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Biological clock

Joseph F O'Grady, Laura S Hoelters, Martin T Swain, David C Wilcockson
BACKGROUND: Talitrus saltator is an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean. T. saltator exhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species...
2016: PeerJ
Carey D Balaban, Joseph M Furman
This study provides the first clear evidence that the generation of optokinetic nystagmus fast phases is a decision process that is influenced by performance of a concurrent disjunctive reaction time task (DRT). Ten subjects performed an auditory DRT during constant velocity optokinetic stimulation. Eye movements were measured in three dimensions with a magnetic search coil. Slow phase (SP) durations were defined as the interval between fast phases (FPs). There were three main findings. Firstly, human optokinetic nystagmus SP durations are consistent with a model of a Gaussian basic interval generator (a type of biological clock), such that FPs can be triggered randomly at the end of a clock cycle (mean duration: 200-250 ms); Kolmogorov-Smirnov tests could not reject the modeled cumulative distribution for any data trials...
October 19, 2016: Journal of Neurophysiology
Brock C Christensen, Karl T Kelsey
A new mitotic clock and mathematical approach that incorporates DNA methylation biology common among human cell types provides a new tool for cancer epigenetics research.
October 19, 2016: Genome Biology
Casey O Diekman, Amitabha Bose
Circadian oscillators found across a variety of species are subject to periodic external light-dark forcing. Entrainment to light-dark cycles enables the circadian system to align biological functions with appropriate times of day or night. Phase response curves (PRCs) have been used for decades to gain valuable insights into entrainment; however, PRCs may not accurately describe entrainment to photoperiods with substantial amounts of both light and dark due to their reliance on a single limit cycle attractor...
October 17, 2016: Journal of Biological Rhythms
Juan A Montero, Cristina Sanchez-Fernandez, Carlos I Lorda-Diez, Juan A Garcia-Porrero, Juan M Hurle
DNA damage independent of caspase activation accompanies programmed cell death in different vertebrate embryonic organs. We analyzed the significance of DNA damage during the regression of the interdigital tissue, which sculpts the digits in the embryonic limb. Interdigit remodeling involves oxidative stress, massive apoptosis and cell senescence. Phosphorylation of H2AX mediated by ATM precedes caspase dependent apoptosis and cell senescence during interdigit regression. The association of γH2AX with other downstream DNA repair factors, including MDC1, Rad50 and 53BP1 suggests a defensive response of cells against DNA damage...
October 18, 2016: Scientific Reports
Rachel A Johnston, Kristina L Paxton, Frank R Moore, Robert K Wayne, Thomas B Smith
The annual migration of a bird can involve thousands of kilometers of non-stop flight, requiring accurately timed seasonal changes in physiology and behavior. Understanding the molecular mechanisms controlling this endogenous programme can provide functional and evolutionary insights into the circannual biological clock and the potential of migratory species to adapt to changing environments. Under naturally-timed photoperiod conditions, we maintained captive Swainson's thrushes (Catharus ustulatus) and performed RNA sequencing (RNA-Seq) of the ventral hypothalamus and optic chiasma to evaluate transcriptome-wide gene expression changes of individuals in migratory condition...
October 16, 2016: Molecular Ecology
Amandine Chaix, Amir Zarrinpar, Satchidananda Panda
Circadian clocks are cell-autonomous timing mechanisms that organize cell functions in a 24-h periodicity. In mammals, the main circadian oscillator consists of transcription-translation feedback loops composed of transcriptional regulators, enzymes, and scaffolds that generate and sustain daily oscillations of their own transcript and protein levels. The clock components and their targets impart rhythmic functions to many gene products through transcriptional, posttranscriptional, translational, and posttranslational mechanisms...
