Funded Research Projects

Permanent URI for this collectionhttps://hdl.handle.net/20.500.14641/189

An index of publicly funded research projects conducted by Texas A&M affiliated researchers.

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Topics in Mathematical Theory of Adaptive Finite Element Methods
Mathematics; TAMU; https://hdl.handle.net/20.500.14641/668; National Science Foundation
Finite element methods (FEM) are widely used to approximately solve partial differential equations in simulations of physical phenomena arising in engineering and the physical sciences. Such simulations are an indispensable tool in the development and testing of new technologies. Adaptive variants of finite element methods are designed to increase the efficiency and accuracy with which simulations can be carried out by making better use of computational resources and to increase confidence in the accuracy of simulations by providing researchers with a computable measure of the errors that arise in approximation techniques. This research project aims to develop new variants of adaptive finite element methods and increase mathematical understanding of their underpinnings. The project has two main foci. The first is adaptive FEM for partial differential equations defined on surfaces, which arise for example in describing fluid flows with multiple components (such as oil and water). The second is development and analysis of adaptive FEM for controlling various measures of the error, especially maximum errors. In the first project the investigator will construct and analyze adaptive variants of surface finite element methods with two main goals in mind. First, while surface FEM are an established finite element methodology with many useful variants defined, adaptive versions of some important variants are missing. This project aims to fill that gap. Secondly, the project will explore the interaction between adaptive surface FEM, the way a given surface is represented in a finite element code, and the smoothness or regularity of the surface. The result will be more robust adaptive surface codes that give users greater flexibility in representing surfaces while also making the best possible use of available information about the surface. The second main project will lead to proof of convergence of adaptive algorithms for controlling maximum errors, and will also provide new adaptive algorithms for controlling maximum errors in a class of singularly perturbed elliptic problems.
SusChEM: Resourceful Polymers Derived from Polyhydroxyl Natural Products
Chemistry; TAMU; https://hdl.handle.net/20.500.14641/598; National Science Foundation
Organic polymer materials, commonly thought of as plastics, are of critical importance to every aspect of human life, from the clothes that we wear to the computers that we use to the tires on which we drive to the devices through which medicines are administered. Two key challenges with polymer materials are their production from petrochemical sources, which are non-renewable, and their persistence in the environment. To address these challenges, Professors Wooley, Darensbourg, and Dr. Sun of Texas A&M University are designing strategies to produce polymer materials from natural building blocks while also incorporating degradable linkages that regenerate those natural building blocks once the material has completed its useful lifetime. This project includes research and educational components to impact fundamental knowledge about polymer materials across the disciplines of chemistry and engineering. The research team is developing synthetic chemistry approaches to the production of a series of polycarbonates and polyphosphoesters that originate from renewable resources, exhibit novel chemical, physical and mechanical properties, and undergo hydrolytic breakdown to biologically-beneficial or benign by-products. In one direction, this project combines polyhydroxyl natural products as the monomeric building blocks and carbonates as the linkages. Hydrolytic degradation of the resulting polymers produces the polyhydroxyl compound plus carbon dioxide. In a second direction, phosphoester linkages are utilized, again borrowing from Nature, in phosphoesters commonly found in biological macromolecules, such as DNA or RNA. The research activities include 1) the synthesis of functional monomers from polyhydroxyl natural products, 2) the transformation of those monomers into linear, branched or crosslinked polymer materials by either step-growth condensation or chain-growth ring-opening polymerizations, 3) rigorous characterization studies to determine the compositions, structures, physicochemical and mechanical properties; and 4) the study of hydrolytic stabilities and degradation products.
Localization of Voltage-Gated Ca2+ Channels and Ca2+-Gated K+ Channels to Specific Active Zone Material Macromolecules at Presynaptic Active Zones and How that Influences Neurotransmitter Secretion
Vet - Pathobiology; TAMU; https://hdl.handle.net/20.500.14641/379; DHHS-NIH-National Institute of Neurological Disorders and Stroke
Synaptic impulse transmission fundamentally relies on the coupling of neuron impulses with neurotransmitter secretion from specialized sites along the presynaptic plasma membrane (PM) of the axon terminals called ac- tive zones. Active zones of all synapses have comparable organelles, called ‘Active Zone Material’ (AZM), which are composed of homologous proteins that assemble to form distinct classes of AZM macromolecules; AZM regulates the events that lead to neurotransmitter secretion from docked synaptic vesicles (SV) (i.e. SVs held in contact with the PM). Determining the identity of the proteins that assemble to form the AZM is neces- sary to understand the general rules that govern the molecular mechanisms that regulate neurotransmitter se- cretion throughout the nervous system under normal, experimental and disease conditions. The arrival of an electrical impulse at an active zone causes voltage-gated Ca2+ (CaV) channels to open and allow Ca2+ to enter the cytosol which results in elevated concentrations of Ca2+ near the mouth of the channel for a very brief peri- od of time. If sufficient concentrations of Ca2+ interact with the SV protein synaptotagmin it triggers membrane fusion and neurotransmitter secretion, which is the defining stage for the described impulse-secretion coupling. The Ca2+ that enters the cytosol also activates Ca2+-gated K+ (KCa) channels to repolarize the PM and deacti- vate the CaV channels to arrest further neurotransmitter secretion. Thus, the relative proximity of CaV channels to docked SVs and KCa channels strongly influences impulse-secretion coupling. In axon terminals of a model synapse, frog neuromuscular junction, it has long been suspected that both CaV and KCa channels are compo- nents of the macromolecules that span the PM at active zones arranged in parallel double row arrays de- scribed in freeze-fracture replicas. Previous studies from our lab used electron tomography to quantitatively study the 3D macromolecular structure of AZM at frog neuromuscular junctions and found that the members of a particular class of AZM macromolecules called pegs are connected to the macromolecules that span the PM. We also found that docked SVs that had the greatest probability of fusing with the PM when an impulse arrives were associated with pegs in the row proximal to the SVs that were displaced closer to them. We proposed that the proximal pegs were connected to CaV channels because the closer the CaV channel is to synaptotag- min when the impulse causes the channel to open and allow an influx of Ca2+ into the cytosol, the higher the concentration of Ca2+ exposure to synaptotagmin and the greater the probability that it will trigger membrane fusion. The objective of the research proposed here is to localize the CaV and KCa channels at active zones of frog neuromuscular junctions with sufficient resolution to determine if they are associated with the pegs that are connected to the macromolecules that span the PM, and if they are, to determine which row each channel is concentrated. To meet this objective, an innovative method involving histochemical labeling of CaV and KCa channels together with quantitative electron tomography will be used.
Conference: International Workshop on Operator Theory and its Applications 2018
Mathematics; TAMU; https://hdl.handle.net/20.500.14641/232; National Science Foundation
This award provides funding to help defray the expenses of participants in the meeting "International Workshop in Operator Theory and its Applications" (IWOTA) a workshop that will take place during July 23-27, 2018, on the campus of the East China Normal University in Shanghai, China. Additional information about the conference can be found on the website http://iwota2018.fudan.edu.cn The 2018 IWOTA meeting will continue the tradition of past meetings in this series going back to 1981. The meeting will be focused on the latest developments in functional analysis, specifically, operator theory and and related fields. This includes applications in engineering and mathematical physics from areas such as differential and integral equations, interpolation theory, system and control theory, signal processing, and scattering theory. The IWOTA meeting will run the week before the international symposium "Mathematical Theory of Networks and Systems"(MTNS) and this pairing provide opportunities for analysts to get exposed to engineering problems. Priority for funding will be given to early career mathematicians, women, members of underrepresented groups and those without other means of support. This is an important conference in operator theory and its applications that will offer participants the opportunity to learn of state-of-the-art research in operator theory with applications to engineering and other sciences. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
Supplement request for PCMHAB: Expanding Harmful Algal Bloom Mitigation in the Gulf of Mexico with Operational Support and Training for the Imaging FlowCytobot Network
Oceanography; TAMU; https://hdl.handle.net/20.500.14641/416; DOC-National Oceanic and Atmospheric Administration
The network of Imaging FlowCytobots (IFCBs) has provided early warning for harmful algal blooms (HABs) along the Texas coast since 2007. The IFCB combines flow cytometry and imaging technology to collect a high resolution (hourly) time series of the phytoplankton dynamics and their response to environmental changes. One extremely valuable product of this decade-long time series of phytoplankton abundance has been the successful early warning of eight HAB events. An automated image classification and notification (email alerts to state managers [Texas Department of State Health Services and Texas Parks and Wildlife Department]) system has been developed based on the IFCB data stream. The lack of any phytoplankton abundance information at this crucial, central Texas coastal station has rendered the early warning system less useful for HAB detection and early warning. The goal of this supplemental funds request is to replace equipment lost or damaged during Hurricane Harvey and its aftermath, and to obtain an IFCB instrument that will permit an uninterrupted time series for the Texas IFCB network. The IFCB in Port Aransas was deployed on the pier of the University of Texas Marine Science Institute and had been in operation since September 2007. The pier was destroyed when a drilling ship broke free of its moorings during the storm and eventually crashed into the pier. IFCB. The loss of the continuous data collection by the IFCB has directly impacted several ongoing projects. The result is a data gap in our time series and loss of HAB early warning capability. The second IFCB deployment site at Surfside Beach, TX was established to expand the HAB early warning network and to look at the coastal connectivity between the Port Aransas and Surfside sites. Models of coastal currents and current velocity/direction data obtained from the Texas Automated Buoy System (TABS) are combined with IFCB data at both locations to determine the connectedness of the two sites to improve early warning of HABs. Gaps in data at the two sites severely impact the effectiveness of the early warning network for HABs. A new IFCB will permit immediate restoration of the time series if a deployed instrument requires maintenance or is damaged at Port Aransas or Surfside Beach deployments.
