bluuebunny/crossref_metadata_2025_split huggingface dataset:
Codenitrification and Denitrification Are Dual Metabolic Pathways through Which Dinitrogen Evolves from Nitrate inStreptomyces antibioticus
Authors: Kumon Yasuyuki , Sasaki Yasuyuki , Kato Isao , Takaya Naoki , Shoun Hirofumi , Beppu Teruhiko 
Published: July 2002

ABSTRACTWe screened actinomycete strains for dinitrogen (N2)-producing activity and discovered thatStreptomyces antibioticusB-546 evolves N2and some nitrous oxide (N2O) from nitrate (NO3−). Most of the N2that evolved from the heavy isotope ([15N]NO3−) was15N14N, indicating that this nitrogen species consists of two atoms, one arising from NO3−and the other from different sources. This phenomenon is similar to codenitrification in fungi. The strain also evolved less, but significant, amounts of15N15N from [15N]NO3−in addition to15N15NO with concomitant cell growth. Prior to the production of N2and N2O, NO3−was rapidly reduced to nitrite (NO2−) accompanied by distinct cell growth, showing that the actinomycete strain is a facultative anaerobe that depends on denitrification and nitrate respiration for anoxic growth. The cell-free activities of denitrifying enzymes could be reconstituted, supporting the notion that the15N15N and15N15NO species are produced by denitrification from NO3−via NO2−. We therefore demonstrated a unique system in an actinomycete that produces gaseous nitrogen (N2and N2O) through both denitrification and codenitrification. The predominance of codenitrification over denitrification along with oxygen tolerance is the key feature of nitrate metabolism in this actinomycete.
Postexponential Regulation of
sin
Operon Expression in
Bacillus subtilis
Authors: Shafikhani Sasha H. , Mandic-Mulec Ines , Strauch Mark A. , Smith Issar , Leighton Terrance 
Published: July 2002

ABSTRACT

The expression of many gene products required during the early stages of
Bacillus subtilis
sporulation is regulated by
sinIR
operon proteins. Transcription of
sinIR
from the P1 promoter is induced at the end of exponential growth. In vivo transcription studies suggest that P1 induction is repressed by the transition-state regulatory protein Hpr and is induced by the phosphorylated form of Spo0A. In vitro DNase I footprinting studies confirmed that Hpr, AbrB, and Spo0A are
trans
-acting transcriptional factors that bind to the P1 promoter region of
sinIR
. We have also determined that the P1 promoter is transcribed in vitro by the major vegetative sigma factor, ς
A
, form of RNA polymerase.
Localization of the Cortex Lytic Enzyme CwlJ in Spores of
Bacillus subtilis
Authors: Bagyan Irina , Setlow Peter 
Published: July 2002

ABSTRACT

The enzyme CwlJ is involved in the depolymerization of cortex peptidoglycan during germination of spores of
Bacillus subtilis
. CwlJ with a C-terminal His tag was functional and was extracted from spores by procedures that remove spore coat proteins. However, this CwlJ was not extracted from disrupted spores by dilute buffer, high salt concentrations, Triton X-100, Ca
2+
-dipicolinic acid, dithiothreitol, or peptidoglycan digestion, disappeared during spore germination, and was not present in
cotE
spores in which the spore coat is aberrant. These findings indicate the following: (i) the reason decoated and
cotE
spores germinate poorly with dipicolinic acid is the absence of CwlJ from these spores; and (ii) CwlJ is located in the spore coat, presumably tightly associated with one or more other coat proteins.
Effect of Different Concentrations of H-NS Protein on Chromosome Replication and the Cell Cycle in
Escherichia coli
Authors: Atlung T. , Hansen F. G. 
Published: July 2002

ABSTRACT

Flow cytometric analysis showed that the
hns205
and
hns206
mutants, lacking the abundant nucleoid-associated protein H-NS, have decreased origin concentration, as well as a low number of origins per cell (ploidy). The most striking observation was that the low ploidy was due to a very short replication time, e.g., at 30°C it was halved compared to that of the

hns
+

strain. The decreased origin concentration was not caused by a decreased
dnaA
gene expression, and the
hns206
mutant had normal DnaA protein concentrations. The replication phenotypes of the
hns206
mutant were independent of RpoS. Cells overproducing H-NS from a LacI-controlled plasmid had a normal origin concentration, indicating that H-NS is not controlling initiation. A wild-type H-NS concentration is, however, required to obtain a wild-type origin concentration, since cells with an intermediate H-NS concentration had an intermediate origin concentration. Two lines of evidence point to an indirect effect of H-NS on initiation. First, H-NS did not show high-affinity binding to any part of
oriC
, and H-NS had no effect on transcription entering
oriC
from the
mioC
promoter. Second, in a shift experiment with the
hns206
mutant, when H-NS protein was induced to wild-type levels within 10 min, it took more than one generation before the origin concentration started to increase.
Use of the
Caulobacter crescentus
Genome Sequence To Develop a Method for Systematic Genetic Mapping
Authors: West Lisandra , Yang Desiree , Stephens Craig 
Published: July 2002

