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https://www.readbyqxmd.com/read/28434151/cbf2a-cbf4b-genomic-region-copy-numbers-alongside-the-circadian-clock-play-key-regulatory-mechanisms-driving-expression-of-fr-h2-cbfs
#1
Taniya Dhillon, Kengo Morohashi, Eric J Stockinger
The C-Repeat Binding Factors (CBFs) are DNA-binding transcriptional activators that were identified using Arabidopsis thaliana. In barley, Hordeum vulgare, a cluster of CBF genes reside at FROST RESISTANCE-H2, one of two loci having major effects on winter-hardiness. FR-H2 was revealed in a population derived from the winter barley 'Nure' and the spring barley 'Trèmois'. 'Nure' harbors two to three copies of CBF2A and CBF4B as a consequence of tandem iteration of the genomic region encompassing these genes whereas 'Trèmois' harbors single copies, and these copy number differences are associated with their transcript level differences...
April 22, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28433925/low-dose-pollutant-mixture-triggers-metabolic-disturbances-in-female-mice-leading-to-common-and-specific-features-as-compared-to-a-high-fat-diet
#2
Emmanuel Labaronne, Claudie Pinteur, Nathalie Vega, Sandra Pesenti, Benoit Julien, Emmanuelle Meugnier-Fouilloux, Hubert Vidal, Danielle Naville, Brigitte Le Magueresse-Battistoni
Environmental pollutants are potential etiologic factors of obesity and diabetes that reach epidemic proportions worldwide. However, it is important to determine if pollutants could exert metabolic defects without directly inducing obesity. The metabolic disturbances triggered in nonobese mice lifelong exposed to a mixture of low-dose pollutants (2,3,7,8-tetrachlorodibenzo-p-dioxine, polychlorinated biphenyl 153, diethylhexyl-phthalate, and bisphenol A) were compared with changes provoked by a high-fat high-sucrose (HFHS) diet not containing the pollutant mixture...
April 8, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28432873/conditional-deletion-of-bmal1-accentuates-microvascular-and-macrovascular-injury
#3
Ashay D Bhatwadekar, Eleni Beli, Diao Yanpeng, Jonathan Chen, Qianyi Luo, Alpha Alex, Sergio Caballero, James M Dominguez, Tatiana E Salazar, Julia V Busik, Mark S Segal, Maria B Grant
The brain and muscle aryl hydrocarbon receptor nuclear translocator-like protein (BMAL)-1 constitutes a major transcriptional regulator of the circadian clock. Here, we explored the impact of conditional deletion of Bmal1 in endothelium and hematopoietic cells in murine models of microvascular and macrovascular injury. We used two models of Bmal1(fx/fx);Tek-Cre mice, a retinal ischemia/reperfusion model and a neointimal hyperplasia model of the femoral artery. Eyes were enumerated for acellular capillaries and were stained for oxidative damage markers using nitrotyrosine immunohistochemistry...
April 19, 2017: American Journal of Pathology
https://www.readbyqxmd.com/read/28432608/fpgasw-accelerating-large-scale-smith-waterman-sequence-alignment-application-with-backtracking-on-fpga-linear-systolic-array
#4
Xia Fei, Zou Dan, Lu Lina, Man Xin, Zhang Chunlei
The Smith-Waterman (SW) algorithm based on dynamic programming is a well-known classical method for high precision sequence matching and has become the gold standard to evaluate sequence alignment software. In this paper, we propose fine-grained parallelized SW algorithms using affine gap penalty and implement a parallel computing structures to accelerating the SW with backtracking on FPGA platform. We analysis the dynamic parallel computing features of anti-diagonal elements and storage expansion problem resulting from backtracking stage, and propose a series of optimization strategies to eliminate data dependency, reduce storage requirements, and overlap memory access latency...
April 21, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28431121/starbeast2-brings-faster-species-tree-inference-and-accurate-estimates-of-substitution-rates
#5
Huw A Ogilvie, Remco R Bouckaert, Alexei J Drummond
Fully Bayesian multispecies coalescent (MSC) methods like *BEAST estimate species trees from multiple sequence alignments. Today thousands of genes can be sequenced for a given study, but using that many genes with *BEAST is intractably slow. An alternative is to use heuristic methods which compromise accuracy or completeness in return for speed. A common heuristic is concatenation, which assumes that the evolutionary history of each gene tree is identical to the species tree. This is an inconsistent estimator of species tree topology, a worse estimator of divergence times, and induces spurious substitution rate variation when incomplete lineage sorting is present...
