A5068760707- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Evolution and Genetic Dynamics
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Bioinformatics and Genomic Networks
- RNA modifications and cancer
- Tuberculosis Research and Epidemiology
- Microbial Metabolic Engineering and Bioproduction
- Mycobacterium research and diagnosis
- Antibiotic Resistance in Bacteria
- Evolutionary Game Theory and Cooperation
- Computational Drug Discovery Methods
- Genomics and Chromatin Dynamics
- Photosynthetic Processes and Mechanisms
- Bacterial Genetics and Biotechnology
- Plant and Biological Electrophysiology Studies
- Microbial Metabolism and Applications
- Innovative Microfluidic and Catalytic Techniques Innovation
- Microbial Community Ecology and Physiology
- Biosimilars and Bioanalytical Methods
- Origins and Evolution of Life
- Genetics, Aging, and Longevity in Model Organisms
- Pharmaceutical and Antibiotic Environmental Impacts
Institute for Systems Biology
2010-2023
European Molecular Biology Laboratory
2016-2023
University of Washington
2010-2014
The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual chromosomes assembled. Here, we describe the consolidation of multiple using advanced endoreduplication intercrossing tRNA expression cassettes to generate strain 6.5 chromosomes. 3D chromosome organization and transcript isoform profiles were evaluated Hi-C long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or...
Here, we report the design, construction, and characterization of a tRNA neochromosome, designer chromosome that functions as an additional, de novo counterpart to native complement Saccharomyces cerevisiae. Intending address one central design principles Sc2.0 project, ∼190-kb neochromosome houses all 275 relocated nuclear genes. To maximize stability, incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, presence 283 rox recombination sites enables...
Sequence features of genes and their flanking regulatory regions are determinants RNA transcript isoform expression have been used as context-independent plug-and-play modules in synthetic biology. However, genetic context—including the adjacent transcriptional environment—also influences levels boundaries. We yeast strains with stochastically repositioned to systematically disentangle effects sequence context. Profiling 120 million full-length molecules across 612 genomic perturbations, we...
Abstract Deep mutational scanning is a powerful approach to investigate wide variety of research questions including protein function and stability. Here, we perform deep on three essential E. coli proteins (FabZ, LpxC MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing, study the effect mutations their original genomic context. We use more than 17,000 variants interrogate importance individual amino acids supporting viability. Additionally, exploit these...
Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological constitute a type Information Communication Technology (ICT): they receive information from the outside inside cells, integrate interpret this information, then activate response. enable molecules within even cells themselves, to communicate with each other their environment. We have become accustomed...
Abstract Microbes can tailor transcriptional responses to diverse environmental challenges despite having streamlined genomes and a limited number of regulators. Here, we present data‐driven models that capture the dynamic interplay environment genome‐encoded regulatory programs two types prokaryotes: E scherichia coli (a bacterium) H alobacterium salinarum (an archaeon). The reveal how genome‐wide distributions cis ‐acting gene elements conditional influences transcription factors at each...
The success of Mycobacterium tuberculosis (Mtb) is largely attributed to its ability physiologically adapt and withstand diverse localized stresses within host microenvironments. Here, we present a data-driven model (EGRIN 2.0) that captures the dynamic interplay environmental cues genome-encoded regulatory programs in Mtb. Analysis EGRIN 2.0 shows how modulation MtrAB two-component signaling system tunes Mtb growth response related microenvironmental cues. Disruption by tunable CRISPR...
In experimental evolution, scientists evolve organisms in the lab, typically by challenging them to new environmental conditions. How best a desired trait? Should challenge be applied abruptly, gradually, periodically, sporadically? one apply chemical mutagenesis, and do strains with high innate mutation rate faster? What are ideal population sizes of evolving populations? There endless strategies, beyond those that can exposed individual labs. We therefore arranged community challenge,...
Abstract The Sc2.0 project is building a eukaryotic synthetic genome from scratch, incorporating thousands of designer features. A major milestone has been achieved with the assembly all individual chromosomes. Here, we describe consolidation multiple chromosomes using endoreduplication intercross to generate strain 6.5 Genome-wide chromosome conformation capture and long-read direct RNA sequencing were performed on this evaluate effects modifications, such as loxPsym site insertion, tRNA...
Expansion of transcription factors is believed to have played a crucial role in evolution all organisms by enabling them deal with dynamic environments and colonize new environments. We investigated how the expansion Feast/Famine Regulatory Protein (FFRP) or Lrp-like proteins into an eight-member family Halobacterium salinarum NRC-1 has aided niche-adaptation this archaeon complex dynamically changing hypersaline environment.We mapped genome-wide binding locations for eight FFRPs, their...
Abstract Here we report the design, construction and characterization of a tRNA neochromosome, designer chromosome that functions as an additional, de novo counterpart to native complement Saccharomyces cerevisiae . Intending address one central design principles Sc2.0 project, ∼190 kb neochromosome houses all 275 relocated nuclear genes. To maximize stability, incorporated orthogonal genetic elements from non- S. yeast species. Furthermore, presence 283 rox recombination sites enable...
There is an urgent need for strategies to discover secondary drugs prevent or disrupt antimicrobial resistance (AMR), which causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (Tet
Abstract The success of Mycobacterium tuberculosis (Mtb) is largely due to its ability withstand multiple stresses encountered in the host. Here, we present a data-driven model that captures dynamic interplay environmental cues and genome-encoded regulatory programs Mtb. genome-wide distribution cis -acting gene elements conditional influences transcription factors at those elicit environment-specific responses. Analysis transcriptional responses may be essential for Mtb survive acidic...
Abstract Deep mutational scanning is a powerful approach to investigate wide variety of research questions including protein function and stability. We performed deep on three essential E. coli proteins (FabZ, LpxC MurA) involved in cell envelope synthesis using high-throughput CRISPR genome editing. This allowed us study the effect introduced mutations their original genomic context. Using more than 17,000 variants FabZ, MurA from saturation editing libraries constructed here, we have...