bluuebunny/crossref_metadata_2025 huggingface dataset:
The inadvertent introduction into Australia of Trypanosoma nabiasi, the trypanosome of the European rabbit (Oryctolagus cuniculus), and its potential for biocontrol
Authors: HAMILTON P. B. , STEVENS J. R. , HOLZ P. , BOAG B. , COOKE B. , GIBSON W. C.
Published: August 2005

Wild rabbits (Oryctolagus cuniculus) in Australia are the descendents of 24 animals from England released in 1859. We surveyed rabbits and rabbit fleas (Spilopsyllus cuniculi) in Australia for the presence of trypanosomes using parasitological and PCR‐based methods. Trypanosomes were detected in blood from the European rabbits by microscopy, and PCR using trypanosome‐specific small subunit ribosomal RNA (SSU rRNA) gene primers and those in rabbit fleas by PCR. This is the first record of trypanosomes from rabbits in Australia. We identified these Australian rabbit trypanosomes as Trypanosoma nabiasi, the trypanosome of the European rabbit, by comparison of morphology and SSU rRNA gene sequences of Australian and European rabbit trypanosomes. Phylogenetic analysis places T. nabiasi in a clade with rodent trypanosomes in the subgenus Herpetosoma and their common link appears to be transmission by fleas. Despite the strict host specificity of trypanosomes in this clade, phylogenies presented here suggest that they have not strictly cospeciated with their vertebrate hosts. We suggest that T. nabiasi was inadvertently introduced into Australia in the 1960s in its flea vector Spilopsyllus cuniculi, which was deliberately introduced as a potential vector of the myxoma virus. In view of the environmental and economic damage caused by rabbits in Australia and other islands, the development of a virulent or genetically modified T. nabiasi should be considered to control rabbits.
Island colonization and founder effects: the invasion of the Guadeloupe islands by ship rats (Rattus rattus)
Authors: ABDELKRIM J. , PASCAL M. , SAMADI S.
Published: August 2005

The stepwise colonization of islands within an archipelago is typically punctuated by successive founder effects, with each newly founded population being a subsample of the gene pool of the source island. Thus, the genetic signature of successive bottlenecks should be detected when analysing the genetic structure between islands of an archipelago. To test this prediction, we investigated introduced ship rat populations, Rattus rattus (Linnaeus, 1758), in the Guadeloupe Archipelago. Three different methods, commonly named the heterozygosity excess, the mode‐shift indicator and the M ratio method, were used to detect bottlenecks from genetic data obtained with eight microsatellite markers on Guadeloupe and two neighbouring islands, Petite‐Terre and Fajou. Moreover, a recent eradication failure on Fajou allowed us to test the accuracy of the methods in an ‘experimental‐like’ situation. The results indicate that rats were introduced on Guadeloupe first, which then became the source population for independent secondary colonization of Fajou and Petite‐Terre. Moreover, the heterozygosity excess and the mode‐shift indicator only detected bottlenecks for the recent colonization of Petite‐Terre and the eradication failure on Fajou. However, bottlenecks were detected for all the populations using the M ratio method. This could be interpreted as the remaining signature of the early introduction of the ship rat in the archipelago.
Phylogeography and demography of Guianan harlequin toads (Atelopus): diversification within a refuge
Authors: NOONAN BRICE P. , GAUCHER PHILIPPE
Published: August 2005

We investigated the genetic structure of populations of Guianan harlequin toads (genus Atelopus) and their evolutionary affinities to extra‐Guianan congeners. Phylogenetic analysis of mitochondrial cytochrome b (cyt b) and NADH dehydrogenase subunit 2 (ND2) gene sequences produced well‐supported clades largely corresponding to the four recognized taxa in the Guianas (Atelopus spumarius hoogmoedi, Atelopus spumarius barbotini, Atelopus franciscus, and Atelopus flavescens). Our findings suggest that the Guianan A. spumarius represent distinct evolutionary lineages that merit distinction from Amazonian conspecifics, and that the status of A. flavescens and A. franciscus is somewhat less clear. Approximately 69% of the observed genetic variation is accounted for by differences between these four recognized taxa. Coalescent‐based estimates of gene flow between taxa suggest that these lineages are largely isolated from one another. Negligible rates of migration between populations and significant divergence within such close proximity suggests that although the region inhabited by these taxa is almost entirely undisturbed, significant habitat heterogeneity exists as to have produced a remarkable diversification of Atelopus within the eastern Guiana Shield. These results contradict the commonly held view of the Guiana Shield as a ‘refuge’ whose stability during late Tertiary and Quaternary climatic fluctuations served as a biotic reservoir. Instead, we provide evidence that climatic fluctuations during this time had a diversifying effect within the Guianan region.
Barcoding generalist predators by polymerase chain reaction: carabids and spiders
Authors: GREENSTONE M. H. , ROWLEY D. L. , HEIMBACH U. , LUNDGREN J. G. , PFANNENSTIEL R. S. , REHNER S. A.
Published: August 2005

