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RNA folding

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https://www.readbyqxmd.com/read/28927104/antisense-rna-transcripts-in-the-blood-may-be-novel-diagnostic-markers-for-colorectal-cancer
#1
Tomohiro Kurokawa, Keisuke Kohno, Kentaro Nagai, Mitsuru Chiba, Sugiru Pak, Soichiro Murata, Kiyoshi Fukunaga, Hiroshi Yasue, Nobuhiro Ohkohchi
Numerous genetic studies have been conducted regarding the occurrence of colorectal cancer (CRC) and the prognosis using microarrays. However, adequate investigations into the diagnostic application of microarrays have yet to be performed. The simplicity and accuracy of diagnosis and prognosis tracking are important requirements for its processes, and the use of blood cells for diagnosis is considered to be suitable to meet these requirements. The patients involved in the study were 28 preoperative patients with CRC and 6 healthy individuals who served as controls...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28927061/5fu-resistance-caused-by-reduced-fluoro-deoxyuridine-monophosphate-and-its-reversal-using-deoxyuridine
#2
Ryutaro Mori, Manabu Futamura, Toshiyuki Tanahashi, Yoshihiro Tanaka, Nobuhisha Matsuhashi, Kazuya Yamaguchi, Kazuhiro Yoshida
The mechanism of 5-fluorouracil (5FU) resistance was investigated, focusing on the level of thymidylate synthase (TS) ternary complex formed with fluoro-deoxyuridine monophosphate (FdUMP). MKN45 and 5FU-resistant MKN45/F2R cells were treated with 5FU and fluoro-deoxyuridine (FdU) in combination with deoxyuridine (dU) and thymidine (dT). Subsequently, the levels of ternary complex were determined by western blotting and the cell viability was calculated using an MTT assay. MKN45/F2R cells exhibited 5FU resistance (56...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28925390/alterations-of-micrornas-throughout-the-malignant-evolution-of-cutaneous-squamous-cell-carcinoma-the-role-of-mir-497-in-epithelial-to-mesenchymal-transition-of-keratinocytes
#3
A Mizrahi, A Barzilai, D Gur-Wahnon, I Z Ben-Dov, S Glassberg, T Meningher, E Elharar, M Masalha, J Jacob-Hirsch, H Tabibian-Keissar, I Barshack, J Roszik, R Leibowitz-Amit, Y Sidi, D Avni
Skin carcinogenesis is known to be a multi-step process with several stages along its malignant evolution. We hypothesized that transformation of normal epidermis to cutaneous squamous cell carcinoma (cSCC) is causally linked to alterations in microRNAs (miRNA) expression. For this end we decided to evaluate their alterations in the pathologic states ending in cSCC. Total RNA was extracted from formalin fixed paraffin embedded biopsies of five stages along the malignant evolution of keratinocytes towards cSCC: Normal epidermis, solar elastosis, actinic keratosis KIN1-2, advanced actinic keratosis KIN3 and well-differentiated cSCC...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28925033/polyamine-mediated-stoichiometric-assembly-of-ribonucleoproteins-for-enhanced-mrna-delivery
#4
Jiahe Li, Yanpu He, Wade Wang, Connie Wu, Celestine Hong, Paula T Hammond
Messenger RNA (mRNA) represents a promising class of nucleic acid drugs. Although numerous carriers have been developed for mRNA delivery, the inefficient mRNA expression inside cells remains a major challenge. Inspired by the dependence of mRNA on 3'-terminal polyadenosine nucleotides (poly A) and poly A binding proteins (PABPs) for optimal expression, we complexed synthetic mRNA containing a poly A tail with PABPs in a stoichiometric manner and stabilized the ribonucleoproteins (RNPs) with a family of polypeptides bearing different arrangements of cationic side groups...
