It has now been more than two years since we said our last goodbye to Jan Svoboda (14 [...].

Department of Biochemistry and Microbiology University of Chemistry and Technology CZ 166 28 Prague Czech Republic

Department of Viral and Cellular Genetics Institute of Molecular Genetics of the Czech Academy of Sciences Videnska 1083 CZ 14220 Prague Czech Republic

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Hejnar J. Jan Svoboda (1934–2017): Sixty Years with Retroviruses. Retrovirology. 2017;14:32. doi: 10.1186/s12977-017-0357-2. PubMed DOI PMC

Weiss R.A. Remembering Jan Svoboda: A Personal Reflection. Viruses. 2018;10:203. doi: 10.3390/v10040203. PubMed DOI PMC

Vogt P.K. The Importance of Being Non-Defective: A Mini Review Dedicated to the Memory of Jan Svoboda. Viruses. 2019;11:80. doi: 10.3390/v11010080. PubMed DOI PMC

Svoboda J., Hejnar J., Geryk J., Elleder D., Vernerová Z. Retroviruses in foreign species and the problem of provirus silencing. Gene. 2000;261:181–188. doi: 10.1016/S0378-1119(00)00481-9. PubMed DOI

Lounková A., Dráberová E., Šenigl F., Trejbalová K., Geryk J., Hejnar J., Svoboda J. Molecular events accompanying rous sarcoma virus rescue from rodent cells and the role of viral gene complementation. J. Virol. 2014;88:3505–3515. doi: 10.1128/JVI.02761-13. PubMed DOI PMC

Elleder D., Plachý J., Hejnar J., Geryk J., Svoboda J. Close linkage of genes encoding receptors for subgroups A and C of avian sarcoma/leucosis virus on chicken chromosome 28. Anim. Genet. 2004;35:176–181. doi: 10.1111/j.1365-2052.2004.01118.x. PubMed DOI

Elleder D., Stepanets V., Melder D.C., Šenigl F., Geryk J., Pajer P., Plachý J., Hejnar J., Svoboda J., Federspiel M.J. The receptor for the subgroup C avian sarcoma and leukosis viruses, Tvc, is related to mammalian butyrophilins, members of the immunoglobulin superfamily. J. Virol. 2005;79:10408–10419. doi: 10.1128/JVI.79.16.10408-10419.2005. PubMed DOI PMC

Elleder D., Melder D.C., Trejbalová K., Svoboda J., Federspiel M.J. Two different molecular defects in the Tva receptor gene explain the resistance of two tvar lines of chickens to infection by subgroup A avian sarcoma and leukosis viruses. J. Virol. 2004;78:13489–13500. doi: 10.1128/JVI.78.24.13489-13500.2004. PubMed DOI PMC

Reinišová M., Šenigl F., Yin X., Plachý J., Geryk J., Elleder D., Svoboda J., Federspiel M.J., Hejnar J. A single-amino-acid substitution in the TvbS1 receptor results in decreased susceptibility to infection by avian sarcoma and leukosis virus subgroups B and D and resistance to infection by subgroup E in vitro and in vivo. J. Virol. 2008;82:2097–2105. doi: 10.1128/JVI.02206-07. PubMed DOI PMC

Reinišová M., Plachý J., Trejbalová K., Šenigl F., Kučerová D., Geryk J., Svoboda J., Hejnar J. Intronic deletions that disrupt mRNA splicing of the tva receptor gene result in decreased susceptibility to infection by avian sarcoma and leukosis virus subgroup A. J. Virol. 2012;86:2021–2030. doi: 10.1128/JVI.05771-11. PubMed DOI PMC

Přikryl D., Plachý J., Kučerová D., Koslová A., Reinišová M., Šenigl F., Hejnar J. The Novel Avian Leukosis Virus Subgroup K Shares Its Cellular Receptor with Subgroup A. J. Virol. 2019;93:e00580-19. doi: 10.1128/JVI.00580-19. PubMed DOI PMC

Kučerová D., Plachý J., Reinišová M., Šenigl F., Trejbalová K., Geryk J., Hejnar J. Nonconserved tryptophan 38 of the cell surface receptor for subgroup J avian leukosis virus discriminates sensitive from resistant avian species. J. Virol. 2013;87:8399–8407. doi: 10.1128/JVI.03180-12. PubMed DOI PMC

Koslová A., Kučerová D., Reinišová M., Geryk J., Trefil P., Hejnar J. Genetic Resistance to Avian Leukosis Viruses Induced by CRISPR/Cas9 Editing of Specific Receptor Genes in Chicken Cells. Viruses. 2018;10:605. doi: 10.3390/v10110605. PubMed DOI PMC

Federspiel M.J. Reverse Engineering Provides Insights on the Evolution of Subgroups A to E Avian Sarcoma and Leukosis Virus Receptor Specificity. Viruses. 2019;11:497. doi: 10.3390/v11060497. PubMed DOI PMC

Munguia A., Federspiel M.J. Avian Sarcoma and Leukosis Virus Envelope Glycoproteins Evolve to Broaden Receptor Usage Under Pressure from Entry Competitors. Viruses. 2019;11:519. doi: 10.3390/v11060519. PubMed DOI PMC

Yin X., Melder D.C., Payne W.S., Dodgson J.B., Federspiel M.J. Mutations in Both the Surface and Transmembrane Envelope Glycoproteins of the RAV-2 Subgroup B Avian Sarcoma and Leukosis Virus Are Required to Escape the Antiviral Effect of a Secreted Form of the TvbS3 Receptor. Viruses. 2019;11:500. doi: 10.3390/v11060500. PubMed DOI PMC

Lounková A., Kosla J., Přikryl D., Štafl K., Kučerová D., Svoboda J. Retroviral host range extension is coupled with Env-activating mutations resulting in receptor-independent entry. Proc. Natl. Acad. Sci. USA. 2017;114:5148–5157. doi: 10.1073/pnas.1704750114. PubMed DOI PMC

Hejnar J., Svoboda J., Geryk J., Fincham V.J., Hák R. High rate of morphological reversion in tumor cell line H-19 associated with permanent transcriptional suppression of the LTR, v-src, LTR provirus. Cell Growth Differ. 1994;5:277–285. PubMed

Hejnar J., Hájková P., Plachý J., Elleder D., Stepanets V., Svoboda J. CpG island protects Rous sarcoma virus-derived vectors integrated into nonpermissive cells from DNA methylation and transcriptional suppression. Proc. Natl. Acad. Sci. USA. 2001;98:565–569. doi: 10.1073/pnas.98.2.565. PubMed DOI PMC

Hejnar J., Plachý J., Geryk J., Machoň O., Trejbalová K., Guntaka R.V., Svoboda J. Inhibition of the rous sarcoma virus long terminal repeat-driven transcription by in vitro methylation: Different sensitivity in permissive chicken cells versus mammalian cells. Virology. 1999;255:171–181. doi: 10.1006/viro.1998.9597. PubMed DOI

Hejnar J., Elleder D., Hájková P., Walter J., Blažková J., Svoboda J. Demethylation of host-cell DNA at the site of avian retrovirus integration. Biochem. Biophys. Res. Commun. 2003;311:641–648. doi: 10.1016/j.bbrc.2003.10.035. PubMed DOI

Lam G., Beemon K. ALV integration-associated hypomethylation at the TERT promoter locus. Viruses. 2018;10:e74. PubMed PMC

Miklík D., Šenigl F., Hejnar J. Proviruses with Long-Term Stable Expression Accumulate in Transcriptionally Active Chromatin Close to the Gene Regulatory Elements: Comparison of ASLV-, HIV- and MLV-Derived Vectors. Viruses. 2018;10:116. doi: 10.3390/v10030116. PubMed DOI PMC

