AnatomyOrganismsDiseasesChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsTechnology, Industry, AgricultureInformation ScienceHealth Care
Arabidopsis ProteinsArabidopsisProteomeGene Expression Regulation, PlantPlant ProteinsGenes, PlantPlants, Genetically ModifiedMolecular Sequence DataAmino Acid SequenceSequence Homology, Amino AcidRNA, PlantPlant LeavesDNA, PlantGenome, PlantMutationSequence AlignmentPlant RootsPhylogenyProteomicsTwo-Hybrid System TechniquesDatabases, ProteinSeedlingFlowersBase SequenceSeedsCloning, MolecularAmino Acid MotifsElectrophoresis, Gel, Two-DimensionalIndoleacetic AcidsPlant Growth RegulatorsGerminationCarrier ProteinsPlant ShootsProtein BindingMeristemPhenotypeAbscisic AcidPlant EpidermisRecombinant ProteinsEthylenesPlant DiseasesOxylipinsSalicylic AcidMass SpectrometryCyclopentanesLightGenetic Complementation TestCotyledonChloroplastsGene Expression ProfilingMADS Domain ProteinsChromatography, LiquidPlastidsMutagenesis, InsertionalCytokininsOryza sativaTandem Mass SpectrometryAGAMOUS Protein, ArabidopsisPseudomonas syringaePlant StomataMultigene FamilySpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationTranscription FactorsPlant StructuresPlant StemsGibberellinsGlucosinolatesPollenSignal TransductionPhytochromeBrassicaceaeTobaccoChromosomes, PlantStress, PhysiologicalGlucuronidaseDNA, ComplementaryPhytochrome BPlant ImmunityGravitropismPhotoperiodDarknessPlant Vascular BundleBrassinosteroidsComputational BiologyEcotypePhotosynthesisDroughtsChlorophyllPhytochrome AProtoplastsModels, BiologicalRNA, MessengerAnthocyaninsChromosome MappingDisease ResistanceInflorescenceProtein TransportThylakoidsOomycetesEvolution, Molecular
ThalianaGenesDetermined the subcellular localization dataOrganismProteomicsAnnotationCharacterizationTranscriptomeMass spectrometryAmino acidsPeptidesInteractionsPrediction2020SpeciesSeed GerminationLocalisationClasses of proteinsCircadian clockTranslational coincidenceSubcellular locationPlastidProteomicBiosynthesisGeneSequencesInteractomeExperimentallySequenceEndoplasmic reticulumMutantsSeedlingsComplexesMetabolitesDatasetsHomologyRevealsInteractionRolesPlantsTAIR10Plasma membraneKinasesDynamicsResponsesMolecularPhosphorylationRiceCellularAnalysisExperimentalMitochondriaDirectly or indirectly2018VariantsFunctionalMediatesStomatalTranscriptsGlycineAbundantMethodsLipidsHomeostasis
Thaliana23
  • Arabidopsis thaliana, the thale cress, mouse-ear cress or arabidopsis, is a small plant from the mustard family (Brassicaceae), native to Eurasia and Africa. (wikipedia.org)
  • Arabidopsis thaliana is an annual (rarely biennial) plant, usually growing to 20-25 cm tall. (wikipedia.org)
  • I discovered a novel polarity protein in Arabidopsis thaliana that polarizes at distinct developmental stages in stomatal precursors. (oeaw.ac.at)
  • Cold stress and freezing tolerance negatively affect the fitness of Arabidopsis thaliana accessions under field and controlled conditions. (mpg.de)
  • Stabilization of Dry Sucrose Glasses by Four LEA_4 Proteins from Arabidopsis thaliana. (mpg.de)
  • Characterisation of the ERF102 to ERF105 genes of Arabidopsis thaliana and their role in the response to cold stress. (mpg.de)
  • Evaluation of seven different rna-seq alignment tools based on experimental data from the model plant arabidopsis thaliana. (mpg.de)
  • Repair of sub-lethal freezing damage in leaves of Arabidopsis thaliana. (mpg.de)
  • Contrary to the persistent endosperm of cereals, the cellular endosperm of Arabidopsis thaliana ( A. thaliana) supports the developing and growing embryo, resulting in a gradually depleted endosperm as the embryo grows. (nature.com)
  • Here, we developed a computational approach for detecting PPIs trained and tested on known PPIs of Arabidopsis thaliana and applied to three plants, Arabidopsis thaliana , Glycine max (soybean), and Zea mays (maize) to discover new PPIs on a genome-scale. (nature.com)
  • Surprisingly, except for Arabidopsis thaliana , virtually no other plant species have experimentally determined PPI data available. (nature.com)
  • Here, we describe the first proteomic analysis of plant (Arabidopsis thaliana) nucleoli, in which we have identified 217 proteins. (hud.ac.uk)
  • Identification and profiling of abiotic stress-responsive proteins in Arabidopsis thaliana and Sorghum bicolor . (agric.za)
