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Clock genes

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https://www.readbyqxmd.com/read/28944015/signatures-of-selection-in-mammalian-clock-genes-with-coding-trinucleotide-repeats-implications-for-studying-the-genomics-of-high-pace-adaptation
#1
Melanie B Prentice, Jeff Bowman, Jillian L Lalor, Michelle M McKay, Lindsay A Thomson, Cristen M Watt, Andrew G McAdam, Dennis L Murray, Paul J Wilson
Climate change is predicted to affect the reproductive ecology of wildlife; however, we have yet to understand if and how species can adapt to the rapid pace of change. Clock genes are functional genes likely critical for adaptation to shifting seasonal conditions through shifts in timing cues. Many of these genes contain coding trinucleotide repeats, which offer the potential for higher rates of change than single nucleotide polymorphisms (SNPs) at coding sites, and, thus, may translate to faster rates of adaptation in changing environments...
September 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28943398/cold-sensing-trpm8-channel-participates-in-circadian-control-of-the-brown-adipose-tissue
#2
Maria Nathália Moraes, Leonardo Vinicius Monteiro de Assis, Felipe Dos Santos Henriques, Miguel Luiz Batista Junior, Ali D Güler, Ana Maria de Lauro Castrucci
Transient receptor potential (TRP) channels are known to regulate energy metabolism, and TRPM8 has become an interesting player in this context. Here we demonstrate the role of the cold sensor TRPM8 in the regulation of clock gene and clock controlled genes in brown adipose tissue (BAT). We investigated TrpM8 temporal profile in the eyes, suprachiasmatic nucleus and BAT; only BAT showed temporal variation of TrpM8 transcripts. Eyes from mice lacking TRPM8 lost the temporal profile of Per1 in LD cycle. This alteration in the ocular circadian physiology may explain the delay in the onset of locomotor activity in response to light pulse, as compared to wild type animals (WT)...
September 21, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28942711/epigenetic-drift-is-a-determinant-of-mammalian-lifespan
#3
Andrew R Mendelsohn, James Larrick
The epigenome, which controls cell identity and function, is not maintained with 100 percent fidelity in somatic animal cells. Errors in the maintenance of the epigenome lead to epigenetic drift, an important hallmark of aging. Numerous studies have described DNA methylation clocks that correlate epigenetic drift with increasing age. The question of how significant a role epigenetic drift plays in creating the phenotypes associated with aging remains open. A recent study describes a new DNA methylation clock that can be slowed by caloric restriction (CR) in a way that correlates with the degree of lifespan and healthspan extension conferred by CR, suggesting that epigenetic drift itself is a determinant of mammalian lifespan...
September 25, 2017: Rejuvenation Research
https://www.readbyqxmd.com/read/28942538/photoperiodism-dynamics-during-the-domestication-and-improvement-of-soybean
#4
REVIEW
Sheng-Rui Zhang, Huan Wang, Zhongyu Wang, Yao Ren, Lifang Niu, Jun Liu, Bin Liu
Soybean (Glycine max) is a facultative short-day plant with a sensitive photoperiod perception and reaction system, which allows it to adjust its physiological state and gene regulatory networks to seasonal and diurnal changes in environmental conditions. In the past few decades, soybean cultivation has spread from East Asia to areas throughout the world. Biologists and breeders must now confront the challenge of understanding the molecular mechanism of soybean photoperiodism and improving agronomic traits to enable this important crop to adapt to geographical and environmental changes...
September 21, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28942468/complete-mitochondrial-genome-of-porzana-fusca-and-porzana-pusilla-and-phylogenetic-relationship-of-16-rallidae-species
#5
Peng Chen, Yuqing Han, Chaoying Zhu, Bin Gao, Luzhang Ruan
The complete mitochondrial genome sequences of Porzana fusca and Porzana pusilla were determined. The two avian species share a high degree of homology in terms of mitochondrial genome organization and gene arrangement. Their corresponding mitochondrial genomes are 16,935 and 16,978 bp and consist of 37 genes and a control region. Their PCGs were both 11,365 bp long and have similar structure. Their tRNA gene sequences could be folded into canonical cloverleaf secondary structure, except for tRNA(Ser (AGY)), which lost its "DHU" arm...
