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https://www.readbyqxmd.com/read/29232716/comparative-transcriptome-analysis-unveils-the-tolerance-mechanisms-of-citrus-hystrix-in-response-to-candidatus-liberibacter-asiaticus-infection
#1
Yan Hu, Xi Zhong, Xuelu Liu, Binghai Lou, Changyong Zhou, Xuefeng Wang
Citrus Huanglongbing (HLB), a highly devastating citrus disease, is associated with 'Candidatus Liberibacter asiacitus' (CLas), a member of phloem-inhabiting α-proteobacteria. HLB can affect all cultivated citrus and no cure is currently available. Previous studies showed that Kaffir lime (Citrus hystrix), primarily grown in South Asia and Southeast Asia, was tolerant to HLB but the molecular mechanism remains unknown. In this study, gene expression profiling experiments were performed on HLB-tolerant C. hystrix and HLB-susceptible C...
2017: PloS One
https://www.readbyqxmd.com/read/29232653/salicylic-acid-and-broad-spectrum-of-nbs-lrr-family-genes-are-involved-in-smv-soybean-interactions
#2
Qiqi Zhao, Haina Li, Hongyu Sun, Aoga Li, Shuxin Liu, Ruonan Yu, Xiuqi Cui, Dejian Zhang, Hada Wuriyanghan
Soybean mosaic virus (SMV) is a severe pathogen reducing crop yield and seed quality of soybean. Although several resistance gene loci including Rsv1, Rsv3 and Rsv4 are identified in some soybean varieties, most of the soybean genes related to SMV infection are still not characterized. In order to reveal genome-wide gene expression profiles in response to SMV infection, we used transcriptome analysis to determine SMV-responsive genes in susceptible variety Hefeng25. Time course RNA-seq analysis at 1, 5 and 10 dpi identified many deregulated pathways and gene families...
December 7, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29231925/expression-profiling-of-the-retina-of-pde6c-a-zebrafish-model-of-retinal-degeneration
#3
Liyun Zhang, Xinlian Zhang, Gaonan Zhang, Chi Pui Pang, Yuk Fai Leung, Mingzhi Zhang, Wenxuan Zhong
Retinal degeneration often affects the whole retina even though the disease-causing gene is specifically expressed in the light-sensitive photoreceptors. The molecular basis of the retinal defect can potentially be determined by gene-expression profiling of the whole retina. In this study, we measured the gene-expression profile of retinas microdissected from a zebrafish pde6cw59 (pde6c) mutant. This retinal-degeneration model not only displays cone degeneration caused by a cone-specific mutation, but also other secondary cellular changes starting from 4 days postfertilization (dpf)...
December 12, 2017: Scientific Data
https://www.readbyqxmd.com/read/29231921/an-rna-seq-atlas-of-gene-expression-in-mouse-and-rat-normal-tissues
#4
Julia F Söllner, German Leparc, Tobias Hildebrandt, Holger Klein, Leo Thomas, Elia Stupka, Eric Simon
Gene functionality is closely connected to its expression specificity across tissues and cell types. RNA-Seq is a powerful quantitative tool to explore genome wide expression. The aim of this study is to provide a comprehensive RNA-Seq dataset across the same 13 tissues for mouse and rat, two of the most relevant species for biomedical research. The dataset provides the transcriptome across tissues from three male C57BL6 mice and three male Han Wistar rats. We also describe our bioinformatics pipeline to process and technically validate the data...
December 12, 2017: Scientific Data
https://www.readbyqxmd.com/read/29231888/analysis-and-prediction-of-exon-skipping-events-from-rna-seq-with-sequence-information-using-rotation-forest
#5
Xiuquan Du, Changlin Hu, Yu Yao, Shiwei Sun, Yanping Zhang
In bioinformatics, exon skipping (ES) event prediction is an essential part of alternative splicing (AS) event analysis. Although many methods have been developed to predict ES events, a solution has yet to be found. In this study, given the limitations of machine learning algorithms with RNA-Seq data or genome sequences, a new feature, called RS (RNA-seq and sequence) features, was constructed. These features include RNA-Seq features derived from the RNA-Seq data and sequence features derived from genome sequences...
