IDconverter and IDClight: Conversion and annotation of gene and protein IDs

Background: Researchers involved in the annotation of large numbers of gene, clone or protein identifiers are usually required to perform a one-by-one conversion for each identifier. When the field of research is one such as microarray experiments, this number may be around 30,000. Results: To help researchers map accession numbers and identifiers among clones, genes, proteins and chromosomal positions, we have designed and developed IDconverter and IDClight. They are two user-friendly, freely available web server applications that also provide additional functional information by mapping the identifiers on to pathways, Gene Ontology terms, and literature references. Both tools are high-throughput oriented and include identifiers for the most common genomic databases. These tools have been compared to other similar tools, showing that they are among the fastest and the most up-to-date. Conclusion: These tools provide a fast and intuitive way of enriching the information coming out of high-throughput experiments like microarrays. They can be valuable both to wet-lab researchers and to bioinformaticiansFunding has been provided by Fundación de Investigatión Médica Mutua Madrileña and Project TIC2003-09331-C02-02 of the Spanish Ministry of Education and Science (MEC). RD-U is partially supported by the Ramón y Cajal programme of the Spanish ME

Pedagogical Content Knowledge Development in the case of the electric charge teaching in high school from classroom practice

La intención de este artículo es abordar las aportaciones más significativas sobre el desarrollo del conocimiento didáctico del contenido (CDC) para la enseñanza de las ciencias y de la física. Presentamos resultados generales de un estudio descriptivo de tipo cualitativo, en el que analizamos a través de un estudio de caso, el desarrollo del CDC sobre la carga eléctrica de un profesor de física colombiano de bachillerato con formación inicial en didáctica de la física. Las categorías consideradas fueron: orientaciones hacia la enseñanza de las ciencias, conocimiento sobre el currículo, conocimiento sobre los estudiantes, conocimiento sobre la evaluación y conocimiento sobre las estrategias de enseñanza. Para la caracterización de cada componente se consideraron los datos analizados a través de Nvivo-10, y las descripciones dadas a estas componentes desde los modelos de enseñanza en didáctica de las ciencias experimentales. Los resultados que presentamos, muestran que a diferencia de las orientaciones sobre la enseñanza de las ciencias, en sus categorías idea de física y carga eléctrica, las tendencias que describen mayoritariamente el resto de componente del CDC no evidencia cambios significativos después de la intervención.The intent of this article is to approach the significant contributions on the development of pedagogical content knowledge (PCK) in science and physics teaching. We present general results of a qualitative study, which we analyzed through a case study, the development of PCK on the electric charge of a Colombian High School Physics Teacher. He has basic training in physics education. The categories were: orientations toward science teaching, knowledge of curriculum, knowledge about students, knowledge on assessment and knowledge of teaching strategies. For the description of each component, we use Nvivo-10, and the descriptions given to these components from teaching models. The results show that the PCK in action is increasingly drawn to the extent that the teacher acquires more confidence and understanding of the content he teaches, and reviews his teaching practices, plans or creates new forms of teaching performance. However, there is no direct causal effect between changes in the orientation component and teaching strategies and objective.The intent of this article is to approach the significant contributions on the development of pedagogical content knowledge (PCK) in science and physics teaching. We present general results of a qualitative study, which we analyzed through a case study, the development of PCK on the electric charge of a Colombian High School Physics Teacher. He has basic training in physics education. The categories were: orientations toward science teaching, knowledge of curriculum, knowledge about students, knowledge on assessment and knowledge of teaching strategies. For the description of each component, we use Nvivo-10, and the descriptions given to these components from teaching models. The results show that the PCK in action is increasingly drawn to the extent that the teacher acquires more confidence and understanding of the content he teaches, and reviews his teaching practices, plans or creates new forms of teaching performance. However, there is no direct causal effect between changes in the orientation component and teaching strategies and objective

Pedagogical content knowledge development in the case of the electric charge teaching in high school from classroom practice

