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rna biology

Mehari B Zerihun, Alexander Schug
Evolution leads to considerable changes in the sequence of biomolecules, while their overall structure and function remain quite conserved. The wealth of genomic sequences, the 'Biological Big Data', modern sequencing techniques provide allows us to investigate biomolecular evolution with unprecedented detail. Sophisticated statistical models can infer residue pair mutations resulting from spatial proximity. The introduction of predicted spatial adjacencies as constraints in biomolecular structure prediction workflows has transformed the field of protein and RNA structure prediction toward accuracies approaching the experimental resolution limit...
October 20, 2017: Biochemical Society Transactions
Zhihao Jiang, Zhaolei Li, Ning Yue, Kun Zhang, Dawei Li, Yongliang Zhang
Lychnis ringspot virus (LRSV, genus Hordeivirus) was first isolated in 1959, and has been shown to infect several dicot plants in nature. However, due to the lack of infectious cDNA clones, the biological properties and mechanisms underlying LRSV infection are obscure. In this work, we constructed infectious cDNA clones of LRSV and have compiled the complete LRSV genomic (g) RNA sequence. Comparison of nucleotide and amino acid sequences between LRSV and barley stripe mosaic virus (BSMV), the type member of genus Hordeivirus, reveals that despite belonging to the same genus, and replicating in chloroplasts, the viruses are only distantly related...
October 17, 2017: Virus Research
R Ciccimarra, S Bussolati, F Grasselli, S Grolli, L Ragionieri, F Ravanetti, M Botti, F Gazza, A Cacchioli, R Di Lecce, A M Cantoni, G Basini
Successful reproduction is strictly linked to metabolic cues. The orexins are a family of hypothalamic neurohormones, well known for their key role in the control of food intake and the involvement in several aspects of the reproductive process. The biological actions of both orexins are carried out through binding to the related Orexin 1 (OX1R) and Orexin 2 (OX2R) G-protein-coupled receptors. The purpose of this study was to investigate the presence of orexin system components in the porcine ovaries, to contribute to expand the knowledge about their pleiotropic role...
September 22, 2017: Domestic Animal Endocrinology
Björn Becker, Manfred J Schmitt
The initial discovery of killer toxin-secreting brewery strains of Saccharomyces cerevisiae (S. cerevisiae) in the mid-sixties of the last century marked the beginning of intensive research in the yeast virology field. So far, four different S. cerevisiae killer toxins (K28, K1, K2, and Klus), encoded by cytoplasmic inherited double-stranded RNA viruses (dsRNA) of the Totiviridae family, have been identified. Among these, K28 represents the unique example of a yeast viral killer toxin that enters a sensitive cell by receptor-mediated endocytosis to reach its intracellular target(s)...
October 20, 2017: Toxins
Charanjeet Kaur, Rashmi Raj, Ashish Srivastava, Susheel Kumar, Shri Krishna Raj
We report the complete genome sequence of five bean yellow mosaic virus (BYMV) isolates (CK-GL1, CK-GL3, CK-GL4, CK-GL5 and Vfaba2) that share 74.6-98.9% (nucleotide) and 81.5-99.1% (amino acid) identity with globally available BYMV sequences. Phylogenetic analysis clustered them specifically in BYMV phylogenetic group-IV within the existing nine groups. The CK-GL1, CK-GL2, CK-GL4 and CK-GL5 isolates formed a discrete cluster within group-IV. The present study suggests subdivision of group-IV into subgroup-IVa and IVb...
October 20, 2017: Archives of Virology
Yang Yu, Yanfei Zhou, Yuchan Zhang, Yueqin Chen
Recent studies have indicated that a special type of small noncoding RNAs, phased small-interfering RNAs (phasiRNAs) play crucial roles in many cellular processes of plant development. PhasiRNAs are generated from long RNA precursors at intervals of 21 or 24 nt in plants, and they are produced from both protein-coding gene and long noncoding RNA genes. Different from those in eudicots, grass phasiRNAs include a special class of small RNAs that are specifically expressed in reproductive organs. These grass phasiRNAs are associated with gametogenesis, especially with anther development and male fertility...
October 18, 2017: Science China. Life Sciences
Maria Dermit, Martin Dodel, Faraz K Mardakheh
Regulation of protein translation constitutes a crucial step in control of gene expression. In comparison to transcriptional regulation, however, translational control has remained a significantly under-studied layer of gene expression. This trend is now beginning to shift thanks to recent advances in next-generation sequencing, proteomics, and microscopy based methodologies which allow accurate monitoring of protein translation rates, from single target messenger RNA molecules to genome-wide scale studies...
