bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coexpression of Genetically Engineered 3-Ketoacyl-ACP Synthase III (
fabH
) and Polyhydroxyalkanoate Synthase (
phaC
) Genes Leads to Short-Chain-Length-Medium-Chain-Length Polyhydroxyalkanoate Copolymer Production from Glucose in
Escherichia coli
JM109
Authors: Nomura Christopher T. , Taguchi Kazunori , Taguchi Seiichi , Doi Yoshiharu 
Published: February 2004

ABSTRACT

Polyhydroxyalkanoates (PHAs) can be divided into three main types based on the sizes of the monomers incorporated into the polymer. Short-chain-length (SCL) PHAs consist of monomer units of C
3
to C
5
, medium-chain-length (MCL) PHAs consist of monomer units of C
6
to C
14
, and SCL-MCL PHAs consist of monomers ranging in size from C
4
to C
14
. Although previous studies using recombinant
Escherichia coli
have shown that either SCL or MCL PHA polymers could be produced from glucose, this study presents the first evidence that an SCL-MCL PHA copolymer can be made from glucose in recombinant
E. coli
. The 3-ketoacyl-acyl carrier protein synthase III gene (
fabH
) from
E. coli
was modified by saturation point mutagenesis at the codon encoding amino acid 87 of the FabH protein sequence, and the resulting plasmids were cotransformed with either the pAPAC plasmid, which harbors the
Aeromonas caviae
PHA synthase gene (
phaC
), or the pPPAC plasmid, which harbors the
Pseudomonas
sp. strain 61-3 PHA synthase gene (
phaC1
), and the abilities of these strains to accumulate PHA from glucose were assessed. It was found that overexpression of several of the mutant
fabH
genes enabled recombinant
E. coli
to induce the production of monomers of C
4
to C
10
and subsequently to produce unusual PHA copolymers containing SCL and MCL units. The results indicate that the composition of PHA copolymers may be controlled by the monomer-supplying enzyme and further reinforce the idea that fatty acid biosynthesis may be used to supply monomers for PHA production.
rpoB
Gene Sequence-Based Identification of Aerobic Gram-Positive Cocci of the Genera
Streptococcus
,
Enterococcus
,
Gemella
,
Abiotrophia
, and
Granulicatella
Authors: Drancourt Michel , Roux Véronique , Fournier Pierre-Edouard , Raoult Didier 
Published: February 2004

ABSTRACT

We developed a new molecular tool based on
rpoB
gene (encoding the beta subunit of RNA polymerase) sequencing to identify streptococci. We first sequenced the complete
rpoB
gene for
Streptococcus anginosus
,
S. equinus
, and
Abiotrophia defectiva
. Sequences were aligned with these of
S. pyogenes
,
S. agalactiae
, and
S. pneumoniae
available in GenBank. Using an in-house analysis program (SVARAP), we identified a 740-bp variable region surrounded by conserved, 20-bp zones and, by using these conserved zones as PCR primer targets, we amplified and sequenced this variable region in an additional 30
Streptococcus
,
Enterococcus
,
Gemella
,
Granulicatella
, and
Abiotrophia
species. This region exhibited 71.2 to 99.3% interspecies homology. We therefore applied our identification system by PCR amplification and sequencing to a collection of 102 streptococci and 60 bacterial isolates belonging to other genera. Amplicons were obtained in streptococci and
Bacillus cereus
, and sequencing allowed us to make a correct identification of streptococci. Molecular signatures were determined for the discrimination of closely related species within the
S. pneumoniae
-
S. oralis
-
S. mitis
group and the
S. agalactiae
-
S. difficile
group. These signatures allowed us to design a
S. pneumoniae
-specific PCR and sequencing primer pair.
Acquisition of High-Risk Human Papillomavirus Infections and Pap Smear Abnormalities among Women in the New Independent States of the Former Soviet Union
Authors: Syrjänen Stina , Shabalova Irena , Petrovichev Nicolay , Kozachenko Vladimir , Zakharova Tatjana , Pajanidi Julia , Podistov Jurij , Chemeris Galina , Sozaeva Larisa , Lipova Elena , Tsidaeva Irena , Ivanchenko Olga , Pshepurko Alla , Zakharenko Sergej , Nerovjna Raisa , Kljukina Ludmila , Erokhina Oksana , Branovskaja Marina , Nikitina Maritta , Grunberga Valerija , Grunberg Alexandr , Juschenko Anna , Tosi Piero , Cintorino Marcella , Santopietro Rosa , Syrjänen Kari 
Published: February 2004

