Arizona State University-Tempe Campus

NIH Research Projects · FY 2025 · 2021-09

OVERALL — PROJECT SUMMARY/ABSTRACT Over the last 20 years, Arizona researchers established NIA's first statewide Alzheimer's Disease Center and the nation's most extensive statewide collaboration in Alzheimer's disease (AD) research. They made pioneering contributions to the unusually early detection, tracking and study of AD and the accelerated evaluation of AD prevention therapies. The Center includes researchers from seven organizations, six in the Phoenix metropolitan area and one in Tucson. It has supported 150 researchers from organizations across the state and helping them to generate more than $2 billion in new grants, contracts, philanthropic, state and organizational investments. The Arizona AD Research Center (ADRC) will capitalize on the Center's leadership, statewide collaborative model, major organizational commitments, and extensively shared scientific resources and its very existence to make the scientific fight against AD a top priority in the state. Its resources, strategic plan, and related programs and prevention trials are specifically intended to set the stage for promising blood tests to transform AD/ADRD research, treatment development, and care, include persons from diverse backgrounds, find an effective prevention therapy by 2025, and fulfill National Alzheimer's Project Act (NAPA) goals. We will use ADRC, organizational and philanthropic funds to provide an extraordinary resource of data and blood samples for neuropathological study and diagnostic validation of BBBs for ADRD using blood samples from several hundred brain donors in the last years of life who have comprehensive neuropathological assessments after they die. The overall goals of the Center will be accomplished through coordinated activities of its six Cores and the Research Education Component (REC). The Administrative Core will provide the scientific leadership to the ADRC as a whole. The multi-site Clinical Core will perform standard evaluations and collect UDS and additional data on all participants, including a large number of Hispanic/Latino and Native American participants. The Neuropathology Core will provide neuropathologic diagnoses and process, store and distribute postmortem brain tissue, including from those who provided blood samples in the last 1-2 years of their lives. The Biomarker Core will support and provide access to genetics, brain imaging (MRI, amyloid PET, tau PET), cerebrospinal fluid (CSF) and BBBs of AD. The Outreach, Recruitment and Engagement (ORE) Core will support the efforts of the Clinical and Neuropathology Core, providing a range of educational and outreach programs for healthy adults, patients and family caregivers in our Center's catchment area, including from Arizona's large Hispanic/Latino and Native American communities. The Data Management and Statistics Core will support all the data management, informatics and statistical needs of the Cores and Center. The REC will coordinate closely with each of the Cores and leverage external partnership with two Resource Centers for Minority Aging Research (RCMARs) to attract and support the development of new researchers and clinicians. Together these activities will help set the stage for BBBs to revolutionize ADRD research, treatment and care, inform the study of preclinical AD, and help provide the best possible change to find and support the approval of an AD prevention therapy in 2025.

NIH Research Projects · FY 2024 · 2021-09

PROJECT SUMMARY / ABSTRACT As of 2015 there were 940 million people with some degree of visual impairment in the world. Visual impairments generate considerable economic burden for the society. The World Health Organization estimates that 80% of visual impairments are either preventable or curable with treatment. Noninvasive imaging techniques have been used extensively by eye specialists for diagnosis and treatment of visual disorders and imaging is one of the priorities in the six core program areas of the National Eye Institute. As a noninvasive high spatial resolution technique for measuring brain activities, functional magnetic resonance imaging (fMRI) has provided a wealth of data on visual cortical organizations. Although numerous studies have been devoted to discovering and validating different retinotopic maps in the human visual system, limited progress has been made in developing software tools that fully consider the intrinsic geometrical features of the underlying cortical structures, enforce diffeomorphic mapping when constructing retinotopic maps and atlases, and integrate both individual and population statistics for more robust data analysis. In preliminary work, we have developed a complete and invertible description of retinotopic maps (U.S. Patent Application Nos. 16/230,284 and 63/004,721, supported by NSF collaborative research awards DMS-1413417 and DMS-1412722). This project will continue developing and applying novel quasiconformal geometry and hierarchical Bayesian modeling (HBM) algorithms to retinotopy data obtained from the Human Connectome Project (HCP), the largest high resolution retinotopy dataset to date. We hypothesize that, by combining Beltrami smoothing, quasiconformal mapping and HBM, the proposed approach will reduce manual annotation work and maximize the statistical power of retinotopic mapping techniques. The project aims to: (1) Develop computational methods to effectively smooth retinotopic maps across multiple visual areas based on Beltrami smoothing. With Beltrami descriptions, the proposed method will simultaneously smooth eccentricity and polar angle retinotopy data in V1, V2 and V3, while preserving the underlying topological continuity; (2) Develop computational methods to effectively register retinotopic maps of multiple visual areas across subjects with quasiconformal mapping. Unlike previous work that relied on either structural MRI (sMRI) or fMRI data only, the proposed method will simultaneously register both sMRI and fMRI data from multiple visual areas across subjects and ensure diffeomorphism; (3) Develop an HBM of the retinotopic maps to capture the hierarchy at both the individual and group levels. The proposed HBM will help overcome measurement noise, reveal both population properties and individual differences, and offer unprecedented accuracy on retinotopic map analysis; (4) Develop and disseminate software tools and atlases of human retinotopic maps. The developed open-source software tools can be extended to analyze data from patients with not only visual impairment but many other neurological and psychiatric disorders.

NIH Research Projects · FY 2025 · 2021-09

Project Summary / Abstract Within 10 years, most persons living with Alzheimer’s disease and related dementias (AD/ADRD; PLWD) will die, creating 13+ million new bereaved AD/ADRD caregivers. 25% of bereaved AD/ADRD caregivers have clinically ‘complicated grief’, which impairs nearly all aspects of their lives. Among bereaved AD/ADRD caregivers who are not clinically impaired, millions still suffer from higher depressive symptoms and loneliness as well as reduced well-being, physical function, self-care, and personal growth. Researchers may be tempted to treat bereaved AD/ADRD caregivers as a homogenous group, but bereavement differs between key kin subgroups of spouses and adult children. Unfortunately, how bereavement differs for extended family is difficult to discern. The long-term goal of this research is to develop interventions to meet the needs of bereaved AD/ADRD caregivers. The objective of this proposal is to test a comprehensive model of bereaved AD/ADRD caregiver needs and identify need satisfying experiences within key kin subgroups that are amenable to future intervention. The central hypothesis is that bereaved AD/ADRD caregivers have a common set of needs that influence clinical and subclinical outcomes, but that subgroups meet those needs in different ways, based on evidence from self-determination theory and 10 months observing bereaved AD/ADRD caregivers. Autonomy, competence, and relatedness are hypothesized to form a common set of needs essential to clinical and subclinical outcomes for bereaved AD/ADRD caregivers (Aim 2; tested in a survey of 400 bereaved AD/ADRD caregivers). Key subgroups are hypothesized to meet these needs differently (Aim 3; tested in semi-structured interviews with 36-45 bereaved AD/ADRD caregivers). Through a tailored training plan and world-renowned- expert mentorship in one of the nation’s foremost schools of public health, the candidate will gain expertise in bereavement, stakeholder engagement, qualitative methods, and mixed methods to facilitate completion of the long-term goal of this research. Complementing the research team, a Community Advisory Board (CAB) of bereaved AD/ADRD caregivers and stakeholders will advise the present project and the PI’s broader research program aimed at helping bereaved AD/ADRD caregivers. CAB members represent different races, ethnicities, sexes, genders, ages, clinical specialties, types of dementia, time since bereavement, community organizations, and geographic locations. After this award, the CAB will help guide development of interventions based on the findings of Aims 2 and 3. The proposed research is innovative in its focus on key subgroups, application of self-determination theory, and diverse CAB focused on bereaved AD/ADRD caregivers. The work will address the NIA’s goal to increase understanding of bereaved AD/ADRD caregivers’ needs, informing future interventions that reduce the clinical and subclinical consequences of bereavement. Together the integrated research strategy and training plan will also facilitate a successful transition to independence for a researcher committed to helping PLWD and their caregivers thrive throughout the dementia caregiving journey.

