bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determinants of the C-Terminal Domain of the
Escherichia coli
RNA Polymerase α Subunit Important for Transcription at Class I Cyclic AMP Receptor Protein-Dependent Promoters
Authors: Savery Nigel J. , Lloyd Georgina S. , Busby Stephen J. W. , Thomas Mark S. , Ebright Richard H. , Gourse Richard L. 
Published: July 2002

ABSTRACT

Alanine scanning of the
Escherichia coli
RNA polymerase α subunit C-terminal domain (αCTD) was used to identify amino acid side chains important for class I cyclic AMP receptor protein (CRP)-dependent transcription. Key residues were investigated further in vivo and in vitro. Substitutions in three regions of αCTD affected class I CRP-dependent transcription from the
CC(−61.5)
promoter and/or the
lacP1
promoter. These regions are (i) the 287 determinant, previously shown to contact CRP during class II CRP-dependent transcription; (ii) the 265 determinant, previously shown to be important for αCTD-DNA interactions, including those required for class II CRP-dependent transcription; and (iii) the 261 determinant. We conclude that CRP contacts the same target in αCTD, the 287 determinant, at class I and class II CRP-dependent promoters. We also conclude that the relative contributions of individual residues within the 265 determinant depend on promoter sequence, and we discuss explanations for effects of substitutions in the 261 determinant.
Pathogenesis of Primary Respiratory Disease Induced by Isolates from a New Genetic Cluster of Bovine Viral Diarrhea Virus Type I
Authors: Baule C. , Kulcsár G. , Belák K. , Albert M. , Mittelholzer C. , Soós T. , Kucsera L. , Belák S. 
Published: July 2002

ABSTRACT
The pathogenesis of infection induced by cytopathogenic isolates from the newly identified genetic cluster Id of bovine viral diarrhea virus (BVDV) type I was studied in two experimental infections of previously seronegative, immunocompetent calves. Experiment 1 focused on the evaluation of clinical patterns, viremia, and serological responses. All infected calves in this experiment developed respiratory symptoms and seroconverted to BVDV positivity. Contact calves also contracted a respiratory tract infection following exposure to infected animals. Viremia was demonstrated between postinfection days 2 and 17, and the virus was detected in organ specimens of all but one each of the infected and contact calves. In experiment 2, the distribution of BVDV in various tissues of calves euthanized at defined days postinfection was studied. In two of these calves recurrent shedding of BVDV in nasal secretions was shown. BVDV was detected in various tissues of all infected calves throughout the experiment and also following seroconversion and the clearance of BVDV from the circulatory system. Despite the widespread distribution of the virus in various organs, significant tissue damage was found mainly in respiratory tract and lymphoid tissues. These experiments revealed that viruses from cluster Id of BVDV are able to induce primary respiratory disease in previously seronegative, immunocompetent calves. Contact transmission and virus recurrence, contrary to observations from acute experimental infections with noncytopathogenic BVDV, are likely to reflect differences in biological features of these cytopathogenic isolates. Virus shedding and its presence in tissues following peripheral clearance and in the presence of antibodies may have implications in the diagnosis, pathogenesis, and epidemiology of BVDV-induced syndromes in cattle.
Simple, Sensitive, and Specific Detection of Human Immunodeficiency Virus Type 1 Subtype B DNA in Dried Blood Samples for Diagnosis in Infants in the Field
Authors: Beck Ingrid A. , Drennan Kathryn D. , Melvin Ann J. , Mohan Kathey M. , Herz Arnd M. , Alarcón Jorge , Piscoya Julia , Velázquez Carlos , Frenkel Lisa M. 
Published: July 2002

