Read by QxMD icon Read

Mammalian circadian

Kevin A McGoff, Xin Guo, Anastasia Deckard, Christina M Kelliher, Adam R Leman, Lauren J Francey, John B Hogenesch, Steven B Haase, John L Harer
We present a novel approach, the Local Edge Machine, for the inference of regulatory interactions directly from time-series gene expression data. We demonstrate its performance, robustness, and scalability on in silico datasets with varying behaviors, sizes, and degrees of complexity. Moreover, we demonstrate its ability to incorporate biological prior information and make informative predictions on a well-characterized in vivo system using data from budding yeast that have been synchronized in the cell cycle...
October 19, 2016: Genome Biology
Aurore Woller, Hélène Duez, Bart Staels, Marc Lefranc
To maintain energy homeostasis despite variable energy supply and consumption along the diurnal cycle, the liver relies on a circadian clock synchronized to food timing. Perturbed feeding and fasting cycles have been associated with clock disruption and metabolic diseases; however, the mechanisms are unclear. To address this question, we have constructed a mathematical model of the mammalian circadian clock, incorporating the metabolic sensors SIRT1 and AMPK. The clock response to various temporal patterns of AMPK activation was simulated numerically, mimicking the effects of a normal diet, fasting, and a high-fat diet...
October 18, 2016: Cell Reports
Jacob J Hughey, Atul J Butte
The daily timing of mammalian physiology is coordinated by circadian clocks throughout the body. Although measurements of clock gene expression indicate that these clocks in mice are normally in phase with each other, the situation in humans remains unclear. We used publicly available data from five studies, comprising over 1000 samples, to compare the phasing of circadian gene expression in human brain and human blood. Surprisingly, after controlling for age, clock gene expression in brain was phase-delayed by ~8...
October 4, 2016: Journal of Biological Rhythms
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
Sahar Farajnia, Johanna H Meijer, Stephan Michel
One feature of the mammalian circadian clock, situated in the suprachiasmatic nucleus (SCN), is its ability to measure day length and thereby contribute to the seasonal adaptation of physiology and behavior. The timing signal from the SCN, namely the 24 hr pattern of electrical activity, is adjusted according to the photoperiod being broader in long days and narrower in short days. Vasoactive intestinal peptide and gamma-aminobutyric acid play a crucial role in intercellular communication within the SCN and contribute to the seasonal changes in phase distribution...
October 2016: ASN Neuro
Yi-Ying Chiou, Yanyan Yang, Naim Rashid, Rui Ye, Christopher P Selby, Aziz Sancar
The mammalian circadian clock is based on a transcription-translation feedback loop (TTFL) consolidated by secondary loops. In the primary TTFL, the circadian locomotor output cycles kaput (CLOCK)-brain and muscle Arnt-like protein-1 (BMAL1) heterodimer acts as the transcriptional activator, and Cryptochrome (CRY) and Period (PER) proteins function as repressors. PER represses by displacing CLOCK-BMAL1 from promoters in a CRY-dependent manner. Interestingly, genes with complex promoters may either be repressed or de-repressed by PER, depending on the particular promoter regulatory elements...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Takafumi Katsumura, Yukiko Fukuyo, Shoji Kawamura, Hiroki Oota
BACKGROUND: The circadian clock is set up around a 24-h period in humans who are awake in the daytime and sleep in the nighttime, accompanied with physiological and metabolic rhythms. Most haplorhine primates, including humans, are diurnal, while most "primitive" strepsirrhine primates are nocturnal, suggesting primates have evolved from nocturnal to diurnal habits. The mechanisms of physiological changes causing the habits and of genetic changes causing the physiological changes are, however, unknown...
September 28, 2016: Journal of Physiological Anthropology
Guocun Huang, Yunfeng Zhang, Yongli Shan, Shuzhang Yang, Yogarany Chelliah, Han Wang, Joseph S Takahashi
It is known that there are mechanistic links between circadian clocks and metabolic cycles. Reduced nicotinamide adenine dinucleotide (NADH) is a key metabolic cofactor in all living cells; however, it is not known whether levels of NADH oscillate or not. Here we employed REX, a bacterial NADH binding protein, fused to the VP16 activator in order to convert intracellular endogenous redox balance into transcriptional readouts by a reporter gene in mammalian cells. EMSA results show that the DNA binding activity of both T-and S-REX::VP16 fusions are decreased with a reduced-to-oxidized cofactor ratio increase...
