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Comparative transcriptome analysis of lufenuron-resistant and susceptible strains of Spodoptera frugiperda (Lepidoptera: Noctuidae)
No full textAbstract\ud
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Background\ud
The evolution of insecticide resistance in Spodoptera frugiperda (Lepidoptera: Noctuidae) has resulted in large economic losses and disturbances to the environment and agroecosystems. Resistance to lufenuron, a chitin biosynthesis inhibitor insecticide, was recently documented in Brazilian populations of S. frugiperda. Thus, we utilized large-scale cDNA sequencing (RNA-Seq analysis) to compare the pattern of gene expression between lufenuron-resistant (LUF-R) and susceptible (LUF-S) S. larvae in an attempt to identify the molecular basis behind the resistance mechanism(s) of S. frugiperda to this insecticide.\ud
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Results\ud
A transcriptome was assembled using approximately 19.6 million 100 bp-long single-end reads, which generated 18,506 transcripts with a N50 of 996 bp. A search against the NCBI non-redundant database generated 51.1 % (9,457) functionally annotated transcripts. A large portion of the alignments were homologous to insects, with the majority (45 %) being similar to sequences of Bombyx mori (Lepidoptera: Bombycidae). Moreover, 10 % of the alignments were similar to sequences of various species of Spodoptera (Lepidoptera: Noctuidae), with 3 % of them being similar to sequences of S. frugiperda. A comparative analysis of the gene expression between LUF-R and LUF-S S. frugiperda larvae identified 940 differentially expressed transcripts (p ≤ 0.05, t-test; fold change ≥ 4). Six of them were associated with cuticle metabolism. Of those, four were overexpressed in LUF-R larvae. The machinery involved with the detoxification process was represented by 35 differentially expressed transcripts; 24 of them belonging to P450 monooxygenases, four to glutathione-S-transferases, six to carboxylases and one to sulfotransferases. RNA-Seq analysis was validated for a number of selected candidate transcripts by using quantitative real time PCR (qPCR).\ud
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Conclusions\ud
The gene expression profile of LUF-R larvae of S. frugiperda differs from LUF-S larvae. In general, gene expression is much higher in resistant larvae when compared to the susceptible ones, particularly for those genes involved with pathways for xenobiotic detoxification, mainly represented by P450 monooxygenases transcripts. Our data indicate that enzymes involved with the detoxification process, and mostly the P450, are one of the resistance mechanisms employed by the LUF-R S. frugiperda larvae against lufenuron.This work was part of research conducted in partial fulfillment of the M.Sc.\ud
Degree in Entomology by ARBN at Escola Superior de Agricultura “Luiz de\ud
Queiroz” (ESALQ/USP). We thank National Council for the Improvement of\ud
Higher Education (CAPES) for the M.Sc. scholarship to ARBN and\ud
postdoctoral fellowship to PF. We also thank National Council for Scientific\ud
and Technological Development (CNPq) for granting research fellowships to\ud
FLC (Process 312094/2013-2) and CO (Process 312086/2013-0)
Technological strategies and learning-by-exporting: the case of brazilian manufacturing firms, 2006–2008
No full textThis article assesses the relationship between learning by exporting and technological strategies for Brazilian manufacturing firms from 2006 to 2008. Technological strategies are characterised by the importance placed on innovation activities, sources of information and cooperation for innovation, and the location of these sources. Combining factor analysis with regression analysis, we find that (i) new exporters become more productive and larger than non-exporters; (ii) technological strategies improve the productivity and size of all firms; and (iii) the differentiated technological strategies of new exporters are generally not correlated with learning by exporting. Learning by exporting might be related to factors that are not captured by the Brazilian Technological Innovation Survey, and the absence of correlation between learning by exporting and technological strategies might reflect some missed opportunities for technological learning from international trad
Automatic counting and measuring fish oocytes from microscopic images
