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https://www.readbyqxmd.com/read/27926877/ptbp1-and-ptbp2-serve-both-specific-and-redundant-functions-in-neuronal-pre-mrna-splicing
#1
John K Vuong, Chia-Ho Lin, Min Zhang, Liang Chen, Douglas L Black, Sika Zheng
Families of alternative splicing regulators often contain multiple paralogs presumed to fulfill different functions. Polypyrimidine tract binding proteins PTBP1 and PTBP2 reprogram developmental pre-mRNA splicing in neurons, but how their regulatory networks differ is not understood. To compare their targeting, we generated a knockin allele that conditionally expresses PTBP1. Bred to a Ptbp2 knockout, the transgene allowed us to compare the developmental and molecular phenotypes of mice expressing only PTBP1, only PTBP2, or neither protein in the brain...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27926863/chronic-infection-depletes-hematopoietic-stem-cells-through-stress-induced-terminal-differentiation
#2
Katie A Matatall, Mira Jeong, Siyi Chen, Deqiang Sun, Fengju Chen, Qianxing Mo, Marek Kimmel, Katherine Y King
Chronic infections affect a third of the world's population and can cause bone marrow suppression, a severe condition that increases mortality from infection. To uncover the basis for infection-associated bone marrow suppression, we conducted repeated infection of WT mice with Mycobacterium avium. After 4-6 months, mice became pancytopenic. Their hematopoietic stem and progenitor cells (HSPCs) were severely depleted and displayed interferon gamma (IFN-γ) signaling-dependent defects in self-renewal. There was no evidence of increased HSPC mobilization or apoptosis...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27926507/macrophage-migration-inhibitory-factor-activates-inflammatory-responses-of-astrocytes-through-interaction-with-cd74-receptor
#3
Yu Su, Yingjie Wang, Yue Zhou, Zhenjie Zhu, Qing Zhang, Xuejie Zhang, Wenjuan Wang, Xiaosong Gu, Aisong Guo, Yongjun Wang
Astrocytes, the major glial cell population of the central nervous system (CNS), play important physiological roles related to CNS homeostasis. Growing evidence demonstrates that astrocytes trigger innate immune responses under challenge of a variety of proinflammatory cytokines. Macrophage migration inhibitory factor (MIF), a proinflammatory cytokine mainly secreted from monocytes/macrophages, is involved in inflammation-associated pathophysiology. Here, we displayed that expression of MIF significantly increased following spinal cord injury, in colocalization with microglia and astrocytes...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27925796/a-severe-asthma-disease-signature-from-gene-expression-profiling-of-peripheral-blood-from-u-biopred-cohorts
#4
Jeannette Bigler, Michael Boedigheimer, James P R Schofield, Paul J Skipp, Julie Corfield, Anthony Rowe, Ana R Sousa, Martin Timour, Lori Twehues, Xuguang Hu, Graham Roberts, Andrew A Welcher, Wen Yu, Kian F Chung, Ian M Adcock, Peter J Sterk, Ratko Djukanović
RATIONALE: Stratification of asthma at the molecular level, especially using accessible biospecimens, could greatly enable patient selection for targeted therapy. OBJECTIVES: To determine the value of blood to identify transcriptional differences between clinically defined asthmatic and non-asthmatic groups, identify potential patient subgroups based on gene expression, and explore biological pathways associated with identified differences. METHODS: Transcriptomics profiles were generated by microarray analysis of blood from 610 asthmatic and control participants in U-BIOPRED...
December 7, 2016: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/27924858/transcriptomic-characterization-and-curation-of-candidate-neuropeptides-regulating-reproduction-in-the-eyestalk-ganglia-of-the-australian-crayfish-cherax-quadricarinatus
#5
Tuan Viet Nguyen, Scott F Cummins, Abigail Elizur, Tomer Ventura
The Australian redclaw crayfish (Cherax quadricarinatus) has recently received attention as an emerging candidate for sustainable aquaculture production in Australia and worldwide. More importantly, C. quadricarinatus serves as a good model organism for the commercially important group of decapod crustaceans as it is distributed worldwide, easy to maintain in the laboratory and its reproductive cycle has been well documented. In order to better understand the key reproduction and development regulating mechanisms in decapod crustaceans, the molecular toolkit available for model organisms such as C...
