Biology Education

The main goal of the project is to characterize fungal calcium carbonate precipitation in microfluidic device as a evaluation of feasibility for concrete crack healing.

Description:

Concrete is the world’s most widely used human-made material, yet its production is responsible for significant environmental impacts: generation of hazardous airborne dust, high energy consumption, and substantial CO₂ emissions. Given the impracticality of replacing concrete, our study proposes a sustainable alternative—concrete crack healing using fungi—to prevent reinforcement corrosion and thereby extend structural service life, ultimately reducing carbon output.

The method using fungi to repair cracks involves Microbial-Induced Calcium Carbonate Precipitation (MICP). MICP is a natural process in which microorganisms precipitate calcium carbonate (CaCO₃), thereby sealing cracks and reinforcing concrete surfaces. This process is primarily influenced by carbonate alkalinity and Ca²⁺ concentration. Ureolytic microorganisms play a key role by breaking down urea, increasing bicarbonate levels and pH, which promotes CaCO₃ precipitation in the presence of calcium ions. As the cement concrete is opaque, it is difficult to understand how they grow and precipitate in the cracks. Therefore, we will employ transparent microfluidic devices that mimic concrete’s porous architecture, enabling real-time visualization of fungal hyphal growth and biomineralization at the single-hypha level.

As part of this project, you will work with microfluidic chips to acquire time-lapse images using an inverted microscope, apply AI-driven object detection to quantify crystal nucleation and growth, and automate fluid delivery with advanced microfluidic pumps. Training in all of these techniques will be provided. The candidate must be proficient in standard microbiological methods, including sterile inoculation and nutrient medium preparation.

This project is interdisciplinary task within biology and engineering. You will primarily work with Dr. Hanbang Zou. This project is designed for a MSc student (optimally 60 cr).

Start Date: Flexible

Contact information: Hanbang Zou: Hanbang.zou@biol.lu.se

We are seeking a Master’s student for a 30, 45, or 60 credit thesis opportunity starting Spring / Summer 2025 to explore the relationship between ambient weather conditions, floral microclimates and resources, and pollinators. Field work will involve floral resource collection and pollinator identification and sampling.

Background:

While there is a fairly good understanding of the negative consequences of pollinator declines for crops, we know very little about the consequences for wild plant communities. Wild plant communities are thought to be more resilient to changes in pollinator communities because they comprise many different species that may show different responses (“response diversity”). Such variation arises from the variability of plant species and taxonomic groups to rely – more or less – on pollinators for reproduction. It is predicted yet barely known whether these differences on pollinator dependence can maintain overall plant diversity but significantly shift plant composition.

Project description:

To address this gap, we will select at least three plant species with different levels of pollinator dependence (low, medium and obligate insect pollinated). For each of these species we will determine the relationship between pollinator visitation rate and diversity with seed set. This will be done experimentally by bagging flowers of plants until they open, exposing individual flowers to a chosen range of visitation rates and species richness of pollinators and then bagging them again until seed set can be estimated. We will also collect body pollen from flower-visiting insects, record the environmental variables, and account for the surrounding plant species composition. We will then analyze these factors to determine how pollinator effectiveness to plant reproduction is mediated on a per-species basis.

You will join us in the field in observing pollinators such as bees, butterflies, and hoverflies. You will learn to develop a research question of your own within the project framework and develop important scientific skills as part of your Master’s studies.

Are you interested?

If you would like to know more about this position and working with insect pollinators, please contact Arrian Karbassioon (arrian.karbassioon@cec.lu.se) for more information.

Caspian terns (Hydroprogne caspia) are long-lived migratory seabirds and constitute the largest tern species in the world. We are currently looking for a dedicated master’s students to study the circadian activities, foraging, rest, sleep during breeding in the largest and oldest Caspian tern colony in Sweden (Stenarna, Björns archipelago, Baltic sea). You will be based in a small village of Fågelsundet (NE of Uppsala) between the end of April/early May and the mid July 2025 and observe Caspian terns in their breeding colony at Stenarna. The study of breeding activities including parents of sleep and behavior expressed during courtship, incubation and feeding of Caspian tern pairs will occur via a combination of direct observation on the island (with overnight stays in the hide on the Stenarna) and by using the surveillance camera that is accessible remotely. You will also have the possibility to partake in chick ringing sessions. Any student interested in this project is encouraged to contact Susanne Åkesson for more information and to discuss specific ideas for their MSc projects.

