2021-11-12T12:28:57-06:00 2020-12-31 910189318 MOSS ADAMS LLP 4747 EXECUTIVE DR SUITE 1300 SAN DIEGO CA 92121 990 2020-01-01 521842938 J CRAIG VENTER INSTITUTE JCRA 8582001800 4120 CAPRICORN LANE LA JOLLA CA 92037 JOHN CRAIG VENTER CHAIRMAN AND CEO 8582001800 2021-11-11 1 JOHN CRAIG VENTER 999009999 PATRICIA J MAYER P00188643 8586271400 2 AAL1 IAL1 2020 2022-09-23 18:48:47Z JOHN CRAIG VENTER 4120 CAPRICORN LANE LA JOLLA CA 92037 28482912 0 X WWW.JCVI.ORG X 1993 MD JCVI IS ADVANCING THE SCIENCE OF GENOMICS THROUGH BOLD INNOVATIONS. OUR MISSION IS TO UNDERSTAND MOREABOUT THE BIOLOGICAL WORLD, AND TO DEVELOP UNIQUE INSIGHTS AND ANSWERSABOUT DISEASE, HEALTH, AND THE ENVIRONMENT FOR THE BENEFIT OF ALL. 8 5 180 7 15294 0 21442951 18613419 420120 123655 1920374 -823759 6009 15294 23789454 17928609 2586471 2842807 0 0 21730028 19124778 0 0 686812 13109263 8407194 37425762 30374779 -13636308 -12446170 108987608 100269815 35167258 36854821 73820350 63414994 X JCVI IS ADVANCING THE SCIENCE OF GENOMICS THROUGH BOLD INNOVATIONS. OUR MISSION IS TO UNDERSTAND MORE ABOUT THE BIOLOGICAL WORLD, AND TO DEVELOP UNIQUE INSIGHTS AND ANSWERS ABOUT DISEASE, HEALTH, AND THE ENVIRONMENT FOR THE BENEFIT OF ALL. 0 0 7864788 2782839 123655 THROUGHOUT THE FISCAL YEAR 2020, THE JCVI RECEIVED FUNDING FROM VARIOUS FEDERAL AND NON-FEDERAL SPONSORING AGENCIES AND FOUNDATIONS SUPPORTING IN EXCESS OF 85 ACTIVE RESEARCH PROJECTS COVERING A RANGE OF RESEARCH AREAS INCLUDING HUMAN HEALTH, ENVIRONMENTAL SUSTAINABILITY, SYNTHETIC BIOLOGY, TECHNOLOGY AND TOOLS, EDUCATION AND POLICY. DEPARTMENT OF HEALTH AND HUMAN SERVICES (DHHS) -FUNDED BY THE NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES (NIAID/NIH) AND IN COLLABORATION WITH THE UNIVERSITY OF CHICAGO, THE JCVI SERVES AS THE MAIN DEVELOPER OF THE VIRAL PATHOGEN RESOURCE (WWW.VIPRBRC.ORG) AND THE INFLUENZA RESEARCH DATABASE (WWW.FLUDB.ORG). THESE RESOURCES SERVE AS FREE PUBLIC PORTALS TO A WIDE RANGE OF INFORMATION, DATA, AND ANALYTICAL TOOLS FOR INTERPRETING VIRAL GENOMES IN THE CONTEXT OF DISEASE. OVER 3000 RESEARCHERS THROUGHOUT THE WORLD USE THESE RESOURCES EVERY WEEK. JCVI CONTINUED TO LEAD A 5-YEAR COLLABORATIVE NATIONAL CENTER FOR ADVANCING TRANSLATIONAL SCIENCES (NCATS/NIH) GRANT WITH THE GOAL TO DEVELOP, VALIDATE AND DISSEMINATE A COMPUTATIONAL INFRASTRUCTURE FOR UNBIASED ANALYSIS OF CYTOMETRY DATA FOR BOTH DIAGNOSTIC AND DISCOVERY APPLICATIONS THAT COULD HELP OVERCOME THE CURRENT LIMITATIONS OF MANUAL ANALYSIS AND PROVIDE FOR MORE EFFICIENT, OBJECTIVE, ACCURATE, AND REPRODUCIBLE ANALYSIS OF CYTOMETRY DATA. FLOW CYTOMETRY ANALYSIS IS WIDELY USED IN TRANSLATIONAL RESEARCH LAB TO EXPLORE THE MECHANISMS OF NORMAL AND ABNORMAL BIOLOGICAL PROCESSES AND IN THE CLINICAL DIAGNOSTIC LAB FOR THE IDENTIFICATION AND CLASSIFICATION OF BLOOD-BORNE MALIGNANCIES. HOWEVER, THE CURRENT PRACTICE FOR CYTOMETRY DATA ANALYSIS RELIES ON SUBJECTIVE AND AD HOC "MANUAL GATING". THE PROJECT TEAM OF JCVI, THE UNIVERSITY OF CALIFORNIA, SAN DIEGO (UCSD), THE UNIVERSITY OF CALIFORNIA, IRVINE (UCI), AND STANFORD UNIVERSITY COLLABORATED TO CONTINUE IMPROVING THE ACCESSIBILITY, FUNCTIONALITY, AND USABILITY OF THE PROPOSED INFRASTRUCTURE. THE PROJECT TEAMS ASSEMBLED MULTIPLE FLOW CYTOMETRY DATASETS FROM IMPORTANT BIOMEDICAL PROJECTS CONDUCTED BY TRANSLATIONAL RESEARCHERS AT UC IRVINE AND FROM THE CLINICAL DIAGNOSTICS LAB AT UCSD. THE JCVI TEAM PROCESSED AND ANALYZED THE DATASETS USING THE COMPUTATIONAL INFRASTRUCTURE AND VALIDATED THE ANALYSIS RESULTS USING FOLLOW-UP STUDIES. THE COMPUTATIONAL ANALYSES OF THESE DATASETS HAVE IDENTIFIED NOVEL CELL SUBSETS FROM HUMAN LEUKOCYTES FOR INDEPENDENT ASTHMA RESEARCH PROJECTS BEING CONDUCTED AT PEDIATRICS OF UC IRVINE. THE ANALYSES HAVE ALSO IDENTIFIED A NOVEL COMBINATION OF CELL SURFACE MARKERS FOR PRECISION DIAGNOSIS OF THE CHRONIC LYMPHOCYTIC LEUKEMIA BASED ON THE CLINICAL FLOW CYTOMETRY DATA PROVIDED BY UCSD. THE RESULTS AND FINDINGS HAVE BEEN PUBLISHED ON PEER-REVIEWED JOURNALS OR REPORTED AT SCIENTIFIC CONFERENCES. THE PROJECT TEAM HAVE ALSO BEEN TRAINING THE TRANSLATIONAL RESEARCHERS OF UCI PEDIATRICS AND HEMATOPATHOLOGISTS OF UCSD PATHOLOGY FOR USING THE ADVANCED DATA ANALYTICS TOOLS ON THE COMPUTATIONAL INFRASTRUCTURE THROUGH IN-PERSON SITE VISITS AND WEBEX MEETINGS. FUNDED THROUGH THE NATIONAL INSTITUTE OF ALLERGY AND IMMUNOLOGY (NIAID/NIH) AND IN COLLABORATION WITH NORTHEASTERN UNIVERSITY. ANTIBIOTIC RESISTANCE CONTINUES TO BE ONE OF THE BIGGEST PUBLIC HEALTH PROBLEMS OF OUR TIME. JCVI IN COLLABORATION WITH NORTHEASTERN UNIVERSITY HAVE DEVELOPED NEW METHODS TO GROW AND EXPLOIT PREVIOUSLY UNCHARACTERIZED MICROBES. JCVI DEVELOPED A TRANSCRIPTION-BASED PLATFORM THAT BIOINFORMATICALLY