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Cooperative Master Thesis: What makes Fusarium aggressive? 
Genetic, epigenetic and bioinformatic genomic analysis of different Fusarium graminearum strains with variable virulence on wheat 

Description
Different strains of the wheat pathogen Fusarium graminearum which were cultivated in different labs around the world over several years, were re-sequenced using Illumina high throughput sequencing. Despite the fact that these strains originate from the same original type strain, their descendants show strongly differing phenotypes in respect to growth, reproduction, secondary metabolite production and plant pathogenicity. The aim of the thesis is to identify structural mutations or putative epimutations (in epigenetic regulators) that are linked to the different phenotypes and identifying putative genes or regulatory regions. The majority of work will be done computationally but some wet lab-work will also be required. 

Required skills:

  • Lab courses in microbiology and molecular biology, e.g. MoBi courses LMBT or Lab Course Agricultural Genetics, or equivalent
  • Experience with any Linux OS
  • Any skills in programming, data analysis and/or R are welcome, e.g. as introduced in the courses “Essentials for Bioinformatics Data Analysis” and “Sequencing Data Analysis”
  • Interest in genetics and epigenetics of microorganisms (fungi)

The student will learn how to work on Linux systems with high throughput sequencing data, data handling, genome mapping, variance analysis, genome wide interpretation and visualization of data using free software including R. Additionally, some lab work on fungi will be done.

General information: Travel expenses to Tulln will be refunded. Extension of the student’s engagement beyond the required six months Master Thesis period will be paid by a student employment contract.
Start: as soon as possible (Sept.2019)
 

Ansprechpersonen: 

Univ.Prof. Dr. Joseph Strauss
Fungal Genetics and Genomics Lab
Department of Applied Genetics and Cell Biology
Campus BiRT-Tulln 
A-3430 Tulln/Donau
e-mail: joseph.strauss(at)boku.ac.at
https://boku.ac.at/dagz/fungal-genetics-and-pathogens		 Univ.Prof. Dr. Heinz Himmelbauer
Bioinformatics Group
Department of Biotechnology
Campus VIBT Muthgasse
A-1190 Wien
e-mail: heinz.himmelbauer(at)boku.ac.at
http://seq.boku.ac.at/foswiki/bin/view/Home/WebHome

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Microbial Communities for Humus Formation in Agricultural Soil / FEMtech Internship & Master Thesis

Description
Modern agriculture has led to a substantial decrease of soil organic carbon. Humus contributes, however, to carbon sequestration, improved plant nutrition and soil water retention. Sustainable agiculture therefore strives for humus formation in depleted soils. Besides approved management techniques like compost addition to soils and reduced tilling, it is generally accepted that soil microbial communities play a pivotal role in soil carbon dynamics. During the master thesis microbial communities from reference soils with and without successful humus formation will be analysed for their microbial communities by cultivation independent high-throughput amplicon sequencing of bacterial and fungal barcodes. Laboratory scale experiments for humus formation under different conditions will provide additional insight into short term processes.

The Master Thesis will be performed in a collaboration between the BOKU Fungal Genetics & Genomics Unit and the AIT Bioresources Unit at the UFT in Tulln.

General Information: Part of the Master Thesis from Sept. 2019 to Feb. 2020 will be financed by a FEMTech Internship (www.ffg.at/femtech-praktika) done at the AIT Austrian Institute of Technology.

Start: earliest April 2019
Duration: 10-12 months
Applicants should be familiar with general microbial and molecular techniques from practical courses.

Ansprechpersonen:
Univ.Prof. Dr. Joseph Strauss  e-mail          
Dr. Markus Gorfer  e-mail

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Expression and glycan engineering of recombinant antibodies

Master Thesis in the field of molecular biotechnology: IgG antibodies are a success-story in medical biotechnology. IgGs are glycoproteins and it is well known that glycosylation impacts IgG functionalities. The aim of the master thesis is to produce and biochemically characterize IgG subclass antibodies with specific glycosylation profiles.

To study the role of glycans on IgG antibodies it is necessary to produce molecules with defined glycan profiles, a challenging issue. The team of Prof. Steinkellner has developed a glyco-engineering approach that allows the rapid expression of proteins with targeted glycan-structures. Appointed students find an excellent infrastructure for efficiently carry out experiments. For immunological studies a cooperation with immunologists at University of Erlangen (Dt) is established.

Tasks:

  • expression of IgGs (subclass1-4) in glycoengineered plants (expression vectors are available)
  • IgG purification (automated chromatography)
  • Mass spectrometric based glycan analyses
  • Biochemical characterisation of IgG (HPLC, immunoblotting)

Start: Early 2019 Duration: 6 months
after 2 months: financial support ~400 €/months

Ansprechperson: Herta Steinkellner  e-mail

Regulation of alternative splicing in plants

The Kalyna research group at the Department of Applied Genetics and Cell Biology is looking for a highly motivated Master’s student who is interested in RNA biology, alternative splicing, and plant molecular biology.

Background:
Alternative splicing results in multiple transcript variants produced from a single gene and is, therefore, a key strategy to increase the diversity of expressed information encoded by eukaryotic genomes. 

Our research has shown that alternative splicing is far more widespread in plants than previously thought. Deep transcriptome sequencing of the model plant Arabidopsis revealed that two-thirds of intron-containing genes undergo alternative splicing (Marquez et al., Genome Res, 2012; Zhang et al., Nucleic Acids Res. 2017). Closer examination of alternative splicing in Arabidopsis and humans led us to the discovery of an unusual type of introns that we termed exitrons (exonic introns) (Marquez et al., Genome Res, 2012; Marquez et al., Genome Res, 2015; featured in Staiger and Simpson, Genome Biol. 2015, Zlotorynski Nat Rev Mol Cell Biol., 2015, and Sibley et al., Nat Rev Genet., 2016). Exitrons are alternatively spliced internal regions of protein-coding exons and have features of both exons and introns. Many plant and human protein-coding genes contain exitrons. A large proportion of our research has been on the Ser/Arg-rich (SR) proteins, major regulators of alternative splicing. For example, together with our collaborators, we showed that chloroplasts signal the nucleus to change alternative splicing of SR genes in response to light or dark (Petrillo et al., Science 2014). 

Our current projects aim to find out more about the mechanisms of alternative splicing in plants, regulation of exitrons, and functions of SR proteins in plant development and stress response.

Requirements and desired qualifications:
- bachelor (or equivalent) degree in molecular biology or a related area
- high accuracy and reliability
- solid written and oral communication skills in English 

Ansprechperson: To apply, please send a CV and cover letter to Mariya Kalyna  e-mail

The position will remain open until it is filled. 

Global profiling of cancer-associated exitron splicing (Bioinformatics)

There is an opportunity for or a Master’s thesis in Bioinformatics in the Kalyna research group. We are looking for a highly motivated student who is interested in RNA biology, alternative splicing, and cancer research.

Background:
Alternative splicing is an essential layer of gene regulation. The majority of human and plant multi-exon genes are alternatively spliced producing from two to thousands of transcript and protein variants with different fates and functions from a single gene.

Closer examination of alternative splicing in humans and model plant Arabidopsis led us to the discovery of an unusual type of introns that we termed exitrons (exonic introns) (Marquez et al., Genome Res, 2012; Marquez et al., Genome Res, 2015; featured in Staiger and Simpson, Genome Biol. 2015, Zlotorynski Nat Rev Mol Cell Biol. 2015, and Sibley et al., Nat Rev Genet., 2016). Exitrons are alternatively spliced internal regions of protein-coding exons and have features of both exons and introns. Many human protein-coding genes, including those with reported functions in cancer, contain exitrons. Our finding brings us to the next research aim, which is to investigate mechanistic basis of exitron regulation and to elucidate a link between exitrons and cancer. To this end, together with our Viennese and Japanese collaborators, we perform large-scale bioinformatics analyses of various cancer RNA-seq and exome datasets.

