Nome Inc

NEW YORK CENTER FOR COLLABORATIVE RESEARCH IN COMMON DISEASE GENOMICS

CENTER FOR INTEGRATED CELLULAR ANALYSIS

INDIAN HSG BLOCK GR

NEW YORK GENOME CHARACTERIZATION CENTER: SOMATIC MOSAICISM ACROSS HUMAN TISSUES - PROJECT SUMMARY/ABSTRACT - NEW YORK GENOME CHARACTERIZATION CENTER LARGE-SCALE SEQUENCING EFFORTS OVER THE LAST TWO DECADES HAVE BEEN FOCUSED ON GENERATING DNA SEQUENCE DATASETS FROM READILY AVAILABLE TISSUES SUCH AS BLOOD OR SALIVA TO IDENTIFY GERMLINE VARIANTS ASSOCIATED WITH DISEASE PHENOTYPES. HOWEVER, LIMITED PROGRESS HAS BEEN MADE IN CHARACTERIZING SOMATIC VARIANTS IN HEALTHY TISSUES AND THEIR CONTRIBUTION TO HEALTH AND DISEASE OVER THE COURSE OF THE HUMAN LIFESPAN. SOMATIC VARIATION HAS HISTORICALLY BEEN STUDIED IN THE CONTEXT OF TUMOR BIOLOGY; HOWEVER, THERE IS MOUNTING EVIDENCE THAT SOMATIC VARIATION PLAYS AN IMPORTANT ROLE IN THE AGING PROCESS, AS WELL AS IN CARDIOVASCULAR, NEURODEGENERATIVE, IMMUNOLOGIC, AND NEURODEVELOPMENTAL DISEASES. THERE IS THEREFORE A CRITICAL NEED TO CHARACTERIZE THE SOMATIC VARIANT LANDSCAPE IN HEALTHY HUMAN TISSUES IN INDIVIDUALS OF DIVERSE RACE AND ETHNICITY ACROSS THE HUMAN LIFESPAN. THE SOMATIC MOSAICISM ACROSS HUMAN TISSUES (SMAHT) PROGRAM WILL ADDRESS THIS GAP BY ESTABLISHING A COHESIVE NETWORK THAT WILL WORK TOGETHER TO CREATE HIGH-QUALITY SOMATIC VARIANT CATALOG; A CATALOG THAT IS BROADLY SHAREABLE ACROSS THE SCIENTIFIC COMMUNITY AND THAT ENABLES STUDIES INVESTIGATING THE RATES AND PATTERNS OF SOMATIC MOSAICISM ACROSS CELL POPULATIONS AND TISSUES, THAT CAN ELUCIDATE THE MECHANISMS UNDERLYING CLONAL DEVELOPMENT, EVOLUTION, AND EXPANSION, AND THAT ENABLES STUDIES OF THE ROLE OF SOMATIC MUTATION IN DISEASE PATHOGENESIS AND PROGRESSION. THE NEW YORK GENOME CHARACTERIZATION CENTER (NYGCC) WILL WORK COLLABORATIVELY WITH OTHER SMAHT NETWORK CENTERS TO GENERATE A HIGH-QUALITY SOMATIC VARIANT CATALOG USING THREE CORE HIGH-DEPTH SEQUENCING ASSAYS: DUPLEX WHOLE GENOME SEQUENCING (WGS), MRNA SEQUENCING, AND LONG- READ OXFORD NANOPORE WGS. THESE THREE CORE ASSAYS WILL PROVIDE AN UNPRECEDENTED AND COMPREHENSIVE VIEW OF SOMATIC MUTATIONS ACROSS A VARIETY OF HEALTHY TISSUES. THE DATA FROM DEEP WGS WILL ENABLE DISCOVERY OF SOMATIC SNVS, INDELS, MOBILE ELEMENTS, COPY NUMBER CHANGES, AND STRUCTURAL VARIANTS. THE RNA SEQUENCING DATA WILL BE USED TO CONFIRM THE PRESENCE OF THOSE VARIANTS THAT FALL IN EXPRESSED GENES, AND FURTHER EVALUATE THEIR EFFECT ON SPLICING. THE LONG READ WGS SEQUENCING WILL BE USED AS A COROLLARY TO SHORT READ WGS TO CONFIRM AND ENHANCE DISCOVERY OF MOBILE ELEMENTS, COPY NUMBER CHANGES AND STRUCTURAL VARIANTS. TO THESE CORE ASSAYS WE PROPOSE ADDING SINGLE CELL WGS SEQUENCING USING DIRECT LIBRARY PREPARATION PLUS (DLP+) AND GENOTYPING OF TRANSCRIPTOMES (GOT). DLP+ IS AN AMPLIFICATION-FREE SINGLE CELL WGS ASSAY THAT ALLOWS HIGH SENSITIVITY DETECTION OF COPY NUMBER CHANGES, LOSS OF HETEROZYGOSITY, AND STRUCTURAL VARIATION. IT FURTHER ENABLES THE STUDY OF REPLICATION TIMING, CLONAL EXPANSION AND FITNESS AND IS COMPATIBLE WITH POOLED PSEUDO-BULK ANALYSIS TO COMPARE AGAINST DEEP BULK WGS. THE GENOTYPING OF TRANSCRIPTOMES ASSAY WILL ALLOW US TO EXPLORE, FOR EXPRESSED SOMATIC VARIANTS, THE CELL TYPE OR LINEAGE IN WHICH THEY OCCURRED AND BY PAIRING WITH SINGLE CELL EXPRESSION DATA (AND CELL SURFACE MARKER DETECTION AND LONG READ TRANSCRIPT SEQUENCING) THE FUNCTIONAL EFFECTS OF THESE MUTATIONS.

INTEGRATED HUMAN GENOME ANNOTATION: GENERATION OF A REFERENCE GENE SET

INTEGRATING SPATIAL MULTI-OMICS AND CLINICAL COVARIATES TO IDENTIFY MECHANISMS OF DISEASE IN ALS-FTD

IN SITU FUNCTIONAL GENOMICS TO UNDERSTAND TRANSCRIPTIONAL REGULATION

SUSTAINED-RELEASE DRUG DELIVERY DEVICE FOR REFILLABLE SUBCUTANEOUS IMPLANTATION

PURPOSE: THE PURPOSE OF THIS AWARD IS TO BUILD THE CAPACITY OF HUD'S TECHNICAL ASSISTANCE CUSTOMER ORGANIZATIONS TO DEPLOY HUD-FUNDED PROGRAMS AND INITIATIVES EFFECTIVELY AND IN COMPLIANCE WITH ASSOCIATED RULES AND REGULATIONS.; ACTIVITIES TO BE PERFORMED: HUD WILL IDENTIFY SPECIFIC TECHNICAL ASSISTANCE NEEDS TO BE ADDRESSED THROUGH A DEMAND-RESPONSE PROGRAM MODEL. THE RECIPIENT MAY RESPOND TO THOSE NEEDS THROUGH A RANGE OF ELIGIBLE ACTIVITIES: NEEDS ASSESSMENTS; DIRECT TECHNICAL ASSISTANCE AND CAPACITY BUILDING; DEVELOPMENT AND MAINTENANCE OF TOOLS AND PRODUCTS; SELF-DIRECTED AND GROUP LEARNING; KNOWLEDGE MANAGEMENT; DATA ANALYSIS, REPORTING, AND PERFORMANCE MEASUREMENT; ADMINISTRATION; AND COORDINATION.; EXPECTED OUTCOMES: OUTCOMES ARE THE RESULTS OF TECHNICAL ASSISTANCE ACTIVITIES, INCLUDING BUT NOT LIMITED TO CHANGES IN MANAGEMENT OR OPERATION OF HUD-FUNDED PROGRAMS OR INITIATIVES. SPECIFIC OUTCOMES WILL VARY BASED ON THE NATURE OF THE ACTIVITIES CARRIED OUT. STANDARD OUTCOME CATEGORIES INCLUDE IMPROVED CAPACITY TO DESIGN PROGRAMS, POLICIES, AND STRATEGIES AS WELL AS TO DELIVER PROJECTS, PROGRAMS, OR SYSTEMS THAT ADDRESS COMMUNITY NEEDS AS DEFINED IN THE TECHNICAL ASSISTANCE (TA) SCOPE.; INTENDED BENEFICIARIES: BENEFICIARIES INCLUDE HUD CUSTOMER ORGANIZATIONS AND WILL VARY BY ACTIVITY. HUD CUSTOMER ORGANIZATIONS INCLUDE STATE AND LOCAL GRANTEES, PUBLIC HOUSING AGENCIES (PHAS), OWNERS AND MANAGERS OF HUD-ASSISTED HOUSING, CONTINUUM OF CARE (COCS), NON-PROFIT GRANTEES, HOMELESS MANAGEMENT INFORMATION SYSTEM (HMIS) LEADS, HUD-APPROVED HOUSING COUNSELING AGENCIES AND COUNSELORS, TRIBAL ORGANIZATIONS, INDIAN TRIBES, TRIBALLY DESIGNATED HOUSING ENTITIES (TDHES), FEDERAL HOUSING ADMINISTRATION (FHA) APPROVED MULTIFAMILY LENDERS, RESIDENTS AND PARTICIPANTS IN HUD-FUNDED PROGRAMS AND INITIATIVES. SELECTED AWARD RECIPIENTS WILL BE DEPLOYED AS HUD DEEMS MOST NECESSARY ACROSS THE COUNTRY TO ASSIST ORGANIZATIONS RECEIVING HUD FUNDS TO IMPROVE PERFORMANCE AND MANAGEMENT OF HUD FUNDS.; SUBRECIPIENT ACTIVITIES: THE SUBRECIPIENT ACTIVITIES ARE UNKNOWN AT THE TIME OF AWARD.

MULTISCALE GENOME ENGINEERING TO MAP CIS-REGULATORY VARIANTS IN HUMAN AND MOUSE - PROJECT SUMMARY GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE LINKED 1000S OF GENOMIC LOCI WITH HUMAN TRAITS AND DISEASES. HOWEVER, THE MECHANISTIC INNER WORKINGS OF THESE LOCI ARE LARGELY UNKNOWN, LEAVING THE PRINCIPAL GOAL OF GWAS – ILLUMINATING THE CAUSAL BIOLOGICAL ETIOLOGY OF HERITABLE PHENOTYPES – UNFULFILLED. MOST GWAS LOCI OCCUR WITHIN NONCODING REGIONS OF THE GENOME WHOSE FUNCTIONAL IMPACT ON GENE REGULATION IS DIFFICULT TO UNRAVEL. HERE, WE PROPOSE TO DEVELOP A HIGH-THROUGHPUT, INTEGRATED GENOME ENGINEERING TOOLBOX TO BUILD CONTEXT-SPECIFIC MAPS OF ENHANCERS AND VARIANTS FOR IMMUNE TRAITS AND AUTOIMMUNE DISORDERS. OUR MULTI-PI TEAM CONSISTS OF EXPERTS IN COMPLEMENTARY FIELDS: MOLECULAR GENOMICS AND CRISPR SCREENS, LARGE-SCALE HUMAN GENETICS AND FUNCTIONAL GENOMICS DATA ANALYSIS, IMMUNOLOGY, STATISTICAL MODELING, AND SINGLE-CELL MULTIOMICS. SPECIFICALLY, WE PROPOSE TO: 1) IDENTIFY GENES AND CIS-REGULATORY ELEMENTS (CRES) RELEVANT FOR T CELL FUNCTION. T CELLS ARE A CENTRAL CELL TYPE IMPLICATED IN MULTIPLE AUTOIMMUNE DISEASES. WE WILL FIRST PERFORM GENOME-WIDE LOSS- AND GAIN-OF-FUNCTION SCREENS FOR 9 PHENOTYPES REFLECTING T-CELL DIFFERENTIATION AND ACTIVATION USING PRIMARY HUMAN T CELLS. FOR TOP- RANKED GENES, WE WILL INTERROGATE CRES NEAR EACH GENE AND EXPLORE THEIR MECHANISMS VIA SINGLE-CELL PROFILING AND SATURATION MUTAGENESIS. 2) BUILD A CONTEXT-SPECIFIC ENHANCER MAP OF GWAS LOCI IN T CELLS. WE WILL TEST 1,000 CANDIDATE CRES THAT OVERLAP GWAS LOCI USING CRISPRI/A SCREENS IN THE SAME PRIMARY T-CELL SYSTEM, COMPLEMENTED BY SINGLE-CELL ECCITE-SEQ TO MEASURE EFFECTS ON THE TRANSCRIPTOME AND SURFACE PROTEOME. THIS WILL PRODUCE A COMPREHENSIVE MAP OF REGULATORY ELEMENTS FOR A LARGE NUMBER OF LOCI, AND THEIR CONTEXT-SPECIFIC IMPACT ON TRANSCRIPTOMIC AND CELLULAR PHENOTYPES. THEN, WE WILL CONSTRUCT A CONTEXT-SPECIFIC VARIANT MAP OF REGULATORY ELEMENTS IN T CELLS BY INSERTING SPECIFIC ALLELES VIA BASE EDITING AT 100 VALIDATED CRES. THIS WILL PRODUCE A FINE-RESOLUTION MAP OF REGULATORY SITES WITHIN CRES. 3) TEST 100 SYNTENIC CRES FROM IN MOUSE MODELS OF GUT HOMEOSTASIS AND INFLAMMATION IN VIVO. WE WILL FOCUS ON T-CELL TISSUE ACCUMULATION (REFLECTING ACTIVATION AND MIGRATION) AND ALTERATIONS IN TRANSCRIPTIONAL AND CELL SURFACE PHENOTYPES OF THE MIGRATING CELLS. BY DOING SO, WE WILL DETERMINE IF THE RELEVANT VARIANTS HAVE SIMILAR ROLES IN HUMAN DISEASE AND PROVIDE PATHWAYS TOWARDS TARGETING THE PATHOGENIC FUNCTIONS OF THOSE GENES. THROUGH THESE AIMS, WE WILL BUILD A HIGHLY-GENERALIZABLE TOOLKIT FOR MULTI-SCALE INTERROGATION OF NONCODING ELEMENTS AND AN ACCESSIBLE, OPEN, AND REUSABLE RESOURCE OF ENHANCER AND VARIANT EFFECTS ON MOLECULAR, CELLULAR, AND PHYSIOLOGICAL TRAITS. ALTOGETHER, WE WILL ANALYZE THE REGULATORY ARCHITECTURE OF THE GENOME, LEVERAGING OUR DIVERSE PERTURBATIONS AND PHENOTYPIC LAYERS, AND CHARACTERIZE FUNCTIONAL MECHANISMS OF LOCI ASSOCIATED WITH AUTOIMMUNE DISORDERS.

LTBR CARS AS NEXT-GENERATION THERAPIES FOR R/R LYMPHOMA - PROJECT SUMMARY UP TO 50% OF PATIENTS WITH DIFFUSE LARGE B-CELL LYMPHOMA (DLBCL) RELAPSE AFTER FIRST-LINE TREATMENT. CHIMERIC ANTIGEN RECEPTOR (CAR) T-CELLS HAVE RECENTLY EMERGED AS A CURATIVE THERAPY FOR RELAPSED OR REFRACTORY (R/R) DLBCL. HOWEVER, ONLY 35% OF R/R DLBCL PATIENTS TREATED WITH CAR T-CELLS HAVE A DURABLE RESPONSE, AND SURVIVAL IS MEASURED IN MONTHS FOR PATIENTS WHO FAIL TO BENEFIT. IMPROVEMENTS IN CAR T-CELLS ARE URGENTLY REQUIRED TO IMPROVE OUTCOMES. RECENTLY, WE IDENTIFIED THE CELL SURFACE LYMPHOTOXIN BETA RECEPTOR (LTBR) AS A POSITIVE T- CELL REGULATOR THAT ENHANCES CD19 CAR T-CELL EFFICACY IN VITRO AND IN VIVO. LTBR IS TYPICALLY EXPRESSED IN A SUBSET OF MYELOID CELLS BUT ABSENT IN LYMPHOCYTES; HOWEVER WHEN EXPRESSED IN T-CELLS, LTBR INDUCES PROINFLAMMATORY CYTOKINE RELEASE, AND IMPROVES ANTIGEN-SPECIFIC CAR T- AND D T-CELL RESPONSES WITH NO APPRECIABLE OFF-TARGET TOXICITY. BASED ON THESE OBSERVATIONS, WE HYPOTHESIZE THAT LTBR CAN EFFECTIVELY POTENTIATE ANTI-TUMOR ACTIVITY IN R/R LYMPHOMA T-CELLS, REDUCING MARKERS OF T CELL EXHAUSTION AND OUTPERFORMING CURRENT FDA-APPROVED CAR-TS ACROSS R/R DLBCL SUBTYPES. IN AIM 1, WE CHARACTERIZE DIFFERENCES IN EXPRESSION OF T-CELL DIFFERENTIATION, ACTIVATION, AND EXHAUSTION MARKERS AND MYELOID POPULATIONS IN 25 TREATMENT-NAIVE AND 25 R/R DLBCL PATIENT SAMPLES. TO UNDERSTAND IF LTBR CAN SIMILARLY IMPROVE CAR-T RESPONSE IN THE R/R CONTEXT, WE WILL USE SINGLE- CELL PROFILING AND FUNCTIONAL ASSAYS TO TEST AUTOLOGOUS CD19+ CELL KILLING, WITH AND WITHOUT LTBR. IN AIM 2 WE WILL EVALUATE THE IMPACT OF DLBCL SUBTYPE ON CAR T-CELL ACTIVITY BY INTRODUCING LTBR AND CAR T-CELLS INTO MICE XENOTRANSPLANTED WITH MULTIPLE GERMINAL CENTER B-CELL (GCB) AND ACTIVATED B-CELL (ABC) CELL LINES. SINCE T-CELL ACTIVATION AND KINETICS ARE FURTHER INFLUENCED BY PATIENT TUMOR BURDEN, WE WILL ALSO INVESTIGATE THE EFFICACY OF LTBR-CAR T-CELL THERAPY IN A HIGH TUMOR BURDEN CONTEXT AND TEST FOR DURABLE IMMUNE MEMORY AFTER COMPLETE TUMOR REGRESSION. RECENTLY, BY FUSING THE INTRACELLULAR SIGNALING DOMAIN OF LBTR DIRECTLY TO EXISTING (CD28 AND 4-1BB) CARS, WE HAVE DEVELOPED A NOVEL CAR CONSTRUCT WITH MORE POTENT ANTITUMOR RESPONSE. IN AIM 3 USING COMPREHENSIVE SCANNING MUTAGENESIS OF THE LTBR DOMAIN, WE WILL CREATE A LIBRARY OF CAR VARIANTS AND TEST THEIR ABILITY TO IMPROVE TUMOR KILLING, RESISTANCE TO EXHAUSTION AND CYTOKINE SECTION. WE WILL ALSO MEASURE CHANGES IN T-TO-B CELL IMMUNE SYNAPSES AND RESISTANCE TO IMMUNOSUPPRESSION BY MYELOID-DERIVED SUPPRESSOR CELLS (MDSCS) IN THE MOST PROMISING LTBR-CARS. THIS PROJECT IS THE FIRST TO COMPREHENSIVELY CHARACTERIZE T CELLS STATES IN TREATMENT-NAIVE AND R/R DLBCL AND EVALUATE LTBR AS A T-CELL ACTIVATING STRATEGY TO MAXIMIZE INTRINSIC ANTI-TUMOR ACTIVITY IN R/R DLBCL. THERE IS SUBSTANTIAL POTENTIAL FOR OUR WORK TO SERVE AS A BRIDGE FROM LABORATORY STUDIES TO CLINICAL TRIALS AND TO HELP THE 40,000 PATIENTS PER YEAR WITH R/R DLBCL AND OTHER B-CELL NHLS.

