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https://www.readbyqxmd.com/read/29153325/genetic-and-epigenetic-strategies-potentiate-gal4-activation-to-enhance-fitness-in-recently-diverged-yeast-species
#1
Varun Sood, Jason H Brickner
Certain genes show more rapid reactivation for several generations following repression, a conserved phenomenon called epigenetic transcriptional memory. Following previous growth in galactose, GAL gene transcriptional memory confers a strong fitness benefit in Saccharomyces cerevisiae adapting to growth in galactose for up to 8 generations. A genetic screen for mutants defective for GAL gene memory revealed new insights into the molecular mechanism, adaptive consequences, and evolutionary history of memory...
November 9, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29130209/live-imaging-of-mrna-synthesis-in-drosophila
#2
Hernan G Garcia, Thomas Gregor
mRNA synthesis is one of the earliest readouts of the activity of a transcribed gene, which is of particular interest in the context of metazoan cell fate specification. These processes are intrinsically dynamic and stochastic, which makes in vivo single-cell measurements inevitable. Here, we present the application of a technology that has been widely used in single celled organisms to measure transcriptional activity in developing embryos of the fruit fly Drosophila melanogaster. The method allows for quantification of instantaneous polymerase occupancy of active gene loci and thereby enables the development and testing of models of gene regulation in development...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29129532/idiosyncratic-genome-degradation-in-a-bacterial-endosymbiont-of-periodical-cicadas
#3
Matthew A Campbell, Piotr Łukasik, Chris Simon, John P McCutcheon
When a free-living bacterium transitions to a host-beneficial endosymbiotic lifestyle, it almost invariably loses a large fraction of its genome [1, 2]. The resulting small genomes often become stable in size, structure, and coding capacity [3-5], as exemplified by Sulcia muelleri, a nutritional endosymbiont of cicadas. Sulcia's partner endosymbiont, Hodgkinia cicadicola, similarly remains co-linear in some cicadas diverged by millions of years [6, 7]. But in the long-lived periodical cicada Magicicada tredecim, the Hodgkinia genome has split into dozens of tiny, gene-sparse circles that sometimes reside in distinct Hodgkinia cells [8]...
November 2, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/29117534/building-predictive-models-of-genetic-circuits-using-the-principle-of-maximum-caliber
#4
Taylor Firman, Gábor Balázsi, Kingshuk Ghosh
Learning the underlying details of a gene network is a major challenge in cellular and synthetic biology. We address this challenge by building a chemical kinetic model that utilizes information encoded in the stochastic protein expression trajectories typically measured in experiments. The applicability of the proposed method is demonstrated in an auto-activating genetic circuit, a common motif in natural and synthetic gene networks. Our approach is based on the principle of maximum caliber (MaxCal)-a dynamical analog of the principle of maximum entropy-and builds a minimal model using only three constraints: 1) protein synthesis, 2) protein degradation, and 3) positive feedback...
November 7, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29116032/single-cell-transcriptomics-suggest-that-human-adipocyte-progenitor-cells-constitute-a-homogeneous-cell-population
#5
Juan R Acosta, Simon Joost, Kasper Karlsson, Anna Ehrlund, Xidan Li, Myriam Aouadi, Maria Kasper, Peter Arner, Mikael Rydén, Jurga Laurencikiene
Regulation of adipose tissue stem cells (ASCs) and adipogenesis impact the development of excess body fat-related metabolic complications. Animal studies have suggested the presence of distinct subtypes of ASCs with different differentiation properties. In addition, ASCs are becoming the biggest source of mesenchymal stem cells used in therapies, which requires deep characterization. Using unbiased single cell transcriptomics we aimed to characterize ASC populations in human subcutaneous white adipose tissue (scWAT)...
November 7, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29108019/stochastic-loss-and-gain-of-symmetric-divisions-in-the-c-elegans-epidermis-perturbs-robustness-of-stem-cell-number
#6
Dimitris Katsanos, Sneha L Koneru, Lamia Mestek Boukhibar, Nicola Gritti, Ritobrata Ghose, Peter J Appleford, Maria Doitsidou, Alison Woollard, Jeroen S van Zon, Richard J Poole, Michalis Barkoulas
Biological systems are subject to inherent stochasticity. Nevertheless, development is remarkably robust, ensuring the consistency of key phenotypic traits such as correct cell numbers in a certain tissue. It is currently unclear which genes modulate phenotypic variability, what their relationship is to core components of developmental gene networks, and what is the developmental basis of variable phenotypes. Here, we start addressing these questions using the robust number of Caenorhabditis elegans epidermal stem cells, known as seam cells, as a readout...
November 2017: PLoS Biology
https://www.readbyqxmd.com/read/29098989/an-application-of-the-krylov-fsp-ssa-method-to-parameter-fitting-with-maximum-likelihood
#7
Khanh N Dinh, Roger B Sidje
Monte Carlo methods such as the stochastic simulation algorithm (SSA) have traditionally been employed in gene regulation problems. However, there has been increasing interest to directly obtain the probability distribution of the molecules involved by solving the chemical master equation (CME). This requires addressing the curse of dimensionality that is inherent in most gene regulation problems. The finite state projection (FSP) seeks to address the challenge and there have been variants that further reduce the size of the projection or that accelerate the resulting matrix exponential...
November 3, 2017: Physical Biology
https://www.readbyqxmd.com/read/29098213/single-cell-analysis-of-early-antiviral-gene-expression-reveals-a-determinant-of-stochastic-ifnb1-expression
#8
Sultan Doğanay, Maurice Youzong Lee, Alina Baum, Jessie Peh, Sun-Young Hwang, Joo-Yeon Yoo, Paul J Hergenrother, Adolfo García-Sastre, Sua Myong, Taekjip Ha
RIG-I-like receptors (RLRs) are cytoplasmic sensors of viral RNA that trigger the signaling cascade that leads to type I interferon (IFN) production. Transcriptional induction of RLRs by IFN is believed to play the role of positive feedback to further amplify viral sensing. We found that RLRs and several other IFN-stimulated genes (ISGs) are induced early in viral infection independent of IFN. Expression of these early ISGs requires IRF3/IRF7 and is highly correlated amongst them. Simultaneous detection of mRNA of IFNB1, viral replicase, and ISGs revealed distinct populations of IFNB1 expressing and non-expressing cells which are highly correlated with the levels of early ISGs but are uncorrelated with IFN-dependent ISGs and viral gene expression...
November 13, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29097405/the-evolution-of-gene-specific-transcriptional-noise-is-driven-by-selection-at-the-pathway-level
#9
Gustavo Valadares Barroso, Natasa Puzovic, Julien Y Dutheil
Biochemical reactions within individual cells result from the interactions of molecules, typically in small numbers. Consequently, the inherent stochasticity of binding and diffusion processes generate noise along the cascade that leads to the synthesis of a protein from its encoding gene. As a result, isogenic cell populations display phenotypic variability even in homogeneous environments. The extent and consequences of this stochastic gene expression have only recently been assessed on a genome-wide scale, in particular owing to the advent of single cell transcriptomics...
November 2, 2017: Genetics
https://www.readbyqxmd.com/read/29093222/host-parasite-fluctuating-selection-in-the-absence-of-specificity
#10
Alex Best, Ben Ashby, Andy White, Roger Bowers, Angus Buckling, Britt Koskella, Mike Boots
Fluctuating selection driven by coevolution between hosts and parasites is important for the generation of host and parasite diversity across space and time. Theory has focused primarily on infection genetics, with highly specific 'matching-allele' frameworks more likely to generate fluctuating selection dynamics (FSD) than 'gene-for-gene' (generalist-specialist) frameworks. However, the environment, ecological feedbacks and life-history characteristics may all play a role in determining when FSD occurs. Here, we develop eco-evolutionary models with explicit ecological dynamics to explore the ecological, epidemiological and host life-history drivers of FSD...
