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Thesis
Peer Reviewed

The human cytomegalovirus (HCMV) IE2 86 kDa protein is an essential viral regulatory factor that has been shown in transient transfection and in vitro assays to transactivate early viral promoters and to interact with many viral and cellular proteins. To understand the functions provided by this protein in the HCMV-infected cell, we have constructed and characterized a family of recombinant viruses containing changes to the IE2 gene and other parts of the HCMV major immediate early (IE) region. The study of these HCMV mutants has allowed us to confirm that several of the predicted functions of IE2 86 are relevant in the virus-infected cell and has identified new functions for the protein. Introducing small deletions into the C-terminus of IE2 86 resulted in viruses that do not support early gene expression, replicate, or repress the major IE promoter. Surprisingly, these constructs also mediated up-regulation of several delayed early and late viral genes, suggesting that IE2 functions are required for the proper regulation of late viral gene expression. By constructing several viruses that do not express the IE2 40 and IE2 60 kDa proteins, which are present in infected cells at late times post infection, we continued to investigate the regulation of late gene expression by IE2. Again, we found that the IE2 40 and IE2 60 proteins are required for proper late gene expression and for repression of the major IE promoter. Interactions between the virus and the host cell are also crucial for proper HCMV replication, and a recombinant virus with a deletion in exon 3 of the major IE region demonstrated that IE2 86 is important not only for transactivation of viral early promoters, but also for dysregulation of the host cell cycle. Cells infected with this recombinant virus fail to exhibit diffuse PML staining at early times post infection and express less cyclin E protein and produce less infectious virus than do wild-type virus-infected controls. The experiments described in this dissertation demonstrate that IE2 86 is a multifunctional protein that contributes many functions, several of which were not previously identified, to HCMV replication in infected cells

Cover page: Functional roles of the human cytomegalovirus IE2 86 kDa protein in HCMV-infected cells

Thesis
Peer Reviewed

Civic Engagement in the Upper Elementary Grades: An Examination of Parent and Teacher Practices and Children's Civic Identity

White, Elizabeth Spalding
Advisor(s): Mistry, Rashmita S.

UCLA Electronic Theses and Dissertations (2012)

This study examines civic identity (i.e., civic values and responsibility to community and to people) in middle childhood, a previously unexplored developmental period in the civic engagement literature, and how adults and socialization processes in the home and school contexts are associated with children's civic outcomes. Middle childhood is a relevant time to explore these processes, as children at this age begin to demonstrate more complex understandings and interactions with their social world (Eccles, 1999). Thus, it is a key time to build a foundation for future civic engagement. This study aimed to determine: 1) child and family characteristics associated with civic outcomes in middle childhood; 2) the extent to which parents' humanitarian values and civic beliefs (social and government trust) are associated with children's civic identity and the ways that parents share these values/beliefs with children; and 3) the types of civic activities used by teachers in the upper elementary grades and the extent to which teacher practices are associated with children's civic outcomes. Survey data were collected from 407 ethnically and economically diverse upper-elementary students (4th- 6th grades), their parents (N = 388), and teachers (N = 22) from seven schools in Southern California. Aim 1: Results indicated that being female, having a need to affiliate with others, and being from a low-income family were associated with children's civic identity. Aim 2: Additionally, parents who more strongly endorsed humanitarian values and were more trusting of others had children with greater civic outcomes, and parents transmitted these values/beliefs to their children by being civically engaged themselves. Parent mistrust in the government was also associated with greater civic outcomes, but only for children from low-income families. Aim 3: Teachers reported using multiple types of civic activities in the classroom, and civic learning opportunities (e.g., service learning) were associated with children's feelings of responsibility to people. This study provides evidence of a civic identity in middle childhood and shows that parents and teachers both matter for children's civic outcomes. Findings also suggest that parents' civic engagement and concrete civic learning experiences are particularly meaningful to children's civic outcomes during middle childhood.

Cover page: Civic Engagement in the Upper Elementary Grades: An Examination of Parent and Teacher Practices and Children's Civic Identity

Article
Peer Reviewed

End-of-Life Care During the Coronavirus Disease 2019 Pandemic: The 3 Wishes Program

UCLA Previously Published Works (2021)

Patient- and family-centered end-of-life care can be difficult to achieve in light of visitation restrictions and infection-prevention measures. We evaluated how the 3 Wishes Program evolved to allow continued provision of compassionate end-of-life care for critically ill patients during the coronavirus disease 2019 pandemic.

Design

This is a prospective observational study where data were collected 1 year prior to the coronavirus disease 2019 pandemic and 1 year after (from March 1, 2019, to March 31, 2021). The number of deceased patients whose care involved the 3 Wishes Program, their characteristics, and wishes were compared between prepandemic and pandemic periods.

Setting

Six adult ICUs of a two-hospital health system in Los Angeles.

Patients

Deceased patients whose care involved the 3 Wishes Program.

Interventions

The 3 Wishes Program is a palliative care intervention in which individualized wishes are implemented for dying patients and their families.

Measurements and main results

During the study period, the end-of-life care for 523 patients involved the 3 Wishes Program; more patients received the 3 Wishes Program as part of their end-of-life care during the pandemic period than during the prepandemic study period (24.8 vs 17.6 patients/mo; p = 0.044). Patients who died during the pandemic compared with prepandemic were less likely to have family at the bedside and more likely to have postmortem wishes fulfilled for their families. Compared with the 736 wishes implemented during the prepandemic period, the 969 wishes completed during the pandemic were more likely to involve keepsakes. Wishes were most commonly implemented by bedside nurses, although the 3 Wishes Program project manager (not involved in the patient's clinical care) was more likely to assist remotely during the pandemic (24.8% vs 12.1%; p < 0.001).

