bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Balm of Gilead: Is the Provision of Treatment to Those Who Seroconvert in HIV Prevention Trials a Matter of Moral Obligation or Moral Negotiation?
Authors: Weijer Charles , LeBlanc Guy J. 
Published: November 2006

Is there no balm in Gilead; is there no physician there? Why then is not the health of the daughter of my people recovered?(Jeremiah 8:22)In July of 2004, Cambodian sex workers staged a protest of an HIV prevention trial set to enroll 900 sex workers in Phnom Penh, charging the study planners with exploitation. The Cambodian study was one of a series of international clinical trials sponsored by the U.S. National Institutes of Health (NIH), U.S. Centers for Disease Control and Prevention (CDC), and the Bill and Melinda Gates Foundation (Gates Foundation) testing the safety and efficacy of tenofovir (Viread), an antiretroviral drug produced by Gilead Sciences, Inc., to prevent HIV transmission. To date, two of these international studies have been closed and one is suspended, prompting calls for re-examination of the ethics of HIV prevention trials.
Homolactate Fermentation by Metabolically Engineered
Escherichia coli
Strains
Authors: Zhu Y. , Eiteman M. A. , DeWitt K. , Altman E. 
Published: November 2006

ABSTRACT

We report the homofermentative production of lactate in
Escherichia coli
strains containing mutations in the
aceEF
,
pfl
,
poxB
, and
pps
genes, which encode the pyruvate dehydrogenase complex, pyruvate formate lyase, pyruvate oxidase, and phosphoenolpyruvate synthase, respectively. The process uses a defined medium and two distinct fermentation phases: aerobic growth to an optical density of about 30, followed by nongrowth, anaerobic production. Strain YYC202 (
aceEF pfl poxB pps
) generated 90 g/liter lactate in 16 h during the anaerobic phase (with a yield of 0.95 g/g and a productivity of 5.6 g/liter · h). Ca(OH)
2
was found to be superior to NaOH for pH control, and interestingly, significant succinate also accumulated (over 7 g/liter) despite the use of N
2
for maintaining anaerobic conditions. Strain ALS961 (YYC202
ppc
) prevented succinate accumulation, but growth was very poor. Strain ALS974 (YYC202
frdABCD
) reduced succinate formation by 70% to less than 3 g/liter.
13
C nuclear magnetic resonance analysis using uniformly labeled acetate demonstrated that succinate formation by ALS974 was biochemically derived from acetate in the medium. The absence of uniformly labeled succinate, however, demonstrated that glyoxylate did not reenter the tricarboxylic acid cycle via oxaloacetate. By minimizing the residual acetate at the time that the production phase commenced, the process with ALS974 achieved 138 g/liter lactate (1.55 M, 97% of the carbon products), with a yield of 0.99 g/g and a productivity of 6.3 g/liter · h during the anaerobic phase.
Comparison of Primer Sets for Use in Automated Ribosomal Intergenic Spacer Analysis of Aquatic Bacterial Communities: an Ecological Perspective
Authors: Jones Stuart E. , Shade Ashley L. , McMahon Katherine D. , Kent Angela D. 
Published: November 2006

ABSTRACT
Two primer sets for automated ribosomal intergenic spacer analysis (ARISA) were used to assess the bacterial community composition (BCC) in Lake Mendota, Wisconsin, over 3 years. Correspondence analysis revealed differences in community profiles generated by different primer sets, but overall ecological patterns were conserved in each case. ARISA is a powerful tool for evaluating BCC change through space and time, regardless of the specific primer set used.
Construction of a
Vibrio splendidus
Mutant Lacking the Metalloprotease Gene
vsm
by Use of a Novel Counterselectable Suicide Vector
Authors: Le Roux Frédérique , Binesse Johan , Saulnier Denis , Mazel Didier 
Published: November 2006

