Reconsidering environmental effects assessment of chemicals: Proposal for a dynamic testing strategy

Certain substances may be hazardous to ecosystems. To be able to preserve the structures and functions of ecosystems, knowledge is required to qualify and quantify such hazards. To this end, biotests are indispensable tools. For the development and/or choice of biotests, special attention has to be drawn to conflicts between scientific demands and practical constraints. From a purely scientific point of view, experiments should be designed to maximise the ecological relevance of the obtained results. However, this often collides with the limited resources (budget, time, manpower) available. Furthermore, societal issues (e.g. animal welfare) have to be taken into account. Thus, it is necessary to develop a scientifically sound testing approach that avoids unnecessary animal testing, keeps the costs low, and can be performed within a short timeframe. The different perspectives of ecology, environmental toxicology, and environmental chemistry should be integrated into a balanced ecotoxicological approach. Accordingly, we propose a dynamic testing strategy, which is adapted to the substance (or substance group) in question and its mode(s) of action.     

Base Excision by Thymine DNA Glycosylase Mediates DNA-Directed Cytotoxicity of 5-Fluorouracil

5-Fluorouracil (5-FU), a chemotherapeutic drug commonly used in cancer treatment, imbalances nucleotide pools, thereby favoring misincorporation of uracil and 5-FU into genomic DNA. The processing of these bases by DNA repair activities was proposed to cause DNA-directed cytotoxicity, but the underlying mechanisms have not been resolved. In this study, we investigated a possible role of thymine DNA glycosylase (TDG), one of four mammalian uracil DNA glycosylases (UDGs), in the cellular response to 5-FU. Using genetic and biochemical tools, we found that inactivation of TDG significantly increases resistance of both mouse and human cancer cells towards 5-FU. We show that excision of DNA-incorporated 5-FU by TDG generates persistent DNA strand breaks, delays S-phase progression, and activates DNA damage signaling, and that the repair of 5-FU–induced DNA strand breaks is more efficient in the absence of TDG. Hence, excision of 5-FU by TDG, but not by other UDGs (UNG2 and SMUG1), prevents efficient downstream processing of the repair intermediate, thereby mediating DNA-directed cytotoxicity. The status of TDG expression in a cancer is therefore likely to determine its response to 5-FU–based chemotherapy.     

Mechanical Network in Titin Immunoglobulin from Force Distribution Analysis

The role of mechanical force in cellular processes is increasingly revealed by single molecule experiments and simulations of force-induced transitions in proteins. How the applied force propagates within proteins determines their mechanical behavior yet remains largely unknown. We present a new method based on molecular dynamics simulations to disclose the distribution of strain in protein structures, here for the newly determined high-resolution crystal structure of I27, a titin immunoglobulin (IG) domain. We obtain a sparse, spatially connected, and highly anisotropic mechanical network. This allows us to detect load-bearing motifs composed of interstrand hydrogen bonds and hydrophobic core interactions, including parts distal to the site to which force was applied. The role of the force distribution pattern for mechanical stability is tested by in silico unfolding of I27 mutants. We then compare the observed force pattern to the sparse network of coevolved residues found in this family. We find a remarkable overlap, suggesting the force distribution to reflect constraints for the evolutionary design of mechanical resistance in the IG family. The force distribution analysis provides a molecular interpretation of coevolution and opens the road to the study of the mechanism of signal propagation in proteins in general.     

Overexpression of the lens epithelium-derived growth factor/p75 integrase binding domain inhibits human immunodeficiency virus replication

We initially identified lens epithelium-derived growth factor/p75 (LEDGF/p75) as a binding partner of human immunodeficiency virus type 1 (HIV-1) integrase. To investigate the role of LEDGF/p75 in HIV replication and its potential as a new antiviral target, we stably overexpressed two different fragments containing the integrase binding domain (IBD) of LEDGF/p75 fused to enhanced green fluorescent protein (eGFP). HIV-1 replication was severely inhibited by overexpression of the eGFP-IBD fusion proteins, while no inhibition was observed in cell lines overexpressing the interaction-deficient D366A mutant. Quantitative PCR pinpointed the block to the integration step, whereas nuclear import was not affected. Competition of the IBD fusion proteins with endogenous LEDGF/p75 for binding to integrase led to a potent defect in HIV-1 replication in both HeLaP4- and MT-4-derived cell lines. A previously described diketo acid-resistant HIV-1 strain remained fully susceptible to inhibition, suggesting that this strategy will also work in patients who harbor strains resistant to the current experimental integrase inhibitors. These data support LEDGF/p75 as an important cofactor for HIV replication and provide proof of concept for the LEDGF/p75-integrase interaction as a novel target for treating HIV-1 infection.     

Effects of light or dark phase testing on behavioural and cognitive performance in DBA mice

Behavioural experiments in mice are often carried out during the resting phase of these nocturnal animals. Ignoring the fact that mice are more active during the dark period, results from resting-phase testing has also been used to characterize these animals. Since the influence of the light/dark cycle on testing is likely to be a relevant factor for the analysis of behavioural results, the aim of this study was to evaluate the effects of the relative time of the day as well as light conditions during testing on behavioural and cognitive performance in inbred mice. Na?ve DBA/2N (DBA) mice were tested in the modified hole board (mHB) either during the dark phase under red light or during the light phase under white light. Different behavioural dimensions and cognitive functions were evaluated in parallel. Depending on the testing conditions, the results showed significant differences in behavioural activity, with DBA mice being less inhibited during dark phase. The same experimental group made fewer memory errors in a visuo-spatial task and showed a faster habituation compared with the group tested during the dark phase. From the results we conclude that testing during the light phase induces a pronounced behavioural inhibition as well as a cognitive disruption in DBA mice, which should be taken into account when cognitively testing these animals.     

