High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

Quantitative analysis of postnatal neurogenesis and neuron number in the macaque monkey dentate gyrus

The dentate gyrus is one of only two regions of the mammalian brain where substantial neurogenesis occurs postnatally. However, detailed quantitative information about the postnatal structural maturation of the primate dentate gyrus is meager. We performed design-based, stereological studies of neuron number and size, and volume of the dentate gyrus layers in rhesus macaque monkeys (Macaca mulatta) of different postnatal ages. We found that about 40% of the total number of granule cells observed in mature 5-10-year-old macaque monkeys are added to the granule cell layer postnatally; 25% of these neurons are added within the first three postnatal months. Accordingly, cell proliferation and neurogenesis within the dentate gyrus peak within the first 3 months after birth and remain at an intermediate level between 3 months and at least 1 year of age. Although granule cell bodies undergo their largest increase in size during the first year of life, cell size and the volume of the three layers of the dentate gyrus (i.e. the molecular, granule cell and polymorphic layers) continue to increase beyond 1 year of age. Moreover, the different layers of the dentate gyrus exhibit distinct volumetric changes during postnatal development. Finally, we observe significant levels of cell proliferation, neurogenesis and cell death in the context of an overall stable number of granule cells in mature 5-10-year-old monkeys. These data identify an extended developmental period during which neurogenesis might be modulated to significantly impact the structure and function of the dentate gyrus in adulthood.

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.

Bone properties and skeletal maturity in adolescent males, as assessed by quantitative ultrasound

ABSTRACT Background: Previous studies have implied that weight-bearing, intense and prolonged physical activities optimize bone accretion during the grow^ing years. The majority of past inquiries have used dual-energy X-ray absorptiometry (DXA) to examine bone strength and hand-wrist radiography to determine skeletal maturity in children. Recently, quantitative ultrasound (QUS) technologies have been developed to examine bone properties and skeletal maturity in a safe, noninvasive and cost-effective manner. Objective: The purpose of this study was to compare bone properties and skeletal maturity in competitive male child and adolescent athletes with minimallyactive, age-matched controls, using QUS technology. >. Methods: In total, 224 males were included in the study. The 115 pre-pubertal boys aged 10-12 years consisted of control, minimally-active children (n=34), soccer players (n=26), gymnasts (n=25) and hockey players (n=30). In addition, the 109 late-pubertal boys aged 14-16 years consisted of control, minimally-active adolescents (n=31), soccer players (n=30), gymnasts (n=17) and hockey players (n=31). The athletic groups were elite level players that predominantly trained year-round. Physical activity, nutrition and sports participation were assessed with various questionnaires. Anthropometries, such as height, weight and relative body fat percentage (BF%) were assessed using standard measures. Skeletal strength and age were evaluated using bone QUS. Lastly, salivary testosterone (sT) concentration was measured using Radioimmunoassay (RIA). Results: Within each age group, there were no significant differences between the activity groups in age and pubertal stage. An age effect was apparent in all variables, as expected. A sport effect was noted in all physical characteristics: the child and adolescent gymnasts were shorter and lighter than other sports groups. Adiposity was greater in the controls and in the hockey players. All child subjects were pubertal stage (fanner) I or II, while adolescent subjects were pubertal stage IV or V. There were no differences in daily energy and mineral intakes between sports groups. In both age groups, gymnasts had a higher training volume than other athletic groups. Bone speed of sound (50s) was higher in adolescents compared with the children. Gymnasts had signifieantly higher radial 50S than controls, hockey and soccer players in both age cohorts. Hockey athletes also had higher radial 50S than controls and soccer players in the child and adolescent groups, respectiyely. Child gymnasts and soccer players had greater tibial 50S compared with the hockey players and control groups. Likewise, adolescent gymnasts and soccer players had higher tibial SoS compared with the control group. No interaction was apparent between age and type of activity in any of the bone measures. » Lastly, maturity as assessed by sT and secondary sex characteristics (Tanner stage) was not different between sports group within each age group. Despite the similarity in chronological age, androgen levels and sexual maturity, differences between activity groups were noted in skeletal maturity. In the younger group, hockey players had the highest bone age while the soccer players had the lowest bone age. In the adolescent group, gymnasts and hockey players were characterized by higher skeletal maturity compared with controls. An interaction between the age and sport type effects was apparent in skeletal maturity, reflecting the fact that among the children, the soccer players were significantly less mature than the rest of the groups, while in the adolescents, the controls were the least skeletally mature. Summary and Conclusions: In summary, radial and tibial SOS are enhanced by the unique loading pattern in each sport (i.e, upper and lower extremities in gymnastics, lower extremities in soccer), with no cumulative effect between childhood and adolescence. That is, the effect of sport participation on bone SOS was apparent already among the young athletes. Enhanced bone properties among athletes of specific sports suggest that participation in these sports can improve bone strength and potential bone health.

