Reverse engineering - defined as extracting information about a product from the product itself - is a design tactic commonly used in industry from competitive benchmarking to product imitation. While reverse engineering is a legitimate practice - as long as the product was legally obtained - innovative products are often reverse engineered at the expense of the pioneering company. However, by designing products with built-in barriers to reverse engineering, competitors are no longer able to effectively extract critical information from the product of interest. Enabling the quantification of barriers to reverse engineering, this dissertation presents a set of metrics and parameters that can be used to calculate the barrier to reverse engineer any product as well as the time required to do so. To the original designer, these numerical representations of the barrier and time can be used to strategically identify and improve product characteristics so as to increase the difficulty and time to reverse engineer them. On the other hand, these quantitative measures enable competitors who reverse engineer original designs to focus their efforts on products that will result in the greatest return on investment. In addition to metrics that estimate the reverse engineering barrier and time, this dissertation also presents a methodology to strategically plan for, select, design, and implement reverse engineering barriers. The methodology presented herein considers barrier development cost, barrier effectiveness in various product components, impact on performance, and return on investment. This process includes sensitivity analysis, modeling of the return on investment, and exploration of multiobjective design spaces. The effectiveness of the presented methodology is demonstrated by making a solar-powered unmanned aerial vehicle difficult to reverse engineer. In the example, the propeller is selected to be the critical component where a series of voids are introduced to decrease the propeller weight and increase the flutter speed (a desirable attribute in propellers). Our tenet is that the use of such a framework contributes greatly to the sustainability of technological, economical, and security advantages enjoyed by those who developed the technology. Designers benefit because (i) products do not readily disclose trade secrets, (ii) competitive advantages can be maintained by impeding competitors from reverse engineering and imitating innovative products, and (iii) the return on investment can be increased.

Le sujet de la thèse vise à développer un imageur neutron portable présentant des performances de détection compatibles avec les besoins de la recherche et de l’industrie nucléaire, notamment ceux du démantèlement. Cette thèse se décompose en trois axes principaux de recherche, précédés d’une phase de recherche bibliographique. Suite à cette dernière, l’approche de localisation retenue est l‘imagerie de neutrons rapides par encodage spatial. Les détecteurs de neutrons ont été étudiés et plusieurs choix, adaptés à cette problématique, ont été retenus pour la suite de l’étude. Le premier axe est consacré aux études sur le développement d’un détecteur de neutrons sensible à la position. Le deuxième axe est lié à la conception et au prototypage d’un imageur neutronique, se reposant sur un masque codé et un détecteur Timepix modifié par une couche de paraffine. Le dernier axe concerne le déploiement et la caractérisation expérimentale de ce prototype. / The subject of the thesis aims at developing a portable neutron imager with detection performance compatible with the needs of the nuclear research and industry, in particular those of decommissioning. This thesis is divided into three main areas of research, preceded by a bibliographic research phase. Following the latter, the localization approach adopted is spatial encoding fast neutron imaging. Neutron detectors were studied and several choices adapted to this challenge were selected for the continuation of the study. The first axis is dedicated to the studies on the development of a position-sensitive neutron detector. The second axis is related to the design and prototyping of a portable neutron imager, based on a coded aperture and a Timepix detector enhanced with a paraffin layer. The last axis concerns the deployment and experimental characterization of this prototype.

