bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Propidium Monoazide in Reverse Transcriptase PCR To Distinguish between Infectious and Noninfectious Enteric Viruses in Water Samples
Authors: Parshionikar Sandhya , Laseke Ian , Fout G. Shay 
Published: May 2010

ABSTRACT
Human enteric viruses can be present in untreated and inadequately treated drinking water. Molecular methods, such as the reverse transcriptase PCR (RT-PCR), can detect viral genomes in a few hours, but they cannot distinguish between infectious and noninfectious viruses. Since only infectious viruses are a public health concern, methods that not only are rapid but also provide information on the infectivity of viruses are of interest. The intercalating dye propidium monoazide (PMA) has been used for distinguishing between viable and nonviable bacteria with DNA genomes, but it has not been used to distinguish between infectious and noninfectious enteric viruses with RNA genomes. In this study, PMA in conjunction with RT-PCR (PMA-RT-PCR) was used to determine the infectivity of enteric RNA viruses in water. Coxsackievirus, poliovirus, echovirus, and Norwalk virus were rendered noninfectious or inactivated by treatment with heat (72°C, 37°C, and 19°C) or hypochlorite. Infectious or native and noninfectious or inactivated viruses were treated with PMA. This was followed by RNA extraction and RT-PCR or quantitative RT-PCR (qRT-PCR) analysis. The PMA-RT-PCR results indicated that PMA treatment did not interfere with detection of infectious or native viruses but prevented detection of noninfectious or inactivated viruses that were rendered noninfectious or inactivated by treatment at 72°C and 37°C and by hypochlorite treatment. However, PMA-RT-PCR was unable to prevent detection of enteroviruses that were rendered noninfectious by treatment at 19°C. After PMA treatment poliovirus that was rendered noninfectious by treatment at 37°C was undetectable by qRT-PCR, but PMA treatment did not affect detection of Norwalk virus. PMA-RT-PCR was also shown to be effective for detecting infectious poliovirus in the presence of noninfectious virus and in an environmental matrix. We concluded that PMA can be used to differentiate between potentially infectious and noninfectious viruses under the conditions defined above.
Burkholderia phymatum
Strains Capable of Nodulating
Phaseolus vulgaris
Are Present in Moroccan Soils
Authors: Talbi C. , Delgado M. J. , Girard L. , Ramírez-Trujillo A. , Caballero-Mellado J. , Bedmar E. J. 
Published: May 2010

ABSTRACT

Phylogenetic analysis of 16S rRNA,
nodC
, and
nifH
genes of four bacterial strains isolated from root nodules of
Phaseolus vulgaris
grown in Morocco soils were identified as
Burkholderia phymatum
. All four strains formed N
2
-fixing nodules on
P. vulgaris
and
Mimosa
,
Acacia
, and
Prosopis
species and reduced acetylene to ethylene when cultured
ex planta
.
Biosynthetic Potential of Phylogenetically Unique Endophytic Actinomycetes from Tropical Plants
Authors: Janso Jeffrey E. , Carter Guy T. 
Published: May 2010

ABSTRACT

The culturable diversity of endophytic actinomycetes associated with tropical, native plants is essentially unexplored. In this study, 123 endophytic actinomycetes were isolated from tropical plants collected from several locations in Papua New Guinea and Mborokua Island, Solomon Islands. Isolates were found to be prevalent in roots but uncommon in leaves. Initially, isolates were dereplicated to the strain level by ribotyping. Subsequent characterization of 105 unique strains by 16S rRNA gene sequence analysis revealed that 17 different genera were represented, and rare genera, such as
Sphaerisporangium
and
Planotetraspora
, which have never been previously reported to be endophytic, were quite prevalent. Phylogenetic analyses grouped many of the strains into clades distinct from known genera within
Thermomonosporaceae
and
Micromonosporaceae
, indicating that they may be unique genera. Bioactivity testing and liquid chromatography-mass spectrometry (LC-MS) profiling of crude fermentation extracts were performed on 91 strains. About 60% of the extracts exhibited bioactivity or displayed LC-MS profiles with spectra indicative of secondary metabolites. The biosynthetic potential of 29 nonproductive strains was further investigated by the detection of putative polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes. Despite their lack of detectable secondary metabolite production in fermentation, most were positive for type I (66%) and type II (79%) PKS genes, and all were positive for NRPS genes. These results suggest that tropical plants from New Guinea and the adjacent archipelago are hosts to unique endophytic actinomycetes that possess significant biosynthetic potential.
Pork Contaminated with
Salmonella
enterica
Serovar 4,[5],12:i:−, an Emerging Health Risk for Humans
Authors: Hauser Elisabeth , Tietze Erhard , Helmuth Reiner , Junker Ernst , Blank Kathrin , Prager Rita , Rabsch Wolfgang , Appel Bernd , Fruth Angelika , Malorny Burkhard 
Published: May 2010

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar 4,[5],12:i:− is a monophasic variant of
S
.
enterica
serovar Typhimurium (antigenic formula 4,[5],12:i:1,2). Worldwide, especially in several European countries and the United States, it has been reported among the 10 most frequently isolated serovars in pigs and humans. In the study reported here, 148 strains of the monophasic serovar isolated from pigs, pork, and humans in 2006 and 2007 in Germany were characterized by various phenotypic and genotypic methods. This characterization was done in order to investigate their clonality, the prevalence of identical subtypes in pigs, pork, and humans, and the genetic relatedness to other
S. enterica
serovar Typhimurium subtypes in respect to the pathogenic and resistance gene repertoire. Two major clonal lineages of the monophasic serovar were detected which can be differentiated by their phage types and pulsed-field gel electrophoresis (PFGE) profiles. Seventy percent of the strains tested belonged to definite phage type DT193, and those strains were mainly assigned to PFGE cluster B. Nineteen percent of the strains were typed to phage type DT120 and of these 86% belonged to PFGE cluster A. Sixty-five percent of the isolates of both lineages carried core multiresistance to ampicillin, streptomycin, tetracycline, and sulfamethoxazole encoded by the genes
bla
TEM1-like
,
strA
-
str
B
,
tet
(B), and
sul2.
No correlation to the source of isolation was observed in either lineage. Microarray analysis of 61
S. enterica
serovar 4,[5],12:i:− and 20
S. enterica
serovar Typhimurium isolates tested determining the presence or absence of 102 representative pathogenicity genes in
Salmonella
revealed no differences except minor variations in single strains within and between the serovars, e.g., by presence of the virulence plasmid in four strains. Overall the study indicates that in Germany
S. enterica
serovar 4,[5],12:i:− strains isolated from pig, pork, and human are highly related, showing their transmission along the food chain. Since the pathogenicity gene repertoire is highly similar to that of
S. enterica
serovar Typhimurium, it is essential that interventions are introduced at the farm level in order to limit human infection.
Diversity of Dissimilatory Sulfite Reductase Genes (
dsrAB
) in a Salt Marsh Impacted by Long-Term Acid Mine Drainage
Authors: Moreau John W. , Zierenberg Robert A. , Banfield Jillian F. 
Published: May 2010

ABSTRACT

Sulfate-reducing bacteria (SRB) play a major role in the coupled biogeochemical cycling of sulfur and chalcophilic metal(loid)s. By implication, they can exert a strong influence on the speciation and mobility of multiple metal(loid) contaminants. In this study, we combined DsrAB gene sequencing and sulfur isotopic profiling to identify the phylogeny and distribution of SRB and to assess their metabolic activity in salt marsh sediments exposed to acid mine drainage (AMD) for over 100 years. Recovered
dsrAB
sequences from three sites sampled along an AMD flow path indicated the dominance of a single
Desulfovibrio
species. Other major sequence clades were related most closely to
Desulfosarcina
,
Desulfococcus
,
Desulfobulbus
, and
Desulfosporosinus
species. The presence of metal sulfides with low δ
34
S values relative to δ
34
S values of pore water sulfate showed that sediment SRB populations were actively reducing sulfate under ambient conditions (pH of ∼2), although possibly within less acidic microenvironments. Interestingly, δ
34
S values for pore water sulfate were lower than those for sulfate delivered during tidal inundation of marsh sediments. 16S rRNA gene sequence data from sediments and sulfur isotope data confirmed that sulfur-oxidizing bacteria drove the reoxidation of biogenic sulfide coupled to oxygen or nitrate reduction over a timescale of hours. Collectively, these findings imply a highly dynamic microbially mediated cycling of sulfate and sulfide, and thus the speciation and mobility of chalcophilic contaminant metal(loid)s, in AMD-impacted marsh sediments.
Cometabolic Degradation of Trichloroethene by
Rhodococcus
sp. Strain L4 Immobilized on Plant Materials Rich in Essential Oils
Authors: Suttinun Oramas , Müller Rudolf , Luepromchai Ekawan 
Published: May 2010

