Article
Virology
Hongliang Wang, Shangrui Guo, Hang Yang
Summary: This study developed a rapid and sensitive coculture system to measure syncytial formation caused by SARS-CoV-2 infection. They found that spike protein, furin cleavage, and TMPRSS2 protease play critical roles in syncytial formation. The system can also be used as a tool for screening anti-syncytial drugs.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Multidisciplinary Sciences
Jordana Munoz-Basagoiti, Fabio Luis Lima Monteiro, Lauren R. H. Krumpe, Victoria Armario-Najera, Shilpa R. Shenoy, Daniel Perez-Zsolt, Harrison James Westgarth, Gemma Villorbina, Larissa Maciel Bomfim, Dalia Raich-Regue, Lara Nogueras, Curtis J. Henrich, Marcal Gallemi, Filipe Romero Rebello Moreira, Pascual Torres, Jennifer Wilson, Mirela D'arc, Silvia Marfil, Alice Laschuk Herlinger, Edwards Pradenas, Luiza Mendonca Higa, Manuel Portero-Otin, Benjamin Trinite, Richard M. Twyman, Teresa Capell, Amilcar Tanuri, Julia Blanco, Nuria Izquierdo-Useros, Elibio L. Rech, Paul Christou, Barry R. O'Keefe
Summary: SARS-CoV-2 is a coronavirus responsible for the COVID-19 pandemic. Targeting the glycosylated Spike protein on the virus surface can prevent infections. Cyanovirin-N (CV-N), a lectin from cyanobacteria, can selectively target SARS-CoV-2 Spike glycans and inhibit viral infection in vitro and in vivo, showing potential as a broad-spectrum antiviral agent.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Virology
Juan Zhao, Ling Wang, Madison Schank, Xindi Dang, Zeyuan Lu, Dechao Cao, Sushant Khanal, Lam N Nguyen, Lam N T Nguyen, Jinyu Zhang, Yi Zhang, James L. Adkins, Evan M. Baird, Xiao Y. Wu, Shunbin Ning, Mohamed El Gazzar, Jonathan P. Moorman, Zhi Q. Yao
Summary: Research shows that COVID-19-recovered individuals exhibit specific T cell responses, potentially offering protection against reinfection for some exposed individuals and inducing protective immunity in unexposed individuals upon vaccination. There is a need for a multi-epitope strategy in COVID-19 vaccine design due to the low immunogenicity of SARS-CoV-2 S and N peptides at inducing robust T cell responses.
Article
Pathology
Andres Santos, Madeline Sauer, Alexander J. Neil, Isaac H. Solomon, Jason L. Hornick, Drucilla J. Roberts, Bradley J. Quade, Carlos Parra-Herran
Summary: This study aimed to investigate the translation and accumulation of Spike protein in placental tissue after mRNA SARC-CoV-2 vaccination during pregnancy. The results showed that there was no significant accumulation of SARS-CoV-2 Spike protein in placental tissue after mRNA vaccination during pregnancy, supporting the safety of mRNA vaccines to the placental-fetal unit.
Article
Multidisciplinary Sciences
Hiam R. S. Arruda, Tulio M. Lima, Renata G. F. Alvim, Fernanda B. A. Victorio, Daniel P. B. Abreu, Federico F. Marsili, Karen D. Cruz, Mayra A. Marques, Patricia Sosa-Acosta, Mauricio Quinones-Vega, Jessica de S. Guedes, Fabio C. S. Nogueria, Jerson L. Silva, Leda R. Castilho, Guilherme A. P. de Oliveira
Summary: The severe acute respiratory syndrome caused a global pandemic. Mutations in the spike protein, an antigenic candidate for COVID-19 vaccines, have been observed in SARS-CoV-2. Comparative data of the ancestral and D614G spike, as well as other variants of concern, show that D614G has lower hydrophobic surface exposure and trimer stability, suggesting a temporary fitness advantage for virus spillover. The adaptation of SARS-CoV-2 also leads to decreased trimer stability and higher ACE-2 affinities in some variants, highlighting the importance of mapping the energetics and flexibility of these variants for vaccine development.
