Major Changes in the Ecology of the Wadden Sea: Human Impacts, Ecosystem Engineering and Sediment Dynamics

Shallow soft-sediment systems are mostly dominated by species that, by strongly affecting sediment dynamics, modify their local environment. Such ecosystem engineering species can have either sediment-stabilizing or sediment-destabilizing effects on tidal flats. They interplay with abiotic forcing conditions (wind, tide, nutrient inputs) in driving the community structure and generating spatial heterogeneity, determining the composition of different communities of associated species, and thereby affecting the channelling of energy through different compartments in the food web. This suggests that, depending on local species composition, tidal flats may have conspicuously different geomorphology and biological functions under similar external conditions. Here we use a historical reconstruction of benthic production in the Wadden Sea to construct a framework for the relationships between human impacts, ecosystem engineering and sediment dynamics. We propose that increased sediment disturbances by human exploitation interfere with biological controls of sediment dynamics, and thereby have shifted the dominant compartments of both primary and secondary production in the Wadden Sea, transforming the intertidal from an internally regulated and spatially heterogeneous, to an externally regulated and spatially homogenous system. This framework contributes to the general understanding of the interaction between biological and environmental control of ecosystem functioning, and suggests a general framework for predicting effects of human impacts on soft-bottom ecosystems.     

The bacterial genus Collimonas: mycophagy,weathering and other adaptive solutions to life in oligotrophic soil environments

This minireview provides a synopsis of past and present research on the biology and ecology of members of the bacterial genus Collimonas. From the distribution, abundance and functional behaviours of these so‐called collimonads emerges a general picture of bacterial adaptation to low‐nutrient soil environments. Among these adaptations is the ability to extract nutrients from living fungi (mycophagy) and from rocks and minerals (weathering). This unique combination of properties will be discussed in the context of other interactions that collimonads have with their biotic and abiotic surroundings, such as the ability to inhibit fungal growth (fungistasis), protect plant roots from fungal disease (biocontrol), and degrade natural polymers and synthetic pollutants (biodegradation). Future research on Collimonas is expected to take advantage of the genomic tools and resources that are becoming available to uncover and describe the genes and gene functions that distinguish this group of bacteria and are the basis for its phenotypes. Potential applications of collimonads include the control of unwanted fungi, for example in agriculture, their use as biological indicators of soil quality and fertility, and as a source of bioactive compounds.     

Large scale comparison of global gene expression patterns in human and mouse

Background  

It is widely accepted that orthologous genes between species are conserved at the sequence level and perform similar functions in different organisms. However, the level of conservation of gene expression patterns of the orthologous genes in different species has been unclear. To address the issue, we compared gene expression of orthologous genes based on 2,557 human and 1,267 mouse samples with high quality gene expression data, selected from experiments stored in the public microarray repository ArrayExpress.     

Different HLA-DRB1 allele distributions in distinct clinical subgroups of sarcoidosis patients

Background

A strong genetic influence by the MHC class II region has been reported in sarcoidosis, however in many studies with different results. This may possibly be caused by actual differences between distinct ethnic groups, too small sample sizes, or because of lack of accurate clinical subgrouping.

Subjects and methods

In this study we HLA typed a large patient population (n = 754) recruited from one single centre. Patients were sub-grouped into those with Löfgren''s syndrome (LS) (n = 302) and those without (non-Löfgren''s) (n = 452), and the majority of them were clinically classified into those with recovery within two years (resolving) and those with signs of disease for more than two years (non-resolving). PCR was used for determination of HLA-DRB1 alleles. Swedish healthy blood donors (n = 1366) served as controls.

Results

There was a dramatic difference in the distribution of HLA alleles in LS compared to non-LS patients (p = 4 × 10^-36). Most notably, DRB1*01, DRB1*03 and DRB1*14, clearly differed in LS and non-LS patients. In relation to disease course, DRB1*07, DRB1*14 and DRB1*15 generally associated with, while DRB1*01 and DRB1*03 protected against, a non-resolving disease. Interestingly, the clinical influence of DRB1*03 (good prognosis) dominated over that of DRB1*15 (bad prognosis).

Conclusions

We found several significant differences between LS and non-LS patients and we therefore suggest that genetic association studies in sarcoidosis should include a careful clinical characterisation and sub-grouping of patients, in order to reveal true genetic associations. This may be particularly accurate to do in the heterogeneous non-LS group of patients.     

L<Subscript>2</Subscript>-norm multiple kernel learning and its application to biomedical data fusion

Background  

This paper introduces the notion of optimizing different norms in the dual problem of support vector machines with multiple kernels. The selection of norms yields different extensions of multiple kernel learning (MKL) such as L _∞, L ₁, and L ₂ MKL. In particular, L ₂ MKL is a novel method that leads to non-sparse optimal kernel coefficients, which is different from the sparse kernel coefficients optimized by the existing L _∞ MKL method. In real biomedical applications, L ₂ MKL may have more advantages over sparse integration method for thoroughly combining complementary information in heterogeneous data sources.     

Thyroid receptor ligands. Part 5: novel bicyclic agonist ligands selective for the thyroid hormone receptor beta

Based on the examination of the crystal structure of rat TRbeta complexed with 3,5,3'-triiodo-l-thyronine (2) a novel TRbeta-selective indole derivative 6b was prepared and tested in vitro. This compound was found to be 14 times selective for TRbeta over TRalpha in binding and its beta-selectivity could be rationalized through the comparison of the X-ray crystallographic structures of 6b complexed with TRalpha and TRbeta.     

Investigation of mechanism-based thrombin inhibitors: Implications of a highly conserved water molecule for the binding of coumarins within the S pocket

The synthesis of novel coumarins bearing on the lateral side chain in the 3-position an amine or a guanidine group is described. In vitro evaluation highlighted 14d which possesses a meta aniline side chain as a very potent THR inhibitor. Surprisingly, the introduction of a guanidine moiety always led to a decrease in THR inhibiting properties. We, thus, used docking experiments to rationalize the SAR in the series. This study showed the crucial role of a conserved water molecule in the specificity pocket of THR during docking simulation in order to explain the inactivity of guanidine derivatives.     

Binding mode of new (thio)hydantoin inhibitors of fatty acid amide hydrolase: comparison with two original compounds, OL-92 and JP104

Substituted (thio)hydantoins (2-thioxoimidazolidinones and imidazolidinediones) were reported as new potential reversible inhibitors of fatty acid amide hydrolase (FAAH). Their binding mode to FAAH was explored to rationalize their activity and give idea to design highly active inhibitors. Starting from the crystal structure of one of these molecules, docking studies provide us with rational basis for the design of new inhibitors within the thiohydantoin family.