The chiral vicinal diamine moiety is “privileged” and is widely found in catalysts and bio-active compounds. A series of seven chiral vicinal diamines with heterocyclic substituents have been synthesized with great enantiospecificity via the resonance assisted hydrogen bond driven diaza-Cope rearrangement reaction using 1,2-bis(2-hydroxyphenyl)-1,2-diaminoethane and heterocyclic aldehydes as starting materials. This thesis will also discuss the development of a new guanidine-based chiral shift rea-gent for determining the enantiopurity and the absolute configuration of α-amino acids by proton nuclear magnetic resonance (1H NMR) spectroscopy. The chiral shift reagent is easily synthesized from the commercially-available 1,2-diphenyl-1,2-diaminoethane. This method is advantageous over many previously described procedures for determining amino acid enantiopurity as it does not require prior derivatization of the analyte.

@font-face { font-family: "Arial"; }@font-face { font-family: "ＭＳ 明朝"; }@font-face { font-family: "Calibri"; }p.MsoNormal, li.MsoNormal, div.MsoNormal { margin: 0in 0in 0.0001pt; text-indent: 0.5in; line-height: 200%; font-size: 11pt; font-family: "Times New Roman"; }p.MsoBodyText, li.MsoBodyText, div.MsoBodyText { margin: 0in 0in 6pt; text-indent: 0.5in; line-height: 200%; font-size: 11pt; font-family: "Times New Roman"; }span.BodyTextChar { font-family: Calibri; }div.Section1 { page: Section1; } A 60 kDa monomeric protein isolated from the defensive purple ink secretion of the sea hare Aplysia californica has broad antimicrobial activity in tryptone peptone rich medium. This protein, which we call ‘escapin’, belongs to an L-amino acid oxidase family. The goals of my project were 1) to determine the products of escapin’s oxidation of its main substrate L-lysine, 2) to characterize the antimicrobial effects of escapin’s products, and 3) determine bactericidal mechanisms of action of these products. Escapin is a powerful bactericidal agent against several bacteria species including Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Vibrio harveyi. Escapin operates through a two-step process: 1) deamination of L-amino acids (especially L-lysine) by enzymatic activity to produce escapin intermediate products of L-lysine (EIP-K), hydrogen peroxide, and ammonia; and 2) EIP-K simultaneously reacts with hydrogen peroxide to generate escapin end products (EEP-K). EIP exists as an equilibrium mixture of the linear a-keto analogue of lysine and its cyclic forms, and the relative amount of the linear form increases with pH decreases. The powerful bactericidal effect of escapin requires the simultaneous presence of hydrogen peroxide and EIP-K in weak acidic conditions, which suggests that linear form of EIP-K with hydrogen peroxide is responsible for the bactericidal effect of escapin. Using E. coli MC4100 as a model, the mechanism of action of escapin was examined. Brief treatment with EIP-K + H2O2, but not EIP-K or H2O2 alone, causes irreversible DNA condensation with a time course similar to the bactericidal effect. A mutant strain resistant to EIP-K + H2O2 was isolated, and a single point mutation was found in the oxidative stress regulator gene (oxyR). Through a complementary assay, it was shown that wild type E. coli is conferred resistance to EIP-K + H2O2 by carrying mutated oxyR plasmid. Furthermore, in this bactericidal effect, heat or cold shock does not substitute for hydrogen peroxide induced oxidative stress. Thus, escapin’s powerful bactericidal effect may be through irreversible DNA condensation mediated through hydrogen peroxide generating an oxidative stress response, but the pathway mediating EIP-K’s synergistic effect is still unclear.

