A5054963404- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- Cancer, Hypoxia, and Metabolism
- RNA and protein synthesis mechanisms
- Animal Genetics and Reproduction
- Nonlinear Partial Differential Equations
- Cancer, Lipids, and Metabolism
- Epigenetics and DNA Methylation
- Advanced Mathematical Modeling in Engineering
- RNA modifications and cancer
- Viral Infectious Diseases and Gene Expression in Insects
- Health, Environment, Cognitive Aging
- Chemical Reactions and Isotopes
- Bioinformatics and Genomic Networks
- Advanced biosensing and bioanalysis techniques
- Pluripotent Stem Cells Research
- Pancreatic function and diabetes
- SARS-CoV-2 detection and testing
- Chromosomal and Genetic Variations
- Gene Regulatory Network Analysis
- Lipid metabolism and biosynthesis
- Intraoperative Neuromonitoring and Anesthetic Effects
- Differential Equations and Numerical Methods
- Genomics and Chromatin Dynamics
- Origins and Evolution of Life
Massachusetts Institute of Technology
2020-2025
Harvard University
2020-2025
Broad Institute
2024-2025
Inspire
2024
Universidade de Brasília
2022-2023
Chalmers University of Technology
2017-2023
Hospital Universitário de Brasília
2023
Universidade Federal do Triângulo Mineiro
2022
Universidad Complutense de Madrid
2007-2021
Boston VA Research Institute
2021
Aerobic glycolysis, or preferential fermentation of glucose-derived pyruvate to lactate despite available oxygen, is associated with proliferation across many organisms and conditions. To better understand that association, we examined the metabolic consequence activating dehydrogenase complex (PDH) increase oxidation at expense fermentation. We find increasing PDH activity impairs cell by reducing NAD+/NADH ratio. This change in caused increased mitochondrial membrane potential electron...
An open-source, genome-scale human metabolic model and a web portal to explore the are generated.
We lack tools to edit DNA sequences at scales necessary study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing insert recombination handles into repetitive sequences, up 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell. tracked these over time measure selection pressures, finding a...
Transcriptional reprogramming is a fundamental process of living cells in order to adapt environmental and endogenous cues. In allow flexible timely control over gene expression without the interference native machinery, large number studies have focused on developing synthetic biology tools for orthogonal transcription. Most recently, nuclease-deficient Cas9 (dCas9) has emerged as tool controlling activation repression target genes, by simple RNA-guided positioning dCas9 vicinity...
Tumors are composed of many different cell types including cancer cells, fibroblasts, and immune cells. Dissecting functional metabolic differences between within a mixed population can be challenging due to the rapid turnover metabolites relative time needed isolate To overcome this challenge, we traced isotope-labeled nutrients into macromolecules that turn over more slowly than metabolites. This approach was used assess fibroblast metabolism in murine pancreatic organoid-fibroblast...
Triacylglycerols (TAGs) are valuable versatile compounds that can be used as metabolites for nutrition and health, well feedstocks biofuel production. Although Saccharomyces cerevisiae is the favored microbial cell factory industrial production of biochemicals, it does not produce large amounts lipids TAGs comprise only ~1% its dry weight. Here, we engineered S. to reorient metabolism overproduction TAGs, by regulating lipid droplet associated-proteins involved in TAG synthesis hydrolysis....
Abstract To extend the frontier of genome editing and enable repetitive elements mammalian genomes, we made use a set dead-Cas9 base editor (dBE) variants that allow at tens thousands loci per cell by overcoming death associated with DNA double-strand breaks single-strand breaks. We used gRNAs targeting elements—ranging in target copy number from about 32 to 161 000 cell. dBEs enabled survival after large-scale editing, allowing targeted mutations up ∼13 200 ∼12 293T human induced...
Large genes including several CRISPR-Cas modules like gene activators (CRISPRa) require dual adeno-associated viral (AAV) vectors for an efficient in vivo delivery and expression. Current AAV vector approaches have important limitations, e.g., low reconstitution efficiency, production of alien proteins, or flexibility split site selection. Here, we present a technology based on via mRNA trans-splicing (REVeRT). REVeRT is flexible selection can efficiently reconstitute different numerous...
