Carbon nanotubes (CNTs) and gold nanoparticles (AuNPs) are widely used for sensing applications due to their distinctive electrical and optical properties, and we have explored the development of methods that enable the incorporation of these nanomaterials into new and improved sensing devices. As a means for fabricating simple, low-cost and fast detection platforms for various applications, we have developed paper-based electrochemical detection platforms based on CNTs or platinum nanoparticle (PtNP)-CNT composite materials. We describe the use of a paper-based, low density, a three-dimensional thin film of interconnected CNTs as an electrode material. We studied the electrochemical properties of these paper-based CNT electrodes and demonstrated their use as an electrochemical sensor for the sensitive detection of guanine-based nucleotides. We further describe the functionalization of this paper-based electrode by fabricating a PtNP-SWCNT hybrid film via a vacuum filtration-based method. The interconnected PtNP structure formed on top of the CNT-coated paper was directly used as an electrocatalyst for methanol oxidation. Compared to paper-based PtNP-SWCNT hybrid films formed by electrochemical deposition, hybrid films formed by vacuum filtration showed a higher electrochemical surface area and enhanced electrocatalytic response to methanol oxidation. We have also developed methods based around DNA-modified AuNPs, which offer an excellent colorimetric platform for target detection. The DNA density on the surface of modified AuNPs affects enzymatic activity, colloidal stability of AuNPs, the orientation of the probe DNA and its hybridization efficiency. The combination of all these factors ultimately dictates the reaction time and sensitivity of colorimetric assays. We demonstrate the use of DTT as a modulator to control DNA surface coverage on the surface of AuNPs. Using this DTT treatment and a novel probe for exonuclease III activity, we have developed a colorimetric assay based on DTT-treated, DNA-modified AuNPs that can achieve more sensitive and rapid detection of DNA and enzymes relative to existing sensor platforms.

The present thesis investigates the electronic and structural properties of adenine, cytosine, and guanine layers on hydrogen passivated silicon (111)(7x7). The (7x7) reconstruction of the silicon surface was achieved by direct current heating of the samples in UHV conditions. After in situ hydrogen passivation layers of the DNA bases were prepared in different thicknesses by means of organic molecular beam deposition, all samples were characterized employing valence band and core level photoemission spectroscopy. Additionally the near edge x-ray absorption fine structure of the DNA base layers was investigated. A detailed and consistent picture of structural and electronic properties of the nucleotide bases in the solid state could be developed by comparison of measurements and DFT/B3LYP calculations.

We have shown previously [Hosohata, K., Logan, J.K., Varga, E., Burkey, T.H., Vanderah, T.W., Porreca, F., Hruby, V.J., Roeske, W.R., Yamamura, H.I., 2000. The role of the G protein γ2 subunit in opioid antinociception in mice. Eur. J. Pharmacol. 392, R9-R11] that intracerebroventricular (i.c.v.) treatment of mice with a phosphorothioate oligodeoxynucleotide antisense to the γ2 subunit (Gγ2) of the heterotrimeric G proteins (antisense ODN) significantly attenuates antinociception by a δ-opioid receptor agonist. In the present study, we examined the involvement of Gγ2 in antinociception mediated by other (μ- or κ-opioid, cannabinoid, α2-adrenoreceptor) analgesic agents in a warm (55°C) water tail-flick test in mice. Interestingly, i.c.v. treatment with the antisense ODN attenuated antinociception by each analgesic agent. Missense phosphorothioate oligodeoxynucleotide treatment, on the other hand, had no effect on antinociception mediated by these agonists. The antinociceptive response recovered in 6 days after the last antisense ODN injection, indicating a lack of nonspecific tissue damage in the animals. These results suggest a pervasive role for the G protein γ2 subunits in supraspinal antinociception.

