Article
Biology
ShylajaNaciyar Mohandass, Mangalalakshmi Ragavan, Dineshbabu Gnanasekaran, Uma Lakshmanan, Prabaharan Dharmar, Sushanta Kumar Saha
Summary: Synthetic azo dyes are widely used but their improper discharge poses a threat to the environment. Genetically modified cyanobacteria with enhanced H2O2 accumulation through SOD overexpression can effectively degrade these dyes, suggesting a valuable bioremediation strategy.
Article
Health Care Sciences & Services
Irina A. Mednova, Liudmila P. Smirnova, Alisa R. Vasilieva, Daria Kazantseva, Elena Epimakhova, Nina M. Krotenko, Arkadiy Semke, Svetlana A. Ivanova
Summary: This study demonstrates that patients with schizophrenia have SOD activity in their IgG, and the highest activity is observed in patients in therapeutic remission. The mechanism of SOD activity in IgG is similar to classical enzyme catalysis, with a higher affinity for the substrate than classical SOD enzyme.
JOURNAL OF PERSONALIZED MEDICINE
(2022)
Article
Cell Biology
Dong-Dong Wu, Sheng Jin, Ruo-Xiao Cheng, Wen-Jie Cai, Wen-Long Xue, Qing-Qing Zhang, Le-Jie Yang, Qi Zhu, Meng-Yao Li, Ge Lin, Yi-Zhen Wang, Xue-Pan Mu, Yu Wang, Igor Ying Zhang, Qi Zhang, Ying Chen, Sheng-Yang Cai, Bo Tan, Ye Li, Yun-Qian Chen, Pu-Juan Zhang, Chen Sun, Yue Yin, Ming-Jie Wang, Yi-Zhun Zhu, Bei-Bei Tao, Jia-Hai Zhou, Wei-Xue Huang, Yi-Chun Zhu
Summary: This study investigates the possibility of a mechanism beyond post-translational modifications to regulate protein function. It shows that hydrogen sulfide (H2S) can bind to the active-site copper of Cu/Zn-SOD, enhancing electrostatic forces and facilitating electron transfer. The physiological relevance of this H2S effect is demonstrated in in vitro and in vivo models where the cardioprotective effects of H2S depend on Cu/Zn-SOD.
Article
Nanoscience & Nanotechnology
Xiangshi Sun, Kongtong Yu, Yulin Zhou, Shiyan Dong, Wenji Hu, Yating Sun, Yuhuan Li, Jing Xie, Robert J. Lee, Fengying Sun, Yifan Ma, Shengnian Wang, Betty Y. S. Kim, Yifan Wang, Zhaogang Yang, Wen Jiang, Youxin Li, Lesheng Teng
Summary: The newly synthesized amphiphilic polymers can self-assemble into micellar nanoparticles with favorable hydrolysis kinetics, biocompatibility, and long circulation time. These materials not only exhibit better inflammation-targeting effects, but also do not induce an acidic microenvironment during degradation.
ACS APPLIED MATERIALS & INTERFACES
(2021)
Article
Biochemistry & Molecular Biology
Bindu Chandrasekharan, Claudia Montllor-Albalate, Alyson E. Colin, Joshua L. Andersen, Young C. Jang, Amit R. Reddi
Summary: Cu/Zn superoxide dismutase (Sod1) catalyzes the breakdown of superoxide radicals into oxygen and hydrogen peroxide, which acts as a signaling molecule. In yeast, Sod1 is involved in a redox signaling pathway that connects nutrient availability to energy metabolism control. This pathway stabilizes plasma membrane kinases Yck1/2, promoting glycolytic growth and repressing respiration.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Guanning Huang, Jiankun Zang, Lizhen He, Huili Zhu, Jiarun Huang, Zhongwen Yuan, Tianfeng Chen, Anding Xu
Summary: This study designed a translational antioxidative agent, HSA-Mn3O4, which effectively inhibits nervous system damage caused by ischemic stroke reperfusion, demonstrating neuroprotective capacity mainly by inhibiting apoptosis and endoplasmic reticulum stress to prevent brain tissue damage.
