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https://www.readbyqxmd.com/read/29245068/overexpression-of-microrna-375-impedes-platelet-derived-growth-factor-induced-proliferation-and-migration-of-human-fetal-airway-smooth-muscle-cells-by-targeting-janus-kinase-2
#1
Yamei Ji, Xin Yang, Huixia Su
The abnormal proliferation and migration of airway smooth muscle (ASM) cells play a critical role in airway remodeling during the development of asthma. MicroRNAs (miRNAs) have emerged as critical regulators of ASM cell proliferation and migration in airway remodeling. In this study, we aimed to investigate the potential role of miR-375 in the regulation of platelet-derived growth factor (PDGF)-induced fetal ASM cell proliferation and migration. Our results showed that miR-375 expression was significantly decreased in fetal ASM cells that were treated with PDGF...
December 12, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29244864/resistant-and-susceptible-responses-in-alfalfa-medicago-sativa-to-bacterial-stem-blight-caused-by-pseudomonas-syringae-pv-syringae
#2
Lev G Nemchinov, Jonathan Shao, Maya N Lee, Olga A Postnikova, Deborah A Samac
Bacterial stem blight caused by Pseudomonas syringae pv. syringae is a common disease of alfalfa (Medicago sativa L). Little is known about host-pathogen interactions and host defense mechanisms. Here, individual resistant and susceptible plants were selected from cultivars Maverick and ZG9830 and used for transcript profiling at 24 and 72 hours after inoculation (hai) with the isolate PssALF3. Bioinformatic analysis revealed a number of differentially expressed genes (DEGs) in resistant and susceptible genotypes...
2017: PloS One
https://www.readbyqxmd.com/read/29244193/comparative-peptidomic-profile-between-human-hypertrophic-scar-tissue-and-matched-normal-skin-for-identification-of-endogenous-peptides-involved-in-scar-pathology
#3
Jingyun Li, Ling Chen, Qian Li, Jing Cao, Yanli Gao, Jun Li
Endogenous peptides recently attract increasing attention for their participation in various biological processes. Their roles in the pathogenesis of human hypertrophic scar remains poorly understood. In this study, we used liquid chromatography-tandem mass spectrometry to construct a comparative peptidomic profiling between human hypertrophic scar tissue and matched normal skin. A total of 179 peptides were significantly differentially expressed in human hypertrophic scar tissue, with 95 upregulated and 84 downregulated peptides between hypertrophic scar tissue and matched normal skin...
December 15, 2017: Journal of Cellular Physiology
https://www.readbyqxmd.com/read/29244056/cscoretool-fast-hi-c-compartment-analysis-at-high-resolution
#4
Xiaobin Zheng, Yixian Zheng
Summary: The genome-wide chromosome conformation capture (Hi-C) has revealed that the eukaryotic genome can be partitioned into A and B compartments that have distinctive chromatin and transcription features. Current Principle Component Analyses (PCA)-based method for the A/B compartment prediction based on Hi-C data requires substantial CPU time and memory. We report the development of a method, CscoreTool, that enables fast and memory-efficient determination of A/B compartments at high resolution even in datasets with low sequencing depth...
December 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29244005/ghost-global-hepatitis-outbreak-and-surveillance-technology
#5
Atkinson G Longmire, Seth Sims, Inna Rytsareva, David S Campo, Pavel Skums, Zoya Dimitrova, Sumathi Ramachandran, Magdalena Medrzycki, Hong Thai, Lilia Ganova-Raeva, Yulin Lin, Lili T Punkova, Amanda Sue, Massimo Mirabito, Silver Wang, Robin Tracy, Victor Bolet, Thom Sukalac, Chris Lynberg, Yury Khudyakov
BACKGROUND: Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Effective HCV outbreak investigation requires comprehensive surveillance and robust case investigation. We previously developed and validated a methodology for the rapid and cost-effective identification of HCV transmission clusters...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29243826/gsslah3-a-glycine-soja-slow-type-anion-channel-homologue-positively-modulates-plant-bicarbonate-stress-tolerance
#6
Xiangbo Duan, Yang Yu, Huizi Duanmu, Chao Chen, Xiaoli Sun, Lei Cao, Qiang Li, Xiaodong Ding, Beidong Liu, Yanming Zhu
Alkaline stress is a major form of abiotic stress that severely inhibits plant growth and development, thus restricting crop productivity. However, little is known about how plants respond to alkali. In this study, a slow-type anion channel homologue 3 gene GsSLAH3 was isolated and functionally characterized. Bioinformatics analysis showed that GsSLAH3 protein contains ten transmembrane helices. Consistently, GsSLAH3 was found to locate on plasma membrane by transient expression in onion epidermal cells. In wild soybeans, GsSLAH3 expression was induced by NaHCO3 treatment, suggesting its involvement in plant response to alkaline stress...
