Charles University in Prague, Faculty of Science, Department of Parasitology, Avian Parasites Study Group
Dynamics and Persistence of Blood Parasite Infection
Topic Overview:

The long term aim of the project is to study the occurrence, dynamics (the age at which hosts are infected), persistence (do individual hosts retain their infection status?), and survival impact of avian parasite haemoproteid genera Plasmodium, Haemoproteus, and Leucocytozoon. By  comparing different avian host and parasite species, we can assess the impact of avian life history traits as well as parasite vectors on the  occurence of different parasite genera.

Task:

To perform diagnostic PCR in blood samples (isolate DNA, do PCR, sequence positive samples, data analysis); eventually, microscopy of blood smears and comparison of methods. The participant can use the acquired laboratory practise in his/her own project or in a diagnostic lab.

Requirements:

PCR theoretical background, Microsoft office.

Outcomes:

Prevalence data, barcoding data.

References:

Valkiunas 2005: Avian Malaria Parasites (General part)
UNIGOU EXCHANGE - AVAILABLE TOPICS
Topic Overview:

Soil microorganisms (especially fungi and bacteria) play important roles in soil quality and plant productivity. The composition of the soil microbial communities may be affected by farming practices. During the internship, the student will get acquainted with a two classical method of isolation soil microorganisms and the method of determining soil basal respiration. Emphasis  will be placed on linking the used methods.

Task:

Students will analyse soil samples in the laboratory under expert supervision (later independently also). The student will write a literature review on the importance of soil microbial activity.

Requirements:

Independence, reliability, patience, accuracy.

References:

Parkinson, D., & Williams, S. T. (1960). A method for isolating fungi from soil microhabitats. Plant and Soil, 13(4), 347-355.
Azaz, A. D. (2003). Isolation and identification of soilborne fungi in fields irrigated by GAP in Harran Plain using two isolation methods. Turkish Journal of Botany, 27(2), 83-92.
Pell, M., Stenstrom, J., & Granhall, U. (2005). 7.2 Soil Respiration. Bloem, J; DW Hopkins & A Benedetti, 117-126.
University of South Bohemia in České Budějovice, Faculty of Agriculture and Technology, Department of Agroecosystems
Soil Microbial Community Composition and Basal Respiration
Topic Overview:

Organic matter is an indispensable component of the soil. It affects the moisture and nutritional regime of soils. It has an irreplaceable role in maintaining soil fertility.  During the internship, the student will get acquainted with a new method of evaluating soil organic matter. Emphasis will be placed on labile fractions of soil organic matter, directly affecting soil fertility.

Task:

Students will analyse soil samples in the laboratory under expert supervision (later independently also). The student will write a literature review on the importance of soil organic matter.

Requirements:

Independence, reliability, patience, accuracy.

References:

Kopecký, Marek, Ladislav Kolář, Kristýna Perná, Radka Váchalová, Petr Mráz, Petr Konvalina, Yves T. Murindangabo, Mohammad Ghorbani, Ladislav Menšík, and Miroslav Dumbrovský. 2022. "Fractionation of Soil Organic Matter into Labile and Stable Fractions" Agronomy 12, no. 1: 73. https://doi.org/10.3390/agronomy12010073
University of South Bohemia in České Budějovice, Faculty of Agriculture and Technology, Department of Agroecosystems
Fractionation of Soil Organic Matter into Labile and Stable Fractions
University of South Bohemia, Faculty of Science, Department of Ecosystem Biology
Effect of Climate Change on Aquatic Invertebrates
Tasks:

You will measure temperature dependence of selected behavioural and physiological traits of model aquatic invertebrates to help understand the ability of species to withstand future effects of climate change. May include limited fieldwork.

Requirements:

Capability of maintaining and running short-term lab experiments, basic knowledge of data manipulation in spreadsheets, knowledge of R and GLMs beneficial.

Recommended for:

Students of ecology, hydrobiology, entomology or zoology programmes.
University of South Bohemia, Faculty of Science, Department of Ecosystem Biology
Behavioral Syndromes in Aquatic Invertebrates
Tasks:

You will measure intraspecific variation in selected behavioural and physiological traits of model aquatic invertebrates to  characterize their behavioural variation and verify or reject the presence of ‘animal personalities‘. May include limited fieldwork.

Requirements:

Capability of maintaining and running short-term lab experiments, basic knowledge of data manipulation in spreadsheets, knowledge of R and GLMs beneficial.

Recommended for:

Students of ecology, hydrobiology, entomology or zoology programmes.
University of South Bohemia, Faculty of Science, Department of Ecosystem Biology
Combined Effects of Warming and Pollutants on Freshwater Communities
Tasks:

You will extract and analyze data from existing literature to understand the combined effects of warming and selected group of pollutants (e.g. pesticides, pharmaceuticals) on individuals, species interactions and/or community structure in freshwater  ecosystems.

Requirements:

Capability of data mining and basic/intermediate knowledge of R, knowledge of meta-analytic techniques beneficial.

