Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds

This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.

Effects of climate change on aquaculture site selection at a temperate estuarine system

Aquaculture is one of the food industries that most evolved in recent years in response to increased human demand for seafood products, which has led to a progressive stock threat in nature. With a high seafood consumption per capita, Portugal has been exploring its coastal systems to improve the cultivation of fish and bivalve species with high commercial value. In this context, this study aims to propose the use of a numerical model as a tool to assess the impact of climate change on aquaculture site selection in a temperate estuarine system (Sado estuary). Therefore, the Delft3D model was calibrated and validated, showing good accuracy in predicting the local hydrodynamics, transport, and water quality. Furthermore, two simulations for the historical and future conditions were performed to establish a Suitability Index capable of identifying the most appropriate sites to exploit two bivalve species (one clam and one oyster), considering both winter and summer seasons. Results suggest that the estuary's northernmost region presents the best conditions for bivalves' exploitation, with more suitable conditions during summer than winter due to the higher water temperature and chlorophyll-a concentrations. Regarding future projections, the model results suggest that environmental conditions will likely benefit the production of both species due to the increase in chlorophyll-a concentration along the estuary.

40 years of changes in sea surface temperature along the Western Iberian Coast

Climate change is causing mean sea surface temperatures (SST) to increase worldwide. However, this increase has not been temporally or spatially uniform, with variations observed depending both on the period considered and the geographic region. In this context, this paper aims to quantify relevant changes in SST along the Western Iberian Coast over the last four decades, through the calculation of trends and anomalies of long-term time series of in situ observations and satellite-derived data. Potential drivers of SST changes were considered using atmospheric and teleconnections time series. Changes in the seasonal cycle of SST were also evaluated. We show that SST has increased since 1982, with regional variations between 0.10 and 0.25 °C per decade, with an increase in air temperature appearing to drive the SST trends along the Iberian coast. In the near-shore area, no significant trends or changes in the seasonal cycle of SST were observed, which is likely due to a buffer effect caused by the seasonal upwelling that characterizes the region. Recent decades show a slowdown in the increase rate of SST along the Western Iberian Coast. An upwelling intensification could justify this observation, along with the effect of teleconnections on the regional climate, such as the North Atlantic Oscillation (NAO) and the Western Mediterranean Oscillation Index (WeMOI). Our results suggest that the WeMOI plays a more important role in coastal SST variability than the other teleconnections. The present study quantifies regional changes in SST and enhances knowledge of the role of ocean-atmosphere interactions in regulating climate and weather conditions. Moreover, it provides a relevant scientific context to the development of regional adaptative and mitigation actions in response to climate change.

Coastal warming under climate change: Global, faster and heterogeneous

The assessment of expected changes in coastal sea surface temperature (SST) on a global scale is becoming increasingly important due to the growing pressure on coastal ecosystems caused by climate change. To achieve this objective, 17 Global Climate Models from CMIP6 were used, with data from historical and hist-1950 experiments spanning 1982-2050. This analysis highlights significant warming of coastal areas worldwide, with higher and more variable rates of warming than observed in previous decades. All basins are projected to experience an increase in coastal SST near 1 °C by mid-century, with some regions exhibiting nearshore SST anomalies exceeding 2 °C for the period 2031-2050 relative to 1995-2014. Regarding the Eastern Upwelling Boundary Systems, only the Canary upwelling system and the southern part of the Humboldt upwelling system manage to show lower-than-average SST warming rates, maintaining, to a certain extent, their ability to buffer global warming.

Climate change in estuarine systems: Patterns and gaps using a meta-analysis approach

Although regional studies and projections suggest the deterioration of estuaries as a consequence of climate change, it is still difficult to fully understand the importance of such changes in estuarine systems. This limitation is particularly important considering their high dynamism and the lack of temporally extended in situ databases with a good spatial coverage for these systems worldwide. Furthermore, contradictory patterns have been observed across the globe. Motivated by these issues, in this study we question the availability of in situ observational evidence of climate change in estuarine systems through a detailed meta-analysis of existing publications. A topic-related search considering the outputs of the Web of Science library was conducted in order to obtain a characterization of the existing studies on climate change in estuarine systems. Results confirmed that climate change has increasingly been studied since 2000 and that marine climate change constituted the focus of 9.69 % of those studies. From these, only 9.30 % encompassed estuarine studies and just 1.13 % used in situ observations from estuarine systems (i.e., 0.11 % of the total climate change publications). Reanalysis products were the most used tools to assess changes in estuarine systems and sea temperature was the most analyzed variable. These results highlight the need to further address such questions using in situ observational data and to implement long-term observatories to fully identify evidence of climate change in estuarine systems, supporting modelling approaches and promoting the development of effective mitigation plans.

Evaluation of future estuarine floods in a sea level rise context

Reliable predictions of future inundation extent within estuaries require a precise evaluation of future extreme sea levels and the application of accurate numerical models that account for the physical processes driving estuarine hydrodynamics. In this study, a methodology that integrates the estimation of local extreme sea levels with high-resolution numerical modeling was applied to assess the future inundation extent in five estuarine systems located on the Portuguese Coast. The main findings obtained were compared with available results from the popular bathtub approach, that disregards the physical processes driving estuarine hydrodynamics and therefore provide imprecise predictions of inundation extent and associated socio-economic impacts. The inundation extent is revealed to be highly dependent on the extreme sea levels and on the estuarine geomorphology, which controls the propagating long-wave. As the long-wave height is highly attenuated within estuaries that have adjacent low-lying areas, restricted inlets, or extensive tidal flats, the results of this study revealed that the extent of inundation is considerably smaller than that obtained by the bathtub approach. The uncertainties associated with mean sea level rise and the estuarine geomorphological evolution constitute the greatest difficulty in assessing the extent of flooding, posing major challenges to the efficient and sustainable management of estuaries.

