Polytechnic University of Valencia

About: Polytechnic University of Valencia is a education organization based out in Valencia, Spain. It is known for research contribution in the topics: Catalysis & Population. The organization has 16282 authors who have published 40162 publications receiving 850234 citations.

Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research

Abstract: Summary: We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. Availability: Blast2GO is freely available via Java Web Start at http://www.blast2go.de Supplementary material:http://www.blast2go.de -> Evaluation Contact:[email protected]; [email protected]

From Microporous to Mesoporous Molecular-Sieve Materials and Their Use in Catalysis

Abstract: It is possible to say that zeolites are the most widely used catalysts in industry They are crystalline microporous materials which have become extremely successful as catalysts for oil refining, petrochemistry, and organic synthesis in the production of fine and speciality chemicals, particularly when dealing with molecules having kinetic diameters below 10 A The reason for their success in catalysis is related to the following specific features of these materials:1 (1) They have very high surface area and adsorption capacity (2) The adsorption properties of the zeolites can be controlled, and they can be varied from hydrophobic to hydrophilic type materials (3) Active sites, such as acid sites for instance, can be generated in the framework and their strength and concentration can be tailored for a particular application (4) The sizes of their channels and cavities are in the range typical for many molecules of interest (5-12 A), and the strong electric fields2 existing in those micropores together with an electronic confinement of the guest molecules3 are responsible for a preactivation of the reactants (5) Their intricate channel structure allows the zeolites to present different types of shape selectivity, ie, product, reactant, and transition state, which can be used to direct a given catalytic reaction toward the desired product avoiding undesired side reactions (6) All of these properties of zeolites, which are of paramount importance in catalysis and make them attractive choices for the types of processes listed above, are ultimately dependent on the thermal and hydrothermal stability of these materials In the case of zeolites, they can be activated to produce very stable materials not just resistant to heat and steam but also to chemical attacks Avelino Corma Canos was born in Moncofar, Spain, in 1951 He studied chemistry at the Universidad de Valencia (1967−1973) and received his PhD at the Universidad Complutense de Madrid in 1976 He became director of the Instituto de Tecnologia Quimica (UPV-CSIC) at the Universidad Politecnica de Valencia in 1990 His current research field is zeolites as catalysts, covering aspects of synthesis, characterization and reactivity in acid−base and redox catalysis A Corma has written about 250 articles on these subjects in international journals, three books, and a number of reviews and book chapters He is a member of the Editorial Board of Zeolites, Catalysis Review Science and Engineering, Catalysis Letters, Applied Catalysis, Journal of Molecular Catalysis, Research Trends, CaTTech, and Journal of the Chemical Society, Chemical Communications A Corma is coauthor of 20 patents, five of them being for commercial applications He has been awarded with the Dupont Award on new materials (1995), and the Spanish National Award “Leonardo Torres Quevedo” on Technology Research (1996) 2373 Chem Rev 1997, 97, 2373−2419

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagy-related protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Chemical Routes for the Transformation of Biomass into Chemicals

Abstract: 3.2.3. Hydroformylation 2467 3.2.4. Dimerization 2468 3.2.5. Oxidative Cleavage and Ozonolysis 2469 3.2.6. Metathesis 2470 4. Terpenes 2472 4.1. Pinene 2472 4.1.1. Isomerization: R-Pinene 2472 4.1.2. Epoxidation of R-Pinene 2475 4.1.3. Isomerization of R-Pinene Oxide 2477 4.1.4. Hydration of R-Pinene: R-Terpineol 2478 4.1.5. Dehydroisomerization 2479 4.2. Limonene 2480 4.2.1. Isomerization 2480 4.2.2. Epoxidation: Limonene Oxide 2480 4.2.3. Isomerization of Limonene Oxide 2481 4.2.4. Dehydroisomerization of Limonene and Terpenes To Produce Cymene 2481

High-throughput functional annotation and data mining with the Blast2GO suite.

Abstract: Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.