PREDICTS WHETHER NEW POTENTIAL COMPOUNDS ARE EXPRESSING ANTIBIOTIC PROPERTIES WITH NOVEL MECHANISMS OF ACTION. PROMISING COMPOUNDS ARE VALIDATED AND BECOME LEAD ANTIMICROBIAL COMPOUNDS FOR FURTHER STUDY. AS PART OF AN NIH GRANT IN COLLABORATION WITH COLLEAGUES AT UC IRVINE, THE RESEARCH TEAM HAVE BEEN APPLYING ADVANCE LABORATORY, COMPUTATIONAL, AND ARTIFICIAL INTELLIGENCE METHODS TO EXPLORE WHY SOME PEOPLE INFECTED WITH SARS-COV-2 DEVELOP SEVERE DISEASE WHILE OTHERS ARE ASYMPTOMATIC OR ONLY DEVELOP MILD SYMPTOMS. WE HAVE ALSO EXPLORED THE IMPACT THAT CORTICOSTEROID TREATMENT HAS ON COVID PATIENTS. WE FOUND THAT WHILE SEVERE COVID PATIENTS MOUNT AN EFFECTIVE ANTIBODY RESPONSE, THEY ALSO DEVELOP A MORE SEVERE GENERAL INFLAMMATORY REACTION, AND THAT THIS INFLAMMATORY RESPONSE WAS DAMPENED WITH STEROID TREATMENT. THESE FINDINGS SUGGEST THAT STEROID-BASED INTERVENTIONS COULD POTENTIAL LIMIT SEVERE COVID DISEASE AND WERE REPORTED IN A RECENT PUBLICATION IN THE JOURNAL OF LEUKOCYTE BIOLOGY (HTTPS://JLB.ONLINELIBRARY.WILEY.COM/DOI/EPDF/10.1002/JLB.4COVA0121-084RR). FUNDED BY NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES (NIEHS/NIH) MICROBIOME IN ASTHMA INDUCED BY ENVIRONMENTAL PARTICLE EXPOSURE. IN COLLABORATION WITH BROWN UNIVERSITY. MICROBIAL DYSBIOSIS IN THE GUT AND THE LUNG IS INCREASINGLY BEING ASSOCIATED WITH THE INCIDENCE AND SEVERITY OF ASTHMA, HOWEVER CAUSALITY STUDIES ARE LACKING. JCVI AND ITS COLLABORATOR, BROWN UNIVERSITY HAVE ADAPTED A MOUSE MODEL THAT FOCUSES ON THE ONSET OF ALLERGIC ASTHMA EARLY IN LIFE AFTER AN IN-UTERO EXPOSURE TO ENVIRONMENTAL PARTICLES TO STUDY HOW MICROBIOME MAY LEAD TO THE ASTHMA ONSET. IN THIS MODEL, THE RESEARCH TEAM HAS SHOWN THAT MATERNAL EXPOSURES TO ALLERGEN OR PARTICULATE MATTER, E.G. CONCENTRATED URBAN AIR PARTICLES (CAP), DIESEL EXHAUST PARTICLES (DEP) AND TITANIUM DIOXIDE PARTICLES (TIO2), TRIGGER INCREASED ASTHMA RISK IN SEVERAL GENERATIONS OF THE OFFSPRING. HUMANS ARE WIDELY EXPOSED TO THESE PARTICULATES, ESPECIALLY IN URBAN AND INDUSTRIAL SETTINGS, WHERE THE INCIDENCE OF ASTHMA IS ALSO HIGHER. RESEARCHERS FOUND THAT THE INCREASED 'PREPAREDNESS' FOR ASTHMA IN THESE NEONATES IS ASSOCIATED WITH DNA METHYLATION CHANGES IN KEY IMMUNE CELLS DENDRITIC CELLS THAT ARE ESSENTIAL IN ASTHMA ORIGIN. IMPORTANT UNANSWERED QUESTIONS ARE WHY THESE EPIGENETIC CHANGES OCCUR, AND WHETHER THERE IS A CAUSATIVE LINK TO THE ABERRANT MICROBIOME SEEN IN ASTHMA. THE JCVI HYPOTHESIZE THAT IN UTERO EXPOSURES TO PARTICLES ALTER THE MICROBIOME OF THE PREGNANT MICE AND THEIR OFFSPRING, WHICH THEN SIGNALS TO THE IMMUNE CELLS IN A WAY THAT PREDISPOSES THE OFFSPRING TO ALLERGY. WE POSTULATE TWO, POTENTIALLY INTERCONNECTED, MECHANISMS IN ASTHMA ONSET: EPIGENETICS AND THE MICROBIOME. BOTH THE EPIGENETIC ALTERATIONS IN IMMUNE CELLS AND THE DYSBIOSIS IN THE GUT AND LUNG HAVE BEEN LINKED TO ASTHMA IN HUMANS AND MOUSE MODELS BUT CAUSALITY STUDIES ARE LACKING. THE PROPOSED RESEARCH ADDRESSES THIS GAP IN KNOWLEDGE IN A STUDY DESIGNED TO TEST BASIC MECHANISMS OF RELATIVELY COMMON ENVIRONMENTAL EXPOSURES. PROJECT FUNDED THROUGH THE NATIONAL INSTITUTE OF ALLERGY AND IMMUNOLOGY (NIAID/NIH) A DEVELOPMENT OF NOVEL PROTEIN-BASED VACCINE FORMULATIONS TO PREVENT PNEUMOCOCCAL COLONIZATION AND DISEASE WITH COLLABORATOR FROM THE UNIVERSITY OF MARYLAND. ONE OF THE MAJOR PROBLEMS OF THE GREAT BURDEN OF COMMUNITY-ACQUIRED PNEUMONIAS CAUSED BY STREPTOCOCCUS PNEUMONIAE (SPN) INFECTION, IS THE ACQUISITION OF ANTIMICROBIAL RESISTANCE AND THE GLOBAL SPREAD OF RESISTANT VARIANTS. THESE PROBLEMS GET ENHANCED BY THE MAJOR DISADVANTAGES OF THE CURRENT CAPSULAR POLYSACCHARIDE-BASED VACCINES, SUCH AS COST, SEROTYPE SPECIFICITY, AND THE RESULTING INCOMPLETE COVERAGE. THIS OCCURS MAINLY BECAUSE OF DISEASE BEING CAUSED BY SEROTYPES NOT PRESENT IN THE VACCINE (MAXIMUM OF 23 OF THE >97 CAPSULE TYPES, ONLY 13 IN THE CONJUGATE VACCINE) AND REPLACEMENT CARRIAGE. THE RATIONALE FOR THIS PROJECT IS THAT DEVELOPMENT OF A SUBUNIT-BASED VACCINE UTILIZING NOVEL CONSERVED ANTIGENIC PROTEINS IN CONJUNCTION WITH NOVEL POLYPHOSPHAZENE (PPZ) ADJUVANTS, PROVEN TO INDUCE ADAPTIVE IMMUNITY WILL DEEPEN THE CURRENT TOOLKIT TO PREVENT PNEUMOCOCCAL DISEASE WITHOUT SEROTYPE LIMITATIONS. THUS, JCVI HYPOTHESIZE THAT ADDITION OF CONSERVED IMMUNOGENIC PROTEINS TO A POTENT ADJUVANT NANO-MOLECULE WILL PROVIDE THE GROUNDWORK FOR THE DEVELOPMENT OF A BROADLY PROTECTIVE PNEUMOCOCCAL SUBUNIT-BASED VACCINE. (SEE FORM 990, PART III, LINE 4A, PROGRAM SERVICE ACCOMPLISHMENTS CONTINUED). 