NIH Research Projects · FY 2025 · 2021-08

1 Current approaches to designing and constructing synthetic gene circuits have reached a 2 dilemma due to the substantial heterogeneity driven by circuit-host interactions, especially for 3 large-scale gene circuits. The conventional trial-and-error iteration approach on synthetic gene 4 circuit development is regarded as inefficient since the assembled gene circuits often are 5 susceptible to experimental conditions. One fundamental reason is that the heterogeneity driven 6 by circuit-host interactions become significant with the increase of the number of components in 7 gene circuits but are often neglected. Moreover, the lack of quantitative frameworks for quantifying, 8 characterizing, and controlling heterogeneity in the host-aware synthetic gene circuits impedes 9 the progress in the field. My laboratory has been focusing on dissecting the mechanisms of how 10 the circuit-host mutual interactions affect the gene circuit functions and developing control 11 strategies targeting circuit-host interactions to optimize engineered synthetic gene circuits. 12 Recently we found a topology-dependent interference of synthetic gene circuit function by growth 13 feedback, which was published in Nature Chemical Biology. We also found winner-takes-all 14 resource competition that redirected cascading cell fate transitions, which is in revision to Nature 15 Communication. In the proposed projects, we will establish experimental and computational 16 frameworks to quantify, characterize, and control the gene expression heterogeneity in the host- 17 aware synthetic gene circuits. The heterogeneity can result from stochastic cellular resource 18 allocation, stochastic biochemical reactions in gene circuits, and stochastic cell divisions. These 19 heterogeneities are intertwined due to the complex interactions between the gene circuits and the 20 host organisms, creating another layer of challenge and complexity to engineering robust gene 21 circuits. We will integrate a microfluidics system for time-lapse live-cell analysis, a Turbidostat 22 platform with Python-based easy-to-use web interface for accurate growth rate control and 23 automatic yet remotely-controllable in-situ fluorescence measurement, and hybrid agent-based 24 modeling algorithms for stochastic simulation of all the single cells in the bacterial community to 25 characterize the heterogeneity from various noise sources in the host-aware synthetic gene 26 circuits. I have built up my research group with all the necessary expertise and capabilities to 27 complete the proposed projects. This work will provide a systematic in-depth mechanical 28 understanding of the heterogeneity driven by circuit-host interactions, and will greatly help us to 29 rationally design and control the synthetic gene circuits for sophisticated clinical applications in a 30 real-world environment, such as bacterial infection and tumor microenvironments.

NIH Research Projects · FY 2025 · 2021-08

PROJECT SUMMARY The human hand plays a critical role in performing many daily activities including self-feeding, tool use, and recreation. Therefore, loss of the hand due to traumatic injury or disease can significantly limit or interfere with the ability of persons with limb loss to perform daily activities and work, thus greatly affecting overall quality of life. Despite advances in prosthetic hand design and research, several barriers to widespread acceptance of prosthetic hands by persons with upper limb loss remain, including limited ability to perform daily activities and poor durability of the prosthetic hand. Therefore, today’s commercially-available myoelectric hand prostheses fail to address the needs of persons with limb loss, i.e., regaining some degree of autonomy, functionality, and re-entry into the work force. To address these gaps, in the past few years we have investigated the extent to which an artificial anthropomorphic hand originally designed for robotic grasping and manipulation – the SoftHand – could be used for prosthetic applications through a non-invasive myoelectric controller – the SoftHand Pro (SHP). The novel design of the SHP is the only prosthetic hand in the world that combines the concept of human hand synergies and soft robotics technologies. The results of preliminary functional assessments and biomechanical analyses revealed that individuals with upper limb loss could perform a variety of grasping and manipulation tasks with the SHP at levels similar or superior to those of their preferred prosthetic device. Additionally, subject surveys reported positive feedback about the ease and comfort associated with using the SHP. This feedback was also instrumental in making software and hardware improvements to make the hand lighter and able to grasp and manipulate small objects. We propose to determine the extent to which the SHP can address three critical needs of transradial amputees that are not met by commercially-available hand prostheses: function, versatility, and robustness. We will attain this objective by comparing its function, versatility, and robustness with a commercially-available multi-digit prosthetic hand, the i-limb (Ossur). We will pursue three aims: (1) to determine the extent to which performance of grasping and manipulation tasks using the SHP is superior to the i-limb, (2) to determine the extent to which daily use of the SHP and i-limb over an extended period of time improves grasping and manipulation performance, and (3) to obtain SHP usage patterns and subjects’ satisfaction ratings from using the SHP and i-limb. We will test the hypotheses that (1) the SHP will outperform the i-limb, and (2) daily use of both prosthetic hands over an 8-week period each will lead to significantly greater improvement in grasping and manipulation performance with the SHP than the i-limb. We will obtain usage and survey data collected through the SHP and i-limb firmware during daily use to complement data obtained in Aims 1 and 2 to explore daily use. This proposed work is significant because it will shed insight on whether an innovative soft synergy- based prosthetic design allows for function, versatility and robustness not available in commercial prostheses.

NIH Research Projects · FY 2025 · 2021-07

PROJECT SUMMARY/ABSTRACT: The goal of this project is to validate a clinically feasible, one-shot contrast-enhanced, multiparametric MRI approach for mapping the morphologic, hemodynamic and metabolic features of brain tumors using a single contrast agent. Contrast-enhanced (CE) MRI is the clinical imaging standard for guiding nearly all aspects of brain tumor management, including surgical biopsy/resection, radiation treatment planning, and post-treatment surveillance for response assessment. Dynamic susceptibility contrast (DSC) MRI is a complementary technique that leverages the dynamic passage of the contrast agents utilized for CE-MRI in order to provide maps of tumor perfusion. An unmet clinical need in the assessment of tumor pathophysiology is the ability to routinely detect hypoxia and its evolution. Brain tumors exhibit considerable hypoxia which leads to therapy resistance, triggers more aggressive and invasive phenotypes, is considered a potential therapeutic target, and is prognostic of overall survival. The most widely used method for interrogating hypoxia in the clinic relies on PET radiotracers, which, in the context of brain tumors, necessitates multiple scans and injections in addition to routine CE-MRI and DSC-MRI. This limitation increases costs, dose and patient discomfort, while reducing efficiency and the likelihood of widespread use, particularly in non-academic community hospitals where patients are unlikely to undergo multi-modality imaging. Consequently, an MRI-based hypoxia imaging approach could significantly enhance the metabolic characterization and therapeutic management of brain tumor patients. We have developed a GdDOTA monoamide conjugate of 2-nitroimidazole (a well-established hypoxia binding moiety), termed GdDO3NI, that enables detection of regional hypoxia. We hypothesize that CE-MRI, DSC-MRI and hypoxia data can be acquired in brain tumors in a single imaging session following a single-injection of GdDO3NI and can help predict outcome of hypoxia targeted therapy. We anticipate that optimal acquisition and analysis protocols for dynamic GdDO3NI MRI will provide hypoxia maps that regionally colocalize with pimonidazole IHC and FMISO PET and will provide congruous estimates of hypoxic tumor fraction between the various techniques. Towards this end we propose to 1) validate GdDO3NI based CE-MRI and DSC-MRI in orthotopic, human-derived glioma preclinical models, 2) establish optimal GdDO3NI based hypoxia mapping protocols and validate using immunohistochemistry (IHC) and clinically comparable PET markers and 3) demonstrate the potential of GdDO3NI to predict response to a hypoxia activated prodrug, evofosfamide. Our innovative, one-shot, multi-parametric strategy represents a transformational shift in brain tumor imaging that could enable personalized therapy based on lesion morphology, regional perfusion and metabolic heterogeneity. The proposed one-shot strategy could also be translated to cancers outside the brain, increasing the range of patients impacted by this research and feasibility of translating GdDO3NI to the clinic.

