Thesis (M.S.)--Texas State University-San Marcos, 2007. / Vita. Includes bibliographical references (leaves 80-85).

Lic.-avh. (sammanfattning) Stockholm : Karol. inst., 2005. / Härtill 2 uppsatser.

Thesis (Ph.D.)--University of Nebraska-Lincoln, 2006. / Title from title screen (site viewed Oct. 10, 2007). PDF text: 234 p. : ill. (some col.) UMI publication number: AAT 3259631. Includes bibliographical references. Also available in microfilm and microfiche formats.

Thesis (M.S.)--Texas State University-San Marcos, 2007. / Vita. Includes bibliographical references (leaves 80-85).

Orientador: Sonia Maria Alves Bueno / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Quimica / Made available in DSpace on 2018-08-13T12:05:33Z (GMT). No. of bitstreams: 1 Goes_LidianaCristinade_M.pdf: 4033239 bytes, checksum: 07d68044592d217e51b3096b35496c87 (MD5) Previous issue date: 2009 / Resumo: Este trabalho visou investigar o efeito dos quelatos IDA-Ni(II), CM-Asp-Ni(II), TED-Ni(II) e TREN-Ni(II) na purificação de pró-insulina humana recombinante com cauda de poli(histidina) (PIS) a partir de solução clarificada, obtida após solubilização dos corpos de inclusão e sulfitólise, proveniente do processo de produção de insulina (BIOMM, MG). Dentre os adsorventes estudados, Sepharose-TREN-Ni (II) apresentou a maior capacidade de adsorção em termos de PIS, cerca de 50% da proteína alimentada. Os demais adsorventes apresentaram a seguinte ordem de capacidade de adsorção IDA > HisTrap > CM-Asp > TED. Em termos de seletividade, os adsorventes com CM-Asp-Ni (II) e TEDNi (II) imobilizados apresentaram maior seletividade. Os dados de adsorção de PIS no equilíbrio a 25°C foram bem representados pelo modelo de Langmuir-Freundlich., fornecendo valores de capacidade máxima de adsorção entre 43,14 mg e 154,56 mg de PIS/g de adsorvente e valores de constante aparente de dissociação entre 10-5 a 10-7 M. O estudo termodinâmico para adsorção de PIS nos adsorventes estudados na faixa de 4 a 25°C (exceto para TED-Ni(II), faixa de temperatura de 25 a 45°C) mostrou diminuição dos valores de Kd com o aumento da temperatura, fornecendo valores de ?H° positivos para todos os casos, indicando que a adsorção de PIS nos quelatos estudados é um processo endotérmico. Os valores de ?Gº foram negativos para todos os sistemas, indicando que a adsorção é espontânea. Os valores de ?Sº encontrados foram positivos e pouco alterados com o aumento de temperatura em todos os casos, favorecendo a complexação proteína-íon metálico. / Abstract: This work sought to investigate the effect of the chelating groups IDA-Ni(II), CMAsp- Ni(II), TED-Ni(II) and TREN-Ni(II) in the purification of a recombinant human proinsulin poly-histidine tagged (PIS) starting from clarified solution, obtained from the dissolution of inclusion bodies and oxidative sulfitolysis, originating from the process of insulin production (BIOMM, MG). Among of the studied adsorbents, Sepharose-TREN-Ni (II) it presented the largest adsorption capacity in terms of PIS, about 50 % of the fed protein. The other adsorbents presented the following order in adsorption capacity IDA > HisTrap > CM-Asp > TED. In selectivity terms, the adsorbents with the chelating groups CM-Asp-Ni (II) and TED-Ni (II) immobilized presented a larger selectivity. The data of adsorption of PIS in the equilibrium to 25°C were well represented by the model of Langmuir-Freundlich, supplying values of maximum adsorption capacity between 43, 14 mg and 154, 56 mg of PIS / g adsorbent and values of apparent constant of dissociation among 10-5 to 10-7 M. The thermodynamic study for adsorption of PIS in the adsorbents considering the range from 4 to 25°C (except for TED-Ni (II), temperature range from 25 to 45°C) showed decrease of the values of Kd with the increase of temperature, providing positive values of ?H° for all of the cases, indicating that the adsorption of PIS in the studied chelating groups is a endothermic process. The values of ?Gº were negative for all of the systems, indicating that the adsorption is spontaneous. The values of ?Sº founded were positive and had little alteration due to temperature increase in all of the cases, favoring the formation of complex protein-metallic ion. / Mestrado / Desenvolvimento de Processos Biotecnologicos / Mestre em Engenharia Química

