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RNA folding

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https://www.readbyqxmd.com/read/27905873/comparative-genomics-of-beauveria-bassiana-uncovering-signatures-of-virulence-against-mosquitoes
#1
Claudio A Valero-Jiménez, Luigi Faino, Daphne Spring In't Veld, Sandra Smit, Bas J Zwaan, Jan A L van Kan
BACKGROUND: Entomopathogenic fungi such as Beauveria bassiana are promising biological agents for control of malaria mosquitoes. Indeed, infection with B. bassiana reduces the lifespan of mosquitoes in the laboratory and in the field. Natural isolates of B. bassiana show up to 10-fold differences in virulence between the most and the least virulent isolate. In this study, we sequenced the genomes of five isolates representing the extremes of low/high virulence and three RNA libraries, and applied a genome comparison approach to uncover genetic mechanisms underpinning virulence...
December 1, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27904556/the-effect-of-%C3%AF-fatty-acids-on-the-expression-of-phospholipase-a2-group-2a-in-human-gastric-cancer-patients
#2
Mahboube Shariati, Mahmoud Aghaei, Ahmad Movahedian, Mohammad Hosein Somi, Homayun Dolatkhah, Ahmad Mirza Aghazade
BACKGROUND: Studies show that polyunsaturated fatty acids (PUFAs) may have an inhibitory role in carcinogenesis. It was previously shown that PLA2 group 2A (PLA2G2A) messenger RNA (mRNA) expression is associated with less frequent metastasis and longer survival in gastric adenocarcinoma. This study intends to investigate the effect of PUFAs on the expression of PLA2G2A in patients with gastric cancer. MATERIALS AND METHODS: Thirty-four patients with gastric cancer (GC) were randomly divided into two groups...
2016: Journal of Research in Medical Sciences: the Official Journal of Isfahan University of Medical Sciences
https://www.readbyqxmd.com/read/27902775/determinants-of-trna-recognition-by-the-radical-sam-enzyme-rlmn
#3
Christina M Fitzsimmons, Danica Galonić Fujimori
RlmN, a bacterial radical SAM methylating enzyme, has the unusual ability to modify two distinct types of RNA: 23S rRNA and tRNA. In rRNA, RlmN installs a methyl group at the C2 position of A2503 of 23S rRNA, while in tRNA the modification occurs at nucleotide A37, immediately adjacent to the anticodon triplet. Intriguingly, only a subset of tRNAs that contain an adenosine at position 37 are substrates for RlmN, suggesting that the enzyme carefully probes the highly conserved tRNA fold and sequence features to identify its targets...
2016: PloS One
https://www.readbyqxmd.com/read/27902457/tfdp3-confers-chemoresistance-in-minimal-residual-disease-within-childhood-t-cell-acute-lymphoblastic-leukemia
#4
Ming Chu, Kailin Yin, Yujun Dong, Pingzhang Wang, Yun Xue, Peng Zhou, Yuqi Wang, Yuedan Wang
Acquired drug resistance in childhood T-cell acute lymphoblastic leukemia (T-ALL) remains a significant clinical problem. In this study, a novel gene therapy target for childhood T-ALL to overcome chemoresistance was discovered: TFDP3 increased in the minimal residual disease (MRD) positive childhood T-ALL patients. Then, we established a preclinical model of resistance to induction therapy to examine the functional relevance of TFDP3 to chemoresistance in MRD derived from Jurkat/E6-1. Jurkat xenografts in NOD/SCID mice were exposed to a four drug combination (VXLD) of vincristine (VCR), dexamethasone (DEX), L-asparaginase (L-asp) and daunorubicin (DNR)...
November 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/27901112/depletion-of-trna-halves-enables-effective-small-rna-sequencing-of-low-input-murine-serum-samples
#5
Alan Van Goethem, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Liselot M Mus, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Tom Van Maerken, Jo Vandesompele
The ongoing ascent of sequencing technologies has enabled researchers to gain unprecedented insights into the RNA content of biological samples. MiRNAs, a class of small non-coding RNAs, play a pivotal role in regulating gene expression. The discovery that miRNAs are stably present in circulation has spiked interest in their potential use as minimally-invasive biomarkers. However, sequencing of blood-derived samples (serum, plasma) is challenging due to the often low RNA concentration, poor RNA quality and the presence of highly abundant RNAs that dominate sequencing libraries...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899983/hur-and-podoplanin-expression-is-associated-with-a-high-risk-of-malignant-transformation-in-patients-with-oral-preneoplastic-lesions
#6
Umma Habiba, Tetsuya Kitamura, Aya Yanagawa-Matsuda, Fumihiro Higashino, Kyoko Hida, Yasunori Totsuka, Masanobu Shindoh
The risk of malignant transformation in oral preneoplastic lesions (OPLs) is challenging to assess. The objective of the present study was to determine the expression of ELAV like RNA binding protein 1 (HuR) and podoplanin in OPLs, and to evaluate the use of each protein as biomarkers for the risk assessment of malignant transformations. Immunohistochemistry for HuR and podoplanin was performed on the tissues of 51 patients with OPL, including cases of low grade dysplasia (LGD) and high grade dysplasia (HGD)...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27899638/structure-and-folding-of-the-tetrahymena-telomerase-rna-pseudoknot
#7
Darian D Cash, Juli Feigon
Telomerase maintains telomere length at the ends of linear chromosomes using an integral telomerase RNA (TER) and telomerase reverse transcriptase (TERT). An essential part of TER is the template/pseudoknot domain (t/PK) which includes the template, for adding telomeric repeats, template boundary element (TBE), and pseudoknot, enclosed in a circle by stem 1. The Tetrahymena telomerase holoenzyme catalytic core (p65-TER-TERT) was recently modeled in our 9 Å resolution cryo-electron microscopy map by fitting protein and TER domains, including a solution NMR structure of the Tetrahymena pseudoknot...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899615/raid-v2-0-an-updated-resource-of-rna-associated-interactions-across-organisms
#8
Ying Yi, Yue Zhao, Chunhua Li, Lin Zhang, Huiying Huang, Yana Li, Lanlan Liu, Ping Hou, Tianyu Cui, Puwen Tan, Yongfei Hu, Ting Zhang, Yan Huang, Xiaobo Li, Jia Yu, Dong Wang
With the development of biotechnologies and computational prediction algorithms, the number of experimental and computational prediction RNA-associated interactions has grown rapidly in recent years. However, diverse RNA-associated interactions are scattered over a wide variety of resources and organisms, whereas a fully comprehensive view of diverse RNA-associated interactions is still not available for any species. Hence, we have updated the RAID database to version 2.0 (RAID v2.0, www.rna-society.org/raid/) by integrating experimental and computational prediction interactions from manually reading literature and other database resources under one common framework...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898685/high-resolution-phenotypic-landscape-of-the-rna-polymerase-ii-trigger-loop
#9
Chenxi Qiu, Olivia C Erinne, Jui M Dave, Ping Cui, Huiyan Jin, Nandhini Muthukrishnan, Leung K Tang, Sabareesh Ganesh Babu, Kenny C Lam, Paul J Vandeventer, Ralf Strohner, Jan Van den Brulle, Sing-Hoi Sze, Craig D Kaplan
The active sites of multisubunit RNA polymerases have a "trigger loop" (TL) that multitasks in substrate selection, catalysis, and translocation. To dissect the Saccharomyces cerevisiae RNA polymerase II TL at individual-residue resolution, we quantitatively phenotyped nearly all TL single variants en masse. Three mutant classes, revealed by phenotypes linked to transcription defects or various stresses, have distinct distributions among TL residues. We find that mutations disrupting an intra-TL hydrophobic pocket, proposed to provide a mechanism for substrate-triggered TL folding through destabilization of a catalytically inactive TL state, confer phenotypes consistent with pocket disruption and increased catalysis...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27898392/colocalization-of-distant-chromosomal-loci-in-space-in-e-coli-a-bacterial-nucleolus
#10
Tamas Gaal, Benjamin P Bratton, Patricia Sanchez-Vazquez, Alexander Sliwicki, Kristine Sliwicki, Andrew Vegel, Rachel Pannu, Richard L Gourse
The spatial organization of DNA within the bacterial nucleoid remains unclear. To investigate chromosome organization in Escherichia coli, we examined the relative positions of the ribosomal RNA (rRNA) operons in space. The seven rRNA operons are nearly identical and separated from each other by as much as 180° on the circular genetic map, a distance of ≥2 million base pairs. By inserting binding sites for fluorescent proteins adjacent to the rRNA operons and then examining their positions pairwise in live cells by epifluorescence microscopy, we found that all but rrnC are in close proximity...
