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https://www.readbyqxmd.com/read/28632769/combining-omics-and-microscopy-to-visualize-interactions-between-the-asian-citrus-psyllid-vector-and-the-huanglongbing-pathogen-candidatus-liberibacter-asiaticus-in-the-insect-gut
#1
Angela Kruse, Somayeh Fattah-Hosseini, Surya Saha, Richard Johnson, EricaRose Warwick, Kasie Sturgeon, Lukas Mueller, Michael J MacCoss, Robert G Shatters, Michelle Cilia Heck
Huanglongbing, or citrus greening disease, is an economically devastating bacterial disease of citrus. It is associated with infection by the gram-negative bacterium Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). For insect transmission to occur, CLas must be ingested during feeding on infected phloem sap and cross the gut barrier to gain entry into the insect vector. To investigate the effects of CLas exposure at the gut-pathogen interface, we performed RNAseq and mass spectrometry-based proteomics to analyze the transcriptome and proteome, respectively, of ACP gut tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28631994/gene-expression-and-morphogenesis-during-the-deposition-of-drosophila-wing-cuticle
#2
Paul N Adler
The exoskeleton of insects and other arthropods is a very versatile material that is characterized by a complex multilayer structure. In Sobala and Adler (2016) we analyzed the process of wing cuticle deposition by RNAseq and electron microscopy. In this extra view we discuss the unique aspects of the envelope the first and most outermost layer and the gene expression program seen at the end of cuticle deposition. We discussed the role of undulae in the deposition of cuticle and how the hydrophobicity of wing cuticle arises...
February 17, 2017: Fly
https://www.readbyqxmd.com/read/28617226/contextualization-of-drug-mediator-relations-using-evidence-networks
#3
Hai Joey Tran, Gil Speyer, Jeff Kiefer, Seungchan Kim
BACKGROUND: Genomic analysis of drug response can provide unique insights into therapies that can be used to match the "right drug to the right patient." However, the process of discovering such therapeutic insights using genomic data is not straightforward and represents an area of active investigation. EDDY (Evaluation of Differential DependencY), a statistical test to detect differential statistical dependencies, is one method that leverages genomic data to identify differential genetic dependencies...
May 31, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28615715/rnaseq-based-transcriptomics-study-of-smcs-from-carotid-atherosclerotic-plaque-bmp2-and-ids-proteins-are-crucial-regulators-of-plaque-stability
#4
Iraide Alloza, Haize Goikuria, Juan Luis Idro, Juan Carlos Triviño, José María Fernández Velasco, Elena Elizagaray, María García-Barcina, Genoveva Montoya-Murillo, Esther Sarasola, Reyes Vega Manrique, Maria Del Mar Freijo, Koen Vandenbroeck
Carotid artery atherosclerosis is a risk factor to develop cerebrovascular disease. Atheroma plaque can become instable and provoke a cerebrovascular event or else remain stable as asymptomatic type. The exact mechanism involved in plaque destabilization is not known but includes among other events smooth muscle cell (SMC) differentiation. The goal of this study was to perform thorough analysis of gene expression differences in SMCs isolated from carotid symptomatic versus asymptomatic plaques. Comparative transcriptomics analysis of SMCs based on RNAseq technology identified 67 significant differentially expressed genes and 143 significant differentially expressed isoforms in symptomatic SMCs compared with asymptomatic...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28614372/intestinal-organoids-model-human-responses-to-infection-by-commensal-and-shiga-toxin-producing-escherichia-coli
#5
Sayali S Karve, Suman Pradhan, Doyle V Ward, Alison A Weiss
Infection with Shiga toxin (Stx) producing Escherichia coli O157:H7 can cause the potentially fatal complication hemolytic uremic syndrome, and currently only supportive therapy is available. Lack of suitable animal models has hindered study of this disease. Induced human intestinal organoids (iHIOs), generated by in vitro differentiation of pluripotent stem cells, represent differentiated human intestinal tissue. We show that iHIOs with addition of human neutrophils can model E. coli intestinal infection and innate cellular responses...
