keyword
MENU ▼
Read by QxMD icon Read
search

gene profile

keyword
https://www.readbyqxmd.com/read/28806730/a-systems-approach-reveals-distinct-metabolic-strategies-among-the-nci-60-cancer-cell-lines
#1
Maike K Aurich, Ronan M T Fleming, Ines Thiele
The metabolic phenotype of cancer cells is reflected by the metabolites they consume and by the byproducts they release. Here, we use quantitative, extracellular metabolomic data of the NCI-60 panel and a novel computational method to generate 120 condition-specific cancer cell line metabolic models. These condition-specific cancer models used distinct metabolic strategies to generate energy and cofactors. The analysis of the models' capability to deal with environmental perturbations revealed three oxotypes, differing in the range of allowable oxygen uptake rates...
August 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28806487/gut-microbiome-response-to-short-term-dietary-interventions-in-reactive-hypoglycemia-subjects
#2
Sara Quercia, Silvia Turroni, Jessica Fiori, Matteo Soverini, Simone Rampelli, Elena Biagi, Andrea Castagnetti, Clarissa Consolandi, Marco Severgnini, Mario Pianesi, Francesco Fallucca, Paolo Pozzilli, Patrizia Brigidi, Marco Candela
BACKGROUND: Reactive hypoglycemia (RH) is a metabolic disorder that provokes severe hypoglycemic episodes after meal. Over recent years, the gut microbiota (GM) has been recognized as potential target for the control of metabolic diseases, and the possibility to correct GM dysbioses through diet, favoring the recovery of metabolic homeostasis, has been considered. METHODS: We investigate the impact of two short-term (3-day) nutritional interventions, based on the macrobiotic Ma-Pi 2 diet and a control Mediterranean diet, on the structure and functionality of the GM in 12 patients affected by RH...
August 14, 2017: Diabetes/metabolism Research and Reviews
https://www.readbyqxmd.com/read/28806393/craf-gene-fusions-in-pediatric-low-grade-gliomas-define-a-distinct-drug-response-based-on-dimerization-profiles
#3
P Jain, T M Fierst, H J Han, T E Smith, A Vakil, P J Storm, A C Resnick, A J Waanders
Pediatric low-grade gliomas (PLGGs) are commonly associated with BRAF gene fusions that aberrantly activate the mitogen-activated protein kinase (MAPK) signaling pathway. This has led to PLGG clinical trials utilizing RAF- and MAPK pathway-targeted therapeutics. Whole-genome profiling of PLGGs has also identified rare gene fusions involving another RAF isoform, CRAF/RAF1, in PLGGs and cancers occuring in adults. Whereas BRAF fusions primarily dysregulate MAPK signaling, the CRAF fusions QKI-RAF1 and SRGAP3-RAF1 aberrantly activate both the MAPK and phosphoinositide-3 kinase/mammalian target of rapamycin (PI3K/mTOR) signaling pathways...
August 14, 2017: Oncogene
https://www.readbyqxmd.com/read/28806280/integrated-analysis-of-biopsies-from-inflammatory-bowel-disease-patients-identifies-saa1-as-a-link-between-mucosal-microbes-with-th17-and-th22-cells
#4
Mei San Tang, Rowann Bowcutt, Jacqueline M Leung, Martin J Wolff, Uma M Gundra, David Hudesman, Lisa B Malter, Michael A Poles, Lea Ann Chen, Zhiheng Pei, Antonio G Neto, Wasif M Abidi, Thomas Ullman, Lloyd Mayer, Richard A Bonneau, Ilseung Cho, Pʼng Loke
BACKGROUND: Inflammatory bowel diseases (IBD) are believed to be driven by dysregulated interactions between the host and the gut microbiota. Our goal is to characterize and infer relationships between mucosal T cells, the host tissue environment, and microbial communities in patients with IBD who will serve as basis for mechanistic studies on human IBD. METHODS: We characterized mucosal CD4 T cells using flow cytometry, along with matching mucosal global gene expression and microbial communities data from 35 pinch biopsy samples from patients with IBD...
August 9, 2017: Inflammatory Bowel Diseases
https://www.readbyqxmd.com/read/28806271/luminal-chemosensing-in-the-gastroduodenal-mucosa
#5
Izumi Kaji, Jonathan D Kaunitz
PURPOSE OF REVIEW: We report recently published knowledge regarding gut chemosensory mechanisms focusing on nutrient-sensing G protein-coupled receptors (GPCRs) expressed on gut enteroendocrine cells (EECs), tuft cells, and in afferent nerves in the gastroduodenal mucosa and submucosa. RECENT FINDINGS: Gene profiling of EECs and tuft cells have revealed expression of a variety of nutrient-sensing GPCRs. The density of EEC and tuft cells is altered by luminal environmental changes that may occur following bypass surgery or in the presence of mucosal inflammation...
August 12, 2017: Current Opinion in Gastroenterology
https://www.readbyqxmd.com/read/28806220/association-of-gender-with-outcome-and-host-response-in-critically-ill-sepsis-patients
#6
Lonneke A van Vught, Brendon P Scicluna, Maryse A Wiewel, Arie J Hoogendijk, Peter M C Klein Klouwenberg, David S Y Ong, Olaf L Cremer, Janneke Horn, Marek Franitza, Mohammad R Toliat, Peter Nürnberg, Marc M J Bonten, Marcus J Schultz, Tom van der Poll
OBJECTIVE: To determine the association of gender with the presentation, outcome, and host response in critically ill patients with sepsis. DESIGN AND SETTING: A prospective observational cohort study in the ICU of two tertiary hospitals between January 2011 and January 2014. PATIENTS: All consecutive critically ill patients admitted with sepsis, involving 1,815 admissions (1,533 patients). INTERVENTIONS: The host response was evaluated on ICU admission by measuring 19 plasma biomarkers reflecting organ systems implicated in sepsis pathogenesis (1,205 admissions) and by applying genome-wide blood gene expression profiling (582 admissions)...
August 11, 2017: Critical Care Medicine
https://www.readbyqxmd.com/read/28805995/germline-pms2-and-somatic-poleexo-mutations-cause-hypermutability-of-the-leading-dna-strand-in-biallelic-mismatch-repair-deficiency-syndrome-brain-tumors
#7
Andrianova Maria, Ghati Kasturirangan Chetan, Madathan Kandi Sibin, Thomas Mckee, Doron Merkler, Rao Kvl Narasinga, Pascale Ribaux, Jean-Louis Blouin, Periklis Makrythanasis, Vladimir B Seplyarskiy, Stylianos E Antonarakis, Sergey I Nikolaev
Biallelic Mismatch Repair Deficiency (bMMRD) in tumors is frequently associated with somatic mutations in the exonuclease domains of DNA polymerases POLE or POLD1 and results to a characteristic mutational profile. In this study we describe the genetic basis of ultramutated high grade brain tumors in the context of bMMRD. We performed exome sequencing of two second-cousin patients from a large consanguineous family of Indian origin with early onset of high grade glioblastoma and astrocytoma. We identified a germline homozygous nonsense variant R802X in the PMS2 gene...
August 14, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28805975/antofine-suppresses-endotoxin-induced-inflammation-and-metabolic-disorder-via-amp-activated-protein-kinase
#8
Shao-Ting Chou, Fang Jung, Shih-Hsing Yang, Hwei-Ling Chou, Guey-Mei Jow, Jau-Chen Lin
The inhibition of activated macrophages has been used to develop anti-inflammatory agents for therapeutic intervention to human diseases that cause excessive inflammatory responses. Antofine, a phenanthroindolizidine alkaloid, has a potent anti-inflammatory effect. However, the molecular mechanisms of its anti-inflammatory activity have not yet been fully detailed. In this study, we comprehensively explored the anti-inflammatory effects of antofine on endotoxin-induced inflammation in macrophages using cDNA microarray analysis, thereby elucidating the potential mechanism by which antofine suppresses inflammation...
August 2017: Pharmacology Research & Perspectives
https://www.readbyqxmd.com/read/28805896/the-composition-of-dietary-fat-alters-the-transcriptional-profile-of-pathways-associated-with-lipid-metabolism-in-the-liver-and-adipose-tissue-in-the-pig
#9
T A Kellner, N K Gabler, J F Patience
The objective was to investigate the of effect chemical composition of dietary fat on transcription of genes involved in lipid metabolism in adipose tissue and the liver via transcriptional profiling in growing pigs. A total of 48 Genetiporc 6.0 × Genetiporc F25 (PIC, Inc., Hendersonville, TN) barrows (initial BW of 44.1 ± 1.2 kg) were randomly allotted to 1 of 6 dietary treatments. Each experimental diet included 95% of a corn-soybean meal basal diet and 5% cornstarch (control; CNTR), animal-vegetable blend (AV), coconut oil (COCO), corn oil (COIL), fish oil (FO), or tallow (TAL)...
August 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28805827/transcriptional-risk-scores-link-gwas-to-eqtls-and-predict-complications-in-crohn-s-disease
#10
Urko M Marigorta, Lee A Denson, Jeffrey S Hyams, Kajari Mondal, Jarod Prince, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace V Crandall, Joel R Rosh, David R Mack, Richard Kellermayer, Melvin B Heyman, Susan S Baker, Michael C Stephens, Robert N Baldassano, James F Markowitz, Mi-Ok Kim, Marla C Dubinsky, Judy Cho, Bruce J Aronow, Subra Kugathasan, Greg Gibson
Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease...