Prof Susanne Åkesson, Department of Biology, Evolutionary Ecology and Disease Biology (Room C221)
Email: susanne.akesson@biol.lu.se

Caspian terns (Hydroprogne caspia) are long-lived migratory seabirds and constitute the largest tern species in the world. We are currently looking for a dedicated master’s students to study the anti-predator behavior, disturbance and nest failure rates during breeding in the largest and oldest Caspian tern colony in Sweden (Stenarna, Björns archipelago, Baltic Sea). The Master’s student will be based in coastal village of Fågelsundet (Uppsala county) between the end of April/early May and mid July 2025 with the fieldwork team and observe Caspian terns in their breeding grounds on Stenarna. The study of anti-predator behavior, mortality and types of disturbances of breeding Caspian terns will occur via a combination of direct observation on the island (with overnight stays in the hide on the Stenarna), by using the surveillance camera that is accessible remotely and tracking data. The student will also have the possibility to partake in chick ringing sessions on Stenarna. Students interested in this project are encouraged to contact Prof Susanne Åkesson for more information and to discuss specific plans for their MSc projects.

Prof Susanne Åkesson, Department of Ecology, Evolutionary Ecology: susanne.akesson@biol.lu.se

Project suggestions 

Supervisor(s): Allan Rasmusson, Bradley Dotson, Dept. Biology, LU 

 Many fungal species of the genus Trichoderma live in symbiosis with plant roots. The fungus produces substances that stimulate plant growth and immune system but also directly attacking other microorganisms, including pathogens. Therefore, some strains of Trichoderma have been used as biocontrol and biostimulants in agriculture, decreasing the need for agrochemical use. The effect of Trichoderma on plants is strongly dependent on the plant genome, which is involved in a mainly unknown intricate interaction with the fungus, likely involving exchange of several signalling biomolecules.  Plant genes that are essential for biostimulation and biocontrol by fungi can be used in breeding, to make plants that can better benefit from biocontrol and biostimulation. However, we presently do not know what genes these are.  

 One possible class of genes that are essential for positive symbiosis with fungi are plant genes encoding proteins that are needed for the plants to avoid being damaged by the Trichoderma. This fungus attacks other microorganisms by secreting enzymes and peptide antibiotics, including so called peptaibols, where alamethicin is the standard model example. This peptide also lyses plant cells, but cellulase secreted from the Trichoderma induces resistance to the alamethicin by modifying the composition of the plant plasma membrane. This process we have named CIRA, and it is likely important for plant symbiosis with Trichoderma, though direct evidence are lacking. We have isolated CIRA-deficient mutants for a range of Arabidopsis genes, indicating that a so far unknown response chain is active. The different mutants belong to the categories Gene expression, Cell wall modifying, Signalling, Membrane lipid modifying and “Unknown”.  

 We can design differently long projects (30-60 credits) at multiple levels: 

• Whole plant level comparison of genetics of inbred sugar beet breeding lines as expressed in their biostimulation phenotypes. Includes work with molecular markers, genotyping and phenotyping on soil. 

• Analysis of particular known Arabidopsis mutants, their (lack of) biostimulation by Trichoderma, and the potential involvement of calcium signalling. This will involve sterile plant growth, fluorescent microscopy and measurements using intracellular fluorescent reporters. 

•  Identification and analysis of novel CIRA genes by mutant screening. Arabidopsis CIRA mutants are identified by a fluorescent phenotypic change and verified by designing PCR assays and analysing a second mutant allele for the same gene. The genes found are analysed in a first line by bioinformatic database mining (e.g. gene expression patterns, protein localisation, post-translational modification, etc). In a longer project additional analyses can be done. Acquired data will be used in order to assemble a preliminary signalling path. 

 For the sugar beet project, background knowledge on plant physiology, genetics and/or agriculture is suitable. For the Arabidopsis projects, background knowledge on plant physiology, molecular cell biology and molecular genetics is suitable. However, a project can usually be designed in accordance with the background of a candidate. 

 For more information and discussions please contact allan.rasmusson@biol.lu.se or bradley.dotson@biol.lu.se.