ABSTRACT

The functional analysis of sequenced genomes will be facilitated by the development of tools for the rapid mapping of mutations. We have developed a systematic approach to genetic mapping in
Caulobacter crescentus
that is based on bacteriophage-mediated transduction of strategically placed antibiotic resistance markers. The genomic DNA sequence was used to identify sites distributed evenly around the chromosome at which plasmids could be nondisruptively integrated. DNA fragments from these sites were amplified by PCR and cloned into a kanamycin-resistant (Kan
r
) suicide vector. Delivery of these plasmids into
C
.
crescentus
resulted in integration via homologous recombination. A set of 41 strains containing Kan
r
markers at 100-kb intervals was thereby generated. These strains serve as donors for generalized transduction using bacteriophage φCr30, which can transduce at least 120 kb of DNA. Transductants are selected with kanamycin and screened for loss of the mutant phenotype to assess linkage between the marker and the site of the mutation. The dependence of cotransduction frequency on sequence distance was evaluated using several markers and mutant strains. With these data as a standard, previously unmapped mutations were readily localized to DNA sequence intervals equivalent to less than 1% of the genome. Candidate genes within the interval were then examined further by subcloning and complementation analysis. Mutations resulting in sensitivity to ampicillin, in nutritional auxotrophies, or temperature-sensitive growth were mapped. This approach to genetic mapping should be applicable to other bacteria with sequenced genomes for which generalized transducing phage are available.
Fluorescent Amplified-Fragment Length Polymorphism Subtyping of the S
almonella enterica
Serovar Enteritidis Phage Type 4 Clone Complex
Authors: Desai Meeta , Threlfall E. John , Stanley John 
Published: July 2002

ABSTRACT

Fluorescent amplified-fragment length polymorphism (FAFLP) analysis, a high-resolution PCR-based genome fingerprinting method, was used to subtype
Salmonella enterica
serovar Enteritidis phage type 4. This single phage type is responsible for the majority of salmonellosis in Europe. Twenty strains isolated from nine outbreaks, five isolates from sporadic cases of human infection, four strains of poultry origin, and one laboratory-derived strain were comparatively studied by pulsed-field gel electrophoresis (PFGE) and FAFLP analysis. Following macrorestriction with
Xba
I, PFGE classified 73% of PT4 strains as a single type. FAFLP analysis was carried out with the primer pair
Eco
RI+0 and
Mse
I+C, by simultaneously sampling 170 to 190 loci throughout the PT4 genome. Twenty-three FAFLP profiles, with 1 to 61 amplified-fragment differences, were found among the 30 strains. The index of discriminatory power of FAFLP analysis was 0.98, compared to 0.47 for PFGE. FAFLP analysis assigned genotypes to each PT4 outbreak, as well as sporadic PT4 infections, a significant development for the epidemiology and control of this zoonotic enteric pathogen.
Rapid Detection of Enterohemorrhagic
Escherichia coli
by Real-Time PCR with Fluorescent Hybridization Probes
Authors: Bellin Tobias , Pulz Matthias , Matussek Andreas , Hempen Hans-Günther , Gunzer Florian 
Published: July 2002

ABSTRACT

In this report, we present a PCR protocol for rapid identification of enterohemorrhagic
Escherichia coli
on a LightCycler instrument. In a multiplex assay, the genes encoding Shiga toxin 1 and Shiga toxin 2 are detected in a single reaction capillary. A complete analysis of up to 32 samples takes about 45 min.
Identification of CTX-M-14 Extended-Spectrum β-Lactamase in Clinical Isolates of
Shigella sonnei
,
Escherichia coli
, and
Klebsiella pneumoniae
in Korea
Authors: Pai Hyunjoo , Choi Eun-Hwa , Lee Hoan-Jong , Hong Jung Yun , Jacoby George A. 
Published: July 2002

