Biocomplex purification

Biocomplex provides purification technologies and expertise specializing in preparative ultracentrifugation, monolithic chromatography and asymmetrical flow field-flow fractionation (AF4). Provided techniques can be used in different combinations to yield high quality samples in quantity. Biosafety level 1 and 2 organisms can be processed.

• Ultracentrifugation combined with swing-out and fixed-angle rotors of different capacities;
• Asymmetrical flow field-flow fractionation (AF4) with online detectors;
• Monolithic ion exchange chromatography;
• Batch mode dynamic light scattering;
• User training, assisted use of instruments, open access for trained users, specialist support and maintenance;
• Project planning;
• Full service packages on sample purification (including analysis of the quality and quantity);
• Collaborative projects;
• Courses in biomolecular complex purification

Ultracentrifugation service

The preparative ultracentrifugation service provides facilities for rate-zonal, equilibrium, flotation and differential centrifugation. It is equipped with a farm of ultracentrifuges as well as swing out and fixed angle rotors with different capacities. We also have instrumentation for gradient making and provide fractionation services. Superspeed centrifuges are available also for the users.

Ultracentrifugation service offers:

• Centrifuges that are regularly serviced;
• Rotors that are regularly inspected by the manufacturer;
• Ultracentrifuge with HEPA filter;
• Piston fractionation of ultracentrifugation tubes using the topdown method with absorbance (A260 and A280) or fluorescence profiling.

Asymmetrical flow field-flow fractionation (AF4) service

AF4 provides size-based separation of sample components. It is applicable for separation of macromolecules, colloids as well as nano- and microparticles. Separation is done in liquid phase without stationary phase.

Biocomplex has an Eclipse NEON AF4 device equipped with five inline detectors. This is the very first new-generation Wyatt FFF-MALS that has been installed in Europe! The premium setup has multiangle (DAWN) and dynamic light scattering (QELS) detectors as well as UV, refractive index (Optilab dRI) and fluorescence detectors. This setup can be used for characterization and purification of samples: the device has automatic and manual sample feeding and a fraction collector. The accompanied software enables simulation of experiments and analysis of the molar mass, size, conformation, conjugation and other physical parameters from experimental data. The service has been supplemented with Mobility EAF4 (Electrical/asymmetrical flow-field flow fractionation) that couples size-based separation to charge-based separation and can be used to determine zeta potential distributions.

The benefits of AF4 are the following:

• Gentle size-based separation in liquid phase;
• Large dynamic size range for separation;
• Rapid analysis time;
• High recovery; 
• Accompanied software: ASTRA enables easy analysis of molar mass and radius; Vision Design enables simulation of experiments for optimal separation.

Dynamic light scattering measurement service

Biocomplex has a DynaPro NanoStar II instrument that enables quick collection of dynamic and static light scattering data in a cuvette for quick testing or using automated data collection for multiple time points or temperature ramp. The accompanied software enables analysis of hydrodynamic size, particle concentration and molar mass in batch mode. 

Chromatography service

CIM® monolithic columns can be utilized for purification of viruses, virus-like particles, extracellular vesicles, nucleic acids, proteins and their complexes. We routinely have weak (DEAE) and strong (QA) anion exchange columns. Please ask for other column types. The benefits of CIM columns are the following:

• Large pore sizes enable entering and binding of large macromolecular complexes to the matrix;
• High flow rates enable fast separation;
• High yields and sample concentrations can be achieved.

• High quality purification of large and fragile macromolecular complexes in quantity;
• Purification based on differences in sedimentation rate (mass, size, shape)  or density (ultracentrifugation), shape or hydrodynamic size (AF4), and surface charge (monoliths);
• Separation and purification of cells, organelles, macromolecules, macromolecular complexes, bacteria, vesicles and viruses etc.
• Analysis of sample quality for size and mass distribution as well as polydisperisty and particle concentration.

Ultracentrifugation

• Six ultracentrifuges of which one has a HEPA filter (Thermo Scientific Sorvall WX Ultra Series);
• Swing-out and fixed angle rotors with different speed and force capacities (Thermo Scientific/Sorvall), see table.
• Instrumentation for gradient making (IBS INTEGRA Biosciences peristaltic pump; BioComp Gradient master)
• Automated BioComp Piston Gradient Fractionator with Triax three wavelength flow cell for UV (A260 and A280) and fluorescence (eGFP or Cy5) profiling. Fractionation utilizes the topdown method where the piston descends from the top, displacing layers through the centre and keeping smooth flow. The method enables minimal disturbation of the gradient. Fractionation and data collection can be performed with:
  • TH641 tubes (SW41, 6*12 ml)
  • AH650 tubes (SW50.1 tubes, 6*5 ml)
  • AH629 (6*36 ml tubes)
• Beckmann Airfuge for fast pelleting of small sample volumes.
  • A-95 fixed angle rotor: 4*450 µl
  • A-110 fixed angle rotor: 6*175 µl

