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RNA folding

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https://www.readbyqxmd.com/read/29352424/cannabinoid-cb1-and-cb2%C3%A2-receptors-and-monoacylglycerol-lipase-gene-expression-alterations-in-the-basal-ganglia-of-patients-with-parkinson-s-disease
#1
Francisco Navarrete, M Salud García-Gutiérrez, Auxiliadora Aracil-Fernández, José L Lanciego, Jorge Manzanares
Previous studies suggest that the endocannabinoid system plays an important role in the neuropathological basis of Parkinson's disease (PD). This study was designed to detect potential alterations in the cannabinoid receptors CB1 (CB1r) and CB2 (A isoform, CB2Ar), and in monoacylglycerol lipase (MAGL) gene expression in the substantia nigra (SN) and putamen (PUT) of patients with PD. Immunohistochemical studies were performed to identify precise CB2r cellular localization in the SN of control and PD patients...
January 19, 2018: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
https://www.readbyqxmd.com/read/29352001/keap1-editing-using-crispr-cas9-for-therapeutic-nrf2-activation-in-primary-human-t-lymphocytes
#2
Sanjeev Noel, Sul A Lee, Mohanraj Sadasivam, Abdel R A Hamad, Hamid Rabb
Oxidant stress modifies T lymphocyte activation and function. Previous work demonstrated that murine T cell-specific kelch like-ECH-associated protein 1 (Keap1) deletion enhances antioxidant capacity and protects from experimental acute kidney injury. In this study, we used CRISPR technology to develop clinically translatable human T cell-specific KEAP1 deletion. Delivery of KEAP1 exon 2 specific Cas9:guide RNA in Jurkat T cells led to significant (∼70%) editing and upregulation of NRF2-regulated antioxidant genes NADPH dehydrogenase quinone 1 (NQO1) (up to 11-fold), heme oxygenase 1 (HO1) (up to 11-fold), and GCLM (up to 2-fold)...
January 19, 2018: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29351962/rna-helicases-in-rna-decay
#3
REVIEW
Vanessa Khemici, Patrick Linder
RNA molecules have the tendency to fold into complex structures or to associate with complementary RNAs that exoribonucleases have difficulties processing or degrading. Therefore, degradosomes in bacteria and organelles as well as exosomes in eukaryotes have teamed-up with RNA helicases. Whereas bacterial degradosomes are associated with RNA helicases from the DEAD-box family, the exosomes and mitochondrial degradosome use the help of Ski2-like and Suv3 RNA helicases.
January 19, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29351764/quantification-and-kinetics-of-viral-rna-transcripts-produced-in-orthohantavirus-infected-cells
#4
Julia Wigren Byström, Jonas Näslund, Fredrik Trulsson, Magnus Evander, Olivia Wesula Lwande, Clas Ahlm, Göran Bucht
BACKGROUND: Rodent borne viruses of the Orthohantavirus genus cause hemorrhagic fever with renal syndrome among people in Eurasia, and hantavirus cardiopulmonary syndrome in the Americas. At present, there are no specific treatments or efficient vaccines against these diseases. Improved understanding of viral transcription and replication may instigate targeted treatment of Orthohantavirus infections. For this purpose, we investigated the kinetics and levels of viral RNA transcription during an ongoing infection in-vitro...
January 19, 2018: Virology Journal
https://www.readbyqxmd.com/read/29348171/a-cationic-c-terminal-patch-and-structural-rearrangements-in-ebola-virus-matrix-vp40-protein-control-its-interactions-with-phosphatidylserine
#5
Kathryn Del Vecchio, Cary T Frick, Jeevan B Gc, Shun-Ichiro Oda, Bernard S Gerstman, Erica Ollmann Saphire, Prem P Chapagain, Robert V Stahelin
Ebola virus (EBOV) is a filamentous lipid-enveloped virus that causes hemorrhagic fever with a high fatality rate. Viral protein 40 (VP40) is the major EBOV matrix protein and regulates viral budding from the plasma membrane. VP40 is a transformer/morpheein that can structurally rearrange its native homodimer into either a hexameric filament that facilitates viral budding or a RNA-binding octameric ring that regulates viral transcription. VP40 associates with plasma-membrane lipids such as phosphatidylserine (PS), and this association is critical to budding from the host cell...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29346617/riboswitching-with-ciprofloxacin-development-and-characterization-of-a-novel-rna-regulator
#6
Florian Groher, Cristina Bofill-Bosch, Christopher Schneider, Johannes Braun, Sven Jager, Katharina Geißler, Kay Hamacher, Beatrix Suess
RNA molecules play important and diverse regulatory roles in the cell. Inspired by this natural versatility, RNA devices are increasingly important for many synthetic biology applications, e.g. optimizing engineered metabolic pathways, gene therapeutics or building up complex logical units. A major advantage of RNA is the possibility of de novo design of RNA-based sensing domains via an in vitro selection process (SELEX). Here, we describe development of a novel ciprofloxacin-responsive riboswitch by in vitro selection and next-generation sequencing-guided cellular screening...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346554/functional-roles-of-sex-biased-growth-hormone-regulated-micrornas-mir-1948-and-mir-802-in-young-adult-mouse-liver
#7
Pengying Hao, David J Waxman
Sex-specific temporal patterns of pituitary GH secretion determine the sex-biased transcription of hundreds of genes in the liver and impart significant sex differences in liver physiology, metabolism and disease. Sex differences in hepatic gene expression vary widely, ranging from <2-fold to >1,000-fold in the mouse. Here, we use small RNA sequencing to discover 24 sex-biased mouse liver miRNAs, and then investigate the roles of two of these miRNAs in GH-regulated liver sex differences. Studies in pre-pubertal and young adult mice, and in mice where pituitary hormones are ablated or where sex-specific hepatic GH signaling is dysregulated, demonstrated that the male-biased miR-1948 and the female-biased miR-802 are both regulated by sex-specific pituitary GH secretory patterns, acquire sex specificity at puberty, and are dependent on the GH-activated transcription factor STAT5 for their sex-specific expression...
January 16, 2018: Endocrinology
https://www.readbyqxmd.com/read/29343718/the-bacterial-type-iii-toxin-antitoxin-system-toxin-is-a-dynamic-protein-rna-complex-with-stability-dependent-antiviral-abortive-infection-activity
#8
Francesca L Short, Chidiebere Akusobi, William R Broadhurst, George P C Salmond
Bacteria have evolved numerous defense systems to protect themselves from viral (bacteriophage) infection. The ToxIN system of Pectobacterium atrosepticum is a Type III toxin-antitoxin complex and "altruistic suicide" anti-phage system, which kills phage-infected cells through the release of a ribonuclease toxin, ToxN. ToxN is counteracted by a co-transcribed antitoxic RNA pseudoknot, ToxI, which self-assembles with ToxN into an inactive 3 ToxI:3 ToxN complex in vitro. However it is not known whether this complex is predominant in vivo, or how the complex is disassembled following infection to trigger a lethal, "altruistic" response...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343207/genome-wide-analysis-identified-a-number-of-dysregulated-long-noncoding-rna-lncrna-in-human-pancreatic-ductal-adenocarcinoma
#9
Sijie Hao, Lie Yao, Jiaxin Huang, Hang He, Feng Yang, Yang Di, Chen Jin, Deliang Fu
BACKGROUND: Long noncoding RNAs have been shown to play crucial roles in cancer biology, while the long noncoding RNA landscapes of pancreatic ductal adenocarcinoma have not been completely characterized. We aimed to determine whether long noncoding RNA could serve as early diagnostic biomarkers for pancreatic ductal adenocarcinoma. METHOD: We conducted a genome-wide microarray analysis on pancreatic ductal adenocarcinoma and their adjacent noncancerous tissues from 8 Chinese patients...
January 1, 2018: Technology in Cancer Research & Treatment
https://www.readbyqxmd.com/read/29342213/circulating-neutrophil-transcriptome-may-reveal-intracranial-aneurysm-signature
#10
Vincent M Tutino, Kerry E Poppenberg, Kaiyu Jiang, James N Jarvis, Yijun Sun, Ashish Sonig, Adnan H Siddiqui, Kenneth V Snyder, Elad I Levy, John Kolega, Hui Meng
BACKGROUND: Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. METHODS: Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls...
