bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monophyly of
nodA
and
nifH
Genes across Texan and Costa Rican Populations of
Cupriavidus
Nodule Symbionts
Authors: Andam Cheryl P. , Mondo Stephen J. , Parker Matthew A. 
Published: May 2007

ABSTRACT

nodA
and
nifH
phylogenies for
Cupriavidus
nodule bacteria from native legumes in Texas and Costa Rica grouped all strains into a single clade nested among neotropical
Burkholderia
strains. Thus,
Cupriavidus
symbiotic genes were not acquired independently in different regions and are derived from other
Betaproteobacteria
rather than from α-rhizobial donors.
Transcriptome Analysis Reveals that Multidrug Efflux Genes Are Upregulated To Protect
Pseudomonas aeruginosa
from Pentachlorophenol Stress
Authors: Muller Jocelyn Fraga , Stevens Ann M. , Craig Johanna , Love Nancy G. 
Published: May 2007

ABSTRACT

Through chemical contamination of natural environments, microbial communities are exposed to many different types of chemical stressors; however, research on whole-genome responses to this contaminant stress is limited. This study examined the transcriptome response of a common soil bacterium,
Pseudomonas aeruginosa
, to the common environmental contaminant pentachlorophenol (PCP). Cells were grown in chemostats at a low growth rate to obtain substrate-limited, steady-state, balanced-growth conditions. The PCP stress was administered as a continuous increase in concentration, and samples taken over time were examined for physiological function changes with whole-cell acetate uptake rates (WAURs) and cell viability and for gene expression changes by Affymetrix GeneChip technology and real-time reverse transcriptase PCR. Cell viability, measured by heterotrophic plate counts, showed a moderately steady decrease after exposure to the stressor, but WAURs did not change in response to PCP. In contrast to the physiological data, the microarray data showed significant changes in the expression of several genes. In particular, genes coding for multidrug efflux pumps, including MexAB-OprM, were strongly upregulated. The upregulation of these efflux pumps protected the cells from the potentially toxic effects of PCP, allowing the physiological whole-cell function to remain constant.
Molecular Characterization of Potential Microcystin-Producing Cyanobacteria in Lake Ontario Embayments and Nearshore Waters
Authors: Hotto A. M. , Satchwell M. F. , Boyer G. L. 
Published: May 2007

ABSTRACT

The distribution and genotypic variation of potential microcystin (MC) producers along the southern and eastern shores of Lake Ontario in 2001 and 2003 were examined using a suite of PCR primers. Cyanobacterial,
Microcystis
sp., and
Microcystis
-specific toxin primer sets identified shoreline distribution of cyanobacterial DNA (in 97% of the stations) and MC synthetase genes (in 50% of the stations). Sequence analysis of a partial
mcyA
amplicon targeting
Microcystis
,
Anabaena
, and
Planktothrix
species indicated that the
Microcystis
sp. genotype was the dominant MC genotype present and revealed a novel
Microcystis
-like sequence containing a 6-bp insert. Analysis of the same samples with genus-specific
mcyE
primers confirmed that the
Microcystis
sp. genotype was the dominant potential MC producer. Genotype compositions within embayments were relatively homogenous compared to those for shoreline and tributary samples. MC concentrations along the shoreline exhibited both temporal and spatial differences as evidenced by the protein phosphatase inhibition assay, at times exceeding the World Health Organization guideline value for drinking water of 1.0 μg MC-LR
eq
liter
−1
. MC genotypes are widespread along the New York State shoreline of Lake Ontario, appear to originate nearshore, and can be carried through the lake via wind and surface water current patterns.
Carvacrol Induces Heat Shock Protein 60 and Inhibits Synthesis of Flagellin in
Escherichia coli
O157:H7
Authors: Burt Sara A. , van der Zee Ruurd , Koets Ad P. , de Graaff Anko M. , van Knapen Frans , Gaastra Wim , Haagsman Henk P. , Veldhuizen Edwin J. A. 
Published: May 2007

