The Zika epidemic in 2015-2016 and COVID-19 pandemic in 2019-2021 are the latest reminders of the enormous impact of viruses on the world. Zika, a flavivirus transmitted by mosquitos, can cause severe neurodevelopmental abnormalities including microcephaly in the newborns of the infected mothers. Vaccine design is complicated by concern that elicited antibodies may also recognize other epidemic-causing flaviviruses that share a similar envelope protein, such as dengue virus, West Nile Virus, and yellow fever virus. This cross-reactivity, if non-neutralizing, may worsen symptoms of a subsequent infection through antibody-dependent enhancement (ADE). To better understand the neutralizing antibody response and risk of ADE, we compared germline and mature antibody binding to Zika and other flaviviruses. We showed that affinity maturation of the light chain variable domain is important for strong binding of VH3-23/VK1-5 neutralizing antibodies to Zika virus envelope domain III (EDIII) and identified interactions that contribute to weak, cross-reactive binding to West Nile Virus EDIII. These findings informed our design of EDIII-conjugated mosaic nanoparticles as a pan-flavivirus vaccine candidate. Sera from immunization trials with nanoparticles displaying EDIIIs of Zika and dengue serotypes 1-4 showed cross-reactive binding to Zika, dengue 1-4, and West Nile Virus, a promising step towards the development of safe and effective flavivirus vaccines.
\r\n\r\nCoronaviruses are another group of viruses responsible for widespread morbidity and mortality, including the severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome coronavirus (MERS-CoV) epidemics and current SARS-CoV-2 pandemic. Given concerns regarding new SARS-CoV-2 variants and the possibility for additional zoonotic betacoronaviruses to cause future outbreaks, we investigated how the epitopes on the SARS-CoV-2 receptor binding domain (RBD) targeted by VH3-30-derived antibodies correlate with their neutralization potency and breadth of betacoronavirus recognition. Analyses showed how variations in antibody light chains and CDRH3 lengths facilitate the diverse RBD epitopes, cross-reactivity, and neutralization profiles of VH3-30 Abs, illustrating their importance for vaccine design and therapeutic antibody development.
" }, { "name": "Grant, Stephen Nicholas", "degree": "PhD", "year": "2022", "title": "Investigation of Some Small Molecule-Protein and Protein-Protein Interactions in Nicotine Addiction, Opioid Use Disorder, and COVID-19", "advisor": "Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07142021-175425546", "creators": [ { "name": { "family": "Grant", "given": "Stephen Nicholas" }, "id": "Grant-Stephen-Nicholas", "orcid": "0000-0003-0923-8886", "display_name": "Grant, Stephen Nicholas" } ], "advisors": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pdtj-8238", "abstract": "Nicotine addiction, opioid use disorder, and COVID-19 have made lasting impacts on every aspect of society. These are complicated conditions, and studies in these fields will likely continue for decades, if not centuries. Here, we make contributions to each of these issues using electrophysiology and microscopy. The first chapter goes into the motivation behind this thesis and the major experiments I used in my graduate career. In the second chapter, we introduce a new amino acid into the mouse muscle nicotinic acetylcholine receptor in an attempt to understand the dynamics of receptor activation. In the third chapter, we continue the Lester lab\u2019s work on the neuroscientific effects of menthol and how it plays a role in nicotine addiction. We found the binding site for menthol on the \u03b14\u03b22 nicotinic acetylcholine receptor, which continues our hypothesis that the neuroscientific effects of menthol are detrimental to cigarette smokers. Fortunately, partly because of our studies, mentholated nicotine products are being phased out of the United States. The fourth and fifth chapters investigate \u03bc-opioid receptor trafficking, both the trafficking from the endoplasmic reticulum and endocytosis from the plasma membrane. Both of these events play a role in inducing opioid use disorder and increasing the danger of using opioids. We hope that these studies will help other researchers understand opioid use disorder and fight the opioid epidemic. Finally, we studied the effects of SARS-COV-2 proteins on epithelial sodium channels. These channels are important for regulating lung fluid levels where their improper function may cause pulmonary edema. Pulmonary edema has been observed in COVID-19 patients. Altogether, we believe that we have made meaningful impacts on these important health concerns in this thesis. We look forward to how the scientific communities continue to build on our results.