Article
Biochemistry & Molecular Biology
Aristotelis Antonopoulos, Steven Broome, Victor Sharov, Christopher Ziegenfuss, Richard L. Easton, Maria Panico, Anne Dell, Howard R. Morris, Stuart M. Haslam
Summary: This study analyzed the glycosylation structure of the novel coronavirus SARS-CoV-2 and identified complex-type N-glycans as well as a single site of O-glycosylation within the receptor-binding domain.
Article
Chemistry, Medicinal
Darya Stepanenko, Stephanie Budhan, Carlos Simmerling
Summary: In this application note, a tool is described that helps structural biologists in studying the SARS-CoV-2 spike glycoprotein. The tool fixes inconsistencies among deposited structures, calculates the distribution of requested distances between atoms, and provides a histogram and cumulative frequency of the calculated distribution.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Biochemical Research Methods
Chu-Wei Kuo, Ning-En Chang, Pei-Yu Yu, Tzu-Jing Yang, Shang-Te Danny Hsu, Kay-Hooi Khoo
Summary: To fully identify all N-glycosylation sites on the SARS-CoV2 spike protein, multiple proteases are needed in addition to trypsin. The commonly used Byonic software for peptide identification often introduces errors due to similar mass differences. By manually interpreting MS2 spectra, this study identifies common errors, especially those caused by chymotrypsin. By using a stringent acceptance threshold and considering results from the pGlyco3 search engine, erroneous assignment can be controlled within 15% in Byonic. A representative N-glycosylation pattern can be constructed by quantifying the overlapping subset of confidently identified N-glycopeptides. Applying two complimentary glycoproteomic software tools, this study confirms significant differences in glycosylation at certain sites between the unstable Omicron spike protein and the stable trimeric form of the parental D614G variant.
Article
Biochemistry & Molecular Biology
Ramirez-Salinas Gema Lizbeth, Garcia-Machorro Jazmin, Correa-Basurto Jose, Martinez-Archundia Marlet
Summary: COVID-19, caused by a virus first identified in China in 2019, has spread to more than 216 countries. Pharmacological treatments based on similarities to the HIV virus have been proposed, as there is currently no vaccine. Research suggests that specific epitopes on the virus surface could be used in future vaccine design.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2021)
Correction
Chemistry, Physical
Ruichao Mao, Lihua Bie, Maofeng Xu, Xiaocong Wang, Jun Gao
Summary: This study focuses on antiviral drug design based on the opening mechanism of the spike glycoprotein in SARS-CoV-2.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Biochemical Research Methods
Eden P. Go, Shijian Zhang, Haitao Ding, John C. Kappes, Joseph Sodroski, Heather Desaire
Summary: The glycosylation analysis of viral glycoproteins plays a significant role in vaccine design and development. While Byonic software has been utilized to facilitate glycopeptide analysis, particularly in vaccine development, it tends to produce more false positives than true positives, indicating the need for careful evaluation and manual correction of the data.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Virology
Hui T. Lin-Wang, Rogerio C. Lemes, Eduardo da Silva Farias, Marcio C. Bajgelman, Kleber G. Franchini, Renata Viana, Carlos Gun
Summary: This study assessed the effectiveness of two COVID-19 vaccines, CoronaVac and AZ, in healthcare workers. The AZ vaccine showed a higher seroconversion rate and more common side effects. One dose of COVID-19 vaccine could produce an effective immune response in convalescent individuals.
JOURNAL OF MEDICAL VIROLOGY
(2022)
Article
Biochemical Research Methods
Jaeyong Jung, Ji-Hong Bong, Hong-Rae Kim, Jun-Hee Park, Chang Kyu Lee, Min-Jung Kang, Hyun Ok Kim, Jae-Chul Pyun
Summary: The study purified antibodies against SARS-CoV-2 NP from pig serum in two steps, demonstrating enhanced specificity through immunoassays and estimating binding constants using a biosensor. Competitive assays showed the potential of these antibodies to detect SARS-CoV-2 and differentiate it from other related coronaviruses in viral fluids.
Article
Chemistry, Analytical
Chang Xu, Xiao-He Ren, Di Han, Yan Peng, Jin-Ju Lei, Luo-Xiao Yu, Ling-Juan Liu, Wei-Chao Xu, Si-Xue Cheng
Summary: In this study, a molecular beacon-based method for precise detection of cell-cell fusion was reported. The method allows easy visualization and quantification of cell fusion using fluorescence microscopy and flow cytometry, providing a convenient and efficient approach for quantitative detection of cell-cell fusion.
ANALYTICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Jamie Guenthoer, Michelle Lilly, Tyler N. Starr, Bernadeta Dadonaite, Klaus N. Lovendahl, Jacob T. Croft, Caitlin I. Stoddard, Vrasha Chohan, Shilei Ding, Felicitas Ruiz, Mackenzie S. Kopp, Jesse D. Bloom, Helen Y. Chu, Kelly K. Lee, Julie Overbaugh
Summary: The antiviral benefit of antibodies can be compromised by viral escape, so durable and effective antibodies that can counter newly emerging virus strains are crucial. Discovery of such antibodies is particularly important for SARS-CoV-2 due to the emergence of new variants that affect the efficacy of therapeutic antibodies and vaccines.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Pharmacology & Pharmacy
Sandra L. Bixler, Thomas M. Bocan, Jay Wells, Kelly S. Wetzel, Sean A. Van Tongeren, Lian Dong, Nicole L. Garza, Ginger Donnelly, Lisa H. Cazares, Jonathan Nuss, Veronica Soloveva, Keith A. Koistinen, Lisa Welch, Carol Epstein, Li-Fang Liang, Dennis Giesing, Robert Lenk, Sina Bavari, Travis K. Warren
ANTIVIRAL RESEARCH
(2018)
Article
Biochemical Research Methods
Michael D. Ward, Ernst E. Brueggemann, Tara Kenny, Raven E. Reitstetter, Christopher R. Mahone, Sylvia Trevino, Kelly Wetzel, Ginger C. Donnelly, Cary Retterer, Robert B. Norgren, Rekha G. Panchal, Travis K. Warren, Sina Bavari, Lisa H. Cazares
CLINICAL PROTEOMICS
(2019)
Article
Virology
M. Jane Morwitzer, Sarah R. Tritsch, Lisa H. Cazares, Michael D. Ward, Jonathan E. Nuss, Sina Bavari, St Patrick Reid
Article
Biochemical Research Methods
Michael D. Ward, Tara Kenny, Ernie Bruggeman, Christopher D. Kane, Courtney L. Morrell, Molly M. Kane, Sandra Bixler, Sarah L. Grady, Rachel S. Quizon, Mekbib Astatke, Lisa H. Cazares
CLINICAL PROTEOMICS
(2020)
Article
Infectious Diseases
Andrew D. Haddow, Unai Perez-Sautu, Michael R. Wiley, Lynn J. Miller, Adrienne E. Kimmel, Lucia M. Principe, Suzanne E. Wollen-Roberts, Joshua D. Shamblin, Stephanie M. Valdez, Lisa H. Cazares, William D. Pratt, Franco D. Rossi, Luis Lugo-Roman, Sina Bavari, Gustavo F. Palacios, Aysegul Nalca, Farooq Nasar, M. Louise M. Pitt
PLOS NEGLECTED TROPICAL DISEASES
(2020)
Article
Biochemical Research Methods
Raghothama Chaerkady, Yebin Zhou, Jared A. Delmar, Shao Huan Samuel Weng, Junmin Wang, Shivangi Awasthi, Dorothy Sims, Michael A. Bowen, Wen Yu, Lisa H. Cazares, Gary P. Sims, Sonja Hess
Summary: This study identified a large number of validated citrullination sites in neutrophil and mast cell proteins, revealing important information about pathways related to innate immune responses. The development of machine learning models successfully predicted the citrullination of proteins in cells.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Microbiology
Daniel P. Strange, Boonyanudh Jiyarom, Hooman Sadri-Ardekani, Lisa H. Cazares, Tara A. Kenny, Michael D. Ward, Saguna Verma
Summary: The study analyzed ZIKV-induced proteome changes in human Sertoli cells using high-throughput liquid chromatography-tandem mass spectrometry, revealing interferon signaling as the significantly enriched pathway and MX1 and IFIT1 as upregulated proteins. MX1 and IFIT1 were found to serve as antiviral effectors against ZIKV, while the antiviral state driven by IFN-I limits ZIKV infection in Sertoli cells, although IFN response is attenuated in these cells compared to other cell types.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Chih-Yuan Chiang, Yang Zhong, Michael D. Ward, Douglas J. Lane, Tara Kenny, Raysa Rosario-Acevedo, Brett P. Eaton, Sylvia R. Trevino, Taylor B. Chance, Meghan Hu, Patricia L. Worsham, David M. Waag, Richard T. Moore, Lisa H. Cazares, Christopher K. Cote, Yingyao Zhou, Rekha G. Panchal