ABSTRACT

The rates of acquisition and the times of incident high-risk (HR) human papillomavirus (HPV) infections and Pap smear abnormalities and their predictive factors were analyzed in women participating in a multicenter screening study in three countries of the New Independent States of the former Soviet Union. The 423 patients were prospectively monitored for a mean of 21.6 months. At the baseline, 118 women were HR HPV DNA negative (Hybrid Capture II assay) and Pap smear negative (group 1), 184 were HPV DNA positive and Pap smear negative (group 2), and 121 were HPV DNA negative and Pap smear positive (group 3). The time to the acquisition of an incident abnormal Pap smear (19.4 months) was significantly longer in group 1 than in group 2 (9.2 months) (
P
= 0.0001). The times of acquisition of incident HR HPV infection were 16.6 and 11.0 months in group 1 and group 3, respectively (
P
= 0.006). The monthly rates of acquisition of incident HR HPV infections were very similar in group 1 (1.0%) and group 3 (0.8%), whereas the rate of acquisition of an abnormal Pap smear was significantly higher in group 2 (3.1%) than in group 1 (1.5%) (
P
= 0.0001). The acquisition of HR HPV infection (but not a positive Pap smear result) was significantly (
P
= 0.0001) age dependent. The only significant independent (
P
= 0.001) predictor of the incidence of an abnormal Pap smear result was a high HR HPV load of >20 relative light units/control value (CO) (rate ratio, 2.050; 95% confidence interval, 1.343 to 3.129). Independent predictors of incident HR HPV infection were patient category (a sexually transmitted disease) and ever having been pregnant. The time of acquisition of HR HPV infection was 3 months shorter than that of an abnormal Pap smear. At the baseline the high load of a particular HR HPV type is the single most important predictor of an incident Pap smear abnormality, whereas young age and having a sexually transmitted disease predict incident HR HPV infections.
High Rate of Transfer of
Staphylococcus aureus
from Parental Skin to Infant Gut Flora
Authors: Lindberg Erika , Adlerberth Ingegerd , Hesselmar Bill , Saalman Robert , Strannegård Inga-Lisa , Åberg Nils , Wold Agnes E. 
Published: February 2004

ABSTRACT

Many Swedish infants carry
Staphylococcus aureus
in their intestinal microflora. The source of this colonization was investigated in 50 families. Infantile
S. aureus
strains were isolated from rectal swabs and stool samples at 3 days and at 1, 2, 4, and 8 weeks of age. The strains were identified by using the random amplified polymorphic DNA method and compared to strains from swab cultures of the mothers' hands, nipples, and nares and from the fathers' hands and nares. Maternal stool samples were also obtained at a later stage to compare infant and adult intestinal
S. aureus
colonization. Although 60% of 1-month-old children had
S. aureus
in the stools, this was true of only 24% of the mothers. The median population numbers in colonized individuals also differed: 10
6.8
CFU/g of feces among infants at 2 weeks of age versus 10
3.2
CFU/g of feces in the mothers. Of
S. aureus
strains in the stools of 3-day-old infants, 90% were identical to a parental skin strain. A total of 96% of infants whose parents were
S. aureus
skin carriers had
S. aureus
in their feces and 91% had the same strain as at least one of the parents. In comparison, only 37% of infants to
S. aureus
-negative parents had
S. aureus
in the stool samples. Thus, infantile intestinal
S. aureus
colonization was strongly associated with parental skin
S. aureus
carriage (
P
= 0.0001). These results suggest that
S. aureus
on parental skin establish readily in the infantile gut, perhaps due to poor competition from other gut bacteria.
International Clones of Methicillin-Resistant
Staphylococcus aureus
in Two Hospitals in Miami, Florida
Authors: Chung Marilyn , Dickinson Gordon , de Lencastre Herminia , Tomasz Alexander 
Published: February 2004