2017: PloS One
https://www.readbyqxmd.com/read/28611744/rnaseq-reveals-complex-response-of-campylobacter-jejuni-to-ovine-bile-and-in-vivo-gallbladder-environment
#6
Amanda J Kreuder, Jennifer A Schleining, Michael Yaeger, Qijing Zhang, Paul J Plummer
Colonization of the gallbladder by enteric pathogens such as Salmonella typhi, Listeria monocytogenes, and Campylobacter jejuni is thought to play a key role in transmission and persistence of these important zoonotic agents; however, little is known about the molecular mechanisms that allow for bacterial survival within this harsh environment. Recently, a highly virulent C. jejuni sheep abortion (SA) clone represented by the clinical isolate IA3902 has emerged as the dominant cause for sheep abortion in the United States...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28601352/comprehensive-genomic-characterization-of-upper-tract-urothelial-carcinoma
#7
Tyler J Moss, Yuan Qi, Liu Xi, Bo Peng, Tae-Beom Kim, Nader E Ezzedine, Maribel E Mosqueda, Charles C Guo, Bogdan A Czerniak, Michael Ittmann, David A Wheeler, Seth P Lerner, Surena F Matin
BACKGROUND: Upper urinary tract urothelial cancer (UTUC) may have unique etiologic and genomic factors compared to bladder cancer. OBJECTIVE: To characterize the genomic landscape of UTUC and provide insights into its biology using comprehensive integrated genomic analyses. DESIGN, SETTING, AND PARTICIPANTS: We collected 31 untreated snap-frozen UTUC samples from two institutions and carried out whole-exome sequencing (WES) of DNA, RNA sequencing (RNAseq), and protein analysis...
June 7, 2017: European Urology
https://www.readbyqxmd.com/read/28596493/upregulation-of-long-noncoding-rna-hoxa-as3-promotes-tumor-progression-and-predicts-poor-prognosis-in-glioma
#8
Fan Wu, Chuanbao Zhang, Jinquan Cai, Fan Yang, Tingyu Liang, Xiaoyan Yan, Haoyuan Wang, Wen Wang, Jing Chen, Tao Jiang
Long noncoding RNAs (lncRNAs) have recently emerged as new potentially promising therapeutic targets in many cancers. However, their prognostic value and biological functions associated with glioma remain to be elucidated. Here, High-throughput RNAseq was performed to detect the expression profiles of lncRNAs in 325 human glioma tissues. It was shown that a novel lncRNA HOXA-AS3 was one of the most significantly upregulated lncRNAs in glioma tissues. Quantitative PCR further verified the increased expression of HOXA-AS3 in patient samples and glioma cell lines...
May 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/28594822/hybridization-and-polyploidy-enable-genomic-plasticity-without-sex-in-the-most-devastating-plant-parasitic-nematodes
#9
Romain Blanc-Mathieu, Laetitia Perfus-Barbeoch, Jean-Marc Aury, Martine Da Rocha, Jérôme Gouzy, Erika Sallet, Cristina Martin-Jimenez, Marc Bailly-Bechet, Philippe Castagnone-Sereno, Jean-François Flot, Djampa K Kozlowski, Julie Cazareth, Arnaud Couloux, Corinne Da Silva, Julie Guy, Yu-Jin Kim-Jo, Corinne Rancurel, Thomas Schiex, Pierre Abad, Patrick Wincker, Etienne G J Danchin
Root-knot nematodes (genus Meloidogyne) exhibit a diversity of reproductive modes ranging from obligatory sexual to fully asexual reproduction. Intriguingly, the most widespread and devastating species to global agriculture are those that reproduce asexually, without meiosis. To disentangle this surprising parasitic success despite the absence of sex and genetic exchanges, we have sequenced and assembled the genomes of three obligatory ameiotic and asexual Meloidogyne. We have compared them to those of relatives able to perform meiosis and sexual reproduction...
June 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28593993/myc-activation-cooperates-with-vhl-and-ink4a-arf-loss-to-induce-clear-cell-renal-cell-carcinoma
#10
Sean T Bailey, Aleisha M Smith, Jordan Kardos, Sara E Wobker, Harper L Wilson, Bhavani Krishnan, Ryoichi Saito, Hyo Jin Lee, Jing Zhang, Samuel C Eaton, Lindsay A Williams, Ujjawal Manocha, Dorien J Peters, Xinchao Pan, Thomas J Carroll, Dean W Felsher, Vonn Walter, Qing Zhang, Joel S Parker, Jen Jen Yeh, Richard A Moffitt, Janet Y Leung, William Y Kim
Renal carcinoma is a common and aggressive malignancy whose histopathogenesis is incompletely understood and that is largely resistant to cytotoxic chemotherapy. We present two mouse models of kidney cancer that recapitulate the genomic alterations found in human papillary (pRCC) and clear cell RCC (ccRCC), the most common RCC subtypes. MYC activation results in highly penetrant pRCC tumours (MYC), while MYC activation, when combined with Vhl and Cdkn2a (Ink4a/Arf) deletion (VIM), produce kidney tumours that approximate human ccRCC...
