Recruitment

PhD students are recruited to the specific research topics offered by potential doctoral advisors. A list of topics is given below. Candidates are expected to contact the faculty members who have announced the topics they are interested in pursuing.

In the Online Application System the topics will be identified by their number. Upon registration the candidates choose up to three research topics. For each declared subject, the candidates will be asked to attach the written approval of the faculty member, confirming that they are willing to academically supervise the candidate, if they pursue the research project subject which they have submitted. 

Please visit Online Application System to find out the information on the recruitment dates, criteria and required documents.

 

IES-1: Experimental model of holobiont evolution: gut bacterial symbionts in bank voles selected for increased herbivorous capability

 Supervisor: Prof. Paweł Koteja (Evolutionary Physiology Research Team, Institute of Environmental Sciences)

Background information: Symbiotic evolution played an important role at all stages of evolution of diverse life strategies. According to the “hologenome” concept, natural selection acts on the holobiont (host and associated microbes) rather than on animals alone. A unique opportunity to test the concept is offered by our artificial selection experiment on bank voles (Myodes glareolus). We observed that voles from lines selected for improved “herbivorous capability” had an altered composition of gut bacterial symbionts, even if the particular individuals had no contact with the special diet.

The main question to be addressed in the project: We ask whether a) the difference in gut bacteria composition occurred in response to the short change of diet in parents, and was merely transmitted to offspring or b) the selected voles evolved genetically-based modifications allowing preferable hosting a modified bacterial community. In the latter case, the project will provide a worldwide-unique experimental demonstration of the “holobiont” evolution, and a promising model for studying the underlying genetic and biochemical mechanisms.

Information on the methods/description of work: The project consists of two main stages: 1) experiments on the voles (manipulation of diet, cross-fostering, measuring physiological traits and the size of internal organs, and collecting gut contents samples), and 2) molecular analyses of bacterial DNA in the samples, leading to description of the bacterial community and statistical analyses of its composition.

Special requirements from the student: An experience in working with terrestrial vertebrate animals (preferably rodents) and in a molecular or biochemical laboratory.

The student will receive a 3000 PLN/month stipend paid from the research grant (independently of regular stipends).

Place/name of potential foreign collaborator: Dr. Kevin Kohl, currently: Vanderbilt University, moving to: University of Pittsburgh, USA.

Reference(s)

Kohl, K.D., Sadowska, E.T., Rudolf, A.M., Dearing, M.D., Koteja, P. 2016. Experimental evolution on a wild mammal species results in modifications of gut microbial communities. Frontiers in Microbiology 7 (634) 1-10 (doi: 10.3389/fmicb.2016.00634) (and all the literature cited in this paper).

  

IES-2: Recombination landscape across the bulb mite genome

Supervisor: Prof. Wiesław Babik (Molecular and Behavioral Ecology Group, Institute of Environmental Sciences)

Background information: In most organisms recombination rate varies across the genome. This variation has fundamental consequences for interpretation of data on genetic variation within and differentiation between populations. It is because intragenomic variation in recombination rate determines the strength of selection at linked sites (background selection). As a consequence, effective population size and genetic diversity are heterogeneous across the genome. This translates into genomic heterogeneity of genetic differentiation between populations and generates signals which may erroneously be identified as signatures of local adaptation or reproductive isolation. Thus, without understanding and accounting for recombination rate variation, studies relying on comparisons between populations to detect and interpret genomic signals of selection and gene flow suffer from high rate of false positives. This issue is not limited to studies of natural populations but is also critical for projects utilizing experimental evolution, which compare replicate lines evolved under different conditions or different selection regimes.

The main question to be addressed: The aim of this project is estimation of recombination rate across the genome of the bulb mite (Rhizoglyphus robinii), an important model in evolutionary studies of sexual selection and sexual conflict, which often employ an experimental evolution approach. The same data will be used to construct high-density linkage map which will improve quality of the reference genome. The existing genomic data on polymorphism and differentiation between populations will be used to check how much intragenomic variation is explained by variation in recombination rate.

Information on the methods: We will use the existing reference genome and low-coverage genome resequencing of parents and numerous offspring.

Collaborators: The project will involve close collaboration with J. Radwan and M. Konczal (Evolutionary Biology Group, AMU, Poznań).

References:

Nachman, M. W. (2002). Variation in recombination rate across the genome: evidence and implications. Current opinion in genetics & development, 12, 657-663.

Webster, M. T., & Hurst, L. D. (2012). Direct and indirect consequences of meiotic recombination: implications for genome evolution. Trends in Genetics, 28, 101-109.

Ellegren, H., & Galtier, N. (2016). Determinants of genetic diversity. Nature Reviews Genetics, 17: 422-433.

 

IES-3: Sexual differences in ontogenetic traits (growth rate and duration) and their effects on other life history traits in decorated cricket

Name of supervisor:  Dr. Paulina Kramarz (Physiological and evolutionary ecology of invertebrates research team, Institute of Environmental Sciences)

Background information: Sexual dimorphism is widespread in nature and is thought to be present in the evolutionary history from the very beginning of sexual reproduction. In spite of its apparent ubiquity and phylogenetic universality, we still know very little about genetic correlations between life history traits within females and males as well as genetic correlations between sexes. Life history traits: growth rate, development time, body size, fecundity, lifespan affect values of the two most important fitness traits: survival and reproduction. In turn, the two shape Darwinian fitness. Sexes differ in Darwinian fitness and thus in the remaining life history traits, possibly as an outcome of different selection forces acting on each sex: selection on fertility in case of females and sexual selection in case of males.

The main question to be addressed in the project: An influence of ontogenetic traits on the level of sexual dimorphism in the other traits and immunological response (as a trait connected to an individual condition). Genetic correlation between studied traits and between females and males in shared traits.

Information on the methods/description of work: Study species, Gryllodes sigillatus, is hemimetabolous insect species with a well-known biology. Reproductive effort of males will be estimated by measuring the amount of time spent calling and size of nuptial gift. All models (life-history, biochemical and behavioral traits) will be subsequently analyzed within the animal model framework.

Special requirements from the student: Knowledge on animal biochemistry and physiology as well as on insect biology.

References

Drayton, J.M. et al. (2012) Sexual signaling and immune function in the black field cricket Teleogryllus commodus. PLoS One 7, e39631

Fairbairn, J.P. et al. (2007) Sex, size, and gender roles evolutionary studies of sexual size dimorphism, Oxford University Press

Gershman, S.N. and Sakaluk, S.K. (2010) Mate quality and novelty influence post-copulatory female choice in decorated crickets, Gryllodes sigillatus. Ethology 116, 1113–1117

 

IES-4: Ecosystem services in environmental governance: a novel paradigm for addressing biodiversity decline

Name of supervisor: Prof. Małgorzata Grodzińska-Jurczak (Environmental Education Research Team, Institute of Environmental Sciences)

Background information: Rich biodiversity and well-functioning ecosystems are pre-requisite for human survival, thus the ongoing biodiversity decline poses threat to our societies. Previous initiatives and policies have failed to halt the decline and there is a need for new environmental governance instruments to address this problem. Recently, ecosystem services (ES) concept has been promoted as a way to improve decision making regarding natural resources, especially maintaining biodiversity. However, ES is still not sufficiently integrated in important environmental decisions and there is a knowledge gap in how to improve its implementation.

The main questions to be addressed in the project: This PhD research project will investigate the ES concept’s assessment by stakeholders at local and regional governance levels in south and eastern Poland. Particularly, the concept’s integration in existing policies, stakeholders’ understanding and acceptance of it, good practices in and challenges of ES implementation, as well as the potential leverage of ES on maintaining endangered core biodiversity areas will be examined.

Information on the methods/description of work: The project will utilise a mixed-mode approach with qualitative (desk research, interviews, Q-method) and quantitative (surveys, statistical analysis) methods. The sample will consist of Polish decision makers and other stakeholders from the Carpathian region related to nature governance. The outputs will be compared with equivalent research in Sweden to validate their relevance and strengthen their practical universality.

Special requirements from the student: A potential candidate should possess knowledge and experience in designing and conducting interdisciplinary research and working in interdisciplinary research teams. Excellent written and oral skills in Polish language are required. A job experience in practical nature conservation (also non-research sector) would be of advantage.

Name of potential foreign collaborator: Dr Małgorzata Blicharska from Uppsala University.  

References

Harrison et al.  2014. Linkages between biodiversity attributes and ecosystem services: a systematic review. Ecosystem Services, 9, 191-203

Paloniemi et. al. 2015. Public participation and environmental justice in biodiversity governance in Finland, Greece, Poland and the UK. Environmental Policy and Governance, 25(5), 330-342

 

IB-5: Taxonomy and evolution of steppe grass species from the tribe Stipeae (Poaceae)

Name of supervisor: Dr. Marcin Nobis (Institute of Botany)

Background information: Steppes are among the most interesting and most diversified ecosystems of temperate zone in the Eurasia. They are also very rich in species of vascular plants. Among the main components of this type of vegetation are grasses, which dominate in many different steppe phytocoenoses. Especially interesting are feather grass steppes, build by different Stipa taxa. Unfortunately, the recognition of particular species representing the tribe is problematic. Selected groups of taxa from the Stipeae is still not sufficiently known and requires modern studies using morphological and molecular methods.

The main questions to be addressed in the project: This PhD research project will investigate taxonomy and phylogeny of feather grasses representing section Leiostipa as well their relation with other members of the genus originating from Old World. Particularly interesting are microevolutionary processes, recognition of natural intra- and intersectional hybridization processes; determination of the origin, stability and fertility of hybrid taxa, introgression events.

Information on the methods/description of work: Realization of this work requires both field and laboratory research: (1) sampling of material from the study area (different parts of Eurasia), (2) taxonomic verification of herbarium materials preserved in the main European and central Asian herbaria; (3) macromorphological, micromorphological, pollen and molecular studies; (4) measurement of morphological and ecological parameters in selected steppe localities (species diversity centers) for hybrids and their parents populations; (5) statistical analyses of obtained results.

Special requirements from the student: A potential candidate should possess experience in working in molecular laboratory, basic knowledge on taxonomy and distribution of feather grasses as well as ability to work in interdisciplinary research teams.

Name of potential collaborator: Dr hab. Jakub Sawicki (Warmia-Mazury University) and Dr Polina Gudkova (Tomsk State University).  

References

Tzvelev, N. (1989). The system of grasses (Poaceae) and their evolution. The Botanical Review, 55(3), 141-203.

Romaschenko, K., Peterson, P. M., Soreng, R. J., Garcia-Jacas, N., Futorna, O., & Susanna, A. (2012). Systematics and evolution of the needle grasses (Poaceae: Pooideae: Stipeae) based on analysis of multiple chloroplast loci, ITS, and lemma micromorphology. Taxon, 61(1), 18-44.

 

IB-6: Anatomy and ultrastructure of needles of relict gymnosperms, with emphasis on the plasmodesmata

Name of supervisor: Dr. Bartosz J. Płachno (Institute of Botany)

Background information: Cathaya argyrophylla Chung & Kuang is an endangered, endemic, relict species. Some anatomical features suggest a closer relationship of Cathaya to genera Picea and Pinus, however, other suggest a relationship to genera Larix and Pseudotsuga. Needle anatomy and ultrastructure of some gymnosperms are well known and documented (e.g. genus Pinus, Metasequoia glyptostroboides), however, still there is not enough data to resolve this controversy. Ultrastructural data may provide the key characters to understand evolutionary and taxonomical position of this ‘living fossil’.

The main question to be addressed in the project: The main aim of this project is to show the similarities and differences in the structure of needles that may indicate relationship between Cathaya and other genera. Another aim is to compare plasmodesmata development in Strasburger cells between Cathaya and other gymnosperm genera.

Information on the methods/description of work: Various anatomical methods will be used with the application of different microscopy techniques, mainly transmission electron microscopy. The samples will consist of gymnosperm needles (Cathaya argyrophylla and other members of subfamily Laricoideae, as well as chosen species from subfamilies Pinoideae and Abietoideae). The following features will be taken into account e.g.: general needle anatomy, structure of resin canals, mesophyll, ultrastructure of Strasburger cells, mesophyll plastids. The plasmodesmata in the Strasburger cells will be analysed in different stages of needle development.​

Special requirements from the student: A potential candidate should possess basic knowledge on plant anatomy and cell structure as well as ability to work in interdisciplinary research teams.

References

Dörken V.M., Nimsch H. (2015) Morpho-anatomical investigations of cones and pollen in Cathaya argyrophylla Chung & Kuang (Pinaceae, Coniferales) under systematical and evolutional aspects. Feddesm Repert. 125: 25-38

Glockmann C., Kollmann R. (1996) Structure and development of cell connections in the phloem of Metasequoia glyptostroboides needles. I. Ultrastructural aspects of modified primary plasmodesmata cells in Strasburger. Protoplasma 193:191–203

 

IES-7: Zooplankton community structure as an indicator of the extent of anthropogenic impact on various types of reservoirs

Name of supervisor: Dr. Wojciech Fiałkowski (Aquatic Biology Group, Institute of Environmental Sciences)

Background information: Water bodies exert significant influence on biodiversity and ecological networks within a landscape. These ecosystems are frequently strongly affected by human activities, e.g. habitat modifications or release of pollutants. How, and to what extent, their biocenoses respond to these stressors has not been fully studied yet. Nonetheless, zooplankton assemblages play an important role in biomonitoring programmes. The project aims at recognising the interplay between natural and anthropogenic factors controlling zooplankton community structure in waterbodies to various degree affected by human influence.

The main questions to be addressed in the project: The project will focus on main components of zooplankton communities – populations of dominant crustacean and rotifer species. Two questions will be addressed: a) how strongly particular characteristics of those communities – species diversity, spatial and temporal distribution of populations – are related to abiotic parameters of water bodies of various type and size; b) how strongly various human activities in investigated waterbodies alter these relationships.

Information on the methods/description of work: Several different reservoirs will be chosen in southern Poland. Samples of zooplankton will be collected over at least one year. Basic chemical and physical parameters of water quality will be concomitantly recorded. The distribution patterns, abundance and diversity of the zooplankton species for each reservoir will be described forming the basis for multivariate comparisons and analyses of the zooplankton communities across the reservoirs. An important part of analyses will be telling apart natural and anthropogenic factors differentiating between waterbodies.

Special requirements from the student: Experience in field and laboratory work in zooplankton research.

Name of potential foreign collaborator: Will be co-opted at later time.

