COLD SPRING HARBOR LABORATORY

1333MF23PNFFM0137

View Award on USAspending website

AWARD

PURCHASE ORDER

Department of Commerce

2023-09-15

10446.00

10446.00

10446.00

PCR AMPLIFY DNA EXTRACTS SEQUENCING SERVICES FOR NOAA/NMFS/NEFSC WOODS HOLE,MA.

541990: ALL OTHER PROFESSIONAL, SCIENTIFIC, AND TECHNICAL SERVICES

F020: NATURAL RESOURCES/CONSERVATION- FISHERIES RESOURCES MANAGEMENT

1263VY19P0026

View Award on USAspending website

AWARD

PURCHASE ORDER

Department of Agriculture

2019-09-16

22590.00

22590.00

22590.00

RNA QC CDNA PREP, LIBRARY PREP, PACBIO II RUN

541715: RESEARCH AND DEVELOPMENT IN THE PHYSICAL, ENGINEERING, AND LIFE SCIENCES (EXCEPT NANOTECHNOLOGY AND BIOTECHNOLOGY)

AA21: R&D- AGRICULTURE: MARKETING (BASIC RESEARCH)

75N95D19P00177

View Award on USAspending website

AWARD

PURCHASE ORDER

Department of Health and Human Services

2019-09-12

17000.00

17000.00

17000.00

COLD SPRING HARBOR LABORATORY:1106189 [19-008563]

541715: RESEARCH AND DEVELOPMENT IN THE PHYSICAL, ENGINEERING, AND LIFE SCIENCES (EXCEPT NANOTECHNOLOGY AND BIOTECHNOLOGY)

Q301: MEDICAL- LABORATORY TESTING

2024-08-06

View on USAspending

National Science Foundation

COLLABORATIVE RESEARCH: PLANTTRANSFORM: MORPHOGENIC-BASED MECHANISMS OF MAIZE REGENERATION -INEFFICIENT METHODS FOR TRANSFORMATION AND REGENERATION OF RECALCITRANT PLANT SPECIES PREVENT WIDESPREAD APPLICATIONS OF GENOME EDITING TECHNOLOGIES FOR BOTH BASIC AND APPLIED RESEARCH IN ESTABLISHED AND EMERGING CROP SPECIES. OVERCOMING THESE LIMITATIONS IS PARTICULARLY RELEVANT IN MONOCOTYLEDONOUS CROPS, SUCH AS MAIZE, WHICH ALONE PROVIDE MOST OF THE CALORIES CONSUMED BY HUMANS. IN THIS PROJECT, MAIZE LINES EXPRESSING GENES THAT PROMOTE REGENERATION, ALSO KNOWN AS MORPHOGENIC FACTORS, WILL BE USED TO PROVIDE A THOROUGH UNDERSTANDING OF THE MOLECULAR EVENTS LEADING TO THE SUCCESSFUL FORMATION OF NEW PLANTS STARTING FROM DIFFERENTIATED TISSUE. THIS KNOWLEDGE WILL BE INSTRUMENTAL IN DEVELOPING NEW STRATEGIES FOR IMPROVING TRANSFORMATION OF MAIZE AND OTHER PLANT SPECIES, AND WILL BE INTEGRATED INTO COURSE-BASED UNDERGRADUATE RESEARCH EXPERIENCES (CURES) AS WELL AS HANDS-ON TRANSFORMATION WORKSHOPS. THE PROPOSED RESEARCH WILL EXPLOIT A MORPHOGENIC-BASED SYSTEM CALLED ?GGB? TO UNDERSTAND HOW CERTAIN MORPHOGENIC REGULATORS REPROGRAM SOMATIC CELLS TO DEVELOP INTO EMBRYOS AND IDENTIFY KEY REGENERATION GENES THAT COULD BE TARGETED TO IMPROVE TRANSFORMATION EFFICIENCY IN RECALCITRANT GENETIC BACKGROUNDS. THIS WILL BE ACCOMPLISHED BY THE IDENTIFICATION OF DIRECT TARGETS OF REGULATION OF THE GGB COMPONENTS VIA SINGLE-CELL TRANSCRIPTOMIC AND DNA-BINDING APPROACHES, AND BY THE DEVELOPMENT OF A DIVERSE PANEL OF MAIZE INBRED LINES EXPRESSING THE GGB MORPHOGENIC REGULATORS. BY EXPLOITING THE REGENERATIVE CAPACITY OF THIS SYSTEM, PROTOPLAST REGENERATION, A CHALLENGING BUT ADVANTAGEOUS SYSTEM FOR THE RAPID GENERATION OF NON-GMO EDITED PLANTS, WILL ALSO BE REVISITED. THIS RESEARCH WILL PROVIDE INSIGHTS INTO THE MOLECULAR BASIS OF TISSUE- AND GENOTYPE-DEPENDENT REGENERATION, HELPING TO IDENTIFY AND EVENTUALLY BYPASS ROADBLOCKS TO REGENERATION, AND WILL FACILITATE THE DEVELOPMENT OF HIGH-THROUGHPUT SYSTEMS FOR GENOME-EDITING AND TRANSGENIC LINE GENERATION IN DIVERSE GENETIC BACKGROUNDS. THIS PROJECT IS JOINTLY FUNDED BY GENETIC MECHANISMS (BIO-MCB). EMERGING FRONTIERS (BIO), AND THE PLANT GENOME RESEARCH PROGRAM (BIO-IOS). 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.

