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Biological clock

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https://www.readbyqxmd.com/read/27913843/molecular-evolution-in-historical-perspective
#1
Edna Suárez-Díaz
In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms...
December 2, 2016: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/27889677/blood-dna-methylation-age-is-not-associated-with-cognitive-functioning-in-middle-aged-monozygotic-twins
#2
A Starnawska, Q Tan, A Lenart, M McGue, O Mors, A D Børglum, K Christensen, M Nyegaard, L Christiansen
The epigenetic clock, also known as DNA methylation age (DNAmAge), represents age-related changes of DNA methylation at multiple sites of the genome and is suggested to be a biomarker for biological age. Elevated blood DNAmAge is associated with all-cause mortality, with the strongest effects reported in a recent intrapair twin study where epigenetically older twins had increased mortality risk in comparison to their co-twins. In the study presented here, we hypothesize that DNAmAge in blood is associated with cross-sectional and longitudinal cognitive abilities in middle-aged individuals...
November 4, 2016: Neurobiology of Aging
https://www.readbyqxmd.com/read/27888113/circadian-urinary-citrate-excretion-in-a-rat-model-of-exercise
#3
Paula Nuñez, Irene Diaz, Carmen Perillan, Juan Arguelles, Elena Diaz
AIMS: Circadian rhythms are the approximate 24h biological cycles that function to prepare an organism for daily environmental changes. Circadian rhythms unquestionably play critical roles in metabolic homeostasis and the exercise has emerged as a strong non-photic time cue or zeitgeber in animal models and humans. Numerous studies on the effects of exercise on the citrate synthase activity have been published. Citrate is used to assess energy production or expenditure because it is a substrate of the Krebs Cycle, a cycle for oxidative energy production...
November 22, 2016: Life Sciences
https://www.readbyqxmd.com/read/27885004/circadian-time-signatures-of-fitness-and-disease
#4
REVIEW
Joseph Bass, Mitchell A Lazar
Biological clocks are autonomous anticipatory oscillators that play a critical role in the organization and information processing from genome to whole organisms. Transformative advances into the clock system have opened insight into fundamental mechanisms through which clocks program energy transfer from sunlight into organic matter and potential energy, in addition to cell development and genotoxic stress response. The identification of clocks in nearly every single cell of the body raises questions as to how this gives rise to rhythmic physiology in multicellular organisms and how environmental signals entrain clocks to geophysical time...
November 25, 2016: Science
https://www.readbyqxmd.com/read/27879317/correlated-evolution-between-ck1%C3%AE-and-the-serine-rich-motif-contributes-to-regulating-the-mammalian-circadian-clock
#5
Lijuan Xing, Yang An, Guangsen Shi, Jie Yan, Pancheng Xie, Zhipeng Qu, Zhihui Zhang, Zhiwei Liu, Dejing Pan, Ying Xu
Understanding the mechanism underlying the physiological divergence of species is a long-standing issue in evolutionary biology. The circadian clock is a highly conserved system existing in almost all organisms that regulates a wide range of physiological and behavioral events to adapt to the day-night cycle. Here, the interactions between hCK1δ/ϵ/DBT (Drosophila ortholog of CK1δ/ϵ) and serine rich (SR) motifs from hPER2 (ortholog of Drosophila per) were reconstructed in a Drosophila circadian system. The results indicated that in Drosophila, the SR mutant form hPER2S662G does not recapitulate the mouse or human mutant phenotype...