2018: PloS One
https://www.readbyqxmd.com/read/29339162/a-method-to-improve-prediction-of-secondary-structure-for-large-single-rna-sequences
#11
Ali El-Lakkani, Eman M Ibrahim
The function of a particular RNA molecule within an organic system is principally determined by its structure. The current physical methods available for structure determination are time consuming and expensive. Hence, computational methods for structure prediction are often used. The prediction of the structure of a large single sequence of RNA needs a lot of research work. In the present work, a method is introduced to improve the prediction of large single sequence RNA secondary structure obtained by Mfold program using the concept of minimum free energy...
January 12, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29335877/development-of-cyclic-amp-receptor-protein-based-artificial-transcription-factor-for-intensifying-gene-expression
#12
Peng Zhao, Wenjuan Wang, Pingfang Tian
Vector-dependent gene overexpression typically relies on an efficient operon and sufficient RNA polymerases (RNAPs). The lac (lactose) operon is a paradigm of transcription control, and cyclic AMP receptor protein (CRP) is a global regulator capable of recruiting RNAPs. However, the gap between lac operon and CRP has not been well bridged. In this work, CRP was fused to lac repressor protein (lacI) to form an artificial transcription factor (ATF) with the expectation that when LacI acted on the lacO-positioned upstream of gene of interest, the LacI-tethered CRP would trap RNAPs and thus improve the expression of PuuC, an aldehyde dehydrogenase catalyzing 3-hydroxypropionaldehyde (3-HPA) to 3-hydroxypropionic acid (3-HP) in Klebsiella pneumoniae...
January 16, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29334891/tuning-iteration-space-slicing-based-tiled-multi-core-code-implementing-nussinov-s-rna-folding
#13
Marek Palkowski, Wlodzimierz Bielecki
BACKGROUND: RNA folding is an ongoing compute-intensive task of bioinformatics. Parallelization and improving code locality for this kind of algorithms is one of the most relevant areas in computational biology. Fortunately, RNA secondary structure approaches, such as Nussinov's recurrence, involve mathematical operations over affine control loops whose iteration space can be represented by the polyhedral model. This allows us to apply powerful polyhedral compilation techniques based on the transitive closure of dependence graphs to generate parallel tiled code implementing Nussinov's RNA folding...
January 15, 2018: BMC Bioinformatics
https://www.readbyqxmd.com/read/29334364/compactness-of-viral-genomes-effect-of-disperse-and-localized-random-mutations
#14
Anže Lošdorfer Božič, Cristian Micheletti, Rudolf Podgornik, Luca Tubiana
Genomes of single-stranded RNA viruses have evolved to optimize several concurrent properties. One of them is the architecture of their genomic folds, which must not only feature precise structural elements at specific positions, but also allow for overall spatial compactness. The latter was shown to be disrupted by random synonymous mutations, a disruption which can consequently negatively affect genome encapsidation. In this study, we use three mutation schemes with different degrees of locality to mutate the genomes of phage MS2 and Brome Mosaic Virus in order to understand the observed sensitivity of the global compactness of their folds...
January 15, 2018: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29331478/comprehensive-analysis-of-lncrnas-and-mrnas-with-associated-co-expression-and-cerna-networks-in-c2c12-myoblasts-and-myotubes
#15
Rui Chen, Ting Jiang, Yanling She, Sidong Xie, Shanyao Zhou, Cheng Li, Jun Ou, Yulin Liu
Long non-coding RNAs (lncRNAs) are emerging as important regulators in the modulation of muscle development and muscle-related diseases. To explore potential regulators of muscle differentiation, we determined the expression profiles of lncRNAs and mRNAs in C2C12 mouse myoblast cell line using microarray analysis. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to explore their function. We also constructed co-expression, cis/trans-regulation, and competing endogenous RNA (ceRNA) networks with bioinformatics methods...
January 10, 2018: Gene
https://www.readbyqxmd.com/read/29331077/optimized-paired-sgrna-cas9-cloning-and-expression-cassette-triggers-high-efficiency-multiplex-genome-editing-in-kiwifruit
#16
Zupeng Wang, Shuaibin Wang, Dawei Li, Qiong Zhang, Li Li, Caihong Zhong, Yifei Liu, Hongwen Huang
Kiwifruit is an important fruit crop; however, technologies for its functional genomic and molecular improvement are limited. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability is variable depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Optimizing conditions for its use within a particular species is therefore needed to achieve highly efficient genome editing...
