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https://www.readbyqxmd.com/read/28724083/identification-of-candidate-genes-responsible-for-stem-pith-production-using-expression-analysis-in-solid-stemmed-wheat
#1
A J Oiestad, J M Martin, J Cook, A C Varella, M J Giroux
The wheat stem sawfly (WSS) is an economically important pest of wheat in the Northern Great Plains. The primary means of WSS control is resistance associated with the single quantitative trait locus (QTL) , which controls most stem solidness variation. The goal of this study was to identify stem solidness candidate genes via RNA-seq. This study made use of 28 single nucleotide polymorphism (SNP) makers derived from expressed sequence tags (ESTs) linked to contained within a 5.13 cM region. Allele specific expression of EST markers was examined in stem tissue for solid and hollow-stemmed pairs of two spring wheat near isogenic lines (NILs) differing for the QTL...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28724071/haplotypes-phased-from-population-transcriptomes-detecting-selection-in-the-initial-adaptation-of-miscanthus-lutarioriparius-to-stressful-environments
#2
Cai-Yun Zhu, Wei Liu, Li-Fang Kang, Qin Xu, Shi-Lai Xing, Yang-Yang Fan, Zhi-Hong Song, Juan Yan, Jian-Qiang Li, Tao Sang
Adaptation is a characteristic that enhances the survival or reproduction of organisms; selection is the critical process leading to adaptive evolution. Therefore, detecting selection is important in studying evolutionary biology. Changes in allele frequency are fundamental to adaptive evolution. The allele frequency of entire genes at the genomic scale is more intensive and precise for analyzing selection effects, compared with simple sequence repeat and single nucleotide polymorphism (SNP) alleles from nuclear gene fragments...
July 2017: Plant Genome
https://www.readbyqxmd.com/read/28723946/the-mitochondrial-genome-of-the-terrestrial-carnivorous-plant-utricularia-reniformis-lentibulariaceae-structure-comparative-analysis-and-evolutionary-landmarks
#3
Saura R Silva, Danillo O Alvarenga, Yani Aranguren, Helen A Penha, Camila C Fernandes, Daniel G Pinheiro, Marcos T Oliveira, Todd P Michael, Vitor F O Miranda, Alessandro M Varani
The carnivorous plants of the family Lentibulariaceae have attained recent attention not only because of their interesting lifestyle, but also because of their dynamic nuclear genome size. Lentibulariaceae genomes span an order of magnitude and include species with the smallest genomes in angiosperms, making them a powerful system to study the mechanisms of genome expansion and contraction. However, little is known about mitochondrial DNA (mtDNA) sequences of this family, and the evolutionary forces that shape this organellar genome...
2017: PloS One
https://www.readbyqxmd.com/read/28723657/an-emerging-function-of-circrna-mirnas-mrna-axis-in-human-diseases
#4
REVIEW
Dawei Rong, Handong Sun, Zhouxiao Li, Shuheng Liu, Chaoxi Dong, Kai Fu, Weiwei Tang, Hongyong Cao
Circular RNAs (circRNAs), a novel class of long noncoding RNAs, are characterized by a covalently closed continuous loop without 5' or 3' polarities structure and have been widely found in thousands of lives including plants, animals and human beings. Utilizing the high-throughput RNA sequencing (RNA-seq) technology, recent findings have indicated thata great deal of circRNAs, which are endogenous, stable, widely expressed in mammalian cells, often exhibit cell type-specific, tissue-specific or developmental-stage-specific expression...
July 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28721901/psmb8-as-a-candidate-marker-of-responsiveness-to-preoperative-radiation-therapy-in-rectal-cancer-patients
#5
Ye Jin Ha, Ka Hee Tak, Chan Wook Kim, Seon Ae Roh, Eun Kyung Choi, Dong Hyung Cho, Jeong Hwan Kim, Seon Kyu Kim, Seon Young Kim, Yong Sung Kim, Jin Cheon Kim
PURPOSE: The ability to predict individual responsiveness to cancer therapy is urgently needed. This is particularly true for patients with locally advanced rectal cancer (LARC) because a large proportion are resistant to preoperative chemoradiation therapy (CRT). In this study, we sought to identify markers that could predict response by comparing the gene expression profiles of the tumors of patients who received preoperative CRT. METHODS AND MATERIALS: The basal gene expression profiles of tumors from 22 LARC patients who were responders (n=9) and nonresponders (n=13) to preoperative CRT were analyzed using RNA sequencing (RNA-Seq)...
