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https://www.readbyqxmd.com/read/27707839/development-of-a-rna-seq-based-prognostic-signature-in-lung-adenocarcinoma
#1
Sudhanshu Shukla, Joseph R Evans, Rohit Malik, Felix Y Feng, Saravana M Dhanasekaran, Xuhong Cao, Guoan Chen, David G Beer, Hui Jiang, Arul M Chinnaiyan
BACKGROUND: Precision therapy for lung cancer will require comprehensive genomic testing to identify actionable targets as well as ascertain disease prognosis. RNA-seq is a robust platform that meets these requirements, but microarray-derived prognostic signatures are not optimal for RNA-seq data. Thus, we undertook the first prognostic analysis of lung adenocarcinoma RNA-seq data and generated a prognostic signature. METHODS: Lung adenocarcinoma RNA-seq and clinical data from The Cancer Genome Atlas (TCGA) were divided chronologically into training (n = 255) and validation (n = 157) cohorts...
January 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/27695782/transcriptomic-signature-of-high-dietary-organic-selenium-supplementation-in-sheep-a-nutrigenomic-insight-using-a-custom-microarray-platform-and-gene-set-enrichment-analysis
#2
R Elgendy, M Giantin, F Castellani, L Grotta, F Palazzo, M Dacasto, G Martino
The objective of this study was to investigate the effect of a high dietary Se supplementation on the whole transcriptome of sheep. A custom sheep whole-transcriptome microarray, with more than 23,000 unique transcripts, was designed and then used to profile the global gene expression of sheep after feeding a high dietary supplementation of organic Se. Lactating crossbred ewes ( = 10; 3 to 4 yr of age and 55 to 65 kg BW) at late lactation (100 ± 8 d in milk) were acclimated to indoor individual pen feeding of a basal control diet (0...
August 2016: Journal of Animal Science
https://www.readbyqxmd.com/read/27695115/comparison-of-the-ability-of-different-clinical-treatment-scores-to-estimate-prognosis-in-high-risk-early-breast-cancer-patients-a-hellenic-cooperative-oncology-group-study
#3
Flora Stavridi, Konstantine T Kalogeras, Kyriaki Pliarchopoulou, Ralph M Wirtz, Zoi Alexopoulou, Flora Zagouri, Elke Veltrup, Eleni Timotheadou, Helen Gogas, Angelos Koutras, Georgios Lazaridis, Christos Christodoulou, George Pentheroudakis, Apostolos Laskarakis, Petroula Arapantoni-Dadioti, Anna Batistatou, Maria Sotiropoulou, Gerasimos Aravantinos, Pavlos Papakostas, Paris Kosmidis, Dimitrios Pectasides, George Fountzilas
BACKGROUND-AIM: Early breast cancer is a heterogeneous disease, and, therefore, prognostic tools have been developed to evaluate the risk for distant recurrence. In the present study, we sought to develop a risk for recurrence score (RRS) based on mRNA expression of three proliferation markers in high-risk early breast cancer patients and evaluate its ability to predict risk for relapse and death. In addition the Adjuvant! Online score (AOS) was also determined for each patient, providing a 10-year estimate of relapse and mortality risk...
2016: PloS One
https://www.readbyqxmd.com/read/27552617/diagnostic-test-accuracy-of-a-2-transcript-host-rna-signature-for-discriminating-bacterial-vs-viral-infection-in-febrile-children
#4
MULTICENTER STUDY
Jethro A Herberg, Myrsini Kaforou, Victoria J Wright, Hannah Shailes, Hariklia Eleftherohorinou, Clive J Hoggart, Miriam Cebey-López, Michael J Carter, Victoria A Janes, Stuart Gormley, Chisato Shimizu, Adriana H Tremoulet, Anouk M Barendregt, Antonio Salas, John Kanegaye, Andrew J Pollard, Saul N Faust, Sanjay Patel, Taco Kuijpers, Federico Martinón-Torres, Jane C Burns, Lachlan J M Coin, Michael Levin
IMPORTANCE: Because clinical features do not reliably distinguish bacterial from viral infection, many children worldwide receive unnecessary antibiotic treatment, while bacterial infection is missed in others. OBJECTIVE: To identify a blood RNA expression signature that distinguishes bacterial from viral infection in febrile children. DESIGN, SETTING, AND PARTICIPANTS: Febrile children presenting to participating hospitals in the United Kingdom, Spain, the Netherlands, and the United States between 2009-2013 were prospectively recruited, comprising a discovery group and validation group...
August 23, 2016: JAMA: the Journal of the American Medical Association
https://www.readbyqxmd.com/read/27440814/schizophyllum-radiatum-an-emerging-fungus-from-human-respiratory-tract
#5
J P Z Siqueira, D Sutton, J Gené, D García, M Guevara-Suarez, C Decock, N Wiederhold, J Guarro
Schizophyllum is an important genus of basidiomycetes that, apart from being of genetic and biotechnological interest, is also reported to be a plant and animal pathogen. Schizophyllum commune is the best-known species and the only one reported from clinical specimens thus far, being recovered mainly from the respiratory tract. The aim of this study was to determine the species diversity of 23 clinical isolates of Schizophyllum from the United States using multilocus phylogenetic analysis and their in vitro susceptibilities to six drugs...
October 2016: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27211267/small-molecule-inhibition-of-camp-response-element-binding-protein-in-human-acute-myeloid-leukemia-cells
#6
B Mitton, H-D Chae, K Hsu, R Dutta, G Aldana-Masangkay, R Ferrari, K Davis, B C Tiu, A Kaul, N Lacayo, G Dahl, F Xie, B X Li, M R Breese, E M Landaw, G Nolan, M Pellegrini, S Romanov, X Xiao, K M Sakamoto
The transcription factor CREB (cAMP Response-Element Binding Protein) is overexpressed in the majority of acute myeloid leukemia (AML) patients, and this is associated with a worse prognosis. Previous work revealed that CREB overexpression augmented AML cell growth, while CREB knockdown disrupted key AML cell functions in vitro. In contrast, CREB knockdown had no effect on long-term hematopoietic stem cell activity in mouse transduction/transplantation assays. Together, these studies position CREB as a promising drug target for AML...
December 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27052474/suppression-of-pcd-related-genes-affects-salt-tolerance-in-arabidopsis
#7
Ahmed Bahieldin, Dhafer A M Alqarni, Ahmed Atef, Nour O Gadalla, Mohammed Al-matary, Sherif Edris, Magdy A Al-Kordy, Rania M Makki, Abdullah A Al-Doss, Jamal S M Sabir, Mohammed H Z Mutwakil, Fotouh M El-Domyati
This work aims at examining a natural exciting phenomenon suggesting that suppression of genes inducing programmed cell death (PCD) might confer tolerance against abiotic stresses in plants. PCD-related genes were induced in tobacco under oxalic acid (OA) treatment (20 mM), and plant cells were characterized to confirm the incidence of PCD. The results indicated that PCD was triggered 24 h after the exposure to OA. Then, RNAs were extracted from tobacco cells 0, 2, 6, 12 and 24 h after treatment for deep sequencing...
March 2016: Comptes Rendus Biologies
https://www.readbyqxmd.com/read/27001218/decorin-over-expression-by-decidual-cells-in-preeclampsia-a-potential-blood-biomarker
#8
Mohammad F Siddiqui, Pinki Nandi, Gannareddy V Girish, Karen Nygard, Genevieve Eastabrook, Barbra de Vrijer, Victor K M Han, Peeyush K Lala
BACKGROUND: Decorin, a leucine-rich proteoglycan that is produced by decidual cells, limits invasion and endovascular differentiation of extravillous trophoblast cells during early placentation by binding to multiple tyrosine kinase receptors, in particular, vascular endothelial growth factor receptor-2. OBJECTIVE: Because many studies have reported an association between poor trophoblast invasion and endovascular differentiation with preeclampsia, the studies reported here tested (1) whether decorin over-expression in the chorionic villi and/or basal decidua is associated with preeclampsia and, if so, (2) whether this association results in a hypoinvasive placenta, and (3) whether elevated plasma decorin concentration in the second trimester is a predictive biomarker for preeclampsia...
