Computational models in immunological methods: an historical review

Deciphering immunodiffusion: In silico optimization for faster protein diagnostics

Immunodiffusion tests offer a simple yet powerful method for detecting protein antigens, but their long assay times hinder clinical utility. We unveil the complex interplay of parameters governing this process using finite element simulations. By meticulously validating our model against real-world data, we elucidate how initial concentrations and diffusivities of antigen and antibody shape the intensity, size, and formation time of the precipitin ring. Our key innovation lies in employing phase diagram analysis to map the combined effects of these parameters on assay performance. This framework enables rapid in silico parameter estimation, paving the way for the design of novel immunodiffusion assays with drastically reduced assay times. The presented approach holds immense potential for optimizing protein diagnostics for fast and reliable diagnostics.

Rapid Detection of Lipopolysaccharide and Whole Cells of Francisella tularensis Based on Agglutination of Antibody-Coated Gold Nanoparticles and Colorimetric Registration

The paper presents development and characterization of a new bioanalytical test system for rapid detection of lipopolysaccharide (LPS) and whole cells of Francisella tularensis, a causative agent of tularemia, in water samples. Gold nanoparticles (AuNPs) coated by the obtained anti-LPS monoclonal antibodies were used for the assay. Their contact with antigen in tested samples leads to aggregation with a shift of absorption spectra from red to blue. Photometric measurements at 530 nm indicated the analyte presence. Three preparations of AuNPs with different diameters were compared, and the AuNPs having average diameter of 34 nm were found to be optimal. The assay is implemented in 20 min and is characterized by detection limits equal to 40 ng/mL for LPS and 3 × 10⁴ CFU/mL for whole cells of F. tularensis. Thus, the proposed simple one-step assay integrates sensitivity comparable with other immunoassay of microorganisms and rapidity. Selectivity of the assay for different strains of F. tularensis was tested and the possibility to choose its variants with the use of different antibodies to distinguish virulent and non-virulent strains or to detect both kinds of F. tularensis was found. The test system has been successfully implemented to reveal the analyte in natural and tap water samples without the loss of sensitivity.

Computational modeling of immune system of the fish for a more effective vaccination in aquaculture

Motivation

A computational model equipped with the main immunological features of the sea bass (Dicentrarchus labrax L.) immune system was used to predict more effective vaccination in fish. The performance of the model was evaluated by using the results of two in vivo vaccinations trials against L. anguillarum and P. damselae.

Results

Tests were performed to select the appropriate doses of vaccine and infectious bacteria to set up the model. Simulation outputs were compared with the specific antibody production and the expression of BcR and TcR gene transcripts in spleen. The model has shown a good ability to be used in sea bass and could be implemented for different routes of vaccine administration even with more than two pathogens. The model confirms the suitability of in silico methods to optimize vaccine doses and the immune response to them. This model could be applied to other species to optimize the design of new vaccination treatments of fish in aquaculture.

Availability and implementation

The method is available at http://www.iac.cnr.it/∼filippo/c-immsim/.

Contact

nromano@unitus.it.

Supplementary information

Supplementary data are available at Bioinformatics online.

Mathematical Modeling of Bioassays

The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand-receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predictive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contemporary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.

Frontiers in epidermal barrier homeostasis--an approach to mathematical modelling of epidermal calcium dynamics

Intact epidermal barrier function is crucial for survival and is associated with the presence of gradients of both calcium ion concentration and electric potential. Although many molecules, including ion channels and pumps, are known to contribute to maintenance of these gradients, the mechanisms involved in epidermal calcium ion dynamics have not been clarified. We have established that a variety of neurotransmitters and their receptors, originally found in the brain, are expressed in keratinocytes and are also associated with barrier homeostasis. Moreover, keratinocytes and neurons show some similarities of electrochemical behaviour. As mathematical modelling and computer simulation have been employed to understand electrochemical phenomena in brain science, we considered that a similar approach might be applicable to describe the dynamics of epidermal electrochemical phenomena associated with barrier homeostasis. Such methodology would also be potentially useful to address a number of difficult problems in clinical dermatology, such as ageing and itching. Although this work is at a very early stage, in this essay, we discuss the background to our approach and we present some preliminary results of simulation of barrier recovery.

Immunological methods for nursing research: from cells to systems

Scientists and clinicians frequently use immunological methods (IMs) to investigate complex biological phenomena. Commonly used IMs include immunocytochemistry (IC), enzyme-linked immunosorbent assays (ELISA) and flow cytometry. Each of these methodologies exploits a common principle in IMs -the binding of an antibody to its antigen. Scientists continue to develop new methodologies, such as high-throughput immunohistochemistry (IHC) and in vivo imaging techniques, which exploit antibody-antigen binding, to more accurately answer complex research questions involving single cells up to whole organ systems. The purpose of this paper is to discuss established and evolving IMs and to illustrate the application of these methods to nursing research.