August 14, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28805815/aav-mediated-direct-in-vivo-crispr-screen-identifies-functional-suppressors-in-glioblastoma
#11
Ryan D Chow, Christopher D Guzman, Guangchuan Wang, Florian Schmidt, Mark W Youngblood, Lupeng Ye, Youssef Errami, Matthew B Dong, Michael A Martinez, Sensen Zhang, Paul Renauer, Kaya Bilguvar, Murat Gunel, Phillip A Sharp, Feng Zhang, Randall J Platt, Sidi Chen
A causative understanding of genetic factors that regulate glioblastoma pathogenesis is of central importance. Here we developed an adeno-associated virus-mediated, autochthonous genetic CRISPR screen in glioblastoma. Stereotaxic delivery of a virus library targeting genes commonly mutated in human cancers into the brains of conditional-Cas9 mice resulted in tumors that recapitulate human glioblastoma. Capture sequencing revealed diverse mutational profiles across tumors. The mutation frequencies in mice correlated with those in two independent patient cohorts...
August 14, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28805813/analysis-of-genome-wide-association-data-highlights-candidates-for-drug-repositioning-in-psychiatry
#12
Hon-Cheong So, Carlos Kwan-Long Chau, Wan-To Chiu, Kin-Sang Ho, Cho-Pong Lo, Stephanie Ho-Yue Yim, Pak-Chung Sham
Knowledge of psychiatric disease genetics has advanced rapidly during the past decade with the advent of genome-wide association studies (GWAS). However, less progress has been made in harnessing these data to reveal new therapies. Here we propose a framework for drug repositioning by comparing transcriptomes imputed from GWAS data with drug-induced gene expression profiles from the Connectivity Map database and apply this approach to seven psychiatric disorders. We found a number of repositioning candidates, many supported by preclinical or clinical evidence...
August 14, 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28805807/notch-signaling-pathway-and-gene-expression-profiles-during-early-in-vitro-differentiation-of-liver-derived-mesenchymal-stromal-cells-to-osteoblasts
#13
Ksymena Urbanek, Marta Lesiak, Daniel Krakowian, Halina Koryciak-Komarska, Wirginia Likus, Piotr Czekaj, Damian Kusz, Aleksander L Sieroń
Notch signaling is a key signaling pathway for cell proliferation and differentiation. Therefore, we formulated a working hypothesis that Notch signaling can be used to detect early osteoblastic differentiation of mesenchymal stromal cells. Changes in expression and distribution of Notch 1, 2, 3, and Delta1 in the cytoplasm and nuclei of rat liver-derived mesenchymal stromal cells differentiating into osteoblasts were investigated, together with the displacement of intracellular domains (ICDs) of the receptors...
August 14, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28805806/lung-tumor-exome-files-with-t-cell-receptor-recombinations-a-mouse-model-of-t-cell-infiltrates-reflecting-mutation-burdens
#14
Yaping N Tu, Wei Lue Tong, Timothy J Fawcett, George Blanck
Tumor exomes and RNASeq data were originally intended for obtaining tumor mutations and gene expression profiles, respectively. However, recent work has determined that tumor exome and RNAseq read files contain reads representing T-cell and B-cell receptor (TcR and BcR) recombinations, presumably due to infiltrating lymphocytes. Furthermore, the recovery of immune receptor recombination reads has demonstrated correlations with specific, previously appreciated aspects of tumor immunology. To further understand the usefulness of recovering TcR and BcR recombinations from tumor exome files, we developed a scripted algorithm for recovery of reads representing these recombinations from a previously described mouse model of lung tumorigenesis...
August 14, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28805715/identification-and-analysis-of-mitogen-activated-protein-kinase-mapk-cascades-in-fragaria-vesca
#15
Heying Zhou, Suyue Ren, Yuanfang Han, Qing Zhang, Ling Qin, Yu Xing
Mitogen-activated protein kinase (MAPK) cascades are highly conserved signaling modules in eukaryotes, including yeasts, plants and animals. MAPK cascades are responsible for protein phosphorylation during signal transduction events, and typically consist of three protein kinases: MAPK, MAPK kinase, and MAPK kinase kinase. In this current study, we identified a total of 12 FvMAPK, 7 FvMAPKK, 73 FvMAPKKK, and one FvMAPKKKK genes in the recently published Fragaria vesca genome sequence. This work reported the classification, annotation and phylogenetic evaluation of these genes and an assessment of conserved motifs and the expression profiling of members of the gene family were also analyzed here...