No full textFish oocyte counting and measuring is an important step for estimating fecundity, which is normally done by analyzing oocytes’s diameters frequency distribution, taking a long time to be done manually and is a laborious task. Oocytes digital images segmentation can make the process faster and more precise. However, proposed methods to address this problem do not deal with overlapped oocyte or tissues and need image processing techniques knowledge to be used. In this paper, we propose a new pipeline to deal with overlapped oocytes so that no image processing knowledge is required for the user. We have used well-known image processing techniques, such as Otsu’s method, Watershed transform, mathematical morphology and regional minimum. Experiments using fish samples from Madeira river show that the proposed pipeline has a huge potential to aid in the task of counting and measuring oocytes. The time spent in this task using the pipeline is twice faster than manual analysis.CNPq (National Council for Scientific and Technological Development) (grant. #350251/2014-2
Portal Min@s: uma ferramenta de apoio ao processamento de córpus de propósito geral
No full textThis paper presents Portal Min@s, a general web-based corpus processing tool. Many corpus processing tools available focus on specific tasks, such as lexicography or translation. Portal, on the other hand, took the challenge of being a general purpose corpus processing tool which deals with different types of corpus, languages and linguistic annotations. We present the features provided by this tool and compare it with two other alternatives.Este artigo apresenta a ferramenta Portal Min@s, criada para apoiar a tarefa de processamento de córpus. Enquanto muitas ferramentas disponíveis focam em pesquisas específicas como lexicografia ou tradução, o Portal fornecendo recursos para tarefas mais gerais, processando córpus com diferentes propósitos, anotação e estruturação. Os recursos disponibilizados são detalhados e comparados com duas ferramentas similares.CAPES (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
Data stream classification guided by clustering on nonstationary environments and extreme verification latency
No full textData stream classification algorithms for nonstationary environments frequently assume the availability of class labels, instantly or with some lag after the classification. However, certain applications, mainly those related to sensors and robotics, involve high costs to obtain new labels during the classification phase. Such a scenario in which the actual labels of processed data are never available is called extreme verification latency. Extreme verification latency requires new classification methods capable of adapting to possible changes over time without external supervision. This paper presents a fast, simple, intuitive and accurate algorithm to classify nonstationary data streams in an extreme verification latency scenario, namely Stream Classification Algorithm Guided by Clustering – SCARGC. Our method consists of a clustering followed by a classification step applied repeatedly in a closed loop fashion. We show in several classification tasks evaluated in synthetic and real data that our method is faster and more accurate than the state-of-the-art.São Paulo Research Foundation (FAPESP) (grant numbers 2011/17698-5, 2012/50714-7, 2013/26151-5)European Commission (project MAESTRA under grant number ICT-2013-612944
Insights into the Skeletonization, Lifestyle, and Affinity of the Unusual Ediacaran Fossil Corumbella
No full textThe Ediacaran fossil Corumbella is important because it is hypothesized to be a scyphozoan\ud
cnidarian, and thus might be one of the rare examples of bona fide Neoproterozoic nimals.\ud
Unfortunately, its mode of life, style of skeletonization, and taxonomic affinity have been very controversial. Here, we use X-ray micro-CT, SEM, and taphonomic analysis to compare preservational modes of Corumbella, in order to better understand the symmetry, mode of construction, preservational style, and taxonomy of this group. Results suggest that articulated and disarticulated specimens of Corumbella from the Ediacaran of Brazil, Paraguay, and the United States, although sometimes preserved very differently, represent\ud
the same taxon—Corumbella werneri. Corumbellids had a thick but flexible theca and probably lived with their basalmost part anchored in the sediment, much like Conotubus. When considered together, these results suggest that Corumbella was one of the first animals to build a skeleton, employing a lamellar microfabric similar to conulariids.FAPESP (Proc. 2009/02312-4)NAPAstrobio (PRP-USP)FAPESP (Proc. 2011/50242-5)CNPq (562143/ 2010-6, 458555/2013-4)CAPES.Astrobiology Laboratory (AstroLab, IAG-USP)LNNano/CNPEMNP-BioMa
Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia)
