keyword
MENU ▼
Read by QxMD icon Read
search

SRNA

keyword
https://www.readbyqxmd.com/read/28724941/novel-small-rna-spike-in-oligonucleotides-enable-absolute-normalization-of-small-rna-seq-data
#1
Stefan Lutzmayer, Balaji Enugutti, Michael D Nodine
Normalization of high-throughput small RNA sequencing (sRNA-Seq) data is required to compare sRNA levels across different samples. Commonly used relative normalization approaches can cause erroneous conclusions due to fluctuating small RNA populations between tissues. We developed a set of sRNA spike-in oligonucleotides (sRNA spike-ins) that enable absolute normalization of sRNA-Seq data across independent experiments, as well as the genome-wide estimation of sRNA:mRNA stoichiometries when used together with mRNA spike-in oligonucleotides...
July 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28720814/small-rna-mediated-repression-of-subtilisin-production-in-bacillus-licheniformis
#2
Robert Hertel, Sandra Meyerjürgens, Birgit Voigt, Heiko Liesegang, Sonja Volland
The species Bacillus licheniformis includes important strains that are used in industrial production processes. Currently the physiological model used to adapt these processes is based on the closely related model organism B. subtilis. In this study we found that both organisms reveal significant differences in the regulation of subtilisin, their main natural protease and a product of industrial fermentation processes. We identified and characterized a novel antisense sRNA AprAs, which represents an RNA based repressor of apr, the gene encoding for the industrial relevant subtilisin protease...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28717590/construction-of-a-fur-null-mutant-and-rna-sequencing-provide-deeper-global-understanding-of-the-aliivibrio-salmonicida-fur-regulon
#3
Sunniva Katharina Thode, Cecilie Bækkedal, Jenny Johansson Söderberg, Erik Hjerde, Hilde Hansen, Peik Haugen
BACKGROUND: The ferric uptake regulator (Fur) is a transcription factor and the main regulator of iron acquisition in prokaryotes. When bound to ferric iron, Fur recognizes its DNA binding site and generally executes its function by repressing transcription of its target genes. Due to its importance in virulence, the Fur regulon is well studied for several model bacteria. In our previous work, we used computational predictions and microarray to gain insights into Fur-regulation in Aliivibrio salmonicida, and have identified a number of genes and operons that appear to be under direct control of Fur...
2017: PeerJ
https://www.readbyqxmd.com/read/28711666/micrornas-associated-with-drought-response-in-the-pulse-crop-common-bean-phaseolus-vulgaris-l
#4
Jing Wu, Lanfen Wang, Shumin Wang
Drought stress significantly reduces common bean yields. Recently, some drought-related miRNAs were found in various plants. However, reports of miRNAs involved in drought stress in common bean are limited. Here, we obtained four sRNA samples from drought-tolerant and -sensitive cultivars of common bean that experienced with or without drought treatment. A total of 49 novel miRNAs and 120 known miRNAs were detected. Under drought treatment, 9 and 7 known miRNAs were down and up-regulated, respectively, and 5 and 3 of the novel miRNAs were increased and decreased, respectively...
July 12, 2017: Gene
https://www.readbyqxmd.com/read/28710366/mirnas-in-the-alga-chlamydomonas-reinhardtii-are-not-phylogenetically-conserved-and-play-a-limited-role-in-responses-to-nutrient-deprivation
#5
Adam Voshall, Eun-Jeong Kim, Xinrong Ma, Tomohito Yamasaki, Etsuko N Moriyama, Heriberto Cerutti
The unicellular alga Chlamydomonas reinhardtii contains many types of small RNAs (sRNAs) but the biological role(s) of bona fide microRNAs (miRNAs) remains unclear. To address their possible function(s) in responses to nutrient availability, we examined miRNA expression in cells cultured under different trophic conditions (mixotrophic in the presence of acetate or photoautotrophic in the presence or absence of nitrogen). We also reanalyzed miRNA expression data in Chlamydomonas subject to sulfur or phosphate deprivation...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28709615/transcriptional-profiling-of-rickettsia-prowazekii-coding-and-non-coding-transcripts-during-in-vitro-host-pathogen-and-vector-pathogen-interactions
#6
Casey L C Schroeder, Hema P Narra, Abha Sahni, Kamil Khanipov, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Natural pathogen transmission of Rickettsia prowazekii, the etiologic agent of epidemic typhus, to humans is associated with arthropods, including human body lice, ticks, and ectoparasites of eastern flying squirrel. Recently, we have documented the presence of small RNAs in Rickettsia species and expression of R. prowazekii sRNAs during infection of cultured human microvascular endothelial cells (HMECs), which represent the primary target cells during human infections. Bacterial noncoding transcripts are now well established as critical post-transcriptional regulators of virulence and adaptation mechanisms in varying host environments...
