Microbial ecology of biotechnological processes

The investigation of phylogenetic diversity and functionality of complex microbial communities in relation to changes in the environmental conditions represents a major challenge of microbial ecology research. Nowadays, particular attention is paid to microbial communities occurring at environmental sites contaminated by recalcitrant and toxic organic compounds. Extended research has evidenced that such communities evolve some metabolic abilities leading to the partial degradation or complete mineralization of the contaminants. Determination of such biodegradation potential can be the starting point for the development of cost effective biotechnological processes for the bioremediation of contaminated matrices. This work showed how metagenomics-based microbial ecology investigations supported the choice or the development of three different bioremediation strategies. First, PCR-DGGE and PCR-cloning approaches served the molecular characterization of microbial communities enriched through sequential development stages of an aerobic cometabolic process for the treatment of groundwater contaminated by chlorinated aliphatic hydrocarbons inside an immobilized-biomass packed bed bioreactor (PBR). In this case the analyses revealed homogeneous growth and structure of immobilized communities throughout the PBR and the occurrence of dominant microbial phylotypes of the genera Rhodococcus, Comamonas and Acidovorax, which probably drive the biodegradation process. The same molecular approaches were employed to characterize sludge microbial communities selected and enriched during the treatment of municipal wastewater coupled with the production of polyhydroxyalkanoates (PHA). Known PHA-accumulating microorganisms identified were affiliated with the genera Zooglea, Acidovorax and Hydrogenophaga. Finally, the molecular investigation concerned communities of polycyclic aromatic hydrocarbon (PAH) contaminated soil subjected to rhizoremediation with willow roots or fertilization-based treatments. The metabolic ability to biodegrade naphthalene, as a representative model for PAH, was assessed by means of stable isotope probing in combination with high-throughput sequencing analysis. The phylogenetic diversity of microbial populations able to derive carbon from naphthalene was evaluated as a function of the type of treatment.

Polychaete fauna of the Northwest Portuguese Coastal Shelf: ecology, diversity and distribution

Polychaetes are one of the larger groups of macroinvertebrates with more than 9000 species recognised, distributed worldwide. Thanks to the broad ecological adaptability and high abundaces, this taxon plays a leading role and is considered an important component of all benthic assemblages. Our knowledge about the West Iberian Coast polychaete fauna are scarce, and the only studies are recent. In this sense, the aim of this work was to investigate the composition and the spatial distribution of the polychaete fauna along the NW Portuguese Coastal Shelf, focusing on their relationship to environmental factors (depth, grain size, longitude and latitude) and to add new data to the existing biological dataset. A total of 39 sites were analysed, collected in an area of about 5665 km², between 20 and 150 m depth, distributed in a way to cover the overall grain size gradient. A total of 9352 specimens belonging to 41 families were found, and the analysis based on the abundance of polychaete species revealed five affinity groups: (a) nearshore medium sand characterised by Pisione parapari and Hesionura elongata; (b) very coarse sand that showed the highest abundance of Syllidae and was characterised by Protodorvillea kefersteini and Syllis garciai; (c) fine sand dominated by Spiophanes bombyx and Glycera tridactyla; (d) very fine sand with Nepthys assimilis and Amage sp. and the highest abundance of Paraonidae; (d) mud characterised by Labioleanira yhleni and Ampharete finmarchica. The combination of the environmental variables and the biological data, done with BIOENV routine, demonstrated that depth, grain size and fine contents were the best related with the biological data (rho=0.598). In general, the results agree with the composition and the spatial distribution of the polychaete fauna in other parts of the world; further polychaete assemblages related to mud sediments were firstly recorded in the Northwestern Portuguese Coastal Shelf.

Surface-acoustic-wave counterflow micropumps for on-chip liquid motion control in two-dimensional microchannel arrays

Fully controlled liquid injection and flow in hydrophobic polydimethylsiloxane (PDMS) two-dimensional microchannel arrays based on on-chip integrated, low-voltage-driven micropumps are demonstrated. Our architecture exploits the surface-acoustic-wave (SAW) induced counterflow mechanism and the effect of nebulization anisotropies at crossing areas owing to lateral propagating SAWs. We show that by selectively exciting single or multiple SAWs, fluids can be drawn from their reservoirs and moved towards selected positions of a microchannel grid. Splitting of the main liquid flow is also demonstrated by exploiting multiple SAW beams. As a demonstrator, we show simultaneous filling of two orthogonal microchannels. The present results show that SAW micropumps are good candidates for truly integrated on-chip fluidic networks allowing liquid control in arbitrarily shaped two-dimensional microchannel arrays.

Design of a semi-implantable hearing device for direct acoustic cochlear stimulation

A new hearing therapy based on direct acoustic cochlear stimulation was developed for the treatment of severe to profound mixed hearing loss. The device efficacy was validated in an initial clinical trial with four patients. This semi-implantable investigational device consists of an externally worn audio processor, a percutaneous connector, and an implantable microactuator. The actuator is placed in the mastoid bone, right behind the external auditory canal. It generates vibrations that are directly coupled to the inner ear fluids and that, therefore, bypass the external and the middle ear. The system is able to provide an equivalent sound pressure level of 125 dB over the frequency range between 125 and 8000 Hz. The hermetically sealed actuator is designed to provide maximal output power by keeping its dimensions small enough to enable implantation. A network model is used to simulate the dynamic characteristics of the actuator to adjust its transfer function to the characteristics of the middle ear. The geometry of the different actuator components is optimized using finite-element modeling.

Life history, ecology and the biogeography of strong genetic breaks among 15 species of PaciWc rockWsh, Sebastes

Strong genetic change over short spatial scales is surprising among marine species with high dispersal potential. Concordant breaks among several species signals a role for geographic barriers to dispersal. Along the coast of California, such breaks have not been seen across the biogeographic barrier of Point Conception, but other potential geographic boundaries have been surveyed less often.;We tested for strong-population structure in 11 species of Sebastes sampled across two regions containing potential dispersal barriers, and conducted a meta-analysis including four additional species. We show two strong breaks north of Monterey Bay, spanning an oceanographic gradient and an upwelling jet. Moderate genetic structure is just as common in the north as it is in the south, across the biogeographic break at Point Conception. Gene Xow is generally higher among deep-water species, but these conclusions are confounded by phylogeny. Species in the subgenus Sebastosomus have higher structure than those in the subgenus;Pteropodus, despite having larvae with longer pelagic phases. DiVerences in settlement behavior in the face of ocean currents might help explain these diVerences. Across similar species across the same coastal environment, we document a wide variety of patterns in gene Xow, suggesting that interaction of individual species traits such as settlement behavior with environmental factors such as;oceanography can strongly impact population structure

Telomeres: Linking stress and survival, ecology and evolution.

Telomeres are protective structures at the ends of eukaryotic chromosomes. The loss of telomeres through cell division and oxidative stress is related to cellular aging, organismal growth and disease. In this way, telomeres link molecular and cellular mechanisms with organismal processes, and may explain variation in a number of important life-history traits. Here, we discuss how telomere biology relates to the study of physiological ecology and life history evolution. We emphasize current knowledge on how telomeres may relate to growth, survival and lifespan in natural populations. We finish by examining interesting new connections between telomeres and the glucocorticoid stress response. Glucocorticoids are often employed as indices of physiological condition, and there is evidence that the glucocorticoid stress response is adaptive. We suggest that one way that glucocorticoids impact organismal survival is through elevated oxidative stress and telomere loss. Future work needs to establish and explore the link between the glucocorticoid stress response and telomere shortening in natural populations. If a link is found, it provides an explanatory mechanism by which environmental perturbation impacts life history trajectories.

Thin-Film Sparse Boundary Array Design for Passive Acoustic Mapping During Ultrasound Therapy

A new 2-D hydrophone array for ultrasound therapy monitoring is presented, along with a novel algorithm for passive acoustic mapping using a sparse weighted aperture. The array is constructed using existing polyvinylidene fluoride (PVDF) ultrasound sensor technology, and is utilized for its broadband characteristics and its high receive sensitivity. For most 2-D arrays, high-resolution imagery is desired, which requires a large aperture at the cost of a large number of elements. The proposed array's geometry is sparse, with elements only on the boundary of the rectangular aperture. The missing information from the interior is filled in using linear imaging techniques. After receiving acoustic emissions during ultrasound therapy, this algorithm applies an apodization to the sparse aperture to limit side lobes and then reconstructs acoustic activity with high spatiotemporal resolution. Experiments show verification of the theoretical point spread function, and cavitation maps in agar phantoms correspond closely to predicted areas, showing the validity of the array and methodology.

Ecology, sexual selection and speciation

The spectacular diversity in sexually selected traits among animal taxa has inspired the hypothesis that divergent sexual selection can drive speciation. Unfortunately, speciation biologists often consider sexual selection in isolation from natural selection, even though sexually selected traits evolve in an ecological context: both preferences and traits are often subject to natural selection. Conversely, while behavioural ecologists may address ecological effects on sexual communication, they rarely measure the consequences for population divergence. Herein, we review the empirical literature addressing the mechanisms by which natural selection and sexual selection can interact during speciation. We find that convincing evidence for any of these scenarios is thin. However, the available data strongly support various diversifying effects that emerge from interactions between sexual selection and environmental heterogeneity. We suggest that evaluating the evolutionary consequences of these effects requires a better integration of behavioural, ecological and evolutionary research.