10,088 research outputs found
Transgenic tomato overexpressing Brassica juncea 3-HYDROXY-3-METHYLGLUTARYL-COA SYNTHASE1 enhances health-promoting vitamin E, carotenoids, squalene and phytosterols
No full textTransgenic tomato overexpressing Brassica juncea 3-HYDROXY-3-METHYLGLUTARYL-COA SYNTHASE1 enhances health-promoting vitamin E, carotenoids, squalene and phytosterols Pan Liao1,2, Xinjian Chen1, Mingfu Wang1, Thomas J. Bach3, Mee-Len Chye1,2* 1School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong, China. 2Partner State Key Laboratory of Agrobiotechnology (CUHK). 3Centre National de la Recherche Scientifique, UPR 2357, Institut de Biologie Moléculaire des Plantes, 67083 Strasbourg, France. *Corresponding author: [email protected] Isoprenoids consist of a large group of functional natural products. For instance, dietary phytosterols are known to lower blood cholesterol levels. 3-Hydroxy-3-methylglutaryl-coenzyme A synthase (HMGS) is the second enzyme in the mevalonate (MVA) pathway which generate isoprenoids including phytosterols [1,2]. Previous studies on the enzyme kinetics of recombinant wild-type (wt) and mutant Brassica juncea HMGS1 had shown that the HMGS mutant enzyme S359A had a 10-fold higher activity [3]. Furthermore, the overexpression of B. juncea wt and mutant (S359A) BjHMGS1 in Arabidopsis upregulated native HMGR, SMT2, DWF1, CYP710A1 and BR60X2, thereby increasing sterol content [4]. Also, tobacco HMGS-overexpressors (OEs) enhanced native NtHMGR1, NtIPI2, NtSQS, NtSMT1-2, NtSMT2-1, NtSMT2-2 and NtCYP85A1 expression in seedlings, improving sterol content, plant growth and seed yield [5]. When wt and mutant (S359A) BjHMGS1 were overexpressed in a crop plant tomato (Solanum lycopersicum), gas chromatography–mass spectrometry (GC-MS) and high-performance liquid chromatography (HPLC) results showed that not only did the MVA-derived squalene and sterols, but also the methylerythritol phosphate (MEP)-derived carotenoids and vitamin E (α-tocopherol), increased, revealing crosstalk between the MVA and MEP pathways. Furthermore, OE-S359A fruits displayed greater squalene and phytosterol content than OE-wtBjHMGS1, as a result of higher expression of SlHMGR2, SlFPS1, SlGPS, SlSQS and SlCYP710A11 [6]. In summary, the manipulation of BjHMGS1 represents a promising strategy to simultaneously enhance health-promoting squalene, phytosterols, carotenoids and vitamin E in an edible fruit. This work was supported by the Wilson and Amelia Wong Endowment Fund, Research Grants Council of Hong Kong (AoE/M-05/12), Innovation Technology Fund of the Innovation Technology Commission (Support to Partner State Key Laboratories in Hong Kong) and HKU CRCG awards (0910159039, 1007160002, 1511159010). PL was supported by a University Postgraduate Fellowship and a Postdoctoral Fellowship. 1. Liao P, Hemmerlin A, Bach TJ, Chye ML. Biotechnol Adv, 2016, 34, 697-713. 2. Liao P, Wang H, Hemmerlin A, Nagegowda DA, Bach TJ, Wang M, Chye ML. Plant Cell Rep, 2014, 33, 1005- 1022. 3. Nagegowda DA, Bach TJ, Chye ML. Biochem J, 2004, 383, 517-527. 4. Wang H, Nagegowda DA, Rawat R, Bouvier-Navé P, Guo D, Bach TJ, Chye ML. Plant Biotechnol J, 2012, 10, 31-42. 5. Liao P, Wang H, Wang M, Hsiao AS, Bach TJ, Chye ML. PLoS One, 2014, 9, e98264. 6. Liao P, Chen X, Wang M, Bach TJ, Chye ML. Plant Biotechnol J, 2017, (DOI: 10.1111/pbi.12828)
Metadata Representations for Queryable ML Model Zoos
No full textMachine learning (ML) practitioners and organizations are building model zoos of pre-trained models, containing metadata describing properties of the ML models and datasets that are useful for reporting, auditing, reproducibility, and interpretability purposes. The metatada is currently not standardised; its expressivity is limited; and there is no interoperable way to store and query it. Consequently, model search, reuse, comparison, and composition are hindered. In this paper, we advocate for standardized ML model metadata representation and management, proposing a toolkit supported to help practitioners manage and query that metadata.Web Information SystemsHuman-Centred Artificial Intelligenc
A Manifesto of Nodalism