June 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28582664/interactions-between-water-activity-and-temperature-on-the-aspergillus-flavus-transcriptome-and-aflatoxin-b1-production
#11
Angel Medina, Matthew K Gilbert, Brian M Mack, Gregory R OBrian, Alicia Rodríguez, Deepak Bhatnagar, Gary Payne, Naresh Magan
Effects of Aspergillus flavus colonization of maize kernels under different water activities (aw; 0.99 and 0.91) and temperatures (30, 37°C) on (a) aflatoxin B1 (AFB1) production and (b) the transcriptome using RNAseq were examined. There was no significant difference (p=0.05) in AFB1 production at 30 and 37°C and 0.99 aw. However, there was a significant (p=0.05) increase in AFB1 at 0.91 aw at 37°C when compared with 30°C/0.99 aw. Environmental stress effects using gene ontology enrichment analysis of the RNA-seq results for increasing temperature at 0...
May 26, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28582519/x-chromosome-inactivation-in-human-pluripotent-stem-cells-as-a-model-for-human-development-back-to-the-drawing-board
#12
Mieke Geens, Susana M Chuva De Sousa Lopes
BACKGROUND: Human pluripotent stem cells (hPSC), both embryonic and induced (hESC and hiPSC), are regarded as a valuable in vitro model for early human development. In order to fulfil this promise, it is important that these cells mimic as closely as possible the in vivo molecular events, both at the genetic and epigenetic level. One of the most important epigenetic events during early human development is X chromosome inactivation (XCI), the transcriptional silencing of one of the two X chromosomes in female cells...
June 5, 2017: Human Reproduction Update
https://www.readbyqxmd.com/read/28578401/rnaseq-analysis-reveals-pathways-and-candidate-genes-associated-with-salinity-tolerance-in-a-spaceflight-induced-wheat-mutant
#13
Hongchun Xiong, Huijun Guo, Yongdun Xie, Linshu Zhao, Jiayu Gu, Shirong Zhao, Junhui Li, Luxiang Liu
Salinity stress has become an increasing threat to food security worldwide and elucidation of the mechanism for salinity tolerance is of great significance. Induced mutation, especially spaceflight mutagenesis, is one important method for crop breeding. In this study, we show that a spaceflight-induced wheat mutant, named salinity tolerance 1 (st1), is a salinity-tolerant line. We report the characteristics of transcriptomic sequence variation induced by spaceflight, and show that mutations in genes associated with sodium ion transport may directly contribute to salinity tolerance in st1...
June 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28577792/genome-wide-analysis-of-gene-expression-of-ems-induced-short-fiber-mutant-ligon-lintless-y-liy-in-cotton-gossypium-hirsutum-l
#14
Marina Naoumkina, Efrem Bechere, David D Fang, Gregory N Thyssen, Christopher B Florane
In this work we describe a chemically-induced short fiber mutant cotton line, Ligon-lintless-y (liy), which is controlled by a single recessive locus and affects multiple traits, including height of the plant, and length and maturity of fiber. An RNAseq analysis was used to evaluate global transcriptional changes during cotton fiber development at 3, 8 and 16days post anthesis. We found that 613, 2629 and 3397 genes were significantly down-regulated, while 2700, 477 and 3260 were significantly up-regulated in liy at 3, 8 and 16 DPA...
May 31, 2017: Genomics
https://www.readbyqxmd.com/read/28575852/increased-transcriptional-and-metabolic-capacity-for-lipid-metabolism-in-the-peripheral-zone-of-the-prostate-may-underpin-its-increased-susceptibility-to-cancer
#15
Omar Al Kadhi, Maria H Traka, Antonietta Melchini, Perla Troncoso-Rey, Wiktor Jurkowski, Marianne Defernez, Purnima Pachori, Robert D Mills, Richard Y Ball, Richard F Mithen
The human prostate gland comprises three distinct anatomical glandular zones, namely the peripheral, central and transitional zones. Although prostate cancer can arise throughout the prostate, it is more frequent in the peripheral zone. In contrast, hyperplasia occurs most frequently in the transitional zone. In this paper, we test the hypothesis that peripheral and transitional zones have distinct metabolic adaptations that may underlie their different inherent predispositions to cancer and hyperplasia. In order to do this, we undertook RNA sequencing and high-throughput metabolic analyses of non-cancerous tissue from the peripheral and transitional zones of patients undergoing prostatectomy...
