Chase L. Beisel
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View article: An updated evolutionary classification of CRISPR–Cas systems including rare variants
An updated evolutionary classification of CRISPR–Cas systems including rare variants Open
The known diversity of CRISPR–Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR–Cas systems. The updated CRISPR–Cas classification includes 2 classes, 7 types an…
View article: YprA family helicases provide the missing link between diverse prokaryotic immune systems
YprA family helicases provide the missing link between diverse prokaryotic immune systems Open
Bacteria and archaea possess an enormous variety of antivirus immune systems that often share homologous proteins and domains, some of which contribute to diverse defense strategies. YprA family helicases are central to widespread defense …
View article: Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes Open
Base editors create precise genomic edits by directing nucleobase deamination or removal without inducing double-stranded DNA breaks. However, a vast chemical space of other DNA modifications remains to be explored for genome editing. Here…
View article: PAM-interacting domain turn-helix 51 motifs can improve Cas9–SpRY activity
PAM-interacting domain turn-helix 51 motifs can improve Cas9–SpRY activity Open
Cas9–SpRY is an engineered variant of the Streptococcus pyogenes Cas9 with relaxed PAM recognition, which can technically be utilized at any target in the genome but some targets are addressed with low efficiency. Here, we show that a prev…
View article: Efficient encapsulation of CRISPR-Cas9 RNP in bioreducible nanogels and release in a cytosol-mimicking environment
Efficient encapsulation of CRISPR-Cas9 RNP in bioreducible nanogels and release in a cytosol-mimicking environment Open
CRISPR/Cas9-mediated programmable gene editing has disrupted the biotechnology industry since it was first described in 2012. Safe in vivo delivery is a key bottleneck for its therapeutic use. Viral vector-mediated delivery raises concerns…
View article: Comprehensive Analysis of CRISPR Array Repeat Mutations Reveals Subtype-Specific Patterns and Links to Spacer Dynamics
Comprehensive Analysis of CRISPR Array Repeat Mutations Reveals Subtype-Specific Patterns and Links to Spacer Dynamics Open
CRISPR–Cas systems are adaptive immune mechanisms in bacteria and archaea that protect against invading genetic elements by integrating short fragments of foreign DNA into CRISPR arrays. These arrays consist of repetitive sequences intersp…
View article: Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system
Streamlined and efficient genome editing in Cupriavidus necator H16 using an optimised SIBR-Cas system Open
Cupriavidus necator H16 is a promising microbial platform strain for CO2 valorisation. While C. necator is amenable to genome editing, existing tools are often inefficient or rely on lengthy protocols, hindering its rapid transi…
View article: RNA-triggered CRISPR-Cas12a2 Preferentially and Cooperatively Cleaves Collateral DNA
RNA-triggered CRISPR-Cas12a2 Preferentially and Cooperatively Cleaves Collateral DNA Open
CRISPR-Cas systems often rely on collateral cleavage activities against nucleic-acid substrates to combat recognized mobile genetic elements. Of the associated RNA-guided Cas effector nucleases, Cas12a2 stands out as the only known example…
View article: Disparate mechanisms counteract extraneous CRISPR RNA production in type II-C CRISPR-Cas systems
Disparate mechanisms counteract extraneous CRISPR RNA production in type II-C CRISPR-Cas systems Open
CRISPR-Cas adaptive immune systems in bacteria and archaea enable precise targeting and elimination of invading genetic elements. An inherent feature of these systems is the ‘extraneous’ CRISPR RNA (ecrRNA), which is produced via the extra…
View article: YprA Family Helicases Provide the Missing Link Between Diverse Prokaryotic Immune Systems
YprA Family Helicases Provide the Missing Link Between Diverse Prokaryotic Immune Systems Open
View article: Cas9-independent tracrRNA cytotoxicity in <i>Lacticaseibacillus paracasei</i>
Cas9-independent tracrRNA cytotoxicity in <i>Lacticaseibacillus paracasei</i> Open
CRISPR-Cas9 systems are widely used for bacterial genome editing, yet their heterologous expression has been associated with cytotoxicity. The Cas9 nuclease from Streptococcus pyogenes (SpyCas9) has been one common source, with reports of …
View article: Streamlined and efficient genome editing in<i>Cupriavidus necator</i>H16 using an optimised SIBR-Cas system
Streamlined and efficient genome editing in<i>Cupriavidus necator</i>H16 using an optimised SIBR-Cas system Open
Cupriavidus necator H16 is a promising microbial platform strain for CO 2 valorisation. While C. necator is amenable to genome editing, existing tools are often inefficient or rely on lengthy protocols, hindering its rapid transition to in…
View article: Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes
Targeted DNA ADP-ribosylation triggers templated repair in bacteria and base mutagenesis in eukaryotes Open
Base editors create precise genomic edits by directing nucleobase deamination or removal without inducing double-stranded DNA breaks. However, a vast chemical space of other DNA modifications remains to be explored for genome editing. Here…
View article: AcrVIB1 inhibits CRISPR-Cas13b immunity by promoting unproductive crRNA binding accessible to RNase attack
AcrVIB1 inhibits CRISPR-Cas13b immunity by promoting unproductive crRNA binding accessible to RNase attack Open
SUMMARY Anti-CRISPR proteins (Acrs) inhibit CRISPR-Cas immune defenses, with almost all known Acrs acting on the Cas nuclease-CRISPR (cr)RNA ribonucleoprotein (RNP) complex. Here, we show that AcrVIB1, the only known Acr against Cas13b, pr…
View article: Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory
Ten Years of the Synthetic Biology Summer Course at Cold Spring Harbor Laboratory Open
The Cold Spring Harbor Laboratory (CSHL) Summer Course on Synthetic Biology, established in 2013, has emerged as a premier platform for immersive education and research in this dynamic field. Rooted in CSHL's rich legacy of biological disc…
