Cellular biology

@incollection{crossref1951v,
    title = "V. CELLULAR BIOLOGY",
    year = "1951",
    booktitle = "A Source Book in Animal Biology",
    url = "https://doi.org/10.4159/harvard.9780674592698.c6",
    doi = "10.4159/harvard.9780674592698.c6",
    pages = "429-470"
}

@article{bullough1958cellular,
    author = "BULLOUGH, W. S.",
    title = "Cellular Biology",
    year = "1958",
    journal = "Nature",
    url = "https://doi.org/10.1038/182551a0",
    doi = "10.1038/182551a0",
    number = "4635",
    pages = "551-551",
    volume = "182"
}

@article{howard1965cellular,
    author = "Howard, Alma",
    title = "Cellular Radiation Biology",
    year = "1965",
    journal = "International Journal of Radiation Biology and Related Studies in Physics, Chemistry and Medicine",
    url = "https://doi.org/10.1080/09553006514550691",
    doi = "10.1080/09553006514550691",
    number = "6",
    pages = "611-611",
    volume = "9"
}

@article{na1965cellular,
    author = "\\&NA;",
    title = "CELLULAR RADIATION BIOLOGY",
    year = "1965",
    journal = "The American Journal of the Medical Sciences",
    url = "https://doi.org/10.1097/00000441-196509000-00017",
    doi = "10.1097/00000441-196509000-00017",
    number = "3",
    pages = "365",
    volume = "250"
}

@article{scott1965cellular,
    author = "Scott, Robert B.",
    title = "Cellular Radiation Biology.",
    year = "1965",
    journal = "Archives of Internal Medicine",
    url = "https://doi.org/10.1001/archinte.1965.03870040147047",
    doi = "10.1001/archinte.1965.03870040147047",
    number = "4",
    pages = "633",
    volume = "116"
}

@misc{ambrose1970cell1,
    author = "Ambrose, E. J. and Easty, D. M",
    title = "Cell Biology",
    year = "1970",
    howpublished = "Reading, Mass., Addison- Wesley",
    note = "talkorigins\_source = {true}; raw\_reference = {Ambrose, E. J., and Easty, D. M., 1970, Cell Biology: Reading, Mass., Addison- Wesley.}"
}

@misc{dowben1971cell2,
    author = "Dowben, R. M",
    title = "Cell Biology",
    year = "1971",
    howpublished = "New York, Harper \& Row",
    note = "talkorigins\_source = {true}; raw\_reference = {Dowben, R. M., 1971, Cell Biology: New York, Harper \& Row.}"
}

Abstract A stable cell line (MCF-7) derived by pleural effusion from a breast cancer patient has been demonstrated to contain significant amounts of 17β-estradiol receptor. This binding protein is specific for 17β-estradiol and has a Kd equal to 2.5 nm, a sedimentation constant of 4.0 S (and 9.2 S), and a mechanism capable of transporting the 17β-estradiol into the nucleus.

@article{doi101016s0021925819435370,
    author = "Brooks, Samuel and Locke, Elizabeth and Soule, Herbert D.",
    title = "Estrogen Receptor in a Human Cell Line (MCF-7) from Breast Carcinoma",
    year = "1973",
    journal = "Journal of Biological Chemistry",
    abstract = "Abstract A stable cell line (MCF-7) derived by pleural effusion from a breast cancer patient has been demonstrated to contain significant amounts of 17β-estradiol receptor. This binding protein is specific for 17β-estradiol and has a Kd equal to 2.5 nm, a sedimentation constant of 4.0 S (and 9.2 S), and a mechanism capable of transporting the 17β-estradiol into the nucleus.",
    url = "https://doi.org/10.1016/s0021-9258(19)43537-0",
    doi = "10.1016/s0021-9258(19)43537-0",
    openalex = "W1495332006"
}

Several properties of lymphoid dendritic cells in situ have been determined, and contrasted to information previously established for lymphocytes and mononuclear phagocytes. Dendritic cells are not found in newborn mice, and their concentration in both spleen and mesenteric lymph node does not reach adult levels until 3–4 wk of age. Dendritic cells largely disappear from adherent populations following administration of steroids (2.5 mg hydrocortisone acetate s.c.) and ionizing radiation (Do of 100 rads for Co60). Splenic dendritic cells can originate from precursors located in both bone marrow and spleen itself, probably the red pulp. The mature splenic population does not actively divide (pulse labeling index with [3H]thymidine of 1.5–2.5%), but does turnover at substantial rate, 10+% of the total pool per day. The influx of new cells appears to be derived from a proliferating precursor compartment, but the mechanism for efflux or turnover is not known. Dendritic cells in spleen and node undergo little or moderate increase in numbers during development of a primary immune response. These in vivo characteristics, taken together, further distinguish dendritic cells as a novel cell type, distinct from mononuclear phagocytes and lymphocytes.

@article{doi101084jem13961431,
    author = "Steinman, Ralph M. and Lustig, Dinah S. and Cohn, Zanvil A.",
    title = "IDENTIFICATION OF A NOVEL CELL TYPE IN PERIPHERAL LYMPHOID ORGANS OF MICE",
    year = "1974",
    journal = "The Journal of Experimental Medicine",
    abstract = "Several properties of lymphoid dendritic cells in situ have been determined, and contrasted to information previously established for lymphocytes and mononuclear phagocytes. Dendritic cells are not found in newborn mice, and their concentration in both spleen and mesenteric lymph node does not reach adult levels until 3–4 wk of age. Dendritic cells largely disappear from adherent populations following administration of steroids (2.5 mg hydrocortisone acetate s.c.) and ionizing radiation (Do of 100 rads for Co60). Splenic dendritic cells can originate from precursors located in both bone marrow and spleen itself, probably the red pulp. The mature splenic population does not actively divide (pulse labeling index with [3H]thymidine of 1.5–2.5\%), but does turnover at substantial rate, 10+\% of the total pool per day. The influx of new cells appears to be derived from a proliferating precursor compartment, but the mechanism for efflux or turnover is not known. Dendritic cells in spleen and node undergo little or moderate increase in numbers during development of a primary immune response. These in vivo characteristics, taken together, further distinguish dendritic cells as a novel cell type, distinct from mononuclear phagocytes and lymphocytes.",
    url = "https://doi.org/10.1084/jem.139.6.1431",
    doi = "10.1084/jem.139.6.1431",
    openalex = "W3098989474",
    references = "doi101001jama195302940280072039"
}

Capacity to resorb bone and calcified cartilage was restored permanently in mice with inherited osteopetrosis by the intravenous administration of cell suspensions prepared from spleen and bone marrow of normal littermates. Beginning near active growth plates as early as 2 weeks after transplantation, replacement of the abnormal spongiosa continued until medullary cavitites were fully expanded.

@article{doi101126science1105786,
    author = "Walker, Donald G.",
    title = "Bone Resorption Restored in Osteopetrotic Mice by Transplants of Normal Bone Marrow and Spleen Cells",
    year = "1975",
    journal = "Science",
    abstract = "Capacity to resorb bone and calcified cartilage was restored permanently in mice with inherited osteopetrosis by the intravenous administration of cell suspensions prepared from spleen and bone marrow of normal littermates. Beginning near active growth plates as early as 2 weeks after transplantation, replacement of the abnormal spongiosa continued until medullary cavitites were fully expanded.",
    url = "https://doi.org/10.1126/science.1105786",
    doi = "10.1126/science.1105786",
    openalex = "W2076263545"
}

Hormones and purine nucleosides and nucleotides induced cultured bone cells to transform transiently from a spherical to a stellate shape. Cytochalasin B also induced the transformation. The change was blocked by colchicine and vinblastine, but not by lumicolchicine or cycloheximide. This morphologic transformation may provide a dynamic model of hormone action and bone cell modulation in vitro.

@article{doi101126science1273593,
    author = "Miller, Sam S. and Wolf, Alice M. and Arnaud, Claude D.",
    title = "Bone Cells in Culture: Morphologic Transformation by Hormones",
    year = "1976",
    journal = "Science",
    abstract = "Hormones and purine nucleosides and nucleotides induced cultured bone cells to transform transiently from a spherical to a stellate shape. Cytochalasin B also induced the transformation. The change was blocked by colchicine and vinblastine, but not by lumicolchicine or cycloheximide. This morphologic transformation may provide a dynamic model of hormone action and bone cell modulation in vitro.",
    url = "https://doi.org/10.1126/science.1273593",
    doi = "10.1126/science.1273593",
    openalex = "W2048169623"
}

Two metabolically distinct types of bone cell populations were isolated from mouse calvaria by a repetitive digestive procedure with a mixture of collagenase and trypsin. Cells released early in the digestion showed approximately two fold increases in cAMP when treated with either parathormone or calcitonin. These populations were denoted CT type. Later eluting cells showed larger parathormone-induced increases in cAMP but did not respond to calcitonin. These populations were denoted PT type. Six metabolic and enzymatic activities were measured in the two types of populations: acid and alkaline phosphatases, hyaluronate synthesis, citrate decarboxylation, prolyl hydroxylase, and general protein synthesis. Although each of these activities was present in both cell types, the basal levels of acid phosphatase and hyaluronate synthesis were higher in the CT cells, whereas alkaline phosphatase, citrate decarboxylation, and prolyl hydroxylase were higher in the PT cells. Parathormone stimulated acid phosphatase and hyaluronate synthesis by 100–200% only in the CT cells; it inhibited alkaline phosphatase, citrate decarboxylation, and prolyl hydroxylase by 75–90% only in the PT cells. Calcitonin alone had no effect on any of these activities other than cAMP production, but it inhibited the action of parathormone in the CT cells. The sensitivities, time courses of development, and magnitudes of these hormonal effects were similar to those observed previously in intact calvaria, indicating that the isolated cell system is a reliable model for the study of bone metabolism. Based on the metabolic responses of the cells, we postulate that the CT type of populations is enriched in osteoclasts and, possibly, osteocytes, and the PT type of population is enriched in osteoblasts. (Endocrinology99: 526, 1976)

@article{doi101210endo992526,
    author = "LUBEN, RICHARD A. and Wong, Glenda L. and Cohn, David V.",
    title = "Biochemical Characterization with Parathormone and Calcitonin of Isolated Bone Cells: Provisional Identification of Osteoclasts and Osteoblasts",
    year = "1976",
    journal = "Endocrinology",
    abstract = "Two metabolically distinct types of bone cell populations were isolated from mouse calvaria by a repetitive digestive procedure with a mixture of collagenase and trypsin. Cells released early in the digestion showed approximately two fold increases in cAMP when treated with either parathormone or calcitonin. These populations were denoted CT type. Later eluting cells showed larger parathormone-induced increases in cAMP but did not respond to calcitonin. These populations were denoted PT type. Six metabolic and enzymatic activities were measured in the two types of populations: acid and alkaline phosphatases, hyaluronate synthesis, citrate decarboxylation, prolyl hydroxylase, and general protein synthesis. Although each of these activities was present in both cell types, the basal levels of acid phosphatase and hyaluronate synthesis were higher in the CT cells, whereas alkaline phosphatase, citrate decarboxylation, and prolyl hydroxylase were higher in the PT cells. Parathormone stimulated acid phosphatase and hyaluronate synthesis by 100–200\% only in the CT cells; it inhibited alkaline phosphatase, citrate decarboxylation, and prolyl hydroxylase by 75–90\% only in the PT cells. Calcitonin alone had no effect on any of these activities other than cAMP production, but it inhibited the action of parathormone in the CT cells. The sensitivities, time courses of development, and magnitudes of these hormonal effects were similar to those observed previously in intact calvaria, indicating that the isolated cell system is a reliable model for the study of bone metabolism. Based on the metabolic responses of the cells, we postulate that the CT type of populations is enriched in osteoclasts and, possibly, osteocytes, and the PT type of population is enriched in osteoblasts. (Endocrinology99: 526, 1976)",
    url = "https://doi.org/10.1210/endo-99-2-526",
    doi = "10.1210/endo-99-2-526",
    openalex = "W2050942360"
}

A liquid culture system is described whereby proliferation of haemopoietic stem cells (CFU-S), production of granulocyte precursor cells (CFU-C), and extensive granulopoiesis can be maintained in vetro for several months. Such cultures consist of adherent and non-adherent populations of cells. The adherent population contains phagocytic mononuclear cells, "epithelial" cells, and "giant fat" cells. The latter appear to be particularly important for stem cell maintenance and furthermore there is a strong tendency for maturing granulocytes to selectively cluster in and around areas of "giant fat" cell aggregations. By "feeding" the cultures at weekly intervals, between 10 to 15 "population doublings" of functionally normal CFU-S regularly occurs. Increased "population doublings" may be obtained by feeding twice weekly. The cultures show initially extensive granulopoiesis followed, in a majority of cases, by an accumulation of blast cells. Eventually both blast cells and granulocytes decline and the cultures contain predominantly phagocytic mononuclear cells. Culturing at 33 degrees C leads to the development of a more profuse growth of adherent cells and these cultures show better maintenance of stem cells and increased cell density. When tested for colony stimulating activity (CSA) the cultures were uniformly negative. Addition of exogenous CSA caused a rapid decline in stem cells, reduced granulopoiesis and an accumulation of phagocytic mononuclear cells.

@article{doi101002jcp1040910303,
    author = "Dexter, T. M. and Allen, Terence and Lajtha, L. G.",
    title = "Conditions controlling the proliferation of haemopoietic stem cells in vitro",
    year = "1977",
    journal = "Journal of Cellular Physiology",
    abstract = {A liquid culture system is described whereby proliferation of haemopoietic stem cells (CFU-S), production of granulocyte precursor cells (CFU-C), and extensive granulopoiesis can be maintained in vetro for several months. Such cultures consist of adherent and non-adherent populations of cells. The adherent population contains phagocytic mononuclear cells, "epithelial" cells, and "giant fat" cells. The latter appear to be particularly important for stem cell maintenance and furthermore there is a strong tendency for maturing granulocytes to selectively cluster in and around areas of "giant fat" cell aggregations. By "feeding" the cultures at weekly intervals, between 10 to 15 "population doublings" of functionally normal CFU-S regularly occurs. Increased "population doublings" may be obtained by feeding twice weekly. The cultures show initially extensive granulopoiesis followed, in a majority of cases, by an accumulation of blast cells. Eventually both blast cells and granulocytes decline and the cultures contain predominantly phagocytic mononuclear cells. Culturing at 33 degrees C leads to the development of a more profuse growth of adherent cells and these cultures show better maintenance of stem cells and increased cell density. When tested for colony stimulating activity (CSA) the cultures were uniformly negative. Addition of exogenous CSA caused a rapid decline in stem cells, reduced granulopoiesis and an accumulation of phagocytic mononuclear cells.},
    url = "https://doi.org/10.1002/jcp.1040910303",
    doi = "10.1002/jcp.1040910303",
    openalex = "W2086793358"
}

@article{doi1010160008874977902635,
    author = "Lachman, Lawrence B. and Hacker, Miles P. and Blyden, Gershwin T. and Handschumacher, Robert E.",
    title = "Preparation of lymphocyte-activating factor from continuous murine macrophage cell lines",
    year = "1977",
    journal = "Cellular Immunology",
    url = "https://doi.org/10.1016/0008-8749(77)90263-5",
    doi = "10.1016/0008-8749(77)90263-5",
    openalex = "W1984359046"
}

@article{doi1010160092867479903179,
    author = "Taylor, Shirley M. and Jones, Peter A.",
    title = "Multiple new phenotypes induced in and 3T3 cells treated with 5-azacytidine",
    year = "1979",
    journal = "Cell",
    url = "https://doi.org/10.1016/0092-8674(79)90317-9",
    doi = "10.1016/0092-8674(79)90317-9",
    openalex = "W1865658459"
}

@article{doi1010160092867480902378,
    author = "Jones, Peter A. and Taylor, Shirley M.",
    title = "Cellular differentiation, cytidine analogs and DNA methylation",
    year = "1980",
    journal = "Cell",
    url = "https://doi.org/10.1016/0092-8674(80)90237-8",
    doi = "10.1016/0092-8674(80)90237-8",
    openalex = "W2145750252"
}

The growth of normal cells is largely controlled by the interplay between several polypeptide hormones and hormone-like growth factors that are present in tissue fluids.1 Many new polypeptide growth factors have recently been identified in blood, serum, tissue fluids, and cellular extracts.2,23 Malignant cells, however, are not subject to all the same growth controls as are normal cells. In general, malignant cells require less of these exogenous growth factors than do their normal counterparts for optimal growth and multiplication, and it has been suggested that "transformed or malignant cells escape from normal growth controls by requiring less of [such] hormones...

@article{doi101056nejm198010093031511,
    author = "Sporn, Michael B. and Todaro, George J.",
    title = "Autocrine Secretion and Malignant Transformation of Cells",
    year = "1980",
    journal = "New England Journal of Medicine",
    abstract = {The growth of normal cells is largely controlled by the interplay between several polypeptide hormones and hormone-like growth factors that are present in tissue fluids.1 Many new polypeptide growth factors have recently been identified in blood, serum, tissue fluids, and cellular extracts.2,23 Malignant cells, however, are not subject to all the same growth controls as are normal cells. In general, malignant cells require less of these exogenous growth factors than do their normal counterparts for optimal growth and multiplication, and it has been suggested that "transformed or malignant cells escape from normal growth controls by requiring less of [such] hormones...},
    url = "https://doi.org/10.1056/nejm198010093031511",
    doi = "10.1056/nejm198010093031511",
    openalex = "W2068961038"
}

Phorbol-12-myristate-13-acetate stimulates a subline of mouse EL-4 thymoma cells to produce, in vitro, in very high titer, T cell growth factor (Interleukin 2, IL 2). The EL-4-derived IL 2 has the same m.w. (30,000) and isoelectric point heterogeneity (pI 3.8-4.4) as the IL 2 produced by Con A-stimulated spleen cells. In addition, the thymoma-derived IL 2 exhibits the same spectrum of biologic activities as has been reported for spleen cell-derived IL 2.

@article{doi104049jimmunol12562555,
    author = "Farrar, Jeremy and Fuller-Farrar, J and Simon, P L and Hilfiker, Mary and Stadler, B. M. and Farrar, William L.",
    title = "Thymoma production of T cell growth factor (Interleukin 2).",
    year = "1980",
    journal = "The Journal of Immunology",
    abstract = "Phorbol-12-myristate-13-acetate stimulates a subline of mouse EL-4 thymoma cells to produce, in vitro, in very high titer, T cell growth factor (Interleukin 2, IL 2). The EL-4-derived IL 2 has the same m.w. (30,000) and isoelectric point heterogeneity (pI 3.8-4.4) as the IL 2 produced by Con A-stimulated spleen cells. In addition, the thymoma-derived IL 2 exhibits the same spectrum of biologic activities as has been reported for spleen cell-derived IL 2.",
    url = "https://doi.org/10.4049/jimmunol.125.6.2555",
    doi = "10.4049/jimmunol.125.6.2555",
    openalex = "W1576863849"
}

The ordered structure of the leading edge (lamellipodium) of cultured fibroblasts is readily revealed in cells extracted briefly in Triton X-100-glutaraldehyde mixtures, fixed further in glutaraldehyde, and then negatively stained for electron microscopy. By this procedure, the leading edge regions show a highly organised, three-dimensional network of actin filaments together with variable numbers of radiating actin filament bundles or microspikes. The use of Phalloidin after glutaraldehyde fixation resulted in a marginal improvement in filament order. Processing of the cytoskeletons though the additional steps generally employed for conventional electron microscopy resulted in a marked deterioration or complete disruption of the order of the actin filament networks. In contrast, the actin filaments of the stress fiber bundles were essentially unaffected. Thus, postfixation in osmium tetroxide (1% for 7 min at room temperature) transformed the networks to a reticulum of kinked fibers, resembling those produced by the exposure of muscle F-actin to OsO4 in vitro (P. Maupin-Szamier and T. D. Pollard. 1978. J. Cell Biol. 77:837--852). While limited exposure to OsO4 (0.2+ for 20 min at 0 degrees C) obviated this destruction, dehydration in acetone or ethanol, with or without post-osmication, caused a further and unavoidable disordering and aggregation of the meshwork filaments. The meshwork regions of the leading edge then showed a striking resemblance to the networks hitherto described in critical point-dried preparations of cultured cells. I conclude that much of the "microtrabecular lattice" described by Wolosewick and Porter (1979. J. Cell Biol. 82:114--139) in the latter preparations constitutes actin meshworks and actin filament arrays, with their associated components, that have been distorted and aggregated by the preparative procedures employed.

@article{doi101083jcb913695,
    author = "Small, J. Victor",
    title = "Organization of actin in the leading edge of cultured cells: influence of osmium tetroxide and dehydration on the ultrastructure of actin meshworks.",
    year = "1981",
    journal = "The Journal of Cell Biology",
    abstract = {The ordered structure of the leading edge (lamellipodium) of cultured fibroblasts is readily revealed in cells extracted briefly in Triton X-100-glutaraldehyde mixtures, fixed further in glutaraldehyde, and then negatively stained for electron microscopy. By this procedure, the leading edge regions show a highly organised, three-dimensional network of actin filaments together with variable numbers of radiating actin filament bundles or microspikes. The use of Phalloidin after glutaraldehyde fixation resulted in a marginal improvement in filament order. Processing of the cytoskeletons though the additional steps generally employed for conventional electron microscopy resulted in a marked deterioration or complete disruption of the order of the actin filament networks. In contrast, the actin filaments of the stress fiber bundles were essentially unaffected. Thus, postfixation in osmium tetroxide (1\% for 7 min at room temperature) transformed the networks to a reticulum of kinked fibers, resembling those produced by the exposure of muscle F-actin to OsO4 in vitro (P. Maupin-Szamier and T. D. Pollard. 1978. J. Cell Biol. 77:837--852). While limited exposure to OsO4 (0.2+ for 20 min at 0 degrees C) obviated this destruction, dehydration in acetone or ethanol, with or without post-osmication, caused a further and unavoidable disordering and aggregation of the meshwork filaments. The meshwork regions of the leading edge then showed a striking resemblance to the networks hitherto described in critical point-dried preparations of cultured cells. I conclude that much of the "microtrabecular lattice" described by Wolosewick and Porter (1979. J. Cell Biol. 82:114--139) in the latter preparations constitutes actin meshworks and actin filament arrays, with their associated components, that have been distorted and aggregated by the preparative procedures employed.},
    url = "https://doi.org/10.1083/jcb.91.3.695",
    doi = "10.1083/jcb.91.3.695",
    openalex = "W2153062931"
}

We developed a method for production of antigen-specific, H-2-restricted T cell hybrids. The tumor cell partner in the fusions was itself a T cell hybrid, FS6-14.13.AG2 (or its derivatives), which could be induced to produce the growth factor, interleukin-2 (IL-2), in response to a challenge with concanavalin A, but had no known antigen specificity. The normal T cell partner in the fusions was a population of lymph node T cell blasts that had been highly enriched in antigen-specific, H-2-restricted T cells by in vivo immunization, followed by in vitro challenge with antigen and clonal expansion in IL-2-containing medium. These fusions produced hybrids that grew constitutively in culture. A sizable proportion of the hybrids demonstrated the ability to produce IL-2 in response to a challenge with specific antigen presented by irradiated spleen cells of the appropriate H-2 type. Four cloned antigen/H-2-specific hybrid lines were produced. AO-40.10 responded to chicken ovalbumin (OVA) when presented by I-A(k)-bearing cells. DC1.18.3 responded to the apo form of beef cytochrome c when presented with I-A(d). AODK-10.4 responded to keyhole limpet hemocyanin (KLH) presented with I-A (d). AODK-1.16 also responded to KLH presented by a product of the I region of H-2(d), but the data were consistent with either a product of the I-J-I-E(d) region or a combinatorial molecule with elements from both I-A(d) and I-E(d)/I-C(d). Coincidentally, AO-40.10 was shown to have an unexpected alloreactivity with a product of H-2(b) mapping to the K-I-A region. These hybrids should prove invaluable as sources of monoclonal material for the study of the receptor(s) on T cells with H-2-restricted antigen specificities. We also generated T cell hybrids with two antigen/H-2 specificities by fusing an azaguanine-resistant clone of AO-40.10 to normal T cells with a different antigen/H-2 specificity. Many of the hybrids retained reactivity to OVA plus H-2(a) and to the second antigen/H-2 combination. None reacted to either OVA plus the second H-2 type or to the second antigen plus H-2(a). One of these hybrids was successfully cloned to produce the line AOFK- 11.11.1. It retained the ability to recognize OVA plus I-A(k) inherited from one parent, and KLH plus IA(f) inherited from the other. It did not recognize OVA plus IA(f) or KLH plus I-A(k). These results have some bearing on models describing the nature of T cell receptors for antigen recognized in association with H-2 products. They do not support models in which antigen and H-2 are recognized separately by two independent T cell receptors.

@article{doi101084jem15351198,
    author = "Kappler, JW and Skidmore, Barry J. and White, John H. and Marrack, Philippa",
    title = "Antigen-inducible, H-2-restricted, interleukin-2-producing T cell hybridomas. Lack of independent antigen and H-2 recognition",
    year = "1981",
    journal = "The Journal of Experimental Medicine",
    abstract = "We developed a method for production of antigen-specific, H-2-restricted T cell hybrids. The tumor cell partner in the fusions was itself a T cell hybrid, FS6-14.13.AG2 (or its derivatives), which could be induced to produce the growth factor, interleukin-2 (IL-2), in response to a challenge with concanavalin A, but had no known antigen specificity. The normal T cell partner in the fusions was a population of lymph node T cell blasts that had been highly enriched in antigen-specific, H-2-restricted T cells by in vivo immunization, followed by in vitro challenge with antigen and clonal expansion in IL-2-containing medium. These fusions produced hybrids that grew constitutively in culture. A sizable proportion of the hybrids demonstrated the ability to produce IL-2 in response to a challenge with specific antigen presented by irradiated spleen cells of the appropriate H-2 type. Four cloned antigen/H-2-specific hybrid lines were produced. AO-40.10 responded to chicken ovalbumin (OVA) when presented by I-A(k)-bearing cells. DC1.18.3 responded to the apo form of beef cytochrome c when presented with I-A(d). AODK-10.4 responded to keyhole limpet hemocyanin (KLH) presented with I-A (d). AODK-1.16 also responded to KLH presented by a product of the I region of H-2(d), but the data were consistent with either a product of the I-J-I-E(d) region or a combinatorial molecule with elements from both I-A(d) and I-E(d)/I-C(d). Coincidentally, AO-40.10 was shown to have an unexpected alloreactivity with a product of H-2(b) mapping to the K-I-A region. These hybrids should prove invaluable as sources of monoclonal material for the study of the receptor(s) on T cells with H-2-restricted antigen specificities. We also generated T cell hybrids with two antigen/H-2 specificities by fusing an azaguanine-resistant clone of AO-40.10 to normal T cells with a different antigen/H-2 specificity. Many of the hybrids retained reactivity to OVA plus H-2(a) and to the second antigen/H-2 combination. None reacted to either OVA plus the second H-2 type or to the second antigen plus H-2(a). One of these hybrids was successfully cloned to produce the line AOFK- 11.11.1. It retained the ability to recognize OVA plus I-A(k) inherited from one parent, and KLH plus IA(f) inherited from the other. It did not recognize OVA plus IA(f) or KLH plus I-A(k). These results have some bearing on models describing the nature of T cell receptors for antigen recognized in association with H-2 products. They do not support models in which antigen and H-2 are recognized separately by two independent T cell receptors.",
    url = "https://doi.org/10.1084/jem.153.5.1198",
    doi = "10.1084/jem.153.5.1198",
    openalex = "W2140985128"
}

The method of embryonic tissue transplantation was used to confirm the dual origin of avian cranial sensory ganglia, to map precise locations of the anlagen of these sensory neurons, and to identify placodal and neural crest-derived neurons within ganglia. Segments of neural crest or strips of presumptive placodal ectoderm were excised from chick embryos and replaced with homologous tissues from quail embryos, whose cells contain a heterochromatin marker. Placode-derived neurons associated with cranial nerves V, VII, IX, and X are located distal to crest-derived neurons. The generally larger, embryonic placodal neurons are found in the distal portions of both lobes of the trigeminal ganglion, and in the geniculate, petrosal and nodose ganglia. Crest-derived neurons are found in the proximal trigeminal ganglion and in the combined proximal ganglion of cranial nerves IX and X. Neurons in the vestibular and acoustic ganglia of cranial nerve VIII derive from placodal ectoderm with the exception of a few neural crest-derived neurons localized to regions within the vestibular ganglion. Schwann sheath cells and satellite cells associated with all these ganglia originate from neural crest. The ganglionic anlagen are arranged in cranial to caudal sequence from the level of the mesencephalon through the third somite. Presumptive placodal ectoderm for the VIIIth, the Vth, and the VIIth, IXth, and Xth ganglia are located in a medial to lateral fashion during early stages of development reflecting, respectively, the dorsolateral, intermediate, and epibranchial positions of these neurogenic placodes.

@article{doi101002aja1001660406,
    author = "D'amico‐Martel, Adele and Noden, Drew M.",
    title = "Contributions of placodal and neural crest cells to avian cranial peripheral ganglia",
    year = "1983",
    journal = "American Journal of Anatomy",
    abstract = "The method of embryonic tissue transplantation was used to confirm the dual origin of avian cranial sensory ganglia, to map precise locations of the anlagen of these sensory neurons, and to identify placodal and neural crest-derived neurons within ganglia. Segments of neural crest or strips of presumptive placodal ectoderm were excised from chick embryos and replaced with homologous tissues from quail embryos, whose cells contain a heterochromatin marker. Placode-derived neurons associated with cranial nerves V, VII, IX, and X are located distal to crest-derived neurons. The generally larger, embryonic placodal neurons are found in the distal portions of both lobes of the trigeminal ganglion, and in the geniculate, petrosal and nodose ganglia. Crest-derived neurons are found in the proximal trigeminal ganglion and in the combined proximal ganglion of cranial nerves IX and X. Neurons in the vestibular and acoustic ganglia of cranial nerve VIII derive from placodal ectoderm with the exception of a few neural crest-derived neurons localized to regions within the vestibular ganglion. Schwann sheath cells and satellite cells associated with all these ganglia originate from neural crest. The ganglionic anlagen are arranged in cranial to caudal sequence from the level of the mesencephalon through the third somite. Presumptive placodal ectoderm for the VIIIth, the Vth, and the VIIth, IXth, and Xth ganglia are located in a medial to lateral fashion during early stages of development reflecting, respectively, the dorsolateral, intermediate, and epibranchial positions of these neurogenic placodes.",
    url = "https://doi.org/10.1002/aja.1001660406",
    doi = "10.1002/aja.1001660406",
    openalex = "W2145454156",
    references = "doi101002cne920200404, doi1010160002941683903329, doi1010970000505319361200000041"
}

Bone morphogenetic protein and bone-derived growth factors are biochemical tools for research on induced cell differentiation and local mechanisms controlling cell proliferation. Bone morphogenetic protein irreversibly induces differentiation of perivascular mesenchymal-type cells into osteoprogenitor cells. Bone-derived growth factors are secreted by and for osteoprogenitor cells and stimulate DNA synthesis. Bone generation and regeneration are attributable to the co-efficiency of bone morphogenetic protein and bone-derived growth factors.