ABSTRACT

The detection of virus is used to diagnose human immunodeficiency virus type 1 (HIV-1) infection in infants due to the persistence of maternal antibodies for a year or more. An HIV-1 DNA PCR assay with simple specimen collection and processing was developed and evaluated. Whole blood was collected on filter paper that lysed cells and bound the DNA, eliminating specimen centrifugation and extraction procedures. The DNA remained bound to the filter paper during PCR amplification. Assays of copy number standards showed reproducible detection of 5 to 10 copies of HIV-1 in 5 μl of whole blood. The sensitivity of the assay did not decrease after storage of the standards on filter paper for 3 months at room temperature or after incubation at 37 or 45°C for 20 h. The primers used for nested PCR of the HIV-1
pol
gene amplified templates from a reference panel of multiple HIV-1 subtypes but did not amplify a subtype A or a subtype C virus from children living in Seattle. The assay had a sensitivity of 98.4% and a specificity of 98.3% for testing of 122 specimens from 35 HIV-1-infected and 16 uninfected children and 43 seronegative adults living in Washington. The assay had a sensitivity of 99% and a specificity of 100% for testing of 102 HIV-1-positive (as determined by enzyme immunoassay) Peruvian women and 6 seropositive and 34 seronegative infants. This assay, with adsorption of whole blood to filter paper and no specimen processing, provides a practical, economical, sensitive, and specific method for the diagnosis of HIV-1 subtype B infection in infants.
Investigation of Optimal Specimen Type and Sampling Time for Detection of Measles Virus RNA during a Measles Epidemic
Authors: Riddell Michaela A. , Chibo Doris , Kelly Heath A. , Catton Michael G. , Birch Christopher J. 
Published: July 2002

ABSTRACT
At various times postonset of rash, 74 patients positive for measles virus-specific immunoglobulin M provided samples for detection of measles virus RNA by a reverse transcriptase PCR. Of lymphocytes, urine, throat swab, and serum specimens, throat swab specimens were optimal for detection of measles virus RNA during the first 2 weeks after the rash.
Coinfection with ThreeEhrlichiaSpecies in Dogs from Thailand and Venezuela with Emphasis on Consideration of 16S Ribosomal DNA Secondary Structure
Authors: Suksawat Jiraporn , Pitulle Christian , Arraga-Alvarado Cruz , Madrigal Karina , Hancock Susan I. , Breitschwerdt Edward B. 
Published: July 2002

ABSTRACTAs part of a larger study to investigate tick-borne infections in dogs from Thailand and Venezuela, documentation of coinfection with threeEhrlichiaspecies in two dogs, one from each country, became the focus of the present study. Although neither dog had clinical signs attributable to ehrlichiosis, both dogs were anemic and neutropenic and the Thai dog was thrombocytopenic. Genus- and species-specific PCR targeting the 16S rRNA genes indicated that both dogs were coinfected withEhrlichia canis,E. platys, andE. equi. To our knowledge, these results provide the first molecular documentation for the presence ofE. equiin dogs from these countries. Using universal bacterial PCR primers, one nearly full-length 16S rRNA gene could be amplified from each dog. The sequences were identical to each other and almost identical to that ofE. platys(AF156784), providing the firstE. platys16S ribosomal DNA (rDNA) sequences reported from these two geographically divergent countries. To determine whether these sequence differences allow differentiation between these two strains and other published 16S rDNAE. platyssequences, we performed a phylogenetic analysis of the rRNA, incorporating the consideration of secondary structure.
Methicillin-Resistant
Staphylococcus aureus
: Comparison of Susceptibility Testing Methods and Analysis of
mecA
-Positive Susceptible Strains
Authors: Sakoulas George , Gold Howard S. , Venkataraman Lata , DeGirolami Paola C. , Eliopoulos George M. , Qian Qinfang 
Published: July 2002