CAREER: Nuclear Microphysics of Neutron Stars, Core-Collapse Supernovae, and Compact Object Mergers
Cyclotron Institute; TAMU; https://hdl.handle.net/20.500.14641/256; National Science Foundation
The structure, phases, and dynamics of nuclear matter are key to answering fundamental questions at the interface of nuclear physics and astrophysics: How are the stable elements heavier than iron synthesized in extreme astrophysical environments? What is the composition and nature of the densest observable matter in the universe? What are the most promising astronomical sources of detectable gravitational waves? This project will integrate research and education while developing new theoretical models of the ultra-hot and ultra-dense matter encountered in core-collapse supernovae, proto-neutron stars, and binary neutron star mergers. The project will also provide theoretical support for the experimental program at rare-isotope beam facilities. As such, this project will also provide new opportunities to disseminate exciting forefront research developments in nuclear physics and nuclear astrophysics to high school students in the Texas Brazos Valley through an integrated lecture and competition series. A major long-term goal is to understand how the strong nuclear force shapes the structure, evolution, and observable emissions of high-energy astrophysical systems, such as core-collapse supernovae, neutron stars, and binary neutron star mergers. To support this effort, this project aims to develop the first microscopic models of hot and dense neutron-rich matter based on the low-energy effective field theory of strong interactions. The nuclear thermodynamic equation of state, governing neutron star structure as well as the hydrodynamic evolution of supernovae and neutron star mergers, will be calculated across the range of conditions needed for numerical simulations. This will enable more reliable predictions for the electromagnetic, neutrino, and gravitational wave signals from supernovae and neutron star mergers. The nucleon single-particle potential in nuclear matter will be computed and parametrized in a form suitable for nucleosynthesis studies of neutrino-driven winds in supernovae and the tidally ejected matter in neutron star mergers. Finally, quantum Monte Carlo simulations of dilute neutron matter at finite temperature will be carried out in order to investigate the effect of neutron pairing on transport and cooling phenomena in proto-neutron stars.
Innovative Statistical Models for Development of First Huntingtons Disease Progression Risk Assessment Tool
Statistics; TAMU; https://hdl.handle.net/20.500.14641/569; DHHS-NIH-National Institute of Neurological Disorders and Stroke
Project Summary/Abstract Huntington's disease (HD) is a progressive, neurodegenerative disorder that can be genetically diagnosed years before clinical symptoms onset. This presents groundbreaking opportunities to learn the overall, dynamic progression of HD which is critical to the timing of therapeutic interventions and design of effective clinical trials. Despite advancements in this area, significant gaps exist about the transitional period from premanifest to manifest HD, particularly how and when overt clinical symptoms and neurological deterioration develop. As part of the candidate's long-term goal to become an independent, lead expert biostatistician for neurodegenerative diseases, the overarching goal of this K01 is to acquire training in the disease-related background and quantitative analytical skills to develop innovative methods that target new discoveries of HD progression. The candidate, Dr. Tanya P. Garcia, is a Huntington's Disease Society of America (HDSA) Human Biology Project Fellow (2013-2015) and has assembled a team of outstanding mentors and collaborators who will provide training to acquire the skills she lacks for an independent, biostatistically-focused, neuroscience career. Her two primary mentors are Dr. Karen Marder and Dr. Raymond J. Carroll. Dr. Marder is the Sally Kerlin Professor of Neurology at Columbia University with over 300 publications in behavioral neurology, neuroepidemiology and neurodegenerative diseases including Huntington's, Alzheimer's, Parkinson's and HIV dementia. Dr. Carroll is Distinguished Professor of Statistics at Texas A&M University with over 400 publications and 5 books in multiple statistics areas, particularly in those needed for this proposal. To conduct high-level research that fills significant gaps about HD progression knowledge, Dr. Garcia proposes in-depth training (i) To learn the latest developments and challenges in clinical and neurological understanding of HD to fine-tune statistical methodology; (ii) To obtain proficiency in analysis of correlated, longitudinal, big data; and (iii) To develop programming expertise to make the proposed methods accessible to neuroscience investigators in user-friendly software. Training in these areas directly support Dr. Garcia's research aims which are (i) To improve prediction of HD motor-diagnosis by modeling the time-varying effects of multiple clinical performance measures; (ii) To improve identification of disease-relevant brain regions in relation to HD motor-diagnosis by modeling the spatial-temporal brain structure; and (iii) To develop the first generation of a HD Progression Risk Assessment Tool (HD-PRAT). Expected research outcomes include models that support President Obama's Precision Medicine Initiative in that they adhere to “2P's” of the NIH New Strategic Vision of the “4P's” of Medicine: they will offer promising ways to Predict the pattern and intensity of an individual's clinical and neurological changes over time; and increase the capacity to Personalize early intervention based on these learned predictions. Having the models available in user-friendly HD-PRAT is of high
CLAP-seq: An Aptamer-Based Platform for Transcriptome-Wide Mapping of RNA Modifications
Chemistry; TAMU; https://hdl.handle.net/20.500.14641/200; DHHS-NIH-Eunice Kennedy Shriver National Institute of Child Health & Human Development
