Bio- ja ympäristötieteiden laitos

Research and Publications

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Research

The research in The Department of Biological and Environmental Sciences encompasses the full biosphere from molecules to populations all the way to complex ecosystems.  Research programs also seek to illuminate connections between biological and non-biological environment, including relationships extending to the larger socio-economic context.

The department has a distinct profile in all research focus areas. Department`s core research strengths include:

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  • Evolutionary Research. In 2012 Finnish Academy appointed the Centre of Excellence in Biological Interactions. This new unit combines functions of two predecessor units; The Centre of Excellence in Evolutionary Research and The Centre of Excellence in Virus Research.
  • Research on Aquatic Ecosystems, Environment and Natural Resources. This program focuses on analyzing ecosystems biology, studying the impact of human actions on nature, researching sustainable usage of natural resources and reducing hazardous effects on natural resources caused by human action.
  • Research on Cells, Viruses and the Structure and Function of Biomolecules. This research program involves nanoscale science and technology.

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See the major research themes listed under each of the departmental divisions

  • welfare of aquatic organisms and ecosystems, integrated research on lake ecosystems, use and regulation of aquatic resources
  • evolutionary research, applied ecology, conservation ecology
  • virology, research on cellular and molecular structure, cell and molecular biological imaging
  • integrated environmental sciences, renewable energy, assessment of environmental impacts

This list covers all the publications in the Department of Bio and Environmental Sciences since year 2003

2003 2004 2005 2006 2007 2008
2009 2010 2011 2012 2013 2014
2015 2016

Recent publications (2017)

Raulinaitis, V., Tossavainen, H., Aitio, O., Seppälä, R., & Permi, P. (2017). 1H, 13C and 15N resonance assignments of the new lysostaphin family endopeptidase catalytic domain from Staphylococcus aureus. Biomolecular NMR Assignments, 11 (1), 69-73. doi:10.1007/s12104-016-9722-7

Luoto, T., Kuhry, P., Holzkämper, S., Solovieva, N., & Self, A. E. (2017). A 2000-year record of lake ontogeny and climate variability from the north-eastern European Russian Arctic. Holocene, 27 (3), 339-348. doi:10.1177/0959683616660168

Ahlstrand, T., Tuominen, H., Beklen, A., Torittu, A., Oscarsson, J., Sormunen, R., . . . Ihalina, R. (2017). A novel intrinsically disordered outer membrane lipoprotein of Aggregatibacter actinomycetemcomitans binds various cytokines and plays a role in biofilm response to interleukin-1β and interleukin-8. Virulence, 8 (2), 115-134. doi:10.1080/21505594.2016.1216294 Open access

Kietäväinen, R., Ahonen, L., Niinikoski, P., Nykänen, H., & Kukkonen, I. T. (2017). Abiotic and biotic controls on methane formation down to 2.5 km depth within the Precambrian Fennoscandian Shield. Geochimica et Cosmochimica Acta, 202, 124-145. doi:10.1016/j.gca.2016.12.020 Open access

Dobrev, P., Donnini, S., Groenhof, G., & Grubmüller, H. (2017). Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations. Journal of Chemical Theory and Computation, 13 (1), 147-160. doi:10.1021/acs.jctc.6b00807

Desrousseaux, M., Kotiaho, J. S., & Kohler, F. (2017). Are Soils Taken into Consideration by the IPBES Assessment on Land Degradation and Restoration?. In H. Ginzky, I. L. Heuser, T. Qin, O. C. Ruppel, & P. Wegerdt (Eds.), International Yearbook of Soil Law and Policy 2016 (pp. 165-177). Springer International Publishing. doi:10.1007/978-3-319-42508-5_13

Salmelin, J., Leppänen, M. T., Karjalainen, A., Vuori, K.-M., Gerhardt, A., & Hämäläinen, H. (2017). Assessing ecotoxicity of biomining effluents in stream ecosystems by in situ invertebrate bioassays : A case study in Talvivaara, Finland. Environmental Toxicology and Chemistry, 36 (1), 147-155. doi:10.1002/etc.3511 Open access

