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https://www.readbyqxmd.com/read/28333289/the-role-of-daf-21-hsp90-in-mouth-form-plasticity-in-pristionchus-pacificus
#1
Bogdan Sieriebriennikov, Gabriel V Markov, Hanh Witte, Ralf J Sommer
Phenotypic plasticity is increasingly recognized to facilitate adaptive change in plants and animals, including insects, nematodes and vertebrates. Plasticity can occur as continuous or discrete (polyphenisms) variation. In social insects, e.g. in ants, some species have workers of distinct size classes while in other closely related species variation in size may be continuous. Despite the abundance of examples in nature, how discrete morphs are specified remains currently unknown. In theory, polyphenisms might require robustness, whereby the distribution of morphologies would be limited by the same mechanisms that execute buffering from stochastic perturbations, a function attributed to heat-shock proteins of the Hsp90 family...
March 13, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28325918/robust-analysis-of-fluxes-in-genome-scale-metabolic-pathways
#2
Michael MacGillivray, Amy Ko, Emily Gruber, Miranda Sawyer, Eivind Almaas, Allen Holder
Constraint-based optimization, such as flux balance analysis (FBA), has become a standard systems-biology computational method to study cellular metabolisms that are assumed to be in a steady state of optimal growth. The methods are based on optimization while assuming (i) equilibrium of a linear system of ordinary differential equations, and (ii) deterministic data. However, the steady-state assumption is biologically imperfect, and several key stoichiometric coefficients are experimentally inferred from situations of inherent variation...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320934/allele-specific-non-cg-dna-methylation-marks-domains-of-active-chromatin-in-female-mouse-brain
#3
Christopher L Keown, Joel B Berletch, Rosa Castanon, Joseph R Nery, Christine M Disteche, Joseph R Ecker, Eran A Mukamel
DNA methylation at gene promoters in a CG context is associated with transcriptional repression, including at genes silenced on the inactive X chromosome in females. Non-CG methylation (mCH) is a distinct feature of the neuronal epigenome that is differentially distributed between males and females on the X chromosome. However, little is known about differences in mCH on the active (Xa) and inactive (Xi) X chromosomes because stochastic X-chromosome inactivation (XCI) confounds allele-specific epigenomic profiling...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28297900/transient-dynamics-and-their-control-in-time-delay-autonomous-boolean-ring-networks
#4
Johannes Lohmann, Otti D'Huys, Nicholas D Haynes, Eckehard Schöll, Daniel J Gauthier
Biochemical systems with switch-like interactions, such as gene regulatory networks, are well modeled by autonomous Boolean networks. Specifically, the topology and logic of gene interactions can be described by systems of continuous piecewise-linear differential equations, enabling analytical predictions of the dynamics of specific networks. However, most models do not account for time delays along links associated with spatial transport, mRNA transcription, and translation. To address this issue, we have developed an experimental test bed to realize a time-delay autonomous Boolean network with three inhibitory nodes, known as a repressilator, and use it to study the dynamics that arise as time delays along the links vary...
February 2017: Physical Review. E
https://www.readbyqxmd.com/read/28291359/challenges-of-integrating-stochastic-dynamics-and-cryo-electron-tomograms-in-whole-cell-simulations
#5
Tyler M Earnest, Reika Watanabe, John E Stone, Julia Mahamid, Wolfgang Baumeister, Elizabeth Villa, Zaida Luthey-Schulten
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle timescales using data taken from -omics, single molecule experiments, and in vitro kinetics. By using real cell geometry derived from cryo-ET data, we have the opportunity to imbue these highly detailed structural data-frozen in time-with realistic biochemical dynamics and investigate how cell structure affects the behavior of the embedded chemical reaction network...
March 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28289838/a-stochastic-analysis-of-autoregulation-of-gene-expression
#6
Renaud Dessalles, Vincent Fromion, Philippe Robert
This paper analyzes, in the context of a prokaryotic cell, the stochastic variability of the number of proteins when there is a control of gene expression by an autoregulation scheme. The goal of this work is to estimate the efficiency of the regulation to limit the fluctuations of the number of copies of a given protein. The autoregulation considered in this paper relies mainly on a negative feedback: the proteins are repressors of their own gene expression. The efficiency of a production process without feedback control is compared to a production process with an autoregulation of the gene expression assuming that both of them produce the same average number of proteins...
