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nucleic acid databases

Guojun Cao, Jilie Kong, Zhifang Xing, Yigui Tang, Xinju Zhang, Xiao Xu, Zhihua Kang, Xueen Fang, Ming Guan
Bleeding and thrombosis represent common complications in myeloproliferative neoplasms (MPN) and significantly contribute to morbidity and mortality. Molecular markers, including CALR mutations, were considered not only as diagnostic markers, but also as risk factors for bleeding and thrombosis associated with MPN, especially for patients in remote primary hospitals. We sought to develop an easy-to-use assay for the rapid detection of CALR type 1 (CALR-1) and type 2 (CALR-2) mutations in Philadelphia chromosome-negative MPN patients...
September 18, 2018: Analytica Chimica Acta
Ezgi Deniz Batu
Systemic lupus erythematosus (SLE) is a complex disease with different genetic, immunologic, and environmental factors contributing to the pathogenesis. Monogenic SLE could help us understand the main phases of immune dysregulation in SLE. The aim of this review is to summarize the current knowledge on monogenic SLE with the implications of the respective genes on disease pathogenesis. A comprehensive literature search on monogenic SLE was conducted utilizing the Cochrane Library and MEDLINE/PubMed databases...
May 15, 2018: Rheumatology International
Christina James-Zorn, Virgilio Ponferrada, Malcolm E Fisher, Kevin Burns, Joshua Fortriede, Erik Segerdell, Kamran Karimi, Vaneet Lotay, Dong Zhuo Wang, Stanley Chu, Troy Pells, Ying Wang, Peter D Vize, Aaron Zorn
Xenbase is the Xenopus model organism database ( ), a web-accessible resource that integrates the diverse genomic and biological data for Xenopus research. It hosts a variety of content including current and archived genomes for both X. laevis and X. tropicalis, bioinformatic tools for comparative genetic analyses including BLAST and GBrowse, annotated Xenopus literature, and catalogs of reagents including antibodies, ORFeome clones, morpholinos, and transgenic lines. Xenbase compiles gene-specific pages which include manually curated gene expression images, functional information including gene ontology (GO), disease associations, and links to other major data sources such as NCBI:Entrez, UniProtKB, and Ensembl...
2018: Methods in Molecular Biology
Yunmeng Yan, Guangzhen Fu, Liang Ming
Pancreatic cancer is one of the most lethal malignancies. Exosomes, which are released by multiple cell types, such as cancer cells, contain functional biomolecules (including proteins, nucleic acids and lipids) that can be horizontally delivered to recipient cells. Exosomes act as the most prominent mediator of intercellular communication and can regulate, instruct and re-educate their surrounding microenvironment and target specific organs. The present review performed an extensive search of multiple databases from 2005 to April 23 2017, for eligible literature relating to exosomes and their role in pancreatic cancer...
May 2018: Oncology Letters
Zhang Yizhi, Launay Hélène, Schramm Antoine, Lebrun Régine, Gontero Brigitte
The content of intrinsically disordered protein (IDP) is related to organism complexity, evolution, and regulation. In the Plantae, despite their high complexity, experimental investigation of IDP content is lacking. We identified by mass spectrometry 682 heat-resistant proteins from the green alga, Chlamydomonas reinhardtii. Using a phosphoproteome database, we found that 331 of these proteins are targets of phosphorylation. We analyzed the flexibility propensity of the heat-resistant proteins and their specific features as well as those of predicted IDPs from the same organism...
May 1, 2018: Scientific Reports
Francesco Fanfani, Giorgia Monterossi, Viola Ghizzoni, Esther D Rossi, Giorgia Dinoi, Frediano Inzani, Anna Fagotti, Salvatore Gueli Alletti, Francesca Scarpellini, Camilla Nero, Angela Santoro, Giovanni Scambia, Gian F Zannoni
INTRODUCTION: The aim of the current study is to evaluate the detection rate of micro- and macro-metastases of the One-Step Nucleic Acid Amplification (OSNA) compared to frozen section examination and subsequent ultra-staging examination in early stage endometrial cancer (EC). MATERIAL AND METHODS: From March 2016 to June 2016, data of 40 consecutive FIGO stage I EC patients were prospectively collected in an electronic database. The sentinel lymph node mapping was performed in all patients...
2018: PloS One
Hugo A Garro, Carlos R Pungitore
BACKGROUND: The discovery of new chemotherapeutic agents still remains a continuous goal to achieve. DNA polymerases and topoisomerases act in nucleic acids metabolism modulating different processes like replication, mitosis, damage repair, DNA topology and transcription. It has been widely documented that Polymerases serve as molecular targets for antiviral and antitumoral chemotherapy. Furthermore, telomerase is a ribonucleoprotein with exacerbated activity in most of tumor cell lines, becoming as an emergent target in Cancer treatment...