ABSTRACT

A total of 202 methicillin-resistant
Staphylococcus aureus
(MRSA) single-patient isolates recovered between January and June 1998 in two hospitals in Miami, Florida, were characterized by a combination of several molecular typing techniques: multilocus sequence typing,
spaA
typing, pulsed-field gel electrophoresis, and determination of the structure of the SCC
mec
element. The overwhelming majority of the isolates—187of 202, or 93%—belonged to one of three internationally spread epidemic clones which were identified on the basis of their multilocus sequence type (ST) as E-MRSA-16 (ST36), the New York clone V (ST8), and the New York/Japan clone (ST5; SCC
mec
II) and its single- and double-locus variants. The rest of the isolates (15 of 202, or 7%) were more genetically diverse and were each recovered from a few patients only. Of the 23 MRSA strains isolated from confirmed human immunodeficiency virus-positive patients, as many as 17 (or 70%) belonged to a single ST8 clone carrying SCC
mec
type IV. The data provide further evidence for the conclusion of earlier studies that most MRSA disease in hospitals is caused by relatively few pandemic clones.
Polymorphism and Drug-Selected Mutations in the Protease Gene of Human Immunodeficiency Virus Type 2 from Patients Living in Southern France
Authors: Colson P. , Henry M. , Tourres C. , Lozachmeur D. , Gallais H. , Gastaut J. A. , Moreau J. , Tamalet C. 
Published: February 2004

ABSTRACT
The susceptibility of human immunodeficiency virus type 2 (HIV-2) to protease inhibitors (PI) is largely unknown. We studied HIV-2 protease genes from 21 HIV-2-infected patients who were exposed or not exposed to PI. The aim of this study was (i) to characterize the polymorphism of HIV-2 protease in the absence of drug, (ii) to know whether the HIV-2 protease gene naturally harbors HIV-1 drug resistance codons, and (iii) to identify mutations emerging under PI-selective pressure. Sixty-five HIV-2 RNA or proviral DNA samples were directly sequenced from the plasma or peripheral blood mononuclear cells of 8 patients who had received PI and 13 patients who had never received any antiretroviral. In untreated patients, the highest amino acid variability in HIV-2 protease was observed at positions 14, 40, 43, 46, 65 and 70, and seven codons (10V, 32I, 36I, 46I, 47V, 71V, and 73A) associated with drug resistance in HIV-1 were highly prevalent. In addition, at six positions (positions 7, 46, 62, 71, 90, and 99), the amino acid variability or the amino acid frequencies or both differed significantly in PI-treated and untreated patients, suggesting that mutations 7K→R, 46V→I, 62V→A/T, 71V→I, 90L→M and 99L→F were occurring under PI-selective pressure. At these positions, at least one sample simultaneously harbored both wild-type and mutated codons, while substitutions at positions 62, 71, 90, and 99 were confirmed in a longitudinal analysis. Moreover, the presence of codons 46I and 99F in the absence of drug in HIV-2 subtype B proteases may reflect natural resistance to PI. In conclusion, the present study revealed that HIV-2 strains harbor specific patterns of natural polymorphism and resistance.
Antigenic and Genetic Characterization of Serotype G2 Human Rotavirus Strains from the African Continent
Authors: Page N. A. , Steele A. D. 
Published: February 2004

ABSTRACT
Serotype G2 rotavirus strains were isolated in seven countries on the African continent during 1999 and 2000. To investigate the associated DS-1 genogroup characteristics, subgroup (VP6) enzyme-linked immunosorbent assay, polyacrylamide gel electrophoresis, and P genotyping were performed on 10 G2 strains. The antigenic and genetic variation of the gene encoding the major neutralization glycoprotein (VP7) was also investigated by using G2-specific monoclonal antibodies and sequence analysis. Alterations in the characteristic DS-1 genogroup gene constellations were more likely to occur in the VP4 gene, and three genotypes were observed: P[4], P[6], and a dual P[4]-P[6] type. The failure of G2-specific monoclonal antibodies to type African G2 strains was more likely due to improper storage of the original stool, although G2 monotypes were detected. Phylogenetic analyses revealed clusters of serotype G2 strains that were more commonly associated with seasons during which G2 was predominant. No rotavirus vaccine trials have been conducted in an area where G2 strains were the predominant circulating serotype, and the continued surveillance of rotavirus epidemics in Africa will be preparation for future vaccine implementation in an area that clearly needs these preventative medicines.
Laboratory Evaluation of a Fully Automated Chemiluminescence Immunoassay for Rapid Detection of HBsAg, Antibodies to HBsAg, and Antibodies to Hepatitis C Virus
Authors: Ismail Nahed , Fish Geoffrey E. , Smith Michael B. 
Published: February 2004

