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Stochastic gene

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https://www.readbyqxmd.com/read/28719044/symmetry-breaking-in-development-and-stochastic-gene-expression
#1
REVIEW
Jonathan R Chubb
The prevailing emphasis in developmental biology since the expansion of the molecular biology age has been that developmental decisions are instructive. A cell differentiates to become a specific cell type because it receives a signal, whereas its neighbor that does not receive the signal adopts a different fate. This emphasis has been generally accepted, largely because of the success of this view in tractable invertebrate model organisms, and the widespread similarities in molecular regulation to the development of more complex species...
July 18, 2017: Wiley Interdisciplinary Reviews. Developmental Biology
https://www.readbyqxmd.com/read/28716960/bacterial-tubulin-a-b-exhibit-polarized-growth-mixed-polarity-bundling-and-destabilization-by-gtp-hydrolysis
#2
César Díaz-Celis, Viviana I Risca, Felipe Hurtado, Jessica K Polka, Scott D Hansen, Daniel Maturana, Rosalba Lagos, R Dyche Mullins, Octavio Monasterio
Bacteria of the genus Prosthecobacter express homologs of eukaryotic α- and β-tubulin, called BtubA and BtubB, that have been observed to assemble into filaments in presence of GTP. BtubA/B polymers are proposed to be composed in vitro by two to six protofilaments, in contrast to in vivo where they have been reported to form 5-protofilaments tubes named bacterial microtubules (bMTs). The btubAB genes likely entered the Prosthecobacter lineage via horizontal gene transfer and may derive from an early ancestor of the modern eukaryotic microtubule (MT)...
July 17, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28714002/identification-of-key-genes-in-gram%C3%A2-positive-and-gram%C3%A2-negative-sepsis-using-stochastic-perturbation
#3
Zhenliang Li, Ying Zhang, Yaling Liu, Yanchun Liu, Youyi Li
Sepsis is an inflammatory response to pathogens (such as Gram‑positive and Gram‑negative bacteria), which has high morbidity and mortality in critically ill patients. The present study aimed to identify the key genes in Gram‑positive and Gram‑negative sepsis. GSE6535 was downloaded from Gene Expression Omnibus, containing 17 control samples, 18 Gram‑positive samples and 25 Gram‑negative samples. Subsequently, the limma package in R was used to screen the differentially expressed genes (DEGs). Hierarchical clustering was conducted for the specific DEGs in Gram‑negative and Gram‑negative samples using cluster software and the TreeView software...
July 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28709943/propagation-and-control-of-gene-expression-noise-with-non-linear-translation-kinetics
#4
J David Van Dyken
Gene expression is a stochastic process involving small numbers of molecules. As a consequence, cells in a clonal population vary randomly and sometimes substantially from one another in the concentration of mRNA and protein species, a phenomenon known as gene expression noise. Previous theoretical models of gene expression noise assumed that translation is first-order (linear) in mRNA concentration, leading to unfiltered propagation of mRNA noise to the protein level. Here I consider the biological ramifications of relaxing this assumption...
