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Variations on a theme: diversification of cuticular hydrocarbons in a clade of cactophilic Drosophila
No full textAbstract\ud
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Background\ud
We characterized variation and chemical composition of epicuticular hydrocarbons (CHCs) in the seven species of the Drosophila buzzatii cluster with gas chromatography/mass spectrometry. Despite the critical role of CHCs in providing resistance to desiccation and involvement in communication, such as courtship behavior, mating, and aggregation, few studies have investigated how CHC profiles evolve within and between species in a phylogenetic context. We analyzed quantitative differences in CHC profiles in populations of the D. buzzatii species cluster in order to assess the concordance of CHC differentiation with species divergence.\ud
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Results\ud
Thirty-six CHC components were scored in single fly extracts with carbon chain lengths ranging from C29 to C39, including methyl-branched alkanes, n-alkenes, and alkadienes. Multivariate analysis of variance revealed that CHC amounts were significantly different among all species and canonical discriminant function (CDF) analysis resolved all species into distinct, non-overlapping groups. Significant intraspecific variation was found in different populations of D. serido suggesting that this taxon is comprised of at least two species. We summarized CHC variation using CDF analysis and mapped the first five CHC canonical variates (CVs) onto an independently derived period (per) gene + chromosome inversion + mtDNA COI gene for each sex. We found that the COI sequences were not phylogenetically informative due to introgression between some species, so only per + inversion data were used. Positive phylogenetic signal was observed mainly for CV1 when parsimony methods and the test for serial independence (TFSI) were used. These results changed when no outgroup species were included in the analysis and phylogenetic signal was then observed for female CV3 and/or CV4 and male CV4 and CV5. Finally, removal of divergent populations of D. serido significantly increased the amount of phylogenetic signal as up to four out of five CVs then displayed positive phylogenetic signal.\ud
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Conclusions\ud
CHCs were conserved among species while quantitative differences in CHC profiles between populations and species were statistically significant. Most CHCs were species-, population-, and sex-specific. Mapping CHCs onto an independently derived phylogeny revealed that a significant portion of CHC variation was explained by species' systematic affinities indicating phylogenetic conservatism in the evolution of these hydrocarbon arrays, presumptive waterproofing compounds and courtship signals as in many other drosophilid species.We thank G. Almeida and A. Tripodi for help with the GC, P.R. Epifânio for\ud
technical assistance, and W. Maddison and M. Laurin for help with Mesquite.\ud
F.F. Franco and A.L.H. Esguicero assisted with field collection of cactus and\ud
flies. WJE and CCO thank L. Jackson for revealing the secrets of Drosophila\ud
hydrocarbon GCMS and for his hospitality in Bozeman. We also thank M.G.\ud
Ritchie and D.C.S.G. Oliveira for their comments on an earlier version of the\ud
manuscript and three anonymous reviewers for valuable criticisms and\ud
insights. Funding was provided by a supplement to National Science\ud
Foundation DEB-0211125 to WJE, a Dissertation Research Award from the J.\ud
William Fulbright College of Arts & Sciences, University of Arkansas to CCO,\ud
and grants from FAPESP, CNPq and USP to MHM and FMS
Germline mutations in BRCA1 and BRCA2 in epithelial ovarian cancer patients in Brazil
No full textAbstract\ud
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Background\ud
Approximately 8–15% epithelial ovarian cancer patients are BRCA1 or BRCA2 germline mutation carriers. Brazilian inhabitants may have peculiar genetic characteristics associated with ethnic diversity, and studies focusing on the entire BRCA1/BRCA2 gene sequencing in Brazilian ovarian cancer patients are still lacking. The aim of this study was to evaluate BRCA1/2 mutations, through entire gene sequencing, in a Brazilian population of women with epithelial ovarian cancer.\ud
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Methods\ud
In a cross sectional study performed in one reference centre for cancer treatment in São Paulo, Brazil, 100 patients diagnosed with epithelial ovarian cancer unselected for family history of breast and/or ovarian cancer were included. The complete coding sequence of BRCA1/2 genes was evaluated through Next-Generation or capillary sequencing. Large deletions were investigated through Multiplex Ligation-dependent Probe Amplification (MLPA).\ud
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Results\ud