Synthesis of isotope-labelled methoxypyrazine compounds as internal standards and quantitative determination of aroma methoxypyrazines in water and wines by solid-phase extraction with isotope dilution-GC-MS /

An efficient way of synthesizing the deuterium labelled analogues of three methoxypyrazine compounds: 2-d3-methoxy-3-isopropylpyrazine, 2-d3-methoxy-3- isobutylpyrazine, and 2-d3-methoxy-3-secbutylpyrazine, has been developed. To confirm that the deuterium labels had been incorporated into the expected positions in the molecules synthesized, the relevant characterization by NMR, HRMS and GC/MS analysis was conducted. Another part of this work involved quantitative determination of methoxypyrazines in water and wines. Solid-phase extraction (SPE) proved to be a suitable means for the sample separation and concentration prior to GC/MS analysis.Such factors as the presence of ethanol, salt, and acid have been investigated which can influence the recovery by SPE for the pyrazines from the water matrix. Significantly, in this work comparatively simple fractional distillation was attempted to replace the conventional steam distillation for pre-concentrating a sample with a relatively large volume prior to SPE. Finally, a real wine sample spiked with the relevant isotope-labelled methoxypyrazines was quantitatively analyzed, revealing that the wine with 10 beetles per litre contained 138 ppt of 2-methoxy-3-isopropylpyrazine. Interestingly, we have also found that 2-methoxy-3-secbutylpyrazine exhibits an extremely low detection limit in GC/MS analysis compared with the detection limit of the other two methoxypyrazines: 2- methoxy-3-isopropylpyrazine and 2-methoxy-3-isobutylpyrazine.

Composition analysis of high-Tc superconducting thin films by quantitative x-ray fluorescence

A method is presented for determining the composition of thin films containing the elements Bi, Sr, Br, Cu, and Ca. Quantitative x-ray fluorescence (XRF) consisting of radioactive sources (secondary foil excitor 241Am-Mo source and 55Pe source), a Si(Li) detector, and a multichannel analyzer were employed. The XRF system was calibrated by using sol gel thin films of known element composition and also by sputtered thin films analyzed by the conventional Rutherford Back Scattering (RBS). The XRF system has been used to assist and optimize the sputter target composition required to produce high-Tc BiSrCaCuO films with the desired metal composition.

Studies on the insecticide - nematicide-oxamyl and its quantitative determination by gas chromatographic method

Ox amyl , an insecticide/nematicide with the chemical name; methyl ~'. ~·-dimethyl-~-(methylcarbamoyl)oxy-l-thiooxamimidate, and its major degradation compound; oxime or oximino compound, methyl ~',~'-dimethyl-~-hydroxy-l-thiooxamimidate were studied in this work. NMR and mass spectrometry were utilized in the structural studies. An attempt was made to explain the fragmentation patterns of some major peaks in the mass spectra of oxamyl and oxime. A new gas chromatographic method for the detection and determination of submicrogram levels of intact oxamyl using a electron-capture detector was developed. The principle of this method is to produce a derivative which is highly sensitive to an electron-capture detector. The derivative described is dinitrophenyl methylamine( DNPMA ) • Experimental conditions such as pH , reaction temperature , reaction time, the amount of reagent ( Dinitrofluaro benzene) etc. were thoroughly investigated and optimized. This method was successfully applied to the determination of oxamyl residues in tobacco leaves and soil. Throughout this J9D:oject , thin layer chromatography was also used in the separation:and clean up of oxamyl and oxime samples.

Exploring Chinese-Canadians' perspectives on health : a quantitative study

Chinese have unique perspectives on health and illness, which is mostly umecognized by western medicine. Immigration may contribute to problems with health consultations, inconvenience, and dissatisfaction. As the largest visible minority in Canada, Chinese- Canadians' perspectives on health should be studied in order to help Chinese immigrants adapt to a new health-care and health-promotion system, and keep them healthy. A quantitative questionnaire was designed based on the findings from a pilot study and previous literature. A hundred participants were recruited from Toronto, Vancouver, Halifax, and St. Catharines. Descriptive analysis and correlation analysis were used to investigate the structure of the variables. Findings indicated that most oftheir attitudes and corresponding practices to the different health aspects were positive. The relation between dietary practices and attitude was only found in small cities. Their attitudes were impacted by their length of stay in Canada. Their attitudes to regularly timed meals and psychological consultation were related to their acculturation level, as was the regularity of their practice of dental flossing. Their self-evaluated general health levels were also found to be affected by their medical history, education level, feeling to talk about • sexual health, and smoking, particularly in the male subjects of the study. In conclusion, they realized that each health aspect w~s important to their health. However, their practices did not bear a strong relation to their beliefs. Traditional thoughts about health reseeded with time. Acculturation level did not affect most of their attitudes or practices. Under pressure, the priority of the daily health practices decreased. Older persons, those with low incomes, lower education levels or families under stress need to pay more attention to their health level. In-depth future research was recommended.

