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Research Output 1996 2019

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2019

Adaptation and application of a two-plasmid inducible CRISPR-Cas9 system in Clostridium beijerinckii

Diallo, M., Hocq, R., Collas, F., Chartier, G., Wasels, F., Wijaya, H. S., Werten, M. W. T., Wolbert, E. J. H., Kengen, S. W. M., van der Oost, J., Ferreira, N. L. & López-Contreras, A. M., 27 Jul 2019, In : Methods. 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clostridium beijerinckii
Clustered Regularly Interspaced Short Palindromic Repeats
Clostridium
Butanols
Plasmids

Addiction systems antagonize bacterial adaptive immunity

van Sluijs, L., van Houte, S., van der Oost, J., Brouns, S. J. J., Buckling, A. & Westra, E. R., 1 Mar 2019, In : FEMS Microbiology Letters. 366, 5, fnz047.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Adaptive Immunity
Plasmids
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Microbial Drug Resistance

Bicistronic Design-Based Continuous and High-Level Membrane Protein Production in Escherichia coli

Claassens, N. J., Finger-Bou, M., Scholten, B., Muis, F., De Groot, J. J., De Gier, J. W., De Vos, W. M. & Van Der Oost, J., 17 Jun 2019, In : ACS synthetic biology. 8, 7, p. 1685-1690 6 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Escherichia coli
Membrane Proteins
Proteins
Membranes
Cell Engineering
4 Citations (Scopus)

Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?

Tytgat, H. L. P., Nobrega, F. L., van der Oost, J. & de Vos, W. M., Jan 2019, In : Trends in Microbiology. 27, 1, p. 17-25

Research output: Contribution to journalArticleAcademicpeer-review

Biofilms
Mucous Membrane
Intestinal Diseases
Health
Colonic Neoplasms
Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Microalgae
Ribonucleoproteins
Homologous Recombination
homology

Distant Non-Obvious Mutations Influence the Activity of a Hyperthermophilic Pyrococcusfuriosus Phosphoglucose Isomerase

Subramanian, K., Mitusińska, K., Raedts, J., Almourfi, F., Joosten, H. J., Hendriks, S., Sedelnikova, S. E., Kengen, S. W. M., Hagen, W. R., Góra, A., Martins Dos Santos, V. A. P., Baker, P. J., van der Oost, J. & Schaap, P. J., 31 May 2019, In : Biomolecules. 9, 6

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Glucose-6-Phosphate Isomerase
Protein Engineering
Metals
Glucose-6-Phosphate
Mutation

DNA-guided DNA cleavage at moderate temperatures by Clostridium butyricum Argonaute

Hegge, J. W., Swarts, D. C., Chandradoss, S. D., Cui, T. J., Kneppers, J., Jinek, M., Joo, C. & van der Oost, J., 20 Jun 2019, In : Nucleic acids research. 47, 11, p. 5809-5821 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clostridium butyricum
DNA Cleavage
Argonaute Proteins
Temperature
DNA
4 Citations (Scopus)

Improved protein production and codon optimization analyses in Escherichia coli by bicistronic design

Nieuwkoop, T., Claassens, N. J. & van der Oost, J., 2019, In : Microbial Biotechnology. 12, 1, p. 173-179

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Codon
Escherichia coli
Proteins
Genes
5' Untranslated Regions

Incorporation of a Synthetic Amino Acid into dCas9 Improves Control of Gene Silencing

Koopal, B., Kruis, A. J., Claassens, N. J., Nobrega, F. L. & Van Der Oost, J., 1 Jan 2019, In : ACS synthetic biology. 8, 2, p. 216-222

Research output: Contribution to journalArticleAcademicpeer-review

Terminator Codon
Gene Silencing
Amino acids
Genes
Amino Acids

Inducible Fibril Formation of Silk-Elastin Diblocks

Willems, L., Roberts, S., Weitzhandler, I., Chilkoti, A., Mastrobattista, E., Van Der Oost, J. & De Vries, R., 23 May 2019, In : ACS Omega. 4, 5, p. 9135-9143 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Elastin
Silk
Block copolymers
Polymers
Tuning