NIH Research Projects · FY 2025 · 2021-07

Project Summary/Abstract Migration affects hundreds of millions of families worldwide. Migrants often leave family members in their origin communities, which can challenge the wellbeing among the children. It is not well understood how migration influences left-behind family members’ socialization of children or children’s social competence and adjustment problems in sending communities. Migration is expected to alter how family members engage with, make expectations for, and provide for children, and alter children’s experiences and resources. These challenges and opportunities are expected to affect children’s social competence and adjustment problems. For instance, family members’ migration is hypothesized to predict less monitoring by left-behind caregivers and, in turn, higher drug and alcohol use for children. Benefits of migration are also anticipated, for instance, children’s increased responsibilities may positively predict their behavioral control. The project will follow children who previously participated in 2 time points of data collection and provide new data on the children, their primary caregivers, and their fathers at 2 additional time points. In combination with the prior waves of data from the same children and their caregivers, the project will yield high-quality information about children (5 to 17 years old at Time 1) across 6 years in a large sample that is representative of the study area. Key developmental transitions into school, adolescence, and adulthood are captured. The research will illustrate the complex ways in which family members’ migration predicts children’s socio-emotional outcomes. The specific aims of the project are: 1) to investigate reciprocal effects of caregivers’ socialization and children’s socio-emotional development, 2) to determine how family members’ migration is associated with socio-emotional outcomes, and how child, family, and migration characteristics moderate associations, and 3) to explore fathers’ roles in children’s socio-emotional outcomes, and compare fathers’ familial relationships and socialization for those who do versus do not participate in migration. This is an innovative extension of prior research; the project will provide a longer and more detailed view of children’s development and the dynamics of migration in and out of their households. Furthermore, including migrating and non-migrating fathers’ interviews supports an innovative investigation of their unique contributions to children’s socio-emotional development that goes beyond their economic contributions. Migrating fathers are expected to have poorer marital quality than non- migrating fathers, which may indirectly affect children’s socio-emotional outcomes via parent-child relationships. The new knowledge developed about migration’s costs and benefits will be useful for families as they adapt to changes migration brings to relationships and caregiving, help policy makers anticipate the challenges migration poses to children’s socio-emotional wellbeing, and inform children’s rights protections.

NIH Research Projects · FY 2024 · 2021-07

Project Summary: This proposal describes a five-year research and career development program to prepare Dr. Razieh Khalifehzadeh for a career as an independent investigator. This program will build upon Dr. Khalifehzadeh’s multidisciplinary background as a bioengineer scientist, trained in bioelectronics, biomaterials and basic cancer research, by providing expertise in designing flexible and highly sensitive pressure sensors for continuous wireless monitoring of intracranial pressure (ICP) associated with brain tumors. The PI will be mentored at Stanford Schools of Engineering and Medicine by Drs. Zhenan Bao (Main mentor, flexible and wearable bioelectronics), Sanjiv S. Gambhir (co-mentor, cancer diagnosis, cancer bioengineering and cancer nanotechnology), Heike Daldrup-Link (co-mentor, brain cancer imaging and therapy, and a leader in promoting diversity), Ada Poon (collaborator, wireless bioelectronics), Melanie Hayden (collaborator, neurosurgery and neurology) and Eric Appel (collaborator, biomaterials and biocompatibility). Brain tumors are usually associated with increased ICP. Delayed diagnosis and treatment of the elevated ICP often results in irreversible neurological damage and even death. The overall goal of the proposed research is to design highly sensitive and brain compatible pressure sensors that can wirelessly detect ICP variations, as a generally neglected neurological marker in brain tumor patients. Recently, I developed ultrasmall (3×3×0.1 mm3), flexible, and implantable pressure sensors that were effective for wireless monitoring of the ICP variations in mice models of growing U87 brain tumor over their 30 day survival period. The key component of these pressure sensors is an intermediate elastomer layer with a specific pressure-responsive micropattern that defines the consistent sensitivity of these devices for long-term accurate measurements in the brain. In Aim 1 of this project, I will study new designs for this elastomer layer, in order to further improve the sensitivity and long- term electro-mechanical stability of my pressure sensors. Additionally, I will use experiments and simulations to find alternative designs for more efficient wireless signal transfer (i.e., higher signal-to-noise ratios) from these sensors. I will also develop a handheld wireless signal recording setup to enable recording and rapid analysis of the wireless pressure data using a smartphone, for easier in vivo measurements and future point-of-care applications. Aim 2 is focused on extending the post-implantation lifetime and brain compatibility of the sensors by coating them with parylene (thickness ~ 1-4 µm). Parylene has been broadly used as a protective coating for neuro-interface and cardiac assist devices to enhance their post-implantation lifetime. Finally, I will use these sensors for continuous wireless monitoring of ICP variations in different mice models of brain tumors, with various survival periods, depending on invasiveness of the tumor (Aim 3). MRI, simulations and histology will be used to verify ICP measurements. These sensors are clinically needed for monitoring ICP in different brain diseases, including tumors, and we envision that their versatile design will facilitate their clinical applications.

NIH Research Projects · FY 2025 · 2021-05

Project Summary/Abstract Overview of Research: The Van Horn lab primarily focuses on elucidating and understanding the molecular mechanisms that underlie membrane protein function in health and disease. To achieve these goals, the laboratory employs a modern state-of-the-art and interdisciplinary approach using biophysical, structural, computational, and functional techniques. We are experts in membrane protein biophysics and make use of advanced NMR studies combined with functional whole-cell patch-clamp electrophysiology. These orthogonal data are linked with Rosetta-based computational techniques to understand protein function. Our primary target is the TRPM8 ion channel which was initially identified as an oncogene that is prognostic for some types of cancer progression. More recently, it has become a focus for therapeutic intervention in pain and obesity. Complicating the potential application of TRPM8 therapies is that it is a molecular integrator that is activated by a number of diverse stimuli. For example, TRPM8 is the primary human cold sensor but is also activated by the chemical menthol from mint, both of which activate TRPM8 signaling networks. The ability to respond to several different stimuli in a polymodal manner makes TRPM8 studies crucial to delineate the independence and interdependence of molecular mechanisms that result in biological function and complicate its therapeutic targeting. In addition to direct stimulation by cold and menthol, TRPM8 is regulated by diverse proteins, including the membrane protein, PIRT, which in turn modulates TRPM8 activation by cold, menthol, and other stimuli. Beyond our research on direct activation of TRPM8 by cold and menthol, we focus on determining the mechanisms whereby PIRT modulates TRPM8 function. This has led to a number of contributions from our lab including, biophysical and structural characterization of TRPM8 and PIRT, TRPM8–PIRT complex stoichiometry, identification of species-dependent regulation, and central insight into molecular regulatory mechanisms. These efforts have led to strong scientific output, including publications, seminars, and patents. Five-year Goals: Broadly defined, we will identify how TRPM8 is directly activated by cold temperatures and other stimuli, map the allosteric networks that allow for polymodal function, and determine structures of TRPM8 and related membrane protein complexes of functional consequence. Research Vision: In the past 8 years, there has been an explosion of TRP channel structural biology with now ~100 discrete TRP channel structures. This represents tremendous development and output. Our research seeks to extend and complement the structural momentum to delineate fundamental mechanistic properties such as allostery, dynamics, and protein complex regulation that determines function. These TRPM8 outcomes are anticipated to have direct impacts on human health and disease but also to serve as a template that defines and identifies fundamental rules and properties of membrane protein function.

NIH Research Projects · FY 2025 · 2021-05

Project Summary/Abstract We have developed a technique for randomizing 23S ribosomal RNA structure, and for selecting modified ribosomes which incorporate into proteins specific types of modified amino acids not ordinarily incorporated by wild-type ribosomes. Species incorporated both in vitro and in vivo have included nucleobase amino acids, dipeptides/dipeptidomimetics, beta-amino acids, phosphorylated amino acids and glycosylated amino acids. The selected ribosomes enable study of two key biochemical regulatory processes, i.e. protein glycosylation and phosphorylation. We will also modify regulatory proteins that interact with nucleic acids, enabling predictable modulation or altered specificity of interactions. We will exemplify new strategies using proteins containing unusual non-proteinogenic amino acids, whose incorporation requires our selected ribosomes. The creation of proteins phosphorylated stoichiometrically at single or multiple positions affords new opportunities. These include the ability to verify natural phosphorylations, and to study their effects. It permits the introduction of (metabolically stable) phosphate groups in vivo, and has enabled new strategies for identifying residues whose phosphorylation modifies function. We showed that phosphorylation of IB- Tyr42 not only relaxes NF-B inhibition, but facilitates the rate of binding to a gene whose expression NF-B regulates. We plan to study two other known phosphorylation sites in IB-, and three in NF-BWhile some sites of serine phosphorylation in NF-B are known, this is not true for Tyr and Thr. Using a new strategy, we have identified four sites of Tyr phosphorylation, and plan to study new Thr and Ser phosphorylation sites. Most mammalian proteins are glycosylated, but understanding/altering carbohydrate functions is challenging. Using a selected ribosome in a cell free system, we prepared murine interferon- (IFN-) containing GlcNAc- Asn at position 29, which can confer antiviral activity. This intermediate acceptor substrate should enable carbohydrate cluster transfer, producing IFN- fully glycosylated at position 29, and expected to have antiviral activity. We have recently introduced the same glycosylated amino acid, and its peracetylated analogue, into a model protein in very good yield in cellulo. This strategy can potentially produce the same intermediate as that prepared in vitro, but in much larger quantities. We wish to prepare fully glycosylated proteins with natural carbohydrate clusters, to simplify these clusters, and to focus on the inclusion of residues such as sialic acid. Cell regulation often involves protein–DNA interactions; low nanomolar affinities and impressive selectivity are typical. Many X-ray crystal structures could guide design changes, but attempts to alter these regulatory processes by changing affinity or specificity have failed. Using Rob proteins having nucleobase amino acids, we modified binding to their micF DNA partners, realizing stronger binding, and enhanced phenotypic cellular responses. We propose to study the Rob–micF DNA interactions further to refine our design techniques. The principles developed will be used to address protein–DNA recognition in a Zn finger system.

NIH Research Projects · FY 2025 · 2021-02

Jensen, Abstract At the founding of population genetics in the early 20th century, S. Wright and R.A. Fisher developed much of the mathematical framework underlying the study of population-level processes dictating variation observed within- and between-species. However, as evidenced by decades of published interactions, they held strongly differing views regarding the relative importance of adaptive vs. non-adaptive processes in driving evolution. As pointed out by J. Crow (2008), these issues were not really resolved, but "rather they were abandoned in favor of more tractable studies." With the proposal of the Neutral Theory by M. Kimura and T. Ohta, the relative contribution of stochastic effects, as earlier advocated by S. Wright, received renewed attention. In the following decades, further theoretical development as well as the availability of large-scale sequencing data have indeed overwhelmingly justified the important role of genetic drift. However, subsequent research related to linked, rather than direct, selection effects have re-ignited previous debates. The primary difficulty in addressing this question has historically stemmed from our lack of an appropriate evolutionary baseline model - that is, a model jointly incorporating constantly and commonly acting evolutionary processes. This would necessarily include genetic drift as modulated by a realistic demographic history, as well as a realistic distribution of fitness effects summarizing the pervasive effects of both direct and linked purifying selection. Without this baseline model incorporating these evolutionary processes that are certain to be occurring, it is simply not feasible to accurately quantify the episodic frequency with which rarer processes (e.g., positive and balancing selection) may be further acting to shape patterns of polymorphism and divergence. During our current funding period, we have addressed this decades old limitation by developing population genetic theory and methodology to jointly estimate the parameters underlying such a baseline model, and we have applied these developments to a number of critical species (including humans, genetic model systems such as Drosophila melanogaster, and critical pathogens including influenza A virus and SARS-CoV- 2). These developments have been made in parallel for organisms well fit by Kingman coalescent assumptions (e.g., mammals) as well as those with highly skewed progeny distributions which necessitate a more generalized multiple-merger coalescent framework (e.g., viruses). In this renewal, I propose to build upon this baseline modeling to additionally infer, identify, and estimate the genomic contributions of the episodic processes of positive and balancing selection, and to extend our evolutionary baseline inference across the primate clade.

NIH Research Projects · FY 2025 · 2021-01

Abstract Traumatic brain injury (TBI) afflicts over 1.7 million persons per year in the U.S. alone, resulting in substantial economic burden annually. To date, despite promising pre-clinical data, no new pharmacological strategies have demonstrated improved patient outcomes in a phase III clinical trial. One significant and often- overlooked pitfall of pharmacological strategies is the use of systemic administration of free drug, where toxic and/or negative side effects may limit the therapeutic threshold at tissue targets. Nanoparticles (NPs) have emerged as an ideal approach to address such drug delivery obstacles. Our long-term goal is to engineer NP delivery systems to improve outcomes in TBI. Here, we will focus on developing a mechanistic understanding of sex-dependent differences in pathophysiology that lead to altered NP delivery to the injured brain of male versus female mice. Our group recently demonstrated that a TBI provides a unique window to deliver NPs to the parenchyma within both of these BBB disruption events. We discovered a sex-dependent response in BBB disruption and subsequent NP delivery profiles, whereby the BBB of females remained open for longer and to a greater extent than males. There is limited understanding of how sex hormones influence TBI induced BBB disruption over the longer term and the potential impact it has on drug delivery. To address this unmet need, we will directly examine the influence of sex hormones on TBI pathophysiology and drug delivery, and we will develop new strategies for targeting sex-dependent injury microenvironments. Our studies will address both mechanistic and therapeutic goals, focusing on NPs composed of poly(lactic acid)-poly(ethylene glycol) (PLA- PEG) and loaded with the histone deacetylase inhibitor quisinostat, which we have already shown are neuroprotective following TBI in mice. We will leverage our existing experience with bacteriophage biopanning to identify sex-targeting ligands to enhance drug delivery to unique, hormone-dependent post injury microenvironments. We hypothesize that differences in NP delivery to male and female mice can be attributed to sex hormone-dependent contributions to TBI pathophysiology, and we predict that improving our understanding of these sex differences will enable us to design more effective NP delivery systems. We will probe this central hypothesis through the following specific aims: (1) Investigate the contribution of hormone mediated sex-dependent injury sequelae on BBB disruption and inflammation, (2) Establish the relationship between hormone mediated sex-dependent injury, drug delivery, and efficacy, and (3) Demonstrate feasibility of sex-specific targeting for NP and drug delivery to TBI. Impact from these studies includes deepened mechanistic understanding of sex-dependent responses to TBI with response to nanoparticle drug delivery, as well as the first exploration of sex-targeted drug delivery to the brain. This will contribute to a thorough understanding of the pathophysiology of TBI and more broadly the potential to exploit inherent biological complexities for developing NP-based drug delivery strategies in context of brain injury.

NIH Research Projects · FY 2025 · 2020-09

PROJECT SUMMARY/ABSTRACT Surface colonization in the form of biofilms or swarms by otherwise free-swimming bacteria is the first step in many bacterial infections, but how bacteria sense surfaces remains unknown. The bacterial flagellar motor has emerged as a key player in surface sensing. Seen traditionally as involved only in motility by rotating helical filaments, new evidence suggests that the motor acts as a mechanosensor to sense bacterial surface interactions. However, the components of the motor-mediated mechanosensing pathway largely remain unidentified. To develop effective strategies for preventing and treating harmful biofilms, there is a critical need to understand how the motor senses forces and transmits information to downstream processes. The objective of this proposal is to characterize the function of motor-mediated mechanosensing and its associated circuitry. The proposed work will utilize novel biophysical methods to precisely control the mechanical load acting on the motor and to measure the motor’s response. Previous results and preliminary data show that the motor adapts to load by changing its torque output via the dynamic self-assembly of torque-generating stator units, providing a possible mechanism for mechanoreception. On the signal transduction side, it is unclear how the mechanosensing information is transmitted from the motor to the biofilm formation pathways, which are regulated by the bacterial second messenger cyclic diguanylate (c-di-GMP). The central hypothesis is that mechanical stimulation of the motor activates local and global responses that trigger c-di-GMP signaling. The central hypothesis will be tested by experimentally characterizing motor mechanoreception and using high-throughput genetics to delineate the mechano-transduction pathways. These goals will utilize a combination of biophysical, imaging, molecular, and genomic tools. The expected outcome of this work is an improved understanding of how the flagellar motor of bacteria is involved in surface sensing. The long-term goal is to study how bacteria generate complex behaviors using simple molecular machinery. The training phase of this career development award outlines a comprehensive plan for the acquisition of technical and professional skills that will enable the PI’s transition into an independent research position. The successful completion of this project will provide a platform for future research aimed at revealing the molecular interactions and the underlying physical biology that enable complex bacterial behavior such as biofilm formation.

NIH Research Projects · FY 2024 · 2020-08

PROJECT SUMMARY DNASU is a 11 year old non-profit, academic-based repository that provides academia, industry and the government with a wide variety of plasmids including specialized vectors, regulatory genetic sequences, and genes from 1,269 organisms, with many complete genome collections, including the first complete human set. Users access the repository through our website, https://dnasu.org/, where they can: view pertinent clone, gene and vector information; order clones; and utilize link-outs to reach external resources such as protocols and publications. DNASU acquires plasmids both through in-house production by our high throughput cloning pipeline and through deposition by outside research groups. In addition, we partnered with the Protein Structure Initiative (PSI), for whom we performed full-length sequence verification and annotation on plasmids from multiple PSI centers before distributing them. Distribution is initiated when a user visits DNASU to request selected construct(s). Technicians subculture and ship the glycerol stocks for a nominal re-charge fee. DNASU maintains and archives over 260,000 unique plasmids. The DNASU website sees an average of 3,000 unique visitors per month, receives 5,000 orders and distributes over 35,000 plasmids per year to scientists worldwide. DNASU received funding from NIGMS through the PSI initiative that enabled the addition of >93,000 plasmids to its collection and the development of software tools for locating and using clones, thus creating a unique worldwide resource. We also received funds from NIGMS Legacy program to improve the infrastructure, member collection, visibility and sustainability of the repository. We have made significant inroads to create a self-sustaining effort whereby we can continue to distribute clones from our existing collection. However, the number of clones we distribute, although large, is small relative to the massive size of the collection we must maintain, so our sales do not support continued database/computer programming, upkeep and updating of our collection, or acquisition of new collections. We recognize that the scientific community needs a comprehensive archival site like ours in order to continue expanding scientific knowledge on the many proteins that have not yet been studied. We are seeking funding to support our operations and customer support to: 1) Maintain and Improve the Physical Plasmid Repository by refining wet lab methods, updating targeted collections to current expression vectors, refreshing clones to ensure viability, and assisting with acquisition of orphaned collections; 2) Enhance Bioinformatics Capabilities of DNASU to stay current with modern hardware, software and operating systems, and to enhance the DNASU database and bioinformatics pipelines for sequence annotation of the physical clones and the related biological information; and 3) Improve Customer Experience and Outreach by re-constructing the DNASU interface for order placement, improving technical support, and engaging scientists through social media support.

NIH Research Projects · FY 2024 · 2020-08

Project Summary Sedentary behavior (i.e., sitting) has emerged as an important risk factor for type 2 diabetes, cardiovascular disease, some cancers, and mortality. Working adults with desk-bound occupations accumulate large volumes of daily sedentary time. Sit-stand workstations are now the fastest growing employee benefit, yet evidence-based interventions are not being implemented to support their use. Our team has completed the largest and most definitive efficacy trial on the impact of an intervention to support use of sit-stand workstations and reduce sedentary behavior in the workplace. Stand & Move at Work (SMW) is a multicomponent, social-ecological behavioral intervention tested in 24 industry, government, and academic worksites (N=630 workers). Intervention effects included: (a) reductions in sedentary time at 12 months (~60 min/8 h workday) that were retained at 24- month follow-up (~30 min/8 h workday); (b) reduced body weight and improved chronic disease risk factors among those with high baseline risk; and (c) reduced musculoskeletal pain. We are now proposing a new trial that tests the role of expert-based facilitation to enhance effectiveness and implementation of the SMW intervention. We use the Integrated - Promoting Action on Research Implementation in Health Services (iPARIHS) framework to inform our new trial through: (a) organizing our implementation outcomes from our efficacy trial; (b) conducting industry-based discovery interviews; and (c) piloting our enhanced implementation strategy in new worksites. We propose a 2-arm group-randomized hybrid effectiveness-implementation (type 2) trial to test the effectiveness of SMW for reducing sedentary time in the workplace, and to test an implementation strategy (i.e., expert facilitation) for improving implementation fidelity. Worksites (N=24) will be observed over 3 months of sit-stand workstation use only, and will then be randomized to 12 months of either: (a) SMW (web- delivered); or (b) SMW+ (web-delivered + expert facilitation). Our dual primary outcomes will be reductions in objectively-measured sedentary time (effectiveness) and intervention fidelity (implementation) over 12 months. Because facilitation increases intervention cost, we will also assess incremental cost benefit of our interventions (secondary aim). Finally, we will explore fidelity as a driver of effectiveness, examine within-worksite differences in sedentary time pre- and post- implementation, and measure organizational sustainability of effectiveness and implementation at 24 months. The potential health benefits of sit-stand workstations and associated worksite health promotion programs will not be realized in the workforce at large until we test the most effective and efficient way to implement evidence-based interventions. This project is among the first initiatives to address this growing trend in worksite health, and will answer important questions related to effectiveness, implementation, and cost benefit. Optimal strategies for delivering the SMW intervention will be identified and new knowledge will be generated on how facilitation can enhance implementation fidelity of workplace health initiatives, both of which will increase the public health impact of evidence-based interventions.

