Analysis of the deep chlorophyll maximum across the Azores Front

Physical, chemical and biological observations made in late July and August 1997 across the Azores Front (37ºN, 32ºW to 32ºN, 29ºW) are presented. The objectives of the study were: (1) to analyse horizontal and vertical profiles of temperature, salinity, density, nutrients and chlorophyll-a (Chl a) of the top 350 m; (2) to identify the main differences in the deep Chl a Maximum (DCM) and hydrographic structure between the water masses that pass north and south of the Azores Front; and (3) to estimate phytoplankton primary production in these water masses. Horizontal and vertical profiles of salinity, temperature, density, nutrients and phytoplankton pigments in the top 350 m were analysed. The Front separates two distinct water types: the 18 ºC ModeWater (18MW) of subtropical origin, and the 15 ºC ModeWater (15MW) of sub-polar origin. Differences in the DCM and hydrographic structure between 18 MW and 15 MW were observed in the contour plots of each section. The average Chl a concentration between 5 and 200 m depth decreased significantly from 15 MW to 18 MW. The same pattern was observed for the Chl a concentration at the DCM depth. A vertical one-dimensional model was used to estimate the phytoplankton primary production in the 15 MW and 18 MW and led to an estimated water column average gross primary productivity (GPP) between 1.08 and 2.71 mg C

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

Nonlinear dynamic analysis for safety assessment of heritage buildings: Church of Santa Maria de Bélem

Despite the remarkable longevity of heritage constructions, they typically present several structural fragilities inherent to their own material and constructive features. This fact is particularly relevant when seismic loads are concerned, because a very significant portion of such constructions lack adequate seismic resistance and require retrofitting interventions in order to mitigate their vulnerability. However, to guarantee the success of the interventions, the interventions should be carefully selected based on a full understanding of the dynamic response of the building and, particularly, its most vulnerable structural elements. Due to many reasons, the issues associated with this kind of analysis are still difficult to address; therefore, research on this subject should be encouraged. Taking this into account, the church of Santa Maria de Belem, one of the most emblematic buildings of the monastery of Jeronimos complex in Lisbon, is used in this work as a case study to discuss the nonlinear dynamic response of cultural heritage buildings. The nonlinear dynamic behavior of the church was numerically simulated with a three-dimensional (3D) model using artificially generated seismic acceleration time histories, in agreement with seismic hazard scenarios for return periods of 475, 975, and 5,000 years. The dynamic response of the church is discussed and a comparison against results derived from a pushover analysis is also presented. Finally, a modal analysis is presented, estimating the damage level that would be present in the church after the occurrence of such seismic scenarios.This work was partly financed by European Regional Development Fund (ERDF) funds through the Operational Programme Competitiveness Factors (COMPETE) and by national funds through the Foundation for Science and Technology (FCT) within the scope of project POCI-01-0145-FEDER-007633. The authors are also grateful to three anonymous reviewers whose comments significantly improved the clarity of the paper

Novel solar absorber surfaces with organic pigments

This paper presents results of application of natural and synthetic organic pigments in selective solar absorber coatings. Some of these photo excite pigments were tested like solar radiation absorber pigments in paint coatings and others as a form to increase the absorption of solar radiation in titanium oxide monolayer selective coatings produced by reactive magnetron sputtering. Morphologic aspects and optical properties are discussed as a function of deposition parameters and of formulation parameters. The main goal is to prepare solar absorber surfaces as a tandem of TiOx thin films, organic pigment using a conductive substrate or of paint with organic and/or inorganic pigments and conductive substrate, all reaching great photo thermal conversion efficiency, high durability and low costs to the ending product and stability at medium range temperatures (120-150ºC). The best optical properties for titanium oxide sputtered films were 88% for solar absorption, with 7% of emissivity for deposition parameters of: pulsed frequency 200kHz, reverse time of 0.4μs, discharge current of 0.7A, argon flow rate of 50ml/min and oxygen flow rate changing from 0 to 2.5ml/min. The results obtained with paints were not satisfactory. The best couple values for solar absorption and emissivity were respectively 94%, and 74

KITE : high-performance accurate modelling of electronic structure and response functions of large molecules, disordered crystals and heterostructures

We present KITE, a general purpose open-source tight-binding software for accurate real-space simulations of electronic structure and quantum transport properties of large-scale molecular and condensed systems with tens of billions of atomic orbitals (N ∼ 10^10). KITE’s core is written in C++, with a versatile Python-based interface, and is fully optimized for shared memory multi-node CPU architectures, thus scalable, efficient and fast. At the core of KITE is a seamless spectral expansion of lattice Green’s functions, which enables large-scale calculations of generic target functions with uniform convergence and fine control over energy resolution. Several functionalities are demonstrated, ranging from simulations of local density of states and photo-emission spectroscopy of disordered materials to large-scale computations of optical conductivity tensors and real-space wave-packet propagation in the presence of magneto-static fields and spin–orbit coupling. On-the-fly calculations of real-space Green’s functions are carried out with an efficient domain decomposition technique, allowing KITE to achieve nearly ideal linear scaling in its multi-threading performance. Crystalline defects and disorder, including vacancies, adsorbates and charged impurity centres, can be easily set up with KITE’s intuitive interface, paving the way to user-friendly large-scale quantum simulations of equilibrium and non-equilibrium properties of molecules, disordered crystals and heterostructures subject to a variety of perturbations and external conditions

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

Hydrogel 3D in vitro tumor models for screening cell aggregation mediated drug response

Hydrogel-based 3D in vitro models comprising tumor ECM-mimetic biomaterials exhibit superlative potential as preclinical testing platforms for drug discovery and bioperformance screening. However, during hydrogel design and testing stages, the ideal selection between cancer cell laden 3D models or spheroid embedded hydrogel platforms remains to be elucidated. Selecting a disease-mimicking cellular arrangement within ECM hydrogels is paramount for anti-cancer therapeutics performance evaluation and may lead to differential outcomes. To investigate the effects assigned to varying cellular-arrangement, we developed dense 3D spheroid microtumors and cell-laden MG-63 osteosarcoma platforms embedded in GelMA and Matrigel ECM-mimetic scaffolds. These platforms enabled cancer cells/3D microtissues maturation and lorlatinib drug performance screening. Initial 3D spheroids assembly via the liquid overlay technique, resulted in the fabrication of dense cellular aggregates with reproducible size, morphology and necrotic core formation, thus mimicking the native tumor. Upon in vitro maturation, MG-63 spheroids encapsulated in hydrogel scaffolds exhibited significantly higher invasion and drug resistance than their cell laden hydrogel counterparts. Such data reveals inherent physiological and drug response variances among randomly distributed osteosarcoma cells and 3D spheroid-laden hydrogels. Overall, this highlights the importance of evaluating different cellular aggregation states when designing ECM-mimetic hydrogels for in vitro tumor modeling and high-throughput screening of anti-cancer therapeutics.publishe

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

High-resolution real-space evaluation of the self-energy operator of disordered lattices : Gade singularity, spin--orbit effects and p-wave superconductivity

Disorder is a key factor influencing the behavior of condensed states of matter, however the true extent of its impact is generally difficult to determine due to the prominent roles played by quantum interference, entanglement between spin and orbital degrees of freedom and proximity to quantum critical points. Here we show that the one-particle disorder self-energy---a direct probe of the renormalization of low-energy excitations due to defects and impurities distributed randomly in a crystal---can be obtained by means of unbiased spectral expansions of lattice Green's functions in a computationally expedient manner. Our scheme provides a powerful framework to map out the frequency and wavevector dependence of electronic excitations in unprecedented large tight-binding systems, up to 109 orbitals, with energy resolution only limited by the mean level spacing. We demonstrate the versatility of our approach in three distinct problems: (i) the Gade singularity in honeycomb layers with dilute topological defects; (ii) the rich landscape of impurity resonances in a spin--orbit-coupled ferromagnet; and (iii) the tailoring of emergent s-wave and p-wave superconducting phases in graphene via atomic defects. These examples reveal rich features in the disorder self-energy that are absent from the self-consistent T-matrix approach and other common approximation schemes, which include regimes of nontrivial wavevector dependence and anomalous dependence upon the impurity concentration. Our study unravels puzzling, and so far largely inaccessible, manifestations of strong nonperturbative quantum interference effects in quantum materials and disordered phases of matter