bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raman Spectroscopy as a Potential Tool for Detection of Brucella spp. in Milk
Authors: Meisel Susann , Stöckel Stephan , Elschner Mandy , Melzer Falk , Rösch Petra , Popp Jürgen 
Published: June 2012

ABSTRACT

Detection of
Brucella
, causing brucellosis, is very challenging, since the applied techniques are mostly time-demanding and not standardized. While the common detection system relies on the cultivation of the bacteria, further classical typing up to the biotype level is mostly based on phenotypic or genotypic characteristics. The results of genotyping do not always fit the existing taxonomy, and misidentifications between genetically closely related genera cannot be avoided. This situation gets even worse, when detection from complex matrices, such as milk, is necessary. For these reasons, the availability of a method that allows early and reliable identification of possible
Brucella
isolates for both clinical and epidemiological reasons would be extremely useful. We evaluated micro-Raman spectroscopy in combination with chemometric analysis to identify
Brucella
from agar plates and directly from milk: prior to these studies, the samples were inactivated via formaldehyde treatment to ensure a higher working safety. The single-cell Raman spectra of different
Brucella
,
Escherichia
,
Ochrobactrum
,
Pseudomonas
, and
Yersinia
spp. were measured to create two independent databases for detection in media and milk. Identification accuracies of 92% for
Brucella
from medium and 94% for
Brucella
from milk were obtained while analyzing the single-cell Raman spectra via support vector machine. Even the identification of the other genera yielded sufficient results, with accuracies of >90%. In summary, micro-Raman spectroscopy is a promising alternative for detecting
Brucella
. The measurements we performed at the single-cell level thus allow fast identification within a few hours without a demanding process for sample preparation.
Respiratory Chain Analysis of Zymomonas mobilis Mutants Producing High Levels of Ethanol
Authors: Hayashi Takeshi , Kato Tsuyoshi , Furukawa Kensuke 
Published: June 2012

ABSTRACT

We previously isolated respiratory-deficient mutant (RDM) strains of
Zymomonas mobilis
, which exhibited greater growth and enhanced ethanol production under aerobic conditions. These RDM strains also acquired thermotolerance. Morphologically, the cells of all RDM strains were shorter compared to the wild-type strain. We investigated the respiratory chains of these RDM strains and found that some RDM strains lost NADH dehydrogenase activity, whereas others exhibited reduced cytochrome
bd
-type ubiquinol oxidase or ubiquinol peroxidase activities. Complementation experiments restored the wild-type phenotype. Some RDM strains seem to have certain mutations other than the corresponding respiratory chain components. RDM strains with deficient NADH dehydrogenase activity displayed the greatest amount of aerobic growth, enhanced ethanol production, and thermotolerance. Nucleotide sequence analysis revealed that all NADH dehydrogenase-deficient strains were mutated within the
ndh
gene, which includes insertion, deletion, or frameshift. These results suggested that the loss of NADH dehydrogenase activity permits the acquisition of higher aerobic growth, enhanced ethanol production, and thermotolerance in this industrially important strain.
Genotypic and Chemotypic Diversity of Neotyphodium Endophytes in Tall Fescue from Greece
Authors: Takach Johanna E. , Mittal Shipra , Swoboda Ginger A. , Bright Sherrita K. , Trammell Michael A. , Hopkins Andrew A. , Young Carolyn A. 
Published: June 2012

ABSTRACT

Epichloid endophytes provide protection from a variety of biotic and abiotic stresses for cool-season grasses, including tall fescue. A collection of 85 tall fescue lines from 15 locations in Greece, including both Continental and Mediterranean germplasm, was screened for the presence of native endophytes. A total of 37 endophyte-infected lines from 10 locations were identified, and the endophytes were classified into five distinct groups (G1 to G5) based on physical characteristics such as colony morphology, growth rate, and conidial morphology. These classifications were supported by phylogenetic analyses of housekeeping genes
tefA
and
tubB
, and the endophytes were further categorized as
Neotyphodium coenophialum
isolates (G1, G4, and G5) or
Neotyphodium
sp. FaTG-2 (
Festuca arundinacea
taxonomic group 2 isolates (G2 and G3). Analyses of the tall fescue
matK
chloroplast genes indicated a population-wide, host-specific association between
N. coenophialum
and Continental tall fescue and between FaTG-2 and Mediterranean tall fescue that was also reflected by differences in colonization of host tillers by the native endophytes. Genotypic analyses of alkaloid gene loci combined with chemotypic (chemical phenotype) profiles provided insight into the genetic basis of chemotype diversity. Variation in alkaloid gene content, specifically the presence and absence of genes, and copy number of gene clusters explained the alkaloid diversity observed in the endophyte-infected tall fescue, with one exception. The results from this study provide insight into endophyte germplasm diversity present in living tall fescue populations.
Stable Isotope Peptide Mass Spectrometry To Decipher Amino Acid Metabolism in Dehalococcoides Strain CBDB1
Authors: Marco-Urrea Ernest , Seifert Jana , von Bergen Martin , Adrian Lorenz 
Published: June 2012

ABSTRACT

Dehalococcoides
species are key players in the anaerobic transformation of halogenated solvents at contaminated sites. Here, we analyze isotopologue distributions in amino acid pools from peptides of
Dehalococcoides
strain CBDB1 after incubation with
13
C-labeled acetate or bicarbonate as a carbon source. The resulting data were interpreted with regard to genome annotations to identify amino acid biosynthesis pathways. In addition to using gas chromatography-mass spectrometry (GC-MS) for analyzing derivatized amino acids after protein hydrolysis, we introduce a second, much milder method, in which we directly analyze peptide masses after tryptic digest and peptide fragments by nano-liquid chromatography-electrospray ionization-tandem mass spectrometry (nano-LC-ESI-MS/MS). With this method, we identify isotope incorporation patterns for 17 proteinaceous amino acids, including proline, cysteine, lysine, and arginine, which escaped previous analyses in
Dehalococcoides
. Our results confirmed lysine biosynthesis via the α-aminoadipate pathway, precluding lysine formation from aspartate. Similarly, the isotopologue pattern obtained for arginine provided biochemical evidence of its synthesis from glutamate. Direct peptide MS/MS analysis of the labeling patterns of glutamine and asparagine, which were converted to glutamate and aspartate during protein hydrolysis, gave biochemical evidence of their precursors and confirmed glutamate biosynthesis via a
Re
-specific citrate synthase. By addition of unlabeled free amino acids to labeled cells, we show that in strain CBDB1 none of the 17 tested amino acids was incorporated into cell mass, indicating that they are all synthesized
de novo
. Our approach is widely applicable and provides a means to analyze amino acid metabolism by studying specific proteins even in mixed consortia.
Comparative Investigation of the Genomic Regions Involved in Antigenic Variation of the TprK Antigen among Treponemal Species, Subspecies, and Strains
Authors: Giacani Lorenzo , Brandt Stephanie L. , Puray-Chavez Maritza , Reid Tara Brinck , Godornes Charmie , Molini Barbara J. , Benzler Martin , Hartig Jörg S. , Lukehart Sheila A. , Centurion-Lara Arturo 
Published: June 2012

ABSTRACTAlthough the threeTreponema pallidumsubspecies (T. pallidumsubsp.pallidum,T. pallidumsubsp.pertenue, andT. pallidumsubsp.endemicum),Treponema paraluiscuniculi, and the unclassified Fribourg-Blanc treponeme cause clinically distinct diseases, these pathogens are genetically and antigenically highly related and are able to cause persistent infection. Recent evidence suggests that the putative surface-exposed variable antigen TprK plays an important role in both treponemal immune evasion and persistence.tprKheterogeneity is generated by nonreciprocal gene conversion between thetprKexpression site and donor sites. Although each of the above-mentioned species and subspecies has a functionaltprKantigenic variation system, it is still unclear why the level of expression and the rate at whichtprKdiversifies during infection can differ significantly among isolates. To identify genomic differences that might affect the generation and expression of TprK variants among these pathogens, we performed comparative sequence analysis of the donor sites, as well as thetprKexpression sites, among eightT. pallidumsubsp.pallidumisolates (Nichols Gen, Nichols Sea, Chicago, Sea81-4, Dal-1, Street14, UW104, and UW126), threeT. pallidumsubsp.pertenueisolates (Gauthier, CDC2, and Samoa D), oneT. pallidumsubsp.endemicumisolate (Iraq B), the unclassified Fribourg-Blanc isolate, and the Cuniculi A strain ofT. paraluiscuniculi. Synteny and sequence conservation, as well as deletions and insertions, were found in the regions harboring the donor sites. These data suggest that thetprKrecombination system is harbored within dynamic genomic regions and that genomic differences might be an important key to explain discrepancies in generation and expression oftprKvariants among theseTreponemaisolates.
Competition injuries in taekwondo: a literature review and suggestions for prevention and surveillance
Authors: Pieter Willy , Fife Gabriel Paul , O'Sullivan David Michael 
Published: June 2012

