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https://www.readbyqxmd.com/read/28322934/comparative-immunogenomics-of-molluscs
#1
Jonathan H Schultz, Coen M Adema
Comparative immunology, studying both vertebrates and invertebrates, provided the earliest descriptions of phagocytosis as a general immune mechanism. However, the large scale of animal diversity challenges all-inclusive investigations and the field of immunology has developed by mostly emphasizing study of a few vertebrate species. In addressing the lack of comprehensive understanding of animal immunity, especially that of invertebrates, comparative immunology helps toward management of invertebrates that are food sources, agricultural pests, pathogens, or transmit diseases, and helps interpret the evolution of animal immunity...
March 18, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28322319/functional-confirmation-of-plag1-as-the-candidate-causative-gene-underlying-major-pleiotropic-effects-on-body-weight-and-milk-characteristics
#2
Tania Fink, Kathryn Tiplady, Thomas Lopdell, Thomas Johnson, Russell G Snell, Richard J Spelman, Stephen R Davis, Mathew D Littlejohn
A major pleiotropic quantitative trait locus (QTL) located at ~25 Mbp on bovine chromosome 14 affects a myriad of growth and developmental traits in Bos taurus and indicus breeds. These QTL have been attributed to two functional variants in the bidirectional promoter of PLAG1 and CHCHD7. Although PLAG1 is a good candidate for mediating these effects, its role remains uncertain given that these variants are also associated with expression of five additional genes at the broader locus. In the current study, we conducted expression QTL (eQTL) mapping of this region using a large, high depth mammary RNAseq dataset representing 375 lactating cows...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28296881/transcriptomic-responses-to-environmental-temperature-by-turtles-with-temperature-dependent-and-genotypic-sex-determination-assessed-by-rnaseq-inform-the-genetic-architecture-of-embryonic-gonadal-development
#3
Srihari Radhakrishnan, Robert Literman, Jennifer Neuwald, Andrew Severin, Nicole Valenzuela
Vertebrate sexual fate is decided primarily by the individual's genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera-GSD), to test whether TSD's and GSD's transcriptional circuitry is identical but deployed differently between mechanisms...
2017: PloS One
https://www.readbyqxmd.com/read/28286708/transcriptomic-analysis-reveals-metabolic-switches-and-surface-remodeling-as-key-processes-for-stage-transition-in-trypanosoma-cruzi
#4
Luisa Berná, Maria Laura Chiribao, Gonzalo Greif, Matias Rodriguez, Fernando Alvarez-Valin, Carlos Robello
American trypanosomiasis is a chronic and endemic disease which affects millions of people. Trypanosoma cruzi, its causative agent, has a life cycle that involves complex morphological and functional transitions, as well as a variety of environmental conditions. This requires a tight regulation of gene expression, which is achieved mainly by post-transcriptional regulation. In this work we conducted an RNAseq analysis of the three major life cycle stages of T. cruzi: amastigotes, epimastigotes and trypomastigotes...
2017: PeerJ
https://www.readbyqxmd.com/read/28286086/hyper-methylation-of-the-upstream-cpg-island-shore-is-a-likely-mechanism-of-gper1-silencing-in-breast-cancer-cells
#5
Mohan C Manjegowda, Paridhi Singhal Gupta, Anil M Limaye
GPER1, also known as GPR30, is a novel seven-transmembrane G-protein coupled estrogen receptor that mediates both short-term (non-genomic) and long-term (genomic) effects of estrogen in target cells and tissues. A substantial body of work over the last two decades has highlighted its therapeutic or prognostic utility. However, the clinical data on the expression of GPER1 in breast tissue is ambiguous. Analysis of TCGA RNAseq data revealed significantly lower mean expression of GPER1 mRNA in primary breast tumors compared to that in normal breast tissues...
