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Items: 1 to 50 of 70

1.

Visualisation of dCas9 target search in vivo using an open-microscopy framework.

Martens KJA, van Beljouw SPB, van der Els S, Vink JNA, Baas S, Vogelaar GA, Brouns SJJ, van Baarlen P, Kleerebezem M, Hohlbein J.

Nat Commun. 2019 Aug 7;10(1):3552. doi: 10.1038/s41467-019-11514-0.

2.

Creation of Conductive Graphene Materials by Bacterial Reduction Using Shewanella Oneidensis.

Lehner BAE, Janssen VAEC, Spiesz EM, Benz D, Brouns SJJ, Meyer AS, van der Zant HSJ.

ChemistryOpen. 2019 Jul 4;8(7):888-895. doi: 10.1002/open.201900186. eCollection 2019 Jul.

3.

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage.

Edwards RA, Vega AA, Norman HM, Ohaeri M, Levi K, Dinsdale EA, Cinek O, Aziz RK, McNair K, Barr JJ, Bibby K, Brouns SJJ, Cazares A, de Jonge PA, Desnues C, Díaz Muñoz SL, Fineran PC, Kurilshikov A, Lavigne R, Mazankova K, McCarthy DT, Nobrega FL, Reyes Muñoz A, Tapia G, Trefault N, Tyakht AV, Vinuesa P, Wagemans J, Zhernakova A, Aarestrup FM, Ahmadov G, Alassaf A, Anton J, Asangba A, Billings EK, Cantu VA, Carlton JM, Cazares D, Cho GS, Condeff T, Cortés P, Cranfield M, Cuevas DA, De la Iglesia R, Decewicz P, Doane MP, Dominy NJ, Dziewit L, Elwasila BM, Eren AM, Franz C, Fu J, Garcia-Aljaro C, Ghedin E, Gulino KM, Haggerty JM, Head SR, Hendriksen RS, Hill C, Hyöty H, Ilina EN, Irwin MT, Jeffries TC, Jofre J, Junge RE, Kelley ST, Khan Mirzaei M, Kowalewski M, Kumaresan D, Leigh SR, Lipson D, Lisitsyna ES, Llagostera M, Maritz JM, Marr LC, McCann A, Molshanski-Mor S, Monteiro S, Moreira-Grez B, Morris M, Mugisha L, Muniesa M, Neve H, Nguyen NP, Nigro OD, Nilsson AS, O'Connell T, Odeh R, Oliver A, Piuri M, Prussin Ii AJ, Qimron U, Quan ZX, Rainetova P, Ramírez-Rojas A, Raya R, Reasor K, Rice GAO, Rossi A, Santos R, Shimashita J, Stachler EN, Stene LC, Strain R, Stumpf R, Torres PJ, Twaddle A, Ugochi Ibekwe M, Villagra N, Wandro S, White B, Whiteley A, Whiteson KL, Wijmenga C, Zambrano MM, Zschach H, Dutilh BE.

Nat Microbiol. 2019 Jul 8. doi: 10.1038/s41564-019-0494-6. [Epub ahead of print]

PMID:
31285584
4.

Conserved motifs in the CRISPR leader sequence control spacer acquisition levels in Type I-D CRISPR-Cas systems.

Kieper SN, Almendros C, Brouns SJJ.

FEMS Microbiol Lett. 2019 Jun 1;366(11). pii: fnz129. doi: 10.1093/femsle/fnz129.

5.

Cas4-Cas1 fusions drive efficient PAM selection and control CRISPR adaptation.

Almendros C, Nobrega FL, McKenzie RE, Brouns SJJ.

Nucleic Acids Res. 2019 Jun 4;47(10):5223-5230. doi: 10.1093/nar/gkz217.

6.

Systematic analysis of Type I-E Escherichia coli CRISPR-Cas PAM sequences ability to promote interference and primed adaptation.