September 23, 2017: Genetica
https://www.readbyqxmd.com/read/28942015/multiple-transmission-chains-of-coxsackievirus-a4-co-circulating-in-china-and-neighboring-countries-in-recent-years-phylogenetic-and-spatiotemporal-analyses-based-on-virological-surveillance
#6
Peng Chen, Haiyan Wang, Zexin Tao, Aiqiang Xu, Xiaojuan Lin, Nan Zhou, Pei Wang, Qian Wang
Coxsackievirus A4 (CV-A4) has been reported frequently in association with many infectious diseases and cases of hand, foot, and mouth disease potentially associated with CV-A4 infection are also identified. This study summarized the Shandong CV-A4 strains isolated from 25 years acute flaccid paralysis surveillance, with an emphasis on exploring the phylogenetic analyses and spatiotemporal dynamics of CV-A4 at the global scale. We sampled 43 CV-A4 isolates and utilized VP1 gene to construct phylogenetic trees...
September 20, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28940754/daily-expression-of-two-circadian-clock-genes-in-compound-eye-of-helicoverpa-armigera-evidence-for-peripheral-tissue-circadian-timing
#7
Shuo Yan, Yan-Jun Liu, Jia-Lin Zhu, Wei-Na Cui, Xin-Fang Zhang, Yu-Hui Yang, Xiao-Ming Liu, Qing-Wen Zhang, Xiao-Xia Liu
Circadian clock genes in peripheral tissues usually play an important role in regulating the circadian rhythms. Light is the most important environmental signal for synchronizing endogenous rhythms with the daily light-dark cycle, and compound eyes are known as the principal circadian photoreceptor for photic entrainment in most moths. However, there is little evidence for circadian timing in the compound eyes. In the current study, we isolated the timeless gene, designated Ha-tim (GenBank accession number: KM233162), from the cotton bollworm Helicoverpa armigera...
September 23, 2017: Insect Science
https://www.readbyqxmd.com/read/28939975/ketamine-induced-glutamatergic-mechanisms-of-sleep-and-wakefulness-insights-for-developing-novel-treatments-for-disturbed-sleep-and-mood
#8
Wallace C Duncan, Elizabeth D Ballard, Carlos A Zarate
Ketamine, a drug with rapid antidepressant effects and well-described effects on slow wave sleep (SWS), is a useful intervention for investigating sleep-wake mechanisms involved in novel therapeutics. The drug rapidly (within minutes to hours) reduces depressive symptoms in individuals with major depressive disorder (MDD) or bipolar disorder (BD), including those with treatment-resistant depression. Ketamine treatment elevates extracellular glutamate in the prefrontal cortex. Glutamate, in turn, plays a critical role as a proximal element in a ketamine-initiated molecular cascade that increases synaptic strength and plasticity, which ultimately results in rapidly improved mood...
September 23, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/28938081/sleep-in-insects
#9
Charlotte Helfrich-Förster
Sleep is essential for proper brain function in mammals and insects. During sleep, animals are disconnected from the external world; they show high arousal thresholds and changed brain activity. Sleep deprivation results in a sleep rebound. Research using the fruit fly, Drosophila melanogaster, has helped us understand the genetic and neuronal control of sleep. Genes involved in sleep control code for ion channels, factors influencing neurotransmission and neuromodulation, and proteins involved in the circadian clock...
September 22, 2017: Annual Review of Entomology
https://www.readbyqxmd.com/read/28937654/genome-wide-analysis-of-cca1-like-proteins-in-soybean-and-functional-characterization-of-gmmyb138a
#10
Shaomin Bian, Donghao Jin, Ruihua Li, Xin Xie, Guoli Gao, Weikang Sun, Yuejia Li, Lulu Zhai, Xuyan Li
Plant CIRCADIAN CLOCK ASSOCIATED1 (CCA1)-like proteins are a class of single-repeat MYELOBLASTOSIS ONCOGENE (MYB) transcription factors generally featured by a highly conserved motif SHAQK(Y/F)F, which play important roles in multiple biological processes. Soybean is an important grain legume for seed protein and edible vegetable oil. However, essential understandings regarding CCA1-like proteins are very limited in soybean. In this study, 54 CCA1-like proteins were identified by data mining of soybean genome...