September 19, 2016: Journal of Biological Chemistry
Jun J Nakano, Kimiko Shimizu, Shigeki Shimba, Yoshitaka Fukada
While disruption of the circadian clock triggers a spectrum of affective abnormalities, how the clock regulates mammalian emotionality remains unclear. Here, we characterized the time-of-day-dependent regulation of mouse anxiety-like behaviors. We show that anxiety-like behaviors are expressed in a circadian manner in mice and demonstrate that the clock machineries in the dorsal telencephalon (dTel) are required for the time-of-day-dependent regulation of anxiety-like behaviors. We identify suprachiasmatic nucleus circadian oscillatory protein (SCOP/PHLPP1β) as an essential intracellular signaling molecule mediating this temporal regulation downstream of the clock...
2016: Scientific Reports
Alexander Andreychenko, Morgan Magnin, Katsumi Inoue
Automated verification of living organism models allows us to gain previously unknown knowledge about underlying biological processes. In this paper we show how parametric time model checking can be applied to define the time behavior of biological oscillatory systems more precisely. In particular, we focus on the resilience properties of such systems. This notion was introduced to understand the behavior of biological systems (e.g. the mammalian circadian rhythm) that are reactive and adaptive enough to endorse major changes in their environment (e...
September 13, 2016: Bio Systems
Marina Maria Bellet, Selma Masri, Giuseppe Astarita, Paolo Sassone-Corsi, Maria Agnese Della Fazia, Giuseppe Servillo
Liver regeneration offers a distinctive opportunity to study cell proliferation in vivo. Mammalian Silent information regulator 1 (SIRT1), a NAD(+)-dependent histone deacetylase, is an important regulator of various cellular processes, including proliferation, metabolism and circadian rhythms. In the liver, SIRT1 coordinates the circadian oscillation of clock-controlled genes, including genes that encode enzymes involved in metabolic pathways. We performed partial hepatectomy in WT and liver-specific Sirt1 deficient mice and analysed the expression of cell cycle regulators in liver samples taken at different times during the regenerative process, by real time PCR, western blotting and immunohistochemistry...
September 15, 2016: Journal of Biological Chemistry
Manish Putteeraj, Tomoko Soga, Takayoshi Ubuka, Ishwar S Parhar
Reproduction is associated with the circadian system, primarily as a result of the connectivity between the biological clock in the suprachiasmatic nucleus (SCN) and reproduction-regulating brain regions, such as preoptic area (POA), anteroventral periventricular nucleus (AVPV), and arcuate nucleus (ARC). Networking of the central pacemaker to these hypothalamic brain regions is partly represented by close fiber appositions to specialized neurons, such as kisspeptin and gonadotropin-releasing hormone (GnRH) neurons; accounting for rhythmic release of gonadotropins and sex steroids...
2016: Frontiers in Endocrinology
Minkyung Kim, Hoyeon Lee, Jin-Hoe Hur, Joonho Choe, Chunghun Lim
Light is one of the strongest environmental time cues for entraining endogenous circadian rhythms. Emerging evidence indicates that CREB-regulated transcription co-activator 1 (CRTC1) is a key player in this pathway, stimulating light-induced Period1 (Per1) transcription in mammalian clocks. Here, we demonstrate a light-independent role of Drosophila CRTC in sustaining circadian behaviors. Genomic deletion of the crtc locus causes long but poor locomotor rhythms in constant darkness. Overexpression or RNA interference-mediated depletion of CRTC in circadian pacemaker neurons similarly impairs the free-running behavioral rhythms, implying that Drosophila clocks are sensitive to the dosage of CRTC...
