Bright-field and fluorescence chip-scale microscopy for biological imaging

Optical microscopy is an essential tool in biological science and one of the gold standards for medical examinations. Miniaturization of microscopes can be a crucial stepping stone towards realizing compact, cost-effective and portable platforms for biomedical research and healthcare. This thesis reports on implementations of bright-field and fluorescence chip-scale microscopes for a variety of biological imaging applications. The term “chip-scale microscopy” refers to lensless imaging techniques realized in the form of mass-producible semiconductor devices, which transforms the fundamental design of optical microscopes.

Our strategy for chip-scale microscopy involves utilization of low-cost Complementary metal Oxide Semiconductor (CMOS) image sensors, computational image processing and micro-fabricated structural components. First, the sub-pixel resolving optofluidic microscope (SROFM), will be presented, which combines microfluidics and pixel super-resolution image reconstruction to perform high-throughput imaging of fluidic samples, such as blood cells. We discuss design parameters and construction of the device, as well as the resulting images and the resolution of the device, which was 0.66 µm at the highest acuity. The potential applications of SROFM for clinical diagnosis of malaria in the resource-limited settings is discussed.

Next, the implementations of ePetri, a self-imaging Petri dish platform with microscopy resolution, are presented. Here, we simply place the sample of interest on the surface of the image sensor and capture the direct shadow images under the illumination. By taking advantage of the inherent motion of the microorganisms, we achieve high resolution (~1 µm) imaging and long term culture of motile microorganisms over ultra large field-of-view (5.7 mm × 4.4 mm) in a specialized ePetri platform. We apply the pixel super-resolution reconstruction to a set of low-resolution shadow images of the microorganisms as they move across the sensing area of an image sensor chip and render an improved resolution image. We perform longitudinal study of Euglena gracilis cultured in an ePetri platform and image based analysis on the motion and morphology of the cells. The ePetri device for imaging non-motile cells are also demonstrated, by using the sweeping illumination of a light emitting diode (LED) matrix for pixel super-resolution reconstruction of sub-pixel shifted shadow images. Using this prototype device, we demonstrate the detection of waterborne parasites for the effective diagnosis of enteric parasite infection in resource-limited settings.

Then, we demonstrate the adaptation of a smartphone’s camera to function as a compact lensless microscope, which uses ambient illumination as its light source and does not require the incorporation of a dedicated light source. The method is also based on the image reconstruction with sweeping illumination technique, where the sequence of images are captured while the user is manually tilting the device around any ambient light source, such as the sun or a lamp. Image acquisition and reconstruction is performed on the device using a custom-built android application, constructing a stand-alone imaging device for field applications. We discuss the construction of the device using a commercial smartphone and demonstrate the imaging capabilities of our system.

Finally, we report on the implementation of fluorescence chip-scale microscope, based on a silo-filter structure fabricated on the pixel array of a CMOS image sensor. The extruded pixel design with metal walls between neighboring pixels successfully guides fluorescence emission through the thick absorptive filter to the photodiode layer of a pixel. Our silo-filter CMOS image sensor prototype achieves 13-µm resolution for fluorescence imaging over a wide field-of-view (4.8 mm × 4.4 mm). Here, we demonstrate bright-field and fluorescence longitudinal imaging of living cells in a compact, low-cost configuration.

Surface-enhanced resonance Raman scattering spectroscopy of single R6G molecules

Surface-enhanced resonance Raman scattering (SERRS) of Rhodamine 6G (R6G) adsorbed on colloidal silver clusters has been studied. Based on the great enhancement of the Raman signal and the quench of the fluorescence, the SERRS spectra of R6G were recorded for the samples of dye colloidal solution with different concentrations. Spectral inhomogeneity behaviours from single molecules in the dried sample films were observed with complementary evidences, such as spectral polarization, spectral diffusion, intensity fluctuation of vibrational lines and even "breathing" of the molecules. Sequential spectra observed from a liquid sample with an average of 0.3 dye molecules in the probed volume exhibited the expected Poisson distribution for actually measuring 0, 1 or 2 molecules. Difference between the SERRS spectra of R6G excited by linearly and circularly polarized light were experimentally measured.

Expression of eph-family receptor tyrosine kinases and ephrins in the tadpole of the frog Xenopus laevis, and possible roles in the development of retinotectal topography

Assembling a nervous system requires exquisite specificity in the construction of neuronal connectivity. One method by which such specificity is implemented is the presence of chemical cues within the tissues, differentiating one region from another, and the presence of receptors for those cues on the surface of neurons and their axons that are navigating within this cellular environment.