" }, { "name": "Gu, Alan Yalun", "degree": "PhD", "year": "2022", "title": "Aqueous Aerosols in Atmospheric Chemistry and Airborne Diseases", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04142022-025410011", "creators": [ { "name": { "family": "Gu", "given": "Alan Yalun" }, "id": "Gu-Alan-Yalun", "orcid": "0000-0001-8095-3634", "display_name": "Gu, Alan Yalun" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "chair", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/4spy-az88", "abstract": "Aqueous atmospheric aerosols are small droplets (typically smaller than 5 \u03bcm) suspended in the air that are comprised of water and water-soluble components. These aerosols provide an air-water interfacial reaction environment on their surfaces, and act as a medium for airborne disease transmission. In this thesis, Chapters II and V explore atmospherically relevant reactions on the aqueous aerosol surface using an online mass spectrometry, while Chapter III investigates the SARS-CoV-2 airborne transmission considering suspended virus-laden aerosols as the transmission media. Spinning off this SARS-CoV-2 work, Chapter IV describes a newly developed quantitative RNA amplification test kit for COVID-19, with an emphasis on the amplification result photo recognition component." }, { "name": "Han, Yanting", "degree": "PhD", "year": "2022", "title": "Emotion Experience from Stories, Videos and Everyday Life: Structure and Individual Differences", "advisor": "Adolphs, Ralph", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272022-181044242", "creators": [ { "name": { "family": "Han", "given": "Yanting" }, "id": "Han-Yanting", "orcid": "0000-0003-3381-2059", "display_name": "Han, Yanting" } ], "advisors": [ { "name": { "family": "Adolphs", "given": "Ralph" }, "id": "Adolphs-R", "orcid": "0000-0002-8053-9692", "role": "advisor", "display_name": "Adolphs, Ralph" } ], "committee": [ { "name": { "family": "Meister", "given": "Markus" }, "id": "Meister-M", "orcid": "0000-0003-2136-6506", "role": "chair", "display_name": "Meister, Markus" }, { "name": { "family": "Eberhardt", "given": "Frederick D." }, "id": "Eberhardt-F-D", "role": "member", "display_name": "Eberhardt, Frederick D." }, { "name": { "family": "Shimojo", "given": "Shinsuke" }, "id": "Shimojo-S", "orcid": "0000-0002-1290-5232", "role": "member", "display_name": "Shimojo, Shinsuke" }, { "name": { "family": "Adolphs", "given": "Ralph" }, "id": "Adolphs-R", "orcid": "0000-0002-8053-9692", "role": "member", "display_name": "Adolphs, Ralph" } ], "option_major": [ "neurobio" ], "doi": "10.7907/yhmt-9t69", "abstract": "Most studies of emotion have as their subject matter the emotion experiences that people can describe and rate. By contrast to this approach from psychology, studies in animals, and some biological studies in humans, focus on behavior and its adaptive function. These two literatures typically use very different corresponding features by which to characterize emotion: categories or dimensions describing feelings for which we have convenient words, for the former (e.g., happiness, pleasantness), and functional properties for the latter (e.g., persistence, generalizability, approachabil- ity). In this thesis I use both sets of ratings, and I ask whether the latter, biologically inspired features could also be used to characterize people\u2019s emotion experiences, and might reveal novel dimensions of variability. They also typically use different sets of stimuli to induce the emotions: lexical stimuli in which participants are asked to imagine something hypothetical are common in human studies; ecologically valid stimuli that at least the subjects cannot distinguish from the real world are common in animal studies. Here I used three domains of stimuli: stories, videos, and real-life experiences, in the same set of participants, permitting a unique comparison.
