FY2023 Annual Report

Kondrashov Unit 2023

Abstract

This year, our lab engaged in a diverse set of research directions, continuing to build our experimental and computational capobilities. These recent publications provide a cohesive look into diverse biological processes, exploring everything from microbial interactions in plants to evolutionary strategies in fish and vaccination responses in humans.

Getzke (2024) sheds light on microbial life in plant roots, where bacterial exometabolites play a crucial role in assembling root-associated microbiota. Published in PNAS, this research reveals that these microbial byproducts are far more than metabolic waste; they are vital signals and resources that guide the establishment of beneficial root communities. Our work underscores the rich interdependencies between plants and microbes, suggesting that microbial metabolites are fundamental players in shaping plant health and ecosystem resilience.

Gert et al. (2023) focused on reproductive boundaries in fish, unveiling how molecular divergences in Bouncer proteins act as a barrier to cross-species fertilization. In the study in Nature Communications, we see how genetic boundaries are reinforced at a molecular level, helping maintain species separation. This research enriches our understanding of speciation, showing that even subtle molecular shifts can define the lines that separate species.

On the front lines of SARS-CoV-2 evolution and vaccine efficacy, Astakhova and our team (2023) employ antigenic mapping to track immune responses after Sputnik V vaccination and revaccination. Published in PubMed, the findings highlight how Omicron subvariants BA.1 and BA.4/BA.5 retain antigenic differences from the original virus strain. This insight is essential as we strategize future vaccination approaches to address ongoing antigenic shifts and ensure enduring immunity against emerging variants.

Yotsui et al. (2023) looked at plant immunity, revealing conserved immune responses in Marchantia polymorpha, a basal land plant. In Current Biology, they explore LysM-mediated signaling, revealing  fundamental aspects of pattern-triggered immunity that are conserved across the plant kingdom. By examining these ancient immune mechanisms, we gain insight into the evolutionary lineage of plant defenses—a shared toolkit that plants have refined over millions of years to fend off pathogens.

Levin et al. (2023) looked into parallel evolution of hypertrophied lips in multiple cyprinid fish lineages. In Ecology and Evolution, this study illustrates how morphological traits can evolve independently yet similarly across species facing comparable ecological challenges, providing a striking example of recurrent patterns in adaptive evolution.

Finally, Rella et al. (2023) propose a novel approach to prevent the emergence of vaccine-resistant strains through complex vaccination strategies. Published in the European Journal of Public Health, this study argues that combining varied vaccination approaches could curtail the virus's ability to adapt and evade immune defenses. By integrating diverse vaccine types, we may reduce the chances of vaccine-resistant variants emerging, offering a proactive pathway for public health resilience.

1. Staff

  • Dr. Shingo Miyauchi, Staff Scientist
  • Dr. Nikolai Iakushev, Staff Scientist
  • Dr. Maria Anastasina, Staff Scientist
  • Arina Mazurova, Research Unit Technician
  • Anna Toidze, Research Unit Technician
  • Aygul Minnegalieva, Research Unit Technician
  • Fedor Gagarin, Research Unit Technician
  • Lada Isakova, Research Unit Technician
  • Saori Chappell, Research Unit Administrator

Research Intern Students/Visiting Researcher

  • Anastasiia Ishchenko, Research Intern
  • Liubov Shestakova, Research Intern
  • Milena Dobronos, Research Intern
  • Aleksei Barykin, Research Intern
  • Maria Gorshkova, Research Intern
  • Daryna Sizon, Research Intern
  • Kateryna Andriienkova, Research Intern
  • Tetiana Salamovska, Research Intern
  • Julia Sakharuk, Research Intern
  • Anton Kulikov, Visiting Researcher
  • Zoe Donaldson, Visiting Researcher

2. Publications

2.1 Journals

  1. Getzke F., Amine Hassan M., Crüsemann M., Malisic M., Zhang P., Ishigaki Y., Böhringer N., Fernández A.J., Wang L., Ordon J., Ma Ka-Wai., Thiergart T., Harbort C.J., Wesseler H., Miyauchi S., Garrido- Oter R., Shirasu K., Schäberle T.F., Hacquard S., Schulze-Lefert P. Cofunctioning of bacterial exometabolites drives root microbiota establishment PNAS, doi:10.1073/pnas.2221508120 (2024)

