Welcome & Contact Information
I am a phytoplankton molecular and cell biologist drawing my scientific inspiration from the diversity of biominerals across the tree of life.
- Jernej Turnšek, PhD
- Department of Plant and Microbial Biology, University of California, Berkeley, 431 Koshland Hall, Berkeley, CA 94720
Biology and Engineering of Phytoplankton Biominerals
The overarching ambition of my research is to understand molecular, cellular, and evolutionary underpinnings of phytoplankton biomineralization, and to turn this knowledge into medical, industrial, and environmental applications.
Background and Motivation
Phytoplankton are photosynthetic microalgae and cyanobacteria living in marine and freshwater habitats worldwide. They form the base of aquatic food webs and account for ~50% of global primary production. Silicon cycle is linked to other major biogeochemical cycles (e.g., carbon, nitrogen, phosphorus, iron) through growth and activity of silicifying phytoplankton. These microorganisms produce intricate silica (glass) skeletons. How they orchestrate the assembly of these ornate biominerals at mild temperatures and pressures is a fascinating question, a bridge between nanoscale and planetary scale biological and geological processes. Additionally, the biocompatibility and hierarchical mesoporous structure of naturally produced silica represent a basis for medical and (bio)technological applications.
Diatoms are a widely distributed group of silicifying microalgae. They account for ~40% of marine primary production and are pivotal to exporting carbon to the deep ocean as part of the biological carbon pump. Ecological and evolutionary success of diatoms has been attributed to their silica-based cell wall called a frustule. There are tens of thousands of different diatom species collectively producing a dazzling variety of frustule shapes and patterns. This makes them a very good model system to study the genetic determinants of biomineral morphogenesis.
I aim to understand the molecular and cellular mechanisms of silica-based cell wall biogenesis and morphogenesis in diatoms. I am employing reverse genetics, imaging, omics, and bioinformatics to achieve these goals. My primary experimental model system is a centric marine diatom Thalassiosira pseudonana.
My current diatom research focuses on:
- molecular links between nitrogen and silicon metabolism;
- trafficking of frustule-associated proteins;
- mechanism(s) of silicic acid sensing and signaling.
How Diatoms Build Their Beautiful Shells is a wonderfully narrated video about diatoms produced by the Journey to the Microcosmos.
Molecular Tools for Diatoms
Biological and technological breakthroughs in diatom research will depend on ease and scale with which these microalgae can be genetically engineered, manipulated, and programmed.
I have recently implemented a novel genome engineering approach in Thalassiosira pseudonana based on bacterial conjugation-mediated transformation method.
Turnšek J et al. Multiplex genome editing in the model marine diatom Thalassiosira pseudonana (in preparation)
I pioneered the use of proximity-dependent proteomic mapping in a pennate model marine diatom Phaeodactylum tricornutum, which led to the discovery of a putative iron trafficking pathway.
Turnšek J et al. 2021. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 10:e52770. DOI
I showed the utility of bacterial conjugation to express biosilica-targeted proteins in Thalassiosira pseudonana.
Faktorová D et al. 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 17:481–494. DOI Revisited Thalassiosira pseudonana (Tp) conjugation protocol enables fusion protein delivery to Tp frustule (protocols.io, Feb 18, 2018)
New Phytoplankton Model Systems for Biosilicification Research
I am establishing a new biosilicification model system, a freshwater alga Synura petersenii. Synurophytes, including Synura petersenii, are heterokont algae related to diatoms. In contrast to diatoms, they don't require silicon for growth and can completely shed off their silica biomineral, which offers some unique research opportunities.
Mathematics of Biomineral Morphogenesis in Microalgae
I am interested in how knowledge of pattern formation in multicellular organisms can inform our description of biomineral growth and morphogenesis in microalgae like diatoms.
Pyrenoids are subchloroplastic RuBisCO-rich proteinaceous compartments crucial for CO2 fixation in many algae and in a group of land plants called hornworths. I worked on an iron- and CO2-sensitive chloroplast-localized disordered protein in a pennate model marine diatom Phaeodactylum tricornutum. We hypothesize this protein, which undergoes a series of post-translational cleavage events, is involved in pyrenoid organization in P. tricornutum. More details about this work can be found in my Doctoral Dissertation.
Flavors and Fragrances Biotechnology
I spent a year at Ginkgo Bioworks engineering Escherichia coli to produce precursor molecules for the flavors and fragrances industry.