Super-speed centrifugation (Thermo Scientific)

• Sorvall LYNX4000 centrifuge
• Superspeed rotors
  • Fiberlite F20-12x50 LEX, 13 000 rpm
  • Fiberlite F12-6x500 LEX, 8000 rpm 
  • Fiberlite F14-6x250y, 10 000 rpm
  • Fiberlite™ F10-4 x 1000 LEX,  max fill ~900 ml, 10 500 rpm.

Eclipse NEON (Wyatt) with MALS, DLS, dRI, UV and fluoresence detectors

• Analytical and semi-preparative separation channels, dispersion inlet channel for aggregation-prone samples, mobility channel for analysis of surface charge
• Temperature controlled channels (+5°C above ambient temperature, up to +75°C), channel cooling possible for analytical channel
• Ultrafiltration membranes with various MWCOs and materials
  • Regenerated cellulose membranes (MWCOs 2, 10 and 30 kDa);
  • Polyethersulfone membranes (MWCOs 10 and 30 kDa);
• Spacers (various thicknesses)
• DAWN 18 angle multiangle light scattering (MALS) detector with embedded QELS dynamic light scattering (DLS) detector (Wyatt)
• Agilent UV-Vis and Fluoresecence Detectors
• Optilab dRI detector (universal concentration detector, Wyatt)
• Dilution control module (to increase signal intensity at the detectors)
• Fraction collection (temperature controlled)
• Autosampler (temperature controlled) or manual injection
• ASTRA 8.2 and Vision 3.2 software
• Electrical/asymmetric-flow field-flow fractionation (EAF4;Mobility) to measure charge and zeta potential (installed Sept 2022)

DynaPro NanoStar II (Wyatt) 

• Batch mode measurement of static and dynamic light scattering:
  • Size; radius of hydration
  • Particle concentration and size
  • Molar mass and size
• Small sample volumes (~4 ul)
• Dynamics 8 software
• Installed December 2023.

CIM monolithic ion-exchange columns

• DEAE and QA anion exchange columns (BiaSeparations)
• Lab-scale chromatography system (ÄKTAPure 25M installed in October 2019)

• Services are open to academic and non-academic national and international users.  
• Services are provided by first come first served principle.   
• New! Project requests and services are requested via iLAB https://hilife-infra.ilab.agilent.com/service_center/show_external/3753/instructhilife. To start a project: Register to iLAB and fill in a Project registration form (Request services -->Select Biocomplex --> Initiate request). Each user needs to fill in the form. Form will be checked and accepted by the core.
• Instruct-HiLIFE reserves the right to ensure that the proposed project is technically and scientifically feasible.  
• Instruct-HiLIFE reserves the right to change the fees for the services and instrument time without further notice. Cancellation fee may apply for unused reservations.  
• Instruct-HiLIFE personnel may cancel the instrument time with short notice in case of instrument failure. Such reservations are not billed.  
• Researchers from Instruct-ERIC member countries can apply for access through Instruct ERIC, in which case the access can be financially supported;   
• It is the user's responsibility to ensure that the safety regulations are followed. This applies to instrument use and to the samples studied. Deviation from the rules will lead to restrictions on using the Instruct-HiLIFE facilities.  
• Biocomplex facilities are classified as Biosafety level 2 laboratories.  
• It is the user's responsibility to ensure that the user has the necessary permits in place (GMO etc.) If you are working with genetically modified organisms, you need to have permits for the intended to work with the specific GMO at the Instruct-HiLIFE facilities;  
• User is responsible for informing Instruct-HiLIFE, when the data is published.   
• User agrees to acknowledge Instruct-HiLIFE in the upcoming publications and theses with the following text:  
•      “The facilities and expertise of the Instruct-HiLIFE Biocomplex unit at the University of Helsinki, a member of Instruct-ERIC Centre Finland, FINStruct, and Biocenter Finland are gratefully acknowledged."  
• Biocomplex keeps the data for 1 month after the end of the experiments. User owns the data collected.  
• Biocomplex stores the samples for 1 month after the end of the experiments.  
• Instruct-HiLIFE may use the information on the registration form for its reporting, e.g. to the host organization, Ministry, the Academy of Finland and Instruct-ERIC.  
   

