Therapeutic Protein and Glycoprotein Production, Optimization, and Analysis Methods

Proteins and glycoproteins have the potential to improve health when used as therapeutic products for prevention or treatment of disease, but methods are needed for solving some remaining challenges to production, optimization, and analysis. In this dissertation, novel glycosylation engineering strategies are used to solve challenges in conventional protein production and are used to improve therapeutic protein stability by blocking asparagine deamidation, a ubiquitous cause of protein degradation. Glycan structures on therapeutic glycoproteins must be optimized to avoid negative impacts on pharmacological properties. Methods to optimize glycans are described within, using novel, extracellular glycan trimming reactions performed with glycosidases that can be implemented without harm to protein activity or stability. Finally, analysis of proteins with mass spectrometric peptide mass fingerprinting techniques can be complex, so mass defect filters used for data analysis were improved by determining the correct filter size, using experimental human protein data

Improving mass defect filters for human proteins

The mass defect of a substance can be used in mass spectral analysis to identify peaks as likely belonging to a compound class, such as peptides, if the mass defect is within the known range for that compound class. For peptides, a range of possible mass defects was calculated previously, using a set of theoretical peptides, where all possible amino acid combinations were considered (Mann, M. Abstract from the 43rd Annual Conference on Mass Spectrometry and Allied Topics; 1995, ASMS). We compare that range of theoretical peptide mass defects to new values obtained from in silico tryptic digests of proteins that are abundant in human serum and human seminal fluid. The range of mass defect values encompassing 95% of peptides for the human protein data sets was found to be up to 50% smaller than the previously reported mass defect range for the theoretical peptides. The smaller range established for human tryptic peptides can be used to improve peptide mass defect filters by excluding more species that are not likely to be peptides, thus improving filter selectivity for peptides during proteomic data analysis

Preconditioning of the background error covariance matrix in data assimilation for the Caspian Sea

Data Assimilation (DA) is an uncertainty quantification technique used for improving numerical forecasted results by incorporating observed data into prediction models. As a crucial point into DA models is the ill conditioning of the covariance matrices involved, it is mandatory to introduce, in a DA software, preconditioning methods. Here we present first studies concerning the introduction of two different preconditioning methods in a DA software we are developing (we named S3DVAR) which implements a Scalable Three Dimensional Variational Data Assimilation model for assimilating sea surface temperature (SST) values collected into the Caspian Sea by using the Regional Ocean Modeling System (ROMS) with observations provided by the Group of High resolution sea surface temperature (GHRSST). We also present the algorithmic strategies we employ

Collision Induced Dissociation Products of Disulfide-bonded Peptides: Ions Result from the Cleavage of More than One Bond

This document is the Accepted Manuscript version of a Published Work that appeared in final form in the Journal of the American Chemical Society, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1007/s13361-010-0064-x.Disulfide bonds are a posttranslational modification (PTM) that can be scrambled or shuffled to non-native bonds during recombinant expression, sample handling, or sample purification. Currently, mapping of disulfide bonds is difficult due, to various sample requirements and data analysis difficulties. One step towards facilitating this difficult work is developing a better understanding of how disulfide-bonded peptides fragment during Collision Induced Dissociation (CID). Most automated analysis algorithms function based on the assumption that the preponderance of product ions observed during the dissociation of disulfide-bonded peptides result from the cleavage of just one peptide bond, and in this report we tested that assumption by extensively analyzing the product ions generated when several disulfide-bonded peptides are subjected to CID on a QTOF instrument. We found that one of the most common types of product ions generated resulted from two peptide bond cleavages, or a double cleavage. We found that for several of the disulfide-bonded peptides analyzed, the number of double cleavage product ions outnumbered those of single cleavages. The influence of charge state and precursor ion size was investigated, to determine if those parameters dictated the amount of double cleavage product ions formed. It was found in this sample set that no strong correlation existed between the charge state or peptide size and the portion of product ions assigned as double cleavages. This data shows that these ions could account for many of the product ions detected in CID data of disulfide bonded peptides. We also showed the utility of double cleavage product ions on a peptide with multiple cysteines present. Double cleavage products were able to fully characterize the bonding pattern of each cysteine where typical single b/y cleavage products could not

Facilitating Mechanical Design with Augmented Reality

By enhancing a real scene with computer generated objects, Augmented Reality (AR), has proven itself as a valuable Human-Computer Interface (HCI) in numerous application areas such as medical, military, entertainment and manufacturing. It enables higher performance of on-site tasks with seamless presentation of up-to-date, task-related information to the users during the operation. AR has potentials in design because the current interface provided by Computer-aided Design (CAD) packages is less intuitive and reports show that the presence of physical objects help design thinking and communication. This research explores the use of AR to improve the efficiency of a design process, specifically in mechanical design.Singapore-MIT Alliance (SMA

Mobility of Chromium and Tin Associated with Geochemical Dynamics in Groundwater in Meboudja Plain

