Article
Biochemistry & Molecular Biology
Harley Gordon, Christin Fellenberg, Nathalie D. Lackus, Finn Archinuk, Amanda Sproule, Yoko Nakamura, Tobias G. Koellner, Jonathan Gershenzon, David P. Overy, C. Peter Constabel
Summary: Knockout of UGT71L1 gene involved in salicinoid biosynthesis in poplars alters salicylic acid and jasmonic acid metabolism and has unexpected effects on plant growth.
Article
Plant Sciences
Franziska Eberl, Thomas Fabisch, Katrin Luck, Tobias G. Koellner, Heiko Vogel, Jonathan Gershenzon, Sybille B. Unsicker
Summary: KTIs in black poplar leaves are induced upon herbivory by three different chewing herbivores, with beetles eliciting higher transcriptional induction than caterpillars, and both caterpillar species inducing similar KTI expression levels. The induction of KTIs is controlled at the transcriptional level in a threshold-based manner and is strongly influenced by the species identity of the herbivore.
Article
Plant Sciences
Nathalie D. Lackus, Axel Schmidt, Jonathan Gershenzon, Tobias G. Kollner
Summary: Benzenoids play vital roles in plant defense, and their biosynthesis in black cottonwood is linked to herbivory. The volatile compounds benzaldehyde, benzylalcohol, and benzyl benzoate are increased upon leaf beetle feeding, while nonvolatile salicinoids remain unaffected. Biosynthesis of benzenoids in poplar involves cinnamic acid and a peroxisomal beta-oxidative pathway, with similarities to petunia flower biosynthesis.
Article
Chemistry, Analytical
Xiaoling Su, Deying Chen, Liang Li, Lanjuan Li
Summary: The study demonstrates that perfusion can significantly alter the liver metabolome, recommending the use of non-perfused liver for comprehensive liver metabolomics analysis for high coverage.
ANALYTICA CHIMICA ACTA
(2021)
Article
Chemistry, Multidisciplinary
Craig S. S. Day, Stephanie J. J. Ton, Clemens Kaussler, Daniel Vronning Hoffmann, Troels Skrydstrup
Summary: Here, a methodology for accessing isotopically labeled esters and amides from carbonates and carbamates utilizing an oxygen deletion strategy is reported. The methodology employs a decarboxylative carbonylation approach using C-12 or C-13 carbon monoxide generated ex situ in near stoichiometric amounts for isotope labeling. The reaction demonstrates a broad scope, functional group tolerance, and high yields, exemplified by the synthesis of structurally complex molecules. Additionally, a complementary method for the catalytic in situ generation of CO from CO2 liberated during decarboxylation is developed as a proof-of-concept approach for converting CO2-derived compounds to CO-containing frameworks. Mechanistic studies provide insights into the catalytic steps and the impact of ligand choice for overcoming challenges in low-pressure carbonylation methodologies, aiding the development of future methodologies.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemical Research Methods
Sha Li, Yao-Yu Chen, Tian-Tian Ye, Quan-Fei Zhu, Yu-Qi Feng
Summary: A method combining chemical isotope labeling and LC-MS was developed for simultaneous determination of central carbon metabolism pathway (CCM) intermediates with high coverage and accuracy. By chemical derivatization, all CCM intermediates achieved better separation and accurate quantification in a single LC-MS run. This method was applied for accurate quantification of 22 CCM intermediates in different biological samples, and also for quantification at the single-cell level.
JOURNAL OF CHROMATOGRAPHY A
(2023)
Article
Chemistry, Analytical
Yan-Qing Chen, Hong Shen, Ru-Jie Yang, Jian-Bo Wan
Summary: A sensitive method was developed to accurately determine 20 NAEs in biological samples by chemical isotope labeling strategy coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Derivatized NAEs provided stable and abundant specific product ions in MS/MS spectrum for quantitation, enhancing detection sensitivity by 6- to 170-fold compared to non-derivatized NAEs. The method was successfully applied to determine NAEs in serum samples and liver tissues, showing practicability in analyzing endogenous NAE in biological samples.
ANALYTICA CHIMICA ACTA
(2021)
Article
Agriculture, Multidisciplinary
Zhihua Li, Ling Dong, Chi Zhao, Fengju Zhang, Shuang Zhao, Jingjing Zhan, Jia Li, Liang Li
Summary: This study presents a four-channel chemical isotope labeling (CIL) LC-MS approach for comprehensive metabolome analysis of high-salt fermented food. The method allows for high coverage identification and quantification of metabolites, revealing the high metabolic diversity in these foods.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Forestry
Vimal K. Balasubramanian, Albert Rivas-Ubach, Tanya Winkler, Hugh Mitchell, James Moran, Amir H. Ahkami
Summary: This study investigates the molecular processes involved in long-distance source-sink carbon allocation in poplar using an "auxin-stimulated carbon sink" approach. The findings show that auxin regulates root dry weight and branching pattern, and increases the allocation of photosynthetically fixed carbon from leaf to root tissues. Transcriptome analysis identifies highly expressed genes in root tissue under auxin enhancer conditions that can increase sink size and activity. Metabolic analysis reveals a shift in overall metabolism and altered levels of galactinol and citrate in root tissue under auxin enhancer and inhibitor conditions. The study suggests that mobile sugar alcohols, starch metabolism-derived sugars, and TCA-cycle intermediates may be key molecular drivers of sink strength in poplar.
