Auf dem Weg der genetischen Information stellt die Translation der RNA in eine Aminosäuresequenz den letzten Schritt dar. In Chloroplasten, den grünen Organellen der Pflanzenzellen, findet ein Großteil der Regulation der Genexpression auf Ebene der Initiation dieses Schrittes statt. Eine Vielzahl von Eigenschaften der RNA und von Faktoren, die an die RNA binden, entfalten einen Einfluss auf diesen Schritt. Bisher unvollständig aufgeklärt ist die Rolle einer konservierten Nukleotidsequenz in der untranslatierten Region der RNA -- der Shine-Dalgarno-Sequenz. Diese stellt in Bakterien, wie z.B. E. coli als Ribosomenbindestelle sicher, dass Ribosomen den Anfang der zu translatierenden Sequenz zuverlässig erkennen. Im Rahmen dieser Arbeit wurden diverse DNA-Konstrukte in Plastiden von Tabak eingebracht. Hierzu zählten Konstrukte, die sowohl eine erhöhte Anzahl von Ribosomenbindestellen enthielten als auch vermehrte Startpunkte der Translation. Zusätzlich wurden Konstrukte hergestellt, die die Situation von mehreren zu translatierenden Regionen in der RNA nachstellten. Es konnte festgestellt werden, dass plastidäre Ribosomen die strangaufwärts gelegenen Translationsstartpunkte bevorzugen -- im Gegensatz zu E. coli, wo alle Startpunkte gleichmäßig genutzt wurden. Hierdurch zeigten die prokaryotischen Ribosomen aus Chloroplasten, die sich aus bakteriellen Systemen ableiten, Eigenschaften von eukaryotischen Ribosomen. Ein zweites Teilprojekt dieser Arbeit beschäftigte sich mit der Inkompatibilität von Chloroplasten mit dem Kerngenom. In Kreuzungen von Arten der Gattung Pelargonium fielen Kombinationen auf, bei denen die Tochterpflanzen bleiche Blattbereiche bis hin zu vollständig weißen Pflanzen zeigten. Dieses Phänomen wird als Bastardbleichheit bezeichnet. In der Gattung Pelargonium werden Chloroplasten von beiden Elternteilen an die Tochterpflanzen vererbt. Da das Phänomen der Bastardbleichheit nur in einem der Plastiden vorkommt, nicht jedoch im anderen in der gleichen Pflanze, muss von einem Effekt ausgegangen werden, der von Plastiden ausgeht. Die Interaktionen zwischen Zellkern und Chloroplasten sind offensichtlich stark gestört. Zur detaillierten Untersuchung dieses Effekts wurde die Nukleotidsequenz von drei Chloroplastengenomen aufgeklärt. Es konnte eine Reihe von Sequenzunterschieden der Genome ermittelt werden. Aus diesen wurde eine Reihe von Unterschieden beobachtet, die einen solchen Effekt zur Folge haben können. Aus diesen Unterschieden wurde eine Reihe von potentiellen Kandidatengenen zusammengestellt, die in weiteren Arbeiten auf ihre Rolle in der Entstehung der Bastardbleichheit untersucht werden. / Chloroplasts are the green organelles of plants with a evolutionary prokaryotic background. During evolution chloroplasts established translation initiation as the major step in regulation of gene expression. A vast number of factors, e.g. sequence elements, secondary structures or RNA binding proteins, influences the regulation of translation initiation. A conserved sequence – Shine-Dalgarno sequence – can be identified both in prokaryotes as well as chloroplasts. In prokaryotes this sequence provides a faithful means for positioning of the ribosome to the start codon. Due to lower conservation of Shine-Dalgarno sequences the role of this sequence in translation initiation is not completely understood. We designed a series of constructs that contain different arrangements of these sequences in the 5’ UTR resulting in an increased number of potential ribosome binding sites or translation initiation sites. Additionally we constructed a series of 5’ UTRs that resembled polycistronic transcripts. The results showed a dramatic effect of the different constructs on the translation efficiency of the reporter protein. It could be shown that numerous translation initiation sites increase translation efficiency, whereas increased numbers of ribosome binding sites do not. Additionally it could be shown, that plastidic ribosomes preferentially initiate on 5’ translations initiation sites in contrast to prokaryotic ribosomes that recognize initiation sites equally. This illustrates that plastidic ribosomes in contrast to prokaryotic ribosomes show a scanning like mechanism. Hence plastidic ribosomes gained some eukaryotic properties during evolution. A second project was dealing with hybrid variegation. This phenomenon is based on plastid-nuclear genome incompatibility. Due to biparental plastid inheritance in Pelargonium hybrids may show chimeric phenotypes with bleached (incompatible) and green (compatible) sectors. This points to the plastome as cause for the hybrid variegation. To this end the nucleotide sequence of three plastid genomes was determined and an array of candidate genes causing the incompatibility could be compiled.

