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This thesis explores bio-mediated processes in geotechnical and petroleum engineering. Worldwide energy consumption is rapidly increasing as the world population and per-capita consumption rises. The US Energy Information Agency (EIA) predicts that hydrocarbons will remain the primary energy source to satisfy the surging energy demands in the near future. The three topics described in detail in this document aim to link microbiology with geotechnical engineering and the petroleum industry. Microorganisms have the potential to exploit residual hydrocarbons in depleted reservoirs in a technique known as microbial enhanced oil recovery, MEOR. The potential of biosurfactants was analyzed in detail with a literature review. Biosurfactant production is the most accepted MEOR technique, and has been successfully implemented in over 700 field cases. Temperature is the main limiting factor for these techniques. The dissolution of carbonates by microorganisms was investigated experimentally. We designed a simple, economical, and robust procedure to monitor diffusion through porous media. This technique determined the diffusion coefficient of H+ in 1.5% agar, 1.122 x 10-5 cm2 sec-1, by using bromothymol blue as a pH indicator and image processing. This robust technique allows for manipulation of the composition of the agar to identify the effect of specific compounds on diffusion. The Red Sea consists of multiple seeps; the nearby sediments are telltales of deeper hydrocarbon systems. Microbial communities associated with the sediments function as in-situ sensors that provide information about the presence of carbon sources, metabolites, and the remediation potential. Sediments seeps in the Red Sea revealed different levels of bioactivity. The more active seeps, from the southern site in the Red Sea, indicated larger pore sizes, higher levels of carbon, and bioactivity with both bacteria and archaeal species present.

Thesis (Ph.D.)--University of Florida, 2004. / Typescript. Title from title page of source document. Document formatted into pages; contains 210 pages. Includes Vita. Includes bibliographical references.

With the increasing demand for assisted reproduction, more knowledge and understanding towards health requirements of oocytes and their inner workings are required. With current IVF success rates of approximately 40%, oocyte and embryo culture conditions in vitro can be improved by first understanding the finer details of oocyte function. As such, there is a need to better understand the mechanisms through which oocytes can acquire certain nutrients. This thesis focuses on the amino acid serine, which has been shown to improve outcome in developing embryos and also plays a variety of roles in the body that may carry over to oocyte health as well. Using radiolabeled [3H] serine, we measured uptake of serine as a function of time throughout growth and meiotic maturation in mouse oocytes. Serine transport appeared in oocytes during growth and became absent in mature eggs. With a competition assay using substrates diagnostic for several different amino acid transporter systems and culture with and without sodium in the external medium, I identified Na+-dependent SNAT7 of the System A/N (SLC38) family to be the most likely transporter in oocytes. Quantitative RT-PCR was consistent with this result. Transporter activity is also not activated by progression of meiotic maturation, as indicated by unperturbed transport when dbcAMP was provided to maintain meiotic arrest. However, a biological regulator of arrest, NPPC, resulted in enhanced transport activity in vitro. This may be due to signalling mechanisms of the NPPC pathway affecting regulation of serine uptake, which presents a direction for future research.

The clearance of circulating glucose and long-chain fatty acids (FA) into skeletal muscle involves the translocation of glucose transporter GLUT4, fatty acid translocase (FAT/CD36), plasma membrane associated fatty acid binding protein (FABPpm) and fatty acid transport protein (FATP) 1 and 4 to the plasma membrane (PM). FAT/CD36 also appears to participate in the regulation of mitochondrial FA oxidation. Metabolic challenges are known to increase FA transport and/or oxidation, but whether this is solely attributable to the translocation of FAT/CD36 to the sarcolemma and/or mitochondria is unknown. Moreover, the signaling and trafficking pathways involved in the translocation of FA transporters are largely unexplored. In this thesis it was found that FA transport was markedly increased following insulin (+2.9-fold) or contraction (+1.7-fold) stimulation of skeletal muscle, along with the PM contents of FAT/CD36 (+78%, +55%,), FABPpm (+61%, +62%), FATP1 (+84%, +61%) and FATP4 (+60%, +66%) (p<0.05). Upon combining the two stimuli, only the translocation of FAT/CD36 (+179%) and FATP1 (+125%) to the PM was additive, suggesting that these transporters may reside in distinct insulin-sensitive and contraction-sensitive intracellular compartments. The translocation of FA transporters may involve the insulin-signaling protein Akt2. It was found that insulin-stimulated FA transport and PM translocation of FA transporters was essentially prevented in Akt2 knockout mice. Following contraction, FA transport was also markedly blunted, along with an impaired translocation of both FAT/CD36 and FATP1, but not FABPpm or FATP4. FA oxidation and mitochondrial FAT/CD36 appearance were also inhibited following muscle contraction in knockout mice (p<0.05). Whether the GLUT4 trafficking protein Munc18c is important for the vesicular re-distribution of FA transporters to the PM or mitochondria was also investigated. FA uptake was comparably increased 1.4 fold with insulin and contraction in both wildtype and heterozygous Munc18c-/+ mice, as were PM FA transporters FAT/CD36 (+82%, +84%), FABPpm (+39%, +43%), FATP1 (+40%, +38%) and FATP4 (+33%, +32%) (p<0.05). Contraction-stimulated mitochondrial FA oxidation was also increased similarly in wildtype (+39%) and Munc18c-/+ mice (+33%). These studies demonstrate that a number of FA transporters are involved in upregulating skeletal muscle FA transport, although their signaling and trafficking pathways may differ from that of GLUT4.

