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https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#1
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29346071/identification-of-potential-inhibitors-against-nuclear-dam1-complex-subunit-ask1-of-candida-albicans-using-virtual-screening-and-md-simulations
#2
Himanshu Tripathi, Feroz Khan
Identification of hit compounds against specific target form the starting point for a drug discovery program. A consistent decline of new chemical entities (NCEs) in recent years prompted a challenge to explore newer approaches to discover potential hit compounds that in turn can be converted into leads, and ultimately drug with desired therapeutic efficacy. The vast amount of omics and activity data available in public databases offers an opportunity to identify novel targets and their potential inhibitors...
January 1, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29345015/dynamic-sex-chromosomes-in-old-world-chameleons-squamata-chamaeleonidae
#3
S V Nielsen, J L Banks, R E Diaz, P A Trainor, T Gamble
Much of our current state of knowledge concerning sex chromosome evolution is based on a handful of 'exceptional' taxa with heteromorphic sex chromosomes. However, classifying the sex chromosome systems of additional species lacking easily identifiable, heteromorphic sex chromosomes is indispensible if we wish to fully understand the genesis, degeneration, and turnover of vertebrate sex chromosomes. Squamate reptiles (lizards and snakes) are a potential model clade for studying sex chromosome evolution as they exhibit a suite of sex determining modes yet most species lack heteromorphic sex chromosomes...
January 18, 2018: Journal of Evolutionary Biology
https://www.readbyqxmd.com/read/29343758/electronic-properties-of-synthetic-shrimp-pathogens-derived-dna-schottky-diodes
#4
Nastaran Rizan, Chan Yen Yew, Maryam Rajabpour Niknam, Jegenathan Krishnasamy, Subha Bhassu, Goh Zee Hong, Sridevi Devadas, Mohamed Shariff Mohd Din, Hairul Anuar Tajuddin, Rofina Yasmin Othman, Siew Moi Phang, Mitsumasa Iwamoto, Vengadesh Periasamy
The exciting discovery of the semiconducting-like properties of deoxyribonucleic acid (DNA) and its potential applications in molecular genetics and diagnostics in recent times has resulted in a paradigm shift in biophysics research. Recent studies in our laboratory provide a platform towards detecting charge transfer mechanism and understanding the electronic properties of DNA based on the sequence-specific electronic response, which can be applied as an alternative to identify or detect DNA. In this study, we demonstrate a novel method for identification of DNA from different shrimp viruses and bacteria using electronic properties of DNA obtained from both negative and positive bias regions in current-voltage (I-V) profiles...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29343059/top-down-characterization-of-heavily-modified-histones-using-193-nm-ultraviolet-photodissociation-uvpd-mass-spectrometry
#5
Sylvester M Greer, Jennifer S Brodbelt
The characterization of protein post-translational modifications (PTMs) remains a significant challenge for traditional bottom-up proteomics methods owing to the lability of PTMs and the difficulty of mapping combinatorial patterns of PTMs based on analysis of small peptides. These shortcomings have accelerated interest in top-down MS/MS methods which focus on analysis of intact proteins. Mapping all protein PTMs simultaneously requires the ability to obtain extensive sequence coverage to allow confident localization of the modifications...
January 18, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29342893/qtl-mapping-for-fiber-quality-and-yield-traits-based-on-introgression-lines-derived-from-gossypium-hirsutum-%C3%A3-g-tomentosum
#6
Ayaz Ali Keerio, Chao Shen, Yichun Nie, Muhammad Mahmood Ahmed, Xianlong Zhang, Zhongxu Lin
The tetraploid species Gossypium hirsutum is cultivated widely throughout the world with high yield and moderate fiber quality, but its genetic basis is narrow. A set of 107 introgression lines (ILs) was developed with an interspecific cross using G. hirsutumacc. 4105 as the recurrent parent and G. tomentosum as the donor parent. A specific locus amplified fragment sequencing (SLAF-seq) strategy was used to obtain high-throughput single nucleotide polymorphism (SNP) markers. In total, 3157 high-quality SNP markers were obtained and further used for identification of quantitative trait loci (QTLs) for fiber quality and yield traits evaluated in multiple environments...
January 14, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29342213/circulating-neutrophil-transcriptome-may-reveal-intracranial-aneurysm-signature
#7
Vincent M Tutino, Kerry E Poppenberg, Kaiyu Jiang, James N Jarvis, Yijun Sun, Ashish Sonig, Adnan H Siddiqui, Kenneth V Snyder, Elad I Levy, John Kolega, Hui Meng
BACKGROUND: Unruptured intracranial aneurysms (IAs) are typically asymptomatic and undetected except for incidental discovery on imaging. Blood-based diagnostic biomarkers could lead to improvements in IA management. This exploratory study examined circulating neutrophils to determine whether they carry RNA expression signatures of IAs. METHODS: Blood samples were collected from patients receiving cerebral angiography. Eleven samples were collected from patients with IAs and 11 from patients without IAs as controls...
