bluuebunny/crossref_metadata_2025 huggingface dataset:
Diversity and Activity of Methanotrophic Bacteria in Different Upland Soils
Authors: Knief Claudia , Lipski André , Dunfield Peter F.
Published: November 2003

Samples from diverse upland soils that oxidize atmospheric methane were characterized with regard to methane oxidation activity and the community composition of methanotrophic bacteria (MB). MB were identified on the basis of the detection and comparative sequence analysis of the
pmoA
gene, which encodes a subunit of particulate methane monooxygenase. MB commonly detected in soils were closely related to
Methylocaldum
spp.,
Methylosinus
spp.,
Methylocystis
spp., or the “forest sequence cluster” (USC α), which has previously been detected in upland soils and is related to
pmoA
sequences of type II MB (
Alphaproteobacteria
). As well, a novel group of sequences distantly related (<75% derived amino acid identity) to those of known type I MB (Gammaproteobacteria) was often detected. This novel “upland soil cluster γ” (USC γ) was significantly more likely to be detected in soils with pH values of greater than 6.0 than in more acidic soils. To identify active MB, four selected soils were incubated with
13
CH
4
at low mixing ratios (<50 ppm of volume), and extracted methylated phospholipid fatty acids (PLFAs) were analyzed by gas chromatography-online combustion isotope ratio mass spectrometry. Incorporation of
13
C into PLFAs characteristic for methanotrophic
Gammaproteobacteria
was observed in all soils in which USC γ sequences were detected, suggesting that the bacteria possessing these sequences were active methanotrophs. A pattern of labeled PLFAs typical for methanotrophic
Alphaproteobacteria
was obtained for a sample in which only USC α sequences were detected. The data indicate that different MB are present and active in different soils that oxidize atmospheric methane.
Application of Real-Time PCR for Quantification of Microcystin Genotypes in a Population of the Toxic CyanobacteriumMicrocystissp
Authors: Kurmayer Rainer , Kutzenberger Thomas
Published: November 2003

The cyanobacteriumMicrocystissp. frequently develops water blooms consisting of organisms with different genotypes that either produce or lack the hepatotoxin microcystin. In order to monitor the development of microcystin (mcy) genotypes during the seasonal cycle of the total population,mcygenotypes were quantified by means of real-time PCR in Lake Wannsee (Berlin, Germany) from June 1999 to October 2000. Standard curves were established by relating cell concentrations to the threshold cycle (the PCR cycle number at which the fluorescence passes a set threshold level) determined by theTaqnuclease assay (TNA) for two gene regions, the intergenic spacer region within the phycocyanin (PC) operon to quantify the total population and themcyBgene, which is indicative of microcystin synthesis. In laboratory batch cultures, the cell numbers inferred from the standard curve by TNA correlated significantly with the microscopically determined cell numbers on a logarithmic scale. The TNA analysis of 10 strains revealed identical amplification efficiencies for both genes. In the field, the proportion ofmcygenotypes made up the smaller part of the PC genotypes, ranging from 1 to 38%. The number ofmcyBgenotypes was one-to-one related to the number of PC genotypes, and parallel relationships between cell numbers estimated via the inverted microscope technique and TNA were found for both genes. It is concluded that the mean proportion of microcystin genotypes is stable from winter to summer and thatMicrocystiscell numbers could be used to infer the mean proportion ofmcygenotypes in Lake Wannsee.
Design and Evaluation of PCR Primers for Analysis of Bacterial Populations in Wine by Denaturing Gradient Gel Electrophoresis
Authors: Lopez Isabel , Ruiz-Larrea Fernanda , Cocolin Luca , Orr Erica , Phister Trevor , Marshall Megan , VanderGheynst Jean , Mills David A.
Published: November 2003

Denaturing gradient gel electrophoresis (DGGE) of PCR-amplified ribosomal DNA (rDNA) is routinely used to compare levels of diversity of microbial communities and to monitor population dynamics. While using PCR-DGGE to examine the bacteria in wine fermentations, we noted that several commonly used PCR primers for amplifying bacterial 16S rDNA also coamplified yeast, fungal, or plant DNA present in samples. Unfortunately, amplification of nonbacterial DNA can result in a masking of bacterial populations in DGGE profiles. To surmount this problem, we developed two new primer sets for specific amplification of bacterial 16S rDNA in wine fermentation samples without amplification of eukaryotic DNA. One primer set, termed WLAB1 and WLAB2, amplified lactic acid bacteria, while another, termed WBAC1 and WBAC2, amplified both lactic acid bacterial and acetic acid bacterial populations found in wine. Primer specificity and efficacy were examined with DNA isolated from numerous bacterial, yeast, and fungal species commonly found in wine and must samples. Importantly, both primer sets effectively distinguished bacterial species in wine containing mixtures of yeast and bacteria.
Peptide Ligands That Bind Selectively to Spores of
Bacillus subtilis
and Closely Related Species
Authors: Knurr Jordan , Benedek Orsolya , Heslop Jennifer , Vinson Robert B. , Boydston Jeremy A. , McAndrew Joanne , Kearney John F. , Turnbough Charles L.
Published: November 2003

