Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Pressure Controlled Self-Assembly of High Quality Three-Dimensional Colloidal Photonic Crystals

A concise pressure controlled isothermal heating vertical deposition (PCIHVD) method is developed, which provides an optimal growing condition with better stability and reproducibility for fabricating photonic crystals (PCs) without the limitation of colloidal sphere materials and sizes. High quality PCs are fabricated with PCIHVD from polystyrene spheres with diameters ranging from 200 nm to 1 mu m. The deep photonic band gap and steep photonic band edge of the samples are most favorable for realizing ultrafast optical devices, photonic chips, and communications. This method makes a meaningful advance in the quality and diversity of PCs and greatly promotes their wide applications.

Rapidly Infrared-Assisted Cooperatively Self-Assembled Highly Ordered Multiscale Porous Materials

In this paper, cooperative self-assembly (CSA) of colloidal spheres with different sizes was studied. It was found that a complicated jamming effect makes it difficult to achieve an optimal self-assembling condition for construction of a well-ordered stacking of colloidal spheres in a relatively short growth time by CSA. Through the use of a characteristic infrared (IR) technique to significantly accelerate local evaporation on the growing interface without changing the bulk growing environment, a concise three-parameter (temperature, pressure, and IR intensity) CSA method to effectively overcome the jamming effect has been developed. Mono- and multiscale inverse opals in a large range of lattice scales can be prepared within a growth time (15-30 min) that is remarkably shorter than the growth times of several hours for previous methods. Scanning electron microscopy images and transmittance spectra demonstrated the superior crystalline and optical qualities of the resulting materials. More importantly, the new method enables optimal conditions for CSA without limitations on sizes and materials of multiple colloids. This strategy not only makes a meaningful advance in the applicability and universality of colloidal crystals and ordered porous materials but also can be an inspiration to the self-assembly systems widely used in many other fields, such as nanotechnology and molecular bioengineering.

A high order accurate difference scheme for complex flow fields

A high order accurate finite difference method for direct numerical simulation of coherent structure in the mixing layers is presented. The reason for oscillation production in numerical solutions is analyzed, It is caused by a nonuniform group velocity of wavepackets. A method of group velocity control for the improvement of the shock resolution is presented. In numerical simulation the fifth-order accurate upwind compact difference relation is used to approximate the derivatives in the convection terms of the compressible N-S equations, a sixth-order accurate symmetric compact difference relation is used to approximate the viscous terms, and a three-stage R-K method is used to advance in time. In order to improve the shock resolution the scheme is reconstructed with the method of diffusion analogy which is used to control the group velocity of wavepackets. (C) 1997 Academic Press.

Depuración de aguas residuales urbanas y concentración de metales en fangos digeridos

[ES] La progresiva implantación de plantas de tratamiento de aguas residuales urbanas ha ido estableciendo una experiencia en el conocimiento de la eficacia de tratamiento de los diversos parámetros en plazos largos de funcionamiento. El análisis y comparación de resultados y tecnologías debe pennitir conocer las características de fiabilidad en la operación y el comportamiento frente a los diversos aspectos de la nonnativa legal. Además, el análisis en diferentes épocas del año puede producir distintos resultados o conclusiones. En este trabajo se ha tomado para el análisis una planta de tratamiento convencional, estudiando inicialmente los porcentajes medios de eliminación de diferentes parámetros, en relación asimismo con las necesidades que debe satisfacer. En condiciones de alta carga orgánica, la concentración de nitrógeno y algún tóxico especial parecen plantear las mayores dificultades. Se ha deseado focalizar la atención en el proceso de concentración de metales que se. produce en las plantas con tratamiento anaerobío de fangos. Por este motivo se Uevó a cabo un estudio de la evolución de metales en la depuración y la concentración de fangos digeridos. El fenómeno resulta de interés para analizar la calidad de las aguas que se obtienen, aunque debe considerarse también la concentración de metales en el destino final que se dé a los fangos tratados.

油藏复杂驱动体系物理模拟相似准则研究进展

综述了水驱油、化学驱油、蒸汽驱、混相驱及非混相驱等复杂油藏驱替体系物理模拟相似准则的研究现状.系统介绍了相似参数敏感性分析方法,定义了表征目标函数对相似参数依赖程度的敏感因子,结合数值方法便可定量地确定复杂体系主要相似参数,并实际应用于工程问题.讨论了水驱和聚合物驱物理模拟应优先满足的相似准则及其随参数范围的变化.