2018: PloS One
https://www.readbyqxmd.com/read/29340898/epidemiological-aspects-of-healthcare-associated-infections-and-microbial-genomics
#8
C Mirande, I Bizine, A Giannetti, N Picot, A van Belkum
Hospital-acquired infections (HAIs) are a cause of continuously increasing morbidity and mortality. Most of these infections are caused by a limited set of bacterial species, which share the capability to efficiently spread from patient to patient and to easily acquire antibiotic resistance determinants. This renders correct and rapid species identification and antibiotic susceptibility testing (AST) important and underscores the relevance of bacterial epidemiological typing. The latter is needed for the sensitive detection and exact tracing of nosocomial spread of these potentially multidrug-resistant microorganisms (MDRO)...
January 17, 2018: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/29340786/in-silico-identification-and-experimental-validation-of-amino-acid-motifs-required-for-the-rho-of-plants-gtpase-mediated-activation-of-receptor-like-cytoplasmic-kinases
#9
Dézi Bianka Lajkó, Ildikó Valkai, Mónika Domoki, Dalma Ménesi, Györgyi Ferenc, Ferhan Ayaydin, Attila Fehér
Several amino acid motifs required for Rop-dependent activity were found to form a common surface on RLCKVI_A kinases. This indicates a unique mechanism for Rho-type GTPase-mediated kinase activation in plants. Rho-of-plants (Rop) G-proteins are implicated in the regulation of various cellular processes, including cell growth, cell polarity, hormonal and pathogen responses. Our knowledge about the signalling pathways downstream of Rops is continuously increasing. However, there are still substantial gaps in this knowledge...
January 16, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29340783/identification-of-bat-trypanosomes-from-minas-gerais-state-brazil-based-on-18s-rdna-and-cathepsin-l-like-targets
#10
Elaine Cristina Bento, César Gómez-Hernández, Lara Rocha Batista, Laís Anversa, André Luiz Pedrosa, Eliane Lages-Silva, Juan David Ramírez, Luis Eduardo Ramirez
Several bat species can be infected by trypanosomes, but there is not much information about which of these parasites infect bats from Triângulo Mineiro and Alto Paranaíba, Minas Gerais state, Brazil, a formerly endemic region for Trypanosoma cruzi, the causative agent of Chagas disease. The aim of this study was to describe, characterize, and identify the presence of trypanosomes in bats. The captured bats (448) belong to four families and to 19 different species. Of those, 37 bats were found to be positive for trypanosomes by microhematocrit, (infection rate 8...
January 16, 2018: Parasitology Research
https://www.readbyqxmd.com/read/29339971/terzyme-a-tool-for-identification-and-analysis-of-the-plant-terpenome
#11
Piyush Priya, Archana Yadav, Jyoti Chand, Gitanjali Yadav
Background: Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data...
2018: Plant Methods
https://www.readbyqxmd.com/read/29339834/use-of-multicolor-fluorescence-in-situ-hybridization-to-detect-deletions-in-clinical-tissue-sections
#12
REVIEW
Maisa Yoshimoto, Olga Ludkovski, Jennifer Good, Ciro Pereira, Robert J Gooding, Jean McGowan-Jordan, Alexander Boag, Andrew Evans, Ming-Sound Tsao, Paulo Nuin, Jeremy A Squire
A variety of laboratory methods are available for the detection of deletions of tumor suppressor genes and losses of their proteins. The clinical utility of fluorescence in situ hybridization (FISH) for the identification of deletions of tumor suppressor genes has previously been limited by difficulties in the interpretation of FISH signal patterns. The first deletion FISH assays using formalin-fixed paraffin-embedded tissue sections had to deal with a significant background level of signal losses affecting nuclei that are truncated by the cutting process of slide preparation...
January 16, 2018: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/29337438/3d-e-chem-structural-cheminformatics-workflows-for-computer-aided-drug-discovery
#13
Albert J Kooistra, Marton Vass, Ross McGuire, Rob Leurs, Iwan Jp de Esch, Gerrit Vriend, Stefan Verhoeven, Chris de Graaf
eScience technologies are needed to process the information available in many heterogeneous types of protein-ligand interaction data and to capture these data into models that enable the design of efficacious and safe medicines. Here we present scientific KNIME tools and workflows that enable the integration of chemical, pharmacological, and structural information for: i) structure-based bioactivity data mapping, ii) structure-based identification of scaffold replacement strategies for ligand design, iii) ligand-based target prediction, iv) protein sequence-based binding site identification and ligand repurposing, and v) structure-based pharmacophore comparison for ligand repurposing across protein families...
