Structural analysis of dihydrofolate reductases enables rationalization of antifolate binding affinities and suggests repurposing possibilities

Antifolates are competitive inhibitors of dihydrofolate reductase ( DHFR), a conserved enzyme that is central to metabolism and widely targeted in pathogenic diseases, cancer and autoimmune disorders. Although most clinically used antifolates are known to be target specific, some display a fair degree of cross-reactivity with DHFRs from other species. A method that enables identification of determinants of affinity and specificity in target DHFRs from different species and provides guidelines for the design of antifolates is currently lacking. To address this, we first captured the potential druggable space of a DHFR in a substructure called the `supersite' and classified supersites of DHFRs from 56 species into 16 `site-types' based on pairwise structural similarity. Analysis of supersites across these site-types revealed that DHFRs exhibit varying extents of dissimilarity at structurally equivalent positions in and around the binding site. We were able to explain the pattern of affinities towards chemically diverse antifolates exhibited by DHFRs of different site-types based on these structural differences. We then generated an antifolate-DHFR network by mapping known high-affinity antifolates to their respective supersites and used this to identify antifolates that can be repurposed based on similarity between supersites or antifolates. Thus, we identified 177 human-specific and 458 pathogen-specific antifolates, a large number of which are supported by available experimental data. Thus, in the light of the clinical importance of DHFR, we present a novel approach to identifying differences in the druggable space of DHFRs that can be utilized for rational design of antifolates.

Phylogeography and non-invasive landscape genetics of the European pine marten ("martes martes" L. 1758) : insights into ancient and contemporary processes shaping genetic variation

283 p. : graf., map.

A bayesian probabilistic approach to structural health monitoring

A Bayesian probabilistic methodology for on-line structural health monitoring which addresses the issue of parameter uncertainty inherent in problem is presented. The method uses modal parameters for a limited number of modes identified from measurements taken at a restricted number of degrees of freedom of a structure as the measured structural data. The application presented uses a linear structural model whose stiffness matrix is parameterized to develop a class of possible models. Within the Bayesian framework, a joint probability density function (PDF) for the model stiffness parameters given the measured modal data is determined. Using this PDF, the marginal PDF of the stiffness parameter for each substructure given the data can be calculated.

Monitoring the health of a structure using these marginal PDFs involves two steps. First, the marginal PDF for each model parameter given modal data from the undamaged structure is found. The structure is then periodically monitored and updated marginal PDFs are determined. A measure of the difference between the calibrated and current marginal PDFs is used as a means to characterize the health of the structure. A procedure for interpreting the measure for use by an expert system in on-line monitoring is also introduced.

The probabilistic framework is developed in order to address the model parameter uncertainty issue inherent in the health monitoring problem. To illustrate this issue, consider a very simplified deterministic structural health monitoring method. In such an approach, the model parameters which minimize an error measure between the measured and model modal values would be used as the "best" model of the structure. Changes between the model parameters identified using modal data from the undamaged structure and subsequent modal data would be used to find the existence, location and degree of damage. Due to measurement noise, limited modal information, and model error, the "best" model parameters might vary from one modal dataset to the next without any damage present in the structure. Thus, difficulties would arise in separating normal variations in the identified model parameters based on limitations of the identification method and variations due to true change in the structure. The Bayesian framework described in this work provides a means to handle this parametric uncertainty.

The probabilistic health monitoring method is applied to simulated data and laboratory data. The results of these tests are presented.

Population connectivity among Dry Tortugas, Florida, and Caribbean populations of mutton snapper (Lutjanus analis), inferred from multiple microsatellite loci

Determining patterns of population connectivity is critical to the evaluation of marine reserves as recruitment sources for harvested populations. Mutton snapper (Lutjanus analis) is a good test case because the last known major spawning aggregation in U.S. waters was granted no-take status in the Tortugas South Ecological Reserve (TSER) in 2001. To evaluate the TSER population as a recruitment source, we genotyped mutton snapper from the Dry Tortugas, southeast Florida, and from three locations across the Caribbean at eight microsatellite loci. Both Fstatistics and individual-based Bayesian analyses indicated that genetic substructure was absent across the five populations. Genetic homogeneity of mutton snapper populations is consistent with its pelagic larval duration of 27 to 37 days and adult behavior of annual migrations to large spawning aggregations. Statistical power of future genetic assessments of mutton snapper population connectivity may benefit from more comprehensive geographic sampling, and perhaps from the development of less polymorphic DNA microsatellite loci. Research where alternative methods are used, such as the transgenerational marking of embryonic otoliths with barium stable isotopes, is also needed on this and other species with diverse life history characteristics to further evaluate the TSER as a recruitment source and to define corridors of population connectivity across the Caribbean and Florida.

Caracterização da distribuição de alelos de loci STR do cromossomo Y com elevada taxa de mutação em uma amostra populacional do Rio de Janeiro

Marcadores genéticos presentes no cromossomo Y, como os microssatélites (Y-STRs) e polimorfismos de único nucleotídeo (Y-SNPs) são utilizados na caracterização de linhagens masculinas, visto que são transmitidos às gerações seguintes sem alterações, a menos que ocorram mutações (Singh et al., 2011; Mitchell & Hammer, 1996; Butler, 2009). Por isso, esses marcadores são amplamente empregados em diversas situações, destacando-se o uso constante dos Y-STRs na genética forense por apresentarem alta capacidade de discriminar linhagens. Recentemente, foram descritos 13 marcadores com taxas de mutação substancialmente superiores àquelas verificadas para loci STR do cromossomo Y, denominados Rapidly Mutating (RM) Y-STRs (Ballantyne et al., 2010; Kayser et al., 2012). Devido às taxas de mutação elevadas, os RM-YSTRs apresentam maior eficiência na discriminação entre indivíduos proximamente relacionados, pertencentes à mesma linhagem patrilínea. O presente trabalho buscou aprofundar o conhecimento acerca das características populacionais e mutacionais dos loci RM-YSTRs em amostra do Rio de Janeiro, contribuindo com estudos desta natureza na população brasileira. Realizou-se a análise de 13 loci do cromossomo Y em 258 indivíduos do sexo masculino, compondo 129 pares de pais e filhos, nascidos no estado do Rio de Janeiro. O DNA das amostras foi extraído, conforme os protocolos vigentes na rotina do LDD-UERJ. As sequências genéticas de interesse foram amplificadas pela técnica de reação em cadeira da polimerase (PCR) através da realização de três PCR multiplex, cujos produtos de amplificação foram separados por eletroforese em sequenciador automático ABI-3500 (Applied Biosystems). Para os pares pai/filho que apresentaram haplótipos mutados, empregou-se a técnica de sequenciamento para confirmação das mutações. Os loci RM-YSTR geraram um poder de discriminação de 1,0 na amostra analisada, o que significa que todos os 129 indivíduos da amostra populacional apresentaram haplótipos diferentes para tais marcadores, com frequências de 0,0077 e diversidade haplotípica igual a 1. Além disso, foram obtidos valores elevados de diversidade gênica para os 13 marcadores. A análise de distância genética e os resultados de AMOVA baseados nos valores de Fst demonstraram que os RM-YSTR não indicam subdivisão populacional e traços ancestrais comuns. Tais valores estão associados às elevadas taxas de mutação encontradas, cuja média foi de 2,11 x 10-2. Foi possível observar que os loci RM-YSTR são muito discriminativos na amostra miscigenada analisada, além de terem maior capacidade de diferenciar indivíduos do que outros conjuntos de marcadores normalmente usados em estudos populacionais e análises forenses. Sendo assim, é possível concluir que os marcadores RM-YSTR são promissores para discriminar indivíduos da mesma linhagem patrilínea, visto que devido às suas elevadas taxas mutacionais e poder de discriminação, são capazes de diferenciar indivíduos de maneira mais eficiente do que os outros conjuntos de STR. Porém, é necessário maior número de estudos para melhor caracterização destes loci em diferentes populações.

Study on the reproductive biology of Pinctada fucata (Gould) (Mollusca: Pteriidae)