Identification of arthropod predators is challenging when closely related species are found at a given locality. Identification of the immature stages is especially problematic, because distinguishing morphological features are difficult to use or have not been described. We used polymerase chain reaction (PCR) to distinguish closely related carabids and spiders, and to match eggs and larvae (or nymphs) with identified adult parents. Within the Carabidae, we amplified species‐specific mitochondrial cytochrome oxidase I (COI) fragments for three species each in the genera Poecilus and Harpalus, and two each in Chlaenius and Bembidion. Within the Araneae, we amplified species‐specific COI fragments for two Hibana species (Anyphaenidae), Pardosa milvina and Rabidosa rabida (Lycosidae), Frontinella communis and Grammonota texana (Linyphiidae), and Cheiracanthium inclusum (Miturgidae). We are able to correctly identify all immature stages tested — eggs, larvae (or nymphs) and pupae — by comparison of the amplified fragments with those of the adults. Using COI markers as species identifiers is a tenet of the Barcode of Life initiative, an international consortium to provide a molecular identifier for every animal species.
Using naturally shed feathers for individual identification, genetic parentage analyses, and population monitoring in an endangered Eastern imperial eagle (Aquila heliaca) population from Kazakhstan
Authors: RUDNICK JAMIE A. , KATZNER TODD E. , BRAGIN EVGENY A. , RHODES O. EUGENE , DEWOODY J. ANDREW
Published: August 2005

Genetic analyses on noninvasively collected samples have revolutionized how populations are monitored. Most noninvasive monitoring studies have used hair or scat for individual identification of elusive mammals, but here we utilize naturally shed feathers. The Eastern imperial eagle (EIE) is a species of conservation concern throughout Central Asia and, like most raptors, EIEs are inherently challenging to study because adults are difficult to capture and band using conventional techniques. Over 6 years, we noninvasively collected hundreds of adult feathers and directly sampled EIE chicks at a national nature reserve in Kazakhstan. All samples were genetically sexed and genotyped at a suite of microsatellite loci. Genetically profiled adult feathers identified and monitored the presence of individual eagles over time, enabling us to address a variety of issues related to the biology, demography, and conservation of EIEs. Specifically, we characterized (i) the genetic mating system, (ii) relatedness among mated pairs, (iii) chick sex ratios, and (iv) annual turnover in an adult breeding population. We show that EIEs are genetically monogamous and furthermore, there is no apparent relatedness‐based system of mate choice (e.g. inbreeding avoidance). Results indicate that annual adult EIE survivorship (84%) is lower than expected for a long‐lived raptor, but initial analyses suggest the current reproductive rate at our study site is sufficient to maintain a stable breeding population. The pristine habitat at our study site supports an EIE population that is probably the most demographically robust in the world; thus, our results caution that populations in marginal habitats may not be self‐sustaining.
Cryptic Neogene vicariance and Quaternary dispersal of the red‐spotted toad (Bufo punctatus): insights on the evolution of North American warm desert biotas
Authors: JAEGER JEF R. , RIDDLE BRETT R. , BRADFORD DAVID F.
Published: August 2005

We define the geographical distributions of mitochondrial DNA (mtDNA) lineages embedded within a broadly distributed, arid‐dwelling toad, Bufo punctatus. These patterns were evaluated as they relate to hypothesized vicariant events leading to the formation of desert biotas within western North America. We assessed mtDNA sequence variation among 191 samples from 82 sites located throughout much of the species’ range. Parsimony‐based haplotype networks of major identified lineages were used in nested clade analysis (NCA) to further elucidate and evaluate shallow phylogeographic patterns potentially associated with Quaternary (Pleistocene–Holocene) vicariance and dispersal. Phylogenetic analyses provided strong support for three monophyletic lineages (clades) within B. punctatus. The geographical distributions of the clades showed little overlap and corresponded to the general boundaries of the Peninsular Desert, and two continental desert regions, Eastern (Chihuahuan Desert–Colorado Plateau) and Western (Mojave–Sonoran deserts), geographically separated along the Rocky Mountains and Sierra Madre Occidental. The observed divergence levels and congruence with postulated events in earth history implicate a late Neogene (latest Miocene–early Pliocene) time frame for separation of the major mtDNA lineages. Evaluation of nucleotide and haplotype diversity and interpretations from NCA reveal that populations on the Colorado Plateau resulted from a recent, likely post‐Pleistocene, range expansion from the Chihuahuan Desert. Dispersal across historical barriers separating major continental clades appear to be recent, resulting in secondary contacts in at least two areas. Given the observed contact between major clades, we speculated as to why the observed deep phylogeographic structure has not been eroded during the multiple previous interglacials of the Pleistocene.
Genomic organization of molecular differentiation in Norway spruce (Picea abies)
Authors: ACHERÉ V. , FAVRE J. M. , BESNARD G. , JEANDROZ S.
Published: August 2005

Diversity and differentiation among three populations representing the geographical domains commonly recognized within the natural distribution area of Picea abies were analysed by using a set of 292 AFLP (amplified fragment length polymorphism), SSR (single sequence repeat) and ESTP (expressed sequence tags polymorphism) markers. As usually observed in forest trees, results showed high within‐population diversity (HS reaching 0.79) and low among‐population differentiation (GST≈ 2%). The genomic organization of differentiation was then investigated on the basis of a subsample of 150 AFLP, SSR and ESTP mapped markers. The number of the loci differentiating the Baltico‐Nordic from the central European populations (25 loci) and, within the central European populations, the Alpine from the Hercyno‐Carpathian populations (12 loci), were different. These 37 differentiated loci, with individual GST values ranging from 0.008 to 0.20, were evenly distributed on all linkage groups and mostly followed the neutral expectations, suggesting genome‐wide effects on differentiation. Nine of them however behave as ‘outlier’ loci indicating possible locus‐specific selective effects. Contribution of ongoing evolutionary forces and historical effects to the geographical differentiation of the species are discussed.
Phylogeography of the longhorn cactus beetle Moneilema appressum LeConte (Coleoptera: Cerambycidae): was the differentiation of the Madrean sky islands driven by Pleistocene climate changes?
Authors: SMITH CHRISTOPHER IRWIN , FARRELL BRIAN D.
Published: August 2005