January 16, 2018: ChemMedChem
https://www.readbyqxmd.com/read/29337219/citrus-bioflavonoid-hesperetin-as-inhibitor-of-two-thrombin-like-snake-venom-serine-proteases-isolated-from-crotalus-simus
#14
Roney Vander Dos Santos, Fabian Villalta-Romero, Danijela Stanisic, Luiz Borro, Goran Neshich, Ljubica Tasic
Around 5.5 million people suffer from snakebites per year, with about 400,000 cases with some type of sequelae, such as amputation, and 20,000 to 125,000 cases with the fatal end. Usually, the victim outcome depends on correct, agile and many times in situ intervention based on the proper identification of the snake venom type and its potential effects, among other factors. Therefore, knowledge on the snake venom composition and a research on inhibitors of snake venom target components might ameliorate envenoming dangerous outcome...
January 11, 2018: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/29336305/inferring-joint-sequence-structural-determinants-of-protein-functional-specificity
#15
Andrew F Neuwald, L Aravind, Stephen F Altschul
Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues distinguishing a protein subgroup from evolutionarily divergent subgroups often constitute an interacting functional network. We identify such networks with the aid of two measures of statistical significance. One measure aids identification of divergent subgroups based on distinguishing residue patterns...
January 16, 2018: ELife
https://www.readbyqxmd.com/read/29336192/how-mass-spectrometric-approaches-applied-to-bacterial-identification-have-revolutionized-the-study-of-human-gut-microbiota
#16
Grégory Dubourg, Hervé Chaudet, Jean-Christophe Lagier, Didier Raoult
Describing the human hut gut microbiota is one the most exciting challenges of the 21st century. Currently, high-throughput sequencing methods are considered as the gold standard for this purpose, however, they suffer from several drawbacks, including their inability to detect minority populations. The advent of mass-spectrometric (MS) approaches to identify cultured bacteria in clinical microbiology enabled the creation of the culturomics approach, which aims to establish a comprehensive repertoire of cultured prokaryotes from human specimens using extensive culture conditions...
January 16, 2018: Expert Review of Proteomics
https://www.readbyqxmd.com/read/29335281/high-throughput-identification-of-rna-nuclear-enrichment-sequences
#17
Chinmay J Shukla, Alexandra L McCorkindale, Chiara Gerhardinger, Keegan D Korthauer, Moran N Cabili, David M Shechner, Rafael A Irizarry, Philipp G Maass, John L Rinn
In the post-genomic era, thousands of putative noncoding regulatory regions have been identified, such as enhancers, promoters, long noncoding RNAs (lncRNAs), and a cadre of small peptides. These ever-growing catalogs require high-throughput assays to test their functionality at scale. Massively parallel reporter assays have greatly enhanced the understanding of noncoding DNA elements en masse Here, we present a massively parallel RNA assay (MPRNA) that can assay 10,000 or more RNA segments for RNA-based functionality...
January 15, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29335005/in-depth-resistome-analysis-by-targeted-metagenomics
#18
Val F Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J Willems, Fernando de la Cruz, Teresa M Coque
BACKGROUND: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29334982/genome-wide-identification-characterization-and-classification-of-ionotropic-glutamate-receptor-genes-iglurs-in-the-malaria-vector-anopheles-sinensis-diptera-culicidae
#19
Ting-Ting Wang, Feng-Ling Si, Zheng-Bo He, Bin Chen
BACKGROUND: Ionotropic glutamate receptors (iGluRs) are conserved ligand-gated ion channel receptors, and ionotropic receptors (IRs) were revealed as a new family of iGluRs. Their subdivision was unsettled, and their characteristics are little known. Anopheles sinensis is a major malaria vector in eastern Asia, and its genome was recently well sequenced and annotated. METHODS: We identified iGluR genes in the An. sinensis genome, analyzed their characteristics including gene structure, genome distribution, domains and specific sites by bioinformatic methods, and deduced phylogenetic relationships of all iGluRs in An...
January 15, 2018: Parasites & Vectors
https://www.readbyqxmd.com/read/29334894/rare-variant-association-analysis-in-case-parents-studies-by-allowing-for-missing-parental-genotypes
#20
Yumei Li, Yang Xiang, Chao Xu, Hui Shen, Hongwen Deng
BACKGROUND: The development of next-generation sequencing technologies has facilitated the identification of rare variants. Family-based design is commonly used to effectively control for population admixture and substructure, which is more prominent for rare variants. Case-parents studies, as typical strategies in family-based design, are widely used in rare variant-disease association analysis. Current methods in case-parents studies are based on complete case-parents data; however, parental genotypes may be missing in case-parents trios, and removing these data may lead to a loss in statistical power...
January 15, 2018: BMC Genetics
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