April 25, 2018: Current Drug Targets
Ling Liu, Yi Xiong, Hongyun Gao, Dong-Qing Wei, Julie C Mitchell, Xiaolei Zhu
January 1, 2018: Database: the Journal of Biological Databases and Curation
S S Patil, K P Suresh, S Saha, A Prajapati, D Hemadri, P Roy
Aim: The aim of the study was to determine the overall prevalence of classical swine fever (CSF) in pigs in India, through a systematic review and meta-analysis of published data. Materials and Methods: Consortium for e-Resources in Agriculture, India, Google Scholar, PubMed, annual reports of All India Coordinated Research Project on Animal Disease Monitoring and Surveillance, and All India Animal Disease database of NIVEDI (NADRES) were used for searching and retrieval of CSF prevalence data (seroprevalence, virus antigen, and virus nucleic acid detection) in India using a search strategy combining keywords and related database-specific subject terms from January 2011 to December 2015 in English only...
March 2018: Veterinary World
Showkat Ahmad Dar, Manoj Kumar
RNA activation (RNAa) is the process of enhancing selective gene expression at transcriptional level using double stranded RNAs, targeting gene promoter. These RNA molecules are usually twenty-one nucleotides long and termed as small activating RNAs (saRNAs). They are involved in gene regulation, epigenetics gain-of-function studies and as have potential therapeutic application for various diseases especially cancer. RNAa is opposite to RNA interference (RNAi) in functionality however; both processes share some protein machinery...
April 3, 2018: Journal of Molecular Biology
Jörg Römbke, Jeannette Bernard, Fabrice Martin-Laurent
The lack of standardized methods to study soil organisms prevents comparisons across datasets and the development of new global and regional experiments and assessments. Moreover, standardized methods are needed to evaluate the impact of anthropogenic stressors such as chemicals on soil organism communities in the regulatory context. The goal of this contribution is to summarize current methodological approaches to measure structural and functional diversity of soil organisms, and to identify gaps and methodological improvements so as to cross datasets generated worldwide...
March 30, 2018: Integrated Environmental Assessment and Management
Marcella A Teixeira, Noa Sela, Hagop S Atamian, Ergude Bao, Ritu Chaudhary, Jacob MacWilliams, Jiangman He, Sophie Mantelin, Thomas Girke, Isgouhi Kaloshian
The potato aphid, Macrosiphum euphorbiae, is an important agricultural pest that causes economic losses to potato and tomato production. To establish the transcriptome for this aphid, RNA-Seq libraries constructed from aphids maintained on tomato plants were used in Illumina sequencing generating 52.6 million 75-105 bp paired-end reads. The reads were assembled using Velvet/Oases software with SEED preprocessing resulting in 22,137 contigs with an N50 value of 2,003bp. After removal of contigs from tomato host origin, 20,254 contigs were annotated using BLASTx searches against the non-redundant protein database from the National Center for Biotechnology Information (NCBI) as well as IntereProScan...
2018: PloS One
Fang Shi, Zhenzhen Liang, Qian Zhang, Chunpeng Wang, Xin Liu
BACKGROUND: One-step nucleic acid amplification (OSNA) assay is a molecular diagnostic method for intraoperative detection of lymph node metastasis by amplifying cytokeratin 19 mRNA. We aim to further evaluate the performance of OSNA assay for the intraoperative diagnosis of sentinel lymph node metastasis in breast cancer. METHODS: PubMed, Cochrane Library, Web of Science databases were searched to retrieve related literature published up until December 2017. This meta-analysis was performed using a random-effects model...
March 22, 2018: Breast: Official Journal of the European Society of Mastology
Mingxue Sun, Yuyan Yang, Wenqi Meng, Qingqiang Xu, Fengwu Lin, Yongchun Chen, Jie Zhao, Kai Xiao
CONTEXT: Sulfur mustard (SM), a bifunctional alkylating agent, can react with a variety of biochemical molecules (DNA, RNA, proteins and other cell components) to cause a series of serious health issues or even death. Although a plethora of research has been done, the pathogenesis of SM poisoning has yet to be fully understood due to its high complexity. As a consequence, a specific antidote has not yet been developed and the treatment of SM poisoning remains a medical challenge. In recent years, various biological products and cell transplantation in the treatment of SM poisoning offered a significant clinical treatment progress...
March 20, 2018: Chemico-biological Interactions
Cheng Zhang, Chun-Dong Zhang, Ming-Hui Ma, Dong-Qiu Dai
AIM: To identify multiple microRNAs (miRNAs) for predicting the prognosis of gastric cancer (GC) patients by bioinformatics analysis. METHODS: The original microarray dataset GSE93415, which included 20 GC and 20 tumor adjacent normal gastric mucosal tissues, was downloaded from the Gene Expression Omnibus database and used for screening differentially expressed miRNAs (DEMs). The cut-off criteria were P < 0.05 and fold change > 2.0. In addition, we acquired the miRNA expression profiles and clinical information of 361 GC patients from The Cancer Genome Atlas database to assess the prognostic role of the DEMs...
March 21, 2018: World Journal of Gastroenterology: WJG
J Kosťun, M Pešta, R Slunečko, P Vlasák, J Bouda, D Berezovskiy, O Topolčan, Z Novotný, J Presl
OBJECTIVE: The article summarizes current possibilities of usage of the One-Step Nucleic Acid Amplification method (OSNA) in the perioperative management of sentinel lymph nodes in oncologic surgery. The principle of this method is the detection of cytokeratin 19 (CK19) in the lymphatic tissue as a marker of the metastatic spread. DESIGN: Review article. SETTINGS: Department of Obstetrics and Gynaecology, University Hospital Pilsen, Faculty of Medicine in Pilsen, Charles University, Prague; Department of Biology, Faculty of Medicine in Pilsen, Charles University, Prague; Department of Immunochemistry, University Hospital Pilsen, Faculty of Medicine in Pilsen, Charles University, Prague; Sikl´s Department of Pathology, University Hospital Pilsen, Faculty of Medicine in Pilsen, Charles University, Prague...
December 0: Ceská Gynekologie
Gilda da Cunha Santos
CONTEXT: - Traditional methods for storing histologic and cytologic specimens for future use in molecular assays have consisted of either snap-freezing with cryopreservation or formalin-fixing, paraffin-embedding the samples. Although snap-freezing with cryopreservation is recommended for better preservation of nucleic acids, the infrastructure and space required for archiving impose challenges for high-volume pathology laboratories. Cost-effective, long-term storage at room temperature; relatively easy shipment; and standardized handling can be achieved with formalin-fixed, paraffin-embedded samples, but formalin fixation induces fragmentation and chemical modification of nucleic acids...
March 2018: Archives of Pathology & Laboratory Medicine
Jaimie Dufresne, Angelique Florentinus-Mefailoski, Pete Bowden, John G Marshall
The proteins identified from endogenous peptides agreed between serum versus plasma, and tryptic versus non-tryptic peptides, when collected by C18 alone and analyzed by liquid chromatography electrospray ionization and tandem mass spectrometry (LC-ESI-MS/MS) including amyloids, apolipoproteins, haptoglobin, complements, fibrinogens, hemopexin, antitrypsin and alpha 2 macroglobulin. Precipitation of polypeptides from plasma in 9 vol of 100% organic solvent followed by stepwise extraction of the insoluble pellet with an increasing fraction of water identified thousands of proteins...
May 15, 2018: Analytical Biochemistry
Courtney M Dewart, Kyle T Bernstein, Nicholas P DeGroote, Raul Romaguera, Abigail Norris Turner
We undertook a systematic review to examine rectal Chlamydia trachomatis (Ct) and Neisseria gonorrhoeae (Ng) infections in women and men who have sex with men (MSM). English-language publications measuring rectal Ct or Ng prevalence using nucleic acid amplification tests were eligible. Searching multiple electronic databases, we identified 115 eligible reports published between January 2000 and November 2016. Overall, the prevalence of rectal Ct (9%) was higher than that of rectal Ng (4.7%). Rectal Ct prevalence was similar in MSM (9%) and women (9...
May 2018: Sexually Transmitted Diseases
Margret I Moré, Yvan Vandenplas
Several properties of the probiotic medicinal yeast Saccharomyces boulardii CNCM I-745 contribute to its efficacy to prevent or treat diarrhoea. Besides immunologic effects, pathogen-binding and anti-toxin effects, as well as positive effects on the microbiota, S boulardii CNCM I-745 also has pronounced effects on digestive enzymes of the brush border membrane, known as trophic effects. The latter are the focus of this review. Literature has been reviewed after searching Medline and PMC databases. All relevant non-clinical and clinical studies are summarized...
2018: Clinical Medicine Insights. Gastroenterology
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