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Rekrutacja 2021/2022 – PhD Programme in Biology (Nauki biologiczne)

Harmonogram rekrutacji

PhD Programme in Biology is carried out in English, in full-time, eight-semester system. 

This PhD programme covers courses representing various areas of biological sciences, including training in modern methodology and mastering skills useful in professional academic and nonacademic career. Choice of facultative classes and possibility of gaining credits for courses offered outside of the University ensures flexibility and helps to adjust participation in classes to the individual research plan of the student. 

For everyone who will be accepted for the PhD programme in Biology a scholarship is guaranteed.

PhD students are recruited to the specific research topics offered by the faculty members. Some of the competitions listed below are held outside the OAS system (Online Application System). We kindly ask you to follow the recruitment rules described in each competition. 

Each year, PhD students and their advisors/promotors write individual research plan for a given year. Until the end of four semester student’s achievements are evaluated (mid-term evaluation) by the committee. 

Doctoral dissertations are prepared under the supervision of scientific staff of the Faculty of Biology (members of the Institute of Botany, Institute of Environmental Sciences or Institute of Zoology and Biomedical Research). PhD programme in Biology lead to the scientific Doctoral title in the discipline of biology. More information about the programme can be found here.

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Lista tematów badawczych

IB – 1: Microbial communities of Dryas octopetala in the era of climate change (Institute of Botany)

Institute: Institute of Botany

Topic:  Microbial communities of Dryas octopetala in the era of climate change

Name of supervisor: dr hab. Piotr Mleczko (piotr.mleczko@uj.edu.pl)

Background information:

Arctic and alpine ecosystems are particularly vulnerable to climate change. Rapid changes in Anthropocene will primarily affect organisms adapted to specific climatic and edaphic conditions of cold environments. One of the typical plants that build arctic-alpine communities is Dryas octopetala, found in Europe in the (sub)arctic zone and temperate alpine areas. Relict sites located beyond the ecological optimum are also known. Extant insular pattern of D. octopetala distribution is a natural consequence of glacial and post-glacial range changes, however, mechanisms of the plant population persistence, as well as building and maintaining linked soil microbial community, are weakly known although of fundamental ecological and biogeographical significance. Insight into functioning of cold-adapted plant populations and related microbial communities in discrete, diversified climatic and habitat contexts (optimum vs relict sites) will provide excellent advance to better understand the resilience of interrelated arctic-alpine communities and thus cold-adapted ecosystems.

The main question to be addressed in the project:

What are the functional composition and species richness of soil microorganisms’ communities developed in the root zones of Dryas octopetala in an altitudinal, and thus climatic, gradient from the relict to optimal (alpine) populations? Which factors are responsible to a greater extent for shaping the microbial soil communities of D. octopetala: plant identity or the climatic and edaphic conditions coupled with the local microbial community?

Information on the methods/description of work:

The project relies on the total soil (rhizosphere) DNA metabarcoding, an effective tool for estimating biodiversity in environmental studies. The research is aimed at understanding the species richness and diversity of the D. octopetala rhizosphere microbiota. It consists of molecular analysis of target (barcode) DNA from environmental samples using High-Throughput Sequencing, bioinformatic data processing and treatment of taxonomic units. Sampling sites will be based on the Western Carpathians, where alpine (optimal) and lower-montane (relict) populations of D. octopetala constitute a unique natural model system for comparative studies on the functional ecology of isolated relict plant populations and related soil microbial communities.

Additional information (e.g. special requirements from the student): 

The student will closely collaborate with the Molecular Biogeography team from the Institute of Botany PAS. The candidate should have a strong interest in modern molecular methods as well as a keen interest in bioinformatics and ecological studies. Strong English language, communication and organisational skills are also essential.

Place/name of potential foreign collaborator:

MNHN, CNRS, Université de Sorbonne, Paris, France, prof. Marc-André Selosse; INRAE, Université de Lorraine, Nancy, France, prof. Marc Buée.

References:

Bjorbækmo, M. et al.  (2010). High diversity of root associated fungi in both alpine and arctic Dryas octopetala. BMC Plant Biology 10(1): 244.

Castilho, R. et al. (2020). Habitat specialization controls ectomycorrhizal fungi above the treeline in the European Alps. New Phytologist 229(5): 2901-2916.

Broadbent, A. et al. (2021). Climate change alters temporal dynamics of alpine soil microbial functioning and biogeochemical cycling via earlier snowmelt. The ISME Journal DOI:10.1038/s41396-021-00922-0.

IB – 2: The structure and immunochemistry of stigma and stylar tissue in Utricularia genus (Institute of Botany)

Institute: Institute of Botany

Topic: The structure and immunochemistry of stigma and stylar tissue in Utricularia genus

Name of supervisor: prof. dr hab. Bartosz J. Płachno (bartosz.plachno@uj.edu.pl)                          

Background information:

In flowering plants, stigma, style, and ovule are essential for pollen grain germination, pollen tube growth and later delivery of male gametes into the female gametophyte for double fertilization. Still, very little is known about the interactions between these maternal tissues and the growing pollen tubes. A subtle dialogue takes place between the mother tissues and the pollen tubes, involving pectins, arabinogalactans and other signaling molecules (1-4). No detailed data are available on the structure of the stigma, the stylar tissues, and the interaction between them and pollen tubes in species from genus Utricularia.

The main question to be addressed in the project:

  1. What is the structure of stigmas in species of bladderworts from different subgenera?
  2. Do species classified in the same section have similar stigma structure?
  3. Do stigma structure and stigma secretion correlate with pollinator type?
  4. Is there one or more types of pistil in the genus Utricularia?
  5. What changes take place in the tissues of the pistil during the growth of pollen tubes?

Information on the methods/description of work:

Anatomy techniques; immunochemistry techniques; light microscopy, electron microscopy (SEM, TEM).

Additional information (e.g. special requirements from the student): 

mobility acceptance, working time flexibility and regularity, English fluency, knowledge about botany.

Place/name of potential foreign collaborator:

São Paulo State University (Unesp), Brazil

References:

(1) Herrero, M. Changes in the ovary related to pollen tube guidance. Ann. Bot. 2000, 85, 79–85.

(2) Herrero, M. Ovary signals for directional pollen tube growth. Sex. Plant Reprod. 2001, 14, 3–7.

(3) Li, H.J.; Meng, J.G.; Yang, W.C. Multilayered signaling pathways for pollen tube growth and guidance. Plant Reprod. 2018, 31, 31–41.

(4) Losada, J.M. Herrero, M. Arabinogalactan proteins mediate intercellular crosstalk in the ovule of apple flowers. Plant Reprod. 2019, 32, 291–305.

IB – 3: Phylogenetic reconstruction of Ranunculus sect. Batrachium (Ranunculaceae, Plantae) using DNA hybridization capture techniques (Institute of Botany)

Institute: Institute of Botany

Topic: Phylogenetic reconstruction of Ranunculus sect. Batrachium (Ranunculaceae, Plantae) using DNA hybridization capture techniques

Name of supervisors: dr hab. Joanna Zalewska-Gałosz, prof. UJ; dr Tomasz Suchan (joanna.zalewska-galosz@uj.edu.pl)                      

Background information:

Section Batrachium (Water Crowfoots) is a monophyletic group of macrophytes classified within cosmopolitan, morphologically, and ecologically diverse genus Ranunculus. In the latest worldwide taxonomic account of the section 30 species, 16 hybrids and 29 hybrid combinations within Batrachium were recognised [1]. Batrachium is regarded as taxonomically the most challenging groups of plants because of extreme phenotypic plasticity, frequent hybridization and introgression, allo- and autopolyploidization, and persistence of genetically independent, sterile lineages. Only recently, thanks to the application of the molecular tools, the modern Batrachium phylogeny starts to clarify. Based on the direct sequencing of selected DNA regions (ITS and cpDNA) some Batrachium taxa were successfully molecularly characterised and general phylogenetic clades were resolved [2]. However, molecular studies revealed also significant intraspecific genetic variation of Ranunculus trichophyllus, not directly related with morphological characters, and genetic split in R. baudotii between populations from coastal regions of the Baltic Sea basin and the populations dispersed though the inland Europe [2].

The main question to be addressed in the project:

We aim to develop a cost-effective hybridization capture approach allowing sequencing of orthologous loci even from highly degraded DNA samples [3] and apply it for the Batrachium specimens preserved in different Herbaria. Based on the obtained markers, we will explore genetic information with taxonomic value from the specimens covering large spatial areas and temporal scales, and resolve phylogeny of Batrachium based on acquired data.

Information on the methods/description of work:

We will develop in-house sequence capture protocols for capturing sets of orthologous loci from degraded DNA form the herbarium specimens. The protocols will be based either on the hyRAD technique [3], allowing the capture of random fraction of the genome, or/and EecSeq, an inexpensive method of exon capture [4]. The student will be in charge of DNA isolation from the vouchers, building genomic libraries and the probes form fresh specimens, testing and performing the hybridization captures. They will characterize the utility of the methods for broader phylogenetic scales and analyse the obtained data to resolve the phylogenetic relationships within the studied group. The training program will equip the student with modern laboratory (the “next-generation sequencing” techniques) as well as bioinformatic skills and taxonomical training.

Additional information (e.g. special requirements from the student): 

Working time flexibility and regularity, English fluency. Experience in basic laboratory skills and willingness to learn next generation DNA sequencing techniques and bioinformatic data analysis.

Place/name of potential foreign collaborator:

Gerhard Wiegleb, Department of Ecology, Brandenburg University of Technology Cottbus, Cottbus, Germany [Herbarium collection]
Bobrov, A. Alexander, I.D. Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia [Herbarium collection]

References:

[1] Wiegleb, G., Bobrov, A. A., Zalewska-Gałosz, J., 2017. A taxonomic account of Ranunculus section Batrachium (Ranunculaceae). Phytotaxa 319: 001–055.

[2] Bobrov, A.A., Zalewska-Gałosz, J., Jopek, M., Movergoz, E.A., 2015. Ranunculus schmalhausenii (section Batrachium, Ranunculaceae), a neglected water Crowfoot endemic to Fennoscandia - a case of rapid hybrid speciation in postglacial environment of North Europe. Phytotaxa 233: 101–138.

[3] Suchan, T. et al. 2016. Hybridization capture using RAD Probes (hyRAD), a new tool for performing genomic analyses on collection specimens. PLoS ONE 11: e0151651.

[4] Puritz, J. B., & Lotterhos, K. E., 2018. Expressed exome capture sequencing: A method for cost‐effective exome sequencing for all organisms. Molecular ecology resources, 18: 1209-1222.

IB – 4: The biochemical and physiological mechanisms preventing seed germination in violets (Institute of Botany)

Institute: Institute of Botany

Topic: The biochemical and physiological mechanisms preventing seed germination in violets

Name of supervisor: dr hab. Aneta Słomka (aneta.slomka@uj.edu.pl)

Background information:
Violets are popular ornamental bedding plants. Currently, horticultural species of long flowering time, high resistance to extreme conditions, e.g., cold and heavy metals are cultivated in gardens thorough the Europe and U.S. However, commercially available seeds, similarly as those of natural origin, germinate poorly unless treated specifically. Osmopriming, halopriming and remining proper relative humidity during seed storage have been found to enhance violets’ germination in laboratory conditions (Dorna et al. 2014 and lit. cited therein), which, however, is unstable and unpredictable, dependent on species and seed origin. Both parameters frequency of germinating seeds and seed vigour (the speed of germination) are reduced in violets. The seed germination process is complex. Even when embryo and endosperm are properly developed there are multiple mechanisms blocking seed germination in unfavoured external conditions (secondary dormancy). In nature, the germination of violets is dependent on cold stratification, temperature, and light conditions. Breaking seed dormancy requires thorough knowledge of the seed intrinsic nature and physiology which both are strongly neglected in violets.

The main question to be addressed in the project:
Since among the most important parameters controlling the process of seed dormancy are changes at molecular levels, including the protein and hormonal alterations, and the balance between abscisic acid and gibberellins, it is planned to perform comparative analyses at different levels using e.g., Viola tricolor differentiated into populations with low and high germination capacity. Firstly, hormonal profile between well and poorly germinating seeds will be established. Secondly, proteomic comparisons with particular emphasis on: (1) proteases (especially caspase-like enzymes) involved in programmed cell death in plants via mobilizing storage proteins to promoting seed germination (e.g., Liu et al. 2018); (2) carbonylated proteins associated with reactive oxygen species production alleviating seed dormancy (Oracz et al. 2007), will be performed. 

The overall project aims will contribute to, at least partial, understanding the mechanisms of poor seed germination in violets and would provide practical advices for horticultural industry how to overcome such difficulty in these and other ornamental species.

Information on the methods/description of work:
Western blot, ligand blotting, high-performance liquid chromatography, one and two-dimensional gel electrophoresis, mass spectrometry technique, seed viability and germination tests, TUNEL assay, etc.

Additional information (e.g., special requirements from the student): 
reliability, working time flexibility, English proficiency.

Place/name of potential foreign collaborator:
 Department of Plant Systems Biology, Ghent University, Belgium and Department of Botany, Palacký University, Faculty of Science, Olomouc, Czech Republic.

References:

Dorna H. et al. 2014. The effect of priming on germination and vigour of pansy (Viola x wittrockiana Gams.) seeds. Acta Sci. Pol. Formatio Circumiectus 13: 15-29.

Liu H. et al. 2018. Role of papain-like cysteine proteases in plant development. Front. Plant Sci. 9: 1717.

Oracz K. et al. 2007. ROS production and protein oxidation as a novel mechanism for seed dormancy alleviation. Plant J. 50: 452-465.

IES – 5: Senescence of avian feathers (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Senescence of avian feathers

Name of supervisor: dr hab. Ulf Bauchinger (ulf.bauchinger@uj.edu.pl)

Background information:

Vertebrate metabolism is subjected to senescence; progressing adult age is known to drive quantitative and qualitative changes in metabolism in mammals and birds. The effects of metabolic aging on fur and the quality of the individual hair are well documented for mammals, but senescence of the avian feather are not known from the literature. The periodic moult represents a demanding period since replacement of the feathers require resources during a time when feather regrowth already impairs flight performance.

First data obtained in the frame of a master thesis on our ageing cohort of zebra finches (Taeniopygia guttata) maintained at the Institute of Environmental Sciences, UJ, unambiguously reveal a decline in feather length, with increasing age. These results of older birds to grow shorter wing feathers must be considered to affect flight performance and maneuverability as wing loading highly depends on feather size.

The main question to be addressed in the project:

Do birds in general reveal similar age effects in feather length?
Do feathers of change in quality in addition to the quantitative changes?
Are the rate of moult and the length of the entire moulting period affected by age?

Information on the methods/description of work:

Measurements of feather length and feather quality from museum specimens of known age will provide a data for multiple species. Morphometric measurements are accompanied with microscopic analysis of feather ultra-structure. Phylogenetic correction will be employed (Question 1 and 2)
Our ageing cohort of zebra finches maintained at INoŚ and at the Max Planck Institute of Ornithology will be used for descriptive analysis of feather length and feather quality based on microscopic analysis of feather ultra-structures (Question 2 and 3) 
Experimental  manipulation of feather regrowth through feather plucking is performed to test for age differences in the rate of moult and the length of the moulting period under specific environmental conditions (Question 2 and 3) 

Additional information:  

Student will have to acquire the necessary certificates for experimental work with animals or (preferable) holds this certificate already. Good English skills. Experience with handling of birds is an advantage.

Place/name of potential foreign collaborator:

Max-Planck Institute for Ornithology, Seewiesen Germany/ Prof. Dr. Manfred Gahr (Director MPIO). Source of the birds currently maintained at UJ.
 
Zoological Staatssammlung Munich, Germany/ Prof. Dr. Gerhard Haszprunar (Director ZSM, Munich, Germany). One of the biggest scientific collection of animals in Europe.

References:

Labocha M. K., Rutkowska J., Cichoń M. and U. Bauchinger. 2015. Age-specific decline in take-off flight performance in a small passerine. Animal Behavior 105: 103-107.
Holmes, D., and K. Martin. 2009. A bird's-eye view of aging: What's in it for ornithologists? Auk 126:1-23.
Swaddle, J. P., and M. S. Witter. 1997. The effects of molt on the flight performance, body mass, and behavior of European starlings (Sturnus vulgaris): An experimental approach. Canadian Journal of Zoology-Revue Canadienne De Zoologie 75:1135-1146.

IES – 6: Biological Clocks in the Wild: the effects of artificial light at night on circadian rhythms of a migratory bird (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Biological Clocks in the Wild: the effects of artificial light at night on circadian rhythms of a migratory bird

Name of supervisor: prof. dr hab. Mariusz Cichoń (mariusz.cichon@uj.edu.pl)

Background information:

It is well established that biological rhythms are fundamental drivers of biochemistry, cell biology, physiology and behaviour (1). The regularity of behaviours is governed by endogenous clocks, which are adjusted and synchronised with environmental cues, primarily light. Rapidly expanding anthropopressure largely disrupts these cues. Yet, it is surprising how little we know about the effects of disorders in the functioning of the internal time-keepers in free-ranging animals. These can range from behavioural and hormonal to immunological responses (2,3).

