Migrating swans profit from favourable changes in wind conditions at low altitude

Because energy reserves limit flight range, wind assistance may be of crucial importance for migratory birds. We tracked eight Bewicks swans Cygnus columbianus bewickii, using 95-g satellite transmitters with altimeters and activity sensors, during their spring migration from Denmark to northern Russia in 1996. During the 82 occasions where a swans location was recorded in flight, average flight altitude was 165 m a.s.l. with a maximum of 759 m a.s.l., despite winds often being more favourable at higher altitudes. We also counted Bewicks swans departing from the Gulf of Finland and subsequently passing an observatory in the next major stop-over area 800 km further north in the White Sea, northern Russia, during the springs of 1994, 1995 and 1996. A comparison of these counts with wind data provided evidence for Bewicks swans using favourable changes in wind conditions to embark on migration. Changes in the numbers of birds arriving in the White Sea correlated best with favourable changes in winds in the Gulf of Finland 1 day earlier. Again, migratory volume showed a correlation with winds at low altitudes only, despite wind conditions for the swans being more favourable at high altitudes. We conclude that the relatively large Bewicks swan tends to gear its migration to wind conditions at low altitude only. We argue that Bewicks swans do not climb to high altitudes because of mechanical and physiological limitations with respect to the generation of power for flight and to avoid rapid dehydration.Communicated by F. Bairlein     

Substrate binding analysis of the 23S rRNA methyltransferase RrmJ

The 23S rRNA methyltransferase RrmJ (FtsJ) is responsible for the 2'-O methylation of the universally conserved U2552 in the A loop of 23S rRNA. This 23S rRNA modification appears to be critical for ribosome stability, because the absence of functional RrmJ causes the cellular accumulation of the individual ribosomal subunits at the expense of the functional 70S ribosomes. To gain insight into the mechanism of substrate recognition for RrmJ, we performed extensive site-directed mutagenesis of the residues conserved in RrmJ and characterized the mutant proteins both in vivo and in vitro. We identified a positively charged, highly conserved ridge in RrmJ that appears to play a significant role in 23S rRNA binding and methylation. We provide a structural model of how the A loop of the 23S rRNA binds to RrmJ. Based on these modeling studies and the structure of the 50S ribosome, we propose a two-step model where the A loop undocks from the tightly packed 50S ribosomal subunit, allowing RrmJ to gain access to the substrate nucleotide U2552, and where U2552 undergoes base flipping, allowing the enzyme to methylate the 2'-O position of the ribose.     

Richness and abundance of stream fish communities in a fragmented neotropical landscape

Environmental Biology of Fishes - Environmental conditions influence ecological processes that shape stream community diversity and abundance. Deforestation has the potential to limit available...     

Impact of land‐use change to Jatropha bioenergy plantations on biomass and soil carbon stocks: a field study in Mali

Small‐scale Jatropha cultivation and biodiesel production have the potential of contributing to local development, energy security, and greenhouse gas (GHG) mitigation. In recent years however, the GHG mitigation potential of biofuel crops is heavily disputed due to the occurrence of a carbon debt, caused by CO₂ emissions from biomass and soil after land‐use change (LUC). Most published carbon footprint studies of Jatropha report modeled results based on a very limited database. In particular, little empirical data exist on the effects of Jatropha on biomass and soil C stocks. In this study, we used field data to quantify these C pools in three land uses in Mali, that is, Jatropha plantations, annual cropland, and fallow land, to estimate both the Jatropha C debt and its C sequestration potential. Four‐year‐old Jatropha plantations hold on average 2.3 Mg C ha^?1 in their above‐ and belowground woody biomass, which is considerably lower compared to results from other regions. This can be explained by the adverse growing conditions and poor local management. No significant soil organic carbon (SOC) sequestration could be demonstrated after 4 years of cultivation. While the conversion of cropland to Jatropha does not entail significant C losses, the replacement of fallow land results in an average C debt of 34.7 Mg C ha^?1, mainly caused by biomass removal (73%). Retaining native savannah woodland trees on the field during LUC and improved crop management focusing on SOC conservation can play an important role in reducing Jatropha's C debt. Although planting Jatropha on degraded, carbon‐poor cropland results in a limited C debt, the low biomass production, and seed yield attained on these lands reduce Jatropha's potential to sequester C and replace fossil fuels. Therefore, future research should mainly focus on increasing Jatropha's crop productivity in these degraded lands.     

Reconciling ecogeographical rules: rainfall and temperature predict global colour variation in the largest bird radiation

Ecogeographical rules that associate climate with organismal form and function can reveal patterns of climatic adaptation. Two rules link animal coloration with climate: Gloger's rule (darker coloration where wet and warm), and Bogert's rule (darker coloration where cold). Whereas Gloger's rule was proposed for endotherms, and Bogert's rule for ectotherms, both rules may apply more broadly, despite their seemingly opposing effects. Here, we test this contradiction on a global scale across passerine birds. Consistent with Gloger's rule, birds were darker in wetter areas and, following Bogert's rule, lighter where warm, although birds became lighter again at very low temperatures. Rainfall and temperature had antagonistic or additive effects depending on their pattern of covariation, and this predicted whether birds followed the rules. We integrate both rules into a general framework to explain heterogeneity in climatic effects on coloration, which has implications to understand patterns of diversification, climatic adaptation and climate change impacts.     

Extra-pair paternity and sexual dimorphism in birds

Differences in the strength of sexual selection between males and females can lead to sexual dimorphism. Extra-pair paternity (EPP) can increase the variance in male reproductive success and hence the opportunity for sexual selection. Previous research on birds suggests that EPP drives the evolution of dimorphism in plumage colour and in body size. Because EPP increases the intensity of sexual selection in males, it should lead to increased dimorphism in species with larger or more colourful males, but decreased dimorphism in species with larger or more colourful females. We explored the covariation between EPP and sexual dimorphism in wing length and plumage colouration in 401 bird species, while controlling for other, potentially confounding variables. Wing length dimorphism was associated positively with the frequency of EPP, but also with social polygamy, sex bias in parental behaviour and body size and negatively with migration distance. The frequency of EPP was the only predictor of plumage colour dimorphism. In support of our prediction, high EPP levels were associated with sexual dichromatism, positively in species in which males are more colourful and negatively in those in which females are more colourful. Contrary to our prediction, high EPP rates were associated with increased wing length dimorphism in species with both male- and female-biased dimorphism. The results support a role for EPP in the evolution of both size and plumage colour dimorphism. The two forms of dimorphism were weakly correlated and predicted by different reproductive, social and life-history traits, suggesting an independent evolution.     

Spike-interval triggered averaging reveals a quasi-periodic spiking alternative for stochastic resonance in catfish electroreceptors

Catfish detect and identify invisible prey by sensing their ultra-weak electric fields with electroreceptors. Any neuron that deals with small-amplitude input has to overcome sensitivity limitations arising from inherent threshold non-linearities in spike-generation mechanisms. Many sensory cells solve this issue with stochastic resonance, in which a moderate amount of intrinsic noise causes irregular spontaneous spiking activity with a probability that is modulated by the input signal. Here we show that catfish electroreceptors have adopted a fundamentally different strategy. Using a reverse correlation technique in which we take spike interval durations into account, we show that the electroreceptors generate a supra-threshold bias current that results in quasi-periodically produced spikes. In this regime stimuli modulate the interval between successive spikes rather than the instantaneous probability for a spike. This alternative for stochastic resonance combines threshold-free sensitivity for weak stimuli with similar sensitivity for excitations and inhibitions based on single interspike intervals.     

Change in sugar, sterol and fatty acid composition in banana meristems caused by sucrose-induced acclimation and its effects on cryopreservation

To understand the mechanisms of sucrose‐induced acclimation in relation to plant cryopreservation, sugars, sterols, fatty acids of different lipid fractions (neutral lipids, glycolipids and sphingolipids and phospholipids), as well as free fatty acids were analyzed in proliferating meristem cultures of different banana varieties. The four banana varieties that were selected show different post‐thaw shoot regeneration rates (0–53.4%). All mentioned parameters were analyzed using (1) control meristems that were cultured on a normal sucrose concentration (0.09 M), which resulted in low survival after cryopreservation; and (2) 2‐week sucrose precultured meristems (0.4 M). This sucrose preculture, essential for regeneration after cryopreservation, resulted in a significant increase of each of seven sugars detected. The ratio of stigmasterol/sitosterol (St/Si) in sucrose‐pretreated meristems significantly increased. The sucrose pretreatment also resulted in a significant increase of total fatty acid content of the neutral lipid fraction and of the glycolipid and sphingolipid fraction, as well as the total free fatty acid content. The individual fatty acid content of the phospholipids was differently changed by the sucrose pretreatment for the given varieties studied. In most cases, sucrose pretreatment resulted in an increase of the double bond index (DBI) in the neutral lipids and a decrease of DBI in the glycolipids and sphingolipids, in phospholipids as well as in free fatty acids. Principal component analysis of all collected data revealed that (1) for the control material, sucrose and total sugar contents were closely linked to the post‐thaw shoot regeneration, suggesting that sucrose and total sugar may be main limiting factors to survive cryopreservation; (2) accumulation of large quantities of sugars (glucose, fructose, sucrose and total sugar) in sucrose‐pretreated material cannot explain the differences in survival after cryopreservation of the four banana varieties. We assume that a minimal amount of sugars is needed in meristem cultures to survive cryopreservation. Still, other limiting factors do influence the survival following the sucrose pretreatment. We observed that the parameters which are closely linked to the post‐thaw shoot regeneration are a minimal change in the ratios of St/Si, the minimal change of the DBI of phospholipids and free fatty acids, as well as linoleic acid content (C18:2); and (3) inositol, raffinose, myristic acid (C14:0) and oleic acid (C18:1) were present in small quantities; however, they could be correlated to survival after cryopreservation, suggesting that they may be also involved in cryopreservation process.     

SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithms

Background  

The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark data sets for which the underlying network is known. Since experimental data sets of the appropriate size and design are usually not available, there is a clear need to generate well-characterized synthetic data sets that allow thorough testing of learning algorithms in a fast and reproducible manner.