bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variation in chicken populations may affect the enzymatic activity of lysozyme
Authors: Downing T. , O’Farrelly C. , Bhuiyan A. K. , Silva P. , Naqvi A. N. , Sanfo R. , Sow R.‐S. , Podisi B. , Hanotte O. , Bradley D. G. 
Published: October 2009

SummaryThe chicken lysozyme gene encodes a hydrolase that has a key role in defence, especially in ovo. This gene was resequenced in global chicken populations [red, grey, Ceylon and green jungle fowl (JF)] and related bird species. Networks, summary statistics and tests of neutrality indicate that although there is extensive variation at the gene, little is present at coding sites, with the exception of one non‐synonymous site. This segregating site and a further fixed non‐synonymous change between red JF and domestic chicken populations are spatially close to the catalytic sites of the enzyme and so might affect its activity.
Remote European mountain lake ecosystems: regionalisation and ecological status
Authors: CATALAN J. , CURTIS C. J. , KERNAN M. 
Published: October 2009

Summary1. A survey of c. 350 remote high altitude and high latitude lakes from 12 different mountain regions across Europe was undertaken to explore ecosystem variability, climate forcing, environmental conditions and pollution threats at a scale not previously attempted.2. Lakes were sampled for a range of contemporary and sub‐fossil organisms including planktonic crustaceans, rotifers, littoral invertebrates, chironomids, diatoms and cladocerans. Survey and cartographic data were used to determine environmental characteristics at each site. Organic pollutants and trace metal concentrations were measured in the lake sediment.3. A number of separate studies were undertaken which examined the environmental characteristics of the surveyed lakes (climate forcing and chemical composition), distribution of biota relative to local, regional and biogeographical factors and pollution threats (acidification, heavy metals and persistent organic pollutants) to these sensitive ecosystems.4. There is a strong regional element to the way that environmental factors combine (including climate and pollution threats) and the biota responds in mountain lakes across Europe. From a management perspective it is clear that lake classification and the development of useful typologies and assessments of reference conditions should be undertaken at regional rather than pan‐European scales.5. There are some common features across lake districts related to the timing of industrialisation, but the studies carried out on metals, organic pollutants and nitrate deposition indicate that each lake district has distinct pollution threats. Climate warming already affects most of the lake districts and there are considerable uncertainties as to how this will modify conditions in remote European mountain systems.6. The lake district concept goes beyond a geographical construct and merits further theoretical and experimental development as an ecological concept.
Interactions of slope and canopy of herbage of three herbage species on transport of faecal indicator bacteria by rain splash
Authors: Boyer D. G. , Belesky D. P. 
Published: October 2009

AbstractThe movement of faecal pathogens from land to surface and ground‐water are of great interest because of the public and livestock health implications. Knowledge of canopy structure and how it might be managed to help mitigate nutrient and pathogen movement in pasture is needed to create management practices that balance livestock production with environmental benefits. An experiment was conducted using a rainfall‐simulating device to test whether canopy structure of species common to pastures in Appalachia, USA could be managed to influence dispersion of faecal pathogens. Seven pots (30‐cm diameter) of white clover, orchardgrass and perennial ryegrass were lined up on horizontal and sloping surfaces under a rainfall simulator. The centre pot was inoculated at the soil surface with 4 × 1010 faecal coliform bacteria (FC) just before rainfall simulation started. The species were maintained under short, moderate and tall canopy management treatments. White clover exhibited the greatest rates of lateral and vertical dispersion of FC into the canopy, especially in the short canopy management treatment following 30 min of rainfall (about 40 mm). Low concentrations of faecal coliform bacteria also dispersed into the canopies of the grass species but the differences in concentration of FC between the grass species were not different. When the proportion of white clover in a pasture is high, the canopy should be relatively taller to reduce the likelihood of infection associated with faecal coliform‐contaminated herbage.
Effects of pasture management and fertilizer regimes on botanical changes in species‐rich mountain calcareous grassland in Central Europe
Authors: Lanta V. , Doležal J. , Lantová P. , Kelíšek J. , Mudrák O. 
Published: October 2009

