Dissecting the sugarcane expressed sequence tag (SUCEST) database: unraveling flower-specific genes

There are almost 260,000 independent clones sequenced from the 5? end in the Sugarcane Expressed Sequence Tag (SUCEST) database, which have been obtained from 37 cDNA libraries prepared from different tissues. This large number of expressed sequence tags (ESTs) provides an opportunity, unprecedented in plants, to perform ?digital differential screening? on selected cDNA libraries. In general, the frequency of a particular EST correlates with transcript accumulation in the tissues from which the cDNA libraries were constructed, so it is possible to compare the whole transcriptome from different tissues using computer-assisted analysis of an EST database. In our research we analyzed sugarcane ESTs according to tissue expression and identified more than 1,000 putative flower-specific genes. The fact that using this technique we were able to identify sugarcane homologues of several genes previously described as pollen-specific justifies this method of assessing tissue specificity. In addition, ESTs similar to genes specific to reproductive organs were detected e.g. a sugarcane gene encoding a meiotic protein essential for assembly of the synaptonemal complex and normal synapsis. This approach also allowed the identification of many flower-specific anonymous sequences that are good candidates for being novel genes involved in plant reproduction. This paper describes the analysis of the gene expression levels of 24 EST clusters during flower development using a ?digital northern blot? constructed from direct EST counts made on the non-normalized sugarcane cDNA libraries.Existem quase 260.000 clones independentes, seqüenciados a partir da extremidade 5?, no banco de dados do SUCEST (Sugarcane Expressed Sequence Tag), os quais foram obtidos a partir de 37 bibliotecas de cDNA preparadas de diferentes tecidos. Este grande número de etiquetas de sequências expressas (ESTs) fornece uma oportunidade, sem precedentes em plantas, de realizar um ?digital differential screening? em bibliotecas de cDNA selecionadas. Geralmente, a frequência de um determinado EST está correlacionada ao acúmulo de transcritos nos tecidos dos quais as bibliotecas de cDNA foram construídas, e desta forma, é possível comparar o transcriptoma completo de diferentes tecidos, usando uma análise computacional de um banco de dados de ESTs. Em nossa pesquisa, analisamos os ESTs de cana-de-açúcar de acordo com sua expressão tecidual e identificamos mais de 1.000 putativos genes específicos de flor. O fato de que usando esta técnica fomos capazes de identificar homológos em cana-de-açúcar, de vários genes previamente descritos como específicos de pólen, sustenta este método de estimar especificidade tecidual. Além disto, ESTs com similaridade a genes específicos de órgãos reprodutivos foram revelados, como por exemplo, o gene que codifica uma proteína meiótica essencial para a montagem do complexo sinaptonêmico e sinapse normal. Esta abordagem também permitiu a identificação de muitas sequências anônimas, específicas de flor, que são boas candidatas para novos genes envolvidos com a reprodução de plantas. Este trabalho descreve a análise dos níveis de expressão gênica de 24 clusters de ESTs, durante o desenvolvimento floral, usando um ?northern blot digital? construído a partir da contagem direta dos ESTs das bibliotecas não-normalizadas de cDNAs de cana-de-açúcar.7784Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Weak Localization Effect in Superconductors by Radiation Damage

Large reductions of the superconducting transition temperature $T_{c}$ and the accompanying loss of the thermal electrical resistivity (electron-phonon interaction) due to radiation damage have been observed for several A15 compounds, Chevrel phase and Ternary superconductors, and $\rm{NbSe_{2}}$ in the high fluence regime. We examine these behaviors based on the recent theory of weak localization effect in superconductors. We find a good fitting to the experimental data. In particular, weak localization correction to the phonon-mediated interaction is derived from the density correlation function. It is shown that weak localization has a strong influence on both the phonon-mediated interaction and the electron-phonon interaction, which leads to the universal correlation of $T_{c}$ and resistance ratio.Comment: 16 pages plus 3 figures, revtex, 76 references, For more information, Plesse see http://www.fen.bilkent.edu.tr/~yjki

Response to “Comment on ‘optimal exposure biomarkers for nonpersistent chemicals in environmental epidemiology’”

We appreciate the opportunity to respond to the letter from Stahlhut et al. regarding our Brief Communication. We stressed the importance of biospecimen integrity and the potential danger of unrecognized contamination of convenience samples, particularly with ubiquitous environmental chemicals such as bisphenol A (BPA) and phthalates

The 2009 edition of the GEISA spectroscopic database

The updated 2009 edition of the spectroscopic database GEISA (Gestionet Etudedes Informations Spectroscopiques Atmospheriques ; Management and Study of Atmospheric Spectroscopic Information) is described in this paper. GEISA is a computer-accessible system comprising three independent sub-databases devoted, respectively, to: line parameters, infrared and ultraviolet/visible absorption cross-sections, microphysical and optical properties of atmospheric aerosols. In this edition, 50 molecules are involved in the line parameters sub-database, including 111 isotopologues, for a total of 3,807,997 entries, in the spectral range from 10-6 to 35,877.031cm-1. GEISA, continuously developed and maintained at LMD (Laboratoirede Meteorologie Dynamique, France) since 1976, is implemented on the IPSL/CNRS(France) ‘‘Ether’’ Products and Services Centre WEB site (http://ether.ipsl.jussieu.fr), where all archived spectroscopic data can be handled through general and user friendly associated managements of software facilities. More than 350 researchers are registered for online use of GEISA

Novel genetic loci associated with hippocampal volume

The hippocampal formation is a brain structure integrally involved in episodic memory, spatial navigation, cognition and stress responsiveness. Structural abnormalities in hippocampal volume and shape are found in several common neuropsychiatric disorders. To identify the genetic underpinnings of hippocampal structure here we perform a genome-wide association study (GWAS) of 33,536 individuals and discover six independent loci significantly associated with hippocampal volume, four of them novel. Of the novel loci, three lie within genes (ASTN2, DPP4 and MAST4) and one is found 200 kb upstream of SHH. A hippocampal subfield analysis shows that a locus within the MSRB3 gene shows evidence of a localized effect along the dentate gyrus, subiculum, CA1 and fissure. Further, we show that genetic variants associated with decreased hippocampal volume are also associated with increased risk for Alzheimer's disease (rg =-0.155). Our findings suggest novel biological pathways through which human genetic variation influences hippocampal volume and risk for neuropsychiatric illness

Ethnographic interpretations of parent-child discourse in huli

This paper seeks to account for a culturally patterned set of analogic renamings found in Huli baby talk, nursery rhymes and children's verbal games. These socialization activities evidence a marked concern with body motifs and appellations. In accordance with ethnographic paradigms of explanation, the frame of reference is broadened to include consideration of inter-adult behaviour involving ‘talk about the body’ to assess what is being learnt from such interactions as well as what communicative intents are encoded. The argument is developed that in addition to the significance of these play routines in sensitizing the child to cultural rules about speaking, these ludic forms also appear implicated in both an evolutionary and logico-operational sense in the conventional anatomical nomenclature

Locking the unlockable: Children's invocation of pretence to define and manage place

Young children use pretense in their interactions with their peers. This paper focuses on their use of pretense to establish, define and formulate places within their peer interaction. A talk-in-interaction approach is used to analyse video-recorded and transcribed interactions of children aged 4-6 years in the block area of an early childhood classroom in Australia. The complex and collaborative interactive work of the children produced shared understandings of pretense, which they used as a device to manage their use of classroom physical and social spaces