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Items: 1 to 50 of 65

1.

Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

Adriaenssens EM, Sullivan MB, Knezevic P, van Zyl LJ, Sarkar BL, Dutilh BE, Alfenas-Zerbini P, Łobocka M, Tong Y, Brister JR, Moreno Switt AI, Klumpp J, Aziz RK, Barylski J, Uchiyama J, Edwards RA, Kropinski AM, Petty NK, Clokie MRJ, Kushkina AI, Morozova VV, Duffy S, Gillis A, Rumnieks J, Kurtböke İ, Chanishvili N, Goodridge L, Wittmann J, Lavigne R, Jang HB, Prangishvili D, Enault F, Turner D, Poranen MM, Oksanen HM, Krupovic M.

Arch Virol. 2020 Mar 11. doi: 10.1007/s00705-020-04577-8. [Epub ahead of print]

PMID:
32162068
2.

Asymmetrical Flow Field-Flow Fractionation on Virus and Virus-Like Particle Applications.

Eskelin K, Poranen MM, Oksanen HM.

Microorganisms. 2019 Nov 12;7(11). pii: E555. doi: 10.3390/microorganisms7110555. Review.

3.

In vitro production of synthetic viral RNAs and their delivery into mammalian cells and the application of viral RNAs in the study of innate interferon responses.

Jiang M, Österlund P, Poranen MM, Julkunen I.

Methods. 2019 Nov 1. pii: S1046-2023(19)30238-5. doi: 10.1016/j.ymeth.2019.10.013. [Epub ahead of print] Review.

PMID:
31682923
4.

Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus.

Ilca SL, Sun X, El Omari K, Kotecha A, de Haas F, DiMaio F, Grimes JM, Stuart DI, Poranen MM, Huiskonen JT.

Nature. 2019 Jun;570(7760):252-256. doi: 10.1038/s41586-019-1229-9. Epub 2019 May 29.

PMID:
31142835
5.

Structural comparison strengthens the higher-order classification of proteases related to chymotrypsin.

Mönttinen HAM, Ravantti JJ, Poranen MM.

PLoS One. 2019 May 17;14(5):e0216659. doi: 10.1371/journal.pone.0216659. eCollection 2019.

6.

Microbial production of lipid-protein vesicles using enveloped bacteriophage phi6.

Lyytinen OL, Starkova D, Poranen MM.

Microb Cell Fact. 2019 Feb 7;18(1):29. doi: 10.1186/s12934-019-1079-z.

7.

Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology.

Mäntynen S, Sundberg LR, Oksanen HM, Poranen MM.

Viruses. 2019 Jan 18;11(1). pii: E76. doi: 10.3390/v11010076. Review.

8.

Efficient Inhibition of Avian and Seasonal Influenza A Viruses by a Virus-Specific Dicer-Substrate Small Interfering RNA Swarm in Human Monocyte-Derived Macrophages and Dendritic Cells.

Jiang M, Österlund P, Westenius V, Guo D, Poranen MM, Bamford DH, Julkunen I.

J Virol. 2019 Feb 5;93(4). pii: e01916-18. doi: 10.1128/JVI.01916-18. Print 2019 Feb 15.

9.
10.

Dual Role of a Viral Polymerase in Viral Genome Replication and Particle Self-Assembly.

Sun X, Ilca SL, Huiskonen JT, Poranen MM.

mBio. 2018 Oct 2;9(5). pii: e01242-18. doi: 10.1128/mBio.01242-18.

11.

RNA Interference as a Prospective Tool for the Control of Human Viral Infections.

Levanova A, Poranen MM.

Front Microbiol. 2018 Sep 11;9:2151. doi: 10.3389/fmicb.2018.02151. eCollection 2018. Review.

12.

Application of steric exclusion chromatography on monoliths for separation and purification of RNA molecules.

Levanova A, Poranen MM.

J Chromatogr A. 2018 Nov 2;1574:50-59. doi: 10.1016/j.chroma.2018.08.063. Epub 2018 Aug 31.

13.

A Systems Approach to Study Immuno- and Neuro-Modulatory Properties of Antiviral Agents.

Zusinaite E, Ianevski A, Niukkanen D, Poranen MM, Bjørås M, Afset JE, Tenson T, Velagapudi V, Merits A, Kainov DE.

Viruses. 2018 Aug 12;10(8). pii: E423. doi: 10.3390/v10080423. Review.

14.

Asymmetrical flow field-flow fractionation in purification of an enveloped bacteriophage ϕ6.

