CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. However, partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, we have developed the CLIPZ database and analysis environment. Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. Individual users can upload their own sequence data sets while being able to limit the access to these data to specific users, and analyses of the public and private data sets can be performed interactively. CLIPZ, available at http://www.clipz.unibas.ch, aims to provide an open access repository of information for post-transcriptional regulatory element

Study of hot deformation behavior of CuFe2 alloy

Nil strength temperature of 1062 degrees C and nil ductility temperature of 1040 degrees C were experimentally set for CuFe2 alloy. The highest formability at approx. 1020 degrees C is unusable due to massive grain coarsening. The local minimum of ductility around the temperature 910 degrees C is probably due to minor formation of gamma-iron. In the forming temperatures interval 650-950 degrees C and strain rate 0.1-10 s(-1) the flow stress curves were obtained and after their analysis hot deformation activation energy of 380 kJ.mol(-1) was achieved. Peak stress and corresponding peak strain values were mathematically described with good accuracy by equations depending on Zener-Hollomon parameter.Web of Science64270670

The Łojasiewicz exponent over a field of arbitrary characteristic

Let K be an algebraically closed field and let K((XQ)) denote the field of generalized series with coefficients in K. We propose definitions of the local Łojasiewicz exponent of F = ( f1, . . . , fm) ∈ K[[X, Y ]]m as well as of the Łojasiewicz exponent at infinity of F = ( f1, . . . , fm) ∈ K[X, Y ]m, which generalize the familiar case of K = C and F ∈ C{X, Y }m (resp. F ∈ C[X, Y ]m), see Cha˛dzy´nski and Krasi´nski (In: Singularities, 1988; In: Singularities, 1988; Ann Polon Math 67(3):297–301, 1997; Ann Polon Math 67(2):191–197, 1997), and prove some basic properties of such numbers. Namely, we show that in both cases the exponent is attained on a parametrization of a component of F (Theorems 6 and 7), thus being a rational number. To this end, we define the notion of the Łojasiewicz pseudoexponent of F ∈ (K((XQ))[Y ])m for which we give a description of all the generalized series that extract the pseudoexponent, in terms of their jets. In particular, we show that there exist only finitely many jets of generalized series giving the pseudoexponent of F (Theorem 5). The main tool in the proofs is the algebraic version of Newton’s Polygon Method. The results are illustrated with some explicit examples

MirZ: an integrated microRNA expression atlas and target prediction resource

MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation of a broad range of biological functions, from development to cardiac and immune system function, to metabolism, to cancer. For most of the over 500 miRNAs that are encoded in the human genome the functions still remain to be uncovered. Identifying miRNAs whose expression changes between cell types or between normal and pathological conditions is an important step towards characterizing their function as is the prediction of mRNAs that could be targeted by these miRNAs. To provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment, we developed the MirZ web server, which is accessible at www.mirz.unibas.ch. The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapien

Fósforo na cultura de girassol.

O objetivo deste trabalho foi avaliar os componentes da produção de girassol cultivado em sistema de semeadura direta, em resposta aos teores de fósforo (P) no solo. O híbrido de girassol Agrobel 960 foi semeado em fevereiro de 2009, em área de Latossolo Vermelho- Amarelo distrófico (LVAd), em experimento de longa duração conduzido em Ponta Grossa, PR. Durante a condução do experimento, as parcelas foram adubadas com 0; 60; 120; 240 e 480 kg ha-1 de P2O5, criando-se uma curva de resposta ao fósforo. No estádio de maturação fisiológica, avaliou-se a produtividade, o número de aquênios por capítulo, o peso de 1000 aquênios e a altura de planta. Os teores de fósforo no solo variaram significativamente em função das doses do nutriente aplicadas no solo. As respostas ao aumento dos teores de P no solo foram semelhantes para todas as variáveis avaliadas. A obtenção de 90 % da produção máxima de grãos foi conseguida quando o teor de P no solo foi de 8,2 mg dm-3. Esse teor de fósforo no solo pode ser considerado o nível crítico do nutriente em latossolos de origem sedimentar do Paraná, para o girassol cultivado na safrinha. Phosporus on sunflower crop. The aim of this study was to evaluate yield components of sunflower grown under notillage system, in response to phosphorus (P) in soil. Sunflower hybrid Agrobel 960 was sown in February 2009 in a dystrophic Typic Hapludoxin long-term experiment runned in Ponta Grossa, PR, Brazil. During the experiment, the plots were fertilized with 0, 60,120, 240 and 480 kg ha-1 P2O5, creating a response curve to phosphorus. At physiological maturity stage, we evaluated yield, number of achenes per head, 1000-seed weight and plant height. The levels of phosphorus in the soil varied significantly depending on the applied rates of the nutrient in the soil. All evaluated parameters present similar reponses to the increase of soil P levels. 90% of the maximum yield was achieved when the P content in soil was 8.2 mg dm-3. This phosphorus content in soil can be considered the critical level of nutrient in oxysols originating from sedimentary rocks in Parana State, for sunflower grown during off-season