ABSTRACT

CTX-M-14 β-lactamase was identified in a stool isolate of
Shigella sonnei
and in blood isolates of
Escherichia coli
(one isolate) and
Klebsiella pneumoniae
(two isolates) from different parts of Korea. The amino acid sequence differed by one amino acid from CTX-M-9 (Ala-231→ Val) and was identical to that of β-lactamases recently found in China and Japan.
Immunofluorescence Method for Detection of Ebola Virus Immunoglobulin G, Using HeLa Cells Which Express Recombinant Nucleoprotein
Authors: Saijo Masayuki , Niikura Masahiro , Morikawa Shigeru , Kurane Ichiro 
Published: July 2002

ABSTRACT
A novel recombinant baculovirus which expresses Ebola virus (EBO) nucleoprotein (NP) under the control of the cytomegalovirus immediate-early promoter was constructed. HeLa cells abortively infected with the baculovirus expressed EBO NP, and this was used as an immunofluorescent (IF) antigen to detect EBO immunoglobulin G (IgG) antibody. This IF method has high efficacy in detecting EBO IgG antibody in clinical specimens, indicating its usefulness in the diagnosis of EBO infections and seroepidemiological studies.
Evaluation of United States-Licensed Human Immunodeficiency Virus Immunoassays for Detection of Group M Viral Variants
Authors: Koch Walter H. , Sullivan Patrick S. , Roberts Charles , Francis Kori , Downing Robert , Mastro Timothy D. , Nkengasong John , Hu Dale , Masciotra Silvina , Schable Charles , Lal Renu B. 
Published: July 2002

ABSTRACT
Six Food and Drug Administration (FDA)-licensed human immunodeficiency virus type 1 (HIV-1) and HIV-1/2 immunoassays, including five enzyme immunoassays and one rapid test, were challenged with up to 250 serum samples collected from various global sites. The serum samples were from individuals known to be infected with variants of HIV-1 including group M subtypes A, B, B′, C, D, E, F, and G and group O. All immunoassays detected the vast majority of samples tested. Three samples produced low signal over cutoff values in one or more tests: a clade B sample, an untypeable sample with a low antibody titer, and a group O sample. It is concluded that HIV-1 immunoassays used in the United States are capable of detecting most HIV-1 group M variants.
Low Prevalence of Community-Acquired Methicillin-Resistant
Staphylococcus aureus
in Adults at a University Hospital in the Central United States
Authors: Suntharam Nila , Hacek Donna , Peterson Lance R. 
Published: July 2002

ABSTRACT

Community-acquired MRSA (CA-MRSA) is potentially a new emerging pathogen with most strains susceptible to many antimicrobials except for β-lactam antibiotics. We retrospectively reviewed MRSA isolates during a 20-month study period (January 1998 through August 1999) and investigated those that were clindamycin susceptible. Patients were not considered to harbor CA-MRSA if they had been admitted to a hospital within the preceding 2 years or if their isolate had been obtained more than 72 h after admission. There were 2,817
S. aureus
isolates, with 1,071 (38%) being MRSA. Of these 1,071 isolates, 161 were clindamycin susceptible; these were recovered from 81 patients. Of these 81 patients, 20 appeared to have community-acquired strains, but only 2 could be confirmed as having CA-MRSA.
Detection of Amantadine-Resistant Influenza A Virus Strains in Nursing Homes by PCR-Restriction Fragment Length Polymorphism Analysis with Nasopharyngeal Swabs
Authors: Saito Reiko , Oshitani Hitoshi , Masuda Hiroki , Suzuki Hiroshi 
Published: July 2002

ABSTRACT

Annual consumption of amantadine increased abruptly after its approval for the treatment of influenza A virus infections in Japan in 1998, and the emergence of amantadine-resistant viruses is now a matter of concern. To detect resistant influenza A virus strains, we have developed a PCR-restriction fragment length polymorphism (PCR-RFLP) analysis for nasopharyngeal swabs. Three different primer sets for nested PCR were designed to incorporate restriction sites into the amplicon to differentiate single-amino-acid substitutions at positions 27, 30, and 31 that confer resistance in the transmembrane domain of the M2 protein. Each PCR product was digested with respective endonucleases (
Bsp
LU11I for amino acid change at position 27,
Hha
I for position 30, and
Sca
I for position 31), and the polymorphisms were determined by electrophoresis. Thirty-four (24.1%) of 141 PCR-positive samples had resistance patterns in eight nursing homes in the 1998–1999 season. Thirty-one viruses (91.2%) showed a change at position 31 (serine to asparagine), three viruses (8.8%) showed a change at position 30 (alanine to threonine), and none showed a change at position 27. The incidence of resistant viruses did not show any significant difference between four facilities where amantadine was used mainly for influenza treatment and four other facilities where it was used only for Parkinson’s disease, values being 27.6 and 16.3%, respectively. We have confirmed that the PCR-RFLP method is useful for detecting amantadine-resistant strains directly from nasopharyngeal swabs and that resistant viruses were circulating in nursing homes where the drug was used not only for influenza virus but also for Parkinson’s disease.
Cryptococcosis in a Bottlenose Dolphin (
Tursiops truncatus
) Caused by
Cryptococcus neoformans
var.
gattii
Authors: Miller W. George , Padhye Arvind A. , van Bonn William , Jensen Eric , Brandt Mary E. , Ridgway Sam H. 
Published: July 2002

