Os rotavírus, membros da família Reoviridae, são uma importante causa de diarreia em mamíferos e aves. São partículas icosaédricas não envelopadas e seu genoma é formado por 11 segmentos de RNA fita dupla que codificam seis proteínas estruturais e seis proteínas não estruturais. O objetivo deste estudo foi caracterizar os genes codificadores das proteínas não estruturais (NSP1-5) e estruturais (VP1-4, VP6-7) dos rotavírus do grupo A em aves de criações comerciais (corte, postura, matrizeiros e avozeiros) localizadas em 12 estados brasileiros, seguido de análises de recombinação e pressão de seleção das amostras definidas. Um total de 226 amostras fecais foram triadas através de reações de RT-PCR tendo como alvo a amplificação da VP6 e NSP5. A frequência de ocorrência, baseada em cada uma destas provas, variou de 9,7% a 18,14%, respectivamente. Em seguida, 10 das amostras positivas foram processadas com primers específicos visando a amplificação dos demais genes, seguido do sequenciamento nucleotídico e filogenia baseada no método de maximum likelihood, tendo como modelos de substituição GTR (NSP1-3, VP1-3, VP4, VP6, VP7) e HKY (NSP4, NSP5) e 1.000 repetições de bootstrap. Foram definidas sequências parciais para os genes codificadores da VP1-4, VP6-7 e NSP1-4 e sequências completas para NSP5. As respectivas árvores demonstraram que as dez amostras definidas se agruparam em clados aviários previamente descritos. Duas constelações genotípicas foram caracterizadas: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 e G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. Estes genotipos são tipicamente encontrados em aves, mas quando analisados em conjunto, esta é a primeira descrição destas constelações. Eventos de recombinação foram observados nos genes NSP2, VP1, VP3 e VP7. Pelo menos um códon com pressão de seleção positiva foi encontrado nos genes codificadores das proteínas NSP1, VP2 e VP3. Este estudo propicia um melhor entendimento acerca da epidemiologia e diversidade viral circulante nas criações aviárias brasileiras, servindo de base para o estabelecimento de medidas profiláticas mais eficazes. / Rotaviruses are members of the Reoviridae family and they are a common cause of acute diarrhea in several mammalian and avian species. They are non-enveloped icosahedral particles and its genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). The objective of this study was to characterize the RVA nonstructural and structural proteins coding genes (NSP1-NSP5, VP1-VP4, VP6 and VP7) from fecal samples from avian farms (broiler breeders, poultry, laying hens, and grandparents) raised in Brazilian commercial farms from 12 states, followed by recombination and selection pressure analysis from samples defined here. A total of 226 fecal samples were screened using a RT-PCR technique targeting the amplification of the VP6 and NSP5. The frequency of occurrence, using these techniques, ranging from 9.7% to 18,14%, respectively; and from these, ten samples were further processed with specific primers to amplify the remaining genes, followed by respective nucleotide sequencing of the amplicons and phylogeny based on method maximum likelihood, as substitutions models GTR (NSP1-3, VP1-3, VP4, VP6, VP7) and HKY (NSP4, NSP5) and 1.000 bootstrap repetitions. Partial nucleotide sequences of VP1-4, VP6-7, and NSP1-4, and complete from NSP5, were obtained in this study. The phylogenetic trees depicted that the ten Brazilian rotavirus strains segregated with previous avian RVA described elsewhere. Two avian genotype constellations have been characterized here: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8, and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. These genotypes are typically found in avian species, although when analyzed together, this is the first report of such constellations. Recombination events were observed in NSP2, VP1, VP3, and VP7 coding genes. At least on positive selected site was observed in NSP1, VP2, and VP3 genes. This study provides a better understanding of rotavirus epidemiology, by the definition of genetic variability of circulating strains.

