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https://www.readbyqxmd.com/read/27926536/a-minimal-titration-model-of-the-mammalian-dynamical-heat-shock-response
#1
Aude Sivéry, Emmanuel Courtade, Quentin Thommen
Environmental stress, such as oxidative or heat stress, induces the activation of the heat shock response (HSR) and leads to an increase in the heat shock proteins (HSPs) level. These HSPs act as molecular chaperones to maintain cellular proteostasis. Controlled by highly intricate regulatory mechanisms, having stress-induced activation and feedback regulations with multiple partners, the HSR is still incompletely understood. In this context, we propose a minimal molecular model for the gene regulatory network of the HSR that reproduces quantitatively different heat shock experiments both on heat shock factor 1 (HSF1) and HSPs activities...
December 7, 2016: Physical Biology
https://www.readbyqxmd.com/read/27924948/foxa1-gata3-and-ppar%C3%A9-cooperate-to-drive-luminal-subtype-in-bladder-cancer-a-molecular-analysis-of-established-human-cell-lines
#2
Joshua I Warrick, Vonn Walter, Hironobu Yamashita, Eunah Chung, Lauren Shuman, Vasty Osei Amponsa, Zongyu Zheng, Wilson Chan, Tiffany L Whitcomb, Feng Yue, Tejaswi Iyyanki, Yuka I Kawasawa, Matthew Kaag, Wansong Guo, Jay D Raman, Joo-Seop Park, David J DeGraff
Discrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA)...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924512/computational-analysis-reveals-microrna-mrna-regulatory-network-in-esophageal-squamous-cell-carcinoma
#3
Jie Zhao, Bi-Cheng Zhang, Li-Fang Yu, Wei-Xing Wang, Yong Zhao, Zhi-Guo Rao
MicroRNAs (miRNAs) are known to regulate post-transcriptional gene expression. They are involved in carcinogenesis and tumor progression. The aim of this study was to explore the microRNA-mRNA regulatory network in esophageal squamous cell carcinoma (ESCC) using comprehensive computational approaches. In this study we have selected a total of 11 miRNAs from one previously reported study in ESCC. The mRNA targets of these miRNAs were predicted using various algorithms. The expression profiles of these mRNA targets were identified on DNA microarray experiment dataset across ESCC tissue samples...
December 2016: Journal of Huazhong University of Science and Technology. Medical Sciences
https://www.readbyqxmd.com/read/27924281/causality-analysis-detects-the-regulatory-role-of-maternal-effect-genes-in-the-early-drosophila-embryo
#4
Zara Ghodsi, Xu Huang, Hossein Hassani
In developmental studies, inferring regulatory interactions of segmentation genetic network play a vital role in unveiling the mechanism of pattern formation. As such, there exists an opportune demand for theoretical developments and new mathematical models which can result in a more accurate illustration of this genetic network. Accordingly, this paper seeks to extract the meaningful regulatory role of the maternal effect genes using a variety of causality detection techniques and to explore whether these methods can suggest a new analytical view to the gene regulatory networks...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/27924033/chipbase-v2-0-decoding-transcriptional-regulatory-networks-of-non-coding-rnas-and-protein-coding-genes-from-chip-seq-data
#5
Ke-Ren Zhou, Shun Liu, Wen-Ju Sun, Ling-Ling Zheng, Hui Zhou, Jian-Hua Yang, Liang-Hu Qu
The abnormal transcriptional regulation of non-coding RNAs (ncRNAs) and protein-coding genes (PCGs) is contributed to various biological processes and linked with human diseases, but the underlying mechanisms remain elusive. In this study, we developed ChIPBase v2.0 (http://rna.sysu.edu.cn/chipbase/) to explore the transcriptional regulatory networks of ncRNAs and PCGs. ChIPBase v2.0 has been expanded with ∼10 200 curated ChIP-seq datasets, which represent about 20 times expansion when comparing to the previous released version...
October 23, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923654/zeb1-is-neither-sufficient-nor-required-for-epithelial-mesenchymal-transition-in-ls174t-colorectal-cancer-cells
#6
Sabine Jägle, Annika Dertmann, Monika Schrempp, Andreas Hecht
Epithelial-mesenchymal transition (EMT) is implicated in metastases formation and acquired therapy resistance in several tumor entities. The two transcription factors SNAIL1 and ZEB1 are thought to be master regulators of EMT and to form a core regulatory network required for EMT-associated transcriptional reprogramming. Yet, inducible EMT models show the sequential upregulation first of SNAIL1 and only subsequently of ZEB1. Therefore, SNAIL1 and ZEB1 might be differentially needed for the onset and propagation of EMT...