ABSTRACT

The cometabolic degradation of trichloroethene (TCE) by
Rhodococcus
sp. L4 was limited by the loss of enzyme activity during TCE transformation. This problem was overcome by repeated addition of inducing substrates, such as cumene, limonene, or cumin aldehyde, to the cells. Alternatively,
Rhodococcus
sp. L4 was immobilized on plant materials which contain those inducers in their essential oils. Cumin seeds were the most suitable immobilizing material, and the immobilized cells tolerated up to 68 μM TCE and degraded TCE continuously. The activity of immobilized cells, which had been inactivated partially during TCE degradation, could be reactivated by incubation in mineral salts medium without TCE. These findings demonstrate that immobilization of
Rhodococcus
sp. L4 on plant materials rich in essential oils is a promising method for efficient cometabolic degradation of TCE.
Exopolysaccharide Synthesized byLactobacillus reuteriDecreases the Ability of EnterotoxigenicEscherichia coliTo Bind to Porcine Erythrocytes
Authors: Wang Yvonne , Gänzle Michael G. , Schwab Clarissa 
Published: May 2010

ABSTRACTThis study investigated the therapeutic potential of bacterial polysaccharides by employing a model system based on enteroxigenicEscherichia coli(ETEC)-induced hemagglutination of erythrocytes. Exopolysaccharides produced by strains ofLactobacillus reuteriinhibited ETEC-induced hemagglutination of porcine erythrocytes. No effect was observed for dextran produced fromWeissella cibariaand commercially available oligo- and polysaccharides.
Microtubule-Dependent mRNA Transport in Fungi
Authors: Zarnack Kathi , Feldbrügge Michael 
Published: May 2010

ABSTRACT

The localization and local translation of mRNAs constitute an important mechanism to promote the correct subcellular targeting of proteins. mRNA localization is mediated by the active transport of mRNPs, large assemblies consisting of mRNAs and associated factors such as RNA-binding proteins. Molecular motors move mRNPs along the actin or microtubule cytoskeleton for short-distance or long-distance trafficking, respectively. In filamentous fungi, microtubule-based long-distance transport of vesicles, which are involved in membrane and cell wall expansion, supports efficient hyphal growth. Recently, we discovered that the microtubule-mediated transport of mRNAs is essential for the fast polar growth of infectious filaments in the corn pathogen
Ustilago maydis
. Combining
in vivo
UV cross-linking and RNA live imaging revealed that the RNA-binding protein Rrm4, which constitutes an integral part of the mRNP transport machinery, mediates the transport of distinct mRNAs encoding polarity factors, protein synthesis factors, and mitochondrial proteins. Moreover, our results indicate that microtubule-dependent mRNA transport is evolutionarily conserved from fungi to higher eukaryotes. This raises the exciting possibility of
U. maydis
as a model system to uncover basic concepts of long-distance mRNA transport.
Systematic Genetic Analysis of the Plasmodium falciparum MSP7-Like Family Reveals Differences in Protein Expression, Location, and Importance in Asexual Growth of the Blood-Stage Parasite
Authors: Kadekoppala Madhusudan , Ogun Solabomi A. , Howell Steven , Gunaratne Ruwani S. , Holder Anthony A. 
Published: May 2010

ABSTRACT

Proteins located on
Plasmodium falciparum
merozoites, the invasive form of the parasite's asexual blood stage, are of considerable interest in vaccine research. Merozoite surface protein 7 (MSP7) forms a complex with MSP1 and is encoded by a member of a multigene family located on chromosome 13. The family codes for MSP7 and five MSP7-related proteins (MSRPs). In the present study, we have investigated the expression and the effect of
msrp
gene deletion at the asexual blood stage. In addition to
msp7
,
msrp2
,
msrp3
, and
msrp5
are transcribed, and mRNA was easily detected by hybridization analysis, whereas mRNA for
msrp1
and
msrp4
could be detected only by reverse transcription (RT)-PCR. Notwithstanding evidence of transcription, antibodies to recombinant MSRPs failed to detect specific proteins, except for antibodies to MSRP2. Sequential proteolytic cleavages of MSRP2 resulted in 28- and 25-kDa forms. However, MSRP2 was absent from merozoites; the 25-kDa MSRP2 protein (MSRP2
25
) was soluble and secreted upon merozoite egress. The
msrp
genes were deleted by targeted disruption in the 3D7 line, leading to ablation of full-length transcripts. MSRP deletion mutants had no detectable phenotype, with growth and invasion characteristics comparable to those of the parental parasite; only the deletion of MSP7 led to a detectable growth phenotype. Thus, within this family some of the genes are transcribed at a significant level in asexual blood stages, but the corresponding proteins may or may not be detectable. Interactions of the expressed proteins with the merozoite also differ. These results highlight the potential for unexpected differences of protein expression levels within gene families.
MoTea4-Mediated Polarized Growth Is Essential for Proper Asexual Development and Pathogenesis in Magnaporthe oryzae
Authors: Patkar Rajesh N. , Suresh Angayarkanni , Naqvi Naweed I. 
Published: May 2010

