81 research outputs found

    Pex3-mediated peroxisomal membrane contact sites in yeast

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    Cell organelles are compartments that occur in eukaryotic cells (for instance plant, animal or fungal cells). Recent studies indicated that cell organelles do not function in isolation, but extensively communicate and collaborate with each other. For these processes membrane contact sites are very important. Membrane contact sites are regions where two membranes form tight physical associations. These contact sites play roles in multiple important cellular processes, such as transport of various molecules like lipids, organelle formation and fission, organelle positioning and degradation. Peroxisomes are cell organelles that occur in almost all eukaryotic cells. Peroxisomes have been implicated in multiple functions including the detoxification of hydrogen peroxide and cellular lipid metabolism. In human, defects in peroxisome formation or function cause various symptoms and often are lethal. The research described in this thesis focuses on peroxisomal contact sites, using yeast as model organism. The research resulted in the identification of two novel contact sites, namely peroxisome-vacuole and peroxisome-plasma membrane contact sites. These contacts are important for peroxisomal membrane expansion and peroxisomal anchoring, respectively. The formation of both contacts require the peroxisomal membrane protein Pex3

    Novel Peroxisome–Vacuole Contacts in Yeast

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    Peroxisomes are important organelles and present in almost all eukaryotic cells. Close associations between peroxisomes and other cell compartments are known for several decades. The first molecular details of physical contacts between peroxisomes and various other organelles are now beginning to emerge. We recently described a novel contact between peroxisomes and vacuoles in the yeast Hansenula polymorpha, which develops during conditions of strong peroxisome proliferation. At such conditions, Pex3-GFP forms focal patches at the peroxisome–vacuole contacts, while overproduction of Pex3 promotes their formation. These results reveal a novel function for Pex3 in the formation of these contacts, where it might act as a tethering protein. We speculate that the peroxisome–vacuole contact is important for membrane lipid transfer at conditions of strong organellar expansion.</p

    Peroxisome retention involves Inp1-dependent peroxisome-plasma membrane contact sites in yeast

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    © 2020 Krikken et al.Retention of peroxisomes in yeast mother cells requires Inp1, which is recruited to the organelle by the peroxisomal membrane protein Pex3. Here we show that Hansenula polymorpha Inp1 associates peroxisomes to the plasma membrane. Peroxisome–plasma membrane contact sites disappear upon deletion of INP1 but increase upon INP1 overexpression. Analysis of truncated Inp1 variants showed that the C terminus is important for association to the peroxisome, while a stretch of conserved positive charges and a central pleckstrin homology-like domain are important for plasma membrane binding. In cells of a PEX3 deletion, strain Inp1-GFP localizes to the plasma membrane, concentrated in patches near the bud neck and in the cortex of nascent buds. Upon disruption of the actin cytoskeleton by treatment of the cells with latrunculin A, Inp1-GFP became cytosolic, indicating that Inp1 localization is dependent on the presence of an intact actin cytoskeleton.China Scholarship Council (NO AWARD)

    Text mining for the biocuration workflow

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    Molecular biology has become heavily dependent on biological knowledge encoded in expert curated biological databases. As the volume of biological literature increases, biocurators need help in keeping up with the literature; (semi-) automated aids for biocuration would seem to be an ideal application for natural language processing and text mining. However, to date, there have been few documented successes for improving biocuration throughput using text mining. Our initial investigations took place for the workshop on ‘Text Mining for the BioCuration Workflow’ at the third International Biocuration Conference (Berlin, 2009). We interviewed biocurators to obtain workflows from eight biological databases. This initial study revealed high-level commonalities, including (i) selection of documents for curation; (ii) indexing of documents with biologically relevant entities (e.g. genes); and (iii) detailed curation of specific relations (e.g. interactions); however, the detailed workflows also showed many variabilities. Following the workshop, we conducted a survey of biocurators. The survey identified biocurator priorities, including the handling of full text indexed with biological entities and support for the identification and prioritization of documents for curation. It also indicated that two-thirds of the biocuration teams had experimented with text mining and almost half were using text mining at that time. Analysis of our interviews and survey provide a set of requirements for the integration of text mining into the biocuration workflow. These can guide the identification of common needs across curated databases and encourage joint experimentation involving biocurators, text mining developers and the larger biomedical research community

