Genomes as geography: using GIS technology to build interactive genome feature maps

BACKGROUND: Many commonly used genome browsers display sequence annotations and related attributes as horizontal data tracks that can be toggled on and off according to user preferences. Most genome browsers use only simple keyword searches and limit the display of detailed annotations to one chromosomal region of the genome at a time. We have employed concepts, methodologies, and tools that were developed for the display of geographic data to develop a Genome Spatial Information System (GenoSIS) for displaying genomes spatially, and interacting with genome annotations and related attribute data. In contrast to the paradigm of horizontally stacked data tracks used by most genome browsers, GenoSIS uses the concept of registered spatial layers composed of spatial objects for integrated display of diverse data. In addition to basic keyword searches, GenoSIS supports complex queries, including spatial queries, and dynamically generates genome maps. Our adaptation of the geographic information system (GIS) model in a genome context supports spatial representation of genome features at multiple scales with a versatile and expressive query capability beyond that supported by existing genome browsers. RESULTS: We implemented an interactive genome sequence feature map for the mouse genome in GenoSIS, an application that uses ArcGIS, a commercially available GIS software system. The genome features and their attributes are represented as spatial objects and data layers that can be toggled on and off according to user preferences or displayed selectively in response to user queries. GenoSIS supports the generation of custom genome maps in response to complex queries about genome features based on both their attributes and locations. Our example application of GenoSIS to the mouse genome demonstrates the powerful visualization and query capability of mature GIS technology applied in a novel domain. CONCLUSION: Mapping tools developed specifically for geographic data can be exploited to display, explore and interact with genome data. The approach we describe here is organism independent and is equally useful for linear and circular chromosomes. One of the unique capabilities of GenoSIS compared to existing genome browsers is the capacity to generate genome feature maps dynamically in response to complex attribute and spatial queries

Teor de compostos fenólicos e capacidade antioxidante encontrados na casca do maná-cubiu (Solanum sessiliflorum Dunal), cultivado na Mata Atlântica Brasileira / Content of phenolic compounds and antioxidant capacity found in cocona peel (Solanum sessiliflorum Dunal), cultived from Brazilian Atlantic Forest

Solanum sessiliflorum Dunal (maná-cubiu) é um fruto da biodiversidade brasileira cultivado na Mata Atlântica do litoral paranaense, cujo suco é utilizado pela medicina tradicional para redução glicêmica. Embora os estudos com frutos tropicais sejam incentivados para caracterização de compostos bioativos, até o momento não foram encontrados relatos acerca do potencial antioxidante desta etnovariedade cultivada no bioma da Mata Atlântica. Esse trabalho teve como objetivo determinar o teor de compostos fenólicos biodisponíveis e a atividade antioxidante nas partes comestíveis: polpa com sementes (P) e casca (C). Extratos metanólicos do maná-cubiu foram utilizados para determinar o teor fenólico total (TFT), atividade antioxidante pelos métodos de 2,2-difenil-1-picryl-hidrazil (DPPH) com inibição de EC50, redução de ferro (FRAP) e captura radical livre de 2,2'-azinobis (3-etilbenzothiazolina-6-sulfônica) (ABTS). A casca do fruto apresentou maior TFT (p = 0,0001). Entretanto, a capacidade antioxidante das frações avaliadas foi similar pelos métodos DPPH (p = 0,0001) e FRAP (p = 0,0662).   A capacidade antioxidante do fruto se apresentou elevada, sendo necessário uma pequena concentração (19,84 g/ L), para redução de 50% do radical DPPH (IC50). O destaque da fração C no elevado conteúdo de fenólicos e na capacidade antioxidante detectada por ABTS comprovam a importância do consumo do fruto com casca, com ingestão de sua porção comestível integral. Além desse achado, os resultados obtidos apontam para um potencial promissor de utilização do maná-cubiu na prevenção ou remoção de danos oxidativos, justificando parcialmente seu uso tradicional no controle glicêmico

