Optimizing the production of useful macromolecules from transgenic microorganisms is crucial to biopharmaceutical companies. Improving bacterial growth and replication depends largely on the efficiency of translation, which is rate-limited by initiation. Among the most important interactions between the mRNA translation initiation region (TIR) and the translation machinery is the association between the Shine-Dalgarno (SD) sequence in the TIR and the complementary anti-SD (aSD) sequence which is located within a short unstructured segment that includes the 3’ terminus (3’ TAIL) of the mature 16S rRNA. However, the mature 3’ TAIL has been poorly characterized in the majority of bacteria, rendering optimal SD/aSD pairing unclear in these species. In light of this, we established a novel strategy to characterize the mature 3’ TAILs of bacterial species that leverages the availability of publically stored RNA sequencing (RNA-Seq) data. In chapter 2, we devised a RNA-Seq-based approach to successfully recover the experimentally verified 3’ TAIL in E. coli (5’-CCUCCUUA-3’) and resolve inconsistencies surrounding the identity of the 3’ TAIL in Bacillus subtilis. In chapter 3 we improve the method introduced in chapter 2 to clearly and more reliably define the 3’ TAIL termini for 13 bacterial species with available protein abundance data. Our results reveal considerable heterogeneity in the termini of 3’ TAILs among closely related species and that sites downstream of the canonical CCUCC aSD motif are more important to initiation than previously believed. My research contributes to advance our understanding in microbial translation efficiency in two significant ways: 1) providing an RNA-Seq-based approach to characterize rRNA transcripts, and 2) elucidating optimal recognition between protein-coding genes and the rRNA translation machinery.

No description available.

2 Abstract Eukaryotic initiation factor 3 (eIF3) is a critical player involved in many steps of translation initiation, which ultimately result in the formation of the elongation competent 80S ribosome. With its 13 subunits (eIF3a - eIF3m) it is the largest and the most complex translation initiation factor composed of three mutually interconnected modules (i - iii), however, the role of individual subunits involved in its structural integrity and proper function is not fully explored. The eIF3e subunit was shown to be a part of the human eIF3 structural core and to help in the mRNA recruitment to the 43S pre-initiation complex by forming a molecular bridge between the 40S ribosomal subunit and the mRNA cap-binding complex. In this study, we employed siRNA-directed downregulation of eIF3e in HeLa cells and analysed its impact on the overall eIF3 integrity and function in vivo. The eIF3e knock-down (eIF3eK.D. ) led to the severe reduction of protein amounts of other three subunits (eIF3d, k and l), which together with the subunit eIF3c and e form module ii of the eIF3 complex. Remaining module i (composed of a, b, g and i) and iii (containing f, h and m) stayed partially bound perhaps thanks to a bridging effect of eIF3c, and showed reduced binding efficiency towards the 40S subunit compared to control...

O objetivo do presente trabalho é a otimização experimental, modelagem matemática e simulação do processo de pré-polimerização fotoiniciada do metacrilato de metila (MMA), visando a produção de um pré-polímero com distribuição estreita de massas moleculares (MWD) e conversão de monômero definida. Os experimentos foram realizados em dois sistemas experimentais em batelada, compostos por reatores fotoquímicos anulares e tanques de recirculação. No primeiro sistema experimental empregou-se uma lâmpada de mercúrio de média pressão, Heraeus TQ 150W. No segundo uma fonte de radiação de excímeros de xenônio e cloro (XeCl) alimentada por um gerador de pulsos e operada em uma larga faixa de freqüências de pulsos (840Hz – 46,4 kHz) foi empregada. Avaliaram-se as evoluções experimentais da concentração de benzoína (iniciador fotoquímico), da concentração do monômero e da concentração e distribuição de massas moleculares do pré-polímero, em função do tempo de irradiação, para diferentes condições de freqüência de pulsos de excitação, de concentração inicial de iniciador e de vazão de circulação. Para tanto, empregaram-se técnicas de análise como espectrofotometria, actinometria química (ferrioxalato), medidas de cromatografia por exclusão de tamanho e em fase reversa. As otimizações foram realizadas segundo dois planejamentos experimentais baseados na matriz Doehlert. As variáveis do processo escolhidas afetam significativamente as características do produto final, devido as diferentes condições de taxa de produção de radicais primários que se mostrou como etapa chave no controle da MWD e conversão do monômero. A modelagem matemática baseou-se nos balanços de massa, quantidade de movimento e transporte de fótons. Os mecanismos de geração de di-radicais monoméricos e dos radicais primários a partir das reações fotoquímicas foram incluídos em um modelo baseado na cinética clássica de polimerização por radicais livres. Os balanços foram desenvolvidos de acordo com o método dos momentos da distribuição de tamanhos de cadeia. O modelo matemático proposto foi validado confrontando-se os dados experimentais com os resultados simulados por um programa de fluido dinâmica computacional (PHOENICS). / The aim of this work is the experimental optimization, the mathematical modeling and the simulation of the photochemically initiated pre-polymerization process of methyl methacrylate (MMA). According to the industrial interests a pre-polymer of narrow molecular weight distribution (MWD) and defined weight concentration was pointed as an optimum since it improves the production process and the characteristics of Plexiglas. The experiments were carried out employing two experimental set-ups, which consist of an annular photochemical reactor connected to reservoir. In the first experimental set-up a medium pressure mercury lamp, Heraeus TQ 150 W was employed. In the second a xenon and chlorine (XeCl) source of radiation was employed. The electricity was supplied by a pulse generator, which operates within a wide frequency range (840Hz – 46,4kHz). The experimental time-evolution of the initiator (benzoin) and the MMA concentration as well as the molecular weight distribution of the pre-polymer were evaluated for different pulse frequencies, initial initiator concentrations and recirculation flow rates conditions. Therefore, analytical techniques were employed as spectrophotometry, chemical actinometry, size exclusion chromatography and reverse phase chromatography. The experimental optimizations were carried out according to two optimal experimental designs based on the classical Doehlert matrix. The chosen variables affect significantly the characteristics of the final product. Mainly due to the different conditions of initial radical production rates, which have shown to be the key on controlling the MWD and the MMA conversion. The mathematical modeling was based on mass, momentum and photons balance equations. The kinetic mechanism of bi-radical and initial radical production from MMA and benzoin respectively, were included in the classical kinetic model of free radical polymerization. The reaction rate equations were developed according to method of the chain size distribution moment. The proposed mathematical model was validated comparing the simulation results obtained with a computational fluid dynamics program (PHOENICS) and the experimental results.