Publications with acknowledgements to the Biocomplex Unit (2017 onwards)

2024

• Henderikx RJM, Mann D, Domanska A, Dong J, Shahzad S, Lak B, Filopoulou A, Ludig D, Grininger M, Momoh J, Laanto E, Oksanen HM, Bisikalo K, Williams PA, Butcher SJ, Peters PJ, Beulen BWAMM. 2024. VitroJet: new features and case studies. Acta Crystallogr D Struct Biol. doi: 10.1107/S2059798324001852. PMID: 38488730.
• Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. 2024. Archaeal virus entry and egress. Microlife. 5:uqad048. doi: 10.1093/femsml/uqad048. PMID: 38234448.

• Levanova AA, Poranen MM. 2024. Utilization of Bacteriophage phi6 for the Production of High-Quality Double-Stranded RNA Molecules. Viruses. 16(1):166. doi: 10.3390/v16010166. PMID: 38275976.

   

2023

• Atanasova N, Salokas J, Sofieva S, Oksanen LM, Sanmark E, Malmgren R, Kuula J, Purhonen R, Bamford D, Romantschuk M. 2023. Evaluating the Effect of Coated Filters and Prefilters on the Infectivity and Concentration of Aerosolized Phi6 Virus. Available at SSRN 4339966.
• De S, Nguyen HM, Liljeström V, Mäkinen K, Kostiainen MA, Vapaavuori J. 2023. Potato virus A particles - A versatile material for self-assembled nanopatterned surfaces. Virology 578:103-110.
• Demina TA, Dyall-Smith M, Jalasvuori M, Du S, Oksanen HM. 2023. ICTV Virus Taxonomy Profile: Sphaerolipoviridae 2023. J. Gen. Virol. 104(3)
• Laanto E, Oksanen HM. Three phages from a boreal lake during ice cover infecting Xylophilus, Caulobacter, and Polaromonas species. Viruses 15(2):307.
• Lampi M, Gregorova P, Qasim MS, Ahlblad NC, Sarin LP. 2023. Bacteriophage Infection of the Marine Bacterium Shewanella glacialimarina Induces Dynamic Changes in tRNA Modifications. Microorganisms 11(2):355.
• Lasanen T, Frejborg F, Lund L, Nyman M, Orpana J, Habib H, Alaollitervo S, Levanova A, Poranen MM, Hukkanen V, Kalke K. 2023. Single therapeutic dose of an antiviral UL29 siRNA swarm diminishes symptoms and viral load of mice infected intranasally with HSV‐1. Smart Medicine 2:e20230009.
• Liu Y, Du S, Chen X, Dyall-Smith M, Jalasvuori M, Oksanen HM. 2023. ICTV Virus Taxonomy Profile: Simuloviridae 2023. J. Gen. Virol. 104(4)
• Malmgren R, Välimaa H, Oksanen L, Sanmark E, Nikuri P, Heikkilä P, Hakala J, Ahola A, Yli-Urpo S, Palomäki V, Asmi E, Sofieva S, Rostedt A, Laitinen S, Romantschuk M, Sironen T, Atanasova N, Paju S, Lahdentausta-Suomalainen L. 2023. High-volume evacuation mitigates viral aerosol spread in dental procedures. Sci Rep. 13:18984.
• Mäntynen S, Salomaa MM, Poranen MM. 2023. Diversity and Current Classification of dsRNA Bacteriophages. Viruses. 15(11):2154. doi: 10.3390/v15112154. PMID: 38005832.
• Norppa AJ, Chowdhury I, van Rooijen LE, Ravantti JJ, Snel B, Varjosalo M, Frilander MJ. 2023. Distinct functions for the paralogous RBM41 and U11/U12-65K proteins in the minor spliceosome. bioRxiv doi: https://doi.org/10.1101/2023.10.12.562036.
• Saari H, Pusa R, Marttila H, Yliperttula M, Laitinen S. 2023. Development of tandem cation exchange chromatography for high purity extracellular vesicle isolation: The effect of ligand steric availability. J Chromatogr A. 1707:464293.
• Sanmark E, Kuula J, Laitinen S, Oksanen LM, Bamford DH, Atanasova NS. 2023. Safe use of PHI6 IN the experimental studies. Heliyon 9 e13565.
• Schwarzer S, Rodrigues-Franco M, Hackl T, Oksanen HM, Quax TEF. 2023. Archaeal host cell recognition and viral binding of HFTV1 to its Haloferax host. mBio 19:e0183322.
• Siddell SG, Smith DB, Adriaenssens E, Alfenas-Zerbini P, Dutilh BE, Garcia ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Mushegian AR, Oksanen HM, Robertson DL, Rubino L,  Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme A-M, Varsani A, Zerbini FM. 2023. Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV). J. Gen. Virol. 104(5)
• Simmonds P, Adriaenssens EM, Zerbini FM, Abrescia NGA, Aiewsakun P, Alfenas-Zerbini P, Bao Y, Barylski J, Drosten C, Duffy S, Duprex WP, Dutilh BE, Elena SF, García ML, Junglen S, Katzourakis A, Koonin EV, Krupovic M, Kuhn JH, Lambert AJ, Lefkowitz EJ, Łobocka M, Lood C, Mahony J, Meier-Kolthoff JP, Mushegian AR, Oksanen HM, Poranen MM, Reyes-Muñoz A, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Siddell S, Skern T, Smith DB, Sullivan MB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A, Vasilakis N. 2023. Four principles to establish a universal virus taxonomy. PLoS Biol. 21:e3001922. 
• Turner D, Shkoporov AN, Lood C, Millard AD, Dutilh BE, Alfenas-Zerbini P, van Zyl LJ, Aziz RK, Oksanen HM, Poranen MM, Kropinski AM, Barylski J, Brister JR, Chanisvili N, Edwards RA, Enault F, Gillis A, Knezevic P, Krupovic M, Kurtböke I, Kushkina A, Lavigne R, Lehman S, Lobocka M, Moraru C, Moreno Switt A, Morozova V, Nakavuma J, Reyes Muñoz A, Rūmnieks J, Sarkar BL, Sullivan MB, Uchiyama J, Wittmann J, Yigang T, Adriaenssens EM. 2023. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch Virol. 168:74.
• Zerbini FM, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Curtis Hendrickson R, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. 2023. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023). Arch Virol. 168:175