Protozoários do gênero Leishmania são parasitas digenéticos, com uma fase no tubo digestório de um hospedeiro invertebrado (promastigota), e uma fase parasita intracelular de macrófagos (amastigotas). Estudar a demanda de L-arginina no parasita é interessante, uma vez que o aminoácido é indispensável para a sobrevida do parasita e, ao mesmo tempo, serve de substrato para a produção de óxido nítrico, principal composto microbicida dos macrófagos. O objetivo deste trabalho foi caracterizar o transporte de arginina em Leishmania (Leishmania) amazonensis do ponto de vista fisiológico e caracterizar o gene que codifica o transportador do aminoácido, bem como a regulação da sua expressão em resposta a diferentes condições biológicas. Para medir o influxo de L-arginina em fagolisossomos, utilizamos macrófagos J774 infectados com L. (L.) amazonensis e desenvolvemos uma metodologia com citometria de fluxo com sorting para a purificação da organela. Validamos microscopicamente a presença do parasita na organela por sua fluorescência, e avaliamos a integridade da membrana externa dessa com marcador de pH ácido. Paralelamente, o gene que codifica o transportador de arginina do parasita foi caracterizado. Foram encontradas duas cópias em tandem que produzem dois transcritos (5.1AAP3 e 4.7AAP3), cujas regiões 5\'UTR e 3\'UTR são diferentes. Por meio de PCR quantitativo em tempo real, avaliamos a expressão desses transcritos e verificamos que 5.1AAP3 é mais expressa ao longo do desenvolvimento do parasita, com um máximo em fase estacionária. A determinação da meia-vida dos mRNA das duas cópias indicou uma duração de 32,6±5,0min para o mRNA de 4.7AAP3, enquanto que o de 5.1AAP3 não apresentou decaimento até 180min do estudo, evidenciando que a estabilidade maior pode ser a razão de sua maior abundância. A submissão de parasitas à privação de arginina levou a aumento na tomada do aminoácido concomitante ao aumento do transcrito 5.1AAP3. Mutantes nulos de arginase submetidos à privação de arginina respondem com uma taxa de incorporação mais baixa em relação aos parasitas selvagens, e mantém a resposta à privação mesmo com os parasitas em fase estacionária, diferente do observado nos parasitas selvagens. Esse conjunto de resultados nos levou a sugerir que a expressão do transportador pode ser regulada pela estabilidade do mRNA, e que o pool de arginina interno ao parasita pode controlar, num mecanismo de retroalimentação negativo, a expressão de seu transportador. / Protozoan of genus Leishmania are digenetic parasites that present a stage in the life in insect gut (promastigotes) and an intracellular phase (amastigotes) inside vertebrate host macrophages. The study of L-arginine influx consists in an interesting matter, since the amino acid is used on NO production pathway (the main macrophage microbial pathway) but are also important for parasites survival. The aim of this work was to perform a genetic and physiological characterization of the arginine transport in Leishmania (Leishmania) amazonensis. To verify how does the arginine uptake occurs in the phagolisosomes, we used J774 macrophages infected with L. (L.) amazonensis to establish a flow cytometry sorting protocol to purify the organelle. Microscopic validation of organelle integrity was achieved by acidic pH marker treatment and detection of fluorescent parasites. The arginine transporter coding gene was characterized. We found two copies in tandem that produces two transcripts, named 5.1AAP3 and 4.7AAP3, with distinct 5\'UTR and 3\'UTR. By quantitative real time PCR we found that 5.1AAP3 mRNA expression varies along parasite development. This copy was, also, more abundant than 4.7AAP3 mRNA. This last mRNA showed a half-life of 32.6±5.0 min, while the 5.1AAP3 mRNA did not decay until 180min. As response to arginine starvation, wild type parasites increase the uptake of arginine, as well as the abundance of 5.1AAP3 mRNA. Arginase null parasites starvation responses showed lower arginine uptake rates compared to wild type responses. Unlike wild type, the null mutants also respond to starvation in stationary phase. This data set allow us to propose that arginine internal pool can downregulate its transporter expression in a feed-back mechanism.

