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Microbial Informatics and Experimentation

Hilde Vinje, Trygve Almøy, Kristian Hovde Liland, Lars Snipen
BACKGROUND: The 16S rRNA is by far the most common genomic marker used for prokaryotic classification, and has been used extensively in metagenomic studies over recent years. Along the 16S gene there are regions with more or less variation across the kingdom of bacteria. Nine variable regions have been identified, flanked by more conserved parts of the sequence. It has been stated that the discriminatory power of the 16S marker lies in these variable regions. In the present study we wanted to examine this more closely, and used a supervised learning method to search systematically for sites that contribute to correct classification at either the phylum or genus level...
2014: Microbial Informatics and Experimentation
Kerensa McElroy, Torsten Thomas, Fabio Luciani
Deep sequencing harnesses the high throughput nature of next generation sequencing technologies to generate population samples, treating information contained in individual reads as meaningful. Here, we review applications of deep sequencing to pathogen evolution. Pioneering deep sequencing studies from the virology literature are discussed, such as whole genome Roche-454 sequencing analyses of the dynamics of the rapidly mutating pathogens hepatitis C virus and HIV. Extension of the deep sequencing approach to bacterial populations is then discussed, including the impacts of emerging sequencing technologies...
2014: Microbial Informatics and Experimentation
Clelia Peano, Alessandro Pietrelli, Clarissa Consolandi, Elio Rossi, Luca Petiti, Letizia Tagliabue, Gianluca De Bellis, Paolo Landini
UNLABELLED: HASH(0x55893db40680) BACKGROUND: Next generation sequencing (NGS) technologies have revolutionized gene expression studies and functional genomics analysis. However, further improvement of RNA sequencing protocols is still desirable, in order to reduce NGS costs and to increase its accuracy. In bacteria, a major problem in RNA sequencing is the abundance of ribosomal RNA (rRNA), which accounts for 95-98% of total RNA and can therefore hinder sufficient coverage of mRNA, the main focus of transcriptomic studies...
January 7, 2013: Microbial Informatics and Experimentation
Susan Joseph, Sumyya Hariri, Naqash Masood, Stephen Forsythe
BACKGROUND: The Cronobacter genus is composed of seven species, and can cause infections in all age groups. Of particular concern is C. sakazakii, as this species is strongly associated with severe and often fatal cases of necrotizing enterocolitis and meningitis in neonates and infants. Whole genome sequencing has revealed that the nanAKT gene cluster required for the utilisation of exogenous sialic acid is unique to the C. sakazakii species (ESA_03609-13).Sialic acid is found in breast milk, infant formula, intestinal mucin, and gangliosides in the brain, hence its metabolism by C...
2013: Microbial Informatics and Experimentation
David J Edwards, Kathryn E Holt
High throughput sequencing is now fast and cheap enough to be considered part of the toolbox for investigating bacteria, and there are thousands of bacterial genome sequences available for comparison in the public domain. Bacterial genome analysis is increasingly being performed by diverse groups in research, clinical and public health labs alike, who are interested in a wide array of topics related to bacterial genetics and evolution. Examples include outbreak analysis and the study of pathogenicity and antimicrobial resistance...
2013: Microbial Informatics and Experimentation
Lijing Xu, Jimmy Kuo, Jong-Kang Liu, Tit-Yee Wong
BACKGROUND: The efficiencies of the stop codons TAA, TAG, and TGA in protein synthesis termination are not the same. These variations could allow many genes to be regulated. There are many similar nucleotide trimers found on the second and third reading-frames of a gene. They are called premature stop codons (PSC). Like stop codons, the PSC in bacterial genomes are also highly bias in terms of their quantities and qualities on the genes. Phylogenetically related species often share a similar PSC profile...
May 31, 2012: Microbial Informatics and Experimentation
Seshan Ananthasubramanian, Rahul Metri, Ankur Khetan, Aman Gupta, Adam Handen, Nagasuma Chandra, Madhavi Ganapathiraju
BACKGROUND: Protein-protein interaction (PPI) networks (interactomes) of most organisms, except for some model organisms, are largely unknown. Experimental methods including high-throughput techniques are highly resource intensive. Therefore, computational discovery of PPIs can accelerate biological discovery by presenting "most-promising" pairs of proteins that are likely to interact. For many bacteria, genome sequence, and thereby genomic context of proteomes, is readily available; additionally, for some of these proteomes, localization and functional annotations are also available, but interactomes are not available...
