Search results for "Computation"
showing 10 items of 7362 documents
Major orchestration of shikimate, early phenylpropanoid and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine
2021
AbstractThe stilbenoid pathway is responsible for the production of resveratrol and its derivatives in grapevine. A few transcription factors (TFs) have been previously identified as regulators of this pathway but the extent of this control is yet to be fully understood. Here we demonstrate how DNA affinity purification sequencing (DAP-Seq) allows for genome-wide TF binding site interrogation in a non-model species. We obtained 5,190 and 4,443 binding events assigned to 4,041 and 3,626 genes for MYB14 and MYB15, respectively (around 40% of peaks being located within -10kb of transcription start sites). DAP-Seq of MYB14 and MYB15 was combined with aggregate gene centred co-expression network…
On Transition Structures for Hydride Transfer Step in Enzyme Catalysis. A Comparative Study on Models of Glutathione Reductase Derived from Semiempir…
1996
As a model of the chemical reactions that take place in the active site of gluthatione reductase, the nature of the molecular mechanism for the hydride transfer step has been characterized by means of accurate quantum chemical characterizations of transition structures. The calculations have been carried out with analytical gradients at AM1 and PM3 semiempirical procedures, ab initio at HF level with 3-21G, 4-31G, 6-31G, and 6-31G basis sets and BP86 and BLYP as density functional methods. The results of this study suggest that the endo relative orientation on the substrate imposed by the active site is optimal in polarizing the C4-Ht bond and situating the system in the neighborhood of the…
Laboratori virtual d'ensenyament-aprenentatge: solució numèrica de les equacions de conservació mitjançant volums finits aplicades a superfícies este…
2014
En este treball es presenta el disseny d’un Laboratori virtual d’ensenyament-aprenentatge per a la resolució d’un problema model de Transferència de la Calor en la matèria d’Enginyeria Tèrmica del II curs del Grau d’Enginyer de Tecnologies Industrials de la Universidad Rey Juan Carlos de Madrid. En l’àmbit de la Dinàmica de Fluids Computacional i per mitjà de l’ús del programari de simulació d’Ansys Fluent s’introduïx l’alumne al disseny, modelatge del sistema, resolució, anàlisi i validació del model. El resultat d’esta experiència d’aprenentatge és no sols la mera resolució del problema, inabordable amb mètodes didàctics tradicionals, sinó el desenvolupament de la combinació de destreses,…
Immunological Methods for Analysis of Recombinant Proteins
1998
We want to introduce researchers to techniques that help to solve some problems in the work of the molecular biologist. After transformation of recombinant DNA in E. coli cells many clones are usually produced, and the same situation appears if recombinant DNA expression libraries are available. Furthermore, if appropriate monoclonal or polyclonal antibodies are available, the method of immunoscreening of colonies for direct immunological detection of translational products of cloned genes can be used. Selected clones could be chosen for further studies such as determination of their primary structure by DNA sequencing and for characterization of an appropriate expressed protein.
On the satisfiability problem for fragments of two-variable logic with one transitive relation
2019
Abstract We study the satisfiability problem for two-variable first-order logic over structures with one transitive relation. We show that the problem is decidable in 2-NExpTime for the fragment consisting of formulas where existential quantifiers are guarded by transitive atoms. As this fragment enjoys neither the finite model property nor the tree model property, to show decidability we introduce a novel model construction technique based on the infinite Ramsey theorem. We also point out why the technique is not sufficient to obtain decidability for the full two-variable logic with one transitive relation; hence, contrary to our previous claim, [FO$^2$ with one transitive relation is deci…
A generalized transitive closure for relational queries
1988
We augment relational algebra with a generalized transitive closure operator that allows for the efficient evaluation of a subclass of recursive queries. The operator is based on a composition operator which is as general as possible when the operator is required to be associative and when only relational algebra operators are used in its definition. The closure of such a composition can be computed using the well-known efficient algorithms designed for the computation of the usual transitive closure. Besides the case in which complete materialization of recursive relations are required, our strategy also yields an efficient solution in the case in which a selection is applied to the closur…
Automatic Extraction of Semantic Roles in Support Verb Constructions
2021
This paper deals with paraphrastic relations in Italian. In the following sentences: (a) Max strappò delle lacrime a Sara 'Max moved Sara to tears' and (b) Max fece piangere Sara 'Max made Sara cry', the verbs differ syntactically and semantically. Strappare 'tear/rip/wring' is transitive, fare ‘have/make’ is a causative, and piangere 'cry' is intransitive. Despite this, a translation of (a) as (b) is legitimate and therefore (a) is a paraphrase of (b). In theoretical linguistics this raises an issue concerning the relationship between strappare and fare/piangere in Italian, and that in English between move and make. In computational linguistics, can such paraphrases be obtained automatical…
Genomic Analysis of Bacterial Outbreaks
2016
The study of outbreaks of infectious diseases has been revolutionized by the current availability of fast and efficient, high-throughput methods capable of yielding the nucleotide sequence of complete genomes of viruses and bacteria within a few days, or even hours. These methods are replacing previous molecular techniques which have been used for the past 30 years, although many of them are still the usual approach for many such investigations. Here we review the major technologies currently in use for high-throughput sequencing of bacterial genomes emphasizing their advantages and drawbacks for the analysis of outbreaks. The use of more efficient methods does not necessarily mean that all…
TAF-ChIP: An ultra-low input approach for genome wide chromatin immunoprecipitation assay
2018
Chromatin immunoprecipitation (ChIP) followed by next generation sequencing is an invaluable and powerful technique to understand transcriptional regulation. However, ChIP is currently limited by the requirement of large amount of starting material. This renders studying rare cell populations very challenging, or even impossible. Here, we present a tagmentation-assisted fragmentation ChIP (TAF-ChIP) and sequencing method to generate high-quality datasets from low cell numbers. The method relies on Tn5 transposon activity to fragment the chromatin that is immunoprecipitated, thus circumventing the need for sonication or MNAse digestion to fragment. Furthermore, Tn5 adds the sequencing adapto…
Common genomic structure for the Lepidoptera cadherin-like genes.
2005
A cadherin-like protein present in the midgut epithelial cells of Lepidoptera is associated with insect resistance to Bacillus thuringiensis Cry toxins. We describe for the first time the genes that encode the cadherin-like proteins in Ostrinia nubilalis, Helicoverpa armigera, and Bombyx mori, and analyze their organization. These genes encompass 19.6 kb, 20.0 kb, and 41.8 kb of genomic DNA, respectively, and despite the size heterogeneity, they are all composed of 35 exons that are linked by 34 introns. In contrast to the high variability noted for the sizes of the introns, the sizes of the coding exons were almost completely preserved among the three species, because the intronic sequence…