September 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28936981/drought-stress-modulates-diurnal-oscillations-of-circadian-clock-and-drought-responsive-genes-in-oryza-sativa-l
#11
Jia Li, Yun-Hua Liu, Yu Zhang, Chen Chen, Xia Yu, Shun-Wu Yu
Endogenous circadian rhythms play a key role in regulating plant growth and development, and in allowing plants to respond and adapt to changing environments. To understand how drought regulates upland rice(Oryza sativa L.) IRAT109, we examined the expression levels of circadian clock and drought-responsive genes through real-time PCR. The results revealed that, first, drought reduced the relative expression level and amplitude of peak expression of several morning circadian clock components (such as OsPRRs, OsLHY and OsZTL1), increased the relative expression level and amplitude of some evening circadian clock components (such as OsTOC1, OsGI and OsELF3), but did not influence OsFKF1...
September 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28933632/influence-of-light-and-food-on-the-circadian-clock-in-liver-of-rainbow-trout-oncorhynchus-mykiss
#12
Juan Hernández-Pérez, Jesús M Míguez, Fatemeh Naderi, José L Soengas, Marcos A López-Patiño
Several reports support the existence of multiple peripheral oscillators in fish, which may be able to modulate the rhythmic functions developed by those tissues hosting them. Thus, a circadian oscillator has been proposed to be located within fish liver. In this vertebrate group, the role played by the circadian system in regulating metabolic processes in liver is mostly unknown. We, therefore investigated the liver of rainbow trout (Oncorhynchus mykiss) as a potential element participating in the regulation of circadian rhythms in fish by hosting a functional circadian oscillator...
September 21, 2017: Chronobiology International
https://www.readbyqxmd.com/read/28933565/sleep-duration-nightshift-work-and-the-timing-of-meals-and-urinary-levels-of-8-isoprostane-and-6-sulfatoxymelatonin-in-japanese-women
#13
Chisato Nagata, Takashi Tamura, Keiko Wada, Kie Konishi, Yuko Goto, Yasuko Nagao, Kazuhiro Ishihara, Satoru Yamamoto
It has been hypothesized that disruption of circadian rhythms affects human health. Shift work and sleep deprivation are thought to disrupt the normal light-dark cycle, although the disruption due to shiftwork may be dependent on sleep deprivation. Both conditions have been suggested to be associated with an increased risk of cardiometabolic disorders. Non-photic environmental factors, such as the timing of eating, are also thought to regulate circadian rhythm and thus, may have effects on health, but the evidence from human studies is scarce...
September 21, 2017: Chronobiology International
https://www.readbyqxmd.com/read/28930051/addiction-and-the-role-of-circadian-genes
#14
Laura A Forde, Gursharan Kalsi
OBJECTIVE: In mammals, intimate interactions exist between the circadian system and other molecular systems, and mounting evidence is suggesting that these relationships may affect substance use disorders. Research in preclinical models supports the role of circadian genes as risk factors for addiction. Here, we explore the evidence and review human genetic studies testing the association between specific circadian genes and substance use disorders. METHOD: A literature search was conducted in PubMed for studies testing variants in eight circadian genes known to be central to the functioning of the master clock in the brain...
September 2017: Journal of Studies on Alcohol and Drugs
https://www.readbyqxmd.com/read/28928952/a-simple-method-to-measure-clock-bmal1-dna-binding-activity-in-tissue-and-cell-extracts
#15
Maud Gillessen, Pieter Bas Kwak, Alfred Tamayo
The proteins CLOCK and BMAL1 form a heterodimeric transcription factor essential to circadian rhythms in mammals.  Daily rhythms of CLOCK-BMAL1 DNA binding activity are known to oscillate with target gene expression in vivo. Here we present a highly sensitive assay that recapitulates native CLOCK-BMAL1 DNA binding rhythms from crude tissue extracts, which we call the Clock Protein-DNA Binding Assay (CPDBA). This method can detect less than 2-fold differences in DNA binding activity, and can deliver results in two hours or less using 10 microliters or less of crude extract, while requiring neither specialized equipment nor expensive probes...
2017: F1000Research
https://www.readbyqxmd.com/read/28928877/mechanisms-of-breast-cancer-in-shift-workers-dna-methylation-in-five-core-circadian-genes-in-nurses-working-night-shifts
#16
Johanna Samulin Erdem, Øivind Skare, Marte Petersen-Øverleir, Heidi Ødegaard Notø, Jenny-Anne S Lie, Edyta Reszka, Beata Pepłońska, Shanbeh Zienolddiny
Shift work has been suggested to be associated with breast cancer risk, and circadian disruption in shift workers is hypothesized as one of the mechanisms of increased cancer risk. There is, however, insufficient molecular evidence supporting this hypothesis. Using the quantitative methodology of pyrosequencing, epigenetic changes in 5-methyl cytosine (5mC) in five circadian genes CLOCK, BMAL1, CRY1, PER1 and PER2 in female nurses working night shift work (278 breast cancer cases, 280 controls) were analyzed...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28923961/evolution-of-the-3-hydroxypropionate-bicycle-and-recent-transfer-of-anoxygenic-photosynthesis-into-the-chloroflexi
#17
Patrick M Shih, Lewis M Ward, Woodward W Fischer
Various lines of evidence from both comparative biology and the geologic record make it clear that the biochemical machinery for anoxygenic photosynthesis was present on early Earth and provided the evolutionary stock from which oxygenic photosynthesis evolved ca. 2.3 billion years ago. However, the taxonomic identity of these early anoxygenic phototrophs is uncertain, including whether or not they remain extant. Several phototrophic bacterial clades are thought to have evolved before oxygenic photosynthesis emerged, including the Chloroflexi, a phylum common across a wide range of modern environments...
September 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28922793/diurnal-cycling-transcription-factors-of-pineapple-revealed-by-genome-wide-annotation-and-global-transcriptomic-analysis
#18
Anupma Sharma, Ching Man Wai, Ray Ming, Qingyi Yu
Circadian clock provides fitness advantage by coordinating internal metabolic and physiological processes to external cyclic environments. Core clock components exhibit daily rhythmic changes in gene expression, and the majority of them are transcription factors (TFs) and transcription coregulators (TCs). We annotated 1,398 TFs from 67 TF families and 80 TCs from 20 TC families in pineapple, and analyzed their tissue-specific and diurnal expression patterns. Approximately 42% of TFs and 45% of TCs displayed diel rhythmic expression, including 177 TF/TCs cycling only in the nonphotosynthetic leaf tissue, 247 cycling only in the photosynthetic leaf tissue, and 201 cycling in both...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28920512/rhythmic-three-part-harmony-the-complex-interaction-of-maternal-placental-and-fetal-circadian-systems
#19
Peter J Mark, Rachael C Crew, Michaela D Wharfe, Brendan J Waddell
From the perspective of circadian biology, mammalian pregnancy presents an unusual biological scenario in which an entire circadian system (i.e., that of the fetus) is embodied within another (i.e., that of the mother). Moreover, both systems are likely to be influenced at their interface by a third player, the placenta. Successful pregnancy requires major adaptations in maternal physiology, many of which involve circadian changes that support the high metabolic demands of the growing fetus. A functional role for maternal circadian adaptations is implied by the effects of circadian disruption, which result in pregnancy complications including higher risks for miscarriage, preterm labor, and low birth weight...
September 1, 2017: Journal of Biological Rhythms
https://www.readbyqxmd.com/read/28919546/phylodynamics-of-the-brazilian-feline-immunodeficiency-virus
#20
Lucía Cano-Ortiz, Dennis Maletich Junqueira, Juliana Comerlato, Cristina Santos Costa, André Zani, Naila Blatt Duda, Caroline Tochetto, Raissa Nunes Dos Santos, Fernanda Vieira Amorim da Costa, Paulo Michel Roehe, Ana Cláudia Franco
Feline immunodeficiency virus (FIV), like other retroviruses, displays large genomic divergence when different isolates are compared. In this study, 31 FIV positive samples of domestic cats from Porto Alegre, RS, Brazil were used aiming at a detailed genomic characterization and a better understanding of the molecular epidemiology of the virus in Brazil. The proviral env genes were partially amplified, sequenced and compared with another 237 sequences from different continents. We identified several Brazilian highly supported clades (A, B1, B2, C and D) that suggest independent events of introduction of FIV in Brazil...
September 13, 2017: Infection, Genetics and Evolution
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