Guanine nucleotide exchange factors (GEFs) regulate and organize diverse cellular processes through their role in converting GTPases from the inactive GDP bound state to the active GTP bound state. An increasing number of GEFs undergo autoregulatory mechanisms through complex intramolecular interactions. Relief of autoinhibition involves specific phosphorylation or binding to lipid and/or effector proteins at sites distal from the catalytic domain, and is often coupled to membrane recruitment. In Cytohesin Arf GEFs, the catalytic Sec7 domain is autoinhibited by a linker region and C-terminal helix flanking a Pleckstrin Homology (PH) domain. Upon binding of the PH domain to low abundance phosphoinositides, the GTPase Arf6-GTP can both relieve autoinhibition and recruit Cytohesins to the plasma membrane. This thesis focuses on determining the molecular mechanism underlying both these functions. The structural mechanisms by which Arf6-GTP binding relieves autoinhibition were studied using biochemical and crystallographic studies. The crystal structure of the Grp1 PH domain in complex with Arf6 revealed that Arf6-GTP binding relieves autoinhibition through competitive sequestration of the inhibitory elements into grooves formed at the periphery of the interface. Importantly, the interaction orients all known membrane targeting components to a common surface. Detailed biochemical studies showed a common mode of binding among Cytohesin family members in which phosphoinositide head group binding primes the interaction with Arf6, and membrane recruitment of both stimulatory and substrate Arf enhances the effect. To assess changes in the Sec7 domain conformation upon activation, Size Exclusion Chromatography in line with Small Angle X-Ray Scattering (SEC-SAXS) was performed. The unique nature of this data led to the development of a novel data analysis and processing strategy. A graphically based, python-extensible software package was created for data normalization, buffer correction, Guinier Analysis, and constant background subtraction. As an unbiased substitute for traditional buffer subtraction, a method to reconstruct the protein scattering through singular value decomposition (SVD) and linear combination of the basis vectors was developed. These methods produced exceptional data quality and allowed versatility for application to other data collection techniques or systems, especially those lacking confident buffer matching or low signal. SEC-SAXS confirmed the overall structure of autoinhibited Grp1 in solution and showed only slight overall changes upon activation by deletion of the autoinhibitory Cterminal helix. Fusion of Arf6 with Grp1 produced a consistently elongated shape in the active state that was incompatible with the autoinhibited or theoretical active positions of the Sec7 domain. Monte Carlo and rigid body modeling using known structural domains revealed a requirement for Sec7-PH linker flexibility in addition to Sec7 domain mobility. These data support an integrated structural model whereby phosphoinositides and Arf-GTP support nucleotide exchange at membranes through allosteric activation, membrane recruitment, and large-scale rearrangement of the Sec7 domain. Overall, these findings offer insight into Cytohesin function that can be applied to assess relief of autoinhibition in the context of other GEFs and GTPases.

Indiana University-Purdue University Indianapolis (IUPUI) / Communication between bone cells is important for the maintenance of bone mass. Although osteocytes are deeply embedded within the mineralized matrix, they are essential for the regulation of osteoblast and osteoclast functions. However, the intracellular proteins that control the morphology and function of osteocytes, and their ability to communicate with other bone cells are still unknown. Kalirin is a novel multi-domain GTP exchange factor (GEF) protein that activates the RhoGTPases. Recently, we found that 14 week old female Kalirin knockout (Kal-KO) mice exhibit a 45% decrease in trabecular bone density and have significantly lower cortical area, perimeter, thickness and polar cross-sectional moment of inertia (-12.6%, -7.2%, -7.6% and -21.9%, respectively) than WT mice. Kalirin was found to be expressed in osteoclasts and osteoblasts but its expression and function in osteocytes is currently unclear. We examined the role of Kalirin on the morphology and function of osteocytes. Primary osteocytes were isolated by sequential collagenase digestions from long bones (femurs and tibias) of 10-week old WT and Kal-KO mice. Immunofluorescent staining revealed Kalirin was localized to the perinuclear region of primary osteocytes and MLO-Y4 cells, and was detected along the cytoplasmic processes of primary osteocytes. We also examined primary osteocytes isolated from the long bones of Kal-KO and WT mice for changes in the length and number of cytoplasmic processes. Kal-KO osteocytes were found to express significantly fewer cytoplasmic processes per cell (3.3±0.21) than WT osteocytes (4.7±0.3). In addition, the cytoplasmic processes of Kal-KO osteocytes were shorter (79.5±4.6 µm) than those observed for WT osteocytes (85.4±3.6 µm) (p <0.01). Quantitative PCR revealed the expression of mRNA for the three major Kalirin isoforms (Kal-7, Kal-9, Kal-12) in primary osteocytes and in MLO-Y4 cells. Moreover, the mRNA levels of osteoprotegerin (OPG) and SOST, which are important for controlling osteoclast differentiation and Wnt signaling leading to bone formation, respectively, were reduced in Kal-KO osteocytes. Next, the role of Kalirin in osteocyte morphology and function was further examined. Treatment of MLO-Y4 cells for 5 days with nerve growth factor, which is known to activate Kalirin in neurons, or over-expression of the Ser-Thr kinase domain of Kal-12, promoted cytoplasmic process elongation and upregulated phosphorylated ERK and RhoA levels. Together, these results suggest that Kalirin controls osteocyte morphology and function in part by regulating cytoskeletal remodeling and the activity of ERK and RhoA. Furthermore, Kalirin may control the bone remodeling cycle by regulating osteocyte signaling to osteoclasts and osteoblasts.

1 Nucleotides are organic molecules that have a wide range of functions in living organisms. They participate in cell signaling, serve as cofactors of enzymatic reactions, play a central role in cellular metabolism, and are the basic monomeric units of nucleic acid polymers. Nucleotides consist of three subunit molecules - nitrogen nucleobase, a five-carbon sugar (ribose or 2'-deoxyribose), and a phosphate group containing one to three phosphates. The subject of this master thesis is the study of various nucleotides and their self-assemblies in water by means of vibrational spectroscopy - Raman scattering and its chirally sensitive variant Raman optical activity (ROA). ROA has the potential to provide new information about the structural arrangement, dynamics, and interactions of nucleotides, as it supposes to be much more sensitive to vibrations of its sugar part containing three to four chiral carbons, compared to Raman scattering. We study spectral manifestations associated with chemical modifications (difference between ribo- and deoxyribonucleotides, the influence of different phosphate positions) and the change of physical conditions (various charge states according to the set pH, effect of concentration, influence of ions). A substantial amount of work is devoted to studying the self-association of...

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第21618号 / 医博第4424号 / 新制||医||1033(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 大森 孝一, 教授 松田 秀一, 教授 安達 泰治 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Lyme disease, the most common tick borne disease in United States, is caused by the bacterial pathogen Borrelia burgdorferi. In nature, B. burgdorferi exists in an enzootic infectious cycle between an arthropod vector and mammalian hosts. Identification and characterization of the genes essential for B. burgdorferi survival throughout its infectious cycle is an important step toward understanding the molecular mechanisms involved in B. burgdorferi pathogenesis. B. burgdorferi contains a small genome, which lacks the genes encoding for the enzymes required for de novo synthesis of amino acids, fatty acids and nucleic acid precursors. Therefore, the spirochete is dependent upon the host environment for the uptake of these essential nutrients. Purines are required for the synthesis of nucleotides for the biosynthesis of DNA and RNA. Due to the lack of de novo purine synthesis, the ability of B. burgdorferi to salvage purines from its host environments is essential to its survival. While the enzymes critical for the B. burgdorferi purine salvage pathway are known, the transporters involved in the uptake of purines from the host environments are not. The work in this thesis is focused on identification of the genes encoding purine permeases in B. burgdorferi and genetic and biochemical characterization of their functions in the infectious cycle of B. burgdorferi. Here, we demonstrate that homologous genes bbb22 and bbb23 present on circular plasmid 26 encode for purine permeases, which are important for transport of hypoxanthine, adenine and guanine. Furthermore, genes bbb22-23 together were essential for B. burgdorferi infection in mice. BBB22 and BBB23 share 78% amino acid identify. And although, individually both BBB22 and BBB23 were found to be capable of purine transport, BBB22 has higher affinity for hypoxanthine and adenine compared to BBB23. Moreover, the bbb22 gene alone was sufficient to restore mouse infectivity to spirochetes lacking both bbb22 and bbb23, whereas, bbb23 was not. Nonetheless, the spirochete loads in the tissues of mice infected with B. burgdorferi carrying bbb22 alone were significantly reduced compared to B. burgdorferi carrying both bbb22 and bbb23, demonstrating the importance of the two genes together for the spirochetes to achieve wild type levels of infection. In ticks, genes bbb22 and bbb23 were dispensable for spirochete survival but contributed to spirochete replication in fed larvae. The replication of spirochetes lacking bbb22-23 in larval ticks was restored to wild type levels by the reintroduction of the low affinity purine transporter encoded by bbb23 alone. Overall, we have identified a purine transport system in B. burgdorferi, which is essential for spirochete survival in the mammalian host and contributes to spirochete replication in the tick vector. As B. burgdorferi lacks typical virulence factors and toxins, these studies highlight the critical role of physiological functions in the virulence of this pathogen. Moreover, the BBB22-23 in vivo essential transport system may represent a novel therapeutic target to deliver antimicrobial drugs to treat Lyme disease.

