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https://www.readbyqxmd.com/read/28651367/alternative-rna-splicing-associated-with-mammalian-neuronal-differentiation
#1
Jiancheng Liu, Anqi Geng, Xiwei Wu, Ren-Jang Lin, Qiang Lu
Alternative pre-mRNA splicing (AS) produces multiple isoforms of mRNAs and proteins from a single gene. It is most prevalent in the mammalian brain and is thought to contribute to the formation and/or maintenance of functional complexity of the brain. Increasing evidence has documented the significant changes of AS between different regions or different developmental stages of the brain, however, the dynamics of AS and the possible function of it during neural progenitor cell (NPC) differentiation is less well known...
June 23, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28651359/altered-mirna-and-pirna-profiles-in-cumulus-cells-from-patients-with-diminished-ovarian-reserve
#2
Dawei Chen, Zhiguo Zhang, Beili Chen, Dongmei Ji, Yan Hao, Ping Zhou, Zhaolian Wei, Yunxia Cao
Diminished ovarian reserve (DOR) is defined as decreased number or quality of follicles and oocytes in a woman at childbearing age. It is estimated that up to 10% of women in the general population may suffer from DOR. The present study aims to comprehensively characterize miRNA and piRNA expression profiles in cumulus cells of DOR patients. Cumulus cells were collected from 20 women of similar chronological age who received assisted reproductive technology treatment, 10 with diminished ovarian reserve (DOR), 10 with normal ovarian reserve (NOR)...
June 23, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28651089/validation-of-commercial-real-time-pcr-arrays-for-environmental-risk-assessment-application-to-the-study-of-p-p%C3%A2-dde-toxicity-in-mus-spretus-mice-liver
#3
Noelia Morales-Prieto, Carmen Pueyo, Nieves Abril
Data on gene transcription profiles provide a comprehensive assessment of the toxic and defensive mechanisms that are triggered by pollutants. PCR-arrays have emerged as a reliable tool for analyzing the expression of a panel of relevant, pathway- or disease-focused genes under uniform cycling conditions. By using SYBR Green-optimized primer assays, it is possible to simultaneously amplify a sample with high specificity and amplification efficiencies. However, commercial PCR-arrays target a limited group of organisms, excluding most of those with environmental relevance, as is the case with Mus spretus mice...
June 23, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28650965/epigenetic-adaptation-of-the-placental-serotonin-transporter-gene-slc6a4-to-gestational-diabetes-mellitus
#4
Sofia Blazevic, Marina Horvaticek, Maja Kesic, Peter Zill, Dubravka Hranilovic, Marina Ivanisevic, Gernot Desoye, Jasminka Stefulj
We tested the hypothesis that gestational diabetes mellitus (GDM) alters the DNA methylation pattern of the fetal serotonin transporter gene (SLC6A4), and examined the functional relevance of DNA methylation for regulation of the SLC6A4 expression in the human placenta. The study included 50 mother-infant pairs. Eighteen mothers were diagnosed with GDM and 32 had normal glucose tolerance (NGT). All neonates were of normal birth weight and born at term by planned Cesarean section. DNA and RNA were isolated from samples of tissue collected from the fetal side of the placenta immediately after delivery...
2017: PloS One
https://www.readbyqxmd.com/read/28650797/larp1-functions-as-a-molecular-switch-for-mtorc1-mediated-translation-of-an-essential-class-of-mrnas
#5
Sungki Hong, Mallory A Freeberg, Ting Han, Avani Kamath, Yao Yao, Tomoko Fukuda, Tsukasa Suzuki, John K Kim, Ken Inoki
The RNA binding protein, LARP1, has been proposed to function downstream of mTORC1 to regulate the translation of 5'TOP mRNAs such as those encoding ribosome proteins (RP). However, the roles of LARP1 in the translation of 5'TOP mRNAs are controversial and its regulatory roles in mTORC1-mediated translation remain unclear. Here we show that LARP1 is a direct substrate of mTORC1 and Akt/S6K1. Deep sequencing of LARP1-bound mRNAs reveal that non-phosphorylated LARP1 interacts with both 5' and 3'UTRs of RP mRNAs and inhibits their translation...
