SAMplus: adaptive optics at optical wavelengths for SOAR

Adaptive Optics (AO) is an innovative technique that substantially improves the optical performance of ground-based telescopes. The SOAR Adaptive Module (SAM) is a laser-assisted AO instrument, designed to compensate ground-layer atmospheric turbulence in near-IR and visible wavelengths over a large Field of View. Here we detail our proposal to upgrade SAM, dubbed SAMplus, that is focused on enhancing its performance in visible wavelengths and increasing the instrument reliability. As an illustration, for a seeing of 0.62 arcsec at 500 nm and a typical turbulence profile, current SAM improves the PSF FWHM to 0.40 arcsec, and with the upgrade we expect to deliver images with a FWHM of $\approx0.34$ arcsec -- up to 0.23 arcsec FWHM PSF under good seeing conditions. Such capabilities will be fully integrated with the latest SAM instruments, putting SOAR in an unique position as observatory facility.Comment: To appear in Proc. SPIE 10703 (Ground-based and Airborne Instrumentation for Astronomy VII; SPIEastro18

Development of molecular and enzymatic kits for the detection of total coliforms and Escherichia coli in water samples

The drinking water is one of the main sources of infectious diseases. It is of major importance to keep a good water quality monitoring. The need for more rapid, sensitive and specific tests is essential; not only for water industry, but for a better public safety. Therefore, detection of microbial indicators of potential pathogens in water is the solution to the prevention and recognition of problems related to human health and safety. The main purpose of this work is to develop commercial kits for the detection of the extensively used as indicator organisms: Escherichia coli and total coliforms. An enzymatic method of detection of these microorganisms is being developed based on the enzymes β-Dglucuronidase and β-D-galactosidase, respectively. The results are visible in 18 h for 1 CFU. In order to achieve a higher level of sensitivity and specificity, molecular detection using the Polymerase Chain Reaction (PCR) technique is being investigated. Three primers were selected for identification of total coliforms, E. coli and E. coli with other enteric pathogens. At this moment, we achieved a sensitivity level of 676 CFU in 8 h, which is already a good achievement but there is still more research to be done in order to accomplish the 1 CFU detection

On the Prospect of Identifying Adaptive Loci in Recently Bottlenecked Populations

Identifying adaptively important loci in recently bottlenecked populations – be it natural selection acting on a population following the colonization of novel habitats in the wild, or artificial selection during the domestication of a breed – remains a major challenge. Here we report the results of a simulation study examining the performance of available population-genetic tools for identifying genomic regions under selection. To illustrate our findings, we examined the interplay between selection and demography in two species of Peromyscus mice, for which we have independent evidence of selection acting on phenotype as well as functional evidence identifying the underlying genotype. With this unusual information, we tested whether population-genetic-based approaches could have been utilized to identify the adaptive locus. Contrary to published claims, we conclude that the use of the background site frequency spectrum as a null model is largely ineffective in bottlenecked populations. Results are quantified both for site frequency spectrum and linkage disequilibrium-based predictions, and are found to hold true across a large parameter space that encompasses many species and populations currently under study. These results suggest that the genomic footprint left by selection on both new and standing variation in strongly bottlenecked populations will be difficult, if not impossible, to find using current approaches

Inconsistency in the Diagnosis of Functional Heartburn: Usefulness of Prolonged Wireless pH Monitoring in Patients With Proton Pump Inhibitor Refractory Gastroesophageal Reflux Disease

Background/Aims The diagnosis of functional heartburn is important for management, however it stands on fragile pH monitoring variables, ie, acid exposure time varies from day to day and symptoms are often few or absent. Aim of this study was to investigate consistency of the diagnosis of functional heartburn in subsequent days using prolonged wireless pH monitoring and its impact on patients' outcome. Methods Fifty proton pump inhibitotor refractory patients (11 male, 48 years [range, 38-57 years]) with a diagnosis of functional heartburn according to Rome III in the first 24 hours of wireless pH monitoring were reviewed. pH variables were analysed in the following 24-hour periods to determine if tracings were indicative of diagnosis of non-erosive reflux disease (either acid exposure time > 5% or normal acid exposure time and symptom index >= 50%). Outcome was assessed by review of hospital files and/or telephone interview. Results Fifteen out of 50 patients had a pathological acid exposure time after the first day of monitoring (10 in the second day and 5 in subsequent days), which changed their diagnosis from functional heartburn to non-erosive reflux disease. Fifty-four percent of non-erosive reflux disease vs 11% of functional heartburn patients (P < 0.003) increased the dose of proton pump inhibitors or underwent fundoplication after the pH test. Outcome was positive in 77% of non-erosive reflux disease vs 43% of functional heartburn patients (P < 0.05). Conclusions One-third of patients classified as functional heartburn at 24-hour pH-monitoring can be re-classified as non-erosive reflux disease after a more prolonged pH recording period. This observation has a positive impact on patients' management