References

Burdis, Robert M., and Jodene K. Hirsch. 2017. “Crustacean Zooplankton Dynamics in a Natural Riverine Lake, Upper Mississippi River.” Journal of Freshwater Ecology 32 (1). Taylor & Francis: 240–58. 

Dembowska, Ewa A., and Paweł Napiórkowski. 2015. “A Case Study of the Planktonic Communities in Two Hydrologically Different Oxbow Lakes, Vistula River, Central Poland.” Journal of Limnology 74 (2): 346–57. 

 

IZBR-8: Pathophysiology of sepsis: involvement of innate immune cells

Supervisor: Dr. Elżbieta Kołaczkowska (Department of Evolutionary Immunology, Institute of Zoology and Biomedical Research)

Background information: Sepsis remains a serious condition, associated with multiple organ dysfunction syndrome and often resulting in mortality. Up till now there is no dedicated therapy to treat sepsis nor exact mechanisms of this condition are known. Innate immune cells, in particular neutrophils and macrophages, are involved in the course of sepsis and their exaggerated activity leads to complications accompanying this condition. Our group studies involvement of the above mentioned leukocytes in pathology of sepsis and one of the foremost studied mechanisms is formation of neutrophil extracellular traps a.k.a. NETs. Although NETs trap pathogens, their persistent presence in vasculature, leads to bystander cell damage as we showed previously (Nat Commun. 2015;6:6673). Involvement of macrophages in NET formation and/or removal in vivo remains unknown, and furthermore, these cells can also release extracellular traps.

The main question to be addressed in the project: The main aim of this project is to scrutinize for yet unrecognized mechanisms of sepsis in relation to activity of innate immune cells with special emphasis on cooperation/interactions of neutrophils and macrophages, predominantly in regard to intravascular NETs.

Information on the methods/description of work: The studies will focus on both human and mouse systems. Mice studies will require induction of experimental sepsis and application of intravital microscopy to image vasculature. Both mouse and human leukocytes will also be studied in vitro by 3D culturing of single and mixed cell populations, and will employ, among others, immunocytochemistry, western blotting and flow cytometry.

Special requirements from the student: Candidates with prior experience conducting immunology research, immunofluorescent/confocal microscopy, flow cytometry, and knowledge of cell culturing, with emphasis on the 3D system, are highly encouraged to apply. Experience with mouse handling and/or Animal Care certificates are an advantage.

References

Kolaczkowska E. The older the faster: aged neutrophils in inflammation. Blood. 2016; 128:2280-2282.

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.

Kolaczkowska E, Kubes P. Neutrophil recruitment and function in health and inflammation. Nat Rev Immunol. 2013;13:159-75.

 

IZBR-9: Reconstruction of the phylogeny of the order Apochela (Tardigrada: Eutardigrada)

Supervisor: Dr. Łukasz Michalczyk (Department of Entomology, Institute of Zoology and Biomedical Research)

Background information: Tardigrades are a phylum of microscopic invertebrates famous for their remarkable resistance to unfavourable conditions. The order Apochela comprises a single family, Milnesiidae, composed of four genera, which have very limited number of meaningful phenotypic traits, making the taxonomy of this group is extremely challenging. Moreover, a recently discovered developmental variability in one of the key diagnostic traits questions at least some of Milnesium spp. diagnoses. So far, Apochela were used only as an outgroup for the order Parachela, thus the phylogenetic relationships between apochelan species and genera are unknown.

The main question to be addressed in the project: The main aim of this project is to reconstruct the phylogeny of the order Apochela based on four genetic markers, both nuclear and mitochondrial. The phylogeny will also allow to formulate hypotheses on the evolution of traits, indicate the ancestral states and identify autapomorphies that may result in erection of new taxa. Thanks to worldwide sampling, the project will allow to test for species crypsis and putative cosmopolitan distribution of some of the known species.

Information on the methods/description of work: About fifty apochelan populations collected worldwide will be examined. Individuals will be extracted from moss and lichen samples both already deposited in the laboratory and newly collected in the field. A comprehensive set of morphological, morphometric, molecular and developmental data will be gathered for each population. The data will be then used to reconstruct the phylogeny and trait evolution.

Special requirements from the student: Knowledge of tardigrade taxonomy, experience in work with LM and SEM, documented experience in molecular laboratory, basic knowledge of statistics and phylogenetic methodology. A track record of tardigrade publications highly desirable.

References

Bertolani, R., Guidetti, R., Marchioro, T., Altiero, T., Rebecchi, L. & Cesari, M. (2014) Phylogeny of Eutardigrada: New molecular data and their morphological support lead to the identification of new evolutionary lineages. Molecular Phylogenetics and Evolution 76: 110–126.

Michalczyk, Ł., Wełnicz, W., Frohme, M. & Kaczmarek, Ł. (2012) Redescriptions of three Milnesium Doyère, 1840 taxa (Tardigrada: Eutardigrada: Milnesiidae), including the nominal species for the genus. Zootaxa 3154: 1‒20.

Morek, W., Gąsiorek, P., Stec, D., Blagden, B. & Michalczyk, Ł. (2016) Experimental taxonomy exposes ontogenetic variability and elucidates the taxonomic value of claw configuration in Milnesium Doyère, 1840 (Tardigrada: Eutardigrada: Apochela). Contributions to Zoology 85: 173–200.

 

IZBR-10: Testing Wallace with microinvertebrates – patterns of diversity and distribution of water bears (Tardigrada)

Supervisor: Dr. Łukasz Michalczyk (Department of Entomology, Institute of Zoology and Biomedical Research)

Background information: Over 150-year ago Wallace postulated a zoogeographic border between the Oriental and the Australian realm that cuts through the Sunda Archipelago. The hypothesis has been positively verified for macroscopic animals, but it is still unclear whether microscopic organisms can be subject to zoogeographic processes similar to those determining the distributions of large animals. Recently, the rapid progress in molecular taxonomy showed that many microscopic animals, such as tardigrades, may exhibit much narrower geographic ranges than it was earlier assumed. Thus, thanks to the modern methods of integrative taxonomy, it will now be possible to confidently test Wallace’s hypothesis also with taxonomically challenging microinvertebrates.

The main question to be addressed in the project: Are there zoogeographic boundaries between the tardigrade faunae of South-Eastern Asia and Australia? If yes, then, (i) is the level of specificity of the fauna of each of the examined regions comparable to that known for macroscopic animals?; and (ii) is the boundary congruent with the Wallace line?

Information on the methods/description of work: The project requires a wide range of field, laboratory and analytical methods. The successful candidate will isolate tardigrades from samples and identify them with the use of integrative taxonomy tools. Then, the data will be used to test the hypotheses by comparing the faunae of the continental Asia, through Sunda Archipelago and Australia. Additionally, the candidate will describe new taxa, with the special attention to the Bornean Echiniscidae.

Special requirements from the student: Candidates must be familiar/skilled with modern animal systematics and phylogeny, fundamentals of theoretical zoogeography, phylogeography and taxonomy, methods of analytical zoogeography, methods of integrative taxonomy, tardigrade taxonomy. A track record of tardigrade publications highly desirable.

References

Condamine, F.L., Toussaint, E.F.A., Clamens, A.-L., Genson, G., Sperling, F.A.H. & Kergoat, G.J. (2015) Deciphering the evolution of birdwing butterflies 150 years after Alfred Russel Wallace. Scientific Reports, 5: 11860.

