GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses

Transcription factors (TFs) are major players in gene regulatory networks and interactions between TFs and their target genes furnish spatiotemporal patterns of gene expression. Establishing the architecture of regulatory networks requires gathering information on TFs, their targets in the genome, and the corresponding binding sites. We have developed GRASSIUS (Grass Regulatory Information Services) as a knowledge-based Web resource that integrates information on TFs and gene promoters across the grasses. In its initial implementation, GRASSIUS consists of two separate, yet linked, databases. GrassTFDB holds information on TFs from maize (Zea mays), sorghum (Sorghum bicolor), sugarcane (Saccharum spp.), and rice (Oryza sativa). TFs are classified into families and phylogenetic relationships begin to uncover orthologous relationships among the participating species. This database also provides a centralized clearinghouse for TF synonyms in the grasses. GrassTFDB is linked to the grass TFome collection, which provides clones in recombination-based vectors corresponding to full-length open reading frames for a growing number of grass TFs. GrassPROMDB contains promoter and cis-regulatory element information for those grass species and genes for which enough data are available. The integration of GrassTFDB and GrassPROMDB will be accomplished through GrassRegNet as a first step in representing the architecture of grass regulatory networks. GRASSIUS can be accessed from www.grassius.org.

Efeito do ganho da antena nas perdas de percurso de uma ligação

O presente trabalho tem como objectivo principal a realização de um estudo do efeito do ganho das antenas nas perdas de percurso de uma ligação na banda de frequência ISM (Insdustrial Scientific and Medical) nos 2,4 GHz. Para tal, foram utilizadas 14 antenas de 7 tipos diferentes (2 monopolo, 2 colineares, 2 grelhas, 2 Yagi, 2 painéis, 2 parabólicas e 2 helicoidais) com ganhos a variar desde os 1,3 a 23 dBi. Inicialmente, obtiveram-se os parâmetros fundamentais das antenas utilizadas, nomeadamente o diagrama de radiação e o ganho. Desenvolveu-se um sistema, que permite a medição do diagrama de radiação de forma automática através de um motor passo a passo. Uma aplicação desenvolvida em ambiente Matlab realiza o controlo do motor e desenha o respectivo diagrama em tempo real. Para a realização das medições da propagação do sinal desenvolveu-se um sistema que interliga a antena receptora a um computador portátil através de um analisador de espectros. À medida que as medições são efectuadas, a atenuação do sinal em função da distância é determinada e apresentada graficamente no computador sendo, ainda, representada a atenuação esperada no espaço livre. Para isto, implementou-se uma aplicação em ambiente Matlab que faz o tratamento e representação dos dados. Tendo-se conhecimento dos parâmetros das antenas, e com o sistema de medição implementado, passou-se às medições da propagação do sinal em diferentes meios, tais como, meio sem obstáculos, meio urbano, meio florestal caracterizado por troncos no percurso de propagação e meio florestal caracterizado por folhagem no percurso de propagação. Em cada meio foram efectuadas medições para 37 combinações de antenas, com ganhos conjuntos a variar desde os 2,6 até o 46 dBi. As medições foram efectuadas com a colocação da antena emissora numa posição fixa e com o afastamento da antena receptora em intervalos de 5 metros, até os 150 metros, seguindo a linha de máxima radiação entre ambas as antenas. Ainda, para os meios sem obstáculos e florestais, foram efectuadas medições para dois ângulos em relação à linha indicada, sendo estes de 30° e 330°, respectivamente. Com base nos resultados obtidos, verificou-se um aumento da atenuação à medida que se passou para meios mais obstruídos, sendo que, para o meio sem obstáculos a atenuação aproxima-se da curva do espaço livre. No meio urbano observou-se que a atenuação aumentou ligeiramente. No entanto, esta não é muito significativa quando comparada com a atenuação no espaço livre. Por último, notou-se um grande aumento da atenuação nos meios florestais, ao nível dos troncos e da vegetação, sendo superior para esta última. Relativamente às antenas, verificou-se que existe um aumento da atenuação na medida que o ganho destas aumenta, sendo mais visível para meios com maior obstrução (florestais). Para a situação em que as antenas encontram-se com desvios de 30° e 330°, verificou-se que este aumento é mais significativo para as antenas directivas (ganhos superiores).

