A5091175771- Chromosomal and Genetic Variations
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genomics and Phylogenetic Studies
- Bacteriophages and microbial interactions
- Bacterial Genetics and Biotechnology
- Genetic diversity and population structure
- CRISPR and Genetic Engineering
- Fungal Infections and Studies
- Genomics and Chromatin Dynamics
- Plant Pathogens and Fungal Diseases
- Plant Molecular Biology Research
- Plant Disease Resistance and Genetics
- Antifungal resistance and susceptibility
- Toxin Mechanisms and Immunotoxins
- Insect-Plant Interactions and Control
- Biochemical and Structural Characterization
- Evolution and Genetic Dynamics
University of California, San Francisco
2020-2025
University of California, Berkeley
2018-2022
Integra (United States)
2022
Mechanistic insights into the role of human microbiome in predisposition to and treatment disease are limited by lack methods precisely add or remove microbial strains genes from complex communities. Here, we demonstrate that engineered bacteriophage M13 can be used deliver DNA Escherichia coli within mouse gastrointestinal (GI) tract. Delivery a programmable exogenous CRISPR-Cas9 system enables strain-specific depletion fluorescently marked isogenic during competitive colonization genomic...
While short-read sequencing technology has resulted in a sharp increase the number of species with genome assemblies, these assemblies are typically highly fragmented. Repeats pose largest challenge for reference assembly, and pericentromeric regions repeat-rich Y chromosome ignored from projects. Here, we assemble Drosophila miranda using long reads contig formation, chromatin interaction maps scaffolding short reads, optical mapping bacterial artificial (BAC) clone consensus validation....
Centromeres are the basic unit for chromosome inheritance, but their evolutionary dynamics is poorly understood. We generate high-quality reference genomes multiple Drosophila obscura group species to reconstruct karyotype evolution. All chromosomes in this lineage were ancestrally telocentric and creation of metacentric some was driven by de novo seeding new centromeres at gene-rich regions, independently chromosomal rearrangements. The emergence resulted a drastic size increase due repeat...
We recently described CRISPR/Cas9-based short homology-dependent genome engineering in the human fungal pathogen Cryptococcus neoformans , a haploid budding yeast that is most common cause of meningitis and an emerging model organism. This was achieved by electroporation strains stably expressing codon-optimized Cas9 with two separate DNA molecules, one encoding selectable marker flanked homology arms second sgRNA under control U6 snRNA promoter. However, efficiency desired repair relative...
Abstract Cryptococcus neoformans is the top-ranked W.H.O. fungal priority pathogen, but tools for generating conditional mutations are limited. Auxin-inducible degron systems permit rapid and effective cellular depletion of a tagged protein interest upon adding small molecule. These invaluable, particularly studying essential genes, which may play important roles in pathogen biology. AID2 one such system that improves on previous strategies. This achieves greater sensitivity specificity...
Abstract The Drosophila nasuta species complex contains over a dozen recently diverged that are distributed widely across South-East Asia, and which shows varying degrees of pre- postzygotic isolation. Here, we assemble high-quality genome for D. albomicans using single-molecule sequencing chromatin conformation capture, draft genomes 11 additional 67 individuals the clade, to infer phylogeny patterns genetic diversity in this group. Our assembly recovers entire chromosomes, date origin...
Sex chromosomes play a special role in the evolution of reproductive barriers between species. Here we describe conflicting roles nascent sex on patterns introgression an experimental hybrid swarm. Drosophila nasuta and albomicans are recently diverged, fully fertile sister species that have different chromosome systems. The fusion autosome (Muller CD) with ancestral X Y gave rise to neo-sex D. albomicans, while Muller CD remains unfused nasuta. We found large block containing overlapping...
Mechanistic insights into the role of human microbiome in predisposition to and treatment disease are limited by lack methods precisely add or remove microbial strains genes from complex communities. Here, we demonstrate that engineered bacteriophage M13 can be used deliver DNA Escherichia coli within mouse gastrointestinal (GI) tract. Delivery a programmable exogenous CRISPR-Cas9 system enabled strain-specific depletion fluorescently marked isogenic during competitive colonization genomic...
While short-read sequencing technology has resulted in a sharp increase the number of species with genome assemblies, these assemblies are typically highly fragmented. Repeats pose largest challenge for reference assembly, and pericentromeric regions repeat-rich Y chromosome ignored from projects. Here, we assemble Drosophila miranda using long reads contig formation, chromatin interaction maps scaffolding short reads, optical mapping BAC clone consensus validation. Our assembly recovers...
Centromeres are the basic unit for chromosome inheritance, but their evolutionary dynamics is poorly understood. We generate high-quality reference genomes multiple Drosophila obscura group species to reconstruct karyotype evolution. All chromosomes in this lineage were ancestrally telocentric and creation of metacentric some was driven by de novo seeding new centromeres at gene-rich regions, independently chromosomal rearrangements. The emergence resulted a drastic size increase due repeat...
Abstract It is increasingly recognized that sex chromosomes are not only the “battlegrounds” between sexes, but also “Great Walls” fencing-off introgression diverging lineages. Here we describe conflicting roles of nascent on patterns in an experimental hybrid swarm. Drosophila nasuta and D. albomicans recently diverged, fully fertile sister species have different chromosome systems. The fusion autosome (Muller CD) with ancestral X Y gave rise to neo-sex , while Muller CDs remains unfused ....
Mechanistic insights into the role of human microbiome in predisposition to and treatment disease are limited by lack methods precisely add or remove microbial strains genes from complex communities. Here, we demonstrate that engineered bacteriophage M13 can be used deliver DNA Escherichia coli within mouse gastrointestinal (GI) tract. Delivery a programmable exogenous CRISPR-Cas9 system enabled strain-specific depletion fluorescently marked isogenic during competitive colonization genomic...