2022

• Aguirre Sourrouille Z, Schwarzer S, Lequime S, Oksanen HM, Quax TEF. 2022. The Viral Susceptibility of the Haloferax Species. Viruses, 4(6):1344. doi: 10.3390/v14061344.
• Andersson Schönn M, Eskelin K, Bamford DH, Poranen MM, Unoson C, Oksanen HM. 2022. Inline-tandem purification of viruses from cell lysate by agarose-based chromatography. J. Chrom. B. 1192, 123140.
• Domanska A, Plavec Z, Ruokolainen V, Löflund B, Marjomäki V, Butcher SJ. 2022. Structural studies reveal that endosomal cations promote formation of infectious CVA9 A particles, facilitating RNA and VP4 release.J Virol 96(24):e0136722, doi: 10.1128/jvi.01367-22.
• Eskelin K, Lampi M, Coustau C, Imani J, Kogel K-H, Poranen MM. 2022. Analysis and purification of ssRNA and dsRNA molecules using asymmetrical flow field flow fractionation. J. Chrom. A. 1683; 463525. https://doi.org/10.1016/j.chroma.2022.463525.
• Eskelin K, Oksanen HM. 2022. Archaeal viruses: production of virus particles and vesicle-like viruses and purification using asymmetrical flow field-flow fractionation. Methods Mol Biol, 2522:449-465. doi:10.1007/978-1-0716-2445-6_31.
• Demina TA, Luhtanen AM, Roux S, Oksanen HM. 2022. Virus-host interactions and genetic diversity of Antarctic sea ice bacteriophages. mBio, 13(3):e0065122. doi: 10.1128/mbio.00651-22.
• Kalke K, Lund LM, Nyman MC, Levanova AA, Urtti A, Poranen MM, Hukkanen V, Paavilainen H. 2022. Swarms of chemically modified antiviral siRNA targeting herpes simplex virus infection in human corneal epithelial cells. PLoS Pathog. 18(7):e1010688. doi: 10.1371/journal.ppat.1010688.
• Levanova AA, Lampi M, Kalke K, Hukkanen V, Poranen MM, Eskelin K. 2022. Native RNA purification method for small RNA molecules based on asymmetrical flow field-flow fractionation. Pharmaceuticals 5(2), 261; https://doi.org/10.3390/ph15020261
• Liu Y, Dyall-Smith M, Oksanen HM and ICTV Report Consortium. 2022. ICTV virus taxonomy profile: Pleolipoviridae 2022. J. Gen. Virol. 103.
• Oksanen L, Auvinen M, Kuula J, Malmgren R, Romantschuk M, Hyvärinen A, Laitinen S, Maunula L, Sanmark E, Geneid A, Sofieva S. 2022. Combining Phi6 as a surrogate virus and computational large‐eddy simulations to study airborne transmission of SARS‐CoV‐2 in a restaurant. Indoor air 32(11):e13165.
• Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Dempsey DM, Dutilh BE, García ML, Curtis Hendrickson R, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A, Zerbini FM. 2022. Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022). Arch Virol. 167:2429-2440
• Zerbini FM, Siddell SG, Mushegian AR, Walker PJ, Lefkowitz EJ, Adriaenssens EM, Alfenas-Zerbini P, Dutilh BE, García ML, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Oksanen HM, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Suzuki N, Van Doorslaer K, Vandamme AM, Varsani A. 2022. Differentiating between viruses and virus species by writing their names correctly. Arch Virol. 167, 1231–1234.