Kauder S.E., Bosque A., Lindqvist A., Planelles V., Verdin E. Epigenetic regulation of HIV-1 latency by cytosine methylation. PloS Pathog. 2009;5:e1000495. doi: 10.1371/journal.ppat.1000495. PubMed DOI PMC

Blažková J., Trejbalová K., Gondois-Rey F., Halfon P., Philibert P., Guiguen A., Verdin E., Olive D., Van Lint C., Hejnar J., et al. CpG methylation controls reactivation of HIV from latency. PLoS Pathog. 2009;5:e1000554. doi: 10.1371/journal.ppat.1000554. PubMed DOI PMC

Darcis G., Das A.T., Berkhout B. Tackling HIV Persistence: Pharmacological versus CRISPR-Based Shock Strategies. Viruses. 2018;10:157. doi: 10.3390/v10040157. PubMed DOI PMC

Elleder D., Pavlíček A., Pačes J., Hejnar J. Preferential integration of human immunodeficiency virus type 1 into genes, cytogenetic R bands and GC-rich DNA regions: Insight from the human genome sequence. FEBS Lett. 2002;517:285–286. doi: 10.1016/S0014-5793(02)02612-1. PubMed DOI

Schroder A.R., Shinn P., Chen H., Berry C., Ecker J.R., Bushman F. HIV-1 Integration in the Human Genome Favors Active Genes and Local Hotspots. Cell. 2002;110:521–529. doi: 10.1016/S0092-8674(02)00864-4. PubMed DOI

Engelman A.N., Singh P.K. Cellular and molecular mechanisms of HIV-1 integration targeting. Cell. Mol. Life Sci. 2018;75:2491–2507. doi: 10.1007/s00018-018-2772-5. PubMed DOI PMC

Debyser Z., Vansant G., Bruggemans A., Janssens J., Christ F. Insight in HIV integration site selection provides a block and lock strategy for a functional cure of HIV infection. Viruses. 2019;11:12. doi: 10.3390/v11010012. PubMed DOI PMC

Rumlová M., Křížová I., Zelenka J., Weber J., Ruml T. Does BCA3 Play a Role in the HIV-1 Replication Cycle? Viruses. 2018;10:212. doi: 10.3390/v10040212. PubMed DOI PMC

Grznárová Prokšová P., Lipov J., Zelenka J., Hunter E., Langerová H., Rumlová M., Ruml T. Mason-Pfizer Monkey Virus Envelope Glycoprotein Cycling and Its Vesicular Co-Transport with Immature Particles. Viruses. 2018;10:575. doi: 10.3390/v10100575. PubMed DOI PMC

Bejarano D.A., Puertas M.C., Börner K., Martinez-Picado J., Müller B., Kräusslich H.-G. Detailed Characterization of Early HIV-1 Replication Dynamics in Primary Human Macrophages. Viruses. 2018;10:620. doi: 10.3390/v10110620. PubMed DOI PMC

Font-Haro A., Janovec V., Hofman T., Machala L., Jilich D., Mělková Z., Weber J., Trejbalová K., Hirsch I. Expression of TIM-3 on Plasmacytoid Dendritic Cells as a Predictive Biomarker of Decline in HIV-1 RNA Level during ART. Viruses. 2018;10:154. doi: 10.3390/v10040154. PubMed DOI PMC

Matoušková M., Blažková J., Pajer P., Pavliček A., Hejnar J. CpG methylation suppresses transcriptional activity of human syncytin-1 in non-placental tissues. Exp. Cell Res. 2006;312:1011–1120. doi: 10.1016/j.yexcr.2005.12.010. PubMed DOI

Trejbalová K., Blažková J., Matoušková M., Kučerová D., Pecnová L., Vernerová Z., Heráček J., Hirsch I., Hejnar J. Epigenetic regulation of transcription and splicing of syncytins, fusogenic glycoproteins of retroviral origin. Nucleic Acids Res. 2011;39:8728–8739. doi: 10.1093/nar/gkr562. PubMed DOI PMC

Benešová M., Trejbalová K., Kovářová D., Vernerová Z., Hron T., Kučerová D., Hejnar J. DNA hypomethylation and aberrant expression of the human endogenous retrovirus ERVWE1/syncytin-1 in seminomas. Retrovirology. 2017;14:20. doi: 10.1186/s12977-017-0342-9. PubMed DOI PMC

Pavlíček A., Pačes J., Elleder D., Hejnar J. Processed pseudogenes of human endogenous retroviruses generated by LINEs: Their integration, stability, and distribution. Genome Res. 2002;12:391–399. doi: 10.1101/gr.216902. PubMed DOI PMC

Hron T., Fábryová H., Pačes J., Elleder D. Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates. Retrovirology. 2014;11:e84. PubMed PMC

Hron T., Farkašová H., Padhi A., Pačes J., Elleder D. Life History of the Oldest Lentivirus: Characterization of ELVgv Integrations in the Dermopteran Genome. Mol. Biol. Evol. 2016;33:2659–2669. doi: 10.1093/molbev/msw149. PubMed DOI

Farkašová H., Hron T., Pačes J., Hulva P., Benda P., Gifford R.J., Elleder D. Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae) Proc. Natl. Acad. Sci. USA. 2017;114:3145–3150. doi: 10.1073/pnas.1621224114. PubMed DOI PMC

Hron T., Farkašová H., Gifford R.J., Benda P., Hulva P., Görföl T., Pačes J., Elleder D. Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae) Viruses. 2018;10:185. doi: 10.3390/v10040185. PubMed DOI PMC

Yao Y., Zhang Y., Tang N., Pedrera M., Shen Z., Nair V. Inhibition of v-rel-Induced Oncogenesis through microRNA Targeting. Viruses. 2018;10:242. doi: 10.3390/v10050242. PubMed DOI PMC

Plachý J. The chicken—A laboratory animal of the class Aves. Folia Biol. 2000;46:17–23. PubMed

. Hron T., Pajer P., Pačes J., Bartůněk P., Elleder D. Hidden genes in birds. Genome Biol. 2015;16:e164. doi: 10.1186/s13059-015-0724-z. PubMed DOI PMC

. Rohde F., Schusser B., Hron T., Farkašová H., Plachý J., Härtle S., Hejnar J., Elleder D., Kaspers B. Characterization of Chicken Tumor Necrosis Factor-α, a Long Missed Cytokine in Birds. Front. Immunol. 2018;9:e605. doi: 10.3389/fimmu.2018.00605. PubMed DOI PMC

Liu W., Qiu X., Song C., Sun Y., Meng C., Liao Y., Tan L., Ding Z., Liu X., Ding C. Deep Sequencing-Based Transcriptome Profiling Reveals Avian Interferon-Stimulated Genes and Provides Comprehensive Insight into Newcastle Disease Virus-Induced Host Responses. Viruses. 2018;10:162. doi: 10.3390/v10040162. PubMed DOI PMC

Schusser B., Collarini E.J., Yi H., Izquierdo S.M., Fesler J., Pedersen D., Klasing K.C., Kaspers B., Harriman W.D., van de Lavoir M.C., et al. Immunoglobulin knockout chickens via efficient homologous recombination in primordial germ cells. Proc. Natl. Acad. Sci. USA. 2013;110:20170–20175. doi: 10.1073/pnas.1317106110. PubMed DOI PMC

Trefil P., Aumann D., Koslová A., Mucksová J., Benešová B., Kalina J., Wurmser C., Fries R., Elleder D., Schusser B., et al. Male fertility restored by transplanting primordial germ cells into testes: A new way towards efficient transgenesis in chicken. Sci. Rep. 2017;7:e14246. doi: 10.1038/s41598-017-14475-w. PubMed DOI PMC

Svoboda J., Svoboda J. The Platonic Receptacle (Hypodoché), Whitehead’s Philosophy, and Genome Evolution. Viruses. 2017;9:381. doi: 10.3390/v9120381. PubMed DOI PMC