Although it has been suggested that Pleistocene climate changes drove population differentiation and speciation in many groups of organisms, population genetic evidence in support of this scenario has been ambiguous, and it has often been difficult to distinguish putative vicariance from simple isolation by distance. The sky island communities of the American Southwest present an ideal system in which to compare late Pleistocene range fragmentations documented by palaeoenvironmental studies with population genetic data from organisms within these communities. In order to elucidate the impact of Pleistocene climate fluctuations on these environments, biogeographic patterns in the flightless longhorn cactus beetle, Moneilema appressum were examined using mitochondrial DNA sequence data. Gene tree relationships between haplotypes were inferred using parsimony, maximum‐likelihood, and Bayesian analysis. Nested clade analysis, Mantel tests, and coalescent modelling were employed to examine alternative biogeographic scenarios, and to test the hypothesis that Pleistocene climate changes drove population differentiation in this species. The program mdiv was used to estimate migration and divergence times between populations, and to measure the statistical support for isolation over ongoing migration. These analyses showed significant geographic structure in genetic relationships, and implicated topography as a key determinant of isolation. However, although the coalescent analyses suggested that a history of past habitat fragmentation underlies the observed geographic patterns, the nested clade analysis indicated that the pattern was consistent with isolation by distance. Estimated divergence times indicated that range fragmentation in M. appressum is considerably older than the end of the most recent glacial, but coincided with earlier interglacial warming events and with documented range expansions in other, desert‐dwelling species of Moneilema.
Detection, identification and geographical distribution of European corn borer larval parasitoids using molecular markers
Authors: AGUSTÍ N. , BOURGUET D. , SPATARO T. , DELOS M. , EYCHENNE N. , FOLCHER L. , ARDITI R.
Published: August 2005

Biological control requires specific tools for the accurate detection and identification of natural enemies, and to detect unusual variations in their density, which may follow changes in agricultural practices. Here we have developed specific molecular markers to detect Lydella thompsoni (Herting) and Pseudoperichaeta nigrolineata (Walker) (Diptera: Tachinidae) within the European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae). Primers amplifying fragments of the mitochondrial COI gene were designed following alignment of comparable sequences for a range of parasitoid and host species. Each of the primer pairs proved to be species specific to a tachinid species, amplifying DNA fragments of 191 and 91 bp in length for L. thompsoni and P. nigrolineata, respectively. This DNA‐based technique allowed molecular evaluation of parasitism in O. nubilalis natural populations. In order to study the geographical distribution of both species in France, O. nubilalis diapausing larvae in maize stalks were collected from 12 locations over the whole country. The molecular evaluation of parasitism was compared with the traditional method of maintaining O. nubilalis populations in controlled conditions before breaking off the diapause. The percentage parasitism found in both species of tachinids was higher — approximately three times — using the molecular method, suggesting an underestimation by the traditional rearing protocol. Tachinid parasitism on O. nubilalis was not significantly different between geographical areas (south, central and north France) for both species. This study shows that molecular methods are very promising for the correct detection and identification of tachinid parasitoids in natural field populations.
Clonal and spatial genetic structures of aspen (Populus tremuloides Michx.)
Authors: NAMROUD MARIE‐CLAIRE , PARK ANDREW , TREMBLAY FRANCINE , BERGERON YVES
Published: August 2005

To portray aspen clonal and spatial genetic structures, we mapped and genotyped trees in two 1‐ha plots, each containing three aspen cohorts originating from fire or subsequent secondary disturbances. We used four microsatellite loci to identify aspen clones and increment core analysis to determine tree age. Clonal dimensions were measured by the maximum distance between two ramets and the number of ramets per genet. Standard normal deviate (SND) was used to assess the spatial distribution of aspen genets and cohorts, and multivariate spatial genetic autocorrelations to assess the spatial distribution of aspen genetic variation. Most aspen genets consisted of only one ramet (> 75%). Median clonal dimensions were 19 and 29 m (maxima: 104 and 72 m in the two plots). No segregation was observed between clones. Aspen cohorts were spatially segregated but trees were spatially aggregated within old and medium‐aged cohorts. In contrast, trees were more randomly distributed within the youngest cohorts. This coincided with a spatial genetic autocorrelation at small scales (up to 30 m) in the older cohorts and a more random genetic distribution in the youngest ones. Our results suggest that aspen spatial genetic structuring reflects the spatial patterns produced by the regeneration of discrete cohorts at different stages of succession. Vegetative reproduction leads to aspen genetic spatial structuring at small scales (few metres) until midsuccession. However, as the stand gets older, the spatial distribution of aspen trees and genetic structure evolve from a structured pattern to a more random one under a gap disturbances regime.
Ten years of AFLP in ecology and evolution: why so few animals?
Authors: BENSCH STAFFAN , ÅKESSON MIKAEL
Published: August 2005

