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EDGAR 2.0: an enhanced software platform for comparative gene content analyses

Jochen Blom, Julian Kreis, Sebastian Spänig, Tobias Juhre, Claire Bertelli, Corinna Ernst, Alexander Goesmann
2016 Nucleic Acids Research  
For the new version, EDGAR 2.0, the gene orthology estimation approach was newly designed and completely re-implemented.  ...  Since initial publication, the EDGAR platform has become one of the most established software tools in the field of comparative genomics.  ...  ACKNOWLEDGEMENT The authors further wish to thank the Bioinformatics Core Facility (BCF) for expert technical support.  ... 
doi:10.1093/nar/gkw255 pmid:27098043 pmcid:PMC4987874 fatcat:5btj3lxjwngs5cqfuakgzestiy

Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins [chapter]

Edna María Hernández-Domínguez, Laura Sofía Castillo-Ortega, Yarely García-Esquivel, Virginia Mandujano-González, Gerardo Díaz-Godínez, Jorge Álvarez-Cervantes
2019 Phylogenetics [Working Title]  
EDGAR 2.0: An enhanced software platform for comparative gene content analyses. Nucleic Acids Research. 2016;44:22-28.  ...  Next-generation whole-genome sequencing platforms and factors to consider for bacterial applications. Journal of Guide to the Analysis of Genes and Proteins. 2nd ed.  ... 
doi:10.5772/intechopen.89594 fatcat:tlvlcnde2bbyniucmaqk2ar6om

Combinatorial Effects of Fatty Acid Elongase Enzymes on Nervonic Acid Production in Camelina sativa

Dongxin Huai, Yuanyuan Zhang, Chunyu Zhang, Edgar B. Cahoon, Yongming Zhou, Thierry Chardot
2015 PLoS ONE  
for oilseed enhancement.  ...  However, compared with that from the LaKCS-expressing lines, nervonic acid content in mature seeds from the co-expressing lines with one or two extra elongase genes did not show further increases.  ...  Nazarenus for support of camelina transformation and Rebecca E. Cahoon for Acyl-CoAs analysis. Author Contributions  ... 
doi:10.1371/journal.pone.0131755 pmid:26121034 pmcid:PMC4485900 fatcat:qqlplfsgafge5cxyyj42avneuy

Identification of placental nutrient transporters associated with intrauterine growth restriction and pre-eclampsia

Xiao Huang, Pascale Anderle, Lu Hostettler, Marc U. Baumann, Daniel V. Surbek, Edgar C. Ontsouka, Christiane Albrecht
2018 BMC Genomics  
Targets of interest were clustered into a substrate-specific interaction network by using Search Tool for the Retrieval of Interacting Genes.  ...  Protein analyses in total placental tissue lysates and membrane fractions isolated from disease and control placentas indicated an altered functional activity of those three nutrient transporters in IUGR  ...  Michael Lüthi for the technical support, Prof. Matthias A. Hediger, Dr. Alexandre Simonin, Dr. Sara El-Gebali and Dr.Cedric Simillion for fruitful discussions.  ... 
doi:10.1186/s12864-018-4518-z pmid:29499643 pmcid:PMC5833046 fatcat:r52c2fpqhrerxpaqscjwy5itha

Toward production of jet fuel functionality in oilseeds: identification of FatB acyl-acyl carrier protein thioesterases and evaluation of combinatorial expression strategies inCamelinaseeds

Hae Jin Kim, Jillian E. Silva, Hieu Sy Vu, Keithanne Mockaitis, Jeong-Won Nam, Edgar B. Cahoon
2015 Journal of Experimental Botany  
Camelina lines presented here provide platforms for additional metabolic engineering targeting fatty acid synthase and specialized acyltransferases for achieving oils with high levels of jet fuel-type  ...  Studies were conducted to test genes, including those from Cuphea, for their ability to confer jet fuel-type fatty acid accumulation in seed oil of the emerging biofuel crop Camelina sativa.  ...  Acknowledgements The research was funded by the Center for Advanced Biofuel Systems (CABS), an Energy Frontier Research Center funded by the US Department of Energy, Office of Basic Energy Sciences under  ... 
doi:10.1093/jxb/erv225 pmid:25969557 pmcid:PMC4493788 fatcat:pfnanlpr3jaonmrg3jctm6gu7e

Single cell transcriptomics identifies focal segmental glomerulosclerosis remission endothelial biomarker