June 26, 2017: ELife
https://www.readbyqxmd.com/read/28650741/microbial-culturomics-application-for-global-health-noncontiguous-finished-genome-sequence-and-description-of-pseudomonas-massiliensis-strain-cb-1-t-sp-nov-in-brazil
#6
Lucie Bardet, Teresa Cimmino, Clémence Buffet, Caroline Michelle, Jaishriram Rathored, Fatalmoudou Tandina, Jean-Christophe Lagier, Saber Khelaifia, Jônatas Abrahão, Didier Raoult, Jean-Marc Rolain
Culturomics is a new postgenomics field that explores the microbial diversity of the human gut coupled with taxono-genomic strategy. Culturomics, and the microbiome science more generally, are anticipated to transform global health diagnostics and inform the ways in which gut microbial diversity contributes to human health and disease, and by extension, to personalized medicine. Using culturomics, we report in this study the description of strain CB1(T) ( = CSUR P1334 = DSM 29075), a new species isolated from a stool specimen from a 37-year-old Brazilian woman...
June 26, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28650433/the-evening-complex-coordinates-environmental-and-endogenous-signals-in-arabidopsis
#7
Daphne Ezer, Jae-Hoon Jung, Hui Lan, Surojit Biswas, Laura Gregoire, Mathew S Box, Varodom Charoensawan, Sandra Cortijo, Xuelei Lai, Dorothee Stöckle, Chloe Zubieta, Katja E Jaeger, Philip A Wigge
Plants maximize their fitness by adjusting their growth and development in response to signals such as light and temperature. The circadian clock provides a mechanism for plants to anticipate events such as sunrise and adjust their transcriptional programmes. However, the underlying mechanisms by which plants coordinate environmental signals with endogenous pathways are not fully understood. Using RNA-sequencing and chromatin immunoprecipitation sequencing experiments, we show that the evening complex (EC) of the circadian clock plays a major role in directly coordinating the expression of hundreds of key regulators of photosynthesis, the circadian clock, phytohormone signalling, growth and response to the environment...
June 26, 2017: Nature Plants
https://www.readbyqxmd.com/read/28650342/inflammatory-ly6chi-monocytes-and-their-conversion-to-m2-macrophages-drive-atherosclerosis-regression
#8
Karishma Rahman, Yuliya Vengrenyuk, Stephen A Ramsey, Noemi Rotllan Vila, Natasha M Girgis, Jianhua Liu, Viktoria Gusarova, Jesper Gromada, Ada Weinstock, Kathryn J Moore, P'ng Loke, Edward A Fisher
Atherosclerosis is a chronic inflammatory disease, and developing therapies to promote its regression is an important clinical goal. We previously established that atherosclerosis regression is characterized by an overall decrease in plaque macrophages and enrichment in markers of alternatively activated M2 macrophages. We have now investigated the origin and functional requirement for M2 macrophages in regression in normolipidemic mice that received transplants of atherosclerotic aortic segments. We compared plaque regression in WT normolipidemic recipients and those deficient in chemokine receptors necessary to recruit inflammatory Ly6Chi (Ccr2-/- or Cx3cr1-/-) or patrolling Ly6Clo (Ccr5-/-) monocytes...
June 26, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28649752/investigating-dna-rna-and-protein-based-features-as-a-means-to-discriminate-pathogenic-synonymous-variants
#9
Mark Livingstone, Lukas Folkman, Yuedong Yang, Ping Zhang, Matthew Mort, David N Cooper, Yunlong Liu, Bela Stantic, Yaoqi Zhou
Synonymous single nucleotide variants (SNVs), although they do not alter the encoded protein sequences, have been implicated in many genetic diseases. Experimental studies indicate that synonymous SNVs can lead to changes in the secondary and tertiary structures of DNA and RNA, thereby impacting translational efficiency, co-translational protein folding as well as the binding of DNA/RNA-binding proteins. However, the importance of these various features in disease phenotypes is not clearly understood. Here we have built a support vector machine model (termed DDIG-SN) as a means to discriminate disease-causing synonymous variants...
