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Gene noise

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https://www.readbyqxmd.com/read/28918301/mathematical-fundamentals-for-the-noise-immunity-of-the-genetic-code
#1
Elena Fimmel, Lutz Strüngmann
Symmetry is one of the essential and most visible patterns that can be seen in nature. Starting from the left-right symmetry of the human body, all types of symmetry can be found in crystals, plants, animals and nature as a whole. Similarly, principals of symmetry are also some of the fundamental and most useful tools in modern mathematical natural science that play a major role in theory and applications. As a consequence, it is not surprising that the desire to understand the origin of life, based on the genetic code, forces us to involve symmetry as a mathematical concept...
September 13, 2017: Bio Systems
https://www.readbyqxmd.com/read/28916451/switches-in-a-genetic-regulatory-system-under-multiplicative-non-gaussian-noise
#2
Xi Chen, Yan-Mei Kang, Yu-Xuan Fu
The non-Gaussian noise is multiplicatively introduced to model the universal fluctuation in the gene regulation of the bacteriophage λ. To investigate the key effect of non-Gaussian noise on the genetic on/off switch dynamics from the viewpoint of quantitative analysis, we employ the high-order perturbation expansion to deduce the stationary probability density of repressor concentration and the mean first passage time from low concentration to high concentration and vice versa. The occupation probability of different concentration states can be estimated from the height and shape of the peaks of the stationary probability density, which could be used to determine the overall expression level...
September 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28912685/neural-code-neural-self-information-theory-on-how-cell-assembly-code-rises-from-spike-time-and-neuronal-variability
#3
Meng Li, Joe Z Tsien
A major stumbling block to cracking the real-time neural code is neuronal variability - neurons discharge spikes with enormous variability not only across trials within the same experiments but also in resting states. Such variability is widely regarded as a noise which is often deliberately averaged out during data analyses. In contrast to such a dogma, we put forth the Neural Self-Information Theory that neural coding is operated based on the self-information principle under which variability in the time durations of inter-spike-intervals (ISI), or neuronal silence durations, is self-tagged with discrete information...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28903980/uniform-gene-expression-in-embryos-is-achieved-by-temporal-averaging-of-transcription-noise
#4
L Carine Stapel, Christoph Zechner, Nadine L Vastenhouw
Transcription is often stochastic. This is seemingly incompatible with the importance of gene expression during development. Here we show that during zebrafish embryogenesis, transcription activation is stochastic due to (1) genes acquiring transcriptional competence at different times in different cells, (2) differences in cell cycle stage between cells, and (3) the stochastic nature of transcription. Initially, stochastic transcription causes large cell-to-cell differences in transcript levels. However, variability is reduced by lengthening cell cycles and the accumulation of transcription events in each cell...
September 13, 2017: Genes & Development
https://www.readbyqxmd.com/read/28900417/integrated-translatome-and-proteome-approach-for-accurate-portraying-of-widespread-multifunctional-aspects-of-trichoderma
#5
REVIEW
Vivek Sharma, Richa Salwan, P N Sharma, Arvind Gulati
Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28895892/a-robotic-platform-for-corn-seedling-morphological-traits-characterization
#6
Hang Lu, Lie Tang, Steven A Whitham, Yu Mei
Crop breeding plays an important role in modern agriculture, improving plant performance, and increasing yield. Identifying the genes that are responsible for beneficial traits greatly facilitates plant breeding efforts for increasing crop production. However, associating genes and their functions with agronomic traits requires researchers to observe, measure, record, and analyze phenotypes of large numbers of plants, a repetitive and error-prone job if performed manually. An automated seedling phenotyping system aimed at replacing manual measurement, reducing sampling time, and increasing the allowable work time is thus highly valuable...
September 12, 2017: Sensors
https://www.readbyqxmd.com/read/28881987/efficient-simulation-of-intrinsic-extrinsic-and-external-noise-in-biochemical-systems
#7
Dennis Pischel, Kai Sundmacher, Robert J Flassig
Motivation: Biological cells operate in a noisy regime influenced by intrinsic, extrinsic and external noise, which leads to large differences of individual cell states. Stochastic effects must be taken into account to characterize biochemical kinetics accurately. Since the exact solution of the chemical master equation, which governs the underlying stochastic process, cannot be derived for most biochemical systems, approximate methods are used to obtain a solution. Results: In this study, a method to efficiently simulate the various sources of noise simultaneously is proposed and benchmarked on several examples...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878825/rna-sequence-data-normalization-through-in-silico-prediction-of-reference-genes-the-bacterial-response-to-dna-damage-as-case-study
#8
Bork A Berghoff, Torgny Karlsson, Thomas Källman, E Gerhart H Wagner, Manfred G Grabherr
BACKGROUND: Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes...