ABSTRACT

Vibrio splendidus
is a dominant culturable
Vibrio
in seawater, and strains related to this species are also associated with mortality in a variety of marine animals. The determinants encoding the pathogenic properties of these strains are still poorly understood; however, the recent sequencing of the genome of
V. splendidus
LGP32, an oyster pathogen, provides an opportunity to decipher the basis of the virulence properties by disruption of candidate genes. We developed a novel suicide vector based on the
pir
-dependent R6K replicative origin, which potentially can be transferred by RP4-based conjugation to any
Vibrio
strain and which also carries the plasmid F toxin
ccdB
gene under control of the P

BAD

promoter. We demonstrated that this genetic system allows efficient counterselection of integrated plasmids in the presence of arabinose in both
V. splendidus
and
Vibrio cholerae
and thus permits efficient markerless allelic replacement in these species. We used this technique to construct several mutants of
V. splendidus
LGP32, including a derivative with a secreted metalloprotease gene,
vsm
, deleted. We found that this gene is essential for LGP32 extracellular product toxicity when the extracellular products are injected into oysters but is not necessary for virulence of bacteria in the oyster infection model when bacteria are injected.
Performance of a Commercial Immunoglobulin M Antibody Capture Assay Using Analyte-Specific Reagents To Screen for Interfering Factors during a West Nile Virus Epidemic Season in Nebraska
Authors: Sambol Anthony R. , Hinrichs Steven H. , Hogrefe Wayne R. , Schweitzer Beth K. 
Published: November 2006

ABSTRACT
In 2003, the Nebraska Public Health Laboratory tested more than 10,371 serum and 516 cerebral spinal fluid specimens. Results showed that without performing the interfering factors screen for specimens in the low positive index value range of >1.1 to ≤3.5, a false positivity rate of 6.5% would have been realized.
Regulation of
Vibrio
Polysaccharide Synthesis and Virulence Factor Production by CdgC, a GGDEF-EAL Domain Protein, in
Vibrio cholerae
Authors: Lim Bentley , Beyhan Sinem , Yildiz Fitnat H. 
Published: November 2006

ABSTRACT

In
Vibrio cholerae
, the second messenger
3′,5′-cyclic diguanylic acid (c-di-GMP) regulates
several cellular processes, such as formation of corrugated colony
morphology, biofilm formation, motility, and virulence factor
production. Both synthesis and degradation of c-di-GMP in the cell are
modulated by proteins containing GGDEF and/or EAL domains, which
function as a diguanylate cyclase and a phosphodiesterase,
respectively. The expression of two genes,
cdgC
and
mbaA
, which encode proteins harboring both GGDEF and EAL
domains is higher in the rugose phase variant of
V. cholerae
than in the smooth variant. In this study, we carried out gene
expression analysis to determine the genes regulated by CdgC in the
rugose and smooth phase variants of
V. cholerae
. We determined
that CdgC regulates expression of genes required for
V.
cholerae
polysaccharide synthesis and of the transcriptional
regulator genes
vpsR
,
vpsT
, and
hapR
. CdgC
also regulates expression of genes involved in extracellular protein
secretion, flagellar biosynthesis, and virulence factor production. We
then compared the genes regulated by CdgC and by MbaA, during both
exponential and stationary phases of growth, to elucidate processes
regulated by them. Identification of the regulons of CdgC and MbaA
revealed that the regulons overlap, but the timing of regulation
exerted by CdgC and MbaA is different, suggesting the interplay and
complexity of the c-di-GMP signal transduction pathways operating in
V.
cholerae
.
Lateral Gene Transfer In Vitro in the Intracellular PathogenChlamydia trachomatis
Authors: DeMars Robert , Weinfurter Jason , Guex Erin , Lin John , Potucek Yvonne 
Published: November 2006

