Biocomplex purification

Biocomplex is specialized in macromolecular sample preparation and purification for functional and structural studies using preparative ultracentrifugation, monolithic chromatography and asymmetrical flow field-flow fractionation technologies.

Biocomplex actively develops new purification methods for large macromolecular complexes, often in co-operation with manufacturers. Our technologies can be used in different combinations to purify large macromolecular complexes such as viruses, virus-like particles, viral subassemblies, exosomes, membrane vesicles, large protein complexes, ribonucleoprotein complexes etc.
We are part of the Faculty of Biological and Environmental Sciences and HiLIFE, University of Helsinki, Biocenter Finland, FINStruct and Instruct-ERIC Centre Finland. Biocomplex is supported by the University of Helsinki (HiLIFE and Faculty of Biological and Environmental Sciences) and Research Council of Finland.

For contact and inquiries: UH users

  • Instruct-HiLIFE units (Biocomplex, CryoEM, and protein crystallisation Xtal) are using the iLAB online system to make project request and to reserve instrument time.
  • Login in using HAKA credentials, i.e. normal UH credentials (UH users only can use the HAKA login).
  • This connects your iLab account to the HAKA directory.
  • During registration, select PI/Lab/Research Group from a dropdown menu. 
  • Group membership connects you with appropriate funds (WBS). 
  • You may need to request group membership, if you have not used iLAB before. You may apply membership in multiple Groups/LabsUH users.
  • Navigate to https://hilife-infra.ilab.agilent.com/service_center/show_external/3753/instructhilife to make a project request and wait for approval from us.
  • Once the group leader has approved your project, you can reserve our ultracentrifuges, piston fractionator, batch DLS and Äkta Pure. AF4 is reserved by Biocomplex personnel.
  • We urge group leaders to give each user a budget (e.g. €1,000), in which case it is possible to reserve equipment without the group leader confirming each reservation.
  • Contact by email: grp-biocomplexservice[at]helsinki.fi
  • We are located at the Viikki campus, Biocenter 1, staircase B, 6th floor (Viikinkaari 9) Google map
  • Shipment address for samples: Biocomplex Unit, Sari Korhonen/Tanja Westerholm, Viikinkaari 9, Biocenter 1, 00790 Helsinki, Finland

External users (non-UH)

  • Note that only UH users can currently use the HAKA credentials.

If your institution or company does not yet have the iLAB account, be in contact with us as we need to be in contact to Agilent to make a valid account. Do not try to make the account yourself. For the account the following information is needed:

  • Official name of the Institution in English;
  • Invoicing address of the institution;
  • Name and email address of the Principal Investigator (PI)/Group leader;
  • Name and email of the persons who should be added to the group

Instruct-ERIC Centre Finland / Biocomplex

Biocomplex services are part of Instruct-ERIC Centre Finland and can be accessed through Instruct-ERIC (Instruct Centre Finland/Biocomplex home page). See funding possibilities for Instruct-ERIC access.

 
Biocomplex services

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.

Link to Ultracentrifugation and fractionation poster:

 

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 and analysis of charge.

Link to AF4 poster:

Dynamic light scattering measurement service

Biocomplex has a DynaPro NanoStar II instrument that enables quick collection of dynamic and static light scattering (90° angle) data in a cuvette for quick testing or using automated data collection for multiple time points or temperature ramp. The accompanied Dynamics software enables analysis of hydrodynamic size, particle concentration and molar mass in batch mode. 

Link to DLS poster:

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.

 
Biocomplex applications
  • 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.
Biocomplex instrumentation

Ultracentrifugation

  • Six ultracentrifuges (U1-U6) of which two have HEPA filters (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

Rotor type

Name*

Recommended capacity

Max speed (rpm)

 Max g**

Amount

swing out

TH641 (SW41 Ti)

6 x 12 ml

35 000

 210 000

4

swing out

AH629 (SW28 Ti)

6 x 36 ml

24 000

 103 500

7

swing out

AH650 (SW50.1)

6 x 5 ml

45 000

 240 000

2
fixed angle F50L 24 x 1.5 ml 50 000 280 000 1
fixed angle T1270 12 x 8-10 ml 55 000 277 000 2

fixed angle

T865

8 x 20 ml

45 000

 205 800

2

fixed angle

T647.5

6 x 60 ml

38 000

 160 500

3
fixed angle A621 6 x 200 ml 21 000 67 000 1
 

* Corresponding Beckman

rotor names in parenthesis

     ** for rotor with the highest speed (rpm)  

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)
Biocomplex user policy and registration
  • 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.  

