Growth

@misc{brody1945bioenergetics2,
    author = "Brody, S",
    title = "Bioenergetics and Growth",
    year = "1945",
    howpublished = "New York, Van Nostrand Reinhold, 1023 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Brody, S., 1945, Bioenergetics and Growth: New York, Van Nostrand Reinhold, 1023 p.}"
}

@article{bertalanffy1957quantitative1,
    author = "Bertalanffy, L",
    title = "Quantitative laws in metabolism and growth",
    year = "1957",
    journal = "Quarterly Review of Biology, v. 32, p. 217-231",
    note = "talkorigins\_source = {true}; raw\_reference = {Bertalanffy, L., 1957, Quantitative laws in metabolism and growth: Quarterly Review of Biology, v. 32, p. 217-231.}"
}

@article{vonbertalanffy1957quantitative,
    author = "von Bertalanffy, Ludwig",
    title = "Quantitative Laws in Metabolism and Growth",
    year = "1957",
    journal = "The Quarterly Review of Biology",
    url = "https://doi.org/10.1086/401873",
    doi = "10.1086/401873",
    number = "3",
    openalex = "W2278685458",
    pages = "217-231",
    volume = "32",
    references = "doi101002ar1091000306, doi101002jcp1030570302, doi101007bf00650112, doi101007bf01722007, doi101016s0021925818555757, doi101016s0021925818566928, doi101021j150446a008, doi101086physzool17130151829, doi101126science1092841579, doi101152physrev1956362255"
}

@book{thompson1961on3,
    author = "Thompson, D'A. W",
    title = "On Growth and Form",
    year = "1961",
    publisher = "Cambridge, Cambridge University Press; [Abriged edition by J.T. Bonner]",
    note = "talkorigins\_source = {true}; raw\_reference = {Thompson, D'A. W., 1961, On Growth and Form: Cambridge, Cambridge University Press; [Abriged edition by J.T. Bonner].}"
}

Abstract Modular (colonial) invertebrates are mostly aquatic, sessile, active or passive suspension feeders. This paper proposes and discusses some generalizations concerning form that apparently are related to the sessile colonial mode of life. In contrast to the size of related unitary forms, the modules are small, maximizing feeding surface relative to metabolic mass and favouring production of a high energy surplus. Increasing colonial integration in ascidians and hydroids is associated with decreasing module size but in Bryozoa, with the lophophore as index, with some increase in size. The smallest lophophores are found in species with apparently primitive, near-linear branching. Among bryozoans with compact encrusting colonies, however, species with larger lophophores can outcompete abutting neighbours with smaller lophophores. Lophophore size may then be a compromise between energetic advantage and competitive disadvantage. Whereas internal filterers tend to have modules grouped to produce larger exhalant openings, favouring stronger discharge flow, in Bryozoa it appears advantageous to attain the maximum coverage of expanded lophophores. In Cheilostomata, lophophores are generally close packed, except at excurrent chimneys, and zooid size and shape are then directly linked to the dimensions of the lophophore. Bryozoa Cyclostomata, however, have evolved away from close-packed lophophores and quincuncial zooids towards fasciculated arrangements, possibly providing structural excurrent channels in a group that lacks the colonial coordination to maintain non-skeletal chimneys. Variations in colony form are related to mode of growth, the disposition of modules to maximize filtration, and interactions with environmental factors. Increasing surface area leads to increased drag imposed by water movements. This may place constraints on growth and form, or may be exploited to augment filtration. Passive filterers often produce erect, branching, planar colonies oriented normal to directional currents. Bilaterally symmetrical, dish-shaped colonies with downstream zooids may occur in unidirectional flow. Erect bryozoan colonies more commonly are irregularly tufted or regularly branched in three dimensions, being then adapted to flows that vary in direction or velocity, or both.

