Integrated Structural Cell Biology /Infrastructures /

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 also actively develops new purification methods for large biopolymers, 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 and Instruct-ERIC. Biocomplex is supported by the University of Helsinki (HiLIFE and Faculty of Biological and Environmental Sciences) and Academy of Finland.

For contact and inquiries

  • email: grp-biocomplexservice[at]helsinki.fi
  • We are located in Viikki campus, Biocenter 1, staircase B, 6th floor (Viikinkaari 9) Google map

COVID-19

  • To protect our users and staff during the ongoing COVID-19 pandemic, Biocomplex has restrictions in the physical visits to its facilities.
  • Please, contact grp-biocomplexservice[at]helsinki.fi in advance if you want to use Biocomplex instrumentation during the restricted access period so that we can book the room for you

Potential down-time periods due to the construction of the tram line

  • Building of the new tram line "Raidejokeri" next to Biocenter 1 induces trembling that may prevent the use of our instruments. Here we announce (possible) bans on the use of ultracentrifuges.
  • Down-time periods of ultracentrifuges
    • March 30 2021
    • April 13 2021

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 applications
Biocomplex instrumentation
Biocomplex user policy and registration
Biocomplex user fees
Frequently asked questions
Biocomplex publications
Further reading

Biocomplex services

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 inline detectors;
  • Monolithic ion exchange chromatography;
  • 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.

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.

Our AF4 services are being renewed. Biocomplex has acquired a new AF4 device (Eclipse NEON) equipped with wonderful 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. Later this year, the service will be 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 yields

  • Accompanied software: ASTRA enables easy analysis of molar mass and radius; Vision Design enables simulation of experiments based on AF4 theory.

Chromatography service

CIM® monolithic columns can be utilized for purification of viruses, virus-like particles, 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.

Please find the downloadable poster of Bíocomplex services below.

Biocomplex service poster

Biocomplex applications

Biocomplex virus structure
  • 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 size (AF4), and surface charge (monoliths);
  • Separation and purification of cells, organelles, macromolecules, macromolecular complexes, bacteria, vesicles and viruses etc.
biocomplex app 2

Biocomplex instrumentation

Biocomplex instrumentation 2 Biocomplex airfuge Biocomplex AF4 channel

Ultracentrifuges

  • Five ultracentrifuges of which one has a HEPA filter (Thermo Scientific Sorvall WX Ultra Series);
  • Swing-out and fixed angle rotors with different capacities (Sorvall and Beckman), see table.
  • Instrumentation for gradient making (IBS INTEGRA Biosciences peristaltic pump; BioComp Gradient master)
  • Gradient fractionator (BioComp Piston Gradient Fractionator, only provided as a service)
  • 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

29 000 -  35 000

 210 000

4

swing out

AH629 (SW 28 Ti)

6 x 36 ml

24 000

 103 500

6

swing out

TH660 (SW 60 Ti)

6 x 4.4 ml

41 000

 228 000

1

swing out

AH650 (SW 50.1)

6 x 5 ml

45 000

 240 000

1
fixed angle T1270 12 x 8-10 ml 55 000 277 000 1

fixed angle

T865

8 x 20 ml

45 000

 205 800

1

fixed angle

T647.5

6 x 60 ml

35 000-   38 000

 160 500

2

fixed angle

A-621 New!

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
  • Superspeed rotors
    • Fiberlite F20-12x50 LEX, 13 000 rpm
    • Fiberlite F12-6x500 LEX, 8000 rpm 
    • Fiberlite F14-6x250y, 10 000 rpm

