Nematode selenoproteome: the use of the selenocysteine insertion system to decode one codon in an animal genome?

Selenocysteine (Sec) is co-translationally inserted into selenoproteins in response to codon UGA with the help of the selenocysteine insertion sequence (SECIS) element. The number of selenoproteins in animals varies, with humans having 25 and mice having 24 selenoproteins. To date, however, only one selenoprotein, thioredoxin reductase, has been detected in Caenorhabditis elegans, and this enzyme contains only one Sec. Here, we characterize the selenoproteomes of C.elegans and Caenorhabditis briggsae with three independent algorithms, one searching for pairs of homologous nematode SECIS elements, another searching for Cys- or Sec-containing homologs of potential nematode selenoprotein genes and the third identifying Sec-containing homologs of annotated nematode proteins. These methods suggest that thioredoxin reductase is the only Sec-containing protein in the C.elegans and C.briggsae genomes. In contrast, we identified additional selenoproteins in other nematodes. Assuming that Sec insertion mechanisms are conserved between nematodes and other eukaryotes, the data suggest that nematode selenoproteomes were reduced during evolution, and that in an extreme reduction case Sec insertion systems probably decode only a single UGA codon in C.elegans and C.briggsae genomes. In addition, all detected genes had a rare form of SECIS element containing a guanosine in place of a conserved adenosine present in most other SECIS structures, suggesting that in organisms with small selenoproteomes SECIS elements may change rapidly.

Small scale underwater change detection

In this paper, we present a method to deal with the constraints of the underwater medium for finding changes between sequences of underwater images. One of the main problems of underwater medium for automatically detecting changes is the low altitude of the camera when taking pictures. This emphasise the parallax effect between the images as they are not taken exactly at the same position. In order to solve this problem, we are geometrically registering the images together taking into account the relief of the scene

Overfishing of small pelagic fishes increases trophic overlap between immature and mature striped dolphins in the Mediterranean Sea

The interactions among diet, ecology, physiology, and biochemistry affect N and C stable isotope signatures in animal tissues. Here, we examined if ecological segregation among animals in relation to sex and age existed by analyzing the signatures of delta15N and delta13C in the muscle of Western Mediterranean striped dolphins. Moreover, we used a Bayesian mixing model to study diet composition and investigated potential dietary changes over the last two decades in this population. For this, we compared isotope signatures in samples of stranded dolphins obtained during two epizootic events occurring in 1990 and 2007-2008. Mean delta13C values for females and males were not significantly different, but age-related variation indicated delta13C enrichment in both sexes, suggesting that females and males most likely fed in the same general areas, increasing their consumption of benthic prey with age. Enrichment of delta15N was only observed in females, suggesting a preference for larger or higher trophic level prey than males, which could reflect different nutritional requirements. delta13C values showed no temporal variation, although the mean delta15N signature decreased from 1990 to 2007-2008, which could indicate a dietary shift in the striped dolphin over the last two decades. The results of SIAR indicated that in 1990, hake and sardine together contributed to 60% on the diet of immature striped dolphins, and close to 90% for mature striped dolphins. Conversely, the diet of both groups in 2007-2008 was more diverse, as hake and sardine contributed to less than 40% of the entire diet. These results suggest a dietary change that was possibly related to changes in food availability, which is consistent with the depletion of sardine stocks by fishing.

Transfer entropy reconstruction and labeling of neuronal connections from simulated calcium imaging

Neuronal dynamics are fundamentally constrained by the underlying structural network architecture, yet much of the details of this synaptic connectivity are still unknown even in neuronal cultures in vitro. Here we extend a previous approach based on information theory, the Generalized Transfer Entropy, to the reconstruction of connectivity of simulated neuronal networks of both excitatory and inhibitory neurons. We show that, due to the model-free nature of the developed measure, both kinds of connections can be reliably inferred if the average firing rate between synchronous burst events exceeds a small minimum frequency. Furthermore, we suggest, based on systematic simulations, that even lower spontaneous inter-burst rates could be raised to meet the requirements of our reconstruction algorithm by applying a weak spatially homogeneous stimulation to the entire network. By combining multiple recordings of the same in silico network before and after pharmacologically blocking inhibitory synaptic transmission, we show then how it becomes possible to infer with high confidence the excitatory or inhibitory nature of each individual neuron.

Imaging polarimetry of the fogbow: polarization characteristics of white rainbows measured in the high Arctic

The knowledge on the optics of fogbows is scarce, and their polarization characteristics have never been measured to our knowledge. To fill this gap we measured the polarization features of 16 fogbows during the Beringia 2005 Arctic polar research expedition by imaging polarimetry in the red, green and blue spectral ranges. We present here the first polarization patterns of the fogbow. In the patterns of the degree of linear polarization p, fogbows and their supernumerary bows are best visible in the red spectral range due to the least dilution of fogbow light by light scattered in air. In the patterns of the angle of polarization α fogbows are practically not discernible because their α-pattern is the same as that of the sky: the direction of polarization is perpendicular to the plane of scattering and is parallel to the arc of the bow, independently of the wavelength. Fogbows and their supernumeraries were best seen in the patterns of the polarized radiance. In these patterns the angular distance δ between the peaks of the primary and the first supernumerary and the angular width σ of the primary bow were determined along different radii from the center of the bow. δ ranged between 6.08° and 13.41° , while σ changed from 5.25° to 19.47° . Certain fogbows were relatively homogeneous, meaning small variations of δ and σ along their bows. Other fogbows were heterogeneous, possessing quite variable δ- and σ-values along their bows. This variability could be a consequence of the characteristics of the high Arctic with open waters within the ice shield resulting in the spatiotemporal change of the droplet size within the fog

Animal sound : què se sent quan s’és una cabra?

Aquest projecte treballa sobre la possibilitat d'aplicar tècniques d'enregistrament binaural en animals, en concret, en una cabra domèstica. Mitjançant uns micròfons col·locats dins les seves orelles i una petita càmera de vídeo muntada sobre el seu cap, s'obté un material audiovisual que permet fer-se una idea aproximada de com és la seva percepció del món. En base a un estudi de cognició comparada, es pretén trobar maneres de transformar els enregistraments obtinguts per tal d'adaptar el marc psicoacústic humà al de l'animal. L'objectiu és que una persona pugui sentir com ho fa un animal, encara que sigui d'una manera aproximada. Els materials obtinguts al llarg dels enregistraments són el punt de partida per a la construcció de paisatges sonors i peces audiovisuals diverses. Així doncs, el treball s'inicia amb el disseny i construcció d'un micròfon binaural, continua amb enregistraments de camp en animals i acaba amb l'edició, el processat i la composició dels paisatges sonors finals.