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Proteins perform an incredible array of functions facilitated by a diverse set of biochemical properties. Changing these properties is an essential molecular mechanism of evolutionary change, with major questions in protein evolution surrounding this topic. How do new functional biochemical features evolve? How do proteins change following gene duplication events? I used the S100 protein family as a model to probe these aspects of protein evolution. The S100s are signaling proteins that play a diverse range of biological roles binding Calcium ions, transition metal ions, and other proteins. Calcium drives a conformational change allowing S100s to bind to diverse peptide regions of target proteins. I used a phylogenetic approach to understand the evolution of these diverse biochemical features. Chapter I comprises an introduction to the disseration. Chapter II is a co-authored literature review assessing available evidence for global trends in protein evolution. Chapter III describes mapping of transition metal binding onto a maximum likelihood S100 phylogeny. Transition metal binding sites and metal-driven structural changes are a conserved, ancestral features of the S100s. However, they are highly labile at the amino acid level. Chapter IV further characterizes the biophysics of metal binding in the S100A5 lineage, revealing that the oft–cited Ca2+/Cu2+ antagonism of S100A5 is likely due to an experimental artifact of previous studies. Chapter V uses the S100 family to investigate the evolution of binding specificity. Binding specificity for a small set of peptides in the duplicate S100A5 and S100A6 clades. Ancestral sequence reconstruction reveals a pattern of clade-level conservation and apparent subfunctionalization along both lineages. In chapter VI, peptide phage display, deep-sequencing, and machine-learning are combined to quantitatively reconstruct the evolution of specificity in S100A5 and S100A6. S100A5 has subfunctionalized from the ancestor, while S100A6 specificity has shifted. The importance of unbiased approaches to measure specificity are discussed. This work highlights the lability of conserved functions at the biochemical level, and measures changes in specificity following gene duplication. Chapter VII summarizes the results of the dissertation, considers the implications of these results, and discusses limitations and future directions. This dissertation includes both previously published/unpublished and co- authored material.

Conselho Nacional de Desenvolvimento Científico e Tecnológico / Early diagnosis of leprosy is an important contribution to reducing the incidence of the disease. For its early detection, the development of new platforms that include the mapping of antigens with potential to be used in immunodiagnostic is of great interest. Among these antigens, the PGL-1 and epitopes derived from specific bacillus proteins have received great attention. Alternatively, due to their versatility to perform the same functions as the protein and non-protein natural antigens, mimetic peptides are considered an important tool. Thus, our goal was to produce mimetic peptides of Mycobacterium leprae antigens that are promising as serological markers, which will be explored in new diagnostic platforms. To produce peptide mimetics, phage display technology was used. In the first case, we used a monoclonal anti-PGL-1 (CS-38) aiming to obtain peptides that mimics the PGL-1. In the second case, the peptides were obtained having purified IgGs from patients with leprosy as target. The sequences of the selected peptides expressed on the phage surface were chemically synthesized. The synthetic peptides were validated by ELISA (case 1 and 2) and by an immunosensor based on Surface Plasmon Resonance (case 1). Aiming to confirm and identify the targets of the mimetic peptides, scFv antibodies were produced by reverse engineering. The PGL-1-M3 peptide that mimics the native PGL-1 had a sensitivity of 89.11% and specificity of 100.00% in the IgM detection, with positivity of 100% in lepromatous (LL). The IgG detection had positivity of 60% for tuberculoid (TT) and 39% for household contacts (HC). This peptide was used in assembling one biophotonics platform, which allowed the differentiation of all forms of