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https://www.readbyqxmd.com/read/28937364/nucleic-acid-amplification-testing-in-indian-blood-banks-a-review-with-perspectives
#1
Kanjaksha Ghosh, Kanchan Mishra
BACKGROUND: Nucleic acid amplification testing (NAT) is restricted to a few blood banks in India since 2008. This review was directed toward understanding NAT yield in different parts of the country and prevalence in the NAT of different types of virus. MATERIALS AND METHODS: English literature was searched from 1990 to 2016 in PubMed, Scopus, Ind med, and Google database using properly constructed key words. Literature was collected and finally the data were synthesized...
July 2017: Indian Journal of Pathology & Microbiology
https://www.readbyqxmd.com/read/28932815/a-multicenter-study-to-evaluate-the-performance-of-high-throughput-sequencing-for-virus-detection
#2
Arifa S Khan, Siemon H S Ng, Olivier Vandeputte, Aisha Aljanahi, Avisek Deyati, Jean-Pol Cassart, Robert L Charlebois, Lanyn P Taliaferro
The capability of high-throughput sequencing (HTS) for detection of known and unknown viruses makes it a powerful tool for broad microbial investigations, such as evaluation of novel cell substrates that may be used for the development of new biological products. However, like any new assay, regulatory applications of HTS need method standardization. Therefore, our three laboratories initiated a study to evaluate performance of HTS for potential detection of viral adventitious agents by spiking model viruses in different cellular matrices to mimic putative materials for manufacturing of biologics...
September 2017: MSphere
https://www.readbyqxmd.com/read/28910345/circulating-mrnas-and-mirnas-as-candidate-markers-for-the-diagnosis-and-prognosis-of-prostate-cancer
#3
Marilesia Ferreira de Souza, Hellen Kuasne, Mateus de Camargo Barros-Filho, Heloísa Lizotti Cilião, Fabio Albuquerque Marchi, Paulo Emilio Fuganti, Alexandre Rossi Paschoal, Silvia Regina Rogatto, Ilce Mara de Syllos Cólus
Circulating nucleic acids are found in free form in body fluids and may serve as minimally invasive tools for cancer diagnosis and prognosis. Only a few studies have investigated the potential application of circulating mRNAs and microRNAs (miRNAs) in prostate cancer (PCa). The Cancer Genome Atlas (TCGA) database was used for an in silico analysis to identify circulating mRNA and miRNA as potential markers of PCa. A total of 2,267 genes and 49 miRNAs were differentially expressed between normal and tumor samples...
2017: PloS One
https://www.readbyqxmd.com/read/28905886/time-series-oligonucleotide-count-to-assign-antiviral-sirnas-with-long-utility-fit-in-the-big-data-era
#4
K Wada, Y Wada, Y Iwasaki, T Ikemura
Oligonucleotides are key elements of nucleic acid therapeutics such as small interfering RNAs (siRNAs). Influenza and Ebolaviruses are zoonotic RNA viruses mutating very rapidly, and their sequence changes must be characterized intensively to design therapeutic oligonucleotides with long utility. Focusing on a total of 182 experimentally validated siRNAs for influenza A, B and Ebolaviruses compiled by the siRNA database, we conducted time-series analyses of occurrences of siRNA targets in these viral genomes...
September 14, 2017: Gene Therapy
https://www.readbyqxmd.com/read/28887714/is-it-time-for-one-step-nucleic-acid-amplification-osna-in-colorectal-cancer-a-systematic-review-and-meta-analysis
#5
J B Wild, N Iqbal, J Francombe, T Papettas, D S Sanders, S Ramcharan
BACKGROUND: Lymph node metastasis (LNM) is prognostic in colorectal cancer (CRC). However, evaluation by routine haematoxylin and eosin histology (HE) limits nodal examination and is subjective. Missed LNMs from tissue allocation bias (TAB) might under-stage disease, leading to under-treatment. One-step nucleic acid amplification (OSNA) for CK19 messenger ribonucleic acid (mRNA), a marker of LNM, analyses the whole node. The aim of the present systematic review and meta-analysis was to assess recent studies on OSNA versus HE and its implications for CRC staging and treatment...