959997.00

0.00

0.00

2024-09-16

View on USAspending

Department of Health and Human Services

A UNIFIED PROBABILISTIC MODEL AND SOFTWARE IMPLEMENTATION FOR ANALYSIS OF NASCENT RNA SEQUENCING DATA - PROJECT SUMMARY THE PROCESS BY WHICH RNA MOLECULES ARE ASSEMBLED FROM DNA TEMPLATES, CALLED TRANSCRIPTION, IS FUNDAMENTAL TO ALL LIFE AND DYSREGULATED IN MANY HUMAN DISEASES. OVER THE PAST 15 YEARS, STUDIES OF THE MECHANISMS AND DYNAMICS OF TRANSCRIPTION HAVE INCREASINGLY RELIED ON A FAMILY OF TECHNIQUES FOR ISOLATING AND SEQUENCING NEWLY TRANSCRIBED, OR “NASCENT” RNAS. IN CONTRAST TO STANDARD RNA-SEQ, THESE NASCENT RNA SEQUENCING (NRS) METHODS ENABLE TRANSCRIPTION TO BE MEASURED SEPARATELY FROM RNA DEGRADATION, RESPOND RAPIDLY TO CHANGES IN TRANSCRIPTION, AND REVEAL THE POSITIONS OF RNA POLYMERASES ALONG A DNA TEMPLATE. HOWEVER, NRS DATA REQUIRE SOPHISTICATED COMPUTATIONAL AND STATISTICAL METHODS FOR ANALYSIS, WHICH ARE ONLY BEGINNING TO EMERGE. HERE, WE PROPOSE TO DEVELOP A POWERFUL AND FLEXIBLE PROBABILISTIC MODELING FRAMEWORK FOR THE ANALYSIS OF NRS DATA. OUR FRAMEWORK IS BASED ON A HIGHLY GENERAL “UNIFIED MODEL” THAT MATHEMATICALLY DESCRIBES BOTH THE KINETICS OF TRANSCRIPTION INITIATION, ELONGATION, AND PROMOTER-PROXIMAL PAUSE RELEASE, AND THE GENERATION OF SEQUENCING READ COUNTS. IT CAN BE USED TO ESTIMATE TRANSCRIPTIONAL RATES DIRECTLY FROM NRS DATA, IN EITHER A STEADY-STATE OR NONEQUILIBRIUM SETTING. OUR PROPOSAL INCLUDES THREE SPECIFIC AIMS, FOCUSED ON THE DEVELOPMENT OF (1) A SERIES OF STATISTICAL TESTS AND MACHINE-LEARNING METHODS FOR DIFFERENTIAL ANALYSIS OF TRANSCRIPTION-ASSOCIATED RATES; (2) A STATISTICAL AND MACHINE-LEARNING FRAMEWORK AND NEW EXPERIMENTAL METHODS FOR CHARACTERIZING VARIATION IN ELONGATION RATE AND ITS DEPENDENCY ON GENOMIC AND EPIGENOMIC COVARIATES; AND (3) AN OPEN-SOURCE SOFTWARE PACKAGE IMPLEMENTING THESE NEW METHODS IN THE R PROGRAMMING ENVIRONMENT (STADYUM), INTEGRATED WITH THE BIOCONDUCTOR, ANVIL, AND PYTORCH ENVIRONMENTS. SUCCESSFUL COMPLETION OF THESE AIMS WILL RESULT IN POWERFUL, VERSATILE, AND HIGHLY ACCESSIBLE NEW COMPUTATIONAL TOOLS THAT WILL ACCELERATE PROGRESS IN TRANSCRIPTIONAL RESEARCH.