December 7, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27924604/exploring-genome-wide-expression-profiles-using-machine-learning-techniques
#6
Moritz Kebschull, Panos N Papapanou
Although contemporary high-throughput -omics methods produce high-dimensional data, the resulting wealth of information is difficult to assess using traditional statistical procedures. Machine learning methods facilitate the detection of additional patterns, beyond the mere identification of lists of features that differ between groups.Here, we demonstrate the utility of (1) supervised classification algorithms in class validation, and (2) unsupervised clustering in class discovery. We use data from our previous work that described the transcriptional profiles of gingival tissue samples obtained from subjects suffering from chronic or aggressive periodontitis (1) to test whether the two diagnostic entities were also characterized by differences on the molecular level, and (2) to search for a novel, alternative classification of periodontitis based on the tissue transcriptomes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924602/genome-wide-analysis-of-periodontal-and-peri-implant-cells-and-tissues
#7
Moritz Kebschull, Claudia Hülsmann, Per Hoffmann, Panos N Papapanou
Omics analyses, including the systematic cataloging of messenger RNA and microRNA sequences or DNA methylation patterns in a cell population, organ or tissue sample, are powerful means of generating comprehensive genome-level data sets on complex diseases. We have systematically assessed the transcriptome, miRNome and methylome of gingival tissues from subjects with different diagnostic entities of periodontal disease, and studied the transcriptome of primary cells ex vivo, or in vitro after infection with periodontal pathogens...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924575/genome-wide-analysis-of-ras-erk-signaling-targets
#8
Joshua P Plotnik, Peter C Hollenhorst
Identifying gene expression changes mediated by signaling pathways is necessary to determine mechanisms that cause phenotypic change. Recent advances in next-generation sequencing and informatic pipelines have streamlined the ability for laboratories to create and analyze transcriptomic data. Here, we describe the preparation of samples and transcriptomic analysis in order to determine gene expression programs regulated by RAS/ERK signaling.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924550/detection-of-transcriptionally-active-mycotoxin-gene-clusters-dna-microarray
#9
Tamás Emri, Anna Zalka, István Pócsi
Various bioanalytical tools including DNA microarrays are frequently used to map global transcriptional changes in mycotoxin producer filamentous fungi. This effective hybridization-based transcriptomics technology helps researchers to identify genes of secondary metabolite gene clusters and record concomitant gene expression changes in these clusters initiated by versatile environmental conditions and/or gene deletions. Such transcriptional data are of great value when future mycotoxin control technologies are considered and elaborated...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924476/competitive-argonaute-based-rna-immunoprecipitation-for-investigation-of-transcriptomic-response-to-anti-mir
#10
John R Androsavich
Identification and validation of microRNA (miRNA) target genes is essential for gaining a better understanding of the many different functions miRNAs have in healthy and diseased cells. From a practical standpoint, validated target genes are also useful for monitoring pharmacological activity of developmental therapeutics that modulate miRNAs, such as anti-miRNA oligonucleotides (anti-miR). Here, we describe a method that uses changes in Argonaute 2-RNA immunoprecipitation in response to competition by anti-miR, titrated ex vivo, as physical evidence for target validation...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924227/otx2-impedes-self-renewal-of-porcine-ips-cells-through-downregulation-of-nanog-expression
#11
Ning Wang, Yaxian Wang, Youlong Xie, Huayan Wang
The transcription factor Otx2 acts as a negative switch in the regulation of transition from naive to primed pluripotency in mouse pluripotent stem cells. However, the molecular features and function of porcine OTX2 have not been well elucidated in porcine-induced pluripotent stem cells (piPSCs). By studying high-throughput transcriptome sequencing and interfering endogenous OTX2 expression, we demonstrate that OTX2 is able to downgrade the self-renewal of piPSCs. OTX2 is highly expressed in porcine brain, reproductive tissues, and preimplantation embryos, but is undetectable in fibroblasts and most somatic tissues...
2016: Cell Death Discovery
https://www.readbyqxmd.com/read/27924117/transcriptome-differences-between-fiber-type-and-seed-type-cannabis-sativa-variety-exposed-to-salinity
#12
Jiajia Liu, Qin Qiao, Xia Cheng, Guanghui Du, Gang Deng, Mingzhi Zhao, Feihu Liu
The industrial hemp varieties 'Yunma 5' and 'Bamahuoma,' which demonstrate growth vigor and environmental adaptability, have been primarily cultivated in Yunnan and Guangxi, China, respectively, for fiber and seeds. The results of physiological measurements showed the phenotypic differences between the two varieties in response to salt stress. RNA-Seq analysis was first performed on leaves of both varieties sampled at four time intervals (0, 2, 4, 6 days) after treatment with salt (500 mM NaCl) We identified 220 co-up-regulated differentially expressed genes (DEGs) in the two varieties, while 26 up-regulated DEGs and 24 down-regulated DEGs were identified exclusively in the single varieties after 2 days of salt stress...
October 2016: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/27923997/insights-into-the-mechanisms-of-eukaryotic-translation-gained-with-ribosome-profiling
#13
Dmitry E Andreev, Patrick B F O'Connor, Gary Loughran, Sergey E Dmitriev, Pavel V Baranov, Ivan N Shatsky
The development of Ribosome Profiling (RiboSeq) has revolutionized functional genomics. RiboSeq is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a 'snapshot' of ribosome positions at the transcriptome wide level. Although the method is predominantly used for analysis of differential gene expression and discovery of novel translated ORFs, the RiboSeq data can also be a rich source of information about molecular mechanisms of polypeptide synthesis and translational control...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923878/neighbor-detection-induces-organ-specific-transcriptomes-revealing-patterns-underlying-hypocotyl-specific-growth
#14
Markus Kohnen, Emanuel Schmid-Siegert, Martine Trevisan, Laure Allenbach Petrolati, Fabien Sénéchal, Patricia Müller-Moulé, Julin N Maloof, Ioannis Xenarios, Christian Fankhauser
In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana...
December 6, 2016: Plant Cell
https://www.readbyqxmd.com/read/27923766/single-cell-analysis-uncovers-clonal-acinar-cell-heterogeneity-in-the-adult-pancreas
#15
Damian Wollny, Sheng Zhao, Isabelle Everlien, Xiaokang Lun, Jan Brunken, Daniel Brüne, Frederik Ziebell, Inna Tabansky, Wilko Weichert, Anna Marciniak-Czochra, Ana Martin-Villalba
Acinar cells make up the majority of all cells in the pancreas, yet the source of new acinar cells during homeostasis remains unknown. Using multicolor lineage-tracing and organoid-formation assays, we identified the presence of a progenitor-like acinar cell subpopulation. These cells have long-term self-renewal capacity, albeit in a unipotent fashion. We further demonstrate that binuclear acinar cells are terminally differentiated acinar cells. Transcriptome analysis of single acinar cells revealed the existence of a minor population of cells expressing progenitor markers...
November 7, 2016: Developmental Cell
https://www.readbyqxmd.com/read/27923621/transcriptomic-analysis-of-gene-expression-profiles-of-stomach-carcinoma-reveal-abnormal-expression-of-mitotic-components
#16
Hongfei Tong, Jisheng Wang, Hui Chen, Zhaohong Wang, Henwei Fan, Zhonglin Ni
AIMS: In order to explore the etiology of gastric cancer on global gene expression level, we developed advanced bioinformatic analysis to investigate the variations of global gene expression and the interactions among them. MAIN METHODS: We downloaded the dataset GSE63288 from Gene Expression Omnibus (GEO) database which included 22 human gastric cancer and 22 healthy control samples. We identified the differential expression genes, and explored the Gene ontology (GO) and pathways of the differentially expressed genes...
December 3, 2016: Life Sciences
https://www.readbyqxmd.com/read/27923398/comparative-transcriptional-profile-of-the-fish-parasite-cryptocaryon-irritans
#17
Ze-Quan Mo, Yan-Wei Li, Hai-Qing Wang, Jiu-Le Wang, Lu-Yun Ni, Man Yang, Guo-Feng Lao, Xiao-Chun Luo, An-Xing Li, Xue-Ming Dan
BACKGROUND: Cryptocaryon irritans is an obligate ectoparasitic ciliate pathogen of marine fishes. It can infect most marine teleosts and cause heavy economic losses in aquaculture. There is currently no effective method of controlling this disease, and little information is available regarding the genes involved in its development and virulence. We aimed to investigate the distinct features of the three major life-cycle stages of C. irritans in terms of gene transcription level, and identify candidate vaccines/drug targets...
December 7, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27923345/combined-transcriptome-and-metabolome-analyses-to-understand-the-dynamic-responses-of-rice-plants-to-attack-by-the-rice-stem-borer-chilo-suppressalis-lepidoptera-crambidae
#18
Qingsong Liu, Xingyun Wang, Vered Tzin, Jörg Romeis, Yufa Peng, Yunhe Li
BACKGROUND: Rice (Oryza sativa L.), which is a staple food for more than half of the world's population, is frequently attacked by herbivorous insects, including the rice stem borer, Chilo suppressalis. C. suppressalis substantially reduces rice yields in temperate regions of Asia, but little is known about how rice plants defend themselves against this herbivore at molecular and biochemical level. RESULTS: In the current study, we combined next-generation RNA sequencing and metabolomics techniques to investigate the changes in gene expression and in metabolic processes in rice plants that had been continuously fed by C...
December 7, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27923066/somatic-genomics-and-clinical-features-of-lung-adenocarcinoma-a-retrospective-study
#19
Jianxin Shi, Xing Hua, Bin Zhu, Sarangan Ravichandran, Mingyi Wang, Cu Nguyen, Seth A Brodie, Alessandro Palleschi, Marco Alloisio, Gianluca Pariscenti, Kristine Jones, Weiyin Zhou, Aaron J Bouk, Joseph Boland, Belynda Hicks, Adam Risch, Hunter Bennett, Brian T Luke, Lei Song, Jubao Duan, Pengyuan Liu, Takashi Kohno, Qingrong Chen, Daoud Meerzaman, Crystal Marconett, Ite Laird-Offringa, Ian Mills, Neil E Caporaso, Mitchell H Gail, Angela C Pesatori, Dario Consonni, Pier Alberto Bertazzi, Stephen J Chanock, Maria Teresa Landi
BACKGROUND: Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and has a high risk of distant metastasis at every disease stage. We aimed to characterize the genomic landscape of LUAD and identify mutation signatures associated with tumor progression. METHODS AND FINDINGS: We performed an integrative genomic analysis, incorporating whole exome sequencing (WES), determination of DNA copy number and DNA methylation, and transcriptome sequencing for 101 LUAD samples from the Environment And Genetics in Lung cancer Etiology (EAGLE) study...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27923061/comparative-transcriptomic-and-epigenomic-analyses-reveal-new-regulators-of-murine-brown-adipogenesis
#20
Reinhard Brunmeir, Jingyi Wu, Xu Peng, Sun-Yee Kim, Sofi G Julien, Qiongyi Zhang, Wei Xie, Feng Xu
Increasing energy expenditure through brown adipocyte recruitment is a promising approach to combat obesity. We report here the comprehensive profiling of the epigenome and transcriptome throughout the lineage commitment and differentiation of C3H10T1/2 mesenchymal stem cell line into brown adipocytes. Through direct comparison to datasets from differentiating white adipocytes, we systematically identify stage- and lineage-specific coding genes, lncRNAs and microRNAs. Utilizing chromatin state maps, we also define stage- and lineage-specific enhancers, including super-enhancers, and their associated transcription factor binding motifs and genes...
December 2016: PLoS Genetics
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