Os rotavírus, membros da família Reoviridae, são uma importante causa de diarreia em mamíferos e aves. São partículas icosaédricas não envelopadas e seu genoma é formado por 11 segmentos de RNA fita dupla que codificam seis proteínas estruturais e seis proteínas não estruturais. O objetivo deste estudo foi caracterizar os genes codificadores das proteínas não estruturais (NSP1-5) e estruturais (VP1-4, VP6-7) dos rotavírus do grupo A em aves de criações comerciais (corte, postura, matrizeiros e avozeiros) localizadas em 12 estados brasileiros, seguido de análises de recombinação e pressão de seleção das amostras definidas. Um total de 226 amostras fecais foram triadas através de reações de RT-PCR tendo como alvo a amplificação da VP6 e NSP5. A frequência de ocorrência, baseada em cada uma destas provas, variou de 9,7% a 18,14%, respectivamente. Em seguida, 10 das amostras positivas foram processadas com primers específicos visando a amplificação dos demais genes, seguido do sequenciamento nucleotídico e filogenia baseada no método de maximum likelihood, tendo como modelos de substituição GTR (NSP1-3, VP1-3, VP4, VP6, VP7) e HKY (NSP4, NSP5) e 1.000 repetições de bootstrap. Foram definidas sequências parciais para os genes codificadores da VP1-4, VP6-7 e NSP1-4 e sequências completas para NSP5. As respectivas árvores demonstraram que as dez amostras definidas se agruparam em clados aviários previamente descritos. Duas constelações genotípicas foram caracterizadas: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8 e G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. Estes genotipos são tipicamente encontrados em aves, mas quando analisados em conjunto, esta é a primeira descrição destas constelações. Eventos de recombinação foram observados nos genes NSP2, VP1, VP3 e VP7. Pelo menos um códon com pressão de seleção positiva foi encontrado nos genes codificadores das proteínas NSP1, VP2 e VP3. Este estudo propicia um melhor entendimento acerca da epidemiologia e diversidade viral circulante nas criações aviárias brasileiras, servindo de base para o estabelecimento de medidas profiláticas mais eficazes. / Rotaviruses are members of the Reoviridae family and they are a common cause of acute diarrhea in several mammalian and avian species. They are non-enveloped icosahedral particles and its genome comprises 11 segments of double-stranded RNA, which encodes six structural proteins (VP1-4, VP6-7) and six nonstructural proteins (NSP1-6). The objective of this study was to characterize the RVA nonstructural and structural proteins coding genes (NSP1-NSP5, VP1-VP4, VP6 and VP7) from fecal samples from avian farms (broiler breeders, poultry, laying hens, and grandparents) raised in Brazilian commercial farms from 12 states, followed by recombination and selection pressure analysis from samples defined here. A total of 226 fecal samples were screened using a RT-PCR technique targeting the amplification of the VP6 and NSP5. The frequency of occurrence, using these techniques, ranging from 9.7% to 18,14%, respectively; and from these, ten samples were further processed with specific primers to amplify the remaining genes, followed by respective nucleotide sequencing of the amplicons and phylogeny based on method maximum likelihood, as substitutions models GTR (NSP1-3, VP1-3, VP4, VP6, VP7) and HKY (NSP4, NSP5) and 1.000 bootstrap repetitions. Partial nucleotide sequences of VP1-4, VP6-7, and NSP1-4, and complete from NSP5, were obtained in this study. The phylogenetic trees depicted that the ten Brazilian rotavirus strains segregated with previous avian RVA described elsewhere. Two avian genotype constellations have been characterized here: G19-P[31]-I11-R6-C6-M7-A16-N6-T8-E10-H8, and G19-P[31]-I4-R4-C4-M4-A16-N4-T4-E4-H4. These genotypes are typically found in avian species, although when analyzed together, this is the first report of such constellations. Recombination events were observed in NSP2, VP1, VP3, and VP7 coding genes. At least on positive selected site was observed in NSP1, VP2, and VP3 genes. This study provides a better understanding of rotavirus epidemiology, by the definition of genetic variability of circulating strains.

