bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Velocity Profiles for Different Flow Chamber Designs Used in Studies of Microbial Adhesion to Surfaces
Authors: Bakker D. P. , van der Plaats A. , Verkerke G. J. , Busscher H. J. , van der Mei H. C. 
Published: October 2003

ABSTRACT

Flow chambers are commonly used to study microbial adhesion to surfaces under environmentally relevant hydrodynamic conditions. The parallel plate flow chamber (PPFC) is the most common design, and mass transport occurs through slow convective diffusion. In this study, we analyzed four different PPFCs to determine whether the expected hydrodynamic conditions, which control both mass transport and detachment forces, are actually achieved. Furthermore, the different PPFCs were critically evaluated based on the size of the area where the velocity profile was established and constant with a range of flow rates, indicating that valid observations could be made. Velocity profiles in the different chambers were calculated by using a numerical simulation model based on the finite element method and were found to coincide with the profiles measured by particle image velocimetry. Environmentally relevant shear rates between 0 and 10,000 s
−1
could be measured over a sizeable proportion of the substratum surface for only two of the four PPFCs. Two models appeared to be flawed in the design of their inlets and outlets and allowed development of a stable velocity profile only for shear rates up to 0.5 and 500 s
−1
. For these PPFCs the inlet and outlet were curved, and the modeled shear rates deviated from the calculated shear rates by up to 75%. We concluded that PPFCs used for studies of microbial adhesion to surfaces should be designed so that their inlets and outlets are in line with the flow channel. Alternatively, the channel length should be increased to allow a greater length for the establishment of the desired hydrodynamic conditions.
Single-Cell Enumeration of an Uncultivated TM7 Subgroup in the Human Subgingival Crevice
Authors: Ouverney Cleber C. , Armitage Gary C. , Relman David A. 
Published: October 2003

ABSTRACT
Specific oligonucleotide hybridization conditions were established for single-cell enumeration of uncultivated TM7 and IO25 bacteria by using clones expressing heterologous 16S rRNA. In situ analysis of human subgingival crevice specimens revealed that a greater proportion of samples from sites of chronic periodontitis than from healthy sites contained TM7 subgroup IO25. In addition, IO25 bacterial cells from periodontitis site samples were more abundant and fourfold longer than IO25 cells from healthy site samples.
Application of Host-Specific Bacteriophages to the Surface of Chicken Skin Leads to a Reduction in Recovery of
Campylobacter jejuni
Authors: Atterbury Robert J. , Connerton Phillippa L. , Dodd Christine E. R. , Rees Catherine E. D. , Connerton Ian F. 
Published: October 2003

ABSTRACT

Retail poultry products are widely purported as the major infection vehicle for human campylobacteriosis. Numerous intervention strategies have sought to reduce
Campylobacter
contamination on broiler carcasses in the abattoir. This study reports the efficacy of bacteriophage in reducing the number of recoverable
Campylobacter jejuni
cells on artificially contaminated chicken skin.
Petroleum Pollution Bioremediation Using Water-Insoluble Uric Acid as the Nitrogen Source
Authors: Koren Omry , Knezevic Vishnia , Ron Eliora Z. , Rosenberg Eugene 
Published: October 2003

ABSTRACT
The biodegradation of hydrocarbon pollutants in open systems is limited by the availability of a utilizable nitrogen source. This limitation can be overcome by using uric acid. Enrichment cultures grown on crude oil-uric acid media yielded mixed and pure cultures that degraded petroleum. In a simulated open system, uric acid bound to crude oil and was available for bacterial growth and petroleum biodegradation.
DpiA Binding to the Replication Origin ofEscherichia coliPlasmids and Chromosomes Destabilizes Plasmid Inheritance and Induces the Bacterial SOS Response
Authors: Miller Christine , Ingmer Hanne , Thomsen Line Elnif , Skarstad Kirsten , Cohen Stanley N. 
Published: October 2003

