Article
Immunology
Sarvin Sanaie, Elham Golipour, Ali Shamekh, Mohammad Reza Sadaie, Ata Mahmoodpoor, Mehdi Yousefi
Summary: The potential for human reinfection with SARS-CoV-2 remains uncertain despite the presence of antibodies and immune cells, as the virus can mutate and affect its spread. Both innate and adaptive immune responses in individuals play a crucial role in the dynamics of virus infection.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
Daseuli Yu, Hee-Jeong Han, Jeonghye Yu, Jihye Kim, Gun-Hee Lee, Ju-Hee Yang, Byeong-Min Song, Dongseob Tark, Byeong-Sun Choi, Sang -Min Kang, Won Do Heo
Summary: CRISPR-Cas13-mediated viral genome targeting is an effective strategy for combating SARS-CoV-2 and its variants. By using mRNA-encoded Cas13b, specifically targeting the ORF1b region, the RNA-dependent RNA polymerase gene can be degraded. Among the designed CRISPR RNAs, those targeting the pseudoknot site upstream of ORF1b were found to be most effective in suppressing viral propagation. Pseudoknot-targeting Cas13b not only reduced spike protein expression and viral replication by 99%, but also inhibited the replication of multiple SARS-CoV-2 variants.
Review
Immunology
James E. Crowe
Summary: Antibodies have been widely used for preventing and treating viral infections since the nineteenth century, and the development of potent human monoclonal antibodies has paved the way for unprecedented activities. Modifications that extend antibody half-life and the clinical development of broad and potent antibodies have the potential to make antibodies the principal tool in managing future viral epidemics. Furthermore, these antibodies are crucial for research and developing effective vaccines.
ANNUAL REVIEW OF IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Joseph L. Harman, Patrick N. Reardon, Shawn M. Costello, Gus D. Warren, Sophia R. Phillips, Patrick J. Connor, Susan Marqusee, Michael J. Harms
Summary: This study identified a mutation in S100A9 protein that simultaneously increased its stability and disrupted its natural ability to regulate Toll-like receptor 4. Structural analysis revealed that the mutation distorted the hydrophobic binding surface of the protein, leading to its functional impairment. Bioinformatic analysis further showed that Phe residues at both positions 37 and 63 are rarely found in S100A9 proteins from different organisms, suggesting that avoiding pathological stabilizing interactions constrains the evolution of S100A9.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Kai Deng, Qing Zhou, Zhanxue Xu, Yuhao Yang, Xi Liu, Chunna Li, Mingxiao Chen, Zhenzhen Zhang, Haihang Chen, Ling Ma, Muhammad Ikram Anwar, Changlong Zheng, Liang Rong, Mingxing Huang, Jinyu Xia, Yuanping Zhou, Yi-Ping Li
Summary: In this study, it was found that IgG antibodies from two chronic hepatitis C (CHC) patients could effectively control HCV infection, with the 1bHVR1 antibody playing a key role. Furthermore, it was discovered that the 1bHVR1 peptide was able to elicit antibodies that neutralized multiple HCV genotypes. The neutralization effect of 1bHVR1 IgG could be enhanced by the HH-1 antibody. Mechanistic studies revealed that the 1bHVR1 antibodies disrupted the interaction of the E2-SR-B1 receptor. This study highlights the importance of HVR1 antibodies generated by CHC patients and HVR1 immunization in neutralizing various HCV genotypes.
Article
Medicine, General & Internal
Peter W. Horby, Marion Mafham, Leon Peto, Mark Campbell, Guilherme Pessoa-Amorim, Enti Spata, Natalie Staplin, Jonathan R. Emberson, Benjamin Prudon, Paul Hine, Thomas Brown, Christopher A. Green, Rahuldeb Sarkar, Purav Desai, Bryan Yates, Tom Bewick, Simon Tiberi, Tim Felton, J. Kenneth Baillie, Maya H. Bitch, Lucy C. Chappell, Saul N. Faust, Thomas Jaki, Katie Jeffery, Edmund Juszczak, Wei Shen Lim, Alan Montgomery, Andrew Mumford, Kathryn Rowan, David M. Weinreich, Richard Haynes, Martin J. Landray
Summary: This study evaluated the efficacy and safety of the combination therapy of casirivimab and imdevimab in patients hospitalized with COVID-19. The results showed that this combination therapy reduced the 28-day mortality rate in patients without detectable antibodies to SARS-CoV-2 infection at baseline, but not in those with detectable antibodies.
Article
Multidisciplinary Sciences
Christian Gaebler, Lilian Nogueira, Elina Stoffel, Thiago Y. Oliveira, Gaelle Breton, Katrina G. Millard, Martina Turroja, Allison Butler, Victor Ramos, Michael S. Seaman, Jacqueline D. Reeves, Christos J. Petroupoulos, Irina Shimeliovich, Anna Gazumyan, Caroline S. Jiang, Nikolaus Jilg, Johannes F. Scheid, Rajesh Gandhi, Bruce D. Walker, Michael C. Sneller, Anthony Fauci, Tae-Wook Chun, Marina Caskey, Michel C. Nussenzweig
Summary: Immunotherapy with anti-HIV-1 antibodies has the potential to suppress infection and increase the rate of clearance of infected cells. A clinical study showed that 76% of HIV-infected individuals who received a combination of antibodies maintained virologic suppression for at least 20 weeks without antiretroviral therapy. The administration of antibodies affected the HIV-1 reservoir, but further research is needed to define the precise effect of antibody immunotherapy.
Article
Biochemical Research Methods
A. Kulandaisamy, R. Sakthivel, M. Michael Gromiha
Summary: Membrane proteins' functions are attributed to their structure and stability, with thermodynamic data aiding in understanding the relationship among these factors. A new database called MPTherm has been developed to provide over 7000 thermodynamic data from around 320 membrane proteins, helping users retrieve and analyze the data effectively. MPTherm serves as a valuable resource for researchers to study membrane protein stability, develop prediction tools, and identify drug targets for diseases associated with membrane proteins.
BRIEFINGS IN BIOINFORMATICS
(2021)
Review
Medical Laboratory Technology
Y. Victoria Zhang, Joesph Wiencek, Qing H. Meng, Elitza S. Theel, Nikolina Babic, Lusia Sepiashvili, Nicole D. Pecora, Patricia Slev, Andrew Cameron, Danijela Konforte
Summary: This document aims to provide a comprehensive reference for laboratory professionals and healthcare workers to appropriately implement SARS-CoV-2 serologic assays in the clinical laboratory and to interpret test results during this pandemic. It discusses the verification and validation of EUA and LDT assays, along with a quality management approach. Recommendations for serologic testing indications, result interpretation and the role of orthogonal testing are presented.
CLINICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Jackson S. Turner, Wooseob Kim, Elizaveta Kalaidina, Charles W. Goss, Adriana M. Rauseo, Aaron J. Schmitz, Lena Hansen, Alem Haile, Michael K. Klebert, Iskra Pusic, Jane A. O'Halloran, Rachel M. Presti, Ali H. Ellebedy
Summary: The study found that individuals who had recovered from mild SARS-CoV-2 infections showed rapid decline of serum anti-SARS-CoV-2 spike protein antibodies in the first 4 months after infection, followed by a more gradual decrease over the following 7 months but remaining detectable at least 11 months after infection. This suggests that mild infection with SARS-CoV-2 can induce robust antigen-specific, long-lived humoral immune memory in humans.
Article
Multidisciplinary Sciences
Christian Gaebler, Zijun Wang, Julio C. C. Lorenzi, Frauke Muecksch, Shlomo Finkin, Minami Tokuyama, Alice Cho, Mila Jankovic, Dennis Schaefer-Babajew, Thiago Y. Oliveira, Melissa Cipolla, Charlotte Viant, Christopher O. Barnes, Yaron Bram, Gaelle Breton, Thomas Hagglof, Pilar Mendoza, Arlene Hurley, Martina Turroja, Kristie Gordon, Katrina G. Millard, Victor Ramos, Fabian Schmidt, Yiska Weisblum, Divya Jha, Michael Tankelevich, Gustavo Martinez-Delgado, Jim Yee, Roshni Patel, Juan Dizon, Cecille Unson-O'Brien, Irina Shimeliovich, Davide F. Robbiani, Zhen Zhao, Anna Gazumyan, Robert E. Schwartz, Theodora Hatziioannou, Pamela J. Bjorkman, Saurabh Mehandru, Paul D. Bieniasz, Marina Caskey, Michel C. Nussenzweig
Summary: After infection with SARS-CoV-2, antibody levels against the spike protein decrease significantly, but the number of memory B cells remain unchanged, indicating an evolving humoral response at 6.2 months after infection.