Seed size variation: magnitude, distribution, and ecological correlates

We examined seed-mass variation in 39 species (46 populations) of plants in eastern-central Illinois, USA. The coefficient of variation of seed mass commonly exceeded 20%. Significant variation in mean seed mass occurred among conspecific plants in most species sampled (by hierarchical ANOVA), averaging 38% of total variance. For most species, within-plant variation was the larger component of total variance, averaging 62% of total variance. Variation in seed mass among fruits within crops was significant in most species tested.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/42741/1/10682_2005_Article_BF02067274.pd

A História da Alimentação: balizas historiográficas

Os M. pretenderam traçar um quadro da História da Alimentação, não como um novo ramo epistemológico da disciplina, mas como um campo em desenvolvimento de práticas e atividades especializadas, incluindo pesquisa, formação, publicações, associações, encontros acadêmicos, etc. Um breve relato das condições em que tal campo se assentou faz-se preceder de um panorama dos estudos de alimentação e temas correia tos, em geral, segundo cinco abardagens Ia biológica, a econômica, a social, a cultural e a filosófica!, assim como da identificação das contribuições mais relevantes da Antropologia, Arqueologia, Sociologia e Geografia. A fim de comentar a multiforme e volumosa bibliografia histórica, foi ela organizada segundo critérios morfológicos. A seguir, alguns tópicos importantes mereceram tratamento à parte: a fome, o alimento e o domínio religioso, as descobertas européias e a difusão mundial de alimentos, gosto e gastronomia. O artigo se encerra com um rápido balanço crítico da historiografia brasileira sobre o tema

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on autosomes: on average, maximal expression is three times lower on the X chromosome than on autosomes. Similarly, autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-autosome retrogenes on autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution

Optimized AAV rh.10 Vectors That Partially Evade Neutralizing Antibodies during Hepatic Gene Transfer

Of the 12 common serotypes used for gene delivery applications, Adeno-associated virus (AAV)rh.10 serotype has shown sustained hepatic transduction and has the lowest seropositivity in humans. We have evaluated if further modifications to AAVrh.10 at its phosphodegron like regions or predicted immunogenic epitopes could improve its hepatic gene transfer and immune evasion potential. Mutant AAVrh.10 vectors were generated by site directed mutagenesis of the predicted targets. These mutant vectors were first tested for their transduction efficiency in HeLa and HEK293T cells. The optimal vector was further evaluated for their cellular uptake, entry, and intracellular trafficking by quantitative PCR and time-lapse confocal microscopy. To evaluate their potential during hepatic gene therapy, C57BL/6 mice were administered with wild-type or optimal mutant AAVrh.10 and the luciferase transgene expression was documented by serial bioluminescence imaging at 14, 30, 45, and 72 days post-gene transfer. Their hepatic transduction was further verified by a quantitative PCR analysis of AAV copy number in the liver tissue. The optimal AAVrh.10 vector was further evaluated for their immune escape potential, in animals pre-immunized with human intravenous immunoglobulin. Our results demonstrate that a modified AAVrh.10 S671A vector had enhanced cellular entry (3.6 fold), migrate rapidly to the perinuclear region (1 vs. >2 h for wild type vectors) in vitro, which further translates to modest increase in hepatic gene transfer efficiency in vivo. More importantly, the mutant AAVrh.10 vector was able to partially evade neutralizing antibodies (~27–64 fold) in pre-immunized animals. The development of an AAV vector system that can escape the circulating neutralizing antibodies in the host will substantially widen the scope of gene therapy applications in humans

New insights into acne pathogenesis: Exploring the role of acne-associated microbial populations

AbstractAcne vulgaris, a prevalent disorder of the skin, is found to increase the incidence of suicidal ideation in acne patients (∼7.1%). This creates a dilemma in the mind whether acne is a life threatening disease among humans. The main inducer for this multifactorial disease is microbial fluctuation of common resident microbes on the skin with each microbe possessing their own purpose and style in protecting the human body. For acne progression, the microbial population has to get around the defense barriers of the host skin and be able to also resist them in order to survive. These matters have been resolved by their pathogenic lifecycle and associated virulence factors coded within their pathogenic islands in the single circular chromosome. This review addresses the different microbial populations residing in acne lesions and promoting acne by emphasizing their pathogenic mechanisms and the genes associated with virulence factors involved in the development of acne. Model systems such as animal models and cell culture models in studying the pathogenic lifestyle of the microbes are also addressed