Musharova O, Sitnik V, Vlot M, Savitskaya E, Datsenko KA, Krivoy A, Fedorov I, Semenova E, Brouns SJJ, Severinov K.

Mol Microbiol. 2019 Jun;111(6):1558-1570. doi: 10.1111/mmi.14237. Epub 2019 Apr 6.

PMID:
30875129
7.

Addiction systems antagonize bacterial adaptive immunity.

van Sluijs L, van Houte S, van der Oost J, Brouns SJ, Buckling A, Westra ER.

FEMS Microbiol Lett. 2019 Mar 1;366(5). pii: fnz047. doi: 10.1093/femsle/fnz047.

8.

CRISPR-Cas Systems Reduced to a Minimum.

Almendros C, Kieper SN, Brouns SJJ.

Mol Cell. 2019 Feb 21;73(4):641-642. doi: 10.1016/j.molcel.2019.02.005.

PMID:
30794791
9.

Using CAPTURE to detect spacer acquisition in native CRISPR arrays.

McKenzie RE, Almendros C, Vink JNA, Brouns SJJ.

Nat Protoc. 2019 Mar;14(3):976-990. doi: 10.1038/s41596-018-0123-5. Epub 2019 Feb 11.

PMID:
30742049
10.

Molecular and Evolutionary Determinants of Bacteriophage Host Range.

de Jonge PA, Nobrega FL, Brouns SJJ, Dutilh BE.

Trends Microbiol. 2019 Jan;27(1):51-63. doi: 10.1016/j.tim.2018.08.006. Epub 2018 Sep 1. Review.

PMID:
30181062
11.

Role of nucleotide identity in effective CRISPR target escape mutations.

Künne T, Zhu Y, da Silva F, Konstantinides N, McKenzie RE, Jackson RN, Brouns SJ.

Nucleic Acids Res. 2018 Nov 2;46(19):10395-10404. doi: 10.1093/nar/gky687.

12.

Targeting mechanisms of tailed bacteriophages.

Nobrega FL, Vlot M, de Jonge PA, Dreesens LL, Beaumont HJE, Lavigne R, Dutilh BE, Brouns SJJ.

Nat Rev Microbiol. 2018 Dec;16(12):760-773. doi: 10.1038/s41579-018-0070-8. Review.

PMID:
30104690
13.

Complete Genome Sequences of Two T4-Like Escherichia coli Bacteriophages.

Costa AR, Brouns SJJ, Nobrega FL.

Genome Announc. 2018 Jun 28;6(26). pii: e00586-18. doi: 10.1128/genomeA.00586-18.

14.

Repetitive DNA Reeling by the Cascade-Cas3 Complex in Nucleotide Unwinding Steps.

Loeff L, Brouns SJJ, Joo C.

Mol Cell. 2018 May 3;70(3):385-394.e3. doi: 10.1016/j.molcel.2018.03.031. Epub 2018 Apr 26.

15.

Cas4 Facilitates PAM-Compatible Spacer Selection during CRISPR Adaptation.

Kieper SN, Almendros C, Behler J, McKenzie RE, Nobrega FL, Haagsma AC, Vink JNA, Hess WR, Brouns SJJ.

Cell Rep. 2018 Mar 27;22(13):3377-3384. doi: 10.1016/j.celrep.2018.02.103.

16.

Complete Genome Sequence of the Escherichia coli Phage Ayreon.

Vlot M, Nobrega FL, Wong CFA, Liu Y, Brouns SJJ.

Genome Announc. 2018 Jan 11;6(2). pii: e01354-17. doi: 10.1128/genomeA.01354-17.

17.

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR-Cas effector complexes.

Vlot M, Houkes J, Lochs SJA, Swarts DC, Zheng P, Kunne T, Mohanraju P, Anders C, Jinek M, van der Oost J, Dickman MJ, Brouns SJJ.

Nucleic Acids Res. 2018 Jan 25;46(2):873-885. doi: 10.1093/nar/gkx1264.

18.

CRISPR-Cas: Adapting to change.