2611197 59968 JCVI IS THE RECIPIENT OF A LARGE COLLABORATIVE ASSISTANCE AWARD FROM THE US DEPARTMENT OF ENERGY. AWARDED TO THE VALUE OF $10.7M. NOW IN ITS 4TH YEAR OF 5,THE JCVI AND ITS COLLABORATORS, COLORADO STATE UNIVERSITY, VANDERBILT UNIVERSITY AND THE UNIVERSITY OF CALIFORNIA, SAN DIEGO, SEEK TO LEVERAGE SIGNIFICANT RECENT ADVANCES IN DIATOM GENOME ENGINEERING AND METABOLIC MODELING; INCLUDING THE ABILITY TO INTRODUCE CHROMOSOME-LIKE EXPRESSION PLATFORMS, WHICH SUBSTANTIALLY ADVANCE POSSIBILITIES FOR HIGH-THROUGHPUT GENERATION AND SCREENING OF GENETICALLY ENGINEERED DIATOMS. RESEARCH PROPOSED HERE WILL RESULT IN DRAMATIC IMPROVEMENTS IN THE PREDICATIVE CAPACITY OF EXISTING GENOME SCALE METABOLIC MODELS OF DIATOM METABOLISM. FOR THE FIRST TIME ON A LARGE SCALE, FLUXOMICS, WHICH IS COMPOUND SPECIFIC INCORPORATION OF AN ISOTOPICALLY-LABELED FEEDSTOCK, WILL BE USED TO PROVIDE BETTER FIRST STEP CONSTRAINTS ON CO2 ASSIMILATION OF IN DIATOMS. STATE-OF-THE-ART HIGH THROUGHPUT IN VITRO EXAMINATIONS OF NEARLY ALL 200 DIATOM TRANSCRIPTION FACTORS WILL BE CONDUCTED TO BETTER UNDERSTAND REGULATORY ARCHITECTURE UNDERLYING DIATOM METABOLISM AS WELL AS SERVE AS A SOURCE FOR NEW TOOLS FOR GENOME ENGINEERING. TAKEN TOGETHER, RESEARCH PROPOSED HERE WILL ADDRESS CURRENTLY LIMITING BOTTLENECKS THROUGH FOSTERING STATE-OF-THE-ART INTEGRATION OF GENOME-SCALE MODELING WITH GENOME ENGINEERING TO OPTIMIZE ENERGY AND METABOLITE FLUX THROUGH SUBCELLULAR COMPARTMENTS TO PROMOTE EFFICIENT PRODUCTION OF HIGH VALUE AND FUEL-RELATED METABOLITES. 2679430 DURING 2020, JCVI HAD MULTIPLE ACTIVE RESEARCH AWARDS FROM THE DEPARTMENT OF DEFENSE (DOD). THESE AWARDS FOCUS ON THE UNDERSTANDING OF POLYMICROBIAL INFECTIONS IN WOUNDS, THE DEVELOPMENT OF SYNTHETIC GENOMIC TECHNOLOGIES FOR MANIPULATION OF CHROMOSOMES AND GENOMES AND FOR THE DEVELOPMENT OF SAFE METHODS FOR DNA ISOLATION AND ANALYSIS FROM BIOTHREAT AGENTS. FUNDED BY THE DEFENSE ADVANCED RESEARCH PROJECTS AGENCY (DARPA) THE JCVI IS PROVIDING LONGITUDINAL DNA METHYLATION PROFILING, LONGITUDINAL HISTONE MODIFICATION PROFILING AND LONGITUDINAL METABOLOME PROFILING ON MULTIPLE SAMPLES IN COLLABORATION WITH DARPA FOR THE SELECTING ELITE-PERFORMERS WITH LONGITUDINAL EPIGENOMIC CHARACTERIZATION AND TRACKING (SELECT) PROJECT. WOUND MICROBIOME PROJECT - CHRONIC WOUNDS ARE WOUNDS THAT FAIL TO HEAL AFTER 3 MONTHS UNDER STANDARD OF CARE WOUND MANAGEMENT. THE GOAL OF THIS DOD STUDY IS TO GAIN A BETTER UNDERSTANDING OF THE DIFFERENT CLASSES OF MICROBES THAT COULD BE PRESENT IN HUMAN CHRONIC WOUNDS (I.E. THE WOUND MICROBIOME), AND ASK WHETHER SPECIFIC MICROBES OR MICROBIAL COMMUNITIES ARE ASSOCIATED WITH NON-HEALING WOUNDS. NEXT GENERATION SEQUENCING WILL BE USED TO IDENTIFY AND CATALOG THE MICROBIAL SPECIES OF BACTERIA, FUNGI, AND VIRUSES THAT ARE PRESENT IN CHRONIC WOUND SPECIMENS. COMPUTATIONAL AND BIOINFORMATICS ANALYSES OF THE MICROBIAL COMMUNITY DNA SEQUENCES WILL BE CARRIED OUT TO CHARACTERIZE THE PRESENCE ANY PATHOGENIC, VIRULENCE, AND ANTIMICROBIAL RESISTANCE-RELATED GENES AND PATHWAYS. THE EVENTUAL GOAL IS TO IDENTIFY ANY PATHOGENIC SPECIES OR FEATURES THAT ARE ASSOCIATED WITH NON-HEALING WOUNDS, AND COULD BE USED AS DIAGNOSTIC AND TREATMENT TARGETS OF CHRONIC WOUNDS. SYNTHETIC ENGINEERING OF BACTERIOPHAGE FOR TREATMENT OF WOUND INFECTIONS ANTIMICROBIAL RESISTANCE IN BACTERIAL PATHOGENS IS STEADILY INCREASING AND RECOGNIZED AS ONE OF THE GREATEST THREATS TO GLOBAL PUBLIC HEALTH. SHORTLY AFTER THE BEGINNING OF THE WARS IN AFGHANISTAN AND IRAQ, THE MILITARY HEALTH SYSTEM EXPERIENCED A MAJOR INCREASE IN WOUND AND HEALTHCARE-ASSOCIATED INFECTIONS CAUSED BY MULTIDRUG RESISTANT ORGANISMS (MDROS) WITH EXTREMELY LIMITED TREATMENT OPTIONS. FUNDED THROUGH THE US MEDICAL RESEARCH ACQUISITION ACTIVITY, THE JCVI IN COLLABORATION WITH THE MILITARY AND THE WALTER REED ARMY INSTITUTE OF RESEARCH, IS COLLABORATING WITH THE GOAL TO DESIGN, BUILD, TEST AND CHARACTERIZE NOVEL ENGINEERED BACTERIOPHAGE BIOLOGICS SPECIFICALLY TARGETING MDROS FOR USE AS NOVEL THERAPEUTICS FOR TREATING AND PREVENTING COMBAT WOUND INFECTIONS USING PIONEERING TECHNOLOGY DEVELOPED AT JCVI. THIS OBJECTIVE WILL BE ACCOMPLISHED THROUGH EXPERIMENTS FOCUSED ON PRODUCING SYNTHETICALLY ENGINEERED PHAGE WITH AN ENHANCED HOST RANGE SUFFICIENT TO COVER CURRENT AND FUTURE CIRCULATING MDR STRAINS OF S. AUREUS AND K. PNEUMONIAE COMMONLY FOUND IN THE MILITARY HEALTH SYSTEM, INCLUDING METHICILLIN-RESISTANT S. AUREUS AND CARBAPENEM-RESISTANT K. PNEUMONIAE STRAINS. CANDIDATE ENGINEERED THERAPEUTIC PHAGE CHASSIS WILL BE PRODUCED, CHARACTERIZED AND TESTED IN MOUSE WOUND INFECTION MODELS BY RESEARCHERS AT WRAIR AS A PRELUDE TO FUTURE HUMAN USE. IT IS ANTICIPATED THAT WE WILL DEVELOP ONE OR MORE PHAGE CHASSIS CAPABLE OF SPECIFICALLY TARGETING AND KILLING EACH PATHOGEN BOTH IN VITRO AND IN VIVO." 3873475 OTHER PROGRAM SERVICES IN THE JCVI RESEARCH