Nineteen pathogenic mutations (BRCA1: n = 17 and BRCA2: n = 2) featuring 14 different mutations, including two large deletions in BRCA1 (exon 1–2 deleted and exon 5–7 deleted) were identified. Three mutations were detected more than once (c.3331_3334delCAAG, c.5266dupC and c.4484G > T). Two novel frameshift mutations were identified, one in BRCA1 (c.961_962delTG) and one in BRCA2 (c.1963_1963delC). BRCA1/2 mutations were seen in 35.5% of the patients with first and/or second-degree relatives with breast and/or ovarian cancer. Nineteen variants of uncertain significance (VUS) were detected (BRCA1: n = 2 and BRCA2: n = 17), including five distinct missense variants (BRCA1: c.5348 T > C; BRCA2: c.2350A > G, c.3515C > T, c.7534C > T, and c.8351G > A).\ud
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Conclusions\ud
Among epithelial ovarian cancer patients unselected for family history of cancer, 19% were BRCA1/2 germline mutation carriers. Almost ¾ of the BRCA mutations, including two large deletions, were detected only once. Our work emphasizes the need of entire gene sequencing and MLPA screening in Brazil.Geertruida Hendrika de Bock received a grant of Coordenação de Aperfeiçoamento\ud
de Pessoal de Nível Superior (CAPES), Programa Pesquisador Visitante Especial (PVE\ud
#029/2012), Simone Maistro received a postdoctoral scholarship by Coordenação\ud
de Aperfeiçoamento de Pessoal de Nível Superior (CAPES, PVE #029/2012), Giselly\ud
Encinas received a PhD scholarship grant by São Paulo Research Foundation\ud
(FAPESP, #2011/09572-1) and Natalia Teixeira received a scholarship grant by São\ud
Paulo Research Foundation (FAPESP, #2012/05754-1).\ud
This work was in part supported by a grant from Diagnósticos da América\ud
-DASA and by a grant from NAP-Biobanco/USP
Comparative phylogeography in the Atlantic forest and Brazilian savannas: pleistocene fluctuations and dispersal shape spatial patterns in two bumblebees
No full textAbstract\ud
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Background\ud
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Bombus morio and B. pauloensis are sympatric widespread bumblebee species that occupy two major Brazilian biomes, the Atlantic forest and the savannas of the Cerrado. Differences in dispersion capacity, which is greater in B. morio, likely influence their phylogeographic patterns. This study asks which processes best explain the patterns of genetic variation observed in B. morio and B. pauloensis, shedding light on the phenomena that shaped the range of local populations and the spatial distribution of intra-specific lineages.\ud
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Results\ud
Results suggest that Pleistocene climatic oscillations directly influenced the population structure of both species. Correlative species distribution models predict that the warmer conditions of the Last Interglacial contributed to population contraction, while demographic expansion happened during the Last Glacial Maximum. These results are consistent with physiological data suggesting that bumblebees are well adapted to colder conditions. Intra-specific mitochondrial genealogies are not congruent between the two species, which may be explained by their documented differences in dispersal ability.\ud
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Conclusions\ud
While populations of the high-dispersal B. morio are morphologically and genetically homogeneous across the species range, B. pauloensis encompasses multiple (three) mitochondrial lineages, and show clear genetic, geographic, and morphological differences. Because the lineages of B. pauloensis are currently exposed to distinct climatic conditions (and elevations), parapatric diversification may occur within this taxon. The eastern portion of the state of São Paulo, the most urbanized area in Brazil, represents the center of genetic diversity for B. pauloensis.Financial support was provided by the Fundação de Amparo à Pesquisa do Estado de São Paulo (Proc. 10/50597-5 and 13/12530-4; PhD and scholarship to EF 2009/07124-1, 2010/20548-2 and 2013/03961-1), and Research Center on Biodiversity and Computing (BioComp), supported by the USP Provost’s Office for Research. A. Carnaval acknowledges funding by FAPESP (BIOTA, 2013/50297-0), National Science Foundation (DOB 1343578 and 1120487), and NASA
Fast unsupervised online drift detection using incremental Kolmogorov-Smirnov test
No full textData stream research has grown rapidly over the last decade. Two major features distinguish data stream from batch learning: stream data are generated on the \ud