La intención de este artículo es abordar las aportaciones más significativas sobre el desarrollo del conocimiento didáctico del contenido (CDC) para la enseñanza de las ciencias y de la física. Presentamos resultados generales de un estudio descriptivo de tipo cualitativo, en el que analizamos a través de un estudio de caso, el desarrollo del CDC sobre la carga eléctrica de un profesor de física colombiano de bachillerato con formación inicial en didáctica de la física. Las categorías consideradas fueron: orientaciones hacia la enseñanza de las ciencias, conocimiento sobre el currículo, conocimiento sobre los estudiantes, conocimiento sobre la evaluación y conocimiento sobre las estrategias de enseñanza. Para la caracterización de cada componente se consideraron los datos analizados a través de Nvivo-10, y las descripciones dadas a estas componentes desde los modelos de enseñanza en didáctica de las ciencias experimentales. Los resultados que presentamos, muestran que a diferencia de las orientaciones sobre la enseñanza de las ciencias, en sus categorías idea de física y carga eléctrica, las tendencias que describen mayoritariamente el resto de componente del CDC no evidencia cambios significativos después de la intervención.The intent of this article is to approach the significant contributions on the development of pedagogical content knowledge (PCK) in science and physics teaching. We present general results of a qualitative study, which we analyzed through a case study, the development of PCK on the electric charge of a Colombian High School Physics Teacher. He has basic training in physics education. The categories were: orientations toward science teaching, knowledge of curriculum, knowledge about students, knowledge on assessment and knowledge of teaching strategies. For the description of each component, we use Nvivo-10, and the descriptions given to these components from teaching models. The results show that the PCK in action is increasingly drawn to the extent that the teacher acquires more confidence and understanding of the content he teaches, and reviews his teaching practices, plans or creates new forms of teaching performance. However, there is no direct causal effect between changes in the orientation component and teaching strategies and objective.Trabajo patrocinado por: Ministerio de Economía y Competitividad. Proyecto: EDU2012-34140 Gobierno de Extremadura y Fondos FEDER. Proyecto GR15009 Universidad de Extremadura. Beca Predoctoral para Lina Viviana Melo NiñopeerReviewe

Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite

Asterias (http://www.asterias.info) is an open-source, web-based, suite for the analysis of gene expression and aCGH data. Asterias implements validated statistical methods, and most of the applications use parallel computing, which permits taking advantage of multicore CPUs and computing clusters. Access to, and further analysis of, additional biological information and annotations (PubMed references, Gene Ontology terms, KEGG and Reactome pathways) are available either for individual genes (from clickable links in tables and figures) or sets of genes. These applications cover from array normalization to imputation and preprocessing, differential gene expression analysis, class and survival prediction and aCGH analysis. The source code is available, allowing for extention and reuse of the software. The links and analysis of additional functional information, parallelization of computation and open-source availability of the code make Asterias a unique suite that can exploit features specific to web-based environments

Asterias: A Parallelized Web-based Suite for the Analysis of Expression and aCGH Data

The analysis of expression and CGH arrays plays a central role in the study of complex diseases, especially cancer, including finding markers for early diagnosis and prognosis, choosing an optimal therapy, or increasing our understanding of cancer development and metastasis. Asterias (http://www.asterias.info) is an integrated collection of freely-accessible web tools for the analysis of gene expression and aCGH data. Most of the tools use parallel computing (via MPI) and run on a server with 60 CPUs for computation; compared to a desktop or server-based but not parallelized application, parallelization provides speed ups of factors up to 50. Most of our applications allow the user to obtain additional information for user-selected genes (chromosomal location, PubMed ids, Gene Ontology terms, etc.) by using clickable links in tables and/or figures. Our tools include: normalization of expression and aCGH data (DNMAD); converting between different types of gene/clone and protein identifiers (IDconverter/IDClight); filtering and imputation (preP); finding differentially expressed genes related to patient class and survival data (Pomelo II); searching for models of class prediction (Tnasas); using random forests to search for minimal models for class prediction or for large subsets of genes with predictive capacity (GeneSrF); searching for molecular signatures and predictive genes with survival data (SignS); detecting regions of genomic DNA gain or loss (ADaCGH). The capability to send results between different applications, access to additional functional information, and parallelized computation make our suite unique and exploit features only available to web-based applications

Conhecimento didático de conteúdo declarado para o Ensino da Força Elétrica na Escola: Um Estudo de Caso