Synthetic molecular machines for active self-assembly : prototype algorithms, designs, and experimental study

Computer science and electrical engineering have been the great success story of the twentieth century. The neat modularity and mapping of a language onto circuits has led to robots on Mars, desktop computers and smartphones. But these devices are not yet able to do some of the things that life takes for granted: repair a scratch, reproduce, regenerate, or grow exponentially fast–all while remaining functional.

This thesis explores and develops algorithms, molecular implementations, and theoretical proofs in the context of “active self-assembly” of molecular systems. The long-term vision of active self-assembly is the theoretical and physical implementation of materials that are composed of reconfigurable units with the programmability and adaptability of biology’s numerous molecular machines. En route to this goal, we must first find a way to overcome the memory limitations of molecular systems, and to discover the limits of complexity that can be achieved with individual molecules.

One of the main thrusts in molecular programming is to use computer science as a tool for figuring out what can be achieved. While molecular systems that are Turing-complete have been demonstrated [Winfree, 1996], these systems still cannot achieve some of the feats biology has achieved.

One might think that because a system is Turing-complete, capable of computing “anything,” that it can do any arbitrary task. But while it can simulate any digital computational problem, there are many behaviors that are not “computations” in a classical sense, and cannot be directly implemented. Examples include exponential growth and molecular motion relative to a surface.

Passive self-assembly systems cannot implement these behaviors because (a) molecular motion relative to a surface requires a source of fuel that is external to the system, and (b) passive systems are too slow to assemble exponentially-fast-growing structures. We call these behaviors “energetically incomplete” programmable behaviors. This class of behaviors includes any behavior where a passive physical system simply does not have enough physical energy to perform the specified tasks in the requisite amount of time.

As we will demonstrate and prove, a sufficiently expressive implementation of an “active” molecular self-assembly approach can achieve these behaviors. Using an external source of fuel solves part of the the problem, so the system is not “energetically incomplete.” But the programmable system also needs to have sufficient expressive power to achieve the specified behaviors. Perhaps surprisingly, some of these systems do not even require Turing completeness to be sufficiently expressive.

Building on a large variety of work by other scientists in the fields of DNA nanotechnology, chemistry and reconfigurable robotics, this thesis introduces several research contributions in the context of active self-assembly.

We show that simple primitives such as insertion and deletion are able to generate complex and interesting results such as the growth of a linear polymer in logarithmic time and the ability of a linear polymer to treadmill. To this end we developed a formal model for active-self assembly that is directly implementable with DNA molecules. We show that this model is computationally equivalent to a machine capable of producing strings that are stronger than regular languages and, at most, as strong as context-free grammars. This is a great advance in the theory of active self- assembly as prior models were either entirely theoretical or only implementable in the context of macro-scale robotics.

We developed a chain reaction method for the autonomous exponential growth of a linear DNA polymer. Our method is based on the insertion of molecules into the assembly, which generates two new insertion sites for every initial one employed. The building of a line in logarithmic time is a first step toward building a shape in logarithmic time. We demonstrate the first construction of a synthetic linear polymer that grows exponentially fast via insertion. We show that monomer molecules are converted into the polymer in logarithmic time via spectrofluorimetry and gel electrophoresis experiments. We also demonstrate the division of these polymers via the addition of a single DNA complex that competes with the insertion mechanism. This shows the growth of a population of polymers in logarithmic time. We characterize the DNA insertion mechanism that we utilize in Chapter 4. We experimentally demonstrate that we can control the kinetics of this re- action over at least seven orders of magnitude, by programming the sequences of DNA that initiate the reaction.

In addition, we review co-authored work on programming molecular robots using prescriptive landscapes of DNA origami; this was the first microscopic demonstration of programming a molec- ular robot to walk on a 2-dimensional surface. We developed a snapshot method for imaging these random walking molecular robots and a CAPTCHA-like analysis method for difficult-to-interpret imaging data.

Bonaparte printzearen inguruko hizkuntz eztabaidak

Lan hau UPV/EHUko Donostiako VII. Udako Ikastaroetan ("Euskalaritza XVIII eta XIX. mendeetan", 1988ko iraila) emandako hitzaldiaren testu zuzendu eta osatua da.

