Apm4, the mu subunit of yeast AP-2 interacts with Pkc1, and mutation of the Pkc1 consensus phosphorylation site Thr176 inhibits AP-2 recruitment to endocytic sites.

The AP-2 endocytic adaptor has been extensively characterized in mammalian cells and is considered to play a role both in cargo binding and in formation of endocytic sites. However, despite our detailed knowledge of mechanistic aspects of endocytic complex assembly and disassembly in the model organism Saccharomyces cerevisiae, no function of AP-2 had been described in wild-type yeast under normal growth conditions. A recent study however revealed that disruption of the complex caused by deletion of the gene encoding its mu subunit (APM4) caused defects in cell polarity such that responses to pheromone, nutritional status and cell wall damage were affected. Furthermore, a homozygous deletion of the mu subunit gene in Candida albicans affected its ability to grow hyphae. Direct binding to the yeast cell wall stress sensor Mid2 was detected, and in an apm4 deletion strain Mid2 showed reduced re-localization to the mother bud neck region following cell wall damage with calcofluor or to the mating projection tip. Here we demonstrate an interaction between Apm4 and the yeast cell wall integrity pathway component Pkc1 and show that mutation of the predicted Pkc1 site in the Apm4 hinge region affects recruitment of the AP-2 complex to endocytic sites

Mems inertial power generators for biomedical applications

Accepted versio

A Four-Antigen Mixture for Rapid Assessment of Onchocerca volvulus Infection

Caused by the filarial parasite Onchocerca volvulus, onchocerciasis is a neglected tropical disease associated with blindness and severe dermatitis. Available diagnostic methods are either invasive, require hours or days to perform, and/or need sophisticated equipment to be conducted. Thus, there is an urgent need for simple and rapid technologies for the specific diagnosis of Onchocerca volvulus infection. Here we investigated whether luciferase immunoprecipitation systems (LIPS) can produce a more rapid and specific test for diagnosis of O. volvulus infection. Using modified versions of previously identified Onchocerca-specific antigens, LIPS tests detected antibodies to all four O. volvulus antigens and easily distinguished the O. volvulus-infected samples from uninfected samples. We also tested these four different antigens in a simpler format as a combined mixture and distinguished 100% of the confirmed cases from the uninfected controls. A rapid 15-minute version of this mixture test (QLIPS) also allowed distinction of 100% of the cases from those uninfected and performed even better in identifying Onchocerca from other cross-reactive parasitic infections. This study suggests that this rapid LIPS test (QLIPS) has the potential to be used in point-of-care detection of onchocerciasis and thereby may provide a new tool for diagnosis and the monitoring of transmission control measures

Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines.

Hundreds of genetically characterized cell lines are available for the discovery of genotype-specific cancer vulnerabilities. However, screening large numbers of compounds against large numbers of cell lines is currently impractical, and such experiments are often difficult to control. Here we report a method called PRISM that allows pooled screening of mixtures of cancer cell lines by labeling each cell line with 24-nucleotide barcodes. PRISM revealed the expected patterns of cell killing seen in conventional (unpooled) assays. In a screen of 102 cell lines across 8,400 compounds, PRISM led to the identification of BRD-7880 as a potent and highly specific inhibitor of aurora kinases B and C. Cell line pools also efficiently formed tumors as xenografts, and PRISM recapitulated the expected pattern of erlotinib sensitivity in vivo

Learning Relations from Social Tagging Data

An interesting research direction is to discover structured knowledge from user generated data. Our work aims to find relations among social tags and organise them into hierarchies so as to better support discovery and search for online users. We cast relation discovery in this context to a binary classification problem in supervised learning. This approach takes as input features of two tags extracted using probabilistic topic modelling, and predicts whether a broader-narrower relation holds between them. Experiments were conducted using two large, real-world datasets, the Bibsonomy dataset which is used to extract tags and their features, and the DBpedia dataset which is used as the ground truth. Three sets of features were designed and extracted based on topic distributions, similarity and probabilistic associations. Evaluation results with respect to the ground truth demonstrate that our method outperforms existing ones based on various features and heuristics. Future studies are suggested to study the Knowledge Base Enrichment from folksonomies and deep neural network approaches to process tagging data

Ferritins: furnishing proteins with iron

Ferritins are a superfamily of iron oxidation, storage and mineralization proteins found throughout the animal, plant, and microbial kingdoms. The majority of ferritins consist of 24 subunits that individually fold into 4-α-helix bundles and assemble in a highly symmetric manner to form an approximately spherical protein coat around a central cavity into which an iron-containing mineral can be formed. Channels through the coat at inter-subunit contact points facilitate passage of iron ions to and from the central cavity, and intrasubunit catalytic sites, called ferroxidase centers, drive Fe2+ oxidation and O2 reduction. Though the different members of the superfamily share a common structure, there is often little amino acid sequence identity between them. Even where there is a high degree of sequence identity between two ferritins there can be major differences in how the proteins handle iron. In this review we describe some of the important structural features of ferritins and their mineralized iron cores and examine in detail how three selected ferritins oxidise Fe2+ in order to explore the mechanistic variations that exist amongst ferritins. We suggest that the mechanistic differences reflect differing evolutionary pressures on amino acid sequences, and that these differing pressures are a consequence of different primary functions for different ferritins