594501.00

0.00

0.00

2024-08-20

View on USAspending

National Science Foundation

GRADUATE RESEARCH FELLOWSHIP PROGRAM (GRFP) -THE NATIONAL SCIENCE FOUNDATION (NSF) GRADUATE RESEARCH FELLOWSHIP PROGRAM (GRFP) IS A HIGHLY COMPETITIVE, FEDERAL FELLOWSHIP PROGRAM. GRFP HELPS ENSURE THE VITALITY AND DIVERSITY OF THE SCIENTIFIC AND ENGINEERING WORKFORCE OF THE UNITED STATES. THE PROGRAM RECOGNIZES AND SUPPORTS OUTSTANDING GRADUATE STUDENTS WHO ARE PURSUING RESEARCH-BASED MASTER'S AND DOCTORAL DEGREES IN SCIENCE, TECHNOLOGY, ENGINEERING, AND MATHEMATICS (STEM) AND IN STEM EDUCATION. THE GRFP PROVIDES THREE YEARS OF FINANCIAL SUPPORT FOR THE GRADUATE EDUCATION OF INDIVIDUALS WHO HAVE DEMONSTRATED THEIR POTENTIAL FOR SIGNIFICANT RESEARCH ACHIEVEMENTS IN STEM AND STEM EDUCATION. THIS AWARD SUPPORTS THE NSF GRADUATE FELLOWS PURSUING GRADUATE EDUCATION AT THIS GRFP INSTITUTION. 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.

