CHILDHOOD INFECTION RESEARCH PROGRAM
R Mark, Professor
Vanderbilt Universitycity: Nashville country: United States (us)
Grant 1T32AI095202-01 from National Institute Of Allergy And Infectious Diseases
Abstract: This application requests support for the Vanderbilt "Childhood Infections Research Program" (ChIRP) a new postdoctoral scientist training program in basic and clinical-translational science for MD and MD/PhD clinical fellows in Pediatric Infectious Diseases and PhD postdoctoral scientists. The goal of the Vanderbilt ChIRP is to train and foster the careers of future leaders in academic biomedical science who are committed to research relevant to infections of children. There is no training program at Vanderbilt focused on the childhood infections, and ChIRP establishes a unique training niche for future basic and clinical investigators. This application proposes an innovative program that uses both 1) mentored research training and 2) "Peer Mentoring and Training" (PMT), a novel program that will partner clinical fellows and postdoctoral scientists to facilitate cross-disciplinary (Med-Grad, Grad-Med) training and experience. ChIRP-PMT training will result in basic scientists with training and in-depth understanding of clinical infectious disease, as well as clinical-translational investigators with a broad knowledge of the basic mechanisms of microbial pathogenesis. Key elements of the training program will be the use of primary mentors, individual development plans, and mentoring committees charged with regular review of scientific progress and career development. The assembled group of faculty mentors has been selected based on demonstrated research excellence, as well as long-term success in training of postdoctoral scientists and clinical fellows for research careers. The investigators hold primary appointments in the Departments of Pediatrics, Medicine, Microbiology and Immunology, and Preventive Medicine and together hold ~$34 million in extramural funding. Training in responsible conduct of research will be incorporated throughout the training term and will establish competencies in emerging areas such as high-biosafety containment, dual-use research, and research ethics in international collaborations. pool results from recruiting efforts focused on MD and MD/PhD Pediatric Infectious Diseases Fellow candidates and from PhD and MD/PhD postdoctoral scientists who apply to individual labs and through novel programs such as the Vanderbilt Office of Postdoctoral Affairs. Recruiting will emphasize clinical fellows and postdoctoral candidates from groups underrepresented in research. The proposal requests funded positions for two postdoctoral trainees each year, with four trainees total in the program during each year after year 1. The goal of ChIRP is to train one clinical fellow and one postdoctoral scientist per year, and to establish a group of clinical and postdoctoral scientists committed to an integrated faculty-and-peer mentoring research culture and experience. This request for support for ChIRP is based on the strength of pool, exceptional opportunities for training scientists in childhood infections, and an institutional commitment to the education of leaders in research in childhood infections. Relevance The broad significance of this program will be realized through the academic and scholarly accomplishments of the trainees and discoveries of basic disease mechanisms and translational-clinical results directly relevant prevention and treatment of infectious diseases. This application proposes a new T32 "Childhood Infections Research Program" (ChIRP). The goal of the program is to train postdoctoral scientists in areas of microbial pathogenesis and infectious diseases of children. The application proposes an innovative program that allows joint training of clinical ID fellows and postdoctoral scientists, resulting in investigators who are able to perform high impact research and train the next generation of scientists
Keywords: Childhood; Infection; programs; Research
Relevance: This application proposes a new T32 "Childhood Infections Research Program" (ChIRP). The goal of the program is to train postdoctoral scientists in areas of microbial pathogenesis and infectious diseases of children. The application proposes an innovative program that allows joint training of clinical ID fellows and postdoctoral scientists, resulting in investigators who are able to perform high impact research and train the next generation of scientists
Project start date: 2011-08-01
Project end date: 2016-07-31
Budget start date: 1-AUG-2011
Budget end date: 31-JUL-2012
PFA/PA: PA-10-036
1T32AI095202-01 (2011): $137833
Sponsored Links Excellgen http://Excellgen.com
Grants awarded to R Mark
RADIOLYTIC FOOTPRINTING METHODS FOR STRUCTURAL MASS SPECTROMETRY
R Mark, Director
Case Western Reserve Universitycity: Cleveland country: United States (us)
Grant 5R01EB009688-02 from National Institute Of Biomedical Imaging And Bioengineering
Abstract: We have developed innovative methods of structural mass spectrometry based on hydroxyl radical modification of proteins. These structural mass spectrometry methods have recently gained widespread acceptance and are ripe for further development. In this proposal we will increase the sensitivity of protein footprinting methods ~1000 fold; integrate docking approaches with protein footprinting data to probe the structure of protein complexes and develop methods to examine the dynamics of water in proteins using footprinting. Our preliminary data has shown feasibility for the examination of the G- protein coupled receptor rhodopsin in its ground and photo-activated states using increased x-ray flux density and shorter exposure times. Within Aim 1 we will use increased x-ray flux density to further explore the structural and solvent dynamics accompanying GPCR activation and the structural mechanism of signaling that mediates information to downstream signaling proteins. Our guiding hypothesis is that highly conserved structural motifs that include bound waters are reorganized to provide a highly controlled signaling channel. In Aim 2 we will further develop a novel O18 water labeling- radiolysis technique to examine the locations and dynamics of structural waters and the exchange properties of bulk water in multiple biological states of interest for rhodopsin and actin. In Aim 3 we will perfect targeted MS approaches to detect low abundance modifications in protein footprinting experiments to enhance the number of amino acids side chains routinely detected by these experiments. In Aim 4 we will develop computational methods of docking that incorporate footprinting data in structure determination. Our hypothesis is that use of footprinting data will drive correct selection of the correct structure among competing docking solutions that are of comparable energies. Optimized algorithmic approaches will be used to model complexes of myosin or cofilin with actin and complexes of rhodopsin and transducin. G-protein coupled receptors are the targets of close to half of all drugs; a better understanding of their activation mechanisms would have a major impact on health and disease. Advanced technologies to examine the structure and dynamics of all proteins are needed in biology and medicine to better correlate structure and function
Keywords: Actins; Adenosine Triphosphatase, Myosin; Ala-Gln; alanyl-glutamine; alanylglutamine; Algorithms; Amino Acids; aminoacid; Asp-Glu; aspartylglutamate; ATPase, Actin-Activated; base; Binding; Binding (Molecular Function); Biological; biological signal transduction; Biology; Cell Communication and Signaling; Cell membrane; Cell Signaling; Cells; Chemistry; cofilin; Collaborations; Complex; computational methodology; computational methods; computer methods; Computing Methodologies; Coupled; Cytoplasmic Membrane; Data; density; Detection; Development; dimer; Disease; disease/disorder; Disorder; Dissociation; Docking; Dose; drug/agent; Drugs; electron transfer; Electron Transport; Environment; Exhibits; experiment; experimental research; experimental study; Filament; Future; G Protein-Complex Receptor; G Protein-Coupled Receptor Genes; G-Protein, Inhibitory Gt; G-Protein-Coupled Receptors; G-Proteins; gene product; Goals; GPCR; GPR; Gt, Transducin G-Protein; GTP-Binding Proteins; GTP-Regulatory Proteins; Guanine Nucleotide Coupling Protein; Guanine Nucleotide Regulatory Proteins; Health; heavy metal lead; heavy metal Pb; Hydrogen Oxide; Hydroxyl; Hydroxyl Radical; innovate; innovation; innovative; instrumentation; Instrumentation, Other; Intracellular Communication and Signaling; Ions; Label; Laboratories; Lead; Location; Lys-Glu; lysylglutamic acid; macromolecular assembly; Mass Spectrum; Mass Spectrum Analysis; Mediating; Medication; Medicine; Membrane Proteins; Membrane-Associated Proteins; Methods; Methods and Techniques; Methods, Other; millisecond; Modeling; Modification; Molecular Interaction; Monitor; monomer; Msec; multiple reaction monitoring; Myosin Adenosinetriphosphatase; myosin ATP phosphohydrolase (actin translocating); Myosin ATPase; Myosins; new approaches; Noise; novel; novel approaches; novel strategies; novel strategy; Pb element; Pharmaceutic Preparations; Pharmaceutical Preparations; Photometry/Spectrum Analysis, Mass; Plasma Membrane; plasmalemma; Post-Translational Modifications; Post-Translational Protein Processing; Posttranslational Modifications; Process; Property; Property, LOINC Axis 2; protein complex; Protein Footprinting; Protein Modification; Protein Modification, Post-Translational; Protein Processing, Post-Translational; Protein Processing, Posttranslational; Protein/Amino Acid Biochemistry, Post-Translational Modification; Proteins; public health relevance; Reaction; research study; Resolution; response; Rhodopsin; Science of Chemistry; Science of Medicine; Side; Signal Transduction; Signal Transduction Systems; Signaling; Signaling Protein; Site; Solutions; Solvents; Spectrometry, Mass; Spectroscopy, Mass; Spectrum Analyses, Mass; Spectrum Analysis, Mass; State Interests; Structure; Surface Proteins; Techniques; Technology; technology development; Time; Transducin; Visual Purple; Water; Work
Relevance: Relevance: G-protein coupled receptors are the targets of close to half of all drugs; a better understanding of their activation mechanisms would have a major impact on health and disease. Advanced technologies to examine the structure and dynamics of all proteins are needed in biology and medicine to better correlate structure and function
Project start date: 2010-05-10
Project end date: 2014-02-28
Budget start date: 1-MAR-2011
Budget end date: 29-FEB-2012
PFA/PA: PA-07-070
5R01EB009688-02 (2011): $254340
R Mark, Deputy Chair And Associate Professor
University Of Texas Md Anderson Can Ctrcity: Houston country: United States (us)
Abstract: To fulfill the overall aim of this SPORE in Brain Cancer, accelerating the clinical testing of new diagnostic and therapeutic approaches for patients with malignant glioma, we need to facilitate the translation of laboratory findings into the necessary clinical and correlative studies. This is the function of Core D. This Clinical Core will provide the infrastructure so that concepts emanating from the projects can be evaluated for translational suitability, formulated into appropriate clinical protocols and these protocols carried out with the appropriate regulatory oversight, safety and collection of clinical data. This core is a necessary and vital component of the SPORE in Brain Cancer, and will streamline and standardize its interaction with the extensive clinical trials infrastructure of The University of Texas M. D. Anderson Cancer Center (UTMDACC). The specific objectives of the Clinical Core are to provide support and resources for completion of the clinical trials or clinically related aspects of each of the Projects, as well as to serve as a resource for the development of promising laboratory findings into clinical concepts. Accordingly, Objective 1 is to provide infrastructure for protocol administration, including the clinical and regulatory aspects. Objective 2 is to provide expert consultation to augment and facilitate the development of clinical trials from promising laboratory data generated by the Projects
Keywords: Address; Adverse event; Aftercare; Back; Biometry; Biostatistics Core; Blood; Brain; Brain Neoplasms; Central Nervous System Neoplasms; Cessation of life; Clinic; Clinical; Clinical Data; Clinical Protocols; Clinical Research; Clinical Trials; Clinical Trials Design; Collaborations; Collection; Complex; Computer Systems; Computer Terminals; Conduct Clinical Trials; Confidentiality of Patient Information; Consult; Consultations; Correlative Study; cost; Data; Data Collection; data management; Data Quality; Data Security; Data Set; Databases; design; Development; Discipline; Doctor of Philosophy; Educational aspects; Eligibility Determination; Enrollment; Ensure; Equipment and supply inventories; European Organization for Research and Treatment of Cancer; Evaluation; experience; Family; Feedback; follow-up; Generations; Glioblastoma; health related quality of life; Human Resources; human subject; improved; Inpatients; Institutional Review Boards; instrument; Laboratories; Laboratory Finding; Learning; Logistics; longitudinal database; Malignant Glioma; Malignant neoplasm of brain; Measures; Medical Informatics; Medicine; meetings; member; Modality; Modification; Molecular Genetics; molecular marker; Monitor; MRI Scans; Names; neuro-oncology; Neurocognitive; neuropathology; Neuropsychology; neurosurgery; novel diagnostics; novel therapeutic intervention; Nurses; Nursing Research; Operative Surgical Procedures; Oral; Outpatients; Pathology; Patient Care; Patient Care Management; Patient Monitoring; Patient Self-Report; Patients; Pediatrics; Performance Status; Pharmacy facility; Phase; Physicians; Population; Primary Brain Neoplasms; Privacy; Procedures; Process; programs; protocol development; Protocols documentation; quality assurance; Quality Control; Quality of life; Quality-of-Life Assessment; Questionnaires; Radiation Oncology; Radiation therapy; Radiation Therapy Oncology Group; Randomized; randomized trial; Records; Regimen; Regulatory Affairs; Reporting; Research; research clinical testing; Research Infrastructure; Research Personnel; Research Training; Resource Development; Resources; response; Review Committee; Running; Safety; Sampling; Schedule; Scientist; Screening procedure; Severities; Specific qualifier value; statistics; Symptoms; System; Systemic Therapy; systems research; Telephone; Testing; Time; Tissue Banking; Tissue Banks; Tissues; tool; Toxic effect; Trail Making Test; Translations; treatment planning; Treatment Protocols; tumor; University of Texas M D Anderson Cancer Center; user-friendly; Validation; Validity and Reliability; Verbal Learning; Vertebral column; Visit; Vital Status; Work; Writing
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
5P50CA127001-04_9003 (2011): $141075
THERMO ELECTRON LTQ ORBITRAP XL ETD WITH ESI AND DIONEX ULTIMATE 3000 HPLC SYSTEM
R Mark, Director
Case Western Reserve Universitycity: Cleveland country: United States (us)
Grant 1S10RR028927-01 from National Center For Research Resources
Abstract: This proposal will enhance mass spectrometry capability and research throughput of the Center for Proteomics and Bioinformatics (CPB) at Case Western Reserve University by the purchase of a Thermo-Scientific LTQ Orbitrap XL (with ETD) and advanced chromatography systems from Dionex. The user group supported by this Center is growing rapidly, as reflected in increases in user fees collected, increases in funded grants, publications, and increases in samples run per month. In particular, user needs and proteomics grants directly tied to techniques that require high-resolution, high-sensitivity, and high mass accuracy mass spectrometry are currently increasing the fastest. The major and minor users´ proteomics research as outlined in the proposal is supported by over forty R-type, P-type (or U-type) grants plus foundation and pilot grant support. Also, the Center operates seven peer-reviewed Cores of major NIH funded Centers, including the Translational Technologies Core of the Center for Translational Science Collaborative and the Cancer Center Proteomics Core. Unfortunately, the two current high-resolution instruments, an Orbitrap and an LTQ-FT, both from Thermo, are overbooked with current projects while the very recent award of a number of NIH grants, including several program project and center grants dependent on high-resolution instruments, suggests that the current backlog will increase substantially over the next 12-24 months. In particular, label-free proteomics studies to identify protein abundance changes, identification of post-translational modifications to understand cell signaling, and structural mass spectrometry studies to understand conformational changes and structure of proteins in solution, are the three most rapidly growing proteomics programs in the Center. These programs will significantly benefit from the high sensitivity and high accuracy of the requested Orbitrap instrument while the ETD capability will enhance protein identification and identification of protein modifications. The research of the users identified in this proposal spans a wide range of biomedical science and many diseases including stem cells, cancer biology, HIV-AIDS pathogenesis, immune activation biomarkers, diabetes and its complications, insulin structure-function, immunity and skin disease, bone marrow transplant rejection, yeast biofilm formation, prion structure and function, cytokine signaling, and many others. They have extensive experience with high-resolution and high accuracy instruments and many publications in proteomics. Knowledge about changes in protein expression, structure, interactions and modifications gives us a crucial information on the changes in signaling pathways underlying development and disease and procuring a novel characterization of phenotype for tissues, cells or cell lines, as well as plasma or other fluids collected non-invasively from patients or animals. This information provides us with understanding of the pathophysiological basis of disease and health while the reliable and reproducible detection of such changes in proteins can be utilized as biomarkers for the presence of disease and its remission. These biomedical science studies support the ARRA goals by providing and retaining jobs in a number of ways. Manufacturing and installation of the LTQ Orbitrap XL ETD and the Ultimate 3000 HPLC System will create or retain at least 5 jobs. Manufacturing the Orbitrap will require between 3-4 months personnel time. Building the Dionex instrument will require 2 months personnel time. Additionally, installation, familiarization, and training on utilization of the Orbitrap and Ultimate 3000 by personnel from Thermo Electron and Dionex will require three weeks. Four project managers are also required, two to oversee manufacturing and two to oversee the installation and training. The proposal also includes a 3-year service contract for the Orbitrap which will require yearly preventive maintenance. Additionally, we will schedule preventative maintenance of the Ultimate 3000
Keywords: Animals; Award; base; Bioinformatics; biomarker; Bone Marrow Transplantation; Cancer Biology; Cancer Center; Cell Line; Cells; Center for Translational Science Activities; Chromatography; Contract Services; Cytokine Signaling; Detection; Development; Diabetes Mellitus; Disease; Disease remission; Electrons; experience; Fees; Foundations; Funding; Goals; Graft Rejection; Grant; Health; High Pressure Liquid Chromatography; Human Resources; immune activation; Immunity; instrument; Insulin; Knowledge; Label; Liquid substance; Maintenance; Mass Spectrum Analysis; Microbial Biofilms; Minor; Modification; novel; Occupations; Pathogenesis; Patients; Peer Review; Phenotype; Plasma; Post-Translational Protein Processing; Preventive; Prions; programs; protein expression; protein structure; Proteins; Proteomics; public health relevance; Publications; Research; Resolution; Running; Sampling; Schedule; Science; Signal Pathway; Signal Transduction; skin disorder; Solutions; Stem cells; Structure; Support Groups; System; Techniques; Technology; Time; Tissues; Training; United States National Institutes of Health; Universities; Yeasts
Project start date: 2010-07-08
Project end date: 2012-07-07
Budget start date: 8-JUL-2010
Budget end date: 7-JUL-2012
PFA/PA: PAR-09-118
1S10RR028927-01 (2010): $982989
CASE PROTEOMICS CENTER FOR HIV/AIDS AND DRUG ABUSE
R Mark, Director
Case Western Reserve Universitycity: Cleveland country: United States (us)
Grant 5P20DA026133-03 from National Institute On Drug Abuse
Abstract: This P20 application proposes the creation of the Case Proteomics Center in HIV/AIDS & Drug Abuse, which is designed to apply state-of-the art proteomics and systems biology tools to investigate HIV pathogenesis in the context of drug abuse and provide significant biomarkers of HIV infection, co-infection with other viruses, and drug abuse. During the pilot phase, we will undertake three inter-related projects designed to provide a better understanding of the impact on immune function and activity in HIV-infected individuals who are also exposed to addictive drugs, and the important viral co-factor Hepatitis C (HCV). In each of these projects there will be a direct examination of the proteomic responses in epithelial or T-cells and parallel examination of plasma readouts from affected patients. A major outcome of these projects will be development of informative biomarkers and methods that can be used in large-scale population studies to further evaluate the impact of drug use on HIV disease. The Center will be directed by Dr Mark Chance, Director of the Case Center for Proteomics, and an internationally recognized expert in proteomics and system biology in collaboration with Dr Jonathan Karn, Chair of the Department of Molecular Biology & Microbiology and Co-Director of the Case Center for AIDS Research (CFAR), and an expert in HIV/AIDS molecular biology. The pilot projects are the work of a strong pre-existing multi-disciplinary team at Case that combines significant biological expertise in HIV/AIDS within the Department of Medicine, the Department of Molecular Biology & Microbiology, the Department of Biological Sciences (Dental School) and CFAR. These investigators have already assembled significant molecular biology and proteomics data to provide testable hypotheses within the context of three Pilot Projects served by a Proteomics and Bioinformatics Core. The three projects, with the cooperation of the clinical core of the Case CFAR, will recruit appropriate patient cohorts to provide relevant samples. The proteomics team in the Core will then conduct proteome expression analysis of cases versus relevant control populations, with statistically significant targets provided to the Bioinformatics team. This team will not only provide network analysis and pathway identification within the context of the biological questions to be addressed, but will correlate the proteomics pathway models with known pathways of drug addiction and HIV pathogenesis and will infer novel sub-networks by combined analysis of proteomics and microarray data
