RanBP2/Nup358 provides a major binding site for NXF1-p15 dimers at the nuclear pore complex and functions in nuclear mRNA export

Metazoan NXF1-p15 heterodimers promote the nuclear export of bulk mRNA across nuclear pore complexes (NPCs). In vitro, NXF1-p15 forms a stable complex with the nucleoporin RanBP2/Nup358, a component of the cytoplasmic filaments of the NPC, suggesting a role for this nucleoporin in mRNA export. We show that depletion of RanBP2 from Drosophila cells inhibits proliferation and mRNA export. Concomitantly, the localization of NXF1 at the NPC is strongly reduced and a significant fraction of this normally nuclear protein is detected in the cytoplasm. Under the same conditions, the steady-state subcellular localization of other nuclear or cytoplasmic proteins and CRM1-mediated protein export are not detectably affected, indicating that the release of NXF1 into the cytoplasm and the inhibition of mRNA export are not due to a general defect in NPC function. The specific role of RanBP2 in the recruitment of NXF1 to the NPC is highlighted by the observation that depletion of CAN/Nup214 also inhibits cell proliferation and mRNA export but does not affect NXF1 localization. Our results indicate that RanBP2 provides a major binding site for NXF1 at the cytoplasmic filaments of the NPC, thereby restricting its diffusion in the cytoplasm after NPC translocation. In RanBP2-depleted cells, NXF1 diffuses freely through the cytoplasm. Consequently, the nuclear levels of the protein decrease and export of bulk mRNA is impaired.     

Cadmium induces nuclear translocation of β-catenin and increases expression of <Emphasis Type="Italic">c-myc</Emphasis> and <Emphasis Type="Italic">Abcb1a</Emphasis> in kidney proximal tubule cells

Cadmium (Cd²⁺) induces renal proximal tubular (PT) damage, including disruption of the E-cadherin/β-catenin complex of adherens junctions (AJs) and apoptosis. Yet, chronic Cd²⁺ exposure causes malignant transformation of renal cells. Previously, we have demonstrated that Cd²⁺-mediated up-regulation of the multidrug transporter Abcb1 causes apoptosis resistance in PT cells. We hypothesized that Cd²⁺ activates adaptive signaling mechanisms mediated by β-catenin to evade apoptosis and increase proliferation. Here we show that 50 μM Cd²⁺, which induces cell death via apoptosis and necrosis, also causes a decrease of the trans-epithelial resistance of confluent WKPT-0293 Cl.2 cells, a rat renal PT cell model, within 45 min of Cd²⁺ exposure, as measured by electric cell-substrate impedance sensing. Immunofluorescence microscopy demonstrates Cd²⁺-induced decrease of E-cadherin at AJs and redistribution of β-catenin from the E-cadherin/β-catenin complex of AJs to cytosol and nuclei after 3 h. Immunoblotting confirms Cd²⁺-induced decrease of E-cadherin expression and translocation of β-catenin to cytosol and nuclei of PT cells. RT-PCR shows Cd²⁺-induced increase of expression of c-myc and of the isoform Abcb1a at 3 h. The data prove for the first time that Cd²⁺ induces nuclear translocation of β-catenin in PT cells. We speculate that Cd²⁺ activates β-catenin/T-cell factor signaling to trans-activate proliferation and apoptosis resistance genes and promote carcinogenesis of PT cells.     

Recognition of different nucleotide-binding sites in primary structures using a property-pattern approach

Consensus sequence patterns for beta-alpha-beta folds binding FAD, NAD and GTP were constructed on the basis of 11 steric and physicochemical properties. These property patterns permit detection and distinction of the respective nucleotide-binding sites on the basis of amino acid sequence analysis alone. The SWISS-PROT database (release 9) was screened with the three calculated patterns, and nucleotide-binding sites identified are presented. They correspond to existing structure data (if known). For the detected sequence segments we are able to predict the beta-alpha-beta motif as well as the respective binding sites. For some of the proteins so detected a nucleotide-binding capacity has not previously been reported.     

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation

Interactive Tree Of Life (iTOL) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. Trees can be interactively pruned and re-rooted. Various types of data such as genome sizes or protein domain repertoires can be mapped onto the tree. Export to several bitmap and vector graphics formats is supported. AVAILABILITY: iTOL is available at http://itol.embl.de     

Characterization of diverse plant communities in Aspen Parkland rangeland using LiDAR data

Question: How effective is high-resolution airborne LiDAR technology for quantifying biophysical characteristics of multiple community types within diverse rangeland environments? Location: Native Aspen Parkland vegetation in central Alberta, Canada. Methods: Vegetation within 117 reference plots stratified across eight types, including forest, shrubland, upland grassland and lowland meadow communities, were assessed in 2001 for the height, cover and density of vegetation within various strata (herb, shrub and tree layers). Actual ground data were subsequently compared against modelled values for each community type and strata derived from the analysis of airborne LiDAR data obtained in 2000. Results: LiDAR data were effective for quantifying vegetation height, cover and density of the overstory within closed- and open Populus forest communities. However, LiDAR measurements typically underestimated the height and cover of shrublands, as well as most of the herbaceous communities. Analysis of LiDAR intensity data indicated reflectance generally decreased as LiDAR sampling points moved upwards from the ground to the vegetation canopy. Conclusions: While LiDAR technology is useful for characterizing deciduous forest properties, the quantification of understory vegetation characteristics, as well as those of individual shrublands and grasslands, was more limiting. Further refinements in analysis methods are necessary to increase the reliability of characterizing these communities.     

A protocol for the update of references to scientific literature in biological databases

Entries in biological databases are usually linked to scientific references. To generate those links and to keep them up-to-date, database maintainers have to continuously scan the scientific literature to select references that are relevant for each single database entry. The continuous growth of both the corpus of scientific literature and the size of biological databases makes this task very hard. We present a protocol intended to assist the updating of an existing set of literature (abstract) links from a single database entry with new references. It consists of taking the set of MEDLINE neighbour references of the existing linked abstracts and evaluating their relevance according to the existing set of abstracts. To test the applicability of the algorithm, we did a simple benchmark of the system using the references associated with the entries of a protein domain database. Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful.