Delayed density‐dependent onset of spring reproduction in a fluctuating population of field voles

Delayed density‐dependent demographic processes are thought to be the basis for multi‐annual cyclic fluctuations in small rodent populations, but evidence for delayed density dependence of a particular demographic trait is rare. Here, using capture–recapture data from 22 sites collected over nine years, we demonstrate a strong effect of population density with a one‐year lag on the timing of the onset of spring reproduction in a cyclically fluctuating population of field voles Microtus agrestis in northern England. The mean date for the onset of spring reproduction was delayed by about 24 days for every additional 100 voles ha^?1 in the previous spring. This delayed density dependence is sufficient to generate the type of cyclic population dynamics described in the study system.     

Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest

Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.     

Investigating environmental variation and landscape characteristics of an urban–rural gradient using woodland carabid assemblages

Aim To investigate environmental variation and associated assemblage changes of carabid beetles along an urban–rural gradient. Location ‘Quercus–Acer’ (oak–sycamore) woodlands in the city of Birmingham, UK. Methods We collected carabid data using pitfall traps on 12 sites in the city. The traps were run from April–September in 2000, and we collected environmental data on 24 individual variables associated with the individual sites and their landscape context. Changes in carabid assemblages were analysed using repeat measures anova and the environment–species relationships with a Redundancy Analyses (RDA) and Generalized Linear Modelling (GLM). Results We found that: (1) species richness and diversity were lower in the urban and suburban zone and higher in the rural zone; (2) Berger Parker dominance index was higher in the urban and suburban zones; (3) the number of woodland and woodland associated species was significantly higher at the rural end of the gradient; (4) the number of short‐winged (brachypterous) species was highest in the rural zone and decreased towards the urban woodlands, whereas the long‐winged species were more abundant in suburban woodlands; (5) the median weight length (WML) of the assemblage declined along the gradient from the rural to the urban zone, as did the number of large species; and (6) five of the 24 environmental variables showed a significant relationship with variation in the carabid assemblage. At site level the carabid assemblages were related to the level of site disturbance and soil penetrability, whereas site size and amount of woodland and urban land within 5 km of the site were important at a larger landscape scale. Main conclusions The results suggest that urbanization has a deleterious impact on carabid assemblages, causing a reduction in species richness from the rural fringe to the centre of the city. Changes in assemblage structure were related to woodland fragmentation, which led to variations in woodland size, woodland location and site disturbance due to trampling. Large, flightless and specialist woodland species are more susceptible to changes associated with urbanization, presumably due to their longer life spans, lower reproductive rates, more specialized niches and more limited dispersal potential.     

Caspase-mediated cleavage of the exosome subunit PM/Scl-75 during apoptosis

Recent studies have implicated the dying cell as a potential reservoir of modified autoantigens that might initiate and drive systemic autoimmunity in susceptible hosts. A number of subunits of the exosome, a complex of 3'→5' exoribonucleases that functions in a variety of cellular processes, are recognized by the so-called anti-PM/Scl autoantibodies, found predominantly in patients suffering from an overlap syndrome of myositis and scleroderma. Here we show that one of these subunits, PM/Scl-75, is cleaved during apoptosis. PM/Scl-75 cleavage is inhibited by several different caspase inhibitors. The analysis of PM/Scl-75 cleavage by recombinant caspase proteins shows that PM/Scl-75 is efficiently cleaved by caspase-1, to a smaller extent by caspase-8, and relatively inefficiently by caspase-3 and caspase-7. Cleavage of the PM/Scl-75 protein occurs in the C-terminal part of the protein at Asp369 (IILD³⁶⁹↓G), and at least a fraction of the resulting N-terminal fragments of PM/Scl-75 remains associated with the exosome. Finally, the implications of PM/Scl-75 cleavage for exosome function and the generation of anti-PM/Scl-75 autoantibodies are discussed.     

De novo designed protein transduction domain mimics from simple synthetic polymers

Protein transduction domains (PTDs) that readily transverse cellular membranes are of great interest and are attractive tools for the intracellular delivery of bioactive molecules. Learning to program synthetic polymers and oligomers with the appropriate chemical information to capture adequately the biological activity of proteins is critical to our improved understanding of how these natural molecules work. In addition, the versatility of these synthetic mimics provides the opportunity to discover analogs with superior properties compared with their native sequences. Here we report the first detailed structure-activity relationship of a new PTD family of polymers based on a completely abiotic backbone. The synthetic approach easily allows doubling the density of guanidine functional groups, which increases the transduction efficiency of the sequences. Cellular uptake studies on three different cell lines (HEK 293T, CHO, and Jurkat T cells) confirm that these synthetic analogs are highly efficient novel protein transduction domain mimics (PTDMs), which are more effective than TAT(49-57) and nonaarginine (R9) and also highlight the usefulness of polymer chemistry at the chemistry-biology interface.     