July 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28709241/careful-accounting-of-extrinsic-noise-in-protein-expression-reveals-correlations-among-its-sources
#5
John A Cole, Zaida Luthey-Schulten
In order to grow and replicate, living cells must express a diverse array of proteins, but the process by which proteins are made includes a great deal of inherent randomness. Understanding this randomness-whether it arises from the discrete stochastic nature of chemical reactivity ("intrinsic" noise), or from cell-to-cell variability in the concentrations of molecules involved in gene expression, or from the timings of important cell-cycle events like DNA replication and cell division ("extrinsic" noise)-remains a challenge...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28706991/multiplexed-gene-control-reveals-rapid-mrna-turnover
#6
Antoine Baudrimont, Sylvia Voegeli, Eduardo Calero Viloria, Fabian Stritt, Marine Lenon, Takeo Wada, Vincent Jaquet, Attila Becskei
The rates of mRNA synthesis and decay determine the mRNA expression level. The two processes are under coordinated control, which makes the measurements of these rates challenging, as evidenced by the low correlation among the methods of measurement of RNA half-lives. We developed a minimally invasive method, multiplexed gene control, to shut off expression of genes with controllable synthetic promoters. The method was validated by measuring the ratios of the nascent to mature mRNA molecules and by measuring the half-life with endogenous promoters that can be controlled naturally or through inserting short sequences that impart repressibility...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28700688/four-simple-rules-that-are-sufficient-to-generate-the-mammalian-blastocyst
#7
Silas Boye Nissen, Marta Perera, Javier Martin Gonzalez, Sophie M Morgani, Mogens H Jensen, Kim Sneppen, Joshua M Brickman, Ala Trusina
Early mammalian development is both highly regulative and self-organizing. It involves the interplay of cell position, predetermined gene regulatory networks, and environmental interactions to generate the physical arrangement of the blastocyst with precise timing. However, this process occurs in the absence of maternal information and in the presence of transcriptional stochasticity. How does the preimplantation embryo ensure robust, reproducible development in this context? It utilizes a versatile toolbox that includes complex intracellular networks coupled to cell-cell communication, segregation by differential adhesion, and apoptosis...
July 2017: PLoS Biology
https://www.readbyqxmd.com/read/28700218/response-of-soil-microbial-communities-to-elevated-antimony-and-arsenic-contamination-indicates-the-relationship-between-the-innate-microbiota-and-contaminant-fractions
#8
Weimin Sun, Enzong Xiao, Tangfu Xiao, Valdis Krumins, Qi Wang, Max M Haggblom, Yiran Dong, Song Tang, Min Hu, Baoqin Li, Bingqing Xia, Wei Liu
Mining of sulfide ore deposits containing metalloids, such as antimony and arsenic, has introduced serious soil contamination around the world, posing severe threats to food safety and human health. Hence, it is important to understand the behavior and composition of the microbial communities that control the mobilization or sequestration of these metal(loid)s. Here, we selected two sites in Southwest China with different levels of Sb and As contamination to study interactions among various Sb and As fractions and the soil microbiota, with a focus on the microbial response to metalloid contamination...
July 12, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28699625/mutation-supply-and-the-repeatability-of-selection-for-antibiotic-resistance
#9
Thomas van Dijk, Sungmin Hwang, Joachim Krug, Arjan Gm de Visser, Mark Peter Zwart
Whether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of antibiotic resistance gene TEM-1 β-lactamase in Escherichia coli, generated by error-prone PCR, were subjected to different antibiotic concentrations...
July 12, 2017: Physical Biology
https://www.readbyqxmd.com/read/28679222/information-based-measures-for-logical-stochastic-resonance-in-a-synthetic-gene-network-under-l%C3%A3-vy-flight-superdiffusion
#10
Juan Wu, Yong Xu, Haiyan Wang, Jürgen Kurths
We investigate the logical information transmission of a synthetic gene network under Lévy flight superdiffusion by an information-based methodology. We first present the stochastic synthetic gene network model driven by a square wave signal under Lévy noise caused by Lévy flight superdiffusion. Then, to quantify the potential of logical information transmission and logical stochastic resonance, we theoretically obtain an information-based methodology of the symbol error rate, the noise entropy, and the mutual information of the logical information transmission...
June 2017: Chaos
https://www.readbyqxmd.com/read/28676075/sgnesr-an-r-package-for-simulating-gene-expression-data-from-an-underlying-real-gene-network-structure-considering-delay-parameters
#11
Shailesh Tripathi, Jason Lloyd-Price, Andre Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib
BACKGROUND: sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles...
July 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28671948/stochasticity-in-the-enterococcal-sex-pheromone-response-revealed-by-quantitative-analysis-of-transcription-in-single-cells
#12
Rebecca J Breuer, Arpan Bandyopadhyay, Sofie A O'Brien, Aaron M T Barnes, Ryan C Hunter, Wei-Shou Hu, Gary M Dunny
In Enterococcus faecalis, sex pheromone-mediated transfer of antibiotic resistance plasmids can occur under unfavorable conditions, for example, when inducing pheromone concentrations are low and inhibiting pheromone concentrations are high. To better understand this paradox, we adapted fluorescence in situ hybridization chain reaction (HCR) methodology for simultaneous quantification of multiple E. faecalis transcripts at the single cell level. We present direct evidence for variability in the minimum period, maximum response level, and duration of response of individual cells to a specific inducing condition...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28671695/engineered-aavs-for-efficient-noninvasive-gene-delivery-to-the-central-and-peripheral-nervous-systems
#13
Ken Y Chan, Min J Jang, Bryan B Yoo, Alon Greenbaum, Namita Ravi, Wei-Li Wu, Luis Sánchez-Guardado, Carlos Lois, Sarkis K Mazmanian, Benjamin E Deverman, Viviana Gradinaru
Adeno-associated viruses (AAVs) are commonly used for in vivo gene transfer. Nevertheless, AAVs that provide efficient transduction across specific organs or cell populations are needed. Here, we describe AAV-PHP.eB and AAV-PHP.S, capsids that efficiently transduce the central and peripheral nervous systems, respectively. In the adult mouse, intravenous administration of 1 × 10(11) vector genomes (vg) of AAV-PHP.eB transduced 69% of cortical and 55% of striatal neurons, while 1 × 10(12) vg of AAV-PHP.S transduced 82% of dorsal root ganglion neurons, as well as cardiac and enteric neurons...
June 26, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28671686/the-methyltransferase-setdb1-regulates-a-large-neuron-specific-topological-chromatin-domain
#14
Yan Jiang, Yong-Hwee Eddie Loh, Prashanth Rajarajan, Teruyoshi Hirayama, Will Liao, Bibi S Kassim, Behnam Javidfar, Brigham J Hartley, Lisa Kleofas, Royce B Park, Benoit Labonte, Seok-Man Ho, Sandhya Chandrasekaran, Catherine Do, Brianna R Ramirez, Cyril J Peter, Julia T C W, Brian M Safaie, Hirofumi Morishita, Panos Roussos, Eric J Nestler, Anne Schaefer, Benjamin Tycko, Kristen J Brennand, Takeshi Yagi, Li Shen, Schahram Akbarian
We report locus-specific disintegration of megabase-scale chromosomal conformations in brain after neuronal ablation of Setdb1 (also known as Kmt1e; encodes a histone H3 lysine 9 methyltransferase), including a large topologically associated 1.2-Mb domain conserved in humans and mice that encompasses >70 genes at the clustered protocadherin locus (hereafter referred to as cPcdh). The cPcdh topologically associated domain (TAD(cPcdh)) in neurons from mutant mice showed abnormal accumulation of the transcriptional regulator and three-dimensional (3D) genome organizer CTCF at cryptic binding sites, in conjunction with DNA cytosine hypomethylation, histone hyperacetylation and upregulated expression...
July 3, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28667450/review-of-stochastic-hybrid-systems-with-applications-in-biological-systems-modeling-and-analysis
#15
REVIEW
Xiangfang Li, Oluwaseyi Omotere, Lijun Qian, Edward R Dougherty
Stochastic hybrid systems (SHS) have attracted a lot of research interests in recent years. In this paper, we review some of the recent applications of SHS to biological systems modeling and analysis. Due to the nature of molecular interactions, many biological processes can be conveniently described as a mixture of continuous and discrete phenomena employing SHS models. With the advancement of SHS theory, it is expected that insights can be obtained about biological processes such as drug effects on gene regulation...