As part of an effort to develop detectors for selected species of bacterial spores, we screened phage display peptide libraries for 7- and 12-mer peptides that bind tightly to spores of
Bacillus subtilis
. All of the peptides isolated contained the sequence Asn-His-Phe-Leu at the amino terminus and exhibited clear preferences for other amino acids, especially Pro, at positions 5 to 7. We demonstrated that the sequence Asn-His-Phe-Leu-Pro (but not Asn-His-Phe-Leu) was sufficient for tight spore binding. We observed equal 7-mer peptide binding to spores of
B. subtilis
and its most closely related species,
Bacillus amyloliquefaciens
, and slightly weaker binding to spores of the closely related species
Bacillus globigii
. These three species comprise one branch on the
Bacillus
phylogenetic tree. We did not detect peptide binding to spores of several
Bacillus
species located on adjacent and nearby branches of the phylogenetic tree nor to vegetative cells of
B. subtilis
. The sequence Asn-His-Phe-Leu-Pro was used to identify
B. subtilis
proteins that may employ this peptide for docking to the outer surface of the forespore during spore coat assembly and/or maturation. One such protein, SpsC, appears to be involved in the synthesis of polysaccharide on the spore coat. SpsC contains the Asn-His-Phe-Leu-Pro sequence at positions 6 to 10, and the first five residues of SpsC apparently must be removed to allow spore binding. Finally, we discuss the use of peptide ligands for bacterial detection and the use of short peptide sequences for targeting proteins during spore formation.
Protistan Grazing Analysis by Flow Cytometry Using Prey Labeled by In Vivo Expression of Fluorescent Proteins
Authors: Fu Yutao , O'Kelly Charles , Sieracki Michael , Distel Daniel L.
Published: November 2003

Selective grazing by protists can profoundly influence bacterial community structure, and yet direct, quantitative observation of grazing selectivity has been difficult to achieve. In this investigation, flow cytometry was used to study grazing by the marine heterotrophic flagellate
Paraphysomonas imperforata
on live bacterial cells genetically modified to express the fluorescent protein markers green fluorescent protein (GFP) and red fluorescent protein (RFP). Broad-host-range plasmids were constructed that express fluorescent proteins in three bacterial prey species,
Escherichia coli
,
Enterobacter aerogenes
, and
Pseudomonas putida. Micromonas pusilla
, an alga with red autofluorescence, was also used as prey. Predator-prey interactions were quantified by using a FACScan flow cytometer and analyzed by using a Perl program described here. Grazing preference of
P. imperforata
was influenced by prey type, size, and condition. In competitive feeding trials,
P. imperforata
consumed algal prey at significantly lower rates than FP (fluorescent protein)-labeled bacteria of similar or different size. Within-species size selection was also observed, but only for
P. putida
, the largest prey species examined; smaller cells of
P. putida
were grazed preferentially. No significant difference in clearance rate was observed between GFP- and RFP-labeled strains of the same prey species or between wild-type and GFP-labeled strains. In contrast, the common chemical staining method, 5-(4,6-dichloro-triazin-2-yl)-amino fluorescein hydrochloride, depressed clearance rates for bacterial prey compared to unlabeled or RFP-labeled cells.
Isolation and Identification of
Photobacterium phosphoreum
from an Unexpected Niche: Migrating Salmon
Authors: Budsberg K. J. , Wimpee C. F. , Braddock J. F.
Published: November 2003

Six luminous bacteria were isolated from migrating salmon in the Yukon River, Alaska. All isolates were identified as
Photobacterium phosphoreum
. Previous studies suggest that
P. phosphoreum
is an exclusively marine bacterium, while our Alaskan isolates are from salmon which migrated up to 1,228 km from the marine environment.
Rectoanal Mucosal Swab Culture Is More Sensitive Than Fecal Culture and Distinguishes
Escherichia coli
O157:H7-Colonized Cattle and Those Transiently Shedding the Same Organism
Authors: Rice Daniel H. , Sheng Haiqing Q. , Wynia Stacey A. , Hovde Carolyn J.
Published: November 2003

Enrichment and direct (nonenrichment) rectoanal mucosal swab (RAMS) culture techniques were developed and compared to traditional fecal culture for the detection of
Escherichia coli
O157:H7 in experimentally infected and naturally infected cattle. Holstein steers (
n
= 16) orally dosed with
E. coli
O157:H7 were sampled after bacterial colonization starting 15 days postinoculation. Enrichment RAMS cultures (70.31% positive) were more sensitive than enrichment fecal cultures with 10 g of feces (46.88% positive) at detecting
E. coli
O157:H7 (
P
< 0.01). Holstein bull calves (
n
= 15) were experimentally exposed to
E. coli
O157:H7 by penning them with
E. coli
O157:H7-positive calves. Prior to bacterial colonization (1 to 14 days postexposure), enriched fecal cultures were more sensitive at detecting
E. coli
O157:H7 than enriched RAMS cultures (
P
< 0.01). However, after colonization (40 or more days postexposure), the opposite was true and RAMS culture was more sensitive than fecal culture (
P
< 0.05). Among naturally infected heifers, enriched RAMS or fecal cultures were equally sensitive (
P
= 0.5), but direct RAMS cultures were more sensitive than either direct or enriched fecal cultures at detecting
E. coli
O157:H7 (
P
< 0.01), with 25 of 144, 4 of 144, and 10 of 108 samples, respectively, being culture positive. For both experimentally and naturally infected cattle, RAMS culture predicted the duration of infection. Cattle transiently shedding
E. coli
O157:H7 for <1 week were positive by fecal culture only and not by RAMS culture, whereas colonized animals (which were culture positive for an average of 26 days) were positive early on by RAMS culture. RAMS culture more directly measured the relationship between cattle and
E. coli
O157:H7 infection than fecal culture.
Novel Enzyme-Linked Minisequence Assay for Genotypic Analysis of Human Immunodeficiency Virus Type 1 Drug Resistance
Authors: Sugiura Wataru , Shimada Kazunori , Matsuda Masakazu , Chiba Tomoko , Myint Lay , Okano Aiko , Yamada Kaneo
Published: November 2003