December 15, 2017: Physiologia Plantarum
https://www.readbyqxmd.com/read/29243775/independent-prognostic-factor-of-low-expressed-lncrna-znf667-as1-for-cervical-cancer-and-inhibitory-function-on-the-proliferation-of-cervical-cancer
#7
L-P Zhao, R-H Li, D-M Han, X-Q Zhang, G-X Nian, M-X Wu, Y Feng, L Zhang, Z-G Sun
OBJECTIVE: To investigate the expression of long non-coding RNA ZNF667-AS1 in cervical cancer and its effect on the proliferation of cervical cancer cell line, SiHa cells. MATERIALS AND METHODS: The expression level of ZNF667-AS1 from two microarray datasets (GSE63514 and GSE6791) and TCGA (The Cancer Genome Atlas) were selected to analyze the difference between cervical cancer tissues and normal cervical tissues with bioinformatics methods. Then, the prognosis of ZNF667-AS1 was calculated in TCGA...
December 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29243131/analysis-of-variability-of-urinary-excreted-jc-virus-strains-in-patients-infected-with-hiv-and-healthy-donors
#8
Danijela Karalic, Ivana Lazarevic, Ana Banko, Maja Cupic, Djordje Jevtovic, Tanja Jovanovic
In immunocompromised individuals, especially in patients with T cell immunodeficiency, reactivation of JCPyV can cause serious life-threatening diseases. Nowadays, HIV infection is one of the most important factor for reactivation of JCPyV and the development of of the progressive multifocal leukoencephalopathy (PML). Mutations in the outer loops of the VP1 region can lead to the selection of the viral variants with changed tropism and increased pathological potential. The aims of this study were to determine sequence variation and amino acid changes within VP1 loops and the structure of non-coding control region (NCCR) of urinary excreted JCPyV isolates among HIV-infected patients and healthy donors...
December 14, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/29243018/decreased-microrna-mir-181c-expression-associated-with-gastric-cancer
#9
Luanna Munhoz Zabaglia, Nicole Chiuso Bartolomeu, Mônica Pezenatto Dos Santos, Rita Luiza Peruquetti, Elizabeth Chen, Marilia de Arruda Cardoso Smith, Spencer Luiz Marques Payão, Lucas Trevizani Rasmussen
PURPOSE: This study investigated miRNA-181c expression in control patients (healthy gastric mucosa), patients with gastritis, and patients with gastric cancer. The presence of Helicobacter pylori was determined, and the associations between H. pylori infection, levels of miRNA-181c expression, and gastric disease were also analyzed. METHODS: A total of 158 subjects were included in the study, and the three groups were respectively composed of 53 controls, 86 patients with gastritis, and 19 patients with gastric cancer...
December 15, 2017: Journal of Gastrointestinal Cancer
https://www.readbyqxmd.com/read/29242834/novel-its1-fungal-primers-for-characterization-of-the-mycobiome
#10
Mykhaylo Usyk, Christine P Zolnik, Hitesh Patel, Michael H Levi, Robert D Burk
Studies of the human microbiome frequently omit characterization of fungal communities (the mycobiome), which limits our ability to investigate how fungal communities influence human health. The internal transcribed spacer 1 (ITS1) region of the eukaryotic ribosomal cluster has features allowing for wide taxonomic coverage and has been recognized as a suitable barcode region for species-level identification of fungal organisms. We developed custom ITS1 primer sets using iterative alignment refinement. Primer performance was evaluated using in silico testing and experimental testing of fungal cultures and human samples...