ABSTRACTThedpiAanddpiBgenes ofEscherichia coli, which are orthologs of genes that regulate citrate uptake and utilization inKlebsiella pneumoniae, comprise a two-component signal transduction system that can modulate the replication of and destabilize the inheritance of pSC101 and certain other plasmids. Here we show that perturbed replication and inheritance result from binding of the effector protein DpiA to A+T-rich replication origin sequences that resemble those in theK. pneumoniaepromoter region targeted by the DpiA ortholog, CitB. Consistent with its ability to bind to A+T-rich origin sequences, overproduction of DpiA induced the SOS response inE. coli, suggesting that chromosomal DNA replication is affected. Bacteria that overexpressed DpiA showed an increased amount of DNA per cell and increased cell size—both also characteristic of the SOS response. Concurrent overexpression of the DNA replication initiation protein, DnaA, or the DNA helicase, DnaB—both of which act at A+T-rich replication origin sequences in theE. colichromosome and DpiA-targeted plasmids—reversed SOS induction as well as plasmid destabilization by DpiA. Our finding that physical and functional interactions between DpiA and sites of replication initiation modulate DNA replication and plasmid inheritance suggests a mechanism by which environmental stimuli transmitted by these gene products can regulate chromosomal and plasmid dynamics.
Spontaneously Arising
mutL
Mutators in Evolving
Escherichia coli
Populations Are the Result of Changes in Repeat Length
Authors: Shaver Aaron C. , Sniegowski Paul D. 
Published: October 2003

ABSTRACT

Over the course of thousands of generations of growth in a glucose-limited environment, 3 of 12 experimental populations of
Escherichia coli
spontaneously and independently evolved greatly increased mutation rates. In two of the populations, the mutations responsible for this increased mutation rate lie in the same region of the mismatch repair gene
mutL
. In this region, a 6-bp repeat is present in three copies in the gene of the wild-type ancestor of the experimental populations but is present in four copies in one of the experimental populations and two copies in the other. These in-frame mutations either add or delete the amino acid sequence LA in the MutL protein. We determined that the replacement of the wild-type sequence with either of these mutations was sufficient to increase the mutation rate of the wild-type strain to a level comparable to that of the mutator strains. Complementation of strains bearing the mutator mutations with wild-type copies of either
mutL
or the mismatch repair gene
uvrD
rescued the wild-type mutation rate. The position of the mutator mutations—in the region of MutL known as the ATP lid—suggests a possible deficiency in MutL's ATPase activity as the cause of the mutator phenotype. The similarity of the two mutator mutations (despite the independent evolutionary histories of the populations that gave rise to them) leads to a discussion of the potential adaptive role of DNA repeats.
Effects of Carboxy-Terminal Modifications and pH on Binding of a
Bacillus subtilis
Small, Acid-Soluble Spore Protein to DNA
Authors: Kosman Jeffrey , Setlow Peter 
Published: October 2003

ABSTRACT

Variants of the wild-type
Bacillus subtilis
α/β-type small, acid-soluble spore protein (SASP) SspC
wt
were designed to evaluate the contribution of C-terminal residues to these proteins' affinity for DNA. SspC variants lacking one to three C-terminal residues were similar to SspC
wt
in DNA binding, but removal of six C-terminal residues greatly decreased DNA binding. In contrast, a C-terminal extension of three residues increased SspC's affinity for DNA 5- to 10-fold. C-terminal and N-terminal changes that independently caused large increases in SspC-DNA binding affinity were combined and produced an additive effect on DNA binding; the affinity of the resulting variant, SspC
ΔN11-D13K-C3
, for DNA was increased ≥20-fold over that of SspC
wt
. For most of the SspC variants tested, lowering the pH from 7 to 6 improved DNA binding two- to sixfold, although the opposite effect was observed with variants having additional C-terminal basic residues. In vitro, the binding of SspC
ΔN11-D13K-C3
to DNA suppressed the formation of cyclobutane-type thymine dimers and promoted the formation of the spore photoproduct upon UV irradiation to the same degree as the binding of SspC
wt
. However,
B. subtilis
spores lacking major α/β-type SASP and overexpressing SspC
ΔN11-D13K-C3
had a 10-fold-lower viability and far less UV and heat resistance than spores overexpressing SspC
wt
. This apparent lack of DNA protection by SspC
ΔN11-D13K-C3
in vivo is likely due to the twofold-lower level of this protein in spores compared to the level of SspC
wt
, perhaps because of effects of SspC
ΔN11-D13K-C3
on gene expression in the forespore during sporulation. The latter results indicate that only moderately strong binding of α/β-type SASP to DNA is important to balance the potentially conflicting requirements for these proteins in DNA transcription and DNA protection during spore formation, spore dormancy, and spore germination and outgrowth.
Analysis of the Mobilization Region of the Broad-Host-Range IncQ-Like Plasmid pTC-F14 and Its Ability To Interact with a Related Plasmid, pTF-FC2
Authors: van Zyl Leonardo J. , Deane Shelly M. , Rawlings Douglas E. 
Published: October 2003

