# data[].attributes.title
Health Outcomes of Youth Who Experience Caregiver Death

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Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)

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Each year, over two million US youth experience the death of a caregiver before the age of 18 (hereafter referred to as caregiver death). Given the syndemic of COVID-19, the opioid crisis, and gun violence, rates of caregiver death among US children are likely to remain elevated or increase in the next decade. US non-Hispanic Black children are three times more likely to experience parent death than White children. Bereaved youth (i.e., who experienced a caregiver death) are vulnerable to adverse emotional and behavioral health (EBH) outcomes, such as higher risks of depression, anxiety, substance use, and suicidality. The goal of this research is to identify opportunities for improving EBH outcomes among bereaved youth. Three knowledge gaps must be filled to achieve this goal. First, we need to evaluate caregiver death in the context of other co-occurring adverse experiences. Second, we need to understand how the caregiving context mediates the relationship between caregiver death and EBH outcomes. Third, we need to learn from the lived experiences of bereaved young people. In addition to our multidisciplinary investigative team with relevant content and methodological expertise, an Advisory Board of bereaved young adults and grief professionals will be developed to inform this research. Guided by a Life Course Framework and Multidimensional Grief Theory, we will use a convergent mixed-method design to achieve three aims and fill the identified knowledge gaps: 1) Assess associations between caregiver death and EBH outcomes in the context of adverse childhood expereinces among young adults from the Future of Families and Child Wellbeing Study (N = ~2900); 2) Determine the extent to which the caregiving context (i.e., material hardship and parental monitoring) mediates the relationship between caregiver death and EBH outcomes; 3) Identify diverse strategies to support bereaved youth using longitudinal survey data and lived experiences (i.e., life history interviews with 80 young adults and consensus building with our Advisory Board). Achieving these aims will improve our ability develop tailored, family-centered interventions, practices and policies that support bereaved youth across sociodemographic groups. Ultimately, study findings will inform theory-driven and data-informed recommendations for future research, practice, and policies to improve EBH outcomes for the growing number of bereaved young people.

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Elucidating the role of the SARS-CoV-2 ORF9b protein in virus replication

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National Institute of Allergy and Infectious Diseases (NIAID)

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Highly pathogenic human coronaviruses encode an array of accessory proteins that are crucial for their virulence, enabling them to effectively manipulate cellular machinery and subvert host defenses. Our research proposal is centered on the SARS-CoV-2 accessory protein, ORF9b, which is known to amplify viral virulence in vivo, yet its specific roles during viral infection remain to be elucidated. Transfection studies suggest that ORF9b prevents innate immune induction by hindering the assembly of the MAVS signalosome, a finding that awaits confirmation in the context of actual SARS-CoV-2 infection. The investigation of ORF9b in virus-infected cells has traditionally been hampered by its integrated localization within the nucleocapsid gene, complicating efforts to manipulate ORF9b without unintentionally interfering in the nucleocapsid functionality. We have successfully overcome this challenge by strategically relocating the ORF9b sequence away from the nucleocapsid gene, creating a SARS-CoV-2 variant that produces native ORF9b levels and replicates as efficiently as the wild-type virus. This engineered virus provides a strong platform for exploring ORF9b functions during infection without unintended impact on the nucleocapsid gene. Further advancing our methodology, we tagged ORF9b in its new locale with an HA tag and TurboID, setting the stage for pioneering investigations of ORF9b networks in SARS-CoV-2-infected cells. Our extensive validation of these viral variants confirmed their ability to replicate comparably to the unmodified virus while preserving the native characteristics of ORF9b. We will employ these advanced tools to rigorously examine the impact of ORF9b phosphorylation on SARS- CoV-2 replication and the protein’s specific functions (Aim 1). Additionally, we will generate a detailed, time- resolved interaction map of ORF9b, uncovering its evolving interactions during infection (Aim 2). Achieving these goals will provide significant insights into the biological mechanisms of ORF9b and enhance our understanding of SARS-CoV-2 pathogenesis. This foundational work will also set the stage for extending similar methodologies to other viral proteins, vastly improving our knowledge of the coronaviral biology and aiding in the identification of new prophylactic and therapeutic avenues.