August 1, 2017: International Journal of Radiation Oncology, Biology, Physics
https://www.readbyqxmd.com/read/28720793/genome-wide-identification-and-characterization-of-natural-antisense-transcripts-by-strand-specific-rna-sequencing-in-ganoderma-lucidum
#6
Junjie Shao, Haimei Chen, Dan Yang, Mei Jiang, Hui Zhang, Bin Wu, Jianqin Li, Lichai Yuan, Chang Liu
Ganoderma lucidum is a white-rot fungus best-known for its medicinal and ligninolytic activities. To discover the underlying genes responsible for these activities, we identified and characterized the natural antisense transcripts (NATs) using strand-specific (ss) RNA-seq data obtained from the mycelia, primordia and fruiting bodies. NATs were identified using a custom pipeline and then subjected to functional enrichment and differential expression analyses. A total of 1613 cis- and 244 trans- sense and antisense transcripts were identified...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720757/integrative-analyses-of-translatome-and-transcriptome-reveal-important-translational-controls-in-brown-and-white-adipose-regulated-by-micrornas
#7
David W Reid, Dan Xu, Peng Chen, Hongyuan Yang, Lei Sun
The epidemic of obesity and diabetes has markedly spurred the research interest in adipocyte biology. Brown adipocytes are specialized for energy expenditure and of therapeutic interest for treatment of metabolic diseases, but how brown adipocytes are distinguished from white adipocytes at the level of translational regulation remains poorly understood. To systemically determine the translational control of gene expression in adipose tissue, we performed ribosome profiling and RNA-seq in parallel to depict the translatome and transcriptome changes during primary brown and white adipogenesis, and between brown and white adipose tissue...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720734/lack-of-acrb-efflux-function-confers-loss-of-virulence-on-salmonella-enterica-serovar-typhimurium
#8
Xuan Wang-Kan, Jessica M A Blair, Barbara Chirullo, Jonathan Betts, Roberto M La Ragione, Alasdair Ivens, Vito Ricci, Timothy J Opperman, Laura J V Piddock
AcrAB-TolC is the paradigm resistance-nodulation-division (RND) multidrug resistance efflux system in Gram-negative bacteria, with AcrB being the pump protein in this complex. We constructed a nonfunctional AcrB mutant by replacing D408, a highly conserved residue essential for proton translocation. Western blotting confirmed that the AcrB D408A mutant had the same native level of expression of AcrB as the parental strain. The mutant had no growth deficiencies in rich or minimal medium. However, compared with wild-type SL1344, the mutant had increased accumulation of Hoechst 33342 dye and decreased efflux of ethidium bromide and was multidrug hypersusceptible...
July 18, 2017: MBio
https://www.readbyqxmd.com/read/28720143/mhc-class-ii-expression-and-potential-antigen-presenting-cells-in-the-retina-during-experimental-autoimmune-uveitis
#9
Deborah A Lipski, Rémi Dewispelaere, Vincent Foucart, Laure E Caspers, Matthieu Defrance, Catherine Bruyns, François Willermain
BACKGROUND: Controversy exists regarding which cell types are responsible for autoantigen presentation in the retina during experimental autoimmune uveitis (EAU) development. In this study, we aimed to identify and characterize the retinal resident and infiltrating cells susceptible to express major histocompatibility complex (MHC) class II during EAU. METHODS: EAU was induced in C57BL/6 mice by adoptive transfer of autoreactive lymphocytes from IRBP1-20-immunized animals...
July 18, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28718511/genome-wide-identification-of-genes-involved-in-the-potato-response-to-drought-indicates-functional-evolutionary-conservation-with-arabidopsis-plants
#10
M Pieczynski, A Wyrzykowska, K Milanowska, D Boguszewska-Mankowska, B Zagdanska, W Karlowski, A Jarmolowski, Z Szweykowska-Kulinska
Potato is one of the four most important food crop plants worldwide and is strongly affected by drought. The following two pairs of potato cultivars, which are related in ancestry but show different drought tolerances, were chosen for comparative gene expression studies: Gwiazda/Oberon and Tajfun/Owacja. Comparative RNA-seq analyses of gene expression differences in the transcriptomes obtained from drought-tolerant versus drought-sensitive plants during water shortage conditions were performed. The twenty-three top-ranking genes were selected, 22 of which are described here as novel potato drought-responsive genes...
July 17, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28718508/development-of-ifox-hunting-as-a-functional-genomics-tool-and-demonstration-of-its-use-to-identify-early-senescence-related-genes-in-the-polyploid-brassica-napus
#11
Juan Ling, Renjie Li, Chinedu Charles Nwafor, Junluo Cheng, Maoteng Li, Qing Xu, Jian Wu, Lu Gan, Qingyong Yang, Chao Liu, Ming Chen, Yongming Zhou, Edgar B Cahoon, Chunyu Zhang
Functional genomics studies of many polyploid crops, including rapeseed (Brassica napus) are constrained by limited tool sets. Here we report development of a gain-of-function platform, termed "iFOX (inducible Full-length cDNA OvereXpressor gene)-Hunting", for inducible expression of B. napus seed cDNAs in Arabidopsis. A Gateway-compatible plant gene expression vector containing a methoxyfenozide-inducible constitutive promoter for transgene expression was developed. This vector was used for cloning of random cDNAs from developing B...
July 17, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28717200/genome-wide-rna-sequencing-analysis-identifies-a-distinct-fibrosis-gene-signature-in-the-conjunctiva-after-glaucoma-surgery
#12
Cynthia Yu-Wai-Man, Nicholas Owen, Jonathan Lees, Aristides D Tagalakis, Stephen L Hart, Andrew R Webster, Christine A Orengo, Peng T Khaw
Fibrosis-related events play a part in most blinding diseases worldwide. However, little is known about the mechanisms driving this complex multifactorial disease. Here we have carried out the first genome-wide RNA-Sequencing study in human conjunctival fibrosis. We isolated 10 primary fibrotic and 7 non-fibrotic conjunctival fibroblast cell lines from patients with and without previous glaucoma surgery, respectively. The patients were matched for ethnicity and age. We identified 246 genes that were differentially expressed by over two-fold and p < 0...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717189/cdk5-mediated-phosphorylation-of-xbp1s-contributes-to-its-nuclear-translocation-and-activation-in-mpp-induced-parkinson-s-disease-model
#13
Feng-Juan Jiao, Qing-Zhi Wang, Pei Zhang, Jian-Guo Yan, Zheng Zhang, Feng He, Qian Zhang, Ze-Xi Lv, Xiang Peng, Hong-Wei Cai, Bo Tian
Parkinson's disease (PD) is an irreversible and progressive neurodegenerative disorder characterized by the selective loss of dopaminergic neurons of the substantia nigra pars compacta. Growing evidence indicates that endoplasmic reticulum stress is a hallmark of PD; however, its exact contribution to the disease process remains poorly understood. Here, we used molecular biology methods and RNA-Seq analysis to explored an unexpected role of spliced X-Box binding protein 1 (XBP1s) in the nervous system. In this study, we determined that the IRE1α/XBP1 pathway is activated in MPP(+)-treated neurons...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717182/widespread-alternative-exon-usage-in-clinically-distinct-subtypes-of-invasive-ductal-carcinoma
#14
Sunniva Stordal Bjørklund, Anshuman Panda, Surendra Kumar, Michael Seiler, Doug Robinson, Jinesh Gheeya, Ming Yao, Grethe I Grenaker Alnæs, Deborah Toppmeyer, Margit Riis, Bjørn Naume, Anne-Lise Børresen-Dale, Vessela N Kristensen, Shridar Ganesan, Gyan Bhanot
Cancer cells can have different patterns of exon usage of individual genes when compared to normal tissue, suggesting that alternative splicing may play a role in shaping the tumor phenotype. The discovery and identification of gene variants has increased dramatically with the introduction of RNA-sequencing technology, which enables whole transcriptome analysis of known, as well as novel isoforms. Here we report alternative splicing and transcriptional events among subtypes of invasive ductal carcinoma in The Cancer Genome Atlas (TCGA) Breast Invasive Carcinoma (BRCA) cohort...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717149/transcriptome-analysis-of-rice-seedling-roots-in-response-to-potassium-deficiency
#15
Xiaoqin Zhang, Hua Jiang, Hua Wang, Jun Cui, Jiahui Wang, Jiang Hu, Longbiao Guo, Qian Qian, Dawei Xue
Rice is one of the most important food crops in the world, and its growth, development, yield, and grain quality are susceptible to a deficiency of the macronutrient potassium (K(+)). The molecular mechanism for K(+) deficiency tolerance remains poorly understood. In this study, K(+) deficient conditions were employed to investigate the resulting changes in the transcriptome of rice seedling roots. Using ribonucleic acid sequencing (RNA-Seq) and analysis, a total of 805 differentially expressed genes were obtained, of which 536 genes were upregulated and 269 were downregulated...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717048/rna-seq-of-rice-yellow-stem-borer-scirpophaga-incertulas-reveals-molecular-insights-during-four-larval-developmental-stages
#16
Renuka P, Maganti S Madhav, Padmakumari A P, Kalyani M Barbadikar, Sathendra K Mangrauthia, Vijaya Sudhakara Rao K, Soma S Marla, Ravindra Babu V
The yellow stem borer (YSB), Scirpophaga incertulas is a prominent pest in the rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on biology and mechanisms underlying growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome at 1(st), 3(rd), 5(th) and 7(th) larval developmental stages employing Illumina Hi-seq...