Project Summary/Abstract Beginning in the 1950s, more than 100 types of posttranscriptional modifications have been identified in cellular RNA. Today, the study of RNA post-transcriptional modifications – known as epitranscriptomics – is a rapidly developing field, which promises to greatly enhance our understanding of human health and disease. Despite the profound implications already assigned to many RNA modifications, their precise functions remain poorly understood. This can be attributed to the lack of sensitive and robust sequencing technologies to detect these epitranscriptomics marks in a transcriptome-wide manner. A key bottleneck is the lack of sensitive and specific enrichment techniques (affinity- or reactivity-based) for RNA molecules containing these modifications. The proposed research takes direct aim at this critical deficit using the aptamer approach, employing in vitro selection methods to identify nucleic acid molecules that bind chemically modified RNAs. These aptamers are unique in that they are comprised of L-(deoxy)ribose-based nucleic acids (L-DNA and L-RNA), which are mirror images (enantiomers) of natural D-nucleotides. L-Aptamers, which are completely orthogonal to natural biology, are extremely well suited for binding RNA targets. Therefore, in vitro selection will be used to isolate novel L- aptamers capable of binding chemically modified mononucleotides, which will enable selective capture of RNA molecules containing the same modified residue. These L-aptamers will then be used in Cross-Linking- Aptamer Pull-down and sequencing (CLAP-seq), the first transcriptome-wide profiling technology employing aptamer-based RNA enrichment prior to next-generation sequencing. CLAP-seq not only promises to open a general and robust route towards transcriptome-wide profiling of the growing list of RNA modifications, but also promises to reinforce our current view of the epitranscriptome. Accordingly, the development of CLAP-seq will have a profound impact on the field of epitranscriptomics, which is well aligned with the mission of the NICHD and the goal of this FOA: to promote research into the role of RNA chemical modifications in development and related disease.
Life history and age validation of blacktip sharks (Carcharhinus limbatus) in the Gulf of Mexico with implications for stock assessment models
Marine Biology; TAMUG; https://hdl.handle.net/20.500.14641/585; DOC-National Oceanic and Atmospheric Administration
The three main objectives of this proposal were as follows: 1. Obtain sex-specific age and growth estimates of blacktip sharks in the eastern and western Gulf, 2. Examine reproduction of blacktip sharks in the eastern and western Gulf, 3. Apply a novel technique (vertebral chemistry) as an age validation method for blacktip sharks. The information gained from this proposed project will provide usable and relevant information to aid fishery researchers, scientists, and managers to make informed management decisions that can be directly utilized for future assessments.
Monitoring of mast cells activation for control of health status in military personnel
Biomedical Engineering; TAMU; https://hdl.handle.net/20.500.14641/242; DOD-Army-Medical Research and Materiel Command
Background: Mast cells are located in various parts of the body, with the highest likelihood of changes introduced from outside: skin, respiratory system, gut and mesentery, along with blood and lymphatic vessels. Mast cells are sensitive to such changes, which may be induced, but not limited by mechanical stress (compression), increases in tissue fluid volume (edema), pH, abnormal temperatures, harmful dust, and ionizing irradiation. Additionally, mast cells are sensitive to the appearance of various antigens/pathogens, chemical and bacterial toxins, traumatic injury (direct cellular/tissue damage and effects of the products of tissue destruction), inflammation, and allergy. Cumulatively, we believe that monitoring ongoing levels of mast cell activation is especially valuable to evaluate and to monitor the pre-existing and ongoing health status of military personnel. Objective/Hypothesis: The determination of pre-existing and monitoring of ongoing levels of mast cell activation is able to provide critical information on healthy reserves of the body and its ability to react to acute challenge. The studies in Aim 1 were designed to establish and characterize correlations between individual variations in resting levels of mast cell activation and the ability to respond/resist effectively to acute infectious challenge. The studies in Aim 2 were designed to establish and to characterize an ability to respond/resist effectively to acute infectious challenge in mast cell-stabilized animals with individual variations in resting levels of mast cell activation. The studies in Aim 3 were developed to design and to test the prototype of an implantable mini-sensor to detect changes in blood histamine and mast cell tryptase as the most important indicators of mast cell activation. In perspective, we believe that the portable reader/scanner will allow performance of periodic measurements of these parameters for fast assessment of individual health status of military personnel in missions. We believe that our innovative research directly targets goals of the FY19 AIMM Focus Area "Algorithms/tools for decision support in a deployed or operational environment to: diagnose military-relevant disease, illness, or injury; prescribe mitigation and treatment strategies; and/or determine risk of Warfighter return to duty." Outcomes of research for military health and medicine: 1. Mast cell activation could be used as an early sign of development of infection. Our approach will provide the ability to start antibacterial therapy even earlier than clinical manifestation of any infection. 2. An ability to monitor mast cell activation in zones contaminated by ionizing irradiation will help to withdraw the most sensitive individuals from such action earlier than the accepted dose of irradiation can be reached. Such ability will help to prevent/diminish the harmful consequences of exposure to irradiation in more sensitive individuals, and to differentiate health risks more precisely on individual basis. 3. Mast cell activation levels could be used as indicators of abnormal reactions to predicted environmental changes (such as harmful dust, extreme heat or cold). In certain situations when personnel cannot be rotated, the therapeutic mast cell stabilization (e.g., masitinib mesylate) could be applied individually with on-time reference to increased levels of histamine and mast cell tryptase. 4. The implantable mini-sensors to detect changes in blood histamine and mast cell tryptase will provide an extremely useful tool to control the health status of military personnel in action. They will permit effective individually based health-oriented decisions in field conditions in accordance with the current situation and therefore diminish the likelihood of a Soldier’s health failure due to unforeseen/unexpected rising health problems. 5. The determination of which level of ongoing mast cell activation and degree of mast cell response could be a useful tool to evaluate the adaptive reserves of the military personnel.
