Harmonization of immune biomarker assays for clinical studies.

Assays that measure a patient's immune response play an increasingly important role in the development of immunotherapies. The inherent complexity of these assays and independent protocol development between laboratories result in high data variability and poor reproducibility. Quality control through harmonization--based on integration of laboratory-specific protocols with standard operating procedures and assay performance benchmarks--is one way to overcome these limitations. Harmonization guidelines can be widely implemented to address assay performance variables. This process enables objective interpretation and comparison of data across clinical trial sites and also facilitates the identification of relevant immune biomarkers, guiding the development of new therapies.

Direct binding of peptides to MHC class I molecules on living cells. Analysis at the single cell level.

To directly assess the binding of exogenous peptides to cell surface-associated MHC class I molecules at the single cell level, we examined the possibility of combining the use of biotinylated peptide derivatives with an immunofluorescence detection system based on flow cytometry. Various biotinylated derivatives of the adenovirus 5 early region 1A peptide 234-243, an antigenic peptide recognized by CTL in the context of H-2Db, were first screened in functional assays for their ability to bind efficiently to Db molecules on living cells. Suitable peptide derivatives were then tested for their ability to generate positive fluorescence signals upon addition of phycoerythrin-labeled streptavidin to peptide derivative-bearing cells. Strong fluorescent staining of Db-expressing cells was achieved after incubation with a peptide derivative containing a biotin group at the C-terminus. Competition experiments using the unmodified parental peptide as well as unrelated peptides known to bind to Kd, Kb, or Db, respectively, established that binding of the biotinylated peptide to living cells was Db-specific. By using Con A blasts derived from different H-2 congenic mouse strains, it could be shown that the biotinylated peptide bound only to Db among > 20 class I alleles tested. Moreover, binding of the biotinylated peptide to cells expressing the Dbm13 and Dbm14 mutant molecules was drastically reduced compared to Db. Binding of the biotinylated peptide to freshly isolated Db+ cells was readily detectable, allowing direct assessment of the relative amount of peptide bound to distinct lymphocyte subpopulations by three-color flow cytometry. While minor differences between peripheral T and B cells could be documented, thymocytes were found to differ widely in their peptide binding activity. In all cases, these differences correlated positively with the differential expression of Db at the cell surface. Finally, kinetic studies at different temperatures strongly suggested that the biotinylated peptide first associated with Db molecules available constitutively at the cell surface and then with newly arrived Db molecules.

"MIATA"-minimal information about T cell assays.

Immunotherapy, especially therapeutic vaccination, has a great deal of potential in the treatment of cancer and certain infectious diseases such as HIV (Allison et al., 2006; Fauci et al., 2008; Feldmann and Steinman, 2005). Numerous vaccine candidates have been tested in patients with a variety of tumor types and chronic viral diseases. Often, the best way to assess the clinical potential of these vaccines is to monitor the induced T cell response, and yet there are currently no standards for reporting these results. This letter is an effort to address this problem.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes.

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

Quantitative multiparameter assays to measure the effect of adjuvants on human antigen-specific CD8 T-cell responses.

Large numbers and functionally competent T cells are required to protect from diseases for which antibody-based vaccines have consistently failed (1), which is the case for many chronic viral infections and solid tumors. Therefore, therapeutic vaccines aim at the induction of strong antigen-specific T-cell responses. Novel adjuvants have considerably improved the capacity of synthetic vaccines to activate T cells, but more research is necessary to identify optimal compositions of potent vaccine formulations. Consequently, there is a great need to develop accurate methods for the efficient identification of antigen-specific T cells and the assessment of their functional characteristics directly ex vivo. In this regard, hundreds of clinical vaccination trials have been implemented during the last 15 years, and monitoring techniques become more and more standardized.

Kinetic studies of the effect of organic sulphides on the oxidation of other sulphides /

The rates of oxidation of three Organic sulphides viz. methyl phenyl sulphide, (P), p -me thoxyphenyl methyl sulphide (M) and methyl p-nitrophenyl sulphide (N). have been obtained in ethanol using MoO-(acac)- as catalyst and Bu OOH as the oxidizing agent. A Hammett plot gave a rho value of -2.1 and the activation energies for the oxidation of P, M and N were estimated to be 63.60, 40.12 and 197.46 Kj mol respectively. The effect of organic sulphide on the oxidation of another sulphide was also ascertained. Positive and negative deviations were observed from the expected slope.

