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Works (13)
Updated: April 5th, 2024 06:19
2022 journal article
Enhancing HR Frequency for Precise Genome Editing in Plants
FRONTIERS IN PLANT SCIENCE, 13.
author keywords: homologous recombination; homology-directed repair; gene targeting; donor template; programmable nucleases
TL;DR:
Various strategies implemented to increase the frequency of HDR in plant cells are summarized, including methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants.
(via Semantic Scholar)
www.frontiersin.org (publisher PDF)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: May 31, 2022
2022 journal article
Identification of Transcription Factors Regulating SARS-CoV-2 Tropism Factor Expression by Inferring Cell-Type-Specific Transcriptional Regulatory Networks in Human Lungs
VIRUSES-BASEL, 14(4).
author keywords: SARS-CoV-2; single-cell RNA-seq; differential network analysis
MeSH headings : COVID-19; Gene Regulatory Networks; Humans; Lung / metabolism; SARS-CoV-2 / genetics; Transcription Factors / genetics; Viral Tropism / genetics
TL;DR:
This work constructed transcriptional regulatory networks (TRNs) controlling SARS-CoV-2 tropism factors for healthy donors and COVID-19 patients using lung single-cell RNA-sequencing (scRNA-seq) data and found that the altered regulatory role of TFs in the same cell types of healthy and Sars-Cov-2-infected networks may be partially responsible for differential tropism factor expression.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science; OpenAlex)
Sources: Web Of Science, ORCID
Added: May 2, 2022
2022 journal article
To Fight or to Grow: The Balancing Role of Ethylene in Plant Abiotic Stress Responses
PLANTS-BASEL, 11(1).
author keywords: ethylene; abiotic stress; hormone crosstalk; growth and defense tradeoff
TL;DR:
The crosstalk between ethylene and other plant hormones in tipping the balance between plant growth and abiotic stress responses is described.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: December 24, 2021
2019 journal article
CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa
NEW PHYTOLOGIST, 222(1), 244–260.
author keywords: co-immunoprecipitation; enzyme activity; monolignol biosynthetic pathway; nuclear magnetic resonance (NMR); Populus trichocarpa; stem-differentiating xylem protein
MeSH headings : Aldehyde Oxidoreductases / genetics; Aldehyde Oxidoreductases / metabolism; Down-Regulation / genetics; Gene Expression Regulation, Plant; Lignin / metabolism; Magnetic Resonance Spectroscopy; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Populus / genetics; Populus / metabolism; RNA Interference; Recombinant Proteins / metabolism; Xylem / metabolism
TL;DR:
Evidence is provided for the formation of PtrCAD1/PtrCCR2 protein complexes in monolignol biosynthesis in planta, and biomolecular fluorescence complementation and pull-down/co-immunoprecipitation experiments supported a hypothesis of P Tr trichocarpa heterodimer formation.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: December 17, 2018
2018 journal article
Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis
Nature Communications, 9(1), 1579.
Contributors: J. Wang n , M. Matthews n, C. Williams n , R. Shi n, C. Yang n, S. Tunlaya-Anukit n, n, Q. Li *
MeSH headings : Gene Expression Regulation, Plant; Lignin / biosynthesis; Lignin / genetics; Plants, Genetically Modified / genetics; Populus / genetics; Populus / metabolism; Transcriptome / genetics; Trees / genetics; Trees / metabolism; Wood / chemistry; Wood / physiology; Xylem / metabolism
TL;DR:
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels and may lead to greater understanding of other pathways for improved growth and adaptation.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018
2017 journal article
Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(45), E9722–E9729.
Contributors: Y. Lin n, n, Q. Li *, W. Li n, J. Wang n , R. Shi n, S. Tunlaya-Anukit n, P. Shuai n
author keywords: reciprocal cross-regulation; NAC transcription factors; alternative splicing; wood formation; Populus trichocarpa
MeSH headings : Alternative Splicing; Cell Wall / genetics; Cell Wall / metabolism; Cloning, Molecular; DNA, Plant; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks; Genes, Plant; Homeostasis; Multigene Family; Nuclear Proteins; Plant Leaves / genetics; Plant Leaves / metabolism; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Shoots / genetics; Plant Shoots / metabolism; Populus / genetics; Populus / metabolism; Recombinant Proteins / genetics; Transcription Factors / genetics; Transcription Factors / metabolism; Transcriptional Activation / genetics; Transcriptome; Wood / genetics; Wood / growth & development; Xylem / genetics; Xylem / growth & development
TL;DR:
The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation, suggesting a general mechanism among NAC domain proteins and likely other transcription factors.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2017 journal article
Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa
PLANTA, 245(5), 927–938.
author keywords: Wood formation; Transcriptome; Fiber cells; Vessel elements; Cell wall biosynthesis; Co-expression network
MeSH headings : Cell Wall / metabolism; Cellulose / metabolism; Cluster Analysis; Gene Expression Regulation, Plant; Lignin / metabolism; Molecular Sequence Annotation; Organ Specificity; Phloem / genetics; Phloem / growth & development; Plant Leaves / genetics; Plant Leaves / growth & development; Plant Proteins / genetics; Populus / genetics; Populus / growth & development; Sequence Analysis, RNA; Transcription Factors / genetics; Transcriptome; Wood / genetics; Wood / growth & development; Xylem / genetics; Xylem / growth & development
TL;DR:
The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2015 journal article
Expression analysis of genes encoding mitogen-activated protein kinases in maize provides a key link between abiotic stress signaling and plant reproduction
FUNCTIONAL & INTEGRATIVE GENOMICS, 15(1), 107–120.