AbstractA 3‐year experiment was conducted in Central Europe to examine the effects of three managements, viz. continuous cattle grazing from April to September, mowing once in July and abandonment of grazing, and two levels of fertilizer application, no fertilizer and 400 kg ha−1of a NPK fertilizer, on changes in plant species composition and summer biomass of dry matter (DM) in a calcareous mountain grassland containing many plant functional types. Different managements led to changes in species composition due to species‐specific responses. Low creeping and rosette species were associated with grazing, while grasses and tall forbs correlated with mowing and abandonment of grazing, probably because of their ability to outcompete rosette species. There was a negative relationship between the number of species and above‐ground biomass and a positive relationship between number of species and below‐ground biomass, suggesting that these species‐rich communities allocate more to below‐ground organs when not grazed. The application of fertilizer had no effect on species composition but it indirectly increased competitive asymmetry for light and increased the number of plant extinctions. It is concluded that continuation of cattle grazing is an acceptable form of grassland management at the study site and that species and functional group compositions can rapidly change with changing environmental conditions such as abandonment of grazing or application of fertilizer.
Relationship of bite mass of cattle to sward structure of four temperate grasses in short‐term grazing sessions
Authors: Soder K. J. , Sanderson M. A. , Gregorini P. , Orr R. J. , Rubano M. D. , Rook A. J. 
Published: October 2009

AbstractThe effect of sward structure of four temperate grass species on the bite mass of cattle was evaluated. Micro‐swards (79 cm × 47 cm; approximately the area of a feeding station) of orchardgrass (Dactylis glomerata L.), quackgrass [Elymus repens (L.) Gould], meadow fescue [Schedonorus pratensis (Huds.) P. Beauv] and reed canarygrass (Phalaris arundinacea L.) were offered to Holstein dairy cows in short‐term grazing sessions in 2006 and 2007 using a 4 × 4 Latin square design. Cows were allowed to take fifty bites in each session. Bite mass was calculated by dividing the adjusted change in weight of the micro‐sward by the number of bites. Sward surface height, bulk density and distribution of herbage dry matter (DM) in the canopy were measured pre‐ and post‐grazing. Sward structure differed among the grass species within years but bite mass (on a fresh or DM basis) was not affected. Higher surface heights and bulk densities in 2006 compared with 2007 (averaged across grass species) resulted in greater bite masses of DM in 2006. Values were 25·7 cm vs. 17·0 cm for surface height; 1219 g m−3 vs. 926 g m−3 for bulk density; and 1·05 g DM bite−1 vs. 0·50 g DM bite−1 for 2006 and 2007 respectively. Within the context of this study, differences between years in bite mass, associated with greater changes in sward structure, were more important than differences among grass species.
Histological grading of invasive breast carcinoma – a simplification of existing methods in a large conservation series with long‐term follow‐up
Authors: Thomas Jeremy St J , Kerr Gillian R , Jack Wilma J L , Campbell Fiona , McKay Laura , Pedersen Hans‐Christian , Kunkler Ian H , Cameron David A , Chetty Udi , Bartlett John M S 
Published: October 2009

Aims:  To assess the validity of grading in the Edinburgh Breast Conservation Series; a consecutive cohort of 1812 early breast cancer patients treated by breast conservation and radiotherapy between 1981 and 1998 in a single specialist centre with ≥9 years’ follow‐up and full staging data.Methods and results:  A single pathologist (J.St.J.T) graded 1650 cases using the Elston and Ellis method (EE) with particular reference to the component data: acinar differentiation, nuclear pleomorphism and mitotic counts. The original method was then compared with binary scoring of the same components and the relationship to prognosis reassessed. EE grades and individual grade components were prognostic (P < 0.0001) with 10‐year cause‐specific survival of 95.6%, 86.4% and 74.7% for EE grades 1, 2 and 3, respectively. A binary scoring of grade components produces four groups, splitting EE grade 2 tumours into two groups with different outcomes – 10‐year survival rates for the four revised grades were 96.0%, 89.0%, 79.7% and 75.4%, respectively.Conclusions:  Existing grading methodology is fully applicable in the narrower context of a conservation series but can be simplified. Subdivision of EE grade 2 into a true intermediate prognosis group and a second group with a worse prognosis also adds benefit.
Caffeine induces ram sperm hyperactivation independent of cAMP‐dependent protein kinase
Authors: Colás C. , Cebrián‐Pérez J. A. , Muiño‐Blanco T. 
Published: October 2009

