A5081784053- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- RNA modifications and cancer
- Plant Virus Research Studies
- Advanced biosensing and bioanalysis techniques
- Prion Diseases and Protein Misfolding
- Nanopore and Nanochannel Transport Studies
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Microfluidic and Capillary Electrophoresis Applications
- Insect symbiosis and bacterial influences
- Molecular Biology Techniques and Applications
- Vibrio bacteria research studies
- Innovation and Socioeconomic Development
Boston VA Research Institute
2024
Harvard University
2023-2024
Massachusetts Institute of Technology
2020-2023
University of California, Berkeley
2014-2017
Berkeley College
2014
In bacteria, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) DNA-targeting complex Cascade (CRISPR-associated for antiviral defense) uses CRISPR RNA (crRNA) guides to bind complementary DNA targets at sites adjacent a trinucleotide signature sequence called protospacer motif (PAM). The then recruits Cas3, nuclease-helicase that catalyzes unwinding and cleavage of foreign double-stranded (dsDNA) bearing matching crRNA. comprises CasA-E proteins one...
CRISPR-Cas adaptive immune systems protect bacteria and archaea against foreign genetic elements. In Escherichia coli, Cascade (CRISPR-associated complex for antiviral defense) is an RNA-guided surveillance that binds DNA recruits Cas3, a trans-acting nuclease helicase target degradation. Here, we use single-molecule imaging to visualize Cas3 binding targets. Our analysis reveals two distinct pathways dictated by the presence or absence of protospacer-adjacent motif (PAM). Binding...
Significance Cas9, a protein derived from the bacterial CRISPR/Cas9 immune system, relies on programmable single-guide RNA (sgRNA) to bind specific genomic sequences. Cas9 complexed with sgRNA readily binds on-target DNA, but models that can predict specificity of this process have proven elusive. To investigate system biophysical perspective, we applied massively parallel method for profiling protein–DNA interactions quantify nuclease-dead (dCas9) binding across thousands off-target We...
The profiling of gene expression by RNA sequencing (RNA-seq) has enabled powerful studies global transcriptional patterns in all organisms, including bacteria. Because the vast majority bacteria is rRNA, it standard practice to deplete rRNA from a total sample such that reads an RNA-seq experiment derive predominantly mRNA. One most commonly used commercial kits for depletion, Ribo-Zero kit Illumina, was recently discontinued abruptly and extended period time. Here, we report development...
Bacteria use diverse immunity mechanisms to defend themselves against their viral predators, bacteriophages. In turn, phages can acquire counter-defense systems, but it remains unclear how such arise and what factors constrain evolution. Here, we experimentally evolved T4 phage overcome a phage-defensive toxin-antitoxin system, toxIN, in Escherichia coli. Through recombination, rapidly acquires segmental amplifications of previously uncharacterized gene, now named tifA, encoding an inhibitor...
The bacterial adaptive immune system CRISPR-Cas9 has been appropriated as a versatile tool for editing genomes, controlling gene expression, and visualizing genetic loci 1 .To analyze Cas9's ability to bind DNA rapidly specifically, we measured the kinetics of catalytically dead Cas9 (dCas9) interactions with library potential binding partners.Using massively parallel assay protein-DNA derived from high-throughput sequencing flow cell (HiTS-FLIP) 2 building on established importance...
Summary Bacteria use diverse immunity mechanisms to defend themselves against their viral predators, bacteriophages. In turn, phages can acquire counter-defense systems, but it remains unclear how such arise and what factors constrain evolution. Here, we experimentally evolved T4 phage overcome a phage-defensive toxin-antitoxin system, toxIN , in E. coli . Through recombination, rapidly acquires segmental amplifications of previously uncharacterized gene, now named tifA encoding an inhibitor...
Abstract Bacteria harbor diverse mechanisms to defend themselves against their viral predators, bacteriophages. In response, phages can evolve counter-defense systems, most of which are poorly understood. T4-like phages, the gene tifA prevents bacterial defense by type III toxin–antitoxin (TA) system toxIN, but mechanism TifA inhibits ToxIN remains unclear. Here, we show that directly binds both endoribonuclease ToxN and RNA, leading formation a high molecular weight ribonucleoprotein...
Abstract The profiling of gene expression by RNA-sequencing (RNA-seq) has enabled powerful studies global transcriptional patterns in all organisms, including bacteria. Because the vast majority RNA bacteria is ribosomal (rRNA), it standard practice to deplete rRNA from a total sample such that reads an RNA-seq experiment derive predominantly mRNA. One most commonly used commercial kits for depletion, Ribo-Zero kit Illumina, was recently discontinued. Here, we report development simple,...