keyword
MENU ▼
Read by QxMD icon Read
search

Expression genomic integration

keyword
https://www.readbyqxmd.com/read/28820946/proteogenomic-investigation-of-strain-variation-in-clinical-mycobacterium-tuberculosis-isolates
#1
Tiaan Heunis, Anzaan Dippenaar, Robin M Warren, Paul D van Helden, Ruben G van der Merwe, Nicolaas C Gey van Pittius, Arnab Pain, Samantha L Sampson, David L Tabb
Mycobacterium tuberculosis consists of a large number of different strains that display unique virulence characteristics. Whole-genome sequencing has revealed substantial genetic diversity among clinical M. tuberculosis isolates, and elucidating the phenotypic variation encoded by this genetic diversity will be of utmost importance to fully understand M. tuberculosis biology and pathogenicity. In this study we integrated whole-genome sequencing and mass spectrometry (GeLC-MS/MS) to reveal strain-specific characteristics in the proteomes of two clinical M...
August 18, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28819308/an-optimal-mean-based-block-robust-feature-extraction-method-to-identify-colorectal-cancer-genes-with-integrated-data
#2
Jian Liu, Yuhu Cheng, Xuesong Wang, Lin Zhang, Hui Liu
It is urgent to diagnose colorectal cancer in the early stage. Some feature genes which are important to colorectal cancer development have been identified. However, for the early stage of colorectal cancer, less is known about the identity of specific cancer genes that are associated with advanced clinical stage. In this paper, we conducted a feature extraction method named Optimal Mean based Block Robust Feature Extraction method (OMBRFE) to identify feature genes associated with advanced colorectal cancer in clinical stage by using the integrated colorectal cancer data...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819235/expression-of-long-non-coding-rna-mfi2-as1-is-a-strong-predictor-of-recurrence-in-sporadic-localized-clear-cell-renal-cell-carcinoma
#3
Ronan Flippot, Roger Mouawad, Jean-Philippe Spano, Morgan Rouprêt, Eva Compérat, Marc-Olivier Bitker, Jérôme Parra, Christophe Vaessen, Frederick Allanic, Quentin Manach, Nizar M Tannir, David Khayat, Xiaoping Su, Gabriel G Malouf
Prediction of recurrence is a challenge for the development of adjuvant treatments in clear-cell renal cell carcinoma (ccRCC). In these tumors, expression of long non-coding RNAs (lncRNAs) are deregulated and closely associated with prognosis. Thus, we aimed to predict ccRCC recurrence risk using lncRNA expression. We identified prognostic lncRNAs in a training set of 351 localized ccRCCs from The Cancer Genome Atlas and validated lncRNA-based recurrence classification in an independent cohort of 167 localized ccRCCs...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818866/systematic-identification-of-determinants-for-single-strand-annealing-mediated-deletion-formation-in-saccharomyces-cerevisiae
#4
Maia Segura-Wang, Megumi Onishi-Seebacher, Adrian M Stütz, Balca R Mardin, Jan O Korbel
To ensure genomic integrity, living organisms have evolved diverse molecular processes for sensing and repairing damaged DNA. If improperly repaired, DNA damage can give rise to different types of mutations, an important class of which are the genomic structural variants (SVs). In spite of their importance for phenotypic variation and genome evolution, potential contributors to SV formation in Saccharomyces cerevisiae (budding yeast), a highly tractable model organism, are not fully recognized. Here we developed and applied a genome-wide assay to identify yeast gene knock-out mutants associated with de novo deletion formation, in particular single strand annealing (SSA) -mediated deletion formation in a systematic manner...
August 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28818737/genome-wide-dna-methylation-profiling-of-articular-cartilage-reveals-significant-epigenetic-alterations-in-kashin-beck-disease-and-osteoarthritis
#5
Wenyu Wang, Yan Yu, Jingcan Hao, Yan Wen, Jing Han, Weikun Hou, Ruiyu Liu, Bo Zhao, Awen He, Ping Li, Qianrui Fan, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Xiong Guo, Feng Zhang
OBJECTIVE: To determine genome-wide DNA methylation profiles of knee cartilage from patients with Kashin-Beck disease (KBD) and osteoarthritis (OA). METHOD: Knee cartilage was collected from 14 grade III KBD patients, 5 primary OA patients and 13 healthy subjects. The genome-wide methylation profiles of 5 KBD cartilage, 5 OA cartilage and 5 normal cartilage were determined by Illumina HumanMethylation450 array. Illumina Methylation Analyzer package was employed for identifying differentially methylated CpG sites...