Lonn, E., Koskela, E., Mappes, T., Mökkönen, M., Sims, A., & Watts, P. (2017). Balancing selection maintains polymorphisms at neurogenetic loci in field experiments. Proceedings of the National Academy of Sciences of the United States of America, 114 (14), 3690-3695. doi:10.1073/pnas.1621228114 Open access

Salomaa, A., Paloniemi, R., Kotiaho, J. S., Kettunen, M., Apostolopoulou, E., & Cent, J. (2017). Can green infrastructure help to conserve biodiversity?. Environment and Planning C: Government and Policy, 35 (2), 265-288. doi:10.1177/0263774X16649363

Hämäläinen, L., Rowland, H. M., Mappes, J., & Thorogood, R. (2017). Can video playback provide social information for foraging blue tits?. PeerJ, 5, e3062. doi:10.7717/peerj.3062 Open access

Belle, S., Luoto, T., Kivilä, H., & Nevalainen, L. (2017). Chironomid paleo diet as an indicator of past carbon cycle in boreal lakes : Lake Kylmänlampi (Kainuu province; Eastern Finland) as a case study. Hydrobiologia, 785 (1), 149-158. doi:10.1007/s10750-016-2914-4

Waissi, G. C., Bold, S., Pakarinen, K., Akkanen, J., Leppänen, M. T., Petersen, E. J., & Kukkonen, J. (2017). Chironomus riparius exposure to fullerene-contaminated sediment results in oxidative stress and may impact life cycle parameters. Journal of Hazardous Materials, 322 (Part A), 301-309. doi:10.1016/j.jhazmat.2016.04.015

Zawiska, I., Luoto, T., Nevalainen, L., Tylmann, W., Jensen, T. C., Obremska, M., . . . Walseng, B. (2017). Climate variability and lake ecosystem responses in western Scandinavia (Norway) during the last Millennium. Palaeogeography, Palaeoclimatology, Palaeoecology, 466, 231-239. doi:10.1016/j.palaeo.2016.11.034 Open access

Kinnula, H., Mappes, J., & Sundberg, L.-R. (2017). Coinfection outcome in an opportunistic pathogen depends on the inter-strain interactions. BMC Evolutionary Biology, 17, 77. doi:10.1186/s12862-017-0922-2 Open access

Eyvindson, K., & Kangas, A. (2017). Comment on “A simple way to incorporate uncertainty and risk into forest harvest scheduling”. Forest Ecology and Management, 386, 86-91. doi:10.1016/j.foreco.2016.03.038

Sánchez-Hernández, J., Eloranta, A., Finstad, A. G., & Amundsen, P.-A. (2017). Community structure affects trophic ontogeny in a predatory fish. Ecology and Evolution, 7 (1), 358-367. doi:10.1002/ece3.2600 Open access

Varga, S., Vega-Frutis, R., & Kytöviita, M.-M. (2017). Competitive interactions are mediated in a sex-specific manner by arbuscular mycorrhiza in Antennaria dioica. Plant Biology, 19 (2), 217-226. doi:10.1111/plb.12510 Open access

Lopes-Lima, M., Sousa, R., Geist, J., Aldridge, D. C., Araujo, R., Bergengren, J., . . . Zogaris, S. (2017). Conservation status of freshwater mussels in Europe: state of the art and future challenges. Biological Reviews, 92 (1), 572-607. doi:10.1111/brv.12244

Galarza, J., Kishor, D., & Mappes, J. (2017). De novo transcriptome assembly and its annotation for the aposematic wood tiger moth (Parasemia plantaginis). Genomics Data, 12, 71-73. doi:10.1016/j.gdata.2017.03.008 Open access

Gopko, M., Mikheev, V. N., & Taskinen, J. (2017). Deterioration of basic components of the anti-predator behavior in fish harboring eye fluke larvae. Behavioral Ecology and Sociobiology, 71 (4), 68. doi:10.1007/s00265-017-2300-x