In this study, firstly the effects of aspartic acid group amino acids -which were reported to be the potential bottleneck in serine alkaline protease (SAP) synthesis- on SAP production were investigated by substituting at a concentration range of 0-15 mM by using recombinant Bacillus subtilis carrying pHV1434::subC gene. All aspartic acid group amino acids except threonine inhibited SAP activity when CAA&amp / #8805 / 2.5 mM. The highest SAP activities with asparagine, aspartic acid, lysine, threonine, isoleucine and methionine werefound to be 1.89-, 1.87-, 1.61-, 1.48-, 1.4-, and 1.4-fold higher than the reference medium activity, respectively, when the concentration of each amino acid was CAA=0.25 mM. The product and by-product distributions in defined and complex media in SAP production were also analyzed and compared in order to obtain a depth in-sight on functioning of the metabolic reaction network. The highest SAP activity in complex medium was found to be 3&ndash / fold higher than defined medium activity, while, specific SAP production rate was 1.2- fold higher. The highest cell concentration in complex medium (CX= 14.3 g/dm-3) was 8.1-fold higher than that obtained in defined medium (CX= 1.75 g/dm-3). In both media, oxaloacetic acid was observed extracellularly and intracellularly. In complex medium there was also succinic acid in the extracellular medium indicating that the operation of TCA cycle was insufficient. In both media serine, valine and glycine were observed neither in the extracellular nor in the intracellular media indicating that the synthesis of these amino acids can be a secondary rate limiting step. In defined medium asparagine was present neither in the cell nor in fermentation broth whereas, methionine was observed in the cell in high amounts, probably due to the lower flux values towards asparagine. Thus, in defined medium the synthesis of asparagine can also be a potential bottleneck in SAP production in defined medium.

Chemical biology encompasses the study and manipulation of biological system using chemistry, often by virtue of small molecules or unnatural amino acids. Much insight has been gained into the mechanisms of biological processes with regards to protein structure and function, metabolic processes and changes between healthy and diseased states. As an ever expanding field, developing new tools to interact with and impact biological systems is an extremely valuable goal. Herein, work is described towards the synthesis of a small library of heterocyclic-containing small molecules and the mechanistic details regarding the interesting and unexpected chemical compounds that arose; an alternative set of non-toxic copper catalyzed azide-alkyne click conditions for in vivo metabolic labelling; and the synthesis of an unnatural amino acid for further chemical modification via [3+2] cycloadditions with nitrones upon incorporation into a peptide of interest. Altogether, these projects strive to supplement pre-existing methodology for the synthesis of small molecule libraries and tools for metabolic labelling, and thus provide further small molecules for understanding biological systems.

Traditional multiple hypothesis testing procedures, such as that of Benjamini and Hochberg, fix an error rate and determine the corresponding rejection region. In 2002 Storey proposed a fixed rejection region procedure and showed numerically that it can gain more power than the fixed error rate procedure of Benjamini and Hochberg while controlling the same false discovery rate (FDR). In this thesis it is proved that when the number of alternatives is small compared to the total number of hypotheses, Storeys method can be less powerful than that of Benjamini and Hochberg. Moreover, the two procedures are compared by setting them to produce the same FDR. The difference in power between Storeys procedure and that of Benjamini and Hochberg is near zero when the distance between the null and alternative distributions is large, but Benjamini and Hochbergs procedure becomes more powerful as the distance decreases. It is shown that modifying the Benjamini and Hochberg procedure to incorporate an estimate of the proportion of true null hypotheses as proposed by Black gives a procedure with superior power.<p> Multiple hypothesis testing can also be applied to regression diagnostics. In this thesis, a Bayesian method is proposed to test multiple hypotheses, of which the i-th null and alternative hypotheses are that the i-th observation is not an outlier versus it is, for i=1,...,m. In the proposed Bayesian model, it is assumed that outliers have a mean shift, where the proportion of outliers and the mean shift respectively follow a Beta prior distribution and a normal prior distribution. It is proved in the thesis that for the proposed model, when there exists more than one outlier, the marginal distributions of the deletion residual of the i-th observation under both null and alternative hypotheses are doubly noncentral t distributions. The outlyingness of the i-th observation is measured by the marginal posterior probability that the i-th observation is an outlier given its deletion residual. An importance sampling method is proposed to calculate this probability. This method requires the computation of the density of the doubly noncentral F distribution and this is approximated using Patnaiks approximation. An algorithm is proposed in this thesis to examine the accuracy of Patnaiks approximation. The comparison of this algorithms output with Patnaiks approximation shows that the latter can save massive computation time without losing much accuracy.<p> The proposed Bayesian multiple outlier identification procedure is applied to some simulated data sets. Various simulation and prior parameters are used to study the sensitivity of the posteriors to the priors. The area under the ROC curves (AUC) is calculated for each combination of parameters. A factorial design analysis on AUC is carried out by choosing various simulation and prior parameters as factors. The resulting AUC values are high for various selected parameters, indicating that the proposed method can identify the majority of outliers within tolerable errors. The results of the factorial design show that the priors do not have much effect on the marginal posterior probability as long as the sample size is not too small.<p> In this thesis, the proposed Bayesian procedure is also applied to a real data set obtained by Kanduc et al. in 2008. The proteomes of thirty viruses examined by Kanduc et al. are found to share a high number of pentapeptide overlaps to the human proteome. In a linear regression analysis of the level of viral overlaps to the human proteome and the length of viral proteome, it is reported by Kanduc et al. that among the thirty viruses, human T-lymphotropic virus 1, Rubella virus, and hepatitis C virus, present relatively higher levels of overlaps with the human proteome than the predicted level of overlaps. The results obtained using the proposed procedure indicate that the four viruses with extremely large sizes (Human herpesvirus 4, Human herpesvirus 6, Variola virus, and Human herpesvirus 5) are more likely to be the outliers than the three reported viruses. The results with thefour extreme viruses deleted confirm the claim of Kanduc et al.

