Iis--integrated Interactome System: A Web-based Platform For The Annotation, Analysis And Visualization Of Protein-metabolite-gene-drug Interactions By Integrating A Variety Of Data Sources And Tools.

High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted. We describe here the Integrated Interactome System (IIS), an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i) Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system); (ii) Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii) Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv) Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web. We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with yeast two-hybrid, proteomics and metabolomics datasets, but it is also extendable to other datasets. IIS is freely available online at: http://www.lge.ibi.unicamp.br/lnbio/IIS/.

Ecosystem Engineering Effects On Species Diversity Across Ecosystems: A Meta-analysis.

Ecosystem engineering is increasingly recognized as a relevant ecological driver of diversity and community composition. Although engineering impacts on the biota can vary from negative to positive, and from trivial to enormous, patterns and causes of variation in the magnitude of engineering effects across ecosystems and engineer types remain largely unknown. To elucidate the above patterns, we conducted a meta-analysis of 122 studies which explored effects of animal ecosystem engineers on species richness of other organisms in the community. The analysis revealed that the overall effect of ecosystem engineers on diversity is positive and corresponds to a 25% increase in species richness, indicating that ecosystem engineering is a facilitative process globally. Engineering effects were stronger in the tropics than at higher latitudes, likely because new or modified habitats provided by engineers in the tropics may help minimize competition and predation pressures on resident species. Within aquatic environments, engineering impacts were stronger in marine ecosystems (rocky shores) than in streams. In terrestrial ecosystems, engineers displayed stronger positive effects in arid environments (e.g. deserts). Ecosystem engineers that create new habitats or microhabitats had stronger effects than those that modify habitats or cause bioturbation. Invertebrate engineers and those with lower engineering persistence (<1 year) affected species richness more than vertebrate engineers which persisted for >1 year. Invertebrate species richness was particularly responsive to engineering impacts. This study is the first attempt to build an integrative framework of engineering effects on species diversity; it highlights the importance of considering latitude, habitat, engineering functional group, taxon and persistence of their effects in future theoretical and empirical studies.

A Decade Of Malaria During Pregnancy In Brazil: What Has Been Done Concerning Prevention And Management.

In Brazil, malaria remains a disease of major epidemiological importance because of the high number of cases in the Amazonian Region. Plasmodium spp infections during pregnancy are a significant public health problem with substantial risks for the pregnant woman, the foetus and the newborn child. In Brazil, the control of malaria during pregnancy is primarily achieved by prompt and effective treatment of the acute episodes. Thus, to assure rapid diagnosis and treatment for pregnant women with malaria, one of the recommended strategy for low transmission areas by World Health Organization and as part of a strategy by the Ministry of Health, the National Malaria Control Program has focused on integrative measures with woman and reproductive health. Here, we discuss the approach for the prevention and management of malaria during pregnancy in Brazil over the last 10 years (2003-2012) using morbidity data from Malaria Health Information System. Improving the efficiency and quality of healthcare and education and the consolidation of prevention programmes will be challenges in the control of malaria during pregnancy in the next decade.

A Metabolomic Protocol For Plant Systematics By Matrix-assisted Laser-desorption/ionization Time-of Flight Mass Spectrometry.

Matrix-assisted laser desorption/ionization time-of flight mass spectrometry (MALDI-TOF MS) has been widely used for the identification and classification of microorganisms based on their proteomic fingerprints. However, the use of MALDI-TOF MS in plant research has been very limited. In the present study, a first protocol is proposed for metabolic fingerprinting by MALDI-TOF MS using three different MALDI matrices with subsequent multivariate data analysis by in-house algorithms implemented in the R environment for the taxonomic classification of plants from different genera, families and orders. By merging the data acquired with different matrices, different ionization modes and using careful algorithms and parameter selection, we demonstrate that a close taxonomic classification can be achieved based on plant metabolic fingerprints, with 92% similarity to the taxonomic classifications found in literature. The present work therefore highlights the great potential of applying MALDI-TOF MS for the taxonomic classification of plants and, furthermore, provides a preliminary foundation for future research.

Phenotypic Polymorphism Of Chrysomya Albiceps (wiedemann) (diptera: Calliphoridae) May Lead To Species Misidentification.

Species identification is an essential step in the progress and completion of work in several areas of biological knowledge, but it is not a simple process. Due to the close phylogenetic relationship of certain species, morphological characters are not always sufficiently distinguishable. As a result, it is necessary to combine several methods of analysis that contribute to a distinct categorization of taxa. This study aimed to raise diagnostic characters, both morphological and molecular, for the correct identification of species of the genus Chrysomya (Diptera: Calliphoridae) recorded in the New World, which has continuously generated discussion about its taxonomic position over the last century. A clear example of this situation was the first record of Chrysomya rufifacies in Brazilian territory in 2012. However, the morphological polymorphism and genetic variability of Chrysomya albiceps studied here show that both species (C. rufifacies and C. albiceps) share very similar character states, leading to misidentification and subsequent registration error of species present in our territory. This conclusion is demonstrated by the authors, based on a review of the material deposited in major scientific collections in Brazil and subsequent molecular and phylogenetic analysis of these samples. Additionally, we have proposed a new taxonomic key to separate the species of Chrysomya found on the American continent, taking into account a larger number of characters beyond those available in current literature.

Levantamento e características ecológicas de orchidacea e da mata ciliar do rio dourados, Dourados-MS

The Orchidaceae is one of the largest flowering plants family and with a great importance to conservation. However, no survey on orchid flowers can be found in Mato Grosso do Sul. Thus, the objective of this work was to make a survey of the Orchidaceae species and of its ecology features in a riparian forest in a fragment of Floresta Estacional Semi-Decidual that belongs to the riparian forest of the Dourados River. The inventory was made by using a sweeping method for collection, and in addition to this the vertical and horizontal position of epiphytes were assessed on the hosts. For characterization of microclimate, it was used a thermohygrometer and luximeter. It was identified 17 species of 13 genera. Of the listed genera, the most abundant ones were: Acianthera, Macradenia and Capanemia. It was also noted a vertical and horizontal distribution of the Orchidaceae in relation to inverse gradient of water and light availability. Some species tended to be sensitive to height level categorization, whereas others seemed to occur with similar frequency along the host. In relation to the cardinal orientation, the apparent preferential response for south and east directions was associated to the low sampling effort and lower water availability, which could occur because the north face is opposed to the water body.

Estrutura de um curso de taxonomia de campo: o modelo aplicado em Ubatuba, São Paulo

The field activities are essential for the education of a good taxonomist. The most common problems found in field activities are: a) large number of students, b) heterogeneous educational background and unlevelled knowledge of the participants, c) repetitions and tendency of collecting the more evidents life-forms. The causes and consequences of such problems are discussed herein. The proposed solution is a methodology, based on many years of experience in field courses for undergraduate and graduate courses. Topics about the ideal number of participants, area of coverage, period of activity, division of work and the necessary material and equipment are discussed. According to the number of species collected at the same place, this methodology may result in a list of local species with precise information about the life-forms, habitat, common names, frequency, uses, phenology and further information in this kind of work. The results of the aplication of this metodology in a field course held in the region of Ubatuba-SP are presented.

Notas sobre duas espécies de Thelypteris Schmidel (Thelypteridaceae - Pterophyta) do Brasil

During the taxonomic study of the Thelypteridaceae from southeastern Brazil was founded Thelypteris polypodioides (Raddi) C. F. Reed and Thelypteris villosa (Link) C. F. Reed, two rare and poorly known species. The taxonomic position of these species is uncertain. This study presents key, descriptions, illustrations, data on geographical distribution, and comments for both species, as well as comments on taxonomic affinity between the two species and Thelypteris subgenera.

Revisão taxonômica de Myrocarpus Allemão (Leguminosae, Papilionoideae, Sophoreae)

In Myrocarpus, an exclusively South American genus, five species are recognised: Myrocarpus frondosus Allemão, M. leprosus Pickel, M. venezuelensis Rudd, M. fastigiatus Allemãoand M. emarginatus A.L.B. Sartori & A.M.G. Azevedo. Morphologic data, habitat information and geographic distribution of each taxon are discussed. Petal morphology and ornamentation of seed chamber are an important character for species identification, though not shown previously. Key to the species, descriptions, illustrations, distribution, and new registers are presented.

Taxonomia do gênero Heliotropium L. (Heliotropiaceae) no Brasil

The taxonomy of the genus Heliotropium L. in Brazil was studied, revealing nine species and two varieties: H. amplexicaule Vahl, H. angiospermum Murray, H. curassavicum L., H. curassavicum var. argentinum I.M. Johnst., H. elongatum (Lehm.) I.M. Johnst., H. elongatum var. burchellii I.M. Johnst., H. indicum L., H. leiocarpum Morong, H. nicotianaefolium Poir., H. phylicoides Cham. and H. transalpinum Vell. Descriptions, illustrations, comments on relationships based on morphology and data on species distribution are presented.

