Disorder prediction methods, their applicability to different protein targets and their usefulness for guiding experimental studies

The role and function of a given protein is dependent on its structure. In recent years, however, numerous studies have highlighted the importance of unstructured, or disordered regions in governing a protein’s function. Disordered proteins have been found to play important roles in pivotal cellular functions, such as DNA binding and signalling cascades. Studying proteins with extended disordered regions is often problematic as they can be challenging to express, purify and crystallise. This means that interpretable experimental data on protein disorder is hard to generate. As a result, predictive computational tools have been developed with the aim of predicting the level and location of disorder within a protein. Currently, over 60 prediction servers exist, utilizing different methods for classifying disorder and different training sets. Here we review several good performing, publicly available prediction methods, comparing their application and discussing how disorder prediction servers can be used to aid the experimental solution of protein structure. The use of disorder prediction methods allows us to adopt a more targeted approach to experimental studies by accurately identifying the boundaries of ordered protein domains so that they may be investigated separately, thereby increasing the likelihood of their successful experimental solution.

Proteins and their interacting partners: an introduction to protein–ligand binding site prediction methods

Elucidating the biological and biochemical roles of proteins, and subsequently determining their interacting partners, can be difficult and time consuming using in vitro and/or in vivo methods, and consequently the majority of newly sequenced proteins will have unknown structures and functions. However, in silico methods for predicting protein–ligand binding sites and protein biochemical functions offer an alternative practical solution. The characterisation of protein–ligand binding sites is essential for investigating new functional roles, which can impact the major biological research spheres of health, food, and energy security. In this review we discuss the role in silico methods play in 3D modelling of protein–ligand binding sites, along with their role in predicting biochemical functionality. In addition, we describe in detail some of the key alternative in silico prediction approaches that are available, as well as discussing the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated Model EvaluatiOn (CAMEO) projects, and their impact on developments in the field. Furthermore, we discuss the importance of protein function prediction methods for tackling 21st century problems.

Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses

We analysed Hordeum spontaneum accessions from 21 different locations to understand the genetic diversity of HsDhn3 alleles and effects of single base mutations on the intrinsically disordered structure of the resulting polypeptide (HsDHN3). HsDHN3 was found to be YSK2-type with a low-frequency 6-aa deletion in the beginning of Exon 1. There is relatively high diversity in the intron region of HsDhn3 compared to the two exon regions. We have found subtle differences in K segments led to changes in amino acids chemical properties. Predictions for protein interaction profiles suggest the presence of a protein-binding site in HsDHN3 that coincides with the K1 segment. Comparison of DHN3 to closely related cereals showed that all of them contain a nuclear localization signal sequence flanking to the K1 segment and a novel conserved region located between the S and K1 segments [E(D/T)DGMGGR]. We found that H. vulgare, H. spontaneum, and Triticum urartu DHN3s have a greater number of phosphorylation sites for protein kinase C than other cereal species, which may be related to stress adaptation. Our results show that the nature and extent of mutations in the conserved segments of K1 and K2 are likely to be key factors in protection of cells.

Seasonality of submesoscale flows in the ocean surface boundary layer

A signature of submesoscale flows in the upper ocean is skewness in the distribution of relative vorticity. Expected to result for high Rossby-number flows, such skewness has implications for mixing, dissipation and stratification within the upper ocean. An array of moorings deployed in the Northeast Atlantic for one year as part of the OSMOSIS experiment reveals that relative vorticity is positively skewed during winter even though the scale of the Rossby number is less than 0.5. Furthermore, this skewness is reduced to zero during spring and autumn. There is also evidence of modest seasonal variations in the gradient Rossby number. The proposed mechanism by which relative vorticity is skewed is that the ratio of lateral to vertical buoyancy gradients, as summarized by the inverse gradient Richardson number, restricts its range during winter but less so at other times of the year. These results support recent observations and model simulations suggesting the upper ocean is host to a seasonal cycle in submesoscale turbulence.

In silico identification and characterization of protein-ligand binding sites

Protein–ligand binding site prediction methods aim to predict, from amino acid sequence, protein–ligand interactions, putative ligands, and ligand binding site residues using either sequence information, structural information, or a combination of both. In silico characterization of protein–ligand interactions has become extremely important to help determine a protein’s functionality, as in vivo-based functional elucidation is unable to keep pace with the current growth of sequence databases. Additionally, in vitro biochemical functional elucidation is time-consuming, costly, and may not be feasible for large-scale analysis, such as drug discovery. Thus, in silico prediction of protein–ligand interactions must be utilized to aid in functional elucidation. Here, we briefly discuss protein function prediction, prediction of protein–ligand interactions, the Critical Assessment of Techniques for Protein Structure Prediction (CASP) and the Continuous Automated EvaluatiOn (CAMEO) competitions, along with their role in shaping the field. We also discuss, in detail, our cutting-edge web-server method, FunFOLD for the structurally informed prediction of protein–ligand interactions. Furthermore, we provide a step-by-step guide on using the FunFOLD web server and FunFOLD3 downloadable application, along with some real world examples, where the FunFOLD methods have been used to aid functional elucidation.

