I started writing down thoughts and ideas on various scientific questions I find interesting in 2016. Heavily influenced by my soon to be completed Ph.D. work in marine microbiology, some of them do touch other fields, mainly neurobiology, evolution, origins of life and gene regulation. This list will grow and its sole intention is to spark scientific discussion. It is open to everyone to comment.
Illuminating evolution one compartment at a time. Pioneering spatial proteomics approaches in photosynthetic microeukaryotes at Harvard University, the Scripps Institution of Oceanography, and the J. Craig Venter Institute (JCVI).
Be part of my efforts to save coral reefs at Let’s all tri our best, TriForOceans!
On Sep 1, 2016, I became a Visiting Graduate Student in Prof. Andrew E. Allen Lab at the Scripps Institution of Oceanography (SIO) and the J. Craig Venter Institute (JCVI) where I am continuing my spatial proteomics work in diatoms. My new mailing address is as follows:
J. Craig Venter Institute
4120 Capricorn Lane
La Jolla, CA 92037
Molecular and cell biologist with broad international academic and industrial research experience. Ph.D. Candidate in Biological and Biomedical Sciences at Harvard University (expected to graduate in 2019), Visiting Graduate Student at The Scripps Institution of Oceanography, University of California, San Diego, and Research Fellow at J. Craig Venter Institute. iGEM 2010 World Champion and protocols.io ambassador. Open science advocate.
In my PhD thesis I am using a genetically encodable tag for electron microscopy and subcellular proteomics to study endocytosis, carbon fixation and biosilicification in diatoms, highly abundant and evolutionarily successful photosynthetic microeukaryotes.
My future interests with tangents to my PhD work are as follows:
1. Continuing my work on systems understanding of the molecular mechanisms guiding the morphogenesis of diatom cell walls. I am particularly interested in polyamines and their role in connecting cell cycle control and call wall formation.
2. Extending my studies on biomineral morphogenesis to non-diatom model systems such as radiolarian protozoa Acantharea which are using strontium sulfate to build their skeletons.
3. Studying evolutionary origins and basic physicochemical principles of protein-induced phase transitions in eukaryotes. I am especially interested in how protein disorder, low amino acid complexity and posttranslational modifications tie to these processes.
4. Investigating antizyme-mediated regulation of polyamine homeostasis and the mechanisms of polyamine-induced ribosomal frameshifting.
I have always been very motivated to balance science with my passion for sports which will extend into all of my future endeavors. I have developed as a triathlete throughout graduate school and am anticipating to participate in my first full Ironman race in 2019 or 2020.
- 1 Contact Info
- 2 Interests
- 3 Projects
- 4 Funding
- 5 Peer reviewed publications
- 6 Preprints
- 7 Open source publications
- 8 Other publications
- 9 Creative writing
- 10 On scientific publishing
- 11 Conferences
- 11.1 Phase Transitions in Polymeric and Protein Systems, 14-15 February 2019, Dresden, Germany
- 11.2 ASCB | EMBO 2018 meeting, 8-12 December 2018, San Diego, CA
- 11.3 ASM Microbe 2018, 7-11 June 2018, GWCC, Atlanta, GA
- 11.4 A New Age of Discovery for Aquatic Microeukaryotes, 26-29 Januar 2016, EMBL Heidelberg, Germany
- 11.5 The Eleventh Annual Broad Institute Retreat, 14-15 December 2015, Hynes Convention Center, Boston, MA
- 11.6 Wyss Institute 7th Annual Retreat, 19 November 2015, Seaport World Trade Center, Boston, MA
- 11.7 Molecular Life of Diatoms 2015, 7-10 July 2015, University of Washington, Seattle, WA
- 11.8 2014 MRS Fall Meeting & Exhibit, 30 November-4 December 2014, Boston, MA
- 12 Talks
- 13 Teaching & Community service
- 14 Outreach
- 15 Resources
- 16 Classic and other interesting papers
- 17 Books to read
- 18 Past Affiliations
- 19 Selected Awards & Accomplishments
- 20 Education
- 21 Sports
- 22 Podcasts
- 23 Web
- 24 Word plays & puns
- Jernej Turnšek | Ph.D. Candidate
- Harvard Medical School | Department of Systems Biology | 200 Longwood Avenue, Boston, MA 02115
- Wyss Institute for Biologically Inspired Engineering at Harvard University | Center for Life Science Boston Bldg., 5th Floor | 3 Blackfan Circle, Boston, MA 02115
- Email: email@example.com | CV as of October 18'
- Biomineralization | Biomaterials | Morphogenesis | Self-assembly | Biomolecular condensates and biological phase transitions
- Marine Microbiome | Marine Natural Products
- Astrobiology | Space Exploration | Origins of Life
- Endurance Sports | Exercise Physiology | Sports Technology
- Spatial biosilicification-specific proteomics in the model diatom Thalassiosira pseudonana.
