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https://www.readbyqxmd.com/read/29150525/distinct-rna-unwinding-mechanisms-of-dead-box-and-deah-box-rna-helicase-proteins-in-remodeling-structured-rnas-and-rnps
#1
REVIEW
Benjamin Gilman, Pilar Tijerina, Rick Russell
Structured RNAs and RNA-protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms...
November 17, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29150011/optimization-of-crispr-cas9-genome-editing-for-loss-of-function-in-the-early-chick-embryo
#2
Shashank Gandhi, Michael L Piacentino, Felipe M Vieceli, Marianne E Bronner
The advent of CRISPR/Cas9 has made genome editing possible in virtually any organism, including those not previously amenable to genetic manipulations. Here, we present an optimization of CRISPR/Cas9 for application to early avian embryos with improved efficiency via a three-fold strategy. First, we employed Cas9 protein flanked with two nuclear localization signal sequences for improved nuclear localization. Second, we used a modified guide RNA (gRNA) scaffold that obviates premature termination of transcription and unstable Cas9-gRNA interactions...
December 1, 2017: Developmental Biology
https://www.readbyqxmd.com/read/29149090/computational-methods-for-modeling-aptamers-and-designing-riboswitches
#3
REVIEW
Sha Gong, Yanli Wang, Zhen Wang, Wenbing Zhang
Riboswitches, which are located within certain noncoding RNA region perform functions as genetic "switches", regulating when and where genes are expressed in response to certain ligands. Understanding the numerous functions of riboswitches requires computation models to predict structures and structural changes of the aptamer domains. Although aptamers often form a complex structure, computational approaches, such as RNAComposer and Rosetta, have already been applied to model the tertiary (three-dimensional (3D)) structure for several aptamers...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29148410/th17-gene-expression-in-psoriatic-arthritis-synovial-fluid-and-peripheral-blood-compared-to-osteoarthritis-and-cutaneous-psoriasis
#4
Fatima Abji, Remy A Pollock, Kun Liang, Vinod Chandran, Dafna D Gladman
OBJECTIVES: The IL-23/IL-17 axis is central to the pathogenesis of psoriatic arthritis (PsA). We aimed to identify Th17 signalling genes that are dysregulated in synovial fluid of PsA compared to osteoarthritis (OA) patients and to determine if differences in peripheral blood can distinguish PsA from psoriasis patients and controls. METHODS: Synovial fluid cells (SFCs) from 14 PsA and 9 OA patients were obtained and stored in TRIzol reagent. RNA was isolated by phenol-chloroform extraction and purified with RNeasy miniprep kits...
November 9, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/29146908/lrpprc-mediated-folding-of-the-mitochondrial-transcriptome
#5
Stefan J Siira, Henrik Spåhr, Anne-Marie J Shearwood, Benedetta Ruzzenente, Nils-Göran Larsson, Oliver Rackham, Aleksandra Filipovska
The expression of the compact mammalian mitochondrial genome requires transcription, RNA processing, translation and RNA decay, much like the more complex chromosomal systems, and here we use it as a model system to understand the fundamental aspects of gene expression. Here we combine RNase footprinting with PAR-CLIP at unprecedented depth to reveal the importance of RNA-protein interactions in dictating RNA folding within the mitochondrial transcriptome. We show that LRPPRC, in complex with its protein partner SLIRP, binds throughout the mitochondrial transcriptome, with a preference for mRNAs, and its loss affects the entire secondary structure and stability of the transcriptome...
November 16, 2017: Nature Communications
https://www.readbyqxmd.com/read/29145027/differential-gene-expression-in-the-intestine-of-sea-cucumber-apostichopus-japonicus-under-low-and-high-salinity-conditions
#6
Libin Zhang, Qiming Feng, Lina Sun, Kui Ding, Da Huo, Yan Fang, Tao Zhang, Hongsheng Yang
Sea cucumber, Apostichopus japonicus is an important species for aquaculture, and its behavior and physiology can change in response to changing salinity conditions. For this reason, it is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity. In this study, RNA-Seq provided a general overview of the gene expression profiles in the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environments. Screening for differentially expressed genes (DEGs) using the NOISeq method identified 109, 100, and 89 DEGs based on a fold change of ≥2 and divergence probability ≥0...