Ce travail de thèse s’inscrit dans le cadre d’une collaboration entre Sanofi à Vitry-sur-Seine et le Laboratoire Hétérochimie Fondamentale et Appliquée (LHFA) à Toulouse, et a pour but de développer de nouveaux nanovecteurs à base de conjugués polymériques biodégradables et biocompatibles capables d’encapsuler, de transporter et de libérer des agents thérapeutiques. Les travaux précédemment réalisés au laboratoire, ont montré que la libération de principes actifs hydrophobes, tels que le Cabazitaxel de la famille des taxanes, pouvait être contrôlée grâce à l’architecture de conjugués de nature PEG-PLA. Dans le premier chapitre, une étude a été menée afin d’améliorer la cinétique de libération du principe actif, en tirant profit de la différence de pH qui réside entre les tissus sains et les tissus cancéreux. Différents liens (reliant le principe actif au copolymère) ayant un comportement pH dépendant ont été étudiés, comme l’hydrazone, l’acétal et le β-thiopropionate. La liaison ester boronique, dynamique en fonction du pH, a aussi été étudiée dans le but de déstructurer la NP et permettre indirectement d’améliorer la libération du principe actif. La synthèse et l’évaluation des divers conjugués ont montré que la structure polymérique amphiphile des conjugués inhibait considérablement le comportement pH dépendant attendu. Dans le second chapitre, plusieurs technologies comme le ciblage, permettant de diriger la NP dans l’organisme, ou l’imagerie permettant de les visualiser, ont été étudiées. L’influence de la structure des conjugués de forme Y et L sur les propriétés de reconnaissance et d’imagerie a été analysée. La structure Y offre quelques avantages quant à la quantité de ligand requise pour obtenir un ciblage actif optimal ainsi qu’une meilleure visualisation, en comparaison des résultats obtenus avec les conjugués L. La méthode de co-nanoformulation a permis de faire varier la quantité de ligand ou de sonde d’imagerie au sein des NPs. Dans le troisième chapitre, la synthèse et l’efficacité de sels de (bi)pyridinium comme catalyseurs pour la ROP de l’ε-caprolactone sont présentées. Un phénomène de coopérativité avec des bipyridiniums, dications donneurs de deux liaisons hydrogènes (IHBD) a été mis en évidence pour l’activation de l’ε-caprolactone, avec des activités en ROP plus importante en comparaison des systèmes impliquant la participation d’une seule liaison H. Les meilleurs systèmes ont pu être évalués plus en détail et ont permis d’accéder à des polymères de masses définies allant jusqu’à 13 000 g/mol. / This PhD thesis is based on a joint between Sanofi in Vitry-sur-Seine and LHFA. This work consists in the development of new nanovectors based on biodegradable and biocompatible polymerics conjugate that enable to encapsulate, transport and deliver therapeutic agents. Previous works in the laboratory have shown that the release of hydrophobic drugs, such as Cabazitaxel, a taxane derivative, could be controlled by the architecture of the conjugated PEG-PLA. In the first chapter, a study was realized to improve the release kinetics of the drug, taking advantage of the difference of pH between healthy and cancerous tissue. Different linkers (linking the drug to the copolymer) having a pH dependent behavior have been studied, such as hydrazone, acetal and β-thiopropionate. The boronic ester bonding, dynamic function of pH, was also studied in order to destroy the NP and indirectly improve the release of drug. The synthesis and the evaluation of various conjugates have shown that the amphiphilic polymeric structure of the conjugates significantly inhibited the expected pH-dependent behavior. In the second chapter, several technologies such as targeting or imaging were studied. The influence of the Y and L-shape on the recognition and imaging properties was analyzed. The Y-shape offers advantages like the amount of ligand required for optimal active targeting and better visualization, in comparison with the results obtained with the L conjugates. The method of co-nanoformulation allowed to adjust the ligand amount or imaging probe within the NPs. In the third chapter, the synthesis and efficiency of (bi)pyridinium salts as catalysts for the ROP of ε-caprolactone are presented. A collaborative behavior with dication bipyridiniums is bearing two hydrogen bonds (IHBD) was demonstrated for the activation of the ε-caprolactone, with greater ROP activities compared to systems involving the participation of only one H bond. The best systems were evaluated in more details and allowed access to polymers with a molecular weight of up to 13 000 g / mol.

The research described in this thesis reviewed previous uses of Interactive Voice Response (IVR), developed appropriate software, and employed IVR to obtain self-report of sensitive issues in surveys and conduct brief public health interventions. Chapter 1 introduces IVR and describes a systematic critical review of the use of IVR. IVR is a telephone interviewing technique where the human speaker is replaced by a high quality recorded interactive script to which the respondent provides answers by pressing the keys of a touch-telephone (touchphone). IVR has numerous advantages, including: economy, autonomy, confidentiality, access to certain population groups, improved data quality, standardised interviewing, multi-lingual interfaces, and detailed longitudinal assessments. Despite this, there have been few survey applications of IVR compared to alternative methods such as Computer-Assisted Telephone Interview (CATI). There has not been any evaluation of the use of IVR for asking sensitive questions in surveys or as a tool for health promotion at the community level. A literature review, described in Chapter 2, was conducted to identify other methods of asking sensitive questions. The literature review identified 19 different methods. Those methods that were most successful were those that provided the greatest degree of anonymity to the respondent. It was suggested that IVR may be a suitable method for community surveys. As described in Chapter 3, a custom software called Generalized Electronic Interviewing System (GEIS) was developed. This provided both CATI and IVR interviewing modes. As described in Chapter 4, it was found that the response rate obtained using IVR was unacceptably low, and an alternative interviewing method, the Hybrid method was developed. In the Hybrid method the interview was initiated by the interviewer but completed using IVR with GEIS. As described in Chapter 5, the IVR, CATI and Hybrid methods were used to investigate self-reported rates of alcohol and drug consumption within a telephone household survey of 2880 households. The self-report rates were compared to the National Drug Strategy Household Survey (NDSHS). Response rates did not differ significantly between the CATI and Hybrid methods, however the response rate for IVR was significantly less than the other methods. The Hybrid and IVR methods obtained significantly higher self-report consumption rates for alcohol and marijuana, and significantly higher hazardous drinking scores using Alcohol Use Disorders Identification Test (AUDIT). In Chapter 6 a pilot of an IVR cervical screening brief advice interface is described. A total of 5000 households were contacted by the IVR system. The system randomly selected an eligible woman aged 18-69 per household and determined her cervical screening status. A total of 661 women listened to the IVR message. The IVR call was shown to be acceptable and inexpensive compared to a mail pamphlet intervention. In Chapter 7 a randomized controlled trial of an IVR cervical screening brief advice involving 17,008 households is described. Cervical screening rate data were obtained from the Health Insurance Commission (HIC) for a period spanning six months before and following the intervention. The cervical screening rate was increased in the intervention postcodes by 0.43% compared to the control postcodes, and the increase was greater for older women at 1.34%. This was a desirable outcome since this group is considered to be an at-risk group. The overall conclusion was that IVR technology could be feasibly used to contact women to deliver brief interventions aimed at increasing cervical screening rates, but the cost per screen was likely to be high. It is suggested that an IVR system could be linked to cervical screening registers to more directly and economically contact women, and provide an efficacious complementary approach to the existing letter reminder system. / PhD Doctorate

<p>The gastric mucosa is frequently exposed to endogenously secreted hydrochloric acid of high acidity. Gastric mucosal defense mechanisms are arranged at different levels of the gastric mucosa and must work in unison to maintain its integrity. </p><p>In this thesis, several mechanisms underlying gastric mucosal resistance to strong acid were investigated in anesthetized rats and mice. The main findings were as follows:</p><p>Only when acid secretion occurred did the pH gradient in the mucus gel withstand back-diffusion of luminal acid (100 mM or 155 mM HCl), and keep the juxtamucosal pH (pH_jm) neutral. Thus, when no acid secretion occurred and the luminal pH was 0.8-1, the pH gradient was destroyed. </p><p>Bicarbonate ions, produced concomitant with hydrogen ions in the parietal cells during acid secretion and blood-borne to the surface epithelium, were carried transepithelially through a DIDS-sensitive transport. </p><p>Prostaglandin-dependent bicarbonate secretion seemed to be less important in maintaining a neutral pH_jm. </p><p>Removal of the loosely adherent mucus layer did not influence the maintenance of the pH_jm. Hence, only the firmly adherent mucus gel layer, approximately 80µm thick, seemed to be important for