y, possibly in a fast and variable rate; and the underlying data distribution can be non-stationary, leading to a phenomenon known as concept drift. Therefore, most of the research on data stream classification focuses on proposing efficient models that can adapt to concept drifts and maintain a stable performance over time. However, specifically for the classification task, the majority of such methods rely on the instantaneous availability of true labels for all already classified instances. This is a strong assumption that is rarely fulfilled in practical applications. Hence there is a clear need for efficient methods that can detect concept drifts in an unsupervised way. One possibility is the well-known Kolmogorov-Smirnov test, a statistical hypothesis test that checks whether two samples differ. This work has two main contributions. The first one is the Incremental Kolmogorov-Smirnov algorithm that allows performing the Kolmogorov-Smirnov hypothesis test instantly using two samples that change over time, where the change is an insertion and/or removal of an observation. Our algorithm employs a randomized tree and is able to perform the insertion and removal operations in O(logN) with high probability and calculate the Kolmogorov-Smirnov test in O(1), where N is the number of sample observations. This is a significant speed-up compared to the O(N logN) cost of the non-incremental implementation. The second contribution is the use of the Incremental Kolmogorov-Smirnov test to detect concept drifts without true labels. Classification algorithms adapted to use the test rely on a limited portion of those labels just to update the classification model after a concept drift is detected.São Paulo Research Foundation (FAPESP) (grants 2014/12333-7, 2015/01701-8 and 2013/50379-6)Natural Sciences and Engineering Research Council of CanadaCALDO ProgrammeNational Research Centre of Poland (NCN) (grant DEC-2013/09/B/-ST6/01549)CNPq (grants 03083/2013-1 and 446330/2014-0
Motion-based wave inference: monitoring campaign on a turret EPSO
No full textIn recent years, considerable effort has been made in order to validate different methods that aim at estimating the wave spectra from the motions recorded on a ship or on an offshore platform. For more than ten years now, the University of São Paulo has been working on a wave inference method for moored oceanic systems, such as Floating Production Storage and Offloading (FPSO) vessels.\ud
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This paper brings the first results from an ongoing field campaign, started in December 2014, for the estimation of wave statistics by means of this system, which is based on a Bayesian inference approach. The performance of the motion-based method is checked against the wave estimations provided by a commercial marine radar system. The radar is installed in a fixed platform close to the FPSO that is being monitored, which is moored in a turret configuration. Comparison between both systems allows one not only to evaluate the performance of the method but also to evaluate the inherent limitations that exist when the estimations are based on a very large vessel, especially one whose heading may be subjected to fast variations.\ud
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In this work, a new algorithm for the partition of the wave spectrum is used, differing from the previous works. This technique allows the identification and combination of energy peaks of the directional spectrum into wave systems, providing better modal wave statistics and less noise in the final spectrum.\ud
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Previously validation of the wave inference method was made through numerical and small-scale experimental analysis. Also, in previous studies, a 9-month field campaign was also used to validate the Bayesian method using a spread-moored FPSO, but no comparison to other measurement technique was made, instead, numerical forecasts were adopted. In this work this objective is achieved: so far, 10 months of estimates from the Bayesian inference algorithm have already been compared to data supplied by a radar system.\ud
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Comparisons with the marine radar readings attest an adequate identification of mean wave directions, with the Bayesian model estimating mean wave directions that are in close agreement to those provided by the radar system most of the time. There are, however, a few cases when the discrepancy is large and the reasons for this are still under investigation.\ud
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The comparison between both sources of data provides some insightful results, which are discussed in this paper. First, they confirm and quantify the main biases of the applied method, which are related to the filtering of the energy from high-frequency waves. On the other hand, they attest that the performance of the method for more severe sea states is good overall, showing that the method is able to provide good estimates of wave height and direction and also to capture situations when wave conditions are changing fast, such as the ones that occur with the incoming of cold fronts from South.CNPqIP
MiRNA-146b-5p upregulates migration and invasion of different Papillary Thyroid Carcinoma cells
No full textAbstract\ud
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Background\ud
Tumor invasiveness is directly related to the ability of tumor cells to migrate and invade surrounding tissues, usually degrading extracellular matrix. Despite significant progress in the knowledge about migration and invasion, there is much more to elucidate about their regulatory mechanisms, especially in cancer cells. MicroRNAs (miRs) were recently described as important regulators of migration. Differential expression of miRs in cancer is frequently associated with progression, invasion and metastasis. In papillary thyroid carcinoma (PTC), miR-146b-5p is highly expressed and positively correlated to the degree of malignancy.\ud
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Methods\ud
This study aimed to investigate the role of miR-146b-5p on the migratory and invasive behaviors of thyroid cells, using a non tumor rat thyroid follicular cell line (PCCl3) transfected with the miR-146b-5p genomic region, and two PTC cell lines (TPC-1 and BCPAP, bearing distinct oncogenic backgrounds), which express high levels of miR-146b-5p, after miR-146b inhibition by antagomiR and miR-146b overexpression by mimics-miR. Migration and invasion were studied by time-lapse and transwell assays (with and without Matrigel®). Gelatin degradation assays were also employed, as well as F-actin staining.\ud
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Results\ud
Migration and invasion of PCCl3 were increased 2-3x after miR-146b-5p overexpression (10X) and large lamellipodia were evident in those cells. After miR-146b-5p inhibition, TPC-1 and BCPAP migration and invasion were significantly reduced, with cells showing several simultaneous processes and low polarity. Gelatin degradation was inhibited in TPC-1 cells after inhibition of miR-146b-5p, but was unaffected in BCPAP cells, which did not degrade gelatin. The inhibition of miR-146b-5p in PCCl3 also inhibited migration and invasion, and additional (exogenous) overexpression of this miR in TPC-1 and BCPAP cells increased migration and invasion, without effects on cell morphology or gelatin degradation. The overexpression of SMAD4 in BCPAP cells, a validated target of miR-146b-5p and key protein in the TGF-β signaling pathway, inhibited migration similarly to the effects observed with the antagomiR 146b-5p.\ud
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Conclusions\ud
miR-146b-5p positively regulates migration and invasion of thyroid normal and tumor follicular cells (independently from their original mutation, either BRAF or RET/PTC), through a mechanism that involves the actin cytoskeleton but not an increased capacity of matrix degradation.This research was supported by Fundação de Amparo à Pesquisa do Estado\ud
de São Paulo (FAPESP, Grants # 2011/18936-7 and #2012/03990-9),\ud
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES,\ud
PNPD), Conselho Nacional de Desenvolvimento Científico e Tecnológico\ud
(CNPq grants #307452/2012-3 and #448052/2014-8) and Pró-Reitoria de\ud
Pesquisa da Universidade de São Paulo (NAPMiR)
Evaluation of functional rehabilitation physiotherapy protocol in the postoperative patients with anterior cruciate ligament reconstruction through clinical prognosis: an observational prospective study
No full textAbstract
Background
The aim of the study was to evaluate the evolution of patients subject to physical treatment based on guidelines of functional rehabilitation after surgery anterior cruciate ligament reconstruction.
Methods
This is a prospective study of 177 patients with anterior cruciate ligament injury, who underwent surgery and physical therapy guideline conducted in an orthopedic clinic in São Paulo, southeastern Brazil. The clinical evolution of patients was made according to Lysholm and IKDC questionnaire on the 1st day after surgery with 30, 90 and 180 days of treatment.
Results
There was statistically significant increase in the gross values of Lysholm and IKDC questionnaires during the treatment (p < 0.001), which indicates progressive gain of function. According to the scores obtained from the IKDC, it can be observed that in stage 1 the average progress was 53.5 %, falling to 50 % in stage 2, and 26.1 % in stage 3. As to Lysholm score, it started with 87.7 %, falling to 62.6 % in the second stage and 7 % in the third stage, both statistically significant (p < 0.001). The rehabilitation-oriented functional objectives priority is to quickly get the exercises to gain breadth, strength and proprioception, optimizing and improving the integration of the athlete back to sport.
Conclusion
Synthesizing the gradual gain of function and according to clinical outcomes assessed by IKDC and Lysholm, the functional guideline presented may be considered an alternative for rehabilitation of patients in postoperative anterior cruciate ligament