    Transcriptome Responses to Combinations of Stresses in Arabidopsis

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    Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity have profound effects on crop performance and yields. Thus, delineation of the regulatory networks and metabolic pathways responding to single and multiple concurrent stresses is required for breeding and engineering crop stress tolerance. Many studies have described transcriptome changes in response to single stresses. However, exposure of plants to a combination of stress factors may require agonistic or antagonistic responses or responses potentially unrelated to responses to the corresponding single stresses. To analyze such responses, we initially compared transcriptome changes in 10 Arabidopsis (Arabidopsis thaliana) ecotypes using cold, heat, high-light, salt, and flagellin treatments as single stress factors as well as their double combinations. This revealed that some 61% of the transcriptome changes in response to double stresses were not predictable from the responses to single stress treatments. It also showed that plants prioritized between potentially antagonistic responses for only 5% to 10% of the responding transcripts. This indicates that plants have evolved to cope with combinations of stresses and, therefore, may be bred to endure them. In addition, using a subset of this data from the Columbia and Landsberg erecta ecotypes, we have delineated coexpression network modules responding to single and combined stresses. Plants are often simultaneousl

    BioCreative III interactive task: an overview

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    The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of biomedical literature, provides a diverse and engaged end user group for text mining tools. Earlier BioCreative challenges involved many text mining teams in developing basic capabilities relevant to biological curation, but they did not address the issues of system usage, insertion into the workflow and adoption by curators. Thus in BioCreative III (BC-III), the InterActive Task (IAT) was introduced to address the utility and usability of text mining tools for real-life biocuration tasks. To support the aims of the IAT in BC-III, involvement of both developers and end users was solicited, and the development of a user interface to address the tasks interactively was requested

    Using Light to Improve Commercial Value

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    The plasticity of plant morphology has evolved to maximize reproductive fitness in response to prevailing environmental conditions. Leaf architecture elaborates to maximize light harvesting, while the transition to flowering can either be accelerated or delayed to improve an individual's fitness. One of the most important environmental signals is light, with plants using light for both photosynthesis and as an environmental signal. Plants perceive different wavelengths of light using distinct photoreceptors. Recent advances in LED technology now enable light quality to be manipulated at a commercial scale, and as such opportunities now exist to take advantage of plants' developmental plasticity to enhance crop yield and quality through precise manipulation of a crops' lighting regime. This review will discuss how plants perceive and respond to light, and consider how these specific signaling pathways can be manipulated to improve crop yield and quality

    The Gene Ontology resource: enriching a GOld mine

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    The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations

    Species-wide variation in shoot nitrate concentration, and genetic loci controlling nitrate, phosphorus and potassium accumulation in Brassica napus L

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    Large nitrogen, phosphorus and potassium fertiliser inputs are used in many crop systems. Identifying genetic loci controlling nutrient accumulation may be useful in crop breeding strategies to increase fertiliser use efficiency and reduce financial and environmental costs. Here, variation in leaf nitrate concentration across a diversity population of 383 genotypes of Brassica napus was characterised. Genetic loci controlling variation leaf nitrate, phosphorus and potassium concentrations, were identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). Leaf nitrate concentration varied over 8-fold across the diversity population. A total of 455 SNP markers were associated with leaf nitrate concentration after false-discovery-rate (FDR) correction. In linkage disequilibrium of highly associated markers are a number of known nitrate transporters and sensors, including a gene thought to mediate expression of the major nitrate transporter NRT1.1. Several genes influencing root and root-hair development co-localise with chromosomal regions associated with leaf P concentration. Orthologues of three ABC-transporters involved in suberin synthesis in roots also co-localise with association peaks for both leaf nitrate and phosphorus. Allelic variation at nearby, highly associated SNPs confers large variation in leaf nitrate and phosphorus concentration. A total of five GEMs associate with leaf K concentration after FDR correction including a GEM that corresponds to an auxin-response family protein. Candidate loci, genes and favourable alleles identified here may prove useful in marker-assisted selection strategies to improve fertiliser use efficiency in B. napus
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