On the context‐dependent scaling of consumer feeding rates

The stability of consumer–resource systems can depend on the form of feeding interactions (i.e. functional responses). Size‐based models predict interactions – and thus stability – based on consumer–resource size ratios. However, little is known about how interaction contexts (e.g. simple or complex habitats) might alter scaling relationships. Addressing this, we experimentally measured interactions between a large size range of aquatic predators (4–6400 mg over 1347 feeding trials) and an invasive prey that transitions among habitats: from the water column (3D interactions) to simple and complex benthic substrates (2D interactions). Simple and complex substrates mediated successive reductions in capture rates – particularly around the unimodal optimum – and promoted prey population stability in model simulations. Many real consumer–resource systems transition between 2D and 3D interactions, and along complexity gradients. Thus, Context‐Dependent Scaling (CDS) of feeding interactions could represent an unrecognised aspect of food webs, and quantifying the extent of CDS might enhance predictive ecology.     

The Nutrient Status of Mgazana,a Warm Temperate Mangrove Estuary in the Transkei,Eastern Cape,South Africa

Mgazana, a rural southern African mangrove system, was visited monthly from August, 1995 to February, 1997 to collect water samples for nutrient analysis. Surface and bottom samples were taken during spring low tide at seven stations along the estuary and the following physico-chemical parameters measured: river flow, temperature, salinity, oxygen, transparency, ammonia, nitrite, nitrate, phosphate, inorganic carbon (IC), organic carbon (OC), total carbon (TC), soluble nitrogen (SN), particulate nitrogen (PN) and total nitrogen (TN). Using correlation matrix analysis and ANOVA, river flow was found to affect estuarine salinity, transparency and stratification, which influenced nutrient dynamics. Significant seasonal (winter and summer) differences were found for temperature, river flow, nitrate, SN, TN, IC and OC. Most nutrients were significantly correlated with river flow showing gradients down the estuary, indicating allochthonous input from the catchment. OC levels within the estuary were high, probably due to autochthonous mangrove leaf-fall processing by the various in-fauna, but high levels measured at the head of the estuary during high river flow suggested additional allochthonous input from coastal forest litter. Conversely, IC was negatively correlated with river flow suggesting that autochthonous faunal and microbial mineralisation of organic matter occurs within creeks, which is then diluted by increased stream-flow. An N:P ratio of 2.7:1 was obtained for this rural mangrove system, which was low compared with Spartina-based East Cape estuaries subject to urban, industrial and agricultural pollution.     

Complete nucleotide sequence of the Escherichia coli ptr gene encoding protease III.

The nucleotide sequence of a 3120 bp region of the E. coli chromosome that includes the entire ptr gene has been determined. The proposed coding region for Protease III is 2889 nucleotides long, which would encode a protein consisting of 962 amino acids with a calculated molecular mass of 107,719 daltons. The predicted primary structure of the protein includes a 23-residue signal sequence, cleavage of which would give rise to a mature protein of molecular mass 105,124 daltons. At its 3' end, the ptr gene overlaps the start of the recB coding sequence by 8 bases, suggesting that these genes may form part of an operon.     

Cloning of the uvrD gene of E. coli and identification of the product

The uvrD gene has been cloned from Escherichia coli chromosomal DNA into phage lambda, cosmid, and low-copy-number plasmid vectors. Comparison of the proteins encoded by the cloned fragments with those encoded by fragments in which the uvrD gene is inactivated by transposon insertion or by deletion shows that the uvrD gene product is a protein of Mr = 73000.     