T2K est une expérience de neutrinos à longue ligne de base à base d'accélérateurs au Japon. Le but principal de l'expérience T2K est la recherche d'une violation de la PC dans le secteur du lepton en mesurant l'apparence (anti)neutrino des électrons dans un faisceau muon (anti)neutrino. Le flux (anti) neutrino initial est produit par les désintégrations des hadrons qui proviennent des interactions et des ré-interactions d'un faisceau de protons de 30 GeV avec une cible en graphite de 90 cm de long. La connaissance du flux de neutrinos T2K est limitée en raison des grandes incertitudes liées à la production de hadrons. Une série de mesures de production d'hadrons a été effectuée pour résoudre ce problème, dans l'expérience NA61/SHINE au CERN. Les mesures ont été effectuées avec un faisceau de protons et deux types de cibles : une cible en graphite mince et une réplique de la cible T2K. Les travaux présentés dans cette thèse se concentrent sur les données cibles de la réplique T2K prises en 2010 et sur le développement du logiciel d'analyse et d'étalonnage. Le but de ces mesures est de contraindre complètement la production de π+, π+, π-, K+, K+, K- et p provenant de la surface cible en mesurant les rendements différentiels en hadrons dans les cellules du momentum de particules sortant (p), l'angle polaire (θ) et la position longitudinale sur la surface cible (z). Cela permettra de réduire les incertitudes du flux de neutrinos T2K d'environ 10 % à moins de 5 %. Les prédictions de Fluka2011.2c.5 Les listes de physique Monte Carlo, NuBeam et QGSP_BERT de Geant4.10.03 ont été comparées aux données et il a été constaté que Fluka2011.c2.5 donne la meilleure prévision. / T2K is an accelerator-based long-baseline neutrino experiment in Japan. The main goal of the T2K experiment is a search for CP violation in the lepton sector by measuring electron (anti) neutrino appearance in a muon (anti)neutrino beam. Initial (anti) neutrino flux is produced in decays of hadrons which originate from the interactions and the re-interactions of a 30 GeV proton beam with a 90 cm long graphite target. Knowledge of the T2K neutrino flux is limited due to large hadron production uncertainties. A series of hadron production measurements were done to solve this problem, in the NA61/SHINE experiment at CERN. Measurements were performed with a proton beam and two target types: a thin graphite target and a replica of the T2K target. Work presented in this thesis concentrates on the T2K replica target data taken in 2010 and the development of the analysis and calibration software. The aim of these measurements is to fully constrain production of π+ , π− , K+ , K− and p coming from the target surface by measuring differential hadron yields in the bins of outgoing particle momentum (p), polar angle (θ) and longitudinal position on the target surface (z). This will allow reduction of the T2K neutrino flux uncertainties from around 10% to below 5%. Predictions of Fluka2011.2c.5 Monte Carlo, NuBeam and QGSP_BERT physics lists from Geant4.10.03 have been compared to the data and it has been found that Fluka2011.c2.5 gives the best prediction.

Translation is a crucial factor in determining the rate of protein biosynthesis; for this reason, bacterial species typically evolve features to improve translation efficiency. Biosynthesis is a finely tuned cellular process aimed at providing the cell with an appropriate amount of proteins and RNAs to fulfill all of its metabolic functions. A key bacterial feature for faster recognition of the start codon on mRNA is the binding between the anti-Shine-Dalgarno (aSD) sequence on prokaryotic ribosomes at the 3’ end of the small subunit (SSU) 16S rRNA and Shine-Dalgarno (SD) sequence, a purine-rich sequence located upstream of the start codon in the mRNA. This binding helps to facilitate positioning of initiation codon at the ribosomal P site. This pairing, as well as factors such as the location of aSD binding relative to the start codon and the sequence of the aSD motif can heavily influence translation efficiency. The objective of this thesis is to understand the SD-aSD interactions and how changes in aSD sequences can affect SD sequences in addition to the underlying impact these changes have on the translational efficiency of prokaryotes. In chapter two, we hypothesized that differences in the prevalence of SD motifs between B. subtilis and E. coli arise as a result of changes in the free 3' end of 16S rRNA which may have led B. subtilis and E. coli to evolve differently. E. coli is expected to be more amenable to the acquisition of SD motifs that do not perfectly correspond with its free 3’ 16S rRNA end than B. subtilis. Further, we proposed that the evolutionary divergence of these upstream sequences may be exacerbated in B. subtilis by the absence of a functional S1 protein. Based on the differences between E. coli and B. subtilis, we were able to identify SD motifs that can only perfectly base pair in one of the two species and are expected to work well in one species, but not the other. Furthermore, we determine the frequency and proportion of these specific SD motifs that are expected to be preferentially present in one of the two species. Our motif detection is in keeping with the expectation that the predicted five categories of SD that are associated with B. subtilis and are expected to be less efficient in E. coli exhibit greater usage in the former than latter. Similarly, the predicted category of SD motifs associated with the E. coli 16S rRNA 3’ end is used more frequently in E. coli.Across prokaryote genomes, translation initiation efficiency varies due to codon usage differences whereas among genes, translation initiation varies because different genes vary in SD strength and location. In chapter 3 we hypothesized that there is differential translation initiation between 16 archaeal and 26 bacterial genomes. Translation initiation was found to be more efficient in Gram-positive than in Gram-negative bacteria and also more efficient in Euryarchaeota than in Crenarchaeota. We assessed the efficiency of translation initiation by measuring: i) the SD sequence’s strength and position and ii) the stability of the secondary structure flanking the start codon, which both affect accessibility of the start codon

No description available.

En quelques années, les domaines des jeux vidéo et des systèmes multi-agents (SMA) ont pris de plus en plus de places dans la vie de chacun. Malgré des similitudes assez fortes (présences d’entité dans les vidéo pouvant être assimilées à des agents), les SMA ne sont presque jamais utilisés dans le développement de jeux. Ce mémoire présente Shine Agent Modeling Platform (SAMP), une plateforme visant intégrer le paradigme multi-agents au sein du développement de jeux vidéo. Cette fusion permet l’utilisation de la puissance des multi-agents au sein des jeux vidéo.SAMP propose une approche au niveau des interactions permettant de réduire le coût de traitement de ces interactions en optimisant le nombre de recherches effectuées dans l’environnement.En plus d’intégrer le paradigme multi-agents, SAMP vise à être accessible à un maximum d’utilisateurs en proposant une interface de modélisation entièrement graphique. Un système d’importation de modèles comportementaux permet de créer deuxniveaux de modélisation : un niveau proche de la logique développement informatique et un niveau proche de la logique métier de l’utilisateur.SAMP est intégré à un moteur de jeux vidéo, Shine Engine, permettant de générer les environnements graphiques dans lesquels les agents évolueront. / In recent years, video games domains and multiagents systems (MAS) domains took more and more place into the life of many pepole. Despite of strong similarities (video games entities wich can be assimilated to agents), MAS are very rarely used during the development of video games. This submission presents the Shine Agent ModelingPlatform (SAMP), a framework trying to integrate the multi-agents paradigm within the development of video games. The purpose is to integrate the efficiency of the MAS within the video games.SAMP provides an approach to enhance the interactions between agents. This approach reduces the number of searches within the environment. In addition to integrate the multi-agents paradigm within the video games, SAMP aims to be userfriendly by proposing a full graphical interface to MAS. An import/export system of these modelsallows users to create two modeling levels: one close to the computer sciences logic and the second close the business logic of the user.SAMP is integrated in a video games engine: Shine Engine. This integration allows to generate the graphic environment in which agents will live.