Aquaculture: global status and trends

Aquaculture contributed 43 per cent of aquatic animal food for human consumption in 2007 (e.g. fish, crustaceans and molluscs, but excluding mammals, reptiles and aquatic plants) and is expected to grow further to meet the future demand. It is very diverse and, contrary to many perceptions, dominated by shellfish and herbivorous and omnivorous pond fish either entirely or partly utilizing natural productivity. The rapid growth in the production of carnivorous species such as salmon, shrimp and catfish has been driven by globalizing trade and favourable economics of larger scale intensive farming. Most aquaculture systems rely on low/uncosted environmental goods and services, so a critical issue for the future is whether these are brought into company accounts and the consequent effects this would have on production economics. Failing that, increased competition for natural resources will force governments to allocate strategically or leave the market to determine their use depending on activities that can extract the highest value. Further uncertainties include the impact of climate change, future fisheries supplies (for competition and feed supply), practical limits in terms of scale and in the economics of integration and the development and acceptability of new bio-engineering technologies.In the medium term, increased output is likely to require expansion in new environments, further intensification and efficiency gains for more sustainable and cost-effective production. The trend towards enhanced intensive systems with key monocultures remains strong and, at least for the foreseeable future, will be a significant contributor to future supplies. Dependence on external feeds (including fish), water and energy are key issues. Some new species will enter production and policies that support the reduction of resource footprints and improve integration could lead to new developments as well as reversing decline in some more traditional systems.     

Treatment with recombinant interferon-β reduces inflammation and slows cartilage destruction in the collagen-induced arthritis model of rheumatoid arthritis

We investigated the therapeutic potential and mechanism of action of IFN-β protein for the treatment of rheumatoid arthritis (RA). Collagen-induced arthritis was induced in DBA/1 mice. At the first clinical sign of disease, mice were given daily injections of recombinant mouse IFN-β or saline for 7 days. Disease progression was monitored by visual clinical scoring and measurement of paw swelling. Inflammation and joint destruction were assessed histologically 8 days after the onset of arthritis. Proteoglycan depletion was determined by safranin O staining. Expression of cytokines, receptor activator of NF-κB ligand, and c-Fos was evaluated immunohistochemically. The IL-1-induced expression of IL-6, IL-8, and granulocyte/macrophage-colony-stimulating factor (GM-CSF) was studied by ELISA in supernatant of RA and osteoarthritis fibroblast-like synoviocytes incubated with IFN-β. We also examined the effect of IFN-β on NF-κB activity. IFN-β, at 0.25 μg/injection and higher, significantly reduced disease severity in two experiments, each using 8–10 mice per treatment group. IFN-β-treated animals displayed significantly less cartilage and bone destruction than controls, paralleled by a decreased number of positive cells of two gene products required for osteoclastogenesis, receptor activator of NF-κB ligand and c-Fos. Tumor necrosis factor α and IL-6 expression were significantly reduced, while IL-10 production was increased after IFN-β treatment. IFN-β reduced expression of IL-6, IL-8, and GM-CSF in RA and osteoarthritis fibroblast-like synoviocytes, correlating with reduced NF-κB activity. The data support the view that IFN-β is a potential therapy for RA that might help to diminish both joint inflammation and destruction by cytokine modulation.     

The human exosome: an autoantigenic complex of exoribonucleases in myositis and scleroderma

The anti-PM/Scl autoantibodies are known to characterize a subset of autoimmune patients with myositis, scleroderma (Scl), and the PM/Scl overlap syndrome. The major autoantigens that are recognized by anti-PM/Scl autoantibodies are designated PM/Scl-100 and PM/Scl-75. These autoantigens have been reported to associate into a large complex consisting of 11 to 16 proteins and to play a role in ribosome synthesis. Recently, it was discovered that the PM/Scl complex is the human counterpart of the yeast (Saccharomyces cerevisiae) exosome, which is an RNA-processing complex consisting of 11 3' → 5' exoribonucleases. To date, 10 human exosome components have been identified, although only some of these were studied in more detail. In this review, we discuss some recent advances in the characterization of the PM/Scl complex.