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Microbial bioinformatics

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https://www.readbyqxmd.com/read/27903821/construction-of-a-minimal-genome-as-a-chassis-for-synthetic-biology
#1
REVIEW
Bong Hyun Sung, Donghui Choe, Sun Chang Kim, Byung-Kwan Cho
Microbial diversity and complexity pose challenges in understanding the voluminous genetic information produced from whole-genome sequences, bioinformatics and high-throughput '-omics' research. These challenges can be overcome by a core blueprint of a genome drawn with a minimal gene set, which is essential for life. Systems biology and large-scale gene inactivation studies have estimated the number of essential genes to be ∼300-500 in many microbial genomes. On the basis of the essential gene set information, minimal-genome strains have been generated using sophisticated genome engineering techniques, such as genome reduction and chemical genome synthesis...
November 30, 2016: Essays in Biochemistry
https://www.readbyqxmd.com/read/27899609/enabling-the-democratization-of-the-genomics-revolution-with-a-fully-integrated-web-based-bioinformatics-platform
#2
Po-E Li, Chien-Chi Lo, Joseph J Anderson, Karen W Davenport, Kimberly A Bishop-Lilly, Yan Xu, Sanaa Ahmed, Shihai Feng, Vishwesh P Mokashi, Patrick S G Chain
Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27896028/the-scavenger-receptor-repertoire-in-six-cnidarian-species-and-its-putative-role-in-cnidarian-dinoflagellate-symbiosis
#3
Emilie F Neubauer, Angela Z Poole, Virginia M Weis, Simon K Davy
Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians have diverse and complex innate immune repertoires that are just beginning to be described. Scavenger receptors (SR) are a diverse superfamily of innate immunity genes that recognize a broad array of microbial ligands and participate in phagocytosis of invading microbes...
2016: PeerJ
https://www.readbyqxmd.com/read/27893735/computational-discovery-of-putative-leads-for-drug-repositioning-through-drug-target-interaction-prediction
#4
Edgar D Coelho, Joel P Arrais, José Luís Oliveira
De novo experimental drug discovery is an expensive and time-consuming task. It requires the identification of drug-target interactions (DTIs) towards targets of biological interest, either to inhibit or enhance a specific molecular function. Dedicated computational models for protein simulation and DTI prediction are crucial for speed and to reduce the costs associated with DTI identification. In this paper we present a computational pipeline that enables the discovery of putative leads for drug repositioning that can be applied to any microbial proteome, as long as the interactome of interest is at least partially known...
November 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27892518/brain-microbiota-disruption-within-inflammatory-demyelinating-lesions-in-multiple-sclerosis
#5
W G Branton, J Q Lu, M G Surette, R A Holt, J Lind, J D Laman, C Power
Microbial communities reside in healthy tissues but are often disrupted during disease. Bacterial genomes and proteins are detected in brains from humans, nonhuman primates, rodents and other species in the absence of neurological disease. We investigated the composition and abundance of microbiota in frozen and fixed autopsied brain samples from patients with multiple sclerosis (MS) and age- and sex-matched nonMS patients as controls, using neuropathological, molecular and bioinformatics tools. 16s rRNA sequencing revealed Proteobacteria to be the dominant phylum with restricted diversity in cerebral white matter (WM) from MS compared to nonMS patients...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27888332/interaction-of-gut-microbiota-with-bile-acid-metabolism-and-its-influence-on-disease-states
#6
REVIEW
Christopher Staley, Alexa R Weingarden, Alexander Khoruts, Michael J Sadowsky
Primary bile acids serve important roles in cholesterol metabolism, lipid digestion, host-microbe interactions, and regulatory pathways in the human host. While most bile acids are reabsorbed and recycled via enterohepatic cycling, ∼5% serve as substrates for bacterial biotransformation in the colon. Enzymes involved in various transformations have been characterized from cultured gut bacteria and reveal taxa-specific distribution. More recently, bioinformatic approaches have revealed greater diversity in isoforms of these enzymes, and the microbial species in which they are found...
November 25, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27884202/extending-colonic-mucosal-microbiome-analysis-assessment-of-colonic-lavage-as-a-proxy-for-endoscopic-colonic-biopsies
#7
Euan Watt, Matthew R Gemmell, Susan Berry, Mark Glaire, Freda Farquharson, Petra Louis, Graeme I Murray, Emad El-Omar, Georgina L Hold
BACKGROUND: Sequencing-based analysis has become a well-established approach to deciphering the composition of the gut microbiota. However, due to the complexity of accessing sufficient material from colonoscopic biopsy samples, most studies have focused on faecal microbiota analysis, even though it is recognised that differences exist between the microbial composition of colonic biopsies and faecal samples. We determined the suitability of colonic lavage samples to see if it had comparable microbial diversity composition to colonic biopsies as they are without the limitations associated with sample size...