December 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29231872/a-deeper-examination-of-thorellius-atrox-scorpion-venom-components-with-omic-techonologies
#6
Teresa Romero-Gutierrez, Esteban Peguero-Sanchez, Miguel A Cevallos, Cesar V F Batista, Ernesto Ortiz, Lourival D Possani
This communication reports a further examination of venom gland transcripts and venom composition of the Mexican scorpion Thorellius atrox using RNA-seq and tandem mass spectrometry. The RNA-seq, which was performed with the Illumina protocol, yielded more than 20,000 assembled transcripts. Following a database search and annotation strategy, 160 transcripts were identified, potentially coding for venom components. A novel sequence was identified that potentially codes for a peptide with similarity to spider ω-agatoxins, which act on voltage-gated calcium channels, not known before to exist in scorpion venoms...
December 12, 2017: Toxins
https://www.readbyqxmd.com/read/29231846/the-discrepant-and-similar-responses-of-genome-wide-transcriptional-profiles-between-drought-and-cold-stresses-in-cassava
#7
Changying Zeng, Zehong Ding, Fang Zhou, Yufei Zhou, Ruiju Yang, Zi Yang, Wenquan Wang, Ming Peng
Background: Cassava, an important tropical crop, has remarkable drought tolerance, but is very sensitive to cold. The growth, development, and root productivity of cassava are all adversely affected under cold and drought. Methods: To profile the transcriptional response to cold and drought stresses, cassava seedlings were respectively subjected to 0, 6, 24, and 48 h of cold stress and 0, 4, 6, and 10 days of drought stress. Their folded leaves, fully extended leaves, and roots were respectively investigated using RNA-seq...
December 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29230913/a-novel-approach-to-single-cell-rna-seq-analysis-facilitates-in-silico-gene-reporting-of-human-pluripotent-stem-cell-derived-retinal-cell-types
#8
M Joseph Phillips, Peng Jiang, Sara Howden, Patrick Barney, Jee Min, Nathaniel W York, Li-Fang Chu, Elizabeth E Capowski, Abigail Cash, Shivani Jain, Katherine Barlow, Tasnia Tabassum, Ron Stewart, Bikash R Pattnaik, James A Thomson, David M Gamm
Cell type-specific investigations commonly employ gene reporters or single-cell (sc) analytical techniques. However, reporter line development is arduous and generally limited to a single gene of interest, while scRNA-seq frequently yields equivocal results that preclude definitive cell identification. To examine gene expression profiles of multiple retinal cell types derived from human pluripotent stem cells (hPSCs), we performed scRNA-seq on optic vesicle-like structures (OVs) cultured under cGMP-compatible conditions...
December 12, 2017: Stem Cells
https://www.readbyqxmd.com/read/29230367/a-novel-approach-for-human-whole-transcriptome-analysis-based-on-absolute-gene-expression-of-microarray-data
#9
Shirley Bikel, Leonor Jacobo-Albavera, Fausto Sánchez-Muñoz, Fernanda Cornejo-Granados, Samuel Canizales-Quinteros, Xavier Soberón, Rogerio R Sotelo-Mundo, Blanca E Del Río-Navarro, Alfredo Mendoza-Vargas, Filiberto Sánchez, Adrian Ochoa-Leyva
Background: In spite of the emergence of RNA sequencing (RNA-seq), microarrays remain in widespread use for gene expression analysis in the clinic. There are over 767,000 RNA microarrays from human samples in public repositories, which are an invaluable resource for biomedical research and personalized medicine. The absolute gene expression analysis allows the transcriptome profiling of all expressed genes under a specific biological condition without the need of a reference sample. However, the background fluorescence represents a challenge to determine the absolute gene expression in microarrays...
2017: PeerJ
https://www.readbyqxmd.com/read/29230237/rna-seq-of-plant-parasitic-nematode-meloidogyne-incognita-at-various-stages-of-its-development
#10
Inchan Choi, Parthiban Subramanian, Donghwan Shim, Byung-Ju Oh, Bum-Soo Hahn
No abstract text is available yet for this article.