Connections from one part of the nervous system to another often take the form of a topographic mapping. One widely studied model system that involves such a mapping is the vertebrate retinotectal projection-the set of connections between the eye and the optic tectum of the midbrain, which is the primary visual center in non-mammals and is homologous to the superior colliculus in mammals. In this projection the two-dimensional surface of the retina is mapped smoothly onto the two-dimensional surface of the tectum, such that light from neighboring points in visual space excites neighboring cells in the brain. This mapping is implemented at least in part via differential chemical cues in different regions of the tectum.

The Eph family of receptor tyrosine kinases and their cell-surface ligands, the ephrins, have been implicated in a wide variety of processes, generally involving cellular movement in response to extracellular cues. In particular, they possess expression patterns-i.e., complementary gradients of receptor in retina and ligand in tectum- and in vitro and in vivo activities and phenotypes-i.e., repulsive guidance of axons and defective mapping in mutants, respectively-consistent with the long-sought retinotectal chemical mapping cues.

The tadpole of Xenopus laevis, the South African clawed frog, is advantageous for in vivo retinotectal studies because of its transparency and manipulability. However, neither the expression patterns nor the retinotectal roles of these proteins have been well characterized in this system. We report here comprehensive descriptions in swimming stage tadpoles of the messenger RNA expression patterns of eleven known Xenopus Eph and ephrin genes, including xephrin-A3, which is novel, and xEphB2, whose expression pattern has not previously been published in detail. We also report the results of in vivo protein injection perturbation studies on Xenopus retinotectal topography, which were negative, and of in vitro axonal guidance assays, which suggest a previously unrecognized attractive activity of ephrins at low concentrations on retinal ganglion cell axons. This raises the possibility that these axons find their correct targets in part by seeking out a preferred concentration of ligands appropriate to their individual receptor expression levels, rather than by being repelled to greater or lesser degrees by the ephrins but attracted by some as-yet-unknown cue(s).

Phospholipids and a protein-conducting channel regulate cotranslational protein targeting

Signal recognition particle (SRP) and signal recognition particle receptor (SR) are evolutionarily conserved GTPases that deliver secretory and membrane proteins to the protein-conducting channel Sec61 complex in the lipid bilayer of the endoplasmic reticulum in eukaryotes or the SecYEG complex in the inner membrane of bacteria. Unlike the canonical Ras-type GTPases, SRP and SR are activated via nucleotide-dependent heterodimerization. Upon formation of the SR•SRP targeting complex, SRP and SR undergo a series of discrete conformational changes that culminate in their reciprocal activation and hydrolysis of GTP. How the SR•SRP GTPase cycle is regulated and coupled to the delivery of the cargo protein to the protein-conducting channel at the target membrane is not well-understood. Here we examine the role of the lipid bilayer and SecYEG in regulation of the SRP-mediated protein targeting pathway and show that they serve as important biological cues that spatially control the targeting reaction.

In the first chapter, we show that anionic phospholipids of the inner membrane activate the bacterial SR, FtsY, and favor the late conformational states of the targeting complex conducive to efficient unloading of the cargo. The results of our studies suggest that the lipid bilayer acts as a spatial cue that weakens the interaction of the cargo protein with SRP and primes the complex for unloading its cargo onto SecYEG.

In the second chapter, we focus on the effect of SecYEG on the conformational states and activity of the targeting complex. While phospholipids prime the complex for unloading its cargo, they are insufficient to trigger hydrolysis of GTP and the release of the cargo from the complex. SecYEG modulates the conformation of the targeting complex and triggers the GTP hydrolysis from the complex, thus driving the targeting reaction to completion. The results of this study suggest that SecYEG is not a passive recipient of the cargo protein; rather, it actively releases the cargo from the targeting complex. Together, anionic phospholipids and SecYEG serve distinct yet complementary roles. They spatially control the targeting reaction in a sequential manner, ensuring efficient delivery and unloading of the cargo protein.

In the third chapter, we reconstitute the transfer reaction in vitro and visualize it in real time. We show that the ribosome-nascent chain complex is transferred to SecYEG via a stepwise mechanism with gradual dissolution and formation of the contacts with SRP and SecYEG, respectively, explaining how the cargo is kept tethered to the membrane during the transfer and how its loss to the cytosol is avoided.