September 2016: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/26866935/immediate-administration-of-intraarticular-triamcinolone-acetonide-after-joint-injury-modulates-molecular-outcomes-associated-with-early-synovitis
#9
Jakob T Sieker, Ugur M Ayturk, Benedikt L Proffen, Manuela H Weissenberger, Ata M Kiapour, Martha M Murray
OBJECTIVE: To test whether intraarticular corticosteroid injection mitigates injury-induced synovitis and collagen degradation after anterior cruciate ligament transection (ACLT) and to characterize the synovial response using a functional genomics approach in a preclinical model of posttraumatic osteoarthritis. METHODS: Yorkshire pigs underwent unilateral ACLT without subsequent corticosteroid injection (the ACLT group; n = 6) or ACLT with immediate injection of 20 mg triamcinolone acetonide (the steroid group; n = 6)...
July 2016: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/26551315/metalaxyl-resistance-in-phytophthora-infestans-assessing-role-of-rpa190-gene-and-diversity-within-clonal-lineages
#10
Michael E H Matson, Ian M Small, William E Fry, Howard S Judelson
Prior work has shown that the inheritance of resistance to metalaxyl, an oomycete-specific fungicide, is complex and may involve multiple genes. Recent research indicated that a single nucleotide polymorphism (SNP) in the gene encoding RPA190, the largest subunit of RNA polymerase I, confers resistance to metalaxyl (or mefenoxam) in some isolates of the potato late blight pathogen Phytophthora infestans. Using both DNA sequencing and high resolution melt assays for distinguishing RPA190 alleles, we show here that the SNP is absent from certain resistant isolates of P...
December 2015: Phytopathology
https://www.readbyqxmd.com/read/26484063/transcriptome-analysis-of-the-mouse-e14-5-ts23-developing-humerus-and-differential-expression-in-muscle-less-mutant-embryos-lacking-mechanical-stimulation
#11
Rebecca A Rolfe, Elaine M Kenny, Paul Cormican, Paula Murphy
Mechanical stimulation is important for the correct formation of the skeleton. Splotch-delayed mutant embryos (Pax3 (Spd/Spd) ) that develop with no limb muscle and therefore no limb movement experience an altered mechanical environment resulting in specific defects in ossification and joint formation, particularly in the forelimb. To test the hypothesis that mechanical stimuli influence the regulation of genes important in skeletal development we generated a transcriptome profile of the developing humerus at Theiler stage 23 (TS23), and then identified differentially expressed genes in muscle-less mutant embryos compared to control littermates...
December 2014: Genomics Data
https://www.readbyqxmd.com/read/26146508/positional-rna-seq-identifies-candidate-genes-for-phenotypic-engineering-of-sexual-traits
#12
Roberto Arbore, Kiyono Sekii, Christian Beisel, Peter Ladurner, Eugene Berezikov, Lukas Schärer
INTRODUCTION: RNA interference (RNAi) of trait-specific genes permits the manipulation of specific phenotypic traits ("phenotypic engineering") and thus represents a powerful tool to test trait function in evolutionary studies. The identification of suitable candidate genes, however, often relies on existing functional gene annotation, which is usually limited in emerging model organisms, especially when they are only distantly related to traditional genetic model organisms. A case in point is the free-living flatworm Macrostomum lignano (Lophotrochozoa: Platyhelminthes: Rhabditophora), an increasingly powerful model organism for evolutionary studies of sex in simultaneous hermaphrodites...
2015: Frontiers in Zoology
https://www.readbyqxmd.com/read/25808638/sirna-mediated-knockdown-of-tissue-factor-expression-in-pigs-for-xenotransplantation
#13
H E Ahrens, B Petersen, D Herrmann, A Lucas-Hahn, P Hassel, M Ziegler, W A Kues, U Baulain, W Baars, R Schwinzer, J Denner, D Rataj, S Werwitzke, A Tiede, A K Bongoni, P S Garimella, A Despont, R Rieben, H Niemann
Acute vascular rejection (AVR), in particular microvascular thrombosis, is an important barrier to successful pig-to-primate xenotransplantation. Here, we report the generation of pigs with decreased tissue factor (TF) levels induced by small interfering (si)RNA-mediated gene silencing. Porcine fibroblasts were transfected with TF-targeting small hairpin (sh)RNA and used for somatic cell nuclear transfer. Offspring were analyzed for siRNA, TF mRNA and TF protein level. Functionality of TF downregulation was investigated by a whole blood clotting test and a flow chamber assay...