We constructed a novel tool for genotypic analysis of human immunodeficiency virus type 1 (HIV-1) drug resistance by using an enzyme-linked minisequence assay (ELMA). ELMA is a combination of hybridization and a 1-base extension reaction, and we designed the assay to detect five mutations conferring nucleoside analogue resistance (M41L, D67N, K70R, T215Y, and M184V) and six mutations conferring protease inhibitor resistance (D30N, M46I, G48V, V82A, I84V, and L90M). At all detection points, ELMA demonstrated high sensitivity and specificity, sufficient for clinical use. Compared to that obtained by direct sequencing, the genotypic information obtained by ELMA is limited to the targeted loci for which it was designed. However, ELMA proves advantageous in several respects. The assay does not require expensive equipment, such as an autosequencer, and can be performed in regular clinical diagnostic laboratories. Therefore ELMA can be a candidate for a drug resistance monitoring assay to be introduced in developing countries. In addition, ELMA demonstrated higher sensitivity in the detection of minor resistant populations. We successfully detected a minor virus population (10%) by the assay. The high sensitivity and specificity of the assay recommend it as a first screening assay for drug resistance surveillance.
Metronidazole-Resistant
Helicobacter pylori
Is More Prevalent in Patients with Nonulcer Dyspepsia than in Peptic Ulcer Patients in a Multiethnic Asian Population
Authors: Lui Sook-Yin , Yeoh Khay-Guan , Ho Bow
Published: November 2003

The trend of increasing prevalence of antibiotic resistance among
Helicobacter pylori
strains has been suggested as a cause of the failure of treatment of
H. pylori
infections. In this study, 120 of 211 antral biopsy specimens from patients with dyspeptic symptoms were found to harbor
H. pylori.
The isolates from the 120 specimens were tested by the agar dilution method, and 38 (31.7%) were found to be metronidazole resistant. Among the 211 subjects, 81 of 115 (70.4%) patients with peptic ulcer (PU) were infected with
H. pylori
, whereas 39 of 96 (40.6%) patients with nonulcer dyspepsia (NUD) were infected with
H. pylori
. Interestingly, significantly more NUD patients than PU patients harbored metronidazole-resistant
H. pylori
(22 of 39 [56.4%] and 16 of 81 [19.8%], respectively;
P
< 0.001). A similar pattern was also observed among NUD patients of different ethnicities but not between male and female patients (23 of 78 [29.5%] and 15 of 42 [35.7%], respectively;
P
= 0.54). In the posttreatment follow-up, five of six patients who had positive urea breath test results, indicating treatment failure, were NUD patients. Of these, four harbored metronidazole-resistant
H. pylori
strains. This further illustrates the relevance of metronidazole-resistant
H. pylori
in NUD patients. The significantly higher percentage of metronidazole-resistant
H. pylori
isolates in NUD patients may be attributed to the protection offered by the mucus layer of the nonulcerated stomach to the bacteria that reside below it, resulting in organism exposure to sublethal concentrations of metronidazole and leading to the induction of metronidazole resistance. The results demonstrate that the
H. pylori
isolates colonizing NUD patients are more likely to be resistant to metronidazole. It will therefore be useful to reevaluate the use of metronidazole in the treatment of NUD patients infected with
H. pylori
.
Distribution of Intimin Subtypes amongEscherichia coliIsolates from Ruminant and Human Sources
Authors: Ramachandran Vidiya , Brett Kim , Hornitzky Michael A. , Dowton Mark , Bettelheim Karl A. , Walker Mark J. , Djordjevic Steven P.
Published: November 2003

The intimin geneeae, located within the locus of enterocyte effacement pathogenicity island, distinguishes enteropathogenicEscherichia coli(EPEC) and some Shiga toxin-producingE. coli(STEC) strains from all other pathotypes of diarrheagenicE. coli. EPEC is a leading cause of infantile diarrhea in developing countries, and intimin-positive STEC isolates are typically associated with life-threatening diseases such as hemolytic-uremic syndrome and hemorrhagic colitis. Here we describe the development of a PCR-restriction fragment length polymorphism (RFLP) assay that reliably differentiates all 11 known intimin types (α1, α2, β, γ, κ, ε, η, ι, λ, θ, and ζ) and three new intimin genes that show less than 95% nucleotide sequence identity with existing intimin types. We designated these new intimin genes Int-μ, Int-ν, and Int-ξ. The PCR-RFLP assay was used to screen 213eae-positiveE. coliisolates derived from ovine, bovine, and human sources comprising 60 serotypes. Of these, 82 were STEC isolates, 89 werestx-negative (stx−) andehxA-positive (ehxA+) isolates, and 42 werestx−andehxA-negative isolates. Int-β, the most commonly identifiedeaesubtype (82 of 213 [38.5%] isolates), was associated with 21 serotypes, followed by Int-ζ (39 of 213 [18.3%] isolates; 11 serotypes), Int-θ (25 of 213 [11.7%] isolates; 15 serotypes), Int-γ (19 of 213 [8.9%] isolates; 9 serotypes), and Int-ε (21 of 213 [9.9%] isolates; 5 serotypes). Intimin subtypes α1, α2, κ, λ, ξ, μ, ν, and ι were infrequently identified; and Int-η was not detected. Phylogenetic analyses with the Phylip package of programs clustered the intimin subtypes into nine distinct families (α, β-ξ, γ, κ, ε-η-ν, ι-μ, λ, θ, and ζ). Our data confirm that ruminants are an important source of serologically and genetically diverse intimin-containingE. colistrains.
Quantifying Adenovirus-Neutralizing Antibodies by Luciferase Transgene Detection: Addressing Preexisting Immunity to Vaccine and Gene Therapy Vectors
Authors: Sprangers Mieke C. , Lakhai Wandena , Koudstaal Wouter , Verhoeven Marielle , Koel Björn F. , Vogels Ronald , Goudsmit Jaap , Havenga Menzo J. E. , Kostense Stefan
Published: November 2003