Kinetic and mechanistic studies for the molybdenum- catalyzed oxidation of organic sulfides and olefins by t- DuO2H

This research was focussed on the effects of light, solvent and substituents in the molybdenum-catalyzed oxidation of phenylmethyl sulfides with t-Bu02H and on the effect of light in the molybdenum-catalyzed epoxidation of l-octene with t-Bu02H. It was shown that the Mo(CO)6-catalyzed oxidation of phenylmethyl sulfide with t-Bu02H~ at 35°C, proceeds 278 times faster underUV light than under laboratory lighting, whereas the Mo02(acac)2-catalyzed oxidation proceeds only 1.7 times faster under UV light than under normal laboratory lighting. The difference between the activities of both catalysts was explained by the formation of the catalytically active species, Mo(VI). The formation of the Mo(VI) species, from Mo(CO)6 was observed from the IR spectrum of Mo(CO)6 in the carbonyl region. The Mo(CO)6-catalyzed epoxidation of l-octene with t-Bu02H showed that the reaction proceeded 4.6 times faster under UV light than in the dark or under normal laboratory lighting; the rates of epoxidations were found to be the same in the dark and under normal laboratory lighting. The kinetics of the epoxidations of l-octene with t-Bu02H, catalyzed by Mo02(acac)2 were found to be complicated; after fast initial rates, the epoxidation rates decreased with time. The effect of phenylmethyl sulfide on the Mo(CO)6-catalyzed epoxidation of l-octene waS studied. It was shown that instead of phenylmethyl sulfide, phenylmethyl sulfone, which formed rapidly at 85°C, lowered the reaction rate. The epoxidation of l-octene was found to be 2.5 times faster in benzene than in ethanol. The substituent effect on the Mo02(acac)2-catalyzed oxidations of p-OH, p-CHgO, P-CH3' p-H, p-Cl, p-Br, p-CHgCO, p-HCO and P-N02 substituted phenylmethyl sulfides were studied. The oxidations followed second order kinetics for each case; first order dependency on catalyst concentration was also observed in the oxidation of p-CHgOPhSMeand PhSMe. It was found that electron-donating groups on the para position of phenylmethyl sulfide increased the rate of reaction, while electronwithdrawing groups caused the reaction rate to decrease. The reaction constants 0 were determined by using 0, 0- and 0* constants. The rate effects were paralleled by the activation energies for oxidation. The decomposition of t-Bu02H in the presence of M.o (CO)6, Mo02 (acac)2 and VO(acac)2 was studied. The rates of decomposition were found to be very small compared to the oxidation rates at high concentration of catalysis. The relative rates of the Mo02(acac)2-catalyzed oxidation of p-N02PhSMe by t-Bu02H in the presence of either p-CH30PhSMe or PhSMe clearly show that PhSMe and p-CHgOPhSMe act as co-catalysts in the oxidation of p-N02PhSMe. Benzene, mesity1ene and cyclohexane were used to determine the effect of solvent in the Mo02 (acac)2 and Mo(CO)6-catalyzed oxidation of phenylmethyl sulfide. The results showed that in the absence of hydroxylic solvent, a second molecule of t-Bu02H was involved in the transition state. The complexation of the solvent with the catalyst could not be explained.The oxidations of diphenyl sulfoxide catalyzed by VO(acac)2, Mo(CO)6 and Mo02(acac)2 showed that VO(acac)2 catalyzed the oxidation faster than Mo(CO)6 and Mo02 (acac)2_ Moreover, the Mo(CO)6-catalyzed oxidation of diphenyl sulfoxide proceeded under UV light at 35°C.

The regulation of oat coleoptile phosphoenolpyruvate carboxylase and malic enzyme by Hâ ½ and metabolites : kinetic evidence for and against a cytosolic pH-stat

Phosphoenolpyruvate carboxylase (PEPC) and malic enzyme activities in soluble protein extracts of Avena coleoptiles were investigated to determine whether their kinetics were consistent with a role in cytosol pH regulation. Malic enzyme activity was specific for NADP+ and Mn2+. Maximal labelled product formation from [14C]-substrates required the presence of all coenzymes, cofactors and substrates. Plots of rate versus malate concentration, and linear transformations there- 2 of, indicated typical Michaelis-Menten kinetics at non-saturating malate levels and substrate inhibition at higher malate levels. pH increases between 6.5 and 7.25 increased near-optimal activity, decreased the degree of substrate inhibition and the Kmapp(Mn2+) but did not affect the Vmax or Kmapp(malate). Transformed data of PEPC activity demonstrated non-linear plots indicative of non-Michaelian kinetics. pH increases between 7.0 and 7.6 increased the Vmax and decreased the Km app (Mg2+) but did not affect the Kmapp(PEP). Various carboxylic acids and phosphorylated sugars inhibited PEPC and malic enzyme activities, and these effects decreased with pH increases. Metabolite inhibited malic enzyme activity was non-competitive and resulted mainly from Mn2+ chelation. In contrast, metabolite inhibited PEPC activity was unique for each compound tested, being variously dependent on the PEP concentration and the pH employed. These results indicate that fluctuations in pH and metabolite levels affect PEPC and malic enzyme activities similarly and that 3 the in vitro properties of PEPC are consistent with its proposed role in a pH-stat, whereas the in vitro properties of the malic enzyme cannot be interpreted in terms of a role in pH regulation.

