Article
Biochemical Research Methods
Chuwei Lin, Dawei Dai, Guimei Zhao, Sarah Joe, Sixue Chen
Summary: In this study, the role of MPK4 in stomatal immune response was explored through overexpression in Arabidopsis. The MPK4-associated protein complex in guard cells was characterized, and four new interacting proteins were identified. These findings shed light on the functions of MPK4 in guard cells and provide new targets for further research.
JOURNAL OF PROTEOMICS
(2023)
Article
Plant Sciences
Young-Sun Riu, Hyun-Geun Song, Hwi-Su Kim, Sam-Geun Kong
Summary: This study used different promoters to alter the response characteristics and growth phenotypes of phototropins in transgenic plants, as well as improve leaf transpiration.
Article
Plant Sciences
Tiantian Liu, Yuxin Li, Chang Wang, Da Zhang, Jiajia Liu, Mingyuan He, Mingxun Chen, Yuan Guo
Summary: This study revealed the function of Brassica napus WRKY transcription factors in leaf senescence, providing a novel strategy for breeding new stay-green cultivars in rapeseed through genetic manipulation.
Article
Plant Sciences
Ke-Lin Huang, Jing Tian, Huan Wang, Yi-Fan Fu, Yang Li, Yong Zheng, Xue-Bao Li
Summary: BnFAX6 mediates fatty acid export from plastids to regulate lipid biosynthesis and release of axillary bud dormancy by enhancing linoleic acid level in Brassica napus buds.
Article
Plant Sciences
Ji Wang, Zhaosheng Zhou, Qing Tao, Xiuping Chen, Chen Shui, Xuyang Ren, Ling Yu, Mingxiang Liang
Summary: The study demonstrates that the miR169 family in rapeseed can cleave the target gene BnaNF-YAs, and these miR169s are responsive to salinity, drought, and abscisic acid. Heterologous expression and gene expression profiling reveal that Bna-miR169n and BnaNF-YA9 co-regulate downstream genes, forming a cascade that regulates plant abiotic stress responses.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Lisa David, Jianing Kang, Josh Nicklay, Craig Dufresne, Sixue Chen
Summary: This study demonstrates that SAR induces altered responses of stomata to pathogens in systemic leaves, with guard cell defense depending on the protein DIR1. By using a multi-omics approach, potential signaling mechanisms specific to guard cells during SAR were identified, which may lead to new avenues for genetic modification and molecular breeding of disease-resistant plants.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Agricultural Engineering
Sayedehsaba Bilgrami, Liezhao Liu, Sara Farokhzadeh, Ahmad Sobhani Najafabadi, Hadi Darzi Ramandi, Najmeh Nasiri, Ibrahim Darwish
Summary: This study collected QTL information from multiple populations and identified overlapping regions associated with seed quality traits in Brassica napus, showing potential for improving multiple desirable traits simultaneously. Enrichment regions with more QTLs in some traits were found, providing clues for discovering varied areas of improvement. Additionally, candidate genes in overlapping regions were analyzed, revealing key known genes, novel genes, and genes with unknown functions involved in different biological processes of quality traits.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Article
Biochemistry & Molecular Biology
Peipei Jiao, Yuanlin Liang, Shaoping Chen, Yang Yuan, Yongqiang Chen, Honghong Hu
Summary: Manipulation of the Bna.EPF2 gene in Brassica napus reduces stomatal density and size, leading to lower transpiration and improved water-use efficiency and drought tolerance without affecting photosynthesis or yield-related traits.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Plant Sciences
Zhiqing Wang, Yao Mu, Xuefeng Hao, Jinbao Yang, Daixuan Zhang, Zhuping Jin, Yanxi Pei
Summary: Hydrogen sulfide and melatonin play important roles in regulating stomatal closure and enhancing osmotic stress resistance in Arabidopsis thaliana. Their crosstalk involves increasing transcription levels of melatonin synthesis-related genes and sulfhydryl modification of enzymes to promote stomatal closure under osmotic stress conditions. This study provides insights into the functions and interactions of hydrogen sulfide and melatonin in response to osmotic stress.
PLANT CELL REPORTS
(2022)
Article
Plant Sciences
Aravind Karanam, David He, Po-Kai Hsu, Sebastian Schulze, Guillaume Dubeaux, Richa Karmakar, Julian Schroeder, Wouter-Jan Rappel
Summary: Signaling networks are crucial in biological processes, with Boolean networks emerging as alternatives to detailed mathematical models. Boolink is a freely available graphical user interface that enables the construction and analysis of Boolean networks, facilitating the generation of testable predictions through iterative modifications based on experimental data.