  • The majority of information related to plant-pathogen interactions originate from studies on model plant species such as Arabidopsis thaliana and Nicotiana spp. (biomedcentral.com)
  • The analytical depth of investigation of the peroxisomal proteome of the model plant Arabidopsis thaliana has not yet reached that of other major cellular organelles such as chloroplasts or mitochondria. (uni-hannover.de)
  • The learning dataset contains 3214 Arabidopsis thaliana proteins classified into 7 subcellular localizations under study (Chloroplast, Cytoplasm, Golgi apparatus, Mitochondrion, Extracellular, Nucleus, Plasma membrane) according to the annotation information available in Swiss-Prot ( release 57.9 ). (zhaolab.org)
  • Finally, our best classifier was run on the complete Arabidopsis thaliana proteome (total 27,379 sequences from TAIR release 9 ) and generate highly reliable predictions for each of the 7 localizations. (zhaolab.org)
  • Arabidopsis thaliana Plant Natriuretic Peptide Active Domain" Encyclopedia , https://encyclopedia.pub/entry/17526 (accessed December 03, 2023). (encyclopedia.pub)
  • Plant natriuretic peptides (PNPs) are hormones that have been extracted from many different species, with the Arabidopsis thaliana PNP (AtPNP-A) being the most studied among them. (encyclopedia.pub)
  • Among its various strains, pathovar tomato strain DC3000 ( PstDC3000 ) is asserted to infect the plant host Arabidopsis thaliana and thus, has been accepted as a model system for experimental characterization of the molecular dynamics of plant-pathogen interactions. (biomedcentral.com)
  • The present work predicts the protein-protein interaction network between Arabidopsis thaliana and Pseudomonas syringae pv. (biomedcentral.com)
  • Among them, pathovar tomato strain DC3000 ( Pst DC3000 ) has been asserted to infect the plant host Arabidopsis thaliana and tomato causing bacterial spec and brown spot. (biomedcentral.com)
  • We used luciferase reporter gene imaging to monitor circadian rhythms in leaves of Arabidopsis thaliana plants, achieving resolution close to the cellular level. (ed.ac.uk)
Genes9
  • Recently, deep sequencing of the transcriptome using high-throughput RNA sequencing (RNAseq) increased this estimate showing that more that 60% of intron-containing genes in Arabidopsis are alternatively spliced [ 12 ]. (biomedcentral.com)
  • The advent of high throughput -omics has made the accumulation of comprehensive data sets possible, consisting of changes in genes, transcripts, proteins and metabolites. (mdpi.com)
  • A number of bleeding disorders arise as a result of mutations in the genes for proteins involved in platelet aggregation. (hindawi.com)
  • The next paper introduces genes from the parasitic plant Striga hermonthica into Arabidopsis to show that strigolactone signaling can replace GA signaling in the control of seed germination. (garnetcommunity.org.uk)
  • They use Hi-C and related techniques to study the control of expression of clustered biosynthetic pathway genes in Arabidopsis. (garnetcommunity.org.uk)
  • Basically, Pseudomonas syringae pathogenesis is dependent on effector proteins and to date, nearly 60 different type III effector proteins encoded by hop genes have been identified [ http://www.pseudomonas-syringae.org/ ]. (biomedcentral.com)
  • Scientists have known for a long time that although the level of some proteins are stable across the day, curiously the genes that dictate their production are still expressed in a rhythmic way. (ed.ac.uk)
  • In all over a third of genes in Arabidopsis show a rhythm in their expression and around 1700 proteins changed their levels according to seasonal daylight hours. (ed.ac.uk)
  • As so many plant genes have rhythmic expression, this type of coincidence detection, termed translational coincidence, affected hundreds of proteins in this study. (ed.ac.uk)
Determined the subcellular localization data1
  • We profiled several thousand proteins and we determined the subcellular localization data for around 5000 of them using the LOPIT-DC spatial proteomics protocol. (bvsalud.org)
Organism3
  • A Pseudomonas protein and an Arabidopsis protein are predicted to interact with each other if an experimentally verified interaction exists between their respective homologous proteins in another organism. (biomedcentral.com)