Conclusions

Bedside innovations, programmatic adaptations, and institutional support made it possible for healthcare workers to continue the 3 Wishes Program and provide compassionate end-of-life care in the ICU during this pandemic.

Cover page: End-of-Life Care During the Coronavirus Disease 2019 Pandemic: The 3 Wishes Program

Article
Peer Reviewed

Identifying predictors of HPV‐related head and neck squamous cell carcinoma progression and survival through patient‐derived models

UC San Diego Previously Published Works (2020)

Therapeutic innovation for human papilloma virus-related (HPV+) head and neck squamous cell carcinomas (HNSCCs) is impaired by inadequate preclinical models and the absence of accurate biomarkers. Our study establishes the first well-characterized panel of patient-derived xenografts (PDXs) and organoids from HPV+ HNSCCs while determining fidelity of the models to the distinguishing genetic features of this cancer type. Despite low engraftment rates, whole exome sequencing showed that PDXs retain multiple distinguishing features of HPV+ HNSCC lost in existing cell lines, including PIK3CA mutations, TRAF3 deletion and the absence of EGFR amplifications. Engrafted HPV+ tumors frequently contained NOTCH1 mutations, thus providing new models for a negatively prognostic alteration in this disease. Genotype-phenotype associations in the models were then tested for prediction of tumor progression and survival in published clinical cohorts. Observation of high tumor mutational burdens (TMBs) in the faster-growing models facilitated identification of a novel association between TMB and local progression in both HPV+ and HPV- patients that was prognostic in HPV- cases. In addition, reduced E7 and p16^INK4A levels found in a PDX from an outlier case with lethal outcome led to detection of similar profiles among recurrent HPV+ HNSCCs. Transcriptional data from the Cancer Genome Atlas was used to demonstrate that the lower E2F target gene expression predicted by reduced E7 levels has potential as a biomarker of disease recurrence risk. Our findings bridge a critical gap in preclinical models for HPV+ HNSCCs and simultaneously reveal novel potential applications of quantifying mutational burden and viral oncogene functions for biomarker development.

Cover page: Identifying predictors of HPV‐related head and neck squamous cell carcinoma progression and survival through patient‐derived models

Article
Peer Reviewed

Defining CD4 T helper and T regulatory cell endotypes of progressive and remitting pulmonary sarcoidosis (BRITE): protocol for a US-based, multicentre, longitudinal observational bronchoscopy study

UC San Francisco Previously Published Works (2021)

Introduction

Sarcoidosis is a multiorgan granulomatous disorder thought to be triggered and influenced by gene-environment interactions. Sarcoidosis affects 45-300/100 000 individuals in the USA and has an increasing mortality rate. The greatest gap in knowledge about sarcoidosis pathobiology is a lack of understanding about the underlying immunological mechanisms driving progressive pulmonary disease. The objective of this study is to define the lung-specific and blood-specific longitudinal changes in the adaptive immune response and their relationship to progressive and non-progressive pulmonary outcomes in patients with recently diagnosed sarcoidosis.

Methods and analysis

The BRonchoscopy at Initial sarcoidosis diagnosis Targeting longitudinal Endpoints study is a US-based, NIH-sponsored longitudinal blood and bronchoscopy study. Enrolment will occur over four centres with a target sample size of 80 eligible participants within 18 months of tissue diagnosis. Participants will undergo six study visits over 18 months. In addition to serial measurement of lung function, symptom surveys and chest X-rays, participants will undergo collection of blood and two bronchoscopies with bronchoalveolar lavage separated by 6 months. Freshly processed samples will be stained and flow-sorted for isolation of CD4 +T helper (Th1, Th17.0 and Th17.1) and T regulatory cell immune populations, followed by next-generation RNA sequencing. We will construct bioinformatic tools using this gene expression to define sarcoidosis endotypes that associate with progressive and non-progressive pulmonary disease outcomes and validate the tools using an independent cohort.

Ethics and dissemination

The study protocol has been approved by the Institutional Review Boards at National Jewish Hospital (IRB# HS-3118), University of Iowa (IRB# 201801750), Johns Hopkins University (IRB# 00149513) and University of California, San Francisco (IRB# 17-23432). All participants will be required to provide written informed consent. Findings will be disseminated via journal publications, scientific conferences, patient advocacy group online content and social media platforms.

Cover page: Defining CD4 T helper and T regulatory cell endotypes of progressive and remitting pulmonary sarcoidosis (BRITE): protocol for a US-based, multicentre, longitudinal observational bronchoscopy study

Creative Commons 'BY-NC' version 4.0 license

Article
Peer Reviewed

Virology—the path forward

UC Davis Previously Published Works (2024)

In the United States (US), biosafety and biosecurity oversight of research on viruses is being reappraised. Safety in virology research is paramount and oversight frameworks should be reviewed periodically. Changes should be made with care, however, to avoid impeding science that is essential for rapidly reducing and responding to pandemic threats as well as addressing more common challenges caused by infectious diseases. Decades of research uniquely positioned the US to be able to respond to the COVID-19 crisis with astounding speed, delivering life-saving vaccines within a year of identifying the virus. We should embolden and empower this strength, which is a vital part of protecting the health, economy, and security of US citizens. Herein, we offer our perspectives on priorities for revised rules governing virology research in the US.

Article
Peer Reviewed

Virology under the Microscope—a Call for Rational Discourse

UC Irvine Previously Published Works (2023)

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Article
Peer Reviewed

Virology under the Microscope-a Call for Rational Discourse.

UC Irvine Previously Published Works (2023)

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.

Article
Peer Reviewed

Virology under the Microscope—a Call for Rational Discourse

UC Irvine Previously Published Works (2023)

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns - conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we - a broad group of working virologists - seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology.