Over the past decade, solid-state nanopores have emerged as a versatile tool for the detection and characterization of single molecules, showing great promise in the field of personalized medicine as diagnostic and genotyping platforms. While solid-state nanopores offer increased durability and functionality over a wider range of experimental conditions compared to their biological counterparts, reliable fabrication of low-noise solid-state nanopores remains a challenge. In this thesis, a methodology for treating nanopores using high electric fields in an automated fashion by applying short (0.1-2 s) pulses of 6-10 V is presented which drastically improves the yield of nanopores that can be used for molecular recognition studies. In particular, this technique allows for sub-nanometer control over nanopore size under experimental conditions, facilitates complete wetting of nanopores, reduces noise by up to three orders of magnitude and rejuvenates used pores for further experimentation. This improvement in fabrication yield (over 90%) ultimately makes nanopore-based sensing more efficient, cost-effective and accessible. Tuning size using high electric fields facilitates nanopore fabrication and improves functionality for single-molecule experiments. Here, the use of nanopores for the detection of DNA-protein complexes is examined. As proof-of-concept, neutravidin bound to double-stranded DNA is used as a model complex. The creation of the DNA-neutravidin complex using polymerase chain reaction with biotinylated primers and subsequent purification and multiplex creation is discussed. Finally, an outlook for extending this scheme for the identification of proteins in a sample based on translocation signatures is presented which could be implemented in a portable lab-on-a-chip device for the rapid detection of disease biomarkers.

This thesis explores ways in which 12 learners of Japanese as a foreign language transform morphologically complex verbs taught as whole words. Written data, collected via a grammar test, and oral data, collected via think-aloud protocols, were used to explore verb-form transformation to the gerund (-te) form. These data were analysed to determine processes participants utilised during derivations. Resulting data indicate participants (1) are largely unaware of morphology, (2) cannot identify consonant-final verb-roots, (3) focus on verb-final characters during categorisation, (4) derive the gerund using prior knowledge – generally grammar rules, (5) link to vocabulary, morphological, phonological, and grammar knowledge during derivations, and (6) differ in performance as measured by the grammar test through utilising types of knowledge differently and in combinations. This implies current pedagogy may not heed learning preferences of learners. This thesis identifies types of knowledge involved during verb transformation tasks and suggests research into task-appropriate lessons.

Proteins play important roles in most cellular functions, such as, replication, transcription regulation, signal transduction, for catalyzing chemical reaction, etc. Technologies developed to identify proteins rely either on observing their own properties such as charge, size, mass to charge ratio or sequence composition; or on using affinity reagents that recognize specific protein targets. Immunoassays utilizing functionalized affinity reagents are powerful for targeted proteomics. Among them, DNA-assisted immunoassays in which affinity reagents are labeled with DNA molecules, offer some unique advantages. In this thesis, I will present works to improve current DNA-assisted immunoassays such as proximity ligation assays (PLA), as well as to take advantage of DNA reactions to adress other problems. In paper I, a new solid support (MBC-Ts) was functionalized with antibodies and used in the solid-phase PLA for detection of VEGF. The assay using MBC-Ts was compared among the commercially available solid supports in different matrices and it was shown to exhibit enhanced limit of detection in complex matrices. In paper II, a two-step protocol was described to prepare high-quality probes used in homogeneous and in situ PLA by purifying DNA-labeled affinity reagents from unconjugated affinity reagents and excess oligonucleotides. In paper III, PLA was applied on a capillary western blotting instrument so that both the sensitivity and specificity of the original assay were improved. In paper IV, a new method was introduced to profile protein components in individual protein complexes by DNA-barcoded antibodies. This method has been used to profile protein complexes such as surface proteins on individual secreted vesicles.