Figure 1 | Overview of the biosilicification process in diatoms. (Left) Diatom cell wall is synthesized inside an acidic compartment called the silica deposition vesicle (SDV). (Right) It is hypothesized that the interaction of silaffins with long-chain polyamines (LCPA) inside the SDV leads to the formation of an organic matrix, the structure of which is controlled by the silaffins (adapted from Kröger, 2007, and Kröger & Poulsen, 2008).
- N. Kröger, Prescribing diatom morphology: toward genetic engineering of biological nanomaterials. Curr. Opin. Chem. Biol. 11, 662–669 (2007).
- N. Kröger, N. Poulsen, Diatoms—From Cell Wall Biogenesis to Nanotechnology. Annu. Rev. Genet. 42, 83–107 (2008).
- M. Hildebrand, S. J. L. Lerch, Diatom silica biomineralization: Parallel development of approaches and understanding. Semin. Cell Dev. Biol. 46, 27–35 (2015).
Figure 2 [A] Morphological diversity of diatom cell walls. The image represents cleaned diatom cell walls arranged in the star-like pattern by the UK-based microscopist and diatom artist Klaus Kemp. [B] SEM image of Thalassiosira pseudonana, the model diatom for biomineralization studies (credit: Nils Kröger). [C] Thalassiosira pseudonana cells. Red and green correspond to plastid autofluorescence and silica, respectively.
See poster links under the "Conferences" section for more details.
My work is supported by the Gordon and Betty Moore Foundation: "The Gordon and Betty Moore Foundation believes in bold ideas that create enduring impact in the areas of science, environmental conservation and patient care. Intel co-founder Gordon and his wife Betty established the foundation to create positive change around the world and at home in the San Francisco Bay Area. Science looks for opportunities to transform–or even create–entire fields by investing in early-stage research, emerging fields and top research scientists. Environmental conservation efforts promote sustainability, protect critical ecological systems and align conservation needs with human development. Patient care focuses on eliminating preventable harms and unnecessary healthcare costs through meaningful engagement of patients and their families in a supportive, redesigned healthcare system." Visit Moore.org or follow @MooreFound and read more about the broader research initiative my projects fall under on the following link.
Peer reviewed publications
- Conrado RJ et al. 2012. DNA-guided assembly of biosynthetic pathways promotes improved catalytic efficiency. Nucleic Acids Res 40:1879–1889. DOI
- Turnšek J, Brunson JK, Deerinck TJ, Oborník M, Horák A, Bielinski VA, Allen AE. 2019. Phytotransferrin endocytosis mediates a direct cell surface-to-chloroplast iron trafficking axis in marine diatoms. bioRxiv DOI
- Faktorová et al. 2019. Genetic tool development in marine protists: Emerging model organisms for experimental cell biology. bioRxiv DOI
Open source publications
- Revisited Thalassiosira pseudonana (Tp) conjugation protocol enables fusion protein delivery to Tp frustule (protocols.io, Feb 18, 2018)
- Vacuole staining in Phaeodactylum tricornutum using RatioWorks™ PDMPO (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)
On scientific publishing
- Reviewers should be paid.
- All science should be free and publicly available.
Phase Transitions in Polymeric and Protein Systems, 14-15 February 2019, Dresden, Germany
This meeting brought soft matter and polymer researchers together with molecular and cell biologists to discuss macromolecular phase separation and the physical nature of protein condensates.
ASCB | EMBO 2018 meeting, 8-12 December 2018, San Diego, CA
Focusing on cell biology as the fundamental basis of biology and exploring more specialized fields, such as neurobiology and stem cell biology. You can find the poster I presented at this conference on this link.
ASM Microbe 2018, 7-11 June 2018, GWCC, Atlanta, GA
Connecting scientists with their science–showcases the best microbial sciences in the world, and provides a one-of-a-kind forum to explore the complete spectrum of microbiology from basic science to translation and application. You can find the poster I presented at the conference on this link.