September 8, 2017: Techniques in Coloproctology
https://www.readbyqxmd.com/read/28869986/diagnostic-accuracy-of-novel-and-traditional-rapid-tests-for-influenza-infection-compared-with-reverse-transcriptase-polymerase-chain-reaction-a-systematic-review-and-meta-analysis
#6
Joanna Merckx, Rehab Wali, Ian Schiller, Chelsea Caya, Genevieve C Gore, Caroline Chartrand, Nandini Dendukuri, Jesse Papenburg
Background: Rapid and accurate influenza diagnostics can improve patient care. Purpose: To summarize and compare accuracy of traditional rapid influenza diagnostic tests (RIDTs), digital immunoassays (DIAs), and rapid nucleic acid amplification tests (NAATs) in children and adults with suspected influenza. Data Sources: 6 databases from their inception through May 2017. Study Selection: Studies in English, French, or Spanish comparing commercialized rapid tests (that is, providing results in <30 minutes) with reverse transcriptase polymerase chain reaction reference standard for influenza diagnosis...
September 19, 2017: Annals of Internal Medicine
https://www.readbyqxmd.com/read/28827558/analysis-of-mononucleotides-by-tandem-mass-spectrometry-investigation-of-fragmentation-pathways-for-phosphate-and-ribose-modified-nucleotide-analogues
#7
Dominika Strzelecka, Sebastian Chmielinski, Sylwia Bednarek, Jacek Jemielity, Joanna Kowalska
Synthetic nucleotide and nucleic acid analogues are useful research tools and modern therapeutics. Hence, methods for the rapid and unambiguous identification of mononucleotides derived from organic syntheses or biological materials are of broad interest. Here, we analysed over 150 mononucleotides (mostly nucleoside 5'-mono-, 5'-di-, and 5'-triphosphates) and their structurally related nucleobase-, phosphate-, and ribose-modified analogues by electrospray tandem mass spectrometry (ESI/MS/MS), identifying characteristic fragmentation ions that may be helpful in structure determination...
August 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28826221/genomic-enzymology-web-tools-for-leveraging-protein-family-sequence-function-space-and-genome-context-to-discover-novel-functions
#8
REVIEW
John A Gerlt
The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of "genomic enzymology" web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis...
August 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/28819973/mobile-platform-for-multiplexed-detection-and-differentiation-of-disease-specific-nucleic-acid-sequences-using-microfluidic-loop-mediated-isothermal-amplification-and-smartphone-detection
#9
Weili Chen, Hojeong Yu, Fu Sun, Akid Ornob, Ryan Brisbin, Anurup Ganguli, Vinay Vemuri, Piotr Strzebonski, Guangzhe Cui, Karen J Allen, Smit A Desai, Weiran Lin, David M Nash, David L Hirschberg, Ian Brooks, Rashid Bashir, Brian T Cunningham
New tools are needed to enable rapid detection, identification, and reporting of infectious viral and microbial pathogens in a wide variety of point-of-care applications that impact human and animal health. We report the design, construction, and characterization of a platform for multiplexed analysis of disease-specific DNA sequences that utilizes a smartphone camera as the sensor in conjunction with a hand-held "cradle" that interfaces the phone with a silicon-based microfluidic chip embedded within a credit-card-sized cartridge...
September 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28797030/one-step-nucleic-acid-amplification-assay-is-an-accurate-technique-for-sentinel-lymph-node-biopsy-of-breast-cancer-patients-a-meta-analysis
#10
Fang Shi, Qian Zhang, Zhenzhen Liang, Mengmeng Zhang, Xin Liu
BACKGROUND: To estimate the accuracy of one-step nucleic acid amplification (OSNA) assay as an intra-operative sentinel lymph node biopsy (SLNB) for sentinel lymph node (SLN) metastasis in breast cancer. METHODS: PubMed, Cochrane Library and Web of Science databases were searched by two independent reviewers to retrieve literature with per-patient analysis. The deadline was up until December 2016. A meta-analysis was performed using STATA, Meta-Disc, and Revman software...
