bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bioenergetic Mechanism for Nisin Resistance, Induced by the Acid Tolerance Response of
Listeria monocytogenes
Authors: Bonnet Marcelo , Rafi Mohamed M. , Chikindas Michael L. , Montville Thomas J. 
Published: April 2006

ABSTRACT

This study examined the bioenergetics of
Listeria monocytogenes
, induced to an acid tolerance response (ATR). Changes in bioenergetic parameters were consistent with the increased resistance of ATR-induced (ATR
+
) cells to the antimicrobial peptide nisin. These changes may also explain the increased resistance of
L. monocytogenes
to other lethal factors. ATR
+
cells had lower transmembrane pH (ΔpH) and electric potential (Δψ) than the control (ATR
−
) cells. The decreased proton motive force (PMF) of ATR
+
cells increased their resistance to nisin, the action of which is enhanced by energized membranes. Paradoxically, the intracellular ATP levels of the PMF-depleted ATR
+
cells were ∼7-fold higher than those in ATR
−
cells. This suggested a role for the F
o
F
1
ATPase enzyme complex, which converts the energy of ATP hydrolysis to PMF. Inhibition of the F
o
F
1
ATPase enzyme complex by

N

′-

N

′-1,3-dicyclohexylcarbodiimide increased ATP levels in ATR
−
but not in ATR
+
cells, where ATPase activity was already low. Spectrometric analyses (surface-enhanced laser desorption ionization-time of flight mass spectrometry) suggested that in ATR
+
listeriae, the downregulation of the proton-translocating c subunit of the F
o
F
1
ATPase was responsible for the decreased ATPase activity, thereby sparing vital ATP. These data suggest that regulation of F
o
F
1
ATPase plays an important role in the acid tolerance response of
L. monocytogenes
and in its induced resistance to nisin.
Both
msa
Genes in
Renibacterium salmoninarum
Are Needed for Full Virulence in Bacterial Kidney Disease
Authors: Coady Alison M. , Murray Anthony L. , Elliott Diane G. , Rhodes Linda D. 
Published: April 2006

ABSTRACT

Renibacterium salmoninarum
, a gram-positive diplococcobacillus that causes bacterial kidney disease among salmon and trout, has two chromosomal loci encoding the major soluble antigen (
msa
) gene. Because the MSA protein is widely suspected to be an important virulence factor, we used insertion-duplication mutagenesis to generate disruptions of either the
msa1
or
msa2
gene. Surprisingly, expression of MSA protein in broth cultures appeared unaffected. However, the virulence of either mutant in juvenile chinook salmon (
Oncorhynchus tshawytscha
) by intraperitoneal challenge was severely attenuated, suggesting that disruption of the
msa1
or
msa2
gene affected in vivo expression.
Identification of
Sinorhizobium meliloti
Early Symbiotic Genes by Use of a Positive Functional Screen
Authors: Zhang Xue-Song , Cheng Hai-Ping 
Published: April 2006

ABSTRACT

The soil bacterium
Sinorhizobium meliloti
establishes nitrogen-fixing symbiosis with its leguminous host plant, alfalfa, following a series of continuous signal exchanges. The complexity of the changes of alfalfa root structures during symbiosis and the amount of
S. meliloti
genes with unknown functions raised the possibility that more
S. meliloti
genes may be required for early stages of the symbiosis. A positive functional screen of the entire
S. meliloti
genome for symbiotic genes was carried out using a modified in vivo expression technology. A group of genes and putative genes were found to be expressed in early stages of the symbiosis, and 23 of them were alfalfa root exudate inducible. These 23 genes were further separated into two groups based on their responses to apigenin, a known nodulation (
nod
) gene inducer. The group of six genes not inducible by apigenin included the
lsrA
gene, which is essential for the symbiosis, and the
dgkA
gene, which is involved in the synthesis of cyclic β-1,2-glucan required for the
S. meliloti-
alfalfa symbiosis. In the group of 17 apigenin-inducible genes, most have not been previously characterized in
S. meliloti
, and none of them belongs to the
nod
gene family. The identification of this large group of alfalfa root exudate-inducible
S. meliloti
genes suggests that the interactions in the early stages of the
S. meliloti
and alfalfa symbiosis could be complex and that further characterization of these genes will lead to a better understanding of the symbiosis.
Detection of Norovirus Capsid Protein in Authentic Standards and in Stool Extracts by Matrix-Assisted Laser Desorption Ionization and Nanospray Mass Spectrometry
Authors: Colquhoun David R. , Schwab Kellogg J. , Cole Robert N. , Halden Rolf U. 
Published: April 2006

