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https://www.readbyqxmd.com/read/28209764/kcnj11-ablation-is-associated-with-increased-nitro-oxidative-stress-during-ischemia-reperfusion-injury-implications-for-human-ischemic-cardiomyopathy
#1
Bo Zhang, Tatiana Novitskaya, Debra G Wheeler, Zhaobin Xu, Elena Chepurko, Ryan Huttinger, Heng He, Saradhadevi Varadharaj, Jay L Zweier, Yanna Song, Meng Xu, Frank E Harrell, Yan Ru Su, Tarek Absi, Mark J Kohr, Mark T Ziolo, Dan M Roden, Christian M Shaffer, Cristi L Galindo, Quinn S Wells, Richard J Gumina
BACKGROUND: Despite increased secondary cardiovascular events in patients with ischemic cardiomyopathy (ICM), the expression of innate cardiac protective molecules in the hearts of patients with ICM is incompletely characterized. Therefore, we used a nonbiased RNAseq approach to determine whether differences in cardiac protective molecules occur with ICM. METHODS AND RESULTS: RNAseq analysis of human control and ICM left ventricular samples demonstrated a significant decrease in KCNJ11 expression with ICM...
February 2017: Circulation. Heart Failure
https://www.readbyqxmd.com/read/28209129/orthograph-a-versatile-tool-for-mapping-coding-nucleotide-sequences-to-clusters-of-orthologous-genes
#2
Malte Petersen, Karen Meusemann, Alexander Donath, Daniel Dowling, Shanlin Liu, Ralph S Peters, Lars Podsiadlowski, Alexandros Vasilikopoulos, Xin Zhou, Bernhard Misof, Oliver Niehuis
BACKGROUND: Orthology characterizes genes of different organisms that arose from a single ancestral gene via speciation, in contrast to paralogy, which is assigned to genes that arose via gene duplication. An accurate orthology assignment is a crucial step for comparative genomic studies. Orthologous genes in two organisms can be identified by applying a so-called reciprocal search strategy, given that complete information of the organisms' gene repertoire is available. In many investigations, however, only a fraction of the gene content of the organisms under study is examined (e...
February 16, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28198009/endoscopic-ultrasound-guided-fine-needle-aspirate-derived-preclinical-pancreatic-cancer-models-reveal-panitumumab-sensitivity-in-kras-wild-type-tumours
#3
William Berry, Elizabeth Algar, Beena Kumar, Christopher Desmond, Michael Swan, Brendan J Jenkins, Daniel Croagh
Pancreatic cancer (PC) is largely refractory to existing therapies used in unselected patient trials, thus emphasizing the pressing need for new approaches for patient selection in personalized medicine. KRAS mutations occur in 90% of PC patients and confer resistance to epidermal growth factor receptor (EGFR) inhibitors (e.g. panitumumab), suggesting that KRAS wild-type PC patients may benefit from targeted panitumumab therapy. Here we use tumour tissue procured by endoscopic ultrasound-guided fine-needle aspirate (EUS-FNA) to compare the in vivo sensitivity in patient derived xenografts (PDXs) of KRAS wild-type and mutant PC tumours to panitumumab, and to profile the molecular signature of these tumours in patients with metastatic or localized disease...
February 15, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28192147/systemic-innate-immune-activation-in-food-protein-induced-enterocolitis-syndrome-fpies
#4
Ritobrata Goswami, Ana Belen Blazquez, Roman Kosoy, Adeeb Rahman, Anna Nowak-Wegrzyn, M Cecilia Berin
BACKGROUND: Food protein induced enterocolitis syndrome (FPIES) is a non-IgE-mediated food allergy of infancy whose pathophysiology is poorly understood. OBJECTIVES: We set out to identify and phenotype allergen-responsive cells in peripheral blood of a cohort of subjects undergoing supervised food challenge for FPIES. METHODS: We profiled antigen-responsive cells in peripheral blood mononuclear cells by flow cytometry, and examined cells in whole blood obtained before and after challenge by CyTOF mass cytometry and RNAseq...