ABSTRACTGenetic recombinants that resulted from lateral gene transfer (LGT) have been detected in sexually transmitted disease isolates ofChlamydia trachomatis, but a mechanism for LGT inC. trachomatishas not been described. We describe here a system that readily detectsC. trachomatisLGT in vitro and that may facilitate discovery of its mechanisms. Host cells were simultaneously infected in the absence of antibiotics with an ofloxacin-resistant mutant and a second mutant that was resistant to lincomycin, trimethoprim, or rifampin. Selection for doubly resistantC. trachomatisisolates in the progeny detected apparent recombinant frequencies of 10−4to 10−3, ∼104times more frequent than doubly resistant spontaneous mutants in progeny from uniparental control infections. Polyclonal doubly resistant populations and clones isolated from them in the absence of antibiotics had the specific resistance-conferring mutations present in the parental mutants; absence of the corresponding normal nucleotides indicated that they had been replaced by homologous recombination. These results eliminate spontaneous mutation, between-strain complementation, and heterotypic resistance as general explanations of multiply resistantC. trachomatisthat originated in mixed infections in our experiments and demonstrate genetic stability of the recombinants. The kind of LGT we observed might be useful for creating new strains for functional studies by creating new alleles or combinations of alleles of polymorphic loci and might also disseminate antibiotic resistance genes in vivo. The apparent absence of phages and conjugative plasmids inC. trachomatissuggests that the LGT may have occurred by means of natural DNA transformation. Therefore, the experimental system may have implications for genetically alteringC. trachomatisby means of DNA transfer.
Integration and Excision of a Newly DiscoveredBacteroidesConjugative Transposon, CTnBST
Authors: Wesslund Neil A. , Wang Gui-Rong , Song Bo , Shoemaker Nadja B. , Salyers Abigail A. 
Published: November 2006

ABSTRACTConjugative transposons (CTns) are major contributors to the spread of antibiotic resistance genes amongBacteroidesspecies. CTnBST, a newly discoveredBacteroidesconjugative transposon, carries an erythromycin resistance gene,ermB, and previously has been estimated to be about 100 kbp in size. We report here the locations and sequencing of both of its ends. We have also located and sequenced the gene that catalyzes the integration of CTnBST,intBST. The integrase gene encodes a 377-amino-acid protein that has the C-terminal R-K-H-R-H-Y motif that is characteristic of members of the tyrosine recombinase family of integrases. DNA sequence comparisons of the ends of CTnBST, the joined ends of the circular intermediate, and the preferred site into which the circular form of CTnBST had integrated revealed that the preferred integration site (attB1) contained an 18-bp sequence of identity to the crossover region,attBST, on CTnBST. Although this site was used in about one-half of the integration events, sequence analysis of these integration events revealed that both CTnBST and a miniature form of CTnBST (miniBST) integrated into a variety of other sites in the chromosome. All of the sites had two conserved regions, AATCTG and AAAT. These two regions flanked a 2-bp sequence, bp 10 and bp 11 of the 18-bp sequence, that varied in some of the different sites and sometimes in theattBSTsequences. Our results suggest that CTnBST integrates site selectively and that the crossover appears to occur within a 12-bp region that contains the two regions of conserved sequences.
Autoregulator Protein PhaR for Biosynthesis of Polyhydroxybutyrate [P(3HB)] Possibly Has Two Separate Domains That Bind to the Target DNA and P(3HB): Functional Mapping of Amino Acid Residues Responsible for DNA Binding
Authors: Yamada Miwa , Yamashita Koichi , Wakuda Akiko , Ichimura Kazuyoshi , Maehara Akira , Maeda Michihisa , Taguchi Seiichi 
Published: November 2006