@article{doi101126science6403986,
    author = "Urist, Marshall R. and DeLange, Robert J. and Finerman, Gerald A. M.",
    title = "Bone Cell Differentiation and Growth Factors",
    year = "1983",
    journal = "Science",
    abstract = "Bone morphogenetic protein and bone-derived growth factors are biochemical tools for research on induced cell differentiation and local mechanisms controlling cell proliferation. Bone morphogenetic protein irreversibly induces differentiation of perivascular mesenchymal-type cells into osteoprogenitor cells. Bone-derived growth factors are secreted by and for osteoprogenitor cells and stimulate DNA synthesis. Bone generation and regeneration are attributable to the co-efficiency of bone morphogenetic protein and bone-derived growth factors.",
    url = "https://doi.org/10.1126/science.6403986",
    doi = "10.1126/science.6403986",
    openalex = "W2005097199",
    references = "doi1010160002941683903329, doi1010160092867479903179, doi1010160092867480902378, doi1010160092867481900374, doi101038225420a0, doi101056nejm198010093031511, doi101073pnas72103925, doi101073pnas7351447, doi101073pnas78127599, doi1010970000308619670700000026, doi101126science1503698893"
}

@article{doi101007bf02406132,
    author = "Parfitt, A. M.",
    title = "The cellular basis of bone remodeling: The quantum concept reexamined in light of recent advances in the cell biology of bone",
    year = "1984",
    journal = "Calcified Tissue International",
    url = "https://doi.org/10.1007/bf02406132",
    doi = "10.1007/bf02406132",
    openalex = "W2114157286",
    references = "doi101007bf02406145, doi101007bf02409454, doi1010160002941683903329, doi1010160021929082902469, doi1010160221874782900029, doi101056nejm198307073090107, doi101126science6403986, doi101172jci111096, doi107326000348199522482, openalexw1585377912"
}

Abstract Most of our current knowledge of cellular ultrastructure is derived from studies of chemically fixed and chemically cryoprotected preparations. In the first part of this review, we document the many artifacts associated with chemical techniques that render them unsuitable for further refinement of our understanding of cellular ultrastructure. The best method currently available for the preservation of cellular ultrastructure is ultrarapid freezing. The second part of this review is a consideration of the physics of ice crystal formation in biological systems, which suggests that ice crystals will be present in any frozen, uncryoprotected specimen. We define an ultrarapidly frozen preparation as one in which the ice crystals are so small as to be invisible at the electron microscopic level. Improvements in the ease of application and reliability of ultrarapid freezing techniques have reached the point that these techniques can be used by anyone requiring the best achievable preservation of cellular ultrastructure. In the third part of this review, we describe and critique the five methods of ultrarapid freezing in current use.

@article{doi101002jemt1060030206,
    author = "Gilkey, John C. and Staehelin, L. Andrew",
    title = "Advances in ultrarapid freezing for the preservation of cellular ultrastructure",
    year = "1986",
    journal = "Journal of Electron Microscopy Technique",
    abstract = "Abstract Most of our current knowledge of cellular ultrastructure is derived from studies of chemically fixed and chemically cryoprotected preparations. In the first part of this review, we document the many artifacts associated with chemical techniques that render them unsuitable for further refinement of our understanding of cellular ultrastructure. The best method currently available for the preservation of cellular ultrastructure is ultrarapid freezing. The second part of this review is a consideration of the physics of ice crystal formation in biological systems, which suggests that ice crystals will be present in any frozen, uncryoprotected specimen. We define an ultrarapidly frozen preparation as one in which the ice crystals are so small as to be invisible at the electron microscopic level. Improvements in the ease of application and reliability of ultrarapid freezing techniques have reached the point that these techniques can be used by anyone requiring the best achievable preservation of cellular ultrastructure. In the third part of this review, we describe and critique the five methods of ultrarapid freezing in current use.",
    url = "https://doi.org/10.1002/jemt.1060030206",
    doi = "10.1002/jemt.1060030206",
    openalex = "W2105773551",
    references = "doi101083jcb173609"
}

Although much attention has been paid to the removal of hormones from sera and to the development of serum-free media for studies on hormone-responsive cells in culture, little consideration has been given to the possibility that the media components themselves may have hormonal activity. We have found that phenol red, which bears a structural resemblance to some nonsteroidal estrogens and which is used ubiquitously as a pH indicator in tissue culture media, has significant estrogenic activity at the concentrations (15-45 microM) at which it is found in tissue culture media. Phenol red binds to the estrogen receptor of MCF-7 human breast cancer cells with an affinity 0.001% that of estradiol (Kd = 2 X 10(-5) M). It stimulates the proliferation of estrogen receptor-positive MCF-7 breast cancer cells in a dose-dependent manner but has no effect on the growth of estrogen receptor-negative MDA-MB-231 breast cancer cells. At the concentrations present in tissue culture media, phenol red causes partial estrogenic stimulation, increasing cell number to 200% and progesterone receptor content to 300% of that found for cells grown in phenol red-free media, thereby reducing the degree to which exogenous estrogen is able to stimulate responses. The antiestrogens tamoxifen and hydroxytamoxifen inhibit cell proliferation below the control level only when cells are grown in the presence of phenol red; in the absence of phenol red, the antiestrogens do not suppress growth. The estrogenic activity of phenol red should be considered in any studies that utilize estrogen-responsive cells in culture.

@article{doi101073pnas8382496,
    author = "Berthois, Yolande and Katzenellenbogen, John A. and Katzenellenbogen, Benita S.",
    title = "Phenol red in tissue culture media is a weak estrogen: implications concerning the study of estrogen-responsive cells in culture.",
    year = "1986",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = "Although much attention has been paid to the removal of hormones from sera and to the development of serum-free media for studies on hormone-responsive cells in culture, little consideration has been given to the possibility that the media components themselves may have hormonal activity. We have found that phenol red, which bears a structural resemblance to some nonsteroidal estrogens and which is used ubiquitously as a pH indicator in tissue culture media, has significant estrogenic activity at the concentrations (15-45 microM) at which it is found in tissue culture media. Phenol red binds to the estrogen receptor of MCF-7 human breast cancer cells with an affinity 0.001\% that of estradiol (Kd = 2 X 10(-5) M). It stimulates the proliferation of estrogen receptor-positive MCF-7 breast cancer cells in a dose-dependent manner but has no effect on the growth of estrogen receptor-negative MDA-MB-231 breast cancer cells. At the concentrations present in tissue culture media, phenol red causes partial estrogenic stimulation, increasing cell number to 200\% and progesterone receptor content to 300\% of that found for cells grown in phenol red-free media, thereby reducing the degree to which exogenous estrogen is able to stimulate responses. The antiestrogens tamoxifen and hydroxytamoxifen inhibit cell proliferation below the control level only when cells are grown in the presence of phenol red; in the absence of phenol red, the antiestrogens do not suppress growth. The estrogenic activity of phenol red should be considered in any studies that utilize estrogen-responsive cells in culture.",
    url = "https://doi.org/10.1073/pnas.83.8.2496",
    doi = "10.1073/pnas.83.8.2496",
    openalex = "W2059153388"
}

@incollection{holahan1987cellular,
    author = "HOLAHAN, EUGENE V.",
    title = "Cellular Radiation Biology",
    year = "1987",
    booktitle = "Military Radiobiology",
    url = "https://doi.org/10.1016/b978-0-12-184050-1.50007-8",
    doi = "10.1016/b978-0-12-184050-1.50007-8",
    pages = "87-110"
}

Bone cells compose a population of cells of heterogeneous origin but restricted function with respect to matrix formation, mineralization, and resorption. The local, mesenchymal origin of the cells which form the skeleton contrasts with their extraskeletal, hemopoietic relatives under which bone resorption takes place. However, the functions of these two diverse populations are remarkably related and interdependent. Bone cell regulation, presently in its infancy, is a complicated cascade involving a plethora of local and systemic factors, including some components of the skeletal matrices and other organ systems. Thus, any understanding of bone cell regulation is a key ingredient in understanding not only the development, maintenance, and repair of the skeleton but also the prevention and treatment of skeletal disorders.

@article{doi101002aja1001830102,
    author = "Marks, Sandy C. and Popoff, Steven N.",
    title = "Bone cell biology: The regulation of development, structure, and function in the skeleton",
    year = "1988",
    journal = "American Journal of Anatomy",
    abstract = "Bone cells compose a population of cells of heterogeneous origin but restricted function with respect to matrix formation, mineralization, and resorption. The local, mesenchymal origin of the cells which form the skeleton contrasts with their extraskeletal, hemopoietic relatives under which bone resorption takes place. However, the functions of these two diverse populations are remarkably related and interdependent. Bone cell regulation, presently in its infancy, is a complicated cascade involving a plethora of local and systemic factors, including some components of the skeletal matrices and other organ systems. Thus, any understanding of bone cell regulation is a key ingredient in understanding not only the development, maintenance, and repair of the skeleton but also the prevention and treatment of skeletal disorders.",
    url = "https://doi.org/10.1002/aja.1001830102",
    doi = "10.1002/aja.1001830102",
    openalex = "W2162552372",
    references = "doi1010160002941683903329"
}

@article{doi101007bf00225804,
    author = "Maniatopoulos, C. and Sodek, Jaro and Melcher, A. H.",
    title = "Bone formation in vitro by stromal cells obtained from bone marrow of young adult rats",
    year = "1988",
    journal = "Cell and Tissue Research",
    url = "https://doi.org/10.1007/bf00225804",
    doi = "10.1007/bf00225804",
    openalex = "W1986276800",
    references = "doi101001jama195302940280072039"
}

High specific activity estradiol labeled with iodine-125 was used to detect approximately 200 saturable, high-affinity (dissociation constant ≅ 1.0 n M) nuclear binding sites in rat (ROS 17/2.8) and human (HOS TE85) clonal osteoblast-like osteosarcoma cells. Of the steroids tested, only testosterone exhibited significant cross-reactivity with estrogen binding. RNA blot analysis with a complementary DNA probe to the human estrogen receptor revealed putative receptor transcripts of 6 to 6.2 kilobases in both rat and human osteosarcoma cells. Type I procollagen and transforming growth factor-β messenger RNA levels were enhanced in cultured human osteoblast-like cells treated with 1 n M estradiol. Thus, estrogen can act directly on osteoblasts by a receptor-mediated mechanism and thereby modulate the extracellular matrix and other proteins involved in the maintenance of skeletal mineralization and remodeling.

@article{doi101126science3164526,
    author = "Komm, Barry S. and Terpening, Christopher and Benz, D. and Graeme, Kimberlie A. and Gallegos, Alfred and Korc, Murray and Greene, Geoffrey L. and O’Malley, Bert W. and Haussler, Mark R.",
    title = "Estrogen Binding, Receptor mRNA, and Biologic Response in Osteoblast-Like Osteosarcoma Cells",
    year = "1988",
    journal = "Science",
    abstract = "High specific activity estradiol labeled with iodine-125 was used to detect approximately 200 saturable, high-affinity (dissociation constant ≅ 1.0 n M) nuclear binding sites in rat (ROS 17/2.8) and human (HOS TE85) clonal osteoblast-like osteosarcoma cells. Of the steroids tested, only testosterone exhibited significant cross-reactivity with estrogen binding. RNA blot analysis with a complementary DNA probe to the human estrogen receptor revealed putative receptor transcripts of 6 to 6.2 kilobases in both rat and human osteosarcoma cells. Type I procollagen and transforming growth factor-β messenger RNA levels were enhanced in cultured human osteoblast-like cells treated with 1 n M estradiol. Thus, estrogen can act directly on osteoblasts by a receptor-mediated mechanism and thereby modulate the extracellular matrix and other proteins involved in the maintenance of skeletal mineralization and remodeling.",
    url = "https://doi.org/10.1126/science.3164526",
    doi = "10.1126/science.3164526",
    openalex = "W2140086733",
    references = "doi101007bf02406132, doi101016s0021925818482580, doi101016s0021925819435370, doi101038316701a0, doi101073pnas8382496, doi101126science1824108126, doi101126science3029866, doi101126science3388021, doi101126science3753802, doi101126science6403986"
}

In seven strains of cultured normal human osteoblast-like cells, a mean of 1615 molecules of tritium-labeled 17 beta-estradiol per cell nucleus could be bound to specific nuclear sites. The nuclear binding of the labeled steroid was temperature-dependent, steroid-specific, saturable, and cell type-specific. These are characteristics of biologically active estrogen receptors. Pretreatment with 10 nanomolar estradiol in vitro increased the specific nuclear binding of progesterone in four of six cell strains, indicating an induction of functional progesterone receptors. RNA blot analysis demonstrated the presence of messenger RNA for the human estrogen receptor. The data suggest that estrogen acts directly on human bone cells through a classical estrogen receptor-mediated mechanism.

@article{doi101126science3388021,
    author = "Eriksen, Erik Fink and Colvard, Douglas S. and Berg, Nicholas J. and Graham, Mark L. and Mann, Kenneth G. and Spelsberg, Thomas C. and Riggs, B. Lawrence",
    title = "Evidence of Estrogen Receptors in Normal Human Osteoblast-Like Cells",
    year = "1988",
    journal = "Science",
    abstract = "In seven strains of cultured normal human osteoblast-like cells, a mean of 1615 molecules of tritium-labeled 17 beta-estradiol per cell nucleus could be bound to specific nuclear sites. The nuclear binding of the labeled steroid was temperature-dependent, steroid-specific, saturable, and cell type-specific. These are characteristics of biologically active estrogen receptors. Pretreatment with 10 nanomolar estradiol in vitro increased the specific nuclear binding of progesterone in four of six cell strains, indicating an induction of functional progesterone receptors. RNA blot analysis demonstrated the presence of messenger RNA for the human estrogen receptor. The data suggest that estrogen acts directly on human bone cells through a classical estrogen receptor-mediated mechanism.",
    url = "https://doi.org/10.1126/science.3388021",
    doi = "10.1126/science.3388021",
    openalex = "W2062729355"
}

Evidence for the hypothesis that there are stromal stem cells present in the soft connective tissues associated with marrow and bone surfaces that are able to give rise to a number of different cell lines is reviewed. The lines are currently designated fibroblastic, reticular, adipocytic and osteogenic. Fibroblastic colonies, each derived from a single colony-forming unit fibroblastic (CFU-F), are formed when marrow cells are cultured in vitro. In vivo assays of tissue formed by CFU-F in open transplant or in diffusion chambers, have demonstrated that some CFU-F have a high ability for self renewal and multipotentiality whereas some have more limited potential. Preliminary investigations in vitro also support the hypothesis and have shown that CFU-F are a heterogeneous population of stem and progenitor cells and that their differentiation in vitro can be modified at the colony level. The stromal cells which survive and proliferate in vitro are highly dependent on culture conditions. The number and hierarchy of cell lines belonging to the stromal fibroblastic system are not yet fully elucidated and more specific markers and better assays for the different phenotypes are required before a greater understanding can be achieved. The possibility that the marrow stromal system is part of a wider stromal cell system of the body is proposed.

@article{doi101242jcs1988supplement105,
    author = "Owen, Maureen",
    title = "Marrow stromal stem cells",
    year = "1988",
    journal = "Journal of Cell Science",
    abstract = "Evidence for the hypothesis that there are stromal stem cells present in the soft connective tissues associated with marrow and bone surfaces that are able to give rise to a number of different cell lines is reviewed. The lines are currently designated fibroblastic, reticular, adipocytic and osteogenic. Fibroblastic colonies, each derived from a single colony-forming unit fibroblastic (CFU-F), are formed when marrow cells are cultured in vitro. In vivo assays of tissue formed by CFU-F in open transplant or in diffusion chambers, have demonstrated that some CFU-F have a high ability for self renewal and multipotentiality whereas some have more limited potential. Preliminary investigations in vitro also support the hypothesis and have shown that CFU-F are a heterogeneous population of stem and progenitor cells and that their differentiation in vitro can be modified at the colony level. The stromal cells which survive and proliferate in vitro are highly dependent on culture conditions. The number and hierarchy of cell lines belonging to the stromal fibroblastic system are not yet fully elucidated and more specific markers and better assays for the different phenotypes are required before a greater understanding can be achieved. The possibility that the marrow stromal system is part of a wider stromal cell system of the body is proposed.",
    url = "https://doi.org/10.1242/jcs.1988.supplement\_10.5",
    doi = "10.1242/jcs.1988.supplement\_10.5",
    openalex = "W2019480285",
    references = "doi101126science6403986"
}

For the past 30 years strategies for the preclinical discovery and development of potential anticancer agents have been based largely upon the testing of agents in mice bearing transplantable leukemias and solid tumors derived from a limited number of murine as well as human sources. The feasibility of implementing an alternate approach, namely combined in vitro/in vivo screening for selective cytotoxicity among panels of human tumor cell lines derived from a broad spectrum of human solid tumors is under investigation. A group of 30 cell lines acquired from a variety of sources and representing 8 lung cancer pathologies as well as 76 cell lines representing 10 other categories of human cancer (carcinomas of colon, breast, kidney, prostate, ovary, head and neck; glioma; leukemia; melanoma; and sarcoma) have exhibited acceptable growth characteristics and suitable colorimetric profiles in a single, standard culture medium. Measurements of in vitro growth in microculture wells by cell-mediated reduction of tetrazolium showed excellent correlation (0.89 less than r2 less than 0.98) with measurements of cellular protein in adherent cell line cultures as well as viable cell count in suspension cell line cultures (0.94 less than r2 less than 0.99). Since the microculture tetrazolium assay provides sensitive and reproducible indices of growth as well as drug sensitivity in individual cell lines over the course of multiple passages and several months' cultivation, it appears suitable for initial-stage in vitro drug screening.

@article{openalexw2120064876,
    author = "Alley, Michael C. and Scudiero, Dominic A. and Monks, Anne and Hursey, Miriam L. and Czerwiński, Maciej and Fine, Donald L. and Abbott, Betty J. and Mayo, Joseph G. and Shoemaker, Robert H. and Boyd, Michael R.",
    title = "Feasibility of drug screening with panels of human tumor cell lines using a microculture tetrazolium assay.",
    year = "1988",
    journal = "PubMed",
    abstract = "For the past 30 years strategies for the preclinical discovery and development of potential anticancer agents have been based largely upon the testing of agents in mice bearing transplantable leukemias and solid tumors derived from a limited number of murine as well as human sources. The feasibility of implementing an alternate approach, namely combined in vitro/in vivo screening for selective cytotoxicity among panels of human tumor cell lines derived from a broad spectrum of human solid tumors is under investigation. A group of 30 cell lines acquired from a variety of sources and representing 8 lung cancer pathologies as well as 76 cell lines representing 10 other categories of human cancer (carcinomas of colon, breast, kidney, prostate, ovary, head and neck; glioma; leukemia; melanoma; and sarcoma) have exhibited acceptable growth characteristics and suitable colorimetric profiles in a single, standard culture medium. Measurements of in vitro growth in microculture wells by cell-mediated reduction of tetrazolium showed excellent correlation (0.89 less than r2 less than 0.98) with measurements of cellular protein in adherent cell line cultures as well as viable cell count in suspension cell line cultures (0.94 less than r2 less than 0.99). Since the microculture tetrazolium assay provides sensitive and reproducible indices of growth as well as drug sensitivity in individual cell lines over the course of multiple passages and several months' cultivation, it appears suitable for initial-stage in vitro drug screening.",
    openalex = "W2120064876"
}

We have previously described the application of an automated microculture tetrazolium assay (MTA) involving dimethyl sulfoxide solubilization of cellular-generated 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)-formazan to the in vitro assessment of drug effects on cell growth (M.C. Alley et al., Proc. Am. Assoc. Cancer Res., 27:389, 1986; M.C. Alley et al., Cancer Res. 48:589-601, 1988). There are several inherent disadvantages of this assay, including the safety hazard of personnel exposure to large quantities of dimethyl sulfoxide, the deleterious effects of this solvent on laboratory equipment, and the inefficient metabolism of MTT by some human cell lines. Recognition of these limitations prompted development of possible alternative MTAs utilizing a different tetrazolium reagent, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl] -2H- tetrazolium hydroxide (XTT), which is metabolically reduced in viable cells to a water-soluble formazan product. This reagent allows direct absorbance readings, therefore eliminating a solubilization step and shortening the microculture growth assay procedure. Most human tumor cell lines examined metabolized XTT less efficiently than MTT; however, the addition of phenazine methosulfate (PMS) markedly enhanced cellular reduction of XTT. In the presence of PMS, the XTT reagent yielded usable absorbance values for growth and drug sensitivity evaluations with a variety of cell lines. Depending on the metabolic reductive capacity of a given cell line, the optimal conditions for a 4-h XTT incubation assay were 50 micrograms of XTT and 0.15 to 0.4 microgram of PMS per well. Drug profiles obtained with representative human tumor cell lines for several standard compounds utilizing the XTT-PMS methodology were similar to the profiles obtained with MTT. Addition of PMS appeared to have little effect on the metabolism of MTT. The new XTT reagent thus provides for a simplified, in vitro cell growth assay with possible applicability to a variety of problems in cellular pharmacology and biology. However, the MTA using the XTT reagent still shares many of the limitations and potential pitfalls of MTT or other tetrazolium-based assays.

@article{openalexw2143811153,
    author = "Scudiero, Dominic A. and Shoemaker, Robert H. and Paull, Kenneth D. and Monks, Anne and Tierney, Sean and Nofziger, T H and Currens, Michael J. and Seniff, D A and Boyd, Michael R.",
    title = "Evaluation of a soluble tetrazolium/formazan assay for cell growth and drug sensitivity in culture using human and other tumor cell lines.",
    year = "1988",
    journal = "PubMed",
    abstract = "We have previously described the application of an automated microculture tetrazolium assay (MTA) involving dimethyl sulfoxide solubilization of cellular-generated 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)-formazan to the in vitro assessment of drug effects on cell growth (M.C. Alley et al., Proc. Am. Assoc. Cancer Res., 27:389, 1986; M.C. Alley et al., Cancer Res. 48:589-601, 1988). There are several inherent disadvantages of this assay, including the safety hazard of personnel exposure to large quantities of dimethyl sulfoxide, the deleterious effects of this solvent on laboratory equipment, and the inefficient metabolism of MTT by some human cell lines. Recognition of these limitations prompted development of possible alternative MTAs utilizing a different tetrazolium reagent, 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl] -2H- tetrazolium hydroxide (XTT), which is metabolically reduced in viable cells to a water-soluble formazan product. This reagent allows direct absorbance readings, therefore eliminating a solubilization step and shortening the microculture growth assay procedure. Most human tumor cell lines examined metabolized XTT less efficiently than MTT; however, the addition of phenazine methosulfate (PMS) markedly enhanced cellular reduction of XTT. In the presence of PMS, the XTT reagent yielded usable absorbance values for growth and drug sensitivity evaluations with a variety of cell lines. Depending on the metabolic reductive capacity of a given cell line, the optimal conditions for a 4-h XTT incubation assay were 50 micrograms of XTT and 0.15 to 0.4 microgram of PMS per well. Drug profiles obtained with representative human tumor cell lines for several standard compounds utilizing the XTT-PMS methodology were similar to the profiles obtained with MTT. Addition of PMS appeared to have little effect on the metabolism of MTT. The new XTT reagent thus provides for a simplified, in vitro cell growth assay with possible applicability to a variety of problems in cellular pharmacology and biology. However, the MTA using the XTT reagent still shares many of the limitations and potential pitfalls of MTT or other tetrazolium-based assays.",
    openalex = "W2143811153",
    references = "doi101002jhet5570250340, doi101007bf00256695, doi1010160022175983903034, doi1010160277537986901628, doi101016s0079633676800150, doi101016s0304383575975060, doi101038bjc198435, doi101093ajcp233218, openalexw2120064876, openalexw2140927361"
}

The National Cancer Institute (NCI) is implementing a large-scale in vitro drug-screening program that requires a very efficient automated assay of drug effects on tumor cell viability or growth. Many laboratories worldwide have adopted a microculture assay based on metabolic reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). However, because of certain technical advantages to use of the protein-binding dye sulforhodamine B (SRB) in a large-scale screening application, a detailed comparison of data generated by each type of assay was undertaken. The MTT and SRB assays were each used to test 197 compounds, on simultaneous days, against up to 38 human tumor cell lines representing seven major tumor categories. On subsequent days, 38 compounds were retested with the SRB assay and 25 compounds were retested with the MTT assay. For each of these three comparisons, we tabulated the differences between the two assays in the ratios of test group values to control values (T/C) for cell survival; calculated correlation coefficients for various T/C ratios; and estimated the bivariate distribution of the values for IC50 (concentration of drug resulting in T/C values of 50%, or 50% growth inhibition) for the two assays. The results indicate that under the experimental conditions used and within the limits of the data analyses, the assays perform similarly. Because the SRB assay has practical advantages for large-scale screening, however, it has been adopted for routine use in the NCI in vitro antitumor screen.

@article{doi101093jnci82131113,
    author = "Rubinstein, Larry and Shoemaker, Robert H. and Paull, Kenneth D. and Simon, Richard and Tosini, S. and Skehan, Philip and Scudiero, Dominic A. and Monks, Anne and Boyd, M.R.",
    title = "Comparison of In Vitro Anticancer-Drug-Screening Data Generated With a Tetrazolium Assay Versus a Protein Assay Against a Diverse Panel of Human Tumor Cell Lines",
    year = "1990",
    journal = "JNCI Journal of the National Cancer Institute",
    abstract = "The National Cancer Institute (NCI) is implementing a large-scale in vitro drug-screening program that requires a very efficient automated assay of drug effects on tumor cell viability or growth. Many laboratories worldwide have adopted a microculture assay based on metabolic reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT). However, because of certain technical advantages to use of the protein-binding dye sulforhodamine B (SRB) in a large-scale screening application, a detailed comparison of data generated by each type of assay was undertaken. The MTT and SRB assays were each used to test 197 compounds, on simultaneous days, against up to 38 human tumor cell lines representing seven major tumor categories. On subsequent days, 38 compounds were retested with the SRB assay and 25 compounds were retested with the MTT assay. For each of these three comparisons, we tabulated the differences between the two assays in the ratios of test group values to control values (T/C) for cell survival; calculated correlation coefficients for various T/C ratios; and estimated the bivariate distribution of the values for IC50 (concentration of drug resulting in T/C values of 50\%, or 50\% growth inhibition) for the two assays. The results indicate that under the experimental conditions used and within the limits of the data analyses, the assays perform similarly. Because the SRB assay has practical advantages for large-scale screening, however, it has been adopted for routine use in the NCI in vitro antitumor screen.",
    url = "https://doi.org/10.1093/jnci/82.13.1113",
    doi = "10.1093/jnci/82.13.1113",
    openalex = "W1993570389"
}

Bone and cartilage formation in the embryo and repair and turnover in the adult involve the progeny of a small number of cells called mesenchymal stem cells. These cells divide, and their progeny become committed to a specific and distinctive phenotypic pathway, a lineage with discrete steps and, finally, end-stage cells involved with fabrication of a unique tissue type, e.g., cartilage or bone. Local cuing (extrinsic factors) and the genomic potential (intrinsic factors) interact at each lineage step to control the rate and characteristic phenotype of the cells in the emerging tissue. The study of these mesenchymal stem cells, whether isolated from embryos or adults, provides the basis for the emergence of a new therapeutic technology of self-cell repair. The isolation, mitotic expansion, and site-directed delivery of autologous stem cells can govern the rapid and specific repair of skeletal tissues.

@article{doi101002jor1100090504,
    author = "Caplan, Arnold I.",
    title = "Mesenchymal stem cells",
    year = "1991",
    journal = "Journal of Orthopaedic Research®",
    abstract = "Bone and cartilage formation in the embryo and repair and turnover in the adult involve the progeny of a small number of cells called mesenchymal stem cells. These cells divide, and their progeny become committed to a specific and distinctive phenotypic pathway, a lineage with discrete steps and, finally, end-stage cells involved with fabrication of a unique tissue type, e.g., cartilage or bone. Local cuing (extrinsic factors) and the genomic potential (intrinsic factors) interact at each lineage step to control the rate and characteristic phenotype of the cells in the emerging tissue. The study of these mesenchymal stem cells, whether isolated from embryos or adults, provides the basis for the emergence of a new therapeutic technology of self-cell repair. The isolation, mitotic expansion, and site-directed delivery of autologous stem cells can govern the rapid and specific repair of skeletal tissues.",
    url = "https://doi.org/10.1002/jor.1100090504",
    doi = "10.1002/jor.1100090504",
    openalex = "W2144268541",
    references = "doi101126science6403986"
}

We describe here the development and implementation of a pilot-scale, in vitro, anticancer drug screen utilizing a panel of 60 human tumor cell lines organized into subpanels representing leukemia, melanoma, and cancers of the lung, colon, kidney, ovary, and central nervous system. The ultimate goal of this disease-oriented screen is to facilitate the discovery of new compounds with potential cell line-specific and/or subpanel-specific antitumor activity. In the current screening protocol, each cell line is inoculated onto microtiter plates, then preincubated for 24-28 hours. Subsequently, test agents are added in five 10-fold dilutions and the culture is incubated for an additional 48 hours. For each test agent, a dose-response profile is generated. End-point determinations of the cell viability or cell growth are performed by in situ fixation of cells, followed by staining with a protein-binding dye, sulforhodamine B (SRB). The SRB binds to the basic amino acids of cellular macromolecules; the solubilized stain is measured spectrophotometrically to determine relative cell growth or viability in treated and untreated cells. Following the pilot screening studies, a screening rate of 400 compounds per week has been consistently achieved.

@article{doi101093jnci8311757,
    author = "Monks, Anne and Scudiero, Dominic A. and Skehan, Philip and Shoemaker, Robert H. and Paull, Kenneth D. and Vistica, David T. and Hose, Curtis and Langley, James W. and Cronise, P. and Vaigro-Wolff, Anne and Gray-Goodrich, M. and Campbell, H. and Mayo, J. and Boyd, Marie",
    title = "Feasibility of a High-Flux Anticancer Drug Screen Using a Diverse Panel of Cultured Human Tumor Cell Lines",
    year = "1991",
    journal = "JNCI Journal of the National Cancer Institute",
    abstract = "We describe here the development and implementation of a pilot-scale, in vitro, anticancer drug screen utilizing a panel of 60 human tumor cell lines organized into subpanels representing leukemia, melanoma, and cancers of the lung, colon, kidney, ovary, and central nervous system. The ultimate goal of this disease-oriented screen is to facilitate the discovery of new compounds with potential cell line-specific and/or subpanel-specific antitumor activity. In the current screening protocol, each cell line is inoculated onto microtiter plates, then preincubated for 24-28 hours. Subsequently, test agents are added in five 10-fold dilutions and the culture is incubated for an additional 48 hours. For each test agent, a dose-response profile is generated. End-point determinations of the cell viability or cell growth are performed by in situ fixation of cells, followed by staining with a protein-binding dye, sulforhodamine B (SRB). The SRB binds to the basic amino acids of cellular macromolecules; the solubilized stain is measured spectrophotometrically to determine relative cell growth or viability in treated and untreated cells. Following the pilot screening studies, a screening rate of 400 compounds per week has been consistently achieved.",
    url = "https://doi.org/10.1093/jnci/83.11.757",
    doi = "10.1093/jnci/83.11.757",
    openalex = "W2155208683",
    references = "doi101093jnci82131113, openalexw2143811153"
}

A new tetrazolium analog of 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) was evaluated as a substitute for MTT in the microculture screening assay for in vitro cell growth. This new tetrazolium compound, 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2- (4-sulfophenyl)-2H-tetrazolium, inner salt (MTS), in the presence of phenazine methosulfate (PMS), gave a water-soluble formazan product that had an absorbance maximum at 490-500 nm in phosphate-buffered saline. The amount of colored product formed was proportional to the number of cells and the time of incubation of the cells with MTS/PMS. MTS/PMS was reactive in all the cell lines tested which included mouse leukemia L1210 cells, mouse Ehrlich tumor cells, mouse 3T3 fibroblasts, and human colon tumor cells (HT-29). HT-29 and 3T3 fibroblasts reduced MTS/PMS more efficiently than they reduced MTT. Comparable to the amount of product formed from MTT, MTS/PMS gave excellent product formation. The IC50 value for pyrazoloimidazole obtained using MTS/PMS was 200 microM; for 5-fluoro-2'-deoxyuridine, the IC50 value was 0.9 nM. These values compared very favorably with the IC50 values obtained by direct cell counts. Further, the same IC50 values were obtained when the absorbances of the formazan product in the 96-well plates were determined after different times of incubation.

