A Brassica exon array for whole-transcript gene expression profiling

Affymetrix GeneChip (R) arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip (R) arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip (R) arrays whose probes are localised primarily in 39 exons. Plant whole-transcript (WT) GeneChip (R) arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip (R) Brassica Exon 1.0 ST Array is a 5 mu M feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E(-5), with <= 98 sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/index.html.

Postpartum GAD is a risk factor for postpartum MDD: the course and longitudinal relationships of postpartum GAD and MDD

Background The objective was to examine the course and longitudinal associations of generalized anxiety disorder (GAD) and major depressive disorder (MDD) in mothers over the postpartum 2 years. Method Using a prospective naturalistic design, 296 mothers recruited from a large community pool were assessed for GAD and MDD at 3, 6, 10, 14, and 24 months postpartum. Structured clinical interviews were used for diagnoses, and symptoms were assessed using self-report questionnaires. Logistic regression analyses were used to examine diagnostic stability and longitudinal relations, and latent variable modeling was employed to examine change in symptoms. Results MDD without co-occurring GAD, GAD without co-occurring MDD, and co-occurring GAD and MDD, displayed significant stability during the postpartum period. Whereas MDD did not predict subsequent GAD, GAD predicted subsequent MDD (in the form of GAD + MDD). Those with GAD + MDD at 3 months postpartum were significantly less likely to be diagnosis free during the follow-up period than those in other diagnostic categories. At the symptom level, symptoms of GAD were more trait-like than those of depression. Conclusions Postpartum GAD and MDD are relatively stable conditions, and GAD is a risk factor for MDD but not vice versa. Given the tendency of MDD and GAD to be persistent, especially when comorbid, and the increased risk for MDD in mothers with GAD, as well as the potential negative effects of cumulative exposure to maternal depression and anxiety on child development, the present findings clearly highlight the need for screening and treatment of GAD in addition to MDD during the postpartum period.

Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs

Although Ca transport in plants is highly complex, the overexpression of vacuolar Ca2+ transporters in crops is a promising new technology to improve dietary Ca supplies through biofortification. Here, we sought to identify novel targets for increasing plant Ca accumulation using genetical and comparative genomics. Expression quantitative trait locus (eQTL) mapping to 1895 cis- and 8015 trans-loci were identified in shoots of an inbred mapping population of Brassica rapa (IMB211 × R500); 23 cis- and 948 trans-eQTLs responded specifically to altered Ca supply. eQTLs were screened for functional significance using a large database of shoot Ca concentration phenotypes of Arabidopsis thaliana. From 31 Arabidopsis gene identifiers tagged to robust shoot Ca concentration phenotypes, 21 mapped to 27 B. rapa eQTLs, including orthologs of the Ca2+ transporters At-CAX1 and At-ACA8. Two of three independent missense mutants of BraA.cax1a, isolated previously by targeting induced local lesions in genomes, have allele-specific shoot Ca concentration phenotypes compared with their segregating wild types. BraA.CAX1a is a promising target for altering the Ca composition of Brassica, consistent with prior knowledge from Arabidopsis. We conclude that multiple-environment eQTL analysis of complex crop genomes combined with comparative genomics is a powerful technique for novel gene identification/prioritization.

Behavioural responses of the seven-spot ladybird Coccinella septempunctata to plant headspace chemicals collected from four crop Brassicas and Arabidopsis thaliana, infested with Myzus persicae

1 Insects using olfactory stimuli to forage for prey/hosts are proposed to encounter a ‘reliability–detectability problem’, where the usability of a stimulus depends on its reliability as an indicator of herbivore presence and its detectability. 2 We investigated this theory using the responses of female seven-spot ladybirds Coccinella septempunctata (Coleoptera: Coccinellidae) to plant headspace chemicals collected from the peach-potato aphid Myzus persicae and four commercially available Brassica cultivars; Brassica rapa L. cultivar ‘turnip purple top’, Brassica juncea L. cultivar ‘red giant mustard’, Brassica napus L. cultivar ‘Apex’, Brassica napus L. cultivar ‘Courage’ and Arabidopsis thaliana. For each cultivar/species, responses to plants that were undamaged, previously infested by M. persicae and infested with M. persicae, were investigated using dual-choice Petri dish bioassays and circular arenas. 3 There was no evidence that ladybirds responded to headspace chemicals from aphids alone. Ladybirds significantly preferred headspace chemicals from B. napus cv. Apex that were undamaged compared with those from plants infested with aphids. For the other four species/cultivars, there was a consistent trend of the predators being recorded more often in the half of the Petri dish containing plant headspace chemicals from previously damaged and infested plants compared with those from undamaged ones. Furthermore, the mean distance ladybirds walked to reach aphid-infested A. thaliana was significantly shorter than to reach undamaged plants. These results suggest that aphid-induced plant chemicals could act as an arrestment or possibly an attractant stimulus to C. septempunctata. However, it is also possible that C. septempunctata could have been responding to aphid products, such as honeydew, transferred to the previously damaged and infested plants. 4 The results provide evidence to support the ‘reliability–detectability’ theory and suggest that the effectiveness of C. septempunctata as a natural enemy of aphids may be strongly affected by which species and cultivar of Brassica are being grown.

