Phosphoproteome profiling approaches for comprehensive monitoring of cell signaling events in interferon-[gamma] stimulated macrophages

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

Strategies for Inverse Profiling of Two Dimensional Dielectric Scatterers Using Electromagnetic Illumination

Electromagnetic tomography has been applied to problems in nondestructive evolution, ground-penetrating radar, synthetic aperture radar, target identification, electrical well logging, medical imaging etc. The problem of electromagnetic tomography involves the estimation of cross sectional distribution dielectric permittivity, conductivity etc based on measurement of the scattered fields. The inverse scattering problem of electromagnetic imaging is highly non linear and ill posed, and is liable to get trapped in local minima. The iterative solution techniques employed for computing the inverse scattering problem of electromagnetic imaging are highly computation intensive. Thus the solution to electromagnetic imaging problem is beset with convergence and computational issues. The attempt of this thesis is to develop methods suitable for improving the convergence and reduce the total computations for tomographic imaging of two dimensional dielectric cylinders illuminated by TM polarized waves, where the scattering problem is defmed using scalar equations. A multi resolution frequency hopping approach was proposed as opposed to the conventional frequency hopping approach employed to image large inhomogeneous scatterers. The strategy was tested on both synthetic and experimental data and gave results that were better localized and also accelerated the iterative procedure employed for the imaging. A Degree of Symmetry formulation was introduced to locate the scatterer in the investigation domain when the scatterer cross section was circular. The investigation domain could thus be reduced which reduced the degrees of freedom of the inverse scattering process. Thus the entire measured scattered data was available for the optimization of fewer numbers of pixels. This resulted in better and more robust reconstructions of the scatterer cross sectional profile. The Degree of Symmetry formulation could also be applied to the practical problem of limited angle tomography, as in the case of a buried pipeline, where the ill posedness is much larger. The formulation was also tested using experimental data generated from an experimental setup that was designed. The experimental results confirmed the practical applicability of the formulation.

Molecular Characterization and Gene Expression Profiling of Antimicrobial Peptides in Penaeid Shrimps

The constitutive production of AMPs in shrimps ensures that animals are able to protect themselves from low-level assaults by pathogens present in the environment. As these molecules play important roles in the shrimp immune defense system, the expression level of these AMPs are possible indicators of the immune state of shrimps. The present study also indicates the antiviral property of AMPs, especially ALF, stressing the importance of their up-regulation through the application of immunostimulants/probiotics as a prophylactic strategy in aquaculture. The present study shows that shrimp defense system is equipped enough to evade WSSV infection to a certain extent, when the animals were maintained on marine yeast and probiotic diet, whereas the control diet fed group succumbed to WSSV infection. This study reveals that marine yeast and probiotic supplemented diet can delay the process of WSSV infection and confer greater protection to the animals. Particularly, the protection conferred by marine yeast, C. haemulonii S27 and Bacillus MCCB101 were highly promising imparting greater hope to the aquaculture community to overcome the prevailing disease problems in aquaculture. It may be inferred from the present study that up-regulation of AMP genes could be effected by the application of immunostimulants and probiotics. Also, AMP expression profile could be used as an effective tool for screening immunostimulants and probiotics for application in shrimp culture. Ultimately, it is likely that no single compound or strategy will provide a solution to the problem of disease within aquaculture and that, in reality, a suite of techniques will be required including the manipulation of the rearing environment, addition of probionts as a matter of routine during culture, and the use of immunostimulants and other supplements during vulnerable growth phases. Finally, the development of good management practices, the control of environmental variables, genetic improvement in the penaeid species, understanding of host-virus interaction, modulation of the shrimp immune system, supported by functional genomics and proteomics of this crustacean, as a whole suggests that the control of WSSV is not far.

Process profiling using frequencies of system calls

In this paper we discuss our research in developing general and systematic method for anomaly detection. The key ideas are to represent normal program behaviour using system call frequencies and to incorporate probabilistic techniques for classification to detect anomalies and intrusions. Using experiments on the sendmail system call data, we demonstrate that we can construct concise and accurate classifiers to detect anomalies. We provide an overview of the approach that we have implemented