@article{doi103727095535491820873191,
    author = "Cory, Ann H. and Owen, Terence C. and Barltrop, J. A. and Cory, Joseph G.",
    title = "Use of an Aqueous Soluble Tetrazolium/Formazan Assay for Cell Growth Assays in Culture",
    year = "1991",
    journal = "Cancer Communications",
    abstract = "A new tetrazolium analog of 3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) was evaluated as a substitute for MTT in the microculture screening assay for in vitro cell growth. This new tetrazolium compound, 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2- (4-sulfophenyl)-2H-tetrazolium, inner salt (MTS), in the presence of phenazine methosulfate (PMS), gave a water-soluble formazan product that had an absorbance maximum at 490-500 nm in phosphate-buffered saline. The amount of colored product formed was proportional to the number of cells and the time of incubation of the cells with MTS/PMS. MTS/PMS was reactive in all the cell lines tested which included mouse leukemia L1210 cells, mouse Ehrlich tumor cells, mouse 3T3 fibroblasts, and human colon tumor cells (HT-29). HT-29 and 3T3 fibroblasts reduced MTS/PMS more efficiently than they reduced MTT. Comparable to the amount of product formed from MTT, MTS/PMS gave excellent product formation. The IC50 value for pyrazoloimidazole obtained using MTS/PMS was 200 microM; for 5-fluoro-2'-deoxyuridine, the IC50 value was 0.9 nM. These values compared very favorably with the IC50 values obtained by direct cell counts. Further, the same IC50 values were obtained when the absorbances of the formazan product in the 96-well plates were determined after different times of incubation.",
    url = "https://doi.org/10.3727/095535491820873191",
    doi = "10.3727/095535491820873191",
    openalex = "W2274550965"
}

Few nonphagocytic cells are known to generate reactive oxygen intermediates. Based on horseradish peroxidase-dependent, catalase-inhibitable oxidation of fluorescent scopoletin, seven human tumor cell lines constitutively elaborated H2O2 at rates (up to 0.5 nmol/10(4) cells/h) large enough that cumulative amounts at 4 h were comparable to the amount of H2O2 produced by phorbol ester-triggered neutrophils. Superoxide dismutase-inhibitable ferricytochrome c reduction was detectable at much lower rates. H2O2 production was inhibited by diphenyleneiodonium, a flavoprotein binder (concentration producing 50% inhibition, 0.3 microM), and diethyldithiocarbamate, a divalent cation chelator (concentration producing 50% inhibition, 3 microM), but not by cyanide or azide, inhibitors of electron transport, or by agents that inhibit xanthine oxidase, polyamine oxidase, or cytochrome P450. Cytochrome b559, present in human phagocytes and lymphocytes, was undetectable in these tumor cells by a sensitive spectrophotometric method. Mouse fibroblasts transfected with human tyrosinase complementary DNA made melanin, but not H2O2. Constitutive generation of large amounts of reactive oxygen intermediates, if it occurs in vivo, might contribute to the ability of some tumors to mutate, inhibit antiproteases, injure local tissues, and therefore promote tumor heterogeneity, invasion, and metastasis.

@article{openalexw1809723326,
    author = "Szatrowski, Ted P. and Nathan, Carl",
    title = "Production of large amounts of hydrogen peroxide by human tumor cells.",
    year = "1991",
    journal = "PubMed",
    abstract = "Few nonphagocytic cells are known to generate reactive oxygen intermediates. Based on horseradish peroxidase-dependent, catalase-inhibitable oxidation of fluorescent scopoletin, seven human tumor cell lines constitutively elaborated H2O2 at rates (up to 0.5 nmol/10(4) cells/h) large enough that cumulative amounts at 4 h were comparable to the amount of H2O2 produced by phorbol ester-triggered neutrophils. Superoxide dismutase-inhibitable ferricytochrome c reduction was detectable at much lower rates. H2O2 production was inhibited by diphenyleneiodonium, a flavoprotein binder (concentration producing 50\% inhibition, 0.3 microM), and diethyldithiocarbamate, a divalent cation chelator (concentration producing 50\% inhibition, 3 microM), but not by cyanide or azide, inhibitors of electron transport, or by agents that inhibit xanthine oxidase, polyamine oxidase, or cytochrome P450. Cytochrome b559, present in human phagocytes and lymphocytes, was undetectable in these tumor cells by a sensitive spectrophotometric method. Mouse fibroblasts transfected with human tyrosinase complementary DNA made melanin, but not H2O2. Constitutive generation of large amounts of reactive oxygen intermediates, if it occurs in vivo, might contribute to the ability of some tumors to mutate, inhibit antiproteases, injure local tissues, and therefore promote tumor heterogeneity, invasion, and metastasis.",
    openalex = "W1809723326"
}

The hydrogen acceptor 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) is commonly utilized to estimate cellular viability in drug screening protocols. The present investigation was prompted, in part, by observations that reduction of MTT to its colored reaction product, MTT formazan, varied between cell lines and with culture age. A correlation was established between the D-glucose concentration of the culture medium at the time of assay and the production of MTT formazan for cell lines representing seven tumor histologies. A decrease in the concentration of D-glucose from culture medium was accompanied by a decrease in MTT specific activity (MTT formazan/microgram cell protein) for a number of cell lines. Cells which extensively metabolized D-glucose exhibited the greatest reduction in MTT specific activity. Further evidence that the D-glucose concentration of the culture medium played an important role in MTT reduction was provided by experiments which demonstrated that transfer of cells to a glucose-free medium (L-15) was accompanied by an immediate decrease in MTT reduction which was pH independent. These studies suggested that cellular transport and constant metabolism of glucose were required for maximum MTT reduction. Decreases in the cellular concentration of the reduced pyridine nucleotides NADH and NADPH were accompanied by concomitant decreases in MTT formazan production. MTT formazan varied significantly among cell lines in both the kinetics of its formation and the degree of saturability exhibited. Apparent IC50 values for Adriamycin varied, in a cell line-specific manner, with MTT exposure time. These results indicate that MTT specific activity is significantly influenced by a number of parameters and suggest that assay conditions should be established which minimize their effects.

@article{openalexw1819048918,
    author = "Vistica, David T. and Skehan, Philip and Scudiero, Dominic A. and Monks, Anne and Pittman, A F and Boyd, Michael R.",
    title = "Tetrazolium-based assays for cellular viability: a critical examination of selected parameters affecting formazan production.",
    year = "1991",
    journal = "PubMed",
    abstract = "The hydrogen acceptor 3-(4,5-dimethylthiazol-2-yl)-2,5 diphenyltetrazolium bromide (MTT) is commonly utilized to estimate cellular viability in drug screening protocols. The present investigation was prompted, in part, by observations that reduction of MTT to its colored reaction product, MTT formazan, varied between cell lines and with culture age. A correlation was established between the D-glucose concentration of the culture medium at the time of assay and the production of MTT formazan for cell lines representing seven tumor histologies. A decrease in the concentration of D-glucose from culture medium was accompanied by a decrease in MTT specific activity (MTT formazan/microgram cell protein) for a number of cell lines. Cells which extensively metabolized D-glucose exhibited the greatest reduction in MTT specific activity. Further evidence that the D-glucose concentration of the culture medium played an important role in MTT reduction was provided by experiments which demonstrated that transfer of cells to a glucose-free medium (L-15) was accompanied by an immediate decrease in MTT reduction which was pH independent. These studies suggested that cellular transport and constant metabolism of glucose were required for maximum MTT reduction. Decreases in the cellular concentration of the reduced pyridine nucleotides NADH and NADPH were accompanied by concomitant decreases in MTT formazan production. MTT formazan varied significantly among cell lines in both the kinetics of its formation and the degree of saturability exhibited. Apparent IC50 values for Adriamycin varied, in a cell line-specific manner, with MTT exposure time. These results indicate that MTT specific activity is significantly influenced by a number of parameters and suggest that assay conditions should be established which minimize their effects.",
    openalex = "W1819048918",
    references = "doi101093jnci82131113, openalexw2143811153"
}

@article{doi101016009286749290115s,
    author = "Hynes, Richard O.",
    title = "Integrins: Versatility, modulation, and signaling in cell adhesion",
    year = "1992",
    journal = "Cell",
    url = "https://doi.org/10.1016/0092-8674(92)90115-s",
    doi = "10.1016/0092-8674(92)90115-s",
    openalex = "W2029231027"
}

The differentiation of adipocytic and osteogenic cells has been investigated in cultures of adult rat marrow stromal cells. Adipocytic differentiation was assessed using morphological criteria, changes in expression of procollagen mRNAs, consistent with a switch from the synthesis of predominantly fibrillar (types I and III) to basement membrane (type IV) collagen, and the induction of expression of aP2, a specific marker for differentiation of adipocytes. Osteogenic differentiation was assessed on the basis of changes in the abundance of the mRNAs for the bone/liver/kidney isozyme of alkaline phosphatase and the induction of mRNAs for bone sialoprotein and osteocalcin. In the presence of foetal calf serum and dexamethasone (10(-8) M) there was always differentiation of both adipocytic and osteogenic cells. When the steroid was present throughout primary and secondary culture the differentiation of osteogenic cells predominated. Conversely, when dexamethasone was present in secondary culture only, the differentiation of adipocytes predominated. When marrow stromal cells were cultured in the presence of dexamethasone in primary culture and dexamethasone and 1,25-dihydroxyvitamin D3 (1,25(OH)2D3; 10(-8) M) in secondary culture, the differentiation of adipocytes was inhibited whereas the differentiation of osteogenic cells was enhanced, as assessed by an increase in expression of osteocalcin mRNA. The results, therefore, demonstrate an inverse relationship between the differentiation of adipocytic and osteogenic cells in this culture system and are consistent with the possibility that the regulation of adipogenesis and osteogenesis can occur at the level of a common precursor in vivo.

@article{doi101242jcs1022341,
    author = "Beresford, J.N. and Bennett, J. and Devlin, C. and Leboy, Phoebe S. and Owen, Maureen",
    title = "Evidence for an inverse relationship between the differentiation of adipocytic and osteogenic cells in rat marrow stromal cell cultures",
    year = "1992",
    journal = "Journal of Cell Science",
    abstract = "The differentiation of adipocytic and osteogenic cells has been investigated in cultures of adult rat marrow stromal cells. Adipocytic differentiation was assessed using morphological criteria, changes in expression of procollagen mRNAs, consistent with a switch from the synthesis of predominantly fibrillar (types I and III) to basement membrane (type IV) collagen, and the induction of expression of aP2, a specific marker for differentiation of adipocytes. Osteogenic differentiation was assessed on the basis of changes in the abundance of the mRNAs for the bone/liver/kidney isozyme of alkaline phosphatase and the induction of mRNAs for bone sialoprotein and osteocalcin. In the presence of foetal calf serum and dexamethasone (10(-8) M) there was always differentiation of both adipocytic and osteogenic cells. When the steroid was present throughout primary and secondary culture the differentiation of osteogenic cells predominated. Conversely, when dexamethasone was present in secondary culture only, the differentiation of adipocytes predominated. When marrow stromal cells were cultured in the presence of dexamethasone in primary culture and dexamethasone and 1,25-dihydroxyvitamin D3 (1,25(OH)2D3; 10(-8) M) in secondary culture, the differentiation of adipocytes was inhibited whereas the differentiation of osteogenic cells was enhanced, as assessed by an increase in expression of osteocalcin mRNA. The results, therefore, demonstrate an inverse relationship between the differentiation of adipocytic and osteogenic cells in this culture system and are consistent with the possibility that the regulation of adipogenesis and osteogenesis can occur at the level of a common precursor in vivo.",
    url = "https://doi.org/10.1242/jcs.102.2.341",
    doi = "10.1242/jcs.102.2.341",
    openalex = "W1943239370"
}

The signaling pathways involved in the long-term metabolic effects of angiotensin II (Ang II) in vascular smooth muscle cells are incompletely understood but include the generation of molecules likely to affect oxidase activity. We examined the ability of Ang II to stimulate superoxide anion formation and investigated the identity of the oxidases responsible for its production. Treatment of vascular smooth muscle cells with Ang II for 4 to 6 hours caused a 2.7 +/- 0.4-fold increase in intracellular superoxide anion formation as detected by lucigenin assay. This superoxide appeared to result from activation of both the NADPH and NADH oxidases. NADPH oxidase activity increased from 3.23 +/- 0.61 to 11.80 +/- 1.72 nmol O2-/min per milligram protein after 4 hours of Ang II, whereas NADH oxidase activity increased from 16.76 +/- 2.13 to 45.00 +/- 4.57 nmol O2-/min per milligram protein. The NADPH oxidase activity was stimulated by exogenous phosphatidic and arachidonic acids and was partially inhibited by the specific inhibitor diphenylene iodinium. NADH oxidase activity was increased by arachidonic and linoleic acids, was insensitive to exogenous phosphatidic acid, and was inhibited by high concentrations of quinacrine. Both of these oxidases appear to reside in the plasma membrane, on the basis of migration of the activity after cellular fractionation and their apparent insensitivity to the mitochondrial poison KCN. These observations suggest that Ang II specifically activates enzyme systems that promote superoxide generation and raise the possibility that these pathways function as second messengers for long-term responses, such as hypertrophy or hyperplasia.

@article{doi10116101res7461141,
    author = "Griendling, Kathy K. and Minieri, C A and Ollerenshaw, Jeremy D. and Alexander, R. Wayne",
    title = "Angiotensin II stimulates NADH and NADPH oxidase activity in cultured vascular smooth muscle cells.",
    year = "1994",
    journal = "Circulation Research",
    abstract = "The signaling pathways involved in the long-term metabolic effects of angiotensin II (Ang II) in vascular smooth muscle cells are incompletely understood but include the generation of molecules likely to affect oxidase activity. We examined the ability of Ang II to stimulate superoxide anion formation and investigated the identity of the oxidases responsible for its production. Treatment of vascular smooth muscle cells with Ang II for 4 to 6 hours caused a 2.7 +/- 0.4-fold increase in intracellular superoxide anion formation as detected by lucigenin assay. This superoxide appeared to result from activation of both the NADPH and NADH oxidases. NADPH oxidase activity increased from 3.23 +/- 0.61 to 11.80 +/- 1.72 nmol O2-/min per milligram protein after 4 hours of Ang II, whereas NADH oxidase activity increased from 16.76 +/- 2.13 to 45.00 +/- 4.57 nmol O2-/min per milligram protein. The NADPH oxidase activity was stimulated by exogenous phosphatidic and arachidonic acids and was partially inhibited by the specific inhibitor diphenylene iodinium. NADH oxidase activity was increased by arachidonic and linoleic acids, was insensitive to exogenous phosphatidic acid, and was inhibited by high concentrations of quinacrine. Both of these oxidases appear to reside in the plasma membrane, on the basis of migration of the activity after cellular fractionation and their apparent insensitivity to the mitochondrial poison KCN. These observations suggest that Ang II specifically activates enzyme systems that promote superoxide generation and raise the possibility that these pathways function as second messengers for long-term responses, such as hypertrophy or hyperplasia.",
    url = "https://doi.org/10.1161/01.res.74.6.1141",
    doi = "10.1161/01.res.74.6.1141",
    openalex = "W2110182057"
}

UNLABELLED: Osteochondral progenitor cells were used to repair large, full-thickness defects of the articular cartilage that had been created in the knees of rabbits. Adherent cells from bone marrow, or cells from the periosteum that had been liberated from connective tissue by collagenase digestion, were grown in culture, dispersed in a type-I collagen gel, and transplanted into a large (three-by-six-millimeter), full-thickness (three-millimeter) defect in the weight-bearing surface of the medial femoral condyle. The contralateral knee served as a control: either the defect in that knee was left empty or a cell-free collagen gel was implanted. The periosteal and the bone-marrow-derived cells showed similar patterns of differentiation into articular cartilage and subchondral bone. Specimens of reparative tissue were analyzed with use of a semiquantitative histological grading system and by mechanical testing with employment of a porous indenter to measure the compliance of the tissue at intervals until twenty-four weeks after the operation. There was no apparent difference between the results obtained with the cells from the bone marrow and those from the periosteum. As early as two weeks after transplantation, the autologous osteochondral progenitor cells had uniformly differentiated into chondrocytes throughout the defects. This repair cartilage was subsequently replaced with bone in a proximal-to-distal direction, until, at twenty-four weeks after transplantation, the subchondral bone was completely repaired, without loss of overlying articular cartilage. The mechanical testing data were a useful index of the quality of the long-term repair. Twenty-four weeks after transplantation, the reparative tissue of both the bone-marrow and the periosteal cells was stiffer and less compliant than the tissue derived from the empty defects but less stiff and more compliant than normal cartilage. CLINICAL RELEVANCE: The current modalities for the repair of defects of the articular cartilage have many disadvantages. The transplantation of progenitor cells that will form cartilage and bone offers a possible alternative to these methods. As demonstrated in this report, autologous, bone-marrow-derived, osteochondral progenitor cells can be isolated and grown in vitro without the loss of their capacity to differentiate into cartilage or bone. Sufficient autologous cells can be generated to initiate the repair of articular cartilage and the reformation of subchondral bone. The repair tissues appear to undergo the same developmental transitions that originally led to the formation of articular tissue in the embryo.(ABSTRACT TRUNCATED AT 400 WORDS)

@article{doi1021060000462319940400000013,
    author = "Wakitani, Shigeyuki and Goto, Tatsuhiko and Pineda, S J and Young, Randell G. and Mansour, Joseph M. and Caplan, Arnold I. and Goldberg, V M",
    title = "Mesenchymal cell-based repair of large, full-thickness defects of articular cartilage.",
    year = "1994",
    journal = "Journal of Bone and Joint Surgery",
    abstract = "UNLABELLED: Osteochondral progenitor cells were used to repair large, full-thickness defects of the articular cartilage that had been created in the knees of rabbits. Adherent cells from bone marrow, or cells from the periosteum that had been liberated from connective tissue by collagenase digestion, were grown in culture, dispersed in a type-I collagen gel, and transplanted into a large (three-by-six-millimeter), full-thickness (three-millimeter) defect in the weight-bearing surface of the medial femoral condyle. The contralateral knee served as a control: either the defect in that knee was left empty or a cell-free collagen gel was implanted. The periosteal and the bone-marrow-derived cells showed similar patterns of differentiation into articular cartilage and subchondral bone. Specimens of reparative tissue were analyzed with use of a semiquantitative histological grading system and by mechanical testing with employment of a porous indenter to measure the compliance of the tissue at intervals until twenty-four weeks after the operation. There was no apparent difference between the results obtained with the cells from the bone marrow and those from the periosteum. As early as two weeks after transplantation, the autologous osteochondral progenitor cells had uniformly differentiated into chondrocytes throughout the defects. This repair cartilage was subsequently replaced with bone in a proximal-to-distal direction, until, at twenty-four weeks after transplantation, the subchondral bone was completely repaired, without loss of overlying articular cartilage. The mechanical testing data were a useful index of the quality of the long-term repair. Twenty-four weeks after transplantation, the reparative tissue of both the bone-marrow and the periosteal cells was stiffer and less compliant than the tissue derived from the empty defects but less stiff and more compliant than normal cartilage. CLINICAL RELEVANCE: The current modalities for the repair of defects of the articular cartilage have many disadvantages. The transplantation of progenitor cells that will form cartilage and bone offers a possible alternative to these methods. As demonstrated in this report, autologous, bone-marrow-derived, osteochondral progenitor cells can be isolated and grown in vitro without the loss of their capacity to differentiate into cartilage or bone. Sufficient autologous cells can be generated to initiate the repair of articular cartilage and the reformation of subchondral bone. The repair tissues appear to undergo the same developmental transitions that originally led to the formation of articular tissue in the embryo.(ABSTRACT TRUNCATED AT 400 WORDS)",
    url = "https://doi.org/10.2106/00004623-199404000-00013",
    doi = "10.2106/00004623-199404000-00013",
    openalex = "W1522229466",
    references = "doi101126science6403986"
}

@article{doi101016089158499400198s,
    author = "Burdon, Roy H.",
    title = "Superoxide and hydrogen peroxide in relation to mammalian cell proliferation",
    year = "1995",
    journal = "Free Radical Biology and Medicine",
    url = "https://doi.org/10.1016/0891-5849(94)00198-s",
    doi = "10.1016/0891-5849(94)00198-s",
    openalex = "W2058461613"
}

Several polycations possessing substantial buffering capacity below physiological pH, such as lipopolyamines and polyamidoamine polymers, are efficient transfection agents per se--i.e., without the addition of cell targeting or membrane-disruption agents. This observation led us to test the cationic polymer polyethylenimine (PEI) for its gene-delivery potential. Indeed, every third atom of PEI is a protonable amino nitrogen atom, which makes the polymeric network an effective "proton sponge" at virtually any pH. Luciferase reporter gene transfer with this polycation into a variety of cell lines and primary cells gave results comparable to, or even better than, lipopolyamines. Cytotoxicity was low and seen only at concentrations well above those required for optimal transfection. Delivery of oligonucleotides into embryonic neurons was followed by using a fluorescent probe. Virtually all neurons showed nuclear labeling, with no toxic effects. The optimal PEI cation/anion balance for in vitro transfection is only slightly on the cationic side, which is advantageous for in vivo delivery. Indeed, intracerebral luciferase gene transfer into newborn mice gave results comparable (for a given amount of DNA) to the in vitro transfection of primary rat brain endothelial cells or chicken embryonic neurons. Together, these properties make PEI a promising vector for gene therapy and an outstanding core for the design of more sophisticated devices. Our hypothesis is that its efficiency relies on extensive lysosome buffering that protects DNA from nuclease degradation, and consequent lysosomal swelling and rupture that provide an escape mechanism for the PEI/DNA particles.

@article{doi101073pnas92167297,
    author = "Boussif, Otmane and Lezoualc’h, Frank and Zanta, Maria Antonietta and Mergny, M D and Scherman, Daniel and Demeneix, Barbara and Behr, Jean‐Paul",
    title = "A versatile vector for gene and oligonucleotide transfer into cells in culture and in vivo: polyethylenimine.",
    year = "1995",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = {Several polycations possessing substantial buffering capacity below physiological pH, such as lipopolyamines and polyamidoamine polymers, are efficient transfection agents per se--i.e., without the addition of cell targeting or membrane-disruption agents. This observation led us to test the cationic polymer polyethylenimine (PEI) for its gene-delivery potential. Indeed, every third atom of PEI is a protonable amino nitrogen atom, which makes the polymeric network an effective "proton sponge" at virtually any pH. Luciferase reporter gene transfer with this polycation into a variety of cell lines and primary cells gave results comparable to, or even better than, lipopolyamines. Cytotoxicity was low and seen only at concentrations well above those required for optimal transfection. Delivery of oligonucleotides into embryonic neurons was followed by using a fluorescent probe. Virtually all neurons showed nuclear labeling, with no toxic effects. The optimal PEI cation/anion balance for in vitro transfection is only slightly on the cationic side, which is advantageous for in vivo delivery. Indeed, intracerebral luciferase gene transfer into newborn mice gave results comparable (for a given amount of DNA) to the in vitro transfection of primary rat brain endothelial cells or chicken embryonic neurons. Together, these properties make PEI a promising vector for gene therapy and an outstanding core for the design of more sophisticated devices. Our hypothesis is that its efficiency relies on extensive lysosome buffering that protects DNA from nuclease degradation, and consequent lysosomal swelling and rupture that provide an escape mechanism for the PEI/DNA particles.},
    url = "https://doi.org/10.1073/pnas.92.16.7297",
    doi = "10.1073/pnas.92.16.7297",
    openalex = "W2010655741",
    references = "doi1010160022175983903034"
}

@article{doi101016s0092867400800859,
    author = "Liu, Xuesong and Kim, Caryn Naekyung and Yang, Jie and Jemmerson, Ronald and Wang, Xiaodong",
    title = "Induction of Apoptotic Program in Cell-Free Extracts: Requirement for dATP and Cytochrome c",
    year = "1996",
    journal = "Cell",
    url = "https://doi.org/10.1016/s0092-8674(00)80085-9",
    doi = "10.1016/s0092-8674(00)80085-9",
    openalex = "W2149967205"
}

Abstract The dye exclusion test is used to determine the number of viable cells present in a cell suspension. It is based on the principle that live cells possess intact cell membranes that exclude certain dyes, such as trypan blue, Eosin, or propidium, whereas dead cells do not. In this test, a cell suspension is simply mixed with dye and then visually examined to determine whether cells take up or exclude dye. In the protocol presented here, a viable cell will have a clear cytoplasm whereas a nonviable cell will have a blue cytoplasm.

@article{doi1010020471142735ima03bs21,
    author = "Strober, Warren",
    title = "Trypan Blue Exclusion Test of Cell Viability",
    year = "1997",
    journal = "Current Protocols in Immunology",
    abstract = "Abstract The dye exclusion test is used to determine the number of viable cells present in a cell suspension. It is based on the principle that live cells possess intact cell membranes that exclude certain dyes, such as trypan blue, Eosin, or propidium, whereas dead cells do not. In this test, a cell suspension is simply mixed with dye and then visually examined to determine whether cells take up or exclude dye. In the protocol presented here, a viable cell will have a clear cytoplasm whereas a nonviable cell will have a blue cytoplasm.",
    url = "https://doi.org/10.1002/0471142735.ima03bs21",
    doi = "10.1002/0471142735.ima03bs21",
    openalex = "W4230982340"
}

3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction is one of the most frequently used methods for measuring cell proliferation and neural cytotoxicity. It is widely assumed that MTT is reduced by active mitochondria in living cells. By using isolated mitochondria from rat brain and B12 cells, we indeed found that malate, glutamate, and succinate support MTT reduction by isolated mitochondria. However, the data presented in this study do not support the exclusive role of mitochondria in MTT reduction by intact cells. Using a variety of approaches, we found that MTT reduction by B12 cells is confined to intracellular vesicles that later give rise to the needle-like MTT formazan at the cell surface. Some of these vesicles were identified as endosomes or lysosomes. In addition, MTT was found to be membrane impermeable. These and other results suggest that MTT is taken up by cells through endocytosis and that reduced MTT formazan accumulates in the endosomal/lysosomal compartment and is then transported to the cell surface through exocytosis.

@article{doi101046j14714159199769020581x,
    author = "Liu, Yuanbin and Peterson, Daniel A. and Kimura, Hideo and Schubert, David",
    title = "Mechanism of Cellular 3‐(4,5‐Dimethylthiazol‐2‐yl)‐2,5‐Diphenyltetrazolium Bromide (MTT) Reduction",
    year = "1997",
    journal = "Journal of Neurochemistry",
    abstract = "3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction is one of the most frequently used methods for measuring cell proliferation and neural cytotoxicity. It is widely assumed that MTT is reduced by active mitochondria in living cells. By using isolated mitochondria from rat brain and B12 cells, we indeed found that malate, glutamate, and succinate support MTT reduction by isolated mitochondria. However, the data presented in this study do not support the exclusive role of mitochondria in MTT reduction by intact cells. Using a variety of approaches, we found that MTT reduction by B12 cells is confined to intracellular vesicles that later give rise to the needle-like MTT formazan at the cell surface. Some of these vesicles were identified as endosomes or lysosomes. In addition, MTT was found to be membrane impermeable. These and other results suggest that MTT is taken up by cells through endocytosis and that reduced MTT formazan accumulates in the endosomal/lysosomal compartment and is then transported to the cell surface through exocytosis.",
    url = "https://doi.org/10.1046/j.1471-4159.1997.69020581.x",
    doi = "10.1046/j.1471-4159.1997.69020581.x",
    openalex = "W1993943341"
}

@article{doi101006excr19973858,
    author = "Johnstone, Brian and Hering, Thomas M. and Caplan, Arnold I. and Goldberg, Victor M. and Yoo, Jung U.",
    title = "In VitroChondrogenesis of Bone Marrow-Derived Mesenchymal Progenitor Cells",
    year = "1998",
    journal = "Experimental Cell Research",
    url = "https://doi.org/10.1006/excr.1997.3858",
    doi = "10.1006/excr.1997.3858",
    openalex = "W1544751778"
}

Stimulation of various cells with growth factors results in a transient increase in the intracellular concentration of H2O2 that is required for growth factor-induced protein tyrosine phosphorylation. The effect of H2O2 produced in response to epidermal growth factor (EGF) on the activity of protein-tyrosine phosphatase 1B (PTP1B) was investigated in A431 human epidermoid carcinoma cells. H2O2 inactivated recombinant PTP1B in vitro by oxidizing its catalytic site cysteine, most likely to sulfenic acid. The oxidized enzyme was reactivated more effectively by thioredoxin than by glutaredoxin or glutathione at their physiological concentrations. Oxidation by H2O2 prevented modification of the catalytic cysteine of PTP1B by iodoacetic acid, suggesting that it should be possible to monitor the oxidation state of PTP1B in cells by measuring the incorporation of radioactivity into the enzyme after lysis of the cells in the presence of radiolabeled iodoacetic acid. The amount of such radioactivity associated with PTP1B immunoprecipitated from A431 cells that had been stimulated with EGF for 10 min was 27% less than that associated with PTP1B from unstimulated cells. The amount of iodoacetic acid-derived radioactivity associated with PTP1B reached a minimum 10 min after stimulation of cells with EGF and returned to base line values by 40 min, suggesting that the oxidation of PTP1B is reversible in cells. These results indicate that the activation of a receptor tyrosine kinase by binding of the corresponding growth factor may not be sufficient to increase the steady state level of protein tyrosine phosphorylation in cells and that concurrent inhibition of protein-tyrosine phosphatases by H2O2 might also be required.