October 10, 2016: Journal of Cell Biology
Jing Men, Yongyang Huang, Jitendra Solanki, Xianxu Zeng, Aneesh Alex, Jason Jerwick, Zhan Zhang, Rudolph E Tanzi, Airong Li, Chao Zhou
Optical coherence tomography (OCT) is a promising research tool for brain imaging and developmental biology. Serving as a three-dimensional optical biopsy technique, OCT provides volumetric reconstruction of brain tissues and embryonic structures with micrometer resolution and video rate imaging speed. Functional OCT enables label-free monitoring of hemodynamic and metabolic changes in the brain in vitro and in vivo in animal models. Due to its non-invasiveness nature, OCT enables longitudinal imaging of developing specimens in vivo without potential damage from surgical operation, tissue fixation and processing, and staining with exogenous contrast agents...
July 2016: IEEE Journal of Selected Topics in Quantum Electronics
Raymond van Ee, Sander Van de Cruys, Luc J M Schlangen, Björn N S Vlaskamp
A daily rhythm that is not in synchrony with the environmental light-dark cycle (as in jetlag and shift work) is known to affect mood and health through an as yet unresolved neural mechanism. Here, we combine Bayesian probabilistic 'cue-conflict' theory with known physiology of the biological clock of the brain, entailing the insight that, for a functional pacemaker, it is sufficient to have two interacting units (reflecting environmental and internal time-of-day cues), without the need for an extra homuncular directing unit...
October 5, 2016: Trends in Neurosciences
Zhen Yang, Andrew Wong, Diana Kuh, Dirk S Paul, Vardhman K Rakyan, R David Leslie, Shijie C Zheng, Martin Widschwendter, Stephan Beck, Andrew E Teschendorff
BACKGROUND: Variation in cancer risk among somatic tissues has been attributed to variations in the underlying rate of stem cell division. For a given tissue type, variable cancer risk between individuals is thought to be influenced by extrinsic factors which modulate this rate of stem cell division. To date, no molecular mitotic clock has been developed to approximate the number of stem cell divisions in a tissue of an individual and which is correlated with cancer risk. RESULTS: Here, we integrate mathematical modeling with prior biological knowledge to construct a DNA methylation-based age-correlative model which approximates a mitotic clock in both normal and cancer tissue...
October 3, 2016: Genome Biology
Lonnele J Ball, Oxana Palesh, Lance J Kriegsfeld
Most physiological processes in the brain and body exhibit daily (circadian) rhythms coordinated by an endogenous master clock located in the suprachiasmatic nucleus of the hypothalamus that are essential for normal health and functioning. Exposure to sunlight during the day and darkness at night optimally entrains biological rhythms to promote homeostasis and human health. Unfortunately, a major consequence of the modern lifestyle is increased exposure to sun-free environments during the day and artificial lighting at night...
October 2016: Endocrine Reviews
Shu-Feng Zhang, Chun-Juan Yuan, Ying Chen, Xiao-Huang Chen, Dong-Xu Li, Jiu-Ling Liu, Lin Lin, Da-Zhi Wang
Phosphorus (P) is a limiting macronutrient for diatom growth and productivity in the ocean. Much effort has been devoted to the physiological response of marine diatoms to ambient P change, however, the whole-genome molecular mechanisms are poorly understood. Here, we utilized RNA-Seq to compare the global gene expression patterns of a marine diatom Skeletonema costatum grown in inorganic P-replete, P-deficient, and inorganic- and organic-P resupplied conditions. In total 34,942 unique genes were assembled and 20...
2016: Frontiers in Microbiology
Judith E Carroll, Michael R Irwin, Morgan Levine, Teresa E Seeman, Devin Absher, Themistocles Assimes, Steve Horvath
BACKGROUND: Insomnia symptoms are associated with vulnerability to age-related morbidity and mortality. Cross-sectional data suggest that accelerated biological aging may be a mechanism through which sleep influences risk. A novel method for determining age acceleration using epigenetic methylation to DNA has demonstrated predictive utility as an epigenetic clock and prognostic of age-related morbidity and mortality. METHODS: We examined the association of epigenetic age and immune cell aging with sleep in the Women's Health Initiative study (N = 2078; mean 64...
