Parasites in peril: abundance of batflies (Diptera: Nycteribiidae) declines along an urbanisation gradient

Journal of Insect Conservation - Urbanisation has a wide range of impacts on biodiversity, but its effects on parasitic arthropods, particularly those of bats, remain poorly studied. Ectoparasites...     

Evaluation of two-dimensional difference gel electrophoresis for protein profiling. Soluble proteins of the marine bacterium Pirellula sp. strain 1

Two-dimensional gel electrophoresis (2DE) is a central tool of proteome research, since it allows separation of complex protein mixtures at highest resolution. Quantification of gene expression at the protein level requires sensitive visualization of protein spots over a wide linear range. Two-dimensional difference gel electrophoresis (2D DIGE) is a new fluorescent technique for protein labeling in 2DE gels. Proteins are labeled prior to electrophoresis with fluorescent CyDyes trade mark and differently labeled samples are then co-separated on the same 2DE gel. We evaluated 2D DIGE for detection and quantification of proteins specific for glucose or N-acetylglucosamine metabolism in the marine bacterium Pirellula sp. strain 1. The experiment was based on 10 parallel 2DE gels. Detection and comparison of the protein spots were performed with the DeCyder trade mark software that uses an internal standard to quantify differences in protein abundance with high statistical confidence; 24 proteins differing in abundance by a factor of at least 1.5 (t test value <10(-9)) were identified. For comparison, another experiment was carried out with four SYPRO-Ruby-stained 2DE gels for each of the two growth conditions; image analysis was done with the ImageMaster trade mark 2D Elite software. Sensitivity of the CyDye fluors was evaluated by comparing Cy2, Cy3, Cy5, SYPRO Ruby, silver, and colloidal Coomassie staining. Three replicate gels, each loaded with 50 microg of protein, were run for each stain and the gels were analyzed with the ImageMaster software. Labeling with CyDyes allowed detection of almost as many protein spots as staining with silver or SYPRO Ruby.     

A fragment-cofragment model of antibody incidence structures

In the predecessor to this paper, "Uncovering Antibody Incidence Structures," Markowsky and Wohlgemuth presented a model which allowed one to calculate best possible solutions for the relation between individuals and antibodies given certain sets of tests each of which is analyzed simply for the presence or absence of a reaction. In this paper, we show that many of the concepts and theorems of the first paper generalize to the case where we actually try to compare the strengths of various reaction tests. As one might expect, the resulting model has a greater ability to detect the presence of antibodies than the model presented in the first paper. Furthermore, the additional information generated by the model described in this paper allows one to present a fairly concise definition of the best possible solution for a given amount of reaction test data.     

A mathematical analysis of human leukocyte antigen serology

This paper presents and explores a comprehensive mathematical model for human leukocyte antigen serology, based on a mathematical formalization of the concept of specificity. This model is general enough to take into account such factors as absorption, elution, cross-reactivity, and incomplete immunization. The paper includes a presentation of the relevant immunological background and a short discussion of the underlying computational difficulty of the basic problems. Upper and lower bounds are derived for the minimal number of specificities required to explain a given set of HLA reactions, and it is shown that the numbers of antibodies and antigens involved must be no less then this minimal number of specificities. Other techniques and theorems are also presented to aid in reducing and analyzing HLA reaction matrices.     

Phage typing set for differentiating Staphylococcus epidermidis

A phage typing set composed of 13 phages is described for characterizing Staphylococcus epidermidis. Isolates (372) from cases of bovine mastitis were used in this study. Of these, 350 or 94% were successfully delineated, and 63 phage types were observed. Twenty two cultures were not typeable.     

Mathematical immunogenetics II antibody incidence structure

Mathematical Immunogenetics I argued for the development of mathematics as a language for immunogenetics. A three-fold factorization of a reaction matrix was seen to be the important form of a model of a first order immunogenetic system. In the present paper, results of the authors on determining this factorization are reworked from a physical perspective and presented in an algorithmic form that can be used to compute a labeling matrix from data. Computer programs to perform these computations are in preparation.     

Mathematical immunogenetics I. Mathematics as language

This paper summarizes approaches to developing mathematics that can act as a language for immunogenetics. The need for this has been documented by showing inadequacies of the standard symbolism. Apparent distinctions in symbolizing and conceptualizing factors involved in immunogenetics are seen to disappear in the mathematical models presented here. One model, a three-fold Boolean matrix factorization, subsumes all approaches to the idea of specificity and yet is general enough to incorporate data beyond that found only in a reaction matrix.