bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequencing and Heterologous Expression of an Epimerase and Two Lyases from Iminodisuccinate-Degrading Bacteria
Authors: Bäuerle Bettina , Cokesa Željko , Hofmann Silvia , Rieger Paul-Gerhard 
Published: April 2006

ABSTRACT

Recently, degradation of all existing epimers of the complexing agent iminodisuccinate (IDS) in the bacterial strain
Agrobacterium tumefaciens
BY6 was proven to depend on an epimerase and a C-N lyase (Cokesa et al., Appl. Environ. Microbiol.
70:
3941-3947, 2004). In the bacterial strain
Ralstonia
sp. strain SLRS7, a corresponding C-N lyase is responsible for the initial degradation step (Cokesa et al., Biodegradation
15:
229-239, 2004). The
ite
gene, encoding the IDS-transforming epimerase, and the genes
icl
B
and
icl
S
, encoding the IDS-converting BY6-lyase and SLRS7-lyase, respectively, were cloned and sequenced. The epimerase gene encodes a protein with a predicted subunit molecular mass of 47.6 kDa. The highest degree of epimerase amino acid sequence identities was found with proteins of unknown function, indicating a novel protein. For the lyases, the deduced amino acid sequences show high similarity to enzymes of the fumarase II family. A classification into a new subfamily within the enzyme family is proposed. The subunit molecular masses of the lyases were calculated to be 54.4 and 54.7 kDa, respectively. In
Agrobacterium tumefaciens
BY6, the
ite
gene was on an approximately 180-kb circular plasmid, whereas the
icl
B
gene was chromosomal like the corresponding
icl
S
gene in
Ralstonia
sp. strain SLRS7. Heterologous expression in
Escherichia coli
and subsequent purification revealed recombinant enzymes with in vitro activity similar to that of the corresponding enzymes from the wild-type strains.
Identification of
Salmonella enterica
Serovar Typhimurium Genes Important for Survival in the Swine Gastric Environment
Authors: Bearson Shawn M. D. , Bearson Bradley L. , Rasmussen Mark A. 
Published: April 2006

ABSTRACT

Since the stomach is a first line of defense for the host against ingested microorganisms, an ex vivo swine stomach contents (SSC) assay was developed to search for genes important for
Salmonella enterica
serovar Typhimurium survival in the hostile gastric environment. Initial characterization of the SSC assay (pH 3.87) using previously identified, acid-sensitive serovar Typhimurium mutants revealed a 10-fold decrease in survival for a
phoP
mutant following 20 min of challenge and no survival for mutants of
rpoS
or
fur
. To identify additional genes, a signature-tagged mutagenesis bank was constructed and screened in the SSC assay. Nineteen mutants were identified and individually analyzed in the SSC and acid tolerance response assays; 13 mutants exhibited a 10-fold or greater sensitivity in the SSC assay compared to the wild-type strain, but only 3 mutants displayed a 10-fold or greater decrease in survival following pH 3.0 acidic challenge. Further examination determined that the lethal effects of the SSC are pH dependent but that low pH is not the sole killing mechanism(s). Gas chromatography analysis of the SSC revealed lactic acid levels of 126 mM. Upon investigating the effects of lactic acid on serovar Typhimurium survival in a synthetic gastric fluid, not only was a concentration- and time-dependent lethal effect observed, but the
phoP
,
rpoS
,
fur
, and
pnp
genes were identified as involved in protection against lactic acid exposure. These studies indicate a role in gastric survival for several serovar Typhimurium genes and imply that the stomach environment is defined by more than low pH.
Molecular Characterization of Subject-Specific Oral Microflora during Initial Colonization of Enamel
Authors: Diaz Patricia I. , Chalmers Natalia I. , Rickard Alexander H. , Kong Colin , Milburn Craig L. , Palmer Robert J. , Kolenbrander Paul E. 
Published: April 2006

