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https://www.readbyqxmd.com/read/29352116/the-chemical-fluctuation-theorem-governing-gene-expression
#1
Seong Jun Park, Sanggeun Song, Gil-Suk Yang, Philip M Kim, Sangwoon Yoon, Ji-Hyun Kim, Jaeyoung Sung
Gene expression is a complex stochastic process composed of numerous enzymatic reactions with rates coupled to hidden cell-state variables. Despite advances in single-cell technologies, the lack of a theory accurately describing the gene expression process has restricted a robust, quantitative understanding of gene expression variability among cells. Here we present the Chemical Fluctuation Theorem (CFT), providing an accurate relationship between the environment-coupled chemical dynamics of gene expression and gene expression variability...
January 19, 2018: Nature Communications
https://www.readbyqxmd.com/read/29346759/nf-%C3%AE%C2%BAb-chromatin-interactions-drive-diverse-phenotypes-by-modulating-transcriptional-noise
#2
Victor C Wong, Victor L Bass, M Elise Bullock, Arvind K Chavali, Robin E C Lee, Walther Mothes, Suzanne Gaudet, Kathryn Miller-Jensen
Noisy gene expression generates diverse phenotypes, but little is known about mechanisms that modulate noise. Combining experiments and modeling, we studied how tumor necrosis factor (TNF) initiates noisy expression of latent HIV via the transcription factor nuclear factor κB (NF-κB) and how the HIV genomic integration site modulates noise to generate divergent (low-versus-high) phenotypes of viral activation. We show that TNF-induced transcriptional noise varies more than mean transcript number and that amplification of this noise explains low-versus-high viral activation...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29342231/mapping-gene-regulatory-networks-from-single-cell-omics-data
#3
Mark W E J Fiers, Liesbeth Minnoye, Sara Aibar, Carmen Bravo González-Blas, Zeynep Kalender Atak, Stein Aerts
Single-cell techniques are advancing rapidly and are yielding unprecedented insight into cellular heterogeneity. Mapping the gene regulatory networks (GRNs) underlying cell states provides attractive opportunities to mechanistically understand this heterogeneity. In this review, we discuss recently emerging methods to map GRNs from single-cell transcriptomics data, tackling the challenge of increased noise levels and data sparsity compared with bulk data, alongside increasing data volumes. Next, we discuss how new techniques for single-cell epigenomics, such as single-cell ATAC-seq and single-cell DNA methylation profiling, can be used to decipher gene regulatory programmes...
January 12, 2018: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29341316/deferoxamine-promotes-mesenchymal-stem-cell-homing-in-noise-induced-injured-cochlea-through-pi3k-akt-pathway
#4
A A Peyvandi, H-A Abbaszadeh, N Ahmady Roozbahany, A Pourbakht, S Khoshsirat, H Haddadzade Niri, H Peyvandi, S Niknazar
OBJECTIVE: Over 5% of the world's population suffers from disabling hearing loss. Stem cell homing in target tissue is an important aspect of cell-based therapy, which its augmentation increases cell therapy efficiency. Deferoxamine (DFO) can induce the Akt activation, and phosphorylation status of AKT (p-AKT) upregulates CXC chemokine receptor-4 (CXCR4) expression. We examined whether DFO can enhance mesenchymal stem cells (MSCs) homing in noise-induced damaged cochlea by PI3K/AKT dependent mechanism...
January 17, 2018: Cell Proliferation
https://www.readbyqxmd.com/read/29340520/analysis-of-serum-microrna-expression-in-male-workers-with-occupational-noise-induced-hearing-loss
#5
Y H Li, Y Yang, Y T Yan, L W Xu, H Y Ma, Y X Shao, C J Cao, X Wu, M J Qi, Y Y Wu, R Chen, Y Hong, X H Tan, L Yang
Occupational noise-induced hearing loss (ONIHL) is a prevalent occupational disorder that impairs auditory function in workers exposed to prolonged noise. However, serum microRNA expression in ONIHL subjects has not yet been studied. We aimed to compare the serum microRNA expression profiles in male workers of ONIHL subjects and controls. MicroRNA microarray analysis revealed that four serum microRNAs were differentially expressed between controls (n=3) and ONIHL subjects (n=3). Among these microRNAs, three were upregulated (hsa-miR-3162-5p, hsa-miR-4484, hsa-miR-1229-5p) and one was downregulated (hsa-miR-4652-3p) in the ONIHL group (fold change >1...
