CONTROL OF GENE EXPRESSION AND LIFE SPAN
L Stephen, Professor Of Biology
Brown Universitycity: Providence country: United States (us)
Grant 5R01AG024353-08 from National Institute On Aging
Abstract: Our long-term goal is to understand the genetic and molecular elements that determine the process of aging and life span. The focus of this proposal is to identify molecular genetic effectors that mediate calorie/dietary restriction (CR/DR) life span extension as a prerequisite to developing molecular genetic and pharmacological interventions that can extend healthy life span. Examination of CR/DR in a variety of species shows changes in a large number of genes and physiological systems. A central question in translating this information to therapeutic interventions is which of the many changes seen are involved in extending healthy life span? In flies molecular genetic studies have led to a model in which a portion of the life span extending effect of CR/DR is mediated by alterations in the activity of the histone deacetylases Rpd3 and Sir2, and the transcription factor p53. This model provides a framework for use in identifying genetic, biochemical, and pharmacological effectors of CR/DR mediated longevity. In this proposal we will (i) further examine the mechanisms by which an increase in dSir2 extends life span in the fly, (ii) confirm the life span extending effect of a gene identified through our genomic analysis of the CR/Sir2/p53 pathway and begin to determine it´s relationship to CR/DR life span extension, (iii) utilize genome based tools to determine genes and gene sets important for CR/DR life span extension in flies and (iv) test the effect of these newly identified genes on life span using molecular genetic tools. Calorie/dietary restriction extends life span and delays the onset of age-related pathology in organisms from worms to mice. Understanding the molecular genetic interactions in the calorie/dietary restriction pathway of Drosophila will contribute to the development of interventions to prevent or delay age-dependent decline in humans
Keywords: Affect; age related; Aging-Related Process; Applications Grants; base; Biochemical; Caloric Restriction; comparative; Comparative Study; Data; dietary restriction; Drosophila genus; Elements; fly; Gene Expression; Genes; Genetic; genetic effector; genetic element; Genome; Genomics; Goals; Health; Histones; Human; Intervention; Longevity; Mediating; Modeling; Molecular; Molecular Genetics; Mus; Mutation; Organism; overexpression; Pathology; Pathway interactions; Physiological; prevent; Role; Study Section; System; Testing; Therapeutic Intervention; therapy development; tool; transcription factor; Translating
Relevance: Narrative Calorie/dietary restriction extends life span and delays the onset of age-related pathology in organisms from worms to mice. Understanding the molecular genetic interactions in the calorie/dietary restriction pathway of Drosophila will contribute to the development of interventions to prevent or delay age-dependent decline in humans
Project start date: 2004-09-30
Project end date: 2014-07-31
Budget start date: 1-AUG-2011
Budget end date: 31-JUL-2012
PFA/PA: PA-07-070
5R01AG024353-08 (2011): $316023
Sponsored Links Excellgen http://Excellgen.com
Grants awarded to L Stephen
MECHANISMS OF RESISTANCE AND SUSCEPTIBILITY TO AFRICAN TRYPANOSOME INFECTION
L Stephen, Professor & Head
University Of Georgia (uga)city: Athens country: United States (us)
Grant 5R01AI039033-12 from National Institute Of Allergy And Infectious Diseases
Abstract: Trypanosoma brucei brucei causes Nagana in cattle but is non-infectious to humans because of its susceptibility to the cytotoxic activity of normal human serum. This innate immune activity is due to a minor subclass of high-density lipoprotein (HDL) termed the Trypanosome Lytic Factor (TLF). TLF contains apolipoprotein A-1 (apoA-1), a protein found in all HDLs, and two primate specific proteins, haptoglobin related protein (Hpr) and apolipoprotein L-1 (apoL-1). Both Hpr and apoL-1 have been shown to be necessary for maximal trypanosome killing in vitro and in a transgenic mouse model. Hpr is a hemoglobin (Hb) binding protein and Hb is an essential co-factor for trypanosome killing by TLF. The cellular pathway of TLF mediated lysis of T. b. brucei initiates with binding of TLF to a high affinity receptor (Tb927.6.440) located in the flagellar pocket. Following binding TLF is rapidly taken up and localized to the lysosome. Within the acidified lysosome TLF is activated and kills T. b. brucei by destabilization of the lysosomal membrane. The human sleeping sickness parasite Trypanosoma brucei rhodesiense has evolved a defense against TLF. T. b. rhodesiense produces a potent inhibitor of TLF, Serum Resistance Associated protein (SRA), which binds apoL-1 and neutralizes the activity of TLF. Trypanosoma brucei gambiense also infects humans but lacks SRA and, as shown in this proposal, resists TLF killing by down regulation of the TLF receptor. In this proposal, we outline a number of experiments that will provide important information on the mechanism of assembly of TLF and how its composition might be altered to produce "variant TLFs" with activity against the human sleeping sickness parasites (Aim 1). To better understand the biophysical basis for membrane destabilization by native TLF and its constituent proteins we will use model liposomes of defined composition in fluorescence based assays to measure TLF induced changes in lipid dynamics (Aim 2). Finally, we will investigate the cellular, molecular and biochemical basis of SRA-dependent and SRA-independent resistance to TLF. In addition to resolving a longstanding question concerning how SRA inhibits TLF activity we will investigate the mechanism of T. b. gambiense resistance to TLF (Aim 3). Our long-term goals are to develop a better understanding of the mechanism of TLF killing and how the human sleeping sickness parasites evade this activity. This may allow us to develop novel approaches for the treatment of this important human disease. African sleeping sickness is a re-emerging human disease in sub- Saharan Africa. It is currently estimated that over 35 million people are at risk and the number of infected people may exceed 300,000. There is no vaccine for African sleeping sickness and most of the drugs have serious toxicity problems. The proposed studies on the mechanism of action of the innate immune complex, TLF, may lead to the identification of novel approaches for therapeutic development
Keywords: Address; Affinity; Africa South of the Sahara; African; African Trypanosomiasis; Anabolism; Antigen-Antibody Complex; Apolipoprotein A-I; Apolipoproteins; base; Binding (Molecular Function); Binding Proteins; Biochemical; Biological Assay; Cattle; Complex; Cytolysis; cytotoxic; Down-Regulation; Environment; Fluorescence; Genes; Goals; Grant; haptoglobin-related protein; Hemoglobin; High Density Lipoproteins; Human; human disease; Immune; Immune system; In Vitro; Infection; inhibitor/antagonist; Killings; Lead; Leishmania (genus); Ligands; Lipids; Lipoproteins; Liposomes; Lysosomes; Lytic; Mammalian Cell; Mammals; Measures; Mediating; Membrane; Minor; Modeling; Molecular; monolayer; mouse model; Multiprotein Complexes; nagana; Natural Immunity; novel strategies; Outcome; Parasite resistance; Parasites; Pathway interactions; Peptide Signal Sequences; Pharmaceutical Preparations; Phospholipids; Plasmodium; Play; Predisposition; Primates; Protein Biosynthesis; Proteins; public health relevance; R Factors; receptor; Relative (related person); research study; Resistance; resistance mechanism; Risk; Role; Serum; Site; Sterility; therapeutic development; Toxic effect; Toxin; Transgenic Mice; Trypanosoma; Trypanosoma brucei brucei; Trypanosoma brucei gambiense; Trypanosoma brucei rhodesiense; Vaccines; Variant
Relevance: . African sleeping sickness is a re-emerging human disease in sub- Saharan Africa. It is currently estimated that over 35 million people are at risk and the number of infected people may exceed 300,000. There is no vaccine for African sleeping sickness and most of the drugs have serious toxicity problems. The proposed studies on the mechanism of action of the innate immune complex, TLF, may lead to the identification of novel approaches for therapeutic development
Project start date: 1996-02-15
Project end date: 2015-05-31
Budget start date: 1-JUN-2011
Budget end date: 31-MAY-2012
PFA/PA: PA-07-070
5R01AI039033-12 (2011): $367538
THE PREVENTION OF HIV/STI AMONG MARRIED WOMEN IN URBAN INDIA
L Stephen
University Of Connecticut Sch Of Med/dntcity: Farmington country: United States (us)
Grant 5R01MH075678-05 from National Institute Of Mental Health
Abstract: This proposal seeks to develop and evaluate a culturally appropriate, health facility-based intervention to promote primary prevention of HIV and other sexually transmitted infections (HIV/STIs) among married women, ages 18-40, living in an economically marginal community in Mumbai (Bombay), India. The proposal responds to the need to develop effective approaches to the global risk of husband to wife transmission of HIV/STIs. This proposed project utilizes an approach to HIV/STI risk reduction among married women that centers on culturally-based gynecological and related health symptoms that women feel more comfortable discussing and presenting for treatment. The specific aims of this proposal are to (1) Conduct formative research on the stakeholders and institutions involved in women´s health including women in the context of the family, women as patients, husbands and their relationship to the health of their wives, and the nature of health care for women in the community; (2) Develop and implement, based on the formative research, Enhanced Care and Couples´ Intervention in an existing public health facility to reduce women´s HIV/STI risk within marriage; (3) Test the efficacy of the interventions, through a randomized clinical trial (RCT), to reduce the risk of HIV/STI transmission, to reduce STIs and women´s gynecological and related symptoms and to improve women´s life situation. The proposed project will be conducted in an urban "slum" community of Mumbai. The project will be organized into three phases Phase I (Year 1) will involve formative research on health and other service providers, married women, and married couples; analysis of these data; and finalization of the intervention design. Phase II (Years 2-4) involves the establishment of a randomized experimental design that will include Enhanced Care plus Couples´ Intervention; Enhanced Care Only; Standard of Care plus Couples´ Intervention; and Standard of Care only; and Phase III (Year 2-5) will evaluate the impact of the interventions on married women. The great majority of women in the world are exposed to HIV/STI risk not through their own agency, but because of the behavior of their spouses. The intent of this study is to develop an approach that will reduce risk among vulnerable married women in these communities and thus serve as a model for India as well as for other vulnerable women in developing and developed countries
Keywords: Address; Age; AIDS prevention; Attention; base; Behavior; Caring; Child Care; Communities; Couples; Data Analyses; Data Collection; Developed Countries; Developing Countries; Distress; efficacy testing; Elements; Epidemic; Etiology; Evaluation; Experimental Designs; Family; Feminization; follow-up; Funding; Gender; Grant; Health; Health care facility; Health Knowledge, Attitudes, Practice; Health Resources; Health Services; Health Status; Healthcare; high risk; HIV; Husband; improved; India; Individual; Infection; Infection prevention; Institution; Institutionalization; instrument; Intervention; Interview; Knowledge; Left; Life; Link; Maintenance; male; Marriage; Maternal and Child Health; Medical; member; men; Methods; Modeling; National Institute of Mental Health (U.S.); Nature; Outcome; Patients; Perception; Phase; Population; Pregnancy; prevention service; Prevention strategy; Primary Prevention; programs; Provider; Psyche structure; psychologic; psychological distress; public health medicine (field); Randomized; Randomized Clinical Trials; Reporting; Research; Research Personnel; Resources; Risk; Risk Reduction; Self Perception; service intervention; Services; sex; Sex Behavior; Sexual Partners; Sexually Transmitted Diseases; Slum; social; Spouses; standard care; standard of care; Symptoms; Syndrome; Testing; theories; therapy design; transmission process; Treatment Efficacy; Urban Health; Wife; Woman; Women`s Health; Women`s Health Services
Project start date: 2007-09-19
Project end date: 2012-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
5R01MH075678-05 (2011): $580926
IMPAIRED MITOCHONDRIAL FUSION IN PULMONARY ARTERIAL HYPERTENSION
L Stephen, Chief Of Cardiology
University Of Chicagocity: Chicago country: United States (us)
Grant 5RC1HL099462-02 from National Heart, Lung, And Blood Institute
Abstract: This proposal responds to the broad challenge area (04) Clinical Research and specific challenge topic 04-HL-102 Develop Integrative Strategies to Elucidate the Mechanisms of Lung Diseases. Pulmonary arterial hypertension (PAH) is a syndrome characterized by obstructive vascular remodeling, inflammation and vasoconstriction of small pulmonary arteries. Despite recent therapeutic advances, 1-year mortality rates remains high (~15%). Although abnormalities of the platelets, endothelium and adventitia contribute critically to the pathogenesis of PAH, excessive proliferation of pulmonary arterial smooth muscle cells (PASMC) is a major contributor to the obstructive vascular pathology. This challenge proposal explores 2 newly-recognized abnormalities that promote PASMC proliferation. We recently discovered that the mitochondrial network is disrupted in PAH PASMC and noted that this is related to the proliferative diathesis of these cells. Fragmentation of the mitochondrial network appears to reflect impaired mitochondrial fusion and is associated with 2 related abnormalities 1) normoxic activation of the master hypoxic transcription factor, hypoxia inducible factor (HIF-1a) and 2) downregulation of mitofusin-2. Normally, mitochondria rapidly join and break apart through highly regulated processes called fusion and fission, respectively. The balance of fusion and fission dynamically regulates the integrity of the reticulum. Fusion is regulated by SNARE-like proteins called mitofusin-1 and mitofusin-2. Fusion redistributes mitochondrial proteins/genes, protecting the cell from oxidant stress, apoptosis and mitochondrial DNA mutations. Impaired fusion alters mitochondrial membrane potential, impairs respiration and promotes SMC proliferation. We evaluate the hypothesis that a HIF-1a-mediated mitofusin-2 deficiency promotes PASMC proliferation and contributes to PAH. Relevant to PAH, mitofusin-2 is a brake on SMC proliferation. Indeed, when first cloned, mitofusin-2 was named hyperplasia suppressor gene. Mitofusin-2 gene therapy reduces intimal hyperplasia in a systemic arterial injury model. HIF-1a is known to downregulate mitofusin-2 expression. Impaired fusion and normoxic HIF-1a activation are found in humans with PAH and fawn-hooded rats (FHR), a strain that spontaneously develops PAH. We are investigating the mechanism of pulmonary arterial hypertension (PAH) in Fawn Hooded Rats (FHR), and have identified problems in the FHR´s mitochondria, namely lower production of hydrogen peroxide and fragmentation of the mitochondrial network, which create a pseudohypoxic environment that favors rapid cell growth and blood vessel blockage. Preliminary studies show that FHR suffer from activation of an hypoxia inducible factor" (HIF-1a) and a related break-up of the mitochondrial network due to a deficiency of mitofusin 2 (which triggers excessive growth of arterial smooth muscle cells and blocks the lung circulation). This proposal seeks to understand the role of the HIF-1a and mitofusin in PAH and develop therapies (inhibition of HIF-1 a and supplementation of mitofusin-2) to restore mitochondrial form and function and cure PAH
Keywords: Address; Apoptosis; Area; Arterial Injury; Award; Basic Science; Blood Circulation; Blood Platelets; Blood Vessels; cell growth; Cell Proliferation; Cell Respiration; Cells; Clinical Research; Cobalt; Consumption; Data; Dichloroacetate; Disease susceptibility; Dose; Down-Regulation; Endothelium; Environment; Equilibrium; fluorodeoxyglucose; gene therapy; Genes; Glycolysis; Grant; Growth; Human; Hydrogen Peroxide; Hyperplasia; Hypoxia; Hypoxia Inducible Factor; in vivo; Inflammation; Injection of therapeutic agent; Investigational Therapies; kinase inhibitor; Lead; Link; Lung; Lung diseases; Mediating; Medicine; Membrane Potentials; Metabolic; Metabolism; Mitochondria; mitochondrial DNA mutation; mitochondrial membrane; Mitochondrial Proteins; Modeling; Mortality Vital Statistics; Names; overexpression; oxidant stress; Oxidation-Reduction; Pathogenesis; Pathology; PDH kinase; Phenotype; Play; Positron-Emission Tomography; Process; Production; Proteins; public health relevance; pulmonary arterial hypertension; Pulmonary artery structure; Pulmonary Hypertension; Rattus; Respiration; Reticulum; Role; Signal Transduction; Small Interfering RNA; Smooth Muscle Myocytes; Structure; Supplementation; Suppressor Genes; Syndrome; Therapeutic; therapeutic target; therapy development; Time; transcription factor; Tunica Adventitia; uptake; Vascular constriction (function); Vascular remodeling
Relevance: We are investigating the mechanism of pulmonary arterial hypertension (PAH) in Fawn Hooded Rats (FHR), and have identified problems in the FHR´s mitochondria, namely lower production of hydrogen peroxide and fragmentation of the mitochondrial network, which create a pseudohypoxic environment that favors rapid cell growth and blood vessel blockage. Preliminary studies show that FHR suffer from activation of an hypoxia inducible factor" (HIF-1¿) and a related break-up of the mitochondrial network due to a deficiency of mitofusin 2 (which triggers excessive growth of arterial smooth muscle cells and blocks the lung circulation). This proposal seeks to understand the role of the HIF-1 and mitofusin in PAH and develop therapies (inhibition of HIF-1 and supplementation of mitofusin-2) to restore mitochondrial form and function and cure PAH
