bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Expressed Sequence Tag Data and Gene Expression Profiles Involved in Conidial Germination of
Fusarium oxysporum
Authors: Deng Ye , Dong Haitao , Jin Qingchao , Dai Cheng'en , Fang Yongqi , Liang Shen , Wang Ke , Shao Jing , Lou Yichun , Shi Wenqin , Vakalounakis Demetrios J. , Li Debao 
Published: February 2006

ABSTRACT

We obtained 3,372 tentative unique transcripts (TUTs) from a cDNA library of
Fusarium oxysporum
. A cDNA array with 3,158 TUTs was produced to analyze gene expression profiles in conidial germination. It seems that
ras
and other signaling genes, e.g.,
ccg
, cooperatively initiate conidial germination in
Fusarium
by increasing protein synthesis.
mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray
Authors: Bodrossy Levente , Stralis-Pavese Nancy , Konrad-Köszler Marianne , Weilharter Alexandra , Reichenauer Thomas G. , Schöfer David , Sessitsch Angela 
Published: February 2006

ABSTRACT
A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities.
Characterization of Bacterial Communities Associated with Deep-Sea Corals on Gulf of Alaska Seamounts
Authors: Penn Kevin , Wu Dongying , Eisen Jonathan A. , Ward Naomi 
Published: February 2006

ABSTRACT

Although microbes associated with shallow-water corals have been reported, deepwater coral microbes are poorly characterized. A cultivation-independent analysis of Alaskan seamount octocoral microflora showed that
Proteobacteria
(classes
Alphaproteobacteria
and
Gammaproteobacteria
),
Firmicutes
,
Bacteroidetes
, and
Acidobacteria
dominate and vary in abundance. More sampling is needed to understand the basis and significance of this variation.
Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental Applications
Authors: Liebich Jost , Schadt Christopher W. , Chong Song C. , He Zhili , Rhee Sung-Keun , Zhou Jizhong 
Published: February 2006

ABSTRACT

To optimize oligonucleotide probe design criteria, PCR products with different similarities to probes were hybridized to a functional gene microarray designed to detect homologous genes from different organisms. In contrast to more restrictive probe designs based on a single criterion, simultaneous consideration of the percent similarity (≤90%), the length of identical sequence stretches (≤20 bases), and the binding free energy (≥−35 kcal mol
−1
) was found to be predictive of probe specificity.
Measurement of Respiration Rates ofMethylobacterium extorquensAM1 Cultures by Use of a Phosphorescence-Based Sensor
Authors: Strovas Tim J. , Dragavon Joe M. , Hankins Tyler J. , Callis James B. , Burgess Lloyd W. , Lidstrom Mary E. 
Published: February 2006

ABSTRACTRespiration rates of bacterial cultures can be a powerful tool in gauging the effects of genetic manipulation and environmental changes affecting overall metabolism. We present an optical method for measuring respiration rates using a robust phosphorescence lifetime-based sensor and off-the-shelf technology. This method was tested with the facultative methylotrophMethylobacterium extorquensAM1 to demonstrate subtle mutant phenotypes.
Caenorhabditis elegans
Is a Model Host for
Listeria monocytogenes
Authors: Thomsen Line E. , Slutz Sandra S. , Tan Man-Wah , Ingmer Hanne 
Published: February 2006

ABSTRACT

Here we report that
Caenorhabditis elegans
nematodes fed
Listeria monocytogenes
die over the course of several days, as a consequence of an accumulation of bacteria in the worm intestine. Mutant strains previously shown to be important for virulence in mammalian models were also found to be attenuated in their virulence in
C. elegans
. However, ActA, which is required for actin-based intracellular motility, appears to be dispensable during infection of
C. elegans
, indicating that
L. monocytogenes
remains extracellular in
C. elegans
.
Freezing Induces Biased Results in the Molecular Detection of
Flavobacterium columnare
Authors: Suomalainen Lotta-Riina , Reunanen Hilkka , Ijäs Ritva , Valtonen E. Tellervo , Tiirola Marja 
Published: February 2006

ABSTRACT

Specific PCR detection and electron microscopy of
Flavobacterium columnare
revealed the risk of false-negative results in molecular detection of this fish pathogen. Freezing and thawing destroyed the cells so that DNA was for the most part undetectable by PCR. The detection of bacteria was also weakened after prolonged enrichment cultivation of samples from infected fish.
Isolation ofRickettsia felisin the Mosquito Cell Line C6/36
Authors: Horta Maurício C. , Labruna Marcelo B. , Durigon Edison L. , Schumaker Teresinha T. S. 
Published: February 2006

