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Stochastic gene

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https://www.readbyqxmd.com/read/28108432/living-on-the-edge-conservation-genetics-of-seven-thermophilous-plant-species-in-a-high-arctic-archipelago
#1
Siri Birkeland, Idunn Elisabeth Borgen Skjetne, Anne Krag Brysting, Reidar Elven, Inger Greve Alsos
Small, isolated, and/or peripheral populations are expected to harbour low levels of genetic variation and may therefore have reduced adaptability to environmental change, including climate warming. In the Arctic, global warming has already caused vegetation change across the region and is acting as a significant stressor on Arctic biodiversity. Many of the rare plants in the Arctic are relicts from early Holocene warm periods, but their ability to benefit from the current warming is dependent on the viability of their populations...
January 20, 2017: AoB Plants
https://www.readbyqxmd.com/read/28100346/-impact-of-cd137-cd137l-signaling-mediated-exocytosis-of-autophagosome-within-vascular-smooth-muscle-cells-on-the-formation-of-atherosclerotic-calcification
#2
B Li, X Y Li, W Zhong, C Shao, Z Q Wang, W Yuan, J C Yan
Objective: To explore whether CD137-CD137L signaling mediated exocytosis of autophagosome within vascular smooth muscle cells (VSMCs) could influence the formation of atherosclerotic calcification. Methods: Fifteen 8-week-old male ApoE(-/-)(C57BL/6J-KO) mice fed with high fat diet for 5 weeks were randomly divided into three groups by using stochastic indicator method as follows: control group, n=5; agonist-CD137 group: agonist-CD137 antibody 200 μg/2 weeks for 4 weeks, ip, n=5; anti-CD137 group: 200 μg anti-CD137 antibody+ 200 μg agonist-CD137 antibody/2 weeks for 4 weeks, ip, n=5...
January 25, 2017: Zhonghua Xin Xue Guan Bing za Zhi
https://www.readbyqxmd.com/read/28096490/comprehensive-essentiality-analysis-of-the-mycobacterium-tuberculosis-genome-via-saturating-transposon-mutagenesis
#3
Michael A DeJesus, Elias R Gerrick, Weizhen Xu, Sae Woong Park, Jarukit E Long, Cara C Boutte, Eric J Rubin, Dirk Schnappinger, Sabine Ehrt, Sarah M Fortune, Christopher M Sassetti, Thomas R Ioerger
: For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28088170/application-of-a-bayesian-dominance-model-improves-power-in-quantitative-trait-genome-wide-association-analysis
#4
Jörn Bennewitz, Christian Edel, Ruedi Fries, Theo H E Meuwissen, Robin Wellmann
BACKGROUND: Multi-marker methods, which fit all markers simultaneously, were originally tailored for genomic selection purposes, but have proven to be useful also in association analyses, especially the so-called BayesC Bayesian methods. In a recent study, BayesD extended BayesC towards accounting for dominance effects and improved prediction accuracy and persistence in genomic selection. The current study investigated the power and precision of BayesC and BayesD in genome-wide association studies by means of stochastic simulations and applied these methods to a dairy cattle dataset...
January 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28077620/mitogen-induced-distinct-epi-alleles-are-phosphorylated-at-either-h3s10-or-h3s28-depending-on-h3k27-acetylation
#5
Dilshad H Khan, Shannon Healy, Shihua He, Daniel Lichtensztejn, Ludger Klewes, Kiran L Sharma, Veronica Lau, Sabine Mai, Geneviève P Delcuve, James R Davie
Stimulation of the MAPK pathway results in mitogen- and stress-activated protein kinase 1/2 (MSK1/2)-catalyzed phosphorylation of histone H3 at serine 10 or 28 and expression of immediate-early (IE) genes. In 10T1/2 mouse fibroblasts, phosphorylation of H3S10 and H3S28 occurs on different H3 molecules and in different nuclear regions. Likewise, we show that mitogen-induced H3S10 and H3S28 phosphorylation occurs in separate pools in human primary fibroblasts. High-resolution imaging studies on both cell types have revealed that H3S10 and H3S28 phosphorylation events can be induced in a single cell but on different alleles, giving rise to H3S10ph and H3S28ph epi-alleles...
January 11, 2017: Molecular Biology of the Cell
https://www.readbyqxmd.com/read/28073363/swept-away-ocean-currents-and-seascape-features-influence-genetic-structure-across-the-18-000-km-indo-pacific-distribution-of-a-marine-invertebrate-the-black-lip-pearl-oyster-pinctada-margaritifera
#6
Monal M Lal, Paul C Southgate, Dean R Jerry, Cyprien Bosserelle, Kyall R Zenger
BACKGROUND: Genetic structure in many widely-distributed broadcast spawning marine invertebrates remains poorly understood, posing substantial challenges for their fishery management, conservation and aquaculture. Under the Core-Periphery Hypothesis (CPH), genetic diversity is expected to be highest at the centre of a species' distribution, progressively decreasing with increased differentiation towards outer range limits, as populations become increasingly isolated, fragmented and locally adapted...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28069947/first-passage-time-approach-to-controlling-noise-in-the-timing-of-intracellular-events
#7
Khem Raj Ghusinga, John J Dennehy, Abhyudai Singh
In the noisy cellular environment, gene products are subject to inherent random fluctuations in copy numbers over time. How cells ensure precision in the timing of key intracellular events despite such stochasticity is an intriguing fundamental problem. We formulate event timing as a first-passage time problem, where an event is triggered when the level of a protein crosses a critical threshold for the first time. Analytical calculations are performed for the first-passage time distribution in stochastic models of gene expression...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28057141/-research-on-spatiotemporal-spread-of-avian-influenza-a-h7n9-virus-based-on-discrete-geographic-information
#8
M X Wang, M Q Yuan, Y Fang
Objective: To establish a dynamic spatiotemporal spread modes of influenza A (H7N9) virus by using discrete geographic information and explore the spatiotemporal transmission of the virus. Methods: The gene sequences of H7N9 virus isolated from human in China, which were available from Global Initiative on Sharing Avian Influenza Data (GISAID), were used in alignment by using software BioEdit 7.0. Spatiotemporal spread model of H7N9 virus was established in a Bayesian statistical framework by using software BEAST 1...
November 10, 2016: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28053113/stochastic-models-of-gene-transcription-with-upstream-drives-exact-solution-and-sample-path-characterization
#9
Justine Dattani, Mauricio Barahona
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells with time-varying (stochastic or deterministic) transcription and degradation rates. Such rates can be understood as upstream cellular drives representing the effect of different aspects of the cellular environment. We show that the full solution of the master equation contains two components: a model-specific, upstream effective drive, which encapsulates the effect of cellular drives (e...
January 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28052327/tissue-disruption-increases-stochastic-gene-expression-thus-producing-tumours-cancer-initiation-without-driver-mutation
#10
REVIEW
Jean-Pascal Capp
Cancer research produced many paradoxical results in recent years. The reductionist approach now shows its limits. Considering the origin of the disease at the tissue level and increased stochastic gene expression (SGE) as a driving force, while admitting a role for genetic alterations in cancer progression, might solve these contradictions. Undifferentiated cells are characterized by open and accessible chromatin generating global and highly SGE (high expression noise) which is a hallmark of pluripotency, while differentiation is associated with progressive chromatin closing and decreased noise...
January 4, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28052139/application-of-stochastic-labeling-with-random-sequence-barcodes-for-simultaneous-quantification-and-sequencing-of-environmental-16s-rrna-genes
#11
Tatsuhiko Hoshino, Fumio Inagaki
Next-generation sequencing (NGS) is a powerful tool for analyzing environmental DNA and provides the comprehensive molecular view of microbial communities. For obtaining the copy number of particular sequences in the NGS library, however, additional quantitative analysis as quantitative PCR (qPCR) or digital PCR (dPCR) is required. Furthermore, number of sequences in a sequence library does not always reflect the original copy number of a target gene because of biases caused by PCR amplification, making it difficult to convert the proportion of particular sequences in the NGS library to the copy number using the mass of input DNA...