The presence of various levels of anti-adenovirus serotype 5 (Ad5)-neutralizing antibodies in humans is thought to contribute to the inconsistent clinical results obtained so far in diverse gene transfer and vaccination studies and might preclude universal dosing with recombinant Ad5. Prescreening of individuals eligible for Ad5 or alternative serotype treatment and subsequently tailoring the vector dose might aid in ensuring the consistency of clinical parameters. For this purpose, a qualified Ad neutralization assay is required. Here we have tested the different protocols used to date to determine anti-Ad neutralizing activity. Based on simplicity, speed, high throughput, sensitivity, and robustness, we propose a qualified assay in which Ad neutralization is monitored by luciferase reporter gene expression.
Genetic Diversity among
Borrelia
Strains Determined by Single-Strand Conformation Polymorphism Analysis of the
ospC
Gene and Its Association with Invasiveness
Authors: Lagal Vanessa , Postic Danièle , Ruzic-Sabljic Eva , Baranton Guy
Published: November 2003

Lyme borreliosis (LB) is a tick-borne spirochetal infection caused by three
Borrelia
species:
Borrelia afzelii
,
B. garinii
, and
B. burgdorferi
sensu stricto. LB evolves in two stages: a skin lesion called erythema migrans and later, different disseminated forms (articular, neurological, cardiac…). Previous research based on analysis of
ospC
sequences allowed the definition of 58 groups (divergence of <2% within a group and >8% between groups). Only 10 of these groups include all of the strains isolated from disseminated forms that are considered invasive. The aim of this study was to determine whether or not invasive strains belong to restricted
ospC
groups by testing human clinical strains isolated from disseminated forms. To screen for
ospC
genetic diversity, we used single-strand conformation polymorphism (SSCP) analysis. Previously known
ospC
sequences from 44 different strains were first tested, revealing that each
ospC
group had a characteristic SSCP pattern. Therefore, we studied 80 disseminated-form isolates whose
ospC
sequences were unknown. Of these, 28 (35%) belonged to previously known invasive groups. Moreover, new invasive groups were identified: six of
B. afzelii
, seven of
B. garinii
, and one of
B. burgdorferi
sensu stricto. This study confirmed that invasive strains are not distributed among all 69
ospC
groups but belong to only 24 groups. This suggests that OspC may be involved in the invasiveness of
B. burgdorferi
.
Comparison of PCR and Serology Assays for Early Diagnosis of Acute Q Fever
Authors: Fournier Pierre-Edouard , Raoult Didier
Published: November 2003

Q fever is a potentially severe disease which can occur in large outbreaks of acute infections and is a possible bioterrorism agent. In order to lessen the delay in diagnosing acute Q fever, we compared LightCycler Nested PCR (LCN
-
PCR), a rapid nested PCR assay that uses serum sampled early during the disease as a specimen and the LightCycler as a thermal cycler, to serology by indirect immunofluorescence. We used the 20-copy
htpAB
-associated element as the DNA target. The detection sensitivity of this method was one
Coxiella burnetii
DNA copy. We applied this method to the first serum samples taken from 100 patients diagnosed in our laboratory as having acute Q fever on the basis of clinical manifestations and serology and to 80 controls. The LCN-PCR had a specificity of 100%. The sensitivity was 26% when no antibodies were detected but only 5% with seropositive patients (
P
< 10
−2
). The technique was most efficient in the first 2 weeks following the onset of symptoms (
P
= 0.02), when its sensitivity was 24% compared with 14% for serology. With combined use of LCN-PCR and serology within the first 2 weeks, the sensitivity was significantly increased over that with serology alone (
P
< 10
−2
). Thus, we propose a strategy for improving the early diagnosis of acute Q fever where LCN-PCR should be performed together with serology in the first 2 weeks of the disease but should be reserved for seronegative patients in the next 2 weeks and not used later than 4 weeks following onset, when serology is highly sensitive.
Application of an rRNA Probe Matrix for Rapid Identification of Bacteria and Fungi from Routine Blood Cultures
Authors: Marlowe Elizabeth M. , Hogan James J. , Hindler Janet F. , Andruszkiewicz Irene , Gordon Pat , Bruckner David A.
Published: November 2003

One of the most important functions of the clinical microbiology laboratory is the identification of the etiology of sepsis. For this study, aliquots from 405 positive blood cultures were tested against a unique array of DNA probes directed against rRNA subsequences of bacteria and fungi for identification. Another 280 samples that were negative after 5 days of incubation were also tested. Blood culture bottles were incubated in a BacT/Alert3D instrument. For the rRNA assay, a 0.4-ml aliquot was removed, and the cells were pelleted by centrifugation. The pellet was washed and frozen at −70°C. Analysis of the pellet involved a lysis step and then the addition of samples to the reaction wells containing the probes in a microtiter plate format. Analysis was performed by using a hybridization protection assay. Results were taken through a series of deductive steps to obtain species, or in some cases genus, identification. Batch sample preparation required approximately 15 min, and sample analysis required another 60 min. Probe results were compared to conventional biochemical identifications. The probe test was negative for the 280 samples that were negative by the BacT/Alert 3D system and for another 21 samples that were false positive (the instrument signaled, but there was no growth). Microorganisms from the remaining 384 signal-positive samples included 60
Enterobacteriaceae
, 10
Pseudomonas aeruginosa
, 10 other gram-negative bacteria, 40
Staphylococcus aureus
, 152 coagulase-negative staphylococci, 28 streptococci, 22 enterococci, 21 other gram-positive bacteria, 8 anaerobes, and 16 yeast organisms. Seventeen cultures were polymicrobial, and one was gram positive and culture negative. Discordance between probe and conventional identification results was noted for only 12 (1.75%) samples. This novel rapid molecular approach to the identification of bacteria and yeast in blood cultures was highly sensitive (100%) and specific (96%).
Multicenter Study To Evaluate the OptiMAL Test for Rapid Diagnosis of Malaria in U.S. Hospitals
Authors: Palmer Carol J. , Bonilla J. Alfredo , Bruckner David A. , Barnett Elizabeth D. , Miller Nancy S. , Haseeb M. A. , Masci Joseph R. , Stauffer William M.
Published: November 2003