Article
Biochemistry & Molecular Biology
Ryo Konno, Takashi Matsui, Hiroaki Ito, Yusuke Kawashima, Makoto Itakura, Yoshio Kodera
Summary: GeLC-MS/MS method coupled with stable isotope dimethyl labeling provides high accuracy and comprehensive peptide comparisons, enabling accurate determination of peptide abundance ratio between samples, unaffected by the reproducibility of gel extraction or LC-MS procedures, thus facilitating the detection of proteolysis events.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Analytical
Kodai Beppu, Daichi Saito, Yoshio Muguruma, Miki Takahashi, Shuichi Harada, Koichi Inoue
Summary: This study developed a new stable isotope labeling method for analyzing residual antibiotics in bacteria culture, achieving acceptable recovery rates and representing a significant improvement over previous methods.
ANALYTICAL SCIENCES
(2021)
Article
Biochemical Research Methods
Sha Li, Zheng Zhang, Fei-Long Liu, Bi-Feng Yuan, Tian-Gang Liu, Yu-Qi Feng
Summary: Phosphomonoester metabolites play a crucial role in microbial biosynthesis and energy metabolism. Researchers have developed a LC-MS method using isotope labeling for the comprehensive analysis of phosphomonoester metabolites. They successfully identified 42 phosphomonoester metabolites, including two that were first detected in Saccharomyces cerevisiae. The relative quantification results showed significant differences in the content of these metabolites between lycopene-producible and wild-type S. cerevisiae, and further experiments confirmed the relationship between lycopene production and the activity of a specific pathway.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Sha Li, Zheng Zhang, Fei-Long Liu, Bi-Feng Yuan, Tian-Gang Liu, Yu-Qi Feng
Summary: We developed an LC-MS method using isotope reagents for the comprehensive analysis of phosphomonoester metabolites. This method allowed for rapid screening, identification, and relative quantification of the metabolites in Saccharomyces cerevisiae. We identified 42 phosphomonoester metabolites, including two that were detected for the first time in S. cerevisiae. The relative quantification results revealed significant differences in certain metabolites between lycopene-producible and wild-type S. cerevisiae, indicating a close relationship between phosphomonoesters and lycopene production.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Xian Luo, Liang Li
Summary: Cellular metabolomics provides insights into metabolic processes in cells, and this study investigates the effects of solvent evaporation equipment and storage conditions on high-coverage cellular metabolomics analysis. The choice of solvent evaporation equipment does not significantly impact the cellular metabolome, but the presence of methanol during storage can lead to notable changes in the metabolome after 7 days. Thoroughly drying cell samples before storage or shipment at room temperature is recommended to ensure high-quality results.
Article
Biochemical Research Methods
Molly Tillmann, Qian Tang, Jerry D. Cohen
Summary: The plant hormone auxin is crucial for plant growth and environmental response. Various pathways exist for the biosynthesis of IAA, the primary auxin, in different plant species. Techniques involving stable isotopes and chemical inhibitors are useful for tracing pathway utilization in vivo.
Article
Plant Sciences
Chhana Ullah, Chung-Jui Tsai, Sybille B. Unsicker, Liangjiao Xue, Michael Reichelt, Jonathan Gershenzon, Almuth Hammerbacher
Article
Plant Sciences
Karolina Heyduk, Jeremy N. Ray, Saaravanaraj Ayyampalayam, Nida Moledina, Anne Borland, Scott A. Harding, Chung-Jui Tsai, Jim Leebens-Mack
JOURNAL OF EXPERIMENTAL BOTANY
(2019)
Article
Plant Sciences
Benjamin A. Babst, Fei Gao, Lucia M. Acosta-Gamboa, Abhijit Karve, Michael J. Schueller, Argelia Lorence
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2019)
Article
Plant Sciences
Chung-Jui Tsai, Peng Xu, Liang-Jiao Xue, Hao Hu, Batbayar Nyamdari, Radnaa Naran, Xiaohong Zhou, Geert Goeminne, Ruili Gao, Erica Gjersing, Joseph Dahlen, Sivakumar Pattathil, Michael G. Hahn, Mark F. Davis, John Ralph, Wout Boerjan, Scott A. Harding
Article
Forestry
Richard Sample, Benjamin A. Babst
TREES-STRUCTURE AND FUNCTION
(2020)
Article
Plant Sciences
Gen Li, Rongshoung Lin, Chioma Egekwu, Joshua Blakeslee, Jinshan Lin, Emily Pettengill, Angus S. Murphy, Wendy A. Peer, Nazrul Islam, Benjamin A. Babst, Fei Gao, Sergey Komarov, Yuan-Chuan Tai, Gary D. Coleman
JOURNAL OF EXPERIMENTAL BOTANY
(2020)
Article
Plant Sciences
Scott A. Harding, Christopher J. Frost, Chung-Jui Tsai
Article
Plant Sciences
Benjamin A. Babst, Abhijit Karve, Anthony Sementilli, Ismail Dweikat, David M. Braun
Summary: The main factor contributing to sugar accumulation in sweet sorghum stems compared to grain sorghum is the higher rate of phloem unloading and storage in the stem, rather than sugar production or export from leaves. Sweet sorghum varieties accumulate high concentrations of fermentable sugars in their stem internodes, making them a valuable feedstock for bioethanol production. The accumulation of sugars in sweet sorghum stems is influenced by the interplay of different sink tissues, with the elevated sugar phloem unloading and uptake capacity in mature stem internodes likely driving the process.