ABSTRACT

The initial microbial colonization of tooth surfaces is a repeatable and selective process, with certain bacterial species predominating in the nascent biofilm. Characterization of the initial microflora is the first step in understanding interactions among community members that shape ensuing biofilm development. Using molecular methods and a retrievable enamel chip model, we characterized the microbial diversity of early dental biofilms in three subjects. A total of 531 16S rRNA gene sequences were analyzed, and 97 distinct phylotypes were identified. Microbial community composition was shown to be statistically different among subjects. In all subjects, however, 4-h and 8-h communities were dominated by
Streptococcus
spp. belonging to the
Streptococcus oralis
/
Streptococcus mitis
group. Other frequently observed genera (comprising at least 5% of clone sequences in at least one of the six clone libraries) were
Actinomyces
,
Gemella
,
Granulicatella
,
Neisseria
,
Prevotella
,
Rothia
, and
Veillonella
. Fluorescence in situ hybridization (FISH) confirmed that the proportion of
Streptococcus
sp. sequences in the clone libraries coincided with the proportion of streptococcus probe-positive organisms on the chip. FISH also revealed that, in the undisturbed plaque, not only
Streptococcus
spp. but also the rarer
Prevotella
spp. were usually seen in small multigeneric clusters of cells. This study shows that the initial dental plaque community of each subject is unique in terms of diversity and composition. Repetitive and distinctive community composition within subjects suggests that the spatiotemporal interactions and ecological shifts that accompany biofilm maturation also occur in a subject-dependent manner.
Toxigenic
Vibrio cholerae
in the Aquatic Environment of Mathbaria, Bangladesh
Authors: Alam Munirul , Sultana Marzia , Nair G. Balakrish , Sack R. Bradley , Sack David A. , Siddique A. K. , Ali Afsar , Huq Anwar , Colwell Rita R. 
Published: April 2006

ABSTRACT

Toxigenic
Vibrio cholerae
, rarely isolated from the aquatic environment between cholera epidemics, can be detected in what is now understood to be a dormant stage, i.e., viable but nonculturable when standard bacteriological methods are used. In the research reported here, biofilms have proved to be a source of culturable
V. cholerae
, even in nonepidemic periods. Biweekly environmental surveillance for
V. cholerae
was carried out in Mathbaria, an area of cholera endemicity adjacent to the Bay of Bengal, with the focus on
V. cholerae
O1 and O139 Bengal. A total of 297 samples of water, phytoplankton, and zooplankton were collected between March and December 2004, yielding eight
V. cholerae
O1 and four O139 Bengal isolates. A combination of culture methods, multiplex-PCR, and direct fluorescent antibody (DFA) counting revealed the Mathbaria aquatic environment to be a reservoir for
V. cholerae
O1 and O139 Bengal. DFA results showed significant clumping of the bacteria during the interepidemic period for cholera, and the fluorescent micrographs revealed large numbers of
V. cholerae
O1 in thin films of exopolysaccharides (biofilm). A similar clumping of
V. cholerae
O1 was also observed in samples collected from Matlab, Bangladesh, where cholera also is endemic. Thus, the results of the study provided in situ evidence for
V. cholerae
O1 and O139 in the aquatic environment, predominantly as viable but nonculturable cells and culturable cells in biofilm consortia. The biofilm community is concluded to be an additional reservoir of cholera bacteria in the aquatic environment between seasonal epidemics of cholera in Bangladesh.
Anaerobic Ammonium-Oxidizing (Anammox) Bacteria and Associated Activity in Fixed-Film Biofilters of a Marine Recirculating Aquaculture System
Authors: Tal Yossi , Watts Joy E. M. , Schreier Harold J. 
Published: April 2006

ABSTRACT

Microbial communities in the biological filter and waste sludge compartments of a marine recirculating aquaculture system were examined to determine the presence and activity of anaerobic ammonium-oxidizing (anammox) bacteria. Community DNA was extracted from aerobic and anaerobic fixed-film biofilters and the anaerobic sludge waste collection tank and was analyzed by amplifying 16S rRNA genes by PCR using anammox-selective and universal GC-clamped primers. Separation of amplified PCR products by denaturing gradient gel electrophoresis and sequencing of the different phylotypes revealed a diverse biofilter microbial community. While
Planctomycetales
were found in all three communities, the anaerobic denitrifying biofilters contained one clone that exhibited high levels of sequence similarity to known anammox bacteria. Fluorescence in situ hybridization studies using an anammox-specific probe confirmed the presence of anammox
Planctomycetales
in the microbial biofilm from the denitrifying biofilters, and anammox activity was observed in these biofilters, as detected by the ability to simultaneously consume ammonia and nitrite. To our knowledge, this is the first identification of anammox-related sequences in a marine recirculating aquaculture filtration system, and our findings provide a foundation for incorporating this important pathway for complete nitrogen removal in such systems.
Overexpression and Characterization of an Iron Storage and DNA-Binding Dps Protein from
Trichodesmium erythraeum
Authors: Castruita M. , Saito M. , Schottel P. C. , Elmegreen L. A. , Myneni S. , Stiefel E. I. , Morel F. M. M. 
Published: April 2006

