Qin Chen, Ph.D. - US grants

Cellular senescence is characterized by the permanent loss of cell proliferation. Little is known about oxidative DNA damage and its relationship to molecular changes during cellular senescence. Hydrogen peroxide can induce human diploid fibroblast cells to develop senescent phenotype, providing an ideal model for determining the contribution of oxidative damage and molecular events in growth cessation. I propose to examine whether oxidative DNA damage serves as a signal activating the tumor suppressor gene p53 and pRB governed cell cycle check points and to explore the synergistic or parallel mechanisms. The experiments are designed to determine cell cycle parameters, involvement of p53 and pRB, contribution of oxidative DNA damage, and gene expressions during the development of hydrogen peroxide induced senescence. The study will provide new insights into the mechanism of growth cessation and cellular aging.

Cardiomyocyte hypertrophy is a common endpoint of heart aging and many cardiac diseases. It is not clear what triggers the change and the mechanism of the change. Oxidants are by-products of aerobic metabolism and increase in the heart under the pathological conditions associated with ischemia-reperfusion. Using H9C2 and primary cultured neonatal rat cardiomyocytes, we found that low concentrations of H2O2 can cause cardiomyocyte hypertrophy. H2O2 treated cells can be 4 times bigger in volume or 4-10 times larger in cell surface area and contain 3 times more proteins per cell. Cardiomyocyte hypertrophy induced by endocrine factors involves elevated expression of a number of genes, activation of MAP kinases and calcium mediated activation of NF-AT3. Since H2O2 has been reported to activate MAP kinases and increase cytosolic calcium, we hypothesize that H2O2 activates MAP kinases or calcium dependent NF-AT3 transcription factor to alter the expression of hypertrophic genes and to induce cardiomyocyte hypertrophy. The expression of the atrial natriuretic factor, beta-myosin heavy chain, skeletal alpha-actin, alpha-myosin heavy chain, ventricular-specific myosin light chain-2 and troponin C genes will be measured by Northern blot in H2O2 treated H9C2 cells. The activity of the stress activated protein kinase, extracellular regulated kinase and p38 MAP kinase will be determined after H2O2 treatment. The inhibitors of these kinases will be tested for their effect on induction of hypertrophic genes and cell enlargement by H2O2. In parallel, cytosolic calcium concentration and DNA binding activity of NF-AT3 will be measured after treating cells with H2O2. Calcium chelators and inhibitors of calcineurin will be tested for their ability to prevent H2O2 induced N-FAT3 activation, activation of hypertrophic genes and cell enlargement. We propose to study the mechanism of oxidant stress by novel and innovative approaches. The results will contribute to the understanding of the process of heart aging and the pathogenesis of heart failure.

Aging is the highest risk factor for many fatal diseases. The Free Radical Theory of Aging argues for a role of oxidant toxicity in aging. Although oxidative damage accumulates during the process of aging, it is not clear how oxidants might cause aging at the mechanistic level. As the gene array technology evolves, it has been shown that tissues from old mice elevate stress responses and decrease metabolism by altering the expression of a large number of genes. Oxidants are known to induce stress responses and alterations of gene expression. In normal human diploid fibroblasts (HDFs) mild doses of oxidants cause the cells to develop a senescent phenotype prematurely. The phenotype switch suggests that multiple intrinsic changes may have been produced at the molecular level following oxidative stress. Elevation of p21 WAF17/Cip1/Sdi1 was found to precede the onset of the senescent phenotype, which involves an elevated expression of 8 senescence-associated genes. Preliminary studies using the microarray technology point to the direction that oxidants induce aging-associated genes as well as senescence- associated genes. These observations lead us to hypothesize that oxidants can induce the expression of aging-associated genes, some of which are controlled by p21. Mouse embryonic fibroblasts (MEFs) will allow us to determine the molecular program of oxidative stress that might be relevant to aging in vivo. Using the senescent phenotype as a marker of multiple molecular changes in MEFs, we will determine the gene expression pattern resulting from oxidative stress using a global and systematic approach involving gene array and Northern blot techniques. Dermal connective tissues from young and old mice will be compared to generate an aging gene profile. Comparison between the pattern of oxidative stress gene expression and the aging gene profile will allow us to critically test the relationship between oxidative stress and aging. This approach will also lead to the identification of important aging-associated changes that can be studied for their mechanisms of regulation at the cellular level. Since p21 has been reported to control the expression of a large number of genes, we will test the relationship between p21 and the expression of a limited number of functionally important genes shared by oxidative stress response and aging of dermal connective tissue using p21 knockout MEFs or HDFs. Finally, the mechanism of sustained p21 elevation following a pulse treatment of H2O2 will be determined by detailed analysis of transcriptional activation or mRNA stabilization. Because of the ubiquitousness of oxidants in our daily life, aging and disease states, it is important to understand the fundamental mechanisms of oxidant toxicity at the molecular level. We have a unique finding of premature senescence with oxidative stress and will combine in vitro and in vivo approaches to uncover the trigger of unwanted effects of aging.

