Comparative transcriptomics of early dipteran development

BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. In particular, this approach holds great promise for emerging model species in fields such as evolutionary developmental biology (evo-devo). RESULTS: We have sequenced early embryonic transcriptomes of two non-drosophilid dipteran species: the moth midge Clogmia albipunctata, and the scuttle fly Megaselia abdita. Our analysis includes a third, published, transcriptome for the hoverfly Episyrphus balteatus. These emerging models for comparative developmental studies close an important phylogenetic gap between Drosophila melanogaster and other insect model systems. In this paper, we provide a comparative analysis of early embryonic transcriptomes across species, and use our data for a phylogenomic re-evaluation of dipteran phylogenetic relationships. CONCLUSIONS: We show how comparative transcriptomics can be used to create useful resources for evo-devo, and to investigate phylogenetic relationships. Our results demonstrate that de novo assembly of short (Illumina) reads yields high-quality, high-coverage transcriptomic data sets. We use these data to investigate deep dipteran phylogenetic relationships. Our results, based on a concatenation of 160 orthologous genes, provide support for the traditional view of Clogmia being the sister group of Brachycera (Megaselia, Episyrphus, Drosophila), rather than that of Culicomorpha (which includes mosquitoes and blackflies).

Dopamine affects parvalbumin expression during cortical development in vitro.

This study was undertaken to determine how dopamine influences cortical development. It focused on morphogenesis of GABAergic neurons that contained the calcium-binding protein parvalbumin (PV). Organotypic slices of frontoparietal cortex were taken from neonatal rats, cultured with or without dopamine, harvested daily (4-30 d), and immunostained for parvalbumin. Expression of parvalbumin occurred in the same regional and laminar sequence as in vivo. Expression in cingulate and entorhinal preceded that in lateral frontoparietal cortices. Laminar expression progressed from layer V to VI and finally II-IV. Somal labeling preceded fiber labeling by 2 d. Dopamine accelerated PV expression. In treated slices, a dense band of PV-immunoreactive neurons appeared in layer V at 7 d in vitro (DIV), and in all layers of frontoparietal cortex at 14 DIV, whereas in control slices such labeling did not appear until 14 and 21 DIV, respectively. The laminar distribution and dendritic branching of PV-immunoreactive neurons were quantified. More labeled neurons were in the superficial layers, and their dendritic arborizations were significantly increased by dopamine. Treatment with a D1 receptor agonist had little effect, whereas a D2 agonist mimicked dopamine's effects. Likewise, the D2 but not the D1 antagonist blocked dopamine-induced changes, indicating that they were mediated primarily by D2 receptors. Parvalbumin expression was accelerated by dopaminergic reinnervation of cortical slices that were cocultured with mesencephalic slices. Coapplication of the glutamate NMDA receptor antagonist MK801 or AP5 blocked dopamine-induced increases in dendritic branching, suggesting that changes were mediated partly by interaction with glutamate to alter cortical excitability.

Differences in phasic development rate amongst wheat cultivars independent of responses to photoperiod and vernalization. A viewpoint of the intrinsic earliness hypothesis

Differences amongst wheat cultivars in the rate of reproductive development are largely dependent on differences in their sensitivity to photoperiod and vernalization. However, when these responses are accounted for, by growing vernalized seedlings under long photoperiods, cultivars can still differ markedly in time to ear emergence. Control of rate of development by this ‘third factor’ has been poorly understood and is variously referred to as intrinsic earliness, earliness in the narrow sense, basic vegetative period, earliness per se, and basic development rate. Certain assumptions are made in the concept of intrinsic earliness. They are that differences in intrinsic earliness (i) are independent of the responses of the cultivars to photoperiod and vernalization, (ii) apply only to the length of the vegetative period up to floral initiation (as suggested by several authors), (iii) are maintained under different temperatures, measured either in days or degree days. As a consequence of this, the ranking of cultivars (from intrinsically early to intrinsically late) must be maintained at different temperatures. This paper, by the re-analysis of published data, examines the extent to which these assumptions can be supported. Although it is shown that intrinsic earliness operates independently of photoperiod and vernalization responses, the other assumptions were not supported. The differences amongst genotypes in time to ear emergence, grown under above-optimum vernalization and photoperiod (that is when the response to these factors is saturated), were not exclusively due to parallel differences in the length of the vegetative phase, and the length of the reproductive phase was independent of that of the vegetative phase. Thus, it would be possible to change the relative allocation of time to vegetative and reproductive periods with no change in the full period to ear emergence. The differences in intrinsic earliness between cultivars were modified by the temperature regime under which they were grown, i.e. the difference between cultivars (both considering the full phase to ear emergence or some sub-phases) was not a constant amount of time or thermal time at different temperatures. In addition, in some instances genotypes changed their ranking for ‘intrinsic earliness’ depending on the temperature regime. This was interpreted to mean that while all genotypes are sensitive to temperature they differ amongst themselves in the extent of that sensitivity. Therefore, ‘intrinsic earliness’ should not be considered as a static genotypic characteristic, but the result of the interaction between the genotype and temperature. Intrinsic earliness is therefore likely to be related to temperature sensitivity. Some implications of these conclusions for plant breeding and crop simulation modelling are discussed.

