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https://www.readbyqxmd.com/read/28444190/biological-aging-and-the-human-gut-microbiota
#1
Vincent J Maffei, Sangkyu Kim, Eugene Blanchard, Meng Luo, S Michal Jazwinski, Christopher M Taylor, David A Welsh
The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity...
April 25, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28443230/prediction-of-optimal-gene-functions-for-osteosarcoma-using-network-based-guilt-by-association-method-based-on-gene-oncology-and-microarray-profile
#2
Xinrang Chen
In the current study, we planned to predict the optimal gene functions for osteosarcoma (OS) by integrating network-based method with guilt by association (GBA) principle (called as network-based gene function inference approach) based on gene oncology (GO) data and gene expression profile. To begin with, differentially expressed genes (DEGs) were extracted using linear models for microarray data (LIMMA) package. Then, construction of differential co-expression network (DCN) relying on DEGs was implemented, and sub-DCN was identified using Spearman correlation coefficient (SCC)...
June 2017: Journal of Bone Oncology
https://www.readbyqxmd.com/read/28439570/epigenomics-of-human-cd8-t-cell-differentiation-and-aging
#3
David M Moskowitz, David W Zhang, Bin Hu, Sabine Le Saux, Rolando E Yanes, Zhongde Ye, Jason D Buenrostro, Cornelia M Weyand, William J Greenleaf, Jörg J Goronzy
The efficacy of the adaptive immune response declines dramatically with age, but the cell-intrinsic mechanisms driving immune aging in humans remain poorly understood. Immune aging is characterized by a loss of self-renewing naïve cells and the accumulation of differentiated but dysfunctional cells within the CD8 T cell compartment. Using ATAC-seq, we inferred the transcription factor binding activities correlated with naive and central and effector memory CD8 T cell states in young adults. Integrating our results with RNA-seq, we identified transcription networks associated with CD8 T cell differentiation, with prominent roles implicated for BATF, ETS1, Eomes, and Sp1...
February 2017: Science Immunology
https://www.readbyqxmd.com/read/28437848/inferring-network-structure-in-non-normal-and-mixed-discrete-continuous-genomic-data
#4
Anindya Bhadra, Arvind Rao, Veerabhadran Baladandayuthapani
Inferring dependence structure through undirected graphs is crucial for uncovering the major modes of multivariate interaction among high-dimensional genomic markers that are potentially associated with cancer. Traditionally, conditional independence has been studied using sparse Gaussian graphical models for continuous data and sparse Ising models for discrete data. However, there are two clear situations when these approaches are inadequate. The first occurs when the data are continuous but display non-normal marginal behavior such as heavy tails or skewness, rendering an assumption of normality inappropriate...
April 24, 2017: Biometrics
https://www.readbyqxmd.com/read/28436883/a-bipartite-network-and-resource-transfer-based-approach-to-infer-lncrna-environmental-factor-associations
#5
Jie Zhou, Yuan-Yuan Shi
Phenotypes and diseases are often determined by the complex interactions between genetic factors and environmental factors (EFs). However, compared with protein-coding genes and microRNAs, there is a paucity of computational methods for understanding the associations between long non-coding RNAs (lncRNAs) and EFs. In this study, we focused on the associations between lncRNA and EFs. By using the common miRNA partners of any pair of lncRNA and EF, based on the competing endogenous RNA (ceRNA) hypothesis and the technique of resources transfer within the experimentally-supported lncRNA-miRNA and miRNA-EF association bipartite networks, we propose an algorithm for predicting new lncRNA-EF associations...
April 18, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28435885/phylogenomic-reconstruction-of-the-oomycete-phylogeny-derived-from-37-genomes
#6
Charley G P McCarthy, David A Fitzpatrick
The oomycetes are a class of microscopic, filamentous eukaryotes within the Stramenopiles-Alveolata-Rhizaria (SAR) supergroup which includes ecologically significant animal and plant pathogens, most infamously the causative agent of potato blight Phytophthora infestans. Single-gene and concatenated phylogenetic studies both of individual oomycete genera and of members of the larger class have resulted in conflicting conclusions concerning species phylogenies within the oomycetes, particularly for the large Phytophthora genus...
March 2017: MSphere
https://www.readbyqxmd.com/read/28433419/disconnect-between-alcohol-induced-alterations-in-chromatin-structure-and-gene-transcription-in-a-mouse-embryonic-stem-cell-model-of-exposure
#7
Kylee J Veazey, Haiqing Wang, Yudhishtar S Bedi, William M Skiles, Richard Cheng-An Chang, Michael C Golding
Alterations to chromatin structure induced by environmental insults have become an attractive explanation for the persistence of exposure effects into subsequent life stages. However, a growing body of work examining the epigenetic impact that alcohol and other drugs of abuse exert consistently notes a disconnection between induced changes in chromatin structure and patterns of gene transcription. Thus, an important question is whether perturbations in the 'histone code' induced by prenatal exposures to alcohol implicitly subvert gene expression, or whether the hierarchy of cellular signaling networks driving development is such that they retain control over the transcriptional program...
