Open doctoral student positions

The Department of Biological and Environmental Science (University of Jyväskylä, Finland) seeks to recruit 4 doctoral students into the Doctoral Programme in Biological and Environmental Science, starting earliest 1.1.2018. The student should complete the doctoral degree in 4 years. Applications, together with all relevant enclosures, should be submitted using electronic application form at latest 31.8.2017 (in Finnish, in English). After the deadline, each supervisor will select one best candidate for their own project. These top candidates will be asked to write a 2-page long research plan on the thesis topic and will be interviewed. Applications sent by email will not be considered. Only one application per candidate is accepted.

For further information on the project, please contact the supervisor (see below).

Further information on the positions and application form: in Finnish, in English.

Descriptions of the projects:

Major subject: Aquatic sciences

1. Eco-evolutionary dynamics of aquatic ecosystems: drivers of resilience and recovery ability (Supervisor: Anna Kuparinen)

Major subject: Cell and molecular biology

2. Evolutionary obstacles and opportunities that govern the dynamics of mobile genetic elements in microbial communities (Supervisor: Matti Jalasvuori)

3. Structural and functional characterization of M23 family metalloendopeptidases that lyse bacterial cell wall peptidoglycans (Supervisors: Perttu Permi & Helena Tossavainen)

4. Virus-nucleus interactions (Supervisor: Maija Vihinen-Ranta)

Major subject: Ecology and evolutionary biology

5. Genetic basis of adaptation to environmental fluctuations (Supervisors: Tarmo Ketola & Ilkka Kronholm)

6. Microbiome-host interactions and developmental polymorphism (Supervisor: Emily Knott)

7. Human induced trans-generational stress tolerance and invasion success (Supervisor: Leena Lindström)

Major subject: Environmental science or Ecology and evolutionary biology

8. Sustainable future use of European forests for developing the bioeconomy (Supervisors: Mikko Mönkkönen, Kyle Eyvindson, Anna Repo & Maria Triviño)

Major subject: Environmental science

9. Climate change and productivity induced shifts in lake food web quality (Supervisors: Sami Taipale & Kimmo Kahilainen)


1. Eco-evolutionary dynamics of aquatic ecosystems: drivers of resilience and recovery ability

The ability of a species to resist change and to recover rapidly from disturbance are the two key determinants of species persistence and viability in a changing world. Apart from their direct ecological impacts, environmental and human-induced drivers can cause rapid evolutionary changes in species life histories. Aquatic ecosystems exposed to fishing provide an optimal context to study eco-evolutionary dynamics within community and ecosystem contexts. Namely, fishes are virtually the only organisms whose natural populations are exposed to systematic and intensive human-induced mortality at a global scale (Darimont et al. 2015) and exploited fish populations worldwide show phenotypic trends towards earlier maturity and smaller body size (Kuparinen & Festa-Bianche 2017).

The objective of the project is to develop simulation models that mechanistically merge ecological and evolutionary dynamics of aquatic ecosystems. To this end, the project will couple the theories of life-history evolution and allometric trophic foodweb models, which are based on the scaling of consumer-resource dynamics by the relative body sizes of the species (Broese et al. 2006, Kuparinen et al. 2016). The project will analyse the eco-evolutionary dynamics of a range of aquatic ecosystems, to identify mechanisms and food web and species properties that make aquatic populations and ecosystems susceptible to disturbances, such as fishing. Mechanistic understanding of these dynamics and their consequences to species and ecosystems has great potential to resolve fundamental yet puzzling patterns observed in natural populations and to identify species and ecosystem properties regulating resilience and recovery ability.

The successful candidate holds an MSc degree in ecology, mathematics, computer sciences, statistics, or comparable skills. Since the project is basis on modelling, the candidate must be comfortable with theoretical work and possess decent programming skills. Knowledge of Matlab is highly beneficial, but solid skills in other another programming language (e.g. C/C++) combined with eagerness to learn Matlab might be sufficient. Experience and/or substantial interest is simulation modelling is also expected. The project includes opportunities for international mobility.

Further information: Associate professor Anna Kuparinen, Email: , Tel. +358 40 8055 046. See profile here.

Brose U., Williams R.J. & Martinez N.D. (2006) Allometric scaling enhances stability in complex food webs. Ecol. Lett. 9: 1228–1236.
Darimont C.T., Fox C.H., Bryan H.M. et al. (2015) The unique ecology of human predators. Science 349: 858–860.
Kuparinen A., Boit A., Valdovinos F.S., Lassaux H. & Martinez N.D. (2016) Fishing-induced life-history changes degrade and destabilize harvested ecosystems. Sci. Rep. 6: 22245.