Eyvindson, K., Petty, A. D., & Kangas, A. S. (2017). Determining the appropriate timing of the next forest inventory : incorporating forest owner risk preferences and the uncertainty of forest data quality. Annals of Forest Science, 74 (1), 2. doi:10.1007/s13595-016-0607-9

Huttunen, M., Turkki, P., Mäki, A., Paavolainen, L., Ruusuvuori, P., & Marjomäki, V. (2017). Echovirus 1 internalization negatively regulates epidermal growth factor receptor downregulation. Cellular Microbiology, 19 (3), e12671. doi:10.1111/cmi.12671 Open access

Enyidi, U., Pirhonen, J., Kettunen, J., & Vielma, J. (2017). Effect of Feed Protein : Lipid Ratio on Growth Parameters of African Catfish Clarias gariepinus after Fish Meal Substitution in the Diet with Bambaranut (Voandzeia subterranea) Meal and Soybean (Glycine max) Meal. Fishes, 2 (1), 1-12. doi:10.3390/fishes2010001 Open access

Salonen, J., & Taskinen, J. (2017). Electrofishing as a new method to search for unknown populations of the endangered freshwater pearl mussel Margaritifera margaritifera. Aquatic Conservation: Marine and Freshwater Ecosystems, 27 (1), 115-127. doi:10.1002/aqc.2667

Papale, M., Giannarelli, S., Francesconi, S., Marco, G. D., Mikkonen, A., Conte, A., . . . Giudice, A. L. (2017). Enrichment, isolation and biodegradation potential of psychrotolerant polychlorinated-biphenyl degrading bacteria from the Kongsfjorden (Svalbard Islands, High Arctic Norway). Marine Pollution Bulletin, 114 (2), 849-859. doi:10.1016/j.marpolbul.2016.11.011

Ojala, A. E. K., Luoto, T., & Virtasalo, J. J. (2017). Establishing a high-resolution surface sediment chronology with multiple dating methods : Testing 137Cs determination with Nurmijärvi clastic-biogenic varves. Quaternary Geochronology, 37, 32-41. doi:10.1016/j.quageo.2016.10.005

Puurtinen, M., & Fromhage, L. (2017). Evolution of male and female choice in polyandrous systems. Proceedings of the Royal Society B : Biological Sciences, 284 (1851), 20162174. doi:10.1098/rspb.2016.2174 Open access

Sipari, S., Ylönen, H., & Palme, R. (2017). Excretion and measurement of corticosterone and testosterone metabolites in bank voles (Myodes glareolus). General and Comparative Endocrinology, 243, 39-50. doi:10.1016/j.ygcen.2016.10.015 Open access

Waldron, S., Endler, J. A., Valkonen, J., Honma, A., Dobler, S., & Mappes, J. (2017). Experimental evidence suggests that specular reflectance and glossy appearance help amplify warning signals. Scientific Reports, 7, 257. doi:10.1038/s41598-017-00217-5 Open access

Ashrafi, R. (2017). Exploring evolutionary responses to increasing temperature in an environmental opportunistic pathogen. Jyväskylä, Finland: University of Jyväskylä. Jyväskylä studies in biological and environmental science, 328. Retrieved from http://urn.fi/URN:ISBN:978-951-39-7007-9 Open access

Pyoriä, L., Toppinen, M., Mäntylä, E., Hedman, L., Aaltonen, L.-M., Vihinen-Ranta, M., . . . Perdomo, M. F. (2017). Extinct type of human parvovirus B19 persists in tonsillar B cells. Nature Communications, 8, 14930. doi:10.1038/ncomms14930 Open access

Mariash, H., Cusson, M., & Rautio, M. (2017). Fall Composition of Storage Lipids is Associated with the Overwintering Strategy of Daphnia. Lipids, 52 (1), 83-91. doi:10.1007/s11745-016-4219-9

Czajlik, A., Kovács, B., Permi, P., & Gáspári, Z. (2017). Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases. Scientific Reports, 7, 44504. doi:10.1038/srep44504 Open access