ABSTRACT

The performance of a fully automated, random access, enhanced chemiluminescence immunoassay (Ortho/ECi) for the detection of antibody to hepatitis C virus (HCV) (anti-HCV), HBsAg, and antibody to HBsAg (anti-HBsAg), in human serum was compared to a Abbott second-generation enzyme immunoassay (EIA 2.0). The Ortho/ECi assays employ an immunometric technique with enhanced chemiluminescence for optimal assay performance. With regard to the study of clinical laboratory performance, six groups of sera prescreened with Abbott EIAs were assayed: anti-HCV-negative samples (
n
= 318), anti-HCV-positive samples (
n
= 177), anti-HBsAg-negative samples (
n
= 241), anti-HBsAg-positive samples (
n
= 239), HBsAg-positive samples (
n
= 158), and HBsAg-negative samples (
n
= 312). Sera with discrepant results in the two serological assays were resolved by confirmatory tests. Sera with indeterminate results by one or more confirmatory tests were evaluated by reviewing medical records. The overall concordance between the Ortho/ECi assay and the Abbott EIA were 97.78, 93.54, and 97.66% for anti-HCV antibodies, anti-HBsAg antibodies, and HBsAg, respectively. After resolving the discrepancies, the specificities of the new assay for anti-HCV and anti-HBsAg antibodies and HBsAg were 98.1, 92.8, and 100%, respectively. The sensitivities of the new assay for anti-HCV, anti-HBsAg, and HBsAg were 100, 98.8, and 97.4%, respectively. In conclusion, The Ortho/ECi assays for diagnosis of HCV and hepatitis B virus (HBV) infections are highly specific and sensitive assays. The rapid turnaround time, random access, full automation, and high throughput make it an effective assay system for clinical laboratory diagnosis of HCV and HBV infections.
Enzyme-Linked Immunosorbent Assay forHelicobacter pyloriNeeds Adjustment for the Population Investigated
Authors: Hoang Thi Thu Ha , Wheeldon Thuc-Uyen , Bengtsson Carina , Phung Dac Cam , Sörberg Mikael , Granström Marta 
Published: February 2004

ABSTRACTHelicobacter pyloriinfection and peptic ulcer disease are common in developing countries, e.g., Vietnam. An enzyme-linked immunosorbent assay (ELISA) for screening of patients and for seroepidemiology is a useful tool but needs to be validated in the population studied. We used in-house ELISA with sonicated Swedish and Vietnamese strains as antigens to measure immunoglobulin G antibodies after absorption with sonicatedCampylobacter jejuniin sera from 270H. pyloriculture-confirmed peptic ulcer patients, 128 Swedish urea-breath test and immunoblot-positive healthy controls, and 432 Vietnamese immunoblot-positive population controls. Sonicated whole-cell antigen based on the local strains showed a significantly better performance. Immunoblot-positive peptic ulcer patients had significantly higher antibody concentrations than immunoblot-positive population controls, necessitating a lower cutoff level if serology is used for screening or epidemiological purposes. The study shows that the parameters of ELISA forH. pylorineed to be adjusted for the population being investigated.
Detection of Species-Specific
Helicobacter
Ribosomal DNA in Intestinal Biopsy Samples from a Population-Based Cohort of Patients with Ulcerative Colitis
Authors: Streutker C. J. , Bernstein C. N. , Chan V. L. , Riddell R. H. , Croitoru K. 
Published: February 2004

ABSTRACT

The inflammatory bowel diseases are considered an abnormal host immune response to an environmental stimulus. Evidence suggests a role for intestinal bacteria in initiating and/or providing an ongoing stimulus for inflammation in inflammatory bowel disease.
Helicobacter pylori
is the major cause of active chronic gastritis and peptic ulcers in humans and has been linked to gastric carcinoma and lymphoma. Studies in various animal models, particularly mice, have identified enterohepatic
Helicobacter
species that are capable of causing hepatitis and enterocolitis. We hypothesize that
Helicobacter
species may have a role in maintaining inflammation in humans with inflammatory bowel disease. In order to investigate this, biopsy specimens were obtained from patients with and without inflammatory bowel disease. DNA was extracted from the tissues and subjected to PCR with primers designed to detect the ribosomal DNA of members of the
Helicobacter
species. DNA from six biopsy samples from 60 inflammatory bowel disease patients tested positive. This included 5 of 33 ulcerative colitis patients that were positive compared to 0 of 29 age-matched controls (
P
< 0.04). Sequencing of the bands produced by PCR amplification revealed ≥99% homology with
H. pylori
. These results indicate that a member of the
Helicobacter
species may be involved in some cases of ulcerative colitis.
Multicenter Comparison of the Sensititre YeastOne Colorimetric Antifungal Panel with the NCCLS M27-A2 Reference Method for Testing New Antifungal Agents against Clinical Isolates of
Candida
spp
Authors: Espinel-Ingroff A. , Pfaller M. , Messer S. A. , Knapp C. C. , Holliday N. , Killian S. B. 
Published: February 2004

