bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discordant 16S and 23S rRNA Gene Phylogenies for the Genus
Helicobacter
: Implications for Phylogenetic Inference and Systematics
Authors: Dewhirst Floyd E. , Shen Zeli , Scimeca Michael S. , Stokes Lauren N. , Boumenna Tahani , Chen Tsute , Paster Bruce J. , Fox James G. 
Published: August 2005

ABSTRACT

Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus
Helicobacter
. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found
Wolinella succinogenes
to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12
Helicobacter
species. IVSs were found in helices 10, 25, and 45, as well as between helices 31′ and 27′. Simultaneous insertion of IVSs at three sites was found in
H. mesocricetorum.
Biodiversity-Based Identification and Functional Characterization of the Mannose-Specific Adhesin ofLactobacillus plantarum
Authors: Pretzer Gabriele , Snel Johannes , Molenaar Douwe , Wiersma Anne , Bron Peter A. , Lambert Jolanda , de Vos Willem M. , van der Meer Roelof , Smits Mari A. , Kleerebezem Michiel 
Published: August 2005

ABSTRACTLactobacillus plantarumis a frequently encountered inhabitant of the human intestinal tract, and some strains are marketed as probiotics. Their ability to adhere to mannose residues is a potentially interesting characteristic with regard to proposed probiotic features such as colonization of the intestinal surface and competitive exclusion of pathogens. In this study, the variable capacity of 14L. plantarumstrains to agglutinateSaccharomyces cerevisiaein a mannose-specific manner was determined and subsequently correlated with anL. plantarumWCFS1-based genome-wide genotype database. This led to the identification of four candidate mannose adhesin-encoding genes. Two genes primarily predicted to code for sortase-dependent cell surface proteins displayed a complete gene-trait match. Their involvement in mannose adhesion was corroborated by the finding that a sortase (srtA) mutant ofL. plantarumWCFS1 lost the capacity to agglutinateS. cerevisiae. The postulated role of these two candidate genes was investigated by gene-specific deletion and overexpression inL. plantarumWCFS1. Subsequent evaluation of the mannose adhesion capacity of the resulting mutant strains showed that inactivation of one candidate gene (lp_0373) did not affect mannose adhesion properties. In contrast, deletion of the other gene (lp_1229) resulted in a complete loss of yeast agglutination ability, while its overexpression quantitatively enhanced this phenotype. Therefore, this gene was designated to encode the mannose-specific adhesin (Msa; gene name,msa) ofL. plantarum. Domain homology analysis of the predicted 1,000-residue Msa protein identified known carbohydrate-binding domains, further supporting its role as a mannose adhesin that is likely to be involved in the interaction ofL. plantarumwith its host in the intestinal tract.
Characterization of the Genome Composition of
Bartonella koehlerae
by Microarray Comparative Genomic Hybridization Profiling
Authors: Lindroos Hillevi L. , Mira Alex , Repsilber Dirk , Vinnere Olga , Näslund Kristina , Dehio Michaela , Dehio Christoph , Andersson Siv G. E. 
Published: August 2005

ABSTRACT

Bartonella henselae
is present in a wide range of wild and domestic feline hosts and causes cat-scratch disease and bacillary angiomatosis in humans. We have estimated here the gene content of
Bartonella koehlerae
, a novel species isolated from cats that was recently identified as an agent of human endocarditis. The investigation was accomplished by comparative genomic hybridization (CGH) to a microarray constructed from the sequenced 1.93-Mb genome of
B. henselae
. Control hybridizations of labeled DNA from the human pathogen
Bartonella quintana
with a reduced genome of 1.58 Mb were performed to evaluate the accuracy of the array for genes with known levels of sequence divergence. Genome size estimates of
B. koehlerae
by pulsed-field gel electrophoresis matched that calculated by the CGH, indicating a genome of 1.7 to 1.8 Mb with few unique genes. As in
B. quintana
, sequences in the prophage and the genomic islands were reported absent in
B. koehlerae
. In addition, sequence variability was recorded in the chromosome II-like region, where
B. koehlerae
showed an intermediate retention pattern of both coding and noncoding sequences. Although most of the genes missing in
B. koehlerae
are also absent from
B. quintana
, its phylogenetic placement near
B. henselae
suggests independent deletion events, indicating that host specificity is not solely attributed to genes in the genomic islands. Rather, the results underscore the instability of the genomic islands even within bacterial populations adapted to the same host-vector system, as in the case of
B. henselae
and
B. koehlerae
.
Domain Structure of HrpE, the Hrp Pilus Subunit of
Xanthomonas campestris
pv. vesicatoria
Authors: Weber Ernst , Koebnik Ralf 
Published: August 2005

