@article{yell_li_2023, title={Scalable, Flexible, and Cost-Effective Seedling Grafting}, volume={1}, ISSN={["1940-087X"]}, url={http://dx.doi.org/10.3791/64519}, DOI={10.3791/64519}, abstractNote={Early-stage seedling grafting has become a popular tool in molecular genetics to study root-shoot relationships within plants. Grafting early-stage seedlings of the small model plant, Arabidopsis thaliana, is technically challenging and time consuming due to the size and fragility of its seedlings. A growing collection of published methods describe this technique with varying success rates, difficulty, and associated costs. This paper describes a simple procedure to make an in-house reusable grafting device using silicone elastomer mix, and how to use this device for seedling grafting. At the time of this publication, each reusable grafting device costs only $0.47 in consumable materials to produce. Using this method, beginners can have their first successfully grafted seedlings in less than 3 weeks from start to finish. This highly accessible procedure will allow plant molecular genetics labs to establish seedling grafting as a normal part of their experimental process. Due to the full control users have in the creation and design of these grafting devices, this technique could be easily adjusted for use in larger plants, such as tomato or tobacco, if desired.}, number={191}, journal={JOVE-JOURNAL OF VISUALIZED EXPERIMENTS}, author={Yell, Victoria and Li, Xu}, year={2023}, month={Jan} }
 @article{li_yell_li_2023, title={Two Arabidopsis promoters drive seed-coat specific gene expression in pennycress and camelina}, volume={19}, ISSN={["1746-4811"]}, url={https://doi.org/10.1186/s13007-023-01114-x}, DOI={10.1186/s13007-023-01114-x}, abstractNote={Abstract}, number={1}, journal={PLANT METHODS}, author={Li, Xin and Yell, Victoria and Li, Xu}, year={2023}, month={Dec} }
 @article{chen_li_chapple_dilkes_li_2023, title={UGT76F1 glycosylates an isomer of the C7-necic acid component of pyrrolizidine alkaloids in Arabidopsis thaliana}, volume={4}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.16211}, DOI={10.1111/tpj.16211}, abstractNote={SUMMARY}, journal={PLANT JOURNAL}, author={Chen, Han-Yi and Li, Xin and Chapple, Clint and Dilkes, Brian and Li, Xu}, year={2023}, month={Apr} }
 @article{lu_li_young_li_linder_suchoff_2022, title={Hyperspectral imaging with chemometrics for non-destructive determination of cannabinoids in floral and leaf materials of industrial hemp (Cannabis sativa L.)}, volume={202}, ISSN={["1872-7107"]}, DOI={10.1016/j.compag.2022.107387}, abstractNote={With the passage of the 2018 Farm Bill, industrial hemp (Cannabis sativa L.) has become a legal and economically promising crop commodity for U.S. farmers. There has been a surge of interest in growing industrial hemp for producing cannabinoids, such as cannabidiol (CBD), because of their medical potential. Quantitative determination of cannabinoids in harvested materials (primarily floral tissues) is critical for cannabinoid production and compliance testing. The concentrations of cannabinoids in hemp materials are conventionally determined using wet-chemistry chromatographic methods, which require destructive sampling, and are time-consuming, costly, and thus not suitable for on-site rapid testing. This study presents a novel effort to utilize hyperspectral imaging technology for non-destructive quantification of major cannabinoids, including CBD, THC (tetrahydrocannabinol), CBG (cannabigerol) and their acid forms in fresh floral and leaf materials of industrial hemp on a dry weight basis. Hyperspectral images in the wavelength range of 400–1000 nm were acquired from floral and leaf tissues immediately after harvest from a total of 100 industrial hemp plants of five cultivars at varied growth stages. Linear discriminant analysis showed hyperspectral imaging could identify CBD-rich/poor and THC-legal/illegal flower samples with accuracies of 99% and 97%, respectively. Quantitative models based on full-spectrum PLS (partial least squares) achieved prediction accuracies of RPD (ratio of prediction to deviation) = 2.5 (corresponding R2 = 0.84) for CBD and THC in floral tissues. Similar accuracies were obtained for their acid forms in flower samples. The predictions for CBG and its acid form in floral tissues and all six cannabinoids in leaf tissues were unsatisfactory with noticeably lower RPD values. Consistently improved accuracies were obtained by parsimonious PLS models based on a wavelength selection procedure for minimized variable collinearity. The best RPD values of approximately 2.6 (corresponding R2 = 0.85) were obtained for CBD and THC in floral materials. This study demonstrates the utility of hyperspectral imaging as a potential valuable tool for rapid quantification of cannabinoids in industrial hemp.}, journal={COMPUTERS AND ELECTRONICS IN AGRICULTURE}, author={Lu, Yuzhen and Li, Xu and Young, Sierra and Li, Xin and Linder, Eric and Suchoff, David}, year={2022}, month={Nov} }