In the fourth chapter, we examine interaction of SecYEG with secretory and membrane proteins and attempt to address the role of a novel insertase YidC in this interaction. We show that detergent-solubilized SecYEG is capable of discriminating between the nascent chains of various lengths and engages a signal sequence in a well-defined conformation in the absence of accessory factors. Further, YidC alters the conformation of the signal peptide bound to SecYEG. The results described in this chapter show that YidC affects the SecYEG-nascent chain interaction at early stages of translocation/insertion and suggest a YidC-facilitated mechanism for lateral exit of transmembrane domains from SecYEG into the lipid bilayer.

Self-assembly of brush polymers

The unique structure and properties of brush polymers have led to increased interest in them within the scientific community. This thesis describes studies on the self-assembly of these brush polymers.

Chapter 2 describes a study on the rapid self-assembly of brush block copolymers into nanostructures with photonic bandgaps spanning the entire visible spectrum, from ultraviolet to near infrared. Linear relationships are observed between the peak wavelengths of reflection and polymer molecular weights. This work enables "bottom-up" fabrication of photonic crystals with application-tailored bandgaps, through synthetic control of the polymer molecular weight and the method of self-assembly.

Chapter 3 details the analysis of the self-assembly of symmetrical brush block copolymers in bulk and thin films. Highly ordered lamellae with domain spacing ranging from 20 to 240 nm are obtained by varying molecular weight of the backbone. The relationship between degree of polymerization and the domain spacing is reported, and evidence is provided for how rapidly the brush block copolymers self-assemble and achieve thermodynamic equilibrium.

Chapter 4 describes investigations into where morphology transitions take place as the volume fraction of each block is varied in asymmetrical brush block copolymers. Imaging techniques are used to observe a transition from lamellar to a cylindrical morphology as the volume fraction of one of the blocks exceeds 70%. It is also shown that the asymmetric brush block copolymers can be kinetically trapped into undulating lamellar structures by drop casting the samples.

Chapter 5 explores the capability of macromolecules to interdigitate into densely grafted molecular brush copolymers using stereocomplex formation as a driving force. The stereocomplex formation between complementary linear polymers and brush copolymers is demonstrated, while the stereocomplex formation between complementary brush copolymers is shown to be restricted.

Interpretation of lunar topography : impact cratering and surface roughness

This work seeks to understand past and present surface conditions on the Moon using two different but complementary approaches: topographic analysis using high-resolution elevation data from recent spacecraft missions and forward modeling of the dominant agent of lunar surface modification, impact cratering. The first investigation focuses on global surface roughness of the Moon, using a variety of statistical parameters to explore slopes at different scales and their relation to competing geological processes. We find that highlands topography behaves as a nearly self-similar fractal system on scales of order 100 meters, and there is a distinct change in this behavior above and below approximately 1 km. Chapter 2 focuses this analysis on two localized regions: the lunar south pole, including Shackleton crater, and the large mare-filled basins on the nearside of the Moon. In particular, we find that differential slope, a statistical measure of roughness related to the curvature of a topographic profile, is extremely useful in distinguishing between geologic units. Chapter 3 introduces a numerical model that simulates a cratered terrain by emplacing features of characteristic shape geometrically, allowing for tracking of both the topography and surviving rim fragments over time. The power spectral density of cratered terrains is estimated numerically from model results and benchmarked against a 1-dimensional analytic model. The power spectral slope is observed to vary predictably with the size-frequency distribution of craters, as well as the crater shape. The final chapter employs the rim-tracking feature of the cratered terrain model to analyze the evolving size-frequency distribution of craters under different criteria for identifying "visible" craters from surviving rim fragments. A geometric bias exists that systematically over counts large or small craters, depending on the rim fraction required to count a given feature as either visible or erased.