September 19, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28924037/intrinsically-disordered-sequences-enable-modulation-of-protein-phase-separation-through-distributed-tyrosine-motifs
#5
Yuan Lin, Simon L Currie, Michael Keith Rosen
Liquid-liquid phase separation (LLPS) is thought to contribute to establishment of many biomolecular condensates, eukaryotic cell structures that concentrate diverse macromolecules but lack a bounding membrane. RNA granules control RNA metabolism and comprise a large class of condensates that are enriched in RNA-binding proteins and RNA molecules. Many RNA granule proteins are composed of both modular domains and intrinsically disordered regions (IDRs) having low amino acid sequence complexity. Phase separation of these molecules likely plays an important role in the generation and stability of RNA granules...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28923079/endoplasmic-reticulum-stress-cooperates-with-toll-like-receptor-ligation-in-driving-activation-of-rheumatoid-arthritis-fibroblast-like-synoviocytes
#6
Pawel A Kabala, Chiara Angiolilli, Nataliya Yeremenko, Aleksander M Grabiec, Barbara Giovannone, Desiree Pots, Timothy R Radstake, Dominique Baeten, Kris A Reedquist
BACKGROUND: Endoplasmic reticulum (ER) stress has proinflammatory properties, and transgenic animal studies of rheumatoid arthritis (RA) indicate its relevance in the process of joint destruction. Because currently available studies are focused primarily on myeloid cells, we assessed how ER stress might affect the inflammatory responses of stromal cells in RA. METHODS: ER stress was induced in RA fibroblast-like synoviocytes (FLS), dermal fibroblasts, and macrophages with thapsigargin or tunicamycin alone or in combination with Toll-like receptor (TLR) ligands, and gene expression and messenger RNA (mRNA) stability was measured by quantitative polymerase chain reaction...
September 18, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28923054/a-novel-method-for-extracting-nucleic-acids-from-dried-blood-spots-for-ultrasensitive-detection-of-low-density%C3%A2-plasmodium-falciparum-and-plasmodium-vivax%C3%A2-infections
#7
Kayvan Zainabadi, Matthew Adams, Zay Yar Han, Hnin Wai Lwin, Kay Thwe Han, Amed Ouattara, Si Thura, Christopher V Plowe, Myaing M Nyunt
BACKGROUND: Greater Mekong Subregion countries are committed to eliminating Plasmodium falciparum malaria by 2025. Current elimination interventions target infections at parasite densities that can be detected by standard microscopy or rapid diagnostic tests (RDTs). More sensitive detection methods have been developed to detect lower density "asymptomatic" infections that may represent an important transmission reservoir. These ultrasensitive polymerase chain reaction (usPCR) tests have been used to identify target populations for mass drug administration (MDA)...
September 18, 2017: Malaria Journal
https://www.readbyqxmd.com/read/28922406/loss-of-liver-specific-and-sexually-dimorphic-gene-expression-by-aryl-hydrocarbon-receptor-activation-in-c57bl-6-mice
#8
Rance Nault, Kelly A Fader, Jack R Harkema, Tim Zacharewski
The aryl hydrocarbon receptor (AhR) is a highly conserved transcription factor that mediates a broad spectrum of species-, strain-, sex-, age-, tissue-, and cell-specific responses elicited by structurally diverse ligands including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Dose-dependent effects on liver-specific and sexually dimorphic gene expression were examined in male and female mice gavaged with TCDD every 4 days for 28 or 92 days. RNA-seq data revealed the coordinated repression of 181 genes predominately expressed in the liver including albumin (3...
2017: PloS One
https://www.readbyqxmd.com/read/28922109/protein-mediated-rna-folding-governs-sequence-specific-interactions-between-rotavirus-genome-segments
#9
Alexander Borodavka, Eric C Dykeman, Waldemar Schrimpf, Don C Lamb
Segmented RNA viruses are ubiquitous pathogens, which include influenza viruses and rotaviruses. A major challenge in understanding their assembly is the combinatorial problem of a non-random selection of a full genomic set of distinct RNAs. This process involves complex RNA-RNA and protein-RNA interactions, which are often obscured by non-specific binding at concentrations approaching in vivo assembly conditions. Here, we present direct experimental evidence of sequence-specific inter-segment interactions between rotavirus RNAs, taking place in a complex RNA- and protein-rich milieu...
September 18, 2017: ELife
https://www.readbyqxmd.com/read/28921531/a-naive-bayes-algorithm-for-tissue-origin-diagnosis-tod-bayes-of-synchronous-multifocal-tumors-in-the-hepatobiliary-and-pancreatic-system
#10
Weiqin Jiang, Yifei Shen, Yongfeng Ding, Chuyu Ye, Yi Zheng, Peng Zhao, Lulu Liu, Zhou Tong, Linfu Zhou, Shuo Sun, Xingchen Zhang, Lisong Teng, Michael P Timko, Longjiang Fan, Weijia Fang
Synchronous multifocal tumors are common in the hepatobiliary and pancreatic system but because of similarities in their histological features, oncologists have difficulty in identifying their precise tissue clonal origin through routine histopathological methods. To address this problem and assist in more precise diagnosis, we developed a computational approach for tissue origin diagnosis based on naive Bayes algorithm (TOD-Bayes) using ubiquitous RNA-Seq data. Massive tissue-specific RNA-Seq data sets were first obtained from The Cancer Genome Atlas (TCGA) and ∼1,000 feature genes were used to train and validate the TOD-Bayes algorithm...
