MSc project in plant-pathogen interactions
In our group we are working on enhancing the knowledge on plant defense mechanisms to various filamentous plant pathogens, with emphasis on disease problems in Scandinavia.
We are currently looking for a highly motivated student(s) who is interested in joining our work to optimize CRISPR-Cas 9 systems for knock-down of selected genes particularly in the pathogens. Such knowledge will greatly facilitate the understanding of what genes that are required to enable infection and disease development in plant hosts.
1. Substantially improve current transformation procedures
2. Establish proof of concept constructs for modification of selected genes
3. Establish knock-down of selected genes
Follow-up work/project could have emphasis on identification of plant interacting proteins and plant modifications.
Required skills and interests
Strong interest in organism biology
Relevant courses in molecular genetics and gene technology
English is the language used in the department.
MSc projects in Sweden are done during the last semester in each MSc program covering at least 30 weeks of work. To be written up and be presented for general public at the BioCenter/Linne Centre.
We are flexible but prefer spring semester.
More information about SLU and the Department of Plant Biology, see www.slu.se or https://www.slu.se/en/departments/plant-biology-forest-genetics/
For further details, contact Christina.Dixelius@slu.se
Master's degree project in plant genetic engineering.
Available earliest from the September 20th 2018.
Alyona Minina, PhD: alena.minina (@) slu.se
Anna Åsman, PhD: anna.asman (@) slu.se
In our group we are currently focusing on investigating the molecular machinery of plant autophagy. We are looking for a highly motivated student who is interested in joining our group to optimize CRISPR-Cas9 system for knock-in modification of plant genes.
Most of the current plant molecular biology studies still rely on the use of crude genetic engineering tools that dramatically limit the capacity of our research. The recent advances in the use of CRISPR-Cas9 system for plants give very promising results that still require some significant modifications.
In this project we aim to optimize the CRISPR-Cas9 for precise knock-in modification of Arabidopsis genes and use the new tool to make reporter lines for detection of plant autophagy-related (ATG) genes activity.
This project, in general, will open up a broad range of new possibilities for investigating plant gene function and in particular, will make a significant contribution to our understanding of ATG-genes regulation.
- Establish proof of concept constructs for knock-in modification of Arabidopsis thaliana genes in protoplasts
- Create a set of constructs for knock-in modification of genes important for regulation of autophagy in Arabidopsis thaliana
- Participate in establishing transgenic lines by knocking in green fluorescent protein and luciferases into Arabidopsis genome
You will acquire skills in
- Genetic engineering
- Use of CRISPR-Cas9 in plants
- Advanced DNA and protein molecular biology methods
- Advanced confocal microscopy
- Plant transformation
- Handling typical plant model organisms: Arabidopsis thaliana plants and tobacco cell cultures
The queen of bites. Help us catch them!
Supervisors: Tessa Visser MSc, and Dr. Sander Koenraadt
Requirements: at least one of the following courses, ENT-30806, ENT-51306, ENT-30306, ENT-54306
Mosquitoes play a key role in the disease transmission of diseases such as dengue, chikungunya and the recently emerged Zika virus. To prevent mosquito-borne disease it is important to gain more knowledge about the behaviour of these pesky biters.
We are looking for an inventive MSc student to help design a new behavioural assay for capturing Aedes aegypti. This mosquito species is vector of all diseases mentioned above. Aedes aegypti is especially dangerous because it’s preference for human blood. This research will contribute to a PhD project in which the final design will be used in a Biosafety level 3 facility to work with real Zika infected mosquitoes. But first we need to design the assay and gain important baseline information. You will work in a team with enthusiastic entomologists!
Learning outcome: performing behaviour studies, statistical analyses, mosquito rearing, design of experiments
Ecosystem Services Valuation in Lacandon Jungle, Mexico
Supervisors: FEM group: Frans Bongers & Carolina Berget.
Other organasation: dr Gerard Verschoor -SDG
Duration: Second half 2018 till Spring 2019
Requirements: Standard for MSc thesis: FEM-30306 Forest Ecology and Forest Management; Or equivalent / Preferably also Social science methods
The general problem:
The search for alternatives to reconcile tradeoffs between biodiversity conservation, agricultural production and local livelihoods relies, among other things, on the understanding of what are the most valued ecosystem services.
The research consortia:
The FOREFRONT project, a joint initiative between Wageningen University, the National Autonomous University of Mexico (UNAM), El Colegio de la Frontera Sur in Mexico, and the Universidad de Minas Gerais in Brasil is exploring these topics for the case of tropical forests in Chiapas, Mexico.