2017: PloS One
https://www.readbyqxmd.com/read/28039387/accounting-for-uncertainty-in-gene-tree-estimation-summary-coalescent-species-tree-inference-in-a-challenging-radiation-of-australian-lizards
#12
Mozes P K Blom, Jason G Bragg, Sally Potter, Craig Moritz
Accurate gene tree inference is an important aspect of species tree estimation in a summary-coalescent framework. Yet, in empirical studies, inferred gene trees differ in accuracy due to stochastic variation in phylogenetic signal between targeted loci. Empiricists should, therefore, examine the consistency of species tree inference, while accounting for the observed heterogeneity in gene tree resolution of phylogenomic data sets. Here, we assess the impact of gene tree estimation error on summary-coalescent species tree inference by screening [Formula: see text] exonic loci based on gene tree resolution prior to phylogenetic inference...
October 6, 2016: Systematic Biology
https://www.readbyqxmd.com/read/28038456/dna-methylation-landscape-of-hepatoblastomas-reveals-arrest-at-early-stages-of-liver-differentiation-and-cancer-related-alterations
#13
Mariana Maschietto, Tatiane Cristina Rodrigues, André Yoshiaki Kashiwabara, Érica Sara Souza de Araujo, Talita Ferreira Marques Aguiar, Cecilia Maria Lima da Costa, Isabela Werneck da Cunha, Luciana Dos Reis Vasques, Monica Cypriano, Helena Brentani, Silvia Regina Caminada de Toledo, Peter Lees Pearson, Dirce Maria Carraro, Carla Rosenberg, Ana Cristina Victorino Krepischi
Hepatoblastomas are uncommon embryonal liver tumors accounting for approximately 80% of childhood hepatic cancer. We hypothesized that epigenetic changes, including DNA methylation, could be relevant to hepatoblastoma onset. The methylomes of eight matched hepatoblastomas and non-tumoral liver tissues were characterized, and data were validated in an independent group (11 hepatoblastomas). In comparison to differentiated livers, hepatoblastomas exhibited a widespread and non-stochastic pattern of global low-level hypomethylation...
December 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/28028208/impact-of-mosquito-gene-drive-on-malaria-elimination-in-a-computational-model-with-explicit-spatial-and-temporal-dynamics
#14
Philip A Eckhoff, Edward A Wenger, H Charles J Godfray, Austin Burt
The renewed effort to eliminate malaria and permanently remove its tremendous burden highlights questions of what combination of tools would be sufficient in various settings and what new tools need to be developed. Gene drive mosquitoes constitute a promising set of tools, with multiple different possible approaches including population replacement with introduced genes limiting malaria transmission, driving-Y chromosomes to collapse a mosquito population, and gene drive disrupting a fertility gene and thereby achieving population suppression or collapse...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28027290/single-cell-based-analysis-highlights-a-surge-in-cell-to-cell-molecular-variability-preceding-irreversible-commitment-in-a-differentiation-process
#15
Angélique Richard, Loïs Boullu, Ulysse Herbach, Arnaud Bonnafoux, Valérie Morin, Elodie Vallin, Anissa Guillemin, Nan Papili Gao, Rudiyanto Gunawan, Jérémie Cosette, Ophélie Arnaud, Jean-Jacques Kupiec, Thibault Espinasse, Sandrine Gonin-Giraud, Olivier Gandrillon
In some recent studies, a view emerged that stochastic dynamics governing the switching of cells from one differentiation state to another could be characterized by a peak in gene expression variability at the point of fate commitment. We have tested this hypothesis at the single-cell level by analyzing primary chicken erythroid progenitors through their differentiation process and measuring the expression of selected genes at six sequential time-points after induction of differentiation. In contrast to population-based expression data, single-cell gene expression data revealed a high cell-to-cell variability, which was masked by averaging...
