Article
Chemistry, Analytical
Runlian Qu, Lu Shan, Qun Sun, Yao Wei, Pengchi Deng, Xiandeng Hou
Summary: A simple, fast, and green method has been established to quantitatively detect isotope labelled compounds in biology and pharmacy using a novel H-1 Nuclear Magnetic Resonance (H-1-NMR) technique. This method removes the coupling between nearby H-1 and C-13, N-15, simplifying the spectrum and enhancing the signal intensity, allowing for the quantitative detection of real polypeptide samples.
Article
Biotechnology & Applied Microbiology
Lea Chuzel, Samantha L. Fossa, Madison L. Boisvert, Samanta Cajic, Rene Hennig, Mehul B. Ganatra, Udo Reichl, Erdmann Rapp, Christopher H. Taron
Summary: This study utilized functional metagenomic screening and glycoanalytics to identify enzymes that act upon the chemical modifications of glycans, demonstrating the feasibility of detecting the presence of GlcNAc-6-SO4 in N-glycans via xCGE-LIF. The discovered enzymes offer new specificities for analyzing N-glycan structures.
MICROBIAL CELL FACTORIES
(2021)
Article
Biochemistry & Molecular Biology
Harri A. Heikkinen, Sofia M. Backlund, Hideo Iwai
Summary: Partially labeling samples with 20% 13C and 100% 15N can reduce chemical costs while maintaining structural information, especially for small proteins. The approach simplifies sample preparation and enhances the efficiency of NMR technology in backbone resonance assignments, structure determination, N15-relaxation analysis, and ligand-protein interactions.
Article
Biochemistry & Molecular Biology
Alexander R. Davis, Elijah T. Roberts, I. Jonathan Amster, Adam W. Barb
Summary: Despite the importance of glycoproteins in human biology, current methods for isotope labeling have limitations. This study presents a system using Saccharomyces cerevisiae for uniform labeling of IgG1, along with strategies to optimize expression yield. Two different media formulations were also developed, providing standardized and rich growth conditions.
JOURNAL OF BIOMOLECULAR NMR
(2023)
Article
Plant Sciences
Maede Faghihinia, Jan Jansa
Summary: The presence of arbuscular mycorrhizal fungi affects resource allocation in mixed plant stands, favoring plants with high-quality partners. However, even lower quality partners can benefit from symbiosis in monoculture systems.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Soil Science
Jim Rasmussen, Dorte Bodin Dresboll, Kirsten Lonne Enggrob, Leanne Peixoto
Summary: Estimates of nitrogen losses from living plants are essential for improving the sustainability of agricultural cropping systems. A novel method using vertical split-root with N-15 placement in deeper soil layers was suggested to enhance the accuracy of tracer-based methods for estimating phyllo- and rhizodeposition. Results showed that nitrogen losses mainly occurred in the soil layers around the roots.
Article
Biotechnology & Applied Microbiology
Oksana Coban, Olivia Rasigraf, Anniek E. E. de Jong, Oliver Spott, Brad M. Bebout
Summary: This study evaluated the occurrence and rates of major nitrogen cycle processes in intact microbial mats from Elkhorn Slough and Baja California Sur using N-15-labeling techniques. The results showed differences in nitrogen cycling between Elkhorn Slough and Baja mats, with differences in ammonium assimilation rates and nitrate affinity. Additionally, low nitrogen fixation rates in Elkhorn Slough mats suggest other processes contribute to nitrogen availability in these ecosystems.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Soil Science
Wang Shichao, Lu Changai, Huai Shengchang, Yan Zhihao, Wang Jinyu, Sun Jiying, Sajjad Raza
Summary: Returning straw to farmlands has the potential to increase C sequestration and decrease losses. Factors such as straw burial depth and manure application play important roles in determining the decomposition or retention of straw C and N in soil. Returning straw to deep soil layers improves the stability of organic C and N in soil, without compromising their sequestration potential.
SOIL & TILLAGE RESEARCH
(2021)
Article
Ecology
Ruzhen Wang, Josep Penuelas, Tian Li, Heyong Liu, Hui Wu, Yuge Zhang, Jordi Sardans, Yong Jiang
Summary: The study investigated the changes in nitrogen isotopes in plants and soil under nitrogen addition, revealing shifts in nitrogen forms and accelerated nitrogen cycling, as well as increased plant reliance on soil NO3-; microbial and plant nitrogen preferences converged, leading to increased competition between them; the changes in plant litter delta C-13 were associated with the abundance of plant species, while plant species' delta C-13 remained unaffected by nitrogen addition.
