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https://www.readbyqxmd.com/read/28747714/transcriptomic-biomarkers-to-discriminate-bacterial-from-nonbacterial-infection-in-adults-hospitalized-with-respiratory-illness
#1
Soumyaroop Bhattacharya, Alex F Rosenberg, Derick R Peterson, Katherine Grzesik, Andrea M Baran, John M Ashton, Steven R Gill, Anthony M Corbett, Jeanne Holden-Wiltse, David J Topham, Edward E Walsh, Thomas J Mariani, Ann R Falsey
Lower respiratory tract infection (LRTI) commonly causes hospitalization in adults. Because bacterial diagnostic tests are not accurate, antibiotics are frequently prescribed. Peripheral blood gene expression to identify subjects with bacterial infection is a promising strategy. We evaluated whole blood profiling using RNASeq to discriminate infectious agents in adults with microbiologically defined LRTI. Hospitalized adults with LRTI symptoms were recruited. Clinical data and blood was collected, and comprehensive microbiologic testing performed...
July 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743761/naturally-segregating-variation-at-ugt86dd-contributes-to-nicotine-resistance-in-drosophila-melanogaster
#2
Chad A Highfill, Jonathan H Tran, Samantha K T Nguyen, Taylor R Moldenhauer, Xiaofei Wang, Stuart J Macdonald
Identifying the sequence polymorphisms underlying complex trait variation is a key goal of genetics research, since knowing the precise causative molecular events allows insight into the pathways governing trait variation. Genetic analysis of complex traits in model systems regularly starts by constructing QTL maps, but generally fails to identify causative sequence polymorphisms. Previously we mapped a series of QTL contributing to resistance to nicotine in a Drosophila melanogaster multiparental mapping resource, and here use a battery of functional tests to resolve QTL to the molecular level...
July 25, 2017: Genetics
https://www.readbyqxmd.com/read/28739731/identification-of-novel-proteins-interacting-with-vascular-endothelial-growth-inhibitor-174-in-renal-cell-carcinoma
#3
Qiang Zhao, Duoer Kun, Baoan Hong, Xiaohu Deng, Sheng Guo, Xingxing Tang, Yong Yang, Kan Gong, Qing Li, Lin Ye, Wen G Jiang, Ning Zhang
BACKGROUND/AIM: Vascular endothelial growth inhibitor (VEGI) is a multipotential cytokine that plays a role in regulating immunity, anti-angiogenesis, and inhibiting tumor growth. However, the proteins that interact with it are still unknown. In the present study, we examined the proteins that interact with VEGI174 and their expression in renal cell carcinoma (RCC). MATERIALS AND METHODS: The proteins that interact with VEGI174 were identified using western blot, pull-down assay, and mass spectrometry...
August 2017: Anticancer Research
https://www.readbyqxmd.com/read/28735299/identification-of-the-first-dominant-mutation-of-lama5-gene-causing-a-complex-multisystem-syndrome-due-to-dysfunction-of-the-extracellular-matrix
#4
Simone Sampaolo, Filomena Napolitano, Alfonsina Tirozzi, Mafalda Giovanna Reccia, Luca Lombardi, Olimpia Farina, Adriano Barra, Ferdinando Cirillo, Mariarosa Anna Beatrice Melone, Fernando Gianfrancesco, Giuseppe Di Iorio, Teresa Esposito
BACKGROUND: The laminin alpha 5 gene (LAMA5) plays a master role in the maintenance and function of the extracellular matrix (ECM) in mammalian tissues, which is critical in developmental patterning, stem cell niches, cancer and genetic diseases. Its mutations have never been reported in human disease so far. The aim of this study was to associate the first mutation in LAMA5 gene to a novel multisystem syndrome. METHODS: A detailed characterisation of a three-generation family, including clinical, biochemical, instrumental and morphological analysis, together with genetics and expression (WES and RNAseq) studies, was performed...
July 22, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28727807/digoxin-reveals-a-functional-connection-between-hiv-1-integration-preference-and-t-cell-activation
#5
Alexander Zhyvoloup, Anat Melamed, Ian Anderson, Delphine Planas, Chen-Hsuin Lee, Janos Kriston-Vizi, Robin Ketteler, Andy Merritt, Jean-Pierre Routy, Petronela Ancuta, Charles R M Bangham, Ariberto Fassati
HIV-1 integrates more frequently into transcribed genes, however the biological significance of HIV-1 integration targeting has remained elusive. Using a selective high-throughput chemical screen, we discovered that the cardiac glycoside digoxin inhibits wild-type HIV-1 infection more potently than HIV-1 bearing a single point mutation (N74D) in the capsid protein. We confirmed that digoxin repressed viral gene expression by targeting the cellular Na+/K+ ATPase, but this did not explain its selectivity. Parallel RNAseq and integration mapping in infected cells demonstrated that digoxin inhibited expression of genes involved in T-cell activation and cell metabolism...