Equilibrium in Multivariate Nonstationary Time Series
Statistics; TAMU; https://hdl.handle.net/20.500.14641/475; National Science Foundation
Nonstationary time series systems appear routinely in economics, seismology, neuroscience, and physics, where stationarity is usually synonymous with equilibrium. Such systems are usually multidimensional, and their modeling, prediction, and control have tremendous social and scientific impacts. Isolating and identifying equilibrium or stationary features are of fundamental importance in prediction and control of such systems. This research project aims to develop methodologies for extracting aspects of multivariate nonstationary processes that display a sense of equilibrium or stationarity. It is interdisciplinary in nature and has immediate applications to the analysis of economics, seismology, and neuroscience data. A graduate student will be involved in the research. This research project aims to elevate the concept and theory of cointegration from multivariate integrated time series rooted in economics theory to the more general multivariate nonstationary time series setup in probability and statistics. In spite of its central role in econometrics in the last four decades and well-founded motivations in economics, the cointegration theory suffers from the requirements that the series be integrated (unit-root nonstationary) and satisfy a vector autoregressive and moving average model. The goal of this project is to avoid such restrictions and focus on general multivariate nonstationary time series. Three distinct methods for computing analogues of cointegrating vectors and the cointegrating rank will be developed. The first is a time-domain method in line with the classical (Johansen's) approach that relies on the reduced rank regression and likelihood ratio tests. The second method is in the spectral domain and relies on the idea of projection pursuit. It searches for coefficients of candidate linear combinations by minimizing a projection index measuring the discrepancy between time-varying and constant spectral density functions. The third method is concerned with a time-varying cointegration setup where the coefficients are piecewise constant over time. Its successful implementation rests on a good solution of the problem of change-point detection for nonstationary processes, and a novel solution is explored in this research. The results will have immediate impact in settings where multivariate time series data are collected, such as in financial markets, epidemiology, environmental monitoring, and global change.
CDS&E: Cyclic Tetrapeptide Probes for Protein Binding
Chemistry; TAMU; https://hdl.handle.net/20.500.14641/216; National Science Foundation
With this award, the Chemistry of Life Processes Program in the Chemistry Division is funding Dr. Kevin Burgess of Texas A & M University to discover small molecules that affect how some proteins bind to each other. Protein-protein interactions are important to many biological processes in cells. Thus having small molecules that can either aid or or hinder protein-protein interactions could lead to potential new drugs to help treat various diseases. The project is creating new small molecules and studying their effect on protein-protein interactions. It also combines chemical synthesis, computer-aided molecular design and data-mining training for graduate and undergraduate students to help them tackle problems in contemporary life science. Cyclic peptides are known to mimic key regions involved in protein-protein interactions, i.e. to be Protein-Protein Interface (PPI) mimics. While cyclic pentapeptides are easy to make they tend to equilibrate between conformers. Conversely cyclic tetrapeptides from natural amino acids are difficult to make but are more conformationally stable. Thus, easily synthesized cyclic peptides from genetically encoded amino acids linked by main-chain amides can have ring sizes of 9, 12, 15, etc. i.e. 3n atoms, (n = # amino acids) which misses ring sizes between 12 and 15 that combine conformational rigidity with ease of synthesis. This work is showing that contrary to some earlier reports, cyclic Tetrapeptides from natural amino acids are conformationally rigid and are more synthetically accessible than previously thought. It is also showing that replacement of a genetically encoded residue with some rigid unnatural amino acids can be used to give cyclic tetrapeptides that rest at a useful crossroads between ease of synthesis and conformational rigidity.
