Computational tools for the study of allergens

Allergy is a major cause of morbidity worldwide. The number of characterized allergens and related information is increasing rapidly creating demands for advanced information storage, retrieval and analysis. Bioinformatics provides useful tools for analysing allergens and these are complementary to traditional laboratory techniques for the study of allergens. Specific applications include structural analysis of allergens, identification of B- and T-cell epitopes, assessment of allergenicity and cross-reactivity, and genome analysis. In this paper, the most important bioinformatic tools and methods with relevance to the study of allergy have been reviewed.

Scabies mite inactivated serine protease paralogues are present both internally in the mite gut and externally in feces

The scabies mite, Sarcoptes scabiei, is the causative agent of scabies, a disease that is common among disadvantaged populations and facilitates streptococcal infections with serious sequelae. Previously, we encountered large families of genes encoding paralogues of house dust mite protease allergens with their catalytic sites inactivated by mutation (scabies mite inactivated protease paralogues [SMIPPs]). We postulated that SMIPPs have evolved as an adaptation to the parasitic lifestyle of the scabies mite, functioning as competitive inhibitors of proteases involved in the host–parasite interaction. To propose testable hypotheses for their functions, it is essential to know their locations in the mite. Here we show by immunohistochemistry that SMIPPs exist in two compartments: 1) internal to the mite in the gut and 2) external to the mite after excretion from the gut in scybala (fecal pellets). SMIPPs may well function in both of these compartments to evade host proteases.

Variance components analyses of multiple asthma traits in a large sample of Australian families ascertained through a twin proband

Background: Intermediate phenotypes are often measured as a proxy for asthma. It is largely unclear to what extent the same set of environmental or genetic factors regulate these traits. Objective: Estimate the environmental and genetic correlations between self-reported and clinical asthma traits. Methods: A total of 3073 subjects from 802 families were ascertained through a twin proband. Traits measured included self-reported asthma, airway histamine responsiveness (AHR), skin prick response to common allergens including house dust mite (Dermatophagoides pteronyssinus [D. pter]), baseline lung function, total serum immunoglobulin E (IgE) and eosinophilia. Bivariate and multivariate analyses of eight traits were performed with adjustment for ascertainment and significant covariates. Results: Overall 2716 participants completed an asthma questionnaire and 2087 were clinically tested, including 1289 self-reported asthmatics (92% previously diagnosed by a doctor). Asthma, AHR, markers of allergic sensitization and eosinophilia had significant environmental correlations with each other (range: 0.23-0.89). Baseline forced expiratory volume in 1 s (FEV1) showed low environmental correlations with most traits. Fewer genetic correlations were significantly different from zero. Phenotypes with greatest genetic similarity were asthma and atopy (0.46), IgE and eosinophilia (0.44), AHR and D. pter (0.43) and AHR and airway obstruction (-0.43). Traits with greatest genetic dissimilarity were FEV1 and atopy (0.05), airway obstruction and IgE (0.07) and FEV1 and D. pter (0.11). Conclusion: These results suggest that the same set of environmental factors regulates the variation of many asthma traits. In addition, although most traits are regulated to great extent by specific genetic factors, there is still some degree of genetic overlap that could be exploited by multivariate linkage approaches.

X-ray properties of the Parkes sample of flat-spectrum radio sources: dust in radio-loud quasars?

We investigate the X-ray properties of the Parkes sample of Bat-spectrum radio sources using data from the ROSAT All-Sky Survey and archival pointed PSPC observations. In total, 163 of the 323 sources are detected. For the remaining 160 sources, 2 sigma upper limits to the X-ray flux are derived. We present power-law photon indices in the 0.1-2.4 keV energy band for 115 sources, which were determined either with a hardness ratio technique or from direct fits to pointed PSPC data if a sufficient number of photons were available. The average photon index is <Gamma > = 1.95(-0.12)(+0.13) for flat-spectrum radio-loud quasars, <Gamma > = 1.70(-0.24)(+0.23) for galaxies, and <Gamma > = 2.40(-0.31)(+0.12) for BL Lac objects. The soft X-ray photon index is correlated with redshift and with radio spectral index in the sense that sources at high redshift and/or with flat (or inverted) radio spectra have flatter X-ray spectra on average. The results are in accord with orientation-dependent unification schemes for radio-loud active galactic nuclei. Webster et al. discovered many sources with unusually red optical continua among the quasars of this sample, and interpreted this result in terms of extinction by dust. Although the X-ray spectra in general do not show excess absorption, we find that low-redshift optically red quasars have significantly lower soft X-ray luminosities on average than objects with blue optical continua. The difference disappears for higher redshifts, as is expected for intrinsic absorption by cold gas associated with the dust. In addition, the scatter in log(f(x)/f(o)) is consistent with the observed optical extinction, contrary to previous claims based on optically or X-ray selected samples. Although alternative explanations for the red optical continua cannot be excluded with the present X-ray data, we note that the observed X-ray properties are consistent with the idea that dust plays an important role in some of the radio-loud quasars with red optical continua.