NW Iberian Peninsula coastal upwelling future weakening: Competition between wind intensification and surface heating

Climate change will modify the oceanographic future properties of the NW Iberian Peninsula due to the projected variations in the meteorological forcing, that will intensify local winds and promote surface heating. The Delft3D-Flow model forced with atmospheric conditions provided within the framework of the CORDEX project under the RCP 8.5 greenhouse emission scenario was used to analyse changes in upwelling. Numerical experiments were conducted under high-extreme upwelling conditions for the historical (1976-2005) and future (2070-2099) period. This study also innovates through the exploitation of a numerical modelling approach that includes both shelf and estuarine processes along the coastal zone. Coastal upwelling will be less effective in the future despite the enhancement of upwelling favorable wind patterns previously predicted for this region. Upwelling weakening is due to the future sea surface warming that will increase the stratification of the upper layers hindering the upward displacement of the underlying water, reducing the surface input of nutrients.

Physical and thermal processing of Waste Printed Circuit Boards aiming for the recovery of gold and copper

The recovery of electronic waste to obtain secondary raw materials is a subject of high relevance in the context of circular economy. Accordingly, the present work relies on the evaluation of mining separation/concentration techniques (comminution, size screening, magnetic separation and gravity concentration) alone as well as combined with thermal pre-treatment to recover gold and copper from Waste Printed Circuit Boards. For that purpose, Waste Printed Circuit Boards were subjected to physical processing (comminution, size screening in 6 classes from <0.425 mm to > 6.70 mm, magnetic separation and gravity concentration) alone and combined with thermal treatment (200-500 °C), aiming the recovery of gold and copper. Mixed motherboards and graphic cards (Lot 1 and 3) and highly rich components (connectors separated from memory cards, Lot 2) were analyzed. Gold and copper concentrations were determined before and after treatment. Before treatment, concentrations from 0.01 to 0.6 % wt. and from 9 to 20 % wt. were found for gold and copper respectively. The highest concentrations were observed in the size fractions between 0.425 and 1.70 mm. The highest copper concentration was around 35 % wt. (class 0.425-0.85 mm) and when analyzing memory card connectors alone, gold concentrations reached almost 2% in the same class, reflecting the interest of separating such components. The physical treatment alone was more effective for Lot 1/3, compared to Lot 2, allowing recoveries of 67 % wt. and 87 % wt. for gold and copper respectively, mostly due to differences in particles size and shape. The thermal treatment showed unperceptive influence on gold concentration but significant effect for copper concentration, mostly attributed to the size of the copper particles. Concentrations increased in a factor of around 10 when the thermal treatment was performed at 300 °C for the larger particles (1.70-6.70 mm); the best results were obtained at 400 °C for the other sizes, when the highest rate of thermal decomposition of the material occurred.

Subtidal variability of the Tagus river plume in winter 2013

The subtidal variability of surface plume response to local wind and river runoff is studied off central Portugal using a hindcast model for the Tagus Estuary (TE) plume. In addition to the model, the main patterns of variability of the TE plume were extracted in an automated mode using Self Organizing Maps (SOM). Three characteristic spatial patterns are extracted in a 3 × 2 SOM array: in synoptic time scales, northward and southward propagation of the plume and transitional periods. Results suggest that river runoff and wind induce strong variability in the coastal ocean, and that the TE plume has a rapid response to their changes. Under high river runoff there is a southern propagation of the plume, even during downwelling favorable winds, revealing bi-directional patterns due to the combined effect of estuarine outflow, wind direction and coastline in establishment the plume direction. The same is found during transitional periods, revealing that the TE plume has significant influence both north and south of the estuary mouth. SOM was applied for the first time to extract spatial and temporal features of the TE plume and prove to be a reliable tool to study large quantities of data in addition to the model results analysis.

Guiding of laser pulses in plasma waveguides created by linearly-polarized femtosecond laser pulses

We experimentally demonstrate that plasma waveguides produced with ultra-short laser pulses (sub-picosecond) in gas jets are capable of guiding high intensity laser pulses. This scheme has the unique ability of guiding a high-intensity laser pulse in a plasma waveguide created by the same laser system in the very simple and stable experimental setup. A hot plasma column was created by a femtosecond class laser that expands into an on-axis parabolic low density profile suitable to act as a waveguide for high intensity laser beams. We have successfully guided ~10¹⁵ W cm⁻² laser pulses in a 8 mm long hydrogen plasma waveguide with a 35% guiding efficiency.

Why coastal upwelling is expected to increase along the western Iberian Peninsula over the next century?

Former studies about coastal upwelling along the Western Iberian Peninsula (WIP) using historical data indicated contradictory results, showing either its strengthening or reduction, while previous studies using Global Climate Models (GCMs) indicated that global warming is likely to intensify this phenomenon although predicting different rates and not justifying the patterns found. Taking advantage of the recent high spatial resolution Regional Climate Models (RCMs) projections from EURO-CORDEX project (Representative Concentration Pathway, RCP 8.5), detailed higher accuracy estimations of the spatio-temporal trends of Upwelling Index (UI) along the WIP coast were performed in this study, integrating the coastal mesoscale effects within the framework of climate change. Additionally, this research brings new insights about the origin of the WIP coastal upwelling intensification over the next century. These new projections clarified the upwelling strengthening rates predicted along the coast of the WIP from 2006 to 2099 revealing more prominent changes in the northern limit of the region (25-30m³s^-1km^-1 per decade between 41.5 and 42.5°N). Trends observed at high latitudes of the region were found to be induced by the displacement of the Azores High, which will intensify (0.03hPa per decade) and drift northeastward (10km per decade) during the 21st century.