November 22, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27856696/the-neurospora-transcription-factor-adv-1-transduces-light-signals-and-temporal-information-to-control-rhythmic-expression-of-genes-involved-in-cell-fusion
#6
Rigzin Dekhang, Cheng Wu, Kristina M Smith, Teresa M Lamb, Matthew Peterson, Erin L Bredeweg, Oneida Ibarra, Jillian M Emerson, Nirmala Karunarathna, Anna Lyubetskaya, Elham Azizi, Jennifer M Hurely, Jay C Dunlap, James E Galagan, Michael Freitag, Matthew S Sachs, Deborah Bell-Pedersen
Light and the circadian clock have a profound effect on the biology of organisms through the regulation of large sets of genes. Towards understanding how light and the circadian clock regulate gene expression, we used genome-wide approaches to identify the direct and indirect targets of the light-responsive and clock-controlled transcription factor ADV-1 in Neurospora crassa A large proportion of ADV-1 targets were found to be light and/or clock-controlled, and enriched for genes involved in development, metabolism, cell growth, and cell fusion...
November 16, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27849618/circadian-rhythms-identified-in-caenorhabditis-elegans-by-in-vivo-long-term-monitoring-of-a-bioluminescent-reporter
#7
María Eugenia Goya, Andrés Romanowski, Carlos S Caldart, Claire Y Bénard, Diego A Golombek
Circadian rhythms are based on endogenous clocks that allow organisms to adjust their physiology and behavior by entrainment to the solar day and, in turn, to select the optimal times for most biological variables. Diverse model systems-including mice, flies, fungi, plants, and bacteria-have provided important insights into the mechanisms of circadian rhythmicity. However, the general principles that govern the circadian clock of Caenorhabditis elegans have remained largely elusive. Here we report robust molecular circadian rhythms in C elegans recorded with a bioluminescence assay in vivo and demonstrate the main features of the circadian system of the nematode...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27846817/micrornas-regulate-gene-plasticity-during-cold-shock-in-zebrafish-larvae
#8
I-Chen Hung, Yu-Chuan Hsiao, H Sunny Sun, Tsung-Ming Chen, Shyh-Jye Lee
BACKGROUND: MicroRNAs (miRNAs) are critical regulators responding to acute environmental stresses in both plants and animals. By modulating gene expression, miRNAs either restore or reconstitute a new expression program to enhance cell tolerance to stresses. Cold shock is one of the stresses that can induce acute physiological responses and transcriptional changes in aquatic creatures. Previous genomic studies have revealed many cold-affected genes in fish larvae and adults, however, the role of miRNAs in acute cold response is still ambiguous...
November 15, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27813571/transcriptome-survey-of-phototransduction-and-clock-genes-in-marine-bivalves
#9
X J Sun, L Q Zhou, J T Tian, Z H Liu, B Wu, Y H Dong, A G Yang, W M Ma
Marine animals exhibit a variety of biological rhythms, such as solar and lunar-related cycles; however, our current molecular understanding of biological rhythms in marine animals is quite limited. Identifying and understanding the expression patterns of clock genes from available transcriptomes will help elucidate biological rhythms in marine species. Here, we perform a comprehensive survey of phototransduction and circadian genes using the mantle transcriptome of the scallop Patinopecten yessoensis and compare the results with those from three other bivalves...
October 24, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27812859/palliative-care-of-cancer-in-the-older-patient
#10
REVIEW
Lodovico Balducci, Dawn Dolan
The scope of palliative care includes goal setting, symptom management, and care of the care giver. Palliative care is essential for patient-centered care of the older cancer patients. The diversity of this population in terms of life expectancy, treatment tolerance, function, disability, and social support mandates personalized treatment plans. The assessment of physiologic age is currently based on a comprehensive geriatric assessment (CGA). A number of biologic markers of aging including the inflammatory index, the genomic clock, the expression of p16INKa4, and the circulating levels of vitamin D may complement the CGA and fine-tune the determination of physiologic age...
December 2016: Current Oncology Reports
https://www.readbyqxmd.com/read/27810175/altered-sleep-wake-patterns-in-blindness-a-combined-actigraphy-and-psychometric-study
#11
S Aubin, C Gacon, P Jennum, M Ptito, R Kupers
OBJECTIVE: Light plays an important role in the synchronization of the internal biological clock and the environmental day/night pattern. Thus, absence of vision is often associated with both increases in reported sleep disturbances and incidence of free-running circadian rhythms. In this study we discuss variability in the sleep-wake pattern between blind and normal-sighted individuals. METHODS: Thirty-day actigraphy recordings were collected from 11 blind individuals without residual light perception and 11 age- and sex-matched normal-sighted controls...
August 2016: Sleep Medicine
https://www.readbyqxmd.com/read/27809780/dual-functions-of-the-zmcct-associated-quantitative-trait-locus-in-flowering-and-stress-responses-under-long-day-conditions
#12
Lixia Ku, Lei Tian, Huihui Su, Cuiling Wang, Xiaobo Wang, Liuji Wu, Yong Shi, Guohui Li, Zhiyong Wang, Huitao Wang, Xiaoheng Song, Dandan Dou, Zhaobin Ren, Yanhui Chen
BACKGROUND: Photoperiodism refers to the ability of plants to measure day length to determine the season. This ability enables plants to coordinate internal biological activities with external changes to ensure normal growth. However, the influence of the photoperiod on maize flowering and stress responses under long-day (LD) conditions has not been analyzed by comparative transcriptome sequencing. The ZmCCT gene was previously identified as a homolog of the rice photoperiod response regulator Ghd7, and associated with the major quantitative trait locus (QTL) responsible for Gibberella stalk rot resistance in maize...
November 3, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27803791/effects-of-lycium-barbarum-polysaccharide-on-type-2-diabetes-mellitus-rats-by-regulating-biological-rhythms
#13
Rui Zhao, Xu Gao, Tao Zhang, Xing Li
OBJECTIVES: Type 2 diabetes mellitus (T2DM) is associated with circadian disruption. Our previous experimental results have showed that dietary Lycium barbarum. polysaccharide (LBP-4a) exhibited hypoglycemic and improving insulin resistance (IR) activities. This study was to explore the mechanisms of LBP-4a for improving hyperglycemia and IR by regulating biological rhythms in T2DM rats. MATERIALS AND METHODS: The rats of T2DM were prepared by the high-sucrose-fat diets and injection of streptozotocin (STZ)...
September 2016: Iranian Journal of Basic Medical Sciences
https://www.readbyqxmd.com/read/27802074/gestational-chronodisruption-impairs-circadian-physiology-in-rat-male-offspring-increasing-the-risk-of-chronic-disease
#14
Natalia Mendez, Diego Halabi, Carlos Spichiger, Esteban R Salazar, Karina Vergara, Pamela Alonso-Vasquez, Pamela Carmona, Jose M Sarmiento, Hans G Richter, Maria Seron-Ferre, Claudia Torres-Farfan
Chronic exposure to light at night, as in shift work, alters biological clocks (chronodisruption), negatively impacting pregnancy outcome in humans. Actually the interaction of maternal and fetal circadian systems could be a key factor determining a fitting health in adults. We propose that chronic photoperiod shift (CPS) during pregnancy alter maternal circadian rhythms and impair circadian physiology in the adult offspring, increasing health risks. Pregnant rats were exposed to normal photoperiod (12 h light, 12 h dark) or to CPS until 85% of gestation...
December 2016: Endocrinology
https://www.readbyqxmd.com/read/27793218/circadian-rhythm-and-the-gut-microbiome
#15
R M Voigt, C B Forsyth, S J Green, P A Engen, A Keshavarzian
Circadian rhythms are 24-h patterns regulating behavior, organs, and cells in living organisms. These rhythms align biological functions with regular and predictable environmental patterns to optimize function and health. Disruption of these rhythms can be detrimental resulting in metabolic syndrome, cancer, or cardiovascular disease, just to name a few. It is now becoming clear that the intestinal microbiome is also regulated by circadian rhythms via intrinsic circadian clocks as well as via the host organism...