Submitted by NATÁLIA GONÇALVES TAKAHASHI GONÇALVES TAKAHASHI (naty_taka@hotmail.com) on 2017-06-07T16:14:24Z No. of bitstreams: 2 Dissertação_Natália_Gonçalves_Takahashi.pdf: 2126549 bytes, checksum: 2e4e7bc6e6b87efa3e00671b6137371c (MD5) Dissertação_Natália_Gonçalves_Takahashi.docx: 17831 bytes, checksum: 978787158c35816170d4451246ee80c5 (MD5) / Approved for entry into archive by Luiz Galeffi (luizgaleffi@gmail.com) on 2017-06-07T16:29:30Z (GMT) No. of bitstreams: 1 takahashi_ng_me_jabo.pdf: 2126549 bytes, checksum: 2e4e7bc6e6b87efa3e00671b6137371c (MD5) / Made available in DSpace on 2017-06-07T16:29:30Z (GMT). No. of bitstreams: 1 takahashi_ng_me_jabo.pdf: 2126549 bytes, checksum: 2e4e7bc6e6b87efa3e00671b6137371c (MD5) Previous issue date: 2017-06-05 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A busca pela diversificação de fontes da matriz energética, priorizando fontes renováveis, acarreta no maior consumo de etanol de primeira geração, podendo este ser insuficiente em suprir a necessidade da frota brasileira. Dessa forma, o etanol de segunda geração (E2G) surge como uma alternativa para aumento da produção de combustíveis renováveis. Ele é produzido a partir da fermentação dos resíduos de glicose após a quebra da celulose presente na biomassa vegetal. Contudo, além da celulose, a biomassa vegetal é também composta pela lignina, composto considerado recalcitrante no processo de obtenção deste tipo de etanol. Para transpor este obstáculo, é necessário encontrar maneiras de diminuir a quantidade ou modificar a composição da lignina. Fatores de transcrição (FTs) são alvos altamente promissores para a modificação deste polímero, uma vez que estão envolvidos com a regulação de sua via de biossíntese, bem como, da formação de toda parede celular secundária (PCS). Plantas de arroz transformadas para a superexpressão de AtSHN2 de Arabdopsis, apresentaram uma diminuição na quantidade de lignina e mostraram uma modulação na via de celulose, enquanto que a superexpressão do outro gene SHN de Arabidopsis (AtSHN1) em Arabidopsis apresentou uma modificação na via de biossíntese de cera e cutina. Isto ressalta a necessidade de avaliar os FTs de maneira espécie-específica. Assim sendo, este trabalho vem com o objetivo de ajudar a elucidar os mecanismos de funcionamento do FT SHINE (SHN), considerado um potencial regulador da PCS em gramíneas. Para a caracterização do FT SbSHN em sorgo foi primeiramente realizado um alinhamento de sequências de aminoácidos, contendo as proteínas codificadas pelos dois genes SHN em sorgo (SbSHN1 – Sb04g006970 e SbSHN2 – Sb10g023600) com outras sequências SHN disponíveis na literatura. Em seguida foi gerada uma árvore filogenética contendo todos esses mesmos SHN. Após isso, foi realizada a clonagem do FT SbSHN1 em vetor comercial pENTR/D-TOPO (Invitrogen), após verificação, a sequência foi recombinada com vetores de destino. Primeiramente, com o vetor pDEST15 para a expressão heteróloga da proteína SHN em E. coli.. De maneira complementar foi produzido um peptídeo sintético para reconhecimento da proteína SbSHN (anticorpo antiSHN). Posteriormente foi produzido um vetor contendo a sequencia de SHN em fusão com GFP, que foi utilizado para agroinfiltração de folhas de N. benthamiana, a fim de observar a localização subcelular do FT SbSHN. Para determinação da expressão através de qPCR em sorgo foram utilizados a folha, dividida em base e ponta, e a inflorescência, imatura e madura. Além disso, foi realizada a imunoprecipitação de cromatina (ChIP) das inflorescências imaturas e maduras de sorgo, com posterior análise inicial por ChIPqPCR para validação de alguns alvos de SbSHN. Como resultados, através da expressão heteróloga foi produzida uma proteína com massa de aproximadamente 52kDa (massa da proteína SHN adicionada de cauda GST), que foi reconhecida pelo anticorpo antSHN produzido. Foi confirmada a presença do FT SbSHN no núcleo celular, através de observação das folhas transformadas por agroinfiltração. As inflorescências imaturas de sorgo apresentaram maior expressão tanto de SbSHN1 quanto de SbSHN2. Com a técnica de ChIPqPCR foi possível validar in vivo os alvos SbNAC91 (Sb07g001550), SbNAC115 (Sb10g000460), SbMYB87 (Sb07g024970) e SbMYB60 (Sb04g031110) do FT SbSHN em sorgo. Em uma perspectiva de longo prazo, acredita-se que o conhecimento obtido a partir destes estudos não só fornecerão informações importantes sobre a função dos reguladores SHN em todo o reino vegetal, mas também fornecer uma poderosa ferramenta para a engenharia metabólica de compostos fenólicos e lignina por meio de melhoramento convencional ou abordagens transgênicas, impactando diretamente sobre a produção de E2G. / The search for alternative sources of the energy, prioritizing renewable sources, increase the consumption of first generation ethanol, which could not be enough to supply the needs of the Brazilian flex fuel car fleet. In this scenario, second generation ethanol (E2G) appears as an alternative to increase production of renewable fuels. E2G it is produced from the fermentation of glucose residues after breaking the cellulose present in the plant biomass. However, adhered to the cellulose is lignin, a compound considered recalcitrant in the process of obtaining this type of ethanol. To overcome this obstacle, it is necessary to find ways to decrease the amount or modify the lignin composition. Transcription factors (TFs) are highly promising targets for the modification of this polymer, since they are involved in the regulation of its biosynthesis pathway, as well as the formation of the whole secondary cell wall (PCS). Rice plants transformed for the overexpression of AtSHN2 from Arabidopsis showed a decrease in the amount of lignin and a modulation of cellulose pathway whereas the overexpression of another gene of SHN (AtSHN1) in Arabidopsis showed a modification in the biosynthesis pathway of wax and cutin. This highlights the need to evaluate TFs in a species-specific manner. Basing on this, the present work has the objective of helping to elucidate the mode of action of TF SHINE (SHN), considered a potential regulator of PCS in grasses. Aiming to characterize SbSHN TF in sorghum, initially an alignment was performed using amino acid sequence of proteins encoded by the two SHN genes in sorghum (SbSHN1 - Sb04g006970 and SbSHN2 - Sb10g023600) with other SHN sequences available in the literature. Then a phylogenetic tree containing all these SHN sequences was generated. After that, the SbSHN1 FT was cloned into commercial vector pENTR / D-TOPO (Invitrogen) and later used to recombinate in different destination vectors using gateway system. First, the vector pDEST15 was used for the production of heterologous expression in E. coli. Complementary, a synthetic peptide was produced for recognition of the SbSHN protein (antiSHN antibody). In parallel, the vector pK7WGF2 was used to obtain SHN phusioned to GFP. This vector was transientilly expressed in leaves of N. benthamiana in order to observe the subcellular location of SbSHN TF. Complementary, to determine the expression through qPCR, sorghum leaves, were splitted in base and tip, and the inflorescence, in immature and mature developmental stages, were used. In addition, chromatin immunoprecipitation (ChIP) of immature and mature sorghum inflorescences was performed, with initial analysis by ChIPqPCR for validation of some SbSHN targets. As results, through heterologous expression, a protein with mass of approximately 52kDa (mass of the SHN protein added with GST tail) was obtained, which was recognized by the antiSHN antibody produced. The presence of SbSHN TF in the cell nucleus was confirmed by observation of the transformed leaves by agroleakage. The immature inflorescences of sorghum presented higher expression level of both SbSHN1 and SbSHN2 genes. With the ChIPqPCR technique it was possible to validate in vivo some SHN targets such as: SbNAC91 (Sb07g001550), SbNAC115 (Sb10g000460), SbMYB87 (Sb07g024970) and SbMYB60 (Sb04g031110) in sorghum. In a long-term perspective, we believe that the knowledge gained from these studies will not only provide important information about the function of SHN as a master regulators throughout the plant kingdom, but also provide a powerful tool for the metabolic engineering of phenolic compounds and lignin using conventional breeding or transgenic approaches, directly impacting the production of E2G.