@article{doi101074jbc2732515366,
    author = "Lee, Seung-Rock and Kwon, Ki‐Sun and Kim, Seung-Ryul and Rhee, Sue Goo",
    title = "Reversible Inactivation of Protein-tyrosine Phosphatase 1B in A431 Cells Stimulated with Epidermal Growth Factor",
    year = "1998",
    journal = "Journal of Biological Chemistry",
    abstract = "Stimulation of various cells with growth factors results in a transient increase in the intracellular concentration of H2O2 that is required for growth factor-induced protein tyrosine phosphorylation. The effect of H2O2 produced in response to epidermal growth factor (EGF) on the activity of protein-tyrosine phosphatase 1B (PTP1B) was investigated in A431 human epidermoid carcinoma cells. H2O2 inactivated recombinant PTP1B in vitro by oxidizing its catalytic site cysteine, most likely to sulfenic acid. The oxidized enzyme was reactivated more effectively by thioredoxin than by glutaredoxin or glutathione at their physiological concentrations. Oxidation by H2O2 prevented modification of the catalytic cysteine of PTP1B by iodoacetic acid, suggesting that it should be possible to monitor the oxidation state of PTP1B in cells by measuring the incorporation of radioactivity into the enzyme after lysis of the cells in the presence of radiolabeled iodoacetic acid. The amount of such radioactivity associated with PTP1B immunoprecipitated from A431 cells that had been stimulated with EGF for 10 min was 27\% less than that associated with PTP1B from unstimulated cells. The amount of iodoacetic acid-derived radioactivity associated with PTP1B reached a minimum 10 min after stimulation of cells with EGF and returned to base line values by 40 min, suggesting that the oxidation of PTP1B is reversible in cells. These results indicate that the activation of a receptor tyrosine kinase by binding of the corresponding growth factor may not be sufficient to increase the steady state level of protein tyrosine phosphorylation in cells and that concurrent inhibition of protein-tyrosine phosphatases by H2O2 might also be required.",
    url = "https://doi.org/10.1074/jbc.273.25.15366",
    doi = "10.1074/jbc.273.25.15366",
    openalex = "W2136573391"
}

Human mesenchymal stem cells are thought to be multipotent cells, which are present in adult marrow, that can replicate as undifferentiated cells and that have the potential to differentiate to lineages of mesenchymal tissues, including bone, cartilage, fat, tendon, muscle, and marrow stroma. Cells that have the characteristics of human mesenchymal stem cells were isolated from marrow aspirates of volunteer donors. These cells displayed a stable phenotype and remained as a monolayer in vitro. These adult stem cells could be induced to differentiate exclusively into the adipocytic, chondrocytic, or osteocytic lineages. Individual stem cells were identified that, when expanded to colonies, retained their multilineage potential.

@article{doi101126science2845411143,
    author = "Pittenger, Mark F. and Mackay, Alastair M. and Beck, Stephen C. and Jaiswal, Rama K. and Douglas, R. Gordon and Mosca, Joseph D. and Moorman, Mark A. and Simonetti, Donald W. and Craig, Stewart and Marshak, Daniel R.",
    title = "Multilineage Potential of Adult Human Mesenchymal Stem Cells",
    year = "1999",
    journal = "Science",
    abstract = "Human mesenchymal stem cells are thought to be multipotent cells, which are present in adult marrow, that can replicate as undifferentiated cells and that have the potential to differentiate to lineages of mesenchymal tissues, including bone, cartilage, fat, tendon, muscle, and marrow stroma. Cells that have the characteristics of human mesenchymal stem cells were isolated from marrow aspirates of volunteer donors. These cells displayed a stable phenotype and remained as a monolayer in vitro. These adult stem cells could be induced to differentiate exclusively into the adipocytic, chondrocytic, or osteocytic lineages. Individual stem cells were identified that, when expanded to colonies, retained their multilineage potential.",
    url = "https://doi.org/10.1126/science.284.5411.143",
    doi = "10.1126/science.284.5411.143",
    openalex = "W2159999899"
}

Adult marrow contains mesenchymal progenitor cells (MPCs) that have multiple differentiation potentials. A conditionally immortalized MPC clone, BMC9, has been identified that exhibits four mesenchymal cell phenotypes: chondrocyte, adipocyte, stromal (support osteoclast formation), and osteoblast. The BMC9 clone, control brain fibroblasts and another marrow-derived clone, BMC10, were isolated from a transgenic mouse (H-2Kb-tsA58) containing a gene for conditional immortality. To test for chondrogenic potential, cells were cultured in defined medium containing 10 ng/ml transforming growth factor beta and 10-7 M dexamethasone in 15-ml polypropylene tubes ("aggregate cultures"). Adipogenic potential was quantitated by flow cytometry of Nile Red-stained cells cultured for 1 and 2 weeks in medium containing isobutyl methylxanthine, indomethacin, insulin, and dexamethasone. Support of osteoclast formation was measured by quantitating multinucleated tartrate-resistant acid phosphatase-positive cells in spleen cell cocultures of test clones (immortomouse clones and positive control ST2 cells) cultured in the presence of 10-7 M vitamin D3 and 150 mM ascorbate-2-phosphate. In vivo osteogenic potential was assayed by histologic examination of bone formation in subcutaneous implants, into athymic mouse hosts, of a composite of cells combined with porous calcium phosphate ceramics. The bone marrow-derived clone BMC9 has the potential to express each of the four mesenchymal characteristics tested, while brain fibroblasts, tested under identical conditions, did not exhibit any of these four mesenchymal characteristics. BMC10 cells exhibited osteogenic and chondrogenic phenotypes, but showed only minimal expression of adipocytic or osteoclast-supportive phenotypes. Clone BMC9 is, minimally, a quadripotential MPC isolated from the marrow of an adult mouse that can differentiate into cartilage and adipose, support osteoclast formation, and form bone. The BMC9 clone is an example of an adult-derived multipotential progenitor cell that is situated early in the mesenchymal lineage.

@article{doi101359jbmr1999145700,
    author = "Dennis, James E. and Merriam, Anita P. and Awadallah, Amad and Yoo, Jung U. and Johnstone, Brian and Caplan, Arnold I.",
    title = "A Quadripotential Mesenchymal Progenitor Cell Isolated from the Marrow of an Adult Mouse",
    year = "1999",
    journal = "Journal of Bone and Mineral Research",
    abstract = {Adult marrow contains mesenchymal progenitor cells (MPCs) that have multiple differentiation potentials. A conditionally immortalized MPC clone, BMC9, has been identified that exhibits four mesenchymal cell phenotypes: chondrocyte, adipocyte, stromal (support osteoclast formation), and osteoblast. The BMC9 clone, control brain fibroblasts and another marrow-derived clone, BMC10, were isolated from a transgenic mouse (H-2Kb-tsA58) containing a gene for conditional immortality. To test for chondrogenic potential, cells were cultured in defined medium containing 10 ng/ml transforming growth factor beta and 10-7 M dexamethasone in 15-ml polypropylene tubes ("aggregate cultures"). Adipogenic potential was quantitated by flow cytometry of Nile Red-stained cells cultured for 1 and 2 weeks in medium containing isobutyl methylxanthine, indomethacin, insulin, and dexamethasone. Support of osteoclast formation was measured by quantitating multinucleated tartrate-resistant acid phosphatase-positive cells in spleen cell cocultures of test clones (immortomouse clones and positive control ST2 cells) cultured in the presence of 10-7 M vitamin D3 and 150 mM ascorbate-2-phosphate. In vivo osteogenic potential was assayed by histologic examination of bone formation in subcutaneous implants, into athymic mouse hosts, of a composite of cells combined with porous calcium phosphate ceramics. The bone marrow-derived clone BMC9 has the potential to express each of the four mesenchymal characteristics tested, while brain fibroblasts, tested under identical conditions, did not exhibit any of these four mesenchymal characteristics. BMC10 cells exhibited osteogenic and chondrogenic phenotypes, but showed only minimal expression of adipocytic or osteoclast-supportive phenotypes. Clone BMC9 is, minimally, a quadripotential MPC isolated from the marrow of an adult mouse that can differentiate into cartilage and adipose, support osteoclast formation, and form bone. The BMC9 clone is an example of an adult-derived multipotential progenitor cell that is situated early in the mesenchymal lineage.},
    url = "https://doi.org/10.1359/jbmr.1999.14.5.700",
    doi = "10.1359/jbmr.1999.14.5.700",
    openalex = "W1986457784"
}

@article{crossref2000announcement,
    title = "ANNOUNCEMENT – Frontiers of Cellular Microbiology and Cell Biology",
    year = "2000",
    journal = "Microbial Pathogenesis",
    url = "https://doi.org/10.1006/mpat.2000.0387",
    doi = "10.1006/mpat.2000.0387",
    number = "1",
    openalex = "W4230669699",
    pages = "61",
    volume = "29"
}

We show here the identity of Alamar Blue as resazurin. The 'resazurin reduction test' has been used for about 50 years to monitor bacterial and yeast contamination of milk, and also for assessing semen quality. Resazurin (blue and nonfluorescent) is reduced to resorufin (pink and highly fluorescent) which is further reduced to hydroresorufin (uncoloured and nonfluorescent). It is still not known how this reduction occurs, intracellularly via enzyme activity or in the medium as a chemical reaction, although the reduced fluorescent form of Alamar Blue was found in the cytoplasm and of living cells nucleus of dead cells. Recently, the dye has gained popularity as a very simple and versatile way of measuring cell proliferation and cytotoxicity. This dye presents numerous advantages over other cytotoxicity or proliferation tests but we observed several drawbacks to the routine use of Alamar Blue. Tests with several toxicants in different cell lines and rat primary hepatocytes have shown accumulation of the fluorescent product of Alamar Blue in the medium which could lead to an overestimation of cell population. Also, the extensive reduction of Alamar Blue by metabolically active cells led to a final nonfluorescent product, and hence an underestimation of cellular activity.

@article{doi101046j14321327200001606x,
    author = "O’Brien, John and Wilson, Ian D. and Orton, Terry C. and Pognan, François",
    title = "Investigation of the Alamar Blue (resazurin) fluorescent dye for the assessment of mammalian cell cytotoxicity",
    year = "2000",
    journal = "European Journal of Biochemistry",
    abstract = "We show here the identity of Alamar Blue as resazurin. The 'resazurin reduction test' has been used for about 50 years to monitor bacterial and yeast contamination of milk, and also for assessing semen quality. Resazurin (blue and nonfluorescent) is reduced to resorufin (pink and highly fluorescent) which is further reduced to hydroresorufin (uncoloured and nonfluorescent). It is still not known how this reduction occurs, intracellularly via enzyme activity or in the medium as a chemical reaction, although the reduced fluorescent form of Alamar Blue was found in the cytoplasm and of living cells nucleus of dead cells. Recently, the dye has gained popularity as a very simple and versatile way of measuring cell proliferation and cytotoxicity. This dye presents numerous advantages over other cytotoxicity or proliferation tests but we observed several drawbacks to the routine use of Alamar Blue. Tests with several toxicants in different cell lines and rat primary hepatocytes have shown accumulation of the fluorescent product of Alamar Blue in the medium which could lead to an overestimation of cell population. Also, the extensive reduction of Alamar Blue by metabolically active cells led to a final nonfluorescent product, and hence an underestimation of cellular activity.",
    url = "https://doi.org/10.1046/j.1432-1327.2000.01606.x",
    doi = "10.1046/j.1432-1327.2000.01606.x",
    openalex = "W2154385453"
}

Neural stem cells exist not only in the developing mammalian nervous system but also in the adult nervous system of all mammalian organisms, including humans. Neural stem cells can also be derived from more primitive embryonic stem cells. The location of the adult stem cells and the brain regions to which their progeny migrate in order to differentiate remain unresolved, although the number of viable locations is limited in the adult. The mechanisms that regulate endogenous stem cells are poorly understood. Potential uses of stem cells in repair include transplantation to repair missing cells and the activation of endogenous cells to provide "self-repair. " Before the full potential of neural stem cells can be realized, we need to learn what controls their proliferation, as well as the various pathways of differentiation available to their daughter cells.

@article{doi101126science28754571433,
    author = "Gage, Fred H.",
    title = "Mammalian Neural Stem Cells",
    year = "2000",
    journal = "Science",
    abstract = {Neural stem cells exist not only in the developing mammalian nervous system but also in the adult nervous system of all mammalian organisms, including humans. Neural stem cells can also be derived from more primitive embryonic stem cells. The location of the adult stem cells and the brain regions to which their progeny migrate in order to differentiate remain unresolved, although the number of viable locations is limited in the adult. The mechanisms that regulate endogenous stem cells are poorly understood. Potential uses of stem cells in repair include transplantation to repair missing cells and the activation of endogenous cells to provide "self-repair. " Before the full potential of neural stem cells can be realized, we need to learn what controls their proliferation, as well as the various pathways of differentiation available to their daughter cells.},
    url = "https://doi.org/10.1126/science.287.5457.1433",
    doi = "10.1126/science.287.5457.1433",
    openalex = "W2084652820",
    references = "doi101126science2715251978"
}

Estrogen deficiency induces bone loss by upregulating osteoclastogenesis by mechanisms not completely defined. We found that ovariectomy-enhanced T-cell production of TNF-alpha, which, acting through the TNF-alpha receptor p55, augments macrophage colony-stimulating factor-induced (M-CSF-induced) and RANKL-induced osteoclastogenesis. Ovariectomy failed to induce bone loss, stimulate bone resorption, or increase M-CSF- and RANKL-dependent osteoclastogenesis in T-cell deficient mice, establishing T cells as essential mediators of the bone-wasting effects of estrogen deficiency in vivo. These findings demonstrate that the ability of estrogen to target T cells, suppressing their production of TNF-alpha, is a key mechanism by which estrogen prevents osteoclastic bone resorption and bone loss.

@article{doi101172jci11066,
    author = "Cenci, Simone and Weitzmann, M. Neale and Roggia, Cristiana and Namba, Noriyuki and Novack, Deborah V. and Woodring, Jessica and Pacifici, Roberto",
    title = "Estrogen deficiency induces bone loss by enhancing T-cell production of TNF-α",
    year = "2000",
    journal = "Journal of Clinical Investigation",
    abstract = "Estrogen deficiency induces bone loss by upregulating osteoclastogenesis by mechanisms not completely defined. We found that ovariectomy-enhanced T-cell production of TNF-alpha, which, acting through the TNF-alpha receptor p55, augments macrophage colony-stimulating factor-induced (M-CSF-induced) and RANKL-induced osteoclastogenesis. Ovariectomy failed to induce bone loss, stimulate bone resorption, or increase M-CSF- and RANKL-dependent osteoclastogenesis in T-cell deficient mice, establishing T cells as essential mediators of the bone-wasting effects of estrogen deficiency in vivo. These findings demonstrate that the ability of estrogen to target T cells, suppressing their production of TNF-alpha, is a key mechanism by which estrogen prevents osteoclastic bone resorption and bone loss.",
    url = "https://doi.org/10.1172/jci11066",
    doi = "10.1172/jci11066",
    openalex = "W2133281510",
    references = "openalexw1585377912"
}

The adult skeleton regenerates by temporary cellular structures that comprise teams of juxtaposed osteoclasts and osteoblasts and replace periodically old bone with new. A considerable body of evidence accumulated during the last decade has shown that the rate of genesis of these two highly specialized cell types, as well as the prevalence of their apoptosis, is essential for the maintenance of bone homeostasis; and that common metabolic bone disorders such as osteoporosis result largely from a derangement in the birth or death of these cells. The purpose of this article is 3-fold: 1) to review the role and the molecular mechanism of action of regulatory molecules, such as cytokines and hormones, in osteoclast and osteoblast birth and apoptosis; 2) to review the evidence for the contribution of changes in bone cell birth or death to the pathogenesis of the most common forms of osteoporosis; and 3) to highlight the implications of bone cell birth and death for a better understanding of the mechanism of action and efficacy of present and future pharmacotherapeutic agents for osteoporosis.

@article{doi101210edrv2120395,
    author = "Manolagas, Stavros C.",
    title = "Birth and Death of Bone Cells: Basic Regulatory Mechanisms and Implications for the Pathogenesis and Treatment of Osteoporosis*",
    year = "2000",
    journal = "Endocrine Reviews",
    abstract = "The adult skeleton regenerates by temporary cellular structures that comprise teams of juxtaposed osteoclasts and osteoblasts and replace periodically old bone with new. A considerable body of evidence accumulated during the last decade has shown that the rate of genesis of these two highly specialized cell types, as well as the prevalence of their apoptosis, is essential for the maintenance of bone homeostasis; and that common metabolic bone disorders such as osteoporosis result largely from a derangement in the birth or death of these cells. The purpose of this article is 3-fold: 1) to review the role and the molecular mechanism of action of regulatory molecules, such as cytokines and hormones, in osteoclast and osteoblast birth and apoptosis; 2) to review the evidence for the contribution of changes in bone cell birth or death to the pathogenesis of the most common forms of osteoporosis; and 3) to highlight the implications of bone cell birth and death for a better understanding of the mechanism of action and efficacy of present and future pharmacotherapeutic agents for osteoporosis.",
    url = "https://doi.org/10.1210/edrv.21.2.0395",
    doi = "10.1210/edrv.21.2.0395",
    openalex = "W2142820105",
    references = "doi101002jcb240550303"
}

OBJECTIVE: To characterize mesenchymal stem cells (MSCs) from human synovial membrane (SM). METHODS: Cell populations were enzymatically released from the SM obtained from knee joints of adult human donors and were expanded in monolayer with serial passages at confluence. Cell clones were obtained by limiting dilution. At different passages, SM-derived cells were subjected to in vitro assays to investigate their multilineage potential. Upon treatments, phenotypes of cell cultures were analyzed by histo- and immunohistochemistry and by semiquantitative reverse transcription-polymerase chain reaction for the expression of lineage-retated marker genes. RESULTS: SM-derived cells could be expanded extensively in monolayer, with limited senescence. Under appropriate culture conditions, SM-derived cells were induced to differentiate to the chondrocyte, osteocyte, and adipocyte lineages. Sporadic myogenesis was also observed. Five independent cell clones displayed multilineage potential. Interestingly, only 1 clone was myogenic. Donor age, cell passaging, and cryopreservation did not affect the multilineage potential of SM-derived cells. In contrast, normal dermal fibroblasts under the same culture conditions did not display this potential. CONCLUSION: Our study demonstrates that human multipotent MSCs can be isolated from the SM of knee joints. These cells have the ability to proliferate extensively in culture, and they maintain their multilineage differentiation potential in vitro, establishing their progenitor cell nature. SM-derived MSCs may play a role in the regenerative response during arthritic diseases and are promising candidates for developing novel cell-based therapeutic approaches for postnatal skeletal tissue repair.

@article{doi101002152901312001084481928aidart33130co2p,
    author = "Bari, Cosimo De and Dell’Accio, Francesco and Tylzanowski, Przemyslaw and Luyten, Frank P.",
    title = "Multipotent mesenchymal stem cells from adult human synovial membrane",
    year = "2001",
    journal = "Arthritis \& Rheumatism",
    abstract = "OBJECTIVE: To characterize mesenchymal stem cells (MSCs) from human synovial membrane (SM). METHODS: Cell populations were enzymatically released from the SM obtained from knee joints of adult human donors and were expanded in monolayer with serial passages at confluence. Cell clones were obtained by limiting dilution. At different passages, SM-derived cells were subjected to in vitro assays to investigate their multilineage potential. Upon treatments, phenotypes of cell cultures were analyzed by histo- and immunohistochemistry and by semiquantitative reverse transcription-polymerase chain reaction for the expression of lineage-retated marker genes. RESULTS: SM-derived cells could be expanded extensively in monolayer, with limited senescence. Under appropriate culture conditions, SM-derived cells were induced to differentiate to the chondrocyte, osteocyte, and adipocyte lineages. Sporadic myogenesis was also observed. Five independent cell clones displayed multilineage potential. Interestingly, only 1 clone was myogenic. Donor age, cell passaging, and cryopreservation did not affect the multilineage potential of SM-derived cells. In contrast, normal dermal fibroblasts under the same culture conditions did not display this potential. CONCLUSION: Our study demonstrates that human multipotent MSCs can be isolated from the SM of knee joints. These cells have the ability to proliferate extensively in culture, and they maintain their multilineage differentiation potential in vitro, establishing their progenitor cell nature. SM-derived MSCs may play a role in the regenerative response during arthritic diseases and are promising candidates for developing novel cell-based therapeutic approaches for postnatal skeletal tissue repair.",
    url = "https://doi.org/10.1002/1529-0131(200108)44:8<1928::aid-art331>3.0.co;2-p",
    doi = "10.1002/1529-0131(200108)44:8<1928::aid-art331>3.0.co;2-p",
    openalex = "W2000097208",
    references = "doi101242jcs11371161"
}

@article{doi101016s0891584900004986,
    author = "Ishige, Kumiko and Schubert, David and Sagara, Yutaka",
    title = "Flavonoids protect neuronal cells from oxidative stress by three distinct mechanisms",
    year = "2001",
    journal = "Free Radical Biology and Medicine",
    url = "https://doi.org/10.1016/s0891-5849(00)00498-6",
    doi = "10.1016/s0891-5849(00)00498-6",
    openalex = "W2133971230",
    references = "doi101046j14714159199769020581x"
}

@article{doi101016s0891584901004804,
    author = "Schäfer, Freya and Buettner, Garry R.",
    title = "Redox environment of the cell as viewed through the redox state of the glutathione disulfide/glutathione couple",
    year = "2001",
    journal = "Free Radical Biology and Medicine",
    url = "https://doi.org/10.1016/s0891-5849(01)00480-4",
    doi = "10.1016/s0891-5849(01)00480-4",
    openalex = "W2132878122"
}

Much of the work conducted on adult stem cells has focused on mesenchymal stem cells (MSCs) found within the bone marrow stroma. Adipose tissue, like bone marrow, is derived from the embryonic mesenchyme and contains a stroma that is easily isolated. Preliminary studies have recently identified a putative stem cell population within the adipose stromal compartment. This cell population, termed processed lipoaspirate (PLA) cells, can be isolated from human lipoaspirates and, like MSCs, differentiate toward the osteogenic, adipogenic, myogenic, and chondrogenic lineages. To confirm whether adipose tissue contains stem cells, the PLA population and multiple clonal isolates were analyzed using several molecular and biochemical approaches. PLA cells expressed multiple CD marker antigens similar to those observed on MSCs. Mesodermal lineage induction of PLA cells and clones resulted in the expression of multiple lineage-specific genes and proteins. Furthermore, biochemical analysis also confirmed lineage-specific activity. In addition to mesodermal capacity, PLA cells and clones differentiated into putative neurogenic cells, exhibiting a neuronal-like morphology and expressing several proteins consistent with the neuronal phenotype. Finally, PLA cells exhibited unique characteristics distinct from those seen in MSCs, including differences in CD marker profile and gene expression.

@article{doi101091mbce02020105,
    author = "Zuk, Patricia A. and Zhu, Min and Ashjian, Peter and Ugarte, Daniel A. De and Huang, Jerry I. and Mizuno, Hiroshi and Alfonso, Zeni C. and Fraser, John K. and Benhaim, Prosper and Hedrick, Marc H.",
    title = "Human Adipose Tissue Is a Source of Multipotent Stem Cells",
    year = "2002",
    journal = "Molecular Biology of the Cell",
    abstract = "Much of the work conducted on adult stem cells has focused on mesenchymal stem cells (MSCs) found within the bone marrow stroma. Adipose tissue, like bone marrow, is derived from the embryonic mesenchyme and contains a stroma that is easily isolated. Preliminary studies have recently identified a putative stem cell population within the adipose stromal compartment. This cell population, termed processed lipoaspirate (PLA) cells, can be isolated from human lipoaspirates and, like MSCs, differentiate toward the osteogenic, adipogenic, myogenic, and chondrogenic lineages. To confirm whether adipose tissue contains stem cells, the PLA population and multiple clonal isolates were analyzed using several molecular and biochemical approaches. PLA cells expressed multiple CD marker antigens similar to those observed on MSCs. Mesodermal lineage induction of PLA cells and clones resulted in the expression of multiple lineage-specific genes and proteins. Furthermore, biochemical analysis also confirmed lineage-specific activity. In addition to mesodermal capacity, PLA cells and clones differentiated into putative neurogenic cells, exhibiting a neuronal-like morphology and expressing several proteins consistent with the neuronal phenotype. Finally, PLA cells exhibited unique characteristics distinct from those seen in MSCs, including differences in CD marker profile and gene expression.",
    url = "https://doi.org/10.1091/mbc.e02-02-0105",
    doi = "10.1091/mbc.e02-02-0105",
    openalex = "W2107503723",
    references = "doi101159000452856, doi101242jcs11371161"
}

At high concentrations, free radicals and radical-derived, nonradical reactive species are hazardous for living organisms and damage all major cellular constituents. At moderate concentrations, however, nitric oxide (NO), superoxide anion, and related reactive oxygen species (ROS) play an important role as regulatory mediators in signaling processes. Many of the ROS-mediated responses actually protect the cells against oxidative stress and reestablish "redox homeostasis." Higher organisms, however, have evolved the use of NO and ROS also as signaling molecules for other physiological functions. These include regulation of vascular tone, monitoring of oxygen tension in the control of ventilation and erythropoietin production, and signal transduction from membrane receptors in various physiological processes. NO and ROS are typically generated in these cases by tightly regulated enzymes such as NO synthase (NOS) and NAD(P)H oxidase isoforms, respectively. In a given signaling protein, oxidative attack induces either a loss of function, a gain of function, or a switch to a different function. Excessive amounts of ROS may arise either from excessive stimulation of NAD(P)H oxidases or from less well-regulated sources such as the mitochondrial electron-transport chain. In mitochondria, ROS are generated as undesirable side products of the oxidative energy metabolism. An excessive and/or sustained increase in ROS production has been implicated in the pathogenesis of cancer, diabetes mellitus, atherosclerosis, neurodegenerative diseases, rheumatoid arthritis, ischemia/reperfusion injury, obstructive sleep apnea, and other diseases. In addition, free radicals have been implicated in the mechanism of senescence. That the process of aging may result, at least in part, from radical-mediated oxidative damage was proposed more than 40 years ago by Harman (J Gerontol 11: 298-300, 1956). There is growing evidence that aging involves, in addition, progressive changes in free radical-mediated regulatory processes that result in altered gene expression.

@article{doi101152physrev000182001,
    author = "Dröge, Wulf",
    title = "Free Radicals in the Physiological Control of Cell Function",
    year = "2002",
    journal = "Physiological Reviews",
    abstract = {At high concentrations, free radicals and radical-derived, nonradical reactive species are hazardous for living organisms and damage all major cellular constituents. At moderate concentrations, however, nitric oxide (NO), superoxide anion, and related reactive oxygen species (ROS) play an important role as regulatory mediators in signaling processes. Many of the ROS-mediated responses actually protect the cells against oxidative stress and reestablish "redox homeostasis." Higher organisms, however, have evolved the use of NO and ROS also as signaling molecules for other physiological functions. These include regulation of vascular tone, monitoring of oxygen tension in the control of ventilation and erythropoietin production, and signal transduction from membrane receptors in various physiological processes. NO and ROS are typically generated in these cases by tightly regulated enzymes such as NO synthase (NOS) and NAD(P)H oxidase isoforms, respectively. In a given signaling protein, oxidative attack induces either a loss of function, a gain of function, or a switch to a different function. Excessive amounts of ROS may arise either from excessive stimulation of NAD(P)H oxidases or from less well-regulated sources such as the mitochondrial electron-transport chain. In mitochondria, ROS are generated as undesirable side products of the oxidative energy metabolism. An excessive and/or sustained increase in ROS production has been implicated in the pathogenesis of cancer, diabetes mellitus, atherosclerosis, neurodegenerative diseases, rheumatoid arthritis, ischemia/reperfusion injury, obstructive sleep apnea, and other diseases. In addition, free radicals have been implicated in the mechanism of senescence. That the process of aging may result, at least in part, from radical-mediated oxidative damage was proposed more than 40 years ago by Harman (J Gerontol 11: 298-300, 1956). There is growing evidence that aging involves, in addition, progressive changes in free radical-mediated regulatory processes that result in altered gene expression.},
    url = "https://doi.org/10.1152/physrev.00018.2001",
    doi = "10.1152/physrev.00018.2001",
    openalex = "W2147993424",
    references = "doi101016030636239190478o, doi10103835021000, doi101093emboj1851321"
}

@article{doi101016jbiocel200311001,
    author = "Barry, Frank and Murphy, Mary",
    title = "Mesenchymal stem cells: clinical applications and biological characterization",
    year = "2004",
    journal = "The International Journal of Biochemistry \& Cell Biology",
    url = "https://doi.org/10.1016/j.biocel.2003.11.001",
    doi = "10.1016/j.biocel.2003.11.001",
    openalex = "W2016931709",
    references = "doi101242jcs11371161"
}

@article{doi101016jtcb200411009,
    author = "McIntosh, Richard and Nicastro, Daniela and Mastronarde, David N.",
    title = "New views of cells in 3D: an introduction to electron tomography",
    year = "2004",
    journal = "Trends in Cell Biology",
    url = "https://doi.org/10.1016/j.tcb.2004.11.009",
    doi = "10.1016/j.tcb.2004.11.009",
    openalex = "W2145778422"
}

@article{doi101016s1534580704000759,
    author = "McBeath, Rowena and Pirone, Dana M. and Nelson, Celeste M. and Bhadriraju, Kiran and Chen, Christopher S.",
    title = "Cell Shape, Cytoskeletal Tension, and RhoA Regulate Stem Cell Lineage Commitment",
    year = "2004",
    journal = "Developmental Cell",
    url = "https://doi.org/10.1016/s1534-5807(04)00075-9",
    doi = "10.1016/s1534-5807(04)00075-9",
    openalex = "W2144023435",
    references = "doi101007bf02406145, doi101016s0142961201000023, doi1015159780691183978018"
}

@article{doi101038nrg1272,
    author = "Barabási, Albert-Ĺaszló and Oltvai, Zoltán N.",
    title = "Network biology: understanding the cell's functional organization",
    year = "2004",
    journal = "Nature Reviews Genetics",
    url = "https://doi.org/10.1038/nrg1272",
    doi = "10.1038/nrg1272",
    openalex = "W2163480486",
    references = "doi101073pnas122653799, doi101103revmodphys7447, doi101126science1073374"
}

Mesenchymal stem cells (MSCs) represent a stem cell population present in adult tissues that can be isolated, expanded in culture, and characterized in vitro and in vivo. MSCs differentiate readily into chondrocytes, adipocytes, osteocytes, and they can support hematopoietic stem cells or embryonic stem cells in culture. Evidence suggests MSCs can also express phenotypic characteristics of endothelial, neural, smooth muscle, skeletal myoblasts, and cardiac myocyte cells. When introduced into the infarcted heart, MSCs prevent deleterious remodeling and improve recovery, although further understanding of MSC differentiation in the cardiac scar tissue is still needed. MSCs have been injected directly into the infarct, or they have been administered intravenously and seen to home to the site of injury. Examination of the interaction of allogeneic MSCs with cells of the immune system indicates little rejection by T cells. Persistence of allogeneic MSCs in vivo suggests their potential "off the shelf" therapeutic use for multiple recipients. Clinical use of cultured human MSCs (hMSCs) has begun for cancer patients, and recipients have received autologous or allogeneic MSCs. Research continues to support the desirable traits of MSCs for development of cellular therapeutics for many tissues, including the cardiovascular system. In summary, hMSCs isolated from adult bone marrow provide an excellent model for development of stem cell therapeutics, and their potential use in the cardiovascular system is currently under investigation in the laboratory and clinical settings.