We consider the problem of local linearization of power series defined over complete valued fields. The complex field case has been studied since the end of the nineteenth century, and renders a delicate number theoretical problem of small divisors related to diophantine approximation. Since a work of Herman and Yoccoz in 1981, there has been an increasing interest in generalizations to other valued fields like p-adic fields and various function fields. We present some new results in this domain of research. In particular, for fields of prime characteristic, the problem leads to a combinatorial problem of seemingly great complexity, albeit of another nature than in the complex field case. In cases for which linearization is possible, we estimate the size of linearization discs and prove existence of periodic points on the boundary. We also prove that transitivity and ergodicity is preserved under the linearization. In particular, transitivity and ergodicity on a sphere inside a non-Archimedean linearization disc is possible only for fields of p-adic numbers.

ABSTRACT CHARACTERIZATION AND IDENTIFICATION OF BACTERIOCINS FROM TWO LACTOCOCCUS LACTIS SUBSP. LACTIS STRAINS Ak&ccedil / elik, Oya M.S., Department of Biotechnology In this study, bacteriocins from two L. lactis subsp. lactis isolates of Turkey origin designated OC1 and OC2, respectively, were characterized and identified. The activity spectra of the bacteriocins were determined by using different indicator bacteria including Listeria, Bacillus and Staphylococcus spp. Bacteriocins were tested for their sensitivity to different enzymes, heat treatments and pH values. Loss of bacteriocin activities after &amp / #61537 / -amylase treatment suggested that they form aggregates with carbohydrates. Molecular masses of partially purified bacteriocins were determined by SDS-polyacrylamide gel electrophoresis. PCR amplification was carried out with different primers for the detection of structural genes of lactococcal bacteriocins. As a result of these studies, the two bacteriocins were characterized as nisin and lacticin 481, respectively. Association of the bacteriocin production with plasmid DNA was examined by using acriflavine as a plasmid curing agent. Plasmid profiles of the wild type and its non-bacteriocin producing mutants were determined by using the alkali lysis method followed by agarose gel electrophoresis. The genetic nature of industrially important characteristics of Lactococcus lactis strains were investigated through gene transfer studies via conjugation. According to the results of plasmid curing and conjugal transfer trials, it was concluded that in Lactococcus lactis subsp. lactis OC1 strain a 39,7 kb plasmid is responsible for nisin production, lactose fermentation and proteolytic activity. In Lactococcus lactis subsp. lactis OC2 strain, on the other hand, a 16 kb plasmid appeared to be responsible for lacticin 481 production and lactose fermentation.

Detailed understanding of electron transfer reactions is important in many aspects of chemistry, biology and solar energy conversion. The main aim of this thesis is to provide further insight into electron transfer through highly conjugated bridge structures. Towards this end, three series of donor-acceptor dyads have been studied, all using an oligo(1,4-phenylene-ethynylene) moiety as the bridge. A common theme in these series is that they explore the effects of having either an ethynylene or phenylene as the attachment group between the bridge and the donor or acceptor. Photophysical characterization of these dyads was carried out by means of time resolved laser spectroscopy. The results show that having an ethynylene as attachment group results in higher rates for bridge mediated electron and energy transfer compared to similar systems, where a phenylene was used. It was also found that most of the investigated systems show a fast back electron transfer. A notable exception is a zinc(II) phthalocyanine- gold(III) porphyrin dyad, where very fast photoinduced electron transfer (kPET = 1.0×1012 s-1) was followed by relatively slow back electron transfer (kBET = 1.0×109 s-1). A complementary DFT investigation indicated that the charge shifted state involves a reduction of the gold ion, rather than the porphyrin ring. This results in lower electronic coupling between the reduced gold porphyrin and the bridge and thus slower back electron transfer. A series of zinc porphyrin platinum acetylide dyads was used to explore the effects on electronic coupling of different attachments points on the porphyrin ring. For the investigated system it was found that linking at the meso-position results in an eight-fold increase in electron transfer rate compared to the β-position. In addition, a series of mixed valence compounds was used to investigate electronic coupling mediated by cross-hyperconjugated or cross-π-conjugated bridges. The results indicate coupling elements of 100-400 cm-1, with the cross-π-conjugated bridge having the largest coupling. A complementary TD-DFT study indicates that both through bond and through space coupling can be active in these systems. The relative contribution of these two mechanisms to the electronic coupling is highly conformer dependent.

Horizontal gene transfer (HGT) is now indisputably the predominant driving force, if not the sole force, behind speciation and the evolution of novelty in bacteria. Of all mechanisms of horizontal gene transfer (HGT), conjugation, the contact-dependent plasmid-mediated transfer of DNA from a bacterial donor to a recipient cell, is probably the most universal. First observed between bacteria, conjugation also mediates gene transfer from bacteria to yeast, plant and even animal cells. The range of environments in which bacteria naturally exchange DNA has not been extensively explored. The interior of the animal cell represents a novel and potentially medically relevant environment for gene transfer. Since most antibiotics are ineffective inside mammalian cells, our cells may be a niche for the evolution of resistance and virulence in invasive pathogens. Invading bacteria accumulate in vacuoles inside human cells, protected from antibiotics. Herein, I demonstrate the ability of intracellular Salmonella typhimurium to meet and exchange plasmid DNA by conjugation within animal cells, revealing the animal intracellular milieu as a permissive environment for gene exchange. This finding evokes a model for the simultaneous dissemination of virulence and antibiotic resistance within a niche protected from both antibiotics and the immune system and extends the variety of environments in which bacteria are known to exchange genes. Unlike conjugation between bacteria, conjugation between bacteria and eukaryotic cells requires the import of transferred DNA into the nucleus before the transferred genes can be expressed and inherited. Plant-cell nuclear transformation by the conjugation system of the Agrobacterium tumefaciens Ti plasmid is believed to be mediated by nuclear localization sequences (NLSs) carried within the proteins that accompany the T-DNA during transfer. Whether NLSs are equally important for transmission of other conjugative plasmids to eukaryotic cells is unknown. Herein, I demonstrate nuclear localization potential within the putative conjugative escort protein TraI of the IncPa plasmid RP4. In contrast, MobA, the putative escort protein from the IncQ plasmid RSF1010, lacked any clear nuclear localization potential. It is therefore likely that specific nuclear localization signals within conjugative proteins are not essential for nuclear transformation per se, although they may assist in efficient plasmid transmission.

Thesis (Ph. D.)--Ohio State University, 2005. / Title from first page of PDF file. Includes bibliographical references.

A literature study was performed on a new type of cancer medicine: antibody drug conjugates, or ADCs. These consist of a monoclonal antibody, chemically linked to a cytotoxic agent. What makes them unique is their selective toxicity against cancer cells. The first approval of such a pharmaceutical was in the year 2000, with three or four available in different regions of the world today. In the range of 50 registered drugs in clinical development were found, by major and minor corporations. These have been presented in a table in the appendix according to their properties such as type of linker, cytotoxin, development status etc. Furthermore, a detailed study has been done of the chemistry of the linker conjugation as well as an attempt at studying the ADC market. Finally, the mentioned strengths of the drug were compared to its weaknesses, mainly instability and otherwise poor pharmacokinetics. The main conclusion is that these drugs are expected to play a major role in oncology in the future.

