bluuebunny/crossref_metadata_2025_split huggingface dataset:
3D Mechanical Properties of the Layered Esophagus: Experiment and Constitutive Model
Authors: Yang W. , Fung T. C. , Chian K. S. , Chong C. K. 
Published: December 2006

Abstract
The identification of a three dimensional constitutive model is useful for describing the complex mechanical behavior of a nonlinear and anisotropic biological tissue such as the esophagus. The inflation tests at the fixed axial extension of 1, 1.125, and 1.25 were conducted on the muscle and mucosa layer of a porcine esophagus separately and the pressure-radius-axial force was recorded. The experimental data were fitted with the constitutive model to obtain the structure-related parameters, including the collagen amount and fiber orientation. Results showed that a bilinear strain energy function (SEF) with four parameters could fit the inflation data at an individual extension very well while a six-parameter model had to be used to capture the inflation behaviors at all three extensions simultaneously. It was found that the collagen distribution was axial preferred in both layers and the mucosa contained more collagen, which were in agreement with the findings through a pair of uniaxial tensile test in our previous study. The model was expected to be used for the prediction of stress distribution within the esophageal wall under the physiological state and provide some useful information in the clinical studies of the esophageal diseases.
Randomized Controlled Comparison of Ofloxacin, Azithromycin, and an Ofloxacin-Azithromycin Combination for Treatment of Multidrug-Resistant and Nalidixic Acid-Resistant Typhoid Fever
Authors: Parry Christopher M. , Ho Vo Anh , Phuong Le Thi , Bay Phan Van Be , Lanh Mai Ngoc , Tung Le Thanh , Tham Nguyen Thi Hong , Wain John , Hien Tran Tinh , Farrar Jeremy J. 
Published: December 2006

ABSTRACT

Isolates of
Salmonella enterica
serovar Typhi that are multidrug resistant (MDR, resistant to chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole) and have reduced susceptibility to fluoroquinolones (nalidixic acid resistant, Na
r
) are common in Asia. The optimum treatment for infections caused by such isolates is not established. This study compared different antimicrobial regimens for the treatment of MDR/Na
r
typhoid fever. Vietnamese children and adults with uncomplicated typhoid fever were entered into an open randomized controlled trial. Ofloxacin (20 mg/kg of body weight/day for 7 days), azithromycin (10 mg/kg/day for 7 days), and ofloxacin (15 mg/kg/day for 7 days) combined with azithromycin (10 mg/kg/day for the first 3 days) were compared. Of the 241 enrolled patients, 187 were eligible for analysis (186
S. enterica
serovar Typhi, 1
Salmonella enterica
serovar Paratyphi A). Eighty-seven percent (163/187) of the patients were children; of the
S. enterica
serovar Typhi isolates, 88% (165/187) were MDR and 93% (173/187) were Na
r
. The clinical cure rate was 64% (40/63) with ofloxacin, 76% (47/62) with ofloxacin-azithromycin, and 82% (51/62) with azithromycin (
P
= 0.053). The mean (95% confidence interval [CI]) fever clearance time for patients treated with azithromycin (5.8 days [5.1 to 6.5 days]) was shorter than that for patients treated with ofloxacin-azithromycin (7.1 days [6.2 to 8.1 days]) and ofloxacin (8.2 days [7.2 to 9.2 days]) (
P
< 0.001). Positive fecal carriage immediately posttreatment was detected in 19.4% (12/62) of patients treated with ofloxacin, 6.5% (4/62) of those treated with the combination, and 1.6% (1/62) of those treated with azithromycin (
P
= 0.006). Both antibiotics were well tolerated. Uncomplicated typhoid fever due to isolates of MDR
S. enterica
serovar Typhi with reduced susceptibility to fluoroquinolones (Na
r
) can be successfully treated with a 7-day course of azithromycin.
Involvement of Pyruvate Oxidase Activity and Acetate Production in the Survival of
Lactobacillus plantarum
during the Stationary Phase of Aerobic Growth
Authors: Goffin Philippe , Muscariello Lidia , Lorquet Frederique , Stukkens Aline , Prozzi Deborah , Sacco Margherita , Kleerebezem Michiel , Hols Pascal 
Published: December 2006

