bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of T helper type 17 and regulatory T cell activity in Citrobacter rodentium invasion and inflammatory damage
Authors: Symonds E L , Riedel C U , O'Mahony D , Lapthorne S , O'Mahony L , Shanahan F 
Published: March 2009

Summary
Citrobacter rodentium is a murine pathogen that transiently colonizes the lumen of the large intestine. C. rodentium induces colitis, but the relative importance and temporal induction of the T helper type 17 (Th17) and regulatory T cell (Treg) pathways in protection from the infection and inflammation have not been assessed. Our aim was to investigate the key immunological signalling events associated with successful clearance of C. rodentium. Mice were challenged with luminescent-tagged C. rodentium and killed at days 3 (early infection), 10 (peak infection) and 21 (late infection) post-infection. Bioluminescent imaging and bacterial culture determined levels of C. rodentium. Distal colon mRNA expression of interleukin (IL)-17, IL-6, IL-1β, tumour necrosis factor (TNF)-α, forkhead box P3 (FoxP3) and ghrelin were assessed using real-time polymerase chain reaction. Results were compared with age-matched non-infected mice. Low levels of C. rodentium were found at day 3, high levels at day 10, with clearance from the majority of the mice by day 21. In the distal colon, there was up-regulation of TNF-α and FoxP3 throughout the study and increases in IL-6 and IL-17 during the peak and late stages of infection. Ghrelin expression was increased at the peak and late stages of infection. This study has characterized changes to the T helper cell pathways, following the course of C. rodentium infection in mice. There were significant immunological changes, with up-regulation of the Th17 and Treg pathways in the distal colon and an increase in ghrelin expression compared with non-infected control mice. These changes may play a role in the pathology and clearance of C. rodentium.
Amelioration of hepatic fibrosis via Padma Hepaten is associated with altered natural killer T lymphocytes
Authors: Ginsburg I , Koren E , Horani A , Mahamid M , Doron S , Muhanna N , Amer J , Safadi R 
Published: March 2009

SummaryHepatic fibrosis is the end-stage consequence of chronic liver disease, affecting many people worldwide. Unlike the anti-fibrotic effect of natural killer (NK) cells, CD8 and NK T subsets are considered as profibrogenic subsets. Padma Hepaten is a multi-compound herbal preparation derived from Tibetan medicine and has proven efficacy in some clinical trials and tests at the cellular level. In this study, we evaluate the immune efficacy of Padma Hepaten administered intraperitoneally (i.p.) and/or orally in a mice model of hepatic fibrosis. Hepatic fibrosis was induced by 6 weeks of biweekly i.p. carbon tetrachloride (CCl4) injections in male C57Bl6 mice. There were four groups, including naive mice, non-treated fibrotic mice and fibrotic mice treated by Padma Hepaten at weeks 5–6 of fibrosis induction either orally or by i.p. injections. Padma Hepaten was prepared at 10 mg/ml in saline and 250 µl (2·5 mg) were administered four times per week. After week 6, animals were killed. To isolate a Padma Hepaten-associated effect on lymphocytes, splenocytes were harvested from either naive or Padma Hepaten-treated non-fibrotic donors. Isolated splenocytes were therefore reconstituted into two groups of irradiated recipients. Recipients were then administered the same CCl4 regimen. Hepatic fibrosis was determined by sirius red staining of liver sections and by assessment of alpha smooth muscle actin expression compared with β-actin (both by mRNA as well as the protein liver extract western blotting). Hepatic fibrosis and alanine aminotransferase serum levels were decreased significantly in both Padma Hepaten-treated groups compared with the non-treated fibrotic group. Padma Hepaten treatment was associated with attenuation of lymphocyte subsets in both treated groups. Using a chemiluminescence technique to assess total anti-oxidant capacities (TAC), it was found that both the plasmas and livers of mice treated by CCl4 had significantly higher TAC compared with controls. However, the levels of TAC in animals treated either by CCl4 alone or CCl4 with Padma Hepaten were similar. Adoptive transfer of Padma Hepaten-treated lymphocytes was associated with fibrosis amelioration compared with recipients with naive lymphocytes. CCl4 generates higher levels of anti-oxidant capacities, probably as a response to oxidative stress. Padma Hepaten administration attenuated hepatic fibrogenesis significantly, accompanied by attenuation of lymphocyte but not anti-oxidant capacities.
Gonadal dysfunction in male cancer patients before cytotoxic treatment
Authors: van Casteren Niels J. , Boellaard Willem P. A. , Romijn Johannes C. , Dohle Gert R. 
Published: March 2009

