bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolomics Reveals Phospholipids as Important Nutrient Sources during Salmonella Growth in Bile In Vitro and
In Vivo
Authors: Antunes L. Caetano. M. , Andersen Sarah K. , Menendez Alfredo , Arena Ellen T. , Han Jun , Ferreira Rosana B. R. , Borchers Christoph H. , Finlay B. Brett 
Published: July 2011

ABSTRACT

During the colonization of hosts, bacterial pathogens are presented with many challenges that must be overcome for colonization to occur successfully. This requires the bacterial sensing of the surroundings and adaptation to the conditions encountered. One of the major impediments to the pathogen colonization of the mammalian gastrointestinal tract is the antibacterial action of bile.
Salmonella enterica
serovar Typhimurium has specific mechanisms involved in resistance to bile. Additionally,
Salmonella
can successfully multiply in bile, using it as a source of nutrients. This accomplishment is highly relevant to pathogenesis, as
Salmonella
colonizes the gallbladder of hosts, where it can be carried asymptomatically and promote further host spread and transmission. To gain insights into the mechanisms used by
Salmonella
to grow in bile, we studied the changes elicited by
Salmonella
in the chemical composition of bile during growth
in vitro
and
in vivo
through a metabolomics approach. Our data suggest that phospholipids are an important source of carbon and energy for
Salmonella
during growth in the laboratory as well as during gallbladder infections of mice. Further studies in this area will generate a better understanding of how
Salmonella
exploits this generally hostile environment for its own benefit.
Genetic Regulation of the
yefM-yoeB
Toxin-Antitoxin Locus of Streptococcus pneumoniae
Authors: Chan Wai Ting , Nieto Concha , Harikrishna Jennifer Ann , Khoo Seok Kooi , Othman Rofina Yasmin , Espinosa Manuel , Yeo Chew Chieng 
Published: July 2011

ABSTRACT

Type II (proteic) toxin-antitoxin systems (TAS) are ubiquitous among bacteria. In the chromosome of the pathogenic bacterium
Streptococcus pneumoniae
, there are at least eight putative TAS, one of them being the

yefM-yoeB
Spn

operon studied here. Through footprinting analyses, we showed that purified YefM
Spn
antitoxin and the YefM-YoeB
Spn
TA protein complex bind to a palindrome sequence encompassing the −35 region of the main promoter (P

yefM2

) of the operon. Thus, the locus appeared to be negatively autoregulated with respect to P

yefM2

, since YefM
Spn
behaved as a weak repressor with YoeB
Spn
as a corepressor. Interestingly, a BOX element, composed of a single copy (each) of the boxA and boxC subelements, was found upstream of promoter P

yefM2

. BOX sequences are pneumococcal, perhaps mobile, genetic elements that have been associated with bacterial processes such as phase variation, virulence regulation, and genetic competence. In the

yefM-yoeB
Spn

locus, the boxAC element provided an additional weak promoter, P

yefM1

, upstream of P

yefM2

which was not regulated by the TA proteins. In addition, transcriptional fusions with a
lacZ
reporter gene showed that P

yefM1

was constitutive albeit weaker than P

yefM2

. Intriguingly, the coupling of the boxAC element to P

yefM1

and

yefM
Spn

in
cis
(but not in
trans
) led to transcriptional activation, indicating that the regulation of the

yefM-yoeB
Spn

locus differs somewhat from that of other TA loci and may involve as yet unidentified elements. Conservation of the boxAC sequences in all available sequenced genomes of
S. pneumoniae
which contained the

yefM-yoeB
Spn

locus suggested that its presence may provide a selective advantage to the bacterium.
Meniscal Root Suturing Techniques
Authors: Kopf Sebastian , Colvin Alexis Chiang , Muriuki Muturi , Zhang Xudong , Harner Christopher Dechant 
Published: July 2011

