bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Early Response to Acid Shock inLactobacillus reuteriInvolves the ClpL Chaperone and a Putative Cell Wall-Altering Esterase
Authors: Wall Torun , Båth Klara , Britton Robert A. , Jonsson Hans , Versalovic James , Roos Stefan 
Published: April 2007

ABSTRACTTo be able to function as a probiotic, bacteria have to survive the passage through the gastrointestinal tract. We have examined survival and gene expression ofLactobacillus reuteriATCC 55730 after a sudden shift in environmental acidity to a pH close to the conditions in the human stomach. More than 80% of theL. reutericells survived at pH 2.7 for 1 h. A genomewide expression analysis experiment using microarrays displayed 72 differentially expressed genes at this pH. The early response to severe acid shock inL. reuteridiffered from long-term acid adaptation to milder acid stress studied in other lactic acid bacteria. The genes induced included the following:clpL, genes putatively involved in alterations of the cell membrane and the cell wall; genes encoding transcriptional regulators; phage genes; and genes of unknown function. Two genes,clpL, encoding an ATPase with chaperone activity, and lr1516, encoding a putative esterase, were selected for mutation analyses. The mutants were significantly more sensitive to acid than the wild type was. Thus, these genes could contribute to the survival ofL. reuteriin the gastrointestinal tract.
DNA Microarray-Based Identification of Serogroups and Virulence Gene Patterns of
Escherichia coli
Isolates Associated with Porcine Postweaning Diarrhea and Edema Disease
Authors: Han Weiqing , Liu Bin , Cao Boyang , Beutin Lothar , Krüger Ulrike , Liu Hongbo , Li Yayue , Liu Yanqun , Feng Lu , Wang Lei 
Published: April 2007

ABSTRACT

Escherichia coli
strains causing postweaning diarrhea (PWD) and edema disease (ED) in pigs are limited to a number of serogroups, with O8, O45, O138, O139, O141, O147, O149, and O157 being the most commonly reported worldwide. In this study, a DNA microarray based on the O-antigen-specific genes of all 8
E. coli
serogroups, as well as 11 genes encoding adhesion factors and exotoxins associated with PWD and ED, was developed for the identification of related serogroups and virulence gene patterns. The microarray method was tested against 186
E. coli
and
Shigella
O-serogroup reference strains, 13
E. coli
reference strains for virulence markers, 43
E. coli
clinical isolates, and 12 strains of other bacterial species and shown to be highly specific with reproducible results. The detection sensitivity was 0.1 ng of genomic DNA or 10
3
CFU per 0.3 g of porcine feces in mock samples. Seventeen porcine feces samples from local hoggeries were examined using the microarray, and the result for one sample was verified by the conventional serotyping methods. This microarray can be readily used to screen for the presence of PWD- and ED-associated
E. coli
in porcine feces samples.
Swarming Behavior of and Hemolysin BL Secretion by
Bacillus cereus
Authors: Ghelardi Emilia , Celandroni Francesco , Salvetti Sara , Ceragioli Mara , Beecher Douglas J. , Senesi Sonia , Wong Amy C. L. 
Published: April 2007

ABSTRACT

An association between swarming and hemolysin BL secretion was observed in a collection of 42
Bacillus cereus
isolates (
P
= 0.029). The highest levels of toxin were detected in swarmers along with swarm cell differentiation (
P
= 0.021), suggesting that swarming
B. cereus
strains may have a higher virulence potential than nonswarming strains.
Diversity and Function of
Chloroflexus
-Like Bacteria in a Hypersaline Microbial Mat: Phylogenetic Characterization and Impact on Aerobic Respiration
Authors: Bachar Ami , Omoregie Enoma , de Wit Rutger , Jonkers Henk M. 
Published: April 2007

ABSTRACT

We studied the diversity of
Chloroflexus
-like bacteria (CLB) in a hypersaline phototrophic microbial mat and assayed their near-infrared (NIR) light-dependent oxygen respiration rates. PCR with primers that were reported to specifically target the 16S rRNA gene from members of the phylum
Chloroflexi
resulted in the recovery of 49 sequences and 16 phylotypes (sequences of the same phylotype share more than 96% similarity), and 10 of the sequences (four phylotypes) appeared to be related to filamentous anoxygenic phototrophic members of the family
Chloroflexaceae
. Photopigment analysis revealed the presence of bacteriochlorophyll
c
(BChl
c
), BChl
d
, and γ-carotene, pigments known to be produced by phototrophic CLB. Oxygen microsensor measurements for intact mats revealed a NIR (710 to 770 nm) light-dependent decrease in aerobic respiration, a phenomenon that we also observed in an axenic culture of
Chloroflexus aurantiacus
. The metabolic ability of phototrophic CLB to switch from anoxygenic photosynthesis under NIR illumination to aerobic respiration under non-NIR illumination was further used to estimate the contribution of these organisms to mat community respiration. Steady-state oxygen profiles under dark conditions and in the presence of visible (VIS) light (400 to 700 nm), NIR light (710 to 770 nm), and VIS light plus NIR light were compared. NIR light illumination led to a substantial increase in the oxygen concentration in the mat. The observed impact on oxygen dynamics shows that CLB play a significant role in the cycling of carbon in this hypersaline microbial mat ecosystem. This study further demonstrates that the method applied, a combination of microsensor techniques and VIS and NIR illumination, allows rapid establishment of the presence and significance of CLB in environmental samples.
Kinetic Constant Variability in Bacterial Oxidation of Elemental Sulfur
Authors: Pokorna Blanka , Mandl Martin , Borilova Sarka , Ceskova Pavla , Markova Romana , Janiczek Oldrich 
Published: April 2007

ABSTRACT

Wide ranges of growth yields on sulfur (from 2.4 × 10
10
to 8.1 × 10
11
cells g
−1
) and maximum sulfur oxidation rates (from 0.068 to 1.30 mmol liter
−1
h
−1
) of an
Acidithiobacillus ferrooxidans
strain (CCM 4253) were observed in 73 batch cultures. No significant correlation between the constants was observed. Changes of the Michaelis constant for sulfur (from 0.46 to 15.5 mM) in resting cells were also noted.
Structure and Function of Methanogens along a Short-Term Restoration Chronosequence in the Florida Everglades
Authors: Smith Jason M. , Castro Hector , Ogram Andrew 
Published: April 2007

ABSTRACT

The removal of plants and soil to bedrock to eradicate exotic invasive plants within the Hole-in-the-Donut (HID) region, part of the Everglades National Park (Florida), presented a unique opportunity to study the redevelopment of soil and the associated microbial communities in the context of short-term primary succession and ecosystem restoration. The goal of this study was to identify relationships between soil redevelopment and activity and composition of methanogenic assemblages in HID soils. Methane production potentials indicated a general decline in methanogenic activity with restoration age. Microcosm incubations strongly suggested hydrogenotrophic methanogenesis as the most favorable pathway for methane formation in HID soils from all sites. Culture-independent techniques targeting methyl coenzyme M reductase genes (
mcrA
) were used to assess the dynamics of methanogenic assemblages. Clone libraries were dominated by sequences related to hydrogenotrophic methanogens of the orders
Methanobacteriales
and
Methanococcales
and suggested a general decline in the relative abundance of
Methanobacteriales mcrA
with time since restoration. Terminal restriction fragment length polymorphism analysis indicated methanogenic assemblages remain relatively stable between wet and dry seasons. Interestingly, analysis of soils across the restoration chronosequence indicated a shift in
Methanobacteriales
populations with restoration age, suggesting genotypic shifts due to site-specific factors.
Quantitative Detection of
Clostridium tyrobutyricum
in Milk by Real-Time PCR
Authors: López-Enríquez Lorena , Rodríguez-Lázaro David , Hernández Marta 
Published: April 2007

ABSTRACT

We developed a real-time PCR assay for the quantitative detection of
Clostridium tyrobutyricum
, which has been identified as the major causal agent of late blowing in cheese. The assay was 100% specific, with an analytical sensitivity of 1 genome equivalent in 40% of the reactions. The quantification was linear (
R
2
> 0.9995) over a 5-log dynamic range, down to 10 genome equivalents, with a PCR efficiency of >0.946. With optimized detergent treatment and enzymatic pretreatment of the sample before centrifugation and nucleic acid extraction, the assay counted down to 300
C. tyrobutyricum
spores, with a relative accuracy of 82.98 to 107.68, and detected as few as 25 spores in 25 ml of artificially contaminated raw or ultrahigh-temperature-treated whole milk.
Shedding of
Escherichia coli
O157:H7 in Calves Is Reduced by Prior Colonization with the Homologous Strain
Authors: Naylor Stuart W. , Flockhart Allen , Nart Pablo , Smith David G. E. , Huntley John , Gally David L. , Low J. Christopher 
Published: April 2007

ABSTRACT

Enterohemorrhagic
Escherichia coli
O157:H7 has a natural reservoir in the intestinal tracts of cattle. Colonization is asymptomatic and transient, but it is not clear if protective immunity is induced. This study demonstrates that prior colonization induces humoral immune responses to bacterial antigens and reduces bacterial shedding after experimental challenge with the homologous strain.
Genomic and Phenotypic Diversity of Coastal
Vibrio cholerae
Strains Is Linked to Environmental Factors
Authors: Keymer Daniel P. , Miller Michael C. , Schoolnik Gary K. , Boehm Alexandria B. 
Published: April 2007

ABSTRACT

Studies of
Vibrio cholerae
diversity have focused primarily on pathogenic isolates of the O1 and O139 serotypes. However, autochthonous environmental isolates of this species routinely display more extensive genetic diversity than the primarily clonal pathogenic strains. In this study, genomic and metabolic profiles of 41 non-O1/O139 environmental isolates from central California coastal waters and four clinical strains are used to characterize the core genome and metabolome of
V. cholerae
. Comparative genome hybridization using microarrays constructed from the fully sequenced
V. cholerae
O1 El Tor N16961 genome identified 2,787 core genes that approximated the projected species core genome within 1.6%. Core genes are almost universally present in strains with widely different niches, suggesting that these genes are essential for persistence in diverse aquatic environments. In contrast, the dispensable genes and phenotypic traits identified in this study should provide increased fitness for certain niche environments. Environmental parameters, measured in situ during sample collection, are correlated to the presence of specific dispensable genes and metabolic capabilities, including utilization of mannose, sialic acid, citrate, and chitosan oligosaccharides. These results identify gene content and metabolic pathways that are likely selected for in certain coastal environments and may influence
V. cholerae
population structure in aquatic environments.
Coprinus comatus
Damages Nematode Cuticles Mechanically with Spiny Balls and Produces Potent Toxins To Immobilize Nematodes
Authors: Luo Hong , Liu Yajun , Fang Lin , Li Xuan , Tang Ninghua , Zhang Keqin 
Published: April 2007

ABSTRACT

We reported recently a unique fungal structure, called the spiny ball, on the vegetative hyphae of
Coprinus comatus
(O. F. Müll.:Fr.) Pers. Although some observations regarding the role of this structure were presented, its function remained largely unknown. In this study, we showed that purified (isolated and washed) spiny balls could immobilize and kill the free-living nematode
Panagrellus redivivus
Goodey highly efficiently. Scanning electron microscopy studies illustrated that the spiny structure damaged the nematode cuticle, suggesting the presence of a mechanical force during the process of nematode immobilization. Severe injuries on nematode cuticles caused the leakage of inner materials of the nematodes. When these structures were ground in liquid nitrogen, their killing efficacy against nematodes was lost, indicating that the shape and the complete structure of the spiny balls are indispensable for their function. However, extraction with organic solvents never lowered their activity against
P. redivivus
, and the extracts showed no obvious effect on the nematode. We also investigated whether
C. comatus
was able to produce toxins which would aid in the immobilization of nematodes. In total, we identified seven toxins from
C. comatus
that showed activity to immobilize the nematodes
P. redivivus
and
Meloidogyne incognita
(Kofoid et White) Chitwood. The chemical structures of these toxins were identified with nuclear magnetic resonance, mass spectrometry, infrared, and UV spectrum analysis. Two compounds were found to be novel. The toxins found in
C. comatus
are O-containing heterocyclic compounds.
Diversity and Mechanisms of Alkali Tolerance in Lactobacilli
Authors: Sawatari Yuki , Yokota Atsushi 
Published: April 2007

ABSTRACT

We determined the maximum pH that allows growth (pHmax) for 34 strains of lactobacilli. High alkali tolerance was exhibited by strains of
Lactobacillus casei
,
L. paracasei
subsp.
tolerans
,
L. paracasei
subsp.
paracasei
,
L. curvatus
,
L. pentosus
, and
L. plantarum
that originated from plant material, with pHmax values between 8.5 and 8.9. Among these,
L. casei
NRIC 1917 and
L. paracasei
subsp.
tolerans
NRIC 1940 showed the highest pHmax, at 8.9. Digestive tract isolates of
L. gasseri
,
L. johnsonii
,
L. reuteri
,
L. salivarius
subsp.
salicinius
, and
L. salivarius
subsp.
salivarius
exhibited moderate alkali tolerance, with pHmax values between 8.1 and 8.5. Dairy isolates of
L. delbrueckii
subsp.
bulgaricus
,
L. delbrueckii
subsp.
lactis
, and
L. helveticus
exhibited no alkali tolerance, with pHmax values between 6.7 and 7.1. Measurement of the internal pH of representative strains revealed the formation of transmembrane proton gradients (ΔpH) in a reversed direction (i.e., acidic interior) at alkaline external-pH ranges, regardless of their degrees of alkali tolerance. Thus, the reversed ΔpH did not determine alkali tolerance diversity. However, the ΔpH contributed to alkali tolerance, as the pHmax values of several strains decreased with the addition of nigericin, which dissipates ΔpH. Although neutral external-pH values resulted in the highest glycolysis activity in the presence of nigericin regardless of alkali tolerance, substantial glucose utilization was still detected in the alkali-tolerant strains, even in a pH range of between 8.0 and 8.5, at which the remaining strains lost most activity. Therefore, the alkali tolerance of glycolysis reactions contributes greatly to the determination of alkali tolerance diversity.
Preliminary Evidence that American Bullfrogs (
Rana catesbeiana
) Are Suitable Hosts for
Escherichia coli
O157:H7
Authors: Gray Matthew J. , Rajeev Sreekumari , Miller Debra L. , Schmutzer A. Chandler , Burton Elizabeth C. , Rogers Emily D. , Hickling Graham J. 
Published: April 2007

ABSTRACT

We orally inoculated
Rana catesbeiana
tadpoles (
n
= 23) and metamorphs (
n
= 24) to test their suitability as hosts for
Escherichia coli
O157:H7. Tadpoles were housed in flowthrough aquaria and did not become infected. Metamorphs were housed in stagnant aquaria, and 54% tested positive through 14 days postinoculation, suggesting that they are suitable hosts for
E. coli
O157:H7.
Recurrent and Sporadic
Listeria monocytogenes
Contamination in Alheiras Represents Considerable Diversity, Including Virulence-Attenuated Isolates
Authors: Felício M. T. S. , Hogg T. , Gibbs P. , Teixeira P. , Wiedmann M. 
Published: April 2007

ABSTRACT

Microbiological characterization of alheiras, traditional smoked meat sausages produced in northern Portugal, had previously shown that more than 60% of the lots analyzed were contaminated with
Listeria monocytogenes
at levels higher than 100 CFU/g. In order to better understand
L. monocytogenes
contamination patterns in alheiras, we characterized 128
L. monocytogenes
isolates from alheiras using a variety of subtyping techniques (i.e., molecular serotyping; arsenic, cadmium, and tetracycline resistance typing; and pulsed-field gel electrophoresis [PFGE]). Subtyping of isolates from products collected on two separate dates provided evidence for the persistence of specific
L. monocytogenes
PFGE types in the production and distribution chains of alheiras from four different processors. A subset of 21 isolates was further characterized using ribotyping and Caco-2 cell invasion assays to evaluate the pathogenic potential of
L. monocytogenes
present in alheiras. Caco-2 invasion assays revealed seven isolates with invasion efficiencies that were less than 20% of that of the control strain 10403S. All seven isolates had premature stop codons in
inlA
that represented three distinct mutations, which had previously been observed in isolates from the United States or France. Our findings indicate the need for a comprehensive approach to control
L. monocytogenes
in alheiras, including strategies to reduce persistence. The presence of considerable diversity in invasion phenotypes among
L. monocytogenes
strains present in alheiras, including the presence of subtypes likely to be virulence attenuated, may provide an opportunity to initially focus control strategies on the subtypes most likely to cause human disease.
Diversity of Environmental
Mycobacterium
Isolates from Hemodialysis Water as Shown by a Multigene Sequencing Approach
Authors: Gomila Margarita , Ramirez Antonio , Lalucat Jorge 
Published: April 2007