An open and parallel multiresolution framework using block-based adaptive grids

A numerical approach for solving evolutionary partial differential equations in two and three space dimensions on block-based adaptive grids is presented. The numerical discretization is based on high-order, central finite-differences and explicit time integration. Grid refinement and coarsening are triggered by multiresolution analysis, i.e. thresholding of wavelet coefficients, which allow controlling the precision of the adaptive approximation of the solution with respect to uniform grid computations. The implementation of the scheme is fully parallel using MPI with a hybrid data structure. Load balancing relies on space filling curves techniques. Validation tests for 2D advection equations allow to assess the precision and performance of the developed code. Computations of the compressible Navier-Stokes equations for a temporally developing 2D mixing layer illustrate the properties of the code for nonlinear multi-scale problems. The code is open source

Diversidade nucleotídica de genes envolvidos na biossíntese de ácidos clorogênicos de cafeeiros.

Os ácidos clorogênicos (CGAs) são compostos químicos importantes de Coffea spp. para a qualidade da bebida, pois eles interferem na adstringência e podem alterar o aroma e sabor da bebida. Aproximadamente 310.000 ESTs de Coffea estão disponíveis e possibilitam o acesso à variabilidade nucleotídica da planta e o desenvolvimento de marcadores moleculares ligados à qualidade da bebida para as principais enzimas da via de biossíntese dos CGAs: PAL, C4H, 4CL, CQT e C3?H. Neste trabalho foram detectados polimorfismos dos tipos SNP, INDEL ou SSR dentro das sequências nucleotídidicas disponíveis no Projeto Genoma Café e no NCBI. As sequências de ESTs de CGAs foram clusterizadas pelo programa Codon Code Aligner, assim como a detecção de polimorfismos e validação dos mesmos (qualidade de cromatograma). Foram identificadas seis isoformas para PAL, uma para C4H, seis para 4CL, duas para CQT e duas para C3?H. Os contigs formados apresentaram um total de 248 polimorfismos (236 SNPs e 12 INDELs), sendo 201 na região codante (127 não sinônimos e 74 sinônimos). A frequência dos polimorfismos foi maior nas regiões UTRs (1pol/54pb), em relação à codante (1pol/81pb). A análise das sequências de C. arabica permitiu a identificação de 2 subgrupos diferentes de sequências, referentes aos seus genomas ancestrais (C. canephora e C. eugenioides). Foi observada a presença de 67,4% dos polimorfismos entre os grupos ancestrais e 32,6% dentro dos grupos em C. arabica. Esses resultados vêm permitindo definir genes tanto para estudos de expressão de homeólogos de CGAs como para o desenvolvimento de marcadores moleculares para o mapeamento genético

Engineering yeast tolerance to inhibitory lignocellulosic biomass

In recent years the necessity for biotechnological manufacturing based on lignocellulosic feedstocks has become evident. However, the pre-treatment step in the production of lignocellulosic bioethanol leads to the accumulation of inhibitory byproducts. Robust second generation bioethanol processes require microorganisms able to ferment these inhibitory lignocellulosic hydrolysates. Significant progress has been made in the understanding of the determinants of yeast tolerance to lignocellulose biomass-derived inhibitors, however further knowledge at the genetic level is of essential importance for the improvement of lignocellulose conversion technology. Based on genome-wide results previously obtained [1], two key genes, PRS3 and RPB4, were found to contribute to the maintenance of cell viability in wheat straw hydrolysate and to the maximal fermentation rate of this substrate. Here we describe the outcome, in bioethanol productivity, of fermentations in Eucalyptus globulus wood hydrolysate, using recombinant Saccharomyces cerevisiae BY4741 overexpressing these genes. Furthermore, we studied their expression in an industrial strain isolated from a Brazilian bioethanol production plant, which was previously demonstrated to have very robust characteristics with outstanding fermentation performances [2]. This expression evaluation was performed during a fermentation mimicking industrial conditions, under the absence and presence of inhibitory compounds, and provides insights into the roles of PRS3 and RPB4 in the adaptation to toxic biomass hydrolysates. This study expands our understanding of the underlying molecular mechanisms involved in yeast response to the multiple stresses occurring during lignocellulose fermentations under industrially relevant conditions. [1] Pereira FB et al. Identification of candidate genes for yeast engineering to improve bioethanol production in very high gravity and lignocellulosic biomass industrial fermentations. Biotechnol Biofuels 2011. 4(1):57. [2] Pereira FB et al. Robust industrial Saccharomyces cerevisiae strains for very high gravity bio-ethanol fermentations. J Biosci Bioeng 2011. 112(2):130-6.Project GlycoCBMs FCT PTDC/AGR-FOR/3090/2012 – FCOMP-01-0124-FEDER-027948, project AshByofactory PTDC/EBB-EBI/101985/2008 – FCOMP-01-0124-FEDER-009701, grant SFRH/BDE/33752/2009 to D Mendes and grant SFRH/BD/64776/2009 to FB Pereira