October 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27897091/inducing-mutations-through-%C3%AE-irradiation-in-seeds-of-mucuna-pruriens-for-developing-high-l-dopa-yielding-genotypes
#11
Susheel Kumar Singh, Deepti Yadav, Raj Kishori Lal, Madan M Gupta, Sunita Singh Dhawan
PURPOSE: To develop elite genotypes in Mucuna pruriens (L.) DC with high L-DOPA (L-3, 4 dihydroxyphenylalanine) yields, with non-itching characteristics and better adaptability by applying γ-irradiation. Molecular and chemical analysis was performed for screening based on specific characteristics desired for developing suitable genotypes. MATERIALS AND METHODS: Developed, mutant populations were analyzed for L-DOPA % in seeds through TLC (thin layer chromatography), and the results obtained were validated with the HPLC (High performance liquid chromatography)...
November 29, 2016: International Journal of Radiation Biology
https://www.readbyqxmd.com/read/27895787/runx2-expression-a-mesenchymal-stem-marker-for-cancer
#12
Maria Teresa Valenti, Paola Serafini, Giulio Innamorati, Anna Gili, Samuele Cheri, Claudio Bassi, Luca Dalle Carbonare
The transcription factor runt-related transcription factor 2 (Runx2) is a master gene implicated in the osteogenic differentiation of mesenchymal stem cells, and thus serves a determinant function in bone remodelling and skeletal integrity. Various signalling pathways regulate Runx2 abundance, which requires a number of molecules to finely modulate its expression. Furthermore, this gene may be ectopically-expressed in cancer cells. Recent studies have reported the involvement of Runx2 in cell proliferation, epithelial-mesenchymal transition, apoptosis and metastatic processes, suggesting it may represent a useful therapeutic target in cancer treatment...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27895662/muscle-enriched-micrornas-isolated-from-whole-blood-are-regulated-by-exercise-and-are-potential-biomarkers-of-cardiorespiratory-fitness
#13
Joshua Denham, Priscilla R Prestes
MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally. Evidence indicating miRNAs influence exercise-induced health and performance adaptations is mounting. Circulating miRNAs are responsible for intercellular communication and could serve as biomarkers for disease and exercise-related traits. Such biomarkers would contribute to exercise screening, monitoring, and the development of personalized exercise prescription. Accordingly, we investigated the impact of long-term strenuous aerobic exercise training and a single bout of maximal aerobic exercise on five muscle-enriched miRNAs implicated in exercise adaptations (miR-1, miR-133a, miR-181a, miR-486, and miR-494)...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27895013/frequent-cross-resistance-to-dapivirine-in-hiv-1-subtype-c-infected-individuals-on-failing-first-line-antiretroviral-therapy-in-south-africa
#14
Kerri J Penrose, Carole L Wallis, Chanson J Brumme, Kristen A Hamanishi, Kelley C Gordon, Raquel V Viana, P Richard Harrigan, John W Mellors, Urvi M Parikh
BACKGROUND: A vaginal ring containing dapivirine (DPV) has shown moderate protective efficacy against HIV-1 acquisition, but the activity of DPV against efavirenz (EFV)- and nevirapine (NVP)-resistant viruses that could be transmitted is not well-defined. We investigated DPV cross-resistance of subtype C HIV-1 from individuals on failing NVP- or EFV-containing antiretroviral therapy (ART) in South Africa (SA). METHODS: Plasma samples were obtained from individuals with >10,000 copies/mL HIV RNA and with HIV-1 containing at least one non-nucleoside reverse transcriptase (NNRTI) mutation...
November 28, 2016: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/27893851/expression-and-regulation-of-piwil-proteins-and-piwi-interacting-rnas-in-rheumatoid-arthritis
#15
Lenka Pleštilová, Michel Neidhart, Giancarlo Russo, Mojca Frank-Bertoncelj, Caroline Ospelt, Adrian Ciurea, Christoph Kolling, Renate E Gay, Beat A Michel, Jiří Vencovský, Steffen Gay, Astrid Jüngel
OBJECTIVE: The PIWIL (P-element induced wimpy testis like protein) subfamily of argonaute proteins is essential for Piwi-interacting RNA (piRNA) biogenesis and their function to silence transposons during germ-line development. Here we explored their presence and regulation in rheumatoid arthritis (RA). METHODS: The expression of PIWIL genes in RA and osteoarthritis (OA) synovial tissues and synovial fibroblasts (SF) was analysed by Real-time PCR, immunofluorescence and Western blot...