[unreadable] DESCRIPTION (provided by applicant): Stress is known to cause an increase in the synthesis of corticosteroids by the adrenal glands. Although corticosteroids have been shown to contribute to the pathophysiology of suppressed Immune response and a number of psychiatric disorders, the effect of CT on the heart remains unclear. Doxorubicin (Dox) is an anti-neoplastic drug that can produce chronic cardiac toxicity which is manifested as dilated cardiomyopathy. An important feature of this form of cardiomyopathy is the apoptosis of cardiomyocytes. Our preliminary studies found that corticosterone (CT) pretreatment prevented Dox from inducing apoptosis of cardiomyocytes. The glucocorticoid receptor antagonist mifepristone prevented CT from inducing a cell survival response. Several forms of g!ucocorticoids, aldosterone, progesterone and retinoic acid but not estrogen, testosterone or L-thyroxin can inhibit apoptosis of cardiomyocytes. Analyses of ERK, Akt and SGK-1 activities or bcl-2 expression indicated that CT neither activated the known survival kinases nor elevated the expression of the anti-apoptotic gene bcl- 2. The conditioned medium of CT-treated cardiomyocytes shows partially cytoprotective effective. The TranSignal array approach found that CT treatment could potentially activate 21 transcription factors. We hypothesize that activation of the glucocorticoid receptor initiates transcriptional activation of survival genes in cardiomyocytes in vitro and in vivo. Specific aims of this grant include: 1) To test if CT binding causes its receptor to interact with and to activate multiple transcription factors in cardiomyocytes; 2) To test that the activation of cell survival genes contributes to CT-induced cytoprotection; and 3) To demonstrate that CT protects the heart from cardiomyopathy induced by Dox in vivo via inducing the transcription of cell survival genes. This project will combine our expertise in genomics, transcriptomics and proteomics to systematically study the linkage between the glucocorticoid receptor and cell survival mechanisms. Given the fact that stress is unavoidable in our daily life, this project will provide novel information to advance our understanding in the biological effect of corticosteroids on the heart. More importantly, since apoptosis has been shown to contribute to heart failure induced by the chemotherapy agent Dox as well as by many forms of cardiovascular disease, our finding and proposed mechanistic study will provide a hope for novel therapy against heart failure in the future. [unreadable] [unreadable] [unreadable]

[unreadable] DESCRIPTION (provided by applicant): The murine eye is composed of tissues that are derived from ectoderm, neuroepithelium, neural crest and mesoderm, which contain different cell lineages. It has been thought that multiple signals are involved in the inductive interactions between these different tissues. Although embryologists have tried to identify the signals that are required for lens induction for many years, these molecules remain poorly defined, and no in vitro assay for the lens induction has been established to date. This proposal aims to establish a stable cell line of embryonic lens progenitor cells, and identify some of the important signals and their downstream target genes required for lens induction. The specific aims of this grant application are: 1) To establish progenitor cell lines from ocular lens pit and from non-lens tissue in the eye field; 2) To assess the gene expression profile in lens progenitor cells before and after initiation of progenitor cell differentiation; 3) To assess external signals as candidates for lens induction. The proposed studies should provide novel strategies for isolation and identification of embryonic lens progenitor cells. These cells should be used for many studies, such as identification of the signals and the molecular pathways involved in lens induction and [unreadable] development, inhibition of cell migration, lens regeneration and cell type conversion. [unreadable] [unreadable] [unreadable]

PROPOSAL NO.: CTS-0547056
PRINCIPAL INVESTIGATORS: QIN CHEN
INSTITUTION: UNIVERSITY OF SOUTH ALABAMA

CAREER: SIMULATIONS OF NONLINEAR WATER WAVES AND AIR-TO-SEA MOMENTUM FLUXES IN THE COASTAL OCEAN

The goal of this project is to develop an integrated research and educational program in coastal engineering and science that will advance the capability of modeling storm surge and wave dynamics, and at the same time educate students and the general public about coastal issues in the Gulf area. According to census data, more than 50% of the U.S. population lives within 50 miles of the shoreline, and the coastal population continues to grow. The nation's near shore regions are severely stressed because of increased human activity and climate change. The continuing popularity of coastal areas and increased development along the coastlines puts more people and property at risk from coastal hazards, such as hurricanes and tsunamis. Winds, surges and waves are the major forcing of coastal flooding and erosion. Mitigating the impacts of such coastal disasters requires an accurate prediction of water surges and ocean waves generated by storms and hurricanes in order to inform the public and decision-makers, facilitate the management of coastal resources and emergency response, and improve engineering design of coastal infrastructure. The research component of this program will employ an innovative, interdisciplinary (civil engineering, physical oceanography and computational science) approach utilizing the PI's advanced coastal wave modeling expertise in computational hydrodynamics. The five-year research plan consists of theoretical formulation and analysis, development and verification of a third-generation Boussinesq-type wave-current model that includes vorticity and wind forcing based on state-of-the-art formulations and spectral-element methods, and the utilization of the new model as a research tool to improve understanding of wind effects on wave-wave interactions as well as air-to-sea momentum fluxes for storm surge modeling. The education component of the program will be coupled with the research component to enhance undergraduate education and research as well as enrich a graduate curriculum with new graduate-level courses. Furthermore, a novel community outreach program will be integrated with the well-established Alabama Dauphin Island Sea Lab's K-12 education programs. The integrated educational program with an emphasis on high-school students and science teachers will enhance ocean-related education and attract U.S. students to the field of ocean science in general and to the profession of coastal engineering in particular. The proposed research and education activities will broaden the participation of the underrepresented Northern Gulf Coast residents and minorities in the discipline of coastal engineering. The multilevel community outreach program will improve the general public's understanding of the destructive forces of storm waves and water surges and their threat to coastal inhabitants and infrastructure. This will raise the public's awareness of the potential risk associated with many residential developments along the coastlines and therefore facilitate coastal zone management.