March 13, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28288800/determining-the-limitations-and-benefits-of-noise-in-gene-regulation-and-signal-transduction-through-single-cell-microscopy-based-analysis
#7
REVIEW
Marie D Harton, Eric Batchelor
Stochastic fluctuations, termed "noise," in the level of biological molecules can greatly impact cellular functions. While biological noise can sometimes be detrimental, recent studies have provided an increasing number of examples in which biological noise can be functionally beneficial. Rather than provide an exhaustive review of the growing literature in this field, in this review we focus on single cell studies based on quantitative microscopy that have generated a deeper understanding of the sources, characteristics, limitations, and benefits of biological noise...
March 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28287985/policy-iteration-algorithm-for-optimal-control-of-stochastic-logical-dynamical-systems
#8
Yuhu Wu, Tielong Shen
This brief investigates the infinite horizon optimal control problem for stochastic multivalued logical dynamical systems with discounted cost. Applying the equivalent descriptions of stochastic logical dynamics in term of Markov decision process, the discounted infinite horizon optimal control problem is presented in an algebraic form. Then, employing the method of semitensor product of matrices and the increasing-dimension technique, a succinct algebraic form of the policy iteration algorithm is derived to solve the optimal control problem...
March 6, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28268604/learning-a-probabilistic-boolean-network-model-from-biological-pathways-and-time-series-expression-data
#9
Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra
The problem of inferring a stochastic model for gene regulatory networks is addressed here. The prior biological data includes biological pathways and time-series expression data. We propose a novel algorithm to use both of these data to construct a Probabilistic Boolean Network (PBN) which models the observed dynamics of genes with a high degree of precision. Our algorithm constructs a pathway tree and uses the time-series expression data to select an optimal level of tree, whose nodes are used to infer the PBN...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28263961/power-analysis-of-single-cell-rna-sequencing-experiments
#10
Valentine Svensson, Kedar Nath Natarajan, Lam-Ha Ly, Ricardo J Miragaia, Charlotte Labalette, Iain C Macaulay, Ana Cvejic, Sarah A Teichmann
Single-cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, thereby revealing new cell types and providing insights into developmental processes and transcriptional stochasticity. A key question is how the variety of available protocols compare in terms of their ability to detect and accurately quantify gene expression. Here, we assessed the protocol sensitivity and accuracy of many published data sets, on the basis of spike-in standards and uniform data processing...
March 6, 2017: Nature Methods
https://www.readbyqxmd.com/read/28259384/biofilms-microbial-cities-wherein-flow-shapes-competition
#11
Su Chuen Chew, Liang Yang
The phenotypic diversity in biofilms allows bacteria to adapt to changing environmental conditions. Stochastic gene expression and structural differentiation are believed to confer phenotypic diversity. However, two recent publications demonstrate how hydrodynamic flow and substrate topography can also alter the competitive outcomes of different bacterial phenotypes, increasing biofilm phenotypic variation.
March 1, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28257645/two-way-learning-with-one-way-supervision-for-gene-expression-data
#12
Monica H T Wong, David M Mutch, Paul D McNicholas
BACKGROUND: A family of parsimonious Gaussian mixture models for the biclustering of gene expression data is introduced. Biclustering is accommodated by adopting a mixture of factor analyzers model with a binary, row-stochastic factor loadings matrix. This particular form of factor loadings matrix results in a block-diagonal covariance matrix, which is a useful property in gene expression analyses, specifically in biomarker discovery scenarios where blood can potentially act as a surrogate tissue for other less accessible tissues...
March 4, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28257471/correction-application-of-stochastic-labeling-with-random-sequence-barcodes-for-simultaneous-quantification-and-sequencing-of-environmental-16s-rrna-genes
#13
Tatsuhiko Hoshino, Fumio Inagaki
[This corrects the article DOI: 10.1371/journal.pone.0169431.].
2017: PloS One
https://www.readbyqxmd.com/read/28256783/the-processive-kinetics-of-gene-conversion-in-bacteria
#14
Johan Paulsson, Meriem El Karoui, Monica Lindell, Diarmaid Hughes
Gene conversion, non-reciprocal transfer from one homologous sequence to another, is a major force in evolutionary dynamics, promoting co-evolution in gene families, and maintaining similarities between repeated genes. However, the properties of the transfer - where it initiates, how far it proceeds, and how the resulting conversion tracts are affected by mismatch repair - are not well understood. Here we use the duplicate tuf genes in Salmonella as a quantitatively tractable model system for gene conversion...