Le code génétique est la table de correspondance entre codons (unité structurelle d'un gène) et acides aminés (brique élémentaire des protéines). Le code génétique est (1) universel, tous les êtres vivants ou presque partagent le même code; (2) univoque, chaque codon spécifie un seul acide aminé et (3) dégénéré, les acides aminés peuvent être codés par plusieurs codons. Ce code dégénéré est donc utilisé par l'ensemble du vivant mais pas de la même manière, certains codons synonymes étant utilisés préférentiellement chez des espèces et pas d'autres. Pour comprendre l'émergence des biais d'usage du code (BUC) génétique entre espèces, je me place dans un contexte évolutif.Dans ce manuscrit, je présente mes travaux de recherche en quatre parties. La première partie introductive décrit la mise en évidence et les propriétés du code génétique, son biais d'usage et les diverses caractéristiques de précédents modèles de codons. La deuxième partie présente le modèle d'évolution de codons SENCA pour Sites Evolution at the Nucleotides, Codons and Amino-acids layers que j'ai développé durant ma thèse. SENCA prend en compte la structure du code génétique. Je valide sa paramétrisation par des simulations numériques et une étude sur des espèces bactériennes ou archées. La partie suivante décrit deux extensions de SENCA qui modélisent plusieurs hypothèses d'origines évolutives du BUC et une application de SENCA sur les conséquences génomiques d'adaptations environnementales. La dernière partie étudie les origines de variations de BUC le long du génome humain par une approche de génomique comparative / In this manuscript, I introduce my doctoral research in four parts. The first introductive part highlights the properties of the genetic code and its usage bias but also the caracteristics of previous published codons models. The second part presents an evolutionary codons models named SENCA for Sites Evolution at the Nucleotides, Codons and Amino-acids layers that I developped. SENCA takes into account the genetic code structure. I perform simulations and study prokaryotes species to confirm its parametrization. The following part provides two extensions of SENCA to test the hypotheses concerning the evolutive origins of CUB and an application of SENCA to study the genomic consequences of an environmental adaptation. The last part studies the origins of CUB variation within the human genome using a comparative genomic strategy

Les éléments transposables (ETs), qui sont présents chez tous les organismes vivants et sont impliqués dans un grand nombre de mutations et de réarrangements chromosomiques, apparaissent comme des composants incontournables des génomes. Ils doivent alors être soumis aux mêmes contraintes que les gènes d'hôte. Afin de tester cette hypothèse, nous avons dans un premier temps analysé l'usage des codons des gènes d'ETs et des gènes d'hôte chez cinq espèces : A. thaliana, C. elegans, D. melanogaster, H. sapiens et S. cerevisiae. Les résultats montrent que les ETs sont riches en AT quelle que soit l'espèce hôte : il s'agit donc d'une propriété intrinsèque aux ETs. L'analyse de la composition en bases aux différentes positions des codons montre que la richesse en AT à la 3ème position est inférieure aux valeurs des régions non contraintes des génomes. Ainsi, les ETs ne subissent pas uniquement des biais mutationnels mais sont aussi soumis à de la sélection. L'usage des codons des ETs n'est cependant pas lié à un taux d'expression fort ou faible, ce qui suggère un pattern d'expression particulier pour ces éléments. Dans un deuxième temps, l'analyse de l'abondance relative en di- et en trinucléotides des ETs et des génomes hôtes montre que les ETs possèdent un pattern d'abondance similaire à celui de leur hôte, indépendamment du biais de composition en bases. Cette analyse montre cependant que les gènes de rétrovirus humains et de rétrotransposons à LTR avec un gène env de drosophile ont un pattern différent des gènes d'hôte. L'abondance en dinucléotides semble être un moyen de détecter les rétroéléments potentiellement infectieux. Ce travail suggère un comportement spécifique des ETs qui semblent soumis à des contraintes de sélection particulières permettant le maintien de leur richesse en AT. Cependant, ils subissent aussi une empreinte du génome hôte, probablement de nature structurale.

Orientador: Marcelo Menossi Teixeira / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-11T20:50:45Z (GMT). No. of bitstreams: 1 Mattioli_MarceloAugustoPortugal_M.pdf: 1336841 bytes, checksum: 296a3b101b6750274ad9c012a8f42161 (MD5) Previous issue date: 2008 / Resumo: O código genético é degenerado, o que permite que um mesmo aminoácido seja codificado por trincas de nucleotídeos distintas. Trincas de um mesmo aminoácido não ocorrem com a mesma freqüência, sugerindo que existe utilização preferencial de codons (codon usage bias). Diferentes organismos geralmente apresentam codon usage bias distintos e estas diferenças podem ser fatores limitantes na expressão heteróloga. Além do codon usage bias existem outros fatores presentes em um gene que podem influenciar a intensidade com que este é traduzido, dentre eles destacam-se: a constituição das regiões gênicas próximas ao códon de iniciação (contexto de iniciação) e a região terminadora da tradução (contexto de terminação). Nosso objetivo foi identificar a presença destes padrões em seqüências ESTs de eucalipto e gerar informações que permitam aumentar os níveis de produção de proteínas de interesse em eucalipto geneticamente modificado. Em concreto, foram alcançados os seguintes objetivos: Identificados os códons mais utilizados em eucalipto; Avaliada as variações na utilização do códon entre genes mais expressos e menos expressos e também entre genes expressos em diferentes tecidos; Identificados os padrões presentes nas regiões iniciadora e terminadora da tradução; Construído um software que indica as alterações necessárias na seqüência de DNA de qualquer gene que se tenha interesse em expressar em eucalipto; Desenhados e construídos genes sintéticos para futura validação in vivo da metodologia de otimização da tradução de proteínas de eucalipto desenvolvida e implementada no software. / Abstract: Most of the amino acids are represented by more than one codon because of that the genetic code is said to be degenerated. Codons from the same amino acid does not occur with the same frequency, suggesting that there is preferential use of codons (codon usage bias). Different organisms often have different codon usage bias and these differences can be limiting factors in heterologous expression. Besides the codon usage bias there are other factors present in a gene that may influence the intensity with which this is translated, among them are: the DNA bases surrounding the initiation codon (initiation context) and the stop codon (termination context). Our goal is to identify the presence of these patterns - codon usage bias, initiation and termination contexts - in eucalyptus EST sets and generate information to increase protein expression in genetically modified eucalyptus. Specifically, the following objectives have been achieved: Identified the set of codons most used in the eucalyptus; Verified changes in the use of codons between genes expressed at different levels and also between genes expressed in different tissues; Identified patterns surrounding the translation initiation and stop sites; Development of a software that indicates the necessary changes in the DNA sequence of any gene to be expressed in eucalyptus Designed and constructed synthetic genes for further validation in vivo of the optimization methodology developed and implemented in the software. / Mestrado / Genetica Vegetal e Melhoramento / Mestre em Genética e Biologia Molecular

Les mutations non sens introduisent un codon stop prématuré dans une phase ouverte de lecture. Ce type de mutation est retrouvé chez environ 11% des patients atteints de maladies génétiques et dans de nombreux cancers. En effet, entre 5 et 40% des mutations affectant des gènes suppresseurs de tumeurs sont des mutations non sens. La conséquence de la présence d’une mutation non sens dans un gène est la dégradation rapide de l’ARN messager correspondant, par l’activation d’un mécanisme de surveillance des ARN appelé NMD (pour nonsense-mediated mRNA decay) conduisant à une absence d’expression du gène mutant. Dans le cas des cancers, l’absence d’expression d’un gène suppresseur de tumeurs tel que TP53, perturbe un ensemble de processus biologiques dont l’apoptose, facilitant ainsi la progression tumorale.En utilisant un système de criblage moyen débit permettant d’identifier des molécules capables de ré-exprimer des gènes porteurs d’une mutation non sens en inhibant le NMD et/ou en activant la translecture, plusieurs molécules ont été identifiées. La translecture est un mécanisme naturel conduisant à l’incorporation d’un acide aminé à la position du codon stop prématuré au cours de la traduction. Parmi les molécules identifiées, je me suis intéressée à un extrait végétal nommé H7 et au composé CNSM1 (pour corrector of nonsense mutation 1) qui permettent une ré-expression très efficace du gène TP53 lorsqu’il est porteur d’une mutation non sens. J’ai caractérisé ces composés en montrant notamment la ré-expression du gène TP53 porteur d’une mutation non sens dans différentes lignées cellulaires issues de différents cancers. J’ai montré également la très faible toxicité de ces molécules, validant leur potentielle utilisation en clinique. Mon étude a aussi permis de montrer que la protéine p53 synthétisée est fonctionnelle puisqu'elle est capable d’induire l’activation transcriptionnelle d’un de ses gènes cibles, le gène TP21.En permettant la ré-expression du gène suppresseur de tumeur mutant, des molécules comme CNSM1 ou H7 restaurent la capacité des cellules à entrer en apoptose et pourraient aussi réduire certaines résistances à la chimiothérapie.De plus, par une approche d’édition du génome, j’ai confirmé le lien existant entre le blocage du cytosquelette et l’inhibition du NMD. J’ai aussi identifié deux protéines impliquées dans le réarrangement du cytosquelette qui pourraient être ciblées pour inhiber le NMD en thérapie et ré-exprimer une protéine tronquée fonctionnelle. L’utilisation de H7 ou de CNMS1 pourrait ainsi être couplée à une inhibition du NMD pour optimiser la correction des mutations non sens. Ces molécules correctrices de mutations non sens représentent de nouvelles approches thérapeutiques ciblées du cancer et des maladies rares liées aux mutations non sens. / Nonsense mutations generate premature termination codons (PTC) within an open reading frame. This type of mutation is found in about 11% of patients with genetic disorders. Concerning cancer, 5 to 40% of mutations affecting tumor-suppressing genes are nonsense mutations. The presence of a PTC in a gene leads to rapid degradation of its mRNA mediated by the RNA surveillance mechanism named NMD (Nonsense-mediated mRNA decay) preventing the synthesis of truncated proteins. In cancer, the absence of expression of tumor suppressing genes such as TP53 interferes with many biological pathways including apoptosis enabling tumor progression.A screening system that allows identifying molecules capable of re-expressing genes