M.A. / The shift from the Old to the New Economy has developed due to four key trends, namely globalisation, consumerism, environmentalism and corporate governance. Globalisation and the Internet has resulted in consumers being able to track the behaviour of corporations (Vise, 2006:119) and consequently, a New Consumer has emerged, where emphasis on corporate transparency and the environment has become a key concern for these New Consumers, as New Consumes are characterised by Lewis and Bridger (2000:21) as independent, sophisticated, involved and well informed about the production of goods and services, where these New Consumers are feeling the pressure to confront and act upon the fact that unbridled production and consumption, which was proliferate in the Old Economy, comes with escalating pollution at a significant human/animal/earth cost (Trendwatching, 2007). Moreover, in the world of globalisation and information overload, Salzer-Mörling and Strannegård (2004:224) argue that the proliferation of brands as well as a cluttered marketplace has meant that corporations now need to not only be differentiated in the marketplace, but also be distinct and one of the ways which corporations in the New Economy are achieving this is by focusing on the corporate brand as the point of differentiation. Hence, by ensuring that the corporate brand is socially responsible, companies are able to use this to stand out from the competition. However, in order to truly become distinct within the marketplace, companies are using a strategy of corporate social responsibility referred to as Cause Related Marketing, which Business in the Community (2004:2) defines as a commercial activity by which businesses and charities or causes form a partnership with each other to market an image, product or service for mutual benefit. Cause Related Marketing thus has the added benefit of creating a win-win-win situation, implying a win for the business, a win for the cause and a win for the consumer (Adkins, 2005:6,101). In addition, the context of symbolic interactionism has been selected as a theoretical base of communication for the process of Cause Related Marketing, whereupon symbolic interactionism relates to the shift from the old to the New Consumer and the resultant implications of the New Economy, as Mead (1962:168) notes that as a rule people assume that the general voice of the community is identical with the larger community of the past and the future and society assumes that an organised custom represents morality, so that the things people cannot do are those that everybody would condemn, which correlates with corporations not being able to pollute the environment and behave in an unethical manner. Consequently, so as to ensure that the corporation creates a successful Cause Related Marketing partnership, it is important that the process of Cause Related Marketing is implemented appropriately. The three key constructs of the process of Cause Related Marketing that have been identified include finding a strategic fit, communicating the partnership and properly assessing the Cause Related Marketing campaign. One company that has created a successful Cause Related Marketing partnership is Nedbank, a South African bank that launched the Green Affinity programme, in partnership with WWF-SA, almost 20 years ago, long before environmentalism, transparency and Cause Related Marketing became corporate buzzwords. Hence, Nedbank has been utilised as an intrinsic case study in order to determine how the process of Cause Related Marketing is utilised by Nedbank’s Green Affinity programme according to a selected group of employees at Nedbank’s Group Marketing department in Sandton. Keywords: New Economy, New Consumer, environmentalism, globalisation, transparency, corporate governance, corporate social responsibility, distinction, Cause Related Marketing, process, symbolic interactionism.