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National Institute of Allergy and Infectious Diseases (NIAID)

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Bats are reservoir hosts of many zoonotic viruses that cause significant disease in humans, including coronaviruses, filoviruses and henipaviruses. It is unknown how bats can host these viruses but some have speculated that tolerance may be a primary factor. What is clear is that infection of bat reservoirs is typically innocuous, without meaningful inflammatory responses, and often with low antibody titers, suggesting poor affinity maturation. T cells are critical arms of the adaptive immune response and it may be that in bats they play a more prominent role during infection than do B cell responses. This project will determine the effector functions of helper (Th) and cytotoxic (CTLs) T cells to H18N11 bat influenza A virus and BANAL-52 coronavirus, determine how vaccination and T cell depletion impact infection, and whether antibody alone is sufficient to control infections. Helper T cell subsets are essential for the orchestration of immune responses to control infections and have critical impacts on B cells, including directing them to undergo somatic hypermutation leading to affinity maturation of antibodies, class switching and clonal expansion, and some account for immunological tolerance. In contrast, CTLs are instrumental in identifying and killing virally-infected cells. This project will use Jamaican fruit bats (Artibeus jamaicensis) from a closed, captive breeding colony to stimulate antigen-specific T cell responses. We will determine if bats possess canonical helper T cell subsets, including Th1, Th2, Tfh, Treg and Th17 cells, and CTLs, and how these subsets participate in the control and clearance of virus with or without vaccination. We will identify subsets using single-cell RNA Seq and qPCR and determine their cytokine and transcription factor profiles in response to antigenic stimulation. We will also deplete T cells from bats to determine the importance of Th cells and CTLs during infection, and determine whether antibody alone is sufficient to protect bats by using adoptive transfer of hyperimmune bat sera to bats depleted of T cells and challenged with virus. Finally, we will establish the methodology for in vitro cultivation of antigen-specific bat T cell clones that can be used for functional studies of effector molecules. Together, this project will be the first to examine antigen-specific T cells from bats in detail, determine their characteristics in response to vaccination and viral challenge, and the role of arms of the adaptive immune response in bats. Collectively, these studies will offer explanations as to how bats control viral infections without disease, and whether T cells are involved in immune tolerance.

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The effect of HIV on SARS-CoV-2 transmission and emergence of variants of concern

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National Institute of Allergy and Infectious Diseases (NIAID)

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The emergence and spread of SARS-CoV-2 variants of concern is threatening global health and our ability to prevent COVID-19 disease, raising concerns about a potential new wave of the pandemic. HIV may complicate the trajectory of the COVID-19 pandemic and efforts to eradicate the virus. While most people with a competent immune system successfully clear SARS-CoV-2 infection within days, people living with HIV with weakened immunity can carry persistent infection for months. Individuals with immunodeficiency may also have a higher risk of SARS-CoV-2 reinfection that can further extend the duration of infectiousness with high viral load. As a result, chronically infected individuals are potentially contagious for an extended period of time and may sustain transmission in the community. Similar to other viruses, SARS-CoV-2 accumulates mutations over time as it replicates within the host. Therefore, chronic SARS-CoV-2 infection in the context of a weakened immune system may provide the time and the environment needed for the virus to replicate and evolve genetic mutations associated with survival advantages, including increased transmissibility and resistance to COVID-19 vaccines or treatment. The proposed research aims to understand the overall impact of HIV infection on the SARS-CoV-2 viral evolution and transmission dynamics in a setting with high HIV prevalence. We will address current knowledge gaps by integrating SARS-CoV-2 genomic data, patient-level clinical data, and epidemiological data to achieve the following aims: 1) we will determine the effect of HIV infection on the transmission dynamics of COVID-19 and emergence of SARS-CoV-2 variants; and 2) we will determine the effect of HIV-associated immunosuppression on the acquisition of SARS-CoV-2 mutations. For the first Aim, advanced phylodynamic methods will be applied to determine how HIV affects the transmission and viral evolution of SARS-CoV-2 on a population scale, as well as to describe risk factors that drive individual and population-level COVID-19 transmission. For the second Aim, we will recruit and follow a cohort of COVID-19 patients with and without HIV infection to determine the effect of HIV-associated immunosuppression on the rate of emerging SARS-CoV-2 mutations. The proposed research will also utilize active case finding to minimize sampling bias. Findings from this project will inform the development of optimal public health interventions to control the pandemic by disrupting transmission chains and prevent the emergence and spread of alarming variants.

