Modelling the Human Immune System by Combining Bioinformatics and Systems Biology Approaches

Over the past decade a number of bioinformatics tools have been developed that use genomic sequences as input to predict to which parts of a microbe the immune system will react, the so-called epitopes. Many predicted epitopes have later been verified experimentally, demonstrating the usefulness of such predictions. At the same time, simulation models have been developed that describe the dynamics of different immune cell populations and their interactions with microbes. These models have been used to explain experimental findings where timing is of importance, such as the time between administration of a vaccine and infection with the microbe that the vaccine is intended to protect against. In this paper, we outline a framework for integration of these two approaches. As an example, we develop a model in which HIV dynamics are correlated with genomics data. For the first time, the fitness of wild type and mutated virus are assessed by means of a sequence-dependent scoring matrix, derived from a BLOSUM matrix, that links protein sequences to growth rates of the virus in the mathematical model. A combined bioinformatics and systems biology approach can lead to a better understanding of immune system-related diseases where both timing and genomic information are of importance.     

NetMHCIIpan-2.0 - Improved pan-specific HLA-DR predictions using a novel concurrent alignment and weight optimization training procedure

Background

Macrophages represent the front lines of our immune system; they recognize and engulf pathogens or foreign particles thus initiating the immune response. Imaging macrophages presents unique challenges, as most optical techniques require labeling or staining of the cellular compartments in order to resolve organelles, and such stains or labels have the potential to perturb the cell, particularly in cases where incomplete information exists regarding the precise cellular reaction under observation. Label-free imaging techniques such as Raman microscopy are thus valuable tools for studying the transformations that occur in immune cells upon activation, both on the molecular and organelle levels. Due to extremely low signal levels, however, Raman microscopy requires sophisticated image processing techniques for noise reduction and signal extraction. To date, efficient, automated algorithms for resolving sub-cellular features in noisy, multi-dimensional image sets have not been explored extensively.

Results

We show that hybrid z-score normalization and standard regression (Z-LSR) can highlight the spectral differences within the cell and provide image contrast dependent on spectral content. In contrast to typical Raman imaging processing methods using multivariate analysis, such as single value decomposition (SVD), our implementation of the Z-LSR method can operate nearly in real-time. In spite of its computational simplicity, Z-LSR can automatically remove background and bias in the signal, improve the resolution of spatially distributed spectral differences and enable sub-cellular features to be resolved in Raman microscopy images of mouse macrophage cells. Significantly, the Z-LSR processed images automatically exhibited subcellular architectures whereas SVD, in general, requires human assistance in selecting the components of interest.

Conclusions

The computational efficiency of Z-LSR enables automated resolution of sub-cellular features in large Raman microscopy data sets without compromise in image quality or information loss in associated spectra. These results motivate further use of label free microscopy techniques in real-time imaging of live immune cells.     

Wet strength improvement of unbleached kraft pulp through laccase catalyzed oxidation

Previous investigations have shown that laccase catalyzed oxidation of lignin containing wood fibers can enhance the strength of medium density fiberboards. In the present work it was investigated if laccase treatment had any impact on the tensile strength of a high yield unbleached kraft pulp. Treatment with laccase alone had only a very little effect on the wet strength of the pulp, whereas addition of lignin rich extractives increased the wet strength after the enzyme treatment significantly. A mediated oxidation gave a similar improvement of the wet tensile strength although no lignin was added to the fiber suspension. Furthermore, it was found that a heat treatment combined with a mediated oxidation gave a higher improvement in wet tensile strength than could be accounted for by the individual treatments. No change in dry tensile strength from the laccase treatment was observed. It is suggested that the observed improvement in wet tensile strength is related to polymerization of lignin on fibers in the hand sheet and/or coupling of phenoxy radicals on lignin associated to adjacent fibers. For the different mediators studied, a correlation was found between oxygen consumption upon mediated oxidation and generation of wet strength in the pulp.     

Lymphotoxin-alpha-deficient mice make delayed,but effective,T and B cell responses to influenza

Lymphotoxin-alpha(-/-) (LTalpha(-/-)) mice are thought to be unable to generate effective T and B cell responses. This is attributed to the lack of lymph nodes and the disrupted splenic architecture of these mice. However, despite these defects we found that LTalpha(-/-) mice could survive infection with a virulent influenza A virus. LTalpha(-/-) mice and normal wild-type mice infected with influenza A generated similar numbers of influenza-specific CD8 T cells that were able to produce IFN-gamma and kill target cells presenting influenza peptides. Furthermore influenza-infected LTalpha(-/-) mice produced high titers of influenza-specific IgM, IgG, and IgA. However, both CD8 and B cell immune responses were delayed in LTalpha(-/-) mice by 2-3 days. The delayed cellular and humoral immune response was sufficient to mediate viral clearance in LTalpha(-/-) mice that were infected with relatively low doses of influenza virus. However, when LTalpha(-/-) mice were infected with larger doses of influenza, they succumbed to infection before the immune response was initiated. These results demonstrate that neither LTalpha nor constitutively organized lymphoid tissues, such as lymph nodes and spleen, are absolutely required for the generation of effective immunity against the respiratory virus influenza A. However, the presence of LTalpha and/or lymph nodes does accelerate the initiation of immune responses, which leads to protection from larger doses of virus.     

