CR-EST: a resource for crop ESTs

The crop expressed sequence tag database, CR-EST (http://pgrc.ipk-gatersleben.de/cr-est/), is a publicly available online resource providing access to sequence, classification, clustering and annotation data of crop EST projects. CR-EST currently holds more than 200 000 sequences derived from 41 cDNA libraries of four species: barley, wheat, pea and potato. The barley section comprises approximately one-third of all publicly available ESTs. CR-EST deploys an automatic EST preparation pipeline that includes the identification of chimeric clones in order to transparently display the data quality. Sequences are clustered in species-specific projects to currently generate a non-redundant set of ∼22 600 consensus sequences and ∼17 200 singletons, which form the basis of the provided set of unigenes. A web application allows the user to compute BLAST alignments of query sequences against the CR-EST database, query data from Gene Ontology and metabolic pathway annotations and query sequence similarities from stored BLAST results. CR-EST also features interactive JAVA-based tools, allowing the visualization of open reading frames and the explorative analysis of Gene Ontology mappings applied to ESTs

Monitoramento hidrometeorológico em bacias rurais do Bioma Mata Atlântica.

Visando estabelecer estudos sobre a hidrologia de bacias com uso agrícola nas regiões tropicais, foram instaladas redes de instrumentação hidrometeorológica em duas bacias rurais. Caracterizadas por um mosaico de classes de cobertura e uso da terra, na Mata Atlântica Fluminense, as bacias são: a do córrego Pito Aceso, no Município de Bom Jardim, região Serrana Fluminense, e a bacia dos Rios Guapiaçu-Macacu, cuja drenagem tem sua foz na Baía de Guanabara. Os resultados obtidos no monitoramento provêm informações essenciais para parametrizar modelos simuladores de processos de fluxo de água e transporte de nutrientes e sedimentos. No projeto AgroHidro, a associação do monitoramento ao uso de modelos visa prover maior conhecimento dos processos de hidrologia em bacias, bem como de suas interações com os sistemas agrícolas

Context Dependence, MOPs,WHIMs and procedures Recanati and Kaplan on Cognitive Aspects in Semantics

After presenting Kripke’s criticism to Frege’s ideas on context dependence of thoughts, I present two recent attempts of considering cognitive aspects of context dependent expressions inside a truth conditional pragmatics or semantics: Recanati’s non-descriptive modes of presentation (MOPs) and Kaplan’s ways of having in mind (WHIMs). After analysing the two attempts and verifying which answers they should give to the problem discussed by Kripke, I suggest a possible interpretation of these attempts: to insert a procedural or algorithmic level in semantic representations of indexicals. That a function may be computed by different procedures might suggest new possibilities of integrating contextual cognitive aspects in model theoretic semanti

The Prenective View of Propositional Content

Beliefs have what I will call ‘propositional content’. A belief is always a belief that so-and-so: a belief that grass is green, or a belief that snow is white, or whatever. Other things have propositional content too, such as sentences, judgments and assertions. The Standard View amongst philosophers is that what it is to have a propositional content is to stand in an appropriate relation to a proposition. Moreover, on this view, propositions are objects, i.e. the kind of thing you can refer to with singular terms. For example, on the Standard View, we should parse the sentence ‘Simon believes that Sharon is funny’ as: [Simon] believes [that Sharon is funny]; ‘Simon’ is a term referring to a thinking subject, ‘that Sharon is funny’ is a term referring to a proposition, and ‘x believes y’ is a dyadic predicate expressing the believing relation. In this paper, I argue against the Standard View. This is how I think we should parse ‘Simon believes that Sharon is funny’: [Simon] believes that [Sharon is funny]; here we have a singular term, ‘Simon’, a sentence ‘Sharon is funny’, and a ‘prenective’ joining them together, ‘x believes that p’. On this Prenective View, we do not get at the propositional content of someone’s belief by referring to a reified proposition with a singular term; we simply use the sentence ‘Sharon is funny’ to express that content for ourselves. I argue for the Prenective View in large part by showing that an initially attractive version of the Standard View is actually vulnerable to the same objection that Wittgenstein used against Russell’s multiple-relation theory of judgment

Priority monism and part/whole dependence

Priority monism is the view that the cosmos is the only independent concrete object. The paper argues that, pace its proponents, Priority monism is in conflict with the dependence of any whole on any of its parts: if the cosmos does not depend on its parts, neither does any smaller composit

Unity through truth

Renewed worries about the unity of the proposition have been taken as a crucial stumbling block for any traditional conception of propositions. These worries are often framed in terms of how entities independent of mind and language can have truth conditions: why is the proposition that Desdemona loves Cassio true if and only if she loves him? I argue that the best understanding of these worries shows that they should be solved by our theory of truth and not our theory of content. Specifically, I propose a version of the redundancy theory according to which ‘it is true that Desdemona loves Cassio’ expresses the same proposition as ‘Desdemona loves Cassio’. Surprisingly, this variant of the redundancy theory treats ‘is true’ as an ordinary predicate of the language, thereby defusing many standard criticisms of the redundancy theory

Acquisition of myogenic specificity through replacement of one amino acid of MASH-1 and introduction of an additional α-helical turn

The homologous transcription factors Myf-5, MyoD, myogenin, MRF-4, and MASH-1 bind with high affinity and modest sequence specificity to DNA containing an E-box (CANNTG). This similarity of the in vitro DNA binding specificity is in sharp contrast to the high physiological specificity displayed by these proteins. Myf-5, MyoD, myogenin, and MRF-4 induce cells to differentiate along a myogenic pathway, while MASH-1 promotes the differentiation of neuronal precursor cells. We show here that MASH-1 can be converted into a protein capable of inducing myogenesis in fibroblasts by replacing leucine (130) of MASH-1 with lysine and introducing an additional turn into its basic recognition helix. These changes do not significantly alter the DNA binding properties of the proteins in cell free conditions. Crystallographic data for the DNA complexes of MyoD and E12 suggest that Leu (130) points away from the DNA into the solvent. We postulate that the identity of the amino acid in position 130 is important for protein-protein interactions that might affect the DNA binding specificities displayed by BHLH-proteins in vivo and form the molecular basis of the different physiological properties of the myogenic and neurogenic BHLH-proteins