November 25, 2016: Microbiome
https://www.readbyqxmd.com/read/27883048/proteomic-profile-of-the-bradysia-odoriphaga-in-response-to-the-microbial-secondary-metabolite-benzothiazole
#8
Yunhe Zhao, Kaidi Cui, Chunmei Xu, Qiuhong Wang, Yao Wang, Zhengqun Zhang, Feng Liu, Wei Mu
Benzothiazole, a microbial secondary metabolite, has been demonstrated to possess fumigant activity against Sclerotinia sclerotiorum, Ditylenchus destructor and Bradysia odoriphaga. However, to facilitate the development of novel microbial pesticides, the mode of action of benzothiazole needs to be elucidated. Here, we employed iTRAQ-based quantitative proteomics analysis to investigate the effects of benzothiazole on the proteomic expression of B. odoriphaga. In response to benzothiazole, 92 of 863 identified proteins in B...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27882328/genomic-analysis-of-a-marine-bacterium-bioinformatics-for-comparison-evaluation-and-interpretation-of-dna-sequences
#9
Bhagwan N Rekadwad, Juan M Gonzalez, Chandrahasya N Khobragade
A total of five highly related strains of an unidentified marine bacterium were analyzed through their short genome sequences (AM260709-AM260713). Genome-to-Genome Distance (GGDC) showed high similarity to Pseudoalteromonas haloplanktis (X67024). The generated unique Quick Response (QR) codes indicated no identity to other microbial species or gene sequences. Chaos Game Representation (CGR) showed the number of bases concentrated in the area. Guanine residues were highest in number followed by cytosine. Frequency of Chaos Game Representation (FCGR) indicated that CC and GG blocks have higher frequency in the sequence from the evaluated marine bacterium strains...
2016: BioMed Research International
https://www.readbyqxmd.com/read/27881978/the-oxidosqualene-cyclase-from-the-oomycete-saprolegnia-parasitica-synthesizes-lanosterol-as-a-single-product
#10
Paul Dahlin, Vaibhav Srivastava, Vincent Bulone, Lauren S McKee
The first committed step of sterol biosynthesis is the cyclisation of 2,3-oxidosqualene to form either lanosterol (LA) or cycloartenol (CA). This is catalyzed by an oxidosqualene cyclase (OSC). LA and CA are subsequently converted into various sterols by a series of enzyme reactions. The specificity of the OSC therefore determines the final composition of the end sterols of an organism. Despite the functional importance of OSCs, the determinants of their specificity are not well understood. In sterol-synthesizing oomycetes, recent bioinformatics, and metabolite analysis suggest that LA is produced...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27881416/metagenomics-of-two-severe-foodborne-outbreaks-provides-diagnostic-signatures-and-signs-of-co-infection-not-attainable-by-traditional-methods
#11
Andrew D Huang, Chengwei Luo, Angela Pena-Gonzalez, Michael R Weigand, Cheryl Tarr, Konstantinos T Konstantinidis
: Diagnostic testing for foodborne pathogens relies on culture-based techniques that are not rapid enough for real-time disease surveillance and do not give a quantitative picture of pathogen abundance or the response of the natural microbiome. Powerful sequence-based, culture-independent approaches such as shotgun metagenomics could sidestep these limitations, and potentially reveal a pathogen-specific signature on the microbiome that would have implications not only for diagnostics but also for better understanding disease progression and pathogen ecology...
November 23, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27877158/ultrastructure-and-viral-metagenome-of-bacteriophages-from-an-anaerobic-methane-oxidizing-methylomirabilis-bioreactor-enrichment-culture
#12
Lavinia Gambelli, Geert Cremers, Rob Mesman, Simon Guerrero, Bas E Dutilh, Mike S M Jetten, Huub J M Op den Camp, Laura van Niftrik
With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bioreactors can experience setbacks due to, for example, bacteriophage blooms. By shaping microbial communities through mortality, horizontal gene transfer, and metabolic reprogramming, bacteriophages are important players in most ecosystems...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27876624/differences-in-structure-and-changes-in-gene-regulation-of-murrel-molecular-chaperone-hsp-family-during-epizootic-ulcerative-syndrome-eus-infection
#13
Akila Sathyamoorthy, Mukesh Kumar Chaurasia, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi, Ramasamy Harikrishnan, Jesu Arockiaraj
Heat shock proteins (HSPs) are immunogenic, ubiquitous class of molecular chaperones, which are induced in response to various environmental and microbial stressful conditions. It plays a vital role in maintaining cellular protein homeostasis in eukaryotic cells. In this study, we described a comprehensive comparative data by bioinformatics approach on three different full length cDNA sequences of HSP family at molecular level. The cDNA sequences of three HSPs were identified from constructed cDNA library of Channa striatus and named as CsCPN60, CsHSP60 and CsHSP70...
November 20, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27864178/microbial-nursery-production-of-high-quality-biological-soil-crust-biomass-for-restoration-of-degraded-dryland-soils
#14
Sergio Velasco Ayuso, Ana Giraldo Silva, Corey J Nelson, Nichole N Barger, Ferran Garcia-Pichel
: Biological soil crusts (biocrusts) are slow growing, phototroph-based microbial assemblages developing on topsoils of drylands. Biocrusts help maintain soil fertility and reduce erosion. Because their loss through human activities has negative ecological and environmental health consequences, biocrust restoration is of interest. Active soil inoculation with biocrust microorganisms can be an important tool in this endeavor. We present a culture-independent, two-step process to grow multispecies biocrusts in open greenhouse nursery facilities, based on inoculation of local soils with local biocrust remnants, and incubation under semi-natural conditions that maintain the essence of the habitat, but lessen its harshness...