Article
Plant Sciences
Chuanlei Xiao, Huimin Guo, Jing Tang, Jiaying Li, Xuan Yao, Honghong Hu
Summary: The study systematically investigated the expression patterns of 19 putative Guard-cell-enriched GDSL Lipases (GGLs) in Arabidopsis, revealing diverse expression patterns in guard cells. Most GGLs were localized in the endoplasmic reticulum, and some in lipid droplets and nucleus. Further analysis showed the correlation of expression pattern and biological function, as well as the functional redundancy of GGLs in plant development and environmental adaptations. Phenotypic identification of ggl mutants indicated unique and redundant roles of GGLs in stomatal dynamics, density, morphology, and plant water relation, providing insights for controlling stomatal dynamics and development, plant growth, and adaptation to the environment.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
A. K. M. Mahmudul Huque, Wonmi So, Minsoo Noh, Min Kyoung You, Jeong Sheop Shin
Summary: AtBBD1 functions as a novel positive regulator of drought responses by enhancing the expression of ABA- and drought stress-responsive genes as well as by increasing proline content, thus conferring plants with enhanced drought tolerance.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Agronomy
Ying Xu, Xiangdong Kong, Yuan Guo, Ruisen Wang, Xiangtan Yao, Xiaoyang Chen, Tao Yan, Dezhi Wu, Yunhai Lu, Jie Dong, Yang Zhu, Mingxun Chen, Haiyan Cen, Lixi Jiang
Summary: We found that the roles of different genes controlling flowering time varied across different environments in a genetic population. Flowering time is crucial for crop life cycle length, yield, and quality. Through analyzing single nucleotide polymorphisms (SNPs) and structural variations (SVs), we provided a high-resolution map of flowering time-related genes (FTRGs) in Brassica napus. Our study revealed the molecular basis of the genotype-by-environment effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.
THEORETICAL AND APPLIED GENETICS
(2023)
Article
Plant Sciences
Kosuke Moriwaki, Shuichi Yanagisawa, Koh Iba, Juntaro Negi
Summary: In this study, two crucial cis-acting elements, 5'-CACGAGA-3 'and 5'-CACATGTTTCCC-3', were found to be essential for the guard cell-specific expression of SCAP1 and HT1. The findings reveal a novel transcriptional regulatory mechanism that synchronously promotes the expression of multiple genes required for stomatal maturation and function.
Article
Plant Sciences
Eigo Ando, Hannes Kollist, Kohei Fukatsu, Toshinori Kinoshita, Ichiro Terashima
Summary: Light and CO2 concentration play important roles in stomatal opening and closure. Changes in light and CO2 concentration can affect the phosphorylation level of guard cell H+-ATPase, which regulates the degree of stomatal aperture.
Article
Biochemistry & Molecular Biology
Clayton Kranawetter, Shuai Zeng, Trupti Joshi, Lloyd W. Sumner
Summary: The study utilized a data visualization tool, the Medicago truncatula Metabolite Atlas, to aid in understanding the accumulation of metabolites in different tissues. By analyzing metabolites in various tissues of Medicago truncatula roots, unique spatial localization of metabolites was revealed.
Article
Endocrinology & Metabolism
Biswapriya B. Misra, Shobana Jayapalan, Alison K. Richards, Ron C. M. Helderman, Elizabeth Rendina-Ruedy
Summary: The study aimed to characterize the distinct metabolic processes and intracellular metabolite profiles in stromal cells throughout osteoblast differentiation using untargeted metabolomics. The results showed that the metabolic footprint of stromal cells undergoing osteoblast differentiation is unique, with oxidative phosphorylation driving ATP generation in early differentiation stages, while mature osteoblasts depend on glycolysis.
Article
Biochemical Research Methods
Saleh Alseekh, Asaph Aharoni, Yariv Brotman, Kevin Contrepois, John D'Auria, Jan Ewald, Jennifer C. Ewald, Paul D. Fraser, Patrick Giavalisco, Robert D. Hall, Matthias Heinemann, Hannes Link, Jie Luo, Steffen Neumann, Jens Nielsen, Leonardo Perez de Souza, Kazuki Saito, Uwe Sauer, Frank C. Schroeder, Stefan Schuster, Gary Siuzdak, Aleksandra Skirycz, Lloyd W. Sumner, Michael P. Snyder, Huiru Tang, Takayuki Tohge, Yulan Wang, Weiwei Wen, Si Wu, Guowang Xu, Nicola Zamboni, Alisdair R. Fernie
Summary: Compound identification and reliable quantification in metabolomics are complicated by the chemical complexity and dynamic range of the metabolome, while quantification in complex mixtures can be further complicated by ion suppression and the presence of isomers.
Article
Microbiology
Robert A. Quinn, Kehau A. Hagiwara, Ken Liu, Maryam Goudarzi, Wimal Pathmasiri, Lloyd W. Sumner, Thomas O. Metz
Summary: Metabolites from the microbiome have significant impacts on health, but their diversity and functional roles are still being explored. Collaboration between microbiome scientists and analytical chemists is crucial to bridge the gap in expertise and communication, ultimately revealing hidden factors within microbiomes that contribute to maintaining healthy humans and environments.