June 29, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28705956/rapid-recovery-gene-downregulation-during-excess-light-stress-and-recovery-in-arabidopsis
#7
Peter Alexander Crisp, Diep Ganguly, Aaron B Smith, Kevin D Murray, Gonzalo M Estavillo, Iain R Searle, Ethan Ford, Ozren Bogdanović, Ryan Lister, Justin O Borevitz, Steven R Eichten, Barry J Pogson
Stress recovery may prove to be a promising approach to increase plant performance, and theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as three minutes. We demonstrate that 87% of the stress-upregulated mRNAs analysed exhibit very rapid recovery. For instance, HSP101 abundance declined two-fold every 5.1 minutes. We term this phenomenon Rapid Recovery Gene Downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting...
July 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28700949/two-sets-of-piwi-proteins-are-involved-in-distinct-srna-pathways-leading-to-elimination-of-germline-specific-dna
#8
Dominique I Furrer, Estienne C Swart, Matthias F Kraft, Pamela Y Sandoval, Mariusz Nowacki
Piwi proteins and piRNAs protect eukaryotic germlines against the spread of transposons. During development in the ciliate Paramecium, two Piwi-dependent sRNA classes are involved in the elimination of transposons and transposon-derived DNA: scan RNAs (scnRNAs), associated with Ptiwi01 and Ptiwi09, and iesRNAs, whose binding partners we now identify as Ptiwi10 and Ptiwi11. scnRNAs derive from the maternal genome and initiate DNA elimination during development, whereas iesRNAs continue DNA targeting until the removal process is complete...
July 11, 2017: Cell Reports
https://www.readbyqxmd.com/read/28699365/activating-the-chromatin-by-non-coding-rnas
#9
Nihay Laham-Karam, Pia Laitinen, Tiia A Turunen, Seppo Ylä-Herttuala
SIGNIFICANCE: The extent and breadth of transcription has recently been uncovered and this has revealed an extensive array of non-coding RNAs (ncRNAs). The biological role and significance of these ncRNAs have been realised and to date it appears that ncRNA may have many important regulatory functions. ncRNAs are multifaceted and they induce a complexity of different types of transcriptional and post-transcriptional regulation including gene activation. Recent Advances: Association of ncRNAs with gene activation is an important finding...
July 12, 2017: Antioxidants & Redox Signaling
https://www.readbyqxmd.com/read/28698160/investigating-the-regulatory-roles-of-the-micrornas-and-the-argonaute-1-enriched-small-rnas-in-plant-metabolism
#10
Jingping Qin, Zhonghai Tang, Xiaoxia Ma, Yijun Meng
The biological roles of small RNAs (sRNAs) in metabolic processes are emerging. However, a systemic study is needed to investigate the wide-spread involvement of the sRNAs in plant metabolism. By using the metabolism-related transcripts retrieved from the public database Plant Metabolic Network, and the publicly available sRNA high-throughput sequencing data, large-scale target identification was performed for microRNAs (miRNAs) and Argonaute 1 (AGO1)-enriched sRNAs in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa)...
July 8, 2017: Gene
https://www.readbyqxmd.com/read/28691898/post-transcriptional-regulation-of-target-genes-by-the-srna-fnrs-in-neisseria-gonorrhoeae
#11
Pooja Tanwer, Susanne Bauer, Elisabeth Heinrichs, Gurudutta Panda, Daman Saluja, Thomas Rudel, Dagmar Beier
Small non-coding RNAs (sRNAs) are well-established post-transcriptional regulators of gene expression in bacteria that respond to a variety of environmental stimuli. They usually act by base-pairing with their target mRNAs, which is commonly facilitated by the RNA chaperone Hfq. In this study we initiated the analysis of the sRNA FnrS of Neisseria gonorrhoeae, which is induced under anaerobic conditions. We identified four putative FnrS target genes using bioinformatics approaches and validated these target genes using translational reporter gene fusions in both Escherichia coli and N...