McInnes, S.J. & Pugh, P.J.A. (2007) An attempt to revisit the global biogeography of limno-terrestrial Tardigrada. Journal of Limnology, 66(S1): 90–96.

Tänzler, R., Toussaint, E.F.A., Suhardjono, Y.R., Balke, M. & Riedel, A. (2014) Multiple transgressions of Wallace’s Line explain diversity of flightless Trigonopterus weevils on Bali. Proceeding of the Royal Society, Series B, 281: 20132528.

 

IZBR-11: The role of glial cells in the regulation of circadian rhythms in Drosophila

Name of supervisor: Prof. Elzbieta Pyza (Department of cell Biology and Imaging, Institute of Zoology and Biomedical Research)

Background information: It is known that circadian rhythms in various processes, including behaviour, are regulated by a circadian system composed of the central clock (pacemaker) and peripheral clocks located in peripheral organs. In the brain of Drosophila melanogaster the pacemaker is composed of about 150 neurons, called clock neurons, which are divided into the morning and evening oscillator cells and their removal leads to arhythmicity or changes in the pattern and/or period of the locomotor activity rhythm. We have found that disruption of glial cells in the brain also results in similar changes in circadian rhythms but the mechanism of this phenomenon is unknown. The aim of this project will be to learn about interactions between clock neurons and glial cells and the role of glial cells in the regulation of circadian rhythms and sleep.

The main question to be addressed in the project: How do glial cells affect clock neuron physiology and morphology in the regulation of circadian rhythms in brain plasticity and behaviour?

Information on the methods/description of  work: In the project transgenic lines of Drosophila will be used to change expression of genes: for example of clock genes, clock-controlled genes in glial cells and to label certain types of glial cells or neurons with fluorescent markers (for example GFP). The effects of genetic manipulations on cell morphology will be studied using confocal and transmission electron microscopes. In addition, molecular methods, as gene expression (RT-PCR) and protein (Western blotting), will be used.

Place/name of potential foreign collaborator: Dr. C. P. Kyriacou, Department of Genetics, Leicester University, UK

References

Pyza E. and Górska-Andrzejak J. (2004).  Involvement of glial cells in rhythmic size changes in neurons of the housefly’s visual system. J. Neurobiol. 59: 205-215.  

Górska-Andrzejak J., Damulewicz M., Pyza E. (2015): Circadian changes in neuronal networks. Current Opinion in Insect Science, 7: 76-81.

 

IZBR-12: BMP signaling upon human MSC culture in 2D, 3D and dynamic (i.e. perfusion bioreactor) environment

Name of supervisor: Dr. Anna M. Osyczka (Department of cell Biology and Imaging, Institute of Zoology and Biomedical Research)

Background information: PhD project is the part of the National Science Centre grant awarded to dr hab. Anna M. Osyczka and entitled: Molecular signature of osteoinductive materials - attempting to standardize in vitro evaluation of biomaterials

The main question to be addressed in the project: Molecular mechanisms by which osteoinductive growth surfaces and scaffolds induce osteogenic differentiation of human mesenchymal stem cells.

Information on the methods/description of work: PhD work will focus on the role of chosen surfaces and scaffolds to induce expression of bone morphogenetic proteins in cultures of human MSC and molecular mechanisms of BMP action in 2D, 3D and dynamic (perfusion bioreactor) cultures. Most promising constructs will be eventually verified in vivoin a rabbit model for ectopic bone formation potential (i.e. “ in vivomeasure” of construct osteoinductivity).

Special requirements from the students: Basic knowledge regarding biomaterials used in regenerative medicine and experimental sciences. Strong background in intracellular signaling mechanisms.

Place/name of potential foreign collaborator: Dr Gwendolen Reilly, University of Sheffield, UK

References

Filipowska J, Reilly GC, Osyczka AM. A single short session of media perfusion induces osteogenesis in hBMSCs cultured in porous scaffolds, dependent on cell differentiation stage. Biotechnol Bioeng. 2016 Aug;113(8):1814-24.

Filipowska J, Pawlik J, Cholewa-Kowalska K, Tylko G, Pamula E, Niedzwiedzki L, Szuta M, Laczka M and Osyczka A. Incorporation of sol–gel bioactive glass into PLGA improves mechanical properties and bioactivity of composite scaffolds and results in their osteoinductive properties. Biomed. Mater. 2014; 9: 065001. 

 

IZBR-13: Vaspin - expression and role in the porcine ovary

Name of supervisor: Dr. Agnieszka Rak (Department of Physiology and Toxicology of Reproduction, Institute of Zoology and Biomedical Research)

Background information: The main scientific objective of the project is examine expression and action of vaspin (VASP) in porcine ovarian physiology. VASP is adipokine isolated in 2005 from the visceral fat strain rats OLETF, animal model of disease with abdominal obesity, diabetes type 2. Literature data describe the participation of VASP in the development of obesity, insulin resistance and pathogenesis of inflammatory (1-4), while a lack information in reproduction. There is a close link between nutritional status and reproductive success of animals, including pigs. Therefore made subject of research for local expression and regulation of the function of the ovary by VASP is extremely important, current and innovative at the same time. We hypothesized that VASP is produced in the ovarian follicle and regulate ovarian physiology such as steroid hormone production, cell proliferation, apoptosis and oocyte maturation, and is new link between metabolism and female reproduction.

The main question to be addressed in the project: i) determine mRNA and protein expression of VASP, their immunolocalization in the ovarian follicles; concentration of VASP in plasma and follicular fluid, ii)  in vitro regulation of ovarian VASP expression, iii) determination of VASP on ovarian function.

Information on the methods: real time PCR, Western blot, ELISA, immunohistochemistry, in vitro culture of porcine ovarian cells, genes silencing, Alamar blue assay, caspases activity.

Name of potential foreign collaborator: Professor Joëlle Dupont, INRA, France

References

Rak A, et al., Adiponectin and resistin: potential metabolic signals affecting hypothalamo-pituitary gonadal axis in females and males of different species. Reproduction. 2017;153(6):R215-R226.

Reverchon M, et al., Adipokines and the female reproductive tract. Int J Endocrinol. 2014;2014:232454.

Dupont J, et al., Involvement of adipokines, AMPK, PI3K and the PPAR signaling pathways in ovarian follicle development and cancer. Int J Dev Biol. 2012;56:959-67.

Tersigni C, et al., Adipokines: new emerging roles in fertility and reproduction. Obstet Gynecol Surv. 2011;66:47-63

 

IES-14: Testing the heat dissipation limitation theory in birds and in the ageing perspective: a study on free-living and captive birds

Supervisors: Dr. Edyta Sadowska (Evolutionary Physiology Research Team, Institute of Environmental Sciences), Dr. Ulf Bauchinger and Prof. Mariusz Cichoń (Population Ecology Research Team, Institute of Environmental Sciences)

Background information: To be able to maintain heat balance is an evolutionary milestone for endotherms, however, the high rates of energy turnover of endotherms also necessitate the dissipation of heat. The dissipation of heat may even become a limiting factor for whole animal performance for example when the surrounding temperature is high or when the metabolic activity is substantial. According to the heat dissipation limits theory (HDL), the rate at which animals can dissipate excess body heat produced through locomotor activity or milk production sets the limit to the total energy budget of endotherms. If the HDL is correct, it can be also hypothesized that the effect of HDL is more profound in old animals, which could explain an age dependent decline of reproductive output. At present, results of empirical testing HDL are not available for birds and are neither available in the ageing context for any endotherm.