August 10, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28753876/emerging-utility-of-urinary-cell-free-nucleic-acid-biomarkers-for-prostate-bladder-and-renal-cancers
#11
REVIEW
Selena Y Lin, Jennifer A Linehan, Timothy G Wilson, Dave S B Hoon
CONTEXT: By 2020 the estimated incidence of genitourinary (GU) cancers (prostate, bladder, and kidney) will be over 2 million worldwide and responsible for ∼800 000 deaths. Current diagnosis and monitoring methods of GU cancer patients are often invasive and/or lack sensitivity and specificity. Given the utility of blood-based cell-free nucleic acid (cfNA) biomarkers, the development of urinary cfNA biomarkers may improve the sensitivity of urine assays utilizing urine sediment for GU cancers...
March 31, 2017: European Urology Focus
https://www.readbyqxmd.com/read/28747168/the-biobank-for-the-molecular-classification-of-kidney-disease-research-translation-and-precision-medicine-in-nephrology
#12
Daniel A Muruve, Michelle C Mann, Kevin Chapman, Josee F Wong, Pietro Ravani, Stacey A Page, Hallgrimur Benediktsson
BACKGROUND: Advances in technology and the ability to interrogate disease pathogenesis using systems biology approaches are exploding. As exemplified by the substantial progress in the personalized diagnosis and treatment of cancer, the application of systems biology to enable precision medicine in other disciplines such as Nephrology is well underway. Infrastructure that permits the integration of clinical data, patient biospecimens and advanced technologies is required for institutions to contribute to, and benefit from research in molecular disease classification and to devise specific and patient-oriented treatments...
July 26, 2017: BMC Nephrology
https://www.readbyqxmd.com/read/28731300/solid-state-structures-of-lead-complexes-with-relevance-for-biological-systems
#13
Katsuyuki Aoki, Kazutaka Murayama, Ning-Hai Hu
Structural information on the interaction between lead ion and its targeting biological substances is important not only for enriching coordination chemistry of lead but for successfully treating lead poisoning that is a present-day problem. This chapter provides structural data, mainly metal binding sites/modes, observed in crystal structures of lead complexes with biorelevant molecules, obtained from the Cambridge Structural Database (the CSD version 5.36 updated to May 2015) and the Protein Data Bank (PDB updated to February 2016)...
April 10, 2017: Metal Ions in Life Sciences
https://www.readbyqxmd.com/read/28688205/utilization-of-organs-from-donors-according-to-hepatitis-c-antibody-and-nucleic-acid-testing-status-time-for-change
#14
C E Kling, J D Perkins, C S Landis, A P Limaye, L Sibulesky
Previous studies have grouped all donors positive for hepatitis C virus (HCV) antibody (Ab). Only recently has donor HCV nucleic acid testing (NAT) become routine, and the impact of Ab and NAT status on organ utilization is unknown. Using the United Network for Organ Sharing database, we identified 9290 donors from 2015 to 2016 for whom both HCV Ab and NAT data were available and compared organ utilization by HCV status. Overall, 93.8% of donors were Ab negative and NAT negative (Ab-NAT-), 0.15% were Ab negative and NAT positive, 1...
June 8, 2017: American Journal of Transplantation
https://www.readbyqxmd.com/read/28666733/virtual-screening-synthesis-and-biological-evaluation-of-dna-intercalating-antiviral-agents
#15
Kyrylo Klimenko, Sergey Lyakhov, Marina Shibinskaya, Alexander Karpenko, Gilles Marcou, Dragos Horvath, Marina Zenkova, Elena Goncharova, Rinat Amirkhanov, Andrei Krysko, Sergei Andronati, Igor Levandovskiy, Pavel Polishchuk, Victor Kuz'min, Alexandre Varnek
This paper describes computer-aided design of new anti-viral agents against Vaccinia virus (VACV) potentially acting as nucleic acid intercalators. Earlier obtained experimental data for DNA intercalation affinities and activities against Vesicular stomatitis virus (VSV) have been used to build, respectively, pharmacophore and QSAR models. These models were used for virtual screening of a database of 245 molecules generated around typical scaffolds of known DNA intercalators. This resulted in 12 hits which then were synthesized and tested for antiviral activity against VaV together with 43 compounds earlier studied against VSV...
