A5025099474- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- Fungal and yeast genetics research
- Evolution and Genetic Dynamics
- Cancer-related gene regulation
- Genomics and Chromatin Dynamics
- RNA regulation and disease
- Bioinformatics and Genomic Networks
- Polyamine Metabolism and Applications
- Single-cell and spatial transcriptomics
- Insect Resistance and Genetics
- Plant and Fungal Interactions Research
- Peptidase Inhibition and Analysis
- Bacterial Genetics and Biotechnology
- Microwave Engineering and Waveguides
- Genetic Associations and Epidemiology
- Adenosine and Purinergic Signaling
- Nanoparticles: synthesis and applications
- Insect-Plant Interactions and Control
- Bacterial biofilms and quorum sensing
- Graphene and Nanomaterials Applications
- Genomics and Rare Diseases
- Pluripotent Stem Cells Research
Stanford University
2017-2024
University of Auckland
2024
New York Genome Center
2023
University of California, Los Angeles
2011-2023
Material Measurement Laboratory
2018
National Institute of Standards and Technology
2018
University of Manchester
2007
Copper formulations have been used for decades antimicrobial and antifouling applications. With the development of nanoformulations copper that are more effective than their ionic microsized analogues, a key regulatory question is whether these materials should be treated as new or existing materials. To address this issue, here we compare magnitude mechanisms toxicity series Cu species (at concentration ranging from 2 to 250 μg/mL), including nano Cu, CuO, Cu(OH)2 (CuPro Kocide), micro Cu2+...
Antimicrobial resistance (AMR) is spreading worldwide and keeps evolving to adapt antibiotics, causing increasing threats in clinics, which necessitates the exploration of antimicrobial agents for not only killing resistant cells but also prevention AMR progression. However, so far, there has been no effective approach. Herein, we designed lanthanum hydroxide graphene oxide nanocomposites (La@GO) confer a synergistic bactericidal effect all tested strains. More importantly, long-term...
In diploid species, genetic loci can show additive, dominance, and epistatic effects. To characterize the contributions of these different types effects to heritable traits, we use a double barcoding system generate phenotype panel ~200,000 yeast strains that be partitioned into hundreds interrelated families. This experiment enables detection thousands loci, many whose vary across Here, traits are largely specified by small number hub with major additive dominance effects, pervasive...
The low costs of array-synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, lack access to individual oligonucleotides limit the true potential these libraries. We have developed a cost-effective method called Recombinase Directed Indexing (REDI), which involves integration complex library into yeast, site-specific recombination index DNA, next-generation sequencing identify...
Abstract We present Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a scalable platform producing autologous organotypic iPS cell-derived induced skin composite (iSC) grafts for definitive treatment. Clinical-grade manufacturing integrates CRISPR-mediated genetic correction with reprogramming into one step, accelerating derivation of COL7A1 -edited cells from patients. Differentiation epidermal, dermal and melanocyte progenitors is followed by CD49f-enrichment, minimizing maturation...
RNA polymerase II (Pol II) transcription termination by the Nrd1p-Nab3p-Sen1p (NNS) pathway is critical for production of stable noncoding RNAs and control pervasive in Saccharomyces cerevisiae To uncover determinants NNS termination, we mapped 3'-ends NNS-terminated transcripts genome-wide. We found that nucleosomes specific DNA-binding proteins, including general regulatory factors (GRFs) Reb1p, Rap1p, Abf1p, Pol III enhance efficiency physically blocking progression. The same DNA-bound...
Large scale perturbation of gene expression in yeast using CRISPR libraries, coupled with high-throughput screening fluorescence-based sorting microfluidic droplets, to identify genes important for increased α-amylase secretion.
Histidine protein methylation is an unusual posttranslational modification. In the yeast Saccharomyces cerevisiae, large ribosomal subunit Rpl3p methylated at histidine 243, a residue that contacts 25S rRNA near P site. dependent upon presence of Hpm1p, candidate seven-beta-strand methyltransferase. this study, we elucidated biological activities Hpm1p in vitro and vivo. Amino acid analyses reveal responsible for all detectable yeast. The modification found on polypeptide corresponding to...
