CleanEST: a database of cleansed EST libraries

The EST division of GenBank, dbEST, is widely used in many applications such as gene discovery and verification of exon–intron structure. However, the use of EST sequences in the dbEST libraries is often hampered by inconsistent terminology used to describe the library sources and by the presence of contaminated sequences. Here, we describe CleanEST, a novel database server that classified dbEST libraries and removes contaminants. We classified all dbEST libraries according to species and sequencing center. In addition, we further classified human EST libraries by anatomical and pathological systems according to eVOC ontologies. For each dbEST library, we provide two different cleansed sequences: ‘pre-cleansed’ and ‘user-cleansed’. To generate pre-cleansed sequences, we cleansed sequences in dbEST by alignment of EST sequences against well-known contamination sources: UniVec, Escherichia coli, mitochondria and chloroplast (for plant). To provide user-cleansed sequences, we built an automatic user-cleansing pipeline, in which sequences of a user-selected library are cleansed on-the-fly according to user-selected options. The server is available at http://cleanest.kobic.re.kr/ and the database is updated monthly

Meiotic Pairing and Segregation of Achiasmate Sex Chromosomes in Eutherian Mammals: The Role of SYCP3 Protein

In most eutherian mammals, sex chromosomes synapse and recombine during male meiosis in a small region called pseudoautosomal region. However in some species sex chromosomes do not synapse, and how these chromosomes manage to ensure their proper segregation is under discussion. Here we present a study of the meiotic structure and behavior of sex chromosomes in one of these species, the Mongolian gerbil (Meriones unguiculatus). We have analyzed the location of synaptonemal complex (SC) proteins SYCP1 and SYCP3, as well as three proteins involved in the process of meiotic recombination (RAD51, MLH1, and γ-H2AX). Our results show that although X and Y chromosomes are associated at pachytene and form a sex body, their axial elements (AEs) do not contact, and they never assemble a SC central element. Furthermore, MLH1 is not detected on the AEs of the sex chromosomes, indicating the absence of reciprocal recombination. At diplotene the organization of sex chromosomes changes strikingly, their AEs associate end to end, and SYCP3 forms an intricate network that occupies the Y chromosome and the distal region of the X chromosome long arm. Both the association of sex chromosomes and the SYCP3 structure are maintained until metaphase I. In anaphase I sex chromosomes migrate to opposite poles, but SYCP3 filaments connecting both chromosomes are observed. Hence, one can assume that SYCP3 modifications detected from diplotene onwards are correlated with the maintenance of sex chromosome association. These results demonstrate that some components of the SC may participate in the segregation of achiasmate sex chromosomes in eutherian mammals

American marsupials chromosomes: Why study them?

Marsupials, one of the three main groups of mammals, are only found in Australia and in the American continent. Studies performed in Australian marsupials have demonstrated the great potential provided by the group for the understanding of basic genetic mechanisms and chromosome evolution in mammals. Genetic studies in American marsupials are relatively scarce and cytogenetic data of most species are restricted to karyotype descriptions, usually without banding patterns. Nevertheless, the first marsupial genome sequenced was that of Monodelphis domestica, a South American species. The knowledge about mammalian genome evolution and function that resulted from studies on M. domestica is in sharp contrast with the lack of genetic data on most American marsupial species. Here, we present an overview of the chromosome studies performed in marsupials with emphasis on the South American species

KARYOTY,PE AND IDENTIFICATION OF SEX IN TWO ENDANGERED CRANE SPECIES

A laboratory procedure for sex identification of monomorphic birds was developed using modern cytological methods of detecting chromosome abnormalities in human amniotic fluid samples. A pin feather is taken from a pre-fledging bird for tissue culture and karyotype analysis. Through this method, the sex was identified and the karyotype described of the whooping crane (Grus americana) and the Mississippi sandhill crane (G. canadensis pulla). Giemsa-stained karyotypes of these species showed an identical chromosome constitution with 2n = 78 ± 2. However, differences in the amount of centromeric heterochromatin were observed in the Mississippi sandhill crane when compared to the whooping crane C-banded karyotype

