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https://www.readbyqxmd.com/read/28092361/designed-cell-consortia-as-fragrance-programmable-analog-to-digital-converters
#1
Marius Müller, Simon Ausländer, Andrea Spinnler, David Ausländer, Julian Sikorski, Marc Folcher, Martin Fussenegger
Synthetic biology advances the rational engineering of mammalian cells to achieve cell-based therapy goals. Synthetic gene networks have nearly reached the complexity of digital electronic circuits and enable single cells to perform programmable arithmetic calculations or to provide dynamic remote control of transgenes through electromagnetic waves. We designed a synthetic multilayered gaseous-fragrance-programmable analog-to-digital converter (ADC) allowing for remote control of digital gene expression with 2-bit AND-, OR- and NOR-gate logic in synchronized cell consortia...
January 16, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28072846/a-hypothesis-testing-based-method-for-normalization-and-differential-expression-analysis-of-rna-seq-data
#2
Yan Zhou, Guochang Wang, Jun Zhang, Han Li
Next-generation sequencing technologies have made RNA sequencing (RNA-seq) a popular choice for measuring gene expression level. To reduce the noise of gene expression measures and compare them between several conditions or samples, normalization is an essential step to adjust for varying sample sequencing depths and other unwanted technical effects. In this paper, we develop a novel global scaling normalization method by employing the available knowledge of housekeeping genes. We formulate the problem from the hypothesis testing perspective and find an optimal scaling factor that minimizes the deviation between the empirical and the nominal type I error...
2017: PloS One
https://www.readbyqxmd.com/read/28069947/first-passage-time-approach-to-controlling-noise-in-the-timing-of-intracellular-events
#3
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/28069594/sigmod-an-exact-and-efficient-method-to-identify-a-strongly-interconnected-disease-associated-module-in-a-gene-network
#4
Yuanlong Liu, Myriam Brossard, Damian Roqueiro, Patricia Margaritte-Jeannin, Chloé Sarnowski, Emmanuelle Bouzigon, Florence Demenais
MOTIVATION: Apart from single marker-based tests classically used in genome-wide association studies (GWAS), network-assisted analysis has become a promising approach to identify a set of genes associated with disease. To date, most network-assisted methods aim at finding genes connected in a background network, whatever the density or strength of their connections. This can hamper the findings as sparse connections are non-robust against noise from either the GWAS results or the network resource...
January 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28068481/micrornas-and-periodontal-homeostasis
#5
X Luan, X Zhou, J Trombetta-eSilva, M Francis, A K Gaharwar, P Atsawasuwan, T G H Diekwisch
MicroRNAs (miRNAs) are a group of small RNAs that control gene expression in all aspects of eukaryotic life, primarily through RNA silencing mechanisms. The purpose of the present review is to introduce key miRNAs involved in periodontal homeostasis, summarize the mechanisms by which they affect downstream genes and tissues, and provide an introduction into the therapeutic potential of periodontal miRNAs. In general, miRNAs function synergistically to fine-tune the regulation of biological processes and to remove expression noise rather than by causing drastic changes in expression levels...
January 1, 2017: Journal of Dental Research
https://www.readbyqxmd.com/read/28068403/normalisation-against-circadian-and-age-related-disturbances-enables-robust-detection-of-gene-expression-changes-in-liver-of-aged-mice
#6
Sara S Fonseca Costa, Daniel Wegmann, Jürgen A Ripperger
The expression of some genes is affected by age. To detect such age-related changes, their expression levels are related to constant marker genes. However, transcriptional noise increasing with advancing age renders difficult the identification of real age-related changes because it may affect the marker genes as well. Here, we report a selection procedure for genes appropriate to normalise the mouse liver transcriptome under various conditions including age. These genes were chosen from an initial set of 16 candidate genes defined based on a RNA-sequencing experiment and published literature...
2017: PloS One
https://www.readbyqxmd.com/read/28065937/dynomics-to-identify-delays-and-co-expression-patterns-across-time-course-experiments
#7
Jasmin Straube, Bevan Emma Huang, Kim-Anh Lê Cao
Dynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and proteins) across time. Integration of such data aims to identify molecules that show similar expression changes over time; such molecules may be co-regulated and thus involved in similar biological processes. Combining data sources presents a systematic approach to study molecular behaviour. It can compensate for missing data in one source, and can reduce false positives when multiple sources highlight the same pathways...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28060821/customized-regulation-of-diverse-stress-response-genes-by-the-multiple-antibiotic-resistance-activator-mara
#8
Nicholas A Rossi, Mary J Dunlop
Stress response networks frequently have a single upstream regulator that controls many downstream genes. However, the downstream targets are often diverse, therefore it remains unclear how their expression is specialized when under the command of a common regulator. To address this, we focused on a stress response network where the multiple antibiotic resistance activator MarA from Escherichia coli regulates diverse targets ranging from small RNAs to efflux pumps. Using single-cell experiments and computational modeling, we showed that each downstream gene studied has distinct activation, noise, and information transmission properties...
January 6, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28060339/the-chip-exo-method-identifying-protein-dna-interactions-with-near-base-pair-precision
#9
Andrea A Perreault, Bryan J Venters
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise...
December 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28056268/-investigation-into-the-relationship-between-mitochondrial-12-s-rrna-gene-trna-gene-and-cytochrome-oxidase-%C3%A2-gene-variations-and-the-risk-of-noise-induced-hearing-loss
#10
J Jiao, G Z Gu, G S Chen, Y H Li, H L Zhang, Q Y Yang, X R Xu, W H Zhou, H Wu, L H He, Y X Zheng, S F Yu
Objective: To explore the relationship between mitochondrial 12 S rRNA gene variation, tRNA gene variation and cytochrome oxidase Ⅱ gene point mutations and the risk of noise-induced hearing loss (NIHL). Methods: A nested case-control study was performed that followed a cohort of 7 445 noise-exposed workers in a steel factory in Henan province, China, from January 1, 2006 to December 31, 2015. Subjects whose average hearing threshold was more than 40 dB(A) in high frequency were defined as the case group, and subjects whose average hearing threshold was less than 35 dB(A) in high frequency and less than 25 dB (A) in speech frequency were defined as the control group...