Relevance: HIV and AIDS are important diseases and growing problems worldwide. Although anti-retroviral therapies are effective, they do not represent a cure. These studies will suggest new treatments for HIV patients with drug use and co-infections based on a molecular understanding of the disease
Project start date: 2009-04-15
Project end date: 2012-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: RFA-DA-08-010
5P20DA026133-03 (2011): $974149
PLATFORMS FOR SYNTHESIS AND TESTING OF EMERGING AND ZOONOTIC VIRUSES
R Mark, Professor
University Of North Carolina Chapel Hillcity: Chapel Hill country: United States (us)
Abstract: There has been an increase in recognized trans-species movement and human disease from zoonotic viruses, as well as increased concern about intentional design and introduction of zoonotic organisms in bioterrorism. Our ability to respond to such emerging zoonotic-human viruses has been limited by our inability to predict the source, frequency, and mechanisms of virus host-species switching and adaptation. Recent advances in bioinformatics, molecular biology, structural biology, and synthetic biology, provide tools to design, synthetically reconstruct, and test new and emerging pathogens from sequence databases alone. However, development of broadly-applicable platforms strategies for emerging viruses has not occurred, in part due to concerns about possible misuse of synthetic biology and engineered host-range variants. We propose that is an essential mission of the RCEs to demonstrate the safe use and potential of synthetic biology in rapid response platforms. SARS-coronavirus (SARS-CoV) is a category C emerging pathogen that caused severe human disease worldwide. SARS-CoV is proposed to have emerged in humans following trans-species movement of Bat-Coronaviruses (Bat-CoV) that have been identified by sequence but have not been grown in culture. This proposal uses SARS-CoV and zoonotic Bat-CoV to establish platforms for recovery and testing of zoonotic viruses. The proposed program is comprised of four integrated Specific Aims that will design and synthetically reconstruct distinct serogroups of zoonotic bat-CoV from sequence databases, and define the determinants of host-species movement and adaptation in culture, and in young and senescent mouse models. Further, the Aims will develop strategies for stable and universal attenuation of pathogenesis of all coronavirus groups. The established approaches will allow rapid response and control of natural and deliberately designed human coronaviruses, and also will be directly applicable to development of similar specific rapid-response systems for recovery, analysis, attenuation and response to other category A, B, or C emerging pathogens of concern for human disease or bioterrorism
Keywords: aged; Animals; Attenuated; attenuation; Bats; Bio-Informatics; biodefense; Bioinformatics; Biological Models; Biological Terrorism; Bioterrorism; body movement; Categories; Chiroptera; Civet Cats; Civets; Clinical; clinical data repository; clinical data warehouse; computational modeling; computational models; computational simulation; computer based models; Computer Simulation; computerized modeling; Computerized Models; computerized simulation; Coronavirus; Coronavirus (genus); coronavirus spike glycoprotein; Cultured Cells; Data Banks; Data Bases; data repository; Databank, Electronic; Databanks; Database, Electronic; Databases; Deletion Mutation; design; designing; Development; Distant; DNA Molecular Biology; drug/agent; Drugs; Engineering; engineering design; Engineerings; Epidemic; Epithelial Cells; Ferrets; Frequencies (time pattern); Frequency; Future; gene product; Gene Transcription; Generalized Growth; Genetic Alteration; Genetic Change; Genetic defect; Genetic Transcription; Genome; genome mutation; Goals; Growth; Homologous Recombinational Repair; Human; human coronavirus; human disease; Human Virus; Human, General; IFN; in silico; In Vitro; in vivo; Interferons; Intervention; Intervention Strategies; interventional strategy; Kinetic; Kinetics; living system; Mammals, Mice; Man (Taxonomy); Man, Modern; Maps; Mathematical Model Simulation; Mathematical Models and Simulations; Medication; Mice; Mission; Model System; Modeling; Models, Biologic; Models, Computer; Molecular Biology; mouse model; Movement; Murine; Mus; Mutation; novel virus; ontogeny; Organism; pandemic; pandemic disease; pathogen; Pathogenesis; Pharmaceutic Preparations; Pharmaceutical Preparations; Phenotype; Phylogenetic Analysis; Phylogenetics; Polyproteins; prevent; preventing; programs; Programs (PT); Programs [Publication Type]; Proteins; Public Health; public health medicine (field); receptor; Receptor Protein; Receptors, Virus; Recombinants; Recombination Repair; recombinational repair; reconstruction; Recovery; relational database; replicase; response; RNA Expression; Role; SARS coronavirus; SARS Virus; SARS-Associated Coronavirus; SARS-CoV; SARS-Related Coronavirus; senescence; Severe Acute Respiratory Syndrome Virus; Simulation, Computer based; social role; Source; structural biology; SUBGP; Subgroup; synthetic biology; System; System, LOINC Axis 4; Testing; Tissue Growth; tool; Transcription; Transcription, Genetic; Transgenic Mice; Transmission; transmission process; Urbani SARS-Associated Coronavirus; Vaccines; Variant; Variation; Viral; Viral Receptor; virtual simulation; Virulence; Virus; Virus Receptors; Viruses, General; Viverridae
Relevance: This program will establish a platform for synthetic reconstruction of emerging zoonotic-human pathogens, using SARS-CoV and zoonotic Bat coronaviruses as a model. The platform will allow testing for determinants of trans-species movement and adaptation. The approaches will allow rapid response and public health interventions for coronaviruses and other pathogens of concern for natural emergence or bioterrorism
Budget start date: 1-MAR-2011
Budget end date: 29-FEB-2012
5U54AI057157-09_5817 (2011): $543438
R Mark, Director
Case Western Reserve Universitycity: Cleveland country: United States (us)
Abstract: The Proteomics Core Facility makes advanced mass spectrometry instruments, expertise, and methods for protein analysis available to the Case Comprehensive Cancer Center (Case CCC) community. The core includes two laboratory sites, one on the Case campus and one the CCF campus, with a current total of 6000 sq. ft. of lab space. The core is directed by Dr. Mark Chance and has a total staff of approximately 20 individuals including scientists specializing in mass spectrometry, protein chemistry, instrument engineering, and bioinformatics. A total of 11 mass spectrometry systems are housed in the laboratories, including both electrospray and Maldi, and ion trap, ToF, QTof, and FTMS systems. The core was established in 1999, became a part of the Case CCC in 2003, and was expanded to its current form in 2005. The services that are offered to the Case CCC community are wide-ranging and range from a drop-off service for protein identification, to collaborative services for the detection and characterization of post-translation modifications, quantitative proteomics, and protein structural analyses to open instrument access for trained users. As a part of the Case CCC, the Proteomics Core has served a growing list of investigators. In 2005, approximately 100 investigators used the facilities, with about 40% being Case CCC members. Greater than 60% of the use was funded by the NIH. The Case CCC users come from 7 of the 9 scientific programs. All Case CCC members receive a 30% discount on the cost of services
Keywords: Bioinformatics; Cancer Center Support Grant; Communities; Comprehensive Cancer Center; Core Facility; cost; Detection; discount; Drops; Engineering; Funding; Housing; Individual; instrument; Ions; Laboratories; Mass Spectrum Analysis; member; Methods; Mission; Modification; programs; Protein Analysis; Protein Chemistry; Proteins; Proteome; Proteomics; Research Personnel; Scientist; Services; Site; Structural Protein; System; Training; Translations; United States National Institutes of Health
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
5P30CA043703-22_9007 (2011): $182905
PROTEOMICS AND BIOINFORMATICS CORE
R Mark, Director
Case Western Reserve Universitycity: Cleveland country: United States (us)
Abstract: The Proteomics and Bioinformatics core (PBC) will provide a powerful and integrated data collection and analysis platform for the pilot projects outlined in this P20 proposal. The specific experimental designs and most of the preliminary data relevant to the individual pilot projects are outlined in those sections. Here we describe the methods of biochemical fractionation, proteomics, bioinformatics and their integration to address the relevant goals of the pilot projects. Aim 1 Develop detailed experimental designs in terms of appropriate biochemical procedures, appropriate choice of proteomics technologies, and appropriate sample numbers based on specific study power for the proteomics studies of all pilot projects. Aim 2 Provide quantitative 2-D gel analysis to discern changes in tissue protein expression for Pilot Projects. Aim 3 Using the high-resolution mass spectrometry instruments of the Center coupled to the advanced bioinformatics and biostatistical pipelines for analysis provide quantitative label free protein expression analysis using a "shotgun" proteomics approach. Aim 4 Using advanced network and pathway tools, provide novel insights into patho-physiological changes in disease cohorts. Based on these data, use conventional biochemical and LC-MS based validation procedures along with novel protein antibody chips to confirm observed and predicted expression changes. Overall the PBC will be closely integrated with the projects through regular meetings and use of the Center´s laboratory information management system, the MIMI
Keywords: Acquired Immunodeficiency Syndrome; Address; AIDS/HIV problem; Anti-Retroviral Agents; Antibodies; base; Biochemical; Bioinformatics; biomarker; Biometry; Cells; Clinical; cohort; Computer software; Coupled; Data; Data Analyses; Data Collection; Disease; Down-Regulation; Drug abuse; Drug usage; effective therapy; Exhibits; experience; Experimental Designs; Fractionation; Gel; Gene Expression; Gene Proteins; Goals; Head; HIV; Housing; Individual; Infection; insight; instrument; Label; Laboratories; Logic; Management Information Systems; Mass Spectrum Analysis; meetings; Methods; Molecular; novel; Pathway Analysis; pathway tools; Patients; Peptide Hydrolases; Peptides; Physiological; Pilot Projects; Plasma; Procedures; protein expression; Protein Microchips; Proteins; Proteomics; Research Personnel; research study; Resolution; Sampling; Scheme; Serum; Shotguns; Signal Pathway; Spottings; Statistical Data Interpretation; Technology; Tissues; Up-Regulation (Physiology); Validation; Western Blotting; Work
Relevance: HIV and AIDS are important diseases and growing problems worldwide. Although anti-retroviral therapies are effective, they do not represent a cure. These studies will suggest new treatments for HIV patients with drug use and co-infections based on a molecular understanding of the disease
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
5P20DA026133-03_8233 (2011): $499670
SURGICAL RESEARCH TRAINING IN GASTROIONTESTINAL DISEASE
R Mark, Associate Professor
University Of Texas Medical Br Galvestoncity: Galveston country: United States (us)
Grant 5T32DK007639-19 from National Institute Of Diabetes And Digestive And Kidney Diseases
Abstract: The primary focus of our training program continues to be to provide intensive and interdisciplinary basic science research training for a minimal period of two years for qualified individuals who are committed to pursuing a career in academic surgery. The purpose of this training program is to provide these trainees with the basic science research skills necessary to become independent investigators in areas of gastrointestinal (Gl) endocrinology, inflammation and cancer when they assume faculty positions. In addition we are adding a new focus area on Gl epidemiology/outcomes research which is assuming a greater importance for future translational investigators. The training faculty is composed of both basic scientists and academic surgeons who are collegial, collaborative and multidisciplinary; each faculty preceptor is a recognized expert in his or her field and has a long record of research productivity in the training of young investigators from the United States and abroad. The diversity of our training program is further enhanced by the inclusion of junior investigators who will act as co-preceptors and further assist in the mentorship of our trainees. The breadth and depth of the research techniques available in the laboratories of the various faculty members allow the trainees to become familiar with and adept at the application of state-of-the-art techniques for the comprehensive study of Gl diseases. All of our trainees are mentored within the context of a multidisciplinary team comprised of clinician-scientists and basic science mentors. The diversity of the experience depends on the needs of the trainees and his or her research interest. In addition to an intensive research experience, the trainee also participates in formal courses in molecular biology, radiation safety and scientific ethics. New courses will be added in epidemiology, outcomes research and translational research. Furthermore, the trainees participate in regularly scheduled departmental seminars and lectures which include a basic science lecture, departmental Grand Rounds and seminars presented by other departments or centers. All of our trainees are required to complete coursework for a Master of Medical Science (MMS) degree, with some of our trainees going on to complete PhD requirements. The Gl research training program in the Department of Surgery at the University of Texas Medical Branch at Galveston has a greater than 35 year history of training surgeons in clinical and basic science investigation. We have demonstrated a strong record of research productivity and have provided a nurturing academic environment for these trainees. Our training program is specifically designed to focus on the research training of academic surgeons so that they will be prepared to become independent scientists and incorporate the new and state-of-the-art techniques learned during their training period into a successful academic career
Keywords: Disease; Research Training; surgical research
Project start date: 1992-09-15
Project end date: 2013-06-30
Budget start date: 1-JUL-2011
Budget end date: 30-JUN-2012
PFA/PA: PA-06-468
5T32DK007639-19 (2011): $37435
DESIGNS FOR PHASE I TRIALS OF COMBINATIONS OF AGENTS
R Mark, Professor
University Of Virginia Charlottesvillecity: Charlottesville country: United States (us)
Grant 5R01CA142859-02 from National Cancer Institute
Abstract: The majority of methods for the design of Phase I trials for in oncology are intended for studies involving a single cytotoxic agent. The goal of these studies is to estimate the ´maximally tolerated dose´, the highest dose that can be administered with an acceptable level of toxicity. A key assumption of these methods is the monotonicity of the dose- response curve. In this case, the dose-response curve is said to follow a ´simple order´ because the ordering of the probabilities of a ´dose-limiting toxicity´ (DLT) for any pair of doses is known; administration of greater doses of the agent can be expected to produce DLT´s in increasing proportions of patients. It is becoming increasingly common for combinations of agents to be tested in phase I trials. In these studies, the probabilities of a DLT associated with the dose combinations often follow a ´partial order´ in that there are pairs of dose combinations for which the ordering of the probabilities is not known. This proposal uses Bayesian methods, combining features of the continual reassessment method and order restricted inference to develop designs for phase I trials in which the probabilities follow a partial order. In addition, we will adapt our methods for cycle-specific toxicities. Finally, we will develop internet-accessible software to assist users in designing and carrying out partially ordered phase I trials. Even though our emphasis is on phase I trials of combinations, the methods we develop can shed light on other issues in phase I trial design, including the study of ordered groups and trials of cancer vaccines. Dose-finding trials of combinations of agents are becoming increasingly common in cancer research. While there are many proposed methods for single agent trials, there are relatively few options for designing phase I trials of combinations. As in single agent trials, it is crucial to find a combination of doses that can be administered with an acceptable level of toxicity in order that these new therapies can be tested for efficacy. Without adequate statistical methods potentially effective combinations may be discarded as too toxic or get tested in subsequent studies at sub-optimal dose combinations. The overall goal of this proposal is to develop designs for phase I trials of combinations of agents
Keywords: Accounting; anticancer research; base; Bayesian Method; Cancer Vaccines; Clinical Trials Design; Computer software; Cytotoxic agent; Data; design; Dimensions; Dose; Dose-Limiting; efficacy testing; Goals; indexing; Internet; Language; Light; Maximum Tolerated Dose; Methods; Modeling; oncology; Outcome; Output; Patient Agents; Patients; phase 1 study; Phase I Clinical Trials; preference; Probability; Property; public health relevance; response; simulation; Site; Statistical Methods; Testing; Time; Toxic effect; Update; Work
Relevance: Dose-finding trials of combinations of agents are becoming increasingly common in cancer research. While there are many proposed methods for single agent trials, there are relatively few options for designing phase I trials of combinations. As in single agent trials, it is crucial to find a combination of doses that can be administered with an acceptable level of toxicity in order that these new therapies can be tested for efficacy. Without adequate statistical methods potentially effective combinations may be discarded as too toxic or get tested in subsequent studies at sub-optimal dose combinations. The overall goal of this proposal is to develop designs for phase I trials of combinations of agents
Project start date: 2010-07-01
Project end date: 2013-06-30
Budget start date: 1-JUL-2011
Budget end date: 30-JUN-2012
PFA/PA: PA-07-070
5R01CA142859-02 (2011): $282619
CORE B - PROTEOMICS & BIO STATISTICS
R Mark, Director
Case Western Reserve Universitycity: Cleveland country: United States (us)
Abstract: The major objective of the Proteomics and Biostatistics Core (PBC) is to perform quantitative analysis of changes in the protein expression for project #1 and project #3 using two dimensional differential in gel electrophoresis (2-D DICE) coupled with mass spectrometry and/or shotgun label-free approaches as well as genotype detections, polymorphism analyses (SNPs and CNPs), time-to-event and disease association studies in project #4. Furthermore, the core will facilitate the interpretation of high throughput data with sophisticated statistical, functional, and Pathway analysis tools. Finally, the core will develop and apply an integrated modeling method to test the fundamental hypothesis of the grant. Specifically, in Aim 1 we will utilize a suite of appropriate proteomics technologies to study changes in protein expression in cells. This Aim will also include validation of expression changes using Western and MSWestern technologies. In Aim 2, we will use statistical, and computational methods to facilitate the interpretation of high throughput data from 2-D DICE and label-free experiments of projects #1 and #3 as well as the genotyping data from SNP arrays in project #4. Furthermore, we will conduct pathway analysis using Ingenuity Pathway software to define the networks and their controlling transcription factors and signaling molecules that are turned on and off based on the proteomics and genomics data. In Aim 3, we will test the fundamental hypothesis of the PPG through a statistical analysis of the outcomes and predictors from the individual projects, based upon common sample usage and/or patient participation
Keywords: Accounting; Algorithms; base; Biostatistics Core; candidate validation; Cells; Classification; Computer software; Computing Methodologies; Coupled; Data; Data Analyses; Data Set; Disease Association; Electrophoresis, Gel, Two-Dimensional; Enrollment; Epithelial Cells; Event; Female; Genetic Markers; Genital system; Genome; Genomics; Genotype; Grant; Haplotypes; Highly Active Antiretroviral Therapy; HIV; HIV Infections; Human; human subject; improved; Individual; insight; interest; Label; Lead; Mass Spectrum Analysis; Methods; Modeling; Molecular; monocyte; Mucosal Immunity; Oral; Oral Manifestations; Oral mucous membrane structure; Outcome; Pathway Analysis; Pathway interactions; Patient Participation; Patients; Polymorphism Analysis; Population; Predictive Value; Process; protein expression; Proteomics; Research; research study; Risk; Sample Size; Sampling; Shotguns; Signaling Molecule; Skin; Statistical Methods; Statistical Models; statistics; Technology; Testing; Time; tool; transcription factor; two-dimensional; Validation
Budget start date: 1-MAY-2011
Budget end date: 30-APR-2012
5P01DE019759-03_7154 (2011): $217603
Sponsored Links Excellgen http://Excellgen.com
VITAMIN D HORMONE SIGNALING IN BONE MINERAL HOMEOSTASIS
R Mark, Regents Professor
University Of Arizonacity: Tucson country: United States (us)
Grant 5R01DK033351-25 from National Institute Of Diabetes And Digestive And Kidney Diseases
Abstract: The goal of this project is to characterize the molecular mechanism of action of the renal vitamin D hormone, 1,25-dihydroxyvitamin D3 (1,25(OH)2D3), in regulating bone mineral ions to prevent diseases such as rickets/osteomalacia and osteoporosis. The hypothesis to be tested is that 1,25(OH)2D3 exerts its actions to support the mineralized skeleton via liganding of the nuclear vitamin D receptor (VDR), which in turn recruits its retinoid X receptor (RXR)heterodimeric partner to recognize vitamin D responsive elements (VDREs) in bone relevant target gene promoters, with 1,25(OH)2D3-VDR-RXR attracting comodulator protein/enzyme complexes that either repress or induce DNA transcription by chromatin remodeling and linkage to RNA polymerase II. Cultured 1,25(OH)2D3target cells will be used as model systems for Specific Aims designed to elucidate the VDR-mediated events in signaling by 1,25(OH)2D3. Aim 1 will determine if 1,25(OH)2D3-VDR modulates osteoblast development/bone formation by impacting the Wnt/LRP5/p-catenin and BMP/SMAD/Runx2 signal cascades, and possibly limits bone overmineralization by controlling a newly recognized phosphate regulatory system, FGF23 and PHEX, in osteoblasts. Aim 2 will probe the role of 1,25(OH)2D3-VDR to stimulate calcium and phosphate translocation in small intestine and kidney through the enhanced expression of epithelial calcium transporter 1 (TRPV6) and sodium-phosphate cotransporter 2c (Npt2c), respectively. Methodology will include genomics and chromatin immunoprecipitation (ChIP) assays to scan for candidate VDREs, plus DNA gel mobility shift, real time PCR and promoter dissection to identify VDR-controlled genes. Comparing 1,25(OH)2D3 to its superactive analogs, ChIP assays will assess intact cell VDR-RXR-VDRE binding and characterize the sequential recruitment of transcriptional comodulators that differentially control the expression of bone mineral target genes. Finally, in Aim 3 ChIP display will be used to reveal novel upstream VDR-controlled genes should any of the proposed VDR targets emerge as secondarily or tertiarily induced/repressed via mediating transfactors. The significance of the proposed studies is that the precise molecular mechanisms whereby 1,25(OH)2D3 maintains proper bone mineralization, as well as the relative importance of novel vitamin D-regulated genes expressed in bone (Aim 1) and small intestine and kidney (Aim 2), are not understood; comprehending these pathways should enhance our ability to develop vitamin D mimetics to prevent and treat osteopenic disorders. Thus, despite the recognized relevance of vitamin D in promoting calcium absorption and bone remodeling to preclude the development of osteoporosis and resulting fractures of the spine, hip and wrist, the manner through which the vitamin D hormone accomplishes this beneficial effect has not been fully elucidated. Defining the molecular pathway of vitamin D action to enhance and preserve the mineralized skeleton may not only reveal new therapeutic strategies to prevent and treat osteoporosis with bone anabolic 1,25(OH)2D3 analogs, but could also shed light on the novel anticancer effects of vitamin D at sites such as the colon, skin, breast and
Keywords: 1 alpha, 25-Dihydroxycholecalciferol; 1 alpha, 25-Dihydroxyvitamin D3; 1, 25-Dihydroxycholecalciferol; 1, 25-Dihydroxycholecalciferol Receptors; 1, 25-Dihydroxyvitamin D3; 1, 25-Dihydroxyvitamin D3 Receptors; 4-Carboxyglutamic Protein, Bone; 9, 10-Secocholesta-5, 7, 10(19)-triene-1, 3, 25-triol, (1alpha, 3beta, 5Z, 7E)-; 9-cis-Retinoic Acid Receptor; Affect; Anabolism; analog; Assay; Autoregulation; backbone; Binding; Binding (Molecular Function); Bioassay; Biologic Assays; Biological Assay; Biological Models; biological signal transduction; biosynthesis; Blood Coagulation Factor IV; Body Tissues; bone; Bone; Bone and Bones; Bone Formation; bone fracture; Bone gamma-Carboxyglutamic Acid Protein; Bone Mineralization; Bone remodeling; bone remodelling; Bone Tissue; Bones and Bone Tissue; bowel; Breast; Ca++ element; Calcification, Physiological; Calcitriol; Calcium; calcium absorption; Calcium Channel; Calcium Channel Antagonist Receptor; calcium phosphate; Calcium-Binding Protein, Vitamin K-Dependent; Cell Communication and Signaling; Cell model; Cell Signaling; Cells; Cellular model; Chemotherapy-Hormones/Steroids; ChIP (chromatin immunoprecipitation); CHIP assay; Cholecalciferol Receptors; chromatin immunoprecipitation; chromatin remodeling; Chronology; clinical relevance; clinically relevant; Coagulation Factor IV; Colon; Complex; Comprehension; Coxa; Cultured Cells; Data; Deoxyribonucleic Acid; design; designing; Development; Differentiation and Growth; Disease; disease/disorder; Disorder; DISSEC; Dissection; DNA; DNA-Dependent RNA Polymerase II; Dysfunction; Elements; Endocrine Gland Secretion; Ensure; enzyme complex; Epithelial; Event; experiment; experimental research; experimental study; Face; facial; Factor IV; familial hypophosphatemia in rickets; Familial hypophosphatemic bone disease; Feedback; Fracture; Functional disorder; gastrointestinal absorption; Gastrointestinal Tract, Small Intestine; Gel; gene product; Gene Targeting; Gene Transcription; Genes; Genes, Regulator; genetic promoter element; Genetic Transcription; Genomics; Gla Protein, Bone; Goals; Hip; Hip region structure; Homeostasis; Hormones; hRANKL2; hypophosphatemia in rickets; In element; Indium; inorganic phosphate; Intestinal; Intestinal Absorption; Intestines; Intestines, Small; Intracellular Communication and Signaling; Investigators; Ion Channels, Calcium; Ions; Kidney; Ligands; Light; Maintenance; Maintenances; Mediating; Messenger RNA; Method LOINC Axis 6; Methodology; mimetics; mineralization; Minerals; Model System; Models, Biologic; Molecular; Molecular Interaction; Molecular Mechanisms of Action; mRNA; Multienzyme Complexes; Na+ - Pi cotransporter; Na-Pi symporter; new therapeutic target; new therapeutics; next generation therapeutics; novel; novel therapeutics; Nuclear; OCIF protein; ODF; opg gene product; OPG protein; OPGL; Osteoblasts; Osteocalcin; osteoclastogenesis; osteoclastogenesis inhibitory factor; Osteoclasts; Osteogenesis; Osteomalacia; Osteoporosis; osteoprotegerin; pathophysiology; pathway; Pathway interactions; Phenotype; Phosphates; Photoradiation; Physiologic; Physiologic calcification; Physiological; Physiological Homeostasis; Physiopathology; prevent; preventing; Production; programs; Programs (PT); Programs [Publication Type]; Promoter; Promoter Regions; Promoter Regions (Genetics); Promoters (Genetics); Promotor; Promotor (Genetics); Promotor Regions; Promotor Regions (Genetics); Proteins; RANKL; receptor; receptor binding; Receptor Protein; Receptors, 1, 25-Dihydroxyvitamin D 3; Receptors, Calcitriol; Receptors, Calcium Channel Blocker; recruit; Recruitment Activity; Regulator Genes; regulatory gene; Relative; Relative (related person); renal; Repression; Research Personnel; research study; Researchers; response; Retinoic Acid Receptor RXR; Retinoid X Receptors; Rickets; Rickets, Hypophosphatemic; Rickets, Vitamin D-Resistant; Risk; RNA Expression; RNA Polymerase B; RNA Polymerase II; RNA, Messenger; Role; RXR; RXR Protein; Scanning; Series; Signal Transduction; Signal Transduction Systems; Signaling; Site; skeletal; Skeleton; Skin; small bowel; Small Intestines; social role; sOdf; sodium phosphate transporter; sodium-phosphate cotransporter; sodium-phosphate cotransporter proteins; Spinal Column; Spine; System; System, LOINC Axis 4; Targetings, Gene; Testing; Therapeutic Hormone; Time; Tissues; TNFRSF11B; TNFRSF11B gene product; TNFSF11; TNFSF11 gene; trans acting element; Transcription; Transcription, Genetic; Transcriptional Regulatory Elements; tumor; Tumor necrosis factor receptor 11b; Tumor Necrosis Factor Receptor Superfamily Member 11B; Urinary System, Kidney; VDCC; VDR; Vertebral column; VIT D; Vitamin D; Vitamin D 3 Receptors; Vitamin D Receptors; Vitamin D3 Receptor; Vitamin K-Dependent Bone Protein; Voltage-Dependent Calcium Channels; Wrist; X linked hypophosphatemia in rickets; X-Linked Hypophosphatemic Rickets
Project start date: 1984-07-01
Project end date: 2011-11-30
Budget start date: 1-DEC-2009
Budget end date: 30-NOV-2011
5R01DK033351-25 (2010): $281318
CASE CENTER FOR SYNCHROTRON BIOSCIENCES
R Mark, Director
Case Western Reserve Universitycity: Cleveland country: United States (us)
Grant 5P30EB009998-03 from National Institute Of Biomedical Imaging And Bioengineering
Abstract: The Case Center for Synchrotron Biosciences (CSB), with state-of-the-art facilities and laboratories at the National Synchrotron Light Source (NSLS) and at Case Western Reserve University School of Medicine (CWRU), is proposing to continue development and operation of a number of novel synchrotron beam lines to support an international clientele of users in the biomedical sciences. The resource currently serves over 550 users at the NSLS through the operation of four synchrotron beamlines that provide state-of-the art equipment, techniques, user support, and training for radiolytic footprinting, x-ray spectroscopy, and macromolecular crystallography experiments. The users come from across the US and from around the world. Three Technology Service Cores are proposed for the P30 Center. These include a footprinting core, based on the world-leading X28C footprinting beamline, which will provide protein, nucleic acid and in vivo footprinting facilities. An x-ray spectroscopy core, based on the X3B beamline, will receive a detector upgrade bringing its capabilities to state-of-the art in the US. The macromolecular crystallography core, particularly the X29 beamline, will expand its world-class productivity. Efficient mechanisms of delivering user service on our synchrotron beamlines will be continued and are contingent on effective training of users by our experienced beamline staff. The P30 proposes the support of 176 service projects across all three cores that are supported by 212 peer-reviewed grants, including 200 from the NIH. The Technology Service Core infrastructure is closely coupled to the needs of over one hundred user groups with peer-reviewed funding in a wide range of biological sciences. Based on specific developmental activities at the beamlines, user staff will enhance the research of the investigators that are presently using the resource´s facilities. Pro-active programs of training and dissemination are outlined that will enhance the reach of the resource´s programs and attract new users, expanding the research base. PUBLIC HEALTH RELEVANCE STATEMENT This project provides resources for the NIH funded scientific community to support the study of the structure and dynamics of macromolecuies. These studies are critical for understanding the normal biology of all organisms and the molecular effects of disease including the design of drugs to control cellular processes and the understanding of the molecular interactions that mediate the spread of viruses and bacteria
Keywords: Accounting; Administrator; Advisory Committees; Bacteria; base; beamline; Binding (Molecular Function); Biological Sciences; Biology; Biomedical Technology; Cell physiology; Communication; Communities; Complex; Conflict (Psychology); cost; Coupled; Crystallography; detector; Development; Disease; Drug Design; Educational workshop; Equipment; experience; Funding; Goals; Grant; in vivo; Individual; Institution; International; laboratory facility; Leadership; lectures; Light; Mediating; medical schools; meetings; Methods; Molecular; Monitor; National Institute of Biomedical Imaging and Bioengineering; novel; Nucleic Acids; Office of Administrative Management; operation; Organism; organizational structure; Output; outreach; Peer Review; Peer Review Grants; posters; Productivity; programs; Progress Reports; Proteins; public health relevance; Publications; ranpirnase; Reporting; Research; Research Infrastructure; Research Personnel; Research Project Grants; research study; Resolution; Resource Allocation; Resources; Science; Services; Source; Spectrum Analysis; Strategic Planning; Structure; Synchrotrons; System; Techniques; Technology; Training; Training Programs; Training Support; United States National Institutes of Health; Universities; Virus; web site
Relevance: This project provides resources for the NIH funded scientific community to support the study of the structure and dynamics of macromolecuies. These studies are critical for understanding the normal biology of all organisms and the molecular effects of disease including the design of drugs to control cellular processes and the understanding of the molecular interactions that mediate the spread of viruses and bacteria
Project start date: 2009-09-01
Project end date: 2014-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
5P30EB009998-03 (2011): $692136
STRUCTURAL EVALUATION OF HIV-1 ENVELOPE GYCOPROTEIN
R Mark
Iowa State Universitycity: Ames country: United States (us)
Abstract: Structure information on HIV glycoproteins (gp120 and gp41) can facilitate the design of envelope-based antigens, and better understanding of HIV fusion process and host immune response. The major objective of Project 2 is to structurally characterize HIV-1 envelope glycoproteins to assist the design of HIV-1 envelope antigens that can elicit broadly cross-reactive neutralizing antibodies, with a long-term goal of developing an envelope-based protective vaccine against HIV infection. All currently known gp41 structures are very similar to each other and represent a post-fusion conformation. Structure of gp41 pre-fusion intermediate is not known. We propose to solve structure for carefully designed gp41 fragments without the N-terminal heptad region. Our approach includes a suite of carefully selected and state-of-the art structural and computational biology approaches, including crystallography, hydroxyl radical footprinting and ab initio modeling. Our current model of the gp41-64 antigen explains its antigenic reactivity and is driving ideas for its engineering. Aim 1 provides a seamless gp41 antigen design-high resolution structure determination-redesign pipeline within the program as a whole. Aim 2 intends to structurally characterize gp120 outer domain (gp120OD) and OD-gp41 constructs using structural mass spectrometry methods. Glycosylation signature of gp120OD would affect the immunogenicity of gp120OD-based antigens. Thus, a design-structural characterization-redesign approach where Project 2 feeds back to the Project 1 team is critical for developing improved gp120-based antigens. Present crystal structures of gp120 are mostly from protein cores, with variable loop regions and N- and Ctermini truncated. Solving a crystal structure of a full-length gp120 with intact variable loops has been extremely difficult due to the flexibility of these loop segments and extensive glycosylation of the protein. In Aim 3, we propose to use, hydroxyl radical footprinting, homology modeling, and docking to characterize the structure of the V1/V2 variable loop regions in the presence and in the absence of the primary receptor CD4. By probing the outer surfaces of proteins accessible to solvents, we will be able to determine the conformational changes in the variable loop regions upon binding of CD4
Keywords: 3-Dimensional; Affect; Antibodies; Antigens; Automobile Driving; Back; base; Binding (Molecular Function); CD4 Antigens; Cells; Chimeric Proteins; Complex; Computational Biology; Computer Simulation; Consensus Sequence; Core Protein; Crystallography; Data; design; Deuterium; Docking; Engineering; Epitopes; Evaluation; Excision; Feeds; flexibility; Glycoproteins; glycosylation; Goals; HIV; HIV Envelope Protein gp120; HIV Infections; HIV-1; Homology Modeling; Hydroxyl Radical; Immune response; Immunodominant Epitopes; immunogenic; immunogenicity; improved; Insecta; Length; Ligands; Maps; Mass Spectrum Analysis; Mediating; Membrane; Membrane Proteins; Methods; Modeling; Molecular Conformation; N-terminal; neutralizing antibody; novel; Principal Investigator; Process; programs; Property; Protein Binding; Protein Footprinting; Protein Glycosylation; protein structure; Proteins; Resolution; simian immunodeficiency virus gp120; Solubility; Solutions; Solvents; structural biology; Structural Models; Structure; Surface; Technology; Trypsin; Vaccines; Variant; Work
Budget start date: 1-MAY-2011
Budget end date: 30-APR-2012
5P01AI074286-04_0001 (2011): $367085
CYTOKINE AND NEUROTRANSMITTER INTERACTIONS IN SLEEP REGULATION
R Mark, Vice Chair For Basic Science
University Of Washingtoncity: Seattle country: United States (us)
Grant 5R01MH064843-09 from National Institute Of Mental Health
Abstract: Sleep presents a conundrum for neurobiology we do not know what function(s) sleep serves for the brain (or the body). We do know, however, that adequate sleep is essential for physical and mental health. In addition to effects on cognition and performance, lack of sleep, or sleep disruption due to sleep disorders may be a contributing factor to multiple pathologies, including but not limited to hypertension, coronary artery disease, cerebrovascular disease, and hyperglycemia. Numerous studies demonstrate that sleep loss impairs immune function and that immune activation from infection alters sleep. Responsiveness to infection varies widely in the extreme, some will live and others will die in response to the same pathogen(s). Numerous systematic pre- clinical studies demonstrate infection-induced alterations in sleep. Most infections increase non-rapid eye movements sleep (NREMS) and decrease rapid eye movements sleep (REMS). Our functional hypothesis is that the manner in which sleep is altered during infection is a critical determinant of clinical outcome. Indeed, one retrospective study demonstrates that specific sleep patterns of rabbits are associated with survival from infection. To further our understanding of central nervous system responses that result in good clinical outcome, we focus on the cytokine interleukin (IL)-1 as one mediator of altered sleep during immune activation. Data indicate IL-1 increases NREMS and suppresses REMS. We propose in this application to focus effort on IL-1-induced suppression of REMS, an effect that has been universally ignored. IL-1 inhibits ACh synthesis and release. Cholinergic neurons of the laterodorsal tegmental (LDT) and pedunculopontine (PPT) nuclei are involved in EEG desynchronization and thalamocortical activation during REMS. REMS- generating structures are under GABAergic inhibition IL-1 enhances GABA inhibitory effects at multiple levels. Studies proposed in this application will test the mechanistic hypothesis that IL-1 suppresses REMS by opposed, yet complementary actions on brainstem cholinergic and GABAergic systems. Our preliminary data indicate IL-1 microinjected into the LDT reduces REMS of rats; IL-1 reduces firing rates of cholinergic neurons in LDT slice preparations; and IL-1 increases the number of c-Fos+ neurons in the ventrolateral periaqueductal grey (vlPAG), a GABA-rich area that projects to the pontine reticular formation and the LDT. In this application, we propose to determine 1) the impact on sleep of IL-1 microinjection into brainstem cholinergic/cholinoceptive nuclei, 2) in vitro effects of IL-1 on electrophysiological properties of cholinergic neurons, and 3) the impact of IL-1 on REMS-relevant brainstem nuclei and neurotransmitter systems using immuno- fluorescence techniques. Successful completion of these aims will provide novel data critical for our understanding of mechanisms by which REMS is suppressed during infection. Determination of whether alterations in sleep contribute to good clinical outcome will only be possible when the neuroanatomic and neurochemical substrates targeted by immune responses to infection are clearly understood. PUBLIC HEALTH RELEVANCE Some individuals live and others die in response to infections. Sleep is dramatically altered during infection. Evidence suggests the manner in which sleep is altered may contribute to survival. This project will determine effects of immune activation on brain systems responsible for regulating one phase of sleep that is suppressed during sickness. Once we understand how (by what means) sleep is altered during infection, we will be able to study why sleep is altered during infection, i.e., does altered sleep facilitate recovery?
Keywords: Acetylcholine; Acute; Anterior Hypothalamus; Area; Arousal; Award; basal forebrain; Bathing; Behavior; Brain; Brain Stem; cell body (neuron); Cell Nucleus; Cells; Cerebrovascular Disorders; cholinergic; cholinergic neuron; Clinical; Cognition; Complex; Coronary Arteriosclerosis; cytokine; Data; dorsal raphe nucleus; Fluorescence; FOS gene; Funding; gamma-Aminobutyric Acid; Health; Hippocampus (Brain); Hyperglycemia; Hypertension; Hypothalamic structure; Immune; immune activation; immune function; Immune response; Immunofluorescence Immunologic; Immunomodulators; In Vitro; Individual; Infection; Interleukin-1; Interleukins; Knowledge; Laboratory Animals; Life; Maintenance; Mediating; Mediator of activation protein; member; Mental Health; Microdialysis; Microinjections; midbrain central gray substance; Modeling; mRNA Expression; Neuraxis; Neurobiology; neurochemistry; Neurons; Neurotransmitters; non rapid eye movement; novel; Oryctolagus cuniculus; Outcome; pathogen; Pathology; Patients; Pattern; Pedunculopontine Tegmental Nucleus; Performance; Phase; physical conditioning; Pituitary Gland; Pontine structure; preclinical study; Preoptic Areas; Preparation; Presynaptic Terminals; Property; Rattus; Recovery; Regulation; REM Sleep; response; Reticular Formation; Retrospective Studies; Seminal; Serotonin; Site; Sleep; Sleep Disorders; sleep regulation; Slice; Structure; Synapses; System; Techniques; Testing; Work
Relevance: Some individuals live and others die in response to infections. Sleep is dramatically altered during infection. Evidence suggests the manner in which sleep is altered may contribute to survival. This project will determine effects of immune activation on brain systems responsible for regulating one phase of sleep that is suppressed during sickness. Once we understand how (by what means) sleep is altered during infection, we will be able to study why sleep is altered during infection, ie., does altered sleep facilitate recovery?