SummaryMale patients diagnosed with cancer are often referred for semen cryopreservation before gonadotoxic treatment but often have low semen quality. The aim of this study was to evaluate which type of cancer affects gonadal function and proposes a risk factor for low pre‐treatment semen quality. Between January 1983 and August 2006, 764 male cancer patients were referred for semen cryopreservation prior to chemotherapy and radiotherapy. We compared semen characteristics and reproductive hormones between different groups of cancer patients. In addition, we evaluated the role of tumour markers in patients with testicular germ‐cell tumours (TGCT) on fertility. Abnormal semen parameters were found in 489 men (64%) before cancer treatment. Patients with TGCT and extragonadal germ‐cell tumours had significantly lower sperm concentrations and inhibin B levels than all other patient groups. No semen could be banked in 93 patients (12.2%). Eight hundred and thirty‐nine of 927 (90%) produced semen samples were adequate for cryopreservation. Inhibin B in all groups showed to be the best predictor of semen quality. Although pre‐treatment raised tumour markers were associated with a decrease in inhibin B and increased follicle stimulating hormone, both predictive for low semen quality; no direct linear association could be found between raised beta‐HCG, alfa‐fetoprotein and semen quality. Only 1/3 of cancer patients had normal semen parameters prior to cancer treatment. Patients with TGCT and extragonadal GCT have the highest risk for impaired semen quality and gonadal dysfunction at the time of semen cryopreservation.
A hierarchical Bayesian approach to multi‐state mark–recapture: simulations and applications
Authors: Calvert Anna M. , Bonner Simon J. , Jonsen Ian D. , Flemming Joanna Mills , Walde Sandra J. , Taylor Philip D. 
Published: March 2009

SummaryMark–recapture models are valuable for assessing diverse demographic and behavioural parameters, yet the precision of traditional estimates is often constrained by sparse empirical data. Bayesian inference explicitly recognizes estimation uncertainty, and hierarchical Bayes has proven particularly useful for dealing with sparseness by combining information across data sets.We developed a general hierarchical Bayesian multi‐state mark–recapture model, tested its performance on simulated data sets and applied it to real ecological data on stopovers by migratory birds.Our hierarchical model performed well in terms of both precision and accuracy of parameters when tested with simulated data of varying quality (sample size, capture and survivorship probabilities). It also provided more precise and accurate parameter estimates than a non‐hierarchical model when data were sparse.A specific version of the model, designed for estimation of daily transience and departure of migratory birds at a mid‐route stopover, was applied to 11 years of autumn migration data from Atlantic Canada. Hierarchical estimates of departure and transience were more precise than those derived from parallel non‐hierarchical and frequentist methods, and indicated that inter‐annual variability in parameters suggested by these other methods was largely due to sampling error.Synthesis and applications. Estimates of demographic parameters, often derived from mark–recapture studies, provide the basis for evaluating the status of species at risk, for developing conservation and management strategies and for evaluating the results of current protocols. The hierarchical Bayesian multi‐state mark–recapture model presented here permits partitioning of complex parameter variation across space or time, and the simultaneous analysis of multiple data sets results in a marked increase in the precision of estimates derived from sparse capture data. Its structural flexibility should make it a valuable tool for conservation ecologists and wildlife managers.
Quantifying historical changes in habitat availability for endangered species: use of pixel‐ and object‐based remote sensing
Authors: Pringle Robert M. , Syfert Mindy , Webb Jonathan K. , Shine Richard 
Published: March 2009