ABSTRACT

Mass spectrometry (MS) represents a rapid technique for the identification of microbial monocultures, and its adaptation to the detection of pathogens in real-world samples is a public health and homeland security priority. Norovirus, a leading cause of gastroenteritis in the world, is difficult to monitor because it cannot be cultured outside the human body. The detection of norovirus capsid protein was explored using three common MS-based methods: scanning of intact proteins, peptide mass fingerprinting, and peptide sequencing. Detection of intact target protein was limited by poor selectivity and sensitivity. Detection of up to 16 target peptides by peptide mass fingerprinting allowed for the reproducible and confident (
P
< 0.05) detection of the 56-kDa norovirus capsid protein in the range of 0.1 × 10
−12
to 50 × 10
−12
mol in authentic standards of recombinant norovirus virus-like particles (VLPs). To explore assay performance in complex matrixes, a non-gel-based, rapid method (2 to 3 h) for virus extraction from human stool was evaluated (72% ± 12% recovery), and additional analyses were performed on norovirus-free stool extracts fortified with VLPs. Whereas peptide mass fingerprinting was rendered impractical by sample interferences, peptide sequencing using nanospray tandem MS facilitated unambiguous identification of ≥250 fmol of capsid protein in stool extracts. This is the first report on MS-based detection of norovirus, accomplished by using structurally identical, noninfective VLPs at clinically relevant concentrations. It represents an important milestone in the development of assays for surveillance of this category B bioterrorism agent.
Lipid II-Based Antimicrobial Activity of the Lantibiotic Plantaricin C
Authors: Wiedemann Imke , Böttiger Tim , Bonelli Raquel Regina , Schneider Tanja , Sahl Hans-Georg , Martínez Beatriz 
Published: April 2006

ABSTRACT

We analyzed the mode of action of the lantibiotic plantaricin C (PlnC), produced by
Lactobacillus plantarum
LL441. Compared to the well-characterized type A lantibiotic nisin and type B lantibiotic mersacidin, which are both able to interact with the cell wall precursor lipid II, PlnC displays structural features of both prototypes. In this regard, we found that lipid II plays a key role in the antimicrobial activity of PlnC besides that of pore formation. The pore forming activity of PlnC in whole cells was prevented by shielding lipid II on the cell surface. However, in contrast to nisin, PlnC was not able to permeabilize
Lactococcus lactis
cells or to form pores in 1,2-dioleoyl-
sn
-glycero-3-phosphocholine liposomes supplemented with 0.1 mol% purified lipid II. This emphasized the different requirements of these lantibiotics for pore formation. Using cell wall synthesis assays, we identified PlnC as a potent inhibitor of (i) lipid II synthesis and (ii) the FemX reaction, i.e., the addition of the first Gly to the pentapeptide side chain of lipid II. As revealed by thin-layer chromatography, both reactions were clearly blocked by the formation of a PlnC-lipid I and/or PlnC-lipid II complex. On the basis of the in vivo and in vitro activities of PlnC shown in this study and the structural lipid II binding motifs described for other lantibiotics, the specific interaction of PlnC with lipid II is discussed.
Bacillus
Endospores Isolated from Granite: Close Molecular Relationships to Globally Distributed
Bacillus
spp. from Endolithic and Extreme Environments
Authors: Fajardo-Cavazos Patricia , Nicholson Wayne 
Published: April 2006

ABSTRACT

As part of an ongoing effort to catalog spore-forming bacterial populations in environments conducive to interplanetary transfer by natural impacts or by human spaceflight activities, spores of
Bacillus
spp. were isolated and characterized from the interior of near-subsurface granite rock collected from the Santa Catalina Mountains, AZ. Granite was found to contain ∼500 cultivable
Bacillus
spores and ∼10
4
total cultivable bacteria per gram. Many of the
Bacillus
isolates produced a previously unreported diffusible blue fluorescent compound. Two strains of eight tested exhibited increased spore UV resistance relative to a standard
Bacillus subtilis
UV biodosimetry strain. Fifty-six isolates were identified by repetitive extragenic palindromic PCR (rep-PCR) and 16S rRNA gene analysis as most closely related to
B. megaterium
(15 isolates),
B. simplex
(23 isolates),
B. drentensis
(6 isolates),
B. niacini
(7 isolates), and, likely, a new species related to
B. barbaricus
(5 isolates). Granite isolates were very closely related to a limited number of
Bacillus
spp. previously found to inhabit (i) globally distributed endolithic sites such as biodeteriorated murals, stone tombs, underground caverns, and rock concretions and (ii) extreme environments such as Antarctic soils, deep sea floor sediments, and spacecraft assembly facilities. Thus, it appears that the occurrence of
Bacillus
spp. in endolithic or extreme environments is not accidental but that these environments create unique niches excluding most
Bacillus
spp. but to which a limited number of
Bacillus
spp. are specifically adapted.
Planktonic Replication Is Essential for Biofilm Formation byLegionella pneumophilain a Complex Medium under Static and Dynamic Flow Conditions
Authors: Mampel Jörg , Spirig Thomas , Weber Stefan S. , Haagensen Janus A. J. , Molin Søren , Hilbi Hubert 
Published: April 2006

