Computational design of self-assembling proteins and protein-DNA nanowires

Computational protein design (CPD) is a burgeoning field that uses a physical-chemical or knowledge-based scoring function to create protein variants with new or improved properties. This exciting approach has recently been used to generate proteins with entirely new functions, ones that are not observed in naturally occurring proteins. For example, several enzymes were designed to catalyze reactions that are not in the repertoire of any known natural enzyme. In these designs, novel catalytic activity was built de novo (from scratch) into a previously inert protein scaffold. In addition to de novo enzyme design, the computational design of protein-protein interactions can also be used to create novel functionality, such as neutralization of influenza. Our goal here was to design a protein that can self-assemble with DNA into nanowires. We used computational tools to homodimerize a transcription factor that binds a specific sequence of double-stranded DNA. We arranged the protein-protein and protein-DNA binding sites so that the self-assembly could occur in a linear fashion to generate nanowires. Upon mixing our designed protein homodimer with the double-stranded DNA, the molecules immediately self-assembled into nanowires. This nanowire topology was confirmed using atomic force microscopy. Co-crystal structure showed that the nanowire is assembled via the desired interactions. To the best of our knowledge, this is the first example of a protein-DNA self-assembly that does not rely on covalent interactions. We anticipate that this new material will stimulate further interest in the development of advanced biomaterials.

Effects produced in GaAs by MeV ion bombardment

Presented in the first part of this thesis is work performed on the ionizing energy beam induced adhesion enhancement of thin (~ 500 Angstrom) Au films on GaAs substrates. The ionizing beam, employed in the present thesis, is the MeV ions (i.e., ¹⁶O, ¹⁹F, and ³⁵Cl), with energies between 1 and 20 MeV. Using the "Scratch" test for adhesion measurement, and ESCA for chemical analysis of the film-substrate interface, the native oxide layer at the interface is shown to play an important role in the adhesion enhancement by the ionizing radiation. A model is discussed which explains the experimental data on the the dependence of adhesion enhancement on the energy which was deposited into electronic processes at the interface. The ESCA data indicate that the chemical bonds (or compounds), which are responsible for the increase in the thin film adherence, are hydroxides rather than oxides.

In the second part of the thesis we present a research performed on the radiation damage in GaAs crystals produced by MeV ions. Lattice parameter dilatation in the surface layers of the GaAs crystals becomes saturated after a high dose bombardment at room temperature. The strain produced by nuclear collisions is shown to relax partially due to electronic excitation (with a functional dependence on the nuclear and electronic stopping power of bombarding ions). Data on the GaAs and GaP crystals suggest that low temperature recovery stage defects produce major crystal distortion. The x-ray rocking curve technique with a dynamical diffraction theory analysis provides the depth distribution of the strain and damage in the MeV ion bombarded crystals.

Estudio de los sueros ricos en factores de crecimiento y de su efecto sobre células de epitelio corneal

Objetivos: Estudiar cómo afecta a la concentración de determinados factores de crecimiento presentes en los sueros la filtración (utilizado como método de esterilización) y el tratamiento por calor (utilizado para la inactivación del complemento). Además de estudiar el efecto de un bioadhesivo (ácido hialurónico, HaNa), aplicado solo o conjuntamente con el suero rico en factores de crecimiento (s-PRGF), sobre la capacidad de las células de epitelio corneal (HCE) para proliferar y migrar. Materiales y métodos: Se midió mediante kits ELISA comerciales la concentración en las diferentes condiciones de filtración y calentamiento de las siguientes biomoléculas EGF (Epidermal Growth Factor), VEGF (Vascular Endothelial Growth Factor), HGF (Hepatocyte Growth Factor), PDGF (Platelet-derived Growth Factor) y la Fibronectina. Teniendo en cuenta el papel de la proliferación y migración celular en los procesos de cicatrización se han realizado dos ensayos diferentes in vitro: un ensayo MTT para estudiar la viabilidad y la proliferación celular y el método de la herida (Scratch wound-healing assay) para determinar la capacidad migratoria de células bajo ciertos tratamientos: BSA (Bovine Serum Albumin) al 1% como control, FBS (Fetal Bovine Serum) al 10%, s-PRGF al 45%, s-PRGF al 45% con HaNa 0,1% y HaNa al 0,1% Resultados: En el caso de la filtración, se observa una mayor pérdida de factores utilizando un filtro con una membrana de PVDF (Durapore®) para todos los factores estudiados. El calentamiento produce una reducción de la concentración superior al 50% en el caso del HGF y EGF, manteniéndose constante en el caso del VEGF.La mezcla de diferentes muestras con el complemento inactivado para formar un pool no presenta cambios en la concentración al compararlo con la media de las muestras utilizadas. Por tanto, la utilización de un pool del hemoderivado no supone perdida de factores de crecimiento, haciendo de ello un procedimiento perfectamente aceptable para los ensayos celulares. El tratamiento con s-PRGF y el combinado con el bioadhesivo promueven la proliferación y migración de las células de epitelio corneal humano(HCE) in vitro de manera similar, no encontrándose diferencias estadísticamente significativas entre ambos. Conclusiones: La adicción del bioadhesivo no produce efecto tóxico en las células, sin embargo, no se han encontrado efectos beneficiosos en cuanto a proliferación y migración se refiere. A este respecto, creemos que hay que dar un paso más haciendo comprobaciones in vivo, ya que, a diferencia de la experimentación in vitro los componentes de los hemoderivados no están indefinidamente en contacto con las células sino por un espacio de tiempo muy reducido. Por ello, la concentración de factores de crecimiento en la aplicación in vivo es especialmente importante, y no sería conveniente reducirla mediante procedimientos físicos como la filtración o el calentamiento.

