bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unusual Microbial Xylanases from Insect Guts
Authors: Brennan YaLi , Callen Walter N. , Christoffersen Leif , Dupree Paul , Goubet Florence , Healey Shaun , Hernández Myrian , Keller Martin , Li Ke , Palackal Nisha , Sittenfeld Ana , Tamayo Giselle , Wells Steve , Hazlewood Geoffrey P. , Mathur Eric J. , Short Jay M. , Robertson Dan E. , Steer Brian A. 
Published: June 2004

ABSTRACT
Recombinant DNA technologies enable the direct isolation and expression of novel genes from biotopes containing complex consortia of uncultured microorganisms. In this study, genomic libraries were constructed from microbial DNA isolated from insect intestinal tracts from the orders Isoptera (termites) and Lepidoptera (moths). Using a targeted functional assay, these environmental DNA libraries were screened for genes that encode proteins with xylanase activity. Several novel xylanase enzymes with unusual primary sequences and novel domains of unknown function were discovered. Phylogenetic analysis demonstrated remarkable distance between the sequences of these enzymes and other known xylanases. Biochemical analysis confirmed that these enzymes are true xylanases, which catalyze the hydrolysis of a variety of substituted β-1,4-linked xylose oligomeric and polymeric substrates and produce unique hydrolysis products. From detailed polyacrylamide carbohydrate electrophoresis analysis of substrate cleavage patterns, the xylan polymer binding sites of these enzymes are proposed.
Discovery of the Novel Candidate Phylum “
Poribacteria
” in Marine Sponges
Authors: Fieseler Lars , Horn Matthias , Wagner Michael , Hentschel Ute 
Published: June 2004

ABSTRACT

Marine sponges (
Porifera
) harbor large amounts of commensal microbial communities within the sponge mesohyl. We employed 16S rRNA gene library construction using specific PCR primers to provide insights into the phylogenetic identity of an abundant sponge-associated bacterium that is morphologically characterized by the presence of a membrane-bound nucleoid. In this study, we report the presence of a previously unrecognized evolutionary lineage branching deeply in the domain
Bacteria
that is moderately related to the
Planctomycetes
,
Verrucomicrobia
, and
Chlamydia
lines of decent. Because members of this lineage showed <75% 16S rRNA gene sequence similarity to known bacterial phyla, we suggest the status of a new candidate phylum, named “
Poribacteria
”, to acknowledge the affiliation of the new bacterium with sponges. The affiliation of the morphologically conspicuous sponge bacterium with the novel phylogenetic lineage was confirmed by fluorescence in situ hybridization with newly designed probes targeting different sites of the poribacterial 16S rRNA. Consistent with electron microscopic observations of cell compartmentalization, the fluorescence signals appeared in a ring-shaped manner. PCR screening with “
Poribacteria
”-specific primers gave positive results for several other sponge species, while samples taken from the environment (seawater, sediments, and a filter-feeding tunicate) were PCR negative. In addition to a report for
Planctomycetes
, this is the second report of cell compartmentalization, a feature that was considered exclusive to the eukaryotic domain, in prokaryotes.
Methods for Enhanced Culture Recovery of
Francisella tularensis
Authors: Petersen Jeannine M. , Schriefer Martin E. , Gage Kenneth L. , Montenieri John A. , Carter Leon G. , Stanley Miles , Chu May C. 
Published: June 2004

ABSTRACT

Francisella tularensis
is found in a wide variety of hosts and extrahost environments, making culture recovery a diagnostic challenge. Here we demonstrate improved recovery times and good sensitivity (90%) when cultures were inoculated on the site of an investigation using fresh tissues. For contaminated specimens, antibiotic supplementation of enriched cysteine heart agar blood culture medium improved recovery of
F. tularensis
by 81.1%. For transport of tissues, immediate freezing yielded culture recovery rates as high as 94%.
Noninvasive Pigment Identification in Single Cells from Living Phototrophic Biofilms by Confocal Imaging Spectrofluorometry
Authors: Roldán M. , Thomas F. , Castel S. , Quesada A. , Hernández-Mariné M. 
Published: June 2004

ABSTRACTA new imaging technique for the analysis of fluorescent pigments from a single cell is reported. It is based on confocal scanning laser microscopy coupled with spectrofluorometric methods. The setup allows simultaneous establishment of the relationships among pigment analysis in vivo, morphology, and three-dimensional localization inside thick intact microbial assemblages.
Bacterial Strains Isolated from Different Niches Can Exhibit Different Patterns of Adhesion to Substrata
Authors: Bakker Dewi P. , Postmus Bart R. , Busscher Henk J. , van der Mei Henny C. 
Published: June 2004