leprosy (p <0.05). The anti-scFv-M3 PGL-1 recognized native PGL-1 and accurately detected the M. leprae in immunohistochemistry tests. The MPML11, MPML14 and MPML12 peptides that mimics M. leprae antigens detect IgG and IgA in patients and HC. In IgG detection, MPML11 peptide showed positivity in 52.2% of TT and 35% of HC, and is also a promising marker of type 2 reaction. MPML12 and MPML14 peptides showed a very similar behavior to the PGL-1, with positivity of 100% and 92.85% in LL, respectively. The three peptides detected IgA in the serum of patients, especially multibacillary (MBs); and IgA in saliva of MBs and HC which index case was multibacillary. Mimetic peptides obtained in this work were confirmed as true mimetics of M. leprae antigens and can be applied in the diagnosis of leprosy in different platforms. / O diagnóstico precoce da hanseníase representa uma contribuição importante para diminuir a incidência da doença. Para isso é fundamental o desenvolvimento de novas plataformas, que incluam o mapeamento de antígenos com potencial para o imunodiagnóstico. Dentre estes destaca-se o PGL-1 e epítopos obtidos de proteínas específicas do bacilo. Alternativamente, peptídeos miméticos apresentam-se como uma importante ferramenta, pela versatilidade em desempenhar as mesmas funções que os antígenos naturais proteicos e não-proteicos. Dessa forma, nosso objetivo foi produzir peptídeos miméticos a antígenos do Mycobacterium leprae e que sejam promissores como marcadores sorológicos, os quais serão explorados em novas plataformas diagnósticas. Para produzir os peptídeos miméticos foi utilizada a tecnologia phage display. No primeiro processo utilizou-se um anticorpo monoclonal anti-PGL-1 (CS-38) para obter peptídeos miméticos ao PGL-1. No segundo processo, os peptídeos foram produzidos tendo como alvo IgGs purificadas de pacientes com hanseníase. As sequências dos peptídeos expressos nos fagos foram sintetizadas quimicamente. Os peptídeos sintéticos foram validados por ELISA (processo 1 e 2) e imunosensor baseado em Ressonância Plasmônica de Superfície (processo 1). Por meio de engenharia reversa, anticorpos scFv foram produzidos para confirmar e identificar alvos dos peptídeos miméticos. O peptídeo PGL-1-M3 mimético ao PGL-1 nativo apresentou sensibilidade de 89,11% e especificidade de 100,00% na detecção de IgM, com positividade de 100% em lepromatosos (LL), bem como títulos de IgG detectaram positividade de 60% para tuberculóides (TT) e 39% para contatos domiciliares (HC). Com este peptídeo foi montada uma plataforma biofotônica, que diferencia todas as formas clínicas de hanseníase (p<0,05). O scFv anti-PGL-1-M3 reconheceu PGL-1 nativo e detectou com precisão o M. leprae na imuno-histoquímica. Os peptídeos MPML11, MPML12 e MPML14 miméticos de antígenos do M.leprae detectam IgG e IgA em pacientes e HC. Na detecção de IgG, MPML11 apresentou positividade de 52,2% em TT e 35% em HC e também é um promissor marcador de reação tipo 2. MPML12 e MPML14 apresentaram um comportamento muito similar ao PGL-1, tendo 100% e 92,85% de positividade em LL, respectivamente. Os três peptídeos detectaram IgA nos soros de pacientes, especialmente multibacilares (MBs); bem como IgA na saliva de MBs e HC cujo caso índice era multibacilar. Os peptídeos miméticos obtidos nesse trabalho foram confirmados como miméticos verdadeiros de antígenos do M. leprae e podem ser aplicados no diagnóstico da hanseníase em diferentes plataformas. / Doutor em Genética e Bioquímica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Alzheimer's Disease (AD) is the most important cause of dementia in the world.The involvement of the immune system in the pathogenic process has been shown by several studies including the description of autoantibodies (AAc) directed to targets in the central nervous system.It is not possible yet to further define what their exact involvement in AD is. In this study, using the methodology of Phage Display we sought to identify AAc specific to patients with the disease and to characterize their antigens using bioinformatics tools. We selected 10 patients with AD according to DSM-IV-TR and NINCDS ASRDA criteria and 10 healthy controls matched for age and sex.Using a library of peptides displayed on M13 phages, we performed biopanning, thus selecting 10 peptides recognized by IgG in sera from patients with AD. The probable epitopes were characterized and their involvement with AD was assessed in the literature.We found alignment with Neurexin 3&#946;, PLK4, Neuroserpin, DNAJ, Mint-1/X11, units of the nicotinic acetylcholine receptor, Trombospondin-1, TRAF6, ACE, GDNF &#945;3 receptor, PRUNE2 and CD44. The Phage display technology, combined with bioinformatics tools, has proven to be an interesting research methodology of AAb present in the serum of patients with AD and may provide new insights into disease mechanisms and therapeutic targets. / A Doença de Alzheimer (DA) é a causa mais importante de demência no mundo. O envolvimento do sistema imunológico no processo patogênico tem sido demonstrado em diversos estudos inclusive com a descrição de autoanticorpos (AAcs) presentes no soro dirigidos a alvos no sistema nervoso central. Não é possível definir ainda qual a sua participação exata na DA. Neste estudo, utilizando a metodologia do Phage Display procuramos identificar AAcs específicos de pacientes com a doença e caracterizar seus antígenos utilizando ferramentas de bioinformática. Foram selecionados 10 pacientes com DA segundo os critérios do DSM-IV TR e NINCDS-ASRDA e 10 controles saudáveis pareados por sexo e idade. Utilizando uma biblioteca de peptídeos expostos em fagos M13, foi realizado biopanning selecionando 10 peptídeos reconhecidos por IgGs no soro de pacientes com DA. Os prováveis epítopos foram caracterizados e seu envolvimento com a DA foi avaliado na literatura. Foram encontrados alinhamentos com a Neurexina 3&#946;, PLK4, Neuroserpina, vários membros da família DNAJ, Mint-1/X11, Gene 2 de susceptibilidade para o Autismo, unidades &#945;2, &#945;3, &#945;4 e &#945;6 do receptor nicotínico da acetilcolina, Trombospondina-1, TRAF6, ECA, receptor &#945; 3 do GDNF, PRUNE2 e CD44. A tecnologia de Phage Display, aliada a ferramentas de bioinformática, demonstrou ser interessante metodologia de investigação de AAcs presentes no soro de pacientes com DA podendo fornecer novas pistas sobre mecanismos da doença e alvos terapêuticos. / Mestre em Ciências da Saúde

Introduction: Tuberculosis is an infectious disease that affects more than 9 million people each year worldwide . For tuberculosis control methods for the study of more accurate diagnostic and monitoring treatment , make it essential . Objectives: To identify biomarkers by Phage display technique and evaluate the immunoreactivity of the IG\'s clones selected sera from patients with tuberculosis to monitor treatment . Methods: Blood samples were collected from 61 individuals over 18 years , both sexes , and performed the tuberculin test ( PPD ) as a control . The samples were subjected to the process of selection of clones, the biopanning using a library of random 12 amino acid region of the protein expressed on the phage pIII . After selecting the ELISA assay was performed to analyze the immunoreactivity of selected clones . Results: after the in silico analysis , it was found that the sequence of clone F10 ( VYKTPNSTANRW ) has similarity to the membrane protein MPT64 low molecular weight , 28 to 32 kDa, immunogenicity of the M. tuberculosis complex. In ELISA clone F10 showed reactivity significant ( p < 0.05 ) and monitoring of individuals in treatment (P < 0.005). Conclusion : the reactivity of clone F10 demonstrated that it can be used for monitoring the treatment of tuberculosis , contributing to its control. / Introdução: A Tuberculose é uma doença infectocontagiosa , que acomete mais de 9 milhões de indivíduos a cada ano em todo o mundo . Para o controle da tuberculose o estudo por métodos de diagnósticos mais acurados e o monitoramento ao tratamento, tornam se imprescindíveis. Objetivos: identificar biomarcadores pela técnica de Phage display e avaliar a imunorreatividade dos clones selecionados ás igG\'s de soros de pacientes com tuberculose para o monitoramento do tratamento. Métodos: foram coletadas amostras de sangue de 61 indivíduos maiores de 18 anos, ambos os sexos, e realizada a prova tuberculina (PPD) como controle. As amostras foram submetidas ao processo de seleções de clones, o Biopanning, utilizando uma biblioteca de 12 aminoácidos randômicos expressos na região da proteína pIII do bacteriófago. Após a seleção foi realizado o ensaio ELISA para analisar a imunorreatividade dos clones selecionados. Resultados: após as análises in silico, observou-se que a sequência do clone F10 (V Y K T P N S T A N RW), possui similaridade com a proteína MPT64 de membrana de baixo peso molecular, 28 a 32 KDa, imunogênica do complexo M.tuberculosis . No ensaio ELISA o clone F10 apresentou uma reatividade significante ( p<0,05 ) e no monitoramento dos indivíduos em tratamento ( p<0,005 ). Conclusão: a reatividade do clone F10 demonstrou que pode ser utilizada para o monitoramento do tratamento da tuberculose, contribuindo para seu controle. / Mestre em Ciências da Saúde