Foraging strategies of natural enemies of the peach-potato aphid Myzus persicae

The foraging strategies of two natural enemies of the peach-potato aphid Myzus persicae: the seven-spot ladybird Coccinella septempunctata and the parasitoid wasp Diaeretiella rapae, were investigated. Specifically the roles of plant semiochemicals in the location of plants infested with M. persicae by these natural enemies were examined. I investigated the olfactory responses of female C. septempunctata to volatiles collected from M. persicae and four Brassica cultivars; Brassica rapa, B. juncea, B. napus cultivar ‘Apex’ and B. napus cultivar ‘Courage’ and wild-type Arabidopsis thaliana that were: undamaged, previously infested by M. persicae and infested with M. persicae. C. septempunctata showed no attraction to volatiles from M. persicae alone. C. septempunctata significantly changed its searching behaviour in response to plant volatiles from B. rapa, B. napus cv. ‘Apex’ and Arabidopsis infested with M. persicae. C. septempunctata was also found to display a significant turning bias when foraging on a branching horizontal wire stem. A model was developed to investigate how turning biases affect the foraging efficiency of C. septempunctata in dichotomous branched environments. Simulations using this model indicated that turning biases could potentially increase searching efficiency. D. rapae showed a significant preference for volatiles from M. persicae infested wild-type Arabidopsis but no preference to volatiles from M. persicae alone or M. persicae honeydew. Volatile emissions by Arabidopsis were shown to be localised to the area of aphid-infestation rather than systemic. Using gas chromatography plants infested with M. persicae were shown to emit a quantitatively different volatile blend than undamaged plants. In experiments with jasmonate mutants of Arabidopsis the jasmonate (octadecanoid) wound response pathway was implicated as being important for the production of M. persicae induced volatiles, attractive to D. rapae. Other wound response pathways were also found to be involved in the production of the full blend of M. persicae induced volatiles.

Assessing the value of imperfect biocontainment nationally: rapeseed in the United Kingdom as an exemplar

Paternal biocontainment methods (PBMs) act by preventing pollen-mediated transgene flow. They are compromised by transgene escape via the crop-maternal line. We therefore assess the efficacy of PBMs for transgenic rapeseed (Brassica napus) biocontainment across the United Kingdom by estimating crop-maternal hybridization with its two progenitor species. We used remote sensing, field surveys, agricultural statistics, and meta-analysis to determine the extent of sympatry between the crop and populations of riparian and weedy B. rapa and B. oleracea. We then estimated the incidence of crop-maternal hybridization across all settings to predict the efficacy of PBMs. Evidence of crop chloroplast capture by the progenitors was expanded to a national scale, revealing that crop-maternal gene flow occurs at widely variable rates and is dependent on both the recipient and setting. We use these data to explore the value that this kind of biocontainment can bring to genetic modification (GM) risk management in terms of reducing the impact that hybrids have on the environment rather than preventing or reducing hybrid abundance per se.

A simple and versatile 2-dimensional platform to study plant germination and growth under controlled humidity

We describe a simple, inexpensive, but remarkably versatile and controlled growth environment for the observation of plant germination and seedling root growth on a flat, horizontal surface over periods of weeks. The setup provides to each plant a controlled humidity (between 56% and 91% RH), and contact with both nutrients and atmosphere. The flat and horizontal geometry of the surface supporting the roots eliminates the gravitropic bias on their development and facilitates the imaging of the entire root system. Experiments can be setup under sterile conditions and then transferred to a non-sterile environment. The system can be assembled in 1-2 minutes, costs approximately 8.78$ per plant, is almost entirely reusable (0.43$ per experiment in disposables), and is easily scalable to a variety of plants. We demonstrate the performance of the system by germinating, growing, and imaging Wheat (Triticum aestivum), Corn (Zea mays), and Wisconsin Fast Plants (Brassica rapa). Germination rates were close to those expected for optimal conditions.

