Molecular biology

@article{crick1968the2,
    author = "Crick, F. H. C",
    title = "The origin of the genetic code",
    year = "1968",
    journal = "Journal of Molecular Biology, v. 38, p. 367-379",
    note = "talkorigins\_source = {true}; raw\_reference = {Crick, F. H. C., 1968, The origin of the genetic code: Journal of Molecular Biology, v. 38, p. 367-379.}"
}

@misc{lewin1985molecular4,
    author = "Lewin, R",
    title = "Molecular clocks scrutinized",
    year = "1985",
    howpublished = "Science, v. 228, p. 571",
    note = "talkorigins\_source = {true}; raw\_reference = {Lewin, R., 1985, Molecular clocks scrutinized: Science, v. 228, p. 571.}"
}

@misc{britten1986rates1,
    author = "Britten, R. J",
    title = "Rates of DNA sequence evolution differ between taxonomic groups",
    year = "1986",
    howpublished = "Science, v. 231, p. 1393-1398",
    note = "talkorigins\_source = {true}; raw\_reference = {Britten, R. J., 1986, Rates of DNA sequence evolution differ between taxonomic groups: Science, v. 231, p. 1393-1398.}"
}

@misc{vawter1986nuclear5,
    author = "Vawter, L. and Brown, W",
    title = "Nuclear and mitochondrial comparisons reveal extreme rate variation in the molecular clock",
    year = "1986",
    howpublished = "Science, v. 234, p. 194-196",
    note = "talkorigins\_source = {true}; raw\_reference = {Vawter, L., and Brown, W., 1986, Nuclear and mitochondrial comparisons reveal extreme rate variation in the molecular clock: Science, v. 234, p. 194-196.}"
}

@book{glover1989genes3,
    author = "Glover, D. M. and Hames, B. D",
    title = "Genes and Embryos",
    year = "1989",
    publisher = "New York, Oxford University Press, 228 p",
    note = "talkorigins\_source = {true}; raw\_reference = {Glover, D. M., and Hames, B. D., 1989, Genes and Embryos: New York, Oxford University Press, 228 p.}"
}

BACKGROUND: Circadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities. RESULTS: We demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase. CONCLUSION: Using data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed.

@article{doi1011861471220231,
    author = "Levine, Joel D and Funes, Pablo and Dowse, Harold B and Hall, Jeffrey C",
    title = "Signal analysis of behavioral and molecular cycles.",
    year = "2002",
    journal = "BMC neuroscience",
    abstract = "BACKGROUND: Circadian clocks are biological oscillators that regulate molecular, physiological, and behavioral rhythms in a wide variety of organisms. While behavioral rhythms are typically monitored over many cycles, a similar approach to molecular rhythms was not possible until recently; the advent of real-time analysis using transgenic reporters now permits the observations of molecular rhythms over many cycles as well. This development suggests that new details about the relationship between molecular and behavioral rhythms may be revealed. Even so, behavioral and molecular rhythmicity have been analyzed using different methods, making such comparisons difficult to achieve. To address this shortcoming, among others, we developed a set of integrated analytical tools to unify the analysis of biological rhythms across modalities. RESULTS: We demonstrate an adaptation of digital signal analysis that allows similar treatment of both behavioral and molecular data from our studies of Drosophila. For both types of data, we apply digital filters to extract and clarify details of interest; we employ methods of autocorrelation and spectral analysis to assess rhythmicity and estimate the period; we evaluate phase shifts using crosscorrelation; and we use circular statistics to extract information about phase. CONCLUSION: Using data generated by our investigation of rhythms in Drosophila we demonstrate how a unique aggregation of analytical tools may be used to analyze and compare behavioral and molecular rhythms. These methods are shown to be versatile and will also be adaptable to further experiments, owing in part to the non-proprietary nature of the code we have developed.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC65508/",
    doi = "10.1186/1471-2202-3-1",
    pmcid = "PMC65508",
    pmid = "11825337"
}

@article{cranston2005molecular,
    author = "Cranston, K and Rannala, B",
    title = "Molecular clocks: Closing the gap between rocks and clocks",
    year = "2005",
    journal = "Heredity",
    url = "https://doi.org/10.1038/sj.hdy.6800644",
    doi = "10.1038/sj.hdy.6800644",
    number = "5",
    pages = "461-462",
    volume = "94"
}

@inproceedings{chapelet2007comparisons,
    author = "Chapelet, F. and Guéna, J. and Rovera, D. and Laurent, P. and Rosenbusch, P. and Santarelli, G. and Bize, S. and Clairon, A. and Tobar, M. E. and Abgrall, M.",
    title = "Comparisons between 3 fountain clocks at LNE-SYRTE",
    year = "2007",
    booktitle = "SPIE Proceedings",
    url = "https://doi.org/10.1117/12.734125",
    doi = "10.1117/12.734125",
    pages = "66730B",
    volume = "6673"
}

@incollection{petit2014atomic,
    author = "Petit, Gérard and Wolf, Peter and Delva, Pacôme",
    title = "Atomic time, clocks, and clock comparisons in relativistic spacetime: a review",
    year = "2014",
    booktitle = "Applications and Experiments",
    url = "https://doi.org/10.1515/9783110345667.249",
    doi = "10.1515/9783110345667.249",
    pages = "249-279"
}

Circadian rhythm is the approximately 24-hour rhythmicity that regulates physiology and behavior in a variety of organisms. The mammalian circadian system is organized in a hierarchical manner. Molecular circadian oscillations driven by genetic feedback loops are found in individual cells, whereas circadian rhythms in different systems of the body are orchestrated by the master clock in the suprachiasmatic nucleus (SCN) of the anterior hypothalamus. SCN receives photic input from retina and synchronizes endogenous rhythms with the external light/dark cycles. SCN regulates circadian rhythms in the peripheral oscillators via neural and humoral signals, which account for daily fluctuations of the physiological processes in these organs. Disruption of circadian rhythms can cause health problems and circadian dysfunction has been linked to many human diseases.