November 4, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/29143424/restoration-of-ribozyme-tertiary-contact-and-function-using-a-molecular-glue-for-rna
#7
Chikara Dohno, Maki Kimura, Kazuhiko Nakatani
Some RNA classes require folding into the proper higher-order structures to exert their functions. Hammerhead ribozyme (HHR) requires a folding conformation stabilized by tertiary interaction for full activity. Here, we developed a rationally engineered HHR that was inactive, but could be activated by a synthetic RNA-binding ligand, naphthyridine carbamate tetramer with Z-stilbene linker (Z-NCTS). Binding of Z-NCTS could induce the formation of an active folding structure and thereby restore ribozyme activity, where Z-NCTS acts as a molecular glue to bring two isolated RNA loops into contact with each other...
November 16, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/29142827/overexpression-of-the-primary-sigma-factor-gene-siga-improved-carotenoid-production-by-corynebacterium-glutamicum-application-to-production-of-%C3%AE-carotene-and-the-non-native-linear-c50-carotenoid-bisanhydrobacterioruberin
#8
Hironori Taniguchi, Nadja A Henke, Sabine A E Heider, Volker F Wendisch
Corynebacterium glutamicum shows yellow pigmentation due to biosynthesis of the C50 carotenoid decaprenoxanthin and its glycosides. This bacterium has been engineered for production of various non-native cyclic C40 and C50 carotenoids such as β-carotene, astaxanthin or sarcinaxanthin. In this study, the effect of modulating gene expression more broadly by overexpression of sigma factor genes on carotenoid production by C. glutamicum was characterized. Overexpression of the primary sigma factor gene sigA improved lycopene production by recombinant C...
June 2017: Metabolic Engineering Communications
https://www.readbyqxmd.com/read/29140303/two-cycloartenol-synthases-for-phytosterol-biosynthesis-in-polygala-tenuifolia-willd
#9
Mei Lan Jin, Woo Moon Lee, Ok Tae Kim
Oxidosqualene cyclases (OSCs) are enzymes that play a key role in control of the biosynthesis of phytosterols and triterpene saponins. In order to uncover OSC genes from Polygala tenuifolia seedlings induced by methyl jasmonate (MeJA), RNA-sequencing analysis was performed using the Illumina sequencing platform. A total of 148,488,632 high-quality reads from two samples (control and the MeJA treated) were generated. We screened genes related to phytosterol and triterpene saponin biosynthesis and analyzed the transcriptional changes of differentially expressed unigene (DEUG) values calculated by fragments per kilobase million (FPKM)...
November 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29139094/investigating-the-therapeutic-potential-and-mechanism-of-curcumin-in-breast-cancer-based-on-rna-sequencing-and-bioinformatics-analysis
#10
Rong Wang, Jinbin Li, Yulan Zhao, Yapeng Li, Ling Yin
BACKGROUND: Breast cancer is a prevalent cancer in female. This study aims to investigate the therapeutic potential and mechanism of curcumin in breast cancer. METHODS: After cultivation, human breast cancer cells (MCF-7 cells) were treated with 0.1% (v/v) 15 µmol/ml curcumin-dimethylsulfoxide solution and 0.1% (v/v) dimethylsulfoxide, respectively, at 37 °C and 5% CO2 for 48 h. Total RNA was extracted, cDNA library was constructed, and cDNAs were amplified and sequenced...
November 14, 2017: Breast Cancer: the Journal of the Japanese Breast Cancer Society
https://www.readbyqxmd.com/read/29138865/silencing-of-vacuolar-atpase-c%C3%A2-subunit-atp6v0c-inhibits-the-invasion-of-prostate-cancer-cells-through-a-lass2-tmsg1-independent-manner
#11
Pengcheng Zou, Yifeng Yang, Xiaoyan Xu, Beiying Liu, Fang Mei, Jiangfeng You, Qichen Liu, Fei Pei
Vacuolar ATPase (V-ATPase), widespread in eukaryotic cells, is extensively expressed in many highly metastatic tumors, of which the V-ATPase c subunit ATP6V0C is particularly associated with the invasion and metastasis of cancer. ATP6V0C was directly found to interact with LASS2/TMSG1 which is a new tumor metastasis inhibitory gene identified by our laboratory in 1999. In order to study the role of ATP6V0C, we generated small interference RNA (siRNA) targeting ATP6V0C and investigated its function on the invasion of human prostate cancer cell line PC-3M-1E8 with high metastatic potential and its interplay with LASS2/TMSG1...
November 10, 2017: Oncology Reports
https://www.readbyqxmd.com/read/29138446/antimicrobial-resistance-and-genetic-diversity-in-ceftazidime-non-susceptible-bacterial-pathogens-from-ready-to-eat-street-foods-in-three-taiwanese-cities
#12
Lin Lin, Sheng-Fan Wang, Tsung-Ying Yang, Wei-Chun Hung, Min-Yu Chan, Sung-Pin Tseng
Bacterial contamination of ready-to-eat (RTE) street foods is a major concern worldwide. Dissemination of antibiotic resistant pathogens from food is an emerging public-health threat. To investigate the prevalence of antibiotic resistance genes and ceftazidime resistance-associated efflux pumps in foodborne pathogens, 270 RTE street foods samples were collected in three densely populated Taiwanese cities. Among 70 ceftazidime non-susceptible isolates, 21 Stenotrophomonas maltophilia, 12 Pseudomonas spp., 22 Acinetobacter spp...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136461/enzyme-free-nucleic-acid-amplification-assay-using-a-cellphone-based-well-plate-fluorescence-reader
#13
Donghyuk Kim, Qingshan Wei, Dong Hyeok Kim, Derek Tseng, Jingzi Zhang, Eric Pan, Omai Brandt Garner, Aydogan Ozcan, Dino Di Carlo
Nucleic acids, DNA and RNA, provide important fingerprint information for various pathogens and have significant diag-nostic value; however, improved approaches are urgently needed to enable rapid detection of nucleic acids in simple point-of-care formats with high sensitivity and specificity. Here, we present a system that utilizes a series of toehold-triggered hy-bridization/displacement reactions that are designed to convert a given amount of RNA molecules (i.e., the analyte) into an amplified amount of signaling molecules without any washing steps or thermocycling...
November 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29136199/site-specific-dual-color-labeling-of-long-rnas-for-single-molecule-spectroscopy
#14
Meng Zhao, Fabio D Steffen, Richard Börner, Michelle F Schaffer, Roland K O Sigel, Eva Freisinger
Labeling of long RNA molecules in a site-specific yet generally applicable manner is integral to many spectroscopic applications. Here we present a novel covalent labeling approach that is site-specific and scalable to long intricately folded RNAs. In this approach, a custom-designed DNA strand that hybridizes to the RNA guides a reactive group to target a preselected adenine residue. The functionalized nucleotide along with the concomitantly oxidized 3'-terminus can subsequently be conjugated to two different fluorophores via bio-orthogonal chemistry...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29136041/profiling-analysis-of-circulating-microrna-in-peripheral-blood-of-patients-with-class-iv-lupus-nephritis
#15
Elkin Navarro-Quiroz, Lisandro Pacheco-Lugo, Roberto Navarro-Quiroz, Hernan Lorenzi, Pierine España-Puccini, Yirys Díaz-Olmos, Lisneth Almendrales, Valeria Olave, Henry Gonzalez-Torres, Anderson Diaz-Perez, Alex Dominguez, Antonio Iglesias, Raul García, Gustavo Aroca-Martinez
Renal involvement in Systemic Lupus Erythematous (SLE) patients is one of the leading causes of morbidity and a significant contributor to mortality. It's estimated that nearly 50% of SLE individuals develop kidney disease in the first year of the diagnosis. Class IV lupus nephritis (LN-IV) is the class of lupus nephritis most common in Colombian patients with SLE. Altered miRNAs expression levels have been reported in human autoimmune diseases including lupus. Variations in the expression pattern of peripheral blood circulating miRNAs specific for this class of lupus nephritis could be correlated with the pathophysiological status of this group of individuals...
2017: PloS One
https://www.readbyqxmd.com/read/29135031/comparative-proteomics-illustrates-the-molecular-mechanism-of-potato-solanum-tuberosum-l-tuberization-inhibited-by-exogenous-gibberellins-in-vitro
#16
Lixiang Cheng, Yuping Wang, Yueshan Liu, Qingquan Zhang, Huihui Gao, Zhang Feng
Among the multiple environmental signals and hormonal factors regulating potato tuberization, gibberellins (GAs) are important components of the signaling pathways in these processes. To understand the GAs-signaling response mechanism of potato tuberization, a comparative proteomics approach was applied to analyze proteome change of potato tuberization in vitro subjected to a range of exogenous GA3 treatments (0, 0.01, 0.1 and 1.0 μΜ) using two-dimensional gel electrophoresis. Quantitative image analyses showed that a total of 37 protein spots have their abundance significantly altered more than 2-fold...