ObjectiveTo review competition injuries in taekwondo and use this information to develop recommendations to reduce the number and severity of injuries in taekwondo competition.MethodsThe available literature was searched for prospective studies on taekwondo injuries in adult athletes. An injury was defined as any circumstance for which the athlete sought the assistance of the on-site medical personnel. Injury rates were expressed per athlete-exposures (A–E) and 95% CIs calculated.ResultsTotal injury rates for elite men varied from 20.6/1000 A–E (95% CI 11.8 to 29.3) to 139.5/1000 A–E (95% CI 94.0 to 185.1). For elite women, the rates varied from 25.3/1000 A–E (95% CI 3.1 to 47.4) to 105.5/1000 A–E (95% CI 89.8 to 121.1). About one-third of all injuries (29.6%) in the men were to the head and neck region, while almost half of the injuries (44.5%) were to the lower extremities. In women, 15.2% of injuries were to the head and neck and 53.1% to the lower extremities. The vast majority of all injuries were contusions (42.7% in the men and 62.7% in the women). Point estimates of rates of head injuries and concussions were found to be higher in taekwondo than in other contact sports such as football (soccer) and American gridiron football. Time-loss injury rates in the men varied from 6.9/1000 A–E (95% CI 1.8 to 11.9) to 33.6/1000 A–E (95% CI 18.9 to 48.3). In the women, they varied from 2.4/1000 A–E (95% CI 2.3 to 7.2) to 23.0/1000 A–E (95% CI 15.7 to 30.4). The turning kick was most often involved in causing injury: 56.9% of all injuries in the men and 49.8% in the women. Lack of blocking skills was identified as one of the main injury mechanisms.ConclusionsRule changes should be considered and it is recommended that governing bodies employ qualified medical personnel. Establishing an ongoing injury surveillance system in taekwondo should be the first priority.
Prostatic needle biopsies following primary high intensity focused ultrasound (HIFU) therapy for prostatic adenocarcinoma: histopathological features in tumour and non-tumour tissue
Authors: Ryan Paul , Finelli Antonio , Lawrentschuk Nathan , Fleshner Neil , Sweet Joan , Cheung Carol , van der Kwast Theodorus , Evans Andrew 
Published: June 2012

AimsHigh intensity focused ultrasound (HIFU) is currently offered as primary treatment for patients with clinically localised prostate cancer. Data on histopathological features of post-treatment biopsies are limited.MethodsPretreatment biopsies were identified in 45 men (age range 41–85) who received primary HIFU therapy. Post-HIFU biopsies were performed in 30 of these patients (67%) at mean 14.1 months (95% CI 11.7 to 16.5) follow-up, 22 due to rising PSA and eight as part of routine follow-up. Biopsies were examined for presence, distribution and extent of adenocarcinoma, Gleason scores, use of standard immunohistochemistry and ablative tissue changes were attributable to HIFU.ResultsIn post-HIFU biopsies performed for biochemical failure, 17/22 (77%) contained adenocarcinoma; 4/22 (18%) had higher post-HIFU Gleason score; 3/22 (14%) had newly recognised bilateral involvement; and 4/22 (18%) had higher percentage tissue involvement compared with pre-HIFU biopsies. Of cases without rising post-HIFU PSA, 2/8 (25%) routine follow-up biopsies contained adenocarcinoma. Stromal fibrosis was the commonest finding in non-tumour post-HIFU biopsy tissue (17/30, 57%) with coagulative necrosis occurring in fewer cases (4/30, 13%) and over a shorter follow-up interval than cases showing fibrosis (8.5 (0.2–16.8) vs 15.3 (11.5–19.1) months). Treatment effects in tumour cells precluding the assignment of Gleason scores or use of immunohistochemistry in post-HIFU biopsies were not identified.ConclusionPost-HIFU biopsies are positive in more than 75% of patients with elevated or rising PSA. Stromal fibrosis is common but the tissue effects of this modality do not appear to impair pathologists' ability to detect and grade adenocarcinoma in follow-up biopsies.
Screening tests forChlamydia trachomatisorNeisseria gonorrhoeaeusing the cobas 4800 PCR system do not require a second test to confirm: an audit of patients issued with equivocal results at a sexual health clinic in the Northwest of England, UK
Authors: Hopkins Mark J , Smith Godfrey , Hart Ian J , Alloba Fath 
Published: June 2012

