Autoantibodies refer to antibodies that target self-antigens, which can play pivotal roles in maintaining homeostasis, distinguishing normal from tumor tissue and trigger autoimmune diseases. In the last three decades, tremendous efforts have been devoted to elucidate the generation, evolution and functions of autoantibodies, as well as their target autoantigens. However, reports of these countless previously identified autoantigens are randomly dispersed in the literature. Here, we constructed an AAgAtlas database 1.0 using text-mining and manual curation. We extracted 45 830 autoantigen-related abstracts and 94 313 sentences from PubMed using the keywords of either ‘autoantigen’ or ‘autoantibody’ or their lexical variants, which were further refined to 25 520 abstracts, 43 253 sentences and 3984 candidates by our bio-entity recognizer based on the Protein Ontology. Finally, we identified 1126 genes as human autoantigens and 1071 related human diseases, with which we constructed a human autoantigen database (AAgAtlas database 1.0). The database provides a user-friendly interface to conveniently browse, retrieve and download human autoantigens as well as their associated diseases. The database is freely accessible at http://biokb.ncpsb.org/aagatlas/. We believe this database will be a valuable resource to track and understand human autoantigens as well as to investigate their functions in basic and translational research.
Rationale: Cell-free protein microarrays display naturally-folded proteins based on just-in-time in situ synthesis, and have made important contributions to basic and translational research. However, the risk of spot-to-spot cross-talk from protein diffusion during expression has limited the feature density of these arrays.Methods: In this work, we developed the Multiplexed Nucleic Acid Programmable Protein Array (M-NAPPA), which significantly increases the number of displayed proteins by multiplexing as many as five different gene plasmids within a printed spot.Results: Even when proteins of different sizes were displayed within the same feature, they were readily detected using protein-specific antibodies. Protein-protein interactions and serological antibody assays using human viral proteome microarrays demonstrated that comparable hits were detected by M-NAPPA and non-multiplexed NAPPA arrays. An ultra-high density proteome microarray displaying > 16k proteins on a single microscope slide was produced by combining M-NAPPA with a photolithography-based silicon nano-well platform. Finally, four new tuberculosis-related antigens in guinea pigs vaccinated with Bacillus Calmette-Guerin (BCG) were identified with M-NAPPA and validated with ELISA.Conclusion: All data demonstrate that multiplexing features on a protein microarray offer a cost-effective fabrication approach and have the potential to facilitate high throughput translational research.
This study is focused on the function of the SHORT VEGETATIVE PHASE gene. Based on morphological observation of flower buds, flower bud differentiation occurs during low-temperature storage of Lilium pumilum bulbs and progresses as the duration of low-temperature storage time. Real-time quantitative PCR analysis showed that the relative expression level of the LpSVP gene first increases and then decreases during low temperature storage. Morphological observation combined with gene expression analyses suggested that LpSVP acts as a repressor of flower meristem identification. To further characterise the function of the LpSVP gene, we constructed the plant expression vector pBI121-LpSVP-GFP, and the fusion protein was transferred into wild-type tobacco via Agrobacterium-mediated transformation of leaf discs. The resulting transgenic plants exhibited delayed flowering and a more lax inflorescence compared with the wild-type plants. This study lays the foundation for further study of the function of the LpSVP gene. Keywords delayed flowering, genetic transformation, lowtemperature storage, real-time quantitative PCR, temperature, SVP gene Significance of this study What is already known on this subject? • The SVP gene inhibits flowering, by protein-protein interactions. What are the new findings? • Flower bud differentiation occurred in bulbs of Lilium pumilum during low-temperature storage time. The expression level of the SVP gene first increased and then decreased during the entire storage process. Transformation of tobacco with the LpSVP gene resulted in delayed flowering. What is the expected impact on horticulture? • Manipulation of LpSVP could help to develop improved Lilium cultivars.
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