Coprocessador para operações quânticas.

A demanda crescente por poder computacional estimulou a pesquisa e desenvolvimento de processadores digitais cada vez mais densos em termos de transistores e com clock mais rápido, porém não podendo desconsiderar aspectos limitantes como consumo, dissipação de calor, complexidade fabril e valor comercial. Em outra linha de tratamento da informação, está a computação quântica, que tem como repositório elementar de armazenamento a versão quântica do bit, o q-bit ou quantum bit, guardando a superposição de dois estados, diferentemente do bit clássico, o qual registra apenas um dos estados. Simuladores quânticos, executáveis em computadores convencionais, possibilitam a execução de algoritmos quânticos mas, devido ao fato de serem produtos de software, estão sujeitos à redução de desempenho em razão do modelo computacional e limitações de memória. Esta Dissertação trata de uma versão implementável em hardware de um coprocessador para simulação de operações quânticas, utilizando uma arquitetura dedicada à aplicação, com possibilidade de explorar o paralelismo por replicação de componentes e pipeline. A arquitetura inclui uma memória de estado quântico, na qual são armazenados os estados individuais e grupais dos q-bits; uma memória de rascunho, onde serão armazenados os operadores quânticos para dois ou mais q-bits construídos em tempo de execução; uma unidade de cálculo, responsável pela execução de produtos de números complexos, base dos produtos tensoriais e matriciais necessários à execução das operações quânticas; uma unidade de medição, necessária à determinação do estado quântico da máquina; e, uma unidade de controle, que permite controlar a operação correta dos componente da via de dados, utilizando um microprograma e alguns outros componentes auxiliares.

Social structure and underwater behavior of harbor seals in southern Monterey Bay, California

To understand harbor seal social and mating strategies, I examined site fidelity, seasonal abundance and distribution, herd integrity, and underwater behavior of individual harbor seals in southern Monterey Bay. Individual harbor seals (n = 444) were identified by natural markings and represented greater than 80% of an estimated 520 seals within this community. Year to year fidelity of individual harbor seals to southern Monterey Bay coastline was 84% (n = 388), and long-term associations (>2 yrs) among individuals were common (>40%). Consistent with these long-term associations, harbor seals were highly social underwater throughout the year. Underwater social behavior included three primary types: (1) visual and acoustic displays, such as vocalizing, surface splashing, and bubble-blowing; (2) playful or agonistic social behavior such as rolling, mounting, attending, and biting; and (3) signal gestures such as head-thrusting, fore-flipper scratch~ng, and growling. Frequency of these types of behavior was related to seal age, gender, season, and resource availability. Underwater behavior had a variety of functions, including promotion of learning and social development, reduction of aggression and preservation of social bonds by maintaining social hierarchy, and facilitation of mate selection during breeding season. Social behavior among adult males was significantly correlated with vocalization characteristics (r = 0.99, X2 = 37.7, p = 0.00087), indicating that seals may assess their competition based on underwater vocalization displays and adopt individual strategies for attracting females during breeding season based on social status. Individual mating strategies may include defending underwater territories, using scramble tactics, and developing social alliances. (PDF contains 105 pages)

Desenvolvimento de um instrumento de avaliação da vulnerabilidade de pacientes imunodeprimidos a infecções zoonóticas a partir de animais de estimação.

Os animais de estimação podem ser fonte de infecções, principalmente para seres humanos imunocomprometidos, em especial, pacientes portadores do vírus HIV. Considerando que o contato com animais pode prover benefícios emocionais, profissionais da área da saúde, em particular médicos e médicos veterinários, devem estar conscientes do papel potencial destes animais na transmissão de doenças de forma a preconizar medidas profiláticas para que esta transmissão não ocorra. As circunstâncias que favorecem a transmissão de doenças a partir dos animais de estimação ainda não são totalmente conhecidas, principalmente na realidade brasileira. Faltam estudos com o objetivo de investigar o risco de doenças de origem zoonótica decorrentes do contato com estes animais, hoje também chamados de animais pet. Ademais, ressente-se da falta de um instrumento devidamente elaborado e validado com a finalidade de captar as informações necessárias para a realização de estudos deste tipo ou mesmo para servir como ferramenta de rastreio de situações de vulnerabilidade de pacientes imunodeprimidos com vistas ao aconselhamento sobre medidas de prevenção. Desta maneira, o objetivo deste estudo é elaborar um instrumento para averiguar a vulnerabilidade de pacientes imunodeprimidos a infecções zoonóticas a partir de animais de estimação. Inicialmente, foram mapeados os animais de estimação mais encontrados no ambiente doméstico e as principais infecções que podem ser transmitidas a partir deles. Selecionaram-se, então, os possíveis mecanismos de transmissão a serem abordados. Dentre as espécies de animais de estimação elencadas, os cães, gatos, aves, répteis e os pequenos roedores foram os selecionados para a confecção deste instrumento. As infecções selecionadas foram: Salmonelose; Criptosporidíase; Giardíase; Dermatofitoses, Esporotricose, Bartonelose; Ancilostomíase; Toxocaríase; Psitacose; Toxoplasmose; Escabiose; Campilobacteriose; Criptococose e Histoplasmose. Considerando as diferentes formas de transmissão de cada infecção foram identificados os possíveis atos e comportamentos no contato com animais de estimação, bem como características destes animais, que poderiam aumentar a probabilidade de transmissão. O instrumento desenvolvido foi composto de uma primeira parte abarcando os critérios de elegibilidade, e de outra envolvendo o escopo principal do instrumento. Como as características de contato e as infecções variam de acordo com a espécie de animal, o instrumento abordou cada um dos cinco grupos de animais separadamente. O instrumento aqui proposto concerne à etapa inicial de um processo de desenvolvimento formal para utilização em futuras pesquisas sobre o papel dos animais de estimação na transmissão de infecções para pacientes imunodeprimidos. Estudos que explorem a confiabilidade e validade do instrumento proposto, assim como sua aceitabilidade, são necessários antes que seu uso seja recomendado.

Designing of a single pack wash primer for aluminium surfaces in a marine environment

Design aspects and comparative performances of different laboratory formulations of wash primers were studied under laboratory and field conditions with reference to scratch hardness, flexibility, stability, resistance to corrosion and adhesiveness. The different formulations of single pack wash primers tested have shown superiority of the formulation prepared out of “mowital” and that it is comparable in performance to double pack wash primer.

Effect of rapid thermal annealing on Ti-AlN interfaces

The interface diffusion, reaction, and adherence of rapid thermal annealed Ti/ALN were investigated by RES, AES, SIMS, XRD and a scratch test. The experimental results show that diffusion and reaction occurs at the interface of Ti/AlN when the sample is rapidly annealed. During annealing, both the O adsorbed on the surface and doped in the AlN substrate diffuse into the Ti film. At low temperature TiO2 is produced. At higher temperature O reacts with the diffused Al in the Ti film and produces an Al2O3 layer in the middle of the film. N diffuses into the Ti film and produces TiN with an interface reaction. Ti oxide is produced at the interface between the film and the substrate. Scratch test results show that interface adherence is distinctly improved by rapid annealing at low temperature and decreases at higher temperature. (C) 1999 Elsevier Science B.V. All rights reserved.

Adhesive strength of new thermal barrier coatings of rare earth zirconates

La2Zr2O7 (LZ) and La-2(Zr0.7Ce0.3)(2)O-7 (LZ7C3) as novel candidate materials for thermal barrier coatings (TBCs) were prepared by electron beam-physical vapor deposition (EB-PVD). The adhesive strength of the as-deposited LZ and LZ7C3 coatings were evaluated by transverse scratch test. Meanwhile, the factors affecting the critical load value were also investigated. The critical load value of LZ7C3 coating is larger than that of LZ coating, whereas both values of these two coatings are lower than that of the traditional coating material, i.e. 8 wt% yttria stabilized zirconia (8YSZ). The micro-cracks formed in the scratch channel can partially release the stress in the coating and then enhance the adhesive strength of the coating. The width of the scratch channel and the surface spallation after transverse scratch test are effective factors to evaluate the adhesive strength of LZ and LZ7C3 coatings.

