Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution

On the consecutive ones property

A binary matrix has the Consecutive Ones Property (CIP) when there is a permutation of its rows that leaves the 1's consecutive in every column. We study the recognition problem for these matrices, giving a structure, PQR trees, generalizing the PQ trees of Booth and Lueker (1976). This new structure is capable of, not only recording all valid permutations when the matrix has the CIP, but also pointing out possible obstructions when the property does not hold. We recast the problem using collections of sets, developing a new theory for it. This problem appears naturally in several applications in molecular biology, for instance, in the construction of physical maps from hybridization data. (C) 1998 Elsevier Science B.V. All right reserved.884169932535

Live Phylogeny

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)The live phylogeny problem generalizes the phylogeny problem while admitting the existence of living ancestors among the taxonomic objects. This problem suits the case of fast-evolving species, like virus, and the construction of phylogenies for nonbiological objects like documents, images, and database records. In this article, we formalize the live phylogeny problem for distances and character states and introduce polynomial-time algorithms for particular versions of the problems. We believe that more general versions of the problems are NP-hard and that many heuristic and approximation approaches may be developed as solution strategies.2013037Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)FINEP [01.08.0166.00]Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)CNPq [305503/2010-3, 306731/2009-6]FINEP [01.08.0166.00

Semantic Wordification of Document Collections

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Word clouds have become one of the most widely accepted visual resources for document analysis and visualization, motivating the development of several methods for building layouts of keywords extracted from textual data. Existing methods are effective to demonstrate content, but are not capable of preserving semantic relationships among keywords while still linking the word cloud to the underlying document groups that generated them. Such representation is highly desirable for exploratory analysis of document collections. In this paper we present a novel approach to build document clouds, named ProjCloud that aim at solving both semantical layouts and linking with document sets. ProjCloud generates a semantically consistent layout from a set of documents. Through a multidimensional projection, it is possible to visualize the neighborhood relationship between highly related documents and their corresponding word clouds simultaneously. Additionally, we propose a new algorithm for building word clouds inside polygons, which employs spectral sorting to maintain the semantic relationship among words. The effectiveness and flexibility of our methodology is confirmed when comparisons are made to existing methods. The technique automatically constructs projection based layouts the user may choose to examine in the form of the point clouds or corresponding word clouds, allowing a high degree of control over the exploratory process.313311451153Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP