Sequential and compartmentalized action of Rabs, SNAREs, and MAL in the apical delivery of fusiform vesicles in urothelial umbrella cells

Uroplakins (UPs) are major differentiation products of urothelial umbrella cells and play important roles in forming the permeability barrier and in the expansion/stabilization of the apical membrane. Further, UPIa serves as a uropathogenic Escherichia coli receptor. Although it is understood that UPs are delivered to the apical membrane via fusiform vesicles (FVs), the mechanisms that regulate this exocytic pathway remain poorly understood. Immunomicroscopy of normal and mutant mouse urothelia show that the UP-delivering FVs contained Rab8/11 and Rab27b/Slac2-a, which mediate apical transport along actin filaments. Subsequently a Rab27b/Slp2-a complex mediated FV–membrane anchorage before SNARE-mediated and MAL-facilitated apical fusion. We also show that keratin 20 (K20), which forms a chicken-wire network ∼200 nm below the apical membrane and has hole sizes allowing FV passage, defines a subapical compartment containing FVs primed and strategically located for fusion. Finally, we show that Rab8/11 and Rab27b function in the same pathway, Rab27b knockout leads to uroplakin and Slp2-a destabilization, and Rab27b works upstream from MAL. These data support a unifying model in which UP cargoes are targeted for apical insertion via sequential interactions with Rabs and their effectors, SNAREs and MAL, and in which K20 plays a key role in regulating vesicular trafficking

Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation

BACKGROUND: High-throughput experiments, such as with DNA microarrays, typically result in hundreds of genes potentially relevant to the process under study, rendering the interpretation of these experiments problematic. Here, we propose and evaluate an approach to find functional associations between large numbers of genes and other biomedical concepts from free-text literature. For each gene, a profile of related concepts is constructed that summarizes the context in which the gene is mentioned in literature. We assign a weight to each concept in the profile based on a likelihood ratio measure. Gene concept profiles can then be clustered to find related genes and other concepts. RESULTS: The experimental validation was done in two steps. We first applied our method on a controlled test set. After this proved to be successful the datasets from two DNA microarray experiments were analyzed in the same way and the results were evaluated by domain experts. The first dataset was a gene-expression profile that characterizes the cancer cells of a group of acute myeloid leukemia patients. For this group of patients the biological background of the cancer cells is largely unknown. Using our methodology we found an association of these cells to monocytes, which agreed with other experimental evidence. The second data set consisted of differentially expressed genes following androgen receptor stimulation in a prostate cancer cell line. Based on the analysis we put forward a hypothesis about the biological processes induced in these studied cells: secretory lysosomes are involved in the production of prostatic fluid and their development and/or secretion are androgen-regulated processes. CONCLUSION: Our method can be used to analyze DNA microarray datasets based on information explicitly and implicitly available in the literature. We provide a publicly available tool, dubbed Anni, for this purpose

Rab27a and Rab27b control different steps of the exosome secretion pathway

Exosomes are secreted membrane vesicles that share structural and biochemical characteristics with intraluminal vesicles of multivesicular endosomes (MVEs). Exosomes could be involved in intercellular communication and in the pathogenesis of infectious and degenerative diseases. The molecular mechanisms of exosome biogenesis and secretion are, however, poorly understood. Using an RNA interference (RNAi) screen, we identified five Rab GTPases that promote exosome secretion in HeLa cells. Among these, Rab27a and Rab27b were found to function in MVE docking at the plasma membrane. The size of MVEs was strongly increased by Rab27a silencing, whereas MVEs were redistributed towards the perinuclear region upon Rab27b silencing. Thus, the two Rab27 isoforms have different roles in the exosomal pathway. In addition, silencing two known Rab27 effectors, Slp4 (also known as SYTL4, synaptotagmin-like 4) and Slac2b (also known as EXPH5, exophilin 5), inhibited exosome secretion and phenocopied silencing of Rab27a and Rab27b, respectively. Our results therefore strengthen the link between MVEs and exosomes, and introduce ways of manipulating exosome secretion in vivo

