keyword
MENU ▼
Read by QxMD icon Read
search

RNA folding

keyword
https://www.readbyqxmd.com/read/28651352/circular-rna-profiling-reveals-that-circular-rnas-from-anxa2-can-be-used-as-new-biomarkers-for-multiple-sclerosis
#1
Iparraguirre Leire, Muñoz-Culla Maider, Prada Iñigo, Castillo-Triviño Tamara, Olascoaga Javier, Otaegui David
Multiple Sclerosis is an autoimmune disease, with higher prevalence in women, in whom the immune system is dysregulated. This dysregulation has been shown to correlate with changes in transcriptome expression as well as in gene-expression regulators, such as non-coding RNAs (e.g. microRNAs). Indeed, some of these have been suggested as biomarkers for multiple sclerosis even though few biomarkers have reached the clinical practice.Recently, a novel family of non-coding RNAs, circular RNAs, has emerged as a new player in the complex network of gene-expression regulation...
June 23, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28650973/interferon-signaling-in-peromyscus-leucopus-confers-a-potent-and-specific-restriction-to-vector-borne-flaviviruses
#2
Adaeze O Izuogu, Kristin L McNally, Stephen E Harris, Brian H Youseff, John B Presloid, Christopher Burlak, Jason Munshi-South, Sonja M Best, R Travis Taylor
Tick-borne flaviviruses (TBFVs), including Powassan virus and tick-borne encephalitis virus cause encephalitis or hemorrhagic fevers in humans with case-fatality rates ranging from 1-30%. Despite severe disease in humans, TBFV infection of natural rodent hosts has little noticeable effect. Currently, the basis for resistance to disease is not known. We hypothesize that the coevolution of flaviviruses with their respective hosts has shaped the evolution of potent antiviral factors that suppress virus replication and protect the host from lethal infection...
2017: PloS One
https://www.readbyqxmd.com/read/28649752/investigating-dna-rna-and-protein-based-features-as-a-means-to-discriminate-pathogenic-synonymous-variants
#3
Mark Livingstone, Lukas Folkman, Yuedong Yang, Ping Zhang, Matthew Mort, David N Cooper, Yunlong Liu, Bela Stantic, Yaoqi Zhou
Synonymous single nucleotide variants (SNVs), although they do not alter the encoded protein sequences, have been implicated in many genetic diseases. Experimental studies indicate that synonymous SNVs can lead to changes in the secondary and tertiary structures of DNA and RNA, thereby impacting translational efficiency, co-translational protein folding as well as the binding of DNA/RNA-binding proteins. However, the importance of these various features in disease phenotypes is not clearly understood. Here we have built a support vector machine model (termed DDIG-SN) as a means to discriminate disease-causing synonymous variants...
June 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28649626/investigation-of-simulated-microgravity-effects-on-streptococcus-mutans-physiology-and-global-gene-expression
#4
Silvia S Orsini, April M Lewis, Kelly C Rice
Astronauts have been previously shown to exhibit decreased salivary lysozyme and increased dental calculus and gingival inflammation in response to space flight, host factors that could contribute to oral diseases such as caries and periodontitis. However, the specific physiological response of caries-causing bacteria such as Streptococcus mutans to space flight and/or ground-based simulated microgravity has not been extensively investigated. In this study, high aspect ratio vessel S. mutans simulated microgravity and normal gravity cultures were assessed for changes in metabolite and transcriptome profiles, H2O2 resistance, and competence in sucrose-containing biofilm media...
2017: NPJ Microgravity
https://www.readbyqxmd.com/read/28648844/novel-functions-for-the-rna-binding-protein-etr-1-in-caenorhabditis-elegans-reproduction-and-engulfment-of-germline-apoptotic-cell-corpses
#5
Ruby Boateng, Ken C Q Nguyen, David H Hall, Andy Golden, Anna K Allen
RNA-binding proteins (RBPs) are essential regulators of gene expression that act through a variety of mechanisms to ensure the proper post-transcriptional regulation of their target RNAs. RBPs in multiple species have been identified as playing crucial roles during development and as having important functions in various adult organ systems, including the heart, nervous, muscle, and reproductive systems. ETR-1, a highly conserved ELAV-Type RNA-binding protein belonging to the CELF/Bruno protein family, has been previously reported to be involved in C...
June 22, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28648754/what-can-human-guided-simulations-bring-to-rna-folding
#6
Liuba Mazzanti, Sébastien Doutreligne, Cedric Gageat, Philippe Derreumaux, Antoine Taly, Marc Baaden, Samuela Pasquali
Inspired by the recent success of scientific-discovery games for predicting protein tertiary and RNA secondary structures, we have developed an open software for coarse-grained RNA folding simulations, guided by human intuition. To determine the extent to which interactive simulations can accurately predict 3D RNA structures of increasing complexity and lengths (four RNAs with 22-47 nucleotides), an interactive experiment was conducted with 141 participants who had very little knowledge of nucleic acids systems and computer simulations, and had received only a brief description of the important forces stabilizing RNA structures...
June 22, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28647196/smooth-muscle-cells-of-human-veins-show-an-increased-response-to-injury-at-valve-sites
#7
Shinsuke Kikuchi, Lihua Chen, Kevin Xiong, Yukihiro Saito, Nobuyoshi Azuma, Gale Tang, Michael Sobel, Thomas N Wight, Richard D Kenagy
OBJECTIVE: Venous valves are essential but are prone to injury, thrombosis, and fibrosis. We compared the behavior and gene expression of smooth muscle cells (SMCs) in the valve sinus vs nonvalve sites to elucidate biologic differences associated with vein valves. METHODS: Tissue explants of fresh human saphenous veins were prepared, and the migration of SMCs from explants of valve sinus vs nonvalve sinus areas was measured. Proliferation and death of SMCs were determined by staining for Ki67 and terminal deoxynucleotidyl transferase dUTP nick end labeling...
June 21, 2017: Journal of Vascular Surgery
https://www.readbyqxmd.com/read/28645721/comparison-of-different-inactivation-methods-on-the-stability-of-indian-vaccine-strains-of-foot-and-mouth-disease-virus
#8
Arunava Sarkar, Ramasamy Periyasamy Tamil Selvan, Subodh Kishore, Kondabattula Ganesh, Veerakyathappa Bhanuprakash
In this study, the efficiency of binary ethyleneimine (BEI) in combination with formaldehyde (FA) and glutaraldehyde (GTA) in inactivating the Indian FMDV vaccine strains is compared. The acceptable safety of virus inactivation was faster and the inactivation rates were increased many-folds with combination of inactivants than BEI alone. FMDV A was inactivated rapidly than the other two serotypes with BEI + FA combination. Inactivation plots were linear for all the serotypes irrespective of inactivation process...
June 20, 2017: Biologicals: Journal of the International Association of Biological Standardization
https://www.readbyqxmd.com/read/28645305/high-expression-of-collagen-triple-helix-repeat-containing-1-cthrc1-facilitates-progression-of-oesophageal-squamous-cell-carcinoma-through-mapk-mek-erk-fra-1-activation
#9
Chunni Wang, Zitong Li, Fei Shao, Xueying Yang, Xiaoli Feng, Susheng Shi, Yibo Gao, Jie He
BACKGROUND: Oesophageal cancer is one of the most common malignancies worldwide,and oesophageal squamous cell carcinoma (ESCC) is the predominant histological type both globally and in China. Collagen triple helix repeat containing 1 (CTHRC1) has been found to be upregulated in ESCC. However, its role in tumourigenesis and progression of ESCC remains unclear. METHODS: Using our previous ESCC mRNA profiling data, we screened upregulated genes to identify those required for proliferation...
June 23, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28644873/circular-rna-expression-profiling-of-human-granulosa-cells-during-maternal-aging-reveals-novel-transcripts-associated-with-assisted-reproductive-technology-outcomes
#10
Jing Cheng, Jia Huang, Suzhen Yuan, Su Zhou, Wei Yan, Wei Shen, Yun Chen, Xi Xia, Aiyue Luo, Da Zhu, Shixuan Wang
Circular RNAs (circRNAs) are a unique class of endogenous RNAs which could be used as potential diagnostic and prognostic biomarkers of many diseases. Our study aimed to investigate circRNA profiles in human granulosa cells (GCs) during maternal aging and to uncover age-related circRNA variations that potentially reflect decreased oocyte competence. CircRNAs in GCs from in vitro fertilization (IVF) patients with young age (YA, ≤ 30 years) and advanced age (AA, ≥ 38 years) were profiled by microarray, and validated in 20 paired samples...
