A simple and rapid method for quantification of hapten specific antibodies

A sensitive and simple method for quantification of antibodies against small molecules is described using DNP-lysozyme as the enzyme conjugate. The anti-DNP antiserum was raised against DNP-bovin serum albumin conjugate. Anti-DNP antibody or its monovalent fragment (Fab) reduced the enzyme activity of DNP-lysozyme conjugate in a concentration-dependent manner. The inhibition of enzyme activity is a specific measure of the antibody and Fab content of the sample. The specificity of the reaction was assessed by reduction of antibody-induced inhibition by DNP-lysine. The ability of DNP-lysine to reduce the antibody-induced inhibition of DNP-lysozyme activity also makes possible a sensitive assay for DNP-lysine.

Systèmes vésiculaires colloïdaux pour la vectorisation de la 1-β-D-arabinofuranosylcytosine

La 1-β-D-arabinofuranosylcytosine (ara-C) demeure l’agent anticancéreux principalement utilisé dans le traitement de la leucémie myéloblastique aiguë (LMA), malgré sa dégradation et son élimination rapide après une administration parentérale. Son encapsulation dans des vecteurs pharmaceutiques, majoritairement des liposomes, a permis de surmonter ces inconvénients. L’objectif général de ce projet de doctorat était de développer deux systèmes à libération prolongée, à base de phospholipides, de cholestérol et de poly(éthylène glycol) (PEG) afin d’encapsuler l’ara-C et ultimement, d’améliorer son efficacité dans le traitement de la LMA. Des Sphérulites® (vésicules multilamellaires d’un type particulier) ont d’abord été étudiées pour leur forte capacité d’encapsulation, due à leur mode de préparation. Par la suite, une formulation liposomale capable, d’une part de cibler spécifiquement les cellules leucémiques et, d’autre part, de promouvoir la libération intracellulaire de l’ara-C grâce à sa sensibilité au pH, a été mise au point. Les deux formulations se devaient d’avoir un faible diamètre, une stabilité en présence de fluides biologiques et des temps de circulation prolongés chez l’animal. Une préparation de Sphérulites®, composée de Phospholipon 90G, de Solutol HS15 et de cholestérol, a permis d’obtenir des vésicules de 300 nm de diamètre. Un dérivé lipidique de PEG a pu être fixé à leur surface, sans modifier la disposition concentrique des lamelles, ni changer leur stabilité. Les Sphérulites® PEGylées ont été chargées d’ara-C et injectées chez le rat par la voie intraveineuse. Elles ont démontré des temps de circulation significativement prolongés comparativement aux Sphérulites® sans PEG. Cependant, l’ara-C s’est retrouvée éliminée de la circulation sanguine très rapidement, révélant une libération précoce du principe actif à partir de ces vésicules. Les liposomes sensibles au pH (~150 nm) ont été obtenus suite à l’insertion d’un copolymère à base de dioctadécyle, de N-isopropylacrylamide (NIPAM) et d’acide méthacrylique. L’anticorps anti-CD33, soit complet soit son fragment Fab’, a été fixé à la surface des liposomes afin de cibler les cellules leucémiques. Les essais in vitro ont démontré la spécificité de la formulation pour différentes cellules leucémiques (CD33+), sa stabilité en présence de protéines plasmatiques et la libération intracellulaire d’un marqueur fluorescent et de l’ara-C. Enfin, des études menées chez la souris saine et immunodéprimée inoculée de cellules HL60 ont montré que la formulation exposant le fragment Fab’ possédait un profil pharmacocinétique et une biodistribution semblables à ceux des liposomes contrôles non-ciblés. L’encapsulation de l’ara-C a permis d’améliorer grandement ses temps de circulation après une administration intraveineuse. Cependant, bien que les immunoliposomes ont permis de prolonger la survie des souris leucémiques comparativement à l’ara-C libre, l’addition du polymère sensible au pH n’a pas permis d’apporter de réel avantage à la formulation lorsque administrée in vivo. Les résultats obtenus dans ce travail de thèse ont, dans un premier temps, mis en évidence que les Sphérulites® pourraient s’avérer utiles dans la vectorisation d’agents anticancéreux si leur capacité à retenir le principe actif in vivo était améliorée. Dans un second temps, les données présentées avec les immunoliposomes suggèrent qu’ils pourraient apporter un bénéfice notable dans le traitement de la LMA.