 @article{linder_young_li_inoa_suchoff_2022, title={The Effect of Harvest Date on Temporal Cannabinoid and Biomass Production in the Floral Hemp (Cannabis sativa L.) Cultivars BaOx and Cherry Wine}, volume={8}, ISSN={["2311-7524"]}, url={https://doi.org/10.3390/horticulturae8100959}, DOI={10.3390/horticulturae8100959}, abstractNote={The objectives of this study were to model the temporal accumulation of cannabidiol (CBD) and tetrahydrocannabinol (THC) in field-grown floral hemp in North Carolina and establish harvest timing recommendations to minimize non-compliant crop production. Field trials were conducted in 2020 and 2021 with BaOx and Cherry Wine cultivars. Harvest events started two weeks after floral initiation and occurred every two weeks for 12 weeks. Per-plant threshed biomass accumulation exhibited a linear plateau trend. The best fit model for temporal accumulation of THC was a beta growth curve. As harvest date was delayed, total THC concentrations increased until concentrations reached their maximum, then decreased as plants approached senescence. Logistic regression was the best fit model for temporal accumulation of CBD. CBD concentrations increased with later harvest dates. Unlike THC concentrations, there was no decline in total CBD concentrations. To minimize risk, growers should test their crop as early as possible within the USDA’s 30-day compliance window. We observed ‘BaOx’ and ‘Cherry Wine’ exceeding the compliance threshold 50 and 41 days after flower initiation, respectively.}, number={10}, journal={HORTICULTURAE}, author={Linder, Eric R. and Young, Sierra and Li, Xu and Inoa, Shannon Henriquez and Suchoff, David H.}, year={2022}, month={Oct} }
 @article{linder_young_li_inoa_suchoff_2022, title={The Effect of Transplant Date and Plant Spacing on Biomass Production for Floral Hemp (Cannabis sativa L.)}, volume={12}, ISSN={["2073-4395"]}, url={https://doi.org/10.3390/agronomy12081856}, DOI={10.3390/agronomy12081856}, abstractNote={Floral hemp cultivated for the extraction of cannabinoids is a new crop in the United States, and agronomic recommendations are scarce. The objective of this study was to understand the effects of plant spacing and transplant date on floral hemp growth and biomass production. Field trials were conducted in North Carolina in 2020 and 2021 with the floral hemp cultivar BaOx. Transplant date treatments occurred every two weeks from 11 May to 7 July (±1 d). Plant spacing treatments were 0.91, 1.22, 1.52, and 1.83 m between plants. Weekly height and width data were collected throughout the vegetative period, and dry biomass was measured at harvest. Plant width was affected by transplant date and spacing. Plant height was affected by transplant date. Earlier transplant dates resulted in taller, wider plants, while larger plant spacing resulted in wider plants. Individual plant biomass increased with earlier transplant dates and larger plant spacing. On a per-hectare basis, biomass increased with earlier transplant dates and smaller transplant spacing. An economic analysis found that returns were highest with 1.22 m spacing and decreased linearly by a rate of −163.098 USD ha−1 d−1. These findings highlight the importance of earlier transplant timing to maximize harvestable biomass.}, number={8}, journal={AGRONOMY-BASEL}, author={Linder, Eric R. and Young, Sierra and Li, Xu and Inoa, Shannon Henriquez and Suchoff, David H.}, year={2022}, month={Aug} }
 @article{tan_wang_schneider_li_souza_tang_grimm_hsieh_wang_li_et al._2021, title={Comparative Phylogenomic Analysis Reveals Evolutionary Genomic Changes and Novel Toxin Families in Endophytic Liberibacter Pathogens}, volume={9}, ISSN={["2165-0497"]}, DOI={10.1128/Spectrum.00509-21}, abstractNote={
            Liberibacter
            pathogens are associated with several severe crop diseases, including citrus Huanglongbing, the most destructive disease to the citrus industry. Currently, no effective cure or treatments are available, and no resistant citrus variety has been found.
          }, number={2}, journal={MICROBIOLOGY SPECTRUM}, author={Tan, Yongjun and Wang, Cindy and Schneider, Theresa and Li, Huan and Souza, Robson Francisco and Tang, Xueming and Grimm, Kylie D. Swisher and Hsieh, Tzung-Fu and Wang, Xu and Li, Xu and et al.}, year={2021}, month={Oct} }
 @article{simpson_wunderlich_li_svedin_dilkes_chapple_2021, title={Metabolic source isotopic pair labeling and genome-wide association are complementary tools for the identification of metabolite-gene associations in plants}, volume={33}, ISSN={["1532-298X"]}, url={https://doi.org/10.1093/plcell/koaa046}, DOI={10.1093/plcell/koaa046}, abstractNote={Abstract}, number={3}, journal={PLANT CELL}, publisher={Oxford University Press (OUP)}, author={Simpson, Jeffrey P. and Wunderlich, Cole and Li, Xu and Svedin, Elizabeth and Dilkes, Brian and Chapple, Clint}, year={2021}, month={Mar}, pages={492–510} }
 @article{wu_la hovary_chen_li_eng_vallejo_qu_dewey_2020, title={An Efficient Stevia rebaudiana Transformation System and In vitro Enzyme Assays Reveal Novel Insights into UGT76G1 Function}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-60776-y}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Wu, Qian and La Hovary, Christophe and Chen, Han-Yi and Li, Xu and Eng, Hayde and Vallejo, Veronica and Qu, Rongda and Dewey, Ralph E.}, year={2020}, month={Feb} }
 @article{panda_li_wager_chen_li_2020, title={An importin-beta-like protein mediates lignin-modification-induced dwarfism in Arabidopsis}, volume={102}, ISSN={["1365-313X"]}, url={https://doi.org/10.1111/tpj.14701}, DOI={10.1111/tpj.14701}, abstractNote={Summary}, number={6}, journal={PLANT JOURNAL}, author={Panda, Chinmayee and Li, Xin and Wager, Amanda and Chen, Han-Yi and Li, Xu}, year={2020}, month={Jun}, pages={1281–1293} }
 @article{yang_zhang_luo_liu_shiga_li_kim_rubinelli_overton_subramanyam_et al._2019, title={Overcoming cellulose recalcitrance in woody biomass for the lignin-first biorefinery}, volume={12}, ISSN={1754-6834}, url={http://dx.doi.org/10.1186/s13068-019-1503-y}, DOI={10.1186/s13068-019-1503-y}, abstractNote={Low-temperature swelling of cotton linter cellulose and subsequent gelatinization in trifluoroacetic acid (TFA) greatly enhance rates of enzymatic digestion or maleic acid-AlCl3 catalyzed conversion to hydroxymethylfurfural (HMF) and levulinic acid (LA). However, lignin inhibits low-temperature swelling of TFA-treated intact wood particles from hybrid poplar (Populus tremula × P. alba) and results in greatly reduced yields of glucose or catalytic conversion compared to lignin-free cellulose. Previous studies have established that wood particles from transgenic lines of hybrid poplar with high syringyl (S) lignin content give greater glucose yields following enzymatic digestion.Low-temperature (- 20 °C) treatment of S-lignin-rich poplar wood particles in TFA slightly increased yields of glucose from enzymatic digestions and HMF and LA from maleic acid-AlCl3 catalysis. Subsequent gelatinization at 55 °C resulted in over 80% digestion of cellulose in only 3 to 6 h with high-S-lignin wood, compared to 20-60% digestion in the wild-type poplar hybrid and transgenic lines high in guaiacyl lignin or 5-hydroxy-G lignin. Disassembly of lignin in woody particles by Ni/C catalytic systems improved yields of glucose by enzymatic digestion or catalytic conversion to HMF and LA. Although lignin was completely removed by Ni/C-catalyzed delignification (CDL) treatment, recalcitrance to enzymatic digestion of cellulose from the high-S lines was reduced compared to other lignin variants. However, cellulose still exhibited considerable recalcitrance to complete enzymatic digestion or catalytic conversion after complete delignification. Low-temperature swelling of the CDL-treated wood particles in TFA resulted in nearly complete enzymatic hydrolysis, regardless of original lignin composition.Genetic modification of lignin composition can enhance the portfolio of aromatic products obtained from lignocellulosic biomass while promoting disassembly into biofuel and bioproduct substrates. CDL enhances rates of enzymatic digestion and chemical conversion, but cellulose remains intrinsically recalcitrant. Cold TFA is sufficient to overcome this recalcitrance after CDL treatment. Our results inform a 'no carbon left behind' strategy to convert total woody biomass into lignin, cellulose, and hemicellulose value streams for the future biorefinery.}, number={1}, journal={Biotechnology for Biofuels}, publisher={Springer Science and Business Media LLC}, author={Yang, Haibing and Zhang, Ximing and Luo, Hao and Liu, Baoyuan and Shiga, Tânia M. and Li, Xu and Kim, Jeong Im and Rubinelli, Peter and Overton, Jonathan C. and Subramanyam, Varun and et al.}, year={2019}, month={Jun} }
 @article{reem_chen_hur_zhao_wurtele_li_li_zabotina_2018, title={Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations}, volume={96}, ISSN={["1573-5028"]}, DOI={10.1007/s11103-018-0714-0}, abstractNote={This research provides new insights into plant response to cell wall perturbations through correlation of transcriptome and metabolome datasets obtained from transgenic plants expressing cell wall-modifying enzymes. Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.}, number={4-5}, journal={PLANT MOLECULAR BIOLOGY}, author={Reem, Nathan T. and Chen, Han-Yi and Hur, Manhoi and Zhao, Xuefeng and Wurtele, Eve Syrkin and Li, Xu and Li, Ling and Zabotina, Olga}, year={2018}, month={Mar}, pages={509–529} }
 @article{pais_li_xiang_2018, title={Discovering variation of secondary metabolite diversity and its relationship with disease resistance in Cornus florida
 L.}, volume={8}, ISSN={2045-7758}, url={http://dx.doi.org/10.1002/ece3.4090}, DOI={10.1002/ece3.4090}, abstractNote={Abstract}, number={11}, journal={Ecology and Evolution}, publisher={Wiley}, author={Pais, Andrew L. and Li, Xu and Xiang, Qiu-Yun (Jenny)}, year={2018}, month={May}, pages={5619–5636} }
 @article{wager_li_2018, title={Exploiting natural variation for accelerating discoveries in plant specialized metabolism}, volume={17}, ISSN={["1572-980X"]}, DOI={10.1007/s11101-017-9524-2}, number={1}, journal={PHYTOCHEMISTRY REVIEWS}, author={Wager, Amanda and Li, Xu}, year={2018}, month={Feb}, pages={17–36} }
 @article{yang_he_kabahuma_chaya_kelly_borrego_bian_el kasmi_yang_teixeira_et al._2017, title={A gene encoding maize caffeoyl-CoA O-methyltransferase confers quantitative resistance to multiple pathogens}, volume={49}, ISSN={1061-4036 1546-1718}, url={http://dx.doi.org/10.1038/ng.3919}, DOI={10.1038/ng.3919}, abstractNote={Alleles that confer multiple disease resistance (MDR) are valuable in crop improvement, although the molecular mechanisms underlying their functions remain largely unknown. A quantitative trait locus, qMdr9.02, associated with resistance to three important foliar maize diseases-southern leaf blight, gray leaf spot and northern leaf blight-has been identified on maize chromosome 9. Through fine-mapping, association analysis, expression analysis, insertional mutagenesis and transgenic validation, we demonstrate that ZmCCoAOMT2, which encodes a caffeoyl-CoA O-methyltransferase associated with the phenylpropanoid pathway and lignin production, is the gene within qMdr9.02 conferring quantitative resistance to both southern leaf blight and gray leaf spot. We suggest that resistance might be caused by allelic variation at the level of both gene expression and amino acid sequence, thus resulting in differences in levels of lignin and other metabolites of the phenylpropanoid pathway and regulation of programmed cell death.}, number={9}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Yang, Qin and He, Yijian and Kabahuma, Mercy and Chaya, Timothy and Kelly, Amy and Borrego, Eli and Bian, Yang and El Kasmi, Farid and Yang, Li and Teixeira, Paulo and et al.}, year={2017}, month={Jul}, pages={1364–1372} }