More than 1,000 cases of malaria are diagnosed each year in the United States. Reported numbers, however, may be artificially low because many clinicians fail to consider the diagnosis on presentation, U.S. hospital laboratory technologists have very limited experience in detecting and identifying malaria parasites, and reporting of malaria to state health departments is sporadic in many states. In this study, a rapid malaria diagnostic test, the OptiMAL test (DiaMed; under license from Flow Inc., Portland, Oreg.) was evaluated in six U.S. hospitals and compared with results of microscopy. The OptiMAL test is a 15-min rapid immunochromatographic test that both identifies and differentiates
Plasmodium falciparum
from non-
P. falciparum
malaria parasites on the basis of the detection of parasite lactate dehydrogenase in a drop of patient blood. A total of 216 specimens from patients suspected of having malaria were tested. Results indicated that 43 samples (20%) were positive for malaria parasites by microscopy (32
P. falciparum
, 11 non-
P. falciparum
) while 42 (19%) were positive by OptiMAL (31
P. falciparum
, 11 non-
P. falciparum
). The sensitivity of the OptiMAL test was 98%; its specificity was 100%, with positive and negative predictive values of 100 and 99%, respectively. Participating hospital physicians and laboratory directors independently reported that the OptiMAL rapid malaria test was accurate, easy to use, and well accepted by those working in their diagnostic laboratories. The overall conclusion was that integration of the OptiMAL rapid malaria test into the U.S. health care infrastructure would provide an important and easy-to-use tool for the timely diagnosis of malaria.
Seroprevalence of Antibodies against Human Herpesvirus 8 in a Population of Renal Transplant Recipients at Hôtel-Dieu de Québec Hospital
Authors: Delorme S. , Houde I. , Deschênes L.
Published: November 2003

We conducted a seroepidemiologic study to determine the prevalence of anti-human herpesvirus 8 antibodies in a renal transplant population at Hôtel-Dieu de Québec Hospital. Testing for immunoglobulin G antibodies against lytic and latent antigens was performed on serum samples from 150 renal transplant patients. Human immunodeficiency virus-positive patients with confirmed Kaposi's sarcoma were used as positive controls. None of the renal transplant patients tested positive.
In Vitro Activities of the New Antifungal Drug Eberconazole and Three Other Topical Agents against 200 Strains of Dermatophytes
Authors: Fernández-Torres Belkys , Inza Isabel , Guarro Josep
Published: November 2003

We have compared the in vitro activity of the new antifungal drug eberconazole with those of three other topical antifungal agents, clotrimazole, ketoconazole, and miconazole, against 200 strains of dermatophytes. MICs were determined by a microdilution method with optimal conditions determined in a previous study (an inoculum of 104CFU/ml, an incubation temperature of 28°C, an incubation period of 7 days, and a MIC endpoint of 100% inhibition of growth). In general, the four drugs tested showed low MICs. However, eberconazole was more active (P< 0.05) than the other three drugs against the majority of the species tested. Eberconazole represents an advantageous alternative for dermatophytoses where a topical therapy is required.
Evaluation of Acridine Orange Staining as a Replacement of Subcultures for BacT/ALERT-Positive, Gram Stain-Negative Blood Cultures
Authors: Adler Hildegard , Baumlin Nathalie , Frei Reno
Published: November 2003

Among 18,424 blood culture sets processed during a study period of 18 months, 85 bottles that were positive by the BacT/ALERT system were Gram stain negative. Both acridine orange staining and subcultures detected microorganisms in a total of 12 bottles. Acridine orange staining can replace subcultures of false-positive blood cultures.
Measurement of Epstein-Barr Virus DNA Loads in Whole Blood and Plasma by TaqMan PCR and in Peripheral Blood Lymphocytes by Competitive PCR
Authors: Wadowsky Robert M. , Laus Stella , Green Michael , Webber Steven A. , Rowe David
Published: November 2003

Epstein-Barr virus (EBV) DNA load values were measured in samples of whole blood (
n
= 60) and plasma (
n
= 59) by TaqMan PCR and in samples of peripheral blood lymphocytes (PBLs) (
n
= 60) by competitive PCR (cPCR). The samples were obtained from 44 transplant recipients. The whole-blood and PBL loads correlated highly (
r
2
> 0.900), whereas the plasma and PBL loads correlated poorly (
r
2
= 0.512). Testing of whole blood by TaqMan PCR is an acceptable alternative to testing of PBLs by cPCR for quantifying EBV DNA load.
Assessment of Laboratory Performance of Nucleic Acid Amplification Tests for Detection of
Mycobacterium tuberculosis
Authors: Ridderhof John C. , Williams Laurina O. , Legois Sue , Shult Peter A. , Metchock Beverly , Kubista Louise N. , Handsfield James H. , Fehd Ronald J. , Robinson Pamela H.
Published: November 2003

During implementation of the Centers for Disease Control and Prevention's
Mycobacterium tuberculosis
nucleic acid amplification (NAA) evaluation program, 27.1% of participants used the same biological safety cabinet for NAA and specimen processing; 28.8% reported not using unidirectional workflow. An association between false positives and adverse responses to quality assurance questions (
P
= 0.04) illustrated the need for following NCCLS recommendations.
Isolation of Members of the
Staphylococcus sciuri
Group from Urine and Their Relationship to Urinary Tract Infections
Authors: Stepanovic Srdjan , Ježek Petr , Vukovic Dragana , Dakic Ivana , Petráš Petr
Published: November 2003

During a 3-year study period, 32,741 urine samples were analyzed for the presence of members of the
Staphylococcus sciuri
group (
S. sciuri
,
S. lentus
, and
S. vitulinus
), and 13 isolates were identified. They presented 0.79% of the total number of coagulase-negative staphylococci isolated. One case of symptomatic urinary tract infection and five possible cases of asymptomatic bacteriuria caused by these bacteria were established. It is noteworthy, however, that over 50% of the isolates originated from hospitalized patients.
Comparison of Etest with Modified Broth Microdilution Method for Testing Susceptibility of
Aspergillus
spp. to Voriconazole
Authors: Serrano M. C. , Morilla D. , Valverde A. , Chávez M. , Espinel-Ingroff A. , Claro R. , Ramírez M. , Mazuelos E. Martín
Published: November 2003