2016: PloS One
https://www.readbyqxmd.com/read/27893832/evolutionary-algorithm-for-rna-secondary-structure-prediction-based-on-simulated-shape-data
#16
Soheila Montaseri, Mohammad Ganjtabesh, Fatemeh Zare-Mirakabad
BACKGROUND: Non-coding RNAs perform a wide range of functions inside the living cells that are related to their structures. Several algorithms have been proposed to predict RNA secondary structure based on minimum free energy. Low prediction accuracy of these algorithms indicates that free energy alone is not sufficient to predict the functional secondary structure. Recently, the obtained information from the SHAPE experiment greatly improves the accuracy of RNA secondary structure prediction by adding this information to the thermodynamic free energy as pseudo-free energy...
2016: PloS One
https://www.readbyqxmd.com/read/27891095/differential-rna-expression-profile-of-skeletal-muscle-induced-by-experimental-autoimmune-myasthenia-gravis-in-rats
#17
Henry J Kaminski, Keiichi Himuro, Jumana Alshaikh, Bendi Gong, Georgiana Cheng, Linda L Kusner
The differential susceptibility of skeletal muscle by myasthenia gravis (MG) is not well understood. We utilized RNA expression profiling of extraocular muscle (EOM), diaphragm (DIA), and extensor digitorum (EDL) of rats with experimental autoimmune MG (EAMG) to evaluate the hypothesis that muscles respond differentially to injury produced by EAMG. EAMG was induced in female Lewis rats by immunization with acetylcholine receptor purified from the electric organ of the Torpedo. Six weeks later after rats had developed weakness and serum antibodies directed against the AChR, animals underwent euthanasia and RNA profiling performed on DIA, EDL, and EOM...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27890659/rna-nanoparticles-harboring-annexin-a2-aptamer-can-target-ovarian-cancer-for-tumor-specific-doxorubicin-delivery
#18
Fengmei Pi, Hui Zhang, Hui Li, Varatharasa Thiviyanathan, David G Gorenstein, Anil K Sood, Peixuan Guo
A novel modified nucleic acid nanoparticle harboring an annexin A2 aptamer for ovarian cancer cell targeting and a GC rich sequence for doxorubicin loading is designed and constructed. The system utilizes a highly stable three-way junction (3WJ) motif from phi29 packaging RNA as a core structure. A phosphorothioate-modified DNA aptamer targeting annexin A2, Endo28, was conjugated to one arm of the 3WJ. The pRNA-3WJ motif retains correct folding of attached aptamer, keeping its functions intact. It is of significant utility for aptamer-mediated targeted delivery...
November 24, 2016: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/27889431/multiclass-cancer-classification-using-a-feature-subset-based-ensemble-from-microrna-expression-profiles
#19
Yongjun Piao, Minghao Piao, Keun Ho Ryu
Cancer classification has been a crucial topic of research in cancer treatment. In the last decade, messenger RNA (mRNA) expression profiles have been widely used to classify different types of cancers. With the discovery of a new class of small non-coding RNAs; known as microRNAs (miRNAs), various studies have shown that the expression patterns of miRNA can also accurately classify human cancers. Therefore, there is a great demand for the development of machine learning approaches to accurately classify various types of cancers using miRNA expression data...
November 21, 2016: Computers in Biology and Medicine
https://www.readbyqxmd.com/read/27889295/novel-t7-like-expression-systems-used-for-halomonas
#20
Han Zhao, Haoqian M Zhang, Xiangbin Chen, Teng Li, Qiong Wu, Qi Ouyang, Guo-Qiang Chen
To engineer non-model organisms, suitable genetic parts must be available. However, biological parts are often host strain sensitive. It is therefore necessary to develop genetic parts that are functional regardless of host strains. Here we report several novel phage-derived expression systems used for transcriptional control in non-model bacteria. Novel T7-like RNA polymerase-promoter pairs were obtained by mining phage genomes, followed by in vivo characterization in non-model strains Halomonas spp TD01 and Pseudomonas entomophila...
November 24, 2016: Metabolic Engineering
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