Irina A. Yushenova Research Scientist Josephine Bay Paul Center for Comparative and Evolution, Marine Biological Laboratory 7 MBL Street, L301/341, Woods Hole, MA 02543 [email protected] ResearchGate ORCID Education and Postdoctoral Training

2011 – 2019 Postdoctoral Arkhipova Lab, Josephine Bay Paul Center for Comparative Scientist Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA. Projects: “Reverse Transcriptase-related genes and their biological significance"; “Horizontal gene transfer as a source of evolutionary innovation in metazoans”; “Structural investigations of a protein-primed reverse transcriptase.” 2007 – 2011 PhD Molecular Basis of Biological Adaptation Laboratory, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, , . Defended Ph.D. on March 17, 2011. Specialization: Molecular biology. Dissertation title: “The peculiarities of the genetic system controlling the thermal adaptation of several Diptera species”, under Olga G. Zatsepina, ScD. 2002 – 2007 DVM Moscow State Academy of Veterinary and Biotechnology named after K.I. Skryabin, Moscow, Russia. Specialization: Biochemistry (major in Bioorganic chemistry; minor in Veterinary medicine). Thesis title: “The variability of hsp70 gene cluster in Drosophila virilis species group”. Defended with Honors. Professional Positions

2019 – Present Research Scientist Arkhipova Lab, Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA. Studying horizontal gene transfer as a source of evolutionary innovation in metazoans using bdelloid rotifers as a model system. 2009 – 2013 Junior Research Molecular Bases of Biological Adaptation Laboratory, Scientist Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. Investigating molecular mechanisms ensured activity of Penelope mobile elements in different Drosophila species, and stress genes expression regulation mechanisms and their role in adaptation to extreme environments.

Publications

1. Craig R.J.*, Yushenova I.A.*, Rodriguez F., Arkhipova I.R. An ancient clade of Penelope-like retroelements with permuted domains is present in the green lineage and protists, and dominates

many invertebrate genomes. bioRxiv 2021.04.23.441226; doi: https://doi.org/10.1101/2021.04.23.441226 (*co-first authors) 2. Vakhrusheva O.A., Mnatsakanova E.A., Galimov Y.R., Neretina T.N., Gerasimov E.S., Naumenko S.A., Ozerova S.G., Zalevsky A.O., Yushenova I.A., Rodriguez F., Arkhipova I.R., Penin A.A., Logacheva M.D., Bazykin G.A., Kondrashov A.S. Recombination in a natural population of the bdelloid rotifer Adineta vaga. Nature Communications. 2020. 11, 6421. https://doi.org/10.1038/s41467-020-19614-y 3. Arkhipova I.R., Yushenova I.A. Giant transposons in eukaryotes: Is bigger better? Genome Biol Evol. 2019. 11(3): 906–918. https://doi.org/10.1093/gbe/evz041 4. Yushenova I.A., Arkhipova I.R. Biochemical properties of bacterial reverse transcriptase-related (rvt) gene products: multimerization, protein priming, and nucleotide preference. Current Genetics. 2018. 64(6): 1287-1301. DOI: 10.1007/s00294-018-0844-6 5. Arkhipova I.R., Yushenova I.A., Rodriguez F. Giant Reverse Transcriptase-Encoding Transposable Elements at Telomeres. Mol. Biol. Evol. 2017. 34(9):2245–2257. DOI: 10.1093/molbev/msx159 6. Zatsepina O.G., Przhiboro A.A., Yushenova I.A., Shilova V.Y., Zelentsova E.S., Shostak N.G., Evgen'ev M.B., Garbuz D.G. A Drosophila Heat Shock Response Represents an Exception Rather than a Rule Among Diptera Species. Insect Mol Biol. 2016. 25(4):431-49. DOI: 10.1111/imb.12235. 7. Arkhipova I.R., Yushenova I.A., Rodrigues F. Endonuclease-containing Penelope retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families. Mobile DNA. 2013. 4:19. DOI: 10.1186/1759-8753-4-19. 8. Flot JF, Hespeels B, Li X, Noel B, Arkhipova I, Danchin EG, Hejnol A, Henrissat B, Koszul R, Aury JM, Barbe V, Barthélémy RM, Bast J, Bazykin GA, Chabrol O, Couloux A, Da Rocha M, Da Silva C, Gladyshev E, Gouret P, Hallatschek O, Hecox-Lea B, Labadie K, Lejeune B, Piskurek O, Poulain J, Rodriguez F, Ryan JF, Vakhrusheva OA, Wajnberg E, Wirth B, Yushenova I, Kellis M, Kondrashov AS, Mark Welch DB, Pontarotti P, Weissenbach J, Wincker P, Jaillon O, Van Doninck K. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga. Nature. 2013. 500(7463):453-7. DOI: 10.1038/nature12326. 9. Rozhkov N.V., Schostak N.G., Zelentsova E.S., Yushenova I.A., Zatsepina O.G., Evgen'ev M.B. Evolution and dynamics of small RNA response to a retroelement invasion in Drosophila. Mol Biol Evol. 2013. 30(2):397-408. DOI: 10.1093/molbev/mss241. 10. Garbuz D.G.*, Yushenova I.A.*, Zatsepina O.G., Przhiboro A.A., Bettencourt B.R., Evgen'ev M.B. Organization and evolution of hsp70 clusters strikingly differ in two species of Stratiomyidae (Diptera) inhabiting thermally contrasting environments. BMC Evol Biol. 2011. 11:74. (*co-first authors) DOI: 10.1186/1471-2148-11-74. 11. Yushenova I.A., Zatsepina O.G., Przhiboro A.A., Evgen'ev M.B., Garbuz D.G. A comparative analysis of the hsp70 genes system in two species of the family Stratiomyidae (Diptera). Moscow University Biological Sciences Bulletin. 2010. 65(4):181-183. https://doi.org/10.3103/S0096392510040164 12. Garbuz D.G., Zatsepina O.G., Yushenova I., Przhiboro A., Evgen’ev M.B. Different Mechanisms Responsible for Stress Resistance Operate in the Same Insect Order (Diptera). In: Handbook of Molecular Chaperones: Roles, Structures and Mechanisms. Nova Pub. 2010. 479-495. 13. Garbuz D.G., Yushenova I.A., Evgen'ev M.B., Zatsepina O.G. Comparative analysis of hsp70 gene cluster in Drosophila virilis species group. Mol Biol (Mosk). 2009. 43(1):44-52. 14. Yushenova I.A., Zatsepina O.G. The investigation of mechanism thermotolerance in species, inhabiting extreme environments. Issues of physico-chemical biology in veterinary : Collection of the scientific works. Moscow: MSAVMB press. 2009. 106-116.

15. Garbuz D.G., Zatsepina O.G., Przhiboro A.A., Yushenova I., Guzhova I.V., Evgen’ev M.B. Larvae of related Diptera species from thermally contrasting habitats exhibit continuous up-regulation of heat shock proteins and high thermotolerance. Mol. Ecol. 2008. 17(21):4763-77. DOI: 10.1111/j.1365-294X.2008.03947.x. Skills and professional training

• Basic molecular biology, biochemical and genetic techniques (including methods of nucleic acids extraction and molecular cloning; EMSA; PCR, Inverse PCR, RT-PCR, qPCR, ddPCR; AGE, Urea- PAGE, SDS-PAGE, isoelectric focusing, 2-D electrophoresis; manipulation with microorganisms (Escherichia coli, Herpetosiphon aurantiacus, Lambda phage); Southern, Northern and Western Blotting; experience with animals (Drosophila sp., larvae of different Diptera species, bdelloid and monogonont rotifers) and fungi (Neurospora crassa); sequencing (Sanger and Next-Generation Seq); expression and purification of recombinant proteins, FPLC using AKTApure system, ultracentrifugation in sucrose/cesium chloride gradients, enzymatic activity assays; microscopy; bioinformatics and data analysis). • Protein crystallization for crystallography: Dr. Phoebe Rice lab, Department of Biochemistry and Molecular Biology, University of Chicago. Oct 19-29, 2015. • Formal training on using AKTA pure FPLC system and Unicorn software. Online Basic Training Course for UNICORN (eSYS1) and UNICORN™ 6 eCourse (eSYS6). Woods Hole, MA. Jun 2015. • “Statistical Analysis and Graphics with R”, Brown-MBL Course, Woods Hole, MA. Jan 7- 22, 2013. • “From Data to Story: A Writing Workshop for Scientists”, MBL, Woods Hole, MA. Nov 8-9, 2013. Mentoring

