Computer aided selection of candidate vaccine antigens

Immunoinformatics is an emergent branch of informatics science that long ago pullulated from the tree of knowledge that is bioinformatics. It is a discipline which applies informatic techniques to problems of the immune system. To a great extent, immunoinformatics is typified by epitope prediction methods. It has found disappointingly limited use in the design and discovery of new vaccines, which is an area where proper computational support is generally lacking. Most extant vaccines are not based around isolated epitopes but rather correspond to chemically-treated or attenuated whole pathogens or correspond to individual proteins extract from whole pathogens or correspond to complex carbohydrate. In this chapter we attempt to review what progress there has been in an as-yet-underexplored area of immunoinformatics: the computational discovery of whole protein antigens. The effective development of antigen prediction methods would significantly reduce the laboratory resource required to identify pathogenic proteins as candidate subunit vaccines. We begin our review by placing antigen prediction firmly into context, exploring the role of reverse vaccinology in the design and discovery of vaccines. We also highlight several competing yet ultimately complementary methodological approaches: sub-cellular location prediction, identifying antigens using sequence similarity, and the use of sophisticated statistical approaches for predicting the probability of antigen characteristics. We end by exploring how a systems immunomics approach to the prediction of immunogenicity would prove helpful in the prediction of antigens.

The effects of oxygen free radicals on the carbohydrate moiety of IgG

The CH2-linked glycoform of rheumatoid IgG is abnormal in having a reduced galactose content. This has been postulated to be a synthetic defect due to a decrease in the level of rheumatoid B cell galactosyltransferase. However, more recent work has indicated that agalactosylation may be common to chronic inflammatory diseases. In this work we have investigated the effect of oxygen free radicals (OFRs), which are generated by activated phagocytic cells at inflammatory sites, on the carbohydrate moiety of IgG. Radiolytically generated peroxy (ROO.) and hydroxyl radicals (OH.) but not superoxide anion radicals (O2.-) were found to destroy galactose on IgG. After OH. attack, this was associated with an increase in the availability of N-acetylglucosamine, possibly due to its presence as a terminal residue. These results suggest that the agalactosylation associated with chronic inflammation may not only be synthetic in nature, but may also be a consequence of post-synthetic degradation by OFRs.

Analysis of Acanthamoeba polyphaga surface carbohydrate exposure by FITC-lectin binding and flourescence evaluation

Aims: Characterization of the representative protozoan Acanthamoeba polyphaga surface carbohydrate exposure by a novel combination of flow cytometry and ligand-receptor analysis. Methods and Results: Trophozoite and cyst morphological forms were exposed to a panel of FITC-lectins. Population fluorescence associated with FITC-lectin binding to acanthamoebal surface moieties was ascertained by flow cytometry. Increasing concentrations of representative FITC-lectins, saturation binding and determination of K d and relative Bmax values were employed to characterize carbohydrate residue exposure. FITC-lectins specific for N-acetylglucosamine, N-acetylgalactosamine and mannose/glucose were readily bound by trophozoite and cyst surfaces. Minor incremental increases in FITC-lectin concentration resulted in significant differences in surface fluorescence intensity and supported the calculation of ligand-binding determinants, Kd and relative B max, which gave a trophozoite and cyst rank order of lectin affinity and surface receptor presence. Conclusions: Trophozoites and cysts expose similar surface carbohydrate residues, foremost amongst which is N-acetylglucosamine, in varying orientation and availability. Significance and Impact of the Study: The outlined versatile combination of flow cytometry and ligand-receptor analysis allowed the characterization of surface carbohydrate exposure by protozoan morphological forms and in turn will support a valid comparison of carbohydrate exposure by other single-cell protozoa and eucaryotic microbes analysed in the same manner.

Vaccine adjuvant systems: enhancing the efficacy of sub-unit protein antigens

Vaccination remains a key tool in the protection and eradication of diseases. However, the development of new safe and effective vaccines is not easy. Various live organism based vaccines currently licensed, exhibit high efficacy; however, this benefit is associated with risk, due to the adverse reactions found with these vaccines. Therefore, in the development of vaccines, the associated risk-benefit issues need to be addressed. Sub-unit proteins offer a much safer alternative; however, their efficacy is low. The use of adjuvanted systems have proven to enhance the immunogenicity of these sub-unit vaccines through protection (i.e. preventing degradation of the antigen in vivo) and enhanced targeting of these antigens to professional antigen-presenting cells. Understanding of the immunological implications of the related disease will enable validation for the design and development of potential adjuvant systems. Novel adjuvant research involves the combination of both pharmaceutical analysis accompanied by detailed immunological investigations, whereby, pharmaceutically designed adjuvants are driven by an increased understanding of mechanisms of adjuvant activity, largely facilitated by description of highly specific innate immune recognition of components usually associated with the presence of invading bacteria or virus. The majority of pharmaceutical based adjuvants currently being investigated are particulate based delivery systems, such as liposome formulations. As an adjuvant, liposomes have been shown to enhance immunity against the associated disease particularly when a cationic lipid is used within the formulation. In addition, the inclusion of components such as immunomodulators, further enhance immunity. Within this review, the use and application of effective adjuvants is investigated, with particular emphasis on liposomal-based systems. The mechanisms of adjuvant activity, analysis of complex immunological characteristics and formulation and delivery of these vaccines are considered.

Induction of inflammatory cytokines and nitric oxide in J774.2 cells and murine macrophages by lipoteichoic acid and related cell wall antigens from Staphylococcus epidermidis

Staphylococcus epidermidis causes infections associated with medical devices including central venous catheters, orthopaedic prosthetic joints and artificial heart valves. This coagulase-negative Staphylococcus produces a conventional cellular lipoteichoic acid (LTA) and also releases a short-glycerophosphate-chain-length form of LTA (previously termed lipid S) into the medium during growth. The relative pro-inflammatory activities of cellular and short-chain-length exocellular LTA were investigated in comparison with peptidoglycan and wall teichoic acid from S. epidermidis and LPS from Escherichia coli O111. The ability of these components to stimulate the production of proinflammatory cytokines [interleukin (IL)-1β, IL-6 and tumour necrosis factor (TNF)-α] and nitric oxide was investigated in a murine macrophage-like cell line (J774.2), and in peritoneal and splenic macrophages. On a weight-for-weight basis the short-chain-length exocellular LTA was the most active of the S. epidermidis products, stimulating significant amounts of each of the inflammatory cytokines and nitric oxide, although it was approximately 100-fold less active than LPS from E. coli. By comparison the full-chain-length cellular LTA and peptidoglycan were less active and the wall teichoic acid had no activity. As an exocellular product potentially released from S. epidermidis biofilms, the short-chain-length exocellular LTA may act as the prime mediator of the host inflammatory response to device-related infection by this organism and act as the Gram-positive equivalent of LPS in Gram-negative sepsis. The understanding of the role of short-chain-length exocellular LTA in Gram-positive sepsis may lead to improved treatment strategies. © 2005 SGM.

Radial growth and carbohydrate levels in the lichen Parmelia conspersa on north and south facing rock surfaces

Parmelia conspersa (Ehrh. Ex Ach.)Ach. is a foliose lichen found more frequently on south facing compared with north facing rock surfaces in South Gwynedd, Wales, UK. The radial growth of thalli of P. conspersa from a north and a south facing rock surface was measured in situ at intervals of two months for 1 yr during 1990/1991. Mean annual radial growth rates were greater on the south compared with the north facing rock surface. In addition, the pattern of radial growth varied during the year with maximum growth recorded in the Feb/Mar. period especially on the south facing rock surface. The levels of ribitol, arabitol and mannitol were measured in individual lobes of P. conspersa collected from the same rock surfaces on 4 days (2 Jun; 7 July and 30 Nov. 1990 and 29 Mar. 1991) during 1990/1991. The total of the three carbohydrates varied between days; the levels of arbitol and ribitol being significantly lower in the 7 July sample on both north and south facing rock surfaces. In addition, the levels ribitol, arabitol and mannitol were higher on the south facing rock surface especially in the summer samples. The ratio of arabitol plus mannitol to ribitol and the mannitol/arabitol ratio varied more between days sampled than between north and south facing rock surfaces. The level of ribitol in individual thalli was positively correlated with arabitol on the north facing and with mannitol on the south facing slope. These results suggest that differences in the radial growth of P. conspersa thalli with aspect are more likely to reflect higher rates of photosynthesis on the south facing rock surface rather than large difference in the way carbohydrates were partitioned on the different surfaces. Lower radial growth rates may place P. conspersa at a competitive disadvantage on north facing rock surfaces.

AntigenDB:an immunoinformatics database of pathogen antigens

The continuing threat of infectious disease and future pandemics, coupled to the continuous increase of drug-resistant pathogens, makes the discovery of new and better vaccines imperative. For effective vaccine development, antigen discovery and validation is a prerequisite. The compilation of information concerning pathogens, virulence factors and antigenic epitopes has resulted in many useful databases. However, most such immunological databases focus almost exclusively on antigens where epitopes are known and ignore those for which epitope information was unavailable. We have compiled more than 500 antigens into the AntigenDB database, making use of the literature and other immunological resources. These antigens come from 44 important pathogenic species. In AntigenDB, a database entry contains information regarding the sequence, structure, origin, etc. of an antigen with additional information such as B and T-cell epitopes, MHC binding, function, gene-expression and post translational modifications, where available. AntigenDB also provides links to major internal and external databases. We shall update AntigenDB on a rolling basis, regularly adding antigens from other organisms and extra data analysis tools. AntigenDB is available freely at http://www.imtech.res.in/raghava/antigendb and its mirror site http://www.bic.uams.edu/raghava/antigendb.