@article{doi101098rstb19860025,
    author = "Ryland, J. S. and Warner, George F.",
    title = "Growth and form in modular animals: ideas on the size and arrangement of zooids",
    year = "1986",
    journal = "Philosophical transactions of the Royal Society of London. Series B, Biological sciences",
    abstract = "Abstract Modular (colonial) invertebrates are mostly aquatic, sessile, active or passive suspension feeders. This paper proposes and discusses some generalizations concerning form that apparently are related to the sessile colonial mode of life. In contrast to the size of related unitary forms, the modules are small, maximizing feeding surface relative to metabolic mass and favouring production of a high energy surplus. Increasing colonial integration in ascidians and hydroids is associated with decreasing module size but in Bryozoa, with the lophophore as index, with some increase in size. The smallest lophophores are found in species with apparently primitive, near-linear branching. Among bryozoans with compact encrusting colonies, however, species with larger lophophores can outcompete abutting neighbours with smaller lophophores. Lophophore size may then be a compromise between energetic advantage and competitive disadvantage. Whereas internal filterers tend to have modules grouped to produce larger exhalant openings, favouring stronger discharge flow, in Bryozoa it appears advantageous to attain the maximum coverage of expanded lophophores. In Cheilostomata, lophophores are generally close packed, except at excurrent chimneys, and zooid size and shape are then directly linked to the dimensions of the lophophore. Bryozoa Cyclostomata, however, have evolved away from close-packed lophophores and quincuncial zooids towards fasciculated arrangements, possibly providing structural excurrent channels in a group that lacks the colonial coordination to maintain non-skeletal chimneys. Variations in colony form are related to mode of growth, the disposition of modules to maximize filtration, and interactions with environmental factors. Increasing surface area leads to increased drag imposed by water movements. This may place constraints on growth and form, or may be exploited to augment filtration. Passive filterers often produce erect, branching, planar colonies oriented normal to directional currents. Bilaterally symmetrical, dish-shaped colonies with downstream zooids may occur in unidirectional flow. Erect bryozoan colonies more commonly are irregularly tufted or regularly branched in three dimensions, being then adapted to flows that vary in direction or velocity, or both.",
    url = "https://doi.org/10.1098/rstb.1986.0025",
    doi = "10.1098/rstb.1986.0025",
    openalex = "W2153028084",
    references = "doi101007bf01722007"
}

Flux balance models of metabolism use stoichiometry of metabolic pathways, metabolic demands of growth, and optimality principles to predict metabolic flux distribution and cellular growth under specified environmental conditions. These models have provided a mechanistic interpretation of systemic metabolic physiology, and they are also useful as a quantitative tool for metabolic pathway design. Quantitative predictions of cell growth and metabolic by-product secretion that are experimentally testable can be obtained from these models. In the present report, we used independent measurements to determine the model parameters for the wild-type Escherichia coli strain W3110. We experimentally determined the maximum oxygen utilization rate (15 mmol of O2 per g [dry weight] per h), the maximum aerobic glucose utilization rate (10.5 mmol of Glc per g [dry weight] per h), the maximum anaerobic glucose utilization rate (18.5 mmol of Glc per g [dry weight] per h), the non-growth-associated maintenance requirements (7.6 mmol of ATP per g [dry weight] per h), and the growth-associated maintenance requirements (13 mmol of ATP per g of biomass). The flux balance model specified by these parameters was found to quantitatively predict glucose and oxygen uptake rates as well as acetate secretion rates observed in chemostat experiments. We have formulated a predictive algorithm in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures. In aerobic experiments we observed acetate secretion, accumulation in the culture medium, and reutilization from the culture medium. In fed-batch cultures acetate is cometabolized with glucose during the later part of the culture period.(ABSTRACT TRUNCATED AT 250 WORDS)

@article{doi101128aem6010372437311994,
    author = "Varma, Amit and Palsson, Bernhard Ø.",
    title = "Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110",
    year = "1994",
    journal = "Applied and Environmental Microbiology",
    abstract = "Flux balance models of metabolism use stoichiometry of metabolic pathways, metabolic demands of growth, and optimality principles to predict metabolic flux distribution and cellular growth under specified environmental conditions. These models have provided a mechanistic interpretation of systemic metabolic physiology, and they are also useful as a quantitative tool for metabolic pathway design. Quantitative predictions of cell growth and metabolic by-product secretion that are experimentally testable can be obtained from these models. In the present report, we used independent measurements to determine the model parameters for the wild-type Escherichia coli strain W3110. We experimentally determined the maximum oxygen utilization rate (15 mmol of O2 per g [dry weight] per h), the maximum aerobic glucose utilization rate (10.5 mmol of Glc per g [dry weight] per h), the maximum anaerobic glucose utilization rate (18.5 mmol of Glc per g [dry weight] per h), the non-growth-associated maintenance requirements (7.6 mmol of ATP per g [dry weight] per h), and the growth-associated maintenance requirements (13 mmol of ATP per g of biomass). The flux balance model specified by these parameters was found to quantitatively predict glucose and oxygen uptake rates as well as acetate secretion rates observed in chemostat experiments. We have formulated a predictive algorithm in order to apply the flux balance model to describe unsteady-state growth and by-product secretion in aerobic batch, fed-batch, and anaerobic batch cultures. In aerobic experiments we observed acetate secretion, accumulation in the culture medium, and reutilization from the culture medium. In fed-batch cultures acetate is cometabolized with glucose during the later part of the culture period.(ABSTRACT TRUNCATED AT 250 WORDS)",
    url = "https://doi.org/10.1128/aem.60.10.3724-3731.1994",
    doi = "10.1128/aem.60.10.3724-3731.1994",
    openalex = "W2143861551"
}

Life is the most complex physical phenomenon in the Universe, manifesting an extraordinary diversity of form and function over an enormous scale from the largest animals and plants to the smallest microbes and subcellular units. Despite this many of its most fundamental and complex phenomena scale with size in a surprisingly simple fashion. For example, metabolic rate scales as the 3/4-power of mass over 27 orders of magnitude, from molecular and intracellular levels up to the largest organisms. Similarly, time-scales (such as lifespans and growth rates) and sizes (such as bacterial genome lengths, tree heights and mitochondrial densities) scale with exponents that are typically simple powers of 1/4. The universality and simplicity of these relationships suggest that fundamental universal principles underly much of the coarse-grained generic structure and organisation of living systems. We have proposed a set of principles based on the observation that almost all life is sustained by hierarchical branching networks, which we assume have invariant terminal units, are space-filling and are optimised by the process of natural selection. We show how these general constraints explain quarter power scaling and lead to a quantitative, predictive theory that captures many of the essential features of diverse biological systems. Examples considered include animal circulatory systems, plant vascular systems, growth, mitochondrial densities, and the concept of a universal molecular clock. Temperature considerations, dimensionality and the role of invariants are discussed. Criticisms and controversies associated with this approach are also addressed.

@article{doi101242jeb01589,
    author = "West, Geoffrey B. and Brown, James H.",
    title = "The origin of allometric scaling laws in biology from genomes to ecosystems: towards a quantitative unifying theory of biological structure and organization",
    year = "2005",
    journal = "Journal of Experimental Biology",
    abstract = "Life is the most complex physical phenomenon in the Universe, manifesting an extraordinary diversity of form and function over an enormous scale from the largest animals and plants to the smallest microbes and subcellular units. Despite this many of its most fundamental and complex phenomena scale with size in a surprisingly simple fashion. For example, metabolic rate scales as the 3/4-power of mass over 27 orders of magnitude, from molecular and intracellular levels up to the largest organisms. Similarly, time-scales (such as lifespans and growth rates) and sizes (such as bacterial genome lengths, tree heights and mitochondrial densities) scale with exponents that are typically simple powers of 1/4. The universality and simplicity of these relationships suggest that fundamental universal principles underly much of the coarse-grained generic structure and organisation of living systems. We have proposed a set of principles based on the observation that almost all life is sustained by hierarchical branching networks, which we assume have invariant terminal units, are space-filling and are optimised by the process of natural selection. We show how these general constraints explain quarter power scaling and lead to a quantitative, predictive theory that captures many of the essential features of diverse biological systems. Examples considered include animal circulatory systems, plant vascular systems, growth, mitochondrial densities, and the concept of a universal molecular clock. Temperature considerations, dimensionality and the role of invariants are discussed. Criticisms and controversies associated with this approach are also addressed.",
    url = "https://doi.org/10.1242/jeb.01589",
    doi = "10.1242/jeb.01589",
    openalex = "W2117184765",
    references = "doi101001jama196203050110085031, doi101016jresp200401006, doi101017cbo9780511608551, doi101021j150446a008, doi10103835098076, doi101113jphysiol1952sp004719, doi101119113295, doi101126science1061967, doi101126science2765309122, doi101126science28454201677, doi103733hilgv06n11p315, openalexw1558456135"
}