The main question to be addressed in the project:

Understanding the effects of disturbance in environmental cues, i.e. light exposure, on circadian clock of a wild migratory bird: collared flycatcher (Ficedula albicollis).

Information on the methods/description of work:

The PhD candidate will actively participate in fieldwork, collecting phenotypic, biological and environmental data, sample preparation and lab work. S/he will be interacting with the supervisor and other team members, collaborators in Poland and worldwide, and attend relevant workshops and conferences. It is expected that the candidate will learn a large ecological skill set that will allow him/her to infer the evolutionary ecology of disturbed photoperiods in wild flycatchers. Specifically, the tasks will involve:

active participation in fieldwork across three breeding seasons (ca. 2-3 months each year) on the Swedish island of Gotland,
assessing the influence of artificial light at night on immune response of birds,
planning and performing PHA immune assays in the field,
analysing gene expression of specific immune genes,
conducting statistical analyses,
presenting the work at local and international conferences and preparing publications in close collaboration with an international team.

Additional information (e.g. special requirements from the student):

strong English language command, communication, organizational and collaboration skills;
experience with molecular laboratory analyses and fieldwork (preferably with birds);
previous experience in statistical analysis of biological data is considered advantageous;
bird ringing/handling experience and ethical permits to work with animals and driving license are a plus.

Place/name of potential foreign collaborator:

Uppsala University/Professor Lars Gustafsson, Groningen University and University of Glasgow/Professor Barbara Helm

References:

1. Bell-Pedersen D, Cassone VM, Earnest DJ, et al (2005) Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat Rev Genet 6:544–556. doi: 10.1038/nrg1633

2. Zhuang X, Magri A, Hill M, et al (2019) The circadian clock components BMAL1 and REV-ERB α regulate flavivirus replication. Nat Commun 10:1–13. doi: 10.1038/s41467-019-08299-7

3. Dominoni DM, Goymann W, Helm B, Partecke J (2013) Urban-like night illumination reduces melatonin release in European blackbirds (Turdus merula): implications of city life for biological time-keeping of songbirds. Front Zool 10: 60. https://doi.org/10.1186/1742-9994-10-60

IES – 7: Nutritional ecology of bees: balancing bee nutrient demands and nutrient supply with a diversity of pollen sources (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Nutritional ecology of bees: balancing bee nutrient demands and nutrient supply with a diversity of pollen sources

Name of supervisor: dr hab. Marcin Czarnołęski, prof UJ (marcin.czarnoleski@uj.edu.pl)

Background information:
For bees, pollen quality determines the overall quality of the larval food, influences the development of individuals and shapes their populations. Not all plants produce pollen that satisfies the nutritional requirements of bees, and we do not know how different plant pollens impact bees’ nutritional demands. Our understanding of the differential contribution of various nutrients to bees’ growth and development is minimal.

The framework of ecological stoichiometry is a promising approach to this issue. It allows questions about the most basic mechanism that shapes the nutritional ecology of bees, i.e., balancing the larval diet to enable larval growth, and development.

The main question to be addressed in the project:
The goal of this project is to determine the nutritional limitations imposed on wild bees by the lack of nutritionally balanced pollen. Therefore, we will (i) determine the nutritional value of the pollen produced by various plant species and (ii) estimate the nutritional needs of different species of wild bees. Finally, the combination of both research aims will enable us to (iii) assess nutritional bottlenecks as determinants of the biodiversity of wild bee species.

Information on the methods/description of work:

We will characterize the stoichiometry of multiple elements for bees and pollen. Within the framework of ecological stoichiometry, the nutritional demand of the bees will be compared with the nutritional supply of the pollen to study if and how the local flora community influence bee communities and populations via the presence or absence of plant species that supply stoichiometrically adequate pollen for bees.

Additional information (e.g special expectations from candidate students):  
Required: (1) Master's level in the studies in the field related to the project’s scope; (2) academic-level knowledge in ecology, evolution and physiology; (3) general experience and interest in any field of ecology; (4) basic knowledge of statistics;  (5) fluency in English.

Preferred: experience in publishing scientific results and application of more complex statistical models (especially in R); either already experience or strong motivation to learn programming in R, MATLAB or Python.

Personal qualities: (1) effective communication; (2) interpersonal abilities and the ability to work well with others; (3) computer and technical literacy; (4) problem-solving/creativity; (5) skills in planning and organizing; (6) high degree of motivation; (7) reliability, diligence, and punctuality; (8) the ability to critically evaluate the obtained results; and (9) willingness to actively participate in conferences, festivals and other forms of dissemination of the project’s results and preparation of scientific publications in English at a high, international level.

Place/name of potential foreign collaborator:

Technical university of Munich, Germany / Prof. Dr. Sara Diana Leonhardt

References:

1. Filipiak, M. (2018). A Better Understanding of Bee Nutritional Ecology Is Needed to Optimize Conservation Strategies for Wild Bees—The Application of Ecological Stoichiometry. Insects.

2. Filipiak, M. & Weiner, J. (2017). Plant-insect interactions: The role of ecological stoichiometry. Acta Agrobot.

IES – 8: Climate crisis: a new paradigm for addressing minimization of plastic harm in the era of COVID-19 pandemic (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Climate crisis: a new paradigm for addressing minimization of plastic harm in the era of COVID-19 pandemic 

Name of supervisor: prof. dr hab. Małgorzata Grodzińska-Jurczak (m.grodzinska-jurczak@uj.edu.pl)                 

Background information:

Contemporary environmental discourses have been largely focused on different contributors to the climate crisis including plastic considered as having the strongest impact on the natural environment and public health. The CO2 emissions directly connected to plastic production, recycling and utilization – estimated to triple by 2050 - requires a re-assessment due to the global COVID-19 pandemic. The already chronic problem of plastic pollution is just becoming more worrying, as the new circumstances result in a constantly growing generation of a new type of pollution originating from single-use items such as gloves, masks, medical suits, cutlery etc. The previously perceived negative roles of plastic experience a major change as health fears appear to outweigh environmental concerns. However, although the effects of the COVID-19 pandemic are more immediate than those of plastic usage, both have a tremendous impact on the environment and public health. Facing both threats requires a major incision into the prevailing plastic governance ensuring a sustainable transition of values and behaviors towards a holistic plastic waste management while considering changing environmental conditions.

The main questions to be addressed in the project:

This research project aims at re-assessing the plastic threat reinforced by the COVID-19 pandemic. It will investigate attitudes and opinions towards the harm of plastic to the environment and health, using the interdisciplinary context, investigating the general public and various stakeholders. Moreover, we’ll develop an inclusive approach aiming at minimizing the new type of plastic pollution, which will comprise a combination of innovative technologies, participatory scenario modelling and knowledge co-creation processes.

Information on the methods/description of work:

The project will utilize a mixed-mode approach with qualitative and quantitative methods. The outputs of the PhD project will be used for comparisons with equivalent research in other countries to validate their relevance and strengthen their practical universality.

Special requirements from the student:

A potential candidate should possess knowledge and experience in working cohesively in an interdisciplinary team environment, demonstrate excellent written and oral English communication skills. A job experience in practical nature conservation (also non-research sector) and participatory research methods would be of advantage.

Place/name of potential foreign collaborator:

Prof. Dietram A. Scheufele, University of Wisconsin, Madison, USA

Prof. Maurie Cohen, New Jersey Institute of Technology, Newark, NJ, USA

References:

Anbumani, S., & Kakkar, P. (2018). Ecotoxicological effects of microplastics on biota: a review. Environmental Science and Pollution Research, 25(15), 14373-14396.
Chen, S., Yang, J., Yang, W., Wang, C., & Bärnighausen, T. (2020). COVID-19 control in China during mass population movements at New Year. The Lancet, 395(10226), 764-766. 
Cohen, M. (2020). Does the COVID-19 outbreak mark the onset of a sustainable consumption transition? Sustainability: Science, Practice and Policy, 16:1, 1-3.
Grodzińska-Jurczak M., A. Krawczyk, A. Jurczak, M. Strzelecka, M. Boćkowski, M. Rechciński. 2020. Environmental choices vs. Covid-19 pandemic fear - Plastic governance re-assessment. Society & Register 4 (2), 34-49.