An ultra-high gain and efficient amplifier based on Raman amplification in plasma

Raman amplification arising from the excitation of a density echelon in plasma could lead to amplifiers that significantly exceed current power limits of conventional laser media. Here we show that 1-100 J pump pulses can amplify picojoule seed pulses to nearly joule level. The extremely high gain also leads to significant amplification of backscattered radiation from "noise", arising from stochastic plasma fluctuations that competes with externally injected seed pulses, which are amplified to similar levels at the highest pump energies. The pump energy is scattered into the seed at an oblique angle with 14 J sr-1, and net gains of more than eight orders of magnitude. The maximum gain coefficient, of 180 cm-1, exceeds high-power solid-state amplifying media by orders of magnitude. The observation of a minimum of 640 J sr-1 directly backscattered from noise, corresponding to ≈10% of the pump energy in the observation solid angle, implies potential overall efficiencies greater than 10%.

Challenges for the WFD second management cycle after the implementation of a regional multi-municipality sanitation system in a coastal lagoon (Ria de Aveiro, Portugal)

In the scope of the first WDF management cycle, a multi-municipality sanitation system with secondary treatment was implemented in 2005 in Ria de Aveiro coastal lagoon, with the treated effluent discharging into the Atlantic Ocean through a submarine outfall. The lagoon water chemical status was evaluated regarding dissolved inorganic nutrients and chlorophyll a before and after 2005. The S. Jacinto outfall has effectively reduced the point source nutrient loads (ammonium and phosphate) into Ria de Aveiro, representing a step forward for the implementation of the WFD, through eutrophication abatement. However, the lagoon remains exposed to non-point nitrogen sources, as a consequence of the current land use and water management, which in a scenario of winter extreme precipitation events, nutrients increase through surface run-off. Besides, in a combined scenario of low freshwater input into the lagoon and favourable oceanic condition, nutrients enter through Ria outer boundary coming from the S. Jacinto outfall. Thus, changes in the system hydrodynamics in the context of global change might pose new challenges regarding the WFD second management cycle involving the second river basin management plan and the first flood risk management plan, foreseeing the 'Good' ecological status in all Ria's Water Bodies.

Torque-angle-velocity Relationships and Muscle Performance of Professional and Youth Soccer Players

Soccer matches consist of a variety of different activities, including repeated sprints. Time to attain velocity (TTAV), load range (LR) and the torque-angle-velocity relationship (TAV_3D) represent an important measurement of muscle performance, however there are few related studies. The aim of this study was to compare these outcomes between soccer players of different age category. 17 professional (PRO) and 17 under-17 (U17) soccer players were assessed for concentric knee flexion/extension at 60, 120 and 300°/s. For the extensor muscles, differences were found in favor of the U17 group for TTAV and LR outcomes at 120°/s, however, the PRO group maintained higher torques in both movement directions in comparison to the U17 in TAV_3D evaluation. These results suggest that muscle performance of the PRO group is more efficient than the U17 group.

Musculoskeletal ultrasound in Paediatric Rheumatology: a retrospective analysis

OBJECTIVES

Musculoskeletal Ultrasound (MSK-US) has become increasingly important in the diagnosis and follow-up of children with rheumatic diseases. We describe the experience of a large Portuguese centre and study the added value of MSK-US in the clinical assessment of paediatric rheumatic diseases.

MATERIAL AND METHODS

Patients were observed by assistant Rheumatologists, a clinical diagnosis was assigned and MSK-US requested. 330 MSK-US exams were performed to 222 children with rheumatic inflammatory diseases. The children's ages were between 1 and 18 years (mean=11.7±4.7 years) and 67.6% were female. Synovial membrane proliferation, intra-articular effusion, cartilage abnormalities, erosions and periarticular affections were searched in each joint. Clinical and ultrasonography data were compared.

RESULTS

MSK-US detected synovitis in 100 of 194 exams (51.5%) of patients with that clinical information and in 36 of 136 exams (26.5%) of patients who presented other clinical findings. In those in which MSK-US did not confirm the clinical information of synovitis (94; 48.5%), we detected tenosynovitis/tendinopathy in 13 cases (13.8%) and synovial cyst in four (4.3%). The remaining patients had no ultrasonography changes and MSK-US helped to exclude synovitis. The sensitivity for arthritis clinical assessment was good (73.5%), with modest specificity (51.5%), an accuracy of 60.6% and precision of 51.5%. Ultrasonography synovitis was mostly found in the knee (37.5%), followed by the ankle (22.8%) and hip (10.3%). Overall, 39 exams showed ultrasonographic tenosynovitis/tendinopathy, 15 of which had the same clinical diagnosis. Tenosynovitis/tendinopathy was mostly found in the ankle (59.0%) and knee (23.1%) areas.

CONCLUSIONS

MSK-US is an important aid to clinical evaluation, allowing both the detection and exclusion of joint pathology in children, contributing to a better assessment.

Compton scattering for spectroscopic detection of ultra-fast, high flux, broad energy range X-rays

Compton side-scattering has been used to simultaneously downshift the energy of keV to MeV energy range photons while attenuating their flux to enable single-shot, spectrally resolved, measurements of high flux X-ray sources to be undertaken. To demonstrate the technique a 1 mm thick pixelated cadmium telluride detector has been used to measure spectra of Compton side-scattered radiation from a Cobalt-60 laboratory source and a high flux, high peak brilliance X-ray source of betatron radiation from a laser-plasma wakefield accelerator.

Salt fluxes in a complex river mouth system of Portugal

Measurements of velocity and salinity near the mouth and head of the Espinheiro channel (Ria de Aveiro lagoon, Portugal) are used to study the local variation of physical water properties and to assess the balance, under steady conditions, between the seaward salt transport induced by river discharge and the landward dispersion induced by various mixing mechanisms. This assessment is made using data sampled during complete tidal cycles. Under the assumption that the estuarine tidal channel is laterally homogeneous and during moderate tidal periods (except for one survey), currents and salinity data were decomposed into various spatial and temporal means and their deviations. Near the channel's mouth, the main contributions to the salt transport are the terms due to freshwater discharge and the tidal correlation. Near the channel's head, this last term is less important than the density driven circulation, which is enhanced by the increase in freshwater discharge. The remaining terms, which are dependent on the deviations from the mean depth have a smaller role in the results of salt transport. The computed salt transport per unit width of a section perpendicular to the mean flow is in close agreement to the sum of the advective and dispersive terms (within or very close to 12%). An imbalance of the salt budget across the sections is observed for all the surveys. Considerations are made on how this approach can inform the management of hazardous contamination and how to use these results to best time the release of environmental flows during dry months.