This thesis explores the complex relationship between food protein structure and digestibility. Food proteins are important nutrients that play a central role in controlling the textural properties of many foods. Processing of food proteins may alter the protein aggregate structure and digestibility. The degree of protein aggregation during food processing depends on the denaturing conditions and the presence of other food components. Sugars and lipids may contribute to protein glycation and protein cross-linking via the Maillard reaction. Furthermore, amino acid residues of food proteins may be chemically modified during processing, thereby influencing both the structure and the nutritional value of proteins. An in vitro digestibility assay was used to investigate the relationship between protein aggregate structure and protein digestibility. Raw and boiled egg whites were exposed to a wide range of conditions: pH 2 - 12, in the presence and absence of 200 mM NaCl. It was found that pH and NaCl treatment prior to in vitro digestion resulted in significantly different protein ultrastructures, but did not markedly influence protein digestibility under the tested conditions. Raw egg white was less digestible than boiled egg white under all test conditions. The inclusion of Maillard reaction partners caused protein cross-linking concurrent with a decrease in digestibility. The digestibility decreased with the reactivity of the Maillard reaction partner and with increasing heating time. Proteomic analysis, using tandem mass spectrometry, of raw and heated egg white showed an increase in hydrothermally induced amino acid modifications. In the presence of glucose and methylglyoxal, a Maillard reaction specific increase in arginine modification to hydroimidazolone was observed with increasing heating times. The observed modifications are likely to contribute to a change in the nutritional quality of egg white. Aggregation kinetics of the major egg white protein, ovalbumin, were studied by dynamic light scattering, small angle X-ray scattering, and transmission electron microscopy. Shape determination was only possible for ordered aggregates, but not for disordered aggregates. Prior to heating, ovalbumin molecules in the presence of water and glucose repelled each other in concentrated solution. The presence of NaCl shielded electrostatic repulsion, leading to early onset dimerisation and disordered aggregation upon heating. Methylglyoxal treated ovalbumin formed more ordered aggregates. The scattering of these structures was able to be fitted to cylindrical shape models showing an increase of cylinder length with time while the cylinder diameter remained near constant over 24 hours of heating. In addition, food protein derived amyloid fibril aggregates were characterised. Amyloid fibrils are a common ordered protein fold that has been linked to neurodegenerative diseases. In the recent literature, amyloid fibrils have been proposed as new functional macromolecules in proteinaceous foods because of their desirable textural properties. Food fibrils formed from whey, egg white, soy bean and kidney bean protein were tested to establish whether they are protease resistant or display toxicity to human Caco-2 cells (a model intestinal cell line). The food fibrils were compared to insulin amyloid fibrils, a well characterised amyloid system. It was shown that the food fibrils displayed some resistance towards in vitro hydrolysis and were not found to be toxic. This work contributes to the understanding of food protein aggregation and digestibility under relevant conditions. It highlights the relationship of aggregate structure and digestibility and the particular role of the Maillard reaction. Moreover, evidence is provided that food protein derived amyloid fibrils may be safe ingredients in consumables. These findings may contribute to optimising industrial food processes and creating safe new food products.