Direct measurement of plowing friction and wear of a polymer thin film using the atomic force microscope

Nanometer-scale plowing friction and wear of a polycarbonate thin film were directly measured using an atomic force microscope (AFM) with nanoscratching capabilities. During the nanoscratch tests, lateral forces caused discrepancies between the maximum forces for the initial loadings prior to the scratch and the unloading after the scratch. In the case of a nanoscratch test performed parallel to the cantilever probe axis, the plowing friction added another component to the moment acting at the cantilevered end compared to the case of nanoindentation, resulting in an increased deflection of the cantilever. Using free-body diagrams for the cases of nanoindentation and nanoscratch testing, the AFM force curves were analyzed to determine the plowing friction during nanoscratch testing. From the results of this analysis, the plowing friction was found to be proportional to the applied contact force, and the coefficient of plowing friction was measured to be 0.56 +/- 0.02. Also, by the combination of nanoscratch and nanoindentation testing, the energetic wear rate of the polycarbonate thin film was measured to be 0.94 +/- 0.05 mm(3)/(N m).

A Robot that Walks: Emergent Behaviors from a Carefully Evolved Network

Most animals have significant behavioral expertise built in without having to explicitly learn it all from scratch. This expertise is a product of evolution of the organism; it can be viewed as a very long term form of learning which provides a structured system within which individuals might learn more specialized skills or abilities. This paper suggests one possible mechanism for analagous robot evolution by describing a carefully designed series of networks, each one being a strict augmentation of the previous one, which control a six legged walking machine capable of walking over rough terrain and following a person passively sensed in the infrared spectrum. As the completely decentralized networks are augmented, the robot's performance and behavior repertoire demonstrably improve. The rationale for such demonstrations is that they may provide a hint as to the requirements for automatically building massive networks to carry out complex sensory-motor tasks. The experiments with an actual robot ensure that an essence of reality is maintained and that no critical problems have been ignored.

Tissue engraftment of hypoxic-preconditioned adipose-derived stem cells improves flap viability.

Adipose-derived stem cells (ASCs) have the ability to release multiple growth factors in response to hypoxia. In this study, we investigated the potential of ASCs to prevent tissue ischemia. We found conditioned media from hypoxic ASCs had increased levels of vascular endothelial growth factor (VEGF) and enhanced endothelial cell tubule formation. To investigate the effect of injecting rat ASCs into ischemic flaps, 21 Lewis rats were divided into three groups: control, normal oxygen ASCs (10(6) cells), and hypoxic preconditioned ASCs (10(6) cells). At the time of flap elevation, the distal third of the flap was injected with the treatment group. At 7 days post flap elevation, flap viability was significantly improved with injection of hypoxic preconditioned ASCs. Cluster of differentiation-31-positive cells were more abundant along the margins of flaps injected with ASCs. Fluorescent labeled ASCs localized aside blood vessels or throughout the tissue, dependent on oxygen preconditioning status. Next, we evaluated the effect of hypoxic preconditioning on ASC migration and chemotaxis. Hypoxia did not affect ASC migration on scratch assay or chemotaxis to collagen and laminin. Thus, hypoxic preconditioning of injected ASCs improves flap viability likely through the effects of VEGF release. These effects are modest and represent the limitations of cellular and growth factor-induced angiogenesis in the acute setting of ischemia.

Two-machine flowshop scheduling problems with no-wait jobs

We study a two-machine flow shop scheduling problem with no-wait in process, in which one of the machines is not available during a specified time interval. We consider three scenarios of handing the operation affected by the nonavailability interval. Its processing may (i) start from scratch after the interval, or (ii) be resumed from the point of interruption, or (iii) be partially restarted after the interval. The objective is to minimize the makespan. We present an approximation algorithm that for all these scenarios delivers a worst-case ratio of 3/2. For the second scenario, we offer a 4/3-approximation algorithm.

A conceptual framework for designing pharmaceutical reverse logistics networks in China

Over latest decade, Reverse Logistics (RL) has gained more and more attention from both industry and academia. In the past, most research on RL has been focused on automobile, electronic waste, computer, paper, package and package material. There is very little research and practice on drug recycling. Nevertheless, it is vital important to properly dispose expired drug because of hazardous contain which may harm to people and environment. In China, public awareness of the harmfulness of expired drugs is still very low and very few efforts have been made to recycle drugs. Therefore, this research aims to build up a conceptual framework to indentify factors of influencing drug recycling in China, from scratch borrowing from existing literature and industry practices in other recycling areas. This framework helps in designing reverse logistic (RL) network and also can provide a useful reference tool for policymakers at the local and national level. Furthermore, a primary research is planed to validate the framework and RL network.

Current-driven atomic waterwheels

A current induces forces on atoms inside the conductor that carries it. It is now possible to compute these forces from scratch, and to perform dynamical simulations of the atomic motion under current. One reason for this interest is that current can be a destructive force—it can cause atoms to migrate, resulting in damage and in the eventual failure of the conductor. But one can also ask, can current be made to do useful work on atoms? In particular, can an atomic-scale motor be driven by electrical current as it can be by other mechanisms. For this to be possible, the current-induced forces on a suitable rotor must be non-conservative, so that net work can be done per revolution. Here we show that current-induced forces in atomic wires are not conservative and that they can be used, in principle, to drive an atomic-scale waterwheel.