bluuebunny/crossref_metadata_2025_split huggingface dataset:
Growth of Enterococci in Unaltered, Unseeded Beach Sands Subjected to Tidal Wetting
Authors: Yamahara Kevan M. , Walters Sarah P. , Boehm Alexandria B. 
Published: January 2009

ABSTRACT
Enterococci are indicator bacteria used to assess the risk of acquiring enteric disease from swimming in marine waters. Previous work identified beach sands as reservoirs of enterococci which can be transported from the sand to the sea, where they may instigate beach advisories. The present study establishes that naturally occurring enterococci can replicate in beach sands under environmentally relevant conditions. In unseeded, nonsterile microcosm experiments, it was shown that intermittent wetting of sands by seawater, like that which would occur at the high tide line, stimulates the transient replication of enterococci at rates of 0.20 to 0.63 per day (equivalent to doubling times of 1.1 to 3.5 days). Replication was not observed in control microcosms that were not subjected to wetting. Enterococci were enumerated using both culture-dependent (membrane filtration and mEI media) and culture-independent (quantitative PCR [QPCR], 23S rRNA gene based) techniques, which allowed tracking of both culturable and total enterococcus populations. Inhibition of QPCR and DNA extraction efficiencies were accounted for in the interpretation of the QPCR results. The results provide evidence that enterococci may not be an appropriate indicator of enteric disease risk at recreational beaches subject to nonpoint sources of pollution.
Bacterial Diversity Analysis of Huanglongbing Pathogen-Infected Citrus, Using PhyloChip Arrays and 16S rRNA Gene Clone Library Sequencing
Authors: Sagaram Uma Shankar , DeAngelis Kristen M. , Trivedi Pankaj , Andersen Gary L. , Lu Shi-En , Wang Nian 
Published: January 2009

ABSTRACT

The bacterial diversity associated with citrus leaf midribs was characterized for citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rRNA gene microarrays and 16S rRNA gene clone library sequencing to determine the microbial community composition for symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria in 15 phyla were present in the citrus leaf midribs, while 20 orders in 8 phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs than in asymptomatic midribs. “
Candidatus
Liberibacter asiaticus” was detected at a very low level in asymptomatic plants but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis results were further verified by sequencing 16S rRNA gene clone libraries, which indicated the dominance of “
Candidatus
Liberibacter asiaticus” in symptomatic leaves. These data implicate “
Candidatus
Liberibacter asiaticus” as the pathogen responsible for HLB disease.
Rapid Oligonucleotide-Based Recombineering of the Chromosome of
Salmonella enterica
Authors: Gerlach Roman G. , Jäckel Daniela , Hölzer Stefanie U. , Hensel Michael 
Published: January 2009

ABSTRACT

Recombinant engineering using Red recombinase-based approaches offers efficient and rapid approaches to deletion and modification of genes. Here we describe a novel application of Red recombinant engineering that enables direct manipulation of chromosomal loci by electroporation with short synthetic DNA molecules. We demonstrate the use of this approach for the generation of scarless in-frame deletions in chromosomal genes of
Salmonella enterica
. Furthermore, we describe rapid site-directed mutagenesis within bacterial chromosomes without any requirement for cloning and mutating genes in vitro or for reintroducing mutant alleles into the chromosome. This approach can be expected to facilitate mutational analysis in
S. enterica
and in other bacterial species able to support Red-mediated recombination.
Prevalence ofRickettsiaSpecies in Canadian Populations ofDermacentor andersoniandD. variabilis
Authors: Dergousoff Shaun J. , Gajadhar Andrew J. A. , Chilton Neil B. 
Published: January 2009

ABSTRACTWe determined the prevalence of rickettsiae inDermacentoradults at 15 localities in Canada.Rickettsia rickettsiiwas not detected in any tick, whereasRickettsia peacockiiwas present in 76% ofDermacentor andersoniadults andRickettsia montanensisin 8% ofDermacentor variabilisadults. This host specificity was maintained in localities where both tick species occurred in sympatry.
Contrasting Soil pH Effects on Fungal and Bacterial Growth Suggest Functional Redundancy in Carbon Mineralization
Authors: Rousk Johannes , Brookes Philip C. , Bååth Erland 
Published: January 2009