Novel on-line methods are presented for the extraction, preconcentration and analysis of zwitterionic biomolecules using sol-gel-coated columns coupled to a conventional UV/visible detector. The presented approaches do not require any additional modification of the commercially available standard CE instrument. Extraction, stacking, and focusing techniques were used in the preconcentration procedures. The positively charged sol-gel coatings were created using N-octadecyldimethyl[3-(trimethoxysilyl) proply]ammonium chloride (C18-TMS) in the coating sol solutions. Due to the presence of a positively charged quaternary ammonium moiety in C18-TMS, the resulting sol-gel coating carried a positive charge. The negatively charged sol-gel coatings were due to the presence of sulfonate groups, which was formed from the oxidation of thiol groups in precursor mercaptopropyltrimethoxysilane (MPTMS) by hydrogen peroxide. Besides MPTMS, tetramethoxysilane (TMOS) and n-octadecyltriethoxysilane (C18-TEOS) were also used to prepare the sol solution for the creation of the negatively charged coatings. For extraction, the pH of the samples was properly adjusted to impart a net charge opposite to the sol-gel coatings. When a long plug of the sample was passed through the sol-gel-coated capillary, extraction was achieved via electrostatic interaction between the charged sol-gel coating and the charged sample molecules. The extracted analytes were then desorbed and focused via local pH change and stacking. The local pH change was accomplished by passing buffer solutions with proper pH values, while a dynamic pH junction between the sample solution and the background electrolyte was utilized to facilitate solute focusing. The developed methods showed excellent extraction and preconcentration effects on both positively and negatively charged sol-gel-coated columns. On-line preconcentration and analysis results obtained on the sol-gel coated columns were compared with those obtained on an uncoated fused silica capillary of identical dimensions using conventional sample injections. The described procedure provided a 150 000-fold enrichment effect for alanine on the positively charged sol-gel-coated column. On the negatively charged sol-gel-coated column, the presented sample preconcentration technique provided a sensitivity enhancement factor (SEF) on the order of 3 x 103 for myoglobin, and 7 x 103 for asparagines. The developed methods provided acceptable repeatability in terms of both peak height and migration time.

