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EDGAR 2.0: an enhanced software platform for comparative gene content analyses
2016
Nucleic Acids Research
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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]
2019
Phylogenetics [Working Title]
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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
2015
PLoS ONE
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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
2018
BMC Genomics
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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
2015
Journal of Experimental Botany
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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
2020
JCI Insight
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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
2017
Plant Biotechnology Journal
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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
2022
Cells
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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
2015
Biomedical Materials
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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
2013
Journal of Experimental Botany
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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
2021
Scientific Reports
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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
2020
PLoS Biology
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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
2020
Neurobiology of Disease
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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)
2021
Journal of Chemical Ecology
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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
2019
F1000Research
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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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