November 14, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/29133898/intertwining-dna-rna-nanocapsules-loaded-with-tumor-neoantigens-as-synergistic-nanovaccines-for-cancer-immunotherapy
#17
Guizhi Zhu, Lei Mei, Harshad D Vishwasrao, Orit Jacobson, Zhantong Wang, Yijing Liu, Bryant C Yung, Xiao Fu, Albert Jin, Gang Niu, Qin Wang, Fuwu Zhang, Hari Shroff, Xiaoyuan Chen
Nanomedicines that co-deliver DNA, RNA, and peptide therapeutics are highly desirable yet remain underdeveloped for cancer theranostics. Herein, we report self-assembled intertwining DNA-RNA nanocapsules (iDR-NCs) that efficiently delivered synergistic DNA CpG and short hairpin RNA (shRNA) adjuvants, as well as tumor-specific peptide neoantigens into antigen presenting cells (APCs) in lymph nodes for cancer immunotherapy. These nanovaccines were prepared by (1) producing tandem CpG and shRNA via concurrent rolling circle replication and rolling circle transcription, (2) self-assembling CpG and shRNA into DNA-RNA microflowers, (3) shrinking microflowers into iDR-NCs using PEG-grafted cationic polypeptides, and (4) physically loading neoantigen into iDR-NCs...
November 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133885/a-conserved-stem-of-the-myxococcus-xanthus-srna-pxr-controls-srna-accumulation-and-multicellular-development
#18
Yuen-Tsu N Yu, Elizabeth Cooper, Gregory J Velicer
The small RNA (sRNA) Pxr negatively controls multicellular fruiting body formation in the bacterium Myxococcus xanthus, inhibiting the transition from growth to development when nutrients are abundant. Like many other prokaryotic sRNAs, Pxr is predicted to fold into three stem loops (SL1-SL3). SL1 and SL2 are highly conserved across the myxobacteria, whereas SL3 is much more variable. SL1 is necessary for the regulatory function of Pxr but the importance of SL3 in this regard is unknown. To test for cis genetic elements required for Pxr function, we deleted the entire pxr gene from a developmentally defective strain that fails to remove Pxr-mediated blockage of development and reintroduced variably truncated fragments of the pxr region to test for their ability to block development...
November 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29133841/nanopore-electric-snapshots-of-an-rna-tertiary-folding-pathway
#19
Xinyue Zhang, Dong Zhang, Chenhan Zhao, Kai Tian, Ruicheng Shi, Xiao Du, Andrew J Burcke, Jing Wang, Shi-Jie Chen, Li-Qun Gu
The chemical properties and biological mechanisms of RNAs are determined by their tertiary structures. Exploring the tertiary structure folding processes of RNA enables us to understand and control its biological functions. Here, we report a nanopore snapshot approach combined with coarse-grained molecular dynamics simulation and master equation analysis to elucidate the folding of an RNA pseudoknot structure. In this approach, single RNA molecules captured by the nanopore can freely fold from the unstructured state without constraint and can be programmed to terminate their folding process at different intermediates...
November 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29133460/elevated-hur-in-pancreas-promotes-a-pancreatitis-like-inflammatory-microenvironment-that-facilitates-tumor-development
#20
Weidan Peng, Narumi Furuuchi, Ludmila Aslanukova, Yu-Hung Huang, Samantha Z Brown, Wei Jiang, Sankar Addya, Vikalp Vishwakarma, Erika Peters, Jonathan R Brody, Dan A Dixon, Janet A Sawicki
Human antigen R (ELAVL1, HuR) is perhaps the best-characterized RNA-binding protein. Through its overexpression in various tumor types, HuR promotes post-transcriptional regulation of target genes in multiple core signaling pathways associated with tumor progression. The role of HuR overexpression in pancreatic tumorigenesis is unknown and led us to explore the consequences of HuR overexpression using a novel transgenic mouse model that has a >2-fold elevation of pancreatic HuR expression. Histologically, HuR overexpressing pancreas displays a fibro-inflammatory response and other pathological features characteristic of chronic pancreatitis...
November 13, 2017: Molecular and Cellular Biology
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