Rivers in peril inside and outside protected areas: a systematic approach to conservation assessment of river ecosystems

This paper establishes a framework within which a rapid and pragmatic assessment of river ecosystems can be undertaken at a broad, subcontinental scale, highlighting some implications for achieving conservation of river biodiversity in water‐limited countries. The status of river ecosystems associated with main rivers in South Africa was assessed based on the extent to which each ecosystem had been altered from its natural condition. This requires consistent data on river integrity for the entire country, which was only available for main rivers; tributaries were thus excluded from the analyses. The state of main river ecosystems in South Africa is dire: 84% of the ecosystems are threatened, with a disturbing 54% critically endangered, 18% endangered, and 12% vulnerable. Protection levels were measured as the proportion of conservation target achieved within protected areas, where the conservation target was set as 20% of the total length of each river ecosystem. Sixteen of the 112 main river ecosystems are moderately to well represented within protected areas; the majority of the ecosystems have very low levels of representation, or are not represented at all within protected areas. Only 50% of rivers within protected areas are intact, but this is a higher proportion compared to rivers outside (28%), providing some of the first quantitative data on the positive role protected areas can play in conserving river ecosystems. This is also the first assessment of river ecosystems in South Africa to apply a similar approach to parallel assessments of terrestrial, marine, and estuarine ecosystems, and it revealed that main river ecosystems are in a critical state, far worse than terrestrial ecosystems. Ecosystem status is likely to differ with the inclusion of tributaries, since options may well exist for conserving critically endangered ecosystems in intact tributaries, which are generally less regulated than main rivers. This study highlights the importance of healthy tributaries for achieving river conservation targets, and the need for managing main rivers as conduits across the landscape to support ecological processes that depend on connectivity. We also highlight the need for a paradigm shift in the way protected areas are designated, as well as the need for integrated river basin management plans to include explicit conservation visions, targets, and strategies to ensure the conservation of freshwater ecosystems and the services they provide.     

Hydrological responses of a valley‐bottom wetland to land‐use/land‐cover change in a South African catchment: making a case for wetland restoration

Valley‐bottom wetlands are valuable assets as they provide many ecosystem services to mankind. Despite their value, valley‐bottom wetlands are often exploited and land‐use/land‐cover (LULC) change results in trade‐offs in ecosystem services. We coupled physically based hydrological modeling and spatial analysis to examine the effects of LULC change on water‐related ecosystem services in the Kromme catchment: an important water‐providing catchment for the city of Port Elizabeth. LULC scenarios were constructed to match 5 different decades in the last 50 years to explore the potential effects of restoring the catchment to different historic benchmarks. In the Kromme catchment, valley‐bottom wetlands have declined by 84%, driven by key LULC changes: an increase in irrigated land (307 ha) and invasion by alien trees (336 ha). If the wetlands were restored to the relatively pristine extent and condition of the 1950s, riverflow could increase by approximately 1.13 million m³/a, about 6% of the current supply to Port Elizabeth. Wetland restoration would also significantly improve the catchment's ability to absorb extreme rainfall events, decreasing flood damage. We conclude that in the face of the water scarcity in this region, all ecosystem services, particularly those related to water flow regulation, should be taken into account by decision makers in charge of land zonation. Zonation decisions should not continue to be made on the basis of provisioning ecosystem services alone (i.e. food provision or dam yield). We recommend prioritization of the preservation and restoration of valley‐bottom wetlands providing water‐related ecosystem services to settlements downstream.     