Annual cycle of gonad development and spawning in pearl oyster, Pinctada ficata (Gould) in Nakhiloo, Northeast Persian Gulf, was investigated over two years from August 1994 to June 1996. Gonadal condition was assessed by staging criteria to describe gametogenic development from histological preparations of randomly collected individuals of all sizes. A bimodal gametogenic pattern with summer and autumn spawning periods was evident throughout the study. Gametogensis commenced in November-December which proceeded by major gonadal maturation during February-April. Summer spawning was observed from April to July with major spawning at the latter end. During spawning peak in July, low level of gametogensis was noticed. Gametogenic activity was picked up again in August-September which proceeded by autumn spawning from September to December. Towards the end of spawning season, incidence of gonadal inactivation increased. Minimum level of gonadal activity was observed in November. Temperature regime appears to have influential role in regulation of gametogenic and spawning processes. Gonadal development and spawning trends were similar in both sexes. P. radiaata was found to be protandrous hermaphrodite which matured as a male at shell height greater than 20 mm. Biseivality was uncommon and the sex ratio was about 1:1. Ultrastructure of gametes were investigated in the Pictada fucata (Gould). "Auxiliary cells" closely accociated with developing oocytes were observed. Each oocyte seems to be associated with only one secretory cell. which is characterized by an abundant rough endoplasmic reticulum at the onset of vitellogenesis. Contact between this cell and a developing oocytes is maintained by a desmosome-like junction which can be observed when the vitelline coat is formed. these "auxiliary or nursing cells" seem to play a tropic role in vitellogenesis, and may be involved in the formation of the vitelline coat of the oocytes. Oocytic degeneration is observed in this species, it is a continuous phenomenon of varing intensity throughout the year. The ultrastructural changes resulting in lysis of the oocyte are described. Mature spermatozoa consist of a broad, cap-shaped acrosomal vesicle, subacrosomal material, a round nucleus, two triplet substructure centrioles surrounded by four spherical mitochondria, and a flagellum anchored to the distal centriole and plasma membrane. Spermatozoa of Plucata closley resemble to those of other investigated Pteriidae. Changes in proximate composition of soft tissue and gonadal cycle of Pinctada fucata was studied. Mobilization and utilization of stored reserves are apparent during gametogenesis and gonadal maturation. Protein reserves are utilized during spermatogenesis while reserved carbohydrates form the main energy donor in oogenesis. The role of lipid as am.: energy reserve is second to that of carbohydrate.

Rao-Blackwellized particle smoothers for mixed linear/nonlinear state-space models

We consider the smoothing problem for a class of conditionally linear Gaussian state-space (CLGSS) models, referred to as mixed linear/nonlinear models. In contrast to the better studied hierarchical CLGSS models, these allow for an intricate cross dependence between the linear and the nonlinear parts of the state vector. We derive a Rao-Blackwellized particle smoother (RBPS) for this model class by exploiting its tractable substructure. The smoother is of the forward filtering/backward simulation type. A key feature of the proposed method is that, unlike existing RBPS for this model class, the linear part of the state vector is marginalized out in both the forward direction and in the backward direction. © 2013 IEEE.

有机结构解析专家系统CAMOS的研制

本文系统地介绍了有机结构解析专家系统CAMOS（Computer Automatted Manipulation of Organic Structures)的研制，建立结构解析专家系统的目的是应用计算机人工智能技术，充分应用化学家的知识和经验，模拟结构解析的思维过程，辅助各种现代结构分析手段，达到用计算机自动解析结构的目的。本文分七个部分介绍CAMOS系统。第一部分介绍系统整体设计和组织以及运行环境。第二部分介绍亚结构的生成和描述。系统从未知物的分子式出发，采用迭代法生成所有符合元素组成的亚结构。生成过程分为两级，先由分子式生成元素组成亚结构（ECSS)，再由EGSS生成键性亚结构（BASS)。然后描述BASS的元素性质（EA)和键性质（BA)。根据集合论，将BASS看成一个集合，则EA和BA为两个子集，通过对EA和BA进行逻辑运算，可以判断任意两个BASS之间是否能成键，生成的亚结构可以用已知的化的亚结构集合。第三部分介绍分子整体结构的生成。作者根据图论，提出了分子结构树生成算法，即用经过挑选的亚结构在一定的约束条件下来构造分子结构树，一棵完整的结构树即为一个候选结构，它必须符合分子式和联接性。算法可迭代生成所有的结构树。生成的候选结构用亚结构联接矩阵SSCM表示。为了减少组合过程中所占存储量，缩短生成时间，本系统中采用了SSGM变换技术，即，将生成的一个候选结构的SSGM进行穷举变换，可得到所有候选结构的SSGM，这对于含多个亚结构的分子的结构生成很有效。第四部分介绍作者提出的一种新的亚结构编码SSTNC（Substructure Tree Numerial Gode)。这种编码可用于亚结构参与结构变换的过程。在GAMOS中，SSTNC用于生成候选分子结构的二维联接表。SSTNC具有很好的唯一性，可减少重复结构的生成。第五部分介绍候选结构的验证。有两个策略，一是模拟候选结构的碳－13核磁共振谱，与未知物的实验谱比较，比较的方法有谱峰个数比较和化学位移比较，去掉与实验谱不符合的候选结构。二是用相似度经验公式计算模拟谱与实验谱的相似性，按相似度排队。第六部分介绍结构的显示。CAMOS系统移植了R.E.Carhart报导的结构显示程序，设计了接口，生成的二维联接表可直接用于结构的显示。最后以一个实例演示CAMOS的解析过程。CAMOS系统目前只是个模型系统，可在小型机或微机上运行。程序用FORTRAN－77语言编写。系统的功能将随着库中内容的增加和推理规则的严格而加强。

Segmented All-Platinum Nanowires with Controlled Morphology through Manipulation of the Local Electrolyte Distribution in Fluidic Nanochannels during Electrodeposition

Synthesis of segmented all-Pt nanowires is achieved by a template-assisted method. The combination of a suitably chosen electrolyte/template system with pulse-reverse electrodeposition allows the formation of well-defined segments linked to nanowires. Manipulation of the morphology is obtained by controlling the electrokinetie effects on the local electrolyte distribution inside the nanochannels during the nanowire growth process, allowing a deviation from the continuously cylindrical geometry given by the nanoporous template. The length of the segments can be adjusted as a function of the cathodic pulse duration. Applying constant pulses leads to segments with homogeneous shape and dimensions along most of the total wire length. X-ray diffraction demonstrates that the preferred crystallite orientation of the polycrystalline wires varies with the average segment length. The results are explained considering transitions in texture formation with increasing thickness of the electrodeposit. A mechanism of segment formation is proposed based on structural characterizations. Nanowires with controlled segmented morphology are of great technological importance, because of the possibility to precisely control their substructure as a means of tuning their electrical, thermal, and optical properties. The concept we present in this work for electrodeposited platinum and track-etched polycarbonate membranes can be applied to other selected materials as well as templates and constitutes a general method to controlled nanostructuring and synthesis of shape controlled nanostructures.

Separation of drug enantiomers by capillary electrophoresis in the presence of neutral cyclodextrins

This is a selected review, highlighting our results obtained in an extended screening program ("The German-Chinese Drug Screening Program"), with a focus on a set of original data obtained with heptakis(2,3,6-tri-O-methyl)-beta-cyclodextrin(TM-beta-CD) as the chiral solvating agent (CSA). The enantioseparation of 86 drugs by capillary zone electrophoresis in the presence of this CSA was successful for 47 drugs. The migration separation factors (alpha(m)) and the migration retardation factors (R-m) were compared with those found for native beta-cyclodextrin (beta-CD). The patterns thus obtained were also compared with those observed for hexakis(2,3,6-tri-O-methyl)-alpha-CD (TM-alpha-CD) and octakis(2,3,6-tri-O-methyl)-gamma-CD (TM-gamma-CD), respectively. From the statistical data, it can be concluded that there is a remarkable influence of the analyte structure on the electrophoretic data. A substructure 4H was found in the analyte structure that has a significant influence on the analytes' behaviour. Thus, analytes bearing the substructure 4H do not only have a strong affinity to the CDs but also a high rate of success of chiral separation in all systems reviewed. In light of this, the different ring sizes of native cyclodextrins (alpha-, beta- and gamma-CD) readily explain their behaviour towards a limited test set of chiral drugs. Sterical considerations point to the significance of side-on-binding versus inclusion in the cavity of the host. In addition to the findings from the screening program, numerous references to the Literature are given. (C) 2000 Elsevier Science B.V. All rights reserved.

EXPERT-SYSTEM FOR ELUCIDATION OF STRUCTURES OF ORGANIC-COMPOUNDS

An expert system for the elucidation of the structures of organic compounds-ESESOC-II has been designed. It is composed of three parts: spectroscopic data analysis, structure generator, and evaluation of the candidate structures. The heart of ESESOC is the structure generator, as an integral part, which accepts the specific types of information, e.g. molecular formulae, substructure constraints, and produces an exhaustive and irredundant list of candidate structures. The scheme for the structural generation is given, in which the depth-first search strategy is used to fill the bonding adjacency matrix (BAM) and a new method is introduced to remove the duplicates.