ABSTRACT

Methicillin-resistant
Staphylococcus aureus
(MRSA) is responsible for an increasing number of serious nosocomial and community-acquired infections. Phenotypic heterogeneous drug resistance (heteroresistance) to antistaphylococcal beta-lactams affects the results of susceptibility testing. The present study compared the MRSA-Screen latex agglutination test (Denka Seiken Co., Ltd., Tokyo, Japan) for detection of PBP 2a with agar dilution, the VITEK-1 and VITEK-2 systems (bioMérieux, St. Louis, Mo.), and the oxacillin agar screen test for detection of MRSA, with PCR for the
mecA
gene used as the “gold standard” assay. Analysis of 107 methicillin-susceptible
S. aureus
(MSSA) isolates and 203 MRSA isolates revealed that the MRSA-Screen latex agglutination test is superior to any single phenotype-based susceptibility testing method, with a sensitivity of 100% and a specificity of 99.1%. Only one isolate that lacked
mecA
was weakly positive by the MRSA-Screen latex agglutination test. This isolate was phenotypically susceptible to oxacillin and did not contain the
mecA
gene by Southern blot hybridization. The oxacillin agar screen test, the VITEK-1 system, the VITEK-2 system, and agar dilution showed sensitivities of 99.0, 99.0, 99.5, and 99%, respectively, and specificities of 98.1, 100, 97.2, and 100%, respectively. The differences in sensitivity or specificity were not statistically significant. Oxacillin bactericidal assays showed that
mecA
- and PBP 2a-positive
S. aureus
isolates that are susceptible to antistaphylococcal beta-lactams by conventional methods are functionally resistant to oxacillin. We conclude that the accuracy of the MRSA-Screen latex agglutination method for detection of PBP 2a approaches the accuracy of PCR and is more accurate than any susceptibility testing method used alone for the detection of MRSA.
In Vitro Culture, Ultrastructure, Antigenic, and Molecular Characterization of
Encephalitozoon cuniculi
Isolated from Urine and Sputum Samples from a Spanish Patient with AIDS
Authors: del Aguila Carmen , Moura Hercules , Fenoy Soledad , Navajas Raquel , Lopez-Velez Rogelio , Li Lixia , Xiao Lihua , Leitch Gordon J. , da Silva Alexandre , Pieniazek Norman J. , Lal Altaf A. , Visvesvara Govinda S. 
Published: July 2002

ABSTRACT

In this report we describe the cultivation of two isolates of microsporidia, one from urine and the other from sputum samples from a Spanish AIDS patient. We identified them as
Encephalitozoon cuniculi
, type strain III (the dog genotype), based on ultrastructure, antigenic characteristics, PCR, and the sequence of the ribosomal DNA internal transcribed spacer region.
Rapid Typing of
Borrelia burgdorferi
Sensu Lato Species in Specimens from Patients with Different Manifestations of Lyme Borreliosis
Authors: Lünemann Jan D. , Zarmas Silvia , Priem Susanne , Franz Juliane , Zschenderlein Rolf , Aberer Elisabeth , Klein Rolf , Schouls Leo , Burmester Gerd R. , Krause Andreas 
Published: July 2002

ABSTRACT

To further investigate the pathogenic potential of different
Borrelia burgdorferi
genospecies, specimens from 27 patients with different manifestations of Lyme borreliosis were analyzed by PCR and reverse line blotting (RLB). In samples from Lyme arthritis patients,
B. burgdorferi
sensu stricto was predominantly identified, while in patients with neuroborreliosis or acrodermatitis,
Borrelia garinii
and
Borrelia afzelii
, respectively, were exclusively detected. The results demonstrate that PCR-RLB is a valuable tool for epidemiological and pathogenetic studies of Lyme borreliosis.
Particular Biochemical Profiles for EnterohemorrhagicEscherichia coliO157:H7 Isolates on the ID 32E System
Authors: Leclercq Alexandre , Lambert Bernard , Pierard Denis , Mahillon Jacques 
Published: July 2002

ABSTRACTThe ability of the ID 32E system to identify and discriminate 74Escherichia coliO157 isolates among 106E. colinon-O157 isolates was evaluated. The results showed atypical biochemical reactions but accurate identification at the species level and no unique biochemical profile numbers forE. coliO157, although these numbers were distinct from those of other serotypes.
Genetic Organization ofPasteurella multocida capLoci and Development of a Multiplex Capsular PCR Typing System
Authors: Townsend Kirsty M. , Boyce John D. , Chung Jing Y. , Frost Alan J. , Adler Ben 
Published: July 2002

