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Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data
Tập 3 Số 1 - 2013
Growth comparison of several Escherichia coli strains exposed to various concentrations of lactoferrin using linear spline regression
- 2012
Abstract 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 ...
Natural genetic engineering: intelligence & design in evolution?
Tập 1 - Trang 1-4 - 2011
There are many things that I like about James Shapiro's new book "Evolution: A
View from the 21st Century" (FT Press Science, 2011). He begins the book by
saying that it is the creation of novelty, and not selection, that is important
in the history of life. In the presence of heritable traits that vary, selection
results in the evolution of a population towards an optimal composition of those
tra...
The zinc-ribbon domain of Helicobacter pylori HP0958: requirement for RpoN accumulation and possible roles of homologs in other bacteria
Tập 1 - Trang 1-10 - 2011
Helicobacter pylori HP0958 protein (FlgZ) prevents the rapid turnover of RpoN
(σ54), 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 Cy...
Bioinformatic identification of Mycobacterium tuberculosis proteins likely to target host cell mitochondria: virulence factors?
Tập 2 - Trang 1-10 - 2012
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, m...
The Regulatory Network of Pseudomonas aeruginosa
Tập 1 - Trang 1-11 - 2011
Pseudomonas aeruginosa is an important bacterial model due to its metabolic and
pathogenic abilities, which allow it to interact and colonize a wide range of
hosts, including plants and animals. In this work we compile and analyze the
structure and organization of an experimentally supported regulatory network in
this bacterium. The regulatory network consists of 690 genes and 1020 regulatory
inte...
Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction
Tập 2 - Trang 1-12 - 2012
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, geno...
Prediction of a novel RNA binding domain in crocodilepox Zimbabwe Gene 157
Tập 1 - Trang 1-7 - 2011
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 no...
A systematic search for discriminating sites in the 16S ribosomal RNA gene
Tập 4 - Trang 1-9 - 2014
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
powe...