DELINEATING THE NETWORK EFFECTS OF MENTAL DISORDER-ASSOCIATED VARIANTS USING CONVEX OPTIMIZATION METHODS - PROJECT SUMMARY/ABSTRACT DRIVEN BY INTERNATIONAL OPEN SCIENTIFIC COLLABORATION THROUGH GROUPS SUCH AS THE PSYCHIATRIC GENOMICS CONSORTIUM (PGC, IN WHICH CO-I MULLINS IS A LEADING ANALYST) BOTH GENOME-WIDE ASSOCIATION STUDIES (GWAS) AND WHOLE EXOME AND GENOME SEQUENCING STUDIES OF NEUROPSYCHIATRIC DISORDERS (NPDS) ARE RAPIDLY INCREASING IN SAMPLE SIZE. WITH THIS INCREASED SAMPLE SIZE COMES INCREASED STATISTICAL POWER TO DETECT MANY MORE, SMALLER GENETIC EFFECTS ON DISEASE RISK, KNOWN AS THE POLYGENIC COMPONENT. THE CHALLENGE NOW IS TO UNDERSTAND WHAT THESE FINDINGS TELL US ABOUT NPD RISK, ETIOLOGY AND BIOLOGY. HERE WE PROPOSE A SUITE OF METHODS FOR MULTI-TRAIT ANALYSIS TO DETERMINE UNDERLYING LATENT STRUCTURE, CAUSAL NETWORKS OF GENES AND TRAITS, AND ENRICHED DATA-DERIVED REGULATORY PATHWAYS. WE MAKE EXTENSIVE USE OF CONVEX OPTIMIZATION METHODS THAT ALLOW BOTH COMPUTATIONAL EFFICIENCY AND GUARANTEES ON REPRODUCIBILITY. IN AIM 1 WE WILL DECOMPOSE A WIDE RANGE OF NPDS AND THEIR SUBPHENOTYPES INTO SHARED AND UNIQUE GENETIC COMPONENTS USING A NOVEL CONVEX FORMULATION OF OBSERVED-WEIGHTED PRINCIPAL COMPONENTS ANALYSIS (PCA) AND DEVELOP EXTENSIONS TO HANDLE SAMPLE OVERLAP, LINKAGE DISEQUILIBRIUM (LD), AND DIFFERENT ANCESTRIES. IN AIM 2 WE WILL EXTEND AND CUSTOMIZE OUR EXISTING WORK ON CAUSAL NETWORK INFERENCE USING BICONVEX OPTIMIZATION TO ESTIMATE BOTH CIS AND TRANS GENE REGULATORY NETWORKS IN THE BRAIN USING LARGE-SCALE UNIFORMLY PROCESSED CHROMATIN ACCESSIBILITY AND EXPRESSION QUANTITATIVE TRAIT LOCI (QTLS). WE WILL REGULARIZE ESTIMATES OF CIS INTERACTIONS USING CHROMATIN CONFORMATION DATA, MODEL LATENT GENETIC CONFOUNDERS IN THESE NETWORKS USING AN EXPECTATION-MAXIMIZATION (EM) APPROACH AND ESTIMATE NETWORKS OVER BOTH GENES AND NPDS IN ORDER TO DETERMINE THE MOST DIRECT CAUSES (“CORE” GENES IN THE OMNIGENIC MODEL). IN AIM 3 WE WILL ANALYZE BOTH RARE AND COMMON GENETIC ASSOCIATIONS IN THEIR GENE REGULATORY NETWORK CONTEXT. BORROWING FROM CANCER GENOMICS, WE WILL USE HEAT DIFFUSION MODELS TO PROPAGATE STATISTICAL INFORMATION ON THE LOCAL NETWORK OVER BOTH GENES AND REGULATORY ELEMENTS (RES) AND THEN USE GRAPH CLUSTERING ALGORITHMS TO EXTRACT “HOT” SUBNETWORKS, CORRESPONDING TO PATHWAYS IMPLICATED IN THE NPD UNDER STUDY. THE METHODS WE DEVELOP FOR THESE ANALYSES WILL BE MADE PUBLICLY AVAILABLE UNDER SOURCE LICENSES WITH EXTENSIVE SUPPORT IN TERMS OF DOCUMENTATION, TUTORIALS, AND VIGNETTES. THROUGH THIS WE HOPE TO EMPOWER FUTURE “POST-GWAS” ANALYSES THAT CAN LEVERAGE THE GENETIC, SUBPHENOTYPE AND TRAIT NETWORKS UNDERLYING HUMAN NEUROPSYCHIATRIC HEALTH, AND EVENTUALLY POINT THE WAY TO THERAPEUTIC INTERVENTIONS.

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

PHARMACOLOGICALLY OPTIMIZED TLR5 AGONIST AS A NOVEL AGAINST IDIOPATHIC PULMONARY FIBROSIS

HIGH ENERGY COST GRANT

SPATIALLY RESOLVED DYNAMICS OF MOLECULAR PATHOLOGY AND INTERCELLULAR INTERACTIONS IN AMYTROPHIC LATERAL SCLEROSIS

DEVELOPMENT OF AN INTERFERON-ALPHA-VELTUZUMAB CONJUGATE FOR CD20-TARGETED THERAPY

LEARNING THE METADATA OF THE CELL WITH SINGLE CELL GENOMICS

PURPOSE: RECONSTRUCT RUNWAY LIGHTING; SHIFT TAXIWAY; CONSTRUCT TAXIWAY; REHABILITATE RUNWAY. ACTIVITIES TO BE PERFORMED/EXPECTED OUTCOMES: THIS PROJECT CONSTRUCTS NEW 573 FOOT TAXIWAY TURNAROUNDS ON THE RUNWAY 17 AND 35 ENDS TO BRING THE AIRPORT INTO CONFORMITY WITH CURRENT STANDARDS. THIS PROJECT RECONSTRUCTS THE EXISTING LIGHTING ON RUNWAY 17/35 THAT HAS REACHED THE END OF ITS USEFUL LIFE. THIS PROJECT REHABILITATES 3,400 FEET OF EXISTING PAVED RUNWAY 17/35 TO MAINTAIN THE STRUCTURAL INTEGRITY AND MINIMIZE FOREIGN OBJECT DEBRIS TO EXTEND ITS USEFUL LIFE. THIS PROJECT SHIFTS EXISTING PAVED TAXIWAY A3 BY 100 FEET TO BRING THE AIRPORT INTO CONFORMITY WITH CURRENT STANDARDS. THIS GRANT FUNDS THE FINAL PHASE, WHICH CONSISTS OF CONSTRUCTION. INTENDED BENEFICIARY: THIS GRANT WILL PROVIDE FEDERAL FUNDING FOR AIRPORTS ASSOCIATED WITH MAHNOMEN, MINNESOTA.

ASSET MGMT TECHNICAL ASSISTANC

NANOMEDEX PROPOFOL MICROEMULSIONS: PRECLINICAL STUDIES TO FDA IND APPLICATION

ORGANOCATALYSIS FOR THE TREATMENT OF SICKLE CELL DISEASE

IMPACT AID PROGRAM, TITLE VII, SECTION 7003

IMPACT AID PROGRAM, TITLE VII, SECTION 7003

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

IMPACT AID PROGRAM, TITLE VII, SECTION 7003

ONECPD TA & CAPACITY BLDG

IMPACT AID PROGRAM, TITLE VII, SECTION 7003

PH CAPITAL FUND M-TA

PUBLIC HOUSING CAPITAL FUND

IMPACT AID PROGRAM, TITLE VII, SECTION 7003

TAS::89 0227::TAS RECOVERY; NEW PHASE I SBIR: RECOVERY ACT; TITLE: RECOVERY ACT - SCALE-UP OF PRODUCTION OF ACTIVE NANOPARTICLES-BASED NOVEL LUBRICAN

DEVELOPMENT OF A COMMERCIAL PLATFORM FOR DISCOVERY AND VALIDATION OF KEY MICROBIAL METABOLITES IN CNS DISORDERS

UNKNOWN TITLE

UNKNOWN TITLE

A PHASE 2, RANDOMIZED, DOUBLE-BLIND, 4-ARM, MULTICENTER STUDY TO DEMONSTRATE THE EFFICACY AND SAFETY OF TOPICAL DOSAGE FORMULATIONS OF A PRESCRIPTION DRUG PRODUCT FOR ACTINIC KERATOSIS - PROJECT SUMMARY / ABSTRACT ACINIC KERATOSES (AK) ARE PREMALIGNANT SKIN LESIONS WITH THE POTENTIAL TO DEVELOP INTO CUTANEOUS SQUAMOUS CELL CARCINOMA (CSCC), WHICH IS THE SECOND MOST COMMON TYPE OF CANCER AND WHEN METASTATIC HAS A MORTALITY RATE THAT IS HIGHER THAN MELANOMA. THERE IS A HIGH UNMET NEED FOR TOPICAL AK MEDICATIONS WITH SHORTER TREATMENT DURATIONS AND ENHANCED EFFICACY THAT CAN ERADICATE AK AND TREAT THE SURROUNDING CANCERIZED FIELD. THE PRODUCT OF THIS SBIR WILL BE A FOOD AND DRUG ADMINISTRATION APPROVED FIXED DOSE COMBINATION CREAM CONTAINING CALCIPOTRIOL (CPO) AND 5-FLUOROURACIL (5-FU) AS A TREATMENT FOR AK IN IMMUNOCOMPETENT PATIENTS. TECHNOLOGICAL INNOVATION: TOPICAL CO-ADMINISTRATION OF CPO / 5-FU ERADICATES AKS BY ACTIVATING CD4+ T CELL DOMINATED IMMUNITY, AN UPSTREAM ACTIVATOR OF THE ADAPTIVE IMMUNE RESPONSE, WHICH THEN RECRUITS AN ARRAY OF DOWNSTREAM EFFECTOR CELLS TO BLOCK CSCC DEVELOPMENT. THE LONG-TERM GOAL IS THE REGISTRATION OF THE SBIR PRODUCT, WHICH DIRECTLY ADDRESSES THE MISSION OF THE NATIONAL CANCER INSTITUTE BY HARNESSING THE POWER OF THE IMMUNE SYSTEM TO TREAT AKS AND PREVENT CSCC. PHASE I SBIR EQUIVALENT STUDIES DEMONSTRATED THE CLINICAL AND COMMERCIAL FEASIBILITY OF THE PHD TECHNOLOGY FOR AK TREATMENT. SUCCESSFULLY COMPLETED RANDOMIZED (N=130) AND OPEN LABEL CLINICAL STUDIES (N=18) DEMONSTRATED THE FEASIBILITY OF THE CPO / 5-FU COMBINATION AS THE BEST-IN-CLASS TREATMENT FOR AK AND THE ONLY PRODUCT EVER REPORTED TO REDUCE THE RISK OF CSCC DEVELOPMENT AT 3-YEARS POST TREATMENT. THE HIGH IMPACT OF THE PUBLISHED DATA HAS RESULTED IN THE NATIONAL COMPREHENSIVE CANCER NETWORK AND THE AMERICAN ACADEMY OF DERMATOLOGY RECOMMENDING CPO / 5-FU AS A TREATMENT FOR AK. MARKET RESEARCH DEMONSTRATED PRESCRIBER AND PATIENT ENTHUSIASM FOR THE PHD PRODUCT AND CONFIRMED THAT HEALTH INSURANCE COMPANIES WILL PROVIDE BROAD COVERAGE TO BENEFICIARIES AT A PRICE THAT WILL GENERATE MEANINGFUL REVENUES FOR THE COMPANY. SPECIFIC AIM 1. COMPLETE A PHASE 2, RANDOMIZED, DOUBLE-BLIND, 4-ARM, MULTICENTER STUDY TO DEMONSTRATE THE EFFICACY AND SAFETY OF TOPICAL DOSAGE FORMULATIONS OF CPO PLUS 5-FU FOR THE TREATMENT OF AK. PHASE II OBJECTIVES: CONDUCT A PHASE 2 CLINICAL TRIAL TO ASSESS THE EFFICACY AND SAFETY OF TOPICAL DOSAGE FORMULATIONS CONTAINING TWO DIFFERENT CONCENTRATIONS OF CPO PLUS 5-FU IN 160 AK PATIENTS. EXPECTED OUTCOMES: 5-FU / CPO IS EXPECTED TO BE WELL-TOLERATED AND SIGNIFICANTLY MORE EFFICACIOUS THAN 5-FU MONOTHERAPY AND PLACEBO. THE DATA WILL ENABLE DOSE SELECTION AND DESIGN OF THE PHASE 3 REGISTRATIONAL STUDIES. COMMERCIAL OPPORTUNITY: THE TARGET CUSTOMER WILL BE DERMATOLOGISTS AND PEAK REVENUES OF $285 MIL ARE PROJECTED AT THE LOWEST PROBABLE LIST PRICE, WITH 93% OF PATIENTS PAYING = $25 OUT-OF-POCKET.

THE DEVELOPMENT OF INORGANIC ULTRAVIOLET FILTERS EXHIBITING IMPROVED TOPICAL RETENTION ON HUMAN SKIN FOR THE PREVENTION OF SKIN CANCER

A PHASE 2 CLINICAL TRIAL OF TOPICAL URACIL FOR THE PREVENTION OF CAPECITABINE INDUCED HAND-FOOT SYNDROME

ROLES OF SMALL RNAS IN GUARDING GERM CELL GENOMES

COMBINED RADIO- AND IMMUNOTHERAPY OF AGGRESSIVE NHL

ONECPD TA & CAPACITY BLDG

ULTRASOUND-BASED DIAGNOSTIC AND MONITORING OF BLADDER CANCER TREATMENT WITH DRUG RELEASED FROM NANOPARTICLES - PROJECT SUMMARY/ABSTRACT: TRANSITIONAL CELL CARCINOMA (TCC) OF THE BLADDER IS THE FIFTH MOST COMMON FORM OF CANCER IN THE U.S., WITH OVER 80,000 NEW CASES EXPECTED IN 2019. FOR EARLY-STAGE CARCINOMAS, PATIENTS RECEIVE INTRAVESICAL BACILLUS CALMETTE-GUERIN (BCG) IMMUNOTHERAPY, OR TRANSURETHRAL RESECTION OF THE BLADDER TUMOR (TURBT) WITH INTRAVESICAL CHEMOTHERAPY. BOTH ARE ASSOCIATED WITH A HIGH RATE OF RECURRENCE AND EVENTUAL PROGRESSION. BCG FAILS MANY PATIENTS WHO ARE IMMUNOCOMPROMISED OR WHO EXPERIENCE ADVERSE REACTIONS, WHILE TURBT WITH CHEMOTHERAPY FAILS BECAUSE THE CHEMOTHERAPEUTIC AGENT IS NOT SUFFICIENTLY RETAINED IN THE BLADDER TO PENETRATE LESIONS THAT AREN’T RESECTED. THUS, THERE IS A NEED FOR AN IMPROVED DRUG FORMULATION FOR EARLY-STAGE (CIS, TA, T1, T2) TCC CAPABLE OF 1) PENETRATING THE TUMOR BEYOND THE SUPERFICIAL CELL LAYERS, AND 2) INCREASING THE DWELL/CONTACT TIME BETWEEN THE CHEMOTHERAPEUTIC AGENT AND THE CANCER CELLS. TO THAT END, NANOMEDTRIX (NMTX) HAS DEVELOPED A PARTICLE BASED ON MESOPOROUS SILICA NANOPARTICLES (MSN) THAT CARRIES KNOWN CHEMOTHERAPEUTIC AGENTS AND IS DESIGNED TO IMPROVE THEIR SPECIFICITY, DWELL TIME, AND TUMOR PENETRATION. OUR PHASE I SBIR PROJECT EXCEEDED OUR GOALS AND DEMONSTRATED THE SAFETY AND EFFICACY OF THE MSN PARTICLES IN CARRYING AND RELEASING EPIRUBICIN IN VIVO IN A MURINE TCC ORTHOTOPIC MODEL AND IN VITRO USING CULTURED HUMAN TCC CELLS. THROUGH OUR PARTICIPATION IN THE NIH I-CORPS PROGRAM WE SPOKE WITH KEY OPINION LEADERS (UROLOGIC ONCOLOGISTS) IN THE CLINICAL BLADDER CANCER SPACE. AS A RESULT, WE ARE COMPLETING OUR PHASE I WORK USING THE MSN TO DELIVER CLINICALLY RELEVANT DOSES OF GEMCITABINE, DOCETAXEL, AND MITOMYCIN-C IN THE SAME MODEL. FOLLOWING OUR PHASE I SUCCESS, OUR PHASE II SBIR IS DESIGNED TO COMPLETE THE ACQUISITION OF DATA REQUIRED BY THE FDA FOR INITIATION OF IND APPROVAL OF NMTX MSN IN HUMAN CLINICAL TRIALS. SPECIFIC AIM 1 DESCRIBES THE NECESSARY IN VITRO TASKS: OPTIMIZING PARTICLE CHEMISTRY AND VALIDATING OUR LARGER CANINE MODEL USING CULTURED CELLS AND CANINE TCC ORGANOIDS. SPECIFIC AIM 2 DESCRIBES COMPLETION OF MURINE ORTHOTOPIC STUDIES AND THE START OF PRE-CLINICAL TRIALS IN DOGS WITH SPONTANEOUSLY OCCURRING TCC. SPECIFIC AIM 3 LAYS OUT OUR PLAN FOR CARRYING OUT CGMP SYNTHESIS, PACKAGING, AND ANALYSIS OF OUR IND. BEYOND SETTING THE STAGE FOR FDA IND APPROVAL AND FIRST-IN-HUMAN CLINICAL TRIALS, PHASE II COMPLETION WILL STRENGTHEN OUR POSITION WITH INVESTORS/PARTNERS IN THE PHARMACEUTICAL INDUSTRY, WITH WHOM WE WILL PARTNER IN SBIR PHASE IIB, PHASE III AND BEYOND TO EXPAND CLINICAL TRIALS AND ULTIMATELY COMMERCIALIZE THE TECHNOLOGY. WE ARE CONTINUING TO WORK WITH THE UROLOGY CONTACTS WE MADE IN I-CORPS WHO ARE EAGER TO PARTICIPATE IN CLINICAL TRIALS, AND WE HAVE RECEIVED INTEREST FROM PHARMA COMPANIES (BRISTOL-MYERS SQUIBB, UROVANT, AND OTHERS). OUR PROPRIETARY TECHNOLOGY WILL PROVIDE LICENSEES WITH IMPROVED PERFORMANCE FROM ESTABLISHED CHEMOTHERAPEUTICS THAT HAVE ALREADY GONE OFF-PATENT, THUS MAKING OUR TECHNOLOGY ATTRACTIVE BOTH CLINICALLY AND COMMERCIALLY. ULTIMATE COMMERCIAL SUCCESS OF THIS SBIR WORK WILL GREATLY BENEFIT HUMAN HEALTH WHILE REDUCING MEDICAL COSTS.

ADAPTATION CC PROGRAM GUAYAS

IMPROVE EXISTING AIRPORT

SINGLE-CELL EPIGENOME ANALYSIS OF THE ALZHEIMER'S DISEASE BRAIN - PROJECT SUMMARY LATE ONSET AD (LOAD) IS A HETEROGENEOUS DISEASE THAT INVOLVES COMPLEX INTERACTIONS BETWEEN GENETIC, EPIGENETIC, AND ENVIRONMENTAL RISK FACTORS. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE IDENTIFIED SEVERAL THOUSAND SEQUENCE VARIANTS LINKED TO INCREASED OR DECREASED RISK OF AD, MOST OF WHICH ARE NONCODING. THE CURRENT PARADIGM POSITS THAT NONCODING VARIANTS CONTRIBUTE TO DISEASE ETIOLOGY BY PERTURBING TRANSCRIPTIONAL REGULATION IN DISEASE-RELEVANT CELL TYPES, WHILE ENVIRONMENTAL RISK FACTORS CONTRIBUTE TO PATHOGENESIS IN PART VIA ALTERATIONS TO THE EPIGENOME. HOWEVER, A LACK OF MAPS AND TOOLS TO EXPLORE GENE ACTIVITIES AND THEIR TRANSCRIPTIONAL REGULATION AT CELLULAR RESOLUTION IN THE BRAIN HAS PRESENTED A MAJOR BOTTLENECK TO THE FUNCTIONAL INTERPRETATION OF NONCODING AD RISK VARIANTS. IN PRIOR WORK, WE APPLIED DROPLET PAIRED-TAG MULTI-OMIC PROFILING OF TRANSCRIPTION AND HISTONE POST-TRANSLATIONAL MODIFICATION TO POST-MORTEM AD AND CONTROL PARIETAL CORTEX, DEMONSTRATING ITS CAPACITY TO PROFILE CELLULAR EPIGENETICS AND TRANSCRIPTION FROM BULK SAMPLES. THIS TECHNOLOGY HAS GARNERED SIGNIFICANT INTEREST THROUGH OUR EARLY-ACCESS PROGRAM. IN THE PROPOSED STUDY, WE WILL DEVELOP A MANUFACTURING QUALITY MANAGEMENT SYSTEM INCORPORATING REFERENCES AND REFERENCE MEASUREMENTS FOR THE PRODUCTION OF DROPLET PAIRED-TAG KITS. WE WILL OPTIMIZE OUR PROTOCOLS SPECIFICALLY ON POST-MORTEM AD AND HEALTHY BRAIN TISSUE FROM HIPPOCAMPUS, WHITE MATTER, AND CEREBELLUM, AS WELL AS ON PERIPHERAL BLOOD; AND FURTHER OPTIMIZE DROPLET PAIRED-TAG FOR APPLICATION TO SORTED NUCLEAR POPULATIONS. WE WILL PUBLISH THE RESULTING DATA AS A COMPREHENSIVE CELLULAR ENCYCLOPEDIA OF DNA ELEMENTS. IF SUCCESSFUL, THE RESEARCH WOULD CATALYZE THE STUDY OF THE EPIGENETICS OF AD, AND ENABLE THE WIDESPREAD APPLICATION OF NEXT-GENERATION MULTI-OMIC ASSAYS TO AD AND OTHER NEUROLOGICAL DISEASES.

HIGH-THROUGHPUT SINGLE CELL CO-ASSAY OF HISTONE MODIFICATIONS ANDTRANSCRIPTOME - SUMMARY DISRUPTION OF GENE REGULATION IS A MAJOR CAUSAL FACTOR IN HERITABLE DISEASE, DEVELOPMENTAL DISORDERS, AND ONCOGENESIS. WHILE CHROMATIN IMMUNOPRECIPITATION FOLLOWED BY SEQUENCING (CHIP-SEQ) AND TN5- TRANSPOSASE BASED TAGGING (CUT&TAG) ENABLE ANALYSIS OF TRANSCRIPTION FACTOR BINDING AND EPIGENETIC STATE PROFILING IN BULK TISSUE SAMPLES AND TUMOR BIOPSIES, THEY PRODUCE ONLY POPULATION AVERAGE SIGNALS. YET REGULATORY NETWORKS AND PERTURBATIONS ARE HETEROGENEOUS BETWEEN CELL CLASSES AND TYPES. SINGLE-CELL TECHNOLOGIES CAN OVERCOME THE CHALLENGE OF CELLULAR HETEROGENEITY AND PROVIDE DEEPER INSIGHT INTO CELL TYPE-SPECIFIC GENE REGULATORY PROGRAMS IN HEALTHY, DISEASED, AND CANCEROUS TISSUES. IN PRIOR WORK, WE DEVELOPED A SINGLE-CELL JOINT ASSAY OF HISTONE MODIFICATION AND RNA EXPRESSION (PAIRED-TAG), ENABLING CELL-TYPE-STRATIFIED EPIGENETIC PROFILING FROM BULK SAMPLES. THIS TECHNOLOGY HAS ATTRACTED CUSTOMERS IN BOTH ACADEMIC AND NONPROFIT RESEARCH. IN THE PROPOSED STUDY, WE WILL DEVELOP AUTOMATED PROTOCOLS AND EFFECT LABORATORY INFORMATICS SYSTEMS TO ESTABLISH A PAIRED-TAG SERVICES LABORATORY, WE WILL REFINE OUR PROTOCOL TO IMPROVE EXPERIMENTAL THROUGHPUT AND REDUCE COST, AND WE WILL DEVELOP A PAIRED-TAG “TF” PROTOCOL FOR PROFILING TRANSCRIPTION FACTOR BINDING PROFILES. IF SUCCESSFUL, THE RESEARCH WOULD ENABLE NEXT- GENERATION MULTI-OMIC ANALYSIS OF TUMOR OR DISEASE SAMPLES AT COMPARABLE COST TO SINGLE-OMIC TECHNOLOGIES.

RESEARCH-PGR: DECIPHERING THE MOLECULAR BASIS OF ELITE RED ALDER LINES AND THEIR FRANKIA ALNI SYMBIONTS

STATISTICAL METHODS FOR CHARACTERIZING MOLECULAR MECHANISMS OF HUMAN TISSUE DEVELOPMENT AND DISEASE - PROJECT SUMMARY THE UNIQUE BIOSPECIMENS AND DATA FROM THE DEVELOPMENTAL GTEX (DGTEX) PROJECT CREATE AN EXCITING OPPORTUNITY AND NEED FOR NOVEL METHODS DEVELOPMENT. IN THIS PROJECT, WE PROPOSE TO DEVELOP A SET OF STATISTICAL METHODS AND ANALYTICAL APPROACHES THAT ARE DESIGNED TO EXTRACT INSIGHTS INTO HUMAN AND NON-HUMAN PRIMATE DEVELOPMENT FROM THE MULTI-MODAL AND MULTI-TISSUE DATA FROM DGTEX POST-MORTEM DONORS. ANALYSIS OF THE DGTEX DATA REQUIRES STATISTICAL MODELS THAT CAN TAKE ADVANTAGE OF THE RICH STRUCTURE AND DIVERSITY OF THE DATA ACROSS AGES AND MODALITIES, WHILE ADDRESSING SOME OF THE INHERENT CHALLENGES. MODELS EXPLICITLY INFORMED BY AGE CAN CAPTURE DEVELOPMENTAL TRAJECTORIES OF GENE REGULATION, GENETIC EFFECTS, AND TISSUE STRUCTURE. THE RANGE OF DATA MODALITIES ALSO CREATES AN OPPORTUNITY FOR NOVEL METHODS TO CAPTURE ADDITIONAL EFFECTS AND IMPROVED RESOLUTION AT THE CELL-TYPE, ISOFORM, AND STRUCTURAL LEVELS. HOWEVER, THESE DATA ARE ALSO INHERENTLY COMPLEX, REPRESENTING A MIXTURE OF CELL TYPES ALONG WITH BIOLOGICAL AND TECHNICAL NOISE. THE AMBITIOUS STUDY DESIGN OF DGTEX ALSO COMES WITH CHALLENGES OF DONOR RECRUITMENT THAT LIMIT SAMPLE SIZE. THE METHODS PROPOSED HERE ARE DESIGNED TO LEVERAGE THE BENEFITS OF TEMPORAL MULTI-MODAL DATA, WHILE ADDRESSING DATA COMPLEXITY AND LIMITED SAMPLE SIZE. IN OUR FIRST AIM, WE WILL ANALYZE TRANSCRIPTOME VARIATION ACROSS THE HUMAN LIFESPAN, WITH IMPROVED TRANSCRIPT ANNOTATION AND NEW METHODS TO CHARACTERIZE HOW GENE EXPRESSION, ALTERNATIVE SPLICING AND CELL TYPE COMPOSITION CHANGE DURING DEVELOPMENT AND HOW THEY CONTRIBUTE IN DRIVING PHENOTYPIC CHANGE. SECONDLY, WE WILL USE MULTI-MODAL DATA FROM GTEX TO CAPTURE CHANGES IN GENE REGULATORY NETWORKS DURING DEVELOPMENT. FROM THE DGTEX HISTOLOGY IMAGES AND SPATIAL TRANSCRIPTOMICS DATA WE WILL MODEL DEVELOPMENTAL TRAJECTORIES OF TISSUE STRUCTURES, AND DESCRIBE THEIR MOLECULAR CHARACTERISTICS AS WELL AS ROLE IN DISEASE. IN OUR THIRD AIM WE WILL MAP AND CHARACTERIZE GENETIC REGULATORY VARIATION IN DGTEX AND APPLY PREDICTIVE MODELS FOR IMPROVED PREDICTIONS OF REGULATORY VARIANTS IN PEDIATRIC TISSUES. IN ADDITION TO EMPOWERING BIOLOGICAL DISCOVERY, THIS WORK HAS THE POTENTIAL TO UNCOVER DISEASE RISK FACTORS AND MECHANISMS THAT ORIGINATE OR MANIFEST DURING EARLY LIFE.

PUBLIC HOUSING CAPITAL FUND

STUDYING THE REGULATORY DYNAMICS WITH SINGLE-CELL MULTIOMICS - PROJECT SUMMARY/ABSTRACT A MULTITUDE OF EPIGENOMIC VARIABLES AND MECHANISMS CONTRIBUTE TO CELL-TYPE-SPECIFIC GENE EXPRESSION PROGRAMS, AND THE SPATIOTEMPORAL DYNAMICS OF THESE COMPLEX GENE REGULATORY MACHINERY LAID THE FOUNDATIONS FOR DIVERSE BIOLOGICAL PROCESSES, PARTICULARLY IN DEVELOPMENT, DISEASE, AND AGING. SINGLE-CELL GENOMICS TECHNOLOGIES ALLOWED CAPTURING THE STATIC SNAPSHOTS, SUCH AS TRANSCRIPTOMIC OR EPIGENOMIC STATES OF THE CELLS; WHILE IT REMAINED CHALLENGING TO STUDY THE TEMPORAL DYNAMICS OF THE CELL’S STATE TRANSITION PROCESSES. WE HYPOTHESIZED THAT THE REGULATORY DYNAMICS ARE SHAPED BY THE BALANCE BETWEEN “WRITING” AND “ERASING” OF EPIGENOMIC VARIABLES, AND THUS CAN BE INFERRED FROM MEASURING THE LINKED MOLECULAR LAYERS THAT MAINTAIN REGULATORY EQUILIBRIUMS BY THE DEVELOPMENT OF SINGLE-CELL MULTIOMICS TECHNOLOGIES. STUDYING THE REGULATORY DYNAMICS OF CELL STATE TRANSITION IS PARTICULARLY CHALLENGING IN AGING BRAINS: AGING OF THE BRAIN INVOLVES COMPLEX CELLULAR AND MOLECULAR CHANGES, INCLUDING VARIATIONS IN MOLECULAR SIGNATURES OF CERTAIN CELL TYPES, CHANGES IN CELL POPULATION COMPOSITIONS, AND DECLINED COMMUNICATIONS BETWEEN NEURON CELLS IN THIS TISSUE WITH THE MOST SOPHISTICATED CELLULAR COMPOSITION AND SPATIAL ORGANIZATIONS. AGING CONTRIBUTES TO MANY DISEASES THAT AFFECT ALL ORGAN SYSTEMS AND IS THE GREATEST RISK FACTOR FOR MULTIPLE DISEASES, INCLUDING NEURODEGENERATION AND CANCERS. UNDERSTANDING THE FUNDAMENTAL BIOLOGY OF AGING IS ESSENTIAL FOR THE DEVELOPMENT OF CLINICAL INTERVENTIONS. BUT CURRENT OMICS ANALYSIS OF AGING CAN ONLY CAPTURE THE STATIC PICTURES OF INDIVIDUAL MODALITIES, WHICH CANNOT DIFFERENTIATE WELL-MAINTAINED COMPONENTS (YOUNG) FROM THOSE WHO ARE ABOUT TO LOSE FIDELITY (PRE-DECAY) NOR RECORD THE COMPLEX RELATIONSHIPS BETWEEN DIFFERENT MOLECULE TYPES. IN THIS PROPOSAL, WE AIM TO FUNDAMENTALLY TRANSFORM OUR APPROACHES TO STUDYING THE PRINCIPLES OF CELL STATE TRANSITION, FOCUSING ON THE MOUSE AGING BRAIN AS A MODEL SYSTEM, BY DEVELOPING INNOVATIVE SINGLE-CELL GENOMICS TECHNOLOGIES FOR JOINT ANALYSIS OF THE CELL’S REGULATORY DYNAMICS AND TRANSCRIPTIONAL STATES. FIRSTLY, WE WILL DEVELOP A SET OF SINGLE-CELL MULTIOMICS TOOLS FOR INTEGRATED ANALYSIS OF THE RATES OF FORWARD AND REVERSE REACTIONS IN MAINTAINING THE CELL’S REGULATORY STATES, INCLUDING EPIGENOME (DNA METHYLATION AND ACTIVE DEMETHYLATION) AND DNA DAMAGES (OXIDATIVE DAMAGES AND BASE EXCISION REPAIR) WITH THE TRANSCRIPTIONAL STATES. NEXT, WE WILL DEVELOP A TECHNOLOGY FOR THE DETECTION OF COLOCALIZED REGULATORY ELEMENTS AND THEIR EPIGENETIC STATES JOINTLY WITH TRANSCRIPTOMES FROM SINGLE CELLS, TO EVALUATE THE CELL’S REGULATORY FUNCTIONALITY. FINALLY, WE WILL DEVELOP A MODULARIZED PLATFORM FOR TISSUE-SCALE HIGH-DEFINITION 3-D SPATIAL REGISTRATION OF SINGLE CELLS (AMBER) AND THEN COMBINE IT WITH THESE SINGLE-CELL MULTIOMICS TOOLS TO RECONSTRUCT THE WHOLE TISSUE STRUCTURE WITH MULTIMODAL MOLECULAR PROFILES. WE WILL APPLY OUR METHODS TO INVESTIGATE THE MOLECULAR CHANGES OF AGING IN NERVOUS SYSTEMS WITH 3-D SPATIAL INFORMATION FROM MOUSE MODELS, AND BELIEVE OUR APPROACH IS BROADLY APPLICABLE TO STUDYING REGULATORY DYNAMICS ACROSS VARIOUS BIOLOGICAL SYSTEMS BOTH IN HEALTH AND DISEASES.

MICROPUBLICATIONS FOR AUTOMATING GENOME SEQUENCE VARIANT INTERPRETATION FROM MEDICAL LITERATURE - PROJECT SUMMARY ACCURATE AND EFFICIENT INTERPRETATION OF GENOMIC VARIANTS FOR CLINICAL DECISION MAKING IS PREDICATED ON READY ACCESS TO AND EXTRACTION OF INFORMATION FROM THE MEDICAL LITERATURE. THE SHEER NUMBER OF POTENTIALLY RELEVANT ARTICLES THAT MUST BE EXAMINED DURING THIS PROCESS POSES A SIGNIFICANT CHALLENGE IN ENSURING THE ACCURACY AND REPRODUCIBILITY OF CLINICAL INTERPRETATION AS IT IS TIME-CONSUMING, ERROR-PRONE, AND HIGHLY USER-DEPENDENT. TO THIS END, WE HAVE DEVELOPED THE MASTERMIND GENOMIC SEARCH ENGINE - A COMMERCIAL DATABASE THAT AUTOMATICALLY ORGANIZES DISEASE, GENE AND VARIANT INFORMATION FROM THE MEDICAL LITERATURE BY SYSTEMATICALLY INDEXING MILLIONS OF SCIENTIFIC ARTICLES. MASTERMIND IS USED BY OVER 9,100 VARIANT SCIENTISTS IN MORE THAN 100 DIFFERENT COUNTRIES TO MORE QUICKLY INTERPRET GENETIC VARIANTS IN CLINICAL SETTINGS. IN PHASE I OF THIS PROJECT, WE DEVELOPED AND TESTED A MICROPUBLICATION PLATFORM WITHIN MASTERMIND THAT ASSEMBLES LITERATURE CURATION ALONG WITH POPULATION FREQUENCY DATA, COMPUTATIONAL PREDICTIONS OF PATHOGENICITY, AND AUTOMATED ACMG/AMP CLASSIFICATIONS THAT IMPROVES THE SPEED OF VARIANT INTERPRETATION BY MORE THAN 70% AND INCREASES THE SENSITIVITY OF THESE RESULTS BY 2-20X. THE PRESENT PROPOSAL SEEKS TO BUILD ON THE SUCCESS OF PHASE I BY 1) INTEGRATING THE MICROPUBLICATION PLATFORM INTO MASTERMIND WITH MIGRATION OF COLLABORATIVE FEATURES FOR COMMUNITY-BASED EVALUATION OF VARIANT INTERPRETATIONS; 2) OPTIMIZING AND IMPROVING AUTOMATED VARIANT INTERPRETATION/PRIORITIZATION OF ARTICLES AND IMPLEMENTING A RIGOROUS QUALITY ASSURANCE PROCESS; AND 3) USING THESE IMPROVEMENTS TO CURATE ALL EVIDENCE IN ALL VARIANTS IN ALL GENES COMPRISING THE ENTIRE HUMAN GENOME, BEGINNING WITH THE CLINICAL EXOME. INTEGRATION OF THE PRE-CURATED GENOME DATA IN THE MICROPUBLICATION PLATFORM WILL RESULT IN MASTERMIND ENTERPRISE, ALLOWING FOR IMMEDIATE AND ACCURATE GENOME-WIDE VARIANT INTERPRETATIONS WITH COLLABORATIVE CURATION IN REAL-TIME AT THE POINT OF INTERACTION WITH SOURCE MATERIAL (I.E. INDIVIDUAL REFERENCES). THIS WORK WILL MITIGATE REPRODUCIBILITY CHALLENGES PLAGUING OTHER LARGE-SCALE CROWD-SOURCED PROJECTS, INCLUDING THOSE UNDERTAKEN BY GROUPS LIKE NIH’S CLINVAR AND QIAGEN’S HGMD. IN ADDITION, OUR NOVEL APPROACH WILL NOT SUFFER FROM POOR SENSITIVITY AS IT RELIES ON A COMPREHENSIVE SOURCE OF MEDICAL LITERATURE PRE-ANNOTATED BASED ON GENETIC CONTENT. THIS WORK WILL PERMIT DRAMATIC SCALING OF VARIANT INTERPRETATION ACTIVITIES AND ALLOW FOR COMPLETE AND ACCURATE CURATION OF THE ENTIRE HUMAN GENOME WITHIN 2 YEARS – A FEAT THAT COULD NOT BE COMPLETED UTILIZING CURRENT MANUAL METHODS FOR VARIANT INTERPRETATION. MASTERMIND ENTERPRISE WILL BE REVOLUTIONARY IN THE GENOMICS INDUSTRY AND WILL REPRESENT A NATURAL NEXT STEP TO BUILD ON THE ACHIEVEMENTS PROVIDED BY THE HUMAN GENOME PROJECT AND THE REDUCED COST OF NEXT-GENERATION SEQUENCING. IT WILL SUBSTANTIALLY IMPROVE DIAGNOSTIC RATES AND ACCURACY IN THE CLINIC, ESPECIALLY IN RARE DISEASE, WHERE A LACK OF GENETIC EVIDENCE OFTEN RESULTS IN SEVERELY DELAYED AND INACCURATE DIAGNOSES. ADDITIONALLY, IT WILL ALLOW THE PHARMACEUTICAL INDUSTRY TO DEVELOP MORE SUCCESSFUL TARGETED THERAPIES AND TO DESIGN MORE INCLUSIVE CLINICAL TRIALS AS WELL AS TO MORE RELIABLY IDENTIFY PATIENTS WHO WOULD BENEFIT FROM THERAPEUTIC INTERVENTION. [WORD COUNT – 468; LINE COUNT – 30]

