Variability patterns and phenology of harmful phytoplankton blooms off southern Portugal: looking for region-specific environmental drivers and predictors

Harmful algal blooms (HABs) negatively impact coastal ecosystems, fisheries, and human health, and their prediction has become imperative for effective coastal management. This study aimed to evaluate spatialtemporal variability patterns and phenology for key toxigenic phytoplankton species off southern Portugal, during a 6-year period, and identify region-specific environmental drivers and predictors. Total abundance of species responsible for amnesic shellfish poisoning (Pseudo-nitzschia spp.), diarrhetic shellfish poisoning (Dinophysis spp.), and paralytic shellfish poisoning (G. catenatum) were retrieved, from the National Bivalve Mollusk Monitoring System public database. Contemporaneous environmental variables were acquired from satellite remote sensing, model-derived data, and in situ observations, and generalized additive models (GAMs) were used to explore the functional relationships between HABs and environmental variables and identify regionspecific predictors. Pseudo-nitzschia spp. showed a bimodal annual cycle for most coastal production areas, with spring and summer maxima, reflecting the increase in light intensity during the mixed layer shoaling stage, and the later stimulatory effects of upwelling events, with a higher bloom frequency over coastal areas subjected to stronger upwelling intensity. Dinophysis spp. exhibited a unimodal annual cycle, with spring/summer maxima associated with stratified conditions, that typically promote dinoflagellates. Dinophysis spp. blooms were delayed with respect to Pseudo-nitzschia spp. spring blooms, and followed by Pseudo-nitzschia spp. summer blooms, probably reflecting upwelling-relaxation cycles. G. catenatum occurred occasionally, namely in areas more influenced by river discharges, under weaker upwelling. Statistical-empirical models (GAMs) explained 7-8%, and 21− 54% of the variability in Pseudo-nitzschia spp. and Dinophysis spp., respectively. Overall, a set of four easily accessible environmental variables, surface photosynthetically available radiation, mixed layer depth, sea surface temperature, and chlorophyll-a concentration, emerged as the most influential predictors. Additionally, over the coastal production areas along the south coast, river discharges exerted minor negative effects on both HAB groups. Despite evidence supporting the role of upwelling intensity as an environmental driver of Pseudonitzschia spp., it was not identified as a relevant model predictor. Future model developments, such as the inclusion of additional environmental variables, and the implementation of species- and period-specific, and hybrid modelling approaches, may further support HAB operational forecasting and managing over complex coastal domains.info:eu-repo/semantics/publishedVersio

Thyr: a volumetric ray-marching tool for simulating microwave emission

Gyrosynchrotron radiation is produced by solar flares, and can be used to infer properties of the accelerated electrons and magnetic field of the flaring region. This microwave emission is highly dependent on many local plasma parameters, and the viewing angle. To correctly interpret observations, detailed simulations of the emission are required. Additionally, gyrosynchrotron emission from the chromosphere has been largely ignored in modelling efforts, and recent studies have shown the importance of thermal emission at millimetric wavelengths. Thyr is a new tool for modelling microwave emission from three-dimensional flaring loops with spatially varying atmosphere and increased resolution in the lower corona and chromosphere. Thyr is modular and open-source, consisting of separate components to compute the thermal and non-thermal microwave emission coefficients and perform three-dimensional radiative transfer (in local thermodynamic equilibrium). The radiative transfer integral is computed by a novel ray-marching technique to efficiently compute the contribution of many volume elements. This technique can also be employed on a variety of astrophysics problems. Herein we present a review of the theory of gyrosynchrotron radiation, and two simulations of identical flare loops in low- and high resolution performed with Thyr, with a spectral imaging analysis of differing regions. The high-resolution simulation presents a spectral hardening at higher frequencies. This hardening originates around the top of the chromosphere due to the strong convergence of the magnetic field, and is not present in previous models due to insufficient resolution. This hardening could be observed with a coordinated flare observation from active radio observatories

Phenotypic analyses of multi-environment data for two diverse tetraploid potato collections: comparing an academic panel with an industrial panel

