LoQAtE--Localization and Quantitation ATlas of the yeast proteomE. A new tool for multiparametric dissection of single-protein behavior in response to biological perturbations in yeast.

Living organisms change their proteome dramatically to sustain a stable internal milieu in fluctuating environments. To study the dynamics of proteins during stress, we measured the localization and abundance of the Saccharomyces cerevisiae proteome under various growth conditions and genetic backgrounds using the GFP collection. We created a database (DB) called 'LoQAtE' (Localizaiton and Quantitation Atlas of the yeast proteomE), available online at http://www.weizmann.ac.il/molgen/loqate/, to provide easy access to these data. Using LoQAtE DB, users can get a profile of changes for proteins of interest as well as querying advanced intersections by either abundance changes, primary localization or localization shifts over the tested conditions. Currently, the DB hosts information on 5330 yeast proteins under three external perturbations (DTT, H₂O₂ and nitrogen starvation) and two genetic mutations [in the chaperonin containing TCP1 (CCT) complex and in the proteasome]. Additional conditions will be uploaded regularly. The data demonstrate hundreds of localization and abundance changes, many of which were not detected at the level of mRNA. LoQAtE is designed to allow easy navigation for non-experts in high-content microscopy and data are available for download. These data should open up new perspectives on the significant role of proteins while combating external and internal fluctuations

Identification of intergeneric and synthetic spring wheat lines with resistance to Fusarium head blight

Non-Peer ReviewedFusarium head blight (FHB) is a serious disease in many cereal crops worldwide, as it can drastically reduce both yield and quality in infected crops. Resistance to FHB is therefore a desirable trait for incorporation into new wheat cultivars. Wild relatives are a source of new genetic variation and have been shown to enhance disease resistance when hybridized with wheat. This research has focused on evaluating intergeneric and interspecific wheat lines for resistance to FHB. Intergeneric hybrids of wheat (Triticum aestivum) and Agropyron repens syn. Elytrigia repens, and synthetic wheat lines produced at CIMMYT, were evaluated under greenhouse conditions for resistance to FHB caused by Fusarium graminearum. Approximately 35% of the intergeneric lines and 15% of the synthetic lines consistently displayed moderate to high levels of Type II resistance. Pollen staining was conducted to determine the fertility levels of the intergeneric lines. 79% of the F3 lines and 72% of the F5 and F6 lines displayed fertility levels above 75%. Control cultivars displayed fertility levels ranging from 88-94%. Generally, lines that rated as moderately to highly resistant were also highly fertile. These lines could be of significant value in wheat breeding programs aimed at integrating new sources of resistance to Fusarium head blight

A survey of visualisation for live cell imaging

Live cell imaging is an important biomedical research paradigm for studying dynamic cellular behaviour. Although phenotypic data derived from images are difficult to explore and analyse, some researchers have successfully addressed this with visualisation. Nonetheless, visualisation methods for live cell imaging data have been reported in an ad hoc and fragmented fashion. This leads to a knowledge gap where it is difficult for biologists and visualisation developers to evaluate the advantages and disadvantages of different visualisation methods, and for visualisation researchers to gain an overview of existing work to identify research priorities. To address this gap, we survey existing visualisation methods for live cell imaging from a visualisation research perspective for the first time. Based on recent visualisation theory, we perform a structured qualitative analysis of visualisation methods that includes characterising the domain and data, abstracting tasks, and describing visual encoding and interaction design. Based on our survey, we identify and discuss research gaps that future work should address: the broad analytical context of live cell imaging; the importance of behavioural comparisons; links with dynamic data visualisation; the consequences of different data modalities; shortcomings in interactive support; and, in addition to analysis, the value of the presentation of phenotypic data and insights to other stakeholders

Metadata management for high content screening in OMERO

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org

High-throughput ultrastructure screening using electron microscopy and fluorescent barcoding.