Project start date: 2009-09-30
Project end date: 2011-08-31
Budget start date: 1-SEP-2010
Budget end date: 31-AUG-2011
PFA/PA: RFA-OD-09-003
5RC1HL099462-02 (2010): $500000
BIOMARKER FOR EARLY DETECTION OF CHRONIC KIDNEY DISEASE
L Stephen
Sequelacity: Falmouth country: United States (us)
Grant 5R43DK089892-02 from National Institute Of Diabetes And Digestive And Kidney Diseases
Abstract: This proposal is submitted in response to the program announcement PA-09-080, "Omnibus Solicitation of the NIH, CDC, and FDA for Small Business Innovation Research Grant Applications (Parent SBIR [R43/R44])" and intended to be directed to the NIDDK, with a potential dual assignment to the NHLBI. There are an estimated 14 million Americans with early chronic kidney disease (CKD). Early diagnosis and treatment of CKD are the only cost-effective means to reverse this growing problem. Current methods and biomarkers that are used to assess CKD are effective once the disease is well established, but , thus far, are reliable for the detection of early renal disease. Existing tests used by physicians today are all essentially markers of kidney filtration function. NIH recognizes the challenge to diagnose CKD early during its initiation and development phases in order to prevent further renal damage, reduce cardiovascular risk, and minimize the economic impact of CKD through program announcements such as PA-09-204 (Development and Validation of Disease Biomarkers) and PA-09-181 (Non-Invasive Methods for Diagnosis and Progression of Diabetes, Kidney, Urological, Hematological and Digestive Diseases). We will produce a new ELISA for CKD based upon the use of a novel biomarker that reflects, in part, the pathophysiology of kidney disease. Detection of this biomarker for CKD will give laboratory results and clinical insight that is complementary to creatinine-based GFR estimates (eGFR) as well as tests for urine albumin. Development of this test should result in a more reliable identification and detection of early CKD patients. In addition, our CKD ELISA would give physicians the ability to evaluate patients that have been recently diagnosed with hypertension or diabetes, the two leading causes of CKD. In turn, this Phase I proposal will evaluate the prototype assay in both populations. We will look for the influence of comorbid conditions and medications on assay performance. Lastly, we will evaluate whether patient characteristics such as age, gender, BMI, ethnicity, and other factors impact on assay performance. The information gained from this test will also lead to a better basic understanding of the biological mechanisms underlying CKD. Sequela requests Phase I support so that we can evaluate a prototype assay and test its feasibility to help identify at-risk patients for early kidney disease and monitor therapy with the ultimate goal of obtaining FDA approval. Chronic Kidney Disease affects nearly 26 million people in the United States, which places them at higher risk of renal failure and hemodialysis. We will develop an ELISA to aid in the diagnosis of early kidney disease to aid physicians in earlier treatment and better assessment of chronic kidney disease
Keywords: Affect; Age; Albumins; American; Antihypertensive Agents; Award; base; Biochemical Markers; Biological; Biological Assay; biomarker; Blood Circulation; Cardiovascular Diseases; cardiovascular disorder risk; cardiovascular risk factor; Cardiovascular system; Centers for Disease Control and Prevention (U.S.); Cessation of life; Characteristics; Chronic Kidney Failure; Clinical; Clinical Trials; Collaborations; Collection; Complement; Confusion; cost; cost effective; Creatinine; Data; Detection; Development; Diabetes Mellitus; diabetic; diabetic patient; Diagnosis; Diagnostic; Diagnostic tests; Dialysis procedure; Diet; Digestive System Disorders; Disease; Disease Outcome; Early Diagnosis; Early treatment; economic impact; Effectiveness; End stage renal failure; Endocrinology; Enzyme-Linked Immunosorbent Assay; Erythrocytes; Essential Hypertension; Ethnicity aspects; Evaluation; Exclusion Criteria; Excretory function; Filtration; Freezing; Functional disorder; Gender; Glomerular Filtration Rate; Goals; Gold; Health; Hematological Disease; Hemodialysis; high risk; Homeostasis; Hormonal; Hospitals; Human; Hypertension; Impairment; improved; Indiana; inorganic phosphate; insight; Institutes; Institutional Review Boards; Intervention; Iothalamate; Israel; Kidney; Kidney Diseases; Kidney Failure; Kidney Transplantation; Laboratories; Lead; Letters; Life; Location; Measurement; Measures; medical schools; Metabolism; Methods; Microalbuminuria; Modeling; Monitor; National Heart, Lung, and Blood Institute; National Institute of Diabetes and Digestive and Kidney Diseases; Nephrology; Nephrons; NIH Program Announcements; novel; novel diagnostics; Parents; Participant; Patients; Performance; Pharmaceutical Preparations; Phase; Physicians; Plasma; Play; Population; Population Control; post gamma-globulins; prevent; Prevention; Production; prohormone; Proteins; Protocols documentation; prototype; prouroguanylin; public health medicine (field); public health relevance; Receiver Operating Characteristics; receptor; Recording of previous events; Renal function; Renal Glycosuria; response; Risk; Risk Factors; Role; Sampling; Series; Serum; Site; Small Business Innovation Research Grant; Sodium; Sodium Chloride; Staging; Technology; Testing; Therapeutic Intervention; tool; Transplant Recipients; Transplantation; Transport Process; Tube; United States; United States National Institutes of Health; Universities; Urine; Urologic Diseases; Validation; Waiting Lists; Water; Weight; Work
Relevance: Chronic Kidney Disease affects nearly 26 million people in the United States, which places them at higher risk of renal failure and hemodialysis. We will develop an ELISA to aid in the diagnosis of early kidney disease to aid physicians in earlier treatment and better assessment of chronic kidney disease
Project start date: 2010-09-20
Project end date: 2012-08-31
Budget start date: 1-SEP-2011
Budget end date: 31-AUG-2012
PFA/PA: PA-09-080
5R43DK089892-02 (2011): $275076
A REAL-TIME ANTIBODY-BASED FIELD ASSAY TO PREDICT CONTAINMENT BIOAVAILABILITY IN
L Stephen
Virginia Institute Of Marine Sciencecity: Gloucester Point country: United States (us)
Grant 1R01ES020949-01 from National Institute Of Environmental Health Sciences
Abstract: This NIEHS-SRP research project will use newly developed biosensor technology to rapidly predict how polycyclic aromatic hydrocarbons (PAH) accumulate in seafood exposed to contaminated sediments. Hydrophobic contaminants such as PAH readily accumulate in shellfish, where they pose a significant human health risk when consumed. Lipid partitioning drives bioaccumulation in shellfish but multiple chemical, physical and environmental factors influence bioavailability and tissue concentrations in dynamic natural systems. Because measuring contaminant uptake in biota is time consuming and expensive, models have been developed to predict contaminant fate and disposition. However, temporal variability and heterogeneity of natural habitats make it difficult to reliably predict bioaccumulation for risk assessments from measured sediment concentrations. Ultimately, site-specific measurements are vital to accurately predict contaminant bioavailability and to evaluate the effectiveness of sediment remediation efforts. Recent advances in biosensor technology now allow near real-time measurement of contaminants at sub part per billion concentrations. This project will evaluate, refine and validate an automated, quantitative, monoclonal antibody-based sensor to measure PAH in sediment-associated water. We will validate the biosensor as a predictor of PAH tissue burdens in shellfish, an important route for PAH exposure to humans from contaminated sediments. This will be accomplished through controlled laboratory dosing of oysters. The biosensor will be then be applied in the highly contaminated Elizabeth River, Norfolk, Virginia to assess the effectiveness of ongoing remediation strategies being employed to reduce the human health risks associated with PAH exposure through the food web. Hypotheses 1. Real-time bio-sensor estimates of PAH concentration in aqueous samples (sediment pore water, surface water) rapidly and specifically predict lipid-normalized PAH concentrations in the tissues of native oysters inhabiting PAH-contaminated sites. 2. Biosensor measurements of aqueous PAH concentrations are specific, dose-responsive, correlate directly with tissue concentrations of PAH in dosed oysters and are therefore predictive surrogates of tissue bioaccumulation. 3. Incorporation of mixed analyte beds with differentative antibody specificities for different PAH classes will provide for more accurate discernment of the relative contribution of these different PAHs in the field and laboratory. Polycyclic aromatic hydrocarbons (PAH) are formed by the combustion of organic matter and they enter the aquatic environment via natural seeps, atmospheric inputs or through spills of petroleum and creosote. Because of their physical properties, PAHs will accumulate in sediments and seafood such as oysters. This research project will develop new antibody-based biosensors to rapidly measure PAHs in the aquatic environment so we can evaluate methods to remediate PAH-contaminated sediments to protect the public from the potential health risks associated with consuming contaminated seafood
Keywords: Adult; Alkylation; Antibodies; Antibody Specificity; Antigens; aqueous; Aromatic Polycyclic Hydrocarbons; base; Beds; bioaccumulation; Biological Assay; Biological Availability; Biosensor; Biota; Carbon; Characteristics; chemical property; Chemicals; Containment; cost effective; Creosote; Detection; Development; Dose; Effectiveness; Environment; Environmental Risk Factor; Evaluation; Exposure to; Food Webs; Habitats; Health; Heterogeneity; Human; Laboratories; Lipids; Measurement; Measures; Methods; Modeling; Monitor; Monoclonal Antibodies; National Institute of Environmental Health Sciences; Oysters; Petroleum; Phase; physical property; Proteins; Relative (related person); remediation; Research Project Grants; Risk; Risk Assessment; Rivers; Route; Sampling; Seafood; sensor; Shellfish - dietary; Signal Recognition Particle; Silicon Dioxide; Site; Specificity; superfund site; Surface; System; Technology; Testing; Time; Tissues; uptake; Variant; Virginia; Water
Relevance: Polycyclic aromatic hydrocarbons (PAH) are formed by the combustion of organic matter and they enter the aquatic environment via natural seeps, atmospheric inputs or through spills of petroleum and creosote. Because of their physical properties, PAHs will accumulate in sediments and seafood such as oysters. This research project will develop new antibody-based biosensors to rapidly measure PAHs in the aquatic environment so we can evaluate methods to remediate PAH-contaminated sediments to protect the public from the potential health risks associated with consuming contaminated seafood
Project start date: 2011-12-12
Project end date: 2014-10-31
Budget start date: 12-DEC-2011
Budget end date: 31-OCT-2012
1R01ES020949-01 (2012): $276184
TREATING ADOLSECENT AND ADULT METHAMPHETAMINE OR INHALANT ABUSE WITH S-(+)-GVG
L Stephen, Investigator
Feinstein Institute For Medical Researchcity: Manhasset country: United States (us)
Grant 5K02DA022346-06 from National Institute On Drug Abuse
Abstract: This is a revised K02 application. Dr. Stephen L. Dewey is a neuroanatomist and a senior scientist. He has a distinguished record in neuroimaging, microdialysis and medications development for drug abuse. His early work focused on imaging neurotransmitter interactions. These pioneering studies produced a paradigm shift that represents one of the most effective applications of PET research today. As a result, Dr. Dewey identified gamma vinyl-GABA, (GVG, vigabatrin) for the treatment of drug abuse. Following the generation of an unprecedented published preclinical database, which produced 9 U.S. patents (1 additional pending), he designed and conducted 2 open labeled clinical trials in adult cocaine and methamphetamine abusers. These trials suggested clinical efficacy and demonstrated visual safety, while also serving as the foundation for 2 Investigative New Drug (IND) applications, recently accepted by the FDA, for Phase I and II clinical trials. Dr. Dewey has successfully graduated 3 doctoral students and is currently a thesis advisor for three additional doctoral candidates as well as being a mentor to several junior scientists. In 1994, Dr. Dewey initiated an outreach program to adolescents that reached more than 55,000 children last year alone (more than 300,000 since its inception), motivating his new research initiative in inhalant abuse. This K02 will release Dr. Dewey from teaching and provide 60% salary support, which will result in at least 75% protected time to focus on the new molecular entity, S- (+)-GVG, for the treatment of adult and adolescent methamphetamine or inhalant abuse. This application proposes 2 synergistic goals (1) Research (60%); to identify optimal treatment regimens with the new molecular entity, S- (+)-GVG, for adult and adolescent methamphetamine or inhalant abuse using the identical strategies he successfully employed with GVG and (2); Mentoring and outreach (15%) to mentor junior investigators, post-doctoral fellows, and graduate and undergraduate students while continuing his extensive outreach program. This research benefits from collaborators at BNL, Stony Brook Univ, New York Univ, St. Johns Univ, and NIDA intramural. Thus, the objectives of this application are to identify optimal treatment regimens for methamphetamine or inhalant abuse while inspiring, teaching, and encouraging young scientists across disciplines to investigate the major public health consequences created by adolescent and adult drug abuse
Keywords: Addictive Behavior; Address; Adolescence; Adolescent; adolescent drug abuse; Adult; Age; Alcohols; Animals; Behavior; Behavioral; Binding (Molecular Function); Biochemical; Brain; Breathing; Child; Chronic; clinical efficacy; Clinical Trials; clinically relevant; Cocaine; cocaine use; Comorbidity; Data; Databases; Decision Making; Dependence; design; Development; Discipline; Dopamine; Dose; Drug abuse; drug of abuse; Educational process of instructing; enantiomer; experience; Foundations; Generations; Goals; Image; Imaging Techniques; inhalation drug abuse; Legal patent; Life; Longevity; Marihuana; mature animal; Mentors; Methamphetamine; methamphetamine abuse; Microdialysis; Modeling; Molecular; Motivation; National Institute of Drug Abuse; neurochemistry; neuroimaging; Neurotransmitters; New York; open label; Opiates; outreach; outreach program; Pattern; Pharmaceutical Preparations; Phase; Positron-Emission Tomography; Postdoctoral Fellow; pre-clinical; preference; Principal Investigator; Process; programs; Property; psychostimulant; Psychotropic Drugs; Puberty; public health medicine (field); Publishing; Raclopride; Recording of previous events; Regimen; Research; Research Personnel; Risk-Taking; Safety; Schedule; Scientist; Self Administration; Senior Scientist; Staging; statistics; Students; Time; Tobacco use; Toluene; Treatment Efficacy; Treatment Protocols; treatment strategy; Vigabatrin; Visual; Vulnerable Populations; Wages; Work
Project start date: 2007-09-01
Project end date: 2012-06-30
Budget start date: 1-JUL-2011
Budget end date: 30-JUN-2012
PFA/PA: PA-06-527
5K02DA022346-06 (2011): $134136
EDUCATING PHYSICIAN-NEUROSCIENTISTS: THE R25 AT UCSF
L Stephen
University Of California San Franciscocity: San Francisco country: United States (us)
Grant 5R25NS070680-02 from National Institute Of Neurological Disorders And Stroke
Abstract: There is a shortage of physician scientists and the number of physicians choosing to enter research careers is declining. This shortage threatens the biomedical research enterprise at a time when the opportunities for physician-neuroscientists to make substantial discoveries contributing to understanding and treatment of nervous system diseases (e.g.-Alzheimer disease, stroke, epilepsy, Parkinson disease) have increased dramatically.1 The National Institute of Health (NIH) has developed a roadmap to encourage disease-oriented research in supportive academic environments, including a special emphasis on improving the success rate of training programs for physician-scientists.2 One reason for the current decline in the physician-scientist pipeline is the long training period required to reach research independence. The average age of a first-time NIH R 01 grant recipient (one commonly used measure of research independence) has reached 43 years for MD applicants who face unique challenges on the path to research independence. By the time physicians have completed clinical residency training and are ready to apply for career development funding, many have reached their late 30s. This period is marked by important lifestyle decisions (e.g.-having a family, becoming financially independent, purchasing a first home) and career development decisions. Coupled with an average debt of approximately $150,000 at the end of medical school, these financial and lifestyle factors combine to discourage potential physician-scientists from embarking on research careers associated with low income, low rates of grant funding, and little long term security. Other career avenues (e.g.-private practice, industry) may seem more attractive for many of the brightest physicians in training. The R25 research education program implements the vision of the NIH roadmap at NINDS by providing new resources to assist promising physician investigators with improved training, mentorship, a supportive research environment, and resources that maximize the probability of a successful transition from the training environment to independent research careers. The Departments of Neurology, Neurosurgery, and Radiology at the University of California, San Francisco (UCSF) are committed to addressing the problem of declining interest in research careers by encouraging residents to develop or extend investigative pursuits during the clinical training years. The Department of Neurology at UCSF is well positioned to serve as the primary sponsor of the clinical neuroscience research education program, detailed below, that is the focus of this application. The development of new treatments and preventions for common nervous system disorders (Alzheimer disease, Parkinson disease, epilepsy, and stroke, among many other maladies) requires the maintenance and renewal of a vital research workforce that understands the relationship between basic neuroscience and clinical care, and is capable of bridging these two worlds. By supporting early research experiences for promising physicians, the R25 education research program is one important step that focuses the biomedical research community on the impending critical manpower shortage. Because of its commitment to training physician-scientists, demonstrated track record of success in this area, and the research accomplishments of its faculty, the clinical neuroscience community at UCSF can provide an outstanding environment for implementation of this program. Although the Department of Neurology is the primary sponsor of this application, the full support and participation of the Departments of Radiology and Neurosurgery for this application (see attached letters of support from Drs. William Dillon and Nicholas Barbaro)
Keywords: Address; Age; Alzheimer`s Disease; Area; Biomedical Research; California; Cancer Education Grant Program; career; career development; Clinical; clinical care; Commit; Communities; Coupled; Development; Disease; Educational aspects; Environment; Epilepsy; experience; Face; Family; Fellowship; Funding; Goals; Grant; Home environment; Human Resources; improved; Industry; interest; Letters; Life Style; lifestyle factors; Low income; Maintenance; Measures; medical schools; Mentorship; National Institute of Neurological Disorders and Stroke; nervous system disorder; Neurology; Neurosciences; Neurosciences Research; neurosurgery; Nursing Faculty; Parkinson Disease; Physicians; Positioning Attribute; Prevention; Private Practice; Probability; programs; public health relevance; Radiology Specialty; Research; Research Personnel; Research Support; Research Training; Residencies; Resources; San Francisco; Scientist; Security; stroke; success; Time; Training; Training Programs; United States National Institutes of Health; Universities; Vision
Relevance: The development of new treatments and preventions for common nervous system disorders (Alzheimer disease, Parkinson disease, epilepsy, and stroke, among many other maladies) requires the maintenance and renewal of a vital research workforce that understands the relationship between basic neuroscience and clinical care, and is capable of bridging these two worlds. By supporting early research experiences for promising physicians, the R25 education research program is one important step that focuses the biomedical research community on the impending critical manpower shortage. Because of its commitment to training physician-scientists, demonstrated track record of success in this area, and the research accomplishments of its faculty, the clinical neuroscience community at UCSF can provide an outstanding environment for implementation of this program. Although the Department of Neurology is the primary sponsor of this application, the full support and participation of the Departments of Radiology and Neurosurgery for this application (see attached letters of support from Drs. William Dillon and Nicholas Barbaro)
Project start date: 2010-04-01
Project end date: 2015-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: RFA-NS-10-002
5R25NS070680-02 (2011): $1
ASTROCYTIC INTEGRINS IN CEREBRAL VESSEL FORMATION
L Stephen, Professor
University Of California San Franciscocity: San Francisco country: United States (us)
Abstract: The long-term goal of this competitive renewal is to understand the mechanistic basis of the cellular interactions required for vessel formation in the central nervous system (CMS). The CMSvasculature differs from the non-CNS vasculature by the presence of the blood-brain barrier (BBB), the formation of which is largely due to interactions with astrocytes. In the past period of support, we have investigated the role that astrocytes play in orchestrating the events that guide proper cerebral vessel development. In particular, we have identified a mechanism for the astrocytic integrin m/p8 in regulating endothelial differentiation. Thus, we have found that astrocytic av(J8-mediatedactivation of TGF-p inhibits endothelial migration and dramatically alters the expression of major endothelial angiogenic and proteolytic factors. This data fills a previous gap in knowledge of the molecular basis for the reciprocal signaling between astrocytes and endothelial cells. Our data suggests that paracrine TGF-p signaling between astrocytes and endothelial cells is the mechanistic basis for the cerebral hemorrhagic phenotype of integrin p8 subunit knock-out mice. TGF-p is essential to normal CNS vasculogenesis since loss of function of the endothelial receptors for active TGF-p, endoglin and Alk-1, lead to hereditary hemorrhagic telangectasia (HHT) in humans and a similar cerebral hemorrhagic disorder in deficient mice. Because TGF-p is ubiquitously expressed in tissues almost entirely in an inactive (latent) state, the avpS-dependent conversion of latent to active TGF-p by astrocytes could be a major regulatory step in the presentation of active TGF-p to CNS endothelial cells. Our preliminary data demonstrate that astrocytes in brain arteriovenous malformation (BAVM) tissues express less P8than control brain tissues; reduced b8 expression is associated with a b8 genotype associated with AVM susceptibility. Furthermore, we have determined that 08 expression in normal astrocytes is dramatically upregulated by IL-10, and that two SNPs in the IL-10 promoter are associated with BAVMsusceptibility and reduced IL-1 ft expression in a cohort of BA VMpatients. These data suggest several mechanisms whereby J38transcription is reduced in BAVMs. We have recently isolated the human and mouse p8 promoters and have identified an IL-1p responsive region. In addition, we have identifiedseveral tag SNPs mapping near the (38 promoter region that show a strong association (p=0.005) with BAVM susceptibility and correlate with reduced expression of (38expression in perivascular cells in BAVM tissue. Finally, we have determined that conditional deletion ofitgbQ in the brain leads to dysplastic neoangiogenesis in response to local VEGF stimulation. Thus, our novel findings support the hypothesis Decreased astrocytic P8 expression results in reduced avpS-dependent activation of TGF-p causing pathologic alterations of cerebral vascular integrity and differentiation. This hypothesis will beexplored in three
Keywords: Adult; Affect; Alleles; angiogenesis; Area; Arteriovenous malformation; Astrocytes; autocrine; base; Binding (Molecular Function); Biological Assay; Biology; Blood - brain barrier anatomy; Blood Vessels; Brain; brain tissue; Brain Vascular Malformation; Cell Communication; Cell Differentiation process; Cell Surface Receptors; cell type; Cells; Cerebral hemisphere hemorrhage; Cerebrum; Chemicals; chromatin immunoprecipitation; chromatin remodeling; Clinical; Coculture Techniques; cohort; Complex; Cues; cytokine; Data; Development; Endoglin; Endothelial Cells; Environment; Event; extracellular; Feedback; Funding; Genes; Genetic Transcription; genetic variant; Genotype; Goals; Hemorrhagic Disorders; Histone Acetylation; Histones; Human; Inflammation Mediators; Inherited; Injection of therapeutic agent; insight; Integrins; Interleukin-1; Interleukin-10; Investigation; Knockout Mice; Knowledge; Lead; Link; loss of function; MADH4 gene; Maps; Mediating; Mediator of activation protein; migration; Modality; Modeling; Molecular; Morphogenesis; Mus; nestin protein; Neuraxis; Neuroepithelial; Neuroepithelial Cells; Neuroglia; Neurons; novel; Nucleic Acid Regulatory Sequences; overexpression; paracrine; Pathogenesis; Pathologic; Pericytes; Phenotype; Play; Predisposition; Pregnancy; prognostic; programs; Promoter Regions (Genetics); Promotor (Genetics); Rattus; receptor; Research Personnel; research study; response; Role; Signal Transduction; Single Nucleotide Polymorphism; Single Nucleotide Polymorphism Map; Testing; Therapeutic; Tissues; Transcription Coactivator; transcription factor; Transcriptional Regulation; Transgenic Organisms; Variant; Variation (Genetics); Vascular Endothelial Growth Factors; vasculogenesis
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
5P01NS044155-08_5204 (2011): $172884
SINGLE GENE MUTANTS THAT CONFER LONGEVITY IN DROSPHILA
L Stephen, Professor Of Biology
Brown Universitycity: Providence country: United States (us)
Grant 5R37AG016667-13 from National Institute On Aging
Abstract: The long-term goal of our studies is to understand the molecular and genetic elements that underlie the process of aging and determine longevity. The aim of this proposal is to understand how mutations in a single gene, Indy, result in a dramatic increase in life span in Drosophila melanogaster without a concomitant loss of reproduction, physical activity or metabolic rate. In particular we will seek to determine where and when Indy mutations act to extend life span. The function of the INDY protein as a tranporter of Krebs cycle intermediates and its preliminary localization to regions of the fly important in uptake, utilization and storage of nutrients, indicate that reductions in the level of INDY protein alters the metabolic state of the fly in a way that favors life span extension. INDY´s similarity in sequence, function, and tissue expression to mammalian and human dicarboxylate transporters suggests that knowledge of how Indy mutations extend life span in flies may be useful for the development of therapeutic interventions for extending healthy life in humans. We will first examine the tissues and times during life INDY expression is altered in the long-lived Indy mutant animals. Using molecular genetic approaches we will restore Indy function to directly determine where and when Indy mutations act to extend life span. Finally we will determine which of the several possible human Indy-like genes can functionally rescue the Indy mutation. A more complete understanding of how mutations in Indy lead to life span extension should yield valuable insights into general mechanisms of life span extension relevant to a variety of organisms including humans
Keywords: Adult; Affect; Aging-Related Process; Animals; Citric Acid Cycle; Development; dicarboxylate-binding protein; Drosophila genus; Drosophila melanogaster; fly; Future; gene therapy; Genes; Genetic; genetic element; Goals; Homologous Gene; Human; Impairment; insight; Intervention; Knowledge; Lead; Life; Longevity; Mammals; Messenger RNA; Metabolic; Molecular Genetics; mutant; Mutation; Nutrient; Organism; Phenotype; Physical activity; Process; Proteins; Reproduction; Research; System; Techniques; Therapeutic Intervention; Time; Tissues; Transgenes; Transgenic Organisms; uptake
Project start date: 1999-04-01
Project end date: 2014-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
5R37AG016667-13 (2011): $295901
3R37AG016667-13S1 (2011): $5000
Sponsored Links Excellgen http://Excellgen.com
5R37AG016667-12 (2010): $328526
OXIDATIVE DAMAGE, AGING AND LIFE SPAN
L Stephen, Professor Of Biology
Brown Universitycity: Providence country: United States (us)
Grant 5R01AG025277-05 from National Institute On Aging
Abstract: The long-term goal of our studies is to understand the molecular and genetic elements that underlie the process of aging and determine longevity. One of the most prominent hypotheses explaining the aging process is the oxidative stress hypothesis, which states that the rate of aging and life span is directly related to the accumulation of oxidative damage to organelles and macromolecules. Comparative studies between species having different life spans have been one of the foundations of the oxidative stress hypothesis, predicting a direct relationship between the accumulation of oxidative damage, the rate of aging and life span. We propose to use the fruit fly model system, Drosophila melanogaster, to compare the relationship between life span and the accrual of oxidative damage within a single, genetically well defined species, using a variety of strains and environmental and genetic conditions known to alter life span. These studies will better define the precise relationship between oxidative damage and life span, laying the foundation for a map detailing the specific quantitative relationship between oxidative damage, aging and life span. An additional advantage of using Drosophila to perform these comparative studies is that the powerful molecular and genetic techniques available in Drosophila can be used to directly identify and test specific physiological systems important in aging
Keywords: 21+ years old; Adult; adult human (21+); Affect; Age; age dependent; age related; Aging; Aging Process; Aging-Related Process; Animals; Biological Models; biomarker; Body Tissues; Comparative Study; Deoxyribonucleic Acid; Development; DNA; DNA Alteration; DNA mutation; Drosophila; Drosophila genus; Drosophila melanogaster; environmental intervention; Foundations; fruit fly; Fruit Fly, Drosophila; Future; Gene Alteration; Gene Mutation; gene product; Genes; Genetic; Genetic Alteration; Genetic Change; Genetic Condition; Genetic defect; Genetic Diseases; genetic disorder; genetic element; Genetic mutation; Genetic Techniques; genome mutation; Goals; Hereditary Disease; hereditary disorder; Human, Adult; Humulin R; Inbred Strain; Individual; insight; Insulin; Insulin (ox), 8A-L-threonine-10A-L-isoleucine-30B-L-threonine-; Insulin, Regular; Intervention; Intervention Strategies; interventional strategy; Knowledge; Length of Life; Life; life span; lifespan; Lipids; Location; Longevity; macromolecule; Maps; Mitochondria; mitochondrial; Model System; Models, Biologic; Molecular; Molecular Disease; Molecular Genetic; Molecular Genetics; Muscle; Muscle Tissue; Mutation; Nature; Nerve Cells; Nerve Unit; Neural Cell; Neurocyte; neuronal; Neurons; Novolin R; Nuclear; Oregon; Organelles; oxidative damage; Oxidative Stress; Physiologic; Physiological; Play; Proteins; receptor; Receptor Protein; reproductive; response; Role; Senescence; senescent; Sequence Alteration; social role; Subcellular Fractions; System; System, LOINC Axis 4; Technics, Genetic; Temperature; Testing; Time; Tissues
Project start date: 2005-09-30
Project end date: 2011-06-30
Budget start date: 15-AUG-2009
Budget end date: 30-JUN-2011
5R01AG025277-05 (2009): $291168
MOLECULAR GENETICS OF HLA AND DISEASE
L Stephen
University Of California San Franciscocity: San Francisco country: United States (us)
Grant 5U19AI067152-05 from National Institute Of Allergy And Infectious Diseases
Abstract: The goal of this application is to identify and characterize the complete repertoire of genes encoded in the MHC region that predispose and/or modulate the expression of autoimmune disease. Following the recent NINDS-sponsored workshop on MHC Genetics in Autoimmune Diseases and the subsequent announcement of an RFA to extend interdisciplinary science in this area, we created a Consortium, named The International MHC and Autoimmunity Genetics Network (IMAGEN) to tackle this problem in a meaningful and decisive manner. The IMAGEN investigators represent a large, diverse, and broad-based collaborative team of scientists at eight academic centers with synergistic skills; demonstrated expertise in MHC genetics and biology; clinical expertise in identifying endophenotypes; history of mutual productive collaborations; and experience in large scale genotyping and state-of-the-art analytical approaches. The basic structure of this collaborative project proposes a common base screen with a panel of more than1500 highly informative SNPs and replication for all diseases. Biologically relevant clinical endpoints will be incorporated into the analysis to assess the role of HLA variants in progression. Specific aim 3 for each project will address disease-specific questions. The primary screen will allow us to 1) map the association signal(s) across the entire MHC to identify regions of the maximal signal; 2) identify extended MHC haplotypes carrying the strongest association signals; 3) identify recombinant chromosomes that maximally delimit the association; 4) make testable hypotheses as to whether different autoimmune diseases are influenced by a single association with a particular locus, or a single association with an extended haplotype or multiple, independent associations across the MHC. The focus is on Multiple Sclerosis, Rheumatoid Arthritis, IgA Deficiency, Common Variable Immunodeficiency, Myasthenia Gravis, Systemic Lupus Erythematosus and Ulcerative Colitis. We believe that the clinical dataset assembled for this project is unmatched anywhere in the world. An Administrative Core at UCSF will coordinate activities and interactions for the overall project. A second Core at the Broad Institute will be responsible for generation of genotypes, data QC, storage, and interaction with BISC
Project start date: 2005-09-01
Project end date: 2011-02-28
Budget start date: 1-MAR-2009
Budget end date: 28-FEB-2011
PFA/PA: RFA-AI-04-039
5U19AI067152-05 (2009): $1774821
O2 SENSING IN THE HUMAN AND RABBIT DUCTUS ARTERIOSUS.
