Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterisation of type 1 cell surface-associated antigens

We have developed a novel multilocus sequence typing (MLST) scheme and database (http://pubmlst.org/pacnes/) for Propionibacterium acnes based on the analysis of seven core housekeeping genes. The scheme, which was validated against previously described antibody, single locus and random amplification of polymorphic DNA typing methods, displayed excellent resolution and differentiated 123 isolates into 37 sequence types (STs). An overall clonal population structure was detected with six eBURST groups representing the major clades I, II and III, along with two singletons. Two highly successful and global clonal lineages, ST6 (type IA) and ST10 (type IB1), representing 64?% of this current MLST isolate collection were identified. The ST6 clone and closely related single locus variants, which comprise a large clonal complex CC6, dominated isolates from patients with acne, and were also significantly associated with ophthalmic infections. Our data therefore support an association between acne and P. acnes strains from the type IA cluster and highlight the role of a widely disseminated clonal genotype in this condition. Characterization of type I cell surface-associated antigens that are not detected in ST10 or strains of type II and III identified two dermatan-sulphate-binding proteins with putative phase/antigenic variation signatures. We propose that the expression of these proteins by type IA organisms contributes to their role in the pathophysiology of acne and helps explain the recurrent nature of the disease. The MLST scheme and database described in this study should provide a valuable platform for future epidemiological and evolutionary studies of P. acnes.

Effectiveness of nonpharmacologic treatments for acute seasonal allergic conjunctivitis

Objective - To investigate whether artificial tears and cold compress alone or in combination provide a treatment benefit and whether they were as effective as or could enhance topical antiallergic medication. Design - Randomized, masked clinical trial. Participants - Eighteen subjects (mean age, 29.5±11.0 years) allergic to grass pollen. Intervention - Controlled exposure to grass pollen using an environmental chamber to stimulate an ocular allergic reaction followed by application of artificial tears (ATs), 5 minutes of cold compress (CC), ATs combined with CC, or no treatment applied at each separate visit in random order. A subset of 11 subjects also had epinastine hydrochloride (EH) applied alone and combined with CC in random order or instillation of a volume-matched saline control. Main Outcome Measures - Bulbar conjunctival hyperemia, ocular surface temperature, and ocular symptoms repeated before and every 10 minutes after treatment for 1 hour. Results - Bulbar conjunctival hyperemia and ocular symptoms decreased and temperature recovered to baseline faster with nonpharmaceutical treatments compared with no treatment (P??0.05). At all measurement intervals, symptoms were reduced for both EH and EH combined with CC than CC or ATs alone or in combination (P?antigenic challenge. Signs of allergic conjunctivitis generally were reduced most by a combination of a CC in combination with ATs or EH.

Production, purification and characterization of recombinant, full-length human claudin-1

The transmembrane domain proteins of the claudin superfamily are the major structural components of cellular tight junctions. One family member, claudin-1, also associates with tetraspanin CD81 as part of a receptor complex that is essential for hepatitis C virus (HCV) infection of the liver. To understand the molecular basis of claudin-1/CD81 association we previously produced and purified milligram quantities of functional, full-length CD81, which binds a soluble form of HCV E2 glycoprotein (sE2). Here we report the production, purification and characterization of claudin-1. Both yeast membrane-bound and detergent-extracted, purified claudin-1 were antigenic and recognized by specific antibodies. Analytical ultracentrifugation demonstrated that extraction with n-octyl-ß-d-glucopyranoside yielded monodispersed, dimeric pools of claudin-1 while extraction with profoldin-8 or n-decylphosphocholine yielded a dynamic mixture of claudin-1 oligomers. Neither form bound sE2 in line with literature expectations, while further functional analysis was hampered by the finding that incorporation of claudin-1 into proteoliposomes rendered them intractable to study. Dynamic light scattering demonstrated that claudin-1 oligomers associate with CD81 in vitro in a defined molar ratio of 1:2 and that complex formation was enhanced by the presence of cholesteryl hemisuccinate. Attempts to assay the complex biologically were limited by our finding that claudin-1 affects the properties of proteoliposomes. We conclude that recombinant, correctly-folded, full-length claudin-1 can be produced in yeast membranes, that it can be extracted in different oligomeric forms that do not bind sE2 and that a dynamic preparation can form a specific complex with CD81 in vitro in the absence of any other cellular components. These findings pave the way for the structural characterization of claudin-1 alone and in complex with CD81.

Effectiveness of nonpharmacologic treatments for acute seasonal allergic conjunctivitis

Objective To investigate whether artificial tears and cold compress alone or in combination provide a treatment benefit and whether they were as effective as or could enhance topical antiallergic medication. Design Randomized, masked clinical trial. Participants Eighteen subjects (mean age, 29.5±11.0 years) allergic to grass pollen. Intervention Controlled exposure to grass pollen using an environmental chamber to stimulate an ocular allergic reaction followed by application of artificial tears (ATs), 5 minutes of cold compress (CC), ATs combined with CC, or no treatment applied at each separate visit in random order. A subset of 11 subjects also had epinastine hydrochloride (EH) applied alone and combined with CC in random order or instillation of a volume-matched saline control. Main Outcome Measures Bulbar conjunctival hyperemia, ocular surface temperature, and ocular symptoms repeated before and every 10 minutes after treatment for 1 hour. Results Bulbar conjunctival hyperemia and ocular symptoms decreased and temperature recovered to baseline faster with nonpharmaceutical treatments compared with no treatment (P <0.05). Artificial tears combined with CC reduced hyperemia more than other treatments (P <0.05). The treatment effect of EH was enhanced by combining it with a CC (P <0.001). Cold compress combined with ATs or EH lowered the antigen-raised ocular surface temperature to less than the pre-exposure baseline. Artificial tear instillation alone or CC combined with ATs or EH significantly reduced the temperature (P <0.05). Cold compress combined with ATs or EH had a similar cooling effect (P > 0.05). At all measurement intervals, symptoms were reduced for both EH and EH combined with CC than CC or ATs alone or in combination (P <0.014). Conclusions After controlled exposure to grass pollen, CC and AT treatment showed a therapeutic effect on the signs and symptoms of allergic conjunctivitis. A CC enhanced the use of EH alone and was the only treatment to reduce symptoms to baseline within 1 hour of antigenic challenge. Signs of allergic conjunctivitis generally were reduced most by a combination of a CC in combination with ATs or EH. © 2014 by the American Academy of Ophthalmology.

SVRMHC prediction server for MHC-binding peptides

The binding between antigenic peptides (epitopes) and the MHC molecule is a key step in the cellular immune response. Accurate in silico prediction of epitope-MHC binding affinity can greatly expedite epitope screening by reducing costs and experimental effort. Recently, we demonstrated the appealing performance of SVRMHC, an SVR-based quantitative modeling method for peptide-MHC interactions, when applied to three mouse class I MHC molecules. Subsequently, we have greatly extended the construction of SVRMHC models and have established such models for more than 40 class I and class II MHC molecules. Here we present the SVRMHC web server for predicting peptide-MHC binding affinities using these models. Benchmarked percentile scores are provided for all predictions. The larger number of SVRMHC models available allowed for an updated evaluation of the performance of the SVRMHC method compared to other well- known linear modeling methods. SVRMHC is an accurate and easy-to-use prediction server for epitope-MHC binding with significant coverage of MHC molecules. We believe it will prove to be a valuable resource for T cell epitope researchers.

The development of a novel Bio-MEMS filtration chip for the separation of specific cells in fluid suspension

In the clinical/microbiological laboratory there are currently several ways of separating specific cells from a fluid suspension. Conventionally cells can be separated based on size, density, electrical charge, light-scattering properties, and antigenic surface properties. Separating cells using these parameters can require complex technologies and specialist equipment. This paper proposes new Bio-MEMS (microelectromechanical systems) filtration chips manufactured using deep reactive ion etching (DRIE) technology that, when used in conjunction with an optical microscope and a syringe, can filter and grade cells for size without the requirement for additional expensive equipment. These chips also offer great versatility in terms of design and their low cost allows them to be disposable, eliminating sample contamination. The pumping mechanism, unlike many other current filtration techniques, leaves samples mechanically and chemically undamaged. In this paper the principles behind harnessing passive pumping are explored, modelled, and validated against empirical data, and their integration into a microfluidic device to separate cells from a mixed population suspension is described. The design, means of manufacture, and results from preliminary tests are also presented. © IMechE 2007.

Predicting class II MHC-Peptide binding:a kernel based approach using similarity scores

Background - Modelling the interaction between potentially antigenic peptides and Major Histocompatibility Complex (MHC) molecules is a key step in identifying potential T-cell epitopes. For Class II MHC alleles, the binding groove is open at both ends, causing ambiguity in the positional alignment between the groove and peptide, as well as creating uncertainty as to what parts of the peptide interact with the MHC. Moreover, the antigenic peptides have variable lengths, making naive modelling methods difficult to apply. This paper introduces a kernel method that can handle variable length peptides effectively by quantifying similarities between peptide sequences and integrating these into the kernel. Results - The kernel approach presented here shows increased prediction accuracy with a significantly higher number of true positives and negatives on multiple MHC class II alleles, when testing data sets from MHCPEP [1], MCHBN [2], and MHCBench [3]. Evaluation by cross validation, when segregating binders and non-binders, produced an average of 0.824 AROC for the MHCBench data sets (up from 0.756), and an average of 0.96 AROC for multiple alleles of the MHCPEP database. Conclusion - The method improves performance over existing state-of-the-art methods of MHC class II peptide binding predictions by using a custom, knowledge-based representation of peptides. Similarity scores, in contrast to a fixed-length, pocket-specific representation of amino acids, provide a flexible and powerful way of modelling MHC binding, and can easily be applied to other dynamic sequence problems.

Statistical deconvolution of enthalpic energetic contributions to MHC-peptide binding affinity

Background - MHC Class I molecules present antigenic peptides to cytotoxic T cells, which forms an integral part of the adaptive immune response. Peptides are bound within a groove formed by the MHC heavy chain. Previous approaches to MHC Class I-peptide binding prediction have largely concentrated on the peptide anchor residues located at the P2 and C-terminus positions. Results - A large dataset comprising MHC-peptide structural complexes was created by re-modelling pre-determined x-ray crystallographic structures. Static energetic analysis, following energy minimisation, was performed on the dataset in order to characterise interactions between bound peptides and the MHC Class I molecule, partitioning the interactions within the groove into van der Waals, electrostatic and total non-bonded energy contributions. Conclusion - The QSAR techniques of Genetic Function Approximation (GFA) and Genetic Partial Least Squares (G/PLS) algorithms were used to identify key interactions between the two molecules by comparing the calculated energy values with experimentally-determined BL50 data. Although the peptide termini binding interactions help ensure the stability of the MHC Class I-peptide complex, the central region of the peptide is also important in defining the specificity of the interaction. As thermodynamic studies indicate that peptide association and dissociation may be driven entropically, it may be necessary to incorporate entropic contributions into future calculations.

Towards the knowledge-based design of universal influenza epitope ensemble vaccines

Motivation: Influenza A viral heterogeneity remains a significant threat due to unpredictable antigenic drift in seasonal influenza and antigenic shifts caused by the emergence of novel subtypes. Annual review of multivalent influenza vaccines targets strains of influenza A and B likely to be predominant in future influenza seasons. This does not induce broad, cross protective immunity against emergent subtypes. Better strategies are needed to prevent future pandemics. Cross-protection can be achieved by activating CD8+ and CD4+ T cells against highly-conserved regions of the influenza genome. We combine available experimental data with informatics-based immunological predictions to help design vaccines potentially able to induce cross-protective T-cells against multiple influenza subtypes. Results: To exemplify our approach we designed two epitope ensemble vaccines comprising highly-conserved and experimentally-verified immunogenic influenza A epitopes as putative non-seasonal influenza vaccines; one specifically targets the US population and the other is a universal vaccine. The USA-specific vaccine comprised 6 CD8+ T cell epitopes (GILGFVFTL, FMYSDFHFI, GMDPRMCSL, SVKEKDMTK, FYIQMCTEL, DTVNRTHQY) and 3 CD4+ epitopes (KGILGFVFTLTVPSE, EYIMKGVYINTALLN, ILGFVFTLTVPSERG). The universal vaccine comprised 8 CD8+ epitopes: (FMYSDFHFI, GILGFVFTL, ILRGSVAHK, FYIQMCTEL, ILKGKFQTA, YYLEKANKI, VSDGGPNLY, YSHGTGTGY) and the same 3 CD4+ epitopes. Our USA-specific vaccine has a population protection coverage (portion of the population potentially responsive to one or more component epitopes of the vaccine, PPC) of over 96% and 95% coverage of observed influenza subtypes. The universal vaccine has a PPC value of over 97% and 88% coverage of observed subtypes.

Utilização de peptídeos sintéticos derivados de moléculas imunodominantes de Toxoplasma gondii para diagnóstico sorológico da toxoplasmose em ovinos e galinhas caipiras

Chapter I - The obligate intracellular parasite Toxoplasma gondii is the causative agent of toxoplasmosis, a disease that affects humans and generates economic losses in farm animals. When prevention fails disease refers to the diagnosis and subsequent treatment if the individual is diagnosed as positive. Therefore, the development of new accurate diagnostic tools for detecting T. gondii infection is a need in particular to determine the environmental source of infection which can result in more appropriate public health policies against different routes of infection and prevent potential damage that toxoplasmosis can cause when animals are infected. Chapter II - The domestic chicken (Gallus gallus domesticus) are considered epidemiological sentinels, still representing a major source of recombinant strains when predated by cats, it is common to find them with multiple infections. We evaluate the diagnostic potential of six synthetic peptides (SAG2Y, MIC1, M2AP, GRA10, ROP2 and ROP7) predicted in silico from tachyzoites immunodominant markers of T. gondii in samples from naturally infected chickens, comparing synthetic peptides with antigen total soluble (STAg). In general, our results demonstrated that reactivity rates and positivity for these peptides are similar to the STAg, and the ROP7 peptide and the combination of peptides MIC1+ROP2 have significant sensitivity, confirming them as potential diagnostic tools for the diagnosis of toxoplasmosis in chickens. Chapter III - Sheep (Ovis aries) are commonly infected with Toxoplasma gondii due to his eating habits. Infection in pregnant sheep can have serious consequences such as embryonic death, fetal resorption, mummification, and neonatal death. One concern regarding the infection in these animals is that the meat can be a source of contamination to humans and other carnivores. Therefore perform accurate diagnosis in these animals is of fundamental importance. In the present study we evaluated the potential of new synthetic peptides as a diagnostic tool. Synthetic peptides (SAG2Y, SRS52A, MIC14, GRA4, GRA10 and GRA15) were predicted in silico from immunodominant proteins of T. gondii. We determine the levels of IgG antibodies using sera obtained from two farms in the city of Uberlândia. Analyzing the results together, the peptide combination GRA10+GRA15 (Accuracy = 0,82) showed better characteristics compared with the other mixtures. This preparation could be better analyzed with an antigenic mixture potential use in the diagnosis of toxoplasmosis in sheep and other species.

