Bristle pattern formation in the thorax formation of Drosophila: a systems level approach

A fundamental question in developmental biology is how tissues are patterned to give rise to differentiated body structures with distinct morphologies. The Drosophila wing disc offers an accessible model to understand epithelial spatial patterning. It has been studied extensively using genetic and molecular approaches. Bristle patterns on the thorax, which arise from the medial part of the wing disc, are a classical model of pattern formation, dependent on a pre-pattern of trans-activators and –repressors. Despite of decades of molecular studies, we still only know a subset of the factors that determine the pre-pattern. We are applying a novel and interdisciplinary approach to predict regulatory interactions in this system. It is based on the description of expression patterns by simple logical relations (addition, subtraction, intersection and union) between simple shapes (graphical primitives). Similarities and relations between primitives have been shown to be predictive of regulatory relationships between the corresponding regulatory factors in other Systems, such as the Drosophila egg. Furthermore, they provide the basis for dynamical models of the bristle-patterning network, which enable us to make even more detailed predictions on gene regulation and expression dynamics. We have obtained a data-set of wing disc expression patterns which we are now processing to obtain average expression patterns for each gene. Through triangulation of the images we can transform the expression patterns into vectors which can easily be analysed by Standard clustering methods. These analyses will allow us to identify primitives and regulatory interactions. We expect to identify new regulatory interactions and to understand the basic Dynamics of the regulatory network responsible for thorax patterning. These results will provide us with a better understanding of the rules governing gene regulatory networks in general, and provide the basis for future studies of the evolution of the thorax-patterning network in particular.

OSIRISv1.2: a named entity recognition system for sequence variants of genes in biomedical literature

Background: Single Nucleotide Polymorphisms, among other type of sequence variants, constitute key elements in genetic epidemiology and pharmacogenomics. While sequence data about genetic variation is found at databases such as dbSNP, clues about the functional and phenotypic consequences of the variations are generally found in biomedical literature. The identification of the relevant documents and the extraction of the information from them are hampered by the large size of literature databases and the lack of widely accepted standard notation for biomedical entities. Thus, automatic systems for the identification of citations of allelic variants of genes in biomedical texts are required. Results: Our group has previously reported the development of OSIRIS, a system aimed at the retrieval of literature about allelic variants of genes http://ibi.imim.es/osirisform.html. Here we describe the development of a new version of OSIRIS (OSIRISv1.2, http://ibi.imim.es/OSIRISv1.2.html webcite) which incorporates a new entity recognition module and is built on top of a local mirror of the MEDLINE collection and HgenetInfoDB: a database that collects data on human gene sequence variations. The new entity recognition module is based on a pattern-based search algorithm for the identification of variation terms in the texts and their mapping to dbSNP identifiers. The performance of OSIRISv1.2 was evaluated on a manually annotated corpus, resulting in 99% precision, 82% recall, and an F-score of 0.89. As an example, the application of the system for collecting literature citations for the allelic variants of genes related to the diseases intracranial aneurysm and breast cancer is presented. Conclusion: OSIRISv1.2 can be used to link literature references to dbSNP database entries with high accuracy, and therefore is suitable for collecting current knowledge on gene sequence variations and supporting the functional annotation of variation databases. The application of OSIRISv1.2 in combination with controlled vocabularies like MeSH provides a way to identify associations of biomedical interest, such as those that relate SNPs with diseases.

A multicase study for the evaluation of a pattern-based visual design process for collaborative learning

Collage is a pattern-based visual design authoring tool for the creation of collaborative learning scripts computationally modelled with IMS Learning Design (LD). The pattern-based visual approach aims to provide teachers with design ideas that are based on broadly accepted practices. Besides, it seeks hiding the LD notation so that teachers can easily create their own designs. The use of visual representations supports both the understanding of the design ideas and the usability of the authoring tool. This paper presents a multicase study comprising three different cases that evaluate the approach from different perspectives. The first case includes workshops where teachers use Collage. A second case implies the design of a scenario proposed by a third-party using related approaches. The third case analyzes a situation where students follow a design created with Collage. The cross-case analysis provides a global understanding of the possibilities and limitations of the pattern-based visual design approach.

From a pattern-language to a pattern ontology approach for CSCL script design

Collaborative activities, in which students actively interact with each other, have proved to provide significant learning benefits. In Computer-Supported Collaborative Learning (CSCL), these collaborative activities are assisted by technologies. However, the use of computers does not guarantee collaboration, as free collaboration does not necessary lead to fruitful learning. Therefore, practitioners need to design CSCL scripts that structure the collaborative settings so that they promote learning. However, not all teachers have the technical and pedagogical background needed to design such scripts. With the aim of assisting teachers in designing effective CSCL scripts, we propose a model to support the selection of reusable good practices (formulated as patterns) so that they can be used as a starting point for their own designs. This model is based on a pattern ontology that computationally represents the knowledge captured on a pattern language for the design of CSCL scripts. A preliminary evaluation of the proposed approach is provided with two examples based on a set of meaningful interrelated patters computationally represented with the pattern ontology, and a paper prototyping experience carried out with two teaches. The results offer interesting insights towards the implementation of the pattern ontology in software tools.