the pH_jm. </p><p>Staining of the mucus gel with a pH-sensitive dye revealed that secreted acid penetrated the mucus gel from the crypt openings toward the gastric lumen only in restricted paths (channels). One crypt opening was attached to one channel, and the channel was irreversibly formed during acid secretion. </p><p>Gastric mucosal blood flow increased on application of strong luminal acid (155 mM HCl). This acid-induced hyperemia involved the inducible but not the neural isoform of nitric oxide synthase. These results suggest a novel role for iNOS in gastric mucosal protection and indicate that iNOS is constitutively expressed in the gastric mucosa. </p><p>It is concluded that a pH gradient in the gastric mucus gel can be maintained during ongoing acid secretion, since the acid penetrates the mucus only in restricted channels and bicarbonate is carried from the blood to the lumen via a DIDS-sensitive transporter.</p>

<p>The field of forensic genetics is growing fast and the development and optimisation of more sensitive, faster and more discriminating forensic DNA analysis methods is highly important. In this thesis, an evaluation of the use of novel DNA technologies and the development of specific applications for use in forensic casework investigations are presented.</p><p>In order to maximise the use of valuable limited DNA samples, a fast and user-friendly Real-time PCR quantification assay, of nuclear and mitochondrial DNA copies, was developed. The system is based on the 5’ exonuclease detection assay and was evaluated and successfully used for quantification of a number of different evidence material types commonly found on crime scenes. Furthermore, a system is described that allows both nuclear DNA quantification and sex determination in limited samples, based on intercalation of the SYBR Green dye to double stranded DNA. </p><p>To enable highly sensitive DNA analysis, Pyrosequencing of short stretches of mitochondrial DNA was developed. The system covers both control region and coding region variation, thus providing increased discrimination power for mitochondrial DNA analysis. Finally, due to the lack of optimal assays for quantification of mitochondrial DNA mixture, an alternative use of the Pyrosequencing system was developed. This assay allows precise ratio quantification of mitochondrial DNA in samples showing contribution from more than one individual.</p><p>In conclusion, the development of optimised forensic DNA analysis methods in this thesis provides several novel quantification assays and increased knowledge of typical DNA amounts in various forensic samples. The new, fast and sensitive mitochondrial DNA Pyrosequencing assay was developed and has the potential for increased discrimination power.</p>

The cardiac sodium-calcium exchanger (NCX) is an important membrane protein which regulates cellular calcium necessary for the optimal contractile function of the heart. NCX has become a focal point in ischemic heart disease (IHD) research as evidence suggests that reactive oxygen species (ROS) produced during IHD can cause NCX to malfunction resulting in an intracellular calcium overload leading to cardiac contractile abnormalities. Therefore, I hypothesized that NCX function is mediated by ROS increasing NCX1 activity during cardiac ischemia-reperfusion. To research this hypothesis, I investigated cellular mechanisms which may play a role in NCX dysfunction and also examined methods to correct NCX function. I found that reactive oxygen species directly and irreversibly modify NCX protein, increasing its activity, thereby worsening the calcium overload which is deleterious to cardiac function. I also elucidated the molecular means by which NCX protein modification occurs. Exploring pharmacological means by which to decrease NCX function to relieve the calcium overload and reduce the damage to the heart, I discovered that ranolazine (Ranexa), indicated for the treatment of angina pectoris inhibits NCX activity directly, thereby further reducing the calcium overload-induced injury to the heart. Furthermore, many IHD patients are also co-morbid for type-2 diabetes. These patients are prescribed sulfonylurea (SU) agents which act at the ATP sensitive K+ channel (KATP). One agent such as glibenclamide is known to have cardiotoxic side effects. Therefore, SUs devoid of any cardiac side effects would beneficial. Interestingly, patients possessing the genetic variant E23K-S1369A KATP channel have improved blood glucose levels with the use of the SU gliclazide. Therefore, I determined the functional mechanism by which gliclazide has increased inhibition at the KATP channel. These findings have implications for type-2 diabetes therapy, in which 20% of the type-2 diabetic population carries the KATP channel variant. In summary, the findings presented in this thesis have implications on treatment strategies in the clinical setting, as a NCX inhibitor can be beneficial in IHD and possibly type-2 diabetes. Moreover, a pharmacogenomic approach in treating type-2 diabetes may also provide a positive outcome when considering co-morbid cardiac complications such as atrial fibrillation and heart failure.