November 2017: MSphere
https://www.readbyqxmd.com/read/29242407/central-role-of-the-p53-pathway-in-the-noncoding-rna-response-to-oxidative-stress
#11
Paola Fuschi, Matteo Carrara, Christine Voellenkle, Jose Manuel Garcia-Manteiga, Paolo Righini, Biagina Maimone, Elena Sangalli, Francesco Villa, Claudia Specchia, Mario Picozza, Giovanni Nano, Carlo Gaetano, Gaia Spinetti, Annibale A Puca, Alessandra Magenta, Fabio Martelli
Oxidative stress plays a fundamental role in many conditions. Specifically, redox imbalance inhibits endothelial cell (EC) growth, inducing cell death and senescence. We used global transcriptome profiling to investigate the involvement of noncoding-RNAs in these phenotypes. By RNA-sequencing, transcriptome changes were analyzed in human ECs exposed to H2O2, highlighting a pivotal role of p53-signaling. Bioinformatic analysis and validation in p53-silenced ECs, identified several p53-targets among both mRNAs and long noncoding-RNAs (lncRNAs), including MALAT1 and NEAT1...
December 12, 2017: Aging
https://www.readbyqxmd.com/read/29242247/chip-regulates-aquaporin-2-quality-control-and-body-water-homeostasis
#12
Qi Wu, Hanne B Moeller, Donté A Stevens, Rebekah Sanchez-Hodge, Gabrielle Childers, Marleen L A Kortenoeven, Lei Cheng, Lena L Rosenbaek, Carrie Rubel, Cam Patterson, Trairak Pisitkun, Jonathan C Schisler, Robert A Fenton
The importance of the kidney distal convoluted tubule (DCT) and cortical collecting duct (CCD) is highlighted by various water and electrolyte disorders that arise when the unique transport properties of these segments are disturbed. Despite this critical role, little is known about which proteins have a regulatory role in these cells and how these cells can be regulated by individual physiologic stimuli. By combining proteomics, bioinformatics, and cell biology approaches, we found that the E3 ubiquitin ligase CHIP is highly expressed throughout the collecting duct; is modulated in abundance by vasopressin; interacts with aquaporin-2 (AQP2), Hsp70, and Hsc70; and can directly ubiquitylate the water channel AQP2 in vitro shRNA knockdown of CHIP in CCD cells increased AQP2 protein t1/2 and reduced AQP2 ubiquitylation, resulting in greater levels of AQP2 and phosphorylated AQP2...
December 14, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29242164/rapid-allopolyploid-radiation-of-moonwort-ferns-botrychium-ophioglossaceae-revealed-by-pacbio-sequencing-of-homologous-and-homeologous-nuclear-regions
#13
Benjamin Dauphin, Jason R Grant, Donald R Farrar, Carl J Rothfels
Polyploidy is a major speciation process in vascular plants, and is postulated to be particularly important in shaping the diversity of extant ferns. However, limitations in the availability of bi-parental markers for ferns have greatly limited phylogenetic investigation of polyploidy in this group. With a large number of allopolyploid species, the genus Botrychium is a classic example in ferns where recurrent polyploidy is postulated to have driven frequent speciation events. Here, we use PacBio sequencing and the PURC bioinformatics pipeline to capture all homeologous or allelic copies of four long (∼1kb) low-copy nuclear regions from a sample of 45 specimens (25 diploids and 20 polyploids) representing 37 Botrychium taxa, and three outgroups...
December 11, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29242124/kinetic-characterization-and-structural-modeling-of-an-nadp-dependent-succinic-semialdehyde-dehydrogenase-from-anabaena-sp-pcc7120
#14
Xiaoqin Wang, Chongde Lai, Guofeng Lei, Fei Wang, Haozhi Long, Xiaoyu Wu, Jinyin Chen, Guanghua Huo, Zhimin Li
Succinic semialdehyde dehydrogenases (SSADH) of cyanobacteria played a pivotal role in completing the cyanobacterial tricarboxylic acid cycle. The structural information of cofactor preference and catalysis for SSADH from cyanobacteria is currently available. However, the detailed kinetics of SSADH from cyanobacteria were not characterized yet. In this study, an all3556 gene encoding SSADH from Anabaena sp. PCC7120 (ApSSADH) was amplified and the recombinant ApSSADH was purified homogenously. Kinetic analysis showed that ApSSADH was an NADP+-dependent SSADH, which utilized NADP+ and succinic semialdehyde (SSA) as its preferred substrates and the activity of ApSSADH was inhibited by its substrate of SSA...