Genetic screens using high-throughput fluorescent microscopes have generated large datasets, contributing many cell biological insights. Such approaches cannot tackle questions requiring knowledge of ultrastructure below the resolution limit of fluorescent microscopy. Electron microscopy (EM) reveals detailed cellular ultrastructure but requires time-consuming sample preparation, limiting throughput. Here we describe a robust method for screening by high-throughput EM. Our approach uses combinations of fluorophores as barcodes to uniquely mark each cell type in mixed populations and correlative light and EM (CLEM) to read the barcode of each cell before it is imaged by EM. Coupled with an easy-to-use software workflow for correlation, segmentation, and computer image analysis, our method, called "MultiCLEM," allows us to extract and analyze multiple cell populations from each EM sample preparation. We demonstrate several uses for MultiCLEM with 15 different yeast variants. The methodology is not restricted to yeast, can be scaled to higher throughput, and can be used in multiple ways to enable EM to become a powerful screening technique.This work was financially supported by grants from the Deutsche Forschungsgemeinschaft (SFB1129 Z2 to J.A.G. Briggs), EMBL (to J.A.G. Briggs), the Medical Research Council (MC_UP_1201/16 to J.A.G. Briggs), and the German Ministry of Education and Research (031A605 to K.R. Patil). The Schuldiner laboratory is supported by the European Research Council CoG 646604 Peroxisystem, the Deutsche Forschungsgemeinschaft (grant SFB1190 and a Deutsch-Israelische Projektkooperation [DIP] collaborative grant). N. Gabrielli was supported by the EMBL interdisciplinary postdoctoral program. M. Schuldiner is an incumbent of the Dr. Gilbert Omenn and Martha Darling Professorial Chair in Molecular Genetics

A new geological map of the Lau Basin (southwestern Pacific Ocean) reveals crustal growth processes in arc-backarc systems

A 1:1,000,000-scale lithostratigraphic assemblage map of the Lau Basin (southwestern Pacific Ocean) has been created using remote predictive mapping (RPM) techniques developed by geological surveys on land. Formation-level geological units were identified in training sets at scales of 1:100,000–1:200,000 in different parts of the basin and then extrapolated to the areas where geological data are sparse. The final compilation is presented together with a quantitative analysis of assemblage-level crustal growth based on area-age relationships of the assigned units. The data sets used to develop mapping criteria and an internally consistent legend for the compilation included high-resolution ship-based multibeam, satellite- and ship-based gravity, magnetics, seafloor imaging, and sampling data. The correlation of units was informed by published geochronological information and kinematic models of basin opening. The map covers >1,000,000 km2 of the Lau-Tonga arc-backarc system, subdivided into nine assemblage types: forearc crust (9% by area), crust of the active volcanic arc (7%), backarc rifts and spreading centers (20%), transitional arc-backarc crust (13%), relict arc crust (38%), relict backarc crust (8%), and undivided arc-backarc assemblages (<5%), plus oceanic assemblages, intraplate volcanoes, and carbonate platforms. Major differences in the proportions of assemblage types compared to other intraoceanic subduction systems (e.g., Mariana backarc, North Fiji Basin) underscore the complex geological makeup of the Lau Basin. Backarc crust formed and is forming simultaneously at 12 different locations in the basin in response to widely distributed extension, and this is considered to be a dominant pattern of crustal accretion in large arc-backarc systems. Accelerated basin opening and a microplate breakout north of the Peggy Ridge has been accommodated by seven different spreading centers. The result is an intricate mosaic of small intact assemblages in the north of the basin, compared to fewer and larger assemblages in the south. Although the oldest rocks are Eocene (~40 m.y. old basement of the Lau and Tonga Ridges), half of the backarc crust in the map area formed within the last 3 m.y. and therefore represents some of the fastest growing crust on Earth, associated with prolific magmatic and hydro-thermal activity. These observations provide important clues to the geological evolution and makeup of ancient backarc basins and to processes of crustal growth that ultimately lead to the emergence of continents

Synthetic protein interactions reveal a functional map of the cell

To understand the function of eukaryotic cells, it is critical to understand the role of protein-protein interactions and protein localization. Currently, we do not know the importance of global protein localization nor do we understand to what extent the cell is permissive for new protein associations – a key requirement for the evolution of new protein functions. To answer this question, we fused every protein in the yeast Saccharomyces cerevisiae with a partner from each of the major cellular compartments and quantitatively assessed the effects upon growth. This analysis reveals that cells have a remarkable and unanticipated tolerance for forced protein associations, even if these associations lead to a proportion of the protein moving compartments within the cell. Furthermore, the interactions that do perturb growth provide a functional map of spatial protein regulation, identifying key regulatory complexes for the normal homeostasis of eukaryotic cells. DOI: http://dx.doi.org/10.7554/eLife.13053.00