March 3, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28256642/identifying-the-optimal-anticancer-targets-from-the-landscape-of-a-cancer-immunity-interaction-network
#15
Chunhe Li
Cancer immunotherapy, an approach of targeting immune cells to attack tumor cells, has been suggested to be a promising way for cancer treatment recently. However, the successful application of this approach warrants a deeper understanding of the intricate interplay between cancer cells and the immune system. Especially, the mechanisms of immunotherapy remain elusive. In this work, we constructed a cancer-immunity interplay network by incorporating interactions among cancer cells and some representative immune cells, and uncovered the potential landscape of the cancer-immunity network...
March 3, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28254434/bimodal-expression-of-yeast-gal-genes-is-controlled-by-a-long-non-coding-rna-and-a-bifunctional-galactokinase
#16
Ioannis Zacharioudakis, Dimitris Tzamarias
Bimodality in gene expression can generate phenotypic heterogeneity facilitating fitness and growth of isogenic cell populations in suboptimal environments. We investigated the mechanism by which, in conditions of limiting galactose, yeast cell populations activate GAL genes in a bimodal fashion with a cell fraction expressing GAL genes (ON), while the rest subpopulation is kept at the non-expressing (OFF) state. We show that a long non-coding RNA (GAL10-ncRNA) crossing the bidirectional GAL1-10 promoter, decreases the rate by which single cells commit transition to the ON state without affecting the rate of GAL transcription per se in ON cells...
April 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28251874/prodigen-visualizing-the-probability-landscape-of-stochastic-gene-regulatory-networks-in-state-and-time-space
#17
Chihua Ma, Timothy Luciani, Anna Terebus, Jie Liang, G Elisabeta Marai
BACKGROUND: Visualizing the complex probability landscape of stochastic gene regulatory networks can further biologists' understanding of phenotypic behavior associated with specific genes. RESULTS: We present PRODIGEN (PRObability DIstribution of GEne Networks), a web-based visual analysis tool for the systematic exploration of probability distributions over simulation time and state space in such networks. PRODIGEN was designed in collaboration with bioinformaticians who research stochastic gene networks...
February 15, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28246332/metabolic-origins-of-spatial-organization-in-the-tumor-microenvironment
#18
Carlos Carmona-Fontaine, Maxime Deforet, Leila Akkari, Craig B Thompson, Johanna A Joyce, Joao B Xavier
The genetic and phenotypic diversity of cells within tumors is a major obstacle for cancer treatment. Because of the stochastic nature of genetic alterations, this intratumoral heterogeneity is often viewed as chaotic. Here we show that the altered metabolism of cancer cells creates predictable gradients of extracellular metabolites that orchestrate the phenotypic diversity of cells in the tumor microenvironment. Combining experiments and mathematical modeling, we show that metabolites consumed and secreted within the tumor microenvironment induce tumor-associated macrophages (TAMs) to differentiate into distinct subpopulations according to local levels of ischemia and their position relative to the vasculature...
February 28, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28226783/learning-a-probabilistic-boolean-network-model-from-biological-pathways-and-time-series-expression-data
#19
Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra, Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra, Vardaan Pahuja, Ritwik Kumar Layek, Pabitra Mitra
The problem of inferring a stochastic model for gene regulatory networks is addressed here. The prior biological data includes biological pathways and time-series expression data. We propose a novel algorithm to use both of these data to construct a Probabilistic Boolean Network (PBN) which models the observed dynamics of genes with a high degree of precision. Our algorithm constructs a pathway tree and uses the time-series expression data to select an optimal level of tree, whose nodes are used to infer the PBN...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28219439/rnas-competing-for-micrornas-mutually-influence-their-fluctuations-in-a-highly-non-linear-microrna-dependent-manner-in-single-cells
#20
Carla Bosia, Francesco Sgrò, Laura Conti, Carlo Baldassi, Davide Brusa, Federica Cavallo, Ferdinando Di Cunto, Emilia Turco, Andrea Pagnani, Riccardo Zecchina
BACKGROUND: Distinct RNA species may compete for binding to microRNAs (miRNAs). This competition creates an indirect interaction between miRNA targets, which behave as miRNA sponges and eventually influence each other's expression levels. Theoretical predictions suggest that not only the mean expression levels of targets but also the fluctuations around the means are coupled through miRNAs. This may result in striking effects on a broad range of cellular processes, such as cell differentiation and proliferation...
February 20, 2017: Genome Biology
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