ABSTRACT

A multicenter (three centers) study compared MICs obtained by the Sensititre YeastOne Colorimetric Antifungal plate to reference microdilution broth (NCCLS M27-A2 document) MICs of three new triazoles (posaconazole, ravuconazole, and voriconazole) and the echinocandin caspofungin acetate for 100 isolates of
Candida
spp. In addition, amphotericin B and fluconazole were tested as control drugs. Colorimetric MICs of caspofungin and amphotericin B corresponded to the first blue well (no growth), and MICs of the other agents corresponded to the first slightly purple or blue well. Two comparisons of MIC pairs by the two methods were evaluated: 24-h colorimetric MICs were compared to NCCLS MICs at 24 and at 48 h. The interlaboratory reproducibility of YeastOne and reference MICs was also examined. The best performance of the YeastOne plate was with 24-h MICs (overall, 95 to 99% agreement) for all the species and antifungal agents. These results suggest the potential value of the YeastOne plate for use in the clinical laboratory for the four new antifungal agents evaluated.
Evaluations of Commercial West Nile Virus Immunoglobulin G (IgG) and IgM Enzyme Immunoassays Show the Value of Continuous Validation
Authors: Malan Annette K. , Martins Thomas B. , Hill Harry R. , Litwin Christine M. 
Published: February 2004

ABSTRACT
West Nile virus was introduced into the United States in 1999 and in only four seasons has become endemic east of the Rocky Mountains. Recently, immunoglobulin M (IgM)-capture enzyme immunoassays for the detection of West Nile virus-specific IgM and indirect IgG enzyme immunoassays for the detection of IgG antibodies against West Nile virus were made available from Focus Technologies and PANBIO, Inc. We evaluated these commercial IgG and IgM test systems and determined agreement, sensitivity, and specificity for the assays, compared to immunofluorescence assay and the Centers for Disease Control and Prevention's IgM-capture enzyme-linked immunosorbent assay (ELISA). Initially, the Focus and PANBIO IgM enzyme immunoassays had at least 95% agreement, sensitivity, and specificity, and, based on the 95% confidence intervals, both IgM-capture assays performed similarly. The IgG assays also performed well, although the Focus IgG assay demonstrated greater specificity (98.8%) and the PANBIO IgG assay demonstrated greater sensitivity (99.3%). However, for 400 samples consecutively submitted for West Nile virus antibody testing during 2 days of the 2003 West Nile virus season, agreement, clinical sensitivity, and clinical specificity were 93.1, 98.0, and 92.4%, respectively, for the PANBIO IgM assay and were 97.4, 100.0, and 97.1%, respectively, for the Focus IgM assay. The specificities observed in this second evaluation equates to an overall false-positivity rate of 6.3% in the PANBIO West Nile virus IgM-capture ELISA versus 2.5% with the Focus West Nile virus IgM-capture ELISA. This experience demonstrates the importance of continuously evaluating the performance of an assay in order to detect any changes in assay performance as the test population evolves.
Prospective Study of Use of PCR Amplification and Sequencing of 16S Ribosomal DNA from Cerebrospinal Fluid for Diagnosis of Bacterial Meningitis in a Clinical Setting
Authors: Schuurman Tim , de Boer Richard F. , Kooistra-Smid Anna M. D. , van Zwet Anton A. 
Published: February 2004

ABSTRACT

We have evaluated the use of a broad-range PCR aimed at the 16S rRNA gene in detecting bacterial meningitis in a clinical setting. To achieve a uniform DNA extraction procedure for both gram-positive and gram-negative organisms, a combination of physical disruption (bead beating) and a silica-guanidiniumthiocyanate procedure was used for nucleic acid preparation. To diminish the risk of contamination as much as possible, we chose to amplify almost the entire 16S rRNA gene. The analytical sensitivity of the assay was approximately 1 × 10
2
to 2 × 10
2
CFU/ml of cerebrospinal fluid (CSF) for both gram-negative and gram-positive bacteria. In a prospective study of 227 CSF samples, broad-range PCR proved to be superior to conventional methods in detecting bacterial meningitis when antimicrobial therapy had already started. Overall, our assay showed a sensitivity of 86%, a specificity of 97%, a positive predictive value of 80%, and a negative predictive value of 98% compared to culture. We are currently adapting the standard procedures in our laboratory for detecting bacterial meningitis; broad-range 16S ribosomal DNA PCR detection is indicated when antimicrobial therapy has already started at time of lumbar puncture or when cultures remain negative, although the suspicion of bacterial meningitis remains.