L Stephen, Chief Of Cardiology
University Of Chicagocity: Chicago country: United States (us)
Grant 2R01HL071115-08 from National Heart, Lung, And Blood Institute
Abstract: The ductus arteriosus (DA) is a fetal artery that allows blood ejected from the right ventricle to bypass the pulmonary circulation in utero. At birth, functional closure of the DA is initiated within minutes by O2-induced vasoconstriction. Functional closure (vasoconstriction) stops right to left shunting of blood and promotes anatomical closure. Failure of these processes leads to persistent ductus arteriosus, a common form of congenital heart disease in premature infants. During the first 5 years of this grant we showed that the DA´s O2- sensing pathway consists of a sensor (the mitochondrial electron transport chain), which produces a diffusible mediator (H2O2), that inhibits voltage-gated K+ channels, such as Kv1.5. At birth, O2-induced increases in mitochondrial H2O2 in DA smooth muscle cells (DASMC) promote constriction by several mechanisms Kv channel inhibition, direct activation of O2-sensitive calcium channels and rho kinase activation. Moreover, preterm DASMC are relatively deficient in these mechanisms, explaining the prevalence of persistent DA in preterm DA. This renewal focuses on a discovery made during a search for splice variants of Kv1.5 in human DASMC. We found a novel K+ channel, Human Oxygen-Sensitive K+ channel (HOSK), that when heterologously expressed creates a current that is voltage-gated, displays K+ specificity (Rb>K>>Cs>Na), and is 4- aminopyridine sensitive. HOSK appears to contribute to the resting membrane potential in human DASMC. HOSK siRNA reduces the O2-sensitive current in human DASMC. HOSK cDNA corresponds to a 3.0 kb neuronal, expressed sequence tag (EST) and has an unusual coding mechanism. HOSK and collagen 12(I) have identical mRNA with the much smaller 21 kDa HOSK resulting from initiation of translation at an internal ribosomal entry site (IRES). In silico modeling suggests that HOSK may have four hydrophobic domains (HD), a unique K+ selectivity filter (GVL, rather than the typical GYG amino acid sequence) and a variant voltage sensor. Phylogenetic analysis suggests HOSK originated in amniotes. In this proposal, the relative importance of HOSK versus canonical O2-sensitive voltage-gated K+ channels, Kv1.5 and Kv2.1, will be compared in term human DA, and two models of impaired O2 constriction preterm rabbit DA and ionically remodeled human DA. Aim 1 HOSK is a novel K+ channel, arising independent of the canonical K+ channel family. Aim 2 HOSK contributes to DA constriction and augmenting HOSK expression will enhance O2- constriction in preterm rabbit DA and ionically remodeled human DA. Aim 3 HIF-11 shifts translation of the collagen gene away from HOSK toward collagen 21(1). HOSK, hidden by its complex encoding mechanism and unique structure, may offer a new explanation for how O2 causes constriction and will shed light on the link between constriction and fibrous obliteration of the DA. Since HOSK may have arisen independent of the canonical K+ channel family, exploring its structure-function relationship will extend our fundamental knowledge K+ channels. With the first breath of life, the ductus arteriosus (DA) constricts in response to increased oxygen, forcing blood to the baby´s newly expanded lungs. Failure of DA closure (persistent DA) is a common form of congenital heart disease. We discovered that the DA senses oxygen using a mitochondrial sensor, which generates hydrogen peroxide, thereby inhibiting voltage-gated K+ channels as oxygen increases, and causing DA constriction. This renewal grant focuses on Human Oxygen-Sensitive K+ channel (HOSK), a novel K+ channel, which we discovered in human DA. Hidden by a complex encoding mechanism and unique structure, HOSK promises new understanding of K+ channel structure-function relationships and may link constriction and fibrous obliteration of the DA
Keywords: 4-Aminopyridine; Air; Amino Acid Sequence; Arteries; Birth; Blood; Breathing; Bypass; Calcium Channel; Chimeric Proteins; Chinese Hamster Ovary Cell; Code; Collagen; Collagen Gene; Complementary DNA; Complex; Computer Simulation; congenital heart disorder; constriction; Cyanosis; Deposition; Down-Regulation; Electron Transport; Electrophysiology (science); Expressed Sequence Tags; Failure (biologic function); Failure to Thrive; Family; fetal; Gene Transfer; Graft vs Leukemia Effect; Grant; Human; human data; Hydrogen Peroxide; Hypoxia Inducible Factor; Ibuprofen; in utero; in vivo; interest; Knowledge; Left; Life; Light; Link; Low Birth Weight Infant; Lung; Mediating; Mediator of activation protein; Medical; Membrane Potentials; Messenger RNA; Mitochondria; Modeling; Molecular; Names; Neurons; new therapeutic target; Newborn Infant; novel; Operative Surgical Procedures; Organism; Oryctolagus cuniculus; overexpression; Oxidation-Reduction; Oxygen; Pathway interactions; Phylogenetic Analysis; Physiology; Potassium Channel; premature; Premature Infant; Prevalence; Process; Production; Prostaglandin-Endoperoxide Synthase; Proteins; Pulmonary Circulation; Relative (related person); research study; response; Rest; Rho-associated kinase; Right ventricular structure; RNA; RNA Splicing; sensor; Shunt Device; Site; Site-Directed Mutagenesis; Smooth Muscle Myocytes; Specificity; Structure; Structure of ductus arteriosus; Structure-Activity Relationship; tissue culture; Translation Initiation; Translations; Variant; Vascular constriction (function); voltage; Voltage-Gated Potassium Channel
Relevance: With the first breath of life, the ductus arteriosus (DA) constricts in response to increased oxygen, forcing blood to the baby´s newly expanded lungs. Failure of DA closure (persistent DA) is a common form of congenital heart disease. We discovered that the DA senses oxygen using a mitochondrial sensor, which generates hydrogen peroxide, thereby inhibiting voltage-gated K+ channels as oxygen increases, and causing DA constriction. This renewal grant focuses on Human Oxygen-Sensitive K+ channel (HOSK), a novel K+ channel, which we discovered in human DA. Hidden by a complex encoding mechanism and unique structure, HOSK promises new understanding of K+ channel structure-function relationships and may link constriction and fibrous obliteration of the DA
Project start date: 2002-07-01
Project end date: 2016-04-30
Budget start date: 1-JUL-2011
Budget end date: 30-APR-2012
PFA/PA: PA-10-067
2R01HL071115-08 (2011): $390000
O2 SENSING IN THE HUMAN AND RABBIT DUCTUS ARTERIOSUS
L Stephen, Chief Of Cardiology
University Of Chicagocity: Chicago country: United States (us)
Grant 5R01HL071115-07 from National Heart, Lung, And Blood Institute
Abstract: The ductus arteriosus (DA) is a fetal artery that allows blood ejected from the right ventricle to bypass the pulmonary circulation in utero. At birth, functional closure of the DA is initiated within minutes by O2-induced vasoconstriction. Functional closure (vasoconstriction) stops right to left shunting of blood and promotes anatomical closure. Failure of these processes leads to persistent ductus arteriosus, a common form of congenital heart disease in premature infants. Although endothelial-derived mediators modulate DA tone, O2 exerts a direct constrictor effect. During the first 5 years of this grant we showed that the DA´s O2-sensing pathway consists of a sensor (the mitochondrial electron transport chain), which produces a diffusible mediator (H2O2), that inhibits voltage-gated K+ channels, such as Kv1.5. At birth, O2-induced increases in mitochondrial H2O2 in DA smooth muscle cells (DASMC) promote constriction by several mechanisms Kv channel inhibition, direct activation of O2-sensitive calcium channels and rho kinase activation. Moreover, preterm DASMC are relatively deficient in these mechanisms, explaining the prevalence of persistent DA in preterm DA. This renewal focuses on a discovery made during a search for splice variants of Kv1.5 in human DASMC. We found a novel K+ channel, Human Oxygen-Sensitive K+ channel (HOSK), that when heterologously expressed creates a current that is voltage-gated, displays K+ specificity (Rb>K>>Cs>Na), and is 4- aminopyridine sensitive. HOSK appears to contribute to the resting membrane potential in human DASMC. HOSK siRNA reduces the O2-sensitive current in human DASMC. HOSK cDNA corresponds to a 3.0 kb neuronal, expressed sequence tag (EST) and has an unusual coding mechanism. HOSK and collagen 12(I) have identical mRNA with the much smaller 21 kDa HOSK resulting from initiation of translation at an internal ribosomal entry site (IRES). In silico modeling suggests that HOSK may have four hydrophobic domains (HD), a unique K+ selectivity filter (GVL, rather than the typical GYG amino acid sequence) and a variant voltage sensor. Phylogenetic analysis suggests HOSK originated in amniotes. In this proposal, the relative importance of HOSK versus canonical O2-sensitive voltage-gated K+ channels, Kv1.5 and Kv2.1, will be compared in term human DA, and two models of impaired O2 constriction preterm rabbit DA and ionically remodeled human DA. Hypothesis 1 HOSK is a novel K+ channel, arising independent of the canonical K+ channel family. Hypothesis 2 HOSK contributes to DA constriction and augmenting HOSK expression will enhance O2- constriction in preterm rabbit DA and ionically remodeled human DA. Significance The proposed experiments will contribute to our understanding of the normal mechanism of DA constriction and functional closure of the human DA. HOSK, hidden by its complex encoding mechanism and unique structure may offer a new explanation for how O2 causes functional closure and shed light on the link between DA constriction and fibrous obliteration of the DA. The ductus arteriosus (DA) is a fetal artery that allows blood ejected from the right ventricle to bypass the pulmonary circulation in utero. The DA closes at birth by a by an O2-induced, vasoconstrictor mechanism that is intrinsic to the smooth muscle cells. Failure of functional closure (vasoconstriction) can cause persistent DA. During the first 5 years of this grant we showed that the DA´s O2-sensing pathway consists of a mitochondrial sensor, which produces diffusible H2O2, that inhibits voltage-gated K+ channels, such as Kv1.5. This renewal assesses a novel voltage-gated K+ channel, Human Oxygen-Sensitive K+ channel (HOSK). Hidden by its complex encoding mechanism within the collagen a2(1) gene HOSK has a unique structure and explain how O2 causes functional closure of the DA and extend our basic knowledge of K+ channel structure/function
Keywords: 4-Aminopyridine; Air; Amino Acid Sequence; Arteries; Birth; Blood; Breathing; Bypass; Calcium Channel; Cell Proliferation; Code; Collagen; Complementary DNA; Complex; Computer Simulation; congenital heart disorder; constriction; COS Cells; Cyanosis; Down-Regulation; Electron Transport; Electrophysiology (science); Expressed Sequence Tags; Failure (biologic function); Failure to Thrive; Family; fetal; Fibrosis; Gene Transfer; Genes; Graft vs Leukemia Effect; Grant; Human; Hydrogen Peroxide; Hypoxia Inducible Factor; Ibuprofen; in utero; inhibitor/antagonist; interest; Knowledge; Left; Light; Link; Lung; Mediator of activation protein; Medical; Membrane Potentials; Messenger RNA; Mitochondria; Modeling; Names; Neurons; Newborn Infant; novel; Operative Surgical Procedures; Organism; Oryctolagus cuniculus; Oxygen; Patent Ductus Arteriosus; Pathway interactions; Pharmacology; Phylogenetic Analysis; Potassium Channel; Pregnancy; premature; Premature Infant; Prevalence; Process; Production; Prostaglandin-Endoperoxide Synthase; Proteins; public health relevance; Pulmonary Circulation; Relative (related person); research study; response; Rest; Rho-associated kinase; Right ventricular structure; RNA; RNA Splicing; sensor; Shunt Device; Site; Site-Directed Mutagenesis; Smooth Muscle Myocytes; Specificity; Structure; Structure of ductus arteriosus; Structure-Activity Relationship; tissue culture; Translation Initiation; Translations; Variant; Vascular constriction (function); Vasoconstrictor Agents; voltage; Voltage-Gated Potassium Channel
Relevance: The ductus arteriosus (DA) is a fetal artery that allows blood ejected from the right ventricle to bypass the pulmonary circulation in utero. The DA closes at birth by a by an O2-induced, vasoconstrictor mechanism that is intrinsic to the smooth muscle cells. Failure of functional closure (vasoconstriction) can cause persistent DA. During the first 5 years of this grant we showed that the DA´s O2-sensing pathway consists of a mitochondrial sensor, which produces diffusible H2O2, that inhibits voltage-gated K+ channels, such as Kv1.5. This renewal assesses a novel voltage-gated K+ channel, Human Oxygen-Sensitive K+ channel (HOSK). Hidden by its complex encoding mechanism within the collagen a2(1) gene HOSK has a unique structure and explain how O2 causes functional closure of the DA and extend our basic knowledge of K+ channel structure/function
Project start date: 2002-07-01
Project end date: 2011-06-30
Budget start date: 1-JUL-2010
Budget end date: 30-JUN-2011
PFA/PA: PA-07-070
5R01HL071115-07 (2010): $466215
2R01HL071115-06 (2009): $454816
LATE TRANSITION METAL CATALYSTS FOR ORGANIC SYNTHESIS
L Stephen, Professor
Massachusetts Institute Of Technologycity: Cambridge country: United States (us)
Grant 5R01GM058160-14 from National Institute Of General Medical Sciences
Abstract: The ability to prepare functionalized organic molecules rationally and predictably, whether individually or in libraries, is central to organic synthesis, medicinal chemistry and the pharmaceutical industry. The aims of this work are to develop new and/or improved methods for the formation of carbon-nitrogen and carbon-oxygen bonds. Included in this work is the development of new strategies and techniques for the preparation of complex heterocycles, which are the building blocks of medicinal chemistry and the pharmaceutical industry, via cross-coupling methodology. Further, information gained from this work will help to understand the mechanism of the processes that are being developed in order to increase the rate of improvement of the techniques that we are studying. The development of new methods for organic synthesis is key to the development of the field of organic chemistry as a whole. These reactions are of critical importance to the pharmaceutical industry. Cross-coupling methods for carbon-heteroatom bond formation are regularly used by those in the pharmaceutical industry for the preparation of analogues with increased potency and reduced side effects. Moreover, the methods can be employed for the preparation of quantities of new substances for preclinical and clinical testing and for the actual manufacture of a pharmaceutical agent. The techniques that are being developed allow for these important functions to be carried out in a more rapid and efficient fashion than previously possible. Moreover, they allow for the preparation of new substances, which have previously been inaccessible. These new compounds have the possibilities of having physiological properties of great importance in medicinal chemistry and the pharmaceutical industry. Further these techniques are used by researchers in both academia and industry in a variety of areas of bioorganic and materials research including in the formation of new sensory materials. The cross-coupling methods we are developing for carbon-heteroatom bond formation are regularly used by those in the pharmaceutical industry for the preparation of analogues with increased potency and reduced side effects. Moreover, the methods can be employed for the preparation of quantities of new substances for preclinical and clinical testing and for the actual manufacture of a pharmaceutical agent
Keywords: Academia; Adverse effects; analog; Area; Carbon; catalyst; Complex; Coupling; design; Development; Drug Industry; Due Process; improved; Industry; interest; Knowledge; Libraries; Ligands; method development; Methodology; Methods; Nitrogen; Organic Chemistry; Organic Synthesis; Oxygen; Pharmaceutical Chemistry; Pharmacologic Substance; Physiological; Preclinical Testing; Preparation; Process; Property; public health relevance; Reaction; Research; research clinical testing; Research Personnel; Sensory; Structure; success; Techniques; Transition Elements; Work