The goal of the Master’s project is to identify and characterize exitrons misregulated in different cancer types. The student will be assisted by an experienced bioinformatician.

Requirements and desired qualifications:
- bachelor (or equivalent) degree in bioinformatics, computational biology or a related area
- high accuracy and reliability
- solid written and oral communication skills in English

Ansprechperson: To apply, please send a CV and cover letter to Mariya Kalyna  e-mail

The position will remain open until it is filled.

O-glycosylation of nuclear proteins in plants

O-glycosylation of cytosolic and nuclear proteins is an important post-translational modification that regulates the molecular function of a large number of proteins. We are interested in understanding the basic principles of how this modification is regulated in plants, and its effects on specific target proteins.
We are currently looking for a Master student to analyse how O-fucoslyation and O-GlcNAcylation affect protein-interactions of a specific transcription factor. The work for this project includes transient expression in tobacco leaves, co-immunoprecipitation and O-glycosylation assays. If you are interested or want to know more about the topic, please contact us!

Ansprechperson: Doris Lucyshyn  e-mail

Characterization of antibody-degrading serine proteases of Nicotiana benthamiana

Plant-based expression platforms are increasingly used for the production of recombinant biotherapeutics such as monoclonal antibodies. However, the expression of monoclonal antibodies in plants is frequently accompanied by unwanted proteolysis. This is also the case for Nicotiana benthamiana, a tobacco-related plant species emerging as a rapid and versatile expression host for complex proteins. This MSc thesis project aims at the recombinant expression and biochemical characterization of N. benthamiana serine proteases potentially involved in antibody degradation. 

Ansprechperson: Lukas Mach  e-mail

Subcellular Mechanisms of Cellular Elongation

The research focus of our group is the regulation of plant growth and development. We are particularly interested in subcellular mechanisms that control cellular elongation. In this master thesis the respective candidate will address how the cell organelles, such as the vacuole, control cell size. We are looking for a motivated student who is willing to work on this project, using state of the art cell biological and molecular methods. The candidate will particularly use high-resolution microscopy, molecular cloning and developmental genetics to advance our current knowledge on cell size determination. If you are interested do not hesitate to contact us!

Ansprechperson: Kai Dünser  e-mail

Erkennungsmechanismen von Metallionenbelastungen bei Pflanzen

Cell walls do not only protect the cell but serves also as signaling platform between the extracellular environment and the intracellular physiology. We are interested in the molecular analysis of cell wall associated receptor kinases which are involved in metal ion sensing. By using molecular genetics, CRISPR/Cas9 gene editing and cell biological approaches this project aims to uncover the role of a class of receptor kinases in the model plant Arabidopsis thaliana.

Keywords: cell wall, kinases, signal transduction, cadmium, nickel, zinc, lead, copper

Ansprechperson: Marie-Theres Hauser  e-mail

Veränderung der Pektinmethylierung bei Metallionenbelastung

The pectin component, homogalacturonan (HG), is synthesized and incorporated in the cell wall in a highly methylesterified form. Upon demethylation HG establishes intramolecular calcium/metal ion bridges, the so-called egg-box structures important for cell wall stiffening. This project tackles the role of HGs in heavy metal ion capturing and sensing using the model plant Arabidopsis thaliana and molecular genetics, cell biological and biochemical approaches.   

Keywords: cell wall, pectin, signal transduction, heavy metals, trace elements, cadmium, nickel, zinc, lead, copper

Ansprechperson: Marie-Theres Hauser  e-mail 

Regulation der Translation bei Stress exponierten Pflanzen

Major efforts were invested in studying transcriptional regulation upon abiotic stresses while understanding of the regulation of protein synthesis is lagging behind. Comparative genomic and proteomic analyses have shown that mRNA and protein levels do not correlate perfectly, highlighting the important contribution of translational control and protein stability to gene expression. This project employs a novel method in combination with genetics to identify regulators of translation which are important for abiotic stress responses.