 @article{chen_li_2017, title={Identification of a residue responsible for UDP-sugar donor selectivity of a dihydroxybenzoic acid glycosyltransferase from Arabidopsis natural accessions}, volume={89}, ISSN={["1365-313X"]}, DOI={10.1111/tpj.13271}, abstractNote={Summary}, number={2}, journal={PLANT JOURNAL}, author={Chen, Han-Yi and Li, Xu}, year={2017}, month={Jan}, pages={195–203} }
 @article{jiao_li_yu_yang_li_shen_2017, title={In situ enhancement of surfactin biosynthesis in Bacillus subtilis
 using novel artificial inducible promoters}, volume={114}, ISSN={0006-3592}, url={http://dx.doi.org/10.1002/BIT.26197}, DOI={10.1002/BIT.26197}, abstractNote={ABSTRACT}, number={4}, journal={Biotechnology and Bioengineering}, publisher={Wiley}, author={Jiao, Song and Li, Xu and Yu, Huimin and Yang, Huan and Li, Xue and Shen, Zhongyao}, year={2017}, month={Apr}, pages={832–842} }
 @article{rathinasabapathy_palatini jackson_thor_buru_esposito_li_pichika_hamzah_komarnytsky_2017, title={Thiazolopyridines Improve Adipocyte Function by Inhibiting 11 Beta-HSD1 Oxoreductase Activity}, volume={2017}, ISSN={2090-9063 2090-9071}, url={http://dx.doi.org/10.1155/2017/3182129}, DOI={10.1155/2017/3182129}, abstractNote={Background. Glucocorticoid excess has been linked to clinical observations associated with the pathophysiology of metabolic syndrome. The intracellular glucocorticoid levels are primarily modulated by 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1) enzyme that is highly expressed in key metabolic tissues including fat, liver, and the central nervous system. Methods. In this study we synthesized a set of novel tetrahydrothiazolopyridine derivatives, TR-01–4, that specifically target 11β-HSD1 and studied their ability to interfere with the glucocorticoid and lipid metabolism in the 3T3-L1 adipocytes. Results. Based on the docking model and structure-activity relationships, tetrahydrothiazolopyridine derivatives TR-02 and TR-04 showed the highest potency against 11β-HSD1 by dose-dependently inhibiting conversion of cortisone to cortisol (IC50 values of 1.8 μM and 0.095 μM, resp.). Incubation of fat cells with 0.1–10 μM TR-01–4 significantly decreased cortisone-induced lipid accumulation in adipocytes and suppressed 11β-HSD1 mRNA expression. Observed reduction in adipocyte fat stores could be partially explained by decreased expression levels of adipogenic markers (PPAR-γ, aP2) and key enzymes of lipid metabolism, including fatty acid synthase (FAS), hormone sensitive lipase (HSL), and lipoprotein lipase (LPL). Conclusions. The tetrahydrothiazolopyridine moiety served as an active pharmacophore for inhibiting 11β-HSD1 and offered a novel therapeutic strategy to ameliorate metabolic alterations found in obesity and diabetes.}, journal={Journal of Chemistry}, publisher={Hindawi Limited}, author={Rathinasabapathy, Thirumurugan and Palatini Jackson, Kimberly Marie and Thor, Yiwen and Buru, Ayuba Sunday and Esposito, Debora and Li, Xu and Pichika, Mallikarjuna Rao and Hamzah, Ahmad Sazali and Komarnytsky, Slavko}, year={2017}, pages={1–10} }
 @article{jacobi_yang_li_menze_laurentz_janle_ferruzzi_mccabe_chapple_kirchmaier_et al._2016, title={Impacts on Sirtuin Function and Bioavailability of the Dietary Bioactive Compound Dihydrocoumarin}, volume={11}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0149207}, abstractNote={The plant secondary metabolite and common food additive dihydrocoumarin (DHC) is an inhibitor of the Sirtuin family of NAD+-dependent deacetylases. Sirtuins are key regulators of epigenetic processes that maintain silent chromatin in yeast and have been linked to gene expression, metabolism, apoptosis, tumorogenesis and age-related processes in multiple organisms, including humans. Here we report that exposure to the polyphenol DHC led to defects in several Sirtuin-regulated processes in budding yeast including the establishment and maintenance of Sir2p-dependent silencing by causing disassembly of silent chromatin, Hst1p-dependent repression of meiotic-specific genes during the mitotic cell cycle. As both transient and prolonged exposure to environmental and dietary factors have the potential to lead to heritable alterations in epigenetic states and to modulate additional Sirtuin-dependent phenotypes, we examined the bioavailability and digestive stability of DHC using an in vivo rat model and in vitro digestive simulator. Our analyses revealed that DHC was unstable during digestion and could be converted to melilotic acid (MA), which also caused epigenetic defects, albeit less efficiently. Upon ingestion, DHC was observed primarily in intestinal tissues, but did not accumulate over time and was readily cleared from the animals. MA displayed a wider tissue distribution and, in contrast to DHC, was also detected in the blood plasma, interstitial fluid, and urine, implying that the conversion of DHC to the less bioactive compound, MA, occurred efficiently in vivo.}, number={2}, journal={PLOS ONE}, author={Jacobi, J. L. and Yang, B. and Li, X. and Menze, A. K. and Laurentz, S. M. and Janle, E. M. and Ferruzzi, M. G. and McCabe, G. P. and Chapple, C. and Kirchmaier, A. L. and et al.}, year={2016}, month={Feb} }
 @article{esposito_damsud_wilson_grace_strauch_li_lila_komarnytsky_2015, title={Black Currant Anthocyanins Attenuate Weight Gain and Improve Glucose Metabolism in Diet-Induced Obese Mice with Intact, but Not Disrupted, Gut Microbiome}, volume={63}, ISSN={["1520-5118"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84937064835&partnerID=MN8TOARS}, DOI={10.1021/acs.jafc.5b00963}, abstractNote={Black currant (Ribes nigrum L.) is a rich source of anthocyanins; however, the relationship between their apparently limited bioavailability and significant protection against metabolic pathologies is poorly understood. This study examined the gastrointestinal distribution of black currant anthocyanins and their phenolic acid metabolites in lean and diet-induced obese mice with healthy and antibiotic-disrupted microbiomes. Daily consumption of low- or high-fat diet supplemented with 1% black currant powdered extract (32% anthocyanins) for 8 weeks reduced body weight gain and improved glucose metabolism only in mice with the intact gut microbiome. Administration of antibiotic cocktail resulted in a 16-25-fold increase (P < 0.001) in anthocyanin content of feces, and cyanidin-based anthocyanins showed the largest increase in fecal content upon disruption of gut microbiome (92.3 ± 16.3 vs 4719 ± 158 μg/g feces), indicating their high susceptibility to microbial degradation in the gut. A 3-fold enrichment (P < 0.05) in gallic over protocatechuic acid was observed in the jejunum of both intact and antibiotic-treated animals, suggesting that this effect was likely independent of their gut microbiome status. Taken together, the data clearly demonstrate that gut microbiome and the type of the anthocyanin aglycone moiety can alter the protective effect of anthocyanins against obesity and associated insulin resistance.}, number={27}, journal={JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Esposito, Debora and Damsud, Thanakorn and Wilson, Mickey and Grace, Mary H. and Strauch, Renee and Li, Xu and Lila, Mary Ann and Komarnytsky, Slavko}, year={2015}, month={Jul}, pages={6172–6180} }
 @article{strauch_svedin_dilkes_chapple_li_2015, title={Discovery of a novel amino acid racemase through exploration of natural variation in Arabidopsis thaliana}, volume={112}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1503272112}, abstractNote={Significance}, number={37}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Strauch, Renee C. and Svedin, Elisabeth and Dilkes, Brian and Chapple, Clint and Li, Xu}, year={2015}, month={Sep}, pages={11726–11731} }
 @article{wang_he_strauch_olukolu_nielsen_li_balint-kurti_2015, title={Maize Homologs of HCT, a Key Enzyme in Lignin Biosynthesis, Bind the NLR Rp1 Proteins to Modulate the Defense Response}, volume={169}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.15.00703}, DOI={10.1104/pp.15.00703}, abstractNote={Homologs of hydroxycinnamoyltransferase, involved in lignin biosynthesis, interact directly with leucine-rich receptor proteins to suppress the hypersensitive response. In plants, most disease resistance genes encode nucleotide binding Leu-rich repeat (NLR) proteins that trigger a rapid localized cell death called a hypersensitive response (HR) upon pathogen recognition. The maize (Zea mays) NLR protein Rp1-D21 derives from an intragenic recombination between two NLRs, Rp1-D and Rp1-dp2, and confers an autoactive HR in the absence of pathogen infection. From a previous quantitative trait loci and genome-wide association study, we identified a single-nucleotide polymorphism locus highly associated with variation in the severity of Rp1-D21-induced HR. Two maize genes encoding hydroxycinnamoyltransferase (HCT; a key enzyme involved in lignin biosynthesis) homologs, termed HCT1806 and HCT4918, were adjacent to this single-nucleotide polymorphism. Here, we show that both HCT1806 and HCT4918 physically interact with and suppress the HR conferred by Rp1-D21 but not other autoactive NLRs when transiently coexpressed in Nicotiana benthamiana. Other maize HCT homologs are unable to confer the same level of suppression on Rp1-D21-induced HR. The metabolic activity of HCT1806 and HCT4918 is unlikely to be necessary for their role in suppressing HR. We show that the lignin pathway is activated by Rp1-D21 at both the transcriptional and metabolic levels. We derive a model to explain the roles of HCT1806 and HCT4918 in Rp1-mediated disease resistance.}, number={3}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Wang, Guan-Feng and He, Yijian and Strauch, Renee and Olukolu, Bode and Nielsen, Dahlia and Li, Xu and Balint-Kurti, Peter}, year={2015}, month={Sep}, pages={pp.00703.2015} }
