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nucleic acid databases

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https://www.readbyqxmd.com/read/28540697/in-silico-pcr-tools-for-a-fast-primer-probe-and-advanced-searching
#1
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
#2
Ruslan Kalendar, Bekbolat Khassenov, Erlan Ramanculov, 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...
May 11, 2017: Genomics
https://www.readbyqxmd.com/read/28490541/exosomes-as-mediators-of-the-systemic-adaptations-to-endurance-exercise
#3
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
https://www.readbyqxmd.com/read/28466064/phylogenetic-analysis-of-classical-swine-fever-virus-from-archival-formalin-fixed-clinical-tissues-reveals-vietnamese-origin-of-the-isolates
#4
Vinod Kumar Singh, Kaushal Kishore Rajak
Detection of Classical swine fever virus (CSFV) nucleic acid in archival formalin fixed tissue samples and their use for phylogenetic analysis was investigated. Ten samples were examined for the presence of CSFV nucleic acid by reverse transcriptase polymerase chain reaction (RT-PCR) amplification of 5'UTR and E2 gene. RT-PCR was found positive for 5'UTR fragment in eight samples while only one tissue samples showed amplification for E2 gene target fragment. For molecular epidemiology of the disease, 5'UTR PCR product of sample from Darbhanga (Bihar), was cloned and sequenced...
March 2017: Virusdisease
https://www.readbyqxmd.com/read/28446765/three-dimensional-modeling-of-single-stranded-dna-hairpins-for-aptamer-based-biosensors
#5
Iman Jeddi, Leonor Saiz
Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility...
April 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420964/identification-of-the-spinal-expression-profile-of-non-coding-rnas-involved-in-neuropathic-pain-following-spared-nerve-injury-by-sequence-analysis
#6
Jun Zhou, Qingming Xiong, Hongtao Chen, Chengxiang Yang, Youling Fan
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. A non-coding Ribose Nucleic Acid (ncRNA) is an RNA molecule that is not translated into a protein. NcRNAs are involved in many cellular processes, and mutations or imbalances of the repertoire within the body can cause a variety of diseases. Although ncRNAs have recently been shown to play a role in NP pathogenesis, the specific effects of ncRNAs in NP remain largely unknown...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28417591/effective-mosquito-and-arbovirus-surveillance-using-metabarcoding
#7
J Batovska, S E Lynch, N O I Cogan, K Brown, J M Darbro, E A Kho, M J Blacket
Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next-generation sequencing (NGS) is a high-throughput technology that has the potential to modernise vector surveillance. When combined with DNA barcoding, it is termed 'metabarcoding'. The aim of our study was to establish a metabarcoding protocol to characterise pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%...
April 18, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28383703/mcsm-na-predicting-the-effects-of-mutations-on-protein-nucleic-acids-interactions
#8
Douglas E V Pires, David B Ascher
Over the past two decades, several computational methods have been proposed to predict how missense mutations can affect protein structure and function, either by altering protein stability or interactions with its partners, shedding light into potential molecular mechanisms giving rise to different phenotypes. Effectively and efficiently predicting consequences of mutations on protein-nucleic acid interactions, however, remained until recently a great and unmet challenge. Here we report an updated webserver for mCSM-NA, the only scalable method we are aware of capable of quantitatively predicting the effects of mutations in protein coding regions on nucleic acid binding affinities...
April 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28370740/a-global-trait-based-approach-to-estimate-leaf-nitrogen-functional-allocation-from-observations
#9
Bardan Ghimire, William J Riley, Charles D Koven, Jens Kattge, Alistair Rogers, Peter B Reich, Ian J Wright
Nitrogen is one of the most important nutrients for plant growth and a major constituent of proteins that regulate photosynthetic and respiratory processes. However, a comprehensive global analysis of nitrogen allocation in leaves for major processes with respect to different plant functional types (PFTs) is currently lacking. This study integrated observations from global databases with photosynthesis and respiration models to determine plant-functional-type-specific allocation patterns of leaf nitrogen for photosynthesis (Rubisco, electron transport, light absorption) and respiration (growth and maintenance), and by difference from observed total leaf nitrogen, an unexplained "residual" nitrogen pool...
March 28, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28291811/systematic-identification-and-characterization-of-long-non-coding-rnas-in-mouse-mature-sperm
#10
Xiaoning Zhang, Fengxin Gao, Jianbo Fu, Peng Zhang, Yuqing Wang, Xuhui Zeng
Increasing studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long non-coding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20,907 known and 4,088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28287524/a-web-tool-for-generating-high-quality-machine-readable-biological-pathways
#11
Miguel Ramirez-Gaona, Ana Marcu, Allison Pon, Jason Grant, Anthony Wu, David S Wishart
PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events...
February 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28266272/multiscale-molecular-simulations-applied-to-nucleic-acid-dendrimer-interactions-studies
#12
Valeria Márquez-Miranda, Ingrid Araya-Durán, Fernando Danilo González-Nilo
BACKGROUND: Dendrimers are monodisperse, regular, three-dimensional and small-scale macromolecules that can be used to release substances such as drugs, markers, and genetic material into the cells. Among these substances, nucleic acids such as plasmid DNA, antisense oligonucleotides (asODN), and small-interfering RNA (siRNA) are widely used as therapeutic macromolecules for the treatment and prevention of diverse diseases. Several studies were focused on the modification of dendrimers aiming to improve their affinity for nucleic acids and their ability to release nucleic acids inside the cells...
March 5, 2017: Current Pharmaceutical Design
https://www.readbyqxmd.com/read/28263762/development-and-evaluation-of-taqman-real-time-pcr-assay-for-detection-of-beak-and-feather-disease-virus
#13
Lenka Černíková, Eliška Vitásková, Alexander Nagy
Psittacine beak and feather disease (PBFD) is one of the most significant viral diseases in psittacine birds. The aim of the presented study was to develop a highly specific and sensitive TaqMan real-time PCR assay for universal detection of beak and feather disease virus (BFDV). Primers and a hydrolysis probe were selected on the highly conserved regions belonging to the ORF1 of the BFDV genome which were identified by aligning 814 genomic sequences downloaded from the GenBank database. The evaluation of the reaction parameters suggested a reaction efficiency of 97...
March 2, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28188804/metabolite-profiling-of-infection-associated-metabolic-markers-of-onchocerciasis
#14
Sasisekhar Bennuru, Sara Lustigman, David Abraham, Thomas B Nutman
The global efforts for onchocerciasis elimination may require additional tools (safe micro and macrofilaricidal drugs, vaccines and biomarkers) as elimination efforts move toward the "end game". Efforts toward the identification of suitable biomarkers have focused on specific protein(s) and/or nucleic acids, but metabolites present an alternative option as they have limited half-lives and are the result of combinatorial effects. In comparison to previously used methodology of LC-MS for metabolomic approaches, we used a non-targeted capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) to analyze the serum metabolic profiles of Ov-infected and -uninfected individuals (n=20)...
July 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28165358/extending-immunological-profiling-in-the-gilthead-sea-bream-sparus-aurata-by-enriched-cdna-library-analysis-microarray-design-and-initial-studies-upon-the-inflammatory-response-to-pamps
#15
Sebastian Boltaña, Barbara Castellana, Giles Goetz, Lluis Tort, Mariana Teles, Victor Mulero, Beatriz Novoa, Antonio Figueras, Frederick W Goetz, Cristian Gallardo-Escarate, Josep V Planas, Simon Mackenzie
This study describes the development and validation of an enriched oligonucleotide-microarray platform for Sparus aurata (SAQ) to provide a platform for transcriptomic studies in this species. A transcriptome database was constructed by assembly of gilthead sea bream sequences derived from public repositories of mRNA together with reads from a large collection of expressed sequence tags (EST) from two extensive targeted cDNA libraries characterizing mRNA transcripts regulated by both bacterial and viral challenge...
February 3, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28100696/the-24th-annual-nucleic-acids-research-database-issue-a-look-back-and-upcoming-changes
#16
Michael Y Galperin, Xosé M Fernández-Suárez, Daniel J Rigden
No abstract text is available yet for this article.
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28093921/microbial-genomics-and-antimicrobial-susceptibility-testing
#17
W Michael Dunne, Magali Jaillard, Olivier Rochas, Alex Van Belkum
Antimicrobial susceptibility testing is key in modern clinical microbiology. With pandemic emergence of (multi-)antibiotic resistance, methods to detect and quantify resistance of clinically important bacterial species are imperative. Historically, antimicrobial susceptibility testing (AST) was mostly performed using methods relying on bacterial growth. Such methods may be time-consuming and more rapid alternatives have been actively sought for. Areas covered: Among the new AST methods there are many that focus on detection of causal resistance genes and/or gene mutations...
March 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28065598/cas13b-is-a-type-vi-b-crispr-associated-rna-guided-rnase-differentially-regulated-by-accessory-proteins-csx27-and-csx28
#18
Aaron A Smargon, David B T Cox, Neena K Pyzocha, Kaijie Zheng, Ian M Slaymaker, Jonathan S Gootenberg, Omar A Abudayyeh, Patrick Essletzbichler, Sergey Shmakov, Kira S Makarova, Eugene V Koonin, Feng Zhang
CRISPR-Cas adaptive immune systems defend microbes against foreign nucleic acids via RNA-guided endonucleases. Using a computational sequence database mining approach, we identify two class 2 CRISPR-Cas systems (subtype VI-B) that lack Cas1 and Cas2 and encompass a single large effector protein, Cas13b, along with one of two previously uncharacterized associated proteins, Csx27 and Csx28. We establish that these CRISPR-Cas systems can achieve RNA interference when heterologously expressed. Through a combination of biochemical and genetic experiments, we show that Cas13b processes its own CRISPR array with short and long direct repeats, cleaves target RNA, and exhibits collateral RNase activity...
February 16, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28056497/taxonomic-distribution-repeats-and-functions-of-the-s1-domain-containing-proteins-as-members-of-the-ob-fold-family
#19
Evgeniia I Deryusheva, Andrey V Machulin, Olga M Selivanova, Oxana V Galzitskaya
Proteins of the nucleic acid-binding proteins superfamily perform such functions as processing, transport, storage, stretching, translation, and degradation of RNA. It is one of the 16 superfamilies containing the OB-fold in protein structures. Here, we have analyzed the superfamily of nucleic acid-binding proteins (the number of sequences exceeds 200,000) and obtained that this superfamily prevalently consists of proteins containing the cold shock DNA-binding domain (ca. 131,000 protein sequences). Proteins containing the S1 domain compose 57% from the cold shock DNA-binding domain family...
January 5, 2017: Proteins
https://www.readbyqxmd.com/read/28053169/nucleic-acids-research-volume-45-database-issue-january-4-2017
#20
(no author information available yet)
No abstract text is available yet for this article.
January 4, 2017: Nucleic Acids Research
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