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https://www.readbyqxmd.com/read/28531322/evaluation-of-ifitm3-rs12252-association-with-severe-pediatric-influenza-infection
#1
Adrienne G Randolph, Wai-Ki Yip, E Kaitlyn Allen, Carrie M Rosenberger, Anna A Agan, Stephanie A Ash, Yu Zhang, Tushar R Bhangale, David Finkelstein, Natalie Cvijanovich, Peter M Mourani, Mark Hall, Helen C Su, Paul G Thomas
Background: Interferon inducible transmembrane protein 3 (IFITM3) restricts endocytic fusion of influenza virus. IFITM3 rs12252_C, a putative alternate splice site, has been associated with influenza severity in adults. IFITM3 has not been evaluated in pediatric influenza. Methods: The PICFLU Study enrolled children with suspected influenza infection across 38 pediatric intensive care units November 2008 to April 2016. IFITM3 was sequenced in patients and parents were genotyped for specific variants for family-based association testing...
May 20, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28520934/the-smap1-2-proteins-of-the-crenarchaeon-sulfolobus-solfataricus-interact-with-the-exosome-and-stimulate-a-rich-tailing-of-transcripts
#2
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28515876/population-genomics-reveals-a-candidate-gene-involved-in-bumble-bee-pigmentation
#3
Meaghan L Pimsler, Jason M Jackson, Jeffrey D Lozier
Variation in bumble bee color patterns is well-documented within and between species. Identifying the genetic mechanisms underlying such variation may be useful in revealing evolutionary forces shaping rapid phenotypic diversification. The widespread North American species Bombus bifarius exhibits regional variation in abdominal color forms, ranging from red-banded to black-banded phenotypes and including geographically and phenotypically intermediate forms. Identifying genomic regions linked to this variation has been complicated by strong, near species level, genome-wide differentiation between red- and black-banded forms...
May 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28514744/characterization-of-mouse-serum-exosomal-small-rna-content-the-origins-and-their-roles-in-modulating-inflammatory-response
#4
Xin Zhou, Zinan Jiao, Juling Ji, Shuyuan Li, Xiaodi Huang, Xiaoshuang Lu, Heng Zhao, Jingwen Peng, Xinya Chen, Qiuhong Ji, Yuhua Ji
In the last decade, although studies on exosomal microRNAs (miRNAs) derived from serum and other body fluids have increased dramatically; the contents and biological significance of serum exosomes under normal conditions remain unclear. In the present study, we profiled the small RNA content of mouse serum exosomes (mSEs) using small RNAseq and found that fragments of transfer RNAs (tRNAs) and miRNAs were the two predominant exosomal RNA species, accounting for approximately 60% and 10% of mapped reads, respectively...
April 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28510484/ethylene-signalling-is-important-for-isoflavonoid-mediated-resistance-to-rhizoctonia-solani-in-roots-of-medicago-truncatula
#5
Yao Liu, Samira Hassan, Brendan N Kidd, Gagan Garg, Ulrike Mathesius, Karam B Singh, Jonathan Anderson
The root-infecting necrotrophic fungal pathogen Rhizoctonia solani causes significant disease to all the world's major food crops. As a model for pathogenesis of legumes, we have examined the interaction of R. solani AG8 with Medicago truncatula. RNAseq analysis of the moderately resistant M. truncatula accession A17 and highly susceptible sickle (skl) mutant (defective in ethylene sensing) identified major early transcriptional reprogramming in A17. Responses specific to A17 included components of ethylene signalling, reactive oxygen species metabolism and consistent up-regulation of the isoflavonoid biosynthesis pathway...
May 16, 2017: Molecular Plant-microbe Interactions: MPMI
https://www.readbyqxmd.com/read/28508121/overexpression-of-smmyb9b-enhances-tanshinone-concentration-in-salvia-miltiorrhiza-hairy-roots
#6
Jingxian Zhang, Lubin Zhou, Xiaoyu Zheng, Jinjia Zhang, Li Yang, Ronghui Tan, Shujuan Zhao
A Salvia miltiorrhiza R2R3-MYB gene, SmMYB9b , has been cloned and characterized. Overexpression of SmMYB9b resulted in a significant improvement of tanshinones, the lipophilic active ingredients in danshen hairy roots. Plant R2R3-MYB transcription factors play important roles in various physiological and biochemical processes. Danshen (Salvia miltiorrhiza bunge) is a valuable medicinal herb with tanshinones and salvianolic acids as the principal bioactive ingredients. A number of putative R2R3-MYB transcription factors have been identified in the plant, but their function remains to be studied...