Researchers in the field of molecular ecology and evolution require versatile and low‐cost genetic typing methods. The AFLP (amplified fragment length polymorphism) method was introduced 10 years ago and shows many features that fulfil these requirements. With good quality genomic DNA at hand, it is relatively easy to generate anonymous multilocus DNA profiles in most species and the start‐up time before data can be generated is often less than a week. Built‐in dynamic, yet simple modifications make it possible to find a protocol suitable to the genome size of the species and to screen thousands of loci in hundreds of individuals for a relatively low cost. Until now, the method has primarily been applied in studies of plants, bacteria and fungi, with a strong bias towards economically important cultivated species and their pests. In this review we identify a number of research areas in the study of wild species of animals where the AFLP method, presently very much underused, should be a very valuable tool. These aspects include classical problems such as studies of population genetic structure and phylogenetic reconstructions, and also new challenges such as finding markers for genes governing adaptations in wild populations and modifications of the protocol that makes it possible to measure expression variation of multiple genes (cDNA‐AFLP) and the distribution of DNA methylation. We hope this review will help molecular ecologists to identify when AFLP is likely to be superior to other more established methods, such as microsatellites, SNP (single nucleotide polymorphism) analyses and multigene DNA sequencing.
Genetic resistance to bovine tuberculosis in the Iberian wild boar
Authors: ACEVEDO‐WHITEHOUSE KARINA , VICENTE JOAQUÍN , GORTAZAR CHRISTIAN , HÖFLE URSULA , FERNÁNDEZ‐DE‐MERA ISABEL G. , AMOS WILLIAM
Published: August 2005

Bovine tuberculosis (bTB) is an important re‐emerging zoonotic disease, causing major economic losses and constraining international trade of animals and their products. Despite eradication programmes, some countries continue to encounter outbreaks, mainly due to wildlife acting as primary hosts or reservoirs. While the genetic component of tuberculosis in humans and cattle is well documented, the role of genetic factors as modulators of bTB resistance remains unclear for natural populations. To address this issue, we investigated the relative contribution of host genetic variability to susceptibility to bTB infection and disease progression in wild boars from southern Spain. We found that genetic heterozygosity is an important predictor of bTB, not only modulating resistance to infection but also influencing containment of disease progression in infected individuals. Our results provide further evidence that host genetic variability plays a central role in natural populations. Testing each marker separately reveals evidence of both general and single‐locus associative effects on bTB and several loci reveal high homology to regions of the genome with known immune function. Our results may prove to be crucial for understanding outbreaks of bTB in wildlife that could potentially affect domestic livestock and humans.
The influence of Pleistocene glacial refugia on tawny owl genetic diversity and phylogeography in western Europe
Authors: BRITO PATRÍCIA H.
Published: August 2005

The glacial refugia hypothesis indicates that during the height of the Pleistocene glaciations the temperate species that are today widespread in western Europe must have survived in small and climatically favourable areas located in the southern peninsulas of Iberia, Italy and Balkans. One such species is the tawny owl, a relatively sedentary, nonmigratory bird presently distributed throughout Europe. It is a tree‐nesting species closely associated with deciduous and mixed coniferous woodlands. In this study I used control region mtDNA sequences from 187 individuals distributed among 14 populations to determine whether current genetic patterns in tawny owl populations were consistent with postglacial expansion from peninsular refugia. European, North African and Asian tawny owls were found to represent three distinct lineages, where North Africa is the sister clade to all European owls. Within Europe, I found three well‐supported clades that correspond to each of the three allopatric refugia. Expansion patterns indicate that owls from the Balkan refugium repopulated most of northern Europe, while expansion out of Iberia and Italy had only regional effects leading to admixture in France. Estimates of population divergence times between refugia populations are roughly similar, but one order of magnitude smaller between Greece and northern Europe. Based on a wide range of mutation rates and generation times, divergence between refugia appears to date to the Pleistocene.
PCR technique detection ofLeishmaniaspp. but notMycobacteriumspp. in canine cutaneous ‘sterile’ pyogranuloma/granuloma syndrome
Authors: CORNEGLIANI L. , FONDEVILA D. , VERCELLI A. , MANTERO G. , FONDATI A.
Published: August 2005

Abstract Cutaneous ‘sterile’ pyogranuloma/granuloma syndrome (SPGS) is an uncommon canine skin disorder of unknown aetiopathogenesis. Histopathological findings and failure to demonstrate an aetiologic agent are suggestive of this syndrome. Nevertheless, it has been hypothesized that SPGS may be related to an immune response against persistent endogenous or exogenous antigens. The presence ofLeishmaniaandMycobacteriumorganisms was investigated by polymerase chain reaction (PCR) techniques in 46 canine skin samples histopathologically diagnosed as SPGS. Concomitantly, an immunohistochemical technique forLeishmaniadetection was applied on the same samples and the results were compared with those from PCR. The PCR technique yielded positive results forLeishmaniaspp. in 21 out of 46 skin samples. The results of immunohistochemical techniques were identical to those obtained by PCR. The PCR technique gave negative results forMycobacteriumspp. in all the samples examined. These results suggest the importance of looking forLeishmaniaspp. in skin biopsies with histopathological findings consistent with the diagnosis of SPGS.
Thymoma‐associated exfoliative dermatitis in a rabbit
Authors: FLORIZOONE KOENRAAD
Published: August 2005

Abstract A 5‐year‐old rabbit with generalized scaling is presented. Multiple skin scrapings and acetate tape impressions were negative for mites andMalassezia. Culture for dermatophytes was also negative. Skin biopsies showed similarities with sebaceous adenitis described in rabbits (absence of sebaceous glands, perifollicular lymphocytic infiltrate at the level of the absent sebaceous glands, lymphocytic mural folliculitis, interface dermatitis). The owners refused any treatment and 2 months later the rabbit was euthanized due to anorexia. At necropsy a mass was found in the anterior mediastinum. Histopathology confirmed a diagnosis of thymoma. A possible paraneoplastic skin disease was suspected, based on similarities with thymoma‐associated exfoliative dermatitis in cats.
Humoral measurement of type‐1 hypersensitivity reactions to a commercialMalasseziaallergen
Authors: FARVER K. , MORRIS D. O. , SHOFER F. , ESCH B.
Published: August 2005