Sialyltransferases, CMP-sialic acid synthetases and CMP-sialic acid transport proteins play a crucial role in the construction of cell surface glycoconjugates. These proteins also have a pivotal role to play in a number of diseases, including cancer. The sialyltransferase enzymes are responsible for transfering sialic acids from the donor substrate (CMP-sialic acid) to growing cell surface glycoconjugate chains within the Golgi apparatus. The CMP-sialic acid synthetase enzymes are responsible for the synthesis of the CMP-sialic acid, the donor substrate of the sialyltransferases in the nucleus, while the CMP-sialic acid transport proteins are responsible for transporting CMP-sialic acid from the Cytosol to the Golgi apparatus. When these proteins function in an abnormal way, hypersialylation results, leading to an increased level of sialylation on the cell surface. This increased level of sialylation aids in the detachment of primary tumour cells due to an increase in the level of overall negative charge, causing repulsion between the cancer cells. Therefore, the sialyltransferase enzymes, CMP-sialic acid synthetases and CMP-sialic acid transport proteins are intimately involved in the metastatic cascade associated with cancer. Chapter 1 provides a general introduction of cancer metastasis, discussing the roles of three target proteins (CMP-sialic acid synthetases, CMP-sialic acid transport proteins and sialyltransferases), as well as discussing their substrate specificities, with an emphasis on their involvements in cancer metastasis. The Chapter concludes with an overview of the types of compounds intended to be utilised as probes or inhibitors of these proteins. Chapter 2 describes the general approach towards the synthesis of CMP-Neu5Ac mimetics with a sulfur linkage in the presence of a phosphate group in the general structure 38. The precursor phosphoramidite derivative 45 was prepared and isolated in a good yield using Py.TFA. Unfortunately, the target compound 38 could not be prepared. Chapter 3 describes an alternative strategy wherein S-linked sialylnucleoside mimetics, of the general structure 39, with a sulfur linkage, but no phosphate group, between the sialylmimetic and the ribose moiety in the base is targeted. A series of these S-linked sialylnucleoside mimetics were successfully prepared. Cytidine, uridine, adenosine and 5-fluorouridine nucleosides were used to create a library of different nucleosides and with structural variability also present in the sialylmimetic portion. This small 'library' of 15 compounds was designed to shed light on the interaction of these compounds with the binding sites of the sialyltranferase, CMP-sialic acid synthetase and/or CM-sialic acid transport protein. Approaches towards the synthesis of O-linked sialylnucleoside mimetics of the general structure 40 are described in Chapter 4. Several methodologies are reported, as well as protecting group manipulations, for successful preparation of these sialylnucleoside mimetics. Cytidine and uridine were employed as the nucleosides, thus allowing a direct comparison between the O- and S-linked sialylnucleoside mimetics in biological evaluation. It appears from these synthetic investigations that gaining access into the O-linked series is not as straightforward as for the S-linked series, with alternative protecting group strategies required for the different nucleosides. The biological evaluation of some of the compounds reported in Chapters 3 and 4 is detailed in Chapter 5. The sialylnucleoside mimetics were evaluated, by 1H NMR spectroscopy, for their ability to inhibit CMP-KDN synthetase. In addition, an initial 1H NMR spectroscopic-based assay was investigated for inhibition studies of α(2,6)sialyltranferase in the absence of potential inhibitors. The final chapter (Chapter 6) brings together full experimental details in support of the compounds described in the preceding Chapters.