Recommended for:

Students of ecology, hydrobiology or environmental pollution programmes.
University of South Bohemia, Faculty of Science, Department of Ecosystem Biology
Are Orchid Localy Adapted to Mycorrhizal Fungi?
Topic Overview:

Orchids produce dust-like seeds with minimum nutrients and successful recruitment is possible only in the presence of one or more suitable mycorrhizal fungi, from which the orchid seedling obtains all nutrients before it becomes  photosynthetically active. Orchids are highly endangered group of plants and the probability that a seed will germinate and  survive till adulthood is extremely low and the abundance of mycorrhizal symbionts is low and patchy. Orchid restoration may benefit from improved seed germination by inoculation of suitable fungi into soil, but so far we know little, how much orchids are adapted to fungi of local origin. This topic will estimate breath of physiological specificity to fungi in several  orchid species differing in ecological fungal specificity using in vitro symbiotic germination experiments.

Task:

The intern will carry out in vitro germination experiment with 4 orchid species and their mycorhizal fungi obtained from home and non-home sites. Student will learn basis of microbial cultivation (how to prepare cultivation media, how to sterilize seeds, work in flowbox) as well as data analysis.

Requirements:

No special skill are needed, except enthusiasm for work and sense of duty.

Outcomes:

Findings will contribute to publication of the laboratory. Intern will be expected to write a brief summary (as a word file or powerpoint presentation) of the results.

Recommended for:

Students of ecology, microbiology and botany programmes.
University of South Bohemia, Faculty of Science, Department of Ecosystem Biology
Can Mycorrhizal Fungi Alleviate Toxicity of Nitrates to Orchid Germination? - 1
Topic Overview:

Many orchid species are threatened, while some disappear from their natural habitats without obvious reasons. Eutrophication has been suggested as a possible factor and nitrate, which is able to suppress non-symbiotic orchid seed germination even at very low concentrations, could pose a serious threat for natural orchid populations. Early ontogenesis of all orchids entirely depends on orchid mycorrhizal symbiosis. We would like to test whether these fungi might also have some non-nutritional roles, i.e., whether they might confer resistance to eutrophication. To test this hypothesis, we plan to co-cultivate in vitro conditions seeds of selected  orchid species with several mycorrhizal fungi that are/are not capable to utilize nitrates.

Task:

The intern will carry out in vitro germination experiment with 3 orchid species and mycorrhizal fungi which differ in their ability to utilize nitrates. Student will learn basis of microbial cultivation (how to prepare cultivation media, how to sterilize seeds,  work in flowbox) as well as data analysis.

Requirements:

No special skill are needed, except enthusiasm for work and sense of duty.

Outcomes:

Findings will contribute to publication of the laboratory. Intern will be expected to write a brief summary (as a word file or powerpoint presentation) of the results.

Recommended for:

Students of ecology, microbiology and botany programmes.
University of South Bohemia, Faculty of Science, Department of Ecosystem Biology
Can Mycorrhizal Fungi Alleviate Toxicity of Nitrates to Orchid Germination? - 2
Topic Overview:

In species rich plant communities coexisting species display different morphological, physiological or life-history characteristics, i.e. functional traits, which directly or indirectly influence species fitness via their effects on survival, growth and reproduction. Differences among species in functional traits may allow complementary strategies of resource acquisition and thus local coexistence of a number of plant species in a small area. We have investigated network of interactions between orchids and their mycorrhizal fungi in species rich habitats and now we would like to test, how functional traits of both orchids and fungi affect the structure of the interaction network within a site.

Task:

The intern will build up a database of orchid and fungal functional traits (e.g. plant height, leaf area, root length, type of storage organs, fungal growth rate) based on the literature survey and data sets already measured by our team at four study sites in the Czechia and France. The student will try to apply multivariate statistical models to test how plant and fungal functional traits shape orchid-fungus interactions.

Requirements:

General knowledge of statistics and Excel software would be advantage, as well as enthusiasm for work and sense of duty.

Outcomes:

Findings will contribute to publication of the laboratory. Intern will be expected to write a brief summary (as a word file or powerpoint presentation) of the results.

Recommended for:

Students of ecology and botany programmes.
University of South Bohemia, Faculty of Science, Department of Molecular Biology and Genetics
Epigenetic Factors of Longevity
Topic Overview:

Epigenetic alterations are associated with aging. We are exploring whether certain epigenetic patterns can be associated with aging (such as enhanced stability of heterochromatin). We bioinformatically identified changes in the expression levels of epigenetic modifiers during aging that are different between short-lived and long-lived species, and we need to confirm the  findings in our tissue samples from young and aged individuals, and analyse the functional consequences of these epigenetic differences at the molecular level.

Task:

Molecular biology experiments - RNA extraction, reverse transcription, real-time PCR (to measure gene expression levels from  tissues), data analysis. Follow up experimenrs will depend on these experiments.  Interested interns can also do literature  search to interpret the results, and potentially bioinformatic analyses to further explore differences in epigenetic factors between short-lived and long-lived species (analyses if gene expression, DNA methylation, histone modifications).