\r\n\r\nI took advantage of a sample of approximately 1000 Americans who were surveyed longitudinally over the internet during the COVID-19 pandemic. I collected ratings of emotion experiences evoked by three classes of stimuli: a validated set of short stories, a validated set of short videos, and actual experiences in real life across multiple waves. I found that all three types of emotion experiences could be characterized by low dimensional spaces, with the first two factors that accounted for most of the variance in people\u2019s ratings corresponding to the dimensions of valence and arousal, in line with prior work. However, I discovered additional novel factors related to generalizability (the extent to which an emotion experience is shared across many different situations and occurrences) or modularity (the extent to which an emotion experience is unique to specific situations). The findings show that emotion features not usually assessed in humans can be recovered from subjective ratings of their experiences. I argue for a revision of current dimensional theories of emotion: they have been incomplete because they were restricted to ratings entrenched in how we think of our conscious experience, and the typical English words we use to describe it. The new dimensions validate some theories of emotion and offer hope for linking psychological studies in humans with behavioral or neurobiological work across species. I also characterized the distributions of the three types of emotion experiences and found that emotions were distributed along continuous gradients, with no well-separated clusters even for emotions belonging to the six basic emotion categories.
\r\n\r\nMy thesis presents two additional topics that capitalize on my unique sample: the emotions experienced during the COVID pandemic, and individual differences. For example, I also found that resilience buffered individuals against the effect of loneliness on depression, and that people who had tested positive for COVID felt more morally disgusted towards acts of violating social norms. I also explored the association between psychological traits and differences in emotion experiences both in terms of the magnitudes of the ratings and the overall correlation structure across scales. Again, the richness of my dataset reveals a number of associations that are theoretically interesting and that will be of relevance to understanding mood and anxiety disorders as well.
\r\n\r\nAll of the data will be made publicly available, and the core parts of many of the investigations were pre-registered.
" }, { "name": "Hoffmann, Magnus Adrian Gero", "degree": "PhD", "year": "2022", "title": "Nanoparticle Technologies to Cure and Prevent Infectious Diseases", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302021-184745797", "creators": [ { "name": { "family": "Hoffmann", "given": "Magnus Adrian Gero" }, "id": "Hoffmann-Magnus-Adrian-Gero", "orcid": "0000-0003-4923-9568", "display_name": "Hoffmann, Magnus Adrian Gero" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "chair", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "orcid": "0000-0001-8723-8190", "role": "member", "display_name": "Baltimore, David L." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "biology" ], "doi": "10.7907/g0w1-rc77", "abstract": "Despite almost 40 years of intensive research, there is still no curative treatment for HIV-1/AIDS. Anti-retroviral therapy (ART) prolongs the life expectancy of HIV-1-infected individuals but is associated with side effects, and multiple drugs need to be given in combination to prevent the development of viral resistance. In addition, treatment must continue for the lifetime of the individual due to the existence of a long-lived latent proviral reservoir. While a \"sterilizing\" cure remains difficult to achieve due to difficulties associated with identifying and clearing latently-infected cells, recent research has focused on designing a \"functional\" cure, i.e., a therapeutic strategy that enables long-term suppression of HIV-1 replication and remission of symptoms in the absence of ART. The work presented here describes a new therapeutic direction for the development of a functional cure against HIV-1. This approach is based on the hypothesis that HIV-1 is unable to escape from a nanoparticle (NP)-based decoy that presents clusters of the HIV-1 receptor CD4, because CD4-NPs mimic viral target cells more accurately than soluble CD4-based inhibitors and permit high-avidity interactions with trimeric HIV-1 Env proteins. We demonstrate that CD4-NPs are >10,000-fold more potent than soluble CD4 (sCD4) and prevent viral escape in vitro. AAV-mediated delivery of self-assembling CD4-NPs produced stable CD4-NP serum concentrations in mice that were almost 1,000-fold higher than concentrations required to neutralize HIV-1 in vitro, suggesting that these concentrations could be therapeutic. Viral challenge studies in non-human primates are underway to evaluate the potential of this therapeutic strategy.