Just add water and salt: the optimisation of petrogenic hydrocarbon biodegradation in soils from semi-arid Barrow Island, Western Australia

We investigated the potential of soil moisture and nutrient amendments to enhance the biodegradation of oil in the soils from an ecologically unique semi-arid island. This was achieved using a series of controlled laboratory incubations where moisture or nutrient levels were experimentally manipulated. Respired CO2 increased sharply with moisture amendment reflecting the severe moisture limitation of these porous and semi-arid soils. The greatest levels of CO2 respiration were generally obtained with a soil pore water saturation of 50–70%. Biodegradation in these nutrient poor soils was also promoted by the moderate addition of a nitrogen fertiliser. Increased biodegradation was greater at the lowest amendment rate (100 mg N kg−1 soil) than the higher levels (500 or 1,000 mg N kg−1 soil), suggesting the higher application rates may introduce N toxicity. Addition of phosphorous alone had little effect, but a combined 500 mg N and 200 mg P kg−1 soil amendment led to a synergistic increase in CO2 respiration (3.0×), suggesting P can limit the biodegradation of hydrocarbons following exogenous N amendment.

Races of Albugo candida causing white blister rust on brassica vegetables in Australia

Albugo Candida races of Australian isolates from B. oleracea var. italica (broccoli), B. rapa var. pekinensis (pak choi) and var. chinensis (Chinese cabbage), and Capsella bursa-pastoris (shepherd's purse) were identified on a set of Brassicaceae hosts. Isolates from broccoli were identified as A. candida race 9 (Ac 9), from pak choi and Chinese cabbage as the sub-race V of Ac 7 or as a mixed population of sub-races A and V of the same race. Isolates from Shepherd's purse were identified as Ac 4. Australian Ac 9 isolates caused white blister disease on broccoli, broccolini, cauliflower, Brussels sprout and other related Brassicaceae hosts including B. nigra (black mustard), B. napus (oilseed rape), and on B. rapa (turnip rape) 'Torch' (a differential host of Ac 7). All cultivars of cabbage (B. oleracea var. capitata) and one new broccoli 'Booster' inoculated with isolates from broccoli were immune to the isolate tested. This result indicates that the Australian A. candida varies from the European one that causes disease on cabbage as well as on other B. oleracea varieties and additionally on shepherd's purse and an American one that causes disease on cabbage. The genotype of B. nigra tested was susceptible to both Ac 9 and Ac 7. This result indicates that B. nigra can serve as a host for both races. This study provides the first record of white blister disease on B. napus ('Hobson' and 'Regent') in Australia.

Os impactos do uso de tecnologia da informação e da identificação e captura automática de dados nos processos operacionais do varejo

Este trabalho objetivou identificar as principais tecnologias disponíveis de TI (Tecnologia da Informação) e de AIDC (Identificação e Captura Automática de Dados) para a área de varejo de autosserviço, para preencher a lacuna existente na literatura, sobre os benefícios de se usar novas tecnologias no ponto de venda, com vistas a otimizar sua operação. Para tanto, foram estudados os principais processos operacionais de uma loja de varejo de autosserviço, com vistas a identificar como as Tecnologias da Informação (TI) e de Identificação e Captura Automática de Dados (AIDC), poderiam ajudar a melhorar os resultados operacionais e agregar valor ao negócio. Para analisar suas proposições (de que o uso de TI e de AIDC podem ajudar na: redução dos tempos dos processos de retaguarda; redução do número de operações no ponto de venda; prevenção de perdas; redução dos custos e dos tempos para a realização dos inventários; redução do número de funcionários nas lojas; redução do tempo de fila no caixa; redução de rupturas e no aumento da eficiência operacional da loja), foram pesquisados diversos estudos de casos mundiais de empresas do segmento de varejo, que implementaram as tecnologias de AIDC e TI, principalmente a de RFID, para saber quais foram os impactos do uso destas tecnologias em suas operações e, em seguida, foi desenvolvido um Estudo de Caso abrangente, por meio do qual se objetivou entender os benefícios empresariais reais do uso destas tecnologias para o varejo de autosserviço. Como resultado final, foi possível identificar as mudanças nos processos operacionais do varejo de autosserviço, bem como os benefícios gerados em termos de custo, produtividade, qualidade, flexibilidade e inovação. O trabalho também evidenciou os pontos críticos de sucesso para a implementação da TI e das AIDC no varejo, que são: a revisão dos processos operacionais; a correta definição do hardware; dos insumos; do software; das interferências do ambiente físico; da disponibilização dos dados/informações dos produtos; das pessoas/funcionários e dos parceiros de negócios/fornecedores. De maneira mais específica, este trabalho buscou contribuir para o enriquecimento do campo de estudos no segmento de varejo e para o uso da tecnologia da informação, no Brasil, já que o assunto sobre o uso e o impacto de novas tecnologias no ponto de vendas, ainda permanece pouco explorado academicamente.