Jackson SA, McKenzie RE, Fagerlund RD, Kieper SN, Fineran PC, Brouns SJ.

Science. 2017 Apr 7;356(6333). pii: eaal5056. doi: 10.1126/science.aal5056. Epub 2017 Apr 6. Review.

PMID:
28385959
19.

Interference-driven spacer acquisition is dominant over naive and primed adaptation in a native CRISPR-Cas system.

Staals RH, Jackson SA, Biswas A, Brouns SJ, Brown CM, Fineran PC.

Nat Commun. 2016 Oct 3;7:12853. doi: 10.1038/ncomms12853.

20.

Cas3-Derived Target DNA Degradation Fragments Fuel Primed CRISPR Adaptation.

Künne T, Kieper SN, Bannenberg JW, Vogel AI, Miellet WR, Klein M, Depken M, Suarez-Diez M, Brouns SJ.

Mol Cell. 2016 Sep 1;63(5):852-64. doi: 10.1016/j.molcel.2016.07.011. Epub 2016 Aug 18.

21.

CRISPR interference and priming varies with individual spacer sequences.

Xue C, Seetharam AS, Musharova O, Severinov K, Brouns SJ, Severin AJ, Sashital DG.

Nucleic Acids Res. 2015 Dec 15;43(22):10831-47. doi: 10.1093/nar/gkv1259. Epub 2015 Nov 19.

22.

CRISPR sabotage.

van der Oost J, Brouns SJ.

Genome Biol. 2015 Nov 9;16:248. doi: 10.1186/s13059-015-0820-0.

23.

An updated evolutionary classification of CRISPR-Cas systems.

Makarova KS, Wolf YI, Alkhnbashi OS, Costa F, Shah SA, Saunders SJ, Barrangou R, Brouns SJ, Charpentier E, Haft DH, Horvath P, Moineau S, Mojica FJ, Terns RM, Terns MP, White MF, Yakunin AF, Garrett RA, van der Oost J, Backofen R, Koonin EV.

Nat Rev Microbiol. 2015 Nov;13(11):722-36. doi: 10.1038/nrmicro3569. Epub 2015 Sep 28. Review.

24.

Electrophoretic Mobility Shift Assay of DNA and CRISPR-Cas Ribonucleoprotein Complexes.

Künne T, Westra ER, Brouns SJ.

Methods Mol Biol. 2015;1311:171-84. doi: 10.1007/978-1-4939-2687-9_11.

PMID:
25981473
25.

Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex.

Blosser TR, Loeff L, Westra ER, Vlot M, Künne T, Sobota M, Dekker C, Brouns SJJ, Joo C.

Mol Cell. 2015 Apr 2;58(1):60-70. doi: 10.1016/j.molcel.2015.01.028. Epub 2015 Mar 5.

26.

Structural biology. Crystal structure of the CRISPR RNA-guided surveillance complex from Escherichia coli.

Jackson RN, Golden SM, van Erp PB, Carter J, Westra ER, Brouns SJ, van der Oost J, Terwilliger TC, Read RJ, Wiedenheft B.

Science. 2014 Sep 19;345(6203):1473-9. doi: 10.1126/science.1256328. Epub 2014 Aug 7.

27.

Archaeal MBF1 binds to 30S and 70S ribosomes via its helix-turn-helix domain.

Blombach F, Launay H, Snijders AP, Zorraquino V, Wu H, de Koning B, Brouns SJ, Ettema TJ, Camilloni C, Cavalli A, Vendruscolo M, Dickman MJ, Cabrita LD, La Teana A, Benelli D, Londei P, Christodoulou J, van der Oost J.

Biochem J. 2014 Sep 1;462(2):373-84. doi: 10.1042/BJ20131474.

PMID:
24825021
28.

Degenerate target sites mediate rapid primed CRISPR adaptation.

Fineran PC, Gerritzen MJ, Suárez-Diez M, Künne T, Boekhorst J, van Hijum SA, Staals RH, Brouns SJ.

