SB students resources

Introduction to our students resources in Synthetic Biology

(Marko Dolinar)

Synthetic biology made a vast progress in good 10 years since it established itself as an interdisciplinary field of research on the interface of molecular biology and engineering. University of Ljubljana Faculty of Chemistry and Chemical Technology has introduced a Synthetic Biology course as a part od Biochemistry MSc programme only in 2013/14. This is relatively late, considering a great success of Slovenian students at iGEM competitions since their first attendance in 2006. On the other hand, the field is still in its first stages if development and a complete textbook for a MSc level course is still missing. This is the reason why our students collaborated on the preparation of a Synthetic Biology textbook with the working title Synthetic Biology - A Students Textbook. It exists as a draft that is not publicly available and is actually part 1 of a (to be) 2-volumes title. Part I is subtitled Engineering Biology, while Part II (that currently doesn't exisist yet) will be subtitled Synthetic Biology Applications.

As in all highly competitive fields of science and technology, students should be following recent progress by reading articles in high quality journals. However, this is often a very difficult task, especially at the BSc level. Specificities of the scientific and technical language, push of publishers towards very short methodological chapters and limited knowledge studens might have about advanced techniques make understanding papers a very challenging task. Therefore, I decided to face MSc students with the challenge to explain selected SB articles in a manner that would make the content of these articles understandable to BSc level students and non-experts.

In 2014/15, seminars in Synthetic Biology include explanations and presentations of some of the top-cited articles from the field of Synthetic Biology. I compiled a list of 95 articles published between 2000 and 2014 having the highest number of citations according to the Web of Science database. The list ended with the paper just exceeding the 100 citations limit. Not included in the list were reviews. With 20 students enrolled in the course, the list has been further reduced to top 40 papers in the field. Students have been asked to check for content (they further eliminated 3 papers which proved to be reviews) and availabitly (they all seemed to be available as full texts with our university subscriptions). My suggestion was to avoid selecting for presentation papers with very similar content. Especially in the field of genome editing there has been a very rapid progress in the past few years resulting in a number of highly-cited articles which could appear very similar in content for a non-specialist. From the shortlist of 37 articles, students selected a topic they believed would be most interesting or easiest to explain. Presentations will be both written (in English, which is not the mother tongue of my students) and oral (in Slovenian, to establish and maintain Slovenian terminology in the field).

List of articles for presentation

This is the list of top-cited papers from the broader field of Synthetic Biology that students chose for explanation in 2014/15 (sorted by year of publication):

1. A synthetic oscillatory network of transcriptional regulators, Michael B. Elowitz & Stanislas Leibler, Letters to Nature, 2000 - Valter Bergant
2. Construction of a genetic toggle switch in Escherichia coli. Gardner et al., Nature, 2000 - Urban Bezeljak
3. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion (2001) - Andreja Bratovš
4. Chemical synthesis of poliovirus cDNA: Generation of infectious virus in the absence of natural template (2002) - Veronika Jarc
5. Combinatorial synthesis of genetic networks. Guet C.C. et al, Science, 2002 - Maja Remškar
6. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids (2003) - Ana Kapraljević
7. Programmed population control by cell-cell communication and regulated killing (2004) - Alja Zottel
8. Gene regulation at the single-cell level (2005) - Katarina Uršič
9. A synthetic multicellular system for programmed pattern formation. (2005) - Mitja Crček
10. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat (2005) - Jana Verbančič
11. Tuning genetic control through promoter engineering (2005) - Špela Pohleven
12. Production of the antimalarial drug precursor artemisinic acid in engineered yeast (2006) - Živa Marsetič
13. An improved zinc-finger nuclease architecture for highly specific genome editing, Miller et al., Nature Biotechnol., 2007 - Eva Knapič
14. Establishment of HIV-1 resistance in CD4(+) T cells by genome editing using zinc-finger nucleases (2008) - Tamara Marić
15. Synthetic protein scaffolds provide modular control over metabolic flux. Dueber et al., Nature Biotechnology, 2009. - Ana Dolinar
16. Creation of a bacterial cell controlled by a chemically synthesized genome. Gibson, D. G. et al., Science, 2010 - Eva Lucija Kozak
17. A TALE nuclease architecture for efficient genome editing, Miller et al, Nature Biotechnol., 2011 - Jernej Mustar
18. Multiplex genome engineering using CRISPR/Cas systems (2013) - Uroš Stupar
19. RNA-guided human genome engineering via Cas9. Mali et al., Science, 2013 - Luka Smole
20. One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering (2013) - Andrej Vrankar

Please link the title of each paper with your written seminar wiki page. Expand the citation according to the following example:

1. Emergent bistability by a growth-modulating positive feedback circuit. Tan et al., Nature Chem. Biol., 2009