ABSTRACT

Although the role of iron in marine productivity has received a great deal of attention, no iron storage protein has been isolated from a marine microorganism previously. We describe an Fe-binding protein belonging to the Dps family (DNA binding protein from starved cells) in the N
2
-fixing marine cyanobacterium
Trichodesmium erythraeum
. A
dps
gene encoding a protein with significant levels of identity to members of the Dps family was identified in the genome of
T. erythraeum
. This gene codes for a putative Dps

T. erythraeurm

protein (Dps
tery
) with 69% primary amino acid sequence similarity to
Synechococcus
DpsA. We expressed and purified Dps
tery
, and we found that Dps
tery
, like other Dps proteins, is able to bind Fe and DNA and protect DNA from degradation by DNase. We also found that Dps
tery
binds phosphate, like other ferritin family proteins. Fe K near-edge X-ray absorption of Dps
tery
indicated that it has an iron core that resembles that of horse spleen ferritin.
Methanosarcina
spp. Drive Vinyl Chloride Dechlorination via Interspecies Hydrogen Transfer
Authors: Heimann Axel C. , Batstone Damien J. , Jakobsen Rasmus 
Published: April 2006

ABSTRACT

Two highly enriched cultures containing
Dehalococcoides
spp. were used to study the effect of aceticlastic methanogens on reductive vinyl chloride (VC) dechlorination. In terms of aceticlastic methanogens, one culture was dominated by
Methanosaeta
, while the other culture was dominated by
Methanosarcina
, as determined by fluorescence in situ hybridization. Cultures amended with 2-bromoethanesulfonate (BES), an efficient inhibitor of methanogens, exhibited slow VC dechlorination when grown on acetate and VC. Methanogenic cultures dominated by
Methanosaeta
had no impact on dechlorination rates, compared to BES-amended controls. In contrast, methanogenic cultures dominated by
Methanosarcina
displayed up to sevenfold-higher rates of VC dechlorination than their BES-amended counterparts.
Methanosarcina
-dominated cultures converted a higher percentage of [2-
14
C]acetate to
14
CO
2
when concomitant VC dechlorination took place, compared to nondechlorinating controls. Respiratory indices increased from 0.12 in nondechlorinating cultures to 0.51 in actively dechlorinating cultures. During VC dechlorination, aqueous hydrogen (H
2
) concentrations dropped to 0.3 to 0.5 nM. However, upon complete VC consumption, H
2
levels increased by a factor of 10 to 100, indicating active hydrogen production from acetate oxidation. This process was thermodynamically favorable by means of the extremely low H
2
levels during dechlorination. VC degradation in nonmethanogenic cultures was not inhibited by BES but was limited by the availability of H
2
as electron donor, in cultures both with and without BES. These findings all indicate that
Methanosarcina
(but not
Methanosaeta
), while cleaving acetate to methane, simultaneously oxidizes acetate to CO
2
plus H
2
, driving hydrogenotrophic dehalorespiration of VC to ethene by
Dehalococcoides
.
Elevated Shear Stress Protects
Escherichia coli
Cells Adhering to Surfaces via Catch Bonds from Detachment by Soluble Inhibitors
Authors: Nilsson Lina M. , Thomas Wendy E. , Sokurenko Evgeni V. , Vogel Viola 
Published: April 2006

ABSTRACT

Soluble inhibitors find widespread applications as therapeutic drugs to reduce the ability of eukaryotic cells, bacteria, or viruses to adhere to surfaces and host tissues. Mechanical forces resulting from fluid flow are often present under in vivo conditions, and it is commonly presumed that fluid flow will further add to the inhibitive effect seen under static conditions. In striking contrast, we discover that when surface adhesion is mediated by catch bonds, whose bond life increases with increased applied force, shear stress may dramatically increase the ability of bacteria to withstand detachment by soluble competitive inhibitors. This shear stress-induced protection against inhibitor-mediated detachment is shown here for the fimbrial FimH-mannose-mediated surface adhesion of
Escherichia coli
. Shear stress-enhanced reduction of bacterial detachment has major physiological and therapeutic implications and needs to be considered when developing and screening drugs.
Culture Conditions of
Roseobacter
Strain 27-4 Affect Its Attachment and Biofilm Formation as Quantified by Real-Time PCR
Authors: Bruhn Jesper Bartholin , Haagensen Janus Anders Juul , Bagge-Ravn Dorthe , Gram Lone 
Published: April 2006