  • Nine eukaryote proteomes have been aligned to the D. pulex genome, with help from Daphnia Genomics Consortium, TeraGrid and Generic Model Organism Database projects. (wfleabase.org)
  • The nine proteomes, with 217,006 total protein sequences, are drawn from organism genome databases, Ensembl and NCBI (see below). (wfleabase.org)
Proteomics10
  • By using label-free quantitative proteomics profiling, we quantified 1,822 proteins across developing barley grains. (nature.com)
  • notably, integration of proteomics data with in situ subcellular microscopic analyses showed a high abundance of cytoskeleton proteins associated with acidified PBs at the early development stages. (nature.com)
  • Spatial proteomics has provided important insights into the relationship between protein function and subcellular location. (bvsalud.org)
  • The issue of abundant (often housekeeping) proteins masking regulatory proteins of lower abundance (such as signaling proteins and cytokines) continues to be a challenging issue for proteomics particularly in the case of biofluids. (hindawi.com)
  • While modern proteomics experiments permit the analysis of hundreds to thousands of proteins in complex samples, the most powerful use of this data would combine information on protein activity with the identities of the active proteins. (hindawi.com)
  • Tools used by Carnegie mass spectrometry facility for analysis of large mass spectrometry proteomics data include Protein Prospector, MaxQuant, Perseus and Skyline. (carnegiescience.edu)
  • Proteomics, generally defined as the simultaneous and high throughput study of protein expression profiles, is used to monitor proteome profiles towards the understanding of molecular mechanisms associated certain biological and environmental cues. (agric.za)
  • Karl Mechtler, Head of the Proteomics Tech Hub at IMP, IMBA, and GMI, is the first Austrian scientist to receive the prestigious Juan Pablo Albar Proteome Pioneer Award from the European Proteomics Association. (oeaw.ac.at)
  • We are using reverse genetics, biochemistry, transcriptomics, proteomics, and metabolomics to understand how these putative signaling proteins affect the plant's resistance to bacterial pathogens. (missouri.edu)
  • A recent plasma membrane (PM) proteomics analysis in our lab revealed a number of proteins that rapidly decrease within one hour of the plants perception of a bacterial pathogen. (missouri.edu)
Annotation1
  • Based on proteome annotation and a homology search, 94 proteins associated with the endomembrane system were identified that exhibited significant changes in abundance during grain development. (nature.com)
Characterization2
  • Characterization of the Heat-Stable Proteome during Seed Germination in Arabidopsis with Special Focus on LEA Proteins. (mpg.de)
  • Proteomic approaches have proven powerful at identifying large numbers of proteins, but there are fewer reports of functional characterization of proteins in biological tissues. (hindawi.com)
Transcriptome3
  • Alternative splicing (AS) is one of the main mechanisms that forge transcriptome plasticity and proteome diversity [ 15 ]. (biomedcentral.com)
  • Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival. (uva.nl)
  • EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula . (biomedcentral.com)
Mass spectrometry5
  • High-accuracy high-throughput mass spectrometry-based methods now exist to map the steady-state localisation and re-localisation of proteins. (bvsalud.org)
  • METHODS: We used high-resolution mass spectrometry, differential ultracentrifugation, machine learning and bioinformatics to investigate both changes in the expression and localization of the human bronchial epithelium CF model (F508del-CFTR CFBE41o-) proteome following treatment with VX-809 (Lumacaftor), a drug able to improve the trafficking of CFTR. (bvsalud.org)
  • We used consecutive orthogonal separation platforms to ensure sensitive detection: (a) ion-exchange of intact proteins, (b) SDS-PAGE separation of ion-exchange fractions and (c) HPLC separation of tryptic digests coupled to electrospray tandem mass spectrometry. (hindawi.com)