View article: Phages to the rescue: in situ editing of the gut microbiota
Phages to the rescue: in situ editing of the gut microbiota Open
The gut microbiome contains numerous bacteria tied to our health. However, genetically modifying this community remains a major challenge. Brödel et al. take a critical step by engineering bacteriophages to efficiently deliver gene editors…
View article: MprF-mediated immune evasion is necessary for Lactiplantibacillus plantarum resilience in the Drosophila gut during inflammation
MprF-mediated immune evasion is necessary for Lactiplantibacillus plantarum resilience in the Drosophila gut during inflammation Open
Multiple peptide resistance factor (MprF) confers resistance to cationic antimicrobial peptides (AMPs) in several pathogens, thereby enabling evasion of the host immune response. The role of MprF in commensals remains, however, uncharacter…
View article: Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins
Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins Open
View article: TracrRNA reprogramming enables direct PAM-independent detection of RNA with diverse DNA-targeting Cas12 nucleases
TracrRNA reprogramming enables direct PAM-independent detection of RNA with diverse DNA-targeting Cas12 nucleases Open
View article: A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria
A cell-free transcription-translation pipeline for recreating methylation patterns boosts DNA transformation in bacteria Open
The bacterial world offers diverse strains for understanding medical and environmental processes and for engineering synthetic biological chassis. However, genetically manipulating these strains has faced a long-standing bottleneck: how to…
View article: Systematic interrogation of CRISPR antimicrobials in <i>Klebsiella pneumoniae</i> reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity
Systematic interrogation of CRISPR antimicrobials in <i>Klebsiella pneumoniae</i> reveals nuclease-, guide- and strain-dependent features influencing antimicrobial activity Open
CRISPR-Cas systems can be utilized as programmable-spectrum antimicrobials to combat bacterial infections. However, how CRISPR nucleases perform as antimicrobials across target sites and strains remains poorly explored. Here, we address th…
View article: Expanding the flexibility of base editing for high-throughput genetic screens in bacteria
Expanding the flexibility of base editing for high-throughput genetic screens in bacteria Open
Genome-wide screens have become powerful tools for elucidating genotype-to-phenotype relationships in bacteria. Of the varying techniques to achieve knockout and knockdown, CRISPR base editors are emerging as promising options. However, th…
View article: An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between <i>Klebsiella</i> species
An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between <i>Klebsiella</i> species Open
Cas9-based gene editing tools have revolutionized genetics, enabling the fast and precise manipulation of diverse bacterial species. However, widely applicable genetic tools for non-model gut bacteria are unavailable. Here, we present a tw…
View article: A Hitchhiker’s guide to CRISPR editing tools in bacteria
A Hitchhiker’s guide to CRISPR editing tools in bacteria Open
View article: CRISPR-based screening of small RNA modulators of bile susceptibility in <i>Bacteroides thetaiotaomicron</i>
CRISPR-based screening of small RNA modulators of bile susceptibility in <i>Bacteroides thetaiotaomicron</i> Open
Microbiota-centric interventions are limited by our incomplete understanding of the gene functions of many of its constituent species. This applies in particular to small RNAs (sRNAs), which are emerging as important regulators in microbio…
View article: Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins
Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins Open
Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challe…
View article: Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration
Improved prediction of bacterial CRISPRi guide efficiency from depletion screens through mixed-effect machine learning and data integration Open
CRISPR interference (CRISPRi) is the leading technique to silence gene expression in bacteria; however, design rules remain poorly defined. We develop a best-in-class prediction algorithm for guide silencing efficiency by systematically in…
View article: MprF-mediated immune evasion is necessary for<i>Lactiplantibacillus plantarum</i>resilience in<i>Drosophila</i>gut during inflammation
MprF-mediated immune evasion is necessary for<i>Lactiplantibacillus plantarum</i>resilience in<i>Drosophila</i>gut during inflammation Open
Background Multiple peptide resistance factor (MprF) confers resistance to cationic antimicrobial peptides (AMPs) in several pathogens, thereby enabling evasion of the host immune response. While MprF has been proven to be crucial for the …
View article: Interrogating two extensively self-targeting Type I CRISPR-Cas systems in <i>Xanthomonas albilineans</i> reveals distinct anti-CRISPR proteins that block DNA degradation
Interrogating two extensively self-targeting Type I CRISPR-Cas systems in <i>Xanthomonas albilineans</i> reveals distinct anti-CRISPR proteins that block DNA degradation Open
CRISPR-Cas systems store fragments of invader DNA as spacers to recognize and clear those same invaders in the future. Spacers can also be acquired from the host's genomic DNA, leading to lethal self-targeting. While self-targeting can be …
View article: An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between<i>Klebsiella</i>species
An adapted method for Cas9-mediated editing reveals the species-specific role of β-glucoside utilization driving competition between<i>Klebsiella</i>species Open
Cas9-based gene editing tools have revolutionized genetics, enabling the fast and precise manipulation of diverse bacterial species. However, widely applicable genetic tools for non-model gut bacteria are unavailable. Here, we present a tw…