Kuparinen A. & Festa-Bianche M. (2017) Harvest-induced evolution: insights from aquatic and terrestrial systems. Phil. Trans. R Soc. B 372: 20160036.

2. Evolutionary obstacles and opportunities that govern the dynamics of mobile genetic elements in microbial communities

Resistance to antibiotics along with increased virulence has turned bacterium Klebsiella pneumoniae into one of the most notorious hospital pathogens. Genetically it is a complex puzzle: K. pneumoniae strains carry large conjugative and smaller non-conjugative plasmids; the number of integrated viruses and integrative and conjugative elements (ICEs) vary between bacteria, and some isolates have multiple CRISPR-loci defending the host against external genetic invaders whereas others have none. While the bacterial chromosome provides much of the genetic background for the mobile elements to operate in, it is usually the mobile elements that determine the resistance and virulence of individual strains. This interaction between chromosomal background (that drift away from each other due to neutral mutations) and mobile elements (that often change from one background to another) is understood only to some extent. Elements that are not adapted to the host induce fitness costs and thus are selected against. On the other hand, acquiring a novel element at the right moment can rescue the strain from otherwise lethal situation (for example during antibiotic therapy) or provide unique openings for reproduction (for example by providing genes that allow exploitation of host resources). Mobile elements can also force their uptake even in conditions where it is not favorable to the host.

In the proposed PhD project, the interaction of conjugative elements acquired from epidemic K. pneumoniae against novel genetic backgrounds (other hosts) are mapped in an attempt to understand evolutionary obstacles and opportunities that govern the dynamics of mobile genetic elements in microbial communities. This research provides insights to the emergence of novel hospital pathogens as well as helps determine fundamental eco-evolutionary rules behind inter-host genetic exchange. Methodologically, the project involves microbiology with bacteria, molecular biology, genetics and some bioinformatics. Also, if the applicant is interested, there are opportunities for developing computational models. The applicant would join a dynamic research group that studies antibiotic resistant bacteria originating from hospitals across the world. The project is done in collaboration with researchers from Karolinska Institute (Sweden), National Center for Biotechonology Information (NCBI, USA) and University of Cambridge (UK).

A successful applicant would have a background in cellular and molecular biology, evolutionary genetics, or a related field.

Further information: Academy Research Fellow Matti Jalasvuori, Email: matti.jalasvuori@jyu.fi.; mattijalasvuoriresearch.blogspot.fi.

Jalasvuori M. & Koonin E. (2015) Classification of prokaryotic genetic replicators: Between selfishness and altruism. Annals of the New York Academy of Sciences 1341: 96–105.
Ojala V., Mattila S., Hoikkala V., Bamford J.K.H., Hiltunen T. & Jalasvuori M. (2016) Scoping the effectiveness and evolutionary obstacles in utilizing plasmid-dependent phages to fight antibiotic resistance. Future microbiology. 11: 999–1009.

3.Structural and functional characterization of M23 family metalloendopeptidases that lyse bacterial cell wall peptidoglycans

Staphylococcus aureus is a major human and veterinary pathogen. The evident increase in S. aureus resistance to antibiotics demands for the development of new, efficient and cost-effective chemotherapeutics. The use of autolysins (bacterial peptidoglycan hydrolases) for the prevention and treatment of S. aureus infections has been under vivid research and shown very promising results. Autolysins play an important role in the maintenance of the bacterial cell wall. The S. aureus cell wall is composed of two polymers, peptidoglycan and teichoic acid. The former provides the structural framework of the bacterium and protects against turgor pressure, whereas the latter controls the overall surface charge affecting e.g. the activity of peptidoglycan hydrolases and surface adherence ability of the bacterium. To date, two autolysins have been tested as potential staphylolytic agents, S. simulans lysostaphin and Pseudomonas aeruginosa LasA. These cleave pentaglycine bridges present in peptidoglycan. Lysostaphin and LasA belong to the M23 family of zinc-dependent peptidases. Other M23 family members that have been structurally and/or functionally characterized are ALE-1 from S. capitis, LytM and LytU from S. aureus, and NMB0315 from Neisseria meningitidis. The overall structures of the enzymes are strikingly similar, the catalytic efficiencies are, nevertheless, markedly different.

The aim of the project is to unravel underlying structural basis for different substrate specificities, catalytic efficiencies as well as the catalytic mechanism of these very similar enzymes by using various biophysical and biochemical approaches. These studies pave the way for development of new therapeutic agents to treat S. aureus infections. The PhD student will engage in structural and functional characterization of this enzyme family by collecting and analyzing data on protein structure and dynamics along with substrate interactions and kinetics. The Permi Lab is the main user of a recently installed, state-of-the-art Bruker Avance III HD NMR spectrometer operating at 800 MHz of 1H frequency, and has access also to a recently upgraded Bruker Avance III 500 MHz NMR spectrometer. The group has also modern facilities for protein production and purification.

We are looking for a motivated PhD applicant having a Master’s degree in Biology/Chemistry or a related field, and some experience at least in one of the following topics: Structural biology/structural bioinformatics, protein biochemistry, biophysical characterization of proteins, NMR spectroscopy, X-ray crystallography. Additional experience on MD simulations, programming, statistics or bioinformatics is beneficial but not essential.

Further information: Professor Perttu Permi, Email: Perttu.Permi@jyu.fi, Tel. +358 (0)40 8054288

Szweda et al. (2012) Peptidoglycan hydrolases-potential weapons against Staphylococcus aureus. Appl Microbiol Biotechnol. 96: 1157–74.


4. Virus-nucleus interactions

Understanding of virus-nucleus interactions is essential for discovering improvements and novel strategies in development of herpes simplex virus type 1 (HSV-1) anti-virals and HSV-1 mediated gene therapy. Moreover, viral infections manipulate the nucleus, and serve as excellent model systems for the characterization of nuclear processes. Our studies advance the current research of virus-nucleus interactions by an interdisciplinary approach involving cell biology and biophysics, combined with state-of-the-art techniques of microscopy imaging, advanced image analysis, and biophysical modeling.

This PhD project aims to unravel the structural changes of chromatin and viral egress dynamics during the lytic infection with HSV-1. In continuation of our prior studies on HSV-1 reorganization of chromatin architecture (1, 2), we will further analyze the mechanisms of viral impact on chromatin structure and detailed dynamics of viral nuclear exit. These studies are done in close collaboration with Prof. Carolyn Larabell (National Center for X-ray Tomography, Lawrence Berkeley National Laboratory, CA, USA; 1, 3) and other collaboration partners with expertise in advanced imaging, modeling, biophysics, virology and viral therapy.

The doctoral student will benefit from supportive research training environment and receive co-supervision by group leader and the senior members of the research team. He/she will use state-of-the-art imaging techniques in University of Jyväskylä, Tampere and Helsinki, attend advanced practical courses on imaging (e.g. EMBO) and national and international scientific meetings, and do site visits in international labs.

We are looking for a highly motivated PhD candidate with a Master’s degree and background in one or several of these areas or a related field: cell biology / microbiology / virology / advanced imaging including live cell imaging, confocal microscopy, EM etc. / biophysics, to conduct the experimental work.

Further information: Group leader, senior lecturer Maija Vihinen-Ranta, Email: maija.vihinen-ranta@jyu.fi

Our most recent publications
Aho V., Myllys M., Ruokolainen V., Hakanen S., Mäntylä E., Virtanen J., Hukkanen V., Kühn T., Timonen J., Mattila K., Larabell C. & Vihinen-Ranta M (2017). Chromatin organization regulates viral egress dynamics Sci Rep 16(7): 3692.
Pyöriä L., Toppinen M., Mäntylä E., Hedman L., Aaltonen L.-M., Vihinen-Ranta M., Söderlund-Venermo M., Hedman K. & Perdomo M.F. (2017). Extinct type of human parvovirus B19 persists in tonsillar B cells. Nat Commun 4(8): 14930.
Myllys M., Ruokolainen V., Aho V., Smith E., Hakanen S., Peri P., Salvetti A., Timonen J., Hukkanen V., Larabell C. & Vihinen-Ranta M. (2016). Herpes simplex virus 1 induces egress channels through marginalized host chromatin. Sci Rep, 28(6): 28844.
Aho V., Mattila K., Kühn T., Kekäläinen P., Pulkkinen O., Brondani Minussi R., Vihinen-Ranta M. & Timonen J. (2016). Diffusion through thin membranes: Modeling across scales. Phys Rev E 93: 043309.

