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65,743 grants matching “single cell sequencing”
THE VAST MAJORITY OF METABOLIC FUNCTIONS IN CONTEMPORARY BIOLOGY IS MADE POSSIBLE ONLY BY THE CATALYTIC AND REGULATORY ACTIVITIES OF PROTEINS. THE CORRESPONDING DIVERSITY OF PROTEIN FUNCTIONS THAT EVOLVED OVER BILLIONS OF YEARS IS SIMPLY ASTOUNDING. WHILE THE RESULT OF THIS EVOLUTIONARY PROCESS CAN BE STUDIED THROUGH ANALYZING MODERN PROTEINS THE MECHANISMS THAT HAVE LIKELY LED TO THE EMERGENCE OF THIS ABUNDANT VARIETY OF PROTEIN STRUCTURES AND FUNCTIONS ARE STILL POORLY UNDERSTOOD. WE WILL EXPERIMENTALLY STUDY THE PROCESS OF HOW PROTEINS CAN ACQUIRE NOVEL FUNCTIONS. WE WILL ADDRESS THE TWO KEY ASPECTS OF THIS FUNDAMENTAL BIOLOGICAL QUESTION: (I) HOW CAN AN EXISTING PROTEIN EVOLVE TO ADOPT NOVEL FUNCTIONS? (II) HOW COULD THE EARLIEST FUNCTIONAL PROTEINS HAVE FIRST APPEARED ON THE STAGE OF DARWINIAN EVOLUTION? WE ANTICIPATE TO DEMONSTRATE POTENTIAL SCENARIOS FOR THE EMERGENCE OF FUNCTIONAL PROTEINS THAT INTERFACE WITH LIVING ORGANISMS. IN OUR APPROACH WE WILL SCREEN COMBINATORIAL LIBRARIES OF TENS OF MILLIONS OF RANDOMIZED PROTEINS FOR VARIANTS WITH NEW FUNCTIONS USING AN IN VIVO SELECTION TECHNIQUE. WE WILL EVALUATE AND COMPARE TWO VERY DIFFERENT PROTEIN LIBRARIES FOR THEIR CAPACITY TO YIELD NOVEL PROTEINS THAT ENABLE BACTERIAL CELL GROWTH THROUGH NEW ENZYMATIC OR REGULATORY ACTIVITIES. OUR SEARCH WILL BEGIN WITH NATURE'S MOST COMMON ENZYME FOLD THE (ALPHA/BETA)8 BARREL. THIS UBIQUITOUS FOLD IS ADOPTED BY ABOUT 10% OF ALL KNOWN ENZYME STRUCTURES UTILIZED IN FIVE OF THE SIX ENZYMATIC CLASSES AND CATALYZES A WIDE ARRAY OF DIFFERENT REACTIONS. DESPITE ITS DOMINANT PRESENCE IN BIOLOGY IT IS NOT FULLY UNDERSTOOD HOW NATURE IS ABLE TO SO READILY REPURPOSE THIS FOLD. WE ENGINEERED A LIBRARY CONTAINING TRILLIONS OF RANDOMIZED YET SOLUBLE (ALPHA/BETA)8 BARREL VARIANTS. A LIBRARY WITH SUCH A HIGH COMPLEXITY AND QUALITY IS UNPRECEDENTED. CONSIDERING THE UNIVERSAL ROLE OF THIS FOLD AMONG NATURAL ENZYMES WE ARE POISED TO SCREEN OUR LIBRARY FOR EMERGING DE NOVO CATALYTIC ACTIVITIES. OUR SECOND LIBRARY CONSISTS OF ENTIRELY RANDOM POLYPEPTIDES OF 80 AMINO ACIDS IN LENGTH. THIS LIBRARY WILL BE USED TO EMULATE THE CONCEIVABLE SCENARIO IN WHICH THE EARLIEST FUNCTIONAL PROTEINS ORIGINATED FROM MIXTURES OF RANDOM-SEQUENCE POLYPEPTIDES. WHILE THIS IS A PLAUSIBLE SCENARIO EXPERIMENTAL DATA IN SUPPORT ARE SURPRISINGLY SPARSE. BOTH LIBRARIES WILL BE SCREENED FOR FUNCTIONAL PROTEINS USING A BACTERIAL GROWTH SELECTION. THIS TECHNIQUE EMPLOYS STRAINS OF THE MODEL ORGANISM ESCHERICHIA COLI WITH SINGLE-GENE DELETIONS RENDERING THEM CONDITIONALLY AUXOTROPHIC - CAPABLE OF GROWTH ON NUTRIENT RICH MEDIUM AND INCAPABLE OF GROWTH ON MINIMAL MEDIUM. THESE AUXOTROPHIC STRAINS ARE DEFICIENT IN A FUNCTION ESSENTIAL FOR CORE METABOLISM SUCH AS A GENE NECESSARY FOR AMINO ACID NUCLEOTIDE OR COFACTOR BIOSYNTHESIS. EACH OF THESE STRAINS WILL BE TRANSFORMED WITH OUR PROTEIN LIBRARIES. GROWTH OF SELECT CLONES ON MINIMAL MEDIUM WILL IDENTIFY PROTEIN VARIANTS WHOSE FUNCTION RESCUED THE WILD TYPE PHENOTYPE. THIS NEW PROTEIN FUNCTION COULD EITHER EFFECTUATE REGULATORY CHANGES IN THE METABOLIC NETWORK OR EVEN PROVIDE A NEW CATALYTIC ACTIVITY. THIS METHOD ALLOWS TO TEST FOR ABOUT 100 DIFFERENT BIOLOGICAL FUNCTIONS. IN A PILOT STUDY WE HAVE ALREADY IDENTIFIED ARTIFICIAL PROTEINS FROM BOTH LIBRARIES THAT COMPENSATE FOR A MISSING ENZYME.