Phenotypic analyses of two different association panels of tetraploid potato cultivars are presented. Association panels are sets of variously related genotypes assembled for association analysis purposes. The aims of this research were to inspect, analyse and compare two phenotypic data sets, a first step in association mapping analysis. A first panel of 205 contemporary and historical cultivars, selected to represent the commercial potato germplasm pool, was evaluated in two trials in 2006, one on sandy soil and the other on clay soil, both with two replications. It was called the academic panel. Data for the second panel with 299 genotypes were compiled from contributions from five breeding companies and included 66 locations and 18 years. Each of the participating breeding companies contributed data from their clonal selection programmes for 38 advanced breeding clones and a series of standard cultivars. It was called the industrial panel. Variance components for genotypic main effects and genotype-by-environment interactions were calculated, and estimates for the random genotypic main effects were produced. The genotypic main effects for 19 agro-morphological and quality traits were used to study trait by trait correlations within each panel. In addition, for the genotypes shared by both panels, the correlation of genetic main effects between the panels was investigated. The heritability of all traits was high and no large differences were observed between panels. Coefficients of trait variation were highly correlated (r¿=¿0.9) for both panels and trait by trait correlations in both panels showed highly similar patterns. These results demonstrate that a single-year balanced field trial as well as using breeders’ records yields robust phenotypic information that can be used in a genome-wide association study. Issues related to data management and definition of traits are discussed

Statistical sampling and modelling for cork oak and eucalyptus stands

This thesis focuses on the use of modern statistical methods to solve problems on sampling, optimal cutting time and agricultural modelling in Portuguese cork oak and eucalyptus stands. The results are contained in five chapters that have been submitted for publication as scientific manuscripts.The thesis first addresses the decision of when to cut a rotation of eucalyptus production forest. The aim is to optimise the long term volume production, corrected for replant costs. On the long term the total financial yield divided by the total rotation time is an important economical asset. Successive rotations and their growth curves are considered as independent realisations of the same generating process. A Bayesian approach was taken, using Shumacher curves. Prior information on the curve parameters was based on a large number of observed growth curves. For known or accurately estimated curves, a 16% gain in optimisation of cutting times could be achieved, as compared to using a common optimal cutting time. It is assumed that a farmer takes two volume measurements to decide upon the cutting time of a rotation, the first measurement at a fixed age, the second at an age that possibly depends upon the first measurement. Finding the optimal second measurement time is entangled with finding the optimal cutting time. In this thesis, simultaneous optimisation is carried out using numerical methods. The gain in using a variable optimised second measurement time, compared with an optimised fixed measurement time, however, was relatively small (up to 0.1%), which is hardly above the numerical noise level.A second problem addressed in this thesis concerns estimation of stem diameter growth curves in cork oaks. A data-set of 24 trees was used. A D-optimal experimental design has been compared with equidistant designs to measure trees at particular ages to allow for an optimal estimation of individual growth curves. An experimental design that is locally D-optimal for a central parameter is proposed. This fixed compromise design can be used for all trees. For individual growth curves and under certain conditions that are discussed in the thesis such a design provides better estimates than an equidistant design.The third study concerns spatial modelling of quantitative cork oak characteristics. Spatial statistical methods are used to analyse cork oak stands, so-called montados. Spatial correlations between neighbouring trees of crown shapes, of crown sizes and of stem sizes are analysed using plots from two montados. A significant correlation is found between tree size and competition from neighbouring trees. In particular, larger trees have a regular spatial distribution in a montado.The final study in this thesis compares three sampling methods for use in cork oak farms. One method is currently in use by Portuguese farmer's associations to estimate cork value prior to stripping and the other two methods are compared to it. The three sampling methods are applied to two cork oak farms and to simulated stands. The latter are generated with spatial simulation methods on the basis of information obtained elsewhere. The current method has a 15-50% larger bias. For a clustered pattern standard errors are lowest for the current method, but these are considerably higher for a regular or a random pattern.In conclusion, this thesis shows that modern statistical methods are valuable to improve modelling and sampling of cork oak and eucalyptus forests. In particular, spatial relations among neighbouring trees should preferably be included into management of cork oak farms. Adequate sampling methods are basic to retrieve information of the highest quality

Transcriptomic analysis of plasmid and plasmid-related chromosomal ORFs in C. trachomatis strains with different cell-appetence