ABSTRACT

PhaR from
Paracoccus denitrificans
functions as a repressor or autoregulator of the expression of genes encoding phasin protein (PhaP) and PhaR itself, both of which are components of polyhydroxyalkanoate (PHA) granules (A. Maehara, S. Taguchi, T. Nishiyama, T. Yamane, and Y. Doi, J. Bacteriol. 184:3992-4002, 2002). PhaR is a unique regulatory protein in that it also has the ability to bind tightly to an effector molecule, PHA polyester. In this study, by using a quartz crystal microbalance, we obtained direct evidence that PhaR binds to the target DNA and poly[(
R
)-3-hydroxybutyrate] [P(3HB)], one of the PHAs, at the same time. To identify the PhaR amino acid residues responsible for DNA binding, deletion and PCR-mediated random point mutation experiments were carried out with the gene encoding the PhaR protein. PhaR point mutants with decreased DNA-binding abilities were efficiently screened by an in vivo monitoring assay system coupled with gene expression of green fluorescent protein in
Escherichia coli
. DNA-binding abilities of the wild-type and mutants of recombinant PhaR expressed in
E. coli
were evaluated using a gel shift assay and a surface plasmon resonance analysis. These experiments revealed that basic amino acids and a tyrosine in the N-terminal region, which is highly conserved among PhaR homologs, are responsible for DNA binding. However, most of the mutants with decreased DNA-binding abilities were unaffected in their ability to bind P(3HB), strongly suggesting that PhaR has two separate domains capable of binding to the target DNA and P(3HB).
Role of GerD in Germination of
Bacillus subtilis
Spores
Authors: Pelczar Patricia L. , Igarashi Takao , Setlow Barbara , Setlow Peter 
Published: November 2006

ABSTRACT

Spores of a
Bacillus subtilis
strain with a
gerD
deletion mutation (Δ
gerD
) responded much slower than wild-type spores to nutrient germinants, although they did ultimately germinate, outgrow, and form colonies. Spores lacking GerD and nutrient germinant receptors also germinated slowly with nutrients, as did Δ
gerD
spores in which nutrient receptors were overexpressed. The germination defect of Δ
gerD
spores was not suppressed by many changes in the sporulation or germination conditions. Germination of Δ
gerD
spores was also slower than that of wild-type spores with a pressure of 150 MPa, which triggers spore germination through nutrient receptors. Ectopic expression of
gerD
suppressed the slow germination of Δ
gerD
spores with nutrients, but overexpression of GerD did not increase rates of spore germination. Loss of GerD had no effect on spore germination induced by agents that do not act through nutrient receptors, including a 1:1 chelate of Ca
2+
and dipicolinic acid, dodecylamine, lysozyme in hypertonic medium, a pressure of 500 MPa, and spontaneous germination of spores that lack all nutrient receptors. Deletion of GerD's putative signal peptide or change of its likely diacylglycerylated cysteine residue to alanine reduced GerD function. The latter findings suggest that GerD is located in a spore membrane, most likely the inner membrane, where the nutrient receptors are located. All these data suggest that, while GerD is not essential for nutrient germination, this protein has an important role in spores' rapid response to nutrient germinants, by either direct interaction with nutrient receptors or some signal transduction essential for germination.
Comparison of Antimicrobial Susceptibility Testing of
Campylobacter
spp. by the Agar Dilution and the Agar Disk Diffusion Methods
Authors: Luangtongkum Taradon , Morishita Teresa Y. , El-Tayeb Amna B. , Ison Aaron J. , Zhang Qijing 
Published: November 2006

ABSTRACT

The correlation and the level of agreement between the standardized agar dilution and the agar disk diffusion methods for antimicrobial susceptibility testing of
Campylobacter
were investigated. A high-level agreement between the two methods was evident for aminoglycosides and fluoroquinolones, while a low-level agreement was observed for other antibiotics.
Determining Human Immunodeficiency Virus Coreceptor Use in a Clinical Setting: Degree of Correlation between Two Phenotypic Assays and a Bioinformatic Model
Authors: Skrabal Katharina , Low Andrew J. , Dong Winnie , Sing Tobias , Cheung Peter K. , Mammano Fabrizio , Harrigan P. Richard 
Published: November 2006