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National Institute of Allergy and Infectious Disease

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Identification and enrichment of signature regions of antimicrobial resistant pathogen genomes for wastewater disease surveillance

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National Institute of Allergy and Infectious Diseases (NIAID)

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Antimicrobial resistance is recognized as a global public health threat that makes infections more difficult to treat and increases the risk of other medical procedures. Global and local surveillance of antimicrobial resistance is critical to understanding transmission of resistant pathogens, detecting the emergence of resistance mechanisms, and mitigating the spread of resistant pathogens. Wastewater surveillance represents a powerful, resource-efficient, and comprehensive approach for population-level surveillance of infectious diseases. It has been widely applied to track COVID-19 and other respiratory virus levels in communities, as well as identify circulating variants. However, wastewater surveillance of antimicrobial resistant pathogens has not been widely implemented because of specific challenges that limit its actionability (i.e., the direct use of the surveillance data to inform public health action). This is because antimicrobial resistance is ubiquitous in the environment and even clinically-important antibiotic resistance genes (ARGs) are abundant and widespread in wastewater. Thus, previous approaches that quantified ARGs generated information that was not specific to antimicrobial resistant pathogens. This proposal focuses on the development of foundational computational tools and laboratory methods necessary to identify and detect signature regions of antimicrobial resistant pathogens for wastewater surveillance. Signature regions are defined as genomic regions that are conserved in a pathogen strain but not found in neighboring strains or other genomes. We propose to develop a genomic language model approach to identify signature regions of target antimicrobial resistant pathogens. This will be integrated with a fully automated design pipeline for quantitative assay design. On the wet lab side, we will use microdroplet encapsulation of wastewater microbes to do high-throughput enrichment and isolation of antimicrobial resistant bacteria. This approach will enable sensitive and specific detection of antimicrobial resistant pathogens by encapsulating individual cells and assaying them for signature regions using digital droplet PCR. The proposed computational and laboratory tools will result in software and wet lab methodologies that can be used by public health laboratories and wastewater surveillance programs for specific and sensitive antimicrobial resistance monitoring. Software, assays, and protocols will be made publicly available and can also be applied for other pathogen targets. Advancing the actionability of antimicrobial resistance wastewater monitoring has the potential to enable the prediction of outbreaks, forecast hospitalizations, guide treatment decisions, understand transmission, and evaluate mitigation strategies for antimicrobial resistant infections.

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Extended spectrum Beta lactamase producing Escherichia coli

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Determining the role of 90K on SARS-CoV-2

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National Institute of Allergy and Infectious Diseases (NIAID)