2017: BioData Mining
https://www.readbyqxmd.com/read/28877184/microgravity-validation-of-a-novel-system-for-rna-isolation-and-multiplex-quantitative-real-time-pcr-analysis-of-gene-expression-on-the-international-space-station
#9
Macarena Parra, Jimmy Jung, Travis D Boone, Luan Tran, Elizabeth A Blaber, Mark Brown, Matthew Chin, Tori Chinn, Jacob Cohen, Robert Doebler, Dzung Hoang, Elizabeth Hyde, Matthew Lera, Louie T Luzod, Mark Mallinson, Oana Marcu, Youssef Mohamedaly, Antonio J Ricco, Kathleen Rubins, Gregory D Sgarlato, Rafael O Talavera, Peter Tong, Eddie Uribe, Jeffrey Williams, Diana Wu, Rukhsana Yousuf, Charles S Richey, Julie Schonfeld, Eduardo A C Almeida
The International Space Station (ISS) National Laboratory is dedicated to studying the effects of space on life and physical systems, and to developing new science and technologies for space exploration. A key aspect of achieving these goals is to operate the ISS National Lab more like an Earth-based laboratory, conducting complex end-to-end experimentation, not limited to simple microgravity exposure. Towards that end NASA developed a novel suite of molecular biology laboratory tools, reagents, and methods, named WetLab-2, uniquely designed to operate in microgravity, and to process biological samples for real-time gene expression analysis on-orbit...
2017: PloS One
https://www.readbyqxmd.com/read/28865426/robust-gene-selection-methods-using-weighting-schemes-for-microarray-data-analysis
#10
Suyeon Kang, Jongwoo Song
BACKGROUND: A common task in microarray data analysis is to identify informative genes that are differentially expressed between two different states. Owing to the high-dimensional nature of microarray data, identification of significant genes has been essential in analyzing the data. However, the performances of many gene selection techniques are highly dependent on the experimental conditions, such as the presence of measurement error or a limited number of sample replicates. RESULTS: We have proposed new filter-based gene selection techniques, by applying a simple modification to significance analysis of microarrays (SAM)...
September 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28862994/fc1000-normalized-gene-expression-changes-of-systematically-perturbed-human-cells
#11
Ingrid M Lönnstedt, Sven Nelander
The systematic study of transcriptional responses to genetic and chemical perturbations in human cells is still in its early stages. The largest available dataset to date is the newly released L1000 compendium. With its 1.3 million gene expression profiles of treated human cells it offers many opportunities for biomedical data mining, but also data normalization challenges of new dimensions. We developed a novel and practical approach to obtain accurate estimates of fold change response profiles from L1000, based on the RUV (Remove Unwanted Variation) statistical framework...
September 26, 2017: Statistical Applications in Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28852133/a-kinetic-model-of-multiple-phenotypic-states-for-breast-cancer-cells
#12
Kang Qiu, Kai-Fu Gao, Li-Jian Yang, Zhao-Kang Zhang, Ran Wang, Hui-Shu Ma, Ya Jia
Quantitative modeling of microscopic genes regulatory mechanisms in an individual cell is a crucial step towards understanding various macroscopic physiological phenomena of cell populations. Based on the regulatory mechanisms of genes zeb1 and cdh1 in the growth and development of breast cancer cells, we propose a kinetic model at the level of single cell. By constructing the effective landscape of underlying stationary probability for the genes expressions, it is found that (i) each breast cancer cell has three phenotypic states (i...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28851906/a-total-variation-constrained-permutation-model-for-revealing-common-copy-number-patterns
#13
Yue Zhang, Yiu-Ming Cheung, Weifeng Su
Variations in DNA copy number carry important information on genome evolution and regulation of DNA replication in cancer cells. The rapid development of single-cell sequencing technology enables exploration of gene-expression heterogeneity among single cells, providing important information on cell evolution. Evolutionary relationships in accumulated sequence data can be visualized by adjacent positioning of similar cells so that similar copy-number profiles are shown by block patterns. However, single-cell DNA sequencing data usually have low amount of starting genome, which requires an extra step of amplification to accumulate sufficient samples, introducing noise and making regular pattern-finding challenging...
August 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28844789/protocadherin-10-alters-%C3%AE-oscillations-amino-acid-levels-and-their-coupling-baclofen-partially-restores-these-oscillatory-deficits
#14
Russell G Port, Christopher Gajewski, Elizabeth Krizman, Holly C Dow, Shinji Hirano, Edward S Brodkin, Gregory C Carlson, Michael B Robinson, Timothy P L Roberts, Steven J Siegel
Approximately one in 45 children have been diagnosed with Autism Spectrum Disorder (ASD), which is characterized by social/communication impairments. Recent studies have linked a subset of familial ASD to mutations in the Protocadherin 10 (Pcdh10) gene. Additionally, Pcdh10's expression pattern, as well as its known role within protein networks, implicates the gene in ASD. Subsequently, the neurobiology of mice heterozygous for Pcdh10 (Pcdh10(+/-)) has been investigated as a proxy for ASD. Male Pcdh10(+/-) mice have demonstrated sex-specific deficits in social behavior, recapitulating the gender bias observed in ASD...