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

Den monstruösa naturen : En ekokritisk analys av fyra skräcknoveller

Den här uppsatsen är en ekokritisk analys av fyra noveller ur Anders Fagers Samlade svenska kulter: skräckberättelser. De undersökta novellerna är ”Furierna från Borås”, ”När döden kom till Bodskär”, ”Leka med Liam” och ”Tre veckor av lycka”. Syftet med uppsatsen är att undersöka hur förhållandet mellan natur och kultur, människa och natur samt människa och icke-människa skildras. Metoden som använts är närläsning. Analysen visar att naturen och de icke-mänskliga varelserna skildras som ett hot mot människorna. Naturskildringen ansluter till tropen vildmark, där naturen är skrämmande och ogästvänlig. Kvinnorna knyts närmare naturen och de framställs som ett hot mot männen. Detta kan dock ses som ett sätt att ge naturen och kvinnorna rollen av aktivt subjekt snarare än passiva objekt.

O uso da representação cartográfica e a cartofobia: analisando a prática e a formação inicial docente na Geografia do ensino público em Teresina-PI

This word has objective to analyzer the relevance of the use of the cartographic representations, in the constructions of the geographical knowledge, during the process of the teaching-learning in the classes of the Geographic of the High School, drawing liam with the formation docent of the regulars courses of teacher training in the regular courses of Degree in Geography. Delimit is the area of empiric search to College State Zacarias de Goes (CEZG) Liceu Piauiense, and to regulars courses of Degree in Geography of the University Federal of the Piauí (UFPI) and University State of the Piauí (UESPI), educational institutions of the public network, located in the city of the Teresina Piauí. Expression of the problematic searched is gaps to been demystified on the vision cartofógica, when has reference to use of the cartographic representations, in the practice, and the initial formation docent in the Geography. To analyze the dynamics of the use of the cartographic resources, tried demystify the Cartography while of the space during the teaching of discipline Geography. So, the lyam with the initial formation in the begree search understand the impasses of construction to academic know and the possibilities of the didactic transposition to the restructure of the know scholar to teacher who works in the Geography, trying to make the teaching of this discipline more interesting and value

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

A França nas crônicas de Mário de Andrade: o nacional e o estrangeiro no periódico Diário Nacional (1929-1932)

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Procedimentos de ensino e de testes de construção e leitura de sentenças com compreensão

Análise de relações ordinais nos quais o responder estaria sob controle de propriedades relacionais do tipo primeiro, segundo, terceiro e assim por diante, a partir do paradigma de equivalência, constitui uma importante forma de compreender o comportamento verbal (sintaxe). Cinco estudos buscaram avaliar a emergência de novas sentenças com três ou quatro palavras (artigos, substantivos, adjetivos ou verbos e advérbios), com base nas posições ocupadas pelas mesmas em cada sentença ensinada independentemente. Participaram do Estudo 1 cinco crianças da pré-escola. Todos os participantes foram submetidos a procedimentos de ensino com três palavras através de emparelhamento de acordo com o modelo, testes de equivalência, treino por encadeamento de respostas, testes de produção de seqüências, conectividade e testes de leitura com compreensão. No Estudo 2, outras cinco crianças do ensino fundamental foram expostas aos mesmos procedimentos de ensino e testes, com quatro palavras. No Estudo 3, quatro crianças eram submetidas ao procedimento por encadeamento, testes de produção de seqüências, conectividade e de leitura com compreensão com quatro palavras. No Estudo 4 outras quatro crianças com história de fracasso escolar foram submetidas ao mesmo procedimento de ensino e testes dos Estudos 1 e 2, com quatro palavras. No Estudo 5 três outras crianças também com história de fracasso escolar foram submetidas ao mesmo procedimento adotado no Estudo 3 com quatro palavras. Os participantes não tinham leitura fluente de frases, mas liam palavras isoladamente. As sessões experimentais ocorreram numa sala da escola freqüentada pelas crianças. Um microcomputador forneceu suporte ao estudo e um software específico exerceu o controle e registro dos dados comportamentais. Utilizaram-se três conjuntos de estímulos: A (desenhos), B (palavras maiúsculas) e C (palavras minúsculas), para ensinar as relações condicionais AB e AC e testes BC/CB. No treino por encadeamento eram usadas três sentenças diferentes. Na primeira tentativa, a palavra UM, por exemplo, era apresentada na área de escolha. Um toque sobre a palavra produzia como conseqüência seu deslocamento para a área de construção na parte superior da tela, uma animação gráfica era apresentada acompanhada de um som muito bem, legal, certo. Em seguida, duas palavras eram apresentadas 10 simultaneamente na tela e o participante deveria tocar em uma delas e depois, na outra. Caso as palavras fossem ordenadas corretamente, a mesma conseqüência anterior era apresentada, e a mesma configuração de palavras era reapresentada em posições diferentes na área de escolha. Caso a resposta fosse diferente da programada pela experimentadora, produzia um escurecimento na tela por 3s e uma nova configuração de palavras era apresentada, lado a lado na área de escolha. Após o ensino da linha de base, testes de produção de seqüências e de conectividade eram aplicados para verificar a emergência de seis novas sentenças (exceto Estudo 1), a partir da recombinação das palavras ensinadas anteriormente. Finalmente, um teste de compreensão de leitura com novas frases era apresentado aos participantes. Por exemplo, na presença de uma figura, três sentenças diferentes em letras maiúsculas eram apresentadas e o participante deveria selecionar qual a sentença correta. Em todos os estudos, os participantes alcançaram o critério de acerto, três vezes consecutivas, sem erro, embora alguns tenham precisado de re-exposições. No Estudo 1 e 2 todos os participantes responderam consistentemente aos testes e leram as novas sentenças fluentemente e com compreensão. No Estudo 3, um participante construiu as seis novas sentenças prontamente. Nenhum participante leu com compreensão aos testes finais de leitura. No Estudo 4, três participantes construíram duas novas sentenças prontamente e um participante não respondeu aos testes de conectividade. Dois participantes responderam aos testes de leitura com compreensão. No Estudo 5 dois participantes construíram quatro novas sentenças prontamente. Nos Estudos 3 e 5 os participantes não responderam aos testes de nomeação oral. Estes resultados demonstraram a emergência de novas sentenças, sem qualquer treino adicional, a partir do ensino com três sentenças independentes. Os resultados dos testes de leitura com compreensão mostraram uma coerência com o paradigma de equivalência. Conclui-se que os estímulos utilizados eram funcionalmente equivalentes e exerceram ainda funções ordinais pela posição que cada um ocupou nas sentenças.