Background: Meniscal root tears have attracted increasing interest in recent years. Fixation is an important factor for rehabilitation and avoidance of early failure. Suture fixations have been the most commonly used techniques. The current study aimed to evaluate the maximum failure load of the native meniscal roots (anteromedial, posteromedial, anterolateral, and posterolateral) and of 3 commonly used meniscal root fixation techniques (2 simple stitches, modified Kessler stitch, and loop stitch). Hypotheses: (1) There will be no difference in maximum failure load between the native meniscal roots. (2) The loop stitch will sustain the greatest maximum load to failure, followed by the modified Kessler stitch and the 2 simple stitches. (3) The maximum failure load of the native meniscal roots will not be restored by the tested fixation methods. Study Design: Controlled laboratory study. Methods: The maximum failure load of the 4 human native meniscal roots was evaluated using 64 human meniscal roots. Additionally, the maximum failure load of the 3 fixation techniques was evaluated on 24 meniscal roots: (1) 2 simple stitches, (2) modified Kessler stitch, and (3) loop stitch using a suture shuttle. Results: The average maximum failure load of the native meniscal roots was 594 ± 241 N (anterolateral: 692 ± 304 N; posterolateral: 648 ± 140 N; anteromedial: 407 ± 180 N; posteromedial: 678 ± 200 N). The anteromedial root was significantly weaker than the posterolateral and posteromedial roots ( P = .04 and P = .01, respectively). Regarding fixation techniques, the maximum failure load of the 2 simple stitches was 64.1 ± 22.5 N, the modified Kessler stitch was 142.6 ± 33.3 N, and the loop was 100.9 ± 41.6 N. None of the fixation techniques recreated the strength of the native roots. Conclusion: The native anterolateral root was the strongest meniscal root, and the anteromedial root was the weakest meniscal root. Regarding primary fixation strength, the modified Kessler stitch was the strongest technique compared with the loop and the 2 simple stitches. Clinical Relevance: None of our tested fixation methods restored the strength of native meniscal roots. Thus, rehabilitation after meniscal root fixation should proceed cautiously.
Monoclonal and polyclonal serum free light chains and clinical outcome in chronic lymphocytic leukemia
Authors: Maurer Matthew J. , Cerhan James R. , Katzmann Jerry A. , Link Brian K. , Allmer Cristine , Zent Clive S. , Call Timothy G. , Rabe Kari G. , Hanson Curtis A. , Kay Neil E. , Slager Susan L. , Witzig Thomas E. , Shanafelt Tait D. 
Published: July 2011

AbstractFree light chains (FLCs) are the most commonly detected paraproteins in chronic lymphocytic leukemia (CLL). We examined the types of FLC abnormalities and prognostic utility of the FLC assay compared with standard prognostic biomarkers in a prospective cohort of 339 patients with newly diagnosed CLL. Three types of FLC abnormalities were identified: monoclonal elevated FLC (elevated κ and/or λ with abnormal FLC ratio), polyclonal elevated FLC (elevated κ and/or λ with normal FLC ratio), and ratio-only FLC abnormality (normal range κ and λ with abnormal FLC ratio). One hundred sixty-five patients (49%) had a FLC abnormality with approximately equal distribution among monoclonal elevation, polyclonal elevation, and ratio-only abnormality. All FLC abnormalities were associated with poor time to first treatment: monoclonal FLC (hazard ratio [HR], 4.99; 95% confidence interval [CI], 2.94-8.48), polyclonal FLC (HR, 2.40; 95% CI, 1.24-4.64), ratio-only FLC (HR, 2.57; 95% CI, 1.40-4.69). Monoclonal FLC and polyclonal FLC were associated with poor overall survival compared with patients with normal FLC. Results remained significant after adjusting for Rai stage. The FLC assay is a simple, widely available clinical test with similar prognostic utility as routinely used prognostic biomarkers for CLL. Among persons with FLC abnormalities, the type of abnormality affects prognostic significance.
Comparative Proteomic Analysis of saccharopolyspora spinosa SP06081 and PR2 strains reveals the differentially expressed proteins correlated with the increase of spinosad yield
Authors: Luo Yushuang , Ding Xuezhi , Xia Liqiu , Huang Fan , Li Wenping , Huang Shaoya , Tang Ying , Sun Yunjun 
Published: July 2011

Abstract

Background

Saccharopolyspora spinosa produces the environment-friendly biopesticide spinosad, a mixture of two polyketide-derived macrolide active ingredients called spinosyns A and D. Therefore considerable interest is in the improvement of spinosad production because of its low yield in wild-type S. spinosa. Recently, a spinosad-hyperproducing PR2 strain with stable heredity was obtained from protoplast regeneration of the wild-type S. spinosa SP06081 strain. A comparative proteomic analysis was performed on the two strains during the first rapid growth phase (RG1) in seed medium (SM) by using label-free quantitative proteomics to investigate the underlying mechanism leading to the enhancement of spinosad yield.

