Article
Chemistry, Multidisciplinary
Page N. Daniels, Hyunji Lee, Rebecca A. Splain, Chi P. Ting, Lingyang Zhu, Xiling Zhao, Bradley S. Moore, Wilfred A. van der Donk
Summary: This study identified a new biosynthetic pathway in which glycyl-tRNA is used to attach amino acids to a ribosomally synthesized peptide, generating amino acid-derived natural products. This pathway involves multiple hydroxylations and chemical modifications.
Article
Multidisciplinary Sciences
Xixi Sun, Yujie Yuan, Qitong Chen, Shiqi Nie, Jiaxuan Guo, Zutian Ou, Min Huang, Zixin Deng, Tiangang Liu, Tian Ma
Summary: The authors develop a new protein assembly strategy using a pool of docking peptides from polyketide synthase and apply it to the biosynthesis of astaxanthin in E. coli, resulting in a 2.4-fold increase in production. This study addresses the challenge of improving cascade catalytic efficiency and highlights the potential for engineering enzyme assembly.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Xianghua Peng, Fang Liu, Ping Liu, Xing Li, Xinguo Lu
Summary: This study introduced a metabolic pathway based driver gene identification method (pathDriver) to distinguish different cancer types/subtypes. By using a protein-protein interaction network combined with metabolic pathways to construct a pathway network, the collaborative impact factor of genes in the pathway network was evaluated using Interaction Frequency (IF) and Inverse Pathway Frequency (IPF) to identify cancer-specific driver genes. The application of this method to 16 types of TCGA cancers for pan-cancer analysis successfully identified biologically significant known cancer genes and potential new candidate genes.
CURRENT BIOINFORMATICS
(2021)
Article
Environmental Sciences
Junfei Zhan, Tao Sun, Xuehong Wang, Huifeng Wu, Junbao Yu
Summary: This study conducted a meta-analysis on published data to investigate the toxicological effects of Cd in marine bivalves. Results showed that there were species-, duration-, and dose-dependent responses to aqueous-phase Cd exposure in bivalves. Clams were the most sensitive species to Cd, and gill, hepatopancreas, and hemolymph were the main tissues indicating Cd-induced toxicity. Oxidative stress and detoxification were the top two subgroups indicating Cd toxicities.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Engineering, Environmental
Qu Zhang, Chao Xue, Gary Owens, Zuliang Chen
Summary: A strain of E2 degrading bacteria, identified as Ochrobactrum sp. strain FJ1, was isolated from activated sludge and showed efficient degradation of E2. The addition of methanol as an additional carbon source increased the biomass of the strain, but slightly inhibited E2 degradation efficiency.
JOURNAL OF HAZARDOUS MATERIALS
(2022)
Article
Biotechnology & Applied Microbiology
Shiyu Chen, Scott Lovell, Sumin Lee, Matthias Fellner, Peter D. Mace, Matthew Bogyo
Summary: A phage display method was developed to screen for covalent inhibitors that bind to protein targets by introducing a reactive linker to form cyclic peptides and an electrophilic 'warhead' to react with target nucleophiles. This approach identified cyclic peptides that irreversibly inhibited cysteine protease and serine hydrolase with high specificity and potency. It enables rapid, unbiased screening to identify new classes of highly selective covalent inhibitors for diverse molecular targets.
NATURE BIOTECHNOLOGY
(2021)
Article
Plant Sciences
Yuping Tan, Jian Yang, Yinyin Jiang, Shufu Sun, Xiaoyan Wei, Ruishan Wang, Junling Bu, Dayong Li, Liping Kang, Tong Chen, Juan Guo, Guanghong Cui, Jinfu Tang, Luqi Huang
Summary: Three O-methyltransferases were identified from Isatis indigotica that have the capacity for O-methylation of C-glycosylflavonoid isoorientin. Type II OMTs IiOMT1 and IiOMT2 efficiently catalyze isoorientin to form isoscoparin and decorate one of the aromatic vicinal hydroxyl groups on flavones. The Type I OMT IiOMT3 exhibited broader substrate promiscuity.
HORTICULTURE RESEARCH
(2022)
Article
Microbiology
Mohammad Mustafa Kazan, Misgana Mengistu Asmare, Rajani Kanta Mahapatra
Summary: Through integrated bioinformatics analysis, this study identified six potential drug target genes involved in the erythrocyte invasion phase, which are related to merozoites motility, cell-cycle regulation, G-dependent protein kinase phosphorylation in schizonts, control of microtubule assembly, and sexual commitment.
CURRENT MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Han Zhang, Jun-Cheng Jiang, Tian-Yi Yan, Lei Ni, Shang-Hao Liu
Summary: This study systematically investigates the pyrolysis hazard characteristics and mechanism of a new versatile ionic liquid, 1-Hexyl-2,3-dimethylimidazolium nitrate ([Hmmim][NO3]). The thermodynamic parameters, safety parameters, and reaction pattern of [Hmmim][NO3] pyrolysis process are obtained. The severity degree and possibility of runaway reaction are evaluated, while the primary noxious gas and reaction steps leading to the thermal hazards of [Hmmim][NO3] are confirmed. This research provides a theoretical basis for improving the intrinsic safety of [Hmmim][NO3] application and formulating corresponding safety preventive measures.
