ORCID Profile
0000-0003-3537-4806
Current Organisations
CSIRO Black Mountain Laboratories
,
CSIRO
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Publisher: Springer Netherlands
Date: 1998
Publisher: Oxford University Press (OUP)
Date: 17-01-2014
DOI: 10.1093/BIOINFORMATICS/BTU024
Abstract: Motivation: Rich collections of bio ersity information such as spatial distributions, species descriptions and trait data are now synthesized in publicly available online sources such as GBIF. Also phylogenetic knowledge now provides a sound understanding of the origin of organisms and their place in the tree of life. We demonstrate with PhyloJIVE that any phylogenetic tree can be linked to online bio ersity data in the browser. This evolutionary view of bio ersity data is demonstrated in a case study that suggests that this approach may be useful to scientists and non-experts users. Contact: joe@acaciamulga.net Supplementary information: Supplementary data are available at Bioinformatics online.
Publisher: Elsevier BV
Date: 1999
DOI: 10.1016/S0145-305X(98)00049-4
Abstract: We have employed a COS cell expression cloning procedure to isolate a full length cDNA clone encoding a hagfish leukocyte-associated membrane protein (HLMP1). The protein, which is identified by a monoclonal antibody (JB3) generated in our laboratory, is present on the majority of hagfish leukocytes and is also expressed on erythrocytes. The cDNA clone contained an open reading frame encoding a 120 residue polypeptide which exhibits 33% amino acid sequence identity with the precursor protein of human CD59, a leukocyte-associated membrane protein which regulates the action of the complement membrane attack complex on homologous cells. CD59 belongs to a family of structurally related glycoproteins which includes the Ly-6 proteins expressed on mouse lymphocytes. In addition to significant overall sequence homology HLMP1 shows conservation of 8 key cysteine residues with members of the CD59/Ly-6 family. Comparison of the hagfish sequence with that of the mature human CD59 protein suggested a processed protein consisting of 74 amino acids associated with the cell membrane via a GPI anchor. The latter was confirmed by immuno-flow cytometry following treatment of transfected COS cells with phospholipase. Phylogenetic analysis and tissue distribution of this protein in the hagfish are consistent with HLMP1 being a homologue of CD59. A three-dimensional model of HLMP1, constructed using the NMR-determined structure for human CD59 as a template, indicated conservation of a core structure of five strands of beta-sheet and a short helix stabilised by four disulfide bonds. These findings, when taken together with our previous identification of C5a-like chemotactic activity in LPS-activated serum, provide indirect evidence for the existence of the terminal lytic complement pathway (C5 to C9) in these primitive vertebrates.
Publisher: Pensoft Publishers
Date: 23-08-2022
DOI: 10.3897/BISS.6.91415
Abstract: Currently, genomics data for living species are stored in public and private repositories online. These repositories remain largely disconnected and only partially findable. The Australian Reference Genome Atlas (ARGA) Project is solving the problem of genomics data obscurity by creating an online platform where life sciences researchers can comprehensively and confidently search for data for taxa relevant to Australian research. At its most basic, ARGA is a tool for aggregating and indexing publicly available genomics (and genetics) data. We aim to improve the experience of discovering and accessing this data by building search functionality, based on features such as phenotypic traits and predicted and observed species distributions, and supporting data packaging and transfer to analysis environments. ARGA will index GenBank (National Institutes of Health (NIH), USA), the European Nucleotide Archive (EMBL-ENA), the database of Bioplatforms Australia, and selected DNA repositories in Australian faunal collections and herbaria. We will integrate these records with the occurrence records and taxonomic framework of the Atlas of Living Australia (ALA) to enrich the data and make it searchable using taxonomy, location, ecological characteristics and selected phenotypic data. The chief aims and outputs for the project are to: create a system to enable contextual metadata about a species to be used as a pointer to a variety of genomic data associated with that species add functionality to that system to enable additional contextual information groupings, and community curation of these created groupings create a user-facing web-accessible interface for the system and devise a mechanism that allows the researchers searching the multiple genomic repositories, via ARGA, to select files for subsequent analysis and export them to other cloud-based analysis infrastructure. create a system to enable contextual metadata about a species to be used as a pointer to a variety of genomic data associated with that species add functionality to that system to enable additional contextual information groupings, and community curation of these created groupings create a user-facing web-accessible interface for the system and devise a mechanism that allows the researchers searching the multiple genomic repositories, via ARGA, to select files for subsequent analysis and export them to other cloud-based analysis infrastructure. Our approach to ARGA incorporates: ingesting species metadata from multiple sequence repositories into a consistent data format using Darwin Core Archive (DwC-A) processing metadata using the Pipelines system developed by the Global Bio ersity Information Facility (GBIF), and as implemented in the ALA and other Living Atlases. indexing metadata using a Solr search engine and providing a front-end web interface for users to find, select and export sequence files to a number of cloud-based analysis platforms. ingesting species metadata from multiple sequence repositories into a consistent data format using Darwin Core Archive (DwC-A) processing metadata using the Pipelines system developed by the Global Bio ersity Information Facility (GBIF), and as implemented in the ALA and other Living Atlases. indexing metadata using a Solr search engine and providing a front-end web interface for users to find, select and export sequence files to a number of cloud-based analysis platforms. Here we will present an overview of the ARGA infrastructure and demonstrate an early prototype of the platform. We will show how ARGA can be used to interrogate DNA sequence records for taxa relevant to Australian research questions, realising a vision where genomics-based solutions to biological questions in conservation, ecology, agriculture and biosecurity can be manifested.
Location: Australia
No related grants have been discovered for Nicholas dos Remedios.