July 26, 2016: Biological Psychiatry
Julia M Selfridge, Tetsuya Gotoh, Samuel Schiffhauer, JingJing Liu, Philip E Stauffer, Andrew Li, Daniel G S Capelluto, Carla V Finkielstein
Circadian rhythms are a collection of endogenously driven biochemical, physiological, and behavioral processes that oscillate in a 24-h cycle and can be entrained by external cues. Circadian clock molecules are responsible for the expression of regulatory components that modulate, among others, the cell's metabolism and energy consumption. In clinical practice, the regulation of clock mechanisms is relevant to biotransformation of therapeutics. Accordingly, xenobiotic metabolism and detoxification, the two processes that directly influence drug effectiveness and toxicity, are direct manifestations of the daily oscillations of the cellular and biochemical processes taking place within the gastrointestinal, hepatic/biliary, and renal/urologic systems...
October 3, 2016: Drugs
Christopher J Sifuentes, Jung-Woong Kim, Anand Swaroop, Pamela A Raymond
Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described, but our understanding of how Müller glial stem cell properties are regulated is incomplete. Mammalian Müller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Müller glia, we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion, prior to the asymmetric division that produces retinal progenitors...
October 1, 2016: Investigative Ophthalmology & Visual Science
S Aubin, R Kupers, M Ptito, P Jennum
As light plays an important role in the synchronisation of the internal biological clock to the environmental day/night schedule, we compared the 24h profiles of biological circadian markers in blind and normal sighted individuals. Salivary melatonin and cortisol concentrations were collected every two hours in eleven blind subjects, reporting no conscious light perception, and eleven age- and sex-matched normal sighted controls. Timing of melatonin onset and associated cortisol quiescence period confirm an increased incidence of abnormal circadian patterns in blindness...
September 27, 2016: Behavioural Brain Research
H J Park, W-Y Kim, J M Pardo, D-J Yun
Plants have adapted to environmental changes and stresses over generations. The decision of transition from the vegetative to reproductive stage is critical, particularly under unfavorable conditions. Thus, plants appear to have developed mechanisms by which environmental factors or inputs are transmitted to stress response signaling pathways to confer tolerance and are simultaneously integrated into flowering regulation pathways (photoperiod, vernalization, autonomous, and gibberellic acid signaling) to propagate the next generation...
2016: International Review of Cell and Molecular Biology
Lucia Mendoza-Viveros, Pascale Bouchard-Cannon, Sara Hegazi, Arthur H Cheng, Stephen Pastore, Hai-Ying Mary Cheng
Circadian timekeeping is a ubiquitous mechanism that enables organisms to maintain temporal coordination between internal biological processes and time of the local environment. The molecular basis of circadian rhythms lies in a set of transcription-translation feedback loops (TTFLs) that drives the rhythmic transcription of core clock genes, whose level and phase of expression serve as the marker of circadian time. However, it has become increasingly evident that additional regulatory mechanisms impinge upon the TTFLs to govern the properties and behavior of the circadian clock...
September 29, 2016: Cellular and Molecular Life Sciences: CMLS
Ashapurna Sarma, Vishal P Sharma, Arindam B Sarkar, M Chandra Sekar, Karunakar Samuel, Michael E Geusz
BACKGROUND: Curcuminoids of the spice turmeric and their enhanced derivatives have much potential as cancer treatments. They act on a wide variety of biological pathways, including those regulating cell division and circadian rhythms. It is known that circadian clocks can modify cancer therapy effectiveness, according to studies aimed at optimizing treatments based on the circadian cycle. It is therefore important to determine whether treatments with curcumin or similar chemotherapeutic agents are regulated by circadian timing...
September 29, 2016: BMC Cancer
E Thomas Danielsen, Kim F Rewitz
Circadian clocks are important timekeepers of physiological processes. A new report shows that silencing the circadian clock specifically in steroid-producing cells of Drosophila disrupts development and causes lethality, and is more detrimental than having no clock at all.
September 26, 2016: Current Biology: CB
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