August 14, 2017: Osteoarthritis and Cartilage
https://www.readbyqxmd.com/read/28817720/targeting-of-cdk9-with-indirubin-3-monoxime-safely-and-durably-reduces-hiv-viremia-in-chronically-infected-humanized-mice
#6
Sandra Medina-Moreno, Thomas C Dowling, Juan C Zapata, Nhut M Le, Edward Sausville, Joseph Bryant, Robert R Redfield, Alonso Heredia
Successful propagation of HIV in the human host requires entry into a permissive cell, reverse transcription of viral RNA, integration into the human genome, transcription of the integrated provirus, and assembly/release of new virus particles. Currently, there are antiretrovirals against each of these viral steps, except for provirus transcription. An inhibitor of HIV transcription could both increase potency of treatment and suppress drug-resistant strains. Cellular cyclin-dependent kinase 9 (CDK9) serves as a cofactor for the HIV Tat protein and is required for effective transcription of the provirus...
2017: PloS One
https://www.readbyqxmd.com/read/28817151/comprehensive-analysis-of-long-noncoding-rna-mrna-co-expression-patterns-in-thyroid-cancer
#7
Yaying Du, Wenfei Xia, Jinjun Zhang, Dongyi Wan, Zhifang Yang, Xingrui Li
Novel molecular-targeted treatments show great prospects for radioiodine-refractory and surgically inoperable thyroid carcinomas. While aberrations in protein-coding genes are a focus in molecular thyroid cancer medicine, the impact of oncogenes on the expression of long noncoding RNAs (lncRNAs) has been largely uncharacterized. We aimed to identify the expression patterns of lncRNAs and mRNAs in high-throughput molecular profiles of 18 papillary thyroid cancer (PTC) patients. We identified 452 mRNAs and 240 unannotated lncRNAs that were differentially expressed in PTC...
August 17, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28817121/meganuclease-assisted-generation-of-stable-transgenics-in-the-sea-anemone-nematostella-vectensis
#8
Eduard Renfer, Ulrich Technau
The sea anemone Nematostella vectensis is a model system used by a rapidly growing research community for comparative genomics, developmental biology and ecology. Here, we describe a microinjection procedure for creating stable transgenic lines in Nematostella based on meganuclease (I-SceI)-assisted integration of a transgenic cassette into the genome. The procedure describes the preparation of the reagents, microinjection of the transgenesis vector and the husbandry of transgenic animals. The microinjection setup differs from those of previously published protocols by the use of a holding capillary mounted on an inverted fluorescence microscope...
September 2017: Nature Protocols
https://www.readbyqxmd.com/read/28815679/-epigallocatechin-3-gallate-and-atorvastatin-treatment-down-regulates-liver-fibrosis-related-genes-in-non-alcoholic-fatty-liver-disease
#9
Le Ying, Feng Yan, Yueling Zhao, Hugh Gao, Bryan Rg Williams, Yiqun Hu, Xiaofang Li, Run Tian, Ping Xu, Yuefei Wang
Non-alcoholic fatty liver disease (NAFLD) and associated advanced liver diseases have become prevalent conditions in many countries and are associated with increased mortality. Gene expression profiles in NAFLD have been examined recently but changes in expression elicited by chemical compound treatments have not been investigated. Since (-)-Epigallocatechin-3-gallate (EGCG) and atorvastatin (ATST) exhibit similar efficacy in NAFLD models, we reasoned that some common key genes might alter after treatment of EGCG and ATST...