ABSTRACTLegionella pneumophilapersists for a long time in aquatic habitats, where the bacteria associate with biofilms and replicate within protozoan predators. WhileL. pneumophilaserves as a paradigm for intracellular growth within protozoa, it is less clear whether the bacteria form or replicate within biofilms in the absence of protozoa. In this study, we analyzed surface adherence of and biofilm formation byL. pneumophilain a rich medium that supported axenic replication. Biofilm formation by the virulentL. pneumophilastrain JR32 and by clinical and environmental isolates was analyzed by confocal microscopy and crystal violet staining. Strain JR32 formed biofilms on glass surfaces and upright polystyrene wells, as well as on pins of “inverse” microtiter plates, indicating that biofilm formation was not simply due to sedimentation of the bacteria. Biofilm formation by anL. pneumophila fliAmutant lacking the alternative sigma factor σ28was reduced, which demonstrated that bacterial factors are required. Accumulation of biomass coincided with an increase in the optical density at 600 nm and ceased when the bacteria reached the stationary growth phase.L. pneumophilaneither grew nor formed biofilms in the inverse system if the medium was exchanged twice a day. However, after addition ofAcanthamoeba castellanii, the bacteria proliferated and adhered to surfaces. Sessile (surface-attached) and planktonic (free-swimming)L. pneumophilaexpressed β-galactosidase activity to similar extents, and therefore, the observed lack of proliferation of surface-attached bacteria was not due to impaired protein synthesis or metabolic activity. Cocultivation of green fluorescent protein (GFP)- and DsRed-labeledL. pneumophilaled to randomly interspersed cells on the substratum and in aggregates, and no sizeable patches of clonally growing bacteria were observed. Our findings indicate that biofilm formation byL. pneumophilain a rich medium is due to growth of planktonic bacteria rather than to growth of sessile bacteria. In agreement with this conclusion, GFP-labeledL. pneumophilainitially adhered in a continuous-flow chamber system but detached over time; the detachment correlated with the flow rate, and there was no accumulation of biomass. Under these conditions,L. pneumophilapersisted in biofilms formed byEmpedobacter breveorMicrobacteriumsp. but not in biofilms formed byKlebsiella pneumoniaeor other environmental bacteria, suggesting that specific interactions between the bacteria modulate adherence.
Diversity and Biocatalytic Potential of Epoxide Hydrolases Identified by Genome Analysis
Authors: van Loo Bert , Kingma Jaap , Arand Michael , Wubbolts Marcel G. , Janssen Dick B. 
Published: April 2006

ABSTRACT

Epoxide hydrolases play an important role in the biodegradation of organic compounds and are potentially useful in enantioselective biocatalysis. An analysis of various genomic databases revealed that about 20% of sequenced organisms contain one or more putative epoxide hydrolase genes. They were found in all domains of life, and many fungi and actinobacteria contain several putative epoxide hydrolase-encoding genes. Multiple sequence alignments of epoxide hydrolases with other known and putative α/β-hydrolase fold enzymes that possess a nucleophilic aspartate revealed that these enzymes can be classified into eight phylogenetic groups that all contain putative epoxide hydrolases. To determine their catalytic activities, 10 putative bacterial epoxide hydrolase genes and 2 known bacterial epoxide hydrolase genes were cloned and overexpressed in
Escherichia coli
. The production of active enzyme was strongly improved by fusion to the maltose binding protein (MalE), which prevented inclusion body formation and facilitated protein purification. Eight of the 12 fusion proteins were active toward one or more of the 21 epoxides that were tested, and they converted both terminal and nonterminal epoxides. Four of the new epoxide hydrolases showed an uncommon enantiopreference for
meso
-epoxides and/or terminal aromatic epoxides, which made them suitable for the production of enantiopure (
S
,
S
)-diols and (
R
)-epoxides. The results show that the expression of epoxide hydrolase genes that are detected by analyses of genomic databases is a useful strategy for obtaining new biocatalysts.
Molecular Epidemiology of Norovirus in Outbreaks of Gastroenteritis in Southwest Germany from 2001 to 2004
Authors: Ike Anthony C. , Brockmann Stefan O. , Hartelt Kathrin , Marschang Rachel E. , Contzen Matthias , Oehme Rainer M. 
Published: April 2006

ABSTRACT

The identification and molecular epidemiology of norovirus in outbreaks of gastroenteritis were studied during a 3-year period in Germany. Specimens (
n
= 316) from 159 nonbacterial gastroenteritis outbreaks from March 2001 to June 2004 were analyzed for the presence of noroviruses by reverse transcriptase PCR. Outbreaks were most frequent in elderly people's homes and care centers (43%), followed by hospitals (24%). Molecular analyses of strains from 148 outbreaks showed that there were up to 12 genotypes involved in the outbreaks. Genogroup II noroviruses were responsible for 95% of the outbreaks. Cocirculation of more than one strain in the same outbreak and cocirculation of genogroup I and II strains in the same place were observed. Genogroup II4 (Grimsby-like) was the most prevalent strain, accounting for 48% and 67% of the outbreaks in 2002 and 2003, respectively. The genogroup IIb (Castell/Suria) genotype was observed in all the years of the study. Epidemiological and molecular data indicated that there was a major shift of the predominant strain that coincided with the appearance of a new variant of genogroup II4 in 2002. By the application of reverse transcriptase PCR, this study has demonstrated the importance and dynamism of noroviruses in Germany.
Genotyping of
Toxoplasma gondii
by Multiplex PCR and Peptide-Based Serological Testing of Samples from Infants in Poland Diagnosed with Congenital Toxoplasmosis
Authors: Nowakowska Dorota , Colón Iris , Remington Jack S. , Grigg Michael , Golab Elzbieta , Wilczynski J. , Sibley L. David 
Published: April 2006

ABSTRACT

Toxoplasma gondii
has a clonal population genetic structure with three (I, II, and III) lineages that predominate in North America and Europe. Type II strains cause most cases of symptomatic human infections in France and the United States, although few other regions have been adequately sampled. Here we determined the parasite genotype in amniotic fluid and cerebrospinal fluid samples from congenital toxoplasmosis cases in Poland. Nineteen confirmed congenital cases of toxoplasmosis were analyzed, including both severe and asymptomatic cases. The genotype of parasite strains causing congenital infection was determined by direct PCR amplification and restriction fragment length polymorphism analysis. Nested multiplex PCR analysis was used to type four independent polymorphic markers. The sensitivity of multiplex nested PCR was ≥25 parasites/ml in amniotic fluid and cerebral spinal fluid samples. Parasite DNA was successfully amplified in 9 of 19 samples (eight severely affected and one asymptomatic fetus). Only genotype II parasites were identified as the source of
T. gondii
infection based on restriction fragment length polymorphism analysis. Strains causing congenital infections were also typed indirectly based on detection of antibodies to strain-specific peptides. Serotyping indicated that 12 of 15 cases tested were caused by type II strains and these positives included both symptomatic and asymptomatic infections. Overall, the combined analysis indicated that 14 of the cases were caused by type II strains. Our results are consistent with the hypothesis that parasite burden is associated with severity of congenital toxoplasmosis and indicate that serological testing provides a promising method for genotypic analysis of toxoplasmosis.
Isothermal Amplification and Molecular Typing of the Obligate Intracellular Pathogen
Mycobacterium leprae
Isolated from Tissues of Unknown Origins
Authors: Groathouse Nathan A. , Brown Susan E. , Knudson Dennis L. , Brennan Patrick J. , Slayden Richard A. 
Published: April 2006

ABSTRACT

Molecular diagnostic and epidemiology studies require appreciable amounts of high-quality DNA. Molecular epidemiologic methods have not been routinely applied to the obligate intracellular organism
Mycobacterium leprae
because of the difficulty of obtaining a genomic DNA template from clinical material. Accordingly, we have developed a method based on isothermic multiple-displacement amplification to allow access to a high-quality DNA template. In the study described in this report, we evaluated the usefulness of this method for error-sensitive, multiple-feature molecular analyses. Using test samples isolated from lepromatous tissue, we also evaluated amplification fidelity, genome coverage, and regional amplification bias. The fidelity of amplified genomic material was unaltered; and while regional differences in global amplification efficiency were seen by using comparative microarray analysis, a high degree of concordance of amplified genomic DNA was observed. This method was also applied directly to archived tissue specimens from leprosy patients for the purpose of molecular typing by using short tandem repeats; the success rate was increased from 25% to 92% without the introduction of errors. This is the first study to demonstrate that serial whole-genome amplification can be coupled with error-sensitive molecular typing methods with low-copy-number sequences from tissues containing an obligate intracellular pathogen.
Multiple-Locus Variable-Number Tandem Repeat Analysis of
Neisseria meningitidis
Yields Groupings Similar to Those Obtained by Multilocus Sequence Typing
Authors: Schouls Leo M. , van der Ende Arie , Damen Marjolein , van de Pol Ingrid 
Published: April 2006

ABSTRACT

We identified many variable-number tandem repeat (VNTR) loci in the genomes of
Neisseria meningitidis
serogroups A, B, and C and utilized a number of these loci to develop a multiple-locus variable-number tandem repeat analysis (MLVA). Eighty-five
N. meningitidis
serogroup B and C isolates obtained from Dutch patients with invasive meningococcal disease and seven reference strains were analyzed using MLVA and multilocus sequence typing (MLST). MLVA, based on eight VNTR loci with limited variability in the number of repeats, yielded clustering of the strains similar to that obtained by MLST, with congruence between both methods amounting to 69%. The ability to recognize clonal complexes makes MLVA a valuable high-throughput method to serve as a tool complementary to MLST. Four highly variable VNTR loci were used in a second assay to analyze
N. meningitidis
serogroup C strains collected during an outbreak of meningococcal disease in The Netherlands. Typing based on the latter VNTR loci enabled differentiation of isolates with identical MLST sequence types and grouped epidemiologically related strains.
Invasive
Haemophilus influenzae
in Manitoba, Canada, in the Postvaccination Era
Authors: Tsang Raymond S. W. , Mubareka Samira , Sill Michelle L. , Wylie John , Skinner Stuart , Law Dennis K. S. 
Published: April 2006

ABSTRACT

Fifty-two
Haemophilus influenzae
isolates from patients with invasive disease in the province of Manitoba, Canada, were examined for serotype, biotype, genotype, and antibiotic susceptibility. Half of the 52 isolates were found to be serotype a, and 38.5% (20 isolates) were found to be nonserotypeable (NST). There were only three serotype b strains and one each for serotypes c, d, and f. All 26 serotype a isolates belonged to biotype II and demonstrated identical or highly similar DNA fingerprints by pulsed-field gel electrophoresis. An analysis of these isolates by multilocus sequence typing showed that they belong to the clonal complex ST-23. While 69% (18 of 26) of the serotype a cases were found in males, only 9 (45%) of the 20 patients with NST isolates were males. Twenty (77%) of the 26 serotype a isolates were from patients who were ≤24 months old. Twelve (63%) of the NST isolates were from adult or adolescent patients. In contrast to the clonal nature of serotype a isolates, the 20 NST isolates were found to belong to 18 different sequence types. Most of these 18 different sequence types were unrelated to each other, with the exception of 7 sequence types grouped into three clonal groups. Two (6.25%) out of 32 serotypeable isolates (1 serotype a and 1 serotype b) and 6 (30%) of 20 NST isolates were resistant to ampicillin due to β-lactamase production. These results suggest a change in the epidemiology of
H. influenzae
disease, with the majority of invasive
H. influenzae
isolates being associated with serotype a and NST strains.
Rapid Identification of
Enterococcus hirae
and
Enterococcus durans
by PCR and Detection of a Homologue of the
E. hirae mur-2
Gene in
E. durans
Authors: Arias Cesar A. , Robredo Beatriz , Singh Kavindra V. , Torres Carmen , Panesso Diana , Murray Barbara E. 
Published: April 2006

ABSTRACT

During an evaluation of PCR for identification of isolates of
Enterococcus hirae
, a homologue with 82% identity to
E. hirae mur-2
was identified in
Enterococcus durans
and was named
mur-2
ed
. PCR using primers for two genes (
copY
and
murG
) of
E. hirae
strains showed amplification with
E. hirae
strains only. PCR (under high-stringency conditions) with primers for the
mur-2
ed
gene gave the expected amplification product only with
E. durans
strains. A combination of
murG
and

mur-2
ed

primers in a multiplex PCR assay differentiated
E. hirae
from
E. durans
in all cases. PCR using these primers appears to be a rapid alternative for identification of
E. hirae
and
E. durans
isolates.