2021

• Adams MP, Atanasova NS, Sofieva S, Ravantti J, Heikkinen A, Brasseur Z, Duplissy J, Bamford DH, Murray BJ. 2021. Ice nucleation by viruses and their potential for cloud glaciation. Biogeosciences 18:4431–4444.
• Duyvesteyn HME, Santos-Pérez I, Peccati F, Martinez-Castillo A, Walter TS, Reguera D, Goñi FM, Jiménez-Osés G, Oksanen HM, Stuart DI, Abrescia NGA. 2021. Bacteriophage PRD1 as a nanoscaffold for drug loading. Nanoscale. 13:19875-19883.
• Demina T, Oksanen HM. 2021. Euryarchaeal viruses. In M. Zuckerman, & DH. Bamford (Eds.), Encyclopedia of Virology (4 ed., Vol. 4, pp. 368-379). Academic Press. https://doi.org/10.1016/B978-0-12-809633-8.20989-8. Eskelin K, Oksanen HM, Poranen MM. 2021. Sample carryover and cleaning procedures for asymmetrical flow field-flow fractionation instrument. J Chromatogr B. 1181:122920. doi: 10.1016/j.jchromb.2021.122920.
• Eskelin , K., & Oksanen, H. M. 2021. Isolating, culturing, and purifying viruses with a focus on bacterial and archaeal viruses. In M. Zuckerman, & DH. Bamford (Eds.), Encyclopedia of Virology (4 ed., Vol. 1, pp. 162-174). Academic Press. https://doi.org/10.1016/B978-0-12-814515-9.00029-1
• Krupovic M, Turner D, Morozova V, Dyall-Smith M, Oksanen HM, Edwards R, Dutilh BE, Lehman SM, Reyes A, Baquero DP, Sullivan MB, Uchiyama J, Nakavuma J, Barylski J, Young MJ, Du S, Alfenas-Zerbini P, Kushkina A, Kropinski AM, Kurtböke I, Brister JR, Lood C, Sarkar BL, Yigang T, Liu Y, Li Huang L, Wittmann J, Chanishvili N, van Zyl LJ, Rumnieks J, Mochizuki T, Jalasvuori M, Aziz RK, Lobocka M, Stedman KM, Shkoporov A, Gillis A, Peng Xu, Enault F, Knezevic P, Lavigne R, Rhee S-K, Cvirkaite-Krupovic V, Moraru C, Moreno-Switt AI, Poranen MM, Millard A, Prangishvili D, Adriaenssens EM. 2021. Bacterial Viruses Subcommittee and Archaeal Viruses Subcommittee of the ICTV: Update of taxonomy changes in 2021. Arch. Virol. 166:3239-3244.
• Levanova AA, Vainio EJ, Hantula J, Poranen MM (2021). RNA-dependent RNA polymerase from Heterobasidion RNA virus 6 is an active replicase in vitro. Viruses 13, 1738.
• Liu Y, Demina TA, Roux S, Aiewsakun P, Kazlauskas D, Simmonds P, Prangishvili D, Oksanen HM, Krupovic M. 2021. Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes. PLoS Biol. 19:e3001442.
• Liu S, Ladera-Carmona MJ, Poranen M, van Bel AJE, Kogel K-H, Imani J (2021). Evaluation of dsRNA delivery methods for targeting macrophage migration inhibitory factor MIF in RNAi-based aphid control. J Plant Dis Prot 128, 1201-1212.
• Mäntynen S, Laanto E, Oksanen HM, Poranen MM, Díaz-Muñoz SL. 2021. Black box of phage-bacterium interactions – Exploring alternative phage infection strategies. Open Biol. 11:210188.
• Mönttinen HAM, Ravantti JJ, Poranen MM (2021). Structure unveils relationships between RNA virus polymerases. Viruses 13, 313.
• Tittes C, Schwarzer S, Pfeiffer F, Dyall-Smith M, Rodriguez-Franco M, Oksanen HM, Quax TEF. 2021. Cellular and genomic properties of Haloferax gibbonsii LR2-5, the host of euryarchaeal virus HFTV1. Front. Microbiol. 12:625599.
• Schwarzer S, Rodriguez-Franco M, Oksanen HM, Quax TEF. 2021. Growth phase dependent cell shape of Haloarcula. Microorganisms. 9:231.
• Walker PJ, Siddell SG, Lefkowitz EJ, Mushegian AR, Adriaenssens EM, Alfenas-Zerbini P, Davison AJ, Dempsey DM, Dutilh BE, García ML, Harrach B, Harrison RL, Hendrickson RC, Junglen S, Knowles NJ, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Nibert ML, Oksanen HM, Orton RJ, Robertson DL, Rubino L, Sabanadzovic S, Simmonds P, Smith DB, Suzuki N, Van Dooerslaer K, Vandamme AM, Varsani A, Zerbini FM. 2021. Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses. Arch Virol. 166:2633-2648.