COMMERCIAL SOFTWARE USING HIGH-THROUGHPUT COMPUTATIONAL TECHNIQUES TO IMPROVE GENOME ANALYSIS

LAUNCH RAMP REPAIR

REGULATORY MODIFIERS OF CODING VARIANT PENETRANCE VIA HAPLOTYPE EPISTASIS IN HUMAN POPULATIONS AND DISEASES

BUILDING KAWERAK REGION TRIBAL CAPACITY FOR EFFECTIVE FISHERIES CO-STEWARDSHIP

UNKNOWN TITLE

SCALABLE MULTI-ANCESTRY FUNCTIONAL GENOMICS OF BLOOD TRAITS AND CARDIOVASCULAR DISEASE - PROJECT SUMMARY CARDIOVASCULAR DISEASE (CVD) IS THE MOST COMMON CAUSE OF MORTALITY IN THE WORLD. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE SUCCESSFULLY IDENTIFIED NUMEROUS GENETIC VARIANTS ASSOCIATED WITH CVD. HOWEVER, MOST VARIANTS DO NOT NECESSARILY CAUSE THE OBSERVED PHENOTYPES, BUT RATHER ARE IN LINKAGE DISEQUILIBRIUM WITH THE TRULY CAUSAL VARIANTS THAT INFLUENCE DISEASE PATHOPHYSIOLOGY VIA LARGELY UNKNOWN MOLECULAR AND CELLULAR MECHANISMS. THUS, THREE CENTRAL CHALLENGES FOR CVD GWAS ARE: 1) IDENTIFYING CAUSAL VARIANTS, 2) UNDERSTANDING WHICH CELL TYPES ARE MOST RELEVANT FOR SPECIFIC VARIANTS, AND 3) IDENTIFYING THE CIS- AND TRANS-REGULATORY TARGET GENES WHOSE EXPRESSION IS MODULATED BY CVD VARIANTS. CURRENTLY, THERE IS NO CONSENSUS ON HOW BEST TO IDENTIFY RELEVANT CELL TYPES AND TARGET GENES. FURTHERMORE, EFFORTS TO CONNECT SPECIFIC NONCODING VARIANTS TO TARGET GENES, SUCH AS CRISPR-BASED INSERTION OF SPECIFIC VARIANTS COUPLED WITH PHENOTYPIC ASSAYS HAVE BEEN HAMPERED BY LOW THROUGHPUT. HERE, WE SEEK TO DEVELOP SCALABLE METHODS TO ADDRESS ALL THREE CENTRAL CHALLENGES FOR CVD DISEASE GWAS, WHILE LEVERAGING THE CONSIDERABLE BENEFITS OF POPULATION-SCALE, MULTI-ANCESTRY GWAS — NAMELY, IMPROVED DISCOVERY OF NOVEL GWAS LOCI AND INCREASED RESOLUTION FOR CAUSAL VARIANTS AT ALREADY KNOWN LOCI. OF THE MANY CELL TYPES AND ORGAN SYSTEMS UNDERLYING CVD PATHOPHYSIOLOGY, WE WILL FOCUS ON BLOOD-RELATED MECHANISMS, WHICH ARE CURRENTLY UNDERSTUDIED DESPITE THE IMPORTANCE OF E.G., IMMUNE RESPONSE AND COAGULATION IN CVD, DEMONSTRATED BY PRIOR WORK AND OUR PRELIMINARY DATA. IN AIM 1, WE WILL PERFORM COLOCALIZATION OF CVD AND BLOOD CELL TRAIT GWASES (AS BLOOD CELLS TRAITS ARE NATURALLY CELL-TYPE-SPECIFIC) AND PRODUCE A REFERENCE ATLAS OF 3D ENHANCER MAPS FOR 13 BLOOD CELL TYPES AND 2 ENDOTHELIAL CELL TYPES IN DONORS OF DIVERSE ANCESTRIES. IN AIM 2, WE WILL COMBINE CRISPR SCREENS AND SINGLE-CELL MULTIOMICS (STING-SEQ) IN BLOOD AND ENDOTHELIAL CELLS TO IDENTIFY CAUSAL VARIANTS AND TARGET GENES FOR CVD. WE WILL FURTHER EXTEND IT BY DEVELOPING BEESTING-SEQ, WHICH COMBINES CYTOSINE AND ADENINE BASE EDITORS WITH A MORE FLEXIBLE CRISPR ENZYME TO INSERT PRECISE SNPS. FOR BOTH STING METHODS, WE WILL USE A THOROUGHLY-VALIDATED COMPUTATIONAL APPROACH TO IDENTIFY CIS AND TRANS TARGET GENES AND REGULATORY NETWORKS. FURTHER, WE WILL DEEPLY VALIDATE TOP VARIANTS USING KEY FUNCTIONAL ASSAYS (ELECTRICAL IMPEDANCE, MIGRATION AND STRESS RESPONSE). THIS PROPOSAL TAKES AN INTERDISCIPLINARY APPROACH WITH A TEAM OF EXPERTS IN NONCODING BIOLOGY AND HIGH-THROUGHPUT SINGLE-CELL CRISPR SCREENS (SANJANA), IN GENETICS AND SYSTEMS BIOLOGY (LAPPALAINEN) AND IN CVD GWAS, CARDIOLOGY AND ENDOTHELIAL CELL FUNCTION (GUPTA). OUR INTEGRATED EXPERIMENTAL AND COMPUTATIONAL APPROACH WILL NOT ONLY REVEAL HOW GENOMIC VARIATION SHAPES CVD RISK, BUT ALSO DEVELOP A GENERALIZABLE TOOLKIT THAT LEVERAGES CUTTING-EDGE 3D GENOME MAPPING, GENE EDITING AND SINGLE-CELL PROFILING TO MAP GENE REGULATORY ELEMENTS, SPECIFIC VARIANTS AND TARGET GENES TO INFORM FUTURE CVD THERAPEUTICS.

A XENOPUS TROPICALIS MUTANT RESOURCE

DESCRIPTION:THIS AGREEMENT PROVIDES FUNDING TO NOME JOINT UTILITY SYSTEM IN ALASKA TO IMPLEMENT ITS PROJECT TO CONNECT UNDERSERVED PROPERTIES (PRIMARILY OWNED BY ALASKA NATIVE RESIDENTS OR ALASKA NATIVE ORGANIZATIONS) TO THE UTILITY'S EXISTING WATER AND SEWER MAIN SYSTEMS AS DIRECTED IN THE 2023 CONSOLIDATED APPROPRIATIONS ACT AND IDENTIFIED IN AN APPROVED TECHNICAL CORRECTION FOR THIS PROJECT.ACTIVITIES:THE ACTIVITIES TO BE PERFORMED INCLUDE THE EXECUTION AND IMPLEMENTATION OF THE DESIGN AND CONSTRUCTION EFFORTS NEEDED TO EXTEND WATER DISTRIBUTION AND WASTEWATER COLLECTION MAINS UNDER (THE EXISTING ROADWAY OF) E 6TH AVE BETWEEN E N ST AND GREG KRUSCHEK AVE. THIS INCLUDES THE SEWER SYSTEM: INSTALLING 3 MANHOLES, 1 LIFT STATION AND 900' OF 8' ARCTIC PIPE SEWER MAIN AND THE WATER SYSTEM: INSTALLING 1100' OF 8' WATER MAIN PIPE WITH A 4' RETURN PIPE. SUBRECIPIENT:NO SUBAWARDS ARE INCLUDED IN THIS ASSISTANCE AGREEMENT.OUTCOMES:THIS PROJECT WILL CONNECT UNDERSERVED RESIDENTS ON E 6TH AVE, BETWEEN E N ST AND GREG KRUSCHEK AVE, TO POTABLE WATER DISTRIBUTION AND WASTEWATER COLLECTION SYSTEMS. EXTENDING THESE UTILITIES WILL ALLOW PROPERTY OWNERS TO SHIFT FROM HAULED POTABLE WATER AND HAULED OFF WASTEWATER. IT WILL ALSO FACILITATE CONSTRUCTION BY THE VILLAGE OF SOLOMON (VOS), KING ISLAND NATIVE COMMUNITY (KINC) AND BERING STRAITS REGIONAL HOUSING AUTHORITY (BSHRA) TO HELP ADDRESS THE COMMUNITY'S CRITICAL HOUSING SHORTAGE. THE INTENDED BENEFICIARIES INCLUDE: RESIDENTS OF CITY OF NOME, HUMAN HEALTH, AND THE ENVIRONMENT.

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

FINE-MAPPING PSYCHIATRIC DISEASE VARIANTS THAT AFFECT POST-TRANSCRIPTIONAL GENE REGULATION - PROJECT SUMMARY NEUROPSYCHIATRIC DISORDERS (NPD) SUCH AS SCHIZOPHRENIA (SZ), AUTISM SPECTRUM DISORDERS (ASD) AND BIPOLAR DISORDERS (BD) ARE REMARKABLY COMMON, WITH SZ ALONE AFFECTING NEARLY THREE MILLION AMERICANS. DESPITE MORE THAN FIFTY YEARS OF RESEARCH, NO CURES EXIST FOR THESE CONDITIONS AND THE STANDARD OF TREATMENT REMAINS UNSATISFACTORY. GENOME-WIDE ASSOCIATION STUDIES (GWAS) INDICATE THAT, IN ADDITION TO HIGHLY PENETRANT RARE MUTATIONS, NPD RISK ALSO REFLECTS THE IMPACT OF HUNDREDS OF COMMON SINGLE NUCLEOTIDE POLYMORPHISMS WITH SMALL EFFECT SIZES. A MAJOR CHALLENGE IN THE FIELD HAS BEEN ILLUMINATING THE PATHWAYS CONNECTING THESE GENETIC VARIANTS (THE VAST MAJORITY OF WHICH FALL IN NON-CODING SEQUENCES) TO TARGET GENES AND CAUSAL CELLULAR PHENOTYPES. TO UNDERSTAND HOW THESE MYRIAD RISK LOCI CAUSALLY CONTRIBUTE TO DISEASE RISK, IT IS ESSENTIAL TO SCREEN FOR PUTATIVELY CAUSAL VARIANT(S) AND DETERMINE HOW THEY INFLUENCE GENE EXPRESSION, WHICH HAS BEEN SHOWN TO BE CELL-TYPE SPECIFIC, AS WELL AS CELLULAR FUNCTION. RECENT EVIDENCE HAS EMERGED INDICATING A SUBSTANTIAL CONTRIBUTION OF RNA SPLICING VARIATION TO HERITABILITY ACROSS MANY COMPLEX GENETIC DISEASES, INCLUDING SZ. BASED ON OUR PRELIMINARY ANALYSES AND THE WORK OF OTHERS, WE HYPOTHESIZE THAT A SUBSTANTIAL PROPORTION OF NPD GWAS LOCI EXERT THEIR PATHOGENIC EFFECTS ON NEURONAL FUNCTION BY IMPACTING RNA: ITS STRUCTURE, MODIFICATIONS, PROTEIN INTERACTIONS AND SPLICING. TO TEST THIS, WE WILL APPLY NOVEL TOOLS AND MACHINE LEARNING METHODS TO PREDICT AND QUANTIFY RNA SPLICING IN THE LARGEST SZ, ASD AND BD GWAS, IN ORDER TO PREDICT SPLICING QUANTITATIVE TRAIT LOCI (SQTLS, AIM 1). TO CONFIRM TRUE EFFECTS ON EXON INCLUSION INDEPENDENTLY IN GLUTAMATERGIC AND GABAERGIC NEURONS (I.E., THE MAJOR CELL-TYPES IMPACTED IN NPD), UP TO SEVERAL THOUSAND OF THE PREDICTED SPLICE VARIANTS WILL BE TESTED BY A MASSIVELY PARALLEL REPORTER ASSAY, MAPSY (AIM 2). FINALLY, IN ORDER TO EVALUATE THE CELL-TYPE-SPECIFIC IMPACT OF PUTATIVE CAUSAL SQTLS IDENTIFIED IN AIMS 1 AND 2 ON NEURONAL MATURATION AND SYNAPTIC FUNCTION, WE WILL USE CRISPR GENE EDITING TO ENGINEER THESE MUTATIONS WITHIN HUMAN INDUCED PLURIPOTENT STEM CELL (HIPSC)-BASED MODELS OF BOTH NEURAL CELL TYPES (AIM 3). OUR OVERARCHING GOAL IS TO MAP AND FUNCTIONALLY EVALUATE THE NPD-GWAS LOCI THAT IMPACT ALTERNATIVE SPLICING AND NEURONAL FUNCTION. OUR WORK MAY IMPACT THE FIELD BY DELIVERING NEW INSIGHTS INTO THE ROLE OF COMMON VARIANTS IN NPD PATHOPHYSIOLOGY, WHICH COULD INFORM WAYS OF IMPROVING DIAGNOSTICS, PREDICTING CLINICAL TRAJECTORIES, AND DEVELOPING NOVEL THERAPEUTIC INTERVENTIONS.

ECONOMIC DEVELOPMENT INITIATIVE, COMMUNITY PROJECT FUNDING, AND MISCELLANEOUS GRANTS

SCHIFF BASE FORMING SUNSCREEN FILTERS FOR LONG-WEAR UV PROTECTION

ONECPD TA & CAP BLDG

THE TRANSLATIONAL DEVELOPMENT OF A THERAPEUTIC FOR TRIPLE NEGATIVE BREAST CANCER

IMPACT AID PROGRAM, TITLE VIII, SECTION 8003

ADVANCED DEVELOPMENT OF LANCET, AN EMERGING TOOL FOR COMPLEX VARIANT CALLING IN CANCER GENOMICS - ABSTRACT ONE OF THE CENTRAL CHALLENGES IN CANCER GENOMICS IS THE ABILITY TO ACCURATELY DETECT SOMATIC MUTATIONS IN HETEROGENEOUS TUMORS, AND PRECISELY DETERMINE THEIR CLONAL ORIGIN AND EVOLUTION. THIS FUNDAMENTAL KNOWLEDGE IS CENTRAL TO THE DISCOVERY OF NEW CANCER THERAPIES. IN RECENT YEARS, REDUCTIONS IN THE COST OF WHOLE-GENOME AND WHOLE-EXOME SEQUENCING HAVE ENABLED RESEARCHERS TO ADDRESS THESE QUESTIONS IN UNPRECEDENTED DETAIL. HOWEVER, A MAJOR LIMITATION IN THE FIELD HAS BEEN A PAUCITY OF METHODS FOR VARIANT CALLING THAT EXTEND BEYOND IDENTIFYING SIMPLE SINGLE-NUCLEOTIDE VARIANTS (SNVS) AND SMALL INDELS TO ALLOW THE CHARACTERIZATION OF COMPLEX STRUCTURAL CHANGES THAT ALSO PLAY A SIGNIFICANT ROLE IN TUMORIGENESIS AND CANCER PROGRESSION. INDELS OF MORE THAN A FEW BASES ARE CHALLENGING TO DISCOVER WITH TYPICALLY USED ALIGNMENT-BASED METHODS. IN ADDITION, MOST VARIANT CALLERS ANALYZE TUMOR AND NORMAL DATA SEPARATELY, WHICH CAN INTRODUCE FALSE POSITIVES SUCH AS WHEN A MUTATION SHOWS PARTIAL SUPPORT IN THE NORMAL SAMPLE. TOWARDS ADDRESSING THESE SHORTCOMINGS, WE RECENTLY INTRODUCED LANCET, A NEW SOMATIC VARIANT CALLER DEVELOPED UNDER THE AUSPICES OF THE ITCR R21. LANCET LEVERAGES LOCAL ASSEMBLY AND JOINT ANALYSIS OF TUMOR-NORMAL PAIRED DATA USING REGION-FOCUSED COLORED DE BRUIJN GRAPHS, WITH ON- THE-FLY REPEAT COMPOSITION ANALYSIS AND A SELF-TUNING K-MER STRATEGY. THIS RESULTS IN RELATIVELY REDUCED REFERENCE BIAS; AN IMPROVED ABILITY TO DETECT VARIATIONS THAT SIGNIFICANTLY DIVERGE FROM THE REFERENCE CHROMOSOME REPRESENTATIONS; A REDUCTION IN THE SCALE OF THE ANALYSIS, LEADING TO INCREASED POWER AND SENSITIVITY TO DETECT VARIANTS THROUGH LOCALIZED, COMPREHENSIVE GRAPH EXPLORATION; AND DYNAMIC ADJUSTMENT OF CALLING BEHAVIOR ACCORDING TO THE SEQUENCE CONDITIONS OF EACH GENOMIC REGION. IN TESTING, LANCET SHOWS SUPERIOR PERFORMANCE TO ALL MAJOR ALIGNMENT-BASED METHODS IN TERMS OF ACCURACY, PARTICULARLY IN THE DETECTION OF ‘TWILIGHT ZONE’ INDELS (30- 250 BP). GIVEN ITS CONTINUED ADOPTION AND SUCCESSFUL APPLICATION IN OVER A DOZEN HIGH-IMPACT PUBLICATIONS, LANCET IS POISED FOR MORE ADVANCED DEVELOPMENT TO ENABLE CONTINUED IMPROVEMENTS IN ITS VARIANT CALLING POWER, PRECISION, AND ANALYTICAL CAPABILITIES. SPECIFICALLY, LANCET IS CURRENTLY LIMITED BY LONGER RUNTIMES THAN ALIGNMENT- BASED METHODS, REDUCED SENSITIVITY FOR LONGER INSERTIONS, LACK OF INTERACTIVE VISUALIZATION OF THE COLORED DE BRUIJN GRAPH, AND THE INABILITY TO JOINTLY ANALYZE LONGITUDINAL DATA. TO ADDRESS THESE LIMITATIONS, WE PROPOSE THE FOLLOWING SPECIFIC AIMS: 1) INCREASE COMPUTATIONAL PERFORMANCE AND FACILITATE USER ADOPTION AND THIRD-PARTY DEVELOPMENT; 2) ADD NEW FEATURES AND ENHANCEMENTS TO IMPROVE VARIANT DETECTION, PHASING, AND DATA VISUALIZATION; AND 3) ENABLE JOINT ASSEMBLY AND ANALYSIS OF LONGITUDINAL DATA. IMPACT: WITH ADDITIONAL DEVELOPMENT, THE NEXT ITERATION OF LANCET WILL FEATURE ADVANCED ALGORITHMS FOR FAST, EFFICIENT, ACCURATE, LOCALIZED, USER-FRIENDLY, AND APPLICATION- MODIFIABLE VARIANT ANALYSIS OF PHASED GENOME-WIDE TIMESERIES DATA, ESTABLISHING IT AS ONE OF THE LEADING METHODS FOR VARIANT CALLING IN CANCER RESEARCH.

A19AV00261

IN-DEPTH STUDY OF THE CELLULAR AND MOLECULAR RESPONSE OF LUNG TISSUES TO ACUTE INJURY BY SMOKE INHALATION.