Evaluation of Novel Interferon Epsilon across Human Pregnancy
Epidemiology And Biostatics; TAMU; https://hdl.handle.net/20.500.14641/560; DHHS-NIH-National Institute of Allergy and Infectious Diseases
Reproductive and pregnancy complications are prevalent, are often recurrent and have poorly understood etiologies. There is mounting evidence that innate immune factors are important for reproductive immune homeostasis to support fertilization, implantation, placentation and overall pregnancy health while maintaining protection against pathogens. This is significant as sexually transmitted infections (STIs), which lead to adverse reproductive and pregnancy outcomes, are currently at an exceptional high in the United States. Furthermore, infection-related pregnancy outcomes, such as preterm birth, occur at the same rate in the U.S. as some middle and low- income countries (11%), particularly in minority populations. Even in the absence of STIs, the genital microbiome may have a significant influence on reproductive immunology. Thus, immune molecules may be targets for novel therapies to improve reproductive and pregnancy health. Recently characterized type I interferon epsilon (IFNe) has been reported in animal and experimental models to maintain reproductive tract IFN-stimulated gene expression and form an innate immune defense against STIs. Indeed, studies suggest that IFNe is a potential novel mucosal therapeutic against genital infections. However, the role of IFNe in human reproductive success is not elucidated. There is a critical need to increase the understanding of the epidemiology, biology and clinical utility of IFNe. Pregnancy is a dynamic immunological state and other type I IFNs, such as IFN-beta, modulate maternal immunity, promote tolerance to the fetus and protect against pathogens. However, type I IFNs can also exacerbate disease, particularly following bacterial infections. This is likely due to increased signaling by the innate immune receptors that regulate IFN expression. However, IFNe is unique as it is regulated by reproductive hormones which makes this type I IFN a more desirable target for mucosal therapeutics. A pilot investigation of 25 pregnant women showed that IFNe is present in the lower genital tract, increases as gestation progresses and is lower in pregnant women with genital infections and high body mass index. The objective of this R21 proposal is to 1) validate prior estimates of vaginal IFNe expression across pregnancy; 2) identify maternal demographic characteristics that influence IFNe levels and 3) determine if lower IFNe levels are associated with maternal and infant health indicators. This study is innovative as it will be the first longitudinal investigation of human IFNe in pregnancy. Data generated from this study will be used for future investigations to determine if IFNe has any clinical utility in protection against genital tract infections and improves reproductive and pregnancy success.
Utilizing geostationary satellite observations to develop a next generation ice cloud optical property model in support of JCSDA Community Radiative Transfer Model (CRTM) and JPSS CAL/VAL
Atmospheric Sciences; TAMU; https://hdl.handle.net/20.500.14641/202; Department of Commerce
SOW As a flagship effort of a multi-agency (NOAA, NASA, Navy and Air Force) Joint Center for Satellite Data Assimilation (JCSDA), the Community Radiative Transfer Model (CRTM) is a powerful and robust tool to facilitate the forward and adjoint radiative transfer simulations involved in satellite remote sensing programs and data assimilation efforts. Although the CRTM is a state-of-the-art radiative transfer package, ice optical property model used in CRTM is obsolete. Ice clouds are ubiquitous in the atmosphere, covering approximately 40% of the tropics and 20% of the globe. These clouds play important roles in the radiative transfer process in the earth-atmosphere coupled system. It is well known that the “equivalent-sphere” model for ice clouds produces significant errors or even misleading results. Progress in developing of more realistic nonspherical ice crystal models has been steady but slow. The existing ice cloud optical property models still suffer various shortcomings, for example, some models lead to inconsistency for applications in the solar and infrared spectral regimes, and some models lacks microphysical consistency in comparison with in situ measurements. In response to this funding opportunity, we propose to develop a next generation ice model in support of the Community Radiative Transfer Model (CRTM) and the improved modeling capability will benefit the CAL/VAL efforts in conjunction with the Joint Polar Satellite System (JPSS). We will use observations made by the Advanced Baseline Imager (ABI) aboard GOES-16 and GOES 17 with high temporal resolution to first infer the radiative and microphysical properties (specifically, optical thickness and the effective particle size) using both the solar bi-spectral technique (i.e., the Nakajima-King method) and the infrared split window technique with daytime ABI observations while only infrared technique will be used for nighttime retrieval. Furthermore, we will collocate the aforesaid retrievals with collocated CALIOP retrieval. In the proposed retrievals, an ice cloud optical property model must be used. We will test various ice cloud models. The optimal model is the one that will lead to spectral consistency between solar-band and IR-band based retrievals and consistency between passive (ABI based) and active (CALIOP based) retrievals. After an optimal ice cloud model is identified, we will implement it in CRTM. Specifically, the implementation will be conducted for the channels of Cross-track infrared Soundar (CrIS) and Visible Infrared Imaging Radiometer Suite (VIIRS) on JPSS. This effort will support JPSS CAL/VAL effort. We call special attention to the optical ice cloud optical properties generated through the proposed project, which can be directly used to generate the forward look-up tables involved in JPSS-based cloud property retrievals in consistent with the improved CRTM so that data assimilation using CRTM and JPSS cloud products are consistent.