The main question to be addressed in the project: The main aim of our study is to check if HDL is responsible for age-dependent decline in reproductive output of small birds.

Information on the methods: We will use two avian model species: great tits (Parus major) in the field and zebra finches (Taenyopyga guttata) in the laboratory. We will measure components of energy budgets in an experiment with manipulation of heat dissipation capacity performed on differently aged animals.

Special requirements from the student: Interest in evolutionary and ecological physiology, experience in experimental work with vertebrates (preferably with small birds), creativity and high motivation in learning new methods, teamwork and communication skills.

Additional information: The student will get 2000 PLN monthly scholarship from NCN project for four years (independently of regular stipends).

Names of potential foreign collaborators: Prof. Wolfgang Goymann, Max Planck Institute for Ornithology, Seewiesen, Germany and Prof. Scott R. McWilliams, University of Rhode Island, Kingston, USA.

References

Speakman, J. R., and E. Król. 2010. Maximal heat dissipation capacity and hyperthermia risk: Neglected key factors in the ecology of endotherms. Journal of Animal Ecology 79:726-746.

Grémillet, D., L. Meslin, and A. Lescroël. 2012. Heat dissipation limit theory and the evolution of avian functional traits in a warming world. Functional Ecology 26:1001-1006.

Hammers, M., D. S. Richardson, T. Burke, and J. Komdeur. 2012. Age-Dependent Terminal Declines in Reproductive Output in a Wild Bird. Plos One 7.

 

IES-15: Testing the heat dissipation limitation theory in the context of ageing: reproductive performance in two mammalian animal models

Supervisors: Dr. Edyta Sadowska, Prof. Paweł Koteja (Evolutionary Physiology Research Team, Institute of Environmental Sciences) and dr. Ulf Bauchinger (Population Ecology Research Team, Institute of Environmental Sciences)

Background information: Both mammals and birds show an age dependent decline in reproductive output, but the causes for this decline are not fully resolved. In general, reproduction represents an extremely energy demanding phase in the life cycle of mammals and birds. According to the heat dissipation limits theory (HDL), the rate at which animals can dissipate excess body heat produced through locomotor activity or milk production sets the limit to the total energy budget of endotherms. If the HDL is correct, it can be also hypothesized that the effect of HDL is more profound in old animals, which could explain the decline of reproductive output. However, results of empirical testing HDL are ambiguous and so far not available in the aging contexts.

The main question to be addressed in the project: The main aim of our study is to check if HDL is responsible for age-dependent decline in reproductive output of small mammals.

Information on the methods: We will use two unique mammalian models: a strain of laboratory mice with ablation of UCP1 and our experimental evolution model system with four lines of bank voles (Myodes glareolus) selected for high metabolic rate and four unselected lines maintained as a control. We will measure components of energy budgets in an experiment with manipulation of heat dissipation capacity performed on differently aged animals.

Special requirements from the student: Interest in evolutionary and ecological physiology, experience in experimental work with vertebrates (preferably with small mammals), creativity and high motivation in learning new methods, teamwork and communication skills.

Additional information: The student will get 2000 PLN monthly scholarship from NCN project for four years (independently of regular stipends).

Place/name of potential foreign collaborator: Jan Nedergaard, Stockholm University, Sweden.

References

Sadowska, E. T., E. Krol, K. M. Chrzascik, A. M. Rudolf, J. R. Speakman, and P. Koteja. 2016. Limits to sustained energy intake. XXIII. Does heat dissipation capacity limit the energy budget of lactating bank voles? Journal of Experimental Biology.

Cannon, B., and J. Nedergaard. 2011. Nonshivering thermogenesis and its adequate measurement in metabolic studies. Journal of Experimental Biology 214:242-253.

Martin, J. G. A., and M. Festa-Bianchet. 2011. Age-independent and age-dependent decreases in reproduction of females. Ecology Letters 14:576-581.

 

IZBR-16: Biologically active substances from Pelargonim sidoides- mechanisms of action in gingivial tissue regeneration; in vitro cell culture studies

Name of supervisors:  Dr. Anna M. Osyczka and/or Dr. Grzegorz Tylko (Department of cell Biology and Imaging, Institute of Zoology and Biomedical Research)

Background information: PhD project is the parts of the European Commission (M-ERA.NET Call 2016) grant awarded collectively to dr hab. Anna M. Osyczka and dr hab. Grzegorz Tylko, who are the partners of the international research team running a project entitled:  "Engineering and functionalization of delivery system with Pelargonium sidoidesbiologically active substance on inflamed periodontal surface area".

The main question to be addressed in the project: Biological mechanisms of action of active substances extracted from Pelargonium sidoidesroots (mainly proanthocyanidins) in relation to human keratinocytes, fibroblasts, periodontal ligament cells and bone marrow mesenchymal stem cells. The active substances reveal anti-microbial potential but little is known about they action on adult and progenitor cells responsible for tissue regeneration.

Information on the methods/description of work: PhD projects will examine the cellular processes triggered by active substances, such as cell cycle/proliferation, differentiation potential, possible apoptotic and related programmed cell death pathways. They will also examine in details the intracellular mechanisms induced by P. sidoides root extracts and proanthocyanidins to acquire the broad knowledge regarding their regenerative potential.

Special requirements from the students: Basic knowledge regarding the differentiation potential of mesenchymal stem cells and periodontal ligament cells, and their application to tissue regeneration. Strong background in intracellular signaling mechanisms, especially those related to cell cycle regulation and programmed cell death.

Place/name of potential foreign collaborator: Lithuanian University of Health Sciences; Centre of Polymer and Carbon Materials Polish Academy of Science; Latvian Institute of Organic Synthesis; Riga Stradins University; Universita Piemonte Oriantale; UAB “Ferentis“

Reference

Pereira A., Bester M., Soundy P., Apostolides Z. 2016. Anti-proliferative properties of commercial Pelargonium sidoidestincture, with cell cycle G0/G1 arrest and apoptosis in Jurkat laeukemia cells. Pharmaceutical Biology 54(9): 1831-1840

 

IZBR-17: Regenerative potential of biomaterials carrying Pelargonium sidoidesactive substances; in vitro cell culture evaluation of delivery vehicles

Name of supervisors: Dr. Anna M. Osyczka and/or Dr. Grzegorz Tylko (Department of cell Biology and Imaging, Institute of Zoology and Biomedical Research)

Background information: PhD project is the parts of the European Commission (M-ERA.NET Call 2016) grant awarded collectively to dr hab. Anna M. Osyczka and dr hab. Grzegorz Tylko, who are the partners of the international research team running a project entitled:  "Engineering and functionalization of delivery system with Pelargonium sidoidesbiologically active substance on inflamed periodontal surface area".

The main question to be addressed in the project: Biological verification of biomaterials (polymers) designated to serve as delivery vehicles of active substances derived from P. sidoides. What are biological mechanisms of polymer and/or its degradation action in relation to human keratinocytes, fibroblasts, periodontal ligament cells and bone marrow mesenchymal stem cells. Most promising delivery constructs will be eventually verified in clinics.