A New Age of Discovery for Aquatic Microeukaryotes, 26-29 Januar 2016, EMBL Heidelberg, Germany
This conference celebrated efforts of three major contributions to microeukaryote biology, ecology, and evolution that are catapulting the field forward: the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP), the Tara Oceans Expeditions, and the Malaspina Expedition. You can find the poster I presented at the conference on this link.
The Eleventh Annual Broad Institute Retreat, 14-15 December 2015, Hynes Convention Center, Boston, MA
This event brings together researchers and affiliates of the Broad Institute to discuss institute's most recent advances at the interface of science and technology. You can find the poster I presented at the retreat here
Wyss Institute 7th Annual Retreat, 19 November 2015, Seaport World Trade Center, Boston, MA
This event brings together researchers and affiliates of the Wyss Institute for Biologically Inspired Engineering to discuss institute's most recent advances at the interface of science and technology. You can find the poster I presented at the retreat on this link.
Molecular Life of Diatoms 2015, 7-10 July 2015, University of Washington, Seattle, WA
Molecular Life of Diatoms 2015 brought together an interdisciplinary mix of scientists to discuss recent advances in our understanding of diatoms and the way they shape our planet. You can find the poster I presented at the conference here.
2014 MRS Fall Meeting & Exhibit, 30 November-4 December 2014, Boston, MA
- ASCB | EMBO 2018 meeting Satellite Event: "Genetic Tool Development in Marine Protists: Emerging New Model Organisms for Cell Biology", 12/12/2018
- SIO262 - Seminars in Marine Chemical Biology and Natural Products, Scripps Insitution of Oceanography, 11/01/2017 slides
- Synthetic Biology Platform Meeting, Wyss Institute for Biologically Inspired Engineering, 03/01/2016 | slides
Teaching & Community service
- protocols.io ambassador, Nov 17'-now.
- Mentoring a B.S. level scientist, JCVI, CA, April 17'-Sep 18'
Molecular cloning & microalgae genetic engineering.
- Biochemistry Bootcamp Mentor, Wellesley College, Wellesley, MA, January 2015
I served as a mentor for the inaugural biochemistry bootcamp aimed at promising undergraduates at Wellesley College. Students expressed a protein in bacteria, purified it, assayed its activity, and presented their findings to their classmates. I directly supervised a pair of undergraduate participants. The administrators at Wellesley agreed to offer this bootcamp opportunity to students again in 2016.
My PhD project in plain English
- A poetronics piece describing my PhD in 15 sec
- 3 slides describing my PhD project in simple terms can be found here.
SITN Waves Correspondent
SITN Waves Expert
- Friend or Foe? Getting the body to make peace with bioengineered drug delivery systems
- Algae: Applications in Removing Arsenic and Beyond
- Can we send a message to the future with DNA?
- Electric Bacteria – Groundbreaking Science or Old News?
- Scientists Learn to 3D Print Cells One Drop at A Time
In the news
- Featured in "VELIKI KORAKI", May 2019
- "Successful first seven decades of Ljubljana's Biotechnical Faculty", February 2017 (in Slovene)
- MetaPHoDcast, January 2016 (in Slovene)
- Wyss Institute, December 2015
- Finance, February 2015 (in Slovene)
- Cal Newport's website
- Izbor misli iz knjige Franceta Cokana: Eno življenje je premalo (in Slovene)
- Starting your own lab - lessons & tips
- Growing list of mostly ambient electronic music artists
Classic and other interesting papers
- Brenner, S. (1997) In theory. Cell. 7, 3: PR202.
- Blobel, G. (1980) Intracellular protein topogenesis. Proc. Natl. Acad. Sci. U. S. A. 77, 3: 1496–1500.
- McFall-Ngai M. et al. (2013), Animals in a bacterial world, a new imperative for the life sciences. Proc. Natl. Acad. Sci. U. S. A. 110, 9: 3229–3236.
- Haldane, J.B.S. (1926) On Being the Right Size.