February 9, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28188910/expression-and-splicing-of-abc-and-slc-transporters-in-the-human-blood-brain-barrier-measured-with-rnaseq
#5
Adam M Suhy, Amy Webb, Audrey C Papp, Ethan G Geier, Wolfgang Sadee
The blood-brain barrier (BBB) expresses numerous membrane transporters that supply needed nutrients to the central nervous system (CNS), consisting mostly of solute carriers (SLC transporters), or remove unwanted substrates via extrusion pumps through the action of ATP binding cassette (ABC) transporters. Previous work has identified many BBB transporters using hybridization arrays or qRT-PCR, using targeted probes. Here we have performed next-generation sequencing of the transcriptome (RNAseq) extracted from cerebral cortex tissues and brain microvessel endothelial cells (BMEC) obtained from two donors...
February 7, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28186107/blubber-transcriptome-response-to-acute-stress-axis-activation-involves-transient-changes-in-adipogenesis-and-lipolysis-in-a-fasting-adapted-marine-mammal
#6
J I Khudyakov, C D Champagne, L M Meneghetti, D E Crocker
Stress can compromise an animal's ability to conserve metabolic stores and participate in energy-demanding activities that are critical for fitness. Understanding how wild animals, especially those already experiencing physiological extremes (e.g. fasting), regulate stress responses is critical for evaluating the impacts of anthropogenic disturbance on physiology and fitness, key challenges for conservation. However, studies of stress in wildlife are often limited to baseline endocrine measurements and few have investigated stress effects in fasting-adapted species...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185541/kaos-a-new-automated-computational-method-for-the-identification-of-overexpressed-genes
#7
Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella, Alfredo Pulvirenti, Antonella Isacchi, Roberta Bosotti
BACKGROUND: Kinase over-expression and activation as a consequence of gene amplification or gene fusion events is a well-known mechanism of tumorigenesis. The search for novel rearrangements of kinases or other druggable genes may contribute to understanding the biology of cancerogenesis, as well as lead to the identification of new candidate targets for drug discovery. However this requires the ability to query large datasets to identify rare events occurring in very small fractions (1-3 %) of different tumor subtypes...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28174601/development-of-a-genetically-programed-vanillin-sensing-bacterium-for-high-throughput-screening-of-lignin-degrading-enzyme-libraries
#8
Barindra Sana, Kuan Hui Burton Chia, Sarada S Raghavan, Balamurugan Ramalingam, Niranjan Nagarajan, Jayasree Seayad, Farid J Ghadessy
BACKGROUND: Lignin is a potential biorefinery feedstock for the production of value-added chemicals including vanillin. A huge amount of lignin is produced as a by-product of the paper industry, while cellulosic components of plant biomass are utilized for the production of paper pulp. In spite of vast potential, lignin remains the least exploited component of plant biomass due to its extremely complex and heterogenous structure. Several enzymes have been reported to have lignin-degrading properties and could be potentially used in lignin biorefining if their catalytic properties could be improved by enzyme engineering...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28171615/the-start-app-a-web-based-rnaseq-analysis-and-visualization-resource
#9
Jonathan W Nelson, Jiri Sklenar, Anthony P Barnes, Jessica Minnier
No abstract text is available yet for this article.
February 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28166733/a-machine-learning-classifier-trained-on-cancer-transcriptomes-detects-nf1-inactivation-signal-in-glioblastoma
#10
Gregory P Way, Robert J Allaway, Stephanie J Bouley, Camilo E Fadul, Yolanda Sanchez, Casey S Greene
BACKGROUND: We have identified molecules that exhibit synthetic lethality in cells with loss of the neurofibromin 1 (NF1) tumor suppressor gene. However, recognizing tumors that have inactivation of the NF1 tumor suppressor function is challenging because the loss may occur via mechanisms that do not involve mutation of the genomic locus. Degradation of the NF1 protein, independent of NF1 mutation status, phenocopies inactivating mutations to drive tumors in human glioma cell lines. NF1 inactivation may alter the transcriptional landscape of a tumor and allow a machine learning classifier to detect which tumors will benefit from synthetic lethal molecules...