Information on the methods/description of work: PhD projects will examine the cellular processes triggered by both polymers and their degradation products, such as cell cycle/proliferation, differentiation potential, possible apoptotic and related programmed cell death pathways. They will also examine in details the active substances delivery vehicles, the rate of the substance release in static and dynamic conditions. Intracellular mechanisms induced by biomaterial/delivery vehicle will be studied in details to acquire the broad knowledge regarding their potential to regenerate periodontal tissue.

Special requirements from the students: Basic knowledge regarding biomaterials used in regenerative medicine and experimental sciences as well as the differentiation potential of mesenchymal stem cells and periodontal ligament cells. Strong background in intracellular signaling mechanisms, cell cycle regulation and programmed cell death mechanisms.

Place/name of potential foreign collaborator: Lithuanian University of Health Sciences; Centre of Polymer and Carbon Materials Polish Academy of Science; Latvian Institute of Organic Synthesis; Riga Stradins University; Universita Piemonte Oriantale; UAB “Ferentis“

References

G. Adamus, P. Kurcok, I. Radecka, M. Kowalczuk, „Bioactive oligomers from natural polyhydroxyalkanoates and their synthetic analogues”, Polimery, 2017, 62(4), 317-322

W. Sikorska, J. Rydz, K. Wolna-Stypka, M. Musioł, G. Adamus, I. Kwiecień, H. Janeczek, K. Duale, M. Kowalczuk "Forensic Engineering of Advanced Polymeric Materials—Part V: Prediction Studies of Aliphatic–Aromatic Copolyester and Polylactide Commercial Blends in View of Potential Applications as Compostable Cosmetic Packages", Polymers, 2017, 9, 257

 

IES-18: Intersexual differences in density-dependent dispersal and their consequences for metapopulation functioning

Supervisor: Dr. Piotr Nowicki (Behavioural Ecology Group, Institute of Environmental Sciences)

Background information: Dispersal is a key driver of evolutionary processes, but at the same time dispersal propensity should be perceived as a life history trait that is subject to evolutionary changes and phenotypic plasticity. Due to different optimal mating strategies of males and females one may expect strong intersexual differences in dispersal, in particular in relation to conspecific density which shapes intraspecific competition and mating chances. Such differences should play a vital role in metapopulation functioning, because while both male and female dispersal contribute to gene flow, only the latter can result in successful colonisations.

The main question to be addressed in the project: The following hypotheses will be tested: (1) male dispersal decreases with conspecific density, and is predominantly driven by the availability of mating partners; (2) female dispersal increases with conspecific density, and is predominantly driven by resource availability. The project will also investigate the consequences of intersexual differences in dispersal for metapopulation functioning by testing the concordance between simulated colonisation rates under various scenarios of sex-biased dispersal and true colonisation rates derived from long‑term monitoring data.

Information on the methods/description of work: The project will involve the analyses of extensive mark-recapture data (mostly already available) collected in metapopulations of several butterfly species (Maculinea spp, Lycaena helle). Density-dependent patterns of male and female dispersal will be analysed using the Virtual Migration model and the multi-state Brownie’s model, whereas the simulations of dispersal within the metapopulations will be run in the VMSIM program.

Special requirements from the student: Interest in metapopulation ecology and mark-recapture models; previous experience in these fields would be of advantage, but is not required.

Place of potential foreign collaboration: Czech University of Life Sciences in Prague

References:

Nowicki P, Vrabec V (2011) Evidence for positive density-dependent emigration in butterfly metapopulations. Oecologia 167: 657–665

Ronce O (2007) How does it feel to be like a rolling stone? Ten questions about dispersal evolution. Annual Review of Ecology Evolution and Systematics 38: 231–253

Timus N, Czekes Z, Rákosy L, Nowicki P (2016) Conservation implications of source-sink dynamics within populations of endangered Maculinea butterflies. Journal of Insect Conservation 21: 369–378

 

IES-19: Using species assembly rules to identify best indicator species in butterfly communities

Supervisor: Dr. Piotr Nowicki (Behavioural Ecology Group, Institute of Environmental Sciences)

Background information: Butterflies are regarded as highly useful biodiversity indicators, but their indicatory potential varies greatly among species. The previous attempts to identify best indicator species based on the species co-occurrence were mostly unsuccessful, because they ignored species traits and phylogeny as well as their environmental preferences. However, with a recent development a novel conceptual framework all these properties shaping species communities can now be accounted for in search for functional associations among species.

The main question to be addressed in the project: The aim of the project will be to identify the species with the strongest associations with all other species within distinct communities of European butterflies. The valuable side result of the project will be evaluation of how well the arbitrarily defined biogeographic regions of Europe reflect the true spatial diversity of butterfly communities.

Information on the methods/description of work: The project will use hierarchical modelling of species communities (HMSC) approach developed by Ovaskainen et al. (2017) to quantify the inter‑specific associations within European butterfly communities. The input data will include the information on species co-occurrence and their habitats obtained from the European Butterfly Monitoring Scheme as well as on the species traits and phylogeny mobilised by the ongoing sECURE project (www.idiv.de/sdiv/working_groups/wg_pool/secure.html).

Special requirements from the student: Experience in working with R packages would be a clear asset.

Place/name of potential foreign collaborator: sECURE project consortium, among others Robert Wilson (University of Exeter); Tim Shreeve (Oxford Brookes University); Josef Settele, Oliver Schweiger, Martin Wiemers (Helmholtz-Centre for Environmental Research UFZ Halle).

References:

Maes D, van Dyck H (2005) Habitat quality and biodiversity indicator performances of a threatened butterfly versus a multispecies group for wet heathlands in Belgium. Biological Conservation 123: 177–187

Ovaskainen O, Tikhonov G, Norberg A, Guillaume Blanchet F, Duan L, Dunson D, Roslin T,  Abrego N (2017), How to make more out of community data? A conceptual framework and its implementation as models and software. Ecology Letters 20: 561–576

 

IZBR-20: Acetylcholine induced bursting activity of midbrain dopaminergic neurons - in vivo electrophysiological and pharmacological studies

Supervisor: Dr Tomasz Błasiak (Department of Neurophysiology and Chronobiology, Institute of Zoology and Biomedical Research)

Background information: Dopamine (DA) synthesizing neurons within ventral tegmental area and substantia nigra pars compacta form the core of reward and motivation system. Basal level of DA is mainly maintained by AMPA dependent, tonic or irregular firing of neurons whereas phasic release of DA is induced by NMDA dependent, bursting pattern of firing. Based on anatomical and electrophysiological results obtained from rodents, acetylcholine is found to have strong modulatory effect on activity of dopaminergic neurons. Previous studies showed, that cholinergic agonists applied directly to VTA induce increase in amount of released dopamine in target structures, however it is not known if acetylcholine alone, i.e. without NMDAr dependent mechanism, can evoke bursting pattern of firing of DA neurons.

The main question to be addressed in the project: The hypothesis underlying this project is that activation of cholinergic receptors is able to evoke bursting activity involving mechanisms independent of NMDA receptor. The objective of proposed project is to describe parameters of bursting activity in dopaminergic neurons evoked by activation of cholinergic receptors in a model of selective, inducible knock-out of NR1 subunit of NMDA receptor in midbrain dopaminergic neurons and to pharmacologically determine subunit clusters involved in this phenomena.

Information on the methods/description of work: Planned experiments will involve extracellular in vivo recordings from urethane anaesthetised mice lacking NR1 subunit of NMDA receptor combined with iontophoretic application of cholinergic agonists and antagonists.