May 15, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28500257/zbtb48-is-both-a-vertebrate-telomere-binding-protein-and-a-transcriptional-activator
#7
Arne Jahn, Grishma Rane, Maciej Paszkowski-Rogacz, Sergi Sayols, Alina Bluhm, Chung-Ting Han, Irena Draškovič, José Arturo Londoño-Vallejo, Alan Prem Kumar, Frank Buchholz, Falk Butter, Dennis Kappei
Telomeres constitute the ends of linear chromosomes and together with the shelterin complex form a structure essential for genome maintenance and stability. In addition to the constitutive binding of the shelterin complex, other direct, yet more transient interactions are mediated by the CST complex and HOT1/HMBOX1, while subtelomeric variant repeats are recognized by NR2C/F transcription factors. Recently, the Kruppel-like zinc finger protein ZBTB48/HKR3/TZAP has been described as a novel telomere-associated factor in the vertebrate lineage...
May 12, 2017: EMBO Reports
https://www.readbyqxmd.com/read/28498607/human-hepatocellular-carcinomas-with-a-periportal-phenotype-have-the-lowest-potential-for-early-recurrence-after-curative-resection
#8
Romain Désert, Florian Rohart, Frédéric Canal, Marie Sicard, Mireille Desille, Stéphanie Renaud, Bruno Turlin, Pascale Bellaud, Christine Perret, Bruno Clément, Kim-Anh Lê Cao, Orlando Musso
Hepatocellular carcinomas (HCCs) exhibit a diversity of molecular phenotypes, raising major challenges in clinical management. HCCs detected by surveillance programs at an early stage are candidates for potentially curative therapies (local ablation, resection or transplantation). In the long term, transplantation provides the lowest recurrence rates. Treatment allocation is based on tumor number, size, vascular invasion, performance status, functional liver reserve and on the prediction of early (< 2 years) recurrence, which reflects the intrinsic aggressiveness of the tumor...
May 12, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28498428/differential-expression-profiles-of-micrornas-as-potential-biomarkers-for-the-early-diagnosis-of-lung-cancer
#9
Yanqiu Zhang, Jing Sui, Xian Shen, Chengyun Li, Wenzhuo Yao, Weiwei Hong, Hui Peng, Yuepu Pu, Lihong Yin, Geyu Liang
Lung cancer is one of the most lethal malignancies worldwide. To reduce the high morbidity and mortality of the disease, sensitive and specific biomarkers for early detection are urgently needed. Tumor-specific microRNAs (miRNAs) seem to be potential biomarkers for the early diagnosis and treatment of cancer. In this study, the microarray of miRNAs and mRNAs on the same samples was performed and the intersection taken with The Cancer Genome Atlas (TCGA) lung cancer miRNA/RNAseq dataset. Then, miRNA-mRNA regulatory network was constructed to identify miRNA candidates associated with lung cancer through integrating gene expression and miRNA-target prediction...
April 28, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28494016/the-host-ubiquitin-dependent-segregase-vcp-p97-is-required-for-the-onset-of-human-cytomegalovirus-replication
#10
Yao-Tang Lin, James Prendergast, Finn Grey
The human cytomegalovirus major immediate early proteins IE1 and IE2 are critical drivers of virus replication and are considered pivotal in determining the balance between productive and latent infection. IE1 and IE2 are derived from the same primary transcript by alternative splicing and regulation of their expression likely involves a complex interplay between cellular and viral factors. Here we show that knockdown of the host ubiquitin-dependent segregase VCP/p97, results in loss of IE2 expression, subsequent suppression of early and late gene expression and, ultimately, failure in virus replication...