Submitted by Napoleana Barros Martins (napoleana_martins@hotmail.com) on 2016-08-08T15:29:51Z No. of bitstreams: 1 Dissertação Leonardo Fontes do Nascimento.pdf: 1675975 bytes, checksum: 22b0c3dd6668766ba6ea72b208d14bf7 (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-08-26T14:01:18Z (GMT) No. of bitstreams: 1 Dissertação Leonardo Fontes do Nascimento.pdf: 1675975 bytes, checksum: 22b0c3dd6668766ba6ea72b208d14bf7 (MD5) / Approved for entry into archive by Divisão de Documentação/BC Biblioteca Central (ddbc@ufam.edu.br) on 2016-08-26T14:03:03Z (GMT) No. of bitstreams: 1 Dissertação Leonardo Fontes do Nascimento.pdf: 1675975 bytes, checksum: 22b0c3dd6668766ba6ea72b208d14bf7 (MD5) / Made available in DSpace on 2016-08-26T14:03:03Z (GMT). No. of bitstreams: 1 Dissertação Leonardo Fontes do Nascimento.pdf: 1675975 bytes, checksum: 22b0c3dd6668766ba6ea72b208d14bf7 (MD5) Previous issue date: 2016-05-29 / FAPEAM - Fundação de Amparo à Pesquisa do Estado do Amazonas / A common concern among researchers is that the results of their research are published in venues of impact in the scientific community. In general, the impact indices are obtained through metrics based on the number of citations that your articles receive. Institutions such as the SCImago and Thomson Reuters provide precise impact indices for major international journals. While this is sufficient for most areas, in Computer Science conferences and other scientific events are also important as publishing venues. However, currently, there is no solution that is universally accepted to obtain accurate indices on conferences, because the tools most commonly used for this purpose have differences between the indices generated for the same conference and year. In this dissertation, we propose a tool called Live SHINE, whose goal is to generate high-precision impact indices of Computer Science Conferences from data provided by Google Scholar. Our tool uses a method based on machine learning techniques that automatically filters the metadata provided by Google Scholar, and considers in the calculation of impact indices only citation data from articles that truly belong to the conference. Our experiments show that our method is effective, achieving an average F1 metric above 0.9 for 30 analyzed conferences. In addition, we also developed a new distributed and collaborative strategy of collecting citations, in which the queries sent to Google Scholar to retrieve the updated values of article citations are triggered by the user interface, avoiding problems such as network overload, delay in update citations and frequent blocking by Google Scholar. Thus, this strategy makes the community of users collaborate to keep updated the data citations for the benefit of all. / Uma preocupação frequente entre os pesquisadores é que os resultados de suas pesquisas sejam publicados em veículos de impacto na comunidade científica. Geralmente, os índices de impacto são obtidos através de métricas baseadas no número de citações que seus artigos recebem. Instituições tais como o SCImago e Thomson Reuters fornecem índices de impacto precisos para os principais periódicos internacionais. Embora isso seja suficiente para a maioria das áreas, para a área de Ciência da Computação as conferências e outros eventos científicos são igualmente importantes como veículos de publicação. No entanto, atualmente não existe nenhuma solução que seja universalmente aceita para se obter índices precisos sobre conferências, pois as ferramentas mais utilizadas para esse fim apresentam divergências entre os índices gerados para uma mesma conferência e ano. Neste trabalho propomos uma ferramenta denominada Live SHINE, cujo objetivo é gerar índices de impacto de alta precisão de conferências de Ciência da Computação a partir de dados fornecidos pelo Google Scholar. Nossa ferramenta utiliza um método baseado em técnicas de aprendizagem de máquina que filtra automaticamente os metadados fornecidos pelo Google Scholar e considera no cálculo dos índices de impacto apenas os dados de citações de artigos que de fato pertencem a conferência. Os experimentos realizados indicam que nosso método é eficaz, alcançando uma métrica F1 média acima de 0.9 considerando 30 conferências analisadas. Além disso, desenvolvemos também uma nova estratégia distribuída e colaborativa de coleta de citações, na qual as consultas enviadas ao Google Scholar para recuperar os valores atualizados de citações de artigos são disparadas pela própria interface do usuário, evitando problemas como sobrecarga da rede, demora na atualização das citações e bloqueio frequente por parte do Google Scholar. Assim, essa estratégia faz com que a comunidade de usuários colabore para manter os dados de citações atualizados para o benefício de todos.

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.

No description available.

No description available.