Thousands of Rab GTPases for the Cell Biologist

Rab proteins are small GTPases that act as essential regulators of vesicular trafficking. 44 subfamilies are known in humans, performing specific sets of functions at distinct subcellular localisations and tissues. Rab function is conserved even amongst distant orthologs. Hence, the annotation of Rabs yields functional predictions about the cell biology of trafficking. So far, annotating Rabs has been a laborious manual task not feasible for current and future genomic output of deep sequencing technologies. We developed, validated and benchmarked the Rabifier, an automated bioinformatic pipeline for the identification and classification of Rabs, which achieves up to 90% classification accuracy. We cataloged roughly 8.000 Rabs from 247 genomes covering the entire eukaryotic tree. The full Rab database and a web tool implementing the pipeline are publicly available at www.RabDB.org. For the first time, we describe and analyse the evolution of Rabs in a dataset covering the whole eukaryotic phylogeny. We found a highly dynamic family undergoing frequent taxon-specific expansions and losses. We dated the origin of human subfamilies using phylogenetic profiling, which enlarged the Rab repertoire of the Last Eukaryotic Common Ancestor with Rab14, 32 and RabL4. Furthermore, a detailed analysis of the Choanoflagellate Monosiga brevicollis Rab family pinpointed the changes that accompanied the emergence of Metazoan multicellularity, mainly an important expansion and specialisation of the secretory pathway. Lastly, we experimentally establish tissue specificity in expression of mouse Rabs and show that neo-functionalisation best explains the emergence of new human Rab subfamilies. With the Rabifier and RabDB, we provide tools that easily allows non-bioinformaticians to integrate thousands of Rabs in their analyses. RabDB is designed to enable the cell biology community to keep pace with the increasing number of fully-sequenced genomes and change the scale at which we perform comparative analysis in cell biology

Reactive magnetron cosputtering of hard and conductive ternary nitride thin films: Ti-Zr-N and Ti-Ta-N

Ternary transition metal nitride thin films, with thickness up to 300 nm, were deposited by dc reactive magnetron cosputtering in Ar-N(2) plasma discharges at 300 degrees C on Si substrates. Two systems were comparatively studied, Ti-Zr-N and Ti-Ta-N, as representative of isostructural and nonisostructural prototypes, with the aim of characterizing their structural, mechanical, and electrical properties. While phase-separated TiN-ZrN and TiN-TaN are the bulk equilibrium states, Ti(1-x)Zr(x)N and Ti(1-y)Ta(y)N solid solutions with the Na-Cl (B1-type) structure could be stabilized in a large compositional range (up to x=1 and y=0.75, respectively). Substituting Ti atoms by either Zr or Ta atoms led to significant changes in film texture, microstructure, grain size, and surface morphology, as evidenced by x-ray diffraction, x-ray reflectivity, and scanning electron and atomic force microscopies. The ternary Ti(1-y)Ta(y)N films exhibited superior mechanical properties to Ti(1-x)Zr(x)N films as well as binary compounds, with hardness as high as 42 GPa for y=0.69. All films were metallic, the lowest electrical resistivity rho similar to 65 mu Omega cm being obtained for pure ZrN, while for Ti(1-y)Ta(y)N films a minimum was observed at y similar to 0.3. The evolution of the different film properties is discussed based on microstructrural investigations. (c) 2010 American Vacuum Society

Tribological Properties at 20 and 500°C of TiN and CrN Cathodic ARC Coatings Deposited on Ti-6Al-4V Alloy

Tribological properties of TiN and CrN coatings deposited by cathodic arc method at three different bias potentials -50, -150 and -300V on Ti-6Al-4V alloy in pair with alumina have been investigated. X-ray diffraction analysis showed that single-phase textured cubic nitrides of TiN and CrN were formed in these coatings. It is shown that the friction coefficient of the coatings is practically equal to that established for the Ti6Al4V alloy, but the wear rate is more than an order of magnitude lower than for the titanium alloy substrate. Coatings deposited at a potential of -50 V show optimal tribological properties at temperatures 20 and 500°C. Friction coefficients for TiN coatings are 0.4-0.8 at 20°C and 0,75 at 500°C; for CrN coatings they are 0.5 at 20°C and 0,7 at 500°C. Wear rates for TiN coatings are 0.86·10-5 мм3/Нм at 20°C and 3.56·10-5 мм3/Нм at 500°C; for CrN coatings they are 1.43·10-5 мм3/Нм at 20°C and 7.13·10-5 мм3/Нм at 500°C