NIH Research Projects · FY 2024 · 2020-08

Between 8-12% of people exposed to opioids develop opioid use disorder (OUD). Developing more effective preventions and treatments for OUD requires a better understanding of genomic and epigenetic mechanisms that underlie individual vulnerability to distinct stages along the OUD trajectory (e.g., initial use, compulsive use, relapse). The overall goal of this proposal is to use an outbred rat model (Sprague-Dawley) to identify novel downstream genes and upstream regulators of gene transcription involved in 3 behavioral phenotypes associated with distinct stages along the OUD trajectory. By comparing rats that show high versus low levels of addiction-like behavior at each stage, we will be able to identify changes in gene expression and their regulation associated specifically with susceptibility to opioid addiction from among the numerous effects of opioids that are unrelated to addiction. Anhedonia produced during withdrawal from acute morphine (i.e., withdrawal-induced anhedonia, WIA) will be used as an addiction phenotype of the earliest phase of OUD, i.e. prior to voluntary drug consumption. We have previously found that WIA is more strongly associated with a range of measures of subsequent i.v. morphine self-administration (SA) than these SA measures are with one another. Economic demand for morphine and reinstatement after extinction will serve as measures of drug reinforcement efficacy and propensity for relapse, respectively, after extensive morphine SA. To identify vulnerability-related genomic targets, we will use Next-Generation Sequencing (NGS) techniques and advanced bioinformatic tools to compare transcriptomic and epigenomic differences in rats exhibiting high versus low levels of WIA (Aim 1), demand (Aim 2) or reinstatement (Aim 3). Our epigenomic assays will map loci of chromosomal accessibility (using ATAC-seq) and of the stable chromatin mark H3K4me3 (using ChIP- seq). We will overlay each of these data sets onto RNA-seq data to identify genes showing differential activation in High- versus Low-Susceptibility rats, as well as upstream regulators of these transcriptional effects. These assays will focus on the medial prefrontal cortex (mPFC), a node within the mesocorticolimbic system that plays a pivotal role in addiction. We will also overlay epigenomic maps derived from our studies onto genotyping data derived from larger studies of Heterogeneous Stock (HS) rats manifesting High- versus Low addiction-related behavioral phenotypes (e.g., drug intake, impulsivity), in other NIDA Animal Genetics Consortium U01/P50 projects. We hypothesize that these comparisons will yield a set of downstream genes and upstream regulators associated with individual differences in early vulnerability to addiction-like behavior and its severity once established. We further hypothesize that our transcriptomic and epigenomic data will provide a viable roadmap for identifying genetic variants from larger genomic datasets associated with individual differences in OUD susceptibility. As such, our studies promise to yield novel genomic and molecular targets for developing more effective, individualized approaches for the prevention and treatment of OUD.

NIH Research Projects · FY 2025 · 2020-06

The 4th chromosome is the final frontier for genetic analysis in Drosophila. Small and devoid of recombination the 4th has long been ignored. Nevertheless, it contains 79 protein coding genes. 92% of the protein coding genes have human counterparts and 68% of these human genes have a disease association. We propose to renew our project to build a Comprehensive Resource for the Drosophila 4th Chromosome. The project is highly visible in the community. It is known as the Fourth Chromosome Resource Project (FCRP) at the Bloomington and Kyoto stock centers as well as in the FlyBase and FlyPush databases. After three years of funding, the FCRP has 446 stocks publicly available and is on track to exceed the proposed goal by 15%. To date, four papers are published and 311 stocks were ordered from Bloomington in 2022. Evidence of impact is that FCRP stocks constitute 0.3% of the Bloomington stock center, but FCRP shipments supported 13% of the NIH grants funding stock orders from Bloomington in 2022. Further evidence of impact is that FCRP stocks for the five most popular 4th genes were ordered at a rate matching the top 3% of all Bloomington stocks. Three of the stock sets have gone well: 1) the UAS.fly cDNA stocks, 2) the UAS.human homolog cDNA stocks and 3) the conversion of MiMIC transgenes to gene trap and protein trap stocks. However, during the project we noted several unmet needs. We propose to address these by continuing to build the two sets that remain incomplete, adding a UAS.RNAi set, plus conducting validation and phenotyping studies on all FCRP stocks. The Specific Aim remains to generate a comprehensive resource enabling modern genetic analysis for protein coding genes on the Drosophila 4th chromosome. One set that will continue is to mutagenize every 4th gene individually on our FRT101F chromosome for loss of function studies and marked single cell clones. The second continuing set is UAS.human cDNA stocks for the top two human relatives of each conserved 4th gene. The need to add a set of UAS.RNAi stocks for genes on the 4th was noted by the PI of the fly Transgenic RNAi Project. Their set of 4th UAS.RNAi stocks is incomplete and the FCRP was encouraged to finish the job. The need for confidence in our stocks will be met with experimental validation. The need to provide investigators with a starting point for genetic analyses will be met by phenotyping. Our systematic observations of phenotypes such as mutant lethality or sterility plus transcript expression and protein localization are the first data for the 58% of 4th genes that were never studied before. Validation of gene trap null mutants and their UAS.fly cDNAs in rescue experiments sets the stage for humanized stocks. When null mutations are rescued by UAS.human cDNAs subsequent mating of rescued flies creates a humanized stock. These stocks provide opportunities to apply Drosophila genetics to the analysis of human gene interactions and function. Taken together, FCRP stocks will facilitate all manner of biochemical, genetic and molecular studies. The resource is readily available to enhance our understanding of conserved molecular mechanisms underlying human health and disease.

NIH Research Projects · FY 2026 · 2019-09

PROJECT SUMMARY Predicting the phenotypic impacts of a mutation is a major goal in biology and medicine. But the paths linking genotype to phenotype are difficult to navigate. For one, some phenotypes impact others, so the impacts of mutation can stretch out across networks of related traits. One of my lab’s goals is to investigate the relationships between basic features of cells (e.g., misfolded protein abundance, levels of protein-folding chaperones, and cell growth rate) so we can predict some phenotypes from others. But doing so is not enough. Predicting phenotype is more challenging than this because the impacts of mutation, and the networks of related traits through which they spread, can change across contexts. By re-measuring the relationships between traits in many different genetic backgrounds and environments, my lab endeavors to make headway on one of the major goals of modern biology: predicting the phenotypic impacts of mutation in diverse contexts. To achieve this goal, my lab conducts high-throughput experiments in the model eukaryote, budding yeast, that simultaneously quantify the phenotypic impacts of many mutations across many environments. We interpret these big datasets using diverse mathematical models and machine learning approaches. In some projects, we quantify the correlations between phenotypes to infer the network through which a mutation’s influence travels and how that network changes across contexts. For example, I recently measured the correlations between yeast single-cell morphological traits, how they change across the cell cycle, and how this predicts which traits are jointly influenced by mutation. In the next five years, my lab plans to apply a similar strategy to study how the impacts of mutation travel through a regulatory network. In other projects, we deconvolute high- dimensional data into an abstract genotype-phenotype map that uses shared mutant behavior across contexts to improve fitness predictions. In the next five years, we plan to apply this approach to make better predictions about how the fitness of drug-resistant yeast mutants changes across subtly different concentrations and combinations of drugs. Some of our work involves engineering libraries of mutant yeast strains to investigate scaling relationships describing how molecular-level phenotypes (e.g., the levels of misfolded proteins or ribosomes) impact higher- level properties (e.g., cell growth and fitness). Other work focuses on large collections of adaptive mutations generated by laboratory evolution experiments. Our overall goal is to build predictive maps from genotype to phenotype and, in so doing, to learn about molecular biology, and also generate tools to measure and predict some phenotypes from others that will be broadly useful to the community.

