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Transcriptomics

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https://www.readbyqxmd.com/read/28545258/marker-assisted-molecular-profiling-deletion-mutant-analysis-and-rna-seq-reveal-a-disease-resistance-cluster-associated-with-uromyces-appendiculatus-infection-in-common-bean-phaseolus-vulgaris-l
#1
Antonette R Todd, Nicole Donofrio, Venkateswara R Sripathi, Phillip E McClean, Rian K Lee, Marcial Pastor-Corrales, Venu Kal Kalavacharla
Common bean (Phaseolus vulgaris L.) is an important legume, useful for its high protein and dietary fiber. The fungal pathogen Uromyces appendiculatus (Pers.) Unger can cause major loss in susceptible varieties of the common bean. The Ur-3 locus provides race specific resistance to virulent strains or races of the bean rust pathogen along with Crg, (Complements resistance gene), which is required for Ur-3-mediated rust resistance. In this study, we inoculated two common bean genotypes (resistant "Sierra" and susceptible crg) with rust race 53 of U...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545234/validation-of-splicing-events-in-transcriptome-sequencing-data
#2
Wolfgang Kaisers, Johannes Ptok, Holger Schwender, Heiner Schaal
Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545146/transcriptomics-technologies
#3
Rohan Lowe, Neil Shirley, Mark Bleackley, Stephen Dolan, Thomas Shafee
Transcriptomics technologies are the techniques used to study an organism's transcriptome, the sum of all of its RNA transcripts. The information content of an organism is recorded in the DNA of its genome and expressed through transcription. Here, mRNA serves as a transient intermediary molecule in the information network, whilst noncoding RNAs perform additional diverse functions. A transcriptome captures a snapshot in time of the total transcripts present in a cell. The first attempts to study the whole transcriptome began in the early 1990s, and technological advances since the late 1990s have made transcriptomics a widespread discipline...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28545064/transcriptomic-analysis-of-the-response-of-pseudomonas-fluorescens-to-epigallocatechin-gallate-by-rna-seq
#4
Xiaoxiang Liu, Bimiao Shen, Peng Du, Nan Wang, Jiaxue Wang, Jianrong Li, Aihua Sun
Epigallocatechin gallate (EGCG) is a main constituent of green tea polyphenols that are widely used as food preservatives and are considered to be safe for consumption. However, the underlying antimicrobial mechanism of EGCG and the bacterial response to EGCG are not clearly understood. In the present study, a genome-wide transcriptional analysis of a typical spoilage bacterium, Pseudomonas fluorescens that responded to EGCG was performed using RNA-seq technology. A total of 26,365,414 and 23,287,092 clean reads were generated from P...
2017: PloS One
https://www.readbyqxmd.com/read/28544973/pegylation-of-a-tlr2-agonist-based-vaccine-delivery-system-improves-antigen-trafficking-and-the-magnitude-of-ensuing-antibody-and-cd8-t-cell-responses
#5
Toshiki Sekiya, Junya Yamagishi, John Henry V Gray, Paul G Whitney, Axel Martinelli, Weiguang Zeng, Chinn Yi Wong, Chihiro Sugimoto, David C Jackson, Brendon Y Chua
The lipopeptide R4Pam2Cys is an agonist for toll-like receptor-2 (TLR2), a key pathogen-associated molecular pattern receptor expressed on many antigen-presenting cells such as dendritic cells (DCs). Electrostatic association of R4Pam2Cys with soluble protein antigens significantly enhances their immunogenicity and there is evidence to suggest that reducing the size of suitably adjuvanted-antigen complexes in solution may further improve their immunostimulatory capabilities. In this study, we investigated how incorporation of polyethylene glycol (PEG) into R4Pam2Cys affects the size, activity and efficacy of formed antigen-lipopeptide complexes...
May 11, 2017: Biomaterials
https://www.readbyqxmd.com/read/28544882/inference-and-evolutionary-analysis-of-genome-scale-regulatory-networks-in-large-phylogenies
#6
Christopher Koch, Jay Konieczka, Toni Delorey, Ana Lyons, Amanda Socha, Kathleen Davis, Sara A Knaack, Dawn Thompson, Erin K O'Shea, Aviv Regev, Sushmita Roy
Changes in transcriptional regulatory networks can significantly contribute to species evolution and adaptation. However, identification of genome-scale regulatory networks is an open challenge, especially in non-model organisms. Here, we introduce multi-species regulatory network learning (MRTLE), a computational approach that uses phylogenetic structure, sequence-specific motifs, and transcriptomic data, to infer the regulatory networks in different species. Using simulated data from known networks and transcriptomic data from six divergent yeasts, we demonstrate that MRTLE predicts networks with greater accuracy than existing methods because it incorporates phylogenetic information...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544881/mammalian-systems-biotechnology-reveals-global-cellular-adaptations-in-a-recombinant-cho-cell-line
#7
Faraaz Noor Khan Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim, Sze Wai Ng, Ai Ping Hiu, Chung Ping Chow, Corrine Wan, Shuwen Chen, Gavin Teo, Gao Song, Ju Xin Chin, Xiaoan Ruan, Ken Wing Kin Sung, Wei-Shou Hu, Miranda Gek Sim Yap, Muriel Bardor, Niranjan Nagarajan, Dong-Yup Lee
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544705/sma3s-a-universal-tool-for-easy-functional-annotation-of-proteomes-and-transcriptomes
#8
Carlos S Casimiro-Soriguer, Antonio Muñoz-Mérida, Antonio J Pérez-Pulido
The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way...
May 20, 2017: Proteomics
https://www.readbyqxmd.com/read/28544664/to-reproduce-or-work-insect-castes-emerge-from-socially-induced-changes-in-nutrition-related-genes
#9
Amy L Toth
In social species, there is a fundamental trade-off between 'me' and 'we'; that is, should I reproduce, or should I work to help others to reproduce? In this issue of Molecular Ecology, Okada et al. () delve into the evolution and genetic mechanisms of this core question, focusing on social caste formation in insects. The authors take advantage of a unique ant in the genus Diacamma, which has secondarily lost the classic, highly different queens and workers found in many other ants, bees and wasps. Instead, Diacamma ant castes are decided via aggressive dominance interactions among adult females, similar to dominance hierarchies seen in primitively social insects and many social vertebrates...
June 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28544438/genome-wide-identification-characterization-and-evolution-of-cuticular-protein-genes-in-the-malaria-vector-anopheles-sinensis-diptera-culicidae
#10
Bai-Qi Liu, Liang Qiao, Qi-Yi He, Yong Zhou, Shuang Ren, Bin Chen
Thirteen cuticular proteins (CPs) families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on motifs and phylogenetic analyses. In 11 other insect species, 9 had CP numbers > 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of 8 species occupied > 1.4% of the total genomic gene number whereas in 3 species the CPs occupied < 1%...
May 24, 2017: Insect Science
https://www.readbyqxmd.com/read/28544196/analysis-of-transcriptional-and-epigenetic-changes-in-hybrid-vigor-of-allopolyploid-brassica-napus-uncovers-key-roles-for-small-rnas
#11
Yifei Shen, Shuo Sun, Shuijin Hua, Enhui Shen, Chu-Yu Ye, Daguang Cai, Michael P Timko, Qian-Hao Zhu, Longjiang Fan
Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared to its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study, we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormones (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines...
May 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28543982/the-rna-binding-protein-caper-is-required-for-sensory-neuron-development-in-drosophila-melanogaster
#12
Eugenia C Olesnicky, Jeremy M Bono, Laura Bell, Logan T Schachtner, Meghan C Lybecker
BACKGROUND: Alternative splicing mediated by RNA-binding proteins (RBPs) is emerging as a fundamental mechanism for the regulation of gene expression. Alternative splicing has been shown to be a widespread phenomenon that facilitates the diversification of gene products in a tissue specific manner. Although defects in alternative splicing are rooted in many neurological disorders, only a small fraction of splicing factors have been investigated in detail. RESULTS: We find that the splicing factor Caper is required for the development of multiple different mechanosensory neuron subtypes at multiple life stages in Drosophila melanogaster...
May 23, 2017: Developmental Dynamics: An Official Publication of the American Association of Anatomists
https://www.readbyqxmd.com/read/28543596/transcriptional-regulation-of-hormone-synthesis-and-signaling-pathways-by-overexpressing-cytokinin-synthesis-contributes-to-improved-drought-tolerance-in-creeping-bentgrass
#13
Yi Xu, Patrick Burgess, Bingru Huang
The objective of this study was to investigate transcriptomic changes and molecular factors regulated by cytokinins that may contribute to improved drought tolerance in creeping bentgrass (Agrostis stolonifera) overexpressing adenine isopentenyltransferase (ipt). Wild-type (WT) and ipt-transgenic plants were maintained well irrigated or exposed to 21 d of drought stress in growth chambers. Transcriptomic analysis conducted by RNA-seq revealed 661 and 648 up-regulated and 764 and 862 down-regulated drought-responsive genes (DRGs) in the WT and ipt-transgenic plants, respectively, under drought stress using adjusted p-value of 0...
May 24, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/28542832/integrated-transcriptomic-and-metabolomic-analysis-reveals-adaptive-changes-of-hibernating-retinas
#14
Yizhao Luan, Jingxing Ou, Vincent P Kunze, Fengyu Qiao, Yan Wang, Lai Wei, Wei Li, Zhi Xie
Hibernation is a seasonally adaptive strategy that allows hibernators to live through extremely cold conditions. Despite the profound reduction of blood flow to the retinas, hibernation causes no lasting retinal injury. Instead, hibernators show an increased tolerance to ischemic insults during the hibernation period. To understand the molecular changes of the retinas in response to hibernation, we applied an integrative transcriptome and metabolome analysis to explore changes in gene expression and metabolites of 13-lined ground squirrel retinas during hibernation...