  • Subcellular location can be determined by fluorescent protein tagging or mass spectrometry detection in subcellular purifications and by prediction using protein sequence features. (suba.live)
  • A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes. (imp.ac.at)
Amino acids1
  • posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
Peptides3
  • Application Flexible and intuitive chromatography system for fast purification of proteins, peptides, and nucleic acids from microgram to gram levels of target product. (carnegiescience.edu)
  • Only Arabidopsis Gene Initiative (AGI) Identifiers OR a Sequences of characters 'ACDEFGHIKLMNPQRSTVWY' representing peptides. (edu.au)
  • Amyloid fibrils are formed by proteins or peptides, that under certain conditions self-assemble into characteristic fibrillar structures [ 1 ] . (encyclopedia.pub)
Interactions10
  • Global mapping of protein-metabolite interactions in Saccharomyces cerevisiae reveals that Ser-Leu dipeptide regulates phosphoglycerate kinase activity. (mpg.de)
  • Protein-protein interactions (PPIs) play essential roles in many biological processes. (nature.com)
  • Identification of protein-protein interactions (PPIs) is important for understanding how proteins work together in a coordinated fashion in a cell to perform cellular functions. (nature.com)
  • Even for Arabidopsis , known PPI data cover interactions with only about 34.55% of proteins. (nature.com)
  • This OpenSPR, a surface plasmon resonance instrument, from Nicoya, provides high quality, label-free interaction analysis for protein-protein, protein-DNA/RNA, protein-small molecules interactions. (carnegiescience.edu)
  • The cropPAL 2020 search interface provides flexible options of refining or interrogating protein data sets by location, interactions, protein properties and bibliographic information. (croppal.org)
  • I am committed to interdisciplinary research, and an example of the successes gained from this approach is the project with Prof A Nabok (Engineering Sheffield Hallam University) using total internal reflection ellipsometry to quantify protein-membrane interactions on native plant membranes and human cell lines. (brookes.ac.uk)
  • Program access grant to the STFC Harwell Laser Facility 'The Plant Cell Initiative: Protein interactions in the higher plant secretory pathway' 2017-2021 (approximate value of £200K). (brookes.ac.uk)
  • Protein-protein interactions (PPIs) play a critical role in initiating pathogenesis and maintaining infection. (biomedcentral.com)
  • In this study, we used two computational approaches, the interolog and the domain-based to predict the interactions between Arabidopsis and PstDC3000 in genome scale. (biomedcentral.com)
Prediction11
  • 2011) The proteome folding project: Proteome-scale prediction of structure and function. (yeastrc.org)
  • This is the first work where a PPI prediction method was developed for is the first PPI prediction method applied on benchmark datasets of Arabidopsis . (nature.com)
  • Proteomic analysis and prediction of amino acid variations that influence protein. (deepdyve.com)
  • To increase the utilization of current computational resources, we 﫿rst provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. (deepdyve.com)
  • Highly accurate protein structure prediction with AlphaFold. (xfam.org)
  • This dataset contains 357 new Arabidopsis sequences never used in the original training/testing process when developing the prediction classifiers. (zhaolab.org)
  • We also developed a corresponding prediction classifier on the combined protein sequences from all the plants and compared with the Arabidopsis-specifc classifier using same encoding schemes. (zhaolab.org)
  • If all the seven models of each location gives negative score, the final prediction would be " Unknown " protein. (zhaolab.org)
  • For wider applicability and increased prediction confidence, we also provide here the complete list of TAIR IDs ( in decreasing order of their reliability confidence ) of the top scoring proteins (>1.0 cutoff) in each class along with their corresponding ' Swiss-Prot ' and ' TAIR ' annotations as well as the PSI-BLAST hit information, if available. (zhaolab.org)
  • The interolog method relies on protein sequence similarity to conduct the PPI prediction. (biomedcentral.com)