In 1999, the Department of Water Affairs and Forestry (DWAF) initiated the development of the Nandoni Dam. A component of this project was the relocation of seven rural villages, which include Mulenzhe, Budeli, Dididi, Mpego, Machivandihala Agricultural College, Mutoti and Tshilangoma. Upon request from the community, DWAF had to provide for the exhumation of approximately 1,000 graves dating to the 20th century. A comprehensive analysis of the 160 skeletons (118 adults and 42 juveniles) found in association with these graves was performed, and a description of the health and disease patterns of these rural communities was provided. A secondary objective of this study was to assess the biological affinity of the Venda by examining both craniometric and odontometric traits. A demographic profile of these communities revealed a high incidence of death in children less than 5 years of age and medium ranged adult mortality that peaked between 45 and 55 years of age. This profile is similar to other contemporary black South African communities, and has been associated with poverty, poor living conditions and poor sanitation. When compared to Iron Age populations, it was noted that a dramatic decline in child mortality and a slight increase in adult longevity has occurred in black South African populations within the past 800 years. This may be associated with a reduction in the number of children born per mother and general improvements in lifestyle and living conditions. Medical researchers suggest that infectious disease and parasite infestation were high in rural Venda communities during the 20th century. Despite the high pathogen load in the environment, skeletal markers of non-specific diseases in this study were found to be minimal. This may be attributed to the administering of medication at both hospitals and local clinics, which would have arrested the development of diseases caused by bacteria and parasites. Overall, it appears that medicine improved health for the individual, but it was relatively ineffective on reducing the number of pathogens in the general environment. Dental health was relatively good for these communities. Tooth decay was more common in Venda than other agricultural based populations and may be related to the increased consumption of western foods such as refined maize and sugar. The results of uni- and multivariate statistical analyses on the craniometric and odontometric traits are indicative of a stronger relationship between the Venda and South African Negroid populations than the East Africa groups. This supports the idea of local development of the Venda people in the Soutpansberg region. These results are also in agreement with other studies that have shown similarities in cranial and dental morphology of South African Negroids with the Venda. Due to the small sample size from K2, it was not possible to establish a direct relationship between this group and the Venda. However, it is prudent to say that both groups can be classified as South African Negroids. / Thesis (DPhil)-University of Pretoria, 2005 / Anatomy / unrestricted

Cette thèse étudie trois sujets relevant de la biologie structurale, de lagénétique et de l'immunologie.Premièrement, nous développons de nouveaux prédicteurs de l'affinité deliaison de complexes protéiques, produisant des résultats de niveau ``état del'art''. Nous calculons d'abord 12 variables modélisant diverses propriétésstructurales des complexes. Nous générons et évaluons des estimateursutilisant des sous ensembles de ces variables, de façon à identifier les plusperformants. Le logiciel associé est distribué dans la Structural BioinformaticsLibrary.Deuxièmement, nous proposons de nouvelles analyses de complexes Ig-Ag.D'une part nous concevons un classificateur distinguant les types de ligand desIg. D'autre part, nous montrons que le modèle précédent prédit fidèlementl'affinité de complexes Ig-Ag. Enfin, nous quantifions la contribution des CDR3de la chaine lourde à l'affinité de liaison, et montrons qu'il contribuesignificativement plus que les autres CDR.Enfin, nous nous intéressons à la modélisation de la diversité des répertoiresde chaîne lourde des Igs, à partir de données de séquençage de CDR3, dans unmodèle de vaccin chez le poisson. Nous analysons les répertoires dans troisconditions: naifs, vaccinés et vaccinés + infectés. Nous comparons lesrépertoires de deux individus en utilisant la « earth-mover distance », laquelleexploite la correspondance entre clonotypes de deux répertoires, révélant ainsides informations inaccessibles aux méthodes basées sur les indices dediversité.Dépôt de thèseDonnées complémentairesPour caractériser la notion de réponse immunitaire publique / privée, nousquantifions le chevauchement des clonotypes exprimés entre individus de lamême ou de différentes conditions / This thesis investigates three topics at the cross-roads of structural biology,genetics and immunology.First, we develop a pipeline to design and select binding affinity predictors forprotein complexes, yielding state-of-the art results. The first step is the designand computation of 12 different variables accounting for geometric andphysico-chemical properties of the complexes. The second step is thegeneration and evaluation of models using subsets of these variables, followedby the selection of the best performing ones. The corresponding software isdistributed within the Structural Bioinformatics Library.Second, we provide an analysis of the interface properties of Ig-Ag complexes.In particular, we design a classifier using two descriptors, which is able todistinguish ligand types. We also apply the previous binding affinity predictionmodel to Ig-Ag complexes and obtain accurate predictions. We then develop aquantitative model for the contribution of VH CDR3 to the binding affinity andinteraction specificity, and show that it contributes significantly more thanother CDRs.Third, we model the diversity of VH CDR3 repertoires from Ig RNA sequencingdata in a fish vaccination model. We analyze repertoires from three conditions:naive, vaccinated and vaccinated + infected fish. Comparison of the repertoiresof two individuals uses the earth-mover distance (EMD). By exploiting amapping between the clonotypes of the repertoires, we show that EMD revealsinformation beyond classical methods based on diversity indexes. Tocharacterize the notion of public / private immune response, we quantify theoverlap of clonotypes between individuals of the same or different conditions