Books to read
- In the Company of Microbes: Ten Years of Small Things Considered (Moselio Schaechter)
- On Growth and Form (D'Arcy Wentworth Thompson)
- Cell Biology by the Numbers (Ron Milo, Rob Phillips, Nigel Orme)
- The Major Transitions in Evolution (Eörs Szathmáry, John Maynard Smith)
- A Brief History of Time (Stephen Hawking)
- Lateral Thinking: Creativity Step by Step (Edward de Bono)
- Ginkgo BioWorks, Inc., Boston, MA (10/2012 - 06/2013) | Ginkgo BioWorks
- Jerala Lab at the National Institute of Chemistry, Ljubljana, Slovenia (05/2010 - 07/2012) | Jerala Lab
Selected Awards & Accomplishments
- Kavčič Prize for young writers in natural sciences, 2013
- University of Ljubljana Prešeren Award for Diploma Thesis, 2012 (in Slovene)
- 42nd Krka Prizes - Krka Prize for Diploma Thesis, 2012 (in Slovene)
- Gold medal, BIOMOD 2011 | Learn more about BIOMOD Slovenia 2011
- Grand Prize, World Champion, iGEM 2010 | Learn more about iGEM Slovenia 2010
- University of Ljubljana, Biotechnical Faculty, Diploma in Biotechnology, 06/2012
- Diploma thesis entitled: "Synthetic biology approach towards improvement of carotenoid biosynthetic pathway using zinc fingers"
- GCN Cycling Club
- Swami's Cycling Club
- Triathlon Club of San Diego
- La Jolla Cove Swim Club
- MIT Triathlon Club
- Harvard University Cycling Association
- Harvard Triathlon Team
- November Project
- 70.3 Ironman triathlon PR | Timberman 2016 08/2016: 5h 24' 02"
You can find reflections on my first Ironman 70.3 journey on this link.
- Olympic distance triathlon PR | Mass State Triathlon 07/2016: 2h 17' 24"
- Sprint distance triathlon PR | Mission Bay Triathlon 10/2017: 58' 33" (qualified for The 2018 Olympic-Distance Age Group National Championship)
- 26.2 PR | Baystate Marathon 10/2013: 3h 30' 55"
- 13.1 PR | Boston's Run to Remember 05/2013: 1h 26' 30"
- 10K PR | Mardi Gras 10K 02/2017: 38' 26"
- 5K PR | Triton 5K 04/2017: 18' 32"
- University of Ljubljana basketball champion in 2008 and 2009.
Science, Technology, Entertainment, Design
- Chemistry World | Disruptive | Discovery | Flash Forward | Hidden Brain | Meet the Microbiologist (MtM) | Nature | Nature Biotechnology | NPR: Invisibilia | NPR: Ted Radio Hour | Science Magazine | Science Talk | Science Weekly | SIT'N Listen! | StarTalk Radio | Stuff You Should Now | The Guardian's Science Weekly | This Week in Microbiology (TWiM | This Week in Virology (TWiV) | WNYC's Radiolab
- Ask a Cycling Coach | Endurance Nation | Locked On Mavericks | Over The Top Cycling | Purple Patch Podcast | Running Rogue | The Freedive Cafe Podcast | The Kona Edge | The Rich Roll Podcast | TOWER26 | Trail Runner Nation | Zen and The Art of Triathlon | 220 Triathlon Magazine
- Apparatus | Frekvenca X | Intelekta | Meta PHoDcast | Podrobnosti | Studio ob 17h | Stevilke | Vroci Mikrofon
- Ask a Manager | Documentaries | Fresh Air | Hello PhD | Stuff You Missed in History Class | The Coffee Podcast | The Joe Rogan Experience | The 5AM Miracle Podcast | Vinyl Schminyl Radio | Waking Up with Sam Harris
- Tara Oceans | The Secret Life of Plankton | Five Reasons to Thank Plankton | Ocean Drifters | The Diatomist
Science, Technology, Entertainment, Design
- Compound Interest | Khan Academy | ScienceDaily | Selected Lectures on Science and Engineering in the Boston Area | TED
- Kraftwerk and Electronic Revolution | Krautrock: The Rebirth of Germany | Sasha - Airdrawndagger | Tycho - Epoch | Tycho - Dive | Tycho - Awake
Word plays & puns
- I know a spunful of them! (referring to puns)
- soupergirl/souperman (when multitasking which involves cooking soup)
- just do it (when sharing words of encouragement with someone named Du)
- room for improvement (e.g. when discussing and referring to downsizing and decluttering your room)
- unbrewlieavable (e.g. coffee cup)
- to hit the grant running (=to start working on your grant proposal)