Biology subjects

Swedlow, J. R.

Publications and source records attributed to Swedlow, J. R..

14 recordsLinked to original sources

bioRxiv2026

The Shape of Biological Metadata: Measuring Repository Richness with Entity-Based NLP Metrics

Ensuring the availability and accessibility of research data is fundamental to advancing knowledge, as codified in the FAIR principles (Findable, Accessible, Interoperable, and Reusable). Accurate metadata documentation is indispensable for meeting these principles; however, entries in deposition databases often contain inadequate, repetitive, or incomplete descriptions. Much of this metadata is captured in free-text fields, motivating the need for scalable, repository-agnostic methods to quantify metadata richness. Here, we quantify free-text metadata richness across three repositories using Natural Language Processing (NLP) methods: BioDare2, an experimental circadian rhythm database; DataShare, a domain-agnostic University of Edinburgh database; and Image Data Resource (IDR), a public repository of biological image datasets from published studies. In general, repositories exhibit distinct distributions of word count and information density, consistent with differences in scope. Named-entity recognition and information-density metrics detected significant category-level differences in BioDare2 (species) and DataShare (communities), while identifying greater consistency in the more curated IDR. The most frequent entities reflected each repository's focus: circadian terminology in BioDare2, microscopy-related entities in IDR, and community-driven terms in DataShare. We develop a scalable framework utilising word counts, named-entity recognition, and entity-derived information density to assess metadata quality across repositories, offering a broadly applicable evaluation tool.

bioinformatics↗

bioRxiv2025

IDR searcher: a search engine solution for public image resource

We introduce the IDR searcher, an open-source search engine designed to ease the exploration of datasets hosted in public bioimaging resources. The application offers a fast, efficient, cost-effective solution for datasets discovery and has the potential to address current disparities in finding quality datasets for exploratory research and to provide the foundation for cross-resource search.

bioinformatics↗

bioRxiv2025

PHD1-dependent hydroxylation of RepoMan (CDCA2) on P604 modulates the control of mitotic progression

Prolyl-hydroxylases (PHDs) are oxygen sensing enzymes that mediate the hydroxylation of proline residues. In mammals, three PHD isoforms (PHD1-3) are responsible for proline hydroxylation of Hypoxia Inducible Factor (HIF) alpha, a key regulator of the hypoxia response. In the accompanying paper (Jiang et. al., 2025) we report development of a mass spectrometry-based method to reliably identify proline hydroxylation (OH-Pro) sites on proteins and use this to identify a PHD-dependent OH-Pro modification at Pro604 on the protein RepoMan (CDCA2), a regulatory subunit for protein phosphatase PP1{gamma}, with important roles in mitotic progression and cell viability. Here, we investigate the functional significance of hydroxylation of RepoMan at P604. During M phase, the PP1-RepoMan complex dephosphorylates Thr3 of Histone H3 (H3T3) on chromosomes arms to ensure the correct localisation of the chromosomal passenger complex (CPC) at centromeres. We show that siRNA depletion of PHD1, but not PHD2, increases H3T3 phosphorylation in prometaphase-arrested cells. In cells depleted of endogenous RepoMan, exogenous expression of wild type RepoMan, but not a RepoMan P604A mutant, restored normal H3T3 phosphorylation localisation in prometaphase arrested cells. RepoMan P604 is located proximal to the Short Linear Motifs (SLiMs) that function as binding sites for the serine/threonine Protein Phosphatase 2A (PP2A). The interaction of RepoMan and PP2A-B56{gamma} is reduced in cells expressing RepoMan P604A. Moreover, analyses in both fixed and live cells released from a prometaphase arrest, show that expression of the RepoMan P604A mutant delays completion of mitosis, results in defects in chromosome alignment and segregation and increases levels of cell death. These data support a role for PHD1-mediated prolyl hydroxylation in controlling progression through mitosis, acting, at least in part, via hydroxylation of RepoMan at P604 regulating the interaction of RepoMan with PP2A during chromosome alignment and thereby controlling the levels of Histone H3 phosphorylation at Thr3.

cell biology↗

bioRxiv2023

Sperm Cell Painting: A Mechanism Driven Approach for Drug Discovery in Human Spermatozoa

We have adapted the cell painting assay developed by Carpenter and colleagues on cultured U2OS cells to human spermatozoa. In Sperm Cell Painting (SCP) we assemble an image-based quantitative fingerprint of the functional state of sperm. We use this assay to gain insight into the mechanism of action of compounds that modify sperm function and as a platform for contraceptive discovery.

cell biology↗

bioRxiv2023

Systematic characterization of site-specific proline hydroxylation using hydrophilic interaction chromatography and mass spectrometry