Yildiz, H. Y., Robaina, L., Pirhonen, J., Mente, E., Domínguez, D., & Parisi, G. (2017). Fish Welfare in Aquaponic Systems : Its Relation to Water Quality with an Emphasis on Feed and Faeces : A Review. Water, 9 (1), 13. doi:10.3390/w9010013 Open access

Oldén, A., Komonen, A., Tervonen, K., & Halme, P. (2017). Grazing and abandonment determine different tree dynamics in wood-pastures. Ambio, 46 (2), 227-236. doi:10.1007/s13280-016-0821-6

Ahonen, H., Koskinen, H., Valtonen, T., & Taskinen, J. (2017). Henneguya zschokkei (Myxozoa) infection in cultured whitefish : Age-dependence, seasonality and distribution within host. Aquaculture, 470, 164-168. doi:10.1016/j.aquaculture.2016.12.018 Open access

Ylönen, H., Kasi, M., Opperbeck, A., Haapakoski, M., & Sundell, J. (2017). How Do Infanticidal Male Bank Voles (Myodes glareolus) Find the Nest with Pups?. Ethology, 123 (2), 105-112. doi:10.1111/eth.12579

Brett, M. T., Bunn, S. E., Chandra, S., Galloway, A. W. E., Guo, F., Kainz, M. J., . . . Wehr, J. D. (2017). How important are terrestrial organic carbon inputs for secondary production in freshwater ecosystems?. Freshwater Biology, 62 (5), 833-853. doi:10.1111/fwb.12909 Open access

Helle, H. (2017, 25.2.2017). Keltasirkku kanarialintuna. Keskisuomalainen, p. 39.

Haimi, J. (2017, 14.1.2017). Kuoriaisia ruokakaapissa?. Keskisuomalainen, p. 36.

Komonen, A. (2017, 28.1.2017). Käpyjen jäytäjät. Keskisuomalainen, p. 33.

Haapakoski, M. (2017, 11.2.2017). Kävynsuomu suksen alla. Keskisuomalainen, p. 33.

Mikonranta, L., Dickel, F., Mappes, J., & Freitak, D. (2017). Lepidopteran species have a variety of defence strategies against bacterial infections. Journal of Invertebrate Pathology, 144, 88-96. doi:10.1016/j.jip.2017.01.012 Open access

Komonen, A. (2017, 11.2.2017). Limasieni - vähän niin kuin eläin. Keskisuomalainen, p. 33.

Haapakoski, M. (2017, 25.2.2017). Lumikolla lämmin talvipesä. Keskisuomalainen, p. 39.

Halme, P. (2017, 2.2.2017). Luonnonsuojelubiologi ja kestävyyspuhe. Tiedeblogi. Open access

Komonen, A. (2017, 11.3.2017). Manto kelpaa kuoriaiselle. Keskisuomalainen, p. 37.

Rissanen, A., Ojala, A., Fred, T., Toivonen, J., & Tiirola, M. (2017). Methylophilaceae and Hyphomicrobium as target taxonomic groups in monitoring the function of methanol-fed denitrification biofilters in municipal wastewater treatment plants. Journal of Industrial Microbiology and Biotechnology, 44 (1), 35-47. doi:10.1007/s10295-016-1860-5 Open access

Poosakkannu, A., Nissinen, R., Männistö, M., & Kytöviita, M.-M. (2017). Microbial community composition but not diversity changes along succession in arctic sand dunes. Environmental Microbiology, 19 (2), 698-709. doi:10.1111/1462-2920.13599 Open access

De Freitas Almeida, G., Ferreira, S. L. C., Philippe, C., & Santos, A. J. (2017). Mimiviruses and the Human Interferon System : Viral Evasion of Classical Antiviral Activities, But Inhibition By a Novel Interferon-β Regulated Immunomodulatory Pathway. Journal of Interferon and Cytokine Research, 37 (1), 1-8. doi:10.1089/jir.2016.0097

Komonen, A. (2017, 25.2.2017). Miten käy kuoriaisten?. Keskisuomalainen, p. 39.