• Summer REU undergraduate students’ supervision: Rachel Urban (Butler University, 2021), Samuel Maffa (Brown University, 2019), Bria Metzger (Brown University, 2018), Laura Swain (University of Chicago, 2017), Katherine Dunham (Brown University, 2017), Jonathan N. Dow (Brown University, 2017), Brandon M. Le (Brown University, 2016, 2017), Vishok Srikanth (University of Chicago, 2016), Samantha Spear (Brown University, 2016), Tatsiana A. Mello (Wellesley College, 2015), Aubrey W. Kenefick (Williams College, 2014). • Blue Economy Internship Program employee: Dakarai Barnard-Pratt (UMass Dartmouth, Jul-Aug 2020), Nevaeh Benoit (Upper Cape Cod Regional Technical School, Jan-Feb 2020). • PhD student rotation research mentoring: Daniel DiCorpo (Brown University, 2013). Professional service and memberships

• American Association for the Advancement of Science (full membership sponsored by AAAS/Science Program for Excellence in Science 2015-2019) • National Shellfisheries Association (invited member since 2020) • MBL Society Member (since 2020) • Genetics Society of America Presidential Membership for 2021 • Society for Molecular Biology and Evolution (since 2021) • Invited Reviewer for Molecular Biology and Evolution, International Journal of Molecular Sciences, BMC Medical Genomics, Cells, Scientific Reports, Mobile DNA, PLOS ONE, Agronomy, Symmetry, Ecology and Evolution, Plasmid, Microorganisms, Antioxidants, Genes. Invited Seminars

1. Department of Biology, University of North Florida. Apr 6, 2018. Title: “From multimerization to protein priming: peculiar properties of a domesticated reverse transcriptase”. 2. Center for Cellular Construction, University of California San Francisco. Dec 21, 2017. Title: “The peculiar properties of a cellular reverse transcriptase from a gliding bacterium Herpetosiphon aurantiacus: from multimerization to protein priming”. 3. Department of Biology, James Madison University. Feb 5, 2016. Title: “Protein priming by a domesticated reverse transcriptase: not for viruses only”. Presentations (presenting author underlined)