ABSTRACT
Various mechanisms have been demonstrated to be operative in bacterial adhesion to surfaces, but whether bacterial adhesion to surfaces can ever be captured in one generally valid mechanism is open to question. Although many papers in the literature make an attempt to generalize their conclusions, the majority of studies of bacterial adhesion comprise only two or fewer strains. Here we demonstrate that three strains isolated from a medical environment have a decreasing affinity for substrata with increasing surface free energy, whereas three strains from a marine environment have an increasing affinity for substrata with increasing surface free energy. Furthermore, adhesion of the marine strains related positively with substratum elasticity, but such a relation was absent in the strains from the medical environment. This study makes it clear that strains isolated from a given niche, whether medical or marine, utilize different mechanisms in adherence, which hampers the development of a generalized theory for bacterial adhesion to surfaces.
Enhancement of Cry19Aa Mosquitocidal Activity against
Aedes aegypti
by Mutations in the Putative Loop Regions of Domain II
Authors: Abdullah Mohd Amir F. , Dean Donald H. 
Published: June 2004

ABSTRACT

Improvements in the mosquitocidal activity of
Bacillus thuringiensis
Cry19Aa were achieved by protein engineering of putative surface loop residues in domain II through rational design. The improvement of
Aedes
toxicity in Cry19Aa was 42,000-fold and did not affect its toxicity against
Anopheles
or
Culex
.
Short-Duration Low-Direct-Current Electrical Field Treatment Is a Practical Tool for Considerably Reducing Counts of Gram-Negative Bacteria Entrapped in Gel Beads
Authors: Zvitov R. , Zohar-Perez C. , Nussinovitch A. 
Published: June 2004

ABSTRACT

Application of a direct-current electrical field for very short times can serve as a practical nonthermal procedure to reduce or modify the microbial distribution in gel beads. The viability of
Escherichia coli
and
Serratia marcescens
entrapped in alginate and agarose beads decreases as the field intensity and duration of electrical field increase.
Differences between Betaproteobacterial Ammonia-Oxidizing Communities in Marine Sediments and Those in Overlying Water
Authors: Freitag Thomas E. , Prosser James I. 
Published: June 2004

ABSTRACT

To assess links between betaproteobacterial ammonia-oxidizing bacteria (AOB) in marine sediment and in overlying water, communities in Loch Duich, Scotland, were characterized by analysis of clone libraries and denaturant gradient gel electrophoresis of 16S rRNA gene fragments.
Nitrosospira
cluster 1-like sequences were isolated from both environments, but different sequence types dominated water and sediment samples. Detailed phylogenetic analysis of marine
Nitrosospira
cluster 1-like sequences in Loch Duich and surrounding regions suggests the existence of at least two different phylogenetic subgroups, potentially indicative of new lineages within the betaproteobacterial AOB, representing different marine ecotypes.
Nocardia arthritidis
sp. nov., a New Pathogen Isolated from a Patient with Rheumatoid Arthritis in Japan
Authors: Kageyama Akiko , Torikoe Kimiaki , Iwamoto Masahiro , Masuyama Jun-Ichi , Shibuya Yasuhiro , Okazaki Hitoaki , Yazawa Katsukiyo , Minota Seiji , Kroppenstedt Reiner M. , Mikami Yuzuru 
Published: June 2004

ABSTRACT

Two different bacterial strains with different drug susceptibilities were isolated from the sputum and an inflammatory discharge from a swelling in the left thigh of a patient with rheumatoid arthritis. Both bacterial strains were provisionally assigned to the genus
Nocardia
on the basis of their morphological and chemotaxonomic characteristics and were further studied in order to establish their taxonomic status. One strain (IFM 10034) was identified as
Nocardia farcinica
on the basis of its physiological characteristics. The other strain, which was designated
Nocardia
sp. strain IFM 10035
T
, revealed a unique pattern of phenotypic properties that distinguished it from other representatives of established
Nocardia
species. Comparative 16S rRNA gene sequence studies of
Nocardia
sp. strain IFM 10035
T
also showed that the bacterium was closely related to the species
Nocardia beijingensis
. Determination of DNA-DNA relatedness, however, indicated that
Nocardia
sp. strain IFM 10035
T
could be delineated from
N. beijingensis
. The genotypic and phenotypic data combined indicated that the bacterium merits description as a new
Nocardia
species. The name proposed for the new species is
Nocardia arthritidis
sp. nov., the type strain being IFM 10035
T
(NBRC 100137
T
, JCM 12120
T
, DSM44731
T
). The present study suggests that
Nocardia
infections can be caused by multiple species of the bacterium.
Implications of Molecular Genotyping of
Helicobacter pylori
Isolates from Different Human Populations by Genomic Fingerprinting of Enterobacterial Repetitive Intergenic Consensus Regions for Strain Identification and Geographic Evolution
Authors: Hussain M. Abid , Kauser Farhana , Khan Aleem A. , Tiwari Santosh , Habibullah Chittoor M. , Ahmed Niyaz 
Published: June 2004