  • Tanz SK, Castleden I, Hooper CM, Vacher M, Small I and Millar AH (2013) SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis. (suba.live)
20204
  • Velanis CN, Perera P, Thomson B, et al (2020) The domesticated transposase ALP2 mediates formation of a novel Polycomb protein complex by direct interaction with MSI1, a core subunit of Polycomb Repressive Complex 2 (PRC2) PLoS Genet. (garnetcommunity.org.uk)
  • Lambing C, Kuo PC, Tock AJ, Topp SD, Henderson IR (2020) A SY1 acts as a dosage-dependent antagonist of telomere-led recombination and mediates crossover interference in Arabidopsis Proc Natl Acad Sci U S A. 2020;201921055. (garnetcommunity.org.uk)
  • The compendium of cropPAL 2020 houses large scale proteomic (MS/MS), fluorescence protein (FP) localisation as well as Protein-Protein Interaction (PPI) inferred from Arabidopsis PPI experimentation. (croppal.org)
  • The compendium of cropPAL 2020 also contains precompiled bioinformatic predictions for protein subcellular localisations and a consensus call (winner-takes-all location) taking predictive and experimental information into account. (croppal.org)
Species7
  • Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for CCT14_ARATH . (yeastrc.org)
  • Here, the spatial proteomes of two African trypanosome species, Trypanosoma brucei and Trypanosoma congolense, are mapped across two life-stages. (bvsalud.org)
  • Other representative plant species cover even less protein involved in known PPIs. (nature.com)
  • This allows a direct comparison of the proteomes of an important nuclear structure between two widely divergent species: human and Arabidopsis. (hud.ac.uk)
  • Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species. (biomedcentral.com)
  • The table below details the number of experimental localisations, the number of distinct proteins localised and available PPI pairs infered from Arabidopsis by homology linking for each species. (croppal.org)
  • In this study, we looked at how levels of proteins change in response to the seasons - recreating seasonal daylight hours for the plant Arabidopsis, a commonly used model for other plant species. (ed.ac.uk)
Seed Germination2
  • Caleosins are proteins involved in storage lipid mobilization during seed germination. (biomedcentral.com)
  • SIMKK-YFP plants showed enhanced activation of Arabidopsis MPK3 and MPK6 kinases upon salt treatment and exhibited high sensitivity against salt stress at the seedling stage, although they were salt insensitive during seed germination. (edu.sa)
Localisation7
  • The steady-state localisation of proteins provides vital insight into their function. (bvsalud.org)
  • Differential localisation, that is a change in the steady-state subcellular location of a protein, provides a step towards mechanistic insight of subcellular protein dynamics. (bvsalud.org)
  • Users can construct powerful queries or interrogate their protein sets resulting in a one-stop-shop for protein localisation and protein location relationships. (croppal.org)
  • Subcellular localisation information can contribute towards our understanding of protein function, protein redundancy and biological relationships. (croppal.org)
  • Here I pursued my scientific interests in subcellular protein localisation, bioinformatics, and mathematical modelling. (brookes.ac.uk)
  • My additional independent research on ER localisation and splicing in auxin biosynthesis showed for the first time ER-localisation for an auxin biosynthetic protein. (brookes.ac.uk)
  • Subcellular Localisation database for Arabidopsis proteins version 5. (suba.live)
Classes of proteins1
  • Plastid lipid-associated proteins (PAPs) and Carotenoid Associated Proteins (CAP) are general terms conferred to two classes of proteins accumulated at high levels in chromoplasts of plant cells [ 1 , 2 ] that are involved in the sequestration of hydrophobic compounds including lipids and carotenoids. (openbiochemistryjournal.com)
Circadian clock1
Translational coincidence1
Subcellular location5
  • Localization of Organelle Proteins by Isotope Tagging (LOPIT) and its variants are proteome-wide techniques, not matched in scale by microscopy-based or proximity tagging-based techniques, allowing holistic mapping of protein subcellular location and re-localization events downstream of cellular perturbations. (bvsalud.org)