August 16, 2017: Clinical and Experimental Pharmacology & Physiology
https://www.readbyqxmd.com/read/28815499/marker-removal-in-transgenic-plants-using-cre-recombinase-delivered-with-potato-virus-x
#10
Lilya Kopertekh, Joachim Schiemann
In this chapter we present an alternative method to develop marker-free transgenic plants. It makes use of the Cre/loxP recombination system from bacteriophage P1 and consists of two essential components. The first component is the transgenic plant containing a loxP-flanked marker gene. The second component is a cre transient expression vector based on potato virus X. The great benefit of this transient delivery method consists in the avoidance of stable integration of the cre recombinase gene into the plant genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28814974/time-resolved-transcriptome-analysis-and-lipid-pathway-reconstruction-of-the-oleaginous-green-microalga-monoraphidium-neglectum-reveal-a-model-for-triacylglycerol-and-lipid-hyperaccumulation
#11
Daniel Jaeger, Anika Winkler, Jan H Mussgnug, Jörn Kalinowski, Alexander Goesmann, Olaf Kruse
BACKGROUND: Oleaginous microalgae are promising production hosts for the sustainable generation of lipid-based bioproducts and as bioenergy carriers such as biodiesel. Transcriptomics of the lipid accumulation phase, triggered efficiently by nitrogen starvation, is a valuable approach for the identification of gene targets for metabolic engineering. RESULTS: An explorative analysis of the detailed transcriptional response to different stages of nitrogen availability was performed in the oleaginous green alga Monoraphidium neglectum...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28814758/targeted-insertion-of-an-anti-cd2-monoclonal-antibody-transgene-into-the-ggta1-locus-in-pigs-using-foki-dcas9
#12
Mark B Nottle, Evelyn J Salvaris, Nella Fisicaro, Stephen McIlfatrick, Ivan Vassiliev, Wayne J Hawthorne, Philip J O'Connell, Jamie L Brady, Andrew M Lew, Peter J Cowan
Xenotransplantation from pigs has been advocated as a solution to the perennial shortage of donated human organs and tissues. CRISPR/Cas9 has facilitated the silencing of genes in donor pigs that contribute to xenograft rejection. However, the generation of modified pigs using second-generation nucleases with much lower off-target mutation rates than Cas9, such as FokI-dCas9, has not been reported. Furthermore, there have been no reports on the use of CRISPR to knock protective transgenes into detrimental porcine genes...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814642/an-indel-in-the-promoter-of-al-activated-malate-transporter-9-selected-during-tomato-domestication-determines-fruit-malate-contents-and-aluminum-tolerance
#13
Jie Ye, Xin Wang, Ti Xu Hu, Feng Xia Zhang, Bing Wang, Chang Xin Li, Tian Xia Yang, Han Xia Li, Yong En Lu, James J Giovannoni, Yuyang Zhang, Zhibiao Ye
Deciphering the mechanism of malate accumulation in plants would contribute to a greater understanding of plant chemistry, which has implications for improving flavor quality in crop species and enhancing human health benefits. However, the regulation of malate metabolism is poorly understood in crops such as tomato (Solanum lycopersicum). Here, we integrated a metabolite-based genome-wide association study (mGWAS) with linkage mapping and gene functional studies to characterize the genetics of malate accumulation in a global collection of tomato accessions with broad genetic diversity...
