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https://www.readbyqxmd.com/read/28342915/redd1-links-stress-with-il-1%C3%AE-mediated-familial-mediterranean-fever-attack-through-autophagy-driven-neutrophil-extracellular-traps
#1
Panagiotis Skendros, Akrivi Chrysanthopoulou, François Rousset, Konstantinos Kambas, Athanasios Arampatzioglou, Alexandros Mitsios, Veronique Bocly, Theocharis Konstantinidis, Philippe Pellet, Iliana Angelidou, Eirini Apostolidou, Dimitrios Ritis, Victoria Tsironidou, Sotiris Galtsidis, Charalampos Papagoras, Dimitrios Stakos, Georgios Kouklakis, Vasiliki Dalla, Maria Koffa, Ioannis Mitroulis, Ioannis Theodorou, Konstantinos Ritis
BACKGROUND: Familial Mediterranean fever (FMF) is an IL-1β-dependent autoinflammatory disease caused by mutations of MEFV encoding pyrin, and characterised by inflammatory attacks, induced by physical or psychological stress. OBJECTIVE: We investigate the underlying mechanism that links stress-induced inflammatory attacks with neutrophil activation and release of IL-1β-bearing neutrophil extracellular traps (NETs) in FMF. METHODS: RNA-seq was performed in peripheral neutrophils from 3 FMF patients, isolated both during attack and remission, 8 patients in remission and 8 healthy individuals...
March 22, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28342759/activation-of-epithelial-stat1-by-interleukin-28-controls-mucosal-healing-in-mice-with-colitis-and-is-increased-in-mucosa-of-patients-with-inflammatory-bowel-disease
#2
Mircea T Chiriac, Barbara Buchen, Alexandra Wandersee, Gheorghe Hundorfean, Claudia Günther, Yvonne Bourjau, Sean E Doyle, Benjamin Frey, Arif B Ekici, Christian Büttner, Benno Weigmann, Raja Atreya, Stefan Wirtz, Christoph Becker, Jürgen Siebler, Markus F Neurath
BACKGROUND & AIMS: We investigated the roles of interleukin 28A (also called IL28A or interferon lambda 2) in intestinal epithelial cell (IEC) activation, studying its effects in mouse models of inflammatory bowel diseases (IBD) and intestinal mucosal healing. METHODS: Colitis was induced in C57BL/6JCrl mice (controls), mice with intestinal epithelial cell-specific disruption of Stat1 (Stat1IEC-KO), mice with disruption of the interferon lambda receptor 1 gene (Il28ra-/-), and mice with disruption of the interferon regulatory factor 3 gene (Irf3-/-), with or without disruption of Irf7 (Irf7-/-)...
March 22, 2017: Gastroenterology
https://www.readbyqxmd.com/read/28340271/snp-detection-using-rna-sequences-of-candidate-genes-associated-with-puberty-in-cattle
#3
M M Dias, A Cánovas, C Mantilla-Rojas, D G Riley, P Luna-Nevarez, S J Coleman, S E Speidel, R M Enns, A Islas-Trejo, J F Medrano, S S Moore, M R S Fortes, L T Nguyen, B Venus, I S D P Diaz, F R P Souza, L F S Fonseca, F Baldi, L G Albuquerque, M G Thomas, H N Oliveira
Fertility traits, such as heifer pregnancy, are economically important in cattle production systems, and are therefore, used in genetic selection programs. The aim of this study was to identify single nucleotide polymorphisms (SNPs) using RNA-sequencing (RNA-Seq) data from ovary, uterus, endometrium, pituitary gland, hypothalamus, liver, longissimus dorsi muscle, and adipose tissue in 62 candidate genes associated with heifer puberty in cattle. RNA-Seq reads were assembled to the bovine reference genome (UMD 3...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340266/rna-seq-based-transcriptome-and-the-reproduction-related-genes-for-the-aphid-schlechtendalia-chinensis-hemiptera-aphididae
#4
P Liu, Z X Yang, X M Chen, P Yang
Chinese galls form on sumac plants (Rhus chinensis) and are used for medicinal and chemical purposes, due to their richness in tannins. The galls are formed by aphids, the most prominent of which is Schlechtendalia chinensis, which forms horn-shaped galls on the winged rachis of R. chinensis. S. chinensis has a complex life cycle, including both R. chinensis and certain mosses as hosts, as well as the existence of both sexual and asexual reproduction (cyclical parthenogenesis). Previous studies have shown that the alternate occurrence of sexual and asexual reproduction relies on many environmental factors, such as temperature, photoperiod, and host-plant...