DESCRIPTION (provide by applicant) The Toxicology Training Program at the University of Arizona has a long-standing reputation for producing many successful Ph.D.s. Graduates are now key players in academia, industry, and government. In response to current and future demand for qualified graduates in the environmental health sciences, the investigators have enhanced their systems-based Toxicology training with an emphasis on cellular and molecular mechanisms that incorporate genomics and proteomics approaches. The cutting-edge interdisciplinary research programs of 21 training grant faculty members, state-of-the-art technologies developed through the Southwest Environmental Health Sciences Center (SWEHSC) and translational approaches undertaken by the NIEHS Superfund Program provide an exceptionally stimulating environment for the training of graduate students and postdoctoral fellows. The Research and Facility Cores supported by the SWEHSC extend the training environment from a single laboratory-oriented domain into a multidisciplinary experience strongly supportive of interactive and collaborative research. The university provides financial support for first year Ph.D. students in the Graduate Programs of Pharmacology and Toxicology, Physiological Sciences, and Cancer Biology, resulting in a large pool of qualified candidates for competitive selection of pre-doctoral trainees. Pre-doctoral training is achieved through a combination of coursework, laboratory research, and supplemental enrichment activities. Postdoctoral trainees have ample opportunities to participate in innovative research programs and to develop their professional skills in oral and written communication and in supervision. Over the past five years, the investigators have generated six new graduate courses: Molecular Toxicology, Toxicogenomics and Proteomics, Advanced Toxicology, Environmental Toxicology Colloquium, Ethics, and Scientific Writing. The curricular changes parallel the evolving expertise of the Training Grant Faculty in genomics and proteomics. They have recruited five senior (Professor) and three junior (Assistant Professor) faculty into the Training Grant, which significantly enhances strength in an evolving theme of molecular toxicology training. The request for continuation of NIEHS support is validated by the highly successful nature of their program, the clear demand for their graduates, the increasing number of students interested in toxicology, institutional commitment, strong and well-funded research programs of the faculty, and the excellence of the training environment.

DESCRIPTION (provided by applicant): Ischemic reperfusion (I/R) is known to trigger an increase of reactive oxygen species in the myocardium. Although high levels of oxidants can cause damages, low doses of oxidant elicit a protective effect, such as during preconditioning induced by cycles of brief I/R. Our recent data suggest that induction of antioxidant and detoxification genes dominates the gene expression network of oxidants in cardiomyocytes. A master switch controlling the expression of these genes is the transcription factor Nrf2. We found that 2 to 4 cycles of 5 min ischemia and 5 min reperfusion cause elevation of Nrf2 protein in the myocardium. With isolated cardiomyocytes, oxidants cause rapid onset of Nrf2 protein translation. Stress generally causes global reduction of protein translation. Recent studies suggest that several genes containing an Internal Ribosomal Entry Site (IRES) in the 5'Untranslated Region (5'UTR) of mRNA can escape the general translational control and undergo stress induced protein translation. A group of IRES Trans-Acting Factors (ITAFs) appears to be critical in recruiting the ribosomes to initiate the translation of these genes. Little is known about which proteins and how they are translated when the myocardium or cardiomyocytes encounter oxidative stress. We plan to take advantage of genomic and proteomic technologies to test the hypothesis that "cycles of brief I/R cause selective increase of Nrf-2 protein in the myocardium through IRES mediated translation". The Specific Aims include 1) Test that Nrf2 protein translation occurs in the myocardium by cycles of brief I/R and mediates preconditioning induced cardiac protection;2) Test that lack of well defined Kozak sequence and formation of stable "stems and loops" secondary structure in 5'UTR enable a battery of genes to undergo I/R induced protein translation;3) Test that Nrf2 mRNA contains an IRES that allows rapid protein translation in cardiomyocytes following cycles of brief I/R or low dose of oxidants;4) Test that cardiomyocytes express a unique set of ITAFs to regulate Nrf2 protein translation in response to I/R. The field of stress induced protein translation is in its stage of infancy. Although Nrf2 plays a critical role in cytoprotection among various cell types, the function and regulation of Nrf2 have not been well studied in cardiomyocytes. Studying the mechanism of protein translation under oxidative stress becomes a necessary task in understanding the transition to heart failure from adaptive response. PUBLIC HEALTH RELEVANCE: This grant proposes to study the mechanism of Nrf2 protein translation in cardiomyocytes and in the myocardium following oxidative stress.