  • While a variety of technologies are currently employed to determine the subcellular location of proteins, much of this information is not available in an integrated manner. (croppal.org)
  • None of the proteins has >30% sequence identity to any other in the same subset (subcellular location). (zhaolab.org)
  • Protein subcellular location and the proximity relationship of proteins are important clues to function within the metabolic household. (suba.live)
  • Heazlewood JL1, Tonti-Filippini J, Verboom RE, Millar AH(2005) Combining experimental and predicted datasets for determination of the subcellular location of proteins in Arabidopsis. (suba.live)
Plastid1
  • We show here that PLASTID REDOX INSENSITIVE 2 (PRIN2) and CHLOROPLAST STEM-LOOP BINDING PROTEIN 41 kDa (CSP41b), two proteins identified in plastid nucleoid preparations, are essential for proper plant embryo development. (frontiersin.org)
Proteomic3
  • Previous proteomic studies of intact platelets have collectively identified hundreds of proteins using a variety of fractionation strategies including 2-dimensional electrophoresis (2DE), multidimensional chromatographic separations, membrane prefractionation techniques, and adsorption to combinatorial hexapeptide ligand libraries [ 1 - 6 ]. (hindawi.com)
  • Proteomic analysis of SIMKK-YFP overexpressors indicated the differential regulation of proteins directly or indirectly involved in salt stress responses. (edu.sa)
  • To uncover new subsets of signaling candidates, my laboratory has developed complementary proteomic approaches to identify proteins undergoing phosphorylation in Arabidopsis within minutes after the application of microbial elicitors. (missouri.edu)
Biosynthesis1
  • I am a plant cell biologist and protein biochemist at Oxford Brookes University with expertise in the structure and function of the plant endoplasmic reticulum (ER), membrane proteins and auxin biosynthesis using biochemical techniques as well as high-resolution live cell imaging. (brookes.ac.uk)
Gene4
  • Natural Variation among Arabidopsis Accessions in the Regulation of Flavonoid Metabolism and Stress Gene Expression by Combined UV Radiation and Cold. (mpg.de)
  • Our method considers a variety of features including protein sequences, gene co-expression, functional association, and phylogenetic profiles. (nature.com)
  • Christos Velanis is first author on this research led by the Goodrich group at the University of Edinburgh that looked at the function of the Arabidopsis ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) gene, which has arose by domestication of the Harbinger class of transposable elements (TEs). (garnetcommunity.org.uk)
  • When this coincides with the right environmental trigger, such as longer daylight hours, it alters the behaviour of the proteins controlled by that gene, triggering flowering. (ed.ac.uk)
Sequences3
  • Peptide sequences (LC_MS/MS spectrum) obtained from CPC and their corresponding proteins were obtained using publically available databases. (openbiochemistryjournal.com)
  • The experimental data is captured and obsolete or non-Ensemble Plant protein IDs are either cross-references or sequences belonging to these IDs are retrieved and BLASTed against the current proteome. (croppal.org)
  • Download predictions for all the 27,379 protein sequences from TAIR 9. (zhaolab.org)
Interactome2
  • To understand the molecular role of polarity proteins in plant development, it is important to characterize their interactome, including their protein-protein interaction partners. (oeaw.ac.at)
  • Firstly a research team led from Oxford highlights an improved protocol for the proteome-analysis technique of RNA interactome capture. (garnetcommunity.org.uk)
Experimentally1
  • Click here to download the combined dataset-II containing these 84 new experimentally proved Arabidopsis-specific proteins. (zhaolab.org)
Sequence4
  • Type or paste your AGIs or Arabidopsis sequence here. (edu.au)
  • AtPNP-A has distant sequence homology with human ANP, a protein that forms amyloid fibrils in vivo . (encyclopedia.pub)
  • Amyloid forming proteins do not share any similarity in sequence or native structure, albeit amyloid fibrils are characterized by a common structure, known as "cross-β" structure. (encyclopedia.pub)
