keyword
MENU ▼
Read by QxMD icon Read
search

RNA folding

keyword
https://www.readbyqxmd.com/read/28108407/purification-and-characterization-of-an-extracellular-ribonuclease-from-a-bacillus-sp-rns3-kx966412
#1
Gupta Shruti, Singh Sukhdev, Kanwar Shamsher Singh
Ribonucleases (RNases) catalyze the degradation of ribonucleic acid (RNA) into smaller nucleotides. RNases display angiogenic, neurotoxic, antitumor and immunosuppressive properties. In the present study, an extracellular RNase was successfully purified to homogeneity from a Bacillus sp. RNS3 (KX966412) by salting out at 0-50% ammonium sulphate saturation followed by the gel permeation (Sephadex G-100) chromatography. The multistep purification resulted in 10.4 fold purification of RNase with a yield of 3.12%...
January 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28108340/rna-seq-transcriptome-analysis-of-the-olive-flounder-paralichthys-olivaceus-kidney-response-to-vaccination-with-heat-inactivated-viral-hemorrhagic-septicemia-virus
#2
Jee Youn Hwang, Mun Gyeoung Kwon, Sung-Hee Jung, Myoung Ae Park, Dong-Wook Kim, Wang Sik Cho, Jeong Woo Park, Maeng-Hyun Son
Viral hemorrhagic septicemia (VHS) is a highly contagious disease of cultured flounder caused by VHS virus (VHSV). To develop effective VHSV vaccines, it is essential to understand the molecular mechanisms underlying the host's protective response against VHSV. The purpose of this study is to clarify which genes are involved in the protective response of olive flounder after VHSV vaccination. We first injected olive flounder intraperitoneally with 10(7) TCID50 heat-inactivated VHSV vaccine and evaluated the vaccine efficacy at 20 °C...
January 17, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28107688/sequencing-and-de-novo-assembly-of-visceral-mass-transcriptome-of-the-critically-endangered-land-snail-satsuma-myomphala-annotation-and-ssr-discovery
#3
Se Won Kang, Bharat Bhusan Patnaik, Hee-Ju Hwang, So Young Park, Jong Min Chung, Dae Kwon Song, Hongray Howrelia Patnaik, Jae Bong Lee, Changmu Kim, Soonok Kim, Young-Su Park, Hong Seog Park, Seung-Hwan Park, Yeon Soo Han, Jun Sang Lee, Yong Seok Lee
Satsuma myomphala is critically endangered through loss of natural habitats, predation by natural enemies, and indiscriminate collection. It is a protected species in Korea but lacks genomic resources for an understanding of varied functional processes attributable to evolutionary success under natural habitats. For assessing the genetic information of S. myomphala, we performed for the first time, de novo transcriptome sequencing and functional annotation of expressed sequences using Illumina Next-Generation Sequencing (NGS) platform and bioinformatics analysis...
October 29, 2016: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28107423/characterization-of-the-drug-resistance-profiles-of-patients-infected-with-crf07_bc-using-phenotypic-assay-and-ultra-deep-pyrosequencing
#4
Szu-Wei Huang, Wei-You Li, Wen-Hung Wang, Yu-Ting Lin, Chih-Hung Chou, Marcelo Chen, Hsien-Da Huang, Yen-Hsu Chen, Po-Liang Lu, Sheng-Fan Wang, Shinichi Oka, Yi-Ming Arthur Chen
The usefulness of ultra-deep pyrosequencing (UDPS) for the diagnosis of HIV-1 drug resistance (DR) remains to be determined. Previously, we reported an explosive outbreak of HIV-1 circulating recombinant form (CRF) 07_BC among injection drug users (IDUs) in Taiwan in 2004. The goal of this study was to characterize the DR of CRF07_BC strains using different assays including UDPS. Seven CRF07_BC isolates including 4 from early epidemic (collected in 2004-2005) and 3 from late epidemic (collected in 2008) were obtained from treatment-naïve patient's peripheral blood mononuclear cells...