 @article{kim_ciesielski_donohoe_chapple_li_2014, title={Chemically Induced Conditional Rescue of the Reduced Epidermal Fluorescence8 Mutant of Arabidopsis Reveals Rapid Restoration of Growth and Selective Turnover of Secondary Metabolite Pools}, volume={164}, ISSN={["1532-2548"]}, DOI={10.1104/pp.113.229393}, abstractNote={Activation of the wild-type gene in an Arabidopsis phenylpropanoid mutant at different developmental stages has distinct impacts on metabolic changes and plant growth. The phenylpropanoid pathway is responsible for the biosynthesis of diverse and important secondary metabolites including lignin and flavonoids. The reduced epidermal fluorescence8 (ref8) mutant of Arabidopsis (Arabidopsis thaliana), which is defective in a lignin biosynthetic enzyme p-coumaroyl shikimate 3′-hydroxylase (C3′H), exhibits severe dwarfism and sterility. To better understand the impact of perturbation of phenylpropanoid metabolism on plant growth, we generated a chemically inducible C3′H expression construct and transformed it into the ref8 mutant. Application of dexamethasone to these plants greatly alleviates the dwarfism and sterility and substantially reverses the biochemical phenotypes of ref8 plants, including the reduction of lignin content and hyperaccumulation of flavonoids and p-coumarate esters. Induction of C3′H expression at different developmental stages has distinct impacts on plant growth. Although early induction effectively restored the elongation of primary inflorescence stem, application to 7-week-old plants enabled them to produce new rosette inflorescence stems. Examination of hypocotyls of these plants revealed normal vasculature in the newly formed secondary xylem, presumably restoring water transport in the mutant. The ref8 mutant accumulates higher levels of salicylic acid than the wild type, but depletion of this compound in ref8 did not relieve the mutant’s growth defects, suggesting that the hyperaccumulation of salicylic acid is unlikely to be responsible for dwarfism in this mutant.}, number={2}, journal={PLANT PHYSIOLOGY}, author={Kim, Jeong Im and Ciesielski, Peter N. and Donohoe, Bryon S. and Chapple, Clint and Li, Xu}, year={2014}, month={Feb}, pages={584–595} }
 @article{li_svedin_mo_atwell_dilkes_chapple_2014, title={Exploiting Natural Variation of Secondary Metabolism Identifies a Gene Controlling the Glycosylation Diversity of Dihydroxybenzoic Acids in Arabidopsis thaliana}, volume={198}, ISSN={0016-6731 1943-2631}, url={http://dx.doi.org/10.1534/genetics.114.168690}, DOI={10.1534/genetics.114.168690}, abstractNote={Abstract}, number={3}, journal={Genetics}, publisher={Genetics Society of America}, author={Li, Xu and Svedin, Elisabeth and Mo, Huaping and Atwell, Susanna and Dilkes, Brian P. and Chapple, Clint}, year={2014}, month={Aug}, pages={1267–1276} }
 @article{rubinelli_chuck_li_meilan_2013, title={Constitutive expression of the Corngrass1 microRNA in poplar affects plant architecture and stem lignin content and composition}, volume={54}, ISSN={0961-9534}, url={http://dx.doi.org/10.1016/j.biombioe.2012.03.001}, DOI={10.1016/j.biombioe.2012.03.001}, abstractNote={A role for microRNAs (miRNAs) in the developmental biology of plants has been established in model annual species, but is poorly understood in perennials, particularly trees. We over-expressed in poplar (genus Populus) a unique miRNA gene from maize belonging to the MIR156 family called Corngrass1 (Cg1) under the control of the cauliflower mosaic virus 35S promoter. Transgenics had significantly greater axillary meristem outgrowth (branching), shorter internode length, and up to a 30% reduction in stem lignin content compared to stem lignin of the wild-type (trunk stem from shoot apex down to node 10). The severity of the phenotype was positively correlated with Cg1 expression level. In addition, the syringyl to guaiacyl ratio (S/G) was lower in 35S:Cg1 lines than in wild-type poplar or a control transgenic line with low abundance of Cg1 transcript. We have demonstrated that over-expression in poplar of a MIR156 class miRNA has dramatic effects on plant architecture, and demonstrated that miRNA over-expression represents a novel approach to altering lignin content and composition in poplar. These transgenic plants may provide a tool for investigating the potential role of MIR156 in regulating developmental processes in poplar. The 35S:Cg1 poplars may also have commercial value as a cellulosic feedstock for biofuel production and in the paper-manufacturing industry.}, journal={Biomass and Bioenergy}, publisher={Elsevier BV}, author={Rubinelli, Peter M. and Chuck, George and Li, Xu and Meilan, Richard}, year={2013}, month={Jul}, pages={312–321} }
 @article{krothapalli_buescher_li_brown_chapple_dilkes_tuinstra_2013, title={Forward Genetics by Genome Sequencing Reveals That Rapid Cyanide Release Deters Insect Herbivory of Sorghum bicolor}, volume={195}, ISSN={0016-6731 1943-2631}, url={http://dx.doi.org/10.1534/genetics.113.149567}, DOI={10.1534/genetics.113.149567}, abstractNote={Abstract}, number={2}, journal={Genetics}, publisher={Genetics Society of America}, author={Krothapalli, Kartikeya and Buescher, Elizabeth M. and Li, Xu and Brown, Elliot and Chapple, Clint and Dilkes, Brian P. and Tuinstra, Mitchell R.}, year={2013}, month={Jul}, pages={309–318} }
