@article{kafle_shi_lee_mittal_park_sun_park_chiang_kim_2014, title={Vibrational sum-frequency-generation (SFG) spectroscopy study of the structural assembly of cellulose microfibrils in reaction woods}, volume={21}, ISSN={["1572-882X"]}, DOI={10.1007/s10570-014-0322-3}, number={4}, journal={CELLULOSE}, author={Kafle, Kabindra and Shi, Rui and Lee, Christopher M. and Mittal, Ashutosh and Park, Yong Bum and Sun, Ying-Hsuan and Park, Sunkyu and Chiang, Vincent and Kim, Seong H.}, year={2014}, month={Aug}, pages={2219–2231} }
 @article{shi_shuford_wang_sun_yang_chen_tunlaya-anukit_li_liu_muddiman_et al._2013, title={Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa}, volume={238}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84882877816&partnerID=MN8TOARS}, DOI={10.1007/s00425-013-1905-1}, abstractNote={Phenylalanine ammonia-lyase (PAL) catalyzes the initial step of phenylpropanoid biosynthesis in plants. Five PAL genes (PtrPAL1 to 5) have been identified in Populus trichocarpa. These genes are classified into two subgroups according to their transcript sequence similarity and tissue specificity. However, the regulation of these genes and their protein functions are not well understood. In this study, enzymatic properties of each PtrPALs were characterized based on their recombinant proteins expressed in E.coli. Subcellular localizations of each PtrPALs in stem wood forming tissue were investigated and individual PtrPAL protein abundances in cytosol and membrane protein fractions were measured using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Protein/mRNA ratios of PtrPALs were further verified using RNA-Seq and gel-enhanced liquid chromatography mass spectrometry (GeLC-MS). All PtrPALs have similar catalytic properties for the deamination of L-phenylalanine, their major substrate. All PtrPALs have similar subcellular locations in stem wood forming tissue, with major amount in the cytosol (93-96 %) and less in the membrane (4-7 %). However, the protein/mRNA ratios of subgroup A (PtrPAL2, 4 and 5) are about five times that of subgroup B (PtrPAL1 and 3) in stem wood forming tissue, while all PtrPALs have similar transcript abundances. These results indicate a greater functional significance of subgroup A PtrPALs for stem wood formation, and highlight the role of gene post-transcriptional regulation.}, number={3}, journal={Planta}, author={Shi, R. and Shuford, C. M. and Wang, Jack P. and Sun, Y. H. and Yang, Z. C. and Chen, H. C. and Tunlaya-Anukit, S. and Li, Q. Z. and Liu, J. and Muddiman, David and et al.}, year={2013}, pages={487–497} }
 @article{shuford_li_sun_chen_wang_shi_sederoff_chiang_muddiman_2012, title={Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry}, volume={11}, ISSN={1535-3893 1535-3907}, url={http://dx.doi.org/10.1021/pr300205a}, DOI={10.1021/pr300205a}, abstractNote={The economic value of wood/pulp from many tree species is largely dictated by the quantity and chemical properties of lignin, which is directly related to the composition and linkages of monolignols comprising the polymer. Although much is known regarding the monolignol biosynthetic pathway, our understanding is still deficient due to the lack of quantitative information at the proteomic level. We developed an assay based on protein cleavage isotope dilution mass spectrometry (PC-IDMS) for the determination of all potential, primary enzymes involved in the biosynthesis of monolignols and the peroxidases responsible for their polymerization to form lignin in the model tree species, Populus trichocarpa. Described is the identification of quantitative surrogate peptides through shotgun analysis of native and recombinant proteins, optimization of trypsin proteolysis using fractional factorial design of experiments, and development of a liquid chromatography-selected reaction monitoring method for specific detection of all targeted peptides. Of the 25 targeted enzymes, three were undetected in the normal xylem tissues, and all but two of the detectable species showed good day-to-day precision (CV < 10%). This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level.}, number={6}, journal={Journal of Proteome Research}, publisher={American Chemical Society (ACS)}, author={Shuford, Christopher M. and Li, Quanzi and Sun, Ying-Hsuan and Chen, Hsi-Chuan and Wang, Jack and Shi, Rui and Sederoff, Ronald. R. and Chiang, Vincent L. and Muddiman, David C.}, year={2012}, month={May}, pages={3390–3404} }