Microbial Diversity and Organic Acid Production of Guinea Pig Faecal Samples

Palakawong Na Ayudthaya, S., van der Oost, H., van der Oost, J., van Vliet, D. M. & Plugge, C. M., Apr 2019, In : Current Microbiology. 76, 4, p. 425-434

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Poaceae
Guinea Pigs
Acids
formic acid
Starch
1 Citation (Scopus)

Multiplex genome editing of microorganisms using CRISPR-Cas

Adiego-Pérez, B., Randazzo, P., Daran, J. M., Verwaal, R., Roubos, J. A., Daran-Lapujade, P. & van der Oost, J., 14 May 2019, In : FEMS Microbiology Letters. 366, 8

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Gene Expression Regulation
Bacteria
Gene Editing
2018
6 Citations (Scopus)

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, S. J. A., Swarts, D. C., Zheng, P., Kunne, T., Mohanraju, P., Anders, C., Jinek, M., Van Der Oost, J., Dickman, M. J. & Brouns, S. J. J., 25 Jan 2018, In : Nucleic acids research. 46, 2, p. 873-885

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Bacteriophages
DNA
T-Phages
6 Citations (Scopus)

Complete Genome Sequence of Geobacillus thermodenitrificans T12, A Potential Host for Biotechnological Applications

Daas, T., Vriesendorp, B., van de Weijer, T., van der Oost, J. & van Kranenburg, R., Jan 2018, In : Current Microbiology. 75, 1, p. 49-56

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Geobacillus
Genome
Denitrification
Lactic Acid
Genes

Contribution of Eat1 and other alcohol acyltransferases to ester production in Saccharomyces cerevisiae

Kruis, A. J., Gallone, B., Jonker, T., Mars, A. E., van Rijswijck, I. M. H., Wolkers-Rooijackers, J. C. M., Smid, E. J., Steensels, J., Verstrepen, K. J., Kengen, S. W. M., van der Oost, J. & Weusthuis, R. A., 21 Dec 2018, In : Frontiers in Microbiology. 9, 11 p., 3202.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Acyltransferases
Saccharomyces cerevisiae
Esters
Transferases
Alcohols
10 Citations (Scopus)

Converting Escherichia coli into an archaebacterium with a hybrid heterochiral membrane

Caforio, A., Siliakus, M. F., Exterkate, M., Jain, S., Jumde, V. R., Andringa, R. L. H., Kengen, S. W. M., Minnaard, A. J., Driessen, A. J. M. & van der Oost, J., 3 Apr 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 14, p. 3704-3709

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Archaea
Escherichia coli
Lipids
Membranes
Membrane Lipids
1 Citation (Scopus)

Engineering Geobacillus thermodenitrificans to introduce cellulolytic activity; expression of native and heterologous cellulase genes

Daas, M. J. A., Nijsse, B., van de Weijer, A. H. P., Groenendaal, B. W. A. J., Janssen, F., van der Oost, J. & van Kranenburg, R., 27 Jun 2018, In : BMC Biotechnology. 18, 1, 42.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Geobacillus
Cellulase
Genes
Glucosides
Hydrolases
1 Citation (Scopus)

Mining for novel bacterial defence systems

Barrangou, R. & van der Oost, J., 30 Apr 2018, In : Nature Microbiology. 3, p. 535-536

Research output: Contribution to journalArticleAcademicpeer-review

Metagenomics
Plasmids
Viruses
Bacteria
Infection
9 Citations (Scopus)

Progress of CRISPR-Cas based genome editing in Photosynthetic microbes

Naduthodi, M. I. S., Barbosa, M. J. & van der Oost, J., Sep 2018, In : Biotechnology Journal. 13, 9

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Carbon Footprint
CRISPR-Cas Systems
Fossil Fuels
Metabolic Engineering
3 Citations (Scopus)

The alcohol acetyltransferase Eat1 is located in yeast mitochondria

Kruis, A. J., Mars, A. E., Kengen, S. W. M., Borst, J. W., van der Oost, J. & Weusthuis, R. A., Oct 2018, In : Applied and Environmental Microbiology. 84, 19, p. 1-11 e01640-18.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
acetyltransferases
Acetyltransferases
mitochondrion
yeast
alcohol
2017
35 Citations (Scopus)