La plupart des sites de liaisons des cibles thérapeutiques sont hydrophobes. La majorité des molécules actives sont donc hydrophobes et difficilement soluble dans l'eau. Pour remédier à ce problème lors des test in vitro, un cosolvant est ajouté dans le milieu de réaction pour augmenter la solubilité des molécules. Le plus commun est le diméthylsulfoxyde (DMSO). Cependant, peu d'études ont regardé l'effet du DMSO sur l'affinité des ligand hydrophobes pour leurs cibles, mais toutes ont montré une modification de l'affinité induite par le DMSO. Pour mieux comprendre l'effet du DMSO il est nécessaire d'étudier un grand nombres de système ligand/récepteur différents. Dans cette étude, nous avons étudié l'effet d'une concentration de 5% de DMSO sur la liaison d'un ligand hydrophobe l'acide adamantane-1-carboxylique (ADA) dans deux cavités hydrophobes la beta et la gamma cyclodextrines (CD). Les deux CD diffèrent par la largeur de leur cavité. Les mesures d'affinités ont été réalisées par mesure de vélocité ultrasonore, résonance magnétique nucléaire et par des simulations moléculaires (MS). Toutes les techniques ont montré que le DMSO n'a pas d'effet sur l'affinité de l'ADA pour la gamma-CD alors qu'il diminue fortement l'affinité de l'ADA pour la beta-CD. L'analyse des MS a montré que le DMSO entre en compétition avec l'ADA pour la petite cavité de la beta-CD alors que pour la large cavité de la gamma-CD cette compétition n'est pas présente. L'effet du DMSO semble plus important lorsque le volume du ligand est parfaitement adapté au volume de la cible. / Most therapeutic targets are proteins whose binding sites are hydrophobic cavities. For this reason, the majority of drugs under development are hydrophobic molecules exhibiting low solubility in water. To tackle this issue, a few percent of cosolvent, such as dimethyl sulfoxide (DMSO), is usually employed to increase drug solubility during the drug screening process. However, the few published studies dealing with the effect of adding DMSO showed that the affinity of hydrophobic ligands is systematically underestimated. To better understand the effect of DMSO, there is a need of studying its effect on a large range of systems. In this work, we used beta and gamma-cyclodextrins (CD) as models of hydrophobic cavities to investigate the effect of the addition 5% DMSO on the affinity of 1-adamantane carboxylic acid (ADA) to these CD. The two systems differ by the size of the CD cavity. The evaluation of binding constants was performed using ultrasound velocimetry, nuclear magnetic resonance spectroscopy, and molecular simulations (MS). All techniques show that the presence of 5% DMSO does not significantly modify the affinity of ADA for gamma-CD, while the affinity is dramatically reduced for beta-CD. MS analysis show a competition between DMSO and ADA for the small cavity of beta-CD, which is not present for the large cavity of gamma-CD. The bias induced by the presence of DMSO is thus more important when the ligand volume better fits the CD cavity.

This thesis focuses mainly on the consequences that single mutations have on structural, functional and energetic aspects of the protein cyanovirin-N. In order to estimate the free energy of single mutations, we have applied thermodynamics integration and Bennett acceptance ratio techniques. Replica exchange molecular dynamics has been applied to accelerate simulations for complicated scenarios. Our studies suggest that certain single mutations may be promising to improve binding affinity to Manα1→2Manα but we also learned that the simplistic view of a strong hydrogen bond correlating to a high binding affinity may not always be correct. Finally, we explored in detail the widely used mutation P51G for its impact on protein rigidity at the very important hinge region as well as for its possible effect on glycan binding.