January 11, 2017: Alcohol
https://www.readbyqxmd.com/read/28430854/dynamic-modeling-and-network-approaches-for-omics-time-course-data-overview-of-computational-approaches-and-applications
#8
Yulan Liang, Arpad Kelemen
Inferring networks and dynamics of genes, proteins, cells and other biological entities from high-throughput biological omics data is a central and challenging issue in computational and systems biology. This is essential for understanding the complexity of human health, disease susceptibility and pathogenesis for Predictive, Preventive, Personalized and Participatory (P4) system and precision medicine. The delineation of the possible interactions of all genes/proteins in a genome/proteome is a task for which conventional experimental techniques are ill suited...
April 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28419235/a-bayesian-group-sparse-multi-task-regression-model-for-imaging-genetics
#9
Keelin Greenlaw, Elena Szefer, Jinko Graham, Mary Lesperance, Farouk S Nathoo
Motivation: Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group l2,1-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided...
April 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28418398/intranasal-oxytocin-enhances-intrinsic-corticostriatal-functional-connectivity-in-women
#10
R A I Bethlehem, M V Lombardo, M-C Lai, B Auyeung, S K Crockford, J Deakin, S Soubramanian, A Sule, P Kundu, V Voon, S Baron-Cohen
Oxytocin may influence various human behaviors and the connectivity across subcortical and cortical networks. Previous oxytocin studies are male biased and often constrained by task-based inferences. Here, we investigate the impact of oxytocin on resting-state connectivity between subcortical and cortical networks in women. We collected resting-state functional magnetic resonance imaging (fMRI) data on 26 typically developing women 40 min following intranasal oxytocin administration using a double-blind placebo-controlled crossover design...
April 18, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28415290/backward-stochastic-differential-equation-approach-to-modeling-of-gene-expression
#11
Evelina Shamarova, Roman Chertovskih, Alexandre F Ramos, Paulo Aguiar
In this article, we introduce a backward method to model stochastic gene expression and protein-level dynamics. The protein amount is regarded as a diffusion process and is described by a backward stochastic differential equation (BSDE). Unlike many other SDE techniques proposed in the literature, the BSDE method is backward in time; that is, instead of initial conditions it requires the specification of end-point ("final") conditions, in addition to the model parametrization. To validate our approach we employ Gillespie's stochastic simulation algorithm (SSA) to generate (forward) benchmark data, according to predefined gene network models...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28412966/tfap2a-is-a-component-of-the-zeb1-2-network-that-regulates-tgfb1-induced-epithelial-to-mesenchymal-transition
#12
Yoana Dimitrova, Andreas J Gruber, Nitish Mittal, Souvik Ghosh, Beatrice Dimitriades, Daniel Mathow, William Aaron Grandy, Gerhard Christofori, Mihaela Zavolan
BACKGROUND: The transition between epithelial and mesenchymal phenotypes (EMT) occurs in a variety of contexts. It is critical for mammalian development and it is also involved in tumor initiation and progression. Master transcription factor (TF) regulators of this process are conserved between mouse and human. METHODS: From a computational analysis of a variety of high-throughput sequencing data sets we initially inferred that TFAP2A is connected to the core EMT network in both species...
April 17, 2017: Biology Direct
https://www.readbyqxmd.com/read/28410408/pleistocene-climate-changes-shaped-the-population-structure-of-partamona-seridoensis-apidae-meliponini-an-endemic-stingless-bee-from-the-neotropical-dry-forest
#13
Elder Assis Miranda, Kátia Maria Ferreira, Airton Torres Carvalho, Celso Feitosa Martins, Carlo Rivero Fernandes, Marco Antonio Del Lama
Partamona seridoensis is an endemic stingless bee from the Caatinga, a Neotropical dry forest in northeastern Brazil. Like other stingless bees, this species plays an important ecological role as a pollinator. The aim of the present study was to investigate the genetic structure and evolutionary history of P. seridoensis across its current geographic range. Workers from 84 nests from 17 localities were analyzed for COI and Cytb genic regions. The population structure tests (Bayesian phylogenetic inference, AMOVA and haplotype network) consistently characterized two haplogroups (northwestern and eastern), with little gene flow between them, generating a high differentiation between them as well as among the populations within each haplogroup...