ABSTRACT

We describe the first case of cryptococcosis caused by
Cryptococcus neoformans
var.
gattii
in a male Atlantic bottlenose dolphin (
Tursiops truncatus
). The dolphin showed clinical signs of tachypnea, transient dyspnea, and mild tachycardia and developed multiple hyperechoic nodules, parenchymal consolidation, and thickening of pleura. A diagnosis of bronchopneumonia with pleuritis was made. Itraconazole therapy was implemented for 120 days, and trough levels in serum were within or above the suggested therapeutic range. Titers of cryptococcal antigen in serum increased eightfold during therapy, and the case had a fatal outcome. Necropsy examination findings included enlarged pulmonary lymph nodes and extensive coalescing granulomatous lesions throughout both lungs. Histologic examination revealed numerous, spherical to ellipsoidal, mucicarmine-positive, 3- to 14-μm, encapsulated, budding cells consistent with
C. neoformans
. Culture of the lung tissue yielded colonies of
C. neoformans
. The isolate was urease positive and nitrate negative and exhibited phenoloxidase activity. It was positive on canavanine-glycine-bromothymol blue agar. When tested by the Iatron serodiagnostic reagent kit (Iatron Laboratories, Inc.), it was shown to belong to serotype B.
Characterization of Shiga Toxin-Producing
Escherichia coli
O26 Strains and Establishment of Selective Isolation Media for These Strains
Authors: Hiramatsu Reiji , Matsumoto Masakado , Miwa Yoshio , Suzuki Yasumoto , Saito Makoto , Miyazaki Yutaka 
Published: July 2002

ABSTRACT

We characterized the carbohydrate-fermenting ability of 31 strains of Shiga toxin-producing
Escherichia coli
(STEC) O26 isolated from diarrhea patients in Aichi Prefecture, Japan, in order to establish selective isolation media for these strains. None of the 31 STEC O26 strains (24 O26:H11, 7 O26:H−) fermented rhamnose, whereas all of the other 108 STEC strains (100 O157, 8 O111) and all of the non-STEC strains except one (i.e., 58 of 59) fermented rhamnose. The great majority of the STEC O26 strains (96.8% [30 of 31]) showed very high resistance to potassium tellurite (MIC ≥ 50 μg/ml), whereas the majority of the non-STEC strains (72.9% [43 of 59]) showed very high sensitivity (MIC ≤ 1.56 μg/ml) to this compound. Accordingly, we developed a rhamnose-MacConkey (RMAC) medium in which the lactose in MacConkey medium was replaced by rhamnose, and cefixime-tellurite-RMAC (CT-RMAC) medium in which potassium tellurite (2.5 mg/liter) and cefixime (0.05 mg/liter) were added to RMAC. All of the STEC O26 strains generated colorless (rhamnose-nonfermented) colonies on both media; the vast majority of selected
E. coli
strains (95.7% [89 of 93; including 26 STEC O157, 8 STEC O111]), other than STEC O26, generated red colonies on RMAC, and most of the non-STEC strains (84.7% [50 of 59]) did not grow on CT-RMAC. We demonstrate that both the RMAC and the CT-RMAC media can be used for the isolation of STEC O26 and that CT-RMAC has better specificity for the routine isolation for STEC O26 in a laboratory.
Prevalence of Parvovirus B19 and Parvovirus V9 DNA and Antibodies in Paired Bone Marrow and Serum Samples from Healthy Individuals
Authors: Heegaard Erik D. , Petersen Bodil Laub , Heilmann Carsten J. , Hornsleth Allan 
Published: July 2002