December 2017: EURASIP Journal on Bioinformatics & Systems Biology
https://www.readbyqxmd.com/read/28667253/inhibitors-alter-the-stochasticity-of-regulatory-proteins-to-force-cells-to-switch-to-the-other-state-in-the-bistable-system
#16
Wun-Sin Jhang, Shih-Chiang Lo, Chen-Chao Yeh, Che-Chi Shu
The cellular behaviors under the control of genetic circuits are subject to stochastic fluctuations, or noise. The stochasticity in gene regulation, far from a nuisance, has been gradually appreciated for its unusual function in cellular activities. In this work, with Chemical Master Equation (CME), we discovered that the addition of inhibitors altered the stochasticity of regulatory proteins. For a bistable system of a mutually inhibitory network, such a change of noise led to the migration of cells in the bimodal distribution...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28665997/independent-regulation-of-gene-expression-level-and-noise-by-histone-modifications
#17
Shaohuan Wu, Ke Li, Yingshu Li, Tong Zhao, Ting Li, Yu-Fei Yang, Wenfeng Qian
The inherent stochasticity generates substantial gene expression variation among isogenic cells under identical conditions, which is frequently referred to as gene expression noise or cell-to-cell expression variability. Similar to (average) expression level, expression noise is also subject to natural selection. Yet it has been observed that noise is negatively correlated with expression level, which manifests as a potential constraint for simultaneous optimization of both. Here, we studied expression noise in human embryonic cells with computational analysis on single-cell RNA-seq data and in yeast with flow cytometry experiments...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28665016/biogeography-and-ecological-diversity-patterns-of-rare-and-abundant-bacteria-in-oil-contaminated-soils
#18
Shuo Jiao, Weimin Chen, Gehong Wei
Revealing the biogeographies and ecologies of rare and abundant microorganisms is crucial to understand ecosystem diversity and function. In this study, we investigated the biogeographic assemblies and ecological diversity patterns of rare and abundant bacteria in long-term oil-contaminated soils at intervals of 46-360 km by performing high-throughput sequencing of 16S rRNA genes. The results clearly revealed distinct distribution patterns for rare and abundant bacteria in soil samples. Rare taxa were unevenly distributed; however, abundant taxa were ubiquitous across all samples...
June 30, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28661893/exact-lower-and-upper-bounds-on-stationary-moments-in-stochastic-biochemical-systems
#19
Khem Raj Ghusinga, Cesar A Vargas-Garcia, Andrew Lamperski, Abhyudai Singh
In the stochastic description of biochemical reaction systems, the time evolution of statistical moments for species population counts is described by a linear dynamical system. However, except for some ideal cases (such as zero- and first-order reaction kinetics), the moment dynamics is underdetermined as lower-order moments depend upon higher-order moments. Here, we propose a novel method to find exact lower and upper bounds on stationary moments for a given arbitrary system of biochemical reactions. The method exploits the fact that statistical moments of any positive-valued random variable must satisfy some constraints that are compactly represented through the positive semidefiniteness of moment matrices...
June 29, 2017: Physical Biology
https://www.readbyqxmd.com/read/28656008/segregation-lag-in-polyploid-cells-of-the-pathogen-genus-borrelia-implications-for-antigenic-variation%C3%A2
#20
Christopher D Crowder, Richard L Denny, Alan G Barbour
Relapsing fever agents like Borrelia hermsii undergo multiphasic antigenic variation that is attributable to spontaneous DNA non-reciprocal transpositions at a particular locus in the genome. This genetic switch results in a new protein being expressed on the cell surface, allowing cells with that phenotype to escape prevailing immunity. But the switch occurs in only one of several genomes in these spirochetes, and a newly-switched gene is effectively "recessive" until homozygosity is achieved. The longer that descendants of the switched cell expressed both old and new proteins, the longer this lineage risks neutralization by antibody to the old protein...
June 2017: Yale Journal of Biology and Medicine
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