Droplet Microfluidic Tools for Sustainable Biotechnology
This PhD project focuses on developing and applying novel user-friendly droplet-based microfluidic pipelines for high-throughput biological assays. This includes employing a vast array of techniques such as hands-on construction and manipulation of microfluidic platforms, generation of small (pico- and nanoliter sized) water-in-oil droplets, biology and chemistry experimental procedures, signal detection or imaging, and image analysis via different software tools.
Droplet-based microfluidic applications are rapidly expanding sustainability in biological research. Encapsulation of study material into microdroplets enables massive high-throughput parallelization, chemical separation, and confined sample analysis. This is unprecedented via classical methods that use flasks, petri dishes, and microtiter plates. However, despite new droplet microfluidic tools evolving and providing new experimental pathways, many obstacles and limitations remain, and the tools are underused in general biology and chemistry labs. There is a need for bridging the gap between state-of-the-art droplet-based microfluidics tools and their easy application for the general scientific community.
The prospective PhD project is developed around these topics pursued currently in the supervising labs:
- Development of user-friendly droplet microfluidic technologies for biotechnology
- Investigation of antimicrobial susceptibility and resistance mechanisms at single cell level in droplets
- Influence of different anthropogenic pollutants (Micro-and nanoplastic, metals, chemicals, etc) to cells and their drug sensitivity
- Development of different labelled or label-free approaches for droplet microfluidics
- Development and validation of active and passive systems for high throughput sorting of droplets
- Functional enrichment of microbial strains and consortia from environmental samples
- Prospective students can also propose and develop their own research directions in the field of droplet microfluidics that align with topics listed above
Ott Scheler (ORCID ID: 0000-0002-8428-1350) has 10 years of work experience in biotechnology and microfluidics, and he is currently the head of the Microfluidics lab at TalTech. He has an interdisciplinary background: initially biotechnologist by training with expertise now in diverse fields such as nucleic acid amplification technologies, diagnostics, bioanalytics, biosensorics, microfluidics, and instrumentation development. His current research interests are: developing droplet tools in biotechnology, antimicrobial susceptibility and impact of different pollutants (metals, plastic, etc), image analysis for microfluidics.
He defended his PhD in University of Tartu, Estonia in 2012 and did his postdoc in Institute of physical chemistry at Polish academy of sciences 2014-2018. He has also been a visiting researcher at University of Illinois, Urbana-Champaign, USA in 2011.
He is currently a PI of HE Pathfinder project Chiralforce (101046961). He has successfully supervised 6 PhD degrees and is currently supervisor of 3 PhD students.
Current research focus: droplet microfluidics, image analysis, biotechnology
Number of Publications: 40+
Key Funding: HE Pathfinder projects: Chiralforce (101046961), 3D-BRICKS (101099125)
Awards, memberships: Member of Estonian Society for Microbiology
Tomasz Kaminski (ORCID ID: 0000-0001-5124-4548) is a group leader at the Faculty of Biology, University of Warsaw. His research interests are focused on developing microfluidic technologies for ultra-high-throughput screening and single-cell genomics. After having graduated in biotechnology (BSc-2009, MSc-2010) from Warsaw University of Life Sciences, Tomasz completed his Ph.D. research (2010-16) in prof. Piotr Garstecki research group at the Institute of Physical Chemistry of Polish Academy of Sciences, Warsaw, Poland. In 2018-20 he was MSCA Postdoctoral Fellow in prof. Florian Hollfelder group at the Department of Biochemistry at the University of Cambridge, and in 2020 he came back to Poland to set up his research group. Tomasz has also worked at the University of Wisconsin-Madison, the University of Oxford and the University of Tokyo. He is an author of 35+ research articles and co-inventor of 26 patents and patent applications, many of them being implemented in the industry. Currently, Tomasz is a supervisor of 3 PhD students.
Simona Bartkova (ORCID ID: 0000-0001-9567-104X) is a researcher at Tallinn University of Technology (TalTech) with expertise in droplet microfluidics, microbiology, image analysis, antibiotics, and microplastics. She has a strong international background, is fluent in five languages, and currently plays a leading role in several interdisciplinary Horizon Europe projects and COST Actions. She recently co-created the award-winning DropliNet project as part of the Horizon Europe Plastic Fantastic program, showcasing her innovative approach to tackling environmental challenges. Alongside her research, she is a dedicated advocate for inclusive science, actively contributing to initiatives that promote gender equality and support mental and physical well-being in academia. Simona is also an engaged educator, teaching across disciplines at TalTech in courses such as genetic engineering, BioMEMS, and bioinformatics.
Currently Simona is a supervisor 2 PhD students.
• We are looking for an open-minded candidate who would like to apply a wide set of multidisciplinary tools for biotechnology
• Candidate must have master’s degree in natural science (e.g in gene technology, microbiology, biotechnology, bioinformatics, bioengineering, biochemistry or similar)
• We expect previous hands-on experience with basic laboratory techniques in at least one of the following areas: molecular biology, microbiology, genetic engineering, biochemistry or similar
• Previous experience in microfluidics is a strong bonus, but not expected
• Experience in any of the following fields is a strong advantage, but is not expected: informatics, statistics, image analysis, engineering, robotics or other similar