ABSTRACT

The essential oils of oregano and thyme are active against a number of food-borne pathogens, such as
Escherichia coli
O157:H7. Carvacrol is one of the major antibacterial components of these oils, and
p
-cymene is thought to be its precursor in the plant. The effects of carvacrol and
p
-cymene on protein synthesis in
E. coli
O157:H7 ATCC 43895 cells were investigated. Bacteria were grown overnight in Mueller-Hinton broth with a sublethal concentration of carvacrol or
p
-cymene, and their protein compositions were analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and confirmed by Western blotting. The presence of 1 mM carvacrol during overnight incubation caused
E. coli
O157:H7 to produce significant amounts of heat shock protein 60 (HSP60) (GroEL) (
P
< 0.05) and inhibited the synthesis of flagellin highly significantly (
P
< 0.001), causing cells to be aflagellate and therefore nonmotile. The amounts of HSP70 (DnaK) were not significantly affected.
p
-Cymene at 1 mM or 10 mM did not induce HSP60 or HSP70 in significant amounts and did not have a significant effect on flagellar synthesis. Neither carvacrol (0.3, 0.5, 0.8, or 1 mM) nor
p
-cymene (0.3, 0.5, or 0.8 mM) treatment of cells in the mid-exponential growth phase induced significant amounts of HSP60 or HSP70 within 3 h, although numerical increases of HSP60 were observed. Motility decreased with increasing concentrations of both compounds, but existing flagella were not shed. This study is the first to demonstrate that essential oil components induce HSP60 in bacteria and that overnight incubation with carvacrol prevents the development of flagella in
E. coli
O157:H7.
Nucleotide Sequence of Plasmid pCNB1 from
Comamonas
Strain CNB-1 Reveals Novel Genetic Organization and Evolution for 4-Chloronitrobenzene Degradation
Authors: Ma Ying-Fei , Wu Jian-Feng , Wang Sheng-Yue , Jiang Cheng-Ying , Zhang Yun , Qi Su-Wei , Liu Lei , Zhao Guo-Ping , Liu Shuang-Jiang 
Published: May 2007

ABSTRACT

The nucleotide sequence of a new plasmid pCNB1 from
Comamonas
sp. strain CNB-1 that degrades 4-chloronitrobenzene (4CNB) was determined. pCNB1 belongs to the IncP-1β group and is 91,181 bp in length. A total of 95 open reading frames appear to be involved in (i) the replication, maintenance, and transfer of pCNB1; (ii) resistance to arsenate and chromate; and (iii) the degradation of 4CNB. The 4CNB degradative genes and arsenate resistance genes were located on an extraordinarily large transposon (44.5 kb), proposed as Tn
CNB1
. Tn
CNB1
was flanked by two IS
1071
elements and represents a new member of the composite I transposon family. The 4CNB degradative genes within Tn
CNB1
were separated by various truncated genes and genetic homologs from other DNA molecules. Genes for chromate resistance were located on another transposon that was similar to the Tn
21
transposon of the class II replicative family that is frequently responsible for the mobilization of mercury resistance genes. Resistance to arsenate and chromate were experimentally confirmed, and transcriptions of arsenate and chromate resistance genes were demonstrated by reverse transcription-PCR. These results described a new member of the IncP-1β plasmid family, and the findings suggest that gene deletion and acquisition as well as genetic rearrangement of DNA molecules happened during the evolution of the 4CNB degradation pathway on pCNB1.
Enteric Virus Survival during Household Laundering and Impact of Disinfection with Sodium Hypochlorite
Authors: Gerba Charles P. , Kennedy Denise 
Published: May 2007

ABSTRACT

This study was conducted to determine whether enteric viruses (adenovirus, rotavirus, and hepatitis A virus) added to cotton cloth swatches survive the wash cycle, the rinse cycle, and a 28-min permanent press drying cycle as commonly practiced in households in the United States. Detergent with and without bleach (sodium hypochlorite) was added to washing machines containing sterile and virus-inoculated 58-cm
2
swatches, 3.2 kg of cotton T-shirts and underwear, and a soiled pillowcase designed to simulate the conditions (pH, organic load, etc.) encountered in soiled laundry. The most important factors for the reduction of virus in laundry were passage through the drying cycle and the addition of sodium hypochlorite. Washing with detergent alone was not found to be effective for the removal or inactivation of enteric viruses, as significant concentrations of virus were found on the swatches (reductions of 92 to 99%). It was also demonstrated that viruses are readily transferred from contaminated cloths to uncontaminated clothes. The use of sodium hypochlorite reduced the number of infectious viruses on the swatches after washing and drying by at least 99.99%. Laundering practices in common use in the United States do not eliminate enteric and respiratory viruses from clothes. The use of bleach can further reduce the numbers of enteric viruses in laundry.
Construction of a Low-Temperature Protein Expression System Using a Cold-Adapted Bacterium,
Shewanella
sp. Strain Ac10, as the Host
Authors: Miyake Ryoma , Kawamoto Jun , Wei Yun-Lin , Kitagawa Masanari , Kato Ikunoshin , Kurihara Tatsuo , Esaki Nobuyoshi 
Published: May 2007

ABSTRACT

A recombinant protein expression system working at low temperatures is expected to be useful for the production of thermolabile proteins. We constructed a low-temperature expression system using an Antarctic cold-adapted bacterium,
Shewanella
sp. strain Ac10, as the host. We evaluated the promoters for proteins abundantly produced at 4°C in this bacterium to express foreign proteins. We used 27 promoters and a broad-host-range vector, pJRD215, to produce β-lactamase in
Shewanella
sp. strain Ac10. The maximum yield was obtained when the promoter for putative alkyl hydroperoxide reductase (AhpC) was used and the recombinant cells were grown to late stationary phase. The yield was 91 mg/liter of culture at 4°C and 139 mg/liter of culture at 18°C. We used this system to produce putative peptidases, PepF, LAP, and PepQ, and a putative glucosidase, BglA, from a psychrophilic bacterium,
Desulfotalea psychrophila
DSM12343. We obtained 48, 7.1, 28, and 5.4 mg/liter of culture of these proteins, respectively, in a soluble fraction. The amounts of PepF and PepQ produced by this system were greater than those produced by the
Escherichia coli
T7 promoter system.
Insertional Mutagenesis To Generate Lantibiotic Resistance in
Lactococcus lactis
Authors: Guinane Caitriona M. , Cotter Paul D. , Lawton Elaine M. , Hill Colin , Ross R. Paul 
Published: May 2007

ABSTRACT

While the potential emergence of food spoilage and pathogenic bacteria with resistance to lantibiotics is a concern, the creation of derivatives of starter cultures and adjuncts that can grow in the presence of these antimicrobials may have applications in food fermentations. Here a bank of
Lactococcus lactis
IL1403 mutants was created and screened, and a number of novel genetic loci involved in lantibiotic resistance were identified.
Mobile Genetic Elements Provide Evidence for a Bovine Origin of Clonal Complex 17 of
Streptococcus agalactiae
Authors: Héry-Arnaud Geneviève , Bruant Guillaume , Lanotte Philippe , Brun Stella , Picard Bertrand , Rosenau Agnès , van der Mee-Marquet Nathalie , Rainard Pascal , Quentin Roland , Mereghetti Laurent 
Published: May 2007

ABSTRACT

We sought an explanation for epidemiological changes in
Streptococcus agalactiae
infections by investigating the link between ecological niches of the bacterium by determining the prevalence of 11 mobile genetic elements. The prevalence of nine of these elements differed significantly according to the human or bovine origin of the isolate. Correlating this distribution with the phylogeny obtained by multilocus sequence analysis, we observed that human isolates harboring GBSi1, a clear marker of the bovine niche, clustered in clonal complex 17. Our results are thus consistent with the emergence of this virulent human clone from a bovine ancestor.
Potential Interactions of Particle-Associated Anammox Bacteria with Bacterial and Archaeal Partners in the Namibian Upwelling System
Authors: Woebken Dagmar , Fuchs Bernhard M. , Kuypers Marcel M. M. , Amann Rudolf 
Published: May 2007

ABSTRACT

Recent studies have shown that the anaerobic oxidation of ammonium by anammox bacteria plays an important role in catalyzing the loss of nitrogen from marine oxygen minimum zones (OMZ). However, in situ oxygen concentrations of up to 25 μM and ammonium concentrations close to or below the detection limit in the layer of anammox activity are hard to reconcile with the current knowledge of the physiology of anammox bacteria. We therefore investigated samples from the Namibian OMZ by comparative 16S rRNA gene analysis and fluorescence in situ hybridization. Our results showed that “
Candidatus
Scalindua” spp., the typical marine anammox bacteria, colonized microscopic particles that were likely the remains of either macroscopic marine snow particles or resuspended particles. These particles were slightly but significantly (
P
< 0.01) enriched in
Gammaproteobacteria
(11.8% ± 5.0%) compared to the free-water phase (8.1% ± 1.8%). No preference for the attachment to particles could be observed for members of the
Alphaproteobacteria
and
Bacteroidetes
, which were abundant (12 to 17%) in both habitats. The alphaproteobacterial SAR11 clade, the
Euryarchaeota
, and group I
Crenarchaeota
, were all significantly depleted in particles compared to their presence in the free-water phase (16.5% ± 3.5% versus 2.6% ± 1.7%, 2.7% ± 1.9% versus <1%, and 14.9% ± 4.6% versus 2.2% ± 1.8%, respectively, all
P
< 0.001). Sequence analysis of the crenarchaeotal 16S rRNA genes showed a 99% sequence identity to the nitrifying “
Nitrosopumilus maritimus
.” Even though we could not observe conspicuous consortium-like structures of anammox bacteria with particle-enriched bacterioplankton groups, we hypothesize that members of
Gammaproteobacteria
,
Alphaproteobacteria
, and
Bacteroidetes
play a critical role in extending the anammox reaction to nutrient-depleted suboxic water layers in the Namibian upwelling system by creating anoxic, nutrient-enriched microniches.
New Insights into the Colonization and Release Processes of
Xenorhabdus nematophila
and the Morphology and Ultrastructure of the Bacterial Receptacle of Its Nematode Host,
Steinernema carpocapsae
Authors: Snyder Holly , Stock S. Patricia , Kim Sam-Kyu , Flores-Lara Yolanda , Forst Steven 
Published: May 2007