ABSTRACT

The plant-pathogenic bacterium
Xanthomonas campestris
pv. vesicatoria possesses a type III secretion (TTS) system necessary for pathogenicity in susceptible hosts and induction of the hypersensitive response in resistant plants. This specialized protein transport system is encoded by a 23-kb
hrp
(hypersensitive response and pathogenicity) gene cluster.
X. campestris
pv. vesicatoria produces filamentous structures, Hrp pili, at the cell surface under
hrp
-inducing conditions. The Hrp pilus acts as a cell surface appendage of the TTS system and serves as a conduit for the transfer of bacterial effector proteins into the plant cell cytosol. The major pilus component, the HrpE pilin, is unique to xanthomonads and is encoded within the
hrp
gene cluster. In this study, functional domains of HrpE were mapped by linker-scanning mutagenesis and by reporter protein fusions to an N-terminally truncated avirulence protein (AvrBs3Δ2). Thirteen five-amino-acid peptide insertion mutants were obtained and could be grouped into six phenotypic classes. Three permissive mutations were mapped in the N-terminal half of HrpE, which is weakly conserved within the HrpE protein family. Four dominant-negative peptide insertions in the strongly conserved C-terminal region suggest that this domain is critical for oligomerization of the pilus subunits. Reporter protein fusions revealed that the N-terminal 17 amino acid residues act as an efficient TTS signal. From these results, we postulate a three-domain structure of HrpE with an N-terminal secretion signal, a surface-exposed variable region of the N-terminal half, and a C-terminal polymerization domain. Comparisons with a mutant study of HrpA, the Hrp pilin from
Pseudomonas syringae
pv. tomato DC3000, and hydrophobicity plot analyses of several nonhomologous Hrp pilins suggest a common architecture of Hrp pilins of different plant-pathogenic bacteria.
Presence of Multiple Sites Containing Polar Material in SphericalEscherichia coliCells That Lack MreB
Authors: Nilsen Trine , Yan Arthur W. , Gale Gregory , Goldberg Marcia B. 
Published: August 2005

ABSTRACTIn rod-shaped bacteria, certain proteins are specifically localized to the cell poles. The nature of the positional information that leads to the proper localization of these proteins is unclear. In a screen for factors required for the localization of theShigellasp. actin assembly protein IcsA to the bacterial pole, a mutant carrying a transposon insertion inmreBdisplayed altered targeting of IcsA. The phenotype of cells containing a transposon insertion inmreBwas indistinguishable from that of cells containing a nonpolar mutation inmreBor that of wild-type cells treated with the MreB inhibitor A22. In cells lacking MreB, a green fluorescent protein (GFP) fusion to a cytoplasmic derivative of IcsA localized to multiple sites. Secreted full-length native IcsA was present in multiple faint patches on the surfaces of these cells in a pattern similar to that seen for the cytoplasmic IcsA-GFP fusion. EpsM, the polarVibrio choleraeinner membrane protein, also localized to multiple sites inmreBcells and colocalized with IcsA, indicating that localization to multiple sites is not unique to IcsA. Our results are consistent with the requirement, either direct or indirect, for MreB in the restriction of certain polar material to defined sites within the cell and, in the absence of MreB, with the formation of ectopic sites containing polar material.
The Active Site Is the Least Stable Structure in the Unfolding Pathway of a Multidomain Cold-Adapted α-Amylase
Authors: Siddiqui Khawar S. , Feller Georges , D'Amico Salvino , Gerday Charles , Giaquinto Laura , Cavicchioli Ricardo 
Published: August 2005