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29230039/gli1-identifies-osteogenic-progenitors-for-bone-formation-and-fracture-repair
#11
Yu Shi, Guangxu He, Wen-Chih Lee, Jennifer A McKenzie, Matthew J Silva, Fanxin Long
Bone formation in mammals requires continuous production of osteoblasts throughout life. A common molecular marker for all osteogenic mesenchymal progenitors has not been identified. Here, by lineage-tracing experiments in fetal or postnatal mice, we discover that Gli1+ cells progressively produce osteoblasts in all skeletal sites. Most notably, in postnatal growing mice, the Gli1+ cells residing immediately beneath the growth plate, termed here "metaphyseal mesenchymal progenitors" (MMPs), are essential for cancellous bone formation...
December 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29230012/estimation-of-immune-cell-content-in-tumour-tissue-using-single-cell-rna-seq-data
#12
Max Schelker, Sonia Feau, Jinyan Du, Nav Ranu, Edda Klipp, Gavin MacBeath, Birgit Schoeberl, Andreas Raue
As interactions between the immune system and tumour cells are governed by a complex network of cell-cell interactions, knowing the specific immune cell composition of a solid tumour may be essential to predict a patient's response to immunotherapy. Here, we analyse in depth how to derive the cellular composition of a solid tumour from bulk gene expression data by mathematical deconvolution, using indication-specific and cell type-specific reference gene expression profiles (RGEPs) from tumour-derived single-cell RNA sequencing data...
December 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29229983/annotation-free-quantification-of-rna-splicing-using-leafcutter
#13
Yang I Li, David A Knowles, Jack Humphrey, Alvaro N Barbeira, Scott P Dickinson, Hae Kyung Im, Jonathan K Pritchard
The excision of introns from pre-mRNA is an essential step in mRNA processing. We developed LeafCutter to study sample and population variation in intron splicing. LeafCutter identifies variable splicing events from short-read RNA-seq data and finds events of high complexity. Our approach obviates the need for transcript annotations and circumvents the challenges in estimating relative isoform or exon usage in complex splicing events. LeafCutter can be used both to detect differential splicing between sample groups and to map splicing quantitative trait loci (sQTLs)...
December 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29229974/ensemble-modeling-approach-targeting-heterogeneous-rna-seq-data-application-to-melanoma-pseudogenes
#14
Enrico Capobianco, Camilo Valdes, Samanta Sarti, Zhijie Jiang, Laura Poliseno, Nicolas F Tsinoremas
We studied the transcriptome landscape of skin cutaneous melanoma (SKCM) using 103 primary tumor samples from TCGA, and measured the expression levels of both protein coding genes and non-coding RNAs (ncRNAs). In particular, we emphasized pseudogenes potentially relevant to this cancer. While cataloguing the profiles based on the known biotypes, all the employed RNA-Seq methods generated just a small consensus of significant biotypes. We thus designed an approach to reconcile the profiles from all methods following a simple strategy: we selected genes that were confirmed as differentially expressed by the ensemble predictions obtained in a regression model...
December 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29229845/brain-urea-increase-is-an-early-huntington-s-disease-pathogenic-event-observed-in-a-prodromal-transgenic-sheep-model-and-hd-cases
#15
Renee R Handley, Suzanne J Reid, Rudiger Brauning, Paul Maclean, Emily R Mears, Imche Fourie, Stefano Patassini, Garth J S Cooper, Skye R Rudiger, Clive J McLaughlan, Paul J Verma, James F Gusella, Marcy E MacDonald, Henry J Waldvogel, C Simon Bawden, Richard L M Faull, Russell G Snell
The neurodegenerative disorder Huntington's disease (HD) is typically characterized by extensive loss of striatal neurons and the midlife onset of debilitating and progressive chorea, dementia, and psychological disturbance. HD is caused by a CAG repeat expansion in the Huntingtin (HTT) gene, translating to an elongated glutamine tract in the huntingtin protein. The pathogenic mechanism resulting in cell dysfunction and death beyond the causative mutation is not well defined. To further delineate the early molecular events in HD, we performed RNA-sequencing (RNA-seq) on striatal tissue from a cohort of 5-y-old OVT73-line sheep expressing a human CAG-expansion HTT cDNA transgene...
December 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29229769/cytoplasmic-polyadenylation-mediated-translational-control-of-maternal-mrnas-directs-maternal-to-zygotic-transition
#16
Cecilia Lanny Winata, Maciej Łapiński, Leszek Pryszcz, Candida Vaz, Muhammad Hisyam Bin Ismail, Srikanth Nama, Hajira Shreen Hajan, Serene Gek Ping Lee, Vladimir Korzh, Prabha Sampath, Vivek Tanavde, Sinnakaruppan Mathavan
In the earliest stages of animal development following fertilization, maternally deposited mRNAs direct biological processes to the point of zygotic genome activation (ZGA). These maternal mRNAs undergo cytoplasmic polyadenylation (CPA), suggesting translational control of their activation. To elucidate the biological role of CPA during embryogenesis, we performed genome-wide polysome profiling at several stages of zebrafish development. Our analysis revealed a correlation between CPA and polysome association dynamics, demonstrating a coupling of translation to the CPA of maternal mRNAs...
December 11, 2017: Development
https://www.readbyqxmd.com/read/29229736/comparison-of-salmonella-enterica-serovars-typhi-and-typhimurium-reveals-typhoidal-specific-responses-to-bile
#17
Rebecca Johnson, Matt Ravenhall, Derek Pickard, Gordon Dougan, Alexander Byrne, Gad Frankel
Salmonella enterica serovars Typhi and Typhimurium cause typhoid fever and gastroenteritis respectively. A unique feature of typhoid infection is asymptomatic carriage within the gallbladder, which is linked with S Typhi transmission. Despite this, S Typhi responses to bile have been poorly studied. RNA-Seq of S Typhi Ty2 and a clinical S Typhi isolate belonging to the globally dominant H58 lineage (129-0238), as well as S Typhimurium 14028, revealed that 249, 389 and 453 genes respectively were differentially expressed in the presence of 3% bile compared to control cultures lacking bile...
December 11, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29229727/high-salt-conditions-alter-transcription-of-helicobacter-pylori-genes-encoding-outer-membrane-proteins
#18
John T Loh, Amber C Beckett, Matthew B Scholz, Timothy L Cover
Helicobacter pylori infection and high dietary salt intake are risk factors for the development of gastric adenocarcinoma. One possible mechanism by which a high salt diet could influence gastric cancer risk is by modulating H. pylori gene expression. In this study, we utilized RNA-seq methodology to compare the transcriptional profiles of H. pylori grown in media containing different concentrations of sodium chloride. We identified 118 differentially expressed genes (65 upregulated and 53 downregulated in response to high salt conditions), including multiple members of 14 operons...
December 11, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29229604/transcription-factor-activities-enhance-markers-of-drug-sensitivity-in-cancer
#19
Luz M Garcia-Alonso, Francesco Iorio, Angela Matchan, Nuno A Fonseca, Patricia Jaaks, Gareth Peat, Miguel Pignatelli, Fiammetta Falcone, Cyril H Benes, Ian Dunham, Graham R Bignell, Simon McDade, Mathew J Garnett, Julio Saez-Rodriguez
Transcriptional dysregulation induced by aberrant Transcription factors (TFs) is a key feature of cancer, but its global influence on drug sensitivity has not been examined. Here we infer the transcriptional activity of 127 TFs through analysis of RNA-seq gene expression data newly generated for 448 cancer cell lines, combined with publicly available datasets to survey a total of 1,056 cancer cell lines and 9,250 primary tumors. Predicted TF activities are supported by their agreement with independent shRNA essentiality profiles and homozygous gene deletions, and recapitulate mutant-specific mechanisms of transcriptional dysregulation in cancer...
December 11, 2017: Cancer Research
https://www.readbyqxmd.com/read/29228974/central-nervous-system-transcriptome-of-biomphalaria-alexandrina-an-intermediate-host-for-schistosomiasis
#20
Tamer A Mansour, Mohamed R Habib, Laura C Vicente Rodríguez, Anthony Hernández Vázquez, Julián Maldonado Alers, Alfredo Ghezzi, Roger P Croll, C Titus Brown, Mark W Miller
OBJECTIVE: Globally, more than 200 million people live at risk of the neglected tropical disease schistosomiasis (or snail fever). Larval schistosomes require the presence of specific snail species that act as intermediate hosts, supporting their multiplication and transformation into forms that can infect humans. This project was designed to generate a transcriptome from the central nervous system (CNS) of Biomphalaria alexandrina, the major intermediate host for Schistosoma mansoni in Egypt...
December 11, 2017: BMC Research Notes
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