Migration of herbaceous plant species across ancient–recent forest ecotones in central Belgium

1 We studied the migration of forest plant species using their percentage cover and frequency in 197 plots distributed over 26 transects across ecotones between ancient and recent deciduous forests in the Meerdaal forest complex in central Belgium. The recent forest stands varied in age between 36 and 132 years, and all occurred on silty, well-drained soils.
2 The total cover, number and diversity of field layer species did not differ significantly between ancient and recent forest stands.
3 The number and cover of the ancient forest plant species and of ant-dispersed species correlated positively with the age of the recent forest and negatively with both the duration of its former agricultural land use and the distance to the ancient forest. This implies a slow colonization of the recent forest stands by these species; all species were, however, able to migrate across the ecotones.
4 The cover of four species ( Anemone nemorosa , Lamium galeobdolon , Convallaria majalis and Polygonatum multiflorum ) declined along the transect, suggesting that they are limited by seed dispersal. Their colonization rates, calculated from the occurrence of the farthest individual, ranged from < 0.05 to 1.15 m year⁻¹ and for other measures from < 0.05 to 0.65 m year⁻¹. Anemone and Lamium appeared to colonize the recent forest by establishment of isolated individuals, while Polygonatum and Convallaria expanded populations from existing patches on the border between ancient and recent forest.
5 Several forest species were able to colonize the recent forest rapidly, where some of them even reached a higher abundance, due to the increased availability of colonization sites with a higher nutrient content and a thinner organic layer.     

Upper Pleistocene cold-water corals from the Inner Sea of the Maldives: taphonomy and environment

Cold-water corals of the Late Pleistocene (21,400–22,500 BP) are recorded from the sea-bottom of two inter-atoll channels (Kardiva Channel at 457-m depth and Malé Vaadhoo Channel at 443-m depth) of the eastern row of the Maldives archipelago. Coral assemblages are composed mainly by Lophelia pertusa and secondarily by Madrepora oculata and Enallopsammia rostrata. These cold-water coral patches are places where the benthic life, mainly sessile, is concentrated, which is clearly absent off-rubble patches. The main epibionts are tube-dwelling polychaetes (mainly Spirorbis and Serpula), bryozoans, siliceous sponges, barnacles, gorgonids, solitary corals, encrusting foraminifera, and microbial mats. The analysis of epibionts assemblages shows different biocoenoses between both studied sites as well as a dependency of the epibiont coverage with regard to the coral genus. Some living benthic organisms such as brachiopods, bivalves, gastropods, barnacles, and ophiuroids find refuge among coral branches. The common record of juvenile specimens of vagile organisms such as small ophiuroids, is probably related to the nursery function of the cold-water corals in spite they are fossils. Environmental requirements of Recent cold-water corals (Lophelia, Madrepora and Enallopsammia) differ of conditions at both sampling sites with sensibly lower oxygenation degree and density of waters than needed for cold-water corals. Therefore, it is proposed that the present-day oxygen and density conditions are the factors which inhibit modern cold-water coral growth in the inter-atoll channels.     

Endostatin's heparan sulfate-binding site is essential for inhibition of angiogenesis and enhances in situ binding to capillary-like structures in bone explants

The functional role of endostatin's affinity for heparan sulfates was addressed using an ex vivo bone angiogenesis model. Capillary-like sprouts showed prominent expression of collagen XVIII/endostatin. Outgrowth of endothelial cells was not altered in the absence of collagen XVIII but inhibited by the addition of recombinant endostatin. Mutant non-heparan sulfate binding endostatin and the collagen XV endostatin homologue were ineffective. The ability of mutant endostatin to bind to capillary structures was reduced when compared to endostatin. Endostatin-XV completely failed to bind to endothelial cells. Our data indicate that endostatin's angiostatic function is heparan sulfate-dependent, and that in situ-binding of endostatin to endothelial cells is increased by heparan sulfates.     

Short term changes in dynamics of C and N in soil when crops are cultivated on permanent raised beds

Densely populated, intensively cropped highland areas in the subtropics are prone to erosion and declining soil fertility, making agriculture unsustainable. Permanent raised bed planting systems, as a form of conservation agriculture, have been developed to reduce production costs while conserving resources and sustaining the environment. In 2004, a new experiment with long term focus was started under rain fed conditions at El Batán (Mexico; 2,240 m a.s.l.; 19.31N, 98.50W; Cumulic Phaeozem), which aims at understanding the effects of (1) tillage (conventionally tilled or permanent raised beds), (2) residue management (retention or removal) and (3) N fertilizer application (0 or 120 kg N/ha) on N availability in a yearly maize/wheat rotation system. Incubation experiments were conducted to establish how the different treatments affect C and N dynamics in the soil. Tillage increases the availability of soil organic matter by soil aggregate disruption, enhancing C and N mineralization. Conventionally tilled raised beds with incorporation of crop residues increased the CO₂ production rate. In both tillage systems, retention of maize or wheat residue without N fertilizer application led to N immobilization. In permanent raised beds, however, the immobilization due to residue retention could be compensated by application of N fertilizer, while conventionally tilled raised beds appeared to use the applied N fertilizer less efficiently.     

