Article
Chemistry, Multidisciplinary
Larissa Bessler, Lea-Marie Vogt, Marc Lander, Christina Dal Magro, Patrick Keller, Jonas Kuehlborn, Christopher J. Kampf, Till Opatz, Mark Helm
Summary: Both RNA modification and RNA damage involve non-canonical nucleoside structures. While RNA modifications improve function, RNA damage has detrimental effects. This study identified and characterized a new structure, 2-methylthio-1,N6-ethenoadenosine (ms(2)epsilon A), related to a lesion resulting from exposure to alkylating chemicals. The formation of ms(2)epsilon A involves cleavage of a prenyl moiety in a known transfer RNA modification.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Biochemistry & Molecular Biology
Fengxia Li, Eugenio F. Fornasiero, Tal M. Dankovich, Verena Kluever, Silvio O. Rizzoli
Summary: By systematically studying probes initially developed for electron microscopy, researchers found that antibodies coupled to 6 nm gold particles exhibit excellent labeling specificity and reliable detection threshold in nanoSIMS imaging. These tools enable accurate visualization and analysis of samples and can be easily combined with other imaging approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Daniele Ubbiali, Marta Fratini, Lolita Piersimoni, Christian H. Ihling, Marc Kipping, Ingo Heilmann, Claudio Iacobucci, Andrea Sinz
Summary: The conformational ensemble of alpha-synuclein shifts during liquid-liquid phase separation, and a novel mass spectrometry-based approach is established to solve open questions in LLPS structural biology.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Dong Xing, Yifan Meng, Xu Yuan, Shuihui Jin, Xiaowei Song, Richard N. Zare, Xinxing Zhang
Summary: Despite the high stability of bulk water, microdroplets exhibit different properties, such as the presence of hydroxyl radicals at the air-water interface. In this study, OH· was detected as (H4O2)+, a hydroxyl radical combined with a hydronium cation, and successfully captured with caffeine and melatonin. Key oxidation radical intermediates were observed, providing important mechanistic information.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Multidisciplinary
Lingqi Qiu, R. Graham Cooks
Summary: Microdroplets exhibit unique chemistry, including simultaneous oxidation and reduction reactions. The active reagent is identified as the water radical cation/anion pair. The coexistence of oxidative and reductive species supports the existence of a double-layer structure at the microdroplet surface.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Review
Neurosciences
Kyle D. Brewer, Sophia M. Shi, Tony Wyss-Coray
Summary: The technological revolution of measuring global gene expression at the single-cell level is changing our understanding of the brain and neurological diseases, leading to a deeper knowledge of gene interactions and biological pathways. The application of new protein labeling, tracking, and detection methods allows researchers to uncover protein mechanisms that were previously only hypothesized, and also aids in discovering new biology. These developments will bring about a transformation in biomedical research and our understanding of the brain, ultimately enabling personalized medicine at the protein level.
MOLECULAR NEURODEGENERATION
(2022)
Article
Food Science & Technology
Jiayin Huang, Zhiheng Hu, Lingping Hu, Gaoshang Li, Chunhong Yuan, Jianchu Chen, Yaqin Hu
Summary: The study investigated the modification effects of a polyvinyl alcohol/hydroxypropyl methylcellulose/roselle anthocyanin-based film on the textural profiles of Penaeus vannamei shrimp. The results showed that the film improved the texture of the shrimp by rearranging water distribution and stabilizing protein conformation.
Review
Biochemistry & Molecular Biology
Alicia L. Richards, Manon Eckhardt, Nevan J. Krogan
Summary: Quantitative mass spectrometry (MS) techniques have enabled unbiased mapping of global changes in protein-protein interactions mediated by diseases, which can reveal disease mechanisms and identify new therapeutic targets.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Article
Biochemical Research Methods
Zhi Cheng, Charles Mobley, Sandeep K. Misra, Rama S. Gadepalli, Rachel Hammond, Leonid S. Brown, John M. Rimoldi, Joshua S. Sharp
Summary: Research shows that the membrane environment does not affect bulk solvent radical scavenging activity, but when present with proteins, the radical scavengers in the membrane compete for the local concentration of hydroxyl radicals, resulting in reduced oxidation of membrane proteins.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Biochemical Research Methods
Hauh-Jyun Candy Chen, Yan-Ling Liao
Summary: Although malondialdehyde and methylglyoxal have the same molecular formula, they have different chemistry in forming protein adducts. The major lysine adduct of malondialdehyde in hemoglobin is the N-propenal type, while that of methylglyoxal is N6-(1-carboxyethyl)lysine. This Letter provides evidence that the methylglyoxal-like hemoglobin adducts are not derived from malondialdehyde. This Letter also discusses the quantification of malondialdehyde-induced post-translational modifications in human hemoglobin by different mass spectrometry-based methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Cell Biology
Devanarayanan Siva Sankar, Joern Dengjel
Summary: Autophagy is a crucial cellular degradation process that helps in maintaining cellular homeostasis through the clearance of damaged organelles and harmful substances. Protein-protein interaction networks play a key role in regulating autophagy, contributing to the degradation process and maintaining cellular function.
Article
Plant Sciences
Ruben Shrestha, Andres V. Reyes, Peter R. Baker, Zhi-Yong Wang, Robert J. Chalkley, Shou-Ling Xu
Summary: This article presents a workflow for N-15 stable-isotope labeled protein quantification and discusses important features such as ratio adjustment, statistical analysis of protein ratios, isotope cluster pattern matching, and fast retrieval of quantification results.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemical Research Methods
Mehar Un Nissa, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, Chetanya Chetanya, Sanjyot Vinayak Shenoy, Robert L. Moritz, Mukunda Goswami, Sanjeeva Srivastava
Summary: Proteomic studies on Labeo rohita provided a comprehensive organ-based protein profiling, identifying a large number of proteins and global post-translational modifications. These findings offer important insights for basic and applied research in aquaculture field.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Environmental Sciences
Chien-Yu Chen, Yi-Chin Cho, Yi-Pin Lin
Summary: In this study, multi-walled carbon nanotubes (MWCNT) were utilized to activate peroxydisulfate (PDS) for the degradation of 2,4-dichlorophenol (2,4-DCP), and the effects of solution pH, PDS concentration, 2,4-DCP concentration, and MWCNT loading on the degradation process were investigated. The results indicated that surface reactions involving both surface-bound radicals and direct electron transfer were responsible for 2,4-DCP degradation, with the rate increasing with higher solution pH, PDS concentration, and MWCNT loading. Reusability tests suggested that surface sites responsible for surface-bound radical formation were deactivated after PDS activation, while those responsible for direct electron transfer remained active.
Article
Engineering, Environmental
Sin-Yi Liou, Michael C. Dodd
Summary: The reaction of hypochlorous acid with superoxide radical can be a novel nonphotochemical advanced oxidation process, generating hydroxyl radical and various reactive chlorine species, with high radical exposures, simplicity, rapid time-scales, and potential for on-site superoxide generation.
Article
Chemistry, Analytical
Sayan Gupta, Yan Chen, Christopher J. Petzold, Daniel P. DePonte, Corie Y. Ralston
ANALYTICAL CHEMISTRY
(2020)
Article
Biochemistry & Molecular Biology
Valentyna Kuznetsova, Maria Agustina Dominguez-Martin, Han Bao, Sayan Gupta, Markus Sutter, Miroslav Kloz, Mateusz Rebarz, Martin Precek, Yan Chen, Christopher J. Petzold, Code Y. Ralston, Cheryl A. Kerfeld, Tomas Polivka
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
(2020)
Article
Chemistry, Multidisciplinary
Jacquelyn M. Blake-Hedges, Jose Henrique Pereira, Pablo Cruz-Morales, Mitchell G. Thompson, Jesus F. Barajas, Jeffrey Chen, Rohith N. Krishna, Leanne Jade. G. Chan, Danika Nimlos, Catalina Alonso-Martinez, Edward E. K. Baidoo, Yan Chen, Jennifer W. Gin, Leonard Katz, Christopher J. Petzold, Paul D. Adams, Jay D. Keasling
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2020)
Article
Biotechnology & Applied Microbiology
Salome C. Nies, Robert Dinger, Yan Chen, Gossa G. Wordofa, Mette Kristensen, Konstantin Schneider, Jochen Buechs, Christopher J. Petzold, Jay D. Keasling, Lars M. Blank, Birgitta E. Ebert
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2020)
Review
Biotechnology & Applied Microbiology
Christopher E. Lawson, Jose Manuel Marti, Tijana Radivojevic, Sai Vamshi R. Jonnalagadda, Reinhard Gentz, Nathan J. Hillson, Sean Peisert, Joonhoon Kim, Blake A. Simmons, Christopher J. Petzold, Steven W. Singer, Aindrila Mukhopadhyay, Deepti Tanjore, Joshua G. Dunn, Hector Garcia Martin
Summary: The review introduces how machine learning can make metabolic engineering more predictable, provides examples and advice, discusses various applications, and examines future prospects.
METABOLIC ENGINEERING
(2021)
Article
Instruments & Instrumentation
Lei Yu, Weishi Wan, Wen-Xin Tang, Jun Feng
Summary: A new method for measuring the transverse momentum and emittance of the photoemitted electron beam from a photocathode has been developed, with systematic analysis of potential errors. Results show that this method can provide accurate measurements of electron beam characteristics.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2021)
Article
Biochemistry & Molecular Biology
N. Sevillano, M. F. Bohn, M. Zimanyi, Y. Chen, C. Petzold, S. Gupta, C. Y. Ralston, C. S. Craik
Summary: Affinity maturation of U33 resulted in improved binding properties, with the creation of an engineered affinity maturation library and identification of eight Fabs with improved binding properties, including the potent inhibitor AB2 with a 13-fold decrease in IC50. X-ray foot-printing and mass spectrometry revealed interfacial residues that might undergo structural rearrangement upon interface formation, providing further insights into the selectivity determinant of the binding mode.