Análise das alterações decorrentes do envelhecimento na mecânica respiratória pela técnica de oscilações forçadas

O crescimento do percentual de idosos na população ocorre mundialmente tornando necessário conhecer o impacto do processo de envelhecimento, neste contexto, do sistema respiratório. O desconhecimento do impacto do envelhecimento associado a diferentes graus de exposição a poluentes e a presença de comorbidade(s) dificulta a diagnose das pneumopatias acarretando aos idosos piora da qualidade de vida. São vantagens da Técnica de Oscilações Forçadas (FOT): alto potencial de aplicação em idosos, fácil realização, análise detalhada da mecânica respiratória, desempenho de papel complementar, bem como de alternativa na impossibilidade de realização dos exames tradicionais. Foi realizado um estudo experimental comparativo que objetivou investigar o impacto do envelhecimento no sistema respiratório pela FOT e pela espirometria entre grupos de diferentes faixas etárias, sendo a idade a variável independente e as variáveis dependentes, os parâmetros oscilométricos resistência em regime contínuo (R0) e das vias aéreas centrais (Rm), inclinação da resistência (S), frequência de ressonância (fr), reatância média (Xm), complacência dinâmica (Cdin,sr) e os parâmetros espirométricos (VEF1, CVF, VEF1/CVF e FEF/CVF). Foram realizados entrevista, exame clínico, radiografia torácica, avaliação da mecânica respiratória pela FOT e da função pulmonar pela espirometria. 255 indivíduos com idades entre 20 e 86 anos foram entrevistados. Destes, 175 foram excluídos, restando os 80 voluntários analisados, que foram divididos em 6 grupos de acordo com a faixa etária (A: 20 a 29 anos; B: 30 a 39 anos; C: 40 a 49 anos; D: 50 a 59 anos; E: 60 a 69 anos; F: 70 anos ou mais). Foram utilizados os testes de Shapiro-Wilkins, na avaliação da normalidade dos dados biométricos em cada grupo, Oneway ANOVA, na comparação entre os grupos, e Tukey HSD na comparação entre as classes subjacentes. A análise da associação entre duas variáveis foi realizada inicialmente pela regressão univariada entre os parâmetros oscilométricos, a idade e a altura. A regressão múltipla entre os parâmetros oscilométricos, idade e altura foi realizada em conjunto. Foi realizada a análise de confundimento ou modificação de efeito sobre o parâmetro altura na relação entre a idade e os parâmetros oscilométricos. A correção pelo fator altura foi realizada quando sua análise apresentava fator de confundimento. Quanto aos parâmetros resistivos, não foram observadas alterações em R0 e Rm com o envelhecimento enquanto que o declínio observado em S é discreto e não-significativo. Em relação aos parâmetros reativos, verificouse que Cdin,sr e Xm diminuem enquanto que fr aumenta com o processo de envelhecimento. Todas estas alterações são significativas. Todavia, a diminuição da Cdin,sr não apresenta relação com a idade e sim com a altura, que constituiu modificação do efeito. Nos demais parâmetros oscilométricos, a altura constituiu fator de confundimento. Quanto à espirometria, observou-se declínio significativo do VEF1, do VEF1/CVF e da CVF. O índice FEF/CVF apresentou declínio nãosignificativo. Concluindo, a resistência do sistema respiratório e a complacência dinâmica não se modificam enquanto a homogeneidade do sistema respiratório diminui com o processo de envelhecimento.

La cerámica de la Segunda Edad del Hierro en el País Vasco: Estudio tecnológico, funcional y social

670 p. Capítulos de introducción, metodología, discusión y conclusiones en castellano e inglés.

Comunicação empática de pais e filhos em situações específicas: bases evolutivas e variáveis associadas