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Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly discovered coronavirus that is responsible for the current pandemic that is plaguing the world and has resulted in millions of dead. Due to the recent emergence of this viral pathogen, there is a dearth of information regarding SARS-CoV-2 infection and the role of cellular host factors associated with it. A better understanding of SARS-CoV-2 infection and the host factors involved with it is necessary for the development of SARS-CoV-2-directed therapeutics. A factor that has been associated with antiviral activity, yet its antiviral mechanism is not elucidated is galectin-3-binding-protein (LGALS3BP/90K). 90K is a secreted glycoprotein that is upregulated during viral infections and is an interferon stimulated gene. Despite the fact that 90K is an interferon stimulated gene, very little is known about its contribution to the antiviral defense of the cell. It is suggested that 90K affects human immunodeficiency virus (HIV) virion biogenesis in a process that is not yet elucidated. Moreover, the antiviral role of 90K has never been studied in other virus families outside of retroviruses. This proposal investigates the role of 90K on SARS-CoV- 2 infection. The goal of this proposal is to provide mechanistic evidence on the effect of 90K during SARS-CoV- 2 infection. Furthermore, many host genes that target viral infections are antagonized by virally encoded genes. There are currently no viral genes known to counteract 90K. SARS-CoV-2 encodes a number of viral accessory proteins, whose function is largely unknown. Therefore, another aspect of this proposal is to identify the mechanism by which SARS-CoV-2 accessory proteins counteract 90K. This study will elucidate the role of 90K during SARS-CoV-2 infections, as a better understanding of host cellular factors that target SARS-CoV-2 is needed and will provide novel valuable information regarding the role of SARS-CoV-2 encoded genes. In conclusion, the identification of host genes that target SARS-CoV-2 infection and their viral antagonists provide possible new targets for the development of SARS-CoV-2 pharmaceutical treatments.

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CSHL 2025 Conference on Eukaryotic mRNA Processing

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The proposed conference on “Eukaryotic mRNA Processing” will convene scientists studying various aspects of mRNA processing, transport, turnover and their roles in human diseases. Major advances have recently been made in all these areas, and the proposed conference will be a timely event for discussing the latest unpublished results and exchanging ideas, thereby fostering new developments in this rapidly moving field. The proposed conference will be the fifteenth meeting in the series that is held every other year at Cold Spring Harbor Laboratory. The most recent meeting was held in August 2023 and attracted 435 scientists internationally, who are actively investigating various aspects of messenger RNA maturation in eukaryotic cells using genetic, biochemical, molecular, cell biological, and computational approaches. The 2025 meeting will be held in person with a virtual audience for broadening access and for those that cannot attend in person. As in the previous meetings, a major focus of the 2025 meeting will be on nuclear events in mRNA maturation, including mRNA splicing and polyadenylation, the connections between transcription and mRNA maturation steps, the roles of mRNA processing events in the biology of viruses, the application of informatics and genome-wide approaches to the analysis of RNA processing, as well as the relevance of mRNA processing to the etiology of cancer and other diseases. We also expect relevant and timely contributions on topics related to the new coronavirus variant SARS-CoV-2, in particular on the experimental vaccines based on messenger RNA. The meeting will include two keynote lectures, eight plenary oral sessions and two poster sessions. Oral sessions will include ten or five 12-minute talks, respectively, with additional time for discussion. In response to major developments in the fields of RNA modification and the roles of RNA structure in processing, we have expanded the sessions devoted to these topics; this adaptability to the major movements in the field helps keep this meeting at the cutting edge and ensures that we will draw participants from traditional as well as emerging areas of RNA research. This subdivision, successfully piloted at the 2019 meeting, allows a broader representation of scientific fields. As always, except for the two keynote lectures, all speakers will be selected on the basis of the submitted abstracts, which encourages active participation by junior scientists. We will particularly encourage presentation of unpublished work by the students and postdoctoral fellows who are leading these projects, as has traditionally been a hallmark and a unique strength of the Cold Spring Harbor meetings.

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A binational cohort of the intersection between substance use, HIV, and associated comorbidities among people who inject drugs in San Diego, CA