ABSTRACT

Biogeographic partitioning of the genome is typical of the gastric pathogen
Helicobacter pylori
. Such population-specific evolution could serve as a model for understanding host-pathogen interaction and the impact of genetic drift and recombination on insular populations. With a total of 320 isolates from six geographic regions (Japan, India, England, Spain, Ireland, Africa, and Peru) analyzed by enterobacterial repetitive intergenic consensus (ERIC)-based genotyping, we examined genetic affinities among various
H. pylori
populations in the world. Several strain-specific and region-specific differences were observed by ERIC-based typing. Polymorphic ERIC patterns indicated that the ERIC sequences are in fact dispersed in the
H. pylori
chromosome at different locations separated by various distances. Phylogenetic analysis of 61 representative isolates revealed three distinct genetic clusters populated by isolates with shared ERIC types independent of the
cag
right-junction motif type and
vacA
allele status. Among the notable genetic relationships were the genotypic similarities between Irish and Japanese and between Peruvian and Japanese isolates. Insular genotypic characteristics of Irish isolates amid genetic similarity to East Asian, as well as North European, strains have been once again proved in this study. Peruvian genotypes were more similar to those of Japanese isolates than to those of Iberian or European isolates. Given the current debate on the origin and age of present-day
H. pylori
, this is a significant finding that supports the possibility of ancient colonization of Amerindians with East Asian strains. Genotypic data presented here will be additionally helpful in realizing the importance of
H. pylori
geographical genomics in the development of gastroduodenal pathology.
Specific T-Cell Epitopes for Immunoassay-Based Diagnosis ofMycobacterium tuberculosisInfection
Authors: Brock Inger , Weldingh Karin , Leyten Eliane M. S. , Arend Sandra M. , Ravn Pernille , Andersen Peter 
Published: June 2004

ABSTRACTThe currently used method for immunological detection of tuberculosis infection, the tuberculin skin test, has low specificity. Antigens specific forMycobacterium tuberculosisto replace purified protein derivative are therefore urgently needed. We have performed a rigorous assessment of the diagnostic potential of four recently identified antigens (Rv2653, Rv2654, Rv3873, and Rv3878) from genomic regions that are lacking from theMycobacterium bovisbacillus Calmette-Guérin (BCG) vaccine strains as well as from the most common nontuberculous mycobacteria. The fine specificity of potential epitopes in these molecules was evaluated by sensitive testing of the T-cell responses of peripheral blood mononuclear cells derived fromM. bovisBCG-vaccinated healthy individuals to synthesized overlapping peptides. Three of the four molecules contained regions with significant specificity problems (Rv2653, Rv3873, and Rv3878). We selected and combined the specific peptide stretches from the four proteins not recognized byM. bovisBCG-vaccinated individuals. These peptide stretches were tested with peripheral blood mononuclear cells obtained from patients with microscopy- or culture-confirmed tuberculosis and from healthyM. bovisBCG-vaccinated controls. The combination of the most promising stretches from this analysis showed a sensitivity level (57%) comparable to the level found with the two well-knownM. tuberculosis-specific proteins ESAT-6 and CFP-10 (75 and 66%, respectively). The combination of ESAT-6, CFP-10, and the novel specific peptide stretches gave an overall sensitivity of 84% at a specificity of 97%. In a validation experiment with new experimental groups, the sensitivities obtained were 57% for the combination of peptides and 90% for the combination of the peptides, ESAT-6, and CFP-10. This combination gave a specificity of 95%.
Development of a Multiplex PCR-Ligase Detection Reaction Assay for Diagnosis of Infection by the Four Parasite Species Causing Malaria in Humans
Authors: McNamara David T. , Thomson Jodi M. , Kasehagen Laurin J. , Zimmerman Peter A. 
Published: June 2004