ABSTRACT
Two recombinant phenotypic assays for human immunodeficiency virus (HIV) coreceptor usage and an HIV envelope genotypic predictor were employed on a set of clinically derived HIV type 1 (HIV-1) samples in order to evaluate the concordance between measures. Previously genotyped HIV-1 samples derived from antiretroviral-naïve individuals were tested for coreceptor usage using two independent phenotyping methods. Phenotypes were determined by validated recombinant assays that incorporate either an ∼2,500-bp (“Trofile” assay) or an ∼900-bp (TRT assay) fragment of the HIV envelope gp120. Population-based HIV envelope V3 loop sequences (∼105 bp) were derived by automated sequence analysis. Genotypic coreceptor predictions were performed using a support vector machine model trained on a separate genotype-Trofile phenotype data set. HIV coreceptor usage was obtained from both phenotypic assays for 74 samples, with an overall 85.1% concordance. There was no evidence of a difference in sensitivity between the two phenotypic assays. A bioinformatic algorithm based on a support vector machine using HIV V3 genotype data was able to achieve 86.5% and 79.7% concordance with the Trofile and TRT assays, respectively, approaching the degree of agreement between the two phenotype assays. In most cases, the phenotype assays and the bioinformatic approach gave similar results. However, in cases where there were differences in the tropism results, it was not clear which of the assays was “correct.” X4 (CXCR4-using) minority species in clinically derived samples likely complicate the interpretation of both phenotypic and genotypic assessments of HIV tropism.
Prevalence and Characterization of Class I Integrons among
Pseudomonas aeruginosa
and
Acinetobacter baumannii
Isolates from Patients in Nanjing, China
Authors: Gu Bing , Tong Mingqing , Zhao Wenjun , Liu Genyan , Ning Mingzhe , Pan Shiyang , Zhao Wangsheng 
Published: November 2006

ABSTRACT

Class I integrons were detected in 40.8% (40/98) of
Pseudomonas aeruginosa
strains and 52.8% (56/106) of
Acinetobacter baumannii
strains in the Nanjing area of China, including several cassette arrays not previously reported.
Molecular Epidemiology of Metallo-β-Lactamase-Producing
Pseudomonas aeruginosa
in the Calgary Health Region: Emergence of VIM-2-Producing Isolates
Authors: Pitout Johann D. D. , Chow Barbara L. , Gregson Daniel B. , Laupland Kevin B. , Elsayed Sameer , Church Deirdre L. 
Published: November 2006

ABSTRACT

A study was designed to describe the molecular epidemiology of carbapenem-resistant (CR)
Pseudomonas aeruginosa
in a large well-defined geographical region with a centralized laboratory system serving one pediatric and three large adult hospitals (acute care centers I, II, and III). Molecular characterization was done using PCR with sequencing of the integron-associated gene cassettes. Pulsed-field gel electrophoresis (PFGE) using a modified combined
Stenotrophomas maltophilia
and
Streptococcus pneumoniae
protocol with SpeI was performed on CR
P. aeruginosa
strains isolated in the Calgary Health Region during 2002-2006. The majority (96%) of metallo-β-lactamase (MBL)-producing isolates produced VIM-2 with gene cassettes
aacC1
and
aacA4
, while 4% produced IMP-7 with gene cassettes
aacC4
and
aacC1
. Eighty-six percent of VIM-2 producers belonged to a cluster (MBLV) that was responsible for nosocomial outbreaks during 2003 (intensive care unit) and 2004 (bone marrow transplant unit) at acute care center I. Environmental isolates from these units also belonged to MBLV. The majority of strains from cluster MBLVR (related to MBLV) were present in acute care center III. Isolates producing IMP-7 belonged to a different cluster (MBLI) and were related to strains described during the 1990s. PFGE of the MBL-negative CR strains showed that 37% belonged to a closely related cluster, NMBL, whose members were predominantly isolated from acute care center II. Our findings suggest that CR and dissemination of MBL clusters among
P. aeruginosa
populations in large geographic healthcare regions are dynamic processes that require continuous molecular surveillance.
Outbreaks of Multidrug-Resistant
Pseudomonas aeruginosa
in Community Hospitals in Japan
Authors: Sekiguchi Jun-Ichiro , Asagi Tsukasa , Miyoshi-Akiyama Tohru , Kasai Atsushi , Mizuguchi Yukie , Araake Minako , Fujino Tomoko , Kikuchi Hideko , Sasaki Satoru , Watari Hajime , Kojima Tadashi , Miki Hiroshi , Kanemitsu Keiji , Kunishima Hiroyuki , Kikuchi Yoshihiro , Kaku Mitsuo , Yoshikura Hiroshi , Kuratsuji Tadatoshi , Kirikae Teruo 
Published: November 2006