Análisis de las transformaciones del dispositivo Manicomial en Córdoba, Argentina

Trabalho de Conclusão de Curso apresentado ao Instituto Latino-Americano de Arte, Cultura e História da Universidade Federal da Integração Latino-Americana, como requisito parcial à obtenção do título de Bacharel em Antropologia – Diversidade Cultural Latino-Americana. Sob a orientação da Profa. Senilde AlcantaraEl siguiente trabajo consiste en una investigación en torno a los dispositivos manicomiales en un contexto de transformación. Se encontrarán definiciones claves para contextualizar histórica y culturalmente estos dispositivos con la finalidad de aportar a una comprensión mas basta de las razones de su funcionamiento actual. El tema es abordado en el contexto de los territorios ocupados por los estados latinoamericanos, específicamente el Estado Argentino. En Argentina la reglamentación reciente de la Ley Nacional de Salud Mental 26.657, introduce un elemento orientador de los procesos de reforma en los diversos niveles jurisdiccionales. Hasta el día de hoy, estas reformas no han sido plenamente ejecutadas. Sirviéndome de la antropología de la dominación como eje que estructura el análisis, mostraré a partir de material etnográfico y de aportes bibliográficos de diversas disciplinas académicas y de textos no académicos algunos elementos que sirven para comprender las razones de la permanencia del sistema manicomial, sin desconocer el enorme esfuerzo de transformación que llevan adelante diversos actores. Con fines analíticos, el siguiente trabajo se divide en tres partes: La primera, presente en el capitulo 1 y 2 es un esquema resultado de un acercamiento a lo que está sucediendo en Argentina tras la aprobación de la ley de Salud Mental que reglamenta la transformación del sistema de salud. A partir de un trabajo de investigación de carácter etnográfico realizado con foco en la ciudad de Córdoba (capital), se propone un análisis que toma en cuenta una dimensión macro y micro política, así como aspectos económicos, históricos y culturales que dan cuenta de cómo se configuran las disputas en el campo de la salud mental hoy. La segunda parte de esta investigación, presente en los capitulos 3, 4 y 5, se desarrolla teniendo como objetivo delinear las formas en que la dominación se ejerce en nuestros territorios y en nuestros cuerpos. Se indaga el carácter capitalista, hetero-patriarcal y racista de la dominación en los territorios ocupados por los Estados Latino Americanos y se argumenta sobre la imposibilidad de comprender el funcionamiento manicomial sin una comprensión profunda de estas tres características de la estructura de dominación. Finalmente, en el capitulo 6 se presentan algunas propuestas que, como lineas de fugas buscan ser un aporte para quienes (aún) entendemos la necesidad de poner fin a la lógica y las prácticas manicomiales como condición necesaria para una vida libre y digna.O seguinte trabalho consiste em uma pesquisa em volta ao dispositivos manicomiais em um contexto de transformação. Podram encontrarse definições chave para contextualizar histórica e culturalmente estes dispsitivos com a finalidade de aportar a uma comprenssão mais avrangente das rações do seu funcionamento atual. O tema é abordado no contexto dos territorios ocupados pelos estados latinoamericanos, específicamente o Estado Argentino. Em Argentina, a regulamentação recente da Ley Nacional de Salud Mental 26.657, intruduz um elemento orientador dos procesos de reforma nos diversos níveis juridiccionales. Até os días de hoje, estas reformas não tem sido plenamente ejecutadas. Serivndo-me da antropología da domnação como eixo que estrutura a análise, mostrarei a partir de material etnográfico e de aportes bibliográficos de diversas disciplinas académicas e de textos não académicos alguns elementos que servem para compreender as razões da permanência do sistema manicomial, sêm desconhecer o gigantesco esforço de transformação que levam adiante diversos atores. Com finalidade analítica, o seguinte trabalho divide-se em tres partes: A primeira, presente no capitulo 1 e 2 é um esquema resultado de uma aproximação a o que está acontecendo em Argentina logo da aprobação da ley de Salud Mental que regulamenta a transformação do sistema de saúde. Partindo dum trabalho de pesquisa de carater etnográfico realizado com foco na cidade de Córodoba (capital), porpo ẽ ;-se uma anãlise que leva em consideração uma dimenssão macro e micro política, assim como aspectos económicos, históricos e culturais que dizem a respeito de cómo se configuram as disputas no campo da saúde mental hoje. A segunda parte de esta pesquisa, presente nos capítulos 3, 4 e 5 desenvolve-se tendo como objetivo disenhar as formas pelas quai a dominação se exerce em nossos territórios e em nossos corpos. Indaga-se o carater capitalista, hetero-patrarcal e racista da dominação nos territorios ocupados pelos estados Latino-americanos e argumenta-se son a impossibilidade de comprender o funcionamento manicomial sem uma comprensão profunda destas tres características da estrutura da dominação. Finalmente, no capitulo 6 se presentam algumas propostas que, como líneas de fuga procuram ser um aporte para quens (aínda) comprendemos a necesidade de colocar fim à lógca e as práticas manicomiais como condição necessaria para uma vida livre e dign

The Genome Sequence DataBase (GSDB): improving data quality and data access.

In 1997 the primary focus of the Genome Sequence DataBase (GSDB; www. ncgr.org/gsdb ) located at the National Center for Genome Resources was to improve data quality and accessibility. Efforts to increase the quality of data within the database included two major projects; one to identify and remove all vector contamination from sequences in the database and one to create premier sequence sets (including both alignments and discontiguous sequences). Data accessibility was improved during the course of the last year in several ways. First, a graphical database sequence viewer was made available to researchers. Second, an update process was implemented for the web-based query tool, Maestro. Third, a web-based tool, Excerpt, was developed to retrieve selected regions of any sequence in the database. And lastly, a GSDB flatfile that contains annotation unique to GSDB (e.g., sequence analysis and alignment data) was developed. Additionally, the GSDB web site provides a tool for the detection of matrix attachment regions (MARs), which can be used to identify regions of high coding potential. The ultimate goal of this work is to make GSDB a more useful resource for genomic comparison studies and gene level studies by improving data quality and by providing data access capabilities that are consistent with the needs of both types of studies

14-3-3 ζ

Abstract 14‐3‐3ζ, a phosphopeptide‐binding molecule, is reportedly overexpressed in the cancerous tissues of patients with hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) protein X (HBx) draws intensive attention in HBV‐related HCC because it not only regulates HBV replication, but also promotes carcinogenesis by interacting with various tumor or antitumor molecules. This study is performed to investigate whether and how 14‐3‐3ζ interacts with HBx. The coimmunoprecipitation (Co‐IP) results showed that 14‐3‐3ζ bond to HBx in HBV‐infected Hep3B HCC cells and CSQT‐2 portal vein tumor thrombosis (PVTT) cells. By performing Co‐IP assay in HBV‐free Huh7 cells expressing wild‐type HBx, mutant HBx‐S31A, or HBx‐S31D (serine31 was mutated into alanine31 or aspartic acid31), we found that the phosphorylated serine31 with its near amino acid residues constituted a RPLphosphoS31GP (R, arginine; P, proline; L, leucine; S, serine; G, glycine) motif in HBx for 14‐3‐3ζ docking. This 14‐3‐3ζ‐HBx interaction was partly impaired when Akt signaling transduction was blocked by LY294002. Furthermore, 14‐3‐3ζ silencing augmented HBx ubiquitination and decreased its expression in cancer cells and xenograft tumor. The migratory and invasive abilities of CSQT‐2 cells were inhibited upon 14‐3‐3ζ silencing, whereas partly restored by HBx overexpression. Additionally, 14‐3‐3ζ positively correlated with HBx to be overexpressed in the primary HCC tissues (r = 0.344) and metastatic PVTT (r = 0.348). In summary, findings of this study reveal a novel 14‐3‐3ζ‐HBx interaction in HCC cells and suggest 14‐3‐3ζ as a candidate target for treating HBV‐related HCC