In this work an intersection between optimization methods and animal cell culture modeling is considered. We present optimization based methods for analyzing and building models of cell culture; models that could be used when designing the environment cells are cultivated in, i.e., medium. Since both the medium and cell line considered are complex, designing a good medium is not straightforward. Developing a model of cell metabolism is a step in facilitating medium design. In order to develop a model of the metabolism the methods presented in this work make use of an underlying metabolic reaction network and extracellular measurements. External substrates and products are connected via the relevant elementary flux modes (EFMs). Modeling from EFMs is generally limited to small networks, because the number of EFMs explodes when the underlying network size increases. The aim of this work is to enable modeling with more complex networks by presenting methods that dynamically identify a subset of the EFMs. In papers A and B we consider a model consisting of the EFMs along with the flux over each mode. In paper A we present how such a model can be decided by an optimization technique named column generation. In paper B the robustness of such a model with respect to measurement errors is considered. We show that a robust version of the underlying optimization problem in paper A can be formed and column generation applied to identify EFMs dynamically. In papers C and D a kinetic macroscopic model is considered. In paper C we show how a kinetic macroscopic model can be constructed from the EFMs. This macroscopic model is created by assuming that the flux along each EFM behaves according to Michaelis-Menten type kinetics. This modeling method has the ability to capture cell behavior in varied types of media, however the size of the underlying network is a limitation. In paper D this limitation is countered by developing an approximation algorithm, that can dynamically identify EFMs for a kinetic model. / I denna avhandling betraktar vi korsningen mellan optimeringsmetoder och modellering av djurcellodling.Vi presenterar optimeringsbaserade metoder för att analysera och bygga modeller av cellkulturer. Dessa modeller kan användas vid konstruktionen av den miljö som cellerna ska odlas i, dvs, medium.Eftersom både mediet och cellinjen är komplexa är det inte okomplicerat att utforma ett bra medium. Att utveckla en modell av cellernas ämnesomsättning är ett steg för att underlätta designen av mediet. För att utveckla en modell av metabolismen kommer de metoder som används i detta arbete att utnyttja ett underliggande metaboliskt reaktions\-nätverk och extracellulära mätningar. Externa substrat och produkter är sammankopplade via de relevanta elementära metaboliska vägarna (EFM).Modellering med hjälp av EFM är i allmänhet begränsad till små nätverk eftersom antalet EFM exploderar när de underliggande nätverket ökar i storlek. Målet med detta arbete är att möjliggöra modellering med mer komplexa nätverk genom att presentera metoder som dynamiskt identifierar en delmängd av EFM. I artikel A och B betraktar vi en modell som består av EFM och ett flöde över varje EFM.I artikel A presenterar vi hur en sådan modell kan bestämmas med hjälp av en optimeringsteknik som kallas kolumngenerering.I artikel A undersöker vi hur robust en sådan modell är med avseende till mätfel. Vi visar att en robust version av det underliggande optimeringsproblemet i artikel A kan konstrueras samt att kolumngenerering kan appliceras för att identifiera EFM dynamiskt. Artikel C och D behandlar en kinetisk makroskopisk modell. Vi visar i artikel C hur en sådan modell kan konstrueras från EFM.Denna makroskopiska modell är skapad genom att anta att flödet genom varje EFM beter sig enligt Michaelis-Menten-typ av kinetik. Denna modelleringsmetod har förmågan att fånga cellernas beteende i olika typer av media, men storleken på nätverket är en begränsning.I artikel D hanterar vi denna begränsing genom att utveckla en approximationsalgoritm som identifierar EFM dynamiskt för en kinetisk modell. / <p>QC 20150827</p>

Many cyanobacteria are reported to produce the nonprotein amino acid β-N-methylamino-L-alanine (BMAA). Cyanobacteria are extensively distributed in terrestrial and aquatic environments and recently BMAA was detected in temperate aquatic ecosystems, e.g. the Baltic Sea. Little is known about developmental effects of the mixed glutamate receptor agonist BMAA. Brain development requires an optimal level of glutamate receptor activity as the glutamatergic system modulates many vital neurodevelopmental processes. The aim of this thesis was to investigate the developmental neurotoxicity of BMAA, and its interaction with the pigment melanin. Autoradiography was utilized to determine the tissue distribution of 3H-labelled BMAA in experimental animals. Behavioral studies and histological techniques were used to study short and long-term changes in the brain following neonatal exposure to BMAA. Long-term changes in protein expression in the brain was also investigated using matrix-assisted laser desorption ionization (MALDI) imaging mass spectrometry (IMS). A notable targeting of 3H-BMAA to discrete brain regions e.g. hippocampus and striatum in mouse fetuses and neonates was determined by autoradiography. BMAA treatment of neonatal rats on postnatal days 9–10 induced acute but transient ataxia and hyperactivity. Postnatal exposure to BMAA also gave rise to reduced spatial learning and memory abilities in adulthood. Neonatal rat pups treated with BMAA at 600 mg/kg showed early neuronal cell death in the hippocampus, retrosplenial and cingulate cortices. In adulthood the CA1 region of the hippocampus displayed neuronal loss and astrogliosis. Lower doses of BMAA (50 and 200 mg/kg) caused impairments in learning and memory function without any acute or long-term morphological changes in the brain. The MALDI IMS studies, however, revealed changes in protein expression in the hippocampus and striatum suggesting more subtle effects on neurodevelopmental processes. The studies also showed that BMAA was bound and incorporated in melanin and neuromelanin, suggesting that pigmented tissues such as in the substantia nigra and eye may be sequestering BMAA. In conclusion, the findings in this thesis show that BMAA is a developmental neurotoxin in rodents. The risks posed by BMAA as a potential human neurotoxin merits further consideration, particularly if the proposed biomagnifications in the food chain are confirmed.

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