Article
Biochemistry & Molecular Biology
Sofia-Iris Bibli, Ingrid Fleming
Summary: This article discusses the impact of changes in oxidative balance on cellular physiology and adaptation, with a focus on the sensitivity of endothelial cells to reactive oxygen species and the role of oxidative modifications in regulating protein function. Persulfidation, a newly identified reversible oxidation modification, plays a crucial role in maintaining cellular redox homeostasis.
ANTIOXIDANTS & REDOX SIGNALING
(2021)
Article
Multidisciplinary Sciences
Wei Lin Lee, Ameya Sinha, Ling Ning Lam, Hooi Linn Loo, Jiaqi Liang, Peiying Ho, Liang Cui, Cheryl Siew Choo Chan, Thomas Begley, Kimberly Ann Kline, Peter Dedon
Summary: A newly discovered RNA modifying enzyme in Enterococcus faecalis regulates translation of stress-response proteins by sensing reactive oxygen species (ROS). The enzyme's activity is inhibited by ROS, leading to reduced levels of N-2-methyladenosine (m(2)A) in ribosomal RNA and transfer RNA. Knockout of the enzyme mimics the oxidative stress response, with increased superoxide dismutase levels and decreased virulence proteins. This study reveals a new mechanism in which RNA modifications directly regulate the proteome in response to oxidative stress.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Mabel Buelna-Chontal, Wylly R. Garcia-Nino, Alejandro Silva-Palacios, Cristina Enriquez-Cortina, Cecilia Zazueta
Summary: Post-translational modifications based on redox reactions play a crucial role in regulating signaling pathways in physiological and pathological conditions. These modifications are dependent on the generation of redox components, such as reactive oxygen species and nitric oxide, and can impact protective signaling in reperfused hearts. Cardioprotective conditioning strategies have been shown to influence these changes at various subcellular levels, particularly in mitochondria. Additionally, potential redox-based therapeutic strategies against reperfusion damage are discussed.
Article
Chemistry, Multidisciplinary
Ahmet Can Timucin, Suleyman Selim Cinaroglu, Osman Ugur Sezerman, Emel Timucin
Summary: The metallation status of human Cu/Zn superoxide dismutase 1 (SOD1) is crucial in the development of amyotrophic lateral sclerosis (ALS). Mutations at the ALS-linked positions H63R and K136A significantly affect dimer dynamics, leading to demetallation and potential ALS toxicity. This study highlights the potential use of atomistic simulations in studying disease variants related to SOD1.
FRONTIERS IN CHEMISTRY
(2021)
Article
Plant Sciences
Pavol Melicher, Petr Dvorak, Yuliya Krasylenko, Alexey Shapiguzov, Jaakko Kangasjarvi, Jozef Samaj, Tomas Takac
Summary: This study characterized the role of FSD1 in response to oxidative stress in Arabidopsis thaliana, and found that its antioxidant function depends on the availability of Cu2+ in the growth media. Chloroplastic localization of FSD1 is crucial for maintaining redox homeostasis.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Environmental Sciences
Ning Sun, Qiang Liu, Jinhu Wang, Falin He, Mingyang Jing, Shanshan Chu, Wansong Zong, Rutao Liu, Canzhu Gao
Summary: The study found that pyrene has strong biological toxicity to earthworms in soil, leading to increased mortality rate, decreased body weight, and decreased reproductive rate, as well as damage to cell membranes, DNA, and proteins. At the molecular level, pyrene inhibits the activity of antioxidant enzymes by changing the amino acid structure.