     
Biocomplex user fees 2025

Fees are collected to cover the service and maintenance costs of the Biocomplex instruments. The prices are without VAT.

  • A kick off meeting/consultation can be requested prior to starting a project. Consultation is free of charge.
  • Prices for full service or collaborative projects should be agreed separately.
  Fees for users from the University of Helsinki (Jan 2024)  
Service/Consumable Description Price and unit

Ultracentrifugation

 

 
Training (8 am - 15 pm)

Technical personnel advice in the use of gradient master and operation of ultracentrifuges and rotors. User learns the safety regulations on using the centrifuges as well as the regular cleaning procedures. Training is provided during the first time of centrifuge use. The centrifuge use and consumables are charged based on the principles provided below. No training fee is charged from the UH users.

Training for Biocomp piston fractionator use must be combined to a centrifugation experiment. For training, only one rotor can be fractionated.

  
Support during centrifugation/Centrifuge operator (8 am - 15 pm) Technical personnel assists the use of centrifuge(s).  
Regular use of ultracentrifuges

Fixed price for unlimited access for one user to use the ultracentrifuges, rotors and gradient master. Valid for one year.

Price includes the use of Biocomp piston fractionator with UV and fluorescence data collection option. Does not include consumables.

 500 €/year
Usage-based pricing

Billing is based on the number of centrifugations. Each individual centrifuge use will be billed. 

  • If you use one centrifuge, but two different rotors, billing is based on two uses.
  • If you use one centrifuge for three consecutive centrifugations with the same rotor, billing is based on three uses.
  • No charge is applied after 25 uses. Uses are counted for one year.
 25 €/use
Centrifugation service and manual fractionation

Technical staff performs the centrifugation experiment.

Price depends on the used work time, consumables and ultracentrifuge use.

 project specific
UC consumables    
Tubes for swing-out rotors TH641, AH629, AH650 4 €/tube
Tubes and caps for fixed angle rotors T-1270 15 €/tube, 30 €/cap
Tubes and caps for fixed angle rotors T865 15 €/tube, 55 €/cap
Tubes and caps for fixed angle rotors T647.5 25 €/tube, 150 €/cap
Tubes and caps for fixed angle rotors F50L 2 €/tube

AF4

    
Machine setup

The requested membrane and spacer are installed. Solvents are filtered and exchanged. System performance is validated with standards such as BSA or polystyrene beads (when applicable).

  • The price contains one day of instrument time. Typically, also the first measurements can be initiated during the first day.
  • The price includes one 0.1 um filter for filtering the solvent, one membrane and one spacer.
  • Sample vials are charged based on consumption.
  • The user provides the solvent (2-5 l). Solvent consumption depends on the used flow conditions and number of experiments performed. The solvent needs to be changed every two days. Solvent needs to be freshly prepared.
 200 €
Independent use of AF4                                                                                            

User operates AF4 instrument independently.

  • A minimum time billed is 2 days.
  • Price for the instrument time does not include consumables.
  • Sample vials, additional filters for solvents, membranes and spacers are charged based on consumption.
  • Price includes the use of ASTRA and Vision Design software for data analysis and method development.
 75 € /day
Technical support or AF4 operator  Technical staff gives practical training and support on AF4 instrument use to promote independent use of AF4 by the user.  
Academic support Academic support for method development and optimization as well as data analysis using Vision and Astra software.  
AF4-service/collaborative projects

Biocomplex personnel performs AF4 experiments. The price is determined by:

  • The used instrument time, 2 days is the minimum charge.
  • The used working time for the staff.
  • The used consumables such as filters for filtering the buffer, membrane, sample vials.

The user is expected to provide the solvent (2 l). The solvent needs to be changed every two days.

