Works (30)

Updated: August 8th, 2023 21:20

2021 journal article

Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa

FRONTIERS IN PLANT SCIENCE, 12.

By: C. Lin n, Y. Sun*, J. Song n, H. Chen n, R. Shi n, C. Yang n, J. Liu n, S. Tunlaya-Anukit n ...

author keywords: protein interaction; monolignol biosynthesis; wood formation; Populus trichocarpa; BiFC; metabolic flux
Sources: Web Of Science, ORCID
Added: November 8, 2021

2021 article

Homoeologous chromosome exchange explains the creation of a QTL affecting soil-borne pathogen resistance in tobacco

Shi, R., Jin, J., Nifong, J. M., Shew, D., & Lewis, R. S. (2021, October 22). PLANT BIOTECHNOLOGY JOURNAL.

By: R. Shi n, J. Jin n, J. Nifong n, D. Shew n & R. Lewis n

author keywords: homoeologous exchange; QTL; resistance; SAR8; 2; tobacco; Phytophthora
MeSH headings : Chromosomes, Plant / genetics; Disease Resistance / genetics; Plant Diseases / genetics; Quantitative Trait Loci / genetics; Soil; Tobacco / genetics
Source: Web Of Science
Added: November 1, 2021

2021 journal article

RNAseq Reveals Differential Gene Expression Contributing to Phytophthora nicotianae Adaptation to Partial Resistance in Tobacco

AGRONOMY-BASEL, 11(4).

By: J. Jin n, R. Shi n, R. Lewis n & H. Shew n

author keywords: RNAseq; Phytophthora nicotianae; adaptation; partial resistance; tobacco
Source: Web Of Science
Added: May 10, 2021

2019 journal article

Genetic Control of Facultative Parthenocarpy in Nicotiana tabacum L.

JOURNAL OF HEREDITY, 110(5), 610–617.

By: A. Dexter-Boone n, M. Humphry*, R. Shi n & R. Lewis n

author keywords: Genomics and gene mapping; haploids; Nicotiana; parthenocarpy; QTL mapping; tobacco
MeSH headings : Chromosome Mapping; Fruit / genetics; Genetic Association Studies; Haploidy; Parthenogenesis / genetics; Quantitative Trait Loci; Quantitative Trait, Heritable; Seeds / genetics; Tobacco / genetics
Source: Web Of Science
Added: September 16, 2019

2019 journal article

Identification and validation of SNP markers associated with Wz-mediated Phytophthora nicotianae resistance in Nicotiana tabacum L.

MOLECULAR BREEDING, 39(7).

By: R. Shi n, H. Hubert n, A. Dexter-Boone n, J. Zeng*, S. Kernodle n & R. Lewis n

author keywords: Nicotiana; Tobacco; RNA-seq; Black shank; Phytophthora nicotianae
Source: Web Of Science
Added: July 22, 2019

2018 journal article

Filter paper-based spin column method for cost-efficient DNA or RNA purification

PLOS ONE, 13(12).

By: R. Shi n, R. Lewis n & D. Panthee n

MeSH headings : Centrifugation / methods; DNA, Plant / chemistry; DNA, Plant / isolation & purification; Solanum lycopersicum / chemistry; Paper; RNA, Plant / chemistry; RNA, Plant / isolation & purification; Tobacco / chemistry
Sources: Web Of Science, ORCID
Added: December 31, 2018

2018 journal article

Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis

Nature Communications, 9(1), 1579.

By: J. Wang*, M. Matthews n, C. Williams n, R. Shi n, C. Yang n, S. Tunlaya-Anukit n, H. Chen 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
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2017 journal article

A novel plant DNA extraction method using filter paper-based 96-well spin plate

Planta, 246(3), 579–584.

By: R. Shi n & D. Panthee n

author keywords: Filter paper; DNA extraction; Inexpensive; Safe; High throughput; Solanum lycopersicum; Ph-3 gene
MeSH headings : Centrifugation / instrumentation; Centrifugation / methods; DNA, Plant / isolation & purification; Electrophoresis / methods; Genetic Markers; Polymerase Chain Reaction; Reproducibility of Results
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.

By: Y. Lin n, H. Chen 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
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.