 @article{wang_shuford_li_song_lin_sun_chen_williams_muddiman_sederoff_et al._2012, title={Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis}, volume={236}, ISSN={["1432-2048"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84865584315&partnerID=MN8TOARS}, DOI={10.1007/s00425-012-1663-5}, abstractNote={Flowering plants have syringyl and guaiacyl subunits in lignin in contrast to the guaiacyl lignin in gymnosperms. The biosynthesis of syringyl subunits is initiated by coniferaldehyde 5-hydroxylase (CAld5H). In Populus trichocarpa there are two closely related CAld5H enzymes (PtrCAld5H1 and PtrCAld5H2) associated with lignin biosynthesis during wood formation. We used yeast recombinant PtrCAld5H1 and PtrCAld5H2 proteins to carry out Michaelis-Menten and inhibition kinetics with LC-MS/MS based absolute protein quantification. CAld5H, a monooxygenase, requires a cytochrome P450 reductase (CPR) as an electron donor. We cloned and expressed three P. trichocarpa CPRs in yeast and show that all are active with both CAld5Hs. The kinetic analysis shows both CAld5Hs have essentially the same biochemical functions. When both CAld5Hs are coexpressed in the same yeast membranes, the resulting enzyme activities are additive, suggesting functional redundancy and independence of these two enzymes. Simulated reaction flux based on Michaelis-Menten kinetics and inhibition kinetics confirmed the redundancy and independence. Subcellular localization of both CAld5Hs as sGFP fusion proteins expressed in P. trichocarpa differentiating xylem protoplasts indicate that they are endoplasmic reticulum resident proteins. These results imply that during wood formation, 5-hydroxylation in monolignol biosynthesis of P. trichocarpa requires the combined metabolic flux of these two CAld5Hs to maintain adequate biosynthesis of syringyl lignin. The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis.}, number={3}, journal={PLANTA}, publisher={Springer Science + Business Media}, author={Wang, Jack P. and Shuford, Christopher M. and Li, Quanzi and Song, Jina and Lin, Ying-Chung and Sun, Ying-Hsuan and Chen, Hsi-Chuan and Williams, Cranos M. and Muddiman, David C. and Sederoff, Ronald R. and et al.}, year={2012}, month={Sep}, pages={795–808} }
 @article{sun_shi_zhang_chiang_sederoff_2012, title={MicroRNAs in trees}, volume={80}, ISSN={["0167-4412"]}, DOI={10.1007/s11103-011-9864-z}, abstractNote={MicroRNAs (miRNAs) are 20-24 nucleotide long molecules processed from a specific class of RNA polymerase II transcripts that mainly regulate the stability of mRNAs containing a complementary sequence by targeted degradation in plants. Many features of tree biology are regulated by miRNAs affecting development, metabolism, adaptation and evolution. MiRNAs may be modified and harnessed for controlled suppression of specific genes to learn about gene function, or for practical applications through genetic engineering. Modified (artificial) miRNAs act as dominant suppressors and are particularly useful in tree genetics because they bypass the generations of inbreeding needed for fixation of recessive mutations. The purpose of this review is to summarize the current status of information on miRNAs in trees and to guide future studies on the role of miRNAs in the biology of woody perennials and to illustrate their utility in directed genetic modification of trees.}, number={1}, journal={PLANT MOLECULAR BIOLOGY}, author={Sun, Ying-Hsuan and Shi, Rui and Zhang, Xing-Hai and Chiang, Vincent L. and Sederoff, Ronald R.}, year={2012}, month={Sep}, pages={37–53} }
 @article{li_lin_sun_song_chen_zhang_sederoff_chiang_2012, title={Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa}, volume={109}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1212977109}, abstractNote={
            Secondary Wall-Associated NAC Domain 1s (SND1s) are transcription factors (TFs) known to activate a cascade of
            TF
            and pathway genes affecting secondary cell wall biosynthesis (xylogenesis) in
            Arabidopsis
            and poplars. Elevated SND1 transcriptional activation leads to ectopic xylogenesis and stunted growth. Nothing is known about the upstream regulators of
            SND1
            . Here we report the discovery of a stem-differentiating xylem (SDX)-specific alternative
            SND1
            splice variant,
            PtrSND1
            -
            A2
            
              IR
            
            , that acts as a dominant negative of SND1 transcriptional network genes in
            Populus trichocarpa
            .