Editorial Material
Psychology, Biological
Tatsuya Amano, Clarissa Rios Rojas, Yap Boum, Margarita Calvo, Biswapriya B. Misra
NATURE HUMAN BEHAVIOUR
(2021)
Article
Biochemistry & Molecular Biology
David S. Wishart, Zinat Sayeeda, Zachary Budinski, AnChi Guo, Brian L. Lee, Mark Berjanskii, Manoj Rout, Harrison Peters, Raynard Dizon, Robert Mah, Claudia Torres-Calzada, Mickel Hiebert-Giesbrecht, Dorna Varshavi, Dorsa Varshavi, Eponine Oler, Dana Allen, Xuan Cao, Vasuk Gautam, Andrew Maras, Ella F. Poynton, Pegah Tavangar, Vera Yang, Jeffrey A. van Santen, Rajarshi Ghosh, Saurav Sarma, Eleanor Knutson, Victoria Sullivan, Amy M. Jystad, Ryan Renslow, Lloyd W. Sumner, Roger G. Linington, John R. Cort
Summary: NP-MRD is a comprehensive electronic resource for NMR data on natural products, metabolites, and other biologically derived chemicals. It is funded by NIH and has quickly become the world's largest repository for NMR data on natural products. The database contains both structural and NMR data for nearly 41,000 natural product compounds from over 7400 different living species, and is accessible at https://np-mrd.org.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Daniel B. Domingo-Fernandez, Yojana Gadiya, Abhishek Patel, Sarah Mubeen, Daniel Rivas-Barragan, Chris Diana, Biswapriya Misra, David Healey, Joe Rokicki, Viswa Colluru, Feilim Mac Gabhann, Carl Herrmann
Summary: Network-based approaches are popular for drug discovery and have shown promise in target discovery, side effect prediction, and drug repurposing. This study presents a novel algorithm, RPath, which prioritizes drugs for a given disease by reasoning over causal paths in a knowledge graph, guided by drug-perturbed and disease-specific transcriptomic signatures. The algorithm consistently prioritizes clinically investigated drug-disease pairs and can also predict novel targets.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Hilal A. Rather, Shalini Mishra, Yixin Su, Ashish Kumar, Sangeeta Singh, Biswapriya B. Misra, Jingyun Lee, Cristina M. Furdui, Lindsey R. Hamilton, Robert W. Gould, Susan H. Nader, Michael A. Nader, Gagan Deep
Summary: This study investigates the effects of prenatal cocaine use on postnatal development and long-term neurobiological outcomes. The researchers found that extracellular vesicles (EVs) could potentially serve as biomarkers to assess the adverse effects due to prenatal cocaine exposure.
Article
Agriculture, Multidisciplinary
Xingxing Li, Saurav J. Sarma, Lloyd W. Sumner, A. Daniel Jones, Robert L. Last
Summary: This study investigated the differences in metabolomes of upland and lowland switchgrass, and revealed significant variations between these two ecotypes as well as at different developmental stages. Terpenoid- and polyphenol-derived specialized metabolites, including steroidal saponins, di- and sesqui-terpenoids, and flavonoids, were identified. The concentrations of saponins were found to be higher in the roots of lowland switchgrass compared to upland switchgrass. These findings provide valuable insights into the potential biological functions and biosynthesis pathways of specialized metabolites in switchgrass, and could contribute to the development of low-input bioenergy crops.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Engineering, Environmental
Mohamed Bayati, Hsin-Yeh Hsieh, Shu-Yu Hsu, Chenhui Li, Elizabeth Rogers, Anthony Belenchia, Sally A. Zemmer, Todd Blanc, Cindy LePage, Jessica Klutts, Melissa Reynolds, Elizabeth Semkiw, Hwei-Yiing Johnson, Trevor Foley, Chris G. Wieberg, Jeff Wenzel, Terri Lyddon, Mary LePique, Clayton Rushford, Braxton Salcedo, Kara Young, Madalyn Graham, Reinier Suarez, Anarose Ford, Zhentian Lei, Lloyd Sumner, Brian P. Mooney, Xing Wei, C. Michael Greenlief, Marc C. Johnson, Chung-Ho Lin
Summary: Recent SARS-CoV-2 wastewater-based epidemiology surveillance has found a positive correlation between the number of COVID-19 patients in a sewershed and the level of viral genetic material in the wastewater. However, the variability in viral load among treatment facilities receiving industrial wastewater has made clinical prediction challenging. This study developed a systematic ranking process and metabolomic analysis to identify wastewater treatment facilities exhibiting SARS-CoV-2 suppression, as well as the chemicals suppressing the signals. It was found that certain bioactive compounds in wastewater can significantly reduce the stability of SARS-CoV-2 genetic marker signals.