ABSTRACT
The influence of pH on the relative importance of the two principal decomposer groups in soil, fungi and bacteria, was investigated along a continuous soil pH gradient at Hoosfield acid strip at Rothamsted Research in the United Kingdom. This experimental location provides a uniform pH gradient, ranging from pH 8.3 to 4.0, within 180 m in a silty loam soil on which barley has been continuously grown for more than 100 years. We estimated the importance of fungi and bacteria directly by measuring acetate incorporation into ergosterol to measure fungal growth and leucine and thymidine incorporation to measure bacterial growth. The growth-based measurements revealed a fivefold decrease in bacterial growth and a fivefold increase in fungal growth with lower pH. This resulted in an approximately 30-fold increase in fungal importance, as indicated by the fungal growth/bacterial growth ratio, from pH 8.3 to pH 4.5. In contrast, corresponding effects on biomass markers for fungi (ergosterol and phospholipid fatty acid [PLFA] 18:2ω6,9) and bacteria (bacterial PLFAs) showed only a two- to threefold difference in fungal importance in the same pH interval. The shift in fungal and bacterial importance along the pH gradient decreased the total carbon mineralization, measured as basal respiration, by only about one-third, possibly suggesting functional redundancy. Below pH 4.5 there was universal inhibition of all microbial variables, probably derived from increased inhibitory effects due to release of free aluminum or decreasing plant productivity. To investigate decomposer group importance, growth measurements provided significantly increased sensitivity compared with biomass-based measurements.
Uneven Distribution of Mating Types among Genotypes of
Candida glabrata
Isolates from Clinical Samples
Authors: Brisse Sylvain , Pannier Christine , Angoulvant Adela , de Meeus Thierry , Diancourt Laure , Faure Odile , Muller Héloïse , Peman Javier , Viviani Maria Anna , Grillot Renée , Dujon Bernard , Fairhead Cécile , Hennequin Christophe 
Published: January 2009

ABSTRACT

In order to shed light on its basic biology, we initiated a population genetic analysis of
Candida glabrata
, an emerging pathogenic yeast with no sexual stage yet recognized. A worldwide collection of clinical strains was subjected to analysis using variable number of tandem repeats (VNTR) at nine loci. The clustering of strains obtained with this method was congruent with that obtained using sequence polymorphism of the
NMT1
gene, a locus previously proposed for lineage assignment. Linkage disequilibrium supported the hypothesis of a mainly clonal reproduction. No heterozygous diploid genotype was found. Minimum-spanning tree analysis of VNTR data revealed clonal expansions and associated genotypic diversification. Mating type analysis revealed that 80% of the strains examined are
MAT
a
and 20%
MAT
α and that the two alleles are not evenly distributed. The
MAT
a
genotype dominated within large clonal groups that contained only one or a few
MAT
α types. In contrast, two groups were dominated by
MAT
α strains. Our data are consistent with rare independent mating type switching events occurring preferentially from type
a
to α, although the alternative possibility of selection favoring type
a
isolates cannot be excluded.
Transcriptional Regulation of an Iron-Inducible Gene by Differential and Alternate Promoter Entries of Multiple Myb Proteins in the Protozoan Parasite
Trichomonas vaginalis
Authors: Hsu Hong-Ming , Ong Shiou-Jeng , Lee Ming-Chun , Tai Jung-Hsiang 
Published: January 2009

ABSTRACT

Iron-inducible transcription of a malic enzyme gene (also reputed to be
ap65-1
) in
Trichomonas vaginalis
was previously shown to involve a Myb1 repressor and a Myb2 activator, each of which may preferentially select two closely spaced promoter sites, MRE-1/MRE-2r, which comprises overlapping promoter elements, and MRE-2f. In the present study, an iron-inducible ∼32-kDa Myb3 nuclear protein was demonstrated to bind only the MRE-1 element. Changes in the iron supply, which produced antagonistic effects on the levels of Myb2 and Myb3 expression, also resulted in temporal and alternate entries of Myb2 and Myb3 into the
ap65-1
promoter. Repression or activation of basal and iron-inducible
ap65-1
transcription was detected in transfected cells when Myb3 was, respectively, substantially knocked down or overexpressed. In the latter case, increased Myb3 promoter entry was detected with concomitant decrease in Myb2 promoter entry under specific conditions, while Myb3 promoter entry was inhibited under all test conditions in cells overexpressing Myb2. In contrast, concomitant promoter entries by Myb2 and Myb3 diminished in cells overexpressing Myb1, except that Myb3 promoter entry was slightly affected under prolonged iron depletion. Together, these results suggest that Myb2 and Myb3 may coactivate basal and iron-inducible
ap65-1
transcription against Myb1 through conditional and competitive promoter entries.
Patterns of Gene-Specific and Total Transcriptional Activity during thePlasmodium falciparumIntraerythrocytic Developmental Cycle
Authors: Sims Jennifer S. , Militello Kevin T. , Sims Peter A. , Patel Vishal P. , Kasper Jacob M. , Wirth Dyann F. 
Published: January 2009