Relevance: The cross-coupling methods we are developing for carbon-heteroatom bond formation are regularly used by those in the pharmaceutical industry for the preparation of analogues with increased potency and reduced side effects. Moreover, the methods can be employed for the preparation of quantities of new substances for preclinical and clinical testing and for the actual manufacture of a pharmaceutical agent
Project start date: 1998-09-01
Project end date: 2014-07-31
Budget start date: 1-AUG-2011
Budget end date: 31-JUL-2012
PFA/PA: PA-07-070
5R01GM058160-14 (2011): $560452
EDUCATING PHYSICIAN-NEUROSCIENTISTS: THE R25 AT UCSF
L Stephen
University Of California San Franciscocity: San Francisco country: United States (us)
Grant 3R25NS070680-02S1 from National Institute Of Neurological Disorders And Stroke
Abstract: Project Summary/ There is a shortage of physician scientists and the number of physicians choosing to enter research careers is declining. This shortage threatens the biomedical research enterprise at a time when the opportunities for physician-neuroscientists to make substantial discoveries contributing to understanding and treatment of nervous system diseases (e.g.-Alzheimer disease, stroke, epilepsy, Parkinson disease) have increased dramatically.1 The National Institute of Health (NIH) has developed a roadmap to encourage disease-oriented research in supportive academic environments, including a special emphasis on improving the success rate of training programs for physician-scientists.2 One reason for the current decline in the physician-scientist pipeline is the long training period required to reach research independence. The average age of a first-time NIH R 01 grant recipient (one commonly used measure of research independence) has reached 43 years for MD applicants who face unique challenges on the path to research independence. By the time physicians have completed clinical residency training and are ready to apply for career development funding, many have reached their late 30s. This period is marked by important lifestyle decisions (e.g.-having a family, becoming financially independent, purchasing a first home) and career development decisions. Coupled with an average debt of approximately $150,000 at the end of medical school, these financial and lifestyle factors combine to discourage potential physician-scientists from embarking on research careers associated with low income, low rates of grant funding, and little long term security. Other career avenues (e.g.-private practice, industry) may seem more attractive for many of the brightest physicians in training. The R25 research education program implements the vision of the NIH roadmap at NINDS by providing new resources to assist promising physician investigators with improved training, mentorship, a supportive research environment, and resources that maximize the probability of a successful transition from the training environment to independent research careers. The Departments of Neurology, Neurosurgery, and Radiology at the University of California, San Francisco (UCSF) are committed to addressing the problem of declining interest in research careers by encouraging residents to develop or extend investigative pursuits during the clinical training years. The Department of Neurology at UCSF is well positioned to serve as the primary sponsor of the clinical neuroscience research education program, detailed below, that is the focus of this application
Keywords: ing; Address; Age; Alzheimer`s Disease; Area; Biomedical Research; California; Cancer Education Grant Program; career; career development; Clinical; clinical care; Commit; Communities; Coupled; Development; Disease; Educational aspects; Environment; Epilepsy; experience; Face; Family; Fellowship; Funding; Goals; Grant; Home environment; Human Resources; improved; Industry; interest; Letters; Life Style; lifestyle factors; Low income; Maintenance; Measures; medical schools; Mentorship; National Institute of Neurological Disorders and Stroke; nervous system disorder; Neurology; Neurosciences; Neurosciences Research; neurosurgery; Nursing Faculty; Parkinson Disease; Physicians; Positioning Attribute; Prevention; Private Practice; Probability; programs; Radiology Specialty; Research; Research Personnel; Research Support; Research Training; Residencies; Resources; San Francisco; Scientist; Security; stroke; success; Time; Training; Training Programs; United States National Institutes of Health; Universities; Vision
Relevance: The development of new treatments and preventions for common nervous system disorders (Alzheimer disease, Parkinson disease, epilepsy, and stroke, among many other maladies) requires the maintenance and renewal of a vital research workforce that understands the relationship between basic neuroscience and clinical care, and is capable of bridging these two worlds. By supporting early research experiences for promising physicians, the R25 education research program is one important step that focuses the biomedical research community on the impending critical manpower shortage. Because of its commitment to training physician-scientists, demonstrated track record of success in this area, and the research accomplishments of its faculty, the clinical neuroscience community at UCSF can provide an outstanding environment for implementation of this program. Although the Department of Neurology is the primary sponsor of this application, the full support and participation of the Departments of Radiology and Neurosurgery for this application (see attached letters of support from Drs. William Dillon and Nicholas Barbaro)
Project start date: 2010-04-01
Project end date: 2015-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: RFA-NS-10-002
3R25NS070680-02S1 (2011): $230723
RARE DISEASE SUSCEPTIBILITY ALLELES IN CHILDREN WITH CROHN DISEASE
L Stephen, Assistant Professor
University Of Utahcity: Salt Lake City country: United States (us)
Grant 1R01DK091374-01A1 from National Institute Of Diabetes And Digestive And Kidney Diseases
Abstract: PROJECT SUMMARY/ The overall goal of this proposed project is to identify rare genetic variants contributing to childhood onset- Crohn disease. Crohn disease is a chronic inflammatory disorder of the gastrointestinal tract of unclear etiology and no known cure. Affected children suffer from diarrhea, abdominal pain, growth disturbances, and an impaired quality of life. The identified Crohn disease susceptibility alleles have improved our understanding of Crohn disease pathogenesis. However, the identified susceptibility alleles do not account for the observed heritability, nor have disease-causing alleles in many genomic regions been identified. For the proposed studies, we will use 1) existing DNA samples collected from high-risk Crohn kindreds identified using the extensive genealogical records available only in Utah, 2) existing DNA samples obtained from very young children with Crohn disease and their parents, and 3) existing DNA samples obtained from healthy controls that are free of a personal or family history of autoimmune disorders. Our overall hypothesis is that childhood- onset Crohn disease is caused in part by rare disease susceptibility alleles. In Aim 1, we will perform shared genomic segment analysis and exome sequencing in children in high-risk Crohn disease kindreds. In Aim 2, we will perform targeted re-sequencing studies and a case-control study in which the cases are very young children with Crohn disease. In Aim 3, we will test the hypothesis that, as a consequence of the evolutionary forces, Crohn disease susceptibility alleles have hitchhiked on a previously identified disease risk haplotype in which the disease-causing variant(s) remains unknown. In this proposal, we will use a novel and powerful resource, the Utah Population Database, and further develop innovative analytical strategies to perform gene- mapping studies in large kindreds. We will utilize a phenotypic extreme-childhood-onset Crohn disease-to characterize the rare genetic variation in known susceptibility alleles. Finally, we will explore the evolutionary forces shaping a Crohn disease susceptibility locus, which may provide insight into the disease-causing gene. These studies will improve our understanding of the causes of Crohn disease, help develop clinically useful molecular classification schemes, and lead to improved therapy. /RELEVANCE TO PUBLIC HEATLH Crohn disease is a chronic inflammatory disorder of the intestine of unclear etiology and no known cure. Affected children suffer from diarrhea, abdominal pain, growth disturbances, and an impaired quality of life. The overall goal of this project is to identify new genetic risk factors by studying high-risk Crohn disease kindreds and very young children affected by Crohn disease. These studies may help us better understand the causes of Crohn disease, and develop clinically relevant tools to classify patients at high risk of developing disease or adverse outcomes of disease
Keywords: 12 year old; Abdominal Pain; ing; Accounting; Adult; adverse outcome; Affect; Age; Alleles; Autoimmune Diseases; base; Base Sequence; Biopsy Specimen; case control; Case-Control Studies; Child; Childhood; Chromosome Mapping; Chronic; Classification Scheme; clinically relevant; Code; Crohn`s disease; Data; density; Diarrhea; Disease; Disease Association; Disease Outcome; Disease susceptibility; disorder risk; DNA; DNA Sequence; Enrollment; Etiology; European; exome; Family history of; fitness; Gastrointestinal tract structure; Gene Frequency; Genes; Genetic; genetic risk factor; Genetic screening method; genetic variant; genome wide association study; Genomic Segment; Genomics; Genotype; Goals; Growth; Haplotypes; Hemorrhage; Heritability; high risk; improved; Individual; Inflammatory; Inflammatory disease of the intestine; innovation; insight; interest; kindred; Lead; Linkage Disequilibrium; member; Meta-Analysis; Molecular; Natural Selections; next generation; novel; Onset of illness; Parents; Pathogenesis; Patients; Phase; Phylogeny; Population; Population Database; Predisposition; Principal Component Analysis; Quality of life; Rare Diseases; Records; rectal; Resources; Sampling; Shapes; statistics; Structure; Testing; tool; Utah; Variant; Variation (Genetics)
Relevance: /RELEVANCE TO PUBLIC HEATLH Crohn disease is a chronic inflammatory disorder of the intestine of unclear etiology and no known cure. Affected children suffer from diarrhea, abdominal pain, growth disturbances, and an impaired quality of life. The overall goal of this project is to identify new genetic risk factors by studying high-risk Crohn disease kindreds and very young children affected by Crohn disease. These studies may help us better understand the causes of Crohn disease, and develop clinically relevant tools to classify patients at high risk of developing disease or adverse outcomes of disease
Project start date: 2011-09-26
Project end date: 2015-06-30
Budget start date: 26-SEP-2011
Budget end date: 30-JUN-2012
PFA/PA: PA-10-067
1R01DK091374-01A1 (2011): $307225
L Stephen
University Of North Carolina Chapel Hillcity: Chapel Hill country: United States (us)
Abstract: PROJECT SUMMARY (See instructions) The Data Compilation Core (Core B) will develop and maintain a central resource of analysis-ready, annotated and documented data sets from clinical trials and related studies to be utilized by the investigators of the program. These data sets will be used to evaluate the methods developed in this program as well as to demonstrate the software developed in the Computational Resource Core (Core C). The primary source of the data will be the clinical trials and related studies of the Cancer and Leukemia Group B (CALGB), one of the major NCI-sponsored cancer cooperative groups. In addition, data from cancer research studies conducted at two large NCI-designated Comprehensive Cancer Centers, the Lineberger Comprehensive Cancer Center at UNC and the Duke Comprehensive Cancer Center, will also be utilized. This is a major advantage for the program in that the data sets provided can be exceptionally well annotated and documented, with the direct involvement of clinical and statistical scientists who were involved in the primary design and analysis of the studies
Keywords: Accounting; Address; anticancer research; Authorization documentation; Biometry; Cancer and Leukemia Group B; Cancer Center; Clinical; Clinical Trials; Comprehensive Cancer Center; Computer software; computing resources; Confidentiality of Patient Information; Data; Data Analyses; Data Collection; Data Set; Data Sources; design; Disadvantaged; distributed data; Documentation; Duke Comprehensive Cancer Center; Head; Information Systems; Information Technology; Instruction; Malignant Neoplasms; Medical; Methods; Mission; Molecular; Process; programs; Recording of previous events; Regulation; Research Design; Research Infrastructure; Research Personnel; Research Project Grants; research study; Resources; Scientist; Secure; Services; software development; statistical center; Statistical Data Interpretation; Statistical Methods; Work
Relevance: A major disadvantage of using public data sets is that the investigator is often unable to understand the clinical and molecular data as the data are provided without appropriate documentation. Indeed, it is not possible to carry out a thorough statistical analysis of data from clinical trials without taking into account and understanding the design of the study, the specifics of the data collection process, the history of the study and the medical issues. This core will address these issues by providing analysis-ready data sets with extensive annotation and documentation
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
5P01CA142538-02_7543 (2011): $320254
Sponsored Links Excellgen http://Excellgen.com
1P01CA142538-01_7543 (2010): $349942
A HAPLOTYPE MAP FOR MULTIPLE SCLEROSIS
L Stephen
University Of California San Franciscocity: San Francisco country: United States (us)
Grant 5R01NS049477-07 from National Institute Of Neurological Disorders And Stroke