Activated carbon modifications to enhance its water treatment applications. An overview

The main objective of this study was to list and compare the advantages and disadvantages of different methodologies to modify the surface of activated carbons (ACs) for their application as adsorbents to remove organic and inorganic pollutants from aqueous phase. These methodologies have been categorized into four broad groups: oxidation, sulfuration, ammonification, and coordinated ligand anchorage. Numerous investigations into the removal of metals from water have modified carbon surfaces to increase their content of acidic surface functional groups by using H(2)O(2), O(3) and HNO(3). Because these treatments can reduce the AC surface area, researchers are seeking alternative methods to modify and/or create surface functional groups without the undesirable effect of pore blockage. The nitrogenation or sulfuration of the AC surface can increase its basicity favoring the adsorption of organic compounds. The introduction of nitrogen or sulfur complexes on the carbon surface increases the surface polarity and, therefore, the specific interaction with polar pollutants. Different coordinated ligands have also been used to modify ACs, showing that coordinated ligand anchorage on the AC surface modifies its textural and chemical properties, but research to date has largely focused on the use of these modified materials to remove heavy metals from water by complexes formation.

Facial exercise therapy for facial palsy: systematic review and meta-analysis

The effectiveness of facial exercises therapy for facial palsy has been debated in systematic reviews but its effects are still not totally explained.

OBJECTIVE

To perform a systematic review with meta-analysis to evaluate the effects of facial exercise therapy for facial palsy.

DATA SOURCES

A search was performed in the following databases: Cochrane Controlled Trials Register Library, Cochrane Disease Group Trials Register, MEDLINE, EMBASE, LILACS, PEDro, Scielo and DARE from 1966 to 2010; the following keywords were used: 'idiopathic facial palsy', 'facial paralysis', 'Bell's palsy', 'physical therapy', 'exercise movement techniques', 'facial exercises', 'mime therapy' 'facial expression', 'massage' and 'randomized controlled trials'.

REVIEW METHODS

The inclusion criteria were studies with facial exercises, associated or not with mirror biofeedback, to treat facial palsy.

RESULTS

One hundred and thirty-two studies were found but only six met the inclusion criteria. All the studies were evaluated by two independent reviewers, following the recommendations of Cochrane Collaboration Handbook for assessment of risk of bias (kappa coefficient = 0.8). Only one study presented sufficient data to perform the meta-analysis, and significant improvements in functionality was found for the experimental group (standardized mean difference (SMD) = 13.90; 95% confidence interval (CI) 4.31, 23.49; P = 0.005).

CONCLUSION

Facial exercise therapy is effective for facial palsy for the outcome functionality.

Electro-optic measurement of terahertz pulse energy distribution

An accurate and direct measurement of the energy distribution of a low repetition rate terahertz electromagnetic pulse is challenging because of the lack of sensitive detectors in this spectral range. In this paper, we show how the total energy and energy density distribution of a terahertz electromagnetic pulse can be determined by directly measuring the absolute electric field amplitude and beam energy density distribution using electro-optic detection. This method has potential use as a routine method of measuring the energy density of terahertz pulses that could be applied to evaluating future high power terahertz sources, terahertz imaging, and spatially and temporarily resolved pump-probe experiments.

Design and characterization of supersonic nozzles for wide focus laser-plasma interactions

In this work we optimize the contour of supersonic nozzles to produce long and stable gas jets suitable to be used in loose focus laser-plasma applications. The nozzle design method takes into account the inclusion of a boundary layer that increases the length of the usable gas jet. Two 8 mm supersonic nozzles were characterized, one with a Mach number of 3 and another with a Mach number of 6, using a Mach-Zehnder interferometer performed with a He:Ne 4 cm expanded laser beam. The experimental results confirm that the inclusion of the boundary layer produces an 8 mm constant longitudinal density profile for the nozzle with a Mach number of 6 (NM6) and a 4.5 mm constant longitudinal density profile for the nozzle with a Mach number of 3 (NM3).

Crystal structure of the 16 heme cytochrome from Desulfovibrio gigas: a glycosylated protein in a sulphate-reducing bacterium

Sulphate-reducing bacteria have a wide variety of periplasmic cytochromes involved in electron transfer from the periplasm to the cytoplasm. HmcA is a high molecular mass cytochrome of 550 amino acid residues that harbours 16 c-type heme groups. We report the crystal structure of HmcA isolated from the periplasm of Desulfovibrio gigas. Crystals were grown using polyethylene glycol 8K and zinc acetate, and diffracted beyond 2.1 A resolution. A multiple-wavelength anomalous dispersion experiment at the iron absorption edge enabled us to obtain good-quality phases for structure solution and model building. DgHmcA has a V-shape architecture, already observed in HmcA isolated from Desulfovibrio vulgaris Hildenborough. The presence of an oligosaccharide molecule covalently bound to an Asn residue was observed in the electron density maps of DgHmcA and confirmed by mass spectrometry. Three modified monosaccharides appear at the highly hydrophobic vertex, possibly acting as an anchor of the protein to the cytoplasmic membrane.