October 20, 2017: Molecular BioSystems
Wenjun Jiang, Baochang Zhang, Chuyao Fan, Min Wang, Jiaxing Wang, Qiang Deng, Xianyu Liu, Ji Chen, Jishen Zheng, Lei Liu, Ting F Zhu
The construction of mirror-image biological systems may open the next frontier for biomedical technology development and discovery. Here we have designed and chemically synthesized a mutant version of the thermostable Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) consisting of d-amino acids. With a total peptide length of 358 amino acid residues, it is the largest chemically synthesized d-amino acid protein reported to date. We show that the d-polymerase is able to amplify a 120-bp l-DNA sequence coding for the Escherichia coli 5S ribosomal RNA gene rrfB by mirror-image polymerase chain reaction, and that both the natural and mirror-image systems operate with strict chiral specificity...
2017: Cell Discovery
Diana Drago-García, Jesús Espinal-Enríquez, Enrique Hernández-Lemus
Over the last years, microRNAs (miRs) have shown to be crucial for breast tumour establishment and progression. To understand the influence that miRs have over transcriptional regulation in breast cancer, we constructed mutual information networks from 86 TCGA matched breast invasive carcinoma and control tissue RNA-Seq and miRNA-Seq sequencing data. We show that miRs are determinant for tumour and control data network structure. In tumour data network, miR-200, miR-199 and neighbour miRs seem to cooperate on the regulation of the acquisition of epithelial and mesenchymal traits by the biological processes: Epithelial-Mesenchymal Transition (EMT) and Mesenchymal to Epithelial Transition (MET)...
October 19, 2017: Scientific Reports
James Chappell, Alexandra Westbrook, Matthew Verosloff, Julius B Lucks
A longstanding goal of synthetic biology has been the programmable control of cellular functions. Central to this is the creation of versatile regulatory toolsets that allow for programmable control of gene expression. Of the many regulatory molecules available, RNA regulators offer the intriguing possibility of de novo design-allowing for the bottom-up molecular-level design of genetic control systems. Here we present a computational design approach for the creation of a bacterial regulator called Small Transcription Activating RNAs (STARs) and create a library of high-performing and orthogonal STARs that achieve up to ~ 9000-fold gene activation...
October 19, 2017: Nature Communications
Wei Wang, Shiping Yang, Chenggui Wang, Lili Shi, Hui Guo, Siuming Chan
The banana shrimp, Fenneropenaeus merguiensis, is an important fishery species in the Indo-West Pacific region. As the shrimp is very sensitive to stressors such as ammonia stress in water, understanding the molecular mechanisms of stress tolerance in F. merguiensis is of pivotal importance for improving its farming performance. In the current study, by using the RNA sequencing platform and comparative transcriptomic analysis, we conducted a comprehensive study on the transcriptomic changes of F. merguiensis in response to ammonia stress...
October 16, 2017: Fish & Shellfish Immunology
Xiaoyun He, Chunlin Ou, Yanhua Xiao, Qing Han, Hao Li, Suxian Zhou
Long non-coding RNAs (LncRNAs) are a class of endogenous RNA molecules, which have a transcribing length of over 200 nt, lack a complete functional open reading frame (ORF), and rarely encode a functional short peptide. Recent studies have revealed that disruption of LncRNAs levels correlates with several human diseases, including diabetes mellitus (DM), a complex multifactorial metabolic disorder affecting more than 400 million people worldwide. LncRNAs are emerging as pivotal regulators in various biological processes, in the progression of DM and its associated complications, involving pancreatic β-cell disorder, insulin resistance, and epigenetic regulation, etc...
September 19, 2017: Oncotarget
Chunqing Dou, Liyuan Sun, Xin Jin, Mingming Han, Bao Zhang, Xian Jiang, Jinyong Lv, Tao Li
Long non-coding RNAs (lncRNAs) play key roles in cancer initiation and progression. The aim was to investigate the biological functions and clinical significance of long non-coding RNA CARLo-5 in hepatocellular carcinoma (HCC). QRT-PCR was performed to investigate CARLo-5 expression in HCC tissues and cells. Kaplan-Meier curve and multivariate analysis validated the association between CARLo-5 expression and overall survival (OS) in HCC patients. Cell proliferation and invasion was performed by CCK8 cell proliferation, cell colony formation and transwell invasion assays...