2017: PloS One
https://www.readbyqxmd.com/read/28106375/acinetodin-and-klebsidin-rna-polymerase-targeting-lasso-peptides-produced-by-human-isolates-of-acinetobacter-gyllenbergii-and-klebsiella-pneumoniae
#5
Mikhail Metelev, Anatolii Arseniev, Leah B Bushin, Konstantin Kuznedelov, Tatiana O Artamonova, Ruslan Kondratenko, Mikhail Khodorkovskii, Mohammad R Seyedsayamdost, Konstantin Severinov
We report the bioinformatic prediction and structural validation of two lasso peptides, acinetodin and klebsidin, encoded by the genomes of several human-associated strains of Acinetobacter and Klebsiella. Computation of the three-dimensional structures of these peptides using NMR NOESY constraints verifies that they contain a lasso motif. Despite the lack of sequence similarity to each other or to microcin J25, a prototypical lasso peptide and transcription inhibitor from Escherichia coli, acinetodin and klebsidin also inhibit transcript elongation by the E...
January 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28105955/small-rna-profiles-in-soybean-primary-root-tips-under-water-deficit
#6
Yun Zheng, Vandana Hivrale, Xiaotuo Zhang, Babu Valliyodan, Christine Lelandais-Brière, Andrew D Farmer, Gregory D May, Martin Crespi, Henry T Nguyen, Ramanjulu Sunkar
BACKGROUND: Soybean (Glycine max) production is significantly hampered by frequent droughts in many regions of the world including the United States. Identifying microRNA (miRNA)-controlled posttranscriptional gene regulation under drought will enhance our understanding of molecular basis of drought tolerance in this important cash crop. Indeed, miRNA profiles in soybean exposed to drought were studied but not from the primary root tips, which is not only a main zone of water uptake but also critical for water stress sensing and signaling...
December 5, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28105110/wt1-shrna-delivery-using-transferrin-conjugated-peg-liposomes-in-an-in-vivo-model-of-melanoma
#7
Santiago Saavedra-Alonso, Pablo Zapata-Benavides, Ana Karina Chavez-Escamilla, Edgar Manilla-Muñoz, Diana Elisa Zamora-Avila, Moisés Armides Franco-Molina, Cristina Rodriguez-Padilla
The global incidence of melanoma is increasing. Mortality from melanoma is influenced primarily by metastasis in advanced stages of the disease. Current treatments are largely ineffective; thus, novel gene delivery approaches that target tumor-specific markers may be useful for the treatment of melanoma. Systemic administration of encapsulated RNA-interference plasmids targeted against tumor cells is a potential alternative therapy for cancer. Formulations of transferrin (Tf)-conjugated polyethylene glycol (PEG) liposomes loaded with short hairpin RNA (shRNA) against WT1 (Lip + RNAi + Tf), PEG liposomes loaded with shRNA against WT1 (Lip + RNAi), Tf-conjugated PEG liposomes loaded with pEGFP-N3 (Lip + GFP + Tf) and saline solution as negative control (untreated) were administered systemically to C57BL/6 mice implanted subcutaneously with a melanoma cell line...
December 2016: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28103507/circular-banp-an-upregulated-circular-rna-that-modulates-cell-proliferation-in-colorectal-cancer
#8
Mingchen Zhu, Yijun Xu, Yun Chen, Feng Yan
Circular RNAs (circRNAs) are recently identified as widespread and diverse endogenous noncoding RNAs that may harbor vital functions in human and animals. However, the role of circRNAs in the process of tumorigenesis and development of colorectal cancer (CRC) remains vague. Here we characterized the circRNA expression profile from three paired CRC cancerous and adjacent normal tissues by human circRNA array, and identified 136 significantly overexpressed circRNAs and 243 downregulated circRNAs in CRC cancerous tissues (>2-fold changes)...
January 16, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28102930/modulation-of-the-thermodynamic-signatures-of-an-rna-thermometer-by-osmolytes-and-salts
#9
Mimi Gao, Loana Arns, Roland Winter
Folding of ribonucleic acids (RNAs) is driven by several factors, such as base pairing and stacking, chain entropy, and ion-mediated electrostatics, which have been studied in great detail. However, the power of background molecules in the cellular milieu is often neglected. Herein, we study the effect of common osmolytes on the folding equilibrium of a hairpin-structured RNA and, using pressure perturbation, provide novel thermodynamic and volumetric insights into the modulation mechanism. The presence of TMAO causes an increased thermal stability and a more positive volume change for the helix-to-coil transition, whereas urea destabilizes the hairpin and leads to an increased expansibility of the unfolded state...
January 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28102265/chemical-and-structural-effects-of-base-modifications-in-messenger-rna
#10
Emily M Harcourt, Anna M Kietrys, Eric T Kool
A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification - the epitranscriptome - is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles...
January 18, 2017: Nature
https://www.readbyqxmd.com/read/28100695/mapping-the-affinity-landscape-of-thrombin-binding-aptamers-on-2-f-ana-dna-chimeric-g-quadruplex-microarrays
#11
Jory Lietard, Hala Abou Assi, Irene Gómez-Pinto, Carlos González, Mark M Somoza, Masad J Damha
In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2'-Fluoroarabinonucleic acid (2'F-ANA) is a prime candidate for such use in microarrays. Indeed, 2'F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered...
January 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28100468/feasibility-of-sample-size-calculation-for-rna-seq-studies
#12
Alicia Poplawski, Harald Binder
Sample size calculation is a crucial step in study design but is not yet fully established for RNA sequencing (RNA-seq) analyses. To evaluate feasibility and provide guidance, we evaluated RNA-seq sample size tools identified from a systematic search. The focus was on whether real pilot data would be needed for reliable results and on identifying tools that would perform well in scenarios with different levels of biological heterogeneity and fold changes (FCs) between conditions. We used simulations based on real data for tool evaluation...
January 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28099441/puma-and-nf-kb-are-cell-signaling-predictors-of-reovirus-oncolysis-of-breast-cancer
#13
Chandini Thirukkumaran, Zhong-Qiao Shi, Ponnampalam Thirukkumaran, Joanne Luider, Karen Kopciuk, Jason Spurrell, Kate Elzinga, Don Morris
BACKGROUND AND PURPOSE: Reovirus is a ubiquitous RNA virus that exploits aberrant signaling pathways for its replication. The oncolytic potential of reovirus against numerous cancers under pre-clinical/clinical conditions has been documented by us and others. Despite its proven clinical activity, the underlying mechanisms of reovirus oncolysis is still not well elucidated. If reovirus therapy is to be optimized for cancer, including breast cancer patients, it is imperative to understand the mechanisms of reovirus oncolysis, especially in treatment of resistant tumour...
2017: PloS One
https://www.readbyqxmd.com/read/28098980/ruthenium-ii-complex-based-luminescent-bifunctional-probe-for-ag-and-phosphate-ions-ag-assisted-detection-and-imaging-of-rrna
#14
Sanjoy Kumar Sheet, Bhaskar Sen, Romita Thounaojam, Kripamoy Aguan, Snehadrinarayan Khatua
A new bis-heteroleptic Ru(II) complex (1) of benzimidazole-substituted 1,2,3-triazole pyridine ligand has been designed and constructed for the photoluminescent detection of cationic and anionic analytes, Ag(+) and phosphate ions. Compound, 1[PF6]2 was fully characterized by various spectroscopic techniques and the solid-state structure was determined via single-crystal X-ray diffraction. The cation and anion sensing properties in 50% aqueous buffer (pH 9.2) and pure acetonitrile were carefully examined in photoluminescence (PL) spectroscopy...
January 18, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28096489/induced-packaging-of-cellular-micrornas-into-hiv-1-virions-can-inhibit-infectivity
#15
Hal P Bogerd, Edward M Kennedy, Adam W Whisnant, Bryan R Cullen
: Analysis of the incorporation of cellular microRNAs (miRNAs) into highly purified HIV-1 virions revealed that this largely, but not entirely, mirrored the level of miRNA expression in the producer CD4(+) T cells. Specifically, of the 58 cellular miRNAs detected at significant levels in the producer cells, only 5 were found in virions at a level 2- to 4-fold higher than that predicted on the basis of random cytoplasmic sampling. Of note, these included two miRNAs, miR-155 and miR-92a, that were reported previously to at least weakly bind HIV-1 transcripts...