1. I.A. Yushenova, F. Rodriguez, S. Maffa, B. Metzger, D. Barnard-Pratt, I.R. Arkhipova. Reverse transcriptase- related genes and their possible role in the host cell response to transition metal pollution. NSA 113th ANNUAL MEETING (virtual). National Shellfisheries Association. Mar 22 – 25, 2021. 2. I.A. Yushenova, F. Rodriguez, S. Maffa, B. Metzger, D. Barnard-Pratt, I.R. Arkhipova. A novel intriguing molecular mechanism of response to transition metals in diverse environments. NSA 113th ANNUAL MEETING (virtual). National Shellfisheries Association. Mar 22 – 25, 2021. 3. I.A. Yushenova, F. Rodriguez, I.R. Arkhipova. Reverse transcriptase-related genes and their possible role in the host cell. 4th Uppsala Transposon Symposium, virtual, September 30 – October 02, 2020. 59. 4. I.A. Yushenova, S. Maffa, F. Rodriguez, B.M. Metzger, I.R. Arkhipova. Reverse-transcriptase related genes and transition metal stress response. Mobile Genetic Elements 2019. MBL, Woods Hole, MA, Aug 29 - 31, 2019. 28. 5. F. Rodriguez, I.A. Yushenova, I.R. Arkhipova. Transposon silencing and non-canonical base modifications of bacterial origin in eukaryotes. Mobile Genetic Elements 2019. MBL, Woods Hole, MA, Aug 29 - 31, 2019. 27. 6. I.R. Arkhipova, F. Rodriguez, I.A. Yushenova. Non-canonical base modifications of bacterial origin in a eukaryotic genome. SMBE19. Manchester Central, England, Jul 21- 25, 2019. 1331. 7. O.A. Vakhrusheva, E.A. Mnatsakanova, Y.R. Galimov, T.V. Neretina, E.S. Gerasimov, S.G. Ozerova, A.O. Zalevsky, I.A. Yushenova, I.R. Arkhipova, A.A. Penin, M.D. Logacheva, G.A. Bazykin, A.S. Kondrashov. Evidence for genetic exchange in the bdelloid rotifer Adineta vaga inferred from multiple genome sequences. SMBE19. Manchester Central, England, Jul 21- 25, 2019. 1259. 8. I.A. Yushenova, F. Rodriguez, B.M. Metzger, I.R. Arkhipova. Reverse-transcriptase related gene products and the transition metal stress response. 2018 Transposable Elements. Cold Spring Harbor Laboratory, New York, Nov 1-4, 2018. 78. 9. I.A. Yushenova, I.R. Arkhipova. A non-canonical base-modifying methyltransferase of bacterial origin in a eukaryote. Mobile Genetic Elements: In Silico, In Vitro, In Vivo. MBL, Woods Hole, MA, Aug 31 - Sep 2, 2017. 10. I.A. Yushenova, I.R. Arkhipova. Functional properties of the unique N- and C-terminal domains in domesticated RVT reverse transcriptases. Mobile Genetic Elements: In Silico, In Vitro, In Vivo. MBL, Woods Hole, MA, Aug 31 - Sep 2, 2017. 11. L. Swain, I.A. Yushenova, I.R. Arkhipova. Identifying extrachromosomal intermediates of transposition in bdelloid rotifers. Mobile Genetic Elements: In Silico, In Vitro, In Vivo. MBL, Woods Hole, MA, Aug 31 - Sep 2, 2017. 12. I.A. Yushenova, P.A. Rice, I.R. Arkhipova. Protein priming by reverse transcriptase-related gene products. 2016 Transposable Elements. Cold Spring Harbor Laboratory, New York, Nov 2-5, 2016. 61. 13. I.R. Arkhipova, F. Rodriguez, I.A. Yushenova. Giant telomeric retroelements of extraordinary complexity. 2016 Transposable Elements. Cold Spring Harbor Laboratory, New York, Nov 2-5, 2016. 86. 14. I.R. Arkhipova, F. Rodriguez, I.A. Yushenova. Giant reverse transcriptase-encoding transposable elements at telomeres. International Congress on Transposable Elements (ICTE-2016). Saint Malo, France. Apr 16 – 19, 2016. T30.