O objetivo do presente trabalho é a otimização experimental, modelagem matemática e simulação do processo de pré-polimerização fotoiniciada do metacrilato de metila (MMA), visando a produção de um pré-polímero com distribuição estreita de massas moleculares (MWD) e conversão de monômero definida. Os experimentos foram realizados em dois sistemas experimentais em batelada, compostos por reatores fotoquímicos anulares e tanques de recirculação. No primeiro sistema experimental empregou-se uma lâmpada de mercúrio de média pressão, Heraeus TQ 150W. No segundo uma fonte de radiação de excímeros de xenônio e cloro (XeCl) alimentada por um gerador de pulsos e operada em uma larga faixa de freqüências de pulsos (840Hz – 46,4 kHz) foi empregada. Avaliaram-se as evoluções experimentais da concentração de benzoína (iniciador fotoquímico), da concentração do monômero e da concentração e distribuição de massas moleculares do pré-polímero, em função do tempo de irradiação, para diferentes condições de freqüência de pulsos de excitação, de concentração inicial de iniciador e de vazão de circulação. Para tanto, empregaram-se técnicas de análise como espectrofotometria, actinometria química (ferrioxalato), medidas de cromatografia por exclusão de tamanho e em fase reversa. As otimizações foram realizadas segundo dois planejamentos experimentais baseados na matriz Doehlert. As variáveis do processo escolhidas afetam significativamente as características do produto final, devido as diferentes condições de taxa de produção de radicais primários que se mostrou como etapa chave no controle da MWD e conversão do monômero. A modelagem matemática baseou-se nos balanços de massa, quantidade de movimento e transporte de fótons. Os mecanismos de geração de di-radicais monoméricos e dos radicais primários a partir das reações fotoquímicas foram incluídos em um modelo baseado na cinética clássica de polimerização por radicais livres. Os balanços foram desenvolvidos de acordo com o método dos momentos da distribuição de tamanhos de cadeia. O modelo matemático proposto foi validado confrontando-se os dados experimentais com os resultados simulados por um programa de fluido dinâmica computacional (PHOENICS). / The aim of this work is the experimental optimization, the mathematical modeling and the simulation of the photochemically initiated pre-polymerization process of methyl methacrylate (MMA). According to the industrial interests a pre-polymer of narrow molecular weight distribution (MWD) and defined weight concentration was pointed as an optimum since it improves the production process and the characteristics of Plexiglas. The experiments were carried out employing two experimental set-ups, which consist of an annular photochemical reactor connected to reservoir. In the first experimental set-up a medium pressure mercury lamp, Heraeus TQ 150 W was employed. In the second a xenon and chlorine (XeCl) source of radiation was employed. The electricity was supplied by a pulse generator, which operates within a wide frequency range (840Hz – 46,4kHz). The experimental time-evolution of the initiator (benzoin) and the MMA concentration as well as the molecular weight distribution of the pre-polymer were evaluated for different pulse frequencies, initial initiator concentrations and recirculation flow rates conditions. Therefore, analytical techniques were employed as spectrophotometry, chemical actinometry, size exclusion chromatography and reverse phase chromatography. The experimental optimizations were carried out according to two optimal experimental designs based on the classical Doehlert matrix. The chosen variables affect significantly the characteristics of the final product. Mainly due to the different conditions of initial radical production rates, which have shown to be the key on controlling the MWD and the MMA conversion. The mathematical modeling was based on mass, momentum and photons balance equations. The kinetic mechanism of bi-radical and initial radical production from MMA and benzoin respectively, were included in the classical kinetic model of free radical polymerization. The reaction rate equations were developed according to method of the chain size distribution moment. The proposed mathematical model was validated comparing the simulation results obtained with a computational fluid dynamics program (PHOENICS) and the experimental results.