We compared the Etest with a broth microdilution method, performed according to a modified National Committee for Clinical Laboratory Standards guideline (M38-A), for determining the in vitro susceptibility of 77 isolates of
Aspergillus
spp. (26
A. fumigatus
, 21
A. flavus
, 10
A. terreus
, 9
A. niger
, 5
A. nidulellus
, 4
A. glaucus
, and 2
A. flavipes
isolates). Overall, there was 92.2% agreement between both methods when Etest MICs were read at 24 h and 83.1% agreement when both methods were read at 48 h. When Etest MICs were read at 24 h, the agreement was >90% for all species tested except for
A. fumigatus
(84.6%). When Etest MICs were read at 48 h, the agreement ranged from 50 to 100%. The poorest agreement was seen with
A. glaucus
(50%) and
A. fumigatus
(65%). Where a discrepancy was observed between Etest and the reference method, the Etest MIC was generally higher. The Etest appears to be a suitable alternative procedure for testing the susceptibility of
Aspergillus
spp. to voriconazole.
Association of Cytolethal Distending Toxin Locus
cdtB
with Enteropathogenic
Escherichia coli
Isolated from Patients with Acute Diarrhea in Calcutta, India
Authors: Pandey Mritunjay , Khan Asis , Das Suresh C. , Sarkar Bhaswati , Kahali Soumen , Chakraborty Subhra , Chattopadhyay Santanu , Yamasaki Shinji , Takeda Yoshifumi , Nair G. Balakrish , Ramamurthy T.
Published: November 2003

Among
Escherichia coli
strains isolated from stool specimens from patients with acute diarrhea, 1.4% were found to harbor
cdtB
by use of enrichment cytolethal distending toxin (CDT) PCR. These isolates were identified as being enteropathogenic
E. coli
(EPEC). In a retrospective study using a probe hybridization assay, 6 of 138 EPEC strains were found to harbor the
cdtB
locus.
cdtB
-positive isolates mostly belong to the O86a and O127a serogroups, with the former being associated with higher expression of CDT. Pulsed-field gel electrophoresis profiles showed that the EPEC strains harboring
cdtB
strains are genetically diverse.
Bacitracin-Resistant Clone of
Streptococcus pyogenes
Isolated from Pharyngitis Patients in Belgium
Authors: Malhotra-Kumar Surbhi , Wang Shuang , Lammens Christine , Chapelle Sabine , Goossens Herman
Published: November 2003

We report 16 bacitracin-resistant
Streptococcus pyogenes
isolates recovered from pharyngitis patients in Belgium, 14 of which belonged to a particular
emm
type (
emm
28). All 16 isolates were constitutively resistant to macrolides and carried
erm
(B). The emergence of a bacitracin-resistant
S. pyogenes
clone raises questions about the continued reliability of bacitracin susceptibility testing for
S. pyogenes
identification.
Pericardial Effusion in a Homeless Man Due to
Bartonella quintana
Authors: Levy P. Y. , Fournier P. E. , Carta M. , Raoult D.
Published: November 2003

Bartonella quintana
may cause trench fever, endocarditis, bacillary angiomatosis, and chronic bacteremia, and a reemergence among homeless populations in cities has been noted. Pericarditis from
Rickettsia conorii
and
Coxiella burnetii
infection has been described, but there have been no reports of pericarditis due to
Bartonella
spp. We report a case of pericardial effusion due to
Bartonella quintana
in a homeless man, diagnosed on the basis of PCR detection of
Bartonella quintana
in a pericardial biopsy sample and a fourfold rise in antibody titers. The patient recovered within 2 weeks with antibiotics active against bartonellae.
Molecular Characterization of
Aegyptianella pullorum
(
Rickettsiales
,
Anaplasmataceae
)
Authors: Rikihisa Yasuko , Zhang Chunbin , Christensen Bruce M.
Published: November 2003

We sequenced the 16S rRNA and
groEL
genes of
Aegyptianella pullorum
, a small bacterium that infects and replicates only in avian red blood cells. A specific PCR test was developed to analyze
A. pullorum
DNA. Phylogenic analysis revealed
A. pullorum
is most closely related to
Anaplasma
spp.
Fatal Case of
Listeria innocua
Bacteremia
Authors: Perrin Monique , Bemer Michel , Delamare Catherine
Published: November 2003

Listeria innocua
is widespread in the environment and in food. This species has to date never been described in association with human disease. We report a case of fatal bacteremia caused by
L. innocua
in a 62-year-old patient.
Fatal Case of Endocarditis Associated with
Bartonella henselae
Type I Infection in a Domestic Cat
Authors: Chomel Bruno B. , Wey Aaron C. , Kasten Rickie W. , Stacy Brian A. , Labelle Philippe
Published: November 2003

We report the first feline case of
Bartonella henselae
endocarditis. Despite negative blood cultures, the cat had high
Bartonella
antibody titers and
B. henselae
type I DNA was detected in the damaged aortic valve. Microscopic examination of the valve revealed endocarditis with small silver positive coccoid structures in endothelial cells.
Relationship of Relapsing Hip Prosthesis Infection by
Staphylococcus aureus
with Gamma Interferon Deficiency
Authors: Honstettre Amélie , Mège Jean-Louis , Lina Gérard , Aubaniac Jean-Manuel , Drancourt Michel
Published: November 2003