 @article{venkata_lauter_li_chapple_krupke_johal_moose_2013, title={crw1 - A Novel Maize Mutant Highly Susceptible to Foliar Damage by the Western Corn Rootworm Beetle}, volume={8}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0071296}, abstractNote={Western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte (Coleoptera: Chrysomelidae), is the most destructive insect pest of corn (Zea mays L.) in the United States. The adult WCR beetles derive their nourishment from multiple sources including corn pollen and silks as well as the pollen of alternate hosts. Conversely, the corn foliage is largely neglected as a food source by WCR beetles, leading to a perception of a passive interaction between the two. We report here a novel recessive mutation of corn that was identified and named after its foliar susceptibility to corn rootworm beetles (crw1). The crw1 mutant under field conditions was exceptionally susceptible to foliar damage by WCR beetles in an age-specific manner. It exhibits pleiotropic defects on cell wall biochemistry, morphology of leaf epidermal cells and lower structural integrity via differential accumulation of cell wall bound phenolic acids. These findings indicate that crw1 is perturbed in a pathway that was not previously ascribed to WCR susceptibility, as well as implying the presence of an active mechanism(s) deterring WCR beetles from devouring corn foliage. The discovery and characterization of this mutant provides a unique opportunity for genetic analysis of interactions between maize and adult WCR beetles and identify new strategies to control the spread and invasion of this destructive pest.}, number={8}, journal={PLOS ONE}, author={Venkata, Bala Puchakayala and Lauter, Nick and Li, Xu and Chapple, Clint and Krupke, Christian and Johal, Gurmukh and Moose, Stephen}, year={2013}, month={Aug} }
 @article{weng_akiyama_bonawitz_li_ralph_chapple_2010, title={Convergent Evolution of Syringyl Lignin Biosynthesis via Distinct Pathways in the Lycophyte Selaginella and Flowering Plants}, volume={22}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.109.073528}, DOI={10.1105/tpc.109.073528}, abstractNote={Abstract}, number={4}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Weng, Jing-Ke and Akiyama, Takuya and Bonawitz, Nicholas D. and Li, Xu and Ralph, John and Chapple, Clint}, year={2010}, month={Apr}, pages={1033–1045} }
 @article{li_ximenes_kim_slininger_meilan_ladisch_chapple_2010, title={Lignin monomer composition affects Arabidopsis cell-wall degradability after liquid hot water pretreatment}, volume={3}, ISSN={1754-6834}, url={http://dx.doi.org/10.1186/1754-6834-3-27}, DOI={10.1186/1754-6834-3-27}, abstractNote={Abstract}, number={1}, journal={Biotechnology for Biofuels}, publisher={Springer Science and Business Media LLC}, author={Li, Xu and Ximenes, Eduardo and Kim, Youngmi and Slininger, Mary and Meilan, Richard and Ladisch, Michael and Chapple, Clint}, year={2010}, pages={27} }
 @article{li_ilarslan_brachova_qian_li_che_wurtele_nikolau_2010, title={Reverse-Genetic Analysis of the Two Biotin-Containing Subunit Genes of the Heteromeric Acetyl-Coenzyme A Carboxylase in Arabidopsis Indicates a Unidirectional Functional Redundancy}, volume={155}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.110.165910}, DOI={10.1104/pp.110.165910}, abstractNote={Abstract}, number={1}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Li, Xu and Ilarslan, Hilal and Brachova, Libuse and Qian, Hui-Rong and Li, Ling and Che, Ping and Wurtele, Eve Syrkin and Nikolau, Basil J.}, year={2010}, month={Oct}, pages={293–314} }
 @article{li_bergelson_chapple_2010, title={The ARABIDOPSIS Accession Pna-10 Is a Naturally Occurring sng1 Deletion Mutant}, volume={3}, ISSN={1674-2052}, url={http://dx.doi.org/10.1093/mp/ssp090}, DOI={10.1093/mp/ssp090}, abstractNote={Sinapoylmalate is the major sinapate ester found in leaves of Arabidopsis thaliana, where it plays an important role in UV-B protection. Metabolic profiling of rosette leaves from 96 Arabidopsis accessions revealed that the Pna-10 accession accumulates sinapoylglucose instead of sinapoylmalate. This unique leaf sinapate ester profile is similar to that of the previously characterized sinapoylglucose accumulator1 (sng1) mutants. SNG1 encodes sinapoylglucose:malate sinapoyltransferase (SMT), a serine carboxypeptidase-like (SCPL) enzyme that catalyzes the conversion of sinapoylglucose to sinapoylmalate. In the reference Columbia genome, the SNG1 gene is located in a cluster of five SCPL genes on Chromosome II. PCR and sequencing analysis of the same genomic region in the Pna-10 accession revealed a 13-kb deletion that eliminates the SNG1 gene (At2g22990) and the gene encoding sinapoylglucose:anthocyanin sinapoyltransferase (SAT) (At2g23000). In addition to its sinapoylmalate-deficient phenotype, and consistent with the loss of SAT, Pna-10 is unable to accumulate sinapoylated anthocyanins. Interestingly, the Pna-17 accession, collected from the same location as Pna-10, has no such deletion. Further analysis of 135 lines collected from the same location as Pna-10 and Pna-17 revealed that four more lines contain the deletion found in Pna-10 accession, suggesting that either the deletion found in Pna-10 is a recent event that has not yet been eliminated through selection or that sinapoylmalate is dispensable for the growth of Arabidopsis under field conditions.}, number={1}, journal={Molecular Plant}, publisher={Elsevier BV}, author={Li, X.u. and Bergelson, Joy and Chapple, Clint}, year={2010}, month={Jan}, pages={91–100} }