ABSTRACT

In addition to the previously characterized pyruvate oxidase PoxB, the
Lactobacillus plantarum
genome encodes four predicted pyruvate oxidases (PoxC, PoxD, PoxE, and PoxF). Each pyruvate oxidase gene was individually inactivated, and only the knockout of
poxF
resulted in a decrease in pyruvate oxidase activity under the tested conditions. We show here that
L. plantarum
has two major pyruvate oxidases: PoxB and PoxF. Both are involved in lactate-to-acetate conversion in the early stationary phase of aerobic growth and are regulated by carbon catabolite repression. A strain devoid of pyruvate oxidase activity was constructed by knocking out the
poxB
and
poxF
genes. In this mutant, acetate production was strongly affected, with lactate remaining the major end product of either glucose or maltose fermentation. Notably, survival during the stationary phase appeared to be dramatically improved in the
poxB poxF
double mutant.
New Rapid and Simple Methods for Detection of Bacteria and Determination of Their Antibiotic Susceptibility by Using Phage Mutants
Authors: Ulitzur Nirit , Ulitzur Shimon 
Published: December 2006

ABSTRACTThree new methods applying a novel approach for rapid and simple detection of specific bacteria, based on plaque formation as the end point of the phage lytic cycle, are described. Different procedures were designed to ensure that the resulting plaques were derived only from infected target bacteria (“infectious centers”). (i) A pair of amber mutants that cannot form plaques at concentrations lower than their reversion rate underwent complementation in the tested bacteria; the number of plaques formed was proportional to the concentration of the bacteria that were coinfected by these phage mutants. (ii) UV-irradiated phages were recovered by photoreactivation and/or SOS repair mediated by target bacteria and plated on arecA uvrAbacterial lawn in the dark to avoid recovery of noninfecting phages. (iii) Pairs of temperature-sensitive mutants were allowed to coinfect their target bacteria at the permissive temperature, followed by incubation of the plates at the restrictive temperature to avoid phage infection of the host cells. This method allowed the omission of centrifuging and washing the infected cells. Only phages that recovered by recombination or complementation were able to form plaques. The detection limit was 1 to 10 livingSalmonellaorEscherichia coliO157 cells after 3 to 5 h. The antibiotic susceptibility of the target bacteria could also be determined in each of these procedures by preincubating the target bacteria with antibiotic prior to phage infection. Bacteria sensitive to the antibiotic lost the ability to form infectious centers.
Sequence Analysis of the
rfb
Loci, Encoding Proteins Involved in the Biosynthesis of the
Salmonella enterica
O17 and O18 Antigens: Serogroup-Specific Identification by PCR
Authors: Fitzgerald Collette , Gheesling Linda , Collins Marcus , Fields Patricia I. 
Published: December 2006

ABSTRACT

We report sequencing of the O antigen encoded by the
rfb
gene cluster of
Salmonella enterica
serotype Jangwani (O17) and
Salmonella
serotype Cerro (O18). We developed serogroup O17- and O18-specific PCR assays based on
rfb
gene targets and found them to be sensitive and specific for rapid identification of
Salmonella
serogroups O17 and O18.
Antimicrobial Use and Resistance in Swine Waste Treatment Systems
Authors: Jindal Archana , Kocherginskaya Svetlana , Mehboob Asma , Robert Matthew , Mackie Roderick I. , Raskin Lutgarde , Zilles Julie L. 
Published: December 2006

ABSTRACT

Chlortetracycline and the macrolide tylosin were identified as commonly used antimicrobials for growth promotion and prophylaxis in swine production. Resistance to these antimicrobials was measured throughout the waste treatment processes at five swine farms by culture-based and molecular methods. Conventional farm samples had the highest levels of resistance with both culture-based and molecular methods and had similar levels of resistance despite differences in antimicrobial usage. The levels of resistance in organic farm samples, where no antimicrobials were used, were very low by a culture-based method targeting fecal streptococci. However, when the same samples were analyzed with a molecular method detecting methylation of a specific nucleotide in the 23S rRNA that results in resistance to macrolides, lincosamides, and streptogramin B (MLS
B
), an unexpectedly high level of resistant rRNA (approximately 50%) was observed, suggesting that the fecal streptococci were not an appropriate target group to evaluate resistance in the overall microbial community and that background levels of MLS
B
resistance may be substantial. All of the feed samples tested, including those from the organic farm, contained tetracycline resistance genes. Generally, the same tetracycline resistance genes and frequency of detection were found in the manure and lagoon samples for each commercial farm. The levels of tetracycline and MLS
B
resistance remained high throughout the waste treatment systems, suggesting that the potential impact of land application of treated wastes and waste treatment by-products on environmental levels of resistance should be investigated further.
Isolation of Two Polyketide Synthase Gene Fragments from the Uncultured Microbial Symbiont of the Marine Bryozoan
Bugula neritina
Authors: Lopanik Nicole B. , Targett Nancy M. , Lindquist Niels 
Published: December 2006

ABSTRACT

“
Candidatus
Endobugula sertula,” the uncultured microbial symbiont of the bryozoan
Bugula neritina
, produces ecologically and biomedically important polyketide metabolites called bryostatins. We isolated two gene fragments from
B. neritina
larvae that have high levels of similarity to polyketide synthase genes. These gene fragments are clearly associated with the symbiont and not with the host.
Diverse Responses to UV-B Radiation and Repair Mechanisms of Bacteria Isolated from High-Altitude Aquatic Environments
Authors: Fernández Zenoff V. , Siñeriz F. , Farías M. E. 
Published: December 2006

ABSTRACT

Acinetobacter johnsonii
A2 isolated from the natural community of Laguna Azul (Andean Mountains at 4,560 m above sea level),
Serratia marcescens
MF42,
Pseudomonas
sp. strain MF8 isolated from the planktonic community, and
Cytophaga
sp. strain MF7 isolated from the benthic community from Laguna Pozuelos (Andean Puna at 3,600 m above sea level) were subjected to UV-B (3,931 J m
−2
) irradiation. In addition, a marine
Pseudomonas putida
strain, 2IDINH, and a second
Acinetobacter johnsonii
strain, ATCC 17909, were used as external controls. Resistance to UV-B and kinetic rates of light-dependent (UV-A [315 to 400 nm] and cool white light [400 to 700 nm]) and -independent reactivation following exposure were determined by measuring the survival (expressed as CFU) and accumulation of cyclobutane pyrimidine dimers (CPD). Significant differences in survival after UV-B irradiation were observed:
Acinetobacter johnsonii
A2, 48%;
Acinetobacter johnsonii
ATCC 17909, 20%;
Pseudomonas
sp. strain MF8, 40%; marine
Pseudomonas putida
strain 2IDINH, 12%;
Cytophaga
sp. strain MF7, 20%; and
Serratia marcescens
, 21%. Most bacteria exhibited little DNA damage (between 40 and 80 CPD/Mb), except for the benthic isolate
Cytophaga
sp. strain MF7 (400 CPD/Mb) and
Acinetobacter johnsonii
ATCC 17909 (160 CPD/Mb). The recovery strategies through dark and light repair were different in all strains. The most efficient in recovering were both
Acinetobacter johnsonii
A2 and
Cytophaga
sp. strain MF7;
Serratia marcescens
MF42 showed intermediate recovery, and in both
Pseudomonas
strains, recovery was essentially zero. The UV-B responses and recovery abilities of the different bacteria were consistent with the irradiation levels in their native environment.
Change in Substrate Preference ofStreptomycesAminopeptidase through Modification of the Environment around the Substrate Binding Site
Authors: Arima Jiro , Uesugi Yoshiko , Iwabuchi Masaki , Hatanaka Tadashi 
Published: December 2006

ABSTRACTWe attempted to alter the substrate preference of aminopeptidase fromStreptomyces septatusTH-2 (SSAP). Because Asp198 and Phe221 of SSAP are located in the substrate binding site, we screened 2,000 mutant enzymes with D198X/F221X mutations. By carrying out this examination, we obtained two enzymes; one specifically hydrolyzed an arginyl derivative, and the other specifically hydrolyzed a cystinyl derivative (65- and 12.5-fold higherkcatvalues for hydrolysis ofp-nitroanilide derivatives than those of the wild type, respectively).
Community Structure Analyses Are More Sensitive to Differences in Soil Bacterial Communities than Anonymous Diversity Indices
Authors: Hartmann Martin , Widmer Franco 
Published: December 2006

ABSTRACT
Changes in the diversity and structure of soil microbial communities may offer a key to understanding the impact of environmental factors on soil quality in agriculturally managed systems. Twenty-five years of biodynamic, bio-organic, or conventional management in the DOK long-term experiment in Switzerland significantly altered soil bacterial community structures, as assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis. To evaluate these results, the relation between bacterial diversity and bacterial community structures and their discrimination potential were investigated by sequence and T-RFLP analyses of 1,904 bacterial 16S rRNA gene clones derived from the DOK soils. Standard anonymous diversity indices such as Shannon, Chao1, and ACE or rarefaction analysis did not allow detection of management-dependent influences on the soil bacterial community. Bacterial community structures determined by sequence and T-RFLP analyses of the three gene libraries substantiated changes previously observed by soil bacterial community level T-RFLP profiling. This supported the value of high-throughput monitoring tools such as T-RFLP analysis for assessment of differences in soil microbial communities. The gene library approach also allowed identification of potential management-specific indicator taxa, which were derived from nine different bacterial phyla. These results clearly demonstrate the advantages of community structure analyses over those based on anonymous diversity indices when analyzing complex soil microbial communities.
Reconstitution of the Myxothiazol Biosynthetic Gene Cluster by Red/ET Recombination and Heterologous Expression in
Myxococcus xanthus
Authors: Perlova Olena , Fu Jun , Kuhlmann Silvia , Krug Daniel , Stewart A. Francis , Zhang Youming , Müller Rolf 
Published: December 2006