Inspired by natural examples of metabolic channeling in enzymes, enzyme complexes, and bacterial microcompartments, we showed that synthetic assemblies of biosynthetic pathways on DNA scaffolds lead to improved metabolite production in Escherichia coli.
Conrado RJ et al. 2012. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 40:1879–1889. DOI
2010 iGEM World Champion
I was a member and a copresenter of the Team Slovenia's Grand Prize-winning iGEM project at the Massachusetts Institute of Technology.
- The Gordon and Betty Moore Foundation Grant GBMF4958 (August 2015–July 2018)
- Turnšek J et al. 2021. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 10:e52770. DOI
- Faktorová D et al. 2020. Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 17:481–494. DOI
- Conrado RJ et al. 2012. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 40:1879–1889. DOI
- Revisited Thalassiosira pseudonana (Tp) conjugation protocol enables fusion protein delivery to Tp frustule (protocols.io, Feb 18, 2018)
- HA tag enables highly efficient detection of heterologous proteins in Phaeodactylum tricornutum (Pt) exconjugants (protocols.io, Oct 5, 2017)
- Guidelines for highly efficient construction of diatom episomes using Gibson Assembly (protocols.io, Sep 21, 2017)
- Pour plating of Thalassiosira pseudonana (Tp) (protocols.io, Aug 16, 2017)
- Simple & rapid genotyping of marine microeukaryotes (protocols.io, Aug 11, 2017)
- Conjugation of Thalassiosira pseudonana (protocols.io, Oct 19, 2016)
- Marine Microbes: Triathlete's Best Friends, January/February 2018
- Diatoms: Nature's Nanotechnologists, May 2014
In the News
- Meta PHoDcast, January 2022 (interview)
- Scientists map how iron is processed by algae, March 2021 (eLife manuscript press release)
- A genetic toolbox for marine protists, April 2020 (Nature Methods manuscript commentary)
- VELIKI KORAKI, May 2019
- Prvih uspešnih sedem desetletij ljubljanske Biotehniške fakultete, February 2017
- Meta PHoDcast, January 2016 (interview)
- Tapping the marine microbiome, December 2015 (GBMF grant press release)
- Slovenec, ki na Harvardu secira alge, February 2015 (interview)
- PhD, Biological and Biomedical Sciences, Harvard University
- MSc, Biotechnology, University of Ljubljana
I am an avid multisport athlete having competed in numerous open water swimming, running, cycling, and triathlon races including two marathons and four Half Ironman triathlons. I was a competitive basketball player prior to transitioning to endurance sports.
- Half Ironman triathlon ~ Ironman 70.3 Santa Cruz 09/2022: 5h 21' 12"
- Olympic distance triathlon ~ Mass State Triathlon 07/2016: 2h 17' 24"
- Sprint distance triathlon ~ Mission Bay Triathlon 10/2017: 58' 33"
- 26.2 ~ Baystate Marathon 10/2013: 3h 30' 55"
- 13.1 ~ Boston's Run to Remember 05/2013: 1h 26' 30"
- 10k ~ Mardi Gras 10K 02/2017: 38' 26"
- 5k ~ Triton 5K 04/2017: 18' 32"
- 1st place (age group), Alpha Win Napa Valley Half Ironman, Lake Berryessa, CA, 10/2021
- 1st place (age group), Rock the Bay Triathlon, San Diego, CA, 09/2018
- 3rd place (age group), Mission Bay Triathlon, San Diego, CA, 10/2017
I've become interested in flash science fiction after learning about postcard-sized stories by Arthur C. Clarke and his contemporaries. "Short Tales from the Mothership" event at the UCSD Geisel Library promotes this elegant genre.
- The Cellist of Sarajevo ~ Steven Galloway
- The Yugoslav Wars of the 1990s ~ Catherine Baker
- Born on a Blue Day ~ Daniel Tammet
- Hero ~ Rhonda Byrne
- The Old Man and the Sea ~ Ernest Hemingway
- Zen Mind, Beginner's Mind ~ Shunryu Suzuki
- Indian running ~ Peter Nabokov
- The Doors of Perception ~ Aldous Huxley
- Deep Simplicity ~ John Gribbin
- Pravica ~ Srečko Kosovel
Advice to a Young Scientist
- The Secret Life of Plankton ~ Five Reasons to Thank Plankton ~ Ocean Drifters ~ The Diatomist ~ Journey to the Microcosmos ~ Planktomania
Slovenian Language and Culture
- I grew up in Slovenia, in the town of Žalec in the Land of Green Gold.
- Izbor misli iz knjige Franceta Cokana "Eno življenje je premalo".