January 11, 2018: Brazilian Journal of Medical and Biological Research, Revista Brasileira de Pesquisas Médicas e Biológicas
https://www.readbyqxmd.com/read/29340399/landscape-of-gene-networks-for-random-parameter-perturbation
#6
Chunhe Li
Landscape approaches have been exploited to study the stochastic dynamics of gene networks. However, how to calculate the landscape with a wide range of parameter variations and how to investigate the influence of the network topology on the global properties of gene networks remain to be elucidated. Here, I developed an approach for the landscape of random parameter perturbation (LRPP) to address this issue. Based on a self-consistent approximation approach, by making perturbations to parameters in a given range, I obtained the landscape for gene network systems...
January 17, 2018: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/29339482/global-spectral-clustering-in-dynamic-networks
#7
Fuchen Liu, David Choi, Lu Xie, Kathryn Roeder
Community detection is challenging when the network structure is estimated with uncertainty. Dynamic networks present additional challenges but also add information across time periods. We propose a global community detection method, persistent communities by eigenvector smoothing (PisCES), that combines information across a series of networks, longitudinally, to strengthen the inference for each period. Our method is derived from evolutionary spectral clustering and degree correction methods. Data-driven solutions to the problem of tuning parameter selection are provided...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29327735/acquired-sensorineural-hearing-loss-in-children-current-research-and-therapeutic-perspectives
#8
M Ralli, R Rolesi, R Anzivino, R Turchetta, A R Fetoni
The knowledge of mechanisms responsible for acquired sensorineural hearing loss in children, such as viral and bacterial infections, noise exposure, aminoglycoside and cisplatin ototoxicity, is increasing and progressively changing the clinical management of affected patients. Viral infections are by far the most relevant cause of acquired hearing loss, followed by aminoglycoside and platinum derivative ototoxicity; moreover, cochlear damage induced by noise overexposure, mainly in adolescents, is an emerging topic...
December 2017: Acta Otorhinolaryngologica Italica
https://www.readbyqxmd.com/read/29322933/integrating-transcriptional-activity-in-genome-scale-models-of-metabolism
#9
Daniel Trejo Banos, Pauline Trébulle, Mohamed Elati
BACKGROUND: Genome-scale metabolic models provide an opportunity for rational approaches to studies of the different reactions taking place inside the cell. The integration of these models with gene regulatory networks is a hot topic in systems biology. The methods developed to date focus mostly on resolving the metabolic elements and use fairly straightforward approaches to assess the impact of genome expression on the metabolic phenotype. RESULTS: We present here a method for integrating the reverse engineering of gene regulatory networks into these metabolic models...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29321537/computational-investigation-of-environment-noise-interaction-in-single-cell-organisms-the-merit-of-expression-stochasticity-depends-on-the-quality-of-environmental-fluctuations
#10
Anja Lück, Lukas Klimmasch, Peter Großmann, Sebastian Germerodt, Christoph Kaleta
Organisms need to adapt to changing environments and they do so by using a broad spectrum of strategies. These strategies include finding the right balance between expressing genes before or when they are needed, and adjusting the degree of noise inherent in gene expression. We investigated the interplay between different nutritional environments and the inhabiting organisms' metabolic and genetic adaptations by applying an evolutionary algorithm to an agent-based model of a concise bacterial metabolism. Our results show that constant environments and rapidly fluctuating environments produce similar adaptations in the organisms, making the predictability of the environment a major factor in determining optimal adaptation...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29320486/systematic-characterization-of-maturation-time-of-fluorescent-proteins-in-living-cells
#11
Enrique Balleza, J Mark Kim, Philippe Cluzel
The slow maturation time of fluorescent proteins (FPs) limits the temporal accuracy of measurements of rapid processes such as gene expression dynamics and effectively reduces fluorescence signal in growing cells. We used high-precision time-lapse microscopy to characterize the maturation kinetics of 50 FPs that span the visible spectrum at two different temperatures in Escherichia coli cells. We identified fast-maturing FPs from this set that yielded the highest signal-to-noise ratio and temporal resolution in individual growing cells...
