Characterization of E. coli Gene Regulatory Network and its Topological Enhancement by Edge Rewiring

2016 ◽  
Author(s):  
Satyaki Roy ◽  
Vijay Shah ◽  
Sajal Das
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
E Coli ◽  
Gene Regulatory

Characterization of a gene regulatory network underlying astringency loss in persimmon fruit

Planta ◽  
2017 ◽  
Vol 247 (3) ◽  
pp. 733-743 ◽  
Author(s):  
Soichiro Nishiyama ◽  
Noriyuki Onoue ◽  
Atsushi Kono ◽  
Akihiko Sato ◽  
Keizo Yonemori ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Persimmon Fruit ◽  
Gene Regulatory

scholarly journals A simple test to infer mode of selection in metagenomics time series of evolving asexual populations

2020 ◽  
Author(s):  
Rohan Maddamsetti ◽  
Nkrumah A. Grant
Keyword(s):  
Time Series ◽  
Positive Selection ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Fine Tuning ◽  
Simple Test ◽  
Regulatory Regions ◽  
E Coli ◽  
Gene Regulatory ◽  
Asexual Populations

ABSTRACTWe introduce a simple test to infer mode of selection (STIMS) in metagenomic time series of evolving asexual populations. STIMS compares the tempo of molecular evolution for a gene set of interest against a null distribution that is bootstrapped on random gene sets. We test STIMS on metagenomic data spanning 62,750 generations of Lenski’s long-term evolution experiment with E. coli (LTEE). Our method successfully recovers signals of purifying selection and positive selection on gold standard sets of genes. We then use STIMS to study the evolution of genetic modules in the LTEE. We find strong evidence of ongoing positive selection on key regulators of the E. coli gene regulatory network. Key regulatory genes show evidence of positive selection over the entire time series, even in some hypermutator populations. By contrast, we found no signal of selection on the genetic modules that show the strongest transcriptional responses to changes in growth conditions. In addition, the cis-regulatory regions of key regulators are evolving faster than the cis-regulatory regions of their downstream regulatory targets. These results indicate that one mechanistic cause for ongoing fitness gains in the LTEE is ongoing fine-tuning of the gene regulatory network.

scholarly journals Chromatin Accessibility-Based Characterization of the Gene Regulatory Network Underlying Plasmodium falciparum Blood-Stage Development

2018 ◽  
Vol 23 (4) ◽  
pp. 557-569.e9 ◽  
Author(s):  
Christa Geeke Toenhake ◽  
Sabine Anne-Kristin Fraschka ◽  
Mahalingam Shanmugiah Vijayabaskar ◽  
David Robert Westhead ◽  
Simon Jan van Heeringen ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Chromatin Accessibility ◽  
Blood Stage ◽  
Stage Development ◽  
Gene Regulatory

scholarly journals Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

2014 ◽  
Vol 25 (1) ◽  
pp. 41-56 ◽  
Author(s):  
Juan L. Mateo ◽  
Debbie L.C. van den Berg ◽  
Maximilian Haeussler ◽  
Daniela Drechsel ◽  
Zachary B. Gaber ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Regulatory Network ◽  
Neural Stem Cell ◽  
Regulatory Network ◽  
Self Renewal ◽  
Gene Regulatory ◽  
Cell Gene ◽  
Stem Cell Gene

scholarly journals Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

2017 ◽  
Vol 27 (12) ◽  
pp. 2129-2129
Author(s):  
Juan L. Mateo ◽  
Debbie L.C. van den Berg ◽  
Maximilian Haeussler ◽  
Daniela Drechsel ◽  
Zachary B. Gaber ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Regulatory Network ◽  
Neural Stem Cell ◽  
Regulatory Network ◽  
Self Renewal ◽  
Gene Regulatory ◽  
Cell Gene ◽  
Stem Cell Gene

scholarly journals IPSC-derived neuronal cultures expressing the Alzheimer’s disease associated rare TREM2 R47H variant enables the construction of an Aβ-induced gene regulatory network

2019 ◽  
Author(s):  
Soraia Martins ◽  
Andreas Müller-Schiffmann ◽  
Martina Bohndorf ◽  
Wasco Wruck ◽  
Kristel Sleegers ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Immune Response ◽  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Molecular Mechanisms ◽  
Late Onset ◽  
Neuronal Cultures ◽  
Gene Regulatory

AbstractRecently, genes associated with immune response and inflammation have been identified as genetic risk factors for late-onset Alzheimer’s disease (LOAD). One of them is the rare p.Arg47His (R47H) variant within triggering receptor expressed on myeloid cells 2 (TREM2), which has been shown to increase the risk for developing AD 2-3-fold. Here, we report the generation and characterization of a model of LOAD using lymphoblast-derived iPSCs from patients harbouring the R47H mutation in TREM2 (AD TREM2 iPSCs), as well as from control individuals without dementia (CON iPSCs). iPSCs efficiently differentiate into mature neuronal cultures and comparative global transcriptome analysis identified a distinct gene expression profile in AD TREM2 neuronal cultures. Furthermore, manipulation of the iPSC-derived functional neuronal cultures with an Aβ-S8C dimer highlighted metabolic pathways, phagosome and immune response as the most perturbed pathways in AD TREM2 neuronal cultures. Through the construction of an Aβ-induced gene regulatory network, we were able to identify an Aβ signature linked to protein processing in the endoplasmic reticulum (ER) which emphasised ER-stress, as a potential causal role in LOAD. Overall, this study has shown that our AD-iPSC based model can be used for in-depth studies to better understand the molecular mechanisms underlying the etiology of LOAD and provides new opportunities for screening of potential therapeutic targets.

scholarly journals Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

2016 ◽  
Vol 26 (11) ◽  
pp. 1626-1626
Author(s):  
Juan L. Mateo ◽  
Debbie L.C. van den Berg ◽  
Maximilian Haeussler ◽  
Daniela Drechsel ◽  
Zachary B. Gaber ◽  
...  
Keyword(s):  
Stem Cell ◽  
Gene Regulatory Network ◽  
Neural Stem Cell ◽  
Regulatory Network ◽  
Self Renewal ◽  
Gene Regulatory ◽  
Cell Gene ◽  
Stem Cell Gene

scholarly journals Characterization of the proneural gene regulatory network during mouse telencephalon development

BMC Biology ◽  
2008 ◽  
Vol 6 (1) ◽  
pp. 15 ◽  
Author(s):  
Julia M Gohlke ◽  
Olivier Armant ◽  
Frederick M Parham ◽  
Marjolein V Smith ◽  
Celine Zimmer ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Regulatory Network ◽  
Proneural Gene ◽  
Gene Regulatory
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