ABSTRACT

Although many secondary metabolites exhibiting important pharmaceutical and agrochemical activities have been isolated from myxobacteria, most of these microorganisms remain difficult to handle genetically. To utilize their metabolic potential, heterologous expression methodologies are currently being developed. Here, the Red/ET recombination technology was used to perform all required gene cluster engineering steps in
Escherichia coli
prior to the transfer into the chromosome of the heterologous host. We describe the integration of the complete 57-kbp myxothiazol biosynthetic gene cluster reconstituted from two cosmids from a cosmid library of the myxobacterium
Stigmatella aurantiaca
DW4-3/1 into the chromosome of the thus far best-characterized myxobacterium,
Myxococcus xanthus
, in one step. The successful integration and expression of the myxothiazol biosynthetic genes in
M. xanthus
results in the production of myxothiazol in yields comparable to the natural producer strain.
Synergistic Inhibition of Microbial Sulfide Production by Combinations of the Metabolic Inhibitor Nitrite and Biocides
Authors: Greene E. Anne , Brunelle Veronique , Jenneman Gary E. , Voordouw Gerrit 
Published: December 2006

ABSTRACT
MICs of six broad-spectrum biocides and two specific metabolic inhibitors and fractional inhibitory concentration indexes (FICIs) for controlling a sulfide-producing consortium were determined. Nitrite was synergistic (FICI < 1) with all but one biocide due to its specific inhibition of dissimilatory sulfite reductase. Hence, combining nitrite with biocides allows more efficient and cost-effective control of sulfate-reducing bacteria.
Studies of the Extracellular Glycocalyx of the Anaerobic Cellulolytic Bacterium
Ruminococcus albus
7
Authors: Weimer Paul J. , Price Neil P. J. , Kroukamp Otini , Joubert Lydia-Marie , Wolfaardt Gideon M. , Van Zyl Willem H. 
Published: December 2006

ABSTRACT

Anaerobic cellulolytic bacteria are thought to adhere to cellulose via several mechanisms, including production of a glycocalyx containing extracellular polymeric substances (EPS). As the compositions and structures of these glycocalyces have not been elucidated, variable-pressure scanning electron microscopy (VP-SEM) and chemical analysis were used to characterize the glycocalyx of the ruminal bacterium
Ruminococcus albus
strain 7. VP-SEM revealed that growth of this strain was accompanied by the formation of thin cellular extensions that allowed the bacterium to adhere to cellulose, followed by formation of a ramifying network that interconnected individual cells to one another and to the unraveling cellulose microfibrils. Extraction of 48-h-old whole-culture pellets (bacterial cells plus glycocalyx [G] plus residual cellulose [C]) with 0.1 N NaOH released carbohydrate and protein in a ratio of 1:5. Boiling of the cellulose fermentation residue in a neutral detergent solution removed almost all of the adherent cells and protein while retaining a residual network of adhering noncellular material. Trifluoroacetic acid hydrolysis of this residue (G plus C) released primarily glucose, along with substantial amounts of xylose and mannose, but only traces of galactose, the most abundant sugar in most characterized bacterial exopolysaccharides. Linkage analysis and characterization by nuclear magnetic resonance suggested that most of the glucosyl units were not present as partially degraded cellulose. Calculations suggested that the energy demand for synthesis of the nonprotein fraction of EPS by this organism represents only a small fraction (<4%) of the anabolic ATP expenditure of the bacterium.
Bestowing Inducibility on the Cloned Methanol Dehydrogenase Promoter (P

mxaF

) of
Methylobacterium extorquens
by Applying Regulatory Elements of
Pseudomonas putida
F1
Authors: Choi Young J. , Morel Lyne , Bourque Denis , Mullick Alaka , Massie Bernard , Míguez Carlos B. 
Published: December 2006

