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https://www.readbyqxmd.com/read/27919219/ston-exploring-biological-pathways-using-the-sbgn-standard-and-graph-databases
#1
Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet, Charles Auffray
BACKGROUND: When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks. RESULTS: We present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database...
December 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27913887/transcriptomics-analysis-of-hulless-barley-during-grain-development-with-a-focus-on-starch-biosynthesis
#2
Yawei Tang, Xingquan Zeng, Yulin Wang, Lijun Bai, Qijun Xu, Zexiu Wei, Hongjun Yuan, Tashi Nyima
Hulless barley, with its unique nutritional value and potential health benefits, has increasingly attracted attentions in recent years. However, the transcription dynamics during hulless barley grain development is not well understood. In the present study, we investigated the transcriptome changes during barley grain development using Illumina paired-end RNA-sequencing. Two datasets of the developing grain transcriptomes from two barley landraces with the differential seed starch synthesis traits were generated, and comparative transcriptome approach in both genotypes was performed...
December 2, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27913250/identification-of-non-coding-and-coding-rnas-in-porcine-endometrium
#3
Yueying Wang, Tao Hu, Lihang Wu, Xiaoran Liu, Songyi Xue, Minggang Lei
One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes...
November 29, 2016: Genomics
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
#4
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/27909803/evolutionary-origin-of-endochondral-ossification-the-transdifferentiation-hypothesis
#5
REVIEW
Fret Cervantes-Diaz, Pedro Contreras, Sylvain Marcellini
The vertebrate endoskeleton results from the piecemeal assembly of bone and cartilage as well as additional types of calcified extracellular matrices produced by seemingly hybrid cell types of intermediate phenotypes between osteoblasts and chondrocytes. Hence, shedding light on the emergence and subsequent diversification of skeletal tissues represents a major challenge in vertebrate evolutionary developmental biology. A 150-year-old debate in the field was recently solved by lineage tracing experiments demonstrating that, during mouse endochondral bone development, a subset of chondrocytes evades apoptosis and transdifferentiate into osteoblasts at the chondro-osseous junction...
December 1, 2016: Development Genes and Evolution
https://www.readbyqxmd.com/read/27908973/environmental-public-health-tracking-a-cost-effective-system-for-characterizing-the-sources-distribution-and-public-health-impacts-of-environmental-hazards
#6
P J Saunders, J D Middleton, G Rudge
BACKGROUND: The contemporary environment is a complex of interactions between physical, biological, socio-economic systems with major impacts on public health. However, gaps in our understanding of the causes, extent and distribution of these effects remain. The public health community in Sandwell West Midlands has collaborated to successfully develop, pilot and establish the first Environmental Public Health Tracking (EPHT) programme in Europe to address this 'environmental health gap' through systematically linking data on environmental hazards, exposures and diseases...
December 1, 2016: Journal of Public Health
https://www.readbyqxmd.com/read/27907891/analysis-of-translation-using-polysome-profiling
#7
Héloïse Chassé, Sandrine Boulben, Vlad Costache, Patrick Cormier, Julia Morales
During the past decade, there has been growing interest in the role of translational regulation of gene expression in many organisms. Polysome profiling has been developed to infer the translational status of a specific mRNA species or to analyze the translatome, i.e. the subset of mRNAs actively translated in a cell. Polysome profiling is especially suitable for emergent model organisms for which genomic data are limited. In this paper, we describe an optimized protocol for the purification of sea urchin polysomes and highlight the critical steps involved in polysome purification...
October 7, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903818/properties-of-alternative-microbial-hosts-used-in-synthetic-biology-towards-the-design-of-a-modular-chassis
#8
REVIEW
Juhyun Kim, Manuel Salvador, Elizabeth Saunders, Jaime González, Claudio Avignone-Rossa, Jose Ignacio Jiménez
The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27902735/role-of-hepatic-specific-transcription-factors-and-polycomb-repressive-complex-2-during-induction-of-fibroblasts-to-hepatic-fate
#9
Shima Rastegar-Pouyani, Niusha Khazaei, Ping Wee, Abdulshakour Mohammadnia, Moein Yaqubi
Direct reprogramming using defined sets of transcription factors (TFs) is a recent strategy for generating induced hepatocytes (iHeps) from fibroblasts for use in regenerative medicine and drug development. Comprehensive studies detailing the regulatory role of TFs during this reprogramming process could help increase its efficiency. This study aimed to find the TFs with the greatest influences on the generation of iHeps from fibroblasts, and to further understand their roles in the regulation of the gene expression program...