March 22, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28340181/different-expression-patterns-of-sperm-motility-related-genes-in-testis-of-diploid-and-tetraploid-cyprinid-fish1
#5
Fangzhou Hu, Kang Xu, Yunfan Zhou, Chang Wu, Shi Wang, Jun Xiao, Min Wen, Rurong Zhao, Kaikun Luo, Min Tao, Wei Duan, Shaojun Liu
Sperm motility is an important standard to measure the fertility of male. In our previous study, we found that the diploid spermatozoa from allotetraploid hybrid (4nAT) had longer durations of rapid and slow progressive motility than haploid spermatozoa from common carp (COC). In this study, to explore sperm motility-related molecular mechanisms, we compared the testis tissues transcriptomes from two years old male COC and 4nAT. The RNA-seq data revealed that 2985 genes were differentially expressed between COC and 4nAT, including 2216 up-regulated and 769 down-regulated genes in 4nAT...
March 7, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28339981/transcriptome-analysis-of-comb-and-testis-from-rose-comb-silky-chicken-r1-r1-and-beijing-fatty-wild-type-chicken-r-r
#6
Y Wang, J Li, C Feng, Y Zhao, X Hu, N Li
Rose-comb was one of the chicken comb-variants first used by Bateson and Punnet in 1902 to demonstrate Mendelian inheritance in animals. Rose-comb is a monogenic trait that has been widely described in chickens. It is caused by a large structural rearrangement that leads to mis-expression of transcription factor MNR2 on chromosome 7. Rose-comb has pleiotropic effects in homozygous roosters, which is associated with poor sperm mobility. It was postulated that this is caused by the disruption of the CCDC108 gene located at the distal inversion breakpoint...
March 2, 2017: Poultry Science
https://www.readbyqxmd.com/read/28338982/rna-editing-during-sexual-development-occurs-in-distantly-related-filamentous-ascomycetes
#7
Ines Teichert, Tim Dahlmann, Ulrich Kück, Minou Nowrousian
RNA editing is a posttranscriptional process that modifies RNA molecules leading to transcript sequences that differ from their template DNA. A-to-I editing was found to be widely distributed in nuclear transcripts of metazoa, but was detected in fungi only recently in a study of the filamentous ascomycete Fusarium graminearum that revealed extensive A-to-I editing of mRNAs in sexual structures (fruiting bodies). Here, we searched for putative RNA editing events in RNA-seq data from Sordaria macrospora and Pyronema confluens, two distantly related filamentous ascomycetes, and in data from the Taphrinomycete Schizosaccharomyces pombe...
March 9, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338870/stmyb44-negatively-regulates-phosphate-transport-by-suppressing-expression-of-phosphate1-in-potato
#8
Xiangjun Zhou, Manrong Zha, Jing Huang, Li Li, Muhammad Imran, Cankui Zhang
Phosphorus is an important macronutrient for plant growth, but often deficient in soil. To understand the molecular basis of the complex responses of potato (Solanum tuberosum L.) to phosphate (Pi) deficiency stress, the RNA-Seq approach was taken to identify genes responding to Pi starvation in potato roots. A total of 359 differentially expressed genes were identified, among which the Solanum tuberosum transcription factor gene MYB44 (StMYB44) was found to be down-regulated by Pi starvation. StMYB44 was ubiquitously expressed in potato tissues and organs, and StMYB44 protein was exclusively localized in the nucleus...
