bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Two-Color Fluorescence In Situ Hybridization Technique for Species-Level Identification of Human-InfectiousCryptosporidiumspp
Authors: Alagappan A. , Bergquist P. L. , Ferrari B. C. 
Published: July 2009

ABSTRACTA two-color fluorescence in situ hybridization assay that allows for the simultaneous identification ofCryptosporidium parvumandC. hominiswas developed. The assay is a simple, rapid, and cost-effective tool for the detection of the majorCryptosporidiumspecies of concern to public health.
Fungal Diversity in Deep-Sea Hydrothermal Ecosystems
Authors: Le Calvez Thomas , Burgaud Gaëtan , Mahé Stéphane , Barbier Georges , Vandenkoornhuyse Philippe 
Published: July 2009

ABSTRACT

Deep-sea hydrothermal ecosystems are considered oases of life in oceans. Since the discovery of these ecosystems in the late 1970s, many endemic species of
Bacteria
,
Archaea
, and other organisms, such as annelids and crabs, have been described. Considerable knowledge has been acquired about the diversity of (micro)organisms in these ecosystems, but the diversity of fungi has not been studied to date. These organisms are considered key organisms in terrestrial ecosystems because of their ecological functions and especially their ability to degrade organic matter. The lack of knowledge about them in the sea reflects the widely held belief that fungi are terrestrial organisms. The first inventory of such organisms in deep-sea hydrothermal environments was obtained in this study. Fungal diversity was investigated by analyzing the small-subunit rRNA gene sequences amplified by culture-independent PCR using DNA extracts from hydrothermal samples and from a culture collection that was established. Our work revealed an unsuspected diversity of species in three of the five fungal phyla. We found a new branch of
Chytridiomycota
forming an ancient evolutionary lineage. Many of the species identified are unknown, even at higher taxonomic levels in the
Chytridiomycota
,
Ascomycota
, and
Basidiomycota
. This work opens the way to new studies of the diversity, ecology, and physiology of fungi in oceans and might stimulate new prospecting for biomolecules. From an evolutionary point of view, the diversification of fungi in the oceans can no longer be ignored.
Genetic Subdivision of Chemosynthetic Endosymbionts of
Solemya velum
along the Southern New England Coast
Authors: Stewart Frank J. , Baik Alan Hyun Y. , Cavanaugh Colleen M. 
Published: July 2009

ABSTRACT

Population-level genetic diversity in the obligate symbiosis between the bivalve
Solemya velum
and its thioautotrophic bacterial endosymbiont was examined. Distinct populations along the New England coast shared a single mitochondrial genotype but were fixed for unique symbiont genotypes, indicating high levels of symbiont genetic structuring and potential symbiont-host decoupling.
Use of Chimeric DNA-RNA Primers in Quantitative PCR for Detection of
Ehrlichia canis
and
Babesia canis
Authors: Peleg Ofer , Baneth Gad , Eyal Osnat , Inbar Jacob , Harrus Shimon 
Published: July 2009

ABSTRACT

To overcome the problem of nonspecific by-products in quantitative PCR (qPCR) assays, we constructed DNA-RNA chimeric primers and evaluated their use in the detection and quantification of the
Ehrlichia canis
16S rRNA,
Babesia canis
Hsp70, and canine β-actin genes. Several RNA bases were incorporated into specific positions in the DNA primers, while no RNA stretches were allowed. qPCR reactions were carried out without preamplification steps. This resulted in decreased formation of undesirable by-products and a 10-fold increase in assay sensitivity.
Isolation and Characterization of “
Dehalococcoides
” sp. Strain MB, Which Dechlorinates Tetrachloroethene to
trans
-1,2-Dichloroethene
Authors: Cheng Dan , He Jianzhong 
Published: July 2009