Orientador: Prof. Dr. Luciano Puzer / Tese (doutorado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biossistemas, 2018. / Serpinas sao proteinas inibidoras de serino-proteases, responsaveis pelo controle dos mais diversos processos fisiologicos e que cujo mecanismo de inibicao consite em formar um complexo covalente com a enzima alvo, em um processo de inibicao irreversivel. A alca de centro reativo (RCL) e responsavel por interagir com a protease, mimetizando um substrato, e quando clivada se insere como uma ¿À-fita no interior da serpina, trazendo a protease e causando uma distorcao no seu sitio ativo. Como as serpinas forma ligacoes covalentes com seus alvos durante a inibicao, essas proteinas tem sido utilizadas para o estudo do mecanismo de hidrolise das serino-proteases. No entanto, elas tambem oferecem a possibilidade do desenvolvimento de novas drogas contra enzimas relacionadas com patologias, como pode ser o caso da Vioserpina, uma serpina bacteriana capaz de inibir serino-proteases do tipo tripsina-like como a calicreina tecidual humana 5. Encontrar uma maneira de produzir uma Vioserpina fluorescente pode resultar no desenvolvimento de uma poderosa ferramenta para moniotramento e controle dessa e outras enzimas envolvidas com processos patologicos, como o antigeno prostatico especifico (PSA). Dessa maneira, realizamos mutacoes pontuais no gene da Vioserpina para a incorporacao do aminoacido cumarinico via par ortogonal tRNA/aaRS por supressao do codon ambar de parada. O aminoacido cumarinico e um aminoacido nao-canonico capaz de emitir fluorescencia na comprimento de onda de 450 nm quando excitado a 363 nm, permitindo o facil monitoramento e deteccao de uma proteina. Tres residuo distintos da Vioserpina foram escolhidos para a incorporacao do aminoacido cumarinico: Trp 208, Ile 342 (P4 da RCL) e Val 343 (P3 da RCL). A incorporacao nas posicoes Trp 208 e Ile 342 resultou em proteina fluorescentes, mas truncadas apos a insercao do aminoacido. Foi possivel obter uma Vioserpina completa com o aminoacido cumarinico na posicao Ile 342, embora com rendimento muito baixo. Tal mutante apresentou capacidade de inibicao e especificidade diferentes da Vioserpina wild type, em ensaios de inibicao enzimatica contra Tripsina e Quimotripsina, indicando que o aminoacido cumarinico em P4 parece causar diferentes interacoes no momento de inibicao da serpina. Para averiguar as melhores sequencias resultantes da incorporacao do aminoacido cumarinico, foi gerada uma biblioteca de genes da Vioserpina variando aleatoriamente as posicoes P4, P2, P1 e P1f da RCL, com incosporacao do aminoacido cumarinico na posicao P3 (Val 343). A biblioteca de Vioserpina foi apresentada por Phage Display no capsideo do fago M13 fusionada a proteina PIII, utilizando Biopanning para selecao das melhores sequencias com incorporacao do aminoacido nao-canonico, contra a serino-protease quimotripsina. A biblioteca de fagos gerou cinco sequencias com melhor inibicao que da Vioserpina, e mostrou que a insercao do aminoacido cumarinico parece acontecer com maior frequencia quando flanqueado por aminoacidos hidrofobicos ou sem cargas. A incorporacao do aminoacido cumarinico em sequencias da Vioserpina foi bem sucedida, sendo possivel avaliar a insercao de tal aminoacido na capacidade inibitoria dessa serpina. A investigacao da insercao de aminoacido nao-canonicos por Phage Display e Biopanning representa um grande passo para entender melhor como ocorre a incorporacao de tais aminoacidos, e quais residuos podem ocupar com maior naturalidade suas posicoes laterais. / Serpins are serine protease inhibitor proteins, responsible for the control of the most diverse physiological processes and