September 19, 2017: Oncotarget
Fanglei Liu, Chunxue Bai, Zhongliang Guo
Osteopontin (OPN) is known to be overexpressed in numerous carcinomas. Although abundant OPN has been reported to be correlated with poor survival in non-small cell lung cancer (NSCLC) but their clinical and prognostic significance in SCLC remains unknown. In this study, RNA-sequencing was used to obtain gene expression data in SCLC tissue samples and OPN expression levels were then investigated using qPCR, immunohistochemical and Western blot. We found OPN was one of the most upregulated genes. Besides, the correlation of OPN with tumor clinicopathological characteristics was evaluated and we found OPN was associated with advanced tumor stages...
September 19, 2017: Oncotarget
Hongxing Li, Bo Li, Dongmei Zhu, Hua Xie, Chunxia Du, Yankai Xia, Weibing Tang
The long noncoding RNA (lncRNA) MEG3 is involved in various biological processes including cell migration and cell proliferation. In present study, it was found that MEG3 and the intronic miR-770-5p were decreased in samples from HSCR patients. Besides, knockdown of MEG3 and miR-770-5p suppressed cell migration and proliferation, while cell cycle and apoptosis were not affected in human 293T and SH-SY5Y cells. SRGAP1 mRNA and protein upregulation was inversely correlated with miR-770-5p expression in tissue samples and cell lines, which was confirmed to be a target gene of miR-770-5p by dual-luciferase reporter assay...
September 19, 2017: Oncotarget
Esteban Cruz, Joel Cain, Ben Crossett, Veysel Kayser
The study of influenza virus evolution in humans has revealed a significant role of glycosylation profile alterations in the viral glycoproteins - hemagglutinin (HA) and neuraminidase (NA), in the emergence of both seasonal and pandemic strains. Viral antigenic drift can modify the number and location of glycosylation sites, altering a wide range of biological activities and the antigenic properties of the strain. In view of the key role of glycans in determining antigenicity, elucidating the glycosylation profiles of influenza strains is a requirement towards the development of improved vaccines...
October 19, 2017: Human Vaccines & Immunotherapeutics
Xiang-Peng Wang, Cai Shan, Xing-Li Deng, Li-Yan Li, Wei Ma
Emerging evidence suggests that long non-coding RNAs (lncRNAs) may be involved in modulating various aspects of tumor biology and serve as potential therapeutic targets as well as novel biomarkers in the treatment of glioma. The present study investigated the role of lncRNA, Prader Willi/Angelman region RNA 5 (PAR5; also known as PWAR5), in glioma and its clinical significance in glioma cases. The expression levels of PAR5 were determined in clinical samples and U87, U251 cells using real-time reverse transcription quantitative polymerase chain reaction (qRT-PCR) analysis...
September 21, 2017: Oncology Reports
Yan Shen, Qi Liu, Shifeng Lou, Yun Luo, Hang Sun, Hanqing Zeng, Jianchuan Deng
Augmenter of liver regeneration (ALR) plays crucial roles in cell survival and growth. Previous studies have demonstrated that ALR exerts a protective effect on toxic agent‑induced cell death in acute T lymphoblastic leukemia cells and ALR knockdown can sensitize cancer cells to radiation. However, the biological functions of ALR against drug resistance in T-cell acute lymphoblastic leukemia are mostly unknown. In the present study, we investigated the effect of small interfering RNA (siRNA)-induced ALR silencing on cell proliferation and sensitivity to vincristine (VCR) of Jurkat cells...
September 21, 2017: Oncology Reports
Nicolai Krogh, Martin Kongsbak-Wismann, Carsten Geisler, Henrik Nielsen
Sequencing-based profiling of ribose methylations is a new approach that allows for experiments addressing dynamic changes on a large scale. Here, we apply such a method to spliceosomal snRNAs present in human whole cell RNA. Analysis of solid tissue samples confirmed all previously known sites and demonstrated close to full methylation at almost all sites. Methylation changes were revealed in biological experimental settings, using T cell activation as an example, and in the T cell leukemia model, Jurkat cells...
October 19, 2017: Organic & Biomolecular Chemistry
Yun Liao, Rui Su, Ping Zhang, Bo Yuan, Ling Li
BACKGROUND: ANFH is a major health problem, to which long lasting and definitive treatments are lacking. The aim of this study is to study RNA alterations attributed to cortisol-induced ANFH. METHODS: Rat models were stratified into three groups: in vitro group (n = 20) for molecular biological assays, control group (n = 3), and ANFH group induced using lipopolysaccharide and dexamethasone (n = 3). Bone marrow-derived endothelial progenitor cells (BM-EPCs) were extracted from the rats...
October 18, 2017: Journal of Orthopaedic Surgery and Research
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