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Coauthors
John van der Oost Department of Agrotechnology and Food Sciences, Wageningen University, the Netherlands
2 protocols

Stan Brouns Department of Agrotechnology and Food Sciences, Wageningen University, the Netherlands
1 protocol

Edze Westra Department of Agrotechnology and Food Sciences, Wageningen University, the Netherlands
1 protocol

Matthijs Jore Department of Agrotechnology and Food Sciences, Wageningen University, The Netherlands
1 protocol
Coreviewers
Aksiniya Asenova UC DAVIS
10 protocols

Arsalan Daudi Department of Plant Pathology, University of California, Davis, CA, USA
137 protocols

Benoit Chassaing Clermont Université, Université d'Auvergne, M2iSH, UMR 1071 INSERM, UNC 2018 INRA, France
11 protocols

Lionel Schiavolin IBENS
4 protocols

Daan C. Swarts
  • Post-Doc, Department of Biochemistry, University of Zurich, Switzerland
Research focus
  • Biochemistry
  • -Structural biology
    -Protein-nucleic acid interactions
    -Nucleases
Contributions
  • 2 Author merit
  • 3 Reviewer merit
  • 6 Editor merit

Education

PhD, Wageningen UR, 2015

Lab information

Martin Jinek lab

Publications

First author publications
7. DC Swarts, J van der Oost, M Jinek (2017). Structural basis for guide RNA processing and seed-dependent DNA targeting by Cas12a. Molecular Cell 66, 221-233
6. DC Swarts*, M Szczepaniak*, G Sheng*, SD Chandradoss, Y Zhu, EM Timmers, Y Zhang, H Zhao, J Lou, Y Wang, C Joo, J van der Oost (2017) Autonomous generation and loading of DNA guides by bacterial Argonaute. Molecular Cell 65, 985-998
5. DC Swarts, JW Hegge, I Hinojo, M Shiimori, M Ellis, J Dumrongkulraksa, RM Terns, MP Terns, J van der Oost (2015) Argonaute of archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA. Nucleic Acids Research, 43: 5120-5129
4. DC Swarts, JJ Koehorst, ER Westra, PJ Schaap, J van der Oost (2015) Effects of Argonaute on gene expression in Thermus thermophilus. PLoS ONE, 10(4): e0124880
3. DC Swarts, K Makarova, Y Wang, K Nakanishi, RF Ketting, EV Koonin, DJ Patel, J van der Oost (2014) The evolutionary journey of Argonaute proteins. Nat. Struc. Mol. Biol. Vol. 21, 743-753
2. DC Swarts*, MJ Jore*, ER Westra, Y Zhu, JH Janssen, AP Snijders, Y Wang, DJ Patel, J Berenguer, SJJ Brouns, J van der Oost (2014) DNA-guided DNA interference by a prokaryotic Argonaute. Nature, Vol. 507, Issue 7491, 258-261
1. DC Swarts, C Mosterd, MWJ van Passel, SJJ Brouns (2012) CRISPR Interference Directs Strand Specific Spacer Acquisition. PLoS ONE, 7(4): e35888

Co-author publications
6. J van der Oost, DC Swarts, MM Jore (2014) Prokaryotic Argonautes – variations on the RNA interference theme. Microbial Cell, Vol. 1, Issue 5, 158-159
5. T Künne, DC Swarts, SJJ Brouns (2014) Planting the seed: Target recognition of short guide RNAs. Trends in Microbiology, Vol. 22, Issue 2, 74-83
4. G Sheng*, H Zhao*, J Wang, Y Rao, W Tian, DC Swarts, J van der Oost, DJ Patel, Y Wang (2014) Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc. Natl. Acad. Sci. USA, Vol. 111, Issue 2, 652-657
3. ER Westra, DC Swarts, RHJ Staals, MM Jore, SJJ Brouns, J van der Oost (2012) The CRISPRs, They Are A-Changin’: How Prokaryotes Generate Adaptive Immunity. Annual Reviews Genetics, Vol. 46
2. CM Plugge, AM Henstra, P Worm, DC Swarts, AH Paultisch-Fuchs, JCM Scholten, A Lykidis, AL Lapidus, E Goltsman, E Kim, E McDonald, L Rohlin, BR Crable, RP Gunsalus, AJM Stams, MJ McInerney (2012) Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOBT). Standards in Genomic Sciences, Vol. 7 91-106
1. F Blombach, H Launay, V Zorraquino, DC Swarts, LD Cabrita, D Benelli, J Christodoulou, P Londei, J van der Oost (2011) An HflX-Type GTPase from Sulfolobus solfataricus binds to the 50S Ribosomal Subunit in All Nucleotide-Bound States. Journal of Bacteriology, Vol. 193 2861-2867