ABSTRACTWe report the isolation and establishment ofRickettsia felisin the C6/36 cell line. Rickettsial growth was intense, always with 90 to 100% of cells being infected after few weeks. The rickettsial isolate was confirmed by testing infected cells by PCR and sequencing fragments of three majorRickettsiagenes (gltA,ompB, and the 17-kDa protein gene).
Activities of Micafungin against 315 Invasive Clinical Isolates of Fluconazole-Resistant
Candida
spp
Authors: Messer S. A. , Diekema D. J. , Boyken L. , Tendolkar S. , Hollis R. J. , Pfaller M. A. 
Published: February 2006

ABSTRACT

Micafungin is a new echinocandin exhibiting broad-spectrum activity against
Candida
spp. The activity of the echinocandins against
Candida
species known to express intrinsic or acquired resistance to fluconazole is of interest. We determined the MICs of micafungin and caspofungin against 315 invasive clinical (bloodstream and other sterile-site) isolates of fluconazole-resistant
Candida
species obtained from geographically diverse medical centers between 2001 and 2004. MICs were determined using broth microdilution according to the CLSI reference method M27-A2. RPMI 1640 was used as the test medium, and we used the MIC endpoint of prominent growth reduction at 24 h. Among the 315 fluconazole-resistant
Candida
isolates, 146 (46%) were
C. krusei
, 110 (35%) were
C. glabrata
, 41 (13%) were
C. albicans
, and 18 (6%) were less frequently isolated species. Micafungin had good in vitro activity against all fluconazole-resistant
Candida
spp. tested; the MICs at which 50% (MIC
50
) and 90% (MIC
90
) of isolates were inhibited were 0.03 μg/ml and 0.06 μg/ml, respectively. All the fluconazole-resistant
Candida
spp. were inhibited at a micafungin MIC that was ≤1 μg/ml. Among the most common fluconazole-resistant
Candida
spp. tested in the collection,
C. glabrata
exhibited the lowest micafungin MICs (MIC
90
, ≤0.015 μg/ml), followed by
C. albicans
(MIC
90
, 0.03 μg/ml) and
C. krusei
(MIC
90
, 0.06 μg/ml). The new echinocandin micafungin has excellent in vitro activity against 315 invasive clinical isolates of fluconazole-resistant
Candida
, which represents the largest collection to date of fluconazole-resistant
Candida
isolates tested against micafungin. Micafungin may prove useful in the treatment of infections due to azole-resistant
Candida
.
Evaluation of the New GenoType Mycobacterium Assay for Identification of Mycobacterial Species
Authors: Russo Cristina , Tortoli Enrico , Menichella Donato 
Published: February 2006

ABSTRACTThe new commercial assay GenoType Mycobacterium, intended for the identification of mycobacteria, was evaluated with a panel of 197 strains belonging to 86 different taxa. The system, which relies on solid-phase reverse hybridization, is composed of two different kits: GenoType CM for the identification of more frequently detected mycobacterial species and GenoType AS for less common species. The sensitivity and specificity were 97.9% and 92.4% for the CM kit and 99.3% and 99.4% for the AS kit. Our results show that the system may represent a useful tool to substantially enlarge the number of mycobacteria that can be reliably identified in clinical laboratories.
Comparison of Two Commercially Available DNA Line Probe Assays for Detection of Multidrug-Resistant
Mycobacterium tuberculosis
Authors: Mäkinen Johanna , Marttila Harri J. , Marjamäki Merja , Viljanen Matti K. , Soini Hanna 
Published: February 2006

ABSTRACT

Two commercially available DNA line probe assays, Genotype MTBDR and INNO-LiPA Rif. TB, were evaluated for their abilities to detect resistance to isoniazid (INH) and rifampin (RIF) in 52
Mycobacterium tuberculosis
isolates. The test results were compared to those obtained by phenotypic drug susceptibility testing and sequencing. Compared to the results of phenotypic drug susceptibility testing, the Genotype MTBDR test results were concordant for INH for 47 of the 52 (90.4%) isolates, and both the Genotype MTBDR and the INNO-LiPA Rif. TB test results were concordant for RIF for 51 of the 52 (98.1%) isolates. The Genotype MTBDR test results correlated with the sequencing results for 48 of the 52 (92.3%) isolates and the INNO-LiPA Rif. TB results for 50 of the 52 (96.2%) isolates. Both assays are useful for the rapid screening of
M. tuberculosis
isolates obtained from patients suspected of having multidrug-resistant tuberculosis, but the GenoType MTBDR assay has the advantage of being able to detect resistance to both INH and RIF simultaneously.
Influence of Anti-FloR Antibody on Florfenicol Accumulation in Florfenicol-Resistant
Escherichia coli
and Enzyme-Linked Immunosorbent Assay for Detection of Florfenicol-Resistant
E. coli
Isolates
Authors: Wu Beibei , Xia Chun , Du Xiangdang , Cao Xingyuan , Shen Jianzhong 
Published: February 2006

