@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={Identification of unknown metabolites and their biosynthetic genes is an active research area in plant specialized metabolism. By following a gene-metabolite association from a genome-wide association study of Arabidopsis stem metabolites, we report a previously unknown metabolite, 2-hydroxy-2-(1-hydroxyethyl)pentanoic acid glucoside, and demonstrated that UGT76F1 is responsible for its production in Arabidopsis. The chemical structure of the glucoside was determined by a series of analyses, including tandem MS, acid and base hydrolysis, and NMR spectrometry. T-DNA knockout mutants of UGT76F1 are devoid of the glucoside but accumulate increased levels of the aglycone. 2-hydroxy-2-(1-hydroxyethyl)pentanoic acid is structurally related to the C7-necic acid component of lycopsamine-type pyrrolizidine alkaloids such as trachelantic acid and viridifloric acid. Feeding norvaline greatly enhances the accumulation of 2-hydroxy-2-(1-hydroxyethyl)pentanoic acid glucoside in wild-type but not the UGT76F1 knockout mutant plants, providing evidence for an orthologous C7-necic acid biosynthetic pathway in Arabidopsis despite the apparent lack of pyrrolizidine alkaloids.}, journal={PLANT JOURNAL}, author={Chen, Han-Yi and Li, Xin and Chapple, Clint and Dilkes, Brian and Li, Xu}, year={2023}, month={Apr} }
 @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={Stevia rebaudiana (Bertoni) is one of a very few plant species that produce zero calorie, sweet compounds known as steviol glycosides (SG). SGs differ in their sweetness and organoleptic properties depending on the number and positioning of sugar groups on the core steviol backbone. There is great interest of modulating the SG profiles of the Stevia plant to enhance the flavor profile for a given application in the food and beverage industries. Here, we report a highly efficient Agrobacterium-mediated stable transformation system using axillary shoots as the initial explant. Using this system, we generated over 200 transgenic Stevia plants overexpressing a specific isoform of UGT76G1. By comparing the SG profiles among independent transgenic events, we demonstrated that altering UGT76G1 expression can change the ratios of specific SG species. Furthermore, using recombinant proteins produced in E. coli, we show that two closely related UGT76G1 isoforms differ in their substrate specificities, providing new insights into mechanisms underlying the diversity of SG profiles that are observed across Stevia germplasm. Finally, we found evidence suggesting that alternative and/or aberrant splicing may serve to influence the ability of the plant to produce functional UGT76G1 transcripts, and possibly produce enzyme variants within the plant.}, 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={Perturbation of lignin biosynthesis often results in severe growth and developmental defects in plants, which imposes practical limitations to genetic enhancement of lignocellulosic biomass for biofuel production. Currently, little information is known about the cellular and genetic mechanisms of this important phenomenon. Here we show that defects in both cell division and cell expansion underlie the dwarfism of an Arabidopsis lignin mutant ref8, and report the identification of a GROWTH INHIBITION RELIEVED 1 (GIR1) gene from a suppressor screen. GIR1 encodes an importin-beta-like protein required for the nuclear import of MYB4, a transcriptional repressor of phenylpropanoid metabolism. Disruption of GIR1 and MYB4 similarly alleviates the cellular defects and growth inhibition in ref8, suggesting that the growth rescue effect of gir1 is likely due to compromised MYB4 transport and function. Importantly, the phenylpropanoid perturbation is not alleviated in gir1 ref8 and myb4 ref8, suggesting that the function of MYB4 in growth inhibition of lignin-modified plants is likely to be distinct from its known role in transcriptional regulation of phenylpropanoid biosynthetic genes. This study also provides evidence that lignin-modification-induced dwarfism is not merely due to compromised water transport brought about by lignin deficiency, as gir1 has no effect on the growth inhibition of other lignin mutants that show the collapsed xylem phenotype.}, 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{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{scully_geib_mason_carlson_tien_chen_harding_tsai_hoover_2018, title={Host-plant induced changes in microbial community structure and midgut gene expression in an invasive polyphage (Anoplophora glabripennis)}, volume={8}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-018-27476-0}, abstractNote={Polyphagous insect herbivores possess diverse mechanisms to overcome challenges of feeding in multiple plant species including, but not limited to, transcriptional plasticity and associations with obligate or facultative symbionts. The Asian longhorned beetle (Anoplophora glabripennis) is a polyphagous wood-feeder capable of developing on over 100 tree