We have developed a robust workflow for the identification of proline hydroxylation sites in proteins, using a combination of hydrophilic interaction chromatography (HILIC) enrichment and high-resolution nano-Liquid Chromatography-Mass Spectrometry (LC-MS) together with refining and filtering parameters during data analysis. Using this approach, we have combined data from cell lines treated with either the prolyl hydroxylase (PHD) inhibitor, Roxadustat (FG-4592), or with the proteasome inhibitor MG-132, or with a DMSO control, to identify a total of 4,993 and 3,247 proline hydroxylation sites, respectively, in HEK293 and RCC4 cells. A subset of 1,954 (HEK293) and 1,253 (RCC4) non-collagen proline hydroxylation sites with high confidence were inhibited by FG-4592 treatment. Features characteristic of proline hydroxylated peptides were identified, which were consistent between the HEK293 and RCC4 datasets. The more hydrophilic HILIC fractions were enriched in peptides containing hydroxylated proline residues, which showed characteristic differences in charge and mass distribution, as compared with either unmodified, or oxidised peptides. Furthermore, we discovered that the intensity of the diagnostic hydroxyproline immonium ion was dependent upon parameters including the MS collision energy setting, parent peptide concentration and the sequence of amino acids adjacent to the modified proline. We show using synthetic peptides that a combination of retention time in LC and optimised MS parameter settings allows reliable identification of proline hydroxylation sites in peptides, even when multiple prolines residues are present. Focussing on proteins in which newly identified proline hydroxylation sites were inhibited by the pan-PHD inhibitor, FG-4592, showed enrichment for proteins involved in metabolism of RNA, mRNA splicing and cell cycle regulation, including the protein phosphatase 1 regulatory subunit, Repo-Man (CDCA2). We show that Repo-Man is hydroxylated at P604 and in the accompanying study by Druker et al. 1, we present a combination of cellular and biochemical evidence that hydroxylation of Repo-Man at P604 is important for its function in controlling mitotic progression.

biochemistry↗

bioRxiv2023

Screening for variable drug responses using human iPSC cohorts

We have developed a laboratory-based drug screening platform that uses a cohort of human induced pluripotent stem cell (hiPSC) lines, derived from different donors, to predict variable drug responses of potential clinical relevance. This builds on recent findings that pluripotent hiPSC lines express a broad repertoire of gene transcripts and proteins, whose expression levels reflect the genetic identity of the donor. We demonstrate that a cohort of hiPSC lines from different donors can be screened efficiently in their pluripotent state, using high-throughput Cell Painting assays. Variable phenotypic responses between hiPSC lines were detected with a wide range of clinically approved drugs, in use across multiple disease areas. Furthermore, information on mechanisms of drug-cell interactions underlying the observed variable responses was derived by using quantitative proteomic analysis to compare sets of hiPSC lines that had been stratified objectively, based upon variable response, Cell Painting data. We propose that information derived from comparative drug screening, using curated libraries of hiPSC lines from different donors, can help to improve the delivery of safe new drugs suitable for a broad range of genetic backgrounds and sexual diversity within human populations.

cell biology↗

bioRxiv2023

Sperm Toolbox - A selection of small molecules to study human spermatozoa

Male contraceptive options and infertility treatments are limited. To help overcome these limitations we established a small molecule library as a toolbox for assay development and screening campaigns using human spermatozoa. We have profiled all compounds in our automated high-throughput screening platform and provide the dataset, which allows direct side-by-side comparisons of compound effects and assays using live human spermatozoa.

pharmacology and toxicology↗

bioRxiv2022

Nucleome Browser: An integrative and multimodal data navigation platform for 4D Nucleome

We introduce Nucleome Browser (http://www.nucleome.org), an interactive, multimodal data visualization and exploration platform for 4D Nucleome research. Our tool effectively integrates heterogeneous datasets (e.g., genomics, imaging, 3D genome structure models, and single-cell data) and external data portals by a new adaptive communication mechanism. Nucleome Browser provides a scalable solution for integrating massive amounts of 4D Nucleome data to navigate multiscale nuclear structure and function in a wide range of biological contexts, enabling hypothesis generation and data sharing with the broad community.

bioinformatics↗

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

Compounds enhancing human sperm motility identified using a high-throughput phenotypic screening platform

Study questionCan a high-throughput screening platform facilitate male fertility drug discovery? Summary answerA high-throughput screening platform identified a large number of compounds that enhanced sperm motility. What is known alreadySeveral efforts to find small molecules modulating sperm function have been performed but not using high-throughput technology. Study design, size, durationHealthy donor semen samples were used and samples were pooled (3-5 donors per pool). Primary screening was performed in singlicate; dose-response screening was performed in duplicate (independent donor pools). Participants/materials, setting, methodsSpermatozoa isolated from healthy donors were prepared by density gradient centrifugation and incubated in 384-well plates with compounds (6.25 uM) to identify those compounds with enhancing effects on motility. A total of [~]17,000 compounds from the following libraries: ReFRAME, Prestwick, Tocris, LOPAC, CLOUD and MMV Pathogen Box were screened. Dose response experiments of screening hits were performed to confirm the enhancing effect on sperm motility. Experiments were performed in a University setting. Main results and the role of chanceFrom our primary single concentration screening, 105 compounds elicited an enhancing effect on sperm motility compared to DMSO treated wells. Confirmed enhancing compounds were grouped based on their annotated targets/target classes. A major target class, phosphodiesterase inhibitors, were identified in particular PDE10A inhibitors as well as number of compounds not previously identified/known to enhance human sperm motility such as those related to GABA signaling. Limitations, reasons for cautionCompounds have been tested with prepared donor spermatozoa and only incubated for a short period of time. Therefore, the effect of compounds on whole semen or with longer incubation time may be different. All experiments were performed in vitro. Wider implications of the findingsThis phenotypic screening assay identified a large number of compounds that increased sperm motility. In addition to furthering our understanding of human sperm function, for example identifying new avenues for discovery, we highlight potential inhibitors as promising start-point for a medicinal chemistry programme for potential enhancement of male infertility. Moreover, with disclosure of the results of screening we present a substantial resource to inform further work in the field Study funding/competing interest(s)This study was supported by the Bill and Melinda Gates Foundation and Scottish Funding Council and Scottish Universities Life Science Alliance.