March 7, 2017: Gene
https://www.readbyqxmd.com/read/28286046/rudimentary-expression-of-ryamide-in-drosophila-melanogaster-relative-to-other-drosophila-species-points-to-a-functional-decline-of-this-neuropeptide-gene
#6
Jan A Veenstra, Hela Khammassi
RYamides are arthropod neuropeptides with unknown function. In 2011 two RYamides were isolated from D. melanogaster as the ligands for the G-protein coupled receptor CG5811. The D. melanogaster gene encoding these neuropeptides is highly unusual, as there are four RYamide encoding exons in the current genome assembly, but an exon encoding a signal peptide is absent. Comparing the D. melanogaster gene structure with those from other species, including D. virilis, suggests that the gene is degenerating. RNAseq data from 1634 short sequence read archives at NCBI containing more than 34 billion spots yielded numerous individual spots that correspond to the RYamide encoding exons, of which a large number include the intron-exon boundary at the start of this exon...
March 7, 2017: Insect Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28282449/infection-with-diverse-immune-modulating-poxviruses-elicits-different-compositional-shifts-in-the-mouse-gut-microbiome
#7
Daniel Aguirre de Cárcer, Bruno Hernáez, Alberto Rastrojo, Antonio Alcamí
It is often not possible to demonstrate causality within the context of gut microbiota dysbiosis-linked diseases. Thus, we need a better understanding of the mechanisms whereby an altered host immunophysiology shapes its resident microbiota. In this regard, immune-modulating poxvirus strains and mutants could differentially alter gut mucosal immunity in the context of a natural immune response, providing a controlled natural in vivo setting to deepen our understanding of the immune determinants of microbiome composition...
2017: PloS One
https://www.readbyqxmd.com/read/28276031/analysis-of-mitochondrial-rna-processing-defects-in-patient-derived-tissues-by-qrt-pcr-and-rnaseq
#8
Robert Kopajtich, Johannes A Mayr, Holger Prokisch
Transcription of the mitochondrial genome yields three large polycistronic transcripts that undergo multiple endonucleolytic processing steps, before resulting in functional mRNAs, tRNAs, and rRNAs. Cleavage of the large precursor transcripts is mainly performed by the RNase P complex and RNase Z that cleave mitochondrial pre-tRNAs at their 5' and 3' ends respectively. Most likely there are additional enzymes involved that still await identification and characterization. Defects in mitochondrial RNA processing have been associated with human disease...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28270590/inhibition-of-mapk-erk-pathway-in%C3%A2-vivo-attenuates-aortic-valve-disease-processes-in-emilin1-deficient-mouse-model
#9
Charu Munjal, Anil G Jegga, Amy M Opoka, Ivan Stoilov, Russell A Norris, Craig J Thomas, J Michael Smith, Robert P Mecham, Giorgio M Bressan, Robert B Hinton
Aortic valve disease (AVD) is a common condition with a progressive natural history, and presently, there are no pharmacologic treatment strategies. Elastic fiber fragmentation (EFF) is a hallmark of AVD, and increasing evidence implicates developmental elastic fiber assembly defects. Emilin1 is a glycoprotein necessary for elastic fiber assembly that is present in both developing and mature human and mouse aortic valves. The Emilin1-deficient mouse (Emilin1(-/-) ) is a model of latent AVD, characterized by activated TGFβ/MEK/p-Erk signaling and upregulated elastase activity...
March 2017: Physiological Reports
https://www.readbyqxmd.com/read/28270101/deciphering-alternative-splicing-and-nonsense-mediated-decay-modulate-expression-in-primary-lymphoid-tissues-of-birds-infected-with-avian-pathogenic-e-coli-apec
#10
Hongyan Sun
BACKGROUND: Avian pathogenic E. coli (APEC) can lead to a loss in millions of dollars in poultry annually because of mortality and produce contamination. Studies have verified that many immune-related genes undergo changes in alternative splicing (AS), along with nonsense mediated decay (NMD), to regulate the immune system under different conditions. Therefore, the splicing profiles of primary lymphoid tissues with systemic APEC infection need to be comprehensively examined. RESULTS: Gene expression in RNAseq data were obtained for three different immune tissues (bone marrow, thymus, and bursa) from three phenotype birds (non-challenged, resistant, and susceptible birds) at two time points...
March 7, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28265491/fuchs-towards-full-circular-rna-characterization-using-rnaseq
#11
Franziska Metge, Lisa F Czaja-Hasse, Richard Reinhardt, Chistoph Dieterich
Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5' splice site is linked to an upstream 3' splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing...
