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Biological clock

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https://www.readbyqxmd.com/read/29784788/mistimed-food-intake-and-sleep-alters-24-hour-time-of-day-patterns-of-the-human-plasma-proteome
#1
Christopher M Depner, Edward L Melanson, Andrew W McHill, Kenneth P Wright
Proteomics holds great promise for understanding human physiology, developing health biomarkers, and precision medicine. However, how much the plasma proteome varies with time of day and is regulated by the master circadian suprachiasmatic nucleus brain clock, assessed here by the melatonin rhythm, is largely unknown. Here, we assessed 24-h time-of-day patterns of human plasma proteins in six healthy men during daytime food intake and nighttime sleep in phase with the endogenous circadian clock (i.e., circadian alignment) versus daytime sleep and nighttime food intake out of phase with the endogenous circadian clock (i...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29768727/a-congenic-line-of-the-c57bl-6j-mouse-strain-that-is-proficient-in-melatonin-synthesis
#2
Zhijing Zhang, Eduardo Silveyra, Nange Jin, Christophe P Ribelayga
The C57BL/6J (B6) is the most common inbred mouse strain used in biomedical research in the United States. Yet, this strain is notoriously known for being deficient in the biosynthesis of melatonin, an important effector of circadian clocks in the brain and in the retina. Melatonin deficiency in this strain results from non-functional alleles of the genes coding two key enzymes of the melatonin synthesis pathway: arylalkylamine-N-acetyltransferase (Aanat) and N-acetylserotonin-O-methyltransferase (Asmt). By introducing functional alleles of the Aanat and Asmt genes from the melatonin-proficient CBA/CaJ (CBA) mouse strain to B6, we have generated a B6 congenic line that has acquired the capacity of rhythmic melatonin synthesis...
May 16, 2018: Journal of Pineal Research
https://www.readbyqxmd.com/read/29768444/ensemble-methods-for-stochastic-networks-with-special-reference-to-the-biological-clock-of-neurospora-crassa
#3
C Caranica, A Al-Omari, Z Deng, J Griffith, R Nilsen, L Mao, J Arnold, H-B Schüttler
A major challenge in systems biology is to infer the parameters of regulatory networks that operate in a noisy environment, such as in a single cell. In a stochastic regime it is hard to distinguish noise from the real signal and to infer the noise contribution to the dynamical behavior. When the genetic network displays oscillatory dynamics, it is even harder to infer the parameters that produce the oscillations. To address this issue we introduce a new estimation method built on a combination of stochastic simulations, mass action kinetics and ensemble network simulations in which we match the average periodogram and phase of the model to that of the data...
2018: PloS One
https://www.readbyqxmd.com/read/29768214/noise-in-the-vertebrate-segmentation-clock-is-boosted-by-time-delays-but-tamed-by-notch-signaling
#4
Sevdenur Keskin, Gnanapackiam S Devakanmalai, Soo Bin Kwon, Ha T Vu, Qiyuan Hong, Yin Yeng Lee, Mohammad Soltani, Abhyudai Singh, Ahmet Ay, Ertuğrul M Özbudak
Taming cell-to-cell variability in gene expression is critical for precise pattern formation during embryonic development. To investigate the source and buffering mechanism of expression variability, we studied a biological clock, the vertebrate segmentation clock, controlling the precise spatiotemporal patterning of the vertebral column. By counting single transcripts of segmentation clock genes in zebrafish, we show that clock genes have low RNA amplitudes and expression variability is primarily driven by gene extrinsic sources, which is suppressed by Notch signaling...
May 15, 2018: Cell Reports
https://www.readbyqxmd.com/read/29756029/circadian-behavioral-responses-to-light-and-optic-chiasm-evoked-glutamatergic-epscs-in-the-suprachiasmatic-nucleus-of-iprgc-conditional-vglut2-knock-out-mice
#5
Michael G Moldavan, Patricia J Sollars, Michael R Lasarev, Charles N Allen, Gary E Pickard
Intrinsically photosensitive retinal ganglion cells (ipRGCs) innervate the hypothalamic suprachiasmatic nucleus (SCN), a circadian oscillator that functions as a biological clock. ipRGCs use vesicular glutamate transporter 2 (vGlut2) to package glutamate into synaptic vesicles and light-evoked resetting of the SCN circadian clock is widely attributed to ipRGC glutamatergic neurotransmission. Pituitary adenylate cyclase-activating polypeptide (PACAP) is also packaged into vesicles in ipRGCs and PACAP may be coreleased with glutamate in the SCN...