159000.00

0.00

0.00

2024-08-13

View on USAspending

Department of Health and Human Services

ION CHANNELS IN SYNAPTIC AND NEURAL CIRCUIT PHYSIOLOGY COURSE (2024-2028) - ABSTRACT ION CHANNELS ARE THE FUNDAMENTAL BUILDING BLOCKS DETERMINING CELLULAR ACTIVITY AND IN PARTICULAR NEURONAL EXCITABILITY. THE MOST ELEMENTARY PROCESSES IN THE NERVOUS SYSTEM, SUCH AS ACTION POTENTIAL FIRING AND SYNAPTIC TRANSMISSION, DEPEND ON THEIR FUNCTION. COORDINATED ACTIVATION OF DISTINCT TYPES OF ION CHANNELS ENABLES INFORMATION TRANSFER THROUGH COMPLEX CIRCUITS AND NEURAL NETWORKS. ADDRESSING THE NEED FOR INTENSIVE RESEARCH TRAINING IN THIS FIELD, COLD SPRING HARBOR LABORATORY WILL OFFER THE ANNUAL THREE-WEEK COURSE ON ION CHANNELS IN SYNAPTIC & NEURAL CIRCUIT PHYSIOLOGY, AS PART OF ITS POSTGRADUATE SUMMER TRAINING PROGRAM IN NEUROBIOLOGY (2024-2028). THE PRIMARY GOAL OF THIS COURSE IS TO DEMONSTRATE, THROUGH LECTURES AND LABORATORY WORK, THE DIFFERENT PROPERTIES OF ION CHANNELS THAT ENABLE NEURONS TO PERFORM UNIQUE PHYSIOLOGICAL FUNCTIONS IN A VARIETY OF NEURAL SYSTEMS. THE COURSE FOCUSES ON: VOLTAGE- AND LIGAND-GATED ION CHANNELS AT CENTRAL AND PERIPHERAL SYNAPSES; SYNAPTIC INTEGRATION AND PLASTICITY; NEURAL CIRCUIT FUNCTION IN VITRO AND IN VIVO; AND OPTOGENETIC STRATEGIES FOR CIRCUIT MANIPULATION. THE LABORATORY COMPONENT OF THE COURSE INTRODUCES STUDENTS TO ELECTROPHYSIOLOGICAL APPROACHES FOR THE STUDY OF ION CHANNELS IN THEIR NATIVE ENVIRONMENTS. THE COURSE PROVIDES TRAINEES WITH HANDS-ON EXPERIENCE IN USING PATCH-CLAMP ELECTROPHYSIOLOGY TO EXAMINE SINGLE CHANNEL ACTIVITY IN CULTURED CELLS, ION CHANNEL BIOPHYSICS IN ACUTELY DISSOCIATED NEURONS, ACTION POTENTIAL FIRING AND SYNAPTIC INTEGRATION, PLASTICITY AND CIRCUIT DYNAMICS IN ACUTE BRAIN SLICES AND IN VIVO. DIFFERENT TYPES OF RECORDINGS WILL BE USED (E.G. CELL-ATTACHED, WHOLE- CELL DENDRITIC AND SOMATIC PATCH, VOLTAGE- AND CURRENT-CLAMP MODES) AND THE ADVANTAGES AND LIMITATIONS OF EACH METHOD WILL BE DISCUSSED IN RELATION TO SPECIFIC SCIENTIFIC QUESTIONS. THE COURSE WILL ALSO PROVIDE PRACTICAL EXPERIENCE IN CELLULAR AND CIRCUIT MANIPULATION TECHNIQUES (I.E. PHARMACOLOGICAL, ELECTROPHYSIOLOGICAL AND OPTOGENETIC) BOTH IN VITRO AND IN VIVO. THE LEAD INSTRUCTORS ARE CHOSEN ON THE BASIS OF THEIR TRAINING, CONTRIBUTIONS TO AND KNOWLEDGE OF THE FIELD. IN TURN, THEY INVITE LECTURERS WHO HAVE MADE SIGNIFICANT CONTRIBUTIONS IN THEIR FIELDS TO GIVE UP-TO-THE-MINUTE REPORTS ON THE UNDERLYING TECHNOLOGY AND THEIR CURRENT RESEARCH. THE TRAINEES ARE CHOSEN BY THE COURSE FACULTY FROM LARGER POOLS OF APPLICANTS AND RANGE FROM GRADUATE STUDENTS TO SENIOR INVESTIGATORS. THIS INTENSIVE RESEARCH TRAINING PROGRAM ENROLLS A DIVERSE CADRE OF RESEARCHERS WHO CAN IMMEDIATELY TRANSFER TECHNIQUES AND CONCEPTS LEARNED DURING THE COURSE TO THEIR OWN RESEARCH PROJECTS AND INTERESTS. THE FACULTY ARE ENCOURAGED TO PRESENT RELEVANT METHODOLOGICAL APPROACHES IN THE BROADER CONTEXT OF BRAIN FUNCTION AND MENTAL HEALTH RESEARCH. THEIR PRESENCE IS NOT LIMITED TO THE CLASSROOM: EACH SPEAKER SPENDS A SIGNIFICANT AMOUNT OF TIME IN THE LABORATORY TO PROVIDE A UNIQUE LEARNING OPPORTUNITY FOR THE ATTENDEES OF THE COURSE. METHODS AND CONCEPTS TAUGHT IN THE COURSE ARE DISSEMINATED TO THE WIDER RESEARCH COMMUNITY THROUGH THE PUBLICATION OF LABORATORY MANUALS AND ONLINE RESOURCES.