November 18, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27832948/up-regulated-of-mir-8159-5p-and-mir-217-5p-by-lps-stimulation-negatively-co-regulate-tlr1-in-miiuy-croaker
#15
Qing Chu, Yuena Sun, Dekun Bi, Junxia Cui, Tianjun Xu
Toll-like receptors (TLRs) are a group of pattern-recognition receptors which play vital roles in ligand recognition and activation of the innate immune response. As an important member of TLRs family, TLR1 is mainly responsible for PAMPs from bacteria and play a pivotal role in sensing microbial products. Recent studies revealed that TLR1 could perceive LPS stimulation and transfer signals to activate the NF-κB pathway, whereas ligands and signaling pathway of TLR1 are still unclear in fish. Growing evidence has shown that miRNAs (microRNAs) play as negative regulators in controlling the diverse of biophysical and biochemical processes at the post-transcriptional level...
February 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27825829/metagenomics-probing-pollutant-fate-in-natural-and-engineered-ecosystems
#16
REVIEW
Emna Bouhajja, Spiros N Agathos, Isabelle F George
Polluted environments are a reservoir of microbial species able to degrade or to convert pollutants to harmless compounds. The proper management of microbial resources requires a comprehensive characterization of their genetic pool to assess the fate of contaminants and increase the efficiency of bioremediation processes. Metagenomics offers appropriate tools to describe microbial communities in their whole complexity without lab-based cultivation of individual strains. After a decade of use of metagenomics to study microbiomes, the scientific community has made significant progress in this field...
November 5, 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/27822553/mockrobiota-a-public-resource-for-microbiome-bioinformatics-benchmarking
#17
Nicholas A Bokulich, Jai Ram Rideout, William G Mercurio, Arron Shiffer, Benjamin Wolfe, Corinne F Maurice, Rachel J Dutton, Peter J Turnbaugh, Rob Knight, J Gregory Caporaso
Mock communities are an important tool for validating, optimizing, and comparing bioinformatics methods for microbial community analysis. We present mockrobiota, a public resource for sharing, validating, and documenting mock community data resources, available at http://caporaso-lab.github.io/mockrobiota/. The materials contained in mockrobiota include data set and sample metadata, expected composition data (taxonomy or gene annotations or reference sequences for mock community members), and links to raw data (e...
September 2016: MSystems
https://www.readbyqxmd.com/read/27822544/multiplexed-metagenomic-deep-sequencing-to-analyze-the-composition-of-high-priority-pathogen-reagents
#18
Michael R Wilson, Greg Fedewa, Mark D Stenglein, Judith Olejnik, Linda J Rennick, Sham Nambulli, Friederike Feldmann, W Paul Duprex, John H Connor, Elke Mühlberger, Joseph L DeRisi
Laboratories studying high-priority pathogens need comprehensive methods to confirm microbial species and strains while also detecting contamination. Metagenomic deep sequencing (MDS) inventories nucleic acids present in laboratory stocks, providing an unbiased assessment of pathogen identity, the extent of genomic variation, and the presence of contaminants. Double-stranded cDNA MDS libraries were constructed from RNA extracted from in vitro-passaged stocks of six viruses (La Crosse virus, Ebola virus, canine distemper virus, measles virus, human respiratory syncytial virus, and vesicular stomatitis virus)...
July 2016: MSystems
https://www.readbyqxmd.com/read/27822515/open-source-sequence-clustering-methods-improve-the-state-of-the-art
#19
Evguenia Kopylova, Jose A Navas-Molina, Céline Mercier, Zhenjiang Zech Xu, Frédéric Mahé, Yan He, Hong-Wei Zhou, Torbjørn Rognes, J Gregory Caporaso, Rob Knight
Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE...
January 2016: MSystems
https://www.readbyqxmd.com/read/27797509/targeting-reactive-carbonyls-for-identifying-natural-products-and-their-biosynthetic-origins
#20
Tucker Maxson, Jonathan I Tietz, Graham A Hudson, Xiao Rui Guo, Hua-Chia Tai, Douglas A Mitchell
Natural products serve important roles as drug candidates and as tools for chemical biology. However, traditional natural product discovery, largely based on bioassay-guided approaches, is biased towards abundant compounds and rediscovery rates are high. Orthogonal methods to facilitate discovery of new natural products are thus needed, and herein we describe an isotope tag-based expansion of reactivity-based natural product screening to address these shortcomings. Reactivity-based screening is a directed discovery approach in which a specific reactive handle on the natural product is targeted by a chemoselective probe to enable its detection by mass spectrometry...
October 31, 2016: Journal of the American Chemical Society
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