By: R. Shi n, J. Wang n, Y. Lin n, Q. Li*, Y. Sun*, H. Chen n, R. Sederoff n, V. Chiang n

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
Sources: Web Of Science, ORCID
Added: August 6, 2018

2016 journal article

A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa

Tree Genetics & Genomes, 12(2).

By: C. Lin n, Q. Li*, S. Tunlaya-Anukit*, R. Shi n, Y. Sun*, J. Wang n, J. Liu n, P. Loziuk n ...

author keywords: Lignin polymerization; Populus trichocarpa; Lignin peroxidase; LC-MS/MS; Lignin systems biology
Sources: Web Of Science, ORCID, Crossref
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.

By: J. Wang n, L. Chuang n, P. Loziuk n, H. Chen 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
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
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.

By: Y. Lin n, W. Li n, H. Chen n, Q. Li n, Y. Sun*, R. Shi n, C. Lin n, J. Wang n ...

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
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Growth under field conditions affects lignin content and productivity in transgenic Populus trichocarpa with altered lignin biosynthesis

BIOMASS & BIOENERGY, 68, 228–239.

By: A. Stout n, A. Davis n, J. Domec n, C. Yang n, R. Shi n & J. King n

author keywords: Populus; Lignin; Field trial; Transgenic; Bioenergy
Sources: Web Of Science, ORCID
Added: August 6, 2018

2014 journal article

Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling

The Plant Cell, 26(3), 876–893.

By: H. Chen n, J. Song n, J. Wang n, Y. Lin n, J. Ducoste n, C. Shuford n, J. Liu n, Q. Li n ...

MeSH headings : Coenzyme A Ligases / genetics; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Immunoprecipitation; Lignin / biosynthesis; Mass Spectrometry; Models, Biological; Populus / metabolism; Propionates; RNA, Messenger / genetics; Substrate Specificity; Systems Biology
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2014 journal article

Vibrational sum-frequency-generation (SFG) spectroscopy study of the structural assembly of cellulose microfibrils in reaction woods

CELLULOSE, 21(4), 2219–2231.

By: K. Kafle*, R. Shi n, C. Lee*, A. Mittal*, Y. Park*, Y. Sun n, S. Park n, V. Chiang n, S. Kim*

author keywords: Reaction wood; Tension wood; Compression wood; Cellulose microfibril assembly; Sum; frequency; generation spectroscopy; X-ray; diffraction
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes

PLANT PHYSIOLOGY, 161(3), 1501–1516.

By: H. Chen n, J. Song n, C. Williams n, C. Shuford n, J. Liu n, J. Wang n, Q. Li n, R. Shi n ...

MeSH headings : Allosteric Regulation / drug effects; Binding Sites; Biosynthetic Pathways / drug effects; Blotting, Western; Caffeic Acids / pharmacology; Coenzyme A / metabolism; Coenzyme A Ligases / antagonists & inhibitors; Coenzyme A Ligases / metabolism; Computer Simulation; Coumaric Acids / chemistry; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Kinetics; Lignin / biosynthesis; Lignin / chemistry; Phenylpropionates / metabolism; Phosphoproteins / metabolism; Phosphorylation / drug effects; Plant Extracts; Populus / drug effects; Populus / enzymology; Propionates; Proteomics; Recombinant Fusion Proteins / metabolism; Sequence Homology, Amino Acid; Substrate Specificity / drug effects; Xylem / drug effects; Xylem / metabolism
Sources: Web Of Science, ORCID
Added: August 6, 2018

2013 journal article

Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa

Planta, 238(3), 487–497.

By: R. Shi n, C. Shuford n, J. Wang n, Y. Sun n, Z. Yang n, H. Chen n, S. Tunlaya-Anukit n, Q. Li n ...

MeSH headings : Gene Expression Regulation, Plant / physiology; Mass Spectrometry; Phenylalanine Ammonia-Lyase / metabolism; Populus / enzymology; Populus / metabolism
Sources: NC State University Libraries, ORCID
Added: August 6, 2018

2013 journal article

The elucidation of the lignin structure effect on the cellulase-mediated saccharification by genetic engineering poplars (Populus nigra L. x Populus maximowiczii A.)