ABSTRACT

Plasmid pTC-F14 is a 14.2-kb plasmid isolated from
Acidithiobacillus caldus
that has a replicon that is closely related to the promiscuous, broad-host-range IncQ family of plasmids. The region containing the mobilization genes was sequenced and encoded five Mob proteins that were related to those of the DNA processing (Dtr or Tra1) region of IncP plasmids rather than to the three-Mob-protein system of the IncQ group 1 plasmids (e.g., plasmid RSF1010 or R1162). Plasmid pTC-F14 is the second example of an IncQ family plasmid that has five
mob
genes, the other being pTF-FC2. The minimal region that was essential for mobilization included the
mobA
,
mobB
, and
mobC
genes, as well as the
oriT
gene. The
mobD
and
mobE
genes were nonessential, but together, they enhanced the mobilization frequency by approximately 300-fold. Mobilization of pTC-F14 between
Escherichia coli
strains by a chromosomally integrated RP4 plasmid was more than 3,500-fold less efficient than the mobilization of pTF-FC2. When both plasmids were coresident in the same
E. coli
host, pTC-F14 was mobilized at almost the same frequency as pTF-FC2. This enhanced pTC-F14 mobilization frequency was due to the presence of a combination of the pTF-FC2
mobD
and
mobE
gene products, the functions of which are still unknown. Mob protein interaction at the
oriT
regions was unidirectionally plasmid specific in that a plasmid with the
oriT
region of pTC-F14 could be mobilized by pTF-FC2 but not vice versa. No evidence for any negative effect on the transfer of one plasmid by the related, potentially competitive plasmid was obtained.
Changes in the Concentrations of Guanosine 5′-Diphosphate 3′-Diphosphate and the Initiating Nucleoside Triphosphate Account for Inhibition of rRNA Transcription in Fructose-1,6-Diphosphate Aldolase (
fda
) Mutants
Authors: Schneider David A. , Gourse Richard L. 
Published: October 2003

ABSTRACT

Early screens for conditional lethal mutations that affected rRNA expression in
Escherichia coli
identified temperature-sensitive
fda
mutants (
fda
encodes the glycolytic enzyme fructose-1,6-diphosphate aldolase). It was shown that these
fda
(Ts) mutants were severely impaired in rRNA synthesis upon shift to the restrictive temperature, although the mechanism of inhibition was never determined. Here, we bring resolution to this long-standing question by showing that changes in the concentrations of guanosine 5′-diphosphate 3′-diphosphate and initiating nucleoside triphosphates can account for the previously observed effects of
fda
mutations on rRNA transcription.
Mutations Affecting DNA-Binding Activity of the MexR Repressor ofmexR-mexA-mexB-oprMOperon Expression
Authors: Saito Kohjiro , Akama Hiroyuki , Yoshihara Eisaku , Nakae Taiji 
Published: October 2003

ABSTRACTWe have isolated 25 MexR mutants that retained their dimerizing ability but were unable to bindmexOPDNA. Surprisingly, 20 mutations were located in the hydrophobic core region at α4, W1, α2, α3, and β2, and only 3 were in positively charged residues. These results verified that DNA binding is mediated by distinct regions of MexR and showed the importance of the hydrophobic core region of the DNA-binding domain.
The SKHR Motif Is Required for Biological Function of the VirR Response Regulator from
Clostridium perfringens
Authors: McGowan Sheena , O'Connor Jennifer R. , Cheung Jackie K. , Rood Julian I. 
Published: October 2003

ABSTRACT

The response regulator VirR and its cognate sensor histidine kinase, VirS, are responsible for toxin gene regulation in the human pathogen
Clostridium perfringens
. The C-terminal domain of VirR (VirRc) contains the functional FxRxHrS motif, which is involved in DNA binding and is conserved in many regulatory proteins. VirRc was cloned, purified, and shown by in vivo and in vitro studies to comprise an independent DNA binding domain. Random and site-directed mutagenesis was used to identify further amino acids that were required for the functional integrity of the protein. Random mutagenesis identified a unique residue, Met-172, that was required for biological function. Site-directed mutagenesis of the SKHR motif (amino acids 216 to 219) revealed that these residues were also required for biological activity. Analysis of the mutated proteins indicated that they were unable to bind to the DNA target with the same efficiency as the wild-type protein.
Nucleotide-Dependent Conformational Changes in the σ54-Dependent Activator DctD
Authors: Wang Ying-Kai , Park Sungdae , Nixon B. Tracy , Hoover Timothy R. 
Published: October 2003