2020

• 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. 2020. Taxonomy of prokaryotic viruses: 2018-2019 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. 2020. Arch Virol. 165(5):1253-1260. doi: 10.1007/s00705-020-04577-8.
• Barylski J, Enault F, Dutilh BE, Schuller MB, Edwards RA, Gillis A, Klumpp J, Knezevic P, Krupovic M, Kuhn JH, Lavigne R, Oksanen HM, Sullivan MB, Jang HB, Simmonds P, Aiewsakun P, Wittmann J, Tolstoy I, Brister JR, Kropinski AM, Adriaenssens EM. 2020. Analysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages. Syst Biol. 69(1):110-123. doi: 10.1093/sysbio/syz036.
• De S, Pollari M, Varjosalo M, Mäkinen K. 2020. Association of host protein VARICOSE with HCPro within a multiprotein complex is crucial for RNA silencing suppression, translation, encapsidation and systemic spread of potato virus A infection. PLoS Pathog. 16(10):e1008956. doi: 10.1371/journal.ppat.1008956.
• Demina T, Oksanen HM. 2020. Pleomorphic archaeal viruses: the family Pleolipoviridae is expanding by seven new species. Arch Virol. 165(11):2723-2731.
• Demina T, Krupovic M, Oksanen HM. 2020. Taxonomy proposal 2019: Create seven new species in the genus Betapleolipovirus, in the family Pleolipoviridae. In ICTV Online: International Committee on Taxonomy of Viruses (ICTV). https://ictv.global/
• Jiang M, Österlund P, Poranen MM, Julkunen I. 2020. 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. Methods.  pii: S1046-2023(19)30238-5. doi: 10.1016/j.ymeth.2019.10.013.
• Kalke K, Lehtinen J, Gnjatovic J, Lund LM, Nyman MC, Paavilainen H, Orpana J, Lasanen T, Frejborg F, Levanova AA, Vuorinen T, Poranen MM, Hukkanen V. 2020. Herpes simplex virus type 1 clinical isolates respond to UL29-targeted siRNA swarm treatment independent of their acyclovir sensitivity. Viruses. 12:1434.
• Krupovic M, Oksanen HM, Prangishvili D, Dyall-Smith ML. 2020. Taxonomy proposal 2019: Create one new family (Halspiviridae), move one unassigned genus (Salterprovirus) to the family and rename the type species. In ICTV Online: International Committee on Taxonomy of Viruses (ICTV).https://ictv.global/
• Laanto E, Mäntynen SS, Sundberg L-R, Kropinski AM, Adriaenssens E, Poranen MM, Oksanen HM. 2020. Taxonomy proposal 2019: Create one new species Flavobacterium virus FLiP, in the new genus Finnlakevirus, in the new family Finnlakeviridae. In ICTV Online: International Committee on Taxonomy of Viruses (ICTV). https://ictv.global/
• Levanova AA, Kalke KM, Lund LM, Sipari N, Sadeghi M, Nyman MC, Paavilainen H, Hukkanen V, Poranen MM. 2020. Enzymatically synthesized 2'-fluoro-modified Dicer-substrate siRNA swarms against herpes simplex virus demonstrate enhanced antiviral efficacy and low cytotoxicity. Antiviral Res. 182:104916. Oksanen HM, Krupovic M. 2020. Taxonomy proposal 2019: Rename the species in the family Pleolipoviridae. In ICTV Online: International Committee on Taxonomy of Viruses (ICTV).
• Mäntynen S, Laanto E, Sundberg LR, Poranen MM, Oksanen HM, Report Consortium I. 2020. ICTV Virus Taxonomy Profile: Finnlakeviridae. J Gen Virol. 101:894-895.
• Saari H, Turunen T, Lõhmus A, Turunen M, Jalasvuori M, Butcher SJ, Ylä-Herttuala S, Viitala T, Cerullo V, Siljander PRM, Yliperttula M. 2020. Extracellular vesicles provide a capsid-free vector for oncolytic adenoviral DNA delivery. Journal of Extracellular Vesicles, 9:1747206, DOI: 10.1080/20013078.2020.
• Seifert M, van Nies P, Papini FS, Arnold JJ, Poranen MM, Cameron CE, Depken M, Dulin D. 2020. Temperature controlled high-throughput magnetic tweezers show striking difference in activation energies of replicating viral RNA-dependent RNA polymerases. Nucleic Acids Res. pii: gkaa233. doi: 10.1093/nar/gkaa233.