Lampi M, Oksanen HM, Meier F, Moldenhauer E, Poranen MM, Bamford DH, Eskelin K.

J Chromatogr B Analyt Technol Biomed Life Sci. 2018 Sep 15;1095:251-257. doi: 10.1016/j.jchromb.2018.07.008. Epub 2018 Jul 10.

PMID:
30098552
15.

Synthetic biology approach for plant protection using dsRNA.

Niehl A, Soininen M, Poranen MM, Heinlein M.

Plant Biotechnol J. 2018 Feb 26. doi: 10.1111/pbi.12904. [Epub ahead of print]

16.

Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee.

Adriaenssens EM, Wittmann J, Kuhn JH, Turner D, Sullivan MB, Dutilh BE, Jang HB, van Zyl LJ, Klumpp J, Lobocka M, Moreno Switt AI, Rumnieks J, Edwards RA, Uchiyama J, Alfenas-Zerbini P, Petty NK, Kropinski AM, Barylski J, Gillis A, Clokie MRC, Prangishvili D, Lavigne R, Aziz RK, Duffy S, Krupovic M, Poranen MM, Knezevic P, Enault F, Tong Y, Oksanen HM, Rodney Brister J.

Arch Virol. 2018 Apr;163(4):1125-1129. doi: 10.1007/s00705-018-3723-z. Epub 2018 Jan 22. No abstract available.

PMID:
29356990
17.

Recognition of six additional cystoviruses: Pseudomonas virus phi6 is no longer the sole species of the family Cystoviridae.

Mäntynen S, Sundberg LR, Poranen MM.

Arch Virol. 2018 Apr;163(4):1117-1124. doi: 10.1007/s00705-017-3679-4. Epub 2017 Dec 19.

PMID:
29260329
18.

ICTV Virus Taxonomy Profile: Cystoviridae.

Poranen MM, Mäntynen S, Ictv Report Consortium.

J Gen Virol. 2017 Oct;98(10):2423-2424. doi: 10.1099/jgv.0.000928. Epub 2017 Sep 20.

19.

Topical treatment of herpes simplex virus infection with enzymatically created siRNA swarm.

Paavilainen H, Lehtinen J, Romanovskaya A, Nygårdas M, Bamford DH, Poranen MM, Hukkanen V.

Antivir Ther. 2017;22(7):631-637. doi: 10.3851/IMP3153. Epub 2017 Mar 13.

PMID:
28287396
20.

Double-stranded RNA virus outer shell assembly by bona fide domain-swapping.

Sun Z, El Omari K, Sun X, Ilca SL, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT.

Nat Commun. 2017 Mar 13;8:14814. doi: 10.1038/ncomms14814.

21.

Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee.

Adriaenssens EM, Krupovic M, Knezevic P, Ackermann HW, Barylski J, Brister JR, Clokie MR, Duffy S, Dutilh BE, Edwards RA, Enault F, Jang HB, Klumpp J, Kropinski AM, Lavigne R, Poranen MM, Prangishvili D, Rumnieks J, Sullivan MB, Wittmann J, Oksanen HM, Gillis A, Kuhn JH.

Arch Virol. 2017 Apr;162(4):1153-1157. doi: 10.1007/s00705-016-3173-4. Epub 2016 Dec 31. No abstract available.

PMID:
28040838
22.

Single-molecule measurements of viral ssRNA packaging.

Hanhijärvi KJ, Ziedaite G, Bamford DH, Hæggström E, Poranen MM.

RNA. 2017 Jan;23(1):119-129. Epub 2016 Nov 1.

23.

Inhibition of clinical pathogenic herpes simplex virus 1 strains with enzymatically created siRNA pools.

Paavilainen H, Lehtinen J, Romanovskaya A, Nygårdas M, Bamford DH, Poranen MM, Hukkanen V.

J Med Virol. 2016 Dec;88(12):2196-2205. doi: 10.1002/jmv.24578. Epub 2016 May 30.

PMID:
27191509
24.

Initiation of RNA Polymerization and Polymerase Encapsidation by a Small dsRNA Virus.

Collier AM, Lyytinen OL, Guo YR, Toh Y, Poranen MM, Tao YJ.

PLoS Pathog. 2016 Apr 14;12(4):e1005523. doi: 10.1371/journal.ppat.1005523. eCollection 2016 Apr.

25.

Common Structural Core of Three-Dozen Residues Reveals Intersuperfamily Relationships.

Mönttinen HA, Ravantti JJ, Poranen MM.

Mol Biol Evol. 2016 Jul;33(7):1697-710. doi: 10.1093/molbev/msw047. Epub 2016 Mar 1.

PMID:
26931141
26.

K2 killer toxin-induced physiological changes in the yeast Saccharomyces cerevisiae.

Orentaite I, Poranen MM, Oksanen HM, Daugelavicius R, Bamford DH.

FEMS Yeast Res. 2016 Mar;16(2):fow003. doi: 10.1093/femsyr/fow003. Epub 2016 Jan 26.

PMID:
26818855
27.

Immuno-modulating properties of saliphenylhalamide, SNS-032, obatoclax, and gemcitabine.

Söderholm S, Anastasina M, Islam MM, Tynell J, Poranen MM, Bamford DH, Stenman J, Julkunen I, Šaulienė I, De Brabander JK, Matikainen S, Nyman TA, Saelens X, Kainov D.

Antiviral Res. 2016 Feb;126:69-80. doi: 10.1016/j.antiviral.2015.12.011. Epub 2015 Dec 29.

28.

Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.

Ilca SL, Kotecha A, Sun X, Poranen MM, Stuart DI, Huiskonen JT.

Nat Commun. 2015 Nov 4;6:8843. doi: 10.1038/ncomms9843.

29.

Backtracking behavior in viral RNA-dependent RNA polymerase provides the basis for a second initiation site.

Dulin D, Vilfan ID, Berghuis BA, Poranen MM, Depken M, Dekker NH.

Nucleic Acids Res. 2015 Dec 2;43(21):10421-9. doi: 10.1093/nar/gkv1098. Epub 2015 Oct 22.

30.

Elongation-Competent Pauses Govern the Fidelity of a Viral RNA-Dependent RNA Polymerase.

Dulin D, Vilfan ID, Berghuis BA, Hage S, Bamford DH, Poranen MM, Depken M, Dekker NH.

Cell Rep. 2015 Feb 17;10(6):983-992. doi: 10.1016/j.celrep.2015.01.031. Epub 2015 Feb 12.

31.

New enveloped dsRNA phage from freshwater habitat.

Mäntynen S, Laanto E, Kohvakka A, Poranen MM, Bamford JKH, Ravantti JJ.

J Gen Virol. 2015 May;96(Pt 5):1180-1189. doi: 10.1099/vir.0.000063. Epub 2015 Jan 22.

PMID:
25614591
32.

MAP kinase p38α regulates type III interferon (IFN-λ1) gene expression in human monocyte-derived dendritic cells in response to RNA stimulation.

Jiang M, Österlund P, Fagerlund R, Rios DN, Hoffmann A, Poranen MM, Bamford DH, Julkunen I.

J Leukoc Biol. 2015 Feb;97(2):307-20. doi: 10.1189/jlb.2A0114-059RR. Epub 2014 Dec 3.

PMID:
25473098
33.

Efficient double-stranded RNA production methods for utilization in plant virus control.

Voloudakis AE, Holeva MC, Sarin LP, Bamford DH, Vargas M, Poranen MM, Tenllado F.

Methods Mol Biol. 2015;1236:255-74. doi: 10.1007/978-1-4939-1743-3_19.

PMID:
25287509
34.

Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases.

Mönttinen HA, Ravantti JJ, Stuart DI, Poranen MM.

Mol Biol Evol. 2014 Oct;31(10):2741-52. doi: 10.1093/molbev/msu219. Epub 2014 Jul 24.

PMID:
25063440
35.

Innate responses to small interfering RNA pools inhibiting herpes simplex virus infection in astrocytoid and epithelial cells.

Paavilainen H, Romanovskaya A, Nygårdas M, Bamford DH, Poranen MM, Hukkanen V.

Innate Immun. 2015 May;21(4):349-57. doi: 10.1177/1753425914537921. Epub 2014 Jul 3.

PMID:
24996409
36.

Electrostatic interactions drive the self-assembly and the transcription activity of the Pseudomonas phage ϕ6 procapsid.

Sun X, Bamford DH, Poranen MM.

J Virol. 2014 Jun;88(12):7112-6. doi: 10.1128/JVI.00467-14. Epub 2014 Apr 9.

37.

Rescue of maturation off-pathway products in the assembly of Pseudomonas phage φ 6.

Sun X, Pirttimaa MJ, Bamford DH, Poranen MM.

J Virol. 2013 Dec;87(24):13279-86. doi: 10.1128/JVI.02285-13. Epub 2013 Oct 2.

38.

Tracking in atomic detail the functional specializations in viral RecA helicases that occur during evolution.