Molecular genetic profiling of functional genes of pearl oyster, Pinctada fucata

There are a number of genes involved in the regulation of functional process in marine bivalves. In the case of pearl oyster, some of these genes have major role in the immune/defence function and biomineralization process involved in the pearl formation in them. As secondary filter feeders, pearl oysters are exposed to various kinds of stressors like bacteria, viruses, pesticides, industrial wastes, toxic metals and petroleum derivatives, making susceptible to diseases. Environmental changes and ambient stress also affect non-specific immunity, making the organisms vulnerable to infections. These stressors can trigger various cellular responses in the animals in their efforts to counteract the ill effects of the stress on them. These include the expression of defence related genes which encode factors such as antioxidant genes, pattern recognition receptor proteins etc. One of the strategies to combat these problems is to get insight into the disease resistance genes, and use them for disease control and health management. Similarly, although it is known that formation of pearl in molluscs is mediated by specialized proteins which are in turn regulated by specific genes encoding them, there is a paucity of sufficient information on these genes.In view of the above facts, studies on the defence related and pearl forming genes of the pearl oyster assumes importance from the point of view of both sustainable fishery management and aquaculture. At present, there is total lack of sufficient knowledge on the functional genes and their expressions in the Indian pearl oyster Pinctada fucata. Hence this work was taken up to identify and characterize the defence related and pearl forming genes, and study their expression through molecular means, in the Indian pearl oyster Pinctada fucata which are economically important for aquaculture at the southeast coast of India. The present study has successfully carried out the molecular identification, characterization and expression analysis of defence related antioxidant enzyme genes and pattern recognition proteins genes which play vital role in the defence against biotic and abiotic stressors. Antioxidant enzyme genes viz., Cu/Zn superoxide dismutase (Cu/Zn SOD), glutathione peroxidise (GPX) and glutathione-S-transferase (GST) were studied. Concerted approaches using the various molecular tools like polymerase chain reaction (PCR), random amplification of cDNA ends (RACE), molecular cloning and sequencing have resulted in the identification and characterization of full length sequences (924 bp) of the Cu/Zn SOD, most important antioxidant enzyme gene. BLAST search in NCBI confirmed the identity of the gene as Cu/Zn SOD. The presence of the characteristic amino acid sequences such as copper/zinc binding residues, family signature sequences and signal peptides were found out. Multiple sequence alignment comparison and phylogenetic analysis of the nucleotide and amino acid sequences using bioinformatics tools like BioEdit,MEGA etc revealed that the sequences were found to contain regions of diversity as well as homogeneity. Close evolutionary relationship between P. fucata and other aquatic invertebrates was revealed from the phylogenetic tree constructed using SOD amino acid sequence of P. fucata and other invertebrates as well as vertebrates

Validierung von HPLC-Methoden zur Bestimmung von Polyphenolen und Carotinoiden in Möhren, Weizen und Mais unterschiedlicher Herkunft