Infections complicate 0.5 to 1% of surgeries for total hip prostheses.
Staphylococcus
species are the most common etiological agents. The role of host factors in the persistence of such infections despite appropriate therapy has yet to be determined. We report the defective immune response characterized by oversecretion of tumor necrosis factor and interleukin 10 and by undersecretion of gamma interferon in such a patient. Further study may determine the prevalence of such deficits and the most appropriate therapy for these patients.
THE ORDER PARAMETER FIELD FOR COSMIC STRING, INFLATION AND DARK ENERGY
Authors: ZHANG PENG-MING , DUAN YI-SHI , CAO LI-MING
Published: November 2003

We present a whole frame for the cosmic strings, inflation and dark energy with the complex scalar field which can be regarded as the order parameter of our universe. One can find that the comic strings emerge in the zeros of the complex scalar field in the early universe. And with the evolution of complex scalar field, inflation and dark energy can be understood in this frame.
SINGULARITY FREE COSMOLOGICAL SOLUTIONS OF EINSTEIN–MAXWELL EQUATIONS
Authors: YAZADJIEV STOYTCHO S. , RIZOV VENTSESLAV A.
Published: November 2003

We report on a new two-parameter class of cosmological solutions of the Einstein–Maxwell equations. The solutions have everywhere regular curvature invariants. We prove that the solutions are geodesically complete and globally hyperbolic.
ON THE FLATTENING OF NEGATIVE CURVATURE VIA T-DUALITY WITH A NON-CONSTANT B-FIELD
Authors: KRAUSE AXEL
Published: November 2003

In an earlier paper, Alvarez, Alvarez-Gaumé, Barbón and Lozano pointed out, that the only way to "flatten" negative curvature by means of a T-duality is by introducing an appropriate, non-constant NS–NS two-form B. In this paper, we are investigating this further and ask, whether it is possible to T-dualize AdS d space to flat space with some suitably chosen B. To answer this question, we derive a relationship between the original curvature tensor and the one of the T-dualized metric involving the B-field. It turns out that there is one component which is independent of B. By inspection of this component, we show that it is not possible to dualize AdS d to flat space irrespective of the choice of B. Finally, we examine the extension of AdS to an AdS 5 × S5 geometry and propose a chain of S- and T-dualities together with an SL (2, ℤ) coordinate transformation, leading to a dual D9-brane geometry.
NONTRIVIAL SOLITON SCATTERING IN PLANAR INTEGRABLE SYSTEMS
Authors: IOANNIDOU THEODORA
Published: November 2003

The behavior of solitons in integrable theories is strongly constrained by the integrability of the theory, that is by the existence of an infinite number of conserved quantities that these theories are known to possess. As a result, the soliton scattering of such theories is expected to be trivial (with no change of direction, velocity or shape). In this paper we present an extended review on soliton scattering of two spatial dimensional integrable systems which have been derived as dimensional reductions of the self-dual Yang–Mills equations and whose scattering properties are highly nontrivial.
CMB ANISOTROPY CONSTRAINTS ON FLAT-Λ AND OPEN CDM COSMOGONIES FROM DMR, UCSB SOUTH POLE, PYTHON, ARGO, MAX, WHITE DISH, OVRO, AND SuZIE DATA
Authors: MUKHERJEE PIA , GANGA KEN , RATRA BHARAT , ROCHA GRACA , SOURADEEP TARUN , SUGIYAMA NAOSHI , GORSKI KRZYSZTOF M.
Published: November 2003

We use joint likelihood analyses of combinations of fifteen cosmic microwave background (CMB) anisotropy data sets from the DMR, UCSB South Pole 1994, Python I–III, ARGO, MAX 4 and 5, White Dish, OVRO, and SuZIE experiments to constrain cosmogonies. We consider open and spatially-flat-Λ cold dark matter cosmogonies, with nonrelativistic-mass density parameter Ω0in the range 0.1–1, baryonic-mass density parameter ΩBin the range (0.005–0.029)h-2, and age of the universe t0in the range (10–20) Gyr.

Marginalizing over all parameters but Ω0, the data favor Ω0≃ 0.9–1 (0.4–0.6) flat-Λ (open) models. The range in deduced Ω0values is partially a consequence of the different combinations of smaller-angular-scale CMB anisotropy data sets used in the analyses, but more significantly a consequence of whether the DMR quadrupole moment is accounted for or ignored in the analysis. While the open model is difficult to reconcile with the results of analyses of more recent CMB anisotropy data, the lower values of Ω0found in this case are more easily reconciled with dynamical estimates of this parameter. For both flat-Λ and open models, after marginalizing over all other parameters, a lower ΩBh2≃ 0.005–0.009 is favored. This is also marginally at odds with estimates from more recent CMB anisotropy data and some estimates from standard nucleosynthesis theory and observed light element abundances. For both sets of models a younger universe with t0≃ 12–15 Gyr is favored, consistent with other recent non-CMB indicators. We emphasize that we have performed an exact analysis (i.e. from data to parameter likelihoods without the intermediate step of data compression into band powers), and since we consider only a small number of data sets, these results are tentative. More importantly, the analyses here do not rule out the currently favored flat-Λ model with Ω0~ 0.3, nor the larger ΩBh2values favored by some other data.
SOLUTION OF THE DIRAC EQUATION FOR POTENTIAL INTERACTION
Authors: ALHAIDARI A. D.
Published: November 2003

An effective approach for solving the three-dimensional Dirac equation for spherically symmetric local interactions, which we have introduced recently, is reviewed and consolidated. The merit of the approach is in producing Schrödinger-like equations for the spinor components that could simply be solved by correspondence with well-known exactly solvable nonrelativistic problems. Taking the nonrelativistic limit will reproduce the nonrelativistic problem. The approach has been used successfully in establishing the relativistic extension of all classes of shape-invariant potentials as well as other exactly solvable nonrelativistic problems. These include the Coulomb, Oscillator, Scarf, Pöschl–Teller, Woods–Saxon, etc.
POINT PARTICLE–SYMMETRIC TENSORS INTERACTION AND GENERALIZED GAUGE PRINCIPLE
Authors: SEGAL ARKADY Y.
Published: November 2003