A Quantitative Study of Social Capital Components, Self-Reported Health Status and Social Determinants of Health

This quantitative descriptive co-relational study used telephone survey interviews and stratified random sampling to collect data related to Social Capital (SC) and its components (trust and safety, reciprocity, civic engagement and collective action) and selected determinants of health variables in Niagara Region, Canada. Among the four components of social capital, trust and safety levels were highest among all participants (m=5.42, SD=1.0), with community engagement yielding the lowest mean score for the sample (m=1.93, SD=.8). Reciprocity had the strongest association with all other components of SC (r=0.51). Those most likely to report low levels of SC and health were unattached and low-income females. Males were more likely to report higher trust and safety levels and higher levels of self-rated health. In this study, a linear relationship between self-reported health status and SC was not found. Marital and employment status were associated with differences in mean scores of SC and self-reported health.

A Quantitative and Qualitative Inquiry Into Positive Involvement Trends of Contemporary Fathers and Influence of Parenting Programs

Parent education programs offered by a variety of public health services are effective support and knowledge resources that enhance positive parenting competencies in early childhood and adolescence. However, parenting education programs are less effective and encompass fewer benefits for fathers in comparison to mothers. This study sought to investigate trends of paternal involvement in early childhood and to compare the influence of parenting education programs on paternal involvement and conceptualization of fathers. A sample of 52 fathers, between the ages of 19 to 54, with children 6 years old and younger completed an electronic or hard copy version of a survey questionnaire reporting on their fathering and experiences as a dad. Findings indicate the sample of Canadian fathers self-reported high levels of paternal involvement, including many who favoured play-based interactions with their children. Although no significant difference in levels of involvement was noted between fathers who had versus those who had not previously participated in a parenting education program, half of the Canadian fathers indicated that supports are needed to strengthen their role as fathers. Results suggest that future initiatives to strengthen parent education program services available in Canada should specifically consider the father’s role.

The Exchange Rate in a Dynamic-Optimizing Current Account Model with Nominal Rigidities: a Quantitative Investigation.

This paper studies a dynamic-optimizing model of a semi-small open economy with sticky nominal prices and wages. the model exhibits exchange rate overshooting in response to money supply shocks. the predicted variability of nominal and real exchange rates is roughly consistent with that of G7 effective exchange rates during the post-Bretton Woods era.

Développement et validation d’un outil clinique pour l’analyse quantitative de la posture auprès de personnes atteintes d’une scoliose idiopathique

La scoliose idiopathique (SI) est une déformation tridimensionnelle (3D) de la colonne vertébrale et de la cage thoracique à potentiel évolutif pendant la croissance. Cette déformation 3D entraîne des asymétries de la posture. La correction de la posture est un des objectifs du traitement en physiothérapie chez les jeunes atteints d’une SI afin d’éviter la progression de la scoliose, de réduire les déformations morphologiques et leurs impacts sur la qualité de vie. Les outils cliniques actuels ne permettent pas de quantifier globalement les changements de la posture attribuables à la progression de la scoliose ou à l’efficacité des interventions thérapeutiques. L’objectif de cette thèse consiste donc au développement et à la validation d’un nouvel outil clinique permettant l’analyse quantitative de la posture auprès de personnes atteintes d’une SI. Ce projet vise plus spécifiquement à déterminer la fidélité et la validité des indices de posture (IP) de ce nouvel outil clinique et à vérifier leur capacité à détecter des changements entre les positions debout et assise. Suite à une recension de la littérature, 34 IP représentant l’alignement frontal et sagittal des différents segments corporels ont été sélectionnés. L’outil quantitatif clinique d’évaluation de la posture (outil 2D) construit dans ce projet consiste en un logiciel qui permet de calculer les différents IP (mesures angulaires et linéaires). L’interface graphique de cet outil est conviviale et permet de sélectionner interactivement des marqueurs sur les photographies digitales. Afin de vérifier la fidélité et la validité des IP de cet outil, la posture debout de 70 participants âgés entre 10 et 20 ans atteints d'une SI (angle de Cobb: 15º à 60º) a été évaluée à deux occasions par deux physiothérapeutes. Des marqueurs placés sur plusieurs repères anatomiques, ainsi que des points de référence anatomique (yeux, lobes des oreilles, etc.), ont permis de mesurer les IP 2D en utilisant des photographies. Ces mêmes marqueurs et points de référence ont également servi au calcul d’IP 3D obtenus par des reconstructions du tronc avec un système de topographie de surface. Les angles de Cobb frontaux et sagittaux et le déjettement C7-S1 ont été mesurés sur des radiographies. La théorie de la généralisabilité a été utilisée pour déterminer la fidélité et l’erreur standard de la mesure (ESM) des IP de l’outil 2D. Des coefficients de Pearson ont servi à déterminer la validité concomitante des IP du tronc de l’outil 2D avec les IP 3D et les mesures radiographiques correspondantes. Cinquante participants ont été également évalués en position assise « membres inférieurs allongés » pour l’étude comparative de la posture debout et assise. Des tests de t pour échantillons appariés ont été utilisés pour détecter les différences entre les positions debout et assise. Nos résultats indiquent un bon niveau de fidélité pour la majorité des IP de l’outil 2D. La corrélation entre les IP 2D et 3D est bonne pour les épaules, les omoplates, le déjettement C7-S1, les angles de taille, la scoliose thoracique et le bassin. Elle est faible à modérée pour la cyphose thoracique, la lordose lombaire et la scoliose thoraco-lombaire ou lombaire. La corrélation entre les IP 2D et les mesures radiographiques est bonne pour le déjettement C7-S1, la scoliose et la cyphose thoracique. L’outil est suffisamment discriminant pour détecter des différences entre la posture debout et assise pour dix des treize IP. Certaines recommandations spécifiques résultents de ce projet : la hauteur de la caméra devrait être ajustée en fonction de la taille des personnes; la formation des juges est importante pour maximiser la précision de la pose des marqueurs; et des marqueurs montés sur des tiges devraient faciliter l’évaluation des courbures vertébrales sagittales. En conclusion, l’outil développé dans le cadre de cette thèse possède de bonnes propriétés psychométriques et permet une évaluation globale de la posture. Cet outil devrait contribuer à l’amélioration de la pratique clinique en facilitant l’analyse de la posture debout et assise. Cet outil s’avère une alternative clinique pour suivre l’évolution de la scoliose thoracique et diminuer la fréquence des radiographies au cours du suivi de jeunes atteints d’une SI thoracique. Cet outil pourrait aussi être utile pour vérifier l’efficacité des interventions thérapeutiques sur la posture.