Estudio genético HLA en poblaciones iraníes: epidemiología, antropología y farmacogenética

The HLA system is the most polymorphic genetic system described in humans. It consists of several closely linked loci encoding cell surface glycoproteins whose best known function is activating immune system response through antigenic presentation. New loci and new alleles have been described since the discovery of this genetic system and the presently available DNA typing and sequencing of these new alleles have increased the variety of HLA allelism. Due to the fact that HLA gene frequencies have a large degree of variability and a remarkable geographical correlation, HLA genes are an important and useful tool to infer genetic background and ethnical composition of modern human populations and also for tracing migration of ancient ones. In addition, certain combinations of contiguous alleles due to the strong linkage disequilibrium between HLA neighbouring loci show a characteristic frequency or are distinctive in many present day populations. Thus, HLA genetic system is a unique tool for studying the origin of relatively isolated groups, like Turkmen, Azeri and Kurd people, the populations under study, living in North Iran, in the surrounding area of Caspian Sea. Finally, HLA polymorphism is crucial for the compatibility between donor and receptor in organ transplantation and several HLA alleles have been linked to diseases and to response to drug treatments, which accomplishes relationships of certain variants with different pathologies treatment including AIDS. This is important in personalized treatments design. Turkmen could be descendants of Oghuz tribes from Seljuq branch coming from Transoxiana region (Central Asia) contemporarily to the foundation of the Seljuk Empire in 10th century AD. Conversely, this people could belong to another group within the Oghuz, arriving to Iran five centuries later. Migrations of this people were initially developed peacefully, being vassals of the Safavid Empire, and later by violent raids. They speak a language belonging to the Turkish-Oghuz group. In Iran, Turkmen live in Golestan province, mainly in Türkmensähra (“Turkmen plain”) area and amount 1.5 million people (2% of Iranian population). Most of this people are Sunni Muslims...

Over 30% of patients with splenic marginal zone lymphoma express the same immunoglobulin heavy variable gene: ontogenetic implications.

We performed an immunogenetic analysis of 345 IGHV-IGHD-IGHJ rearrangements from 337 cases with primary splenic small B-cell lymphomas of marginal-zone origin. Three immunoglobulin (IG) heavy variable (IGHV) genes accounted for 45.8% of the cases (IGHV1-2, 24.9%; IGHV4-34, 12.8%; IGHV3-23, 8.1%). Particularly for the IGHV1-2 gene, strong biases were evident regarding utilization of different alleles, with 79/86 rearrangements (92%) using allele (*)04. Among cases more stringently classified as splenic marginal-zone lymphoma (SMZL) thanks to the availability of splenic histopathological specimens, the frequency of IGHV1-2(*)04 peaked at 31%. The IGHV1-2(*)04 rearrangements carried significantly longer complementarity-determining region-3 (CDR3) than all other cases and showed biased IGHD gene usage, leading to CDR3s with common motifs. The great majority of analyzed rearrangements (299/345, 86.7%) carried IGHV genes with some impact of somatic hypermutation, from minimal to pronounced. Noticeably, 75/79 (95%) IGHV1-2(*)04 rearrangements were mutated; however, they mostly (56/75 cases; 74.6%) carried few mutations (97-99.9% germline identity) of conservative nature and restricted distribution. These distinctive features of the IG receptors indicate selection by (super)antigenic element(s) in the pathogenesis of SMZL. Furthermore, they raise the possibility that certain SMZL subtypes could derive from progenitor populations adapted to particular antigenic challenges through selection of VH domain specificities, in particular the IGHV1-2(*)04 allele.