 Project specific
AF4 consumables    
Membranes for analytical or semipreparative channel Regenerated cellulose (RC) and polyethersulfone (PES) membranes with different MWCOs available 50 €/membrane
Spacers for analytical or semipreparative channel Different spacer thicknesses available for analytical long channel and semipreparative channel 50 €/spacer
Filter PAL filter for filtering of the solvents, 0.1 um pore size. 35 € /filter
Sample vials and caps

Glass vials (amber), 1 ml max volume

Plastic vials, 0.3 ml max volume

 1 € /vial
     

ÄktaPure chromatography

    
Independent use of ÄktaPure chromatography instrument User operates chromatography equipment independently and rinses the instrument after the use and sets it to the storage solution. The price includes the possibility to use CIM monolithic anion exchange columns with QA or DEAE chemistry. 40 €/day
Regular use of ÄktaPure Fixed price for unlimited use of Äkta Pure for one calendar year. 400 €/year
User support Technical staff  support  
Chromatography service/   Project specific

Dynapro Nanostar II batch DLS

    
Instrument time User operates instrument independently using the quartz cuvette.  
Consumables    
Single use plastic cuvette Min volume 4 ul 12 € / piece
Filtterit Whatman Anotop syringe filter 0.01 um Price includes the syringe (Hence Jet 1 ml) 15 €/piece
Filtterit Whatman Anotop syringe filter 0.2 um Price includes the syringe (Hence Jet 1 ml) 13 €/piece
Gel loading tips   18 € /box

 
Answers to frequently asked questions

Ultracentrifugation

  • For safety reasons we do not borrow our rotors.
  • Safety training is mandatory for new users of the ultracentrifugation facility. This is also true for experienced ultracentrifuge users. This for your own safety and for the safety of our customers and other personnel.

Asymmetrical flow field-flow fractionation

  • The number of analysis that can be performed with the same membrane depends on the sample properties, the manufacturer's estimate is 30-50 analysis per one membrane.
  • The number of analysis that can be performed during one working day depends on the method used and also on the sample. Some sticky samples may need rinses or blank runs between analysis.

Monolithic ion exchange chromatography

  • Biocomplex has currently only monolithic DEAE and QA columns available that can be used. However, you are allowed to bring your own columns.

User policies

  • Project sheets are user specific as is the billing. Thus each user should fill in their own project sheet.
  • Project and service requests are done in iLAB.
Biocomplex publications

Publications where services of Biocomplex Unit were utilized (2020 onwards)

2025

  • Gregorova P, Isada M, DiRuggiero J, Sarin LP (2025). Purification of micrococcal nuclease for use in ribosomal profiling of high-salinity extremophiles. J. Biol. Chem. 301(1):108020. 
  • Demina T, Marttila H, Pessi IS, Männistö MK, Dutilh BE, Roux S, Hultman. 2025. Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils. J. Microbiome 20;13(1):79. 
  • Dutta P, Mäkinen K. 2025. Mapping and quantification of potato virus A RNA genomes within viral particles and polysomes in infected plant cells. J. Virol. Methods. 332:115066. 
  • Moorlach BW, Sede AR, Hermann KM, Levanova AA, Poranen MM, Westphal M, Wortmann M, Stepula E, Jakobs-Schönwandt D, Heinlein M, Keil W, Patel AV. 2025. Interpolyelectrolyte complexes of in vivo produced dsRNA with chitosan and alginate for enhanced plant protection against tobacco mosaic virus. Int. J. Biol. Macromol. 306(Pt 2):141579. 

2024

  • De S, Nguyen HM, Zou F, Basarir F, Mousavi M, Mäkinen K, Kostiainen MA, Vapaavuori J. 2024. Bio-templated silver nanopatterns for photothermal and antifogging coatings. Adv. Mater. Interfaces, 11:2300828
  • García-Arribas AB, Ibáñez-Freire P, Carlero D, Palacios-Alonso P, Cantero-Reviejo M, Ares P, López-Polín G, Yan H, Wang Y, Sarkar S, Chhowalla M, Oksanen HM, Martín-Benito J, de Pablo PJ, Delgado-Buscalioni R. 2024. Broad Adaptability of Coronavirus Adhesion Revealed from the Complementary Surface Affinity of Membrane and Spikes. Adv. Sci. (Weinh). 11(41):e2404186. doi: 10.1002/advs.202404186.
  • 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.
  • Jiang M, Laine L, Kolehmainen P, Kakkola L, Avelin V, Väisänen E, Poranen MM, Österlund P, Julkunen I. 2024. Virus-specific Dicer-substrate siRNA swarms inhibit SARS-CoV-2 infection in TMPRSS2-expressing Vero E6 cells. Front. Microbiol, 15:1432349. 
  • Kohvakka A, Sattari M, Nättinen J, Aapola U, Gregorová P, Tammela TLJ, Uusitalo H, Sarin LP, Visakorpi T, Latonen L. 2024. Long noncoding RNA EPCART regulates translation through PI3K/AKT/mTOR pathway and PDCD4 in prostate cancer. Cancer Gene Ther. 31(10):1536-1546. 
  • 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.
  • Latimer-Smith M, Salgado PS, Forsyth I, Makeyev E, Poranen MM, Stuart DI, Grimes JM, El Omari K. 2024. Structure of the RNA-dependent RNA polymerase P2 from the cystovirus φ8. Sci. Rep. 4(1):23540. doi: 10.1038/s41598-024-75213-7.
  • Lem O, Kekki R, Koivuniemi A, Efimov A, Laaksonen T, Durandin N. 2024. The role of lipid oxidation pathway in reactive oxygen species-mediated cargo release from liposomes. Mater Adv. 5(22):8878-8888. 
  • León MJ, Sánchez-Porro C, de la Haba RR, Pfeiffer F, Dyall-Smith M, Oksanen HM, Ventosa A. 2024. Halobacterium hubeiense sp. nov., a haloarchaeal species isolated from a bore core drilled in Hubei Province, PR China. Int. J. Syst. Evol. Microbiol. 74(3):006296. doi: 10.1099/ijsem.0.006296. PMID: 38512754 
  • 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.
  • Malmgren R, Sofieva-Rios S, Lakkala K, Asmi E, Sun Y, Todt M, Heikkilä P, Bamford D, Romantschuk M, Atanasova N. 2024. Phi6 virus transmission in Arctic outdoor air and the effects of solar UV radiation on virus and host viability. Environmental Advances, 18:100600.
  • Palviainen M, Puutio J, Østergaard RH, Eble JA, Maaninka K, Butt U, Ndika J, Kari OK, Kamali-Moghaddam M, Kjaer-Sorensen K, Oxvig C, Aransay AM, Falcon-Perez JM, Federico A, Greco D, Laitinen S, Hayashi Y, Siljander PR. 2024. Beyond basic characterization and omics: Immunomodulatory roles of platelet-derived extracellular vesicles unveiled by functional testing. J Extracell Vesicles. 13(10):e12513. doi: 10.1002/jev2.12513. PMID: 39330919 
  • Saari H, Marttila H, Poranen MM, Oksanen HM, Zini J, Laitinen S. 2024. Inline Raman Spectroscopy Provides Versatile Molecular Monitoring for Platelet Extracellular Vesicle Purification with Anion-Exchange Chromatography. 2024. Int. J. Mol. Sci. 25(15):8130. doi: 10.3390/ijms25158130. PMID: 39125704 
  • Simmonds P, Adriaenssens EM, Lefkowitz EJ, Oksanen HM, Siddell SG, Zerbini FM, Alfenas-Zerbini P, Aylward FO, Dempsey DM, Dutilh BE, Freitas-Astúa J, García ML, Hendrickson RC, Hughes HR, Junglen S, Krupovic M, Kuhn JH, Lambert AJ, Łobocka M, Mushegian AR, Penzes J, Muñoz AR, Robertson DL, Roux S, Rubino L, Sabanadzovic S, Smith DB, Suzuki N, Turner D, Van Doorslaer K, Vandamme AM, Varsani A. 2024. Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024). Arch Virol. 169:236. 
  • Stuart DI, Oksanen HM, Abrescia NGA. 2024. Integrative approaches to study virus structures. Subcell Biochem. 105:247-297. 
  • Zhang DX, Isupov MN, Davies BM, Schwarzer S, McLaren M, Stuart WS, Gold VAM, Oksanen HM, Quax TEF, Daum B. 2024. CryoEM resolves the structure of the halophile virus HFTV1 from head to toe.  bioRxiv doi: https://doi.org/10.1101/2024.12.09.627619 

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.

 

 

 
Further reading

Here are some reading tips for techniques utilized for biological macromolecular complexes

Ultracentrifugation

Mohr, H. and Völkl, A. (2017). Ultracentrifugation. In eLS, John Wiley & Sons, Ltd (Ed.). doi:10.1002/9780470015902.a0002969.pub3

Chromatography

Lewis, A. C. (2015). Chromatographic Techniques. In eLS, John Wiley & Sons, Ltd (Ed.). doi:10.1002/9780470015902.a0002705.pub2

Sheehan, D. and O'Sullivan, S. (2001). Ion Exchange Chromatography. In eLS, (Ed.). doi:10.1038/npg.els.0002677

Mansoor, M. A. (2015). Liquid Chromatography. In eLS, John Wiley & Sons, Ltd (Ed.). doi/10.1002/9780470015902.a0002679.pub3