2017: PeerJ
https://www.readbyqxmd.com/read/28263985/robust-stratification-of-breast-cancer-subtypes-using-differential-patterns-of-transcript-isoform-expression
#12
Thomas P Stricker, Christopher D Brown, Chaitanya Bandlamudi, Megan McNerney, Ralf Kittler, Vanessa Montoya, April Peterson, Robert Grossman, Kevin P White
Breast cancer, the second leading cause of cancer death of women worldwide, is a heterogenous disease with multiple different subtypes. These subtypes carry important implications for prognosis and therapy. Interestingly, it is known that these different subtypes not only have different biological behaviors, but also have distinct gene expression profiles. However, it has not been rigorously explored whether particular transcriptional isoforms are also differentially expressed among breast cancer subtypes, or whether transcript isoforms from the same sets of genes can be used to differentiate subtypes...
March 6, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28263756/neuregulin-1%C3%AE-induces-proliferation-survival-and-paracrine-signaling-in-normal-human-cardiac-ventricular-fibroblasts
#13
Annet Kirabo, Sergey Ryzhov, Manisha Gupte, Seng Sengsayadeth, Richard J Gumina, Douglas B Sawyer, Cristi L Galindo
Neuregulin-1β (NRG-1β) is critical for cardiac development and repair, and recombinant forms are currently being assessed as possible therapeutics for systolic heart failure. We previously demonstrated that recombinant NRG-1β reduces cardiac fibrosis in an animal model of cardiac remodeling and heart failure, suggesting that there may be direct effects on cardiac fibroblasts. Here we show that NRG-1β receptors (ErbB2, ErbB3, and ErbB4) are expressed in normal human cardiac ventricular (NHCV) fibroblast cell lines...
March 3, 2017: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/28263224/acute-ischemia-induced-by-high-density-culture-increases-cytokine-expression-and-diminishes-the-function-and-viability-of-highly-purified-human-islets-of-langerhans
#14
Kate E Smith, Amy C Kelly, Catherine G Min, Craig S Weber, Fiona M McCarthy, Leah V Steyn, Vasudeo Badarinarayana, J Brett Stanton, Jennifer P Kitzmann, Peter Strop, Angelika C Gruessner, Ronald M Lynch, Sean W Limesand, Klearchos K Papas
BACKGROUND: Encapsulation devices have the potential to enable cell based insulin replacement therapies (such as human islet or stem cell derived β cell transplantation) without immunosuppression. However, reasonably sized encapsulation devices promote ischemia due to high β cell densities creating prohibitively large diffusional distances for nutrients. It is hypothesized that even acute ischemic exposure will compromise the therapeutic potential of cell based insulin replacement. In this study, the acute effects of high-density ischemia were investigated in human islets to develop a detailed profile of early ischemia induced changes and targets for intervention...
March 3, 2017: Transplantation
https://www.readbyqxmd.com/read/28258137/metatranscriptomic-evidence-for-direct-interspecies-electron-transfer-between-geobacter-and-methanothrix-species-in-methanogenic-rice-paddy-soils
#15
Dawn E Holmes, Pravin M Shrestha, David J F Walker, Yan Dang, Kelly P Nevin, Trevor L Woodard, Derek R Lovley
The possibility that Methanothrix (formerly Methanosaeta) and Geobacter species cooperate via direct interspecies electron transfer (DIET) in terrestrial methanogenic environments was investigated in rice paddy soils. Genes with high sequence similarity to the gene for the PilA pilin monomer of the electrically conductive pili (e-pili) of Geobacter sulfurreducens accounted for over half of the PilA gene sequences in metagenomic libraries and 42% of the mRNA transcripts in RNAseq libraries. This abundance of e-pilin genes and transcripts is significant because e-pili can serve as conduits for DIET...