species and, like other polyphages, its genome contains amplifications of digestive and detoxification genes. This insect also possesses a diverse gut microbial community, which has the metabolic potential to augment digestive physiology. While the genomic repertoires of A. glabripennis and its microbial community have been studied previously, comparatively less is known about how the gut transcriptome and community change in response to feeding in different hosts. In this study, we show that feeding in two suitable hosts (Acer spp. and Populus nigra) altered the expression levels of multicopy genes linked to digestion and detoxification. However, feeding in a host with documented resistance (Populus tomentosa) induced changes in the transcriptome and community beyond what was observed in insects reared in P. nigra, including the downregulation of numerous β-glucosidases, odorant binding proteins, and juvenile hormone binding proteins, the upregulation of several cuticular genes, and the loss of one major bacterial family from the gut community.}, journal={SCIENTIFIC REPORTS}, author={Scully, Erin D. and Geib, Scott M. and Mason, Charles J. and Carlson, John E. and Tien, Ming and Chen, Han-Yi and Harding, Scott and Tsai, Chung-Jui and Hoover, Kelli}, year={2018}, month={Jun} }
 @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 UDP ‐glycosyltransferase ( UGT ) plays a major role in the diversity and reactivity of plant specialized metabolites by catalyzing the transfer of the sugar moiety from activated UDP ‐sugars to various acceptors. Arabidopsis UGT 89A2 was previously identified from a genome‐wide association study as a key factor that affects the differential accumulation of dihydroxybenzoic acid ( DHBA ) glycosides in distinct Arabidopsis natural accessions, including Col‐0 and C24. The in vitro enzyme assays indicate that these distinct metabolic phenotypes reflect the divergence of UGT 89A2 enzyme properties in the Col‐0 and C24 accessions. UGT 89A2 from Col‐0 is highly selective toward UDP ‐xylose as the sugar donor, and the isoform from C24 can utilize both UDP ‐glucose and UDP ‐xylose but with a higher affinity to the glucose donor. The sequences of the two isozymes only differ at six amino acid residues. Examination of these amino acid residues in more natural accessions revealed a strong correlation between the amino acid polymorphism at position 153 and the DHBA glycoside accumulation pattern. Site‐directed mutagenesis that swapped residue 153 between UGT 89A2 from Col‐0 and C24 reversed the UDP ‐sugar preferences, indicating that residue 153 plays an important role in determining sugar donor specificity of UGT 89A2. This study provides insight into the key amino acid changes that confer sugar donor selectivity on UGT s, and demonstrates the usefulness of natural variation in understanding the structure–function relationship of enzymes involved in specialized metabolism.}, number={2}, journal={PLANT JOURNAL}, author={Chen, Han-Yi and Li, Xu}, year={2017}, month={Jan}, pages={195–203} }
 @article{chen_park_heitmann_hubbe_2009, title={Importance of Cellulosic Fines Relative to the Dewatering Rates of Fiber Suspensions}, volume={48}, ISSN={["0888-5885"]}, DOI={10.1021/ie9006613}, abstractNote={When cellulosic fines are present in significant amounts, they can have a dominant influence on dewatering. Pulp suspensions drain rapidly if the fines have been removed. In this study, the dependency of gravity dewatering rates on the level and properties of cellulosic fine matter was quantified. Bleached hardwood kraft pulp was used as a source of primary fines (collected before refining) and secondary fines (collected after refining of fines-free fiber suspensions). Fractions of fine matter also were obtained from chemithermomechanical (CTMP) pulp. Size distributions of these fines were characterized using a laser diffraction method. Results were explainable by a mechanism in which unattached fines are able to move relative to adjacent fibers during the dewatering and consolidation of a mat of fibers. Due to such movement, fines end up in locations where they plug drainage channels in the mat. The contribution of the fines to dewatering increased in inverse proportion to particle size and with increasing surface area, as calculated from the light scattering analysis.}, number={20}, journal={INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH}, author={Chen, Hao and Park, Andrew and Heitmann, John A. and Hubbe, Martin A.}, year={2009}, month={Oct}, pages={9106–9112} }