2016: PloS One
https://www.readbyqxmd.com/read/27897008/tracing-co-regulatory-network-dynamics-in-noisy-single-cell-transcriptome-trajectories
#10
Pablo Cordero, Joshua M Stuart
The availability of gene expression data at the single cell level makes it possible to probe the molecular underpinnings of complex biological processes such as differentiation and oncogenesis. Promising new methods have emerged for reconstructing a progression 'trajectory' from static single-cell transcriptome measurements. However, it remains unclear how to adequately model the appreciable level of noise in these data to elucidate gene regulatory network rewiring. Here, we present a framework called Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR) that infers progressions from static single-cell transcriptomes by employing a continuous parametrization of Gaussian mixtures in high-dimensional curves...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896968/exploring-the-reproducibility-of-probabilistic-causal-molecular-network-models
#11
Ariella Cohain, Aparna A Divaraniya, Kuixi Zhu, Joseph R Scarpa, Andrew Kasarskis, Jun Zhu, Rui Chang, Joel T Dudley, Eric E Schadt
Network reconstruction algorithms are increasingly being employed in biomedical and life sciences research to integrate large-scale, high-dimensional data informing on living systems. One particular class of probabilistic causal networks being applied to model the complexity and causal structure of biological data is Bayesian networks (BNs). BNs provide an elegant mathematical framework for not only inferring causal relationships among many different molecular and higher order phenotypes, but also for incorporating highly diverse priors that provide an efficient path for incorporating existing knowledge...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896738/inferring-genome-wide-interaction-networks
#12
Gökmen Altay, Onur Mendi
The inference of gene regulatory networks is an important process that contributes to a better understanding of biological and biomedical problems. These networks aim to capture the causal molecular interactions of biological processes and provide valuable information about normal cell physiology. In this book chapter, we introduce GNI methods, namely C3NET, RN, ARACNE, CLR, and MRNET and describe their components and working mechanisms. We present a comparison of the performance of these algorithms using the results of our previously published studies...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27894849/a-global-view-of-regulatory-networks-in-lung-cancer-an-approach-to-understand-homogeneity-and-heterogeneity
#13
REVIEW
Jiapei Lu, William Wang, Menglin Xu, Yuping Li, Chengshui Chen, Xiangdong Wang
A number of new biotechnologies are used to identify potential biomarkers for the early detection of lung cancer, enabling a personalized therapy to be developed in response. The combinatorial cross-regulation of hundreds of biological function-specific transcription factors (TFs) is defined as the understanding of regulatory networks of molecules within the cell. Here we integrated global databases with 537 patients with lung adenocarcinoma (ADC), 140 with lung squamous carcinoma (SCC), 9 with lung large-cell carcinoma (LCC), 56 with small-cell lung cancer (SCLC), and 590 without cancer with the understanding of TF functions...
November 25, 2016: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/27894672/microrna-145-regulates-the-rlr-signaling-pathway-in-miiuy-croaker-after-poly-i-c-stimulation-via-targeting-mda5
#14
Jingjing Han, Yuena Sun, Weihua Song, Tianjun Xu
MicroRNAs (miRNAs) are endogenous small non-coding RNAs that participate in diverse biological processes via degrading the target mRNAs or repressing translation. In this study, the regulation of miRNA to the RLR (RIG-I-like receptor) signaling pathway by degrading the target mRNAs was researched in miiuy croaker. MDA5, a microRNA-145-5p (miR-145-5p) putative target gene, was predicted by bioinformatics, and the target sites from the 3'untranslated region of MDA5 transcripts were confirmed using luciferase reporter assays...