$569,334Regents Of The University Of Minnesota · · FY2020 · National Aeronautics and Space Administration
Therapeutic targeting of MUC5B in a novel ferret model of idiopathic pulmonary fibrosis
$569,331Steven Mark Rowe · University Of Alabama At Birmingham · U01 · FY2023 · HL
MicroRNA regulation of neural tube closure
$569,324Ronald J Parchem · Baylor College Of Medicine · R01 · FY2022 · HD
MicroRNA regulation of neural tube closure
$569,324Ronald J Parchem · Baylor College Of Medicine · R01 · FY2021 · HD
MicroRNA regulation of neural tube closure
$569,324Ronald J Parchem · Baylor College Of Medicine · R01 · FY2023 · HD
FXPOI: Mechanisms and Modifiers
$569,247Emily Graves Allen · Baylor College Of Medicine · P50 · FY2023 · HD
A dialogue between neutrophils and monocytes for effective resolution of inflammation following acute myocardial injury
$569,242Prabhakara Reddy Nagareddy · University Of Oklahoma Hlth Sciences Ctr · R01 · FY2025 · HL
Dietary modulation of Paneth cells
$569,241Ta-Chiang Liu · Washington University · R01 · FY2025 · DK
Deciphering the Role of Mycobiome (Fungus) in Lung Carcinogenesis
$569,229Joyce Huanhuan Chen · University Of Chicago · R37 · FY2025 · CA
Biomarkers of dasatinib response and resistance in T-cell acute lymphoblastic leukemia
$569,213Jun J. Yang · St. Jude Children'S Research Hospital · R01 · FY2024 · CA
Investigating the Molecular Determinants Driving Response and Resistance to HDAC6 Targeted Therapy in Breast Cancer
$569,181Jose M Silva · Icahn School Of Medicine At Mount Sinai · R01 · FY2025 · CA
Cellular and circuitry mechanisms of NRTI-induced pain pathogenesis in the context of opioids and HIV
$569,163Shao-Jun Tang · State University New York Stony Brook · R01 · FY2023 · DA
Cellular and circuitry mechanisms of NRTI-induced pain pathogenesis in the context of opioids and HIV
$569,163Shao-Jun Tang · State University New York Stony Brook · R01 · FY2022 · DA
Cellular and circuitry mechanisms of NRTI-induced pain pathogenesis in the context of opioids and HIV
$569,163Shao-Jun Tang · State University New York Stony Brook · R01 · FY2025 · DA
Population Genetic Mapping of Tourette Syndrome
$569,104Nelson B Freimer · University Of California Los Angeles · R01 · FY2007 · NS
Gene Therapy for HIV Using Aptamers that Target Reverse Transcriptase
$569,073Donald H Burke · University Of Missouri-Columbia · R01 · FY2014 · AI
Molecular pathways controlling alveolar epithelial remodeling in development and regeneration
$569,053Edward E Morrisey · University Of Pennsylvania · R01 · FY2020 · HL
Advancing Precision Oncology in a Humanized, Fully Autologous Mouse Model
$569,047Ryan C Fields · Washington University · R01 · FY2024 · CA
The Role of CD3z ITAM (Immunoreceptor Tyrosine-Based Activation Motif) diversity in CAR T cell Force and Function
$569,047Matthew Bettini · Utah State Higher Education System--University Of Utah · R01 · FY2025 · CA
Neutrophil Metabolism Regulates Hematopoiesis After Trauma
$569,019Robert Tower · Ut Southwestern Medical Center · R01 · FY2025 · AI
Digestive Health and Diseases (DHD) Training Grant
$568,921Eugene B Chang · University Of Chicago · T32 · FY2024 · DK
Viscoelasticity and T Cell Production
$568,911David J Mooney · Harvard University · R01 · FY2023 · CA
Antigenic basis of immune responses after immune modulatory therapies post-HCT
$568,895Catherine Ju-Ying Wu · Dana-Farber Cancer Inst · P01 · FY2023 · CA
Uncovering mechanisms and developing novel therapeutic strategies for TBCD-related developmental and epileptic encephalopathy
$568,866Allison M Bradbury · Research Inst Nationwide Children'S Hosp · R01 · FY2025 · NS
Mapping proximal and distal splicing-regulatory elements
$568,846Chaolin Zhang · Columbia University Health Sciences · R56 · FY2022 · HG