SCFFbxw5 targets kinesin‐13 proteins to facilitate ciliogenesis

Microtubule depolymerases of the kinesin‐13 family play important roles in various cellular processes and are frequently overexpressed in different cancer types. Despite the importance of their correct abundance, remarkably little is known about how their levels are regulated in cells. Using comprehensive screening on protein microarrays, we identified 161 candidate substrates of the multi‐subunit ubiquitin E3 ligase SCF^Fbxw5, including the kinesin‐13 member Kif2c/MCAK. In vitro reconstitution assays demonstrate that MCAK and its closely related orthologs Kif2a and Kif2b become efficiently polyubiquitylated by neddylated SCF^Fbxw5 and Cdc34, without requiring preceding modifications. In cells, SCF^Fbxw5 targets MCAK for proteasomal degradation predominantly during G₂. While this seems largely dispensable for mitotic progression, loss of Fbxw5 leads to increased MCAK levels at basal bodies and impairs ciliogenesis in the following G₁/G₀, which can be rescued by concomitant knockdown of MCAK, Kif2a or Kif2b. We thus propose a novel regulatory event of ciliogenesis that begins already within the G₂ phase of the preceding cell cycle.     

One-Way Allosteric Communication between the Two Disulfide Bonds in Tissue Factor

Tissue factor (TF) is a transmembrane glycoprotein that plays distinct roles in the initiation of extrinsic coagulation cascade and thrombosis. TF contains two disulfide bonds, one each in the N-terminal and C-terminal extracellular domains. The C-domain disulfide, Cys186-Cys209, has a ?RHStaple configuration in crystal structures, suggesting that this disulfide carries high pre-stress. The redox state of this disulfide has been proposed to regulate TF encryption/decryption. Ablating the N-domain Cys49-Cys57 disulfide bond was found to increase the redox potential of the Cys186-Cys209 bond, implying an allosteric communication between the domains. Using molecular dynamics simulations, we observed that the Cys186-Cys209 disulfide bond retained the ?RHStaple configuration, whereas the Cys49-Cys57 disulfide bond fluctuated widely. The Cys186-Cys209 bond featured the typical ?RHStaple disulfide properties, such as a longer S-S bond length, larger C-S-S angles, and higher bonded prestress, in comparison to the Cys49-Cys57 bond. Force distribution analysis was used to sense the subtle structural changes upon ablating the disulfide bonds, and allowed us to identify a one-way allosteric communication mechanism from the N-terminal to the C-terminal domain. We propose a force propagation pathway using a shortest-pathway algorithm, which we suggest is a useful method for searching allosteric signal transduction pathways in proteins. As a possible explanation for the pathway being one-way, we identified a pronounced lower degree of conformational fluctuation, or effectively higher stiffness, in the N-terminal domain. Thus, the changes of the rigid domain (N-terminal domain) can induce mechanical force propagation to the soft domain (C-terminal domain), but not vice versa.     

Spatiotemporal variability of grassland vegetation cover in a catchment in Inner Mongolia, China, derived from MODIS data products

Conditions, distribution and development of vegetation in semi arid regions are highly variable. In this study we detected the temporal and spatial variability of vegetation in the Xilin river catchment from 2000 to 2008 by analysis of Moderate Resolution Imaging Spectroradiometer (MODIS) data products of that period. The study is based on LAI (Leaf area index) and supported by NDVI (Normalized difference vegetation index) and LST (Land surface temperature) data with a spatial resolution of 1 km. The mean LAI of the catchment from 2000 to 2008 is 0.59. Precipitation data of the study period governs the conditions and distribution of vegetation in the catchment. In dry years, e.g. 2001 and 2005, LAI was clearly lower (0.52) compared to 2003 (LAI?=?0.72) which was a wet year. As precipitation generally decreases from south-east to north-west, LAI values decrease according to this gradient. The influence of heavy grazing in the vicinity of the Xilin river is obvious as LAI is low (0.4) in these areas. The high temporal variability of the LAI is displayed by its high mean CV (coefficient of variation) which is 48% for the observed years. The analysis of sample areas illustrates temporal and spatial differences in vegetation development within the catchment and shows a generally delayed growth start in the north-west of the catchment.     

In Vitro DNA Tethering of HIV-1 Integrase by the Transcriptional Coactivator LEDGF/p75

Although LEDGF/p75 is believed to act as a cellular cofactor of lentiviral integration by tethering integrase (IN) to chromatin, there is no good in vitro model to analyze this functionality. We designed an AlphaScreen assay to study how LEDGF/p75 modulates the interaction of human immunodeficiency virus type 1 IN with DNA. IN bound with similar affinity to DNA mimicking the long terminal repeat or to random DNA. While LEDGF/p75 bound DNA strongly, a mutant of LEDGF/p75 with compromised nuclear localization signal (NLS)/AT hook interacted weakly, and the LEDGF/p75 PWWP domain did not interact, corroborating previous reports on the role of NLS and AT hooks in charge-dependent DNA binding. LEDGF/p75 stimulated IN binding to DNA 10-fold to 30-fold. Stimulation of IN-DNA binding required a direct interaction between IN and the C-terminus of LEDGF/p75. Addition of either the C-terminus of LEDGF/p75 (amino acids 325-530) or LEDGF/p75 mutated in the NLS/AT hooks interfered with IN binding to DNA. Our results are consistent with an in vitro model of LEDGF/p75-mediated tethering of IN to DNA. The inhibition of IN-DNA interaction by the LEDGF/p75 C-terminus may provide a novel strategy for the inhibition of HIV IN activity and may explain the potent inhibition of HIV replication observed after the overexpression of C-terminal fragments in cell culture.