IMPACT AID PROGRAM, TITLE VIII, SECTION 8003

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

2/5 CLINICAL OUTCOME PREDICTION OF PSYCHOSIS FROM ELECTRONIC HEALTH RECORDS (COPPER) - PROJECT SUMMARY CLINICAL PREDICTORS ARE NOW FIRMLY INCORPORATED INTO ROUTINE STANDARD-OF-CARE IN MANY FIELDS OF MEDICINE, IN CONTRAST WITH PSYCHIATRY WHERE QUANTITATIVE PREDICTORS THAT GUIDE CLINICAL DECISION-MAKING REMAIN EXTREMELY LIMITED. PSYCHOSIS-RELATED DISORDERS ARE RESPONSIBLE FOR A SUBSTANTIAL PUBLIC HEALTH BURDEN, FOR WHICH THERE ARE SIGNIFICANT UNMET NEEDS THAT WOULD BE SUBSERVED BY CLINICAL PREDICTORS. FOR EXAMPLE, LONG-TERM OUTCOMES VARY WIDELY AND IDENTIFYING INDIVIDUALS WITH POOR OR ADVANTAGEOUS FUTURE OUTCOMES WOULD HELP TO OPTIMIZE TREATMENT PLANNING AND RESOURCE ALLOCATION. FURTHERMORE, ANTIPSYCHOTICS ARE ASSOCIATED WITH ADVERSE SIDE EFFECTS, SUCH AS INCREASED RISK OF DIABETES. IN THIS APPLICATION, WE PROPOSE TO USE MACHINE LEARNING APPROACHES TO BUILD PREDICTORS AND IDENTIFY SUBTYPES OF CLINICAL OUTCOMES AMONG INDIVIDUALS WITH SCHIZOPHRENIA, THROUGH INTEGRATION OF LONGITUDINAL ELECTRONIC HEALTH RECORDS (EHRS), DIMENSIONAL PHENOTYPING, AND GENETIC ANALYSES. WE WILL ALSO EXPLORE THE PSYCHOSOCIAL AND ETHICAL IMPLICATIONS OF PSYCHIATRIC CLINICAL PREDICTORS. OUR LONG-TERM OBJECTIVE IS TO ADVANCE THE GOALS OF PRECISION PSYCHIATRY TO ACHIEVE INDIVIDUALIZED TREATMENT PLANNING, OUTCOME MONITORING, AND PREVENTIVE INTERVENTIONS. WE PROPOSE THE FOLLOWING SPECIFIC AIMS: AIM 1: LEVERAGE TWO INDEPENDENT EHR DATABASES FOR OUTCOME PREDICTION AND SUB-CLASSIFICATION OF PSYCHOSIS-RELATED DISORDERS. (A) WE WILL USE THE LONGITUDINAL PSYCKES AND MARKETSCAN DATABASES TO BUILD MACHINE LEARNING-BASED INDIVIDUAL-LEVEL PREDICTION MODELS TO FORECAST THE ONSET OF FOUR MAJOR PROGNOSTIC OUTCOMES: TREATMENT RESPONSE (ANTIPSYCHOTIC RESISTANCE), ILLNESS SEVERITY (LONG-TERM HOSPITALIZATION), MEDICAL COMORBIDITY (DIABETES), AND DIAGNOSTIC TRANSITION FROM A PSYCHOSIS-RELATED DISORDER TO SCHIZOPHRENIA. (B) WE WILL PERFORM COHORT-LEVEL ANALYSES USING UNSUPERVISED METHODS TO DISCOVER NOVEL PSYCHOSIS-RELATED DIAGNOSIS AND PROGNOSIS SUBTYPES. AIM 2: ENHANCE PREDICTIVE MODELING THROUGH DIMENSIONAL PHENOTYPING AND WHOLE GENOME SEQUENCING. (A) WE WILL RECRUIT N = 10,000 PATIENTS WITH SCHIZOPHRENIA FROM THE PSYCKES DATABASE POPULATION FOR ENRICHED DATA COLLECTION: 1) DIMENSIONAL PHENOTYPING (COGNITION, EXPOSOME, AND SOCIAL DETERMINANTS OF HEALTH), AND 2) WHOLE GENOME SEQUENCING TO ENABLE CALLING OF RARE VARIANTS, STRUCTURAL VARIANTS, AND COMMON VARIANTS (POLYGENIC RISK). (B) WE WILL INVESTIGATE THE EXTENT TO WHICH DIMENSIONAL PHENOTYPES AND GENOMIC DATA CAN IMPROVE THE MODELS DEVELOPED IN AIM 1. AIM 3: EXPLORE THE PSYCHOSOCIAL AND ETHICAL IMPLICATIONS OF PSYCHIATRIC CLINICAL PREDICTORS. (A) WE WILL SURVEY A SUBSET OF PATIENTS AND THEIR CLINICIANS REGARDING THEIR ATTITUDES TOWARDS IMPLEMENTATION OF CLINICAL OUTCOME PREDICTORS. (B) WE WILL RETURN PATHOGENIC FINDINGS TO PATIENTS THROUGH GENETIC COUNSELING AND SURVEY THE EXPERIENCE OF PATIENTS AND THEIR CLINICIANS ON THEIR EMOTIONAL REACTIONS AND PERCEPTIONS OF IMPAIRMENT, TREATABILITY, AND LIFE-PLANNING.

IMPACT AID PROGRAM, TITLE VII, SECTION 7003

PLASMA PROTEIN BIOMARKER-BASED DIAGNOSTICS OF OUTCOME I*

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

SBIR PHASE II: HIGH-RESOLUTION SHOP FLOOR VIDEO-RATE SURFACE METROLOGY SYSTEM

COLLABORATIVE RESEARCH: TRTECH-PGR: FUNCTIONAL PANGENOMIC AND MACHINE LEARNING TOOLS FOR EXPLORING GENETIC DIVERSITY IN PLANTS -AS CLIMATE CHANGE ACCELERATES, THE ABILITY OF PLANTS TO ADAPT WILL BE CRITICAL IN ENSURING THEIR ABILITY TO SURVIVE IN FUTURE DECADES. A PLANT POPULATION THAT HAS A MORE DIVERSE SET OF GENES AND OTHER GENETIC MATERIAL IS MORE LIKELY TO SURVIVE CLIMATE SHIFTS AND CLIMATE EXTREMES. HOWEVER, AS PLANTS ARE FORCED TO ADAPT TO HARSHER CONDITIONS, MANY PLANTS WILL DIE OFF, REDUCING THE DIVERSITY OF THE GENES AVAILABLE FOR FUTURE ADAPTATION OF THE POPULATION. BECAUSE CHANGING CLIMATES ARE REQUIRING ORGANISMS TO ADAPT AT MUCH FASTER RATES THAN IN THE PAST, UNDERSTANDING THE GENETIC DIVERSITY PRESENT IN A POPULATION AND HOW THAT DIVERSITY IS CHANGING IS CRITICAL FOR UNDERSTANDING WHICH PLANTS ARE IN DANGER. THIS KNOWLEDGE IS CRITICAL TO MAINTAINING STRONG FOOD SYSTEMS AND ECOSYSTEMS. BREAKTHROUGHS IN DNA SEQUENCING TECHNOLOGY AND ARTIFICIAL INTELLIGENCE ENABLE, FOR THE FIRST TIME, THE ABILITY TO LOOK AT THE GENES AND GENOMES IN MANY INDIVIDUALS OF THE SAME PLANT SPECIES AT ONCE TO UNDERSTAND THEIR GENETIC DIVERSITY. THIS PROJECT WILL USE THIS COMPUTATIONAL APPROACH TO CONNECT DIFFERENT VERSIONS OF GENES WITH SUCCESSFUL GROWTH IN DIFFERENT CLIMATE CONDITIONS, REVEALING WHICH VERSIONS OF SPECIFIC GENES PLANTS WILL NEED AS THE CLIMATE AROUND THEM CHANGES. THE METHODS DEVELOPED WILL BE INCORPORATED INTO A SOFTWARE TOOL THAT WILL HELP SCIENTISTS STUDY GENETIC DIVERSITY IN MANY DIFFERENT PLANT SPECIES AND OTHER ORGANISMS. ADDITIONALLY, OUR K-12, UNDERGRADUATE, AND GRADUATE OUTREACH PROGRAMS WILL HELP TRAIN SCIENTISTS AND ENABLE THEM TO USE THE SOFTWARE TOOL TO COMBAT THE EFFECTS OF CLIMATE CHANGE. GIVEN RAPID AND UNPRECEDENTED CHANGES IN CLIMATE THAT THREATEN GLOBAL FOOD SECURITY AND INCREASE PLANT EXTINCTION RISK, THE NEED FOR METHODS THAT ENHANCE AND EXPEDITE INSIGHTS INTO PLANT GENETIC DIVERSITY CRITICAL FOR ADAPTATION IS WIDESPREAD AND IMMEDIATE. THE EXPONENTIAL GROWTH OF COMPLETE, HIGH-QUALITY GENOMES, FUNCTIONAL SEQUENCING DATA SETS THAT HELP DELINEATE PROMOTERS AND ENHANCERS, AND LARGE-SCALE PHENOTYPIC DATA SETS, HAS CREATED OPPORTUNITY FOR ALGORITHMIC INNOVATION TO BETTER UNDERSTAND EXTANT GENETIC DIVERSITY, HOW IT IS CHANGING, AND THE GENES AND REGULATORY SEQUENCES THAT DRIVE ADAPTATION. THIS PROJECT WILL CREATE A MODULAR SOFTWARE TOOL FOR BIOLOGISTS THAT WILL ENABLE IDENTIFICATION OF CIS-REGULATORY ELEMENTS USING FUNCTIONAL SEQUENCE AND PANGENOME-WIDE NUCLEOTIDE SIGNALS, CONNECTING THESE AND OTHER GENOMIC FEATURES TO EXPRESSION DATA AND CLIMATE VARIABLES. THIS TOOL WILL COMBINE A NOVEL GRAPH MODEL WITH RECENT INNOVATIONS IN ARTIFICIAL INTELLIGENCE, IMPROVING PANGENOMIC ANALYSES BY INCORPORATING ANNOTATION OF GENES AND THEIR CONTROL REGIONS WITH CLADE-WIDE GENOMIC VARIATION AND PHENOTYPIC VARIANCE TO IDENTIFY GENOMIC DRIVERS OF PHENOTYPIC DIFFERENCES THAT ENABLE ADAPTATION. TO TEST AND CHARACTERIZE THE TOOL, THIS PROJECT WILL FOCUS ON PUBLICLY AVAILABLE DATA SETS FROM PLANTS, WHOSE COMPLEX GENOMES PROVIDE AN IMPORTANT STRESS TEST AND WHOSE GENETIC DIVERSITY IS CRITICAL TO AGRICULTURAL SYSTEMS, FOOD SECURITY, AND ECOSYSTEM HEALTH. THE PROPOSED TOOL HAS CROSS-DISCIPLINARY IMPLICATIONS, ALLOWING ANY RESEARCHER WITH GENOME ASSEMBLIES, FUNCTIONAL SEQUENCE, AND PHENOTYPIC DATA TO PERFORM UNBIASED, COMPREHENSIVE ANALYSES OF A CLADE?S GENETIC DIVERSITY AND EXPLORE HOW THAT DIVERSITY DRIVES PHENOTYPIC ADAPTATION. THIS AWARD REFLECTS NSF'S STATUTORY MISSION AND HAS BEEN DEEMED WORTHY OF SUPPORT THROUGH EVALUATION USING THE FOUNDATION'S INTELLECTUAL MERIT AND BROADER IMPACTS REVIEW CRITERIA.- SUBAWARDS ARE NOT PLANNED FOR THIS AWARD.

NOME - FY 14 TPA BASE CR1 DIST

IMPACT AID PROGRAM, TITLE VIII, SECTION 8003

PV MODULE SOILING SPECTRAL DEPOSITION DETECTOR

BIFACIAL PV SYSTEM LOW-COST HIGH-ACCURACY IRRADIANCE MEASUREMENTS

PH CAPITAL FUND M-TA

CD74 IMMUNOTHERAPY OF SYSTEMIC LUPUS ERYTHEMATOSUS

NOME ESKIMO COMMUNITY - TPA BASE CR1 DISTRIBUTION

IMPACT AID PROGRAM, TITLE VIII, SECTION 8003

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

NOME ESKIMO COMMUNITY

RAT GERMLINE GENE EDITING PRODUCTS AND SERVICES

IMPACT AID PROGRAM, TITLE VIII, SECTION 8003

TRTECH-PGR: UNLOCKING BREAD WHEAT GENOME DIVERSITY: FOUNDATIONAL GENOME SEQUENCES AND RESOURCES TO ADVANCE BREEDING AND BIOTECHNOLOGICAL IMPROVEMENT OF A GLOBAL FOOD SECURITY CROP -COMMON BREAD WHEAT (TRITICUM AESTIVUM L.) IS A MAJOR FOOD SECURITY CROP, PROVIDING ~20% OF HUMAN DIETARY CALORIES AND PROTEINS WORLDWIDE. GENETIC DIVERSITY UNDERLIES THE PRODUCTIVITY AND ADAPTIVE CAPACITY OF AGRICULTURE; YET, TODAY?S HIGH-YIELDING WHEAT VARIETIES CONTAIN ONLY A SMALL FRACTION OF THE AVAILABLE GENE POOL, RAISING CONCERNS THAT OVERRELIANCE ON EXISTING BREEDING STOCKS COULD LIMIT FUTURE GAINS IN WHEAT PRODUCTION. SIGNIFICANT GENETIC DIVERSITY IS HELD WITHIN LANDRACES THAT WERE TRADITIONALLY FARMED ACROSS EUROPE, NORTHERN AFRICA, AND ASIA FOR THOUSANDS OF YEARS PRIOR TO THEIR DISPLACEMENT BY MODERN AGRICULTURE. THIS PROJECT ADDRESSES A CRITICAL NEED TO PRESERVE, DISCOVER, AND MOBILIZE THESE GENETIC RESOURCES BY GENERATING GENOME SEQUENCES OF EIGHT LANDRACES THAT ARE FOUNDATIONAL TO EARLY REGIONAL GROWING CENTERS AND ENCOMPASS THE WORLDWIDE DIVERSITY OF BREAD WHEAT. IN ADDITION, THIS PROJECT WILL UPDATE THE INTERNATIONAL WHEAT GENOME SEQUENCING CONSORTIUM (IWGSC) CHINESE SPRING REFERENCE GENOME SEQUENCE, AN IMPORTANT COMMUNITY-RESOURCE THAT HAS SERVED AS A SPRINGBOARD FOR ADVANCEMENTS IN WHEAT GENETICS, EVOLUTION, BREEDING AND BIOTECHNOLOGY RESEARCH. WITH RESPECT TO TRAINING AND PUBLIC OUTREACH, THIS PROJECT WILL CONTINUE ESTABLISHED EDUCATION, OUTREACH AND TRAINING ACTIVITIES, INCLUDING SUMMER UNDERGRADUATE RESEARCH INTERNSHIPS, ANNUAL INTERNATIONAL WORKSHOPS, EARLY CAREER SPEAKER AWARDS, AND MONTHLY WEBINAR SERIES. THE PROJECT WILL FURTHER INCREASE SCIENCE, TECHNOLOGY, ENGINEERING AND MATHEMATICS (STEM) EDUCATOR TRAINING, PUBLIC SCIENTIFIC LITERACY, AND CONTRIBUTE TO A DIVERSIFIED WORKFORCE. GENERATION OF GENOME SEQUENCE AND ANNOTATION OF EIGHT STRATEGICALLY SELECTED LANDRACES, ALONG WITH THE UPDATED INTERNATIONAL WHEAT GENOME SEQUENCING CONSORTIUM CHINESE SPRING REFERENCE GENOME SEQUENCE, WILL PROVIDE A CRUCIAL STEP FORWARD IN WORLD-WIDE EFFORTS TO IMPROVE WHEAT BY IDENTIFYING THE EXTENT OF GENOMIC DIVERSITY THAT UNDERLIES ADAPTIVE TRAITS. LANDRACES ARE A PARTICULARLY IMPORTANT RESERVOIR OF PHENOTYPIC TRAITS, HAVING ADAPTED OVER MANY GENERATIONS TO LOCALIZED ENVIRONMENTS AND AGRONOMIC SYSTEMS. THE NINE GENOME ASSEMBLIES WILL BE GENERATED BY APPLYING RECENT ADVANCES IN LONG-READ SEQUENCING, OPTICAL MAPS, AND CHROMOSOME CONFORMATION CAPTURE SEQUENCING, WHICH HAVE BEEN DEMONSTRATED TO PROVIDE LOW-COST, PLATINUM-QUALITY ASSEMBLIES OF EVEN LARGE AND COMPLEX GENOMES SUCH AS HEXAPLOID WHEAT (TRITICUM AESTIVUM L. 2N = 6X = 42, AABBDD). ALL GENOMES WILL BE ANNOTATED USING ESTABLISHED PIPELINES AND ACCESSION-DERIVED TRANSCRIPTOME DATA TO INFORM GENE MODELS ACROSS THE DIVERSITY PANEL. EXISTING ANNOTATIONS IN THE CHINESE SPRING REFERENCE GENOME SEQUENCE, INCLUDING THOUSANDS OF COMMUNITY-CONTRIBUTED AND MANUALLY CURATED GENE MODELS, WILL BE PRESERVED IN THE NEW REFSEQ VERSION, WITH SYNTELOGS IDENTIFIED IN THE EIGHT LANDRACE GENOMES. TO MAKE THIS RESOURCE APPLICABLE TO ADVANCED METHODS OF GENETIC AND BREEDING RESEARCH, THE PROJECT WILL DEVELOP A PRACTICAL HAPLOTYPE GRAPH REPRESENTATION OF THESE AND ADDITIONAL PUBLIC REFERENCE GENOME SEQUENCES DEVELOPED BY THE COMMUNITY AT LARGE. THESE PRODUCTS WILL EXCEED PREVIOUS WHEAT PAN-GENOME EFFORTS AND EMPOWER THE WHEAT COMMUNITY TO STRATEGICALLY INCORPORATE UNDERUTILIZED GERMPLASMS TO MEET CURRENT AND FUTURE CHALLENGES IN CROP RESEARCH AND IMPROVEMENT. PUBLIC ACCESS TO ALL PROJECT OUTCOMES WILL BE PROVIDED THROUGH LONG-TERM REPOSITORIES SUCH AS NCBI (FOR DATA ORIGINATING IN THE UNITED STATES) OR EMBL-EBI (FOR DATA ORIGINATING IN EUROPE) AND FURTHER RELEASED TO THE COMMUNITY VIA THE IWGSC DATA REPOSITORY, GRAINGENES, ENSEMBL PLANTS, AND THROUGH DATA PUBLICATION. THIS AWARD REFLECTS NSF'S STATUTORY MISSION AND HAS BEEN DEEMED WORTHY OF SUPPORT THROUGH EVALUATION USING THE FOUNDATION'S INTELLECTUAL MERIT AND BROADER IMPACTS REVIEW CRITERIA.- SUBAWARDS ARE PLANNED FOR THIS AWARD.

NOME ESKIMO COMMUNITY - TPA BASE CR1 DIST.

NOME - INITIAL WELFARE ASSISTANCE GRANT DIST.

IMPACT AID PROGRAM, TITLE VIII, SECTION 8003

INITIAL TPA BASE DISTRIBUTION UNDER C.R. #1 (THROUGH MARCH 27, 2013)

IMPACT AID PROGRAM, TITLE VIII, SECTION 8003

GOLDMANN CONTACT TONOMETRY WITH OPTIMIZED ERROR CORRECTION

IMPACT AID PROGRAM TITLE VIII SECTION 8003

F-18 LABELED PEPTIDES FOR PRETARGETED PET IMAGING OF PANCREATIC CANCER

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

INDIAN COMMUNITY DEVELOPMENT BLOCK GRANT (ICDBG)

METHODS FOR EFFICIENT DETECTION OF MUTATIONS IN ZEBRAFISH

NSP3 TA GRANTS

DOCK CONSTRUCTION

IMPACT AID PROGRAM TITLE VIII SECTION 8003

SBIR PHASE II: RAPID AND ACCURATE MULTI-VARIABLE OPTIMIZATION SOFTWARE FOR ARRAYS OF HEAT SINKS

MAB-BASED TARGETED CHEMOTHERAPY OF LUNG CANCER

WHOLE GENOME CHROMATIN INTERACTION ANALYSIS USING PAIR-END-DITAGGING (CIA-PET)

PROJECT TITLE: NOME ESKIMO COMMUNITY TRANSPORTATION PROGRAM FUNDING FY 2024 :::: PROJECT DESCRIPTION: ALL TRANSPORTATION FUNDING PROVIDED BY FHWA TO NOME ESKIMO COMMUNITY UNDER THE FHWA OTT PROGRAM AGREEMENT FOR FY24

RURAL HIT NETWORK PROGRAM

BROADLY ACCESSIBLE TECHNOLOGIES FOR SINGLE-CELL JOINT ANALYSIS OF TRANSCRIPTOME AND EPIGENOME - ABSTRACT HISTONE MODIFICATIONS CARRY RICH INFORMATION OF CELLULAR MEMORY AND GENE REGULATORY MECHANISMS. SINGLE CELL ANALYSIS OF HISTONE MODIFICATION IN CONJUNCTION WITH TRANSCRIPTOME COULD RECOVER THIS CRITICAL LAYER OF CELL IDENTITY AND HELP TO DISSECT THE CELLULAR AND MOLECULAR COMPOSITION OF COMPLEX TISSUES SUCH AS THE BRAIN. WE RECENTLY DEVELOPED AN ULTRA-HIGH THROUGHPUT SINGLE CELL MULTI-OMICS ASSAY, PAIRED-TAG, THAT CAN JOINTLY MAP TRANSCRIPTOME AND HISTONE MODIFICATIONS FROM UP TO A MILLION SINGLE CELLS IN PARALLEL. IN ORDER TO TRANSLATE THIS NOVEL TECHNOLOGY TO THE MARKETPLACE AND TO ADVANCE THE GOALS OF THE BRAIN INITIATIVE, WE PROPOSE TO OPTIMIZE AND FURTHER DEVELOP PAIRED-TAG TO ENABLE ITS BROAD USE IN THE RESEARCH COMMUNITY. SPECIFICALLY, WE WILL DEVELOP PAIRED-TAG KITS TO ALLOW FOR GENERAL ACCESSIBILITY OF THE METHOD IN MOLECULAR BIOLOGY LABORATORIES. WE WILL THEN CARRY OUT EXTENSIVE FIELD TESTS OF THE PAIRED-TAG KIT IN THE LABORATORIES OF CURRENT BRAIN INITIATIVE INVESTIGATORS, AND FURTHER IMPROVE IT BASED ON THE FEEDBACKS. FINALLY, WE WILL ADAPT THE PAIRED-TAG PROCEDURE TO LONG-READ SEQUENCING TECHNOLOGIES TO ENABLE HIGH THROUGHPUT DETECTION OF SPLICING ISOFORMS IN BRAIN CELLS AT SINGLE CELL RESOLUTION. IF SUCCESSFUL, THE PROPOSED RESEARCH WOULD PROVIDE RESEARCHERS WITH A POWERFUL NEW TOOL FOR SINGLE CELL TRANSCRIPTOMICS AND EPIGENOMICS ANALYSIS.

