22 papers · ranked by Valyu relevance
Min Jiang, Changyin Fang, Yongping Ma
Antigenic drift is the biggest challenge for mutagenic RNA virus vaccine development. The most fundamental but neglected thing is to determine the immune escape mutation map (IEMM) of 20 amino acids to reveal the rule of the viral immune escape. We use universal protein tags as a linear epitope model to determine the…
Min Jiang, Changyin Fang, Yongping Ma
Purpose Antigenic drift is the biggest challenge for mutagenic RNA virus vaccine development. The primary purpose is to determine the IEMM (immune escape mutation map) of 20 amino acids’ replacement to reveal the rule of the viral immune escape. Methods To determine the relationship between epitope mutation and immune…
Yongping Ma, Changyin Fang
The biggest challenge of influenza A virus vaccine development is the constant mutation of the virus, especially the antigenic drift. Therefore, we suggest establishing a research system for upgrading of current influenza A vaccines. The most fundamental but neglected thing is to determine the immune escape mutation…
Stephen Lindsly, Maya R. Gupta, Alnawaz Rehemtulla, Indika Rajapakse
The mammalian adaptive immune system has evolved over millions of years to become an incredibly effective defense against foreign antigens. The adaptive immune system's humoral response creates plasma B cells and memory B cells, each with their own immunological objectives. The affinity maturation process is widely…
Thomas B. Kepler, Supriya Munshaw, Kevin Wiehe, Ruijun Zhang + 9 more
'Jae-Sung Yu' 'Christopher W. Woods' 'Thomas N. Denny' 'Georgia D. Tomaras' 'S. Munir Alam' 'M. Anthony Moody' 'Garnett Kelsoe' 'Hua-Xin Liao' 'Barton F. Haynes'] Affinity maturation of the antibody response is a fundamental process in adaptive immunity during which B-cells activated by infection or vaccination undergo…
Alexandre de Castro, Carlos Frederico Fronza, Domingos Alves
Immunological systems have been an abundant inspiration to contemporary computer scientists. Problem solving strategies, stemming from known immune system phenomena, have been successfully applied to challenging problems of modern computing (MONROY, SAAB, GODÍNEZ, 2004). Simulation systems and mathematical modeling are…
Marcos Costa Vieira, Daniel Zinder, Sarah Cobey
High-affinity antibodies arise within weeks of infection from the evolution of B cell receptors under selection to improve antigen recognition. This rapid adaptation is enabled by the frequency and distribution of highly mutable “hotspotx” motifs in B cell receptor genes. High mutability in antigen binding regions…
Gao-De Li
Site-directed mutagenesis refers to a man-made molecular biology method that is used to make genetic alterations in the DNA sequence of a gene of interest. But based on our recently published experimental findings, we propose that "natural site-directed mutagenesis" might exist in eukaryotic cells, which is triggered…
Aurelien Pelissier, Maria Stratigopoulou, Naomi Donner, Evangelos Dimitriadis + 4 more
Germinal centers (GCs) are specialized compartments within the secondary lymphoid organs where B cells proliferate, differentiate, and mutate their antibody genes in response to the presence of foreign antigens. They play a central role in generating an effective immune response against infectious pathogens, and…
Liping Zhou, Leyun Wu, Cheng Peng, Yanqing Yang + 3 more
The emergence of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been bringing the world to a standstill. Beyond all doubt, the most striking therapeutic target for antibody development is the spike (S) protein on the surface of virus. In contrast…
Marco Molari, Klaus Eyer, Jean Baudry, Simona Cocco + 1 more
Affinity maturation is a complex dynamical process allowing the immune system to generate antibodies capable of recognizing antigens. We introduce a model for the evolution of the distribution of affinities across the antibody population in germinal centers. The model is amenable to detailed mathematical analysis, and…
Chao Zhang, Andrey V. Bzikadze, Yana Safonova, Siavash Mirarab
Affinity maturation (AM) of antibodies through somatic hypermutations (SHMs) enables the immune system to evolve to recognize diverse pathogens. The accumulation of SHMs leads to the formation of clonal trees of antibodies produced by B cells that have evolved from a common naive B cell. Recent advances in…
Armita Nourmohammad, Jakub Otwinowski, Joshua B. Plotkin
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens. Yet, viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system, forming an evolutionary arms race. Here we introduce a mathematical framework to study the…
Thiago Detanico, Matthew Phillips, Lawrence J. Wysocki
In systemic autoimmunity, autoantibodies directed against nuclear antigens (Ags) often arise by somatic hypermutation (SHM) that converts AGT and AGC (AGY) Ser codons into Arg codons. This can occur by three different single-base changes. Curiously, AGY Ser codons are far more abundant in complementarity-determining…
Irène Balelli, Vuk Milišić, Gilles Wainrib
Within the germinal center in follicles, B-cells proliferate, mutate and dierentiate, while being submitted to a powerful selection : a microevolutionary mechanism at the heart of adaptive immunity. A new foreign pathogen is confronted to our immune system, the mutation mechanism that allows B-cells to adapt to it is…
liu wenzhong, li hualan
The high mortality of COVID-19 is related to poor antigen presentation and lymphopenia. In this present study, domain search results showed that many proteins of the SARS-COV-2 virus had MHC-like domains, which were similar to decoys for the human immune system. MHC-like structures could bind to MHC receptors of immune…
Chaim A. Schramm, Daniel C. Douek
The evolution of antibodies in an individual during an immune response by somatic hypermutation (SHM) is essential for the ability of the immune system to recognize and remove the diverse spectrum of antigens that may be encountered. These mutations are not produced at random; nucleotide motifs that result in increased…
Anja Schrade, Alexander Bujotzek, Christian Spick, Martina Wagner + 5 more
'Johannes Goerl' 'Xenia Wezler' 'Guy Georges' 'Roland E. Kontermann' 'Ulrich Brinkmann'] Bispecific antibodies (bsAbs) with avidity-enhanced specificity can be used to address target cells with increased specificity, ideally binding efficiently to cells that express two cognate antigens, yet not to cells that express…
Nicolas Strauli, Ryan Hernandez
Vaccines dramatically affect an individual’s adaptive immune system, and thus provide an excellent means to study human immunity. Upon vaccination, the B cells that express antibodies (Abs) that happen to bind the vaccine are stimulated to proliferate and undergo mutagenesis at their Ab locus. This process may alter…
Saeed Mahdisoltani, Pranav Murugan, Arup K. Chakraborty, Mehran Kardar
'Mehran Kardar'] A persistent public health challenge is finding immunization schemes that are effective in combating highly mutable pathogens such as HIV and influenza viruses. To address this, we analyze a simplified model of affinity maturation, the Darwinian evolutionary process B cells undergo during immunization.…
Ufuk Kirik, Helena Persson, Fredrik Levander, Lennart Greiff + 1 more
'Mats Ohlin'] B cells produce antibodies, key effector molecules in health and disease. They mature their properties, including their affinity for antigen, through hypermutation events; processes that involve, e.g., base substitution, codon insertion and deletion, often in association with an isotype switch.…
Annmaree K. Warrender, William Kelton
Polymorphic diversity in antibody constant domains has long been defined by allotypic motifs that cross react with the sera of other individuals. Improvements in sequencing technologies have led to the discovery of a large number of new allelic sequences that underlie this diversity. Many of the point mutations lie…