May 25, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/28542617/inflammatory-and-apoptotic-remodeling-in-autonomic-nervous-system-following-myocardial-infarction
#15
Chen Gao, Kimberly Howard-Quijano, Christoph Rau, Tatsuo Takamiya, Yang Song, Kalyanam Shivkumar, Yibin Wang, Aman Mahajan
BACKGROUND: Chronic myocardial infarction (MI) triggers pathological remodeling in the heart and cardiac nervous system. Abnormal function of the autonomic nervous system (ANS), including stellate ganglia (SG) and dorsal root ganglia (DRG) contribute to increased sympathoexcitation, cardiac dysfunction and arrythmogenesis. ANS modulation is a therapeutic target for arrhythmia associated with cardiac injury. However, the molecular mechanism involved in the pathological remodeling in ANS following cardiac injury remains to be established...
2017: PloS One
https://www.readbyqxmd.com/read/28542579/transcriptomic-dissection-reveals-wide-spread-differential-expression-in-chickpea-during-early-time-points-of-fusarium-oxysporum-f-sp-ciceri-race-1-attack
#16
Sumanti Gupta, Anirban Bhar, Moniya Chatterjee, Amartya Ghosh, Sampa Das
Plants' reaction to underground microorganisms is complex as sessile nature of plants compels them to prioritize their responses to diverse microorganisms both pathogenic and symbiotic. Roots of important crops are directly exposed to diverse microorganisms, but investigations involving root pathogens are significantly less. Thus, more studies involving root pathogens and their target crops are necessitated to enrich the understanding of underground interactions. Present study reported the molecular complexities in chickpea during Fusarium oxysporum f...
2017: PloS One
https://www.readbyqxmd.com/read/28542576/ebola-virus-glycoprotein-directly-triggers-t-lymphocyte-death-despite-of-the-lack-of-infection
#17
Mathieu Iampietro, Patrick Younan, Andrew Nishida, Mukta Dutta, Ndongala Michel Lubaki, Rodrigo I Santos, Richard A Koup, Michael G Katze, Alexander Bukreyev
Fatal outcomes of Ebola virus (EBOV) infections are typically preceded by a 'sepsis-like' syndrome and lymphopenia despite T cells being resistant to Ebola infection. The mechanisms that lead to T lymphocytes death remain largely unknown; however, the degree of lymphopenia is highly correlative with fatalities. Here we investigated whether the addition of EBOV or its envelope glycoprotein (GP) to isolated primary human CD4+ T cells induced cell death. We observed a significant decrease in cell viability in a GP-dependent manner, which is suggestive of a direct role of GP in T cell death...
May 22, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28542535/a-trichostatin-a-expression-signature-identified-by-tempo-seq-targeted-whole-transcriptome-profiling
#18
Joanne M Yeakley, Peter J Shepard, Diana E Goyena, Harper C VanSteenhouse, Joel D McComb, Bruce E Seligmann
The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0...
2017: PloS One
https://www.readbyqxmd.com/read/28542527/genomic-and-transcriptomic-analyses-reveal-adaptation-mechanisms-of-an-acidithiobacillus-ferrivorans-strain-yl15-to-alpine-acid-mine-drainage
#19
Tangjian Peng, Liyuan Ma, Xue Feng, Jiemeng Tao, Meihua Nan, Yuandong Liu, Jiaokun Li, Li Shen, Xueling Wu, Runlan Yu, Xueduan Liu, Guanzhou Qiu, Weimin Zeng
Acidithiobacillus ferrivorans is an acidophile that often occurs in low temperature acid mine drainage, e.g., that located at high altitude. Being able to inhabit the extreme environment, the bacterium must possess strategies to copy with the survival stress. Nonetheless, information on the strategies is in demand. Here, genomic and transcriptomic assays were performed to illuminate the adaptation mechanisms of an A. ferrivorans strain YL15, to the alpine acid mine drainage environment in Yulong copper mine in southwest China...
2017: PloS One
https://www.readbyqxmd.com/read/28542439/host-mediated-inflammatory-influence-on-glioblastoma-multiforme-recurrence-following-high-dose-ionizing-radiation
#20
J Tyson McDonald, Xuefeng Gao, Cole Steber, Jawon Lee Breed, Caitlin Pollock, Lili Ma, Lynn Hlatky
Despite optimal clinical treatment, glioblastoma multiforme (GBM) inevitably recurs. Standard treatment of GBM, exposes patients to radiation which kills tumor cells, but also modulates the molecular fingerprint of any surviving tumor cells and the cross-talk between those cells and the host. Considerable investigation of short-term (hours to days) post-irradiation tumor cell response has been undertaken, yet long-term responses (weeks to months) which are potentially even more informative of recurrence, have been largely overlooked...
2017: PloS One
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