Tidal transport and dispersal of marine toxic microalgae in a shallow, temperate coastal lagoon

A numerical model was used to predict toxic microalgal transport and dispersion in Ria de Aveiro in Portugal. A previously developed Lagrangean particle tracking model coupled to a calibrated two-dimensional hydrodynamic model of Ria de Aveiro was used. Microalgae were regarded as passive particles and the methodology used allowed the determination of their trajectories, as induced by the tidal currents predicted by the hydrodynamic model. The model assumes Ria de Aveiro as vertically homogeneous and does not take into account the vertical distribution patterns of microalgae. Simulations were carried out during extreme spring and neap tides, with microalgal released at the mouth of the lagoon at the local flood. The maximum and minimum areas affected during the occurrence of toxic microalgal blooms were estimated to evaluate the suitability of the distribution of the sampling stations included in the local monitoring program. It was found that the tidal currents greatly determine the microalgal horizontal distribution and dispersal in the lagoon. The results confirmed that the locations of water and bivalve shellfish sampling stations, postulated by INIAP/IPIMAR, in the context of the local harmful algal bloom (HAB) program, were appropriate, although some possible refinements were identified.

Bacterial productivity distribution during a rainy year in an estuarine system

Bacterial density and productivity were investigated along four salinity gradients within the estuary Ria de Aveiro. Bacterial variables and environmental parameters were measured at three to four stations spanning the entire salinity gradient of the four channels. The rather high variation in bacterial productivity (0.16-7.6 microg C L(-1) h(-1)) along the profiles of salinity indicates that bacterial activity shows a reactive behavior to environmental changing. Bacterial density (0.5-11.2 x 10(9) cells L(-1)) with a comparative smaller variation showed a more conservative behavior, mainly reflecting the phytoplankton distribution. Contrary to expectation, minimal values of bacterial productivity were not observed in November-December but in June. In fact, in November-December, the deep zone near the mouth showed the highest values of bacterial activity. At the upper stations, the highest values were observed in October. The relatively high values of bacterial production during the cold rainy season suggest that allochthonous substrates leached out from the surroundings by rain controlled the distribution of bacterial activity in the estuarine system. The substantial decrease in salinity during the rainy season negatively affected bacterial productivity, namely in the marine zone, where water column was highly stratified. Salinity seems to play an indirect role in the regulation of estuarine bacteria because there are different bacterial communities adapted to a wide salinity range.

The water quality of the Ria de Aveiro lagoon, Portugal: from the observations to the implementation of a numerical model

Ria de Aveiro is a very important area of the Portuguese coast, which has been under an increasing anthropogenic pressure for several decades and, contributes to the degradation of the lagoon's water quality. This work presents both a characterisation of the water quality of the Ria de Aveiro lagoon, using physical, chemical and biological experimental data, and an implementation of a numerical model for the water quality of the lagoon. The ultimate goal is to obtain an accurate numerical model able to simulate major water quality features of the lagoon under the influence of different forcing conditions. Data analysis reveals good correlations between the salinity and almost all the water quality variables as well as between the different variables. The maximum biochemical oxygen demand concentration (BOD) depends on the light intensity, the temperature and the river inputs. The main vulnerable areas of the lagoon, from the water quality point of view, seem to be the far end of the main channels, where low dissolved oxygen concentration (DO) and high BOD concentrations are observed. The numerical model of the Ria de Aveiro has reproduced both winter-spring and spring-summer events related to the lagoon water quality as well as its main pattern. Both data and modelling results show that the BOD5 concentrations (where the subscript '5' means that the BOD measurements were conducted for five days, without inhibitor of nitrification) are driven by the river influence, during the winter-spring period, and by the biological activity during the spring-summer period. The DO concentrations show high values in the spring-summer period and smaller concentrations in the winter-spring period at the far end of the lagoon. The application of the model to the study of scenarios has demonstrated the role of nutrients and light in the phytoplankton growth, the relationship between DO and phytoplankton concentrations, as well as the effect of the BOD degradation in the ammonia (NH4) regeneration.

Plasma channels produced by a laser-triggered high-voltage discharge

A plasma waveguide scheme for high-intensity laser guiding with densities and lengths suitable for laser-plasma particle accelerators is presented. This scheme uses a laser-triggered high-voltage discharge, presents negligible jitter, allows full access to the plasma, and can be scaled to large distances. Experimental results showing the feasibility of this scheme are presented.

Photon acceleration of ultrashort laser pulses by relativistic ionization fronts

We present experimental results from the collision of weak ultrashort pulses with relativistic ionization fronts in copropagation and counterpropagation. The observed frequency upshifts of the probe pulses provide not only information about the electron density of the ionization front but also reveal the fine structure of the front. The connection between the correlation lengths for copropagation and counterpropagation and the longitudinal and transverse dimensions of the ionization front is also demonstrated thus showing the feasibility of using the frequency upshift experienced by short probe pulses to fully characterize relativistic ionization fronts and other relativistic coherent structures in laser-produced plasmas.

Two-dimensional collision of probe photons with relativistic ionization fronts

The collision of a probe laser pulse with a relativistic ionization front is analyzed via two-dimensional ray-tracing theory and simulations. It is shown that collisions in higher dimensions lead to new regimes for the frequency upshift of the probe photons; the frequency upshift can be considerably higher for particular collision angles that maximize the interaction length with the ionization front gradient. Finite ionization fronts also lead to angle-dependent frequency upshifts, thus acting as diffraction gratings.

Structure refinement of the aldehyde oxidoreductase from Desulfovibrio gigas (MOP) at 1.28 A

The sulfate-reducing bacterium aldehyde oxidoreductase from Desulfovibrio gigas (MOP) is a member of the xanthine oxidase family of enzymes. It has 907 residues on a single polypeptide chain, a molybdopterin cytosine dinucleotide (MCD) cofactor and two [2Fe-2S] iron-sulfur clusters. Synchrotron data to almost atomic resolution were collected for improved cryo-cooled crystals of this enzyme in the oxidized form. The cell constants of a=b=141.78 A and c=160.87 A are about 2% shorter than those of room temperature data, yielding 233,755 unique reflections in space group P6(1)22, at 1.28 A resolution. Throughout the entire refinement the full gradient least-squares method was used, leading to a final R factor of 14.5 and Rfree factor of 19.3 (4sigma cut-off) with "riding" H-atoms at their calculated positions. The model contains 8146 non-hydrogen atoms described by anisotropic displacement parameters with an observations/parameters ratio of 4.4. It includes alternate conformations for 17 amino acid residues. At 1.28 A resolution, three Cl- and two Mg2+ ions from the crystallization solution were clearly identified. With the exception of one Cl- which is buried and 8 A distant from the Mo atom, the other ions are close to the molecular surface and may contribute to crystal packing. The overall structure has not changed in comparison to the lower resolution model apart from local corrections that included some loop adjustments and alternate side-chain conformations. Based on the estimated errors of bond distances obtained by blocked least-squares matrix inversion, a more detailed analysis of the three redox centres was possible. For the MCD cofactor, the resulting geometric parameters confirmed its reduction state as a tetrahydropterin. At the Mo centre, estimated corrections calculated for the Fourier ripples artefact are very small when compared to the experimental associated errors, supporting the suggestion that the fifth ligand is a water molecule rather than a hydroxide. Concerning the two iron-sulfur centres, asymmetry in the Fe-S distances as well as differences in the pattern of NH.S hydrogen-bonding interactions was observed, which influences the electron distribution upon reduction and causes non-equivalence of the individual Fe atoms in each cluster.

Purification, crystallization and identification by X-ray analysis of a prostate kallikrein from horse seminal plasma

The purification, crystallization and identification by X-ray diffraction analysis of a horse kallikrein is reported. The protein was purified from horse seminal plasma. Crystals belong to space group C2 and the structure was solved by the MIRAS method, with two heavy-atom derivatives of mercury and platinum. X-ray diffraction data to 1.42 A resolution were collected at the ESRF synchrotron-radiation source.

Tungsten-containing formate dehydrogenase from Desulfovibrio gigas: metal identification and preliminary structural data by multi-wavelength crystallography

The tungsten-containing formate dehydrogenase (W-FDH) isolated from Desulfovibrio gigas has been crystallized in space group P2(1), with cell parameters a = 73.8 A, b = 111.3 A, c = 156.6 A and beta = 93.7 degrees. These crystals diffract to beyond 2.0 A on a synchrotron radiation source. W-FDH is a heterodimer (92 kDa and 29 kDa subunits) and two W-FDH molecules are present in the asymmetric unit. Although a molecular replacement solution was found using the periplasmic nitrate reductase as a search model, additional phasing information was needed. A multiple-wavelength anomalous dispersion (MAD) dataset was collected at the W- and Fe-edges, at four different wavelengths. Anomalous and dispersive difference data allowed us to unambiguously identify the metal atoms bound to W-FDH as one W atom with a Se-cysteine ligand as well as one [4Fe-4S] cluster in the 92 kDa subunit, and three additional [4Fe-4S] centers in the smaller 29 kDa subunit. The D. gigas W-FDH was previously characterized based on metal analysis and spectroscopic data. One W atom was predicted to be bound to two molybdopterin guanine dinucleotide (MGD) pterin cofactors and two [4Fe-4S] centers were proposed to be present. The crystallographic data now reported reveal a selenium atom (as a Se-cysteine) coordinating to the W site, as well as two extra [4Fe-4S] clusters not anticipated before. The EPR data were re-evaluated in the light of these new results.

Gene sequence and crystal structure of the aldehyde oxidoreductase from Desulfovibrio desulfuricans ATCC 27774

The aldehyde oxidoreductase (MOD) isolated from the sulfate reducer Desulfovibrio desulfuricans (ATCC 27774) is a member of the xanthine oxidase family of molybdenum-containing enzymes. It has substrate specificity similar to that of the homologous enzyme from Desulfovibrio gigas (MOP) and the primary sequences from both enzymes show 68 % identity. The enzyme was crystallized in space group P6(1)22, with unit cell dimensions of a=b=156.4 A and c=177.1 A, and diffraction data were obtained to beyond 2.8 A. The crystal structure was solved by Patterson search techniques using the coordinates of the D. gigas enzyme. The overall fold of the D. desulfuricans enzyme is very similar to MOP and the few differences are mapped to exposed regions of the molecule. This is reflected in the electrostatic potential surfaces of both homologous enzymes, one exception being the surface potential in a region identifiable as the putative docking site of the physiological electron acceptor. Other essential features of the MOP structure, such as residues of the active-site cavity, are basically conserved in MOD. Two mutations are located in the pocket bearing a chain of catalytically relevant water molecules. As deduced from this work, both these enzymes are very closely related in terms of their sequences as well as 3D structures. The comparison allowed confirmation and establishment of features that are essential for their function; namely, conserved residues in the active-site, catalytically relevant water molecules and recognition of the physiological electron acceptor docking site.

Screening and characterization of Bacillus thuringiensis isolates from Brazil for the presence of coleoptera-specific cry genes

Forty-three Bacillus thuringiensis isolates from Brazil and 3 from Argentina were screened, using the polymerase chain reaction (PCR), for various coleoptera-specific cry genes. Seven isolates produced specific and/or nonspecific DNA fragments in a PCR reaction with primers specific for two coleopteran cry genes and 4 of these produced DNA fragments with primers specific for 7 known coleopteran cry genes. These isolates showed, by electron microscopy, the presence of spherical crystals. They also showed proteins of around 70 kDa which were immunologically similar to the Cry3Aa protein from B. thuringiensis subsp. tenebrionis. The 3 isolates from Argentina were toxic to T. molitor, and although no isolate from Brazil showed toxicity, they might show toxicity to another insect species.

Biochemical/spectroscopic characterization and preliminary X-ray analysis of a new aldehyde oxidoreductase isolated from Desulfovibrio desulfuricans ATCC 27774

Aldehyde oxidoreductase (AOR) activity has been found in different sulfate reducing organisms (Moura, J. J. G., and Barata, B. A. S. (1994) in Methods in Enzymology (Peck, H. D., Jr., and LeGall, J., Eds.), Vol. 243, Chap. 4. Academic Press; Romão, M. J., Knäblein, J., Huber, R., and Moura, J. J. G. (1997) Prog. Biophys. Mol. Biol. 68, 121-144). The enzyme was purified to homogeneity from extracts of Desulfovibrio desulfuricans (Dd) ATCC 27774, a sulfate reducer that can use sulfate or nitrate as terminal respiratory substrates. The protein (AORDd) is described as a homodimer (monomer, circa 100 kDa), contains a Mo-MCD pterin, 2 x [2Fe-2S] clusters, and lacks a flavin group. Visible and EPR spectroscopies indicate a close similarity with the AOR purified from Desulfovibrio gigas (Dg) (Barata, B. A. S., LeGall, J., and Moura, J. J. G. (1993) Biochemistry 32, 11559-11568). Activity and substrate specificity for different aldehydes were determined. EPR studies were performed in native and reduced states of the enzyme and after treatment with ethylene glycol and dithiothreitol. The AORDd was crystallized using ammonium sulfate as precipitant and the crystals belong to the space group P6(1)22, with unit cell dimensions a = b = 156.4 and c = 177.1 A. These crystals diffract to beyond 2.5 A resolution and a full data set was measured on a rotating anode generator. The data were used to solve the structure by Patterson Search methods, using the model of AORDg.

Crystallization and preliminary X-ray analysis of a membrane-bound nitrite reductase from Desulfovibrio desulfuricans ATCC 27774

Nitrite reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is a multihaem (type c) membrane-bound enzyme that catalyzes the dissimilatory conversion of nitrite to ammonia. Crystals of the oxidized form of this enzyme were obtained using PEG and CaCl(2) as precipitants in the presence of 3--(decylmethylammonium)propane-1-sulfonate and belong to the space group P2(1)2(1)2(1), with unit-cell parameters a = 78.94, b = 104.59, c = 143.18 A. A complete data set to 2.30 A resolution was collected using synchrotron radiation at the ESRF. However, the crystals may diffract to beyond 1.7 A and high-resolution data will be collected in the near future.

Expression of cre recombinase as a reporter of signal transduction in mammalian cells

BACKGROUND

Cell-based reporter assays, which rely on a reporter gene under the control of a regulated promoter, are widely used to screen chemical libraries for novel receptor ligands. Here, we describe a reporter system that is based on ligand-induced DNA recombination to express the reporter gene. This system converts a transient activation of a signal transduction pathway into an amplified, constitutive and heritable expression of the reporter gene.

RESULTS

We constructed gene fusions of Cre recombinase and mammalian promoters regulated by calcium, nuclear receptors or cyclic AMP. Reporter systems, comprising a Cre gene fusion and a loxP/reporter gene, were used to study the kinetics and dose responses to compounds that activate or inhibit the corresponding signal transduction pathway. We compared these reporters with conventional reporter systems in which the reporter gene is under the direct control of the responsive promoter. Reporter gene expression of the Cre reporters was greater than that of conventional reporters and could be measured more than a week after adding the stimulus. For all pathways studied here, the dose responses of the Cre reporters are nearly identical to those of conventional reporter systems.

CONCLUSIONS

We have shown that Cre recombinase can be regulated by a variety of signal transduction pathways. It should therefore be possible to use receptor ligands to induce phenotypic conversion of mammalian cells for use in a variety of applications. One such application is high-throughput screening, and we developed loxP/luciferase reporter genes that provide an amplified and sustained luminescent response.

Crystallization and preliminary x-ray analysis of a nitrate reductase from Desulfovibrio desulfuricans ATCC 27774

Periplasmic nitrate reductase from the sulfate-reducing bacterium Desulfovibrio desulfuricans ATCC 27774 contains two molybdopterin guanine dinucleotide cofactors and one [4Fe-4S] cluster as prosthetic groups and catalyzes the conversion of nitrate to nitrite. Crystals of the oxidized form of this enzyme were obtained using PEG as precipitant and belong to space group P3121 or P3221, with unit-cell dimensions a = b = 106.3, c = 135.1 A. There is one monomer of 80 kDa in the asymmetric unit, which corresponds to a Matthews ratio of 2.75 A3 Da-1. Using cryo-cooling procedures and X-rays from a rotating-anode generator, diffraction was observed to beyond 3.0 A resolution.

Larvicidal activity of Bacillus sphaericus 2362 against Anopheles nuneztovari, Anopheles darlingi and Anopheles braziliensis (Diptera, Culicidae)

In this present study, preliminary data was obtained regarding the mortality rate of the Amazonian anophelines, Anopheles nuneztovari, Anopheles darlingi and Anopheles braziliensis when subjected to treatment with Bacillus sphaericus strain 2362, the WHO standard strain. Initially, experiments were conducted to test the mortality rate of the three species of anopheline larvae. The third larval instar of An. nuneztovari and the second and third larval instars of An. darlingi proved to be the least susceptible. In other experiments, the same three mosquito species were tested with the standard strain 2362, An. nuneztovari was the least susceptible to this insect pathogen, while An. braziliensis was the most susceptible. This latter species showed a difference in the level of LC50 concentration, when compared to the former, of 2.4, 2.5 and 1.8 in readings taken 24, 48 and 72 hours after exposure to the bacillus.

Crystal structure of the first dissimilatory nitrate reductase at 1.9 A solved by MAD methods

BACKGROUND

The periplasmic nitrate reductase (NAP) from the sulphate reducing bacterium Desulfovibrio desulfuricans ATCC 27774 is induced by growth on nitrate and catalyses the reduction of nitrate to nitrite for respiration. NAP is a molybdenum-containing enzyme with one bis-molybdopterin guanine dinucleotide (MGD) cofactor and one [4Fe-4S] cluster in a single polypeptide chain of 723 amino acid residues. To date, there is no crystal structure of a nitrate reductase.

RESULTS

The first crystal structure of a dissimilatory (respiratory) nitrate reductase was determined at 1.9 A resolution by multiwavelength anomalous diffraction (MAD) methods. The structure is folded into four domains with an alpha/beta-type topology and all four domains are involved in cofactor binding. The [4Fe-4S] centre is located near the periphery of the molecule, whereas the MGD cofactor extends across the interior of the molecule interacting with residues from all four domains. The molybdenum atom is located at the bottom of a 15 A deep crevice, and is positioned 12 A from the [4Fe-4S] cluster. The structure of NAP reveals the details of the catalytic molybdenum site, which is coordinated to two MGD cofactors, Cys140, and a water/hydroxo ligand. A facile electron-transfer pathway through bonds connects the molybdenum and the [4Fe-4S] cluster.

CONCLUSIONS

The polypeptide fold of NAP and the arrangement of the cofactors is related to that of Escherichia coli formate dehydrogenase (FDH) and distantly resembles dimethylsulphoxide reductase. The close structural homology of NAP and FDH shows how small changes in the vicinity of the molybdenum catalytic site are sufficient for the substrate specificity.

Studies on the Bacillus sphaericus larvicidal activity against malarial vector species in Amazonia

In this work, bioassays were carried out in laboratory conditions (average temperature 26 +/- 2 degrees C) to test ten strains of Bacillus sphaericus, isolated from Brazilian soils against third instar larvae from anopheline species recorded as malaria vectors in Amazonian-Anopheles nuneztovari and An. darlingi. With the former mosquito, three strains--S2, S20 and S46 showed relative activity, in 24 and 48 hr exposure to the B. spahericus strains. With the latter only the S2 and S20 were effective in the 48 hr reading. The studied strains that showed the most adequate response in the Amazonian region were S2 and S20 showing broader and more efficient results. Therefore, S2 was the most effective when the 24 and 48 hr readings were considered, because it showed the greatest relative activity values.

Genetic recombination as a reporter for screening steroid receptor agonists and antagonists

Reporter cell lines are often used for high throughput screening of chemical libraries to identify new receptor ligands. Here we show how Cre recombinase can be used in mammalian cells to screen for steroid receptor ligands. A translational fusion of Cre recombinase and the ligand binding domain of the human glucocorticoid receptor was transfected into mammalian cells with a loxP/luciferase reporter gene. The recombinase function of the fusion is dependent on ligand binding to the receptor, and Cre-mediated recombination results in constitutive expression of luciferase from the reporter gene. A stable transfected clone was isolated and used to characterize the kinetics, ligand specificity, and dose response to various receptor ligands. The Cre fusion system, unlike a transcriptional reporter using the mouse mammary tumor virus promoter, can detect binding of the receptor antagonist RU486. We also studied the Cre reporter in a sensitive, miniaturized, assay format using an 864-well plate and show that as few as 560 cells per assay well was sufficient to measure a dose response to ligand.

Crystal structure of acidic seminal fluid protein (aSFP) at 1.9 A resolution: a bovine polypeptide of the spermadhesin family

We report the three-dimensional crystal structure of acidic seminal fluid protein (aSFP), a 12.9 kDa polypeptide of the spermadhesin family isolated from bovine seminal plasma, solved by the multiple isomorphous replacement method and refined with data to 1.9 A resolution with a final R-factor of 17.3%. aSFP is built by a single CUB domain architecture, a 100 to 110 amino-acid-residue extracellular module found in 16 functionally diverse proteins. The structure of aSFP reveals that the CUB domain displays a beta-sandwich topology organised into two 5-stranded beta-sheets, each of which contain two parallel and four antiparallel strands. The structure of aSFP is almost identical to that of porcine spermadhesins PSP-I and PSP-II, which in turn show limited structural similarity with jellyroll topologies of certain virus capsid proteins. Essentially, topologically conserved residues in these proteins are those internal amino acids forming the hydrophobic core of the CUB and the jellyroll domains, suggesting their importance in maintaining the integrity of these protein folds. On the other hand, the structure of aSFP shows structural features that are unique to this protein and which may provide a structural ground for understanding the distinct biological properties of different members of the spermadhesin protein family.

The crystal structures of two spermadhesins reveal the CUB domain fold

Spermadhesins, 12,000-14,000 M(r) mammalian proteins, include lectins involved in sperm-egg binding and display a single CUB domain architecture. We report the crystal structures of porcine seminal plasma PSP-I/PSP-II, a heterodimer of two glycosylated spermadhesins, and bovine aSFP at 2.4 A and 1.9 A resolution respectively.

Crystallization and preliminary X-ray diffraction studies of aSFP, a bovine seminal plasma protein with a single CUB domain architecture

Bovine acidic seminal fluid protein (aSFP) is a 1.29 kDa polypeptide of the spermadhesin family built by a single CUB domain architecture. The CUB domain is an extracellular module present in 16 functionally diverse proteins. To determine the three-dimensional structure of aSFP, the protein was crystallized at 21 degrees C by vapor diffusion in hanging drops, using ammonium sulfate, pH 4.7, and polyethyleneglycol 4,000 as precipitants, containing 10% dioxane to avoid the formation of clustered crystals. Elongated prismatic crystals with maximal size of 0.6 x 0.3 x 0.2 mm3 diffract to beyond 1.9 A resolution and belong to space group P2(1)2(1)2(1), with cell parameters a = 52.4 A, b = 41.5 A, c = 48.2 A. There is one aSFP molecule per asymmetric unit, which corresponds to a crystal volume per unit molecular mass of 2.04 A3/Da, and analytical ultracentrifugation analysis show that aSFP is a monomeric protein.