Characterizing the regulation of mitochondrial nucleoids

Mitochondria contain a 16.6 kb circular genome encoding 13 proteins as well as mitochondrial tRNAs and rRNAs. Copies of the genome are organized into nucleoids containing both DNA and proteins, including the machinery required for mtDNA replication and transcription. Although mtDNA integrity is essential for cellular and organismal viability, regulation of proliferation of the mitochondrial genome is poorly understood. To elucidate the mechanisms behind this, we chose to study the interplay between mtDNA copy number and the proteins involved in mitochondrial fusion, another required function in cells. Strikingly, we found that mouse embryonic fibroblasts lacking fusion also had a mtDNA copy number deficit. To understand this phenomenon further, we analyzed the binding of mitochondrial transcription factor A, whose role in transcription, replication, and packaging of the genome is well-established and crucial for cellular maintenance. Using ChIP-seq, we were able to detect largely uniform, non-specific binding across the genome, with no occupancy in the known specific binding sites in the regulatory region. We did detect a single binding site directly upstream of a known origin of replication, suggesting that TFAM may play a direct role in replication. Finally, although TFAM has been previously shown to localize to the nuclear genome, we found no evidence for such binding sites in our system.

To further understand the regulation of mtDNA by other proteins, we analyzed publicly available ChIP-seq datasets from ENCODE, modENCODE, and mouseENCODE for evidence of nuclear transcription factor binding to the mitochondrial genome. We identified eight human transcription factors and three mouse transcription factors that demonstrated binding events with the classical strand asymmetrical morphology of classical binding sites. ChIP-seq is a powerful tool for understanding the interactions between proteins and the mitochondrial genome, and future studies promise to further the understanding of how mtDNA is regulated within the nucleoid.

Mechanisms of substrate selection by the signal recognition particle

The signal recognition particle (SRP) targets membrane and secretory proteins to their correct cellular destination with remarkably high fidelity. Previous studies have shown that multiple checkpoints exist within this targeting pathway that allows ‘correct cargo’ to be quickly and efficiently targeted and for ‘incorrect cargo’ to be promptly rejected. In this work, we delved further into understanding the mechanisms of how substrates are selected or discarded by the SRP. First, we discovered the role of the SRP fingerloop and how it activates the SRP and SRP receptor (SR) GTPases to target and unload cargo in response to signal sequence binding. Second, we learned how an ‘avoidance signal’ found in the bacterial autotransporter, EspP, allows this protein to escape the SRP pathway by causing the SRP and SR to form a ‘distorted’ complex that is inefficient in delivering the cargo to the membrane. Lastly, we determined how Trigger Factor, a co-translational chaperone, helps SRP discriminate against ‘incorrect cargo’ at three distinct stages: SRP binding to RNC; targeting of RNC to the membrane via SRP-FtsY assembly; and stronger antagonism of SRP targeting of ribosomes bearing nascent polypeptides that exceed a critical length. Overall, results delineate the rich underlying mechanisms by which SRP recognizes its substrates, which in turn activates the targeting pathway and provides a conceptual foundation to understand how timely and accurate selection of substrates is achieved by this protein targeting machinery.

[B_Zalla_Bolunburu] Documentación Geométrica de la Ferrería Bolunburu (Zalla, Bizkaia)

[ES] El conjunto de dos edificios divididos en varias estancias, un canal de captación de aguas y un puente, todo ello arruinado. Los muros aún se mantienen en pie aunque ya no quedan restos de los tejados ni del mobiliario, maquinaria o decoración.

Bioestímulo e bioaumento na remediação de solo contaminado com óleo lubrificante usado escala piloto

