Innovations of wide-field optical-sectioning fluorescence microscopy : toward high-speed volumetric bio-imaging with simplicity

Optical microscopy has become an indispensable tool for biological researches since its invention, mostly owing to its sub-cellular spatial resolutions, non-invasiveness, instrumental simplicity, and the intuitive observations it provides. Nonetheless, obtaining reliable, quantitative spatial information from conventional wide-field optical microscopy is not always intuitive as it appears to be. This is because in the acquired images of optical microscopy the information about out-of-focus regions is spatially blurred and mixed with in-focus information. In other words, conventional wide-field optical microscopy transforms the three-dimensional spatial information, or volumetric information about the objects into a two-dimensional form in each acquired image, and therefore distorts the spatial information about the object. Several fluorescence holography-based methods have demonstrated the ability to obtain three-dimensional information about the objects, but these methods generally rely on decomposing stereoscopic visualizations to extract volumetric information and are unable to resolve complex 3-dimensional structures such as a multi-layer sphere.

The concept of optical-sectioning techniques, on the other hand, is to detect only two-dimensional information about an object at each acquisition. Specifically, each image obtained by optical-sectioning techniques contains mainly the information about an optically thin layer inside the object, as if only a thin histological section is being observed at a time. Using such a methodology, obtaining undistorted volumetric information about the object simply requires taking images of the object at sequential depths.

Among existing methods of obtaining volumetric information, the practicability of optical sectioning has made it the most commonly used and most powerful one in biological science. However, when applied to imaging living biological systems, conventional single-point-scanning optical-sectioning techniques often result in certain degrees of photo-damages because of the high focal intensity at the scanning point. In order to overcome such an issue, several wide-field optical-sectioning techniques have been proposed and demonstrated, although not without introducing new limitations and compromises such as low signal-to-background ratios and reduced axial resolutions. As a result, single-point-scanning optical-sectioning techniques remain the most widely used instrumentations for volumetric imaging of living biological systems to date.

In order to develop wide-field optical-sectioning techniques that has equivalent optical performance as single-point-scanning ones, this thesis first introduces the mechanisms and limitations of existing wide-field optical-sectioning techniques, and then brings in our innovations that aim to overcome these limitations. We demonstrate, theoretically and experimentally, that our proposed wide-field optical-sectioning techniques can achieve diffraction-limited optical sectioning, low out-of-focus excitation and high-frame-rate imaging in living biological systems. In addition to such imaging capabilities, our proposed techniques can be instrumentally simple and economic, and are straightforward for implementation on conventional wide-field microscopes. These advantages together show the potential of our innovations to be widely used for high-speed, volumetric fluorescence imaging of living biological systems.

Geochemistry and resonance ionization of platinum-group elements

Experimental studies were conducted with the goals of 1) determining the origin of Pt- group element (PGE) alloys and associated mineral assemblages in refractory inclusions from meteorites and 2) developing a new ultrasensitive method for the in situ chemical and isotopic analysis of PGE. A general review of the geochemistry and cosmochemistry of the PGE is given, and specific research contributions are presented within the context of this broad framework.

An important step toward understanding the cosmochemistry of the PGE is the determination of the origin of POE-rich metallic phases (most commonly εRu-Fe) that are found in Ca, AJ-rich refractory inclusions (CAI) in C3V meteorites. These metals occur along with γNi-Fe metals, Ni-Fe sulfides and Fe oxides in multiphase opaque assemblages. Laboratory experiments were used to show that the mineral assemblages and textures observed in opaque assemblages could be produced by sulfidation and oxidation of once homogeneous Ni-Fe-PGE metals. Phase equilibria, partitioning and diffusion kinetics were studied in the Ni-Fe-Ru system in order to quantify the conditions of opaque assemblage formation. Phase boundaries and tie lines in the Ni-Fe-Ru system were determined at 1273, 1073 and 873K using an experimental technique that allowed the investigation of a large portion of the Ni-Fe-Ru system with a single experiment at each temperature by establishing a concentration gradient within which local equilibrium between coexisting phases was maintained. A wide miscibility gap was found to be present at each temperature, separating a hexagonal close-packed εRu-Fe phase from a face-centered cubic γNi-Fe phase. Phase equilibria determined here for the Ni-Fe-Ru system, and phase equilibria from the literature for the Ni-Fe-S and Ni-Fe-O systems, were compared with analyses of minerals from opaque assemblages to estimate the temperature and chemical conditions of opaque assemblage formation. It was determined that opaque assemblages equilibrated at a temperature of ~770K, a sulfur fugacity 10 times higher than an equilibrium solar gas, and an oxygen fugacity 10⁶ times higher than an equilibrium solar gas.

Diffusion rates between -γNi-Fe and εRu-Fe metal play a critical role in determining the time (with respect to CAI petrogenesis) and duration of the opaque assemblage equilibration process. The diffusion coefficient for Ru in Ni (D^Ru_Ni) was determined as an analog for the Ni-Fe-Ru system by the thin-film diffusion method in the temperature range of 1073 to 1673K and is given by the expression:

D^Ru_Ni (cm² sec^-1) = 5.0(±0.7) x 10^-3 exp(-2.3(±0.1) x 10¹² erg mole^-1/RT) where R is the gas constant and T is the temperature in K. Based on the rates of dissolution and exsolution of metallic phases in the Ni-Fe-Ru system it is suggested that opaque assemblages equilibrated after the melting and crystallization of host CAI during a metamorphic event of ≥ 10³ years duration. It is inferred that opaque assemblages originated as immiscible metallic liquid droplets in the CAI silicate liquid. The bulk compositions of PGE in these precursor alloys reflects an early stage of condensation from the solar nebula and the partitioning of V between the precursor alloys and CAI silicate liquid reflects the reducing nebular conditions under which CAI were melted. The individual mineral phases now observed in opaque assemblages do not preserve an independent history prior to CAI melting and crystallization, but instead provide important information on the post-accretionary history of C3V meteorites and allow the quantification of the temperature, sulfur fugacity and oxygen fugacity of cooling planetary environments. This contrasts with previous models that called upon the formation of opaque assemblages by aggregation of phases that formed independently under highly variable conditions in the solar nebula prior to the crystallization of CAI.

Analytical studies were carried out on PGE-rich phases from meteorites and the products of synthetic experiments using traditional electron microprobe x-ray analytical techniques. The concentrations of PGE in common minerals from meteorites and terrestrial rocks are far below the ~100 ppm detection limit of the electron microprobe. This has limited the scope of analytical studies to the very few cases where PGE are unusually enriched. To study the distribution of PGE in common minerals will require an in situ analytical technique with much lower detection limits than any methods currently in use. To overcome this limitation, resonance ionization of sputtered atoms was investigated for use as an ultrasensitive in situ analytical technique for the analysis of PGE. The mass spectrometric analysis of Os and Re was investigated using a pulsed primary Ar⁺ ion beam to provide sputtered atoms for resonance ionization mass spectrometry. An ionization scheme for Os that utilizes three resonant energy levels (including an autoionizing energy level) was investigated and found to have superior sensitivity and selectivity compared to nonresonant and one and two energy level resonant ionization schemes. An elemental selectivity for Os over Re of ≥ 10³ was demonstrated. It was found that detuning the ionizing laser from the autoionizing energy level to an arbitrary region in the ionization continuum resulted in a five-fold decrease in signal intensity and a ten-fold decrease in elemental selectivity. Osmium concentrations in synthetic metals and iron meteorites were measured to demonstrate the analytical capabilities of the technique. A linear correlation between Os⁺ signal intensity and the known Os concentration was observed over a range of nearly 10⁴ in Os concentration with an accuracy of ~ ±10%, a millimum detection limit of 7 parts per billion atomic, and a useful yield of 1%. Resonance ionization of sputtered atoms samples the dominant neutral-fraction of sputtered atoms and utilizes multiphoton resonance ionization to achieve high sensitivity and to eliminate atomic and molecular interferences. Matrix effects should be small compared to secondary ion mass spectrometry because ionization occurs in the gas phase and is largely independent of the physical properties of the matrix material. Resonance ionization of sputtered atoms can be applied to in situ chemical analysis of most high ionization potential elements (including all of the PGE) in a wide range of natural and synthetic materials. The high useful yield and elemental selectivity of this method should eventually allow the in situ measurement of Os isotope ratios in some natural samples and in sample extracts enriched in PGE by fire assay fusion.

Phase equilibria and diffusion experiments have provided the basis for a reinterpretation of the origin of opaque assemblages in CAI and have yielded quantitative information on conditions in the primitive solar nebula and cooling planetary environments. Development of the method of resonance ionization of sputtered atoms for the analysis of Os has shown that this technique has wide applications in geochemistry and will for the first time allow in situ studies of the distribution of PGE at the low concentration levels at which they occur in common minerals.

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.