Développement et évaluation pré-clinique de nouveaux vaccins inactivés contre l’influenza et suivi de l’évolution des souches virales A/H3N2

Les virus influenza de type A sont des pathogènes respiratoires causant des épidémies saisonnières et des pandémies de manière plus occasionnelles. Au cours d’une saison, 10 à 20 % de la population mondiale est touchée, ce qui constitue un problème majeur de santé publique. Les virus de sous-type A/H3N2 sont associés à une plus forte morbidité et mortalité que les virus de sous-type A/H1N1. La vaccination reste le moyen le plus efficace de contrôler les infections, cependant l’efficacité de ces vaccins est de courte durée et compromise en cas de non-appariemment entre les souches circulantes et vaccinales. La première partie de cette thèse a été consacrée à l’optimisation des vaccins inactivés A/H3N2 en testant de nouveaux adjuvants et de nouvelles voies d’administration chez la souris et le furet. Nous avons démontré que l’adjuvant AS25 semble prometteur pour le développement de vaccins plus efficaces. La seconde partie de cette thèse a été consacrée à suivre l’évolution moléculaire et antigénique des souches A/H3N2 circulantes au Québec entre 2009 et 2011. Notre conclusion est qu’il n’y a pas que le nombre de mutations dans la HA qui est important, en ce sens que la nature et la localisation de ces dernières jouent un rôle clé lors d’une dérive antigénique. Après avoir suivi les souches A/H3N2 sous pression immunitaire, nous avons suivi dans la troisième partie de cette thèse une souche A/H3N2 sous pression d’un nouvel antiviral; le laninamivir. Les antiviraux sont la première ligne de défense en cas de pandémie ou lors d’une épidémie lorsqu’il y a un mésappariemment entre les souches circulante et vaccinale. Notre conclusion est que la réplication de notre mutant est conservé in vitro mais non in vivo. Les différentes expériences effectuées au cours de cette thèse ont permis de suivre l’évolution des souches A/H3N2 et de mettre en œuvre de nouveaux moyens de prévention et de traitement.

Irrigação em Endodontia

Introdução e objectivos - O número de casos com reincidência de infecções póstratamento endodôntico, resultantes de uma incompleta desinfecção dos canais radiculares ainda é significativo e requer aperfeiçoamento. A complexidade do sistema de canais radiculares constitui o principal obstáculo à instrumentação e desinfecção dos mesmos em toda a sua extensão. A irrigação é um passo chave durante a instrumentação que possibilita a limpeza e desinfecção dos canais radiculares e através da qual, as bactérias, toxinas e os seus bio-produtos são eliminados. Este trabalho tem como objectivo descrever as várias técnicas de irrigação actualmente em uso na prática clínica. Materiais e métodos – Para elaboração deste trabalho de revisão foi efectuada uma pesquisa bibliográfica nos motores de busca: PubMed e Science Direct, utilizando como palavras-chave “endodontic irrigation”, “endodontic irrigants” e “sodium hypochloride”. Foram incluídos artigos desde 1915 a 2016 e a pesquisa foi realizada nos meses de Abril a Junho de 2016. Desenvolvimento - Um irrigante endodôntico deve responder a um conjunto de requisitos, entre os quais a eficácia na desinfecção total e definitiva dos canais radiculares, a eliminação da smear layer, deve ser não-antigénico, não tóxico e não carcinogénico e preservar a função do dente. O irrigante mais utilizado é o hipoclorito de sódio, mas alternativas têm sido amplamente utilizadas, tais como clorexidina, ácido etilenodiaminotetra-acético, e irrigantes combinados, tais como uma mistura de tetraciclina, um ácido e um detergente (MTAD), o Hypoclean® e o QMix®. Conlusão - Embora o NaOCl seja a solução que mais se aproxime do irrigante perfeito, a sua toxicidade representa um risco para o paciente e as suas limitações enquanto desinfectante são factores a considerar. A conjugação do NaOCl com outros irrigantes, bem como a formulação dos irrigantes compostos, tem vindo a melhorar a eficiência dos tratamentos endodônticos. No entanto, justifica-se o permanente investimento científico nesta área para que se reduza para níveis esporádicos os casos de reinfecção.