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Genetics, Microbial (0):
Recent article
Genetics, Microbial
Biomacromolecules (12)9 2011
Abstract
Polyhydroxyalkanoates (PHA) synthesis genes phbC and orfZ cloned from Ralstonia eutropha H16 were transformed into beta-oxidation weakened Pseudomonas putida KTOY08ΔGC, a mutant of P. putida KT2442. The recombinant P. putida strain termed KTHH06 was able to produce a short-chain-len...
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PMID: 21863836
PDF is available here.
PDF is available here.
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Abstract
We use a simpler and more intuitive approach to evaluate patterns of genome structure....
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PMID: 21304908
PDF is available here.
PDF is available here.
Abstract
We developed novel promoter-probe and terminator-probe vectors based on the Streptococcus agalactiae pMV158 plasmid, which replicates autonomously in numerous Gram-positive bacteria. As reporter gene, a gfp allele encoding a variant of the green fluorescent protein was used. These genetic tools were...
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PMID: 20801171
PDF is available here.
PDF is available here.
Abstract
V-Xtractor (http://www.cmde.science.ubc.ca/mohn/software.html) uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences. With a detection efficiency of 99.6% and low susceptibility to fa...
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PMID: 20804791
PDF is available here.
PDF is available here.
Abstract
We describe the testing of these vectors through marker gene expression in Coprinopsis cinerea. This work also extends the range of marker genes available for use in C. cinerea with the first report of DsRed and monomeric red fluorescent protein (mRFP) expression in C. cinerea and further demonstrat...
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PMID: 20570599
PDF is available here.
PDF is available here.
Abstract
We still have no answer to the fundamental question regarding sexual development: 'what triggers gametocytogenesis'? In the current climate of eradication/elimination, tackling transmission by killing gametocytes has an important place on the agenda because most antimalarial drugs, whilst killing as...
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PMID: 20381542
PDF is available here.
PDF is available here.
Journal of Virology (84)16 2010
Abstract
We have constructed a novel oncolytic HSV-1 recombinant, KTR27, whose replication can be tightly controlled and regulated by tetracycline in a dose-dependent manner. Infection of normal replicating cells as well as multiple human cancer cell types with KTR27 in the presence of tetracycline led to 1,...
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PMID: 20519407
PDF is available here.
PDF is available here.
Abstract
We measured the frequency of appearance of spontaneous mutants resistant to gentamicin, kanamycin, streptomycin, and spectinomycin in saprophytic and pathogenic Leptospira strains. The mutations responsible for the spontaneous resistance to streptomycin and spectinomycin were identified in the rpsL...
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PMID: 20511419
PDF is available here.
PDF is available here.
Journal of Virology (84)13 2010
Abstract
We report here a reverse genetics system for RV based on the preferential packaging of rearranged RNA segments. Using this system, wild-type or in vitro-engineered forms of rearranged segment 7 from a human rotavirus (encoding the NSP3 protein), derived from cloned cDNAs and transcribed in the cytop...
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PMID: 20427539
PDF is available here.
PDF is available here.
Abstract
We designed a screening procedure to enrich for phenotypes with defects in induced egress. The procedure is based on in vitro induced egress and the efficient separation of intracellular from extracellular parasites. Attachment and fast reinvasion of egressed parasites are prevented by the addition...
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PMID: 20227445
PDF is available here.
PDF is available here.
Abstract
We report the development of protoplast and transformation system for U. oxytropis. Fungal mycelia required for generating protoplasts were grown in liquid culture, then harvested and processed with various enzymes. Protoplasts were transformed with a fungal specific vector driving the expression of...
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PMID: 20211666
PDF is available here.
PDF is available here.
Abstract
Extraction of genomic DNA from mycobacteria requires special consideration because (i) many mycobacterial species exhibit extremely slow growth, and thus produce only small amounts of starting material, and (ii) a robust and waxy cell wall renders mycobacteria difficult to lyse. Hence, mycobacterial...
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PMID: 20360362
PDF is available here.
PDF is available here.
Abstract
We developed a common oligonucleotide reference standard (CORS) method to address this problem. A unique 50-mer reference oligonucleotide probe was selected to co-spot with gene probes for each array feature. The complementary sequence was synthesized and labeled for use as the reference target, whi...