O presente estudo pretende suprir parcialmente algumas lacunas nos estudos sobre o desenvolvimento da empatia. A primeira lacuna se refere a incluir os pais, além das mães, na pesquisa, uma vez que aqueles podem ter um papel ainda pouco explorado no desenvolvimento. A segunda se refere a abordar a empatia tanto por uma visão ontogenética como filogenética, pois ambas se complementam na compreensão das nossas capacidades e habilidades, essencialmente muito semelhantes às de nossos ancestrais no ambiente de nossa evolução. Presume-se que no ambiente de adaptação evolutiva (AAE) da nossa espécie as habilidades sociais foram importantes na resolução de conflitos e na manutenção da coesão intragrupais. A empatia, habilidade social foco desta dissertação, é definida como a capacidade de compreender e expressar compreensão sobre os pensamentos e sentimentos de outra pessoa e é uma característica da espécie que sofre desenvolvimento ontogenético, em culturas e nichos específicos de desenvolvimento. Esta dissertação tem como objetivo geral abordar a comunicação empática entre pais e mães e seus filhos pelo olhar da Psicologia Evolucionista do Desenvolvimento. Participaram deste estudo 10 crianças, entre oito e 11 anos e seus respectivos pais e mães, sendo cinco meninos e cinco meninas, todos da cidade do Rio de Janeiro. A empatia dos pais e dos filhos foi avaliada por meio de instrumentos (Inventário de Empatia e Entrevista sobre Cenas de Curta Duração), assim como as crenças parentais sobre a importância e o desenvolvimento das habilidades empáticas, por instrumento desenvolvido para este estudo (Crenças Parentais sobre Habilidades). As famílias participaram ainda de uma sessão de filmagem em três situações específicas de 10 minutos cada: jogo com peças de montar para construção conjunta de escolha livre e a representação de papéis em duas cenas do cotidiano familiar (conversar sobre um boletim da criança com notas vermelhas e sobre um problema que a criança trouxe para os pais). Os resultados foram apresentados e discutidos para cada uma das famílias. Pode-se observar que existem relações entre os escores de empatia dos pais e da criança nos instrumentos utilizados e que, em geral, os pais valorizam habilidades empáticas e atribuem seu desenvolvimento, principalmente ao exemplo e à aprendizagem e não a maturação e características de temperamento da criança. No entanto, nas tarefas propostas, dificuldades de comunicação empática são observadas, levando a que se hipotetize que não é direta a relação entre crenças, habilidades individuais e práticas em família. Reconhecem-se as limitações do presente estudo, de caráter exploratório. Novas investigações com observação da comunicação pais-filhos em situações cotidianas do ambiente natural podem contribuir para o avanço do conhecimento nessa área.

Measurement of the neutron beta decay asymmetry using ultracold neutrons

The free neutron beta decay correlation A₀ between neutron polarization and electron emission direction provides the strongest constraint on the ratio λ = g_A/g_V of the Axial-vector to Vector coupling constants in Weak decay. In conjunction with the CKM Matrix element V_ud and the neutron lifetime τ_n, λ provides a test of Standard Model assumptions for the Weak interaction. Leading high-precision measurements of A₀ and τ_n in the 1995-2005 time period showed discrepancies with prior measurements and Standard Model predictions for the relationship between λ, τ_n, and V_ud. The UCNA experiment was developed to measure A₀ from decay of polarized ultracold neutrons (UCN), providing a complementary determination of λ with different systematic uncertainties from prior cold neutron beam experiments. This dissertation describes analysis of the dataset collected by UCNA in 2010, with emphasis on detector response calibrations and systematics. The UCNA measurement is placed in the context of the most recent τ_n results and cold neutron A₀ experiments.

A comunidade disciplinar de ensino de Biologia na produção de políticas de currículo

Esta dissertação se insere no estudo de políticas de currículo em múltiplos contextos educacionais, com base na abordagem teórico-metodológica do ciclo de políticas de Stephen Ball, na forma como interpretado para o campo do Currículo por Lopes e Macedo. Essa análise é subsidiada também pela concepção de comunidade disciplinar de Ivor Goodson e pela teoria do discurso de Ernesto Laclau. O objeto desta pesquisa é a investigação da produção de políticas curriculares pela comunidade disciplinar de ensino de Biologia. Para tanto, são analisados os principais documentos curriculares relacionados à Biologia no nível médio produzidos em âmbito federal os Parâmetros Curriculares Nacionais para o Ensino Médio (PCNEm), as Orientações Complementares aos Parâmetros Curriculares Nacionais para o Ensino Médio (PCN+) e as Orientações Curriculares Nacionais para o Ensino Médio (OCNEM). Igualmente buscando entender o processo de produção da política, foram realizadas entrevistas com professores e pesquisadores reconhecidos nessa comunidade disciplinar que participaram da elaboração dos documentos curriculares supramencionados. Nessa análise, são identificadas demandas em disputa no âmbito dessa comunidade disciplinar assim como distanciamentos e aproximações entre esses documentos. Concluímos que mesmo em governos diferentes, representantes das comunidades disciplinares podem se manter atuantes no contexto de produção de textos das políticas e produzir sentidos e significados semelhantes nas políticas.

The avifauna of Laguna Llancanelo (Mendoza, Argentina), a South American wetland of international importance

Laguna Llancanelo is a large (40,000 ha), very shallow (less than 3 m deep), inland saline waterbody, located in southern Mendoza, Argentina. A survey of the avifauna was undertaken during 1983 to 1985; field trips were made mostly to the northeastern and central-western sectors of the lagoon, in the months of April, May, September, October and December. Complementary studies were made by an aerial survey and assessments of terrestrial birds in the surroundings of the lagoon. A total of 64 species in 22 families of birds usually associated with aquatic environments were recorded. The best-represented families of aquatic birds in terms of numbers of species were: Anatidae (13 swans, geese, ducks), Scolopacidae (7 sandpipers and other small waders), Ardeidae (6 herons, bitterns, egrets, Podicipedidae (4 grebes), Rallidae (4 rails, coots) and Charadriidae (4 plovers, lapwings). The most abundant nesting birds on the lagoon were: Black-necked swan Cygnus melancoryphus (824), silvery grebe Podiceps occipitalis (202) and black-crowned night heron Nycticorax nycticorax (100).

Polilaktida oinarri duten 3D zelula-euskarri (scaffold) polimeriko biodegradagarrien diseinu, fabrikazio eta propietateak

[EU]Hiru dimentsioko inprimaketa etorkizun handiko teknologia bezala azaltzen zaigu gaur egun. Esate baterako, biomedikuntza arloan aukera berritzaileak ekar ditzake, baina baita hezkuntza, heziketa eta ikerketa munduetan ere. Teknologia berri honen abantailarik nagusiena prototipatze azkarrean datza, eta honi esker, mikro- eta makro- egitura definituak dituzten objektuak diseinatu eta fabrikatu daitezke modu lehiakorrean. Lan honen helburua 3D inprimagailu baten bitartez inprimaturiko polimero biobateragarri eta biodegradagarrietan oinarrituriko ereduen garapen eta fabrikazioan datza. Hala ere, lehenik eta behin, lehengaiak bai fisikoki eta bai termikoki karakterizatu behar dira, ondoren, 3D inprimagailuaren parametroen arteko erlazioa ezarri, eta azkenik, produktu finalaren egitura propietateak eta kalitatea aztertu. Aipaturiko lana aurrera eramateko erabili den materiala polilaktida (PLA) izan da, zeinen erabilera oso zabaldua dagoen medikuntza arloan inplante (torloju, iltze, plaka eta abar) moduan eta ehun ingeniaritzaren munduan.

Structure-, stereochemistry-, and metal-regulated DNA binding/cleaving molecules

In the cell, the binding of proteins to specific sequences of double helical DNA is essential for controlling the processes of protein synthesis (at the level of DNA transcription) and cell proliferation (at the level of DNA replication). In the laboratory, the sequence-specific DNA binding/cleaving properties of restriction endonuclease enzymes (secreted by microorganisms to protect them from foreign DNA molecules) have helped to fuel a revolution in molecular biology. The strength and specificity of a protein:DNA interaction depend upon structural features inherent to the protein and DNA sequences, but it is now appreciated that these features (and therefore protein:DNA complexation) may be altered (regulated) by other protein:DNA complexes, or by environmental factors such as temperature or the presence of specific organic molecules or inorganic ions. It is also now appreciated that molecules much smaller than proteins (including antibiotics of molecular weight less than 2000 and oligonucleotides) can bind to double-helical DNA in sequence-specific fashion. Elucidation of structural motifs and microscopic interactions responsible for the specific molecular recognition of DNA leads to greater understanding of natural processes and provides a basis for the design of novel sequence-specific DNA binding molecules. This thesis describes the synthesis and DNA binding/cleaving characteristics of molecules designed to probe structural, stereochemical, and environmental factors that regulate sequence-specific DNA recognition.