A MSc thesis can be undertaken within this context to assess what are the most valued ecosystem services by the local farmers in the Marques de Comillas Municipality in Chiapas Mexico.
A standard protocol will be followed to undertake approx. 30 individual interviews to farmers from different locations within the study area.
The individual interviews will depart from a fixed list of ecosystem services elaborated by the FOREFRONT team, and depicted into individual drawings by a graphic designer. Each interviewee will be asked to order the services from the most to the least important and to explain the reasons for this ordering. Basic socioeconomic information will be requested from each interviewee.
The resulting flipchart will be digitized and the position of each service will be used as a metric of its importance. The reasons associated to the choices will be analyzed using qualitative analyses. General patterns as well as differences among communities and types of interviewees will be explored.
Who can participate:
Students with very diverse backgrounds in biological sciences, environmental sciences, anthropology, sociology, economics, geography, rural development, philosophy are most welcome. Students need to be 100% proficient in spoken and written Spanish and be willing to live in rural tropical humid areas.
Effects of grazing and enhanced nutrients on the ecosystem services, resilience and competitive abilities of native and invasive seagrass.
Master thesis or internship
30, 33, 36 credits
Supervisors: F.O.H. Smulders (Fee.Smulders@wur.nl)
Contact info: Marine Ecology: Noël Diepens 0317-489701 (Noel.Diepens@wur.nl)
Begin date: September/October/November 2018
End date: 5 or 6 months after the begin date
In this project, you will research the impact of grazing and nutrients on the ecosystem services and the resilience (ability to recover from disturbance) of seagrass. As an invasive seagrass species (H. stipulacaea) is spreading in Bonaire, we also want to study competition between native (T. testudinum) and invasive seagrass. You will be part of a large Caribbean wide project on turtlegrass. Additionally, there are many options to design and carry out side experiments of your choice.
Used skills: Scientific diving, designing ecological experiments, nutrient analysis in the lab.
Requirements: Diving certificate (min. 30 dives), driver's license.
Understanding nutrient cycling in cocoa production systems in Ivory Coast (Theobroma cacao L.)
Supervisors: A. (Ambra) Tosto MSc; Prof. Dr. P.A. (Pieter) zuidema; L. S. (Lotte) Woittiez MSc
Contact: Ambra.email@example.com; firstname.lastname@example.org; email@example.com
Requirements: REG-31806 Ecological Methods I or other basic statistics course
Cacao is the most important export crop in west African countries, with Ivory Coast and Ghana producing 70% of the world production, mostly in smallholder plantations. Realized yields however are much less than the potential value calculated for the region. One of the suggested causes of this low yield is poor nutrient availability. To better understand possible nutrient limitations, basic information on nutrient cycling in the cocoa tree is required.
Theobroma cacao is a cauliflorous species with flowers appearing both on the main stem and in the canopy. This project aims to understand and quantify the nutrient content (NPK) of organs of cocoa trees (fruit, leaves, stem, roots) and flows of nutrients (leaf loss, fruit harvest, root turnover) and to use this data to quantify a nutrient balance of cocoa production systems. Some basic information is available already from a previous MSc thesis study.
The project comprises field work with a duration of 2-3 months in the research station of CNRA in Divo, Ivory coast. The field work consists of sample collection from different types of cocoa tissue within a newly set up experiment. Field work will be in November-December 2018 or June-July 2019. In addition, nutrient analyses will be conducted and interpreted, and optionally results may be used to update/expand a simple nutrient cycling model.
Learning outcome: Cocoa nutrient cycling, statistical analyses, field work skills, simple nutrient modelling
Required skills: We are looking for an enthusiastic student, with very good adaptation skills and a working knowledge of French since in the research stations very few people speak English.
Agroforestry/ Ecophysiology /Africa/ Tropical zone
Quantifying the effect of pruning on cocoa (Theobroma cacao) architecture in Ivory Coast
Supervisors: A. (Ambra) Tosto MSc; Prof. Dr. P.A. (Pieter) zuidema; Dr. J.B. (Jochem) Evers
Contact: Ambra.firstname.lastname@example.org; email@example.com; firstname.lastname@example.org
Requirements: REG-31806 Ecological Methods I
Cocoa (or cacao) is the most important export crop in west African countries: Ivory Coast and Ghana produce 70% of the world production, mostly by smallholder farmers. Realized yield however falls way below the potential value calculated for the region. Pruning is suggested to be an effective measure to increase yield. It creates a more open canopy with greater penetration of light to lower levels in the cacao crowns. Little is known though about how cocoa responds to pruning and how this changes the 3D architecture of the tree. We are conducting a study on the effects of pruning on the architecture of cacao trees, in which we combine pruning experiments and plant modelling.