15. I.A. Yushenova, I.R. Arkhipova. Domesticated reverse transcriptase RVT exhibits protein priming activity. Mobile Genetic Elements: In Silico, In Vitro, In Vivo. MBL, Woods Hole, MA, Sep 3-5, 2015. 16. Arkhipova, F. Rodriguez, I. Yushenova. Giant reverse transcriptase-encoding transposable elements reveal unexpected links to the viral world. Abstracts, FASEB SRC "Mobile DNA in Mammalian Genomes", Jun 14- 19, 2015, West Palm Beach, FL. 17. I.R. Arkhipova, I.A. Yushenova, F. Rodriguez. Diversified coding potential of retroelements from bdelloid rotifers reveals multiple links to the viral world. Abstracts, Keystone Symposium “Mobile Genetic Elements and Genome Evolution”, Santa Fe, NM, Mar 2014. 44. 18. I.R. Arkhipova, I.A. Yushenova, F. Rodriguez. Phylogenetic relationships in diverse superfamilies of eukaryotic transposable elements. Contributions to the 4th Moscow International Conference “Molecular Phylogenetics” (MolPhy-4). Moscow: Torus Press, 2014. 5-6. 19. I.A. Yushenova, F. Rodriguez, I.R. Arkhipova. Penelope-like retrotransposons in the bdelloid rotifer Adineta vaga exhibit unusual structural features and play a role in expansion of host gene families. Regional Meeting on Mobile Genetic Elements. Cold Spring Harbor Laboratory, New York, Oct 24-26, 2013. 20. E.A. Gladyshev, F. Rodrigues, I.A. Yushenova, and I.R. Arkhipova. Use of phylogenetic approaches to study horizontal gene transfer and evolutionary history of gene families. Molecular Phylogenetics: Contributions to the 3rd Moscow International Conference “Molecular Phylogenetics”. Moscow, Russia, Jul 31 – Aug 4, 2012. / Moscow: TORUS PRESS, 2012. 13-14. 21. I.R. Arkhipova, I.A. Yushenova. Two Types of Penelope-like Elements (PLEs) in Rotifers of the Class Bdelloidea. 3rd International Congress on Transposable Elements (Saint Malo, France, Apr 21-24, 2012). 22. I.R. Arkhipova, I.A. Yushenova. Two Types of Penelope-like Elements (PLEs) in the Phylum Rotifera. 3rd International Conference/Workshop “Genomic Impact of Eukaryotic Transposable Elements”. The Asilomar Conference Center, Pacific Grove, CA, USA. Feb 24-28, 2012. 23. I.A. Yushenova, K. Yan, I.R. Arkhipova. Genomes of monogonont rotifers contain both telomere-associated (endonuclease-deficient) and conventional (endonuclease-containing) Penelope-like elements. 3rd Northeast Mobile DNA Meeting. MBL, Woods Hole, MA, Sep 1-3, 2011. 24. I.A. Yushenova, O.G. Zatsepina, A.A. Przhiboro, M.B. Evgen`ev, D.G. Garbuz. Analysis nucleotide and aminoacid sequences hsp70 in two Stratiomyidae (Diptera) species. Biology – The Science of ХХI age: 15-th Puschino International school-conference young scientist, (Pushchino, Apr 18 – 22, 2011). 28. 25. I.A. Yushenova, O.G. Zatsepina, A.A. Przhiboro, M.B. Evgen`ev, D.G. Garbuz. The comparative analysis of the hsp70 genes clusters in the Diptera species, dwelling in contrasting environments. IV International young scientists’ workshop on molecular genetics “Genomics and ” (, Nov 29 – Dec 3, 2010). 228 – 229. 26. D.G. Garbuz, I.A. Yushenova, M.B. Evgen'ev, O.G. Zatsepina. Diversity of thermal adaptation mechanisms for species dwelling in unfavorable climatic condition. ХХI Congress of The Physiological Society named after I.P. Pavlov. Theses of reports. – M. – Kaluga: OOO “Best-print”. 2010. 137. 27. I.A. Yushenova, O.G. Zatsepina, A.A. Przhiboro, M.B. Evgen'ev, D.G. Garbuz. The investigation of molecular mechanisms expression HSP70 in species, dwelling in extreme natural condition. Biology – The Science of ХХI age: 14-th Puschino International school-conference young scientist, (Pushchino, Apr 19 – 23, 2010). 205. 28. I.A. Yushenova, O.G. Zatsepina, A.A. Przhiboro, M.B. Evgen'ev, D.G. Garbuz. A comparative analysis of the hsp70 genes system in two species of the family Stratiomyidae (Diptera). Molecular Phylogenetics: Thesis of the 2nd Moscow International Conference “Molecular Phylogenetics” (Moscow, Russia, May 18-21, 2010). 189. 29. O.G. Zatsepina, D.G. Garbuz, Zelentsova E.S., Shilova V.Iu., I.A. Yushenova. The investigation of mechanisms thermotolerance: the evolution of genetic loci and mutagenesis. Contributions to the Conference: «Biodiversity and genepool`s dynamics». Moscow, 2008. 132-135.