author keywords: Maize; MAPK; Gene family; Gene expression; Abiotic stress; Plant reproduction
MeSH headings : Abscisic Acid / pharmacology; Amino Acid Motifs; Chromosomes, Plant / genetics; Cold Temperature; Conserved Sequence / genetics; Droughts; Exons / genetics; Gene Duplication; Gene Expression Profiling; Gene Expression Regulation, Enzymologic / drug effects; Gene Expression Regulation, Plant / drug effects; Genes, Plant; Introns / genetics; Mitogen-Activated Protein Kinases / chemistry; Mitogen-Activated Protein Kinases / genetics; Mitogen-Activated Protein Kinases / metabolism; Multigene Family; Organ Specificity / drug effects; Organ Specificity / genetics; Phylogeny; Plant Proteins / chemistry; Plant Proteins / genetics; Plant Proteins / metabolism; Promoter Regions, Genetic / genetics; Protein Structure, Tertiary; Reproduction / drug effects; Reproduction / genetics; Signal Transduction / genetics; Sodium Chloride / pharmacology; Stress, Physiological / drug effects; Stress, Physiological / genetics; Zea mays / drug effects; Zea mays / enzymology; Zea mays / genetics
TL;DR:
expression analyses indicated that ZmMPKs might serve as linkers between abiotic stress signaling and plant reproduction, and will deepen the understanding of the complexity of the maize MAPK gene family and provide new clues to investigate their functions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2015 journal article
Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis
Proceedings of the National Academy of Sciences, 112(27), 8481–8486.
Contributors: J. Wang n , L. Chuang n, P. Loziuk n, n, Y. Lin n, R. Shi n, G. Qu *, D. Muddiman n , R. Sederoff n, V. Chiang n
author keywords: AldOMT; COMT; lignin; phosphoproteomics; phosphoregulation
MeSH headings : Acrolein / analogs & derivatives; Acrolein / metabolism; Amino Acid Sequence; Binding Sites / genetics; Biocatalysis; Catechols / metabolism; Chromatography, Liquid; Electrophoresis, Polyacrylamide Gel; Green Fluorescent Proteins / genetics; Green Fluorescent Proteins / metabolism; Isoenzymes / genetics; Isoenzymes / metabolism; Lignin / biosynthesis; Methyltransferases / genetics; Methyltransferases / metabolism; Microscopy, Confocal; Molecular Sequence Data; Mutation; Phosphoproteins / metabolism; Phosphorylation; Plant Proteins / genetics; Plant Proteins / metabolism; Populus / enzymology; Populus / genetics; Populus / metabolism; Proteomics / methods; Protoplasts / enzymology; Protoplasts / metabolism; Sequence Homology, Amino Acid; Tandem Mass Spectrometry
TL;DR:
It is shown that reversible monophosphorylation at Ser123 or Ser125 acts as an on/off switch for the activity of 5-hydroxyconiferaldehyde O-methyltransferase 2 (PtrAldOMT2), an enzyme central to monolignol biosynthesis for lignification in stem-differentiating xylem of Populus trichocarpa.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018
2014 journal article
A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue
NATURE PROTOCOLS, 9(9), 2180–2193.
MeSH headings : Base Sequence; Chromatin Immunoprecipitation / methods; DNA / metabolism; DNA Fragmentation; Histones / metabolism; Immunoprecipitation; Molecular Sequence Data; Populus / cytology; Populus / metabolism; Sequence Analysis, DNA; Transcription Factors / metabolism; Wood / cytology; Xylem / genetics; Xylem / metabolism
TL;DR:
This protocol is the only working ChIP system for wood-forming tissue and uses stem-differentiating xylem to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
A simple improved-throughput xylem protoplast system for studying wood formation
NATURE PROTOCOLS, 9(9), 2194–2205.
MeSH headings : Cell Wall / metabolism; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Green Fluorescent Proteins; Populus / cytology; Populus / growth & development; Protoplasts / metabolism; Transfection / methods; Wood / cytology; Wood / growth & development; Xylem / chemistry
TL;DR:
A protocol for the isolation and transfection of protoplasts from wood-forming tissue, the stem-differentiating xylem (SDX), in the model woody plant Populus trichocarpa is presented.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2012 journal article
Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(36), 14699–14704.
MeSH headings : Blotting, Western; Cloning, Molecular; DNA Primers / genetics; Dimerization; Electrophoresis, Polyacrylamide Gel; Gene Regulatory Networks / genetics; Homeostasis / physiology; Models, Biological; Plasmids / genetics; Populus / genetics; Protein Isoforms / genetics; Protein Transport; Real-Time Polymerase Chain Reaction; Transcription Factors / genetics
TL;DR:
A stem-differentiating xylem (SDX)-specific alternative SND1 splice variant, PtrSND1-A2IR, that acts as a dominant negative of S ND1 transcriptional network genes in Populus trichocarpa is discovered and may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
journal article
Permeability reduction phenomena in packed beds, fiber mats, and wet webs of paper exposed to flow of liquids and suspensions: A review
Hubbe, M. A., Chen, H., & Heitmann, J. A. BioResources, 4(1), 405–451.
Source: NC State University Libraries
Added: August 6, 2018
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