Fusogenics: a recombinant immunotoxin-based screening platform to select internalizing tumor-specific antibody fragments

Antibody-based therapeutics play a vital role in the treatment of certain cancers; however, despite commercial success, various strategies are being pursued to increase their potency and hence improve patient outcomes. The use of antibodies to deliver a cytotoxic payload offers a promising alternative for more efficacious therapies. Immunotoxins are composed of an internalizing antibody fragment linked to a bacterial or plant toxin. Once internalized, the payload, such as Pseudomonas exotoxin A (PE), blocks protein synthesis and induces apoptosis. Typically, immunotoxins are developed by first isolating a tumor-specific antibody, which is then either chemically linked to a toxin or reengineered as a fusion protein. Here, the authors describe the development of Fusogenics, an immunotoxin-based screening method that selects internalizing tumor-specific antibodies using a functional assay. Selected immune library clones were characterized and shown to be selective against normal tissues and specific to tumor tissues. In summary, the Fusogenics immunotoxin platform represents a unique, single-step selection approach combining specificity and functionality to isolate novel internalizing tumor-specific antibody fragments with potential for direct clinical application in the treatment of cancer.     

Plasma proteome analysis in HTLV-1-associated myelopathy/tropical spastic paraparesis

Background

A new subgroup of HIV-1, designated Group P, was recently detected in two unrelated patients of Cameroonian origin. HIV-1 Group P phylogenetically clusters with SIVgor suggesting that it is the result of a cross-species transmission from gorillas. Until today, HIV-1 Group P has only been detected in two patients, and its degree of adaptation to the human host is largely unknown. Previous data have shown that pandemic HIV-1 Group M, but not non-pandemic Group O or rare Group N viruses, efficiently antagonize the human orthologue of the restriction factor tetherin (BST-2, HM1.24, CD317) suggesting that primate lentiviruses may have to gain anti-tetherin activity for efficient spread in the human population. Thus far, three SIV/HIV gene products (vpu, nef and env) are known to have the potential to counteract primate tetherin proteins, often in a species-specific manner. Here, we examined how long Group P may have been circulating in humans and determined its capability to antagonize human tetherin as an indicator of adaptation to humans.

Results

Our data suggest that HIV-1 Group P entered the human population between 1845 and 1989. Vpu, Env and Nef proteins from both Group P viruses failed to counteract human or gorilla tetherin to promote efficient release of HIV-1 virions, although both Group P Nef proteins moderately downmodulated gorilla tetherin from the cell surface. Notably, Vpu, Env and Nef alleles from the two HIV-1 P strains were all able to reduce CD4 cell surface expression.

Conclusions

Our analyses of the two reported HIV-1 Group P viruses suggest that zoonosis occurred in the last 170 years and further support that pandemic HIV-1 Group M strains are better adapted to humans than non-pandemic or rare Group O, N and P viruses. The inability to antagonize human tetherin may potentially explain the limited spread of HIV-1 Group P in the human population.     

Tracing B-genome chromatin in Brassica napus x B. juncea interspecific progeny.

We used polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH) techniques to demonstrate the presence of Brassica B-genome chromosomes and putative B-genome introgressions in B. napus x B. juncea interspecific progeny. The B-genome--specific repeat sequence pBNBH35 was used to generate PCR products and FISH probes. The highest frequencies of viable progeny were obtained when B. napus was the maternal parent of the interspecific hybrid and the first backcross. B-genome--positive PCR assays were found in 34/51 fertile F2 progeny (67%), which was more than double the proportion found in fertile BC(1) progeny. Four B-genome--positive F(2)-derived families and 1 BC(1)-derived family were fixed or segregating for B. juncea morphology in the F(4) and BC(1)S(2), respectively, but in only 2 of these families did B. juncea-type plants exhibit B. juncea chromosome count (2n = 36) and typical B-genome FISH signals on 16 chromosomes. The remaining B. juncea-type plants had B. napus chromosome count (2n = 38) and no B-genome FISH signals, except for 1 exceptional F(4)-derived line that exhibited isolated and weak B-genome FISH signals on 11 chromosomes and typical A-genome FISH signals. B. juncea morphology was associated with B-genome--positive PCR signals but not necessarily with 16 intact B-genome chromosomes as detected by FISH. B-genome chromosomes tend to be eliminated during selfing or backcrossing after crossing B. juncea with B. napus, and selection of lines containing B-genome chromatin during early generations would be promoted by use of this B-genome repetitive marker.     

