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https://www.readbyqxmd.com/read/27932388/from-embryo-to-adult-pirna-mediated-silencing-throughout-germline-development-in-drosophila
#1
Pauline P Marie, Stéphane Ronsseray, Antoine Boivin
In metazoan germ cells, transposable element activity is repressed by small noncoding PIWI-associated RNAs (piRNAs). Numerous studies in Drosophila have elucidated the mechanism of this repression in the adult germline. However, when and how transposable element repression is established during germline development, has not been addressed. Here, we show that homology-dependent trans silencing is active in female primordial germ cells from late embryogenesis through pupal stages, and that genes related to the adult piRNA pathway are required for silencing during development...
December 7, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27928055/minimum-noise-production-of-translation-factor-eif4g-maps-to-a-mechanistically-determined-optimal-rate-control-window-for-protein-synthesis
#2
Xiang Meng, Helena Firczuk, Paola Pietroni, Richard Westbrook, Estelle Dacheux, Pedro Mendes, John E G McCarthy
Gene expression noise influences organism evolution and fitness. The mechanisms determining the relationship between stochasticity and the functional role of translation machinery components are critical to viability. eIF4G is an essential translation factor that exerts strong control over protein synthesis. We observe an asymmetric, approximately bell-shaped, relationship between the average intracellular abundance of eIF4G and rates of cell population growth and global mRNA translation, with peak rates occurring at normal physiological abundance...
December 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27927198/a-computational-method-for-the-investigation-of-multistable-systems-and-its-application-to-genetic-switches
#3
Miriam Leon, Mae L Woods, Alex J H Fedorec, Chris P Barnes
BACKGROUND: Genetic switches exhibit multistability, form the basis of epigenetic memory, and are found in natural decision making systems, such as cell fate determination in developmental pathways. Synthetic genetic switches can be used for recording the presence of different environmental signals, for changing phenotype using synthetic inputs and as building blocks for higher-level sequential logic circuits. Understanding how multistable switches can be constructed and how they function within larger biological systems is therefore key to synthetic biology...
December 7, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27923068/gene-expression-correlates-with-the-number-of-herpes-viral-genomes-initiating-infection-in-single-cells
#4
Efrat M Cohen, Oren Kobiler
Viral gene expression varies significantly among genetically identical cells. The sources of these variations are not well understood and have been suggested to involve both deterministic host differences and stochastic viral host interactions. For herpesviruses, only a limited number of incoming viral genomes initiate expression and replication in each infected cell. To elucidate the effect of this limited number of productively infecting genomes on viral gene expression in single cells, we constructed a set of fluorescence-expressing genetically tagged herpes recombinants...
December 6, 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27920382/adaptation-to-fragmentation-evolutionary-dynamics-driven-by-human-influences
#5
REVIEW
Pierre-Olivier Cheptou, Anna L Hargreaves, Dries Bonte, Hans Jacquemyn
Fragmentation-the process by which habitats are transformed into smaller patches isolated from each other-has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions...
January 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/27919068/capturing-pairwise-and-multi-way-chromosomal-conformations-using-chromosomal-walks
#6
Pedro Olivares-Chauvet, Zohar Mukamel, Aviezer Lifshitz, Omer Schwartzman, Noa Oded Elkayam, Yaniv Lubling, Gintaras Deikus, Robert P Sebra, Amos Tanay
Chromosomes are folded into highly compacted structures to accommodate physical constraints within nuclei and to regulate access to genomic information. Recently, global mapping of pairwise contacts showed that loops anchoring topological domains (TADs) are highly conserved between cell types and species. Whether pairwise loops synergize to form higher-order structures is still unclear. Here we develop a conformation capture assay to study higher-order organization using chromosomal walks (C-walks) that link multiple genomic loci together into proximity chains in human and mouse cells...
November 30, 2016: Nature
https://www.readbyqxmd.com/read/27917954/regional-variations-in-the-diversity-and-predicted-metabolic-potential-of-benthic-prokaryotes-in-coastal-northern-zhejiang-east-china-sea
#7
Kai Wang, Xiansen Ye, Huajun Zhang, Heping Chen, Demin Zhang, Lian Liu
Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27911933/driving-cells-to-the-desired-state-in-a-bimodal-distribution-through-manipulation-of-internal-noise-with-biologically-practicable-approaches
#8
Che-Chi Shu, Chen-Chao Yeh, Wun-Sin Jhang, Shih-Chiang Lo
The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end...
2016: PloS One
https://www.readbyqxmd.com/read/27911801/mechanical-bounds-to-transcriptional-noise
#9
Stuart A Sevier, David A Kessler, Herbert Levine
Over the past several decades it has been increasingly recognized that stochastic processes play a central role in transcription. Although many stochastic effects have been explained, the source of transcriptional bursting (one of the most well-known sources of stochasticity) has continued to evade understanding. Recent results have pointed to mechanical feedback as the source of transcriptional bursting, but a reconciliation of this perspective with preexisting views of transcriptional regulation is lacking...
December 6, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27909780/interrogating-the-variation-of-element-masses-and-distribution-patterns-in-single-cells-using-icp-ms-with-a-high-efficiency-cell-introduction-system
#10
Hailong Wang, Meng Wang, Bing Wang, Lingna Zheng, Hanqing Chen, Zhifang Chai, Weiyue Feng
Cellular heterogeneity is an inherent condition of cell populations, which results from stochastic expression of genes, proteins, and metabolites. The heterogeneity of individual cells can dramatically influence cellular decision-making and cell fate. So far, our knowledge about how the variation of endogenous metals and non-metals in individual eukaryotic cells is limited. In this study, ICP-MS equipped with a high efficiency cell introduction system (HECIS) was developed as a method of single-cell ICP-MS (SC-ICP-MS)...
December 1, 2016: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/27902489/effects-of-cell-cycle-noise-on-excitable-gene-circuits
#11
Alan Veliz-Cuba, Chinmaya Gupta, Matthew R Bennett, Krešimir Josić, William Ott
We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most likely occur just after cell division and that this concentration effect intensifies in the presence of transcriptional delay. We explain this concentration effect with a three-states stochastic model. For genetic oscillators, we quantify the temporal correlations between daughter cells induced by cell division. Temporal correlations must be captured properly in order to accurately quantify noise sources within gene networks...
November 30, 2016: Physical Biology
https://www.readbyqxmd.com/read/27893965/single-cell-and-single-molecule-analysis-of-gene-expression-regulation
#12
Maria Vera, Jeetayu Biswas, Adrien Senecal, Robert H Singer, Hye Yoon Park
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells...
November 23, 2016: Annual Review of Genetics
https://www.readbyqxmd.com/read/27893768/macromolecular-crowding-regulates-the-gene-expression-profile-by-limiting-diffusion
#13
Mahdi Golkaram, Stefan Hellander, Brian Drawert, Linda R Petzold
We seek to elucidate the role of macromolecular crowding in transcription and translation. It is well known that stochasticity in gene expression can lead to differential gene expression and heterogeneity in a cell population. Recent experimental observations by Tan et al. have improved our understanding of the functional role of macromolecular crowding. It can be inferred from their observations that macromolecular crowding can lead to robustness in gene expression, resulting in a more homogeneous cell population...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27884781/epigenetic-mechanisms-underlying-lifespan-and-age-related-effects-of-dietary-restriction-and-the-ketogenic-diet
#14
Cesar L Moreno, Charles V Mobbs
Aging constitutes the central risk factor for major diseases including many forms of cancer, neurodegeneration, and cardiovascular diseases. The aging process is characterized by both global and tissue-specific changes in gene expression across taxonomically diverse species. While aging has historically been thought to entail cell-autonomous, even stochastic changes, recent evidence suggests that modulation of this process can be hierarchal, wherein manipulations of nutrient-sensing neurons (e.g., in the hypothalamus) produce peripheral effects that may modulate the aging process itself...
November 21, 2016: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/27883889/inferring-cell-state-transition-dynamics-from-lineage-trees-and-endpoint-single-cell-measurements
#15
Sahand Hormoz, Zakary S Singer, James M Linton, Yaron E Antebi, Boris I Shraiman, Michael B Elowitz
As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees)...