This MSc project aims to explore methods to quantify the architecture of cacao trees and capture changes in architecture due to pruning. It will be conducted in an ongoing pruning experiment (first pruning in April 2018) in a 10-year old stand.
Type of work
The project comprises field work for approximately 2 months in the research station of CNRA (National Agricultural Research Centre of Ivory Coast) in Divo, Ivory Coast. Field work will consist of measurements of dimensions (length, diameter) and orientation of stems and (main) branches. This will take place for both pruned and unpruned trees.
Understand and measure tree architecture, understand effects of pruning, statistical analyses, field work skills.
We are looking for an enthusiastic student, with very good adaptation skills and a working knowledge of French since in the research stations very few people speak English.
Agroforestry/ Africa/ Tropical zone
Join the Biodiversity Genomics Team for your internship in subtropical China!
As a Wageningen Biologist (graduated 2005), it is my pleasure to send out this invitation to BVW for internship applications! I am leading the Biodiversity Genomics Team at Guangxi University, hosted at the Plant Ecophysiology and Evolution Group (College of Forestry).
Within the Team we conduct research on some of the largest families of tropical trees which are complex clusters of young, closely related species with often poorly defined morphologies. Our goal is to quantify and assess patterns of genomic diversity, to unravel evolutionary relationships, reconstruct historical biogeography, speciation patterns and describe trends in assembly of the tropical forest biome. To this end, we apply the latest NextGen sequencing techniques, bioinformatics and technological advances (e.g. DoveTail, Nanopore). We don’t concern us with PCR-based single marker approaches but focus explicitly on collecting and sequencing on a large scale, targeting organellar genomes and specific whole genomes in key lineages. Our research involves extensive molecular laboratory work, computer analyses and bioinformatics, and periodical fieldwork in protected areas, botanical gardens and the permanent forest plot system of Guangxi University.
The Team has a growing herbarium collection of tropical tree specimens (BGT herbarium) which is under active construction (data basing/digitizing). A taxonomic angle to your internship is certainly possible, in combination with a molecular/genomic component.
During your internship, you will be exposed to all the aspects of the work we do, from fieldwork to the lab to learning how to write scripts and analyze data using genomic software. For us as a Team, our goal is to get you to leave at the end of your internship with one submitted article. So far, all Team members have succeeded in publishing in their first year, and given the amount of data available, this is a feasible target!
In principle, multiple positions are available, for periods of 3-6 months. Exact topics can be discussed via email. Housing is available through Guangxi University on our large Nanning City campus. Unfortunately, travel funding to cover your flight is not available. I recommend approaching funding bodies like the Wageningen University Fund, to apply for a travel grant. I was fortunate to obtain this when studying in Wageningen for a Philippines-based MSc.
Nanning is a large city (~5 million) and the new subway makes getting around easy. It is nicknamed “the Green City” and has a subtropical climate, with warm-hot summers and mild winters. The new international airport gets you to almost every regional Asian capital. By road, you can get to Hanoi or the coast in about 3-4 hours. Hong Kong is about 2 hours by plane.
Guangxi University is based on a very large and green campus, with about 20,000 students. Almost everyone lives on the campus and everything you need for daily life is available on site or near one of the campus gates (restaurants, fast food and coffee). Life in Nanning is not expensive – a meal at one of the 15! canteens on campus will set you back 1-3 euro.
The Team currently consists of 4 postdocs, 2 MSc and one PhD student. The College of Forestry is unique in Guangxi University for the cluster of foreign professors leading research teams staring in 2014. Since then, six teams have emerged with different backgrounds, and now we have a stable population of 35-40 (Chinese and foreign) faculty, postdocs, PhD and MSc students. In my team I have people from France, Spain, the US, Serbia, Ecuador, India and China. Other groups have members of Sri Lanka, Indonesia, Colombia, Madagascar, Malaysia and Cyprus, making our community highly diverse and dynamic. Daily language within the teams is English.
A picture impression of life on campus and some facilities is available here: http://www.plant-ecophysiology-evolution.com/contact-us/
If you’d like to learn more about coming to China and joining the Team for your internship, please send an email to email@example.com , and let’s see what we can do! We look forward to hearing from you.
Joeri Sergej Strijk
Biodiversity Genomics Team
Guangxi University, Nanning, China