Abstract Malassezia pachydermatisis considered to be a contributing factor to canine atopic dermatitis (AD). The purpose of this study was to investigate the humoral response to a commercially producedM. pachydermatisextract. Fifteen atopic dogs withMalasseziaovergrowth on the skin (MD), 16 atopic dogs without MD, three atopic dogs with overgrowth ofMalasseziain the ears only (MO), and 12 normal dogs were intradermally tested withM. pachydermatisextract at 50, 100, 250, 500, 1000, 2000 and 4000 PNU mL−1. All dogs were evaluated cytologically by cutaneous tape strip and bilateral ear exudate sampling to determine presence of MD or MO. Each had serum evaluated for anti‐MalasseziaIgE using threeMalasseziaextracts with an ELISA assay. The irritant threshold concentration at which healthy nonatopic dogs ceased to react was 1000 PNU mL−1. There was a significant difference in intradermal test reactivity between the atopic groups. At this dilution, 93% (14/15) of the atopic MD group, 31% (5/16) of the atopic group without MD or MO, and 100% (3/3) of the atopic MO only group reacted. There were no significant differences in the serum IgE levels as measured by the Greer ELISA assay, between any groups using any of the three extracts. These results support that Greer'sM. pachydermatisextract is useful for intradermal testing of dogs with an allergic phenotype, and that atopics with MD are more likely to have a type‐1Malasseziahypersensitivity than those without. The ELISA assay may require further development in order to be useful for the diagnosis ofMalasseziahypersensitivity.
Mechanisms of lymphocyte migration in autoimmune disease
Authors: Norman M.U. , Hickey M.J.
Published: August 2005

Abstract:  The recruitment of leukocytes to inflamed tissues plays an essential role in combating infection and promoting wound healing. However, in autoimmune diseases such as multiple sclerosis and diabetes, leukocytes enter tissues and contribute to inappropriate inflammatory responses, which cause tissue injury and dysfunction. In diseases of this type, lymphocytes play critical roles in initiating and maintaining these aberrant inflammatory responses. The aim of this review is to examine the mechanisms whereby T‐lymphocytes enter tissues in autoimmune diseases and to compare these mechanisms between various organs and diseases. An overview of the mechanisms of leukocyte recruitment and the techniques used to study leukocyte trafficking is provided, focusing on the use of intravital microscopy as a tool to assess the functional microvasculature in vivo. We also discuss the series of tissue homing events which allow naïve lymphocytes to first enter lymph nodes and undergo activation, then subsequently to home to the peripheral organ where their cognate antigen is present. Finally, we examine mechanisms of leukocyte recruitment in diseases such as multiple sclerosis, autoimmune diabetes, systemic lupus erythematosus, rheumatoid arthritis, inflammatory bowel disease and asthma.
A novel HLA allele, DRB1*1609, identified in the Chinese Han population*
Authors: Miao K.R. , Pan Q.Q. , Xue M. , Zhou X.Y. , Fei X.M. , Tang Y.H. , Xu R. , Zhang J.W. , Zhao X. , Osowski L. , Shi W.X. , Xu A.L. , Wang C.Y. , KuKuruga D.
Published: August 2005

Abstract:  A novel human leucocyte antigen‐DRB1*16 (HLA‐DRB1*16) allele (DRB1*1609) has been identified by sequencing‐based typing (SBT) in Chinese Han population. This new allele has identical nucleotide sequence to DRB1*160101 in exon 2, except for a single‐nucleotide substitution from A to T at position 127. This change leads to an amino acid change from tyrosine to phenylalanin at residue 47 (Y47F). SBT was performed for cloned DRB1*16‐specific polymerase chain reaction fragment. The serological phenotype of DRB1*1609 is equivalent to DR16 antigen.
Identification of four novel HLA‐DOA alleles, DOA*010106, DOA*0102, DOA*0103, and DOA*0104N, by sequence‐based typing*
Authors: Moon S.‐M. , Gu H. , Ryu H.‐J. , Kim J.‐J. , Kim H.‐T. , Han B.‐G. , Kimm K. , Lee J.‐K. , Oh B.
Published: August 2005

Abstract:  DOA sequences are currently known to have identical protein sequences. However, in this study, we report four novel allele types of human leucocyte antigen‐DOA, including one synonymous and three non‐ synonymous amino acid changes from the Korean population. DOA*010106 has identical protein sequence with previously known DOA*010103 except one nucleotide difference at codon 45 (TCG→TCA). In contrast, DOA*0102 and DOA*0103 have a sequence change at codon 99 (CTG→GTG) and codon 105 (CGC→TGC), causing non‐synonymous amino acid changes, Leu99Val and Arg105Cys, respectively. In addition, DOA*0104N has a sequence deletion at codon 36 (CCC→CC‐), resulting in a frame shift leading to a stop codon at codon 62.
Identification of a novel human DRB1*13 allele by sequence‐based DRB typing
Authors: Caggiari L. , Simula M.P. , Marzotto A. , Caragnano A. , Luchetti M. , Gabrielli A. , De Re V.
Published: August 2005