Results
In total, 224 proteins from the SP06081 strain and 204 proteins from the PR2 strain were unambiguously identified by liquid chromatography-tandem mass spectrometry analysis, sharing 140 proteins. A total of 12 proteins directly related to spinosad biosynthesis were identified from the two strains in RG1. Comparative analysis of the shared proteins revealed that approximately 31% of them changed their abundance significantly and fell in all of the functional groups, such as tricarboxylic acid cycles, glycolysis, biosynthetic processes, catabolic processes, transcription, translation, oxidation and reduction. Several key enzymes involved in the synthesis of primary metabolic intermediates used as precursors for spinosad production, energy supply, polyketide chain assembly, deoxysugar methylation, and antioxidative stress were differentially expressed in the same pattern of facilitating spinosad production by the PR2 strain. Real-time reverse transcriptase polymerase chain reaction analysis revealed that four of five selected genes showed a positive correlation between changes at the translational and transcriptional expression level, which further confirmed the proteomic analysis.

Conclusions
The present study is the first comprehensive and comparative proteome analysis of S. spinosa strains. Our results highlight the differentially expressed proteins between the two S. spinosa strains and provide some clues to understand the molecular and metabolic mechanisms that could lead to the increased spinosad production yield.
Evaluation of 19 Autoimmune Disease-associated Loci with Rheumatoid Arthritis in a Colombian Population: Evidence for Replication and Gene-Gene Interaction
Authors: DESHMUKH HARSHAL A. , MAITI AMIT K. , KIM-HOWARD XANA R. , ROJAS-VILLARRAGA ADRIANA , GUTHRIDGE JOEL M. , ANAYA JUAN-MANUEL , NATH SWAPAN K. 
Published: July 2011

Objective.Recent studies have identified several common genes associated with multiple autoimmune diseases that support the hypothesis of the presence of shared or general autoimmunity genes. However, most of this work has been performed in populations of white origin. The main objectives of this study are to replicate the genotype-phenotype correlation between 19 such variants and rheumatoid arthritis (RA), and to evaluate gene-gene interactions between these genes in individuals from an ethnically homogenous nonwhite Colombian population.Methods.Nineteen single-nucleotide polymorphisms (SNP) from 16 genes/loci were genotyped in 353 RA cases and 368 controls. For each SNP, allelic and genotype-based association tests were applied to evaluate genotype-phenotype correlation. Permutation-based tests were used to validate the statistical significance. Gene-gene interactions were assessed by logistic regression.Results.We replicated the genetic association with rs13277113 (p = 0.0009, OR 1.46) and rs2736340 (p = 0.0001, OR 1.63) from C8orf13-BLK (8p23.1, associated with RA and systemic lupus erythematosus), and rs763361 (p = 0.03) from CD226 (18q22.3, associated with multiple sclerosis and type 1 diabetes) in the Colombian population. The population-attributable risks were estimated as 27%, 34%, and 16% for rs13277113, rs2736340, and rs763361, respectively. We also detected evidence for gene-gene interaction between SNP in MMEL1 (rs3890745) and C80rf13-BLK (rs13277113; p = 0.0002).Conclusion.Our results demonstrate that the IL2/IL21 region, C8orf13-BLK, and CD226 influence RA in Colombians, and RA shares some of the pathogenic mechanisms associated with other autoimmune diseases.
Molecular Analysis of the Metabolic Rates of Discrete Subsurface Populations of Sulfate Reducers
Authors: Miletto M. , Williams K. H. , N'Guessan A. L. , Lovley D. R. 
Published: July 2011

ABSTRACT

Elucidating the
in situ
metabolic activity of phylogenetically diverse populations of sulfate-reducing microorganisms that populate anoxic sedimentary environments is key to understanding subsurface ecology. Previous pure culture studies have demonstrated that the transcript abundance of dissimilatory (bi)sulfite reductase genes is correlated with the sulfate-reducing activity of individual cells. To evaluate whether expression of these genes was diagnostic for subsurface communities, dissimilatory (bi)sulfite reductase gene transcript abundance in phylogenetically distinct sulfate-reducing populations was quantified during a field experiment in which acetate was added to uranium-contaminated groundwater. Analysis of
dsrAB
sequences prior to the addition of acetate indicated that
Desulfobacteraceae
,
Desulfobulbaceae
, and
Syntrophaceae
-related sulfate reducers were the most abundant. Quantifying
dsrB
transcripts of the individual populations suggested that
Desulfobacteraceae
initially had higher
dsrB
transcripts per cell than
Desulfobulbaceae
or
Syntrophaceae
populations and that the activity of
Desulfobacteraceae
increased further when the metabolism of dissimilatory metal reducers competing for the added acetate declined. In contrast,
dsrB
transcript abundance in
Desulfobulbaceae
and
Syntrophaceae
remained relatively constant, suggesting a lack of stimulation by added acetate. The indication of higher sulfate-reducing activity in the
Desulfobacteraceae
was consistent with the finding that
Desulfobacteraceae
became the predominant component of the sulfate-reducing community. Discontinuing acetate additions resulted in a decline in
dsrB
transcript abundance in the
Desulfobacteraceae
. These results suggest that monitoring transcripts of dissimilatory (bi)sulfite reductase genes in distinct populations of sulfate reducers can provide insight into the relative rates of metabolism of different components of the sulfate-reducing community and their ability to respond to environmental perturbations.
Coassimilation of Organic Substrates via the Autotrophic 3-Hydroxypropionate Bi-Cycle in Chloroflexus aurantiacus
Authors: Zarzycki Jan , Fuchs Georg 
Published: July 2011