Immunoinformatics: an overview of computational tools and techniques for understanding immune function

In recent years, there has been a rapid expansion in the application of information technology to biological data. Although the use of information science techniques is less common for the discipline of immunology, this field has seen great strides in recent years. This review addresses why in silico modeling is needed in immunology research, highlights some of the major areas of research and suggests what may be important for the future of immunoinformatics.

Characterization and Optimization of Gold Nanoparticle-Based Silver-Enhanced Immunoassays

Silver-enhanced nanoparticle-labeled immunoassays provide a simple, low-cost, and effective way of detecting antigens in dilute solutions. The physical mechanisms behind their operation, however, have not been fully investigated. We present a semiquantitative approach for optimizing sandwich nanoparticle immunoassays using an adsorption-controlled kinetic model. Primary antibodies were immobilized on a solid substrate to bind the target antigens in solution. An optical signal was measured by secondary labeling of antigens with gold nanoparticles and their enhancement by silver nucleation. The opacity of the silver-enhanced spots was quantified by densitometry. The selectivity of the sandwich immunoassays was adequately high, and antigen concentrations as low as 0.1 microg cm(-3) (4 ng total) were detected reproducibly. The role of mass transfer was investigated, and a model was developed to optimize the performance of immunoassays by correlating the opacities of silver spots to the concentration and incubation times of antigens and gold nanoparticles. The results could allow the development of more rapid and reliable nanoparticle immunoassays.

Mathematical modeling of humoral immune response suppression by passively administered antibodies in mice

Although passively administered antibodies are known to suppress the humoral immune response, the mechanism is not fully understood. Here, we developed a mathematical model to better understand the suppression phenomena in mice. Using this model, we tested the generally accepted but difficult to prove "epitope masking hypothesis." To simulate the hypothesis and clearly observe masking of epitopes, we modeled epitope-antibody and epitope-B-cell receptor interactions at the epitope level. To validate this model, we simulated the effect of the antibody affinity and quantity as well as the timing of administration on the suppression, and we compared the results with experimental observations reported in the literature. We then developed a simulation to determine whether the epitope-masking hypothesis alone can explain known immune suppression phenomena, especially the conflicting results on F(ab')2 fragment-induced suppression, which has been shown to be no suppression, or similar to or up to 1000-fold weaker than the suppression by intact antibody. We found that suppression was caused by a synergistic effect of both epitope masking and rapid antigen clearance. Although the latter hypothesis has lost support because FcgammaRI/III mutant mice show antibody-mediated suppression, our simulations predict that, even in FcgammaRI/III mutant mice, the immune response can be suppressed according to the antibody affinity. Our model also effectively reproduced the conflicting results obtained using F(ab')2 fragments. Thus, in contrast to the idea that the F(ab')2 results prove the FcgammaRIIb involvement in suppression, our mathematical model suggests that the epitope-masking hypothesis together with rapid antigen clearance explains the conflicting results.

Experimental study and mathematical modeling of the interaction between antibodies and antigens on the surface of liposomes

Unilamellar liposomes with incorporated hapten-phospholipid conjugates were proposed as models of polyvalent antigens with migrating determinants for quantitative analysis of their interaction with antibodies. The monovalent pesticide atrazine was used as a model antigen. For its incorporation into the lipid bilayer, the atrazine carboxylated derivative was conjugated with dimyristoylphosphatidylethanolamine (DMPE). Unilamellar liposomes were prepared with dimyristoylphosphatidylcholine/atrazine-DMPE at molar ratios of 90:10, 95:5, 98:2, 99:1 and 99.5:0.5. Their interaction with the peroxidase-labeled anti-atrazine antibodies was studied by enzyme immunoassay and polarization fluoroimmunoassay techniques. It was shown that the increase in hapten content in the liposomes from 0.5 to 10 mol% led to an increase in the equilibrium constants of the interaction with antibodies from 0.093 x 10(8) to 0.303 x 10(8)M-1. The association rate constants varied from 1.45 x 10(5) to 15.5 x 10(5)M-1 s-1 depending on the antigen content in liposomes and experimental conditions. The measured constants were applied for a mathematical model describing multi-step interaction between antibodies and polyvalent liposomal antigens. The model adequately describes the quantitative regularities of the influence of antigen content and the affinity of immunochemical interaction on the quantity and the dynamics of the immune complexes forming.

Molecular immunology databases and data repositories

Over recent years databases have become an extremely important resource for biomedical research. Immunology research is increasingly dependent on access to extensive biological databases to extract existing information, plan experiments, and analyse experimental results. This review describes 15 immunological databases that have appeared over the last 30 years. In addition, important issues regarding database design and the potential for misuse of information contained within these databases are discussed. Access pointers are provided for the major immunological databases and also for a number of other immunological resources accessible over the World Wide Web (WWW).