ABSTRACTCurrent serotyping methods classifyPasteurella multocidainto five capsular serogroups (serogroups A, B, D, E, and F) and 16 somatic serotypes (serotypes 1 to 16). In the present study, we have developed a multiplex PCR assay as a rapid alternative to the conventional capsular serotyping system. The serogroup-specific primers used in this assay were designed following identification, sequence determination, and analysis of the capsular biosynthetic loci of each capsular serogroup. The entire capsular biosynthetic loci ofP. multocidaA:1 (X-73) and B:2 (M1404) have been cloned and sequenced previously (J. Y. Chung, Y. M. Zhang, and B. Adler, FEMS Microbiol. Lett. 166:289–296, 1998; J. D. Boyce, J. Y. Chung, and B. Adler, Vet. Microbiol. 72:121–134, 2000). Nucleotide sequence analysis of the biosynthetic region (region 2) from each of the remaining three serogroups, serogroups D, E, and F, identified serogroup-specific regions and gave an indication of the capsular polysaccharide composition. The multiplex capsular PCR assay was highly specific, and its results, with the exception of those for some serogroup F strains, correlated well with conventional serotyping results. Sequence analysis of the strains that gave conflicting results confirmed the validity of the multiplex PCR and indicated that these strains were in fact capsular serogroup A. The multiplex PCR will clarify the distinction between closely related serogroups A and F and constitutes a rapid assay for the definitive classification ofP. multocidacapsular types.
Biochemical Identification and Characterization of DNA Groups within the
Proteus vulgaris
Complex
Authors: Janda J. Michael , Abbott Sharon L. , Khashe Shideh , Probert Will 
Published: July 2002

ABSTRACT

We placed 43 isolates belonging to the
Proteus vulgaris
complex into proposed DNA groups (genomovars) using five previously recommended tests (tests for esculin hydrolysis, production of acid from salicin,
l
-rhamnose fermentation, and elaboration of DNase and lipase). On the basis of the results of these five tests, 49% of the isolates fell into DNA groups 5 and 6, 37% fell into DNA group 2, and the remaining 14% fell into DNA groups 3 and 4. Sequencing of the 16S rRNA genes of 11 members of DNA groups 5 and 6 indicated that 10 of these isolates (91%) could be unambiguously assigned to one of these two genomospecies. Overall expression of selected enzymatic and virulence-associated characteristics did not differ significantly among DNA groups.
Comparison of Sequence Analysis and the INNO-LiPA HBV DR Line Probe Assay for Detection of Lamivudine-Resistant Hepatitis B Virus Strains in Patients under Various Clinical Conditions
Authors: Aberle Stephan W. , Kletzmayr Josef , Watschinger Bruno , Schmied Brigitte , Vetter Norbert , Puchhammer-Stöckl Elisabeth 
Published: July 2002

ABSTRACTA line probe assay (INNO-LiPA HBV DR) detecting drug-resistant hepatitis B virus (HBV) strains was evaluated. Results concordant with sequence analysis were obtained with 48 of 56 serum samples from HBV-infected patients undergoing lamivudine therapy. In eight cases, additional minor subpopulations could be identified by the line probe assay.
Helicobacter winghamensis
sp. nov., a Novel
Helicobacter
sp. Isolated from Patients with Gastroenteritis
Authors: Melito P. L. , Munro C. , Chipman P. R. , Woodward D. L. , Booth T. F. , Rodgers F. G. 
Published: July 2002