ABSTRACT

In an attempt to understand the microorganisms involved in the generation of
trans
-1,2-dichloroethene (
trans
-DCE), pure-culture “
Dehalococcoides
” sp. strain MB was isolated from environmental sediments. In contrast to currently known tetrachloroethene (PCE)- or trichloroethene (TCE)-dechlorinating pure cultures, which generate
cis
-DCE as the predominant product,
Dehalococcoides
sp. strain MB reductively dechlorinates PCE to
trans
-DCE and
cis
-DCE at a ratio of 7.3 (±0.4):1. It utilizes H
2
as the sole electron donor and PCE or TCE as the electron acceptor during anaerobic respiration. Strain MB is a disc-shaped, nonmotile bacterium. Under an atomic force microscope, the cells appear singly or in pairs and are 1.0 μm in diameter and ∼150 nm in depth. The purity was confirmed by culture-based approaches and 16S rRNA gene-based analysis and was corroborated further by putative reductive dehalogenase (RDase) gene-based, quantitative real-time PCR. Although strain MB shares 100% 16S rRNA gene sequence identity with
Dehalococcoides ethenogenes
strain 195, these two strains possess different dechlorinating pathways. Microarray analysis revealed that 10 putative RDase genes present in strain 195 were also detected in strain MB. Successful cultivation of strain MB indicates that the biotic process could contribute significantly to the generation of
trans
-DCE in chloroethene-contaminated sites. It also enhances our understanding of the evolution of this unusual microbial group,
Dehalococcoides
species.
Overexpression of the
groESL
Operon Enhances the Heat and Salinity Stress Tolerance of the Nitrogen-Fixing Cyanobacterium
Anabaena
sp. Strain PCC7120
Authors: Chaurasia Akhilesh Kumar , Apte Shree Kumar 
Published: July 2009

ABSTRACT

The bicistronic
groESL
operon, encoding the Hsp60 and Hsp10 chaperonins, was cloned into an integrative expression vector, pFPN, and incorporated at an innocuous site in the
Anabaena
sp. strain PCC7120 genome. In the recombinant
Anabaena
strain, the additional
groESL
operon was expressed from a strong cyanobacterial P

psbA1

promoter without hampering the stress-responsive expression of the native
groESL
operon. The net expression of the two
groESL
operons promoted better growth, supported the vital activities of nitrogen fixation and photosynthesis at ambient conditions, and enhanced the tolerance of the recombinant
Anabaena
strain to heat and salinity stresses.
Genome-Wide Identification of
S
accharomyces cerevisiae
Genes Required for Maximal Tolerance to Ethanol
Authors: Teixeira Miguel C. , Raposo Luís R. , Mira Nuno P. , Lourenço Artur B. , Sá-Correia Isabel 
Published: July 2009

ABSTRACT

The understanding of the molecular basis of yeast resistance to ethanol may guide the design of rational strategies to increase process performance in industrial alcoholic fermentations. In this study, the yeast disruptome was screened for mutants with differential susceptibility to stress induced by high ethanol concentrations in minimal growth medium. Over 250 determinants of resistance to ethanol were identified. The most significant gene ontology terms enriched in this data set are those associated with intracellular organization, biogenesis, and transport, in particular, regarding the vacuole, the peroxisome, the endosome, and the cytoskeleton, and those associated with the transcriptional machinery. Clustering the proteins encoded by the identified determinants of ethanol resistance by their known physical and genetic interactions highlighted the importance of the vacuolar protein sorting machinery, the vacuolar H
+
-ATPase complex, and the peroxisome protein import machinery. Evidence showing that vacuolar acidification and increased resistance to the cell wall lytic enzyme β-glucanase occur in response to ethanol-induced stress was obtained. Based on the genome-wide results, the particular role of the
FPS1
gene, encoding a plasma membrane aquaglyceroporin which mediates controlled glycerol efflux, in ethanol stress resistance was further investigated.
FPS1
expression contributes to decreased [
3
H]ethanol accumulation in yeast cells, suggesting that Fps1p may also play a role in maintaining the intracellular ethanol level during active fermentation. The increased expression of
FPS1
confirmed the important role of this gene in alcoholic fermentation, leading to increased final ethanol concentration under conditions that lead to high ethanol production.
rhs
Genes Are Potential Markers for Multilocus Sequence Typing of
Escherichia coli
O157:H7 Strains
Authors: Liu K. , Knabel S. J. , Dudley E. G. 
Published: July 2009