November 25, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27890633/comparison-analysis-of-micrornas-in-response-to-ev71-and-ca16-infection-in-human-bronchial-epithelial-cells-by-high-throughput-sequencing-to-reveal-differential-infective-mechanisms
#15
Yajie Hu, Jie Song, Longding Liu, Jing Li, Beibei Tang, Ying Zhang, Jingjing Wang, Lichun Wang, Shengtao Fan, Ming Feng, Qihan Li
Hand, foot, and mouth disease (HFMD) mainly caused by Enterovirus 71 (EV71) and coxsackievirus A16 (CA16) infections which presented significantly different clinical manifestations. Nevertheless, the factors underlying these differences remain unclear. Recently, the functions of microRNAs (miRNAs) in pathogen-host interactions have been highlighted. Here, we performed comprehensive miRNA profiling in EV71- and CA16-infected human bronchial epithelial (16HBE) cells at multiple time points using high-throughput sequencing...
November 24, 2016: Virus Research
https://www.readbyqxmd.com/read/27890449/independent-evolution-of-genomic-characters-during-major-metazoan-transitions
#16
REVIEW
Oleg Simakov, Takeshi Kawashima
Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages...
November 25, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27886593/the-evolution-of-micrornas-in-plants
#17
REVIEW
Jie Cui, Chenjiang You, Xuemei Chen
MicroRNAs (miRNAs) are a central player in post-transcriptional regulation of gene expression and are involved in numerous biological processes in eukaryotes. Knowledge of the origins and divergence of miRNAs paves the way for a better understanding of the complexity of the regulatory networks that they participate in. The biogenesis, degradation, and regulatory activities of miRNAs are relatively better understood, but the evolutionary history of miRNAs still needs more exploration. Inverted duplication of target genes, random hairpin sequences and small transposable elements constitute three main models that explain the origination of miRNA genes (MIR)...
November 22, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27885004/circadian-time-signatures-of-fitness-and-disease
#18
REVIEW
Joseph Bass, Mitchell A Lazar
Biological clocks are autonomous anticipatory oscillators that play a critical role in the organization and information processing from genome to whole organisms. Transformative advances into the clock system have opened insight into fundamental mechanisms through which clocks program energy transfer from sunlight into organic matter and potential energy, in addition to cell development and genotoxic stress response. The identification of clocks in nearly every single cell of the body raises questions as to how this gives rise to rhythmic physiology in multicellular organisms and how environmental signals entrain clocks to geophysical time...
November 25, 2016: Science
https://www.readbyqxmd.com/read/27881070/pregnancy-specific-%C3%AE-1-glycoproteins-combined-biomarker-roles-structure-function-relationships-and-implications-for-drug-design
#19
Nurbubu T Moldogazieva, Innokenty M Mokhosoev, Alexander A Terentiev
BACKGROUND: Pregnancy specific β1-glycoproteins (PSGs) have long been recognized as trophoblast quality and embryo viability markers. However, biological roles of PSGs remain obscure, and structure/function relationships to other feto-placental proteins as well as implications for drug design have not been reviewed. This review summarizes and discusses advances in 45-year studies of PSGs with focus on the latest achievements and the challenges for future investigations. METHODS: Literature search was performed to review the majority of recent PSG studies with emphasis on usage of high-throughput integrated proteomic profiling technologies, systems biology and bioinformatics approaches that enhance novel biomarker and drug target discovery as well as protein structure/activity analysis...
November 22, 2016: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/27879480/adaptive-modelling-of-gene-regulatory-network-using-bayesian-information-criterion-guided-sparse-regression-approach
#20
Ming Shi, Weiming Shen, Hong-Qiang Wang, Yanwen Chong
Inferring gene regulatory networks (GRNs) from microarray expression data are an important but challenging issue in systems biology. In this study, the authors propose a Bayesian information criterion (BIC)-guided sparse regression approach for GRN reconstruction. This approach can adaptively model GRNs by optimising the l1-norm regularisation of sparse regression based on a modified version of BIC. The use of the regularisation strategy ensures the inferred GRNs to be as sparse as natural, while the modified BIC allows incorporating prior knowledge on expression regulation and thus avoids the overestimation of expression regulators as usual...
December 2016: IET Systems Biology
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