Protein structure refinement algorithms

Protein structure prediction has remained a major challenge in structural biology for more than half a century. Accelerated and cost efficient sequencing technologies have allowed researchers to sequence new organisms and discover new protein sequences. Novel protein structure prediction technologies will allow researchers to study the structure of proteins and to determine their roles in the underlying biology processes and develop novel therapeutics.

Difficulty of the problem stems from two folds: (a) describing the energy landscape that corresponds to the protein structure, commonly referred to as force field problem; and (b) sampling of the energy landscape, trying to find the lowest energy configuration that is hypothesized to be the native state of the structure in solution. The two problems are interweaved and they have to be solved simultaneously. This thesis is composed of three major contributions. In the first chapter we describe a novel high-resolution protein structure refinement algorithm called GRID. In the second chapter we present REMCGRID, an algorithm for generation of low energy decoy sets. In the third chapter, we present a machine learning approach to ranking decoys by incorporating coarse-grain features of protein structures.

Toxic blue-green algae: The "problem" in perspective

The incidence of blue-green algal blooms and surface scum-formation are certainly not new phenomena. Many British and European authors have been faithfully describing the unmistakable symptoms of blue-green algal scums for over 800 years. There is no disputing that blue-green algal toxins are extremely harmful. Three quite separate categories of compound have been separated: neurotoxins; hepatotoxins and lipopolysaccharides. There is a popular association between blue-green algae and eutrophication. Certainly the main nuisance species - of Microcystis, Anabaena and Aphanizomenon are rare in oligotrophic lakes and reservoirs. Several approaches have been proposed for the control of blue-green algae. Distinction is made between methods for discharging algae already present (eg algicides; straw bales; viruses; parasitic fungi and herbivorous ciliates), and methods for averting an anticipated abundance in the future (phosphorous control, artificial circulation etc).

Resolution and noise in ghost imaging with classical thermal light

The resolution and classical noise in ghost imaging with a classical thermal light are investigated theoretically. For ghost imaging with a Gaussian Schell model source, the dependences of the resolution and noise on the spatial coherence of the source and the aperture in the imaging system are discussed and demonstrated by using numerical simulations. The results show that an incoherent source and a large aperture will lead to a good image quality and small noise.

High-resolution automatic water quality monitoring systems applied to catchment and reservoir monitoring

Automatic recording instruments provide the ideal means of recording the responses of rivers, lakes and reservoirs to short-term changes in the weather. As part of the project ‘Using Automatic Monitoring and Dynamic Modelling for the Active Management of Lakes and Reservoirs', a family of three automatic monitoring stations were designed by engineers at the Centre for Ecology and Hydrology in Windermere to monitor such responses. In this article, the authors describe this instrument network in some detail and present case studies that illustrate the value of high resolution automatic monitoring in both catchment and reservoir applications.

On the problem of the distribution of Acanthocyclops viridis Jurine in the Rybinsk reservoir. [Translation from: Byulleten' Institute Biologii Vodokhranilishch 1958(1), 36-39, 1958. ]

Observations of individual weight, duration of development and production of different stages of Tropodiaptomus incognitus are presented. The study is based on data gathered from Lake Chad in 1968.

Vulnerabilidades da Mulher idosa frente ao HIV/AIDS

Tratou-se de um estudo descritivo exploratório com abordagem quantitativa acerca da vulnerabilidade de mulheres com mais de 60 anos em relação ao HIV/AIDS, cujo problema foi descobrir qual o processo de vulnerabilidade auto referido por mulheres de 60 anos e mais em relação ao HIV/AIDS a partir de suas atitudes sexuais.Os objetivos foram: Descrever o processo de vulnerabilidade auto referido por mulheres com 60 anos e mais em relação ao HIV/AIDS a partir de suas atitudes sexuais. Identificar atitudes sexuais entre mulheres com mais de 60 anos e mais. Descrever o conhecimento sobre HIV/AIDS das mulheres com mais de 60 anos.Descrever o processo de vulnerabilidade auto referido por mulheres com mais de 60 anos em relação ao HIV/AIDS.O estudo foi realizado com mulheres com mais de 60 anos freqüentadoras das atividades do Projeto Longegividade da Secretária Especial de Envelhecimento Saudável e Qualidade de vida do Rio de Janeiro. O local escolhido foram espaços públicos aonde se realizavam as atividades do Projeto. A coleta de dados aconteceu no período dos meses de setembro e outubro de 2009. Em atendimento ao preconizado pela resolução 196/96, todos os sujeitos assinaram o termo de consentimento livre e esclarecido. O estudo foi submetido à apreciação do Comitê de Ética da Prefeitura do Rio de Janeiro a fim obter a autorização para a divulgação do nome da Instituição aonde foi realizada a pesquisa, sob o parecer de número 84 A-2009. Participaram do estudo 256 mulheres. O questionário foi criado à partir de quatro dimensões estabelecidas. Dimensão sócio econômico e demográfica, processo de vulnerabilidade auto referido, conhecimento sobre HIV/AIDS e práticas sexuais. Os dados coletados foram organizados em bancos de dados, criados pelo pesquisador através de um sistema Gerenciador de Banco de Dados Microsoft Excel versão 2003. Foram utilizadas medidas estatísticas descritivas como freqüência absoluta e a freqüência relativa para atender aos objetivos do estudo. Concluiu-se que em nossa amostra as mulheres idosas se colocam em situação de risco, quando ao possuir vida sexual ativa não usam preservativos. Compõem um grupo bem informado acerca dos métodos de prevenção, porém a utilização do preservativo esta relacionada, a muito mais do que informação e sim a um objeto de confiança nas relações. Entendeu-se que a prevenção ao HIV/AIDS em mulheres com mais de 60 anos deveria incluir, além de estratégias de repasse de repasse de informação, estratégia de fortalecimento individual, reforço na auto estima e estimulo a autonomia de uma forma geral.

