Biology subjects

Hartley, M.

Publications and source records attributed to Hartley, M..

8 recordsLinked to original sources

bioRxiv2025

Chart Builder: An Interactive Tool for User Driven Data Visualization in the Electron Microscopy Data Bank

The cryogenic sample-electron microscopy (cryoEM) field has generated significant amounts of 3D Electron Microscopy (3DEM) volumetric data and associated metadata, now comprehensively archived in the Electron Microscopy Data Bank (EMDB - www.emdatabank.org) and the Electron Microscopy Public Image Archive (EMPIAR - www.empiar.org). Harnessing the full potential of these resources requires robust, flexible, and publicly accessible tools for data exploration, analysis and retrieval. Here, we present Chart Builder, an interactive web-based platform that enables researchers to create customizable, publication-quality visualizations directly from archival metadata, validation assessments, and cross-reference annotations. Chart Builder integrates the same query-driven and flexible Solr search system as EMDB search, into a user interface with tools to assist users to filter, group, and compare data without programming expertise. It supports multiple chart types (including line, bar, area, scatter (2D and 3D), histogram, bubble, pie, geographic and Venn diagrams) with customizable axes, data series, and statistical operators. Users can apply global filters, define temporal, categorical, or custom query-based axes, and explore multi-dimensional relationships interactively. Chart data-points are linked to their underlying datasets, such that visualisation interaction opens entry-level or archive-level search results for inspection and datasets from charts may be exported in several ways. Findability, accessibility, interoperability and reusability of data are facilitated by these direct access and export mechanisms, including HTML embedding, persistent URL sharing and chart/data download options. By combining interactivity and ease of use with up-to-date access to the EMDB and EMPIAR archive metadata, both computational and experimental communities may explore and visualize current metadata and export to formats for further analysis or as publication-ready figures. Chart Builder promotes community-driven data analysis and empowers users to evaluate trends in the biological 3DEM field. Chart Builder is freely accessible and fully integrated into the EMDB website at https://www.ebi.ac.uk/emdb/statistics/builder/.

biophysics↗

bioRxiv2023

OME-Zarr: a cloud-optimized bioimaging file format with international community support

A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the cloud-optimized format itself - OME-Zarr - along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain -- the file format that underlies so many personal, institutional, and global data management and analysis tasks.

bioinformatics↗

bioRxiv2022

Integrating analog and digital modes of gene expression at Arabidopsis FLC

Quantitative gene regulation at the cell population-level can be achieved by two fundamentally different modes of regulation at individual gene copies. A "digital" mode involves binary ON/OFF expression states, with population-level variation arising from the proportion of gene copies in each state, while an "analog" mode involves graded expression levels at each gene copy. At the Arabidopsis floral repressor FLOWERING LOCUS C (FLC), "digital" Polycomb silencing is known to facilitate quantitative epigenetic memory in response to cold. However, whether FLC regulation before cold involves analog or digital modes is unknown. Using quantitative fluorescent imaging of FLC mRNA and protein, together with mathematical modelling, we find that FLC expression before cold is regulated by both analog and digital modes. We observe a temporal separation between the two modes, with analog preceding digital. The analog mode can maintain intermediate expression levels at individual FLC gene copies, before subsequent digital silencing, consistent with the copies switching OFF stochastically and heritably without cold. This switch leads to a slow reduction in FLC expression at the cell population-level. These data present a new paradigm for gradual repression, elucidating how analog transcriptional and digital epigenetic memory pathways can be integrated.

molecular biology↗

bioRxiv2022

Species identification of early colonial bone artefacts excavated from Pyrmont, Australia, by mass spectrometric identification of collagen peptides

Zooarchaeology by Mass Spectrometry (ZooMS) is a rapidly developing and increasingly utilised peptide mass fingerprinting (PMF) technique that analyses Collagen 1A1 and 1A2 marker peptides for the genus- or species-level identification of fragmentary bones in the archaeological record. Traditionally, this analysis is performed using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF-MS) to identify characteristic m/z values of known marker peptides. Here we present data on the application of a modified ZooMS approach, using nanoflow liquid chromatography - tandem mass spectrometry proteomics, to the analysis of a collection of six early colonial Australian (early to mid-19th Century CE) worked bone artefacts, believed to be mostly knife handles, excavated from a site in Pyrmont, Sydney, Australia in 2017. We were successfully able to identify characteristic marker peptides for bovine COL1A1 and COL1A2 in all six bone artefacts.

biochemistry↗

bioRxiv2022

A scalable phenotyping approach for female floral organ development and senescence in the absence of pollination in wheat

In the absence of pollination, female reproductive organs senesce leading to an irrevocable loss in the reproductive potential of the flower and directly affecting seed set. In self-pollinating crops like wheat (Triticum aestivum), the post-anthesis viability of the unpollinated carpel has been overlooked, despite its importance for hybrid seed production systems. To advance our knowledge of carpel development in the absence of pollination, we created a relatively high-throughput phenotyping approach to quantify stigma and ovary morphology. We demonstrate the suitability of the approach, which is based on light microscopy imaging and machine learning, for the detailed study of floral organ traits in field grown plants using both fresh and fixed samples. We show that the unpollinated carpel undergoes a well-defined initial growth phase, followed by a peak phase (in which stigma area reaches its maximum and the radial expansion of the ovary slows), and a final deterioration phase. These developmental dynamics were largely consistent across years and could be used to classify male sterile cultivars, however the absolute duration of each phase varied across years. This phenotyping approach provides a new tool for examining carpel morphology and development which we hope will help advance research into this field and increase our mechanistic understanding of female fertility in wheat.