Chapter One introduces the DNA minor groove binding antibiotics Netropsin and Distamycin A, which are di- and tri(N-methylpyrrolecarboxamide) peptides, respectively. The method of DNA affinity cleaving, which has been employed to determine DNA binding properties of designed synthetic molecules is described. The design and synthesis of a series of Netropsin dimers linked in tail-to-tail fashion (by oxalic, malonic, succinic, or fumaric acid), or in head-to-tail fashion (by glycine, β-alanine, and γ-aminobutanoic acid (Gaba)) are presented. These Bis(Netropsin)s were appended with the iron-chelating functionality EDTA in order to make use of the technique of DNA affinity cleaving. Bis(Netropsin)-EDTA compounds are analogs of penta(N-methylpyrrolecarboxamide)-EDTA (P5E), which may be considered a head-to-tail Netropsin dimer linked by Nmethylpyrrolecarboxamide. Low- and high-resolution analysis of pBR322 DNA affinity cleaving by the iron complexes of these molecules indicated that small changes in the length and nature of the linker had significant effects on DNA binding/cleaving efficiency (a measure of DNA binding affinity). DNA binding/cleaving efficiency was found to decrease with changes in the linker in the order β-alanine > succinamide > fumaramide > N-methylpyrrolecarboxamide > malonamide >glycine, γ-aminobutanamide > oxalamide. In general, the Bis(Netropsin)-EDTA:Fe compounds retained the specificity for seven contiguous A:T base pairs characteristic of P5E:Fe binding. However, Bis(Netropsin)Oxalamide- EDTA:Fe exhibited decreased specificity for A:T base pairs, and Bis(Netropsin)-Gaba-EDT A:Fe exhibited some DNA binding sites of less than seven base pairs. Bis(Netropsin)s linked with diacids have C₂-symmmetrical DNA binding subunits and exhibited little DNA binding orientation preference. Bis(Netropsin)s linked with amino acids lack C₂-symmetrical DNA binding subunits and exhibited higher orientation preferences. A model for the high DNA binding orientation preferences observed with head-to-tail DNA minor groove binding molecules is presented.

Chapter Two describes the design, synthesis, and DNA binding properties of a series of chiral molecules: Bis(Netropsin)-EDTA compounds with linkers derived from (R,R)-, (S,S)-, and (RS,SR)-tartaric acids, (R,R)-, (S,S)-, and (RS,SR)-tartaric acid acetonides, (R)- and (S)-malic acids, N ,N-dimethylaminoaspartic acid, and (R)- and (S)-alanine, as well as three constitutional isomers in which an N-methylpyrrolecarboxamide (P1) subunit and a tri(N-methylpyrrolecarboxamide)-EDTA (P3-EDTA) subunit were linked by succinic acid, (R ,R)-, and (S ,S)-tartaric acids. DNA binding/cleaving efficiencies among this series of molecules and the Bis(Netropsin)s described in Chapter One were found to decrease with changes in the linker in the order β-alanine > succinamide > P1-succinamide-P3 > fumaramide > (S)-malicamide > N-methylpyrrolecarboxamide > (R)-malicamide > malonamide > N ,N-dimethylaminoaspanamide > glycine = Gaba = (S,S)-tartaramide = P1-(S,S)-tanaramide-P3 > oxalamide > (RS,SR)-tartaramide = P1- (R,R)-tanaramide-P3 > (R,R)-tartaramide (no sequence-specific DNA binding was detected for Bis(Netropsin)s linked by (R)- or (S)-alanine or by tartaric acid acetonides). The chiral molecules retained DNA binding specificity for seven contiguous A:T base pairs. From the DNA affinity cleaving data it could be determined that: 1) Addition of one or two substituents to the linker of Bis(Netropsin)-Succinamide resulted in stepwise decreases in DNA binding affinity; 2) molecules with single hydroxyl substituents bound DNA more strongly than molecules with single dimethylamino substituents; 3) hydroxyl-substituted molecules of (S) configuration bound more strongly to DNA than molecules of (R) configuration. This stereochemical regulation of DNA binding is proposed to arise from the inherent right-handed twist of (S)-enantiomeric Bis(Netropsin)s versus the inherent lefthanded twist of (R)-enantiomeric Bis(Netropsin)s, which makes the (S)-enantiomers more complementary to the right-handed twist of B form DNA.