O óleo lubrificante mineral é amplamente utilizado no cenário mundial no funcionamento de máquinas e motores. No entanto, o ciclo de vida deste petro-derivado resulta na geração de um resíduo (óleo lubrificante usado), o qual é nocivo ao meio ambiente quando não descartado adequadamente ou reciclado. No Brasil, apesar das normas que tratam especificamente do armazenamento, recolhimento e destino de óleo lubrificante usado, grande parte do mesmo ainda é despejado diretamente no meio ambiente, sem qualquer tratamento, sendo de grande importância estudos que visem o entendimento dos processos e o desenvolvimento de tecnologias de remediação de áreas contaminadas por esse resíduo. O objetivo geral do presente trabalho foi conduzir estudos de tratabilidade de solo arenoso contaminado experimentalmente com 5% (m m-1 seco) de óleo lubrificante usado, através de duas diferentes estratégias de biorremediação: bioestímulo e bioaumento. Foram conduzidos dois experimentos. No primeiro, foi avaliada a atividade microbiana aeróbia na biodegradação do OLU através do método respirométrico de Bartha. No segundo, foram montados três biorreatores de fase sólida simulando biopilhas estáticas com aeração forçada, cada um contendo 125 kg de solo e 5% (m m-1 seco) de óleo lubrificante automotivo usado, os quais receberam como tratamento: bioestímulo por ajuste de pH e umidade (BIOSca); bioestímulo por ajuste de pH e umidade associado ao bioaumento com a adição de composto maduro (BIOA1ca) ; e bioestímulo por ajuste de pH e umidade associado ao bioaumento com a adição de composto jovem (BIOA2ca). Foram também montados três biorreatores de bancada simulando biopilhas estáticas sem aeração forçada, cada um contendo 3 kg de solo e 5% (m m-1) do mesmo contaminante, sendo que o primeiro continha solo sem contaminação - CONTsa, o segundo, solo contaminado com ajuste de pH BIOSsa e o terceiro, solo contaminado com adição de 0,3% de azida sódica - ABIOsa. Os tratamentos foram avaliados pela remoção de hidrocarbonetos totais de petróleo (HTPs) e após 120 dias de experimento obteve-se remoções de HTPs de 84,75%, 99,99% e 99,99%, com BIOS, BIOA1 e BIOA2, respectivamente, demonstrando que a estratégia de bioestímulo associada ao bioaumento foram promissoras na remediação do solo contaminado pelo óleo lubrificante usado. Os tratamentos que receberam composto (BIOA1 e BIOA2) não apresentaram diferenças quanto à remoção de HTPs, evidenciando que a fase de maturação dos compostos não apresentou influência na eficiência do processo. No entanto, verificou-se uma eficiência nos tratamentos que receberam composto quando comparado ao tratamento sem adição de composto

Quantitative, Time-Resolved Proteomic Analysis Using Bio-Orthogonal Non-Canonical Amino Acid Tagging

Bio-orthogonal non-canonical amino acid tagging (BONCAT) is an analytical method that allows the selective analysis of the subset of newly synthesized cellular proteins produced in response to a biological stimulus. In BONCAT, cells are treated with the non-canonical amino acid L-azidohomoalanine (Aha), which is utilized in protein synthesis in place of methionine by wild-type translational machinery. Nascent, Aha-labeled proteins are selectively ligated to affinity tags for enrichment and subsequently identified via mass spectrometry. The work presented in this thesis exhibits advancements in and applications of the BONCAT technology that establishes it as an effective tool for analyzing proteome dynamics with time-resolved precision.

Chapter 1 introduces the BONCAT method and serves as an outline for the thesis as a whole. I discuss motivations behind the methodological advancements in Chapter 2 and the biological applications in Chapters 2 and 3.

Chapter 2 presents methodological developments that make BONCAT a proteomic tool capable of, in addition to identifying newly synthesized proteins, accurately quantifying rates of protein synthesis. I demonstrate that this quantitative BONCAT approach can measure proteome-wide patterns of protein synthesis at time scales inaccessible to alternative techniques.

In Chapter 3, I use BONCAT to study the biological function of the small RNA regulator CyaR in Escherichia coli. I correctly identify previously known CyaR targets, and validate several new CyaR targets, expanding the functional roles of the sRNA regulator.

In Chapter 4, I use BONCAT to measure the proteomic profile of the quorum sensing bacterium Vibrio harveyi during the time-dependent transition from individual- to group-behaviors. My analysis reveals new quorum-sensing-regulated proteins with diverse functions, including transcription factors, chemotaxis proteins, transport proteins, and proteins involved in iron homeostasis.

Overall, this work describes how to use BONCAT to perform quantitative, time-resolved proteomic analysis and demonstrates that these measurements can be used to study a broad range of biological processes.

Biological Activity of Rhodium Metalloinsertors and the Design of Bifunctional Conjugates

The Barton laboratory has established that octahedral rhodium complexes bearing the sterically expansive 5,6-chrysene diimine ligand can target thermodynamically destabilized sites, such as base pair mismatches, in DNA with high affinity and selectivity. These complexes approach DNA from the minor groove, ejecting the mismatched base pairs from the duplex in a binding mode termed metalloinsertion. In recent years, we have shown that these metalloinsertor complexes also exhibit cytotoxicity preferentially in cancer cells that are deficient in the mismatch repair (MMR) machinery.

Here, we establish that a sensitive structure-activity relationship exists for rhodium metalloinsertors. We studied the relationship between the chemical structures of metalloinsertors and their effect on biological activity for ten complexes with similar DNA binding affinities, but wide variation in their lipophilicity. Drastic differences were observed in the selectivities of the complexes for MMR-deficient cells. Compounds with hydrophilic ligands were highly selective, exhibiting preferential cytotoxicity in MMR-deficient cells at low concentrations and short incubation periods, whereas complexes with lipophilic ligands displayed poor cell-selectivity. It was discovered that all of the complexes localized to the nucleus in concentrations sufficient for mismatch binding; however, highly lipophilic complexes also exhibited high mitochondrial uptake. Significantly, these results support the notion that mitochondrial DNA is not the desired target for our metalloinsertor complexes; instead, selectivity stems from targeting mismatches in genomic DNA.

We have also explored the potential for metalloinsertors to be developed into more complex structures with multiple functionalities that could either enhance their overall potency or impart mismatch selectivity onto other therapeutic cargo. We have constructed a family of bifunctional metalloinsertor conjugates incorporating cis-platinum, each unique in its chemical structure, DNA binding interactions, and biological activity. The study of these complexes in MMR-deficient cells has established that the cell-selective biological activity of rhodium metalloinsertors proceeds through a critical cellular pathway leading to necrosis.

We further explored the underlying mechanisms surrounding the biological response to mismatch recognition by metalloinsertors in the genome. Immunofluorescence assays of MMR-deficient and MMR-proficient cells revealed that a critical biomarker for DNA damage, phosphorylation of histone H2AX (γH2AX) rapidly accumulates in response to metalloinsertor treatment, signifying the induction of double strand breaks in the genome. Significantly, we have discovered that our metalloinsertor complexes selectively inhibit transcription in MMR-deficient cells, which may be a crucial checkpoint in the eventual breakdown of the cell via necrosis. Additionally, preliminary in vivo studies have revealed the capability of these compounds to traverse the complex environments of multicellular organisms and accumulate in MMR-deficient tumors. Our ever-increasing understanding of metalloinsertors, as well as the development of new generations of complexes both monofunctional and bifunctional, enables their continued progress into the clinic as promising new chemotherapeutic agents.

Análise dinâmica de plataformas de aço para produção de petróleo com base na consideração do efeito da interação solo-estrutura

Atualmente, as tendências competitivas do mercado mundial, têm forçado os engenheiros estruturais a desenvolver soluções de projeto que acarretem em menor peso e custo de execução. Uma consequência direta desta nova tendência de projeto é o aumento considerável de problemas relacionados a vibrações de piso indesejadas. Por esta razão, os sistemas estruturais de pisos podem tornar-se vulneráveis a vibrações excessivas, como por exemplo, aquelas induzidas por equipamentos mecânicos (máquinas rotativas). Deste modo, este trabalho objetiva investigar o comportamento dinâmico de uma plataforma de aço para produção de petróleo, localizada na bacia de Santos (campo de Merluza), São Paulo, Brasil. Para tal, investiga-se a influência das ações dinâmicas oriundas dos equipamentos mecânicos localizados sobre os decks metálicos da plataforma. A resposta dinâmica do modelo estrutural foi determinada através de um extenso estudo numérico, a partir da análise de suas frequências naturais, deslocamentos, velocidades e acelerações de pico. Nesta investigação, as cargas dinâmicas provenientes dos equipamentos mecânicos (máquinas rotativas) foram aplicadas sobre o piso metálico do sistema estrutural. Com base obtenção da resposta dinâmica da estrutura (deslocamentos, velocidades e acelerações), foi possível avaliar a performance do modelo estrutural em termos de critérios de conforto humano e das tolerâncias máximas referentes aos equipamentos mecânicos, de acordo com normas e recomendações de projeto.

Informe técnico sobre posibles alternativas de valorización energética de residuos forestales

[ES]Mediante este proyecto, se trata de buscar diferentes alternativas de valorización energética de residuos forestales, analizar su proceso y los equipos involucrados, y al final elegir la más adecuada en base a ciertos criterios.