ObjectivesTo assess the clinical utility of supplementary PCRs following a positive cobas 4800 CT/NG PCR screening test result.MethodsLaboratory reports, forChlamydia trachomatisorNeisseria gonorrhoeae, issued to genitourinary medicine patients between April 2010 and April 2011 were reviewed retrospectively. Positive reports were routinely confirmed by supplementary PCRs andN gonorrhoeaeculture. Clinical records of patients with unconfirmed positive (equivocal) reports were retrieved to determine if the infection was confirmed by a second sample obtained at patient recall and the impact of this process on antibiotic management.ResultsOver 15 000 patients were tested during the study period. The prevalence of chlamydia and gonorrhoea was 972 (5.75%) and 76 (0.50%), respectively. A further 78 chlamydia and 2 gonorrhoea equivocal reports were issued. Only 56 (72%) patients with an equivocal chlamydia report returned to the clinic, and of these, only 41 (73%) gave a second sample to retest. Positive predictive value (PPV) of the PCR screening test was calculated at 98.0% and 97.5% for detection of chlamydia infection from urine and rectal swabs, respectively. Most patients accepted antibiotic treatment before their infection status had been confirmed. Prevalence of gonorrhoea infection was low but the PPV of the screening PCR in urine specimens remained high (98.75%).ConclusionsEquivocal reports introduce delays to patient management, while the risk of unnecessary antibiotic therapy appears acceptable to most patients. The cobas 4800 CT/NG PCR screening assay can achieve UK testing standards (PPV >90%) for chlamydia, and low prevalence gonorrhoea in urine without supplementary tests. A patient-led confirmation algorithm is proposed.
Effects of pollen availability on pollen immigration and pollen donor diversity in riparian dioecious trees (Salix arbutifolia)
Authors: Hoshikawa Takeshi , Nagamitsu Teruyoshi , Tomaru Nobuhiro 
Published: June 2012

Reduced pollen availability in a fragmented population may affect pollen immigration and diversity of pollen donors in the population. To test this prediction, tree locations, tree sizes, and nuclear microsatellite genotypes were determined for 182 offspring, their 8 mothers, and 194 males of a wind-pollinated, dioecious Salix arbutifolia Pallas population along a river isolated over 4 km from other populations. The effects of the distance between the mother and male trees and the size of the male trees on pollen dispersal as well as fractional paternity allocation for the offspring and the number of unsampled males were estimated simultaneously. Based on the estimated parameters of pollen dispersal, the availability of pollen from the males along the river was obtained for the individual mother trees. The pollen availability was not correlated with the proportion of offspring sired by immigrating pollen from unsampled males (8%–50%), but was positively correlated with the effective number of pollen donors in sampled males (1–8). The results suggest that the reduced pollen donor diversity owing to low pollen availability increases the fraction of full-sibs in offspring and subsequent reduction in genetic diversity, but that pollen immigration compensates the offspring for the reduced genetic diversity.
Rock denudation rates and organic carbon exports along a latitudinal gradient in the Hudson, James, and Ungava bays watershed
Authors: Rosa Eric , Gaillardet Jérôme , Hillaire-Marcel Claude , Hélie Jean-François , Richard Louis-Filip 
Published: June 2012

This study documents chemical denudation rates (CDR) in the Canadian Shield and Interior Platform. It focuses on the dissolved chemistry of rivers flowing into the Hudson, James, and Ungava bays (HJUB). Major ions, strontium, neodymium, and dissolved organic carbon (DOC) concentrations were monitored in four rivers (Koksoak, Great Whale, La Grande, and Nelson). Six other rivers flowing into the HJUB were sampled during baseflow and snowmelt conditions. The rivers of the Canadian Shield exhibit major cation concentrations ranging between 62 and 360 µmol/L, [Nd] of 0.57–4.72 nmol/L, and variable [DOC] of 241–1777 µmol/L. In comparison, the Nelson River (Interior Platform) shows higher major cation concentrations (1200–2276 µmol/L), lower [Nd] (0.14–0.45 nmol/L), and intermediate [DOC] (753–928 µmol/L). Altogether, the studied rivers export 8 × 106 t/year of dissolved major cations and 50 t/year of dissolved Nd towards the HJUB. Basin-scale rock denudation rates (RDR) range from 1.0 to 5.3 t·km–2·year–1 and are essentially controlled by lithology, as illustrated by the relationship established between RDR and the proportion of sedimentary and volcanic rocks (%S + %V) within the basins: RDR = 0.08(%S + %V) + 0.9. In contrast, dissolved Nd exports (and likely other insoluble elements) seem to be dependent upon organic matter leaching, as illustrated by the empirical coupling between Nd and DOC exports. These fluxes decrease northwards, likely in response to the hydroclimatic gradient. The CDR evaluated within the Canadian Shield are among the lowest on the planet, and the alkalinity generated by rock weathering remains small with respect to DOC exports.
Pharmacogenomic Profiling and Pathway Analyses Identify MAPK-Dependent Migration as an Acute Response to SN38 in p53 Null and p53-Mutant Colorectal Cancer Cells
Authors: Allen Wendy L. , Turkington Richard C. , Stevenson Leanne , Carson Gail , Coyle Vicky M. , Hector Suzanne , Dunne Philip , Van Schaeybroeck Sandra , Longley Daniel B. , Johnston Patrick G. 
Published: June 2012