ABSTRACT

DNA sequence-based molecular subtyping methods such as multilocus sequence typing (MLST) are commonly used to generate phylogenetic inferences for monomorphic pathogens. The development of an effective MLST scheme for subtyping
Escherichia coli
O157:H7 has been hindered in the past due to the lack of sequence variation found within analyzed housekeeping and virulence genes. A recent study suggested that
rhs
genes are under strong positive selection pressure, and therefore in this study we analyzed these genes within a diverse collection of
E. coli
O157:H7 strains for sequence variability. Eighteen O157:H7 strains from lineages I and II and 15 O157:H7 strains from eight clades were included. Examination of these
rhs
genes revealed 44 polymorphic loci (PL) and 10 sequence types (STs) among the 18 lineage strains and 280 PL and 12 STs among the 15 clade strains. Phylogenetic analysis using
rhs
genes generally grouped strains according to their known lineage and clade classifications. These findings also suggested that O157:H7 strains from clades 6 and 8 fall into lineage I/II and that strains of clades 1, 2, 3, and 4 fall into lineage I. Additionally, unique markers were found in
rhsA
and
rhsJ
that might be used to define clade 8 and clade 6. Therefore,
rhs
genes may be useful markers for phylogenetic analysis of
E. coli
O157:H7.
In Vitro Kinetics of Prebiotic Inulin-Type Fructan Fermentation by Butyrate-Producing Colon Bacteria: Implementation of Online Gas Chromatography for Quantitative Analysis of Carbon Dioxide and Hydrogen Gas Production
Authors: Falony Gwen , Verschaeren An , De Bruycker Feije , De Preter Vicky , Verbeke Kristin , Leroy Frédéric , De Vuyst Luc 
Published: July 2009

ABSTRACTKinetic analyses of bacterial growth, carbohydrate consumption, and metabolite production of five butyrate-producing clostridial cluster XIVa colon bacteria grown on acetate plus fructose, oligofructose, inulin, or lactate were performed. A gas chromatography method was set up to assess H2and CO2production online and to ensure complete coverage of all metabolites produced. Method accuracy was confirmed through the calculation of electron and carbon recoveries. Fermentations withAnaerostipes caccaeDSM 14662T,Roseburia faecisDSM 16840T,Roseburia hominisDSM 16839T, andRoseburia intestinalisDSM 14610Trevealed similar patterns of metabolite production with butyrate, CO2, and H2as the main metabolites.R. faecisDSM 16840TandR. intestinalisDSM 14610Twere able to degrade oligofructose, displaying a nonpreferential breakdown mechanism. Lactate consumption was only observed withA. caccaeDSM 14662T.Roseburia inulinivoransDSM 16841Twas the only strain included in the present study that was able to grow on fructose, oligofructose, and inulin. The metabolites produced were lactate, butyrate, and CO2, without H2production, indicating an energy metabolism distinct from that of otherRoseburiaspecies. Oligofructose degradation was nonpreferential. In a coculture ofR. inulinivoransDSM 16841Twith the highly competitive strainBifidobacterium longumsubsp.longumLMG 11047 on inulin, hardly any production of butyrate and CO2was detected, indicating a lack of competitiveness of the butyrate producer. Complete recovery of metabolites during fermentations of clostridial cluster XIVa butyrate-producing colon bacteria allowed stoichiometric balancing of the metabolic pathway for butyrate production, including H2formation.
Identification of a Basic Helix-Loop-Helix-Type Transcription Regulator Gene in
Aspergillus oryzae
by Systematically Deleting Large Chromosomal Segments
Authors: Jin Feng Jie , Takahashi Tadashi , Machida Masayuki , Koyama Yasuji 
Published: July 2009

ABSTRACT

We previously developed two methods (loop-out and replacement-type recombination) for generating large-scale chromosomal deletions that can be applied to more effective chromosomal engineering in
Aspergillus oryzae
. In this study, the replacement-type method is used to systematically delete large chromosomal DNA segments to identify essential and nonessential regions in chromosome 7 (2.93 Mb), which is the smallest
A. oryzae
chromosome and contains a large number of nonsyntenic blocks. We constructed 12 mutants harboring deletions that spanned 16- to 150-kb segments of chromosome 7 and scored phenotypic changes in the resulting mutants. Among the deletion mutants, strains designated Δ5 and Δ7 displayed clear phenotypic changes involving growth and conidiation. In particular, the Δ5 mutant exhibited vigorous growth and conidiation, potentially beneficial characteristics for certain industrial applications. Further deletion analysis allowed identification of the AO090011000215 gene as the gene responsible for the Δ5 mutant phenotype. The AO090011000215 gene was predicted to encode a helix-loop-helix binding protein belonging to the bHLH family of transcription factors. These results illustrate the potential of the approach for identifying novel functional genes.
Macrolide Resistance in Microorganisms at Antimicrobial-Free Swine Farms
Authors: Zhou Zhi , Raskin Lutgarde , Zilles Julie L. 
Published: July 2009