@misc{crossref2007bioenergetics,
    title = "Bioenergetics and Metabolism",
    year = "2007",
    booktitle = "Principles and Practice of Resistance Training",
    url = "https://doi.org/10.5040/9781492596875.part-002",
    doi = "10.5040/9781492596875.part-002",
    openalex = "W4251395485",
    pages = "61-62"
}

The growth rate-dependent regulation of cell size, ribosomal content, and metabolic efficiency follows a common pattern in unicellular organisms: with increasing growth rates, cell size and ribosomal content increase and a shift to energetically inefficient metabolism takes place. The latter two phenomena are also observed in fast growing tumour cells and cell lines. These patterns suggest a fundamental principle of design. In biology such designs can often be understood as the result of the optimization of fitness. Here we show that in basic models of self-replicating systems these patterns are the consequence of maximizing the growth rate. Whereas most models of cellular growth consider a part of physiology, for instance only metabolism, the approach presented here integrates several subsystems to a complete self-replicating system. Such models can yield fundamentally different optimal strategies. In particular, it is shown how the shift in metabolic efficiency originates from a tradeoff between investments in enzyme synthesis and metabolic yields for alternative catabolic pathways. The models elucidate how the optimization of growth by natural selection shapes growth strategies.

@article{doi101038msb200982,
    author = "Molenaar, Douwe and van Berlo, Rogier and de Ridder, Dick and Teusink, Bas",
    title = "Shifts in growth strategies reflect tradeoffs in cellular economics",
    year = "2009",
    journal = "Molecular Systems Biology",
    abstract = "The growth rate-dependent regulation of cell size, ribosomal content, and metabolic efficiency follows a common pattern in unicellular organisms: with increasing growth rates, cell size and ribosomal content increase and a shift to energetically inefficient metabolism takes place. The latter two phenomena are also observed in fast growing tumour cells and cell lines. These patterns suggest a fundamental principle of design. In biology such designs can often be understood as the result of the optimization of fitness. Here we show that in basic models of self-replicating systems these patterns are the consequence of maximizing the growth rate. Whereas most models of cellular growth consider a part of physiology, for instance only metabolism, the approach presented here integrates several subsystems to a complete self-replicating system. Such models can yield fundamentally different optimal strategies. In particular, it is shown how the shift in metabolic efficiency originates from a tradeoff between investments in enzyme synthesis and metabolic yields for alternative catabolic pathways. The models elucidate how the optimization of growth by natural selection shapes growth strategies.",
    url = "https://doi.org/10.1038/msb.2009.82",
    doi = "10.1038/msb.2009.82",
    openalex = "W2107275175",
    references = "doi101016jccr200604023, doi101016jcell200808021, doi101038nrmicro1023, doi101073pnas91156808, doi10109900221287193592, doi101126science1058079, doi101126science1233191309, doi101126science2785338680, doi101128aem6010372437311994, doi101146annurevmi03100149002103"
}

@article{bouillaud2010ucp2,
    author = "Bouillaud, Frédéric and Pecqueur, Claire",
    title = "UCP2 bioenergetics and metabolism",
    year = "2010",
    journal = "Biochimica et Biophysica Acta (BBA) - Bioenergetics",
    url = "https://doi.org/10.1016/j.bbabio.2010.04.252",
    doi = "10.1016/j.bbabio.2010.04.252",
    openalex = "W2000325152",
    pages = "84",
    volume = "1797"
}