June 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28649496/de-novo-transcriptome-assembly-of-loggerhead-sea-turtle-nesting-of-the-colombian-caribbean
#10
Javier Hernández-Fernández, Andrés Pinzón, Leonardo Mariño-Ramírez
Loggerhead sea turtle Caretta caretta is widely distributed in the oceans of tropical and subtropical latitude. This turtle is an endangered species due to anthropic and natural factors that have decreased their population levels. In this study, RNA sequencing and de-novo assembly of genes expressed in blood were performed. The raw FASTQ files have been deposited on NCBI's SRA database with accession number SRX2629512. A total of 5.4 Gb raw sequence data were obtained, corresponding to 48,257,019 raw reads...
September 2017: Genomics Data
https://www.readbyqxmd.com/read/28649404/comparative-transcriptomic-analysis-of-gardnerella-vaginalis-biofilms-vs-planktonic-cultures-using-rna-seq
#11
Joana Castro, Angela França, Katie R Bradwell, Myrna G Serrano, Kimberly K Jefferson, Nuno Cerca
Bacterial vaginosis is the most common gynecological disorder affecting women of reproductive age. Bacterial vaginosis is frequently associated with the development of a Gardnerella vaginalis biofilm. Recent data indicates that G. vaginalis biofilms are more tolerant to antibiotics and are able to incorporate other bacterial vaginosis -associated species, yielding a multi-species biofilm. However, despite its apparent role in bacterial vaginosis, little is known regarding the molecular determinants involved in biofilm formation by G...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28649357/rna-editing-by-the-host-adar-system-affects-the-molecular-evolution-of-the-zika-virus
#12
Helen Piontkivska, Madeline Frederick, Michael M Miyamoto, Marta L Wayne
Zika virus (ZIKV) is a mosquito-transmitted flavivirus, linked to microcephaly and fetal death in humans. Here, we investigate whether host-mediated RNA editing of adenosines (ADAR) plays a role in the molecular evolution of ZIKV. Using complete coding sequences for the ZIKV polyprotein, we show that potential ADAR substitutions are underrepresented at the ADAR-resistant GA dinucleotides of both the positive and negative strands, that these changes are spatially and temporally clustered (as expected of ADAR editing) for three branches of the viral phylogeny, and that ADAR mutagenesis can be linked to its codon usage...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649315/effects-of-a-social-stimulus-on-gene-expression-in-a-mouse-model-of-fragile-x-syndrome
#13
Tiffany D Rogers, Allison M J Anacker, Travis M Kerr, C Gunnar Forsberg, Jing Wang, Bing Zhang, Jeremy Veenstra-VanderWeele
BACKGROUND: People with fragile X syndrome (FXS) often have deficits in social behavior, and a substantial portion meet criteria for autism spectrum disorder. Though the genetic cause of FXS is known to be due to the silencing of FMR1, and the Fmr1 null mouse model representing this lesion has been extensively studied, the contributions of this gene and its protein product, FMRP, to social behavior are not well understood. METHODS: Fmr1 null mice and wildtype littermates were exposed to a social or non-social stimulus...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28649263/survey-of-high-throughput-rna-seq-data-reveals-potential-roles-for-lncrnas-during-development-and-stress-response-in-bread-wheat
#14
Shumayla, Shailesh Sharma, Mehak Taneja, Shivi Tyagi, Kashmir Singh, Santosh K Upadhyay
Long non-coding RNAs (lncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of lncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 lncRNAs in T. aestivum genome, which were characterized in comparison to the coding sequences (mRNAs)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28648779/natural-rna-polymerase-aptamers-regulate-transcription-in-e-coli
#15
Nadezda Sedlyarova, Philipp Rescheneder, Andrés Magán, Niko Popitsch, Natascha Rziha, Ivana Bilusic, Vitaly Epshtein, Bob Zimmermann, Meghan Lybecker, Vitaly Sedlyarov, Renée Schroeder, Evgeny Nudler
In search for RNA signals that modulate transcription via direct interaction with RNA polymerase (RNAP), we deep sequenced an E. coli genomic library enriched for RNAP-binding RNAs. Many natural RNAP-binding aptamers, termed RAPs, were mapped to the genome. Over 60% of E. coli genes carry RAPs in their mRNA. Combining in vitro and in vivo approaches, we characterized a subset of inhibitory RAPs (iRAPs) that promote Rho-dependent transcription termination. A representative iRAP within the coding region of the essential gene, nadD, greatly reduces its transcriptional output in stationary phase and under oxidative stress, demonstrating that iRAPs control gene expression in response to changing environment...