ABSTRACTThe relationships among gene regulatory mechanisms in the malaria parasitePlasmodium falciparumthroughout its asexual intraerythrocytic developmental cycle (IDC) remain poorly understood. To investigate the level and nature of transcriptional activity and its role in controlling gene expression during the IDC, we performed nuclear run-on on whole-transcriptome samples from time points throughout the IDC and found a peak in RNA polymerase II-dependent transcriptional activity related to both the number of nuclei per parasite and variable transcriptional activity per nucleus over time. These differential total transcriptional activity levels allowed the calculation of the absolute transcriptional activities of individual genes from gene-specific nuclear run-on hybridization data. For half of the genes analyzed, sense-strand transcriptional activity peaked at the same time point as total activity. The antisense strands of several genes were substantially transcribed. Comparison of the transcriptional activity of the sense strand of each gene to its steady-state RNA abundance across the time points assayed revealed both correlations and discrepancies, implying transcriptional and posttranscriptional regulation, respectively. Our results demonstrate that such comparisons can effectively indicate gene regulatory mechanisms inP. falciparumand suggest that genes with diverse transcriptional activity levels and patterns combine to produce total transcriptional activity levels tied to parasite development during the IDC.
Correlation between Biofilm Formation and the Hypoxic Response in
Candida parapsilosis
Authors: Rossignol Tristan , Ding Chen , Guida Alessandro , d'Enfert Christophe , Higgins Desmond G. , Butler Geraldine 
Published: January 2009

ABSTRACT

The ability of
Candida parapsilosis
to form biofilms on indwelling medical devices is correlated with virulence. To identify genes that are important for biofilm formation, we used arrays representing approximately 4,000 open reading frames (ORFs) to compare the transcriptional profile of biofilm cells growing in a microfermentor under continuous flow conditions with that of cells in planktonic culture. The expression of genes involved in fatty acid and ergosterol metabolism and in glycolysis, is upregulated in biofilms. The transcriptional profile of
C. parapsilosis
biofilm cells resembles that of
Candida albicans
cells grown under hypoxic conditions. We therefore subsequently used whole-genome arrays (representing 5,900 ORFs) to determine the hypoxic response of
C. parapsilosis
and showed that the levels of expression of genes involved in the ergosterol and glycolytic pathways, together with several cell wall genes, are increased. Our results indicate that there is substantial overlap between the hypoxic responses of
C. parapsilosis
and
C. albicans
and that this may be important for biofilm development. Knocking out an ortholog of the cell wall gene
RBT1
, whose expression is induced both in biofilms and under conditions of hypoxia in
C. parapsilosis
, reduces biofilm development.
Phylogeny and Phenotypic Characterization of PathogenicCryptococcusSpecies and Closely Related Saprobic Taxa in the Tremellales
Authors: Findley Keisha , Rodriguez-Carres Marianela , Metin Banu , Kroiss Johannes , Fonseca Álvaro , Vilgalys Rytas , Heitman Joseph 
Published: January 2009