2016: Scientific Reports
Qun-Yong Zhou, Katherine J Burton, Matthew L Neal, Yu Qiao, Anumantha G Kanthasamy, Yanjun Sun, Xiangmin Xu, Yuanye Ma, Xiaohan Li
The temporal organization of activity/rest or sleep/wake rhythms for mammals is regulated by the interaction of light/dark cycle and circadian clocks. The neural and molecular mechanisms that confine the active phase to either day or night period for the diurnal and the nocturnal mammals are unclear. Here we report that prokineticin 2, previously shown as a circadian clock output molecule, is expressed in the intrinsically photosensitive retinal ganglion cells, and the expression of prokineticin 2 in the intrinsically photosensitive retinal ganglion cells is oscillatory in a clock-dependent manner...
2016: Molecular Brain
Hyeon-Young Min, Kyeong-Min Kim, Gabbine Wee, Eun-Jung Kim, Won-Gu Jang
AIMS: Mammalian circadian rhythms regulate many metabolic processes. Recent studies suggest that brain and muscle Arnt-like 1 (BMAL1), an important component of mammalian circadian rhythm, is associated with insulin signaling. Several studies have shown that insulin is associated with bone metabolism; however, the relationship between BMAL1 and osteoblasts remains unclear. MAIN METHODS: Expression of osteogenic markers and Bmal1 in MC3T3-E1 cells was measured by RT-PCR and Western blotting...
October 1, 2016: Life Sciences
N S Foulkes, D Whitmore, D Vallone, C Bertolucci
The utility of any model species cannot be judged solely in terms of the tools and approaches it provides for genetic analysis. A fundamental consideration is also how its biology has been shaped by the environment and the ecological niche which it occupies. By comparing different species occupying very different habitats we can learn how molecular and cellular mechanisms change during evolution in order to optimally adapt to their environment. Such knowledge is as important as understanding how these mechanisms work...
2016: Advances in Genetics
Sue Goo Rhee, In Sup Kil
Mitochondria produce hydrogen peroxide (H2O2) during energy metabolism in most mammalian cells as well as during the oxidation of cholesterol associated with the synthesis of steroid hormones in steroidogenic cells. Some of the H2O2 produced in mitochondria is released into the cytosol, where it serves as a key regulator of various signaling pathways. Given that mitochondria are equipped with several H2O2-eliminating enzymes, however, it had not been clear how mitochondrial H2O2 can escape destruction by these enzymes for such release...
August 4, 2016: Free Radical Biology & Medicine
Arjun Sengupta, Saikumari Y Krishnaiah, Seth Rhoades, Jacqueline Growe, Barry Slaff, Anand Venkataraman, Anthony O Olarerin-George, Chi Van Dang, John B Hogenesch, Aalim M Weljie
Oscillations in circadian metabolism are crucial to the well being of organism. Our understanding of metabolic rhythms has been greatly enhanced by recent advances in high-throughput systems biology experimental techniques and data analysis. In an in vitro setting, metabolite rhythms can be measured by time-dependent sampling over an experimental period spanning one or more days at sufficent resolution to elucidate rhythms. We hypothesized that cellular metabolic effects over such a time course would be influenced by both oscillatory and circadian-independent cell metabolic effects...
July 27, 2016: Metabolites
Charles L Nunn, David R Samson, Andrew D Krystal
Sleep is essential to cognitive function and health in humans, yet the ultimate reasons for sleep-i.e. 'why' sleep evolved-remain mysterious. We integrate findings from human sleep studies, the ethnographic record, and the ecology and evolution of mammalian sleep to better understand sleep along the human lineage and in the modern world. Compared to other primates, sleep in great apes has undergone substantial evolutionary change, with all great apes building a sleeping platform or 'nest'. Further evolutionary change characterizes human sleep, with humans having the shortest sleep duration, yet the highest proportion of rapid eye movement sleep among primates...
2016: Evolution, Medicine, and Public Health
Pauline Traynard, Céline Feillet, Sylvain Soliman, Franck Delaunay, François Fages
Experimental observations have put in evidence autonomous self-sustained circadian oscillators in most mammalian cells, and proved the existence of molecular links between the circadian clock and the cell cycle. Some mathematical models have also been built to assess conditions of control of the cell cycle by the circadian clock. However, recent studies in individual NIH3T3 fibroblasts have shown an unexpected acceleration of the circadian clock together with the cell cycle when the culture medium is enriched with growth factors, and the absence of such acceleration in confluent cells...
July 18, 2016: Bio Systems
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"