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 1.1.2019. The student should complete the doctoral degree in 4 years. Applications for the positions together with all relevant enclosures, should be submitted using electronic application form at latest 31.8.2018 (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. Further information on the positions in Saima (salary etc.) and application form: in Finnish, in English.

For further information on the project, please contact the supervisor (see below).
Descriptions of the projects:

Major subject: Aquatic sciences

1. CoreSex: Experimental behavioural biology of fish (Supervisor: Juha Karjalainen)

Major subject: Cell and molecular biology

2. Fight against multi-resistant bacteria - Assessing and tuning target cell specificity of antimicrobial enzymes (Supervisor: Perttu Permi)

3. Signaling pathways associated with mechanosensitive muscle abnormalities in Drosophila melanogaster (Supervisors: Jari Ylänne)

Major subject: Ecology and evolutionary biology

4. Costs and benefits of larval cannibalism in a species threatened by a deadly disease (Supervisor: Bibiana Rojas)

5. Theoretical studies of the evolution of mating systems and parental care (Supervisor: Lutz Fromhage)

6. WILD HEALTH: How does environmental biodiversity affect wildlife health? (Supervisor: Tapio Mappes)

Major subject: Environmental science

7. Occurrence of selected antibiotics and antibiotic resistance bacteria and genes in untreated and treated wastewaters and sludge and the risk reduction with multi-barrier approach (Supervisor: Tuula Tuhkanen)

8. Optical properties regulate the food web structure and fish biomass in lakes (Supervisor: Anssi Vähätalo)

1. CoreSex: Experimental behavioural biology of fish

A high proportion of freshwater fish catches in Europe and North America consist of coregonid fishes and despite their intensive exploitation, many key questions of their biology, such as details of their mating system and spawning behaviour, are still unanswered. Coregonid species have versatile life histories and reproductive strategies and e.g. a small-sized schooling species vendace,  Coregonus albula, clearly responds to fishing mortality differently from many other important commercial species including whitefish (C. lavaretus) with longer life cycle and larger maturation size. Yet, majority of harvest models and management advice has been developed for fishes in the latter category and thus, with incorrect life history information for small-sized, short-living schooling species. Further, recently it has become self-evident that in order to understand the requirements for sustainable harvesting, one needs individual level knowledge on key biological parameters in addition to the traditional population/cohort averages.

The project CoreSex aims to experimentally disentangle 1) the characteristics and differences in mate choice of vendace and whitefish, 2) the importance of chemical clues in their mate choice and 3) in kinship recognition in the spawning occurring in the dark, and 4) whether industrial or municipal waste waters affect reproduction behaviour of coregonids by confusing their olfactory sensing.

In all, the questions in the focus of the PhD thesis project bear significance to the ecologically sustainable fisheries management of not only coregonids, but more generally on any small-sized, short-living species experiencing low stock levels either due to natural or human induced causes.

We are looking for an enthusiastic PhD student with firm knowledge on fish biology and ecology and skills to collaborate within the international Coregonid Fish Research Team in experimental research on behavioural biology of coregonid fish reproduction.

Further information: Professor Juha Karjalainen, Email: juha.karjalainen@jyu.fi

Karjalainen Research group page, Juha Karjalainen Research Gate, Timo Marjomäki, Research gate

2. Fight against multi-resistant bacteria - Assessing and tuning target cell specificity of antimicrobial enzymes

Increasing bacterial multi-drug resistance calls for new therapeutic strategies. Gram-positive Staphylococcus aureus and especially its methicillin-resistant strain (MRSA) is responsible for a myriad of diseases, including severe wound and bloodstream infections in hospital-acquired MRSA or skin and soft tissue infections in community-associated MRSA settings. S. aureus is also a major veterinary pathogen, and it has a major contribution to food-borne diseases. In February 2017 WHO published a first ever list of the 12 most threatening antibiotic-resistant families of bacteria to promote development of new antibiotics. Together with Enterococcus faecium, S. aureus hold the two first positions in the second-most threatening class “HIGH priority”1. The evident increase in S. aureus resistance to antibiotics demands for the development of new, efficient and cost-effective chemotherapeutics.

Our group is focused on structural and functional studies of peptidoglycan hydrolases (PGHs), a novel group of alternative, potential antibacterial agents to combat infections caused by Gram-positive bacteria. Whereas the majority of antibiotics target cell wall synthesis, including penicillin and other beta-lactam antibiotics, our approach aims to harness PGHs to selectively “seek and destroy” the bacterial envelope without disrupting natural microflora. Externally administered PHGs target the bacterial cell wall, the thick (up to 40 layers), highly cross-linked peptidoglycan network embracing surface proteins and carbohydrates. PGHs cleave specific chemical bonds in peptidoglycan, which induces bacterial cell lysis and death.