Article
Biochemistry & Molecular Biology
Garry W. Buchko, Mowei Zhou, Cat Hoang Vesely, Jinhui Tao, Wendy J. Shaw, Ryan A. Mehl, Richard B. Cooley
Summary: In this study, the researchers successfully expressed and purified C-13-, N-15-labeled murine amelogenin protein with phosphorylation at Ser-16 using a modified genetic code expansion protocol. This protein will be a valuable tool for studying the process of amelogenesis and mineralization.
Article
Biochemical Research Methods
Qiong Wang, Tiexin Wang, Wells W. Wu, Chang-Yi Lin, Shuang Yang, Ganglong Yang, Ewa Jankowska, Yifeng Hu, Rong-Fong Shen, Michael J. Betenbaugh, John F. Cipollo
Summary: This study reports the glycoproteomic analysis of three commonly used Chinese hamster ovary (CHO) cell lines in biopharmaceutical settings. Differences were observed in the types and abundance of N- and O-glycopeptides, their glycans, and the complexity of glycoproteins. The study also revealed differences in pathways and cellular compartments between the cell lines.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Chemistry, Multidisciplinary
Jean-Guy Boiteau, Gregoire Mouis, Kevin Reverse, Estelle Surget, Gaetan Boccadifuoco, Sophie Dufay
Summary: Codeine N-oxide 2, an active metabolite of codeine, is produced through oxidation and observed as a degradation product in codeine drug products. This study thoroughly characterizes and assigns the isomers of Codeine N-oxide using experimental and analytical techniques, and investigates the effects of N-oxidation on the chemical shifts of codeine.
MAGNETIC RESONANCE IN CHEMISTRY
(2022)
Article
Environmental Sciences
Nele Engel, Teresa Aguado, Mark Maraun
Summary: Marine polychaetes are a diverse group of organisms with various feeding modes. Identifying their diets and trophic positions in the food web is crucial for understanding their interactions and community dynamics in marine ecosystems. This study used stable isotope and lipid fatty acid analyses, as well as carbon and nitrogen stoichiometry, to investigate the feeding habits of three widely distributed marine polychaete species. The results showed that each species had different trophic ecologies, with Eurythoe complanata mainly feeding on algae, cyanobacteria, and fungi, Syllis malaquini mainly feeding on algae and bacteria, and Platynereis massiliensis mainly feeding on algae, especially diatoms. The combination of these methods proved useful in identifying the diet and trophic position of marine polychaetes and providing insights into their feeding habits and position in marine food webs.
MARINE ENVIRONMENTAL RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Haci Mehmet Kayili, Rokia Sakhta, Bekir Salih
Summary: Glycosylation is an essential posttranslational modification in the living proteome and plays a crucial role in the early diagnosis of cancer. This study compares the effectiveness of different detergent combinations in the N-glycan release method and finds that the SDS + SDC combination provides the highest signal areas and intensities in N-glycan analysis.
TURKISH JOURNAL OF CHEMISTRY
(2022)
Article
Plant Sciences
Eduardo Mariano, Beatriz N. Boschiero, Luis F. Merlotti, Alexandre Pedrinho, Miriam G. Chaves, Siu M. Tsai, Paulo C. O. Trivelin
Summary: The study demonstrates that the use of nitrification inhibitor DCD can reduce nitrogen losses in sugarcane production, while altering the composition of microbial populations in the soil.
JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION
(2022)
Article
Biochemical Research Methods
Jacob T. Roberts, Kashyap R. Patel, Adam W. Barb
MOLECULAR & CELLULAR PROTEOMICS
(2020)
Article
Biochemistry & Molecular Biology
Paul G. Kremer, Adam W. Barb
Summary: Fc gamma receptor IIIa/CD16a is a crucial receptor involved in regulating cellular immune responses. Genetic polymorphism and N-glycan composition of CD16a can affect its binding affinity and kinetics with antibodies, thus impacting immune responses and therapeutic efficacy of antibodies.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Anjali Shenoy, Alexander R. Davis, Elijah T. Roberts, I. Jonathan Amster, Adam W. Barb
Summary: This study describes a novel yeast-based expression platform that simultaneously expresses the Kar2p chaperone and protein disulfide isomerase to facilitate the expression of secreted proteins. High-quality 15N-labeled human immunoglobulin fragments were successfully obtained by optimizing yeast expression conditions and developing a new growth medium. The interaction between the labeled immunoglobulin fragments and another protein was studied using NMR spectroscopy.