Analyse quantitative des cyanotoxines d'eau douce par LDTD-APCI-MS/MS

Avec la hausse mondiale de la fréquence des floraisons de cyanobactéries (CB), dont certaines produisent des cyanotoxines (CT), le développement d’une méthode de détection/quantification rapide d’un maximum de CT s’impose. Cette méthode permettrait de faire un suivi quotidien de la toxicité de plans d’eau contaminés par des CB et ainsi d’émettre rapidement des avis d’alerte appropriés afin de protéger la santé publique. Une nouvelle technologie utilisant la désorption thermique induite par diode laser (LDTD) couplée à l’ionisation chimique sous pression atmosphérique (APCI) et reliée à la spectrométrie de masse en tandem (MS/MS) a déjà fait ses preuves avec des temps d'analyse de l’ordre de quelques secondes. Les analytes sont désorbés par la LDTD, ionisés en phase gazeuse par APCI et détectés par la MS/MS. Il n’y a donc pas de séparation chromatographique, et la préparation de l’échantillon avant l’analyse est minimale selon la complexité de la matrice contenant les analytes. Parmi les quatre CT testées (microcystine-LR, cylindrospermopsine, saxitoxine et anatoxine-a (ANA-a)), seule l’ANA-a a généré une désorption significative nécessaire au développement d’une méthode analytique avec l’interface LDTD-APCI. La forte polarité ou le poids moléculaire élevé des autres CT empêche probablement leur désorption. L’optimisation des paramètres instrumentaux, tout en tenant compte de l’interférence isobarique de l’acide aminé phénylalanine (PHE) lors de la détection de l’ANA-a par MS/MS, a généré une limite de détection d’ANA-a de l’ordre de 1 ug/L. Celle-ci a été évaluée à partir d’une matrice apparentée à une matrice réelle, démontrant qu’il serait possible d’utiliser la LDTD pour effectuer le suivi de l’ANA-a dans les eaux naturelles selon les normes environnementales applicables (1 à 12 ug/L). Il a été possible d’éviter l’interférence isobarique de la PHE en raison de sa très faible désorption avec l’interface LDTD-APCI. En effet, il a été démontré qu’une concentration aussi élevée que 500 ug/L de PHE ne causait aucune interférence sur le signal de l’ANA-a.

Pauvreté, criminalité et problèmes de santé mentale : une évaluation qualitative et quantitative des interventions communautaires et policières dans un taudis mal famé

L'analyse quantitative a été réalisée en cotutelle avec Rémi Boivin et Pierre Tremblay et publiée dans la Revue de Criminologie: Boivin, R., Lamige, C,. Tremblay, P. (2009) La police devrait-elle cibler les taudis malfamés? Criminologie, (42)1, 225-266.