Transport of anti-IL-6 antigen binding fragments into cartilage and the effects of injury

The efficacy of biological therapeutics against cartilage degradation in osteoarthritis is restricted by the limited transport of macromolecules through the dense, avascular extracellular matrix. The availability of biologics to cell surface and matrix targets is limited by steric hindrance of the matrix, and the microstructure of matrix itself can be dramatically altered by joint injury and the subsequent inflammatory response. We studied the transport into cartilage of a 48 kDa anti-IL-6 antigen binding fragment (Fab) using an in vitro model of joint injury to quantify the transport of Fab fragments into normal and mechanically injured cartilage. The anti-IL-6 Fab was able to diffuse throughout the depth of the tissue, suggesting that Fab fragments can have the desired property of achieving local delivery to targets within cartilage, unlike full-sized antibodies which are too large to penetrate beyond the cartilage surface. Uptake of the anti-IL-6 Fab was significantly increased following mechanical injury, and an additional increase in uptake was observed in response to combined treatment with TNFα and mechanical injury, a model used to mimic the inflammatory response following joint injury. These results suggest that joint trauma leading to cartilage degradation can further alter the transport of such therapeutics and similar-sized macromolecules.

Development of a recombinant Fab-fragment based electrochemical immunosensor for deoxynivalenol detection in food samples

A reliable and cost-effective electrochemical method for the detection of deoxynivalenol (DON) in cereals and cereal-based food samples based on the use of a novel anti-DON Fab fragment is presented. The analytical system employed, Enzyme-Linked-Immunomagnetic-Electrochemical (ELIME) assay, is based on the use of immunomagnetic beads (IMBs) coupled with eight magnetized screen-printed electrodes (8-mScPEs) as electrochemical transducers.

Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab fragment of a human IgM antibody: Structural basis for recognition of B-cell receptors and superantigen activity

Staphylococcus aureus produces a virulence factor, protein A (SpA), that contains five homologous Ig-binding domains. The interactions of SpA with the Fab region of membrane-anchored Igs can stimulate a large fraction of B cells, contributing to lymphocyte clonal selection. To understand the molecular basis for this activity, we have solved the crystal structure of the complex between domain D of SpA and the Fab fragment of a human IgM antibody to 2.7-Å resolution. In the complex, helices II and III of domain D interact with the variable region of the Fab heavy chain (VH) through framework residues, without the involvement of the hypervariable regions implicated in antigen recognition. The contact residues are highly conserved in human VH3 antibodies but not in other families. The contact residues from domain D also are conserved among all SpA Ig-binding domains, suggesting that each could bind in a similar manner. Features of this interaction parallel those reported for staphylococcal enterotoxins that are superantigens for many T cells. The structural homology between Ig VH regions and the T-cell receptor Vβ regions facilitates their comparison, and both types of interactions involve lymphocyte receptor surface remote from the antigen binding site. However, T-cell superantigens reportedly interact through hydrogen bonds with T-cell receptor Vβ backbone atoms in a primary sequence-independent manner, whereas SpA relies on a sequence-restricted conformational binding with residue side chains, suggesting that this common bacterial pathogen has adopted distinct molecular recognition strategies for affecting large sets of B and T lymphocytes.

Crystal structure of the complex of a catalytic antibody Fab fragment with a transition state analog: structural similarities in esterase-like catalytic antibodies.

The x-ray structure of the complex of a catalytic antibody Fab fragment with a phosphonate transition-state analog has been determined. The antibody (CNJ206) catalyzes the hydrolysis of p-nitrophenyl esters with significant rate enhancement and substrate specificity. Comparison of this structure with that of the uncomplexed Fab fragment suggests hapten-induced conformational changes: the shape of the combining site changes from a shallow groove in the uncomplexed Fab to a deep pocket where the hapten is buried. Three hydrogen-bond donors appear to stabilize the charged phosphonate group of the hapten: two NH groups of the heavy (H) chain complementarity-determining region 3 (H3 CDR) polypeptide chain and the side-chain of histidine-H35 in the H chain (His-H35) in the H1 CDR. The combining site shows striking structural similarities to that of antibody 17E8, which also has esterase activity. Both catalytic antibody ("abzyme") structures suggest that oxyanion stabilization plays a significant role in their rate acceleration. Additional catalytic groups that improve efficiency are not necessarily induced by the eliciting hapten; these groups may occur because of the variability in the combining sites of different monoclonal antibodies that bind to the same hapten.