PORTFOLIO ALSO INCLUDED SUPPORT FROM FOUNDATIONS AND INDUSTRIAL COLLABORATIONS.: NATIONAL SCIENCE FOUNDATION COLLABORATIVE RESEARCH: IRON BIOAVAILABILITY IN HIGH-CO2 OCEANS: NEW PERSPECTIVES ON IRON ACQUISITION MECHANISMS IN DIATOMS WITH THIS PROJECT THE JCVI SEEKS TO UNDERSTAND THE DIFFERENTIAL SENSITIVITY OF DIATOM IRON ACQUISITION STRATEGIES TO CHANGES IN SEAWATER PH AND CARBONATE CHEMISTRY. ULTIMATELY A MORE THOROUGH AND DETAILED MECHANISTIC UNDERSTANDING OF DIATOM IRON UPTAKE PATHWAYS WILL FACILITATE A MUCH-IMPROVED ABILITY TO FORECAST THE IMPACT OF ANTICIPATED CHANGES IN OCEAN PH AND INORGANIC CARBON CHEMISTRY ON RATES OF IRON UPTAKE BY DIATOMS. THIS CRITICAL BIOGEOCHEMICAL ISSUE IS ADDRESSED THROUGH TRACE METAL CLEAN MANIPULATION EXPERIMENTS INCORPORATING STATE-OF-THE-ART ANALYTICAL METHODOLOGY TO PROBE PHYTOPLANKTON CELLULAR PHYSIOLOGY AND BIOGEOCHEMISTRY IN LABORATORY CULTURES AND NATURAL COMMUNITIES. IN THE FIRST YEAR, LABORATORY EXPERIMENTS WITH A MODEL PENNATE DIATOM LEVERAGE A COLLECTION OF TARGETED KNOCKOUT TRANSGENIC LINES TO EVALUATE THE SUBSTRATE SPECIFICITY AND RELATIVE IMPORTANCE OF DISTINCT IRON ASSIMILATION PATHWAYS UNDER A RANGE OF PCO2 AND IRON AVAILABILITY CONDITIONS. ADDITIONALLY, QUANTITATION OF MRNA AND PROTEINS FOR KEY DIATOM IRON ASSIMILATION PATHWAYS IN NATURAL COMMUNITIES IN THE SOUTHERN CALIFORNIA CURRENT FURTHER CLARIFY THE RELATIVE IMPORTANCE AND SENSITIVITY OF DISTINCT IRON ASSIMILATION PATHWAYS IN RELATION TO PCO2 AND IRON AVAILABILITY. IN YEAR TWO A LAGRANGIAN STUDY OF IRON UPTAKE RATES AND ASSOCIATED MRNA AND PROTEIN ABUNDANCE IS PERFORMED ON UPWELLED HIGH PCO2 WATER OVER THE COURSE OF OFFSHORE ADVECTION. ADDITIONALLY, WE CONDUCT MESOCOSM EXPERIMENTS USING NATURALLY ELEVATED HIGH PCO2 SEAWATER AS WELL AS LABORATORY EXPERIMENTS ON MULTIPLEX KNOCKOUT LINES. YEAR THREE IS DEDICATED TO DATA ANALYSES AND OVERALL PROJECT SYNTHESIS. OVERALL AIMS OF THE RESEARCH ACTIVITIES INCLUDE, 1) DEVELOPMENT AND VALIDATION OF A REFINED CONCEPTUAL MODEL OF IRON UPTAKE IN KEY MARINE PHYTOPLANKTON AND SUBSEQUENT UTILIZATION OF THE MODEL TO CHARACTERIZE THE SENSITIVITY OF DISTINCT IRON UPTAKE PATHWAYS TO THE EFFECTS OF OCEAN ACIDIFICATION, AND 2) DETERMINATION OF THE EFFECTS OF ACIDIFICATION ON IRON UPTAKE, AND QUANTIFICATION OF THE RELATIVE CONTRIBUTION OF DISTINCT IRON ACQUISITION PATHWAYS IN HIGH PCO2 PHYTOPLANKTON COMMUNITIES. GORDON AND BETTY MOORE FOUNDATION GENETIC DIVERSITY IS A HALLMARK OF ADAPTABILITY; THE RIGHT AMOUNT GIVES A THEORETICAL ADVANTAGE IN SHIFTING ENVIRONMENTS. HOWEVER, TOO MUCH DIVERSITY MAY LEAD TO DECREASED FITNESS RESULTING FROM GENETIC BOTTLENECKS, KNOWN AS MULLER'S RATCHET. THE EXTENT OF GENETIC VARIATION AMONG INDIVIDUALS CAN SET A SPECIES' ADAPTIVE POTENTIAL AND INFLUENCE ITS PERSISTENCE OVER TIME. FOR THESE REASONS, THE AMOUNT OF GENETIC VARIABILITY WITHIN SPECIES HAS BEEN A FOCUS OF POPULATION GENETICS AND EVOLUTIONARY BIOLOGY FOR NEARLY 100 YEARS. FROM AN ECOLOGICAL PERSPECTIVE, RECENT WORK IN BOTH TERRESTRIAL AND MARINE SYSTEMS HAS SHOWN THAT INTRASPECIFIC GENETIC DIVERSITY CAN MODULATE INTERSPECIFIC INTERACTIONS AND THUS INFLUENCE LEVELS OF PRIMARY PRODUCTIVITY AND FUNCTIONAL RESPONSES TO CHANGING ENVIRONMENTS. THESE COMPLEXITIES GUIDE OUR RATIONALE FOR SEEKING CELLULAR-LEVEL DATA TO ADDRESS HIGHER-ORDER ECO-EVOLUTIONARY DYNAMICS. IN THIS PROJECT, FUNDED BY THE GORDON AND BETTY MOORE FOUNDATION, THE JCVI HAVE TAKEN A CELLULAR APPROACH TO CAPTURE GENETIC DIVERSITY OF A MARINE EUKARYOTIC PHYTOPLANKTON POPULATION OF CYLINDROTHECA. DURING THIS WORK, JCVI HAS ISOLATED NOVEL RNA VIRUSES INFECTING THIS DIATOM AND GENERATED HOST/VIRUS GENOMIC AND TRANSCRIPT EXPRESSION DATA. JCVI HAVE ALSO DEVELOPED NEW AND MORE EFFICIENT METHODS FOR OBTAINING THESE DATA. USING THIS INFORMATION, WE HAVE EMPIRICALLY DERIVED THE HETEROGENEOUS NATURE OF PHYTOPLANKTON POPULATIONS AND GAINED INSIGHT INTO HOW THE INDIVIDUAL'S METABOLIC CAPACITY MAY NOT TRANSLATE TO THE POPULATION AS A WHOLE. THE LARRY L HILLBOM FOUNDATION - OVER THE LAST FEW YEARS, ADVANCES IN STEM CELL RESEARCH AND SYNTHETIC BIOLOGY HAVE CATALYZED AN EXTRAORDINARY EXPANSION OF ORGANOID TECHNOLOGY THAT IS BRINGING CHANGES TO TRANSLATIONAL MEDICINE, PHARMACEUTICAL RESEARCH, AND STRATEGIES FOR TREATING VARIOUS HUMAN PATHOLOGIES. USING STEM CELLS, ORGANOIDS HAVE BEEN DEVELOPED FOR MULTIPLE ORGANS INCLUDING LIVER, INTESTINE, KIDNEY, BRAIN, STOMACH, SKIN, OVARY, AND LUNG (1). A NETWORK OF SCIENTISTS LED BY THE JCVI AND IN COLLABORATION WITH STANFORD UNIVERSITY, UNIVERSITY OF CALIFORNIA, SAN DIEGO, AND THE SALK INSTITUTE FOR BIOLOGICAL STUDIES ARE DEVELOPING ORGANOIDS THAT CAN SERVE AS SURROGATES FOR BETA CELLS, WHICH ARE THE CELLS IN THE