On the inhibitory action of cadmium on the donor side of photosystem II in isolated chloroplasts.

The inhibitory effect of the Cd2+ in the electron transport of the isolated chloroplasts has been observed by measuring the oxygen uptake from the solution and the fluorescence induction. Cd2+ is found to be an inhibitor on the donor side of Photosystem II and its action site, as determined by experiments using hydroxylamine and exogenous Mn, is supposed to be on the water-splitting enzyme itself. Moreover, physicochemical and physiological studies indicate that only the ionic form of Cd is acting at the level of the manganoprotein. It is not possible, from this work, to define precisely in which form Cd is taken up through the thylakoid membranes.     

bioRad: biological analysis and visualization of weather radar data

Weather surveillance radars are increasingly used for monitoring the movements and abundances of animals in the airspace. However, analysis of weather radar data remains a specialised task that can be technically challenging. Major hurdles are the difficulty of accessing and visualising radar data on a software platform familiar to ecologists and biologists, processing the low‐level data into products that are biologically meaningful, and summarizing these results in standardized measures. To overcome these hurdles, we developed the open source R package bioRad, which provides a toolbox for accessing, visualizing and analyzing weather radar data for biological studies. It provides functionality to access low‐level radar data, process these data into meaningful biological information on animal speeds and directions at different altitudes in the atmosphere, visualize these biological extractions, and calculate further summary statistics. The package aims to standardize methods for extracting and reporting biological signals from weather radars. Here we describe a roadmap for analyzing weather radar data using bioRad. We also define weather radar equivalents for familiar measures used in the field of migration ecology, such as migration traffic rates, and recommend several good practices for reporting these measures. The bioRad package integrates with low‐level data from both the European radar network (OPERA) and the radar network of the United States (NEXRAD). bioRad aims to make weather radar studies in ecology easier and more reproducible, allowing for better inter‐comparability of studies.     

Developing products for conservation decision-making: lessons from a spatial biodiversity assessment for South Africa

South Africa's first national assessment of spatial priorities for biodiversity conservation, released in 2005, aimed to identify conservation priority areas for mainstreaming into all sectors at national and provincial scales. This National Spatial Biodiversity Assessment (NSBA) was based on a planning for implementation approach in order to deliver defensible products useful to decision-makers. The NSBA aimed to produce a map of broad-scale priority areas for future finer-scale assessment and conservation action. This map summarized information on species, ecosystems, ecological processes, and the pressures they face from human activities. Owing to the complexity of the priority area map, two additional user-friendly products — maps of ecosystem status and protection levels — were developed. These products represented the habitat loss and protected area coverage of South Africa's ecosystems relative to their conservation targets. A year after release, we reflect on the NSBA process, products and uptake by implementing agencies (with a specific focus on the terrestrial biodiversity assessment) in order to contribute to the growing body of documented best practice in conservation planning. The ecosystem status product has been widely used at national and provincial scales due in large to its clear and compelling message. The protection level and overall priority map have also witnessed uptake, the former in guiding the expansion of protected areas and the latter as an integrated map of national biodiversity status. The strong collaboration of local planners and implementers with in-depth experience of biodiversity assessment, using a systematic approach and focusing on communicating a few high level messages, appears to have contributed to the initial, successful uptake of the NSBA. We conclude with a call to address data and monitoring shortcomings before the next NSBA in 2010.     

Influence of a natural and a synthetic inhibitor of factor XIIIa on fibrin clot rheology

We investigated the origins of greater clot rigidity associated with FXIIIa-dependent cross-linking. Fibrin clots were examined in which cross-linking was controlled through the use of two inhibitors: a highly specific active-center-directed synthetic inhibitor of FXIIIa, 1,3-dimethyl-4,5-diphenyl-2[2(oxopropyl)thio]imidazolium trifluoromethylsulfonate, and a patient-derived immunoglobulin directed mainly against the thrombin-activated catalytic A subunits of thrombin-activated FXIII. Cross-linked fibrin chains were identified and quantified by one- and two-dimensional gel electrophoresis and immunostaining with antibodies specific for the alpha- and gamma-chains of fibrin. Gamma-dimers, gamma-multimers, alpha(n)-polymers, and alpha(p)gamma(q)-hybrids were detected. The synthetic inhibitor was highly effective in preventing the production of all cross-linked species. In contrast, the autoimmune antibody of the patient caused primarily an inhibition of alpha-chain cross-linking. Clot rigidities (storage moduli, G') were measured with a cone and plate rheometer and correlated with the distributions of the various cross-linked species found in the clots. Our findings indicate that the FXIIIa-induced dimeric cross-linking of gamma-chains by itself is not sufficient to stiffen the fibrin networks. Instead, the augmentation of clot rigidity was more strongly correlated with the formation of gamma-multimers, alpha(n)-polymers, and alpha(p)gamma(q)-hybrid cross-links. A mechanism is proposed to explain how these cross-linked species may enhance clot rigidity.     

Peptide-protein microarrays for the simultaneous detection of pathogen infections

We describe novel peptide-protein microarrays, which were fabricated using semicarbazide glass slides that permitted the immobilization of glyoxylyl peptides by site-specific ligation and the immobilization of proteins by physisorption. The arrays permitted the simultaneous serodetection of antibodies directed against hepatitis C virus (HCV core p21 15-45 peptide, NS4 1925-1947 peptide, core, NS3, NS4, and mixture of core, NS3, NS4, and NS5 antigens), hepatitis B virus (HBc, HBe, and HBs), human immunodeficiency virus (Gp41 and Gp120 for HIV-I and Gp36 for HIV-II), Epstein-Barr virus (VCAp18 153-176 peptide), and syphilis (rTpN47 and rTpN17) antigens using an immunofluorescence assay. Peptide-protein microarrays displayed high signal-to-noise ratios, sensitivities, and specificities for the detection of antibodies as revealed by the analysis of a collection of human sera referenced against these five pathogens.     

Development and application of cytotoxic T lymphocyte-associated antigen 4 as a protein scaffold for the generation of novel binding ligands

We have explored the possibilities of using human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) as a single immunoglobulin fold-based scaffold for the generation of novel binding ligands. To obtain a suitable protein library selection system, the extracellular domain of CTLA-4 was first displayed on the surface of a filamentous phage as a fusion product of the phage coat protein p3. CTLA-4 was shown to be functionally intact by binding to its natural ligands B7-1 (CD80) and B7-2 (CD86) both in vitro and in situ. Secondly, the complementarity determining region 3 (CDR3) loop of the CTLA-4 extracellular domain was evaluated as a permissive site. We replaced the nine amino acid CDR3-like loop of CTLA-4 with the sequence XXX-RGD-XXX (where X represents any amino acid). Using phage display we selected several CTLA-4-based variants capable of binding to human alphavbeta3 integrin, one of which showed binding to integrins in situ. To explore the construction of bispecific molecules we also evaluated one other potential permissive site diametrically opposite the natural CDR-like loops, which was found to be tolerant of peptide insertion. Our data suggest that CTLA-4 is a suitable human scaffold for engineering single-domain molecules with one or possibly more binding specificities.