March 21, 2012: Microbial Informatics and Experimentation
Torsten Thomas, Jack Gilbert, Folker Meyer
Metagenomics applies a suite of genomic technologies and bioinformatics tools to directly access the genetic content of entire communities of organisms. The field of metagenomics has been responsible for substantial advances in microbial ecology, evolution, and diversity over the past 5 to 10 years, and many research laboratories are actively engaged in it now. With the growing numbers of activities also comes a plethora of methodological knowledge and expertise that should guide future developments in the field...
February 9, 2012: Microbial Informatics and Experimentation
María Maximina Bertha Moreno-Altamirano, Iris Selene Paredes-González, Clara Espitia, Mauricio Santiago-Maldonado, Rogelio Hernández-Pando, Francisco Javier Sánchez-García
UNLABELLED: HASH(0x55893d9585f0) BACKGROUND: M. tuberculosis infection either induces or inhibits host cell death, depending on the bacterial strain and the cell microenvironment. There is evidence suggesting a role for mitochondria in these processes.On the other hand, it has been shown that several bacterial proteins are able to target mitochondria, playing a critical role in bacterial pathogenesis and modulation of cell death. However, mycobacteria-derived proteins able to target host cell mitochondria are less studied...
2012: Microbial Informatics and Experimentation
Lars Snipen, Trudy M Wassenaar, Eric Altermann, Jonathan Olson, Sophia Kathariou, Karin Lagesen, Monica Takamiya, Susanne Knøchel, David W Ussery, Richard J Meinersmann
UNLABELLED: HASH(0x55893dde6fa8) BACKGROUND: The thermophilic Campylobacter jejuni and Campylobacter coli are considered weakly clonal populations where incongruences between genetic markers are assumed to be due to random horizontal transfer of genomic DNA. In order to investigate the population genetics structure we extracted a set of 1180 core gene families (CGF) from 27 sequenced genomes of C. jejuni and C. coli. We adopted a principal component analysis (PCA) on the normalized evolutionary distances in order to reveal any patterns in the evolutionary signals contained within the various CGFs...
2012: Microbial Informatics and Experimentation
Fathiah Zakham, Othmane Aouane, David Ussery, Abdelaziz Benjouad, Moulay Mustapha Ennaji
UNLABELLED: HASH(0x55893dd748d0) BACKGROUND: The genus Mycobacterium comprises different species, among them the most contagious and infectious bacteria. The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have killed human and other mammals since millennia. Additionally, with the many different mycobacterial sequences available, there is a crucial need for the visualization and the simplification of their data. In this present study, we aim to highlight a comparative genome, proteome and phylogeny analysis between twenty-one mycobacterial (Tuberculosis and non tuberculosis) strains using a set of computational and bioinformatics tools (Pan and Core genome plotting, BLAST matrix and phylogeny analysis)...
2012: Microbial Informatics and Experimentation
Camilla Sekse, Jon Bohlin, Eystein Skjerve, Gerd E Vegarud
BACKGROUND: We wanted to compare growth differences between 13 Escherichia coli strains exposed to various concentrations of the growth inhibitor lactoferrin in two different types of broth (Syncase and Luria-Bertani (LB)). To carry this out, we present a simple statistical procedure that separates microbial growth curves that are due to natural random perturbations and growth curves that are more likely caused by biological differences.Bacterial growth was determined using optical density data (OD) recorded for triplicates at 620 nm for 18 hours for each strain...
2012: Microbial Informatics and Experimentation
Manal Helal, Fanrong Kong, Sharon Ca Chen, Fei Zhou, Dominic E Dwyer, John Potter, Vitali Sintchenko
BACKGROUND: Comparative genomics has put additional demands on the assessment of similarity between sequences and their clustering as means for classification. However, defining the optimal number of clusters, cluster density and boundaries for sets of potentially related sequences of genes with variable degrees of polymorphism remains a significant challenge. The aim of this study was to develop a method that would identify the cluster centroids and the optimal number of clusters for a given sensitivity level and could work equally well for the different sequence datasets...
