Human protein reference database—2006 update

Human Protein Reference Database (HPRD) () was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein–protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest database for literature-derived protein–protein interactions (>30 000) and PTMs (>8000) for human proteins. We have also introduced several new features in HPRD including: (i) protein isoforms, (ii) enhanced search options, (iii) linking of pathway annotations and (iv) integration of a novel browser, GenProt Viewer (), developed by us that allows integration of genomic and proteomic information. With the continued support and active participation by the biomedical community, we expect HPRD to become a unique source of curated information for the human proteome and spur biomedical discoveries based on integration of genomic, transcriptomic and proteomic data

Investigating the consistency of extracellular vesicle production from breast cancer subtypes using CELLine adherent bioreactors

Abstract Extracellular vesicle (EV) research has grown rapidly in recent years, largely due to the potential use of EVs as liquid biopsy biomarkers or therapeutics. However, in‐depth characterisation and validation of EVs produced using conventional in vitro cultures can be challenging due to the large area of cell monolayers and volumes of culture media required. To overcome this obstacle, multiple bioreactor designs have been tested for EV production with varying success, but the consistency of EVs produced over time in these systems has not been reported previously. In this study, we demonstrate that several breast cancer cell lines of different subtypes can be cultured simultaneously in space, resource, and time efficient manner using CELLine AD 1000 systems, allowing the consistent production of vast amounts of EVs for downstream experimentation. We report an improved workflow used for inoculating, maintaining, and monitoring the bioreactors, their EV production, and the characterisation of the EVs produced. Lastly, our proteomic analyses of the EVs produced throughout the lifetime of the bioreactors show that core EV‐associated proteins are relatively consistent, with few minor variations over time, but that tracking the production of EVs is a convenient method to indirectly monitor the bioreactor and consistency of the yielded EVs. These findings will aid future studies requiring the simultaneous production of large amounts of EVs from several cell lines of different subtypes of a disease and other EV biomanufacturing applications

Statistics pertaining to HPRD growth, experimental types for protein–protein interactions and a breakdown of PTMs

<p><b>Copyright information:</b></p><p>Taken from "Human protein reference database—2006 update"</p><p>Nucleic Acids Research 2005;34(Database issue):D411-D414.</p><p>Published online 28 Dec 2005</p><p>PMCID:PMC1347503.</p><p>© The Author 2006. Published by Oxford University Press. All rights reserved</p> () Growth of HPRD over the last 3 years with respect to protein entries, protein–protein interactions and PTMs. () Distribution of protein–protein interactions in HPRD based on the type of the experimental method. () Distribution of various types of PTMs in HPRD. The percentage of the respective PTM is indicated only when it is greater than or equal to 2