August 16, 2017: Plant Cell
https://www.readbyqxmd.com/read/28811643/overexpressed-somatic-alleles-are-enriched-in-functional-elements-in-breast-cancer
#14
Paula Restrepo, Mercedeh Movassagh, Nawaf Alomran, Christian Miller, Muzi Li, Chris Trenkov, Yulian Manchev, Sonali Bahl, Stephanie Warnken, Liam Spurr, Tatiyana Apanasovich, Keith Crandall, Nathan Edwards, Anelia Horvath
Asymmetric allele content in the transcriptome can be indicative of functional and selective features of the underlying genetic variants. Yet, imbalanced alleles, especially from diploid genome regions, are poorly explored in cancer. Here we systematically quantify and integrate the variant allele fraction from corresponding RNA and DNA sequence data from patients with breast cancer acquired through The Cancer Genome Atlas (TCGA). We test for correlation between allele prevalence and functionality in known cancer-implicated genes from the Cancer Gene Census (CGC)...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811563/crosstalk-between-diurnal-rhythm-and-water-stress-reveals-an-altered-primary-carbon-flux-into-soluble-sugars-in-drought-treated-rice-leaves
#15
Seo-Woo Kim, Sang-Kyu Lee, Hee-Jeong Jeong, Gynheung An, Jong-Seong Jeon, Ki-Hong Jung
Plants retain rhythmic physiological responses when adapting to environmental challenges. However, possible integrations between drought conditions and those responses have not received much focus, especially regarding crop plants, and the relationship between abiotic stress and the diurnal cycle is generally not considered. Therefore, we conducted a genome-wide analysis to identify genes showing both diurnal regulation and water-deficiency response in rice (Oryza sativa). Among the 712 drought-responsive genes primary identified, 56...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811362/nuclear-envelope-rupture-is-enhanced-by-loss-of-p53-or-rb
#16
Zhe Yang, John Maciejowski, Titia de Lange
The mammalian nuclear envelope (NE) forms a stable physical barrier between the nucleus and the cytoplasm, normally breaking down only during the cell cycle phase of mitosis. However, spontaneous transient NE rupture in interphase can occur when NE integrity is compromised such as when the nucleus experiences mechanical stress. For instance, deficiencies in the nuclear lamins and their associated proteins can cause NE rupture that is promoted by forces exerted by actin filaments. NE rupture can allow cytoplasmic nucleases to access chromatin, potentially compromising genome integrity...
August 15, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28810930/sex-differences-in-microrna-mrna-networks-examination-of-novel-epigenetic-programming-mechanisms-in-the-sexually-dimorphic-neonatal-hypothalamus
#17
Christopher P Morgan, Tracy L Bale
BACKGROUND: Sexual differentiation of the male brain, and specifically the stress circuitry in the hypothalamus, is primarily driven by estrogen exposure during the perinatal period. Surprisingly, this single hormone promotes diverse programs of sex-specific development that vary widely between different cell types and across the developing male brain. The complexity of this phenomenon suggests that additional layers of gene regulation, including microRNAs (miRNAs), must act downstream of estrogen to mediate this specificity...
August 15, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/28810832/genome-wide-analysis-of-basic-helix-loop-helix-bhlh-transcription-factors-in-brachypodium-distachyon
#18
Xin Niu, Yuxiang Guan, Shoukun Chen, Haifeng Li
BACKGROUND: As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS: A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28809126/comprehensive-epigenetic-analysis-of-the-signature-genes-in-lung-adenocarcinoma
#19
Yunfeng Zhang, Weidong Zhao, Jia Zhang
AIM: This study aimed to explore the epigenetic modifications of signature genes in lung adenocarcinoma. MATERIALS & METHODS: The data of miRNA expression, mRNA expression and DNA methylation were downloaded from The Cancer Genome Atlas. Differential analysis was performed, followed by correlation analysis of miRNA-mRNA and DNA methylation-mRNA. RESULTS: A total of 14 significant inverse correlations between gene expression and DNA methylation were identified, the expressions of which were selected for further validation via GSE27262, displaying similar pattern with that of the integrated analysis...
August 15, 2017: Epigenomics
https://www.readbyqxmd.com/read/28809021/genetic-manipulation-of-the-avian-urogenital-system-using-in-ovo-electroporation
#20
Claire E Hirst, Olivier Serralbo, Katie L Ayers, Kelly N Roeszler, Craig A Smith
One of the advantages of the avian embryo as an experimental model is its in ovo development and hence accessibility for genetic manipulation. Electroporation has been used extensively in the past to study gene function in chicken and quail embryos . Readily accessible tissues such as the neural tube, somites, and limb bud, in particular, have been targeted. However, more inaccessible tissues, such as the embryonic urogenital system , have proven more challenging to study. Here, we describe the use of in ovo electroporation of TOL2 vectors or RCASBP avian viral vectors for the rapid functional analysis of genes involved in avian sex determination and urogenital development ...
2017: Methods in Molecular Biology
keyword
keyword
40958
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"