Identifying regional dust transport pathways: Application of kinematic trajectory modelling to a trans-Tasman case

PI kinematic trajectory model is used to investigate potential pathways of dust transport from Australia to New Zealand. Historically, these have been assumed to follow rather direct west-east trajectories spanning 2 to 3 days, often resulting in red snow events in the Southern Alps of New Zealand. However, results from the present study which examined the route taken by air parcels originating in southern Australia during dust storms on 24 and 25 May 1994, indicate that trans-Tasman dust transport trajectories are more diverse than previously thought, and display considerable variation during single events. These mon divergent pathways tie in more closely with aeolian dust sedimentation patterns identified by ocean coring in the Tasman Sea, and may account for the deposition of Australian dust on sub-Antarctic islands located well south of the Australian continent. Copyright 2000 John Wiley Sons, Ltd.

Allergen databases

Allergies represent a significant medical and industrial problem. Molecular and clinical data on allergens are growing exponentially and in this article we have reviewed nine specialized allergen databases and identified data sources related to protein allergens contained in general purpose molecular databases. An analysis of allergens contained in public databases indicates a high level of redundancy of entries and a relatively low coverage of allergens by individual databases. From this analysis we identify current database needs for allergy research and, in particular, highlight the need for a centralized reference allergen database.

The 23rd October 2002 dust storm in eastern Australia: characteristics and meteorological conditions

The dust storm of 23 October 2002 covered most of eastern Australia and carried one of the largest recorded dust loads in Australia. In the 6 months leading up to the event, severe drought conditions in eastern Australia, plus above average maximum temperatures resulted in high potential evapo-transpiration rates, producing severe soil moisture deficits and reduced vegetation cover. Although increased wind speeds associated with a fast moving cold front were the meteorological driving force, these winds speeds were lower than those for the previously documented large dust storms. The dust storm was 2400 km long, up to 400 km across and 1.5-2.5 km in height. The plume area was estimated at 840,860 km 2 and the dust load at 0900 h was 3.35-4.85 million tones (Mt). These dust load estimates are highly sensitive to assumptions, regarding visibility-dust concentration relationships, vertical dust concentration profiles and dust ceilings. The event is examined using meteorological records, remote sensing and air quality monitoring. (C) 2004 Elsevier Ltd. All rights reserved.

Host plant specificity in several species of generalist mite predators

1. Species in the genus Neoseiulus are considered to be generalist predators. with some species used in biological control programmes against phytophagous mites and insects. 2. A general survey of Neoseiulus species in inland Australia indicated that different species are associated with particular tree species. This pattern of host plant use was investigated for four Neoseiulus species (N. buxeus, N. cappari, N. brigarinus, N. eremitus) by means of a sampling programme through time and across space. 3. Each species of Neoseiulus was collected entirely or mostly from one species of tree: little or no overlap was detected despite the tree species growing in well-mixed stands. Host plant specificity thus appears to be strong in this genus. 4. Species in two other genera (Pholaseius and Australiseiulus), also considered to be predatory, showed a similar association with particular tree species. 5. The implications for the use of these predators in biological control are considerable. In particular, phytoseiid species with specific needs in terms of host plants may not be suitable for use as general purpose predators. Meeting the needs of phytoseiids through the modification of host plant attributes may be a step towards enhancing their efficacy as biological control agents.