January 17, 2017: MBio
https://www.readbyqxmd.com/read/28096444/single-molecule-fret-rosetta-reveals-rna-structural-rearrangements-during-human-telomerase-catalysis
#16
Joseph W Parks, Kalli Kappel, Rhiju Das, Michael D Stone
Maintenance of telomeres by telomerase permits continuous proliferation of rapidly dividing cells, including the majority of human cancers. Despite its direct biomedical significance, the architecture of the human telomerase complex remains unknown. Generating homogeneous telomerase samples has presented a significant barrier to developing improved structural models. Here we pair single-molecule Förster resonance energy transfer (smFRET) measurements with Rosetta modeling to map the conformations of the essential telomerase RNA core domain within the active ribonucleoprotein...
February 2017: RNA
https://www.readbyqxmd.com/read/28096403/crystal-structure-of-pistol-a-class-of-self-cleaving-ribozyme
#17
Laura A Nguyen, Jimin Wang, Thomas A Steitz
Small self-cleaving ribozymes have been discovered in all evolutionary domains of life. They can catalyze site-specific RNA cleavage, and as a result, they have relevance in gene regulation. Comparative genomic analysis has led to the discovery of a new class of small self-cleaving ribozymes named Pistol. We report the crystal structure of Pistol at 2.97-Å resolution. Our results suggest that the Pistol ribozyme self-cleavage mechanism likely uses a guanine base in the active site pocket to carry out the phosphoester transfer reaction...
January 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28096217/high-throughput-analysis-reveals-novel-maternal-germline-rnas-crucial-for-primordial-germ-cell-preservation-and-proper-migration
#18
Dawn A Owens, Amanda M Butler, Tristan H Aguero, Karen M Newman, Derek Van Booven, Mary Lou King
During oogenesis, hundreds of maternal RNAs are selectively localized to the animal or vegetal pole, including determinants of somatic and germline fates. Although microarray analysis has identified localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high-throughput RNA-sequencing analysis to comprehensively interrogate animal and vegetal pole RNAs in the fully grown Xenopus laevis oocyte. We identified 411 (198 annotated) and 27 (15 annotated) enriched mRNAs at the vegetal and animal pole, respectively...
January 15, 2017: Development
https://www.readbyqxmd.com/read/28094339/massive-effect-on-lncrnas-in-human-monocytes-during-fungal-and-bacterial-infections-and-in-response-to-vitamins-a-and-d
#19
Konstantin Riege, Martin Hölzer, Tilman E Klassert, Emanuel Barth, Julia Bräuer, Maximilian Collatz, Franziska Hufsky, Nelly Mostajo, Magdalena Stock, Bertram Vogel, Hortense Slevogt, Manja Marz
Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown...
January 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28091876/hypermethylation-of-ifn-%C3%AE-in-oral-cancer-tissues
#20
Songbo Tian, Chunyang Jiang, Xiaoqin Liu, Sheng Xu, Zhiyong Zhang, Huizhen Chen, Yinghuai Zhang, Yanping Liu, Dong Ma
OBJECTIVES: The study aimed to evaluate the methylation pattern of the interferon-gamma (IFN-γ) gene in oral cancer tissues compared with normal and benign oral disease tissues. MATERIALS AND METHODS: The oral tissues were gained from the patients of 85 cases of oral squamous cell carcinoma (OSCC), 47 cases of oral dysplastic lesions, and 53 normal biopsies. IFN -γ methylation in oral tissues was verified through methylation-specific polymerase chain reaction (PCR) and DNA sequencing analyses, and the expression levels of IFN-γ messenger RNA (mRNA) and protein were detected using real-time reverse transcription (RT)-PCR and enzyme-linked immunosorbent assays, respectively...
January 13, 2017: Clinical Oral Investigations
keyword
keyword
60696
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"