May 2018: ENeuro
https://www.readbyqxmd.com/read/29755411/time-of-day-effects-on-metabolic-and-clock-related-adjustments-to-cold
#6
Frederico Sander Mansur Machado, Zhi Zhang, Yan Su, Paul de Goede, Remi Jansen, Ewout Foppen, Cândido Celso Coimbra, Andries Kalsbeek
Background: Daily cyclic changes in environmental conditions are key signals for anticipatory and adaptive adjustments of most living species, including mammals. Lower ambient temperature stimulates the thermogenic activity of brown adipose tissue (BAT) and skeletal muscle. Given that the molecular components of the endogenous biological clock interact with thermal and metabolic mechanisms directly involved in the defense of body temperature, the present study evaluated the differential homeostatic responses to a cold stimulus at distinct time-windows of the light/dark-cycle...
2018: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29754901/nocte-is-required-for-integrating-light-and-temperature-inputs-in-circadian-clock-neurons-of-drosophila
#7
Chenghao Chen, Min Xu, Yuto Anantaprakorn, Mechthild Rosing, Ralf Stanewsky
Circadian clocks organize biological processes to occur at optimized times of day and thereby contribute to overall fitness. While the regular daily changes of environmental light and temperature synchronize circadian clocks, extreme external conditions can bypass the temporal constraints dictated by the clock. Despite advanced knowledge about how the daily light-dark changes synchronize the clock, relatively little is known with regard to how the daily temperature changes influence daily timing and how temperature and light signals are integrated...
May 8, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29753700/spectrum-and-prevalence-of-genetic-predisposition-in-medulloblastoma-a-retrospective-genetic-study-and-prospective-validation-in-a-clinical-trial-cohort
#8
Sebastian M Waszak, Paul A Northcott, Ivo Buchhalter, Giles W Robinson, Christian Sutter, Susanne Groebner, Kerstin B Grund, Laurence Brugières, David T W Jones, Kristian W Pajtler, A Sorana Morrissy, Marcel Kool, Dominik Sturm, Lukas Chavez, Aurelie Ernst, Sebastian Brabetz, Michael Hain, Thomas Zichner, Maia Segura-Wang, Joachim Weischenfeldt, Tobias Rausch, Balca R Mardin, Xin Zhou, Cristina Baciu, Christian Lawerenz, Jennifer A Chan, Pascale Varlet, Lea Guerrini-Rousseau, Daniel W Fults, Wiesława Grajkowska, Peter Hauser, Nada Jabado, Young-Shin Ra, Karel Zitterbart, Suyash S Shringarpure, Francisco M De La Vega, Carlos D Bustamante, Ho-Keung Ng, Arie Perry, Tobey J MacDonald, Pablo Hernáiz Driever, Anne E Bendel, Daniel C Bowers, Geoffrey McCowage, Murali M Chintagumpala, Richard Cohn, Timothy Hassall, Gudrun Fleischhack, Tone Eggen, Finn Wesenberg, Maria Feychting, Birgitta Lannering, Joachim Schüz, Christoffer Johansen, Tina V Andersen, Martin Röösli, Claudia E Kuehni, Michael Grotzer, Kristina Kjaerheim, Camelia M Monoranu, Tenley C Archer, Elizabeth Duke, Scott L Pomeroy, Redmond Shelagh, Stephan Frank, David Sumerauer, Wolfram Scheurlen, Marina V Ryzhova, Till Milde, Christian P Kratz, David Samuel, Jinghui Zhang, David A Solomon, Marco Marra, Roland Eils, Claus R Bartram, Katja von Hoff, Stefan Rutkowski, Vijay Ramaswamy, Richard J Gilbertson, Andrey Korshunov, Michael D Taylor, Peter Lichter, David Malkin, Amar Gajjar, Jan O Korbel, Stefan M Pfister
BACKGROUND: Medulloblastoma is associated with rare hereditary cancer predisposition syndromes; however, consensus medulloblastoma predisposition genes have not been defined and screening guidelines for genetic counselling and testing for paediatric patients are not available. We aimed to assess and define these genes to provide evidence for future screening guidelines. METHODS: In this international, multicentre study, we analysed patients with medulloblastoma from retrospective cohorts (International Cancer Genome Consortium [ICGC] PedBrain, Medulloblastoma Advanced Genomics International Consortium [MAGIC], and the CEFALO series) and from prospective cohorts from four clinical studies (SJMB03, SJMB12, SJYC07, and I-HIT-MED)...
May 9, 2018: Lancet Oncology
https://www.readbyqxmd.com/read/29751158/tritiated-water-exposure-disrupts-myofibril-structure-and-induces-mis-regulation-of-eye-opacity-and-dna-repair-genes-in-zebrafish-early-life-stages
#9
Caroline Arcanjo, Olivier Armant, Magali Floriani, Isabelle Cavalie, Virginie Camilleri, Olivier Simon, Daniel Orjollet, Christelle Adam-Guillermin, Béatrice Gagnaire
Tritium (3 H) is a radioactive isotope of hydrogen. In the environment, the most common form of tritium is tritiated water (HTO). The present study aimed to identify early biomarkers of HTO contamination through the use of an aquatic model, the zebrafish (Danio rerio). We used the zebrafish embryo-larvae model to investigate the modes of action of HTO exposure at dose rates of 0.4 and 4 mGy/h, dose rates expected to induce deleterious effects on fish. Zebrafish were exposed to HTO from 3 hpf (hours post fertilization) to 96 hpf...