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

  • Analytical and semi-preparative separation channels, dispersion inlet channel for sticky samples
  • Temperature controlled channels (+5°C above ambient temperature, up to +75 °C), channel cooling possible for analytica channel
  • Ultrafiltration membranes with various MWCOs and materials
    • Regenerated cellulose membranes (MWCOs 10 and 30 kDa);
    • Polyethersulfone membranes (MWCOs 10 and 30 kDa);
    • Other MWCOs and membrane materials possible also;
  • Spacers (various thicknesses)
  • DAWN 18 angle multiangle light scattering (MALS) detector with embedded QELS dynamic light scattering (DLS) detector
  • Agilent UV-Vis and Fluoresecence Detectors
  • Optilab dRI detector (universal concentration detector)
  • Dilution control module (to increase signal intensity at the detectors)
  • Fraction collection (temperature controlled)
  • Autosampler or manual injection
  • ASTRA and Vision software
  • Electrical/asymmetric-flow field-flow fractionation (EAF4;Mobility) to measure charge and zeta potential (coming in 2021)

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

Biocomplex UC farm2
  • Our service is open for all users;
  • Our facility can be used for organisms of the biosafety levels 1 and 2;
  • We serve on a first-come-first-served basis. Access is prioritized based on the scientific feasibility peer-review of the project summary within the units;
  • Register your project by filling the Biocomplex User Registration e-form https://elomake.helsinki.fi/lomakkeet/93251/lomake.html for approval (feasibility, technical checking; safety issues) and contact grp-biocomplexservice[at]helsinki.fi to gain access to the premises. Note that the registration is valid for one calendar year and it is personal (not project specific);
  • We recommend users to register as a member of Instruct-ERIC (Instruct registration);
  • Researchers from Instruct ERIC member countries can apply for access through Instruct ERIC, in which case it can be financially supported;
  • Training is obligatory before the first use. After your project has been approved by the Biocomplex personnel, please contact us for reserving the time for training (grp-biocomplexservice[at]helsinki.fi). Training includes introdution to the centrifugation facilities, to safe operation of centrifuges, as well as hands-on support for the first centrifugation experiment;
  • Users are expected to clean up the work places immediately after they have completed their work; 
  • Acknowledgements: User agrees to acknowledge research infrastructures (RIs) in the upcoming publications and theses with i.e. the following text:
    “The facilities and expertise of the HiLIFE Biocomplex unit at the University of Helsinki, a member of Instruct-ERIC Centre Finland, FINStruct, and Biocenter Finland are gratefully acknowledged."
  • Users agree to send the bibliography of the published material (scientific papers, theses) to biocomplexservice[at]helsinki.fi.

Frequently asked questions

Centrifugation

  • Do you borrow the rotors for centrifuges?

For safety reasons we do not borrow our rotors.

  • I have obtained the training for centrifuges from another unit/university. Do I need the training from Biocomplex unit?

Yes you do. This for your own safety and for the safety of our customers and other personnel.

  • I am an experienced centrifuge user. Can I do the training?

Unfortunately not. This for your own safety and for the safety of our customers and other personnel.

Asymmetrical flow field-flow fractionation

  • How many samples can be analyzed by the same membrane used in AF4?

Obviously this depends on the sample that is being analyzed, but the manufacturer's estimate is 30-50 analysis per one membrane.

  • How many AF4 analysis can be performed during one working day?

This depends on the type of analysis that is done. Minimum number is ~7 analysis, if the anaysis time is ~1 hour.

Monolithic ion exchange chromatography

  • Do you provide other column types as well?

Currently, we only have the DEAE and QA chemistries available routinely. If you have other types of columns in mind, please contact us.

User policies

  • Does the PI of the project need to fill in his/her own Biocomplex service request form?

No. It is enough that the PI signs the service request form that is filled in by the User. By signing the PI agrees to cover the costs from the service.

  • I have already registered as a Biocomplex user for 2018. Do I need to register again for 2019?

Yes you do. From 2019 we start to collect the registration forms electronically. While renewing your registration, please check that the information for invoicing is still valid?