The study analyzes the characterization of pedagogical content knowledge (pck) of a Colombianhigh school physics teacher about the electric force, before and after of an intervention program.The coding scheme was: orientations to science teaching; knowledge of the curriculum; knowledgeof pupils’ understanding of science; knowledge of evaluation, and knowledge of representations andinstructional strategies. The results show that during the two years, there were disagreements betweenideas about teaching and learning of physics, the knowledge of the curriculum and evaluation, whichinfluence the teacher’s instructional strategies. As result, his teaching shows a more teacher-centeredteaching. Finally, the logic that articulates the class’ content does not consider the teacher’s reflectionson the needs and difficulties of his students on the learning of the electric force.El estudio analiza el conocimiento didáctico del contenido (cdc) que un profesorcolombiano de física, que enseña en bachillerato, declara sobre el concepto defuerza eléctrica antes y después de un programa de intervención basado en lareflexión. Las categorías consideradas fueron: orientaciones hacia la enseñanzade las ciencias, conocimiento sobre el currículo, conocimiento de los estudiantes,conocimiento sobre las estrategias de enseñanza y conocimiento sobre la evaluación.Los resultados muestran que durante los dos años de la investigación, existendesacuerdos entre las ideas sobre la enseñanza y el aprendizaje de la física, elconocimiento curricular y la evaluación, los cuales condicionan fuertemente lasestrategias de enseñanza que utiliza el profesor. Por consiguiente, su instrucciónmuestra una enseñanza más centrada en el profesor. Finalmente, la lógica quearticula la proposición de los contenidos no tiene en cuenta las reflexiones que elprofesor ha realizado sobre las necesidades y dificultades de sus estudiantes conrespecto al aprendizaje de la fuerza eléctrica.O estudo analisa o conhecimento didático do conteúdo (cdc) de um professor de física do ensinomédio de Colômbia, sobre o conceito de força elétrica antes e após um programa de intervenção combase na reflexão. As categorias consideradas foram: orientações para o ensino de ciência, o conhecimentocurricular, o conhecimento dos alunos, o conhecimento sobre estratégias de ensino e oconhecimento sobre avaliação. Os resultados mostram que durante os dois anos da pesquisa, hádivergências entre as ideias sobre o ensino e a aprendizagem da física e o conhecimento curriculare avaliação, que influenciam fortemente as estratégias de ensino utilizadas pelo professor. Em consequênciaseu método de ensino mostra-se mais centrado no professor. Finalmente, a lógica quearticula a colocação de conteúdos, não considera as reflexões que o professor tem realizado emrelação às necessidades e dificuldades dos seus alunos ao respeito da força elétrica

A glucotolerant β-glucosidase from the fungus Talaromyces amestolkiae and its conversion into a glycosynthase for glycosylation of phenolic compounds

The interest for finding novel β-glucosidases that can improve the yields to produce second-generation (2G) biofuels is still very high. One of the most desired features for these enzymes is glucose tolerance, which enables their optimal activity under high-glucose concentrations. Besides, there is an additional focus of attention on finding novel enzymatic alternatives for glycoside synthesis, for which a mutated version of glycosidases, named glycosynthases, has gained much interest in recent years. Results In this work, a glucotolerant β-glucosidase (BGL-1) from the ascomycete fungus Talaromyces amestolkiae has been heterologously expressed in Pichia pastoris, purified, and characterized. The enzyme showed good efficiency on p-nitrophenyl glucopyranoside (pNPG) (Km= 3.36 ± 0.7 mM, kcat= 898.31 s−1), but its activity on cellooligosaccharides, the natural substrates of these enzymes, was much lower, which could limit its exploitation in lignocellulose degradation applications. Interestingly, when examining the substrate specificity of BGL-1, it showed to be more active on sophorose, the β-1,2 disaccharide of glucose, than on cellobiose. Besides, the transglycosylation profile of BGL-1 was examined, and, for expanding its synthetic capacities, it was converted into a glycosynthase. The mutant enzyme, named BGL-1-E521G, was able to use α-d-glucosyl-fluoride as donor in glycosylation reactions, and synthesized glucosylated derivatives of different pNP-sugars in a regioselective manner, as well as of some phenolic compounds of industrial interest, such as epigallocatechin gallate (EGCG). Conclusions In this work, we report the characterization of a novel glucotolerant 1,2-β-glucosidase, which also has a considerable activity on 1,4-β-glucosyl bonds, that has been cloned in P. pastoris, produced, purified and characterized. In addition, the enzyme was converted into an efficient glycosynthase, able to transfer glucose molecules to a diversity of acceptors for obtaining compounds of interest. The remarkable capacities of BGL-1 and its glycosynthase mutant, both in hydrolysis and synthesis, suggest that it could be an interesting tool for biotechnological applications

Identification of a New HIV-1 BC Intersubtype Circulating Recombinant Form (CRF108_BC) in Spain.