Chapter Three describes the design and synthesis of molecules for the study of metalloregulated DNA binding phenomena. Among a series of Bis(Netropsin)-EDTA compounds linked by homologous tethers bearing four, five, or six oxygen atoms, the Bis(Netropsin) linked by a pentaether tether exhibited strongly enhanced DNA binding/cleaving in the presence of strontium or barium cations. The observed metallospecificity was consistent with the known affinities of metal cations for the cyclic hexaether 18-crown-6 in water. High-resolution DNA affinity cleaving analysis indicated that DNA binding by this molecule in the presence of strontium or barium was not only stronger but of different sequence-specificity than the (weak) binding observed in the absence of metal cations. The metalloregulated binding sites were consistent with A:T binding by the Netropsin subunits and G:C binding by a strontium or barium:pentaether complex. A model for the observed positive metalloregulation and novel sequence-specificity is presented. The effects of 44 different cations on DNA affinity cleaving by P5E:Fe were examined. A series of Bis(Netropsin)-EDTA compounds linked by tethers bearing two, three, four, or five amino groups was also synthesized. These molecules exhibited strong and specific binding to A:T rich regions of DNA. It was found that the iron complexes of these molecules bound and cleaved DNA most efficiently at pH 6.0-6.5, while P5E:Fe bound and cleaved most efficiently at pH 7.5-8.0. Incubating the Bis(Netropsin) Polyamine-EDTA:Fe molecules with K₂PdCl₄ abolished their DNA binding/cleaving activity. It is proposed that the observed negative metalloregulation arises from kinetically inert Bis(Netropsin) Polyamine:Pd(II) complexes or aggregates, which are sterically unsuitable for DNA complexation. Finally, attempts to produce a synthetic metalloregulated DNA binding protein are described. For this study, five derivatives of a synthetic 52 amino acid residue DNA binding/cleaving protein were produced. The synthetic mutant proteins carried a novel pentaether ionophoric amino acid residue at different positions within the primary sequence. The proteins did not exhibit significant DNA binding/cleaving activity, but they served to illustrate the potential for introducing novel amino acid residues within DNA binding protein sequences, and for the development of the tricyclohexyl ester of EDTA as a superior reagent for the introduction of EDT A into synthetic proteins.

Chapter Four describes the discovery and characterization of a new DNA binding/cleaving agent, [SalenMn(III)]OAc. This metal complex produces single- and double-strand cleavage of DNA, with specificity for A:T rich regions, in the presence of oxygen atom donors such as iodosyl benzene, hydrogen peroxide, or peracids. Maximal cleavage by [SalenMn(III)]OAc was produced at pH 6-7. A comparison of DNA singleand double-strand cleavage by [SalenMn(III)]⁺ and other small molecules (Methidiumpropyl-EDTA:Fe, Distamycin-EDTA:Fe, Neocarzinostatin, Bleomycin:Fe) is presented. It was found that DNA cleavage by [SalenMn(III)]⁺ did not require the presence of dioxygen, and that base treatment of DNA subsequent to cleavage by [SalenMn(III)]⁺ afforded greater cleavage and alterations in the cleavage patterns. Analysis of DNA products formed upon DNA cleavage by [SalenMn(III)] indicated that cleavage was due to oxidation of the sugar-phosphate backbone of DNA. Several mechanisms consistent with the observed products and reaction requirements are discussed.

Chapter Five describes progress on some additional studies. In one study, the DNA binding/cleaving specificities of Distamycin-EDTA derivatives bearing pyrrole N-isopropyl substituents were found to be the same as those of derivatives bearing pyrrole N-methyl substituents. In a second study, the design of and synthetic progress towards a series of nucleopeptide activators of transcription are presented. Five synthetic plasmids designed to test for activation of in vitro run-off transcription by DNA triple helix-forming oligonucleotides or nucleopeptides are described.

Chapter Six contains the experimental documentation of the thesis work.

Panpinan egindako bihotz-biriketako berpizte maniobran bularra bere onera bueltatzearen analisia

[EU]Dokumentu honek "Panpinan Egindako Bihotz-Biriketako Berpizte Maniobran Bularra Bere Onera Bueltatzearen Analisia" izena duen Gradu Amaierako Lanaren memoria eta eranskinak biltzen ditu. Bertan, lan horren bitartez lorturiko helburuak, horiek nola lortu diren eta burutu ahal izateko egin beharreko pausuak aurkezten dira. Bihotz-biriketako berpizterako berrelikadura gailuek berpizte maniobren kalitateari buruzko informazioa momentuan ematen dute. Proiektua berrelikadurarako laguntza gailuen parametroen kalitatea hobetzeko ikerlan bat egitera bideratuta dago, zehazki bularra bere onera bueltatzen den jakiteko metodoen azterketan sakontzen duelarik interesa duelarik. Alde batetik, benetako sakoneraren kalkulu zehatzari buruzko ikerketa bat egiten da, horretarako aukera ezberdinak aztertuz, metodo desberdinen analisia eginez. Bestetik, berrelikaduran zehar bularra bere onera bueltatzen den ohartarazteko (esate baterako, alarma sistema baten bitartez) parametroan egiten da ikerketa, horretarako indar sentsore gehigarri bat erabiliz.