March 1, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338822/gene-expression-atlas-of-pigeonpea-and-its-application-to-gain-insights-into-genes-associated-with-pollen-fertility-implicated-in-seed-formation
#9
Lekha T Pazhamala, Shilp Purohit, Rachit K Saxena, Vanika Garg, L Krishnamurthy, Jerome Verdier, Rajeev K Varshney
Pigeonpea (Cajanus cajan) is an important grain legume of the semi-arid tropics, mainly used for its protein rich seeds. To link the genome sequence information with agronomic traits resulting from specific developmental processes, a Cajanus cajan gene expression atlas (CcGEA) was developed using the Asha genotype. Thirty tissues/organs representing developmental stages from germination to senescence were used to generate 590.84 million paired-end RNA-Seq data. The CcGEA revealed a compendium of 28 793 genes with differential, specific, spatio-temporal and constitutive expression during various stages of development in different tissues...
February 23, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28338820/evolutionary-dynamics-of-regulatory-changes-underlying-gene-expression-divergence-among-saccharomyces-species
#10
Brian P H Metzger, Patricia J Wittkopp, Joseph D Coolon
Heritable changes in gene expression are important contributors to phenotypic differences within and between species and are caused by mutations in cis-regulatory elements and trans-regulatory factors. While previous work has suggested that cis-regulatory differences preferentially accumulate with time, technical restrictions to closely related species and limited comparisons have made this observation difficult to test. To address this problem, we used allele-specific RNA-seq data from Saccharomyces species and hybrids to expand both the evolutionary timescale and number of species in which the evolution of regulatory divergence has been investigated...
February 22, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338816/conserved-patterns-of-sex-chromosome-dosage-compensation-in-the-lepidoptera-wz-zz-insights-from-a-moth-neo-z-chromosome
#11
Liuqi Gu, James R Walters, Douglas C Knipple
Where previously described, patterns of sex chromosome dosage compensation in the Lepidoptera (moths and butterflies) have several unusual characteristics. Other female-heterogametic (ZW/ZZ) species exhibit female Z-linked expression that is reduced compared to autosomal expression and male Z expression. In the Lepidoptera, however, Z expression typically appears balanced between sexes but overall reduced relative to autosomal expression, i.e. Z ≈ ZZ < AA. This pattern is not easily reconciled with theoretical expectations for the evolution of sex chromosome dosage compensation...
March 2, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28338730/genetic-variability-of-the-activity-of-bidirectional-promoters-a-pilot-study-in-bovine-muscle
#12
Cédric Meersseman, Rabia Letaief, Véronique Léjard, Emmanuelle Rebours, Gabriel Guillocheau, Diane Esquerré, Anis Djari, Amanda Chamberlain, Christy Vander Jagt, Christophe Klopp, Mekki Boussaha, Gilles Renand, Abderrahman Maftah, Daniel Petit, Dominique Rocha
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters...
February 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338719/the-legume-mir1514a-modulates-a-nac-transcription-factor-transcript-to-trigger-phasirna-formation-in-response-to-drought
#13
Guadalupe Sosa-Valencia, Miguel Palomar, Alejandra A Covarrubias, José L Reyes
Recent studies have identified microRNAs as post-transcriptional regulators involved in stress responses. miR1514a is a legume microRNA that is induced in response to drought stress in Phaseolus vulgaris (common bean) and shows differential accumulation levels in roots during water deficit in two cultivars with different drought tolerance phenotypes. A recent degradome analysis revealed that miR1514a targets the transcripts of two NAC transcription factors (TFs), Phvul.010g121000 and Phvul.010g120700. Furthermore, expression studies and small RNA-seq data indicate that only Phvul...