January 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28056267/-association-between-eye-absent-homolog-4-gene-polymorphisms-and-occupational-noise-induced-hearing-loss
#11
Q Y Yang, X R Xu, J Jiao, Y X Zheng, L H He, S F Yu, G Z Gu, G S Chen, W H Zhou, H Wu, Y H Li, H L Zhang, Z R Zhang
Objective: To identify the association between genetic polymorphisms in the eye absent homolog 4 (EYA4) gene and noise-induced hearing loss (NIHL). Method: A nested case control study was conducted based on a cohort of noise-exposed subjects. In total, 292 cases were selected from a steel factory from 6 297 subjects during Jan 1, 2006 to Dec 12, 2015,who had an average hearing threshold of more than 40 dB(A); 584 matched control subjects for each case were designated on the basis of matched criteria including same gender, age (±5 years) and duration of exposure to noise (±2 years)...
January 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28056266/-association-between-variations-in-protocadherin-15-gene-and-occupational-noise-induced-hearing-loss
#12
X R Xu, Q Y Yang, J Jiao, Y X Zheng, L H He, S F Yu, G Z Gu, G S Chen, W H Zhou, H Wu, Y H Li, H L Zhang, Z R Zhang
Objective: The aim of this study was to investigate whether genetic variability in the protocadherin 15 (PCDH15) gene may correspond with increased susceptibility to noise-induced hearing loss (NIHL) in a Chinese population. Methods: A nested case-control study was performed that followed a cohort of 7 445 noise-exposed workers in a steel factory of Henan province in China from January 1, 2006 to December 31, 2015. In this study, 394 cases who had an average hearing threshold of more than 40 dB (A) in high frequency were defined as the case group, and 721 controls who had an average hearing threshold of less than 35 dB (A) in high frequency and less than 25 dB (A) in speech frequency were defined as the control group...
January 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/28056182/noise-stress-induces-an-epidermal-growth-factor-receptor-xeroderma-pigmentosum-a-response-in-the-auditory-nerve
#13
O'neil W Guthrie
In response to toxic stressors, cancer cells defend themselves by mobilizing one or more epidermal growth factor receptor (EGFR) cascades that employ xeroderma pigmentosum-A (XPA) to repair damaged genes. Recent experiments discovered that neurons within the auditory nerve exhibit basal levels of EGFR+XPA co-expression. This finding implied that auditory neurons in particular or neurons in general have the capacity to mobilize an EGFR+XPA defense. Therefore, the current study tested the hypothesis that noise stress would alter the expression pattern of EGFR/XPA within the auditory nerve...
December 1, 2016: Journal of Histochemistry and Cytochemistry: Official Journal of the Histochemistry Society
https://www.readbyqxmd.com/read/28053113/stochastic-models-of-gene-transcription-with-upstream-drives-exact-solution-and-sample-path-characterization
#14
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
#15
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/28045081/batch-effects-and-the-effective-design-of-single-cell-gene-expression-studies
#16
Po-Yuan Tung, John D Blischak, Chiaowen Joyce Hsiao, David A Knowles, Jonathan E Burnett, Jonathan K Pritchard, Yoav Gilad
Single-cell RNA sequencing (scRNA-seq) can be used to characterize variation in gene expression levels at high resolution. However, the sources of experimental noise in scRNA-seq are not yet well understood. We investigated the technical variation associated with sample processing using the single-cell Fluidigm C1 platform. To do so, we processed three C1 replicates from three human induced pluripotent stem cell (iPSC) lines. We added unique molecular identifiers (UMIs) to all samples, to account for amplification bias...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28043818/molecular-noise-can-minimize-the-collective-sensitivity-of-a-clonal-heterogeneous-cell-population
#17
Marzo Forment, Guillermo Rodrigo
It is now widely accepted that molecular noise, rather than be always detrimental, introduces in many circumstances the required boost to reach fundamental cellular activities or strategies otherwise unattainable. In threshold-like genetic systems, molecular noise serves to generate heterogeneous responses in a clonal population, also in a tissue, due to cell-to-cell variability. Here, we derived a mathematical framework from which we could study in detail this effect. We focused on a minimal decision-making gene circuit implemented as a transcriptional positive-feedback loop...
December 31, 2016: Journal of Theoretical Biology
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
#18
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/28034617/cochlear-hair-cell-regeneration-after-noise-induced-hearing-loss-does-regeneration-follow-development
#19
REVIEW
Fei Zheng, Jian Zuo
Noise-induced hearing loss (NIHL) affects a large number of military personnel and civilians. Regenerating inner-ear cochlear hair cells (HCs) is a promising strategy to restore hearing after NIHL. In this review, we first summarize recent transcriptome profile analysis of zebrafish lateral lines and chick utricles where spontaneous HC regeneration occurs after HC damage. We then discuss recent studies in other mammalian regenerative systems such as pancreas, heart and central nervous system. Both spontaneous and forced HC regeneration occurs in mammalian cochleae in vivo involving proliferation and direct lineage conversion...
December 26, 2016: Hearing Research
https://www.readbyqxmd.com/read/28025271/no-evidence-that-protein-noise-induced-epigenetic-epistasis-constrains-gene-expression-evolution
#20
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
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