Modelling the effects of bone fragment contact in fracture healing

The fracture healing process is modulated by the mechanical environment created by imposed loads and motion between the bone fragments. Contact between the fragments obviously results in a significantly different stress and strain environment to a uniform fracture gap containing only soft tissue (e.g. haematoma). The assumption of the latter in existing computational models of the healing process will hence exaggerate the inter-fragmentary strain in many clinically-relevant cases. To address this issue, we introduce the concept of a contact zone that represents a variable degree of contact between cortices by the relative proportions of bone and soft tissue present. This is introduced as an initial condition in a two-dimensional iterative finite element model of a healing tibial fracture, in which material properties are defined by the volume fractions of each tissue present. The algorithm governing the formation of cartilage and bone in the fracture callus uses fuzzy logic rules based on strain energy density resulting from axial compression. The model predicts that increasing the degree of initial bone contact reduces the amount of callus formed (periosteal callus thickness 3.1mm without contact, down to 0.5mm with 10% bone in contact zone). This is consistent with the greater effective stiffness in the contact zone and hence, a smaller inter-fragmentary strain. These results demonstrate that the contact zone strategy reasonably simulates the differences in the healing sequence resulting from the closeness of reduction.

Campylobacter jejuni and campylobacter coli genotyping by high-resolution melting analysis of a flaA fragment

The highly variable flagellin-encoding flaA gene has long been used for genotyping Campylobacter jejuni and Campylobacter coli. High-resolution melting (HRM) analysis is emerging as an efficient and robust method for discriminating DNA sequence variants. The objective of this study was to apply HRM analysis to flaA-based genotyping. The initial aim was to identify a suitable flaA fragment. It was found that the PCR primers commonly used to amplify the flaA short variable repeat (SVR) yielded a mixed PCR product unsuitable for HRM analysis. However, a PCR primer set composed of the upstream primer used to amplify the fragment used for flaA restriction fragment length polymorphism (RFLP) analysis and the downstream primer used for flaA SVR amplification generated a very pure PCR product, and this primer set was used for the remainder of the study. Eighty-seven C. jejuni and 15 C. coli isolates were analyzed by flaA HRM and also partial flaA sequencing. There were 47 flaA sequence variants, and all were resolved by HRM analysis. The isolates used had previously also been genotyped using single-nucleotide polymorphisms (SNPs), binary markers, CRISPR HRM, and flaA RFLP. flaAHRManalysis provided resolving power multiplicative to the SNPs, binary markers, and CRISPR HRM and largely concordant with the flaA RFLP. It was concluded that HRM analysis is a promising approach to genotyping based on highly variable genes.

FAB-MAP + RatSLAM : appearance-based SLAM for multiple times of day

Appearance-based mapping and localisation is especially challenging when separate processes of mapping and localisation occur at different times of day. The problem is exacerbated in the outdoors where continuous change in sun angle can drastically affect the appearance of a scene. We confront this challenge by fusing the probabilistic local feature based data association method of FAB-MAP with the pose cell filtering and experience mapping of RatSLAM. We evaluate the effectiveness of our amalgamation of methods using five datasets captured throughout the day from a single camera driven through a network of suburban streets. We show further results when the streets are re-visited three weeks later, and draw conclusions on the value of the system for lifelong mapping.

Augmenting RatSLAM using FAB-MAP-based visual data association

This paper investigates the use of the FAB-MAP appearance-only SLAM algorithm as a method for performing visual data association for RatSLAM, a semi-metric full SLAM system. While both systems have shown the ability to map large (60-70km) outdoor locations of approximately the same scale, for either larger areas or across longer time periods both algorithms encounter difficulties with false positive matches. By combining these algorithms using a mapping between appearance and pose space, both false positives and false negatives generated by FAB-MAP are significantly reduced during outdoor mapping using a forward-facing camera. The hybrid FAB-MAP-RatSLAM system developed demonstrates the potential for successful SLAM over large periods of time.