whose mechanism of inhibition consists in forming a covalent complex with the target enzyme, in an irreversible inhibition process. The reactive center loop (RCL) acts as a bait for the protease, and when cleaved it inserts as a â-strand inside the molecule, distorting the protease active site. As serpins form covalent bonds with their targets, these proteins have been used to study the hydrolysis mechanism of serine proteases. However, they also offer the possibility of developing new drugs against disease-related enzymes, as is the case of Vioserpin, a bacterial serpin capable of inhibiting trypsin-like serine proteases such as human tissue kallikrein. Finding a way of producing fluorescent Vioserpin may result in the development of a powerful tool for monitoring and controlling this and other enzymes involved in pathological processes, such as prostate specific antigen (PSA). Thus, we performed point mutations in the Vioserpin gene for incorporation of the coumarin amino acid through tRNA/aaRS orthogonal pair by suppression of the amber stop codon. The coumarin amino acid is a non-canonical amino acid capable of emitting fluorescence at 450 nm when excited at 363 nm, allowing for easy detection of a protein. Three different residues of Vioserpin were chosen for incorporation of the coumarin amino acid: Trp 208, Ile 342 (P4 in RCL) and Val 343 (P3 in RCL). Incorporation at positions Trp 208 and Ile 342 resulted in fluorescent but truncated proteins following amino acid insertion. A complete Vioserpin bearing the coumarin amino acid at the Ile 342 position was possible, although at very low yield. Such a mutant exhibited different inhibition and specificity compared to Vioserpin wild type in enzymatic inhibition assays against trypsin and chymotrypsin, indicating that the coumarin amino acid at P4 appears to cause different interactions during serpin inhibition. To ascertain the best sequences resulting from coumarin amino acid incorporation, a Vioserpin gene library was generated by randomly varying the P4, P2, P1 and P1' positions in RCL, with coumarin amino acid incorporated at the P3 (Val 343) position. The Vioserpin library was exhibited by Phage Display in the M13 phage capsid fused to the PIII protein, using Biopanning against chymotrypsin to select the best sequences with incorporation of the non-canonical amino acid. The phage library generated five sequences with better inhibition than Vioserpin, and pointed to coumarin amino acid insertion appearing to occur more frequently when flanked by hydrophobic or uncharged amino acids. The incorporation of the coumarin amino acid into Vioserpin sequences was successful, and it is possible to evaluate the insertion of such amino acid in the inhibitory capacity of this serpin. The investigation of non-canonical amino acid insertion by Phage Display and Biopanning represents a great step to better understand how the incorporation of such amino acids occurs, and which residues may more naturally occupy their lateral positions

The increasing incidence of infections due to antibiotic resistant bacteria has led to renewed interest in bacteriophages (= phages) and phage therapy. Although phage therapy has been applied to control bacterial diseases in plants, poultry, livestock and humans, its application in aquaculture is still relatively limited. The emergence of phage-resistant bacterial mutants has been considered to be one of the major limitations of phage therapy. This study aimed to (i) isolate and characterise phages; (ii) select phages and their bacterial hosts to set up in vivo phage therapy models with aquaculture animals, and estimate the efficiency of phage therapy; (iii) investigate the generation and characteristics of phage-resistant mutants, and thus estimate the consequence of applying phage therapy when phage-resistant mutants emerge; and (iv) discuss the prospects for application of phages in aquaculture. Two Vibrio isolates and their phages were isolated from a Scottish marine fish farm. Based on the results of conventional phenotype testing and 16S rRNA gene sequencing analysis, the two vibrios, V9 and V13, were identified as Vibrio splendidus and Vibrio cyclitrophicus, respectively. The bacterial characteristics including morphology, temperature and salinity range of growth, production of extracellular