Kinetic and product studies for the oxidtion of organic sulfides and sulfoxides in the presence of transition metal complexes

Rates and products of the oxidation of diphenyl sulfide, phenyl methyl sulfide, p-chlorophenyl methyl sulfide and diphenyl sulfoxide have been determined. Oxidants included t-Bu02H alone, t-Bu02H plus molybdenum or vanadium catalysts and the molybdenum peroxo complex Mo0(02)2*HMPT. Reactions were chiefly carried out in ethanol at temperatures ranging from 20° to 65°C. Oxidation of diphenyl sulfide by t-Bu02H in absolute ethanol at 65°C followed second-order kinetics with k2 = 5.61 x 10 G M~1s"1, and yielded only diphenyl sulfoxide. The Mo(C0)g-catalyzed reaction gave both the sulfoxide and the sulfone with consecutive third-order kinetics. Rate = k3[Mo][t-Bu02H][Ph2S] + k^[Mo][t-Bu02H][Ph2S0], where log k3 = 12.62 - 18500/RT, and log k^ = 10.73 - 17400/RT. In the absence of diphenyl sulfide, diphenyl sulfoxide did not react with t-Bu02H plus molybdenum catalysts, but was oxidized by t-Bu02H-V0(acac)2. The uncatalyzed oxidation of phenyl methyl sulfide by t-Bu02H in absolute ethanol at 65°C gave a second-order rate constant, k = 3.48 x 10~"5 M^s""1. With added Mo(C0)g, the product was mainly phenyl methyl sulfoxide; Rate = k3[Mo][t-Bu02H][PhSCH3] where log k3 = 22.0 - 44500/RT. Both diphenyl sulfide and diphenyl sulfoxide react readily with the molybdenum peroxy complex, Mo0(02)2'HMPT in absolute ethanol at 35°C, yielding diphenyl sulfone. The observed features are mainly in agreement with the literature on metal ion-catalyzed oxidations of organic compounds by hydroperoxides. These indicate the formation of an active catalyst and the complexation of t-Bu02H with the catalyst. However, the relatively large difference between the activation energies for diphenyl sulfide and phenyl methyl sulfide, and the non-reactivity of diphenyl sulfoxide suggest the involvement of sulfide in the production of an active species.

Hyperosmotic Stress and the Impact on Metabolite Formation and Redox Balance in Saccharomyces cerevisiae and Saccharomyces bayanus strains

Wine produced using an appassimento-type process represents a new and exciting innovation for the Ontario wine industry. This process involves drying grapes that have already been picked from the vine, which increases the sugar content due to dehydration and induces a variety of changes both within and on the surface of the grapes. Increasing sugar contents in musts subject wine yeast to conditions of high osmolarity during alcoholic fermentations. Under these conditions, yeast growth can be inhibited, target alcohol levels may not be attained and metabolic by-products of the hyperosmotic stress response, including glycerol and acetic acid, may impact wine composition. The further metabolism of acetic acid to acetylCoA by yeast facilitates the synthesis of ethyl acetate, a volatile compound that can also impact wine quality if present in sufficiently high concentrations. The first objective of this project was to understand the effect of yeast strain and sugar concentration on fermentation kinetics and metabolite formation, notably acetic acid and ethyl acetate, during fermentation in appassimento-type must. Our working hypotheses were that (1) the natural isolate Saccharomyces bayanus would produce less acetic acid and ethyl acetate compared to Saccharomyces cerevisiae strain EC-1118 fermenting the high and low sugar juices; (2) the wine produced using the appassimento process would contain higher levels of acetic acid and lower levels of ethyl acetate compared to table wine; (3) and the strains would be similar in the kinetic behavior of their fermentation performances in the high sugar must. This study determined that the S. bayanus strain produced significantly less acetic acid and ethyl acetate in the appassimento wine and table wine fermentations. Differences in acetic acid and ethyl acetate production were also observed within strains fermenting the two sugar conditions. Acetic acid production was higher in table wine fermented by S. bayanus as no acetic acid was produced in appassimento-style wine, and 1.4-times higher in appassimento wine fermented by EC-1118 over that found in table wine. Ethyl acetate production was 27.6-times higher in table wine fermented by S. bayanus, and 5.2-times higher by EC-1118, compared to that in appassimento wine. Sugar utilization and ethanol production were comparable between strains as no significant differences were determined. The second objective of this project was to bring a method in-house for measuring the concentration of pyridine nucleotides, NAD+, NADP+, NADH and NADPH, in yeast cytosolic extract. Development of this method is of applicative interest for our lab group as it will enable the redox balance of the NAD+/ NADH and NADP+/ NADPH systems to be assessed during high sugar fermentations to determine their respective roles as metabolic triggers for acetic acid production. Two methods were evaluated in this study including a UV-endpoint method using a set of enzymatic assay protocols outlined in Bergmeyer (1974) and a colorimetric enzyme cycling method developed by Sigma-Aldrich® using commercial kits. The former was determined to be limited by its low sensitivity following application to yeast extract and subsequent coenzyme analyses, while the latter was shown to exhibit greater sensitivity. The results obtained from the kits indicated high linearity, accuracy and precision of the analytical method for measuring NADH and NADPH, and that it was sensitive enough to measure the low coenzyme concentrations present in yeast extract samples. NADtotal and NADPtotal concentrations were determined to be above the lower limit of quantification and within the range of the respective calibration curves, making this method suitable for our research purposes.