Humoral and cellular immune response generated by different vaccine programs before and after Salmonella Enteritidis challenge in chickens

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Experimental infection of commercial layers with wild or attenuated Salmonella Gallinarum mutant strains: Anatomic pathology, total blood cell count and serum protein levels

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Resposta imune celular e humoral em aves (Gallus gallus) vacinadas, antes e após o desafio com Salmonella enteritidis

Pós-graduação em Medicina Veterinária - FCAV

Genome Sequence of the Bacterioplanktonic, Mixotrophic Vibrio campbellii Strain PEL22A, Isolated in the Abrolhos Bank

Vibrio campbellii PEL22A was isolated from open ocean water in the Abrolhos Bank. The genome of PEL22A consists of 6,788,038 bp (the GC content is 45%). The number of coding sequences (CDS) is 6,359, as determined according to the Rapid Annotation using Subsystem Technology (RAST) server. The number of ribosomal genes is 80, of which 68 are tRNAs and 12 are rRNAs. V. campbellii PEL22A contains genes related to virulence and fitness, including a complete proteorhodopsin cluster, complete type II and III secretion systems, incomplete type I, IV, and VI secretion systems, a hemolysin, and CTX Phi.

A revision of Evaniscus (Hymenoptera, Evaniidae) using ontology-based semantic phenotype annotation

The Neotropical evaniid genus Evaniscus Szepligeti currently includes six species. Two new species are described, Evaniscus lansdownei Mullins, sp. n. from Colombia and Brazil and E. rafaeli Kawada, sp. n. from Brazil. Evaniscus sulcigenis Roman, syn. n., is synonymized under E. rufithorax Enderlein. An identification key to species of Evaniscus is provided. Thirty-five parsimony informative morphological characters are analyzed for six ingroup and four outgroup taxa. A topology resulting in a monophyletic Evaniscus is presented with E. tibialis and E. rafaeli as sister to the remaining Evaniscus species. The Hymenoptera Anatomy Ontology and other relevant biomedical ontologies are employed to create semantic phenotype statements in Entity-Quality (EQ) format for species descriptions. This approach is an early effort to formalize species descriptions and to make descriptive data available to other domains.

A hymenopterists' guide to the Hymenoptera Anatomy Ontology: utility, clarification, and future directions

Hymenoptera exhibit an incredible diversity of phenotypes, the result of similar to 240 million years of evolution and the primary subject of more than 250 years of research. Here we describe the history, development, and utility of the Hymenoptera Anatomy Ontology (HAO) and its associated applications. These resources are designed to facilitate accessible and extensible research on hymenopteran phenotypes. Outreach with the hymenopterist community is of utmost importance to the HAO project, and this paper is a direct response to questions that arose from project workshops. In a concerted attempt to surmount barriers of understanding, especially regarding the format, utility, and development of the HAO, we discuss the roles of homology, "preferred terms", and "structural equivalency". We also outline the use of Universal Resource Identifiers (URIs) and posit that they are a key element necessary for increasing the objectivity and repeatability of science that references hymenopteran anatomy. Pragmatically, we detail a mechanism (the "URI table") by which authors can use URIs to link their published text to the HAO, and we describe an associated tool (the "Analyzer") to derive these tables. These tools, and others, are available through the HAO Portal website (http://portal.hymao.org). We conclude by discussing the future of the HAO with respect to digital publication, cross-taxon ontology alignment, the advent of semantic phenotypes, and community-based curation.

Identification of intracellular peptides in rat adipose tissue: Insights into insulin resistance

Intracellular peptides generated by the proteasome and oligopeptidases have been suggested to function in signal transduction and to improve insulin resistance in mice fed a high-caloric diet. The aim of this study was to identify specific intracellular peptides in the adipose tissue of Wistar rats that could be associated with the physiological and therapeutic control of glucose uptake. Using semiquantitative mass spectrometry and LC/MS/MS analyses, we identified ten peptides in the epididymal adipose tissue of the Wistar rats; three of these peptides were present at increased levels in rats that were fed a high-caloric Western diet (WD) compared with rats fed a control diet (CD). The results of affinity chromatography suggested that in the cytoplasm of epididymal adipose tissue from either WD or CD rats, distinctive proteins bind to these peptides. However, despite the observed increase in the WD animals, the evaluated peptides increased insulin-stimulated glucose uptake in 3T3-L1 adipocytes treated with palmitate. Thus, intracellular peptides from the adipose tissue of Wistar rats can bind to specific proteins and facilitate insulin-induced glucose uptake in 3T3-L1 adipocytes.