ABSTRACT

From 1997 to 1999 seven isolates of
Campylobacter
-like organisms from five patients that were exhibiting symptoms of gastroenteritis, including fever, stomach malaise, and diarrhea, were investigated. The organisms were isolated from stool samples and found to exhibit a diverse colony morphology; hence multiple isolates were submitted from one of the patients. All isolates were found to be identical. The organisms were catalase, urease, alkaline phosphatase, and nitrate negative but oxidase and indoxyl acetate positive. They grew at 37°C but not at 42°C, and three of the isolates from two different patients were sensitive to nalidixic acid and cephalothin. Full 16S rRNA sequence analysis not only grouped these organisms within the
Helicobacter
genus but also differentiated them from previously identified
Helicobacter
species. The closest relative by phylogenetic analysis was
Helicobacter
sp. flexispira taxon 1. Electron microscopy showed that these isolates had one or two bipolar flagella; however, the periplasmic fibers, a characteristic of the known
Helicobacter
sp. flexispira taxa, were not observed. The present isolates also lacked a flagellar sheath, a trait shared with four other
Helicobacter
spp.,
H. canadensis
,
H. mesocricetorum
,
H. pullorum
, and
H. rodentium
. On the basis of the unique phenotypic properties of these isolates and 16S rRNA sequence analysis, we propose the classification of a new
Helicobacter
species,
Helicobacter winghamensis
sp. nov.
Fourth-Generation Enzyme-Linked Immunosorbent Assay for the Simultaneous Detection of Human Immunodeficiency Virus Antigen and Antibody
Authors: Saville Rebecca D. , Constantine Niel T. , Cleghorn Farley R. , Jack Noreen , Bartholomew Courtenay , Edwards Jeffrey , Gomez Perry , Blattner William A. 
Published: July 2002

ABSTRACT
The VIDAS HIV DUO Ultra, a fourth-generation immunoassay under development for the simultaneous detection of human immunodeficiency virus type 1 (HIV-1) p24 antigen and antibodies to HIV-1 and HIV-2, was evaluated. The enzyme-linked fluorescence immunoassay, performed on the automated VIDAS instrument, is claimed to detect early and established HIV infection. The assay was challenged with a total of 2,847 samples that included 74 members of 10 seroconversion panels, 9 p24 antigen-only-reactive members of a panel of group M clades, 503 consecutively collected samples from individuals seeking care in the University of Maryland Medical System, 1,010 samples from U.S. blood donors, 1,141 samples from patients in a high-incidence population in Trinidad, 83 samples from a clinic for sexually transmitted diseases in the Bahamas, 10 confirmed HIV-1 group O samples, and 16 confirmed HIV-2 samples from the Cote d'Ivoire. Reference tests were U.S. Food and Drug Administration-licensed HIV antibody screening, p24 antigen tests, HIV confirmatory assays, and the Roche Diagnostics Amplicor HIV-1 Monitor. The VIDAS HIV DUO Ultra demonstrated 100% sensitivity and 99.5% specificity overall, with a 99.7% specificity in low-risk individuals. The analytical sensitivity, as assessed by seroconversion panels and p24 antigen in samples, was equivalent to the sensitivity of the reference assays used to characterize these panels. The VIDAS HIV DUO Ultra is accurate, offers potential advantages over conventional HIV testing for time and cost savings, has walk-away capability, and correctly identifies both early and established HIV infections.
Cryptococcus neoformans
var.
neoformans
(Serotype D) Strains Are More Susceptible to Heat than
C. neoformans
var.
grubii
(Serotype A) Strains
Authors: Martinez Luis. R , Garcia-Rivera Javier , Casadevall Arturo 
Published: July 2002

ABSTRACT

Cryptococcus neoformans
var.
neoformans
(serotype D) and
C. neoformans
var.
grubii
(serotype A) differ in geographic prevalence and dermatotropism, with
C. neoformans
var.
neoformans
strains being more prevalent among isolates from temperate countries as well as from skin infections. Analysis of 19 strains from each serotype revealed wide variation in thermal susceptibility, with
C. neoformans
var.
neoformans
strains being more susceptible, on average, to heat killing. The results suggest a consistent explanation for the geographic differences between serotype A and D strains and for the dermatotropism of serotype D strains.
Molecular Characterization of Methicillin-Resistant
Staphylococcus epidermidis
Clones: Evidence of Geographic Dissemination
Authors: Miragaia Maria , Couto Isabel , Pereira Sandro F. F. , Kristinsson Karl G. , Westh Henrik , Jarløv Jens O. , Carriço João , Almeida Jonas , Santos-Sanches Ilda , de Lencastre Hermínia 
Published: July 2002

ABSTRACT

Denmark and Iceland are countries where the frequency of methicillin-resistant
Staphylococcus aureus
is very low due to strict infection control and restrictive antibiotic use policies. In contrast, methicillin-resistant
S. epidermidis
(MRSE) continues to be isolated as a nosocomial pathogen. The molecular typing by pulsed-field gel electrophoresis (PFGE) of 136 MRSE isolates from five hospitals in Denmark and 94 MRSE isolates from one hospital in Iceland collected in 1997 and 1998 defined 40 different patterns. Closely related PFGE types were found in isolates recovered in Iceland, Denmark, Mexico, Uruguay, Greece, and Cape Verde, evidencing for the first time the geographic clonal dissemination of MRSE strains. The large majority (87.4%) of the MRSE isolates studied were multiresistant.
Detection ofEhrlichia canisin Canine Carrier Blood and in Individual Experimentally Infected Ticks with ap30-Based PCR Assay
Authors: Stich Roger W. , Rikihisa Yasuko , Ewing S. A. , Needham Glen R. , Grover Debra L. , Jittapalapong Sathaporn 
Published: July 2002

ABSTRACTDetection of vector-borne pathogens is necessary for investigation of their association with vertebrate and invertebrate hosts. The ability to detectEhrlichiaspp. within individual experimentally infected ticks would be valuable for studies to evaluate the relative competence of different vector species and transmission scenarios. The purpose of this study was to develop a sensitive PCR assay based on oligonucleotide sequences from the uniqueEhrlichia canisgene,p30, to facilitate studies that require monitoring this pathogen in canine and tick hosts during experimental transmission. Homologous sequences forEhrlichia chaffeensis p28were compared to sequences of primers derived from a sequence conserved amongE. canisisolates. Criteria for primer selection included annealing scores, identity of the primers to homologousE. chaffeensissequences, and the availability of similarly optimal primers that were nested within the target template sequence. Thep30-based assay was at least 100-fold more sensitive than a previously reported nested 16S ribosomal DNA (rDNA)-based assay and did not amplify the 200-bp target amplicon fromE. chaffeensis,the human granulocytic ehrlichiosis agent, orEhrlichia murisDNA. The assay was used to detectE. canisin canine carrier blood and in experimentally infectedRhipicephalus sanguineusticks. Optimized procedures for preparing tissues from these hosts for PCR assay are described. Our results indicated that thisp30-based PCR assay will be useful for experimental investigations, that it has potential as a routine test, and that this approach to PCR assay design may be applicable to other pathogens that occur at low levels in affected hosts.
Results of Human Papillomavirus DNA Testing with the Hybrid Capture 2 Assay Are Reproducible
Authors: Castle Philip E. , Lorincz Attila T. , Mielzynska-Lohnas Iwona , Scott David R. , Glass Andrew G. , Sherman Mark E. , Schussler John E. , Schiffman Mark 
Published: July 2002

ABSTRACT
Reproducibility of the Hybrid Capture 2 Test (HC 2) for human papillomavirus (HPV) DNA detection was evaluated by assaying frozen cervical specimens in 1997 and again in 2001 from 1,775 women with normal cervical cytology. Using a cutoff point of 1.0 pg of HPV DNA/ml between a negative and a positive test result, the result of the kappa test for agreement was 0.72 (a kappa value of >0.60 is considered good agreement). Using cutoff points of 1.0 and 10.0 pg/ml between negative and low positive and between low positive and high positive, respectively, the kappa was 0.68 and the linear-weighted kappa was 0.76. The results of this study indicate that HC 2 testing is reproducible even among cytologically normal women with low test values.