October 7, 2016: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28337281/c-myc-induced-upregulation-of-lncrna-snhg12-regulates-cell-proliferation-apoptosis-and-migration-in-triple-negative-breast-cancer
#14
Ouchen Wang, Fan Yang, Yehuan Liu, Lin Lv, Ruimin Ma, Chuanzhi Chen, Jiao Wang, Qiufan Tan, Yue Cheng, Erjie Xia, Yizuo Chen, Xiaohua Zhang
Triple-negative breast cancer (TNBC) is one of the most aggressive subtypes of breast cancer, with a significantly higher recurrence and mortality rate. There is an urgent need to uncover the mechanism underlying TNBC and establish therapeutic targets. Long non-coding RNAs (lncRNAs) are involved in a series of biological functions and provide novel insights into the molecular mechanism of cancer. Based on their expression specificity and large number, lncRNAs are likely to serve as the basis for clinical applications in oncology...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28337215/root-adaptive-responses-to-aluminum-treatment-revealed-by-rna-seq-in-two-citrus-species-with-different-aluminum-tolerance
#15
Peng Guo, Yi-Ping Qi, Lin-Tong Yang, Ning-Wei Lai, Xin Ye, Yi Yang, Li-Song Chen
Seedlings of aluminum (Al)-tolerant Citrus sinensis and Al-intolerant Citrus grandis were fertigated daily with nutrient solution containing 0 and 1.0 mM AlCl3●6H2O for 18 weeks. The Al-induced decreases of biomass and root total soluble proteins only occurred in C. grandis, demonstrating that C. sinensis had higher Al-tolerance than C. grandis. Under Al-treatment, C. sinensis roots secreted more citrate and malate than C. grandis ones; less Al was accumulated in C. sinenis than in C. grandis leaves. The Al-induced reduction of phosphorus was lesser in C...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28337209/transcriptional-responses-of-chilean-quinoa-chenopodium-quinoa-willd-under-water-deficit-conditions-uncovers-aba-independent-expression-patterns
#16
Andrea Morales, Andres Zurita-Silva, Jonathan Maldonado, Herman Silva
HIGHLIGHTS R49 genotype displayed best performance on selected physiological parameters and highest tolerance to drought.R49 drought over-represented transcripts has exhibited 19% of genes (306 contigs) that presented no homology to published databases.Expression pattern for canonical responses to drought such as ABA biosynthesis and other genes induced in response to drought were assessed by qPCR. Global freshwater shortage is one of the biggest challenges of our time, often associated to misuse, increased consumption demands and the effects of climate change, paralleled with the desertification of vast areas...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28336542/seten-a-tool-for-systematic-identification-and-comparison-of-processes-phenotypes-and-diseases-associated-with-rna-binding-proteins-from-condition-specific-clip-seq-profiles
#17
Gungor Budak, Rajneesh Srivastava, Sarath Chandra Janga
RNA-binding proteins (RBPs) control the regulation of gene expression in eukaryotic genomes at post-transcriptional level by binding to their cognate RNAs. Although several variants of CLIP (crosslinking and immunoprecipitation) protocols are currently available to study the global protein-RNA interaction landscape at single nucleotide resolution in a cell, currently there are very few tools which can facilitate understanding and dissecting the functional associations of RBPs from the resulting binding maps...
March 23, 2017: RNA
https://www.readbyqxmd.com/read/28335741/high-throughput-sequencing-of-pituitary-and-hypothalamic-microrna-transcriptome-associated-with-high-rate-of-egg-production
#18
Nan Wu, Qing Zhu, Binlong Chen, Jian Gao, Zhongxian Xu, Diyan Li
BACKGROUND: MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. RESULTS: In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high- and 3 low-rate egg production Luhua chickens at the age of 300 days...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335739/identification-of-long-non-coding-transcripts-with-feature-selection-a-comparative-study
#19
Giovanna M M Ventola, Teresa M R Noviello, Salvatore D'Aniello, Antonietta Spagnuolo, Michele Ceccarelli, Luigi Cerulo
BACKGROUND: The unveiling of long non-coding RNAs as important gene regulators in many biological contexts has increased the demand for efficient and robust computational methods to identify novel long non-coding RNAs from transcripts assembled with high throughput RNA-seq data. Several classes of sequence-based features have been proposed to distinguish between coding and non-coding transcripts. Among them, open reading frame, conservation scores, nucleotide arrangements, and RNA secondary structure have been used with success in literature to recognize intergenic long non-coding RNAs, a particular subclass of non-coding RNAs...
March 23, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28335720/widespread-promoter-methylation-of-synaptic-plasticity-genes-in-long-term-potentiation-in-the-adult-brain-in-vivo
#20
Jesper L V Maag, Dominik C Kaczorowski, Debabrata Panja, Timothy J Peters, Clive R Bramham, Karin Wibrand, Marcel E Dinger
BACKGROUND: DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS: To investigate the occurrence of DNA methylation changes in LTP, we undertook the first detailed study to describe the methylation status of all known LTP-associated genes during LTP induction in the dentate gyrus of live rats...
March 23, 2017: BMC Genomics
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