August 15, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28660575/lipid-identification-by-untargeted-tandem-mass-spectrometry-coupled-with-ultra-high-pressure-liquid-chromatography
#16
Gabriel B Gugiu
Lipidomics refers to the large-scale study of lipids in biological systems (Wenk, Nat Rev Drug Discov 4(7):594-610, 2005; Rolim et al., Gene 554(2):131-139, 2015). From a mass spectrometric point of view, by lipidomics we understand targeted or untargeted mass spectrometric analysis of lipids using either liquid chromatography (LC) (Castro-Perez et al., J Proteome Res 9(5):2377-2389, 2010) or shotgun (Han and Gross, Mass Spectrom Rev 24(3):367-412, 2005) approaches coupled with tandem mass spectrometry. This chapter describes the former methodology, which is becoming rapidly the preferred method for lipid identification owing to similarities with established omics workflows, such as proteomics (Washburn et al...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28654728/finding-similar-nucleotide-sequences-using-network-blast-searches
#17
Istvan Ladunga
The Basic Local Alignment Search Tool (BLAST) is the first tool in the annotation of nucleotide or amino acid sequences. BLAST is a flagship of bioinformatics due to its performance and user-friendliness. Beginners and intermediate users will learn how to design and submit blastn and Megablast searches on the Web pages at the National Center for Biotechnology Information. We map nucleic acid sequences to genomes, find identical or similar mRNAs, expressed sequence tag, and noncoding RNA sequences, and run Megablast searches, which are much faster than blastn...
June 27, 2017: Current Protocols in Bioinformatics
https://www.readbyqxmd.com/read/28540697/in-silico-pcr-tools-for-a-fast-primer-probe-and-advanced-searching
#18
Ruslan Kalendar, Alexandr Muterko, Malika Shamekova, Kabyl Zhambakin
The polymerase chain reaction (PCR) is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. The principle of this technique has been further used and applied in plenty of other simple or complex nucleic acid amplification technologies (NAAT). In parallel to laboratory "wet bench" experiments for nucleic acid amplification technologies, in silico or virtual (bioinformatics) approaches have been developed, among which in silico PCR analysis. In silico NAAT analysis is a useful and efficient complementary method to ensure the specificity of primers or probes for an extensive range of PCR applications from homology gene discovery, molecular diagnosis, DNA fingerprinting, and repeat searching...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28502701/fastpcr-an-in-silico-tool-for-fast-primer-and-probe-design-and-advanced-sequence-analysis
#19
Ruslan Kalendar, Bekbolat Khassenov, Yerlan Ramankulov, Olga Samuilova, Konstantin I Ivanov
Polymerase chain reaction (PCR) is one of the most important laboratory techniques used in molecular biology, genetics and molecular diagnostics. The success of a PCR-based method largely depends on the correct nucleic acid sequence analysis in silico prior to a wet-bench experiment. Here, we report the development of an online Java-based software for virtual PCR on linear or circular DNA templates and multiple primer or probe search from large or small databases. Primer or probe sensitivity and specificity are predicted by searching a database to find sequences with an optimal number of mismatches, similarity and stability...
July 2017: Genomics
https://www.readbyqxmd.com/read/28490541/exosomes-as-mediators-of-the-systemic-adaptations-to-endurance-exercise
#20
Adeel Safdar, Mark A Tarnopolsky
Habitual endurance exercise training is associated with multisystemic metabolic adaptations that lower the risk of inactivity-associated disorders such as obesity and type 2 diabetes mellitus (T2DM). Identification of complex systemic signaling networks responsible for these benefits are of great interest because of their therapeutic potential in metabolic diseases; however, specific signals that modulate the multisystemic benefits of exercise in multiple tissues and organs are only recently being discovered...
May 10, 2017: Cold Spring Harbor Perspectives in Medicine
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