Along with our recent structural and functional studies of lysostaphin and LytM, well-known members of the M23 metallopeptidase family, we have identified the product of the S. aureus gene sa0205, dubbed as LytU as a novel PGH3-5. In contrast to the common beta-lactam antibiotics, whose mechanism of action and antimicrobial resistance e.g. in MRSA are well-established, a profound understanding of PGHs’ structural and functional role, their evolutionary aspects, and mechanisms in cell wall recognition is currently lacking. In this project, we are addressing the underlying questions regarding target cell and substrate specificity as well as catalytic efficiency of these enzymes by using various approaches in molecular biology and biophysics. Another goal is to decipher the activation and regulation mechanisms of LytU in vivo. In addition, monitoring of lytic efficiency of these enzymes against different S. aureus strains, including the notorious MRSA, and biofilms will be tested. These studies pave the way for the development of new therapeutic agents to treat S. aureus infections.

The PhD student will have the possibility to work on an interdisciplinary project with medical relevance, using state-of-the-art methodology and instrumentation e.g., high-field NMR spectrometers or electron and helium ion microscopes, in a highly motivated research team. 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 1H frequency and has access also to a recently upgraded Bruker Avance III 500 MHz NMR spectrometer. The group has modern facilities for protein production and purification.

We are looking for a motivated PhD applicant having a Master’s degree in molecular biology, (bio)chemistry, (bio)physics or a related field. Experience in one or more of the following topics are considered as an asset: bacterial cell biology, biophysical characterization of proteins, imaging (electron or helium ion microscopy), protein biochemistry, structural biology (NMR spectroscopy, X-ray crystallography) and structural bioinformatics. Additional experience on simulations, programming or statistics is beneficial but not essential.

Further information: Professor Perttu Permi, Email: perttu.permi@jyu.fi

Permi Research group page

“WHO Publishes List of Bacteria For Which New Antibiotics are Urgently Needed” WHO News Releases (2017), http://www.who.int/mediacentre/news/releases/2017/bacteria-antibiotics-needed/en/
Szweda et al. (2012) Peptidoglycan hydrolases-potential weapons against Staphylococcus aureus. Appl Microbiol Biotechnol. 96:1157-74.
Raulinaitis et al. (2017) 1H, 13C and 15N resonance assignments of the new lysostaphin family endopeptidase catalytic domain from Staphylococcus aureus. Biomol. NMR Assign. 11, 69.
Raulinaitis et al. (2017) Identification and structural characterization of LytU, a unique peptidoglycan endopeptidase from the lysostaphin family. Sci. Rep. 7, 6020.
Tossavainen et al. (2018) Structural and functional insights into lysostaphin-substrate interaction. Front. Mol. Biosci. (in press).

3. Signaling pathways associated with mechanosensitive muscle abnormalities in Drosophila melanogaster

In tissues, cell differentiation is partially controlled by mechanical forces. Individual cells sense the forces generated by neighbouring cells and also actively probe the surrounding tissue by pulling on it. Cell adhesion molecules and actin cytoskeleton play a central role in this mechanosensing. We have found that alterations in the integrin-associated mechanosensitive proteins talin and vinculin and in the actin cross-linking protein filamin lead to defects in Drosophila indirect flight muscle structure and function. The aim of the project is to characterize the intracellular signalling pathways involved.

We are seeking for a PhD candidate with a strong cell and molecular biology or developmental biology background. Experience in confocal microscopy and Drosophila genetics is an advantage.

Further information: Professor Jari Ylänne, Email: jari.p.ylanne@jyu.fi

Ylänne Research group page

Green, H.J., Griffiths, A.G.M., Ylänne, J., and Brown, N.H. (2018). Novel functions for integrin-associated proteins revealed by analysis of myofibril attachment in Drosophila. ELife 7, e35783.
Huelsmann, S., Rintanen, N., Sethi, R., Brown, N.H., and Ylänne, J. (2016). Evidence for the mechanosensor function of filamin in tissue development. Scientific Reports 6, srep32798.
Maartens, A.P., Wellmann, J., Wictome, E., Klapholz, B., Green, H., and Brown, N.H. (2016). Drosophila vinculin is more harmful when hyperactive than absent, and can circumvent integrin to form adhesion complexes. J. Cell. Sci. 129, 4354–4365.