HUMAN PANCREAS THAT CONTROL BLOOD GLUCOSE LEVELS BY SYNTHESIZING INSULIN. THE GOAL IS THAT THESE ORGANOIDS, WHEN IMPLANTED IN TYPE 1 DIABETICS (T1D), WILL RESULT IN A BETTER TREATMENT AND BETTER LIVES FOR THOSE PATIENTS. THE INSULIN INFUSION PUMPS USED BY MANY T1D PATIENTS ARE IN ESSENCE, MECHANICAL ORGANOIDS. WHILE EFFECTIVE, THEY DO NOT COMPLETELY PROTECT THE PATIENTS FROM THE LONG-TERM EFFECTS OF THE DISEASE OR ENABLE A NORMAL NONDIABETIC LIFESTYLE. IN T1D PATIENTS, THE PANCREATIC BETA CELLS ARE DESTROYED BY AN AUTOIMMUNE RESPONSE. ONE THEME OF RESEARCH FOR MANY YEARS HAS BEEN TO TRANSPLANT BETA CELLS FROM CADAVERS INTO DIABETIC PATIENTS. MORE RECENTLY, RESEARCHERS ARE DEVELOPING METHODS TO PROGRAM STEM CELLS TO BECOME BETA CELLS THAT WOULD BE TRANSPLANTED INTO PATIENTS. FOR THIS TO BE SUCCESSFUL, THE PATIENTS ARE FORCED TO TAKE IMMUNOSUPPRESSIVE DRUGS FOR THE REST OF THEIR LIVES, OR TO SEQUESTER THE TRANSPLANTED BETA CELLS FROM THE PATIENT'S IMMUNE SYSTEM BY PLACING THEM IN PLASTIC CAPSULES. NEITHER OF THESE APPROACHES HAVE PROVEN SATISFACTORY. SUPPORT FROM LARRY L HILLBOM FOUNDATION IS ENABLING THE RESEARCH TEAM TO TEST TWO NOVEL APPROACHES TO MAKE INSULIN-PRODUCING BIOLOGICAL ORGANOIDS THAT WOULD CONTROL DIABETICS' BLOOD GLUCOSE LEVELS BUT NOT BE AFFECTED BY THE PATIENTS' AUTOIMMUNE SYSTEM, WHICH KILLED THE PATIENTS' NATURAL BETA CELLS. THE FIRST APPROACH IS TO USE STEM CELL AND SYNTHETIC BIOLOGY TECHNOLOGY TO DEVELOP ORGANOIDS THAT RESEMBLE THE EYE AND USE THEM TO HOUSE BETA CELLS. THE EYE IS A WELL-CHARACTERIZED "IMMUNE PRIVILEGE" SITE WHERE IMMUNE ACTIVITY IS REDUCED TO ALLOW FOR OTHER ESSENTIAL FUNCTIONS. THE GENERATED EYE/BETA CELL ORGANOIDS WILL BE IMPLANTED IN THE PATIENT'S SKIN AND REPLACE THE CURRENT INSULIN INFUSION THERAPY. THE SECOND APPROACH CAPITALIZES ON THE RECENT DISCOVERY BY THE RESEARCH TEAM THAT BACTERIA LIVE IN THE DEEPEST LAYERS OF THE SKIN. WE PROPOSE TO HARVEST THOSE BACTERIA AND USING SYNTHETIC BIOLOGY, GENETICALLY ENGINEER THEM TO SENSE BLOOD GLUCOSE IN THE SKIN AND SYNTHESIZE INSULIN IN RESPONSE TO ELEVATED GLUCOSE LEVELS. THEY WOULD BE ORGANOIDS THAT ARE LIKE NATURAL BETA CELLS, BUT NOT AFFECTED BY PATIENTS' AUTOIMMUNE RESPONSES. ORGANOIDS FROM BOTH APPROACHES SHOULD ENABLE AN AUTONOMOUS, CLOSED-LOOP SYSTEMS THAT ARE NOT MACHINEBASED WITH NO PAINFUL NEEDLES AND NO SENSATION OF WEARING A DEVICE. WE BELIEVE THAT ORGANOID-BASED THERAPIES COULD BE A BREAKTHROUGH THAT WILL BRING NORMAL LIFESTYLES TO T1D PATIENTS.SYNTHETIC-GESTALT - MORE AND MORE CHEMICALS TO SUPPORT VARIOUS INDUSTRIES WILL COME FROM ENGINEERED BACTERIA IN THE FUTURE, BUT CONCERNS REMAIN ABOUT THE SAFETY OF THE ORGANISMS OR UNINTENDED BYPRODUCTS. MINIMAL BACTERIAL CELLS OFFER A UNIQUE PLATFORM FOR BIOPRODUCTION. BECAUSE A LARGER FRACTION OF BIOLOGICAL PROCESSES ARE UNDERSTOOD IN THESE SIMPLE CELLS, THEY CAN EASILY BE MADE SAFE AND MORE EFFICIENT IN PRODUCING TARGET COMPOUNDS. THE COLLABORATION BETWEEN SYNTHETIC GESTALT AND JCVI IN 2020 LED TO THE DEVELOPMENT OF A DIGITAL TWIN, A COMPUTATIONAL MODEL, FOR A MINIMAL CELL THAT CAN BE USED TO OPTIMIZE METABOLIC REACTIONS IN THE CELL. THIS RESEARCH ALSO GAVE RISE TO STRAINS WITH METABOLIC PATHWAY GENES ADDED FROM OUTSIDE TOWARD ESTABLISHING A MINIMAL BACTERIAL CELL AS A FUTURE INDUSTRIAL PRODUCTION HOST. 3873475 17028890 1 1 0 0 0 0 0 1 0 0 1 0 0 0 1 1 1 0 0 0 1 1 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 1 56 0 1 180 1 1 1 0 0 0 0 0 0 0 0 0 1 0 X 8 5 1 0 0 0 0 0 0 1 1 0 0 1 1 1 1 1 1 1 1 0 CA MD X DR JOHN CRAIG VENTER 8582001800 4120 CAPRICORN LANE LA JOLLA CA 92037 VENTER JOHN CRAIG CHAIRMAN & CEO 40.00 X X 1194335 0 45300 NELSON KAREN PRESIDENT 40.00 X X 711001 0 61532 KOWALSKI HEATHER CHIEF OPERATING OFFICER 40.00 X X 449321 0 36738 MULLEN JILL SR. VP OF PHILANTHROPY AND STRATEGIC ALLIANCES 40.00 X 350060 0 63009 SCHEUERMANN RICHARD H DIRECTOR, LA JOLLA CAMPUS 40.00 X 348827 0 56459 STOUT MARTIN CHIEF TECHNOLOGY OFFICER 40.00 X 308171 0 36227 PEAKE ANTONY G VP FOR RESEARCH ADMINISTRATION 40.00 X 294523 0 30633 YUMULMARY VP OF HUMAN RESOURCES 40.00 X 253229 0 65398 KIRKNESS EWEN PROFESSOR 40.00 X 257034 0 54754 STAYEAS TIMOTHY NETWORK TEAM LEAD 40.00 X 214440 0 60471 ADELSON JULIE VP, LEG. AFFRS/GENERAL COUNSEL 40.00 X 210151 0 36765 PRATTE EDWARD DIRECTOR OF SECURITY 40.00 X 226695 0 7187 FRIEDMAN ROBERT M VP FOR POLICY & UNIV. RELATIONS 40.00 X 143182 0 52666 BADR-EL-DIN AMIN PHD TRUSTEE 4.00 X 0 0 0 HOROWITZREENA TRUSTEE (THRU 2/27/2020) 4.00 X 0 0 0 KNIGHT JESSIE TRUSTEE (THRU 2/27/2020) 4.00 X 0 0 0 MCGRORY JACK TRUSTEE 4.00 X 0 0 0 NORRBY ERLING TRUSTEE 4.00 X 0 0 0 RUGGLES RUDY TRUSTEE 4.00 X 0 0 0 WEI WU TRUSTEE (AS OF 2/27/2020) 4.00 X 0 0 0 4960969 0 607139 58 0 1 0 TB CONSULTING 8328 E HARTFORD DRIVE SUITE 102 SCOTTSDALE AZ 85255 COMPUTER SERVICE CONSULTANT 216901 MOSS ADAMS LLP 4747 EXECUTIVE DRIVE SUITE 1300 SAN DIEGO CA 92121 ACCOUNTING AND AUDIT SERVICES 165285 2 15140853 3472566 18613419 SEQUENCING SERVICES REVENUE 900099 120988 120988 CLONE REVENUE 900099 2667 2667 123655 905885 905885 8729641 95018 10552212 2091 -1822571 92927 -1729644 -1729644 K-1 PASSTHROUGH 900099 15294 15294 15294 17928609 123655 15294 -823759 2782839 2782839 59968 59968 4015830 1037747 2945546 32537 12209265 7678994 4135691 394580 407174 202230 182191 22753 1476838 674939 706100 95799 1015671 430211 537894 47566 54871 54871 133112 133112 108379 108379 210121 70000 140121 37579 37579 361311 121628 221868 17815 973958 31911 942047 2041396 1371259 626438 43699 30595 17920 4647 8028 52041 44395 6505 1141 66954 66954 2051976 1051885 984247 15844 477540 108701 366868 1971 LAB EQUIPMENT/SUPPLIES 1726041 1335945 390096 BOOKS AND SUBSCRIPTIONS 26646 36 21646 4964 54674 8282 46277 115 30374779 17028890 12659077 686812 4765643 2188334 12285562 7177016 3868838 4135631 260317 16925 1022612 884675 69065155 24415322 46530181 44649833 36161170 37353456 1253071 1087432 2840214 2776513 108987608 100269815 6031343 4481086 2528751 2353045 26524485 24942805 82679 5077885 35167258 36854821 X 73084655 62937864 735695 477130 73820350 63414994 108987608 100269815 X -12446170 2056108 -15294 X 0 1 X 1 1 1 X 26768604 20421917 30012027 21442951 18613419 117258918 26768604 20421917 30012027 21442951 18613419 117258918 4002103 113256815 1482196 1373809 1387304 1158537 905885 6307731 123566649 1757477 0.91660 0.76300 X RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED RESTRICTED 2545000 X X X 0 53875009 10050198 43824811 15190146 14365124 825022 44649833 LEASES PAYABLE 33024 PPP LOAN 5044861 5077885 X 20221044 2056108 360000 2416108 17804936 108379 15294 123673 17928609 30626400 360000 360000 30266400 108379 108379 30374779 PART III, LINE 4: COLLECTION OF SCIENTIFIC WRITINGS RELEVANT TO GENOMIC RESEARCH. PART X, LINE 2: THE INSTITUTE IS A NOT-FOR-PROFIT ORGANIZATION EXEMPT FROM FEDERAL INCOME TAXES UNDER SECTION 501(C)(3) OF THE INTERNAL REVENUE CODE. THE INSTITUTE DOES NOT BELIEVE THERE ARE ANY MATERIAL UNCERTAIN TAX POSITIONS AND ACCORDINGLY, NO PROVISION FOR INCOME TAXES HAS BEEN MADE IN THE ACCOMPANYING FINANCIAL STATEMENTS. THE INSTITUTE IS SUBJECT TO ROUTINE AUDITS BY TAXING JURISDICTIONS; HOWEVER, THERE ARE CURRENTLY NO AUDITS FOR ANY TAX PERIOD IN PROGRESS. PART XI, LINE 4B - OTHER ADJUSTMENTS: K-1 PASSTHROUGH 15,294. 1 EAST ASIA AND THE PACIFIC - AUSTRALIA, BRUNEI, BURMA, CAMBODIA, PROGRAM SERVICES RESEARCH SUBGRANTS 59986 CAYMAN ISLANDS INVESTMENTS 143279 0 0 0 0 0 0 203265 0 203265 EAST ASIA AND THE PACIFIC PROGRAM SERVICES 59986 WIRE 1 1 0 0 1 1 0 PART I, LINE 2: EACH SUBGRANT IS A PASS THROUGH GRANT FROM A FEDERAL OR NON-FEDERAL GRANT OR CONTRACT AWARDED TO J. CRAIG VENTER INSTITUTE. ALL EXPENSES ARE MONITORED AS INVOICED AT LEAST QUARTERLY, BUT IN MOST CASES MONTHLY. THE INVOICES ARE REVIEWED AND APPROVED BASED ON RECEIPT OF GOODS OR SERVICES AND AGAINST AN APPROVED BUDGET. PART I, LINE 3: ACCRUAL BASIS PART III ACCOUNTING METHOD: PART II, LINE 1: ACCRUAL BASIS 1 UNIVERSITY OF CALIFORNIA SAN DIEGO 9500 GILMAN DR LA JOLLA CA 92037 566001393 501(C)(3) 646423 RESEARCH SUBGRANT UNIVERSITY OF CALIFORNIA IRVINE 120 THEORY SUITE 200 IRVINE CA 92697 952226406 501(C)(3) 73149 RESEARCH SUBGRANT COLORADO STATE UNIVERSITY 6015 CAMPUS DELIVERY FORT COLLINS CO 80523 846000545 501(C)(3) 441120 RESEARCH SUBGRANT MRI GLOBAL 425 VOLKER BLVD KANSAS CITY MO 641102241 440545878 501(C)(3) 117251 RESEARCH SUBGRANT REGENTS UNIVERSITY OF MINNESOTA 700 ROSEDALE AVE ST LOUIS MO 63112 430653611 501(C)(3) 46643 RESEARCH SUBGRANT VANDERBILT UNIVERSITY 2201 WEST END AVE NASHVILLE TN 37235 620476822 501(C)(3) 236730 RESEARCH SUBGRANT RHODE ISLAND HOSPITAL 1 HOPPIN STREET BOX 42 SUITE 1300 PROVIDENCE RI 029034923 050258954 501(C)(3) 393803 RESEARCH SUBGRANT SALK INSTITUTE 10010 N TORREY PINES ROAD LA JOLLA CA 92037 952160097 501(C)(3) 123771 RESEARCH SUBGRANT SANTA FE INSTITUTE 1399 HYDE PARK ROAD SANTA FE NM 875018943 850325494 501(C)(3) 46969 RESEARCH SUBGRANT SEQUELLA FOUNDATION INC 9610 MEDICAL CENTER DRIVE 200 ROCKVILLE MD 20850 522044703 501(C)(3) 5378 RESEARCH SUBGRANT LELAND STANFORD JR UNIVERSITY 3145 PORTER DRIVE PALO ALTO CA 94304 941156365 501(C)(3) 254611 RESEARCH SUBGRANT CAL POLY CORPORATION 1 GRAND AVE SAN LUIS OBSISPO CA 93407 951648180 501(C)(3) 30426 RESEARCH SUBGRANT GLOBAL ALGAE INNOVATIONS 486 LIVE OAK DRIVE EL CAJON CA 92020 455319556 326567 RESEARCH SUBGRANT LAWRENCE LIVERMORE NATIONAL LABORATORY 7000 EAST