IES – 9: Reimagining River Stewardship- the role of values embedded in leisure activities ‘with’ rivers (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Reimagining River Stewardship- the role of values embedded in leisure activities ‘with’ rivers

Name of supervisor: prof. dr hab. Małgorzata Grodzińska-Jurczak (m.grodzinska-jurczak@uj.edu.pl)

Background information:

River stewardship is an increasingly important approach to preserve the European countryside and rivers flowing through rural areas. It “comprises all efforts to create, nurture and enable responsibility of landowners and resource users to manage and protect land and its natural and cultural heritage”. One way to conceptualize this kind of stewardship is through people-nature relationships. The contemporary western-scientific discourse understands people-nature relationship through the lens of ‘ecosystem services’ (ES) or more recently Nature-Contribution-to-People (N-C-P), which puts emphasis on cultural and emotional aspects .

This project concerns rivers that are important locally and essential to the wellbeing of communities on the Polish and Swedish countryside. By focusing on locally significant rivers, this study will expose the complexity of relations between outdoor leisure and river stewardship between cases in Poland and Sweden.

The main question to be addressed in the project:

In what ways relational values embedded in outdoor leisure alongside rivers flowing through rural areas translate into river stewardship?

The overall goal: to explore the transformative capacity of outdoor leisure practices to pave the way for river stewardship on the Polish and Swedish countryside.

Information on the methods/description of work:

This research utilizes a sequential exploratory mixed methods approach integrating both qualitative and quantitative tools for data collection. Additionally, the study targets rural river sites in Poland (cases) and Sweden (cases) with the goal to capitalize on potential differences in terms of local environmental heritage. Specific rural river sites are to be determined through spatial analysis of social media data.

Special requirements from the student:

A potential candidate should possess knowledge in designing and executing interdisciplinary research. Foundations to work in an R environment are an additional advantage. Evidence of high-quality academic writing in English is necessary.

Place/Name of potential foreign collaborator: 

Marianna Strzelecka, PhD, Linnaeus University, Sweden

References:

Brown J, & Mitchell B. (2000) The stewardship approach and its relevance for protected landscapes. The George Wright Forum, 7, 70–79.
Creswell, J.W. & Plano Clark, V.L. (2017). Designing and conducting mixed methods research (3rd ed.). Thousand Oaks, CA: Sage.

IES – 10: The role of ultrasounds in biology, communication and sexual selection of voles (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: The role of ultrasounds in biology, communication and sexual selection of voles.

Name of supervisor: dr hab. Joanna Kapusta (joanna.kapusta@uj.edu.pl)       

Background information:

It is commonly known that rodent communication appears to be based primarily on the well-developed olfactory system. Many studies suggest that vocalization, especially in the high frequency range (ultrasounds) form a significant element of communication within many species of rodents. Previous studies conducted on laboratory animals (mainly mice and rats) have shown that ultrasounds emitted by pups elicit maternal care, especially retrieval behavior. Adult animals produce ultrasounds during amicable and aggressive interactions, and they occur during male-female sexual encounters. Moreover, vocalization of males depends on male sex hormones – androgens. Androgens are critically involved in the development and expression of secondary sex characters essential for attraction and acquisition of mates. In this context it may therefore be hypothesized that ultrasounds are a part of sexual behaviour and play an important role in mate choice.

The main question to be addressed in the project:

The primary purpose of this project is to assess the importance of ultrasounds for the sexual selection of voles. Do the ultrasounds emitted by males influence the behaviour of females and are these sounds involved in intrasexual competition?

Information on the methods/description of work:

This research project will study the reaction of females to the play back of male ultrasounds and will also assess the influence of ultrasounds emitted by males of voles on the hormonal activity of conspecific and heterospecific females and on their sexual behavior. It will also examine the impact of ultrasounds emitted by males on the interaction between males which may be part of the competition. The main model for studying all these interactions will be two species of voles: bank vole and common vole. The behavioural and physiological reactions of voles will be analysed using preference tests and behavioural confrontation tests. All recordings will be later analyzed using computer software dedicated to sound analysis.

Additional information (e.g., Special requirements from the student): 

Recommended: previous experience in research on rodents, knowledge of behavioral tests on rodents as well as bioacoustics methods. Appropriate ethical permissions to work with vertebrate animals. Good English language, communication, and organizational skills.

Place/name of potential foreign collaborator:

Direct foreign collaboration is not planned but it is possible.

References:

1. Kapusta J and Kruczek M. (2016). Ultrasonic reaction of bank vole males to the presence of

females varying in hormonal activity. Ethology 122: 468-480.

2. Marchlewska-Koj A, Kapusta J (2018). Vocalization of Adult Bank Voles. In: Stefan M.

Brudzynski, editor: Handbook of Ultrasonic Vocalization, Vol 25, HBBN, UK: Academic Press, 2018, pp. 217-225.

3. Merten S, Hoier S, Pfeifle Ch, Tautz D. (2014). A role for ultrasonic vocalization in social

communication and divergence of natural populations of the house mouse (Mus musculus

domesticus). PLoS  ONE 9: e97244.

IES – 11: Mechanisms determining predatory behavior: insights from an experimental evolution on bank vole (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Title: Mechanisms determining predatory behavior: insights from an experimental evolution on bank vole

Name of supervisor: prof. dr hab. Paweł Koteja (pawel.koteja@uj.edu.pl)/dr Edyta Sadowska (edyta.sadowska@uj.edu.pl)

Background information:

One of the main challenges in biology is to understand the evolution of complex adaptations that allow realization of the astonishing variety of "lifestyles." Predator-prey interactions are important components in ecological communities, where under the pressure of natural selection, predators have evolved a variety of behavioral, morphological and/or physiological adaptations for detecting, catching, killing, and digesting prey. The examples include the wolf with its cooperate hunting skills, the cheetah - the world’s fastest land animal, the golden eagle with excellent eyesight that allows to spot even a small prey from the great height, or the grasshopper mouse Onychomys, hunting on cotton rats that are three times their weight. The predatory behavior is important not only from the ecological and evolutionary, but also from biomedical perspective. It is surprising that our knowledge concerning biological mechanism determining the predatory aggression is very limited, especially in comparison with that concerning conspecific-directed aggressive behavior.

The main question to be addressed in the project:

Characterization of details of the predatory behavior to learn whether the selection increased only the propensity to attack, or also the hunting skills.
Is selection for predatory behavior caused changes in conspecific-directed aggression?
Assessing the contribution of “nature – nurture” effects on the behavioral differences between the predatory and control lines.
Uncovering the mechanisms underlying the differences due to selection for predatory behavior, we will investigate hormones, neurotransmitters and brain activity activated by recent experience with crickets.

Information on the methods/description of work:

We will use our unique experimental evolution model system: lines of a rodent, the bank vole, selected for predatory behaviour. The biochemical and neurological methods will be used to uncover the mechanisms underlying the differences due to selection for predatory behaviour. We will apply a cross-fostering experiment in which new born voles will be exchanged between mothers from the selected and control lines. This will allow to test whether rearing by a predatory mother increases predatory propensity of an individual independently of its genetic background. Samples of tissues will be preserved for follow-up project focused on for investigation of the molecular background (gene expression level).

Additional information:

- strong English language, communication, organizational and collaboration skills.

- Previous experience with small mammals, neuro-physiology, and/or evolutionary biology are considered advantageous.

Place/name of potential foreign collaborator:

Jennifer Hoy, University of Nevada, Reno

References:

1. Sadowska, E. T., K. Baliga-Klimczyk, K. M. Chrzascik, and P. Koteja. 2008. Laboratory model of adaptive radiation: A selection experiment in the bank vole. Physiological and Biochemical Zoology 81:627-640

2. Hoy, J. L. et al. 2019. Defined cell types in superior colliculus make distinct contributions to prey capture behavior in the mouse. Current Biology. 29, 4130-8 e5.

3. Shang, C. et al. 2 A subcortical excitatory circuit for sensory-triggered predatory hunting in mice. Nature Neuroscience 22, 909-920.

IES – 12: The ecological dynamics of insect microbiomes (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: The ecological dynamics of insect microbiomes

Name of supervisor: dr hab. Piotr Łukasik (p.lukasik@uj.edu.pl)

Background information:

Insects frequently associate with microbes, forming different types of symbiotic associations that often play critical roles in insect biology. We know that the microbial abundance, community composition, and roles vary among insect species, but they also differ among populations, sampling dates, and among individuals sampled from a population at the same time. However, our understanding of the microbiome abundance and diversity patterns across insects, and factors that drive these patterns, remain very limited.

The goal of the proposed project is a broad, comprehensive survey of insect microbial symbioses. We will do this in close collaboration with Insect Biome Atlas (IBA), a project that samples flying insects at hundreds of sites in Sweden and Madagascar. We will use large numbers of insects from that collection for the microbiome characterization using high-throughput next-generation sequencing. This approach will allow us to understand the microbiome composition across the taxonomic diversity of insects and describe the seasonal changes, geographic variation, and the effects of environmental factors on microbiomes of selected, broadly distributed species.