2019

• De Colibus L, Roine E, Walter TS, Ilca SL, Wang X, Wang N, Roseman AM, Bamford D, Huiskonen JT, Stuart DI. 2019. Assembly of complex viruses exemplified by a halophilic euryarchaeal virus. Nat Commun. 10:1456. doi:10.1038/s41467-019-09451-z
• Eskelin K, Poranen MM, Oksanen HM. 2019. Asymmetrical Flow Field-Flow Fractionation on Virus and Virus-Like Particle Applications. Microorganisms. 7(11). pii: E555. doi: 10.3390/microorganisms7110555.
• El Omari K, Li S, Kotecha A, Walter TS, Bignon EA, Harlos K, Somerharju P, De Haas F, Clare DK, Molin M, Hurtado F, Li M, Grimes JM, Bamford DH, Tischler ND, Huiskonen JT, Stuart DI, Roine E. 2019. The structure of a prokaryotic viral envelope protein expands the landscape of membrane fusion proteins. Nat Commun. 10:846. doi:10.1038/s41467-019-08728-7
• Ilca SL, Sun X, El Omari K, Kotecha A, de Haas F, DiMaio F, Grimes JM, Stuart DI, Poranen MM, Huiskonen JT. 2019. Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus. Nature. 570(7760):252-256. doi: 10.1038/s41586-019-1229-9.
• Jiang M, Österlund P, Poranen MM, Julkunen I. 2019. 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.Methods. pii: S1046-2023(19)30238-5. doi: 10.1016/j.ymeth.2019.10.013.
• Mennesson M, Rydgren E, Lipina T, Sokolowska E, Kulesskaya N, Morello F, Ivakine E, Voikar V, Risbrough V, Partanen J, Hovatta I. 2019. Kainate receptor auxiliary subunit NETO2 is required for normal fear expression and extinction. Neuropsychopharmacology. 44(11):1855-1866. doi: 10.1038/s41386-019-0344-5.
• Mizuno CM, Prajapati B, Lucas-Staat S, Sime-Ngando T, Forterre P, Bamford DH, Prangishvili D, Krupovic M, Oksanen HM. 2019. Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species. Environ Microbiol. 21(6):2129-2147. https://doi.org/10.1111/1462-2920.14604
• Mäntynen S, Sundberg LR, Oksanen HM, Poranen MM. 2019. Half a century of research on membrane-containing bacteriophages: bringing new concepts to modern virology. Viruses 11: e76. https://doi.org/10.3390/v11010076
• Mönttinen HAM, Ravantti JJ, Poranen MM. 2019. Structural comparison strengthens the higher-order classification of proteases related to chymotrypsin. PLoS One. 14(5):e0216659. doi: 10.1371/journal.pone.0216659.
• Lyytinen OL, Starkova D, Poranen MM. 2019. Microbial production of lipid-protein vesicles using enveloped bacteriophage phi6. Microb Cell Fact. 18:29. doi:10.1186/s12934-019-1079-z
• Oksanen HM, and Abrescia NGA. 2019. Membrane-containing icosahedral bacteriophage PRD1: the dawn of viral lineages. In: Advances in Experimental Medicine and Biology - 'Physical Virology - Virus Structure and Mechanics’. Ed: Greber, U. Springer. 1140:85-109. In Press
• Santos-Pérez I, Charro D, Gil-Carton D, Azkargorta M, Elortza F, Bamford DH, Oksanen HM, Abrescia NGA. 2019. Structural basis for assembly of vertical single β-barrel viruses. Nat Commun. 10:1184. doi: 10.1038/s41467-019-08927-2.

