A5032908241- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Gene Regulatory Network Analysis
- Viral Infectious Diseases and Gene Expression in Insects
- Microbial Metabolic Engineering and Bioproduction
- Advanced biosensing and bioanalysis techniques
- RNA Research and Splicing
- Bacteriophages and microbial interactions
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Biofuel production and bioconversion
- Molecular Communication and Nanonetworks
- Advanced Fluorescence Microscopy Techniques
- Enzyme Catalysis and Immobilization
- Protein Structure and Dynamics
- Evolutionary Algorithms and Applications
- Advanced Nanomaterials in Catalysis
- Antimicrobial Peptides and Activities
- RNA regulation and disease
- Selenium in Biological Systems
- Cell Image Analysis Techniques
- Birth, Development, and Health
- Machine Learning in Bioinformatics
- 3D Printing in Biomedical Research
Pennsylvania State University
2015-2024
FORTH Institute of Chemical Engineering Sciences
2015
University of California, San Francisco
2008-2009
University of Minnesota
2004-2006
Abstract The ribosome’s interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. Long, structured 5′ untranslated regions (5′ UTRs) are commonly found in bacterial mRNAs, though physical mechanisms that determine how ribosome binds these upstream remain poorly defined. Here, we systematically investigate standby sites, Shine–Dalgarno sequences, show can modulate initiation rates by over 100-fold. We find an mRNA’s is controlled amount...
The dynamical solution of a well-mixed, nonlinear stochastic chemical kinetic system, described by the Master equation, may be exactly computed using simulation algorithm. However, because computational cost scales with number reaction occurrences, systems one or more “fast” reactions become costly to simulate. This paper describes hybrid method that partitions system into subsets fast and slow reactions, approximates as continuous Markov process, Langevin accurately dynamics integral form...
Riboswitches are shape-changing regulatory RNAs that bind chemicals and regulate gene expression, directly coupling sensing to cellular actuation. However, it remains unclear how their sequence controls the physics of riboswitch switching activation, particularly when changing ligand-binding aptamer domain. We report development a statistical thermodynamic model predicts sequence-structure-function relationship for translation-regulating riboswitches activate characterized inside cells...
Abstract Transcription rates are regulated by the interactions between RNA polymerase, sigma factor, and promoter DNA sequences in bacteria. However, it remains unclear how non-canonical sequence motifs collectively control transcription rates. Here, we combine massively parallel assays, biophysics, machine learning to develop a 346-parameter model that predicts site-specific initiation for any σ 70 sequence, validated across 22132 bacterial promoters with diverse sequences. We apply predict...
Abstract Genetic circuits and metabolic pathways can be reengineered to allow organisms process signals manufacture useful chemicals. However, their functions currently rely on organism-specific regulatory parts, fragmenting synthetic biology engineering into host-specific domains. To unify efforts, here we have engineered a cross-species expression resource that enables reuse the same genetic while functioning similarly across diverse organisms. Our system combines mixed feedback control...
RNA folding plays an important role in controlling protein synthesis as well other cellular processes. Existing models have focused on how energetics control translation initiation rate under equilibrium conditions but largely ignored the effects of nonequilibrium folding. We introduce a new mechanism, called "ribosome drafting", that explains mRNA's kinetics and ribosome's binding collectively its rate. During cycles translation, ribosome drafting emerges whenever successive ribosomes bind...
A mRNA's translation rate is controlled by several sequence determinants, including the presence of RNA structures within N-terminal regions its coding sequences. However, physical rules that govern when such mRNA will inhibit remain unclear. Here, we introduced systematically designed hairpins into region a reporter protein with steadily increasing distances from start codon, followed characterization their and expression levels in Escherichia coli. We found mRNAs' rates were repressed, up...
Gene expression models greatly accelerate the engineering of synthetic metabolic pathways and genetic circuits by predicting sequence-function relationships reducing trial-and-error experimentation. However, developing with more accurate predictions remains a significant challenge. Here we present model test system that combines advanced statistics, machine learning, database 9862 characterized systems to automatically quantify accuracies, accept or reject mechanistic hypotheses, identify...
Energy from remote methane reserves is transformative; however, unintended release of this potent greenhouse gas makes it imperative to convert efficiently into more readily transported biofuels. No pure microbial culture that grows on anaerobically has been isolated, despite capture through anaerobic processes efficient than aerobic ones. Here we engineered the archaeal methanogen Methanosarcina acetivorans grow as a and biofuel precursor acetate. To methane, cloned enzyme methyl-coenzyme M...
The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical engineering applications. CRISPR/Cas9 (Type II) system binds cuts DNA using guide RNAs, though the variables that control its on-target off-target activity remain poorly characterized. Here, we develop parameterize a system-wide biophysical model of Cas9-based genome editing gene regulation predict how changing RNA sequences, superhelical densities, Cas9 crRNA expression levels,...
Natural and engineered genetic systems require the coordinated expression of proteins. In bacteria, translational coupling provides a genetically encoded mechanism to control level ratios within multi-cistronic operons. We have developed sequence-to-function biophysical model predict in natural operons design synthetic with desired ratios. To quantitatively measure ribosome re-initiation rates, we designed characterized 22 bi-cistronic operon variants systematically modified intergenic...
mRNA degradation is a central process that affects all gene expression levels, and yet, the determinants control decay rates remain poorly characterized. Here, we applied synthetic biology, learn-by-design approach to elucidate sequence structural stability in bacterial operons. We designed, constructed, characterized 82 operons Escherichia coli, systematically varying RNase binding site characteristics, translation initiation rates, transcriptional terminator efficiencies 5′ untranslated...
Abstract Cell-free genetically encoded biosensors have been developed to detect small molecules and nucleic acids, but they yet be reliably engineered proteins. Here we develop an automated platform convert protein-binding RNA aptamers into riboswitch sensors that operate within low-cost cell-free assays. We demonstrate the by engineering 35 protein-sensing riboswitches for human monomeric C-reactive protein, interleukin-32γ, phage MS2 coat protein. The regulate output expression levels up...
Abstract Background Stochastic simulation has become a useful tool to both study natural biological systems and design new synthetic ones. By capturing the intrinsic molecular fluctuations of "small" systems, these simulations produce more accurate picture single cell dynamics, including interesting phenomena missed by deterministic methods, such as noise-induced oscillations transitions between stable states. However, computational cost original stochastic algorithm can be high, motivating...
Stochastic chemical kinetics more accurately describes the dynamics of "small" systems, such as biological cells. Many real systems contain dynamical stiffness, which causes exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend majority their time executing frequently occurring reaction events. Previous have successfully applied a type probabilistic steady-state approximation by deriving an evolution equation, master for relaxed fast and using solution that...
Gene expression is a complex phenomenon involving numerous interlinked variables, and studying these variables to control essential in bioengineering biomanufacturing. While cloning techniques for achieving plasmid libraries that cover large design spaces exist, multiplex offering cell culture screening at similar scales are still lacking. We introduced microcapillary array-based platform aimed high-throughput, of miniature cultures through fluorescent reporters.