No full textThis paper proposes the notion of Nodalism as a means describing contemporary culture and of understanding my own creative practice in electronic music composition. It draws on theories and ideas from Kirby, Bauman, Bourriaud, Deleuze, Guatarri, and Gochenour, to demonstrate how networks of ideas or connectionist neural models of cognitive behaviour can be used to contextualize, understand and become a creative tool for the creation of contemporary electronic music
Single amino acid substitutions at the acyl-CoA-binding domain interrupt 14[C]palmitoyl-CoA binding of ACBP2, an Arabidopsis acyl-CoA-binding protein with ankyrin repeats
No full textCytosolic acyl-CoA-binding proteins (ACBPs) are small proteins (ca. 10 kDa) that bind long-chain acyl-CoAs and are involved in the storage and intracellular transport of acyl-CoAs. Previously, we have characterized an Arabidopsis thaliana cDNA encoding a novel membrane-associated ACBP, designated ACBP1, demonstrating the existence of a new form of ACBP in plants (M.-L. Chye. Plant Mol. Biol. 38 (1998) 827-838). ACBPI likely participates in intermembrane lipid transport from the ER to the plasma membrane, where it could maintain a membrane-associated acyl pool (Chye et al., Plant J. 18 (1999) 205-214). Here we report the isolation of cDNAs encoding ACBP2 (Mr 38 479) that shows conservation in the acyl-CoA-binding domain to previously reported ACBPs, and contains ankyrin repeats at its carboxy terminus. These repeats, which likely mediate protein-protein interactions, could constitute a potential docking site in ACBP2 for an enzyme that uses acyl-CoAs as substrate. In vitro binding assays on recombinant (His)6-ACBP2 expressed in Escherichia coli show that it binds 14[C]palmitoyl-CoA preferentially to 14[C]oleoyl-CoA. Analysis of the acyl-CoA-binding domain in ACBP2 was carried out by in vitro mutagenesis. Mutant forms of recombinant (His)6-ACBP2 with single amino acid substitutions at conserved residues within the acyl-CoA-binding domain were less effective in binding14[C]palmitoyl-CoA. Northern blot analysis showed that the 1.6 kb ACBP2 mRNA, like that of ACBP1, is expressed in all plant organs. Analysis of the ACBP2 promoter revealed that, like the ACBP1 promoter, it lacks a TATA box suggesting the possibility of a housekeeping function for ACBP2 in plant lipid metabolism.link_to_subscribed_fulltex
Optimizing ML Inference Queries Under Constraints
No full textThe proliferation of pre-trained ML models in public Web-based model zoos facilitates the engineering of ML pipelines to address complex inference queries over datasets and streams of unstructured content. Constructing optimal plan for a query is hard, especially when constraints (e.g. accuracy or execution time) must be taken into consideration, and the complexity of the inference query increases. To address this issue, we propose a method for optimizing ML inference queries that selects the most suitable ML models to use, as well as the order in which those models are executed. We formally define the constraint-based ML inference query optimization problem, formulate it as a Mixed Integer Programming (MIP) problem, and develop an optimizer that maximizes accuracy given constraints. This optimizer is capable of navigating a large search space to identify optimal query plans on various model zoos.Green Open Access added to TU Delft Institutional Repository ‘You share, we take care!’ – Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Web Information SystemsHuman-Centred Artificial Intelligenc
Characterization of acyl-coenzyme A-binding proteins from rice
No full textAcyl-CoA-binding proteins (ACBPs) show conservation in an acyl-CoA-binding domain (ACB domain) which binds acyl-CoA esters. The 10-kDa ACBP represents the highly-conserved prototype that occurs in animals, plants, fungi and protists. Previous phylogenetic analysis of the 10-kDa ACBP from metazoans and nonmetazoans showed lineage-specific duplication and purifying selection during evolution. Besides the 10-kDa ACBPs, large multifunctional proteins containing a predicted ACB domain have been identified in many eukaryotes. However, the evolutionary relationships of these larger ACBPs had not been investigated. The aim of this study is to investigate the phylogeny of plant ACBPs, 10-kDa ACBPs as well as the larger ACBPs, and to characterize the ACBP family from the monocot model plant, rice.