January 2018: Nature Methods
https://www.readbyqxmd.com/read/29317620/experimental-noise-cutoff-boosts-inferability-of-transcriptional-networks-in-large-scale-gene-deletion-studies
#12
C F Blum, N Heramvand, A S Khonsari, M Kollmann
Generating a comprehensive map of molecular interactions in living cells is difficult and great efforts are undertaken to infer molecular interactions from large-scale perturbation experiments. Here, we develop the analytical and numerical tools to quantify the fundamental limits for inferring transcriptional networks from gene knockout screens and introduce a network inference method that is unbiased with respect to measurement noise and scalable to large network sizes. We show that network asymmetry, knockout coverage and measurement noise are central determinants that limit prediction accuracy, whereas the knowledge about gene-specific variability among biological replicates can be used to eliminate noise-sensitive nodes and thereby boost the performance of network inference algorithms...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29315915/a-comparison-of-2-hydroxyglutarate-detection-at-3-and-7%C3%A2-t-with-long-te-semi-laser
#13
Adam Berrington, Natalie L Voets, Sarah J Larkin, Nick de Pennington, James Mccullagh, Richard Stacey, Christopher J Schofield, Peter Jezzard, Stuart Clare, Tom Cadoux-Hudson, Puneet Plaha, Olaf Ansorge, Uzay E Emir
Abnormally high levels of the 'oncometabolite' 2-hydroxyglutarate (2-HG) occur in many grade II and III gliomas, and correlate with mutations in the genes of isocitrate dehydrogenase (IDH) isoforms. In vivo measurement of 2-HG in patients, using magnetic resonance spectroscopy (MRS), has largely been carried out at 3 T, yet signal overlap continues to pose a challenge for 2-HG detection. To combat this, several groups have proposed MRS methods at ultra-high field (≥7 T) where theoretical increases in signal-to-noise ratio and spectral resolution could improve 2-HG detection...
January 5, 2018: NMR in Biomedicine
https://www.readbyqxmd.com/read/29309409/weighted-functional-linear-regression-models-for-gene-based-association-analysis
#14
Nadezhda M Belonogova, Gulnara R Svishcheva, James F Wilson, Harry Campbell, Tatiana I Axenovich
Functional linear regression models are effectively used in gene-based association analysis of complex traits. These models combine information about individual genetic variants, taking into account their positions and reducing the influence of noise and/or observation errors. To increase the power of methods, where several differently informative components are combined, weights are introduced to give the advantage to more informative components. Allele-specific weights have been introduced to collapsing and kernel-based approaches to gene-based association analysis...
2018: PloS One
https://www.readbyqxmd.com/read/29303479/intrinsic-adaptive-value-and-early-fate-of-gene-duplication-revealed-by-a-bottom-up-approach
#15
Guillermo Rodrigo, Mario A Fares
The population genetic mechanisms governing the preservation of gene duplicates, especially in the critical very initial phase, have remained largely unknown. Here, we demonstrate that gene duplication confers per se a weak selective advantage in scenarios of fitness trade-offs. Through a precise quantitative description of a model system, we show that a second gene copy serves to reduce gene expression inaccuracies derived from pervasive molecular noise and suboptimal gene regulation. We then reveal that such an accuracy in the phenotype yields a selective advantage in the order of 0...
