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https://www.readbyqxmd.com/read/28747168/the-biobank-for-the-molecular-classification-of-kidney-disease-research-translation-and-precision-medicine-in-nephrology
#1
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
#2
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
#3
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
#4
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...
June 13, 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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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...
July 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
#16
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
#17
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
#18
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
#19
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
#20
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
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