Nicastrin, a presenilin-interacting protein, contains an aminopeptidase/transferrin receptor superfamily domain

Nicastrin, a protein implicated in Alzheimer's disease, has a domain that is found in the aminopeptidase/transferrin receptor superfamily. In nicastrin, this domain might possess catalytic activity (as observed with aminopeptidases) or it could serve merely as a binding domain (with analogy to the transferrin receptors) for the beta-amyloid precursor protein.     

Application of deglycosylation to SDS PAGE analysis improves calibration of influenza antigen standards

Each year the production of seasonal influenza vaccines requires antigen standards to be available for the potency assessment of vaccine batches. These are calibrated and assigned a value for haemagglutinin (HA) content. The calibration of an antigen standard is carried out in a collaborative study amongst a small number of national regulatory laboratories which are designated by WHO as Essential Regulatory Laboratories (ERLs) for the purposes of influenza vaccine standardisation. The calibration involves two steps; first the determination of HA protein in a primary liquid standard by measurement of total protein in a purified influenza virus preparation followed by determination of the proportion of HA as determined by PAGE analysis of the sample; and second, the calibration of the freeze-dried reference antigen against the primary standard by single radial immunodiffusion (SRD) assay. Here we describe a collaborative study to assess the effect of adding a deglycosylation step prior to the SDS-PAGE analysis for the assessment of relative HA content. We found that while the final agreed HA value of the samples tested was not significantly different with or without deglycosylation, the deglycosylation step greatly improved between-laboratory agreement.     

Quantification of the Effects of Age on the Dose Response of Variola major in Suckling Mice

Dose-response data for Variola major (V. major), the causative agent of smallpox, were obtained from the open literature, summarized, and fitted with three dose-response models. It is known from prior outbreak experience that there is generally a difference in infectivity of the agent and its subsequent mortality depending on the age of the patient. A source of animal dose-response data were found with age delineation for the exposure group (suckling mice, intraperitoneal exposure). This delineation was used to adapt current dose-response models to include an age dependency parameter. The degree of the models' fit to the data was ascertained using maximum likelihood estimation (MLE). The effect of host age could be described quantitatively using modifications to the beta Poisson and exponential dose-response models. The modifications improvement in the accuracy of risk prediction by 72% for the beta Poisson model and 7% for the exponential model, compared to the original (unmodified) models.     

Effects of population structure and admixture on exact tests for association between Loci

The probability of multilocus genotype counts conditional on allelic counts and on allelic independence provides a test statistic for independence within and between loci. As the number of loci increases and each sampled genotype becomes unique, the conditional probability becomes a function of total heterozygosity. In that case, it does not address between-locus dependence directly but only indirectly through detection of the Wahlund effect. Moreover, the test will reject the hypothesis of allelic independence only for small values of heterozygosity. Low heterozygosity is expected for population subdivision but not for population admixture. The test may therefore be inappropriate for admixed populations. If individuals with parents in two different populations are always considered to belong to one of the populations, then heterozygosity is increased in that population and the exact test should not be used for sparse data sets from that population. If such a case is suspected, then alternative testing strategies are suggested.     

Formatting antibody fragments to mediate specific therapeutic functions

Monoclonal antibodies are increasingly being used as therapeutic agents in a wide range of indications, including oncology, inflammation and infectious disease. In most cases the basis of the therapeutic function is the high degree of specificity and affinity the antibody-based drug has for its target antigen. However, the mechanism of action (MOA), the way the drug takes advantage of this specificity to mediate a therapeutic effect, varies considerably from drug to drug. Three basic potential categories of MOAs exist: antagonists, agonists and specific delivery mechanisms to target an active function to a particular cell type. The latter functions include selective cell killing, based on Fc-mediated events, recruitment of effector cells, and drug or radioisotope delivery. The majority of these mechanisms are not necessarily optimally mediated by an IgG structure; clearly, in the case of antibody-dependent cellular cytotoxicity or complement-mediated lysis, Fc is required. However, Fab fragments (the fragment comprising one antigen-binding arm of the Y-shaped IgG molecule) can be formatted to mediate most mechanisms and have the advantage that valency and half-life can be controlled to simplify the drug and address only the mechanism required. Moreover, Fab fragments can be produced in microbial expression systems which address manufacturing issues such as scale of supply and cost of goods.     

Moment estimation of population diversity and genetic distance from data on recessive markers

A moment-based method for estimating a measure of population diversity, theta or Wright's FST, is given for dominant markers such as amplified fragment length polymorphisms (AFLPs) or RAPDs in noninbred populations. Basic assumptions are that there is random mating, Hardy-Weinberg equilibrium, linkage equilibrium, no mutation from common ancestor and equally distant populations. It is based on the variances between and within populations of genotype frequencies, whereas previously moment methods for dominant markers have been indirect in that they have been based on first estimating allele frequencies and then using the variances of those frequencies. The use of genotype frequencies directly appears to be more robust. Approximate sampling errors of the estimates are given. Methods are extended to estimate genetic distances and their sampling errors. The AFLP data from samples of breeds of pig are used for illustration.     

Inflammatory bowel disease: the role of inflammatory cytokine gene polymorphisms

The mechanisms responsible for development of inflammatory bowel disease (IBD) have not been fully elucidated, although the main cause of disease pathology is attributed to up-regulated inflammatory processes. The aim of this study was to investigate frequencies of polymorphisms in genes encoding pro-inflammatory and anti-inflammatory markers in IBD patients and controls. We determined genotypes of patients with IBD (n= 172) and healthy controls (n= 389) for polymorphisms in genes encoding various cytokines (interleukin (IL)-1beta, IL-6, tumour necrosis factor (TNF), IL-10, IL-1 receptor antagonist). Association of these genotypes to disease incidence and pathophysiology was investigated. No strong association was found with occurrence of IBD. Variation was observed between the ulcerative colitis study group and the control population for the TNF-alpha-308 polymorphism (p= 0.0135). There was also variation in the frequency of IL-6-174 and TNF-alpha-308 genotypes in the ulcerative colitis group compared with the Crohn's disease group (p= 0.01). We concluded that polymorphisms in inflammatory genes are associated with variations in IBD phenotype and disease susceptibility. Whether the polymorphisms are directly involved in regulating cytokine production, and consequently pathophysiology of IBD, or serve merely as markers in linkage disequilibrium with susceptibility genes remains unclear.     

Stigmatomyces from New Zealand and New Caledonia: new records, new species and two new host families

Seven new records and three new species of Stigmatomyces (S. australis, S. baeopteri and S. clasiopellae), a genus of Laboulbeniales associated only with Diptera, are described from New Zealand and New Caledonia. Two new host families for Laboulbeniales are recorded, and a dichotomous key to Stigmatomyces species in New Zealand and New Caledonia is presented.     

Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays

MOTIVATION: Li and Wong have described some useful statistical models for probe-level, oligonucleotide array data based on a multiplicative parametrization. In earlier work, we proposed similar analysis-of-variance-style mixed models fit on a log scale. With only subtle differences in the specification of their mean and stochastic error components, a question arises as to whether these models could lead to varying conclusions in practical application. RESULTS: In this paper, we provide an empirical comparison of the two models using a real data set, and find the models perform quite similarly across most genes, but with some interesting and important distinctions. We also present results from a simulation study designed to assess inferential properties of the models, and propose a modified test statistic for the Li-Wong model that provides an improvement in Type 1 error control. Advantages of both methods include the ability to directly assess and account for key sources of variability in the chip data and a means to automate statistical quality control.