@article{doi10116101res0000135902993836f,
    author = "Pittenger, Mark F. and Martin, Bradley J.",
    title = "Mesenchymal Stem Cells and Their Potential as Cardiac Therapeutics",
    year = "2004",
    journal = "Circulation Research",
    abstract = {Mesenchymal stem cells (MSCs) represent a stem cell population present in adult tissues that can be isolated, expanded in culture, and characterized in vitro and in vivo. MSCs differentiate readily into chondrocytes, adipocytes, osteocytes, and they can support hematopoietic stem cells or embryonic stem cells in culture. Evidence suggests MSCs can also express phenotypic characteristics of endothelial, neural, smooth muscle, skeletal myoblasts, and cardiac myocyte cells. When introduced into the infarcted heart, MSCs prevent deleterious remodeling and improve recovery, although further understanding of MSC differentiation in the cardiac scar tissue is still needed. MSCs have been injected directly into the infarct, or they have been administered intravenously and seen to home to the site of injury. Examination of the interaction of allogeneic MSCs with cells of the immune system indicates little rejection by T cells. Persistence of allogeneic MSCs in vivo suggests their potential "off the shelf" therapeutic use for multiple recipients. Clinical use of cultured human MSCs (hMSCs) has begun for cancer patients, and recipients have received autologous or allogeneic MSCs. Research continues to support the desirable traits of MSCs for development of cellular therapeutics for many tissues, including the cardiovascular system. In summary, hMSCs isolated from adult bone marrow provide an excellent model for development of stem cell therapeutics, and their potential use in the cardiovascular system is currently under investigation in the laboratory and clinical settings.},
    url = "https://doi.org/10.1161/01.res.0000135902.99383.6f",
    doi = "10.1161/01.res.0000135902.99383.6f",
    openalex = "W2154502936",
    references = "doi101242jcs11371161"
}

Mesenchymal stem cells (MSCs) are multipotent cells found in several adult tissues. Transplanted allogeneic MSCs can be detected in recipients at extended time points, indicating a lack of immune recognition and clearance. As well, a role for bone marrow-derived MSCs in reducing the incidence and severity of graft-versus-host disease (GVHD) during allogeneic transplantation has recently been reported; however, the mechanisms remain to be investigated. We examined the immunomodulatory functions of human MSCs (hMSCs) by coculturing them with purified subpopulations of immune cells and report here that hMSCs altered the cytokine secretion profile of dendritic cells (DCs), naive and effector T cells (T helper 1 [T(H)1] and T(H)2), and natural killer (NK) cells to induce a more anti-inflammatory or tolerant phenotype. Specifically, the hMSCs caused mature DCs type 1 (DC1) to decrease tumor necrosis factor alpha (TNF-alpha) secretion and mature DC2 to increase interleukin-10 (IL-10) secretion; hMSCs caused T(H)1 cells to decrease interferon gamma (IFN-gamma) and caused the T(H)2 cells to increase secretion of IL-4; hMSCs caused an increase in the proportion of regulatory T cells (T(Regs)) present; and hMSCs decreased secretion of IFN-gamma from the NK cells. Mechanistically, the hMSCs produced elevated prostaglandin E2 (PGE(2)) in co-cultures, and inhibitors of PGE(2) production mitigated hMSC-mediated immune modulation. These data offer insight into the interactions between allogeneic MSCs and immune cells and provide mechanisms likely involved with the in vivo MSC-mediated induction of tolerance that could be therapeutic for reduction of GVHD, rejection, and modulation of inflammation.

@article{doi101182blood2004041559,
    author = "Aggarwal, Sudeepta and Pittenger, Mark F.",
    title = "Human mesenchymal stem cells modulate allogeneic immune cell responses",
    year = "2004",
    journal = "Blood",
    abstract = "Mesenchymal stem cells (MSCs) are multipotent cells found in several adult tissues. Transplanted allogeneic MSCs can be detected in recipients at extended time points, indicating a lack of immune recognition and clearance. As well, a role for bone marrow-derived MSCs in reducing the incidence and severity of graft-versus-host disease (GVHD) during allogeneic transplantation has recently been reported; however, the mechanisms remain to be investigated. We examined the immunomodulatory functions of human MSCs (hMSCs) by coculturing them with purified subpopulations of immune cells and report here that hMSCs altered the cytokine secretion profile of dendritic cells (DCs), naive and effector T cells (T helper 1 [T(H)1] and T(H)2), and natural killer (NK) cells to induce a more anti-inflammatory or tolerant phenotype. Specifically, the hMSCs caused mature DCs type 1 (DC1) to decrease tumor necrosis factor alpha (TNF-alpha) secretion and mature DC2 to increase interleukin-10 (IL-10) secretion; hMSCs caused T(H)1 cells to decrease interferon gamma (IFN-gamma) and caused the T(H)2 cells to increase secretion of IL-4; hMSCs caused an increase in the proportion of regulatory T cells (T(Regs)) present; and hMSCs decreased secretion of IFN-gamma from the NK cells. Mechanistically, the hMSCs produced elevated prostaglandin E2 (PGE(2)) in co-cultures, and inhibitors of PGE(2) production mitigated hMSC-mediated immune modulation. These data offer insight into the interactions between allogeneic MSCs and immune cells and provide mechanisms likely involved with the in vivo MSC-mediated induction of tolerance that could be therapeutic for reduction of GVHD, rejection, and modulation of inflammation.",
    url = "https://doi.org/10.1182/blood-2004-04-1559",
    doi = "10.1182/blood-2004-04-1559",
    openalex = "W2095666785",
    references = "doi101242jcs11371161"
}

@article{doi101016jcell200508020,
    author = "Boyer, Laurie A. and Lee, Tong Ihn and Cole, Megan F. and Johnstone, Sarah E. and Levine, Stuart S. and Zucker, Jacob and Guenther, Matthew G. and Kumar, Roshan and Murray, Heather L. and Jenner, Richard G. and Gifford, David K. and Melton, Douglas A. and Jaenisch, Rudolf and Young, Richard A.",
    title = "Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells",
    year = "2005",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2005.08.020",
    doi = "10.1016/j.cell.2005.08.020",
    openalex = "W2107575419"
}

@misc{doi101016s1387265605110047,
    author = "Berridge, Michael V. and Herst, Patries M. and Tan, An S.",
    title = "Tetrazolium dyes as tools in cell biology: New insights into their cellular reduction",
    year = "2005",
    booktitle = "Biotechnology annual review",
    url = "https://doi.org/10.1016/s1387-2656(05)11004-7",
    doi = "10.1016/s1387-2656(05)11004-7",
    openalex = "W1849819493",
    references = "doi101001jama195302940280072039, doi101006abbi19931311, doi1010160003269771903708, doi1010160022175983903034, doi101016030636239190478o, doi101038nri1312, doi101046j14714159199769020581x, doi101093jnci82131113, doi103727095535491820873191, openalexw2143811153"
}

Adult stem cells provide replacement and repair descendants for normal turnover or injured tissues. These cells have been isolated and expanded in culture, and their use for therapeutic strategies requires technologies not yet perfected. In the 1970s, the embryonic chick limb bud mesenchymal cell culture system provided data on the differentiation of cartilage, bone, and muscle. In the 1980s, we used this limb bud cell system as an assay for the purification of inductive factors in bone. In the 1990s, we used the expertise gained with embryonic mesenchymal progenitor cells in culture to develop the technology for isolating, expanding, and preserving the stem cell capacity of adult bone marrow-derived mesenchymal stem cells (MSCs). The 1990s brought us into the new field of tissue engineering, where we used MSCs with site-specific delivery vehicles to repair cartilage, bone, tendon, marrow stroma, muscle, and other connective tissues. In the beginning of the 21st century, we have made substantial advances: the most important is the development of a cell-coating technology, called painting, that allows us to introduce informational proteins to the outer surface of cells. These paints can serve as targeting addresses to specifically dock MSCs or other reparative cells to unique tissue addresses. The scientific and clinical challenge remains: to perfect cell-based tissue-engineering protocols to utilize the body's own rejuvenation capabilities by managing surgical implantations of scaffolds, bioactive factors, and reparative cells to regenerate damaged or diseased skeletal tissues.

@article{doi101089ten2005111198,
    author = "Caplan, Arnold I.",
    title = "Review: Mesenchymal Stem Cells: Cell–Based Reconstructive Therapy in Orthopedics",
    year = "2005",
    journal = "Tissue Engineering",
    abstract = "Adult stem cells provide replacement and repair descendants for normal turnover or injured tissues. These cells have been isolated and expanded in culture, and their use for therapeutic strategies requires technologies not yet perfected. In the 1970s, the embryonic chick limb bud mesenchymal cell culture system provided data on the differentiation of cartilage, bone, and muscle. In the 1980s, we used this limb bud cell system as an assay for the purification of inductive factors in bone. In the 1990s, we used the expertise gained with embryonic mesenchymal progenitor cells in culture to develop the technology for isolating, expanding, and preserving the stem cell capacity of adult bone marrow-derived mesenchymal stem cells (MSCs). The 1990s brought us into the new field of tissue engineering, where we used MSCs with site-specific delivery vehicles to repair cartilage, bone, tendon, marrow stroma, muscle, and other connective tissues. In the beginning of the 21st century, we have made substantial advances: the most important is the development of a cell-coating technology, called painting, that allows us to introduce informational proteins to the outer surface of cells. These paints can serve as targeting addresses to specifically dock MSCs or other reparative cells to unique tissue addresses. The scientific and clinical challenge remains: to perfect cell-based tissue-engineering protocols to utilize the body's own rejuvenation capabilities by managing surgical implantations of scaffolds, bioactive factors, and reparative cells to regenerate damaged or diseased skeletal tissues.",
    url = "https://doi.org/10.1089/ten.2005.11.1198",
    doi = "10.1089/ten.2005.11.1198",
    openalex = "W2013970253",
    references = "doi101126science6403986"
}

Electron tomography (ET) is uniquely suited to obtain three-dimensional reconstructions of pleomorphic structures, such as cells, organelles or supramolecular assemblies. Although the principles of ET have been known for decades, its use has gathered momentum only in recent years, thanks to technological advances and its combination with improved specimen preparation techniques. The rapid freezing/freeze-substitution preparation is applicable to whole cells and tissues, and it is the method of choice for ET investigations of cellular ultrastructure. The frozen-hydrated preparation provides the best possible structural preservation and allows the imaging of molecules, complexes, and supramolecular assemblies in their native state and their natural environment. Devoid of staining and chemical fixation artifacts, cryo-ET provides a faithful representation of both the surface and internal structure of molecules. In combination with advanced computational methods, such as molecular identification based on pattern recognition techniques, cryo-ET is currently the most promising approach to comprehensively map macromolecular architecture inside cellular tomograms.

@article{doi101146annurevbiochem73011303074112,
    author = "Lučić, Vladan and Förster, Friedrich and Baumeister, Wolfgang",
    title = "STRUCTURAL STUDIES BY ELECTRON TOMOGRAPHY: From Cells to Molecules",
    year = "2005",
    journal = "Annual Review of Biochemistry",
    abstract = "Electron tomography (ET) is uniquely suited to obtain three-dimensional reconstructions of pleomorphic structures, such as cells, organelles or supramolecular assemblies. Although the principles of ET have been known for decades, its use has gathered momentum only in recent years, thanks to technological advances and its combination with improved specimen preparation techniques. The rapid freezing/freeze-substitution preparation is applicable to whole cells and tissues, and it is the method of choice for ET investigations of cellular ultrastructure. The frozen-hydrated preparation provides the best possible structural preservation and allows the imaging of molecules, complexes, and supramolecular assemblies in their native state and their natural environment. Devoid of staining and chemical fixation artifacts, cryo-ET provides a faithful representation of both the surface and internal structure of molecules. In combination with advanced computational methods, such as molecular identification based on pattern recognition techniques, cryo-ET is currently the most promising approach to comprehensively map macromolecular architecture inside cellular tomograms.",
    url = "https://doi.org/10.1146/annurev.biochem.73.011303.074112",
    doi = "10.1146/annurev.biochem.73.011303.074112",
    openalex = "W2123176293"
}

Cellular senescence suppresses cancer by arresting cells at risk of malignant tumorigenesis. However, senescent cells also secrete molecules that can stimulate premalignant cells to proliferate and form tumors, suggesting the senescence response is antagonistically pleiotropic. We show that premalignant mammary epithelial cells exposed to senescent human fibroblasts in mice irreversibly lose differentiated properties, become invasive and undergo full malignant transformation. Moreover, using cultured mouse or human fibroblasts and non-malignant breast epithelial cells, we show that senescent fibroblasts disrupt epithelial alveolar morphogenesis, functional differentiation and branching morphogenesis. Furthermore, we identify MMP-3 as the major factor responsible for the effects of senescent fibroblasts on branching morphogenesis. Our findings support the idea that senescent cells contribute to age-related pathology, including cancer, and describe a new property of senescent fibroblasts - the ability to alter epithelial differentiation - that might also explain the loss of tissue function and organization that is a hallmark of aging.

@article{doi101242jcs01635,
    author = "Parrinello, Simona and Coppé, Jean‐Philippe and Krtolica, Ana and Campisi, Judith",
    title = "Stromal-epithelial interactions in aging and cancer: senescent fibroblasts alter epithelial cell differentiation",
    year = "2005",
    journal = "Journal of Cell Science",
    abstract = "Cellular senescence suppresses cancer by arresting cells at risk of malignant tumorigenesis. However, senescent cells also secrete molecules that can stimulate premalignant cells to proliferate and form tumors, suggesting the senescence response is antagonistically pleiotropic. We show that premalignant mammary epithelial cells exposed to senescent human fibroblasts in mice irreversibly lose differentiated properties, become invasive and undergo full malignant transformation. Moreover, using cultured mouse or human fibroblasts and non-malignant breast epithelial cells, we show that senescent fibroblasts disrupt epithelial alveolar morphogenesis, functional differentiation and branching morphogenesis. Furthermore, we identify MMP-3 as the major factor responsible for the effects of senescent fibroblasts on branching morphogenesis. Our findings support the idea that senescent cells contribute to age-related pathology, including cancer, and describe a new property of senescent fibroblasts - the ability to alter epithelial differentiation - that might also explain the loss of tissue function and organization that is a hallmark of aging.",
    url = "https://doi.org/10.1242/jcs.01635",
    doi = "10.1242/jcs.01635",
    openalex = "W2128668256",
    references = "doi103727095535491820873191"
}

@article{doi101016jcell200607024,
    author = "Takahashi, Kazutoshi and Yamanaka, Shinya",
    title = "Induction of Pluripotent Stem Cells from Mouse Embryonic and Adult Fibroblast Cultures by Defined Factors",
    year = "2006",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2006.07.024",
    doi = "10.1016/j.cell.2006.07.024",
    openalex = "W2125987139",
    references = "doi101016037811199190434d, doi101016jcell200508020, doi101016s0092867400817699, doi101016s0092867403003921, doi101016s0092867403003933, doi101038292154a0, doi101038385810a0, doi10103874199, doi101073pnas78127634, doi101126science28253911145"
}

Due to strong electric fields at the surface, the absorption and scattering of electromagnetic radiation by noble metal nanoparticles are strongly enhanced. These unique properties provide the potential of designing novel optically active reagents for simultaneous molecular imaging and photothermal cancer therapy. It is desirable to use agents that are active in the near-infrared (NIR) region of the radiation spectrum to minimize the light extinction by intrinsic chromophores in native tissue. Gold nanorods with suitable aspect ratios (length divided by width) can absorb and scatter strongly in the NIR region (650-900 nm). In the present work, we provide an in vitro demonstration of gold nanorods as novel contrast agents for both molecular imaging and photothermal cancer therapy. Nanorods are synthesized and conjugated to anti-epidermal growth factor receptor (anti-EGFR) monoclonal antibodies and incubated in cell cultures with a nonmalignant epithelial cell line (HaCat) and two malignant oral epithelial cell lines (HOC 313 clone 8 and HSC 3). The anti-EGFR antibody-conjugated nanorods bind specifically to the surface of the malignant-type cells with a much higher affinity due to the overexpressed EGFR on the cytoplasmic membrane of the malignant cells. As a result of the strongly scattered red light from gold nanorods in dark field, observed using a laboratory microscope, the malignant cells are clearly visualized and diagnosed from the nonmalignant cells. It is found that, after exposure to continuous red laser at 800 nm, malignant cells require about half the laser energy to be photothermally destroyed than the nonmalignant cells. Thus, both efficient cancer cell diagnostics and selective photothermal therapy are realized at the same time.

@article{doi101021ja057254a,
    author = "Huang, Xiaohua and El‐Sayed, Ivan H. and Qian, Wei and El‐Sayed, Mostafa A.",
    title = "Cancer Cell Imaging and Photothermal Therapy in the Near-Infrared Region by Using Gold Nanorods",
    year = "2006",
    journal = "Journal of the American Chemical Society",
    abstract = "Due to strong electric fields at the surface, the absorption and scattering of electromagnetic radiation by noble metal nanoparticles are strongly enhanced. These unique properties provide the potential of designing novel optically active reagents for simultaneous molecular imaging and photothermal cancer therapy. It is desirable to use agents that are active in the near-infrared (NIR) region of the radiation spectrum to minimize the light extinction by intrinsic chromophores in native tissue. Gold nanorods with suitable aspect ratios (length divided by width) can absorb and scatter strongly in the NIR region (650-900 nm). In the present work, we provide an in vitro demonstration of gold nanorods as novel contrast agents for both molecular imaging and photothermal cancer therapy. Nanorods are synthesized and conjugated to anti-epidermal growth factor receptor (anti-EGFR) monoclonal antibodies and incubated in cell cultures with a nonmalignant epithelial cell line (HaCat) and two malignant oral epithelial cell lines (HOC 313 clone 8 and HSC 3). The anti-EGFR antibody-conjugated nanorods bind specifically to the surface of the malignant-type cells with a much higher affinity due to the overexpressed EGFR on the cytoplasmic membrane of the malignant cells. As a result of the strongly scattered red light from gold nanorods in dark field, observed using a laboratory microscope, the malignant cells are clearly visualized and diagnosed from the nonmalignant cells. It is found that, after exposure to continuous red laser at 800 nm, malignant cells require about half the laser energy to be photothermally destroyed than the nonmalignant cells. Thus, both efficient cancer cell diagnostics and selective photothermal therapy are realized at the same time.",
    url = "https://doi.org/10.1021/ja057254a",
    doi = "10.1021/ja057254a",
    openalex = "W2080376276"
}

Mesenchymal stem cells (MSCs) represent a promising tool for new clinical concepts in supporting cellular therapy. Bone marrow (BM) was the first source reported to contain MSCs. However, for clinical use, BM may be detrimental due to the highly invasive donation procedure and the decline in MSC number and differentiation potential with increasing age. More recently, umbilical cord blood (UCB), attainable by a less invasive method, was introduced as an alternative source for MSCs. Another promising source is adipose tissue (AT). We compared MSCs derived from these sources regarding morphology, the success rate of isolating MSCs, colony frequency, expansion potential, multiple differentiation capacity, and immune phenotype. No significant differences concerning the morphology and immune phenotype of the MSCs derived from these sources were obvious. Differences could be observed concerning the success rate of isolating MSCs, which was 100% for BM and AT, but only 63% for UCB. The colony frequency was lowest in UCB, whereas it was highest in AT. However, UCB-MSCs could be cultured longest and showed the highest proliferation capacity, whereas BM-MSCs possessed the shortest culture period and the lowest proliferation capacity. Most strikingly, UCB-MSCs showed no adipogenic differentiation capacity, in contrast to BM- and AT-MSCs. Both UCB and AT are attractive alternatives to BM in isolating MSC: AT as it contains MSCs at the highest frequency and UCB as it seems to be expandable to higher numbers.

@article{doi101634stemcells20050342,
    author = "Kern, Susanne and Eichler, Hermann and Stoeve, Johannes and Klüter, Harald and Bieback, Karen",
    title = "Comparative Analysis of Mesenchymal Stem Cells from Bone Marrow, Umbilical Cord Blood, or Adipose Tissue",
    year = "2006",
    journal = "Stem Cells",
    abstract = "Mesenchymal stem cells (MSCs) represent a promising tool for new clinical concepts in supporting cellular therapy. Bone marrow (BM) was the first source reported to contain MSCs. However, for clinical use, BM may be detrimental due to the highly invasive donation procedure and the decline in MSC number and differentiation potential with increasing age. More recently, umbilical cord blood (UCB), attainable by a less invasive method, was introduced as an alternative source for MSCs. Another promising source is adipose tissue (AT). We compared MSCs derived from these sources regarding morphology, the success rate of isolating MSCs, colony frequency, expansion potential, multiple differentiation capacity, and immune phenotype. No significant differences concerning the morphology and immune phenotype of the MSCs derived from these sources were obvious. Differences could be observed concerning the success rate of isolating MSCs, which was 100\% for BM and AT, but only 63\% for UCB. The colony frequency was lowest in UCB, whereas it was highest in AT. However, UCB-MSCs could be cultured longest and showed the highest proliferation capacity, whereas BM-MSCs possessed the shortest culture period and the lowest proliferation capacity. Most strikingly, UCB-MSCs showed no adipogenic differentiation capacity, in contrast to BM- and AT-MSCs. Both UCB and AT are attractive alternatives to BM in isolating MSC: AT as it contains MSCs at the highest frequency and UCB as it seems to be expandable to higher numbers.",
    url = "https://doi.org/10.1634/stemcells.2005-0342",
    doi = "10.1634/stemcells.2005-0342",
    openalex = "W2036348189",
    references = "doi101242jcs11371161"
}

Structural cell biology, which we define as electron microscopic analysis of intact cells, suffered a loss of interest and activity following the advances in light microscopy beginning in the 1990s. Interestingly, it is the wealth of detailed observation in the light microscope that is one of the driving forces for the current renewed interest in electron microscopy (EM). A great many cellular details are simply beyond the resolving power of the light microscope. In this article, we describe how electron microscopists are responding to the demands for better preservation of cells and for ways to view cell ultrastructure in three dimensions at high resolution. We discuss how low temperature methods, especially high-pressure freezing and freeze substitution, reduce the artifacts of conventional EM specimen preparation. We also give a brief introduction to cellular electron tomography, a powerful analytical method that can give near-atomic resolution of cell ultrastructure in three-dimensional (3-D) models.

@article{doi102144000112226,
    author = "McDonald, Kent and Auer, Manfred",
    title = "High-Pressure Freezing, Cellular Tomography, and Structural Cell Biology",
    year = "2006",
    journal = "BioTechniques",
    abstract = "Structural cell biology, which we define as electron microscopic analysis of intact cells, suffered a loss of interest and activity following the advances in light microscopy beginning in the 1990s. Interestingly, it is the wealth of detailed observation in the light microscope that is one of the driving forces for the current renewed interest in electron microscopy (EM). A great many cellular details are simply beyond the resolving power of the light microscope. In this article, we describe how electron microscopists are responding to the demands for better preservation of cells and for ways to view cell ultrastructure in three dimensions at high resolution. We discuss how low temperature methods, especially high-pressure freezing and freeze substitution, reduce the artifacts of conventional EM specimen preparation. We also give a brief introduction to cellular electron tomography, a powerful analytical method that can give near-atomic resolution of cell ultrastructure in three-dimensional (3-D) models.",
    url = "https://doi.org/10.2144/000112226",
    doi = "10.2144/000112226",
    openalex = "W2150218224",
    references = "doi101002jemt1060030206, doi10100797815974529468, doi10100797836427281507, doi10100797836427281508, doi1010160300962988909802, doi101016jtcb200411009, doi101038sjemboj7600366, doi101083jcb913695, doi101146annurevbiochem73011303074112, doi1015159783112366967"
}

@article{doi101016jcell200711019,
    author = "Takahashi, Kazutoshi and Tanabe, Koji and Ohnuki, Mari and Narita, Megumi and Ichisaka, Tomoko and Tomoda, Kiichiro and Yamanaka, Shinya",
    title = "Induction of Pluripotent Stem Cells from Adult Human Fibroblasts by Defined Factors",
    year = "2007",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2007.11.019",
    doi = "10.1016/j.cell.2007.11.019",
    openalex = "W2138977668",
    references = "doi101016jcell200607024"
}

The process of programmed cell death, or apoptosis, is generally characterized by distinct morphological characteristics and energy-dependent biochemical mechanisms. Apoptosis is considered a vital component of various processes including normal cell turnover, proper development and functioning of the immune system, hormone-dependent atrophy, embryonic development and chemical-induced cell death. Inappropriate apoptosis (either too little or too much) is a factor in many human conditions including neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. The ability to modulate the life or death of a cell is recognized for its immense therapeutic potential. Therefore, research continues to focus on the elucidation and analysis of the cell cycle machinery and signaling pathways that control cell cycle arrest and apoptosis. To that end, the field of apoptosis research has been moving forward at an alarmingly rapid rate. Although many of the key apoptotic proteins have been identified, the molecular mechanisms of action or inaction of these proteins remain to be elucidated. The goal of this review is to provide a general overview of current knowledge on the process of apoptosis including morphology, biochemistry, the role of apoptosis in health and disease, detection methods, as well as a discussion of potential alternative forms of apoptosis.

@article{doi10108001926230701320337,
    author = "Elmore, Susan A.",
    title = "Apoptosis: A Review of Programmed Cell Death",
    year = "2007",
    journal = "Toxicologic Pathology",
    abstract = "The process of programmed cell death, or apoptosis, is generally characterized by distinct morphological characteristics and energy-dependent biochemical mechanisms. Apoptosis is considered a vital component of various processes including normal cell turnover, proper development and functioning of the immune system, hormone-dependent atrophy, embryonic development and chemical-induced cell death. Inappropriate apoptosis (either too little or too much) is a factor in many human conditions including neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. The ability to modulate the life or death of a cell is recognized for its immense therapeutic potential. Therefore, research continues to focus on the elucidation and analysis of the cell cycle machinery and signaling pathways that control cell cycle arrest and apoptosis. To that end, the field of apoptosis research has been moving forward at an alarmingly rapid rate. Although many of the key apoptotic proteins have been identified, the molecular mechanisms of action or inaction of these proteins remain to be elucidated. The goal of this review is to provide a general overview of current knowledge on the process of apoptosis including morphology, biochemistry, the role of apoptosis in health and disease, detection methods, as well as a discussion of potential alternative forms of apoptosis.",
    url = "https://doi.org/10.1080/01926230701320337",
    doi = "10.1080/01926230701320337",
    openalex = "W2008757142"
}

Somatic cell nuclear transfer allows trans-acting factors present in the mammalian oocyte to reprogram somatic cell nuclei to an undifferentiated state. We show that four factors (OCT4, SOX2, NANOG, and LIN28) are sufficient to reprogram human somatic cells to pluripotent stem cells that exhibit the essential characteristics of embryonic stem (ES) cells. These induced pluripotent human stem cells have normal karyotypes, express telomerase activity, express cell surface markers and genes that characterize human ES cells, and maintain the developmental potential to differentiate into advanced derivatives of all three primary germ layers. Such induced pluripotent human cell lines should be useful in the production of new disease models and in drug development, as well as for applications in transplantation medicine, once technical limitations (for example, mutation through viral integration) are eliminated.

@article{doi101126science1151526,
    author = "Yu, Junying and Vodyanik, Maxim A. and Smuga-Otto, Kim and Antosiewicz‐Bourget, Jessica and Frane, Jennifer L. and Tian, Shulan and Nie, Jeff and Jónsdóttir, Guðrún A. and Ruotti, Victor and Stewart, Ron and Slukvin, Igor I. and Thomson, James A.",
    title = "Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells",
    year = "2007",
    journal = "Science",
    abstract = "Somatic cell nuclear transfer allows trans-acting factors present in the mammalian oocyte to reprogram somatic cell nuclei to an undifferentiated state. We show that four factors (OCT4, SOX2, NANOG, and LIN28) are sufficient to reprogram human somatic cells to pluripotent stem cells that exhibit the essential characteristics of embryonic stem (ES) cells. These induced pluripotent human stem cells have normal karyotypes, express telomerase activity, express cell surface markers and genes that characterize human ES cells, and maintain the developmental potential to differentiate into advanced derivatives of all three primary germ layers. Such induced pluripotent human cell lines should be useful in the production of new disease models and in drug development, as well as for applications in transplantation medicine, once technical limitations (for example, mutation through viral integration) are eliminated.",
    url = "https://doi.org/10.1126/science.1151526",
    doi = "10.1126/science.1151526",
    openalex = "W2142046859",
    references = "doi101016jcell200607024, doi101016jstem200705014, doi101038385810a0, doi101038nature05874, doi101038nature05934, doi101038nature05944, doi101038nbt1335, doi101038nbt788, doi101126science28253911145, doi101182blood2004041649"
}

Irrespective of the morphological features of end-stage cell death (that may be apoptotic, necrotic, autophagic, or mitotic), mitochondrial membrane permeabilization (MMP) is frequently the decisive event that delimits the frontier between survival and death. Thus mitochondrial membranes constitute the battleground on which opposing signals combat to seal the cell's fate. Local players that determine the propensity to MMP include the pro- and antiapoptotic members of the Bcl-2 family, proteins from the mitochondrialpermeability transition pore complex, as well as a plethora of interacting partners including mitochondrial lipids. Intermediate metabolites, redox processes, sphingolipids, ion gradients, transcription factors, as well as kinases and phosphatases link lethal and vital signals emanating from distinct subcellular compartments to mitochondria. Thus mitochondria integrate a variety of proapoptotic signals. Once MMP has been induced, it causes the release of catabolic hydrolases and activators of such enzymes (including those of caspases) from mitochondria. These catabolic enzymes as well as the cessation of the bioenergetic and redox functions of mitochondria finally lead to cell death, meaning that mitochondria coordinate the late stage of cellular demise. Pathological cell death induced by ischemia/reperfusion, intoxication with xenobiotics, neurodegenerative diseases, or viral infection also relies on MMP as a critical event. The inhibition of MMP constitutes an important strategy for the pharmaceutical prevention of unwarranted cell death. Conversely, induction of MMP in tumor cells constitutes the goal of anticancer chemotherapy.

@article{doi101152physrev000132006,
    author = "Kroemer, Guido and Galluzzi, Lorenzo and Brenner, Catherine",
    title = "Mitochondrial Membrane Permeabilization in Cell Death",
    year = "2007",
    journal = "Physiological Reviews",
    abstract = "Irrespective of the morphological features of end-stage cell death (that may be apoptotic, necrotic, autophagic, or mitotic), mitochondrial membrane permeabilization (MMP) is frequently the decisive event that delimits the frontier between survival and death. Thus mitochondrial membranes constitute the battleground on which opposing signals combat to seal the cell's fate. Local players that determine the propensity to MMP include the pro- and antiapoptotic members of the Bcl-2 family, proteins from the mitochondrialpermeability transition pore complex, as well as a plethora of interacting partners including mitochondrial lipids. Intermediate metabolites, redox processes, sphingolipids, ion gradients, transcription factors, as well as kinases and phosphatases link lethal and vital signals emanating from distinct subcellular compartments to mitochondria. Thus mitochondria integrate a variety of proapoptotic signals. Once MMP has been induced, it causes the release of catabolic hydrolases and activators of such enzymes (including those of caspases) from mitochondria. These catabolic enzymes as well as the cessation of the bioenergetic and redox functions of mitochondria finally lead to cell death, meaning that mitochondria coordinate the late stage of cellular demise. Pathological cell death induced by ischemia/reperfusion, intoxication with xenobiotics, neurodegenerative diseases, or viral infection also relies on MMP as a critical event. The inhibition of MMP constitutes an important strategy for the pharmaceutical prevention of unwarranted cell death. Conversely, induction of MMP in tumor cells constitutes the goal of anticancer chemotherapy.",
    url = "https://doi.org/10.1152/physrev.00013.2006",
    doi = "10.1152/physrev.00013.2006",
    openalex = "W1964483580"
}

Mesenchymal stem cells or multipotent stromal cells (MSCs) isolated from the bone marrow of adult organisms were initially characterized as plastic adherent, fibroblastoid cells with the capacity to generate heterotopic osseous tissue when transplanted in vivo. In recent years, MSCs or MSC-like cells have been shown to reside within the connective tissue of most organs, and their surface phenotype has been well described. A large number of reports have also indicated that the cells possess the capacity to transdifferentiate into epithelial cells and lineages derived from the neuroectoderm. The broad developmental plasticity of MSCs was originally thought to contribute to their demonstrated efficacy in a wide variety of experimental animal models of disease as well as in human clinical trials. However, new findings suggest that the ability of MSCs to alter the tissue microenvironment via secretion of soluble factors may contribute more significantly than their capacity for transdifferentiation in tissue repair. Herein, we critically evaluate the literature describing the plasticity of MSCs and offer insight into how the molecular and functional heterogeneity of this cell population, which reflects the complexity of marrow stroma as an organ system, may confound interpretation of their transdifferentiation potential. Additionally, we argue that this heterogeneity also provides a basis for the broad therapeutic efficacy of MSCs.

@article{doi101634stemcells20070637,
    author = "Phinney, Donald G. and Prockop, Darwin J.",
    title = "Concise Review: Mesenchymal Stem/Multipotent Stromal Cells: The State of Transdifferentiation and Modes of Tissue Repair—Current Views",
    year = "2007",
    journal = "Stem Cells",
    abstract = "Mesenchymal stem cells or multipotent stromal cells (MSCs) isolated from the bone marrow of adult organisms were initially characterized as plastic adherent, fibroblastoid cells with the capacity to generate heterotopic osseous tissue when transplanted in vivo. In recent years, MSCs or MSC-like cells have been shown to reside within the connective tissue of most organs, and their surface phenotype has been well described. A large number of reports have also indicated that the cells possess the capacity to transdifferentiate into epithelial cells and lineages derived from the neuroectoderm. The broad developmental plasticity of MSCs was originally thought to contribute to their demonstrated efficacy in a wide variety of experimental animal models of disease as well as in human clinical trials. However, new findings suggest that the ability of MSCs to alter the tissue microenvironment via secretion of soluble factors may contribute more significantly than their capacity for transdifferentiation in tissue repair. Herein, we critically evaluate the literature describing the plasticity of MSCs and offer insight into how the molecular and functional heterogeneity of this cell population, which reflects the complexity of marrow stroma as an organ system, may confound interpretation of their transdifferentiation potential. Additionally, we argue that this heterogeneity also provides a basis for the broad therapeutic efficacy of MSCs.",
    url = "https://doi.org/10.1634/stemcells.2007-0637",
    doi = "10.1634/stemcells.2007-0637",
    openalex = "W2012549032",
    references = "doi101242jcs11371161"
}

@article{doi101038cdd2008150,
    author = "Kroemer, Guido and Galluzzi, Lorenzo and Vandenabeele, Peter and Abrams, John and Alnemri, E S and Baehrecke, Eric H. and Blagosklonny, Mikhail V. and El‐Deiry, Wafik S. and Golstein, Pierre and Green, Douglas R. and Hengartner, Michael O. and Knight, Richard A. and Kumar, Sharad and Lipton, Stuart A. and Malorni, Walter and Núñez, Gabriel and Peter, Marcus E. and Tschopp, J and Yuan, Junying and Piacentini, Mauro and Zhivotovsky, Boris and Melino, Gerry",
    title = "Classification of cell death: recommendations of the Nomenclature Committee on Cell Death 2009",
    year = "2008",
    journal = "Cell Death and Differentiation",
    url = "https://doi.org/10.1038/cdd.2008.150",
    doi = "10.1038/cdd.2008.150",
    openalex = "W1976881265",
    references = "doi101016jcub200610053"
}

@article{doi101038nchembio85,
    author = "Winterbourn, Christine C.",
    title = "Reconciling the chemistry and biology of reactive oxygen species",
    year = "2008",
    journal = "Nature Chemical Biology",
    url = "https://doi.org/10.1038/nchembio.85",
    doi = "10.1038/nchembio.85",
    openalex = "W1991952977",
    references = "doi101038nri1312, doi101126science1130481"
}

Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP) developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA-damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial-mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL)-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced senescence. Moreover, they suggest a cell-nonautonomous mechanism by which p53 can restrain, and oncogenic RAS can promote, the development of age-related cancer by altering the tissue microenvironment.

@article{doi101371journalpbio0060301,
    author = "Coppé, Jean‐Philippe",
    title = "Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor",
    year = "2008",
    abstract = "Cellular senescence suppresses cancer by arresting cell proliferation, essentially permanently, in response to oncogenic stimuli, including genotoxic stress. We modified the use of antibody arrays to provide a quantitative assessment of factors secreted by senescent cells. We show that human cells induced to senesce by genotoxic stress secrete myriad factors associated with inflammation and malignancy. This senescence-associated secretory phenotype (SASP) developed slowly over several days and only after DNA damage of sufficient magnitude to induce senescence. Remarkably similar SASPs developed in normal fibroblasts, normal epithelial cells, and epithelial tumor cells after genotoxic stress in culture, and in epithelial tumor cells in vivo after treatment of prostate cancer patients with DNA-damaging chemotherapy. In cultured premalignant epithelial cells, SASPs induced an epithelial-mesenchyme transition and invasiveness, hallmarks of malignancy, by a paracrine mechanism that depended largely on the SASP factors interleukin (IL)-6 and IL-8. Strikingly, two manipulations markedly amplified, and accelerated development of, the SASPs: oncogenic RAS expression, which causes genotoxic stress and senescence in normal cells, and functional loss of the p53 tumor suppressor protein. Both loss of p53 and gain of oncogenic RAS also exacerbated the promalignant paracrine activities of the SASPs. Our findings define a central feature of genotoxic stress-induced senescence. Moreover, they suggest a cell-nonautonomous mechanism by which p53 can restrain, and oncogenic RAS can promote, the development of age-related cancer by altering the tissue microenvironment.",
    url = "https://doi.org/10.1371/journal.pbio.0060301",
    doi = "10.1371/journal.pbio.0060301",
    openalex = "W2010417927",
    references = "doi101111j155856461957tb02911x"
}

@article{doi101038nrm2766,
    author = "MacArthur, Ben D. and Ma’ayan, Avi and Lemischka, Ihor R.",
    title = "Systems biology of stem cell fate and cellular reprogramming",
    year = "2009",
    journal = "Nature Reviews Molecular Cell Biology",
    url = "https://doi.org/10.1038/nrm2766",
    doi = "10.1038/nrm2766",
    openalex = "W1971445167",
    references = "doi1010160020711x94901198, doi101016jcell200508020, doi101016jcell200607024, doi101016jcell200711019, doi10106314823332, doi101073pnas0506580102, doi101126science1151526, doi101126science2845411143, doi101126science28754571433, openalexw2799004609"
}

In contrast to normal differentiated cells, which rely primarily on mitochondrial oxidative phosphorylation to generate the energy needed for cellular processes, most cancer cells instead rely on aerobic glycolysis, a phenomenon termed "the Warburg effect." Aerobic glycolysis is an inefficient way to generate adenosine 5'-triphosphate (ATP), however, and the advantage it confers to cancer cells has been unclear. Here we propose that the metabolism of cancer cells, and indeed all proliferating cells, is adapted to facilitate the uptake and incorporation of nutrients into the biomass (e.g., nucleotides, amino acids, and lipids) needed to produce a new cell. Supporting this idea are recent studies showing that (i) several signaling pathways implicated in cell proliferation also regulate metabolic pathways that incorporate nutrients into biomass; and that (ii) certain cancer-associated mutations enable cancer cells to acquire and metabolize nutrients in a manner conducive to proliferation rather than efficient ATP production. A better understanding of the mechanistic links between cellular metabolism and growth control may ultimately lead to better treatments for human cancer.

@article{doi101126science1160809,
    author = "Heiden, Matthew G. Vander and Cantley, Lewis C. and Thompson, Craig B.",
    title = "Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation",
    year = "2009",
    journal = "Science",
    abstract = {In contrast to normal differentiated cells, which rely primarily on mitochondrial oxidative phosphorylation to generate the energy needed for cellular processes, most cancer cells instead rely on aerobic glycolysis, a phenomenon termed "the Warburg effect." Aerobic glycolysis is an inefficient way to generate adenosine 5'-triphosphate (ATP), however, and the advantage it confers to cancer cells has been unclear. Here we propose that the metabolism of cancer cells, and indeed all proliferating cells, is adapted to facilitate the uptake and incorporation of nutrients into the biomass (e.g., nucleotides, amino acids, and lipids) needed to produce a new cell. Supporting this idea are recent studies showing that (i) several signaling pathways implicated in cell proliferation also regulate metabolic pathways that incorporate nutrients into biomass; and that (ii) certain cancer-associated mutations enable cancer cells to acquire and metabolize nutrients in a manner conducive to proliferation rather than efficient ATP production. A better understanding of the mechanistic links between cellular metabolism and growth control may ultimately lead to better treatments for human cancer.},
    url = "https://doi.org/10.1126/science.1160809",
    doi = "10.1126/science.1160809",
    openalex = "W2097259163",
    references = "doi1010160307441278900493"
}

@article{ito2010cellular,
    author = "Ito, Yutaka and Selenko, Philipp",
    title = "Cellular structural biology",
    year = "2010",
    journal = "Current Opinion in Structural Biology",
    url = "https://doi.org/10.1016/j.sbi.2010.07.006",
    doi = "10.1016/j.sbi.2010.07.006",
    number = "5",
    pages = "640-648",
    volume = "20"
}

The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay is based on the conversion of MTT into formazan crystals by living cells, which determines mitochondrial activity. Since for most cell populations the total mitochondrial activity is related to the number of viable cells, this assay is broadly used to measure the in vitro cytotoxic effects of drugs on cell lines or primary patient cells. In this chapter the protocol of the assay is described including important considerations relevant for each step of the assay as well as its limitations and possible applications.

@article{doi101007978161779080520,
    author = "van Meerloo, Johan and Kaspers, Gertjan J.L. and Cloos, Jacqueline",
    title = "Cell Sensitivity Assays: The MTT Assay",
    year = "2011",
    journal = "Methods in molecular biology",
    abstract = "The MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay is based on the conversion of MTT into formazan crystals by living cells, which determines mitochondrial activity. Since for most cell populations the total mitochondrial activity is related to the number of viable cells, this assay is broadly used to measure the in vitro cytotoxic effects of drugs on cell lines or primary patient cells. In this chapter the protocol of the assay is described including important considerations relevant for each step of the assay as well as its limitations and possible applications.",
    url = "https://doi.org/10.1007/978-1-61779-080-5\_20",
    doi = "10.1007/978-1-61779-080-5\_20",
    openalex = "W2341769195"
}

@article{doi101016jcell201101032,
    author = "Young, Richard A.",
    title = "Control of the Embryonic Stem Cell State",
    year = "2011",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2011.01.032",
    doi = "10.1016/j.cell.2011.01.032",
    openalex = "W2017050785",
    references = "doi101038nrm2766"
}

@article{doi101016jstem201109010,
    author = "Suda, Toshio and Takubo, Keiyo and Semenza, Gregg L.",
    title = "Metabolic Regulation of Hematopoietic Stem Cells in the Hypoxic Niche",
    year = "2011",
    journal = "Cell stem cell",
    url = "https://doi.org/10.1016/j.stem.2011.09.010",
    doi = "10.1016/j.stem.2011.09.010",
    openalex = "W1995091371",
    references = "doi101038nrm2766"
}

@article{doi101038cdd201196,
    author = "Galluzzi, Lorenzo and Vitale, Ilio and Abrams, John and Alnemri, Emad S. and Baehrecke, Eric H. and Blagosklonny, Mikhail V. and Dawson, T M and Dawson, Valina L. and El‐Deiry, Wafik S. and Fulda, Simone and Gottlieb, Eyal and Green, Douglas R. and Hengartner, Michael O. and Kepp, Oliver and Knight, R A and Kumar, Sharad and Lipton, Stuart A. and Lü, Xin and Madeo, Frank and Malorni, Walter and Mehlen, Patrick and Núñez, Gabriel and Peter, Marcus E. and Piacentini, Mauro and Rubinsztein, David C. and Shi, Yufang and Simon, H-U and Vandenabeele, Peter and White, Eileen and Yuan, Jing and Zhivotovsky, Boris and Melino, Gerry and Kroemer, Guido",
    title = "Molecular definitions of cell death subroutines: recommendations of the Nomenclature Committee on Cell Death 2012",
    year = "2011",
    journal = "Cell Death and Differentiation",
    url = "https://doi.org/10.1038/cdd.2011.96",
    doi = "10.1038/cdd.2011.96",
    openalex = "W2030864103",
    references = "doi101038nrd3373"
}

Warburg's observation that cancer cells exhibit a high rate of glycolysis even in the presence of oxygen (aerobic glycolysis) sparked debate over the role of glycolysis in normal and cancer cells. Although it has been established that defects in mitochondrial respiration are not the cause of cancer or aerobic glycolysis, the advantages of enhanced glycolysis in cancer remain controversial. Many cells ranging from microbes to lymphocytes use aerobic glycolysis during rapid proliferation, which suggests it may play a fundamental role in supporting cell growth. Here, we review how glycolysis contributes to the metabolic processes of dividing cells. We provide a detailed accounting of the biosynthetic requirements to construct a new cell and illustrate the importance of glycolysis in providing carbons to generate biomass. We argue that the major function of aerobic glycolysis is to maintain high levels of glycolytic intermediates to support anabolic reactions in cells, thus providing an explanation for why increased glucose metabolism is selected for in proliferating cells throughout nature.

@article{doi101146annurevcellbio092910154237,
    author = "Lunt, Sophia Y. and Heiden, Matthew G. Vander",
    title = "Aerobic Glycolysis: Meeting the Metabolic Requirements of Cell Proliferation",
    year = "2011",
    journal = "Annual Review of Cell and Developmental Biology",
    abstract = "Warburg's observation that cancer cells exhibit a high rate of glycolysis even in the presence of oxygen (aerobic glycolysis) sparked debate over the role of glycolysis in normal and cancer cells. Although it has been established that defects in mitochondrial respiration are not the cause of cancer or aerobic glycolysis, the advantages of enhanced glycolysis in cancer remain controversial. Many cells ranging from microbes to lymphocytes use aerobic glycolysis during rapid proliferation, which suggests it may play a fundamental role in supporting cell growth. Here, we review how glycolysis contributes to the metabolic processes of dividing cells. We provide a detailed accounting of the biosynthetic requirements to construct a new cell and illustrate the importance of glycolysis in providing carbons to generate biomass. We argue that the major function of aerobic glycolysis is to maintain high levels of glycolytic intermediates to support anabolic reactions in cells, thus providing an explanation for why increased glucose metabolism is selected for in proliferating cells throughout nature.",
    url = "https://doi.org/10.1146/annurev-cellbio-092910-154237",
    doi = "10.1146/annurev-cellbio-092910-154237",
    openalex = "W2095987251",
    references = "doi1010160307441278900493, doi101016s0021925818711794, doi1012019781315735368"
}

High-throughput and high-content databases are increasingly important resources in molecular medicine, systems biology, and pharmacology. However, the information usually resides in unwieldy databases, limiting ready data analysis and integration. One resource that offers substantial potential for improvement in this regard is the NCI-60 cell line database compiled by the U.S. National Cancer Institute, which has been extensively characterized across numerous genomic and pharmacologic response platforms. In this report, we introduce a CellMiner (http://discover.nci.nih.gov/cellminer/) web application designed to improve the use of this extensive database. CellMiner tools allowed rapid data retrieval of transcripts for 22,379 genes and 360 microRNAs along with activity reports for 20,503 chemical compounds including 102 drugs approved by the U.S. Food and Drug Administration. Converting these differential levels into quantitative patterns across the NCI-60 clarified data organization and cross-comparisons using a novel pattern match tool. Data queries for potential relationships among parameters can be conducted in an iterative manner specific to user interests and expertise. Examples of the in silico discovery process afforded by CellMiner were provided for multidrug resistance analyses and doxorubicin activity; identification of colon-specific genes, microRNAs, and drugs; microRNAs related to the miR-17-92 cluster; and drug identification patterns matched to erlotinib, gefitinib, afatinib, and lapatinib. CellMiner greatly broadens applications of the extensive NCI-60 database for discovery by creating web-based processes that are rapid, flexible, and readily applied by users without bioinformatics expertise.

@article{doi10115800085472can121370,
    author = "Reinhold, William C. and Sunshine, Margot and Liu, Hongfang and Varma, Sudhir and Kohn, Kurt W. and Morris, Joel and Doroshow, James H. and Pommier, Yves",
    title = "CellMiner: A Web-Based Suite of Genomic and Pharmacologic Tools to Explore Transcript and Drug Patterns in the NCI-60 Cell Line Set",
    year = "2012",
    journal = "Cancer Research",
    abstract = "High-throughput and high-content databases are increasingly important resources in molecular medicine, systems biology, and pharmacology. However, the information usually resides in unwieldy databases, limiting ready data analysis and integration. One resource that offers substantial potential for improvement in this regard is the NCI-60 cell line database compiled by the U.S. National Cancer Institute, which has been extensively characterized across numerous genomic and pharmacologic response platforms. In this report, we introduce a CellMiner (http://discover.nci.nih.gov/cellminer/) web application designed to improve the use of this extensive database. CellMiner tools allowed rapid data retrieval of transcripts for 22,379 genes and 360 microRNAs along with activity reports for 20,503 chemical compounds including 102 drugs approved by the U.S. Food and Drug Administration. Converting these differential levels into quantitative patterns across the NCI-60 clarified data organization and cross-comparisons using a novel pattern match tool. Data queries for potential relationships among parameters can be conducted in an iterative manner specific to user interests and expertise. Examples of the in silico discovery process afforded by CellMiner were provided for multidrug resistance analyses and doxorubicin activity; identification of colon-specific genes, microRNAs, and drugs; microRNAs related to the miR-17-92 cluster; and drug identification patterns matched to erlotinib, gefitinib, afatinib, and lapatinib. CellMiner greatly broadens applications of the extensive NCI-60 database for discovery by creating web-based processes that are rapid, flexible, and readily applied by users without bioinformatics expertise.",
    url = "https://doi.org/10.1158/0008-5472.can-12-1370",
    doi = "10.1158/0008-5472.can-12-1370",
    openalex = "W2103196126",
    references = "doi101093jnci82131113"
}

@article{doi101038cdd201375,
    author = "Martins, Isabel and Wang, Yan and Michaud, Michael and Ma, Yuting and Sukkurwala, Abdul Qader and Shen, Shensi and Kepp, Oliver and Métivier, David and Galluzzi, Lorenzo and Perfettini, J-L and Zitvogel, Laurence and Kroemer, Guido",
    title = "Molecular mechanisms of ATP secretion during immunogenic cell death",
    year = "2013",
    journal = "Cell Death and Differentiation",
    url = "https://doi.org/10.1038/cdd.2013.75",
    doi = "10.1038/cdd.2013.75",
    openalex = "W1991505853",
    references = "doi101038nrd3373"
}

@article{doi101038cdd2014137,
    author = "Galluzzi, Lorenzo and Pedro, José Manuel Bravo‐San and Vitale, Ilio and Aaronson, Stuart A. and Abrams, John and Adam, Dieter and Alnemri, Emad S. and Altucci, Lucia and Andrews, David W. and Annicchiarico‐Petruzzelli, Margherita and Baehrecke, Eric H. and Bazán, Nicolás G. and Bertrand, Mathieu J.M. and Bianchi, Katiuscia and Blagosklonny, Mikhail V. and Blomgren, Klas and Borner, Christoph and Bredesen, Dale E. and Brenner, Catherine and Campanella, Michelangelo and Candi, Eleonora and Cecconi, Francesco and Chan, Francis Ka-Ming and Chandel, Navdeep S. and Cheng, Emily H. and Chipuk, Jerry E. and Cidlowski, John A. and Ciechanover, Aaron and Dawson, Ted M. and Dawson, Valina L. and Laurenzi, Vincenzo De and Maria, Ruggero De and Debatin, K-M and Daniele, N Di and Dixit, Vishva M. and Dynlacht, Brian David and El‐Deiry, Wafik S. and Fimia, Gian María and Flavell, Richard A. and Fulda, Simone and Garrido, Carmen and Gougeon, M-L and Green, Douglas R. and Gronemeyer, Hinrich and Hajnóczky, György and Hardwick, J. Marie and Hengartner, Michael O. and Ichijo, Hidenori and Joseph, Bertrand and Jost, Philipp J. and Kaufmann, Thomas and Kepp, Oliver and Klionsky, Daniel J. and Knight, Richard A. and Kumar, Sharad and Lemasters, John J. and Levine, Beth and Linkermann, Andreas and Lipton, Stuart A. and Lockshin, Richard A. and López-Otı́n, Carlos and Lugli, Enrico and Madeo, Frank and Malorni, Walter and Marine, J-C and Martin, Séamus J. and Martinou, J-C and Medema, Jan Paul and Meier, Pascal and Melino, Sonia and Mizushima, Noboru and Moll, Ute M. and Muñoz‐Pinedo, Cristina and Núñez, Gabriel and Oberst, Andrew and Panaretakis, Theocharis and Penninger, Josef and Peter, Marcus E. and Piacentini, Mauro and Pinton, Paolo and Prehn, Jochen H.M. and Puthalakath, Hamsa and Rabinovich, Gabriel A. and Ravichandran, Kodi S. and Rizzuto, Rosario and Rodrigues, Cecília M. P. and Rubinsztein, David C. and Rudel, Thomas and Shi, Yufang and Simon, H-U and Stockwell, Brent R. and Szabadkai, György and Tait, Stephen W. G. and Tang, Ho Lam and Tavernarakis, N and Tsujimoto, Yoshihide and Berghe, Tom Vanden and Vandenabeele, Peter and Villunger, Andreas and Wagner, Erwin F.",
    title = "Essential versus accessory aspects of cell death: recommendations of the NCCD 2015",
    year = "2014",
    journal = "Cell Death and Differentiation",
    url = "https://doi.org/10.1038/cdd.2014.137",
    doi = "10.1038/cdd.2014.137",
    openalex = "W1997128330",
    references = "doi101038nrd3373, doi101038nri3244"
}

and to screen large chemical libraries for putative ICD inducers, based on a high-content, high-throughput platform that we recently developed. Such a platform allows for the detection of multiple DAMPs, like cell surface-exposed calreticulin, extracellular ATP and high mobility group box 1 (HMGB1), and/or the processes that underlie their emission, such as endoplasmic reticulum stress, autophagy and necrotic plasma membrane permeabilization. We surmise that this technology will facilitate the development of next-generation anticancer regimens, which kill malignant cells and simultaneously convert them into a cancer-specific therapeutic vaccine.

@article{doi104161216240112014955691,
    author = "Kepp, Oliver and Senovilla, Laura and Vitale, Ilio and Vacchelli, Erika and Adjemian, Sandy and Agostinis, Patrizia and Apétoh, Lionel and Aranda, Fernando and Barnaba, Vincenzo and Bloy, Norma and Bracci, Laura and Breckpot, Karine and Brough, David and Buqué, Aitziber and Castro, María G. and Cirone, Mara and Colombo, María I. and Cremer, Isabelle and Demaria, Sandra and Dini, Luciana and Eliopoulos, Aristides G. and Faggioni, Alberto and Formenti, Silvia C. and Fučíková, Jitka and Gabriele, Lucia and Gaipl, Udo S. and Galon, Jérôme and Garg, Abhishek D. and Ghiringhelli, François and Giese, Nathalia A. and Guo, Zong Sheng and Hemminki, Akseli and Herrmann, Martin and Hodge, James W. and Holdenrieder, Stefan and Honeychurch, Jamie and Hu, Hong‐Ming and Huang, Xing and Illidge, Tim and Kono, Koji and Korbelik, Mladen and Krysko, Dmitri V. and Loi, Sherene and Löwenstein, Pedro R. and Lugli, Enrico and Ma, Yuting and Madeo, Frank and Manfredi, Angelo A. and Martins, Isabelle and Mavilio, Domenico and Menger, Laurie and Merendino, Nicolò and Michaud, Michael and Mignot, Grégoire and Mossman, Karen and Multhoff, Gabriele and Oehler, Rudolf and Palombo, Fabio and Panaretakis, Theocharis and Pol, Jonathan and Proietti, Enrico and Ricci, Jean‐Ehrland and Riganti, Chiara and Rovere–Querini, Patrizia and Rubartelli, Anna and Sistigu, Antonella and Smyth, Mark J. and Sonnemann, Juergen and Špíšek, Radek and Stagg, John and Sukkurwala, Abdul Qader and Tartour, Éric and Thorburn, Andrew and Thorne, Stephen H. and Vandenabeele, Peter and Velotti, Francesca and Workenhe, Samuel T. and Yang, Haining and Zong, Wei‐Xing and Zitvogel, Laurence and Kroemer, Guido and Galluzzi, Lorenzo",
    title = "Consensus guidelines for the detection of immunogenic cell death",
    year = "2014",
    journal = "OncoImmunology",
    abstract = "and to screen large chemical libraries for putative ICD inducers, based on a high-content, high-throughput platform that we recently developed. Such a platform allows for the detection of multiple DAMPs, like cell surface-exposed calreticulin, extracellular ATP and high mobility group box 1 (HMGB1), and/or the processes that underlie their emission, such as endoplasmic reticulum stress, autophagy and necrotic plasma membrane permeabilization. We surmise that this technology will facilitate the development of next-generation anticancer regimens, which kill malignant cells and simultaneously convert them into a cancer-specific therapeutic vaccine.",
    url = "https://doi.org/10.4161/21624011.2014.955691",
    doi = "10.4161/21624011.2014.955691",
    openalex = "W2163252162",
    references = "doi101038nrd3373"
}

@incollection{hendry2014cellular,
    author = "Hendry, J.H.",
    title = "Cellular Radiation Biology",
    year = "2014",
    booktitle = "Comprehensive Biomedical Physics",
    url = "https://doi.org/10.1016/b978-0-444-53632-7.00804-2",
    doi = "10.1016/b978-0-444-53632-7.00804-2",
    pages = "63-74"
}

The protocol described in this appendix allows for light microscopic quantitation of cell viability. Cells are suspended in PBS containing trypan blue and then examined to determine the percentage of cells that have clear cytoplasm (viable cells) versus cells that have blue cytoplasm (nonviable cells).

@article{doi1010020471142735ima03bs111,
    author = "Strober, Warren",
    title = "Trypan Blue Exclusion Test of Cell Viability",
    year = "2015",
    journal = "Current Protocols in Immunology",
    abstract = "The protocol described in this appendix allows for light microscopic quantitation of cell viability. Cells are suspended in PBS containing trypan blue and then examined to determine the percentage of cells that have clear cytoplasm (viable cells) versus cells that have blue cytoplasm (nonviable cells).",
    url = "https://doi.org/10.1002/0471142735.ima03bs111",
    doi = "10.1002/0471142735.ima03bs111",
    openalex = "W2110378444"
}

@article{doi101016jcell201511018,
    author = "Battich, Nico and Stoeger, Thomas and Pelkmans, Lucas",
    title = "Control of Transcript Variability in Single Mammalian Cells",
    year = "2015",
    journal = "Cell",
    url = "https://doi.org/10.1016/j.cell.2015.11.018",
    doi = "10.1016/j.cell.2015.11.018",
    openalex = "W2211016425",
    references = "doi101038nrm2766"
}

Super-resolution microscopy can unravel previously hidden details of cellular structures but requires high irradiation intensities to use the limited photon budget efficiently. Such high photon densities are likely to induce cellular damage in live-cell experiments. We applied single-molecule localization microscopy conditions and tested the influence of irradiation intensity, illumination-mode, wavelength, light-dose, temperature and fluorescence labeling on the survival probability of different cell lines 20-24 hours after irradiation. In addition, we measured the microtubule growth speed after irradiation. The photo-sensitivity is dramatically increased at lower irradiation wavelength. We observed fixation, plasma membrane permeabilization and cytoskeleton destruction upon irradiation with shorter wavelengths. While cells stand light intensities of ~1 kW cm(-2) at 640 nm for several minutes, the maximum dose at 405 nm is only ~50 J cm(-2), emphasizing red fluorophores for live-cell localization microscopy. We also present strategies to minimize phototoxic factors and maximize the cells ability to cope with higher irradiation intensities.

@article{doi101038srep15348,
    author = "Wäldchen, Sina and Lehmann, Julian and Klein, Teresa and van de Linde, Sebastian and Sauer, Markus",
    title = "Light-induced cell damage in live-cell super-resolution microscopy",
    year = "2015",
    journal = "Scientific Reports",
    abstract = "Super-resolution microscopy can unravel previously hidden details of cellular structures but requires high irradiation intensities to use the limited photon budget efficiently. Such high photon densities are likely to induce cellular damage in live-cell experiments. We applied single-molecule localization microscopy conditions and tested the influence of irradiation intensity, illumination-mode, wavelength, light-dose, temperature and fluorescence labeling on the survival probability of different cell lines 20-24 hours after irradiation. In addition, we measured the microtubule growth speed after irradiation. The photo-sensitivity is dramatically increased at lower irradiation wavelength. We observed fixation, plasma membrane permeabilization and cytoskeleton destruction upon irradiation with shorter wavelengths. While cells stand light intensities of \textasciitilde 1 kW cm(-2) at 640 nm for several minutes, the maximum dose at 405 nm is only \textasciitilde 50 J cm(-2), emphasizing red fluorophores for live-cell localization microscopy. We also present strategies to minimize phototoxic factors and maximize the cells ability to cope with higher irradiation intensities.",
    url = "https://doi.org/10.1038/srep15348",
    doi = "10.1038/srep15348",
    openalex = "W1782900133",
    references = "doi101006abbi19931311"
}

BACKGROUND: The tetrazolium-based MTT assay has long been regarded as the gold standard of cytotoxicity assays as it is highly sensitive and has been miniaturised for use as a high-throughput screening assay. However, various reports refer to interference by different test compounds, including the glycolysis inhibitor 3-bromopyruvate, with the conversion of the dye to coloured formazan crystals. This study assessed the linear range and reproducibility of three commonly used cell enumeration assays; the neutral red uptake (NRU), resazurin reduction (RES) and sulforhodamine B (SRB) assays, in comparison to the MTT assay. Interference between the MTT assay and three glycolysis inhibitors, 2-deoxyglucose, 3-bromopyruvate and lonidamine, was investigated. RESULTS: Data indicate that the NRU, RES and SRB assays showed the smallest variability across the linear range, while the largest variation was observed for the MTT assay. This implies that these assays would more accurately detect small changes in cell number than the MTT assay. The SRB assay provided the most reproducible results as indicated by the coefficient of determination after a limited number of experiments. The SRB assay also produced the lowest variance in the derived 50% inhibitory concentration (IC50), while IC50 concentrations of 3-bromopyruvate could not be detected using either the MTT or RES assays after 24 hours incubation. Interference in the MTT assay was observed for all three tested glycolysis inhibitors in a cell-free environment. No interferences were observed for the NRU, SRB or RES assays. CONCLUSIONS: This study demonstrated that the MTT assay was not the best assay in a number of parameters that must be considered when a cell enumeration assay is selected: the MTT assay was less accurate in detecting changes in cell number as indicated by the variation observed in the linear range, had the highest variation when the IC50 concentrations of the glycolysis inhibitors were determined, and interference between the MTT assay and all the glycolysis inhibitors tested were observed. The SRB assay performed best overall considering all of the parameters, suggesting that it is the most suitable assay for use in preclinical screening of novel therapeutic compounds with oxido-reductive potential.