  2. R.B. Gert K., Panser K., Surm J., Steinmetz B.J., Schleiffer A., Jovine L., Moran Y., Kondrashov F., & Pauli A. Divergent molecular signatures in fish Bouncer proteins define cross-fertilization boundaries, nature communications, doi:10.1038/s41467-023-39317-4 (2023)

  3. Astakhova E.A., Morozov A.A, Byazrova M.G., Sukhova M.M., Mikhailov A.A., Minnegalieva A.R., Gorchakov A.A., Filatov A.V. Antigenic Cartography Indicates That the Omicron BA.1 and BA.4/BA.5 Variants Remain Antigenically Distant to Ancestral SARS-CoV-2 after Sputnik V Vaccination Followed by Homologous (Sputnik V) or Heterologous (Comirnaty) Revaccination, Pub Med, doi: 10.3390/ijms241310493 (2023)

  4. Yotsui I., Matsui H., Miyauchi S., Iwakawa H., Melkonian K., Schluter T., Michavila S., Kanazawa T., Nomura Y., Stolze S.C., Jeon H-W., Yan Y., Harzen A., Sugano S.S., Shirakawa M., Nishihama R., Ichihashi Y., Ibanez S.G., Shirasu K., Ueda T., Kohchi T., Nakagami H. LysM-mediated signaling in Marchantia polymorpha highlights the conservation of pattern-triggered immunity in land plants, Current Biology (Volume 33, Issue 17) doi: /10.1016/j.cub.2023.07.068 (2023)

  5. Levin B., Komaroval A., Simonov E., Tiunov A., Levina M., Golubtsov A., Kondrashov F.,  Meyer A. Speciation and repeated origins of hypertrophied lips in parallel adaptive radiations of cyprinid fish from East Africa, Ecology and Evolution doi: 10.1002/ece3.10523 (2023)

  6. Rella S.A., Kulikova Y.A., Minnegalieva A.R., Kondrashov F.A. Complex vaccination strategies prevent the emergence of vaccine resistance, European Journal of Public Health (Volume 33, Issue Supplement_2) doi: 10.1093/eurpub/ckad160.597 (2023)

2.2 Oral and Poster Presentations

  1. Isakova L., Bochkareva O., Streltsova E., Buianova S., Vlasov P., Kondrashov F. The geometric and topological properties of sequence space reflect the rate of evolution of protein families, Poster Presentation, Society for Molecular Biology and Evolution 2023 Annual Congress, Ferrara, Italy, 2023.July 23-27

  2. Kondrashov F. Diversity of fitness peak shapes in the Green Fluorescent Protein, The 3rd AsiaEvo Conference, National University of Singapore, Singapore, 2023.12.16

  3. Kondrashov F. Genetic bottlenecks and potential threats, International Workshop on Migratory Waterbird Flyways and Habitats Conservation, Shenzhen, China 2024.01.26

 

3. Meetings and Events

 

3.1 Seminar and Talk

The interaction of amino acid states in the course of molecular evolution

  • Date: July 4, 2023
  • Speaker: Prof. Fyodor Kondrashov
  • Invited talk: Bio Data Science^3

Composition of negative data impacts machine learning generalization and biological rule discovery: lessons for in silico biologics sequence design

  • Date: Nov 8, 2023
  • Speaker: Aygul Minnegalieva
  • OIST Mini Symposium: Library Design for Protein Engineering 2023

Diversity of fitness peak shapes in the Green Fluorescent Protein

  • Date: Nov 9, 2023
  • Speaker: Prof. Fyodor Kondrashov
  • OIST Mini Symposium: Library Design for Protein Engineering 2023

Perceptual dysfunctions impair fear memory in models of autism

  • Date: Nov 9, 2023
  • Venue: OIST
  • Speaker: Prof. Maximilian Jösch, Institute of Science and Technology, Austria
  • Guest seminar

Machine Learning and Modeling Evolutionary Protein Mutation

  • Date: Nov 28, 2023
  • Venue: Davis Center for Russian and Eurasian Studies at Harvard University
  • Speaker: Prof. Fyodor Kondrashov
  • Virtual talk

Geometric and topological properties of protein sequence space and molecular evolution

  • Date: Feb 5, 14, 2024
  • Venue: University of Arizona/ Columbia University
  • Speaker: Lada Isakova
  • Invited talk

4. Other

We organize two summer schools: The School of Molecular and Theoretical Biology and the Biological Data Science Summer School.