Barley development as affected by rate of change of photoperiod

The rate of leaf appearance of barley varies substantially with time of sowing. This variation has been related to both the length and the rate of change of photoperiod at the time of plant emergence. An outdoor pot experiment was conducted to test if rate of change of photoperiod directly affects phasic development and rate of leaf emergence of spring barley. Two photoperiod-sensitive cultivars (Bandulla and Galleon) were subjected to five photoperiod regimes: two constant photoperiods, of 14 and 15·5 h, and three different rates of change of photoperiod of c. 2, 9 and 13 min/day from seedling emergence to awn initiation. Photoperiod treatments significantly affected the duration from seedling emergence to awn initiation in both cultivars. Rate of change of photoperiod did not affect the rate of development towards awn initiation independently of the absolute daylength it produced. Although Bandulla had a longer duration than Galleon at any photoperiod regime, the cultivars did not vary in their sensitivity to photoperiod. When this phase was divided into the leaf initiation (LI) and spikelet initiation (SI) phases, it was evident that the sensitivity to photoperiod was not constant, being in general higher during the SI than during the LI phase. However, the magnitude of the change in sensitivity was cultivar-dependent, indicating that sensitivity to photoperiod during the different phases could be under independent genetic control. Final numbers of primordia (leaves together with maximum spikelet number) were negatively affected by increasing photoperiods, but once again, there was no evidence of any effect of the rate of change of photoperiod which was independent of the average photoperiod. Both cultivars showed similar sensitivities for final leaf number but maximum spikelet number was more sensitive to photoperiod in Galleon than in Bandulla. Highly significant linear relationships between leaf number and thermal time were found for all combinations of cultivars and photoperiod regimes (r2 > 0·98). The rate of leaf appearance (RLA) was similar for both cultivars (c. 0·0185 leaves/°Cd) and did not alter during plant development or in response to the change in photoperiod at awn initiation. The range in RLA was greater for Galleon (0·0170–0·0205 leaves/°Cd) than for Bandulla (0·0173–0·0186 leaves/°Cd). Neither of these cultivars exhibited a significant relationship between rate of leaf emergence and photoperiod or rate of change of photoperiod. The lack of significant relationships between RLA and length or rate of change of photoperiod is in contrast with previous reports using time of sowing as a main treatment.

Seedling development and biomass as affected by seed size and morphology in durum wheat

This work evaluated the effect of seed size and morphology on the development and biomass of durum wheat seedlings. Three different seed-grading sizes selected by sieving were used in glasshouse experiments, and a set of three developmental and 23 biomass-related indices were measured on eight genotypes, at two moisture levels. The influence of seed size on seedling development was studied at high and low temperatures (22\12 mC, and 15\5 mC day\night temperatures, respectively), in growth chambers. The area of the seed and the area of the embryo were the seed morphological traits most affected by seed size. Seed size was strongly associated with seedling development and seedling biomass until the complete extension of the first two leaves, at the fourth leaf stage. The rate of first-leaf growth and the area of the first leaf were the developmental and biomass traits, respectively, most sensitive to seed-grading size.

A Semantic wiki for quality management in software development projects

Quality management has become a strategic issue for organisations and is very valuable to produce quality software. However, quality management systems (QMS) are not easy to implement and maintain. The authors' experience shows the benefits of developing a QMS by first formalising it using semantic web ontologies and then putting them into practice through a semantic wiki. The QMS ontology that has been developed captures the core concepts of a traditional QMS and combines them with concepts coming from the MPIu'a development process model, which is geared towards obtaining usable and accessible software products. Then, the ontology semantics is directly put into play by a semantics-aware tool, the Semantic MediaWiki. The developed QMS tool is being used for 2 years by the GRIHO research group, where it has manages almost 50 software development projects taking into account the quality management issues. It has also been externally audited by a quality certification organisation. Its users are very satisfied with their daily work with the tool, which manages all the documents created during project development and also allows them to collaborate, thanks to the wiki features.

Background, current status and future prospects of transgenic crop plant development

Les plantes transgèniques són una part integral de l’agricultura contemporània. Durant l’any 2006 més de noranta milions d’hectàrees de plantes transgèniques van ser cultivades en vint-i-un països. Des de la comercialització de la primera planta transgènica el 1996 els nivells d’adopció d’aquests cultius han augmentat anualment amb percentatges de dos dígits. El desenvolupament i la comercialització de les plantes transgèniques van lligats estretament al comerç mundial, a la globalització, a la disponibilitat de suficient menjar, a la protecció del medi ambient i del consumidor i a la propietat intel·lectual. En aquest article exposem els avenços més recents i les tendències actuals en el desenvolupament dels cultius transgènics i de la seva utilització. També ens fem ressò d’alguns assumptes no científics que s’han de solucionar abans que aquests cultius arribin al màxim del seu potencial, proporcionant una agricultura més sostenible i ecològica. Finalment, ressaltarem la importància de com les plantes transgèniques poden contribuir en la disponibilitat de menjar i en la millora de la pobresa en els països en vies de desenvolupament.

Modelling leaf development in Oxalis latifolia

This study was carried to develop functions that could explain the growth of Oxalis latifolia, in both early stages and throughout the season, contributing to the improvement of its cultural control. Bulbs of the Cornwall form of O. latifolia were buried at 1 and 8 cm in March 1999 and 2000. Samples were destructive at fixed times, and at each time the corresponding BBCH scale codes as well as the absolute number of growing and adult leaves were noted. Using the absolute number of adult leaves (transformed to percentages), a Gaussian curve of three parameters that explains the growth during the season (R2=0.9355) was developed. The BBCH scale permitted the fit of two regression lines that were accurately adjusted for each burial depth (R2=0.9969 and R2=0.9930 respectively for 1 and 8 cm). The best moment for an early defoliation in Northern Spain could be calculated with these regression lines, and was found to be the second week of May. In addition, it was observed that a burial depth of 8 cm does not affect the growing pattern of the weed, but it affects the number of leaves they produce, which decreases to less than a half of those produced at 1 cm.

MPRO-Spanish: development and experiments with a linguistic parser for Spanish texts

This paper describes the main features and present results of MPRO-Spanish, a parser for morphological and syntactic analysis of unrestricted Spanish text developed at the IAI1. This parser makes direct use of X-phrase structure rules to handle a variety of patterns from derivational morphology and syntactic structure. Both analyses, morphological and syntactic, are realised by two subsequent modules. One module analyses and disambiguates the source words at morphological level while the other consists of a series of programs and a deterministic, procedural and explicit grammar. The article explains the main features of MPRO and resumes some of the experiments on some of its applications, some of which still being implemented like the monolingual and bilingual term extraction while others need further work like indexing. The results and applications obtained so far with simple and relatively complex sentences give us grounds to believe in its reliability.

Analysis of vineyard differential management zones and relation to vine development, grape maturity and quality

The objective of research was to analyse the potential of Normalized Difference Vegetation Index (NDVI) maps from satellite images, yield maps and grapevine fertility and load variables to delineate zones with different wine grape properties for selective harvesting. Two vineyard blocks located in NE Spain (Cabernet Sauvignon and Syrah) were analysed. The NDVI was computed from a Quickbird-2 multi-spectral image at veraison (July 2005). Yield data was acquired by means of a yield monitor during September 2005. Other variables, such as the number of buds, number of shoots, number of wine grape clusters and weight of 100 berries were sampled in a 10 rows × 5 vines pattern and used as input variables, in combination with the NDVI, to define the clusters as alternative to yield maps. Two days prior to the harvesting, grape samples were taken. The analysed variables were probable alcoholic degree, pH of the juice, total acidity, total phenolics, colour, anthocyanins and tannins. The input variables, alone or in combination, were clustered (2 and 3 Clusters) by using the ISODATA algorithm, and an analysis of variance and a multiple rang test were performed. The results show that the zones derived from the NDVI maps are more effective to differentiate grape maturity and quality variables than the zones derived from the yield maps. The inclusion of other grapevine fertility and load variables did not improve the results.

Evaluation of the Development of Metacognitive Knowledge Supported by the KnowCat System

The aim of this study was to examine the development of the metacognitive knowledge of a group of higher education students who participated actively in an experiment based on a Computer Supported Collaborative Learning environment called KnowCat. Eighteen university students participated in a 12-month learning project during which the KnowCat learning environment was used to support scaffolding process among equals during problem-solving tasks. After using KnowCat, the students were interviewed over their work in this shared workspace. Qualitative analysis revealed that the educational application of KnowCat can favour and improve the development of metacognitive knowledge.

