A5005439170- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Insect symbiosis and bacterial influences
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Gene Regulatory Network Analysis
- Vibrio bacteria research studies
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
Delft University of Technology
2017-2022
Institute for Atomic and Molecular Physics
2021-2022
University of Otago
2014-2016
Clustered regularly interspaced short palindromic repeats (CRISPR), in combination with CRISPR associated (cas) genes, constitute CRISPR-Cas bacterial adaptive immune systems. To generate immunity, these systems acquire sequences of nucleic acids from foreign invaders and incorporate into their arrays as spacers. This adaptation process is the least characterized step immunity. Here, we used Pectobacterium atrosepticum to investigate Type I-F Pre-existing spacers that matched plasmids...
CRISPR-Cas systems adapt their immunological memory against invaders by integrating short DNA fragments into clustered regularly interspaced palindromic repeat (CRISPR) loci. While Cas1 and Cas2 make up the core machinery of CRISPR integration process, various class I II encode Cas4 proteins for which role is unknown. Here, we introduced adaptation genes cas1, cas2, cas4 from type I-D system Synechocystis sp. 6803 Escherichia coli observed that strictly required selection targets with...
Microbes have the unique ability to acquire immunological memories from mobile genetic invaders protect themselves predation. To confer CRISPR resistance, new spacers need be compatible with a targeting requirement in invader's DNA called protospacer adjacent motif (PAM). Many systems encode Cas4 proteins ensure are integrated that meet this prerequisite. Here we report gene fusion between cas4 and cas1 Geobacter sulfurreducens I-U CRISPR–Cas system is capable of introducing functional...
The last decade has witnessed a remarkable increase in our ability to measure genetic information. Advancements of sequencing technologies are challenging the existing methods data storage and analysis. While cope with deluge progressing, many biologists have lagged behind due fast pace computational advancements tools available address their scientific questions. Future generations must be more computationally aware capable. This means they should trained give them skills keep technological...
Prokaryotes use primed CRISPR adaptation to update their memory bank of spacers against invading genetic elements that have escaped interference through mutations in protospacer target site. We previously observed a trend nucleotide-dependent mismatches between crRNA and the strongly influence efficiency adaptation. Here we show guanine-substitutions strand are highly detrimental interference-dependent priming, while cytosine-substitutions more readily tolerated. Furthermore, this effect is...
CRISPR-Cas systems are adaptive immune in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers used interference stage to guide effector associated (Cas) protein(s) target complementary invading Cas1 integrase enzyme central catalysis of spacer integration. There many diverse types systems, including type I-F which...
Abstract CRISPR-Cas defence is a combination of adaptation to new invaders by spacer acquisition, and interference targeted nuclease activity. While these processes have been studied on population level, the individual cellular variability has remained unknown. Here, using microfluidic device combined with time-lapse microscopy, we monitor invader clearance in Escherichia coli across multiple generations. We observed that CRISPR fast narrow distribution times. In contrast, for escaping PAM...