179836.00

0.00

0.00

2024-08-15

View on USAspending

Department of Health and Human Services

BLOCKADE OF CMYC ONCOGENIC FUNCTION BY PREGNANCY-INDUCED ALTERATIONS AND REMODELING OF THE MAMMARY GLAND - ABSTRACT/PROJECT SUMMARY THE GOAL OF THIS PROPOSAL IS TO UNDERSTAND HOW TRANSITIONS THROUGH PREGNANCY INFLUENCE THE MOLECULAR AND CELLULAR STATE OF MAMMARY EPITHELIAL CELLS AND ONCOGENESIS. NUMEROUS EPIDEMIOLOGICAL STUDIES HAVE FOUND THAT PREGNANCY ALTERS THE RISK OF BREAST CANCER. THESE STUDIES HAVE SHOWN CONSISTENTLY THAT A FULL-TERM PREGNANCY PRIOR TO THE AGE OF 25 IS ASSOCIATED WITH A ONE-THIRD DECREASE IN THE LIFE-TIME INCIDENCE OF BREAST CANCER. WHILE A PROTECTIVE EFFECT OF PREGNANCY HAS BEEN VALIDATED IN RODENT MODELS OF CANCER, THE UNDERLYING MOLECULAR BASIS FOR THIS EFFECT REMAINS UNCLEAR. WE HAVE FOUND THAT PREGNANCY LEADS TO PERSISTENT CHANGES IN THE EPIGENOME AND ENHANCER LANDSCAPE OF MECS. USING AN INDUCIBLE C-MYC MOUSE MODEL, WE ALSO FIND THAT ONCOGENESIS AND THE TRANSCRIPTIONAL OUTPUT DOWNSTREAM OF THIS ONCOGENE ARE REDUCED IN POST-PREGNANCY MECS. IN THIS PROPOSAL WE WILL INVESTIGATE THE MOLECULAR BASIS UNDERLYING THESE ROBUST PHENOTYPES. WE WILL USE EPIGENOMICS, EX VIVO, IN VIVO AND BIOCHEMICAL METHODS TO DEFINE HOW THE TRANSCRIPTIONAL FUNCTION OF C-MYC IS MODULATED BY PREGNANCY. WE HYPOTHESIZE THAT C- MYC INTERACTIONS WITH COFACTORS AND WITH SPECIFIC CIS-REGULATORY ELEMENTS ARE ALTERED IN THIS SYSTEM. WE WILL ALSO STUDY HOW SPECIFIC CHROMATIN REGULATORS CONTRIBUTE TO PREGNANCY-MEDIATED EPIGENOMIC REWIRING. THESE EFFORTS WILL BUILD UPON OUR RECENT DATA SUGGESTING THAT EZH2 SUPPORTS THE POST-PREGNANCY EPIGENOME IN WILD-TYPE MICE. COLLECTIVELY, THIS RESEARCH WILL PROVIDE FUNDAMENTAL INSIGHTS INTO THE CELL BIOLOGY OF THE MAMMARY GLAND AND CARRY THE POTENTIAL FOR DISCOVERIES THAT COULD BE HARNESSED TO DEVELOP PREVENTATIVE TREATMENTS THAT MODULATE BREAST CANCER RISK IN HUMANS.

953150.00

0.00

0.00

11-2013303

% LARI RUSSO CFO

Educational Organization, Scientific Organization, Local Association of Employees, Horticultural Organization, Business League, Voluntary Employees' Beneficiary Association (Govt. Emps.), Mutual Ditch or Irrigation Co., Cemetery Company, Other Mutual Corp. or Assoc.

1964-08

Type of organization and use of contribution: A public charity. Deductibility Limitation: 50% (60% for cash contributions)

Intrastate Hazmat

(516) 367-8339

(516) 367-6873

2009-10-08

Private(Property)

13

8

0

View on FMCSA website

2010-02-16

Terminated

no monetary award

Neither plaintiff nor defendant demands jury

Patent

COLD SPRING HARBOR LABORATORY

Plaintiff

ROPES & GRAY LLP

Defendant

COLD SPRING HARBOR LABORATORY

Plaintiff

2009-08-11

Terminated

no monetary award

Plaintiff demands jury

Trademark

COLD SPRING HARBOR LABORATORY

Plaintiff

COLD SPRING PUBLISHING, LLC

Defendant

2003-08-18

Terminated

Missing

Missing

Patent

COLD SPRING HARBOR LABORATORY

Plaintiff

INVITROGEN CORPORATION

Defendant

COLD SPRING HARBOR LABORATORY

Plaintiff