April 14, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28431105/extinction-vs-rapid-radiation-the-juxtaposed-evolutionary-histories-of-coelotine-spiders-support-the-eocene-oligocene-orogenesis-of-the-tibetan-plateau
#6
Zhe Zhao, Shuqiang Li
Evolutionary biology has long been concerned with how changing environments affect and drive the spatiotemporal development of organisms. Coelotine spiders (Agelenidae: Coelotinae) are common species in the temperate and subtropical areas of the Northern Hemisphere. Their long evolutionary history and the extremely imbalanced distribution of species richness suggest that Eurasian environments, especially since the Cenozoic, are the drivers of their diversification. We use phylogenetics, molecular dating, ancestral area reconstructions, diversity, and ecological niche analyses to investigate the spatiotemporal evolution of 286 coelotine species from throughout the region...
April 20, 2017: Systematic Biology
https://www.readbyqxmd.com/read/28430521/perinatal-light-imprinting-of-circadian-clocks-and-systems-pliccs-a-signature-of-photoperiod-around-birth-on-circadian-system-stability-and-association-with-cancer
#7
Philip Lewis, Thomas C Erren
Recent findings from animal models suggest that plasticity of human circadian clocks and systems may be differentially affected by different paradigms of perinatal photoperiod exposure to the detriment of health in later life, including cancer development. Focusing on the example of cancer, we carry out a series of systematic literature reviews concerning perinatal light imprinting of circadian clocks and systems (PLICCS) in animal models, and concerning the risk of cancer development with the primary determinants of the perinatal photoperiod, namely season of birth or latitude of birth...
April 21, 2017: Chronobiology International
https://www.readbyqxmd.com/read/28430519/energy-resolved-ultrashort-delays-of-photoelectron-emission-clocked-by-orthogonal-two-color-laser-fields
#8
Xiaochun Gong, Cheng Lin, Feng He, Qiying Song, Kang Lin, Qinying Ji, Wenbin Zhang, Junyang Ma, Peifen Lu, Yunquan Liu, Heping Zeng, Weifeng Yang, Jian Wu
A phase-controlled orthogonal two-color (OTC) femtosecond laser pulse is employed to probe the time delay of photoelectron emission in the strong-field ionization of atoms. The OTC field spatiotemporally steers the emission dynamics of the photoelectrons and meanwhile allows us to unambiguously distinguish the main and sideband peaks of the above-threshold ionization spectrum. The relative phase shift between the main and sideband peaks, retrieved from the phase-of-phase of the photoelectron spectrum as a function of the laser phase, gradually decreases with increasing electron energy, and becomes zero for the fast electron which is mainly produced by the rescattering process...
April 7, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28430027/a-comparison-of-the-performance-of-2-5-to-3-5-year-old-children-without-disabilities-using-animated-and-cursor-based-scanning-in-a-contextual-scene
#9
John W McCarthy, Jamie B Boster
Although recent evidence suggests learning demands for children can be reduced by organizing augmentative and alternative communication (AAC) displays in contextual scenes, there is little evidence on how such scenes could be made accessible for children who cannot use direct selection. Using a line drawn scene of a living room, a traditional traveling cursor (a green outline of objects within the scene) was compared with sequential animation-logically matching the function of items in the scene (e.g., hands of a clock moving, a lamp turning on and off, etc...
April 21, 2017: Assistive Technology: the Official Journal of RESNA
https://www.readbyqxmd.com/read/28429400/the-circadian-clock-component-lhy-tells-a-plant-when-to-respond-photosynthetically-to-light-in-nature
#10
Youngsung Joo, Variluska Fragoso, Felipe Yon, Ian T Baldwin, Sang-Gyu Kim
The circadian clock is known to increase plant growth and fitness, and thought to prepare plants for photosynthesis at dawn and dusk; whether this happens in nature was unknown. We transformed the native tobacco, Nicotiana attenuata to silence two core clock components, NaLHY (irLHY) and NaTOC1 (irTOC1). We characterized growth and light-and dark-adapted photosynthetic rates (Ac ) throughout a 24 h day in empty vector-transformed (EV), irLHY, and irTOC1 plants in the field, and in NaPhyA-and NaPhyB1-silenced plants in the glasshouse...
April 21, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28429123/optical-coherence-tomography-angiography-vessel-density-mapping-at-various-retinal-layers-in-healthy-and-normal-tension-glaucoma-eyes
#11
Joong Won Shin, Kyung Rim Sung, Ji Yun Lee, Junki Kwon, Mincheol Seong
PURPOSE: To investigate peripapillary vessel density at various spatial locations and layers in healthy and normal tension glaucoma eyes using optical coherence tomography angiography (OCTA). METHODS: A commercial OCTA device (AngioPlex; Carl Zeiss Meditec) was used to image microvasculature in a 6 × 6-mm optic disc region. Vessel densities of superficial and deep retinal layers were calculated using an automatic thresholding algorithm. Vessel density maps were plotted by averaging individual angiogram images...
April 20, 2017: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/28428829/semivariogram-analysis-of-bone-images-implemented-on-fpga-architectures
#12
Mukul Shirvaikar, Yamuna Lagadapati, Xuanliang Dong
Osteoporotic fractures are a major concern for the healthcare of elderly and female populations. Early diagnosis of patients with a high risk of osteoporotic fractures can be enhanced by introducing second-order statistical analysis of bone image data using techniques such as variogram analysis. Such analysis is computationally intensive thereby creating an impediment for introduction into imaging machines found in common clinical settings. This paper investigates the fast implementation of the semivariogram algorithm, which has been proven to be effective in modeling bone strength, and should be of interest to readers in the areas of computer-aided diagnosis and quantitative image analysis...
March 2017: J Real Time Image Process
https://www.readbyqxmd.com/read/28425955/homomorphic-filtering-for-improving-time-synchronization-in-wireless-networks
#13
José María Castillo-Secilla, José Manuel Palomares, Fernando León, Joaquín Olivares
Wireless sensor networks are used to sample the environment in a distributed way. Therefore, it is mandatory for all of the measurements to be tightly synchronized in order to guarantee that every sensor is sampling the environment at the exact same instant of time. The synchronization drift gets bigger in environments suffering from temperature variations. Thus, this work is focused on improving time synchronization under deployments with temperature variations. The working hypothesis demonstrated in this work is that the clock skew of two nodes (the ratio of the real frequencies of the oscillators) is composed of a multiplicative combination of two main components: the clock skew due to the variations between the cut of the crystal of each oscillator and the clock skew due to the different temperatures affecting the nodes...
April 20, 2017: Sensors
https://www.readbyqxmd.com/read/28425940/circadian-clock-cell-division-and-cancer-from-molecules-to-organism
#14
REVIEW
Anton Shostak
As a response to environmental changes driven by the Earth's axial rotation, most organisms evolved an internal biological timer-the so called circadian clock-which regulates physiology and behavior in a rhythmic fashion. Emerging evidence suggests an intimate interplay between the circadian clock and another fundamental rhythmic process, the cell cycle. However, the precise mechanisms of this connection are not fully understood. Disruption of circadian rhythms has a profound impact on cell division and cancer development and, vice versa, malignant transformation causes disturbances of the circadian clock...
April 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28425528/chemomechanical-oscillations-with-a-non-redox-non-oscillatory-reaction
#15
J Horváth
Periodic length changes, over 20%, were sustained in a pH-responsive gel by associating the methylene glycol-sulphite OH-producing clock-reaction with variations of the exchange time induced between the core of the gel and a steady chemical environment. This is the first synergistic actuator that operates beyond acid-producing redox reactions.