ABSTRACTTo investigate the relationship between agricultural antimicrobial use and resistance, a variety of methods for quantification of macrolide-lincosamide-streptogramin B (MLSB) resistance were applied to organic swine farm manure samples. Fluorescence in situ hybridization was used to indirectly quantify the specific rRNA methylation resulting in MLSBresistance. Using this method, an unexpectedly high prevalence of ribosomal methylation and, hence, predicted MLSBresistance was observed in manure samples from two swine finisher farms that reported no antimicrobial use (37.6% ± 6.3% and 40.5% ± 5.4%, respectively). A culture-based method targeting relatively abundant clostridia showed a lower but still unexpectedly high prevalence of resistance at both farms (27.7% ± 11.3% and 11.7% ± 8.6%, respectively), while the prevalence of resistance in cultured fecal streptococci was low at both farms (4.0%). These differences in the prevalence of resistance across microorganisms suggest the need for caution when extrapolating from data obtained with indicator organisms. A third antimicrobial-free swine farm, a breeder-to-finisher operation, had low levels of MLSBresistance in manure samples with all methods used (<9%). Tetracycline antimicrobials were detected in manure samples from one of the finisher farms and may provide a partial explanation for the high level of MLSBresistance. Taken together, these findings highlight the need for a more fundamental understanding of the relationship between antimicrobial use and the prevalence of antimicrobial resistance.
Interactions of Typical and Atypical EnteropathogenicEscherichia coliStrains with the Calf Intestinal Mucosa Ex Vivo
Authors: Girard Francis , Dziva Francis , Stevens Mark P. , Frankel Gad 
Published: July 2009

ABSTRACTEnteropathogenicEscherichia coli(EPEC) can be found in healthy and diarrheic cattle; however, little is known about the role of attaching and effacing (A/E) lesion formation in colonization of bovine intestinal mucosa by such strains. We show that typical and atypical EPEC induce A/E lesions on calf intestinal explants independently of Tir tyrosine phosphorylation and TccP. Our data support the existence of conserved Tir- and TccP-independent mechanisms of A/E lesion formation in a range of hosts and reinforce the zoonotic potential of EPEC in cattle.
Distribution of Sulfonamide Resistance Genes inEscherichia coliandSalmonellaIsolates from Swine and Chickens at Abattoirs in Ontario and Québec, Canada
Authors: Kozak Gosia K. , Pearl David L. , Parkman Julia , Reid-Smith Richard J. , Deckert Anne , Boerlin Patrick 
Published: July 2009

ABSTRACTSulfonamide-resistantEscherichia coliandSalmonellaisolates from pigs and chickens in Ontario and Québec were screened forsul1,sul2, andsul3by PCR. Eachsulgene was distributed differently across populations, with a significant difference between distribution in commensalE. coliandSalmonellaisolates andsul3restricted mainly to porcineE. coliisolates.
Influence of Vegetation on the In Situ Bacterial Community and Polycyclic Aromatic Hydrocarbon (PAH) Degraders in Aged PAH-Contaminated or Thermal-Desorption-Treated Soil
Authors: Cébron Aurélie , Beguiristain Thierry , Faure Pierre , Norini Marie-Paule , Masfaraud Jean-François , Leyval Corinne 
Published: July 2009