AbstractIn the region of Sidi Amar Annaba South. Storage of industrial waste from the Arcelor-Mittal steel complex directly on the floor produced an infiltration of heavy metals to the under saturated and groundwater area. To know the exact origin of some pollutants and their evolution in time, monthly monitoring of water chemistry (potential hydrogen, potential of oxydo-reduction, temperature, conductivity, Oxygen, Calcium, Magnesium, Sodium, Potassium, Chlorine, sulfate, bicarbonate, Nitrate, Strontium, total Chrome, total Tin) was performed on wells for water cycle.Statistical analysis shows a common origin of chromium and tin that would be due to electroplating waste. The temporal evolution of these elements highlights the influence of several factors (potential hydrogen, potential of oxydo-reduction, rainfall and pumping) in the dissolution of these species and the evolution of the dominant aqueous species. There presentation of water points on the Eh-pH equilibrium diagram indicates that chromium may appear in the water table in two complex forms, trivalent and hexavalent by against the tin is in the hexavalent form

Etude éco-biologique d’Artémia salina des zones humides de l’Ouest Algérien

L’Artémie (Artémia salina) est une espèce de crustacé vivant dans les lacs salés, les chotts et les marais salants .Elle est en abondance dans les salines de l’ouest Algérien. Ce genre de crustacé est très demandé dans le domaine d’exploitation des ressources hydriques et en aquaculture. Dans le présent travail on a étudié, en premier lieu l’aspect biologique et écologique de ce crustacé dans les salines de Bathioua (wilaya d’Oran) et Oued Djemaa (wilaya de Relizane), en deuxième lieu on a étudié son accommodation à différentes doses de salinité dans un milieu même quand les conditions de vie sont défavorables. L’Artémie salina est capable de produire des cystes qui ont la capacité de donner naissance à une larve appelée nauplius. La résistivité des cystes au stress du milieu en état de cryptobiose, leur permet de subsister à des températures extrêmes. Les nauplius sont distribués dès l’éclosion ou après 24 à 48 h d’enrichissement en protéines et en lipides. Les résultats obtenus lors de ce travail ont montré que le taux de reproduction varie en fonction des changements saisonniers des différents facteurs écologiques et des éléments physico chimiques de son environnement.Mots-clés: Artémia salina, aspect biologique, adaptation, salines, Ouest Algérien. Eco-biological study of Artemia salina wetlands of West AlgeriaThe Artemia (Artemia salina) is a species of crustacean living in salt lakes, chotts and salt marshes. It is in abundance in the salt mines of western Algeria. This kind of crustacean is highly demanded in the fields of water exploitation and aquaculture. In this study, the observation is drawn on the biological and ecological aspects of this crustacean in the salt mines of Bathioua (Oran wilaya) and Oued Djemaa (Relizane wilaya), according to the seasonal variations. Artemia salina is able to produce cysts that have the ability to give birth to a larva called nauplius. The resistivity of cysts at environment stress on cryptobiosis state allows them to survive in extreme temperatures. Nauplii begin hatching after 24 to 48 h enrichment in proteins and lipids. The results obtained in this work showed that the reproduction rate varies according to seasonal changes in different ecological factors and the physical and chemical elements of its environment.Keywords : Artemia salina, biological aspect, adaptation, salt, West Algeria

Equilibria-based Probabilistic Model Checking for Concurrent Stochastic Games

Probabilistic model checking for stochastic games enables formal verification of systems that comprise competing or collaborating entities operating in a stochastic environment. Despite good progress in the area, existing approaches focus on zero-sum goals and cannot reason about scenarios where entities are endowed with different objectives. In this paper, we propose probabilistic model checking techniques for concurrent stochastic games based on Nash equilibria. We extend the temporal logic rPATL (probabilistic alternating-time temporal logic with rewards) to allow reasoning about players with distinct quantitative goals, which capture either the probability of an event occurring or a reward measure. We present algorithms to synthesise strategies that are subgame perfect social welfare optimal Nash equilibria, i.e., where there is no incentive for any players to unilaterally change their strategy in any state of the game, whilst the combined probabilities or rewards are maximised. We implement our techniques in the PRISM-games tool and apply them to several case studies, including network protocols and robot navigation, showing the benefits compared to existing approaches

Automated verification of concurrent stochastic games

We present automatic verifcation techniques for concurrent stochastic multi-player games (CSGs) with rewards. To express properties of such models, we adapt the temporal logic rPATL (probabilistic alternating-time temporal logic with rewards), originally introduced for the simpler model of turn-based games, which enables quantitative reasoning about the ability of coalitions of players to achieve goals related to the probability of an event or reward measures. We propose and implement a modelling approach and model checking algorithms for property verifcation and strategy synthesis of CSGs, as an extension of PRISMgames. We evaluate the performance, scalability and applicability of our techniques on case studies from domains such as security, networks and finance, showing that we can analyse systems with probabilistic, cooperative and competitive behaviour between concurrent components, including many scenarios that cannot be analysed with turn-based models