Digit Ratio (2D:4D), Aggression, and Testosterone in Men Exposed to an Aggressive Video Stimulus

The relative lengths of the 2nd and 4th digits (2D:4D) is a negative biomarker for prenatal testosterone, and low 2D:4D may be associated with aggression. However, the evidence for a 2D:4D-aggression association is mixed. Here we test the hypothesis that 2D:4D is robustly linked to aggression in challenge situations in which testosterone is increased. Participants were exposed to an aggressive video and a control video. Aggression was measured after each video and salivary free testosterone levels before and after each video. Compared to the control video, the aggressive video was associated with raised aggression responses and a marginally significant increase in testosterone. Left 2D:4D was negatively correlated with aggression after the aggressive video and the strength of the correlation was higher in those participants who showed the greatest increases in testosterone. Left 2D:4D was also negatively correlated to the difference between aggression scores in the aggressive and control conditions. The control video did not influence testosterone concentrations and there were no associations between 2D:4D and aggression. We conclude that 2D:4D moderates the impact of an aggressive stimulus on aggression, such that an increase in testosterone resulting from a challenge is associated with a negative correlation between 2D:4D and aggression.

Padrões de busca e uso de artigos científicos: um estudo com pós-graduandos em educação brasileiros

This article presents part of a larger study on the use of reference sources to perform bibliographical search by graduate students in Education. Data relating to the use of the scientific journals by these students are presented and discussed. Sixty Education graduate students, 28 Master degree and 32 Doctoral, answered an electronic questionnaire. The students indicated the types of articles usually read and the importance attributed to each one. For each of treated themes in the electronic questionnaire, data are initially presented and analyzed in the set of the 60 participants of the study and then compared between master and doctoral students. Were used the Chi-squared (?2) test, the Fisher exact test and the Spearman’s correlation coefficient. Research reports were more frequently pointed out but less valued in comparison to articles referring to critical review and theoretical essay. Methodological articles, appearing in fourth position according to reading frequency and importance attributed, are more valued by doctoral than master students. The students read these articles using different procedures. The possible reasons for the students valorizing the articles of critical review and theoretical essays are discussed. The present study intends to offer a contribution to understand the use of scientific information by students, describing some graduate students’ habits related to information seeking in scientific journals, and reading of the articles published.

Narrow-band search of continuous gravitational-wave signals from Crab and Vela pulsars in Virgo VSR4 data

In this paper we present the results of a coherent narrow-band search for continuous gravitational-wave signals from the Crab and Vela pulsars conducted on Virgo VSR4 data. In order to take into account a possible small mismatch between the gravitational-wave frequency and two times the star rotation frequency, inferred from measurement of the electromagnetic pulse rate, a range of 0.02 Hz around two times the star rotational frequency has been searched for both the pulsars. No evidence for a signal has been found and 95% confidence level upper limits have been computed assuming both that polarization parameters are completely unknown and that they are known with some uncertainty, as derived from x-ray observations of the pulsar wind torii. For Vela the upper limits are comparable to the spin-down limit, computed assuming that all the observed spin-down is due to the emission of gravitational waves. For Crab the upper limits are about a factor of 2 below the spin-down limit, and represent a significant improvement with respect to past analysis. This is the first time the spin-down limit is significantly overcome in a narrow-band search.