\r\n\r\nAs an alternative approach to generate decoys against HIV-1, we generated engineered red blood cells (RBCs) that expressed viral receptors and potently inhibited HIV-1 infection of target cells in vitro. Because RBCs do not contain nuclei or functional organelles required for protein translation, infection of engineered RBCs represents a dead-end for a lentivirus such as HIV-1, which must integrate into the host cell genome as part of its lifecycle. We generated stable erythroid progenitor cell lines that continuously produced HIV-1 receptor-expressing RBCs that could be administered to HIV-1-infected individuals. As RBCs vastly outnumber CD4+ T-cells, HIV-1\u2019s main target cells, and have extended lifetimes, only a fraction of an individual\u2019s RBCs would need to be replaced with the engineered RBC viral traps in order to suppress HIV-1 infection in vivo.
\r\n\r\nMy work on CD4-NP therapeutics against HIV-1 also led to the invention and development of the EBR NP technology that is ideally suited for vaccine design applications. This technology can be used to modify any type of membrane protein to self-assemble into enveloped virus-like NPs without the need for additional proteins. EBR NP assembly is induced by inserting a short amino acid sequence into the cytoplasmic tail of the membrane protein, which was designed to recruit host proteins from the endosomal sorting complex required for transport (ESCRT) pathway. We applied this technology to design protein NP-based vaccines against Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), which elicited potent serum neutralizing antibody responses in mice. The EBR NP technology is also ideally suited for the development of hybrid vaccine approaches that allow genetic encoding of protein-based NPs, thereby combining attributes of mRNA and protein-based NP vaccines. Pilot studies demonstrated that mRNA and DNA vaccines encoding the self-assembling SARS-CoV-2 spike-EBR construct elicited ~10-fold higher neutralizing antibody responses than mRNA and DNA vaccines encoding the unmodified spike protein. This hybrid approach has the potential to substantially enhance the potency of mRNA vaccines and could become a leading vaccine platform technology. Future applications for the EBR NP technology are discussed, including the development of a universal coronavirus vaccine to prevent future pandemics, and engineering EBR NPs to mRNA vaccines or therapeutic cargoes for efficient and targeted delivery.
" }, { "name": "Jette, Claudia Angela", "degree": "PhD", "year": "2022", "title": "Targeting Fusion Proteins of HIV-1 and SARS-CoV-2", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechThesis:04282022-192922044", "creators": [ { "name": { "family": "Jette", "given": "Claudia Angela" }, "id": "Jette-Claudia-Angela", "orcid": "0000-0002-5085-8027", "display_name": "Jette, Claudia Angela" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "orcid": "0000-0001-8723-8190", "role": "member", "display_name": "Baltimore, David L." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "biochem" ], "doi": "10.7907/pxa2-dy41", "abstract": "Viruses are disease-causing pathogenic agents that require host cells to replicate. Fusion of host and viral membranes is critical for the lifecycle of enveloped viruses. Studying viral fusion proteins can allow us to better understand how they shape immune responses and inform the design of therapeutics such as drugs, monoclonal antibodies, and vaccines. This thesis discusses two approaches to targeting two fusion proteins: Env from HIV-1 and S from SARS-CoV-2. The first chapter of this thesis is an introduction to viruses with a specific focus on HIV-1 CD4 mimetic drugs and antibodies against SARS-CoV-2. It discusses the architecture of these viruses and fusion proteins and how small molecules, peptides, and antibodies can target these proteins successfully to treat and prevent disease. In addition, a brief overview is included of the techniques involved in structural biology and how it has informed the study of viruses. For the interested reader, chapter 2 contains a review article that serves as a more in-depth introduction for both viruses as well as how the use of structural biology has informed the study of viral surface proteins and neutralizing antibody responses to them. The subsequent chapters provide a body of work divided into two parts. The first part in chapter 3 involves a study on conformational changes induced in the HIV-1 Env protein by CD4-mimemtic drugs using single particle cryo-EM. The second part encompassing chapters 4 and 5 includes two studies on antibodies isolated from convalescent COVID-19 donors. The former involves classification of antibody responses to the SARS-CoV-2 S receptor-binding domain (RBD). The latter discusses an anti-RBD antibody class that binds to a conserved epitope on the RBD and shows cross-binding and cross-neutralization to other coronaviruses in the sarbecovirus subgenus.