Geochemistry of lipids in lacustrine sediments

An explanation of the basic premises of the subject and its terminology is given. The article then outlines aspects of research on the organic material found in lacustrine sediments, and the analytical methods involved.

Valoración de bio-oil completo por craqueo catalítico en condiciones de la unidad FCC de refinería

351 p.

Poly(lactic acid)-based bio-blends and nanocomposites

172 p.

Avaliação da acidez de bio-óleos obtidos pela pirólise de óleos vegetais pós-consumo

O descarte irregular do óleo vegetal pós-consumo diretamente na rede de esgoto vem causando grandes problemas para o meio ambiente. Atualmente, essa problemática tem se intensificado devido ao aumento de produção e consumo destes óleos, o que por conseqüência aumenta o despejo desordenado. No presente estudo foi realizada a obtenção do bio-óleo a partir da pirólise térmica em atmosfera de nitrogênio, a 400C, por 20 minutos, do óleo vegetal pós-consumo, provenientes das seguintes oleoginosas: soja, milho, girassol e canola. As pirólises não-catalíticas apresentaram uma geração média entre 40 e 50% de um bio-óleo, de elevado índice de acidez, 81,8 mg NaOH/g. Na pirólise catalítica, a argila ácida K10 foi o catalisador que apresentou melhor eficácia para geração de um bio-óleo de menor índice de acidez. A concentração ótima do catalisador foi de 5%(m/m), gerando 482 % de um bio-óleo com índice de acidez de 43,8 mg NaOH/g. A caracterização dos líquidos pirolíticos obtidos foi realizada através da técnica de espectrofotometria na região do infravermelho (FTIR) e cromatografia em fase gasosa acoplada a espectrômetro de massas (CG/EM) que monstraram que a trioleína, o triglicerídeo do ácido oléico, foi craqueado, gerando o hexadecanoato de octadecila e o oleato de eicosila, ésteres do respectivo ácido graxo

White spot syndrome virus (WSSV) transmission risk through infected cooked shrimp products assessed by polymerase chain reaction (PCR) and bio-inoculation studies

The aim of the study was to evaluate the resistance of white spot syndrome virus (WSSV) in shrimps (Penaeus monodon) to the process of cooking. The cooking was carried out at 1000C six different durations 5, 10, 15, 20, 25 and 30 min. The presence of WSSV was tested by single step and nested polymerase chain reaction (PCR). In the single step PCR, the primers 1s5 & 1a16 and IK1 & IK2 were used. While in the nested PCR, primers IK1 &IK2 – IK3 & IK4 were used for the detection of WSSV. WSSV was detected in the single step PCR with the primers 1s5 and 1a16 and the nested PCR with the primers IK1 and IK2 – IK3 & IK4 from the cooked shrimp samples. The cooked shrimps, which gave positive results for WSSV by PCR, were further confirmed for the viability of WSSV by conducting the bio-inoculation studies. Mortality (100%) was observed within 123 h of intra-muscular post injection (P.I) into the live healthy WSSV-free shrimps (P. monodon). These results show that the WSSV survive the cooking process and even infected cooked shrimp products may pose a transmission risk for WSSV to the native shrimp farming systems.

Variation des bio-volumes des zooplancton du plateau continental entre le Cap des Palmes et le Cap des Trois Pointes

Three years of weekly sampling from a coastal station and 29 monthly cruises over the whole continental shelf were studied for zooplankton quantitative variation. Settled volumes were preferred to displacement volumes. At the coastal station, near Abidjan, a negative correlation was found between the log2 of zooplankton volume and the preceding fortnight temperature. On the whole shelf, the differences between the 6 considered areas were tested by the variance analysis. There were significative differences in shallow waters only (20 m). During the main cold season, the upwelling of Tabou causes a very important enrichment 30 to 60 nautical miles to the east. Eastwards the plankton drifts and decreases in abundance. The zooplankton maximum is not always inshore, but often in the middle of the shelf and sometimes over the slope. During the little cold season the enrichments caused by coastal upwelling are less abundant and restricted to smaller areas. During the warm season, the waters are uniformly poor. During the cold season, over the 60m depths, the zooplankton maximum lies between 10 and 20 m and seems to sink in deeper waters. In warm season the vertical repartition is rather homogeneous in the first 40 meters. The diel vertical migrations show a very consistent rhythm, varying with the season.