July 10, 2017: Microbiology
https://www.readbyqxmd.com/read/28689267/the-novel-srna-s015-improves-nisin-yield-by-increasing-acid-tolerance-of-lactococcus-lactis-f44
#12
Jiakun Qi, Qinggele Caiyin, Hao Wu, Kairen Tian, Binbin Wang, Yanni Li, Jianjun Qiao
Nisin, a polycyclic antibacterial peptide produced by Lactococcus lactis, is stable at low pH. Improving the acid tolerance of L. lactis could thus enhance nisin yield. Small non-coding RNAs (sRNAs) play essential roles in acid tolerance by regulating their target mRNAs at the post-transcriptional level. In this study, a novel sRNA, s015, was identified in L. lactis F44 via the use of RNA sequencing, qRT-PCR analysis, and Northern blotting. s015 improved the acid tolerance of L. lactis and boosted nisin yield at low pH...
July 9, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28686301/mirpursuit-a-pipeline-for-automated-analyses-of-small-rnas-in-model-and-non-model-plants
#13
Inês Chaves, Bruno Costa, Andreia S Rodrigues, Andreas Bohn, Célia M Miguel
MiRPursuit is a pipeline developed for running end-to-end analyses of high-throughput small RNA (sRNA) sequence data in model and non-model plants, from raw data to identified and annotated conserved and novel sequences. It consists of a series of UNIX shell scripts, which connect open-source sRNA analysis software. The involved parameters can be combined with convenient workflow management by users without advanced computational skills. miRPursuit presents several advantages when compared to other tools, including the possibility of processing several sRNA libraries in parallel, thus easily allowing a comparison of the differences in sRNA read accumulation among sRNA libraries...
July 7, 2017: FEBS Letters
https://www.readbyqxmd.com/read/28682306/unique-roles-for-histone-h3k9me-states-in-rnai-and-heritable-silencing-of-transcription
#14
Gloria Jih, Nahid Iglesias, Mark A Currie, Natarajan V Bhanu, Joao A Paulo, Steven P Gygi, Benjamin A Garcia, Danesh Moazed
Heterochromatic DNA domains play important roles in regulation of gene expression and maintenance of genome stability by silencing repetitive DNA elements and transposons. From fission yeast to mammals, heterochromatin assembly at DNA repeats involves the activity of small noncoding RNAs (sRNAs) associated with the RNA interference (RNAi) pathway(1-9). Typically, sRNAs, originating from long noncoding RNAs, guide Argonaute-containing effector complexes to complementary nascent RNAs to initiate histone H3 lysine 9 di- and tri-methylation (H3K9me2 and H3K9me3, respectively) and heterochromatin formation(10-17)...
June 22, 2017: Nature
https://www.readbyqxmd.com/read/28677390/quantitative-proteomics-reveals-potential-crosstalk-between-a-small-rna-coar-and-a-two-component-regulator-slr1037-in-synechocystis-sp-pcc6803
#15
Tao Sun, Lei Chen, Weiwen Zhang
Bacterial small RNAs (sRNAs) and two-component systems (TCSs) were two vital regulatory mechanisms employed by microorganisms to respond to environmental changes and stresses. As a promising "autotrophic cell factory", photosynthetic cyanobacteria have attracted a lot of concentrations these years. Though most studies focused on studying the roles of sRNAs or TCS regulators in stress response in photosynthetic cyanobacteria, limited work has elucidated their potential crosstalk. Our previous work has identified a negative sRNA regulator CoaR and a positive response regulator Slr1037 both related with 1-butanol stress regulation in Synechocystis sp...