分子生物光子学的进展

随着分子生物学和标记技术的进步，光学成像和分析有了很快的发展，无论是从理论上还是应用上都有所突破，展现了良好的前景。本文综述了近年来在分子生物探测中光子学的情况，简介了几种突破光学衍射极限的探测方法，着重阐明了与生化技术密切相关的荧光共振能量转移和荧光相关光谱显微术及其在分子生物学中的应用。

基于同步移相技术的1/4波片相位延迟量的快速测量

提出了一种基于同步移相技术的1/4波片相位延迟量的快速测量方法。由正交光栅、光阑、检偏器组和四象限探测器实现同步移相功能。检偏器组由4个不同方位角的检偏器组成。通过检偏器组的四束光束的光强由四象限探测器同时测量。1/4波片的相位延迟量由这四光束的光强得到。该方法中波片的快轴不需被事先确定。另外光源光强的波动对测量结果没有影响。通过实验验证了该方法的有效性。

Theoretical investigations of experimental gravitation

This thesis has two basic themes: the investigation of new experiments which can be used to test relativistic gravity, and the investigation of new technologies and new experimental techniques which can be applied to make gravitational wave astronomy a reality.

Advancing technology will soon make possible a new class of gravitation experiments: pure laboratory experiments with laboratory sources of non-Newtonian gravity and laboratory detectors. The key advance in techno1ogy is the development of resonant sensing systems with very low levels of dissipation. Chapter 1 considers three such systems (torque balances, dielectric monocrystals, and superconducting microwave resonators), and it proposes eight laboratory experiments which use these systems as detectors. For each experiment it describes the dominant sources of noise and the technology required.

The coupled electro-mechanical system consisting of a microwave cavity and its walls can serve as a gravitational radiation detector. A gravitational wave interacts with the walls, and the resulting motion induces transitions from a highly excited cavity mode to a nearly unexcited mode. Chapter 2 describes briefly a formalism for analyzing such a detector, and it proposes a particular design.

The monitoring of a quantum mechanical harmonic oscillator on which a classical force acts is important in a variety of high-precision experiments, such as the attempt to detect gravitational radiation. Chapter 3 reviews the standard techniques for monitoring the oscillator; and it introduces a new technique which, in principle, can determine the details of the force with arbitrary accuracy, despite the quantum properties of the oscillator.

The standard method for monitoring the oscillator is the "amplitude- and-phase" method (position or momentum transducer with output fed through a linear amplifier). The accuracy obtainable by this method is limited by the uncertainty principle. To do better requires a measurement of the type which Braginsky has called "quantum nondemolition." A well-known quantum nondemolition technique is "quantum counting," which can detect an arbitrarily weak force, but which cannot provide good accuracy in determining its precise time-dependence. Chapter 3 considers extensively a new type of quantum nondemolition measurement - a "back-action-evading" measurement of the real part X₁ (or the imaginary part X₂) of the oscillator's complex amplitude. In principle X₁ can be measured arbitrarily quickly and arbitrarily accurately, and a sequence of such measurements can lead to an arbitrarily accurate monitoring of the classical force.

Chapter 3 describes explicit gedanken experiments which demonstrate that X₁ can be measured arbitrarily quickly and arbitrarily accurately, it considers approximate back-action-evading measurements, and it develops a theory of quantum nondemolition measurement for arbitrary quantum mechanical systems.

In Rosen's "bimetric" theory of gravity the (local) speed of gravitational radiation v_g is determined by the combined effects of cosmological boundary values and nearby concentrations of matter. It is possible for v_g to be less than the speed of light. Chapter 4 shows that emission of gravitational radiation prevents particles of nonzero rest mass from exceeding the speed of gravitational radiation. Observations of relativistic particles place limits on v_g and the cosmological boundary values today, and observations of synchrotron radiation from compact radio sources place limits on the cosmological boundary values in the past.

Reprodução e biopolítica: infertilidades e práticas de saúde em um serviço público no Rio de Janeiro

Apesar de a reprodução assistida possibilitar transformações importantes na parentalidade e nas relações familiares, suas tecnologias têm sido mais frequentemente usadas para reiterar o modelo tradicional de reprodução biológica e social. Este estudo qualitativo, de cunho exploratório, analisou quais normas estariam presentes nas práticas de saúde relativas à dificuldade de engravidar e o que poderia ser revelado a partir destas práticas. Foram observadas interações entre profissionais e pacientes atendidos em um serviço público de reprodução humana no Rio de Janeiro. A discussão dos diagnósticos de infertilidade e de risco, duas importantes estratégias biopolíticas usadas como critério de elegibilidade para o acesso às novas tecnologias reprodutivas, revelou como algumas práticas de saúde reiteram normas de gênero e de reprodução social. Atrelados à condição socioeconômica de seus usuários, estes diagnósticos tendem a agravar exclusões e desigualdades no exercício dos direitos reprodutivos no país. A análise da atenção médica possibilitou conhecer em parte o difícil cotidiano não apenas de homens e mulheres, que por anos persistem em seus desejos por filhos, mas também de profissionais que enfrentam antigas barreiras políticas, econômicas e burocráticas do serviço público de saúde. Este estudo corrobora a visão de que o serviço representa um avanço em termos de direitos sexuais e reprodutivos, apesar de ainda ser longo o caminho para o acesso igualitário e equânime às tecnologias reprodutivas pelo sistema único de saúde brasileiro (SUS).