4. Costs and benefits of larval cannibalism in a species threatened by a deadly disease

Cannibalism is common among animals because eating conspecifics confers nutritional benefits that can make the difference between survival and death. However, cannibals should recognise their kin; if not, they decrease the amount of family genes passed onto the next generation, and are more likely to acquire infectious diseases. Here, we will study the cannibalistic behaviour between tadpoles of an Amazonian frog species which devotedly cares of its offspring, and which develops in unstable environments that can suddenly dry out. This project aims to establish if cannibalism confers benefits that make tadpoles more likely to survive until metamorphosis, and have larger size and better performance when they start terrestrial life; but also to determine if cannibals pay the cost of acquiring infectious diseases more easily. Our study will provide new insights into the spread mechanisms of a disease that is largely responsible for amphibian declines worldwide, and into the potential role of parental decision-making in the regulation of this counterintuitive behaviour. The project will entail both field work and experiments with captive animals.

 I am seeking a highly motivated candidate with good background in behavioural and/or evolutionary ecology or related areas, excellent written and oral communication skills in English and a strong interest in interdisciplinary research. Prior experience doing fieldwork in the tropics is not required but will be considered a bonus.

Further information: Academy Research Fellow Bibiana Rojas, Email: bibiana.rojas@jyu.fi

Rojas Research group page

Pfennig, D. W. 1999. Cannibalistic tadpoles that pose the greatest threat to kin are most likely to discriminate kin. - Proceedings of the Royal Society B-Biological Sciences 266: 57-61
Rojas, B. 2014. Strange parental decisions: fathers of the dyeing poison frog deposit their tadpoles in pools occupied by large cannibals. . - Behavioral Ecology and Sociobiology 68: 551-559.
 Rojas, B. 2015. Mind the gap: treefalls as drivers of parental tradeoffs. - Ecology and Evolution 5 4028-4036.
Summers, K. and McKeon, C. S. 2004. The evolutionary ecology of phytotelmata use in neotropical poison frogs. - Miscellaneous Publications Museum of Zoology University of Michigan 193: 55-73.
Stynoski, J. L., Schulte, L. M. and Rojas, B. 2015. Poison frogs. - Current Biology 25: R1026–R1028.

 5. Theoretical studies of the evolution of mating systems and parental care

A fundamental question in evolutionary biology is why anisogamy, the difference in gamete size that defines the sexes, has repeatedly led to large differences in behaviours such as mate searching, mating competition, and parental care. Recent theory has made progress in this area based on mathematical models of the feedback loops that link sex-specific selection pressures with the current state of a population (including current sex differences).

The objective of the project is to develop mathematical and simulation models to study this topic further. Specific points of interest include (1) the evolution of “mating windows” (intervals in a female’s life cycle during which the exact timing of mating does not affect the timing of offspring production, e.g. due to sperm storage; Fromhage et al. 2016); (2) the origin of sex-specific “time-out” durations (the time needed to recover after reproduction; Fromhage and Jennions 2016); and (3) the role of seasonal versus continuous reproduction. The candidate will be encouraged to also develop own ideas within this field of study.

The successful candidate should hold an MSc degree in a relevant area (e.g. behavioural ecology, evolutionary biology, economics with focus on game theory, physics, mathematics, computer science), with some mathematical and computing skills and a keen interest in evolutionary biology.

Further information: Academy Research Fellow Lutz Fromhage, Email: lutz.fromhage@jyu.fi

Fromhage Research group page

Fromhage, L., and M. D. Jennions. 2016. Coevolution of parental investment and sexually selected traits drives sex-role divergence. Nature Communications 7:12517.
Fromhage, L., M. D. Jennions, and H. Kokko. 2016. The evolution of sex roles in mate-searching. Evolution 70:617–624.

6. WILD HEALTH: How does environmental biodiversity affect wildlife health?

Biodiversity has a multifunctional role in maintaining ecosystem goods and services. Biodiversity has been hypothesised to positively impact human health (Hanski et al. 2012) via a co-association with the host’s microbiome (an associated community of microscopic organisms), but it is unknown whether biodiversity confers a comparable benefit to wildlife. The Phd student will test the hypothesis that environmental biodiversity has positive effect on wildlife health by combining state-of-the-art genomics methods, molecular biology and bioinformatics, with community ecology, empirical data and field experiments. Phd student examine the health of mammals (bank voles) inhabiting forests that experience contrasting human impacts.