Abstract:  Herein, we report on a novel DRB1 allele (DRB1*1368) identified during sequence‐based HLA‐DRB typing. This new DRB1 allele is identical to DRB1*1301 at exon 2 except for a single‐nucleotide substitution at codon 37, changing the amino acid Asn to Asp.
Novel HLA‐Cw*01 allele, Cw*010203, identified by sequence‐based typing*
Authors: Kwon O.‐J. , Hwang S.‐H. , Hur S.‐S. , Lee M.‐N. , Oh H.‐B.
Published: August 2005

Abstract:  In this report, we describe the identification of an human leucocyte antigen‐Cw*0102 (HLA‐Cw*0102) nucleotide sequence variant, a new HLA‐Cw*010203, in a case – control study by using sequence‐based typing. Allele HLA‐Cw*010203 showed one nucleotide difference with HLA‐Cw*010201 by a silent substitution at codon 130 (CTG→CTA).
The haplotype block, NFKBIL1‐ATP6V1G2‐BAT1‐MICB‐MICA, within the class III – class I boundary region of the human major histocompatibility complex may control susceptibility to hepatitis C virus‐associated dilated cardiomyopathy
Authors: Shichi D. , Kikkawa E.F. , Ota M. , Katsuyama Y. , Kimura A. , Matsumori A. , Kulski J.K. , Naruse T.K. , Inoko H.
Published: August 2005

Abstract:  Cardiomyopathy is a heart muscle disease with impaired stretch response that can result in severe heart failure and sudden death. A small proportion of hepatitis C virus (HCV)‐infected patients may be predisposed to develop dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). The molecular mechanisms involved in the predisposition remain unknown due in part to the lack of information on their genetic background. Because the human leukocyte antigen (HLA) region has a pivotal role in controlling the susceptibility to HCV‐induced liver disease, we hypothesized that particular HLA alleles and/or non‐HLA gene alleles within the human major histocompatibility complex (MHC) genomic region might control the predisposition to HCV‐associated DCM (HCV‐DCM) and/or HCV‐associated HCM (HCV‐HCM). Here, we present mapping results of the MHC‐related susceptibility gene locus for HCV‐associated cardiomyopathy by analyzing microsatellite and single nucleotide polymorphism markers. To delineate the susceptibility locus, we genotyped 44 polymorphic markers scattered across the entire MHC region in a total of 59 patients (21 HCV‐DCM and 38 HCV‐HCM) and 120 controls. We mapped HCV‐DCM susceptibility to a non‐HLA gene locus spanning from NFKBIL1 to MICA gene loci within the MHC class III – class I boundary region. Our results showed that HCV‐DCM was more strongly associated with alleles of the non‐HLA genes rather than the HLA genes themselves. In addition, no significant association was found between the MHC markers and HCV‐HCM. This marked difference in the MHC‐related disease susceptibility for HCV‐ associated cardiomyopathy strongly suggests that the development of HCV‐ DCM and HCV‐HCM is under the control of different pathogenic mechanisms.
Frequency and distribution of alleles of canine MHC‐II DLA‐DQB1, DLA‐DQA1 and DLA‐DRB1 in 25 representative American Kennel Club breeds
Authors: Angles J.M. , Kennedy L.J. , Pedersen N.C.
Published: August 2005

Abstract:  The frequency and distribution of dog leucocyte antigens (DLA) class II ‐DQA1, ‐DQB1 and ‐DRB1 alleles were determined for 25 American Kennel Club (AKC) registered dog breeds, representing 360 dogs from each of the seven major performance categories. Six to twenty‐eight (average n = 11) dogs were studied per group, with the exception of the Akita dog (n = 94). All dogs were unrelated with no common grandparents based on AKC pedigree records (F‐value <0.125). DLA class II allelic diversity was broad across breeds; 31/61 published DLA‐DRB1 alleles, 11/18 published DLA‐DQA1 alleles and 31/47 published DLA‐DQB1 alleles were found among the 25 breeds. However, allelic diversity was severely limited within a breed. Seventeen of the DLA‐DRB1 alleles were each found in only a single breed, and only seven alleles were shared by seven or more breeds. DLA‐DRB1*00101 and DLA‐DRB1*01501 were shared by 16 and 19 breeds, respectively. DLA‐DQA1*00101 and DLA‐DQA1*00601 alleles were shared by many breeds. The Rough Collie (DLA‐DQA1*00901), English Setter (DLA‐DQA1*00101) and Scottish Terrier (DLA‐DQA1*00101) were monoallelic for DLA‐DQA1. Eleven DLA‐DQB1 alleles were each found only in a single breed and only seven alleles were shared by six or more breeds. DLA‐DQB1*00201 and DLA‐DQB1*02301 were shared by 17 and 18 breeds, respectively. Forty per cent of dogs typed were homozygous at DLA‐DRB1, 52% at DLA‐DQA1 and 44% at DLA‐DQB1. Nine new DLA class II alleles were identified; three for DRB1 and six for DQB1. Comparison of our study of North American purebred dogs to previous European DLA surveys showed a similar use of common alleles consistent with known founder effects. However, more alleles were detected in European breeds, compared to their North American descendents, indicating that additional DLA class II diversity was lost when European breeds were established in North America.
Epitope analysis of immunoglobulins against gp20, a GPI‐anchored protein of the human sperm surface homologous to leukocyte antigen CD52
Authors: Flori F. , Giovampaola C. Della , Focarelli R. , Secciani F. , La Sala G.B. , Nicoli A. , Hale G. , Rosati F.
Published: August 2005

Abstract:  Gp20 is a sialylglycoprotein of the human sperm surface related to maturation and capacitation and is homologous to CD52, a glycosyl‐  phosphatidyl‐inositol (GPI)‐anchored protein highly expressed in lymphocytes, monocytes, eosinophils, and epididymal cells, described by the monoclonal antibody family CAMPATH. The CAMPATH antigen is characterized by a very short peptide (12 amino acids) and an N‐linked oligosaccharide chain bound to the asparagine located in the third position and a GPI anchor bound to the C‐terminal serine. The CAMPATH epitope includes three amino acids at the C‐terminus and part of the GPI anchor. It has been suggested that anti‐gp20 interacts with the same peptide recognized by CAMPATH antibodies but with a different epitope, since it describes the corresponding antigen in a different way. For example, it localizes the corresponding antigen in the equatorial region of the sperm head when sperm are capacitated, whereas CAMPATH antibodies bind all over the sperm surface. Our results indicate that the anti‐gp20 epitope does not include the peptide backbone, the GPI anchor, or the N‐glycans but consists of O‐linked oligosaccharide chains bound to a unique CD52 glycoform present both in sperm and leukocytes. This is suggested by results obtained using many different approaches, such as immunoblot analysis of gp20 after removal of N‐ and O‐glycans and after jacalin (Artocarpus integrifolia agglutinin)‐affinity chromatography.
HLA class I and II polymorphisms in Azores show different settlements in Oriental and Central islands
Authors: Spínola H. , Brehm A. , Bettencourt B. , Middleton D. , Bruges‐Armas J.
Published: August 2005

Abstract:  Human leucocyte antigen‐A, ‐B, ‐Cw, ‐DRB1, ‐DQA1 and ‐DQB1 polymorphisms were examined in the Azorean population. The data were obtained at high‐resolution level, using polymerase chain reaction (PCR) with sequence‐specific primer, PCR‐sequence‐specific oligonucleotides and sequence‐based typing. The most frequent allele in each locus was: A*0201 (24.5%), B*510101 (9.8%), Cw*0401 (14.8%), DRB1*070101 (18.3%), DQA1*0201 (17.4%) and DQB1*0301 (19.4%). The predominant extended haplotype was A*0202‐B*1503‐Cw*0202‐DRB1*090102‐DQA1*0303‐  DQB1*0202 (1.9%), which was found to be absent in the Portuguese mainland. The present study corroborates historical sources that say the Azores were populated not only by Portuguese but also by other Europeans, mostly Flemish people. Despite dendrogram analysis showing some remote Asian genetic affinities, the lack of specific alleles and haplotypes from those populations does not allow us to conclude for direct influence. Haplotype and allele frequencies in Azores show no homogeneous distribution between Oriental and Central islands of this archipelago. The Oriental islands harbour several haplotypes already found in mainland Portugal and identified as Mediterranean and European. The Central group of islands on the contrary clearly shows an influence of north Europeans (most probably derived from a well‐documented Flemish settlement), with much less affinity to mainland Portugal.
Transjugular liver biopsy is a safe and effective intervention to guide management for patients with a congenital bleeding disorder infected with hepatitis C
Authors: Dawson M. A. , McCarthy P. H. , Walsh M. E. , McLean C. A. , Thomson K. , Roberts S. , Street A. M.
Published: August 2005

Abstract

The prevalence of hepatitis C virus (HCV) infection in adult patients with a congenital bleeding disorder (CBD) approaches 95% and is a major cause of morbidity and mortality. Histological examination of the liver remains the cornerstone of management decisions in patients without a CBD. The reluctance to perform liver biopsies in patients with a CBD has been a major limitation in the management of these patients. We are currently the only haemophilia centre in Australasia performing liver biopsies in patients with a CBD for the purpose of guiding prognostic and therapeutic decisions. We report here the results of our centre's experience with transjugular liver biopsy (TJLB) in patients with a CBD. An adequate specimen for histological assessment was attained from all of the patients. There were no major complications recorded. Patients were hospitalized for ≤ 48 h for haemostasis prophylaxis. The diagnostic specimen obtained from patients was integral in guiding their future management. We suggest that with a coordinated multidisciplinary approach, TJLB can be performed in patients with a CBD. (Intern Med J 2005; 35: 556–559)
Effects of opioids and sedatives on survival in an Australian inpatient palliative care population
Authors: Good P. D. , Ravenscroft P. J. , Cavenagh J.
Published: August 2005

Abstract

Aims: To assess whether opioid and sedative medication use affects survival (from hospice admission to death) of patients in an Australian inpatient palliative care unit.

Background: Retrospective audit. Newcastle Mercy Hospice – a tertiary referral palliative care unit. All patients who died in the hospice between 1 February and 31 December 2000.

Methods: Length of survival from hospice admission to death, and the median and mean doses of opioids and sedatives used in the last 24 h of life. Comparison of these with published studies outside of Australia.

Results: In this study, the use of opioids, benzodiazepines and haloperidol did not have an association with shortened survival and the only statistical significant finding was an increased survival in patients who were on 300 mg/day or more of oral morphine equivalent (OME). The proportion of patients requiring greater than or equal to 300 mg OME/day (at 28%) was higher than published studies, but the mean dose of 371 mg OME/day was within the range of other studies. The proportion of patients receiving sedatives (94%) was higher than other studies, but the median dose of parenteral midazolam equivalent of 12.5 mg per 24 h was lower than other studies from outside Australia.