ABSTRACTParvovirus B19 (hereafter referred to as B19) exhibits a marked tropism to human bone marrow (BM), and infection may lead to erythema infectiosum, arthropathy, hydrops fetalis, and various hematologic disorders. Recently, a distinct parvovirus isolate termed V9 with an unknown clinical spectrum was discovered. In contrast to the many studies of B19 serology and viremia, valid information on the frequency of B19 or V9 DNA in the BM of healthy individuals is limited. To develop a reference value, paired BM and serum samples from healthy subjects were tested for the presence of B19 and V9 DNA and specific antibodies. Immunoglobulin M (IgM) was not found in any of the serum samples. The prevalence of IgG showed a gradual and steady increase from 37% in children aged 1 to 5 years to 87% in people aged >50 years. When 190 well-characterized subjects were examined, B19 DNA was detected in the BM of 4 individuals (2.1%; 95% confidence interval, 0.58 to 5.3%) while none of the paired serum samples showed evidence of circulating viral DNA. V9 DNA was not found in any of the BM or serum samples. The finding of B19 DNA probably indicated a primary infection in one 7-year-old individual and reinfection or reactivation of persistent infection in the remaining three persons, aged 47 to 58 years. Serving as a benchmark for future studies, these findings are useful when interpreting epidemiologic data, performing BM transplantation, or considering clinical implications of parvovirus infection.
Biofilm Production by Isolates of
Candida
Species Recovered from Nonneutropenic Patients: Comparison of Bloodstream Isolates with Isolates from Other Sources
Authors: Shin Jong Hee , Kee Seung Jung , Shin Myung Geun , Kim Soo Hyun , Shin Dong Hyeon , Lee Sang Ku , Suh Soon Pal , Ryang Dong Wook 
Published: July 2002

ABSTRACT

Biofilm production has been implicated as a potential virulence factor of some
Candida
species responsible for catheter-related fungemia in patients receiving parenteral nutrition. We therefore compared clinical bloodstream isolates representing seven different
Candida
species to each other and to those from other anatomical sites for the capacity to form biofilms in glucose-containing medium. Potential associations between the capacity to form biofilms and the clinical characteristics of fungemia were also analyzed. Isolates included the following from nonneutropenic patients: 101 bloodstream isolates (35
C. parapsilosis
, 30
C. albicans
, 18
C. tropicalis
, 8
C. glabrata
, and 10 other
Candida
species isolates) and 259 clinical isolates from other body sites (116
C. albicans
, 53
C. glabrata
, 43
C. tropicalis
, 17
C. parapsilosis
, and 30 other
Candida
species isolates). Organisms were grown in Sabouraud dextrose broth (SDB) containing a final concentration of 8% glucose to induce biofilm formation, as published previously. Biofilm production was determined by both visual and spectrophotometric methods. In this medium, biofilm production by
C. albicans
isolates was significantly less frequent (8%) than that by non-
C. albicans Candida
species (61%;
P
< 0.0001). The overall proportion of non-
C. albicans Candida
species isolates from the blood that produced biofilms was significantly higher than that of non-
C. albicans Candida
isolates obtained from other sites (79% versus 52%;
P
= 0.0001). Bloodstream isolates of
C. parapsilosis
alone were significantly more likely to be biofilm positive than were
C. parapsilosis
isolates from other sites (86% versus 47%;
P
= 0.0032). Non-
C. albicans Candida
species, including
C. parapsilosis
, were more likely to be biofilm positive if isolates were derived from patients whose candidemia was central venous catheter (CVC) related (95%;
P
< 0.0001) and was associated with the use of total parenteral nutrition (TPN) (94%;
P
< 0.005). These data suggest that the capacity of
Candida
species isolates to produce biofilms in vitro in glucose-containing SDB may be a reflection of the pathogenic potential of these isolates to cause CVC-related fungemia in patients receiving TPN.
Detection of a Human Rotavirus with G12 and P[9] Specificity in Thailand
Authors: Pongsuwanna Y. , Guntapong R. , Chiwakul M. , Tacharoenmuang R. , Onvimala N. , Wakuda M. , Kobayashi N. , Taniguchi K. 
Published: July 2002

ABSTRACT
G12 rotavirus has not been detected anywhere in the world since the first detection of a human strain, L26 (G12, P1B[4]), in the Philippines in 1990. In this study, we isolated a human rotavirus (strain T152) with a VP7 of G12 specificity from the stool of an 11-month-old diarrheic patient in Thailand. The strain T152 exhibited a long RNA pattern and subgroup I specificity. In the comparison of the nucleotide and amino acid sequences of the VP7 gene of strain T152 with those of rotaviruses with different G type specificities, strain T152 showed the highest identity, 90.9 and 93.9%, respectively, to G12 prototype strain L26. In contrast, the VP4 gene of strain T152 showed the highest identity with P[9] specificity of human strains K8 and AU-1 and feline strains Cat2 and FRV-1, with homologies of 89.3 to 90.6% at the nucleotide level and 93.9 to 95.6% at the amino acid level. Thus, strain T152 was found to be a natural reassortant strain with G12 and P[9] specificities.