Requirements:

Experience with molecular biology techniques, or at least pipetting, is beneficial, but not strictly required. Basic knowledge of molecular biology is required (what is RNA transcription, what is epigenetics, etc).

Outcomes:

Findings will contribute to publication(s) of the laboratory. Intern will be expected to write a brief summary (as a word file or powerpoint presentation) of their results.

References:

https://link.springer.com/article/10.1007/s40520-019-01430-0; 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5821249/; 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4966880/;
https://www.nature.com/articles/s41580-019-0204-5

Recommended for:

Students of molecular biology and genetics programmes, or with interest in these topics.
University of South Bohemia, Faculty of Science, Department of Molecular Biology and Genetics
Search for Dnmt3l Promoter in Guinea Pig Oocytes
Topic Overview:

DNMT3L is considered a key factor for DNA methylation establishment in mammalian oocytes. Our results show that it is not true and its activity is restricted to only few mammalian species. Because of the bad quality of guinea pig genome assembly at the region of potential Dnmt3l promoter, we are unable to analyse the situation in this species, although our results suggest that Dnmt3l may be expressed from an evolutionary unique promoter absent in other species.

Task:

Molecular biology experiments – DNA and RNA extraction, reverse transcription, cloning, PCR, Sanger sequencing, data analysis, work with genome browser.

Requirements:

Experience with molecular biology techniques, or at least pipetting, is beneficial, but not strictly required. Basic knowledge of molecular biology is required (what is RNA transcription, epigenetics, PCR etc).

Outcomes:

Findings will contribute to publication(s) of the laboratory. Intern will be expected to write a brief summary (as a word file or powerpoint presentation) of their results.

References:

https://f1000research.com/articles/9-146;
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6093373/

Recommended for:

Students of molecular biology and genetics programmes, or with interest in these topics.
University of South Bohemia, Faculty of Science, Department of Molecular Biology and Genetics
Endogenous Retroviruses and Their Activity
Topic Overview:

Endogenous retroviruses and other retrotransposons are integral parts of mammalian genomes, they share characteristics  with classical retroviruses except the ability of infecting other cells or individuals. Generally, retrotransposons and endogenous retroviruses are silenced by epigenetic mechanisms, but in specific biological contexts in mammals they are relatively active  (in the oocytes, early embryos and placenta). We are studying the activity of these elements in the oocytes, changes of activity during aging, and the consequences of low/no activity of these elements for oocyte transcriptomes and epigenomes.

Task:

Depending on their skills and interest, the intern will perform bioinformatic analysis in R and/or by programming (work with large text files and tables, data analysis, potentially sequence analysis and next-generation sequencing data processing and analysis).

Requirements:

Required skills: R and/or programming in Python or Perl (to be able to work relatively independently).

Outcomes:

Findings will contribute to publication(s) of the laboratory. Intern will be expected to write a brief summary (as a word file or powerpoint presentation) of their results.

References:

https://www.sciencedirect.com/science/article/pii/S0168952522000361?via%3Dihub; https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1577-z; https://www.sciencedirect.com/science/article/pii/S0168952518301197?via%3Dihub

Recommended for:

Students studying or with interest in molebular biology, genetics, bioinformatics.
Czech Academy of Science, Institute of Parasitology, Biology Centre, Laboratory of Molecular Ecology and Evolution
Population Genomics of Host-Parasite Co-Evolution
Topic Overview:

Hosts and parasites interact at multiple ecological and evolutionary levels. Here we focus at the population genomic level of diversification in several species of parasites in response to their host evolution or behaviour.

Task:

Analyse population structure and search for genes under selection in parasites co-evolving with their hosts. Participate in the analysis of Illumina reads, their mapping on genome and population genomic statistics.

Requirements:

Basic molecular laboratory skills (pipetting), experience with bioinformatics or at least willingness to learn (unix, R, python, etc.).

Outcomes:

Presentation.

References:

https://global.oup.com/academic/product/ecological-speciation-9780199587117?cc=cz&lang=en&; https://www.biorxiv.org/content/10.1101/2020.02.28.969279v1
Czech Academy of Science, Institute of Parasitology, Biology Centre, Laboratory of Molecular Ecology and Evolution
Biodiversity of Mesozoan Parasites from Cephalopods
Topic Overview:

Mesozoa (dicyemida) are an enigmatic group of marine parasites/symbionts of octopuses and cuttlefish with unknown evolutionary history.

Task:

Explore dicyemid species diversity using DNA barcoding (amplicon sequencing) and reconstruct phylogenetic relationships of multiple species using genomic data. Participate in the preparation of DNA samples for sequencing.

Requirements:

Basic molecular laboratory skills (pipetting), experience with computing or at least willingness to learn (unix, R, python, etc.).

Outcomes:

Presentation.

References:

https://www.frontiersin.org/articles/10.3389/fphys.2; https://www.nature.com/articles/s41598-019-50555-9
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