Plant carbon balance, evolutionary innovation and extinction in land plants

The plant fossil record was reviewed to highlight how consideration of plant carbon balance strengthens our understanding of various evolutionary innovation and extinction events. Following a brief physiological primer to carbon acquisition and allocation in C3‐plants, specific evolutionary events are discussed in connection with postulated carbon‐based mechanisms. Primary topics include: (i) the evolution of plants with the C4‐photosynthetic pathway; (ii) the surprising lack of plant extinctions during the Pleistocene (1.6 million years ago, Ma); (iii) the trend toward declining plant diversity and increasing rates of herbivory across the Palaeocene/Eocene transition (57–52 Ma); and (iv) megaherbivore extinctions at the end of the Pleistocene (10 thousand years ago, Ka). A framework is presented for testing hypotheses on the cause–effect relationships between global carbon cycling, plant carbon dynamics and the evolution of terrestrial ecosystems.     

An Assessment of Habitat Diversity and Transformation on La Réunion Island (Mascarene Islands,Indian Ocean) as a Basis for Identifying Broad-scale Conservation Priorities

Most natural habitat in the Mascarene Islands (Mauritius, La Réunion and Rodrigues) has been transformed. Although urbanisation, agriculture and alien plant invasions have transformed large areas in La Réunion, the island has by far the greatest area of intact habitats in the Mascarenes, but remaining natural areas are under threat. We propose a protocol for defining a system of habitat types and for using these to provide a preliminary assessment of conservation priorities for La Réunion. The protocol draws on existing data and expert knowledge to map habitat types, assesses the extent of habitat transformation, and quantifies heterogeneity between habitat types based on climate, topography and geology. The pattern of habitat transformation was uneven among the nineteen habitat types identified. While three habitats have lost > 95% of their original area, four still retain> 80% of their original extent. Habitat types could be grouped into the following categories: (i) transformed habitats with low levels of plant endemism, (ii) habitats confined to homogenous geology with high levels of plantendemism, and (iii) species-rich heterogeneous habitats on diverse geological types. Priority habitats were also identified using municipalities as a basis for implementation. Urgent action is required for several habitat types where a large part of the original extent has been transformed. Three municipalities which contain more than 10 habitat types should receive conservation priority. The analysis provides the basis for setting conservation priorities in La Réunion at the regional and local scale. Implications of the results are discussed with reference to requirements for finer-scale conservation planning.     

Potentials for win-win alliances among animal agriculture and forest products industries: Application of the principles of industrial ecology and sustainable development

Commercial forests in many parts of the world are deficient in nitrogen and phosphorus. These nutrient-deficient forests often exist in close proximity to large animal feeding operations, meat processing and other food, textile, or other biomass-processing plants, and municipal waste treatment facilities. Many of these facilities produce large surpluses of nitrogen, phosphorus, and organic matter as gaseous ammonia, urea, uric acid, phosphorus compounds, bacterial sludges, and partially treated municipal wastewaters. These co-existing and substantial nutrient deficiencies and surpluses offer ready-made opportunities for discovery, demonstration, and commercial development of science-based, technology-facilitated, environmentally sound, economically viable, and socially acceptable "win-win alliances" among these major industries based on the principles of industrial ecology and sustainable development. The major challenge is to discover practical means to capture the surplus nutrients and put them to work in forest stands from which value-added products can be produced and sold at a profit.     

Evaluation of fluorescence-based thermal shift assays for hit identification in drug discovery

The fluorescence-based thermal shift assay is a general method for identification of inhibitors of target proteins from compound libraries. Using an environmentally sensitive fluorescent dye to monitor protein thermal unfolding, the ligand-binding affinity can be assessed from the shift of the unfolding temperature (Delta Tm) obtained in the presence of ligands relative to that obtained in the absence of ligands. In this article, we report that the thermal shift assay can be conducted in an inexpensive, commercially available device for temperature control and fluorescence detection. The binding affinities obtained from thermal shift assays are compared with the binding affinities measured by isothermal titration calorimetry and with the IC(50) values from enzymatic assays. The potential pitfalls in the data analysis of thermal shift assays are also discussed.