DESCRIPTION (provided by applicant): Multiple lines of evidence point to the existence of cellular defense against xenobiotic chemical stress in mammalian cells. Increased expression of antioxidant and detoxification genes contributes to cell survival. While induction of oxidative stress represents one component in the mechanism of toxicity of many types of xenobiotics, our recent data suggest that induction of Phase II detoxification pathway dominates the gene expression network of oxidants. A master switch controlling the expression of Phase II antioxidant and detoxification enzymes is the transcription factor Nrf2. We found that oxidants cause rapid translation of endogenous Nrf2 protein. Little is known about the selectivity and mechanisms of protein translation under oxidative stress. We hypothesize that "IRES mediates oxidant induced selective translation of Nrf2 protein". The Specific Aims include 1). Test that oxidants turn on Nrf2 protein translation due to Internal Ribosomal Entry Site (IRES) in the 5'UTR;2). Apply proteomic technology to address the mechanism of stress induced protein translation by identifying the proteins bound to Nrf2 5'UTR. Cell survival represents a critical layer of defense against chemical toxicity. Therefore studying the mechanism of stress induced protein translation is an imperative task for understanding the etiology of diseases associated with chemical exposure. PUBLIC HEALTH RELEVANCE: This proposal plans to study the mechanism of oxidative stress induced Nrf2 protein translation.

Research and Education Cyberinfrastructure Investments to Develop the Coastal Hazards Collaboratory in the Northern Gulf Coast

Proposal Number: EPS - 1010640
Lead Institution: Louisiana Board of Regents
Project Director: Michael M Khonsari
Linked to: EPS-1010578 (Sandra H Harpole, Mississippi State University)
Linked to: EPS-1010607 (Sara J Graves, University of Alabama in Huntsville)


The Northern Gulf Coast is essential to the sustainability of economically important coastal fisheries, marine transportation, energy development and strategic national defense. The project supported by this EPSCoR Research Infrastructure Improvement (RII) Track-2 award establishes the Northern Gulf Coastal Hazards Collaboratory (NG-CHC) to: (1) enhance the research competitiveness of the region, (2) advance economic opportunities for citizens by reducing risks to coastal vulnerabilities, and (3) catalyze collaborative research via enhanced cyberinfrastructure (CI) that addresses problems of major national importance, viz., engineering design, coastal system response, and risk management of coastal hazards. The three states in the consortium, Louisiana (LA), Mississippi (MS), and Alabama (AL), are leveraging their partnerships, proximity, and significant prior investments in CI to advance science and engineering of coastal hazards across the region.

The NG-CHC has the opportunity to capitalize upon strong CI and coastal hazards research infrastructure to address issues of national importance. The challenge is to develop a framework and strategies for organizing the resources in the region in a manner that transcends boundaries among state lines. The principal barrier to date has been the lack of CI that enables rapid sharing of available data resources and tools and advance new discoveries in geosciences and engineering associated with coastal hazards in this vulnerable coastal region. The Research Infrastructure Improvement Track-2 cyberinfrastructure (CI) investments will focus on enhancement of the data storage, sensor network, computing and instrumentation systems that are essential for addressing the challenges of a distributed Coastal Hazard Collaboratory.

Intellectual Merit
The NG-CHC is focused on a strategic plan to develop integrated CI for a research and education environment to promote the capability in simulating coastal hazards by enhancing the linkages between modeling and observations in a multidisciplinary environment that couples geoscience, engineering, geoinformatics, computational science, and economic development. One of the grand challenges for earth system science is to characterize dynamic environmental processes at appropriate space and time scales with integrated observation networks and models. Such capabilities are critical to societal needs for reduction of risks to built, human and natural environments. The observational and data storage systems located at university, government and private industries in the Northern Gulf Coast have increased capacity due to recent major investments, but this region lacks the CI necessary to integrate these data inventories into information and knowledge that will reduce risks to coastal hazards. An integrated CI capable of simulating all relevant interacting processes from the watershed to the coast is needed to implement a system that captures the dynamic nature of these earth surface processes. This includes the ability to couple models, invoke dynamic algorithms based on streams of sensor and satellite data, locate appropriate data and computational resources, create necessary workflows associated with different simulation demands, and provide visualization tools for analysis of results.
The collaborative research program within NG-CHC is organized around three prototype simulation experiments: (1) Surge Guidance System; (2) River/Watershed Flood Modeling; and (3) Ecosystem Restoration and Flood Risks Reduction.

Broader Impacts
Coastal hazards represent generic environmental, engineering and social problems worldwide in which human and natural dynamics are strongly and inherently coupled. Thus, the proposed CI in the NG-Coastal Hazards Collaboratory may have national and international implications to living and working in coastal environments. The challenges to promoting resilience of the Northern Gulf Coast region, including the urban, industrial, and natural landscape components, provide a laboratory to develop new technologies that reduce risks to both natural and built environments. The key is close integration among coastal scientists, coastal engineers, and social scientists, with a comprehensive commitment to producing results that advance science and provide a sound basis for designing more sustainable landscapes. The proposed NG-CHC would develop a more integrated research environment by interpreting landscape patterns, forecasting landscape dynamics, and applying critical thinking and problem solving techniques in 'system designs'.