The gastric mucosa is frequently exposed to endogenously secreted hydrochloric acid of high acidity. Gastric mucosal defense mechanisms are arranged at different levels of the gastric mucosa and must work in unison to maintain its integrity. In this thesis, several mechanisms underlying gastric mucosal resistance to strong acid were investigated in anesthetized rats and mice. The main findings were as follows: Only when acid secretion occurred did the pH gradient in the mucus gel withstand back-diffusion of luminal acid (100 mM or 155 mM HCl), and keep the juxtamucosal pH (pHjm) neutral. Thus, when no acid secretion occurred and the luminal pH was 0.8-1, the pH gradient was destroyed. Bicarbonate ions, produced concomitant with hydrogen ions in the parietal cells during acid secretion and blood-borne to the surface epithelium, were carried transepithelially through a DIDS-sensitive transport. Prostaglandin-dependent bicarbonate secretion seemed to be less important in maintaining a neutral pHjm. Removal of the loosely adherent mucus layer did not influence the maintenance of the pHjm. Hence, only the firmly adherent mucus gel layer, approximately 80µm thick, seemed to be important for the pHjm. Staining of the mucus gel with a pH-sensitive dye revealed that secreted acid penetrated the mucus gel from the crypt openings toward the gastric lumen only in restricted paths (channels). One crypt opening was attached to one channel, and the channel was irreversibly formed during acid secretion. Gastric mucosal blood flow increased on application of strong luminal acid (155 mM HCl). This acid-induced hyperemia involved the inducible but not the neural isoform of nitric oxide synthase. These results suggest a novel role for iNOS in gastric mucosal protection and indicate that iNOS is constitutively expressed in the gastric mucosa. It is concluded that a pH gradient in the gastric mucus gel can be maintained during ongoing acid secretion, since the acid penetrates the mucus only in restricted channels and bicarbonate is carried from the blood to the lumen via a DIDS-sensitive transporter.

The field of forensic genetics is growing fast and the development and optimisation of more sensitive, faster and more discriminating forensic DNA analysis methods is highly important. In this thesis, an evaluation of the use of novel DNA technologies and the development of specific applications for use in forensic casework investigations are presented. In order to maximise the use of valuable limited DNA samples, a fast and user-friendly Real-time PCR quantification assay, of nuclear and mitochondrial DNA copies, was developed. The system is based on the 5’ exonuclease detection assay and was evaluated and successfully used for quantification of a number of different evidence material types commonly found on crime scenes. Furthermore, a system is described that allows both nuclear DNA quantification and sex determination in limited samples, based on intercalation of the SYBR Green dye to double stranded DNA. To enable highly sensitive DNA analysis, Pyrosequencing of short stretches of mitochondrial DNA was developed. The system covers both control region and coding region variation, thus providing increased discrimination power for mitochondrial DNA analysis. Finally, due to the lack of optimal assays for quantification of mitochondrial DNA mixture, an alternative use of the Pyrosequencing system was developed. This assay allows precise ratio quantification of mitochondrial DNA in samples showing contribution from more than one individual. In conclusion, the development of optimised forensic DNA analysis methods in this thesis provides several novel quantification assays and increased knowledge of typical DNA amounts in various forensic samples. The new, fast and sensitive mitochondrial DNA Pyrosequencing assay was developed and has the potential for increased discrimination power.