NIH Research Projects · FY 2025 · 2018-06

PROJECT SUMMARY The proposed project is a competing renewal of R01AA017608, which investigated the influence of young men's alcohol intoxication, sexual aggression perpetration history, and partner condom negotiation on their sexual risk behavior through two alcohol administration experiments and follow-up surveys. Findings from the original project suggest that alcohol intoxication and sexual aggression history are predictive of greater condom use resistance and other sexual risk behaviors (e.g., unprotected sex) at both proximal and event levels. Moreover, preliminary results suggest that emotional factors may play a role in these associations, suggesting a promising avenue for continued research. The proposed renewal aims to build upon these findings through investigation of the emotional mechanisms involved in young men's alcohol-related sexual risk behavior to provide an empirical foundation for developing evidence-based sexual risk prevention programs. The proposed project continues and extends the original line of research through multiple methods designed to evaluate distal and proximal emotional factors implicated in alcohol-related sexual risk. Male drinkers aged 21- 30 who use condoms inconsistently (n = 600) will first complete a screening procedure followed by a baseline survey which will assess relevant constructs including negative emotional traits, emotion dysregulation tendencies, and alcohol expectancies. They will then complete a 30 day daily diary assessment of their daily emotional states, daily coping motives pertaining to drinking and sex, and daily drinking and sexual risk behaviors in order to evaluate daily relationships among these factors. Upon completion of the daily monitoring period, the same participants will complete an in-lab experiment assessing in-the-moment effects of alcohol intoxication and provocation on negative emotional states and sexual risk intentions. Generalized linear mixed models will be used to examine the daily influence of emotional states and coping motives on alcohol consumption and sexual risk behaviors. Structural equation modeling and other regression-based analyses will be used to examine experimental effects of alcohol intoxication and provocation on negative emotional states and other mediators, as well as sexual risk intentions. Moderating effects of negative emotional traits, emotion dysregulation tendencies, and alcohol expectancies will also be examined for both daily and in-the-moment processes, and the linkages between event-level and experimental relationships will be investigated. The proposed renewal is both significant and innovative in that it will address the public health concern of men's sexual risk behaviors including condom use resistance; will evaluate the role of emotional processes in men's alcohol-related sexual risk; and will use multiple methods to gather complementary types of data that will elucidate the mechanisms underlying alcohol-related sexual risk behaviors and provide an empirical evidence base from which to develop and inform prevention and intervention programs.

NIH Research Projects · FY 2026 · 2017-08

Elevated rates of childhood obesity are a lingering public health concern. Recent national statistics indicate Mexican American youth are nearly twice as likely to be obese as non-Hispanic white youth. Cardiometabolic risk indicators are also elevated among Mexican American children relative to children of other ethnicities. The identification of risk and resiliency predictors of poor health during childhood and adolescence from a longitudinal and developmental perspective will provide specific targets amenable to preventive public health interventions. We propose to capitalize on longitudinal data collected by an NIH-funded study of very low income Mexican American mothers and youth (LMN) that assessed a multitude of individual, biological, family, and environmental risk and protective factors from the prenatal period through ten years of age, including 13 objective measures of child weight and health beginning at birth. We propose to leverage this existing longitudinal dataset and evaluate weight gain and cardiometabolic health trajectories, and additional risk and resiliency factors at child ages 12-13 and 15-16. In combination, we will: 1) Examine trajectories of child weight gain from birth to age 15-16 years and associated cardiometabolic health consequences (e.g., blood pressure, HbA1c, cholesterol, CRP, IL-6); 2) Examine macro-level social and environmental risk and protective factors that influence developmental trajectories in weight gain and cardiometabolic health. 3) Examine proximal influences (e.g., maternal and child mental health; family feeding and behavioral practices) on trajectories of weight gain and cardiometabolic health; 4) Conduct a nuanced examination of ecological and salient stressors that potentially alter weight gain and cardiometabolic trajectories, focusing on the unique characteristics of youth who are relatively unaffected, recover, or are chronically affected. The proposed study will analyze data from biological measures, anthropometric measures, parent report, youth report, medical records, and observational protocols. Our scientific approach emphasizes the view that positive health can best be achieved by understanding social and economic forces that shape eating behavior and weight gain. This project holds great potential to address central questions about contributors to weight gain and obesity risk in a high-risk group, and enhance opportunities for prevention of obesity and associated health problems.

NIH Research Projects · FY 2025 · 2017-05

Abstract This project focuses on elucidating the mechanisms of evolution at the molecular and population-genetic levels by integrating theoretical and experimental work in a wide phylogenetic framework. The molecular focus is on cellular rates of error production in prokaryotic and eukaryotic species, in particular erroneous protein production resulting from messenger RNA mistranslation. This work will test the drift-barrier hypothesis, which postulates that the level of refinement that natural selection can achieve with any trait is limited by the power of random drift but enhanced by the effective genome size and/or number of molecular transactions. Newly developed methods in proteomics will yield rigorous estimates of the apparently high rates at which erroneous amino acids are incorporated into proteins, complementing prior work at DNA and RNA levels. The genetic mechanisms of evolution will be clarified by integrating population-genomic surveys of 1000s of genotypic isolates of the model microcrustacean Daphnia pulex and related species with functional analyses of key genes known to be involved phenotypic divergence. This work will reveal the relative magnitudes of drift, mutation, and recombination in a collection of ~30 populations, far beyond that for any other species. Combined with a long-term temporal survey, the results will enable a test of the hypothesis that variation at the level of gene structure and genomic architecture is directly driven by the local population-genetic environment. The D. pulex system has unique features for gaining insights into major unsolved mysteries in evolutionary genetics, including the causes and consequences of the loss of meiotic recombination, the genetic mechanisms of sex determination, and the coevolutionary constraints within and among mitochondrial and nuclear-encoded genes as determinants of ribosome structure and bioenergetic capacity. A third project develops evolutionary theory, which combined with the empirical observations, is designed to clarify how phenotypic divergence emerges among isolated lineages. Special attention will be given to the joint roles played by genetic drift and fluctuating selection in driving adaptive and nonadaptive patterns of evolution, as well as to matters of molecular coevolution that form the basis of most intracellular features. Because cellular integrity depends on the production of proper proteins, our work on translation fidelity has broad significance for diverse human-health issues, including matters related to cellular toxicity and protein aggregation. By integrating direct observations on the relative power of drift, mutation, recombination, and fluctuating selection, the population-genomics work will yield insight into the factors driving the efficiencies and mechanisms by which all species respond to natural selection. Elucidation of the molecular/cellular mechanisms converting sexual reproduction to asexual propagation via unfertilized eggs and the separate mechanisms preventing male production will open up possibilities of clonal propagation in diverse species as well as possible strategies for pest control.

NIH Research Projects · FY 2025 · 2016-09

PROJECT SUMMARY For persons with cancer and their intimate partners, the ability to communicate effectively about cancer-related issues impacts the adjustment of both individuals and their relationships. However, the vast majority of research on couple communication in cancer has been limited by reliance on global self-report measures of communication that focus on a single dimension of communication behavior (e.g., disclosure versus avoidance) without consideration of other potentially important processes such as emotional arousal, the quality of emotions expressed, and sequences and trajectories of communication behaviors. This narrow focus has prohibited advancements in our understanding of communication processes which, in turn, limits efforts to develop efficacious interventions and target them to couples most at risk of poor adjustment. The proposed study will address these limitations by leveraging a large longitudinal, multi-method dataset we collected among 353 couples coping with stage II-IV breast, colon, rectal, and lung cancer (R01 CA201179). Participants completed global self-report measures of communication four times over a one-year period; twice-daily ecological momentary assessments (EMA) over two weeks; and audio- and video-recorded couple conversations of cancer-related topics from which we coded affective expressions and communicative behaviors and obtained data on fundamental frequency, a novel objective indicator of vocally expressed emotional arousal. Preliminary results provided support for two theories of couple communication in cancer (Social Cognitive Processing and Relationship Intimacy) and underscored the utility of different indicators of communication in predicting adjustment. While these findings are promising, our original aims and methods relied on single indicators of communication in isolation, and thus did not fully capitalize on the integrative potential of the dataset. Recent advances in relationship science suggest that the integration of self-report, behavioral, and fundamental frequency data can provide a richer and more sophisticated picture of communication processes and their impacts on intra- and interpersonal outcomes. This in turn can inform the development of more targeted and efficacious interventions. Specific aims of this proposal are: (1) To identify communication profiles of couples based on EMA and observational data. (2) To examine the predictive relationship of these communication profiles to outcomes including patient and partner psychological adjustment, relational functioning, and physical and functional well-being collected at the 12-month follow up. (3a) To develop, using machine learning, a brief self-report screening tool that will identify couples most at risk for poor outcomes based on the communication profiles developed and tested in Aims 1-2. (3b) To concurrently and prospectively validate this brief screening tool in a new sample of 270 couples (patients with stage II-IV breast, colorectal, or lung cancer and their partners). (3c) To identify facilitators and barriers to implementation of the screener in a clinical setting. The goal is development of an efficient, empirically-derived measure that can be administered to patients and partners in real-world clinical settings.