ABSTRACT

To detect florfenicol-resistant
Escherichia coli
isolates by enzyme-linked immunosorbent assay (ELISA), anti-FloR1 antibodies were produced in mice using a recombinant glutathione
S
-transferase (GST)-FloR1 protein, which was expressed in a prokaryote expression system, as the antigen. The specificity of the murine anti-GST-FloR1 antibody and its influence on florfenicol accumulation in florfenicol-resistant isolates were investigated using Western blotting and high-performance liquid chromatography, respectively. Western blotting using the anti-FloR1 antibody showed specific binding of the antibody to the florfenicol-resistant FloR protein. Preincubation of florfenicol-resistant strains with the antibody significantly increased the intracellular accumulation of florfenicol and enhanced the bacterial susceptibility to florfenicol, suggesting that antibody binding to the FloR protein inhibited the activity of the efflux protein conferred by the
floR
gene. Analyses of florfenicol-resistant and -sensitive isolates by ELISA using the anti-FloR1 antibody showed good correlation between FloR protein expression and the
floR
genotype. The anti-FloR1 antibody-based ELISA is a useful tool for the detection of florfenicol-resistant bacteria harboring the
floR
gene.
Neisseria bacilliformis
sp. nov. Isolated from Human Infections
Authors: Han Xiang Y. , Hong Tao , Falsen Enevold 
Published: February 2006

ABSTRACT

Most
Neisseria
species are gram-negative cocci or diplococci; currently,
N. elongata
is the only species of human origin with a bacillary morphology. Here, we report isolation and characterization of eight strains of another bacillary
Neisseria
species from human infections. The organisms caused or contributed to either oral cavity-related or respiratory tract infections, and two strains were isolated from blood cultures. The 16S rRNA gene sequences of these organisms, being homogenous or nearly so (99.4 to 100% identity), matched at <96% known
Neisseria
species and formed a distinct group within the genus. Analysis of the cellular fatty acids showed broad similarity with a few
Neisseria
species. The organisms were gram negative and measured 0.6 μm by 1.3 to 3.0 μm. They grew well on chocolate agar and on sheep blood agar but did not grow on modified Thayer-Martin agar. They were positive for oxidase and negative for indole production. There was no acid production from dextrose, lactose, maltose, or sucrose. The tests for catalase reaction, nitrate reduction, and tributilin varied with the strains. These results suggest that these organisms represent a novel species within the genus
Neisseria
, for which the name
Neisseria bacilliformis
sp. nov. is proposed. The type strain is MDA2833 = ATCC BAA-1200
T
= CCUG50858
T
. Distinction between
N. bacilliformis
and
N. elongata
can be made confidently by 16S rRNA gene sequencing or cellular fatty acid profiling but may be difficult by morphology or routine biochemical tests.
Genotyping Measles Virus by Real-Time Amplification Refractory Mutation System PCR Represents a Rapid Approach for Measles Outbreak Investigations
Authors: Waku-Kouomou Diane , Alla Amal , Blanquier Bariza , Jeantet Damien , Caidi Hayat , Rguig Ahmed , Freymuth François , Wild Fabian T. 
Published: February 2006

ABSTRACT
Real-time PCR has been developed to genotype measles virus (MV) isolates. MV strains circulating in epidemics in Gabon in 1984, Cameroon in 2001, Morocco in 2003, and France in 2004 were investigated. We developed a real-time amplification refractory mutation system PCR (RT-AMRS PCR) using SYBR green fluorescent dye. Six pairs of primers for RT-ARMS PCR were designed to specifically amplify genotypes A, B2, B3.1, B3.2, C2, and D7. Genotypes could be differentiated by melting curve analysis. All strains were also confirmed by direct sequencing. Using the result obtained by direct sequencing and phylogenetic analysis as the reference, the accuracy of MV by RT-ARMS PCR and melting curve analysis was 97%. However, the latter method is more rapid and sensitive than the former method. This method could be a useful tool for molecular epidemiological studies of MV, providing an efficient alternative for large-scale studies.
Multilocus Microsatellite Typing as a New Tool for Discrimination of
Leishmania infantum
MON-1 Strains
Authors: Ochsenreither Sebastian , Kuhls Katrin , Schaar Matthias , Presber Wolfgang , Schönian Gabriele 
Published: February 2006