Summary

Establishing medium‐ to long‐term trends in habitat availability for endangered species is important for determining the causes of historical population declines and for designing effective management plans. For some animal species, relative habitat availability can be estimated using time series of aerial photographs, but the limited information in old black‐and‐white images makes it challenging to estimate accurately at large spatial scales.
Australia's most endangered snake, the broad‐headed snake Hoplocephalus bungaroides, requires unshaded, exfoliated sandstone rocks for shelter. Using digitized aerial photographs of four sites from 1941 and 1971, and a Quickbird satellite image from 2006, we estimated the trend in habitat availability for a well‐studied population of H. bungaroides in New South Wales. We did this using both traditional, pixel‐based classifications and a more recently developed object‐based approach.
Both classification methods revealed substantial, monotonic decreases (by 24–77%) in the percentage cover of bare rock from 1941 to 2006 at all sites, with concomitant (although non‐monotonic) net increases in percentage tree‐canopy cover of 3–70%. The cover of herbaceous and low‐shrub vegetation appeared variable and was poorly resolved in the classifications.
Both classification methods yielded adequate (> 70%) accuracy for most images, but the object‐based classifications were consistently more accurate than the pixel‐based classifications and performed better when analysing images (from 1971) with comparatively low resolution.
Synthesis and applications. Our study indicates that habitat availability for broad‐headed snakes has decreased considerably over 65 years due to increased shading from vegetation, and that object‐based image analysis is a promising tool for assessing habitat trends using historical photographs. Multiple studies have reported woody‐vegetation increases over multi‐decadal time‐scales in Australia and elsewhere, but few have tied these trends to habitat availability for animal species of concern. The phenomenon we document may therefore be quite widespread, and advances in remote sensing (including applications and refinements of the methods presented here) will be invaluable for revealing these trends and designing ameliorative management strategies. Management plans to conserve broad‐headed snakes and similarly threatened species should include either controlled burns or regular targeted removal of vegetation, preferably after a rigorous comparison of the relative economic and biological costs and benefits of each.
Phenotypic, serological and genetic characterization of Flavobacterium psychrophilum strains isolated from salmonids in Chile
Authors: Valdebenito S , Avendaño‐Herrera R 
Published: March 2009

AbstractCharacterization of 20 Flavobacterium psychrophilum strains isolated from farmed Atlantic salmon and rainbow trout in Chile was done using phenotypic, antigenic and genetic techniques. Experimental infections were also performed to assess the virulence of two representative isolates and of the type strain. Biochemical and physiological analyses showed that Chilean F. psychrophilum strains, regardless of the host species, constitute a phenotypically very homogeneous group matching with previous descriptions of this pathogen. However, serological assays indicated the existence of antigenic heterogeneity with four patterns of serological reactions. The first group contained most (14 of 20) of the F. psychrophilum isolates showing cross‐reaction with the antisera obtained against Atlantic salmon and rainbow trout isolates. Group 2 corresponded to four other rainbow trout isolates (1658, 1731, 1762 and 29009) that did not agglutinate with anti‐1150 serum. Two minor serological groups were identified for the remaining isolates (Groups 3 and 4). Marked homogeneity was also revealed by genetic studies including 16S rRNA alleles, random amplified polymorphic DNA and REP‐PCR showing that a major genetic group of F. psychrophilum may be dominant in disease outbreaks in farms. Restriction fragment length polymorphism of PCR analysis showed that gyrase genotypes B‐S or B‐R were found in Chilean isolates from rainbow trout and Atlantic salmon, whereas genotype A was not found. Virulence assays using Atlantic salmon indicated no relationship between the degree of pathogenicity and the host origin of the F. psychrophilum strains.
Genetic characterization of Streptococcus phocae strains isolated from Atlantic salmon, Salmo salar L., in Chile
Authors: Valdés I , Jaureguiberry B , Romalde J L , Toranzo A E , Magariños B , Avendaño‐Herrera R 
Published: March 2009

Abstract Streptococcus phocae is a beta‐haemolytic bacterium frequently involved in disease outbreaks in seals causing pneumonia or respiratory infection. Since 1999, this pathogen has been isolated from diseased Atlantic salmon, Salmo salar, causing serious economic losses in the salmon industry in Chile. In this study, we used different molecular typing methods, such as pulsed‐field gel electrophoresis (PFGE), randomly amplified polymorphic DNA (RAPD), enterobacterial repetitive intergenic consensus sequence PCR (ERIC‐PCR), repetitive extragenic palindromic PCR (REP‐PCR) and restriction of 16S–23S rDNA intergenic spacer regions to evaluate the genetic diversity in S. phocae. Thirty‐four strains isolated in different years were analysed. The S. phocae type strain ATCC 51973T was included for comparative purposes. The results demonstrated genetic homogeneity within the S. phocae strains isolated in Chile over several years, suggesting the existence of clonal relationships among S. phocae isolated from Atlantic salmon. The type strain ATCC 51973T presented a different genetic pattern with the PFGE, RAPD, ERIC‐PCR and REP‐PCR methods. However, the fingerprint patterns of two seal isolates were distinct from those of the type strain.
Better adherence to antihypertensive agents and risk reduction of chronic heart failure
Authors: Perreault S. , Dragomir A. , White M. , Lalonde L. , Blais L. , Bérard A. 
Published: March 2009