2017: PloS One
https://www.readbyqxmd.com/read/28410373/parallel-reorganization-of-protein-function-in-the-spindle-checkpoint-pathway-through-evolutionary-paths-in-the-fitness-landscape-that-appear-neutral-in-laboratory-experiments
#14
Alex N Nguyen Ba, Bob Strome, Selma Osman, Elizabeth-Ann Legere, Taraneh Zarin, Alan M Moses
Regulatory networks often increase in complexity during evolution through gene duplication and divergence of component proteins. Two models that explain this increase in complexity are: 1) adaptive changes after gene duplication, such as resolution of adaptive conflicts, and 2) non-adaptive processes such as duplication, degeneration and complementation. Both of these models predict complementary changes in the retained duplicates, but they can be distinguished by direct fitness measurements in organisms with short generation times...
April 14, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28408966/gene-network-reconstruction-using-global-local-shrinkage-priors
#15
Gwenaël G R Leday, Mathisca C M de Gunst, Gino B Kpogbezan, Aad W van der Vaart, Wessel N van Wieringen, Mark A van de Wiel
Reconstructing a gene network from high-throughput molecular data is an important but challenging task, as the number of parameters to estimate easily is much larger than the sample size. A conventional remedy is to regularize or penalize the model likelihood. In network models, this is often done locally in the neighbourhood of each node or gene. However, estimation of the many regularization parameters is often difficult and can result in large statistical uncertainties. In this paper we propose to combine local regularization with global shrinkage of the regularization parameters to borrow strength between genes and improve inference...
March 2017: Annals of Applied Statistics
https://www.readbyqxmd.com/read/28407042/incorporating-prior-information-into-differential-network-analysis-using-nonparanormal-graphical-models
#16
Xiao-Fei Zhang, Le Ou-Yang, Hong Yan
Motivation: Understanding how gene regulatory networks change under different cellular states is important for revealing insights into network dynamics. Gaussian graphical models, which assume that the data follow a joint normal distribution, have been used recently to infer differential networks. However, the distributions of the omics data are nonnormal in general. Furthermore, althoughmuch biological knowledge (or prior information) has been accumulated, most existing methods ignore the valuable prior information...
April 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28406900/gene-co-expression-network-connectivity-is-an-important-determinant-of-selective-constraint
#17
Niklas Mähler, Jing Wang, Barbara K Terebieniec, Pär K Ingvarsson, Nathaniel R Street, Torgeir R Hvidsten
While several studies have investigated general properties of the genetic architecture of natural variation in gene expression, few of these have considered natural, outbreeding populations. In parallel, systems biology has established that a general feature of biological networks is that they are scale-free, rendering them buffered against random mutations. To date, few studies have attempted to examine the relationship between the selective processes acting to maintain natural variation of gene expression and the associated co-expression network structure...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28406896/inferring-modulators-of-genetic-interactions-with-epistatic-nested-effects-models
#18
Martin Pirkl, Madeline Diekmann, Marlies van der Wees, Niko Beerenwinkel, Holger Fröhlich, Florian Markowetz
Maps of genetic interactions can dissect functional redundancies in cellular networks. Gene expression profiles as high-dimensional molecular readouts of combinatorial perturbations provide a detailed view of genetic interactions, but can be hard to interpret if different gene sets respond in different ways (called mixed epistasis). Here we test the hypothesis that mixed epistasis between a gene pair can be explained by the action of a third gene that modulates the interaction. We have extended the framework of Nested Effects Models (NEMs), a type of graphical model specifically tailored to analyze high-dimensional gene perturbation data, to incorporate logical functions that describe interactions between regulators on downstream genes and proteins...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28404936/systematic-identification-and-comparison-of-expressed-profiles-of-lncrnas-and-circrnas-with-associated-co-expression-and-cerna-networks-in-mouse-germline-stem-cells
#19
Xiaoyong Li, Junping Ao, Ji Wu
Accumulating evidence indicates that long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) involve in germ cell development. However, little is known about the functions and mechanisms of lncRNAs and circRNAs in self-renewal and differentiation of germline stem cells. Therefore, we explored the expression profiles of mRNAs, lncRNAs, and circRNAs in male and female mouse germline stem cells by high-throughput sequencing. We identified 18573 novel lncRNAs and 18822 circRNAs in the germline stem cells and further confirmed the existence of these lncRNAs and circRNAs by RT-PCR...
February 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28403823/empirical-bayes-method-for-reducing-false-discovery-rates-of-correlation-matrices-with-block-diagonal-structure
#20
Clare Pacini, James W Ajioka, Gos Micklem
BACKGROUND: Correlation matrices are important in inferring relationships and networks between regulatory or signalling elements in biological systems. With currently available technology sample sizes for experiments are typically small, meaning that these correlations can be difficult to estimate. At a genome-wide scale estimation of correlation matrices can also be computationally demanding. RESULTS: We develop an empirical Bayes approach to improve covariance estimates for gene expression, where we assume the covariance matrix takes a block diagonal form...
April 12, 2017: BMC Bioinformatics
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