The main question to be addressed in the project:

The Ph.D. Student will address the questions of how the microbiomes vary across insect diversity, space, and time, and how host-specific symbiotic microbes are.

Information on the methods/description of work:

The student's main task will be the bioinformatic analysis of large amounts of insect microbiome composition and abundance data. They may also participate in phylogenomics and comparative genomics characterization of broadly distributed microbial clades. They will be encouraged to contribute to field collections, to work with international collaborators on the selection and preparation of insect specimens for the microbiome characterization, and to participate in high-throughput sample processing and next-generation sequencing library preparation. The student will be encouraged to work closely with other team members and project collaborators, including Insect Biome Atlas consortium members in Sweden and prof. Rudolf Meier at Humboldt University in Berlin.

Additional information (e.g special requirements from the student):

The successful candidate will have an M.Sc. degree in a relevant field by September 2020. They will be able to demonstrate interest in Evolution, Entomology, Microbiology, and/or Genomics; experience with, or a keen interest in learning, Bioinformatics and Computational Biology; and strong English language, communication, and organizational skills. Previous experience in ecology, evolution and especially symbioses, molecular biology, microbiome surveys, phylogenomics and/or comparative genomics, and willingness to travel are advantageous.

For more information about the project and the research group, please check symbio.eko.uj.edu.pl

Place/name of potential foreign collaborator:

Fredrik Ronquist, Swedish Museum of Natural History

Rudolf Meier, Humboldt University, Berlin.

References:

1. Moran N.A., McCutcheon J.P. & Nakabachi A. (2008): Genomics and evolution of heritable bacterial symbionts. Annual Review of Genetics 42:165-190.

https://www.annualreviews.org/doi/full/10.1146/annurev.genet.41.110306.130119

2. Oliver K.M., Smith A.H., Russell J.A. (2014): Defensive symbiosis in the real world–advancing ecological studies of heritable, protective bacteria in aphids and beyond.

Functional Ecology 28(2): 341-355. https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/1365-2435.12133

3. Turelli M., Cooper B.S., Richardson K.M., et al. (2018): Rapid global spread of wRi-like Wolbachia across multiple Drosophila. Current Biology 28:963-971. https://www.sciencedirect.com/science/article/pii/S0960982218301696

IES – 13: Soil temperature sensitivity under different stresses, the role of soil microbial communities (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Soil temperature sensitivity under different stresses, the role of soil microbial communities

Name of supervisor: prof. dr hab. Maria Niklińska (maria.niklinska@uj.edu.pl)/dr Beata Klimek (beata.klimek@uj.edu.pl)

Background information:

One of the major consequences of climate change in European forest areas will be increased frequency and severity of heat and drought events. Despite decades of empirical research, the nature and magnitude of global warming on C cycling in European forest ecosystems are still uncertain. This is mainly due to independent or interactive effects of both biotic and abiotic factors. The chemical composition of the organic matter and temperature changes connected with soil moisture content are the main factors influencing soil microbiome and thus affecting the turnover rate of different elements in the soil environment.

Soil and its associated microbiome are fundamental and still often ignored components of the climate system. The distribution and function of soil microorganisms are important for the flow or organic matter and the biogeochemical cycles. However different group of microbes in different environmental conditions (e.g. pollution) may respond differently by accelerating or by alleviating, human caused climate change. Rapidly warming climate enhancing organic matter decomposition, creating a climate warming positive feedback loop which accelerates global warming.

The main question to be addressed in the project:

The main objective of the planed research is to better understanding and harness forest soil microbiome responses to higher temperatures and altered soil water content and identification of soil parameters and microbiological factors controlling mitigation potential.

The more detailed  purpose of this project is to test if fungi dominated in coniferous, Pine forest growing in different polluted areas are the key microbial group responsible for soil temperature sensitivity.

Working with PhD student we want to compare the sensitivity of Scots pine forest organic matter to different temperature and try to find the not only physicochemical factors responsible for the diverse answer but also estimate relationship between microbial genetic and physiological diversity for temperature and water stress sensitivity. And the futher perspective, we want to check if still after more than three decades the pattern observed by our group for organic matter sensitivity to temperature changes is similar and close to our previous research and prediction and if exactly fungi in soil microbiome are the most responsible in carbon cycling process.

Information on the methods/description of work:

Planned experiments will based on soil laboratory incubation in different combinations of temperature and humidity and on measuring the soil respiration rates and different soil microbial communities properties like genetic structure of community (using Illumina sequencing), physiological profiles (using Biolog test),  microbial community structure (using PLFA method) and enzyme activities.

Additional information (e.g Special requirements from the student): 

The student will focus on the field and laboratory analysis of different soil and microbial properties. The PhD student should have base knowledge in ecology, especially global changes and their effects on global ecological processes. The experience in microbiological and molecular methods will be another advantage. Of course English language and team laboratory skills are also expected.

Place/name of potential foreign collaborator:

dr Hamed Azarbad Philipps University Marburg, Germany
Prof. Rosa Margesin Professor of Microbiology. Institute of Microbiology Technikerstrasse 25 6020 Innsbruck Austria.

References:

1. Klimek B., Chodak M., Jaźwa M., Azarbad H., Niklińska M. 2020. Soil physicochemical and microbial drivers of temperature sensitivity of soil organic matter decomposition under boreal forests. Pedosphere 30(4): 528-534.

2. Niklińska M., Maryański M., Laskowski R. 1999. Effect of temperature on humus respiration rate and nitrogen mineralization: Implication for global climate change. Biogeochemistry 44:239-257.

3. Tuomi M., Vanhala P, Karhu K., Fritze H., Liski J. 2008. Heterotrophic soil respiration- comparison of different models describing its temperature dependence. Ecological Modelling 211: 182-190.

IES – 14: Population genomics of outbreaks - adaptive evolution in spruce bark beetle (Institute of Environmental Sciences)

Institute:  Institute of Environmental Sciences

Topic: Population genomics of outbreaks - adaptive evolution in spruce bark beetle

Name of supervisor: dr hab. Krystyna Nadachowska-Brzyska (krystyna.nadachowska@uj.edu.pl)

Background information:

A major goal in evolutionary biology is to understand which processes shape genetic diversity observed in natural populations. Classic population genetic theory provides a solid mathematical framework to study genetic variation and predict efficacy of natural selection relative to drift in equilibrium conditions, for example under constant population size. However, the majority of natural populations often experience large size fluctuations that make prediction less straightforward. For example, many pests experience epidemic outbreaks characterized by sudden changes in population size, often spanning orders of magnitude. Such outbreaks are known from ecological studies of closely monitored species of economic importance. However, little is known about the genetic consequences of outbreaks. Specifically, the rate of adaptive evolution during relatively short periods of large population size remains unknown. This can be studied in species which experience extreme fluctuations of population size, such as spruce bark beetle (Ips typographus). Spruce bark beetle is the most destructive pest of Norway spruce forests because under specific conditions (e.g. storms) populations may outbreak, causing mass mortalities of spruce stands.

The main question to be addressed in the project:

The main purpose of this project is to test how extreme fluctuations in population size of outbreaking species affect the dynamics of adaptive genetic variation.

Information on the methods/description of work:

The PhD student will be working with large, whole genome resequencing data obtained from several populations and >500 individuals (short and long read sequencing). The PhD student will investigate selection patterns along the spruce bark beetle and among outbreaking and non-outbreaking populations. The analysis will include standard selection scans as well novel approaches to detect and distinguish between hard and soft sweeps.

Additional information (e.g Special requirements from the student): 

The PhD project is a part of recently awarded project Population genomics of outbreaks - neutral and adaptive evolution in spruce bark beetle. The student will focus on the analysis of adaptive genome-wide variation and will closely collaborate with other members of the team that are focusing on theoretical investigations, neutral genome-wide variation and demographic history inference. The PhD student should have strong interest in Evolution, Molecular Ecology, Population Genetics and/or Genomics as well as experience with, or a keen interest in learning, Bioinformatics and Computational Biology. Strong English language, communication, and organizational skills are essential.

Place/name of potential foreign collaborator:

prof. Fredrik Schlyter (SLU, Sweden), Prof. Paal Krokene (NIBIO, Norway)

References:

1. Mayer, F. et al. Comparative multilocus phylogeography of two Palaearctic spruce bark beetles: Influence of contrasting ecological strategies on genetic variation. Mol. Ecol. 24, 1292–1310 (2015).

2. Pélissié, B. et al. Rapid evolution in insect pests: the importance of space and time in population genomics studies. Curr. Opin. Insect Sci. 1–9 (2018).

3. Hermisson J, Pennings PS. Soft sweeps and beyond: understanding the patterns and probabilities of selection footprints under rapid adaptation. Methods Ecol. Evol. 8:700–716 (2017).