July 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28723760/bioinformatics-analysis-to-identify-the-critical-genes-micrornas-and-long-noncoding-rnas-in-melanoma
#6
Qian Zhang, Yang Wang, Jiulong Liang, Yaguang Tian, Yu Zhang, Kai Tao
Melanoma, which is usually induced by ultraviolet light exposure and the following DNA damage, is the most dangerous skin cancer. The purpose of the present study was to screen key molecules involved in melanoma.Microarray data of E-MTAB-1862 were downloaded from the ArrayExpress database, which included 21 primary melanoma samples and 11 benign nevus samples. In addition, the RNASeq version 2 and microRNA (miRNA) sequencing data of cutaneous melanoma were downloaded from The Cancer Genome Atlas database. After identifying the differentially expressed genes (DEGs) using Limma package, enrichment analysis and protein-protein interaction (PPI) network analysis were performed separately for them using DAVID software and Cytoscape software...
July 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28722115/transcriptional-profiling-of-mechanically-and-genetically-sink-limited-soybeans
#7
Anne V Brown, Karen A Hudson
The absence of a reproductive sink causes physiological and morphological changes in soybean plants. These include increased accumulation of nitrogen and starch in the leaves and delayed leaf senescence. To identify transcriptional changes that occur in leaves of these sink-limited plants, we used RNAseq to compare gene expression levels in trifoliate leaves from depodded and ms6 male sterile soybean plants and control plants. In both sink-limited tissues, we observed a deferral of the expression of senescence-associated genes and a continued expression of genes associated with leaf maturity...
July 19, 2017: Plant, Cell & Environment
https://www.readbyqxmd.com/read/28722025/nanopore-long-read-rnaseq-reveals-widespread-transcriptional-variation-among-the-surface-receptors-of-individual-b-cells
#8
Ashley Byrne, Anna E Beaudin, Hugh E Olsen, Miten Jain, Charles Cole, Theron Palmer, Rebecca M DuBois, E Camilla Forsberg, Mark Akeson, Christopher Vollmers
Understanding gene regulation and function requires a genome-wide method capable of capturing both gene expression levels and isoform diversity at the single-cell level. Short-read RNAseq is limited in its ability to resolve complex isoforms because it fails to sequence full-length cDNA copies of RNA molecules. Here, we investigate whether RNAseq using the long-read single-molecule Oxford Nanopore MinION sequencer is able to identify and quantify complex isoforms without sacrificing accurate gene expression quantification...
July 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28717593/short-reads-from-honey-bee-apis-sp-sequencing-projects-reflect-microbial-associate-diversity
#9
Michael Gerth, Gregory D D Hurst
High throughput (or 'next generation') sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and 'contaminating' material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome...
2017: PeerJ
https://www.readbyqxmd.com/read/28717417/analysis-of-extracellular-rna-in-cerebrospinal-fluid
#10
Julie A Saugstad, Theresa A Lusardi, Kendall R Van Keuren-Jensen, Jay I Phillips, Babett Lind, Christina A Harrington, Trevor J McFarland, Amanda L Courtright, Rebecca A Reiman, Ashish S Yeri, M Yashar S Kalani, P David Adelson, Jorge Arango, John P Nolan, Erika Duggan, Karen Messer, Johnny C Akers, Douglas R Galasko, Joseph F Quinn, Bob S Carter, Fred H Hochberg
We examined the extracellular vesicle (EV) and RNA composition of pooled normal cerebrospinal fluid (CSF) samples and CSF from five major neurological disorders: Alzheimer's disease (AD), Parkinson's disease (PD), low-grade glioma (LGG), glioblastoma multiforme (GBM), and subarachnoid haemorrhage (SAH), representing neurodegenerative disease, cancer, and severe acute brain injury. We evaluated: (I) size and quantity of EVs by nanoparticle tracking analysis (NTA) and vesicle flow cytometry (VFC), (II) RNA yield and purity using four RNA isolation kits, (III) replication of RNA yields within and between laboratories, and (IV) composition of total and EV RNAs by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and RNA sequencing (RNASeq)...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28716741/inferring-the-shallow-phylogeny-of-true-salamanders-salamandra-by-multiple-phylogenomic-approaches
#11
Ariel Rodríguez, James D Burgon, Mariana Lyra, Iker Irisarri, Denis Baurain, Leon Blaustein, Bayram Göcmen, Sven Künzel, Barbara Mable, Arne W Nolte, Michael Veith, Sebastian Steinfartz, Kathryn R Elmer, Hervé Philippe, Miguel Vences
The rise of high-throughput sequencing techniques provides the unprecedented opportunity to analyse controversial phylogenetic relationships in great depth, but also introduce the risk of being misinterpreted by high node support values influenced by unevenly distributed missing data or unrealistic model assumptions. Here, we use three largely independent phylogenomic data sets to reconstruct the controversial phylogeny of true salamanders of the genus Salamandra. a group of amphibians providing an intriguing model to study the evolution of aposematism and viviparity...