September 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28921495/probing-rna-folding-pathways-by-rna-fingerprinting
#11
Sarah A Woodson
This unit provides protocols for using native polyacrylamide gel electrophoresis to distinguish folding and unfolding conformers of RNA. It is useful for studying conformers that can exchange in a period of minutes or seconds, and that are thus difficult to study by solution-based methods. Conformers that have been separated and immobilized in the gel matrix can be used to study catalytic activity with or without being eluted from the gel. The method can be applied to a wide variety of catalytic RNAs and RNA-protein complexes...
September 18, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28920960/long-noncoding-rna-egfr-as1-mediates-epidermal-growth-factor-receptor-addiction-and-modulates-treatment-response-in-squamous-cell-carcinoma
#12
Daniel S W Tan, Fui Teen Chong, Hui Sun Leong, Shen Yon Toh, Dawn P Lau, Xue Lin Kwang, Xiaoqian Zhang, Gopinath M Sundaram, Gek San Tan, Mei Mei Chang, Boon Tin Chua, Wan Teck Lim, Eng Huat Tan, Mei Kim Ang, Tony K H Lim, Prabha Sampath, Balram Chowbay, Anders J Skanderup, Ramanuj DasGupta, N Gopalakrishna Iyer
Targeting EGFR is a validated approach in the treatment of squamous-cell cancers (SCCs), although there are no established biomarkers for predicting response. We have identified a synonymous mutation in EGFR, c.2361G>A (encoding p.Gln787Gln), in two patients with head and neck SCC (HNSCC) who were exceptional responders to gefitinib, and we showed in patient-derived cultures that the A/A genotype was associated with greater sensitivity to tyrosine kinase inhibitors (TKIs) as compared to the G/A and G/G genotypes...
September 18, 2017: Nature Medicine
https://www.readbyqxmd.com/read/28919414/changes-in-related-circular-rnas-following-er%C3%AE-knockdown-and-the-relationship-to-rbmsc-osteogenesis
#13
Xiaoyun Li, Bojia Peng, Xiaofeng Zhu, Panpan Wang, Yingquan Xiong, Hengrui Liu, Kehuan Sun, Haixia Wang, Ling Ou, Zhidi Wu, Xiaoguang Liu, Haibin He, Shu Mo, Xunqian Peng, Ya Tian, Ronghua Zhang, Li Yang
Recently, several studies have indicated that circular RNAs (circRNAs) play significant roles in various disease; however, Little is known about the chronology of estrogen receptor beta (ERβ) deficiency and altered circRNA expression, or their relationship with osteogenesis. Herein, we show through western-blot and quantitative real-time PCR assays, that when ERβ is silenced, the expression of osteogenesis-related proteins and mRNAs were down-regulated. We then performed RNA-Seq to analyze differential circRNA expression between the control and ERβ knockdown group...
September 15, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28919035/development-of-a-fast-and-efficient-method-for-hepatitis-a-virus-concentration-from-green-onion
#14
Yan Zheng, Yuan Hu
Hepatitis A virus (HAV) can cause serious liver disease and even death. HAV outbreaks are associated with the consumption of raw or minimally processed produce, making it a major public health concern. Infections have occurred despite the fact that effective HAV vaccine has been available. Development of a rapid and sensitive HAV detection method is necessary for an investigation of an HAV outbreak. Detection of HAV is complicated by the lack of a reliable culture method. In addition, due to the low infectious dose of HAV, these methods must be very sensitive...
September 14, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28918093/topological-structure-determination-of-rna-using-small-angle-x-ray-scattering
#15
Yuba R Bhandari, Linxin Fan, Xianyang Fang, George Zaki, Eric A Stahlberg, Wei Jiang, Charles D Schwieters, Jason R Stagno, Yun-Xing Wang
Knowledge of RNA three-dimensional topological structures provides important insight into the relationship between RNA structural components and function. It is often likely that near complete sets of biochemical and biophysical data containing structural restraints are not available but one still wants to obtain knowledge about approximate topological folding of RNA. In this regard, general methods for determining such topological structures with minimum readily available restraints are lacking. Naked RNAs are difficult to crystallize and NMR spectroscopy is generally limited to small RNA fragments...