            PtrSND1
            -
            A2
            
              IR
            
            derives from
            PtrSND1-A2
            , one of the four fully spliced
            PtrSND1
            gene family members (
            PtrSND1
            -
            A1
            , -
            A2
            , -
            B1
            , and -
            B2
            ). Each full-size PtrSND1 activates its own gene, and all four full-size members activate a common
            MYB
            gene (
            PtrMYB021
            ). PtrSND1-A2
            IR
            represses the expression of its
            PtrSND1
            member genes and
            PtrMYB021
            . Repression of the autoregulation of a TF family by its only splice variant has not been previously reported in plants. PtrSND1-A2
            IR
            lacks DNA binding and transactivation abilities but retains dimerization capability. PtrSND1-A2
            IR
            is localized exclusively in cytoplasmic foci. In the presence of any full-size PtrSND1 member, PtrSND1-A2
            IR
            is translocated into the nucleus exclusively as a heterodimeric partner with full-size PtrSND1s. Our findings are consistent with a model in which the translocated PtrSND1-A2
            IR
            lacking DNA-binding and transactivating abilities can disrupt the function of full-size PtrSND1s, making them nonproductive through heterodimerization, and thereby modulating the SND1 transcriptional network. PtrSND1-A2
            IR
            may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth.
          }, number={36}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Li, Quanzi and Lin, Ying-Chung and Sun, Ying-Hsuan and Song, Jian and Chen, Hao and Zhang, Xing-Hai and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2012}, month={Sep}, pages={14699–14704} }
 @article{hung_sun_chen_darlington_williams_burkey_xie_2010, title={Identification of a Mg-protoporphyrin IX monomethyl ester cyclase homologue, EaZIP, differentially expressed in variegated Epipremnum aureum 'Golden Pothos' is achieved through a unique method of comparative study using tissue regenerated plants}, volume={61}, ISSN={["1460-2431"]}, DOI={10.1093/jxb/erq020}, abstractNote={Variegated plants provide a valuable tool for studying chloroplast biogenesis by allowing direct comparison between green and white/yellow sectors within the same leaf. While variegated plants are abundant in nature, the mechanism of leaf variegation remains largely unknown. Current studies are limited to a few mutants in model plant species, and are complicated by the potential for cross-contamination during dissection of leaf tissue into contrasting sectors. To overcome these obstacles, an alternative approach was explored using tissue-culture techniques to regenerate plantlets from unique sectors. Stable green and pale yellow plants were developed from a naturally variegated Epipremnum aureum 'Golden Pothos'. By comparing the gene expression between green and pale yellow plants using suppression subtractive hybridization in conjunction with homologous sequence search, nine down-regulated and 18 up-regulated genes were identified in pale yellow plants. Transcript abundance for EaZIP (Epipremnum aureum leucine zipper), a nuclear gene homologue of tobacco NTZIP and Arabidopsis CHL27, was reduced more than 4000-fold in qRT-PCR analysis. EaZIP encodes the Mg-protoporphyrin IX monomethyl ester cyclase, one of the key enzymes in the chlorophyll biosynthesis pathway. Examination of EaZIP expression in naturally variegated 'Golden Pothos' confirmed that EaZIP transcript levels were correlated with leaf chlorophyll contents, suggesting that this gene plays a major role in the loss of chlorophyll in the pale yellow sectors of E. aureum 'Golden Pothos'. This study further suggests that tissue-culture regeneration of plantlets from different coloured sectors of variegated leaves can be used to investigate the underlying mechanisms of variegation.}, number={5}, journal={JOURNAL OF EXPERIMENTAL BOTANY}, author={Hung, Chiu-Yueh and Sun, Ying-Hsuan and Chen, Jianjun and Darlington, Diane E. and Williams, Alfred L. and Burkey, Kent O. and Xie, Jiahua}, year={2010}, month={Mar}, pages={1483–1493} }