ABSTRACT

The
Leishmania donovani
complex, which consists of
L. donovani
,
L. infantum
-
L. chagasi
, and
L. archibaldi
, is responsible for visceral manifestations of leishmaniasis. Multilocus enzyme electrophoresis is the standard method for the characterization and identification of strains of
Leishmania.
For
L. infantum
, the predominance of zymodeme MON-1 significantly reduces the discriminative power of this approach. In the present study, we developed 17 independent polymorphic microsatellite markers for the typing of strains of
L. infantum
, with the main emphasis on zymodeme MON-1. The discriminative powers of 11 markers selected from among these markers were tested by using a panel of 63 isolates of the
L. donovani
complex. Unique multilocus genotypes were observed for the strains analyzed, with only three exceptions. Model-based and distance-based analyses of the data set showed comparable results. It was possible to discriminate between
L. donovani
sensu stricto, a non-MON-1 group of
L. infantum
isolates, and a MON-1 group of
L. infantum
isolates. Within MON-1, three clusters with geographical correlations became apparent. The frequency of heterozygosity in the alleles analyzed varied extremely between the different groups of isolates. The main clusters described are not consistent with species definitions based on isoenzyme analysis but confirm the results of former PCR-based investigations.
Bead-Based Multiplex Genotyping of Human Papillomaviruses
Authors: Schmitt Markus , Bravo I. G. , Snijders Peter J. F. , Gissmann Lutz , Pawlita Michael , Waterboer Tim 
Published: February 2006

ABSTRACT
Typing of human papillomaviruses (HPV) by DNA hybridization procedures, such as reverse line blot (RLB) assay, is sensitive and well validated. However, the application of these assays to high-throughput analyses is limited. Here, we describe the development of multiplex human papillomavirus genotyping (MPG), a quantitative and sensitive high-throughput procedure for the identification of multiple high- and low-risk genital HPV genotypes in a single reaction. MPG is based on the amplification of HPV DNA by a general primer PCR (GP5+/6+) and the subsequent detection of the products with type-specific oligonucleotide probes coupled to fluorescence-labeled polystyrene beads (Luminex suspension array technology). Up to 100 different HPV types can be detected simultaneously with MPG, and the method is fast and labor saving. We detected all 22 HPV types examined with high specificity and reproducibility (the median interplate coefficient of variation was below 10%). Detection limits for the different HPV types varied between 100 and 800 pg of PCR products. We compared the performance of MPG to an established RLB assay on GP5+/6+-PCR products derived from 94 clinical samples. The evaluation showed an excellent agreement (kappa = 0.922) but also indicated a higher sensitivity of MPG. In conclusion, MPG appears to be highly suitable for large-scale epidemiological studies and vaccination trials as well as for routine diagnostic purposes.
Two New Colorimetric Methods for Early Detection of Vancomycin and Oxacillin Resistance in
Staphylococcus aureus
Authors: Coban Ahmet Y. , Bozdogan Bülent , Cihan Cigdem Cekic , Cetinkaya Ebru , Bilgin Kemal , Darka Ozge , Akgunes Alper , Durupinar Belma , Appelbaum Peter C. 
Published: February 2006

ABSTRACT

We developed two colorimetric methods for the detection of vancomycin- and oxacillin-resistant
Staphylococcus aureus
in ≤6 h: (i) a nitrate reductase assay and (ii) a resazurin microplate method. MICs agreed with results obtained by CLSI methods for oxacillin. However, detection of vancomycin resistance required a larger inoculum. These methods may be recommended for the detection of vancomycin- and oxacillin-resistant
S. aureus.
Use of Different Stains for Microscopic Evaluation of Corneal Scrapings for Diagnosis of Microsporidial Keratitis
Authors: Joseph Joveeta , Murthy Somasheila , Garg Prashant , Sharma Savitri 
Published: February 2006

ABSTRACT

Retrospective evaluation of potassium hydroxide plus calcofluor white (KOH+CFW), Gram, Giemsa, and modified Ziehl-Neelsen (1% H
2
SO
4
, cold) stains for the detection of microsporidia in corneal scrapings from 30 patients showed KOH+CFW and acid-fast stains to be most efficient (29/30 [96.7%] and 28/30 [93.3%], respectively) in the diagnosis of microsporidial keratitis.
Use of Cefoxitin-Based Selective Broth for Improved Detection of Methicillin-Resistant
Staphylococcus aureus
Authors: Fang Hong , Hedin Göran 
Published: February 2006

