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https://www.readbyqxmd.com/read/28526789/a-novel-iron-dependent-enzyme-that-catalyzes-the-initial-step-in-the-biodegradation-of-n-nitroglycine-by-variovorax-sp-strain-js1663
#1
Kristina M Mahan, Hangping Zheng, Tekle T Fida, Ronald J Parry, David E Graham, Jim C Spain
Nitramines are key constituents of most of the explosives in current use and consequently contaminate soil and groundwater at many military facilities around the world. Toxicity from nitramine contamination poses a health risk to plants and animals, thus understanding how nitramines are biodegraded is critical to environmental remediation. The biodegradation of synthetic nitramine compounds such as hexahydro-1,3,5-trinitro-1,3,5- triazine (RDX) has been studied for decades, but little is known about the catabolism of naturally produced nitramine compounds...
May 19, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28526529/adding-biological-meaning-to-human-protein-protein-interactions-identified-by-yeast-two-hybrid-screenings-a-guide-through-bioinformatics-tools
#2
Juliana Felgueiras, Joana Vieira Silva, Margarida Fardilha
"A man is known by the company he keeps" is a popular expression that perfectly fits proteins. A common approach to characterize the function of a target protein is to identify its interacting partners and thus infer its roles based on the known functions of the interactors. Protein-protein interaction networks (PPINs) have been created for several organisms, including humans, primarily as results of high-throughput screenings, such as yeast two-hybrid (Y2H). Their unequivocal use to understand events underlying human pathophysiology is promising in identifying genes and proteins associated with diseases...
May 16, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28525954/construction-of-various-%C3%AE-34-5-deleted-fluorescent-expressing-oncolytic-herpes-simplex-type-1-ohsv-for-generation-and-isolation-of-hsv-based-vectors
#3
REVIEW
Shahriyar Abdoli, Farzin Roohvand, Ladan Teimoori-Toolabi, Mohammad Ali Shokrgozar, Mina Bahrololoumi, Kayhan Azadmanesh
Background: Oncolytic herpes simplex virus (oHSV)-based vectors lacking γ34.5 gene, are considered as ideal templates to construct efficient vectors for (targeted) cancer gene therapy. Herein, we reported the construction of three single/dually-flourescence labeled and γ34.5-deleted, recombinant HSV-1 vectors for rapid generation and easy selection/isolation of different HSV-Based vectors. Methods: Generation of recombinant viruses was performed with conventional homologous recombination methods using green fluorescent protein (GFP) and BleCherry harboring shuttle vectors...
July 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28523076/metaproteomics-guided-selection-of-targeted-enzymes-for-bioprospecting-of-mixed-microbial-communities
#4
Jutta Speda, Bengt-Harald Jonsson, Uno Carlsson, Martin Karlsson
BACKGROUND: Hitherto, the main goal of metaproteomic analyses has been to characterize the functional role of particular microorganisms in the microbial ecology of various microbial communities. Recently, it has been suggested that metaproteomics could be used for bioprospecting microbial communities to query for the most active enzymes to improve the selection process of industrially relevant enzymes. In the present study, to reduce the complexity of metaproteomic samples for targeted bioprospecting of novel enzymes, a microbial community capable of producing cellulases was maintained on a chemically defined medium in an enzyme suppressed metabolic steady state...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28523007/transcriptomic-identification-of-drought-related-genes-and-ssr-markers-in-sudan-grass-based-on-rna-seq
#5
Yongqun Zhu, Xia Wang, Linkai Huang, Chaowen Lin, Xinquan Zhang, Wenzhi Xu, Jianhua Peng, Zhou Li, Haidong Yan, Fuxiang Luo, Xie Wang, Li Yao, Dandan Peng
Sudan grass (Sorghum sudanense) is an annual warm-season gramineous forage grass that is widely used as pasture, hay, and silage. However, drought stress severely impacts its yield, and there is limited information about the mechanisms of drought tolerance in Sudan grass. In this study, we used next-generation sequencing to identify differentially expressed genes (DEGs) in the Sudan grass variety Wulate No.1, and we developed simple sequence repeat (SSR) markers associated with drought stress. From 852,543,826 raw reads, nearly 816,854,366 clean reads were identified and used for analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28521526/the-impact-of-genetics-on-future-drug-discovery-in-schizophrenia
#6
Mitsuyuki Matsumoto, Noah M Walton, Hiroshi Yamada, Yuji Kondo, Gerard J Marek, Katsunori Tajinda
Failures of investigational new drugs (INDs) for schizophrenia have left huge unmet medical needs for patients. Given the recent lackluster results, it is imperative that new drug discovery approaches (and resultant drug candidates) target pathophysiological alterations that are shared in specific, stratified patient populations that are selected based on pre-identified biological signatures. One path to implementing this paradigm is achievable by leveraging recent advances in genetic information and technologies...