Proc Natl Acad Sci U S A. 2014 Apr 22;111(16):E1629-38. doi: 10.1073/pnas.1400071111. Epub 2014 Apr 7.

29.

DNA-guided DNA interference by a prokaryotic Argonaute.

Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, van der Oost J.

Nature. 2014 Mar 13;507(7491):258-261. doi: 10.1038/nature12971. Epub 2014 Feb 16.

30.

Planting the seed: target recognition of short guide RNAs.

Künne T, Swarts DC, Brouns SJ.

Trends Microbiol. 2014 Feb;22(2):74-83. doi: 10.1016/j.tim.2013.12.003. Epub 2014 Jan 14. Review.

PMID:
24440013
31.

Type I-E CRISPR-cas systems discriminate target from non-target DNA through base pairing-independent PAM recognition.

Westra ER, Semenova E, Datsenko KA, Jackson RN, Wiedenheft B, Severinov K, Brouns SJ.

PLoS Genet. 2013;9(9):e1003742. doi: 10.1371/journal.pgen.1003742. Epub 2013 Sep 5.

32.

Differential translation tunes uneven production of operon-encoded proteins.

Quax TE, Wolf YI, Koehorst JJ, Wurtzel O, van der Oost R, Ran W, Blombach F, Makarova KS, Brouns SJ, Forster AC, Wagner EG, Sorek R, Koonin EV, van der Oost J.

Cell Rep. 2013 Sep 12;4(5):938-44. doi: 10.1016/j.celrep.2013.07.049. Epub 2013 Sep 5.

33.

Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG.

Douillard FP, Ribbera A, Kant R, Pietilä TE, Järvinen HM, Messing M, Randazzo CL, Paulin L, Laine P, Ritari J, Caggia C, Lähteinen T, Brouns SJ, Satokari R, von Ossowski I, Reunanen J, Palva A, de Vos WM.

PLoS Genet. 2013;9(8):e1003683. doi: 10.1371/journal.pgen.1003683. Epub 2013 Aug 15.

34.

A capture approach for supercoiled plasmid DNA using a triplex-forming oligonucleotide.

Ruigrok VJ, Westra ER, Brouns SJ, Escudé C, Smidt H, van der Oost J.

Nucleic Acids Res. 2013 May 1;41(10):e111. doi: 10.1093/nar/gkt239. Epub 2013 Apr 9.

35.

CRISPR-Cas systems preferentially target the leading regions of MOBF conjugative plasmids.

Westra ER, Staals RH, Gort G, Høgh S, Neumann S, de la Cruz F, Fineran PC, Brouns SJ.

RNA Biol. 2013 May;10(5):749-61. doi: 10.4161/rna.24202. Epub 2013 Mar 27.

36.

CRISPRTarget: bioinformatic prediction and analysis of crRNA targets.

Biswas A, Gagnon JN, Brouns SJ, Fineran PC, Brown CM.

RNA Biol. 2013 May;10(5):817-27. doi: 10.4161/rna.24046. Epub 2013 Mar 14.

37.

The CRISPRs, they are a-changin': how prokaryotes generate adaptive immunity.

Westra ER, Swarts DC, Staals RH, Jore MM, Brouns SJ, van der Oost J.

Annu Rev Genet. 2012;46:311-39. doi: 10.1146/annurev-genet-110711-155447. Review.

PMID:
23145983
38.

Cascade-mediated binding and bending of negatively supercoiled DNA.

Westra ER, Nilges B, van Erp PB, van der Oost J, Dame RT, Brouns SJ.

RNA Biol. 2012 Sep;9(9):1134-8. doi: 10.4161/rna.21410. Epub 2012 Sep 1. Review.

39.

Native tandem and ion mobility mass spectrometry highlight structural and modular similarities in clustered-regularly-interspaced shot-palindromic-repeats (CRISPR)-associated protein complexes from Escherichia coli and Pseudomonas aeruginosa.

van Duijn E, Barbu IM, Barendregt A, Jore MM, Wiedenheft B, Lundgren M, Westra ER, Brouns SJ, Doudna JA, van der Oost J, Heck AJ.