January 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29330371/transcriptional-inaccuracy-threshold-attenuates-differences-in-rna-dependent-dna-synthesis-fidelity-between-retroviral-reverse-transcriptases
#17
Alba Sebastián-Martín, Verónica Barrioluengo, Luis Menéndez-Arias
In M13mp2 lacZα forward mutation assays measuring intrinsic fidelity of DNA-dependent DNA synthesis, wild-type human immunodeficiency virus type 1 (HIV-1) RTs of group M/subtype B previously showed >10-fold higher error rates than murine leukaemia virus (MLV) and avian myeloblastosis virus (AMV) RTs. An adapted version of the assay was used to obtain error rates of RNA-dependent DNA synthesis for several RTs, including wild-type HIV-1BH10, HIV-1ESP49, AMV and MLV RTs, and the high-fidelity mutants of HIV-1ESP49 RT K65R and K65R/V75I...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330365/engineered-nanointerfaces-for-microfluidic-isolation-and-molecular-profiling-of-tumor-specific-extracellular-vesicles
#18
Eduardo Reátegui, Kristan E van der Vos, Charles P Lai, Mahnaz Zeinali, Nadia A Atai, Berent Aldikacti, Frederick P Floyd, Aimal H Khankhel, Vishal Thapar, Fred H Hochberg, Lecia V Sequist, Brian V Nahed, Bob S Carter, Mehmet Toner, Leonora Balaj, David T Ting, Xandra O Breakefield, Shannon L Stott
Extracellular vesicles (EVs) carry RNA, DNA, proteins, and lipids. Specifically, tumor-derived EVs have the potential to be utilized as disease-specific biomarkers. However, a lack of methods to isolate tumor-specific EVs has limited their use in clinical settings. Here we report a sensitive analytical microfluidic platform (EVHB-Chip) that enables tumor-specific EV-RNA isolation within 3 h. Using the EVHB-Chip, we achieve 94% tumor-EV specificity, a limit of detection of 100 EVs per μL, and a 10-fold increase in tumor RNA enrichment in comparison to other methods...
January 12, 2018: Nature Communications
https://www.readbyqxmd.com/read/29329159/overexpression-of-the-long-noncoding-rna-homeboxa-transcript-at-the-distal-tip-predicts-poor-prognosis-in-a-kras-independent-manner-in-periampullary-region-tumors
#19
Ozkan Balcin, Secil Ak Aksoy, Berrin Tunca, Ekrem Kaya, Unal Egeli, Gulcin Tezcan, Nesrin Ugras, Gulsah Cecener, Ozgen Isik, Halit Ziya Dundar, Omer Yerci
OBJECTIVES: Periampullary region tumors (PRTs) are the fifth highest cause of cancer-related deaths worldwide. Although recent studies have highlighted the prognostic value of the long noncoding RNA HomeboxA transcript at the distal tip (HOTTIP) in patients with pancreatic ductal adenocarcinoma, the relationship between HOTTIP and clinical outcome of all PRTs remains obscure. The aim of this study was to clarify the prognostic significance of HOTTIP in patients with all PRTs related to KRAS mutational status...
January 12, 2018: Pancreas
https://www.readbyqxmd.com/read/29329019/salidroside-influences-the-cellular-cross-talk-of-human-fetal-lung-diploid-fibroblasts-a-proteomic-approach
#20
Wenmin Xing, Wenyan Gao, Huili Su, Sanying Wang, Jing Zhang, Genxiang Mao, Jing Yan
Senescence is a complex multiple factor proces, which is still poorly understood. The purpose of this study was to find the proteome of cultured human fetal lung diploid fibroblasts (2BS) of different population doubling (PD), as well as the altered proteome induced by salidroside (SAL) in 2BS cells. Proteins were identified by two-dimensional electrophoresis (2-DE) combining matrix-assisted laser desorption/ionization-time and flight mass spectrometry (MAL DI-TOF/MS). As a result, we found 16 proteins with two-fold variations in senescent cells or after SAL treatment, some being reduced such as reticulocalbin-1, heat shock protein beta-6, elongation factor 1-delta, F-actin-capping protein subunit alpha-1, and chloride intracellular channel 1...
January 5, 2018: Environmental Toxicology and Pharmacology
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