Adaptations of archaeal and bacterial membranes to variations in temperature, pH and pressure

Siliakus, M. F., van der Oost, J. & Kengen, S. W. M., 2017, In : Extremophiles. 21, 4, p. 651-670

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Lipids
Pressure
Temperature
Membranes
Archaea
1 Citation (Scopus)

A growth- and bioluminescence-based bioreporter for the in vivo detection of novel biocatalysts

van Rossum, T., Muras, A., Baur, M. J. J., Creutzburg, S. C. A., van der Oost, J. & Kengen, S. W. M., 2017, In : Microbial Biotechnology. 10, 3, p. 625-641

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bioluminescence
Biocatalysts
Isomerases
Screening
Arabinose
16 Citations (Scopus)

Autonomous Generation and Loading of DNA Guides by Bacterial Argonaute

Swarts, D. C., Szczepaniak, M., Sheng, G., Chandradoss, S. D., Zhu, Y., Timmers, E. M., Zhang, Y., Zhao, H., Lou, J., Wang, Y., Joo, C. & van der Oost, J., 2017, In : Molecular Cell. 65, 6, p. 985-998

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Argonaute Proteins
Thermus thermophilus
Deoxycytidine
Deoxyguanosine
DNA
3 Citations (Scopus)

Biochemical characterization of the xylan hydrolysis profile of the extracellular endo-xylanase from Geobacillus thermodenitrificans T12

Daas, T., Martínez, P. M., van de Weijer, T., van der Oost, J., de Vos, W. M., Kabel, M. A. & van Kranenburg, R., 2017, In : BMC Biotechnology. 17, 1, 44.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Geobacillus
Xylans
Hydrolysis
Triticum
Enzymes
22 Citations (Scopus)

Characterizing a thermostable Cas9 for bacterial genome editing and silencing

Mougiakos, I., Mohanraju, P., Bosma, E. F., Vrouwe, V., Finger Bou, M., Naduthodi, M. I. S., Gussak, A., Brinkman, R. B. L., Van Kranenburg, R. & Van Der Oost, J., 1 Dec 2017, In : Nature Communications. 8, 1, 1647.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacterial Genomes
editing
genome
deletion
Clustered Regularly Interspaced Short Palindromic Repeats
13 Citations (Scopus)

Efficient Genome Editing of a Facultative Thermophile Using Mesophilic spCas9

Mougiakos, I., Bosma, E. F., Weenink, K., Vossen, E., Goijvaerts, K., van der Oost, J. & van Kranenburg, R., 2017, In : ACS synthetic biology. 6, 5, p. 849-861

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Streptococcus pyogenes
Genes
Gene Knockout Techniques
Insertional Mutagenesis
Gene Deletion
23 Citations (Scopus)

Ethyl acetate production by the elusive alcohol acetyltransferase from yeast

Kruis, A., Levisson, M., Mars, A. E., van der Ploeg, M., Garcés Daza, F., Ellena, V., Kengen, S. W. M., van der Oost, J. & Weusthuis, R. A., 2017, In : Metabolic Engineering. 41, p. 92-101

Research output: Contribution to journalArticleAcademicpeer-review

Acetyltransferases
Yeast
Alcohols
Yeasts
Saccharomyces cerevisiae
23 Citations (Scopus)

FnCpf1: a novel and efficient genome editing tool for Saccharomyces cerevisiae

Swiat, M. A., Dashko, S., den Ridder, M., Wijsman, M., van der Oost, J., Daran, J. M. & Daran-Lapujade, P., 1 Dec 2017, In : Nucleic acids research. 45, 21, p. 12585-12598

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Saccharomyces cerevisiae
Acidaminococcus
Francisella
Yeasts
5 Citations (Scopus)

Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms

Claassens, N. J., Siliakus, M. F., Spaans, S. K., Creutzburg, S. C. A., Nijsse, B., Schaap, P. J., Quax, T. E. F. & Van Der Oost, J., 2017, In : PLoS ONE. 12, 9, e0184355.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
codons
Codon
membrane proteins
Escherichia coli
Membrane Proteins
2 Citations (Scopus)

Monascus ruber as cell factory for lactic acid production at low pH

Weusthuis, R. A., Mars, A. E., Springer, J., Wolbert, E. J. H., van der Wal, H., de Vrije, T. G., Levisson, M., Leprince, A., Houweling-Tan, B., Moers, A., Hendriks, S. N. A., Mendes, O., Griekspoor, Y., Werten, M. W. T., Schaap, P. J., van der Oost, J. & Eggink, G., 2017, In : Metabolic Engineering. 42, p. 66-73

Research output: Contribution to journalArticleAcademicpeer-review

Monascus
Lactic acid
Industrial plants
Lactic Acid
Glucose
210 Citations (Scopus)

Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array

Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., Degennaro, E. M., Winblad, N., Choudhury, S. R., Abudayyeh, O. O., Wu, W. Y. & van der Oost, J., 2017, In : Nature Biotechnology. 35, 1, p. 31-34

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
RNA
Genes
Brain
Cells
5 Citations (Scopus)

Streptococcus caviae sp. nov., isolated from Guinea pig faecal samples

Palakawong Na Ayudthaya, S., Hilderink, L. J., van der Oost, J., de Vos, W. M. & Plugge, C. M., 2017, In : International Journal of Systematic and Evolutionary Microbiology. 67, 5, p. 1551-1556

Research output: Contribution to journalArticleAcademicpeer-review

Streptococcus
Poaceae
pig
guinea pigs
Guinea Pigs
71 Citations (Scopus)

Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a

Swarts, D. C., van der Oost, J. & Jinek, M., 2017, In : Molecular Cell. 66, 2, p. 221-233.e4

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Seeds
DNA
DNA Cleavage
2016
4 Citations (Scopus)

Complete genome sequence of thermophilic Bacillus smithii type strain DSM 4216T

Bosma, E. F., Koehorst, J. J., van Hijum, S. A. F. T., Renckens, B., Vriesendorp, B., van de Weijer, T., Schaap, P. J., de Vos, W. M., van der Oost, J. & van Kranenburg, R., 2016, In : Standards in Genomic Sciences. 11, 11 p., 52.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Nucleic Acid Databases
formate C-acetyltransferase
Bacillus
Acetates
Phosphate Acetyltransferase
19 Citations (Scopus)

CRISPR-Cas9 gene editing: Delivery aspects and therapeutic potential

Oude Blenke, E., Evers, M. J. W., Mastrobattista, E. & van der Oost, J., 2016, In : Journal of Controlled Release. 244, p. 139-148

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
CRISPR-Associated Proteins
Therapeutics
Nobel Prize
Inborn Genetic Diseases
202 Citations (Scopus)

Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems

Mohanraju, P., Makarova, K. S., Zetsche, B., Zhang, F., Koonin, E. V. & van der Oost, J., 2016, In : Science. 353, 6299, 14 p., aad5147.

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Adaptive Immunity
Parasites
Genome
43 Citations (Scopus)

Harnessing the power of microbial autotrophy

Claassens, N. J., Machado de Sousa, D., Martins dos Santos, V., de Vos, W. M. & van der Oost, J., 2016, In : Nature Reviews Microbiology. 14, p. 692-706

Research output: Contribution to journalArticleAcademicpeer-review

Autotrophic Processes
Light
Semiconductors
Genetic Engineering
Biofuels
108 Citations (Scopus)

Healthy human gut phageome

Manrique, P., Bolduc, B., Walk, S. T., van der Oost, J., de Vos, W. M. & Young, M. J., 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 37, p. 10400-10405

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Bacteriophages
Metagenomics
Microbiota
6 Citations (Scopus)

Integrated in silico analysis of pathway designs for synthetic photo-electro-autotrophy

Volpers, M., Claassens, N. J., Noor, E., van der Oost, J., de Vos, W. M., Kengen, S. W. M. & Martins dos Santos, V., 2016, In : PLoS ONE. 11, 6, e0157851.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Autotrophic Processes
Carbon Cycle
autotrophs
Computer Simulation
Calvin cycle
10 Citations (Scopus)

Isolation of a genetically accessible thermophilic xylan degrading bacterium from compost

Daas, T., van de Weijer, T., de Vos, W. M., van der Oost, J. & van Kranenburg, R., 2016, In : Biotechnology for Biofuels. 9, 210.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Xylans
Lactic acid
compost
Lactic Acid
Bacteria
7 Citations (Scopus)