Keywords: UV-B, heavy metals, protein synthesis, translation initiation factors  

Ansprechperson: Marie-Theres Hauser  e-mail 

Epigenetische Regulation ribosomaler RNA               

Transcriptome-wide analyses have shown that RNA modifications occur on all major classes of RNA including ribosomal RNA. Recently a member of an evolutionarily conserved family of methyltransferases has been identified in the model plant Arabidopsis thaliana which is responsible to methylate the 25S rRNA of the large ribosomal subunit. With the help of genetic and molecular biological analyses the project analyses the dynamics of rRNA methylation during development and in response to abiotic stressors and aims to reveal the functional role of this epigenetic modification on the translational efficiency, growth and fecundity. 

Keywords: UV-B, heavy metals, protein synthesis, rRNA, RNA methylation, methyltransferases 

Ansprechperson: Marie-Theres Hauser  e-mail 

Untersuchungen über Metallionen induzierten epigenetischen Veränderungen bei Pflanzen 

Plants are sessile organisms and cannot escape adverse environmental conditions as for example the increase of heavy metals and trace elements in soils due to air pollution but also heavy use of fertilizers and fungicides. In this project the impact on the epigenome should be analyzed upon chronic exposure to elevated concentrations of metal ions. Quantitative gene expression analyses will be combined with experiments using epigenetically silenced reporter lines of the model plant Arabidopsis thaliana.      

Keywords: cadmium, nickel, zinc, lead, copper, DNA methylation, chromatin remodeling, small RNA expression, gene silencing

Ansprechperson: Marie-Theres Hauser  e-mail

Molecular characterization of a cell wall associated kinase involved in heavy metal sensing

Phytoremediation, the extraction of heavy metals and other contaminates through plants might be a cost effective method to restore metal polluted soils. We have isolated a heavy metal induced cell wall associated kinase of a heavy metal tolerant willow. To characterize its function we transferred this gene fused with a fluorescing protein gene to the model plant Arabidopsis thaliana. To characterize the protein domains necessary for the cell wall association and triggering heavy metal responses, microscopic analyses (CLSM) will be employed combined with cell fractionations and Western blots. Since it is anticipated that the project needs many hours on high end confocal laser scanning microscopes only students should take this project which love microscopy. 

Keywords: Microscopy, Western blot, heavy metals

Ansprechperson: Marie-Theres Hauser  e-mail 

Epigenetic control of fungal secondary metabolism

The role of H4K20 methylation in Aspergillus nidulans
Fungi are known to produce a plethora of secondary metabolites (SMs) with toxic and carcinogenic properties, while others are used as antoibiotics and other medicinal drugs. One important regulatory layer in SM biosynthesis involves histone modifications, which define the amounts and timing of SM gene expression. The master student will elucidate the role of histone methylation (H4K20me) on fungal development and SM biosynthesis in the model organism Aspergillus nidulans by employing general mycology methods, reverse and molecular genetics and state-of-the-art technologies, such as Chromatin Immunoprecipitation. The master thesis will be carried out in the lab of Prof. Dr. Strauss at the BOKU Campus in Tulln (train connection from U4/U6, ~ 20min. ride to Tulln).

Allgemeine Information: Die „Abteilung Mikrobielle Genetik & Pathogen-Interaktionen“ bietet die Möglichkeit am Standort Tulln eine Masterarbeit durchzuführen. Für den Zeitraum der Masterarbeit (6 Monate) wird eine Reisekostenentschädigung Wien-Tulln angeboten. Arbeitszeit über die Masterarbeit hinaus wird im Rahmen einer Anstellung als studentische/r Mitarbeiter/in abgegolten.

Start: möglich ab Dezember 2016
Bewerber/innen sollten die wichtigsten mikrobiologischen und molekularbiologischen Techniken aus Praktika kennen.

Ansprechperson: Lena Studt  e-mail

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