 @misc{shi_sun_li_heber_sederoff_chiang_2010, title={Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes}, volume={51}, ISSN={["1471-9053"]}, DOI={10.1093/pcp/pcp175}, abstractNote={As a step toward a comprehensive description of lignin biosynthesis in Populus trichocarpa, we identified from the genome sequence 95 phenylpropanoid gene models in 10 protein families encoding enzymes for monolignol biosynthesis. Transcript abundance was determined for all 95 genes in xylem, leaf, shoot and phloem using quantitative real-time PCR (qRT-PCR). We identified 23 genes that most probably encode monolignol biosynthesis enzymes during wood formation. Transcripts for 18 of the 23 are abundant and specific to differentiating xylem. We found evidence suggesting functional redundancy at the transcript level for phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), p-hydroxycinnamoyl-CoA:quinate shikimate p-hydroxycinnamoyltransferase (HCT), caffeoyl-CoA O-methyltransferase (CCoAOMT) and coniferyl aldehyde 5-hydroxylase (CAld5H). We carried out an enumeration-based motif identification and discriminant analysis on the promoters of all 95 genes. Five core motifs correctly discriminate the 18 xylem-specific genes from the 77 non-xylem genes. These motifs are similar to promoter elements known to regulate phenylpropanoid gene expression. This work suggests that genes in monolignol biosynthesis are regulated by multiple motifs, often related in sequence.}, number={1}, journal={PLANT AND CELL PHYSIOLOGY}, author={Shi, Rui and Sun, Ying-Hsuan and Li, Quanzi and Heber, Steffen and Sederoff, Ronald and Chiang, Vincent L.}, year={2010}, month={Jan}, pages={144–163} }
 @article{lu_sun_chiang_2009, title={Adenylation of plant miRNAs}, volume={37}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkp031}, abstractNote={The modification or degradation of RNAs including miRNAs may play vital roles in regulating RNA functions. The polyadenylation- and exosome-mediated RNA decay is involved in the degradation of plant RNAs including the primary miRNA processing intermediates. However, plant miRNA levels are not affected by exosome depletion. Here, we report the cloning of a large number of 5′ and/or 3′ truncated versions of the known miRNAs from various tissues of Populus trichocarpa (black cottonwood). It suggests that plant miRNAs may be degraded through either 5′ to 3′ or 3′ to 5′ exonucleolytic digestion. We also show that a significant portion of the isolated miRNAs contains, at the 3′-end, one or a few post-transcriptionally added adenylic acid residues, which are distinct in length from the polyadenylate tail added to other plant RNAs for exosome-mediated degradation. Using an in vitro miRNA degradation system, where synthesized miRNA oligos were degraded in extracts of P. trichocarpa cells, we revealed that the adenylated miRNAs were degraded slower than others without adenylation. It indicates that addition of adenylic acid residues on the 3′-end plays a negative role in miRNA degradation. Our results provide new information for understanding the mechanism of miRNA degradation.}, number={6}, journal={NUCLEIC ACIDS RESEARCH}, author={Lu, Shanfa and Sun, Ying-Hsuan and Chiang, Vincent L.}, year={2009}, month={Apr}, pages={1878–1885} }
 @article{yeh_wang_rui_sun_chiang_2008, title={A novel O-Methyltransferase-like gene with a drastic extopic expression in response to tension wood formation in Poupulus trichocarpa}, volume={41}, number={9-10}, journal={Cellulose Chemistry and Technology}, author={Yeh, T. F. and Wang, J. and Rui, S. and Sun, Y. H. and Chiang, V. L.}, year={2008}, pages={521–528} }
 @article{lu_sun_chiang_2008, title={Stress-responsive microRNAs in Populus}, volume={55}, ISSN={["1365-313X"]}, DOI={10.1111/j.1365-313X.2008.03497.x}, abstractNote={Summary}, number={1}, journal={PLANT JOURNAL}, author={Lu, Shanfa and Sun, Ying-Hsuan and Chiang, Vincent L.}, year={2008}, month={Jul}, pages={131–151} }