BIOMASS & BIOENERGY, 58, 52–57.

By: D. Min n, C. Yang n, R. Shi n, H. Jameel n, V. Chiang n & H. Chang n

author keywords: Transgenic hybrid poplar; Pretreatment; S to V Ratio; Delignification; Enzymatic saccharification
Source: Web Of Science
Added: August 6, 2018

2012 journal article

A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities

PLANTA, 236(3), 879–885.

By: J. Liu n, R. Shi n, Q. Li n, R. Sederoff n & V. Chiang n

author keywords: Monolignols; Enzyme activity; Populus trichocarpa; Pinus taeda; Angiosperm; Gymnosperm
MeSH headings : Biosynthetic Pathways; Chromatography, High Pressure Liquid; Enzyme Assays; Lignin / biosynthesis; Methyltransferases / metabolism; Mixed Function Oxygenases / metabolism; Oxidoreductases / metabolism; Pinus taeda / enzymology; Plant Proteins / analysis; Plant Stems / enzymology; Populus / enzymology; Substrate Specificity; Xylem / enzymology
Source: Web Of Science
Added: August 6, 2018

2012 journal article

Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry

Journal of Proteome Research, 11(6), 3390–3404.

By: C. Shuford n, Q. Li n, Y. Sun n, H. Chen n, J. Wang n, R. Shi n, R. Sederoff n, V. Chiang n, D. Muddiman n

author keywords: quantification; isotope dilution mass spectrometry; selected reaction monitoring; filter-aided sample preparation; monolignol biosynthesis
MeSH headings : Amino Acid Sequence; Biosynthetic Pathways; Isotope Labeling; Molecular Sequence Data; Plant Proteins / chemistry; Plant Proteins / metabolism; Populus / enzymology; Proteome / chemistry; Proteome / metabolism; Reference Standards; Spectrometry, Mass, Electrospray Ionization / standards; Xylem / enzymology
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018

2012 journal article

MicroRNAs in trees

PLANT MOLECULAR BIOLOGY, 80(1), 37–53.

By: Y. Sun n, R. Shi n, X. Zhang n, V. Chiang n & R. Sederoff n

author keywords: MicroRNA; Woody plant; Gene regulation; Plant development; Plant stress response; Artificial microRNA
MeSH headings : Gene Expression Regulation, Plant; MicroRNAs / genetics; MicroRNAs / metabolism; Models, Genetic; Phylogeny; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Plant / genetics; RNA, Plant / metabolism; Trees / classification; Trees / genetics; Trees / metabolism
Source: Web Of Science
Added: August 6, 2018

2010 journal article

Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa

PLANTA, 232(6), 1281–1288.

By: R. Shi n, C. Yang n, S. Lu n, R. Sederoff n & V. Chiang n

author keywords: Artificial microRNA; Phenylalanine ammonia-lyase; Populus trichocarpa transformation; Down-regulation; PolyA tailing-based real time RT-PCR; Quantitation
MeSH headings : Base Sequence; DNA Primers; Down-Regulation; Genes, Plant; MicroRNAs / physiology; Mutation; Populus / genetics; Reverse Transcriptase Polymerase Chain Reaction; Sequence Homology, Nucleic Acid
Source: Web Of Science
Added: August 6, 2018

2010 review

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes

[Review of ]. PLANT AND CELL PHYSIOLOGY, 51(1), 144–163.

By: R. Shi n, Y. Sun n, Q. Li n, S. Heber n, R. Sederoff n & V. Chiang n

author keywords: Lignin systems biology; Monolignol biosynthesis; Populus trichocarpa; Promoter motifs; Transcript abundance; Xylem-specific expression
MeSH headings : Amino Acid Motifs / genetics; Biosynthetic Pathways / genetics; Enzymes / biosynthesis; Enzymes / genetics; Gene Expression Regulation, Enzymologic / physiology; Gene Expression Regulation, Plant / physiology; Genome, Plant / genetics; Lignin / biosynthesis; Lignin / genetics; Phloem / enzymology; Phloem / genetics; Plant Shoots / enzymology; Plant Shoots / genetics; Populus / genetics; Populus / metabolism; Promoter Regions, Genetic / genetics; RNA, Messenger / analysis; RNA, Messenger / genetics; RNA, Messenger / metabolism; RNA, Plant / analysis; RNA, Plant / genetics; RNA, Plant / metabolism; Transcription, Genetic / physiology; Xylem / enzymology; Xylem / genetics
Sources: Web Of Science, ORCID
Added: August 6, 2018

2009 journal article

Isolation of expressed sequences from a specific chromosome of Thinopyrum intermedium infected by BYDV

GENOME, 52(1), 68–76.