ABSTRACT

We previously reported an outbreak in a neurosurgery ward of catheter-associated urinary tract infection with multidrug-resistant (MDR)
Pseudomonas aeruginosa
strain IMCJ2.S1, carrying the 6′-
N
-aminoglycoside acetyltransferase gene [
aac(6
′
)-Iae
]. For further epidemiologic studies, 214 clinical isolates of MDR
P. aeruginosa
showing resistance to imipenem (MIC ≥ 16 μg/ml), amikacin (MIC ≥ 64 μg/ml), and ciprofloxacin (MIC ≥ 4 μg/ml) were collected from 13 hospitals in the same prefecture in Japan. We also collected 70 clinical isolates of
P. aeruginosa
that were sensitive to one or more of these antibiotics and compared their characteristics with those of the MDR
P. aeruginosa
isolates. Of the 214 MDR
P. aeruginosa
isolates, 212 (99%) were serotype O11. We developed a loop-mediated isothermal amplification (LAMP) assay and a slide agglutination test for detection of the
aac(6
′
)-Iae
gene and the AAC(6′)-Iae protein, respectively. Of the 212 MDR
P. aeruginosa
isolates, 212 (100%) and 207 (98%) were positive in the LAMP assay and in the agglutination test, respectively. Mutations of
gyrA
and
parC
genes resulting in amino acid substitutions were detected in 213 of the 214 MDR
P. aeruginosa
isolates (99%). Of the 214 MDR
P. aeruginosa
isolates, 212 showed pulsed-field gel electrophoresis patterns with ≥70% similarity to that of IMCJ2.S1 and 83 showed a pattern identical to that of IMCJ2.S1, indicating that clonal expansion of MDR
P. aeruginosa
occurred in community hospitals in this area. The methods developed in this study to detect
aac(6
′
)-Iae
were rapid and effective in diagnosing infections caused by various MDR
P. aeruginosa
clones.
Evaluation of the Sensitivities of DNA Extraction and PCR Methods for Detection of
Giardia duodenalis
in Stool Specimens
Authors: Nantavisai Kwannan , Mungthin Mathirut , Tan-ariya Peerapan , Rangsin Ram , Naaglor Tawee , Leelayoova Saovanee 
Published: November 2006

ABSTRACT

Sensitivities of DNA extraction methods and PCR methods for
Giardia duodenalis
were evaluated. A combination of the most sensitive methods, i.e., FTA filter paper and a PCR protocol using RH11/RH4 and GiarF/GiarR primers, showed no significant differences compared to immunofluorescence assay in terms of their sensitivities and specificities.
Usefulness of the BACTEC MGIT 960 System for Isolation of
Mycobacterium tuberculosis
from Sputa Subjected to Long-Term Storage
Authors: Pardini Manuela , Varaine Francis , Bonnet Maryline , Orefici Graziella , Oggioni Marco Rinaldo , Fattorini Lanfranco 
Published: November 2006

ABSTRACT

The recovery of
Mycobacterium tuberculosis
from sputa positive or negative for acid-fast bacilli that were stored for 17 ± 7 days and inoculated in the BACTEC MGIT 960 system (MGIT) was higher than that from sputa inoculated in Lowenstein-Jensen medium. MGIT is useful for isolation of
M. tuberculosis
from sputa subjected to long-term storage.