" }, { "name": "Savela, Emily Sue", "degree": "PhD", "year": "2022", "title": "Nucleic Acid Measurements for Antibiotic Susceptibility Testing and Early Detection of SARS-CoV-2", "advisor": "Ismagilov, Rustem F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10072021-173853251", "creators": [ { "name": { "family": "Savela", "given": "Emily Sue" }, "id": "Savela-Emily-Sue", "orcid": "0000-0001-9614-4276", "display_name": "Savela, Emily Sue" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "advisor", "display_name": "Ismagilov, Rustem F." } ], "committee": [ { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "chair", "display_name": "Pierce, Niles A." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "bioeng" ], "doi": "10.7907/vp9a-n206", "abstract": "Nucleic-acid-amplification tests (NAATs) are widely used in microbial detection both in environmental characterization and human diagnostics. NAATs offer highly sensitive and specific detection of target molecules among the noise of complex samples. This thesis covers two important applications of nucleic-acid quantification techniques in human clinical samples. First, I co-developed a new phenotypic antibiotic susceptibility test that uses species-specific DNA detection to detect bacterial cell-wall damage following incubation with beta-lactam antibiotics. Second, I helped compile a longitudinal dataset of SARS-CoV-2 viral loads during a community-based COVID-19 study run by the Ismagilov Lab through October 2020 \u2013 April 2021 in the greater Los Angeles County area, USA. Sensitive and specific nucleic-acid tests allowed for robust detection of pathogenic microbes in both these applications. Designing and implementing NAATs for these applications required consideration of biological constraints of the microorganisms, molecular stability over the time of quantification, and the practical constraints of acquiring and transporting samples. Continued innovation of NAAT technologies will be critical to contain present and future pandemics and empower medical professionals with data to inform treatment options.
" }, { "name": "Banerjee, Abhik Kumar", "degree": "PhD", "year": "2021", "title": "Diverse Roles of RNA-protein Interactions: From Viral Antagonism to Mammalian Development", "advisor": "Guttman, Mitchell; Rothenberg, Ellen V.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02032021-180657616", "creators": [ { "name": { "family": "Banerjee", "given": "Abhik Kumar" }, "id": "Banerjee-Abhik-Kumar", "orcid": "0000-0002-9797-0104", "display_name": "Banerjee, Abhik Kumar" } ], "advisors": [ { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "advisor", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "co-advisor", "display_name": "Rothenberg, Ellen V." } ], "committee": [ { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "chair", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "orcid": "0000-0001-8723-8190", "role": "member", "display_name": "Baltimore, David L." }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "role": "member", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "member", "display_name": "Rothenberg, Ellen V." } ], "option_major": [ "biology" ], "doi": "10.7907/tfb9-n887", "abstract": "RNA is a widely utilized and integrated component of core cellular function because of its abilities to recognize and hybridize to nucleic acid templates, spatially localize to different compartments within the cell, bind combinatorially to effector molecules, and in some cases directly catalyze chemical reactions. In this thesis, I describe three cases, illustrating the biomolecule\u2019s unique importance in several different aspects of cellular homeostasis. Chapter 1 provides historical context for studying RNA-protein interactions within RNA biology and Virology. Chapter 2 details experiments in which we explored RNA as a central target of host cell takeover by SARS-CoV-2. In the process, we highlight the importance of RNA in many integral complexes within the cell, including components of the spliceosome, the eukaryotic ribosome, and signal recognition particle. Chapter 3 presents data from our consideration of RNA within the context of cis gene regulation. We specifically focus on a model RNA-binding protein, SMRT/HDAC1 Associated Repressor Protein (SHARP), and the paternally imprinted long non-coding RNA, Kcnq1ot1, as case studies. Chapter 4 describes our dissection of a transcriptional circuit involving SHARP and discusses implications of RNA-binding to developmentally sensitive circuits and processes. Finally, Chapter 5 poses new questions raised by these studies. Together these data emphasize the diverse and unique role RNA plays in cellular homeostasis and suggest additional roles in nuclear compartment stabilization and crosstalk.
" } ]