December 3, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27923054/fused-regression-for-multi-source-gene-regulatory-network-inference
#7
Kari Y Lam, Zachary M Westrick, Christian L Müller, Lionel Christiaen, Richard Bonneau
Understanding gene regulatory networks is critical to understanding cellular differentiation and response to external stimuli. Methods for global network inference have been developed and applied to a variety of species. Most approaches consider the problem of network inference independently in each species, despite evidence that gene regulation can be conserved even in distantly related species. Further, network inference is often confined to single data-types (single platforms) and single cell types. We introduce a method for multi-source network inference that allows simultaneous estimation of gene regulatory networks in multiple species or biological processes through the introduction of priors based on known gene relationships such as orthology incorporated using fused regression...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27922680/identification-of-key-genes-induced-by-platelet-rich-plasma-in-human-dermal-papilla-cells-using-bioinformatics-methods
#8
Haiyan Shen, Hanxiao Cheng, Haihua Chen, Jufang Zhang
Dermal papilla cells (DPCs) are located at the base of hair follicles, and are known to induce hair follicle regeneration. Platelet-rich plasma (PRP) functions in hair follicle regeneration. To investigate the influence of PRP on DPCs, the present study analyzed RNA‑seq data of human hair dermal papilla cells (HHDPCs) that were treated or untreated by PRP. The data included in the RNA‑seq were from two normal and two treated HHDPC samples. Following identification by Cuffdiff software, differentially expressed genes (DEGs) underwent enrichment analyses, and protein-protein interaction networks were constructed using Cytoscape software...
December 6, 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27922095/co-expression-network-analyses-identify-functional-modules-associated-with-development-and-stress-response-in-gossypium-arboreum
#9
Qi You, Liwei Zhang, Xin Yi, Kang Zhang, Dongxia Yao, Xueyan Zhang, Qianhua Wang, Xinhua Zhao, Yi Ling, Wenying Xu, Fuguang Li, Zhen Su
Cotton is an economically important crop, essential for the agriculture and textile industries. Through integrating transcriptomic data, we discovered that multi-dimensional co-expression network analysis was powerful for predicting cotton gene functions and functional modules. Here, the recently available transcriptomic data on Gossypium arboreum, including data on multiple growth stages of tissues and stress treatment samples were applied to construct a co-expression network exploring multi-dimensional expression (development and stress) through multi-layered approaches...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922078/malat1-and-hotair-long-non-coding-rnas-play-opposite-role-in-estrogen-mediated-transcriptional-regulation-in-prostate-cancer-cells
#10
Aurora Aiello, Lorenza Bacci, Agnese Re, Cristian Ripoli, Francesco Pierconti, Francesco Pinto, Riccardo Masetti, Claudio Grassi, Carlo Gaetano, Pier Francesco Bassi, Alfredo Pontecorvi, Simona Nanni, Antonella Farsetti
In the complex network of nuclear hormone receptors, the long non-coding RNAs (lncRNAs) are emerging as critical determinants of hormone action. Here we investigated the involvement of selected cancer-associated lncRNAs in Estrogen Receptor (ER) signaling. Prior studies by Chromatin Immunoprecipitation (ChIP) Sequencing showed that in prostate cancer cells ERs form a complex with the endothelial nitric oxide synthase (eNOS) and that in turn these complexes associate with chromatin in an estrogen-dependent fashion...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922073/a-single-step-method-for-rna-isolation-from-tropical-crops-in-the-field
#11
J-C Breitler, C Campa, F Georget, B Bertrand, H Etienne
The RNAzol RT reagent was used to provide pure RNA from human cells. We develop a protocol using RNAzol RT reagent to extract pure RNA from plants tissues and demonstrate that this RNA extraction method works not only at room temperature but also at elevated temperatures and provides the simplest and most effective single-step method to extract pure and undegraded RNA directly from tropical plants in the field. RNA extraction directly in a complex field environment opens up the way for studying gene-environment interactions at transcriptome level to decipher the complex regulatory network involved in multiple-stress responses...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922056/identification-and-functional-analysis-of-long-intergenic-noncoding-rna-genes-in-porcine-pre-implantation-embryonic-development
#12
Jingyu Li, Zhengling Gao, Xingyu Wang, Hongbo Liu, Yan Zhang, Zhonghua Liu
Genome-wide transcriptome studies have identified thousands of long intergenic noncoding RNAs (lincRNAs), some of which play important roles in pre-implantation embryonic development (PED). Pig is an ideal model for reproduction, however, porcine lincRNAs are still poorly characterized and it is unknown if they are associated with porcine PED. Here we reconstructed 195,531 transcripts in 122,007 loci, and identified 7,618 novel lincRNAs from 4,776 loci based on published RNA-seq data. These lincRNAs show low exon number, short length, low expression level, tissue-specific expression and cis-acting, which is consistent with previous reports in other species...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920338/the-plethora-gene-regulatory-network-guides-growth-and-cell-differentiation-in-arabidopsis-roots
#13
Luca Santuari, Gabino Sanchez-Perez, Marijn Luijten, Bas Rutjens, Inez Terpstra, Lidija Berke, Maartje Gorte, Kalika Prasad, Dongping Bao, Johanna L P M Timmermans-Hereijgers, Kenichiro Maeo, Kenzo Nakamura, Akie Shimotohno, Ales Pencik, Ondřej Novák, Karin Ljung, Sebastiaan van Heesch, Ewart de Bruijn, Edwin Cuppen, Viola Willemsen, Ari Pekka Mähönen, Wolfgang Lukowitz, Berend Snel, Dick de Ridder, Ben Scheres, Renze Heidstra
Organ formation in animals and plants relies on precise control of cell state transitions to turn stem cell daughters into fully differentiated cells. In plants, cells cannot rearrange due to shared cell walls. Thus, differentiation progression and the accompanying cell expansion must be tightly coordinated across tissues. PLETHORA (PLT) transcription factor gradients are unique in their ability to guide the progression of cell differentiation at different positions in the growing Arabidopsis root, which contrasts with well-described transcription factor gradients in animals specifying distinct cell fates within an essentially static context...
