A5090046581- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Plant Virus Research Studies
- Salmonella and Campylobacter epidemiology
- Hypothalamic control of reproductive hormones
- Neuroendocrine regulation and behavior
- Neuropeptides and Animal Physiology
- Vibrio bacteria research studies
- Receptor Mechanisms and Signaling
- Bacterial Genetics and Biotechnology
- Viral Infections and Immunology Research
- Insect symbiosis and bacterial influences
- Autophagy in Disease and Therapy
- Digital Innovation in Industries
- Advanced biosensing and bioanalysis techniques
- Ubiquitin and proteasome pathways
- Neuroscience and Neuropharmacology Research
- Virus-based gene therapy research
- Microbial infections and disease research
- Pharmacological Receptor Mechanisms and Effects
- Microbial Community Ecology and Physiology
- RNA modifications and cancer
- Viral gastroenteritis research and epidemiology
University of California, Berkeley
2018-2025
QB3
2021-2025
Innovative Genomics Institute
2020-2025
Howard Hughes Medical Institute
2024
Montana State University
2023
Lawrence Berkeley National Laboratory
2023
National Alliance on Mental Illness
2015
Rice University
2013
Adler
2005
Microsharp (United Kingdom)
2001
Abstract CRISPR-Cas13 proteins are RNA-guided RNA nucleases that defend against incoming and DNA phages by binding to complementary target phage transcripts followed general, non-specific degradation. Here we analysed the defensive capabilities of LbuCas13a from Leptotrichia buccalis found it have robust antiviral activity unaffected gene essentiality, expression timing or sequence location. Furthermore, find be broadly effective a wide range challenging nine E. coli diverse phylogenetic...
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities drive processes as diverse global biogeochemical cycles human health. Phages tend to be predators finely tuned attack specific hosts, even down strain level, which turn defend themselves using an array mechanisms. However, date, efforts rapidly comprehensively identify bacterial host factors important phage infection resistance have yet fully realized. Here, we globally map genetic determinants...
Abstract CRISPR-Cas12a is an RNA-guided, programmable genome editing enzyme found within bacterial adaptive immune pathways. Unlike CRISPR-Cas9, Cas12a uses only a single catalytic site to both cleave target double-stranded DNA (dsDNA) (cis-activity) and indiscriminately degrade single-stranded (ssDNA) (trans-activity). To investigate how the relative potency of cis- versus trans-DNase activity affects Cas12a-mediated editing, we first used structure-guided engineering generate variants...
Abstract Large-genome bacteriophages (jumbo phages) of the proposed family Chimalliviridae assemble a nucleus-like compartment bounded by protein shell that protects replicating phage genome from host-encoded restriction enzymes and DNA-targeting CRISPR-Cas nucleases. While nuclear provides broad protection against host nucleases, it necessitates transport mRNA out for translation ribosomes, specific proteins into to support DNA replication transcription. Here, we identify conserved...
Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes a nucleus-like replication compartment composed of protein chimallin (ChmA) excludes ribosomes decouples transcription from translation. These selectively partition between phage nucleus bacterial cytoplasm. Currently, genes signals govern selective import into are unknown. Here, we identify two components this...
Recent evidence suggests that γ-aminobutyric acid (GABA)-containing neurons may inhibit LH release under certain circumstances. The present experiments tested whether GABA agonists block the surge induced in ovariectomized rats by estradiol benzoate (EB) plus progesterone (P) treatment and these agents affect concentration turnover of hypothalamic catecholamines, assessed from depletion occurs after synthesis inhibition. Ovariectomized received EB, followed 2 days later P. Simultaneously...
Recent pharmacological studies have suggested a role for neuropeptide Y (NPY) in control of LH secretion. The present study examined the effects estradiol benzoate (EB) given alone or combination with progesterone (P), on concentrations immunoreactive NPY microdissected nuclei rat brain, association changes LHRH and release. Forty-eight hours after administration EB to ovariectomized rats, serum was significantly reduced. Concentrations NPY, measured by sensitive specific RIA, were also...
Many eukaryotic viruses require membrane-bound compartments for replication, but no such organelles are known to be formed by prokaryotic
RNA-guided endonucleases form the crux of diverse biological processes and technologies, including adaptive immunity, transposition, genome editing. Some these enzymes are components insertion sequences (IS) in IS200/IS605 IS607 transposon families. Both IS families encode a TnpA transposase TnpB nuclease, an enzyme ancestral to CRISPR-Cas12s. In eukaryotes, homologs occur as two distinct types, Fanzor1s Fanzor2s. We analyzed evolutionary relationships between prokaryotic TnpBs eukaryotic...
Abstract Bacteriophages constitute one of the largest sources unknown gene content in biosphere. Even for well-studied model phages, robust experimental approaches to identify and study their essential genes remain elusive. We uncover exploit conserved vulnerability phage transcriptome facilitate genome-wide protein expression knockdown via programmable RNA-binding dRfxCas13d (CRISPRi-ART) across diverse phages host. Establishing first broad-spectrum functional genomics platform, we predict...