Article
Biochemistry & Molecular Biology
Sherif G. Ahmed, Casey A. Maguire, Shiliang Alice Cao, Gary J. Brenner
Summary: Schwannomas are tumors derived from Schwann-lineage cells. Currently, treatment options for schwannomas are limited and associated with significant complications. Researchers have successfully reduced tumor volume and pain in experimental models using gene therapy. The safety and efficacy data support the translation of this gene therapy strategy to clinical trials.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Matthijs Meijers, Kanika Vanshylla, Henning Gruell, Florian Klein, Michael Laessig
Summary: Broadly neutralizing antibodies show promise in treating and preventing HIV-1 infections, but the virus often evolves resistance. A fitness model based on in vivo data accurately predicts the dynamics of HIV-1 escape during antibody treatment, highlighting an evolutionary trade-off between antibody resistance and its collateral cost.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biotechnology & Applied Microbiology
Arpana Khatri, Rajani Shelke, Shunjie Guan, Suryanarayan Somanathan
Summary: This study evaluated the incidence of AAV neutralizing antibodies (NAbs) among a panel of vectors in healthy donors within the United States. The findings showed a higher incidence of NAbs among black and Hispanic donors, highlighting the importance of considering the seroprevalence within the patient population when selecting AAV capsids and the need to eliminate bias in sample data sets.
HUMAN GENE THERAPY
(2022)
Article
Virology
Widade Ziani, Anya Bauer, Hong Lu, Xiaolei Wang, Xueling Wu, Katharine J. Bar, Hui Li, Dongfang Liu, George M. Shaw, Ronald S. Veazey, Huanbin Xu
Summary: The newly developed SHIV.C.CH848 can establish sustained viremia and viral reservoirs in rhesus macaques with clinical immunodeficiency consequences, providing a valuable SHIV model for HIV research. The findings suggest that this CCR5-tropic, SHIVC strain is valuable for testing responses to HIV vaccines and therapeutics in nonhuman primate models.
JOURNAL OF VIROLOGY
(2021)
Article
Ecology
Weronika Jasinska, Michael Manhart, Jesse Lerner, Louis Gauthier, Adrian W. R. Serohijos, Shimon Bershtein
NATURE ECOLOGY & EVOLUTION
(2020)
Article
Biophysics
Rostam M. Razban, Pouria Dasmeh, Adrian W. R. Serohijos, Eugene Shakhnovich
Summary: The study reveals that protein stability evolution is better explained by the misfolding avoidance fitness function than the flux dynamics fitness function. Further experiments show that only the unfolded state, not all misfolded states, are avoided. The research also provides a closed-form expression linking protein abundance to evolutionary rate without fitted parameters for Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens.
BIOPHYSICAL JOURNAL
(2021)
Article
Biochemical Research Methods
Ankur Sarkar, Edward Y. Kim, Taehwan Jang, Akarawin Hongdusit, Hyungjun Kim, Jeong-Mo Choi, Jerome M. Fox
Summary: The study introduces a novel approach to utilize microbial hosts for targeted natural product discovery and biosynthesis, leading to the identification and synthesis of two potential protein tyrosine phosphatase 1B inhibitors for the treatment of diabetes and cancer. The findings demonstrate the scalability and versatility of the method, as well as the potential of using microbes to discover and produce bioactive compounds with unique structures and binding sites.
ACS SYNTHETIC BIOLOGY
(2021)
Article
Evolutionary Biology
Arnaud N'Guessan, Ilana Lauren Brito, Adrian W. R. Serohijos, B. Jesse Shapiro
Summary: The study investigates the evolution of pangenomes and finds that sequence evolution of mobile genes within human microbiomes is primarily determined by gene families rather than human social attributes. Results indicate that gene-specific selective pressures dominate over human or bacterial host-specific pressures on relatively short evolutionary time scales.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biochemistry & Molecular Biology
Joanna Zell, Katerina Duskova, Leila Chouh, Madeleine Bossaert, Nicolas Cheron, Anton Granzhan, Sebastien Britton, David Monchaud
Summary: DNA is a dynamic molecule that can fold into alternative higher-order structures like G-quadruplexes (G4s) and three-way DNA junctions (TWJs). Ligands targeting both TWJs and G4s in vitro show distinct cellular effects, suggesting a pivotal role of TWJs in cells. These dual TWJ-/G4-ligands can be combined with DDR inhibitors for an efficient synthetic lethality strategy.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Chemistry, Multidisciplinary
Min-kyung Jo, Young Shin Cho, Gabor Hollo, Jeong-Mo Choi, Istvan Lagzi, Sung Ho Yang
Summary: The study revealed the asymmetric crystal growth in individual bands of Liesegang patterns, which was not observed in previous research. Through a combination of microscopic and spatiotemporal analyses based on nucleation theory, the formation process of asymmetric bands was explained, focusing on the inhomogeneity within a single band.