Mol Cell Proteomics. 2012 Nov;11(11):1430-41. doi: 10.1074/mcp.M112.020263. Epub 2012 Aug 23.

40.

Molecular biology. A Swiss army knife of immunity.

Brouns SJ.

Science. 2012 Aug 17;337(6096):808-9. doi: 10.1126/science.1227253. No abstract available.

PMID:
22904002
41.

The rise and fall of CRISPRs--dynamics of spacer acquisition and loss.

Westra ER, Brouns SJ.

Mol Microbiol. 2012 Sep;85(6):1021-5. doi: 10.1111/j.1365-2958.2012.08170.x. Epub 2012 Jul 23.

42.

CRISPR interference directs strand specific spacer acquisition.

Swarts DC, Mosterd C, van Passel MW, Brouns SJ.

PLoS One. 2012;7(4):e35888. doi: 10.1371/journal.pone.0035888. Epub 2012 Apr 27.

43.

CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3.

Westra ER, van Erp PB, Künne T, Wong SP, Staals RH, Seegers CL, Bollen S, Jore MM, Semenova E, Severinov K, de Vos WM, Dame RT, de Vries R, Brouns SJ, van der Oost J.

Mol Cell. 2012 Jun 8;46(5):595-605. doi: 10.1016/j.molcel.2012.03.018. Epub 2012 Apr 19.

44.

Structures of the RNA-guided surveillance complex from a bacterial immune system.

Wiedenheft B, Lander GC, Zhou K, Jore MM, Brouns SJJ, van der Oost J, Doudna JA, Nogales E.

Nature. 2011 Sep 21;477(7365):486-489. doi: 10.1038/nature10402.

45.

Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence.

Semenova E, Jore MM, Datsenko KA, Semenova A, Westra ER, Wanner B, van der Oost J, Brouns SJ, Severinov K.

Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10098-103. doi: 10.1073/pnas.1104144108. Epub 2011 Jun 6.

46.

Evolution and classification of the CRISPR-Cas systems.

Makarova KS, Haft DH, Barrangou R, Brouns SJ, Charpentier E, Horvath P, Moineau S, Mojica FJ, Wolf YI, Yakunin AF, van der Oost J, Koonin EV.

Nat Rev Microbiol. 2011 Jun;9(6):467-77. doi: 10.1038/nrmicro2577. Epub 2011 May 9. Review.

47.

Structural basis for CRISPR RNA-guided DNA recognition by Cascade.

Jore MM, Lundgren M, van Duijn E, Bultema JB, Westra ER, Waghmare SP, Wiedenheft B, Pul U, Wurm R, Wagner R, Beijer MR, Barendregt A, Zhou K, Snijders AP, Dickman MJ, Doudna JA, Boekema EJ, Heck AJ, van der Oost J, Brouns SJ.

Nat Struct Mol Biol. 2011 May;18(5):529-36. doi: 10.1038/nsmb.2019. Epub 2011 Apr 3.

PMID:
21460843
48.

RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements.

Jore MM, Brouns SJ, van der Oost J.

Cold Spring Harb Perspect Biol. 2012 Jun 1;4(6). pii: a003657. doi: 10.1101/cshperspect.a003657.

49.

Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes.

Al-Attar S, Westra ER, van der Oost J, Brouns SJ.

Biol Chem. 2011 Apr;392(4):277-89. doi: 10.1515/BC.2011.042. Epub 2011 Feb 7. Review.

PMID:
21294681
50.

Assembling the archaeal ribosome: roles for translation-factor-related GTPases.

Blombach F, Brouns SJ, van der Oost J.

Biochem Soc Trans. 2011 Jan;39(1):45-50. doi: 10.1042/BST0390045. Review.

PMID:
21265745

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