@article{doi101186s1310401510008,
    author = "van Tonder, Alet and Joubert, Annie and Cromarty, Duncan",
    title = "Limitations of the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay when compared to three commonly used cell enumeration assays",
    year = "2015",
    journal = "BMC Research Notes",
    abstract = "BACKGROUND: The tetrazolium-based MTT assay has long been regarded as the gold standard of cytotoxicity assays as it is highly sensitive and has been miniaturised for use as a high-throughput screening assay. However, various reports refer to interference by different test compounds, including the glycolysis inhibitor 3-bromopyruvate, with the conversion of the dye to coloured formazan crystals. This study assessed the linear range and reproducibility of three commonly used cell enumeration assays; the neutral red uptake (NRU), resazurin reduction (RES) and sulforhodamine B (SRB) assays, in comparison to the MTT assay. Interference between the MTT assay and three glycolysis inhibitors, 2-deoxyglucose, 3-bromopyruvate and lonidamine, was investigated. RESULTS: Data indicate that the NRU, RES and SRB assays showed the smallest variability across the linear range, while the largest variation was observed for the MTT assay. This implies that these assays would more accurately detect small changes in cell number than the MTT assay. The SRB assay provided the most reproducible results as indicated by the coefficient of determination after a limited number of experiments. The SRB assay also produced the lowest variance in the derived 50\% inhibitory concentration (IC50), while IC50 concentrations of 3-bromopyruvate could not be detected using either the MTT or RES assays after 24 hours incubation. Interference in the MTT assay was observed for all three tested glycolysis inhibitors in a cell-free environment. No interferences were observed for the NRU, SRB or RES assays. CONCLUSIONS: This study demonstrated that the MTT assay was not the best assay in a number of parameters that must be considered when a cell enumeration assay is selected: the MTT assay was less accurate in detecting changes in cell number as indicated by the variation observed in the linear range, had the highest variation when the IC50 concentrations of the glycolysis inhibitors were determined, and interference between the MTT assay and all the glycolysis inhibitors tested were observed. The SRB assay performed best overall considering all of the parameters, suggesting that it is the most suitable assay for use in preclinical screening of novel therapeutic compounds with oxido-reductive potential.",
    url = "https://doi.org/10.1186/s13104-015-1000-8",
    doi = "10.1186/s13104-015-1000-8",
    openalex = "W2117653463",
    references = "doi101016jacthis201201006"
}

Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a 'resolution revolution', owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM.

@article{doi101016jymeth201602017,
    author = "Thompson, Rebecca F. and Walker, Matt and Siebert, C. Alistair and Muench, Stephen P. and Ranson, Neil A.",
    title = "An introduction to sample preparation and imaging by cryo-electron microscopy for structural biology",
    year = "2016",
    journal = "Methods",
    abstract = "Transmission electron microscopy (EM) is a versatile technique that can be used to image biological specimens ranging from intact eukaryotic cells to individual proteins >150kDa. There are several strategies for preparing samples for imaging by EM, including negative staining and cryogenic freezing. In the last few years, cryo-EM has undergone a 'resolution revolution', owing to both advances in imaging hardware, image processing software, and improvements in sample preparation, leading to growing number of researchers using cryo-EM as a research tool. However, cryo-EM is still a rapidly growing field, with unique challenges. Here, we summarise considerations for imaging of a range of specimens from macromolecular complexes to cells using EM.",
    url = "https://doi.org/10.1016/j.ymeth.2016.02.017",
    doi = "10.1016/j.ymeth.2016.02.017",
    openalex = "W2292743908",
    references = "doi102144000112226"
}

Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile. But how progenitor cells overcome the stability of their gene expression configuration (attractor) to exit the attractor in one direction remains elusive. Here we show that commitment of blood progenitor cells to the erythroid or myeloid lineage is preceded by the destabilization of their high-dimensional attractor state, such that differentiating cells undergo a critical state transition. Single-cell resolution analysis of gene expression in populations of differentiating cells affords a new quantitative index for predicting critical transitions in a high-dimensional state space based on decrease of correlation between cells and concomitant increase of correlation between genes as cells approach a tipping point. The detection of "rebellious cells" that enter the fate opposite to the one intended corroborates the model of preceding destabilization of a progenitor attractor. Thus, early warning signals associated with critical transitions can be detected in statistical ensembles of high-dimensional systems, offering a formal theory-based approach for analyzing single-cell molecular profiles that goes beyond current computational pattern recognition, does not require knowledge of specific pathways, and could be used to predict impending major shifts in development and disease.

@article{doi101371journalpbio2000640,
    author = "Mojtahedi, Mitra and Skupin, Alexander and Zhou, Joseph and Castaño, Ivan G. and Leong-Quong, Rebecca Y. Y. and Chang, Hannah and Trachana, Kalliopi and Giuliani, Alessandro and Huang, Sui",
    title = "Cell Fate Decision as High-Dimensional Critical State Transition",
    year = "2016",
    journal = "PLoS Biology",
    abstract = {Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile. But how progenitor cells overcome the stability of their gene expression configuration (attractor) to exit the attractor in one direction remains elusive. Here we show that commitment of blood progenitor cells to the erythroid or myeloid lineage is preceded by the destabilization of their high-dimensional attractor state, such that differentiating cells undergo a critical state transition. Single-cell resolution analysis of gene expression in populations of differentiating cells affords a new quantitative index for predicting critical transitions in a high-dimensional state space based on decrease of correlation between cells and concomitant increase of correlation between genes as cells approach a tipping point. The detection of "rebellious cells" that enter the fate opposite to the one intended corroborates the model of preceding destabilization of a progenitor attractor. Thus, early warning signals associated with critical transitions can be detected in statistical ensembles of high-dimensional systems, offering a formal theory-based approach for analyzing single-cell molecular profiles that goes beyond current computational pattern recognition, does not require knowledge of specific pathways, and could be used to predict impending major shifts in development and disease.},
    url = "https://doi.org/10.1371/journal.pbio.2000640",
    doi = "10.1371/journal.pbio.2000640",
    openalex = "W2952938648",
    references = "doi101038nrm2766, doi101093aibsbulletin6323c"
}

Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes.

@article{doi1021741389201017666160808160513,
    author = "Adan, Aysun and Kiraz, Yağmur and Baran, Yusuf",
    title = "Cell Proliferation and Cytotoxicity Assays",
    year = "2016",
    journal = "Current Pharmaceutical Biotechnology",
    abstract = "Cell viability is defined as the number of healthy cells in a sample and proliferation of cells is a vital indicator for understanding the mechanisms in action of certain genes, proteins and pathways involved cell survival or death after exposing to toxic agents. Generally, methods used to determine viability are also common for the detection of cell proliferation. Cell cytotoxicity and proliferation assays are generally used for drug screening to detect whether the test molecules have effects on cell proliferation or display direct cytotoxic effects. Regardless of the type of cell-based assay being used, it is important to know how many viable cells are remaining at the end of the experiment. There are a variety of assay methods based on various cell functions such as enzyme activity, cell membrane permeability, cell adherence, ATP production, co-enzyme production, and nucleotide uptake activity. These methods could be basically classified into different categories: (I) dye exclusion methods such as trypan blue dye exclusion assay, (II) methods based on metabolic activity, (III) ATP assay, (IV) sulforhodamine B assay, (V) protease viability marker assay, (VI) clonogenic cell survival assay, (VII) DNA synthesis cell proliferation assays and (V) raman micro-spectroscopy. In order to choose the optimal viability assay, the cell type, applied culture conditions, and the specific questions being asked should be considered in detail. This particular review aims to provide an overview of common cell proliferation and cytotoxicity assays together with their own advantages and disadvantages, their methodologies, comparisons and intended purposes.",
    url = "https://doi.org/10.2174/1389201017666160808160513",
    doi = "10.2174/1389201017666160808160513",
    openalex = "W2518046346",
    references = "doi1010020471142735ima03bs21, doi101002sici109746522000031823311aidjcp130co29, doi101006abbi19931311, doi101007978161779080520, doi1010160022175994903964, doi101016s1387265605110047, doi101038nprot2006179, doi101038nprot2006339, doi103727095535491820873191, openalexw2143811153"
}

This chapter is an introductory overview of the most commonly used assay methods to estimate the number of viable cells in multi-well plates. This chapter describes assays where data are recorded using a plate-reader; it does not cover assay methods designed for flow cytometry or high content imaging. The assay methods covered include the use of different classes of colorimetric tetrazolium reagents, resazurin reduction and protease substrates generating a fluorescent signal, the luminogenic ATP assay, and a novel real-time assay to monitor live cells for days in culture. The assays described are based on measurement of a marker activity associated with viable cell number. These assays are used for measuring the results of cell proliferation, testing for cytotoxic effects of compounds, and for multiplexing as an internal control to determine viable cell number during other cell-based assays.

@article{openalexw319133514,
    author = "Riss, Terry and Moravec, Richard A and Niles, Andrew L. and Duellman, Sarah and Benink, Hélène A and Worzella, Tracy J and Minor, Lisa",
    title = "Cell Viability Assays",
    year = "2016",
    journal = "Europe PMC (PubMed Central)",
    abstract = "This chapter is an introductory overview of the most commonly used assay methods to estimate the number of viable cells in multi-well plates. This chapter describes assays where data are recorded using a plate-reader; it does not cover assay methods designed for flow cytometry or high content imaging. The assay methods covered include the use of different classes of colorimetric tetrazolium reagents, resazurin reduction and protease substrates generating a fluorescent signal, the luminogenic ATP assay, and a novel real-time assay to monitor live cells for days in culture. The assays described are based on measurement of a marker activity associated with viable cell number. These assays are used for measuring the results of cell proliferation, testing for cytotoxic effects of compounds, and for multiplexing as an internal control to determine viable cell number during other cell-based assays.",
    openalex = "W319133514",
    references = "doi101006abbi19931311"
}

, implying that these proteins may function upstream in the same pathway. Building on these genetic interactions, we explored the role of LEM2 during nuclear envelope reformation in human cells. We found that CHMP7 and LEM2 enrich at the same region of the chromatin disk periphery during this window of cell division and that CHMP7 can bind directly to the C-terminal domain of LEM2 in vitro. We further found that, during nuclear envelope formation, recruitment of the ESCRT factors CHMP7, CHMP2A, and IST1/CHMP8 all depend on LEM2 in human cells. We conclude that Lem2p/LEM2 is a conserved nuclear site-specific adaptor that recruits Cmp7p/CHMP7 and downstream ESCRT factors to the nuclear envelope.

@article{doi101073pnas1613916114,
    author = "Gu, Mingyu and LaJoie, Dollie and Chen, Opal S. and von Appen, Alexander and Ladinsky, Mark S. and Redd, Michael J. and Nikolova, Linda S. and Björkman, Pamela J. and Sundquist, Wesley I. and Ullman, Katharine S. and Frost, Adam",
    title = "LEM2 recruits CHMP7 for ESCRT-mediated nuclear envelope closure in fission yeast and human cells",
    year = "2017",
    journal = "Proceedings of the National Academy of Sciences",
    abstract = ", implying that these proteins may function upstream in the same pathway. Building on these genetic interactions, we explored the role of LEM2 during nuclear envelope reformation in human cells. We found that CHMP7 and LEM2 enrich at the same region of the chromatin disk periphery during this window of cell division and that CHMP7 can bind directly to the C-terminal domain of LEM2 in vitro. We further found that, during nuclear envelope formation, recruitment of the ESCRT factors CHMP7, CHMP2A, and IST1/CHMP8 all depend on LEM2 in human cells. We conclude that Lem2p/LEM2 is a conserved nuclear site-specific adaptor that recruits Cmp7p/CHMP7 and downstream ESCRT factors to the nuclear envelope.",
    url = "https://doi.org/10.1073/pnas.1613916114",
    doi = "10.1073/pnas.1613916114",
    openalex = "W2592379452",
    references = "doi102144000112226"
}

@article{doi101016jacthis201802005,
    author = "Stockert, Juan C. and Horobin, Richard W. and Colombo, Lucas L. and Blázquez‐Castro, Alfonso",
    title = "Tetrazolium salts and formazan products in Cell Biology: Viability assessment, fluorescence imaging, and labeling perspectives",
    year = "2018",
    journal = "Acta Histochemica",
    url = "https://doi.org/10.1016/j.acthis.2018.02.005",
    doi = "10.1016/j.acthis.2018.02.005",
    openalex = "W2793210811",
    references = "doi101006abbi19931311, doi101007978161779080520, doi1010160022175983903034, doi101016jacthis201201006, doi101016s1387265605110047, doi101046j14714159199769020581x, doi101093jnci82131107, doi101126science1160809, doi101146annurevcellbio092910154237, doi103727095535491820873191, openalexw1553088832, openalexw2140927361"
}

Rapid progress in the development of next-generation sequencing (NGS) technologies in recent years has provided many valuable insights into complex biological systems, ranging from cancer genomics to diverse microbial communities. NGS-based technologies for genomics, transcriptomics, and epigenomics are now increasingly focused on the characterization of individual cells. These single-cell analyses will allow researchers to uncover new and potentially unexpected biological discoveries relative to traditional profiling methods that assess bulk populations. Single-cell RNA sequencing (scRNA-seq), for example, can reveal complex and rare cell populations, uncover regulatory relationships between genes, and track the trajectories of distinct cell lineages in development. In this review, we will focus on technical challenges in single-cell isolation and library preparation and on computational analysis pipelines available for analyzing scRNA-seq data. Further technical improvements at the level of molecular and cell biology and in available bioinformatics tools will greatly facilitate both the basic science and medical applications of these sequencing technologies.

@article{doi101038s1227601800718,
    author = "Hwang, Byungjin and Lee, Ji Hyun and Bang, Duhee",
    title = "Single-cell RNA sequencing technologies and bioinformatics pipelines",
    year = "2018",
    journal = "Experimental \& Molecular Medicine",
    abstract = "Rapid progress in the development of next-generation sequencing (NGS) technologies in recent years has provided many valuable insights into complex biological systems, ranging from cancer genomics to diverse microbial communities. NGS-based technologies for genomics, transcriptomics, and epigenomics are now increasingly focused on the characterization of individual cells. These single-cell analyses will allow researchers to uncover new and potentially unexpected biological discoveries relative to traditional profiling methods that assess bulk populations. Single-cell RNA sequencing (scRNA-seq), for example, can reveal complex and rare cell populations, uncover regulatory relationships between genes, and track the trajectories of distinct cell lineages in development. In this review, we will focus on technical challenges in single-cell isolation and library preparation and on computational analysis pipelines available for analyzing scRNA-seq data. Further technical improvements at the level of molecular and cell biology and in available bioinformatics tools will greatly facilitate both the basic science and medical applications of these sequencing technologies.",
    url = "https://doi.org/10.1038/s12276-018-0071-8",
    doi = "10.1038/s12276-018-0071-8",
    openalex = "W2886347923",
    references = "doi105694j132653771958tb86500x"
}

Single-cell RNA-seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single-cell analysis methods. As more analysis tools are becoming available, it is becoming increasingly difficult to navigate this landscape and produce an up-to-date workflow to analyse one's data. Here, we detail the steps of a typical single-cell RNA-seq analysis, including pre-processing (quality control, normalization, data correction, feature selection, and dimensionality reduction) and cell- and gene-level downstream analysis. We formulate current best-practice recommendations for these steps based on independent comparison studies. We have integrated these best-practice recommendations into a workflow, which we apply to a public dataset to further illustrate how these steps work in practice. Our documented case study can be found at https://www.github.com/theislab/single-cell-tutorial This review will serve as a workflow tutorial for new entrants into the field, and help established users update their analysis pipelines.

@article{doi1015252msb20188746,
    author = "Luecken, Malte D. and Theis, Fabian J.",
    title = "Current best practices in single‐cell RNA‐seq analysis: a tutorial",
    year = "2019",
    journal = "Molecular Systems Biology",
    abstract = "Single-cell RNA-seq has enabled gene expression to be studied at an unprecedented resolution. The promise of this technology is attracting a growing user base for single-cell analysis methods. As more analysis tools are becoming available, it is becoming increasingly difficult to navigate this landscape and produce an up-to-date workflow to analyse one's data. Here, we detail the steps of a typical single-cell RNA-seq analysis, including pre-processing (quality control, normalization, data correction, feature selection, and dimensionality reduction) and cell- and gene-level downstream analysis. We formulate current best-practice recommendations for these steps based on independent comparison studies. We have integrated these best-practice recommendations into a workflow, which we apply to a public dataset to further illustrate how these steps work in practice. Our documented case study can be found at https://www.github.com/theislab/single-cell-tutorial This review will serve as a workflow tutorial for new entrants into the field, and help established users update their analysis pipelines.",
    url = "https://doi.org/10.15252/msb.20188746",
    doi = "10.15252/msb.20188746",
    openalex = "W2949237386"
}

Abstract Recently, the interest in the application of cell viability assays has been increasing in various fields. Cell viability assays may be broadly classified as (a) dye exclusion assays, (b) colorimetric assays, (c) fluorometric assays, (d) luminometric assays, and (e) flow cytometric assays. Dye exclusion assays include trypan blue, eosin, congo red, and erythrosine B stain assays, whereas 3‐[4,5‐dimethylthiazol‐2‐yl]‐2,5 diphenyl tetrazolium bromide (MTT), 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium (MTS), 2,3‐bis‐(2‐methoxy‐4‐nitro‐5‐sulfophenyl)‐2H‐tetrazolium‐5‐carboxanilide (XTT), 2‐(4‐iodophenyl)‐3‐(4‐nitrophenyl)‐5‐(2,4‐disulfophenyl)‐2H tetrazolium, monosodium salt (WST‐1), 2‐(2‐methoxy‐4‐nitrophenyl)‐3‐(4‐nitrophenyl)‐5‐(2,4‐disulfophenyl)‐2H‐tetrazolium, monosodium salt (WST‐8), lactate dehydrogenase (LDH), sulforhodamine B (SRB), neutral red uptake (NRU), and crystal violet stain (CVS) assays are among the colorimetric assays. Similarly, resazurin and 5‐carboxyfluorescein diacetate acetoxymethyl ester (5‐CFDA‐AM) assays are based on fluorometric measurements, whereas luminometric assays comprise adenosine triphosphate and real‐time viability assays. Major flow cytometric assays include membrane asymmetry, membrane permeability, and mitochondria assays. In this guideline, the mechanisms and the practice of assessment of the most common cell viability assays applied in research labs are discussed in detail. An ideal cell viability assay should be safe, rapid, reliable, efficient, and time‐ and cost‐effective, and should not interfere with the test compound. Overall, it can be concluded that more than one cell viability assay should be applied in order to obtain reliable results.

@article{doi101002fft244,
    author = "Kamiloğlu, Senem and Sarı, Gülce and Özdal, Tuğba and Çapanoğlu, Esra",
    title = "Guidelines for cell viability assays",
    year = "2020",
    journal = "Food Frontiers",
    abstract = "Abstract Recently, the interest in the application of cell viability assays has been increasing in various fields. Cell viability assays may be broadly classified as (a) dye exclusion assays, (b) colorimetric assays, (c) fluorometric assays, (d) luminometric assays, and (e) flow cytometric assays. Dye exclusion assays include trypan blue, eosin, congo red, and erythrosine B stain assays, whereas 3‐[4,5‐dimethylthiazol‐2‐yl]‐2,5 diphenyl tetrazolium bromide (MTT), 3‐(4,5‐dimethylthiazol‐2‐yl)‐5‐(3‐carboxymethoxyphenyl)‐2‐(4‐sulfophenyl)‐2H‐tetrazolium (MTS), 2,3‐bis‐(2‐methoxy‐4‐nitro‐5‐sulfophenyl)‐2H‐tetrazolium‐5‐carboxanilide (XTT), 2‐(4‐iodophenyl)‐3‐(4‐nitrophenyl)‐5‐(2,4‐disulfophenyl)‐2H tetrazolium, monosodium salt (WST‐1), 2‐(2‐methoxy‐4‐nitrophenyl)‐3‐(4‐nitrophenyl)‐5‐(2,4‐disulfophenyl)‐2H‐tetrazolium, monosodium salt (WST‐8), lactate dehydrogenase (LDH), sulforhodamine B (SRB), neutral red uptake (NRU), and crystal violet stain (CVS) assays are among the colorimetric assays. Similarly, resazurin and 5‐carboxyfluorescein diacetate acetoxymethyl ester (5‐CFDA‐AM) assays are based on fluorometric measurements, whereas luminometric assays comprise adenosine triphosphate and real‐time viability assays. Major flow cytometric assays include membrane asymmetry, membrane permeability, and mitochondria assays. In this guideline, the mechanisms and the practice of assessment of the most common cell viability assays applied in research labs are discussed in detail. An ideal cell viability assay should be safe, rapid, reliable, efficient, and time‐ and cost‐effective, and should not interfere with the test compound. Overall, it can be concluded that more than one cell viability assay should be applied in order to obtain reliable results.",
    url = "https://doi.org/10.1002/fft2.44",
    doi = "10.1002/fft2.44",
    openalex = "W3088986342",
    references = "doi1010020471142735ima03bs111, doi101007978161779080520, doi1010160022175983903034, doi101016s1387265605110047, doi101038nprot2006179, doi101038nprot200875, doi101038nrc3064, doi101046j14321327200001606x, doi101093jnci82131107, doi1021741389201017666160808160513, doi103727095535491820873191, openalexw2143811153"
}

@article{doi101016jejcb2020151108,
    author = "Kamal, Nor Shaheera Mohamad and Safuan, Sabreena and Shamsuddin, Shaharum and Foroozandeh, Parisa",
    title = "Aging of the cells: Insight into cellular senescence and detection Methods",
    year = "2020",
    journal = "European Journal of Cell Biology",
    url = "https://doi.org/10.1016/j.ejcb.2020.151108",
    doi = "10.1016/j.ejcb.2020.151108",
    openalex = "W3042119537",
    references = "doi1021741389201017666160808160513"
}

Understanding cellular heterogeneity is the holy grail of biology and medicine. Cells harboring identical genomes show a wide variety of behaviors in multicellular organisms. Genetic circuits underlying cell-type identities will facilitate the understanding of the regulatory programs for differentiation and maintenance of distinct cellular states. Such a cell-type-specific gene network can be inferred from coregulatory patterns across individual cells. Conventional methods of transcriptome profiling using tissue samples provide only average signals of diverse cell types. Therefore, reconstructing gene regulatory networks for a particular cell type is not feasible with tissue-based transcriptome data. Recently, single-cell omics technology has emerged and enabled the capture of the transcriptomic landscape of every individual cell. Although single-cell gene expression studies have already opened up new avenues, network biology using single-cell transcriptome data will further accelerate our understanding of cellular heterogeneity. In this review, we provide an overview of single-cell network biology and summarize recent progress in method development for network inference from single-cell RNA sequencing (scRNA-seq) data. Then, we describe how cell-type-specific gene networks can be utilized to study regulatory programs specific to disease-associated cell types and cellular states. Moreover, with scRNA data, modeling personal or patient-specific gene networks is feasible. Therefore, we also introduce potential applications of single-cell network biology for precision medicine. We envision a rapid paradigm shift toward single-cell network analysis for systems biology in the near future.

@article{doi101038s12276020005280,
    author = "Cha, Junha and Lee, Insuk",
    title = "Single-cell network biology for resolving cellular heterogeneity in human diseases",
    year = "2020",
    journal = "Experimental \& Molecular Medicine",
    abstract = "Understanding cellular heterogeneity is the holy grail of biology and medicine. Cells harboring identical genomes show a wide variety of behaviors in multicellular organisms. Genetic circuits underlying cell-type identities will facilitate the understanding of the regulatory programs for differentiation and maintenance of distinct cellular states. Such a cell-type-specific gene network can be inferred from coregulatory patterns across individual cells. Conventional methods of transcriptome profiling using tissue samples provide only average signals of diverse cell types. Therefore, reconstructing gene regulatory networks for a particular cell type is not feasible with tissue-based transcriptome data. Recently, single-cell omics technology has emerged and enabled the capture of the transcriptomic landscape of every individual cell. Although single-cell gene expression studies have already opened up new avenues, network biology using single-cell transcriptome data will further accelerate our understanding of cellular heterogeneity. In this review, we provide an overview of single-cell network biology and summarize recent progress in method development for network inference from single-cell RNA sequencing (scRNA-seq) data. Then, we describe how cell-type-specific gene networks can be utilized to study regulatory programs specific to disease-associated cell types and cellular states. Moreover, with scRNA data, modeling personal or patient-specific gene networks is feasible. Therefore, we also introduce potential applications of single-cell network biology for precision medicine. We envision a rapid paradigm shift toward single-cell network analysis for systems biology in the near future.",
    url = "https://doi.org/10.1038/s12276-020-00528-0",
    doi = "10.1038/s12276-020-00528-0",
    openalex = "W3108451992",
    references = "doi101038nmeth2016, doi101038nmeth4463, doi101038nrg1272, doi101038nri201776, doi101038s1227601800718, doi101093nargku1003, doi101126science1087447, doi101186147121059559, doi101371journalpone0012776, doi1015252msb20188746"
}

Cells succumbing to stress via regulated cell death (RCD) can initiate an adaptive immune response associated with immunological memory, provided they display sufficient antigenicity and adjuvanticity. Moreover, multiple intracellular and microenvironmental features determine the propensity of RCD to drive adaptive immunity. Here, we provide an updated operational definition of immunogenic cell death (ICD), discuss the key factors that dictate the ability of dying cells to drive an adaptive immune response, summarize experimental assays that are currently available for the assessment of ICD in vitro and in vivo, and formulate guidelines for their interpretation.

@article{doi101136jitc2019000337,
    author = "Galluzzi, Lorenzo and Vitale, Ilio and Warren, Sarah H. and Adjemian, Sandy and Agostinis, Patrizia and Martinez, Aitziber Buqué and Chan, Timothy A. and Coukos, George and Demaria, Sandra and Deutsch, Éric and Draganov, Dobrin and Edelson, Richard L. and Formenti, Silvia C. and Fučíková, Jitka and Gabriele, Lucia and Gaipl, Udo S. and Gameiro, Sofia R. and Garg, Abhishek D. and Golden, Encouse B. and Han, Jian and Harrington, Kevin J. and Hemminki, Akseli and Hodge, James W. and Hossain, Dewan Md Sakib and Illidge, Tim and Karin, Michael and Kaufman, Howard L. and Kepp, Oliver and Kroemer, Guido and Lasarte, Juan José and Loi, Sherene and Lotze, Michael T. and Manic, Gwenola and Merghoub, Taha and Melcher, Alan and Mossman, Karen and Prósper, Felipe and Rekdal, Øystein and Rescigno, María and Riganti, Chiara and Sistigu, Antonella and Smyth, Mark J. and Špíšek, Radek and Stagg, John and Strauss, Bryan E. and Tang, Daolin and Tatsuno, Kazuki and Gool, Stefaan Van and Vandenabeele, Peter and Yamazaki, Takahiro and Zamarin, Dmitriy and Zitvogel, Laurence and Cesano, Alessandra and Marincola, Francesco M.",
    title = "Consensus guidelines for the definition, detection and interpretation of immunogenic cell death",
    year = "2020",
    journal = "Journal for ImmunoTherapy of Cancer",
    abstract = "Cells succumbing to stress via regulated cell death (RCD) can initiate an adaptive immune response associated with immunological memory, provided they display sufficient antigenicity and adjuvanticity. Moreover, multiple intracellular and microenvironmental features determine the propensity of RCD to drive adaptive immunity. Here, we provide an updated operational definition of immunogenic cell death (ICD), discuss the key factors that dictate the ability of dying cells to drive an adaptive immune response, summarize experimental assays that are currently available for the assessment of ICD in vitro and in vivo, and formulate guidelines for their interpretation.",
    url = "https://doi.org/10.1136/jitc-2019-000337",
    doi = "10.1136/jitc-2019-000337",
    openalex = "W3011642937",
    references = "doi101038nrd3373"
}

extract and evaluation of the cellular and molecular mechanism of apoptosis.

@article{doi10115520201215395,
    author = "Ullah, Ikram and Khalil, Ali Talha and Ali, Muhammad and Iqbal, Javed and Ali, Waqar and Alarifi, Saud and Shinwari, Zabta Khan",
    title = "Green-Synthesized Silver Nanoparticles Induced Apoptotic Cell Death in MCF-7 Breast Cancer Cells by Generating Reactive Oxygen Species and Activating Caspase 3 and 9 Enzyme Activities",
    year = "2020",
    journal = "Oxidative Medicine and Cellular Longevity",
    abstract = "extract and evaluation of the cellular and molecular mechanism of apoptosis.",
    url = "https://doi.org/10.1155/2020/1215395",
    doi = "10.1155/2020/1215395",
    openalex = "W3092593061",
    references = "doi101016jacthis201201006"
}

cell cultures for many years. With the increase of 3D systems in cellular biology research to determine therapeutic efficacy, two-dimensional assays that measure cell viability are being used outside their intended use on 3D constructs. In this study, we assess the accuracy of using various commercially available cell viability assays on different 3D hydrogel constructs to help researchers understand expected variability in their experimentation along microscopic imaging validation.

@article{doi101089tentec20210060,
    author = "Dominijanni, Anthony and Devarasetty, Mahesh and Forsythe, Steven D. and Votanopoulos, Konstantinos I. and Söker, Shay",
    title = "Cell Viability Assays in Three-Dimensional Hydrogels: A Comparative Study of Accuracy",
    year = "2021",
    journal = "Tissue Engineering Part C Methods",
    abstract = "cell cultures for many years. With the increase of 3D systems in cellular biology research to determine therapeutic efficacy, two-dimensional assays that measure cell viability are being used outside their intended use on 3D constructs. In this study, we assess the accuracy of using various commercially available cell viability assays on different 3D hydrogel constructs to help researchers understand expected variability in their experimentation along microscopic imaging validation.",
    url = "https://doi.org/10.1089/ten.tec.2021.0060",
    doi = "10.1089/ten.tec.2021.0060",
    openalex = "W3165104736",
    references = "doi101002fft244"
}

/pRB tumor suppressor pathways play a central role in regulating senescence. Several other pathways have recently been implicated in mediating senescence and the senescent phenotype. Herein we review the molecular mechanisms that underlie cellular senescence and the senescence associated growth arrest with a particular focus on why cells stop dividing, the stability of the growth arrest, the hypersecretory phenotype and how the different pathways are all integrated.

@article{doi103389fcell2021645593,
    author = "Kumari, Ruchi and Jat, Parmjit",
    title = "Mechanisms of Cellular Senescence: Cell Cycle Arrest and Senescence Associated Secretory Phenotype",
    year = "2021",
    journal = "Frontiers in Cell and Developmental Biology",
    abstract = "/pRB tumor suppressor pathways play a central role in regulating senescence. Several other pathways have recently been implicated in mediating senescence and the senescent phenotype. Herein we review the molecular mechanisms that underlie cellular senescence and the senescence associated growth arrest with a particular focus on why cells stop dividing, the stability of the growth arrest, the hypersecretory phenotype and how the different pathways are all integrated.",
    url = "https://doi.org/10.3389/fcell.2021.645593",
    doi = "10.3389/fcell.2021.645593",
    openalex = "W3146579363",
    references = "doi1021741389201017666160808160513"
}

The rapid development of single-cell technologies allows for dissecting cellular heterogeneity at different omics layers with an unprecedented resolution. In-dep analysis of cellular heterogeneity will boost our understanding of complex biological systems or processes, including cancer, immune system and chronic diseases, thereby providing valuable insights for clinical and translational research. In this review, we will focus on the application of machine learning methods in single-cell multi-omics data analysis. We will start with the pre-processing of single-cell RNA sequencing (scRNA-seq) data, including data imputation, cross-platform batch effect removal, and cell cycle and cell-type identification. Next, we will introduce advanced data analysis tools and methods used for copy number variance estimate, single-cell pseudo-time trajectory analysis, phylogenetic tree inference, cell-cell interaction, regulatory network inference, and integrated analysis of scRNA-seq and spatial transcriptome data. Finally, we will present the latest analyzing challenges, such as multi-omics integration and integrated analysis of scRNA-seq data.