Abstract: Multiple sclerosis (MS) is a common and severe disorder of the central nervous system characterized by chronic inflammation, myelin loss, gliosis, varying degrees of axonal and oligodendrocyte pathology, and progressive neurological dysfunction. MS pathogenesis includes a complex genetic component. In spite of intensive long-standing efforts, the knowledge of MS genetics remains incomplete. Our overall objective is to characterize the repertoire of genes that predispose to MS and modulate its presentation. Their identification is now possible as a result of rapid progress in defining the landscape of genetic organization and cataloging variation across the human genome. This proposal builds on the availability of second generation, high-quality genome-wide association results and comprehensive phenotypic data in a large MS cohort. We propose four main research goals In Specific Aim 1 high-coverage genome-wide genetic data from a total of approximately 17,000 subjects affected with MS will be pooled and analyzed using a multi-stage and multi- analytical approach to map unambiguous association signals from sequence (SNPs) and copy number (CNVs) polymorphisms and identify novel disease candidate genes, leading to robust and testable hypotheses as to which are the specific common allelic variants conferring susceptibility. Using the meta-analysis-derived genotypes, together with open databases and novel algorithms, we will develop a composite global map of the effects of epistatic interactions and biochemical networks of genomic variation underlying MS pathogenesis. Specific Aim 2 takes advantage of the wealth of phenotypic data available for the different datasets to assess disease course variables and correlations to genotype. Important clinical metrics such as age and site of disease onset, disability at entry of study and progression, and changes in lesion distribution and burden will be incorporated into the analysis of genetic data. This aim directly addresses the question of clinical heterogeneity in MS and the correlation between different phenotypes and genotypes. In Specific Aim 3 we intend to generate high-coverage sequence information for the regulatory regions, exons and flanking regions of genes with unequivocal evidence of association for the discovery of rare variants associated with MS. To efficiently resequence DNA in a large dataset (3,000 patients / 3,000 controls), we will create 120 pools of 50 DNA samples each. Approximately 1,000 low-frequency variants will be genotyped in a validation cohort consisting of 10,000 MS subjects and 10,000 control subjects. As technologies advance and costs retreat, whole exome re-sequencing will be pursued in the second half of the funding cycle. Finally, in Specific Aim 4 we will integrated all the generated data and build an array, the "MS Fine-Mapping Gene-chip," consisting of a comprehensive compendium of common and rare variants covering and flanking confirmed associations with susceptibility and disease expression. All relevant variants will be tested in an independent dataset (10,000 cases / 10,000 controls) for association individually and by combining multiple alleles within a single gene and across multiple genes to assess of causative cumulative effects. From this dataset, we expect to generate a minimal set of DNA variants that individually or in combination can aid in prediction of disease risk and/or progression. The availability of a large and well-characterized cohort as described here, coupled with the aid of high-powered laboratory technologies, provides an outstanding opportunity to identify and characterize MS-related genes. This information may translate into clinically useful genetic biomarkers and reveal novel targets for therapy. Public Health Relevance Statement Multiple sclerosis (MS) is a common cause of severe neurological disability resulting from the interruption of myelinated tracts in the central nervous system. MS is second only to trauma as a cause of neurologic disability in young adults, affecting approximately 2 million people worldwide and more than 400,000 individuals in the US. Remarkably, the incidence of MS seems to have increased considerably over the last century, and this increase may have occurred primarily in women. The socioeconomic consequences of this long-lasting disease are staggering as 75- 85% of patients are eventually unemployed and at high risk for social isolation. Conservative estimates indicate that this chronic illness results in healthcare costs exceeding $200 billion annually in the United States alone. Thus, MS is the second most costly neurological disorder after Alzheimer´s disease. Despite important advances in therapeutics, of the currently available disease-modifying drugs convincingly alter the long-term prognosis of the disease. Clinical manifestations are extremely diverse, but very little is known about the underlying cause of this variability. It can vary from a benign illness to a rapidly evolving and incapacitating disease. Onset may be abrupt or insidious, and early symptoms may be severe or seem so trivial that a patient may not seek medical attention for months or years. Most patients ultimately experience progressive disability and twenty-five years after onset approximately 80% of affected individuals will require assistance with ambulation. Thus over the long-term, MS is most often a severe disease requiring profound lifestyle adjustments to the affected and their families. We aim to identify the genes and the gene-specific variants that code for products involved in MS susceptibility. We anticipate that there may be several genes involved in MS risk. These genes may work independently or together, and affect susceptibility in concert with environmental factors. Particular combinations of inherited genetic variants may also determine when symptoms develop, or how the disease progresses. Their identification will help to define the basic etiology of MS, improve risk assessment, and influence therapeutics
Keywords: Address; Affect; Age; Algorithms; Alleles; Alzheimer`s Disease; arm; Autoimmune Diseases; Automobile Driving; base; Benign; Biochemical; biomarker; Candidate Disease Gene; Cataloging; Catalogs; Central Nervous System Diseases; Chronic; Chronic Disease; Clinical; Code; cohort; Complex; cost; Coupled; Data; Data Analyses; Data Set; Databases; Development; Diagnosis; disability; Disease; Disease susceptibility; disorder risk; DNA; DNA Resequencing; Environmental Risk Factor; Etiology; exome; Exons; experience; Family; Family Study; Frequencies (time pattern); Funding; Gene Chips; gene discovery; Gene Frequency; Generations; Genes; Genetic; genetic analysis; Genetic Polymorphism; Genetic Processes; Genetic Risk; genetic variant; Genome; genome wide association study; genome-wide; Genomics; Genotype; Gliosis; Goals; Haplotypes; Health Care Costs; Heterogeneity; high risk; Human Genome; improved; Incidence; Individual; Inflammation; Inherited; insight; Interruption; Knowledge; Laboratories; Lesion; Life Style; Magnetic Resonance Imaging; Maps; medical attention; Meta-Analysis; Methods; Metric; Multiple Sclerosis; Myelin; nervous system disorder; Neuraxis; Neurologic; Neurologic Dysfunctions; novel; Nucleic Acid Regulatory Sequences; Odds Ratio; Oligodendroglia; Onset of illness; outcome forecast; Pathogenesis; Pathology; Pathway interactions; Patients; Peptide Signal Sequences; Pharmaceutical Preparations; Phenotype; Play; Population; Predisposition; Prevention; public health relevance; Relapse; Research; Risk; Risk Assessment; Role; Sample Size; Sampling; Signal Transduction; Site; Social isolation; socioeconomics; Staging; Stratification; Susceptibility Gene; Symptoms; Technology; Testing; Therapeutic; tool; Translating; Trauma; TYK2; Unemployment; United States; Validation; Variant; Variation (Genetics); Woman; Work; young adult
Relevance: Public Health Relevance Statement Multiple sclerosis (MS) is a common cause of severe neurological disability resulting from the interruption of myelinated tracts in the central nervous system. MS is second only to trauma as a cause of neurologic disability in young adults, affecting approximately 2 million people worldwide and more than 400,000 individuals in the US. Remarkably, the incidence of MS seems to have increased considerably over the last century, and this increase may have occurred primarily in women. The socioeconomic consequences of this long-lasting disease are staggering as 75- 85% of patients are eventually unemployed and at high risk for social isolation. Conservative estimates indicate that this chronic illness results in healthcare costs exceeding $200 billion annually in the United States alone. Thus, MS is the second most costly neurological disorder after Alzheimer´s disease. Despite important advances in therapeutics, of the currently available disease-modifying drugs convincingly alter the long-term prognosis of the disease. Clinical manifestations are extremely diverse, but very little is known about the underlying cause of this variability. It can vary from a benign illness to a rapidly evolving and incapacitating disease. Onset may be abrupt or insidious, and early symptoms may be severe or seem so trivial that a patient may not seek medical attention for months or years. Most patients ultimately experience progressive disability and twenty-five years after onset approximately 80% of affected individuals will require assistance with ambulation. Thus over the long-term, MS is most often a severe disease requiring profound lifestyle adjustments to the affected and their families. We aim to identify the genes and the gene-specific variants that code for products involved in MS susceptibility. We anticipate that there may be several genes involved in MS risk. These genes may work independently or together, and affect susceptibility in concert with environmental factors. Particular combinations of inherited genetic variants may also determine when symptoms develop, or how the disease progresses. Their identification will help to define the basic etiology of MS, improve risk assessment, and influence therapeutics
Project start date: 2004-07-01
Project end date: 2015-05-31
Budget start date: 1-JUN-2011
Budget end date: 31-MAY-2012
PFA/PA: PA-10-067
5R01NS049477-07 (2011): $1025276
MECHANISM OF TRNA IMPORT INTO TRYPANOSOME MITOCHONDRIA
L Stephen, Professor & Head
University Of Georgia (uga)city: Athens country: United States (us)
Grant 5R01AI061356-06 from National Institute Of Allergy And Infectious Diseases
Abstract: Mitochondria are essential organelles found in most eukaryotic cells and provide for diverse metabolic functions. Fully active mitochondria require proteins and RNAs encoded both by the mitochondrial and nuclear genomes. In humans, at least 600 nuclear encoded proteins are imported into mitochondria and another 13 proteins are encoded by mitochondrial genes. The translation of this limited number of mitochondria-encoded proteins requires mitochondrial ribosomes, translation factors and transfer RNAs. Recent studies, of evolutionary diverse organisms, have shown that some or all of the mitochondrial tRNAs can be nuclear-encoded and must be imported into the mitochondria. In trypanosomes, all mitochondrial tRNAs are nuclear encoded and most are localized to both the mitochondrion and cytosol. While remarkable progress has been made in the elucidation of the mechanism of protein import into fungal and mammalian mitochondria, little is known about the mechanism of mitochondrial RNA import. The overall goal of this proposal is to dissect the pathway of tRNA biosynthesis and trafficking in African trypanosomes. To accomplish this goal the following specific aims are proposed. In Specific Aim I, the biosynthetic pathway for trypanosome tRNAs will be investigated by in vitro transcription and kinetic analysis of tRNA trafficking in intact cells. In Specific Aim II, the role of specific sequence and/or structural motifs in tRNA export from the nucleus and import into the mitochondria will be determined. Finally, in Specific Aim III, trypanosome proteins that interact with precursor and mature tRNAs to influence tRNA trafficking and ultimately mitochondrial import will be identified. Trypanosomes offer an attractive model to study tRNA trafficking pathways since both in vitro and in vivo systems have recently been developed to study both tRNA synthesis and mitochondrial import. In addition, mitochondrial tRNA import may have therapeutic potential since, in contrast to trypanosomes, all mammalian mitochondrial tRNAs are encoded by mitochondrial genes
Keywords: Affinity Chromatography; affinity purification; African; Assay; base; Binding; Binding (Molecular Function); Bioassay; Biologic Assays; Biological Assay; Cell Fractionation; Cell Line; Cell Lines, Strains; Cell Nucleus; CellLine; Cells; Chromatography, Affinity; Complex; Conserved Sequence; Coupled; cross-link; crosslink; cultured cell line; Cytosol; defined contribution; Development; Elements; Eukaryote; Eukaryotic Cell; eukaryotida; experiment; experimental research; experimental study; Gel; gene product; Gene Products, RNA; Gene Transcription; Genes; Genetic Alteration; Genetic Change; Genetic defect; Genetic Transcription; Genome; genome mutation; Goals; Human; Human, General; In element; In Vitro; in vivo; Indium; Investigators; Kinetic; Kinetics; knockout gene; Label; living system; Man (Taxonomy); Man, Modern; Metabolic; Mitochondria; Mitochondria RNA; mitochondrial; mitochondrial membrane; Mitochondrial RNA; Modeling; Molecular Interaction; mtRNA; Mutate; Mutation; novel; Nuclear; Nucleus; Organelles; Organism; pathway; Pathway interactions; Peptide Biosynthesis, Ribosomal; Post-Transcriptional Gene Silencing; Post-Transcriptional Gene Silencings; Posttranscriptional Gene Silencing; Posttranscriptional Gene Silencings; Production; programs; Programs (PT); Programs [Publication Type]; Promoter; Promoters (Genetics); Promotor; Promotor (Genetics); Protein Binding; Protein Biosynthesis; Protein Biosynthesis, Ribosomal; protein function; Protein Import; protein synthesis; Protein Synthesis, Ribosomal; Proteins; Proteomics; Quelling; Relative; Relative (related person); Research Personnel; research study; Researchers; reverse transcriptase PCR; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleic Acid; Ribonucleic acids, transfer; Ribosomes; RNA; RNA Expression; RNA Interference; RNA Silencing; RNA Silencings; RNA, Non-Polyadenylated; RNAi; Role; RT-PCR; RTPCR; Sequence-Specific Posttranscriptional Gene Silencing; Site; social role; Structure; subcellular fractionation; System; System, LOINC Axis 4; Therapeutic; trafficking; Transcription; Transcription Initiation; Transcription Initiation Site; Transcription Start Site; Transcription, Genetic; Transfection; Transfer RNA; translation factor; Translations; Triplet Codon-Amino Acid Adaptor; tRNA; tRNA Biosynthesis (Eukaryotes); tRNA Biosynthesis Pathway; Trypanosoma; Trypanosome; Work
Project start date: 2005-03-01
Project end date: 2011-02-28
Budget start date: 1-MAR-2009
Budget end date: 28-FEB-2011
5R01AI061356-06 (2009): $342998
ANTIBODY-BASED DETECTION OF TRANSLOCATIONS IN PEDIATRIC CANCER
L Stephen, Associate Professor
University Of Utahcity: Salt Lake City country: United States (us)
Grant 5R21CA138295-03 from National Cancer Institute
Abstract: Many cancers are associated with recurrent abnormalities of chromosome structure. One abnormality, a chromosomal translocation, occurs when portions of two normal chromosomes are exchanged. In the cancer setting, translocations may change the expression of genes near the chromosomal breakpoint, or may cause an abnormal "fusion oncogene" to be formed when portions of two genes at the breakpoint become linked together in an abnormal way. The products of these fusion oncogenes induce cancer development in the cells where they occur. In many instances, the presence of these fusion oncogenes may provide diagnostic, prognostic, or therapeutic information about the tumor. A highly sensitive and specific approach for detecting these chromosomal translocations would allow new information to be developed about cancers that contain them, and would also be of great use to the clinical care of these patients with these tumors. Unfortunately, although current approaches have been useful in detecting translocations and their products, they have a number of shortcomings that limit their use. We now propose to develop a new approach for translocation detection that avoids many of the difficulties associated with current methods antibody detection of translocations (ADOT). We plan to develop two versions of this technology, one that can analyze thousands of potential translocations at a time, but is somewhat costly, and one that can analyze a limited number of translocations at once, but is relatively cheap. We will determine the functional characteristics of these approaches, and compare them to current methodologies. At the end of these studies, we will have developed and characterized a technique for detecting these important chromosomal abnormalities that may be ready for clinical and research applications
Keywords: Affinity; Antibodies; base; Base Sequence; Basic Science; Biological Assay; Blood specimen; cancer diagnosis; cancer therapy; Caring; Cell Line; Cells; Characteristics; Chromosomal translocation; Chromosome abnormality; Chromosome Structures; Chromosomes; Clinical; clinical application; clinical care; Clinical Research; Clinical Trials; Common Neoplasm; Cost Effectiveness Analysis; Detection; Development; Diagnostic; Discrimination (Psychology); Disease; DNA; Ewings sarcoma; Exons; Fission Yeast; fluorophore; Formalin; Fungal Genome; Gene Expression; Gene Mutation; Genes; Genetic Transcription; Genome; Goals; Gold; Human; Human Development; Hybrids; improved; Institutes; leukemia/lymphoma; Link; Malignant Childhood Neoplasm; Malignant neoplasm of prostate; Malignant Neoplasms; Methodology; Methods; Molecular; Molecular Profiling; Monoclonal Antibodies; neoplastic cell; new technology; novel strategies; Oligonucleotides; Oncogenes; Paraffin Embedding; Pathway interactions; Patient Care; patient population; Patients; peripheral blood; Procedures; Process; prognostic; Reagent; Recurrence; Research; Reverse Transcriptase Polymerase Chain Reaction; RNA; RNA Binding; Sampling; sarcoma; Sensitivity and Specificity; Specimen; System; t(11;22)(q24;q12); Techniques; Technology; Therapeutic; Time; Transcript; Translocation Breakpoint; tumor; tumor xenograft; Whole Blood