ABSTRACT

The diagnosis of infections caused by
Plasmodium
species is critical for understanding the nature of malarial disease, treatment efficacy, malaria control, and public health. The demands of field-based epidemiological studies of malaria will require faster and more sensitive diagnostic methods as new antimalarial drugs and vaccines are explored. We have developed a multiplex PCR-ligase detection reaction (LDR) assay that allows the simultaneous diagnosis of infection by all four parasite species causing malaria in humans. This assay exhibits sensitivity and specificity equal to those of other PCR-based assays, identifying all four human malaria parasite species at levels of parasitemias equal to 1 parasitized erythrocyte/μl of blood. The multiplex PCR-LDR assay goes beyond other PCR-based assays by reducing technical procedures and by detecting intraindividual differences in species-specific levels of parasitemia. Application of the multiplex PCR-LDR assay will provide the sensitivity and specificity expected of PCR-based diagnostic assays and will contribute new insight regarding relationships between the human malaria parasite species and the human host in future epidemiological studies.
Development of a Species-Specific Probe forPythium insidiosumand the Diagnosis of Pythiosis
Authors: Schurko Andrew M. , Mendoza Leonel , de Cock Arthur W. A. M. , Bedard James E. J. , Klassen Glen R. 
Published: June 2004

ABSTRACTPythium insidiosum, the only species in the genus that infects mammals, is the etiological agent of pythiosis, a granulomatous disease characterized by cutaneous and subcutaneous lesions and vascular diseases. Accurate diagnosis of pythiosis and identification of its causal agent are often inconsistent with current immunological diagnostic methods. A species-specific DNA probe was constructed by using a 530-bp HinfI fragment from the ribosomal DNA intergenic spacer ofP. insidiosum.When the probe was incubated with dot blots of genomic DNA from 104Pythiumspecies, it hybridized only to the DNA ofP. insidiosumandP. destruens—two species that have been considered conspecific. The probe also hybridized to DNA from 22P. insidiosumisolates in this study, regardless of their geographic origin or animal host. When tested against genomic DNA from other pathogenic organisms (Aspergillus fumigatus,Basidiobolus ranarum,Conidiobolus coronatus,Lagenidium giganteum,Paracoccidioides brasiliensis, andPrototheca wickerhamii), no cross-hybridization of the probe was detected. The specificity of the probe to hybridize to genomic DNA from all isolates ofP. insidiosumand not cross-react with DNA from otherPythiumspecies or pathogens that cause symptoms similar to pythiosis in their hosts makes it a powerful tool for the accurate diagnosis of pythiosis. In addition, the probe has the potential for pathological and environmental diagnostic applications.
Analysis of the Allelic Diversity of the Mycobacterial Interspersed Repetitive Units inMycobacterium tuberculosisStrains of the Beijing Family: Practical Implications and Evolutionary Considerations
Authors: Mokrousov Igor , Narvskaya Olga , Limeschenko Elena , Vyazovaya Anna , Otten Tatiana , Vyshnevskiy Boris 
Published: June 2004

ABSTRACTA study set comprised 44Mycobacterium tuberculosisstrains of the Beijing family selected for their representativeness among those previously characterized by IS6110-RFLP and spoligotyping (Northwest Russia, 1997 to 2003). In the present study, these strains were subjected to mycobacterial interspersed repetitive units (MIRU) typing to assess a discriminatory power of the 12-MIRU-loci scheme (P. Supply et al., J. Clin. Microbiol. 39:3563-3571, 2001). The 44 Russian Beijing strains were subdivided into 12 MIRU types with identical profiles: 10 unique strains and two major types shared by 10 and 24 strains. Thus, basically, two distinct sublineages appear to shape the evolution of the Beijing strains in Russia. Most of the MIRU loci were found to be (almost) monomorphic in the Russian Beijing strains; the Hunter-Gaston discriminatory index (HGDI) for all 12 loci taken together was 0.65, whereas MIRU26 (the most variable in our study) showed a moderate level of discrimination (0.49). The results were compared against all available published MIRU profiles of Beijing strains from Russia (3 strains) and other geographic areas (51 strains in total), including South Africa (38 strains), East Asia (7 strains), and the United States (4 strains). A UPGMA (unweighted pair-group method with arithmetic averages)-based tree was constructed. Interestingly, no MIRU types were shared by Russian and South African strains (the two largest samples in this analysis), whereas both major Russian types included also isolates from other locations (United States and/or East Asia). This implies the evolution of the Beijing genotype to be generally strictly clonal, although a possibility of a convergent evolution of the MIRU loci cannot be excluded. We propose a dissemination of the prevailing local Beijing clones to have started earlier in South Africa rather than in Russia since more monomorphic loci were identified in Russian samples than in South African samples (mean HGDI scores, 0.08 versus 0.17). To conclude, we suggest to use a limited number of MIRUs for preliminary subdivision of Beijing strains in Russian (loci 26 + 31), South African (10 + 26 + 39), and global settings (10 + 26 + 39).
Hepatitis B Virus Genotypes and Precore and Core Mutants in Brazilian Patients
Authors: Sitnik Roberta , Pinho João Renato Rebello , Bertolini Dennis Armando , Bernardini Antonio Plinio , da Silva Luiz Caetano , Carrilho Flair José 
Published: June 2004