ABSTRACTThe basidiomycetous yeastsCryptococcus neoformansandCryptococcus gattiiare closely related sibling species that cause respiratory and neurological disease in humans and animals. Within these two recognized species, phylogenetic analysis reveals at least six cryptic species defined as molecular types (VNI/II/B, VNIV, VGI, VGII, VGIII, and VGIV) that comprise the pathogenicCryptococcusspecies complex. These pathogenic species are clustered in theFilobasidiellaclade within the order Tremellales. Previous studies have shown that theFilobasidiellaclade also includes several saprobic fungi isolated from insect frass, but information evaluating the relatedness of the saprobes and pathogens within this cluster is limited. Here, the phylogeny encompassing a subset of species in the Tremellales lineage that clusters closely with the pathogenicCryptococcusspecies complex was resolved by employing a multilocus sequencing approach for phylogenetic analysis. Six highly conserved genomic loci from 15 related basidiomycete species were sequenced, and the alignments from the concatenated gene sequences were evaluated with different tree-building criteria. Furthermore, these 15 species were subjected to virulence and phenotype assays to evaluate their pathogenic potential. These studies revealed thatCryptococcus amylolentusandTsuchiyaea wingfieldii, two nonpathogenic sibling species, are the taxa most closely related to the pathogensC. neoformansandC. gattiiand together withFilobasidiella depauperataform aCryptococcussensu stricto group. Five other saprobic yeast species form theKwoniellaclade, which appears to be a part of a more distantly related sensu lato group. This study establishes a foundation for future comparative genomic approaches that will provide insight into the structure, function, and evolution of the mating type locus, the transitions in modes of sexual reproduction, and the emergence of human pathogenic species from related or ancestral saprobic species.
Contribution of Peroxisomes to Penicillin Biosynthesis in
Aspergillus nidulans
Authors: Spröte Petra , Brakhage Axel A. , Hynes Michael J. 
Published: January 2009

ABSTRACT

Peroxisomal localization of the third enzyme of the penicillin biosynthesis pathway of
Aspergillus nidulans
, acyl-coenzyme A:IPN acyltransferase (IAT), is mediated by its atypical peroxisomal targeting signal 1 (PTS1). However, mislocalization of IAT by deletion of either its PTS1 or of genes encoding proteins involved in peroxisome formation or transport does not completely abolish penicillin biosynthesis. This is in contrast to the effects of IAT mislocalization in
Penicillium chrysogenum
.
Identification of
ENA1
as a Virulence Gene of the Human Pathogenic Fungus
Cryptococcus neoformans
through Signature-Tagged Insertional Mutagenesis
Authors: Idnurm Alexander , Walton Felicia J. , Floyd Anna , Reedy Jennifer L. , Heitman Joseph 
Published: January 2009

ABSTRACT

A library of more than 4,500 signature-tagged insertion mutants of the human pathogenic fungus
Cryptococcus neoformans
was generated, and a subset was screened in a murine inhalation model to identify genes required for virulence. New genes that regulate aspects of
C. neoformans
virulence were also identified by screening the entire library for in vitro phenotypes related to the ability to cause disease, including melanin production, growth at high temperature, and growth under conditions of nutrient limitation. A screen of 10% of the strain collection in mice identified an avirulent mutant strain with an insertion in the
ENA1
gene, which is predicted to encode a fungus-specific sodium or potassium P-type ATPase. The results of the deletion of the gene and complementation experiments confirmed its key role in mammalian virulence.
ena1
mutant strains exhibited no change in sensitivity to high salt concentrations but were sensitive to alkaline pH conditions, providing evidence that the fungus may have to survive at elevated pH during infection of the mammalian host. The mutation of the well-characterized virulence factor calcineurin (
CNA1
) also rendered
C. neoformans
strains sensitive to elevated pH.
ENA1
transcripts in wild-type and
cna1
mutant strains were upregulated in response to high pH, and
cna1 ena1
double mutant strains exhibited increased sensitivity to elevated pH, indicating that at least two pathways in the fungus mediate survival under alkaline conditions. Signature-tagged mutagenesis is an effective strategy for the discovery of new virulence genes in fungal pathogens of animals.
Property Differences among the Four Major
Candida albicans
Strain Clades
Authors: MacCallum Donna M. , Castillo Luis , Nather Kerstin , Munro Carol A. , Brown Alistair J. P. , Gow Neil A. R. , Odds Frank C. 
Published: January 2009