December 11, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29242049/rational-library-design-by-functional-cdr-resampling
#15
Qi Zhao, Diane Buhr, Courtney Gunter, Jenny Frenette, Mary Ferguson, Eric Sanford, Erika Holland, Chitra Rajagopal, Melissa Batonick, Margaret M Kiss, Michael P Weiner
Successful antibody discovery relies on diversified libraries, where two aspects are implied, namely the absolute number of unique clones and the percentage of functional clones. Instead of pursuing the absolute quantity thresholded by current display technology, we have sought to maximize the effective diversity by improving functional clone percentage. With the combined effort of bioinformatics, structural biology, molecular immunology and phage display technology, we devised a bioinformatic pipeline to construct and validate libraries via combinatorial assembly of sequences from a database of experimentally validated antibodies...
December 11, 2017: New Biotechnology
https://www.readbyqxmd.com/read/29241190/circrna-expression-profile-in-early-stage-lung-adenocarcinoma-patients
#16
Jiangmin Zhao, Le Li, Qian Wang, Hongxiu Han, Qing Zhan, Ming Xu
BACKGROUND/AIMS: Lung adenocarcinoma, a form of non-small cell lung cancer with high lethality at an advanced stage, is becoming more common in women, non- or never-smokers, and even young adults. At present, there are still no effective early diagnosis methods for patients to be cured in a timely manner. Circular RNAs (circRNAs), which are stable and conserved non-coding RNA in mammalian cells, have been reported to be widely involved in the processes of cancer disease. However, it is still a puzzle as to which specific circRNAs are involved in the development of early-stage lung adenocarcinoma...
December 12, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/29240934/a-peculiar-iclr-family-transcription-factor-regulates-para-hydroxybenzoate-catabolism-in-streptomyces-coelicolor
#17
Rui Zhang, Dana M Lord, Rakhi Bajaj, Wolfgang Peti, Rebecca Page, Jason K Sello
In Streptomyces coelicolor, we identified a para-hydroxybenzoate (PHB) hydroxylase, encoded by gene pobA (SCO3084), which is responsible for conversion of PHB into PCA (protocatechuic acid), a substrate of the β-ketoadipate pathway which yields intermediates of the Krebs cycle. We also found that the transcription of pobA is induced by PHB and is negatively regulated by the product of SCO3209, which we named PobR. The product of this gene is highly unusual in that it is the apparent fusion of two IclR family transcription factors...
December 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29240760/novel-linear-motif-filtering-protocol-reveals-the-role-of-the-lc8-dynein-light-chain-in-the-hippo-pathway
#18
Gábor Erdős, Tamás Szaniszló, Mátyás Pajkos, Borbála Hajdu-Soltész, Bence Kiss, Gábor Pál, László Nyitray, Zsuzsanna Dosztányi
Protein-protein interactions (PPIs) formed between short linear motifs and globular domains play important roles in many regulatory and signaling processes but are highly underrepresented in current protein-protein interaction databases. These types of interactions are usually characterized by a specific binding motif that captures the key amino acids shared among the interaction partners. However, the computational proteome-level identification of interaction partners based on the known motif is hindered by the huge number of randomly occurring matches from which biologically relevant motif hits need to be extracted...
December 14, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29240723/identi%C3%AF-cation-of-key-genes-and-pathways-in-tongue-squamous-cell-carcinoma-using-bioinformatics-analysis
#19
Huayong Zhang, Jianmin Liu, Xiaoyan Fu, Ankui Yang
BACKGROUND Tongue squamous cell carcinoma (TSCC) is a major type of oral cancers and has remained an intractable cancer over the past decades. The aim of this study was to identify differentially expressed genes (DEGs) during TSCC and reveal their potential mechanisms. MATERIAL AND METHODS The gene expression profiles of GSE13601 were downloaded from the GEO database. The GSE13601 dataset contains 57 samples, including 31 tongue SCC samples and 26 matched normal mucosa samples. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were performed; Cytoscape software was used for the protein-protein interaction (PPI) network and module analysis of the DEGs...
December 14, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29240691/absence-of-correlation-between-chimeric-rna-and-aging
#20
Reyna Huang, Shailesh Kumar, Hui Li
Chimeric RNAs have been recognized as a phenomenon not unique to cancer cells. They also exist in normal physiology. Aging is often characterized by deregulation of molecular and cellular mechanisms, including loss of heterochromatin, increased transcriptional noise, less tight control on alternative splicing, and more stress-induced changes. It is thus assumed that chimeric RNAs are more abundant in older people. In this study, we conducted a preliminary investigation to identify any chimeric RNAs with age-based trends in their expression levels in blood samples...
December 14, 2017: Genes
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