enzymes, and the possession of virulence genes were examined. According to the morphological characteristics observed using transmission electron microscopy by negative staining, phage PVS9 of V. splendidus V9 was identified as a myophage, while phage PVC13 of V. cyclitrophicus V13 was identified as a siphophage. The phages could only lyse one bacterial host strain and their genomic DNA was double stranded with a size of ~46 kb. The two Vibrio isolates were found to be non- or of low virulence to rainbow trout, goldsinny wrasse and Artemia in pathogenicity experiments. Thus an in vivo phage therapy model could not be set up using these Vibrio isolates and their phages. Two phages pAS-3 and pAS-6 were isolated using the Aeromonas salmonicida subsp. salmonicida Hooke strain as the host. Phages pAS-3 and pAS-6 had a similar genome size of ~50 kb, and the same relatively narrow host range within A. salmonicida subsp. salmonicida strains. The siphophage pAS-3 formed clear plaques and inhibited A. salmonicida Hooke growth in vitro completely for at least 18 hours when using MOI = 1,000, whereas the podophage pAS-6 formed turbid plaques and weakly inhibited Hooke growth. Rainbow trout exposed by intraperitoneal injection with 0.1 mL of the raw phage preparations at a concentration of 108 PUF mL-1 showed no adverse effects over 14 days. In the phage therapy trial, fish were firstly injected with 1 x 102 CFU fish-1 of A. salmonicida Hooke, then immediately injected with phage preparations of pAS-3 and pAS-6, respectively, using MOI = 10,000. Compared with the control group (which did not receive phage treatment), phage treated groups showed a delay in the time to death, and lower mortalities. However, the mortalities and time to death between phage treated and non-treated groups were not significantly different. Phage-resistant mutants of pathogenic A. salmonicida strain Hooke were induced by repeatedly challenging with phage pAS-3. One of the mutants, termed HM, was chosen to compare the characteristics with the parental wild-type strain Hooke. Test results including the formation of ‘smooth’ colonies on TSA, autoagglutination negative, the formation of creamy colonies on Coomassie Brilliant Blue agar, and the degradation of a thick/furry layered structure on the cell surface indicated a deficiency of the A-layer in the phage-resistant mutant HM. Therefore, it was deduced that the A-layer either directly acted as the receptor of A. salmonicida phage pAS-3, or was affected indirectly by the change of an unknown phage receptor. The greater wax moth larvae model was used to compare the virulence of the phage-resistant mutant HM and the parental wild-type strain Hooke, as it is an ethically acceptable animal model, which has the advantages of being low cost and convenient for injection, and is also a recognised alternative model for bacterial pathogens of fish. The results showed that virulence of the phage-resistant mutant HM did not decline in the greater wax moth larvae model compared with that of the parental wild-type strain Hooke. In conclusion, different approaches were used to isolate and characterise phages from different aquaculture environments for potential use in phage therapy. A rainbow trout model was set up using pathogenic A. salmonicida strain Hooke and two A. salmonicida phages pAS-3 and pAS-6. The use of phage treatment led to lower cumulative mortalities and delay to the time of death, although the differences between the groups were not significant, futher work is required to determine if these phages have potential in phage therapy. The consequence of applying phage therapy when phage-resistant mutants emerge was estimated based on their characteristics and virulence, and no decline in virulence of the phage-resistant mutant from this study indicates the importance of fully testing the virulence of phage-resistant mutants before carrying out large scale field trials of phage therapy. It appears feasible to use phage therapy as an alternative approach to control bacterial infections in aquaculture, but further studies are required to focus on improving effectiveness, and also to overcome the concrete limitations and hurdles in application and commercialisation. Moreover, a broader range of applications of phages in aquaculture should be explored.