 @article{li_bonawitz_weng_chapple_2010, title={The Growth Reduction Associated with Repressed Lignin Biosynthesis in Arabidopsis thaliana Is Independent of Flavonoids}, volume={22}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.110.074161}, DOI={10.1105/tpc.110.074161}, abstractNote={This study reexamines the relationship between flavonoid accumulation and the growth reduction exhibited by Arabidopsis plants that are defective in lignin biosynthesis. It shows that flavonoids are not responsible for the observed growth inhibition, contrary to a previous report. Defects in phenylpropanoid biosynthesis arising from deficiency in hydroxycinnamoyl CoA:shikimate hydroxycinnamoyl transferase (HCT) or p-coumaroyl shikimate 3′-hydroxylase (C3′H) lead to reduced lignin, hyperaccumulation of flavonoids, and growth inhibition in Arabidopsis thaliana. It was previously reported that flavonoid-mediated inhibition of auxin transport is responsible for growth reduction in HCT-RNA interference (RNAi) plants. This conclusion was based on the observation that simultaneous RNAi silencing of HCT and chalcone synthase (CHS), an enzyme essential for flavonoid biosynthesis, resulted in less severe dwarfing than silencing of HCT alone. In an attempt to extend these results using a C3′H mutant (ref8) and a CHS null mutant (tt4-2), we found that the growth phenotype of the ref8 tt4-2 double mutant, which lacks flavonoids, is indistinguishable from that of ref8. Moreover, using RNAi, we found that the relationship between HCT silencing and growth inhibition is identical in both the wild type and tt4-2. We conclude from these results that the growth inhibition observed in HCT-RNAi plants and the ref8 mutant is independent of flavonoids. Finally, we show that expression of a newly characterized gene bypassing HCT and C3′H partially restores both lignin biosynthesis and growth in HCT-RNAi plants, demonstrating that a biochemical pathway downstream of coniferaldehyde, probably lignification, is essential for normal plant growth.}, number={5}, journal={The Plant Cell}, publisher={American Society of Plant Biologists (ASPB)}, author={Li, Xu and Bonawitz, Nicholas D. and Weng, Jing-Ke and Chapple, Clint}, year={2010}, month={May}, pages={1620–1632} }
 @article{li_chapple_2010, title={Understanding Lignification: Challenges Beyond Monolignol Biosynthesis}, volume={154}, ISSN={0032-0889 1532-2548}, url={http://dx.doi.org/10.1104/pp.110.162842}, DOI={10.1104/pp.110.162842}, abstractNote={Lignin, a major component of vascular plant cell wall, provides mechanical support for plants to stand upright and enables xylems to withstand the negative pressure generated during water transport. Although important for plant growth, the presence of lignin limits access to cell wall}, number={2}, journal={Plant Physiology}, publisher={American Society of Plant Biologists (ASPB)}, author={Li, Xu and Chapple, Clint}, year={2010}, month={Oct}, pages={449–452} }
 @article{weng_li_bonawitz_chapple_2008, title={Emerging strategies of lignin engineering and degradation for cellulosic biofuel production}, volume={19}, ISSN={0958-1669}, url={http://dx.doi.org/10.1016/j.copbio.2008.02.014}, DOI={10.1016/j.copbio.2008.02.014}, abstractNote={Ethanol and other biofuels produced from lignocellulosic biomass represent a renewable, more carbon-balanced alternative to both fossil fuels and corn-derived or sugarcane-derived ethanol. Unfortunately, the presence of lignin in plant cell walls impedes the breakdown of cell wall polysaccharides to simple sugars and the subsequent conversion of these sugars to usable fuel. Recent advances in the understanding of lignin composition, polymerization, and regulation have revealed new opportunities for the rational manipulation of lignin in future bioenergy crops, augmenting the previous successful approach of manipulating lignin monomer biosynthesis. Furthermore, recent studies on lignin degradation in nature may provide novel resources for the delignification of dedicated bioenergy crops and other sources of lignocellulosic biomass.}, number={2}, journal={Current Opinion in Biotechnology}, publisher={Elsevier BV}, author={Weng, Jing-Ke and Li, Xu and Bonawitz, Nicholas D and Chapple, Clint}, year={2008}, month={Apr}, pages={166–172} }
 @article{li_weng_chapple_2008, title={Improvement of biomass through lignin modification}, volume={54}, ISSN={0960-7412 1365-313X}, url={http://dx.doi.org/10.1111/j.1365-313x.2008.03457.x}, DOI={10.1111/j.1365-313x.2008.03457.x}, abstractNote={Summary}, number={4}, journal={The Plant Journal}, publisher={Wiley}, author={Li, Xu and Weng, Jing-Ke and Chapple, Clint}, year={2008}, month={May}, pages={569–581} }
 @article{weng_li_stout_chapple_2008, title={Independent origins of syringyl lignin in vascular plants}, volume={105}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.0801696105}, DOI={10.1073/pnas.0801696105}, abstractNote={
            Lycophytes arose in the early Silurian (≈400 Mya) and represent a major lineage of vascular plants that has evolved in parallel with the ferns, gymnosperms, and angiosperms. A hallmark of vascular plants is the presence of the phenolic lignin heteropolymer in xylem and other sclerified cell types. Although syringyl lignin is often considered to be restricted in angiosperms, it has been detected in lycophytes as well. Here we report the characterization of a cytochrome P450-dependent monooxygenase from the lycophyte
            Selaginella moellendorffii
            . Gene expression data, cross-species complementation experiments, and
            in vitro
            enzyme assays indicate that this P450 is a ferulic acid/coniferaldehyde/coniferyl alcohol 5-hydroxylase (F5H), and is capable of diverting guaiacyl-substituted intermediates into syringyl lignin biosynthesis. Phylogenetic analysis indicates that the
            Selaginella
            F5H represents a new family of plant P450s and suggests that it has evolved independently of angiosperm F5Hs.
          }, number={22}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Weng, J.-K. and Li, X. and Stout, J. and Chapple, C.}, year={2008}, month={May}, pages={7887–7892} }