January 5, 2018: ELife
https://www.readbyqxmd.com/read/29301492/effect-of-grm7-polymorphisms-on-the-development-of-noise-induced-hearing-loss-in-chinese-han-workers-a-nested-case-control-study
#16
Peipei Yu, Jie Jiao, Guoshun Chen, Wenhui Zhou, Huanling Zhang, Hui Wu, Yanhong Li, Guizhen Gu, Yuxin Zheng, Yue Yu, Shanfa Yu
BACKGROUND: Noise-induced hearing loss (NIHL) is a complex, irreversible disease caused by the interaction of genetic and environmental factors. In recent years, a great many studies have been done to explore the NIHL susceptibility genes among humans. So far, high powerful detections have been founded that genes of potassium ion channel genes (KCNQ4 and KCNE1), catalase (CAT), protocadherin 15 (PCDH15), myosin 14 (MYH14) and heart shock protein (HSP70) which have been identified in more than one population may be associated with the susceptibility to NIHL...
January 5, 2018: BMC Medical Genetics
https://www.readbyqxmd.com/read/29280088/visnormsc-a-graphical-user-interface-to-normalize-single-cell-rna-sequencing-data
#17
Lijun Tang, Nan Zhou
Single-cell RNA sequencing (RNA-seq) allows the analysis of gene expression with high resolution. The intrinsic defects of this promising technology imports technical noise into the single-cell RNA-seq data, increasing the difficulty of accurate downstream inference. Normalization is a crucial step in single-cell RNA-seq data pre-processing. SCnorm is an accurate and efficient method that can be used for this purpose. An R implementation of this method is currently available. On one hand, the R package possesses many excellent features from R...
December 26, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29274763/the-neural-response-of-female-zebra-finches-taeniopygia-guttata-to-conspecific-heterospecific-and-isolate-song-depends-on-early-life-song-exposure
#18
Adriana Diez, Alice Cui, Scott A MacDougall-Shackleton
The auditory forebrain regions caudo-medial nidopallium (NCM) and caudo-medial mesopallium (CMM) of songbirds exhibit differential expression of the immediate-early gene ZENK in response to playback of different song stimuli, and dependent on early-life auditory experience. Similarly, song preferences depend both on auditory experience and unlearned biases for particular song features. We explored the contributions of early-life auditory experience and the type of song stimuli on the Zenk response in the auditory forebrain of female zebra finches...
December 21, 2017: Behavioural Processes
https://www.readbyqxmd.com/read/29246519/hybrid-method-based-on-information-gain-and-support-vector-machine-for-gene-selection-in-cancer-classification
#19
Lingyun Gao, Mingquan Ye, Xiaojie Lu, Daobin Huang
It remains a great challenge to achieve sufficient cancer classification accuracy with the entire set of informative genes, due to the high dimensions, small sample size, and big noise of gene expression data. We thus proposed a hybrid gene selection method, Information Gain-Support Vector Machine (IG-SVM) in this study. IG was initially employed to filter irrelevant and redundant genes. Then, further removal of redundant genes was performed using SVM to eliminate the noise in the datasets more effectively...
December 12, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29242599/stochastic-gene-expression-in-arabidopsis-thaliana
#20
Ilka Schultheiß Araújo, Jessica Magdalena Pietsch, Emma Mathilde Keizer, Bettina Greese, Rachappa Balkunde, Christian Fleck, Martin Hülskamp
Although plant development is highly reproducible, some stochasticity exists. This developmental stochasticity may be caused by noisy gene expression. Here we analyze the fluctuation of protein expression in Arabidopsis thaliana. Using the photoconvertible KikGR marker, we show that the protein expressions of individual cells fluctuate over time. A dual reporter system was used to study extrinsic and intrinsic noise of marker gene expression. We report that extrinsic noise is higher than intrinsic noise and that extrinsic noise in stomata is clearly lower in comparison to several other tissues/cell types...
December 14, 2017: Nature Communications
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