April 27, 2018: Aquatic Toxicology
https://www.readbyqxmd.com/read/29751019/nighttime-light-exposure-enhances-rev-erb%C3%AE-targeting-micrornas-and-contributes-to-hepatic-steatosis
#10
Patricia C Borck, Thiago M Batista, Jean F Vettorazzi, Gabriela M Soares, Camila Lubaczeuski, Dongyin Guan, Antonio C Boschero, Elaine Vieira, Mitchell A Lazar, Everardo M Carneiro
OBJECTIVE: The exposure to artificial light at night (ALAN) disrupts the biological rhythms and has been associated with the development of metabolic syndrome. MicroRNAs (miRNAs) display a critical role in fine-tuning the circadian system and energy metabolism. In this study, we aimed to assess whether altered miRNAs expression in the liver underlies metabolic disorders caused by disrupted biological rhythms. RESULTS: We found that C3H/HePas mice exposed to ALAN developed obesity, and hepatic steatosis, which was paralleled by decreased expression of Rev-erbα and up-regulation of its lipogenic targets ACL and FAS in liver...
May 8, 2018: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/29746298/perinatally-acquired-hiv-infection-accelerates-epigenetic-aging-in-south-african-adolescents
#11
Steve Horvath, Nicole Phillips, Sarah J Heany, Michael S Kobor, David Ts Lin, Landon Myer, Heather J Zar, Dan J Stein, Andrew J Levine, Jacqueline Hoare
OBJECTIVE: Recent studies demonstrate that infection with the Human Immunodeficiency Virus-1 (HIV) is associated with accelerated aging effects in adults according to a highly accurate epigenetic biomarker of aging known as epigenetic clock. However, it not yet known whether epigenetic age acceleration occurs as early as adolescence in perinatally HIV-infected (PHIV+) youth. DESIGN: Observational study of PHIV and HIV-uninfected adolescents enrolled in the Cape Town Adolescent Antiretroviral Cohort (CTAAC) Study...
May 8, 2018: AIDS
https://www.readbyqxmd.com/read/29739910/comparative-population-genomics-analysis-of-the-mammalian-fungal-pathogen-pneumocystis
#12
Ousmane H Cissé, Liang Ma, Da Wei Huang, Pavel P Khil, John P Dekker, Geetha Kutty, Lisa Bishop, Yueqin Liu, Xilong Deng, Philippe M Hauser, Marco Pagni, Vanessa Hirsch, Richard A Lempicki, Jason E Stajich, Christina A Cuomo, Joseph A Kovacs
Pneumocystis species are opportunistic mammalian pathogens that cause severe pneumonia in immunocompromised individuals. These fungi are highly host specific and uncultivable in vitro Human Pneumocystis infections present major challenges because of a limited therapeutic arsenal and the rise of drug resistance. To investigate the diversity and demographic history of natural populations of Pneumocystis infecting humans, rats, and mice, we performed whole-genome and large-scale multilocus sequencing of infected tissues collected in various geographic locations...
May 8, 2018: MBio
https://www.readbyqxmd.com/read/29739445/setting-the-pace-host-rhythmic-behaviour-and-gene-expression-patterns-in-the-facultatively-symbiotic-cnidarian-aiptasia-are-determined-largely-by-symbiodinium
#13
Michal Sorek, Yisrael Schnytzer, Hiba Waldman Ben-Asher, Vered Chalifa Caspi, Chii-Shiarng Chen, David J Miller, Oren Levy
BACKGROUND: All organisms employ biological clocks to anticipate physical changes in the environment; however, the integration of biological clocks in symbiotic systems has received limited attention. In corals, the interpretation of rhythmic behaviours is complicated by the daily oscillations in tissue oxygen tension resulting from the photosynthetic and respiratory activities of the associated algal endosymbiont Symbiodinium. In order to better understand the integration of biological clocks in cnidarian hosts of Symbiodinium, daily rhythms of behaviour and gene expression were studied in symbiotic and aposymbiotic morphs of the sea-anemone Aiptasia diaphana...
