A5008617222- CRISPR and Genetic Engineering
- Fungal Infections and Studies
- SARS-CoV-2 detection and testing
- SARS-CoV-2 and COVID-19 Research
- Immune Cell Function and Interaction
- Respiratory viral infections research
- Animal Virus Infections Studies
- Phytoplasmas and Hemiptera pathogens
- Plant Pathogens and Fungal Diseases
- Biosensors and Analytical Detection
- RNA regulation and disease
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Infectious Diseases and Mycology
- Viral Infections and Outbreaks Research
- Mycorrhizal Fungi and Plant Interactions
- interferon and immune responses
University of California, San Francisco
2020-2024
Gladstone Institutes
2023-2024
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across world and effectively evaded immune responses, its viral fitness in cell animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent genomes is challenging because length genome (~30 kb). Here, we present a plasmid-based assembly rescue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons single ligation reaction with...
Abstract As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that recapitulate the cell-intrinsic response arising viral variants are needed. Here we describe an adult stem cell-derived human organoid model overexpressing ACE2 receptor (ACE2-OE) supports robust replication while maintaining 3D architecture and cellular diversity of epithelium. ACE2-OE organoids were infected with subjected single-cell RNA-sequencing. Interferon-lambda was upregulated in cells...
The COVID-19 pandemic has been driven by SARS-CoV-2 variants with enhanced transmission and immune escape. Apart from extensive evolution in the Spike protein, non-Spike mutations are accumulating across entire viral genome their functional impact is not well understood. To address contribution of these mutations, we reconstructed genomes recent Omicron disabled expression (replicons) to systematically compare RNA replication capabilities independently Spike. We also used a single reference...
The COVID-19 pandemic has been driven by SARS-CoV-2 variants with enhanced transmission and immune escape. Apart from extensive evolution in the Spike protein, non-Spike mutations are accumulating across entire viral genome their functional impact is not well understood. To address contribution of these mutations, we reconstructed genomes recent Omicron disabled expression (replicons) to systematically compare RNA replication capabilities independently Spike. We also used a single reference...
Histoplasma is a primary fungal pathogen with the ability to infect otherwise healthy mammalian hosts, causing systemic and sometimes life-threatening disease. Thus far, molecular genetic manipulation of this organism has utilized RNA interference, random insertional mutagenesis, homologous recombination protocol that highly variable often inefficient. Targeted gene manipulations have been challenging due poor rates events in Histoplasma. Interrogation virulence strategies would be...
Although the SARS-CoV-2 Omicron variant (BA.1) spread rapidly across world and effectively evaded immune responses, its viral fitness in cell animal models was reduced. The precise nature of this attenuation remains unknown as generating replication-competent genomes is challenging because length genome (30kb). Here, we designed a plasmid-based assembly resc ue strategy (pGLUE) that constructs complete infectious viruses or noninfectious subgenomic replicons single ligation reaction with...
Abstract As SARS-CoV-2 continues to spread worldwide, tractable primary airway cell models that accurately recapitulate the cell-intrinsic response arising viral variants are needed. Here we describe an adult stem cell-derived human organoid model overexpressing ACE2 receptor supports robust replication while maintaining 3D architecture and cellular diversity of epithelium. ACE2-OE organoids were infected with subjected single-cell RNA-sequencing. NF-κB inhibitor alpha was consistently...
Next generation sequencing has unlocked a wealth of genotype information for microbial populations, but phenotyping remains bottleneck exploiting this information, particularly pathogens that are difficult to manipulate. Here, we establish method high-throughput mixed cultures, in which the pattern naturally occurring single-nucleotide polymorphisms each isolate is used as intrinsic barcodes can be read out by sequencing. We demonstrate our correctly deconvolute strain proportions simulated...
Abstract Coccidioides spp . are highly understudied but significant dimorphic fungal pathogens that can infect both immunocompetent and immunocompromised people. In the environment, they grow as multicellular filaments (hyphae) produce vegetative spores called arthroconidia. Upon inhalation by mammals, arthroconidia undergo a process spherulation. They enlarge numerous nuclear divisions to form spherical structure, then internally segment until spherule is filled with multiple cells...
Targeted gene disruption is challenging in the dimorphic fungal pathogen Histoplasma due to low frequency of homologous recombination. Transformed DNA either integrated ectopically into genome or maintained extra chromosomally by de novo addition telomeric sequences. Based on a system developed Blastomyces, we adapted CRISPR/Cas9 facilitate targeted with high efficiency. We express codon-optimized version Cas9 as well guide RNAs from single ectopic vector carrying selectable marker. Once...