Conclusions: There was no association between the doses of opioids and sedatives on the last day of life and survival (from hospice admission to death) in this population of palliative care patients. (Intern Med J 2005; 35: 512–517)
Randomized double‐blind trial of sotalol versus lignocaine in out‐of‐hospital refractory cardiac arrest due to ventricular tachyarrhythmia
Authors: Kovoor P. , Love A. , Hall J. , Kruit R. , Sadick N. , Ho D. , Adelstein B.‐A. , Ross D. L.
Published: August 2005

Abstract

Aim: We aimed to compare the efficacy of sotalol versus lignocaine for the treatment of patients with out‐of‐hospital ventricular fibrillation refractory to ≥4 defibrillatory shocks.

Background: The outcome of patients in ventricular fibrillation refractory to ≥4 defibrillatory shocks is poor. In a previous randomized trial, sotalol was superior to lignocaine for acute termination of ventricular tachycardia not causing loss of consciousness.

Methods: Patients of the Ambulance Service of New South Wales treated by paramedics with continued ventricular fibrillation despite standard resuscitation and ≥4 defibrillatory monophasic shocks were eligible. Drug doses were sotalol 100 mg or lignocaine 100 mg, given as i.v. boluses. A further 2 min of cardiopulmonary resuscitation was given and then defibrillation was repeated twice. If this failed, half the initial dose of the trial drug was repeated and a further ≥2 shocks were given.

Results: Sixty patients were randomized to sotalol and 69 randomized to lignocaine. There was no significant difference between the two groups in the clinical characteristics of the patients or in the number of shocks received. Outcomes in the sotalol and lignocaine groups were survival to hospital admission in 7 (12%) and 16 (23%), respectively (P = 0.09), and survival to hospital discharge in 2 (3%) and 5 (7%), respectively (P = 0.33).

Conclusions: Sotalol is not superior to lignocaine for treatment of ventricular fibrillation refractory to multiple shocks. The overall outcome of this group of patients is poor regardless of the pharmacological intervention (lignocaine or sotalol). (Intern Med J 2005; 35: 518–525)
Use of a quantitative point‐of‐care test for the detection of serum cardiac troponin T in patients with suspected acute coronary syndromes
Authors: Hallani H. , Leung D. Y. , Newland E. , Juergens C. P.
Published: August 2005

Abstract

We compared a third generation quantitative cardiac troponin T (cTnT) point‐of‐care testing (POCT) from Roche Diagnostics with the laboratory assay (Roche Elecsys 2010 immunoassay analyser). Heparin‐treated blood and serum were collected simultaneously in 133 unselected patients (mean age 62 ± 14 years, 38% females) presenting to our hospital with possible cardiac chest pain. Results of the POCT were measured against the laboratory‐based assay considered as the gold standard. There were 18 POCT positive versus 24 laboratory assay positive (≥0.03 ng/mL) patients. POCT was falsely negative in six patients, with values between 0.03 and 0.1 ng/mL. The POCT had a sensitivity of 75%, specificity of 100%, positive predictive value of 100%, negative predictive value of 95% and a total accuracy of 95%; kappa = 0.831 (P < 0.001). There was good correlation between the values of POCT and the laboratory assay: Y = 1.195X + 0.002, r2 = 0.94 (P < 0.0001). Whereas cTnT levels >0.1 mg/mL were reliably detected with this current generation of POCT, cTnT levels between 0.03 and 0.10 ng/mL were not. Future generations of devices will need to improve sensitivity to reliably risk stratify patients with suspected acute coronary syndromes. (Intern Med J 2005; 35: 560–562)
Stool antigen testing for the diagnosis and confirmation of eradication of Helicobacter pylori infection: a prospective blinded trial
Authors: Islam S. , Weilert F. , Babington R. , Dickson G. , Smith A. C.
Published: August 2005

Abstract

Background and aims:  Helicobacter pylori is an established pathogen for a wide spectrum of gastroduodenal diseases. We investigated the usefulness of H. pylori stool antigen test (HpSA) before and after eradication therapy on patients referred for gastroscopy.

Methods:  Over a 12‐month period, 127 adult patients (47% males) underwent HpSA and gastroscopy with dual biopsies from the antrum and proximal body of the stomach for urease and histology. The positive patients (histology, urease or combined positive) received triple therapy consisting of clarithromycin 500 mg, amoxycillin 1 g and omeprazole 20 mg, each given twice daily for 7 days. Six weeks post‐therapy, eradication was verified with the 13C‐urea breath test (UBT) and the HpSA results compared on a second stool sample.

Results:  Pre‐therapy, 23/113 patients were positive by urease test, 22/112 by histology and 22/112 were combined positive. For the HpSA, compared to combined urease and histology as the reference standards, the sensitivity and specificity were 79 and 92% while the positive and negative predictive values (PPV and NPV) were 68 and 96%, respectively. Post‐therapy, UBT was adopted as the reference standard and 18 paired samples were available for analysis: three were positive and 15 were negative. Sensitivity and specificity were 67 and 100% while the PPV and NPV were 100 and 94%, respectively.

Conclusions:  In this prospective study, HpSA was found to be a reasonably useful diagnostic test for H. pylori infection. Post‐eradication, it was highly specific and similar to UBT in terms of PPV and NPV. The test is non‐invasive and cheaper than the urease test or the UBT, making it a candidate in the investigation of dyspepsia. (Intern Med J 2005; 35: 526–529)