August 13, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28805547/the-association-between-methylation-levels-of-targeted-genes-and-albuminuria-in-patients-with-early-diabetic-kidney-disease
#16
Ozgur Aldemir, Faruk Turgut, Cumali Gokce
OBJECTIVE: The incidence of diabetes and its complications are greatly increasing world-wide. Diabeticnephropathy (DN) is the main cause of end-stage renal disease and is associated with high morbidity and mortality. It is important to predict patients with high risk for DN in the early stage. We selected the genes which have an important role on diabetic kidney disease. We aimed to investigate the association between DNA methylation levels of targeted genes and albuminuria in patients with early DN...
November 2017: Renal Failure
https://www.readbyqxmd.com/read/28805537/high-prevalence-of-extended-spectrum-%C3%AE-lactamase-producing-enterobacteriaceae-in-wild-fish-from-the-mediterranean-sea-in-algeria
#17
Soumia Brahmi, Abdelaziz Touati, Catherine Dunyach-Remy, Albert Sotto, Alix Pantel, Jean-Philippe Lavigne
AIM: We investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae among wild fish from the coast of Bejaia (Algeria) in the Mediterranean Sea. RESULTS: From March 2012 to August 2013, gut and gill samples of wild fish were screened for the presence of ESBL-producing Enterobacteriaceae. Strains were characterized with regard to antibiotic resistance, β-lactamase content, plasmid-mediated quinolone resistance, aminoglycoside resistance genes, and clonality (repetitive sequence-based polymerase chain reaction profiles and multilocus sequence typing)...
August 14, 2017: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/28805233/analytic-and-dynamic-secretory-profile-of-patient-derived-cytokine-induced-killer-cells
#18
Giulia Mesiano, Roberta Zini, Giulia Montagner, Nicoletta Bianchi, Rossella Manfredini, Antonella Chillemi, Massimo Aglietta, Giovanni Grignani, Ilaria Lampronti, Erika Fiorino, Fabio Malavasi, Dario Sangiolo, Roberto Gambari, Davide Ferrari
Adoptive immunotherapy with Cytokine Induced Killer (CIK) cells has shown antitumor activity against several kinds of cancers in preclinical models and clinical trials. CIK cells are a subset of ex vivo expanded T lymphocytes with T-NK phenotype and MHC-unrestricted antitumor activity. Literature provides scanty information on cytokines, chemokines and growth factors secreted by CIK cells. Therefore, we investigated the secretory profile of CIK cells generated from tumor patients. The secretome analysis was performed at specific time points (day 1, day 14 and day 21) of CIK cells expansion...
August 9, 2017: Molecular Medicine
https://www.readbyqxmd.com/read/28805067/the-lncrna-nespas-is-associated-with-osteoarthritis-progression-and-serves-as-a-potential-new-prognostic-biomarker
#19
Sujung Park, Myeungsoo Lee, Churl-Hong Chun, Eun-Jung Jin
INTRODUCTION: In this article, we explored the hypothesis that the long noncoding RNA, Nespas, promotes osteoarthritis (OA) by supporting abnormal lipid metabolism in human chondrocytes. MATERIALS AND METHODS: Human articular chondrocytes from osteoarthritis patients were used and expression level of Nespas were determined by real-time polymerase chain reaction. Introduction of Nespas and Nespas-associated genes/miRNAs were performed by using a lentiviral system...
August 1, 2017: Cartilage
https://www.readbyqxmd.com/read/28805015/stromelysin-2-mmp-10-a-novel-mediator-of-vascular-remodeling-underlying-pulmonary-hypertension-associated-with-systemic-sclerosis
#20
Jérôme Avouac, Christophe Guignabert, Anna Maria Hoffmann-Vold, Barbara Ruiz, Peter Dorfmuller, Sonia Pezet, Olivia Amar, Ly Tu, Jérôme Van Wassenhove, Jérémy Sadoine, David Launay, Muriel Elhai, Anne Cauvet, Arun Subramaniam, Robert Resnick, Eric Hachulla, Øyvind Molberg, André Kahan, Marc Humbert, Yannick Allanore
OBJECTIVE: To decipher the role of gene candidates involved in pulmonary hypertension (PH) associated with systemic sclerosis (SSc). METHODS: Gene candidates were identified through microarray experiments performed on Affymetrix GeneChip(®) Human Exon 1.0 ST Arrays in endothelial progenitor cell (EPC)-derived endothelial cells (ECs) issued from patients with SSc-PH, SSc without PH and controls. Expression of identified candidates was assessed by quantitative sandwich ELISA in the serum and by immunohistochemistry in lesional lung tissue...
August 13, 2017: Arthritis & Rheumatology
keyword
keyword
76949
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"