Lipase-Mediated Enzymatic Catalysis For The Synthesis of New Chiral Polymers

Immobilized lipase B from Candida antarctica (N435) was investigated as a potential biocatalyst to generate silicone-based chiral polymers from monomers derived from the enzymatic dihydroxylation of bromobenzene. Several conditions and parameters have been investigated for this purpose and lipase transesterification preference to each of the free secondary alcohols in the chiral monomers was documented. The N435 was challenged with a series of substrates where the free alcohol moieties were systematically protected in order to study the substrate preference(s) for the transesterification reactions.

Standardization of cytokine flow cytometry assays

Affiliation: Faculté de médecine, Université de Montréal & CANVAC

Études Structurales par Résonance Magnétique Nucléaire (RMN) du Site Actif du Ribozyme VS de Neurospora.

Nous étudions le ribozyme VS de Neurospora, en tant que système modèle, pour augmenter nos connaissances sur la relation entre la structure et la fonction chez les ARNs, ainsi que pour mieux comprendre le mécanisme de clivage de ce ribozyme. Il a été proposé précédemment que la boucle interne A730 dans la tige-boucle VI (SLVI) contient le site actif du ribozyme et lie un ou plusieurs ions métalliques qui pourraient participer au mécanisme réactionnel. Nous avons déterminé par spectroscopie RMN la structure de la tige-boucle SLVI contenant la boucle A730 afin d’éclaircir ce mécanisme. La structure obtenue est en accord avec les études biochimiques antérieures et présente un ou plusieurs sites de liaison au magnésium associé à la boucle interne. Suite à des études de cinétique et de mutagenèse, il a été proposé qu’une adénine localisée dans le site actif, A756, participe à la catalyse par acide/base générale. Des études de pH effectuées précédemment ont identifié un pKa catalytique (5.2-5.8) qui correspond probablement à l’équilibre de protonation du A756. À l’aide de méthodes utilisant le carbone-13, nous avons identifié un pKa modifié appartenant au A756, ce qui supporte le rôle de ce résidu dans la catalyse par acide/base générale. Les études structurales présentées ici aident donc à augmenter notre compréhension du mécanisme de clivage chez le ribozyme VS.

Étude structurale de la fructoselysine 6-kinase d’Escherichia coli : reconnaissance de substrats et mécanisme enzymatique

Quelques enzymes sont connus pour déglyquer les kétoamines résultants de la réaction de Maillard entre des sucres et des amines primaires. Il a été démontré qu’Escherichia coli possède un opéron afin de métaboliser la fructoselysine. La fructoselysine 6-kinase, de la famille des PfkB, initie le processus de déglycation permettant l’utilisation ultérieure du glucose-6-P par la bactérie. La résolution de la structure de la FL6K par cristallographie et diffraction des rayons X a permis d’identifier son site actif en présence d’ATP, d’ADP et d’AMP-PNP. La modélisation de la fructoselysine au site actif de la kinase a permis d’identifier des résidus pouvant être importants pour sa liaison et son mécanisme enzymatique. De plus, les résultats de cinétique suggèrent que le mécanisme utilisé par la FL6K semble passer par un état ternaire de type SN2. Des modifications structurales à la FL6K pourraient permettre d’augmenter la taille des substrats afin de permettre ultimement la déglycation de protéines.

New high through-put assays for detecting transglutaminase activity

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal