Phytochrome degradation

Plants actively modulate the levels of the various phyto-chrome isoforms during their life cycle to optimize light absorption and perception. For phytochrome A (phyA), one of the most influential methods of control is selective turnover of the photoreceptor upon photoconversion from the red-absorbing form (Pr) to the far-red-absorbing form (Pfr). Whereas the Pr form has a half-life of approximately 1 week, the Pfr form is rapidly degraded with a half-life of 1–2 h. The ubiquitin/26S proteasome pathway has been implicated in phyA breakdown. In this proteolytic pathway, multiple ubiquitins are covalently attached to proteins committed for degradation; these ubiquitin-protein conjugates then serve as intermediates in the breakdown of the target protein by the 26S proteasome, a multi-subunit proteolytic complex. In several plant species, ubiquitin-phyA conjugates have been detected in vivo following Pfr formation that show accumulation and decay kinetics expected for Pfr degradation intermediates. Analyses of phyA mutants and phyA/phyB chimeras expressed in transgenic plants have been particularly useful in mapping domains within the chromoprotein that are necessary for Pfr degradation. Several domains have been identified within both the N- and C-terminal portions of the photoreceptor that presumably serve as recognition and/or acceptor sites for ubiquitination     

Detecting the impact of oceano-climatic changes on marine ecosystems using a multivariate index: The case of the Bay of Biscay (North Atlantic-European Ocean)

Large‐scale univariate climate indices (such as NAO) are thought to outperform local weather variables in the explanation of trends in animal numbers but are not always suitable to describe regional scale patterns. We advocate the use of a Multivariate Oceanic and Climatic index (MOCI), derived from ‘synthetic’ and independent variables from a linear combination of the total initial variables objectively obtained from Principal Component Analysis. We test the efficacy of the index using long‐term data from marine animal populations. The study area is the southern half of the Bay of Biscay (43°–47°N; western Europe). Between 1974 and 2000 we monitored cetaceans and seabirds along 131000 standardized line transects from ships. Fish abundance was derived from commercial fishery landings. We used 44 initial variables describing the oceanic and atmospheric conditions and characterizing the four annual seasons in the Bay of Biscay. The first principal component of our MOCI is called the South Biscay Climate (SBC) index. The winter NAO index was correlated to this SBC index. Inter‐annual fluctuations for most seabird, cetacean and fish populations were significant. Boreal species (e.g. gadiformes fish species, European storm petrel and Razorbill …) with affinities to cold temperate waters declined significantly over time while two (Puffin and Killer Whale) totally disappeared from the area during the study period. Meridional species with affinities to hotter waters increased in population size. Those medium‐term demographic trends may reveal a regime shift for this part of the Atlantic Ocean. Most of the specific observed trends were highly correlated to the SBC index and not to the NAO. Between 40% and 60% of temporal variations in species abundance were explained by the multivariate SBC index suggesting that the whole marine ecosystem is strongly affected by a limited number of physical parameters revealed by the multivariate SBC index. Aside the statistical error of the field measurements, the remaining variation unexplained by the physical characteristics of the environment correspond to the impact of anthropogenic activities such overfishing and oil‐spills.     

Diurnal fluctuations of dissolved nitrous oxide (N2O) concentrations and estimates of N2O emissions from a spring-fed river: implications for IPCC methodology

There is uncertainty in the estimates of indirect nitrous oxide (N₂O) emissions as defined by the Intergovernmental Panel on Climate Change (IPCC). The uncertainty is due to the challenge and dearth of in situ measurements. Recent work in a subtropical stream system has shown the potential for diurnal variability to influence the downstream N transfer, N form, and estimates of in‐stream N₂O production. Studies in temperate stream systems have also shown diurnal changes in stream chemistry. The objectives of this study were to measure N₂O fluxes and dissolved N₂O concentrations from a spring‐fed temperate river to determine if diurnal cycles were occurring. The study was performed during a 72 h period, over a 180 m reach, using headspace chamber methodology. Significant diurnal cycles were observed in radiation, river temperature and chemistry including dissolved N₂O‐N concentrations. These data were used to further assess the IPCC methodology and experimental methodology used. River NO₃‐N and N₂O‐N concentrations averaged 3.0 mg L⁻¹ and 1.6 μg L⁻¹, respectively, with N₂O saturation reaching a maximum of 664%. The N₂O‐N fluxes, measured using chamber methodology, ranged from 52 to 140 μg m⁻² h⁻¹ while fluxes predicted using the dissolved N₂O concentration ranged from 13 to 25 μg m⁻² h⁻¹. The headspace chamber methodology may have enhanced the measured N₂O flux and this is discussed. Diurnal cycles in N₂O% saturation were not large enough to influence downstream N transfer or N form with variability in measured N₂O fluxes greater and more significant than diurnal variability in N₂O% saturation. The measured N₂O fluxes, extrapolated over the study reach area, represented only 6 × 10⁻⁴% of the NO₃‐N that passed through the study reach over a 72 h period. This is only 0.1% of the IPCC calculated flux.     

Phylogenetic systematics and biogeography of the poison frogs: evidence from mitochondrial DNA sequences

Regions of the mitochondrial genome were sequenced and analysed in representative species of poison frogs, in order to investigate phylogenetic relationships within the family Dendrobatidae. Mitochondrial DNA (mfDNA) fragments from three gene regions; cytochrome b, 16S ribosomal RNA (rRNA), and 12S rRNA, provided 1198 base pairs of DNA sequence and 589 informative sites. Phylogenetic analysis using parsimony was used to infer the evolutionary relationships among the species in the survey. Our analysis supported previous partitions of species into the genera Epipedobates, Phyllobates and Dendrobates , with two exceptions; Epipedobates (Allobates) femoralis was placed outside the clade containing the other toxic dendrobatids, and Minyobates minutus was placed within the genus Dendrobates. Genetic distances estimated between all pairs of taxa using the Kimura 2-parameter model indicated substantial genetic divergence between species, particularly those found in Amazonia. Time of divergence estimates were highly variable depending on gene region, but even the lowest estimates were inconsistent with the Pleistocene Refugia hypothesis.     

Origins of irruptive migrations by Common Crossbills Loxia curvirostra into northwestern Europe revealed by stable isotope analysis

We used analyses of stable hydrogen isotope (δ²H) measurements in Common Crossbill feathers (δ²H_f) to infer the region of origin of Crossbills collected from different irruptions into Britain, Iceland and the Faeroes, comparing these values with those from birds sampled in breeding areas in Britain and elsewhere in the western Palaearctic. No differences in δ²H_f values were found between different species or sexes of Crossbills that could be presumed to have grown their feathers in the same region, but juveniles had lower δ²H_f values than adults that had grown their feathers in the same region. On the basis mainly of museum skins, immigrant birds were sampled from 30 different irruption years, spanning the period 1866–2009, with annual samples varying from one to 29 individuals. The variation in δ²H_f values within irruptions was substantially less than the variation between irruptions, indicating that irruptions in different years originated in different parts of the western Palaearctic boreal zone. Birds with lower δ²H_f values tended to arrive later in the migration season, which was consistent with the idea that they had travelled further. In 17 of the irruption years, the birds had mean δ²H_f values more than ?120‰, suggesting that they had originated somewhere in the region extending from northern Scandinavia to northwestern Russia. In these years the birds arrived early, in June and July. In 10 of the irruption years, the mean δ²H_f values were between ?120 and ?130‰, suggesting origins further east, in northern Russia, east of Archangel (about 40°E). In only three of the 30 years (1898, 2002, 2009) the mean δ²H_f values were even lower (< 130‰), and these birds arrived in late July, August and September. Birds in these three irruptions had probably come from Siberia, east of the Ural Mountains. In at least three irruption years (1898, 1927, 1985) the observed range of δ²H_f values suggested that birds had come from more than one of these regions, including east of the Urals in 1898 and 1927.     

The interrelationships of all major groups of Platyhelminthes: phylogenetic evidence from morphology and molecules

We used a data matrix of 65 morphological characters from 25 ingroup and 6 outgroup taxa, and an alignment comprising complete 18S rDNA sequences from 82 species of parasitic and free-living Platyhelminthes and from 19 species of lower invertebrates to analyse phylogenetic relationships of various platyhelminth taxa. Of the 1358 unambiguously alignablc molecular positions, 995 were variable and 757 were phylogenctically informative (parsimony criterion); complete 18S rDNA sequences ranged in length from 1755 to 2873 bp. Main conclusions are: Ncodermata are monophylctic, and the Trematoda, Monogenca and Cestoda within them are monophylctic as well. The sister group of the Ncodermata is all the other Ncoophora; the Kalyptorhynchia, Typhloplanida, Dalyelliida and Tcmnocephalida form one clade, and the last three another. Monophyly of the Seriata is rejected, but Polycladida/ Macrostomida/Haplopharyngida are monophylctic, as arc the last two taxa. As a consequence, validity of the taxon Trepaxonemata is rejected. Further studies must show the correct position of the Acocla and Nemertodermatida. It is stressed that morphological and molecular data in some respects lead to contradictory results, for instance concerning the position of the Fecampiidac/ Urastoma/Ichthyophaga and the relative position of the Lccithoepitheliata. Denser sampling of taxa for molecular data, complementary sequences from independent genes, and inclusion of additional morphological data are necessary to resolve these contradictions.