No full textBackground: Gene duplication followed by adaptive selection is a well-accepted process leading to toxin diversification in venoms. However, emergent genomic, transcriptomic and proteomic evidence now challenges this role to be at best equivocal to other processess . Cnidaria are arguably the most ancient phylum of the extant metazoa that are venomous and such provide a definitive ancestral anchor to examine the evolution of this trait.\ud
Methods: Here we compare predicted toxins from the translated genome of the coral Acropora digitifera to putative toxins revealed by proteomic analysis of soluble proteins discharged from nematocysts, to determine the extent to which gene duplications contribute to venom innovation in this reef-building coral species. A new bioinformatics tool called HHCompare was developed to detect potential gene duplications in the genomic data, which is made freely available (https://github.com/rgacesa/HHCompare).\ud
Results: A total of 55 potential toxin encoding genes could be predicted from the A. digitifera genome, of which 36 (65 %) had likely arisen by gene duplication as evinced using the HHCompare tool and verified using two standard phylogeny methods. Surprisingly, only 22 % (12/55) of the potential toxin repertoire could be detected\ud
following rigorous proteomic analysis, for which only half (6/12) of the toxin proteome could be accounted for as peptides encoded by the gene duplicates. Biological activities of these toxins are dominatedby putative phospholipases and toxic peptidases.\ud
Conclusions: Gene expansions in A. digitifera venom are the most extensive yet described in any venomous animal, and gene duplication plays a significant role leading to toxin diversification in this coral species. Since such low numbers of toxins were detected in the proteome, it is unlikely that the venom is evolving rapidly by preydriven positive natural selection. Rather we contend that the venom has a defensive role deterring predation or\ud
harm from interspecific competition and overgrowth by fouling organisms. Factors influencing translation of toxin encoding genes perhaps warrants more profound experimental consideration.United Kingdom Medical Research Council (MRC grant G82144A to R. Gacesa, D. Hranueli and P. F. Long)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP grants 2010/50174-7 to A. C. Morandini and 2011/50242-5 to A. C. Marques)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq grant 301039/2013-5 to A. C. Morandini)Universidade de São Paulo (USP grant 13.1.1502.9.8)NP-BioMar program at the Universidade de São Paul
Vulnerability to climate warming and acclimation capacity of tropicaland temperate coastal organisms
No full texttEcological forecasting on the likely impacts of climate warming is crucial at a time when several ecosys-tems seem to be responding to this environmental threat. Among the most important questions are:which are the most vulnerable organisms to climate warming and where are they? Recently, there hasbeen debate on whether the tropics or temperate zones are more vulnerable to warming. Vulnerabilitytoward higher temperatures will depend on the organisms’ thermal limits and also on their acclimationcapacity, which remains largely unknown for most species. The aim of the present work was to estimate(1) the upper thermal limits (Critical Thermal Maximum (CTMax)), (2) the warming tolerance (CTMax –Maximum Habitat Temperature) and (3) the acclimation capacity of tropical and temperate rocky shoreorganisms. Differences in biological groups (decapod crustaceans vs fish) were investigated and the effectof region (tropical vs temperate) and habitat (intertidal vs subtidal) was tested. Overall, 35 species weretested. For the assessment of the acclimation capacity, tropical-temperate pairs of closely related speciesof shrimp, crab and fish were selected. Warming tolerance was higher for temperate species than fortropical species and higher for subtidal species than for intertidal species, confirming that species withthe highest thermal limits have the lowest warming tolerance. All species tested presented some accli-mation capacity (CTMaxTrial− CTMaxControl), with the exception of gobiid fish, which was not observed toacclimate. The tropical species tested showed a lower acclimation capacity than their temperate counter-parts. Given that tropical rocky shore organisms are already living very close to their thermal limits andthat their acclimation capacity is limited, it is likely that the impacts of global warming will be evidentsooner in the tropics than in the temperate zone.Portuguese Foundation for Scienceand Technology through the WarmingWebs project, PTDC/MAR-EST/2141/2012, the grant SFRH/BD/80613/201
