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https://www.readbyqxmd.com/read/29779095/crispr-cas13a-targeting-of-rna-virus-in-plants
#1
Kulbhushan Chaudhary
This approach is quite promising to control plant viral diseases and create synthetic networks to better understand the structure/function relationship in RNA and proteins. Plant viruses are obligate intracellular parasites which causes enormous losses in crop yield worldwide. These viruses replicate into infected cells by highjacking host cellular machinery. Over the last two decades, diverse approaches such as conventional breeding, transgenic approach and gene silencing strategies have been used to control RNA viruses, but escaped due to high rate of mutation...
May 19, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29778844/identification-of-micrornas-with-heat-stress-responsive-and-immune-properties-in-marsupenaeus-japonicus-based-on-next-generation-sequencing-and-bioinformatics-analysis-essential-regulators-in-the-heat-stress-host-interactions
#2
Jinbin Zheng, Jiawen Cao, Yong Mao, Yongquan Su, Jun Wang
Summer mortality syndrome is one of the most serious issue for Marsupenaeus japonicus aquaculture in China. Since it causes massive economic loss and threatens sustainability of M. japonicus aquaculture industry, thus, there is an urgent desire to reveal the heat stress-host interactions mechanisms that lead to mass mortalities of M. japonicus in hot summer months. MicroRNAs (miRNAs) are small noncoding RNAs that involved in regulation of diverse biological processes, including stress and immune response, and might serve as potential regulators in the heat stress-host interactions...
May 17, 2018: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29778222/exploring-dinoflagellate-biology-with-high-throughput-proteomics
#3
REVIEW
David Morse, Sirius P K Tse, Samuel C L Lo
Dinoflagellates are notorious for their ability to form the harmful algal blooms known as "red tides," yet the mechanisms underlying bloom formation remain poorly understood. Despite recent advances in nucleic acid sequencing, which have generated transcriptomes from a wide range of species exposed to a variety of different conditions, measuring changes in RNA levels have not generally produced great insight into dinoflagellate cell biology or environmental physiology, nor do we have a thorough grasp on the molecular events underpinning bloom formation...
May 2018: Harmful Algae
https://www.readbyqxmd.com/read/29777445/a-reverse-genetics-system-for-enterovirus-d68-using-human-rna-polymerase-i
#4
Minglei Pan, Shuai Gao, Zhenwei Zhou, Keke Zhang, Sihua Liu, Zhiyun Wang, Tao Wang
Human enterovirus D68 (EV-D68) is a highly contagious virus, which causes respiratory tract infections. However, no effective vaccines are currently available for controlling EV-D68 infection. Here, we developed a reverse genetics system to recover EV-D68 minireplicons and infectious EV-D68 from transfected plasmids using the RNA polymerase I (Pol I) promoter. The EV-D68 minireplicons contained the luciferase reporter gene, which flanked by the non-coding regions of the EV-D68 RNA. The luciferase signals could be detected in cells after transfection and Pol I promoter-mediated luciferase signal was significantly stronger than that mediated by the T7 promoter...
May 17, 2018: Virus Genes
https://www.readbyqxmd.com/read/29777050/the-yeast-telomerase-recruitment-module-requires-a-specific-rna-architecture
#5
Nancy Laterreur, Bruno Lemieux, Hannah Neumann, Jean-Christophe Berger-Dancause, Daniel Lafontaine, Raymund J Wellinger
Telomerases are ribonucleoprotein (RNP) enzymes that are related to reverse transcriptases. While they maintain genome stability, their composition varies significantly between species. Yeast telomerase RNPs contain an RNA that is comparatively large and its overall folding shows long helical segments with distal functional parts. Here we investigated the essential stem IVc module of the budding yeast telomerase RNA, called Tlc1. The distal part of stem IVc includes a conserved sequence element CS2a and structurally conserved features to which bind the Pop1/Pop6/Pop7 proteins and which together function analogously to the P3 domains of the RNase P/MRP RNPs...