Urban Water Provisioning Systems and Household Water Security
Geography; TAMU; https://hdl.handle.net/20.500.14641/592; National Science Foundation
Water security remains a major challenge for rapidly growing urban areas of the developing world and impoverished areas in developed countries where unregulated and informal domestic water provisioning practices persist despite increases in household access to piped water. Urban water provision is an assemblage of water vendors, networked pipes, plastic jugs, standpipes, water meters, rainwater and greywater collection tanks, and water trucks that convey and manage domestic water provision to help households cope and meet needs of everyday life. This project examines how and why urban households obtain water through these hybrid infrastructure systems and tests their efficacy in terms of household water security, defined as reliable, adequate and affordable water for a healthy life, using a scaled metric developed by the investigator. The project will be conducted in metropolitan Fortaleza, Brazil, where domestic water provision reflects typical configurations of water provision in the developing world. Research outcomes will provide meaningful insights as to the benefits and limitations of hybrid water-provisioning systems and inform development interventions, technological innovations for water provision, and infrastructure investments. Investigators will create a publicly available online portal to disseminate project information and photos, research findings, and a computational tool to standardize the household water security metric for cross-regional comparisons, allowing researchers to examine impacts of household water insecurity on diverse areas such as public health and water infrastructure planning. The project will also deepen research networks between Brazilian and US researchers, broaden participation of underrepresented groups in science through its research design, and contribute to the development of a globally competitive STEM workforce by training one computer science undergraduate and one geography graduate student. The emergence of regulated and unregulated water provisioning systems begs the question of its efficacy for human development and water security: Do hybrid urban water systems increase or decrease household water security? What particular configuration of formal and informal technologies and practices enhances or reduces household water security? How do different hybrid water-provisioning systems compare in terms of household water security? The major social scientific contribution of this project is to answer these questions by employing a mix of qualitative (observation; open-ended and semi-structured interviews), participatory (photovoice), and quantitative (survey) methods. The investigator will describe and develop a typology of water provision, assess how households interact with the existing systems, and measure household-level water security in selected urban communities. The household water security metric calculated from the survey data can be used to statistically test and model the relationship of water insecurity to several factors, including water-provisioning type, income, education, and health. This project will provide new empirical data to engage larger theoretical debates on the benefits of coexistence, the efficacy of centralized, piped water networks as the modern ideal of water provision, and urban water governance, more broadly.
TRIM Proteins Polarize DNA Sensing Outcomes During the Innate Immune Response to Mycobacterium Tuberculosis
Microbial Pathogenesis And Immunology; TAMHSC; https://hdl.handle.net/20.500.14641/513; National Institutes of Health
Project Summary Mycobacterium tuberculosis (Mtb) is an incredibly successful human pathogen that currently infects one-third of the world's population and kills 1.5 million people every year. While interaction of Mtb bacilli and macrophages activates numerous antimicrobial pathways, this bacterium has evolved an exquisite array of adaptations to counteract such responses in order to establish a niche and promote infection. As such, when Mtb is internalized into macrophages, innate immune sensing of bacterial DNA in the host cell cytosol triggers both anti-bacterial and pro-bacterial responses: selective autophagy destroys a population of bacilli and restricts Mtb growth, while activation of the antiviral type I interferon response promotes bacterial infection and pathogenesis. An innate immune kinase called TBK1 is central to both of these processes; however, the mechanism by which this kinase comprises both selective autophagy and type I interferon signaling complexes is unknown. Our new work has uncovered an important role for the tripartite motif protein TRIM14 in regulating the kinase TBK1 and eliciting the type I IFN response during Mtb infection. We hypothesize that TRIM14 is a key modulator of DNA sensing during Mtb infection and that post-translational modification of TRIM14 influences the shuttling of TBK1 away from selective autophagy to promote type I IFN production. Using biochemical, proteomic and microscopy-based approaches we will (1) determine the mechanism by which TRIM14 influences DNA sensing outcomes during Mtb infection (2) elucidate the role of post-translational modifications in regulating TRIM14 and (3) determine the role of TRIM30a in negatively regulating type I IFN production and controlling Mtb pathogenesis. Because these two DNA sensing pathways lead to such strikingly different disease outcomes, there is an obvious opportunity to develop therapeutics that target molecules like TRIMs, in hopes of activating selective autophagy while inhibiting the type I interferon response during Mtb infection.
Convective-Environmental Interactions in the Tropics
Atmospheric Sciences; TAMU; https://hdl.handle.net/20.500.14641/651; DOE-Office Of Science
During the four years of this grant performance, the PI and her research group have made a number of significant contributions toward better understanding convective processes over the Amazon. First, she made available to the broader community a two-year data set of convective storm metrics based on SIPAM radar data from the central Amazon that has been utilized widely. Second, her students analyzed cold pool and heating characteristics of Amazonian convection and showed in heretofore unknown ways how both can impact new convective initiation (e.g., through multiple cold pool interactions and gravity waves formed via pulsed heating). Finally, her group more broadly showed how Amazonian and Indian Ocean convection interacts with the large-scale environment, especially low-level winds (e.g., the nocturnal Amazonian low-level jet) and deeper tropospheric moisture, to help it organize and how this interaction is represented in climate models.
Digital Humanities and the Infrastructures of Race in African-American Literature
English; TAMU; https://hdl.handle.net/20.500.14641/669; National Endowment for the Humanities
"Can a Computer Be Racist?" examines how technological infrastructure and algorithms interact with African- American authored literary texts to construct and deconstruct racial identities. By employing multiple lenses of data, digital tools, and analysis, the project reveals how seemingly naturalized technological infrastructures impact meaning through an interactive Scalar project and reposited data, visualizations and project documents for use and remix. Further, the digital project is designed to explore questions of preservation and open data, particularly important to Black literary studies where we continue to struggle to represent the fullness of cultural expression within current infrastructures.