Continous annular chromatography for the separation of carbohydrate mixtures

The continuous separation of beet molasses resulting in a sucrose rich product and a non-sugar waste product was carried out using a rotating annular chromatograph. The annulus was 12 mm wide and 1.4 m long and was packed with a sodium charged 5.5% cross-linked polystyrene ion exchange resin. Separation was achieved by the simultaneous mechanisms of ion exclusion, size exclusion and partition chromatography. The entire packed bed was slowly rotated while beet molasses was fed continuously through a stationary feed nozzle to the top of the bed. Each molasses constituent having a different relative affinity for the packing and the deionised water mobile phase describes a characteristic helical path as it progresses from the stationary feed point to the bottom of the rotating bed. Each solute then elutes from the annulus at a different angular distance from the feed and separation of the multicomponent mixture is thereby achieved. When a 35% w/w sucrose beet molasses feed was used the throughput achievable was 45.1 kg sucrose m~3 resin h"1. In addition to beet molasses separation other carbohydrate mixtures were separated. In particular the separation of glucose and fructose by Ligand exchange chromatography on a calcium charged ion exchange bed was carried out. The effects of flowrates, concentration, rotation rate, temperature and particle size on resolution and dilution of constituents in the mixtures to be separated were studied. A small test rig was designed and built to determine the cause of liquid maldistribution around the annulus. The problem was caused by the porous bed support media becoming clogged with fines being introduced by eluent flows and off the resin. An outer ring was constructed to house the bed support which could be quickly replaced with the onset of maldistribution. The computer simulation of the operation of the rotating annular chromatograph has been carried out successfully.

The production of fructose from carbohydrate feedstocks

A review of the general chromatographic theory and of continuous chromatographic techniques has been carried out. Three methods of inversion of sucrose to glucose and fructose in beet molasses were explored. These methods were the inversion of sucrose using the enzyme invertase, by the use of hydrochloric acid and the use of the resin Amberlite IR118 in the H+ form. The preferred method on economic and purity considerations was by the use of the enzyme invertase. The continuous chromatographic separation of inverted beet molasses resulting in a fructose rich product and a product containing glucose and other non-sugars was carried out using a semi-continuous counter-current chromatographic refiner (SCCR6), consisting of ten 10.8cm x 75cm long stainless steel columns packed with a calcium charged 8% cross-linked polystyrene resin Zerolit SRC 14. Based on the literature this is the first time such a continuous separation has been attempted. It was found that the cations present in beet molasses displaced the calcium ions from the resin resulting in poor separation of the glucose and fructose. Three methods of maintaining the calcium form of the resin during the continuous operation of the equipment were established. Passing a solution of calcium nitrate through the purge column for half a switch period was found to be most effective as there was no contamination of the main fructose rich product and the product concentrations were increased by 50%. When a 53% total solids (53 Brix) molasses feedstock was used, the throughput was 34.13kg sugar solids per m3 of resin per hour. Product purities of 97% fructose in fructose rich (FRP) and 96% glucose in the glucose rich (GRP) products were obtained with product concentrations of 10.93 %w/w for the FRP and 10.07 %w/w for the GRP. The effects of flowrates, temperature and background sugar concentration on the distribution coefficients of fructose, glucose, betaine and an ionic component of beet molasses were evaluated and general relationships derived. The computer simulation of inverted beet molasses separations on an SCCR system has been carried out successfully.

The chromatographic separation of carbohydrate mixtures

The separation performance of a semicontinuous counter-current chromatographic refiner (SCCR7), consisting of twelve 5.4 cm id x 75cm long columns packed with calcium charged cross-linked polysytrene resin (KORELA VO7C), was optimised. An industrial barley syrup was used containing 42% fructose, 52% glucose and 6% maltose and oligosaccharides. The effects of temperature, flow rates and concentration on the distribution coefficients were evaluated and quantified by deriving general relationships. The effects of flow rates, feed composition and concentration on the separation performance of the SCCR7 were identified and general relationships between them and the switch time, which was found to be the controlling parameter, were developed. Fructose rich (FRP) and glucose rich (GRP) product purities of 99.9% were obtained at 18.6% w/v feed concentrations. When a 66% w/v feed concentration was used and product splitting technique was employed, the throughput was 32.1 kg sugar solids/m3 resin/hr. The GRP contained less than 4.5% fructose, the FRP was over 95% pure, and the respective concentrations were 22.56 and 11.29% w/v. Over 94% of the glucose and 95.78% of the fructose in the feed were recovered in the GRP and FRP respectively. By recycling the dilute product split fractions, the GRP and FRP concentrations were increased to 25.4 and 12.96% w/v; the FRP was 90.2% pure and the GRP contained 6.69% w/v fructose. A theoretical link between batch and semicontinuous chromatographic equipments has been determined. A computer simulation was developed predicting successfully the purging concentration profiles at `pseudo-equilibrium', and also certain system design parameters. An important further aspect of the work has been to study the behaviour of chromatographic bioreactor-separators. Such batch systems of 5.4cm id and lengths varying between 30 and 230cm, were used to investigate the effect of scaling up on the conversion of sucrose into dextran and fructose in the presence of the dextransucrase enzyme. Conversions of over 80% were achieved at 4 hr sucrose residence times. The crude dextransucrase was purified using centrifugation, ultrafiltration and cross-flow microfiltration techniques. Better enzyme stability was obtained by first separating the non-solid impurities using cross-flow microfiltration, and then removing the cells from the enzyme immediately before use by continuous centrifugation.