IES – 15: Winter feeding ecology of Eurasian lynx (Lynx lynx) (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Winter feeding ecology of Eurasian lynx (Lynx lynx)

Name of supervisor: dr hab. Izabela Wierzbowska (i.wierzbowska@uj.edu.pl)

Background information:

The Eurasian lynx (Lynx lynx) is a stalking predator that mainly hunts on ungulates. In Northern and Central Europe lynxes forage on their prey, mainly roe deer (Capreolus capreolus), between 2 and 8 days but consumption time can increase with a larger prey, e.g. red deer (Cervus elaphus). The choice of the most suitable hunting areas can be driven by prey abundance and landscape attributes influencing prey catchability. There are several factors which can affect feeding behaviour of lynxes including habitat and seasonal characteristics such as presence of snow and vegetation as well as scavenging and kleptoparasitism. The presence of lynx in the proximity of its prey can be prolonged mainly to prevent prey losses.

The main question to be addressed in the project:

The aim of this project is to find out information about lynx behaviour in context of its prey: i) to study type and fate of lynx prey mainly ii) how long lynx is foraging on its prey and iii) if there are other species present near the prey utilizing it as well. At present, most studies have been done in Białowieża Primeval Forest and almost nothing is known about lynx population in southern Poland.

Information on the methods/description of work:

The use of non-invasive methods including camera traps. The potential candidate of this project will be involved in the fieldwork in Małopolska region (mainly Gorce National Park and Babia Góra National Park (tracking on snow, search of lynx prey in winter, location and deployment of camera traps in close proximity to lynx prey) and using multidimensional statistical geospatial analyses of collected data.

Special requirements from the student:
experience in field work, ability to track animals on snow and experience with the use of camera traps. Good or very good command of English.

Place/name of potential foreign collaborator:
Dr John D.C. Linnell Norwegian Institute for Nature Research, Norway

Reference(s):

Duľa, M., Krofel, M. 2020. A cat in paradise: hunting and feeding behaviour of Eurasian lynx among abundant naive prey. Mamm Biol 100:685–690.
Herrero, A., Heikkinen, J. & Holmala, K. 2020. Movement patterns and habitat selection during dispersal in Eurasian lynx. Mamm Res 65:523–533.
Teurlings, I.J.M.; Odden, J.; Linnell, J.D.C.; Melis, C. 2020. Caching Behavior of Large Prey by Eurasian Lynx: Quantifying the Anti-Scavenging Benefits. Diversity 12, 350. https://doi.org/10.3390/d12090350

IZBR –16: Infant social development, breastfeeding, and breast milk composition (Institute of Zoology and Biomedical Research)

Institute: Institute of Zoology and Biomedical Research    

Topic: Infant social development, breastfeeding, and breast milk composition

Supervisor: dr hab. Anna Ziomkiewicz-Wichary (anna.ziomkiewicz-wichary@uj.edu.pl

Background information:

The development of early social communication skills in infants and young children remains under the constant interest of psychologists (Hansen et al., 2018). These early social skills, such as eye gaze, joint attention, social referencing, and social orienting, are typically developed in the first two years of life in the context of everyday interactions (DeQuinzio et al. 2016). While several psychological factors were identified to drive the development of these skills, studies in this area usually ignore the effect of biological factors such as breastfeeding. Meanwhile, research shows that breastfeeding is an essential factor in facilitating the neurocognitive and temperamental development of infants and, as such, might be critical for the formation of communication skills.

The main question to be addressed in the project:

This project seeks to understand the association between breastfeeding and the development of infant social skills during the first year of life. In particular, this project will investigate the effect of breastfeeding patterns (number and duration of breastfeeding episodes during the day) and breast milk composition (main milk nutrients and fatty acids) are related to the development of early social communication skills in 1-year old infants.

Information on the methods/description of work:

The project is based on the pre-existing data set collected during the grant awarded to the supervisor. During the project, around 150 infants, aged about 12 months, were filmed while participating in The Early Social Communication Scales (ESCS) tasks (Mundy et al., 2003).

ESCS is a videotaped structured observation designed to provide measures of individual differences in nonverbal communication skills that typically emerge in children between 8 and 30 months of age. Also, data about breastfeeding pattern and breastmilk composition (the content of lactose, protein, fats, fatty acids, and energy value of milk) was collected when infants were around five and twelve months old. The examined associations will be controlled for infant temperamental characteristics and markers of infant biological development. The role of a Ph.D. candidate will be to analyze the videotaped tasks and further to conduct the necessary statistical analysis to test the potential associations. During her/his work, the candidate will collaborate with the Institute of Psychology, Department of Developmental Psychology, and if agreed with program COGNES (Ph.D. in Cognitive Neuroscience) of Jagiellonian University.

Place/name of potential foreign collaborator:

Leiden University, Department of Clinical Psychology, Dr Marieke Tollenaar

References:

 Hansen, S. G., Carnett, A., & Tullis, C. A. (2018). Defining early social communication skills: A systematic review and analysis. Advances in Neurodevelopmental Disorders, 2(1), 116-128.
 DeQuinzio, J. A., Poulson, C. L., Townsend, D. B., & Taylor, B. A. (2016). Social referencing and children with autism. The Behavior Analyst, 39(2), 319–331.
 Mundy, P., Delgado, C., Block, J., Venezia, M., Hogan, A., & Seibert, J. (2003). Early social communication scales (ESCS). Coral Gables, FL: University of Miami.

IZBR –17: Macrophage polarization and osteoclast formation on contact with bioactive materials (growth surfaces and scaffolds) (Institute of Zoology and Biomedical Research)

Institute: Institute Zoology and Biomedical Research

Topic: Macrophage polarization and osteoclast formation on contact with bioactive materials (growth surfaces and scaffolds)

Name of supervisor: dr hab. Anna M. Osyczka, prof. UJ.

Background information:
Bioactive materials are cell-friendly materials that are not bioinert and display some benefits to the given cell population due to their inherent physico-chemical properties. We study the materials that contain bioactive glasses and/or polyphenols, both well recognized in literature for their osteoinductive and/or anti-inflammatory properties, respectively. We wish to explore the potential of some of them to drive macrophage polarization and/or osteoclast formation and bone remodeling.

The main question to be addressed in the project:
To what extend the selected osteoinductive materials display anti-inflammatory properties (this includes the studies on macrophage polarization) and affect bone remodeling (with the focus on osteoclast formation) and by what biological mechanisms

Information on the methods/description of work: The work will focus on in vitro cell culture on the selected bioactive materials and cell molecular analyses (gene and protein expression, signal transduction mechanisms and related standard cell biology technics) using animal and human cell lines and/or primary cells. Some of the results may be eventually verified in vivo in an animal model (most likely a rabbit model). 

Additional information (e.g Special requirements from the student):
The candidate should have proven experience in cell culture and standard molecular analyses of celsl and tissues, such as gene and protein expression analyses, immunohistochemistry, cytometry etc . She/he should also have good knowledge (the experience is a plus) regarding the biomaterials, their physico-chemical properties and biological responses to them.

Place/name of potential foreign collaborator:
The potential collaborators may include several different Institutes/Universities placed in Poland, but they may as well extend at some point to collaborators in the UK, USA and other countries.

References:

Jumana R. Alhamdi et al. Controlled M1-to-M2 transition of aged macrophages by calcium phosphate coatings; Biomaterials 196 (2019) 90e99
Krzysztof Łukowicz et al. The role of CaO/SiO2 ratio and P2O5 content in gel-derived bioactive glass-polymer composites in the modulation of their bioactivity and osteoinductivity in human BMSCs; Materials Science & Engineering C 109 (2020) 110535
M. Łączka et al. Bioactivity and osteoinductivity of glasses and glass-ceramics and their material determinants; Ceramics International 42 (2016) 14313–14325

IZBR –18: Astrocytes as the target of anti-epileptic action of ketogenic diet (Institute of Zoology and Biomedical Research)

Institute: Institute of Zoology and Biomedical Reasearch

Topic: Astrocytes as the target of anti-epileptic action of ketogenic diet

Name of supervisor: prof. dr hab. Zuzanna Setkowicz-Janeczko (zuzanna.setkowicz-janeczko@uj.edu.pl)  

Background information:

Traumatic brain injury (TBI) brings serious therapeutic problems to clinical neurology. Its pathogenesis is complex and multifactorial. One of the most common consequences of traumatic brain injury is epilepsy. The current state of knowledge resulting from experimental and clinical trials clearly indicates the strong need for further search for new effective strategies to minimize consequences of brain damage and, at the same time, prevent the development of epilepsy. Among the various treatments ameliorating neurodegenerative changes in the posttraumatic conditions, a ketogenic diet (KD) was used. This is a special, restrictive high-fat diet without carbohydrates and with very low protein content. As demonstrated by the ketogenic diet used after TBI in one-month-old rats, it reduces the area of brain damage, suppresses apoptosis, and improves results in neurological tests. In response to CNS damage, astrocytes react with a series of morphological and functional changes and contribute to  the glial scar formation, which, among others, can interfere with neuronal excitability triggering seizures and epileptogenesis or can also increase susceptibility to seizuregenic agents.