ABSTRACT

The cold-active α-amylase from the Antarctic bacterium
Pseudoalteromonas haloplanktis
(AHA) is the largest known multidomain enzyme that displays reversible thermal unfolding (around 30°C) according to a two-state mechanism. Transverse urea gradient gel electrophoresis (TUG-GE) from 0 to 6.64 M was performed under various conditions of temperature (3°C to 70°C) and pH (7.5 to 10.4) in the absence or presence of Ca
2+
and/or Tris (competitive inhibitor) to identify possible low-stability domains. Contrary to previous observations by strict thermal unfolding, two transitions were found at low temperature (12°C). Within the duration of the TUG-GE, the structures undergoing the first transition showed slow interconversions between different conformations. By comparing the properties of the native enzyme and the N12R mutant, the active site was shown to be part of the least stable structure in the enzyme. The stability data supported a model of cooperative unfolding of structures forming the active site and independent unfolding of the other more stable protein domains. In light of these findings for AHA, it will be valuable to determine if active-site instability is a general feature of heat-labile enzymes from psychrophiles. Interestingly, the enzyme was also found to refold and rapidly regain activity after being heated at 70°C for 1 h in 6.5 M urea. The study has identified fundamental new properties of AHA and extended our understanding of structure/stability relationships of cold-adapted enzymes.
Using Multilocus Sequence Data To Define the Pneumococcus
Authors: Hanage William P. , Kaijalainen Tarja , Herva Elja , Saukkoriipi Annika , Syrjänen Ritva , Spratt Brian G. 
Published: August 2005

ABSTRACT

We investigated the genetic relationships between serotypeable pneumococci and nonserotypeable presumptive pneumococci using multilocus sequence typing (MLST) and partial sequencing of the pneumolysin gene (
ply
). Among 121 nonserotypeable presumptive pneumococci from Finland, we identified isolates of three classes: those with sequence types (STs) identical to those of serotypeable pneumococci, suggesting authentic pneumococci in which capsular expression had been downregulated or lost; isolates that clustered among serotypeable pneumococci on a tree based on the concatenated sequences of the MLST loci but which had STs that differed from those of serotypeable pneumococci in the MLST database; and a more diverse collection of isolates that did not cluster with serotypeable pneumococci. The latter isolates typically had sequences at all seven MLST loci that were 5 to 10% divergent from those of authentic pneumococci and also had distinct and divergent
ply
alleles. These isolates are proposed to be distinct from pneumococci but cannot be resolved from them by optochin susceptibility, bile solubility, or the presence of the
ply
gene. Complete resolution of pneumococci from the related but distinct population is problematic, as recombination between them was evident, and a few isolates of each population possessed alleles at one or occasionally more MLST loci from the other population. However, a tree based on the concatenated sequences of the MLST loci in most cases unambiguously distinguished whether a nonserotypeable isolate was or was not a pneumococcus, and the sequence of the
ply
gene fragment was found to be useful to resolve difficult cases.
An assessment of dermal exposure to semi-synthetic metal working fluids by different methods to group workers for an epidemiological study on dermatitis
Authors: van Wendel de Joode B , Bierman E P B , Brouwer D H , Spithoven J , Kromhout H 
Published: August 2005