April 20, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28425502/revealing-hidden-conformational-space-of-lov-protein-vivid-through-rigid-residue-scan-simulations
#16
Hongyu Zhou, Brian D Zoltowski, Peng Tao
VIVID(VVD) protein is a Light-Oxygen-Voltage(LOV) domain in circadian clock system. Upon blue light activation, a covalent bond is formed between VVD residue Cys108 and its cofactor flavin adenine dinucleotide(FAD), and prompts VVD switching from Dark state to Light state with significant conformational deviation. However, the mechanism of this local environment initiated global protein conformational change remains elusive. We employed a recently developed computational approach, rigid residue scan(RRS), to systematically probe the impact of the internal degrees of freedom in each amino acid residue of VVD on its overall dynamics by applying rigid body constraint on each residue in molecular dynamics simulations...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28425198/the-cell-adhesion-molecule-epha4-is-involved-in-circadian-clock-functions
#17
Silke Kiessling, Emma K O'Callaghan, Marlène Freyburger, Nicolas Cermakian, Valérie Mongrain
Circadian (~24 h) rhythms of cellular network plasticity in the central circadian clock, the suprachiasmatic nucleus (SCN), have been described. The neuronal network in the SCN regulates photic resetting of the circadian clock as well as stability of the circadian system during both entrained and constant conditions. EphA4, a cell adhesion molecule regulating synaptic plasticity by controlling connections of neurons and astrocytes, is expressed in the SCN. To address whether EphA4 plays a role in circadian photoreception and influences the neuronal network of the SCN, we have analysed circadian wheel-running behavior of EphA4 knockout (EphA4(-/-) ) mice under different light conditions and upon photic resetting, as well as their light-induced protein response in the SCN...
April 20, 2017: Genes, Brain, and Behavior
https://www.readbyqxmd.com/read/28423315/mir-132-212-modulates-seasonal-adaptation-and-dendritic-morphology-of-the-central-circadian-clock
#18
Lucia Mendoza-Viveros, Cheng-Kang Chiang, Jonathan L K Ong, Sara Hegazi, Arthur H Cheng, Pascale Bouchard-Cannon, Michael Fana, Christopher Lowden, Peng Zhang, Béatrice Bothorel, Matthew G Michniewicz, Stephen T Magill, Melissa M Holmes, Richard H Goodman, Valérie Simonneaux, Daniel Figeys, Hai-Ying M Cheng
The central circadian pacemaker, the suprachiasmatic nucleus (SCN), encodes day length information by mechanisms that are not well understood. Here, we report that genetic ablation of miR-132/212 alters entrainment to different day lengths and non-24 hr day-night cycles, as well as photoperiodic regulation of Period2 expression in the SCN. SCN neurons from miR-132/212-deficient mice have significantly reduced dendritic spine density, along with altered methyl CpG-binding protein (MeCP2) rhythms. In Syrian hamsters, a model seasonal rodent, day length regulates spine density on SCN neurons in a melatonin-independent manner, as well as expression of miR-132, miR-212, and their direct target, MeCP2...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28423013/mapping-the-co-localization-of-the-circadian-proteins-per2-and-bmal1-with-enkephalin-and-substance-p-throughout-the-rodent-forebrain
#19
Ariana Frederick, Jory Goldsmith, Nuria de Zavalia, Shimon Amir
Despite rhythmic expression of clock genes being found throughout the central nervous system, very little is known about their function outside of the suprachiasmatic nucleus. Determining the pattern of clock gene expression across neuronal subpopulations is a key step in understanding their regulation and how they may influence the functions of various brain structures. Using immunofluorescence and confocal microscopy, we quantified the co-expression of the clock proteins BMAL1 and PER2 with two neuropeptides, Substance P (SubP) and Enkephalin (Enk), expressed in distinct neuronal populations throughout the forebrain...
2017: PloS One
https://www.readbyqxmd.com/read/28422759/ryr2r420q-catecholaminergic-polymorphic-ventricular-tachycardia-mutation-induces-bradycardia-by-disturbing-the-coupled-clock-pacemaker-mechanism
#20
Yue Yi Wang, Pietro Mesirca, Elena Marqués-Sulé, Alexandra Zahradnikova, Olivier Villejoubert, Pilar D'Ocon, Cristina Ruiz, Diana Domingo, Esther Zorio, Matteo E Mangoni, Jean-Pierre Benitah, Ana María Gómez
Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a lethal genetic arrhythmia that manifests syncope or sudden death in children and young adults under stress conditions. CPVT patients often present bradycardia and sino-atrial node (SAN) dysfunction. However, the mechanism remains unclear. We analyzed SAN function in two CPVT families and in a novel knock-in (KI) mouse model carrying the RyR2R420Q mutation. Humans and KI mice presented slower resting heart rate. Accordingly, the rate of spontaneous intracellular Ca2+ ([Ca2+]i) transients was slower in KI mouse SAN preparations than in WT, without any significant alteration in the "funny" current (If )...
April 20, 2017: JCI Insight
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