May 2015: American Journal of Transplantation
https://www.readbyqxmd.com/read/25798844/mir-200-promotes-the-mesenchymal-to-epithelial-transition-by-suppressing-multiple-members-of-the-zeb2-and-snail1-transcriptional-repressor-complexes
#14
R Perdigão-Henriques, F Petrocca, G Altschuler, M P Thomas, M T N Le, S M Tan, W Hide, J Lieberman
The miR-200 family promotes the epithelial state by suppressing the Zeb1/Zeb2 epithelial gene transcriptional repressors. To identify other miR-200-regulated genes, we isolated mRNAs bound to transfected biotinylated miR-200c in mouse breast cancer cells. In all, 520 mRNAs were significantly enriched in miR-200c binding at least twofold. Putative miR-200-regulated genes included Zeb2, enriched 3.5-fold in the pull down. However, Zeb2 knockdown does not fully recapitulate miR-200c overexpression, suggesting that regulating other miR-200 targets contributes to miR-200's enhancement of epithelial gene expression...
January 14, 2016: Oncogene
https://www.readbyqxmd.com/read/25637493/pivotal-role-of-cerebral-interleukin-23-during-immunologic-injury-in-delayed-cerebral-ischemia-in-mice
#15
Y Zheng, D Zhong, H Chen, S Ma, Y Sun, M Wang, Q Liu, G Li
BACKGROUND: Interleukin-23 (IL-23) is required for T helper 17 (Th17) cell responses and IL-17 production in ischemic stroke. We previously showed that the IL-23/IL-17 axis aggravates immune injury after cerebral infarction in mice. However, IL-23 might activate other cytokines and transcription factor forkhead box P3 (Foxp3) production in cerebral ischemia. We aimed to determine whether IL-23p19 knockdown prevents cerebral ischemic injury by reducing ischemic-induced inflammation. METHODS: Ischemic stroke models were established by permanent middle cerebral arterial occlusion (pMCAO) in male C57BL/6 mice...
April 2, 2015: Neuroscience
https://www.readbyqxmd.com/read/25538794/an-integrated-transcriptome-and-expressed-variant-analysis-of-sepsis-survival-and-death
#16
Ephraim L Tsalik, Raymond J Langley, Darrell L Dinwiddie, Neil A Miller, Byunggil Yoo, Jennifer C van Velkinburgh, Laurie D Smith, Isabella Thiffault, Anja K Jaehne, Ashlee M Valente, Ricardo Henao, Xin Yuan, Seth W Glickman, Brandon J Rice, Micah T McClain, Lawrence Carin, G Ralph Corey, Geoffrey S Ginsburg, Charles B Cairns, Ronny M Otero, Vance G Fowler, Emanuel P Rivers, Christopher W Woods, Stephen F Kingsmore
BACKGROUND: Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor outcomes, though current clinical characterizations fail to identify those at greatest risk of progression and mortality. METHODS: The Community Acquired Pneumonia and Sepsis Outcome Diagnostic study enrolled 1,152 subjects with suspected sepsis...
2014: Genome Medicine
https://www.readbyqxmd.com/read/25518432/an-outbreak-of-mycobacterium-genavense-infection-in-a-flock-of-captive-diamond-doves-geopelia-cuneata
#17
Mohie Haridy, Mayumi Fukuta, Yasuyuki Mori, Hideyuki Ito, Masahito Kubo, Hiroki Sakai, Tokuma Yanai
Two diamond doves (Geopelia cuneata) in a flock of 23 birds housed in an aviary in a zoo in central Japan were found dead as a result of mycobacteriosis. Fecal samples of the remaining doves were positive for mycobacterial infection, and thus they were euthanatized. Clinical signs and gross pathology, including weight loss and sudden death and slight enlargement of the liver and intestine, were observed in a small number of birds (3/23). Disseminated histiocytic infiltration of either aggregates or sheets of epithelioid cells containing acid-fast bacilli, in the absence of caseous necrosis, were observed in different organs of the infected doves, especially lungs (23/23), intestines (9/23), livers (7/23), and hearts (6/23)...