Touch ‘n’ sketch: pen and fingers on a multi-touch sketch application for tablet PC’s

In many creative and technical areas, professionals make use of paper sketches for developing and expressing concepts and models. Paper offers an almost constraint free environment where they have as much freedom to express themselves as they need. However, paper does have some disadvantages, such as size and not being able to manipulate the content (other than remove it or scratch it), which can be overcome by creating systems that can offer the same freedom people have from paper but none of the disadvantages and limitations. Only in recent years has the technology become massively available that allows doing precisely that, with the development in touch‐sensitive screens that also have the ability to interact with a stylus. In this project a prototype was created with the objective of finding a set of the most useful and usable interactions, which are composed of combinations of multi‐touch and pen. The project selected Computer Aided Software Engineering (CASE) tools as its application domain, because it addresses a solid and well‐defined discipline with still sufficient room for new developments. This was the result from the area research conducted to find an application domain, which involved analyzing sketching tools from several possible areas and domains. User studies were conducted using Model Driven Inquiry (MDI) to have a better understanding of the human sketch creation activities and concepts devised. Then the prototype was implemented, through which it was possible to execute user evaluations of the interaction concepts created. Results validated most interactions, in the face of limited testing only being possible at the time. Users had more problems using the pen, however handwriting and ink recognition were very effective, and users quickly learned the manipulations and gestures from the Natural User Interface (NUI).

Nutritional composition, phenolic compounds, nitrate content in eatable vegetables obtained by conventional and certified organic grown culture subject to thermal treatment

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Diferentes níveis de torta de nabo forrageiro (Raphanus sativus) como aditivo na silagem de capim elefante

The aim of the study was to evaluate the effects of the inclusion of different levels of turnip cake (TNF) on the chemical composition, digestibility and quality of elephant grass silage. Due to the quality of the oil extracted from the seeds, the turnip is being considered as an important option for the biodiesel industry in Brazil. The turnip cake is obtained from the mechanical pressing of the seeds to produce oil, and it differs from the meal by the content of fat. In the meal the fat is less than 1%, due to the use of solvents for the oil extraction. Experimental silos were used in a completely randomized design, in factorial arrangement 2 x 3 (two types of material and four levels of inclusion). The materials were represented for original material (fresh) and ensiled material, with four levels of inclusion of TNF (0, 3, 6, and 9%). Dry matter (DM), ether extract (EE), crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), nitrogen indigestible neutral detergent (NIDN), nitrogen indigestible acid detergent (NIDA), ash (MM), lignin (LIG), buffer power (PT), calcium (Ca), phosphorus (P) and in vitro dry matter digestibility (IVDDM) were determined in all materials. In silage, additionally, were determined pH and amoniacal nitrogen (NH3-N). There were effects of inclusion of TNF and the type of material on the DM, CP, ADF, NIDA, P, and MM contents and on IVDDM. The interaction of the two factors was observed to the contents of CP, NDF, ADF, NIDA, Ca and IVDDM. In silage, the DM levels were lower (P < 0.05) than in original material. The values of DM were increased linearly as increased levels of inclusion of TNF. The fibrous components, including NIDN and NIDA, decreased linearly when the TNF increased. In all treatments, values of pH and N-NH3 considered ideal for good silage were observed. The IVDDM was reduced, linearly, with the addition of increasing levels of TNF. A negative correlation (-0.95) between IVDDM and content of EE may explain the tendency of this variable, due to the EE content increased linearly with the addition of TNF. The addition of TNF as an additive in silage of elephant diminished IVDDM. Considering the changes observed in the chemical composition and digestibility of elephant grass silage with TNF as additive, suggests that this should not be included at levels exceeding 3%. On the other hand, the silages with TNF as additive showed appropriate fermentation characteristics.

Influence of storage on chemical properties of different peats

The change of chemical properties during storage of 12 fertilized bagged peats of different origins at high temperature was investigated. The average values for N, soluble salts and EC decreased significantly, whereas the pH as well as P and K contents changed only slightly. Differences in N were observed between the peats. The contents of CAT soluble N in the two dredged frozen black peats did not change during storage. However, a decrease in N was found when water extraction was used. In the case of the 10 white peats the loss of N differed considerably, but it was independent of the method of peat harvest. The N decrease resulted mainly from reduced levels of NO3-N. Substances damaging to plant growth do not seem to have developed during storage as shown by trials on the germination and the growth of Chinese cabbage. There were no significant differences between the peats, whether stored or not.

Carbono orgânico e carbono residual do solo em sistema de plantio direto, submetido a diferentes manejos

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)