ABSTRACT

Polarized growth is essential for cellular development and function and requires coordinated organization of the cytoskeletal elements. Tea4, an important polarity determinant, regulates localized F-actin assembly and bipolar growth in fission yeast and directional mycelial growth in
Aspergillus
. Here, we characterize Tea4 in the rice blast fungus
Magnaporthe oryzae
(MoTea4). Similar to its orthologs, MoTea4-green fluorescent protein (MoTea4-GFP) showed punctate distribution confined to growth zones, particularly in the mycelial tips, aerial hyphae, conidiophores, conidia, and infection structures (appressoria) in
Magnaporthe
. MoTea4 was dispensable for vegetative growth in
Magnaporthe
. However, loss of MoTea4 led to a zigzag morphology in the aerial hyphae and a huge reduction in conidiation. The majority of the
tea4
Δ conidia were two celled, as opposed to the tricellular conidia in the wild type. Structure-function analysis indicated that the SH3 and coiled-coil domains of MoTea4 are necessary for proper conidiation in
Magnaporthe
. The
tea4
Δ conidia failed to produce proper appressoria and consequently failed to infect the host plants. The
tea4
Δ conidia and germ tubes showed disorganized F-actin structures with significantly reduced numbers of cortical actin patches. Compared to the wild-type conidia, the
tea4
Δ conidia showed aberrant germination, poor cytoplasmic streaming, and persistent accumulation of lipid droplets, likely due to the impaired F-actin cytoskeleton. Latrunculin A treatment of germinating wild-type conidia showed that an intact F-actin cytoskeleton is indeed essential for appressorial development in
Magnaporthe
. We show that MoTea4 plays an important role in organizing the F-actin cytoskeleton and is essentially required for polarized growth and morphogenesis during asexual and pathogenic development in
Magnaporthe
.
Unconventional Secretion of AcbA in Dictyostelium discoideum through a Vesicular Intermediate
Authors: Cabral Matthew , Anjard Christophe , Malhotra Vivek , Loomis William F. , Kuspa Adam 
Published: May 2010

ABSTRACT

The acyl coenzyme A (CoA) binding protein AcbA is secreted unconventionally and processed into spore differentiation factor 2 (SDF-2), a peptide that coordinates sporulation in
Dictyostelium discoideum
. We report that AcbA is localized in vesicles that accumulate in the cortex of prespore cells just prior to sporulation. These vesicles are not observed after cells are stimulated to release AcbA but remain visible after stimulation in cells lacking the Golgi reassembly stacking protein (GRASP). Acyl-CoA binding is required for the inclusion of AcbA in these vesicles, and the secretion of AcbA requires
N
-ethylmaleimide-sensitive factor (NSF). About 1% of the total cellular AcbA can be purified within membrane-bound vesicles. The yield of vesicles decreases dramatically when purified from wild-type cells that were stimulated to release AcbA, whereas the yield from GRASP mutant cells was only modestly altered by stimulation. We suggest that these AcbA-containing vesicles are secretion intermediates and that GRASP functions at a late step leading to the docking/fusion of these vesicles at the cell surface.
Sensor Kinases RetS and LadS RegulatePseudomonas syringaeType VI Secretion and Virulence Factors
Authors: Records Angela R. , Gross Dennis C. 
Published: May 2010

ABSTRACTPseudomonas syringaepv. syringae B728a is a resident on leaves of common bean, where it utilizes several well-studied virulence factors, including secreted effectors and toxins, to develop a pathogenic interaction with its host. The B728a genome was recently sequenced, revealing the presence of 1,297 genes with unknown function. This study demonstrates that a 29.9-kb cluster of genes in the B728a genome shares homology to the novel type VI secretion system (T6SS) locus recently described for other Gram-negative bacteria. Western blot analyses showed that B728a secretes Hcp, a T6SS protein, in culture and that this secretion is dependent onclpV, a gene that likely encodes an AAA+ATPase. In addition, we have identified two B728a sensor kinases that have homology to theP. aeruginosaproteins RetS and LadS. We demonstrate that B728a RetS and LadS reciprocally regulate the T6SS and collectively modulate several virulence-related activities. Quantitative PCR analyses indicated that RetS and LadS regulate genes associated with the type III secretion system and that LadS controls the expression of genes involved in the production of the exopolysaccharides alginate and levan. These analyses also revealed that LadS and the hybrid sensor kinase GacS positively regulate the expression of a putative novel exopolysaccharide called Psl. Plate assays demonstrated that RetS negatively controls mucoidy, while LadS negatively regulates swarming motility. A mutation inretSaffected B728a population levels on the surfaces of bean leaves. A model for the LadS and RetS control of B728a virulence activities is proposed.
Variation among Genome Sequences of H37Rv Strains of
Mycobacterium tuberculosis
from Multiple Laboratories
Authors: Ioerger Thomas R. , Feng Yicheng , Ganesula Krishna , Chen Xiaohua , Dobos Karen M. , Fortune Sarah , Jacobs William R. , Mizrahi Valerie , Parish Tanya , Rubin Eric , Sassetti Chris , Sacchettini James C. 
Published: May 2010

ABSTRACT

The publication of the complete genome sequence for
Mycobacterium tuberculosis
H37Rv in 1998 has had a great impact on the research community. Nonetheless, it is suspected that genetic differences have arisen in stocks of H37Rv that are maintained in different laboratories. In order to assess the consistency of the genome sequences among H37Rv strains in use and the extent to which they have diverged from the original strain sequenced, we carried out whole-genome sequencing on six strains of H37Rv from different laboratories. Polymorphisms at 73 sites were observed, which were shared among the lab strains, though 72 of these were also shared with H37Ra and are likely to be due to sequencing errors in the original H37Rv reference sequence. An updated H37Rv genome sequence should be valuable to the tuberculosis research community as well as the broader microbial research community. In addition, several polymorphisms unique to individual strains and several shared polymorphisms were identified and shown to be consistent with the known provenance of these strains. Aside from nucleotide substitutions and insertion/deletions, multiple IS
6110
transposition events were observed, supporting the theory that they play a significant role in plasticity of the
M. tuberculosis
genome. This genome-wide catalog of genetic differences can help explain any phenotypic differences that might be found, including a frameshift mutation in the mycocerosic acid synthase gene which causes two of the strains to be deficient in biosynthesis of the surface glycolipid phthiocerol dimycocerosate (PDIM). The resequencing of these six lab strains represents a fortuitous “
in vitro
evolution” experiment that demonstrates how the
M. tuberculosis
genome continues to evolve even in a controlled environment.
Down-Regulation of theEscherichia coliK-12nrfPromoter by Binding of the NsrR Nitric Oxide-Sensing Transcription Repressor to an Upstream Site
Authors: Browning Douglas F. , Lee David J. , Spiro Stephen , Busby Stephen J. W. 
Published: May 2010

ABSTRACTFNR-dependent activation of theEscherichia coliK-12nrfpromoter is downregulated by the nitric oxide-sensitive NsrR protein together with the nucleoid-associated protein IHF, which bind to overlapping targets adjacent to the DNA site for FNR. The NsrR target is inactivated by mutation at theSalmonella entericaserovar Typhimuriumnrfpromoter.
The Genetic Basis of Laboratory Adaptation in
Caulobacter crescentus
Authors: Marks Melissa E. , Castro-Rojas Cyd Marie , Teiling Clotilde , Du Lei , Kapatral Vinayak , Walunas Theresa L. , Crosson Sean 
Published: May 2010

ABSTRACT

The dimorphic bacterium
Caulobacter crescentus
has evolved marked phenotypic changes during its 50-year history of culture in the laboratory environment, providing an excellent system for the study of natural selection and phenotypic microevolution in prokaryotes. Combining whole-genome sequencing with classical molecular genetic tools, we have comprehensively mapped a set of polymorphisms underlying multiple derived phenotypes, several of which arose independently in separate strain lineages. The genetic basis of phenotypic differences in growth rate, mucoidy, adhesion, sedimentation, phage susceptibility, and stationary-phase survival between
C. crescentus
strain CB15 and its derivative NA1000 is determined by coding, regulatory, and insertion/deletion polymorphisms at five chromosomal loci. This study evidences multiple genetic mechanisms of bacterial evolution as driven by selection for growth and survival in a new selective environment and identifies a common polymorphic locus,
zwf
, between lab-adapted
C. crescentus
and clinical isolates of
Pseudomonas aeruginosa
that have adapted to a human host during chronic infection.