December 2016: PLoS Biology
https://www.readbyqxmd.com/read/28025271/no-evidence-that-protein-noise-induced-epigenetic-epistasis-constrains-gene-expression-evolution
#16
Gábor Boross, Balázs Papp
Changes in gene expression can affect phenotypes and therefore both its level and stochastic variability are frequently under selection. It has recently been proposed that epistatic interactions influence gene expression evolution: gene pairs where simultaneous knockout is more deleterious than expected should evolve reduced expression noise to avoid concurrent low expression of both proteins. In apparent support, yeast genes with many epistatic partners have low expression variation both among isogenic individuals and between species...
November 8, 2016: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28009485/heterogeneity-and-concordance-in-locus-specific-differentiation-and-introgression-between-species-of-towhees
#17
Sarah E Kingston, Thomas L Parchman, Zachariah Gompert, C Alex Buerkle, Michael J Braun
The maintenance or breakdown of reproductive isolation are observable outcomes of secondary contact between species. In cases where hybrids beyond the F1 are formed, the representation of each species' ancestry can vary dramatically among genomic regions. This genomic heterogeneity in ancestry and introgression can offer insight into evolutionary processes, particularly if introgression is compared in multiple hybrid zones. Similarly, considerable heterogeneity exists across the genome in the extent to which populations and species have diverged, reflecting the combined effects of different evolutionary processes on genetic variation...
December 23, 2016: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/28009264/noise-induces-hopping-between-nf-%C3%AE%C2%BAb-entrainment-modes
#18
Mathias Heltberg, Ryan A Kellogg, Sandeep Krishna, Savaş Tay, Mogens H Jensen
Oscillations and noise drive many processes in biology, but how both affect the activity of the transcription factor nuclear factor κB (NF-κB) is not understood. Here, we observe that when NF-κB oscillations are entrained by periodic tumor necrosis factor (TNF) inputs in experiments, NF-κB exhibits jumps between frequency modes, a phenomenon we call "cellular mode-hopping." By comparing stochastic simulations of NF-κB oscillations to deterministic simulations conducted inside and outside the chaotic regime of parameter space, we show that noise facilitates mode-hopping in all regimes...
December 21, 2016: Cell Systems
https://www.readbyqxmd.com/read/28003475/single-cell-transcriptomics-reveals-unanticipated-features-of-early-hematopoietic-precursors
#19
Jennifer Yang, Yoshiaki Tanaka, Montrell Seay, Zhen Li, Jiaqi Jin, Lana Xia Garmire, Xun Zhu, Ashley Taylor, Weidong Li, Ghia Euskirchen, Stephanie Halene, Yuval Kluger, Michael P Snyder, In-Hyun Park, Xinghua Pan, Sherman Morton Weissman
Molecular changes underlying stem cell differentiation are of fundamental interest. scRNA-seq on murine hematopoietic stem cells (HSC) and their progeny MPP1 separated the cells into 3 main clusters with distinct features: active, quiescent, and an un-characterized cluster. Induction of anemia resulted in mobilization of the quiescent to the active cluster and of the early to later stage of cell cycle, with marked increase in expression of certain transcription factors (TFs) while maintaining expression of interferon response genes...
December 20, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27997556/self-organizing-global-gene-expression-regulated-through-criticality-mechanism-of-the-cell-fate-change
#20
Masa Tsuchiya, Alessandro Giuliani, Midori Hashimoto, Jekaterina Erenpreisa, Kenichi Yoshikawa
BACKGROUND: A fundamental issue in bioscience is to understand the mechanism that underlies the dynamic control of genome-wide expression through the complex temporal-spatial self-organization of the genome to regulate the change in cell fate. We address this issue by elucidating a physically motivated mechanism of self-organization. PRINCIPAL FINDINGS: Building upon transcriptome experimental data for seven distinct cell fates, including early embryonic development, we demonstrate that self-organized criticality (SOC) plays an essential role in the dynamic control of global gene expression regulation at both the population and single-cell levels...
2016: PloS One
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