The problem of the co-existence of Arctodiaptomus bacillifer (Koelb.), Acanthodiaptomus denticornis (Wierz.) and Heterocope saliens Lill [Translation from: Memorie dell'Istituto Italiano di Idrobiologia Dott.Marco de Marchi 8 81-94, 1954]

In freshwater environments of modest size and without notable ecological structure, there is usually present only one diaptomid species. When two or more diaptomid species are present in the same habitat, generally their body dimensions are distinctly different. There are only four examples of co-existence of Arctodiaptomus bacillifer (Koelb.) and Acanthodiaptomus denticornis (Wierz.) situated at higher altitudes alpine lakes. The article discusses the results of sampling in the summer of 1953 and the problem of the co-existence of Arctodiaptomus bacillifer, Acanthodiaptomus denticornis and Heterocope saliens.

Preparation and attempted resolution of benzoyl-malic acid

The final object of this research was to prepare m-nitrobenzoyl malic acid and to separate it, if possible, into the four stereoisomers predicted by the Huggins' theory of the benzene ring. Inasmuch as the quantity of m-nitro- benzoyl chloride available was limited it was thought better to first prepare i-benzoyl malic acid and then attempt to resolve it. The resolution of m-nitrobenzoyl malic acid could probably be accomplished by a similar method.

Fiber Bragg grating temperature sensor for multiplexed measurement with high resolution

A novel fiber Bragg grating temperature sensor is proposed and experimentally demonstrated with a long-period grating as a linear response edge filter to convert wavelength into intensity-encoded information for interrogation. The sensor is embedded into an aluminum substrate with a larger coefficient of thermal expansion to enhance its temperature sensitivity. A large dynamic range of 110 degreesC and a high resolution of 0.02 degreesC are obtained in the experiments. The technique can be used for multiplexed measurements with one broadband source and one long-period grating, and therefore is low Cost. (C) 2004 Society of PhotoOptical Instrumentation Engineers.

High resolution electron microscope studies of chromosomal fibers

Techniques are described for mounting and visualizing biological macromolecules for high resolution electron microscopy. Standard techniques are included in a discussion of new methods designed to provide the highest structural resolution. Methods are also discussed for handling samples on the grid, for making accurate size measurements at the 20 Å level, and for photographically enhancing image contrast.

The application of these techniques to the study of the binding of DNA polymerase to DNA is described. It is shown that the electron micrographs of this material are in agreement with the model proposed by Dr. Arthur Kornberg. A model is described which locates several active sites on the enzyme.

The chromosomal material of the protozoan tetrahymena has been isolated and characterized by biochemical techniques and by electron microscopy. This material is shown to be typical of chromatin of higher creatures.

Comparison with other chromatins discloses that the genome of tetrahymena is highly template active and has a relatively simple genetic construction.

High resolution electron microscope procedures developed in this work have been combined with standard biochemical techniques to give a comprehensive picture of the structure of interphase chromosome fibers. The distribution of the chromosomal proteins along its DNA is discussed.

Filtering N.M.R. spectra

Methods of filtering an n.m.r. spectrum which can improve the resolution by as much as a factor of ten are examined. They include linear filters based upon an information theory approach and non-linear filters based upon a statistical approach. The appropriate filter is determined by the nature of the problem. Once programmed on a digital computer they are both simple to use.

These filters are applied to some examples from ¹³C and ¹⁵N n.m.r. spectra.