Rajasree Menon, Edgar A. Otto, Paul J. Hoover, Sean Eddy, Laura H. Mariani, Bradley Godfrey, Celine C. Berthier, Felix Eichinger, Lalita Subramanian, Jennifer L. Harder, Wenjun Ju, Viji Nair (+9 others)
2020 JCI Insight  
The mRNA content and number of genes of doublets are comparatively higher than mRNA content and number of genes of single cells.  ...  This cluster had a comparatively higher mRNA content (Supplemental Figure 1B ).  ... 
doi:10.1172/jci.insight.133267 pmid:32107344 pmcid:PMC7213795 fatcat:sns2bgfq3bhwtdh2olkudqerhm

Development of iFOX-hunting as a functional genomic tool and demonstration of its use to identify early senescence-related genes in the polyploid Brassica napus

Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xu, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou (+2 others)
2017 Plant Biotechnology Journal  
Here we report development of a gain-of-function platform, termed 'iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting', for inducible expression of B. napus seed cDNAs in Arabidopsis.  ...  The integrated B. napus cDNA was identified as a homolog of an Arabidopsis acyl-CoA binding protein (ACBP) gene designated BnACBP1-like.  ...  We thank Zhengwei Shang for care of plant material. We thank Dr. Chibuzo Nwaoguala of University of Benin Nigeria for critical comments on the manuscript. The authors declare no conflict of interest.  ... 
doi:10.1111/pbi.12799 pmid:28718508 pmcid:PMC5787830 fatcat:gsj3axdvwfe6xi335jhrvmhqwa

Identification of a Potent Cytotoxic Pyrazole with Anti-Breast Cancer Activity That Alters Multiple Pathways

Denisse A. Gutierrez, Lisett Contreras, Paulina J. Villanueva, Edgar A. Borrego, Karla Morán-Santibañez, Jessica D. Hess, Rebecca DeJesus, Manuel Larragoity, Ana P. Betancourt, Jonathon E. Mohl, Elisa Robles-Escajeda, Khodeza Begum (+4 others)
2022 Cells  
In support of our in vitro assays, transcriptome analyses of two distinct TNBC cell lines (MDA-MB-231 and MDA-MB-468 cells) treated with P3C revealed 28 genes similarly affected by the treatment implicated  ...  Acknowledgments: The authors thank Gladys Almodovar for the cell culture expertise and services provided, and personnel of the Genomic Analysis and the Cell Characterization and Biorepository Core Facilities  ...  with a cut-off of ≥2.0 or ≤−2.0-fold change for upand down-regulated genes, respectively.  ... 
doi:10.3390/cells11020254 pmid:35053370 pmcid:PMC8773755 fatcat:ifpb3njj6jhsbhqegbtuyuvcka

Bone regeneration and gene expression in bone defects under healthy and osteoporotic bone conditions using two commercially available bone graft substitutes

Claire I A van Houdt, Carla R Tim, Murilo C Crovace, Edgar D Zanotto, Oscar Peitl, Dietmar J O Ulrich, John A Jansen, Nivaldo A Parizotto, Ana C Renno, Jeroen J J P van den Beucken
2015 Biomedical Materials  
The relative gene expression was increased with Biosilicate ® for all genes in OVX rats and for Runx-2, ALP, OC and RANKL in SHAM rats.  ...  In contrast, with Bio-Oss ® , the relative gene expression of OVX rats was similar for all three groups. For SHAM rats it was increased for Runx-2, ALP, OC and RANKL.  ...  Acknowledgments The authors thank CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior) for financial support. Author 1 and Author 2 contributed equally to this work.  ... 
doi:10.1088/1748-6041/10/3/035003 pmid:25953955 fatcat:75pjk2rt2rguljro4cfgb3abzq

A thraustochytrid diacylglycerol acyltransferase 2 with broad substrate specificity strongly increases oleic acid content in engineered Arabidopsis thaliana seeds

Chunyu Zhang, Umidjon Iskandarov, Elliott T. Klotz, Robyn L. Stevens, Rebecca E. Cahoon, Tara J. Nazarenus, Suzette L. Pereira, Edgar B. Cahoon
2013 Journal of Experimental Botany  
These results suggest that increased seed oleic acid content mediated by TaDGAT2 is influenced in part by the fatty acid composition of host cells and occurs not by enhancing oleic acid content at the  ...  Diacylglycerol acyltransferase (DGAT) catalyses the last step in acyl-CoA-dependent triacylglycerol (TAG) biosynthesis and is an important determinant of cellular oil content and quality.  ...  Acknowledgements The authors thank the Center for Advanced Biofuel Systems (CABS), an Energy Frontier Research Center funded by the US Department of Energy, Office of Basic Energy Sciences for funding  ... 
doi:10.1093/jxb/ert156 pmid:23814277 pmcid:PMC3733143 fatcat:q6kybd4hrrf6xf53ho5tcnqkje

Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics

Carola Berger, Christian Rückert, Jochen Blom, Korneel Rabaey, Jörn Kalinowski, Miriam A. Rosenbaum
2021 Scientific Reports  
For both of these, the increased virulence has been directly linked to their accessory genome before.  ...  AbstractThe isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes.  ...  Tobias Busche and Anika Winkler from the CeBiTec in Bielefeld for generating the MinION library, performing the sequencing and in general for the excellent technical assistance.  ... 
doi:10.1038/s41598-020-80592-8 pmid:33446769 fatcat:7rf7oadpg5echkonblxq7b4dxi

Snail synchronizes endocycling in a TOR-dependent manner to coordinate entry and escape from endoreplication pausing during the Drosophila critical weight checkpoint

Jie Zeng, Nhan Huynh, Brian Phelps, Kirst King-Jones, Bruce Edgar
2020 PLoS Biology  
is terminated through a cascade of peptide and steroid hormones that end larval feeding behavior and trigger metamorphosis, a nonfeeding stage during which the larval body plan is remodeled to produce an  ...  Before and during the CW checkpoint, snail is highly expressed in the larval prothoracic gland (PG), an endocrine tissue undergoing endoreplication and primarily dedicated to the production of the steroid  ...  Hwei-Jan Hsu for providing important fly stocks, as well as Dr. Julia Zeitlinger for generously sending anti-Snail antibodies. We greatly appreciate the help and advice from Dr.  ... 
doi:10.1371/journal.pbio.3000609 pmid:32097403 pmcid:PMC7041797 fatcat:dfawygw4w5hytjsd7af3jxydju

Parkin deficiency perturbs striatal circuit dynamics

Magdalena K. Baaske, Edgar R. Kramer, Durga Praveen Meka, Gerhard Engler, Andreas K. Engel, Christian K.E. Moll
2020 Neurobiology of Disease  
Loss-of-function mutations in the parkin-encoding PARK2 gene are a frequent cause of young-onset, autosomal recessive Parkinson's disease (PD).  ...  The entire transgenic striatal microcircuit showed enhanced and phase-shifted phase coupling to slow (1-3 Hz) cortical population oscillations.  ...  analyses.  ... 
doi:10.1016/j.nbd.2020.104737 pmid:31923460 fatcat:eqrxqplh5bhdpbt3xlhweb2cja

Green Chemistry Production of Codlemone, the Sex Pheromone of the Codling Moth (Cydia pomonella), by Metabolic Engineering of the Oilseed Crop Camelina (Camelina sativa)

Yi-Han Xia, Hong-Lei Wang, Bao-Jian Ding, Glenn P. Svensson, Carin Jarl-Sunesson, Edgar B. Cahoon, Per Hofvander, Christer Löfstedt
2021 Journal of Chemical Ecology  
Camelina (Camelina sativa) has emerged as an ideal, non-food biotech oilseed platform for production of oils with modified fatty acid compositions.  ...  Different transgene combinations were investigated for increasing pheromone precursor yield.  ...  The analyses of the entire fatty acid profile (Fig. 6 ) showed that 83 of the CPRQ2.1 transformants (Fig. 6c ) had reduced content of 12:0.  ... 
doi:10.1007/s10886-021-01316-4 pmid:34762210 pmcid:PMC8642345 fatcat:mhh5wt5rlbhndetse2m3d26ria

An in vitro model for studying CNS white matter: functional properties and experimental approaches

Silvia Bijland, Gemma Thomson, Matthew Euston, Kyriakos Michail, Katja Thümmler, Steve Mücklisch, Colin L. Crawford, Susan C. Barnett, Mark McLaughlin, T. James Anderson, Christopher Linington, Euan R. Brown (+2 others)
2019 F1000Research  
Further, we show they are (i) amenable to siRNA making them suitable for testing gene-silencing strategies; (ii) can be established on microelectrode arrays (MEAs) for electrophysiological studies; and  ...  Together, these advances increase the utility of this in vitro tool for studying normal and pathological development and function of white matter, and for screening therapeutic molecules or gene targets  ...  Further, the possibility of modifying it for use as an electrophysiological or gene silencing assay has not been explored.  ... 
doi:10.12688/f1000research.16802.1 pmid:31069065 pmcid:PMC6489523 fatcat:qthxuma4cfbi5mthz2nhhxyesq
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