By: S. Jiang n, W. Yin n, J. Hu n, R. Shi n, R. Zhou n, Y. Chen n, G. Zhou n, R. Wang n, L. Song n, Z. Hu n

author keywords: TAi-27; Thinopyrum intermedium; chromosome microdissection; hybridization-specific amplification (HSA); expressed sequences; barley yellow dwarf virus (BYDV)
MeSH headings : Chromosome Mapping; Chromosomes / ultrastructure; Chromosomes, Plant; Cloning, Molecular; DNA, Complementary / metabolism; DNA, Plant / metabolism; Expressed Sequence Tags; Gene Expression Regulation; Genes, Plant; Genome, Plant; Luteovirus / genetics; Models, Genetic; Oligonucleotides / genetics; RNA, Messenger / metabolism; Triticum / genetics; Triticum / virology
Source: Web Of Science
Added: August 6, 2018

2008 journal article

Rapid EST isolation from chromosome IR of rye

BMC PLANT BIOLOGY, 8.

By: R. Zhou*, R. Shi*, S. Jiang*, W. Yin*, H. Wang*, Y. Chen*, J. Hu*, R. Wang*, X. Zhang*, Z. Hu*

MeSH headings : Chromosomes, Plant / genetics; DNA, Complementary / genetics; DNA, Plant / genetics; Expressed Sequence Tags; Immunoblotting; Secale / genetics
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Facile means for quantifying microRNA expression by real-time PCR

BIOTECHNIQUES, 39(4), 519–525.

By: R. Shi n & V. Chiang*

MeSH headings : Arabidopsis / genetics; Base Sequence; Benzothiazoles; Blotting, Northern; DNA Primers / chemistry; DNA, Complementary / metabolism; Diamines; Fluorescent Dyes / pharmacology; Genes, Plant / genetics; MicroRNAs / analysis; Molecular Sequence Data; Organic Chemicals / pharmacology; Plant Leaves / metabolism; Plant Stems / metabolism; Polymerase Chain Reaction; Quinolines; RNA / metabolism; Reverse Transcriptase Polymerase Chain Reaction / methods; Sensitivity and Specificity; Temperature; Tissue Distribution; Transcription, Genetic
Source: Web Of Science
Added: August 6, 2018

2005 journal article

Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis

Plant Cell, 17(8), 2186–2203.

By: S. Lu n, Y. Sun n, R. Shi n, C. Clark n, L. Li n & V. Chiang n

MeSH headings : Arabidopsis / genetics; Base Sequence; Conserved Sequence; Gene Expression Regulation, Plant; MicroRNAs / chemistry; MicroRNAs / genetics; Molecular Sequence Data; Plant Stems / genetics; Populus / genetics; RNA, Plant / genetics; Species Specificity; Transcription, Genetic
Source: NC State University Libraries
Added: August 6, 2018

2004 journal article

RNA silencing in plants by the expression of siRNA duplexes

NUCLEIC ACIDS RESEARCH, 32(21).

By: S. Lu*, R. Shi, C. Tsao, X. Yi, L. Li & V. Chiang

MeSH headings : Gene Expression Regulation, Plant; Genetic Vectors; Glucuronidase / analysis; Glucuronidase / genetics; Humans; Molecular Sequence Data; Promoter Regions, Genetic; RNA / genetics; RNA Interference; RNA, Small Cytoplasmic / genetics; RNA, Small Interfering / biosynthesis; RNA, Small Interfering / chemistry; RNA, Small Interfering / genetics; Signal Recognition Particle / genetics; Tobacco / genetics; Tobacco / metabolism
Source: Web Of Science
Added: August 6, 2018