STAR Protoc
J. Craig Venter Institute, La Jolla, CA 92037, USA; Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA. Electronic address:
Published: December 2022
Evaluating the neutralizing antibody titer following SARS-CoV-2 vaccination is essential in defining correlates of protection. We describe an assay that uses single-cycle vesicular stomatitis virus (VSV) pseudoviruses linking a fluorophore with a spike (S) from a variant of concern (VOC). Using two fluorophores linked to two VOC S, respectively, allows us to determine the neutralization titer against two VOCs in a single run. This is a generalizable approach that saves time, samples, and run-to-run variability. For complete details on the use and execution of this protocol, please refer to Sievers et al. (2022)..
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http://dx.doi.org/10.1016/j.xpro.2022.101835 | DOI Listing |
Bioinformatics
March 2025
European Commission, Joint Research Centre (JRC), Geel, Belgium.
Motivation: Recommendations on the use of genomics for pathogens surveillance are evidence that high-throughput genomic sequencing plays a key role to fight global health threats. Coupled with bioinformatics and other data types (e.g.
View Article and Find Full Text PDFJ Biol Chem
March 2025
Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA; Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA. Electronic address:
The kinase-like NiRAN domain of nsp12 in SARS-CoV-2 catalyzes the formation of the 5' RNA cap structure. This activity is required for viral replication, offering a new target for the development of antivirals. Here, we develop a high-throughput assay to screen for small molecule inhibitors targeting the SARS-CoV-2 NiRAN domain.
View Article and Find Full Text PDFJACS Au
February 2025
Laboratory for Chemistry and Life Science, Institute of Integrated Research, Institute of Science Tokyo, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8501, Japan.
A quenchbody (Q-body) is a fluorophore-labeled homogeneous immunosensor in which the fluorophore is quenched by tryptophan (Trp) residues in the vicinity of the antigen-binding paratope and dequenched in response to antigen binding. Developing Q-bodies against targets on demand remains challenging due to the large sequence space of the complementarity-determining regions (CDRs) related to antigen binding and fluorophore quenching. In this study, we pioneered a strategy using high-throughput screening and a protein language model (pLM) to predict the effects of mutations on fluorophore quenching with single amino acid resolution, thereby enhancing the performance of Q-bodies.
View Article and Find Full Text PDFJACS Au
February 2025
Department of Cardiovascular Sciences, University of Leicester, University Road, Leicester, Leicester LE1 7RH, U.K.
Mass spectrometry (MS) is a potentially powerful approach for the diagnostic detection of SARS-CoV-2 and other viruses. However, MS detection is compromised when viral antigens are present at low concentrations, especially in complex biological media. We hypothesized that viral receptors could be used for viral target capture to enable detection by MS under such conditions.
View Article and Find Full Text PDFFront Bioinform
February 2025
Department of Biotechnology, Kulliyyah of Science, International Islamic University Malaysia, Kuantan, Pahang, Malaysia.
Antibodies are naturally produced safeguarding proteins that the immune system generates to fight against invasive invaders. For centuries, they have been produced artificially and utilized to eradicate various infectious diseases. Given the ongoing threat posed by COVID-19 pandemics worldwide, antibodies have become one of the most promising treatments to prevent infection and save millions of lives.
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