This proposal develops an accurate and efficient method for modeling the interaction of fluid with numerous flexible plant stems (modeled as bendable cylinders) at a wide range of Reynolds numbers. Research activities include deriving new mathematics of kernel functions for bottom-clamped and bendable cylinders, verifying and validating model output, investigating the relation between the drag force and the bending angle and the link between the lateral clearance in a cylinder cluster and the effectiveness of wave and surge attenuation, and upscaling the model to infer macroscale parameters for large-scale simulations to test hypotheses of wetland resilience and flood risk reduction. Three educational programs: Summer Outreach, Minority Internship, and Graduate Student Exchange, provide opportunities for communities and minorities to participate in research and inter-university collaborations.

Continued climate change and sea level rise pose a major threat to coastal habitats and communities worldwide. The impact of sea level rise has caused increased coastal erosion and flooding. For example, owing to subsidence, sea level rise and human interventions, the Mississippi River Delta and the Louisiana coast lose one acre of wetland every 24 minutes, which accounts for 80% of the total annual loss of coastal wetlands in the continental United States. The chronic wetland loss in south Louisiana has considerably weakened the natural defense against catastrophic floods, such as Hurricanes Katrina and Rita (2005). Over 1,500 people lost their lives and several major coastal populations were crippled for months after the hurricanes passed. Mitigating flood damage and reducing the threat of storm surges are imperative. It has been recognized that vegetation in wetlands can effectively reduce the flow speed. Results from the proposed research will not only provide insight to wave and surge attenuation in coastal wet-lands for coastal engineers and managers, but also serve as useful references for mechanical, civil, environmental, and ocean engineering concerning interactions of fluid with structures and plant canopies. The developed simulation tools will benefit society in better protecting the coastal ecosystem from impacts of storms and sea level rise and reducing the risk of flooding. Knowledge gained from the research will be assimilated in multi-channel education to train two graduate students, to involve minorities in mathematical science, and to stimulate the interest of communities in computational mathematics. This project will educate the public about the gravity of coastal flooding and erosion in Louisiana.

DESCRIPTION (provided by applicant): The Toxicology Graduate Program at the University of Arizona has a long-standing reputation for excellence in training Ph.D. scientist. Many of our graduates are now leaders in academia, industry, and government. Current trainees are now selected through a University-wide competition. The graduate program has evolved from a systems-based toxicology experience to training students to apply state-of-the art techniques to solve mechanisms of environmental toxicity affecting complex diseases in various organ systems. The cutting-edge basic science research programs of 22 Training Grant Faculty members, state-of-the-art technologies developed at the University of Arizona in association with the Southwest Environmental Health Sciences Center and Bio5, and translational approaches undertaken by our NIEHS Superfund Program and US-Mexico Binational Center provide an exceptionally stimulating environment for the training of graduate students and postdoctoral fellows. The interactive research of our Training Grant Faculty and our state-of-the-art Facility Cores extend the training environment from a single laboratory-oriented domain into a multidisciplinary experience strongly supportive of collaborative research. The University provides financial support for first year Ph.D. students, providing a large pool of highly qualified candidates for competitive selection of predoctoral trainees. Predoctoral training is achieved through a combination of coursework, laboratory research, and supplemental enrichment activities. Postdoctoral trainees participate in innovative research programs and are guided to develop professional skills in oral and written communication and in supervision. Over past five years, the curricular changes parallel the evolving expertise of the Training Grant Faculty in utilizing state-of-the-art technology for research projects. We have recruited 3 senior (Professor) and 3 junior (Assistant Professor) faculty into the Training Grant, which significantly enhances the strength in the core of mechanistic based molecular toxicology training. We have opened the Training Grant for University-wide selection to further stimulate interdisciplinary/multidisciplinary approaches in research and training. The request for continuation of NIEHS support is validated by the highly successful nature of our program, the clear demand for our graduates, the strong emphasis we place on leadership skills for our trainees and postdoctoral fellows, the increasing number of students interested in toxicology, substantial institutional commitment, strong and well-funded research programs of our faculty, and the excellence of the training environment. PUBLIC HEALTH RELEVANCE: This training grant seeks the support from NIEHS for 9 predoctoral and 3 postdoctoral fellows in training of toxicology at the University of Arizona.

This is an award to acquire a compute cluster at LSU. The computer is a heterogeneous HPC cluster named SuperMIC containing both Intel Xeon Phi and NVIDIA Kepler K20X GPU (graphics processing unit) accelerators. The intent is to conduct research on programming such clusters while advancing projects that are dependent on HPC. The efforts range from modeling conditions which threaten coastal environments and test mitigation techniques; to simulating the motions of tumors/organs in cancer patients due to respiratory actions to aid radiotherapy planning and management. The burden of learning highly complex hybrid programming models presents an enormous software development crisis and demands a better solution. SuperMIC will serve as the development platform to extend current programming frameworks, such as Cactus, by incorporating GPU and Xeon Phi methods. Such frameworks allow users to move seamlessly from serial to multi-core to distributed parallel platforms without changing their applications, and yet achieve high performance. The SuperMIC project will include training and education at all levels, from a Beowulf boot camp for high school students to more than 20 annual LSU workshops and computational sciences distance learning courses for students at LONI (Louisiana Optical Network Initiative) and LA-SiGMA (Louisiana Alliance for Simulation-Guided Materials Applications) member institutions. These include Southern University, Xavier University, and Grambling State University - all historically black colleges and universities (HBCU) which have large underrepresented minority enrollments. The SuperMIC cluster will be used in the LSU and LA-SiGMA REU and RET programs. It will impact the national HPC community through resources committed to the NSF XSEDE program and the Southeastern Universities Research Association SURAgrid. The SuperMIC will commit 40% of the usage of the machine to the XSEDE XRAC allocation committee.