March 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28253318/transgenic-expression-of-fungal-accessory-hemicellulases-in-arabidopsis-thaliana-triggers-transcriptional-patterns-related-to-biotic-stress-and-defense-response
#16
Alex Yi-Lin Tsai, Kin Chan, Chi-Yip Ho, Thomas Canam, Resmi Capron, Emma R Master, Katharina Bräutigam
The plant cell wall is an abundant and renewable resource for lignocellulosic applications such as the production of biofuel. Due to structural and compositional complexities, the plant cell wall is, however, recalcitrant to hydrolysis and extraction of platform sugars. A cell wall engineering strategy to reduce this recalcitrance makes use of microbial cell wall modifying enzymes that are expressed directly in plants themselves. Previously, we constructed transgenic Arabidopsis thaliana constitutively expressing the fungal hemicellulases: Phanerochaete carnosa glucurnoyl esterase (PcGCE) and Aspergillus nidulans α-arabinofuranosidase (AnAF54)...
2017: PloS One
https://www.readbyqxmd.com/read/28252016/an-antimicrobial-peptide-resistant-minor-subpopulation-of-photorhabdus-luminescens-is-responsible-for-virulence
#17
Annabelle Mouammine, Sylvie Pages, Anne Lanois, Sophie Gaudriault, Gregory Jubelin, Maurine Bonabaud, Stéphane Cruveiller, Emeric Dubois, David Roche, Ludovic Legrand, Julien Brillard, Alain Givaudan
Some of the bacterial cells in isogenic populations behave differently from others. We describe here how a new type of phenotypic heterogeneity relating to resistance to cationic antimicrobial peptides (CAMPs) is determinant for the pathogenic infection process of the entomopathogenic bacterium Photorhabdus luminescens. We demonstrate that the resistant subpopulation, which accounts for only 0.5% of the wild-type population, causes septicemia in insects. Bacterial heterogeneity is driven by the PhoPQ two-component regulatory system and expression of pbgPE, an operon encoding proteins involved in lipopolysaccharide (LPS) modifications...
March 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28245801/differentiation-of-ncrnas-from-small-mrnas-in-escherichia-coli-o157-h7-edl933-ehec-by-combined-rnaseq-and-riboseq-ryhb-encodes-the-regulatory-rna-ryhb-and-a-peptide-ryhp
#18
Klaus Neuhaus, Richard Landstorfer, Svenja Simon, Steffen Schober, Patrick R Wright, Cameron Smith, Rolf Backofen, Romy Wecko, Daniel A Keim, Siegfried Scherer
BACKGROUND: While NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA. RESULTS: Based on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E...
February 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28240256/a-comparison-of-host-gene-expression-signatures-associated-with-infection-in-vitro-by-the-makona-and-ecran-mayinga-variants-of-ebola-virus
#19
Andrew Bosworth, Stuart D Dowall, Isabel Garcia-Dorival, Natasha Y Rickett, Christine B Bruce, David A Matthews, Yongxiang Fang, Waleed Aljabr, John Kenny, Charlotte Nelson, Thomas R Laws, E Diane Williamson, James P Stewart, Miles W Carroll, Roger Hewson, Julian A Hiscox
The Ebola virus (EBOV) variant Makona (which emerged in 2013) was the causative agent of the largest outbreak of Ebola Virus Disease recorded. Differences in virus-host interactions between viral variants have potential consequences for transmission, disease severity and mortality. A detailed profile of the cellular changes induced by the Makona variant compared with other Ebola virus variants was lacking. In this study, A549 cells, a human cell line with a robust innate response, were infected with the Makona variant or with the Ecran variant originating from the 1976 outbreak in Central Africa...
February 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28237718/endogenous-beta-cell-cart-regulates-insulin-secretion-and-transcription-of-beta-cell-genes
#20
L Shcherbina, A Edlund, J L S Esguerra, M Abels, Y Zhou, E Ottosson-Laakso, C B Wollheim, O Hansson, L Eliasson, N Wierup
Impaired beta-cell function is key to the development of type 2 diabetes. Cocaine- and amphetamine-regulated transcript (CART) is an islet peptide with insulinotropic and glucagonostatic properties. Here we studied the role of endogenous CART in beta-cell function. CART silencing in INS-1 (832/13) beta-cells reduced insulin secretion and production, ATP levels and beta-cell exocytosis. This was substantiated by reduced expression of several exocytosis genes, as well as reduced expression of genes important for insulin secretion and processing...
February 22, 2017: Molecular and Cellular Endocrinology
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