Article
Plant Sciences
Chhana Ullah, Axel Schmidt, Michael Reichelt, Chung-Jui Tsai, Jonathan Gershenzon
Summary: SA and JA pathways interact positively in poplar, resulting in the accumulation of flavonoid phytoalexins and enhanced resistance to pathogens.
Article
Materials Science, Paper & Wood
Gurshagan Kandhola, Angele Djioleu, Kalavathy Rajan, Joseph Batta-Mpouma, Nicole Labbe, Joshua Sakon, Benjamin A. Babst, Anindya Ghosh, Danielle Julie Carrier, Jin-Woo Kim
Summary: Cellulose nanocrystals (CNCs) are renewable and biocompatible nanomaterials with unique properties. The production and properties of CNCs from different wood species were investigated. The results showed that the type of wood species had an impact on the yield, purity, and properties of CNCs. This study provides insights into optimizing CNC production and usage for different applications.
Article
Plant Sciences
Scott A. Harding, Trevor T. Tuma, Kavita Aulakh, Maria A. Ortega, Dong Ci, Yongbin Ou, Chung-Jui Tsai
Summary: Leaf osmotic adjustment plays an important role in drought tolerance of plants. This study investigates the role of PtaSUT4 gene in regulating sucrose and turgor in European aspen under water deficit. The results show that downregulation of PtaSUT4 affects starch utilization and leaf relative water content dynamics. PtaSUT4 is also involved in regulating reactive oxygen species and antioxidants. These findings contribute to our understanding of plant responses to water stress.
PLANT AND CELL PHYSIOLOGY
(2022)
Article
Forestry
Richard D. Sample, James Cook, Benjamin A. Babst
Summary: Shumard oak seedlings are intolerant of dormant season flood, while Nuttall oak seedlings are tolerant. Flooding for more than 1-2 months beyond budbreak may have persistent negative impacts on Nuttall oaks.
TREES-STRUCTURE AND FUNCTION
(2023)
Article
Plant Sciences
Benjamin A. Babst, David M. Braun, Abhijit A. Karve, R. Frank Baker, Thu M. Tran, Douglas J. Kenny, Julia Rohlhill, Jan Knoblauch, Michael Knoblauch, Gertrud Lohaus, Ryan Tappero, Soenke Scherzer, Rainer Hedrich, Kaare H. Jensen
Summary: Phloem transport of photoassimilates plays a crucial role in plant growth and yield. This study demonstrates that sugar import is not necessary for phloem sap flow, and increased potassium loading compensates for decreased sucrose loading to maintain phloem pressure and transport.
Article
Biochemistry & Molecular Biology
Xi Gu, Ing-Gin Chen, Chung-Jui Tsai
Summary: Phylloquinone biosynthesis is retained in nonphotosynthetic holoparasitic plants, potentially enabling them to sense changes in the redox environment during host interactions through plasma membrane phylloquinone. This suggests an ancient origin of distinct phylloquinone pathways predating the evolution of parasitic plants in the Orobanchaceae.
PLANT SIGNALING & BEHAVIOR
(2021)
Article
Plant Sciences
Xi Gu, Ing-Gin Chen, Scott A. Harding, Batbayar Nyamdari, Maria A. Ortega, Kristen Clermont, James H. Westwood, Chung-Jui Tsai
Summary: Nonphotosynthetic holoparasites utilize flexible targeting of phylloquinone biosynthesis for plasma membrane redox signaling, with evidence of biosynthesis in Phelipanche aegyptiaca. This suggests a noncanonical role for phylloquinone in seed germination and haustorium development, with genes coexpressed with oxidoreductases involved in PM electron transport. Similar pathways are present in photoautotrophic taxa, indicating a potential ancient origin of multifunctionality.