July 14, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28712804/identifying-cell-populations-with-scrnaseq
#12
REVIEW
Tallulah S Andrews, Martin Hemberg
Single-cell RNASeq (scRNASeq) has emerged as a powerful method for quantifying the transcriptome of individual cells. However, the data from scRNASeq experiments is often both noisy and high dimensional, making the computational analysis non-trivial. Here we provide an overview of different experimental protocols and the most popular methods for facilitating the computational analysis. We focus on approaches for identifying biologically important genes, projecting data into lower dimensions and clustering data into putative cell-populations...
July 13, 2017: Molecular Aspects of Medicine
https://www.readbyqxmd.com/read/28712319/primary-liver-cancer-genome-sequencing-translational-implications-and-challenges
#13
Demosthenes E Ziogas, Ioannis D Kyrochristos, Georgios K Glantzounis, Dimitrios Christodoulou, Evangelos Felekouras, Dimitrios H Roukos
The prognosis of primary liver cancer (PLC) remains poor and is explained by the slow progress in understanding the molecular pathways driving tumorigenesis, therapeutic resistance and relapse. For early PLCs, complete surgical resection is the only effective treatment, with sorafenib and, more recently, regorafenib prolonging overall survival by a few months. Areas covered: Application of next-generation sequencing (NGS), including targeted NGS (tNGS), whole-exome sequencing (WES), whole-genome sequencing (WGS) and RNA sequencing (RNAseq), on clinical samples from patients with hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC) could aid in comprehending tumorigenesis, genetic and genomic heterogeneity, as well as developing molecular classifications for specialized targeted therapy...
July 26, 2017: Expert Review of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28711856/rnaseq-based-transcriptome-comparison-of-saccharomyces-cerevisiae-strains-isolated-from-diverse-fermentative-environments
#14
Clara Ibáñez, Roberto Pérez-Torrado, Miguel Morard, Christina Toft, Eladio Barrio, Amparo Querol
Transcriptome analyses play a central role in unraveling the complexity of gene expression regulation in Saccharomyces cerevisiae. This species, one of the most important microorganisms for humans given its industrial applications, shows an astonishing degree of genetic and phenotypic variability among different strains adapted to specific environments. In order to gain novel insights into the Saccharomyces cerevisiae biology of strains adapted to different fermentative environments, we analyzed the whole transcriptome of three strains isolated from wine, flor wine or mezcal fermentations...
July 6, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28711779/hyperactive-foxo1-results-in-lack-of-tip-stalk-identity-and-deficient-microvascular-regeneration-during-kidney-injury
#15
Lan T H Dang, Takahide Aburatani, Graham A Marsh, Bryce G Johnson, Stella Alimperti, Christine J Yoon, Angela Huang, Suzanne Szak, Naoki Nakagawa, Ivan Gomez, Shuyu Ren, Sarah K Read, Chris Sparages, Alfred C Aplin, Roberto F Nicosia, Chris Chen, Giovanni Ligresti, Jeremy S Duffield
Loss of the microvascular (MV) network results in tissue ischemia, loss of tissue function, and is a hallmark of chronic diseases. The incorporation of a functional vascular network with that of the host remains a challenge to utilizing engineered tissues in clinically relevant therapies. We showed that vascular-bed-specific endothelial cells (ECs) exhibit differing angiogenic capacities, with kidney microvascular endothelial cells (MVECs) being the most deficient, and sought to explore the underlying mechanism...
July 7, 2017: Biomaterials
https://www.readbyqxmd.com/read/28704618/paracoccidioides-brasiliensis-presents-metabolic-reprogramming-and-secretes-a-serine-proteinase-during-murine-infection
#16
Laurine Lacerda Pigosso, Lilian Cristiane Baeza, Mariana Vieira Tomazett, Mariana Batista Rodrigues Faleiro, Veridiana Maria Brianezi Dignani de Moura, Alexandre Melo Bailão, Clayton Luiz Borges, Juliana Alves Parente Rocha, Gabriel Rocha Fernandes, Gregory M Gauthier, Celia Maria de Almeida Soares
Paracoccidoides brasiliensis and Paracoccidioides lutzii, the etiologic agents of paracoccidioidomycosis, cause disease in healthy and immunocompromised persons in Latin America. We developed a method for harvesting P. brasiliensis yeast cells from infected murine lung to facilitate in vivo transcriptional and proteomic profiling. P. brasiliensis harvested at 6 h post-infection were analyzed using RNAseq and LC-MS(E). In vivo yeast cells had 594 differentially expressed transcripts and 350 differentially expressed proteins...
July 13, 2017: Virulence
https://www.readbyqxmd.com/read/28701920/tlx3-function-in-the-dorsal-root-ganglion-is-pivotal-to-itch-and-pain-sensations
#17
Chengcheng Huang, Fumin Lu, Ping Li, Cheng Cao, Zijing Liu
Itch, a sensation eliciting a desire to scratch, is distinct from but not completely independent of pain. Inspiring achievements have been made in the characterization of itch-related receptors and neurotransmitters, but the molecular mechanisms controlling the development of pruriceptors remain poorly understood. Here, our RNAseq and in situ hybridization data show that the transcription factor Tlx3 is required for the expression of a majority of itch-related molecules in the dorsal root ganglion (DRG). As a result, Tlx3(F/F);Nav1...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28700589/ank1-is-up-regulated-in-laser-captured-microglia-in-alzheimer-s-brain-the-importance-of-addressing-cellular-heterogeneity
#18
Diego Mastroeni, Shobana Sekar, Jennifer Nolz, Elaine Delvaux, Katie Lunnon, Jonathan Mill, Winnie S Liang, Paul D Coleman
Recent epigenetic association studies have identified a new gene, ANK1, in the pathogenesis of Alzheimer's disease (AD). Although strong associations were observed, brain homogenates were used to generate the data, introducing complications because of the range of cell types analyzed. In order to address the issue of cellular heterogeneity in homogenate samples we isolated microglial, astrocytes and neurons by laser capture microdissection from CA1 of hippocampus in the same individuals with a clinical and pathological diagnosis of AD and matched control cases...
2017: PloS One
https://www.readbyqxmd.com/read/28694034/insertion-and-deletion-derived-tumour-specific-neoantigens-and-the-immunogenic-phenotype-a-pan-cancer-analysis
#19
Samra Turajlic, Kevin Litchfield, Hang Xu, Rachel Rosenthal, Nicholas McGranahan, James L Reading, Yien Ning S Wong, Andrew Rowan, Nnennaya Kanu, Maise Al Bakir, Tim Chambers, Roberto Salgado, Peter Savas, Sherene Loi, Nicolai J Birkbak, Laurent Sansregret, Martin Gore, James Larkin, Sergio A Quezada, Charles Swanton
BACKGROUND: The focus of tumour-specific antigen analyses has been on single nucleotide variants (SNVs), with the contribution of small insertions and deletions (indels) less well characterised. We investigated whether the frameshift nature of indel mutations, which create novel open reading frames and a large quantity of mutagenic peptides highly distinct from self, might contribute to the immunogenic phenotype. METHODS: We analysed whole-exome sequencing data from 5777 solid tumours, spanning 19 cancer types from The Cancer Genome Atlas...
July 7, 2017: Lancet Oncology
https://www.readbyqxmd.com/read/28688370/whole-transcriptome-rnaseq-analysis-of-oenococcus-oeni-reveals-distinct-intra-specific-expression-patterns-during-malolactic-fermentation-including-genes-involved-in-diacetyl-metabolism
#20
Peter R Sternes, Peter J Costello, Paul J Chambers, Eveline J Bartowsky, Anthony R Borneman
We report the first whole transcriptome RNAseq analysis of the wine-associated lactic acid bacterium Oenococcus oeni using a combination of reference-based mapping and de novo transcript assembly in three distinct strains during malolactic fermentation in Cabernet Sauvignon wine. Two of the strains (AWRIB551 and AWRIB552) exhibited similar transcriptomes relative to the third strain (AWRIB419) which was dissimilar by comparison. Significant intra-specific variation for genes related to glycolysis/gluconeogenesis, purine metabolism, aminoacyl-tRNA biosynthesis, ABC transporters and phosphotransferase systems was observed...
June 28, 2017: International Journal of Food Microbiology
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