Fragment-based version management for repositories of business process models

As organizations reach higher levels of Business Process Management maturity, they tend to accumulate large collections of process models. These repositories may contain thousands of activities and be managed by different stakeholders with varying skills and responsibilities. However, while being of great value, these repositories induce high management costs. Thus, it becomes essential to keep track of the various model versions as they may mutually overlap, supersede one another and evolve over time. We propose an innovative versioning model and associated storage structure, specifically designed to maximize sharing across process model versions, and to automatically handle change propagation. The focal point of this technique is to version single process model fragments, rather than entire process models. Indeed empirical evidence shows that real-life process model repositories have numerous duplicate fragments. Experiments on two industrial datasets confirm the usefulness of our technique.

Fragment-based version management for repositories of business process models

As organizations reach higher levels of Business Process Management maturity, they tend to accumulate large collections of process models. These repositories may contain thousands of activities and be managed by different stakeholders with varying skills and responsibilities. However, while being of great value, these repositories induce high management costs. Thus, it becomes essential to keep track of the various model versions as they may mutually overlap, supersede one another and evolve over time. We propose an innovative versioning model, and associated storage structure, specifically designed to maximize sharing across process models and process model versions, reduce conflicts in concurrent edits and automatically handle controlled change propagation. The focal point of this technique is to version single process model fragments, rather than entire process models. Indeed empirical evidence shows that real-life process model repositories have numerous duplicate fragments. Experiments on two industrial datasets confirm the usefulness of our technique.

A fragment of the LG3 peptide of endorepellin is present in the urine of physically active mining workers : a potential marker of physical activity

Biomarker analysis has been implemented in sports research in an attempt to monitor the effects of exertion and fatigue in athletes. This study proposed that while such biomarkers may be useful for monitoring injury risk in workers, proteomic approaches might also be utilised to identify novel exertion or injury markers. We found that urinary urea and cortisol levels were significantly elevated in mining workers following a 12 hour overnight shift. These levels failed to return to baseline over 24h in the more active maintenance crew compared to truck drivers (operators) suggesting a lack of recovery between shifts. Use of a SELDI-TOF MS approach to detect novel exertion or injury markers revealed a spectral feature which was associated with workers in both work categories who were engaged in higher levels of physical activity. This feature was identified as the LG3 peptide, a C-terminal fragment of the anti-angiogenic / anti-tumourigenic protein endorepellin. This finding suggests that urinary LG3 peptide may be a biomarker of physical activity. It is also possible that the activity mediated release of LG3 / endorepellin into the circulation may represent a biological mechanism for the known inverse association between physical activity and cancer risk / survival.

The phylogeny of Ureaplasma urealyticum based on the mba gene fragment

Sequencing of mba gene fragments of reference strains of Ureaplasma urealyticum serovars 1, 3, 6, 14, in addition to 33 clinical U. urealyticum isolates is reported. A phylogenetic tree deduced from an alignment of these sequences clearly demonstrates two major clusters (confidence limit 100%), which equate to the parvo and T960 biovars, and five types which we have designated mba 1, 3, 6, 8 and X. These relationships are supported by bootstrap analysis. Polymorphisms within the mba fragment of types mba 1, 3, and 6 were used to define nine subtypes (mba 1a, 1b, 3a, 3b, 3c, 3d, 3e, 6a, and 6b) thus facilitating high resolution typing of U. urealyticum. Inclusion of the reference strains for serovars 1, 3, 6, and 8 in the mba typing scheme showed that the results of this analysis are broadly consistent with currently accepted serotyping. In addition a ure gene fragment from nine of the clinical isolates was amplified and sequenced. Comparisons of the sequences clearly distinguished the two biovars of U. urealyticum; however this fragment was invariant within the parvo biovar. This study has shown that the sequence of the mba can reveal the fine details of the relationships between U. urealyticum isolates and also supports the significant evolutionary gap between the two biovars.