JOURNAL OF BIOMOLECULAR NMR
(2022)
Article
Immunology
William D. D. Tolbert, Neelakshi Gohain, Paul G. G. Kremer, Andrew P. P. Hederman, Dung N. N. Nguyen, Verna Van, Rebekah Sherburn, George K. K. Lewis, Andres Finzi, Justin Pollara, Margaret E. E. Ackerman, Adam W. W. Barb, Marzena Pazgier
Summary: Fc mediated effector functions of antibodies are crucial in immunotherapies and vaccine efficacy. The Ile/Val(158) polymorphism in Mm Fc gamma RIII and glycan composition variations affect the affinity of allelic variants, providing important insights for nonhuman primate studies and human effector cell studies.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Maria Carolina Rodriguez Benavente, Harrison B. Hughes, Paul G. Kremer, Ganesh P. Subedi, Adam W. Barb
Summary: Novel approaches, including cytokine treatment and NK cell receptor engineering, are being explored to improve antibody-dependent cell-mediated cytotoxicity (ADCC) in immunotherapies. This study evaluated the impact of kifunensine, an inhibitor of N-linked glycan processing, on ADCC using primary and cultured human NK cells. The results showed that kifunensine treatment doubled ADCC in a CD16a-dependent manner and increased the antibody-binding affinity of CD16a. Structural analysis identified a CD16a region perturbed by N-glycan composition. Additionally, combining kifunensine treatment with afucosylated antibodies further increased ADCC by 33%. These findings highlight the importance of N-glycan processing in limiting NK cell ADCC and provide insights into optimizing antibody and CD16a glycoforms for enhanced ADCC activity.
Article
Biochemistry & Molecular Biology
Alexander R. Davis, Elijah T. Roberts, I. Jonathan Amster, Adam W. Barb
Summary: Despite the importance of glycoproteins in human biology, current methods for isotope labeling have limitations. This study presents a system using Saccharomyces cerevisiae for uniform labeling of IgG1, along with strategies to optimize expression yield. Two different media formulations were also developed, providing standardized and rich growth conditions.
JOURNAL OF BIOMOLECULAR NMR
(2023)
Article
Biochemistry & Molecular Biology
Jesus S. Aguilar Diaz de Leon, Isaac Aguilar, Adam W. Barb
Summary: N-glycan processing plays an important role in regulating macrophage effector function in antibody-mediated therapies. Inhibition of N-glycan processing by kifunensine enhances target binding and phagocytosis of antibody-coated target cells by macrophages. CD64, CD32, and CD16 are the crucial Fcγ receptors involved in macrophage ADCP. Differential phosphorylation levels of immune receptors correlate with increased ADCP.
Meeting Abstract
Biochemistry & Molecular Biology
Maria Carolina Rodriguez Benavente, Harrison Hughes, Paul G. Kremer, Adam W. Barb
Article
Immunology
Anjali Shenoy, Srisaimaneesh Yalamanchili, Alexander R. Davis, Adam W. Barb
Summary: Interaction with cell surface receptors plays a crucial role in enhancing the therapeutic properties of antibodies, including Fc gamma Rs. A novel Saccharomyces cerevisiae strain was engineered to specifically modify the IgG1 Fc with a truncated N-glycan consisting of a single N-acetylglucosamine residue. This glycoengineered Fc displayed on the yeast surface maintained high affinity for receptors, demonstrating potential for antibody production.
Article
Biochemistry & Molecular Biology
Kashyap R. Patel, Maria C. Rodriguez Benavente, W. Walter Lorenz, Emily M. Mace, Adam W. Barb
Summary: This study identified substantial differences in CD16a processing by NK cells from different origins, suggesting that CD16a N-glycan composition is influenced by gene expression regulation, and different cell types show high variability in processing the same human protein.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Adam W. Barb
Summary: Fc gamma receptors play a critical role in activating or suppressing cellular responses by binding with antibody-coated targets, yet research and development efforts in this area are currently limited. The success of engineered cell-based immunotherapies has provided a pathway for introducing modified Fc gamma receptors into clinical settings, showing potential for enhancing their function.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Meeting Abstract
Biochemistry & Molecular Biology
Maria C. Rodriguez Benavente, Kashyap R. Patel, W. Walter Lorenz, Emily M. Mace, Adam W. Barb
Article
Biochemistry & Molecular Biology
Kashyap R. Patel, Jacob T. Roberts, Adam W. Barb
Review
Biochemistry & Molecular Biology
Yoshiki Yamaguchi, Adam W. Barb
Review
Immunology
Kashyap R. Patel, Jacob T. Roberts, Adam W. Barb
FRONTIERS IN IMMUNOLOGY
(2019)