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We will prospectively study the intersection between substance use, HIV and related co-morbidities in a cohort of people who use drugs (PWUD) in San Diego County (SD). For >25 years, Strathdee has studied the epidemiology of HIV and related co-infections among PWUD across North America, with N=500-1000 and annual retention ≥90%. Since 2020, our La Frontera I cohort situated on the U.S.-Mexico border has documented the highest HIV and HCV incidence among people who inject drugs in North America. Currently, HIV prevalence among former injectors in SD is 16% compared to 10% among current injectors. Consistent with other U.S. cities, we observed a dramatic shift from injection to non-injection of opiates in recent years, leading us to propose cohort expansion to non-injectors. Due to our location on a major drug trafficking corridor, we observe a wide range of substances (e.g., heroin, fentanyl, methamphetamine, xylazine, benzodiazepines). We previously leveraged La Frontera I to evaluate initiatives to improve uptake of PrEP, COVID-19 testing and vaccination. We propose: 1) To characterize trends and predictors of use of established and emerging drugs, drug use transitions (e.g., shifts from IDU to non-IDU & vice versa) and their impact on HIV incidence and utilization of HIV prevention and treatment. 2) To study prevalence and incidence of the following co-morbidities and their relationship to HIV incidence and utilization of HIV prevention and treatment: i) HCV; ii) STIs (i.e., syphilis, gonorrhea, Chlamydia, MPox), iii) neurobehavioral disturbances. 3) To evaluate the influence of structural interventions on HIV-related risk behaviors and utilization of HIV prevention and treatment including: i) new homelessness policies; ii) drug checking services; iii) vending machines. 4) To contribute to a shared database and biorepositories that serve as a platform for collaborations with end users and community partners. To meet these aims, we will continue to follow PWUD from La Frontera I who are actively using illicit substances, replenishing to arrive at 500 PWID and 500 PWUD (non-injectors) for a total sample of 1000. This will include subgroups vulnerable to HIV in SD (e.g., sex workers, people experiencing homelessness) among whom we expect 52 HIV seroconversions after 5 years of follow-up. Our cohort will include at least 50 PWUD living with HIV who will provide samples for viral load, sequencing and biobanking. All participants will undergo semi-annual interviews and specimen collection. SD is designated as a high priority jurisdiction for the Ending the HIV Epidemic Initiative (EHE) and a high intensity drug trafficking area by the DEA. La Frontera II leverages NIH-funded T32s, the California NeuroHIV Tissue Network, Last Gift Study brain/tissue repositories and the PREPARE Institute which tracks emerging and re-emerging infectious disease threats. Our work is aligned with priorities identified by RFA-DA-25-003, the NIH Office of AIDS Research and the EHE.

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United States National Institutes of Health

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Vitamin C protect against nicotine induced lung ailment

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Smoking has been demonstrated to induce oxidative stress, which is compounded with significantly reduced antioxidant availability, increased production of inflammatory cytokines as well as neutrophilic infiltration that are implicated in pathogenic processes in the lungs. Additionally, studies involving mice exposed to cigarette smoke reveal impaired pulmonary anti-bacterial and anti-viral defenses in response to infections. Other research has found that smokers also exhibit increased susceptibility to infections including influenza and SARS-CoV2. Investigations concerning the harmful effects that tobacco use exerts to lower bodily defenses are undeniably urgent, particularly those that address strategies for amelioration of smoking-induced health risks. Nicotine is the main component among the thousands of chemicals in all tobacco products including e-cigarettes. Nicotine binds to a family of nicotinic acetylcholine receptors (nAChRs) like acetylcholine (ACh). nAChRs are highly expressed in the lung fibroblasts and epithelial cells. Nicotine functions as an immunomodulator and has been reported to impair the immune response of smokers to infections. Vitamin C (vitC; ascorbic acid: AA) is an essential water- soluble vitamin with known respiratory health enhancing properties. Humans cannot synthesize vitC endogenously and thus obtain it from dietary sources via intestinal absorption. Dietary vitC is absorbed from the intestine via carrier-mediated sodium-dependent vitC transporters (SVCT1 and SVCT2, the products of the SLC23A1 and SLC23A2 genes, respectively). Low plasma levels of vitC have been found in patients with viral infections and other critical illnesses. Many previous studies have highlighted the role of vitC in protection against lung infections. Administration of vitC to patients with pneumonia, for example, can reduce the severity and duration of the disease. Pneumonia and influenza infections and related pathologies are also more severe in Gulo KO mice (a mouse model that cannot synthesize vitC endogenously, similar to humans). Both smokers and passive smokers have lower plasma and leukocyte vitC levels than non-smokers. Mean serum concentrations of vitC in adults who smoke have been found to be one-third lower than those of non-smokers. Our preliminary studies showed that nicotine reduces the functional expression of vitC transporters in the intestine and lung epithelial cells. We therefore hypothesize that nicotine induced vitC deficiency/insufficiency is a major factor in increasing the risk of respiratory viral infections in smokers. To test this hypothesis we propose two specific aims: Aim 1: To determine the mechanisms underlying nicotine-mediated impaired uptake of vitC by intestinal and lung epithelial cells using in vitro and in vivo models. Aim 2: To determine whether vitC supplementation is able to overcome the increased susceptibility to viral infections induced by nicotine. The expected outcomes of this project will advance our knowledge regarding the changes in uptake of vitC in the intestine and in the lungs, which is essential to develop novel therapeutics to improve vitC deficiency and insufficiency while also addressing ensuing lung viral infections and injury found in smoking population.