Within the immune system, Y-shaped proteins known as antibodies play crucial roles in detecting and blocking the harmful effects of foreign pathogens. Antibodies are naturally synthesized in our bodies by plasma B-cells, but they can also be synthesized and manufactured in labs through methods of recombinant antibody technology. Today, the field of antibody research and development is a competitive area of study due to the great promise it carries. In this study, 4 clones were developed as phage linked and soluble scFv proteins in order to be tested for their specificity against an RTK antigen, T1. T1 was of interest due to its hypothesized involvement in a breast cancer causing pathway. Subsequent selection assays in the form of ELISA and Western Blot were performed in order to identify a promising antibody candidate both robust in expression and specific in binding. The ELISA results pointed to Clone A1 as having the greatest potency and specificity for the T1 target antigen when it was presented as a phage linked and soluble scFv protein. Evaluation of the expression profiles for the 4 soluble and phage linked clones also pointed to clone A1 as being the most robust and potent. In conclusion, clone A1 exhibited the greatest ability in expression and detection of the T1 antigen and was thereby determined to be the most promising candidate in further development and optimization procedures. A1’s results in the preliminary tests also suggests strong performance in its translation into a successful therapeutic drug.

Mass production of translationally optimized bacteriophages (hereafter referred to as phages) is the need of the hour in the application of phages to therapy. Understanding translational efficiency of phages is the major preliminary step for mass producing efficient phages. The objective of this thesis is to understand factors affecting translational efficiency of phages. In chapter two, we hypothesized that weak translation initiation efficiency is responsible for weak codon concordance of Escherichia coli lambdoid phages with that of their hosts. We measured the strength of translation initiation using two indices namely minimum folding energy (MFE) and proportion of Shine-Dalgarno sequence (PSD). Empirical results substantiate our hypothesis suggesting lack of strong selection for improving codon adaptation in these phages is due to their weak translation initiation. In chapter three, we measured codon usage concordance between GC-rich and GC-poor Aeromonas phages with their GC-rich host Aeromonas salmonicida. We found low codon usage concordance in the GC-poor Aeromonas phages. We were interested in testing for the role of tRNAs in the GC-poor phages. We observed that the GC-poor phages carry tRNAs for codons that are overused by the phages and underused by the host. These findings suggest that the GC-poor Aeromonas phages carry their own tRNAs for compensating for the compositional difference between their genomes and that of their host. Previously several studies have reported observed avoidance of stable secondary structures in start site of mRNA in a wide range of species. We probed the genomes of 422 phage species and measured their secondary structure stability using MFE. We observed strong patterns of secondary structure avoidance (less negative MFE values) in the translation initiation region (TIR) and translation termination region (TTR) of all analyzed phages. These findings imply selection is operating at these translationally important sites to control stable secondary structures in order to maintain efficient translation.

Homogeneous hydrogels made of an interpenetrating network of poly(N-isopropylacrylamide) (PNIPAm) and poly(acrylic acid) (PAAc) are synthesized by a two-step process; first making PNIPAm hydrogels and then interpenetrating acrylic acid throughout the hydrogel through polymerization. The kinetic growth of the IPN is plotted and an equation is fitted to the data. When diluted to certain concentrations in water, the hydrogels show reversible, inverse thermal gelation at about 34°C. This shows unique application to the medical field, as the transition is just below body temperature. A drug release experiment is performed using high molecular weight dyes, and a phase diagram is created through observation of the purified, concentrated gel at varying concentrations and temperatures.