November 15, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/29084263/a-plasmid-based-escherichia-coli-gene-expression-system-with-cell-to-cell-variation-below-the-extrinsic-noise-limit
#11
Zach Hensel
Experiments in synthetic biology and microbiology can benefit from protein expression systems with low cell-to-cell variability (noise) and expression levels precisely tunable across a useful dynamic range. Despite advances in understanding the molecular biology of microbial gene regulation, many experiments employ protein-expression systems exhibiting high noise and nearly all-or-none responses to induction. I present an expression system that incorporates elements known to reduce gene expression noise: negative autoregulation and bicistronic transcription...
2017: PloS One
https://www.readbyqxmd.com/read/29080679/sfrp2-dpp4-and-fmo1-lsp1-define-major-fibroblast-populations-in-human-skin
#12
Tracy Tabib, Christina Morse, Ting Wang, Wei Chen, Robert Lafyatis
Fibroblasts produce matrix, regulate inflammation, mediate reparative processes, and serve as pluripotent mesenchymal cells. Analyzing digested normal human skin by single cell RNA-seq (scRNA-seq), we explored different fibroblast populations. T-distributed stochastic neighbor embedding and clustering of scRNA-seq data from six biopsies revealed two major fibroblast populations, defined by distinct genes, including SFRP2 and FMO1, expressed exclusively by these two major fibroblast populations. Further subpopulations were defined within each of the SFRP2 and FMO1 populations, as well as five minor fibroblast populations, each expressing discrete genes: CRABP1, COL11A1, FMO2, PRG4 or C2ORF40...
October 25, 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/29077012/clinical-and-functional-assays-of-radiosensitivity-and-radiation-induced-second-cancer
#13
REVIEW
Mohammad Habash, Luis C Bohorquez, Elizabeth Kyriakou, Tomas Kron, Olga A Martin, Benjamin J Blyth
Whilst the near instantaneous physical interaction of radiation energy with living cells leaves little opportunity for inter-individual variation in the initial yield of DNA damage, all the downstream processes in how damage is recognized, repaired or resolved and therefore the ultimate fate of cells can vary across the population. In the clinic, this variability is observed most readily as rare extreme sensitivity to radiotherapy with acute and late tissue toxic reactions. Though some radiosensitivity can be anticipated in individuals with known genetic predispositions manifest through recognizable phenotypes and clinical presentations, others exhibit unexpected radiosensitivity which nevertheless has an underlying genetic cause...
October 27, 2017: Cancers
https://www.readbyqxmd.com/read/29065388/targeted-sequencing-of-clade-specific-markers-from-skin-microbiomes-for-forensic-human-identification
#14
Sarah E Schmedes, August E Woerner, Nicole M M Novroski, Frank R Wendt, Jonathan L King, Kathryn M Stephens, Bruce Budowle
The human skin microbiome is comprised of diverse communities of bacterial, eukaryotic, and viral taxa and contributes millions of additional genes to the repertoire of human genes, affecting human metabolism and immune response. Numerous genetic and environmental factors influence the microbiome composition and as such contribute to individual-specific microbial signatures which may be exploited for forensic applications. Previous studies have demonstrated the potential to associate skin microbial profiles collected from touched items to their individual owner, mainly using unsupervised methods from samples collected over short time intervals...
October 18, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/29058744/hybrid-deterministic-stochastic-simulation-of-complex-biochemical-systems
#15
Paola Lecca, Fabio Bagagiolo, Marina Scarpa
In a biological cell, cellular functions and the genetic regulatory apparatus are implemented and controlled by complex networks of chemical reactions involving genes, proteins, and enzymes. Accurate computational models are indispensable means for understanding the mechanisms behind the evolution of a complex system, not always explored with wet lab experiments. To serve their purpose, computational models, however, should be able to describe and simulate the complexity of a biological system in many of its aspects...