Submitted by Maria Medeiros (maria.dilva1@ufcg.edu.br) on 2018-09-25T15:07:35Z No. of bitstreams: 1 PATRÍCIA TATIANA ARAÚJO DOS SANTOS - TESE (PPGEP) 2011.pdf: 1900230 bytes, checksum: 89561c399b083520a1b499f7b2a0e152 (MD5) / Made available in DSpace on 2018-09-25T15:07:35Z (GMT). No. of bitstreams: 1 PATRÍCIA TATIANA ARAÚJO DOS SANTOS - TESE (PPGEP) 2011.pdf: 1900230 bytes, checksum: 89561c399b083520a1b499f7b2a0e152 (MD5) Previous issue date: 2011 / Capes / Nanopartículas de ZnAl1,9Eu0,1O4 foram modificadas a superfície usando agentes amino-silanos, e funcionalizadas a partir de monômeros do tipo metilmetacrilato, etilenodiamina e quitosana como moléculas biocompatíveis. As nanopartículas do ZnAl1,9Eu0,1O4 foram obtidas por reação de combustão, e silanizadas com os agentes silanos 3 – aminopropiltrimetoxisilano e 3 – aminopropiltrietoxisilano, com o intuito de tornar o caráter do espinélio hidrofóbico e em seguida funcionalizadas. As amostras resultantes foram caracterizadas por Difração de raios X, Espectroscopia de Infra Vermelho com Transformada de Fourrier, Microscopia Eletrônica de Transmissão, Espectroscopia de Excitação e Emissão e Rendimento quântico. Os resultados revelaram a formação da fase cúbica ZnAl1,9Eu0,1O4 e traços de EuAlO3. Para as amostras funcionalizadas com quitosana observa-se a formação da fase espinélio e da fase quitosana. Mediante os espectros de FTIR observou-se bandas abaixo de 1000 cm-1 atribuídas às vibrações dos sítios tetraédricos e octaédricos. As amostras funcionalizadas com quitosana apresentaram melhor complexação (interação óxido /polímero) e presença de estiramento NH atribuído ao grupo NH2 da quitosana. A banda de C=O observada para o espinélio ZnAl1,9Eu0,1O4 com quitosana evidenciou a funcionalização das nanopartículas. As nanopartículas ZnAl1,9Eu0,1O4 apresentaram morfologia constituída de aglomerados com formato de agulhas, constituídos de partículas com formato aproximadamente hexagonal, e tamanho menores que 100 nm. Após funcionalização as nanopartículas ZnAl1,9Eu0,1O4 apresentaram morfologia não homogênea, composta por um filme e partículas impregnadas de formato aproximadamente esférica, contendo fases amorfas e cristalinas, com partículas menores que 100 nm. As amostras silanizadas, funcionalizadas com os monômeros e a amostra funcionalizada com quitosana na proporção 5:1, apresentaram as linhas espectrais do íon Eu3+ correspondentes as transições 5D0 → 7F0, 5D0 → 7F1, 5D0 → 7F2, 5D0 → 7F3 e 5D0 → 7F4. O maior rendimento quântico foi observado para a amostra funcionalizada com a mistura dos monômeros utilizando o 3- aminopropiltrimetoxisilano. / Nanoparticles ZnAl1,9Eu0,1O4 were surface modified using amino-silane agents, and from functionalized monomers like methylmethacrylate, ethylenediamine and chitosan as biocompatible molecules. Nanoparticles of ZnAl1,9Eu0,1O4 were obtained by combustion reaction, and silanized with silane agents and 3- aminopropyltrimethoxysilane and 3 -aminopropyltriethoxysilane, in order to make the hydrophobic character of the spinel and then functionalized. The resulting samples were characterized by X-ray Diffraction, Infrared Spectroscopy Fourier Transform, Transmission Electron Microscopy, Excitation and Emission Spectroscopy and quantum yield. The results revealed the formation of cubic phase ZnAl1,9Eu0,1O4 and traces of EuAlO3. For samples functionalized with chitosan, we observed the formation of spinel phase and phase chitosan. Through the FTIR spectra observed bands below 1000 cm-1 assigned to the vibrations of tetrahedral and octahedral sites. The samples functionalized with chitosan showed better complexation (interaction oxide / polymer) and the presence of NH stretch assigned to NH2 group of chitosan. C = O band observed for the spinel ZnAl1,9Eu0,1O4 with chitosan showed the functionalization of nanoparticles. Nanoparticles ZnAl1,9Eu0,1O4 showed morphology composed of needle-shaped clusters consisting of particles with roughly hexagonal shape, and size smaller than 100 nm. Nanoparticles ZnAl1,9Eu0,1O4 after functionalization showed inhomogeneous morphology, consisting of a film and impregnated particles of roughly spherical shape containing amorphous and crystalline phases, with particles smaller than 100 nm. The silanized samples, functionalized with monomers functionalized with chitosan and the sample in 5:1 ratio showed the spectral lines corresponding Eu3+ ion transitions 5D0 → 7F0, 7F1 → 5D0, 5D0 → 7F2, 5D0 → 7F3 and 5D0 → 7F4. The higher quantum yield observed for the sample was functionalized with a mixture of monomers using the 3-aminopropyltrimethoxysilane.