DESCRIPTION (provided by applicant): Inhibition of protein synthesis is a general measurement of toxicity. Evolutionarily while inhibition of protein synthesis serves to save energy and prevents aberrant proteins being made, increasing evidence suggests that selective protein translation occurs and determines the cell fate. Arsenic and many environmental toxicants are known to induce oxidative stress. We found that treatment of human cells in culture with arsenic or oxidants causes rapid elevation Nrf2 protein due to de novo protein translation. Nrf2 encodes a transcription factor regulating a network of antioxidant and detoxification genes, functioning as a safeguard in multiple organ systems. Nrf2 knockout mice show an increased sensitivity to tissue injury by arsenic. Understanding how cells orchestrate molecular events leading to de novo Nrf2 protein translation under oxidative stress is important for dialing up this pathway for organ protection. Human Nrf2 gene encodes an mRNA species containing 555 nucleotides (nt) of 5' Untranslated Region (5'UTR). Several genes containing an Internal Ribosomal Entry Site (IRES) in 5'UTR can bypass 5' 7-methyl Guanine cap dependent translation and undergo stress induced protein translation. We found a consensus G-quadruplex sequence in -195 to - 168 nucleotide region of Nrf2 5'UTR. An RNA fragment from the region forms the 3-D structure of G-quadruplex as measured by Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), Electrophoretic Mobility Shift Assay and Dimethyl Sulfate footprinting. LC-MS/MS based proteomics has led to the discovery of EF1a as a binding partner of Nrf2 5'UTR G-quadruplex. At the cellular level, oxidants cause an increased association of EF1a with Nrf2 5'UTR G-quadruplex and eliminating the G- quadruplex structure prohibited the activation of Nrf2 5'UTR. Since an RNA strand in cells is rarely free of protein binding, the G-quadruplex structure forms in solution from a naked RNA fragment, and oxidation of Guanine does not affect G-quadruplex formation, we hypothesize that oxidative stress causes changes in the proteins binding to Nrf2 5'UTR at the cellular level, resulting in G-quadruplex formation and recruitment of specific proteins for interaction with eIFs to initiate Nrf2 protein translation. Ai 1 will define the impact of oxidative stress on proteins binding to Nrf2 5'UTR at the cellular level. Proteins binding to Nrf2 5'UTR will be isolated from cells with or without oxidative stress for identification by LC-MS/MS based proteomics. Aim 2 will address the interplay of EF1a with translational machinery in oxidative stress induced Nrf2 protein translation. Whether EF1a binding to Nrf2 5'UTR causes recruitment of translational machinery will be addressed by examining the interaction of EF1a/Nrf2 mRNA with eIFs, ribosomes and ribosome associated proteins. Aim 3 will confirm the biological significance of EF1a interaction with Nrf2 5'UTR in Nrf2 protein translation, cell survival and protection against arsenic toxicity. Using a G-quadruplex aptamer and pharmacological enhancers or inhibitors of G-quadruplex, we will test the effect of de novo Nrf2 protein translation in cell survival and mouse tissue injury by arsenic.

The most populated cities in the world are located on deltaic coastal floodplains because of their rich fertile soils and plentiful natural resources. River deltas are disappearing at increasing rates due to human-caused changes to sediment supply and river flow, gradual sinking of land, and rising sea level, threatening the sustainability of human settlements on coastal river deltas. River management projects, including those designed to promote navigation and reduce flooding, have in some cases accelerated land loss and increased the threat of hurricane flooding. This project will explore the relationships among human river management, sediment supply, wetland building capacity, coastal flood risk, and human perception of flood risk. Testing the connections between river management, wetland loss, and flood risks will improve prediction of future coastal system states and produce guidelines for how to sustainably manage sediment supply and maintain human settlement in coastal areas. Other broader impact activities will include graduate and undergraduate education, application to public policy, and public and K-12 outreach. These are all unified through the general recognition in Louisiana (like many other deltaic coasts) that the science of deltaic restoration has strong and direct impacts on local welfare and economies. This project is supported as part of the National Science Foundation's Coastal Science, Engineering, and Education for Sustainability program - Coastal SEES.

This project will explore the co-evolution of deltaic landscapes and human system response by focusing on changes in coastal flood risks due to human manipulations of sediment delivery. Three experimental coastal basins in the central Mississippi River Deltaic Plain with distinct histories of sediment delivery by rivers and wetland loss responses will be investigated. An interdisciplinary team of researchers will combine field studies and modeling approaches to characterize: 1) feedbacks between human river management strategies that reduce sediment delivery and corresponding landscape degradation and 2) causal links between landscape degradation resulting from reduced sediment delivery, increased flood risks from hurricane storm surges, and human responses to perceived flood risks. The team will explore historical and future outcomes of river management strategies, including reorganization of human settlement in coastal areas using computer simulations incorporating how sediment supply builds land and human response to flood risks. Testing these system interactions in a modeling framework will produce foundational knowledge that can inform management decisions and promote sustainable human settlements on deltaic landscapes.