PROCESS SAFETY AND ENVIRONMENTAL PROTECTION
(2023)
Article
Multidisciplinary Sciences
Guifa Zhai, Yan Zhu, Guo Sun, Fan Zhou, Yangning Sun, Zhou Hong, Chuan Dong, Peter F. Leadlay, Kui Hong, Zixin Deng, Fuling Zhou, Yuhui Sun
Summary: Revealed the intermodular recognition mechanism in modular polyketide synthase, providing insights into the biosynthetic process and guidance for engineering. Demonstrated that KS4 in module 4 acts as a gatekeeper for cross-module enoylreduction. Discovered the evolutionary homology between module 3 and module 6 in AZL PKS, enabling evolution-oriented engineering.
NATURE COMMUNICATIONS
(2023)
Article
Plant Sciences
Zhi-Xin Leng, Ying Liu, Zhan-Yu Chen, Jun Guo, Jun Chen, Yong-Bin Zhou, Ming Chen, You-Zhi Ma, Zhao-Shi Xu, Xi-Yan Cui
Summary: DUF4228 proteins are important in plant response to abiotic stresses, and in soybean, 81 DUF4228 genes were identified with uneven distribution across chromosomes. GmDUF4228 genes are widely expressed in various organs, and GmDUF4228-70 was found to be up-regulated under drought and salt stresses, promoting stress tolerance and physiological changes in transgenic plants. These results suggest that GmDUF4228 genes play crucial roles in soybean response to abiotic stresses.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Microbiology
Lydia Alberti, Patricia Koenig, Sabine Zeidler, Anja Poehlein, Rolf Daniel, Beate Averhoff, Volker Mueller
Summary: Acinetobacter baumannii, a nosocomial pathogen, exhibits significant metabolic diversity. Growth on L-arabinose was found, and transcriptome analyses identified two gene clusters responsible for the oxidation of pentonates to a-ketoglutarate. These clusters also encode an uptake system and a regulator for specific pentonate oxidation pathways. Despite a cross-talk between these pathways, growth on pentoses was observed in pathogenic Acinetobacter species, while growth on L-arabinose provided benefits for long-term survival and desiccation resistance in A. baumannii ATCC 19606.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Toxicology
Shujie Liu, Toru Kawanishi, Atsuko Shimada, Naohiro Ikeda, Masayuki Yamane, Hiroyuki Takeda, Junichi Tasaki
Summary: Craniofacial anomalies are common birth defects caused by genetic and environmental factors. The identification of adverse outcome pathways (AOPs) for evaluating teratogenicity in craniofacial anomalies has been challenging. This study establishes zebrafish as a model for studying craniofacial anomalies and identifies the AOPs involved. The findings can be extrapolated to mammalian craniofacial development and help in predicting craniofacial anomalies in humans.
TOXICOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Zsolt Durvanger, Eszter Boros, Zoltan Attila Nagy, Rozsa Hegedus, Marton Megyeri, Jozsef Dobo, Peter Gal, Gitta Schlosser, Annamaria F. Angyan, Zoltan Gaspari, Andras Perczel, Veronika Harmat, Gabor Mezo, Dora K. Menyhard, Gabor Pal
Summary: Researchers have developed SFMIs, peptide inhibitors of MASP proteases, with high structural plasticity through directed evolution. They have also modified MASP-2-specific SFMI2 to create a versatile scaffold that is resistant to reducing environments and possesses near-native potency. These synthetic inhibitors could be potential drug candidates for coronavirus, particularly in thrombosis associated with COVID-19.
ACS CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Wasantha Lankathilaka Karunagala Pathiranage, Natalie Gumataotao, Adam T. Fiedler, Richard C. Holz, Brian Bennett
Summary: A new method was employed to trap catalytic intermediate species in Fe-type nitrile hydratase ReNHase. The reaction induced significant changes in EPR spectra, with a previously unobserved signal indicating a catalytically competent intermediate. Density functional theory calculations facilitated the assignment of observed EPR signals, providing new insights into the catalytic mechanism of NHase.
