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nucleic acid databases

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...
2018: 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, 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...
February 24, 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 (9.0%) was higher than rectal Ng (4.7%). Rectal Ct prevalence was similar in MSM (9%) and women (9...
November 1, 2017: 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
Nastassya L Chandra, Claire Broad, Kate Folkard, Katy Town, Emma M Harding-Esch, Sarah C Woodhall, John M Saunders, S Tariq Sadiq, J Kevin Dunbar
OBJECTIVES: Chlamydia trachomatis is the most commonly diagnosed bacterial STI. Lack of prevalence and risk factor data for rectal chlamydia in women has testing and treatment implications, as azithromycin (a first-line urogenital chlamydia treatment) may be less effective for rectal chlamydia. We conducted a systematic review of studies on women in high-income countries to estimate rectal chlamydia prevalence, concurrency with urogenital chlamydia and associations with reported anal intercourse (AI)...
February 3, 2018: Sexually Transmitted Infections
Courtney Olson-Chen, Kripa Balaram, David N Hackney
OBJECTIVES: We conducted a meta-analysis to determine the association between Chlamydia trachomatis and adverse perinatal outcomes. METHODS: Electronic databases were searched between 1970 and 2013. Included studies reported perinatal outcomes in women with and without chlamydia. Summary odds ratios were calculated using fixed- and random-effects models. Study bias was assessed using a Funnel Plot and Begg's test. RESULTS: Of 129 articles identified, 56 studies met the inclusion criteria encompassing 614,892 subjects...
February 7, 2018: Maternal and Child Health Journal
Kyson X Chou, Donna M Williams-Hill
Rapid advancement in genomics and bioinformatics in recent years holds great promise for research and development in many disciplines including public health. For the detection of pathogens, methods based on nucleic acid amplification need to be re-evaluated periodically to ensure the validity of signature primers and probes as more and more outbreak strains are sequenced and collected into databases in public domains. In this study, a previous assay designed computationally for detecting hepatitis A virus (HAV) was re-examined...
January 31, 2018: Journal of Virological Methods
Mutsumi Watanabe, Takayuki Tohge, Salma Balazadeh, Alexander Erban, Patrick Giavalisco, Joachim Kopka, Bernd Mueller-Roeber, Alisdair R Fernie, Rainer Hoefgen
Leaf senescence is an essential developmental process that involves diverse metabolic changes associated with degradation of macromolecules allowing nutrient recycling and remobilization. In contrast to the significant progress in transcriptomic analysis of leaf senescence, metabolomics analyses have been relatively limited. A broad overview of metabolic changes during leaf senescence including the interactions between various metabolic pathways is required to gain a better understanding of the leaf senescence allowing to link transcriptomics with metabolomics and physiology...
2018: Methods in Molecular Biology
Mahesh S Krishna, A Aneesh Kumar, K A Abdul Jaleel
Adipogenesis is a complex biological process involving synchronised interplay of different nuclear receptors. Aberration in the process leads to obesity and associated disorders. Addressing the complexity of molecular mechanisms, we worked on characterising the changes in NR1C3/PPARγ-, NR1H3/LXRα- and NCoAs/SRCs-associated microRNA, genes and proteins during different time points of adipogenesis. Glucose uptake of differentiating cells was checked at selected time points with FACS. Observations on gene expression pattern pointed a correlation in adipogenic-related genes and increased expression of PPARγ, but not LXRα...
February 1, 2018: Molecular and Cellular Biochemistry
Sean M Mythen, Saravanan Devendran, Celia Méndez-García, Isaac Cann, Jason M Ridlon
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids on gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDH) are pyridine nucleotide-dependent enzymes with stereo-specificity and regio-specificity for bile acid and steroid hydroxyl groups...
January 12, 2018: Applied and Environmental Microbiology
Daniel J Rigden, Xosé M Fernández
The 2018 Nucleic Acids Research Database Issue contains 181 papers spanning molecular biology. Among them, 82 are new and 84 are updates describing resources that appeared in the Issue previously. The remaining 15 cover databases most recently published elsewhere. Databases in the area of nucleic acids include 3DIV for visualisation of data on genome 3D structure and RNArchitecture, a hierarchical classification of RNA families. Protein databases include the established SMART, ELM and MEROPS while GPCRdb and the newcomer STCRDab cover families of biomedical interest...
January 4, 2018: Nucleic Acids Research
Z Dou, Z Jiang, P L Pan, W L Song, J Xu, Z Y Wu
Objective: To compare the community viral load (CVL) among MSM in 15 cities in China using standardized national reference sources. Methods: The study analyzed the existing database of National Major Science and Technology Project of China. The database was established with serial random survey of MSM HIV CVL among MSM in 15 cities from 2013 to 2015. VL tests were conducted in 15 laboratories with different equipment and methods, including RT-PCR, nucleic acid sequence based amplification (NASBA), branched DNA testing (bDNA) and Abbott M2000 RealTime system (M2000)...