Disponibilidade de níquel associada a características químicas e texturais de solos destinados ao cultivo de soja

O níquel (Ni) foi o último elemento inserido entre os micronutrientes de plantas, entretanto, poucos são os estudos sobre seu efeito na cultura da soja. Assim como para os demais nutrientes, a resposta da soja à adubação com este micronutriente está diretamente relacionada aos teores disponíveis no solo. O objetivo do trabalho foi correlacionar a disponibilidade de Ni com atributos químicos e físicos de solos representativos das principais regiões produtoras de soja no Brasil. Foi realizada a caracterização química e textural em oito amostras de solo coletadas na profundidade de 0-20 cm nos seguintes locais: Bahia, Goiás, Maranhão, Mato Grosso, Paraná (Londrina e Palotina) e Rio Grande do Sul (Campo Novo e Coxilha). Os teores de Ni disponíveis foram extraídos em DTPA e determinados por ICP-OES. Os teores de Ni variaram de <0,013 a 0,27 mg dm-3 e apresentaram correlação com os atributos texturais, bem como com os teores de potássio, cobre, manganês e boro

Tolerância de girassol (Helianthus annuus L.) ao alumínio.

O girassol é uma planta muito sensível à acidez do solo, não tolerando, de modo geral, saturação por alumínio (Al) trocável superior a 5 %. Nessas condições o desenvolvimento radicular é drasticamente afetado reduzindo a capacidade das plantas de explorar maior volume de solo, consequentemente de água e nutrientes. O objetivo deste trabalho foi avaliar a tolerância de genótipos de girassol a diferentes concentrações de alumínio. O experimento foi conduzido no Laboratório de Sementes da Embrapa Soja. Sementes de dez genótipos (Pioneer 6510, CF 101, Embrapa 122, BRS 323, BRS 322, V 70004, SYN 045, BRS G 32, HLA 211 CL e Catissol) foram embebidas com quatro doses de alumínio (0, 0,4, 0,8 e 1,2 mg dm-3 de Al), em papel de germinação, com três repetições. Foi avaliada a massa seca das raízes aos sete dias após a germinação. A massa seca das raízes dos genótipos de girassol foi afetada significativamente pelos teores de alumínio em solução. O método é capaz de separar os genótipos de girassol em função do desenvolvimento das raízes em diferentes concentrações de alumínio. SUNFLOWER (Helianthus annuus L.) TOLERANCE TO ALUMINUM. Sunflower is a very sensitive to soil acidity and cannot tolerate, in general, Al saturation greater than 5%. Under these conditions, root growth is affected drastically reducing the ability of plants to explore larger volume of soil, therefore water and nutrients. The aim of this study was to evaluate the tolerance of sunflower genotypes to different concentrations of aluminum. An experiment was carried out at the Seed Laboratory of Embrapa Soja. Seeds of ten sunflower genotypes (Pioneer 6510, CF 101, Embrapa 122, BRS 323, BRS 322, V 70004, SYN 045, BRS G 32, HLA 211 CL and Catissol) were soaked in germination paper with four doses of aluminum (0, 0.4, 0.8 and 1.2 mg dm-3 Al), with three replications. Dry weight of roots was evaluated at seven days after germination. Dry weight of roots of sunflower genotypes was significantly affected by levels of aluminum in solution. The method is able to separate sunflower genotypes by development of roots under different concentrations of aluminum