2016: International Review of Neurobiology
https://www.readbyqxmd.com/read/27792172/circadian-rhythm-shapes-the-gut-microbiota-affecting-host-radiosensitivity
#16
Ming Cui, Huiwen Xiao, Dan Luo, Xin Zhang, Shuyi Zhao, Qisheng Zheng, Yuan Li, Yu Zhao, Jiali Dong, Hang Li, Haichao Wang, Saijun Fan
Modern lifestyles, such as shift work, nocturnal social activities, and jet lag, disturb the circadian rhythm. The interaction between mammals and the co-evolved intestinal microbiota modulates host physiopathological processes. Radiotherapy is a cornerstone of modern management of malignancies; however, it was previously unknown whether circadian rhythm disorder impairs prognosis after radiotherapy. To investigate the effect of circadian rhythm on radiotherapy, C57BL/6 mice were housed in different dark/light cycles, and their intestinal bacterial compositions were compared using high throughput sequencing...
October 26, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27786253/synchronizing-stochastic-circadian-oscillators-in-single-cells-of-neurospora-crassa
#17
Zhaojie Deng, Sam Arsenault, Cristian Caranica, James Griffith, Taotao Zhu, Ahmad Al-Omari, Heinz-Bernd Schüttler, Jonathan Arnold, Leidong Mao
The synchronization of stochastic coupled oscillators is a central problem in physics and an emerging problem in biology, particularly in the context of circadian rhythms. Most measurements on the biological clock are made at the macroscopic level of millions of cells. Here measurements are made on the oscillators in single cells of the model fungal system, Neurospora crassa, with droplet microfluidics and the use of a fluorescent recorder hooked up to a promoter on a clock controlled gene-2 (ccg-2). The oscillators of individual cells are stochastic with a period near 21 hours (h), and using a stochastic clock network ensemble fitted by Markov Chain Monte Carlo implemented on general-purpose graphical processing units (or GPGPUs) we estimated that >94% of the variation in ccg-2 expression was stochastic (as opposed to experimental error)...
October 27, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27781473/resynchronization-of-circadian-oscillators-and-the-east-west-asymmetry-of-jet-lag
#18
Zhixin Lu, Kevin Klein-Cardeña, Steven Lee, Thomas M Antonsen, Michelle Girvan, Edward Ott
Cells in the brain's Suprachiasmatic Nucleus (SCN) are known to regulate circadian rhythms in mammals. We model synchronization of SCN cells using the forced Kuramoto model, which consists of a large population of coupled phase oscillators (modeling individual SCN cells) with heterogeneous intrinsic frequencies and external periodic forcing. Here, the periodic forcing models diurnally varying external inputs such as sunrise, sunset, and alarm clocks. We reduce the dimensionality of the system using the ansatz of Ott and Antonsen and then study the effect of a sudden change of clock phase to simulate cross-time-zone travel...
September 2016: Chaos
https://www.readbyqxmd.com/read/27775529/a-biochemical-oscillator-using-excitatory-molecules-for-nanonetworks
#19
Ethungshan Shitiri, Ho-Shin Cho
For nanonetworks to be able to achieve large-scale functionality, such as to respond collectively to a trigger, synchrony between nanomachines is essential. However, to facilitate synchronization, some sort of physical clocking mechanism is required, such as the oscillators driven by auto-inhibitory molecules or by auto-inducing molecules. In this study, taking inspiration from the widely studied biological oscillatory phenomena called Calcium (Ca2+) oscillations, we undertake a different approach to design an oscillator...
October 18, 2016: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/27774300/exploring-the-temporal-structure-of-heterochronous-sequences-using-tempest-formerly-path-o-gen
#20
Andrew Rambaut, Tommy T Lam, Luiz Max Carvalho, Oliver G Pybus
Gene sequences sampled at different points in time can be used to infer molecular phylogenies on a natural timescale of months or years, provided that the sequences in question undergo measurable amounts of evolutionary change between sampling times. Data sets with this property are termed heterochronous and have become increasingly common in several fields of biology, most notably the molecular epidemiology of rapidly evolving viruses. Here we introduce the cross-platform software tool, TempEst (formerly known as Path-O-Gen), for the visualization and analysis of temporally sampled sequence data...
January 2016: Virus Evolution
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