Abstract While protein-coding genes are characterized increasingly well, 99% of the human genome is non-coding and poorly understood. This gap due to a lack tools for engineering variants that affect sequence necessary extent. To bridge this gap, we have developed toolbox create deletions, inversions, translocations, extrachromosomal circular DNA at scale by highly multiplexed insertion recombinase recognition sites into repetitive sequences with CRISPR prime editing. Using strategy, derived...
We study the blow-up phenomenon for non-negative solutions to following parabolic problem: where 0 < p − = min ≤ p(x) max + is a smooth bounded function. After discussing existence and uniqueness, we characterize critical exponents this problem. prove that there are with in finite time if only > 1. When Ω ℝ N show 1 2/ , then global non-trivial solutions, while all problem blow up time. Moreover, case when +, functions such possesses solutions. domain domains On other hand, small...
Significance Replacement of nonrenewable petrochemicals and liquid fuels requires sustainable production oleochemicals. Free fatty acids (FFAs) are versatile molecules that can be produced by microbial fermentation used as precursors for these In the past few years, we have seen major advancements in improving yeast Saccharomyces cerevisiae FFA production. Despite successes, lipid metabolism is highly complex, pathways metabolites involved formation FFAs remain incompletely understood. this...
Engineering Saccharomyces cerevisiae for industrial-scale production of valuable chemicals involves extensive modulation its metabolism. Here, we identified novel gene expression fine-tuning set-ups to enhance endogenous metabolic fluxes toward increasing levels acetyl-CoA and malonyl-CoA. dCas9-based transcriptional regulation was combined together with a malonyl-CoA responsive intracellular biosensor select beneficial set-ups. The candidate genes screening were predicted using genome-scale...
Programmable technologies that sense specific nucleic acid signatures in living cells and trigger cellular functions hold significant potential for biotechnology medicine. Here, we developed SONAR (Sensing Of Nucleic acids using ASOs Reverse-transcriptases), a platform enables the detection of target DNA RNA sequences triggers controlled gene expression human cells. operates through circularizable single-stranded (ssDNA) sensors that, upon hybridization with complementary or...
In vivo production of fatty acid-derived chemicals in Saccharomyces cerevisiae requires strategies to increase the intracellular supply either acyl-CoA or free acids (FFAs), since their cytosolic concentrations are quite low a natural state for this organism. Deletion synthetase genes FAA1 and FAA4 is an effective straightforward way disable re-activation drastically FFA levels. However, strategy causes over-accumulation consequential release extracellular medium, which results significant...
Metabolic reprogramming is considered a hallmark of malignant transformation. However, it not clear whether the network metabolic reactions expressed by cancers different origin differ from each other or normal human tissues. In this study, we reconstructed functional and connected genome-scale models for 917 primary tumor samples across 13 types based on probability expression 3765 reference genes in sample. This network-centric approach revealed that networks are largely similar terms...
Efficient production of sesquiterpenes in Saccharomyces cerevisiae requires a high flux through the mevalonate pathway. To achieve this, supply acetyl-CoA plays crucial role, partially because nine moles are necessary to produce one mole farnesyl diphosphate, but also overcome thermodynamic constraint imposed on first reaction, which acetoacetyl-CoA is produced from two by thiolase. Recently, novel synthase (nphT7) has been identified Streptomyces sp. strain CL190, catalyzes irreversible...
The coronavirus disease 2019 (COVID-19) pandemic has brought about the unprecedented expansion of highly sensitive molecular diagnostics as a primary infection control strategy. At same time, many laboratories have shifted focus to severe acute respiratory syndrome 2 (SARS-CoV-2) research and diagnostic development, leading large-scale production SARS-CoV-2 nucleic acids that can interfere with these tests. We identified multiple instances, in independent laboratories, which generated...
Abstract To extend the frontier of genome editing and enable radical redesign mammalian genomes, we developed a set dead-Cas9 base editor (dBE) variants that allow at tens thousands loci per cell by overcoming death associated with DNA double-strand breaks (DSBs) single-strand (SSBs). We used gRNAs targeting repetitive elements – ranging in target copy number from about 31 to 124,000 cell. dBEs enabled survival after large-scale editing, allowing targeted mutations up ~13,200 ~2610 293T...