ABSTRACT

A cefoxitin-based selective broth was evaluated for its efficiency in detecting methicillin-resistant
Staphylococcus aureus
(MRSA) by the use of laboratory reference strains, clinical isolates of different clones, and clinical samples. The cefoxitin-based broth was proved to be more sensitive and rapid for the detection of MRSA strains, especially heterogeneously resistant strains, than the oxacillin-based broth.
Proximal Region of the Gene Encoding Cytadherence-Related Protein Permits Molecular Typing of
Mycoplasma genitalium
Clinical Strains by PCR-Restriction Fragment Length Polymorphism
Authors: Musatovova Oxana , Herrera Caleb , Baseman Joel B. 
Published: February 2006

ABSTRACT

Restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified proximal region of the gene encoding cytadherence accessory protein P110 (MG192) revealed DNA sequence divergences among 54
Mycoplasma genitalium
clinical strains isolated from the genitourinary tracts of women attending a sexually transmitted disease-related health clinic, plus one from the respiratory tract and one from synovial fluid. Seven of 56 (12.5%) strains exhibited RFLPs following digestion of the proximal region with restriction endonuclease MboI or RsaI, or both. No sequence variability was detected in the distal portion of the gene.
Unique NS5b Hepatitis C Virus Gene Sequence Consensus Database Is Essential for Standardization of Genotype Determinations in Multicenter Epidemiological Studies
Authors: Laperche Syria , Saune Karine , Dény Paul , Duverlie Gilles , Alain Sophie , Chaix Marie-Laure , Gaudy Catherine , Lunel Françoise , Pawlotsky Jean-Michel , Payan Christopher , Pozzetto Bruno , Tamalet Catherine , Thibault Vincent , Vallet Sophie , Bouchardeau Françoise , Izopet Jacques , Lefrère Jean-Jacques 
Published: February 2006

ABSTRACT
A multicenter study of NS5b hepatitis C virus (HCV) genotype determination involving 12 laboratories demonstrates that any laboratory with expertise in sequencing techniques would be able to provide a reliable HCV genotype for clinical and epidemiological purposes as long as they are provided a consensus reference sequence database.
Timely Diagnosis of Disseminated Toxoplasmosis by Sputum Examination
Authors: Laibe Sophy , Ranque Stéphane , Curtillet Catherine , Faraut Françoise , Dumon Henri , Franck Jacqueline 
Published: February 2006

ABSTRACT

The diagnosis of disseminated toxoplasmosis in a 14-year-old allogeneic bone marrow recipient with graft-versus-host disease was determined by the detection of
Toxoplasma gondii
tachyzoites in sputum smears. Sputum analysis is a valuable alternative in the clinical assessment of pulmonary toxoplasmosis, especially when conventional invasive techniques are not practicable.
Capnocytophaga canimorsus
Mycotic Abdominal Aortic Aneurysm: Why the Mailman Is Afraid of Dogs
Authors: Tierney David M. , Strauss Leigh P. , Sanchez Jason L. 
Published: February 2006

ABSTRACT

We describe the first case report of a mycotic abdominal aortic aneurysm secondary to
Capnocytophaga canimorsus
in an immunocompetent 65-year-old man. The exposure occurred after his dog scratched his arm and subsequently licked the wound. A review of
C. canimorsus
, a rarely pathogenic but potentially devastating bacterium, is also presented.
Direct Detection of
Cardiobacterium hominis
in Serum from a Patient with Infective Endocarditis by Broad-Range Bacterial PCR
Authors: Gatselis N. , Malli E. , Papadamou G. , Petinaki E. , Dalekos G. N. 
Published: February 2006

ABSTRACT

Bacterial DNA was detected directly in the serum of a patient with endocarditis by broad-range 16S rRNA PCR followed by sequencing and analysis of the results by the BLAST search. Using these methods,
Cardiobacterium hominis
was identified in 2 days from the date of serum collection. The microorganism was also isolated and identified using conventional methods (bacterial culture and biochemical tests) 17 days from the date of sample collection. This is the first report showing the direct detection of
C. hominis
in a patient's serum using molecular-based methods, emphasizing their potential usefulness as additional and rapid diagnostic tools for the detection and identification of fastidious bacteria.