Summary: Burkholderia mallei, the causative agent of glanders, poses a serious biological threat due to its infectivity, antibiotic resistance, and lack of approved vaccines. Studying host responses in non-human primates has revealed insights into the pathogenesis of glanders. Integration of proteomics data has led to the construction of a predictive protein-protein interaction network, shedding light on the molecular mechanisms underlying B. mallei infections.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Cristina Di Poto, Xiang Tian, Xuejun Peng, Heino M. Heyman, Matthias Szesny, Sonja Hess, Lisa H. Cazares
Summary: The identification of metabolites in urine samples is challenging due to its complexity. Ion mobility spectrometry (IMS) coupled with LC-PASEF TIMS-qTOF platform can provide robust CCS values for metabolite identification. Using untargeted metabolomics, a total of 362 urine metabolites were characterized, with three analytes targeted for quantification.
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY
(2021)
Article
Immunology
Sergei Biryukov, Jennifer L. Dankmeyer, Zain Shamsuddin, Ivan Velez, Nathaniel O. Rill, Raysa Rosario-Acevedo, Christopher P. Klimko, Jennifer L. Shoe, Melissa Hunter, Michael D. Ward, Lisa H. Cazares, David P. Fetterer, Joel A. Bozue, Patricia L. Worsham, Christopher K. Cote, Kei Amemiya
Summary: Research shows that by incorporating multiple toll-like receptor agonists into the F1-V plague vaccine regimen, it is possible to further enhance the immune response, optimize, and augment vaccine efficacy.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Medicine, Research & Experimental
Lina Chakrabarti, Raghothama Chaerkady, Junmin Wang, Shao Huan Samuel Weng, Chunlei Wang, Chen Qian, Lisa Cazares, Sonja Hess, Peter Amaya, Jie Zhu, Diane Hatton
Summary: In this study, we enriched Chinese hamster ovary (CHO) host cells with high mitochondrial membrane potential (MMP) to enhance protein productivity and biomanufacturing capability. Stable transfectant pools and clonal cell lines expressing difficult-to-express bispecific molecules were generated from the MMP-enriched host. The MMP-enriched host exhibited improved fed-batch productivity, enhanced cell viability, favorable lactate metabolism, and improved cell cloning efficiency. Proteomic analysis and Western blot validation revealed the underlying mechanisms by which high MMP influenced production performance.
Article
Microbiology
Qingbo Shu, Tara Kenny, Jia Fan, Christopher J. Lyon, Lisa H. Cazares, Tony Y. Hu
Summary: This study introduced six ebolavirus species, emphasizing the importance of species identification and viral burden quantification for timely and effective treatment. The authors developed an IP-MS assay for VP40 antigen detection and quantification, selecting specific regions of VP40 for antibody generation and successfully differentiating four EBV species using this assay.
Meeting Abstract
Hematology
Minal B. Mehta, Benji Gill, Marta Szydlowska, Liang Guo, Taylor Cohen, Cristina Di Poto, Matthew Glover, Erik Allman, Lisa Cazares, Sonja Hess
ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY
(2022)
Article
Immunology
Jill R. Wells, Ian Crozier, Colleen S. Kraft, Mary Elizabeth Sexton, Charles E. Hill, Bruce S. Ribner, Sina Bavari, Gustavo Palacios, William A. Pearce, Russell Van Gelder, Hans Grossniklaus, Lisa Cazares, Xiankung Zeng, Jessica G. Shantha, Steven Yeh
EMERGING INFECTIOUS DISEASES
(2020)