ENVIRONMENTAL POLLUTION
(2021)
Article
Plant Sciences
Li Tian, Junjiao Li, Caimin Huang, Dandan Zhang, Yan Xu, Xingyong Yang, Jian Song, Dan Wang, Nianwei Qiu, Dylan P. G. Short, Patrik Inderbitzin, Krishna Subbarao, Jieyin Chen, Xiaofeng Dai
Summary: The accumulation of ROS is a common defense mechanism in higher plants against pathogen attack. Previous studies showed that Cu/Zn-SOD1 (VdSOD1) in plants is upregulated following infection, indicating its role in pathogen virulence. Deletion of VdSOD1 leads to increased sensitivity to ROS generator menadione and relies on Golgi reassembly stacking protein for secretion. Overall, VdSOD1 plays a significant role in scavenging ROS and promoting virulence in V. dahliae.
MOLECULAR PLANT PATHOLOGY
(2021)
Article
Microbiology
Cindy Staerck, Hajar Yaakoub, Patrick Vandeputte, Julie Tabiasco, Charlotte Godon, Amandine Gastebois, Sandrine Giraud, Thomas Guillemette, Alphonse Calenda, Yves Delneste, Maxime Fleury, Jean-Philippe Bouchara
Summary: The mutation of the SODD gene in S. apiospermum fungi increases susceptibility to oxidizing agents and antifungal drugs, as well as intracellular killing by human macrophages. Furthermore, the study suggests a potential indirect role of SodD in the synthesis or assembly of cell wall components.
Article
Biochemistry & Molecular Biology
Yoshiaki Furukawa, Atsuko Shintani, Teppei Kokubo
Summary: The study demonstrates that the disulfide-reduced SodC can secure copper and zinc ions through thiolate groups, and binds cuprous and cupric ions more tightly than SodC with the disulfide bond, leading to the production of enzymatically active SodC.
Article
Oncology
Elizabeth C. Randall, Begona G. C. Lopez, Sen Peng, Michael S. Regan, Walid M. Abdelmoula, Sankha S. Basu, Sandro Santagata, Haejin Yoon, Marcia C. Haigis, Jeffrey N. Agar, Nhan L. Tran, William F. Elmquist, Forest M. White, Jann N. Sarkaria, Nathalie Y. R. Agar
Article
Cell Biology
Yagmur Micoogullari, Sankha S. Basu, Jessie Ang, Nina Weisshaar, Nicholas D. Schmitt, Walid M. Abdelmoula, Begona Lopez, Jeffrey N. Agar, Nathalie Agar, John Hanna
MOLECULAR BIOLOGY OF THE CELL
(2020)
Article
Multidisciplinary Sciences
Krishna C. Aluri, Joseph P. Salisbury, Jochen H. M. Prehn, Jeffrey N. Agar
SCIENTIFIC REPORTS
(2020)
Article
Biochemical Research Methods
Kristina Srzentic, Luca Fornelli, Yury O. Tsybin, Joseph A. Loo, Henrique Seckler, Jeffrey N. Agar, Lissa C. Anderson, Dina L. Bai, Alain Beck, Jennifer S. Brodbelt, Yuri E. M. van der Burgt, Julia Chamot-Rooke, Sneha Chatterjee, Yunqiu Chen, David J. Clarke, Paul O. Danis, Jolene K. Diedrich, Robert A. D'Ippolito, Mathieu Dupre, Natalia Gasilova, Ying Ge, Young Ah Goo, David R. Goodlett, Sylvester Greer, Kim F. Haselmann, Lidong He, Christopher L. Hendrickson, Joshua D. Hinkle, Matthew Holt, Sam Hughes, Donald F. Hunt, Neil L. Kelleher, Anton N. Kozhinov, Ziqing Lin, Christian Malosse, Alan G. Marshall, Laure Menin, Robert J. Millikin, Konstantin O. Nagornov, Simone Nicolardi, Ljiljana Pasa-Tolic, Stuart Pengelley, Neil R. Quebbemann, Anja Resemann, Wendy Sandoval, Richa Sarin, Nicholas D. Schmitt, Jeffrey Shabanowitz, Jared B. Shaw, Michael R. Shortreed, Lloyd M. Smith, Frank Sobott, Detlev Suckau, Timothy Toby, Chad R. Weisbrod, Norelle C. Wildburger, John R. Yates, Sung Hwan Yoon, Nicolas L. Young, Mowei Zhou