Project start date: 2001-03-15
Project end date: 2013-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: PA-07-070
5R01MH064843-09 (2011): $377230
FLEXIBILITY AND COMMITMENT IN POST-EFFECTOR CD4 LYMPHOCYTES
R Mark, Professor
Vanderbilt Universitycity: Nashville country: United States (us)
Grant 5R01AI077528-03 from National Institute Of Allergy And Infectious Diseases
Abstract: Signaling and gene activation mechanisms in the initial phase of effector CD4 T cell responses restrict the expression of cytokine and trafficking genes to functionally distinct programs. Production of IFN-? by Th1 cells is central to immunity against many intracellular pathogens, but induction of this gene is blocked in activated Th2 cells. In contrast to the information available about mechanisms programming the acute effector response, relatively little is known about molecular regulation in post-effector populations. Antigenic experience is central to the diverse processes involved in immunologic memory. Memory is essential for the efficacy of vaccines, the most cost-effective of medical interventions and a key to potential protection against bioweapons, so a better understanding of the molecular regulation of antigen (Ag)-experienced helper cells is a vital priority. The goal of this research program is to elucidate molecular mechanisms involved in programming cytokine gene activity in CD4 T cells that have had prior antigenic experience and then become quiescent after their first period of activation. The central hypothesis of this proposal is that commitment to one aspect of Th2 identity - chromatin marks establishing transcriptional competence of the Th2 cytokine locus - is maintained in Ag-experienced cells by persistence of GATA3 protein after initial development, but this committed population regains a capacity to activate T-bet, the IFN-? locus, and perhaps other Th1-specific genes. Using CD4 T cells purified via a lineage-marking approach, we have evidence that Ag-experienced Th2 cells can become IFN-? producers with a substantial efficiency once they have been parked in vivo for weeks, yet the population and the individual IFN-3-producing cells retain a commitment to reactivation of their Th2 program. The proposed studies will answer a few main questions (a) What mechanisms give rise to the flexibility in IFN-? gene activation, which should be ´forbidden´ in a "differentiated Th2 cell", and what are the consequences? (b) In T cells that differentiated from cells with an active IL-4 locus, is commitment to transcriptional competence of the IL-4 gene fixed or can its molecular programming be altered if expression of a developmental regulator is terminated? To answer these questions, we will analyze Th1-like flexibility (Ifng locus & other endpoints) and Th2 locus commitment after Th1-biasing immune challenges in vivo, e.g. with influenza virus (Specific Aim 1). Further, we will elucidate mechanisms by which IFN-? gene expression is induced in memory-like Th2 cells after their re-activation and growth in Th1 conditions (Aim 2). In Aim 3, we will determine if persistence of GATA3, a master regulator of initial Th2 locus activation, is required for maintenance of IL-4 locus competence and chromatin marks in the population derived from Ag-experienced IL-4 locus-activated CD4 T cells. We propose that loss of the transcription factor GATA-3 from differentiated Th2 cells will alter the functional capabilities of their recall response in terms of localization, IL-4 production, & allergic inflammation. Together, the proposed studies will provide new insights into the programming of antigen-experienced helper populations. The properties of T lymphocytes that have previously been activated by the target for which they are specific are crucial for normal immunity to pathogens, effective vaccines, and biodefense. This type of "antigen-experienced" cell contributes in important ways to immune memory, and also influences flares of allergic disease such as asthma. By exploring a new and unexpected finding about flexibility in the gene expression program of these cells, the proposed research will generate important new insights into the regulation of which genes get expressed in helper T cells, the quarterbacks of adaptive immunity, after cells have been activated once by antigen, picked up specific types of function, and then gone into a resting state
Keywords: Acute; adaptive immunity; Allergic Disease; Allergic inflammation; Antigens; Asthma; base; biodefense; CD4 Positive T Lymphocytes; Cells; Characteristics; chemokine receptor; Chromatin; chromatin modification; Commit; Competence; cost effective; cytokine; Cytokine Gene; Defect; Development; Effectiveness; Epigenetic Process; Exhibits; experience; Flare; flexibility; Frequencies (time pattern); GATA3 transcription factor; Gene Activation; Gene Expression; Gene Expression Regulation; gene induction; Genes; Genetic Transcription; Goals; Growth; Health; Helper-Inducer T-Lymphocyte; histone modification; Host Defense; Immune; Immune response; Immunity; Immunologic Memory; in vivo; Individual; influenzavirus; insight; Interferon Type II; Interferons; Interleukin-17; Interleukin-4; Intervention; Lead; Lymphocyte; Maintenance; Mediating; Medical; Memory; Modification; Molecular; Mus; Outcome; pathogen; Pathogenesis; Pattern; Phase; Phenotype; Play; Population; Process; Production; programs; Property; Proteins; Regulation; Research; Resolution; response; Rest; Role; Signal Transduction; Sorting - Cell Movement; T cell response; T-Lymphocyte; Th2 Cells; trafficking; transcription factor; Tumor stage; vaccine efficacy; Vaccines; Work
Relevance: NARRATIVE The properties of T lymphocytes that have previously been activated by the target for which they are specific are crucial for normal immunity to pathogens, effective vaccines, and biodefense. This type of "antigen-experienced" cell contributes in important ways to immune memory, and also influences flares of allergic disease such as asthma. By exploring a new and unexpected finding about flexibility in the gene expression program of these cells, the proposed research will generate important new insights into the regulation of which genes get expressed in helper T cells, the quarterbacks of adaptive immunity, after cells have been activated once by antigen, picked up specific types of function, and then gone into a resting state
Project start date: 2009-09-01
Project end date: 2014-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
PFA/PA: PA-07-070
5R01AI077528-03 (2011): $382239
PRETERM BIRTH, LUNG INNATE IMMUNITY, AND RSV
R Mark, Professor
Iowa State Universitycity: Ames country: United States (us)
Grant 5R01AI062787-05 from National Institute Of Allergy And Infectious Diseases
Abstract: Respiratory syncytial virus (RSV) infection is the most common cause of respiratory disease leading to hospitalization in children. Preterm infants are especially susceptible to severe RSV infection. Respiratory epithelium is an initial site of RSV infection and epithelial cells along with alveolar macrophages (AM) and dendritic cells (DC) are vital to innate and adaptive immune responses. However, the extent of innate immune gene expression by epithelia and AM-DC in preterm infants can be variable/limited. The hypothesis is that Reduced innate immunity by respiratory epithelia and AM-DC preterm enhances susceptibility to RSV infection This hypothesis is based on the facts above and our preliminary data in lambs demonstrating limited expression of surfactant proteins A and D (SP-AD), sheep beta-defensin-1 (SBD-1), and Toll-like receptor 4 (TLR4) preterm. It will be tested in preterm lambs which have close similarities with human disease including susceptibility, lesions, and innate immunity. Specific Aim 1 compares expression of key innate immune genes (SBD-1, SP-AD, TLR4) and protein/peptide production in vivo as well as AM-DC cytokine expression in pre- and full-term lung. It also tests the hypothesis that limited epithelial cell proliferation and/or differentiation pre-term underlie(s) the mechanistic basis for limited SP-AD, SDB-1 expression and tests this by comparing transcriptional activity, protein/peptide production in pre- and full term cultured cells with or without cell proliferation and differentiation. Specific Aim 2 tests the hypothesis that SP-AD, SBD-1 and AM-DC responses to RSV are less at pre- than full-term in the lamb model and in vitro with cultured epithelial cells. A second hypothesis, that increased cell proliferation and/or differentiation of epithelia protects against RSV infection, will be tested in vitro with treatments from Aim 1. The extent to which SP-AD, SBD-1 directly prevent RSV infection will be tested with RNAi assays. Specific Aim 3 tests the hypothesis that yet other innate immune genes expressed with cell proliferation/differentiation prevent RSV infection. This Aim uses gene expression profiling of primary polarized human lung cells and a respiratory epithelia-specific probe set (Unigene) that is the most well-annotated and defined gene target set to date. It also identifies ovine orthologs of human genes and test for impaired/reduced expression preterm. This team combines veterinary and human medical expertise to attain the goal of this project to discover the reason(s) for inadequate expression of SP-AD, SBD-1 and other innate immune genes as well as AMDC responses at preterm that predispose to RSV infection. The work is significant because it discovers the underlying basis for RSV susceptibility preterm and mechanistic approaches to enhance innate immunity
Keywords: Admission activity; Affect; Age; Alveolar Macrophages; Alveolus; Animal Diseases; Antigen-Presenting Cells; antimicrobial; antimicrobial peptide; Area; base; beta-Defensins; Biological; Biological Assay; Birth; bronchial epithelium; Cell Proliferation; Cells; Child; Clinical; Clinical Pathology; Collaborations; college; Computer Analysis; Cultured Cells; cytokine; Cytokine Gene; Data; Defensins; Dendritic Cells; Dentistry; effective therapy; Electronic Mail; Epithelial Cell Proliferation; Epithelial Cells; Epithelium; experience; Funding; Gene Expression; Gene Expression Profiling; Gene Proteins; Gene Targeting; Genes; Genetic Transcription; Goals; Grant; Growth; Hospitalization; Human; human DEFB1 protein; human disease; IL8 gene; Immune; Immune response; Immunity; in vitro Model; in vitro testing; in vivo; Infant; Infection; Intensive Care Units; Interferon-alpha; Interleukin-10; interleukin-12 subunit p35; laser capture microdissection; Lesion; Lung; Lung diseases; Manuscripts; Mechanical ventilation; Medical; Medicine; meetings; Modeling; Molecular Profiling; National Institute of Allergy and Infectious Disease; Natural Immunity; novel; Orthologous Gene; Outcome; Oxygen; pathogen; pediatrician; Peptides; Persons; Predisposition; Pregnancy; Premature Birth; Premature Infant; prevent; Principal Investigator; Production; programs; Proliferating; Proteins; Publishing; Pulmonary Surfactant-Associated Protein A; Pulmonary Surfactant-Associated Protein D; Recording of previous events; Regulator Genes; release factor; Research; Research Personnel; Research Project Grants; respiratory; Respiratory syncytial virus; Respiratory Syncytial Virus Infections; Respiratory System; Respiratory tract structure; response; RNA Interference; Role; Ruminants; Scientist; Severities; Severity of illness; Sheep; Site; Structure of respiratory epithelium; surfactant; Telephone; Testing; Tissues; toll-like receptor 4; Type II Epithelial Receptor Cell; United States National Institutes of Health; Vascular Endothelial Growth Factors; Veterinarians; Veterinary Medicine; Viral; Virus Activation; Virus Diseases; Work
Project start date: 2005-08-15
Project end date: 2011-01-31
Budget start date: 1-FEB-2009
Budget end date: 31-JAN-2011
5R01AI062787-05 (2009): $466565
5R01AI062787-04 (2008): $451544
5R01AI062787-03 (2007): $475144
5R01AI062787-02 (2006): $380843
POLYMERASE PROTEINS IN CORONAVIRUS REPLICATION
R Mark, Professor
Vanderbilt Universitycity: Nashville country: United States (us)
Grant 5R01AI026603-22 from National Institute Of Allergy And Infectious Diseases
Abstract: Replication of positive-strand RNA viruses requires processing of virus-encoded polyproteins by viral proteases. Proteases mediate temporal and hierarchical processing of constantly changing polyprotein precursors, which in turn determine the successful viral replication and pathogenesis. Proteases of RNA viruses therefore represent important targets for development of broadly applicable inhibitors of virus replication. Rational design of protease inhibitors has targeted conserved structure/function elements such as active-site cavities and substrate-binding domains. However, RNA viruses have shown the capacity to select for resistance to these types of inhibitors. Thus, it is important to identify determinants of protease activity that are independent from catalytic or substrate sites, and which can be targeted by inhibitors that can prevent emergence of resistance. The goals of this proposal are to use the coronavirus murine hepatitis nsp5 protease as a model to 1) test the role of nsp5 precursors, and non-catalytic, non-substrate binding structure-function determinants, in protease activity and specificity; and 2) identify and test the role of novel intramolecular residue networks in nsp5 polyprotein processing in vitro and during virus replication in culture. Coronaviruses are positive-strand RNA viruses, important pathogens of humans, and express a polyprotein composed of sixteen nonstructural replicase protein domains (nsp1-16), of which nsp4-16 are processed by the nsp5 protease (3CLpro, Mpro) at eleven cleavage sites. Nsp5 possesses two chymotrypsin-like domains, whose interface comprises the active-site cavity and substrate-binding regions, and a unique domain 3 of unknown function. In vitro biochemical and structural studies have concluded that functional nsp5 dimeric, and have identified structure/function determinants of dimerization and catalysis, but of these have been tested in a replicating virus. Specific Aims 1 and 2 will test predicted nsp5 structure/function determinants in the context of intermediate precursors and membrane-associated complexes. Experiments in Specific Aim 3 will perform bioinformatic analysis of extensive sequence and structure datasets of nsp5 and related proteases, in order to predict intramolecular residue networks based on a) iterative mutation and reversion of conditional temperature sensitive mutant viruses; b) co-evolution and structural proximity; and c) protein flexibility and movement. The role of predicted network residues will be tested in reverse genetic replication studies of mutant viruses, and by in vitro biochemical assays of purified nsp5. The proposed studies will answer fundamental questions in coronavirus polyprotein processing and will define critical new intramolecular networks, communication pathways, and determinants of the evolution and function of nidovirus nsp5 and orthologs. The outcome of the proposed experiments will be of high impact and significance by establishing universally applicable systems for identification and testing of novel non-catalytic RNA virus protease targets for inhibition or attenuation of virus replication. RNA viruses such as coronaviruses are important pathogens of humans, and RNA virus proteases are important targets for development of inhibitors. Coronavirus nsp5 protease is essential for virus replication and mediates processing of the replicase polyprotein. The Aims of this proposal will define novel conserved structure and sequence determinants of coronavirus nsp5 during replication, and identify and test the role of intramolecular networks of residues as regulators of RNA virus protease activity and specificity during replication
Keywords: Active Sites; Alanine; attenuation; Binding (Molecular Function); Binding Sites; Biochemical; Bioinformatics; Biological Assay; Catalysis; Cellular Membrane; Chimeric Proteins; chymotrypsin; Communication; Complex; Coronavirus (genus); Data Set; design; Development; dimer; Dimerization; Elements; Engineering; Evolution; Fingers; flexibility; Genetic; Goals; Hepatitis; Human; human disease; In Vitro; Infection; inhibitor/antagonist; Location; Mediating; Membrane; Modeling; Movement; Murine hepatitis virus; Mus; Mutagenesis; mutant; Mutation; Network-based; Nonstructural Protein; novel; Orthologous Gene; Outcome; pathogen; Pathogenesis; Pathway interactions; Peptide Hydrolases; Polymerase; Polyproteins; positional cloning; prevent; Process; Protease Inhibitor; Proteins; public health relevance; Regulation; replicase; research study; Resistance; RNA chemical synthesis; RNA Viruses; Role; Site; Specificity; Structure; System; Temperature; temperature sensitive mutant; Tertiary Protein Structure; Testing; Variant; Viral; Viral Proteins; Virus; Virus Diseases; virus host interaction; Virus Replication
Project start date: 1991-09-30
Project end date: 2015-04-30
Budget start date: 1-MAY-2011
Budget end date: 30-APR-2012
PFA/PA: PA-07-070
5R01AI026603-22 (2011): $317256
Sponsored Links Excellgen http://Excellgen.com
TARGETING PANCREATIC CANCER USING PEPTIDE CHEMISTRY: FROM BENCH TO BEDSIDE
R Mark, Professor And Consultant
Mayo Cliniccity: Rochester country: United States (us)
Grant 5R01CA150190-02 from National Cancer Institute
Abstract: Pancreatic adenocarcinoma (PCA) is an almost invariably fatal disease. Furthermore, conventional treatment generally fails because of a significant gap in translating the molecular mechanisms of carcinogenesis into feasible therapeutics. Overexpression of many mitogenic growth factors and their receptors, in particular the overexpression of IGF-1R and EGFR, has been observed with a high frequency in patients with advanced pancreatic cancer. Several studies have been completed in an attempt to understand the pathways that lead to IGF-1R and EGFR-mediated signaling, but the molecular mechanism of receptor overexpression remains unclear. In our published as well as preliminary studies, we have defined a unique mechanism of IGF-1R and EGFR overexpression in PCA. Our data also define a novel regulatory role of GIPC, a RGS/PDZ binding protein, which controls both IGF-1R and EGFR expression by two distinct mechanisms. Moreover, we have also shown that pancreatic cancer cells expressed shRNA of GIPC grow significantly slower than that of parental cells, and their metastasis capabilities are restricted. Our recent published results have also encouraged us to propose a targeted therapeutic approach using nanotechnology to improve drug delivery methods. Taken together, these observations have led us to hypothesize that inactivation of GIPC function can be exploited to inhibit IGF-1R and EGFR overexpression in a targeted manner that would have important clinical implications in PCA. To test our hypothesis, we have proposed four aims. Aim 1 will examine the molecular mechanism of the regulatory role of GIPC on IGF-1R and EGFR overexpression in PCA cells. Aim 2 will develop chemical discovery platforms for identifying novel peptide-based ligands for GIPC. In Aim 3, we will focus on biochemical characterization and cellular probe development of peptide-based ligands for GIPC. Aim 4 will focus on the development of nanotechnology-based targeted therapeutics. We will synthesize and characterize in vitro the different combinations of anti-IGF-1R antibody, GIPC peptides (IGF-1R and EGFR inhibitors) attached onto the surface of gold nanoparticles with or without gemcitabine. In the later part of this aim, we will extrapolate the knowledge and reagents from the previous aims to the animal model of orthotropic pancreatic cancer that can mimic human diseases. We will examine the in vivo efficacy of the nanogold conjugated drugs in vivo seeking to understand the importance of multi-targeted, combination drugs in PCA progression and metastasis. Furthermore, we will determine pharmacokinetics, pharmacodynamics, bio-distribution, and bio-toxicity of the effective drugs that will lead us toward clinical trials in the near future. Overall, our highly collaborative proposed experiments will identify specific targets for therapeutic interventions for pancreatic adenocarcinoma where no current therapy is available. Pancreatic adenocarcinoma (PaCA) is, almost invariably, a fatal disease. This work will focus on the prevention and therapeutic aspects of this cancer. Overall, our proposed experiments will define the regulatory role of GIPC and their downstream molecules that can influence the tumor growth and metastasis. The proposed study might define the mechanism of pancreatic cancer growth and progression and identify specific targets for therapeutic interventions for pancreatic adenocarcinoma where no current therapy is available