CRYSTAL GROWTH & DESIGN
(2021)
Review
Biochemistry & Molecular Biology
Je-Kyung Ryu, Da-Eun Hwang, Jeong-Mo Choi
Summary: Biomolecular phase separation is a common phenomenon in cells, particularly involved in the formation and regulation of chromosome structures. Understanding the fundamental principles, experimental and computational methods, and the recent bridging-induced phase separation model can provide insights into this process.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Multidisciplinary
Dongjoon Im, Chae Eun Heo, Myung Kook Son, Chae Ri Park, Hugh Kim, Jeong-Mo Choi
Summary: This study focuses on protein mutations related to neurodegenerative diseases and their impact on fibril formation. Using a multidisciplinary approach and in silico analyses, the researchers designed mutant candidates that could inhibit fibrillation and reduce toxicity. The structural basis for this inhibition was revealed through various biophysical techniques. This study offers new insights into modulating amyloid aggregation based on the understanding of intrinsically disordered proteins.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Biochemistry & Molecular Biology
Dooam Paik, Hankyul Lee, Hyungjun Kim, Jeong-Mo Choi
Summary: The pi-pi interaction is a major driving force in protein folding and liquid-liquid phase separation. Our computational study of the solvation effect on pi-pi interactions in water reveals that solvation influences the association free energies of benzene and phenol dimers, but not significantly when no direct hydrogen-bond-type interaction exists between two monomeric units.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Jaegeon Joo, Sunghyun Cho, Sukbum Hong, Sunwoo Min, Kyukwang Kim, Rajeev Kumar, Jeong-Mo Choi, Yongdae Shin, Inkyung Jung
Summary: This study introduces a novel computational method to systematically characterize inter-chromosomal interactions using in situ Hi-C results. The research identifies two hub-like inter-chromosomal contacts associated with nuclear speckles and nucleoli, respectively, and finds that speckle-associated inter-chromosomal interactions are highly cell-type invariant with a marked enrichment of cell-type common super-enhancers (CSEs). The study also demonstrates the importance of MAZ binding in regulating speckle-associated inter-chromosomal contacts.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Chemistry, Multidisciplinary
Dongjoon Im, Soohyeong Kim, Gyusub Yoon, Da Gyeong Hyun, Yu-Gon Eom, Ye Eun Lee, Chang Ho Sohn, Jeong-Mo Choi, Hugh I. Kim
Summary: This study identified three key hydrophobic sites on amyloid-fi (1-42) protein and investigated their involvement in the self-assembly process, providing important information for the development of aggregation inhibitors.
Article
Chemistry, Physical
Jihye Park, Hee-Seung Lee, Hyungjun Kim, Jeong-Mo Choi
Summary: In this study, we assessed the performance of three popular force fields in predicting the conformational propensities of a beta-peptide foldamer. Our results showed the unanimous role of hydrogen bonds in shaping energy landscapes. These findings contribute to the improvement of force fields and understanding the role of solvents in peptide folding, crystallization, and engineering.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Review
Biochemistry & Molecular Biology
Chan-Geun Kim, Da-Eun Hwang, Rajeev Kumar, Min Chung, Yu-Gon Eom, Hyunji Kim, Da-Hyun Koo, Jeong-Mo Choi
Summary: Biomolecular phase separation is a crucial phenomenon that plays a significant role in the compartmentalization of living cells. It can be explained by simple physical principles and replicated in vitro. This Mini review provides an overview of the current understanding and recent progress in the fundamental principles of biomolecular phase separation.
Article
Chemistry, Multidisciplinary
Francesco Rota Sperti, Baptiste Dupouy, Jeremie Mitteaux, Angelique Pipier, Marc Pirrotta, Nicolas Cheron, Ibai E. Valverde, David Monchaud
Summary: This study demonstrates the versatility of a biomimetic G4 ligand called TASQ, providing important tools for investigating G-quadruplex biology in human cells and gaining insights into its mechanism of action.
Article
Physics, Fluids & Plasmas
Jeong-Mo Choi, Anthony A. Hyman, Rohit V. Pappu