ABSTRACT

We present results from epifluorescence, differential interference contrast, and transmission electron microscopy showing that
Xenorhabdus nematophila
colonizes a receptacle in the anterior intestine of the infective juvenile (IJ) stage of
Steinernema carpocapsae
. This region is connected to the esophagus at the esophagointestinal junction. The process by which
X. nematophila
leaves this bacterial receptacle had not been analyzed previously. In this study we monitored the movement of green fluorescent protein-labeled bacteria during the release process. Our observations revealed that
Xenorhabdus
colonizes the distal region of the receptacle and that exposure to insect hemolymph stimulated forward movement of the bacteria to the esophagointestinal junction. Continued exposure to hemolymph caused a narrow passage in the distal receptacle to widen, allowing movement of
Xenorhabdus
down the intestine and out the anus. Efficient release of both the wild type and a nonmotile strain was evident in most of the IJs incubated in hemolymph, whereas only a few IJs incubated in nutrient-rich broth released bacterial cells. Incubation of IJs in hemolymph treated with agents that induce nematode paralysis dramatically inhibited the release process. These results suggest that bacterial motility is not required for movement out of the distal region of the receptacle and that hemolymph-induced esophageal pumping provides a force for the release of
X. nematophila
out of the receptacle and into the intestinal lumen.
Serial Analysis of rRNA Genes and the Unexpected Dominance of Rare Members of Microbial Communities
Authors: Ashby Matthew N. , Rine Jasper , Mongodin Emmanuel F. , Nelson Karen E. , Dimster-Denk Dago 
Published: May 2007

ABSTRACT
The accurate description of a microbial community is an important first step in understanding the roles of its components in ecosystem function. A method for surveying microbial communities termed serial analysis of rRNA genes (SARD) is described here. Through a series of molecular cloning steps, short DNA sequence tags are recovered from the fifth variable (V5) region of the prokaryotic 16S rRNA genes from microbial communities. These tags are ligated to form concatemers comprised of 20 to 40 tags which are cloned and identified by DNA sequencing. Four agricultural soil samples were profiled with SARD to assess the method's utility. A total of 37,008 SARD tags comprising 3,127 unique sequences were identified. A comparison of duplicate profiles from one soil genomic DNA preparation revealed that the method was highly reproducible. The large numbers of singleton tags, together with nonparametric richness estimates, indicated that a significant amount of sequence tag diversity remained undetected with this level of sampling. The abundance classes of the observed tags were scale-free and conformed to a power law distribution. Numerically, the majority of the total tags observed belonged to abundance classes that were each present at less than 1% of the community. Over 99% of the unique tags individually made up less than 1% of the community. Therefore, from either a numerical or diversity standpoint, taxa with low abundance comprised a significant proportion of the microbial communities examined and could potentially make a large contribution to ecosystem function. SARD may provide a means to explore the ecological roles of these rare members of microbial communities in qualitative and quantitative terms.
Development and Application of Two Multiplex Real-Time PCR Assays for the Detection of
Mycobacterium ulcerans
in Clinical and Environmental Samples
Authors: Fyfe Janet A. M. , Lavender Caroline J. , Johnson Paul D. R. , Globan Maria , Sievers Aina , Azuolas Joseph , Stinear Timothy P. 
Published: May 2007