ABSTRACT

Chloroflexus aurantiacus
is a facultative autotrophic green nonsulfur bacterium that grows phototrophically in thermal springs and forms microbial mats with cyanobacteria. Cyanobacteria produce glycolate during the day (photorespiration) and excrete fermentation products at night.
C. aurantiacus
uses the 3-hydroxypropionate bi-cycle for autotrophic carbon fixation. This pathway was thought to be also suited for the coassimilation of various organic substrates such as glycolate, acetate, propionate, 3-hydroxypropionate, lactate, butyrate, or succinate. To test this possibility, we added these compounds at a 5 mM concentration to autotrophically pregrown cells. Although the provided amounts of H
2
and CO
2
allowed continuing photoautotrophic growth, cells immediately consumed most substrates at rates equaling the rate of autotrophic carbon fixation. Using [
14
C]acetate, half of the labeled organic carbon was incorporated into cell mass. Our data suggest that
C. aurantiacus
uses the 3-hydroxypropionate bi-cycle, together with the glyoxylate cycle, to channel organic substrates into the central carbon metabolism. Enzyme activities of the 3-hydroxypropionate bi-cycle were marginally affected when cells were grown heterotrophically with such organic substrates. The 3-hydroxypropionate bi-cycle in
Chloroflexi
is unique and was likely fostered in an environment in which traces of organic compounds can be coassimilated. Other bacteria living under oligotrophic conditions acquired genes of a rudimentary 3-hydroxypropionate bi-cycle, possibly for the same purpose. Examples are
Chloroherpeton thalassium
,
Erythrobacter
sp. strain NAP-1,
Nitrococcus mobilis
, and marine gammaproteobacteria of the OM60/NOR5 clade such as
Congregibacter litoralis
.
Trophic Links between the Acetogen Clostridium glycolicum KHa and the Fermentative Anaerobe Bacteroides xylanolyticus KHb, Isolated from Hawaiian Forest Soil
Authors: Hunger Sindy , Gößner Anita S. , Drake Harold L. 
Published: July 2011

ABSTRACT

Isolate KH was obtained from Hawaiian forest soil and found to be composed of two functionally linked anaerobes, KHa and KHb. Gene analyses (16S rRNA,
fhs
,
cooS
) identified KHa as an acetogenic strain of
Clostridium glycolicum
and KHb as
Bacteroides xylanolyticus
. KHb fermented xylan and other saccharides that KHa could not utilize and formed products (e.g., ethanol and H
2
) that supported the acetogenic growth of KHa.
Vacuolar Protein Sorting Protein 13A, TtVPS13A, Localizes to the Tetrahymena thermophila Phagosome Membrane and Is Required for Efficient Phagocytosis
Authors: Samaranayake Haresha S. , Cowan Ann E. , Klobutcher Lawrence A. 
Published: July 2011

ABSTRACT

Vacuolar protein sorting 13 (VPS13) proteins have been studied in a number of organisms, and mutations in
VPS13
genes have been implicated in two human genetic disorders, but the function of these proteins is poorly understood. The TtVPS13A protein was previously identified in a mass spectrometry analysis of the
Tetrahymena thermophila
phagosome proteome (M. E. Jacobs et al., Eukaryot. Cell 5:1990–2000, 2006), suggesting that it is involved in phagocytosis. In this study, we analyzed the structure of the macronuclear
TtVPS13A
gene, which was found to be composed of 17 exons spanning 12.5 kb and was predicted to encode a protein of 3,475 amino acids (aa). A strain expressing a TtVPS13A-green fluorescent protein (GFP) fusion protein was constructed, and the protein was found to associate with the phagosome membrane during the entire cycle of phagocytosis. In addition,
Tetrahymena
cells with a
TtVPS13A
knockout mutation displayed impaired phagocytosis. Specifically, they grew slowly under conditions where phagocytosis is essential, they formed few phagosomes, and the digestion of phagosomal contents was delayed compared to wild-type cells. Overall, these results provide evidence that the TtVPS13A protein is required for efficient phagocytosis.
Identification of Rgg Binding Sites in the Streptococcus pyogenes Chromosome
Authors: Anbalagan Srivishnupriya , McShan W. Michael , Dunman Paul M. , Chaussee Michael S. 
Published: July 2011