 

 

 

Biocomplex publications

Biocomplex publications

Publications with acknowledgements to the Biocomplex Unit (Instruct Centre for Virus and Macromolecular Complex Production, ICVIR 2009-2017)

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. Euryarchaeal viruses. In Zuckerman M, Bamford DH, editors, Encyclopedia of Virology, 4th edition. Elsevier. In Press.
  • Demina T, Oksanen HM. 2020. Pleomorphic archaeal viruses: the family Pleolipoviridae is expanding by seven new species. Arch Virol. In Press.
  • 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).
  • Eskelin K, Oksanen HM. 2020. Isolating, culturing, and purifying viruses with a focus on bacterial and archaeal viruses. In Zuckerman M, Bamford DH, editors, Encyclopedia of Virology, 4th edition. Elsevier. In Press.
  • 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).
  • 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).
  • 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

2016

  • Atanasova NS, Bamford DH, Oksanen HM. 2016. Virus-host interplay in high salt environments. Environmental microbiology reports. Environ. Microbiol. Rep. 8:431-44.
  • Demina TA, Atanasova NS, Pietilä MK, Oksanen HM, Bamford DH. 2016. Vesicle-like virion of Haloarcula hispanica pleomorphic virus 3 preserves high infectivity in saturated salt. Virology 499:40-51.
  • Demina TA, Pietilä MK, Svirskaite J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM. 2016. Archaeal virus HCIV-1 highlights conserved elements in icosahedral membrane-containing DNA viruses from extreme environments. mBio 7(4):e00699-16.
  • Eskelin K, Lampi M, Meier F, Moldenhauer E, Bamford DH, Oksanen HM. 2016. Asymmetric flow field flow fractionation methods for virus purification. J. Chromatogr. A. 1469:108-119.
  • Hanhijärvi KJ, Ziedaite G, Hæggström E, Bamford DH. 2016. Temperature and pH dependence of DNA ejection from archaeal lemon-shaped virus His1. Eur. Biophys. J. 45:435-442.
  • Ivanov KI, Eskelin K, Bašić M, De S, Lõhmus A, Varjosalo M, Mäkinen K. 2016. Molecular insights into the function of the viral RNA silencing suppressor HCPro. Plant. J. 85:30-45.
  • Orentaite, I., Poranen, M. M., Oksanen, H. M., Daugelavicius, R. & Bamford, D. H. 2016. K2 killer toxin-induced physiological changes in the yeast Saccharomyces cerevisiae. FEMS Yeast Research. 16:1-8.  
  • Pietilä MK, Roine E, Sencilo A, Bamford DH, Oksanen HM. 2016. Pleolipoviridae, a newly proposed family comprising archaeal pleomorphic viruses with single-stranded or double-stranded DNA genomes. Arch. Virol. 161:249-56.
  • Svirskaitė J, Oksanen HM, Daugelavičius R, Bamford DH. 2016. Monitoring Physiological Changes in Haloarchaeal Cell during Virus Release. Viruses. 8(3). pii: E59.