May 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28493130/a-bioinformatics-pipeline-for-the-identification-of-cho-cell-differential-gene-expression-from-rna-seq-data
#11
Craig Monger, Krishna Motheramgari, John McSharry, Niall Barron, Colin Clarke
In recent years, the publication of genome sequences for the Chinese hamster and Chinese hamster ovary (CHO) cell lines has facilitated study of these biopharmaceutical cell factories with unprecedented resolution. Our understanding of the CHO cell transcriptome, in particular, has rapidly advanced through the application of next-generation sequencing (NGS) technology to characterize RNA expression (RNA-Seq). In this chapter, we present a computational pipeline for the analysis of CHO cell RNA-Seq data from the Illumina platform to identify differentially expressed genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28486694/differential-microrna-expression-in-cultured-palatal-fibroblasts-from-infants-with-cleft-palate-and-controls
#12
Christian Schoen, Jeffrey C Glennon, Shaghayegh Abghari, Marjon Bloemen, Armaz Aschrafi, Carine E L Carels, Johannes W Von den Hoff
Background: The role of microRNAs (miRNAs) in animal models of palatogenesis has been shown, but only limited research has been carried out in humans. To date, no miRNA expression study on tissues or cells from cleft palate patients has been published. We compared miRNA expression in palatal fibroblasts from cleft palate patients and age-matched controls. Material and Methods: Cultured palatal fibroblasts from 10 non-syndromic cleft lip and palate patients (nsCLP; mean age: 18 ± 2 months), 5 non-syndromic cleft palate only patients (nsCPO; mean age: 17 ± 2 months), and 10 controls (mean age: 24 ± 5 months) were analysed with next-generation small RNA sequencing...
May 9, 2017: European Journal of Orthodontics
https://www.readbyqxmd.com/read/28484437/a-novel-raym_rs09735-raym_rs09740-two-component-signaling-system-regulates-gene-expression-and-virulence-in-riemerella-anatipestifer
#13
Ying Wang, Ti Lu, Xuehuan Yin, Zutao Zhou, Shaowen Li, Mei Liu, Sishun Hu, Dingren Bi, Zili Li
The Gram-negative bacterium Riemerella anatipestifer is an important waterfowl pathogen, causing major economic losses to the duck-producing industry. However, little is known of the virulence factors that mediate pathogenesis during R. anatipestifer infection. In this study, RAYM_RS09735 and RAYM_RS09740 were predicted to form a two-component signaling system (TCS) through bioinformatics analysis. This TCS was highly conserved across the Flavobacteriaceae. A mutant YMΔRS09735/RS09740 strain was constructed to investigate the role of the RAYM_RS09735/RAYM_RS09740 TCS in R...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28483704/genome-wide-analysis-of-ar-binding-and-comparison-with-transcript-expression-in-primary-human-fetal-prostate-fibroblasts-and-cancer-associated-fibroblasts
#14
REVIEW
Claire Nash, Nadia Boufaied, Ian G Mills, Omar E Franco, Simon W Hayward, Axel A Thomson
The androgen receptor (AR) is a transcription factor, and key regulator of prostate development and cancer, which has discrete functions in stromal versus epithelial cells. AR expressed in mesenchyme is necessary and sufficient for prostate development while loss of stromal AR is predictive of prostate cancer progression. Many studies have characterized genome-wide binding of AR in prostate tumour cells but none have used primary mesenchyme or stroma. We applied ChIPseq to identify genomic AR binding sites in primary human fetal prostate fibroblasts and patient derived cancer associated fibroblasts, as well as the WPMY1 cell line overexpressing AR...
May 5, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28475687/the-quinoline-bromoquinol-exhibits-broad-spectrum-antifungal-activity-and-induces-oxidative-stress-and-apoptosis-in-aspergillus-fumigatus
#15
Dafna Ben Yaakov, Yana Shadkchan, Nathaniel Albert, Dimitrios P Kontoyiannis, Nir Osherov
Objectives: Over the last 30 years, the number of invasive fungal infections among immunosuppressed patients has increased significantly, while the number of effective systemic antifungal drugs remains low. The aim of this study was to identify and characterize antifungal compounds that inhibit fungus-specific metabolic pathways not conserved in humans. Methods: We screened a diverse compound library for antifungal activity in the pathogenic mould Aspergillus fumigatus ...
May 5, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/28475646/parallel-clickseq-and-nanopore-sequencing-elucidates-the-rapid-evolution-of-defective-interfering-rnas-in-flock-house-virus
#16
Elizabeth Jaworski, Andrew Routh
Defective-Interfering RNAs (DI-RNAs) have long been known to play an important role in virus replication and transmission. DI-RNAs emerge during virus passaging in both cell-culture and their hosts as a result of non-homologous RNA recombination. However, the principles of DI-RNA emergence and their subsequent evolution have remained elusive. Using a combination of long- and short-read Next-Generation Sequencing, we have characterized the formation of DI-RNAs during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms of DI-RNA emergence and evolution...
May 5, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28470431/radiogenomics-of-lower-grade-glioma-algorithmically-assessed-tumor-shape-is-associated-with-tumor-genomic-subtypes-and-patient-outcomes-in-a-multi-institutional-study-with-the-cancer-genome-atlas-data
#17
Maciej A Mazurowski, Kal Clark, Nicholas M Czarnek, Parisa Shamsesfandabadi, Katherine B Peters, Ashirbani Saha
Recent studies identified distinct genomic subtypes of lower-grade gliomas that could potentially be used to guide patient treatment. This study aims to determine whether there is an association between genomics of lower-grade glioma tumors and patient outcomes using algorithmic measurements of tumor shape in magnetic resonance imaging (MRI). We analyzed preoperative imaging and genomic subtype data from 110 patients with lower-grade gliomas (WHO grade II and III) from The Cancer Genome Atlas. Computer algorithms were applied to analyze the imaging data and provided five quantitative measurements of tumor shape in two and three dimensions...
May 3, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28465297/comprehensive-transcriptome-and-mutational-profiling-of-endemic-burkitt-lymphoma-reveals-ebv-type-specific-differences
#18
Yasin Kaymaz, Cliff I Oduor, Hongbo Yu, Juliana A Otieno, John Michael 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 with sBL tumors. Within eBL tumors, minimal expression differences were found based on: anatomical presentation site, in-hospital survival rates, and EBV genome type, suggesting that eBL tumors are homogeneous without marked subtypes...
May 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28457995/schistosoma-mansoni-off-target-analyses-using-nonspecific-double-stranded-rnas-as-control-for-rnai-experiments-in-schistosomula
#19
Sandra Grossi Gava, Naiara Clemente Tavares, Anna Christina de Matos Salim, Flávio Marcos Gomes de Araújo, Guilherme Oliveira, Marina Moraes Mourão
RNA interference is a well established and widely used reverse genetic tool available for gene functional studies in trematodes. This technique requires the use of nonrelevant double-stranded RNA as control. However, several authors have reported inconsistencies associated with RNAi. We used RNASeq to analyze genes affected by nonspecific dsRNA exposure. We found only few genes presenting altered expression in schistosomula exposed to GFP or mCherry nonspecific-dsRNAs, most of them encoding uncharacterized proteins...
April 27, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28455238/a-novel-ex-vivo-immunoproteomic-approach-characterising-fasciola-hepatica-tegumental-antigens-identified-using-immune-antibody-from-resistant-sheep
#20
Timothy C Cameron, Ira Cooke, Pierre Faou, Hayley Toet, David Piedrafita, Neil Young, Vignesh Rathinasamy, Travis Beddoe, Glenn Anderson, Robert Dempster, Terry W Spithill
A more thorough understanding of the immunological interactions between Fasciola spp. and their hosts is required if we are to develop new immunotherapies to control fasciolosis. Deeper knowledge of the antigens that are the target of the acquired immune responses of definitive hosts against both Fasciola hepatica and Fasciola gigantica will potentially identify candidate vaccine antigens. Indonesian Thin Tail sheep express a high level of acquired immunity to infection by F. gigantica within 4weeks of infection and antibodies in Indonesian Thin Tail sera can promote antibody-dependent cell-mediated cytotoxicity against the surface tegument of juvenile F...
April 26, 2017: International Journal for Parasitology
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