The extraordinary genetic variability of human immunodeficiency virus type 1 (HIV-1) group M has led to the identification of 10 subtypes, 102 circulating recombinant forms (CRFs) and numerous unique recombinant forms. Among CRFs, 11 derived from subtypes B and C have been identified in China, Brazil, and Italy. Here we identify a new HIV-1 CRF_BC in Northern Spain. Originally, a phylogenetic cluster of 15 viruses of subtype C in protease-reverse transcriptase was identified in an HIV-1 molecular surveillance study in Spain, most of them from individuals from the Basque Country and heterosexually transmitted. Analyses of near full-length genome sequences from six viruses from three cities revealed that they were BC recombinant with coincident mosaic structures different from known CRFs. This allowed the definition of a new HIV-1 CRF designated CRF108_BC, whose genome is predominantly of subtype C, with four short subtype B fragments. Phylogenetic analyses with database sequences supported a Brazilian ancestry of the parental subtype C strain. Coalescent Bayesian analyses estimated the most recent common ancestor of CRF108_BC in the city of Vitoria, Basque Country, around 2000. CRF108_BC is the first CRF_BC identified in Spain and the second in Europe, after CRF60_BC, both phylogenetically related to Brazilian subtype C strains.This work was funded through Acción Estratégica en Salud Intramural (AESI), Instituto de Salud Carlos III, projects “Estudios sobre vigilancia epidemiológica molecular del VIH- 1 en España,” PI16CIII/00033, and “Epidemiología molecular del VIH-1 en España y su utilidad para investigaciones biológicas y en vacunas”, PI19CIII/00042; Red de Investigación en SIDA (RIS), Instituto de Salud Carlos III, Subdirección General de Evaluación y Fondo Europeo de Desarrollo Regional (FEDER), Plan Nacional I + D + I, project RD16ISCIII/0002/0004; and scientific agreement with Osakidetza-Servicio Vasco de Salud, Government of Basque Country, MVI 1001/16. JC was supported by the Social European Fund through the Youth Employment Operational Program and the Youth Employment Initiative and by the Comunidad de Madrid.S

Serum Phospholipids Fatty Acids and Breast Cancer Risk by Pathological Subtype

This study evaluates whether serum phospholipids fatty acids (PL-FAs) and markers of their endogenous metabolism are associated with breast cancer (BC) subtypes. EpiGEICAM is a Spanish multicenter matched case-control study. A lifestyle and food frequency questionnaire was completed by 1017 BC cases and healthy women pairs. Serum PL-FA percentages were measured by gas chromatography-mass spectrometry. Conditional and multinomial logistic regression models were used to quantify the association of PL-FA tertiles with BC risk, overall and by pathological subtype (luminal, HER2+ and triple negative). Stratified analyses by body mass index and menopausal status were also performed. Serum PL-FAs were measured in 795 (78%) pairs. Women with high serum levels of stearic acid (odds ratio (OR)T3vsT1 = 0.44; 95% confidence interval (CI) = 0.30-0.66), linoleic acid (ORT3vsT1 = 0.66; 95% CI = 0.49-0.90) and arachidonic to dihomo-γ-linolenic acid ratio (OR T3vsT1 = 0.64; 95% CI = 0.48-0.84) presented lower BC risk. Participants with high concentrations of palmitoleic acid (ORT3vsT1 = 1.65; 95% CI = 1.20-2.26), trans-ruminant palmitelaidic acid (ORT3vsT1 = 1.51; 95% CI = 1.12-2.02), trans-industrial elaidic acid (ORT3vsT1 = 1.52; 95% CI = 1.14-2.03), and high oleic to stearic acid ratio (ORT3vsT1 = 2.04; 95% CI = 1.45-2.87) showed higher risk. These associations were similar in all BC pathological subtypes. Our results emphasize the importance of analyzing fatty acids individually, as well as the desaturase activity indices

A Fungal Versatile GH10 Endoxylanase and Its Glycosynthase Variant: Synthesis of Xylooligosaccharides and Glycosides of Bioactive Phenolic Compounds

The study of endoxylanases as catalysts to valorize hemicellulosic residues and to obtain glycosides with improved properties is a topic of great industrial interest. In this work, a GH10 β-1,4-endoxylanase (XynSOS), from the ascomycetous fungus Talaromyces amestolkiae, has been het- erologously produced in Pichia pastoris, purified, and characterized. rXynSOS is a highly glycosylated monomeric enzyme of 53 kDa that contains a functional CBM1 domain and shows its optimal activity on azurine cross-linked (AZCL)–beechwood xylan at 70 ◦C and pH 5. Substrate specificity and kinetic studies confirmed its versatility and high affinity for beechwood xylan and wheat arabi- noxylan. Moreover, rXynSOS was capable of transglycosylating phenolic compounds, although with low efficiencies. For expanding its synthetic capacity, a glycosynthase variant of rXynSOS was developed by directed mutagenesis, replacing its nucleophile catalytic residue E236 by a glycine (rXynSOS-E236G). This novel glycosynthase was able to synthesize β-1,4-xylooligosaccharides (XOS) of different lengths (four, six, eight, and ten xylose units), which are known to be emerging prebiotics. rXynSOS-E236G was also much more active than the native enzyme in the glycosylation of a broad range of phenolic compounds with antioxidant properties. The interesting capabilities of rXynSOS and its glycosynthase variant make them promising tools for biotechnological application.This research was funded by the MICIU/AEI/FEDER [RTI2018-093683-B-I00, RTI2018- 094751-B-C22, PID2019-107476GB-I00], Comunidad de Madrid [RETOPROSOST-2-CM P2018/EMT- 4459], and CIBERES (an initiative from the Spanish Institute of Health Carlos IPeer reviewe