Special requirements from the student: Candidates with prior experience in electrophysiological in vivo recordings are encouraged to apply.

References:

Grace AA, Bunney BS (1984) The control of firing pattern in nigral dopamine neurons: burst firing. J Neurosci 4:2877–2890

Jastrzębska K, Walczak M, Cieślak PE, Szumiec Ł, Turbasa M, Engblom D, Błasiak T, Parkitna JR (2016) Loss of NMDA receptor-dependent activity in dopamine neurons leads to the development of affective disorder-like symptoms in mice. Sci Rep. 6:37171.

Gronier B, Rasmussen K. (1998) Activation of midbrain presumed dopaminergic neurones by muscarinic cholinergic receptors: an in vivo electrophysiological study in the rat. Br J Pharmacol. 124(3):455-64.

 

IZBR-21: Dopaminergic control of the nucleus incertus in control conditions and after stress experience

Supervisor: Prof. Grzegorz Hess (Department of Neurophysiology & Chronobiology, Institute of Zoology and Biomedical Research)

Background information: Nucleus incertus (NI) is a brainstem structure rich in relaxin-3 peptide synthesising neurons. NI is highly sensitive to stress and is involved in compulsive behaviours development [1]. Recently, the presence of dopamine receptors in NI neurons has been revealed [2], however, the influence of the activation of these receptors on electrophysiological properties of NI neurons and its consequences for the behaviour remain unknown. The dopaminergic system is the main component of the brain reward system. One of the most severe factors that dysregulate the reward system in adult brain are adverse childhood experiences. Accordingly, maternal separation stress (MS), the animal model of human childhood maltreatment, was shown to dysregulate the dopaminergic system [3] and increase the likelihood of the occurrence of compulsive behaviours. The neuronal mechanism of MS pathophysiological consequences most likely involves dysregulation of the mechanisms of dopamine influence on the activity of NI neurons.

Therefore the main aims of the project are as follows: 1. To investigate the effects of the activation of dopamine D1 and D2 receptors on NI neurons electrical activity. 2. To describe the influence of MS on the reactivity of NI neurons to dopamine. 3. To define the source of dopamine in NI. 4. To describe the influence of dopamine receptors activation in the NI on compulsive-like behaviors in control and MS conditions.

Information on the methods/description of work: To answer aims 1 and 2 whole-cell patch clamp electrophysiological recordings will be performed, with the use of dopamine receptors agonists and a subsequent verification of the neurochemical nature of the recorded neurons. To answer question 3 track-tracing studies will be conducted. Behavioral experiments using intra-NI infusions of dopamine receptors agonists/antagonists will address the question regarding the involvement of NI dopaminergic modulation in compulsive-like behaviors in control and MS conditions.

Special requirements from the student: An experience in whole-cell patch clamp recording technique.

Place/name of potential foreign collaborator: Prof. Andrew Gundlach, Florey Institute of Neuroscience and Mental Health, Australia

References

[1] Lenglos C, Mitra A, Guèvremont G, Timofeeva (2013) Sex differences in the effects of chronic stress and food restriction on body weight gain and brain expression of CRF and relaxin-3 in rats. Genes Brain Behav., 12(4):370-87

[2] Kumar JR, Rajkumar R, Farooq U, Lee LC, Tan FC, Dawe GS (2015) Evidence of D2 receptor expression in the nucleus incertus of the rat. Physiol. Behav., 151, 525-534

[3] Nishi M, Horii-Hayashi N, Sasagawa T (2014) Effects of early life adverse experiences on the brain: implications from maternal separation models in rodents. Front Neurosci 8, 166

 

IZBR-22: Molecular mechanism of exogenous hormonally active compounds in the biology of human granulosa tumors

Name of supervisor: Dr. Anna Ptak (Department of Physiology and Toxicology of Reproduction, Institute of Zoology and Biomedical Research)

Background information: Endocrine disrupting chemicals (EDCs) are natural or synthetic chemicals that alter the functions of the endocrine system and thereby cause adverse health effects. Recently, epidemiological studies have measured unconjugated concentrations of a number EDCs such as polychlorinated biphenyls (PCBs), 2,2-dichlorodiphenyldichlorethylene (DDE), hexchlorobenzene (HCB), perfluorooctanoate (PFOA) and perfluorooctane sulfonate (PFOS), and in follicular fluid from women undergoing assisted reproductive technology [1,2]. These compounds may further exert their potential direct effects on oocyte, cumulus and granulosa cell function. These observations raised the intriguing hypothesis that EDCs mixture present in follicular fluid may be involved in the pathogenesis and progression of human granulosa tumors.

The main question to be addressed in the project: Thus, it is hypothesized that mixtures of EDCs presents in follicular fluid activate directly granulosa tumor receptors or acts indirectly by change levels of signaling factors contributes to granulosa cell growth and function and by both mechanisms lead to granulosa tumor progression.

Information on the methods/description of work: To verify the hypothesis, we intend to identify whether EDCs mixture could stimulate human granulosa tumors spheroids (3D architecture) viability, resistant to anoikis, and invasion which are essential for cancer progression.

Special requirements from the student: An experience in working with cell culturing with emphasis on the 3D system and documented experience in molecular laboratory.

References

[1] Petro EM, Leroy JL, Covaci A, Fransen E, De Neubourg D, Dirtu AC, De Pauw I, Bols PE. Endocrine-disrupting chemicals in human follicular fluid impair in vitro oocyte developmental competence. Hum Reprod. 2012;27:1025-33.

[2] Petro EM, D'Hollander W, Covaci A, Bervoets L, Fransen E, De Neubourg D, De Pauw I, Leroy JL, Jorssen EP, Bols PE. Perfluoroalkyl acid contamination of follicular fluid and its consequence for in vitro oocyte developmental competence. Sci Total Environ. 2014;496:282-8. 

 

IZBR-23: Developing an environmental DNA (eDNA) protocol for characterizing freshwater biodiversity

Name of supervisor: Dr. Maciej Pabijan (Department of Comparative Anatomy
Institute of Zoology and Biomedical Research)

Background information: All living organisms expel DNA into their environments in the form of faeces, urine, skin cells or gametes. Recently, techniques have emerged that can reliably assess presence-absence of species in samples of water, sediment, soil or air from natural environments. These methods, collectively called environmental DNA (eDNA) analyses, either have a specific target (e.g. endangered or invasive species) or use a non-targeted approach and identify entire communities (e.g. metazoans) from samples. The eDNA approach has tremendous potential for contributing to the understanding of the ecology and conservation of biotic communities. However, as with all emerging scientific fields, there are currently a number of diverse protocols for sampling and interpreting eDNA data.

The main question to be addressed in the project: This project will develop an eDNA laboratory workflow and analysis pipeline to track the presence of indicator amphibian and fish species in freshwater ponds along with their coexisting macroinvertebrate communities. Depending upon the interests of the candidate, these data can then be used to address issues in ecology and conservation such as detection of illusive species, tracking of invasive fish species and their influence on freshwater communities, or testing the reliability of indicator species in determining overall species richness in ponds and small wetlands.

Information on the methods/description of work: The project consists of fieldwork (sampling water from ponds) and extensive laboratory work: DNA extraction, PCR primer development and validation, library preparation and high-throughput DNA sequencing (Illumina). The candidate will use bioinformatics techniques for preparing raw sequence data for taxonomic assignment using clustering methods and reference databases.