5. Genetic basis of adaptation to environmental fluctuations

Global change is expected not only to increase mean temperatures but also to increase fluctuations in temperature. However, very little is known about adaptation to fluctuations in comparison to evolution in constant environments. Theories and an array of well reported physiological adaptations suggest that different sorts of fluctuations can have drastically different evolutionary outcomes.

We hypothesize that if genetic strategies, transgenerationally mediated effects, phenotypic plasticity, mutator strategies, bet hedging, and coping mechanisms for acute and chronic stress affect fitness depending on the frequency and predictability of environmental fluctuations, as vast body of literature expects, we will see differing genetic variances, differing genetic background and specialized adaptations to differently fluctuating environments. Interestingly, this has not been tested before and majority of research considers all fluctuations the same, or considers that fitness under fluctuations can be described with measurements done at constant environments, i.e. via tolerance curves or reaction norms. Information on which is the case is crucial for predicting how climate change induced fluctuations affect biota.

We approach these questions with experimental evolution methodologies and experiments with sequenced strains, using Bacteria and Neurospora crassa –fungi.

We expect enthusiast applicants with dire interest on evolutionary consequences of fluctuating environments with good writing and communication skills. Previous expertise on microbiological methods, quantitative genetics or genetic analyses of sequenced strains is a bonus, but not a prerequisite.

Further information: Academy Research Fellow Tarmo Ketola, e-mail: tketola@jyu.fi; www.ketolalab.com

6. Microbiome-host interactions and developmental polymorphism

The poecilogonous polychaete Pygospio elegans is able to produce different kinds of larvae: planktonic larvae, capable of dispersal, that complete most of their development in the plankton, and benthic larvae that do not disperse, but develop in brood capsules maintained by the mother. Neither a genetic nor an environmental basis for this polymorphism has been determined. Recently, two species of marine gregarine (Selenidium spp.) have been noted in P. elegans. Transcriptome data collected in the group (Heikkinen et al. in review) suggest that high parasite loads might be more common in populations of P. elegans that produce planktonic larvae.

This PhD project will investigate the role of co-habiting parasitic intestinal protozoa on host physiology and larval developmental mode variation (poecilogony) exhibited by polychaete worms. The work aims to: 1) document the extent of infection by marine gregaines (Apicomplexa) in spionid polychaetes that exhibit poecilogony and in their non-poecilogonous relatives; 2) use an experimental approach in combination with a survey of natural populations to clarify the role of infection by Selenidium spp. in developmental variation of Pygospio elegans; and 3) identify physiological responses, i.e. gene expression signatures of both Apicomplexa and the host, that could shed light on the molecular mechanisms involved in infection and defense.

I am seeking a highly motivated candidate with a Master’s degree and background in evolutionary biology, genetics, molecular biology, or a related field, to explore the above questions. Experience working with DNA laboratory is required.

Further information: Academy Research Fellow Emily Knott, Email: emily.knott@jyu.fi. See research group's webpages here.

7. Human induced trans-generational stress tolerance and invasion success

We all know that human induced changes on Earth mark the new geological era, anthropocene. Despite the ongoing sixth mass extinction, we witness the success and rapid spread of invasive species into new areas. Stress tolerance and rapid adaptation to stressful environments are suggested to be among the most important factors affecting the invasion success of invasive species whereas the disability to cope with rapid changes and habitat loss are considered to be the major drivers of species extinctions. To understand the causal links which species succeed and why, we need a more thorough understanding of the factors which promote stress tolerance and adaptation to stressful environments. Furthermore we need to understand what role human induced stress can play in the rapid adaptation to stressful conditions.

This PhD-project aims to assess the human contribution for the development of stress resistance on the invasive pest Colorado potato beetle (Leptinotarsa decemlineata). We are going to estimate the relative roles of genetic background, trans-generational effects and human induced selection (pesticides) on stress tolerance and link this to invasion success. These results will serve both basic research and improve sustainable implementation of invasive species strategy. 

I am seeking a highly motivated candidate with a Master’s degree and a keen interest in ecology and evolutionary biology, or related areas (applied ecology, genetics, molecular biology). The recruited PhD candidate is expected to have excellent English communication skills. 

Further information: Senior lecturer Leena Lindström,  E.mail: leena.m.lindstrom@jyu.fi, More information on group website.

Lehmann, P. Lyytinen, A., Piiroinen, S. and Lindström, L. 2015. Latitudinal differences in diapause related photoperiodic responses of European Colorado potato beetles (Leptinotarsa decemlineata). Evolutionary Ecology 29:269-282.