November 23, 2016: Cell Systems
https://www.readbyqxmd.com/read/27879115/preface
#16
Avner Friedman, Mirosław Lachowicz, Urszula Ledzewicz, Monika Joanna Piotrowska, Zuzanna Szymanska
This volume was inspired by the topics presented at the international conference "Micro and Macro Systems in Life Sciences" which was held on Jun 8-12, 2015 in Będlewo, Poland. System biology is an approach which tries to understand how micro systems, at the molecular and cellular levels, affect macro systems such as organs, tissue and populations. Thus it is not surprising that a major theme of this volume evolves around cancer and its treatment. Articles on this topic include models for tumor induced angiogenesis, without and with delays, metastatic niche of the bone marrow, drug resistance and metronomic chemotherapy, and virotherapy of glioma...
February 1, 2017: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/27875323/estimating-intrinsic-and-extrinsic-noise-from-single-cell-gene-expression-measurements
#17
Audrey Qiuyan Fu, Lior Pachter
Gene expression is stochastic and displays variation ("noise") both within and between cells. Intracellular (intrinsic) variance can be distinguished from extracellular (extrinsic) variance by applying the law of total variance to data from two-reporter assays that probe expression of identically regulated gene pairs in single cells. We examine established formulas [Elowitz, M. B., A. J. Levine, E. D. Siggia and P. S. Swain (2002): "Stochastic gene expression in a single cell," Science, 297, 1183-1186.] for the estimation of intrinsic and extrinsic noise and provide interpretations of them in terms of a hierarchical model...
December 1, 2016: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/27872476/new-insights-into-the-immunopathogenesis-of-systemic-lupus-erythematosus
#18
REVIEW
George C Tsokos, Mindy S Lo, Patricia Costa Reis, Kathleen E Sullivan
The aetiology of systemic lupus erythematosus (SLE) is multifactorial, and includes contributions from the environment, stochastic factors, and genetic susceptibility. Great gains have been made in understanding SLE through the use of genetic variant identification, mouse models, gene expression studies, and epigenetic analyses. Collectively, these studies support the concept that defective clearance of immune complexes and biological waste (such as apoptotic cells), neutrophil extracellular traps, nucleic acid sensing, lymphocyte signalling, and interferon production pathways are all central to loss of tolerance and tissue damage...
November 22, 2016: Nature Reviews. Rheumatology
https://www.readbyqxmd.com/read/27869821/synthetic-recording-and-in-situ-readout-of-lineage-information-in-single-cells
#19
Kirsten L Frieda, James M Linton, Sahand Hormoz, Joonhyuk Choi, Ke-Huan K Chow, Zakary S Singer, Mark W Budde, Michael B Elowitz, Long Cai
Reconstructing the lineage relationships and dynamic event histories of individual cells within their native spatial context is a long-standing challenge in biology. Many biological processes of interest occur in optically opaque or physically inaccessible contexts, necessitating approaches other than direct imaging. Here, we describe a new synthetic system that enables cells to record lineage information and event histories in the genome in a format that can be subsequently read out in single cells in situ...
November 21, 2016: Nature
https://www.readbyqxmd.com/read/27858532/tracking-the-evolution-of-epialleles-during-neural-differentiation-and-brain-development-d-aspartate-oxidase-as-a-model-gene
#20
Ermanno Florio, Simona Keller, Lorena Coretti, Ornella Affinito, Giovanni Scala, Francesco Errico, Annalisa Fico, Francesca Boscia, Maria Josè Sisalli, Mafalda Giovanna Reccia, Gennaro Miele, Antonella Monticelli, Antonella Scorziello, Francesca Lembo, Luca Colucci-D'Amato, Gabriella Minchiotti, Vittorio Enrico Avvedimento, Alessandro Usiello, Sergio Cocozza, Lorenzo Chiariotti
We performed ultra-deep methylation analysis at single molecule level of the promoter region of developmentally regulated D-Aspartate oxidase (Ddo), as a model gene, during brain development and embryonic stem cell neural differentiation. Single molecule methylation analysis enabled us to establish the effective epiallele composition within mixed or pure brain cell populations. In this framework, an epiallele is defined as a specific combination of methylated CpG within Ddo locus and can represent the epigenetic haplotype revealing a cell-to-cell methylation heterogeneity...
November 18, 2016: Epigenetics: Official Journal of the DNA Methylation Society
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