The main question to be addressed in the project:

In this situation, given the results of our recent research (1,2), it is important to verify the hypothesis that a long-term ketogenic diet, applied after the brain damage, will change the properties of astrocytes, thereby weakening the epileptogenic nature of the glial scar. To verify this hypothesis, we suggest a sequence experiments generally described below:

Information on the methods/description of work:

1. Mechanical damage of the cerebral hemisphere in rats at two stages of postnatal life, followed by 4-month-lasting treatment with the ketogenic diet;

2. Induction of seizures (in rats treated with ketogenic diet after the brain damage) combined with electroencephalographic recordings before, during and after seizures occurrence;

3. Assessments of changes in behavioral symptoms, EEG spectra and transformations of cellular elements in the injured brains of rats treated with ketogenic diet.

Additional information (e.g Special requirements from the student):

Practical experience and theoretical knowledge concerning the following research activities, techniques and methods is expected in candidates: diet administration, blood collection (every week for about 500 animals), nervous tissue histological processing, immunohistochemical staining, behavioral tests, observation and scoring of animal seizure behavior, preliminary data analysis, animal care under anesthesia conditions, following EEG transmitter implantation and during EEG signal acquisition, photographic documentation, assistance in preparation of scientific reports. Of particular importance is the ability to perform statistical calculations and present their results at conferences.

References:

1. MRI spectroscopic and tractography studies indicate consequences of long-term ketogenic diet.

Brain Struct Funct. 2020 Sep;225(7):2077-2089.

2. The Impact of the Ketogenic Diet on Glial Cells Morphology. A Quantitative Morphological Analysis. Neuroscience. 2019 Aug 10;413:239-251.

3. Various ketogenic diets can differently support brain resistance against experimentally evoked seizures and seizure-induced elemental anomalies of hippocampal formation. J Trace Elem Med Biol. 2017 Jul;42:50-58.

IZBR –19: The influence of interspecific gene flow on the integrity of mitonuclear coadaptation (Institute of Zoology and Biomedical Research)

Institute: Institute of Zoology and Biomedical Research

Topic: The influence of interspecific gene flow on the integrity of mitonuclear coadaptation 

Name of supervisor: Dr hab. Maciej Pabijan (maciej.pabijan@uj.edu.pl)  

Background information:

Proteins encoded by interacting mitochondrial and nuclear genes catalyze essential metabolic processes such as oxidative phosphorylation (OXPHOS) in the mitochondria of eukaryotic cells. The direct interaction of these proteins requires cooperation between mitonuclear allele combinations. However, the two genomes have different modes of inheritance, recombination and mutation rates. These differences have the potential to coerce reciprocal changes in interacting OXPHOS genes (mitonuclear coadaptation). In hybridizing species, mismatched combinations (mitonuclear incompatibilities), i.e. OXPHOS protein complexes with subunits from both of the parental species, could result in inferior enzymatic performance and reduced fitness of hybrid progeny. Selection for the maintenance of integrity of coadapted mitonuclear gene complexes may have major consequences for local adaptation, reproductive isolation and speciation. However, apart from a few systems, little is known of the role of mitonuclear match and mismatch on speciation. In particular, the extent of mitonuclear coadaptation among closely related species and the dynamics of mitonuclear associations in hybridizing species are not well understood. Moreover, the fitness effects of mitonuclear incompatibilities have been assessed in very few species.

The main question to be addressed in the project:

What is the effect of gene flow via hybridization on co-adapted mitonuclear gene complexes? Do co-adapted complexes flow more freely between hybridizing species than randomly chosen nuclear loci?

The 1st aim of the project will be an assessment of mitonuclear co-adaptation across a broad panel of hybridizing amphibian species, including deeply divergent lineages within species.

The 2nd stage of the project will take advantage of several amphibian species complexes in which the mtDNA of one species has introgressed onto the nuclear background of a different species, with purportedly little or no nuclear gene flow. We will test the hypothesis that mtDNA replacement has entailed the introgression of coadapted nuclear genes due to strong selection for mitonuclear integrity.

The third aim of the project, contingent on the results of stage 2, will check for differential performance of lineages with mismatched mitochondrial and nuclear OXPHOS components, with an aim to assess whole organism (i.e. tadpole) fitness. We hypothesize that mismatched individuals will have lower fitness under a range of environmental gradients.

Information on the methods/description of work:

A major component of the project will involve labwork and bioinformatics using targeted sequencing approaches after establishing gene models from transcriptome/genomic data for each of the species complexes. Samples from some systems, as well as transcriptomes, will be available from collaborators. In other systems, the project will involve de novo collection of data, including field work (collection of tissue samples from selected species complexes including Pelophylax, Lissotriton, Ichthyosaura). New transcriptomes will be generated if necessary. Hypothesis tests will be centered around the assumptions that, if there is selection maintaining the integrity of co-adapted OXPHOS complexes across species boundaries, then genetic differentiation between hybridizing species at OXPHOS genes should be lower compared to a random sample of nuclear genes. On the other hand, we should observe higher linkage disequilibrium among OXPHOS genes as well as genealogical discordance between OXPHOS genes and a randomly selected set of nuclear genes. Further work will involve the husbandry of amphibian larvae for experimental fitness assays.

Additional information (e.g Special requirements from the student):
Candidates are expected to have a strong interest in evolutionary biology and a basic knowledge of molecular ecology. The PhD student may be entitled to a separate stipend from the National Science Centre of Poland.

Place/name of potential foreign collaborator:
CIBIO - Research Center in Biodiversity and Genetic Resources, InBIO Associate Laboratory, University of Porto, Portugal

References:

Gershoni, M., Templeton, A. R., & Mishmar, D. (2009). Mitochondrial bioenergetics as a major motive force of speciation. Bioessays, 31(6), 642-650.
Morales, H. E., Pavlova, A., Amos, N., Major, R., Kilian, A., Greening, C., & Sunnucks, P. (2018). Concordant divergence of mitogenomes and a mitonuclear gene cluster in bird lineages inhabiting different climates. Nature Ecology & Evolution 2(8), 1258.
Hill, G. E. (2019). Reconciling the mitonuclear compatibility species concept with rampant mitochondrial introgression. Integrative and Comparative Biology, doi: 10.1093/icb/icz019

IZBR –20: An evaluation of the action of next-generation bisphenols in the ovary (Institute of Zoology and Biomedical Research)

Institute: Institute of Zoology and Biomedical Research

Topic: An evaluation of the action of next-generation bisphenols in the ovary.

Name of supervisor: dr hab. Anna Ptak, prof. UJ (anna.ptak@uj.edu.pl)             

Background information:
Bisphenol A (BPA) was an important chemical building block in the plastics industry, making it one of the most common commercial products in the world. Increasing concern over BPA, as an endocrine-disrupting chemical (EDC) and its possible effect on human health, has prompted the removal of BPA from consumer products, often labelled “BPA-free”. We believe that the subsequent introduction of BPA-free products, although a master marketing strategy, is in reality only the beginning of a new chapter of the BPA story. Bisphenol-S, F, B, and AF named next-generation bisphenols (NextGen bisphenols), are already used as the main BPA alternatives in consumer goods [1]. As a consequence, the presence of many NextGen bisphenols in environmental media, foodstuffs, consumer products, and humans urine from different regions of the world are observing [2]. Considering that the worldwide production and consumption of NextGen bisphenols are increasing dramatically, the number of individuals that are occupationally exposed to these compounds is, consequently, increasing every year. Thus, it is of pivotal importance for humans health to characterize their biological effects, especially on the reproductive system, which is a target for EDCs [3].

The main question to be addressed in the project:
The main aim of the project is to verify if NextGen bisphenols are endocrine-disrupting chemicals in the ovary and which disorders are connected with these exposures.

Information on the methods/description of work:
Experiments in the proposed research project will be performed using in vitro methods. We intend to identify whether individual NextGen bisphenols (like BPS, BPF), could disrupt human ovarian steroidogenesis by modulating the expression of key steroidogenic enzyme. Next, we plan determinate whether NextGen bisphenols could modulate the biology of ovarian cells via the “classical” and “non-classical” estrogen receptor signaling pathways. Importantly, the animal model will allow for the evaluation of NextGen bisphenols influence at oocyte quality and potential success in the reproduction.

