Enquête beek(dal)herstelprojecten 2004-2008 : evaluatie van beekherstel over de periode 1960-2008 en analyse van effecten van 9 voorbeeldprojecten

Om inzicht te krijgen in de stand van de aquatisch-ecologische aspecten van beekherstel zijn door Alterra in de jaren 1993 (uitgebreid), 1998 (verkort) en 2003 (verkort) beekherstelenquêtes uitgevoerd en gerapporteerd. De Nederlandse natuur- en waterbeheerders hebben behoefte aan de resultaten van dergelijke enquêtes om (1) van elkaar te leren en (2) om nieuwe inzichten en mogelijkheden te leren kennen. OBN heeft de resultaten nodig om een scherp beeld van de mogelijkheden en onmogelijkheden van verschillende herstelmaatregelen onder verschillende omstandigheden te krijgen. In 2008 is een opnieuw een enquête gehouden, welke een vervolg is op de voorgaande beekherstelenquêtes. Deze laatste enquête echter richtte zich naast beekherstel ook op beekdalherstel. In dit rapport wordt de actuele stand (2004-2008) omtrent beek(dal)herstel in Nederland gerapporteerd. (zie ook Alterra rapport 1858)

Sequence annotation of nuclear receptor ligand-binding domains by automated homology modeling

The quality of three-dimensional homology models derived from protein sequences provides an independent measure of the suitability of a protein sequence for a certain fold. We have used automated homology modeling and model assessment tools to identify putative nuclear hormone receptor ligand-binding domains in the genome of Caenorhabditis elegans. Our results indicate that the availability of multiple crystal structures is crucial to obtaining useful models in this receptor family. The majority of annotated mammalian nuclear hormone receptors could be assigned to a ligand-binding domain fold by using the best model derived from any of four template structures. This strategy also assigned the ligand-binding domain fold to a number of C.elegans sequences without prior annotation. Interestingly, the retinoic acid receptor crystal structure contributed most to the number of sequences that could be assigned to a ligand-binding domain fold. Several causes for this can be suggested, including the high quality of this protein structure in terms of our assessment tools, similarity between the biological function or ligand of this receptor and the modeled genes and gene duplication in C.elegans

Coping strategies in farmed African catfish Clarias gariepinus. Does it affect their welfare?

The objective of this study was to assess whether and how coping strategies affect the welfare of African catfish Clarias gariepinus housed at low and high densities. Group composition influenced feed intake; re-active groups (comprised of 100% re-active fish) had a lower specific growth rate (G) and feed intake and a higher feed conversion ratio (RFC) than pro-active groups. Furthermore, re-active groups had a lower energy retention than pro-active groups. The latter was fully due to differences in feed intake, since energy partitioning (on % total gross energy intake basis) was similar among the group composition treatments. Fish held at high stocking density showed a higher RFC and feeding speed and a lower energy retention and agonistic behaviour. None of the measured variables was influenced by the interaction effect. In mixed groups, G and number of skin lesions seemed to be affected by different behavioural phenotypes at low stocking density, but not at high density. These results indicate that both stocking density and group composition affect physical and behavioural responses of C. gariepinus. Furthermore, physical and behavioural data of individual fish housed in mixed groups suggest that coping strategy affects the fitness of different behavioural phenotypes at low, but not at high, stocking densit

Crystal structure at 2.3 A resolution and revised nucleotide sequence of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermo-sulfurigenes EM1

The crystal structure of the cyclodextrin glycosyltransferase (CGTase) from the thermophilic microorganism Thermoanaerobacterium thermosulfurigenes EM1 has been elucidated at 2.3 Angstrom resolution. The final model consists of all 683 amino acid residues, two calcium ions and 343 water molecules, and has a crystallographic X-factor of 17.9% (R(free) 24.9%) with excellent stereochemistry. The overall fold of the enzyme is highly similar to that reported for mesophilic CGTases and differences are observed only at surface loop regions. Closer inspection of these loop regions and comparison with other CGTase structures reveals that especially loops 88-95, 335-339 and 534-539 possibly contribute with novel hydrogen bonds and apolar contacts to the stabilization of the enzyme. Other structural features that might confer thermostability to the T. thermosulfurigenes EM1 CGTase are the introduction of five new salt-bridges and three Gly to Ala/Pro substitutions. The abundance of Ser, Thr and Tyr residues near the active site and oligosaccharide binding sites might explain the increased thermostability of CGTase in the presence of starch, by allowing amylose chains to bind non-specifically to the protein. Additional stabilization of the A/E domain interface through apolar contacts involves residues Phe273 and Tyr187. No additional or improved calcium binding is observed in the structure, suggesting that the observed stabilization in the presence of calcium ions is caused by the reduced exchange of calcium from the protein to the solvent, rendering it less susceptible to unfolding. The 50% decrease in cyclization activity of the T. thermosulfurigenes EM1 CGTase compared with that of B. circulans strain 251 appears to be caused by the changes in the conformation and amino acid composition of the 88-95 loop. In the T. thermosulfurigenes EM1 CGTase there is no residue homologous to Tyr89, which was observed to take part in stacking interactions with bound substrate in the case of the B. circulans strain 251 CGTase. The lack of this interaction in the enzyme-substrate complex is expected to destabilize bound substrates prior to cyclization. Apparently, some catalytic functionality of CGTase has been sacrificed for the sake of structural stability by modifying loop regions near the active site. (C) 1996 Academic Press Limite