References:

Valentini, A., Taberlet, P., Miaud, C., et al. (2016). Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology, 25, 929-942.

Goldberg, C. S., Turner, C. R., Deiner, K., et al. (2016). Critical considerations for the application of environmental DNA methods to detect aquatic species. Methods in Ecology and Evolution, 7, 1299-1307.

Thomsen, P., Kielgast, J. O. S., Iversen, L. L., et al. (2012). Monitoring endangered freshwater biodiversity using environmental DNA. Molecular Ecology, 21, 2565-2573.

 

IZBR-24: Formation of the cytoplasmic asymmetry in oocytes of non-model insects

Name of supervisor: Dr. Mariusz Jaglarz (Department of Invertebarte Development and Morphology, Institute of Zoology and Biomedical Research)

Background information: In recent years, convincing structural and molecular evidence has indicated that macromolecules and organelles are distributed asymmetrically (unevenly) in the cytoplasm of different cell types and that this phenomenon is indispensable for normal cell functioning (reviewed in Lecuyer et al., 2007). In the female germline cells (oogonia, oocytes and egg cells), the asymmetric distribution of cytoplasmic constituents is vital not only for differentiation of  these cells, but also for proper development of the future embryo (reviewed in Kloc and Etkin, 2005). Studies in model species revealed that central to the understanding of  the oocyte symmetry-breaking are processes occurring during early stages of meiosis and that there is a link between nuclear and cytoplasmic events (Elkouby, 2017). In insects, the formation of  the oocyte early asymmetry is well characterized in the model species, the fruit fly Drosophila melanogaster.  However, there is only limited information how such asymmetry is created in other insect species (Tworzydlo et al., 2016).

The main question to be addressed in the project: The proposed Ph.D. project aims to elucidate the  sequence of events leading to the oocyte symmetry-breaking in non-model insects and to identify cellular and molecular factors responsible for this process. The obtained results will enable to make a comparison of  the symmetry-breaking mechanisms in different insect groups and to draw conclusions how these processes might have changed during evolution of insects.

Information on the methods: The project will require the use of modern technics of light, electron and confocal microscopy, supplemented with molecular methods, e.g. in situ hybridization and antibody labelling.

Special requirements from the student: Basic microscopy skills and good background in cell and developmental biology.

Place/name of potential foreign collaborator: Prof. Siegfried Roth, University of Cologne, Germany

References

Elkouby Y.M. 2017.  All in one – integrating cell polarity, meiosis, mitosis and mechanical forces in early oocyte differentiation in vertebrates. Int. J. Dev. Biol. 61: 179-193.

Kloc M., Etkin L.D. 2005. RNA localization mechanisms in oocytes. J. Cell Sci. 118: 269-282.

Lecuyer E., Yoshida H., Parthasarathy N., Alm C., Babak T., Cerovina T., Hughes T.R., Tomancak P., Krause H.M. 2007. Global analysis of mRNA localization reveals a prominent role in organizing cellular architecture and function. Cell 131: 174–187.

Tworzydlo W., Marek M., Kisiel E., Bilinski S.M. 2017. Meiosis, Balbiani body and early asymmetry of Thermobia oocyte. Protoplasma 254: 649-655.

 

IES-25: Sex and adaptation: the many-faced problem

Supervisors: Prof. Wiesław Babik and Dr. Zofia Prokop (Molecular and Behavioral Ecology Group, Institute of Environmental Sciences)

Background information: Predominance of sexual reproduction among eukaryotes has been puzzling evolutionary biologists for decades because of its apparent high fitness costs relative to asexuality. Theoretical explanations considered as most likely relate to the role of recombination: by shuffling alleles among individuals, sex may facilitate the spread of beneficial and the removal of deleterious genetic variants. However, sexual reproduction also sets the stage for sexual antagonism, whereby selection on (some) traits acts in different directions on males than on females and hence (some) mutations favorable to one sex are harmful for the other. This could further exacerbate the cost of sex, decreasing mean fitness of sexual populations and hampering their adaptation to novel environments. On the other hand, continuous environmental changes can align selection between the sexes, reducing sexual antagonism. Moreover, if selection on males and females is largely aligned, strong sexual selection acting on males may additionally facilitate adaptation.

The main question to be addressed: The main aim of this project is to unify theoretical models concerning the roles of recombination, sexual antagonism, and sexual selection in adaptation to constant vs. changing environments. Additionally, empirical part of the project will involve testing some of the models’ predictions using experimental evolution of nematode populations.

Information on the methods: Theoretical part will involve mathematical modelling and computer simulations. Empirical part will involve laboratory work on nematode populations, as a part of a team working on an ongoing experimental evolution project.

References:

Candolin, U and Heuschele J. "Is sexual selection beneficial during adaptation to environmental change?." Trends in Ecology & Evolution 23.8 (2008): 446-452.

Connallon, T, and Hall, MD. "Genetic correlations and sex‐specific adaptation in changing environments." Evolution 70.10 (2016): 2186-2198.

Otto, SP. "The evolutionary enigma of sex." The American Naturalist 174.S1 (2009): S1-S14.

 

IZBR-26: Glycosylation of T helper lymphocytes in Graves’s disease: the role of cytokines in regulation of glycosylation

Name of supervisor: Dr. Ewa Pocheć (Department of Glycoconjugate Biochemistry, Institute of Zoology and Biomedical Research)

Background information: Although glycosylation is critical for the proper function of the immune system and its changes were observed in autoimmune diseases, glycosylation of immune cells was not studied in autoimmune thyroid diseases (AITD) so far. The previous studies of glycosylation in Graves’ disease (GD) focused on the impact of altered glycosylation on antigenic properties of thyroid proteins that are targets of immune cell attack. T cells that are involved in the recognition and immune response directed against the autoantigens, are also strongly glycosylated. The purpose of this study is to evaluate the glycosylation of CD4+ T helper (Th) cells in AITD and to determine the role of cytokines in regulation of glycosylation.

The main question to be addressed in the project: PhD project is a part of the grant founded by the National Center of Sciences, aimed at the characterization of Th N-glycosylation in AITD. The purpose of the PhD project is to answer the following questions: (1) whether Th cell proteins in GD are otherwise post-translationally modified than in healthy people, (2) whether glycosylation is influenced by taken medication, (3) which Th supopulation(s) is/are subject to change glycosylation and (4) whether cytokines regulate glycosylation.

Information on the methods/description of work: Glycosylation of Th cells will be assessed at the level of glycosyltransferases (rtPCR) and N-glycans (HPLC). The role of cytokines, which levels change during GD development, will be determined in the regulation of T cells glycosylation using cell culture model. Flow cytometry will be used for immunophenotyping.

Special requirements from the student: An experience in work with glycan analysis, flow cytometry, isolation of white blood cells and cell culture. Knowledge in the fields of glycobiology and immunology.

Place/name of potential foreign collaborator: Prof. Gordan Lauc, Genos Glycoscience Research Laboratory, Zagreb, Croatia

References

Zhao L, Liu M, Gao Y, Huang Y, Lu G, Gao Y, Guo Y, Shi B. Glycosylation of sera thyroglobulin antibody in patients with thyroid diseases. Eur J Endocrinol., 2013, 168(4): 585-92.

Rabinovich GA, van Kooyk Y, Cobb BA. Glycobiology of immune responses. Ann N Y Acad Sci. 2012, 1253: 1-15.