No / The protein O6-alkylguanine-DNA alkyltransferase (Atase) is responsible for the repair of DNA lesions generated by several clinically important anti-cancer drugs; this is manifest as active resistance in those cancer cell lines proficient in Atase expression. Novel O6-substituted guanine analogues have been synthesized, bearing acidic, basic and hydrogen bonding functional groups. In contrast to existing O6-modified purine analogues, such as methyl or benzyl, the new compounds were found to resist repair by Atase even when tested at concentrations much higher than O6-benzylguanine, a well-established Atase substrate active both in vitro and in vivo. The inactivity of the new purines as covalent substrates for Atase indicates that agents to deliver these groups to DNA would represent a new class of DNA-modifying drug that circumvents Atase-mediated resistance.

Vias redox são importantes reguladores da homeostase e sinalização celular, mas o entendimento dos mecanismos desses processos é incompleto. Tiol-proteínas como a dissulfeto isomerase proteica (PDI) podem ser moduladores dessas vias. A PDI(PDIA1) é o protótipo da família das PDIs, cuja função canônica é o enovelamento redox de proteínas no retículo endoplasmático. Além disso, PDI exerce regulação de NADPH oxidases, as principais fontes de oxidantes celulares, e é necessária para ativação de RhoGTPases, organização do citoesqueleto e migração de células vasculares. No estudo de mecanismos pelos quais a PDI regula RhoGTPases, mostramos, em redes computacionais e em experimentos de co-imunoprecitação, associação entre PDIA1 e o regulador de RhoGTPases RhoGDIalfa. Além disso, identificamos forte proximidade entre os genes codificando estas proteínas. Neste estudo, caracterizamos o perfil e implicações desta sintenia gênica.A análise bioinformática pelos programs Ensembl, NCBI e UCSC evidencia um padrão de sintenia entre diferentes isoformas destas duas famílias: PDIA1 (P4HB), PDIA2 (PDIP) e PDIA8 (Erp27) são vizinhos, respectivamente, a RhoGDIbeta, RhoGDIy e RHOGDIalfa, com correspondentes regiões intergênicas de 7.1, 2.9 e 0.14 kb em distintos cromossomos em H. sapiens. O padrão dessa sintenia foi fortemente conservado emC. elegans, alguns peixes e uniformemente em anfíbios, répteis, aves e mamíferos. Leveduras expressam no mesmo cromossomo , porém em locais distantes (i.emacrossintenia) ortólogos da PDIA1 e RhoGDI?, mas não expressam outras PDIs e RhoGDIssintênicasnos eucariotos complexos. No entanto, sintenia entre PDI e RhoGDI foi também observada na planta A. thaliana, sem evidência de um ancestral comum. Os pares sintênicos associam-se a blocos vizinhos conservados, porém diversos para cada par, enquanto cada bloco contem um gene codificando um distinto regulador da PP1 (fosfatase proteica-1). Análise filogenética mostrou topologia semelhante entre as duas famílias.Análise dos dados do estudo ENCODE e predição pelo Softberry identificou sítios de ligação a fatores de transcrição comuns entre os distintos pares, cuja ontologia indicou principalmente desenvolvimento, processos metabólicos e resposta imune. O estudo de possíveis implicações funcionais dessa sintenia mostrou que manipulações da expressão proteica de PDIA1 não promovem mudança consistente na expressão proteica de RhoGDIalfa, tanto in vitro (silenciamento da PDI por siRNA e superexpressão por vetor lentiviral induzível) como in vivo (camundongo transgênico com superexpressão constitutiva da PDIA1). No entanto, as mudanças da expressãogênica de ambos os genes na camada íntima de artérias carótidas de camundongo durante remodelamento induzido por fluxo foram fortemente correlacionadas. Experimentos de coimunoprecipitação e co-localização à microscopia confocal sugeriram interação física entre PDIA1 e RhoGDIAalfa. Deste modo, estes dados mostram um intrigante padrão de conservação evolutiva da proximidade gênica