Ambrosio Leal Dutra, L., Almeida, G. M. d. F., Oliveira, G. P., Abrahão, J. S., Kroon, E. G., & Trindade, G. d. S. (2017). Molecular evidence of Orthopoxvirus DNA in capybara (Hydrochoerus hydrochaeris) stool samples. Archives of Virology, 162 (2), 439-448. doi:10.1007/s00705-016-3121-3

Kytöviita, M.-M. (2017, 14.1.2017). Männyn monet kävyt. Keskisuomalainen, p. 36.

Avila, P. (2017). New insights on the role of ecology and life-history in social evolution. Jyväskylä, Finland: University of Jyväskylä. Jyväskylä studies in biological and environmental science, 326. Retrieved from http://urn.fi/URN:ISBN:978-951-39-6904-2 Open access

Triviño, M., Pohjanmies, T., Mazziotta, A., Juutinen, A., Podkopaev, D., Le tortorec, E., & Mönkkönen, M. (2017). Optimizing management to enhance multifunctionality in a boreal forest landscape. Journal of Applied Ecology, 54 (1), 61-70. doi:10.1111/1365-2664.12790 Open access

Merikanto, I., Laakso, J., & Kaitala, V. (2017). Outside-host predation as a biological control against an environmental opportunist disease. Ecological Modelling, 347, 85-93. doi:10.1016/j.ecolmodel.2017.01.002

Gopala Krishnan, M. K., Brader, G., Sessitsch, A., Mäki, A., Elsas, J. D. V., & Nissinen, R. (2017). Plants Assemble Species Specific Bacterial Communities From Common Core Taxa in Three Arcto-Alpine Climate Zones. Frontiers in Microbiology, 8, 12. doi:10.3389/fmicb.2017.00012 Open access

Felton, A., Ranius, T., Roberge, J.-M., Öhman, K., Lämås, T., Hynynen, J., . . . Nordin, A. (2017). Projecting biodiversity and wood production in future forest landscapes: 15 key modeling considerations. Journal of Environmental Management, 197 (July), 404-414. doi:10.1016/j.jenvman.2017.04.001

Elzinga, J. A., & Varga, S. (2017). Prolonged stigma and flower lifespan in females of the gynodioecious plant Geranium sylvaticum. Flora, 226, 72-81. doi:10.1016/j.flora.2016.11.007 Open access

Mazziotta, A., Podkopaev, D., Triviño, M., Miettinen, K., Pohjanmies, T., & Mönkkönen, M. (2017). Quantifying and resolving conservation conflicts in forest landscapes via multiobjective optimization. Silva Fennica, 51 (1), 1778. doi:10.14214/sf.1778 Open access

Gordon, S., Lopez Sepulcre, A., Rumbo, D., & Reznick, D. N. (2017). Rapid Changes in the Sex Linkage of Male Coloration in Introduced Guppy Populations. American Naturalist, 189 (2), 196-200. doi:10.1086/689864

Gaelings, L., Söderholm, S., Bugai, A., Fu, Y., Nandania, J., Schepens, B., . . . Kainov, D. E. (2017). Regulation of Kynurenine Biosynthesis during Influenza Virus Infection. FEBS Journal, 284 (2), 222-236. doi:10.1111/febs.13966 Open access

Nevalainen, L., & Luoto, T. (2017). Relationship between cladoceran (Crustacea) functional diversity and lake trophic gradients. Functional Ecology, 31 (2), 488-498. doi:10.1111/1365-2435.12737 Open access

Helama, S., Luoto, T., Nevalainen, L., & Edvardsson, J. (2017). Rereading a tree-ring database to illustrate depositional histories of subfossil trees. Palaeontologia Electronica, 20 (1), 2A. Retrieved from http://palaeo-electronica.org/content/2017/1735-depositional-histories Open access

