Lake water level increase during spring affects the breeding success of bream Abramis brama (L.)

In Lake Constance, Eurasian bream Abramis brama (L.) spawn in very shallow littoral areas by the beginning of May. They attach their adhesive eggs to pebble and cobble substratum at <40 cm depth. Increasing water levels before spawning inundate bare substratum to which bream eggs may attach better than to deeper substratum covered by epilithon. Consequently, the water level increase prior to spawning should determine the amount of pristine spawning substratum available to bream and thus influence their breeding success. In order to test this hypothesis, the influence of hydrology and climate on the abundance of age-0 bream was combined with the results from field investigations on the egg survival and abundance of age-0 bream. A strong positive correlation between the mean water level increase during the spawning season of bream (April–May) and the abundance of juvenile bream was found. In contrast, the absolute water level during spawning and during the nursery stage in summer, the cumulative temperature during the egg, larval and juvenile stages and two North Atlantic Oscillation (NAO) indices did not affect the abundance of juvenile bream. The field investigations confirmed that bream eggs attach better to and have higher survival rates on bare substratum than on substratum with epilithon cover. Accordingly, eggs within a spawning habitat of bream were most abundant between 10 and 20 cm depth, where the epilithon cover was lower than at depths exceeding 30 cm. The results of this study confirm an adverse influence of epilithon cover on the attachment and subsequent survival of bream eggs and emphasize the importance of spring inundations for the successful breeding of the bream. Handling editor: J. A. Cambray     

Syntheses and structures of mononuclear manganese(II) complexes bearing bis(1-methylimidazol-2-yl)ketone ligands

The ligand bis(1-methylimidazol-2-yl)ketone (bik) (1) was applied in the synthesis of mononuclear manganese(II) complexes. The complexes [Mn(bik)₂Cl₂] (2), [Mn(bik)₂(OH₂)Br]Br × H₂O (3b) and [Mn(bik)₃](ClO₄) (4) were characterised by X-ray crystallography, ESR and UV-Vis methods.     

Docking and scoring with alternative side-chain conformations

We describe a scoring and modeling procedure for docking ligands into protein models that have either modeled or flexible side-chain conformations. Our methodical contribution comprises a procedure for generating new potentials of mean force for the ROTA scoring function which we have introduced previously for optimizing side-chain conformations with the tool IRECS. The ROTA potentials are specially trained to tolerate small-scale positional errors of atoms that are characteristic of (i) side-chain conformations that are modeled using a sparse rotamer library and (ii) ligand conformations that are generated using a docking program. We generated both rigid and flexible protein models with our side-chain prediction tool IRECS and docked ligands to proteins using the scoring function ROTA and the docking programs FlexX (for rigid side chains) and FlexE (for flexible side chains). We validated our approach on the forty screening targets of the DUD database. The validation shows that the ROTA potentials are especially well suited for estimating the binding affinity of ligands to proteins. The results also show that our procedure can compensate for the performance decrease in screening that occurs when using protein models with side chains modeled with a rotamer library instead of using X-ray structures. The average runtime per ligand of our method is 168 seconds on an Opteron V20z, which is fast enough to allow virtual screening of compound libraries for drug candidates.     

How to monitor elusive lizards: comparison of capture–recapture methods on giant day geckos (Gekkonidae, Phelsuma madagascariensis grandis) in the Masoala rainforest exhibit, Zurich Zoo

Rapid and reliable estimation of population size is needed for the efficient monitoring of animal populations of conservation concern. Unfortunately, technical advances in this area have not been paralleled in uptake in conservation, which may be due to difficulties in implementation or the lack of general guidelines for application. Here we tested five different methods used to estimate population size [capture–mark–recapture (CMR), finite-mixture models, model averaging of finite-mixture models, accumulation curve methods (ACM), and the line transect method (LT)] using extensive capture–recapture data of the giant day gecko (Gekkonidae, Phelsuma madagascariensis grandis, Gray 1870) at the Masoala rainforest exhibit, Zurich Zoo. When the complete data were analyzed [30 sessions (and 27 sessions for the LT)], all methods except the LT produced similar estimates of population size. The simple ACM gave a small coefficient of variation (CV), but did not cover the most likely value of population size at moderate sampling effort. Nevertheless, the ACM was the only method that showed a reasonable convergence when subsets of data were used. CMR and Pledger models included the reference value in their confidence intervals (CI) after 25 and 30 sessions, respectively. Although model averaging did slightly improve the estimate, the CV was still high for the full dataset. Our method of using subsets of data to test the robustness of estimates is simple to apply and could be adopted more widely in such analyzes to evaluate sensitivity to method of evaluation. In conclusion, simple accumulation methods showed similar efficiency to more complex statistical models, and are likely to be sufficiently precise for most conservation monitoring purposes. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Realities in breed improvement programmes for dairy goats in East and Central Africa

Increasing population pressure, land scarcity and diminishing production resources are promoting goat production in the tropics. Dairy goat breeding (DGB) projects have been implemented by development agencies, governments and the private sector with the objective of improving the dairy merits genetically through crossbreeding with exotic genotypes. The performance of these projects is still a cause for concern. Therefore, sustainable dairy goat breeding forces various stakeholders to re-orient their breeding goals, strategies and design of breeding programmes towards a sustainability perspective. This paper highlights a set of key requirements for establishing sustainable dairy goat breeding programmes. Conclusions are drawn based on the lessons learnt from numerous examples of DGB projects in East and Central Africa keeping sustainability concerns insight to inform on-going and future projects.     

Toward visualization of nanomachines in their native cellular environment

The cellular nanocosm is made up of numerous types of macromolecular complexes or biological nanomachines. These form functional modules that are organized into complex subcellular networks. Information on the ultra-structure of these nanomachines has mainly been obtained by analyzing isolated structures, using imaging techniques such as X-ray crystallography, NMR, or single particle electron microscopy (EM). Yet there is a strong need to image biological complexes in a native state and within a cellular environment, in order to gain a better understanding of their functions. Emerging methods in EM are now making this goal reachable. Cryo-electron tomography bypasses the need for conventional fixatives, dehydration and stains, so that a close-to-native environment is retained. As this technique is approaching macromolecular resolution, it is possible to create maps of individual macromolecular complexes. X-ray and NMR data can be ‘docked’ or fitted into the lower resolution particle density maps to create a macromolecular atlas of the cell under normal and pathological conditions. The majority of cells, however, are too thick to be imaged in an intact state and therefore methods such as ‘high pressure freezing’ with ‘freeze-substitution followed by room temperature plastic sectioning’ or ‘cryo-sectioning of unperturbed vitreous fully hydrated samples’ have been introduced for electron tomography. Here, we review methodological considerations for visualizing nanomachines in a close-to-physiological, cellular context. EM is in a renaissance, and further innovations and training in this field should be fully supported. Robert Feulgen Lecture 2009 presented at the 51st symposium of the Society for Histochemistry in Stubai, Austria, October 7–10, 2009.     

A hybrid life cycle assessment model for comparison with conventional methodologies in Australia

Background, aim, and scope  

One barrier to the further implementation of LCA as a quantitative decision-support tool is the uncertainty created by the diversity of available analytical approaches. This paper compares conventional (‘process analysis’) and alternative (‘input–output analysis’) approaches to LCA, and presents a hybrid LCA model for Australia that overcomes the methodological limitations of process and input–output analysis and enables a comparison between the results achieved using each method. A case study from the water industry illustrates this comparison.