September 2014: Avian Diseases
https://www.readbyqxmd.com/read/25382608/pathogenetic-and-diagnostic-significance-of-microrna-deregulation-in-peripheral-t-cell-lymphoma-not-otherwise-specified
#18
M A Laginestra, P P Piccaluga, F Fuligni, M Rossi, C Agostinelli, S Righi, M R Sapienza, G Motta, A Gazzola, C Mannu, E Sabattini, F Bacci, V Tabanelli, C A S Sacchetti, T Z Barrese, M Etebari, F Melle, A Clò, D Gibellini, C Tripodo, G Inghirami, C M Croce, S A Pileri
Peripheral T-cell lymphomas not otherwise specified (PTCLs/NOS) are rare and aggressive tumours whose molecular pathogenesis and diagnosis are still challenging. The microRNA (miRNA) profile of 23 PTCLs/NOS was generated and compared with that of normal T-lymphocytes (CD4+, CD8+, naive, activated). The differentially expressed miRNA signature was compared with the gene expression profile (GEP) of the same neoplasms. The obtained gene patterns were tested in an independent cohort of PTCLs/NOS. The miRNA profile of PTCLs/NOS then was compared with that of 10 angioimmunoblastic T-cell lymphomas (AITLs), 6 anaplastic large-cell lymphomas (ALCLs)/ALK+ and 6 ALCLs/ALK-...
2014: Blood Cancer Journal
https://www.readbyqxmd.com/read/25344240/rotavirus-genotypes-in-sewage-treatment-plants-and-in-children-hospitalized-with-acute-diarrhea-in-italy-in-2010-and-2011
#19
Franco M Ruggeri, Paolo Bonomo, Giovanni Ianiro, Andrea Battistone, Roberto Delogu, Cinzia Germinario, Maria Chironna, Maria Triassi, Rosalba Campagnuolo, Antonella Cicala, Giovanni M Giammanco, Paolo Castiglia, Caterina Serra, Andrea Gaggioli, Lucia Fiore
Although the molecular surveillance network RotaNet-Italy provides useful nationwide data on rotaviruses causing severe acute gastroenteritis in children in Italy, scarce information is available on rotavirus circulation in the general Italian population, including adults with mild or asymptomatic infection. We investigated the genotypes of rotaviruses present in urban wastewaters and compared them with those of viral strains from clinical pediatric cases. During 2010 and 2011, 285 sewage samples from 4 Italian cities were tested by reverse transcription-PCRs (RT-PCRs) specific for rotavirus VP7 and VP4 genes...
January 2015: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/25225260/nesterenkonia-rhizosphaerae-sp-nov-an-alkaliphilic-actinobacterium-isolated-from-rhizosphere-soil-in-a-saline-alkaline-desert
#20
Hong-Fei Wang, Yong-Guang Zhang, Ji-Yue Chen, Wael N Hozzein, Li Li, Mohammed A M Wadaan, Yuan-Ming Zhang, Wen-Jun Li
An alkaliphilic actinobacterial strain, designated EGI 80099(T), was isolated from a rhizosphere soil sample of Reaumuria soongorica found in the desert soils of Fukang, Xinjiang, north-west China. Cells of strain EGI 80099(T) were Gram-stain-positive, non-motile, non-endospore-forming cocci. The predominant menaquinones were MK-7, MK-8 and MK-9. The major cellular fatty acids (>10 %) were anteiso-C15 : 0 and anteiso-C17 : 0. Analysis of the cell wall showed the presence of peptidoglycan of the type l-Lys-Gly-l-Glu, variation A4α...
December 2014: International Journal of Systematic and Evolutionary Microbiology
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