Jensen, H., Kiljunen, M., Knudsen, R., & Amundsen, P.-A. (2017). Resource Partitioning in Food, Space and Time between Arctic Charr (Salvelinus alpinus), Brown Trout (Salmo trutta) and European Whitefish (Coregonus lavaretus) at the Southern Edge of Their Continuous Coexistence. PLoS ONE, 12 (1), e0170582. doi:10.1371/journal.pone.0170582 Open access

Juutilainen, K., Mönkkönen, M., Kotiranta, H., & Halme, P. (2017). Resource use of wood-inhabiting fungi in different boreal forest types. Fungal Ecology, 27 (Part A), 96-106. doi:10.1016/j.funeco.2017.03.003

Lonn, E. (2017). Selection on two behavioral genes : fitness effects of receptor genes for arginine vasopressin 1a and oxytocin in the bank vole Myodes glareolus. Jyväskylä, Finland: University of Jyväskylä. Jyväskylä studies in biological and environmental science, 327. Retrieved from http://urn.fi/URN:ISBN:978-951-39-6969-1 Open access

Halme, P. (2017). Sieniatlas tarvitsee jokaisen harrastajan työpanosta. Sienilehti, 69 (1), 4-5.

Kytöviita, M.-M. (2017, 25.3.2017). Silmut kevätvireessä. Keskisuomalainen, p. 33.

Cairns, J., Becks, L., Jalasvuori, M., & Hiltunen, T. (2017). Sublethal streptomycin concentrations and lytic bacteriophage together promote resistance evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 372 (1712), 20160040. doi:10.1098/rstb.2016.0040

Raatikainen, K., Mussaari, M., Raatikainen, K. M., & Halme, P. (2017). Systematic targeting of management actions as a tool to enhance conservation of traditional rural biotopes. Biological Conservation, 207, 90-99. doi:10.1016/j.biocon.2017.01.019 Open access

Cayol, C., Koskela, E., Mappes, T., Siukkola, A., & Kallio, E. (2017). Temporal dynamics of the tick Ixodes ricinus in northern Europe : epidemiological implications. Parasites and Vectors, 10 (1), 166. doi:10.1186/s13071-017-2112-x Open access

Antonovics, J., Wilson, A. J., Forbes, M. R., Hauffe, H. C., Kallio, E., Leggett, H. C., . . . Webster, J. P. (2017). The evolution of transmission mode. Philosophical Transactions of the Royal Society B: Biological Sciences, 372 (1719), 0083. doi:10.1098/rstb.2016.0083 Open access

Kuusela, S., Anttila, S., Halme, P., & Juslén, A. (2017). Tutkimus tehostaa suojelutoimia : yhteenveto Puutteellisesti tunnettujen ja uhanalaisten metsälajien tutkimusohjelman vaikuttavuudesta. Metsätieteen Aikakauskirja, 2017. doi:10.14214/ma.6987 Open access

Jones, S., Ahonen, H., Granlund, L., Arsiola, T., & Taskinen, J. (2017). Two Novel Microsporidia in Skeletal Muscle of Pike-Perch (Sander Lucioperca) and Burbot (Lota Lota) in Finland. Journal of Parasitology, 103 (1), 95-102. doi:10.1645/16-24

Kytöviita, M.-M. (2017, 28.1.2017). Uusia näkökulmia. Keskisuomalainen, p. 33.

Mustonen, M., Haimi, J., Kesäniemi, J., Högmander, H., & Knott, E. (2017). Variation in gene expression within clones of the earthworm Dendrobaena octaedra. PLoS ONE, 12 (4), e0174960. doi:10.1371/journal.pone.0174960 Open access

Klemme, I., & Karvonen, A. (2017). Vertebrate defense against parasites: Interactions between avoidance, resistance, and tolerance. Ecology and Evolution, 7 (2), 561-571. doi:10.1002/ece3.2645 Open access

Abrego, N., Dunson, D., Halme, P., Salcedo, I., & Ovaskainen, O. (2017). Wood-inhabiting fungi with tight associations with other species have declined as a response to forest management. Oikos, 126 (2), 269-275. doi:10.1111/oik.03674 Open access

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