Metabolism generates oxygen radicals, which contribute to oncogenic mutations. Activated oncogenes and loss of tumor suppressors in turn alter metabolism and induce aerobic glycolysis. Aerobic glycolysis or the Warburg effect links the high rate of glucose fermentation to cancer. Together with glutamine, glucose via glycolysis provides the carbon skeletons, NADPH, and ATP to build new cancer cells, which persist in hypoxia that in turn rewires metabolic pathways for cell growth and survival. Excessive caloric intake is associated with an increased risk for cancers, while caloric restriction is protective, perhaps through clearance of mitochondria or mitophagy, thereby reducing oxidative stress. Hence, the links between metabolism and cancer are multifaceted, spanning from the low incidence of cancer in large mammals with low specific metabolic rates to altered cancer cell metabolism resulting from mutated enzymes or cancer genes.

@article{doi101101gad189365112,
    author = "Dang, Chi V.",
    title = "Links between metabolism and cancer",
    year = "2012",
    journal = "Genes \& Development",
    abstract = "Metabolism generates oxygen radicals, which contribute to oncogenic mutations. Activated oncogenes and loss of tumor suppressors in turn alter metabolism and induce aerobic glycolysis. Aerobic glycolysis or the Warburg effect links the high rate of glucose fermentation to cancer. Together with glutamine, glucose via glycolysis provides the carbon skeletons, NADPH, and ATP to build new cancer cells, which persist in hypoxia that in turn rewires metabolic pathways for cell growth and survival. Excessive caloric intake is associated with an increased risk for cancers, while caloric restriction is protective, perhaps through clearance of mitochondria or mitophagy, thereby reducing oxidative stress. Hence, the links between metabolism and cancer are multifaceted, spanning from the low incidence of cancer in large mammals with low specific metabolic rates to altered cancer cell metabolism resulting from mutated enzymes or cancer genes.",
    url = "https://doi.org/10.1101/gad.189365.112",
    doi = "10.1101/gad.189365.112",
    openalex = "W2105665764",
    references = "doi101016jcellsig201201008, doi101016jcmet200602002, doi101038nature08617, doi101038nrc2981, doi101038nrc3038, doi101038nrm3025, doi101056nejmoa0808710, doi101126science1160809, doi101126science1164382, doi101126science1233191309"
}

Growth is a fundamental process of life. Growth requirements are well-characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale and capable of explaining the high-level behavior of the cell as a whole. Here, we construct an ME-Model for Escherichia coli--a genome-scale model that seamlessly integrates metabolic and gene product expression pathways. The model computes ~80% of the functional proteome (by mass), which is used by the cell to support growth under a given condition. Metabolism and gene expression are interdependent processes that affect and constrain each other. We formalize these constraints and apply the principle of growth optimization to enable the accurate prediction of multi-scale phenotypes, ranging from coarse-grained (growth rate, nutrient uptake, by-product secretion) to fine-grained (metabolic fluxes, gene expression levels). Our results unify many existing principles developed to describe bacterial growth.

@article{doi101038msb201352,
    author = "O’Brien, Edward J. and Lerman, Joshua A. and Chang, Roger L. and Hyduke, Daniel R. and Palsson, Bernhard Ø.",
    title = "Genome‐scale models of metabolism and gene expression extend and refine growth phenotype prediction",
    year = "2013",
    journal = "Molecular Systems Biology",
    abstract = "Growth is a fundamental process of life. Growth requirements are well-characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale and capable of explaining the high-level behavior of the cell as a whole. Here, we construct an ME-Model for Escherichia coli--a genome-scale model that seamlessly integrates metabolic and gene product expression pathways. The model computes \textasciitilde 80\% of the functional proteome (by mass), which is used by the cell to support growth under a given condition. Metabolism and gene expression are interdependent processes that affect and constrain each other. We formalize these constraints and apply the principle of growth optimization to enable the accurate prediction of multi-scale phenotypes, ranging from coarse-grained (growth rate, nutrient uptake, by-product secretion) to fine-grained (metabolic fluxes, gene expression levels). Our results unify many existing principles developed to describe bacterial growth.",
    url = "https://doi.org/10.1038/msb.2013.52",
    doi = "10.1038/msb.2013.52",
    openalex = "W2122860350",
    references = "doi101038msb200982"
}