Communities on modern river deltas with total populations greater than 500 million people face threats from global reductions in river sediment, land subsidence and rising sea level. Risk mitigation efforts may require intensive computer simulations that are integrated with data collection and engineering analytics for guidance. This project establishes a Coastal Resilience Collaboratory with a three-fold mission: 1) enhance the collaboration among earth scientists, computer scientists, cyberinfrastructure specialists and coastal engineers tasked with solving the sustainability issues of deltaic coasts; 2) identify risk mitigation for coastal communities subject to flooding hazards using approaches that integrate restoration and protection; and 3) leverage NSF investments in cyberinfrastructure to address problems of major national importance involving engineering design guided by coastal system responses to specific hazard mitigation projects. Effective linkages of cyberinfrastructure that enables rapid sharing and integration of available data resources and computational tools will be evaluated. The project will also evaluate how effectively these cyberinfrastructure products promote the wider use of high-performance computing and data analytics in the coastal engineering and science research community. The proposed project has a wide range of broader impacts, ranging from education and workforce development, to dissemination of research results to the general public, K-12 students, and coastal managers and decision makers.

The Coastal Resilience Collaboratory core research program builds on a recently funded Coastal SEES project (EAR-1427389), which serves as the science driver for the cyberinfrastructre development and its enabled simulation experiments. One of the grand challenges for earth system science is to characterize dynamic environmental processes at appropriate space and time scales with integrated observation networks and models. The project advances four elements: 1) A simulation management system for a high-level web-based interface, improving multiphysics model usability for coastal scientists/engineers not familiar with advanced computing resources; 2) Application packaging for cloud-computing using Docker container technology to facilitate prototype simulation experiments in two large river deltas to test a range of hypotheses; 3) Accelerator technology to achieve high performance levels aimed at making a GPU- accelerated Boussinesq code base available to coastal engineers for the design of sustainable infrastructure; and 4)Aapplications for visualization and access to toolkits on mobile devices to support decision-making and educational activities. The three simulation experiments that test system interactions in the modeling framework proposed is expected to produce foundational knowledge that can evaluate potential impacts of deltaic landscape change on coasts around the world and suggest mitigation solutions.

The ability to construct flood hydrographs in urban areas in real-time during flash floods, hurricanes, and other extreme weather events is difficult because of the low spatial density of water level measurements and the complex interactions of built infrastructure, ground topography, and natural landscape with flowing water. The goal of this RAPID project is to leverage perishable images and video footage from traffic intersection and interstate highway cameras, major news media outlets, and social media along with reference objects/points. Subsequent photo image processing, scaled to the reference objects, will enable development of a more continuous, accurate hydrograph in the Houston metropolitan area. By reconstructing the flood hydrographs at a large number of locations in flooded highways, streets and residential subdivisions, high-resolution, process-based urban inundation modeling from hurricane-generated surge and rainfall will become significantly more accurate. For example, it will facilitate a better understanding of transport of sediments and pollutants in and out of Houston during Hurricane Harvey. Such a model validated by the reconstructed hydrographs will also aid state and local governments in making timely evacuation decisions for low-lying areas to mitigate the impact of similar hurricane-induced hazards.

This RAPID project based on reconstruction of flood hydrographs in Houston using image processing and in-situ measurements has significant intellectual merit: (1) The proposed methodology is innovative and creative because it does not employ any traditional stream gages. Instead, it relies on a unique form of existing data employed for a new application. (2) The reconstructed flood hydrographs will significantly improve the understanding of the hydrological processes of this unprecedented flood event caused by the extreme rainfall of Hurricane Harvey. (3) The data will benefit the development of a new flood model for Houston. (4) The developed algorithms and software for processing the traffic image data, which will be available on the NHERI DesignSafe-CI platform, can be readily applied to many other flood-prone urban centers, such as New York City, New Orleans, and Miami.