Structural and biochemical characterisation of Archaeoglobus fulgidus esterase reveals a bound CoA molecule in the vicinity of the active site

Sayer, C., Finnigan, W., Isupov, M. N., Levisson, M., Kengen, S. W. M., van der Oost, J., Harmer, N. J. & Littlechild, J. A., 10 May 2016, In : Scientific Reports. 6, 25542.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Esterases
Coenzyme A
Molecules
Enzymes
Pantetheine
2015
12 Citations (Scopus)

Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry

Sharma, K., Hrle, A., Kramer, K., Sachsenberg, T., Staals, R. H. J., Randau, L., Marchfelder, A., van der Oost, J., Kohlbacher, O., Conti, E. & Urlaub, H., 2015, In : Methods : a companion to Methods in enzymology. 89, p. 138-148

Research output: Contribution to journalArticleAcademicpeer-review

Clustered Regularly Interspaced Short Palindromic Repeats
Mass spectrometry
Mass Spectrometry
RNA
Proteins
716 Citations (Scopus)

An updated evolutionary classification of CRISPR-Cas systems

Makarova, K. S., Wolf, Y. I., Alkhnbashi, O. S., Brouns, S. J. J. & Van Der Oost, J., 2015, In : Nature Reviews Microbiology. 13, 11, p. 722-736

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Archaea
Immune System
Bacteria
49 Citations (Scopus)

Argonaute of the archaeon Pyrococcus furiosus is a DNA-guided nuclease that targets cognate DNA

Swarts, D. C., Hegge, J. W., Hinojo, I., Shiimori, M., Ellis, M. A., Dumrongkulraksa, J., Terns, R. M., Terns, M. P. & Van Der Oost, J., 2015, In : Nucleic acids research. 43, 10, p. 5120-5129

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Pyrococcus furiosus
Deoxyribonucleases
Archaea
DNA
Guide RNA
12 Citations (Scopus)

Bacteriophage exclusion, a new defense system

Barrangou, R. & van der Oost, J., 2015, In : The EMBO Journal. 34, 2, p. 134-135

Research output: Contribution to journalArticleAcademicpeer-review

Bacteriophages
Clustered Regularly Interspaced Short Palindromic Repeats
Bacterial Genomes
Genes
DNA Restriction-Modification Enzymes
1 Citation (Scopus)

Beat their swords into ploughshares

van der Oost, J., 2015, In : Microbial Biotechnology. 8, 1, p. 34-35

Research output: Contribution to journalArticleAcademicpeer-review

Biotechnology
90 Citations (Scopus)

Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity

Charpentier, E., Richter, H., van der Oost, J. & White, M. F., 2015, In : FEMS Microbiology Reviews. 39, 3, p. 428-441

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
Guide RNA
Adaptive Immunity
CRISPR-Associated Proteins
RNA
183 Citations (Scopus)

Codon Bias as a Means to Fine-Tune Gene Expression

Quax, T. E. F., Claassens, N. J. H. P., Söll, D. & van der Oost, J., 2015, In : Molecular Cell. 59, 2, p. 149-161

Research output: Contribution to journalArticleAcademicpeer-review

Codon
Gene Expression
Synthetic Biology
Genetic Code
Proteins
1062 Citations (Scopus)

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

Zetsche, B., Gootenberg, JS., Abudayyeh, OO., Slaymaker, IM., Makarova, KS., Essletzbichler, P., Volz, SE., Joung, J., van der Oost, J., Regev, A., Koonin, EV. & Zhang, F., 2015, In : Cell. 163, 3, p. 759-771

Research output: Contribution to journalArticleAcademicpeer-review

CRISPR-Cas Systems
Clustered Regularly Interspaced Short Palindromic Repeats
Endonucleases
RNA
Acidaminococcus
2 Citations (Scopus)

CRISPR sabotage

van der Oost, J. & Brouns, S. J. J., 2015, In : Genome Biology. 16, 1, 248.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
Clustered Regularly Interspaced Short Palindromic Repeats
coevolution
CRISPR-Cas Systems
virus
Viruses