plant biology↗

bioRxiv2021

The BioImage Archive - home of life-sciences microscopy data

Despite the huge impact of data resources in genomics and structural biology, until now there has been no central archive for biological data for all imaging modalities. The BioImage Archive is a new data resource at the European Bioinformatics Institute (EMBL-EBI) designed to fill this gap. In its initial development BioImage Archive accepts bioimaging data associated with publications, in any format, from any imaging modality from the molecular to the organism scale, excluding medical imaging. The BioImage Archive will ensure reproducibility of published studies that derive results from image data and reduce duplication of effort. Most importantly, the BioImage Archive will help scientists to generate new insights through reuse of existing data to answer new biological questions, and provision of training, testing and benchmarking data for development of tools for image analysis. The archive is available at https://www.ebi.ac.uk/bioimage-archive/. HighlightsO_LIThe BioImage Archive is a new archival data resource at the European Bioinformatics Institute (EMBL-EBI). C_LIO_LIThe BioImage Archive aims to accept all biological imaging data associated with peer-reviewed publications using approaches that probe biological structure, mechanism and dynamics, as well as other important datasets that can serve as reference examples for particular biological or technical domains. C_LIO_LIThe BioImage Archive aims to encourage the use of valuable imaging data, to improve reproducibility of published results that rely on image data, and to facilitate extraction of novel biological insights from existing data and development of new image analysis methods. C_LIO_LIThe BioImage Archive forms the foundation for an ecosystem of related databases, supporting those resources with storage infrastructure and indexing across databases. C_LIO_LIAcross this ecosystem, the BioImage Archive already stores and provides access to over 1.5 petabytes of image data from many different imaging modalities and biological domains. C_LIO_LIFuture development of the BioImage Archive will support the fast-emerging next generation file formats (NGFFs) for bioimaging data, providing access mechanisms tailored toward modern visualisation and data exploration tools, as well as unlocking the power of modern AI-based image-analysis approaches. C_LI

bioinformatics↗

bioRxiv2021

STARCH SYNTHASE 4 is required for normal starch granule initiation in amyloplasts of wheat endosperm

O_LIStarch granule initiation is poorly understood at the molecular level. The glucosyltransferase, STARCH SYNTHASE 4 (SS4), plays a central role in granule initiation in Arabidopsis leaves, but its function in cereal endosperms is unknown. We investigated the role of SS4 in wheat, which has a distinct spatiotemporal pattern of granule initiation during grain development. C_LIO_LIWe generated TILLING mutants in tetraploid wheat (Triticum turgidum) that are defective in both SS4 homoeologs. The morphology of endosperm starch was examined in developing and mature grains. C_LIO_LISS4 deficiency led to severe alterations in endosperm starch granule morphology. During early grain development, while the wild type initiated single A-type granules per amyloplast, most amyloplasts in the mutant formed compound granules due to multiple initiations. This phenotype was similar to mutants deficient in B-GRANULE CONTENT 1 (BGC1). SS4 deficiency also reduced starch content in leaves and pollen grains. C_LIO_LIWe propose that SS4 and BGC1 are required for the proper control of granule initiation during early grain development that leads to a single A-type granule per amyloplast. The absence of either protein results in a variable number of initiations per amyloplast and compound granule formation. C_LI

plant biology↗

bioRxiv2017

Morphometrics of complex cell shapes: Lobe Contribution Elliptic Fourier Analysis (LOCO-EFA)

Quantifying cell morphology is fundamental to the statistical study of cell populations, and can help us unravel mechanisms underlying cell and tissue morphogenesis. Current methods, however, require extensive human intervention, are highly sensitive to parameter choice, or produce metrics that are difficult to interpret biologically. We therefore developed a novel method, Lobe Contribution Elliptical Fourier Analysis (LOCO-EFA), which generates from digitalised cell outlines meaningful descriptors that can be directly matched to morphological features. We show that LOCO-EFA provides a tool to phenotype efficiently and objectively populations of cells by applying it to the complex shaped pavement cells of Arabidopsis thaliana wild type and speechless leaves. To further validate our method, we analysed computer-generated tissues, where cell shape can be specified in a controlled manner. LOCO-EFA quantifies deviations between the specified shape that an individual in silico cell takes up when in isolation and the resultant shape when they are allowed to interact within a confluent tissue, thereby assessing the role of cell-cell interactions on population cell shape distributions.\n\nSummary statement\n\nNovel method (LOCO-EFA) quantifies complex cell shapes, extracting meaningful biological features such as protrusion number and amplitude; here shown for plant pavement cells and validated on in silico tissues.

developmental biology↗