Oxidative stress is an important component of disease etiology and progression. At the cellular level, while inhibition of overall protein synthesis is a measure of stress in general, increasing evidence suggests that selective protein translation occurs and determines cell fate. Many xenobiotics or disease states cause an increase in oxidative stress. We have found that low to mild doses of oxidants trigger de novo translation of Nrf2 protein, a transcription factor regulating a network of antioxidant and detoxification genes. Deficiency of Nrf2 protein results in an increased sensitivity to a variety of chemical and pathophysiological stresses. It is not known the components in the translation machinery responsible for Nrf2 protein translation. Normally, initiation of protein translation requires recognition of 7-methyl Guanine cap at the 5' end (5' m7G) of an mRNA strand by eIF4E in the eIF4F complex, and recruitment of the 43S pre- initiation complex. Human Nrf2 gene encodes an mRNA species containing a 555 nucleotide 5' Untranslated Region (5'UTR). Genes containing an Internal Ribosomal Entry Site (IRES) in 5'UTR can bypass 5' m7G cap-dependent translation and undergo stress-induced protein translation. Using LC-MS/MS based proteomics, we have identified the La autoantigen as a binding partner of Nrf2 5'UTR. Oxidants induce La protein to translocate from the nucleus to the cytoplasm, where it exhibits increased binding to Nrf2 mRNA and ribosomes, resulting in Nrf2 protein translation. Nrf2 is typically activated when modification of redox-sensitive cysteine residues in Keap1 renders it incapable of mediating Nrf2 ubiquitination. Whether or not de novo Nrf2 protein translation is sufficient for activating the Nrf2 transcription network has not been addressed. We hypothesize that La facilitates the assembly of the 48S Initiation Complex for de novo Nrf2 protein translation, and La-Nrf2 signaling is essential for cytoprotection via controlling gene expression under oxidative stress. Aim 1 will test whether RNA recognition motifs of La protein form physical contact with a specific region of Nrf2 5'UTR to mediate de novo Nrf2 protein translation. The region of Nrf2 5'UTR for La binding will be mapped using an RNA Electrophoretic Mobility Shift Assay (EMSA) in combination with RNase/Chemical probing. The motif of La protein responsible for binding to Nrf2 5'UTR will be identified by deletion or mutation. Aim 2 will test whether La coordinates the assembly of the 48S Initiation Complex to drive new protein translation under oxidative stress. The eIF4E, 4G, 4A, 4B, 4H, 1, 1A, 2, 3, 5, 5B, and PABP are essential elements of the 48S Initiation Complex (48S IC) and will be examined for interactions with La and La/Nrf2 5'UTR complex under oxidative stress. Proteins associated with the La or the La binding site of Nrf2 5'UTR will be revealed using high resolution LC-MS/MS proteomics. The role of these proteins will be tested for assembly of 48S IC and de novo Nrf2 protein translation. Aim 3 will test whether de novo Nrf2 protein translation mediates cytoprotection and expression of antioxidant and detoxification genes independent of Keap1 during oxidative stress. La will be knocked out using siRNA and CRISPR, and knocked in using Nrf2 5'UTR binding null mutant to investigate its cytoprotective role. We will further define the La-Nrf2 axis of gene expression using microarray and RNAseq. Keap1 null cells and conditional Keap1 knockout mice will be tested for Nrf2 induction via de novo protein translation, and subsequent cytoprotection (in vitro) or cardiac protection against ischemic injury (in vivo). The PI has expertise for contemporary state-of-the-art cell and molecular biology research. This project will advance our understanding on the mechanism and functional impact of de novo Nrf2 protein translation under oxidative stress.

Project Summary/Abstract: Myocardial infarction (MI) is an emergency state that requires immediate medical intervention. Coronary artery bypass graft (CABG) surgery or angioplasty procedures have becoming standard but effective treatment. Biomarkers of myocardial cell death are detected postoperatively in nearly all CABG patients or about 30% of angioplasty patients. Cell death remains detectable in the myocardium even when patients appear to have recovered from MI. The degree of cell death predicts the risk of developing heart failure and other complications. Identifying cytoprotective genes and uncovering their mechanisms of action pave the way for developing new therapies to reduce cardiac injury. Oxidative stress, as a result of ischemic or reperfusion and/or major surgery, usually causes an inhibition of protein synthesis. We found that Nrf2 mRNA can escape such general inhibition and be translated selectively. 5'UTR of Nrf2 mRNA was found to recruit La autoantigen for ribosomal association and de novo Nrf2 protein translation. Nrf2 is best known as a transcription factor for regulating the expression of antioxidant and detoxification genes. We have found that Nrf2 protects mitochondria from oxidative injury by physical association. We propose to utilize high resolution LC-MS/MS based proteomics, novel Nrf2 inducers in combination with transgenic animals, and in vitro and in vivo experimental models to test the hypothesis that elevated Nrf2 protein plays an important role in preservation of mitochondria and protection against myocardial injury. Aim 1 will investigate a novel pathway of Nrf2 induction by de novo Nrf2 protein translation. Components in the La and ribosomal protein complexes will be uncovered in an effort to understand the translational machinery under oxidative or ischemic stress in cardiomyocytes. Aim 2 will reveal a novel mechanism of Nrf2 mediated cytoprotection by testing Nrf2 participation in maintenance of mitochondrial integrity and metabolism. The domain of Nrf2 protein for physical interaction with mitochondria or mitochondrial outer membrane proteins will be identified for testing the significance in mitochondrial integrity, metabolism and mitophagy. Aim 3 will provide preclinical evidence for Nrf2 as the lead for cardiac protection. The importance of de novo Nrf2 protein translation for cardiac protection will be demonstrated using siRNA against La autoantigen. Contracting cardiomyocytes will be established for selection of Nrf2 inducers with suitable therapeutic indices. Mitochondrial preservation and cardiac protective effect of these compounds will be tested using Nrf2 overexpressing transgenics as a positive control. We have accumulated a large volume of data to support the success of the project. Accomplishment of the proposed work will not only provide needed answers to basic science questions, but also present the feasibility of a new category of drugs for cardiac protection.