 @article{chen_allen_2001, title={Human milk antibacterial factors - The effect of temperature on defense systems}, DOI={10.1007/978-1-4615-1371-1_42}, abstractNote={Bovine milk will eventually spoil at refrigeration temperatures, but endogenous or exogenous pathogenic or spoilage bacteria in human milk stored for delayed feeding will die. We investigated the mechanism for these antibacterial properties and their response to high-tempertature, short-time (HTST, 72°C-75°C, 15 sec) and low-temperature long-time (LTLT, 65°C, 30min) pasteurization. NonpathogenicListeria innocua(106cfu/mL) was inoculated into raw and processed bovine and human milk; bacterial plate counts twice weekly determined antibacterial activities. Up to 99% ofL. innocuawere killed and further growth was inhibited in raw and pasteurized human milk for at least 60 days at 4°C. Reactive IgA antibodies againstListeriaantigens were demonstrated by enzyme immunoassay in some human milk samples; sIgA activity againstEscherichia coliO antigens was significantly decreased by heat treatments (raw, 1.8; HTST, 1.1; LTLT, 1.3 activity units). Adding human lactoferrin (0.5-20 mg/mL) to theListeriainoculum (-107cfu/mL) in 1% peptone water did not inhibit bacterial growth.}, journal={Bioactive components of human milk (Advances in experimental medicine and biology; v. 501)}, publisher={New York: Kluwer Academic/Plenum Publishers}, author={Chen, H. Y. and Allen, J. C.}, year={2001}, pages={341–348} }
 @article{chen_pilkington_tharrington_allen_1997, title={Developing a dry-cured ham nutritional database}, volume={10}, DOI={10.1006/jfca.1997.0534}, abstractNote={Manufacturers of country ham, a dry-cured ham with a minimum 4% NaCl in the finished product, are required by Food Safety and Inspection Service (FSIS) to declare the nutrient content on the label. This study investigated the distribution of nutrients within whole hams to permit calculation of nutrient content for various cuts. Results of a preliminary experiment utilizing six country hams to develop sampling techniques were used to develop the final study protocol. The final study measured the nutrient content of 15 whole hams representative of Southeastern country hams and 7 side meats. Each ham was divided into four sections (butt, center, shank, and hock), which were subdivided into bone and skin, fat, and muscle groups. All muscle and fat samples were analyzed for moisture, protein, fat, sugar profile, cholesterol, fatty acid profile, and minerals (Ca, Fe, K, Na, Zn). Significant variations (P< 0.05) were found between different hams as well as between different muscle groups. Nutrition Facts labels of 19 typical country ham products were then computed from chemical analysis and tissue and muscle composition and put into standard formats. All ham products contained a very high amount of sodium (>28% DV), were high in protein and fat (>20% DV), and were “good” to “high” in cholesterol (16 to 28% DV). The lean muscle products contained higher sodium and protein, but lower amounts of fat, cholesterol, and calories compared to untrimmed products. Side meat was higher in calories, fat, and cholesterol but lower in protein and sodium content than country ham products. Country ham products and side meats were low (<2% DV) in total carbohydrate, sugars, and calcium. The data presented for nutrient content of all the muscle systems in whole country hams permit calculations for a nutritional label for virtually all of the subdivided portions of country ham that are currently being marketed.}, number={3}, journal={Journal of Food Composition and Analysis}, author={Chen, H. Y. and Pilkington, D. H. and Tharrington, J. B. and Allen, J. C.}, year={1997}, pages={190–204} }
 @article{chen_schwartz_spanos_1992, title={FRACTIONATION OF BUTTER OIL BY SUPERCRITICAL CARBON-DIOXIDE}, volume={75}, ISSN={["0022-0302"]}, DOI={10.3168/jds.S0022-0302(92)78027-8}, abstractNote={The use of supercritical CO 2 to fractionate butter oil into various triglyceride groups with unique physical and chemical properties was investigated.Experiments were conducted at 40 'C and at 10.3, 13.8, 17.2, 20.7, 24.1, and 27.6 MPa in a continuous flow extraction system.Solubility of butter oil triglycerides in supercritical C02 of various temperatures (35, 40, 50, and 60'C) and pressures (10.3, 13.8, 17.2, 20.7, 24.1, and 27.6 MPa) was also studied.Triglyceride extractability was enhanced by raising the pressure and lowering the temperature of extraction.The mean molecular weight of fractions, estimated by high performance gel permeation chromatography, ranged from 703 amu (atomic mass unit; 40°C, 10.3 MPa) to 794 amu (40°C, 27.6 MPa).The fatty acid composition of triglycerides, determined by HPLC, showed that fractions extracted at lower pressure contained higher concentrations of short-chain C4 to CS) and medium-chain (CI0 to C12) fatty acids and lower concentrations of long-chain (C14 to CIS) fatty acids.Melting behavior of the various fractions, studied by differential scanning calorimetry, reflected the alterations in triglyceride composition.Fractions with unique melting behavior (i.e., a single narrow melting zone and a melting peak maximum}, number={10}, journal={JOURNAL OF DAIRY SCIENCE}, author={CHEN, H and SCHWARTZ, SJ and SPANOS, GA}, year={1992}, month={Oct}, pages={2659–2669} }
 @article{chen_schwartz_1991, title={Fractionation of butter oil with supercritical carbon dioxide}, volume={74}, journal={Journal of Dairy Science}, author={Chen, H. and Schwartz, S. J.}, year={1991}, pages={130} }