Piiroinen, S., Boman, S., Lyytinen, A., Mappes, J. & Lindström, L 2014. Sublethal effects of deltamethrin exposure of parental generations on physiological traits and overwintering in Leptinotarsa decemlineata. Journal of Applied Entomology 138: 149-158.

8. Sustainable future use of European forests for developing the bioeconomy

Work description. The PhD student will work in the project “Sustainable future use of European forests for developing the bioeconomy“. In this project, we assess the potential of EU forestry policy and practice to increase the delivery of wood products while contributing to climate change mitigation in such a way that the delivery of other ecosystem services and the persistence of forest species are also warranted in the long-term from the Finnish perspective. For this holistic evaluation, our international team includes forest researchers, life cycle analysis experts and biologists together with target stakeholders of the forestry and environmental sectors that will work on developing a novel integrative framework for forest management. We aim to identify forest management plans that can provide optimal solutions to potential conflicts across the full array of considered objectives (ecosystem services and biodiversity). We consider a wide set of valuable provisioning (i.e. collectable goods), regulating (i.e. climate regulation) and cultural (i.e. recreation) ecosystem services that boreal forests can provide. We consider alternative aspects of biodiversity including habitat availability for indicator and umbrella species, availability of critical resources, and plant species richness.

Qualifications. The research tasks will require the development and use of mathematical models in forecasting resource development, potential for ecosystem service provisioning and biodiversity conservation. To be successful, applicants should be able to express themselves fluently in both written and verbal communication and possess good analytical and problem-solving skills. Applicants should be familiar with a computer programming language (e.g. python or R) and database management tools (i.e. SQL). An ability to work with large data sets is necessary. Familiarity with operations research methods is considered an asset. Potential candidates are required to be eligible to start doctoral training and to have a master’s degree e.g. in ecology, economics, forestry, mathematics, statistics or systems analysis.

Further information: Professor Mikko Mönkkönen, Email: mikko.monkkonen@jyu.fi

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.
Mönkkönen M., Juutinen A., Mazziotta A., Miettinen K., Podkopaev D., Reunanen P., Salminen H. & Tikkanen O.-P. (2014) Spatially dynamic forest management to sustain biodiversity and economic returns. Journal of Environmental Management 134: 80–89.

9. Climate change and productivity induced shifts in lake food web quality

Climate change is major environmental challenge in northern lake ecosystems influencing energy sources and flows, but very little is known of how it affects the synthesis and transfer of essential biomolecules in freshwater food webs (Taipale et al. 2016). These consequences are likely to vary along different climatic zones, but climate change may indirectly affect the synthesis and transfer of essential fatty acids, especially on EPA (20:5ω3) and DHA (22:6ω3), which are physiologically the most important fatty acids for zooplankton, fish, birds, mammals and humans. Since EPA and DHA is directly related to the somatic growth and reproduction of consumers, the lower availability of these essential fatty acids can decrease productivity of freshwater ecosystems, but can have severe impact on development and survival of consumers e.g. fish larvae. In addition, increasing temperature and precipitation in northern regions may change the biomagnification dynamics of fatty acids in food webs and subsequent accumulation in fish, thus potentially minimizing the positive health effects of EPA and DHA for humans. On this project, climate change and land-use impact on food web quality will be studied in the best climatic and land-use gradient in Finland (from Kilpisjärvi to Arctic circle). Along this gradient of 20 lakes temperature (+3°C), precipitation (+30 %) and nutrient (TP) concentration (+45 µg/L) increase significantly. The most of samples are already collected, but this project would also include lake sampling on this area. Goals of this PhD project is to 1) define ecological consequences of climate and productivity on pelagic and benthic fatty acid coupling of generalist fish, 2) is to study how climate change and land-use will affect the content of polyunsaturated fatty acids of common fish species in local subsistence catches, and 3) to study climatic and land-use stressors influence on biomagnification of essential fatty acids in lake food webs from primary producers to top consumers.

I am seeking a highly motivated candidate with a Master’s degree and background in ecology / fish biology / toxicology / organic chemistry or related areas. Prior expertise on working in laboratory and field is acknowledged and should mentioned in motivation letter.

Further information: Senior Lecturer Sami J. Taipale, Email: sami.taipale@jyu.fi

Taipale S.J., Vuorio K., Strandberg U. Kahilainen K.K., Järvinen M., Hiltunen M., Peltomaa E. & Kankaala P. (2016) Lake eutrophication and brownification downgrade availability and transfer of essential fatty acids for human consumption. Environment International 96: 156–166.