Meeting Abstract
Oncology
Raghu G. Nath, B. R. Sonawane, S. V. Vulimiri, Y. S. Lin
Review
Environmental Sciences
Gary Ginsberg, Suryanarayana V. Vulimiri, Yu-Sheng Lin, Jayaram Kancherla, Brenda Foos, Babasaheb Sonawane
JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH-PART A-CURRENT ISSUES
(2017)
Review
Toxicology
Jennifer Jinot, Jason M. Fritz, Suryanarayana V. Vulimiri, Nagalakshmi Keshava
TOXICOLOGY MECHANISMS AND METHODS
(2018)
Review
Toxicology
Jennifer Jinot, Jason M. Fritz, Suryanarayana V. Vulimiri, Nagalakshmi Keshava
TOXICOLOGY MECHANISMS AND METHODS
(2018)
Editorial Material
Environmental Sciences
Suryanarayana V. Vulimiri, Ofelia Olivero
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2019)
Review
Environmental Sciences
Channa Keshava, J. Allen Davis, John Stanek, Kristina A. Thayer, Audrey Galizia, Nagalakshmi Keshava, Jeff Gift, Suryanarayana V. Vulimiri, George Woodall, Carolyn Gigot, Kelly Garcia, Andrew Greenhalgh, Brittany Schulz, Savannah Volkoff, Krisa Camargo, Amanda S. Persad
ENVIRONMENT INTERNATIONAL
(2020)
Review
Environmental Sciences
Erin E. Yost, Audrey Galizia, Dustin F. Kapraun, Amanda S. Persad, Suryanarayana V. Vulimiri, Michelle Angrish, Janice S. Lee, Ingrid L. Druwe
Summary: The study summarized literature on naphthalene toxicity, indicating that animal studies are more suitable for deriving reference values.
ENVIRONMENTAL HEALTH PERSPECTIVES
(2021)
Article
Environmental Sciences
Kristina A. Thayer, Michelle Angrish, Xabier Arzuaga, Laura M. Carlson, Allen Davis, Laura Dishaw, Ingrid Druwe, Catherine Gibbons, Barbara Glenn, Ryan Jones, J. Phillip Kaiser, Channa Keshava, Nagalakshmi Keshava, Andrew Kraft, Lucina Lizarraga, Amanda Persad, Elizabeth G. Radke, Glenn Rice, Brittany Schulz, Rachel M. Shaffer, Teresa Shannon, Andrew Shapiro, Shane Thacker, Suryanarayana V. Vulimiri, Antony J. Williams, George Woodall, Erin Yost, Robyn Blain, Katherine Duke, Alexandra E. Goldstone, Pam Hartman, Kevin Hobbie, Brandall Ingle, Courtney Lemeris, Cynthia Lin, Alex Lindahl, Kristen McKinley, Parnian Soleymani, Nicole Vetter
Summary: This article describes the typical methods used to produce systematic evidence maps (SEMs) for the IRIS and PPRTV Programs. It provides examples of applications and workflows for rapid production of SEMs, as well as methods for literature search, screening, and data extraction. The article also presents approaches for study evaluation and offers interactive visual formats and downloadable data.
ENVIRONMENT INTERNATIONAL
(2022)
Article
Environmental Sciences
Kristina A. Thayer, Rachel M. Shaffer, Michelle Angrish, Xabier Arzuaga, Laura M. Carlson, Allen Davis, Laura Dishaw, Ingrid Druwe, Catherine Gibbons, Barbara Glenn, Ryan Jones, J. Phillip Kaiser, Channa Keshava, Nagalakshmi Keshava, Andrew Kraft, Lucina Lizarraga, Kristan Markey, Amanda Persad, Elizabeth G. Radke, Glenn Rice, Brittany Schulz, Teresa Shannon, Andrew Shapiro, Shane Thacker, Suryanarayana Vulimiri, George Woodall, Erin Yost
Summary: Systematic evidence maps (SEMs) are increasingly utilized in the environmental health field to enhance transparency and efficiency in data gathering, and to promote coordination and sharing among the community.
ENVIRONMENT INTERNATIONAL
(2022)
Meeting Abstract
Environmental Sciences
Channa Keshava, Vulimiri V. Suryanarayana, Suna Nicolai, Florenz A. Cruz, Ariane Lenzner, Patrick Tarnow, Narges Ghoreishi, Sven Knueppel, Amanda S. Persad, Kristina A. Thayer, Antony J. Williams, Nancy Baker, Jens T. Vanselow, Ralph Pirow
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)
Meeting Abstract
Environmental Sciences
Nagalakshmmi Keshava, Brittany Schulz, Suryanarayana V. Vulimiri, Jeff Gift, Geoffrey Peterson, Catheryne Chiang, Chelsea A. Weitekamp, David M. Lehmann, Amanda S. Persad, Yu-Sheng Lin, Anuradha Mudipalli, Michelle Angrish, Andrew Hotchkiss, Kristina A. Thayer
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2022)
Meeting Abstract
Environmental Sciences
C. Keshava, A. Davis, J. Stanek, K. Thayer, A. Galizia, N. Keshava, J. Gift, S. V. Vulimiri, G. Woodall, C. Gigot, A. Greenhalgh, Z. B. Schult, S. Volkoff, K. Camargo, A. S. Persad
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2019)
Meeting Abstract
Environmental Sciences
S. V. Vulimiri
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2016)
Meeting Abstract
Environmental Sciences
B. R. Sonawane, S. V. Vulimiri, L. S. Adams, R. G. Nath, J. M. Fritz
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2015)
Meeting Abstract
Environmental Sciences
R. G. Nath, B. R. Sonawane, S. V. Vulimiri, Y-S Lin
ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
(2014)