May 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28559982/long-noncoding-rnas-and-novel-inflammatory-genes-determined-by-rna-sequencing-in-human-lymphocytes-are-up-regulated-in-permanent-atrial-fibrillation
#16
Xue-Jing Yu, Li-Hui Zou, Jun-Hua Jin, Fei Xiao, Li Li, Nan Liu, Jie-Fu Yang, Tong Zou
Atrial fibrillation (AF) is a common arrhythmia in clinical practice. Currently, approximately 33.5 million individuals are affected by AF globally. AF involves multiple complicated mechanisms which have not been fully investigated yet. RNA sequencing (RNAseq) is an outstanding method for investigation of diseases due to its high-throughput information. Here, RNAseq was applied to determine mRNA and long noncoding RNA (lncRNA) expression profiles in human lymphocytes from 6 permanent atrial fibrillation (pmAF) patients and 6 healthy controls...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28559853/proteogenomics-reveals-enriched-ribosome-assembly-and-protein-translation-in-pectoralis-major-of-high-feed-efficiency-pedigree-broiler-males
#17
Walter G Bottje, Kentu Lassiter, Alissa Piekarski-Welsher, Sami Dridi, Antonio Reverter, Nicholas J Hudson, Byung-Whi Kong
Background: In production animal agriculture, the cost of feed represents 60-70% of the total cost of raising an animal to market weight. Thus, development of viable biomarkers for feed efficiency (FE, g gain/g feed) to assist in genetic selection of breeding stock remains an important goal in commercial breeding programs. Methods: Global gene (cDNA microarray, RNAseq) and protein expression (shotgun proteomics) analyses have been conducted on breast muscle samples obtained from pedigree broiler males (PedM) exhibiting high and low FE phenotypes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28548943/intra-tumour-molecular-heterogeneity-of-clear-cell-renal-cell-carcinoma-reveals-the-diversity-of-the-response-to-targeted-therapies-using-patient-derived-xenograft-models
#18
Baoan Hong, Yong Yang, Sheng Guo, Shayiremu Duoerkun, Xiaohu Deng, Dawei Chen, Shijun Yu, Wubin Qian, Qixiang Li, Qing Li, Kan Gong, Ning Zhang
Inter- and intra-tumour molecular heterogeneity is increasingly recognized in clear cell renal cell carcinoma (ccRCC). It may partially explain the diversity of responses to targeted therapies and the various clinical outcomes. In this study, a 56-year-old male ccRCC patient with multiple metastases received radical nephrectomy and resection of the metastatic tumour in chest wall. The surgical specimens were implanted into nude mice to establish patient-derived xenograft (PDX) models with KI2367 model derived from the primary tumour and KI2368 model from the metastastic tumour...
May 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28548877/role-of-osgin1-in-mediating-smoking-induced-autophagy-in-the-human-airway-epithelium
#19
Guoqing Wang, Haixia Zhou, Yael Strulovici-Barel, Mohammed Al-Hijji, Xuemei Ou, Jacqueline Salit, Matthew S Walters, Michelle R Staudt, Robert J Kaner, Ronald G Crystal
Enhanced macroautophagy/autophagy is recognized as a component of the pathogenesis of smoking-induced airway disease. Based on the knowledge that enhanced autophagy is linked to oxidative stress and the DNA damage response, both of which are linked to smoking, we used microarray analysis of the airway epithelium to identify smoking upregulated genes known to respond to oxidative stress and the DNA damage response. This analysis identified OSGIN1 (oxidative stress induced growth inhibitor 1) as significantly upregulated by smoking, in both the large and small airway epithelium, an observation confirmed by an independent small airway microarray cohort, TaqMan PCR of large and small airway samples and RNA-Seq of small airway samples...
May 26, 2017: Autophagy
https://www.readbyqxmd.com/read/28548123/infrequently-expressed-mirnas-in-colorectal-cancer-tissue-and-tumor-molecular-phenotype
#20
Martha L Slattery, Frances Y Lee, Andrew J Pellatt, Lila E Mullany, John R Stevens, Wade S Samowitz, Roger K Wolff, Jennifer S Herrick
We have previously shown that commonly expressed miRNAs influenced tumor molecular phenotype in colorectal cancer. We hypothesize that infrequently expressed miRNAs, when showing higher levels of expression, help to define tumor molecular phenotype. In this study, we examine 304 miRNAs expressed in at least 30 individuals, but in <50% of the population and with a mean level of expression above 1.0 relative florescent unit. We examine associations in 1893 individuals who have the tumor molecular phenotype data as well as miRNA expression levels for both carcinoma and normal colorectal tissue...
May 26, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
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