@article{doi103389fgene2021655536,
    author = "Liu, Jiajia and Fan, Zhiwei and Zhao, Weiling and Zhou, Xiaobo",
    title = "Machine Intelligence in Single-Cell Data Analysis: Advances and New Challenges",
    year = "2021",
    journal = "Frontiers in Genetics",
    abstract = "The rapid development of single-cell technologies allows for dissecting cellular heterogeneity at different omics layers with an unprecedented resolution. In-dep analysis of cellular heterogeneity will boost our understanding of complex biological systems or processes, including cancer, immune system and chronic diseases, thereby providing valuable insights for clinical and translational research. In this review, we will focus on the application of machine learning methods in single-cell multi-omics data analysis. We will start with the pre-processing of single-cell RNA sequencing (scRNA-seq) data, including data imputation, cross-platform batch effect removal, and cell cycle and cell-type identification. Next, we will introduce advanced data analysis tools and methods used for copy number variance estimate, single-cell pseudo-time trajectory analysis, phylogenetic tree inference, cell-cell interaction, regulatory network inference, and integrated analysis of scRNA-seq and spatial transcriptome data. Finally, we will present the latest analyzing challenges, such as multi-omics integration and integrated analysis of scRNA-seq data.",
    url = "https://doi.org/10.3389/fgene.2021.655536",
    doi = "10.3389/fgene.2021.655536",
    openalex = "W3169674085",
    references = "doi101038s12276020005280"
}

The MTT assay for cellular metabolic activity is almost ubiquitous to studies of cell toxicity; however, it is commonly applied and interpreted erroneously. We investigated the applicability and limitations of the MTT assay in representing treatment toxicity, cell viability, and metabolic activity. We evaluated the effect of potential confounding variables on the MTT assay measurements on a prostate cancer cell line (PC-3) including cell seeding number, MTT concentration, MTT incubation time, serum starvation, cell culture media composition, released intracellular contents (cell lysate and secretome), and extrusion of formazan to the extracellular space. We also assessed the confounding effect of polyethylene glycol (PEG)-coated gold nanoparticles (Au-NPs) as a tested treatment in PC-3 cells on the assay measurements. We additionally evaluated the applicability of microscopic image cytometry as a tool for measuring intracellular MTT reduction at the single-cell level. Our findings show that the assay measurements are a result of a complicated process dependant on many of the above-mentioned factors, and therefore, optimization of the assay and rational interpretation of the data is necessary to prevent misleading conclusions on variables such as cell viability, treatment toxicity, and/or cell metabolism. We conclude, with recommendations on how to apply the assay and a perspective on where the utility of the assay is a powerful tool, but likewise where it has limitations.

@article{doi103390ijms222312827,
    author = "Ghasemi, Mahshid and Turnbull, Tyron and Sebastian, Sonia and Kempson, Ivan M.",
    title = "The MTT Assay: Utility, Limitations, Pitfalls, and Interpretation in Bulk and Single-Cell Analysis",
    year = "2021",
    journal = "International Journal of Molecular Sciences",
    abstract = "The MTT assay for cellular metabolic activity is almost ubiquitous to studies of cell toxicity; however, it is commonly applied and interpreted erroneously. We investigated the applicability and limitations of the MTT assay in representing treatment toxicity, cell viability, and metabolic activity. We evaluated the effect of potential confounding variables on the MTT assay measurements on a prostate cancer cell line (PC-3) including cell seeding number, MTT concentration, MTT incubation time, serum starvation, cell culture media composition, released intracellular contents (cell lysate and secretome), and extrusion of formazan to the extracellular space. We also assessed the confounding effect of polyethylene glycol (PEG)-coated gold nanoparticles (Au-NPs) as a tested treatment in PC-3 cells on the assay measurements. We additionally evaluated the applicability of microscopic image cytometry as a tool for measuring intracellular MTT reduction at the single-cell level. Our findings show that the assay measurements are a result of a complicated process dependant on many of the above-mentioned factors, and therefore, optimization of the assay and rational interpretation of the data is necessary to prevent misleading conclusions on variables such as cell viability, treatment toxicity, and/or cell metabolism. We conclude, with recommendations on how to apply the assay and a perspective on where the utility of the assay is a powerful tool, but likewise where it has limitations.",
    url = "https://doi.org/10.3390/ijms222312827",
    doi = "10.3390/ijms222312827",
    openalex = "W3216591159",
    references = "doi1010160022175983903034, doi1010160022175989903979, doi101016jacthis201201006, doi101016jacthis201802005, doi101016s1387265605110047, doi101038bjc1987190, doi101038cdd2008150, doi101039df9511100055, doi101046j14714159199769020581x, doi10108001926230701320337, doi101146annurevpathol121808102144, doi101371journalpbio0060301"
}

Background. Among cancer patients receiving radiotherapy about 5–15 % may have adverse reactions in normal tissues and organs that limit their treatment in a full, originally scheduled regimen. The development of biomarkers and assays for radiation oncology allowing the prediction of patients’ normal tissue toxicity requires a lot of resourses, threfore its current status amd potential directions for future research have to be periodically analyzed and re-evaluated. Purpose – this review summarizes the methodological approaches and developments in the area of functional laboratory assays based on ex vivo cell survival for the prediction of the individual clinical radiosensitivity. Materials and methods. Data for the analysis and systematization were obtained from the full-text articles published in peer review international scientific journals (in English) in 1990–2020, which were selected by the extensive search in PubMed information database and cross references on the topic “Functional cellular tests for intrinsic radiosensitivity to predict adverse radiation effects and radiotherapy complications”. Results. In theory, it might be expected that clonogenic cell survival after ex vivo irradiation can surve as the best individual predictor of radiation toxicity, as it is an integral indicator of cell damage and decline of their regenerative potential. Tendentially, fibroblasts, as a test system for such studies, did not show significant advantages over lymphocytes either in detecting inter-individual variations in the intrinsic cellular radiosensitivity or in predicting clinical radiation toxicity, even for that in skin. It was found that clonogenic cell survival assay, being very time consuming and technically demanding, also suffers from the lack of sensitivity and specificity, essential uncertainty and low reproducibility of the results, and thus is not suitable for the sceening for the abnormal intrinsic radiosensitivity. However, this type of assays is applicable for the radiobiological expertise post factum in individual cases with unexpected, extreme radiation lesions. Radiation-induced lymphocyte apoptosis assay seems to be more promising however still requires further fundamental research for better understanding of its background and more validation studies in order to assess the optimum patient groups, radiotherapy regimens and adverse effects for its confident use in clinical practice. Changes in the regulation of cell cycle check-points (radiationinduced delay) ex vivo can have either positive or inverted association, or no correlation with clinical radiation responses in tissues, thus so far cannot be included in the toolbox of applied radiobiological tests. Conclusions. To date, in the practice of clinical radiobiology, there are no fully validated and standardized functional tests based on the cell survival after ex vivo irradiation, which would allow a sufficiently accurate prediction of adverse radiation effects in normal tissues of radiotherapy patients. In general, ex vivo tests based on the evaluation of only one form of cell death in one cell type are not fully reliable as a “stand alone” assay, because different pathways of cell death probably play different roles and show different dose response within the overal reaction of the irradiated tissue or critical organ. Such tests should become a part of the multiparametric predictive platforms.

@article{doi1046879ukroj1202189118,
    author = "Vinnikov, Volodymyr and Rublova, T.V.",
    title = "Predictors of radiation-induced complications in radiation oncology based on cell survival tests after ex vivo exposure: literature review",
    year = "2021",
    journal = "Український радіологічний та онкологічний журнал",
    abstract = "Background. Among cancer patients receiving radiotherapy about 5–15 \% may have adverse reactions in normal tissues and organs that limit their treatment in a full, originally scheduled regimen. The development of biomarkers and assays for radiation oncology allowing the prediction of patients’ normal tissue toxicity requires a lot of resourses, threfore its current status amd potential directions for future research have to be periodically analyzed and re-evaluated. Purpose – this review summarizes the methodological approaches and developments in the area of functional laboratory assays based on ex vivo cell survival for the prediction of the individual clinical radiosensitivity. Materials and methods. Data for the analysis and systematization were obtained from the full-text articles published in peer review international scientific journals (in English) in 1990–2020, which were selected by the extensive search in PubMed information database and cross references on the topic “Functional cellular tests for intrinsic radiosensitivity to predict adverse radiation effects and radiotherapy complications”. Results. In theory, it might be expected that clonogenic cell survival after ex vivo irradiation can surve as the best individual predictor of radiation toxicity, as it is an integral indicator of cell damage and decline of their regenerative potential. Tendentially, fibroblasts, as a test system for such studies, did not show significant advantages over lymphocytes either in detecting inter-individual variations in the intrinsic cellular radiosensitivity or in predicting clinical radiation toxicity, even for that in skin. It was found that clonogenic cell survival assay, being very time consuming and technically demanding, also suffers from the lack of sensitivity and specificity, essential uncertainty and low reproducibility of the results, and thus is not suitable for the sceening for the abnormal intrinsic radiosensitivity. However, this type of assays is applicable for the radiobiological expertise post factum in individual cases with unexpected, extreme radiation lesions. Radiation-induced lymphocyte apoptosis assay seems to be more promising however still requires further fundamental research for better understanding of its background and more validation studies in order to assess the optimum patient groups, radiotherapy regimens and adverse effects for its confident use in clinical practice. Changes in the regulation of cell cycle check-points (radiationinduced delay) ex vivo can have either positive or inverted association, or no correlation with clinical radiation responses in tissues, thus so far cannot be included in the toolbox of applied radiobiological tests. Conclusions. To date, in the practice of clinical radiobiology, there are no fully validated and standardized functional tests based on the cell survival after ex vivo irradiation, which would allow a sufficiently accurate prediction of adverse radiation effects in normal tissues of radiotherapy patients. In general, ex vivo tests based on the evaluation of only one form of cell death in one cell type are not fully reliable as a “stand alone” assay, because different pathways of cell death probably play different roles and show different dose response within the overal reaction of the irradiated tissue or critical organ. Such tests should become a part of the multiparametric predictive platforms.",
    url = "https://doi.org/10.46879/ukroj.1.2021.89-118",
    doi = "10.46879/ukroj.1.2021.89-118",
    openalex = "W3156546532",
    references = "doi101016jacthis201802005"
}

Analysis of the toxicity of chemotherapeutic drugs is one of the main tasks of clinical pharmacology. Decreased viability of tumor cells may reflect two important physiological processes, namely the arrest of proliferation associated with disturbances in cellular metabolism or actual cell death. Elucidation of the exact processes mediating a reduction in the number of cells is fundamentally important to establish the mechanisms of drug action. Only the use of a combination of cell biological and biochemical approaches makes it possible to understand these mechanisms. Here, using various lines of tumor cells and a set of methodological approaches, we carried out a detailed comparative analysis and demonstrated the possible ways to overcome the uncertainties in establishing the mechanisms of cell response to the action of chemotherapeutic drugs and their toxicity.

@article{doi101038s4142002201207x,
    author = "Sazonova, Elena V. and Chesnokov, Mikhail S. and Zhivotovsky, Boris and Kopeina, Gelina S.",
    title = "Drug toxicity assessment: cell proliferation versus cell death",
    year = "2022",
    journal = "Cell Death Discovery",
    abstract = "Analysis of the toxicity of chemotherapeutic drugs is one of the main tasks of clinical pharmacology. Decreased viability of tumor cells may reflect two important physiological processes, namely the arrest of proliferation associated with disturbances in cellular metabolism or actual cell death. Elucidation of the exact processes mediating a reduction in the number of cells is fundamentally important to establish the mechanisms of drug action. Only the use of a combination of cell biological and biochemical approaches makes it possible to understand these mechanisms. Here, using various lines of tumor cells and a set of methodological approaches, we carried out a detailed comparative analysis and demonstrated the possible ways to overcome the uncertainties in establishing the mechanisms of cell response to the action of chemotherapeutic drugs and their toxicity.",
    url = "https://doi.org/10.1038/s41420-022-01207-x",
    doi = "10.1038/s41420-022-01207-x",
    openalex = "W4306164209",
    references = "doi101002fft244, doi101016jacthis201802005, doi103390ijms222312827"
}

Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.

@article{doi101186s1302402200517z,
    author = "Wang, Minghui and Song, Won‐Min and Chen, Ming and Wang, Qian and Zhou, Xianxiao and Xu, Peng and Krek, Azra and Yoon, Yonejung and Ho, Lap and Orr, Miranda E. and Yuan, Guo‐Cheng and Zhang, Bin",
    title = "Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer’s disease: review, recommendation, implementation and application",
    year = "2022",
    journal = "Molecular Neurodegeneration",
    abstract = "Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.",
    url = "https://doi.org/10.1186/s13024-022-00517-z",
    doi = "10.1186/s13024-022-00517-z",
    openalex = "W4214892207",
    references = "doi101038s12276020005280"
}

@article{doi10100797810716305252,
    author = "Ghasemi, Mahshid and Liang, Sisi and Luu, Quang Minh and Kempson, Ivan M.",
    title = "The MTT Assay: A Method for Error Minimization and Interpretation in Measuring Cytotoxicity and Estimating Cell Viability",
    year = "2023",
    journal = "Methods in molecular biology",
    url = "https://doi.org/10.1007/978-1-0716-3052-5\_2",
    doi = "10.1007/978-1-0716-3052-5\_2",
    openalex = "W4371783751",
    references = "doi103390ijms222312827"
}

Cultivated meat production requires an efficient, robust and highly optimized serum-free cell culture media for the needed upscaling of muscle cell expansion. Existing formulations of serum-free media are complex, expensive and have not been optimized for muscle cells. Thus, we undertook this work to develop a simple and robust serum-free media for the proliferation of bovine satellite cells (SCs) through Design of Experiment (DOE) and Response Surface Methodology (RSM) using precise and high-throughput image-based cytometry. Proliferative attributes were investigated with transcriptomics and long-term performance was validated using multiple live assays. Here we formulated a media based on three highly optimized components; FGF2 (2 ng/mL), fetuin (600 µg/mL) and BSA (75 µg/mL) which together with an insulin-transferrin-selenium (1x) supplement, sustained the proliferation of bovine SCs, porcine SCs and murine C2C12 muscle cells. Remarkably, cells cultured in our media named Tri-basal 2.0+ performed better than cell cultured in 10% FBS, with respect to proliferation. Hence, the optimized Tri-basal 2.0+ enhanced serum-free cell attachment and long-term proliferation, providing an alternative solution to the use of FBS in the production of cultivated meat.

@article{doi101016jfoodres2023113194,
    author = "Skrivergaard, Stig and Young, J.F. and Sahebekhtiari, Navid and Semper, Cameron and Venkatesan, Meenakshi and Savchenko, Alexei and Stogios, P.J. and Therkildsen, Margrethe and Rasmussen, Martin Krøyer",
    title = "A simple and robust serum-free media for the proliferation of muscle cells",
    year = "2023",
    journal = "Food Research International",
    abstract = "Cultivated meat production requires an efficient, robust and highly optimized serum-free cell culture media for the needed upscaling of muscle cell expansion. Existing formulations of serum-free media are complex, expensive and have not been optimized for muscle cells. Thus, we undertook this work to develop a simple and robust serum-free media for the proliferation of bovine satellite cells (SCs) through Design of Experiment (DOE) and Response Surface Methodology (RSM) using precise and high-throughput image-based cytometry. Proliferative attributes were investigated with transcriptomics and long-term performance was validated using multiple live assays. Here we formulated a media based on three highly optimized components; FGF2 (2 ng/mL), fetuin (600 µg/mL) and BSA (75 µg/mL) which together with an insulin-transferrin-selenium (1x) supplement, sustained the proliferation of bovine SCs, porcine SCs and murine C2C12 muscle cells. Remarkably, cells cultured in our media named Tri-basal 2.0+ performed better than cell cultured in 10\% FBS, with respect to proliferation. Hence, the optimized Tri-basal 2.0+ enhanced serum-free cell attachment and long-term proliferation, providing an alternative solution to the use of FBS in the production of cultivated meat.",
    url = "https://doi.org/10.1016/j.foodres.2023.113194",
    doi = "10.1016/j.foodres.2023.113194",
    openalex = "W4382559755",
    references = "doi103390ijms222312827"
}

Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims to unravel the complex relationships between genes and their regulators. Deciphering these networks plays a critical role in understanding the underlying regulatory crosstalk that drives many cellular processes and diseases. Recent advances in sequencing technology have led to the development of state-of-the-art GRN inference methods that exploit matched single-cell multi-omic data. By employing diverse mathematical and statistical methodologies, these methods aim to reconstruct more comprehensive and precise gene regulatory networks. In this review, we give a brief overview on the statistical and methodological foundations commonly used in GRN inference methods. We then compare and contrast the latest state-of-the-art GRN inference methods for single-cell matched multi-omics data, and discuss their assumptions, limitations and opportunities. Finally, we discuss the challenges and future directions that hold promise for further advancements in this rapidly developing field.

@article{doi101038s41540023003126,
    author = "Kim, Daniel and Tran, Andy and Kim, Hani Jieun and Lin, Yingxin and Yang, Jean and Yang, Pengyi",
    title = "Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data",
    year = "2023",
    journal = "npj Systems Biology and Applications",
    abstract = "Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims to unravel the complex relationships between genes and their regulators. Deciphering these networks plays a critical role in understanding the underlying regulatory crosstalk that drives many cellular processes and diseases. Recent advances in sequencing technology have led to the development of state-of-the-art GRN inference methods that exploit matched single-cell multi-omic data. By employing diverse mathematical and statistical methodologies, these methods aim to reconstruct more comprehensive and precise gene regulatory networks. In this review, we give a brief overview on the statistical and methodological foundations commonly used in GRN inference methods. We then compare and contrast the latest state-of-the-art GRN inference methods for single-cell matched multi-omics data, and discuss their assumptions, limitations and opportunities. Finally, we discuss the challenges and future directions that hold promise for further advancements in this rapidly developing field.",
    url = "https://doi.org/10.1038/s41540-023-00312-6",
    doi = "10.1038/s41540-023-00312-6",
    openalex = "W4387774515",
    references = "doi101038s12276020005280"
}

BACKGROUND: Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution. RESULTS: We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay. CONCLUSIONS: This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.

@article{doi101186s13059023030326,
    author = "Zhu, Xiangqian and Xu, Zhongping and Wang, Guanying and Cong, Yulong and Lu, Yu and Jia, Ruoyu and Qin, Yuan and Zhang, Guangyu and Li, Bo and Yuan, Daojun and Tu, Lili and Yang, Xiyan and Lindsey, Keith and Zhang, Xianlong and Jin, Shuangxia",
    title = "Single-cell resolution analysis reveals the preparation for reprogramming the fate of stem cell niche in cotton lateral meristem",
    year = "2023",
    journal = "Genome biology",
    abstract = "BACKGROUND: Somatic embryogenesis is a major process for plant regeneration. However, cell communication and the gene regulatory network responsible for cell reprogramming during somatic embryogenesis are still largely unclear. Recent advances in single-cell technologies enable us to explore the mechanism of plant regeneration at single-cell resolution. RESULTS: We generate a high-resolution single-cell transcriptomic landscape of hypocotyl tissue from the highly regenerable cotton genotype Jin668 and the recalcitrant TM-1. We identify nine putative cell clusters and 23 cluster-specific marker genes for both cultivars. We find that the primary vascular cell is the major cell type that undergoes cell fate transition in response to external stimulation. Further developmental trajectory and gene regulatory network analysis of these cell clusters reveals that a total of 41 hormone response-related genes, including LAX2, LAX1, and LOX3, exhibit different expression patterns in the primary xylem and cambium region of Jin668 and TM-1. We also identify novel genes, including CSEF, PIS1, AFB2, ATHB2, PLC2, and PLT3, that are involved in regeneration. We demonstrate that LAX2, LAX1 and LOX3 play important roles in callus proliferation and plant regeneration by CRISPR/Cas9 editing and overexpression assay. CONCLUSIONS: This study provides novel insights on the role of the regulatory network in cell fate transition and reprogramming during plant regeneration driven by somatic embryogenesis.",
    url = "https://doi.org/10.1186/s13059-023-03032-6",
    doi = "10.1186/s13059-023-03032-6",
    openalex = "W4386167342",
    references = "doi101038s12276020005280"
}

Cell viability and cytotoxicity assays play a crucial role in drug screening and evaluating the cytotoxic effects of various chemicals. The quantification of cell viability and proliferation serves as the cornerstone for numerous in vitro assays that assess cellular responses to external factors. In the last decade, several studies have developed guidelines for defining and interpreting cell viability and cytotoxicity based on morphological, biochemical, and functional perspectives. As this domain continues to experience ongoing growth, revealing new mechanisms orchestrating diverse cell cytotoxicity pathways, we suggest a revised classification for multiple assays employed in evaluating cell viability and cell death. This classification is rooted in the cellular compartment and/or biochemical element involved, with a specific focus on mechanistic and essential aspects of the process. The assays are founded on diverse cell functions, encompassing metabolic activity, enzyme activity, cell membrane permeability and integrity, adenosine 5'-triphosphate content, cell adherence, reduction equivalents, dye inclusion or exclusion, constitutive protease activity, colony formation, DNA fragmentation and nuclear splitting. These assays present straightforward, reliable, sensitive, reproducible, cost-effective, and high-throughput approaches for appraising the effects of newly formulated chemotherapeutic biomolecules on the cell survival during the drug development process.

@article{doi101002cbf4007,
    author = "Lefsih, Khalef and Lydia, Radja and Filicia, Khettar and Moussa, Berkoud",
    title = "Cell viability and cytotoxicity assays: Biochemical elements and cellular compartments",
    year = "2024",
    journal = "Cell Biochemistry and Function",
    abstract = "Cell viability and cytotoxicity assays play a crucial role in drug screening and evaluating the cytotoxic effects of various chemicals. The quantification of cell viability and proliferation serves as the cornerstone for numerous in vitro assays that assess cellular responses to external factors. In the last decade, several studies have developed guidelines for defining and interpreting cell viability and cytotoxicity based on morphological, biochemical, and functional perspectives. As this domain continues to experience ongoing growth, revealing new mechanisms orchestrating diverse cell cytotoxicity pathways, we suggest a revised classification for multiple assays employed in evaluating cell viability and cell death. This classification is rooted in the cellular compartment and/or biochemical element involved, with a specific focus on mechanistic and essential aspects of the process. The assays are founded on diverse cell functions, encompassing metabolic activity, enzyme activity, cell membrane permeability and integrity, adenosine 5'-triphosphate content, cell adherence, reduction equivalents, dye inclusion or exclusion, constitutive protease activity, colony formation, DNA fragmentation and nuclear splitting. These assays present straightforward, reliable, sensitive, reproducible, cost-effective, and high-throughput approaches for appraising the effects of newly formulated chemotherapeutic biomolecules on the cell survival during the drug development process.",
    url = "https://doi.org/10.1002/cbf.4007",
    doi = "10.1002/cbf.4007",
    openalex = "W4394595909",
    references = "doi101002fft244, doi103390ijms222312827"
}

The exponential growth of big data in RNA biology (RB) has led to the development of deep learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL studies in other fields, the successful implementation of DL in RB depends heavily on the effective utilization of large-scale datasets from public databases. In achieving this goal, data encoding methods, learning algorithms, and techniques that align well with biological domain knowledge have played pivotal roles. In this review, we provide guiding principles for applying these DL concepts to various problems in RB by demonstrating successful examples and associated methodologies. We also discuss the remaining challenges in developing DL models for RB and suggest strategies to overcome these challenges. Overall, this review aims to illuminate the compelling potential of DL for RB and ways to apply this powerful technology to investigate the intriguing biology of RNA more effectively.

@article{doi101038s1227602401243w,
    author = "Hwang, Hyeonseo and Jeon, Hyeonseong and Yeo, Nagyeong and Baek, Daehyun",
    title = "Big data and deep learning for RNA biology",
    year = "2024",
    journal = "Experimental \& Molecular Medicine",
    abstract = "The exponential growth of big data in RNA biology (RB) has led to the development of deep learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL studies in other fields, the successful implementation of DL in RB depends heavily on the effective utilization of large-scale datasets from public databases. In achieving this goal, data encoding methods, learning algorithms, and techniques that align well with biological domain knowledge have played pivotal roles. In this review, we provide guiding principles for applying these DL concepts to various problems in RB by demonstrating successful examples and associated methodologies. We also discuss the remaining challenges in developing DL models for RB and suggest strategies to overcome these challenges. Overall, this review aims to illuminate the compelling potential of DL for RB and ways to apply this powerful technology to investigate the intriguing biology of RNA more effectively.",
    url = "https://doi.org/10.1038/s12276-024-01243-w",
    doi = "10.1038/s12276-024-01243-w",
    openalex = "W4399691497",
    references = "doi101038s12276020005280"
}

In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies have established themselves as key tools for dissecting genetic sequences at the level of single cells. These technologies reveal cellular diversity and allow for the exploration of cell states and transformations with exceptional resolution. Unlike bulk sequencing, which provides population-averaged data, scRNA-seq can detect cell subtypes or gene expression variations that would otherwise be overlooked. However, a key limitation of scRNA-seq is its inability to preserve spatial information about the RNA transcriptome, as the process requires tissue dissociation and cell isolation. Spatial transcriptomics is a pivotal advancement in medical biotechnology, facilitating the identification of molecules such as RNA in their original spatial context within tissue sections at the single-cell level. This capability offers a substantial advantage over traditional single-cell sequencing techniques. Spatial transcriptomics offers valuable insights into a wide range of biomedical fields, including neurology, embryology, cancer research, immunology, and histology. This review highlights single-cell sequencing approaches, recent technological developments, associated challenges, various techniques for expression data analysis, and their applications in disciplines such as cancer research, microbiology, neuroscience, reproductive biology, and immunology. It highlights the critical role of single-cell sequencing tools in characterizing the dynamic nature of individual cells.

@article{doi103389abp202513922,
    author = "Desta, Getnet Molla and Birhanu, Alemayehu Godana",
    title = "Advancements in single-cell RNA sequencing and spatial transcriptomics: transforming biomedical research",
    year = "2025",
    journal = "Acta Biochimica Polonica",
    abstract = "In recent years, significant advancements in biochemistry, materials science, engineering, and computer-aided testing have driven the development of high-throughput tools for profiling genetic information. Single-cell RNA sequencing (scRNA-seq) technologies have established themselves as key tools for dissecting genetic sequences at the level of single cells. These technologies reveal cellular diversity and allow for the exploration of cell states and transformations with exceptional resolution. Unlike bulk sequencing, which provides population-averaged data, scRNA-seq can detect cell subtypes or gene expression variations that would otherwise be overlooked. However, a key limitation of scRNA-seq is its inability to preserve spatial information about the RNA transcriptome, as the process requires tissue dissociation and cell isolation. Spatial transcriptomics is a pivotal advancement in medical biotechnology, facilitating the identification of molecules such as RNA in their original spatial context within tissue sections at the single-cell level. This capability offers a substantial advantage over traditional single-cell sequencing techniques. Spatial transcriptomics offers valuable insights into a wide range of biomedical fields, including neurology, embryology, cancer research, immunology, and histology. This review highlights single-cell sequencing approaches, recent technological developments, associated challenges, various techniques for expression data analysis, and their applications in disciplines such as cancer research, microbiology, neuroscience, reproductive biology, and immunology. It highlights the critical role of single-cell sequencing tools in characterizing the dynamic nature of individual cells.",
    url = "https://doi.org/10.3389/abp.2025.13922",
    doi = "10.3389/abp.2025.13922",
    openalex = "W4407184228",
    references = "doi101038s12276020005280"
}

Skeletal stem cells (SSCs) are well characterized in humans and mice, providing valuable insights into bone development and regeneration. However, their identification in poultry, particularly in chicken embryos, remains limited. In the present study, we used single-cell transcriptomic profiling to compare the cellular composition and functionality of human and chicken embryonic limb buds. Our cross-species analysis revealed high conservation of key cell types, such as mesenchymal and osteochondral progenitors, alongside notable heterogeneity in individual gene expression profiles. We identified the conserved and species-specific gene expression patterns in chicken SSCs. Differential expression analysis combined with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein-protein interaction (PPI) networks suggested that COL5A2, COL1A2, PRRX1, and TGFβ2 may serve as key regulators of chicken SSCs. Immunofluorescence assays confirmed the predominant localization of these genes in the periosteal region, with minor expression in the primary ossification centers. This study enhances our understanding of cellular diversity in chicken embryonic limb buds and highlights conserved and divergent mechanisms across species, offering insights for future SSC research and animal model selection in skeletal biology.

@article{doi101371journalpone0346514,
    author = "Zhao, Ruohan and Jian, Zonghui and Yang, Fangxiao and Wang, Kun and Liu, Lixian and Xu, Zhiqiang and Jia, Junjing and Dou, Tengfei and He, Xiaoming",
    title = "Single-cell profiling unveils key regulators of skeletal stem cells in chicken and human embryonic limb development.",
    year = "2026",
    journal = "PloS one",
    abstract = "Skeletal stem cells (SSCs) are well characterized in humans and mice, providing valuable insights into bone development and regeneration. However, their identification in poultry, particularly in chicken embryos, remains limited. In the present study, we used single-cell transcriptomic profiling to compare the cellular composition and functionality of human and chicken embryonic limb buds. Our cross-species analysis revealed high conservation of key cell types, such as mesenchymal and osteochondral progenitors, alongside notable heterogeneity in individual gene expression profiles. We identified the conserved and species-specific gene expression patterns in chicken SSCs. Differential expression analysis combined with Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and protein-protein interaction (PPI) networks suggested that COL5A2, COL1A2, PRRX1, and TGFβ2 may serve as key regulators of chicken SSCs. Immunofluorescence assays confirmed the predominant localization of these genes in the periosteal region, with minor expression in the primary ossification centers. This study enhances our understanding of cellular diversity in chicken embryonic limb buds and highlights conserved and divergent mechanisms across species, offering insights for future SSC research and animal model selection in skeletal biology.",
    url = "https://pubmed.ncbi.nlm.nih.gov/42048409/",
    doi = "10.1371/journal.pone.0346514",
    pmid = "42048409"
}

@misc{sadguna2026cellular,
    author = "Sadguna, V.",
    title = "Cellular Biology",
    year = "2026",
    url = "https://doi.org/10.70593/978-93-7185-293-7",
    doi = "10.70593/978-93-7185-293-7"
}

@misc{crossrefNoneinternational,
    title = "International Journal of Cell Biology and Cellular Functions",
    year = "None",
    url = "https://doi.org/10.37591/ijcbcf",
    doi = "10.37591/ijcbcf",
    openalex = "W4379209419"
}

@misc{crossrefNonejournal,
    title = "Journal of Cellular Toxicology and Cell Biology",
    year = "None",
    url = "https://doi.org/10.29199/ctcb",
    doi = "10.29199/ctcb",
    openalex = "W4252752144"
}