ABSTRACT

The fish probiotic bacterium
Roseobacter
strain 27-4 grows only as rosettes and produces its antibacterial compound under static growth conditions. It forms three-dimensional biofilms when precultured under static conditions. We quantified attachment of
Roseobacter
strain 27-4 using a direct real-time PCR method and demonstrated that the bacteria attached more efficiently to surfaces during static growth than under aerated conditions.
Does Green Light Influence the Fluorescence Properties and Structure of Phototrophic Biofilms?
Authors: Roldán M. , Oliva F. , Gónzalez del Valle M. A. , Saiz-Jimenez C. , Hernández-Mariné M. 
Published: April 2006

ABSTRACTArtificial illumination can harm works of art by inducing the development of photosynthetic biofilms. With the aim of preventing biodeterioration or esthetic damage to such surfaces, we evaluated and compared the effects of illuminating biofilms formed byGloeothece membranacea(cyanobacteria) andChlorella sorokiniana(Chlorophyta) using exclusively white or green light.
Laboratory-Dependent Bacterial Ecology: a Cautionary Tale
Authors: O'Keefe K. J. , Morales N. M. , Ernstberger H. , Benoit G. , Turner P. E. 
Published: April 2006

ABSTRACT

Although laboratory dependence is an acknowledged problem in microbiology, it is seldom intensively studied or discussed. We demonstrate that laboratory dependence is real and quantifiable even in the popular model
Escherichia coli
. Here laboratory effects alter the equilibrium composition of a simple community composed of two strains of
E. coli
. Our data rule out changes in the bacterial strains, chemical batches, and human handling but implicate differences in growth medium, especially the water component.
Antimicrobial Susceptibility and Characterization ofSalmonellaIsolates from Processed Bison Carcasses
Authors: Li Qiongzhen , Skyberg Jerod A. , Fakhr Mohamed K. , Sherwood Julie S. , Nolan Lisa K. , Logue Catherine M. 
Published: April 2006

ABSTRACTSeventeenSalmonella entericaserovar Hadar isolates recovered from bison were found to possess a range of virulence genes and resistance to tetracycline, gentamicin, sulfamethoxazole, and streptomycin simultaneously. A 1-kb class 1 integron containing theaadA1gene was identified in all isolates. Pulsed-field gel electrophoresis found that all isolates were closely related, indicating the possibility of cross-contamination during processing.
Safety Assessment of the Oral Cavity Probiotic
Streptococcus salivarius
K12
Authors: Burton Jeremy P. , Wescombe Philip A. , Moore Chris J. , Chilcott Chris N. , Tagg John R. 
Published: April 2006

ABSTRACT

Streptococcus salivarius
is a prominent member of the oral microbiota and has excellent potential for use as a probiotic targeting the oral cavity. In this report we document safety data relating to
S. salivarius
K12, including assessment of its antibiogram, metabolic profiles, and virulence determinants, and we examine the microbial composition of saliva following the dosing of subjects with K12.
Prevalence of
Borrelia burgdorferi
Sensu Lato and
Anaplasmataceae
Members in
Ixodes ricinus
Ticks in Alsace, a Focus of Lyme Borreliosis Endemicity in France
Authors: Ferquel Elisabeth , Garnier Martine , Marie Jérôme , Bernède-Bauduin Claire , Baranton Guy , Pérez-Eid Claudine , Postic Danièle 
Published: April 2006

ABSTRACT

Due to the high Lyme borreliosis incidence in Alsace, in northeastern France, we investigated in 2003-2004 three cantons in this region in order to determine the density of
Ixodes ricinus
ticks infected by
Borrelia burgdorferi
sensu lato and
Anaplasmataceae
. The peak density of nymphs infected by
B. burgdorferi
sensu lato at Munster and Guebwiller, where the disease incidence was high, was among the highest reported in Europe (105 and 114 per 100 m
2
, respectively). In contrast, the peak density of infected nymphs was low in the canton of Dannemarie (5/100 m
2
), where the disease incidence was low. The two main species detected in ticks were
Borrelia afzelii
, more frequent in nymphs, and
Borrelia garinii
, more frequent in adult ticks. The rates of tick infection by
Anaplasma phagocytophilum
were 0.4% and 1.2% in nymphs and adults, respectively.
Use of Semiconductor-Based Oligonucleotide Microarrays for Influenza A Virus Subtype Identification and Sequencing
Authors: Lodes Michael J. , Suciu Dominic , Elliott Mark , Stover Axel G. , Ross Marty , Caraballo Marcelo , Dix Kim , Crye James , Webby Richard J. , Lyon Wanda J. , Danley David L. , McShea Andrew 
Published: April 2006

ABSTRACT
In the face of concerns over an influenza pandemic, identification of virulent influenza A virus isolates must be obtained quickly for effective responses. Rapid subtype identification, however, is difficult even in well-equipped virology laboratories or is unobtainable in the field under more austere conditions. Here we describe a genome assay and microarray design that can be used to rapidly identify influenza A virus hemagglutinin subtypes 1 through 15 and neuraminidase subtypes 1 through 9. Also described is an array-based enzymatic assay that can be used to sequence portions of both genes or any other sequence of interest.
Evaluation of the IDI-MRSA Assay for Detection of Methicillin-Resistant
Staphylococcus aureus
from Nasal and Rectal Specimens Pooled in a Selective Broth
Authors: Desjardins M. , Guibord Christiane , Lalonde B. , Toye B. , Ramotar K. 
Published: April 2006

ABSTRACT

Rapid detection of methicillin-resistant
Staphylococcus aureus
(MRSA) by PCR can be performed directly from nasal specimens with the IDI-MRSA assay. To improve the efficiency of screening, we evaluated the performance of the IDI-MRSA assay for the detection of MRSA from pooled and unpooled specimens cultured in a selective broth. Of the 287 specimens evaluated, 71 were culture and PCR positive, 203 were culture and PCR negative, 3 were culture positive and PCR negative, 8 were culture negative and PCR positive, and 2 remained inhibited. A methicillin-susceptible
Staphylococcus aureus
isolate was recovered from five of the eight specimens with false-positive PCR results. Compared to the results of culture, the sensitivity, specificity, and negative and positive predictive values of the IDI-MRSA assay for detection of MRSA from broth were 96%, 96%, 90%, and 98%, respectively. Following implementation of the IDI-MRSA assay, PCR-positive broths were subcultured for evaluation of assay performance. Of the 298 IDI-MRSA assay-positive broths, the results for 103 could not be confirmed by culture. A methicillin-susceptible
S. aureus
(MSSA) isolate was recovered from 77 of these 103 broths. Repeat testing by the IDI-MRSA assay directly with the MSSA isolates confirmed the original positive PCR result. The positive predictive value of the IDI-MRSA assay fell from 90% during the evaluation phase to 65% postimplementation. The IDI-MRSA assay performed well for the detection of MRSA from a selective broth compared to the performance of the detection of MRSA from culture. However, because of the burden associated with implementation of infection control precautions, cultures remain essential in confirming positive IDI-MRSA results.
Sequence Variation in the T-Cell Epitopes of thePlasmodium falciparumCircumsporozoite Protein among Field Isolates Is Temporally Stable: a 5-Year Longitudinal Study in Southern Vietnam
Authors: Jalloh Amadu , van Thien Huynh , Ferreira Marcelo U. , Ohashi Jun , Matsuoka Hiroyuki , Kanbe Toshio , Kikuchi Akihiko , Kawamoto Fumihiko 
Published: April 2006

ABSTRACTIn an effort to decipher the nature and extent of antigen polymorphisms of malaria parasites in a setting where malaria is hypomesoendemic, we conducted a 5-year longitudinal study (1998 to 2003) by sequencing the Th2R and Th3R epitopes of the circumsporozoite protein (CSP) of 142Plasmodium falciparumfield isolates from Bao Loc, Vietnam. Samples were collected during the high-transmission season, September through December 1998 (n =43), as well as from July 2000 to August 2001 (n= 34), September 2001 to July 2002 (n = 33), and August 2002 to July 2003 (n =32). Marked sequence diversity was noted during the high-transmission season in 1998, but no significant variation in allele frequencies was observed over the years (χ2 = 70.003, degrees of freedom = 57,P= 0.116). The apparent temporal stability in allele frequency observed in this Bao Loc malaria setting may suggest that polymorphism in the Th2R and Th3R epitopes is not maintained by frequency-dependent immune selection. By including 36 isolates from Flores Island, Indonesia, and 19 isolates from Thaton, Myanmar, we investigated geographical patterns of sequence polymorphism for these epitopes in Southeast Asia; among the characterized isolates, a globally distributed variant appears to be predominant in Vietnam (75 of 142 isolates, or 52.8%) as well as in Myanmar (15 of 19 isolates, or 78.9%) and Indonesia (31 of 36 isolates, or 86.1%). Further analyses involving worldwide CSP sequences revealed distinct regional patterns, a finding which, together with the unique mutations observed here, may suggest a possible role for host or local factors in the generation of sequence diversity in the T-cell epitopes of CSP.