ABSTRACT

P

mxaF

is a strong methanol-inducible promoter in
Methylobacterium extorquens
. When this promoter is cloned in expression vectors and used to drive heterologous gene expression, methanol inducibility is either greatly reduced or entirely lost. In order to bestow inducibility upon the cloned P

mxaF

promoter in expression vectors, we adopted combinational methods (regulatory elements of the
Pseudomonas putida
F1
cym
and
cmt
operons and Tn
7
transposon system) to control reporter gene expression at the transcriptional level in
M. extorquens
. An operator fragment (26 nucleotides) of the
cmt
operon was inserted downstream of the cloned P

mxaF

promoter in the broad-host-range expression vector (pCHOI3). The repressor gene (
cymR
) located upstream of the
cym
operon in
P. putida
F1 was amplified by PCR. To avoid cellular toxicity for
M. extorquens
caused by the overexpression of CymR, single and/or double copies of
cymR
were integrated into the chromosome of
M. extorquens
using the mini-Tn
7
transposon system. Cultures containing the chromosomally integrated
cymR
gene were subsequently transformed with pCHOI3 containing modified P

mxaF

(i.e., P

mxaF

plus operator). In this construct, inducibility is afforded by cumate (
p
-isopropylbenzoate). In this report, we describe the inducible and tightly regulated expression of heterologous genes (
bgl
[for β-galactosidase],
est
[for esterase], and
gfp
[for green fluorescent protein]) in
M. extorquens
. This is the first documented example of an inducible/regulated heterologous gene expression system in
M. extorquens
.
Glycoprotein Hypersecretion Alters the Cell Wall in
Trichoderma reesei
Strains Expressing the
Saccharomyces cerevisiae
Dolichylphosphate Mannose Synthase Gene
Authors: Perlińska-Lenart Urszula , Orłowski Jacek , Laudy Agnieszka E. , Zdebska Ewa , Palamarczyk Grażyna , Kruszewska Joanna S. 
Published: December 2006

ABSTRACT

Expression of the
Saccharomyces cerevisiae DPM1
gene (coding for dolichylphosphate mannose synthase) in
Trichoderma reesei (Hypocrea jecorina
) increases the intensity of protein glycosylation and secretion and causes ultrastructural changes in the fungal cell wall. In the present work, we undertook further biochemical and morphological characterization of the
DPM1-
expressing
T. reesei
strains. We established that the carbohydrate composition of the fungal cell wall was altered with an increased amount of
N
-acetylglucosamine, suggesting an increase in chitin content. Calcofluor white staining followed by fluorescence microscopy indicated changes in chitin distribution. Moreover, we also observed a decreased concentration of mannose and alkali-soluble β-(1,6) glucan. A comparison of protein secretion from protoplasts with that from mycelia showed that the cell wall created a barrier for secretion in the
DPM1
transformants. We also discuss the relationships between the observed changes in the cell wall, increased protein glycosylation, and the greater secretory capacity of
T. reesei
strains expressing the yeast
DPM1
gene.
Destruction of Spores on Building Decontamination Residue in a Commercial Autoclave
Authors: Lemieux P. , Sieber R. , Osborne A. , Woodard A. 
Published: December 2006

ABSTRACT

The U.S. Environmental Protection Agency conducted an experiment to evaluate the effectiveness of a commercial autoclave for treating simulated building decontamination residue (BDR). The BDR was intended to simulate porous materials removed from a building deliberately contaminated with biological agents such as
Bacillus anthracis
(anthrax) in a terrorist attack. The purpose of the tests was to assess whether the standard operating procedure for a commercial autoclave provided sufficiently robust conditions to adequately destroy bacterial spores bound to the BDR. In this study we investigated the effects of several variables related to autoclaving BDR, including time, temperature, pressure, item type, moisture content, packing density, packing orientation, autoclave bag integrity, and autoclave process sequence. The test team created simulated BDR from wallboard, ceiling tiles, carpet, and upholstered furniture, and embedded in the BDR were
Geobacillus stearothermophilus
biological indicator (BI) strips containing 10
6
spores and thermocouples to obtain time and temperature profile data associated with each BI strip. The results indicated that a single standard autoclave cycle did not effectively decontaminate the BDR. Autoclave cycles consisting of 120 min at 31.5 lb/in
2
and 275°F and 75 min at 45 lb/in
2
and 292°F effectively decontaminated the BDR material. Two sequential standard autoclave cycles consisting of 40 min at 31.5 lb/in
2
and 275°F proved to be particularly effective, probably because the second cycle's evacuation step pulled the condensed water out of the pores of the materials, allowing better steam penetration. The results also indicated that the packing density and material type of the BDR in the autoclave could have a significant impact on the effectiveness of the decontamination process.