The PhD project is adopts a holistic approach to quantifying both biodiversity and wildlife health across appropriate biological hierarchies: from communities to individuals; PhD student also use field experiments to quantify the fitness role of the microbiome in nature and test the efficacy of selection on the host and its commensal microbes (the holobiont). Thus, (s)he address the multiple dimensions and accumulating ecosystem services of structural and biological diversity of the environment to the microbial diversity of individuals’ and, finally, the physiology and health of individuals.

We are looking for a motivated PhD applicant having a Master’s degree  in ecology, evolutionary biology, molecular biology or environmental sciences

Further information: Senior lecturer Tapio Mappes, Email: tapio.mappes@jyu.fi

Mappes Research group page

Hanski I et al. 2012 Environmental biodiversity, human microbiota, and allergy are interrelated. PNAS, 109, 8334-8339.

7. Occurrence of selected antibiotics, antibiotic resistant bacteria and resistance genes in untreated and treated wastewaters and sludge and the risk reduction with multi-barrier approach

Antibiotic resistance is currently identified as one of the most serious global health threats by the World Health Organization WHO. Antibiotics are often found in the environment in sub-inhibitory concentrations, which has the potential to promote the development antibiotic resistance. Mixtures of various pharmaceuticals used to treat infectious diseases such as pneumonia, HIV/AIDS and tuberculosis, are excreted from the body via urine and released to the environment in waste waters.  The long term environmental and health effects of these cocktails remain largely unknown even though there is existing evidence of the wide spread evidence of the occurrence of antibiotic resistance bacteria and genes in the wastewater treatment plants and environments exposed to the point and non-point load. Thus, the high antibiotic concentrations measured in hospital wastewaters and developing and middle income countries (such as in Zambia and Kenya) calls for establishment of effective risk identification, management and communication strategies as a priority (Ngumba et al 2016a, b). Even though several individual studies of antibiotics in environmental compartments have been conducted, comprehensive surveys of antibiotics and ARGs in the environment are still scanty.

The objective of the PhD project is to study the occurrence of selected antibiotics in wastewater and sludge. In addition to the chemical analyses the candidate shall determine bacterial load and diversity in selected environmental samples as well as the presence of various antibiotic resistance genes (ARGs).

We are hence looking for a motivated PhD applicant having a Master’s degree and a background in environmental science, microbiology or a related field.

Further information: Professor Tuula Tuhkanen, Email: tuula.tuhkanen@jyu.fi

Ngumba, E., Kosunen, P.,  Gachanja, A and  Tuhkanen, T.  (2016) A multiresidue analytical method for trace level determination of antibiotics and antiretroviral drugs in wastewater and surface water using SPE-LC-MS/MS and matrix-matched standards, Analytical Methods, DOI: 10.1039/c6ay01695b
Ngumba, E, Gachanjah, A., Tuhkanen. T (2016) Occurrence of selected antibiotics and antiretroviral drigs in Nairobi River Basin, Kenya, Sci Total Environ. 539, 206-213

 8. Optical properties regulate food web structure and fish biomass in lakes

A novel initiative of project – a transition from fieldwork-based assessment towards a satellite-based assessment of food web structure and fish biomass in surface waters.

This PhD-project will examine how optical properties regulate phytoplankton communities, aquatic food webs and fish biomass in lakes. Optical properties of lakes refer to the light absorption and scattering properties of water that determine light availability for phytoplankton and affect their community composition. Phytoplankton serves as a basal resource for consumers up to fish (autochthony).  Consumers may alternatively use organic matter (CDOM) imported from the catchment to the lake as their basal resource (allochthony) but only with low efficiency. The light absorption by phytoplankton and by brown allochthonous organic matter can be measured from water samples in laboratory, but also monitored in situ and by remote sensing techniques. The PhD-project seeks for a robust model that explains food web structure and fish biomass based on optical properties of lake water.

The Ph.D. thesis will address three related topics:

1 Optical properties and light availability as the regulators for the composition of phytoplankton communities in lakes. 2 The variability of allochthony in the food webs of lakes assessed by stable isotopes and optical properties in lake water. 3 The relationship between the optical properties of lake water and fish biomass.

We seek a motivated student with a background in natural science (biology, physics, aquatic or environmental science).

Further information: Senior lecturer Anssi Vähätalo, Email: anssi.vahatalo@jyu.fi