2018

• 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. 2018. Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee. Arch Virol. 163:1125-1129.
• Atanasova NS, Demina TA, Krishnam Rajan Shanthi SV, Oksanen HM, and Bamford DH. 2018. Extremely halophilic pleomorphic archaeal virus HRPV9 extends the diversity of pleolipoviruses with integrases. Res Microbiol. 169:500-504 doi: 10.1016/j.resmic.2018.04.004.
• Atanasova NS, Heiniö CHE, Demina T, Bamford DH, Oksanen HM. 2018. The unexplored diversity of pleolipoviruses: the surprising case of two viruses with identical major structural modules. Genes 9:131.
• Azinas S, Bano F, Torca I, Bamford DH, Schwart GA, Esnaola J, Oksanen HM, Richter R, Abrescia NGA. 2018. Membrane-containing virus particle exhibits mechanics of a composite material for genome protection. Nanoscale 10(16):7769-7779.
• Duyvesteyn HME, Ginn HM, Pietilä MK, Wagner A, Hattne J, Grimes JM, Hirvonen E, Evans G, Parsy M-L, Sauter NK, Brewster AS, Huiskonen JT, Stuart DI, Sutton G, Bamford DH. 2018. Towards in cellulo virus crystallography. Sci. Rep. 8:3771.
• Eskelin K, Poranen MM. 2018. Controlled disassembly and purification of functional viral subassemblies using asymmetrical flow field-flow fractionation (AF4). Viruses, 10(11), 579; https://doi.org/10.3390/v10110579
• Lampi M, Oksanen HM, Meier F, Moldenhauer E, Poranen MM, Bamford DH, and Eskelin K. 2018. Asymmetrical flow field-flow fractionation in purification of an enveloped bacteriophage ɸ6. J Chrom B. 1095: 251-257.
• Leigh B, Breitbart M, Oksanen HM, Bamford DH & Dishaw L. 2018. Genome sequence of PM2-like phage Cr39582 induced from Pseudoalteromonas sp. isolated from the gut of Ciona robusta. Genome Announc 6(21): e00368-18.
• Levanova A, Poranen MM. 2018. Application of steric exclusion chromatography on monoliths for separation and purification of RNA molecules. J Chrom A.1574:50-59. doi: 10.1016/j.chroma.2018.08.063.
• Luhtanen AM, Eronen-Rasimus E, Oksanen HM, Tison J-L, Delille B, Dieckmann G, Rintala J-M, Bamford DH. 2018. The first known virus isolates from Antarctic sea ice have complex infection patterns. FEMS Microbiol Ecol. 94:fiy028. 
• Niehl A, Soininen M, Poranen MM, Heinlein M. 2018. Synthetic biology approach for plant protection using dsRNA. Plant Biotechnol J. 16(9): 1679-1687. doi: 10.1111/pbi.12904
• Pietilä MK, van Hemert MJ, Ahola T. 2018. Purification of highly active alphavirus replication complexes demonstrates altered fractionation of multiple cellular membranes. J Virol. 92:e01852-17.
• Sun X, Ilca SL, Huiskonen JT, Poranen MM. 2018. Dual role of a viral polymerase in viral genome replication and particle self-assembly. mBio. 9(5): e01242-18. doi: 10.1128/mBio.01242-18.

2017

• 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. 2017. Taxonomy of prokaryotic viruses: 2016 update from the ICTV bacterial and archaeal viruses subcommittee. Arch. Virol. 162:1153-1157.
• Coloma SE, Dienstbier A, Bamford DH, Sivonen K, Roine E, Hiltunen T. 2017. Newly isolated Nodularia phage influences cyanobacterial community dynamics. Environ. Microbiol. 19:273-286.
• Demina TA, Pietilä MK, Svirskaitė J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM. 2017. HCIV-1 and other tailless icosahedral internal membrane-containing viruses of the family Sphaerolipoviridae. Viruses. 9:32.
• Eskelin K., Lampi M, Meier F, Moldenhauer E, Bamford DH, and Oksanen HM. Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation. Extremophiles. 21:1119-1132.
• Hanhijärvi KJ, Ziedaite G, Bamford DH, Hæggström E, Poranen MM. 2017. Single-molecule measurements of viral ssRNA packaging. RNA. 23:119-129.
• Pietilä MK, Albulescu IC, Hemert MJV, Ahola T. 2017. Polyprotein processing as a determinant for in vitro activity of Semliki Forest virus replicase. Viruses. 9:292.
• Prangishvili D, Bamford DH, Forterre P, Iranzo J, Koonin EV, Krupovic M. 2017. The enigmatic archaeal virosphere. Nat. Rev. Microbiol. 15:724-739.
• Sinclair RM, Ravantti JJ, Bamford DH. 2017. Nucleic and amino acid sequences support structure-based viral classification. J. Virol. 91:e02275-16.                                    
• Santos-Pérez I, Oksanen HM, Bamford DH, Goñi FM, Reguera D, Abrescia NG. 2017. Membrane-assisted viral DNA ejection. Biochim. Biophys. Acta. 1861:664-672.
• Sun Z, El Omari K, Sun X, Ilca SL, Kotecha A, Stuart DI, Poranen MM, Huiskonen JT. 2017. Double-stranded RNA virus outer shell assembly by bona fide domain-swapping. Nat. Commun. 8:14814