ABSTRACT

A selection of 43
Candida albicans
isolates, chosen to represent the four major strain clades of the species and also intraclade diversity, was screened for their virulence in the murine intravenous challenge model of
C. albicans
infection, for a range of properties measurable in vitro that might relate to virulence, and for the numbers of midrepeat sequences in genes of the
ALS
and
HYR
families. Heterozygosity at the mating type locus and low whole-cell acid phosphatase activity and growth rate at 40°C were found to be significantly positively associated with the most virulent isolates. Acid phosphatase activity and growth in 2 M NaCl were statistically significant variables between clades by univariate analysis. Isolates in different clades also differed significantly in midrepeat sequence alleles of
ALS2
,
ALS4
,
ALS6
,
ALS7
,
ALS9
,
HYR1
, and
HYR2
. There was no association between the midrepeat alleles of any
ALS
or
HYR
gene and the virulence of isolates to mice. Genome-wide transcript profiles of 20 isolates (5 per clade) grown under two conditions showed considerable variation between individual isolates, but only a small number of genes showed statistically significant differential gene expression between clades. Analysis of the expression profiles by overall strain virulence revealed 18 open reading frames differing significantly between isolates of high, intermediate, and low virulence. Four of these genes encoded functions related to phosphate uptake and metabolism. This finding and the significant association between whole-cell acid phosphatase activity and virulence led us to disrupt
PHO100
, which encodes a predicted periplasmic acid phosphatase. The
pho100
Δ mutant was mildly but significantly attenuated in terms of survival curves in the mouse model. The study has extended the range of properties known to differ between
C. albicans
clades and suggests a possible but minor role of phosphate metabolism in the virulence of the species.
Population Variability of the FimH Type 1 Fimbrial Adhesin in
Klebsiella pneumoniae
Authors: Stahlhut Steen G. , Chattopadhyay Sujay , Struve Carsten , Weissman Scott J. , Aprikian Pavel , Libby Stephen J. , Fang Ferric C. , Krogfelt Karen Angeliki , Sokurenko Evgeni V. 
Published: January 2009

ABSTRACT

FimH is an adhesive subunit of type 1 fimbriae expressed by different enterobacterial species. The enteric bacterium
Klebsiella pneumoniae
is an environmental organism that is also a frequent cause of sepsis, urinary tract infection (UTI), and liver abscess. Type 1 fimbriae have been shown to be critical for the ability of
K. pneumoniae
to cause UTI in a murine model. We show here that the
K. pneumoniae fimH
gene is found in 90% of strains from various environmental and clinical sources. The
fimH
alleles exhibit relatively low nucleotide and structural diversity but are prone to frequent horizontal-transfer events between different bacterial clones. Addition of the
fimH
locus to multiple-locus sequence typing significantly improved the resolution of the clonal structure of pathogenic strains, including the K1 encapsulated liver isolates. In addition, the
K. pneumoniae
FimH protein is targeted by adaptive point mutations, though not to the same extent as FimH from uropathogenic
Escherichia coli
or TonB from the same
K. pneumoniae
strains. Such adaptive mutations include a single amino acid deletion from the signal peptide that might affect the length of the fimbrial rod by affecting FimH translocation into the periplasm. Another FimH mutation (S62A) occurred in the course of endemic circulation of a nosocomial uropathogenic clone of
K. pneumoniae.
This mutation is identical to one found in a highly virulent uropathogenic strain of
E. coli
, suggesting that the FimH mutations are pathoadaptive in nature. Considering the abundance of type 1 fimbriae in
Enterobacteriaceae
, our present finding that
fimH
genes are subject to adaptive microevolution substantiates the importance of type 1 fimbria-mediated adhesion in
K. pneumoniae
.
Differential Interactions between Tat-Specific Redox Enzyme Peptides and Their Chaperones
Authors: Chan Catherine S. , Chang Limei , Rommens Kenton L. , Turner Raymond J. 
Published: January 2009

ABSTRACT

The twin-arginine translocase (Tat) system is used by many bacteria to move proteins across the cytoplasmic membrane. Tat substrates are prefolded and contain a conserved SRRxFLK twin-arginine (RR) motif at their N termini. Many Tat substrates in
Escherichia coli
are cofactor-containing redox enzymes that have specific chaperones called redox enzyme maturation proteins (REMPs). Here we characterized the interactions between 10 REMPs and 15 RR peptides of known and predicted Tat-specific redox enzyme subunits. A combination of in vitro and in vivo experiments demonstrated that some REMPs were specific to a redox enzyme(s) of similar function, whereas others were less specific and bound peptides of unrelated enzymes. Results from Biacore surface plasmon resonance (SPR) and bacterial two-hybrid experiments identified interactions in addition to those found in far-Western experiments, suggesting that conformational freedom and/or other cellular factors may be required. Furthermore, we show that the interaction of the two prevents both from being proteolytically degraded in vivo, and kinetic data from SPR show up to 10-fold-tighter binding to the expected RR substrate when multiple binding partners existed. Investigations using full-length sequences of the RR proteins showed that the mature portion for some redox enzyme subunits is required for detection of the interactions. Sequence alignments among the REMPs and RR peptides indicated that homology between the REMPs and the hydrophobic regions following the RR motifs in the peptides correlates to cross-recognition.