2012: Microbial Informatics and Experimentation
Lynda Bm Ellis, Lawrence P Wackett
Microorganisms are ubiquitous on earth and have diverse metabolic transformative capabilities important for environmental biodegradation of chemicals that helps maintain ecosystem and human health. Microbial biodegradative metabolism is the main focus of the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD). UM-BBD data has also been used to develop a computational metabolic pathway prediction system that can be applied to chemicals for which biodegradation data is currently lacking. The UM-Pathway Prediction System (UM-PPS) relies on metabolic rules that are based on organic functional groups and predicts plausible biodegradative metabolism...
2012: Microbial Informatics and Experimentation
Sónia Carneiro, Anália Lourenço, Eugénio C Ferreira, Isabel Rocha
BACKGROUND: Understanding the mechanisms responsible for cellular responses depends on the systematic collection and analysis of information on the main biological concepts involved. Indeed, the identification of biologically relevant concepts in free text, namely genes, tRNAs, mRNAs, gene products and small molecules, is crucial to capture the structure and functioning of different responses. RESULTS: In this work, we review literature reports on the study of the stringent response in Escherichia coli...
December 30, 2011: Microbial Informatics and Experimentation
Nicole S Little, Taylor Quon, Chris Upton
BACKGROUND: Although the crocodilepox virus (CRV) is currently unclassified, phylogenetic analyses suggest that its closest known relatives are molluscum contagiosum virus (MCV) and the avipox viruses. The CRV genome is approximately 190 kb and contains a large number of unique genes in addition to the set of conserved Chordopoxvirus genes found in all such viruses. Upon sequencing the viral genome, others noted that this virus was also unusual because of the lack of a series of common immuno-suppressive genes...
November 21, 2011: Microbial Informatics and Experimentation
Ivaylo Kostadinov, Renzo Kottmann, Alban Ramette, Jost Waldmann, Pier Luigi Buttigieg, Frank Oliver Glöckner
BACKGROUND: DNA-binding transcription factors (TFs) regulate cellular functions in prokaryotes, often in response to environmental stimuli. Thus, the environment exerts constant selective pressure on the TF gene content of microbial communities. Recently a study on marine Synechococcus strains detected differences in their genomic TF content related to environmental adaptation, but so far the effect of environmental parameters on the content of TFs in bacterial communities has not been systematically investigated...
September 7, 2011: Microbial Informatics and Experimentation
Lara E Pereira, Jennifer Tsang, Jan Mrázek, Timothy R Hoover
BACKGROUND: Helicobacter pylori HP0958 protein (FlgZ) prevents the rapid turnover of RpoN (σ(54)), a transcription factor required for expression of several flagellar genes in H. pylori. FlgZ possesses a zinc-ribbon domain (DUF164) that contains two conserved CXXC motifs which coordinate a zinc ion and is thought to interact with nucleic acids or proteins. Two conserved cysteine residues in FlgZ (Cys-202 and Cys-223) were replaced with serine to assess their significance in FlgZ function...
August 23, 2011: Microbial Informatics and Experimentation
Andrea Squartini
BACKGROUND: The associations between bacteria and environment underlie their preferential interactions with given physical or chemical conditions. Microbial ecology aims at extracting conserved patterns of occurrence of bacterial taxa in relation to defined habitats and contexts. RESULTS: In the present report the NCBI nucleotide sequence database is used as dataset to extract information relative to the distribution of each of the 24 phyla of the bacteria superkingdom and of the Archaea...
2011: Microbial Informatics and Experimentation
W Nicholson Price, Samuel K Handelman, John K Everett, Saichiu N Tong, Ana Bracic, Jon D Luff, Victor Naumov, Thomas Acton, Philip Manor, Rong Xiao, Burkhard Rost, Gaetano T Montelione, John F Hunt
The biochemical and physical factors controlling protein expression level and solubility in vivo remain incompletely characterized. To gain insight into the primary sequence features influencing these outcomes, we performed statistical analyses of results from the high-throughput protein-production pipeline of the Northeast Structural Genomics Consortium. Proteins expressed in E. coli and consistently purified were scored independently for expression and solubility levels. These parameters nonetheless show a very strong positive correlation...
2011: Microbial Informatics and Experimentation
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