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PMID: 20038701
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)4 2010
Abstract
We establish for the first time, through a combination of reverse genetics, mass spectrometry, and mutagenesis, that these genes encode a functional lantibiotic. We also reveal that Bsa is identical to the previously identified bacteriocin staphylococcin Au-26, produced by an S. aureus strain of vag...
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PMID: 20023032
PDF is available here.
PDF is available here.
Abstract
In 1944, Oswald T. Avery and his associates reported that DNA was the chemical substance acting to genetically transform species of pneumococcal bacteria. Many believe that Avery warranted the Nobel Prize for this discovery. Avery's work is evaluated here in light of the Nobel archives, which have m...
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PMID: 21037409
PDF is available here.
PDF is available here.
Methods in Molecular Biology (551)551 2009
Abstract
We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison...
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PMID: 19521870
PDF is available here.
PDF is available here.
Abstract
We present a novel approach to metagenomic data analysis, called Metagenomic ORFome Assembly (MetaORFA). The whole computational framework consists of three steps. Each read from a metagenomics project will first be annotated with putative open reading frames (ORFs) that likely encode proteins. Next...
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PMID: 19507285
PDF is available here.
PDF is available here.
Methods in Molecular Biology (532)532 2009
Abstract
The subject of this chapter is to describe the methodology for assessing the power of phylogenetic HGT detection methods. Detection power is defined in the framework of hypothesis testing. Rates of false positives and false negatives can be estimated by testing HGT detection methods on HGT-free orth...
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PMID: 19271188
PDF is available here.
PDF is available here.
Methods in Molecular Biology (532)532 2009
Abstract
We point to a prodigious but little-known symbiogenesis literature that contrasts the transfer of sets of genes with HGT taken to mean one or a-very-few-genes at a time....
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PMID: 19271185
PDF is available here.
PDF is available here.
Methods in Molecular Biology (532)532 2009
Abstract
Comparative genomics have identified two loosely defined classes of genes: widely distributed core genes that encode proteins for central functions in the cell and accessory genes that are patchily distributed across lineages and encode taxa-specific functions. Studies of microbial eukaryotes show t...
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PMID: 19271202
PDF is available here.
PDF is available here.
Methods in Molecular Biology (532)532 2009
Abstract
We present cases in which HGT has been demonstrated to contribute to the dissemination of genes that provide adaptation to contaminant stress (i.e., toxic heavy metals and radionuclides). In addition, we present directions for future studies that could provide even greater insights into the contribu...
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PMID: 19271201
PDF is available here.
PDF is available here.
Methods in Molecular Biology (532)532 2009
Abstract
We developed a set of user-friendly MatLab routines, which are deposited in the public domain. We hope that the availability of these routines will encourage the computationally untrained microbiologist to make use of these mathematical models. Finally, further permutations, as well as limitations o...
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PMID: 19271192
PDF is available here.
PDF is available here.
Methods in Molecular Biology (532)532 2009
Abstract
We discuss a simple theoretical analysis based on the in silico artificial addition of known foreign genes from different prokaryotic groups into the genome of Escherichia coli K12 MG1655. Using this dataset as a control, we have tested the efficiency of four methodologies commonly employed to detec...
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PMID: 19271187
PDF is available here.
PDF is available here.
Abstract
We understand how the assayed variation accumulates. We discuss this with specific reference to three classes of methods: those based on gel electrophoresis of fragments generated by restriction enzymes or polymerase chain reaction (PCR), those based on microsatellites and other repeat elements, and...
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PMID: 19521881
PDF is available here.
PDF is available here.
Abstract
We discuss recent insights gained from different methodological approaches used to characterize the biodiversity and ecology of MGE in marine environments and their contributions to HGT. In addition, we present case studies that highlight specific HGT examples in coastal, open-ocean, and deep-sea ma...
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PMID: 19271200
PDF is available here.
PDF is available here.
Abstract
The deep terrestrial subsurface is a vast, largely unexplored environment that is oligotrophic, highly heterogeneous, and may contain extremes of both physical and chemical factors. In spite of harsh conditions, subsurface studies at several widely distributed geographic sites have revealed diverse...
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PMID: 19271199
PDF is available here.
PDF is available here.
Abstract
I stress one more time the urgency to better connect molecular epidemiology and evolutionary biology. I show how much population genetics and phylogenetic analyses can confer a considerable added value to all attempts to characterize strains and species of pathogens. The problems dealing with the me...
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PMID: 19521862
PDF is available here.
PDF is available here.
Abstract
A universal Tree of Life has been a longstanding goal of the biosciences. The most common Tree of Life, based on the small subunit rRNA gene, may or may not represent the phylogenetic history of microorganisms. The horizontal transfer of genes from one taxon to another provides a means by which each...
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PMID: 19271183
PDF is available here.
PDF is available here.
Abstract
A new plasmid pCASE1 was isolated from Gram-positive Corynebacterium casei JCM 12072. It comprised a 2.4-kb nucleotide sequence with three ORFs, two of which were indispensable for autonomous replication in Corynebacterium glutamicum. Homology search identified these two ORFs as repA and repB, areas...
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PMID: 18936936
PDF is available here.
PDF is available here.
Abstract
Short-insert shotgun sequencing approaches have been applied in recent years to environmental genomic libraries. In the case of complex multispecies microbial communities, there can be many sequence reads that are not incorporated into assemblies, and thus need to be annotated and accessible as sing...
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PMID: 19090024
PDF is available here.
PDF is available here.
Infection and Immunity (76)10 2008
Abstract
We developed a novel approach for plasmid selection based on immunity to the antimicrobial peptide microcin H47 (MccH47). Two expression plasmids encoding the reporter green fluorescent protein (GFPuv) were constructed; selection markers comprised either mchI, conferring immunity to MccH47 (pGEN222I...
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PMID: 18663003
PDF is available here.
PDF is available here.
Abstract
We highlight the ongoing historical transition in the field of infectious disease research and clinical practice in the new era of genomics....
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PMID: 18767959
PDF is available here.
PDF is available here.
Abstract
Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically coevolving relationships with the habitats they occupy without having to culture community members. Uniting metagenomics with analyses of the products of microbial community metabolis...
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PMID: 18775300
PDF is available here.
PDF is available here.
Theory in Biosciences (127)3 2008
Abstract
I review past and present uses of the niche concept in ecology and in microbiological studies, showing that a new, updated definition need to be used in the context of the metagenomics. Finally, I give some insights into a more adequate conceptual background for the utilisation of the niche concept...
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PMID: 18421492
PDF is available here.
PDF is available here.
Abstract
Abstract
We propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species comi...
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PMID: 18331337
PDF is available here.
PDF is available here.
Abstract
Clostridium proteoclasticum is commonly associated with the rumen microflora of pasture-fed cattle and sheep and has significant hemicellulose degradation abilities. Genes involved in plant fibre breakdown are commonly identified by producing site-specific mutations. However, the genetics of C. prot...
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PMID: 18346802
PDF is available here.
PDF is available here.
Abstract
We describe a method that combines PCR and Gateway cloning technology together with use of the I-SceI homing endonuclease to generate precise deletion constructs in a very simple, universal and robust manner in just 2 days. These constructs are then used to produce deletion mutants in the organism o...
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PMID: 18248826
PDF is available here.
PDF is available here.
Abstract
This transformation method significantly improves the classical heat shock treatment. SIGNIFICANCE AND IMPACT OF THE STUDY: This method might be useful to those laboratories that cannot afford an electroporation apparatus....
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PMID: 18284557
PDF is available here.
PDF is available here.
ISME Journal (2)3 2008
Abstract
Microbial ecology is a field that applies molecular techniques to analyze genes and communities associated with a plethora of unique environments on this planet. In the past, low biomass and the predominance of a few abundant community members have impeded the application of techniques such as PCR,...
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PMID: 18256705
PDF is available here.
PDF is available here.
Revue medicale suisse (4)143 2008
Abstract
Microbiology (154)Pt 2 2008
Abstract
Microbial genome sequencing has, for the first time, made accessible all the components needed for both the elaboration and the functioning of a cell. Associated with other global methods such as protein and mRNA profiling, genomics has considerably extended our knowledge of physiological processes...
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PMID: 18227239
PDF is available here.
PDF is available here.
Abstract
Six out of ten completely sequenced bacterial genomes are pathogenic or opportunistic bacteria. The genome sequence of at least one strain of all the principal pathogenic bacteria will soon be available. This information should enable us to identify genes that encode virulence factors. As these gene...
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PMID: 18341921
PDF is available here.
PDF is available here.
Abstract
We then focus on the use of microarrays to examine genome dynamics, to uncover novel functional elements in genomes, to unravel the evolution of regulatory networks, to identify genes important for behavioral and phenotypic plasticity, and to determine microbial community diversity in environmental...
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PMID: 17091126
PDF is available here.
PDF is available here.
Abstract
We report the first demonstration of conjugation between Escherichia coli and Leptospira spp. by using RP4 derivative conjugative plasmids. The DNA transfer described here was due to authentic conjugation, as shown by the requirement for cell-to-cell contact and the resistance of DNA transfers to th...
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PMID: 17993560
PDF is available here.
PDF is available here.
Abstract
We validated using a model system: Pseudomonas putida mt-2 degrading toluene. cDNA from P. putida mt-2 grown on toluene (model pollutant) or acetate (control substrate) was subjected to our prokaryotic SSH PCR cDNA subtraction protocol to generate subtraction clone libraries. Over 90% of the sequenc...
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PMID: 17993561
PDF is available here.
PDF is available here.
Abstract
We compared the metagenomes of 10 successive layers of a phylogenetically complex hypersaline mat from Guerrero Negro, Mexico. We found pronounced millimeter-scale genetic gradients that were consistent with the physicochemical profile of the mat. Despite these gradients, all layers displayed near-i...
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PMID: 18523433
PDF is available here.
PDF is available here.
Abstract
We describe experiments with a fusion protein that allows positive selection for genome integration followed by CRE recombinase-mediated excision of the marker cassette that can be selected by ganciclovir, although the excision event is so efficient that selection is not strictly necessary. We descr...
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PMID: 18006158
PDF is available here.
PDF is available here.
Abstract
We report the development and validation of transfection methodology for this parasite. We first selected from our P. marinus EST collection a highly expressed gene, which we designated "MOE" (PmMOE), to which we fused at the C-terminus the enhanced green fluorescent protein (GFP) as a reporter gene...
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PMID: 17996961
PDF is available here.
PDF is available here.
New Phytologist (177)3 2008
Abstract
Abstract
Research in Microbiology (158)10 2007
Abstract
Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences (38)4 2007
Abstract
We know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively mor...
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PMID: 18053938
PDF is available here.
PDF is available here.
Abstract
This method can be used for rapid construction of Camp. jejuni deletion mutants. SIGNIFICANCE AND IMPACT OF THE STUDY: The use of this method should facilitate functional characterization of various Camp. jejuni genes....
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PMID: 17908230
PDF is available here.
PDF is available here.
Molecular Microbiology (66)1 2007
Abstract
Borrelia burgdorferi, the agent of Lyme disease, disseminates from the site of deposition by Ixodes ticks to cause systemic infection. Dissemination occurs through the circulation and through tissue matrices, but the B. burgdorferi molecules that mediate interactions with the endothelium in vivo hav...
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PMID: 17784908
PDF is available here.
PDF is available here.
Microbiology (153)Pt 8 2007
Abstract
Most of the spontaneous poly-gamma-glutamate (gamma-PGA)-deficient mutants of Bacillus subtilis (natto) appear to have resulted from the insertion of IS4Bsu1 exclusively into the comP gene. However, complete genomic analysis of B. subtilis 168, a close relative of B. subtilis (natto), revealed no IS...
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PMID: 17660419
PDF is available here.
PDF is available here.
Abstract
We study the problem of selecting control clones in DNA array hybridization experiments. The problem arises in the OFRG method for analyzing microbial communities. The OFRG method performs classification of rRNA gene clones using binary fingerprints created from a series of hybridization experiments...
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PMID: 17787064
PDF is available here.
PDF is available here.