May 18, 2018: RNA
https://www.readbyqxmd.com/read/29775757/molecular-characterization-of-physis-tissue-by-rna-sequencing
#6
Christopher R Paradise, Catalina Galeano-Garces, Daniela Galeano-Garces, Amel Dudakovic, Todd A Milbrandt, Daniel B F Saris, Aaron J Krych, Marcel Karperien, Gabriel B Ferguson, Denis Evseenko, Scott M Riester, Andre J van Wijnen, A Noelle Larson
The physis is a well-established and anatomically distinct cartilaginous structure that is crucial for normal long-bone development and growth. Abnormalities in physis function are linked to growth plate disorders and other pediatric musculoskeletal diseases. Understanding the molecular pathways operative in the physis may permit development of regenerative therapies to complement surgically-based procedures that are the current standard of care for growth plate disorders. Here, we performed next generation RNA sequencing on mRNA isolated from human physis and other skeletal tissues (e...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29775626/microrna-21-up-regulates-metalloprotease-by-down-regulating-timp3-during-cumulus-cell-oocyte-complex-in-vitro-maturation
#7
Bo Pan, Julang Li
Cumulus cells and the remodeling of their extracellular matrix around oocytes are essential for oocyte maturation and ovulation in the ovary. An important extracellular metalloprotease, ADAMTS1, and its partner VERSICAN, mediate essential cumulus-oocyte-complex (COC) structural remodeling. However, how the expression of these proteinases is regulated during oocyte maturation is unclear. Here we report that both ADAMTS1 and VERSICAN significantly increased in porcine cumulus cells during COC in vitro maturation (IVM)...
May 15, 2018: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/29775593/structure-of-telomerase-with-telomeric-dna
#8
Jiansen Jiang, Yaqiang Wang, Lukas Sušac, Henry Chan, Ritwika Basu, Z Hong Zhou, Juli Feigon
Telomerase is an RNA-protein complex (RNP) that extends telomeric DNA at the 3' ends of chromosomes using its telomerase reverse transcriptase (TERT) and integral template-containing telomerase RNA (TER). Its activity is a critical determinant of human health, affecting aging, cancer, and stem cell renewal. Lack of atomic models of telomerase, particularly one with DNA bound, has limited our mechanistic understanding of telomeric DNA repeat synthesis. We report the 4.8 Å resolution cryoelectron microscopy structure of active Tetrahymena telomerase bound to telomeric DNA...
May 17, 2018: Cell
https://www.readbyqxmd.com/read/29775584/conformational-activation-of-argonaute-by-distinct-yet-coordinated-actions-of-the-hsp70-and-hsp90-chaperone-systems
#9
Kotaro Tsuboyama, Hisashi Tadakuma, Yukihide Tomari
Loading of small RNAs into Argonaute, the core protein in RNA silencing, requires the Hsp70/Hsp90 chaperone machinery. This machinery also activates many other clients, including steroid hormone receptors and kinases, but how their structures change during chaperone-dependent activation remains unclear. Here, we utilized single-molecule Förster resonance energy transfer (smFRET) to probe the conformational changes of Drosophila Ago2 mediated by the chaperone machinery. We found that empty Ago2 exists in various closed conformations...
May 17, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29775224/circular-rnas-are-differentially-expressed-in-liver-ischemia-reperfusion-injury-model
#10
Zhiqiang Ye, Qinglei Kong, Jianhua Han, Jingyi Deng, Miaolue Wu, Hong Deng
Liver ischemia/reperfusion (I/R) injury has high mortality due to the intense inflammatory process occurs in the liver. However, the pathological mechanism underlying I/R injury is still not clear. Recent works showed that circular RNAs play critical roles in many human diseases. In this study, the occurrence of liver I/R injury was validated by an analysis of the blood samples and hematoxylin-eosin (HE) staining of liver tissues. Total RNA was purified and followed by RNA-seq in the purpose of screening the circRNAs in significant differentially expression, which were validated by quantitative PCR...
May 18, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/29773918/rna-modifying-proteins-as-anticancer-drug-targets
#11
REVIEW
P Ann Boriack-Sjodin, Scott Ribich, Robert A Copeland
All major biological macromolecules (DNA, RNA, proteins and lipids) undergo enzyme-catalysed covalent modifications that impact their structure, function and stability. A variety of covalent modifications of RNA have been identified and demonstrated to affect RNA stability and translation to proteins; these mechanisms of translational control have been termed epitranscriptomics. Emerging data suggest that some epitranscriptomic mechanisms are altered in human cancers as well as other human diseases. In this Review, we examine the current understanding of RNA modifications with a focus on mRNA methylation, highlight their possible roles in specific cancer indications and discuss the emerging potential of RNA-modifying proteins as therapeutic targets...
May 18, 2018: Nature Reviews. Drug Discovery
https://www.readbyqxmd.com/read/29773840/rna-seq-and-uhplc-q-tof-ms-based-lipidomics-study-in-lysiphlebia-japonica
#12
Xueke Gao, Junyu Luo, Limin Lü, LiJuan Zhang, Shuai Zhang, Jinjie Cui
Lipids play an important role in energy storage, membrane structure stabilization and signaling. Parasitoids are excellent models to study lipidomics because a majority of them do not accumulate during their free-living life-stage. Studies on parasitoids have mostly focused on the changes in the lipids and gene transcripts in hosts and little attention has been devoted to lipidomics and transcriptomics changes in parasitoids. In this study, a relative quantitative analysis of lipids and their gene transcripts in 3-days-old Lysiphlebia japonica larva (3 days after spawning) and pupae were performed using liquid chromatography, mass spectrometry and RNA-seq...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773839/layer-by-layer-sirna-poly-l-lysine-multilayers-on-polydopamine-coated-surface-for-efficient-cell-adhesion-and-gene-silencing
#13
Cheol Am Hong, Ho Yeon Son, Yoon Sung Nam
For tissue engineering applications, small interfering RNA (siRNA) is an attractive agent for controlling cellular functions and differentiation. Although polyionic condensation of nucleic acids with polycations has been widely used for gene delivery, siRNA is not strongly associated with cationic carriers due to its low charge density and rigid molecular structures. The use of an excess amount of cationic carriers is often used for siRNA condensation, though they can induce severe cytotoxicity. Here we introduce the self-assembly of siRNA with mild polyelectrolytes into multilayers for efficient gene silencing during cell proliferation...
May 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29773599/tgf%C3%AE-1-mediated-functional-inhibition-of-mesenchymal-stromal-cells-in-myelodysplastic-syndromes-and-acute-myeloid-leukemia
#14
Stefanie Geyh, Manuel Rodríguez-Paredes, Paul Jäger, Annemarie Koch, Felix Bormann, Julian Gutekunst, Christoph Zilkens, Ulrich Germing, Guido Kobbe, Frank Lyko, Rainer Haas, Thomas Schroeder
Mesenchymal stromal cells are involved in the pathogenesis of myelodysplastic syndromes and acute myeloid leukemia, but the underlying mechanisms are incompletely understood. To further characterize the pathological phenotype we performed RNA sequencing of mesenchymal stromal cells from patients with myelodysplastic syndromes and acute myeloid leukemia revealing a specific molecular signature of genes commonly deregulated in myelodysplastic syndromes and acute myeloid leukemia. Pathway analysis showed a strong enrichment of genes related to osteogenesis, senescence, inflammation and inhibitory cytokines thereby reflecting the structural and functional deficits of mesenchymal stromal cells in myelodysplastic syndromes and acute myeloid leukemia on a molecular level...
May 17, 2018: Haematologica
https://www.readbyqxmd.com/read/29773130/identification-of-emu-tegp11-an-ef-hand-domain-containing-tegumental-protein-of-echinococcus-multilocularis
#15
Yadong Zheng, Xiaola Guo, Meng Su, Xiaoqian Chen, Xiaoliang Jin, Juntao Ding, Zhengrong Wang, Xinwen Bo, Mazhar Ayaz, Ivan Kutyrev, Wanzhong Jia, Xichen Zhang, Jing Zhang
Tegumental proteins (TegPs) are a group of proteins that coat on the surface of worms, mainly being involved in ion uptake and immune evasion. Echinococcus species have many TegPs, but none of them have been characterized and their role remains unclear. The genome-wide analysis revealed that there were at least 14 tegp genes (tegp1 - 14) in Echinococcus species, the majority of which were found to contain an EF-hand domain or a dynein light chain-like domain or both. Despite low identity, all TegP11 proteins from 25 flatworms were conserved in structure...