On Directional Selectivity in Vertebrate Retina: An Experimental and Computational Study

This thesis describes an investigation of retinal directional selectivity. We show intracellular (whole-cell patch) recordings in turtle retina which indicate that this computation occurs prior to the ganglion cell, and we describe a pre-ganglionic circuit model to account for this and other findings which places the non-linear spatio-temporal filter at individual, oriented amacrine cell dendrites. The key non-linearity is provided by interactions between excitatory and inhibitory synaptic inputs onto the dendrites, and their distal tips provide directionally selective excitatory outputs onto ganglion cells. Detailed simulations of putative cells support this model, given reasonable parameter constraints. The performance of the model also suggests that this computational substructure may be relevant within the dendritic trees of CNS neurons in general.

A puzzle with many pieces: the genetic structure and diversity of Phaeocystis antarctica Karsten (Prymnesiophyta)

Strong ocean current systems characterize the Southern Ocean. The genetic structure of marine phytoplankton species is believed to depend mainly on currents. Genetic estimates of the relatedness of populations of phytoplankton species therefore should provide a proxy showing to what extent different geographic regions are interconnected by the ocean current systems. In this study, spatial and temporal patterns of genetic diversity were studied in the circumpolar prymnesiophyte Phaeocystis antarctica Karsten using seven nuclear microsatellite loci. Analyses were conducted for 86 P. antarctica isolates sampled around the Antarctic continent between 1982 and2007. The resultsrevealed highgenetic diversity without singlegenotypes recurringeven amongisolateswithin a bloom or originating from the same bucket of water. Populations of P. antarctica were significantly differentiated among the oceanic regions. However, some geographically distant populations were more closely related to each other than they were to other geographically close populations. Temporal haplotype turnover within regions was also suggested by the multilocus fingerprints. Our data suggest that even within blooms of P. antarctica genetic diversity and population sizes are large but exchange between different regions canbe limited. Positive and significant inbreeding coefficients hint at further regional substructure of populations, suggestingthat patches, once isolated from one another, may not reconnect. These data emphasize that even for planktonic species in a marine ecosystem that is influenced by strong currents, significant breaks in geneflow may occur.

Observations of the interstellar medium in the Magellanic Bridge.

We present ultraviolet and optical spectra of DI 1388, a young star in the Magellanic Bridge, a region of gas between the Small and Large Magellanic Clouds. The data have signal-to-noise ratios of 20-45 and a spectral resolution of 6.5 km s-1. Interstellar absorption by the Magellanic Bridge at vLSR~200 km s-1 is visible in the lines of C I, C II, C II*, C IV, N I, O I, Al II, Si II, Si III, Si IV, S II, Ca II, Fe II, and Ni II. The relative gas-phase abundances of C II, N I, O I, Al II, Si II, Fe II, and Ni II with respect to S II are similar to those found in Galactic halo clouds, despite a significantly lower metallicity in the Magellanic Bridge. The higher ionization species in the cloud have a column density ratio N(C+3)/N(Si+3)~1.9, similar to that inferred for collisionally ionized Galactic cloud interfaces at temperatures ~105 K. We identify substructure in the stronger interstellar lines, with a broad component (FWHM~20 km s-1) at ~179 km s-1 and a sharp component (FWHM~11 km s-1) at 198 km s-1. The abundance analysis for these clouds indicates that the feature at 198 km s-1 consists of a low electron density, mainly neutral gas that may be associated with an interface responsible for the highly ionized gas. The 179 km s-1 cloud consists of warmer, lower density gas that is partially ionized.

The production and characterisation of dinitrocarbanilide antibodies raised using antigen mimics.

Polyclonal antibodies were produced to detect the coccidiostat nicarbazin. Due to structural constraints of the active component of nicarbazin, dinitrocarbanilide (DNC), three different compounds that shared a common substructure with DNC were used as antigen mimics. The compounds (N-suceinyl-L-alanyl-L-alanyl-L-alanine 4-nitroanilide (SAN), L-glutamic acid gamma-(p-nitroanilide) (GAN) and p-nitrosuccinanilic acid (NSA)) were conjugated to a carrier protein and used in the immunisation of rabbits. Five different polyclonal sera were produced and consequently characterised. The antibodies exhibited an IC50 range of 2.3-7.6 ng/ml using a competitive ELISA procedure, Serum from one rabbit, R555, exhibited an IC50 of 2.9 ng/ml for DNC and cross-reactivity studies showed that this serum was specific for DNC and did not cross-react with other coccidiostats such as halofuginone, toltrazuril or ronidazole. (C) 2002 Elsevier Science B.V. All rights reserved.