Peer-reviewed protocol publications
2. DC Swarts, ER Westra, SJJ Brouns, J van der Oost (2014) Purification and Sequencing of DNA guides from Prokaryotic Argonaute. Bio-protocol, Vol 4, Issue 22
1. DC Swarts, MM Jore, John van der Oost (2014) Expression and Purification of the Thermus thermophilus Argonaute Protein. Bio-protocol, Vol 4, Issue 19

*These authors contributed equally

2 Protocols published
Purification and Sequencing of DNA Guides from Prokaryotic Argonaute
Authors:  Daan C. Swarts, Edze R. Westra, Stan J. J. Brouns and John van der Oost, date: 11/20/2014, view: 4034, Q&A: 0
Some proteins utilize nucleic acids to guide them to complementary nucleic acid targets. One example is prokaryotic Argonaute protein, which, binds small single stranded DNA molecules as guides (Swarts et al., 2014). This protocol describes ...
Expression and Purification of the Thermus thermophilus Argonaute Protein
Authors:  Daan C. Swarts, Matthijs M. Jore and John van der Oost, date: 10/05/2014, view: 3530, Q&A: 0
The Argonaute protein of Thermus thermophilus (TtAgo) has recently been studied in detail. For its in vitro characterization, TtAgo was purified after heterologous expression in Escherichia coli (E. coli ...
3 Protocols reviewed
Determination of (p)ppGpp Levels During Stringent Response in Streptomyces coelicolor by Thin Layer Chromatography
Authors:  Smitha Sivapragasam and Anne Grove, date: 11/05/2016, view: 1977, Q&A: 0
The stringent response in bacteria is a stress response that is mediated by the signaling molecules guanosine tetraphosphate and pentaphosphate [(p)ppGpp], alarmones that are also directly related to virulence. Therefore, determination of (p)ppGpp ...
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Measurement of Intracellular cAMP Levels Using the Cyclic Nucleotide XP Enzymatic Immunoassay Kit in Bacteria
Authors:  Sarah K Giles, Uwe H Stroeher and Melissa H Brown, date: 04/20/2016, view: 2757, Q&A: 0
Cyclic AMP (cAMP) is a ubiquitous secondary signaling molecule, commonly associated with many bacterial processes, including the regulation of virulence factors, such as biofilms, pellicles and motility (Wolfgang, 2003). The quantity of available ...
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6 Protocols edited
Conjugation Assay for Testing CRISPR-Cas Anti-plasmid Immunity in Staphylococci
Authors:  Forrest C. Walker and Asma Hatoum-Aslan, date: 05/05/2017, view: 1217, Q&A: 0
CRISPR-Cas is a prokaryotic adaptive immune system that prevents uptake of mobile genetic elements such as bacteriophages and plasmids. Plasmid transfer between bacteria is of particular clinical concern due to increasing amounts of antibiotic ...
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Transformation of Thermus Species by Natural Competence
Authors:  Alba Blesa and José Berenguer, date: 11/20/2016, view: 1604, Q&A: 0
Many Thermus species harbour genomes scourged with horizontally transferred signatures. Thermus thermophilus (Tth) has been characterized as naturally competent. The transformation protocol described here is based on the ...
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