harboring nonsense mutations by inhibiting the NMD system and/or by activating readthrough has been developed in the lab. Readthrough is a natural mechanism, which occurs during translation, leading to the incorporation of an amino acid at the PTC position. Among the molecules that have been identified thanks to the screen, a natural extract named H7 and a compound named CNSM1 efficiently rescues the expression of the nonsense-mutated TP53 gene carrying a PTC.CNSM1 and H7 induces the expression of full-length proteins from PTC-containing genes indicating that these compounds are capable of activating readthrough. I validated the screen results on several cancer cell lines harboring an endogenous nonsense mutation in TP53 gene and showed that the function of p53 was restored in the presence of CNSM1 or H7. I also investigated the cellular toxicity related with the use of CMNS1 on cultured cells and the in vivo effect of H7 in a mouse model harboring a nonsense mutation in dystrophin gene. My results demonstrate that these compounds have a mild cellular toxicity. In addition, using a genome editing approach I confirmed the relationship between the cytoskeletal blockage and the NMD inhibition. I identified two proteins that are implicated in the cytoskeletal rearrangement, which might be targeted to induce NMD inhibition and then the expression of truncated but functional protein from the mutated mRNA. H7 or CNMS1 might be coupled to an NMD inhibition strategy to improve the nonsense mutation correction. Knowing CNSM1 and H7 are so far the most efficient molecule capable of rescuing the expression of PTC-containing genes, these compounds represents a realistic hope for a new-targeted therapy for pathologies associated with nonsense mutations.

<p>In prokaryotes, several mRNA sequences surrounding the initiation codon have been found to influence the translation process; these include the downstream region and its codon context, the Shine-Dalgarno sequence and the S1 ribosomal protein-binding site. In this thesis, the purpose has been to study the role of the downstream region and Shine-Dalgarno-like sequences on early translation elongation and gene expression in <i>Escherichia coli</i>.</p><p>The downstream region (DR) after the initiation codon (around five to seven codons), has an important role in the initiation of translation. We find that most of the codons which give very low gene expression at +2 (considering AUG as +1), reach 5 to 10 fold higher expression when those codons are positioned posteriori to +2, with the exception of the NGG codons. The NGG codons abort the translation process if located within the first five codons of the DR, due to peptidyl-tRNA drop-off. However, when the NGG codons are situated further down from the DR, the protein expression was increased at the same level of expression as in the presence of any other codon.</p><p>The Shine-Dalgarno (SD) is an important region of initiation in translation of bacteria. In spite of this, it has been found that Gram-negative bacteria could translate mRNAs with weak or non-functional SD, while the DR carries out a main role in the efficiency of translation. In addition, positions of SD and SD-like sequences are very important to direct initiation of translation in the choice between two possible initiation codons. A strong SD between two initiation sites will favor the second initiation site if it consists of a canonical start codon followed by a good DR.</p><p>The results suggest that the mRNA sequences surrounding the initiation codon: the downstream region and the Shine-Dalgarno and SD-like sequences, are very important contributors to the translation level and gene expression in <i>Escherichia coli</i>.</p>

In prokaryotes, several mRNA sequences surrounding the initiation codon have been found to influence the translation process; these include the downstream region and its codon context, the Shine-Dalgarno sequence and the S1 ribosomal protein-binding site. In this thesis, the purpose has been to study the role of the downstream region and Shine-Dalgarno-like sequences on early translation elongation and gene expression in Escherichia coli. The downstream region (DR) after the initiation codon (around five to seven codons), has an important role in the initiation of translation. We find that most of the codons which give very low gene expression at +2 (considering AUG as +1), reach 5 to 10 fold higher expression when those codons are positioned posteriori to +2, with the exception of the NGG codons. The NGG codons abort the translation process if located within the first five codons of the DR, due to peptidyl-tRNA drop-off. However, when the NGG codons are situated further down from the DR, the protein expression was increased at the same level of expression as in the presence of any other codon. The Shine-Dalgarno (SD) is an important region of initiation in translation of bacteria. In spite of this, it has been found that Gram-negative bacteria could translate mRNAs with weak or non-functional SD, while the DR carries out a main role in the efficiency of translation. In addition, positions of SD and SD-like sequences are very important to direct initiation of translation in the choice between two possible initiation codons. A strong SD between two initiation sites will favor the second initiation site if it consists of a canonical start codon followed by a good DR. The results suggest that the mRNA sequences surrounding the initiation codon: the downstream region and the Shine-Dalgarno and SD-like sequences, are very important contributors to the translation level and gene expression in Escherichia coli.

Cette thèse regroupe des travaux concernant le biais d'usage de codons et son rôle chez les bactéries et leurs phages, en particulier sur les processus de traduction et l'organisation des génomes bactériens. Après une introduction portant sur i) la traduction chez les procaryotes, et ii) les techniques de classification et leurs liens avec la théorie de l'information, un nouvel algorithme de partition d'un ensemble de gènes en fonction de leur usage de codons est présenté. Son application aux génomes d'E. coli et de B. subtilis permet de mettre en évidence plusieurs phénomènes. Le génome de ces organismes se décompose respectivement en 4 et 5 groupes de gènes ayant des usages de codons distincts. Les gènes du même groupe tendent à partager des fonctions similaires, et sont organisés sur le chromosome en domaines cohérents d'une longueur de 10 à 15 gènes. Cette organisation non triviale pourrait permettre une régulation de la vitesse de traduction des gènes en fonction de leur similarité avec leur environnement génétique. <br />Dans la seconde partie le biais de codons et le contenu en ARN de transfert (ARNt) de bactériophages sont analysés, comparativement à ceux de leurs hôtes. L'étude statistique montre que le contenu en ARNt des phages n'est pas aléatoire, mais biaisé en faveur d'ARNt complémentaires aux codons fréquents dans le génome du phage. Un modèle d'équation maîtresse montre que cette distribution des ARNt au sein des génomes de phages pourrait être le résultat de deux processus : l'acquisition aléatoire par le phage d'ARNt, parmi ceux de l'hôte, et la perte préférentielle des ARNt correspondants à des codons moins utilisés par le phage que par son hôte. Un tel mécanisme permettrait au phage de s'adapter en ne conservant au final que les ARNt présents en quantité insuffisante chez son hôte pendant l'infection. Finalement, on observe plus d'ARNt chez les phages lytiques que chez les tempérés, laissant supposer que les processus de traduction sont soumis à une plus forte pression de sélection chez eux.

The standard genetic code (SGC) is the cipher used by nearly all organisms to transcribe information stored in DNA and translate it into its amino acid counterparts. Since the early 1960s, researchers have observed that the SGC is structured so that similar codons encode amino acids with similar physiochemical properties. This structure has been hypothesized to buffer the SGC against transcription or translational error because single nucleotide mutations usually either are silent or impart minimal effect on the containing protein. We herein briefly review different theories for the origin of that structure. We also briefly review different computational experiments designed to quantify buffering capacity for the SGC. We report on computational Monte Carlo simulations that we performed using a computer program that we developed, AGCT. In the simulations, the SGC was ranked against other, hypothetical genetic codes (HGC) for its ability to minimize physiochemical distances between amino acids encoded by codons separated by single nucleotide mutations. We analyzed unappreciated structural aspects and neglected properties in the SGC. We found that error measure type affected SGC ranking. We also found that altering stop codon positions had no effect on SGC ranking, but including stop codons in error calculations improved SGC ranking. We analyzed 49 properties individually and identified conserved properties. Among these, we found that long-range non-bonded energy is more conserved than is polar requirement, which previously was considered to be the most conserved property in the SGC. We also analyzed properties in combinations. We hypothesized that the SGC is organized as a compromise among multiple properties. Finally, we used AGCT to test whether different theories on the origin of the SGC could explain more convincingly the buffering capacity in the SGC. We found that, without accounting for transition/transversion biases, the SGC ranking was modest enough under constraints imposed by the coevolution and four column theories that it could be explained due to constraints associated with either theory (or both theories); however, when transition/transversion biases were included, only the four column theory returned a SGC ranking modest enough that it could be explained due to constraints associated with that theory. / Thesis / Master of Science (MSc) / The standard genetic code (SGC) is the cipher used almost universally to transcribe information stored in DNA and translate it to amino acid counterparts. Since the mid 1960s, researchers have recognized that the SGC is organized so that similar three-nucleotide RNA codons encode amino acids with similar properties; researchers consequently hypothesized that the SGC is structured to minimize effects from transcription or translation errors. This hypothesis has been tested using computer simulation. I briefly review results from those studies, complement them by analyzing unappreciated structural aspects and neglected properties, and test two theories on the origin of the SGC.