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false/arabidopsis
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Assessing the Performances of Protein Function Prediction Algorithms from the Perspectives of Identification Accuracy and False Discovery Rate.
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The function of a protein is of great interest in the cutting-edge research of biological mechanisms, disease development and drug/target discovery. Besides experimental explorations, a variety of computational methods have been designed to predict protein function. Among these in silico methods,
High Throughput Screening Method for Identifying Potential Agonists and Antagonists of Arabidopsis thaliana Cytokinin Receptor CRE1/AHK4.
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The CRE1/AHK4 cytokinin receptor is an important component of plants' hormone signaling systems, and compounds that can alter its activity have potential utility for studying the receptor's functions and/or developing new plant growth regulators. A high throughput method was developed for screening
A Holistic Approach to Analyze Systemic Jasmonate Accumulation in Individual Leaves of Arabidopsis Rosettes Upon Wounding.
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Phytohormones, especially jasmonates, are known to be mediators of the plant responses to wounding and herbivore feeding. Their role in such stress responses has been largely studied locally in treated leaves. However, less is known about the induced systemic distribution of phytohormone signals
Evaluation of MeDIP-chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis.
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Studies of DNA methylation in Arabidopsis have rapidly advanced from the analysis of a single reference accession to investigations of large populations. The goal of emerging population studies is to detect differentially methylated regions (DMRs) at the genome-wide scale, and to relate this
UvHrip1, an Effector Secreted by Ustilaginoidea Virens, Suppresses Basal Defense and Promotes Disease Development in Arabidopsis Thaliana
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Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most detrimental rice fungal diseases and pose a severe threat to rice production and quality. Effectors in U. virens often act as a set of essential virulence factors that play crucial roles in the interaction between host and
Computational analysis of auxin responsive elements in the Arabidopsis thaliana L. genome.
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Auxin responsive elements (AuxRE) were found in upstream regions of target genes for ARFs (Auxin response factors). While Chip-seq data for most of ARFs are still unavailable, prediction of potential AuxRE is restricted by consensus models that detect too many false positive sites. Using sequence
Arabidopsis galactinol synthase AtGolS2 improves drought tolerance in the monocot model Brachypodium distachyon.
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Brachypodium distachyon (purple false brome) is a herbaceous species belonging to the grass subfamily Pooideae, which also includes major crops like wheat, barley, oat and rye. The species has been established as experimental model organism for understanding and improving cereal crops and temperate
Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field.
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The circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. Under natural field conditions, however, little is known about the significance of the circadian clock in plants. By time-course transcriptome analyses of rice
Hierarchical nuclear and cytoplasmic genetic architectures for plant growth and defense within Arabidopsis.
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To understand how genetic architecture translates between phenotypic levels, we mapped the genetic architecture of growth and defense within the Arabidopsis thaliana Kas × Tsu recombinant inbred line population. We measured plant growth using traditional size measurements and size-corrected growth
Response to the note to editor: Comments on "transcriptomic response of Arabidopsis thaliana exposed to hydroxylated polychlorinated biphenyls (OH-PCBs)".
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In response to Dr. Yang et al.'s comments on our article "Transcriptomic response of Arabidopsis thaliana exposed to hydroxylated polychlorinated biphenyls (OH-PCBs)", additional details were provided regarding the analysis of the gene expression level (One-Way
Workflow for large scale detection and validation of peptide modifications by RPLC-LTQ-Orbitrap: application to the Arabidopsis thaliana leaf proteome and an online modified peptide library.
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Post-translational modifications (PTMs) of proteins add to the complexity of proteomes, thereby complicating the task of proteome characterization. An efficient strategy to identify this peptide heterogeneity is important for determination of protein function, as well as for mass spectrometry-based
Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis).
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The largest group of deubiquitinases-ubiquitin-specific proteases (UBPs)-perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study
iTRAQ protein profile analysis of Arabidopsis roots reveals new aspects critical for iron homeostasis.
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Iron (Fe) deficiency is a major constraint for plant growth and affects the quality of edible plant parts. To investigate the mechanisms underlying Fe homeostasis in plants, Fe deficiency-induced changes in the protein profile of Arabidopsis (Arabidopsis thaliana) roots were comprehensively analyzed
The transcriptome of syncytia induced by the cyst nematode Heterodera schachtii in Arabidopsis roots.
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Arabidopsis thaliana is a host for the sugar beet cyst nematode Heterodera schachtii. Juvenile nematodes invade the roots and induce the development of a syncytium, which functions as a feeding site for the nematode. Here, we report on the transcriptome of syncytia induced in the roots of
Infrared microspectroscopic imaging of plant tissues: spectral visualization of Triticum aestivum kernel and Arabidopsis leaf microstructure.
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Infrared microspectroscopy is a tool with potential for studies of the microstructure, chemical composition and functionality of plants at a subcellular level. Here we present the use of high-resolution bench top-based infrared microspectroscopy to investigate the microstructure of Triticum aestivum
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