The role of fibroblast growth factor (FGF) and type beta transforming growth factot beta (TGF beta1, beta2 and beta3) during rat craniofacial development

Growth factors seem to be part of a complex cellular signalling language, in which individual growth factors are the equivalents of the letters that compose words. According to this analogy, informational content lies, not in an individual growth factor, but in the entire set of growth factors and others signals to which a cell is exposed. The ways in which growth factors exert their combinatorial effects are becoming clearer as the molecular mechanisms of growth factors actions are being investigated. A number of related extracellular signalling molecules that play widespread roles in regulating development in both invertebrates and vertebrates constitute the Fibroblast Growth Factor (FGF) and type beta Transforming Growth Factor ((TGF beta). The latest research literature about the role and fate of these Growth factors and their influence in the craniofacial bone growth ad development is reviewed

The role of fibroblast growth factor (FGF) and type beta transforming growth factot beta (TGF beta1, beta2 and beta3) during rat craniofacial development

Growth factors seem to be part of a complex cellular signalling language, in which individual growth factors are the equivalents of the letters that compose words. According to this analogy, informational content lies, not in an individual growth factor, but in the entire set of growth factors and others signals to which a cell is exposed. The ways in which growth factors exert their combinatorial effects are becoming clearer as the molecular mechanisms of growth factors actions are being investigated. A number of related extracellular signalling molecules that play widespread roles in regulating development in both invertebrates and vertebrates constitute the Fibroblast Growth Factor (FGF) and type beta Transforming Growth Factor ((TGF beta). The latest research literature about the role and fate of these Growth factors and their influence in the craniofacial bone growth ad development is reviewed

Humeral development from neonatal period to skeletal maturity—application in age and sex assessment

The goal of the present study is to examine cross-sectional information on the growth of the humerus based on the analysis of four measurements, namely, diaphyseal length, transversal diameter of the proximal (metaphyseal) end of the shaft, epicondylar breadth and vertical diameter of the head. This analysis was performed in 181 individuals (90 ♂ and 91 ♀) ranging from birth to 25 years of age and belonging to three documented Western European skeletal collections (Coimbra, Lisbon and St. Bride). After testing the homogeneity of the sample, the existence of sexual differences (Student"s t- and Mann-Whitney U-test) and the growth of the variables (polynomial regression) were evaluated. The results showed the presence of sexual differences in epicondylar breadth above 20 years of age and vertical diameter of the head from 15 years of age, thus indicating that these two variables may be of use in determining sex from that age onward. The growth pattern of the variables showed a continuous increase and followed first- and second-degree polynomials. However, growth of the transversal diameter of the proximal end of the shaft followed a fourth-degree polynomial. Strong correlation coefficients were identified between humeral size and age for each of the four metric variables. These results indicate that any of the humeral measurements studied herein is likely to serve as a useful means of estimating sub-adult age in forensic samples.

Aspirin and statin use and the subsequent development of depression in men and women: Results from a longitudinal population-based study.

OBJECTIVE: Low-grade chronic inflammation is one potential mechanism underlying the well-established association between major depressive disorder (MDD) and increased cardiovascular morbidity. Both aspirin and statins have anti-inflammatory properties, which may contribute to their preventive effect on cardiovascular diseases. Previous studies on the potentially preventive effect of these drugs on depression have provided inconsistent results. The aim of the present paper was to assess the prospective association between regular aspirin or statin use and the incidence of MDD. METHOD: This prospective cohort study included 1631 subjects (43.6% women, mean age 51.7 years), randomly selected from the general population of an urban area. Subjects underwent a thorough physical evaluation as well as semi-structured interviews investigating DSM-IV mental disorders at baseline and follow-up (mean duration 5.2 years). Analyses were adjusted for a wide array of potential confounders. RESULTS: Our main finding was that regular aspirin or statin use at baseline did not reduce the incidence of MDD during follow-up, regardless of sex or age (hazard ratios, aspirin: 1.19; 95%CI, 0.68-2.08; and statins: 1.25; 95%CI, 0.73-2.14; respectively). LIMITATIONS: Our study is not a randomized clinical trial and could not adjust for all potential confounding factors, information on aspirin or statin use was collected only for the 6 months prior to the evaluations, and the sample was restricted to subjects between 35 and 66 years of age. CONCLUSION: Our data do not support a large scale preventive treatment of depression using aspirin or statins in subjects aged from 35 to 66 years from the community.