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS
(2021)
Article
Cell Biology
Hualan Liu, Anthony L. Shiver, Morgan N. Price, Hans K. Carlson, Valentine V. Trotter, Yan Chen, Veronica Escalante, Jayashree Ray, Kelsey E. Hern, Christopher J. Petzold, Peter J. Turnbaugh, Kerwyn Casey Huang, Adam P. Arkin, Adam M. Deutschbauer
Summary: This study reveals the functions of numerous genes in a gut commensal Bacteroides thetaiotaomicron under different conditions, providing insights into gene functions. For example, key enzymes important for specific carbohydrate utilization and bile salt tolerance were identified. Additionally, alternative enzymes for synthesizing nitrogen-containing metabolic precursors were found to be used in a diet-dependent manner.
Article
Multidisciplinary Sciences
Nicole Ing, Kai Deng, Yan Chen, Martina Aulitto, Jennifer W. Gin, Thanh Le Mai Pham, Christopher J. Petzold, Steve W. Singer, Benjamin Bowen, Kenneth L. Sale, Blake A. Simmons, Anup K. Singh, Paul D. Adams, Trent R. Northen
Summary: This study integrated two nanostructure-initiator mass spectrometry-based assays into a single multiplexed assay for quickly detecting glycan and lignin deconstruction enzymes, providing a tool for characterizing crude commercial enzyme mixtures. By applying this method, mixtures of enzymes suitable for biomass pretreatment can be discovered.
SCIENTIFIC REPORTS
(2021)
Article
Instruments & Instrumentation
Chunlin Song, Boyuan Huang, Jun Feng, Jiangyu Li
Summary: In this study, a sequential excitation (SE) module was developed to achieve high fidelity piezoresponse force microscopy (PFM) by using a customized discrete frequency sweep signal for drive excitation and sampling the AC component of piezoresponse using an oscilloscope. A fast analysis method was also developed for efficient fitting of the cantilever's transfer function during scanning.
REVIEW OF SCIENTIFIC INSTRUMENTS
(2022)
Article
Chemistry, Physical
Yingkai Hua, Zhiyuan Huang, Sen Li, Siyuan Chen, Xin He, Haodong Liu, Jun Feng
Summary: Ni-rich layered transition metal oxides have the potential to be cathodes for Li-ion batteries due to their cost-effectiveness and high capacity. However, the capacity fading caused by inherent lattice structure variations has hindered their practical applications. By using in situ neutron powder diffraction, this study investigated the structural evolution of LiNi0.5Co0.2Mn0.3O2 during synthesis, revealing the correlation between annealing time, structural instability, and battery performance. These findings provide useful insights for synthesizing high-performance transition metal layered oxide materials.
ACS APPLIED ENERGY MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Sen Li, Zhiyuan Huang, Yafei Ding, Chao Zhang, Jingyan Yu, Qi Feng, Jun Feng
Summary: In this study, single-crystalline BiSBr was synthesized and characterized for its photoelectric properties and photovoltaic performances. The results showed that BiSBr is a p-type semiconductor with high electrical conductivity and light absorption capability. By fabricating BiSBr microsheet array films, the photovoltaic efficiency was significantly enhanced.
Review
Biochemistry & Molecular Biology
Noel S. Ha, Markus de Raad, La Zhen Han, Amber Golini, Christopher J. Petzold, Trent R. Northen
Summary: High-throughput screening technologies, integrated with mass spectrometry and microfluidics, offer high throughput, sensitivity, and specificity in analysis by enabling rapid manipulation of small volumes, improved control of reaction conditions, faster assays, and reduced reagent consumption. Recent applications include single-cell analysis, compound screening, and microbiology research. Future outlooks focus on online coupling, enhancing sensitivity, and integrating multi-omics into a single platform.
RSC CHEMICAL BIOLOGY
(2021)
Article
Physics, Multidisciplinary
C. Feng, J. Feng, R. Saha, Y. Arakawa, J. Gleeson, S. Sprunt, C. Zhu, A. Jakli
PHYSICAL REVIEW RESEARCH
(2020)
Article
Biotechnology & Applied Microbiology
Tadas Jakociunas, Andreas K. Klitgaard, Eftychia Eva Kontou, Julie Bang Nielsen, Emil Thomsen, David Romero-Suarez, Kai Blin, Christopher J. Petzold, Jennifer W. Gin, Yaojun Tong, Charlotte Held Gotfredsen, Pep Charusanti, Rasmus J. N. Frandsen, Tilmann Weber, Sang Yup Lee, Michael K. Jensen, Jay D. Keasling
SYNTHETIC AND SYSTEMS BIOTECHNOLOGY
(2020)