In Utero Third-Hand Smoke Impact on Platelet Function and Thrombogenesis
Cop-Pharmaceutical Sciences; TAMHSC; https://hdl.handle.net/20.500.14641/689; DHHS-NIH-National Institute of Environmental Health Sciences
While the involvement of in utero exposure to first-hand smoke (FHS) and second-hand smoke (SHS) in the pathogenesis of thrombotic diseases is well documented, the contribution of the newly “discovered” third-hand form (THS) in such disease processes remains unknown. This derives, in part, from: (1) initial lack of knowledge of THS existence; (2) lack of appreciation for its “real” negative health consequences; (3) lack of a THS-exposure animal model that mimics real-world scenarios; and (4) lack of studies regarding such consequences on platelet biology. The present application proposes experiments that address fundamental, mechanistic, epigenetic and clinically-relevant translational aspects of the adverse-health effects of the newly “realized” form of smoking, THS, in utero and in the context of thrombotic disease and platelet biology, and gender. Studies are also proposed to investigate, in a similar fashion, the toxicants that underlie THS effects on platelets and associated diseases. These studies are of paramount significance given that the dangers of THS are underestimated/unappreciated, despite evidence that it is more toxic than SHS, especially in vulnerable populations such as children and minorities (e.g., Hispanic Americans). The Aims of our proposal are: Aim 1. Investigate the impact of in utero THS-exposure on platelet-dependent diseases. While in utero exposure to the well-known FHS and SHS was found to contribute to the genesis of myocardial infarctions, whether in utero exposure to THS is also associated with an increased risk of thrombotic disorders, is yet to be determined. To address this issue, we will determine the ramifications of in utero THS exposure on normal hemostasis, platelet counts, as well as on clotting factors and other thrombosis mediators, in a dose-, and time dependent fashion. Subsequent studies will examine whether in utero THS participates in the development of thrombotic disorders. Aim 2. Investigate the mechanism by which in utero THS-exposure modulates platelet function. Our recently published findings show, for the first time, that adult THS exposure modulates physiological hemostasis, and increases the risk of thrombogenesis, via enhancing platelet activation. However, whether in utero THS is associated with similar effects, and if so, the mechanism by which it modulates platelet function remain to be investigated. Thus, the overall goal of the experiments proposed in this section is to determine the significance, toxicants and mechanism of the impact of in utero THS-exposure on various platelet functional responses, platelet epigenetics, its effect on other blood cells (e.g., leukocytes) and thrombosis “markers”, as well as its major route of exposure. Collectively, these experiments will make significant contributions to our understanding of the consequences of in utero THS exposure on platelet activation and cardiovascular human health, its epigenetics, and the mechanism and toxicants by which THS exerts its effects
Origin of yellowfin tuna in the western Atlantic Ocean: importance of outside production to US fisheries
Marine Biology; TAMUG; https://hdl.handle.net/20.500.14641/522; DOC-NOAA-National Marine Fisheries Services
Several novel tools are currently being used to investigate the natal origin and stock structure of Atlantic tunas, including natural chemical markers in hard parts (Rooker et al. 2008, 2014, 2019). Natural markers in otoliths (ear stones) show significant potential for determining origin and quantifying population connectivity. This is due to the fact that otoliths precipitate material (primarily calcium carbonate) as a fish grows, and the chemical composition of each newly accreted layer is often associated with physicochemical conditions of the water mass they inhabit. As a result, material deposited in the otolith during the first year of life serves as a natural marker of the individual’s nursery or place of origin. Previous studies have demonstrated that trace elements and stable isotopes in otoliths can be used to determine the origin of both temperate and tropical tunas (Wells et al. 2012, Kitchens et al. 2018, Rooker et al. 2019). The goal of the SK-funded study was to determine the origin and migratory histories of yellowfin tuna from U.S. fisheries in the Atlantic: 1) Gulf of Mexico [GoM], 2) Mid Atlantic Bight [MAB], and 3) US territories in the Caribbean [CAR]. Our efforts centered on two questions: Q1) Are yellowfin tuna in U.S. fisheries derived from local production or from more distant production zones in the eastern Atlantic Ocean (EAO), and Q2) Are trans-Atlantic movements (E to W) common for yellowfin tuna caught in U.S. waters? Such questions are important to fishery managers because this species is currently managed as a single, panmictic stock, despite the fact that trans-Atlantic movement is well documented. Similar to previous studies, we used natural tracers in otoliths that are linked to ambient physicochemical conditions of the ocean to develop ‘birth certificates’ for individuals from different regions or nurseries in the Atlantic Ocean. Thus, the first step was to develop reliable baseline chemical signatures for young-of-the-year (YOY) tuna from all sources or production areas in the Atlantic Ocean. As demonstrated in Kitchens et al. (2018), classification success to regional nurseries is relatively high, supporting the use of these reference signatures to source yellowfin tuna to their place of origin.

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