Cell polarity in plants: a PARspective on PINs

Plants have acquired the ability for organized multicellular development independent from animals. Because of this, they represent an independent example in nature for the development of coordinated, complex cell polarity from the simple polarity found in unicellular eukaryotes. Plants display a striking array of polarized cell types, with different axes of polarity being defined in one cell. The most investigated and best understood aspect of plant polarity is the apical-basal polarity of the PIN family of auxin efflux facilitators, which are of crucial importance for the organization of the entire plant body. Striking differences exist between the PAR-polarity modules known in animals and the ways PINs polarize plant cells. Nonetheless, a common regulatory logic probably applies to all polarizing eukaryotic cells, which includes self-reinforcing, positive feedback loops, intricate interactions between membrane-attached proteins, lipid signatures, and the targeting of transmembrane proteins to the correct domains of the plasma membrane.     

Volatile constituents of Erodium cicutarium (L.) L’ Hérit. (Geraniaceae)

Essential oils from Erodium cicutarium were obtained by hydrodistillation (samples consisting of entire plants (ec1), leaves and stems (ec2)) and analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC/MS), resulting in a total of 177 components being identified. The essential oils were of a very similar chemical composition and consisted mainly of aliphatic compounds and their derivatives. Fatty acids and fatty acid derived compounds were the most common, 51.3% (ec1) and 60.1% (ec2), followed by carotenoid derived compounds, 12.6% (ec1) and 20.2% (ec2), and then terpenoids, 14.9% (ec1) and 14.2% (ec2). The main constituents in the oils were hexadecanoic acid, 22.8% (ec2) and 35.9% (ec1) and hexahydrofarnesyl acetone, 10.8% (ec2) and 11.6% (ec1). The results obtained differ markedly from those previously reported for the same species.     

Crystal structure of yeast peroxisomal multifunctional enzyme: structural basis for substrate specificity of (3R)-hydroxyacyl-CoA dehydrogenase units

(3R)-hydroxyacyl-CoA dehydrogenase is part of multifunctional enzyme type 2 (MFE-2) of peroxisomal fatty acid beta-oxidation. The MFE-2 protein from yeasts contains in the same polypeptide chain two dehydrogenases (A and B), which possess difference in substrate specificity. The crystal structure of Candida tropicalis (3R)-hydroxyacyl-CoA dehydrogenase AB heterodimer, consisting of dehydrogenase A and B, determined at the resolution of 2.2A, shows overall similarity with the prototypic counterpart from rat, but also important differences that explain the substrate specificity differences observed. Docking studies suggest that dehydrogenase A binds the hydrophobic fatty acyl chain of a medium-chain-length ((3R)-OH-C10) substrate as bent into the binding pocket, whereas the short-chain substrates are dislocated by two mechanisms: (i) a short-chain-length 3-hydroxyacyl group ((3R)-OH-C4) does not reach the hydrophobic contacts needed for anchoring the substrate into the active site; and (ii) Leu44 in the loop above the NAD(+) cofactor attracts short-chain-length substrates away from the active site. Dehydrogenase B, which can use a (3R)-OH-C4 substrate, has a more shallow binding pocket and the substrate is correctly placed for catalysis. Based on the current structure, and together with the structure of the 2-enoyl-CoA hydratase 2 unit of yeast MFE-2 it becomes obvious that in yeast and mammalian MFE-2s, despite basically identical functional domains, the assembly of these domains into a mature, dimeric multifunctional enzyme is very different.     

Evolution on distributive lattices

We consider the directed evolution of a population after an intervention that has significantly altered the underlying fitness landscape. We model the space of genotypes as a distributive lattice; the fitness landscape is a real-valued function on that lattice. The risk of escape from intervention, i.e., the probability that the population develops an escape mutant before extinction, is encoded in the risk polynomial. Tools from algebraic combinatorics are applied to compute the risk polynomial in terms of the fitness landscape. In an application to the development of drug resistance in HIV, we study the risk of viral escape from treatment with the protease inhibitors ritonavir and indinavir.