Coordination pattern variability provides functional adaptations to constraints in swimming performance.

In a biophysical approach to the study of swimming performance (blending biomechanics and bioenergetics), inter-limb coordination is typically considered and analysed to improve propulsion and propelling efficiency. In this approach, 'opposition' or 'continuous' patterns of inter-limb coordination, where continuity between propulsive actions occurs, are promoted in the acquisition of expertise. Indeed a 'continuous' pattern theoretically minimizes intra-cyclic speed variations of the centre of mass. Consequently, it may also minimize the energy cost of locomotion. However, in skilled swimming performance there is a need to strike a delicate balance between inter-limb coordination pattern stability and variability, suggesting the absence of an 'ideal' pattern of coordination toward which all swimmers must converge or seek to imitate. Instead, an ecological dynamics framework advocates that there is an intertwined relationship between the specific intentions, perceptions and actions of individual swimmers, which constrains this relationship between coordination pattern stability and variability. This perspective explains how behaviours emerge from a set of interacting constraints, which each swimmer has to satisfy in order to achieve specific task performance goals and produce particular task outcomes. This overview updates understanding on inter-limb coordination in swimming to analyse the relationship between coordination variability and stability in relation to interacting constraints (related to task, environment and organism) that swimmers may encounter during training and performance.

The pattern of health care use of older prisoners in Switzerland.

Introduction: Population ageing is a worldwide phenomenon that forces us to make radical changes on multiple levels of society. So far, studies have concluded that the health, both physical and mental, of prisoners in general and older prisoners in particular is worse than that of the general population. Prisoners are reported to age faster as compared to adults in the community. However, to date, very little is known about the actual healthcare conditions of older prisoners and almost no substantial knowledge is available concerning their patterns of healthcare use. Method: A quantitative study was conducted in four prisons for male prisoners in Switzerland, including two open and two closed prisons situated in different cantons. In this study, medical records of older prisoners (50+) were obtained from the respective authority upon consent and total anonymity was ensured. Data gathered from all available medical records included basic demographic information, education and prison sentencing. Healthcare data obtained were extensive in nature encompassing data related to illness types, number of visits to different health care providers and hospitals. The corresponding reasons for visits and outcomes of these visits were extracted. All data are analysed using statistical software SPSS 20.0. Results: Data were extracted for a total of 50 older prisoners living in Switzerland. The chosen prisons are located in German-speaking cantons. Preliminary results show that the age average was 56 years. For more than half, this was their first imprisonment. Nevertheless, a third of them were sentenced to measures (Art. 64 Swiss Criminal Code) which means that the length of the detention is indefinite and while release is possible it is in most cases not very likely. This entails that these prisoners will grow old in prison and some will even spend their remaining years there. Concerning their health, a third of the sample reported respiratory and cardiovascular illnesses and half reported suffering from some form of musculoskeletal related pain. Older prisoners were prescribed on average only 3.5 medications, which is significantly fewer than the number of medication prescribed to younger prisoners, whose data were also sampled. Conclusion: Access to healthcare is a right given to all prisoners through the principle of equivalence which is generally exercised in Switzerland. Prisoners growing old in prison will represent a challenge for prison health care services.

The art and learning patterns of knowing in nursing

Objective To identify the perception of the students about the use of art as a pedagogical strategy in learning the patterns of knowing in nursing; to identify the dimensions of each pattern valued in the analysis of pieces of art. Method Descriptive mixed study. Data collection used a questionnaire applied to 31 nursing students. Results In the analysis of the students’ discourse, it was explicit that empirical knowledge includes scientific knowledge, tradition and nature of care. The aesthetic knowledge implies expressiveness, subjectivity and sensitivity. Self-knowledge, experience, reflective attitude and relationships with others are the subcategories of personal knowledge and the moral and ethics support ethical knowledge. Conclusion It is possible to learn patterns of knowledge through art, especially the aesthetic, ethical and personal. It is necessary to investigate further pedagogical strategies that contribute to the learning patterns of nursing knowledge.

A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants.

BACKGROUND: Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species. RESULTS: Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic self-incompatibility. CONCLUSIONS: We present a new systematic strategy of gene discovery based on conservation of the protein-coding sequence that complements classical forward and reverse genetics. This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest.

The night and day of dung beetles (Coleoptera, Scarabaeidae) in the Serra do Japi, Brazil: elytra colour related to daily activity

In the present study 387 dung beetles (Coleoptera: Scarabaeidae) were surveyed at the Serra do Japi, in the Atlantic Forest in São Paulo State, with four baited pitfall traps during the months of December, 1998, and January, 1999 during eight 24 hour cycles. A total of 30 species were identified and temporal variation in activity patterns among the species shows a specialization in the use of food resources: 9 species were classified as nocturnal and 13 as diurnal. The daily activity pattern of dung beetles does not necessarily correspond to the taxonomic classification, but is strongly related to the colouring of species, determined by predominant elytra colour: nocturnal species have 89 % more chances of being black as opposed to colourful. Black nocturnal species might have evolved as an interspecific adaptation to avoid predation (cryptic colouring). Among the colourful diurnal dung beetles, measure of body length of each species shows that development of bright colouring was more often found in medium to large species, which suggests that colouring evolved as a response to intraspecific pressures, important in agonistic encounters among males.

Biologia de Neotrioza tavaresi Crawford, 1925 (Hemiptera, Psyllidae), galhador da folha do araçazeiro (Psidium cattleianum)

Biology of the leaf gall inducer Neotrioza tavaresi Crawford, 1925 (Hemiptera, Psyllidae) on strawberry guava tree (Psidium cattleianum). A field study was conducted in Curitiba region, State of Paraná, southern Brazil, to describe the life cycle of Neotrioza tavaresi Crawford, 1925, a leaf galling insect in strawberry guava trees (Psidium cattleianum). Three cycles were observed (1997, 1998, 1999) during regular field trips and the insects were observed in Piraquara municipality, where 15 samples with 50 infested leaves were sampled in the 1997-98 cycle. Galls were dissected for detailed studies. Neotrioza tavaresi has a univoltine cycle in which adult individuals were found inside the galls from August onwards. The sexually mature insects with sex ratio 1, emerged from the galls after their dehiscence caused by feeding of the adult insects on the gall walls. Adult emergence started in early October and ended by early December, with its peak in November. Copulation took place as soon as adults exit the gall and egg laying started the next day. Females had more than 100 ovarioles containing 218.7±44.7 (n=50) fully formed eggs. This indicated the short sexual adult life-span (aprox. 5-7 days) of the species, also characterized by a concentrated oviposition. Adult individuals fed and laid their eggs on younger shoots of the plant. The bottoms of the yellowish eggs were inserted into the leaf tissue, mainly on its adaxial edge (78.1%). The nymphs hatched and, as they fed on the adaxial side of expanding leaves, modified the cell growth pattern and the round-shape galls developed on the adaxial side with one insect inside. The gall wall showed distinct layers, with the inner one suppliyng the food to the insects, and the outer layer supplying gall protection. Nymphs went through five instars and the exuviae remained stuck on a ball of wax inside the gall. All parasitoids found were Hymenoptera belonging to Chalcidoidea: Eulophidae (1 sp), Pteromalidae (2 spp) and Encyrtidae (3 spp). The findings suggest that leaf gall inducer and parasitoids insects and plant life cycles are closely connected and both leaf sprouting and gall opening seem to be triggered by the same environmental and plant conditions. The high abundance of shoots may favor insect performance as adult individuals can easily find an ideal place for feeding, copulating and laying eggs.

Distribuição de abundância e tamanho do corpo de invertebrados do folhiço em uma floresta de terra firme na Amazônia Central, Brasil

Abundace and body size distribution of invertebrates of leaf litter in Amazonian forest, Brazil. Based on 605 invertebrates sampled of the litter in an Amazonian Forest, some basic macroecological patterns for this assemblage were described. The relationship between abundance and body size, at logarithmic scale, was triangular, and the distribution of species was constrained in an asymmetric triangular envelope, that was tested using null model procedures in ECOSIM (P= 0,0002). The most abundant species were at an intermediated body size. The relationship between maximum abundance with different mean body size classes confirmed the Energetic Equivalent Rule (b = -1,069; t-0,75 = -2,13; P = 0.079). This way, species tend to consume energy from the community independent of their body size, since requirements are compensated by local population density.

Spatial pattern of floral morphology: a possible insight into the effects of pollinators on plant distribution

Pollination syndromes involve convergent evolution towards phenotypes composed of specific scents, colours or floral morphologies that attract or restrict pollinator access to reward. How these traits might influence the distributions of plant species in interaction with pollinators has rarely been investigated. We sampled 870 vegetation plots in the western Swiss Alps and classified the plant species into seven blossom types according to their floral morphology (wind, disk, funnel, tube, bilabiate, head or brush). We investigated the environmental features of plots with functional diversity (FD) lower than expected by chance alone to detect potential pollination filtering and related the proportions of the seven blossom types to a combination of environmental descriptors. From these results, we inferred the potential effect of the pollinator on the spatial distribution of plant species. The vegetation plots with significantly lower FD of blossom types than expected by chance were found at higher altitudes, and the proportions of blossom types were strongly patterned along the same gradient. These results support a biotic filtering effect on plant species assemblages through pollination: disk blossoms became dominant at higher altitudes, resulting in a lower FD. In harsh conditions at high altitudes, pollinators usually decrease in activity, and the openness of the disk blossom grants access to any available pollinator. Inversely, bilabiate blossoms, which are mostly pollinated by bees, were more abundant at lower elevations, which are characterised by greater abundance and diversity of bees. Generalisation through openness of the blossom could be advantageous at high elevations, while specialisation could be a successful alternative strategy at lower elevations. The approach used in this study is purely correlative, and further investigations should be conducted to infer the nature of the causal relationship between plant and pollinator distributions.

Elytra colour polymorphism and randomness of matings in Chauliognathus fallax Germar 1824 from southern Brazil (Coleoptera, Cantharidae)

Beetles of the species Chauliognathus fallax Germar 1824 are polymorphic for elytron colouration with six morphs distinguished on the basis of black pigmentation on a yellow background. We investigated samples of C. fallax taken in eight consecutive weeks aiming to determine the frequency of the morphs which were grouped, for statistical analysis, into three classes according to elytra pigmentation as well as the possible occurrence of assortative mating. Our results showed a variation in the frequency of the classes throughout the season, both in males and females, with the maximum frequency of each class at the fourth and fifth week. The three classes (A, B, C) showed the same pattern of variation, and class B was always the more frequent. To test randomness of matings two approaches were taken: in the first, we compared the frequency of each class in copulating and non-copulating insects. In the second, the frequency of each class in the whole sample was taken as the probability of occurrence of the respective class; then, using the criterion of the probability of independent events we calculated the expected proportion of copulating insects for each pair of events. Both methods gave non-significant differences, suggesting that the matings were random.

Efeitos do sexo, do vigor e do tamanho da planta hospedeira sobre a distribuição de insetos indutores de galhas em Baccharis pseudomyriocephala Teodoro (Asteraceae)

Several hypotheses have been proposed to explain the patterns of host plant utilization by herbivorous insects in natural communities. We tested four hypotheses aiming to understand the pattern of attack by gall-inducing insects on the dioecious shrub, Baccharis pseudomyriocephala (Asteraceae). The shrub occurs in the Parque Estadual do Itacolomi, Southeastern Brazil, and supports ten species of galling insects. The following hypotheses were tested: i) male plants are more attacked by galling insects than female plants; ii) larger plant modules are preferentially attacked by galling insects; iii) galling insects perform better on larger modules than on smaller modules; iv) galling insects increase in abundance with meristematic availability. To address these questions, 240 plants (120 of each sex) were sampled in both reproductive and vegetative periods. We recorded the growth rate (4 cm), inflorescence and fruit production, attack rates of the galling insects, and their survivorship and mortality per shoot (module). Modules were separated into size classes (cm) and analyzed by regressions and ANCOVAs. Module size and reproductive effort were positively correlated with host plant size. We did not observe any effect of host plant gender on either variables. In the same way, host plant sex did not show any influence on the abundance and richness of galling insects. Although the abundance of galling insects showed a positive correlation with shoot size, the trend disappeared when the analyses were performed taking into consideration the number of galls per unit of growth (number of galls/cm of shoot) or biomass (number of galls/dry weight). Larval survivorship was not influenced by shoot size. Also, we observed that the abundance of one species of hemipteran galling insect showed a positive relation with leaf biomass. Therefore, we conclude that gender and vigor of this plant species do not influence the community structure of its galling herbivores.

Aspectos biológicos de Zabrotes subfasciatus (Bohemann, 1833) (Coleoptera, Bruchidae) em Phaseolus vulgaris L., cv. Carioca (Fabaceae), sob condições de laboratório

Zabrotes subfasciatus is a serious pest of common beans, P. vulgaris L.. In Brazil there are several studies dealing with resistance of bean genotypes to this insect, while other studies have emphasized the utilization of oils and powders from plants to repel their attack. In this paper, fecundity, fertility, pattern of oviposition, life cycle and longevity were evaluated for a Brazilian stock from the Goiás State on P. vulgaris cv. Carioca, at 30ºC and 70% R.H. The mean fecundity was 38 eggs per female and 73% of viability. Egg laying showed an aggregated pattern. Males and females lived an average of 13 and 9 days, respectively. The total life cycle lasted for about 28 days.