May 9, 2018: Microbiome
https://www.readbyqxmd.com/read/29735680/diurnal-down-regulation-of-ethylene-biosynthesis-mediates-biomass-heterosis
#14
Qingxin Song, Atsumi Ando, Dongqing Xu, Lei Fang, Tianzhen Zhang, Enamul Huq, Hong Qiao, Xing Wang Deng, Z Jeffrey Chen
Heterosis is widely applied in agriculture; however, the underlying molecular mechanisms for superior performance are not well understood. Ethylene biosynthesis and signaling genes are shown to be down-regulated in Arabidopsis interspecific hybrids. Ethylene is a plant hormone that promotes fruit ripening and maturation but inhibits hypocotyl elongation. Here we report that application of exogenous ethylene could eliminate biomass vigor in Arabidopsis thaliana F1 hybrids, suggesting a negative role of ethylene in heterosis...
May 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29730779/the-role-of-circadian-rhythms-in-the-hypertension-of-diabetes-mellitus-and-the-metabolic-syndrome
#15
REVIEW
Björn Lemmer, Henrik Oster
PURPOSE OF THE REVIEW: Cellular circadian clocks regulate physiological functions during day and night. It has been convincingly demonstrated that hypertension in patients suffering from diabetes mellitus or metabolic syndrome is characterized in most cases by a disturbed 24-h profile resulting in a nondipper pattern. We consider possible correlation between biological clocks and symptoms of the metabolic syndrome. RECENT FINDINGS: Changes in circadian clock function have been linked to metabolic disorders in genome-wide association studies...
May 5, 2018: Current Hypertension Reports
https://www.readbyqxmd.com/read/29729018/the-role-of-dynamic-m-6-a-rna-methylation-in-photobiology
#16
Myles Robinson, Palak Shah, Yanhong Cui, Yu-Ying He
N6 -methyladenosine (m6 A) is the most abundant internal RNA modification among numerous post-transcriptional modifications identified in eukaryotic mRNA. m6 A modification of RNA is catalyzed by the "writer" m6 A methyltransferase enzyme complex, consisting of METTL3, METTL14, WTAP, and KIAA1429. The m6 A modification is reversible, and can be removed by "eraser" m6 A demethylase enzymes, namely, FTO and ALKBH5. The biological function of m6 A modification on RNA is carried out by RNA-binding effector proteins called "readers"...
May 4, 2018: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/29727574/reconstitution-of-an-ultradian-oscillator-in-mammalian-cells-by-a-synthetic-biology-approach
#17
Marco Santorelli, Daniela Perna, Akihiro Isomura, Immacolata Garzilli, Francesco Annunziata, Lorena Postiglione, Barbara Tumaini, Ryoichiro Kageyama, Diego di Bernardo
The Notch effector gene Hes1 is an ultradian clock exhibiting cyclic gene expression in several progenitor cells, with a period of a few hours. Because of the complexity of studying Hes1 in the endogenous setting, and the difficulty of imaging these fast oscillations in vivo, the mechanism driving oscillations has never been proven. Here, we applied a "build it to understand it" synthetic biology approach to construct simplified 'hybrid' versions of the Hes1 ultradian oscillator combining synthetic and natural parts...
May 4, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29721962/the-retinal-circadian-clock-and-photoreceptor-viability
#18
Kenkichi Baba, Christophe P Ribelayga, P Michael Iuvone, Gianluca Tosini
Circadian rhythms are present in most living organisms, and these rhythms are not just a consequence of the day/night fluctuation, but rather they are generated by endogenous biological clocks with a periodicity of about 24 h. In mammals, the master pacemaker of circadian rhythms is localized in the suprachiasmatic nuclei (SCN) of the hypothalamus. The SCN controls circadian rhythms in peripheral organs. The retina also contains circadian clocks which regulate many aspects of retinal physiology, independently of the SCN...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29707543/modeling-based-investigation-of-the-effect-of-noise-in-cellular-systems
#19
REVIEW
Didier Gonze, Claude Gérard, Benjamin Wacquier, Aurore Woller, Alen Tosenberger, Albert Goldbeter, Geneviève Dupont
Noise is pervasive in cellular biology and inevitably affects the dynamics of cellular processes. Biological systems have developed regulatory mechanisms to ensure robustness with respect to noise or to take advantage of stochasticity. We review here, through a couple of selected examples, some insights on possible robustness factors and constructive roles of noise provided by computational modeling. In particular, we focus on (1) factors that likely contribute to the robustness of oscillatory processes such as the circadian clocks and the cell cycle, (2) how reliable coding/decoding of calcium-mediated signaling could be achieved in presence of noise and, in some cases, enhanced through stochastic resonance, and (3) how embryonic cell differentiation processes can exploit stochasticity to create heterogeneity in a population of identical cells...
2018: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29706671/review-of-methods-in-enzymology-volumes-551-and-552-circadian-rhythms-and-biological-clocks-part-a-and-b-edited-by-amita-sehgal
#20
Brian R Crane
No abstract text is available yet for this article.
June 2017: Quarterly Review of Biology
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