Karlovsky lab: BSc and MSc topics

In addition to the projects listed here, further MSc and BSc topics are available. Contact Petr Karlovsky (pkarlov at gwdg.de) if you are interested.

MSc project: Characterization of fungal isolates from maize harvested in the Philippines

This project will be supervised by Prof. Christian Cumagun. A set of fungal isolates (Aspergillus spp., Fusarium spp.) from maize grown in the Philippines will be characterized regarding their taxonomic affiliation, genetic diversity and potential to produce mycotoxins.

Contact: Prof. Ch. Cumagun, Prof. P. Karlovsky

MSc project: Metabolic diversity of endophytic fungi acting as antagonists of plant pathogens

This project will be supervised by Prof. Christian Cumagun. A set of fungal endophytes from the Philippines selected due to their ability to suppress fungal pathogens will be characterized their production of volatile compounds (collaboration with Prof. C. Müller, Bielefeld) and soluble metabolites (Dr. Anna Rathgeb).

Contact: Prof. Ch. Cumagun, Prof. P. Karlovsky

MSc project: Function of MAR pathway in fungi

Fungi produce a range of species-specific secondary metabolites. It is assumed that the biological function of these metabolites relies in modulating ecological interactions of fungi with other organisms. A new biosynthetis pathway hypothesized to be involved in ecological relationships has recently been discovered in our laboratory. We named the pathway MAR. Gene disruption mutants were generated for the key gene of the pathway. The task of the MSc proeject is to test the effect of the gene disruption on a range of organisms (nematodes, arthropodes, mycoparasites) in order to discover the natural target of the metabolites.

Contact: Mohammad Alhussein, Maria Vinas, Prof. P. Karlovsky

BSc project: Review of the function of NLPs in the pathogenicity of fungi on plants

NLPs are small proteins produced by many bacteria and fungi. Because NLPs of phytopathogenic fungi are cytotoxic, causing strong necrosis in the leaves of dicotyledoneous plants, the role of NLPs in the aggressiveness (virulence) of many plant pathogenic fungi has been studied. The task is to review this literature and summarize the findings.

Contact: Mohammad Alhussein, Ling Su, Prof. P. Karlovsky

MSc project: Alternative biological functions of fungal NLP proteins

NLPs are small proteins produced by many bacteria and fungi. NLPs of phytopathogenic fungi are cytotoxic, cause strong necrosis in the leaves of dicotyledoneous plants. The role of NLPs in plant infection is unknown.
The task is to test fungal mutants with disrupted production of NLPs in different systems in order to reveal the biological function of the proteins. Nonhost plants and unconventional targets will be tested to solve the puzzle that most mutants of pathogenic fungi that do not produce NLPs are not impaired in their pathogenicity.

Contact: Mohammad Alhussein, Ling Su, Prof. P. Karlovsky

MSc project: infecton of Brassica napus with Verticillium longisporum and the role of NLP proteins

V. longisporum is a fungal pathogen infecting oilseed rape and other crucifers. The pathogen invades plant roots and colonizes hypocotyl. At late stages of infection the fungus invades the entire stem and produces microsclerotia. The disease caused by "V. longisporum" is different from "Verticillium wilt" caused by other Verticillium species in vegetables, cotton and other plants because V. longisporum does not cause wilting.
NLPs are small proteins secreted by V. longisporum and other phytopathogenic fungi. NLPs are cytotoxic, causing necrosis after infiltration into plant leaves. The role of NLPs in plant infection is unknown.
The task is to culture a special variety of B. napus called Rapid Cycling Brassica, which completes its entire growth cycle within two months, inoculate plants with V. longisporum strains (wild-type and strains impaired in the production of NLPs) by dipping their roots to spore suspension, monitor disease progress, take samples and analyze the expression of NLP genes by RT qPCR and the presence of NLP proteins in the plant by Western Blotting.

Contact: Ling Su, Prof. P. Karlovsky

MSc project: Analysis of fungal colonization of maize

Maize grains collected at several sampling locations in Germany in 1998 and 2005-2007 and kept deep frozen since then will be used. It was not possible at the time when the samples were collected to quantify the biomass of fungal pathogens infecting maize in a species-specic way. The task is to extract total DNA and determine the content of DNA of fungal pathogens using species-specific real-time PCR assays in 384-well microplates. The assays comprise all important mycotoxin-producing fungi colonizing maize grains, including seven Fusarium species and aflatoxin-forming Aspergillus species. The results on historical material will be compared with the current situation. The study should reveal whether species spectrum of fungi infecting maize ears changed during the last 18 years.

Prerequisites: Understanding maize production and plant pathology.
Hands-on experience with classical PCR and/or qPCR would be useful but is not obligatory.