August 24, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28842224/an-efficient-and-assumption-free-method-to-approximate-protein-level-distribution-in-the-two-states-gene-expression-model
#15
Bingxiang Xu, Hao Ge, Zhihua Zhang
Stochastic fluctuations at each step of gene expression might influence protein levels distributions across cell populations. However, current methods to model protein distribution of intrinsic gene expression dynamics are either computationally inefficient or rely on ad hoc assumptions, e.g., that the gene is always active. Taking advantage of the simple form of lower-order moments of distribution, we developed an efficient and assumption-free protein distribution approximation method (EFPD), for the two state gene expression model to accurately approximate the distribution...
August 24, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28839042/evolutionarily-conserved-alternative-splicing%C3%A2-across-monocots
#16
Wenbin Mei, Lucas Boatwright, Guanqiao Feng, James C Schnable, W Brad Barbazuk
One difficulty when identifying alternative splicing (AS) events in plants is distinguishing functional AS from splicing noise. One way to add confidence to the validity of a splice isoform is to observe that it is conserved across evolutionarily related species. We use a high throughput method to identify junction based conserved AS events from RNA-Seq data across nine plant species including: five grass monocots (maize, sorghum, rice, Brachpodium and foxtail millet), plus two non-grass monocots (banana and African oil palm), the eudicot Arabidopsis and the basal angiosperm Amborella In total, 9,804 AS events were found to be conserved between 2 or more species studied...
August 24, 2017: Genetics
https://www.readbyqxmd.com/read/28835372/pervasive-coexpression-of-spatially-proximal-genes-is-buffered-at-the-protein-level
#17
Georg Kustatscher, Piotr Grabowski, Juri Rappsilber
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of bidirectional gene pairs, and closeby genes in general, is buffered at the protein level. Taking into account the 3D architecture of the genome, we find that co-regulation of spatially close, functionally unrelated genes is pervasive at the transcriptome level, but does not extend to the proteome...
August 23, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/28826607/a-strategy-to-find-suitable-reference-genes-for-mirna-quantitative-pcr-analysis-and-its-application-to-cervical-specimens
#18
Iris Babion, Barbara C Snoek, Mark A van de Wiel, Saskia M Wilting, Renske D M Steenbergen
miRNAs represent an emerging class of promising biomarkers for cancer diagnostics. To perform reliable miRNA expression analysis using quantitative PCR, adequate data normalization is essential to remove nonbiological, technical variations. Ideal reference genes should be biologically stable and reduce technical variability of miRNA expression analysis. Herein is a new strategy for the identification and evaluation of reference genes that can be applied for miRNA-based diagnostic tests without entailing excessive additional experiments...
September 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28822748/an-integrated-approach-to-identify-critical-transcription-factors-in-the-protection-against-hydrogen-peroxide-induced-oxidative-stress-by-danhong-injection
#19
Jingjing Zhang, Feifei Guo, Junying Wei, Minghua Xian, Shihuan Tang, Ye Zhao, Mingwei Liu, Lei Song, Ya Geng, Hongjun Yang, Chen Ding, Luqi Huang
Oxidative stress plays a vital role in many pathological processes of the cardiovascular diseases. However, the underlying mechanism remains unclear, especially on a transcription factor (TF) level. In this study, a new method, concatenated tandem array of consensus transcription factor response elements (catTFREs), and an Illumina-based RNA-seq technology were integrated to systematically investigate the role of TFs in hydrogen peroxide (H2O2)-induced oxidative stress in cardiomyocytes; the damage was then rescued by Danhong injection (DHI), a Chinese standardized product approved for cardiovascular diseases treatment...
August 16, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28819158/discovering-condition-specific-gene-co-expression-patterns-using-gaussian-mixture-models-a-cancer-case-study
#20
Stephen P Ficklin, Leland J Dunwoodie, William L Poehlman, Christopher Watson, Kimberly E Roche, F Alex Feltus
A gene co-expression network (GCN) describes associations between genes and points to genetic coordination of biochemical pathways. However, genetic correlations in a GCN are only detectable if they are present in the sampled conditions. With the increasing quantity of gene expression samples available in public repositories, there is greater potential for discovery of genetic correlations from a variety of biologically interesting conditions. However, even if gene correlations are present, their discovery can be masked by noise...
August 17, 2017: Scientific Reports
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