Hachiman is a broad-spectrum antiphage defense system of unknown function. We show here that comprises heterodimeric nuclease-helicase complex, HamAB. HamA, previously protein function, the effector nuclease. HamB sensor helicase. constrains HamA activity during surveillance intact dsDNA. When HamAB complex detects DNA damage, helicase liberates unleashing nuclease activity. activation degrades all in cell, creating ‘phantom’ cells devoid both phage and host DNA. demonstrate absence by...
Results from previous investigations have suggested an important role for central epinephrine (EPI) systems in mediating the stimulatory effects of ovarian hormones on LH release ovariectomized female rats. The purpose these experiments was 1) to test whether selective inhibition EPI synthesis blocks sequential accumulation and decline LHRH concentrations median eminence that precedes hormone-induced surge 2) hormone regimen enhances activity hypothalamus. Ovariectomized rats were treated...
CRISPR-Cas systems provide bacteria and archaea with programmable immunity against mobile genetic elements. Evolutionary pressure by has driven bacteriophage to evolve small protein inhibitors, anti-CRISPRs (Acrs), that block Cas enzyme function wide-ranging mechanisms. We show here the inhibitor AcrVA4 uses a previously undescribed strategy recognize
Though bacteriophages (phages) are known to play a crucial role in bacterial fitness and virulence, our knowledge about the genetic basis of their interaction, cross-resistance host-range is sparse. Here, we employed genome-wide screens Salmonella enterica serovar Typhimurium discover host determinants involved resistance eleven diverse lytic phages including four new isolated from therapeutic phage cocktail. We uncovered 301 factors essential infection, many which shared between multiple...
Abstract Single-strand RNA (ssRNA) Fiersviridae phages cause host lysis with a product of single gene ( sgl for single-gene lysis; Sgl) that induces autolysis. Many different Sgls have been discovered, but the molecular targets only few identified. In this study, we used high-throughput genetic screen to uncover genome-wide suppressors diverse Sgls. addition validating known mechanisms, discovered Sgl PP7, an ssRNA phage Pseudomonas aeruginosa , MurJ, flippase responsible lipid II export,...
Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated (Cas9, Cas12 Cas13 families), have been deployed numerous research, clinical agricultural applications. However, immense genetic biochemical diversity of these proteins in public domain poses a barrier researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), Cas Protein...
Abstract Genome editing is transforming plant biology by enabling precise DNA modifications. However, delivery of systems into plants remains challenging, often requiring slow, genotype-specific methods such as tissue culture or transformation. Plant viruses, which naturally infect and spread to most tissues, present a promising system for reagents. But viruses have limited cargo capacities, restricting their ability carry large CRISPR-Cas systems. Here, we engineered tobacco rattle virus...
Abstract Bacteriophages constitute one of the largest reservoirs genes unknown function in biosphere. Even well-characterized phages, functions most remain unknown. Experimental approaches to study phage gene fitness and at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d selectively interfere with protein translation measure a transcriptome-wide scale. We find CRISPR Interference through Antisense...
Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signaling that share mechanistic features with human anti-viral systems. In these pathways, including CBASS type III CRISPR systems in bacteria cGAS-STING humans, synthesis occurs upon detection of virus or foreign genetic material the cell, triggering antiviral response. a surprising inversion this process, we show here CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as...
The analgesic potency and toxicity (lethality) of morphine were increased 2.5 times after implantation 7.5-mg s.c. naltrexone pellets in the mouse for 8 days. Implantation days also resulted a 41% [3H][D-Ala2-D-Leu5]enkephalin 55% [3H] [D-Ala2-MePhe4-Gly(ol)5]enkephalin increase radiolabeled opioid binding brain relative to placebo-implanted controls. Treatment 1 day did not produce any significant increases or morphine's potency. Brain concentrations differ dose (8 mg/kg) that produced...
Previous studies have shown that the stimulation of LH release by opiate receptor blocker, naloxone, can be prevented catecholamine synthesis inhibitors, suggesting regulation release. The present study tested whether an agonist and antagonist would affect depletion hypothalamic catecholamines observed after inhibition, as a measure activity, concomitant with changes in secretion. Administration naloxone to estradiol-primed rats increased potentiated norepinephrine preoptic-anterior...
The RNA-guided ribonuclease CRISPR-Cas13 enables adaptive immunity in bacteria and programmable RNA manipulation heterologous systems. Cas13s share limited sequence similarity, hindering discovery of related or ancestral To address this, we developed an automated structural-search pipeline to identify clade Cas13 (Cas13an) further trace origins defense-associated ribonucleases. Despite being one-third the size other Cas13s, Cas13an mediates robust depletion defense against diverse...