May 15, 2018: Veterinary Parasitology
https://www.readbyqxmd.com/read/29773099/-toxoplasma-gondii-rop38-promotes-the-maturation-of-dendritic-cells-mediated-by-tlr4
#16
Heng Zhang, Shanghua Wu, Zhiqiang Shi, Shan Wang, Wei Lu, Yizhen Wu, Pei Sun, Qianming Xu
Objective To investigate the effect of rhoptry protein 38 (ROP38) from Toxoplasma gondii (T. gondii) on the maturation of dendritic cells (DCs) by Toll-like receptor 4 (TLR4) induction in vitro. Methods The total RNA from T. gondii RH strain was extracted by guanidine thiocyanate method, and then cDNA was synthesized with reverse transcription reaction. After ROP38 gene was amplified by PCR, the recombinant pGEX-4T-ROP38 was constructed and expressed under IPTG induction. The recombinant ROP38 protein was detected by SDS-PAGE and Western blot analysis...
March 2018: Xi Bao Yu Fen Zi Mian Yi Xue za Zhi, Chinese Journal of Cellular and Molecular Immunology
https://www.readbyqxmd.com/read/29771928/chip-exo-interrogation-of-crp-dna-and-rnap-holoenzyme-interactions
#17
Haythem Latif, Stephen Federowicz, Ali Ebrahim, Janna Tarasova, Richard Szubin, Jose Utrilla, Karsten Zengler, Bernhard O Palsson
Numerous in vitro studies have yielded a refined picture of the structural and molecular associations between Cyclic-AMP receptor protein (Crp), the DNA motif, and RNA polymerase (RNAP) holoenzyme. In this study, high-resolution ChIP-exonuclease (ChIP-exo) was applied to study Crp binding in vivo and at genome-scale. Surprisingly, Crp was found to provide little to no protection of the DNA motif under activating conditions. Instead, Crp demonstrated binding patterns that closely resembled those generated by σ70...
2018: PloS One
https://www.readbyqxmd.com/read/29771365/the-landscape-of-the-non-canonical-rna-binding-site-of-gemin5-unveils-a-feedback-loop-counteracting-the-negative-effect-on-translation
#18
Rosario Francisco-Velilla, Javier Fernandez-Chamorro, Ivan Dotu, Encarnación Martinez-Salas
Gemin5 is a predominantly cytoplasmic protein that downregulates translation, beyond controlling snRNPs assembly. The C-terminal region harbors a non-canonical RNA-binding site consisting of two domains, RBS1 and RBS2, which differ in RNA-binding capacity and the ability to modulate translation. Here, we show that these domains recognize distinct RNA targets in living cells. Interestingly, the most abundant and exclusive RNA target of the RBS1 domain was Gemin5 mRNA. Biochemical and functional characterization of this target demonstrated that RBS1 polypeptide physically interacts with a predicted thermodynamically stable stem-loop upregulating mRNA translation, thereby counteracting the negative effect of Gemin5 protein on global protein synthesis...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#19
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29769717/swi2-snf2-atpase-chr2-remodels-pri-mirnas-via-serrate-to-impede-mirna-production
#20
Zhiye Wang, Zeyang Ma, Claudia Castillo-González, Di Sun, Yanjun Li, Bin Yu, Baoyu Zhao, Pingwei Li, Xiuren Zhang
Chromatin remodelling factors (CHRs) typically function to alter chromatin structure. CHRs also reside in ribonucleoprotein complexes, but little is known about their RNA-related functions. Here we show that CHR2 (also known as BRM), the ATPase subunit of the large switch/sucrose non-fermentable (SWI/SNF) complex, is a partner of the Microprocessor component Serrate (SE). CHR2 promotes the transcription of primary microRNA precursors (pri-miRNAs) while repressing miRNA accumulation in vivo. Direct interaction with SE is required for post-transcriptional inhibition of miRNA accumulation by CHR2 but not for its transcriptional activity...
May 16, 2018: Nature
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