May 18, 2017: Expert Opinion on Drug Discovery
https://www.readbyqxmd.com/read/28520805/identification-of-key-contributors-in-complex-population-structures
#7
Markus Neuditschko, Herman W Raadsma, Mehar S Khatkar, Elisabeth Jonas, Eike J Steinig, Christine Flury, Heidi Signer-Hasler, Mirjam Frischknecht, Ruedi von Niederhäusern, Tosso Leeb, Stefan Rieder
Evaluating the genetic contribution of individuals to population structure is essential to select informative individuals for genome sequencing, genotype imputation and to ascertain complex population structures. Existing methods for the selection of informative individuals for genomic imputation solely focus on the identification of key ancestors, which can lead to a loss of phasing accuracy of the reference population. Currently many methods are independently applied to investigate complex population structures...
2017: PloS One
https://www.readbyqxmd.com/read/28520401/identification-of-galnac-conjugated-antisense-oligonucleotide-metabolites-using-an-untargeted-and-generic-approach-based-on-high-resolution-mass-spectrometry
#8
Christophe Husser, Andreas Brink, Manfred Zell, Martina B Müller, Erich Koller, Simone Schadt
Antisense oligonucleotides linked by phosphorothioates are an important class of therapeutics under investigation in various pharmaceutical companies. Antisense oligonucleotides may be coupled to high-affinity ligands (triantennary N-acetyl ga-lactosamine = GalNAc) for hepatocyte-specific asialoglycoprotein receptors (ASGPR) to enhance uptake to hepatocytes and to increase potency. Since disposition and biotransformation of GalNAc-conjugated oligonucleotides is different from unconjugated oligonucleotides, appropriate analytical methods are required to identify main cleavage sites and degradation products of GalNAc conjugated and unconjugated oligonucleotides in target cells...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28517930/middle-down-193-nm-ultraviolet-photodissociation-for-unambiguous-antibody-identification-and-its-implications-for-immunoproteomic-analysis
#9
Victoria C Cotham, Andrew Pitchford Horton, Jiwon Lee, George Georgiou, Jennifer S Brodbelt
Mass spectrometry (MS) has emerged as a powerful tool within the growing field of immunoproteomics, which aims to understand antibody-mediated immunity at the molecular-level based on the direct determination of serological antibody repertoire. To date, these methods have relied on the use of high-resolution bottom-up proteomic strategies that require effective sampling and characterization of low abundance peptides derived from the antigen-binding domains of polyclonal antibody mixtures. Herein, we describe a method that uses restricted Lys-C enzymatic digestion to increase the average mass of proteolytic IgG peptides (≥4...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28516911/electrostatic-melting-in-a-single-molecule-field-effect-transistor-with-applications-in-genomic-identification
#10
Sefi Vernick, Scott M Trocchia, Steven B Warren, Erik F Young, Delphine Bouilly, Ruben L Gonzalez, Colin Nuckolls, Kenneth L Shepard
The study of biomolecular interactions at the single-molecule level holds great potential for both basic science and biotechnology applications. Single-molecule studies often rely on fluorescence-based reporting, with signal levels limited by photon emission from single optical reporters. The point-functionalized carbon nanotube transistor, known as the single-molecule field-effect transistor, is a bioelectronics alternative based on intrinsic molecular charge that offers significantly higher signal levels for detection...