Abstract.Aims.  Antihypertensive (AH) agents have been shown to reduce the risk of major cardiovascular events including chronic heart failure (CHF). However, the impact of changes in patterns of AH agents use on CHF is unknown. Our objective was to estimate to which different patterns of AH agent use is associated with the occurrence of CHF in a population‐based study.Method and results.  A cohort of 82 320 patients was reconstructed using the Régie de l’assurance maladie du Québec’s databases. Patients were eligible if they were between 45 to 85 years of age, had no indication of cardiovascular disease and were newly treated with AH therapy between 1999 and 2004. A nested case–control design was used to study the occurrence of CHF. Every case of CHF was matched for age and duration of follow‐up to a maximum of 15 randomly selected controls. Adherence level was reported as a medication possession ratio. Conditional logistic regression models were used to estimate the rate ratio (RR) of CHF adjusting for different covariables. The mean patient age was 65 years, 37% were male, 8% had diabetes, 19% had dyslipidaemia and mean time of follow‐up at 2.7 years. High adherence level (95%) to AH therapy compared with lower adherence level (60%) was associated with an additional reduction of CHF events (RR: 0.89; 0.80–0.99). Risk factors for CHF were being on social assistance, diabetes, dyslipidaemia, higher chronic disease score and developing a cardiovascular condition during follow‐up.Conclusion.  Our study suggests that a better adherence is associated with a significant risk reduction of CHF. Adherence to AH therapy needs to be improved to optimize benefits.
Escherichia coli DnaA forms helical structures along the longitudinal cell axis distinct from MreB filaments
Authors: Boeneman Kelly , Fossum Solveig , Yang Yanhua , Fingland Nicholas , Skarstad Kirsten , Crooke Elliott 
Published: March 2009

SummaryDnaA initiates chromosomal replication in Escherichia coli at a well‐regulated time in the cell cycle. To determine how the spatial distribution of DnaA is related to the location of chromosomal replication and other cell cycle events, the localization of DnaA in living cells was visualized by confocal fluorescence microscopy. The gfp gene was randomly inserted into a dnaA‐bearing plasmid via in vitro transposition to create a library that included internally GFP‐tagged DnaA proteins. The library was screened for the ability to rescue dnaAts mutants, and a candidate gfp–dnaA was used to replace the dnaA gene of wild‐type cells. The resulting cells produce close to physiological levels of GFP–DnaA from the endogenous promoter as their only source of DnaA and somewhat under‐initiate replication with moderate asynchrony. Visualization of GFP‐tagged DnaA in living cells revealed that DnaA adopts a helical pattern that spirals along the long axis of the cell, a pattern also seen in wild‐type cells by immunofluorescence with affinity purified anti‐DnaA antibody. Although the DnaA helices closely resemble the helices of the actin analogue MreB, co‐visualization of GFP‐tagged DnaA and RFP‐tagged MreB demonstrates that DnaA and MreB adopt discrete helical structures along the length of the longitudinal cell axis.
Trichomonas vaginalis: metronidazole and other nitroimidazole drugs are reduced by the flavin enzyme thioredoxin reductase and disrupt the cellular redox system. Implications for nitroimidazole toxicity and resistance
Authors: Leitsch David , Kolarich Daniel , Binder Marina , Stadlmann Johannes , Altmann Friedrich , Duchêne Michael 
Published: March 2009