Rpl3, a highly conserved ribosomal protein, is methylated at histidine 243 by the Hpm1 methyltransferase in Saccharomyces cerevisiae . Histidine lies close to peptidyl transferase center functionally important region of Rpl3 designated as basic thumb that coordinates decoding, transfer, and translocation steps translation elongation. was recently implicated ribosome biogenesis translation. However, biological role methylation its substrate has not been identified. Here we interrogate H243...
Summary Background Gene editing in induced pluripotent stem (iPS) cells has been hailed to enable new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa (DEB). However, manufacturing, efficacy and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. Methods We developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a generation GMP-compatible (cGMP), reproducible, scalable platform...
Abstract Interactions between genetic perturbations and segregating loci can cause to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing measure the fitness of 8046 CRISPRi targeting 1721 genes 169 yeast cross progeny (or segregants). We identified 460 whose perturbation has segregants. Several factors caused variable effects, including baseline segregant...
The fidelity of splice site selection is critical for proper gene expression. In particular, recognition 3'-splice (3'SS) sequences by the spliceosome challenging considering low complexity 3'SS consensus sequence YAG. Here, we show that absence Prp18p splicing factor results in genome-wide activation alternative S. cerevisiae, including highly unusual non-YAG sequences. Usage these non-canonical enhanced upstream poly(U) tracts and their potential to interact with first intronic nucleoside,...
Bromodomain proteins are key regulators of gene expression. How the levels these factors regulated in specific environmental conditions is unknown. Previous work has established that expression yeast factor 2 (BDF2) limited by spliceosome-mediated decay (SMD). Here we show BDF2 subject to an additional layer post-transcriptional control through RNase III-mediated (RMD). We found III Rnt1p cleaves a stem-loop structure within mRNA down-regulate its However, two nuclear RNA degradation...
Methylation of various components the translational machinery has been shown to globally affect protein synthesis. Little is currently known about role lysine methylation on elongation factors. Here we show that in Saccharomyces cerevisiae, product EFM3/YJR129C gene responsible for trimethylation 509 factor 2. Deletion EFM3 or previously described EFM2 increases sensitivity antibiotics target translation and decreases fidelity. Furthermore, amino acid sequences Efm3 Efm2, as well their...
3'-end poly(A)+ sequencing is an efficient and economical method for global measurement of mRNA levels alternative poly(A) site usage. A common involves oligo(dT)19V reverse-transcription (RT)-based library preparation high-throughput with a custom primer ending in (dT)19. While the majority products have first sequenced nucleotide reflect bona fide (pA), substantial fraction reads arise from various mis-priming events. These can result incorrect pA calls anywhere several nucleotides...
To date, 12 protein lysine methyltransferases that modify translational elongation factors and ribosomal proteins (Efm1–7 Rkm 1–5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, five (Efm1 Efm4–7) appear to be specific factor 1A (EF1A), responsible for bringing aminoacyl-tRNAs ribosome. In S. cerevisiae, functional implications of methylation translation are mostly unknown. this work, we assessed physiological impact disrupting EF1A a strain where four most...
CRISPR-Cas9 genome editing technology is widely used in scientific research and biotechnology. As this becomes a staple tool life sciences research, it increasingly important to incorporate into biology curricula train future scientists.
Abstract Interactions between genetic perturbations and segregating loci can cause to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing measure the fitness of 7,700 CRISPRi targeting 1,712 genes 169 yeast cross progeny (or segregants). We identified 460 whose perturbation has segregants. Several factors caused variable effects, including baseline segregant...
Genome editing technologies have the potential to transform our understanding of how genetic variation gives rise complex traits through systematic engineering and phenotypic characterization variants. However, there has yet be a system with sufficient efficiency, fidelity, throughput comprehensively identify causal variants at genome scale. Here we explored ability templated CRISPR systems install natural genome-wide in budding yeast. We optimized several approaches enhance...
Non-genetic variations derived from expression noise at transcript or protein levels can result in cell-to-cell heterogeneity within an isogenic population. Although cells have developed strategies to reduce some cellular functions, this also facilitate varying of regulation and provide evolutionary benefits specific environments. Despite several general characteristics having been revealed, the detailed molecular pathways underlying remain elusive. Here, we established a dual-fluorescent...