In den vorliegenden Untersuchungen wurde der Gehalt von Carotinoiden in Weizen, Mais und Möhren sowie der Polyphenolgehalt in Möhren mit analytischen Methoden zum Nachweis dieser Substanzen gemessen. Der Gehalt der Carotinoide in Mais und der Gehalt der phenolischen Bestandteile in Möhren wurde mit Messungen mittels HPLC-Analytik gemessen. Die Methoden wurden aus literaturbekannten Verfahren abgeleitet und an die Anforderungen der untersuchten Probenmatrices angepasst und validiert. Dem Verfahren lag die Frage zugrunde, ob es möglich ist, Kulturpflanzen aus verschiedenen Anbausystemen auf der Basis des Gehaltes bestimmter sekundärer Pflanzeninhaltsstoffe zu differenzieren und aufgrund von Unterschieden im Gehalt der sekundären Pflanzeninhaltsstoffe zu klassifizieren. Die Gesamtverfahren wurden dabei gemäß der ISO 17025 validiert. Für die Messungen standen Proben aus definierten Langzeitversuchen und Erzeugerproben ausgesuchter ökologisch bzw. konventionell arbeitender Anbaubetriebe zur Verfügung. Als Grundlage für eine valide Methodeneinschätzung wurden die Messungen an codierten Proben vorgenommen. Eine Decodierung der Proben erfolgte erst nach der Vorlage der Messergebnisse in den genannten Projekten. Die Messung und Auswertung des Carotinoidgehaltes in Weizen, Mais und Möhren vor dem Hintergrund der Differenzierung und Klassifizierung erfolgte in Proben eines Erntejahres. Die Messung des Gehaltes phenolischer Substanzen in Möhren erfolgte in Möhren aus 3 Erntejahren. Die verwendeten HPLC-Verfahren konnten in Bezug auf den analytischen Teil der Messungen in den einzelnen Verfahrensschritten Linearität, Spezifität, Präzision und Robustheit erfolgreich überprüft werden. Darüber hinaus wurden wichtige Einflussgrößen auf die Messungen bestimmt. Für die Verfahren zur photometrischen Bestimmung der Gesamtcarotinoide konnte eine Grundkalibrierung der Parameter Präzision und Linearität des Verfahrens erfolgreich durchgeführt werden. Während der Anwendung der HPLC-Methoden an codierten Proben konnten in allen untersuchten Probenmatrices quantitativ bedeutende Inhaltsstoffe nachgewiesen und identifiziert werden. Eine vollständige Identifizierung aller dargestellten Peaks konnte in den Untersuchungen der Polyphenole in Möhren und der Carotinoide in Mais nicht erfolgen. Im Hinblick auf die Frage nach der Differenzierung und Klassifizierung ergab sich in den verschiedenen Proben ein unterschiedliches Bild. Sowohl durch den Carotinoid- als auch den Polyphenolgehalt konnten einzelne Proben statistisch signifikant differenziert werden. Die Trennleistung hing dabei sowohl von den jeweiligen Komponenten als auch von der untersuchten Probenmatrix ab. Ein durchgängig höherer Gehalt sekundärer Pflanzeninhaltsstoffe in Proben aus ökologischem Anbau konnte nicht bestätigt werden. Für die Klassifizierung der Proben verschiedener Anbauvarianten und konnten multivariate statistische Methoden, wie lineare Diskriminantenanalyse (LDA) und Classification and Regression Tree (CART), erfolgreich angewandt werden. Eine Klassifizierung mit unterschiedlichen statistischen Verfahren erbrachte dabei unterschiedliche Ergebnisse. In der Klassifizierung der decodierten Proben mittels LDA wirkten sich die Faktoren Sorte und Standort stärker auf das Klassifizierungsergebnis aus als der Faktor Anbausystem. Eine Klassifizierung der decodierten Proben nach dem Anbausystem wurde mit dem CART-Verfahren durchgeführt. Auf dieser Basis wurden für die Polyphenole in Möhren 97 % der Proben richtig klassifiziert. Durch die Messwerte des Carotinoidgehaltes und des Luteingehaltes in Weizen konnte der größere Teil der Proben (90 %) korrekt klassifiziert werden. Auf der Basis des Carotinoidgehaltes in Mais wurde der Großteil der Proben (95 %) korrekt nach dem Anbausystem klassifiziert. Auf der Basis des mittels HPLC gemessenen Carotinoidgehaltes in Möhren konnten die Proben 97 % korrekt klassifiziert werden (97 %). Insgesamt erscheint der Grundgedanke der Klassifizierung durch den Gehalt sekundärer Pflanzeninhaltsstoffe vielversprechend. Durch die vielfältigen Einflussgrößen auf den Sekundärstoffwechsel von Pflanzen müssten Veränderungen, die durch Sorte und Standort auftreten, über mehrere Jahre erhoben und systematisiert werden.

SCAPA (Spacially Addressable Protein Array) – a Novel Protein Array for the Differential Profiling of Ligand-receptor Induced Signalling

While protein microarray technology has been successful in demonstrating its usefulness for large scale high-throughput proteome profiling, performance of antibody/antigen microarrays has been only moderately productive. Immobilization of either the capture antibodies or the protein samples on solid supports has severe drawbacks. Denaturation of the immobilized proteins as well as inconsistent orientation of antibodies/ligands on the arrays can lead to erroneous results. This has prompted a number of studies to address these challenges by immobilizing proteins on biocompatible surfaces, which has met with limited success. Our strategy relates to a multiplexed, sensitive and high-throughput method for the screening quantification of intracellular signalling proteins from a complex mixture of proteins. Each signalling protein to be monitored has its capture moiety linked to a specific oligo ‘tag’. The array involves the oligonucleotide hybridization-directed localization and identification of different signalling proteins simultaneously, in a rapid and easy manner. Antibodies have been used as the capture moieties for specific identification of each signaling protein. The method involves covalently partnering each antibody/protein molecule with a unique DNA or DNA derivatives oligonucleotide tag that directs the antibody to a unique site on the microarray due to specific hybridization with a complementary tag-probe on the array. Particular surface modifications and optimal conditions allowed high signal to noise ratio which is essential to the success of this approach.