2015

  • Atanasova NS, Oksanen HM, and Bamford DH. 2015. Haloviruses of archaea, bacteria, and eukaryotes. Curr. Opin. Microbiol. 25:40-48.
  • Atanasova NS, Bamford DH, Oksanen HM. 2015. Haloarchaeal virus morphotypes. Biochimie. 118:333-343.
  • Atanasova NS, Demina TA, Buivydas A, Bamford DH, and Oksanen HM. 2015. Archaeal viruses multiply: temporal screening in a solar saltern. Viruses. 7:1902-1926.
  • Atanasova NS, Senčilo A, Pietilä MK, Roine E, Oksanen HM, and Bamford DH. 2015. Comparison of lidip-containing bacterial and archaeal viruses. Adv. Virus Res. 92:1-61.
  • Gil-Carton D, Jaakkola ST, Charro D, Peralta B, Castaño-Díez, Oksanen HM, Bamford DH, Abrescia NGA. 2015. Insight into the assembly of viruses with vertical single β-barrel major capsid proteins. Structure. 23:1866-1877.
  • Hong C, Pietilä MK, Fu C, Schmid MF, Bamford DH, and Chiu W. 2015. Lemon-shaped halo archaeal virus His1 with uniform tail but variable capsid structure. Proc. Natl. Acad. Sci USA 112:2449-2454.
  • Karttunen J, Mäntynen S, Ihalainen TO, Bamford JKH and Oksanen HM. 2015. Non-structural proteins P17 and P33 are involved in the assembly of the internal membrane-containing virus PRD1. Virology. 482:225-233.
  • Liu Y, Wang J, Liu Y, Wang Y, Zhang Z, Oksanen HM, Bamford DH and Chen X. 2015. Identification and characterization of SNJ2, the first temperate pleolipovirus integrating into the genome of the SNJ1-lysogenic archaeal strain. Mol. Microbiol. 98:1002-1020.
  • Mattila SP, Oksanen HM, and Bamford JKH. 2015. Probing of protein interactions in the membrane-containing virus PRD1. J. Gen. Virol. 96: 453-462.
  • Mäntynen S, Laanto E, Kohvakka A, Poranen MM, Bamford JK, Ravantti JJ. 2015. New enveloped dsRNA phage from freshwater habitat. J. Gen. Virol. 96:1180-1189.
  • Poranen MM, Bamford DH, and Oksanen HM. 2015. Membrane-containing bacteriophages. In: eLS. John Wiley & Sons, Ltd: Chichester. DOI: 10.1002/9780470015902.a0000779.pub3
  • Quemin ERJ, Pietilä MK, Oksanen HM, Forterre P, Rijpstra WIC, Schouten S, Bamford DH, Prangishvili D, Krupovic M. 2015. Sulfolobus spindle-shaped virus 1 contains glycosylated capsid proteins, a cellular chromatin protein and host-derived lipids. J Virol. 15:11681-11691.
  • Sencilo A, Luhtanen A-M, Saarijärvi M, Bamford DH, Roine E. 2015. Cold-active bacteriophages from the Baltic Sea ice have diverse genomes and virus-host interactions. Environ Microbiol. 17:3628-41.

2014

  • Hong C, Oksanen HM, Liu X, Jakana J, Bamford DH, and Chiu W. 2014. A structural model of the genome packaging process in a membrane-containing double stranded DNA virus. PLoS Biol. 12:e1002024.
  • Krupovic M, Bamford DH, Koonin EV. 2014. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol. Direct. 9:6
  • Luhtanen A-M, Eronen-Rasimus E, Kaartokallio H, Rintala J-M, Autio R, and Roine E. 2014. Isolation and characterization of phage-host systems from the Baltic Sea ice. Extremophiles. 18:121-130.
  • Mönttinen HAM, Ravantti JJ, Stuart DI, and Poranen MM. 2014. Automated structural comparisons clarify the phylogeny of the right-hand-shape polymerases. Mol Biol Evol. 31:2741-52.
  • Pietilä MK, Demina TA, Atanasova NS, Oksanen HM, and Bamford DH. 2014. Archaeal viruses and bacteriophages: comparisons and contrasts. Trends in Microbiol. 22:334-344.
  • Sun X, Bamford DH, Poranen MM. 2014. Electrostatic interactions drive the self-assembly and the transcription activity of the Pseudomonas phage Ф6 procapsid. J Virol. 88:7112-7116.