SummaryWe have previously shown that a cocktail‐containing phosphodiesterase inhibitors (theophylline and caffeine), a phosphatase inhibitor (okadaic acid) and dibutyryl‐cAMP promoted specific protein tyrosine phosphorylation in ram spermatozoa during incubation in capacitating conditions. Here, we show, for the first time, that this cocktail induced a progressive time‐dependent increase in the capacitated‐sperm subpopulation.The addition of either the analogue of adenosine, 2‐chloro‐2′‐deoxyadenosine (Cl‐Ado) or caffeine provided a significant increase in the proportion of capacitated spermatozoa and total tyrosine phosphorylation. Computer‐assisted semen analysis was used to identify hyperactivated spermatozoa by setting maximum threshold for linearity (≤45%) and minimum for amplitude of lateral head displacement (≥3.5 μm). Our results showed that ram spermatozoa can be capacitated in vitro without displaying hyperactivated movement. Among the above‐mentioned compounds, only caffeine was able to induce hyperactivation that achieved the maximal response at 8 min of incubation, with a significant increase in hyperactivated spermatozoa of 44.4 ± 5.6% related to control samples. Flow cytometry analyses showed that caffeine induced a significant increase in the content of calcium in viable spermatozoa during the time‐course of incubation in capacitating conditions. BAPTA‐AM, a cell‐permeable calcium chelator, did not suppress the caffeine‐dependent hyperactivation. Quantitative analysis revealed that the addition of caffeine or Cl‐Ado accounted for an increase in intracellular cAMP level. However, this increase in cAMP does not seem to be responsible for the caffeine‐induced hyperactivation because the cAMP‐elevating agents (cocktail) did not promote hyperactivation either, although they greatly induced capacitation and protein tyrosine phosphorylation. The inhibition of PKA with H89 reduced both capacitation and protein tyrosine phosphorylation although hyperactivation increased. These results suggest that calcium from internal stores would be enough to initiate the hyperactivated movement, and that protein tyrosine phosphorylation implicated in ram sperm hyperactivation would be regulated by calcium rather than by PKA‐dependent cAMP.
The predictive value of testicular ultrasound abnormalities for carcinoma in situ of the testis in men at risk for testicular cancer
Authors: Elzinga‐Tinke J. E. , Sirre M. E. , Looijenga L. H. J. , Van Casteren N. , Wildhagen M. F. , Dohle G. R. 
Published: October 2009

SummaryTesticular microlithiasis (TM) is sometimes observed during scrotal ultrasound examinations in men. It has been suggested that TM is more prevalent in testes of men at risk for testicular carcinoma in situ (CIS), the precursor cells of all testicular germ cell tumours (TGCT). We have performed a retrospective analysis of ultrasound images and additional clinical data of a selected cohort of men and have determined the risk factor of TM and other ultrasound abnormalities for testicular CIS. Between 2002 and 2007, 176 testicular biopsies were performed in men with abnormalities found on the scrotal ultrasound. TM was found in 76/176 men (43.2%) and CIS was diagnosed in 20 of these men (26.3%). Here, we focused on the group of 76 men with TM to determine additional risk factors, besides TM, for CIS. In both groups, those with and without CIS, reproductive hormones, scrotal ultrasound images and patient history were compared. Predictive ultrasound findings for CIS were TM (sensitivity 100%, 95% CI: 0.8–1.0; specificity 64.1%, 95% CI: 0.6–0.7; PPV 26.3%, 95% CI: 0.2–0.4) and within this group an inhomogeneous testicular parenchyma (OR 16.1, 95% CI 2.4–106.8; sensitivity 75.0%, 95% CI: 0.5–0.9; specificity 79.0%, 95% CI: 0.7–0.9; PPV 50.0%, 95% CI: 0.3–0.7). Other significantly ultrasound characteristics for CIS in this population with TM were clusters of TM (p = 0.02) and intra‐testicular lesions (p = 0.01). Men with CIS were found to have significantly lower values of inhibin‐B (p = 0.02). Clusters of TM, intra‐testicular lesions and lower values of inhibin‐B were not significantly different in logistic regression analysis. TM on scrotal ultrasound of men with risk factors for TGCT and men with clinical signs of testicular maldevelopment has a high predictive value for CIS. However, the predictive value of an inhomogeneous testicular parenchyma, besides TM, for CIS is much higher.
Genetic relatedness in groups of the humbug damselfish Dascyllus aruanus: small, similar‐sized individuals may be close kin
Authors: BUSTON PETER M. , FAUVELOT CÉCILE , WONG MARIAN Y. L. , PLANES SERGE 
Published: October 2009

AbstractKin selection plays an important role in the evolution of social behaviour in terrestrial systems. The extent to which kin selection influences the evolution of social behaviour in marine systems is largely unexplored. Generally, it is considered that kin selection is irrelevant in marine systems, because it is assumed that the dispersing larval phase of marine organisms will break up kin associations. Here, we challenge this assumption and investigate the opportunity for kin selection in a coral reef fish: the humbug damselfish Dascyllus aruanus. This fish lives in groups composed of a large male and a number of smaller females and nonbreeders. We use 10 polymorphic microsatellite loci to assess the relatedness of 265 individuals from 35 groups. The mean coefficient of relatedness among group members is 0.01 ± 0.04, suggesting that individuals are not associated with close relatives. However, the distribution of pairwise relatedness of individuals within groups has an overabundance of positive values, and indicates that there might be 35 pairs of close relatives within groups. Further analyses reveal that close relatives likely are similar in size and small in size, suggesting that they might have recruited together. We conclude that it is possible for kin selection to operate in D. aruanus, but kin recognition will be a prerequisite for such selection. This study reveals that individuals can be associated with close relatives, and there is a hidden potential for kin selection, during certain parts of the life cycle of coral reef fishes.
Contrasting mtDNA diversity and population structure in a direct‐developing marine gastropod and its trematode parasites
Authors: KEENEY DEVON B. , KING TANIA M. , ROWE DIANE L. , POULIN ROBERT 
Published: October 2009

AbstractThe comparative genetic structure of hosts and their parasites has important implications for their coevolution, but has been investigated in relatively few systems. In this study, we analysed the genetic structure and diversity of the New Zealand intertidal snail Zeacumantus subcarinatus (n = 330) and two of its trematode parasites, Maritrema novaezealandensis (n = 269) and Philophthalmus sp. (n = 246), using cytochrome c oxidase subunit I gene (COI) sequences. Snails and trematodes were examined from 11 collection sites representing three regions on the South Island of New Zealand. Zeacumantus subcarinatus displayed low genetic diversity per geographic locality, strong genetic structure following an isolation by distance pattern, and low migration rates at the scale of the study. In contrast, M. novaezealandensis possessed high genetic diversity, genetic homogeneity among collection sites and high migration rates. Genetic diversity and migration rates were typically lower for Philophthalmus sp. compared to M. novaezealandensis and it displayed weak to moderate genetic structure. The observed patterns likely result from the limited dispersal ability of the direct developing snail and the utilization of bird definitive hosts by the trematodes. In addition, snails may occasionally experience long‐distance dispersal. Discrepancies between trematode species may result from differences in their effective population sizes and/or life history traits.
Major histocompatibility complex variation at class II DQA locus in the brown hare (Lepus europaeus)
Authors: KOUTSOGIANNOULI E. A. , MOUTOU K. A. , SARAFIDOU T. , STAMATIS C. , SPYROU V. , MAMURIS Z. 
Published: October 2009

AbstractThe major histocompatability complex (MHC) is a multigene family of receptors that bind and present antigenic peptides to T‐cells. Genes of the MHC are characterized by an outstanding genetic polymorphism, which is considered to be maintained by positive selection. Sites involved in peptide binding form binding pockets (P) that are collectively termed the peptide‐binding region (PBR). In this study, we examined the level of MHC genetic diversity within and among natural populations of brown hare (Lepus europaeus) from Europe and Anatolia choosing for analysis of the second exon of the DQA locus, one of the most polymorphic class II loci. We aimed at an integrated population genetic analysis of L. europeaus by (i) correlating MHC polymorphism to genetic variability and phylogenetic status estimated previously from maternally (mtDNA) and biparentally (allozymes, microsatellites) inherited loci; and (ii) comparing full‐length exon amino acid polymorphism with functional polymorphism in the PBR and the binding pockets P1, P6 and P9. A substantial level of DQA exon 2 polymorphism was detected with two completely different set of alleles between the Anatolian and European populations. However, the phylogeny of full‐length exon 2 Leeu‐DQA alleles did not show a strong phylogeographic signal. The presence of balancing selection was supported by a statistically significant excess of nonsynonymous substitutions over synonymous in the PBR and a trans‐species pattern of evolution detected after phylogenetic reconstruction. The differentiating patterns detected between genetic and functional polymorphism, i.e. the number and the distribution of pocket variants within and among populations, indicated a hierarchical action of selection pressures.
Noonan syndrome and neurofibromatosis type I in a family with a novel mutation in NF1
Authors: Nyström AM , Ekvall S , Allanson J , Edeby C , Elinder M , Holmström G , Bondeson ML , Annerén G 
Published: October 2009

Noonan syndrome (NS) and neurofibromatosis type I (NF1) belong to a group of clinically related disorders that share a common pathogenesis, dysregulation of the RAS‐MAPK pathway. NS is characterized by short stature, heart defect, pectus deformity and facial dysmorphism, whereas skin manifestations, skeletal defects, Lisch nodules and neurofibromas are characteristic of NF1. Both disorders display considerable clinical variability. Features of NS have been observed in individuals with NF1 –a condition known as neurofibromatosis–Noonan syndrome (NFNS). The major gene causing NFNS is NF1. Rarely, a mutation in PTPN11 in addition to an NF1 mutation is present.We present the clinical and molecular characterization of a family displaying features of both NS and NF1, with complete absence of neurofibromas. To investigate the etiology of the phenotype, mutational analysis of NF1 was conducted, revealing a novel missense mutation in exon 24, p.L1390F, affecting the GAP‐domain. Additional RAS‐MAPK pathway genes were examined, but no additional mutations were identified. We confirm that NF1 mutations are involved in the etiology of NFNS. Furthermore, based on our results and previous studies we suggest that evaluation of the GAP‐domain of NF1 should be prioritized in NFNS.
A high‐throughput Taqman® approach for the discrimination of HLA‐E alleles
Authors: Paquay M. M. , Schellekens J. , Tilanus M. G. J. 
Published: October 2009

AbstractAn association between human leukocyte antigen (HLA) molecules and the incidence of various diseases has been recognized for years. Molecules of the HLA system also exert an important role on the clinical outcome after transplantation such as stem cell transplantation. The conventional HLA typing method is sequence based typing (SBT) which is reliable but laborious. The goal of this study was to develop a high‐throughput Taqman® assay to screen large panels for HLA‐E alleles. Two functional HLA‐E alleles, *0101 and *0103, have been identified. We set up the Taqman® assay with genomic DNA as template to discriminate the three HLA‐E genotypes: homozygous HLA‐E*0101, heterozygous *0101, *0103 and homozygous *0103. This Taqman® approach was validated by the comparison of results obtained with the typing results acquired by sequenced base typing (SBT). Additional screening of a large panel showed the pronounced discriminative capacity of the Taqman® assay for HLA‐E allele typing. The Taqman® assay is a fast, reliable and consistent HLA‐E allele typing method, especially useful to screen large panels.
IL‐21: roles in immunopathology and cancer therapy
Authors: Søndergaard H. , Skak K. 
Published: October 2009

AbstractCytokines are secreted signalling molecules with decisive effects on haematopoiesis, innate and adaptive immunity, and immunopathology. Interleukin (IL)‐21 is a novel cytokine produced by activated CD4+ T cells and natural killer T (NKT) cells. IL‐21 is part of a family of cytokines which include IL‐2, ‐4, ‐7, ‐9 and ‐15 that all share the common IL‐2 receptor γ chain (γc) in their individual receptor complexes. IL‐21 receptor (IL‐21R) is widely expressed on both myeloid and lymphoid cell lineages and IL‐21 actions include co‐stimulation of B cell differentiation and immunoglobulin (Ig) production, co‐mitogen of T cells, and stimulation of NK and CD8+ T cell cytotoxic function. Initially, IL‐21 was recognized for its anti‐tumour effects in several preclinical tumour models, warranting its currently ongoing clinical development as a cancer immunotherapeutic. More recently, IL‐21 has been associated with the development of a panel of autoimmune and inflammatory diseases, where neutralization of IL‐21 has been suggested as a potential new therapy. In this review, we will cover the latest discoveries of IL‐21 as a cancer therapy and its implications in immunopathologies.