October 23, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29053427/canine-distemper-virus-in-a-wild-far-eastern-leopard-panthera-pardus-orientalis
#16
Nadezhda S Sulikhan, Martin Gilbert, Ekaterina Yu Blidchenko, Sergei V Naidenko, Galina V Ivanchuk, Tatiana Yu Gorpenchenko, Mikhail V Alshinetskiy, Elena I Shevtsova, John M Goodrich, John C M Lewis, Mikhail S Goncharuk, Olga V Uphyrkina, Vyatcheslav V Rozhnov, Sergey V Shedko, Denise McAloose, Dale G Miquelle
The critically endangered population of Far Eastern leopards (Panthera pardus orientalis) may number as few as 60 individuals and is at risk from stochastic processes such as infectious disease. During May 2015, a case of canine distemper virus (CDV) was diagnosed in a wild leopard exhibiting severe neurologic disease in the Russian territory of Primorskii Krai. Amplified sequences of the CDV hemagglutinin gene and phosphoprotein gene aligned within the Arctic-like clade of CDV, which includes viruses from elsewhere in Russia, China, Europe, and North America...
October 20, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/29046735/identification-of-a-key-role-of-widespread-epigenetic-drift-in-barrett-s-esophagus-and-esophageal-adenocarcinoma
#17
E Georg Luebeck, Kit Curtius, William D Hazelton, Sean Maden, Ming Yu, Prashanthi N Thota, Deepa T Patil, Amitabh Chak, Joseph E Willis, William M Grady
BACKGROUND: Recent studies have identified age-related changes in DNA methylation patterns in normal and cancer tissues in a process that is called epigenetic drift. However, the evolving patterns, functional consequences, and dynamics of epigenetic drift during carcinogenesis remain largely unexplored. Here we analyze the evolution of epigenetic drift patterns during progression from normal squamous esophagus tissue to Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) using 173 tissue samples from 100 (nonfamilial) BE patients, along with publically available datasets including The Cancer Genome Atlas (TCGA)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29045390/the-dynamics-of-molecular-evolution-over-60-000-generations
#18
Benjamin H Good, Michael J McDonald, Jeffrey E Barrick, Richard E Lenski, Michael M Desai
The outcomes of evolution are determined by a stochastic dynamical process that governs how mutations arise and spread through a population. However, it is difficult to observe these dynamics directly over long periods and across entire genomes. Here we analyse the dynamics of molecular evolution in twelve experimental populations of Escherichia coli, using whole-genome metagenomic sequencing at five hundred-generation intervals through sixty thousand generations. Although the rate of fitness gain declines over time, molecular evolution is characterized by signatures of rapid adaptation throughout the duration of the experiment, with multiple beneficial variants simultaneously competing for dominance in each population...
November 2, 2017: Nature
https://www.readbyqxmd.com/read/29042584/the-role-of-chromatin-density-in-cell-population-heterogeneity-during-stem-cell-differentiation
#19
Mahdi Golkaram, Jiwon Jang, Stefan Hellander, Kenneth S Kosik, Linda R Petzold
We incorporate three-dimensional (3D) conformation of chromosome (Hi-C) and single-cell RNA sequencing data together with discrete stochastic simulation, to explore the role of chromatin reorganization in determining gene expression heterogeneity during development. While previous research has emphasized the importance of chromatin architecture on activation and suppression of certain regulatory genes and gene networks, our study demonstrates how chromatin remodeling can dictate gene expression distribution by folding into distinct topological domains...
October 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29040384/selansi-a-toolbox-for-simulation-of-stochastic-gene-regulatory-networks
#20
Manuel Pájaro, Irene Otero-Muras, Carlos Vázquez, Antonio A Alonso
Motivation: Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort...
October 11, 2017: Bioinformatics
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