[2019-03-14] Barbara Terebieniec, PhD student at the Department of Plant Physiology, wanted to identify the factors that determine the shape of a leaf. Using different systems biology approaches, she and her colleagues identified genes that are controlling leaf shape in European aspen. Barbara Terebieniec successfully defended her PhD thesis today at Umeå University.
Why did you choose your project?
I was interested in working with populations and phenotypic traits and leaf shape is one of the most obvious characteristics of the plant phenotype.
What was most fascinating during your PhD?
I was collecting buds throughout the summer and cross-sectioned them to prepare them for the microscope. Like this, I could follow the full development of a leaf from the start until the bud flash under the microscope. That was very fascinating to see.
What was most disappointing during your PhD?
In collaboration with SciLifeLab, we developed and optimized the Spatial Transcriptomics (ST) method for our poplar bud samples. After we successfully optimized the ST method for our bud samples, we realized that the current resolution of this technique for plant samples is too low for the tiny buds. So, we could not answer all our questions even though we achieved what we planned in this project.
What do you like about UPSC?
UPSC with all the people from different countries creates this nice multicultural bubble. I met many nice people and made lots of new friendships.
What are your plans for the future?
Two years ago, I started working on my own start-up. I was very frustrated about keeping track of my lab samples in commonly used -80°C freezers. Our idea was to develop FreezFiler, a digital, non-intrusive system using computer vision. It can be placed on the -80°C freezer to read barcode tagged samples and simplifies the inventory of the freezers. We are now on the way to register a company and launch our first product. It means a lot of work, but also a lot of excitement and I am looking forward for these new challenges.
About the PhD thesis
Barbara Terebieniec and her colleagues exploited several different bioinformatics approaches to identify genes that are controlling leaf shape. Their results show that leaf shape is controlled by a complex network of many different genes and that each of those genes contributes minorly to the final leaf shape.
They compared the genetic setup of a collection of aspen trees with different leaf shape and identified genes that are associated with leaf shape. In a next step, they showed that a number those genes also play a role during leaf development. For this, they compared the genetic setup of leaves of different age, developing on one individual tree.
In an additional approach, Barbara Terebieniec optimized successfully the method spatial transcriptomics for aspen buds together with researchers from SciLifeLab. With this technique they hoped to identify those genes that are specifically expressed in the developing leaf within the bud. Even though they successfully established the method, they could not resolve spatially which genes were active during leaf development in the very young leaf because the size of the tissue was too small for the technique.
About the defence:
Barbara Terebieniec defended her thesis entitled “Using systems genetics to explore the complexity of leaf shape variation in Populus tremula” on Thursday, 14th of March. The public defence took place at 10:00am in Lilla hörsalen (KB.E3.01) in the KBC building, Umeå University. Faculty opponent was Chung-Jui Tsai from the Department of Genetics, University of Georgia, USA. Supervisor of the PhD thesis was Nathaniel Street.
Link to the thesis: urn:nbn:se:umu:diva-156464
For more information, please contact:
Umeå Plant Science Centre
Department of Plant Physiology