entre PDIs e RhoGDIs, não usual em eucariotos. Genes sintênicos frequentemente codificam proteínas que tendem a interagir física e/ou funcionalmente. Com efeito, nosso dados sugerem co-regulação e interação física entre PDIA1 e RhoGDIAalfa, corroborando a convergência entre essas proteínas como possível mecanismo envolvido na regulação redox do citoesqueleto pela PDIA1 / Redox pathways are important regulators of homeostasis and cell signaling, but the understanding of the mechanisms of these processes is incomplete. Thiol proteins such as protein disulfide isomerase (PDI) can be modulators of these pathways. PDI (PDIA1) is the prototype of the family of PDIs whose canonical function is a redox protein folding in the endoplasmic reticulum. In addition, PDI exerts regulatory NADPH oxidase, the main sources of cellular oxidant, and is required for activation RhoGTPases, cytoskeletal organization and migration of vascular cells. In the study of mechanisms by which regulates PDI RhoGTPases, we showed in computer networks and co-imunoprecitation experiments association between PDIA1 and the regulator of RhoGTPases, RhoGDI?. In addition, we identified strong proximity of the genes encoding these proteins. In this study, we characterize the profile and implications of this synteny. .A bioinformatic analysis by programs Ensembl, NCBI and UCSC shows a pattern of synteny between different isoforms of these two families: PDIA1 (P4HB), PDIA2 (PDIP) and PDIA8 (Erp27) are neighbors , respectively RhoGDIalfa, and RhoGDIy RHOGDIbeta with corresponding intergenic regions 7.1, 2.9 and 0:14 kb in different chromosomes of H. sapiens. The pattern of this synteny was strongly maintained in C. elegans, some fish and evenly amphibians, reptiles, birds and mammals. Yeasts express on the same chromosome, but in distant places (i.e macrosintenia) orthologs of PDIA1 and RhoGDI?, but do not express other syntenics PDIs and RhoGDIs in complex eukaryotes. However, synteny between PDI and RhoGDI was also observed in the plant A. thaliana, no evidence of a common ancestor. The syntenic pairs are associated with the stored neighboring blocks, but different for each pair, while each block contains a gene encoding a regulator of distinct PP1 (protein phosphatase-1). Phylogenetic analysis showed similar topology between the two famílias. The identified binding sites common transcription factors between different pairs, which mainly indicated ontology development, metabolic and immune response. The study of possible functional implications of synteny showed that manipulations of PDIA1 protein expression do not promote consistent change in protein expression RhoGDI, both in vitro (silencing of PDI by siRNA and overexpression of inducible lentiviral vector) and in vivo (transgenic mice overexpressing constitutive of PDIA1). The study of possible functional implications of synteny showed that manipulations of PDIA1 protein expression do not promote consistent change in protein expression RhoGDIalfa, both in vitro (silencing of PDI by siRNA and overexpression of inducible lentiviral vector) and in vivo (transgenic mice overexpressing constitutive of PDIA1). However, changes of gene expression of both genes in the intima of mouse carotid arteries during remodeling induced by flow were strongly correlated. Immunoprecipitation experiments and co-location to confocal microscopy suggested physical interaction between PDIA1 and RhoGDIAalfa. Thus, these data show an intriguing pattern of evolutionary conservation of gene proximity between POIs and RhoGDIs not common in eukaryotes. sintênicos genes often encode proteins that tend to interact physically and / or functionally. Indeed, our data suggest co-regulation and physical interaction between PDIA1 and RhoGDIAalfa, supporting the convergence of these proteins as a possible mechanism involved in redox regulation of cytoskeleton by PDIA1