February 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28165003/alterations-in-rice-chloroplast-integrity-photosynthesis-and-metabolome-associated-with-pathogenesis-of-rhizoctonia-solani
#11
Srayan Ghosh, Poonam Kanwar, Gopaljee Jha
Sheath blight disease is caused by a necrotrophic fungal pathogen Rhizoctonia solani and it continues to be a challenge for sustainable rice cultivation. In this study, we adopted a multi-pronged approach to understand the intricacies of rice undergoing susceptible interactions with R. solani. Extensive anatomical alteration, chloroplast localized ROS, deformed chloroplast ultrastructure along with decreased photosynthetic efficiency were observed in infected tissue. GC-MS based metabolite profiling revealed accumulation of glycolysis and TCA cycle intermediates, suggesting enhanced respiration...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28159858/transcriptomic-alterations-in-the-brain-of-painted-turtles-chrysemys-picta-developmentally-exposed-to-bisphenol-a-or-ethinyl-estradiol
#12
Lindsey K Manshack, Caroline M Conard, Sara J Bryan, Sharon L Deem, Dawn K Holliday, Nathan J Bivens, Scott A Givan, Cheryl Susan Rosenfeld
Developmental exposure of turtles and other reptiles to endocrine disrupting chemicals (EDCs), including bisphenol A (BPA) and ethinyl estradiol (EE), can stimulate partial to full gonadal sex-reversal in males. We have also recently shown that in ovo exposure to either EDC can induce similar sex-dependent behavioral changes typified by improved spatial learning and memory or possibly feminized brain responses. Observed behavioral changes are presumed to be due to BPA- and EE-induced brain transcriptomic alterations during development...
February 3, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28158604/pathway-inspector-a-pathway-based-web-application-for-rnaseq-analysis-of-model-and-non-model-organisms
#13
Luca Bianco, Samantha Riccadonna, Enrico Lavezzo, Marco Falda, Elide Formentin, Duccio Cavalieri, Stefano Toppo, Paolo Fontana
No abstract text is available yet for this article.
February 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28152580/quantifying-three-dimensional-morphology-and-rna-from-individual-embryos
#14
Rebecca M Green, Courtney L Leach, Natasha Hoehn, Ralph S Marcucio, Benedikt Hallgrímsson
Quantitative analysis of morphogenesis aids our understanding of developmental processes by providing a method to link changes in shape with cellular and molecular processes. Over the last decade many methods have been developed for 3D imaging of embryos using microCT scanning to quantify the shape of embryos during development. These methods generally involve a powerful, cross-linking fixative such as paraformaldehyde to limit shrinkage during the CT scan. However, the extended time frames that these embryos are incubated in such fixatives prevent use of the tissues for molecular analysis after microCT scanning...
February 2, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28152011/dengue-virus-serotype-2-infection-alters-midgut-and-carcass-gene-expression-in-the-asian-tiger-mosquito-aedes-albopictus
#15
Hitoshi Tsujimoto, Kathryn A Hanley, Anitha Sundararajan, Nicholas P Devitt, Faye D Schilkey, Immo A Hansen
BACKGROUND: The Asian tiger mosquito, Aedes albopictus is currently an important vector for dengue, chikungunya and Zika virus, and its role in transmission of arthropod-borne viruses (arboviruses) may increase in the future due to its ability to colonize temperate regions. In contrast to Aedes aegypti, the dominant vector of dengue, chikungunya and Zika virus, genetic responses of Ae. albopictus upon infection with an arbovirus are not well characterized. Here we present a study of the changes in transcript expression in Ae...
2017: PloS One
https://www.readbyqxmd.com/read/28151934/hepatitis-b-virus-modulates-store-operated-calcium-entry-to-enhance-viral-replication-in-primary-hepatocytes
#16
Jessica C Casciano, Nicholas J Duchemin, R Jason Lamontagne, Laura F Steel, Michael J Bouchard
Many viruses modulate calcium (Ca2+) signaling to create a cellular environment that is more permissive to viral replication, but for most viruses that regulate Ca2+ signaling, the mechanism underlying this regulation is not well understood. The hepatitis B virus (HBV) HBx protein modulates cytosolic Ca2+ levels to stimulate HBV replication in some liver cell lines. A chronic HBV infection is associated with life-threatening liver diseases, including hepatocellular carcinoma (HCC), and HBx modulation of cytosolic Ca2+ levels could have an important role in HBV pathogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28148532/meta-analysis-of-polycystic-kidney-disease-expression-profiles-defines-strong-involvement-of-injury-repair-processes
#17
Tareq B Malas, Chiara Formica, Wouter N Leonhard, Pooja Rao, Zoraide Granchi, Marco Roos, Dorien J M Peters, Peter A C 't Hoen
Polycystic Kidney Disease is a major cause of end-stage renal disease. The disease mechanisms are not well understood and the pathogenesis towards renal failure remains elusive. In this study, we present the first RNASeq analysis of a Pkd1-mutant mouse model in a combined meta-analysis with other published PKD expression profiles. We introduce the PKD signature, a set of 1515 genes that are commonly dysregulated in PKD studies. We show that the signature genes include many known and novel PKD-related genes and functions...
February 1, 2017: American Journal of Physiology. Renal Physiology
https://www.readbyqxmd.com/read/28148395/tissue-factor-factor-viia-complex-triggers-protease-activated-receptor-2-dependent-growth-factor-release-and-migration-in-ovarian-cancer
#18
Alice Chanakira, Pamela R Westmark, Irene M Ong, John P Sheehan
OBJECTIVE: Enhanced tissue factor (TF) expression in epithelial ovarian cancer (EOC) is associated with aggressive disease. Our objective was to evaluate the role of the TF-factor VIIa-protease-activated receptor-2 (PAR-2) pathway in human EOC. METHODS: TCGA RNAseq data from EOC databases were analyzed for PAR expression. Cell and microparticle (MP) associated TF protein expression (Western blot) and MP-associated coagulant activity were determined in human EOC (SKOV-3, OVCAR-3 and CaOV-3) and control cell lines...
January 29, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28138401/t-cadherin-in-prostate-cancer-relationship-with-cancer-progression-differentiation-and-drug-resistance
#19
Boris Dasen, Tatjana Vlajnic, Chantal Mengus, Christian Ruiz, Lukas Bubendorf, Giulio Spagnoli, Stephen Wyler, Paul Erne, Thérèse J Resink, Maria Philippova
Prostate cancer represents the second leading cause of cancer-related death in men. T-cadherin (CDH13) is an atypical GPI-anchored member of the cadherin family of adhesion molecules. Its gene was reported to be downregulated in a small series of prostate tumours. T-cadherin protein expression/localisation in prostate tissue has never been investigated. The purpose of our study was to analyse CDH13 gene and protein levels in large sets of healthy and cancer prostate tissue specimens and evaluate CDH13 effects on the sensitivity of prostate cancer cells to chemotherapy...
January 2017: Journal of Pathology. Clinical Research
https://www.readbyqxmd.com/read/28137761/comprehensive-transcriptome-and-mutational-profiling-of-endemic-burkitt-lymphoma-reveals-ebv-type-specific-differences
#20
Yasin Kaymaz, Cliff I Oduor, Hongbo Yu, Juliana A Otieno, John M Ong'echa, Ann M Moormann, Jeffrey A Bailey
: Endemic Burkitt lymphoma (eBL) is the most common pediatric cancer in malaria-endemic equatorial Africa and nearly always contains Epstein-Barr virus (EBV), unlike sporadic Burkitt Lymphoma (sBL) that occurs with a lower incidence in developed countries. Given these differences and the variable clinical presentation and outcomes, we sought to further understand pathogenesis by investigating transcriptomes using RNA sequencing (RNAseq) from multiple primary eBL tumors compared to sBL tumors...
January 30, 2017: Molecular Cancer Research: MCR
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