ABSTRACT
A method for genotyping hepatitis B virus by partial HBsAg gene sequencing with primers common to all known genotypes was developed. Mutations related to anti-HBs resistance are also detected with this method. Samples from 103 Brazilian patients were analyzed. Precore and core region of these viruses were also sequenced in 101 patients. Genotypes A, B, C, D, and F were found with frequencies of 49.5, 2.9, 13.6, 24.3, and 9.7%, respectively. Genotypes B and C were found only in Asian patients, whereas genotypes A, D, and F were more common in patients without an Asian background. Precore mutants were found in 32 (31.7%) of 101 patients, with a higher frequency in those infected with genotype D (22 of 25 [88.0%]). Analysis of nucleotide 1858 showed presence of thymine in all patients with genotypes B, C, and D and in a few patients with genotypes A (10.0%) and F (30.0%), who showed more frequently the presence of cytosine. This nucleotide was closely related to the presence of precore mutants. Mutations in the basal core promoter were found in 64 of 101 (63.4%) samples. These mutations were more frequent in patients infected with genotype F (90.0%) and less frequent in patients infected with genotype B (33.3%). Deletions in this region were found in two genotype C-infected patients.
Human Papillomavirus Testing with the Hybrid Capture 2 Assay and PCR as Screening Tools
Authors: Kulmala S.-M. , Syrjänen S. , Shabalova I. , Petrovichev N. , Kozachenko V. , Podistov J. , Ivanchenko O. , Zakharenko S. , Nerovjna R. , Kljukina L. , Branovskaja M. , Grunberga V. , Juschenko A. , Tosi P. , Santopietro R. , Syrjänen K. 
Published: June 2004

ABSTRACT

The recognition of high-risk human papillomaviruses (HPVs) as etiological agents of cervical cancer has increased the demands to use testing for HPV for the detection of abnormal cervical smears and for cervical cancer screening. The present study compared the performance of the Hybrid Capture 2 (HC2) assay with that of PCR for the detection of significant cervical lesions in 1,511 women with different risks for HPV infections in three New Independent States of the former Soviet Union. The results showed that the level of agreement between the HC2 assay and PCR was substantial, with a kappa (Cohen) value of 0.669 (95% confidence interval [CI], 0.629 to 0.709). Of the 228 samples with discrepant results, 92 were positive by the HC2 assay but negative by PCR, whereas 136 samples were PCR positive but HC2 assay negative. The positive predictive values (PPVs) of the HC2 assay and PCR in detecting high-grade intraepithelial lesions (HSILs) were 4.5% (95% CI, 3.5 to 5.5%) and 3.6% (95% CI, 2.7 to 4.5%), respectively, and the negative predictive values (NPVs) were 99.6% (95% CI, 99.3 to 99.9%) and 99.3% (95% CI, 98.9 to 99.7%), respectively. The sensitivities of the HC2 assay and PCR for the detection of HSILs were 85.2 and 74.0%, respectively, and the specificities were 67.2 and 64.1%, respectively. In receiver operating characteristic (ROC) analysis, the performance of the HC2 assay for the detection of HSILs was excellent (
P
= 0.0001); the area under the ROC analysis curve was 0.858 (95% CI, 0.811 to 0.905), and the optimal balance between sensitivity (86.5%) and specificity (80%) was obtained with an HC2 assay cutoff level of 15.6 relative light units/positive control. Use of this cutoff would increase the specificity of the HC2 assay to 80.0% without compromising sensitivity. In conclusion, the results of PCR and the HC2 assay were concordant for 85% of samples, resulting in substantial reproducibility. Both tests had low PPVs, equal specificities, and equal (almost 100%) NPVs for the detection of HSILs; but the sensitivity of the HC2 assay was slightly better.