ABSTRACT

Here we used a multigene sequencing approach for the identification and molecular typing of environmental mycobacteria of the fast-growing subgroup. Strains were isolated from hemodialysis water and clinical samples. Eleven type strains of related species of the genus were also included in this study. To gain further insight into the diversity of the environmental mycobacteria, we analyzed several housekeeping genes (16S rRNA, ITS1,
gyrB
,
hsp65
,
recA
,
rpoB
, and
sodA
). No individual phylogenetic tree allowed good discrimination of all of the species studied. However, a concatenated and a consensus analysis, combining the genes, allowed better discrimination of each strain to the species level, and the increase in sequence size also led to greater tree robustness. This approach is useful not only for the discrimination and identification of environmental mycobacteria but also for their molecular typing and studies of population genetics. Our results demonstrate high genetic diversity among the isolates obtained, which are probably new species of the genus.
Transcriptome Analysis in Response to Heat Shock and Cadmium in the Aquatic Fungus
Blastocladiella emersonii
Authors: Georg Raphaela C. , Gomes Suely L. 
Published: April 2007

ABSTRACT

The global transcriptional response of the chytridiomycete
Blastocladiella emersonii
to environmental stress conditions was explored by sequencing a large number of expressed sequence tags (ESTs) from three distinct cDNA libraries, constructed with mRNA extracted from cells exposed to heat shock and different concentrations of cadmium chloride. A total of 6,350 high-quality EST sequences were obtained and assembled into 2,326 putative unigenes, 51% of them not previously described in
B. emersonii
. To approximately 59% of the unigenes it was possible to assign an orthologue in another organism, whereas 41% of them remained without a putative identification, with transcripts related to protein folding and antioxidant activity being highly enriched in the stress libraries. A microarray chip was constructed encompassing 3,773 distinct ESTs from the
B. emersonii
transcriptome presently available, which correspond to a wide range of biological processes. Global gene expression analysis of
B. emersonii
cells exposed to stress conditions revealed a large number of differentially expressed genes: 122 up- and 60 downregulated genes during heat shock and 189 up- and 110 downregulated genes during exposure to cadmium. The main functional categories represented among the upregulated genes were protein folding and proteolysis, proteins with antioxidant properties, and cellular transport. Interestingly, in response to cadmium stress,
B. emersonii
cells induced genes encoding six different glutathione
S
-transferases and six distinct metacaspases, as well as genes coding for several proteins of sulfur amino acid metabolism, indicating that cadmium causes oxidative stress and apoptosis in this fungus.
Carbohydrate Metabolism in theToxoplasma gondiiApicoplast: Localization of Three Glycolytic Isoenzymes, the Single Pyruvate Dehydrogenase Complex, and a Plastid Phosphate Translocator
Authors: Fleige Tobias , Fischer Karsten , Ferguson David J. P. , Gross Uwe , Bohne Wolfgang 
Published: April 2007

ABSTRACTMany apicomplexan parasites, such asToxoplasma gondiiandPlasmodiumspecies, possess a nonphotosynthetic plastid, referred to as the apicoplast, which is essential for the parasites’ viability and displays characteristics similar to those of nongreen plastids in plants. In this study, we localized several key enzymes of the carbohydrate metabolism ofT. gondiito either the apicoplast or the cytosol by engineering parasites which express epitope-tagged fusion proteins. The cytosol contains a complete set of enzymes for glycolysis, which should enable the parasite to metabolize imported glucose into pyruvate. All the glycolytic enzymes, from phosphofructokinase up to pyruvate kinase, are present in theT. gondiigenome, as duplicates and isoforms of triose phosphate isomerase, phosphoglycerate kinase, and pyruvate kinase were found to localize to the apicoplast. The mRNA expression levels of all genes with glycolytic products were compared between tachyzoites and bradyzoites; however, a strict bradyzoite-specific expression pattern was observed only for enolase I. TheT. gondiigenome encodes a single pyruvate dehydrogenase complex, which was located in the apicoplast and absent in the mitochondrion, as shown by targeting of epitope-tagged fusion proteins and by immunolocalization of the native pyruvate dehydrogenase complex. The exchange of metabolites between the cytosol and the apicoplast is likely to be mediated by a phosphate translocator which was localized to the apicoplast. Based on these localization studies, a model is proposed that explains the supply of the apicoplast with ATP and the reduction power, as well as the exchange of metabolites between the cytosol and the apicoplast.