DOCK AND LOCK: NOVEL PROTEIN ENGINEERING

LARGE SCALE GENERATION OF ANTI-ZEBRAFISH MONOCLONAL ANTIBODIES

BIOMARKER DISCOVERY IN COLON CANCER THROUGH NEXT-GENERATION METABOLOMICS - PROJECT SUMMARY METABOLOMICS IS THE STUDY OF SMALL MOLECULE METABOLITES AND HAS DRASTICALLY IMPROVED HEALTH RESEARCH, DIAGNOSTICS, AND PATIENT TREATMENT. METABOLOMIC APPROACHES QUANTIFY THE ABUNDANCE OF SMALL MOLECULES WITHIN BIOLOGICAL SAMPLES USING LIQUID CHROMATOGRAPHY COUPLED TO MASS SPECTROMETRY (LC/MS), WHICH IS CAPABLE OF SIMULTANEOUS DETECTION OF 1,000S OF METABOLITES. CANCER, A FUNDAMENTALLY METABOLIC DISEASE, HAS BENEFITTED GREATLY FROM METABOLOMICS, HAVING ENABLED THE DISCOVERY OF TUMOR HETEROGENEITY, NOVEL BIOMARKERS, AND INDIVIDUALIZED TREATMENTS. UNTIL RECENTLY, HOWEVER, NEARLY ALL LARGE-SCALE METABOLOMICS ANALYSES HAVE BEEN LIMITED TO TARGETED STUDIES OF A FEW HUNDRED PRE-DISCOVERED METABOLITES. IN PART, THIS IS DUE TO THE DATA BURDEN AND UNCERTAINTY IN GLOBAL ANALYSIS OF ALL DETECTED METABOLITES (I.E., UNTARGETED METABOLOMICS). RESEARCHERS HAVE BEEN SLOW TO ADOPT UNTARGETED METABOLOMICS BECAUSE IT RELIES HEAVILY ON SOFTWARE TO EVALUATE THE LARGE NUMBER OF SIGNALS DETECTED. UNFORTUNATELY, CURRENT SOFTWARE ARE LIMITED BY TWO MAJOR FACTORS: (1) ~90% OF THE DETECTED SIGNALS DO NOT REPRESENT UNIQUE METABOLITES BUT ARE FALSE POSITIVES OR REDUNDANT COMPOUND DETECTIONS DERIVED FROM CHEMICAL OR ELECTRONIC NOISE THAT CURRENT SOFTWARE DOES NOT ADDRESS, AND (2) MORE THAN 80% OF MEASURED METABOLITES ARE REMOVED FROM DOWNSTREAM ANALYSIS DUE TO AMBIGUOUS IDENTIFICATIONS, IN LARGE PART DUE TO SOFTWARE PROGRAMS NOT PROVIDING STATISTICAL SCORES FOR METABOLITE IDENTIFICATION CERTAINTY. THESE LIMITATIONS LEAD TO AN INFLATED DATA BURDEN, POOR METABOLOME COVERAGE, AND MISIDENTIFIED METABOLITES, DIMINISHING THE VALUE AND IMPACT OF UNTARGETED METABOLOMICS TO CANCER RESEARCH. AT PANOME BIO, WE ARE THE FIRST METABOLOMICS CRO TO BRING A TRULY UNTARGETED METABOLOMICS APPROACH TO BIOMEDICAL RESEARCHERS. OUR COMPANY CURRENTLY OFFERS UNTARGETED METABOLOMICS IN A FEE-FOR-SERVICE MODEL AND HAS ACHIEVED STRONG INITIAL TRACTION, COMPLETING >100 CUSTOMER PROJECTS TO DATE. AN IMPORTANT ASPECT TO THIS PLATFORM IS MASSID, OUR NEXT-GENERATION UNTARGETED METABOLOMICS ANALYSIS SOFTWARE. WHILE EFFECTIVE, OUR CURRENT VERSION OF MASSID (MASSID 1.0) IS DESIGNED TO FOCUS ONLY ON THE MOST CONFIDENTLY IDENTIFIED METABOLITES AT THE EXPENSE OF REMOVING AMBIGUOUS (BUT INFORMATIVE) DATA. HERE, WE PROPOSE TO DEVELOP TWO SOFTWARE COMPONENTS THAT WILL IMPROVE THE SCORING AND FILTERING SYSTEMS USED DURING METABOLITE IDENTIFICATION: PEAKDEFRAG AND DECOID2. THESE WILL BE INTEGRATED INTO A SECOND-GENERATION ANALYSIS SOFTWARE (MASSID 2.0) THAT IS HOSTED ON THE CLOUD AND AVAILABLE THROUGH A WEB APPLICATION, OFFERING ALL RESEARCHERS STRAIGHTFORWARD ACCESS TO THEIR DATA. THE GRANT WILL BE COMPLETED BY BENCHMARKING MASSID 2.0 AGAINST MASSID 1.0 AND OTHER UNTARGETED SOFTWARE APPROACHES IN A COLON CANCER COHORT. WITH THESE RESULTS, WE PLAN TO BE THE FIRST METABOLOMICS COMPANY TO BACK METABOLITE IDENTIFICATIONS WITH STATISTICAL VALUES AND TO FURTHER OUR POSITION AS THE LEADING PLATFORM IN ELIMINATING THE NUMBER OF SIGNALS DERIVED FROM NOISE. WE EXPECT MASS ID 2.0 TO TRANSFORM UNTARGETED METHODS BY INCREASING THE NUMBER OF STATISTICALLY SIGNIFICANT METABOLITE IDENTIFICATIONS AND TO ADVANCE PANOME BIO AS AN INDUSTRY LEADER IN MULTI-OMICS DISCOVERY RESEARCH, A MARKET VALUED AT $750M.

SINGLE NUCLEUS TRANSCRIPTOMIC PROFILING IN POSTMORTEM SPINAL CORD OF ALS PATIENTS

PRIVACY PRESERVATION IN TRANSCRIPTOMIC DATA ANALYSIS - PROJECT SUMMARY UNDERSTANDING THE MECHANISM BEHIND CELLULAR ACTIVITIES REQUIRES LARGE-SCALE MINING OF GENETIC AND TRANSCRIPTOMIC OBSERVATIONS FROM LARGE AMOUNTS OF HUMAN DATA. WIDESPREAD AND EASY ACCESS TO SUCH DATA IS IMPERATIVE TO MAKE BIOLOGICAL CONNECTIONS BETWEEN GENES AND DISEASES. HOWEVER, THERE IS A DIRECT CONFLICT BETWEEN PROTECTING THE PRIVACY OF PATIENTS AND RESEARCH PARTICIPANTS AND BROAD SHARING OF GENETIC AND TRANSCRIPTOMIC DATA FOR BIOMEDICAL ADVANCES. IN ORDER TO ADDRESS THESE PRIVACY CONCERNS DURING TRANSCRIPTOMIC ANALYSIS, WE PROPOSE TO TAKE ADVANTAGE OF CRYPTOGRAPHIC APPROACHES THAT ENABLE DIRECT COMPUTATIONS ON ENCRYPTED DATA WITHOUT REVEALING THE SENSITIVE INFORMATION IN THEM. WE WILL CREATE AN EVOLVING AND MODULAR TOOL SUITE TO PRESERVE PRIVACY; THIS SUITE WILL HAVE THE ABILITY TO BE ADOPTED TO NEW DATA MODALITIES AND ANALYSIS NEEDS AS THEY ARISE. IN PARTICULAR, WE PROPOSE TO DEVELOP A SERIES OF TOOLS THAT CAN QUANTIFY THE BULK TRANSCRIPT AND SINGLE-CELL GENE EXPRESSION AND PERFORM EQTL MAPPING ON THE ENCRYPTED GENOTYPES IN A SHARED SERVER AND CLOUD SETTING. THE PROPOSED TOOLS WILL HELP PREVENT FUTURE CATASTROPHIC PRIVACY LEAKS, WHICH MAY RESULT IN A LOSS OF ACCESS TO ALL MEDICALLY ACTIONABLE DATA. OUR LONG-TERM GOAL IS TO DEMOCRATIZE DATA ACCESS FOR ALL RESEARCHERS AND CREATE TRUST BETWEEN PATIENTS AND RESEARCHERS, THUS INCREASING PARTICIPATION IN STUDIES.

LEGUME INFORMATION SYSTEM AND NETWORK - A LEGUME BIOINFORMATICS RESOURCE

LEGUME INFORMATION SYSTEM AND NETWORK - A LEGUME BIOINFORMATICS RESOURCE

LEGUME INFORMATION SYSTEM AND NETWORK - A LEGUME BIOINFORMATICS RESOURCE

LEGUME INFORMATION SYSTEM AND NETWORK - A LEGUME BIOINFORMATICS RESOURCE

LEGUME INFORMATION SYSTEM AND NETWORK-A LEGUME BIOINFORMATICS RESOURCE

LEGUME INFORMATION SYSTEM AND NETWORK-A LEGUME BIOINFORMATICS RESOURCE

INDIAN HSG BLOCK GR

PUB HSG RECEIVERSHIP

AN ANTI-CD74 MAB-DRUG CONJUGATE FOR B-CELL MALIGNANCIES

OFFICE OF NATIVE AMERICAN PROGRAMS TRAINING AND TECHNICAL ASSISTANCE FOR INDIAN HOUSING BLOCK GRANT PROGRAM

LEGUME INFORMATION SYSTEM AND NETWORK-A LEGUME BIOINFORMATICS RESOURCE

INDIAN HSG BLOCK GR

INDIAN HSG BLOCK GR

THIS PROJECT WILL COMPLETE THE REPLACEMENT OF FAILING UTILITY MAINS AND ASSOCIATED WATER AND SEWER SERVICE LINES IN THE EAST G STREET TO EAST K STREE

MASSIVELY PARALLEL MULTI-MODAL SINGLE-CELL PHENOTYPING USING A PORTABLE DEVICE

DEVICE FOR NONINVASIVE DETECTION OF CORONARY ARTERY DISEASE - REVISED

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

PUBLIC HOUSING CAPITAL FUND

THE INTERNATIONAL MAMMALIAN GENOME CONFERENCE

ALASKA NATIVE EDUCATION

STUDYING THE MAMMALIAN REGULATORY CIRCUITS BY DEVELOPING SINGLE-CELL MULTI-OMICS TECHNOLOGIES - PROJECT SUMMARY/ABSTRACT HOW THE IDENTICAL GENOME SEQUENCE PRODUCES DIVERSE CELL TYPES DURING DEVELOPMENT REMAINS A FUNDAMENTAL QUESTION IN BIOLOGY. RECENT TECHNOLOGY ADVANCEMENTS IN SINGLE-CELL GENOMICS PROVIDED EXCELLENT OPPORTUNITIES TO STUDY THE MOLECULAR PROFILES DURING DEVELOPMENT AND IN DISEASE AT UNPRECEDENTED RESOLUTION. HOWEVER, MONITORING INDIVIDUAL MODALITIES FROM SINGLE CELLS AT A TIME RUNS THE RISK OF OBTAINING ONLY PARTIAL PICTURES FROM THE COMPLEX REGULATORY NETWORK. MULTI-MODAL SINGLE-CELL GENOMICS TOOLS WOULD BE DESIRED TO OVERCOME THIS LIMITATION. I RECENTLY INVENTED A METHOD FOR ULTRA-HIGH-THROUGHPUT JOINT ANALYSIS OF OPEN CHROMATIN AND TRANSCRIPTOME FROM THE SAME SINGLE CELLS (PAIRED-SEQ) AND DEMONSTRATED ITS POTENTIAL FOR COMPREHENSIVE INVESTIGATIONS OF THE CELL- TYPE-SPECIFIC REGULATORY PROGRAMS FROM HETEROGENOUS BRAIN TISSUES. IN THIS K99/R00 APPLICATION, I PROPOSE TO FURTHER DEVELOP A SET OF NEW SINGLE-CELL MULTI-OMICS TOOLS TO STUDY THE DYNAMIC AND CELL-TYPE-SPECIFIC REGULATORY CIRCUITS DURING MAMMALIAN DEVELOPMENT. I WILL IMPROVE THE SENSITIVITIES AND COVERAGES OF PAIRED-SEQ AND DEVELOP A COMPUTATIONAL METHOD FOR SINGLE-CELL MULTI-OMICS ANALYSIS FROM THE PHENOTYPIC LEVEL (AIM1). SUBSEQUENTLY, I WILL FURTHER DEVELOP A METHOD FOR HIGH-THROUGHPUT SINGLE-CELL JOINT ANALYSIS OF HISTONE MODIFICATIONS/TRANSCRIPTION FACTORS BINDING WITH GENE EXPRESSION (PAIRED-TAG) FOR ANALYSIS OF MOLECULAR PROGRAMS FROM THE MECHANISTIC LEVEL (AIM2). FINALLY, I WILL APPLY THESE TECHNOLOGIES TO STUDY THE DYNAMIC AND CELL-TYPE-SPECIFIC MOLECULAR PROGRAMS IN MAMMALIAN DEVELOPING GERM CELLS, AND TO IDENTIFY AND VALIDATE NOVEL REGULATORS DURING THIS PROCESS (AIM3). OVERALL, THE RESULTS FROM THIS PROPOSAL WILL PROVIDE NEW TECHNOLOGIES FOR THE STUDY OF EPIGENETIC PROGRAMS IN COMPLEX TISSUES AND DURING DEVELOPMENT AT SINGLE-CELL RESOLUTION, AND PROVIDING MORE COMPLETE VIEWS OF THE GENE REGULATORY CIRCUITS DURING MAMMALIAN GERM CELL DEVELOPMENT. MY CAREER GOAL IS TO LEAD AN INDEPENDENT RESEARCH GROUP FOCUSING ON INTEGRATING NOVEL EXPERIMENTAL AND COMPUTATIONAL TECHNOLOGIES TO UNDERSTAND THE UNDERLYING PRINCIPLES CONTROLLING MAMMALIAN DEVELOPMENT. DURING THE K99 PHASE, I WILL CONTINUE TO RECEIVE EXPERIMENTAL AND COMPUTATIONAL TRAINING FROM MY POSTDOCTORAL MENTOR DR. REN AND COLLABORATORS/ADVISORY COMMITTEE AT UC SAN DIEGO AND THE SALK INSTITUTE. THE RIGOROUS MENTORED SUPPORT AND RESULTS OBTAINED IN THE K99 PHASE WILL FACILITATE MY TRANSITION TO AN INDEPENDENT INVESTIGATOR IN THE R00 PHASE AND LAY THE FOUNDATION FOR MY FUTURE CAREER.

LEGUME INFORMATION SYSTEM AND NETWORK-A LEGUME BIOINFORMATICS RESOURCE

GENOME ENGINEERING TOOLS FOR FUNCTIONAL SCREENING OF NON-CODING ELEMENTS

INDIAN HSG BLOCK GR

COMMUNITY COMPASS TECHNICAL ASSISTANCE AND CAPACITY BUILDING

A CRISPR/CAS13 APPROACH FOR IDENTIFYING INDIVIDUAL TRANSCRIPT ISOFORM FUNCTION IN CANCER - ABSTRACT ONE OF THE MAJOR CHALLENGES IN CHARACTERIZING TRANSCRIPT ISOFORM CELLULAR FUNCTION IN HEALTH AND DISEASE IS THE LACK OF METHODS TO SPECIFICALLY AND EFFICIENTLY DOWNREGULATE THEIR EXPRESSION. RNA-TARGETING RNA-GUIDED TYPE VI CRISPR/CAS13 SYSTEMS CONSTITUTE A RECENTLY DEVELOPED TOOL TO KNOCKDOWN TRANSCRIPTS IN MAMMALIAN CELLS. THEIR RNASE ACTIVITY IS ACTIVATED BY BINDING OF A CRISPR RNA GUIDE (GRNA) COMPLEMENTARY TO A SINGLE-STRANDED RNA TARGET. THE CRISPR/CAS13 SYSTEMS TESTED TO DATE HAVE BEEN SHOWN TO ACHIEVE HIGHLY SPECIFIC KNOCKDOWN OF ENDOGENOUS TRANSCRIPTS, WITH MINIMAL OFF-TARGET EFFECTS, OUTPERFORMING CURRENT METHODOLOGIES SUCH AS RNAI. WHILE CRISPR/CAS13 HAS BEEN SHOWN TO WORK EFFICIENTLY WHEN TARGETED TO THE PRE-MRNA, TRANSCRIPTOME-WIDE STRATEGIES THAT WOULD ALLOW KNOCKDOWN OF TRANSCRIPT ISOFORMS BY TARGETING UNIQUE JUNCTIONS IN THE MATURE MRNA MOLECULE HAVE NOT BEEN EXPLORED. SELECTING THE BEST GRNA SEQUENCES IS CRUCIAL FOR SUCCESSFUL AND SPECIFIC RNA KNOCKDOWN MEDIATED BY CAS13. PRELIMINARY DATA FROM OUR LAB SHOWS THAT USING GRNAS TARGETING SEQUENCES SPANNING EXON-EXON JUNCTIONS IN MATURE MRNA MOLECULES WITH CRISPR/CAS13D (THE SMALLEST CAS13 EFFECTOR) EFFICIENTLY REDUCES TRANSCRIPT EXPRESSION UP TO 80%. MOREOVER, TARGETING ISOFORM-SPECIFIC JUNCTIONS ALLOWS FOR THEIR INDIVIDUAL KNOCKDOWN WITHOUT AFFECTING NON-TARGETED ISOFORMS. THESE RESULTS SUGGEST THAT THERE IS NO STERIC CONSTRAINT IN TARGETING JUNCTIONS IN MATURE MRNA MOLECULES. TRANSCRIPTOME ANALYSES OF TUMORS AND CANCER CELL LINES HAVE COMPREHENSIVELY DESCRIBED THE EXPRESSION LEVELS AND IDENTITIES OF ALTERNATIVE TRANSCRIPT ISOFORMS. IN PARALLEL, A NUMBER OF STUDIES HAVE SHOWN THAT SPLICING DYSREGULATION IS A HALLMARK OF CANCER. THE CAUSAL LINK BETWEEN TRANSCRIPT ISOFORM EXPRESSION AND CANCER RELATED PHENOTYPES HAS NOT BEEN THOROUGHLY STUDIED. HERE, WE WILL EXPAND THE APPLICABILITY OF CRISPR/CAS13 SYSTEMS TO THE SYSTEMATIC STUDY OF TRANSCRIPT ISOFORMS IN CANCER BY 1) COMBINING LARGE-SCALE EXPERIMENTAL DATA WITH MACHINE LEARNING APPROACHES TO DEFINE RULES FOR GRNA DESIGN WHEN TARGETING SPECIFIC TRANSCRIPT JUNCTIONS 2) OPTIMIZING A PIPELINE AND THE COMPUTATIONAL ANALYSIS REQUIRED FOR USING CRISPR/CAS13 SYSTEMS IN FORWARD TRANSCRIPTOMIC POOLED SCREENS TO INTERROGATE THE CELLULAR FUNCTION OF TRANSCRIPT ISOFORMS. BY BROADENING THE APPLICATION OF THE CRISPR/CAS13 SYSTEM, OUR PIPELINE WILL PROVIDE THE MOLECULAR TOOLS AND COMPUTATIONAL ANALYSIS REQUIRED FOR INTERROGATING TRANSCRIPT ISOFORM FUNCTION IN A ROBUST, UNBIASED AND HIGHLY EXPANDABLE MANNER. WE EXPECT THAT OUR CRISPR/CAS13 APPROACH WILL BE ABLE TO OVERCOME THE LIMITATIONS OF CURRENT METHODS IN IDENTIFYING CELL-SPECIFIC ISOFORM EXPRESSION AND/OR RATIOS UNDERLYING TUMORIGENESIS AND DRUG RESISTANCE. LASTLY, THE CRISPR/CAS13 APPROACH COULD BE FURTHER ADAPTED TO PERFORM TARGETING OF TRANSCRIPT ISOFORMS IN VIVO AS AN RNA-BASED THERAPEUTIC.

REDUCING ALCOHOL-RELATED CRIME IN TRIBAL YOUNG ADULTS

NEXTGEN LAB-ON-BEAD: HARNESSING ION TORRENT SEQUENCING FOR CANCER DRUG DISCOVERY

ROBUST STR CALLING FROM HIGH-THROUGHPUT SEQUENCING TECHNOLOGIES

CONTR GRANTS AGREE

IMPACT AID PROGRAM TITLE VIII SECTION 8003

IMPROVE EXISTING AIRPORT

IMPACT AID PROGRAM TITLE VIII SECTION 8003 AND SECTION 8007(A)

PAIR-END-DITAG TECHNOLOGIES FOR THE COMPLETE ANNOTATION OF FUSION GENES

IMPROVE EXISTING AIRPORT

GENERAL RESEARCH AND TECHNOLOGY ACTIVITY

INDIAN HOUSING BLOCK GRANTS

LAUNCH RAMP REPAIR

LEGUME INFORMATION SYSTEM - A LEGUME BIOINFORMATICS RESOURCE

NATIVE AMERICAN HSNG BLOCK GRA

2021 CCDF TRIBAL CONSTRUCTION

SHOREBIRD NETWORK AND WINGS ACROSS THE AMERICAS

A METHOD FOR EARLY AND EASY DETECTION OF ALZHEIMER'S DISEASE

A VIRTUAL PLANT INFORMATION NETWORK (VPIN)

THREE PRIMARY OBJECTIVES ARE IDENTIFIED AS PROGRAM COMPONENTS: BUILD THE TRIBE'S ADMINISTRATIVE CAPACITY TO SUCCESSFULLY MANAGE ENVIRONMENTAL PROGRAM

AUTOLOGOUS HIV-1 RESISTANT T CELLS THROUGH ACCELERATED CCR5 GENE DISRUPTION

PNM DRUG FREE YOUTH

PURCHASE GENOM EQUIPMENT

THIS PROPOSAL IS FOR A TWO YEAR PERIOD AND CONTAINS THREE PRIMARY OBJECTIVES IDENTIFIED AS PROGRAM COMPONENTS. THE FIRST WILL FOCUS ON DEVELOPMENT AN

PUBLIC HOUSING CAPITAL FUND

CONTR GRANTS AGREE

SINGLE-CELL EPIGENOME ANALYSIS OF THE ALZHEIMER'S DISEASE BRAIN - TITLE: SINGLE-CELL EPIGENOME ANALYSIS OF THE ALZHEIMER’S DISEASE BRAIN (PI: HARTL) ALZHEIMER’S DISEASE (AD) AFFECTS MORE THAN 6 MILLION AMERICAN BUT NO CURES AND FEW EFFECTIVE TREATMENTS ARE AVAILABLE. GENOME-WIDE ASSOCIATION STUDIES (GWAS) HAVE UNCOVERED THOUSANDS OF SEGREGATING MUTATIONS THAT SIGNIFICANTLY INCREASE AD RISK. MOST OF THESE VARIANTS ALTER NON-PROTEIN-CODING SEQUENCE AND LACK CLEAR FUNCTIONAL ANNOTATION, HINDERING EFFORTS TO TRANSLATE RISK-CONFERRING MUTATIONS INTO CURATIVE OR PREVENTATIVE THERAPIES. HERITABILITY PARTITIONING SUGGESTS THAT THESE VARIANTS LIKELY PERTURB GENE EXPRESSION IN GLIAL CELLS (ESPECIALLY MICROGLIA), ULTIMATELY LEADING TO AD PATHOLOGY. LINKING THESE VARIANTS – AND THEIR DOWNSTREAM EFFECTS – TO SPECIFIC REGULATORY NETWORKS AND PATHWAYS HAS BEEN HINDERED BY A LACK OF CIS-REGULATORY ELEMENT MAPS FOR THESE MAJOR GLIAL CELL CLASSES AND THEIR SUBTYPES. THE PROPOSED STUDY ADDRESSES THIS CRITICAL KNOWLEDGE GAP BY APPLYING A CUTTING-EDGE SINGLE CELL MULTI-OMIC TECHNOLOGY TO POSTMORTEM HUMAN BRAIN SAMPLES FROM PHENOTYPICALLY NORMAL DONORS AND AD PATIENTS. SPECIFICALLY, THE CHROMATIN ACCESSIBILITY OR HISTONE MODIFICATIONS WILL BE INTERROGATED JOINTLY WITH GENE EXPRESSION AT SINGLE CELL RESOLUTION IN DORSOLATERAL PREFRONTAL CORTEX (DLPFC) FROM MULTIPLE DONORS, TO IDENTIFY AND CHARACTERIZE THE CELL-TYPE-SPECIFIC GENE REGULATORY ELEMENTS THAT DRIVE ABERRANT CELL STATES AND DISEASE-RELEVANT CELLULAR RESPONSES IN HUMAN AD BRAINS. THE SINGLE CELL CHROMATIN STATE AND GENE EXPRESSION ATLASES FROM PHENOTYPICALLY NORMAL INDIVIDUALS WILL BE COMPARED TO THOSE FROM AD SUBJECTS TO DETERMINE THE BRAIN CELL TYPES, GENES AND REGULATORY ELEMENTS THAT EXHIBIT SIGNIFICANT CHANGES IN PATHOLOGICAL CONDITIONS. FINALLY, THE NEWLY GENERATED CELL-TYPE RESOLVED EPIGENOME MAPS WILL BE INTEGRATED WITH PUBLIC GENOMIC RESOURCES TO PROVIDE FUNCTIONAL ANNOTATION OF THE AD RISK VARIANTS, IDENTIFY DISEASE-RELEVANT CELL TYPES, PRIORITIZE GENES, TRANSCRIPTION FACTORS, AND MOLECULAR PATHWAYS FOR FUTURE MECHANISTIC INVESTIGATION. RESULTS OF THE PROPOSED STUDY WILL PROVIDE A MUCH-NEEDED TOOL FOR STUDY OF AD PATHOGENESIS AND DEVELOPMENT OF IMPROVED AD THERAPIES.

PUBLIC HOUSING CAPITAL FUND

PURPOSE: REHABILITATE AIRPORT ROTATING BEACON; RECONSTRUCT RUNWAY VISUAL GUIDANCE SYSTEM; REHABILITATE TAXILANE; RECONSTRUCT AIRFIELD EQUIPMENT. ACTIVITIES TO BE PERFORMED/EXPECTED OUTCOMES: THIS PROJECT RECONSTRUCTS PRECISION APPROACH PATH INDICATOR SYSTEMS FOR RUNWAY 17/35, AT BOTH RUNWAY THRESHOLDS, THAT HAVE REACHED THE END OF THEIR USEFUL LIVES. THIS PROJECT RECONSTRUCTS RUNWAY END IDENTIFIER LIGHTS SYSTEMS FOR RUNWAY 17/35, AT BOTH RUNWAY THRESHOLDS, THAT HAVE REACHED THE END OF THEIR USEFUL LIVES. THIS PROJECT REHABILITATES 1,365 FEET OF EXISTING TAXILANE B PAVEMENT THAT HAS REACHED THE END OF ITS USEFUL LIFE. THIS PROJECT REHABILITATES ONE EXISTING AIRPORT ROTATING BEACON TO EXTEND ITS USEFUL LIFE. THIS PROJECT REPLACES THE EXISTING WIND CONE THAT HAS REACHED THE END OF ITS USEFUL LIFE. THIS GRANT FUNDS THE FINAL PHASE, WHICH CONSISTS OF CONSTRUCTION. INTENDED BENEFICIARY: THIS GRANT WILL PROVIDE FEDERAL FUNDING FOR AIRPORTS ASSOCIATED WITH MAHNOMEN, MINNESOTA.

THE EFFECTS OF UNDERAGE DRINKING ENFORCEMENT

THE CONSENSUS LEGUME DATABASE II: BIOLOGICAL INFERENCE FROM DISTRIBUTED INTEROPERABLE DATABASES52.

BROCKTON, MASSACHUSETTS IS A FANTASTICALLY DIVERSE BUT IMPOVERISHED CITY AND DESIGNATED ENVIRONMENTAL JUSTICE COMMUNITY WITH A RICH HISTORY. IT IS HIGHLY VULNERABLE TO FLOODING, POLLUTION, AND WATER SUPPLY DISRUPTIONS RELATED TO CLIMATE CHANGE, AND ITS SCHOOL SYSTEM FACES SIGNIFICANT CHALLENGES. IT HAS BEEN HARD-HIT BY COVID-19. BROCKTON IS ALSO A CITY WITH A LONG HISTORY OF RESILIENCE IN THE FACE OF ECONOMIC CHALLENGES AND A THIRST FOR EMPOWERMENT AND OPPORTUNITY. THIS PROJECT WILL BOOST CLIMATE RESILIENCE IN BROCKTON BY PARTNERING WITH SCHOOLS TO (1) SUSTAINABLY BOOST SCHOOL CAPACITY TO DEVELOP ENVIRONMENTAL STEWARDSHIP AND RESILIENCE IN STUDENTS BY COLLABORATING TO DESIGN AND BUILD OUTDOOR LEARNING SPACES ON SCHOOL GROUNDS, AND TO PROVIDE TEACHERS WITH CURRICULAR TOOLS AND TRAINING FOR USE, (2) EMPOWER ELEMENTARY STUDENTS AND TEACHERS AS ENVIRONMENTAL STEWARDS THROUGH OUTDOOR ENVIRONMENTAL EDUCATION, ENGAGING IN STEWARDSHIP ACTION TO BUILD GREEN INFRASTRUCTURE, AND CIVIC ENGAGEMENT

SHORE BIRD RECOVERY PROJECT

PUBLIC HOUSING CAPITAL FUND

WESTERN HEMISPHERE SHOREBIRD RESERVE NETWORK

CSC6-2021

CPD'S TRANSFORMATION INTITIATIVE TECHNICIAL ASSISTANCE

NOVEL VACCINES AGAINST JOHNE'S DISEASE: PHASE II TRIALS

IMPROVE EXISTING AIRPORT

THIS PROJECT WILL INCREASE ADMINISTRATIVE CAPACITY TO CREATE, OPERATE, AND MANAGE AN ENVIRONMENTAL PROGRAM IN THE NOME ESKIMO COMMUNITY. THE PROGRAM

MOUSE TRANSCRIPTOMIC FINGERPRINTS AS BIOMARKERS FOR CHRONIC ALCOHOL ABUSE

A NOVEL CTDNA ANALYSIS SOLUTION FOR THE NEXT-GENERATION OF LIQUID BIOPSY ASSAYS - PROJECT SUMMARY/ABSTRACT DETECTION AND ANALYSIS OF THE MUTATIONS AND METHYLATION CHANGES THAT OCCUR IN CANCER CELLS IS A FOUNDATIONAL ELEMENT OF CANCER RESEARCH AND CARE. RAPIDLY EMERGING TECHNOLOGIES SUCH AS ‘LIQUID BIOPSY’ (LBX) BASED ON CIRCULATING TUMOR DNA (CTDNA) ARE HINDERED BY THE LIMITATIONS OF CURRENT DNA ANALYSIS METHODS, PRIMARILY NEXT- GENERATION SEQUENCING (NGS). THESE LIMITATIONS INCLUDE LOW ACCURACY AND THE REQUIREMENT FOR INDIRECT, EVEN MORE INACCURATE METHODS TO READOUT METHYLATION. TO ADDRESS THIS CHALLENGE, XGENOMES IS DEVELOPING AN ENTIRELY NOVEL DNA ANALYSIS PLATFORM THAT DIRECTLY READS BOTH MUTATIONS AND METHYLATION CHANGES, ACHIEVING ACCURACY FOR EACH OVER 100X GREATER THAN CURRENT DNA SEQUENCING PLATFORMS. THIS TECHNOLOGY IS BASED AROUND MEASURING THE KINETIC BINDING OF A REPERTOIRE OF SHORT, FLUORESCENTLY LABELLED OLIGONUCLEOTIDE PROBES, USING SUPER-RESOLUTION MICROSCOPY. THE CHANGES IN BINDING KINETICS ALLOW FOR DIRECT MEASUREMENT OF METHYLATION, WITHOUT THE NEED FOR PRIOR BISULFITE CONVERSION OR SIMILAR TREATMENT. AS EACH NUCLEOTIDE OF THE TARGET DNA IS MEASURED BY MULTIPLE OVERLAPPING PROBES, THIS TECHNIQUE PROVIDES UNPRECEDENTED ACCURACY. THIS TECHNOLOGY WILL FACILITATE A TRANSFORMATIVE ADVANCEMENT IN BOTH CANCER RESEARCH AND CLINICAL CARE. XGENOMES HAS DEMONSTRATED ALL KEY ELEMENTS OF THE PLATFORM IN PRINCIPLE. IN THIS PROJECT, THE PLATFORM WILL BE FURTHER DEVELOPED TO THE POINT WHERE PROOF-OF-CONCEPT (POC) ASSAYS IN CANCER THERAPY SELECTION AND METHYLATION ANALYSIS CAN BE CONDUCTED. SPECIFIC AIM 1 INVOLVES INTEGRATING HYBRIDIZATION CAPTURE INTO XGENOMES' WORKFLOW. SPECIFIC AIM 2 WILL FOCUS ON DESIGNING AND OPTIMIZING A TARGETED METHYLATION ASSAY FOR THE BRCA1 GENE PROMOTER—A CRITICAL FACTOR IN BREAST AND OVARIAN CANCER. THE TESTS DEVELOPED IN THIS PROJECT WILL ACT AS PROOF OF CONCEPT FOR BROADER APPLICATIONS, LAYING THE FOUNDATION FOR DEVELOPMENT OF MORE COMPLEX ASSAYS. THIS VALIDATION OF XGENOMES’ PLATFORM ACHIEVED IN THIS PROJECT WILL HELP SECURE FURTHER INVESTMENT, BOTH FEDERAL AND VENTURE, THEREBY ACCELERATING THE PLATFORM'S APPLICATION ACROSS CANCER RESEARCH AND CARE, AND ULTIMATELY TRANSFORMING THE FIELD.

LIGNOCELLULOSE DEGRADATION BY SHIPWORMS AND THEIR BACTERIAL ENDOSYMBIONTS

FURTHERING THE CLINICAL DEVELOPMENT OF A FIRST IN CLASS, WATER RESISTANT SUNSCREEN TO MEET EMERGING ENVIRONMENTAL REGULATIONS - PROJECT SUMMARY / ABSTRACT PROBLEM TO BE SOLVED AND SIGNIFICANCE: EXPOSURE TO ULTRAVIOLET RADIATION (UVR) IS A RISK FACTOR FOR THE DEVELOPMENT OF SKIN CANCER, AND HEALTH CARE AGENCIES RECOMMEND THAT SUNSCREENS BE USED AS A PREVENTATIVE MEASURE. RECENT LEGISLATION IN THE U.S. AND INTERNATIONALLY HAS BANNED THE SALE OF INGREDIENTS THAT ARE FUNDAMENTAL TO WATER-RESISTANT SUNSCREENS, CREATING AN URGENT NEED FOR NEW PRODUCTS THAT SATISFY EXISTING AND EMERGING LEGISLATION. PRODUCT AND LONG-TERM GOAL: THE PRODUCT OF THIS SBIR WILL BE A WHOLLY BIOCOMPATIBLE SPF 30 BROAD SPECTRUM SUNSCREEN CREAM, SOLD IN 6-OZ TUBES, THAT SATISFIES FDA’S CRITERIA TO BE LABELED AS ‘WATER RESISTANT (80 MIN)’ AND IS BASED ON THE NANOMETICS (D.B.A. PHD BIOSCIENCES [PHD]) PROPRIETARY ELASTOMER TECHNOLOGY. SUCCESSFUL DEVELOPMENT OF THIS SUNSCREEN PRODUCT DIRECTLY ADDRESSES THE MISSION OF THE NATIONAL CANCER INSTITUTE BY IMPROVING PROTECTION AGAINST UVR AND DECREASING THE RISK OF SKIN CANCER. TECHNOLOGICAL INNOVATION: THE PHD SUNSCREEN INCORPORATES PHD’S PROPRIETARY BIODEGRADABLE ELASTOMER TECHNOLOGY, WHICH IS THE FIRST PLANT DERIVED ELASTOMER FOR TOPICAL PRODUCTS THAT PROVIDES WATER RESISTANCE, IS COMPATIBLE WITH ALL FOOD AND DRUG ADMINISTRATION APPROVED UV FILTERS, AND RECAPITULATES THE FAVORABLE AESTHETIC PROPERTIES OF SILICONE ELASTOMERS. SPECIFIC AIM #1. TO DEMONSTRATE THAT THE PHD SUNSCREEN IS WATER RESISTANT FOR AT LEAST 80 MIN ON HEALTHY VOLUNTEERS. STUDIES IN THIS AIM WILL BE CONDUCTED UNDER FDA GUIDANCE AND WILL DEMONSTRATE THE FEASIBILITY THAT THE PHD SUNSCREEN IS RESISTANT TO REMOVAL WITH WATER AFTER 80 MIN OF CONTINUOUS IMMERSION IN WATER. SUCCESS CRITERION: THIS AIM WILL BE SUCCESSFUL IF AFTER 80 MIN OF WATER IMMERSION, THE MEAN SPF FALLS WITHIN ONE STANDARD DEVIATION OF THE PRE-IMMERSION SPF OF 30. COMMERCIAL OPPORTUNITY: THE GLOBAL SUNSCREEN MARKET IS PROJECTED TO EXCEED $2.5 BILLION BY 2023. PRIMARY AND SECONDARY MARKET RESEARCH SUPPORTS THE NEED FOR THE PHD SUNSCREEN TO MEET THE EMERGING NEEDS CREATED BY NEW LEGISLATION. PHASE II SBIR STUDIES WILL INCLUDE ADDITIONAL STUDIES TO CONFIRM SAFETY ON A LARGER NUMBER OF VOLUNTEERS; COMPARE PERFORMANCE TO LEADING COMMERCIAL SUNSCREENS; AND OPTIMIZE THE CHEMISTRY, MANUFACTURING, AND CONTROL (CMC) PROCESSES TO PRODUCE THE PRODUCT AT COMMERCIAL SCALE.

SEQUENCING OF EPIGENETIC MODIFICATIONS ACROSS THE GENOME BY SINGLE-MOLECULE DETECTION OF OLIGONUCLEOTIDE BINDING KINETICS - PROJECT SUMMARY/ABSTRACT DNA METHYLATION IS A CRUCIAL EPIGENETIC MODIFICATION THAT PLAYS A PIVOTAL ROLE IN REGULATING GENE EXPRESSION AND MAINTAINING GENOMIC STABILITY. DYSREGULATED DNA METHYLATION IS LINKED TO VARIOUS PATHOLOGICAL CONDITIONS, INCLUDING CANCER, AUTOIMMUNE DISEASES, AND NEUROLOGICAL DISORDERS, UNDERSCORING ITS SIGNIFICANCE IN BOTH HEALTH AND DISEASE. ACCORDINGLY, ANALYSIS OF DNA METHYLATION IS FUNDAMENTAL IN BIOMEDICAL RESEARCH AND HAS GROWING CLINICAL USES, PARTICULARLY AS A CANCER BIOMARKER. NEXT-GENERATION SEQUENCING (NGS), THE CORNERSTONE OF CURRENT GENETIC AND EPIGENETIC ANALYSIS METHODS, IS INCAPABLE OF DIRECTLY READING METHYLATION. AS A RESULT, INDIRECT TECHNIQUES LIKE BISULFITE SEQUENCING (BS-SEQ) ARE USED. BS-SEQ IS LIMITED BY LOW ACCURACY, HIGH LOSSES OF INPUT DNA, AND AN INABILITY TO CONCURRENTLY READ GENETIC SEQUENCE. ALTERNATIVE CONVERSION APPROACHES AND 'THIRD GENERATION’ SEQUENCING RESOLVE SOME ISSUES BUT FAIL TO SIGNIFICANTLY IMPROVE UPON BS-SEQ'S ACCURACY AND HAVE DRAWBACKS IN OTHER AREAS. THE LIMITATIONS OF CURRENT DNA METHYLATION ANALYSIS METHODS BECOME INCREASINGLY APPARENT WITH THE DEVELOPMENT OF VARIOUS METHODS THAT ALLOW FOR THE DETERMINATION OF DNA SEQUENCE AT INCREASINGLY HIGH ACCURACY. FOR EXAMPLE, USING UNIQUE MOLECULAR IDENTIFIERS (UMI) ANALYSIS OF DNA SEQUENCE AT ACCURACY EXCEEDING 99.999% IS POSSIBLE (ALBEIT AT THE COST OF COMPLEX WORKFLOWS AND HIGH SEQUENCING COSTS). BY CONTRAST, ALL CURRENT METHYLATION ANALYSIS METHODS DELIVER ACCURACY BELOW 99% AND ARE INCOMPATIBLE WITH ERROR SUPPRESSION METHODS LIKE UMI. THUS, FOR KEY APPLICATIONS LIKE LIQUID BIOPSY, WHICH REQUIRE HIGH ACCURACY TO DETECT CANCER DNA PRESENT AS AN EXTREME MINORITY OF TOTAL DNA, NO HIGHLY ACCURATE METHOD IS AVAILABLE FOR THE DETECTION OF METHYLATION. XGENOMES IS DEVELOPING A RADICALLY NOVEL EPIGENETIC ANALYSIS METHOD WHICH OVERCOMES KEY LIMITATIONS OF EXISTING TECHNOLOGY. XGENOMES’ SINGLE-MOLECULE PLATFORM MEASURES THE TRANSIENT REPETITIVE BINDING OF SHORT (5- LETTER), FLUORESCENTLY LABELED PROBES TO SINGLE-STRANDED TARGET DNA. PROBES EXHIBIT A REPETITIVE KINETIC BINDING PATTERN, WHICH ALTERS IN THE PRESENCE OF METHYLATION. THIS EFFECT IS REPLICATED ACROSS ALL PROBES BINDING A METHYLATED SITE. COMBINING DATA FROM MULTIPLE PROBES ALLOWS FOR DETERMINATION OF THE METHYLATION STATUS OF EACH POSITION IN THE TARGET DNA MOLECULE WITH UNPRECEDENTED ACCURACY. XGENOMES’ PRIOR WORK HAS VALIDATED THE FUNDAMENTAL APPROACH. THIS PHASE I PROJECT WILL BUILD OUT THE TECHNOLOGY THROUGH TWO SPECIFIC AIMS. IN AIM 1, THE CHEMISTRY OF THE PROBE LIBRARY AND BUFFER COMPOSITION WILL BE OPTIMIZED FOR METHYLATION DISCRIMINATION. IN AIM 2, WE WILL REFINE, VALIDATE, AND DEMONSTRATE OUR EPI-SEQUENCING PLATFORM IN COMPARISON WITH EXISTING TECHNOLOGIES.

MICROFLUIDIC FLOW RETARDATION DEVICE FOR TAGLESS CANCER CELL ANALYSIS FOR METASTATIC POTENTIAL

SUPER-RESOLUTION SINGLE-MOLECULE SEQUENCING BY OBSERVING THE DYNAMIC HYBRIDIZATION OF A REPERTOIRE OF OLIGONUCLEOTIDES TO DNA TARGETS - PROJECT SUMMARY/ABSTRACT THE GENOME IS A CRITICAL FACTOR IN OUR HEALTH. HOWEVER, THE COST AND PERFORMANCE OF CURRENT SEQUENCING TECHNOLOGIES ARE LIMITING GENOMICS FROM REALIZING ITS FULL POTENTIAL IN HEALTHCARE, INCLUDING MONITORING OF CANCER DEVELOPMENT AND RECURRENCE. THE GOAL OF THE PROJECT IS TO DEVELOP A REVOLUTIONARY SEQUENCING PLATFORM THAT IS SUPERIOR TO EXISTING TECHNOLOGIES ACROSS A RANGE OF METRICS. RATHER THAN READING ONE BASE OR LETTER AT A TIME, THE PROPOSED TECHNOLOGY READS SHORT SEGMENTS OF SEQUENCE OR “WORDS”, BY MEASURING THE KINETICS OF SHORT OLIGONUCLEOTIDE PROBE BINDING TO THEIR COMPLEMENTARY SEQUENCE IN THE TARGET USING SUPER-RESOLUTION FLUORESCENCE IMAGING. EACH NUCLEOTIDE IS READ MULTIPLE TIMES DURING SEQUENCING. SUPER-RESOLUTION IMAGING ENABLES THE SEQUENCING OF A HIGH MOLECULAR DENSITY OF TARGETS. ADVANCED STATISTICAL AND MACHINE LEARNING ALGORITHMS ARE USED FOR IMAGE PROCESSING, BASE CALLING AND SEQUENCE ASSEMBLY. ONCE DEVELOPED, THIS PLATFORM WILL SURPASS EXISTING SEQUENCING TECHNOLOGY BY ONE OR MORE ORDERS OF MAGNITUDE IN FACTORS INCLUDING ACCURACY AND SEQUENCING COST. XGENOMES’ PRIOR WORK HAS VALIDATED THE FUNDAMENTAL APPROACH. THIS PHASE I PROJECT WILL DEVELOP A FULL-STACK PROOF-OF-CONCEPT THROUGH THREE SPECIFIC AIMS. IN AIM 1, WE WILL APPLY OUR EXPERIENCE TO EXPAND THE PROBE SET TO THE 96 WE WILL REQUIRE FOR DEMONSTRATING SEQUENCING IN AIM 3. IN AIM 2, THE BIOINFORMATICS PIPELINE WILL BE FULLY IMPLEMENTED AND OUR PROTOTYPE FLUIDICS PLATFORM WILL BE SCALED UP TO DELIVER AND IMAGE 96 PROBES. FINALLY, IN AIM 3 WE WILL CONSTRUCT THE SYNTHETIC TEST TARGETS AND DEMONSTRATE Q50 SEQUENCING OF TARGETED VARIANTS OF A CLINICALLY RELEVANT LOCI. THE SUCCESSFUL COMPLETION OF THESE AIMS WILL PROVE THE TECHNOLOGY WORKS AND POSITION XGENOMES TO SCALE UP TO THE COMPLETE PLATFORM.

PNM DRUG FREE YOUTH

IMPROVE EXISTING AIRPORT C

THIS PROJECT WILL ASSIST NOME ESKIMO COMMUNITY IN BUILDING CAPACITY AND DEVELOPING PROGRAMS TO PROTECT THE TRIBAL ENVIRONMENT AND HEALTH. TASKS INCLUDE MANAGING AN ENVIRONMENTAL OFFICE TO SUSTAIN A SUCCESSFUL TRIBAL ENVIRONMENTAL PROGRAM; CONTINUE DEVELOPING WATER QUALITY MONITORING CAPACITY; IMPLEMENT A RECYCLING AND COMMUNITY EDUCATION PROGRAM; AND WORK TO ESTABLISH PARTNERSHIPS TOWARDS DEVELOPING A SUSTAINABLE TRIBAL SOLID WASTE REMOVAL PROGRAM.

SOMATIC VARIANT CALLING AND PHASING USING COLORED DE BRUIJN GRAPHS IN HETEROGENEOUS TUMORS

HIGH-THROUGHPUT SINGLE CELL CO-ASSAY OF HISTONE MODIFICATIONS AND TRANSCRIPTOME - ABSTRACT EPIGENOME ANALYSIS CAN HELP DISSECT THE TRANSCRIPTIONAL REGULATORY SEQUENCES THAT CONTROL SPATIOTEMPORAL PATTERNS OF GENE EXPRESSION DURING ANIMA DEVELOPMENT AND DISEASE PATHOGENESIS, BUT A MAJOR CHALLENGE TO EPIGENOME ANALYSIS IS THE HETEROGENEITY OF PRIMARY TISSUES. CONVENTIONAL EPIGENOME ASSAYS THAT TAKE BULK TISSUES AS INPUT ONLY PRODUCE POPULATION AVERAGE SIGNALS. TO ADDRESS THIS MAJOR BOTTLENECK, WE PROPOSE TO DEVELOP AN ULTRA-HIGH THROUGHPUT SINGLE-CELL MULTI-OMICS METHOD, PAIRED-TAG, FOR JOINT PROFILING OF HISTONE MODIFICATIONS AND TRANSCRIPTOME. IN PRELIMINARY EXPERIMENTS, WE HAVE DEMONSTRATED THE FEASIBILITY AND UTILITY OF THIS METHOD THROUGH ANALYSIS OF THE NUCLEAR TRANSCRIPTOME AND MULTIPLE HISTONE MODIFICATIONS AT SINGLE CELL RESOLUTION IN THE ADULT MOUSE FRONTAL CORTEX AND HIPPOCAMPUS. IN THE PROPOSED STUDY, WE WILL FURTHER OPTIMIZE THE CURRENT PAIRED-TAG PROTOCOL AND DEMONSTRATE ITS UTILITY IN CANCER EPIGENOME ANALYSIS. IF SUCCESSFUL, THE RESEARCH WOULD ADD A MAJOR TOOLKIT FOR THE PRODUCTION OF CELL-TYPE-RESOLVED MAPS OF CHROMATIN STATE AND TRANSCRIPTOME IN COMPLEX TISSUES AND ENABLE NEXT GENERATION EPIGENOME ANALYSIS OF TUMOR SAMPLES.

ULTRASOUND-BASED DIAGNOSTIC AND MONITORING OF BLADDER CANCER TREATMENT WITH DRUG RELEASED FROM NANOPARTICLES

ACHIEVING ULTRA-HIGH-DENSITY, ULTRA-HIGH-PRECISION SINGLE MOLECULE LOCALIZATION MICROSCOPY WITH WHOLE-VIDEO DEEP LEARNING ARCHITECTURES - PROJECT SUMMARY/ABSTRACT SUPERRESOLUTION MICROSCOPY IS AN INCREDIBLE FAMILY OF APPROACHES THAT HAVE PROVIDED EASIER OBSERVABILITY OF NANOMETER-SCALE FEATURES USING VISIBLE-LIGHT FLUORESCENCE WHICH WAS PREVIOUSLY LIMITED TO ~200-300 NM. THE HIGHEST RESOLUTION OF THESE TECHNIQUES IS SINGLE MOLECULE LOCALIZATION MICROSCOPY (SMLM), IN WHICH AN OTHERWISE DARK FIELD HAS RANDOM, SPARSE FLUORESCENT FLASHES. THESE FLASHES MAY BE ACHIEVED EITHER THROUGH A PHOTOPHYSICAL PROCESS ON A STATIONARY FLUOROPHORE (STORM/PALM) OR THROUGH A KINETIC PROCESS WHERE A MOBILE FLUOROPHORE IS TRANSIENTLY FIXED TO A TARGET (PAINT). A POINT-SOURCE DIFFRACTION-LIMITED FLASH CAN BE LOCALIZED WITH PRECISION ON THE ORDER OF 1-20 NM. HOWEVER, THE REQUIREMENT FOR SPARSITY MEANS THAT THE FLUOROPHORE BLINKING RATES NEED TO BE CAREFULLY OPTIMIZED, THE ACQUISITION TIME FOR A VIDEO CAN BE QUITE LONG, AND MOST LOCALIZATION METHODS SCALE POORLY WITH THE NUMBER OF LOCALIZATIONS. THESE AND OTHER ISSUES ARE CHALLENGING FOR ROUTINE USAGE OF SMLM, INCLUDING IN THE SINGLE-MOLECULE DIAGNOSTIC ASSAY AND SEQUENCING PLATFORM THAT XGENOMES IS DEVELOPING. IN THIS PHASE I PROJECT, XGENOMES WILL BUILD MACHINE LEARNING ALGORITHMS TO ANALYZE WHOLE SMLM VIDEOS TO IDENTIFY EMITTER POSITIONS AT ULTRA-HIGH PRECISIONS AND ULTRA-HIGH DENSITIES. IN AIM 1, WE WILL CREATE THE SMLM VIDEO SIMULATOR NECESSARY TO GENERATE TRAINING DATA. IN AIM 2, WE WILL BUILD A MACHINE LEARNING-BASED GROUPING ALGORITHM THAT CAN WORK WITH EXISTING LOCALIZATION DATA AND PRIMARILY IMPROVE THE SPEED AND ACCURACY OF ANALYSIS. IN AIM 3, WE WILL BUILD A MACHINE LEARNING MODEL TO ANALYZE WHOLE SMLM VIDEOS AT ONCE AND PUSHING THE DENSITY UP AN ORDER OF MAGNITUDE HIGHER THAN CURRENT ALGORITHMS CAN ACHIEVE. THIS WORK WILL BE MADE FREELY AVAILABLE FOR USE TO THE ACADEMIC RESEARCH COMMUNITY. THE SUCCESSFUL COMPLETION OF THESE AIMS WILL CREATE A LEAP FORWARD IN SMLM AND WILL UNLOCK NEW USES FOR THESES TECHNOLOGIES.

COLLABORATIVE RESEARCH: ABI DEVELOPMENT: A NEW PLATFORM FOR HIGHLY-OPTIMIZED, LOW-LATENCY PIPELINES FOR GENOMIC DATA ANALYSIS

PROJECT TITLE: NOME ESKIMO COMMUNITY FY2025 TRIBAL TRANSPORTATION PROGRAM FUNDING :::: PROJECT DESCRIPTION: ALL FY25 FUNDS TRANSFERRED UNDER THE NOME ESKIMO COMMUNITY TRIBAL TRANSPORTATION PROGRAM AGREEMENT.

WESTERN HEMISPHERE SHOREBIRD RESERVE NETWORK

NANOSENSOR DEVICE FOR THE DETECTION OF H. PYLORI AND PREVENTION OF GASTRIC CANCER

TRIBAL TRANSPORTATION PROGRAM

WE PROPOSE TO CONDUCT A SHOREBIRD SURVEY OF THE COASTAL PORTIONS OF THE NPR-A, INCLUDING THE TLSA AND PORTIONS OF THE WESTERN NPR-A BELOW 350 METERS IN ELEVATION, FOLLOWING PROTOCOLS DEVELOPED BY THE PROGRAM FOR REGIONAL AND INTERNATIONAL SHOREBIRD MONITORING (PRISM). WE PROPOSE TO SURVEY THE TLSA AND WILLOW PROJECT AREAS IN YEARS 1 AND 2, AND WESTERN COASTAL AREAS INCLUDING THE KASEGALUK LAGOON SPECIAL AREA IN YEARS 3 AND 4. THIS SURVEY WILL PROVIDE THE FIRST COMPARISON OF CHANGES IN SHOREBIRD POPULATIONS AND DISTRIBUTION SINCE INITIAL SURVEYS WERE CONDUCTED IN NPR-A IN 2007-8. THESE DATA WILL SUPPORT BOTH THE RANGE-WIDE POPULATION TREND ESTIMATION GOALS OF PRISM, AND ALSO PROVIDE IMPORTANT BASELINE DATA ON SHOREBIRD STATUS, TRENDS, AND DISTRIBUTION BEFORE PLANNED OIL AND GAS INFRASTRUCTURE DEVELOPMENT IN THE WILLOW PROJECT AREA OCCURS. NEW POPULATION ESTIMATES FOR THE NPR-A WILL HELP TARGET CONSERVATION ACTIONS BOTH LOCALLY AND RANGE-WIDE IF EXISTING DECLINES ARE CONFIRMED (OR NEW ONES ARE DETECTED) FOR ONE OR MORE SHOREBIRD SPECIES. UP TO DATE POPULATION ESTIMATES IN THE TLSA AND OTHER COASTAL AREAS OF NPR-A WILL ALLOW FOR MITIGATION MEASURES TO BE DESIGNED, IMPLEMENTED, AND ANALYZED FOR EFFECTIVENESS BY THE LAND MANAGER IN ORDER TO MITIGATE IMPACTS TO SHOREBIRDS FROM INFRASTRUCTURE DEVELOPMENT OF VARIOUS KINDS.WE WILL ALSO USE AUTOMATED RECORDING UNITS TO EVALUATE A POTENTIAL NEW METHOD TO SURVEY SHOREBIRDS AND TO DETERMINE HOW ANTHROPOGENIC AND NATURAL SOUNDS CHANGE AS THE WILLOW MASTER DEVELOPMENT PLAN (WILLOW) PROJECT AREA IS DEVELOPED, PROVIDING INFORMATION ON HOW SOUNDSCAPES CHANGE AND HOW THOSE CHANGES MAY INFLUENCE ANIMALS THROUGH TIME. AUTOMATED RECORDING UNITS (ARUS) WILL BE DEPLOYED AT A SAMPLE OF PRISM SITES ACROSS THE NPR-A TO DETERMINE IF ARUS COULD BE A COST EFFECTIVE AND LESS INVASIVE APPROACH TO SURVEYING SHOREBIRDS AS COMPARED TO PRISM RAPID SURVEYS IN THE FUTURE. USING ARUS COULD DRAMATICALLY DECREASE COSTS FOR OBTAINING DATA ON STATUS AND TRENDS OF MANY WILDLIFE SPECIES. FINALLY, ARUS WILL BE USED TO MEASURE CHANGES IN ANTHROPOGENIC AND NATURAL SOUNDS NEAR THE PROPOSED WILLOW PROJECT AREA BETWEEN 2023-2026 AS THE AREA UNDERGOES DEVELOPMENT OF OIL AND GAS INFRASTRUCTURE FOR THE PROPOSED WILLOW PROJECT.THIS PROJECT DIRECTLY ADDRESSES THREE BLM ALASKA WILDLIFE PROGRAM PRIORITY WORK AREAS THROUGH APPLICATION OF PRISM SURVEY PROTOCOLS FOR SHOREBIRDS, AND BY COLLECTION OF SOUNDSCAPE DATA THROUGH THE USE OF AUTOMATED RECORDING UNITS, INCLUDING INVENTORYING WILDLIFE POPULATIONS AND DISTRIBUTION, AND LEVERAGING RESOURCES THROUGH PARTNERSHIPS. SPECIFIC BLM MANAGEMENT ACTIONS THE PROJECT CAN HELP INFORM INCLUDE FUTURE IAPS, DEVELOPMENT OF PERMITS OF ALL TYPES, AND MANAGEMENT AND MITIGATION MEASURES FOCUSED ON SHOREBIRDS AND WATERFOWL. PUBLIC BENEFITS FROM THE PROJECT OUTCOMES WILL INCLUDE DISSEMINATION OF DATA IMPORTANT FOR ASSESSING STATUS AND TRENDS OF DECLINING SHOREBIRD SPECIES, DATA FOR ASSESSING WHETHER MORE COST EFFECTIVE SURVEY METHODS CAN BE DEVELOPED BASED ON ARUS, AND DATA ON BASELINE ANTHROPOGENIC SOUNDSCAPES PRIOR TO AND AFTER DEVELOPMENT.