@misc{cao2019molecular,
    author = "Cao, Ruifeng",
    title = "Molecular Biology and Physiology of Circadian Clocks",
    year = "2019",
    booktitle = "Oxford Research Encyclopedia of Neuroscience",
    abstract = "Circadian rhythm is the approximately 24-hour rhythmicity that regulates physiology and behavior in a variety of organisms. The mammalian circadian system is organized in a hierarchical manner. Molecular circadian oscillations driven by genetic feedback loops are found in individual cells, whereas circadian rhythms in different systems of the body are orchestrated by the master clock in the suprachiasmatic nucleus (SCN) of the anterior hypothalamus. SCN receives photic input from retina and synchronizes endogenous rhythms with the external light/dark cycles. SCN regulates circadian rhythms in the peripheral oscillators via neural and humoral signals, which account for daily fluctuations of the physiological processes in these organs. Disruption of circadian rhythms can cause health problems and circadian dysfunction has been linked to many human diseases.",
    url = "https://doi.org/10.1093/acrefore/9780190264086.013.28",
    doi = "10.1093/acrefore/9780190264086.013.28"
}

@article{xu2021molecular,
    author = "Xu, Weiyi and Jain, Mukesh K and Zhang, Lilei",
    title = "Molecular link between circadian clocks and cardiac function: a network of core clock, slave clock, and effectors",
    year = "2021",
    journal = "Current Opinion in Pharmacology",
    url = "https://doi.org/10.1016/j.coph.2020.10.006",
    doi = "10.1016/j.coph.2020.10.006",
    pages = "28-40",
    volume = "57"
}

Horloges à réseau optique au strontium: comparaisons d'horloges pour des applications en physique fondamentale et échelles de temps Cette thèse est consacrée aux progrès récents des horloges à réseau optique au strontium du LNE-SYRTE, Observatoire de Paris. L'incertitude systématique et la stabilité des horloges optiques sont 2 ordres de grandeur meilleures que les horloges atomiques micro-ondes au cesium qui réalisent la seconde SI, bénéficiant maintenent a des applications en physique fondamentale, astronomie et géosciences. Dans un futur proche, une redéfinition de la seconde SI est attendue, quand les horloges optiques se seront révélées aussi fiables et reproductibles que les horloges a micro-ondes. La thèse présente trois étapes décisives dans cette direction. Nous présentons un fonctionnemment operation quasi-continu de nos horloges Sr pendant plusieurs semaines. Des comparaisons de fréquences locales et à distance avec diverses références de fréquence micro-ondes et optiques montrent que les horloges optiques sont reproductibles par des laboratoires independants. Nous avons démontré un premier réseau tout optique entre des horloges optiques à l'échelle continentale. Les horloges au Sr ont été utilisées pour préparer 5 rapports de calibration du Temps Atomique International (TAI) qui ont été validés par le BIPM comme première contribution au TAI par des horloges optiques. Certains de ces résultats ont été utilisés pour borner l'amplitude d'une possible violation de l'invariance de Lorentz analysant les comparaisons d'horloges distantes. Enfin, nous avons effectué une caractérisation complète des déplacements de fréquence associés aux sources laser à semiconducteur utilisées pour le piégeage des atomes dans l'optique d'applications pour des horloges transportables et spatiales.

@misc{andbilickiNonestrontium,
    author = "Bilicki, Sławomir",
    title = "Strontium optical lattice clocks: clock comparisons for timescales and fundamental physics applications",
    year = "None",
    abstract = "Horloges à réseau optique au strontium: comparaisons d'horloges pour des applications en physique fondamentale et échelles de temps Cette thèse est consacrée aux progrès récents des horloges à réseau optique au strontium du LNE-SYRTE, Observatoire de Paris. L'incertitude systématique et la stabilité des horloges optiques sont 2 ordres de grandeur meilleures que les horloges atomiques micro-ondes au cesium qui réalisent la seconde SI, bénéficiant maintenent a des applications en physique fondamentale, astronomie et géosciences. Dans un futur proche, une redéfinition de la seconde SI est attendue, quand les horloges optiques se seront révélées aussi fiables et reproductibles que les horloges a micro-ondes. La thèse présente trois étapes décisives dans cette direction. Nous présentons un fonctionnemment operation quasi-continu de nos horloges Sr pendant plusieurs semaines. Des comparaisons de fréquences locales et à distance avec diverses références de fréquence micro-ondes et optiques montrent que les horloges optiques sont reproductibles par des laboratoires independants. Nous avons démontré un premier réseau tout optique entre des horloges optiques à l'échelle continentale. Les horloges au Sr ont été utilisées pour préparer 5 rapports de calibration du Temps Atomique International (TAI) qui ont été validés par le BIPM comme première contribution au TAI par des horloges optiques. Certains de ces résultats ont été utilisés pour borner l'amplitude d'une possible violation de l'invariance de Lorentz analysant les comparaisons d'horloges distantes. Enfin, nous avons effectué une caractérisation complète des déplacements de fréquence associés aux sources laser à semiconducteur utilisées pour le piégeage des atomes dans l'optique d'applications pour des horloges transportables et spatiales.",
    url = "https://doi.org/10.70675/4b3e81f4z8872z4d16z8156z517133a256ac",
    doi = "10.70675/4b3e81f4z8872z4d16z8156z517133a256ac"
}