December 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
Fredmoore L Orosco, Arturo O Lluisma
Marine animals typically harbor a community of viruses, a number of which are known to cause diseases. In shrimp aquaculture, viral pathogens are the principal causes of major economic losses. However, the composition of the viral load of shrimps in wild population is poorly known. In this study, we explored the viral diversity in the microbiome of wild Penaeus monodon collected from six sites in the Philippines, with a view to detecting pathogenic forms. We employed a metagenomic approach via particle-associated nucleic acid isolation, sequence-independent single primer amplification, and pyrosequencing...
September 2017: Virusdisease
Leonie J Barnett, Terrence L Miller
Species-level relationships of a complex of six putative acanthocolpid cercariae with ventral keels from nassariid gastropods from Capricornia, Queensland (Cercaria capricornia I-VI) were explored using mitochondrial and nuclear DNA sequence data. Analysis of the large subunit of nuclear ribosomal DNA (rDNA), the internal transcribed spacer 2 rDNA and subunit 3 of the nicotinamide-adenine-dinucleotide dehydrogenase mitochondrial gene indicates that the six distinct morphotypes previously identified relate to only three discrete genotypes...
December 26, 2017: Parasitology International
Kerri Basile, Jen Kok, Dominic E Dwyer
Successful treatment outcomes for viral respiratory tract infections presenting from primary health care to quaternary hospitals will only be achieved with rapid, sensitive and specific identification of pathogens to allow effective pathogen-specific antiviral therapy and infection control measures. Areas covered: This review aims to explore the different point-of-care tests currently available to diagnose viral respiratory tract infections, discuss the advantages and limitations of point-of-care testing, and provide insights into the future of point-of-care tests...
January 2018: Expert Review of Molecular Diagnostics
Nelson Gil, Andras Fiser
Motivation: Multiple sequence alignments (MSAs) can provide essential input to many bioinformatics applications, including protein structure prediction and functional annotation. However, the optimal selection of sequences to obtain a biologically informative MSAs for such purposes is poorly-explored, and has traditionally been performed manually. Results: We present SAMMI, an automated, sequence-based approach to objectively select an optimal MSA from a large set of alternatives sampled from a general sequence database search...
December 1, 2017: Bioinformatics
Priscyla Maria Vieira Mendes, Daila Leite Chaves Bezerra, Loanne Rocha Dos Santos, Raísa de Oliveira Santos, Stéfany Rodrigues de Sousa Melo, Jennifer Beatriz Silva Morais, Juliana Soares Severo, Sabas Carlos Vieira, Dilina do Nascimento Marreiro
Breast cancer is a disease of high mortality, characterized by the progressive accumulation of mutations that contribute to the uncontrolled development of breast tissue cells. Literature shows that disturbances in mineral homeostasis, such as magnesium, may interfere with tumor progression. The objective of this study is to provide updated information about magnesium's role in the pathogenesis of breast cancer. A review of literature was carried out from a search for articles in the PubMed and CAPES Periodicals databases published between 1995 and 2016 with the cross-references of the descriptors "magnesium," "breast neoplasms," and "oxidative stress" and the corresponding words in Portuguese...
December 2, 2017: Biological Trace Element Research
Claudio Campa, Carla Enrica Gallenga, Elena Bolletta, Paolo Perri
Background: Gene therapy represents the therapeutic delivery of nucleic acid polymers into a patient's cells with the aim of treating an underlying disease. Over the past 2 decades this new therapy has made substantial progress owing to better understanding of the pathobiologic basis of various diseases coupled with growth of gene transfer biotechnologies. The eye, in particular, represents a suitable target for such therapy due to the immune privilege provided by the blood-ocular barrier, the ability to directly visualize, access and locally treat the cells and the minimal amount of vector needed given the size of this organ...
November 16, 2017: Current Gene Therapy
Ali Amini, Olivia Varsaneux, Helen Kelly, Weiming Tang, Wen Chen, Debrah I Boeras, Jane Falconer, Joseph D Tucker, Roger Chou, Azumi Ishizaki, Philippa Easterbrook, Rosanna W Peeling
BACKGROUND: Chronic Hepatitis B Virus (HBV) infection is characterised by the persistence of hepatitis B surface antigen (HBsAg). Expanding HBV diagnosis and treatment programmes into low resource settings will require high quality but inexpensive rapid diagnostic tests (RDTs) in addition to laboratory-based enzyme immunoassays (EIAs) to detect HBsAg. The purpose of this review is to assess the clinical accuracy of available diagnostic tests to detect HBsAg to inform recommendations on testing strategies in 2017 WHO hepatitis testing guidelines...
November 1, 2017: BMC Infectious Diseases
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