Contact: Prof. Petr Karlovsky

MSc project: biological function of fumonisins

Fumonisins are mycotoxins produced mainly by Fusarium verticillioides and Fusarium proliferatum in maize and other host plants. Fumonisins are tocix to farm animals, causing pulmonary edema in pigs and encephalomalacia in horses. They have been proven to act as carcinogents in rodents and suspected to contribute to cancer of the esophagus and spina bifida in humans. The biological function of fumonisins remains unknown. Infection experiments with Fusarium verticillioides strains with disrupted fumonisin synthesis lead to controversial results; in some experiment fumonisins appeared to be involved in disease development, in other experimehts the disrupted mutants were as virulent as fumonisin-producing strains (e.g., Dastjerdi and Karlovsky 2015). The goal of the MSc project is to clarify whether fumonisins are involved in interactons between Fusarium verticillioides and fungivorous arthropods. Small arthropods (springtails and woodlice) will be fed with wild-type Fusarium verticillioides strains and with genetically engineered strains with disrupted fumonisin synthesis pathway. Food preference and the fitness of fungivores feeding on strains producting and not producing fumonisins will be recorded and compared. The fate of fumonisins ingested by the animals will be monitored by HPLC-MS/MS.

Contact: Dr. Katharina Pfohl

Masterarbeit: Inhibition des Pilzwachstums durch Metaboliten von Landasseln

Ziel der Arbeit besteht in der Untersuchung von antifungalen Substanzen, die (i) auf der Kutikula von Landasseln und (ii) als Rückstände der Asselaktivität im besiedelten Substrat vorkommen, und die Überprüfung ihrer Wirksamkeit an Pilzkulturen. Solche Substanzen sind für die Entwicklung von antifungalen Wirkstoffen für den Pflanzenschutz und die Humanmedizin interessant. Darüber hinaus wird die Untersuchung unser Verständnis der chemischen Ökologie von Landasseln erweitern.

- Pflege von Asselkulturen, Anzucht von Pilzkulturen
- Extraktion antifungaler Substanzen aus Bestandsmaterial
- experimentelle Überprüfung extrahierter Substanzen an Pilzkulturen
- Datenanalyse und -auswertung

Bachelor- bzw. Masterarbeit: Futterwahl von Landasseln im natürlichen Habitat

Ziel der Arbeit besteht in der Untersuchung von Pilzen, die im Verdauungstrakt diverser Landassel-arten aufzufinden sind, mithilfe von DNA-analytischen Methoden.

Methoden: Sammeln von Asseln im Freiland, Mikroskopische Präparation der Verdauungstrakte, DNA-Extraktion, DGGE und artspezifische qPCR.

Fungal diet of soil mesofauna

Many small soil invertebrates (soil mesofauna, defined by size between 0.1 and 2.0 mm) feed on fungi. Colembola, mites and fungivorous nematodes have been studied extensively in this respect. The goal of this project is to look at other, less known invertebrates that feed on fungi and study their diet and food preference.
Techniques: Barlese funnel, microscopy, PCR, DGGE.

Volatile compounds in soil ecology

Plant roots and microbes in the rhizosphere secrete diverse metabolites to modulate symbiotic and/or pathogenic interactions. Richard Splivallo's group addresses the role of bacteria-truffle interactions in truffle aroma and studies plant root volatiles. Interesting topics are available in both fields. A new portable GC-FAIMS system will be available for the project.
Techniques: Analysis of volatiles (SPME, GC), microscopy.

Enzymatic detoxification of mycotoxins

Genes encoding enzymes that detoxify mycotoxins will be overexpressed and their enzymatic activities will be studied. The project will be supported by Ruth Pilot. (Screening for new active microbial strains is not intended in this project.)
Techniques: Heterologous gene expression, purification of recombinant proteins, enzymatic assays with TLC or HPLC.

Mycotoxins and Fusarium species in Amaranthus

Raana Dastjerdi in our lab found out that certain weeds are heavily colonized with Fusarium spp. Amaranthus, which is grown for organic markets, is one of these weeds. The goal is to study how Fusarium spp. infect the plant and which role mycotoxin play in this process.
Techniques: Plant inoculation, qPCR, mycotoxin analysis.

Ecological role of mycotoxins in nematode/fungus interactions

Free-living nematode Aphelenchoides saprophilus feeds on fungi. Certain mycotoxins may protect fungi from predation. The task is to study ecological role of mycotoxins in the protection of fungi against nematodes or (by interest) other soil invertebrates. This project was initiated by Marie Reuther.
Techniques: Nematological methods, qPCR, mycotoxin analysis.

Secondary metabolites of Botrytis cinerea

Interesting secondary metabolites of B. cinerea have been identified in collaboration with TU Kaiserslautern by metabolic profiling. The task is to purify these metabolites and study their biological activities. The work may involve genetically engineered Botrytis strains, the project is supported by Kuang Yi.
Techniques: Purification of natural products by flash chromatography, preparative HPLC and TLC; bioassays.

Mycotoxins in fungal interactions

Secondary metabolites play key roles in interactions among fungi such as competition and mycoparasitism. The goal is to study fungal fitness in mixed cultures involving genetically engineered strains with modified abilities to synthesize and/or inactivate mycotoxins.
Techniques: Microbial techniques, DNA-based techniques for biomass analysis.