Influencia de la internacionalización en el desempeño social de las empresas

[ES] Recientemente estudios previos han comenzado a plantear la posible relación entre el fenómeno de la internacionalización y responsabilidad social corporativa de las organizaciones. En este trabajo analizamos en qué medida la internacionalización contribuye a una mejora sustancial del desempeño social de las empresas. Usando una muestra de 102 empresas estadounidenses de los sectores químico, energético y de maquinaria industrial, nuestros resultados muestran que no todas las dimensiones de la internacionalización permiten a las empresas adquirir conocimiento valioso que conduzca a una mejora de su desempeño social. Concretamente, comprobamos que, mientras el porcentaje de ventas en mercados extranjeros y la diversificación internacional cultural favorecen la puesta en marcha de prácticas de responsabilidad social corporativa avanzadas que redundan en un mejor desempeño social (cumpliendo con las demandas sociales de los grupos de interés de los distintos mercados donde operan), la diversificación internacional geográfica no tiene efecto directo en el desempeño social de las empresas. Por tanto, no es tan importante el número de mercados donde la empresa actúa, sino el grado de diferenciación cultural existente entre los mismos lo que hace que la propia empresa mejore su desempeño social. El presente trabajo incluye implicaciones relevantes para el mundo académico, directivos y reguladores públicos.

Leukemia-Associated Mutations in Nucleophosmin Alter Recognition by CRM1: Molecular Basis of Aberrant Transport

Nucleophosmin (NPM) is a nucleocytoplasmic shuttling protein, normally enriched in nucleoli, that performs several activities related to cell growth. NPM mutations are characteristic of a subtype of acute myeloid leukemia (AML), where mutant NPM seems to play an oncogenic role. AML-associated NPM mutants exhibit altered subcellular traffic, being aberrantly located in the cytoplasm of leukoblasts. Exacerbated export of AML variants of NPM is mediated by the nuclear export receptor CRM1, and due, in part, to a mutationally acquired novel nuclear export signal (NES). To gain insight on the molecular basis of NPM transport in physiological and pathological conditions, we have evaluated the export efficiency of NPM in cells, and present new data indicating that, in normal conditions, wild type NPM is weakly exported by CRM1. On the other hand, we have found that AML-associated NPM mutants efficiently form complexes with CRM1HA (a mutant CRM1 with higher affinity for NESs), and we have quantitatively analyzed CRM1HA interaction with the NES motifs of these mutants, using fluorescence anisotropy and isothermal titration calorimetry. We have observed that the affinity of CRM1HA for these NESs is similar, which may help to explain the transport properties of the mutants. We also describe NPM recognition by the import machinery. Our combined cellular and biophysical studies shed further light on the determinants of NPM traffic, and how it is dramatically altered by AML-related mutations.

Latt-Mayer, um estudo de caso: tecnologia na história do design gráfico brasileiro.

Nosso objetivo neste trabalho é investigar como o design gráfico se relaciona com os meios de produção da indústria gráfica brasileira. Não é comum encontrar referências abordando temas que relacionam design e tecnologia em livros sobre a história do Brasil, o que demonstra a urgência do resgate histórico de indústrias que implementaram novas tecnologias para atender a demandas projetuais e mercadológicas. Sediada na cidade do Rio de Janeiro, a clicheria Latt-Mayer como era comumente chamada, era sinônimo de qualidade e tecnologia. Entre seus clientes podemos apontar agências de publicidade, editoras, escritórios de designers e gráficas de todo país. Esta pesquisa se baseia em um corpus composto por imagens, documentos, manuais técnicos, reportagens, matrizes e depoimentos com pessoas que estiveram diretamente envolvidas com essa empresa. Catalogamos maquinaria e técnicas utilizadas, além de projetos gráficos relevantes que tiveram matrizes e provas produzidas na empresa. Por meio deste trabalho, é possível visualizar um abrangente painel histórico, que contempla um período em que ocorreram significativas transformações na relação entre designers e tecnologia na indústria gráfica brasileira.

Diseño de una tarjeta de drivers para un inversor de potencia.

[EN]The purpose of this project is to design a system which improves the e ciency of power inverters. The project is focused in the analysis of the di erent power semiconductors (based on silicon, silicon carbide and gallium nitride) and driver applications. This system can be implemented in di erent future versions of power inverters and in many kind of applications like electrical vehicles. Other than that, it can be also implemented on any machinery requiring an inverter obtaining more energy and reduce manufacturing costs.