2013

  • Atanasova NS, Pietilä M, and Oksanen HM. 2013. Diverse antimicrobial interactions of halophilic archaea and bacteria extend over geographical distances and cross the domain barrier. MicrobiologyOpen. 2:811-825.
  • Badia-Martinez D, Oksanen HM, Stuart, DI, and Abrescia NGA. 2013. Combined approaches to study virus structures. In: Structure and Physics of Viruses: An intergrated Textbook, Subcellular Biochemistry 68. Ed: Mateu MG. Springer. pp. 203-246.
  • Hanhijärvi KJ, Žiedaitė G, Pietilä MK, Haeggström E, and Bamford DH. 2013. DNA ejection from an archaeal virus - a single-molecule approach. Biophys. J. 104:2264-2272.
  • Peralta B, Gil-Carton D, Castaño-Díez D, Bertin A, Boulogne C, Oksanen HM, Bamford DH, and Abrescia NGA. 2013. Mechanism of membranous tunnelling nanotube formation in viral genome delivery. PLoS Biol. 11: e1001667.
  • Pietilä MK, Atanasova NS, Oksanen HM, and Bamford DH. 2013. Modified coat protein forms the flexible spindle-shaped virion of haloarchaeal virus His1. Environ. Microbiol. 15:1674-1686.
  • Pietilä MK, Laurinmäki P, Russell DA, Ko C-C, Jacobs-Sera D, Butcher SJ, Bamford DH, and Hendrix RW. 2013. Insights into head-tailed viruses infecting extremely halophilic archaea. J. Virol. 87:5057-5079.
  • Pietilä MK, Laurinmäki P, Russell DA, Ko C-C, Jacobs-Sera D, Hendrix RW, Bamford DH, and Butcher SJ. 2013. Structure of the archaeal head-tailed virus HSTV-1 compleates the HK97-fold story. Proc. Natl. Acad. Sci. USA. 110:10604-10609.
  • Ravantti JJ, Bamford DH, and Stuart DI.  2013. Automatic comparison and classification of protein structures. J. Struct. Biol. 183:47-56.
  • Senčilo A, Jacobs-Sera D, Russell DA, Ko C-C, Bowman CA, Atanasova NS, Österlund E, Oksanen HM, Bamford DH, Hatfull GF, and Roine E, and Hendrix RW. 2013. Snapshot of haloarchaeal tailed virus genomes. RNA Biol. 10:33-46.
  • Sun X, Pirttimaa MJ, Bamford DH, and Poranen MM. 2013. Rescue of maturation off-pathway products in the assembly of Pseudomonas phage φ6. J. Virol. 87:13279-13286.
  • Vitale R, Roine E, Bamford, DH, and Corcelli A. 2013. Lipid fingerprints of intact viruses by MALDI-TOF mass spectrometry. Biochim Biophys Acta. 1831:872-879.

2012

  • Aalto AP, Bitto D, Ravantti JJ, Bamford DH, Huiskonen JT, and Oksanen HM. 2012. A snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing Salisaeta icosahedral phage 1. Proc. Natl. Acad. Sci. USA. 109: 7079–7084.
  • Jaakkola ST, Penttinen RK, Vilén ST, Jalasvuori M,  Rönnholm G, Bamford JKH, Bamford DH, and Oksanen HM. 2012. Closely related archaeal Haloarcula hispanica icosahedral viruses HHIV-2 and SH1 have nonhomologous genes encoding host recognition functions. J. Virol. 86:4734-4742.
  • Kandiba L, Aitio O, Helin J, Guan Z, Permi P, Bamford DH, Eichler J, and Roine E. 2012. Diversity in prokaryotic glycosylation: an archaeal-derived N-linked glycan contains legionaminic acid. Mol. Microbiol. 84:578-593.
  • Oksanen HM, Domanska A, and Bamford DH. 2012. Monolithic ion exchange chromatography methods for virus purification. Virology. 434:271-277.
  • Pietilä M, Atanasova NS, Manole V, Liljeroos L, Butcher SJ, Oksanen HM, and Bamford DH. 2012. Virion architecture unifies globally distributed pleolipoviruses infecting halophilic archaea. J. Virol. 86:5067-5079.
  • Senčilo A, Paulin L, Kellner S, Helm M, and Roine E. 2012. Related haloarchaeal pleomorphic viruses contain different genome types. Nucleic Acids Res. 40:5523-5534.
  • Sun X, Bamford DH, and Poranen MM. 2012. Probing, by self-assembly, the number of potential binding sites for minor protein subunits in the procapsid of double-stranded RNA bacteriophage φ6. J. Virol. 86:12208–12216.

Further reading

Here are some reading tips for technicues 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