Induction of a protective response in mice by the dengue virus NS3 protein using DNA vaccines

The dengue non-structural 3 (NS3) is a multifunctional protein, containing a serino-protease domain, located at the N-terminal portion, and helicase, NTPase and RTPase domains present in the C-terminal region. This protein is considered the main target for CD4+ and CD8+ T cell responses during dengue infection, which may be involved in protection. However, few studies have been undertaken evaluating the use of this protein as a protective antigen against dengue, as well as other flavivirus. In the present work, we investigate the protective efficacy of DNA vaccines based on the NS3 protein from DENV2. Different recombinant plasmids were constructed, encoding either the full-length NS3 protein or only its functional domains (protease and helicase), fused or not to a signal peptide (t-PA). The recombinant proteins were successfully expressed in transfected BHK-21 cells, and only plasmids encoding the t-PA signal sequence mediated protein secretion. Balb/c mice were immunized with the different DNA vaccines and challenged with a lethal dose of DENV2. Most animals immunized with plasmids encoding the full-length NS3 or the helicase domain survived challenge, regardless of the presence of the t-PA. However, some mice presented clinical signs of infection with high morbidity (hind leg paralysis and hunched posture), mainly in animal groups immunized with the DNA vaccines based on the helicase domain. On the other hand, inoculation with plasmids encoding the protease domain did not induce any protection, since mortality and morbidity rates in these mouse groups were similar to those detected in the control animals. The cellular immune response was analyzed by ELISPOT with a specific-CD8+ T cell NS3 peptide. Results revealed that the DNA vaccines based on the full-length protein induced the production of INF-γ, thus suggesting the involvement of this branch of the immune system in the protection.     

Persistent negative effects of pesticides on biodiversity and biological control potential on European farmland

During the last 50 years, agricultural intensification has caused many wild plant and animal species to go extinct regionally or nationally and has profoundly changed the functioning of agro-ecosystems. Agricultural intensification has many components, such as loss of landscape elements, enlarged farm and field sizes and larger inputs of fertilizer and pesticides. However, very little is known about the relative contribution of these variables to the large-scale negative effects on biodiversity. In this study, we disentangled the impacts of various components of agricultural intensification on species diversity of wild plants, carabids and ground-nesting farmland birds and on the biological control of aphids.In a Europe-wide study in eight West and East European countries, we found important negative effects of agricultural intensification on wild plant, carabid and bird species diversity and on the potential for biological pest control, as estimated from the number of aphids taken by predators. Of the 13 components of intensification we measured, use of insecticides and fungicides had consistent negative effects on biodiversity. Insecticides also reduced the biological control potential. Organic farming and other agri-environment schemes aiming to mitigate the negative effects of intensive farming on biodiversity did increase the diversity of wild plant and carabid species, but – contrary to our expectations – not the diversity of breeding birds.We conclude that despite decades of European policy to ban harmful pesticides, the negative effects of pesticides on wild plant and animal species persist, at the same time reducing the opportunities for biological pest control. If biodiversity is to be restored in Europe and opportunities are to be created for crop production utilizing biodiversity-based ecosystem services such as biological pest control, there must be a Europe-wide shift towards farming with minimal use of pesticides over large areas.     

Bird communities across varying landcover types in a Neotropical city

Urbanization poses a serious threat to local biodiversity, yet towns and cities with abundant natural features may harbor important species populations and communities. While the contribution of urban greenspaces to conservation has been demonstrated by numerous studies within temperate regions, few consider the bird communities associated with different landcovers in Neotropical cities. To begin to fill this knowledge gap, we examined how the avifauna of a wetland city in northern Amazonia varied across six urban landcover types (coastal bluespace; urban bluespace; managed greenspace; unmanaged greenspace; dense urban; and sparse urban). We measured detections, species richness, and a series of ground cover variables that characterized the heterogeneity of each landcover, at 114 locations across the city. We recorded >10% (98) of Guyana's bird species in Georgetown, including taxa of conservation interest. Avian detections, richness, and community composition differed with landcover type. Indicator species analysis identified 29 species from across dietary guilds, which could be driving community composition. Comparing landcovers, species richness was highest in managed greenspaces and lowest in dense urban areas. The canal network had comparable levels of species richness to greenspaces. The waterways are likely to play a key role in enhancing habitat connectivity as they traverse densely urbanized areas. Both species and landcover information should be integrated into urban land-use planning in the rapidly urbanizing Neotropics to maximize the conservation value of cities. This is imperative in the tropics, where anthropogenic pressures on species are growing significantly, and action needs to be taken to prevent biodiversity collapse.     

pH-Dependent Conformational Changes in the HCV NS3 Protein Modulate Its ATPase and Helicase Activities

The hepatitis C virus (HCV) infects 170 to 200 million people worldwide and is, therefore, a major health problem. The lack of efficient treatments that specifically target the viral proteins or RNA and its high chronicity rate make hepatitis C the cause of many deaths and hepatic transplants annually. The NS3 protein is considered an important target for the development of anti-HCV drugs because it is composed of two domains (a serine protease in the N-terminal portion and an RNA helicase/NTPase in the C-terminal portion), which are essential for viral replication and proliferation. We expressed and purified both the NS3 helicase domain (NS3hel) and the full-length NS3 protein (NS3FL) and characterized pH-dependent structural changes associated with the increase in their ATPase and helicase activities at acidic pH. Using intrinsic fluorescence experiments, we have observed that NS3hel was less stable at pH 6.4 than at pH 7.2. Moreover, binding curves using an extrinsic fluorescent probe (bis-ANS) and ATPase assays performed under different pH conditions demonstrated that the hydrophobic clefts of NS3 are significantly more exposed to the aqueous medium at acidic pH. Using fluorescence spectroscopy and anisotropy assays, we have also observed more protein interaction with DNA upon pH acidification, which suggests that the hydrophobic clefts exposure on NS3 might be related to a loss of stability that could lead it to adopt a more open conformation. This conformational change at acidic pH would stimulate both its ATPase and helicase activities, as well as its ability to bind DNA. Taken together, our results indicate that the NS3 protein adopts a more open conformation due to acidification from pH 7.2 to 6.4, resulting in a more active form at a pH that is found near Golgi-derived membranes. This increased activity could better allow NS3 to carry out its functions during HCV replication.     

Eimeria species and genetic background influence the serum protein profile of broilers with coccidiosis

Background

Coccidiosis is an intestinal disease caused by protozoal parasites of the genus Eimeria. Despite the advent of anti-coccidial drugs and vaccines, the disease continues to result in substantial annual economic losses to the poultry industry. There is still much unknown about the host response to infection and to date there are no reports of protein profiles in the blood of Eimeria-infected animals. The objective of this study was to evaluate the serum proteome of two genetic lines of broiler chickens after infection with one of three species of Eimeria.

Methodology/Principal Findings

Birds from lines A and B were either not infected or inoculated with sporulated oocysts from one of the three Eimeria strains at 15 d post-hatch. At 21 d (6 d post-infection), whole blood was collected and lesion scoring was performed. Serum was harvested and used for 2-dimensional gel electrophoresis. A total of 1,266 spots were quantitatively assessed by densitometry. Protein spots showing a significant effect of coccidia strain and/or broiler genetic line on density at P<0.05−0.01 (250 spots), P<0.01−0.001 (248 spots), and P<0.001 (314 spots) were excised and analyzed by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry. Proteins were identified in 172 spots. A total of 46 different proteins were identified. Of the spots with a corresponding protein identification, 57 showed a main effect of coccidia infection and/or 2-way interaction of coccidia infection×broiler genetic line at P<0.001.

Conclusions/Significance

Several of the metabolic enzymes identified in this study are potential candidates for early diagnostic markers of E. acervulina infection including malate dehydrogenase 2, NADH dehydrogenase 1 alpha subcomplex 9, and an ATP synthase. These proteins were detected only in Line A birds that were inoculated with E. acervulina. Results from this study provide a basic framework for future research aimed at uncovering the complex biochemical mechanisms involved in host response to Eimeria infection and in identifying molecular targets for diagnostic screening and development of alternative preventative and therapeutic methods.