A comparison of the predicted and X-ray structures of angiogenin. Implications for further studies of model building of homologous proteins

The three-dimensional structure of human angiogenin has been determined by X-ray crystallography and is compared here with an earlier model which predicted its structure, based on the homology of angiogenin with bovine pancreatic ribonuclease A. Comparison of the predicted model and crystal structure shows that the active-site histidine residues and the core of the angiogenin molecule, including most of the-strands and-helices, were predicted reasonably well. However, the structure of the surface loop regions and residues near the truncated C-terminus differs significantly. The C-terminal segment includes the active-site residues Asp-116, Gln-117, and Ser-118; Gln-117 in particular has been shown to be important in affecting the ribonucleolytic activity of angiogenin. Also, the orientation of one helix in the model differed from the orientation observed experimentally by about 20°, resulting in a large displacement of this chain segment. The difficulty encountered in predicting the surface loop regions has led to a new algorithm [Palmer and Scheraga (1991),J. Comput. Chem.,12, 505–526; (1992),J. Comput. Chem.,13, 329–350] for predicting the conformations of surface loops.     

Tricyclic 3,4-dihydropyrimidine-2-thione derivatives as potent TRPA1 antagonists

The transient receptor potential A1 (TRPA1) channel has been implicated in a number of inflammatory and nociceptive processes, and antagonists of the TRPA1 receptor could offer a potential treatment for conditions such as inflammatory or neuropathic pain, airway disorders, and itch. In a high throughput screen aimed at the identification of TRPA1 antagonists, 4-phenyl-2-thioxo-1,2,3,4-tetrahydro-indeno[1,2-d]pyrimidin-5-one (1) was identified as a potent TRPA1 receptor antagonist. A series of analogous tricyclic 3,4-dihydropyrimidine-2-thiones has been prepared via the multi-component Biginelli reaction and subsequent derivatization. This has led to TRPA1 antagonists with potencies around 10nM for both rat and human derived TRPA1 receptors. The activity was shown to reside exclusively in the 4R-enantiomers.     

Cotransformation of Aspergillus nidulans: a tool for replacing fungal genes

Summary When a non-selected DNA sequence was added during the transformation of amdS320 deletion strains of Aspergillus nidulans with a vector containing the wild-type amdS gene the AmdS⁺ transformants were cotransformed at a high frequency. Cotransformation of an amdS320, trpC801 double mutant strain showed that both the molar ratio of the two vectors and the concentration of the cotransforming vector affected the cotransformation frequency. The maximum frequency obtained was defined by the gene chosen as selection marker for transformation. Cotransformation was used to induce a gene replacement in A. nidulans. An amdS320 strain was transformed to AmdS⁺ and cotransformed with a DNA fragment containing a fusion between a non-functional A. nidulans trpC gene and the Escherichia coli lacZ gene. Ten AmdS⁺, LacZ⁺ transformants with a Trp^– mutant phenotype were selected. All of these strains could be transformed with a functional copy of the A. nidulans trpC gene, but only two strains yielded TrpC⁺ transformants which, with a low frequency, had a LacZ^– phenotype. These latter transformants had also lost the AmdS⁺ phenotype. Southern blotting analysis of DNA from these transformants confirmed the inactivation of the wild-type trpC gene, but revealed that amdS vector sequences were also involved in the gene replacement events.     

Water Scarcity in the Andes: A Comparison of Local Perceptions and Observed Climate, Land Use and Socioeconomic Changes

In the Andean region of South America, understanding communities’ water perceptions is particularly important for water management as many rural communities must decide by themselves if and how they will protect their micro-watersheds and distribute their water. In this study we examine how Water User Associations in the Eastern Andes of Colombia perceive water scarcity and the relationship between this perception and observed climate, land use, and demographic changes. Results demonstrate a complex relationship between perceptions and observed changes. On the one hand, observed changes in land cover match perceptions of deforestation as the primary cause of increasing water scarcity. On the other hand, perceptions of climate driven changes in water availability are not reflected in observed precipitation data. Furthermore, water scarcity was perceived in regions where seasonal rainfall variability is higher but not in regions where annual rainfall is lower. We discuss how these results contribute to our understanding of adaptation to climate change and the implications of possible mismatches between environmental changes and local perceptions.     

Virgin forests in Romania and Bulgaria: results of two national inventory projects and their implications for protection

Despite extensive forest destruction in the Middle Ages and later intensive commercial forest management, remnants of virgin forests remained spared in some Central, Eastern and South-Eastern European countries. These virgin forests are the last examples of original forests in this part of Europe. That is why their protection becomes an important issue of current European forestry and nature protection policy. But the knowledge about the location and the area of virgin forests in these countries is incomplete up till now. This article has the prime goal to present a conceptual framework what virgin forests might be (“A conceptual framework for defining of virgin forests” section). Based on this framework, a working methodology has been tested in Bulgaria and Romania (“Results of the two national projects in Romania and in Bulgaria” section and further). For this reason two projects have been carried out by the Royal Dutch Society of Nature Conservation (KNNV) in close co-operation with the Forestry Institutes in Romania and in Bulgaria. The results of these projects are described in general terms and further analysis in the future is necessary to describe specific features like forest structure and spatial heterogeneity of these forests. Based on the results of the inventory, principles of sustainable protection and management of the mapped virgin forests were defined and described in the research reports. The usefulness of the inventory became evident already during the EU pre-accession period of both countries while preparing the NATURA 2000 network. The remaining virgin forests of temperate Europe are an inexhaustible source of ecological information about biodiversity, structure, natural processes and overall functioning of undisturbed forest ecosystems. Their research will reveal information which can be used for ecological restoration of man-made forests which are degraded through intensive forestry practices over the last centuries. The last virgin forests of temperate Europe represent an irreplaceable part of the natural capital of Europe and are worth to be protected by law. Their last remnants in South-Eastern and Eastern Europe are endangered by commercial activities. A full inventory of remaining virgin forests in all countries of temperate Europe is a matter of highest urgency. A representative selection of virgin forest sites should be declared by UNESCO as World Heritage Sites.     

Acquisition of ionic copper by the bacterial outer membrane protein OprC through a novel binding site

Copper, while toxic in excess, is an essential micronutrient in all kingdoms of life due to its essential role in the structure and function of many proteins. Proteins mediating ionic copper import have been characterised in detail for eukaryotes, but much less so for prokaryotes. In particular, it is still unclear whether and how gram-negative bacteria acquire ionic copper. Here, we show that Pseudomonas aeruginosa OprC is an outer membrane, TonB-dependent transporter that is conserved in many Proteobacteria and which mediates acquisition of both reduced and oxidised ionic copper via an unprecedented CxxxM-HxM metal binding site. Crystal structures of wild-type and mutant OprC variants with silver and copper suggest that acquisition of Cu(I) occurs via a surface-exposed “methionine track” leading towards the principal metal binding site. Together with whole-cell copper quantitation and quantitative proteomics in a murine lung infection model, our data identify OprC as an abundant component of bacterial copper biology that may enable copper acquisition under a wide range of conditions.

How do Gram-negative bacteria acquire copper? This study shows that the outer membrane protein OprC from Pseudomonas aeruginosa is abundant during infection and mediates highly selective acquisition of both copper redox states via an extracellular "methionine track" and an unprecedented near-irreversible binding site.     

Zinc tolerance and hyperaccumulation are genetically independent characters

The hyperaccumulation of metals by a rare class of plants is a fascinating and little understood phenomenon. No genetic analysis has been possible since no intraspecific variation is known for this character. Here, we report on crosses between the zinc-hyperaccumulating and -tolerant species Arabidopsis halleri and the non-hyperaccumulating, non-tolerant species Arabidopsis petraea. The F2 segregates for both characters and it appears that the two characters are genetically independent. The data for tolerance are consistent with a single major gene for this character (although the number of genes for hyperaccumulation cannot be determined), and is probably not very large.     

Validation of lactose[15N,15N]ureide as a tool to study colonic nitrogen metabolism

In vitro experiments have shown that fermentation of carbohydrates prevents accumulation of nitrogen in the colon. Variable results have been obtained on modulation of dietary intakes in vivo. Lactose[15N,15N]-labeled ureide has been proposed as a tool to study colonic nitrogen metabolism. However, on oral administration of the marker, different urinary excretion patterns of the 15N label have been found. In this study, 50 mg lactose[15N,15N]ureide was directly instilled in the colon through an orocecal tube to investigate the colonic handling of this molecule in a direct way. In basal conditions, 42% (range, 37-48%) of labeled nitrogen administered as lactose[15N,15N]ureide was retrieved in urine after 72 h. A substantial variability in total urinary excretion of the label was found, but the urinary excretion pattern of the label was similar in all volunteers. When inulin, a fermentable carbohydrate, was administered together with the labeled marker, a significant decrease in urinary excretion of 15N after 72 h was found, to 29% (range, 23-34%). The effect of a smaller dose of inulin (250 mg) on colonic handling of lactose[15N,15N]ureide (50 mg), was investigated in another group of volunteers, and this time, fecal excretion of the marker was also evaluated. The results seem to indicate that fermentation of inulin causes an increased fecal excretion of the marker, thereby reducing urinary excretion but not retention in the human nitrogen pool. This instillation study shows that lactose[15N,15N]ureide is a tool with good properties to investigate the effect of different types of carbohydrates on nitrogen metabolism in the proximal colon in vivo.