June 19, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28648749/transcriptome-profiling-of-3d-co-cultured-cardiomyocytes-and-endothelial-cells-under-oxidative-stress-using-a-photocrosslinkable-hydrogel-system
#16
Xiaoshan Yue, Aylin Acun, Pinar Zorlutuna
Myocardial infarction (MI) is one of the most common among cardiovascular diseases. Endothelial cells (ECs) are considered to have protective effects on cardiomyocytes (CMs) under stress conditions such as MI; however, the paracrine CM-EC crosstalk and the resulting endogenous cellular responses that could contribute to this protective effect are not thoroughly investigated. Here we created biomimetic synthetic tissues containing CMs and human induced pluripotent stem cell (hiPSC)-derived ECs (iECs), which showed improved cell survival compared to single cultures under conditions mimicking the aftermath of MI, and performed high-throughput RNA-sequencing to identify target pathways that could govern CM-iEC crosstalk and the resulting improvement in cell viability...
June 22, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28648396/25-years-of-serving-the-community-with-ribosomal-rna-gene-reference-databases-and-tools
#17
Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, Wolfgang Ludwig
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis...
June 22, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28648085/specifying-rna-binding-regions-in-proteins-by-peptide-cross-linking-and-affinity-purification
#18
Meeli Mullari, David Lyon, Lars Juhl Jensen, Michael L Nielsen
RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, with aberrations in RBP functions linked to many diseases including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins with unique RNA-binding properties. These properties are regulated through modularity of a large variety of RNA-binding domains, rendering RNA-protein interactions difficult to study. Recently, the introduction of proteomics methods has provided novel insights into RNA-binding proteins at a systems level...
June 25, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28647987/-distribution-of-hiv-1-subtypes-among-foreign-patients-in-guangzhou-between-2008-and-2010-and-in-2015
#19
Z G Han, H Wu, C Y Liang, K Gao, H X Mai, Y S Cai, H F Xu
Objective: To understand the characteristic of subtype distribution among foreigners who were living with HIV-1, in Guangzhou. Methods: HIV-1 RNAs were extracted from 114 serum specimens in foreigners diagnosed with HIV-1 infections between 2008 and 2010, and in 2015. Partial pol gene of HIV-1 genome from these RNA samples were amplified by nested reverse transcription polymerase chain reaction (nested-PCR) with nucleotide sequenced. Subsequently, phylogenetic tree was reconstructed using the pol sequences of samples and references...
June 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28647582/comparison-of-sequencing-the-d2-region-of-the-large-subunit-ribosomal-rna-gene-microseq%C3%A2-versus-the-internal-transcribed-spacer-its-regions-using-two-public-databases-for-identification-of-common-and-uncommon-clinically-relevant-fungal-species
#20
S Arbefeville, A Harris, P Ferrieri
CONTEXT: Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. OBJECTIVE: The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data...
June 21, 2017: Journal of Microbiological Methods
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