Review
Biochemistry & Molecular Biology
David S. Wishart, Leo L. Cheng, Valerie Copie, Arthur S. Edison, Hamid R. Eghbalnia, Jeffrey C. Hoch, Goncalo J. Gouveia, Wimal Pathmasiri, Robert Powers, Tracey B. Schock, Lloyd W. Sumner, Mario Uchimiya
Summary: Metabolomics investigates the global metabolic alterations associated with various processes, and NMR-based methods have considerable benefits and advantages. The growing number of publications on NMR-based metabolomics suggests its continuous development and contributions to the scientific community.
Article
Agronomy
Khanh-Van Ho, Novianus Efrat, Kathy L. Schreiber, Phuc H. Vo, Marco N. De Canha, Analike Blom van Staden, Bianca D. Payne, Carel B. Oosthuizen, Danielle Twilley, Zhentian Lei, Lloyd W. Sumner, Charles R. Brown, Namrita Lall, Chung-Ho Lin
Summary: This study evaluated the anti-inflammatory properties of switchgrass and identified compounds in switchgrass extracts that inhibit the expression of inflammatory mediators. Different cultivars of switchgrass showed varying degrees of inhibition on the secretion of inflammatory mediators. Metabolomics and chromatography-mass spectrometry analyses were used to identify bioactive anti-inflammatory compounds in switchgrass. The Alamo and Kanlow cultivars of switchgrass showed potential as a natural source of anti-inflammatory compounds.
Article
Nutrition & Dietetics
Dominick J. Lemas, Xinsong Du, Bethany Dado-Senn, Ke Xu, Amanda Dobrowolski, Marina Magalhaes, Juan J. Aristizabal-Henao, Bridget E. Young, Magda Francois, Lindsay A. Thompson, Leslie A. Parker, Josef Neu, Jimena Laporta, Biswapriya B. Misra, Ismael Wane, Samih Samaan, Timothy J. Garrett
Summary: This study aims to identify unique metabolites that may impact infant health outcomes by analyzing the metabolome of human and bovine milk at 2 weeks of life. The results showed that more than 80% of the milk metabolome is shared between human and bovine milk during early lactation. These findings highlight untargeted metabolomics as a potential strategy to identify unique and shared metabolites in bovine and human milk that may relate to and impact infant health outcomes.
Review
Chemistry, Analytical
Biswapriya B. Misra
Summary: Gas chromatography-mass spectrometry (GC-MS) is a versatile analytical platform that is widely used in metabolomics and exposomics research, especially with the development of high-resolution accurate mass (HRAM) GC-MS systems. These systems generate rich data, which are crucial for data processing and information sharing.
ANALYTICAL METHODS
(2021)
Article
Biotechnology & Applied Microbiology
Alexander A. Aksenov, Ivan Laponogov, Zheng Zhang, Sophie L. F. Doran, Ilaria Belluomo, Dennis Veselkov, Wout Bittremieux, Louis Felix Nothias, Melissa Nothias-Esposito, Katherine N. Maloney, Biswapriya B. Misra, Alexey V. Melnik, Aleksandr Smirnov, Xiuxia Du, Kenneth L. Jones, Kathleen Dorrestein, Morgan Panitchpakdi, Madeleine Ernst, Justin J. J. van der Hooft, Mabel Gonzalez, Chiara Carazzone, Adolfo Amezquita, Chris Callewaert, James T. Morton, Robert A. Quinn, Amina Bouslimani, Andrea Albarracin Orio, Daniel Petras, Andrea M. Smania, Sneha P. Couvillion, Meagan C. Burnet, Carrie D. Nicora, Erika Zink, Thomas O. Metz, Viatcheslav Artaev, Elizabeth Humston-Fulmer, Rachel Gregor, Michael M. Meijler, Itzhak Mizrahi, Stav Eyal, Brooke Anderson, Rachel Dutton, Raphael Lugan, Pauline Le Boulch, Yann Guitton, Stephanie Prevost, Audrey Poirier, Gaud Dervilly, Bruno Le Bizec, Aaron Fait, Noga Sikron Persi, Chao Song, Kelem Gashu, Roxana Coras, Monica Guma, Julia Manasson, Jose U. Scher, Dinesh Kumar Barupal, Saleh Alseekh, Alisdair R. Fernie, Reza Mirnezami, Vasilis Vasiliou, Robin Schmid, Roman S. Borisov, Larisa N. Kulikova, Rob Knight, Mingxun Wang, George B. Hanna, Pieter C. Dorrestein, Kirill Veselkov
Summary: This study developed a machine learning approach that enables auto-deconvolution of gas chromatography-mass spectrometry data for the analysis and comparison of chemical compounds.
NATURE BIOTECHNOLOGY
(2021)