physiology↗

bioRxiv2021

OME-NGFF: scalable format strategies for interoperable bioimaging data

Biological imaging is one of the most innovative fields in the modern biological sciences. New imaging modalities, probes, and analysis tools appear every few months and often prove decisive for enabling new directions in scientific discovery. One feature of this dynamic field is the need to capture new types of data and data structures. While there is a strong drive to make scientific data Findable, Accessible, Interoperable and Reproducible (FAIR 1), the rapid rate of innovation in imaging impedes the unification and adoption of standardized data formats. Despite this, the opportunities for sharing and integrating bioimaging data and, in particular, linking these data to other "omics" datasets have never been greater. Therefore, to every extent possible, increasing "FAIRness" of bioimaging data is critical for maximizing scientific value, as well as for promoting openness and integrity. In the absence of a common, FAIR format, two approaches have emerged to provide access to bioimaging data: translation and conversion. On-the-fly translation produces a transient representation of bioimage metadata and binary data but must be repeated on each use. In contrast, conversion produces a permanent copy of the data, ideally in an open format that makes the data more accessible and improves performance and parallelization in reads and writes. Both approaches have been implemented successfully in the bioimaging community but both have limitations. At cloud-scale, those shortcomings limit scientific analysis and the sharing of results. We introduce here next-generation file formats (NGFF) as a solution to these challenges.

bioinformatics↗

bioRxiv2019

Community Standards for Open Cell Migration Data

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited due to the diversity of experimental protocols and non-standardised output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardised data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardisation efforts by the Cell Migration Standardisation Organization, CMSO, an open community-driven organisation to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools, and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration.

bioinformatics↗

bioRxiv2019

Numerically enhanced adaptive optics-based 3D STED microscopy for deep-tissue super-resolved imaging

In stimulated emission depletion (STED) nanoscopy, the major origin of decreased signal-to-noise ratio within images can be attributed to sample photobleaching and strong optical aberrations. This is due to STED utilising both a high power depletion laser (increasing risk of photodamage), while the depletion beam is very sensitive to sample-induced aberrations. Here we demonstrate a custom-built 3D STED microscope with automated aberration correction that is capable of 3D super-resolution imaging through thick, highly aberrating, tissue. We introduce and investigate image denoising by block-matching and collaborative filtering (BM3D) to numerically enhance fine object details otherwise mixed with noise. Numerical denoising provides an increase in the final effective resolution of the STED imaging of 31% using the well-established Fourier ring correlation metric. Experimental validation of the proposed method is achieved through super-resolved 3D imaging of axons in differentiated induced pluripotent stem cells growing under a 80{micro}m thick layer of tissue with lateral and axial resolution of 256nm and 300nm, respectively.

biophysics↗

bioRxiv2017

The Ndc80 complex targets Bod1 to human mitotic kinetochores

Regulation of protein phosphatase activity by endogenous protein inhibitors is an important mechanism to control protein phosphorylation in cells. We recently identified Biorientation defective 1 (Bod1) as a small protein inhibitor of PP2A-B56. This phosphatase controls the amount of phosphorylation of mitotic kinetochore proteins and thus the establishment of load-bearing chromosome-spindle attachments in time for accurate separation of sister chromatids in mitosis. The PP2A-B56 regulatory protein Bod1 directly localises to mitotic kinetochores and is required for correct segregation of mitotic chromosomes. In this report, we have probed the spatio-temporal regulation of Bod1 during mitotic progression. Kinetochore localisation of Bod1 increases from nuclear envelope breakdown until metaphase. Phosphorylation of Bod1 at threonine 95 (T95), which increases Bod1s binding and inhibition of PP2A-B56, peaks in prometaphase, when PP2A-B56 localisation to kinetochores is highest. Kinetochore targeting of Bod1 depends on the outer kinetochore protein Ndc80 and not PP2A-B56. Additionally, Bod1 depletion leads to a defect in the phosphorylation kinetics of Ndc80 at serine 55 (S55) within its N-terminus. Therefore, Ndc80 recruits a phosphatase inhibitor to kinetochores which directly feeds forward to regulate Ndc80 phosphorylation and the stability of the attachments of microtubules to kinetochores.

cell biology↗