ABSTRACTActivators of σ54-RNA polymerase holoenzyme couple ATP hydrolysis to formation of an open promoter complex. DctDΔ1-142, a truncated and constitutively active form of the σ54-dependent activator DctD fromSinorhizobium meliloti, displayed an altered DNase I footprint at its binding site located upstream of thedctApromoter in the presence of ATP. The altered footprint was not observed for a mutant protein with a substitution at or near the putative arginine finger, a conserved arginine residue thought to contact the nucleotide. These data suggest that structural changes in DctDΔ1-142during ATP hydrolysis can be detected by alterations in the DNase I footprint of the protein and may be communicated by interactions between bound nucleotide and the arginine finger. In addition, kinetic data for changes in fluorescence energy transfer upon binding of 2′(3′)-O-(N-methylanthraniloyl)-ATP (Mant-ATP) to DctDΔ1-142and DctD suggested that these proteins undergo multiple conformational changes following ATP binding.
Molecular Subtyping of
Vibrio cholerae
O1 and O139 by Pulsed-Field Gel Electrophoresis in Hong Kong: Correlation with Epidemiological Events from 1994 to 2002
Authors: Kam Kai Man , Luey Cindy Kit Yee , Tsang Yee Man , Law Choi Ping , Chu Man Yu , Cheung Tze Leung , Chiu Agatha Wai Huen 
Published: October 2003

ABSTRACT

Two hundred twenty isolates of
Vibrio cholerae
O1 and O139 collected from 1994 to 2002 in Hong Kong were analyzed by pulsed-field gel electrophoresis (PFGE). Chromosomal DNAs from all
V. cholerae
isolates in agarose plugs were digested with the restriction enzyme
Not
I, resulting in 20 to 27 bands. Sixty distinctive PFGE patterns in the range of 10 to 300 kb were noted among 213 isolates typeable by PFGE. By comparing the common PFGE patterns obtained from four well-defined outbreaks of
V. cholerae
O1 and O139 with those obtained from other, epidemiologically unrelated isolates during the study period, indistinguishable and similar PFGE patterns were identified, indicating their close relatedness, in agreement with the results of epidemiological investigations. Heterogeneous PFGE patterns (with four to six banding differences), however, were identified among strains that were imported from other parts of Asia, including Indonesia, India, and Pakistan. Correlations with epidemiological information further support the usefulness of PFGE as an epidemiological tool in laboratory investigations of suspected outbreaks. Standardization of PFGE methodology will allow international comparison of fingerprint patterns and will form the basis of a laboratory network for tracking
V. cholerae
.
Evaluation of Reverse Transcription-PCR Assays for Rapid Diagnosis of Severe Acute Respiratory Syndrome Associated with a Novel Coronavirus
Authors: Yam W. C. , Chan K. H. , Poon L. L. M. , Guan Y. , Yuen K. Y. , Seto W. H. , Peiris J. S. M. 
Published: October 2003

ABSTRACT
The reverse transcription (RT)-PCR protocols of two World Health Organization (WHO) severe acute respiratory syndrome (SARS) network laboratories (WHO SARS network laboratories at The University of Hong Kong [WHO-HKU] and at the Bernhard-Nocht Institute in Hamburg, Germany [WHO-Hamburg]) were evaluated for rapid diagnosis of a novel coronavirus (CoV) associated with SARS in Hong Kong. A total of 303 clinical specimens were collected from 163 patients suspected to have SARS. The end point of both WHO-HKU and WHO-Hamburg RT-PCR assays was determined to be 0.1 50% tissue culture infective dose. Using seroconversion to CoV as the “gold standard” for SARS CoV diagnosis, WHO-HKU and WHO-Hamburg RT-PCR assays exhibited diagnostic sensitivities of 61 and 68% (nasopharyngeal aspirate specimens), 65 and 72% (throat swab specimens), 50 and 54% (urine specimens), and 58 and 63% (stool specimens), respectively, with an overall specificity of 100%. For patients confirmed to have SARS CoV and from whom two or more respiratory specimens were collected, testing the second specimen increased the sensitivity from 64 and 71% to 75 and 79% for the WHO-HKU and WHO-Hamburg RT-PCR assays, respectively. Testing more than one respiratory specimen will maximize the sensitivity of PCR assays for SARS CoV.
New Real-Time Reverse Transcriptase-Initiated PCR Assay with Single-Copy Sensitivity for Human Immunodeficiency Virus Type 1 RNA in Plasma
Authors: Palmer Sarah , Wiegand Ann P. , Maldarelli Frank , Bazmi Holly , Mican JoAnn M. , Polis Michael , Dewar Robin L. , Planta Angeline , Liu Shuying , Metcalf Julia A. , Mellors John W. , Coffin John M. 
Published: October 2003

ABSTRACT

More sensitive assays for human immunodeficiency virus type 1 (HIV-1) RNA are needed to detect, quantify, and characterize persistent viremia in patients who are receiving antiretroviral therapy and whose plasma HIV-1 RNA levels are suppressed to less than 50 to 75 copies/ml. We therefore developed an internally controlled real-time reverse transcriptase-initiated PCR assay that quantifies HIV-1 RNA concentrations down to 1 copy per ml of plasma. This assay with single-copy sensitivity (the single-copy assay) generates a reproducible linear regression plot of input copy number versus threshold cycle by using HIV-1 RNA transcripts at copy numbers ranging from 1 to 10
6
per reaction mixture. The single-copy assay was compared to the ultrasensitive AMPLICOR HIV-1 MONITOR assay and a more sensitive modification of the ultrasensitive assay by repeatedly testing a low-copy-number panel containing 200 to 0.781 copies of HIV-1 RNA per ml of plasma. This comparison showed that the single-copy assay had a greater sensitivity than the other assays and was the only assay that detected HIV-1 RNA at levels as low as 0.781 copies/ml. Testing of plasma samples from 15 patients who were receiving antiretroviral therapy and who had <75 HIV-1 RNA copies/ml revealed persistent viremia in all 15 patients, with HIV-1 RNA levels ranging from 1 to 32 copies/ml (median, 13 copies/ml). The greater sensitivity of the single-copy assay should allow better characterization of persistent viremia in patients who are receiving antiretroviral therapy and whose HIV-1 RNA levels are suppressed to below the detection limits of present assays.
Madurella mycetomatisStrains from Mycetoma Lesions in Sudanese Patients Are Clonal
Authors: Ahmed Abdalla , van de Sande Wendy , Verbrugh Henri , Fahal Ahmed , van Belkum Alex 
Published: October 2003

ABSTRACTMolecular diversity among clinical isolates ofMadurella mycetomatis, the prime fungal agent of human mycetoma in Sudan, could possibly explain the diverse clinical presentations of this severely debilitating infectious disease. In addition, culture-independent DNA-mediated typing tests need to be developed for this organism, sinceM. mycetomatisDNA, but not the organism itself, can be identified in soil, the material from which infections are thought to originate. A collection of 38 different clinicalM. mycetomatisisolates was characterized by large-scale random amplification of polymorphic DNA using 20 different primer species. These analyses, involving at least 2,600 annealing sites, showed a complete lack of DNA fingerprint variation among the various isolates. From the resulting homogeneous DNA fingerprints, seven fragments were cloned and sequenced, and novel, species-specific PCR restriction fragment length polymorphism (RFLP) tests were designed. The seven PCR RFLP tests were successfully performed on the 38 differentM. mycetomatisstrains. However, again allM. mycetomatisDNA patterns obtained appeared to be identical, whereas patterns produced using DNAs from other fungal species were clearly discriminatory. These results suggest that there is little genetic variation among clinically relevantM. mycetomatisstrains from Sudan. The data tentatively imply that different manifestations of mycetoma are due to differences in host susceptibility rather than differential virulence of the causative agent.
Clonal Characterization of
Staphylococcus aureus
by Multilocus Restriction Fragment Typing, a Rapid Screening Approach for Molecular Epidemiology
Authors: Diep Binh An , Perdreau-Remington Françoise , Sensabaugh George F. 
Published: October 2003

ABSTRACT

We have developed a rapid and simplified approach for the strain characterization of
Staphylococcus aureus
on the basis of multilocus sequence typing (MLST) in which sequence variations in the MLST housekeeping gene loci are detected by restriction fragment pattern analysis rather than sequencing; we refer to this approach as multilocus restriction fragment typing (MLRFT). Briefly, MLRFT for
S. aureus
involves the PCR amplification of each of the seven MLST housekeeping gene loci by using the same primer pairs used in MLST. The amplicons are then digested directly with one or two restriction enzymes and the restriction fragments are resolved by agarose gel electrophoresis. Projection from published MLST data shows that MLRFT captures about 95% of the genetic diversity detected by MLST. The MLRFT approach was validated with a set of 59 methicillin-susceptible and 44 methicillin-resistant
S. aureus
isolates from community-acquired and nosocomial sources which had previously been characterized by pulsed-field gel electrophoresis (PFGE). MLRFT resolved the 103 isolates into 15 restriction fragment types, giving a discrimination index of 89.0%. Clonal groupings established by MLRFT correlated well with those established by PFGE. In short, MLRFT provides a convenient alternative to MLST and PFGE because it requires minimal laboratory facilities and is relatively simple and inexpensive to perform.