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2020)
Article
Limnology
Jeffrey A. Hawkes, Juliana D'Andrilli, Jeffrey N. Agar, Mark P. Barrow, Stephanie M. Berg, Nuria Catalan, Hongmei Chen, Rosalie K. Chu, Richard B. Cole, Thorsten Dittmar, Remy Gavard, Gerd Gleixner, Patrick G. Hatcher, Chen He, Nancy J. Hess, Ryan H. S. Hutchins, Amna Ijaz, Hugh E. Jones, William Kew, Maryam Khaksari, Diana Catalina Palacio Lozano, Jitao Lv, Lynn R. Mazzoleni, Beatriz E. Noriega-Ortega, Helena Osterholz, Nikola Radoman, Christina K. Remucal, Nicholas D. Schmitt, Simeon K. Schum, Quan Shi, Carsten Simon, Gabriel Singer, Rachel L. Sleighter, Aron Stubbins, Mary J. Thomas, Nikola Tolic, Shuzhen Zhang, Phoebe Zito, David C. Podgorski
LIMNOLOGY AND OCEANOGRAPHY-METHODS
(2020)
Article
Biochemistry & Molecular Biology
Amanda R. Clark, Elizabeth C. Randall, Begona G. C. Lopez, Michael S. Regan, Jeffrey N. Agar, Benjamin J. Andreone, Chenghua Gu, Nathalie Y. R. Agar
Summary: Omega-3 phospholipid species in brain endothelial cells play a crucial role in maintaining low transcytosis rate and regulating the blood brain barrier mechanism. Advanced mass spectrometry imaging techniques were used to map the spatial distribution of these phospholipids in the brain, and the impact of omega-3 dietary deprivation was explored on the brain phospholipid profile. The study identified unique spatial distribution of DHA-containing phospholipids and changes in phospholipid species under omega-3 deficiency.
ACS CHEMICAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Krishna C. Aluri, Md Amin Hossain, Ninad Kanetkar, Brandon C. Miller, Matthew G. Dowgiallo, Durgalakshmi Sivasankar, Matthew R. Sullivan, Roman Manetsch, Tania Konry, Adam Ekenseair, Jeffrey N. Agar
Summary: This study presents a novel class of cross-linkers, cyclic thiosulfinates, for the facile synthesis of biodegradable hydrogels. The synthesized hydrogel can release proteins in vitro and support cell growth with acceptable cytotoxicity. The hydrogel can be modulated in mechanical properties and degradation kinetics with physiological concentrations of glutathione.
BIOCONJUGATE CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Morgan R. Packer, Jillian A. Parker, Jean K. Chung, Zhenlu Li, Young Kwang Lee, Trinity Cookis, Hugo Guterres, Steven Alvarez, Md Amin Hossain, Daniel P. Donnelly, Jeffrey N. Agar, Lee Makowski, Matthias Buck, Jay T. Groves, Carla Mattos
Summary: Studies demonstrate that Raf-Ras binding domain (Raf-RBD) can induce Ras dimerization at low surface densities and in solution, with robust connections between two Raf-RBD D113 residues confirmed by molecular dynamics simulations. These results suggest that Raf-RBD binding and Ras dimerization occur together, forming a high-affinity signaling complex.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Analytical
Nicholas D. Schmitt, Joshua M. Berger, Jeremy B. Conway, Jeffrey N. Agar
Summary: Intact protein fragmentation often lacks sequence coverage within proteins' interiors. Collisionally activated dissociation (CAD) produces internal fragmentation within proteins' interiors, filling existing gaps in sequence coverage. Challenges in identifying internal fragments, such as "frameshift ambiguity," can be overcome through optimizing methods and considering fragmentation propensities.
ANALYTICAL CHEMISTRY
(2021)
Article
Oncology
Begona G. C. Lopez, Ishwar N. Kohale, Ziming Du, Ilya Korsunsky, Walid M. Abdelmoula, Yang Dai, Sylwia A. Stopka, Giorgio Gaglia, Elizabeth C. Randall, Michael S. Regan, Sankha S. Basu, Amanda R. Clark, Bianca-Maria Marin, Ann C. Mladek, Danielle M. Burgenske, Jeffrey N. Agar, Jeffrey G. Supko, Stuart A. Grossman, Louis B. Nabors, Soumya Raychaudhuri, Keith L. Ligon, Patrick Y. Wen, Brian Alexander, Eudocia Q. Lee, Sandro Santagata, Jann Sarkaria, Forest M. White, Nathalie Y. R. Agar
Summary: The study developed an integrative platform using mass spectrometry imaging, phosphoproteomics, and multiplexed tissue imaging to map drug distribution, target engagement, and adaptive response in glioblastoma. The platform identified new markers of molecular response to adavosertib and demonstrated potential in studying patient's response to the drug in clinical trials. This approach may provide valuable insights for optimizing clinical trial design and guiding future application into clinical practice.
Article
Multidisciplinary Sciences
Walid M. Abdelmoula, Begona Gimenez-Cassina Lopez, Elizabeth C. Randall, Tina Kapur, Jann N. Sarkaria, Forest M. White, Jeffrey N. Agar, William M. Wells, Nathalie Y. R. Agar
Summary: This study demonstrates the application of artificial intelligence in mining Mass Spectrometry Imaging (MSI) data to reveal biologically relevant metabolomic and proteomic information acquired from different mass spectrometry platforms. By utilizing a fully connected variational autoencoder, the researchers developed the msiPL method to learn and visualize the underlying non-linear spectral manifold in MSI data, uncovering biologically relevant clusters of tissue anatomy and tumor heterogeneity in various tissue types.
NATURE COMMUNICATIONS
(2021)
Article
Biochemical Research Methods
Walid M. Abdelmoula, Sylwia A. Stopka, Elizabeth C. Randall, Michael Regan, Jeffrey N. Agar, Jann N. Sarkaria, William M. Wells, Tina Kapur, Nathalie Y. R. Agar
Summary: This paper proposes a deep learning model, massNet, for the analysis of mass spectrometry imaging (MSI) data. The massNet model achieves better accuracy and speed compared to traditional machine learning methods.
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Article
Biochemistry & Molecular Biology
Anya B. Zhong, Isabella H. Muti, Stephen J. Eyles, Richard W. Vachet, Kristen N. Sikora, Cedric E. Bobst, David Calligaris, Sylwia A. Stopka, Jeffery N. Agar, Chin-Lee Wu, Mari A. Mino-Kenudson, Nathalie Y. R. Agar, David C. Christiani, Igor A. Kaltashov, Leo L. Cheng
Summary: This article presents the application of a multiplatform approach combining NMR and MS imaging in metabolomics studies of human prostate and lung cancers. The combined analysis enhances the ability to conduct comprehensive metabolomics research.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Proceedings Paper
Computer Science, Theory & Methods
Ross L. Bobb, Jeffry A. Coady, Virgil O. Barnard, Matthew A. Mueller, William D. Casebeer, Joseph P. Salisbury
Summary: This article describes a virtual reality framework and environment for evaluating computer vision algorithms and augmented reality interfaces to enhance the situational awareness of dismounted soldiers. By simulating combat scenarios and using trained models to process input from a virtual camera, as well as adding digital information in the augmented reality display, the impact of these technologies on soldiers' perception abilities can be evaluated.
VIRTUAL, AUGMENTED, AND MIXED REALITY (XR) TECHNOLOGY FOR MULTI-DOMAIN OPERATIONS III
(2022)