Bacteria must constantly adapt their growth to changes in nutrient availability; yet despite large-scale changes in protein expression associated with sensing, adaptation, and processing different environmental nutrients, simple growth laws connect the ribosome abundance and the growth rate. Here, we investigate the origin of these growth laws by analyzing the features of ribosomal regulation that coordinate proteome-wide expression changes with cell growth in a variety of nutrient conditions in the model organism Escherichia coli. We identify supply-driven feedforward activation of ribosomal protein synthesis as the key regulatory motif maximizing amino acid flux, and autonomously guiding a cell to achieve optimal growth in different environments. The growth laws emerge naturally from the robust regulatory strategy underlying growth rate control, irrespective of the details of the molecular implementation. The study highlights the interplay between phenomenological modeling and molecular mechanisms in uncovering fundamental operating constraints, with implications for endogenous and synthetic design of microorganisms.

@article{doi1015252msb20145379,
    author = "Scott, Matthew P. and Klumpp, Stefan and Mateescu, Eduard M. and Hwa, Terence",
    title = "Emergence of robust growth laws from optimal regulation of ribosome synthesis",
    year = "2014",
    journal = "Molecular Systems Biology",
    abstract = "Bacteria must constantly adapt their growth to changes in nutrient availability; yet despite large-scale changes in protein expression associated with sensing, adaptation, and processing different environmental nutrients, simple growth laws connect the ribosome abundance and the growth rate. Here, we investigate the origin of these growth laws by analyzing the features of ribosomal regulation that coordinate proteome-wide expression changes with cell growth in a variety of nutrient conditions in the model organism Escherichia coli. We identify supply-driven feedforward activation of ribosomal protein synthesis as the key regulatory motif maximizing amino acid flux, and autonomously guiding a cell to achieve optimal growth in different environments. The growth laws emerge naturally from the robust regulatory strategy underlying growth rate control, irrespective of the details of the molecular implementation. The study highlights the interplay between phenomenological modeling and molecular mechanisms in uncovering fundamental operating constraints, with implications for endogenous and synthetic design of microorganisms.",
    url = "https://doi.org/10.15252/msb.20145379",
    doi = "10.15252/msb.20145379",
    openalex = "W2111354165",
    references = "doi101038msb200982"
}

Introduction John Tyler Bonner VII 1. Introductory 2. On magnitude 3. The forms of cells 4. The forms of tissues, of cell-aggregates 5. On spicules and spicular skeletons 6. The equiangular spiral 7. The shapes of horns and of teeth or tusks 8. On form and mechanical efficiency 9. On the theory of transformations, or the comparison of related forms 10. Epilogue Index.

@book{doi1015159780691183978018,
    author = "Thompson, D’Arcy Wentworth",
    title = "On Growth and Form, 1917",
    year = "2019",
    booktitle = "Princeton University Press eBooks",
    abstract = "Introduction John Tyler Bonner VII 1. Introductory 2. On magnitude 3. The forms of cells 4. The forms of tissues, of cell-aggregates 5. On spicules and spicular skeletons 6. The equiangular spiral 7. The shapes of horns and of teeth or tusks 8. On form and mechanical efficiency 9. On the theory of transformations, or the comparison of related forms 10. Epilogue Index.",
    url = "https://doi.org/10.1515/9780691183978-018",
    doi = "10.1515/9780691183978-018",
    openalex = "W2100983000"
}

@incollection{chatterjee2023bioenergetics,
    author = "Chatterjee, Sankar",
    title = "Bioenergetics and Primitive Metabolism",
    year = "2023",
    booktitle = "From Stardust to First Cells",
    url = "https://doi.org/10.1007/978-3-031-23397-5\_7",
    doi = "10.1007/978-3-031-23397-5\_7",
    openalex = "W4386903178",
    pages = "67-74",
    references = "doi101007bf01808115, doi101016jcell201702001, doi101017cbo9780511614736, doi101038355125a0, doi101038nchem2202, doi101093oso97801951175470010001, doi101126science1251653, doi101126science2765311390, doi101126science2815377670, doi1015259780520948952"
}