The model of a point particle in the background of external symmetric tensor fields is analyzed from the higher spin theory perspective. It is proposed that the gauge transformations of the infinite collection of symmetric tensor fields may be read off from the covariance properties of the point particle action w.r.t. general canonical transformations. The gauge group turns out to be a semidirect product of all phase space canonical transformations to an Abelian ideal of "hyperWeyl" transformations and includes U(1) and general coordinate symmetries as a subgroup. A general configuration of external fields includes rank-0,1,2 symmetric tensors, so the whole system may be truncated to ordinary particle in Einstein–Maxwell backgrounds by switching off the higher-rank symmetric tensors. When otherwise all the higher rank tensors are switched on, the full gauge group provides a huge gauge symmetry acting on the whole infinite collection of symmetric tensors. We analyze this gauge symmetry and show that the symmetric tensors which couple to the point particle should not be interpreted as Fronsdal gauge fields, but rather as gauge fields of some conformal higher spin theories. It is shown that the Fronsdal fields system possesses twice as many symmetric tensor fields as is contained in the general background of the point particle. Besides, the particle action in general backgrounds is shown to reproduce De Wit–Freedman point particle–symmetric tensors first order interaction suggested many years ago, and extends their result to all orders in interaction, while the generalized equivalence principle completes the first order covariance transformations found in their paper, in all orders.
THE ANTICOMMUTATOR SPIN ALGEBRA, ITS REPRESENTATIONS AND QUANTUM GROUP INVARIANCE
Authors: ARIK M. , KAYSERILIOGLU U.
Published: November 2003

We define a 3-generator algebra obtained by replacing the commutators with anticommutators in the defining relations of the angular momentum algebra. We show that integer spin representations are in one to one correspondence with those of the angular momentum algebra. The half-integer spin representations, on the other hand, split into two representations of dimension [Formula: see text]. The anticommutator spin algebra is invariant under the action of the quantum group SO q(3) with q=-1.
DIRECT PHOTON PRODUCTION IN HIGH ENERGY HADRONIC AND NUCLEAR COLLISIONS: MEASURED DATA VERSUS A MODEL
Authors: GUPTAROY P. , DE BHASKAR , BHATTACHARYYA S.
Published: November 2003

This work is in response to the stimulus received from our fairly successful attempt at understanding in the recent past the problem of direct photon production only in gold–gold and lead–lead collisions from the viewpoint of a non-standard approach. The same nonconventional formalism would, once again, be applied to analyze the vast array of measurements on the inclusive cross sections of direct photons produced in several purely nuclear or hadronuclear collisions at very high energies. Besides, some of the cross section ratios would also be calculated and be compared with data on them. All this reveals and indicates a modest agreement between the model-based calculations and the actual measurements. The authors would also endeavor here to adduce the reasons for the discrepancies, if any.
MONOPOLES NEAR THE PLANCK SCALE AND UNIFICATION
Authors: LAPERASHVILI L. V. , RYZHIKH D. A. , NIELSEN H. B.
Published: November 2003

Considering our (3+1)-dimensional space–time as, in some way, discrete or lattice with a parameter a = λP, where λP is the Planck length, we have investigated the additional contributions of lattice artifact monopoles to beta functions of the renormalization group equations for the running fine structure constants αi(μ) (i = 1,2,3 correspond to the U(1), SU(2) and SU(3) gauge groups of the Standard Model) in the Family Replicated Gauge Group Model (FRGGM) which is an extension of the Standard Model at high energies. It was shown that monopoles have N fam times smaller magnetic charge in FRGGM than in SM (N fam is the number of families in FRGGM). We have estimated also the enlargement of a number of fermions in FRGGM leading to the suppression of the asymptotic freedom in the non-Abelian theory. We have shown that, in contrast to the case of anti-GUT when the FRGGM undergoes the breakdown at μ = μG ~ 1018 GeV , we have the possibility of unification if the FRGGM-breakdown occurs at μG ~ 1014 GeV . By numerical calculations we obtained an example of the unification of all gauge interactions (including gravity) at the scale μ GUT ≈ 1018.4 GeV . We discussed the possibility of [ SU (5)]3 or [ SO (10)]3 (SUSY or not SUSY) unifications.
NONCOMMUTATIVE EXTENDED WAVES AND SOLITON-LIKE CONFIGURATIONS IN N = 2 STRING THEORY
Authors: IHL MATTHIAS , UHLMANN SEBASTIAN
Published: November 2003

The Seiberg–Witten limit of fermionic N = 2 string theory with nonvanishing B-field is governed by noncommutative self-dual Yang–Mills theory (ncSDYM) in 2+2 dimensions. Conversely, the self-duality equations are contained in the equation of motion of N = 2 string field theory in a B-field background. Therefore finding solutions to noncommutative self-dual Yang–Mills theory on ℝ2,2 might help to improve our understanding of nonperturbative properties of string (field) theory. In this paper, we construct nonlinear soliton-like and multi-plane wave solutions of the ncSDYM equations corresponding to certain D-brane configurations by employing a solution generating technique, an extension of the so-called dressing approach. The underlying Lax pair is discussed in two different gauges, the unitary and the Hermitian gauge. Several examples and applications for both situations are considered, including Abelian solutions constructed from GMS-like projectors, noncommutative U(2) soliton-like configurations and interacting plane waves. We display a correspondence to earlier work on string field theory and argue that the solutions found here can serve as a guideline in the search for nonperturbative solutions of nonpolynomial string field theory.
AN ALGEBRAIC APPROACH TO LOGARITHMIC CONFORMAL FIELD THEORY
Authors: GABERDIEL MATTHIAS R.
Published: November 2003

A comprehensive introduction to logarithmic conformal field theory, using an algebraic point of view, is given. A number of examples are explained in detail, including the c=-2 triplet theory and the k=-4/3 affine su(2) theory. We also give some brief introduction to the work of Zhu.