July 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28716420/characterization-of-bdcbf-genes-and-genome-wide-transcriptome-profiling-of-bdcbf3-dependent-and-independent-cold-stress-responses-in-brachypodium-distachyon
#17
Jingjie Hao, Jinliang Yang, Jiangli Dong, Shui-Zhang Fei
Freezing stress substantially reduces crop yields and limits plant distribution. The identification of genes critical for cold acclimation is thus of great importance. C-repeat binding factors (CBFs) are transcription factors that play key regulatory roles in the cold acclimation process, which dramatically increases freezing tolerance in plants. We report here that B. distachyon can successfully cold acclimate and we identified a CBF gene family consisting of eight genes in a tandem array and are designated as BdCBF1-8...
September 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28715507/independent-component-analysis-ica-based-clustering-of-temporal-rna-seq-data
#18
Moysés Nascimento, Fabyano Fonseca E Silva, Thelma Sáfadi, Ana Carolina Campana Nascimento, Talles Eduardo Maciel Ferreira, Laís Mayara Azevedo Barroso, Camila Ferreira Azevedo, Simone Eliza Faccione Guimarães, Nick Vergara Lopes Serão
Gene expression time series (GETS) analysis aims to characterize sets of genes according to their longitudinal patterns of expression. Due to the large number of genes evaluated in GETS analysis, an useful strategy to summarize biological functional processes and regulatory mechanisms is through clustering of genes that present similar expression pattern over time. Traditional cluster methods usually ignore the challenges in GETS, such as the lack of data normality and small number of temporal observations...
2017: PloS One
https://www.readbyqxmd.com/read/28715477/the-rhlr-quorum-sensing-receptor-controls-pseudomonas-aeruginosa-pathogenesis-and-biofilm-development-independently-of-its-canonical-homoserine-lactone-autoinducer
#19
Sampriti Mukherjee, Dina Moustafa, Chari D Smith, Joanna B Goldberg, Bonnie L Bassler
Quorum sensing (QS) is a bacterial cell-to-cell communication process that relies on the production, release, and response to extracellular signaling molecules called autoinducers. QS controls virulence and biofilm formation in the human pathogen Pseudomonas aeruginosa. P. aeruginosa possesses two canonical LuxI/R-type QS systems, LasI/R and RhlI/R, which produce and detect 3OC12-homoserine lactone and C4-homoserine lactone, respectively. Here, we use biofilm analyses, reporter assays, RNA-seq studies, and animal infection assays to show that RhlR directs both RhlI-dependent and RhlI-independent regulons...
July 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28715466/the-antenna-transcriptome-changes-in-mosquito-anopheles-sinensis-pre-and-post-blood-meal
#20
Qian Chen, Di Pei, Jianyong Li, Chengyu Jing, Wenjian Wu, Yahui Man
Antenna is the main chemosensory organ in mosquitoes. Characterization of the transcriptional changes after blood meal, especially those related to chemoreception, may help to explain mosquito blood sucking behavior and to identify novel targets for mosquito control. Anopheles sinensis is an Asiatic mosquito species which transmits malaria and lymphatic filariasis. However, studies on chemosensory biology in female An. sinensis are quite lacking. Here we report a transcriptome analysis of An. sinensis female antennae pre- and post- blood meal...
2017: PloS One
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