2017: PloS One
https://www.readbyqxmd.com/read/28640636/cross-reactive-synbody-affinity-ligands-for-capturing-diverse-noroviruses
#11
Nidhi Gupta, John C Lainson, Paul E Belcher, Luhui Shen, Hugh S Mason, Stephen Albert Johnston, Chris W Diehnelt
Noroviruses are the most common cause of acute gastroenteritis in the developed world. Noroviruses are a diverse group of nonenveloped RNA viruses that are continuously evolving. This leads to the rise of immunologically distinct strains of the same genotype on a frequent basis. This diversity presents a unique challenge for detection and tracking of new strains, with the continuous need for new norovirus affinity ligands. Our group developed a family of bivalent synbody affinity ligands using a virus-like particle (VLP) from the 2006 GII...
June 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28639574/mir-551b-5p-contributes-to-pathogenesis-of-vein-graft-failure-via-upregulating-early-growth-response-1-expression
#12
Ran Dong, Kui Zhang, Yue-Li Wang, Feng Zhang, Jian Cao, Ju-Bing Zheng, Hong-Jia Zhang
BACKGROUND: Vein graft failure (VGF) is a serious complication of coronary artery bypass graft, although the mechanism remains unclear. The study aimed to investigate the effects of microRNAs (miRNAs) on the endothelial dysfunction involved in VGF. METHODS: Human umbilical vein endothelial cells (HUVECs) were subjected to mechanical stretch stimulation to induce endothelial dysfunction. Genome-wide transcriptome profiling was performed using the Human miRNA OneArray® V4 (PhalanxBio Inc...
July 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28639228/role-of-20-hydroxyeicosatetraenoic-acid-20-hete-in-androgen-mediated-cell-viability-in-prostate-cancer-cells
#13
Cecilia Colombero, Daniela Papademetrio, Paula Sacca, Eduardo Mormandi, Elida Alvarez, Susana Nowicki
20-Hydroxyeicosatetraenoic acid (20-HETE) is generated intracellularly through the ω-hydroxylation of arachidonic acid by the cytochrome P450 (in humans, CYP4A11 and CYP4F2). 20-HETE induces mitogenic responses in different cancer cells. The aim of this study was to analyze how 20-HETE impacts cell survival, proliferation, and apoptosis in prostate cancer cells. Incubation of the human androgen-sensitive cells (LNCaP) with 1-10 μM HET0016 (a selective inhibitor of 20-HETE synthesis) reduced cell viability by 49*-64%* (*p < 0...
June 21, 2017: Hormones & Cancer
https://www.readbyqxmd.com/read/28638804/pkc-%C3%AE-marcks-signaling-promotes-intracellular-survival-of-unopsonized-burkholderia-thailandensis
#14
Sofiya N Micheva-Viteva, Yulin Shou, Kumkum Ganguly, Terry H Wu, Elizabeth Hong-Geller
Pathogenic Burkholderia rely on host factors for efficient intracellular replication and are highly refractory to antibiotic treatment. To identify host genes that are required by Burkholderia spp. during infection, we performed a RNA interference (RNAi) screen of the human kinome and identified 35 host kinases that facilitated Burkholderia thailandensis intracellular survival in human monocytic THP-1 cells. We validated a selection of host kinases using imaging flow cytometry to assess efficiency of B. thailandensis survival in the host upon siRNA-mediated knockdown...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28637794/a-trpv1-to-secretagogin-regulatory-axis-controls-pancreatic-%C3%AE-cell-survival-by-modulating-protein-turnover
#15
Katarzyna Malenczyk, Fatima Girach, Edit Szodorai, Petter Storm, Åsa Segerstolpe, Giuseppe Tortoriello, Robert Schnell, Jan Mulder, Roman A Romanov, Erzsébet Borók, Fabiana Piscitelli, Vincenzo Di Marzo, Gábor Szabó, Rickard Sandberg, Stefan Kubicek, Gert Lubec, Tomas Hökfelt, Ludwig Wagner, Leif Groop, Tibor Harkany
Ca(2+)-sensor proteins are generally implicated in insulin release through SNARE interactions. Here, secretagogin, whose expression in human pancreatic islets correlates with their insulin content and the incidence of type 2 diabetes, is shown to orchestrate an unexpectedly distinct mechanism. Single-cell RNA-seq reveals retained expression of the TRP family members in β-cells from diabetic donors. Amongst these, pharmacological probing identifies Ca(2+)-permeable transient receptor potential vanilloid type 1 channels (TRPV1) as potent inducers of secretagogin expression through recruitment of Sp1 transcription factors...