Keywords: 1-(2-Oxo-4-amino-1, 2-dihydropyrimidin-1-yl)-2-deoxy-2, 2-difluororibose; 1H-Thieno(3, 4-d)imidazole-4-pentanoic acid, hexahydro-2-oxo-, (3aS-(3aalpha, 4beta, 6aalpha))-; 2`, 2`-DFDC; 2`, 2`-difluoro-2`-deoxycytidine; 2`, 2`-difluorodeoxycytidine; 2`-deoxy-2`-difluorocytidine; 2`Deoxy-2`, 2`-Difluorocytidine; 2, 2 difluorodexoycytidine; Adenocarcinoma Cell; Affinity; Animal Model; Animal Models and Related Studies; Antibodies; Assay; Au element; bacterial virus; Bacteriophage T7; Bacteriophages; base; bench bed side; bench bedside; bench to bed side; bench to bedside; Binding; Binding (Molecular Function); Binding Proteins; Bioassay; Biochemical; Biologic Assays; Biological; Biological Assay; biological signal transduction; Biotin; c-erbB-1; c-erbB-1 Protein; Calorimetry; Cancer Cause; Cancer Etiology; cancer metastasis; Cancers; Carcinogenesis Mechanism; cell biology; Cell Communication and Signaling; Cell Line; Cell Lines, Strains; Cell Signaling; CellLine; Cells; Cellular biology; Cessation of life; Chemicals; Chemistry; Clinic; Clinical; clinical investigation; Clinical Trials; Clinical Trials, Unspecified; coenzyme R; Coliphage T7; conventional therapy; cultured cell line; Data; Death; design; designing; Development; dFdC; dFdCyd; Diagnosis; Difluorodeoxycytidine; Disease; Disease Progression; disease/disorder; Disorder; Drug Combinations; Drug Delivery; Drug Delivery Systems; drug development; Drug Kinetics; Drug Targeting; Drug Targetings; drug/agent; Drugs; effective therapy; EGFR; EGFR Blocker; EGFR Inhibitor; EGFR Tyrosine Kinase Inhibitor; EGFR-TK Inhibitor; ELISA; Enterobacteria phage T7; Enzyme-Linked Immunosorbent Assay; Epidermal Growth Factor Receptor; Epidermal Growth Factor Receptor Inhibitor; Epidermal Growth Factor Receptor Kinase; Epidermal Growth Factor Receptor Protein-Tyrosine Kinase; Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor; ERBB Protein; erbB-1; erbB-1 Proto-Oncogene Protein; ERBB1; erbBl; Esteroproteases; Exhibits; experiment; Experimental Designs; experimental research; experimental study; Expression Profiling; Expression Signature; Extracellular Matrix, Integrins; Family; Fluorescence; Frequencies (time pattern); Frequency; Future; gemcitabine; gene product; Generalized Growth; GFAC; Gold; Growth; Growth Agents; Growth Factor; Growth Factors, Proteins; Growth Substances; heavy metal lead; heavy metal Pb; HER1; human disease; improved; In Vitro; in vivo; Individual; inhibitor; inhibitor/antagonist; Integrins; intervention therapy; Intracellular Communication and Signaling; Investigation; Knowledge; Laboratories; language translation; Lead; Libraries; Ligand Binding; Ligand Binding Protein; Ligands; Link; Lipids; malignancy; Malignant Glandular Cell; Malignant neoplasm of pancreas; Malignant Neoplasms; Malignant Pancreatic Neoplasm; Malignant Tumor; Mediating; Medication; Metastasis; Metastasize; Metastatic Neoplasm; Metastatic Tumor; Methods; Methods and Techniques; Methods, Other; Microarray Analysis; microarray technology; Microarray-Based Analysis; model organism; Modification; molecuar profile; Molecular; Molecular Fingerprinting; Molecular Interaction; Molecular Profiling; molecular signature; mouse model; Mutagenesis, Site-Directed; nano; nano gold; nano particle; nano probe; nano scale Science; nano tech; nano technology; nanoGold; nanoparticle; nanoprobe; Nanoscale Science; nanotech; Nanotechnology; Neoplasm Metastasis; neoplasm/cancer; new approaches; novel; novel approaches; novel strategies; novel strategy; ontogeny; overexpression; Pancreas Adenocarcinoma; Pancreas Cancer; Pancreatic Adenocarcinoma; Pancreatic Cancer; pancreatic¿cancer¿cells; pathway; Pathway interactions; Patients; Pattern; Pb element; Peptidases; Peptide Hydrolases; Peptide Library; Peptides; peptidomimetics; Phage Display; Phages; Pharmaceutic Preparations; Pharmaceutical Preparations; Pharmacodynamics; Pharmacokinetics; pre-clinical; preclinical; preclinical study; Preclinical Testing; Preparation; Prevention; Principal Investigator; Property; Property, LOINC Axis 2; Proteases; Protein Binding Domain; Protein Binding Motif; Protein Family; Protein Trafficking; protein transport; Protein-Protein Interaction Domain; Proteinases; Proteins; Proteolytic Enzymes; proto-oncogene protein c-erbB-1; public health relevance; Publishing; Reagent; receptor; Receptor Protein; Receptor, EGF; Receptor, TGF-alpha; Receptor, Urogastrone; Receptors, Epidermal Growth Factor-Urogastrone; Relative; Relative (related person); research study; Role; Science of Chemistry; screening; Screening procedure; screenings; Secondary Neoplasm; Secondary Tumor; short hairpin RNA; shRNA; Signal Transduction; Signal Transduction Systems; Signaling; Site-Directed Mutagenesis; Site-Specific Mutagenesis; small hairpin RNA; small molecule libraries; social role; Staging; Surface; T7 Phage; Targeted DNA Modification; Targeted Modification; Techniques; Testing; Therapeutic; Therapeutic Intervention; therapeutic target; Tissue Arrays; Tissue Chip; Tissue Growth; Tissue Microarray; Titrations; Toxic effect; Toxicities; Traffickings, Protein; Transforming Growth Factor alpha Receptor; Translating; Translatings; translational approach; tumor; Tumor Cell Migration; tumor growth; United States; Vitamin H; Work; Xenograft Model
Relevance: Pancreatic adenocarcinoma (PaCA) is, almost invariably, a fatal disease. This work will focus on the prevention and therapeutic aspects of this cancer. Overall, our proposed experiments will define the regulatory role of GIPC and their downstream molecules that can influence the tumor growth and metastasis. The proposed study might define the mechanism of pancreatic cancer growth and progression and identify specific targets for therapeutic interventions for pancreatic adenocarcinoma where no current therapy is available
Project start date: 2010-04-07
Project end date: 2015-01-31
Budget start date: 1-FEB-2011
Budget end date: 31-JAN-2012
PFA/PA: PA-07-070
5R01CA150190-02 (2011): $552353
BEDSIDE-TO-BENCH RESEARCH TRAINING FOR PEDIATRIC INFECTIOUS DISEASES FELLOWS
R Mark, Professor
University Of Minnesota Twin Citiescity: Minneapolis country: United States (us)
Grant 1T32HD068229-01 from Eunice Kennedy Shriver National Institute Of Child Health & Human Development
Abstract: Our primary objective in this new T32 proposal, "Bedside-to-Bench Research Training for Pediatric Infectious Diseases Fellows" is to train highly skilled academic physicians in translational research relevant to infectious diseases of global importance to infants and children. The long-term goal of the program is to train pediatric physician-scientists who will become NIH-funded investigators skilled in multidisciplinary research initiatives. The title of our application reflects the emphasis that will be placed on preparing trainees to become pediatric infectious disease experts capable of managing complex patient populations prior to initiation of research training. This goal will be realized by providing trainees in the first year of fellowship with intense and diverse inpatient and outpatient clinical experiences in children´s hospitals in the Twin Cities. Following the first year, two years of research support will be provided for intense, mentored investigation of pathogens and pathogen-host interactions. Mentored training will take place at the recently opened Center for Infectious Diseases and Microbiology Translational Research (CIDMTR) at the University of Minnesota. The CIDMTR is a collaborative, multi-departmental facility consisting of investigators from the Departments of Microbiology, Pediatrics, and Internal Medicine. CIDMTR-affiliate faculty in the Department of Microbiology will also be mentors on the T32. Of the 27 investigators identified as mentors or prospective mentors, 11 are pediatricians or have a primary appointment in the Department of Pediatrics. A core group of senior faculty with independent NIH funding and training experience will be designated as primary mentors for this program. Investigators at the CIDMTR have strong translational research programs in infectious diseases of global health significance to children, including herpesviruses, malaria, tuberculosis, salmonella, and HIV infection. Additional opportunities will be available for T32 scholars to interface with experts in genomics, pharmacology, veterinary medicine, epidemiology, and clinical trials. Fellows elect to pursue research in a translational track, or a basic science track. Within both pathways, we have developed programs to ensure that fellows will acquire the scientific background and investigative skills necessary to conduct independent translational research. In either track, fellows have opportunities to pursue a graduate course work. Fellows may register as nonmatriculated graduate students in microbiology graduate course work, or pursue a novel Master´s in Translational Research program. Safeguards will ensure that graduate work does not interfere with protected time to perform research. Two MD post-doctoral fellow slots/year are requested. A Scholarship Oversight Committee and an external advisory committee of NIH-funded pediatric investigators will monitor progress of the T32 scholars. We anticipate that our trainees will be uniquely well prepared to lead translational investigative programs in pediatric infectious diseases in their academic research careers. Infectious diseases continue to extract considerable morbidity and mortality in infants and children globally. There is a major need to translate basic research findings into more effective disease control interventions, including preventative strategies such as vaccines, and novel antimicrobial interventions. A group of experienced mentors with extensive research experience will educate pediatric infectious diseases physicians in how to conduct translational research on infectious diseases that are of importance to children throughout the world
Keywords: bench to bedside; Childhood; Communicable Diseases; Research Training
Project start date: 2011-05-10
Project end date: 2016-04-30
Budget start date: 10-MAY-2011
Budget end date: 30-APR-2012
PFA/PA: PA-10-036
1T32HD068229-01 (2011): $132660
THE ROLE OF APE1 IN NEUROTOXICITY OF CANCER TREATMENTS
R Mark, Chair
Indiana Univ-purdue Univ At Indianapoliscity: Indianapolis country: United States (us)
Grant 5R01CA121168-04 from National Cancer Institute
Abstract: Numerous neurotoxic side effects of cancer treatments include cognitive dysfunction, commonly called chemobrain and peripheral neuropathy. The mechanisms for these side-effects and ways to protect neurons remain to be elucidated. The DNA base excision repair (BER) pathway including the abasic- endonuclease1/redox factor (Ape1/Ref-1 or Ape1) has been shown to be the major DNA repair pathway for oxidative and alkylating agent damage that occurs with chemotherapy and ionizing radiation (IR). Additionally, Ape1 interacts with a number of transcription factors, especially NFB, AP1 and p53 to regulate their function through redox signaling. In neurons, these transcription factors mediate the expression of a number of proteins involved in neuronal survival and altered excitability in response to injury and inflammation. Thus, Ape1 could play a critical role in maintaining homeostasis in neuronal tissue through its DNA repair and/or its redox function. The overall hypothesis of the proposed work is that Ape1 acts to enhance neuronal survival and function after injury by chemotherapy or IR and helps to maintain normal neuronal function by minimizing alkylation and oxidative damage to DNA as well as by regulating the activity of AP1, NFkB and p53. We will determine if Ape1 is involved in the neurotoxicity and neuronal function associated with chemotherapy and IR using primary rat central nervous system (hippocampal) and sensory neuronal cells (dorsal root ganglia or DRG). We will reduce or augment Ape1 expression in these neurons under normal and following the addition of cancer chemotherapeutic agents and IR and ascertain the effects on various aspects of neuronal function and survival. We also will use Ape1 mutant proteins that only have either the redox or repair functions or drugs that inhibit only the repair or redox activity to ascertain which functions of Ape1 are critical for neuroprotection/function. Finally, we will determine whether the redox activity of Ape1 alters the activity of downstream stress response factors such as AP1, NFkB and p53 in neuronal cultures following chemotherapy and IR.Experiments in this application will form the basis for mechanistic studies into neurocognitive ("chemobrain") and peripheral neuropathy experienced by patients following chemotherapy and IR. Understanding the mechanism for neuroprotection during cancer therapy will be critical in providing patients with neuroprotection that can help alleviate these serious side effects
Keywords: Accounting; Activator Protein-1; Active Oxygen; Adverse effects; Afferent Neurons; Alkylating Agents; Alkylation; Alkylators; Ammon Horn; Anti-Cancer Agents; Anti-Tumor Agents; Anti-Tumor Drugs; anticancer agent; anticancer drug; anticancer therapy; Antineoplastic Agents; Antineoplastic Drugs; Antineoplastics; Antiproliferative Agents; Antiproliferative Drugs; AP-1; AP-1 Enhancer-Binding Protein; AP1; AP1 protein; Autoregulation; base; Base Excision Repairs; biological adaptation to stress; biological signal transduction; Body Tissues; Cancer Drug; cancer therapy; Cancer Treatment; Cancers; Causality; Cell Communication and Signaling; Cell Signaling; Cells; Central Nervous System; chemobrain; chemotherapeutic agent; Chemotherapeutic Agents, Neoplastic Disease; chemotherapy; Clinical; Cognitive decline; Cognitive Disturbance; cognitive dysfunction; Cognitive function abnormal; Cognitive Impairment; cognitive loss; cognitively impaired; Common Rat Strains; Cornu Ammonis; cross-link; crosslink; Data; Deoxyribonucleic Acid; disease causation; disease etiology; disease/disorder etiology; disorder etiology; Disturbance in cognition; DNA; DNA Base Excision Repair; DNA Damage; DNA Damage Repair; DNA Injury; DNA Repair; DNA Repair Enzymes; DNA Repair Pathway; Dorsal Root Ganglia; dorsal root ganglion; drug/agent; Drugs; Electromagnetic Radiation, Ionizing; endonuclease; Enhancer-Binding Protein AP1; Etiology; experience; experiment; experimental research; experimental study; Exposure to; Ganglia, Spinal; gene product; Gene Transcription; Genes, p53; Genetic Alteration; Genetic Change; Genetic defect; Genetic Transcription; Genome; genome mutation; hippocampal; Hippocampus; Hippocampus (Brain); Homeostasis; Impaired cognition; Inflammation; INFLM; inhibitor; inhibitor/antagonist; Injury; injury response; Intracellular Communication and Signaling; Ionizing radiation; Maintenance; Maintenances; malignancy; Malignant Neoplasm Therapy; Malignant Neoplasm Treatment; Malignant Neoplasms; Malignant Tumor; Mammals, Rats; Measures; Mediating; Medication; Medulla Spinalis; Methods; Mitochondria; mitochondrial; mitochondrial genome; mutant; Mutation; neoplasm/cancer; Nerve Cells; Nerve Unit; Nervous System, CNS; Neural Cell; Neuraxis; Neurocognitive; Neurocyte; neuron toxicity; neuronal; neuronal survival; neuronal toxicity; Neurons; Neurons, Afferent; Neurons, Sensory; neuroprotection; neurotoxic; neurotoxicity; neurotransmitter release; overexpression; oxidation reduction reaction; Oxidation-Reduction; oxidative damage; Oxidative Stress; Oxygen Radicals; P53; pathway; Pathway interactions; Patients; Peripheral Nerve Diseases; Peripheral Nervous System; Peripheral Nervous System Diseases; Peripheral Nervous System Disorders; Peripheral Neuropathy; Pharmaceutic Preparations; Pharmaceutical Preparations; Physiological Homeostasis; Play; PNS Diseases; Preparation; prevent; preventing; Pro-Oxidants; Production; Proteins; Protocols, Treatment; Radiation-Ionizing Total; Rat; Rattus; reaction; crisis; Reactive Oxygen Species; Redox; Regimen; repair; repaired; Repairs, Base Excision; research study; response; response to injury; RGM; RNA Expression; RNA, Small Interfering; Role; Secondary to; Sensory; Sensory Cell Afferent Neuron; side effect; Signal Transduction; Signal Transduction Systems; Signaling; siRNA; Site; Slice; Small Interfering RNA; small molecule; social role; Spinal Cord; Spinal Ganglia; stress response; stress; reaction; Study Section; Therapeutic Effect; therapy adverse effect; Tissues; TP53; TP53 gene; Transcription; transcription factor; Transcription Factor AP-1; Transcription, Genetic; treatment adverse effect; Treatment Protocols; Treatment Regimen; Treatment Schedule; Treatment Side Effects; TRP53; Tumor Protein p53 Gene; Tumor-Specific Treatment Agents; Unscheduled DNA Synthesis; Viral Diseases; viral infection; Virus Diseases; virus infection; Work
Project start date: 2008-04-01
Project end date: 2013-01-31
Budget start date: 1-FEB-2011
Budget end date: 31-JAN-2012
PFA/PA: PA-07-070
5R01CA121168-04 (2011): $385578
INFLUENZA VACCINATION USING A MICRONEEDLE PATCH
R Mark, Professor
Georgia Institute Of Technologycity: Atlanta country: United States (us)
Grant 5U01EB012495-02 from National Institute Of Biomedical Imaging And Bioengineering
Abstract: Influenza is a major cause of morbidity and mortality worldwide. Although vaccination is the most effective Strategy to prevent infection, influenza vaccination coverage is insufficient and improved vaccine immunogenicity is needed. We propose development of a microneedle patch that is simple enough to increase vaccination coverage by enabling self-administration and specifically designed to improve immunogenicity by targeting dendritic cells in skin. Microneedles (MN) are micron-scale, solid needles that administer vaccine directly into skin using a simple, painless and minimally invasive approach. The patch is designed to enable skin vaccination with a patch application time of just seconds, generation of no sharp biohazardous waste, and antigen stability during storage without refrigeration. The goal of this milestone-driven project is to develop a MN patch for influenza vaccination and assess its safety and immunogenicity in a Phase I clinical trial. In Aim 1, based at Georgia Tech, we will design, formulate, and fabricate MN for simple, rapid application and long-term stability. In Aim 2, based at Emory, we will assess MN vaccination in three animal models with the goals of validating suitability for human trials and enhancing immunogenicity. Aim 3 will be achieved with external contractors and consultants to develop and validate cGMP manufacturing, conduct GLP preclinical studies and obtain an IND. This work will culminate in a Phase I clinical trial carried out in Aim 4 at Emory´s Hope Clinic to assess safety, tolerability, immunogenicity and acceptability of influenza vaccination using a MN patch. Finally, Aim 5 will be based at PATH to assess regulatory, cost and policy issues associated with self-administered influenza vaccination. Expected outcomes from this research are (i) development of a low-cost MN patch that administers influenza vaccine in a simple, rapid manner, (ii) identification of immunologic differences and advantages of MN-based influenza vaccination compared to IM vaccination that will be used to improve the MN patch, (iii) production of MN patches for influenza vaccination under cGMP and IND approval from FDA, (iv) completion of a Phase I clinical trial assessing safety, tolerability, immunogenicity and acceptability of influenza vaccination using MN and (v) identification of regulatory, cost and policy issues to guide development and future introduction of our MN patch into clinical practice. These outcomes not only impact influenza vaccination, but also provide a basis for delivery of other vaccines and drugs using MN patches. Despite annual influenza vaccination campaigns, CDC attributes 36,000 deaths and 226,000 hospitalizations per year in the US to influenza, with an associated cost of ~$100 billion per year. As a quantum advance, this project will develop a novel microneedle patch designed to increase vaccination coverage by enabling simple, self-vaccination and increase vaccine immunogenicity by targeting antigen delivery to skin. The proposed Phase I clinical trial will provide the first human study of this technology
Keywords: Address; Adopted; analytical method; Animal Model; Animals; Antibodies; antigen processing; Antigen Targeting; Antigen-Presenting Cells; Antigens; base; Cadaver; Cavia; Cells; Centers for Disease Control and Prevention (U.S.); Cessation of life; Clinic; clinical practice; Clinical Trials; Consultations; Contractor; Contracts; cost; Cost Effectiveness Analysis; Dendritic Cells; design; Development; Devices; Dose; Drug Formulations; Drug usage; Engineering; Exhibits; experience; Ferrets; Future; Generations; Goals; Good Clinical Practice; good laboratory practice; Hemagglutination; Hospitalization; Human; human study; human subject; Immune response; Immune system; Immunity; immunogenicity; Immunologics; improved; In Vitro; in vivo; Infection prevention; Influenza; Influenza vaccination; Influenza virus vaccine; Investigational Drugs; Investigational New Drug Application; Laboratories; Legal; Licensure; Logistics; Manufacturer Name; Measurement; Measures; Mediating; Medical; Medical Economics; Methods; minimally invasive; Monitor; Morbidity - disease rate; Mortality Vital Statistics; Mus; Needles; New Drug Approvals; novel; Outcome; Outcomes Research; Painless; Pathway interactions; Patients; Phase I Clinical Trials; Policies; policy implication; preclinical study; Process; Production; Prophylactic treatment; Protocols documentation; public health relevance; quantum; Refrigeration; Relative (related person); response; Route; Safety; Sagittaria; seasonal influenza; Self Administration; Self-Administered; Skin; social; Solid; System; Technology; Technology Transfer; Time; Universities; Vaccination; Vaccine Antigen; Vaccines; wasting; Work
Project start date: 2010-09-30
Project end date: 2015-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
PFA/PA: RFA-EB-09-003
5U01EB012495-02 (2011): $1503781
REGULATION OF CYCLOOXYGENASE-2 BY ERBB4 IN COLON EPITHELIAL CELLS
R Mark
Children´s Hospital Los Angelescity: Los Angeles country: United States (us)
Grant 1R03DK090295-01 from National Institute Of Diabetes And Digestive And Kidney Diseases
Abstract: Inflammatory bowel diseases are associated with an increased risk of early-onset colorectal cancer, resulting in great cost both economically and in patient morbidity and mortality. Intensive research has been focused on identifying signaling pathways active in both inflammation and cancer, which may thus be targets of therapy or chemoprevention. The ErbB4 tyrosine kinase, a member of the epidermal growth factor-related ErbB growth factor receptor family, is expressed at elevated levels in colitis and in a subset of human colorectal cancers. This receptor is thus a candidate participant in colitis-associated tumorigenesis. We recently demonstrated that ErbB4 expression and activity are induced by tumor necrosis factor, and that ErbB4 in turn promotes colon epithelial cell survival in the presence of pro-inflammatory cytokines. Preliminary data developed for this application further show that ErbB4 promotes colon epithelial cell transformation in both in vitro and in vivo models. Furthermore, ErbB4-induced cell survival and transformation are associated with increased mRNA stability and protein levels for the prostaglandin synthase cyclooxygenase-2 (COX-2). Thus, this application proposes to test the hypothesis that ErbB4 promotes colon epithelial cell survival and transformation in the inflammatory milieu through a COX-2-dependent mechanism. Planned experiments will use coordinated in vitro (signal transduction analysis, apoptosis & and colony formation assays) and in vivo (nude mouse xenograft tumor formation assays) approaches to (1) Identify signaling pathways involved in ErbB4-induced COX-2 expression, and (2) investigate cooperation between ErbB4 and COX-2 in colon epithelial cell survival and transformation. Patients with inflammatory bowel diseases are at elevated risk for the development of colorectal cancer, but the exact molecular mechanisms underlying this increased risk are poorly understood. The proposed studies will advance our mechanistic understanding of cellular signaling in inflammation and carcinogenesis, with implications for the development of novel clinical therapies targeting ErbB4 and COX-2. NOTE The criteria scores and the critiques given below were provided by the reviewers assigned to this application. These do not necessarily reflect the positions of the reviewers at the close of the group discussion or the final majority opinion of the group, although the reviewers were asked to amend their criteria scores and critiques if their positions changed during the discussion. Please note that the criteria scores are not averaged in arriving at the final overall impact scores. If the reviewers have not changed their criteria scores after the discussion, those shown in the critiques may reflect the opinion of the reviewers before the meeting. The Resume and other initial sections of the summary statement are the authoritative representations of the final outcome of the group discussion. If there is any discrepancy between the reviewers´ commentaries and the priority/impact score on the face page of this summary statement, the priority/impact score should be considered the most accurate representation of the final outcome of the group discussion