Abstract
The topoisomerase I inhibitor irinotecan is used to treat advanced colorectal cancer and has been shown to have p53-independent anticancer activity. The aim of this study was to identify the p53-independent signaling mechanisms activated by irinotecan. Transcriptional profiling of isogenic HCT116 p53 wild-type and p53 null cells was carried out following treatment with the active metabolite of irinotecan, SN38. Unsupervised analysis methods showed that p53 status had a highly significant impact on gene expression changes in response to SN38. Pathway analysis indicated that pathways involved in cell motility [adherens junction, focal adhesion, mitogen-activated protein kinase (MAPK), and regulation of the actin cytoskeleton] were significantly activated in p53 null cells, but not p53 wild-type cells, following SN38 treatment. In functional assays, SN38 treatment increased the migratory potential of p53 null and p53-mutant colorectal cancer cell lines, but not p53 wild-type lines. Moreover, p53 null SN38-resistant cells were found to migrate at a faster rate than parental drug-sensitive p53 null cells, whereas p53 wild-type SN38-resistant cells failed to migrate. Notably, cotreatment with inhibitors of the MAPK pathway inhibited the increased migration observed following SN38 treatment in p53 null and p53-mutant cells. Thus, in the absence of wild-type p53, SN38 promotes migration of colorectal cancer cells, and inhibiting MAPK blocks this potentially prometastatic adaptive response to this anticancer drug. Mol Cancer Ther; 11(8); 1724–34. ©2012 AACR.
Sorafenib Inhibits Many Kinase Mutations Associated with Drug-Resistant Gastrointestinal Stromal Tumors
Authors: Heinrich Michael C. , Marino-Enriquez Adrian , Presnell Ajia , Donsky Rachel S. , Griffith Diana J. , McKinley Arin , Patterson Janice , Taguchi Takahiro , Liang Cher-Wei , Fletcher Jonathan A. 
Published: June 2012

Abstract
Sorafenib has substantial clinical activity as third- or fourth-line treatment of imatinib- and sunitinib-resistant gastrointestinal stromal tumors (GIST). Because sorafenib targets both angiogenesis-related kinases (VEGFR) and the pathogenetic kinases found in GIST (KIT or PDGFRA), the molecular basis for sorafenib efficacy in this setting remains unknown. We sought to determine the spectrum of activity of sorafenib against different mutant kinases associated with drug-sensitive and drug-resistant GIST. We compared the activity of imatinib and sorafenib against transiently expressed mutant forms of KIT and PDGFRA, including various secondary mutations that have been identified in imatinib-resistant or sunitinib-resistant GISTs. We also examined these drugs against four GIST cell lines, three of which are imatinib resistant. In our in vitro studies, we determined that sorafenib inhibited imatinib-resistant mutations in exons encoding the ATP/drug-binding pocket and in exons encoding the activation loop, with the exception of substitutions at KIT codon D816 and PDGFRA codon 842. Notably our data indicate that sorafenib is more effective than imatinib or sunitinib for inhibiting the kinase activity of drug-resistant KIT mutants (as assessed by biochemical IC50). We hypothesize that a major determinant of the efficacy of sorafenib for treatment of advanced GIST is the activity of this agent against KIT or PDGFRA-mutant kinases. These results have implications for the further development of treatments for drug-resistant GIST. Mol Cancer Ther; 11(8); 1770–80. ©2012 AACR.