ABSTRACT

Streptococcus pyogenes
Rgg is a regulatory protein that controls the transcription of 588 genes in strain NZ131 during the post-exponential phase of growth, including the virulence-associated genes encoding the extracellular SpeB protease, pullulanase A (PulA), and two extracellular nucleases (SdaB and Spd-3). Rgg binds to DNA proximally to the
speB
promoter (P
speB
) to activate transcription; however, it is not known if Rgg binds to the promoters of other genes to influence expression, or if the perturbation of other global regulons accounts for the genome-wide changes in expression associated with the mutant. To address this issue, chromatin immunoprecipitation followed by DNA microarray analysis (ChIP-chip) was used to identify the DNA binding sites of Rgg. Rgg bound to 65 sites in the chromosome. Thirty-five were within noncoding DNA, and 43% of these were adjacent to genes previously identified as regulated by Rgg. Electrophoretic mobility shift assays were used to assess the binding of Rgg to a subset of sites bound
in vivo
, including the noncoding DNA upstream of
speB
, the genes encoding PulA, Spd-3, and a transcriptional regulator (SPY49_1113), and prophage-associated genes encoding a putative integrase (SPY49_0746) and a surface antigen (SPY49_0396). Rgg bound to all target DNAs
in vitro
, consistent with the
in vivo
results. Finally, analyses with a transcriptional reporter system showed that the DNA bound by Rgg contained an active promoter that was regulated by Rgg. Overall, the results indicate that Rgg binds specifically to multiple sites in the chromosome, including prophage DNA, to influence gene expression.
Data Impediments to Empirical Work on Health Insurance Markets
Authors: Dafny Leemore , Dranove David , Limbrock Frank , Scott Morton Fiona 
Published: July 2011

Abstract
We compare four datasets that researchers might use to study competition in the health insurance industry. We show that the two datasets most commonly used to estimate market concentration differ considerably from each other (both in levels and in changes over time), and reflect implausibly high volatility in market shares. By comparison, market share volatility is much lower in a private dataset gathered by a leading investment bank, and in state-level hospital discharge data. We also demonstrate that the outcome of regressions using these data vary considerably by the source used. We conclude that researchers should be cautious about using available data and recommend a new source be developed for public use.
Prescription for Education: Development, Evaluation, and Implementation of a Successful Interprofessional Education Program for Adults with Inflammatory Arthritis
Authors: KENNEDY CAROL A. , BEATON DORCAS E. , WARMINGTON KELLY , SHUPAK RACHEL , JONES CAROLINE , HOGG-JOHNSON SHEILAH 
Published: July 2011

Objective.To assess the feasibility of recruitment and standardize care delivery for an interprofessional program for inflammatory arthritis education (Prescription for Education, or RxEd), and to explore outcomes relevant to arthritis patient education.Methods.A patient-based needs assessment and ongoing patient feedback guided program development. An interprofessional team was involved in developing program content and delivering and adapting the program to patient needs. A quasiexperimental, waitlisted control with crossover design was used to evaluate the program. Data were collected at baseline, immediately following intervention, at 6 months (when the crossover control group received intervention), and at 1 year. Self-report measures included demographics, disorder-related data, Arthritis Self-efficacy Scale, arthritis knowledge, coping efficacy, and illness intrusiveness. Analysis included baseline comparisons and longitudinal trends; direct between-group comparison at 6 months; and generalized estimating equations (GEE) analysis to evaluate the main effect of the intervention on the primary outcome (arthritis self-efficacy) and secondary outcomes.Results.Program modifications based on patient input made recruitment possible. Forty-two persons participated (including 19 controls), with 93% followup at 1 year. Comparison of change shows moderate effect sizes (standardized effect size 0.5 to 0.7). GEE analysis showed significant main effect, before to after the program, in both groups for primary outcome (arthritis self-efficacy) and most secondary outcomes.Conclusion.Program feasibility was dependent on patient feedback. Our pilot study provides evidence that the RxEd program is feasible and improves arthritis self-efficacy and other outcomes.