December 5, 2016: Plant Cell
https://www.readbyqxmd.com/read/27920295/a-novel-transcriptional-regulator-related-to-thiamine-phosphate-synthase-controls-thiamine-metabolism-genes-in-archaea
#14
Dmitry A Rodionov, Semen A Leyn, Xiaoqing Li, Irina A Rodionova
: Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamin biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages from the Crenarchaeota phylum, as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain that is similar to the archaeal thiamin phosphate synthase ThiN...
December 5, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27919733/variable-neighborhood-search-for-reverse-engineering-of-gene-regulatory-networks
#15
Charles Nicholson, Leslie Goodwin, Corey Clark
A new search heuristic, Divided Neighborhood Exploration Search, designed to be used with inference algorithms such as Bayesian networks to improve on the reverse engineering of gene regulatory networks is presented. The approach systematically moves through the search space to find topologies representative of gene regulatory networks that are more likely to explain microarray data. In empirical testing it is demonstrated that the novel method is superior to the widely employed greedy search techniques in both the quality of the inferred networks and computational time...
December 2, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27919219/ston-exploring-biological-pathways-using-the-sbgn-standard-and-graph-databases
#16
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/27918942/molecular-networks-orchestrating-plant-cell-growth
#17
REVIEW
Anna Franciosini, Bart Rymen, Michitaro Shibata, David S Favero, Keiko Sugimoto
Plant cell growth can broadly be categorized into either diffuse or tip growth. Here we compare gene regulatory networks (GRNs) controlling growth of hypocotyls and root hairs as examples for diffuse and tip growth, respectively. Accumulating evidence shows that GRNs in both cell types are multi-layered in structure and fine-tuned by transcriptional and post-translational mechanisms. We discuss how these GRNs regulate the expression of proteins controlling cell wall remodeling or other growth regulatory processes...
December 2, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27918939/the-shady-side-of-leaf-development-the-role-of-the-revoluta-kanadi1-module-in-leaf-patterning-and-auxin-mediated-growth-promotion
#18
REVIEW
Paz Merelo, Esther Botterweg Paredes, Marcus G Heisler, Stephan Wenkel
Leaves are present in all land plants and are specialized organs for light harvesting. They arise at the flanks of the shoot apical meristem (SAM), and develop into lamina structures that exhibit adaxial/abaxial (upper/lower side of the leaf) polarity. At the molecular level, an intricate regulatory network determines ad-/abaxial polarity in Arabidopsis thaliana leaves, where the Class III Homeodomain Leucine Zipper (HD-ZIPIII) and KANADI (KAN) proteins are key mediators. The HD-ZIPIII REVOLUTA (REV) is expressed in the adaxial domain of lateral organs, whereas KAN1 is involved in abaxial differentiation...
December 2, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27918583/the-gene-regulatory-network-of-lens-induction-is-wired-through-meis-dependent-shadow-enhancers-of-pax6
#19
Barbora Antosova, Jana Smolikova, Lucie Klimova, Jitka Lachova, Michaela Bendova, Iryna Kozmikova, Ondrej Machon, Zbynek Kozmik
Lens induction is a classical developmental model allowing investigation of cell specification, spatiotemporal control of gene expression, as well as how transcription factors are integrated into highly complex gene regulatory networks (GRNs). Pax6 represents a key node in the gene regulatory network governing mammalian lens induction. Meis1 and Meis2 homeoproteins are considered as essential upstream regulators of Pax6 during lens morphogenesis based on their interaction with the ectoderm enhancer (EE) located upstream of Pax6 transcription start site...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27918582/investigating-conservation-of-the-cell-cycle-regulated-transcriptional-program-in-the-fungal-pathogen-cryptococcus-neoformans
#20
Christina M Kelliher, Adam R Leman, Crystal S Sierra, Steven B Haase
The pathogenic yeast Cryptococcus neoformans causes fungal meningitis in immune-compromised patients. Cell proliferation in the budding yeast form is required for C. neoformans to infect human hosts, and virulence factors such as capsule formation and melanin production are affected by cell-cycle perturbation. Thus, understanding cell-cycle regulation is critical for a full understanding of virulence factors for disease. Our group and others have demonstrated that a large fraction of genes in Saccharomyces cerevisiae is expressed periodically during the cell cycle, and that proper regulation of this transcriptional program is important for proper cell division...
December 2016: PLoS Genetics
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