ABSTRACT

The polycyclic aromatic hydrocarbon (PAH) contamination, bacterial community, and PAH-degrading bacteria were monitored in aged PAH-contaminated soil (Neuves-Maisons [NM] soil; with a mean of 1,915 mg of 16 PAHs·kg
−1
of soil dry weight) and in the same soil previously treated by thermal desorption (TD soil; with a mean of 106 mg of 16 PAHs·kg
−1
of soil dry weight). This study was conducted in situ for 2 years using experimental plots of the two soils. NM soil was colonized by spontaneous vegetation (NM-SV), planted with
Medicago sativa
(NM-Ms), or left as bare soil (NM-BS), and the TD soil was planted with
Medicago sativa
(TD-Ms). The bacterial community density, structure, and diversity were estimated by real-time PCR quantification of the 16S rRNA gene copy number, temporal thermal gradient gel electrophoresis fingerprinting, and band sequencing, respectively. The density of the bacterial community increased the first year during stabilization of the system and stayed constant in the NM soil, while it continued to increase in the TD soil during the second year. The bacterial community structure diverged among all the plot types after 2 years on site. In the NM-BS plots, the bacterial community was represented mainly by
Betaproteobacteria
and
G
ammaproteobacteria
. The presence of vegetation (NM-SV and NM-Ms) in the NM soil favored the development of a wider range of bacterial phyla (
Alphaproteobacteria
,
Betaproteobacteria
,
G
ammaproteobacteria
,
Verrucomicrobia
,
Actinobacteria
,
Firmicutes
, and
Chlorof
l
exi
) that, for the most part, were not closely related to known bacterial representatives. Moreover, under the influence of the same plant, the bacterial community that developed in the TD-Ms was represented by different bacterial species (
Alphaproteobacteria
,
Betaproteobacteria
,
Gammaproteobacteria
, and
Actinobacteria
) than that in the NM-Ms. During the 2 years of monitoring, the PAH concentration did not evolve significantly. The abundance of gram-negative (GN) and gram-positive (GP) PAH-degrading bacteria was estimated by real-time PCR quantification of specific functional genes encoding the α subunit of PAH-ring hydroxylating dioxygenase (PAH-RHD
α
). The percentage of the PAH-RHD
α
GN bacterial genes relative to 16S rRNA gene density decreased with time in all the plots. The GP PAH-RHD
α
bacterial gene proportion decreased in the NM-BS plots but stayed constant or increased under vegetation influence (NM-SV, NM-Ms, and TD-Ms).
The tRNA Modification Complex Elongator Regulates the Cdc42-Dependent Mitogen-Activated Protein Kinase Pathway That Controls Filamentous Growth in Yeast
Authors: Abdullah Ummi , Cullen Paul J. 
Published: July 2009

ABSTRACT

Signal transduction pathways control multiple aspects of cellular behavior, including global changes to the cell cycle, cell polarity, and gene expression, which can result in the formation of a new cell type. In the budding yeast
Saccharomyces cerevisiae
, the mitogen-activated protein kinase (MAPK) pathway that controls filamentous growth induces a dimorphic foraging response under nutrient-limiting conditions. How nutritional cues feed into MAPK activation remains an open question. Here we report a functional connection between the elongator tRNA modification complex (
ELP
genes) and activity of the filamentous growth pathway. Elongator was required for filamentous growth pathway signaling, and
elp
mutants were defective for invasive growth, cell polarization, and MAPK-dependent mat formation. Genetic suppression analysis showed that elongator functions at the level of Msb2p, the signaling mucin that operates at the head of the pathway, which led to the finding that elongator regulates the starvation-dependent expression of the
MSB2
gene. The Elp complex was not required for activation of related pathways (pheromone response or high osmolarity glycerol response) that share components with the filamentous growth pathway. Because protein translation provides a rough metric of cellular nutritional status, elongator may convey nutritional information to the filamentous growth pathway at the level of
MSB2
expression.
How a Cell Crawls and the Role of Cortical Myosin II
Authors: Soll David R. , Wessels Deborah , Kuhl Spencer , Lusche Daniel F. 
Published: July 2009

ABSTRACT

The movements of
Dictyostelium discoideum
amoebae translocating on a glass surface in the absence of chemoattractant have been reconstructed at 5-second intervals and motion analyzed by employing 3D-DIAS software. A morphometric analysis of pseudopods, the main cell body, and the uropod provides a comprehensive description of the basic motile behavior of a cell in four dimensions (4D), resulting in a list of 18 characteristics. A similar analysis of the myosin II phosphorylation mutant 3XASP reveals a role for the cortical localization of myosin II in the suppression of lateral pseudopods, formation of the uropod, cytoplasmic distribution of cytoplasm in the main cell body, and efficient motility. The results of the morphometric analysis suggest that pseudopods, the main cell body, and the uropod represent three motility compartments that are coordinated for efficient translocation. It provides a contextual framework for interpreting the effects of mutations, inhibitors, and chemoattractants on the basic motile behavior of
D. discoideum
. The generality of the characteristics of the basic motile behavior of
D. discoideum
must now be tested by similar 4D analyses of the motility of amoeboid cells of higher eukaryotic cells, in particular human polymorphonuclear leukocytes.