Overview of coded light projection techniques for automatic 3D profiling

Obtaining automatic 3D profile of objects is one of the most important issues in computer vision. With this information, a large number of applications become feasible: from visual inspection of industrial parts to 3D reconstruction of the environment for mobile robots. In order to achieve 3D data, range finders can be used. Coded structured light approach is one of the most widely used techniques to retrieve 3D information of an unknown surface. An overview of the existing techniques as well as a new classification of patterns for structured light sensors is presented. This kind of systems belong to the group of active triangulation method, which are based on projecting a light pattern and imaging the illuminated scene from one or more points of view. Since the patterns are coded, correspondences between points of the image(s) and points of the projected pattern can be easily found. Once correspondences are found, a classical triangulation strategy between camera(s) and projector device leads to the reconstruction of the surface. Advantages and constraints of the different patterns are discussed

Team Working and Profiling Handout

Exercise and Handout for use in conjunction with Lecture on team working and profiling. Refers to Belbin model of team development. If you have missed the class, you should work through the activity, ideally find some other students to work with. It consists of a number of parts in addition to a self-evaluation checklist 1) A personal reflection activity (for use as the class settles) 2) A brief group activity to use during the lecture 3) A follow up activity, to complete an evaluation online from the belbin website 4) A follow up activity to work through the videos which have been produced by the LearnHigher Project

ELEC1032 Team Working and Profiling

Powerpoint Slide set used to manage in class activity based introduction to team profiling from the Belbin perspective.

Team Working and Profiling

slides and accompanying handouts for hectic classroom activity bases session. See also notes on ECS module page: https://secure.ecs.soton.ac.uk/module/1617/COMP1205/33423/

Bibliography profiling of undergraduate theses in a professional psychology program

The bibliographic profile of 125 undergraduate (licentiate) theses was analyzed, describing absolute quantities of several bibliometric variables, as well as within-document indexes and average lags of the references. The results show a consistent pattern across the years in the 6 cohorts included in the sample (2001-2007), with variations, which fall within the robust confi dence intervals for the global central tendency. The median number of references per document was 52 (99% CI 47-55); the median  percentage of journal articles cited was 55%, with a median age for journal references of 9 years. Other highlights of the bibliographic profile were the use of foreign language references (median 61%), and low reliance on open web documents (median 2%). A cluster analysis of the bibliometric indexes resulted  in a typology of 2 main profiles, almost evenly distributed, one of them with the makeup of a natural science bibliographic profile and the second within the style of the humanities. In general, the number of references, proportion of papers, and age of the references are close to PhD dissertations and Master theses, setting a rather high standard for undergraduate theses.

Profiling of phenols in human fecal water after raspberry supplementation.

The phenolic compositions of fecal water samples from ten free-living human subjects without marked dietary restrictions were monitored before and after intake of raspberry puree (200 g/day, 4 days) using gas chromatography-mass spectrometry. No single phenolic component was increased in all subjects after intake, but a majority of subjects had significant elevations in phenylacetic acid (7/10), 4-hydroxyphenylacetic acid (6/10), 3-hydroxyphenylacetic acid (5/10), 3-phenylpropionic acid and 3-(4-hydroxyphenyl)propionic acid. The levels of 3,4-dihydroxbenzoic acid were elevated in 8/10 subjects, significantly for 6 subjects (p < 0.05), and not significantly reduced in the other 2 subjects. In addition, unlike most other fecal metabolites, the increase was always >2-fold. This metabolite may be representative of the increased colonic dose of cyanidin anthocyanins. The colonic microbiota varied greatly between individuals, and supplementation with raspberries did not produce any statistically significant alterations in the profile of colonic bacteria, nor was a common pattern revealed to account for the interindividual variations observed in the fecal water phenolic profiles.

The effect of consumption volume on profile and liking of oral nutritional supplements of varied sweetness: sequential profiling and boredom tests

Oral nutrition supplements (ONS) are routinely prescribed to those with, or at risk of, malnutrition. Previous research identified poor compliance due to taste and sweetness. This paper investigates taste and hedonic liking of ONS, of varying sweetness and metallic levels, over consumption volume; an important consideration as patients are prescribed large volumes of ONS daily. A sequential descriptive profile was developed to determine the perception of sensory attributes over repeat consumption of ONS. Changes in liking of ONS following repeat consumption were characterised by a boredom test. Certain flavour (metallic taste, soya milk flavour) and mouthfeel (mouthdrying, mouthcoating) attributes built up over increased consumption volume (p 0.002). Hedonic liking data from two cohorts, healthy older volunteers (n = 32, median age 73) and patients (n = 28, median age 85), suggested such build-up was disliked. Efforts made to improve the palatability of ONS must take account of the build up of taste and mouthfeel characteristics over increased consumption volume.