May 18, 2017: Nature Communications
https://www.readbyqxmd.com/read/28516206/identification-expression-and-characterization-of-an-r-%C3%AF-transaminase-from-capronia-semiimmersa
#11
César Iglesias, Paola Panizza, Sonia Rodriguez Giordano
Chiral amines are essential precursors in the production of biologically active compounds, including several important drugs. Among the biocatalytic strategies that have been developed for their synthesis, the use of ω-transaminases (ω-TA) appears as an attractive alternative allowing the stereoselective amination of prochiral ketones. However, the problems associated with narrow substrate specificity, unfavourable reaction equilibrium and expensive amine donors still hamper its industrial application. The search for novel enzymes from nature can contribute to expand the catalytic repertoire of ω-TA and help to circumvent some of these problems...
May 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28515718/fungal-diversity-in-field-mold-damaged-soybean-fruits-and-pathogenicity-identification-based-on-high-throughput-rdna-sequencing
#12
Jiang Liu, Jun-Cai Deng, Cai-Qiong Yang, Ni Huang, Xiao-Li Chang, Jing Zhang, Feng Yang, Wei-Guo Liu, Xiao-Chun Wang, Tai-Wen Yong, Jun-Bo Du, Kai Shu, Wen-Yu Yang
Continuous rain and an abnormally wet climate during harvest can easily lead to soybean plants being damaged by field mold (FM), which can reduce seed yield and quality. However, to date, the underlying pathogen and its resistance mechanism have remained unclear. The objective of the present study was to investigate the fungal diversity of various soybean varieties and to identify and confirm the FM pathogenic fungi. A total of 62,382 fungal ITS1 sequences clustered into 164 operational taxonomic units (OTUs) with 97% sequence similarity; 69 taxa were recovered from the samples by internal transcribed spacer (ITS) region sequencing...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28515314/the-mzidentml-data-standard-version-1-2-supporting-advances-in-proteome-informatics
#13
Juan Antonio Vizcaíno, Gerhard Mayer, Simon R Perkins, Harald Barsnes, Marc Vaudel, Yasset Perez-Riverol, Tobias Ternent, Julian Uszkoreit, Martin Eisenacher, Lutz Fischer, Juri Rappsilber, Eugen Netz, Mathias Walzer, Oliver Kohlbacher, Alexander Leitner, Robert J Chalkley, Fawaz Ghali, Salvador Martínez-Bartolomé, Eric W Deutsch, Andrew R Jones
The first stable version of the Proteomics Standards Initiative mzIdentML open data standard (version 1.1) was published in 2012 - capturing the outputs of peptide and protein identification software. In the intervening years, the standard has become well supported in both commercial and open software, as well as a submission and download format for public repositories. Here we report a new release of mzIdentML (version 1.2) that is required to keep pace with emerging practice in proteome informatics. New features have been added to support: (i) scores associated with localization of modifications on peptides; (ii) statistics performed at the level of peptides; (iii) identification of cross-linked peptides; and (iv) support for proteogenomics approaches...
May 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28514720/new-application-for-haplotype-specific-extraction-separation-of-mitochondrial-dna-mixtures
#14
J Zander, J Rothe, J Dapprich, M Nagy
A particularly challenging aspect of forensic casework is the accurate interpretation of samples that contain DNA from more than one contributor, since DNA analysis of specific identification markers often results in ambiguous mixed profiles. Physically separating the various haploid components of a diploid or polyploid DNA sample or of a specimen containing DNA from multiple individuals can resolve this problem. We adapted and combined previously developed methods of haplotype-specific extraction (HSE) to separate and analyze mitochondrial DNA (mtDNA) in samples containing DNA from two individuals...
May 6, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28513534/unraveling-prion-protein-interactions-with-aptamers-and-other-prp-binding-nucleic-acids
#15
REVIEW
Bruno Macedo, Yraima Cordeiro
Transmissible spongiform encephalopathies (TSEs) are a group of neurodegenerative disorders that affect humans and other mammals. The etiologic agents common to these diseases are misfolded conformations of the prion protein (PrP). The molecular mechanisms that trigger the structural conversion of the normal cellular PrP (PrP(C)) into the pathogenic conformer (PrP(Sc)) are still poorly understood. It is proposed that a molecular cofactor would act as a catalyst, lowering the activation energy of the conversion process, therefore favoring the transition of PrP(C) to PrP(Sc)...
May 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28512371/first-report-of-the-spiral-nematode-helicotylenchus-microlobus-infecting-soybean-in-north-dakota
#16
Guiping Yan, Addison Plaisance, Danqiong Huang, Zafar A Handoo
Spiral nematodes (Helicotylenchus spp.) are common plant-parasitic nematodes in fields of many crops. In June 2015, two soil samples were collected from a soybean field in Richland County, ND. Nematodes were extracted from soil using the sugar centrifugal flotation method (Jenkins, 1964). Plant-parasitic nematodes were identified to genus based on morphological features and counted. Both samples contained spiral nematodes from 1,500 to 3,300 per kilogram of soil. In June and August 2016, 10 soil samples were collected from the same field...
March 2017: Journal of Nematology
https://www.readbyqxmd.com/read/28511691/tomato-root-microbiota-and-phytophthora-parasitica-associated-disease
#17
Marie Larousse, Corinne Rancurel, Camille Syska, Ferran Palero, Catherine Etienne, Benoît Industri, Xavier Nesme, Marc Bardin, Eric Galiana
BACKGROUND: Interactions between pathogenic oomycetes and microbiota residing on the surface of the host plant root are unknown, despite being critical to inoculum constitution. The nature of these interactions was explored for the polyphagous and telluric species Phytophthora parasitica. RESULTS: Composition of the rhizospheric microbiota of Solanum lycopersicum was characterized using deep re-sequencing of 16S rRNA gene to analyze tomato roots either free of or partly covered with P...
May 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28510639/toward-an-elucidation-of-the-molecular-genetics-of-inherited-retinal-degenerations
#18
G Jane Farrar, Matthew Carrigan, Adrian Dockery, Sophia Millington Ward, Arpad Palfi, Naomi Chadderton, Marian Humphries, Anna Sophia Kiang, Paul F Kenna, Pete Humphries
While individually classed as rare diseases, hereditary retinal degenerations (IRDs) are the major cause of registered visual handicap in the developed world. Given their hereditary nature, some degree of intergenic heterogeneity was expected, with genes segregating in autosomal dominant, recessive, X-linked recessive, and more rarely in digenic or mitochondrial modes. Today, it is recognized that IRDs, as a group, represent one of the most genetically diverse of hereditary conditions - at least 260 genes having been implicated, with 70 genes identified in the most common IRD, retinitis pigmentosa (RP)...
May 16, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28508728/high-frequency-of-identical-clonal-immunoglobulin-dna-in-pre-treatment-tumor-and-plasma-from-untreated-patients-with-hiv-associated-lymphoma-prospective-multicenter-trial-of-the-aids-malignancies-consortium-amc-064
#19
Nina D Wagner-Johnston, Shelly Lensing, Ariela Noy, Lee Ratner, David Henry, Jeannette Y Lee, Sylvia Silver, Malek Faham, Richard F Ambinder
Patients with HIV are at increased risk for developing B-cell lymphomas likely due in part to chronic antigen stimulation leading to clonal immunoglobulin (Ig) gene rearrangements. Next-generation sequencing (NGS)-based identification of circulating Ig clonotypes has not been well-characterized in HIV-related lymphomas. The AIDS Malignancies Consortium (AMC) enrolled 51 untreated patients with HIV-related B-cell lymphomas and analyzed paired tumor/plasma specimens for Ig clonotypes using an NGS approach (AMC064, NCT00981097)...
May 16, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/28508147/identification-of-beta-lactamases-and-beta-lactam-related-proteins-in-human-pathogenic-bacteria-using-a-computational-search-approach
#20
Aniel Jessica Leticia Brambila-Tapia, Ernesto Perez-Rueda, Humberto Barrios, Nory Omayra Dávalos-Rodríguez, Ingrid Patricia Dávalos-Rodríguez, Ernesto Germán Cardona-Muñoz, Mario Salazar-Páramo
A systematic analysis of beta-lactamases based on comparative proteomics has not been performed thus far. In this report, we searched for the presence of beta-lactam-related proteins in 591 bacterial proteomes belonging to 52 species that are pathogenic to humans. The amino acid sequences for 19 different types of beta-lactamases (ACT, CARB, CifA, CMY, CTX, FOX, GES, GOB, IMP, IND, KPC, LEN, OKP, OXA, OXY, SHV, TEM, NDM, and VIM) were obtained from the ARG-ANNOT database and were used to construct 19 HMM profiles, which were used to identify potential beta-lactamases in the completely sequenced bacterial proteomes...
May 16, 2017: Current Microbiology
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