Background:Assessment of exposure assessment to metal working fluids (MWF) has almost exclusively focused on inhalation exposure.Aims:To assess levels of, and factors affecting, dermal and inhalation exposure to semi-synthetic MWF, and to identify suitable dermal exposure grouping schemes among metal workers for an epidemiological survey on dermatitis of hands, forearms, and head.Methods:A cross-sectional survey was conducted in four metal working machining departments of a truck manufacturing plant, estimating dermal and inhalation exposure levels to semi-synthetic metal working fluids (SMWF) in machine operators. Dermal exposure levels to SMWF were estimated by three different methods for dermal exposure assessment (VITAE, surrogate skin pad method, and a semi-quantitative dermal exposure assessment method (DREAM)).Results:The identified factors affecting dermal exposure were similar for the three methods, although differences were found for estimated variability in dermal exposure levels between groups, within groups (among workers), and from day to day. With the VITAE method differences in exposure levels were detected between workers that were not detected with the surrogate skin pad method, and only partly with the DREAM method.Conclusions:Considering the additional effort and costs that use of the VITAE method entailed, the observational semi-quantitative DREAM method appeared to be more efficient for grouping of dermal exposure levels for the epidemiological study on dermatitis.
The impact of overtime and long work hours on occupational injuries and illnesses: new evidence from the United States
Authors: Dembe A E , Erickson J B , Delbos R G , Banks S M 
Published: August 2005

Aims:To analyse the impact of overtime and extended working hours on the risk of occupational injuries and illnesses among a nationally representative sample of working adults from the United States.Methods:Responses from 10 793 Americans participating in the National Longitudinal Survey of Youth (NLSY) were used to evaluate workers’ job histories, work schedules, and occurrence of occupational injury and illness between 1987 and 2000. A total of 110 236 job records were analysed, encompassing 89 729 person-years of accumulated working time. Aggregated incidence rates in each of five exposure categories were calculated for each NLSY survey period. Multivariate analytical techniques were used to estimate the relative risk of long working hours per day, extended hours per week, long commute times, and overtime schedules on reporting a work related injury or illness, after adjusting for age, gender, occupation, industry, and region.Results:After adjusting for those factors, working in jobs with overtime schedules was associated with a 61% higher injury hazard rate compared to jobs without overtime. Working at least 12 hours per day was associated with a 37% increased hazard rate and working at least 60 hours per week was associated with a 23% increased hazard rate. A strong dose-response effect was observed, with the injury rate (per 100 accumulated worker-years in a particular schedule) increasing in correspondence to the number of hours per day (or per week) in the workers’ customary schedule.Conclusions:Results suggest that job schedules with long working hours are not more risky merely because they are concentrated in inherently hazardous industries or occupations, or because people working long hours spend more total time “at risk” for a work injury. Strategies to prevent work injuries should consider changes in scheduling practices, job redesign, and health protection programmes for people working in jobs involving overtime and extended hours.
STUDY OF THE FUNDAMENTAL STRUCTURE OF MATTER WITH AN ELECTRON-ION COLLIDER
Authors: Deshpande Abhay , Milner Richard , Venugopalan Raju , Vogelsang and Werner 
Published: August 2005

▪ Abstract  We present an overview of the scientific opportunities that would be offered by a high-energy electron-ion collider. We discuss the relevant physics of polarized and unpolarized electron-proton collisions and of electron-nucleus collisions. We also describe the current accelerator and detector plans for a future electron-ion collider. This review is dedicated to the memory of Professor Vernon W. Hughes.
Extensions of Bailey′s transform and applications
Authors: Joshi C. M. , Vyas Yashoverdhan 
Published: August 2005

The well‐known Bailey′s transform is extended. Using the extended
transform, we derive hitherto undiscovered ordinary and
q‐hypergeometric identities and discuss their particular cases
of importance, namely, two new q‐sums for Saalschützian
4Φ3, new double series Rogers‐Ramanujan‐type identities
of modulo 81, discrete extension of the q‐analogs of two
quadratic transformations of  2F1, and two new
quadratic‐cubic transformations of  3F2.
Neurocognitive Consequences of Risk-Adapted Therapy for Childhood Medulloblastoma
Authors: Mulhern Raymond K. , Palmer Shawna L. , Merchant Thomas E. , Wallace Dana , Kocak Mehmet , Brouwers Pim , Krull Kevin , Chintagumpala Murali , Stargatt Robyn , Ashley David M. , Tyc Vida L. , Kun Larry , Boyett James , Gajjar Amar 
Published: August 2005

Purpose This prospective, longitudinal study examined the effects of risk-adapted craniospinal irradiation (CSI) dose and the interactions of dose with age and time from diagnosis on intelligence quotient (IQ) and academic achievement (reading, spelling, and math) among patients treated for medulloblastoma (MB). Patients and Methods Patients received serial neurocognitive testing spanning from 0 to 6.03 years after diagnosis (median, 3.14 years). The multi-institutional study included 111 patients, who were 3 to 20 years of age at diagnosis (median age, 7.4 years), treated for MB with risk-adapted CSI followed by four cycles of high-dose chemotherapy (cyclophosphamide, cisplatin, and vincristine) with stem-cell support. High-risk patients (HR; n = 37) received CSI to 36 to 39.6 Gy and conformal boost treatment of the primary site to 55.8 to 59.4 Gy. Average-risk patients (AR; n = 74) received CSI to 23.4 Gy and conformal boost treatment of the posterior fossa to 36.0 Gy and primary site to 55.8 Gy. Results Multivariate modeling revealed statistically significant declines in mean IQ (−1.59 points/yr; P = .006), reading (−2.95 points/yr; P < .0001), spelling (−2.94 points/yr; P < .0001), and math (−1.87 points/yr; P = .003) scores for the entire group. The effects of risk-adapted radiation therapy on IQ, reading, and spelling were moderated by age, with the greatest rates of decline observed for the HR patients who were younger (< 7 years old) at diagnosis. Conclusion Young age at diagnosis was the most prominent risk factor for neurocognitive deficits among survivors of MB despite reductions in CSI dosing and efforts to limit the boost volume. Younger patients exhibited substantial problems with the development of reading skills.
Bilateral Risk for Subsequent Breast Cancer After Lobular Carcinoma-In-Situ: Analysis of Surveillance, Epidemiology, and End Results Data
Authors: Chuba Paul J. , Hamre Merlin R. , Yap Johnny , Severson Richard K. , Lucas David , Shamsa Falah , Aref Amr 
Published: August 2005

Purpose Noninvasive lesions involving the lobules of the breast are increasingly diagnosed as incidental microscopic findings at the time of lumpectomy or core-needle biopsy. We investigated the incidence rates of invasive breast cancer (IBC) after a diagnosis of lobular carcinoma-in-situ (LCIS) by using Surveillance, Epidemiology, and End Results (SEER) data. Patients and Methods Patients (N = 4,853) having a diagnosis of primary LCIS in the time period of 1973 to 1998 were identified using the SEER Public Use CD-ROM data. The database was then searched for patients with subsequent primary IBC occurrences (n = 350). The clinical and pathologic characteristics of patients with subsequent primary IBCs were compared with the characteristics of patients with primary IBCs attained during the same time period (N = 255,114). Results The incidence of IBC increased over time from diagnosis of LCIS, with 7.1% ± 0.5% incidence of IBC at 10 years. IBCs detected after partial mastectomy occurred in either breast (46% ipsilateral and 54% contralateral); however, after mastectomy, most IBCs were contralateral (94.7%). IBCs occurring after LCIS more often represented invasive lobular histology (23.1%) compared with primary IBCs (6.5%). The standardized incidence ratio (the ratio of observed to expected cases) for developing IBC was 2.4 (95% CI, 2.1 to 2.6) adjusted for age and year of diagnosis. Conclusion LCIS is associated with increased risk of subsequent invasive disease, with equal predisposition in either breast. The minimum risk of developing IBC after LCIS is 7.1% at 10 years.