QuMinS: fast and scalable querying, mining and summarizing multi-modal databases

Given a large image set, in which very few images have labels, how to guess labels for the remaining majority? How to spot images that need brand new labels different from the predefined ones? How to summarize these data to route the user’s attention to what really matters? Here we answer all these questions. Specifically, we propose QuMinS, a fast, scalable solution to two problems: (i) Low-labor labeling (LLL) – given an image set, very few images have labels, find the most appropriate labels for the rest; and (ii) Mining and attention routing – in the same setting, find clusters, the top-'N IND.O' outlier images, and the 'N IND.R' images that best represent the data. Experiments on satellite images spanning up to 2.25 GB show that, contrasting to the state-of-the-art labeling techniques, QuMinS scales linearly on the data size, being up to 40 times faster than top competitors (GCap), still achieving better or equal accuracy, it spots images that potentially require unpredicted labels, and it works even with tiny initial label sets, i.e., nearly five examples. We also report a case study of our method’s practical usage to show that QuMinS is a viable tool for automatic coffee crop detection from remote sensing images.

Matriz de Butler de Banda Ancha en Banda X para Antenas Reconfigurables

The work presented in this document shows the complete simulation of a Butler matrix. This circuit will be used in the feeding of a steerable on board antenna in X band. The antenna consists of printed elements grouped in an array. This terminal works in a frequency band from 7.25 up to 8.4 GHz (15% of bandwidth), where both bands, reception (7.25 – 7.75 GHz) and transmission (7.9–8.4 GHz), are included simultaneously. The whole antenna reaches 31 dBi, with a beam width smaller than 10º and a dual circular polarization. This antenna also includes the capability of electronic steering in elevation ±45º and mechanically motorized junction 360º in azimuth.

Electronic Steering antenna onboard for satellite communications in X band.

The antenna presented in this article will be developed for satellite communications onboard systems based on the recommendations ITU-R S.580-6 and ITU-R S.465-5. The antenna consists of printed elements grouped in an array, this terminal works in a frequency band from 7.25 up to 8.4 GHz (14.7% of bandwidth), where both bands, reception (7.25 - 7.75 GHz) and transmission (7.9 - 8.4 GHz), are included simultaneously. The antenna reaches a gain about 31 dBi, and it has a radiation pattern with a beamwidth smaller than 10° and a dual circular polarization. The antenna has the capability to steer in elevation from 90° to 40° electronically and 360° in azimuth with a motorized junction.

Mutual Coupling Reduction Techniques in Electronic Steering Antennas in X Band

This work provides the development of an antenna for satellite communications onboard systems based on the recommendations ITU-R S.580-6 [1] and ITU-R S.465-5 [2]. The antenna consists of printed elements grouped in an array, working in a frequency band from 7.25 up to 8.4 GHz (15% of bandwidth). In this working band, transmission and reception are included simultaneously. The antenna reaches a gain about 31 dBi, has a radiation pattern with a beam width smaller than 10oand dual circular polarization. It has the capability to steer in elevation through a Butler matrix to 45

Low-Profile Dual Circularly Polarized Antenna Array for Satellite Communications in the X Band

A planar antenna is introduced that works as a portable system for X-band satellite communications. This antenna is low-profile and modular with dimensions of 40 × 40 × 2.5 × cm. It is composed of a square array of 144 printed circuit elements that cover a wide bandwidth (14.7%) for transmission and reception along with dual and interchangeable circular polarization. A radiation efficiency above 50% is achieved by a low-loss stripline feeding network. This printed antenna has a 3 dB beamwidth of 5°, a maximum gain of 26 dBi and an axial ratio under 1.9 dB over the entire frequency band. The complete design of the antenna is shown, and the measurements are compared with simulations to reveal very good agreement.

Dual circular polarized steering antenna for satellite communications in X band

In this work, a dual circular polarized steering antenna for satellite communications in X band is presented. The antenna consists of printed elements grouped in an array. This terminal works in a frequency band from 7.25 GHz up to 8.4 GHz (15% of bandwidth), where both bands, reception (RX) and transmission (TX) are included simultaneously and Left Handed Circular Polarization (LHCP) and Right Handed Circular Polarization (RHCP) are interchangeable. The antenna is compact, narrow bandwidth and reaches a gain of 16 dBi. It has the capability to steer in elevation to 45±, 75±, 105± and 135± electronically with a Butler matrix and 360± in azimuth with a motorized junction.