Despite the undergoing chromosomal size-reduction of Chlamydia trachomatis, almost all strains maintain the conserved 7,5kb plasmid. It has been recently considered a virulence factor, as plasmid-bearing strains evidenced a higher ability to successfully colonize epithelial cells and sustain infection than plasmidless strains. However, the biological role of the eight plasmid ORFs remains poorly characterized. Thus, we aim to correlate the relative expression of each plasmid ORFs with the number of plasmids per genome as well as with the relative expression of chromosomal genes that seem to be regulated by the plasmid, during the whole Chlamydia developmental cycle. Both the transcriptomic analysis of all the selected ORFs and the determination of the plasmid copy number were performed by qPCR in prototype and currently circulating strains with distinct cell-appetence and ecological success, throughout Chlamydia developmental cycle. So far, our results indicate: 1) huge differences (up to 100-fold) in the expression levels between plasmid ORFs; 2) for the same ORF, different expression levels and profiles among strains; 3) variation in the number of plasmids per genome during the infectious cycle; 4) the higher expression level of the plasmid ORFs do not seem to correlate with a higher number of plasmids per genome. These results, together with our ongoing transcriptomic survey of the plasmid-related chromosomal genes, will contribute to shed some light on the molecular function of the plasmid ORFs in chlamydial biology

Molecular features underlying the higher ecological success of C. trachomatis E and F genotypes

In the light of the >98% genomic similarity among Chlamydia trachomatis serovars, the higher worldwide ecological success of E and F is enigmatic. We intend to provide a quick overview of the molecular data that distinguish these from the remaining strains. Examples are: - E and F possess a similar chromosomal genetic make-up distinct from the remaining genotypes. Some loci linked to this independent co-segregation comprehend membrane proteins, hypothetical virulence factors, and regulatory regions (published data). - Some loci reveal nonrandom mutational patterns, where mutations exclusive of E and F are clustered in specific protein domains, likely promoting strains functional and/or structural attributes (published data). - Based on data from a worldwide survey, MOMP of E and F exhibit the lowest mutation rate (22.3-fold lower), implying more fitted antigenic profiles to deal with host immunity (published data). - The likelihood of E and F strains to undergo genetic recombination is about 12-fold lower than that of the other genotypes (P<10-2), suggesting a putative clonal evolution, where superimposed favorable clones may be strongly maintained in vivo (preliminary data from our lab). - Strains E and F do not seem to originate higher infectious load in vivo, when compared with other genital genotypes (published data). Full-genomic data from multiple and diverse clinical isolates will be essential to decipher the secret behind the higher ecological success of E and F strains

Chlamydia trachomatis infection in patients selected for HPV detection

Background: The significance of the association between the human papillomavirus (HPV) and other sexually transmitted infections in the development of cervical, penile or anal neoplasias has been investigated, and the more consistent data have pointed to an association with Chlamydia trachomatis. In Portugal, the lack of information on STI precludes any knowledge on this subject. Objective: To determine CT infection in a group of individuals selected for HPV detection in the major Portuguese STD clinic. Methods: This opportunistic screening comprehended 177 outpatients (148 women, 29 men; age: 16-61 years) suspected of HPV infection (warts, abnormal histology) between 2008 and 2010. Demographic and sexual behaviour data and a full medical history were obtained at enrolment. Genital samples (cervical, vulvar, vaginal, penile or anal) were collected from all the subjects. HPV DNA was detected by CLART HPV2 assay, which allowed the detection of 35 genotypes. CT DNA was detected by Cobas 4800. Results and Discussion: Overall, 84.5% of the individuals had at least one of the infections. Evidencing an excellent correlation with clinical signs, HPV infection was detected in 68.2% of the women and in 75.9% of the men, where CT positivity was 10.1% and 13.8%, respectively. Coinfection was observed in 8.9% of the women and in 13.8% of the men. No correlation with HPV or CT genotypes could be established. HPV infection was more frequent in CT negative (87.1%) than in CT positive women (13.8%), and the same was observed for men (81.8% versus 18.2%). Full results will be presented and discussed. Conclusions: No correlation between HPV-CT coinfection, and clinical signs was observed. However, further long-term studies are needed to elucidate the effects of HPV-CT coinfection in the clinical history of the infected patient, which would greatly contribute towards a better management of patients

Normalization strategies for real-time expression data in Chlamydia trachomatis

Since Chlamydia trachomatis is a genetically non-tractable pathogen, transcriptomics assumes a fundamental role for the better understanding of its biology. However, the suitability of endogenous controls for normalization of transcriptomic data in this bacterium still needs validation. We aimed to assess the stability of 10 genes for their potential use as endogenous controls in qPCR at both normal and stress (antibiotic treatment) growth conditions throughout the developmental cycle of three strains with different cell-appetence. Normalization was performed using the quantified bacterial genomes. We also tested the applicability of two widely used softwares (geNorm and Normfinder) to our data. For all strains, we found that 16SrRNA was the most stably expressed gene throughout the normal developmental cycle, but it was highly unstable under antibiotic exposure, suggesting prudence when using ribosomal genes as endogenous controls in expression experiments involving stress environments. The geNorm and Normfinder algorithms revealed contrasting results and seem inappropriate for the selected pool of genes. Considering the multiplicity of experimental conditions, there should be an in loco validation of endogenous controls, where 16SrRNA appears to be in the front line. Alternatively, normalization of expression data against genomic DNA, which is less influenced by experimental constraints (especially relevant for intracellular organisms) and stress conditions, likely constitutes a good option. The present study constitutes the first evaluation of putative endogenous controls for real-time expression assays in C. trachomati

In silico scrutiny of genes revealing phylogenetic congruence with clinical prevalence or tropism properties of Chlamydia trachomatis strains

Microbes possess a multiplicity of virulence factors that confer them the ability to specifically infect distinct biological niches. Contrary to what is known for other bacteria, for the obligate intracellular human pathogen Chlamydia trachomatis, the knowledge of the molecular basis underlying serovars’ tissue specificity is scarce. We examined all ~900 genes to evaluate the association between individual phylogenies and cell-appetence or ecological success of C. trachomatis strains. Only ~1% of the genes presented a tree topology showing the segregation of all three disease groups (ocular, urogenital, and lymphatic) into three wellsupported clades. Approximately 28% of the genes, which include the majority of the genes encoding putative type III secretion system effectors and Inc proteins, present a phylogenetic tree where only lymphogranuloma venereum strains form a clade. Similarly, an exclusive phylogenetic segregation of the most prevalent genital serovars was observed for 61 proteins. Curiously, these serovars are phylogenetically cosegregated with the lymphogranuloma venereum serovars for ~20% of the genes. Some clade-specific pseudogenes were identified (novel findings include the conserved hypothetical protein CT037 and the predicted a-hemolysin CT473), suggesting their putative expendability for the infection of particular niches. Approximately 3.5% of the genes revealed a significant overrepresentation of nonsynonymous mutations, and the majority encode proteins that directly interact with the host. Overall, this in silico scrutiny of genes whose phylogeny is congruent with clinical prevalence or tissue specificity of C. trachomatis strains may constitute an important database of putative targets for future functional studies to evaluate their biological role in chlamydial infections.This work was supported by a grant, ERA-PTG/0004/2010, from Fundação para a Ciência e a Tecnologia (FCT) (to J.P.G.), in the frame of ERA-NET PathoGenoMics. A.N. is recipient of a FCT post-doctoral fellowship (SFRH/BPD/75295/2010), V.B. and R.F. are recipients of Ph.D. fellowships (SFRH/BD/68527/2010 and SFRH/BD/68532/2010, respectively) from FCT, and V.D. is a recipient of fellowship on behalf of the grant ERA-PTG/0004/2010

GFC-Robust Risk Management under the Basel Accord using Extreme Value Methodologies

In this paper we provide further evidence on the suitability of the median of the point VaR forecasts of a set of models as a GFC-robust strategy by using an additional set of new extreme value forecasting models and by extending the sample period for comparison. These extreme value models include DPOT and Conditional EVT. Such models might be expected to be useful in explaining financial data, especially in the presence of extreme shocks that arise during a GFC. Our empirical results confirm that the median remains GFC-robust even in the presence of these new extreme value models. This is illustrated by using the S&P500 index before, during and after the 2008-09 GFC. We investigate the performance of a variety of single and combined VaR forecasts in terms of daily capital requirements and violation penalties under the Basel II Accord, as well as other criteria, including several tests for independence of the violations. The strategy based on the median, or more generally, on combined forecasts of single models, is straightforward to incorporate into existing computer software packages that are used by banks and other financial institutions