NIH Research Projects · FY 2026 · 2016-08

Project Summary Pediatric chronic pain is a common but understudied health problem, with prevalence increasing from childhood to adolescence, particularly among girls. Moreover, prevalence rates have increased over the past 20 years for unknown reasons. Despite the high prevalence and enduring impact, we know little about its etiology and developmental progression. The literature documents associations between exposure to early adversity and chronic pain among adults, but little is known about the early developmental time course, key mechanisms, and social resilience that can mitigate risk in youth. Critical questions need to be addressed before efforts at prevention and intervention can have maximum impact. To that end, the proposed competing continuation project focuses on four aims: identify the genetic and environmental influences on growth in pain across childhood and adolescence (Aim1); examine the role of stress exposure in the development of children's chronic pain (Aim 2); and evaluate two potential mechanisms linking stress and pain, problems with emotion regulation (Aim 3), and epigenetics (Aim 4). Under a recalibration model, we also explore social resilience in adolescence as a buffer of these risk processes. To accomplish our aims, we propose to conduct intensive longitudinal follow-up assessments (at 14, 15, and 16 years of age) of a birth-records-based community sample of 350 pairs of twins who are diverse in ethnicity and socioeconomic status. Stress, emotion regulation, and recurring pain during early and middle childhood have already been well characterized. Assessments during adolescence will take a multi-method approach that includes clinical and diary assessments of pain frequency, intensity, duration; objective, diary, and questionnaire assessments of emotion regulation, stress, and social resilience; and objective assessments of epigenetics. Our genetically informed developmental approach to understanding the etiology and mechanisms of pain in youth is critical to determining when benign chronic pain is clinically significant and identifying key targets for intervention efforts to prevent the development of and promote recovery from chronic pain among youth.

NIH Research Projects · FY 2025 · 2015-12

ABSTRACT: Type 2 diabetes (T2D) disproportionately impacts Latino children, families and communities. T2D disparities are the result of complex interactions that involve biological susceptibility and various interdependent social determinants that represent the root causes of disease. The Diabetes Prevention Program (DPP) established that T2D can be prevented in high-risk adults through intensive lifestyle intervention. Although the DPP has been translated to a variety of adult populations and settings, engagement and effectiveness is diminished in minority communities and there are no family-focused diabetes prevention trials for Latinos. For over a decade, our team has collaborated to address the social and cultural determinants of diabetes among Latino youth, in the midst of extant disparities in access to care, low health literacy, and certain cultural norms that may increase diabetes risk. Our culturally-grounded approach is guided by an Ecodevelopmental model that considers community, family, peer, and individual-level factors that influence health behaviors and health outcomes over time. Through a series of increasingly rigorous studies we established that a lifestyle intervention can significantly reduce T2D risk factors and increase Quality of Life (QoL) among Latino adolescents with obesity. We now propose to build upon our extensive experience working with the local Latino community to rigorously test the efficacy of a family-focused diabetes prevention intervention for reducing T2D risk and increasing QoL among high-risk Latino families. We will use Integrative Mixed Methods to understand how family structures and processes influence intervention outcomes. We will examine the sustainability of the intervention at 12-months and explore mediators and moderators of long-term changes. Lastly, we acknowledge that the current translational gap between scientific discovery and real-world impact must be closed so that evidence-based interventions are expeditiously scaled to advance towards health equity for vulnerable and underserved populations. Therefore, we will use the Exploration, Preparation, Implementation, Sustainment (EPIS) framework to guide areas for adaptation and integration within key community-based organizations that may be well-positioned to adopt and implement family-focused diabetes prevention programs. Our long-term goal is to build the evidence, network, and capacity to scale multi-level, family-focused diabetes prevention programs across systems that serve vulnerable and disadvantaged communities. As the next step towards this goal, we propose the following Primary Aim: Test the efficacy of a 4-month, family-focused diabetes prevention intervention, compared to a family control condition, for improving glucose tolerance and increasing QoL among high-risk Latino families. Secondary Aim: Understand how family structure and family processes influence the reach, diffusion, and impact of the intervention on the family system. Exploratory Aim: Examine mediators and moderators of 12- month changes in glucose tolerance and QoL. Implementation Aim: Create a statewide, stakeholder- informed plan to take family diabetes prevention to scale by 1) generating a rapid learning community with organizations that serve Latino families in Arizona, 2) exploring the need, readiness, costs of, and capacity for implementation across these organizations, and 3) planning adaptations and activities to enhance fit and function of the intervention within these organizations.

NIH Research Projects · FY 2025 · 2015-07

Abstract Despite clear and convincing evidence for the efficacy of preventive interventions in preventing substance use and abuse (SU/A), the public health impact of these programs has been limited by inadequate uptake in community settings. This application seeks to train 3 pre-doctoral and 3 post-doctoral fellows annually to conduct research that reduces the gap between real-world practice and evidence-based preventive interventions targeting SU/A. The proposed background is a renewal of our current NIDA-funded T32 (currently in Year 5) and builds on a lengthy and successful 33-year history of T32 training that has been funded by NIMH from 1987-2014 and NIDA from 2014-present. Our training program is informed by the translational research cycle and Chambers and Proctor's recommendations on training for early career Dissemination & Implementation (D&I) researchers. The training is housed at ASU's REACH Institute, and participating units include the Arizona State University (ASU) Department of Psychology and School for Social and Family Dynamics. The interdisciplinary training faculty will be drawn from these units, as well as existing collaborators from College of Health Solutions, W.P. Carey Colleges of Business, Edson College of Nursing and Health Innovation, Fulton Schools of Engineering, Hugh Downs School of Human Communications, School of Criminology and Social Justice, and the School of Social Work. Training faculty conduct numerous NIH-funded projects in which collaborative research teams design, implement, and evaluate theory-based preventive interventions in natural service delivery settings and study the implementation science questions related to successful program uptake. Training faculty have unique strengths in SU/A prevention, D&I, culture and health disparities, and research methodology (particularly quantitative methods). The program is guided by an External Training Faculty of national experts in implementation science and a Community Advisory Board composed of decision leaders from service delivery settings (schools, courts, health care, and mental health care settings), with whom we partner on community-based research projects. Training consists of mentored research apprenticeships, an ongoing training seminar (including training in ethics and career development), required courses in SU/A and D&I, and other relevant experiences based on Individualized Training Plans that will be co-created with mentors. Through this tailored combination of coursework and research apprenticeships, trainees acquire skills in designing interventions for implementation, models of cultural adaptation, technology-based interventions, community-based participatory research, implementation theory and design, organizational characteristics, and economic analysis. The research contributions of our trainees will increase the adoption of evidence-based interventions in real world practice, helping to realize their public health impact at the population level.