A questão cultural enquanto formação humana: investigando os interesses em disputa nas políticas culturais da cidade de São Gonçalo

A presente dissertação para o Mestrado em Educação da UERJ/FFP intenciona apresentar a questão cultural enquanto formação humana, buscando, assim, compreender a intrínseca relação entre a conjuntura histórico-social universal e a formação cultural gonçalense, e sua implicação na formulação de Políticas Públicas de Cultura no município de São Gonçalo. Na construção da pesquisa foi necessário, primeiramente, investigar e conceituar os sentidos ideológicos das palavras cultura e política, que contribuísse para fundamentar o pressuposto dos interesses em disputa que atravessam a formulação das políticas públicas, tendo como referencial a perspectiva gramsciana. Delimitamos a pesquisa empírica no cenário da IV Conferência Municipal de Cultura em São Gonçalo, por se tratar de um dos mecanismos de controle social que congrega a participação do Estado (no sentido estrito) e da sociedade civil, situando essa relação na perspectiva gramsciana em contraposição a perspectiva neoliberal. Através das falas dos cinco entrevistados, dos documentos e dos bastidores do cenário conferencista, foi possível visualizar as possibilidades e limites inerentes a formação humana gonçalense. Sem ter a pretensão de esgotar uma temática tão complexa e abrangente, a produção dissertativa objetiva avançar no debate da questão cultural enquanto uma das ferramentas na disputa por um projeto societário contra-hegemônico.

Um estudo histórico e conceitual sobre a clínica da reforma psiquiátrica brasileira

Este trabalho discute os fundamentos históricos e conceituais do movimento da reforma psiquiátrica brasileira. A questão principal que se coloca é como realizar a transformação da assistência em saúde mental sem recorrer a teorias reducionistas psiquiátricas, psicanalíticas ou culturais, mas apontando para um pluralismo clínico. Para responder a essa questão percorremos os trabalhos de autores que fizeram uma abordagem Epistemológica sobre a constituição da psiquiatria colocando em debate duas idéias centrais. A primeira idéia é defendida por Foucault que considera a invenção da psiquiatria e de seu objeto, a doença mental, uma redução indesejável da loucura cuja conseqüência é sua exclusão do mundo. A segunda idéia defendida por Gauchet e Swain se opõe à anterior e procura mostrar que a psiquiatria foi um avanço no entendimento de um fenômeno complexo. No entanto, o modelo assistencial promovido pela psiquiatria baseado no manicômio faliu ao não oferecer eficácia terapêutica e inclusão social para uma grande parcela de pacientes. Em conseqüência desse processo iniciaram-se movimentos de reforma psiquiátrica na maior parte do mundo. Experiências pioneiras foram capazes de formular novas formas de tratamento, em que teorias psicanalíticas, fenomenológicas e sociológicas tiveram um importante papel. Baseadas nessas experiências foram formuladas políticas públicas em saúde mental que tentaram conciliar o tratamento com a não exclusão. Examinamos, a partir daí, as principais experiências de reforma, seu estado atual e suas influências no Brasil. Analisamos a reforma psiquiátrica brasileira e as críticas que lhe são feitas. Em seguida procuramos entender as bases teóricas que fundamentam a experiência reformista no país. Descrevemos três vertentes de pensamento que fundamentam as ações dos novos serviços criados pela reforma psiquiátrica. Essas vertentes, embora em alguns aspectos se superpõem, em outros se antagonizam frontalmente. São elas as perspectivas basagliana, lacaniana e pluralista. Visando fundamentar essa última perspectiva, discutimos autores que fazem a interface da psiquiatria com a filosofia pragmática e também aproximamos essa concepção do pensamento do psicanalista Donald Winnicott como uma forma de contribuição à clínica da reforma. O estudo considera a possibilidade de abordar a reforma psiquiátrica a partir da concepção de uma clínica plural que autorize a incorporação de outros referenciais teóricos e que sirvam como instrumentos de reflexão e ação prática na condução de situações clínicas complexas e multifacetadas.