  • SUBA5 contains a subcellular data query platform, protein sequence BLAST alignment, a high confidence subcellular locations reference standard and analytic tools. (suba.live)
Endoplasmic reticulum1
  • These proteins included catalase, peroxiredoxin, glutathione S-transferase, nucleoside diphosphate kinase 1, endoplasmic reticulum luminal-binding protein 2, and finally plasma membrane aquaporins. (edu.sa)
Mutants2
  • Ion Homeostasis and Metabolome Analysis of Arabidopsis 14-3-3 Quadruple Mutants to Salt Stress. (mpg.de)
  • A substantial number of proteins that are involved in the heat-acclimatization process such as the proteins related to cellular redox status and heat shock, are already altered in the type-A arr mutants without a prior exposure to stress conditions. (frontiersin.org)
Seedlings1
  • In conclusion, Arabidopsis seedlings overexpressing SIMKK-YFP exhibited higher salt sensitivity consistent with their proteome composition and with the presumptive MPK3/MPK6 hijacking of the salt response pathway. (edu.sa)
Complexes1
  • The facility is also providing cross-linking analysis for mapping protein structure of functional protein complexes. (carnegiescience.edu)
Metabolites1
  • At the sub-cellular scale, maps document the spatial organization of proteins, RNA, DNA, and metabolites with nanometer precision and temporal acuity on the order of seconds. (stanford.edu)
Datasets1
  • The four resulting datasets provide evidence of expression of approximately 5500 proteins per cell-type. (bvsalud.org)
Homology1
  • The table below shows the number of studies that have been linked to the Ensembl proteomes as well as the number of PPI studies that were derived from Arabidopsis through homology linking. (croppal.org)
Reveals1
  • Subcellular Localization of Seed-Expressed LEA_4 Proteins Reveals Liquid-Liquid Phase Separation for LEA9 and for LEA48 Homo- and LEA42-LEA48 Heterodimers. (mpg.de)
Interaction5
  • Following up on the top hits obtained by proximity labeling, I study co-localization, protein-protein interaction, and genetics to expand our knowledge on the molecular networks that regulate stomatal development. (oeaw.ac.at)
  • These proteins may modulate the interaction of platelets with their local cellular environment. (hindawi.com)
  • The protein located on the outside might rather play a function in pollen-stigma interaction during pollen hydration and germination. (biomedcentral.com)
  • The domain-based method uses domain interaction information, which is derived from known protein 3D structures, to infer the potential PPIs. (biomedcentral.com)
  • This can be a useful resource to the plant community to characterize the host-pathogen interaction in Arabidopsis and Pseudomonas system. (biomedcentral.com)
Roles1
  • Plants produce a vast number of proteins with different roles in their biology. (ed.ac.uk)
Plants4
  • During my postdoc, I characterize novel mechanisms and polarity proteins in the development of stomata, the major drivers of gas exchange and carbon fixation in the leaf epidermis of vascular plants. (oeaw.ac.at)
  • The comparison identified many common proteins, plant-specific proteins, proteins of unknown function found in both proteomes, and proteins that were nucleolar in plants but nonnucleolar in human. (hud.ac.uk)
  • SIMKK function was further studied in Arabidopsis plants overexpressing SIMKK-yellow fluorescent protein (YFP) fusions. (edu.sa)
  • Like high street shops stocking up for the upcoming season - whether it is swimwear or winter coats - plants must also select the right options from their extensive protein catalogue. (ed.ac.uk)
TAIR101
  • SUBA5 contains more experimental data increasing proteome coverage (TAIR10) to 44% (53% incl. (suba.live)
Plasma membrane1
  • I adapted the biotin ligase (BirA)-based proximity labeling method for polarity proteins in the stomatal lineage and identified the respective plasma membrane proteomes. (oeaw.ac.at)
Kinases1
  • Dual-specificity mitogen-activated protein kinases kinases (MAPKKs) are the immediate upstream activators of MAPKs. (edu.sa)
Dynamics1
  • Using genetic tools and confocal microscopy, I study the role and protein dynamics of this novel polarity domain in stomatal development (and beyond). (oeaw.ac.at)
Responses2
  • Plant responses to ambient temperature fluctuations and water-limiting conditions: a proteome-wide perspective. (muni.cz)
  • One of the major classes of virulence factors includes effector proteins that are delivered into the host through a type III protein secretion system (TTSS) to suppress plant immune responses, and also to facilitate disease development [ 6 ]. (biomedcentral.com)
Molecular1
  • For instance, a number of studies have used 1D SDS-PAGE to separate proteins by molecular weight prior to MS analysis [ 12 - 15 ]. (hindawi.com)
Phosphorylation1
  • The facility provides analysis for identification of both proteins and post-translation modifications, including phosphorylation, ubiquitination, methylation and O-GlcNAcylation. (carnegiescience.edu)
Rice1
Cellular2
  • Here, we describe a principled Bayesian approach, BANDLE, that uses these data to compute the probability that a protein differentially localises upon cellular perturbation. (bvsalud.org)
  • PPIs are essential for individual protein functions, forming various cellular pathways, and are also involved in the development of diseases. (nature.com)
Analysis5
  • Protein and peptide chromatography prior to MS analysis can partly address this issue. (hindawi.com)
  • An important step in the functional analysis of the nucleolus is to determine the complement of proteins of this nuclear compartment. (hud.ac.uk)
  • The development of better methods for mutation analysis-related protein PTMs will help to facilitate the development of personalized precision medicine. (deepdyve.com)
  • Guayule Proteome Analysis: Towards development of a sustainable low tech-hypoallergenic latex (and by products) agroprocessing system designed for South African small-holder farmers. (agric.za)
  • Western blot analysis showed that Fribrillin and Or-protein were present in chromoplast-enriched suspensions of yellow root but not in the complex or white root. (openbiochemistryjournal.com)
Experimental1
  • Here, we describe an experimental approach that fractionates proteins released from human platelets, linking bioassay activity to identity. (hindawi.com)
Mitochondria1
  • RESULTS: The data suggested no stark changes in protein expression, yet subtle localization changes of proteins of the mitochondria and peroxisomes were detected. (bvsalud.org)
Directly or indirectly1
  • Consequently, amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence PTM of protein and bring about a detrimental effect on protein function. (deepdyve.com)
20181
  • For instance, the SwissVariant database (http://swissvar.expasy.org/) contained 76 613 variants in 20 244 human proteins on 10 January 2018. (deepdyve.com)
Variants1
  • A new eLife paper by Fred Berger uncovers the key role histone variants play in establishing chromatin states in Arabidopsis. (oeaw.ac.at)
Functional1
  • Heat shock proteins (HSPs) and antioxidant enzymes are the two major classes of functional proteins that are induced during HSR. (frontiersin.org)
Mediates1
Stomatal2
  • Polarity proteins orient divisions in stomatal precursor cells to determine stomatal fate and patterning. (oeaw.ac.at)
  • The next paper is from Durham and looks at the role of GA-regulated DELLA proteins in the regulation of stomatal aperature. (garnetcommunity.org.uk)
Transcripts1
  • Moreover, endosomal sorting complex required for transport (ESCRT)-related proteins and their transcripts are most abundant at early and mid-development. (nature.com)
Glycine1
  • For instance, the Type I protein arginine methyltransferases are known to methylate a number of proteins that contain an arginine glycine glycine (RGG)-motif [6]. (deepdyve.com)
Abundant1
Methods1
  • Using fluorescence and transmission electron microscopic immunolocalization methods, the protein was first localized in the tapetal cells at the free microspore stage. (biomedcentral.com)
Lipids1
  • Unfavorably high temperature causes heat stress in all organisms and leads to disintegration of membrane lipids, protein misfolding and denaturation, oxidative burst, and increased membrane fluidity. (frontiersin.org)
Homeostasis1
  • Collectively, our results suggest that the type-A ARRs play an important role in heat stress response by affecting the redox homeostasis in Arabidopsis. (frontiersin.org)