Estudo de pirólise catalítica de biomassa em escala piloto para melhoramento da qualidade do bio-óleo

A pirólise rápida é um processo para conversão térmica de uma biomassa sólida em altos rendimentos de um produto líquido chamado de bio-óleo. Uma das alternativas para geração de um bio-óleo com menor teor de oxigênio é uso de catalisadores nos reatores de pirólise, ao invés de um inerte, num processo chamado de pirólise catalítica. O objetivo deste trabalho foi testar catalisadores comerciais, um ácido e outro básico, em uma unidade piloto de leito fluidizado circulante. O catalisador ácido utilizado foi o Ecat, proveniente de uma unidade industrial de craqueamento catalítico fluido (FCC), e como catalisador básico foi utilizado uma hidrotalcita. Os resultados foram comparados com testes utilizando um material inerte, no caso uma sílica. Uma unidade piloto de FCC do CENPES foi adaptada para realizar os testes de pirólise catalítica. Após fase de modificação e testes de condicionamento, foi comprovada a viabilidade na utilização da unidade piloto adaptada. Contudo, devido a limitações operacionais, maiores tempos de residência tiveram que ser aplicados no reator, configurando o processo como pirólise intermediária. Foram então realizados testes com os três materiais nas temperaturas de 450C e 550C. Os resultados mostraram que o aumento do tempo de residência dos vapores de pirólise teve um impacto significativo nos rendimentos dos produtos quando comparada com o perfil encontrado na literatura para pirólise rápida, pois devido ao incremento das reações secundárias, produziu maiores rendimentos de coque e água, e menores rendimentos de bio-óleo. O Ecat e a hidrotalcita se apresentaram mais efetivos em termos de desoxigenação. O primeiro apresentou maiores taxas de desoxigenação via desidratação e a hidrotalcita apresentou maior capacidade para descarboxilação. Contudo, o uso de Ecat e hidrotalcita não se mostrou adequado para uso em reatores de pirólise intermediária, pois acentuou ainda mais as reações secundárias, gerando um produto com alto teor de água e baixo teor de compostos orgânicos no bio-óleo, além de produzirem mais coque. À temperatura de 450C estes efeitos foram mais pronunciados. Em termos de caracterização química, a condição de pirólise intermediária apontou para a produção de bio-óleos com perfil fenólico, sendo a sílica o que proporcionou os melhores rendimentos, principalmente a temperatura de 550C, sendo superiores aos encontrados na literatura. Analisando as composições dos bio-óleos sob a ótica da produção de biocombustíveis, nenhum dos materiais testados apresentou rendimentos consideráveis em hidrocarbonetos. De maneira geral, a sílica foi o que proporcionou os melhores resultados em termos de rendimento e qualidade do bio-óleo. Sua menor área superficial e sua característica de inerte se mostraram mais adequados para o processo de pirólise intermediária, onde a contribuição das reações secundárias em fase gasosa é elevada em função do tempo de residência no reator

Estudo para minimização do processo de fumigação empregado na limpeza e desinfecção de salas limpas em Bio-Manguinhos/ FIOCRUZ

As indústrias farmacêuticas que utilizam salas limpas, em seus processos produtivos, devem controlar ao máximo o nível de contaminantes microbiológicos, baseada na legislação RDC 210 que determina o cumprimento das diretrizes estabelecidas no Regulamento Técnico das Boas Práticas para a Fabricação de Medicamentos. Diante deste cenário, a proposta deste trabalho é avaliar o processo de fumigação com o reagente formaldeído, para a limpeza e desinfecção de salas limpas do Instituto de Tecnologia de Imunobiológicos Bio-Manguinhos. Então, foram desenvolvidas as seguintes etapas: diagnóstico com as indústrias farmacêuticas para traçar um perfil quanto ao uso da fumigação; quantificação de resíduos gerados; avaliação da exposição dos operadores ao formaldeído que é cancerígeno e acompanhamento dos resultados do monitoramento ambiental do ar e de superfícies, inicialmente na sala limpa do SEFBC, cuja atividade principal é a formulação de vacinas bacterianas e biofármacos, após a implantação do espaçamento da fumigação. Os resultados discutidos na presente dissertação mostraram, que a maior parte das indústrias farmacêuticas, não realiza a desinfecção por intermédio da fumigação e que o resíduo gerado neste processo é o mais crítico. E, sobretudo, o monitoramento microbiológico do ar e de superfícies da sala limpa do SEFBC, a partir da metodologia adotada de espaçamento da fumigação, comprovou que não é necessário o emprego deste processo de forma rotineira, para garantir os níveis exigidos de limpeza e desinfecção da respectiva área