June 21, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28637405/molecular-dynamics-simulations-challenges-and-opportunities-a-biologist-s-prospective
#16
Indu Kumari, Padmani Sandhu, Mushtaq Ahmed, Yusuf Akhter
Molecular dynamics (MD) is a computational technique which is used to study biomolecules in virtual environment. Each of the constituent atoms represents a particle and hence the biomolecule embodies a multi-particle mechanical system analyzed within a simulation box during MD analysis. The potential energies of the atoms are explained by a mathematical expression consisting of different forces and space parameters. There are various software and force fields that have been developed for MD studies of the biomolecules...
June 21, 2017: Current Protein & Peptide Science
https://www.readbyqxmd.com/read/28637286/structure-seq2-sensitive-and-accurate-genome-wide-profiling-of-rna-structure-in-vivo
#17
Laura E Ritchey, Zhao Su, Yin Tang, David C Tack, Sarah M Assmann, Philip C Bevilacqua
RNA serves many functions in biology such as splicing, temperature sensing, and innate immunity. These functions are often determined by the structure of RNA. There is thus a pressing need to understand RNA structure and how it changes during diverse biological processes both in vivo and genome-wide. Here, we present Structure-seq2, which provides nucleotide-resolution RNA structural information in vivo and genome-wide. This optimized version of our original Structure-seq method increases sensitivity by at least 4-fold and improves data quality by minimizing formation of a deleterious by-product, reducing ligation bias, and improving read coverage...
June 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28636618/de-novo-transcriptome-of-the-mayfly-cloeon-viridulum-and-transcriptional-signatures-of-prometabola
#18
Qin Si, Juan-Yan Luo, Ze Hu, Wei Zhang, Chang-Fa Zhou
Mayflies (Ephemeroptera) display many primitive characters and a unique type of metamorphosis (Prometabola). However, information on the genomes and transcriptomes of this insect group is limited. The RNA sequencing study presented here generated the first de novo transcriptome assembly of Cloeon viridulum (Ephemeroptera: Baetidae), and compared gene expression signatures among the young larva (YL), mature larva (ML), subimago (SI), and imago (IM) stages of this mayfly. The transcriptome, based on 88 Gb of sequence data, comprised a set of 81,185 high quality transcripts...
2017: PloS One
https://www.readbyqxmd.com/read/28636433/immunogenicity-of-ags-004-dendritic-cell-therapy-in-patients-treated-during-acute-hiv-infection
#19
Cynthia L Gay, Mark A DeBenedette, Irina Y Tcherepanova, Alicia Gamble, Whitney E Lewis, Anna B Cope, JoAnn D Kuruc, Kara S McGee, Mary F Kearney, John M Coffin, Nancie M Archin, Charles B Hicks, Joseph J Eron, Charles A Nicolette, David M Margolis
AGS-004 consists of matured autologous dendritic cells co-electroporated with in vitro transcribed RNA encoding autologous HIV antigens. In an open-label, single arm sub-study of AGS-004-003, AGS-004 was administered monthly to suppressed participants who started antiretroviral therapy (ART) during acute HIV infection. HIV-1 specific T cell responses were measured by multicolor flow cytometry after 3-4 doses. The frequency of resting CD4(+) T-cell infection (RCI) was measured by quantitative viral outgrowth assay...
June 21, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28636268/high-throughput-sequencing-reveals-drosophila-suzukii-responses-to-insecticides
#20
Ruchir Mishra, Joanna C Chiu, Gang Hua, Nilesh R Tawari, Michael J Adang, Ashfaq A Sial
Global climate change and acquired resistance to insecticides are threats to world food security. Drosophila suzukii, a devastating invasive pest in many parts of the world, causes substantial economic losses to fruit production industries, forcing farmers to apply broad-spectrum insecticides frequently. This could lead to the development of insecticide resistance. We determined the Lethal Concentration50 (median lethal concentration) values of zeta-cypermethrin, spinosad, and malathion insecticides against D...
June 21, 2017: Insect Science
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"