AVE LIVERMORE CA 94550 205624386 GOVT 40000 RESEARCH SUBGRANT 13 1 PART I, LINE 2: EACH SUBGRANT IS A PASS THROUGH GRANT FROM A FEDERAL OR NON-FEDERAL GRANT OR CONTRACT AWARDED TO J. CRAIG VENTER INSTITUTE. ALL EXPENSES ARE MONITORED AS INVOICED AT LEAST QUARTERLY, BUT IN MOST CASES MONTHLY. THE INVOICES ARE REVIEWED AND APPROVED BASED ON RECEIPT OF GOODS OR SERVICES AND AGAINST AN APPROVED BUDGET. X X X 1 1 X X X X 0 0 0 0 0 0 0 0 0 VENTER JOHN CRAIG CHAIRMAN & CEO 1178618 0 0 0 15717 0 11400 0 33900 0 1239635 0 0 0 NELSON KAREN PRESIDENT 705214 0 0 0 5787 0 11400 0 50132 0 772533 0 0 0 KOWALSKI HEATHER CHIEF OPERATING OFFICER 446179 0 0 0 3142 0 11400 0 25338 0 486059 0 0 0 MULLEN JILL SR. VP OF PHILANTHROPY AND STRATEGIC 342958 0 0 0 7102 0 11400 0 51609 0 413069 0 0 0 SCHEUERMANN RICHARD H DIRECTOR, LA JOLLA CAMPUS 340418 0 0 0 8409 0 11400 0 45059 0 405286 0 0 0 STOUT MARTIN CHIEF TECHNOLOGY OFFICER 299769 0 0 0 8402 0 11400 0 24827 0 344398 0 0 0 PEAKE ANTONY G VP FOR RESEARCH ADMINISTRATION 291936 0 0 0 2587 0 11400 0 19233 0 325156 0 0 0 YUMULMARY VP OF HUMAN RESOURCES 250697 0 0 0 2532 0 10400 0 54998 0 318627 0 0 0 KIRKNESS EWEN PROFESSOR 256212 0 0 0 822 0 10400 0 44354 0 311788 0 0 0 STAYEAS TIMOTHY NETWORK TEAM LEAD 212920 0 0 0 1520 0 8986 0 51485 0 274911 0 0 0 ADELSON JULIE VP, LEG. AFFRS/GENERAL COUNSEL 197625 0 0 0 12526 0 8015 0 28750 0 246916 0 0 0 PRATTE EDWARD DIRECTOR OF SECURITY 223817 0 0 0 2878 0 0 0 7187 0 233882 0 0 0 FRIEDMAN ROBERT M VP FOR POLICY & UNIV. RELATIONS 126606 0 0 0 16576 0 5305 0 47361 0 195848 0 0 0 PART I, LINE 1A SCHEDULE J, PART I, LINE 1A: TAX INDEMIFICATION AND GROSS-UP PAYMENTS - CERTAIN AWARDS ARE GROSSED UP FOR INCOME TAX AND INCLUDED AS TAXABLE COMPENSATION. SCHEDULE J, PART I, LINE 1A; FIRST-CLASS OR CHARTER TRAVEL - THE ORGANIZATION PROVIDES THE CEO FIRST CLASS AND CHARTER TRAVEL FOR BUSINESS PURPOSES. NO PART OF THIS BENEFIT IS TREATED AS TAXABLE COMPENSATION. SCHEDULE J, PART I, LINE 1A; PERSONAL SERVICES - THE ORGANIZATION PROVIDES THE CEO SERVICES OF BODYGUARDS WHEN HE TRAVELS. NO PART OF THIS BENEFIT IS TREATED AS TAXABLE COMPENSATION. FORM 990, PART III, LINE 4A, PROGRAM SERVICE ACCOMPLISHMENTS (CONTINUED): THE GAPS IN KNOWLEDGE WE AIM TO BRIDGE ARE TO DEFINE AND CHARACTERIZE NOVEL PNEUMOCOCCAL ANTIGENIC PROTEINS AND POLYELECTROLYTE ADJUVANTS FORMULATIONS THAT WILL INITIATE ADAPTIVE IMMUNE RESPONSES AND LEAD TO PROTECTION AGAINST DISEASE IN A SEROTYPE INDEPENDENT MANNER. THE PROPOSED WORK IS SIGNIFICANT DUE TO THE HIGH INCIDENCE SEROTYPE REPLACEMENT THAT CURRENT POLYSACCHARIDE-BASED VACCINES ARE PRONE TO, WHICH LEADS TO INCREASE SUSCEPTIBILITY OF CHILDREN AND THE ELDERLY TO SPN CARRIAGE AND SEVERE INFECTIONS (E.G., PNEUMONIA, BACTEREMIA, AND MENINGITIS); AND INNOVATIVE SINCE IT WILL USE NOVEL FORMULATIONS OF ANTIGENIC AND CONSERVED PNEUMOCOCCAL PROTEINS TO INDUCE POTENT ADAPTIVE IMMUNE RESPONSES, THAT WILL NOT BE SEROTYPE DEPENDENT. FUNDED THROUGH THE NATIONAL INSTITUTE OF ALLERGY AND IMMUNOLOGY (NIAID/NIH) INTERPLAY BETWEEN THE HEAT SHOCK RESPONSE AND HISTIDINE KINASE PATHWAYS IN THE THERMALLY DIMORPHIC FUNGAL PATHOGEN HISTOPLASMA CAPSULATUM. HISTOPLASMA CAPSULATUM IS ONE OF SEVERAL SYSTEMIC DIMORPHIC FUNGAL PATHOGENS THAT SWITCH THEIR GROWTH PROGRAM FROM AN INFECTIOUS MOLD FORM IN THE SOIL TO A PATHOGENIC YEAST FORM IN MAMMALIAN HOSTS. H. CAPSULATUM CAUSES UP TO 25,000 LIFE-THREATENING INFECTIONS PER YEAR IN THE U.S. ALONE WITH UP TO 50% MORTALITY RATE AND IS THE MOST COMMON CAUSE OF FUNGAL RESPIRATORY INFECTIONS IN HEALTHY HOSTS. INFECTION OCCURS WHEN THE SOIL IS DISRUPTED, FACILITATING DISPERSION OF HYPHAL FRAGMENTS OR SPORES THAT ARE INHALED BY HUMANS. SPORES AND HYPHAL FRAGMENTS ARE THE PRIMARY INFECTIOUS AGENTS; HOWEVER, ONCE INTRODUCED INTO THE HOST, THE PATHOGEN CONVERTS TO A BUDDING-YEAST FORM, WHICH SURVIVES AND REPLICATES WITHIN HOST MACROPHAGES. HUMAN BODY TEMPERATURE IS THE PRIMARY SIGNAL FOR CONVERSION FROM AN INFECTIOUS TO A PARASITIC FORM IN HISTOPLASMA. DESPITE ITS IMPORTANCE TO HUMAN HEALTH, VERY LITTLE IS KNOWN ABOUT HOW H. CAPSULATUM SENSES AND RESPONDS TO HUMAN BODY TEMPERATURE. THE JCVI IN OUR FUNDED NIH R01 PROJECT, HAS PROPOSED TO BUILD UPON ITS PREVIOUS FINDINGS AND FULLY CHARACTERIZE THE INVOLVEMENT OF THE HEAT SHOCK RESPONSE AND HISTIDINE KINASE PATHWAYS IN REGULATING CELL MORPHOLOGY AND VIRULENCE TRAITS IN H. CAPSULATUM IN RESPONSE TO HOST TEMPERATURE. JCVI HAS BEEN WORKING ON IMPROVING H. CAPSULATUM GENOME ASSEMBLY. TO THIS END, IT USED LONG-READ SEQUENCING TECHNOLOGY AND SUCCESSFULLY COMPLETED CHROMOSOMAL LEVEL ASSEMBLIES OF FIVE COMMONLY USED HISTOPLASMA STRAINS, WHICH HAVE SIX OR SEVEN CHROMOSOMES. JCVI DESCRIBED ITS FINDINGS IN A MANUSCRIPT THAT IS CURRENTLY UNDER REVISION AT THE MBIO JOURNAL. JCVI WILL BE UTILIZING ITS NEW ASSEMBLIES AND ANNOTATIONS IN THE TRANSCRIPTOME STUDIES THAT IT HAS BEEN PERFORMING WITHIN THE SCOPE OF OUR FUNDED PROJECT. RESULTS OF THIS PROJECT WILL PROVIDE FUNDAMENTAL INFORMATION ON HOW CELLS SENSE TEMPERATURE AND TURN ON THE APPROPRIATE VIRULENCE PATHWAYS IN THE HOST. ULTIMATELY, THE INFORMATION OBTAINED FROM THIS PROJECT CAN BE USED TO DEVELOP THERAPEUTICS FOR H. CAPSULATUM INFECTIONS AND HELP PREVENT OTHER DIMORPHIC FUNGAL INFECTIONS. GREATER THAN 10% OF HIV PATIENTS INJECT ILLICIT DRUGS AND WITH THE RISING OPIOID CRISIS AND THE INCREASED RISK OF HIV IN THESE PATIENTS, IT IS CRITICAL WE UNDERSTAND HOW SUBSTANCE USE INFLUENCES THE SPREAD AND COURSE OF HIV INFECTION AND DISEASE. FUNDED BY THE NATIONAL INSTITUTE OF DRUG ABUSE (NIDA/NIH) AND IN COLLABORATION WITH BOSTON UNIVERSITY, THIS STUDY SPECIFICALLY ADDRESSES HOW OPIOID ABUSE ALTERS THE IMMUNE RESPONSE IN HIV PATIENTS AND WITH THIS CAN DIRECTLY CONTRIBUTE TO HIDDEN RESERVOIRS OF HIV. SUCCESSFUL COMPLETION OF THESE STUDIES WILL PROVIDE INSIGHTS INTO POTENTIAL STRATEGIES FOR TREATING HIV IN THIS GROWING POPULATION OF HIV PATIENTS. OUR CENTRAL HYPOTHESIS IS THAT OPIOID MISUSE EXACERBATES HIV PATHOGENESIS AND THE ESTABLISHMENT OF HIV LATENCY BY DYSREGULATING THE HOST IMMUNE RESPONSE. OUR OVERALL OBJECTIVE IS TO EXPLOIT TRANSCRIPTOMIC INFORMATION FROM PATIENT SAMPLES TO CHARACTERIZE THE EFFECTS OF OPIOID USE DISORDER ON HOST IMMUNE FUNCTION, HIV REPLICATION, AND HIV LATENCY. WE WILL CHARACTERIZE SINGLE CELL GENE EXPRESSION AND IDENTIFY DYSREGULATED GENE REGULATORY NETWORKS IN IMMUNE CELLS ASSOCIATED WITH OPIOID MISUSE IN PLWH. WE WILL ALSO PERFORM COMPUTATIONAL ANALYSIS TO IDENTIFY IMMUNE CELL GENE REGULATORY NETWORKS ALTERED BY OPIOID MISUSE AND WE WILL COMBINE SINGLE CELL RNA-SEQ AND FLUORESCENT IN SITU HYBRIDIZATION FLOW CYTOMETRY (FLOW-FISH) TO CHARACTERIZE THE TRANSCRIPTOME IN CELL MODELS OF LATENT HIV INFECTION. SUCCESSFUL COMPLETION OF THESE AIMS WILL HAVE SIGNIFICANT RESEARCH AND CLINICAL IMPACT BY: 1) ELUCIDATING HOW OPIOID MISUSE ALTERS HIV PATHOGENESIS; 2) PRODUCING NOVEL TOOLS FOR CHARACTERIZING HIV LATENCY; AND 3) DISCOVERING CANDIDATE MOLECULES TO REGULATE HIV EXPRESSION IN THE CONTEXT OF OPIOID MISUSE. SEVERAL ADDITIONAL DHHS GRANTS AT JCVI ARE RELATED TO HUMAN MICROBIOME STUDIES. THE MICROBIOME IS THE COLLECTION OF MICROBES THAT LIVE IN AND ON THE HUMAN BODY; THESE SPECIES HAVE RECEIVED CONSIDERABLE ATTENTION IN RECENT YEARS BECAUSE A NEW APPRECIATION OF THE COMPLEX ROLES THAT THEY PLAY IN HEALTH AND DISEASE. SOME OF THESE STUDIES ARE AIMED AT BASIC CHARACTERIZATION OF THE COMPOSITION AND ACTIVITY OF THE MICROBIOME, WHILE OTHERS SEEK TO UNDERSTAND THE CONTRIBUTION OF THE MICROBIOME TO THE DEVELOPMENT OF VARIOUS DISEASES INCLUDING ALCOHOLIC HEPATITIS, TYPE 1 DIABETES, DENTAL CARIES, DIARRHEA, AND ESOPHAGEAL CANCER, AMONG OTHERS. THE INSTITUTE IS AN ACTIVE PARTICIPATANT IN THE H3AFRICA PROGRAM VIA A COLLABORATION WITH THE UNIVERSITY OF CAPE TOWN, SOUTH AFRICA, TRAINING COLLABORATORS IN HUMAN MICROBIOME ANALYSIS. THE PROGRAM IS SPONSORED BY THE NIH COMMON FUND TO BRING TECHNOLOGICAL RESOURCES AND TRAINING IN A CAPITAL INVESTMENT-INTENSIVE FIELD (GENOMICS) TO THE AFRICAN CONTINENT VIA COLLABORATIONS WITH US SCIENTISTS WITH EXPERTISE IN THIS FIELD. FORM 990, PART VI, SECTION A, LINE 2 BOARD MEMBERS HEATHER KOWALSKI AND J. CRAIG VENTER HAVE A FAMILY RELATIONSHIP. FORM 990, PART VI, SECTION B, LINE 11B THE FORM 990 IS REVIEWED BY MANAGEMENT. A COMPLETE COPY OF THE FORM 990 AND SUPPORTING SCHEDULES WAS PROVIDED TO THE FULL BOARD FOR REVIEW PRIOR TO BEING FILED. FORM 990, PART VI, SECTION B, LINE 12C JCVI MONITORS COMPLIANCE OF ITS CONFLICT OF INTEREST POLICY THROUGH AN ANNUAL SOLICITATION OF CONFLICT OF INTEREST STATEMENTS FROM TRUSTEES, OFFICERS, AND EMPLOYEES. IF A PERSON HAS A CONFLICT WITH RESPECT TO A TRANSACTION, SUCH PERSON IS NOT ALLOWED TO VOTE. FORM 990, PART VI, SECTION B, LINE 15 JCVI USES AN OUTSIDE COMPENSATION CONSULTANT, TO PROVIDE A LIST OF COMPARABLE SALARIES FOR THE CEO AND OFFICERS THESE ARE REVIEWED BY THE JCVI COMPENSATION COMMITTEE AND CEO BEFORE A FINAL DETERMINATION IS MADE. THIS PROCESS WAS DOCUMENTED AND LAST DONE IN OCTOBER 2018. FORM 990, PART VI, SECTION C, LINE 19 THE ORGANIZATION'S FINANCIAL STATEMENTS, GOVERNING DOCUMENTS, AND CONFLICT OF INTEREST POLICY ARE MADE AVAILABLE TO THE PUBLIC UPON REQUEST. FORM 990, PART XI, LINE 9: K-1 PASSTHROUGH -15,294. J CRAIG VENTER INSTITUTE MEDICAL GROUP 4120 CAPRICORN LANE LA JOLLA CA 92037 833574850 MEDICAL OFFICE CA N/A C 1.00000 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0