ABSTRACT

Mycobacterium ulcerans
is a slow-growing environmental bacterium that causes a severe skin disease known as Buruli ulcer. PCR has become a reliable and rapid method for the diagnosis of
M. ulcerans
infection in humans and has been used for the detection of
M. ulcerans
in the environment. This paper describes the development of a TaqMan assay targeting IS
2404
multiplexed with an internal positive control to monitor inhibition with a detection limit of less than 1 genome equivalent of DNA. The assay improves the turnaround time for diagnosis and replaces conventional gel-based PCR as the routine method for laboratory confirmation of
M. ulcerans
infection in Victoria, Australia. Following analysis of 415 clinical specimens, the new test demonstrated 100% sensitivity and specificity compared with culture. Another multiplex TaqMan assay targeting IS
2606
and the ketoreductase-B domain of the
M. ulcerans
mycolactone polyketide synthase genes was designed to augment the specificity of the IS
2404
PCR for the analysis of a variety of environmental samples. Assaying for these three targets enabled the detection of
M. ulcerans
DNA in soil, sediment, and mosquito extracts collected from an area of endemicity for Buruli ulcer in Victoria with a high degree of confidence. Final confirmation was obtained by the detection and sequencing of variable-number tandem repeat (VNTR) locus 9, which matched the VNTR locus 9 sequence obtained from the clinical isolates in this region. This suite of new methods is enabling rapid progress in the understanding of the ecology of this important human pathogen.
New
Trypanosoma cruzi
Repeated Element That Shows Site Specificity for Insertion
Authors: Souza Renata T. , Santos Márcia R. M. , Lima Fábio M. , El-Sayed Najib M. , Myler Peter J. , Ruiz Jeronimo C. , da Silveira José Franco 
Published: May 2007

ABSTRACT

A new family of site-specific repeated elements identified in
Trypanosoma cruzi
, which we named TcTREZO, is described here. TcTREZO appears to be a composite repeated element, since three subregions may be defined within it on the basis of sequence similarities with other
T. cruzi
sequences. Analysis of the distribution of TcTREZO in the genome clearly indicates that it displays site specificity for insertion. Most TcTREZO elements are flanked by conserved sequences. There is a highly conserved 68-bp sequence at the 5′ end of the element and a sequence domain of ∼500 bp without a well-defined borderline at the 3′ end. Northern blot hybridization and reverse transcriptase PCR analyses showed that TcTREZO transcripts are expressed as oligo(A)-terminated transcripts whose length corresponds to the unit size of the element (1.6 kb). Transcripts of ∼0.2 kb derived from a small part of TcTREZO are also detected in steady-state RNA. TcTREZO transcripts are unspliced and not translated. The copy number of TcTREZO sequences was estimated to be ∼173 copies per haploid genome. TcTREZO appears to have been assembled by insertions of sequences into a progenitor element. Once associated with each other, these subunits were amplified as a new transposable element. TcTREZO shows site specificity for insertion, suggesting that a sequence-specific endonuclease could be responsible for its insertion at a unique site.
Saccharomyces cerevisiae
Vacuole in Zinc Storage and Intracellular Zinc Distribution
Authors: Simm Claudia , Lahner Brett , Salt David , LeFurgey Ann , Ingram Peter , Yandell Brian , Eide David J. 
Published: May 2007

ABSTRACT

Previous studies of the yeast
Saccharomyces cerevisiae
indicated that the vacuole is a major site of zinc storage in the cell. However, these studies did not address the absolute level of zinc that was stored in the vacuole nor did they examine the abundances of stored zinc in other compartments of the cell. In this report, we describe an analysis of the cellular distribution of zinc by use of both an organellar fractionation method and an electron probe X-ray microanalysis. With these methods, we determined that zinc levels in the vacuole vary with zinc status and can rise to almost 100 mM zinc (i.e., 7 × 10
8
atoms of vacuolar zinc per cell). Moreover, this zinc can be mobilized effectively to supply the needs of as many as eight generations of progeny cells under zinc starvation conditions. While the Zrc1 and Cot1 zinc transporters are essential for zinc uptake into the vacuole under steady-state growth conditions, additional transporters help mediate zinc uptake into the vacuole during “zinc shock,” when zinc-limited cells are resupplied with zinc. In addition, we found that other compartments of the cell do not provide significant stores of zinc. In particular, zinc accumulation in mitochondria is low and is homeostatically regulated independently of vacuolar zinc storage. Finally, we observed a strong correlation between zinc status and the levels of magnesium and phosphorus accumulated in cells. Our results implicate zinc as a major determinant of the ability of the cell to store these other important nutrients.