Relevance: Chromosomal translocations are a type of genetic mutation that are highly associated with the development of human cancers. Detection of translocations, then, has important implications for the diagnosis of cancer, for providing prognostic information to patients with this disease, and in some cases, for deciding on the appropriate anti-cancer treatment for patients. We propose to develop a new technology that will circumvent many of the shortcomings associated with current technologies for translocation detections, and thus provide critical information to improve the care of patients with cancer
Project start date: 2009-04-01
Project end date: 2012-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: RFA-CA-08-006
5R21CA138295-03 (2011): $178794
GENETICS OF LATENT ZEBRAFISH MELANOBLASTS
L Stephen, Associate Professor Of Genetics
Washington Universitycity: Saint Louis country: United States (us)
Grant 5R01GM056988-13 from National Institute Of General Medical Sciences
Abstract: Growth, repair and homeostasis of adult tissues suggests that they are monitored and maintained by adult, or quiescent, stem cells. In turn, growth control of the quiescent stem cell requires mechanisms whereby their target tissues keep them in check, allowing stem cell activation when needed. We use developmental and genetic analysis to explore these mechanisms in the zebrafish melanocyte pigment pattern. In this proposal, we take advantage of chemically-induced melanocyte-ablation followed by larval melanocyte regeneration to explore mechanisms of quiescent stem cell growth control. Analyses include (i) BrdU incorporation to study growth histories and relationships of stem cell populations and clonal analysis of GFP expression in mosaic animals, (ii) identification of mutants that are specifically defective for melanocyte regeneration, and identification of the mutated gene, and (iii) whether or how mutant target tissues suppress or keep their sustaining stem cells in check. Thus, this proposal will provide novel insights into the developmental and genetic mechanisms of growth control of quiescent or adult stem cells that will in turn facilitate our ability to harness them for medical applications. Using embryonic or adult stem cells in regenerative medicine to replace damaged or missing tissues requires that we know and can manipulate the signals that act to recruit or drive the stem cells to differentiate, or act to repress their development. We use melanocyte regeneration in zebrafish to identify the developmental and genetic mechanisms that regulate the melanocyte stem cell, towards understanding the general mechanisms that positively and negatively regulate stem cell development in vivo
Keywords: Ablation; Adult; adult stem cell; Alleles; Animals; Biological Assay; Bromodeoxyuridine; cell growth; Chimera organism; Development; developmental genetics; Embryo; Engineering; Feedback; gene function; Genes; Genetic; genetic analysis; Growth; Homeostasis; In Situ; in vivo; insight; Label; Life Cycle Stages; Medical; melanoblast; melanocyte; Monitor; mutant; Mutate; Mutation; Natural regeneration; novel; Pattern; Pigments; Population; Recording of previous events; Recruitment Activity; Regenerative Medicine; Regulation; repaired; Role; self-renewal; Signal Transduction; Staging; Stem Cell Development; stem cell population; Stem cells; Temperature; Tissues; Zebrafish
Project start date: 1998-01-01
Project end date: 2012-07-31
Budget start date: 1-AUG-2011
Budget end date: 31-JUL-2012
PFA/PA: PA-07-070
5R01GM056988-13 (2011): $372438
INTEGRIN ALPHAVBETA8 INHIBITS AIRWAY EPITHELIAL CELL GROWTH
L Stephen, Professor
University Of California San Franciscocity: San Francisco country: United States (us)
Grant 5R01HL063993-10 from National Heart, Lung, And Blood Institute
Abstract: Failure of therapeutic trials for Chronic Obstructive Lung Disease (COPD) reflects our poor mechanistic understanding of the disease. The long term goal of this project is to improve the mechanistic understanding of COPD. The two major pathologic features of COPD that contribute to airway obstruction are loss of alveolar walls and wall thickening of small airways (<2mm). Small airway changes progress with increasing severity of COPD and therefore represent a therapeutic target to stabilize or potentially reverse airway obstruction. Recent investigation suggests that TGF¿ is likely to play a major mechanistic role in wall thickening in COPD by regulating the balanced autocrine and paracrine interactions between airway epithelial and mesenchymal cell types, collectively known as the epithelial-mesenchymal trophic unit (EMTU). These autocrine and paracrine interactions dictate cellular differentiation during lung development. Imbalances in these interactions could result from chronic airway injury (e.g. tobacco smoke) and lead to airway remodeling. TGF¿ isoforms are expressed by all cell types within the EMTU, but almost entirely in an inactive form. Hence, activation of TGF¿ is a major point of regulation of TGF¿ function. We have recently developed one of the first in vitro models of the human EMTU (Araya, et al, Am. J. Path, 2006) and have used it to determine that the integrin av¿8 plays a major role in TGF¿ activation, and subsequent autocrine and paracrine interactions between airway epithelial cells and fibroblasts. Using human COPD samples, we demonstrate increased ¿8 expression in both the airway epithelium and small airway fibroblasts, which significantly correlates with declining pulmonary function and airway wall thickening. These findings have led us to our overall hypothesis Increased av¿8-dependent activation of TGF¿ in COPD airway epithelial cells and fibroblasts leads to inappropriate reactivation of morphogenic programs within the EMTU, which leads to airway remodeling. Using physiologically relevant primary human airway epithelial and fibroblast cell culture systems, we will 1) determine the mechanism of increased (38 expression in COPD by airway epithelial cells and fibroblasts; 2) determine mechanism of increased av¿8-mediated activation of TGF¿ in COPD; 3) determine the functional consequence of increased av¿8-mediated activation of TGF¿ in autocrine and paracrine interactions between airway epithelial and fibroblast cell types. TGF¿ is one of the most fibrogenic cytokines known, but because of its normal homeostatic role in virtually all tissues, therapies targeted at global TGF¿ neutralization will also have undesired systemic effects. The TGF¿ activating integrin, av¿8, is upregulated in COPD but has a highly restricted pattern of expression in normal human tissues making it a possible therapeutic target to specifically inhibit TGF¿ in COPD. This proposal is the first step in testing the therapeutic potential of inhibiting av¿8 function in COPD
Keywords: Accounting; Air; airway epithelium; Airway Obstruction; airway remodeling; Alveolar wall; autocrine; Cell Culture System; cell growth; Cell Proliferation; cell type; Cells; chromatin immunoprecipitation; Chronic; Chronic Obstructive Airway Disease; Coculture Techniques; Complex; cytokine; Data; Disease; Disease Progression; Dominant-Negative Mutation; EMSA; Epithelial; Epithelial Cells; Equilibrium; Event; Failure (biologic function); Fibroblasts; Gene Silencing; Goals; Histone Acetylation; Histone Deacetylase; Human; human tissue; Immune; improved; in vitro Model; Inflammatory; injured airway; integrin alphavbeta8; Integrins; Interleukin-1; Interleukin-16; Investigation; Lead; Liquid substance; Lung; lung development; MAPK14 gene; Mediating; Mesenchymal; migration; MMP14 gene; Modeling; Obstruction; overexpression; Oxidative Stress; Oxidative Stress Pathway; paracrine; Pathologic; Pathway interactions; Pattern; Play; Process; programs; Promotor (Genetics); Protein Isoforms; Publishing; pulmonary function decline; Regulation; response; response to injury; Role; Sampling; Severities; Signal Transduction; small airways disease; spatiotemporal; Stress; System; Testing; Therapeutic; therapeutic target; Therapy Clinical Trials; Tissue Therapy; Tissues; Tobacco smoke; transcription factor; Transcriptional Regulation; two-dimensional; Work
Project start date: 1999-12-01
Project end date: 2012-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
5R01HL063993-10 (2011): $347625
EWS/FLI AND ITS TARGETS IN EWING´S SARCOMA
L Stephen, Associate Professor
University Of Utahcity: Salt Lake City country: United States (us)
Grant 5R01CA140394-02 from National Cancer Institute
Abstract: Ewing´s sarcoma is a highly malignant bone-associated cancer of children and young adults that usually expresses the EWS/FLI fusion protein. EWS/FLI is the key oncoprotein in Ewing´s sarcoma, and functions as an aberrant transcription factor. We recently demonstrated that EWS/FLI downregulates many more genes than it upregulates, and that a portion of these are directly regulated by EWS/FLI binding. This suggests that the widely-accepted model of EWS/FLI functioning as a transcriptional activator may be incomplete, and that it may act as a transcriptional repressor in some settings. Furthermore, our work identified a number of dysregulated genes that are required for the oncogenic behavior of Ewing´s sarcoma cells, but suggested that additional targets remain to be identified. Finally, we made the unexpected discovery that EWS/FLI upregulates some of its targets by binding to GGAA-containing microsatellites. This was surprising because these microsatellites do not conform to known EWS/FLI binding sites, nor have they been previously implicated in cancer development. Based on our preliminary data, we hypothesize that EWS/FLI functions as a transcriptional activator at some loci, and as a repressor at other loci, that both of these functions are required to dysregulate critical target genes to induce oncogenic transformation, and that polymorphisms that effect transcriptional function at these loci modulate Ewing´s sarcoma susceptibility or prognosis. Experiments are now proposed to test this hypothesis. The transcriptional repression domain of EWS/FLI will be defined, and its role in both the transcriptional and oncogenic function of EWS/FLI determined. Identification and analysis of genes directly regulated by EWS/FLI using both experimental and computational approaches will allow for the identification of new key targets that are involved in the development of Ewing´s sarcoma. Analysis of microsatellites in patients and populations will help to define the role of these elements in disease phenotypes and susceptibility to Ewing´s sarcoma. At the completion of these studies, we will have developed a deeper understanding of the mechanistic basis of Ewing´s sarcoma and applied it translationally. This may allow for the development of new prognostic or therapeutic approaches to this disease, and may impact on our understanding of other ETS-associated cancers as well. Many cancers are associated with abnormal ETS proteins, such as prostate cancer, leukemia, breast cancer, and sarcoma. Ewing´s sarcoma, with its abnormal ETS protein EWS/FLI, serves as a paradigm to understand the function of ETS proteins in cancer. Thus, understanding the mechanisms by which EWS/FLI causes Ewing´s sarcoma may identify new approaches for treating this very aggressive cancer of children and young adults, and may also allow for an improved understanding and treatments of other ETS-associated cancers as well
Keywords: base; Behavior; Binding (Molecular Function); Binding Sites; bone; Cell Line; Cells; Child; Chimeric Proteins; Clinical; Data; Data Set; Dependency (Psychology); Development; Disease; disease phenotype; Disease susceptibility; DNA Binding; ETS Family Protein; Event; Ewings sarcoma; Gene Expression; gene repression; Gene Targeting; Genes; Genetic Polymorphism; Genetic Transcription; improved; In Vitro; in vivo; Indium; Individual; insight; leukemia; Link; Malignant - descriptor; malignant breast neoplasm; Malignant neoplasm of prostate; Malignant Neoplasms; Maps; Mediating; Microsatellite Repeats; Modeling; new therapeutic target; novel strategies; Oncogene Proteins; Oncogenic; Outcome; outcome forecast; Pathway interactions; patient population; Patients; Phenotype; Predisposition; Primary Neoplasm; Process; prognostic; Promotor (Genetics); Proteins; public health relevance; Repression; research study; Role; sarcoma; Screening procedure; small hairpin RNA; Structure; System; Techniques; Testing; Therapeutic; Therapeutic Intervention; Transcription Coactivator; transcription factor; Transcription Repressor/Corepressor; tumorigenesis; Work; young adult
Relevance: Many cancers are associated with abnormal ETS proteins, such as prostate cancer, leukemia, breast cancer, and sarcoma. Ewing´s sarcoma, with its abnormal ETS protein EWS/FLI, serves as a paradigm to understand the function of ETS proteins in cancer. Thus, understanding the mechanisms by which EWS/FLI causes Ewing´s sarcoma may identify new approaches for treating this very aggressive cancer of children and young adults, and may also allow for an improved understanding and treatments of other ETS-associated cancers as well
Project start date: 2010-03-01
Project end date: 2015-02-28
Budget start date: 1-MAR-2011
Budget end date: 29-FEB-2012
PFA/PA: PA-07-070
5R01CA140394-02 (2011): $279814
ADVANCING REAL TIME DATA COLLECTION: ADAPTIVE SAMPLING AND INNOVATIVE TECHNOLOGY
L Stephen, Professor
University Of Pittsburgh At Pittsburghcity: Pittsburgh country: United States (us)
Grant 1R01HL107370-01 from National Heart, Lung, And Blood Institute
Abstract: Ecological momentary assessment (EMA) is a data collection method that assesses individual´s experiences as they occur in real time and in the natural environment. Its usefulness has been limited, however, by the available technology and the burden it places on the participant. We propose to improve EMA by further developing and testing an adaptive assessment system designed by our interdisciplinary team using state-of-the-science hardware and software that limits subject burden while facilitating real-time data collection. Our modifications to EMA are designed to increase data quality by optimizing the sampling schedule for random prompts measuring momentary covariates, while reducing the burden on study participants. We hypothesize that our proposed method will mitigate limitations associated with EMA and provide a means to quantify variables not traditionally measured in EMA, e.g., duration and quality of sleep, physical activity, daily weight and location, in a study of intentional, supervised weight loss in adults. We will test our hypothesis by using real-time transmission of data to link information from smart-phones, weight scales, daily diaries, actigraphs, and accelerometers. Modified-EMA sampling will be response adaptive - increasing the frequency of random assessments in response to indicators of increased risk, such as low mood for 3 days or high levels of stress. The value of the models we propose to further develop here will be applicable to a wide range of conditions in which the process of self-imposed behavior change is maintained or reversed, including adherence to self-management of chronic diseases (e.g., diabetes, kidney disease, cancer). Additionally, the framework for EMA sampling design and model fitting that we propose to develop is anticipated to be broadly applicable not only to EMA, but also to survival analysis in biomedicine, spatial epidemiology in environmental health, and to event history data in the social and behavioral sciences. We suspect that individuals´ moods, feelings and environments affect their behaviors, and the best way to understand their effect on behaviors is to collect data throughout the day, in real- time with participant in their real environment using a smart phone so data can be transmitted in real time. However, there is a balance between collecting data too frequently and potentially over-burdening participants, and collecting data too infrequently and not being able to answer our research questions. Thus, we will examine the data to determine how frequent and the best times of day we should ask participants to answer our brief survey questions via the smart phone. For our study we are researching relapse following intentional weight loss, but more importantly, we are advancing a data collection method that can be applied to a wide variety of health behaviors
Keywords: Accounting; actigraphy; Adherence (attribute); Adult; Affect; Area; Attention; base; Behavior; behavior change; Behavior monitoring; Behavioral; Behavioral Sciences; behavioral/social science; Body Weight; Body Weight decreased; Calculi; Cardiovascular system; Cellular Phone; Chronic Disease; Complex; Computer software; Data; Data Collection; data exchange; Data Quality; Data Sources; design; Development; Devices; Diabetes Mellitus; diaries; Eating; Elements; Environment; Environmental Health; Epidemiology; Equilibrium; Event; Exercise; experience; Feeling; Food; Frequencies (time pattern); Future; hazard; Health behavior; improved; Individual; innovative technologies; insight; instrument; Investigation; Kidney Diseases; Length; Link; Location; longitudinal design; Malignant Neoplasms; Measurement; Measures; Methodology; Methods; model design; Modeling; Modification; Monitor; Moods; Natural Sciences; Pain; Paper; Participant; Patient Self-Report; Patients; Pattern; Physical activity; Probability Samples; Process; programs; Recording of previous events; Relapse; Reporting; Research; Research Design; Research Personnel; research study; response; Risk; Sampling; Schedule; Science; Self Efficacy; Self Management; Sleep; smoking relapse; Social Interaction; Social Sciences; Statistical Models; Stress; Study models; Study Subject; Surveys; Survival Analysis; System; Technology; Telephone; Testing; Time; Time Study; Tooth structure; Weight; Work
Relevance: We suspect that individuals´ moods, feelings and environments affect their behaviors, and the best way to understand their effect on behaviors is to collect data throughout the day, in real- time with participant in their real environment using a smart phone so data can be transmitted in real time. However, there is a balance between collecting data too frequently and potentially over-burdening participants, and collecting data too infrequently and not being able to answer our research questions. Thus, we will examine the data to determine how frequent and the best times of day we should ask participants to answer our brief survey questions via the smart phone. For our study we are researching relapse following intentional weight loss, but more importantly, we are advancing a data collection method that can be applied to a wide variety of health behaviors
Project start date: 2011-04-15
Project end date: 2015-03-31
Budget start date: 15-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: PAR-08-212
1R01HL107370-01 (2011): $699897
MOLECULAR COORDINATION OF IRON HOMEOSTASIS BY MICRORNAS
L Stephen
Oklahoma State University Stillwatercity: Stillwater country: United States (us)
Grant 1R15DK088721-01 from Office Of The Director, National Institutes Of Health
Abstract: Diseases of iron metabolism continue to be a major health concern in the United States. Iron deficiency remains the most common single nutrient deficiency in the US and individuals experience negative health consequences due to iron deficiency in the absence of anemia, primarily due to alterations in iron metabolism in skeletal muscle. Surprisingly little is known about the molecular mechanisms regulating iron metabolism in skeletal muscle and how alterations in this tissue affects iron homeostasis. The long-term research goal of our laboratory is to advance understanding of how iron metabolism coordinated, and how alterations in iron sensing can lead to the development or prevention of disease. There is evidence suggesting expression of genes involved in iron metabolism is regulated by ID, however, the molecular mechanisms remain poorly characterized. Only recently has the role of small regulatory RNA molecules called microRNAs (miRNAs) been identified as an important mechanism for regulating various cellular processes. Our preliminary in silico analysis of miRNA targets resulted in the identification of mRNAs encoding proteins involved in iron metabolism. Thus our primary objectives are to determine the extent to which expression of miRNAs is regulated in response to ID and to characterize the impact of miRNA expression on potential regulatory targets involved in iron metabolism. We will critically evaluate targets of differentially expressed miRNAs and examine the roles of these targets in cellular iron metabolism. The central hypothesis is that miRNA expression is regulated in response to ID and that changes in expression are associated with changes in the expression target mRNAs resulting in the homeostatic regulation of cellular iron metabolism. To test this hypothesis, this proposal encompasses two specific aims. In Aim 1 we will evaluate and characterize iron-dependent changes in miRNA expression using a weanling rat model of ID. In Aim 2 we will determine the extent to which miRNAs contribute to the regulation cellular iron metabolism through modulating the expression of proteins involved in cellular iron homeostasis. MicroRNA expression profiles in the liver and skeletal muscle will be determined using miRNA microarrays and validated using qPCR. Combining in vivo and in vitro studies, we will identify and characterize target mRNAs and determine the role of these mRNAs in iron metabolism. We will also determine the extent to which changes in miRNA expression are due to alterations in iron status versus alterations in iron sensing. The proposed research is relevant to the maintenance of optimal health in light of the prevalence ID, and by taking an interdisciplinary approach to examine the relationships between iron status and cellular metabolism, we will expand our understanding of how iron contributes to the maintenance of optimal health. Iron deficiency continues to be the most common nutrient deficiency and is associated with alterations ranging from impairment in immune function, delayed cognitive development, and decreased capacity of work in skeletal muscle. The focus of this project is to examine the extent to which iron status is associated with alterations in microRNA expression that may contribute to some of the tissue-specific effects of iron deficiency. The results of this study will inform our understanding of the molecular mechanisms coordinating the cellular response to iron deficiency and may have implications in understanding alterations in iron metabolism observed in chronic diseases such as cancer and diabetes
Keywords: Affect; Anemia; Animals; Applications Grants; biological adaptation to stress; cell growth regulation; Cell physiology; Chronic Disease; Cognitive; Computer Simulation; Development; Diabetes Mellitus; Dietary Iron; Disease; disorder prevention; experience; Extramural Activities; Foundations; Future; Gene Expression; Gene Expression Regulation; Goals; Health; Homeostasis; immune function; impaired capacity; Impairment; In Vitro; in vivo; Individual; innovation; insight; interdisciplinary approach; Iron; Iron deficiency anemia; iron metabolism; Laboratories; Lead; Light; Liver; Maintenance; Malignant Neoplasms; Messenger RNA; Metabolism; MicroRNAs; Modeling; Molecular; Molecular Profiling; Motor; novel; Nutrient; Physiological; Population; Positioning Attribute; Prevalence; protein expression; Proteins; public health relevance; Rattus; Research; response; RNA; Role; Skeletal muscle structure; Solid; Testing; Tissues; United States; uptake; Work
Relevance: Iron deficiency continues to be the most common nutrient deficiency and is associated with alterations ranging from impairment in immune function, delayed cognitive development, and decreased capacity of work in skeletal muscle. The focus of this project is to examine the extent to which iron status is associated with alterations in microRNA expression that may contribute to some of the tissue-specific effects of iron deficiency. The results of this study will inform our understanding of the molecular mechanisms coordinating the cellular response to iron deficiency and may have implications in understanding alterations in iron metabolism observed in chronic diseases such as cancer and diabetes
Project start date: 2010-05-01
Project end date: 2013-04-30
Budget start date: 1-MAY-2010
Budget end date: 30-APR-2013
PFA/PA: RFA-OD-09-007
1R15DK088721-01 (2010): $436143
CULTURE-BASED PREDICTION OF ADOLESCENT HIV RISK
L Stephen
University Of California San Franciscocity: San Francisco country: United States (us)
Grant 5R01HD051438-05 from Eunice Kennedy Shriver National Institute Of Child Health & Human Development
Abstract: Consisting of ideas, understandings, beliefs, and subjective knowledge, culture is a determinant of adolescent risk behavior that is shared by adolescents in a given social group. Culture affects adolescent risk behavior because individuals choose roles and select situations leading to risky behavior from among culturally posited options. In this proposed five year community-based research project, we plan to study a particular domain of adolescent culture, that of sex and romantic relationships. We focus on two populations that have high levels of risk for HIV infection associated with sex and romantic relationships- mid-low to low SES African American heterosexual late adolescents and mid-low to low SES African American sexual minority late adolescents. The goal of the research is to identify cultural predictors of HIV risk that are generalizable, respectively, to mid-low to low SES African American adolescents of either heterosexual or sexual minority orientation. Our first specific aim is to identify, using qualitative methods, cultural models of sex and romantic relationships in samples drawn from heterosexual and sexual minority communities in three geographically distal cities Oakland, CA, Chicago, IL and Birmingham, AL. Our second specific aim is to compare, using a survey, cultural models related to sex and romantic relationships among samples drawn from the same three heterosexual and the same three sexual minority groups. Our third specific aim is to study the effect of cultural model-determined culturally specified attributes (CS As) related to sex and romantic relationships on the HIV risk behaviors of each sexual orientation group. Using new samples, we will test the hypothesis that these CSA measures will predict HIV risk behaviors of the corresponding sexual orientation group better than non-cultural self-report measures that have previously been shown to predict HIV risk behaviors in these populations. The proposed research tests an innovative method for identification of group- specific cultural knowledge related to sex and romantic relationships, calibrates findings to account for inter-group differences, and develops cultural measures that can be used both to explain HIV risk behavior and to design HIV risk reduction interventions suited to specific populations
Keywords: Accounting; Adolescent; Adolescent Risk Behavior; Affect; African American; age group; base; Behavior; Belief; Characteristics; Chicago; Cities; Communities; Data; design; Distal; Event; Goals; Group Identifications; Health; Health behavior; Health Promotion; Heterosexuals; HIV; HIV Infections; Individual; innovation; Intervention; Knowledge; Lead; Location; Measures; Medical; member; Methods; Minority; Minority Groups; Modeling; Morbidity - disease rate; Mortality Vital Statistics; Nature; Patient Self-Report; Play; Population; psychologic; Psychological adjustment; Qualitative Methods; Research; Research Project Grants; Resources; Risk; Risk Behaviors; Risk Reduction; Risk-Taking; Role; Sampling; sex; Sex Behavior; Sex Orientation; Sexually Transmitted Diseases; social group; Specific qualifier value; Surveys; Testing; theories; transmission process; Unwanted pregnancy; Youth
Project start date: 2007-08-15
Project end date: 2012-06-30
Budget start date: 1-JUL-2011
Budget end date: 30-JUN-2012
5R01HD051438-05 (2011): $517201
Sponsored Links Excellgen http://Excellgen.com
CONNECTIVITY PATTERNS OF RETINAL BIPOLAR CELLS
L Stephen, Professor
University Of Texas Hlth Sci Ctr Houstoncity: Houston country: United States (us)
Grant 5R01EY010121-16 from National Eye Institute
Abstract: About 15 types of retinal ganglion cell, each type tuned to different aspects of the visual scene, independently sample the visual space. About half are coupled via gap junctions to amacrine cells and/or their neighboring ganglion cells of the same type. Very few of these ganglion cell types are well characterized with regard to either their function or what other cells they contact to form their individual circuit. The PI has developed usage of a gap junctional-permeant fluorescent tracer (Hoshi and Mills, 2006) that allows in vivo identification of cells electrically coupled to the injected cell. This tracer, PoPro1, provides the PI with a unique opportunity to examine the properties of coupled ganglion and amacrine cells. This proposal uses this novel technique to investigate this important, but almost completely-unexplored feature of network coupling, namely, the functional consequences of heterologous coupling between amacrine and ganglion cells. The proposal involves (1) recording from a ganglion cell type called the G3 ganglion cell, which preliminary data shows has an orientation bias and determining how this function arises, and (2) discovering the manner in which amacrine cells coupled to ganglion cells participate in synchronized firing of ganglion cells. Synchrony is emerging as an important process in coding and possibly decoding of visual signals. The processes that lead to synchrony are also important in pathologies such as seizures. The studies in this grant are directed toward two elements pertinent to public health ganglion cell circuits and gap junctions. The importance of gap junctions has been established in photoreceptor death (the "bystander" effect), but as the extent and function of gap junctions in ganglion cell circuitry is not well known, the involvement of gap junctions in ganglion cell death in diseases such as glaucoma is a topic worthy of investigation
Keywords: Amacrine Cells; Bystander Effect; Cell Death; cell type; Cells; Cessation of life; Chemical Synapse; Code; Color; Coupled; Coupling; Data; density; design; Discrimination (Psychology); Disease; Electrical Synapse; Elements; Ganglia; ganglion cell; Gap Junctions; Glaucoma; Glutamates; Grant; Health; in vivo; Individual; Inhibitory Synapse; Investigation; Lead; Length; Life; Myxoid cyst; Nature; novel; Oryctolagus cuniculus; Pathology; Pathway interactions; Pattern; Photoreceptors; Physiological; Process; Property; public health medicine (field); receptive field; Relative (related person); response; Retina; Retinal; Retinal Ganglion Cells; Role; Sampling; Seizures; Signal Transduction; Staining method; Stimulus; success; Techniques; Testing; Time; Tissues; Tracer; Visual; Work
Project start date: 1994-01-01
Project end date: 2013-03-31
Budget start date: 1-APR-2011
Budget end date: 31-MAR-2012
PFA/PA: PA-07-070
5R01EY010121-16 (2011): $263331
L Stephen
Duke Universitycity: Durham country: United States (us)
Keywords: ing; anticancer research; Applications Grants; Area; Basic Science; Bioinformatics; Biometry; Biostatistics Shared Resource; Cancer and Leukemia Group B; Cancer Center; Cancer Research Project; Clinical Sciences; Clinical Trials; Collaborations; Consultations; design; Faculty; Grant; Institutes; Malignant Neoplasms; Manuscripts; member; Peer Review; Pilot Projects; Preparation; protocol development; Protocols documentation; Publications; Reporting; Research Personnel; Research Project Grants; Resource Sharing; Resources; Review Committee; Services; Work
Budget start date: 1-JAN-2011
Budget end date: 31-DEC-2011
5P30CA014236-37_6454 (2011): $238123