El Omari K, Meier C, Kainov D, Sutton G, Grimes JM, Poranen MM, Bamford DH, Tuma R, Stuart DI, Mancini EJ.

Nucleic Acids Res. 2013 Nov;41(20):9396-410. doi: 10.1093/nar/gkt713. Epub 2013 Aug 11.

39.

High-throughput purification of double-stranded RNA molecules using convective interaction media monolithic anion exchange columns.

Romanovskaya A, Sarin LP, Bamford DH, Poranen MM.

J Chromatogr A. 2013 Feb 22;1278:54-60. doi: 10.1016/j.chroma.2012.12.050. Epub 2012 Dec 29.

PMID:
23332782
40.

Enzymatically produced pools of canonical and Dicer-substrate siRNA molecules display comparable gene silencing and antiviral activities against herpes simplex virus.

Romanovskaya A, Paavilainen H, Nygårdas M, Bamford DH, Hukkanen V, Poranen MM.

PLoS One. 2012;7(11):e51019. doi: 10.1371/journal.pone.0051019. Epub 2012 Nov 30.

41.

Probing, by self-assembly, the number of potential binding sites for minor protein subunits in the procapsid of double-stranded RNA bacteriophage Φ6.

Sun X, Bamford DH, Poranen MM.

J Virol. 2012 Nov;86(22):12208-16. doi: 10.1128/JVI.01505-12. Epub 2012 Aug 29.

42.

Incoming influenza A virus evades early host recognition, while influenza B virus induces interferon expression directly upon entry.

Österlund P, Strengell M, Sarin LP, Poranen MM, Fagerlund R, Melén K, Julkunen I.

J Virol. 2012 Oct;86(20):11183-93. Epub 2012 Aug 1.

43.

Evidence for a non-catalytic ion-binding site in multiple RNA-dependent RNA polymerases.

Mönttinen HA, Ravantti JJ, Poranen MM.

PLoS One. 2012;7(7):e40581. doi: 10.1371/journal.pone.0040581. Epub 2012 Jul 11.

44.

The C-terminal priming domain is strongly associated with the main body of bacteriophage ϕ6 RNA-dependent RNA polymerase.

Sarin LP, Wright S, Chen Q, Degerth LH, Stuart DI, Grimes JM, Bamford DH, Poranen MM.

Virology. 2012 Oct 10;432(1):184-93. doi: 10.1016/j.virol.2012.05.035. Epub 2012 Jul 6.

45.

Bacteriophage ϕ6 nucleocapsid surface protein 8 interacts with virus-specific membrane vesicles containing major envelope protein 9.

Sarin LP, Hirvonen JJ, Laurinmäki P, Butcher SJ, Bamford DH, Poranen MM.

J Virol. 2012 May;86(9):5376-9. doi: 10.1128/JVI.00172-12. Epub 2012 Feb 29.

46.

Assembly of large icosahedral double-stranded RNA viruses.

Poranen MM, Bamford DH.

Adv Exp Med Biol. 2012;726:379-402. doi: 10.1007/978-1-4614-0980-9_17. Review.

PMID:
22297523
47.

Noncatalytic ions direct the RNA-dependent RNA polymerase of bacterial double-stranded RNA virus ϕ6 from de novo initiation to elongation.

Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM.

J Virol. 2012 Mar;86(5):2837-49. doi: 10.1128/JVI.05168-11. Epub 2011 Dec 28.

48.

Innate immune responses in human monocyte-derived dendritic cells are highly dependent on the size and the 5' phosphorylation of RNA molecules.

Jiang M, Osterlund P, Sarin LP, Poranen MM, Bamford DH, Guo D, Julkunen I.

J Immunol. 2011 Aug 15;187(4):1713-21. doi: 10.4049/jimmunol.1100361. Epub 2011 Jul 8.

49.

The DNA/RNA-dependent RNA polymerase QDE-1 generates aberrant RNA and dsRNA for RNAi in a process requiring replication protein A and a DNA helicase.

Lee HC, Aalto AP, Yang Q, Chang SS, Huang G, Fisher D, Cha J, Poranen MM, Bamford DH, Liu Y.

PLoS Biol. 2010 Oct 5;8(10). pii: e1000496. doi: 10.1371/journal.pbio.1000496.

50.

In vitro activities of the multifunctional RNA silencing polymerase QDE-1 of Neurospora crassa.

Aalto AP, Poranen MM, Grimes JM, Stuart DI, Bamford DH.

J Biol Chem. 2010 Sep 17;285(38):29367-74. doi: 10.1074/jbc.M110.139121. Epub 2010 Jul 20.

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