Thesis (Ph. D.)--University of Lund, 1995. / Published dissertation. Includes bibliographical references.

Thesis (Ph. D.)--University of Lund, 1995. / Published dissertation. Includes bibliographical references.

The mutated forms of the Discs overgrown gene causes overproliferation of imaginal discs of Drosophila melanogaster. Somatic mutations in its human counterpart, casein kinase I epsilon, were strongly associated with human breast cancer. Using the advantage of a high conservancy between fly's dco and human casein kinase I epsilon genes we have chosen D. melanogaster as a model organism to provide a list of probable Dco interaction partners via tandem affinity purification and mass spectrometry analysis. However, these proteins need to be independently verified as true Dco interaction partners.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20764号 / 工博第4416号 / 新制||工||1686(附属図書館) / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 浜地 格, 教授 跡見 晴幸, 教授 秋吉 一成 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

Indiana University-Purdue University Indianapolis (IUPUI) / The discovery and isolation of naturally occurring fluorescent proteins, FPs, have provided much needed tools for molecular and cellular level studies. Specifically the cloning of green fluorescent protein, GFP, revolutionized the field of biotechnology and biochemical research. Recently, a red fluorescent protein, DsRed, isolated from the Discosoma coral has further expanded the pallet of available fluorescent tools. DsRed shares only 23 % amino acid sequence homology with GFP, however the X-ray crystal structures of the two proteins are nearly identical. DsRed has been subjected to a number of mutagenesis studies, which have been found to offer improved physical and spectral characteristics. One such mutant, DsRed-Monomer, with a total of 45 amino acid substitutions in native DsRed, has shown improved fluorescence characteristics without the toxic oligomerization seen for the native protein. In our laboratory, we have demonstrated that DsRed proteins have a unique and selective copper-binding affinity, which results in fluorescence quenching. This copper-binding property was utilized in the purification of DsRed proteins using copper-bound affinity columns. The work presented here has explored the mechanism of copper-binding by DsRed-Monomer using binding studies, molecular biology, and other biochemical techniques. Another focus of this thesis work was to demonstrate the applications of DsRed-Monomer in biochemical studies based on the copper-binding affinity and fluorescence properties of the protein. To achieve this, we have focused on genetic fusions of DsRed-Monomer with peptides and proteins. The work with these fusions have demonstrated the feasibility of using DsRed-Monomer as a dual functional tag, as both an affinity tag and as a label in the development of a fluorescence assay to detect a ligand of interest. Further, a complex between DsRed-Monomer-bait peptide/protein fusion and an interacting protein has been isolated taking advantage of the copper-binding affinity of DsRed-Monomer. We have also demonstrated the use of non-natural amino acid analogues, incorporated into the fluorophore of DsRed-Monomer, as a tool for varying the spectral properties of the protein. These mutations demonstrated not only shifted fluorescence emission compared to the native protein, but also improved extinction coefficients and quantum yields.

Reliable prediction of binding affinity of peptides is one of the most challenging but important complex modelling problems in the post-genome era due to the diversity and functionality of the peptides discovered. Generally, peptide binding prediction models are commonly used to find out whether a binding exists between a certain peptide(s) and a major histocompatibility complex (MHC) molecule(s). Recent research efforts have been focused on quantifying the binding predictions. The objective of this thesis is to develop reliable real-value predictive models through the use of fuzzy systems. A non-linear system is proposed with the aid of support vector-based regression to improve the fuzzy system and applied to the real value prediction of degree of peptide binding. This research study introduced two novel methods to improve structure and parameter identification of fuzzy systems. First, the support-vector based regression is used to identify initial parameter values of the consequent part of type-1 and interval type-2 fuzzy systems. Second, an overlapping clustering concept is used to derive interval valued parameters of the premise part of the type-2 fuzzy system. Publicly available peptide binding affinity data sets obtained from the literature are used in the experimental studies of this thesis. First, the proposed models are blind validated using the peptide binding affinity data sets obtained from a modelling competition. In that competition, almost an equal number of peptide sequences in the training and testing data sets (89, 76, 133 and 133 peptides for the training and 88, 76, 133 and 47 peptides for the testing) are provided to the participants. Each peptide in the data sets was represented by 643 bio-chemical descriptors assigned to each amino acid. Second, the proposed models are cross validated using mouse class I MHC alleles (H2-Db, H2-Kb and H2-Kk). H2-Db, H2-Kb, and H2-Kk consist of 65 nona-peptides, 62 octa-peptides, and 154 octa-peptides, respectively. Compared to the previously published results in the literature, the support vector-based type-1 and support vector-based interval type-2 fuzzy models yield an improvement in the prediction accuracy. The quantitative predictive performances have been improved as much as 33.6\% for the first group of data sets and 1.32\% for the second group of data sets. The proposed models not only improved the performance of the fuzzy system (which used support vector-based regression), but the support vector-based regression benefited from the fuzzy concept also. The results obtained here sets the platform for the presented models to be considered for other application domains in computational and/or systems biology. Apart from improving the prediction accuracy, this research study has also identified specific features which play a key role(s) in making reliable peptide binding affinity predictions. The amino acid features "Polarity", "Positive charge", "Hydrophobicity coefficient", and "Zimm-Bragg parameter" are considered as highly discriminating features in the peptide binding affinity data sets. This information can be valuable in the design of peptides with strong binding affinity to a MHC I molecule(s). This information may also be useful when designing drugs and vaccines.

The final goal of this study is to establish a microscale analysis method that allows solution phase characterization of interactions between β2-glycoprotein I (β2gpI) and some of its ligands. Human β2gpI is a phospholipid- and heparin-binding plasma glycoprotein. The physiological role of the protein in normal blood coagulation is not entirely known, nor is its role in autoimmune diseases characterized by blood clotting disturbances (thrombosis). Quantitative binding data of β2gpI interactions with some of its ligands may help elucidating the mechanisms behind these diseases and in the development of new approaches for diagnostics, prevention, and therapy. In this thesis, capillary electrophoresis (CE) was used as methodological platform for the interaction studies. The analysis of peptides and proteins by CE is desirable due to low sample consumption, possibilities for non-denaturing and highly effective separations. The first objective of this thesis was to find an approach to prevent charge dependent adsorption of β2gpI to the inner surface of the capillaries. Analyte adsorption at the negatively charged inner surface of fused silica capillaries is detrimental to interaction analyses. This phenomenon is especially pronounced in the analysis of basic proteins and proteins containing exposed positively charged domains, such as β2gpI. A new strategy to suppress these solute-wall interactions was devised, investigated and optimized. This strategy exploits the pH hysteresis behavior of fused silica surfaces, by simply performing an acidic pretreatment of the capillary. The results in this thesis show that the acidic pretreatment efficiently prevents protein adsorption. / <p>Papper 4 Estimation of the amount of β₂-glycoprotein I adsorbed at the inner surface of fused silica capillaries after acidic, neutral and alkaline pretreatment ingick som manuskript i avhandlingen, nu publicerad.</p>

