Distribution of CK2, its substrate MAP1B and phosphatases in neuronal cells

Neuronal morphogenesis depends on the organization of cytoskeletal elements among which microtubules play a very important role. The organization of microtubules is controlled by the presence of microtubule-associated proteins (MAPs), the activity of which is modulated by phosphorylation and dephosphorylation. One of these MAPs is MAP1B, which is very abundant within growing axons of developing neurons where it is found phosphorylated by several protein kinases including CK2. The expression of MAP1B is notably decreased after neuronal maturation in parallel with a change in the localization of the protein, which becomes largely concentrated in neuronal cell bodies and dendrites. Interestingly, MAP1B remains highly phosphorylated at sites targeted by protein kinase CK2 in mature neurons.We have analyzed the expression and localization of CK2 catalytic subunits along neuronal development. CK2 subunit appears early during development whereas CK2 subunit appears within mature neurons at the time of dendrite maturation and synaptogenesis, in parallel with the change in the localization of MAP1B. CK2 subunit is found associated with microtubule preparations obtained from either grey matter or white matter from adult bovine brain, whereas CK2 subunit is highly enriched in microtubules obtained from grey matter. These results lend support to the hypothesis that CK2 subunit is concentrated in neuronal cell bodies and dendrites, where it associates with microtubules, thus contributing to the increased phosphorylation of MAP1B in this localization in mature neurons.     

Protein translocation through a tunnel induces changes in folding kinetics: a lattice model study

Compaction of a nascent polypeptide chain inside the ribosomal exit tunnel, before it leaves the ribosome, has been proposed to accelerate the folding of newly synthesized proteins following their release from the ribosome. Thus, we used Kinetic Monte Carlo simulations of a minimalist on-lattice model to explore the effect that polypeptide translocation through a variety of channels has on protein folding kinetics. Our results demonstrate that tunnel confinement promotes faster folding of a well-designed protein relative to its folding in free space by displacing the unfolded state towards more compact structures that are closer to the transition state. Since the tunnel only forbids rarely visited, extended configurations, it has little effect on a "poorly designed" protein whose unfolded state is largely composed of low-energy, compact, misfolded configurations. The beneficial effect of the tunnel depends on its width; for example, a too-narrow tunnel enforces unfolded states with limited or no access to the transition state, while a too-wide tunnel has no effect on the unfolded state entropy. We speculate that such effects are likely to play an important role in the folding of some proteins or protein domains in the cellular environment and might dictate whether a protein folds co-translationally or post-translationally.     

Geographic variation in beak colouration in gentoo penguins <Emphasis Type="Italic">Pygoscelis papua</Emphasis>

Ornamental colouration is often due to carotenoid pigments and varies inter- and intra-specifically. This paper reports on variation in beak colour of the gentoo penguin, Pygoscelis papua, corresponding to different geographical locations along a latitudinal gradient in the Antarctic Peninsula (from King George Island (62o15′S–58o37′W) to Rongé Island (64o40′S–62o40′W). The gentoo penguin has a conspicuous red spot on both sides of the beak that indicates the presence of the carotenoid pigment, astaxanthin. Beak colouration was measured with a portable spectrophotometer for 20 individuals in three locations, along the Western coast of the Antarctic Peninsula. In the study area, marked variation can be found in terms of factors such us parasite load, human impact, variations in UV radiation and the abundance of krill; all possibly affecting carotenoid availability for signalling purposes. Colour traits were expected to be more intense, that is more vivid, saturated and pure, in places where there is diminished pressure from factors such as contamination, parasites or diseases, all of which may reduce the availability of carotenoids for other functions, such as antioxidant or immune stimulation involving physiological trade-offs. Likewise, colour traits might be predicted to be more intense where carotenoid sources, krill in the case of gentoo penguins, are more available. However, contrary to this initial expectation, our results indicate that northerly penguins’ populations, which are in the most polluted and parasitized areas, have more saturated beaks. An alternative hypothesis suggests that environmental constraints relating to the variation in abundance of krill may explain the geographical variation in colour expression found among gentoo penguins.     

Significant ecosystem-wide effects of the swiftly spreading invasive freshwater bivalve <Emphasis Type="Italic">Limnoperna</Emphasis> <Emphasis Type="Italic">fortunei</Emphasis>

Since its introduction in South America around 1990, the freshwater Asian mussel Limnoperna fortunei has been shown to strongly interact with several components of the local biota. However, investigation of its ecosystem-wide effects was hindered by (1) difficulties associated with evaluation of its densities over large spatial scales and (2) scarcity of pre-invasion environmental data. The present survey overcomes these shortcomings and addresses the question whether Limnoperna’s impact on the ecosystem-wide scale is measurable and significant. On the basis of diver-collected bottom samples, we estimated the overall density of this mussel in a reservoir (Embalse de Río Tercero, Argentina), where Limnoperna is present since 1998 and analyzed changes in several water-column properties before and after the invasion. The 47 km² reservoir hosts around 45 billion mussels; at these densities, a volume equivalent to that of this water body can potentially be filtered by the bivalves every 2–3 days. Data collected regularly since 1996 indicate that after the invasion water transparency increased, and suspended matter, chlorophyll a, and primary production decreased significantly, with strong changes occurring in the area with highest mussel densities. Our results indicate that the ecosystem-wide impacts of Limnoperna are generally comparable to those described in Europe and North America for another invasive mussel—Dreissena polymorpha. However, given Limnoperna’s wider tolerance limits, its influence on newly invaded water bodies, potentially including Europe and North America, will probably be stronger.     

Testing the threat-sensitive predator avoidance hypothesis: physiological responses and predator pressure in wild rabbits

Predation is a strong selective force with both direct and indirect effects on an animal’s fitness. In order to increase the chances of survival, animals have developed different antipredator strategies. However, these strategies have associated costs, so animals should assess their actual risk of predation and shape their antipredator effort accordingly. Under a stressful situation, such as the presence of predators, animals display a physiological stress response that might be proportional to the risk perceived. We tested this hypothesis in wild European rabbits (Oryctolagus cuniculus), subjected to different predator pressures, in Doñana National Park (Spain). We measured the concentrations of fecal corticosterone metabolites (FCM) in 20 rabbit populations. By means of track censuses we obtained indexes of mammalian predator presence for each rabbit population. Other factors that could modify the physiological stress response, such as breeding status, food availability and rabbit density, were also considered. Model selection based on information theory showed that predator pressure was the main factor triggering the glucocorticoid release and that the physiological stress response was positively correlated with the indexes of the presence of mammalian carnivore predators. Other factors, such as food availability and density of rabbits, were considerably less important. We conclude that rabbits are able to assess their actual risk of predation and show a threat-sensitive physiological response.     

Exogenous strigolactones impact metabolic profiles and phosphate starvation signalling in roots

Strigolactones (SLs) are important ex-planta signalling molecules in the rhizosphere, promoting the association with beneficial microorganisms, but also affecting plant interactions with harmful organisms. They are also plant hormones in-planta, acting as modulators of plant responses under nutrient-deficient conditions, mainly phosphate (Pi) starvation. In the present work, we investigate the potential role of SLs as regulators of early Pi starvation signalling in plants. A short-term pulse of the synthetic SL analogue 2′-epi-GR24 promoted SL accumulation and the expression of Pi starvation markers in tomato and wheat under Pi deprivation. 2′-epi-GR24 application also increased SL production and the expression of Pi starvation markers under normal Pi conditions, being its effect dependent on the endogenous SL levels. Remarkably, 2′-epi-GR24 also impacted the root metabolic profile under these conditions, promoting the levels of metabolites associated to plant responses to Pi limitation, thus partially mimicking the pattern observed under Pi deprivation. The results suggest an endogenous role for SLs as Pi starvation signals. In agreement with this idea, SL-deficient plants were less sensitive to this stress. Based on the results, we propose that SLs may act as early modulators of plant responses to P starvation.     

Gene set analysis in the cloud

Cloud computing offers low cost and highly flexible opportunities in bioinformatics. Its potential has already been demonstrated in high-throughput sequence data analysis. Pathway-based or gene set analysis of expression data has received relatively less attention. We developed a gene set analysis algorithm for biomarker identification in the cloud. The resulting tool, YunBe, is ready to use on Amazon Web Services. Moreover, here we compare its performance to those obtained with desktop and computing cluster solutions. AVAILABILITY AND IMPLEMENTATION: YunBe is open-source and freely accessible within the Amazon Elastic MapReduce service at s3n://lrcv-crp-sante/app/yunbe.jar. Source code and user's guidelines can be downloaded from http://tinyurl.com/yunbedownload.     

Testing the Performance of Fourteen Native Tropical Tree Species in Two Abandoned Pastures of the Lacandon Rainforest Region of Chiapas,Mexico

The rainforest of Mexico has been degraded and severely fragmented, and urgently require restoration. However, the practice of restoration has been limited by the lack of species‐specific data on survival and growth responses to local environmental variation. This study explores the differential performance of 14 wet tropical early‐, mid‐ or late‐successional tree species that were grown in two abandoned pastures with contrasting land‐use histories. After 18 months, seedling survival and growth of at least 7 of the 14 tree species studied were significantly higher in the site with a much longer history of land use (site 2). Saplings of the three early‐successional species showed exceptional growth rates. However, differences in performance were noted in relation to the differential soil properties between the experimental sites. Mid‐successional species generally showed slow growth rates but high seedling survival, whereas late‐successional species exhibited poor seedling survival at both the study sites. Stepwise linear regressions revealed that the species integrated response index combining survivorship and growth measurements, was influenced mostly by differences in soil pH between the two abandoned pastures. Our results suggest that local environmental variation among abandoned pastures of contrasting land‐use histories influences sapling survival and growth. Furthermore, the similarity of responses among species with the same successional status allowed us to make some preliminary site and species‐specific silvicultural recommendations. Future field experiments should extend the number of species and the range of environmental conditions to identify site “generalists” or more narrowly adapted species, that we would call “sensitive.”     

Impact of Daily Thermocycles on Hatching Rhythms,Larval Performance and Sex Differentiation of Zebrafish

In the wild, water temperature cycles daily: it warms up after sunrise, and cools rapidly after sunset. Surprisingly, the impact of such daily thermocycles during the early development of fish remains neglected. We investigated the influence of constant vs daily thermocycles in zebrafish, from embryo development to sexual differentiation, by applying four temperature regimens: two constant (24°C and 28°C) and two daily thermocycles: 28:24°C, TC (thermophase coinciding with daytime, and cryophase coinciding with night-time) and 24:28°C, CT (opposite to TC) in a 12:12 h light:dark cycle (LD). Embryo development was temperature-dependent but enhanced at 28°C and TC. Hatching rhythms were diurnal (around 4 h after lights on), but temperature- and cycle-sensitive, since hatching occurred sooner at 28°C (48 hours post fertilization; hpf) while it was delayed at 24°C (96 hpf). Under TC, hatching occurred at 72 hpf, while under CT hatching displayed two peaks (at 70 hpf and 94 hpf). In constant light (LL) or darkness (DD), hatching rhythms persisted with tau close to 24 h, suggesting a clock-controlled “gating” mechanism. Under 28°C or TC, larvae showed the best performance (high growth and survival, and low malformations). The sex ratio was strongly influenced by temperature, as the proportion of females was higher in CT and TC (79 and 83% respectively), contrasting with 28°C and 24°C, which led to more males (83 and 76%). Ovarian aromatase (cyp19a) expression in females was highest in TC and CT (6.5 and 4.6 fold higher than at 28°C, respectively); while anti-müllerian hormone (amh) expression in males increased in testis at 24°C (3.6 fold higher compared to TC) and particularly at 28°C (14.3 fold increase). Taken together, these findings highlight the key role of environmental cycles during early development, which shaped the daily rhythms in fish embryo and larvae, and ultimately influenced sex differentiation.