July 5, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28676719/srna-and-cis-antisense-srna-identification-in-staphylococcus-aureus-highlights-an-unusual-srna-gene-cluster-with-one-encoding-a-secreted-peptide
#16
Julie Bronsard, Gaetan Pascreau, Mohamed Sassi, Tony Mauro, Yoann Augagneur, Brice Felden
The human pathogen Staphylococcus aureus expresses a set of transcriptional factors and small RNAs (sRNAs) to adapt to environmental variations. Recent harmonization of staphylococcal sRNA data allowed us to search for novel sRNAs using DETR'PROK, a computational pipeline for identifying sRNA in prokaryotes. We performed RNA-Seq on Newman strain and identified a set of 48 sRNA candidates. To avoid bioinformatic artefacts, we applied a series of cut-offs and tested experimentally each selected intergenic region...
July 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28669956/-changes-in-expressions-of-srna-spr19-and-its-potential-target-groel-in-streptococcus-mutans-strains-with-different-cariogenicity-cultured-under-different-ph-conditions
#17
Tong-Nan Hu, Wei Zheng, Shao-Hua Li, Jie Dong, Xin-Ling Wang, Cheng-Long Wang, Ning-Sheng Shao, Bing-Feng Chu
OBJECTIVE: To investigate the changes in the expression level of sRNA SpR19 and its potential target protein GroEL in clinical isolates of Streptococcus mutans with different cariogenicity exposed to different pH conditions and explore the possibility of using these molecules as biomarkers for assessing the cariogenicity of the bacteria. METHODS: The total RNAs were extracted from the clinical isolates of Streptococcus mutans with high (strain 17) and low cariogenicity (strain 5) for high-throughput sequencing for profiling of the differentially expressed sRNAs...
June 20, 2017: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
https://www.readbyqxmd.com/read/28669526/attenuating-staphylococcus-aureus-virulence-by-targeting-flotillin-protein-scaffold-activity
#18
Gudrun Koch, Charlotte Wermser, Ivan C Acosta, Lara Kricks, Stephanie T Stengel, Ana Yepes, Daniel Lopez
Scaffold proteins are ubiquitous chaperones that bind proteins and facilitate physical interaction of multi-enzyme complexes. Here we used a biochemical approach to dissect the scaffold activity of the flotillin-homolog protein FloA of the multi-drug-resistant human pathogen Staphylococcus aureus. We show that FloA promotes oligomerization of membrane protein complexes, such as the membrane-associated RNase Rny, which forms part of the RNA-degradation machinery called the degradosome. Cells lacking FloA had reduced Rny function and a consequent increase in the targeted sRNA transcripts that negatively regulate S...
July 20, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28666873/overexpression-of-mica-induces-production-of-ompc-enriched-outer-membrane-vesicles-that-protect-against-salmonella-challenge
#19
Hyun-Il Choi, Moonjeong Kim, Jinseong Jeon, Jin Kwan Han, Kwang-Sun Kim
Outer membrane vesicles (OMVs) derived from bacteria are promising candidates for subunit vaccines. Stresses that modulate the composition of outer membrane proteins (OMPs) are important for OMV synthesis. Small RNAs (sRNAs) expressed in response to stress regulate OMPs, although the mechanism underlying sRNA-mediated OMV biogenesis and its utility for developing vaccine platforms remains to be elucidated. Here, we characterized the role of a sRNA, MicA, which regulates OmpA, a major OMP involved in both production of OMVs and reactive immunity against Salmonella challenge...
June 27, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28665976/the-papi-1-pathogenicity-island-encoded-small-rna-pesa-influences-pseudomonas-aeruginosa-virulence-and-modulates-pyocin-s3-production
#20
Silvia Ferrara, Marilena Falcone, Raffaella Macchi, Alessandra Bragonzi, Daniela Girelli, Lisa Cariani, Cristina Cigana, Giovanni Bertoni
Small non-coding RNAs (sRNAs) are post-transcriptional regulators of gene expression that have been recognized as key contributors to bacterial virulence and pathogenic mechanisms. In this study, we characterized the sRNA PesA of the opportunistic human pathogen Pseudomonas aeruginosa. We show that PesA, which is transcribed within the pathogenicity island PAPI-1 of P. aeruginosa strain PA14, contributes to P. aeruginosa PA14 virulence. In fact, pesA gene deletion resulted in a less pathogenic strain, showing higher survival of cystic fibrosis human bronchial epithelial cells after infection...
2017: PloS One
keyword
keyword
30226
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"