September 13, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28918047/long-noncoding-rna-bc032913-as-a-novel-therapeutic-target-for-colorectal-cancer-that-suppresses-metastasis-by-upregulating-timp3
#16
Jiaxin Lin, Xin Tan, Lin Qiu, Long Huang, Yi Zhou, Zhizhong Pan, Ranyi Liu, Shuai Chen, Rong Geng, Jiangxue Wu, Wenlin Huang
Long noncoding RNAs (lncRNAs) have been shown to play critical roles in the biology of various cancers. However, their expression patterns and biological functions in human colorectal cancer (CRC) remain largely unknown. The aim of this study was to explore lncRNA profiles in CRC and investigate key lncRNAs involved in CRC tumorigenesis and progression. The microarray data of six CRC and matched non-cancerous tissues revealed distinct lncRNA profiles, including 899 upregulated and 1,646 downregulated lncRNAs (p < 0...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28916391/zika-virus-structural-biology-and-progress-in-vaccine-development
#17
REVIEW
Hsiao-Han Lin, Bak-Sau Yip, Li-Min Huang, Suh-Chin Wu
The growing number of zika virus (ZIKV) infections plus a 20-fold increase in neonatal microcephaly in newborns in Brazil have raised alarms in many countries regarding the threat to pregnant women. Instances of microcephaly and central nervous system malformations continue to increase in ZIKV outbreak regions. ZIKV is a small enveloped positive-strand RNA virus belonging to the Flavivirus genus of the Flaviviridae family. High-resolution ZIKV structures recently identified by cryo-electron microscopy indicate that the overall ZIKV structure is similar to those of other flaviviruses...
September 12, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28915405/hepatic-immunopathology-during-occult-hepacivirus-re-infection
#18
Cordelia Manickam, Amanda J Martinot, Rhianna A Jones, Valerie Varner, R Keith Reeves
Despite drug advances for Hepatitis C virus (HCV), re-infections remain prevalent in high-risk populations. Unfortunately, the role of preexisting viral immunity and how it modulates re-infection is unclear. GBV-B infection of common marmosets is a useful model to study tissue immune responses in hepacivirus infections, and in this study we re-challenged 4 animals after clearance of primary viremia. Although only low-to-absent viremia was observed following re-challenge, GBV-B viral RNA was detectable in liver, confirming re-infection...
September 12, 2017: Virology
https://www.readbyqxmd.com/read/28912799/triportheus-albus-cope-1872-in-the-blackwater-clearwater-and-whitewater-of-the-amazon-a-case-of-phenotypic-plasticity
#19
José D A Araújo, Andrea Ghelfi, Adalberto L Val
The Amazon basin includes 1000s of bodies of water, that are sorted according to their color in three types: blackwater, clearwater, and whitewater, which significantly differ in terms of their physicochemical parameters. More than 3,000 species of fish live in the rivers of the Amazon, among them, the sardine, Triportheus albus, which is one of the few species that inhabit all three types of water. The purpose of our study was to analyze if the gene expression of T. albus is determined by the different types of water, that is, if the species presents phenotypic plasticity to live in blackwater, clearwater, and whitewater...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28911167/in-utero-exposure-to-a-high-fat-diet-programs-hepatic-hypermethylation-and-gene-dysregulation-and-development-of-metabolic-syndrome-in-male-mice
#20
Yoshinori Seki, Masako Suzuki, Xingyi Guo, Alan Scott Glenn, Patricia M Vuguin, Ariana Fiallo, Quan Du, Yi-An Ko, Yiting Yu, Katalin Susztak, Deyou Zheng, John M Greally, Ellen B Katz, Maureen J Charron
Exposure to a high-fat (HF) diet in utero is associated with increased incidence of cardiovascular disease, diabetes, and metabolic syndrome later in life. However, the molecular basis of this enhanced susceptibility for metabolic disease is poorly understood. Gene expression microarray and genome-wide DNA methylation analyses of mouse liver revealed that exposure to a maternal HF milieu activated genes of immune response, inflammation, and hepatic dysfunction. DNA methylation analysis revealed 3360 differentially methylated loci, most of which (76%) were hypermethylated and distributed preferentially to hotspots on chromosomes 4 [atherosclerosis susceptibility quantitative trait loci (QTLs) 1] and 18 (insulin-dependent susceptibility QTLs 21)...
September 1, 2017: Endocrinology
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