Tissue engineering active biological machines : bio-inspired design, directed self-assembly, and characterization of muscular pumps simulating the embryonic heart

Biological machines are active devices that are comprised of cells and other biological components. These functional devices are best suited for physiological environments that support cellular function and survival. Biological machines have the potential to revolutionize the engineering of biomedical devices intended for implantation, where the human body can provide the required physiological environment. For engineering such cell-based machines, bio-inspired design can serve as a guiding platform as it provides functionally proven designs that are attainable by living cells. In the present work, a systematic approach was used to tissue engineer one such machine by exclusively using biological building blocks and by employing a bio-inspired design. Valveless impedance pumps were constructed based on the working principles of the embryonic vertebrate heart and by using cells and tissue derived from rats. The function of these tissue-engineered muscular pumps was characterized by exploring their spatiotemporal and flow behavior in order to better understand the capabilities and limitations of cells when used as the engines of biological machines.

Coupled effects of mechanics, geometry, and chemistry on bio-membrane behavior

Lipid bilayer membranes are models for cell membranes--the structure that helps regulate cell function. Cell membranes are heterogeneous, and the coupling between composition and shape gives rise to complex behaviors that are important to regulation. This thesis seeks to systematically build and analyze complete models to understand the behavior of multi-component membranes.

We propose a model and use it to derive the equilibrium and stability conditions for a general class of closed multi-component biological membranes. Our analysis shows that the critical modes of these membranes have high frequencies, unlike single-component vesicles, and their stability depends on system size, unlike in systems undergoing spinodal decomposition in flat space. An important implication is that small perturbations may nucleate localized but very large deformations. We compare these results with experimental observations.

We also study open membranes to gain insight into long tubular membranes that arise for example in nerve cells. We derive a complete system of equations for open membranes by using the principle of virtual work. Our linear stability analysis predicts that the tubular membranes tend to have coiling shapes if the tension is small, cylindrical shapes if the tension is moderate, and beading shapes if the tension is large. This is consistent with experimental observations reported in the literature in nerve fibers. Further, we provide numerical solutions to the fully nonlinear equilibrium equations in some problems, and show that the observed mode shapes are consistent with those suggested by linear stability. Our work also proves that beadings of nerve fibers can appear purely as a mechanical response of the membrane.

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.

Diseño y despliegue de una red inalámbrica segura y control de acceso de sensores IP

[ES]El proyecto está orientado a conseguir una comunicación inalámbrica y segura de una red de sensores IP. Por un lado, mediante el protocolo 6LoWPAN se consigue que los datos se transmitan mediante IPv6 y, por otro lado, gracias al protocolo LADON se establecen los servicios de seguridad de autenticación, integridad de datos, autorización y control de acceso.

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.

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

351 p.

CICLOADICIONES [3+2] Y [8+2] Y SU APLICACIÓN A LA SÍNTESIS DE MOLÉCULAS MARCADAS Y SENSORES DE ADN FLUORESCENTES

La presente Tesis Doctoral está encaminada hacia el estudio de las cicloadiciones y su aplicación a la síntesis de moléculas marcadas y sensores de ADN fluorescentes. La primera línea de trabajo se basará en el diseño y síntesis de dos nuevos grupos de moléculas fluorescentes basadas en las benzo[a]imidazo[5,1,2-cd]indolizinas y en las 2,3,9c-triazociclo-penta[j,k]fluorenos mediante la cicloadición [8 + 2]. También se lleva a cabo la síntesis de los derivados los aductos [8+2] que pudieran interaccionar con el ADN y posteriores experimentos de unión al ADN de los compuestos sintetizados. Por otro lado, la segunda línea de investigación consistirá en la búsqueda de estrategias sintéticas para la obtención de un precursor de un inhibidor de HDAC para su utilización en estudios de biodistribución mediante técnicas basados en radioactividad, como son la de tomografía por emisión de positrones y el método de disección.

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