Plant protein sequences from 16 plant genomes consisting of an ACB domain were identified using Arabidopsis AtACBP1, AtACBP3, AtACBP4 or AtACBP6 sequences as independent probes. Phylogenetic analyses were conducted by maximum likelihood (ML) analysis and neighbor-joining (NJ) methods. The ACBP family was found to diversify as land plants evolved. Classes I and IV showed lineage-specific gene expansion while Classes II and III were closely-related phylogenetically. Similar to the eudicot, Arabidopsis, six genes (designated OsACBP1 to OsACBP6) encode rice ACBPs, but their distribution into various classes differed from Arabidopsis.
Expression profiles of rice ACBPs under normal growth and biotic and abiotic stress conditions, as well as when subject to phytohormone treatments, were examined by quantitative real-time reverse-transcription polymerase chain reactions. Rice ACBP mRNAs showed ubiquitous expression. OsACBP5 is unique because it was highly-expressed throughout the whole reproductive stage. OsACBP1, OsACBP2 and OsACBP3 were abscisic acid (ABA)-and salicylic acid (SA)-inducible. OsACBP4, OsACBP5 were stress (drought and salt) - and ABA/SA-responsive while OsACBP6 was wound-inducible.
In vitro acyl-CoA-binding assays and phospholipid binding assays were conducted using bacterial-expressed recombinant (His)6-tagged OsACBPs to determine their potential lipid binding abilities. Other than a common affinity to [14C]linolenoyl-CoA, recombinant rice ACBPs demonstrated specific acyl-CoA ester preferences. All recombinant OsACBPs could bind many species of phosphatidic acid (PA) and phosphatidylcholine (PC) with the exception of recombinant OsACBP4 which was the only OsACBP to bind 16:0 PA.
To better understand the potential roles of rice ACBPs in lipid trafficking, the subcellular localization of rice ACBPs was investigated by western blot analysis, transient expression in tobacco leaf cells and stable expression in transgenic Arabidopsis of autofluorescence-tagged OsACBPs, respectively. OsACBP-GFP fusions were observed to be targeted to the cytosol, plasma membrane, endoplasmic reticulum (ER) or peroxisome.
Results from phylogeny, gene expression, biochemical analysis and subcellular localization investigation suggest that rice ACBP paralogues, within and across classes, are not redundant proteins. From results on differences in gene expression, acyl-CoA ester/phospholipid binding and subcellular localization between Arabidopsis and rice ACBPs, the function of ACBPs occur to have diverged with the split between eudicots and monocots. Besides performing conserved basal functions, multi-domain rice ACBPs appear to be associated with stress responses which makes them attractive candidates for potential applications in agriculture.published_or_final_versionBiological SciencesDoctoralDoctor of Philosoph
Identification of mutants in genes encoding arabidopsis acyl-coenzyme A binding proteins ACBP3, ACBP4 and ACBP5
No full textpublished_or_final_versionabstractBotanyMasterMaster of Philosoph
Characterization of protein interactors of Arabidopsis acyl-coenzymea-binding protein 2
No full textpublished_or_final_versionBiological SciencesDoctoralDoctor of Philosoph
Overexpression of rice acyl-CoA-binding protein confers salinity tolerance in transgenic plants
No full textPlants are continuously affected by the adverse effects from the ongoing climate change, which alter the abiotic conditions required for plant growth. In rice (Oryza sativa), a gene family encoding six members of acyl-CoA-binding proteins (ACBPs) co-exist designated as OsACBP1 to OsACBP6. These proteins have been reported to play pivotal roles in plant lipid metabolism and in biotic and abiotic stress responses. Based on its structure, rice OsACBP4, belongs to the same Class II ACBPs as AtACBP2 in Arabidopsis, containing a conserved acyl-CoA-binding domain that facilitates binding activities to various acyl-CoA esters, and ankyrin repeats that mediate protein-protein interactions. In this study, the distinct roles of rice OsACBP4 were studied in transgenic rice and Arabidopsis.
Electrophoretic mobility shift assays identified four salinity-responsive elements in the rice OsACBP4 5'-flanking region which bind salt-treated rice nuclear proteins and provide a molecular basis for salt-inducible regulation of OsACBP4 expression, indicating a potential role in plant abiotic stress tolerance. High OsACBP4 expression in rice leaves and roots was confirmed by histochemical staining and quantitative β-glucuronidase (GUS) analysis of OsACBP4pro::GUS transgenic plants. When salt treatments were performed on rice, in the wild-type (WT), the vector-transformed control (VC), rice OsACBP4-overexpressors (OEs), OsACBP4-RNAi lines and AtACBP2-OEs, the OsACBP4-OEs conferred greatest protection. In addition, rice AtACBP2-OEs were more tolerant than the controls as well, but less tolerant than OsACBP4-OEs, whereas OsACBP4-RNAi lines were more sensitive than the controls. In the experiments on transgenic Arabidopsis, OsACBP4-OEs were more salt-tolerant than AtACBP2-OEs.
RNA-sequencing of transgenic rice OsACBP4-OEs revealed significant upregulation of phospholipase-encoding genes involved in salt stress tolerance and genes encoding acyl-CoA synthetase (E.C. 6.2.1.3) in the fatty acid biosynthesis pathway, and which were all further confirmed by quantitative real-time polymerase chain reactions. Taken together, these results suggested that the salinity tolerance mechanism in rice OsACBP4-OEs may involve the phospholipid signaling pathway. Gas chromatography mass spectrometry (GC/MS) revealed increased levels of palmitic, stearic, linoleic and linolenic fatty acids, but no oleic acid in transgenic rice OsACBP4-OEs over the controls. Fatty acid content in OsACBP4-RNAi lines was lower than that of the controls. Inductively coupled plasma optical emission spectrometry (ICP-OE) ion content analysis revealed fewer toxic ions accumulated in stress-tolerant transgenic rice OsACBP4-OEs, followed by AtACBP2-OEs and then the controls, whereas the sensitive OsACBP4-RNAi lines accumulated the most. Antioxidant enzymes such as superoxide-dismutase (SOD), peroxidase (POD) and catalase (CAT) show higher enzyme activity in salt-tolerant transgenic rice OsACBP4-OEs when compared to the controls, whereas the activity decreased in the OsACBP4-RNAi lines. In the isothermal titration calorimetry experiments (ITC), His(6)-OsACBP4 had binding affinity for palmitoyl-CoA, stearoyl-CoA, linoleoyl-CoA and linolenoyl-CoA. Uniquely to the rice ACBPs, His(6)-OsACBP4 had ability to bind oleoyl-CoA. It is envisaged that the overexpression of OsACBP4 achieves protection against salinity stress, through its abilities to bind LC-CoAs and to interact with yet unidentified protein partners.published_or_final_versionBiological SciencesDoctoralDoctor of Philosoph
Investigations on recombinant Arabidopsis acyl-coenzyme A binding protein 1
No full textpublished_or_final_versionabstractBotanyMasterMaster of Philosoph
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