SummaryInfections with the microaerophilic parasiteTrichomonas vaginalisare treated with the 5‐nitroimidazole drug metronidazole, which is also in use againstEntamoeba histolytica,Giardia intestinalisand microaerophilic/anaerobic bacteria. Here we report that inT. vaginalisthe flavin enzyme thioredoxin reductase displays nitroreductase activity with nitroimidazoles, including metronidazole, and with the nitrofuran drug furazolidone. Reactive metabolites of metronidazole and other nitroimidazoles form covalent adducts with several proteins that are known or assumed to be associated with thioredoxin‐mediated redox regulation, including thioredoxin reductase itself, ribonucleotide reductase, thioredoxin peroxidase and cytosolic malate dehydrogenase. Disulphide reducing activity of thioredoxin reductase was greatly diminished in extracts of metronidazole‐treated cells and intracellular non‐protein thiol levels were sharply decreased. We generated a highly metronidazole‐resistant cell line that displayed only minimal thioredoxin reductase activity, not due to diminished expression of the enzyme but due to the lack of its FAD cofactor. Reduction of free flavins, readily observed in metronidazole‐susceptible cells, was also absent in the resistant cells. On the other hand, iron‐depletedT. vaginaliscells, expressing only minimal amounts of PFOR and hydrogenosomal malate dehydrogenase, remained fully susceptible to metronidazole. Thus, taken together, our data suggest a flavin‐based mechanism of metronidazole activation and thereby challenge the current model of hydrogenosomal activation of nitroimidazole drugs.
The biogenic origin of needle fibre calcite
Authors: CAILLEAU GUILLAUME , VERRECCHIA ERIC P. , BRAISSANT OLIVIER , EMMANUEL LAURENT 
Published: March 2009

AbstractNeedle fibre calcite is one of the most ubiquitous habits of calcite in vadose environments (caves deposits, soil pores, etc.). Its origin, either through inorganic, indirect or direct biological processes, has long been debated. In this study, investigations at 11 sites in Europe, Africa and Central America support arguments for its biogenic origin. The wide range of needle morphologies is the result of a gradual evolution of the simplest type, a rod. This rod is the elementary brick which, by aggregation and welding, builds more complex needles. The absence of cross‐welded needles implies that they are welded in a mould, or under a longitudinal and unidirectional constraint, before being released inside the soil pores. The difference between the lengthening of the needles and the c axis can be explained by the existence of needles observed under a scanning electron microscope in organic sleeves, which can act as a mould during rod growth. Complex morphologies with epitaxial outgrowths on straight rods cannot have grown entirely inside organic microtubes; they must result from soil diagenesis after the release of straight rods in a soil‐free medium. Whisker crystals are interpreted as the result of growth and coalescence of euhedral crystals on a rod. Rhomb chains are considered to be the consequence of successive epitaxial growth steps on a needle during variations in growth conditions. Isotopic signatures for needle fibre calcite vary from −16·63‰ to +1·10‰ and from −8·63‰ to −2·25‰ for δ13C and δ18O, respectively. The absence of high δ18O values for needle fibre calcite precludes a purely physicochemical origin (evaporative) for this particular habit of calcite. As epitaxial growth cannot precipitate in the same conditions as initial needles, needle fibre calcite stable isotopic signatures should be used with caution as a proxy for palaeoenvironmental reconstructions. In addition, it is suggested that the term needle fibre calcite should be kept for the original biogenic form. The other habit should be referred to as epitaxial forms of needle fibre calcite.
Local adaptation of stress related traits in Drosophila buzzatii and Drosophila simulans in spite of high gene flow
Authors: SARUP P. , FRYDENBERG J. , LOESCHCKE V. 
Published: March 2009

AbstractWe addressed the question if local adaptation to a thermal gradient is possible in spite of a high gene flow among closely spaced populations of two species of Drosophila from the island of La Gomera (Canary Islands). Variation in multiple traits related to stress resistance in different life stages was measured in both species in flies collected from five localities at different altitudes and thereby with different climatic conditions. Based on microsatellite loci, the populations were not genetically differentiated. However, 18 of the 24 independent traits measured showed significant differentiation among populations of Drosophila buzzatii, but only nine of 25 for Drosophila simulans. This difference in the number of traits might reflect higher habitat specificity and thus higher potential for local adaptation of D. buzzatii than D. simulans. We found clinal variation, as some traits showed significant linear regressions on altitude, but more on altitude cubed.