Keywords: 1-Phosphatidylinositol 3-Kinase; Ablation; Agar; Apoptosis; betacellulin; Biological Assay; cancer cell; carcinogenesis; Cell Survival; cell transformation; Cells; Chemoprevention; Clinical; Colitis; Colon; colon carcinogenesis; Colon Carcinoma; Colorectal Cancer; cost; Critiques; cyclooxygenase 2; cytokine; Data; Development; DTR gene; early onset; Epidermal Growth Factor; Epidermal Growth Factor Receptor; Epiregulin; Epithelial Cells; ErbB4 gene; Face; Family; Funding; Genetic; Goals; Growth; Growth Factor Receptors; Half-Life; Human; human FRAP1 protein; In Vitro; in vivo; in vivo Model; Individual; Inflammation; Inflammatory; Inflammatory Bowel Diseases; Ligands; Malignant Neoplasms; Mediator of activation protein; meetings; member; Messenger RNA; metaplastic cell transformation; Molecular; Morbidity - disease rate; Mortality Vital Statistics; mRNA Stability; Mucous Membrane; Mus; North America; novel; Nude Mice; Outcome; overexpression; Participant; Pathway interactions; Patients; Positioning Attribute; Prevention; Prostaglandin-Endoperoxide Synthase; protein expression; Protein Tyrosine Kinase; Proteins; PTGS2 gene; public health relevance; Published Comment; receptor; Receptor Protein-Tyrosine Kinases; Regulation; Research; research study; response; Risk; Role; Signal Pathway; Signal Transduction; Testing; Tumor Necrosis Factor-alpha; Tumor Necrosis Factors; tumor xenograft; tumorigenesis; Xenograft procedure; young adult
Relevance: Relevance Patients with inflammatory bowel diseases are at elevated risk for the development of colorectal cancer, but the exact molecular mechanisms underlying this increased risk are poorly understood. The proposed studies will advance our mechanistic understanding of cellular signaling in inflammation and carcinogenesis, with implications for the development of novel clinical therapies targeting ErbB4 and COX-2
Project start date: 2011-04-01
Project end date: 2013-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: PAR-09-230
1R03DK090295-01 (2011): $80000
REGULATED GENETICS STUDIES OF MEMORY FORMATION
R Mark, Associate Professor
Scripps Research Institutecity: La Jolla country: United States (us)
Grant 5R01MH057368-13 from National Institute Of Mental Health
Abstract: Impairments in memory function can range from the moderately inconvenient benign forgetfulness with normal aging to the devastating losses associated with Alzheimer´s disease. In addition, alterations in the mechanisms that underlie normal memory are thought to underlie psychiatric disorders such as depression and post-traumatic stress disorder and may contribute to relapse in addiction. This grant uses animal models to identify the cellular and molecular mechanisms of memory formation. We use a genetic technique that allows us to introduce genes into specific parts of the brain and to turn them on or off at different times either during learning or during memory retrieval. For example, in one study we looked at a mouse model of a human genetic disorder (Rubenstein Taybi Syndrome) associated with both developmental abnormalities and severe cognitive impairment. One question that we addressed was whether the cognitive defects found in adults were due a defect in brain development or due to abnormal gene function in the adult brain. By inducing the genetic lesion only in the adult we could show that it produced learning and memory defects acutely and that these defects could be reversed by turning off the defective gene. We also showed that the behavioral defects could be reversed in this mouse model with a drug that targeted the biochemical defect. We apply this approach to a number of different cellular signaling pathways in neurons that are thought to underlie memory. We also use a genetic approach to analyze the anatomical structure of memory. Using this approach we hope to identify the individual neurons that contribute specific memories. We use this to address questions such as "Are the neurons activated during learning reactivated during recall?" and "Does the pattern of neuronal activation change as memories consolidate over time?" By studying the specific cellular circuits that underlie memory we hope to more readily identify the underlying cellular and molecular mechanisms. PUBLIC HEALTH RELEVANCE This grant examines the mechanisms of learning and memory, from how brain cells are activated with learning to what genes and molecules in the cells are important for the formation of memories. We do these studies in mice because they are surprisingly similar to humans both genetically and in terms of brain structure. Memory is a basic element of brain function that is altered in many disease states from the degenerative diseases of aging like Alzheimer´s to psychiatric disorders such as schizophrenia and post-traumatic stress disorder. One of the genes we work on is the mouse analogue of a gene that produces a form of mental retardation in humans
Keywords: 21+ years old; addiction; Address; Adult; adult human (21+); Aging; Alzheimer; Alzheimer disease; Alzheimer sclerosis; Alzheimer syndrome; Alzheimer`s; Alzheimer`s Disease; Alzheimers Dementia; Alzheimers disease; Ammon Horn; Amygdala; Amygdaloid Body; amygdaloid nuclear complex; Amygdaloid Nucleus; Amygdaloid structure; analog; Anatomic; Anatomical Sciences; Anatomy; anatomy; Animal Model; Animal Models and Related Studies; Animals; Behavioral; Benign; Biochemical; biological signal transduction; Brain; brain cell; Brain Part; Cell Communication and Signaling; Cell Signaling; Cells; Cognitive; Cognitive decline; Cognitive Disturbance; cognitive dysfunction; Cognitive function abnormal; Cognitive Impairment; cognitive loss; cognitively impaired; Cornu Ammonis; Defect; degenerative condition; degenerative disease; Degenerative Disorder; dementia of the Alzheimer type; dementia praecox; Dementia, Alzheimer Type; Dementia, Primary Senile Degenerative; Dementia, Senile; Depression; Development; Disease; disease/disorder; Disorder; Disturbance in cognition; Drug Delivery; Drug Delivery Systems; Drug Targeting; Drug Targetings; Elements; Encephalon; Encephalons; Fore-Brain; Forebrain; Gene Expression; gene function; Genes; Genetic; Genetic Condition; Genetic Diseases; genetic disorder; Genetic Techniques; Grant; Health; Hereditary Disease; hereditary disorder; hippocampal; Hippocampus; Hippocampus (Brain); Hour; Human; Human Genetics; Human, Adult; Human, General; Impaired cognition; Impairment; Individual; Intracellular Communication and Signaling; Learning; Lesion; long term memory; Mammals, Mice; Mammals, Rodents; Man (Taxonomy); Man, Modern; Medial; Memory; memory recall; memory retrieval; Mental Depression; Mental disorders; Mental health disorders; mental illness; Mental Retardation; Mice; model organism; Molecular; Molecular Disease; molecular marker; mouse model; Murine; Mus; Nature; Nerve Cells; Nerve Unit; Nervous System, Brain; Neural Cell; Neurocyte; neuronal; neuronal patterning; Neurons; Neuroses, Post-Traumatic; Neuroses, Posttraumatic; normal aging; Nuclear; otopalatodigital (OPD) syndrome I; otopalatodigital syndrome I; Performance; Phase; Post-Traumatic Stress Disorders; primary degenerative dementia; Primary Senile Degenerative Dementia; Process; Prosencephalon; Psychiatric Disease; Psychiatric Disorder; psychological disorder; PTSD; recruit; Recruitment Activity; Relapse; Research; Retrieval; Rodent; Rodentia; Rodentias; Role; Schizophrenia; schizophrenic; Schizophrenic Disorders; Science of Anatomy; Senescence; senescent; senile dementia of the Alzheimer type; Signal Pathway; Signal Transduction; Signal Transduction Systems; Signaling; social role; Stress Disorders, Post-Traumatic; Stress Disorders, Posttraumatic; Structure; Synapses; Synaptic; System; System, LOINC Axis 4; Taybi syndrome; Technics, Genetic; temporal cortex; Temporal Lobe; temporal lobe/cortex; Testing; Tetracycline Antibiotic; Tetracyclines; Time; Training; Transgenes; Transgenic Mice; traumatic neurosis; Unspecified Mental Disorder; Work
Project start date: 1997-07-01
Project end date: 2012-12-31
Budget start date: 1-JAN-2011
Budget end date: 31-DEC-2011
PFA/PA: PA-07-070
5R01MH057368-13 (2011): $345364
VACCINE-MEDIATED TARGETING OF VIRAL IL10 TO CONTROL HCMV SHEDDING AND REINFECTION
R Mark
University Of California Daviscity: Davis country: United States (us)
Grant 1R01AI097629-01 from National Institute Of Allergy And Infectious Diseases
Abstract: Immune responses to human cytomegalovirus (HCMV) infection in immunocompetent hosts present paradoxes with potentially devastating ramifications for those without immune competency. The long quest for a protective HCMV vaccine has been impeded by multiple factors, including two contradictions about HCMV natural history. (1) HCMV is considered to be a virus with low disease potential in immunocompetent hosts. Yet, the virus efficiently maintains a lifelong persistence in the presence of those immune responses that limit clinical outcomes. A hallmark of HCMV persistence is the reactivation of latent viral genomes and shedding of virus. Horizontal transmission represents an infectious threat to those at-risk for primary HCMV infection, particularly fetuses borne by mothers without prior HCMV immunity. Accumulating evidence highlights another ambiguity about HCMV immunity. (2) The immune responses to HCMV generated during primary and long-term infection, which protect against viral sequelae, are incompletely protective against reinfection with horizontally transmitted virions. It is well- established that women with prior immunity can be reinfected with antigenic variants of HCMV that can then be transmitted to their fetuses. This proposal hypothesizes that there is a key nexus linking virus-host interactions, persistence, and reinfection that is susceptible to vaccine- mediated intervention. Specifically, HCMV modulation of host immunity through the functionality of the HCMV-encoded interleukin-10 protein (cmvIL10), enables both viral reactivation and systemic spread of virions beyond sites of reinfection. HYPOTHESIS post-exposure increases of neutralizing antibody (NAb) titers to cmvIL10 in HCMV-infected individuals will (1) reduce HCMV shedding and (2) increase resistance to reinfection. This study extends our work on the in vitro functionality of cmvIL10 and the in vivo modulation of host immunity by rhesus CMV (RhCMV)-encoded IL-10 (rhcmvIL10). Aim 1) Quantification of RhCMV shedding in RhCMV- infected monkeys following immunization with functionally inactive rhcmvIL10. Aim 2) Comparison of RhCMV reinfection in RhCMV-immune monkeys that differ in their NAb titers to rhcmvIL10. Aim 3) Characterization of rhcmvIL-10-induced alterations to host immunity. The goal of this proposal is the shift the paradigm for the prevention of congenital HCMV infection by expanding the target population for an HCMV vaccine beyond just women without preconceptional HCMV immunity. Targeting those who shed virus to reduce shedding and also targeting those women with preconceptional immunity to reduce reinfection would greatly reduce the rate of congenital infection
Keywords: acquired immunity; Age; Antibody Formation; Antigens; Antiviral Agents; Attenuated; attenuation; base; Chronic; Clinical; congenital infection; cost; Cytomegalovirus; Cytomegalovirus Infections; Cytomegalovirus Vaccines; cytotoxic; Development; Disease; Equilibrium; Female of child bearing age; Fetus; Frequencies (time pattern); Gap Junctions; Goals; Herpesviridae; high risk; Horizontal Disease Transmission; Immune; Immune response; Immunity; Immunization; Immunocompetent; In Vitro; in vivo; Individual; Infection; Interleukin-10; Intervention; Lead; Licensing; Link; Liquid substance; Macaca mulatta; Mediating; Memory; Modeling; Monkeys; Mothers; mucosal site; Natural History; Neurologic; neutralizing antibody; Outcome; Pathogenesis; Population; Pregnancy; prevent; Prevention; Production; Proteins; Resistance; Resolution; response; Risk; Saliva; Seroprevalences; Site; Staging; Systemic infection; Target Populations; Testing; transmission process; Urine; Vaccination; Vaccine Design; Vaccines; Variant; Viral; Viral Genome; Virion; Virus; virus host interaction; Virus Shedding; Woman; Work
Relevance: The goal of this proposal is the shift the paradigm for the prevention of congenital HCMV infection by expanding the target population for an HCMV vaccine beyond just women without preconceptional HCMV immunity. Targeting those who shed virus to reduce shedding and also targeting those women with preconceptional immunity to reduce reinfection would greatly reduce the rate of congenital infection
Project start date: 2011-12-01
Project end date: 2016-11-30
Budget start date: 1-DEC-2011
Budget end date: 30-NOV-2012
1R01AI097629-01 (2012): $624587
STRUCTURE STUDIES ON PROTEINS THAT MODULATE IL-10 ACTION
R Mark, Associate Professor
University Of Alabama At Birminghamcity: Birmingham country: United States (us)
Grant 5R01AI047300-10 from National Institute Of Allergy And Infectious Diseases
Abstract: IL-10 is a multifunctional cytokine that regulates complex immune responses. Its normal function is to protect the host from uncontrolled inflammatory responses. However, IL-10 has also been implicated as an autocrine growth factor in several B-cell malignancies and stimulates B-cell mediated autoimmune disease. The normal and pathological functions of IL-10 are initiated by IL-10 receptor engagement and assembly into a signaling competent IL-10/IL-10R1/IL-10R2 complex. In addition to cellular IL-10 (clL-10), Epstein Barr virus (EBV) and cytomegalovirus (CMV) harbor viral IL-10 mimics (ebvlL-10 and cmvlL-10) in their genomes that activate the IL-10 signaling complex, resulting in overlapping and distinct biological properties. In the past funding period, we determined crystal structures of clL-10, cmvlL-10, and ebvlL-10 bound to the high affinity IL-10R1 chain. In this proposal we will use surface plasmon resonance, site-directed mutagenesis, NMR spectroscopy, X-ray crystallography, and FRET methods to study cellular and viral IL-10 receptor interactions. These studies will be complemented by the analysis of the cellular IL-10 homologs IL- 22 and IL-20. The long term goal of this proposal is to derive a quantitative structural/computational model of IL-10 family signaling that might explain how cellular and viral IL-10s shape immune responses and allow the rational design of cytokine therapeutics
Keywords: Affinity; autocrine; Autoimmune Diseases; B lymphoid malignancy; B-Lymphocytes; base; Binding (Molecular Function); Binding Sites; Biological; Biology; Cell surface; Cell Surface Receptors; cell type; Cellular Structures; Complement; Complex; Computer Simulation; Congenital Abnormality; Crystallography; cytokine; Cytomegalovirus; Cytomegalovirus Infections; Data; defined contribution; design; Employee Strikes; Exhibits; Family; Fluorescence Resonance Energy Transfer; Funding; Genome; Goals; Growth Factor; Homologous Gene; Human; Human Herpesvirus 4; IL10RB gene; Immune response; improved; Infection; Inflammatory Response; Interferons; interleukin 20; Interleukin-10; interleukin-22; Kinetics; Measurable; Measures; Mediating; metaplastic cell transformation; Methods; mutant; NMR Spectroscopy; programs; Property; Protein Dynamics; Proteins; receptor; receptor binding; Research Personnel; response; Shapes; Signal Transduction; Site-Directed Mutagenesis; Solutions; Structural Models; Structure; Surface Plasmon Resonance; System; Techniques; Therapeutic; three-dimensional modeling; Viral; Virus; Virus Diseases; X ray diffraction analysis; X-Ray Crystallography
Project start date: 2000-04-01
Project end date: 2012-04-30
Budget start date: 1-MAY-2011
Budget end date: 30-APR-2012
5R01AI047300-10 (2011): $316851
ETHANOL ON OVERNIGHT GLUCOSE REGULATION IN DIABETES
R Mark
University Of New Mexicocity: Albuquerque country: United States (us)
Grant 5R01DK061990-05 from National Institute Of Diabetes And Digestive And Kidney Diseases
Abstract: Hypoglycemia is the principal barrier to the achievement of target glycemic goals in type 2 diabetes. Alcohol consumption is very prevalent in our society and a proven cause of hypoglycemia. Population studies suggest that elderly, insulin requiring type 2 diabetes patients are particularly vulnerable to severe hypoglycemia and that this problem accounts for an estimated $50 million or more in healthcare costs in the USA each year. We hypothesize that low dose ethanol significantly increases the vulnerability to overnight hypoglycemia and impairs the recovery of plasma glucose in elderly, insulin requiring patients with type 2 diabetes. Our preliminary studies suggest that low dose ethanol impairs recovery from day time insulin-induced hypoglycemia in type 2 diabetes patients but not in age matched healthy control subjects. The proposed studies will examine the effects of low dose ethanol on overnight glucose regulation in elderly, insulin requiring type 2 diabetes patients and will establish the mechanism of these impairments through a series of systematic evaluations. Specifically, these studies will document suppression of the dawn phenomenon by ethanol, and/or exacerbation of a deficient counterregulatory response to hypoglycemia during sleep, especially growth hormone. Specific mechanisms for the suppression of growth hormone to be examined include that evening ethanol (3) inhibits peak overnight ghrelin secretion and/or (4) reduces pituitary sensitivity to GHRH. Additionally, these studies will characterize (5) the dose response characteristics of ethanol on overnight glucose homeostasis and will (6) carefully evaluate the effect of the timing of ethanol administration in relation to meal ingestion on overnight hypoglycemic vulnerability. To address these aims, we will assess the effect of moderate doses of orally administered ethanol or placebo on overnight growth hormone release, ghrelin, total IGF- 1, free IGF- 1, insulin-like growth factor binding protein 1 (IGFBP- 1) concentrations, glucose production and other parameters of glucose homeostasis among elderly control subjects versus elderly, insulin requiring subjects with type 2 diabetes. These important studies will provide a scientific basis for the prevention of overnight hypoglycemia (and the attendant cost savings) by providing mechanistic insights into the causes of nocturnal hypoglycemia
Keywords: Absolute ethanol; Accounting; Achievement; Achievement Attainment; Address; adult onset diabetes; advanced age; AFBP; Age; Aged 65 and Over; Agonist; Alcohol consumption; Alcohol Drinking; alcohol ingestion; alcohol intake; alcohol product use; alcohol use; Alcohol, Ethyl; alcoholic beverage consumption; alcoholic drink intake; Alpha-Pregnancy-Associated Endometrial Globulin; Amniotic Fluid Binding Protein; antihyperglycemic; base; Binding Protein-25; Binding Protein-26; Binding Protein-28; blood glucose regulation; Blood Plasma; Characteristics; Chemotherapy-Hormones/Steroids; Classification; Cost Savings; D-Glucose; day; Dextrose; diabetes; Diabetes Mellitus; Diabetes Mellitus, Adult-Onset; Diabetes Mellitus, Ketosis-Resistant; Diabetes Mellitus, Non-Insulin-Dependent; Diabetes Mellitus, Noninsulin Dependent; Diabetes Mellitus, Slow-Onset; Diabetes Mellitus, Stable; Diabetes Mellitus, Type 2; Diabetes Mellitus, Type II; Dose; Elderly; Elderly, over 65; elders; Endocrine Gland Secretion; Ethanol; ethanol consumption; ethanol drinking; ethanol ingestion; ethanol intake; ethanol product use; ethanol use; ETOH; EtOH drinking; etoh use; Evaluation; geriatric; GHN; ghrelin; GHRH; GHRH(1-29)NH2; Glucose; glucose control; glucose homeostasis; glucose production; glucose RA; glucose rate of appearance; glucose regulation; Goals; Grain Alcohol; GRF(1-29)NH2; GRH; Growth Hormone; Growth Hormone 1; Growth Hormone Independent-Binding Protein; Growth Hormone Releasing Hormone, human; Growth Hormone-Releasing Factor; Growth Hormone-Releasing Factor(1-29)Amide; Growth Hormone-Releasing Hormone; Health Care Costs; Health Costs; Healthcare Costs; hGHN; hGHRH(1-29)NH2; Hormones; Human Pancreatic Growth Hormone-Releasing Factor; Humulin R; Hypoglycemia; hypoglycemic; Hypoglycemic Agents; Hypoglycemic Drugs; hypoglycemic episodes; Hypoglycemics; Hypophysis; Hypophysis Cerebri; IBP-1; IGF; IGF-Binding Protein 1; IGFBP-1; IGFBP1; Impairment; Ingestion; insight; Insulin; Insulin (ox), 8A-L-threonine-10A-L-isoleucine-30B-L-threonine-; Insulin, Regular; Insulin-Like Growth Factors; Insulin-Like Growth-Factor Binding Protein 1; insulinlike growth factor; ketosis resistant diabetes; late life; later life; maturity onset diabetes; Maturity-Onset Diabetes Mellitus; Methylcarbinol; MODY; Nervous System, Pituitary; NIDDM; Non-Insulin Dependent Diabetes; Non-Insulin-Dependent Diabetes Mellitus; Novolin R; older adult; older person; Oral; Patients; PBO; Pituitary; Pituitary Gland; Pituitary Growth Hormone; Placebos; placental protein 12; Plasma; Population Study; PP12; Prevention; Recovery; response; Reticuloendothelial System, Serum, Plasma; Saving, Cost; senior citizen; Series; Sermorelin; Serum, Plasma; sham therapy; Sham Treatment; Sleep; Societies; Somatocrinin; Somatoliberin; Somatomedins; somatotropic hormone; Somatotropin; Somatotropin-Releasing Hormone; Somatotropin-Releasing-Hormone(1-29)Amide; STH; Sulfation Factor; Systematics; T2D; T2DM; Therapeutic Hormone; Time; Type 2 diabetes; Type II diabetes
Project start date: 2004-02-01
Project end date: 2011-04-30
Budget start date: 1-JAN-2008
Budget end date: 30-APR-2011
5R01DK061990-05 (2008): $262040
SURGICAL STUDIES OF GI PEPTIDES - MECHANISMS OF ACTION
R Mark, Associate Professor
University Of Texas Medical Br Galvestoncity: Galveston country: United States (us)
Grant 5R01DK048345-14 from National Institute Of Diabetes And Digestive And Kidney Diseases
Abstract: Gastrointestinal (GI) cancers continue to be a significant and challenging clinical problem. Surgical resection is the mainstay for cure of GI malignancies; however, cure can only be achieved if the tumors are localized and have not spread to lymph nodes and distant organs. Increased understanding of the molecular mechanisms controlling GI cancer cell growth is required for the development of novel thera-peutic strategies to be used in combination with surgical resection. GI peptide hormones can stimulate the growth of normal and neoplastic gut tissues. For years, our studies have focused on determining the molecular mechanisms by which the gut peptide, gastrin (G-17), and its cognate receptors, regulate cell growth. Recently, we have discovered a novel splice variant of the CCK-B/gastrin receptor called CCK-BRi4sv that is expressed in colonic and pancreatic cancers, but not the normal tissues. CCK-BRi4sv exhibit distinctly different signaling properties when compared to the previously characterized wild-type CCK-BR (CCK-BRwt) including G-17-independent stimulation of cell growth, regulation of intracellular Ca 2+and subcellular trafficking. Also, we found that mitogen-activated protein kinases (MAPKs) play a key role in CCK-BR-mediated signaling both before and after agonist stimulation. MAPK kinase (MEK) regulates CCK-BRwt sensitivity to G-17 stimulation and mediates the effects of G-17 stimulation on downstream effectors. Finally, we found that CCK-BRi4sv and CCK-BRwt mediate G-17-induction of COX-2 gene expression. Based on our findings, we hypothesize that CCK-BR variants regulate GI cell growth by both agonist-dependent and -independent mechanisms, and that MAPKs play a central role in receptor-mediated regulation of cell growth by modulating the sensitivity of the receptor to agonist stimulation and by acting as downstream effectors of agonist-induced signal transduction. To examine these hypotheses, we have planned experiments with three Specific Aims. Aim 1 To define the mechanisms of CCK-BRwt and CCK-BRi4sv internalization and intracellular receptor trafficking. Aim 2 To define the role of MAPKs in CCK-BRwt- and CCK-BRi4sv-mediated intracellular signal transduction. Aim 3 To determine the effects of CCK-BRi4sv and CCK-BRwt expression on gene expression
Keywords: Abscission; Act-2; ACT2; Agonist; Aminoacetic Acid; Anthelone U; AT744.1; base; beta-Urogastrone; biological signal transduction; Body Tissues; cancer cell; Cancer Cell Growth; Cancer of the Fundus of the Stomach; Cancer of the Gastric Body; Cancer of the Gastric Cardia; Cancer of the Gastric Fundus; Cancer of the Gastric Pylorus; Cancer of the Gastrointestinal Tract; Cancer of the Pylorus of the Stomach; Cancers; CCK; CCK-B Receptor; CCK-BR; CCK2 Receptor; CCKBR; CCKRB; CCL4; CCL4 gene; Cell Communication and Signaling; cell growth; cell growth regulation; Cell membrane; Cell Signaling; Cell Surface Receptors; cell type; Cells; Cellular Expansion; Cellular Growth; Cellular Regulation; Cholecystokinin; Cholecystokinin B Receptor; Cholecystokinin Receptor; Cholecystokinin Type B Receptor; Cholecystokinin-2 Receptor; CKK-2 Receptor; Clinical; Cloning; Cola; Colon; colon polyp; Colonic Polyps; Colorectal Cancer; COX-2; COX2; CSBP1; CSBP2; CSPB1; Cytoplasmic Membrane; Data; Development; digestive neoplasm; Digestive Tumor; Distant; Doctor of Medicine; EC 2.7.2-; Effectiveness; EGF; Epidermal Growth Factor; Epidermal Growth Factor-Urogastrone; ERK 2; ERK MAP Kinases; Excision; Exhibits; EXIP; experiment; experimental research; experimental study; Extirpation; Extracellular Signal Regulated Kinases; extracellular signal related kinase; Extracellular Signal-Regulated Kinase 2; Extracellular Signal-Regulated Kinases; Extracellular Signal-Regulated MAP Kinases; Fibroblasts; Funding; G Protein-Complex Receptor; G-Protein-Coupled Receptors; GASR; Gastric Cancer; Gastric Carcinoma; Gastrins; gastrointestinal; Gastrointestinal Cancer; Gastrointestinal Neoplasms; Gastrointestinal Tract, Pancreas; Gastrointestinal Tumor; Gene Expression; Generalized Growth; Genus Cola; GI Neoplasm; GI Tumor; Glycine; Growth; hCOX-2; Human; Human Urinary Gastric Inhibitor; Human, General; innovate; innovation; innovative; Intervening Sequences; Intracellular Communication and Signaling; Introns; Invasive; Investigators; LAG1; Ligands; Localized; lymph gland; Lymph node proper; lymph nodes; M.D.; malignancy; Malignant Cell; Malignant Gastric Neoplasm; Malignant Gastric Tumor; Malignant Gastrointestinal Neoplasm; Malignant neoplasm of gastrointestinal tract; Malignant neoplasm of pancreas; Malignant neoplasm of stomach; Malignant Neoplasms; Malignant Pancreatic Neoplasm; malignant stomach neoplasm; Malignant Tumor; Malignant Tumor of the Stomach; Man (Taxonomy); Man, Modern; MAP kinase; MAP Kinase 1; MAP Kinase 2; MAP Kinase Kinases; MAP-ERK Kinase; MAPK; MAPK ERK Kinases; MAPK Kinases; MAPK1; MAPK1 Mitogen-Activated Protein Kinase; MAPK14; MAPK14 gene; MAPK2 Mitogen-Activated Protein Kinase; MAPKKs; Mediating; MEKs; MIP-1-beta; MIP1B; Mitogen Activated Protein Kinase 1; Mitogen-Activated Protein Kinase 2; Mitogen-Activated Protein Kinase Kinases; Mitogen-Activated Protein Kinases; Modeling; Molecular; Mxi2; Neoplasm of the Digestive Tract; Neoplasm of the Gastrointestinal Tract; Neoplasm of the GI Tract; neoplasm/cancer; neoplastic; new approaches; Normal Cell; Normal Tissue; Normal tissue morphology; novel; novel approaches; novel strategies; novel strategy; Numbers; ontogeny; Operation; Operative Procedures; Operative Surgical Procedures; Organ; p38; p38 MAPK Gene; p38Alpha; p42 MAP Kinase; p42 MAPK; p42(Mapk) Kinase; p42(Mitogen-Activated Protein Kinase); P42MAPK; Pancreas; Pancreas Cancer; Pancreatic; Pancreatic Cancer; Pancreozymin; pathway; Pathway interactions; peptide hormone; Peptides; PGG/HS; PGHS-2; PHS-2; Plasma Membrane; plasmalemma; Play; Pre-Malignant; precancerous; Premalignant; PRKM1; PRKM14; PRKM15; programs; Programs (PT); Programs [Publication Type]; Property; Property, LOINC Axis 2; PTGS2; PTGS2 gene; Rate; receptor; receptor internalization; Receptor Mediated Signal Transduction; Receptor Protein; receptor sensitivity; Receptors, CCK; Receptors, Gastrin; Receptors, Pancreozymin; Regulation; Removal; Research Personnel; research study; Researchers; resection; Reticuloendothelial System, Lymph Node; RNA Splicing; Role; SAPK2A; SCYA4; Signal Transduction; Signal Transduction Systems; Signaling; social role; Splicing; Stomach Cancer; Stomach Carcinoma; surgery; Surgical; Surgical Interventions; Surgical Procedure; Surgical Removal; Systemic disease; Therapeutic; Threonine/Tyrosine Protein Kinase; Tissue Growth; Tissues; trafficking; tumor; Tumor of the Digestive Tract; Tumor of the Gastrointestinal Tract; Tumor of the GI Tract; Urogastrone; Uropancreozymin; Variant; Variation
Project start date: 1994-08-01
Project end date: 2011-07-31
Budget start date: 1-AUG-2007
Budget end date: 31-JUL-2011
5R01DK048345-14 (2007): $467010
Sponsored Links Excellgen http://Excellgen.com
ENDOCRINOLOGY OF MOSQUITO REPRODUCTION
R Mark, Professor
University Of Georgia (uga)city: Athens country: United States (us)
Grant 5R01AI033108-18 from National Institute Of Allergy And Infectious Diseases
Abstract: Ecdysteroid hormones are key regulators of development and reproduction in the mosquitoes, Aedes aegypti and Anopheles gambiae. The proposed research will focus on the molecular characterization and expression of two types of peptide hormones involved in the activation of ecdysteroid hormone production in females of these species. First, the secretion of ovary ecdysteroidogenic hormone (OEM) and insulin-like peptides (ILPs) will be characterized. Second, their receptors and signalling pathways will be delineated. Third, activation of ecdysteroid biosynthesis by peptide hormones provides an experimental approach to identify .new proteins and their genes specifically involved in this essential process, which is incompletely known for insects. Indeed, the mosquito ovary is an exceptionally robust model for such discoveries. Peptide-treated and control ovaries will be compared by proteomic analysis to reveal translational and post- translational changes in particular proteins that then will be identified in genome databases. In addition, suppressive subtractive hybridization of cDNAs from experimental ovaries will be used to obtain a cDNA library that will be examined for novel and known gene products transcribed in response to peptide hormone activation of ecdysteroid biosynthesis. Candidate genes and proteins then will be subjected to quantitative PCR and immunoassays, and to RNA interference knockdown in vivo and in bioassays to substantiate the observed changes. The proposed work has practical import for public health in that the identification of mosquito-specific enzymes involved in ecdysteroid biosynthesis may provide targets for novel substrate poisons. As well, knowledge of peptide hormones and their receptors may allow design of bioactive, stable peptide mimics that disrupt key regulatory processes. Such chemicals may lead to the development of new pesticides that provide cost-effective and strategic reductions in mosquito populations and lessen their nuisance and ability to transmit pathogens
Keywords: Address; Aedes; Aedes (genus); Affinity; Anabolism; Anopheles gambiae; Assay; Binding; Binding (Molecular Function); Binding Proteins; Bioassay; Biologic Assays; Biological Assay; biosynthesis; Blood; bovid; bovine; Bovine Species; Brain; Candidate Disease Gene; Candidate Gene; Cattle; cDNA; cDNA Library; Cells; Chemicals; Chemotherapy-Hormones/Steroids; communicable disease transmission; Complementary DNA; Complex; cost effective; cow; Culicidae; Deposit; Deposition; design; designing; Development; Disease; disease transmission; disease/disorder; Disorder; DNA, Complementary; Dose; Ecdysteroids; egg; Encephalon; Encephalons; Endocrine Gland Secretion; Endocrinology; Enzymes; Fat Body; feeding; Female; Funding; gene product; Gene Proteins; GeneHomolog; Genes; Genital System, Female, Ovary; genome database; GFAC; Goals; Growth Agents; Growth Factor; Growth Factors, Proteins; Growth Substances; heavy metal lead; heavy metal Pb; Homolog; Homologous Gene; Homologue; Hormonal; Hormones; Humulin R; Immunoassay; in vivo; infectious disease transmission; Ingestion; Insecta; Insects; Insulin; Insulin (ox), 8A-L-threonine-10A-L-isoleucine-30B-L-threonine-; Insulin, Regular; Invertebrates, Insects; Knowledge; Lead; Ligand Binding Protein; Metabolism and Endocrinology; Modeling; Molecular; Molecular Interaction; Mosquitoes; Names; Nervous System, Brain; Neurohormones; Neuropeptides; novel; Novolin R; Nutrient; Ovary; Parasites; pathogen; pathway; Pathway interactions; Pb element; peptide hormone; peptide hormone biosynthesis; Peptide Receptor; Peptides; Pesticides; poison; Poisons; Population; Post-Transcriptional Gene Silencing; Post-Transcriptional Gene Silencings; Posttranscriptional Gene Silencing; Posttranscriptional Gene Silencings; Process; Production; Protein Family; Protein Gene Products; Proteins; Proteomics; Public Health; public health medicine (field); Quelling; receptor; Receptor Protein; Receptor Signaling; Regulation; Reproduction; Reproductive Physiology; Research; Research Resources; Resources; response; Reticuloendothelial System, Blood; RNA Interference; RNA Silencing; RNA Silencings; RNAi; Sequence-Specific Posttranscriptional Gene Silencing; Signal Pathway; Testing; Therapeutic Hormone; Time; Toxic Chemical; toxic compound; Toxic Substance; Transmission; transmission process; vertebrata; Vertebrate Animals; Vertebrates; Work
Project start date: 1992-07-01
Project end date: 2011-12-31
Budget start date: 1-JAN-2011
Budget end date: 31-DEC-2011
5R01AI033108-18 (2011): $241243
TYPE B HISTONE ACETYLTRANSFERASES AND THE ASSEMBLY OF CHROMATIN STRUCTURE
R Mark, Associate Professor
Ohio State Universitycity: Columbus country: United States (us)
Grant 2R01GM062970-10A1 from National Institute Of General Medical Sciences
Abstract: Each time a eukaryotic cell divides it must duplicate, not only its genomic DNA, but the underlying chromatin structure, as well. The faithful propagation of chromatin structure is necessary for the packaging and protection of the eukaryotic genome as well as for the maintenance of epigenetically inherited transcriptional programs. The primary goal of our research program is to decipher the mechanisms by which the primary protein components of chromatin (the core histones H2A, H2B H3 and H3 and the linker histone H1) are brought together with genomic DNA to form chromatin. The specific focus of this proposal is the characterization of a class of enzymes known as type B histone acetyltransferases. These enzymes are responsible for the post-translational acetylation of newly synthesized histones. While it has been known for decades that newly synthesized histones are acetylated during the process of chromatin assembly, the function of these modifications is not known. We have proposed a number of studies that will help to identify the role of the type B histone acetyltransferase Hat1p in chromatin assembly. The first specific aim utilizes S. cerevisiae as a model system to study Hat1p and the acetylation of newly synthesized histones. We will use experimental systems that will allow us to directly assay for the effect of Hat1p on chromatin assembly in several different contexts. In addition, will use a variety of yeast molecular genetic techniques to decipher the unique and overlapping functions of the multiple sites of acetylation that have been identified on newly synthesized histones. Finally, we will continue the isolation and characterization of a novel chromatin assembly factor that we have identified in yeast extracts. The second specific aim extends our studies of the yeast enzyme, to the characterization of mammalian Hat1. We will use biochemical techniques to isolate and characterize complexes containing the human Hat1 enzyme. In addition, we will characterize a Hat1 mouse knockout model in order to identify the function of this type B histone acetyltransferase in a complex organism. Eukaryotic cells contain an enormous linear length of DNA that must be highly condensed to be packaged inside cells. This packaging results from the formation of a structure known as chromatin that plays an important role in regulating most processes that occur in the nucleus. The importance of chromatin structure is evidenced by the numerous examples of defects in chromatin structure that cause serious human diseases. This proposal seeks to understand the mechanisms by which chromatin is assembled and regulated which will aid in our understanding and treatment of these diseases
Keywords: Acetylation; Animal Model; Area; base; Biochemical; Biological; Biological Assay; Biological Models; Biological Process; Birth; Categories; Cell Nucleus; Cells; Chromatin; Chromatin Modeling; Chromatin Structure; Complex; Coupled; Data; Defect; Deposition; Disease; DNA; DNA Double Strand Break; Enzymes; Eukaryotic Cell; Gene Deletion; Generations; Genetic Models; Genetic Techniques; Genome; Genomics; Goals; Histone Acetylation; histone acetyltransferase; Histone H1; Histone H1(s); Histone H2A; Histone H3; Histone H4; Histones; Human; human disease; Inherited; interest; Investigation; Knockout Mice; Laboratories; Length; Link; Lysine; Maintenance; Mammalian Cell; member; Modeling; Modification; Molecular Chaperones; Molecular Genetics; Mus; novel; Nuclear; Organism; Pathway interactions; Play; Process; programs; Property; protein complex; Proteins; public health relevance; recombinational repair; Regulation; Research; research study; RNA; Role; Saccharomyces cerevisiae; Series; Site; Specificity; Structure; System; Techniques; Testing; Time; Transcriptional Regulation; Work; Yeasts
Relevance: Eukaryotic cells contain an enormous linear length of DNA that must be highly condensed to be packaged inside cells. This packaging results from the formation of a structure known as chromatin that plays an important role in regulating most processes that occur in the nucleus. The importance of chromatin structure is evidenced by the numerous examples of defects in chromatin structure that cause serious human diseases. This proposal seeks to understand the mechanisms by which chromatin is assembled and regulated which will aid in our understanding and treatment of these diseases
Project start date: 2001-07-01
Project end date: 2015-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: PA-10-067
2R01GM062970-10A1 (2011): $314150
ROLES OF RICTOR IN MTOR SIGNALING, DIFFERENTIATION & IMMUNE MEMORY VIA AKT & PKC
R Mark, Professor
Vanderbilt Universitycity: Nashville country: United States (us)
Grant 1R01HL106812-01 from National Heart, Lung, And Blood Institute
Abstract: Analyses of signaling mechanisms drive fundamental insights into biological regulation as well as important targets for possible therapeutic interventions. Adaptive immunity and autoimmune disease are determined by signal transduction pathways that regulate the balance among differentiation and fate choices for CD4 and CD8 T cells, and the capacities of different subsets to generate immunological memory. Signals initiated through PI 3-kinases (PI3K) are relayed in part by the pro-survival kinase Akt, whose activation and downstream targets such as the mammalian Target of Rapamycin (mTOR) regulate survival and proliferation. Functions of rapamycin, an immune suppressive drug useful in transplantation medicine, had been equated with mTOR inhibition, but recent findings show that mTOR functions through at least two mutually exclusive classes of multiprotein complexes. The first, mTORC1, is rapamycin-sensitive and regulates aspects of protein translation and cellular growth. However, a second class of mTOR complex, termed mTORC2, is relatively rapamycin-resistant, with inhibition depending on the effective concentration of the drug. While the signaling and biology of mTORC1 have been investigated extensively, little is known about the roles of mTORC2 in normal cell physiology, and nothing in cells of the immune system. Evidence as to the function of mTORC2 in immunity (if any), the mechanism(s) for any such function or its relation to Akt vs. PKC pathways, and whether or not the lack of mTORC2 would mitigate abnormalities stemming from loss of PTEN in lymphocytes are all unknown. Exciting indications suggest complex roles of rapamycin in regulating a balance between effector and memory states for CTL, but nothing is known about the helper lineages in this regard, nor is there insight into how mTORC2 relates to the effect of rapamycin on CTL memory. Thus, the need to understand functions of the mTORC2 complex as part of new frontiers for mTOR signaling in immunity and memory is especially great. Based on our preliminary findings, the central hypotheses of this proposal are (i) that the mTORC2 signaling complex mediates the acquisition of full and appropriately balanced functional capabilities by mature T cells, and (ii) that it regulates their properties and capacity to participate in immunity and autoimmunity using different downstream signal relays depending on the biological target process. To test the central hypothesis and elucidate related mechanisms, we propose to define the roles of mTORC2 in T cell- mediated primary and recall immunity (Aim 1), elucidate mechanisms by which mTORC2 effects T helper differentiation via the HM modifications of Akt- and PKC-8 (Aim 2), and dissect the interplay between mTORC2 and PTEN in regulating T cells (Aim 3). The expected outcome of the proposed studies is that we will (i) change concepts and elucidate how mTOR signaling affects immunity and CD4 T cell fates, & (ii) identify new mechanisms by which signaling through Akt and PKC influence the balance of gene expression programs acquired by this class of T cells, thereby offering the potential for more selective therapeutic targeting. The precise properties of a class of white blood cells called lymphocytes are central to the effectiveness of immune responses and vaccines but also cause autoimmune diseases and the rejection of organ transplants. Lymphocytes acquire their specific properties as a result of passing signals inside the cell, a feature exploited by effective but problematic immune suppressant drugs such as rapamycin. This research proposal seeks to understand key aspects of how proteins whose function is blocked by rapamycin function in immunity by regulating lymphocytes, and enhance understanding of the way in which vaccines work through ´immune memory´
Keywords: 1-Phosphatidylinositol 3-Kinase; Acute; adaptive immunity; Affect; Alleles; Allelomorphs; anamnestic reaction; ATP[{..}]1-phosphatidyl-1D-myo-inositol 3-phosphotransferase; Autoimmune Diseases; autoimmune disorder; Autoimmune Status; Autoimmunity; balance; balance function; base; Biological; biological signal transduction; Biology; Blood leukocyte; body system, allergic/immunologic; BZS; Calcium Phospholipid-Dependent Protein Kinase; Calcium-Activated Phospholipid-Dependent Kinase; Cancers; CD4 lymphocyte; CD4 Positive T Lymphocytes; CD4 T cells; CD4+ T cell; CD4+ T-Lymphocyte; CD4-Positive Lymphocytes; CD8; CD8B; CD8B1; CD8B1 gene; Cell Communication and Signaling; Cell Function; cell growth; Cell Line; Cell Lines, Strains; Cell physiology; Cell Process; Cell Signaling; CellLine; Cells; Cells, CD4; Cellular Expansion; Cellular Function; Cellular Growth; Cellular Physiology; Cellular Process; Chronic; Clinical, Transplantation, Organ; Clonal Expansion; Complex; cultured cell line; Cytosolic Protein Tyrosine Phosphastase; drug/agent; Drugs; EC 2.7; Effectiveness; Equilibrium; Event; frontier; Gene Expression; gene product; Genes, Class I; Genes, MHC Class I; Grafting Procedure; helper T cell; host response; Immune; Immune response; Immune system; Immunity; Immunologic Memory; Immunological Memory; immunological synapse; immunoresponse; insight; intervention therapy; Intracellular Communication and Signaling; Isoforms; Kinases; Leukocytes; Light; Lipids; lymph cell; Lymphocyte; Lymphocytic; LYT3; Macromolecular Protein Complexes; malignancy; Malignant Neoplasms; Malignant Tumor; mammalian target of rapamycin (mTOR); Marrow leukocyte; Mature T-Cell; Mature T-Lymphocyte; Measures; Mediating; Medication; Memory; memory T lymphocyte; MHAM; MHC Class I; MHC Class I Genes; MMAC1; Modification; mTOR gene product; mTOR protein; Multiprotein Complexes; neoplasm/cancer; Normal Cell; Nuclear; organ allograft; organ graft; organ system, allergic/immunologic; Organ Transplantation; Organ Transplants; Organ Transplants, Including Bone Marrow for DCT; organ xenograft; Outcome; pathway; Pathway interactions; Pharmaceutic Preparations; Pharmaceutical Preparations; Phase; Phosphatase and Tensin Homolog; Phosphatidylinositol 3-Kinase; Phosphatidylinositol-3-OH Kinase; Phosphoinositide 3-Hydroxykinase; Phospholipid-Sensitive Calcium-Dependent Protein Kinase; Phosphorylation; Phosphotransferases; Phosphotyrosine Phosphatase; Phosphotyrosyl Protein Phosphatase; Photoradiation; PI-3 Kinase; PI-3K; PI3-Kinase; PKC; Play; Process; programs; Programs (PT); Programs [Publication Type]; Property; Property, LOINC Axis 2; protein complex; Protein Isoforms; Protein Kinase C; Protein Phosphorylation; Protein Tyrosine Phosphatase; protein tyrosine phosphate phosphohydrolase; Protein-Serine Kinase; Protein-Serine-Threonine Kinases; Protein-Threonine Kinase; Proteins; PtdIns 3-Kinase; PTEN; PTEN gene; PTEN1; PTPase; public health relevance; RAFT-1 gene product; Rapamune; Rapamycin; Regulation; Research Proposals; Resistance; resistant; response; Reticuloendothelial System, Leukocytes; Role; secondary immune response; self recognition (immune); Serine Kinase; Serine-Threonine Kinases; Signal Transduction; Signal Transduction Pathway; Signal Transduction Systems; Signaling; Sirolimus; social role; Specificity; stem; Subcellular Process; T cell response; T memory cell; T-Cells; T-Lymphocyte; T4 Cells; T4 Lymphocytes; Testing; Therapeutic Intervention; therapeutic target; Threonine Kinase; thymus derived lymphocyte; Thymus-Dependent Lymphocytes; transcription factor; transgenic; Transgenic Organisms; Translations; Transphosphorylases; transplant; transplant medicine; Transplantation; transplantation medicine; Transplantation Surgery; Type I Phosphatidylinositol Kinase; Type III Phosphoinositide 3-Kinase; Tyrosine Phosphatase; Tyrosyl Phosphoprotein Phosphatase; Vaccines; white blood cell; White Blood Cells; white blood corpuscle; White Cell; Work
Relevance: NARRATIVE The precise properties of a class of white blood cells called lymphocytes are central to the effectiveness of immune responses and vaccines but also cause autoimmune diseases and the rejection of organ transplants. Lymphocytes acquire their specific properties as a result of passing signals inside the cell, a feature exploited by effective but problematic immune suppressant drugs such as rapamycin. This research proposal seeks to understand key aspects of how proteins whose function is blocked by rapamycin function in immunity by regulating lymphocytes, and enhance understanding of the way in which vaccines work through ´immune memory´
Project start date: 2011-01-15
Project end date: 2014-11-30
Budget start date: 15-JAN-2011
Budget end date: 30-NOV-2011
PFA/PA: PA-10-067
1R01HL106812-01 (2011): $388542
REDOX PROTEIN APE1/REF-1 AS A TARGET FOR AGE-RELATED MACULAR DEGENERATION (AMD)
R Mark
Apex Therapeutics, Inc.city: Indianapolis country: United States (us)
Grant 1R41EY019784-01 from National Eye Institute
Abstract: Age-related macular degeneration (AMD) is the leading cause of severe vision loss in people over age 60 and an estimated 8 million older-age Americans are at high risk to develop advanced AMD. Among two types of AMD, neovascular (wet) and non-neovascular (dry), neovascular AMD causes 90% of the vision loss. The key pathogenesis of the neovascular AMD is neovascularization and its associated increased vascular permeability in the macula. It eventually leads to photoreceptor degeneration causing central vision loss. Although with the most advanced treatment including the newly FDA approved anti-VEGF treatments (Macugen(R), Lucentis(R)/Avastin(R)), there are only 25-33% patients with visual acuity improvement. Even for the well-responded individual, re-occurring neovascularization after a few months often require repeated treatments. Therefore, AMD clinical management remains a great challenge with the need for more effective therapies. The multifactor nature involved in the pathogenic process of AMD requires pursuing novel agents to target other factors promoting angiogenesis, such as inflammation, as an alternative therapy or in combination therapy with anti-VEGF agents. The objective of this proposal is to determine the role of APE1/Ref-1 in retinal angiogenesis and evaluate the potential of APE1/Ref1 as a new therapeutic target for treatment of neovascularization using in vitro retinal endothelial cells and in vivo animal models of AMD with subretinal and choroidal neovascularization. The hypothesis of the proposed research is that blocking APE1/Ref-1 redox function will lead to inhibition of retinal neovascularization as a single agent efficacy, as well as enhancement of anti-VEGF treatments in AMD. Specific Aim 1 Characterization of the novel agent, (2E)-3-[5-(2, 3-dimethoxy-6-methyl-1,4-benzoquinoyl)]-2- nonyl-2-propenoic acid (APX3330) and new novel analogues of APX3330 on APE1/Ref-1´s function in retinal vascular endothelial cells (RVEC). Specific Aim 2 Determination of APX3330 and new novel analogues on APE1/Ref-1´s function in animal models of AMD. We will study the anti-angiogenic effects of APX3330 on subretinal neovascularization (SNV) in vldlr-/- mice and on choroidal neovascularization (CNV) in laser-induced CNV animal model. We anticipate two outcomes enhancement of currently used anti-VEGF agents such as Macugen and Lucentis(R) and the development of a new single agent that would augment or supplement current and future use of anti-VEGF treatments. This enhanced anti-angiogenic effect may allow for longer treatment intervals or enhance the efficacy of anti-VEGF agents. Other indications/utility We also see potential utility of APE1/Ref-1 redox inhibition in other indications such as diabetic retinopathy and other scenarios where anti-angiogenic agents could or are being used such as cancer, glaucoma and other diseases. Age-related macular degeneration (AMD) is the leading cause of severe vision loss in people over age 60 and an estimated 8 million older-age Americans are at high risk to develop advanced AMD. AMD clinical management remains a great challenge with the need for more effective therapies. The proposed work will look at the effects of APE1/Ref-1 redox inhibitors in cells and in animals toward the goal of enhancing of current therapies and the development of a new therapy for treating AMD
Keywords: 2-propenoic acid; acrylic acid; advanced age; Age; Age related macular degeneration; Aged 65 and Over; Alternative Therapies; American; analog; angiogenesis; Angiogenesis Antagonists; Angiogenesis Blockers; Angiogenesis Inhibitors; Angiogenetic Antagonists; Angiogenic Antagonists; Angiostatic Agents; Animal Model; Animal Models and Related Studies; Animals; Anti-Angiogenesis; Anti-Angiogenetic Agents; Anti-Angiogenic Agents; Anti-Angiogenic Drugs; Anti-VEGF; Anti-VEGF Humanized Monoclonal Antibody; Anti-VEGF RhuMAb; Antiangiogenesis; Antiangiogenesis Agents; antiangiogenesis therapy; antiangiogenic; Antiangiogenic Agents; Area; Automobile Driving; Avastin; base; bevacizumab; Bevacizumab (rhuMAb VEGF); Blindness; Cancer of Breast; Cancers; Causality; cell growth; Cell Growth in Number; Cell Multiplication; Cell Proliferation; Cells; Cellular Expansion; Cellular Growth; Cellular Proliferation; Choroidal Neovascularization; Clinical Management; combination therapy; Combined Modality Therapy; combined modality treatment; combined treatment; Data; Deoxyribonucleic Acid; Development; Diabetic Retinopathy; Disciform macular degeneration; Disciform senile macular retinal degeneration; Disease; disease causation; disease etiology; disease/disorder; disease/disorder etiology; Disorder; disorder etiology; DNA; DNA Repair Enzymes; driving; Drivings, Automobile; drug/agent; Drugs; effective therapy; Elderly; Elderly, over 65; elders; Electromagnetic, Laser; Endothelial Cells; Etiology; Exudative age-related macular degeneration; Exudative AMD; FDA approved; Future; gene product; geriatric; Glaucoma; glaucomatous; Goals; heavy metal lead; heavy metal Pb; high risk; In Vitro; in vivo; Individual; Inflammation; INFLM; inhibitor; inhibitor/antagonist; Inhibitors, Angiogenetic; Inhibitors, Angiogenic; intervention development; Lasers; late life; later life; Lead; Legal patent; Lucentis; macula; macular; Maculopathy, Age-Related; malignancy; malignant breast neoplasm; Malignant neoplasm of breast; Malignant Neoplasms; Malignant Tumor; Malignant Tumor of the Breast; Mammals, Mice; Medication; Mice; MoAb VEGF; model organism; Modeling; Monoclonal Antibody Anti-VEGF; Multimodal Therapy; Multimodal Treatment; multimodality therapy; Multimodality Treatment; Multiple Myeloma; Murine; Mus; myeloma; Myeloma, Plasma-Cell; myelomatosis; Nature; neoplasm/cancer; neovascular; Neovascular age-related macular degeneration; Neovascular AMD; neovascularization; Neovascularization Inhibitors; Neovascularization, Choroid; new therapeutic target; novel; older adult; older person; Outcome; oxidation reduction reaction; Oxidation-Reduction; Patents; Pathogenesis; Patients; Pb element; Pharmaceutic Preparations; Pharmaceutical Preparations; photoreceptor degeneration; Process; Proteins; public health relevance; Radiation, Laser; Recombinant Humanized Anti-VEGF Monoclonal Antibody; Recombinant Humanized Monoclonal Antibody to Vascular Endothelial Growth Factor; Redox; Research; Retinal; retinal angiogenesis; Retinal Neovascularization; RhuMAb VEGF; rhuMabVEGF; Role; senile macular disease; senior citizen; Signaling Protein; small molecule; social role; Therapeutic; therapy development; transcription factor; treatment development; treatment strategy; Vascular Endothelial Cell; Vascular Permeabilities; Visual Acuity; Wet AMD; Work
Relevance: ApeX Therapeutics, Inc. Age-related macular degeneration (AMD) is the leading cause of severe vision loss in people over age 60 and an estimated 8 million older-age Americans are at high risk to develop advanced AMD. AMD clinical management remains a great challenge with the need for more effective therapies. The proposed work will look at the effects of APE1/Ref-1 redox inhibitors in cells and in animals toward the goal of enhancing of current therapies and the development of a new therapy for treating AMD
Project start date: 2009-09-30
Project end date: 2011-06-29
Budget start date: 30-SEP-2009
Budget end date: 29-JUN-2011
PFA/PA: PA-08-051
1R41EY019784-01 (2009): $225064
PROTEOGENOMICS OF DYSREGULATED PROTEIN INTERACTION NETWORKS IN MTB INFECTION
R Mark
Case Western Reserve Universitycity: Cleveland country: United States (us)
Grant 5R01HL106798-02 from National Heart, Lung, And Blood Institute
Abstract: Aerosolized Mycobacterium tuberculosis (MTB) is readily transmitted from person to person. Mycobacteria infect the distal alveoli where they replicate unfettered in the face of innate responses. As adaptive T cell immunity develops, MTB growth is controlled but bacilli are not eradicated. The interactions between T cells and MTB infected antigen presenting cells (APC) are central for the organism to evade/resist host immunity to establish latent infection. In this application in response to RFA-HL-10-015 "Systems Biology Approach to the Mechanisms of TB Latency and Reactivation" we bring together a multidisciplinary team of experts in proteomics, computer science, bioinformatics, genetic epidemiology, epidemiology, immunology, lung biology and pulmonary medicine coupled to access to a unique set of cohorts of epidemiologically and clinically well characterized persons with the spectrum of MTB exposure, infection and disease in the US, Uganda and S. Africa, in order to apply novel systems biology approaches to latent MTB infection. Recent studies suggest that proteomic approaches aimed at identifying protein-protein interaction networks result in the identification of functional sub-networks with a role in disease pathogenesis. We propose to apply this approach to the analysis of latent MTB infection (LTBI) in humans, and to link proteomic results with parallel studies using human genetic and systemic chemo-/cytokine approaches to understanding MTB pathogenesis. The general hypothesis of this proposal is that proteomic seeds identify sub-networks of proteins that differentiate persons at different stages of MTB infection and disease, and provide insight into the mechanism(s) responsible for progression from LTBI to active TB. The aims are Aim 1 To determine dysregulated protein-protein interaction sub-networks in mononuclear phagocytes and CD4+ T cells of persons in households heavily exposed to MTB who do not become infected compared to those with LTBI who do not progress to disease and those who develop TB. Aim 2 To determine the relationship between protein-protein interaction sub-networks to whole genome and targeted gene analyses, and peripheral chemo-/cytokine responses detected by multiplex chemo-/cytokine assays in the same population as in Aim 1. Aim 3 To determine which of the protein-protein interaction and chemo-/cytokine sub-networks analyzed in Aims 1 and 2 are most relevant for lung CD4+ T cells and macrophages from persons with LTBI. This proposal combines access to unique clinical specimens (peripheral blood cells, plasma, broncho- alveolar lavage specimens) from epidemiologically well characterized persons with MTB infection in US, Uganda and South Africa with experts in the use of proteomics, genetic epidemiology and cytokine biology for a multidisciplinary systems biology approach to LTBI and its progression to active TB. Systems biology is ideally suited to analyze the complex interaction between humans and M. tuberculosis (MTB), the cause of tuberculosis (TB), and is particularly powerful when applied to tissues from persons in different stages of MTB exposure, infection and disease. Using systems biology to find key host proteins disturbed by MTB exposure or infection allows us to identify persons at risk for progression to active TB and find out what we need to be naturally or through vaccination protected against TB
Keywords: aerosolized; Africa; Alveolar; Alveolus; Antigen-Presenting Cells; Bacillus (bacterium); Bioinformatics; Biological; Biological Assay; Biology; Blood Cells; case control; CD4 Positive T Lymphocytes; Cells; Chronic; Clinical; cohort; Colon Carcinoma; Complex; computer science; Coupled; cytokine; Disease; Distal; Epidemiology; Exposure to; Gene Targeting; genetic epidemiology; Genome; Genus Mycobacterium; Growth; HIV; Household; Human; Human Genetics; Immune response; Immunity; Immunology; Infection; innovation; insight; Irrigation; latent infection; Learning; Link; Lung; macrophage; Malignant - descriptor; Malignant Neoplasms; Mononuclear; multidisciplinary; Mycobacterium tuberculosis; Non-Malignant; novel; novel strategies; Ohio; Organism; Pathogenesis; Pathologic; Pattern; Peripheral; peripheral blood; Persons; Phagocytes; Phenotype; Plasma; Population; protein protein interaction; Proteins; Proteome; Proteomics; public health relevance; Pulmonary Disease (Specialty); reactivation from latency; Research Personnel; response; Risk; Role; Sampling; Seeds; South Africa; Specimen; Staging; Systems Biology; T-Lymphocyte; Tissues; transcriptomics; Tuberculosis; tumor; Uganda; Vaccination; Validation
Relevance: Narrative Systems biology is ideally suited to analyze the complex interaction between humans and M. tuberculosis (MTB), the cause of tuberculosis (TB), and is particularly powerful when applied to tissues from persons in different stages of MTB exposure, infection and disease. Using systems biology to find key host proteins disturbed by MTB exposure or infection allows us to identify persons at risk for progression to active TB and find out what we need to be naturally or through vaccination protected against TB
Project start date: 2010-09-17
Project end date: 2014-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
5R01HL106798-02 (2011): $705283
1R01HL106798-01 (2010): $752076
TRANSGENIC PROBES OF ACTIVE CIRCUITS
R Mark, Associate Professor
Scripps Research Institutecity: La Jolla country: United States (us)
Grant 5R01DA028300-03 from National Eye Institute
Abstract: A key question in attempts to understand brain function is how does the electrical activity of neurons give rise to specific perceptions or memories? What is the neural representation of the external world or of past events? While there is a basic understanding of brain circuits at the macroscopic level between defined anatomical regions and to a lesser extent locally within brain regions, there are currently no techniques that allow the identification or manipulation of neuronal ensembles that represent a specific external stimulus or event. The primary goal of this proposal is to improve and extend upon a genetic approach that we have developed that uses the cfos promoter and the tetracycline system to allow the introduction of long lasting genetic tags into active neuronal ensembles (Reijmers et al. 2007; Matsuo et al. 2008). We will develop and validate transgenic mouse lines that allow the direct electrical and biochemical manipulation of environmentally activated neuronal ensembles. If successful, these mice will provide a tool that should be generally useful throughout a wide range of neuroscience disciplines. The human mind is made up of specific bits of knowledge and memories that are integrated within a relational network. Many neurological and neuropsychiatric disorders lead to a disruption of memories or of the cognitive framework in which these memories exists. In this proposal we develop mouse models that allow us to genetically alter, and thus manipulate electrically and molecularly, neurons that make up specific memories. These tools should be useful in dissecting the underlying circuit structure of specific memories, how they are accessed, and how they are disrupted in disease models
Keywords: Allatostatin; Area; base; Biochemical; Boxing; Brain; brain cell; Brain region; Cell Separation; cell type; Cells; Cognitive; Color; Complex; design; Discipline; Disease; Disease model; Dominant-Negative Mutation; Enterobacteria phage P1 Cre recombinase; Episodic memory; Event; Gene Expression Regulation; Genes; Genetic; genetic manipulation; Goals; Grant; Health; Hippocampus (Brain); Human; improved; information processing; Knowledge; Lead; Learning; Ligands; Light; Memory; memory retrieval; Mind; Modeling; Molecular; mouse model; Mus; Mutant Strains Mice; neural circuit; Neurologic; Neurons; Neurophysiology - biologic function; neuropsychiatry; Neurosciences; Nuclear; Pattern; Perception; Plastics; Process; Promotor (Genetics); receptor; Regulation; relating to nervous system; Resolution; response; Retrieval; Sensory; Series; Signal Transduction; Specific qualifier value; Stimulus; Structure; Synapses; System; Techniques; Tetracyclines; Time; tool; Toxin; Transgenic Mice; Transgenic Organisms
Relevance: Narrative The human mind is made up of specific bits of knowledge and memories that are integrated within a relational network. Many neurological and neuropsychiatric disorders lead to a disruption of memories or of the cognitive framework in which these memories exists. In this proposal we develop mouse models that allow us to genetically alter, and thus manipulate electrically and molecularly, neurons that make up specific memories. These tools should be useful in dissecting the underlying circuit structure of specific memories, how they are accessed, and how they are disrupted in disease models
Project start date: 2009-09-01
Project end date: 2014-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
PFA/PA: RFA-MH-09-030
5R01DA028300-03 (2011): $455902
TARGETING PANCREATIC CANCER USING PEPTIDE CHEMISTRY: FROM BENCH TO BEDSIDE
R Mark
Mayo Cliniccity: Rochester country: United States (us)
Grant 5R01CA150190-03 from National Cancer Institute
Keywords: Adenocarcinoma Cell; Affinity; Animal Model; Antibodies; Bacteriophage T7; Bacteriophages; base; bench to bedside; Binding (Molecular Function); Binding Proteins; Biochemical; Biological; Biological Assay; Biotin; Calorimetry; Cancer Etiology; Carcinogenesis Mechanism; Cell Line; Cells; Cellular biology; Cessation of life; Chemicals; Chemistry; Clinic; Clinical; Clinical Trials; conventional therapy; Data; design; Development; Diagnosis; Disease; Disease Progression; Drug Combinations; Drug Delivery Systems; drug development; Drug Kinetics; effective therapy; Enzyme-Linked Immunosorbent Assay; Epidermal Growth Factor Receptor; Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor; Exhibits; Experimental Designs; Family; Fluorescence; Frequencies (time pattern); Future; gemcitabine; Gold; Growth; Growth Factor; human disease; improved; In Vitro; in vivo; Individual; inhibitor/antagonist; Integrins; Investigation; Knowledge; Laboratories; Lead; Libraries; Ligand Binding; Ligands; Link; Lipids; Malignant neoplasm of pancreas; Malignant Neoplasms; Mediating; Methods; Microarray Analysis; Modification; Molecular; Molecular Profiling; mouse model; nano; nanoGold; nanoparticle; nanoprobe; Nanotechnology; Neoplasm Metastasis; novel; novel strategies; overexpression; Pancreatic Adenocarcinoma; pancreatic cancer cells; Pathway interactions; Patients; Pattern; Peptide Hydrolases; Peptide Library; Peptides; peptidomimetics; Phage Display; Pharmaceutical Preparations; Pharmacodynamics; pre-clinical; preclinical study; Preclinical Testing; Preparation; Prevention; Principal Investigator; Property; Protein Binding Domain; Protein Family; protein transport; Proteins; public health relevance; Publishing; Reagent; receptor; Relative (related person); research study; Role; Screening procedure; Signal Transduction; Site-Directed Mutagenesis; small hairpin RNA; small molecule libraries; Staging; Surface; Techniques; Testing; Therapeutic; Therapeutic Intervention; therapeutic target; Tissue Microarray; Titrations; Toxic effect; Translating; translational approach; tumor; tumor growth; United States; Work; Xenograft Model
Relevance: Pancreatic adenocarcinoma (PaCA) is, almost invariably, a fatal disease. This work will focus on the prevention and therapeutic aspects of this cancer. Overall, our proposed experiments will define the regulatory role of GIPC and their downstream molecules that can influence the tumor growth and metastasis. The proposed study might define the mechanism of pancreatic cancer growth and progression and identify specific targets for therapeutic interventions for pancreatic adenocarcinoma where no current therapy is available
Project start date: 2010-04-07
Project end date: 2015-01-31
Budget start date: 1-FEB-2012
Budget end date: 31-JAN-2013
5R01CA150190-03 (2012): $572715
THE ROLE OF ERBB-4 IN INFLAMMATION-INDUCED COLON CARCINOGENESIS
R Mark
Children´s Hospital Los Angelescity: Los Angeles country: United States (us)
Grant 5K01DK077956-06 from National Institute Of Diabetes And Digestive And Kidney Diseases
Keywords: Address; Allografting; base; Biological Assay; carcinogenesis; Cell Survival; cell transformation; Cells; Chemoprevention; Chronic; Colitis; Colon; colon carcinogenesis; Colon Carcinoma; Colorectal Cancer; cost; cytokine; Data; Disease; early onset; Environment; Epidermal Growth Factor Receptor; Epithelial Cells; Epithelium; ErbB4 gene; Family; Family member; high risk; In Vitro; in vitro Model; in vivo; In-Migration; Individual; Inflammation; Inflammatory; Inflammatory Bowel Diseases; intestinal epithelium; Intestinal Neoplasms; Intestines; Large Intestine Carcinoma; Length; member; migration; Modeling; Morbidity - disease rate; Mortality Vital Statistics; Mus; novel; overexpression; Pathologic; Patients; Protein Isoforms; Receptor Protein-Tyrosine Kinases; Relative (related person); Reporting; Research; research study; Risk; Role; Signal Pathway; Testing; Tissues; TNF gene; tumor; tumorigenesis
Project start date: 2007-04-01
Project end date: 2012-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: PAR-05-066
5K01DK077956-06 (2011): $127602
STRUCTURE, DYNAMICS & ACTIVATION MECHANISMS OF CHEMOKINE RECEPTORS
R Mark, Director
University Of California San Diegocity: La Jolla country: United States (us)
Budget start date: 1-JUL-2011
Budget end date: 30-JUN-2012
5U01GM094612-02_5949 (2011): $123788
Sponsored Links Excellgen http://Excellgen.com