The analysis will be carried out with the use of following assays: in vitro cell culture, RT-qPCR, siRNA transfection, Western blot, ELISA assay, Fluorescence assay and staining, Luminescence assay.

Special requirements from the student:
Experience in cell culture, molecular biology techniques like ELISA, fluorometric and/or colorimetric analysis, and proteomic analysis; ii) completed courses on Endocrinology and Hormonally Active Compounds in the Environment.

References:

[1] Lehmler HJ, Liu B, Gadogbe M, Bao W. Exposure to Bisphenol A, Bisphenol F, and Bisphenol S in U.S. Adults and Children: The National Health and Nutrition Examination Survey 2013–2014. ACS Omega 2018; 3, 6523-6532.

[2] Chen D, Kannan K, Tan H, Zheng Z, Feng YL, Wu Y, Widelka M. Bisphenol Analogues Other Than BPA: Environmental Occurrence, Human Exposure, and Toxicity-A Review. Environ Sci Technol. 2016; 50: 5438-53.

[3] Ptak A, Hoffmann M, Rak A. The ovary as a target organ for bisphenol a toxicity. Book title: Bisphenol A: exposure and health risks, 2017;  57-73, ISBN 978-935-51-3218-9, Publisher: InTech.

IZBR –21: The role of interpeduncular nucleus – ventral hippocampus axis in anxiety-related behaviours (Institute of Zoology and Biomedical Research) 

Institute: Institute of Zoology and Biomedical Research

Topic: The role of interpeduncular nucleus – ventral hippocampus axis in anxiety-related behaviours

Name of supervisor: dr hab. Anna Błasiak (anna.blasiak@uj.edu.pl)

Background information:

Anxiety disorders are currently the most common neuropsychiatric condition, affecting up to 34% of the global population. Yet the precise neural circuits and molecular mechanisms involved in anxiety control remain unclear (Bandelow and Michaelis, 2015). Considerable experimental data indicate that the midbrain interpeduncular nucleus (IPN) and innervated by this structure ventral hippocampus (vHipp), are critical for anxiety expression and necessary for the emergence of aversive states (McLaughlin et al., 2017). Importantly, environmental stressors, aggressiveness and anxiety-like behaviours significantly affect the expression of nerve-growth factor (NGF) in certain brain areas and NGF levels in the bloodstream both in animal models and in humans (Bersani et al., 2000). In this regard, it was show that the brain area that is characterized by one of the highest expression levels of NGF receptor - tropomyosin receptor kinase-A (TrkA), is the IPN. These data underpin the hypothesis that the IPN-vHipp axis is a crucial component of the network controlling anxiety behaviour and that IPN is a site of anxiety related NGF action.

The main question to be addressed in the project:

Despite emerging evidence for a role of IPN and vHipp in the control of anxiety, the nature of IPN-vHipp innervation and its role in shaping anxiety behaviour remain uncharacterized. Therefore, the major goals of the proposed research are to investigate the functional connectivity and neurochemical profile of the IPN-vHipp circuit, the role of this pathway in anxiety-related behaviours, and the impact of NGF signaling in shaping IPN neuronal activity, and consequently, anxiety behaviours.

Information on the methods/description of work:

In studies to elucidate the nature of the interaction between IPN and vHipp at the cellular level, ex vivo patch-clamp recordings of rat vHipp neuronal activity during optogenetic activation of fibres originating in IPN will be performed. Moreover, patch clamp recordings will be used to verify NGF actions on IPN neurons. Multiplex in situ hybridization, immunohistochemical and neural tract-tracing studies in rats, will characterize the neurotransmitters and receptors expressed by neurons comprising the IPN-vHipp circuit. Finally, behavioral experiments in rats, employing chemogenetics will test how the IPN-vHipp circuit is involved in anxiety-related behaviours.

Additional information (e.g Special requirements from the student):

Candidates with previous experience in electrophysiological ex vivo recordings, analysis of electrophysiological data, preparation of tissues for subsequent anatomical studies and immunohistochemical techniques.

Place/name of potential foreign collaborator:

Florey Institute of Neuroscience and Mental Health, Melbourne, Australia/Professor Andrew Gundlach

References:

1.  Bandelow, B., Michaelis, S., 2015. Epidemiology of anxiety disorders in the 21st century. Dialogues Clin. Neurosci. 17, 327–335.

2.  Bersani, G., Iannitelli, A., Fiore, M., Angelucci, F., Aloe, L., 2000. Data and hypotheses on the role of nerve growth factor and other neurotrophins in psychiatric disorders. Med. Hypotheses 55, 199–207.

3.  McLaughlin, I., Dani, J.A., De Biasi, M., 2017. The medial habenula and interpeduncular nucleus circuitry is critical in addiction, anxiety, and mood regulation. J. Neurochem. 142,

IZBR –22: Immunometabolism of leukocytes of innate immunity: intravital imaging approach (Institute of Zoology and Biomedical Research)

Institute: Institute of Zoology and Biomedical Research 

Topic: Immunometabolism of leukocytes of innate immunity: intravital imaging approach

Name of supervisor: dr hab. Elżbieta Kołaczkowska, prof. UJ (ela.kolaczkowska@uj.edu.pl)                                                     

Background information:

Immunometabolism, an interdisciplinary branch of biomedical research, focuses on intracellular metabolic pathways in leukocytes that alter their function and thus impact immune responses. Also the other way around, metabolic state of the organism impacts behavior and functioning of immune cells. Thus overall, the immunometabolism at either cellular or organismal level is a deciding factor in disease development and/or course and represents a potential therapeutic goal. Whereas majority of studies on immunometabolism focuses on either macrophages or lymphocytes and in in vitro settings, herein we aim to investigate the metabolic-immune interactions also of other innate immune cells, especially of neutrophils, and follow them in vivo, in a living organism. Any disease is connected to inflammation, be it the inducing factor that becomes chronic or a consequence of malfunctioning of a given molecule or process. But whereas the inflammatory response follows similar steps independently of the cause, its consequences differ in regard to its duration (acute vs. chronic) and extend/severity (local vs. systemic). These aspects of immunometabolism were not explored thus far whereas remain critical in our understanding of (any) disease progression.

The main questions to be addressed in the project:

Does what we know on immunometabolism from in vitro studies apply also to complex biological in vivo milieu? If so, can we manipulate metabolically either the environment or leukocytes to adjust their parameters/functions in favor of disease ceasing? What are the differences between leukocyte metabolism in the course of acute/chronic and local/systemic inflammation? To answer the questions, extensive studies on mouse disease(s) models will be undertaken and apart of standard biomedical tools intravital microscopic analyses will be employed to investigate dynamic biological processes occurring in live mice in real time.

Information on the methods/description of work:

Intravital (in vivo) microscopy, confocal microscopy, large-scale studies on mouse models,  Western blot, ELISA, immunocytochemistry, ex vivo cell culture (siRNA silencing, miRNA).

Additional information:

Special requirements from the student: experience in working with mice, knowledge of confocal microscopy, ability to use the above mentioned methods, knowledge of English in speech and writing, openness to learning, teamwork skills. Experience is immunometabolic studies (immunological and biochemical methods and/or degree in immunology/biochemistry) is highly welcome although not required.

Place/name of potential foreign collaborator:

-Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium / Prof. Ghislain Opdenakker

- Centre for Inflammatory Disease Monash Health, Monash University, Sydney, Australia / Prof. Connie Wong

References:

Cichon I, Ortmann W, Santocki M, Opydo-Chanek M, Kolaczkowska E. Scrutinizing Mechanisms of the 'Obesity Paradox in Sepsis': Obesity Is Accompanied by Diminished Formation of Neutrophil Extracellular Traps (NETs) Due to Restricted Neutrophil-Platelet Interactions. Cells. 2021;10:384.
Kolaczkowska E, Jenne CN, Surewaard BG, Thanabalasuriar A, Lee WY, Sanz MJ, Mowen K, Opdenakker G, Kubes P. Molecular mechanisms of NET formation and degradation revealed by intravital imaging in the liver vasculature. Nat Commun. 2015;6:6673.
Dal-Secco D, Wang J, Zeng Z, Kolaczkowska E, Wong CH, Petri B, Ransohoff RM, Charo IF, Jenne CN, Kubes P. A dynamic spectrum of monocytes arising from the in situ reprogramming of CCR2+ monocytes at a site of sterile injury. J Exp Med. 2015;212:447-56.
Kolaczkowska E, Kubes P. Neutrophil recruitment and function in health and inflammation. Nat Rev Immunol. 2013;13:159-75.