The effect of coal particle size on colorimetric analysis of roadway dust

Colorimetric analysis of roadway dust is currently a method for monitoring the incombustible content of mine roadways within Australian underground coal mines. To test the accuracy of this method, and to eliminate errors of judgement introduced by human operators in the analysis procedure, a number of samples were tested using scanning software to determine absolute greyscale values. High variability and unpredictability of results was noted during this testing, indicating that colorimetric testing is sensitive to parameters within the mine that are not currently reproduced in the preparation of reference samples. This was linked to the dependence of colour on particle surface area, and hence also to the size distribution of coal particles within the mine environment. (C) 2001 Elsevier Science Ltd. All rights reserved.

First record of the mite Hirstiella diolii Baker (Prostigmata : Pterygosomatidae) from Australia, with a review of mites found on Australian lizards

We report the First occurrence in Australia of an exotic mite parasite of lizards, Hirstiella diolii Baker (Prostigmata, Pterygosomatidae), and its association with iguanas at the Taronga Zoo in Sydney. We also report on the spread of the exotic snake mite Ophionyssus natricis (Gervais) to native populations of skinks, provide a key to the mites associated with Australian lizards and review how to distinguish chiggers from pterygosomatid mites.

Of mites and bees: A review of mite-bee associations in Australia and a revision of Raymentia Womersley (Acari : Mesostigmata : Laelapidae), with the description of two new species of mites from Lasioglossum (Parasphecodes) spp. (Hymenoptera : Halictidae)

Social bees have a diverse fauna of symbiotic mesostigmatic mites, including highly pathogenic parasites of the honeybee, but there are few reports of Mesostigmata phoretic on or inhabiting the nests of solitary or communal, ground-nesting bees. In south-eastern Australia, however, native bees in the family Halictidae carry what appears to be a substantial radiation of host-specific mesostigmatans in the family Laelapidae. Herein, we redescribe the obscure genus Raymentia , associated with Lasioglossum (Parasphecodes ) spp. bees (Halictidae) and describe two new species, R. eickwortiana from L. lacthium (Smith) and R. walkeriana from L. atronitens (Cockerell). The type species, R. anomala Womersley, is associated with L. altichum (Smith). In addition, we review the mites known to be associated with Australian bees, provide a key to differentiate them, and describe and illustrate acarinaria of the Halictinae. We also report on the first occurrences in Australia of the genera Trochometridium Cross (Heterostigmata: Trochometridiidae), from L. eremaean Walker (Halictidae), and Cheletophyes Oudemans (Prostigmata: Cheyletidae) from Xylocopa Latreille (Xylocopinae), and on the previously unknown association between a Neocypholaelaps Vitzthum (Mesostigmata: Ameroseiidae) and Lipotriches tomentifera (Friese) (Halictidae).

Coal dust exposures in the longwall mines of New South Wales, Australia: a respiratory risk assessment

This paper presents an analysis of personal respirable coal dust measurements recorded by the Joint Coal Board in the underground longwall mines of New South Wales from 1985 to 1999. A description of the longwall mining process is given. In the study, 11 829 measurements from 33 mines were analysed and the results given for each occupation, for seven occupational groups, for individual de-identified mines and for each year of study. The mean respirable coal dust concentration for all jobs was 1.51 mg/m(3) (SD 1.08 mg/m(3)). Only 6.9% of the measurements exceeded the Australian exposure standard of 3 mg/m(3). Published exposure-response relationships were used to predict the prevalence of progressive massive fibrosis and the mean loss of FEV1, after a working lifetime (40 years) of exposure to the mean observed concentration of 1.5 mg/m(3). Prevalences of 1.3 and 2.9% were predicted, based on data from the UK and the USA, respectively. The mean loss of FEV1 was estimated to be 73.7 ml.

A new mite from an arboreal ant (Formicidae : Polyrachis sp.): Myrmozercon iainkayi n. sp (Mesostigmata : Laelapidae)

Previously, two species of Myrmozercon (= Myrmonyssus) have been described from ground-nesting Australian ants in the genus Iridiomyrmex. Herein a new species, Myrmozercon iainkayi, infesting workers and alate adults of a leaf-nesting species of Polyrachis ant is described. The new species has a number of unusual or unique characters, including coxal hypertrichy (6-6-6-4 for legs I-IV, respectively), and based on the structure of its mouthparts, appears to be a haemolymph-feeding parasite.