O gênero Nectandra Rol. ex Rottb. (Lauraceae) no Estado do Paraná, Brasil

Nectandra Rol. ex Rottb. has 14 species in Paraná: Nectandra angustifolia (Schrader) Nees & Mart., N. cissiflora Nees, N. cuspidata Nees & Mart., N. grandiflora Nees & Mart., N. hihua (Ruiz & Pav.) Rohwer, N. lanceolata Nees & Mart., N. leucantha Nees & Mart., N. megapotamica (Sprengel) Mez, N. membranacea (Sw.) Griseb., N. nitidula Nees & Mart., N. oppositifolia Nees & Mart., N. paranaensis Coe-Teixeira, N. puberula (Schott) Nees and N. reticulata (Ruiz & Pav.) Mez. We present an identification key and species descriptions, as well as illustrations and data on phenology and geographic distribution. N. hihua is cited for the first time in Paraná State.

Números cromossômicos em espécies de Acosmium Schott e Leptolobium Vogel (Leguminosae, Papilionoideae)

A cytotaxonomic analysis of species of Acosmium Schott e Leptolobium Vogel was carried out, by determining their chromosome numbers. The three species of Acosmium and five species of Leptolobium (representing 50% of the genus) were studied from seeds obtained from different regions of Brazil. Chromosome counts were new for all Acosmium species and for four Leptolobium species. For Acosmium cardenasii, 2n = 18 was constantly observed, while occurring at the same meristem were found 2n = 18, 24 e 32 in A. diffusissimum and 2n = 18 e 32 in A. lentiscifolium. For Leptolobium, all studied species had 2n = 18, confirming a previous count for L. dasycarpum. The results showed that chromosome numbers of Acosmium and Leptolobium species are homogeneous, confirming the basic number x = 9 for both genera. Therefore, chromosome numbers do not provide a useful taxonomic character distinguishing Acosmium from Leptolobium.

Taxonomia do gênero Euploca Nutt. (Heliotropiaceae) no Brasil

This work deals with a taxonomic study of the genus Euploca (Heliotropiaceae) in Brazil; seventeen species are recorded. A keyfor identification, descriptions, illustrations and comments, besides distribution, habitat, flowering and fruiting data for the species are presented.

Revisão taxonômica de Leptolobium (Papilionoideae, Leguminosae)

This revision of Leptolobium Vogel includes an identification key, descriptions, illustrations, and distribution maps for the taxa. Leptolobium comprises 12 species, and is characterized by its arboreal or shrubby habit, flowers with white, actinomorphic or slightly zygomorphic corollas, 10 free stamens, a stipitate ovary with many ovules, indehiscent (samara-like or nut-like) fruits, compressed seeds, and a bulbose hypocotyl-radicle axis. Leptolobium is a neotropical genus that occurs from Mexico to northern Argentina. Eleven species are found in Brazil, seven of which are endemic to the country. The lectotype of Sweetia glazioviana Harms is designated in this paper. In addition, information about uses, common names, geographical distribution, and habitats are provided.

Revisão taxonômica de Lonchocarpus s. str. (Leguminosae, Papilionoideae) do Brasil

A revision of the Brazilian species of Lonchocarpus s. str. is presented. This study is based on field observation and an analysis of approximately 1,200 herbarium collections. Nine species are recognized, L. cultratus, L. hedyosmus, L. latifolius, L. macrocarpus, L. nitidus, L. pluvialis, L. sericeus, L. spiciflorus, and L. violaceus, which grow in forests and are usually associated with river banks. Lonchocarpus sericeus and L. cultratus have a wide distribution throughout Brazil, whereas L. hedyosmus, L. macrocarpus, L. spiciflorus, and L. latifolius are restricted to the Amazonian domain. Lonchocarpus pluvialis occurs in the Central-West (Mato Grosso do Sul and Goiás) and Southeast (São Paulo) regions. Lonchocarpus violaceus is found in the states of Bahia and Espírito Santo, and is reported for the first time for Brazil. Identification keys, descriptions, and illustrations, in addition to information about habitat, geographic distribution and taxonomic and nomenclatural comments, are provided for the species. Four new synonyms and five lectotypifications are proposed.