Thesis (MSc)--Stellenbosch University, 2015. / ENGLISH ABSTRACT: During the last two and a half decades a large body of research has accumulated indicating the presence of various natural and synthetic chemical compounds within the environment capable of inducing hormone-like responses in humans and animals. Such compounds, termed endocrine disruptors, have been implicated in a variety of developmental, reproductive and physiological abnormalities which have been shown to converge on the endocrine system. Given that endocrine disrupters are comprised of a diverse group of molecules with dissimilar chemical structures, general screening techniques are not feasible for effective environmental monitoring. A primary method of action by which these exogenous molecules affect the homeostatic regulation of the endocrine system is believed to be via the modulation of gene transcription. It is now well established that many endocrine disrupting compounds act upon a principal group of transcription factors, the nuclear receptors, by chance interaction with the ligand binding domains of these proteins. With a view to ultimately design a portable kit for the detection of endocrine disrupting compounds in water based on the bio-specific immobilisation of nuclear receptor ligand binding domains to a stationary membrane matrix, this study specifically describes: 1. The effects on recombinant protein expression by the addition of small molecules to the cultivation media of bacteria. 2. The optimisation of conditions for the lysis of bacterial cells to increase the solubility of heterologously expressed proteins. 3. The purification of recombinant proteins from bacterial cell lysates by means of a two-step chromatographic methodology. 4. The cloning of the genes for the human androgen and estrogen receptors’ ligand binding domains into baculovirus transfer plasmids. 5. Transfer of genetic material from the created baculovirus transfer plasmids to a linearised baculovirus genome for the generation of recombinant viruses. 6. The cultivation, and baculoviral infection, of Spodoptera frugiperda and Trichoplusia ni cell lines. 7. Expression and purification of N-terminal hexahistidine-tagged human nuclear receptor LBDs from insect cell lysates by means of immobilised metal affinity chromatography. / AFRIKAANSE OPSOMMING: Die teenwoordigheid van natuurlike en sintetiese chemiese middels wat oor die vermoë beskik om die aksies van hormone in die mens en dier na te boots het toenemend aftrek gekry in navorsing gedurende die laaste twee en ’n halwe dekades. 'n Verskeidenheid van ontwikkelings-, reproduktiewe- en fisiologiese abnormaliteite ontstaan as gevolg van die aksies van hierdie molekule, genaamd endokriene-ontwrigters, op die natuurlike funksionering van die endokriene-sisteem. Gegewe dat die groep chemiese middels waaruit endokriene-ontwrigters bestaan van diverse oorsprong afkomstig is lei dit daartoe dat algemene analitiese tegnieke nie in alle gevalle geskik is vir effektiewe omgewingsmonitering is nie. Die modulasie van geentranskripsie is een van die metodes wat voorgestel word as ’n metode waarop hierdie eksogene molekule die homeostatiese regulering deur die endokriene-sisteem omverwerp. ’n Algemene metode waarop vele endokrien-ontwrigtende stowwe geentranskripsie beïnvloed, is deur interaksie met die hormoon-bindende gedeeltes van ’n belangrike groep transkripsiefaktore, die nukluêre reseptore. Hierdie studie, met die uiteindelike ontwikkeling van ’n draagbare toetsstelsel vir die opsporing van endokrien-ontwrigtende-stowwe in water, gebasseer op die bio-spesifieke immobilisering van nukluêre reseptor ligand bindingsdomeins op ’n stasionêre membraanmatriks, het ten doel om die volgende te beskryf: 1. Die effek wat die byvoeging van klein molekule tot die groeimedium van bakteriëe het op die uitdrukking van rekombinante proteïene. 2. Die optimisering van bakteriese sel-lisering in terme van verhoging in die oplosbaarheid van heteroloë proteïene. 3. Die suiwering van rekombinante proteïen vanuit bakteriese sellisate deur middel van ’n twee-stap chromatografiese sisteem. 4. Die klonering van die gene vir die menslike androgeen en estrogeen reseptore se ligand bindingsdomeine in bakulovirus oordragplasmiede. 5. Die oordrag van genetiese materiaal vanaf hierdie bakulovirus oordragplasmiede na ’n gelineariseerde bakulovirus genoom deur middel van homoloë rekombinasie vir die produksie van rekombinante virusse. 6. Die groei en infeksie van Spodoptera frugiperda en Trichoplusia ni sellyne wat lei tot die uitdrukking van menssoortgelyke nukluêre reseptor ligandbindingsdomains. 7. Suiwering van N-terminaal heksahistidien-etiket-gekoppelde menslike nukluêre reseptor ligandbindingsdomeins vanuit inseksellisate deur middel van geïmmobiliseerde metaal affiniteitschromatografie.

Thesis (MSc)--Stellenbosch University, 2016. / ENGLISH ABSTRACT: Tuberculosis (TB) is one of the world’s deadliest diseases, with one third of the population being infected by it. The diagnosis of active tuberculosis entails finding and identifying Mycobacterium tuberculosis (Mtb), the causative pathogen in a specimen of bodily fluid from the patient. Multiple samples will improve the diagnostic yield and specimen volumes should therefore be as large as possible, which is often challenging for patients and especially younger children. Alternatively, a smaller volume could be required if there was a manner in which to concentrate the bacteria within a specimen, through use of a substrate which has an affinity for the pathogenic species. Polymers having intrinsic cellular activity are of interest as such substrates, one such being the natural polysaccharide, chitosan. In this thesis, a variety of modified chitosan derivatives were prepared as potential Mtb-capturing substrates. This was achieved by modifying chitosan with a variety of moieties, selected based on possible interactions with the Mtb cell wall, to render various quaternary ammonium salts of the polymer chitosan. The quaternized chitosan derivatives were then used to synthesize nano-substrates having an affinity for Mtb. Polymer coated superparamagnetic magnetite nanoparticles (SPMNs) were synthesized via an in situ co-precipitation technique, in which modified chitosan is able to chelate with the metal core. Polymer nanofibers were also electrospun via the electrospinning technique. The prepared derivative, N-trimethylammonium chitosan chloride (TMC), was electrospun into nanofibers by blending with suitable non-ionogenic polymers, namely polyvinyl alcohol (PVA), polyethylene oxide (PEO), polyvinyl pyrrolidone (PVP) and polyacrylamide (PAM), required to facilitate nanofiber formation. Affinity studies were conducted between the modified chitosan nano-substrates and the bacillus Calmette-Guérin (BCG) strain of Mycobacterium bovis, the attenuated Mtb-mimic bacteria, for evaluation as mycobacterium capturing substrates. The successful capture of BCG onto the surfaces of the various modified chitosan nanofibers and modified chitosan coated superparamagnetic nanoparticles was confirmed by fluorescence microscopy (FM), light microscopy (LM), transmission electron microscopy (TEM) and field emission scanning electron microscopy (FE-SEM). Analysis of the FM, TEM and FE-SEM images indicated that the chitosan coated nanoparticles functionalized with a C12 aliphatic quaternary ammonium moiety (CS-qC12), captured the most BCG through a combination of ionic and hydrophobic interaction. TMC blended with PVA, to produce nanofibers crosslinked with genipin, were found to have the strongest interaction with BCG of the nanofibrous mats tested. These findings were corroborated by water contact angle measurements, which established that PVA was the least hydrophilic of the non-ionogenic polymers and had hydrogen bond donating groups only, factors influencing the cellular adhesive properties of affinity substrates. / AFRIKAANSE OPSOMMING: Tuberkulose (TB) is een van die wêreld se mees dodelikste siektes, met ‘n derde van die bevolking wat geïnfekteer is daarmee. Ten einde aktiewe TB te diagnoseer moet Mycobacterium tuberculosis (Mtb), die voorsakende patogeen in ʼn monster van die pasiënt se liggaamlike vloeistof, gevind en ïdentifiseer word. Veelvuldige monsters sal die diagnotiese opbrengs verhoog en monster volumes moet dus so groot as moontlik wees wat dikwels ʼn uitdaging vir pasiënte en veral jonger kinders kan bied. Alternatiewelik kan ʼn kleiner monster van die pasiënt vereis word indien daar ʼn manier was om die bakterieë in ʼn monster te konsentreer deur die gebruik van ʼn substraat wat ʼn affiniteit toon vir die patogeniese spesie. Polimere met ʼn intrinsieke sellulêre aktiwiteit, wek belangstelling as sodanige substraat, een synde die natuurlike polisakkaried, chitosan. In hierdie tesis is ʼn verskeidenheid gemodifiseerde chitosan afgeleides voorberei as potensiële Mtb-vaslegging substrate. Dit is gedoen deur chitosan te modifiseer met ʼn verskeidenheid funksionele groepe, gekies op grond van moontlike interaksies met die Mtb selwand, ten einde ʼn verskeidenheid kwaternêre ammonium soute van die chitosan polimeer te bekom. Die kwaternêre chitosan afgeleides is gevolglik gebruik om nano-substrate te sintetiseer wat ʼn affiniteit toon vir Mtb. Polimeer bedekte superparamagnetiese magnetiet nanopartikels (SPMNs) is gesintetiseer via ʼn in situ mede-neerslag metode, waarvolgens die gemodifiseerde chitosan polimere in staat is om met die metaal kern te chelaat. Polimeer nanovesels is ook geëlektrospin deur die elektrospin tegniek te gebruik. Die voorbereide afgeleide N-trimetielammonium chitosan chloried (TMC) is tot nanovesels geëlektrospin deur vermenging met geskikte nie-ionogeniese polimere, naamlik poliviniel-alkohol (PVA), polietilene-oksied (PEO), poliviniel-pirrolidoon (PVP) en poliakrielamied (PAM), wat vereis word ten einde nanovesels te produseer. Affiniteit studies is uitgevoer tussen die gemodifiseerde chitosan nano-substrate en die bacillus Calmette-Guérin (BCG) stam van Mycobacterium bovis, die verswakte Mtb-mimiek bakterieë vir evaluering as mycobakterium-vaslegging substrate. Die suksesvolle vasvang van BCG op die oppervlaktes van die verskillende gemodifiseerde chitosan nanovesels en gemodifiseerde chitosan bedekte SPMNs is bevestig deur fluoressensie mikroskopie (FM), lig mikroskopie (LM), transmissie elektron mikroskopie (TEM) en veld-emissie-skandering elektron mikroskopie (FE-SEM). Analise van die FM, TEM en FE-SEM beelde het getoon dat die chitosan bedekte nanopartikels met byvoeging van ʼn C12 alifatiese kwaternêre ammonium groep, die meeste BCG vasgevang het deur ʼn kombinasie van ioniese en hidrofobiese interaksie. TMC vermeng met PVA om nanovesels te vorm, gekruisbind met genipin, is gevind om die sterkste interaksie met BCG te toon. Hierdie bevindings is bevestig deur water-kontak-hoek-metings, wat getoon het dat PVA die minste hidrofilies van die nie-ionogeniese polimere was en slegs waterstof-binding skenkings groepe het, alles faktore wat die sellulêre bindingskwaliteite van affiniteit-substrate sal beïnvloed.

We live in a world where social media allows everyone to have a voice regardless of their expertise on any subject. With so many anonymous voices giving their opinions are the expert reviews of film critics no longer as useful? Some may believe there is a disconnect between what critics like and what people like. With this in mind, this research puts the usefulness of expert movie reviews and word of mouth against each other as can be seen through the need for cognition scale and social media affinity scale. / text