Chaperone activity of a chimeric GroEL protein that can exist in a single or double ring form.

The molecular chaperone GroEL is a protein complex consisting of two rings each of seven identical subunits. It is thought to act by providing a cavity in which a protein substrate can fold into a form that has no propensity to aggregate. Substrate proteins are sequestered in the cavity while they fold, and prevented from diffusion out of the cavity by the action of the GroES complex, that caps the open end of the cavity. A key step in the mechanism of action of GroEL is the transmission of a conformational change between the two rings, induced by the binding of nucleotides to the GroEL ring opposite to the one containing the polypeptide substrate. This conformational change then leads to the discharge of GroES from GroEL, enabling polypeptide release. Single ring forms of GroEL are thus predicted to be unable to chaperone the folding of GroES-dependent substrates efficiently, since they are unable to discharge the bound GroES and unable to release folded protein. We describe here a detailed functional analysis of a chimeric GroEL protein, which we show to exist in solution in equilibrium between single and double ring forms. We demonstrate that whereas the double ring form of the GroEL chimera functions effectively in refolding of a GroES-dependent substrate, the single ring form does not. The single ring form of the chimera, however, is able to chaperone the folding of a substrate that does not require GroES for its efficient folding. We further demonstrate that the double ring structure of GroEL is likely to be required for its activity in vivo.     

N-Acetylglutamate in rat liver during foetal development.

N-Acetylglutamate is present in foetal rat liver at 17 days' gestation. The tissue content (approx. 50 nmol/g wet wt.) remains constant during later foetal life. The appearance of N-acetylglutamate does not parallel the developmental pattern of the urea cycle.     

Family studies of hereditary hemochromatosis in Denmark and the Faroe Islands

Summary Pedigree studies were performed based on one Faroese and four Danish probands with overt idiopathic hemochromatosis (IH). The study consisted of HLA typing and determination of biochemical iron status indicators (serum transferrin saturation, serum ferritin). In total, 130 persons were evaluated. The screening identified 6 homozygous (h/h) subjects with preclinical IH, 46 heterozygous (h/n), and 8 normal (n/n) subjects, while 39 subjects were classified as normal or heterozygous (n/h?). One family demonstrated both a homozygous x heterozygous as well as a heterozygous x heterozygous mating. Recombination between the HLA region and IH locus occurred possibly in three subjects in three different families. The significance of detailed screening in families with probands with IH is discussed.     

Susceptibility of Campylobacter jejuni and Yersinia enterocolitica to UV radiation

Two enteric pathogens, Campylobacter jejuni and Yersinia enterocolitica serogroup O:3, together with Escherichia coli, were investigated for susceptibility to UV radiation at 254 nm. The UV dose required for a 3-log reduction (99.9% inactivation) of C. jejuni, Y. enterocolitica, and E. coli was 1.8, 2.7, and 5.0 mWs/cm2, respectively. Using E. coli as the basis for comparison, it appears that C. jejuni and Y. enterocolitica serogroup O:3 are more sensitive to UV than many of the pathogens associated with waterborne disease outbreaks and can be easily inactivated in most commercially available UV reactors. No association was found between the sensitivity of Y. enterocolitica to UV and the presence of a 40- to 50-megadalton virulence plasmid.     

o,p'-DDD in the mouse lung: selective uptake, covalent binding and effect on drug metabolism

By means of autoradiography a high and selective accumulation was observed in the lung alveolar region of C57Bl mice injected with o,p'-[14C]DDD. Exhaustive extraction of lung tissue showed that a large fraction of the radioactivity was covalently bound to protein. Covalent binding in liver was 20-30 times lower and represented a smaller fraction of the total radioactivity present in this tissue. Formation of a cytochrome P-450 catalysed reactive metabolite in lung and liver was indicated by a decreased covalent binding in these tissues in mice pretreated with metyrapone. Both beta-naphthoflavone (beta NF) and phenobarbital (PB) pretreatment decreased binding of o,p'-DDD in lung tissue, while binding in the liver was induced by PB but remained unaffected by beta NF. Pretreatment with high doses of o,p'-DDD and p,p'-DDT gave a significantly decreased binding of o,p'-[14C]DDD in lung, whereas binding in liver remained unchanged. Conjugation with glutathione does not appear to be a major inactivation pathway for the reactive lung metabolite, since a high dose of o,p'-DDD did not deplete non-protein thiols (NPSH) in lung tissue. Pretreatment with o,p'-DDD decreased the N-demethylation of [dimethyl-14C]aminopyrine in both lung and liver in a dose-dependent manner, suggesting that the drug-metabolizing enzyme system may be a target for o,p'-DDD in vivo.