 @misc{lu_sun_amerson_chiang_2007, title={MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development}, volume={51}, ISSN={["1365-313X"]}, DOI={10.1111/j.1365-313x.2007.03208.x}, abstractNote={Summary}, number={6}, journal={PLANT JOURNAL}, author={Lu, Shanfa and Sun, Ying-Hsuan and Amerson, Henry and Chiang, Vincent L.}, year={2007}, month={Sep}, pages={1077–1098} }
 @article{suzuki_li_sun_chiang_2006, title={The cellulose synthase gene superfamily and biochemical functions of xylem-specific cellulose synthase-like genes in Populus trichocarpa}, volume={142}, ISSN={["1532-2548"]}, DOI={10.1104/pp.106.086678}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Suzuki, Shiro and Li, Laigeng and Sun, Ying-Hsuan and Chiang, Vincent L.}, year={2006}, month={Nov}, pages={1233–1245} }
 @article{lu_sun_shi_clark_li_chiang_2005, title={Novel and mechanical stress-responsive microRNAs in Populus trichocarpa that are absent from Arabidopsis}, volume={17}, DOI={10.1105/tpc.105.033456}, abstractNote={Abstract}, number={8}, journal={Plant Cell}, author={Lu, S. F. and Sun, Y. H. and Shi, R. and Clark, C. and Li, L. G. and Chiang, V. L.}, year={2005}, pages={2186–2203} }
 @article{jaaskelainen_sun_argyropoulos_tamminen_hortling_2003, title={The effect of isolation method on the chemical structure of residual lignin}, volume={37}, ISSN={["0043-7719"]}, DOI={10.1007/s00226-003-0163-y}, number={2}, journal={WOOD SCIENCE AND TECHNOLOGY}, author={Jaaskelainen, AS and Sun, Y and Argyropoulos, DS and Tamminen, T and Hortling, B}, year={2003}, month={Oct}, pages={91–102} }
 @inproceedings{sun_cheng_2002, title={Dilute sulfuric acid pretreatment of agricultural residues for ethanol production}, volume={2}, booktitle={ASAE annual International Meeting/CIGR World Congress : July 28-31, 2002, Chicago, Illinois : engineering for a sustainable world}, author={Sun, Y. and Cheng, J.}, year={2002}, pages={6198} }
 @inproceedings{sun_adney_bergmann_cheng_decker_freer_himmel_nishimura_skory_stomp_et al._2002, title={Expression of endoglucanase E1 in transgenic duckweed Lemna minor}, ISBN={1588293874}, booktitle={Biotechnology for fuels and chemicals : proceedings of the Twenty-Fourth Symposium on Biotechnology for Fuels and Chemicals, held April 28-May 1, 2002, in Gatlinburg, TN}, author={Sun, Y. and Adney, W. S. and Bergmann, B. A. and Cheng, J. and Decker, S. R. and Freer, S. and Himmel, M. E. and Nishimura, Y. and Skory, C. D. and Stomp, A.-M and et al.}, year={2002} }
 @article{whetten_sun_zhang_sederoff_2001, title={Functional genomics and cell wall biosynthesis in loblolly pine}, volume={47}, ISSN={0167-4412}, url={http://dx.doi.org/10.1023/a:1010652003395}, DOI={10.1023/A:1010652003395}, number={1/2}, journal={Plant Molecular Biology}, publisher={Springer Science and Business Media LLC}, author={Whetten, Ross and Sun, Ying-Hsuan and Zhang, Yi and Sederoff, Ron}, year={2001}, month={Sep}, pages={275–291} }
 @article{bergmann_sun_stomp_1997, title={Harvest time and nitrogen source influence in vitro growth of apical buds from Fraser fir seedlings}, volume={32}, ISSN={["0018-5345"]}, DOI={10.21273/HORTSCI.32.1.125}, abstractNote={Information was obtained concerning appropriate bud harvest time and nitrogen source to be used in the tissue culture of Fraser fir [Abies fraseri (Pursh) Poir] apical buds from 2-year-old seedlings. April was the preferred time to harvest buds for culture, as summer buds had a high contamination frequency, and fall and winter buds did not develop well. Shoot elongation of buds collected in April (1.6 cm) was more than twice that of buds collected in February (0.7 cm) after 100 days in culture; during the same period, shoot fresh mass increased 5-fold (0.21 g in April, 0.04 g in February). Inclusion of a nitrate source reduced the frequency of bud browning, and glutamine was superior to ammonium as a source of reduced nitrogen. Litvay's basal medium containing 10 mm glutamine and 10 mm nitrate was the best nitrogen source combination tested when considering bud browning frequency and shoot fresh mass and length after 100 days in culture.}, number={1}, journal={HORTSCIENCE}, author={Bergmann, BA and Sun, YH and Stomp, AM}, year={1997}, month={Feb}, pages={125–128} }