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sodium DEPENDENDENT vitamin C transporter 1

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sodium-dependent vitamin C transporter 2

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The role of the mRNA-based or Newcastle disease virus (NDV)-based vaccine platform in mucosal B cell priming and recirculation

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National Institute of Allergy and Infectious Diseases (NIAID)

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The experiences and lessons learned from the COVID-19 pandemic geared our interests towards investigating the mechanism of action of different vaccine platforms and vaccination strategies that aim to induce long-lasting protective systemic and mucosal immune responses to prevent disease and transmission via the mucosal route. Dr. Weina Sun co-developed a Newcastle disease virus vector (NDV)-based COVID-19 vaccine that can be used either as an injectable inactivated whole virion vaccine or a live intranasal vaccine, the latter of which can elicit mucosal immune responses as a “stand-alone” vaccine platform. In naïve mice, a 2-dose regimen of intranasal NDV-based vaccine induced a high level of mucosal IgA antibodies. In mice that were pre- vaccinated with mRNA-LNP COVID-19 vaccines via the intramuscular route, a third intranasal NDV booster also substantially enhanced nasal wash antigen-specific IgA. By closely examining samples obtained from different anatomical mucosal sites in mRNA-LNP vaccinated mice without the NDV booster, spike-specific IgA were detected in nasal wash, intestinal lavage as well as vaginal lavage, among which Intestinal lavage contained the highest levels of IgA. Dr. Jennifer Gommerman is an immunologist with special interests studying mucosal B lymphocytes. In humans, she developed methods to detect salivary antibodies. While SARS-CoV-2 infection induces high levels of spike-specific salivary IgG and IgA, salivary IgG are also abundantly found after intramuscular 2-dose mRNA vaccinations. Intriguingly, some of the mRNA-vacccinated individuals developed and maintained modest salivary secretory-IgA that were resistence to decay after a 2-dose mRNA vaccine. Given that both in mice and humans, mucosal antigen-specific IgA were detected after mRNA-LNP vaccination, we hypothesize that mRNA-LNP vaccines can prime de novo mucosal B cells that are close to the administration sites, which are able to recirculate to other mucosal surfaces. Consequently, a further mucosal booster vaccine, such as the intranasal live NDVvaccine, would be able to recall pre-exisiting memory B cell responses. We will follow two specific aims to test our hypothesis, utilizing mRNA-LNP vaccine and NDV vaccine encoding the spike of Beta variant as a proof of concept: (Aim 1) To examine temporal and spatial dynamics of antigen-specific IgA and IgG secreting B cells in the mucosa-associated lymphoid tissues after mRNA and NDV vaccination in mice. (Aim 2) To track circulation of antigen-specific mucosal B cells in photoconvertible Kikume mice after mRNA prime followed by NDV vaccination or infection by flowcytometry. The proposed work entails innovative approaches and mouse models to test our hypothesis. We believe the outcomes of the study can inform the mechanism of action of not only mRNA-based and NDV-based SARS-CoV-2 vaccines, but also the same types of vaccines against other respiratory or enteric viral pathogens, in which mucosal antibody responses plays a critical role to mitigate virus infection and transmission.