The unique native structure is a basic requirement for normal functioning of most proteins. Many diseases stem from mutations in proteins that destabilize the protein structure thereby resulting in impairment or loss of function (Sunyaev et al. 2000). Therefore, it is important from both fundamental and applied points of view, to elucidate the sequence determinants of protein structure and function. With the advent of recombinant DNA techniques for modifying protein sequences, studies on the effect of amino acid replacements on protein structure and function have acquired momentum. It is well established from previous mutagenesis studies that buried residues in a protein are important determinants of protein structure or stability while surface residues are involved in protein function (Rennell et al. 1991; Terwilliger et al. 1994; Axe et al. 1998). Inspite of this, there is no universally accepted definition and probe to distinguish and identify buried residues from exposed residues. A part of this thesis aims to examine the feasibility of using scanning mutagenesis to distinguish between buried and exposed positions in the absence of three-dimensional structure and also to arrive at an experimental definition of the appropriate accessibility cut-off to distinguish between buried and exposed residues. Proline, being an unusual amino acid is usually exploited to determine sites in a protein important for protein stability (Sauer et al. 1992). This thesis also explores the use of proline scanning mutagenesis to make inferences about protein structure and stability. Temperature sensitive mutant proteins, which result from single amino acid substitutions, are particularly useful in elucidating the determinants of protein folding and stability (Grutter et al. 1987; Sturtevant et al. 1989). Temperature sensitive (ts) mutants are an important class of conditional mutants which are widely used to study gene function in vivo and in cell culture (Novick and Schekman 1979; Novick and Botstein 1985). They display a marked drop in the level or activity of the gene product when the gene is expressed above a certain temperature (restrictive temperature). Below this temperature (permissive temperature), the level or activity of the mutant is very similar to that of the wild type. Inspite of their widespread use, little is known about the molecular mechanisms responsible for generating a Ts phenotype. A part of this thesis discusses a set of sequence/structure-based strategies for the successful design and isolation of ts mutants of a globular protein, inferred from saturation mutagenesis of CcdB. The experimental system, CcdB (Controller of Cell Division or Death B protein), is a 101 residue, homodimeric protein encoded by F plasmid. The protein is an inhibitor of DNA gyrase and is a potent cytotoxin in E.coli (Bernard et al. 1993). Crystallographic structures of CcdB in the free and gyrase bound forms (Loris et al. 1999; Dao-Thi et al. 2005) are also available. Expression of the CcdB functional protein results in cell death, thus providing a rapid and easy assay for the protein (Chakshusmathi et al. 2004). This dissertation focuses on understanding the determinants of globular protein stability and temperature sensitivity using saturation mutagenesis of E.coli CcdB. Towards this objective, we attempted to replace each of the 101 residues of CcdB with 19 other amino acids using high throughput mutagenesis tools. A total of 1430 (~75%) of all possible single site mutants of the CcdB saturation mutagenesis library could be isolated. These mutants were characterized in terms of their activity at different expression levels. The correlation between the observed mutant phenotypes with residue burial, nature of substitution and expression level was examined. The introductory chapter (Chapter 1) describes the use of mutagenesis as a tool to understand the relationship between protein sequence, structure and function. It represents an overview of previous large scale mutagenesis studies from the literature. It also addresses the motivation behind this work and problems which we have attempted to address in these studies. Chapter 2 discusses mutagenesis based definitions and probes for residue burial in proteins as derived from alanine and charged scanning mutagenesis of CcdB. Every residue of the 101 amino acid E. coli toxin CcdB was substituted with Ala, Asp, Glu, Lys and Arg using site directed mutagenesis. The activity of each mutant in vivo was characterized as a function of CcdB transcriptional level. The mutation data suggest that an accessibility value of 5% is an appropriate cutoff for definition of buried residues. At all buried positions, introduction of Asp results in an inactive phenotype at all CcdB transcriptional levels. The average amount of destabilization upon substitution at buried positions decreases in the order Asp>Glu>Lys>Arg>Ala. Asp substitutions at buried sites in two other proteins, MBP and Thioredoxin were also shown to be severely destabilizing. Ala and Asp scanning mutagenesis, in combination with dose dependent expression phenotypes, was shown to yield important information on protein structure and activity. These results also suggest that such scanning mutagenesis data can be used to rank order sequence alignments and their corresponding homology models, as well as to distinguish between correct and incorrect structural alignments. When incorporated into a polypeptide chain, Proline (Pro) differs from all other naturally occurring amino acids in two important respects. The  dihedral angle of Pro is constrained to values close to –65o and Pro lacks an amide hydrogen. Chapter 3 describes a procedure to accurately predict the effects of proline introduction on protein stability. 77 of the 97 non-Pro amino acid residues in the model protein, CcdB, were individually mutated to proline and the in vivo activity of each mutant was characterized. A decision tree to classify the mutation as perturbing or non-perturbing was created by correlating stereochemical properties of mutants to activity data. The stereochemical properties, including main chain dihederal angle and main chain amide hydrogen bonds, were determined from 3D models of the mutant proteins built using MODELLER. The performance of the decision tree was assessed on 74 nsSNPs and 37 other proline substitutions from the literature. The overall accuracy of this algorithm was found to be 89% in case of CcdB, 71% in case of nsSNPs and 83% in case of other proline substitution data. Contrary to previous assertions, Proline scanning mutagenesis cannot be reliably used to make secondary structural assignments in proteins. The studies will be useful in annotating uncharacterized nsSNPs of disease-associated proteins and for protein engineering and design. Mutants of CcdB were also characterized in terms of their activity at two different temperatures (30oC and 37oC) to screen for temperature sensitive (ts) mutants. The isolation and structural analysis of Ts mutants of CcdB is dealt with in Chapter 4. Of the total 1430 single site mutants, 12% showed a ts phenotype and were mapped onto the crystal structure of the protein. Almost all the ts mutants could be interpreted in terms of the wild type, native structure. ts mutants were found at all buried sites and all active sites (except one). ts mutants were also obtained at sites in close proximity to active site residues where polar side-chains were involved in H-bonding interaction with active site residues. Several proline substitutions also displayed a ts phenotype. The effect of expression level on ts phenotype was also studied. 78% of the mutants that showed an inactive phenotype at the lowest expression level and an active phenotype at highest expression level, resulted in a ts phenotype at an intermediate expression level. The molecular determinant responsible for the ts phenotype of buried site ts mutant is suggested to be the thermodynamic destabilization of the protein which results in a reduced steady state in vivo level of soluble, functional protein relative to wild type. The active site ts mutants probably lower the specific activity of the protein and hence the total activity relative to wild type. However these effects might be less severe at lower temperature. Specific structure/function based mutagenesis strategies are suggested to design ts mutant of a protein. These studies will simplify the design of ts mutants for any globular protein and will have applications in diverse biological systems to study gene function in vivo. Chapter 5 represents the structural and sequence correlations of a CcdB saturation mutagenesis library which was obtained by replacing each of 101 amino acid residues with 19 other amino acids. Polar substitutions i.e. Asn, Gln, Ser, Thr and His were poorly tolerated at buried sites at lower expression levels. Aromatic substitutions and Gly were also not well tolerated at buried positions at lower expression levels. Trp was poorly tolerated at residues with accessibility <15%. However, most of the surface exposed residues with accessibility >40% (except functional ones) could tolerate all kinds of substitutions. Chapter 6 deals with the thermodynamic characterization of monomeric and dimeric forms of CcdB. The stability and aggregation state of CcdB have been characterized as a function of pH and temperature. Size exclusion chromatography revealed that the protein is a dimer at pH 7.0, but a monomer at pH 4.0. CD analysis and fluorescence spectroscopy showed that the monomer is well folded, and has similar tertiary structure to the dimer. Hence intersubunit interactions are not required for folding of individual subunits. The oligomeric status of CcdB at pH 7.0 at physiologically relevant low concentrations of protein, was characterized by labeling the protein with two different pairs of donor and acceptor fluorescent dyes (Acrylodan-Pyrene and IAF-IAEDANS) separately and carrying out fluorescence resonance energy transfer (FRET) measurements by mixing them together. CcdB exists in a dimeric state even at nanomolar concentrations, thus indicating that the dimeric form is likely to be the physiologically active form of CcdB. The stability of the dimeric form at pH 7.0 and the monomeric form at pH 4.0 was characterized by isothermal denaturant unfolding and calorimetry. The free energies of unfolding were found to be 9.2 kcal/mol (1 cal=4.184 J) and 21 kcal/mol at 298 K for the monomer and dimer respectively. The denaturant concentration at which one-half of the protein molecules are unfolded (Cm) for the dimer is dependent on protein concentration, whereas the Cm of the monomer is independent of protein concentration, as expected. Although thermal unfolding of the protein in aqueous solution is irreversible at neutral pH, it was found that thermal unfolding is reversible in the presence of GdnCl (guanidinium chloride). Differential scanning calorimetry in the presence of low concentrations of GdnCl in combination with isothermal denaturation melts as a function of temperature were used to derive the stability curve for the protein. The value of Cp (representing the change in excess heat capacity upon protein denaturation) is 2.8 ± 0.2 kcalmol-1K-1 for unfolding of dimeric CcdB, and only has a weak dependence on denaturant concentration. These studies advanced the understanding of protein folding of oligomeric proteins. The concluding section summarizes all the chapters in a nutshell and addresses the future directions provided by these investigations.