SURF 2022
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Works (24)
1. Transcriptional Role of SPT6 at the Histone Locus Body
- Title Tesim:
- Transcriptional Role of SPT6 at the Histone Locus Body
- Creator:
- Mia Hoover
- Date of publication:
- August 12, 2022
- Abstract Tesim:
- Histones are essential for packaging DNA, with their expression tightly controlled and coupled to replication. In Drosophila, replication-dependent (RD) histone mRNAs are transcribed from a single locus at which a specific phase-separated nuclear body forms — the histone locus body (HLB). We investigated the spatiotemporal localization of factors controlling RD-histone mRNA synthesis, particularly the elongation factor SPT6, at the HLB in the developing Drosophila embryo. Through RNA FISH, we also correlated the localization of these factors to the presence of histone mRNA at the HLB. We built upon previous work in the lab (White, 2011) which suggested that SPT6 remains enriched at the HLB through S phase of the earlier nuclear cycles yet was transient at the HLB during cycle 14. Here, utilizing better microscopy with increased resolution, we show that SPT6 was enriched at the HLB only briefly (for eight to 10 minutes) at the beginning of nuclear cycle 14, with no noticeable enrichment as the embryo enters G2 for the first time. In contrast, RNA Pol II and histone mRNA remain enriched at the HLB during this phase, showing an unexpecting decoupling of the association between SPT6 and RNA Pol II and suggesting that in G2, SPT6 is no longer needed for production of histone mRNA. RNA FISH against the 5’ vs 3’ ends of the histone mRNAs suggest that RNA Pol II is not paused but still actively transcribing. Our next steps include using the JabbaTrap system to remove SPT6 from the HLB in the developing embryo to determine whether it is necessary for transcription of RD histone genes and localization of HLB factors.
- Affiliation Label Tesim:
- Department of Biology
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/a5b5-4341
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Mia Hoover
- Rights Statement Label:
- In Copyright
2. In vivo targeted CRISPR based loss-of-function mutations during neonatal mouse heart development
- Title Tesim:
- In vivo targeted CRISPR based loss-of-function mutations during neonatal mouse heart development
- Creator:
- Qian, Yunzhe
- Date of publication:
- August 10, 2022
- Abstract Tesim:
- Technologies that aim to alter DNA advances ever since the discovery of DNA double helix. Previous studies showed that Clustered Regularly Interspaced Short Palindromic Repeats pathway (CRISPR) can edit mammalian genomes in a cost-effective and user-friendly method1. Together with sgRNA (single-guide RNA), CRISPR/Cas9 can be effectively used in vivo to generate controlled mutations with specific cell targets2-3. By simply altering the sequence of sgRNA, we can reprogram Cas9 to target different genomic sites2-3,4. To achieve cardiomyocyte-specific knockout (KO) of the target genes with CRISPR/Cas9, we adopted CRISPR/Cas9 into AAV vector to create recombinant AAV serotype 9 (AAV9) to deliver single guide RNA (sgRNA) into the cardiomyocytes (CM), named CASAAV5. This project is a part of the on-going project in Qian lab. In this project, we will use in vivo perturb-seq to study CM maturation. Briefly, CASAAV will be used in a pooled approach to introduce mutations in each of the selected risk genes and interrogate each gene’s KO effect with single cell RNA-seq (scRNA-seq). We will knock out the risk genes identified from previous Genome-wide Association Studies (GWAS) of congenital and hypertrophic heart disease during neonatal heart maturation and study their function on CM maturation6. As the first in vivo Perturb-Seq on mouse heart development, the project could significantly deepen our understanding of CM maturation. Moreover, compared to classic approach to study gene’s function, in vivo Perturb-Seq can identify cardiac specific effects of genetic perturbations in a high-throughput manner7. and References 1. Doudna J. and Charpentier E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014;346:1258096. 10.1126/science.1258096 2. Jin X, Simmones S, Guo A, Shetty A, Ko M, Nguyen L, Jokhi V, Robinson E, Oyler P, Curry N, Deangeli G, Lodato S, Levin J, Regev A, Zhang F, Arlotta P. In vivo Perturb- Seq reveals neuronal and glial abnormalities associated with autism risk genes. Science. 2020;370:aaz6063. 10.1126/science.aaz6063 3. Dixit A, Parnas O, Li B, Chen J, Fulco C, Jerby-Arnon L, Marjanovic N, Dionne D, Burks T, Raychowdhury R, Adamson B, Norman T, Lander E, Weissman J, Friedman N, Regev A. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell. 2016;167: 1853-1866.e17. https://doi.org/10.1016/j.cell.2016.11.038. 4. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2016;337(6096):816-821. doi:10.1126/science.1225829 5. VanDusen N, Guo Y, Gu W, Pu W. CASAAV: A CRISPR-Based Platform for Rapid Dissection of Gene Function In Vivo. Curr. Protoc. Mol. Biol. 2017;120:31.11.1- 31.11.14. doi: 10.1002/cpmb.46. 6. Harper A, Goel A, Grace C. Common genetic variants and modifiable risk factors underpin hypertrophic cardiomyopathy susceptibility and expressivity. Nat. Genet. 2021;53:135–142. https://doi.org/10.1038/s41588-020-00764-0 7. Carroll K, Makarewich C, McAnally J, Anderson D, Zentilin L, Liu N, Giacca M, Bassel-Duby R, Olson EN. A mouse model for adult cardiac-specific gene deletion with CRISPR/Cas9. Proc. Natl. Acad. Sci. U. S. A. 2016;113(2):338–343. doi: 10.1073/pnas.1523918113.
- Affiliation Label Tesim:
- Department of Pathology and Laboratory Medicine
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/83gc-5y91
- Language Label:
- English
- ORCID:
- 0000-0002-8404-692
- Other Affiliation:
- Person:
- Qian, Yunzhe
- Rights Statement Label:
- In Copyright
3. Testing Novel Podocyte Slit Diaphragm Protein Conservation in Danio rerio (Zebrafish)
- Title Tesim:
- Testing Novel Podocyte Slit Diaphragm Protein Conservation in Danio rerio (Zebrafish)
- Creator:
- Imseis, Zachary, Gerlach, Gary, and O'Brien, Lori
- Date of publication:
- September 22, 2022
- Abstract Tesim:
- Kidneys are vital organs responsible for filtering and removing toxins from the blood. The major filtration unit of the kidney is the nephron. The nephron consists of the glomerulus and tubules. The glomerulus consists of three components: fenestrated endothelium, the glomerular basement membrane (GBM), and podocytes. Podocytes are highly specialized epithelial cells with long protrusions called foot processes that connect to each other via specialized junctions called slit diaphragms (SD). The SD is largely responsible for the integrity of the glomerulus. Lack of the SD contributes to a loss of podocyte integrity; however, only a small number of proteins are known to localize in the SD. One protein known to localize in the SD is podocin. We utilized proximity-dependent Biotin Identification (BioID). We utilized CRISPR-Cas9-based gene editing to knock in the BioID moiety to the endogenous NPHS2 locus (Podocin). BioID allows for the biotinylation of a protein of interest (POI) by fusing a mutated promiscuous prokaryotic biotin ligase to the endogenous locus of our target gene, NPHS2 (Podocin). This biochemical assay allowed us to identify the repertoire of proteins within the podocyte foot process. We identified a novel Immunoglobulin-like domain-containing receptor 2 (Ildr2) within the podocyte SD. Recent data from sc-RNAseq databases evince Ildr2 expression in human podocytes. By utilizing zebrafish and mice, the importance of this novel immunoglobulin family protein can be tested in podocyte integrity. Our innovative method has allowed us to identify novel proteins of the SD and potential new therapeutic targets for kidney disease.
- Affiliation Label Tesim:
- College of Arts and Sciences and Department of Cell Biology and Physiology
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/5yqx-b411
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Imseis, Zachary, Gerlach, Gary, and O'Brien, Lori
- Rights Statement Label:
- In Copyright
4. Equilibrium Thermodynamic Effects of Sugar-based Polymers on Protein-complex Formation
- Title Tesim:
- Equilibrium Thermodynamic Effects of Sugar-based Polymers on Protein-complex Formation
- Creator:
- Redvanly, Thomas
- Date of publication:
- September 22, 2022
- Abstract Tesim:
- The insides of cells are crowded. To model these conditions, synthetic crowders like Ficoll can be used to create crowded environments in vitro. Classic crowding models suggest that hard-core repulsions have the only effect on protein-complex stability. However, these theories neglect the contribution of “soft” chemical interactions. Such interactions can be stabilizing, if repulsive, and destabilizing, if attractive. To study how protein-protein interactions are affected by crowding, I investigated the effects of Ficoll on the equilibrium thermodynamics of protein complexes. Specifically, I quantified the temperature-dependence of this interaction to determine the enthalpic contribution. I found that Ficoll has a measurable enthalpic contribution to protein complex stability that was otherwise disregarded in classic crowding theories.
- Affiliation Label Tesim:
- Department of Chemistry
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/yk81-2c75
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Redvanly, Thomas
- Rights Statement Label:
- In Copyright
5. SURF 2022- Design and Analysis of Organometallic Catalysts for the Synthesis of Better Fuels
- Title Tesim:
- SURF 2022- Design and Analysis of Organometallic Catalysts for the Synthesis of Better Fuels
- Creator:
- Eblen, Anna
- Date of publication:
- September 22, 2022
- Abstract Tesim:
- Research performed under SURF 2022 funding. Various catalyst designs were synthesized and tested for converting ethanol to longer chain alcohol to be used as fuel additives. From these results various design principles were observed. These principles were then used to advance and narrow down what catalyst design routes should be pursued.
- Affiliation Label Tesim:
- Department of Chemistry
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/9wec-z237
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Eblen, Anna
- Rights Statement Label:
- In Copyright
6. Function of βII-Spectrin (SPTBN1) in Skeletal Muscle Metabolism
- Title Tesim:
- Function of βII-Spectrin (SPTBN1) in Skeletal Muscle Metabolism
- Creator:
- Choi, Grace
- Date of publication:
- August 23, 2022
- Abstract Tesim:
- The aim of this project is to characterize the role of the cytoskeletal protein βII-spectrin in skeletal muscle (SKM) structure and metabolism. Using a novel conditional SKM-specific βII-spectrin knockout (SKM-βII-spectrin-KO) I recently validated, I will determine structural and functional consequences of βII-spectrin deficiency in SKM. Based on known functions of βII-spectrin and preliminary findings, I hypothesize that βII-spectrin is required for maintaining the structural integrity, mitochondrial content, and bioenergetic capacity of SKM fibers. Results from this study will increase our understanding of the contribution of the cytoskeleton to SKM energetics and the mechanistic basis of muscle-related deficiencies found in individuals with impaired βII-spectrin function.
- Resource type:
- Presentation
- Location:
- Chapel Hill, North Carolina, United States
- Affiliation Label Tesim:
- Department of Cell Biology and Physiology and Department of Biology
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/hfcr-4j35
- Keyword:
- skeletal muscle, metabolic disease, cytoskeletal protein, spectrins, mitochondrial homeostasis, western blotting, qpcr
- Language Label:
- English
- ORCID:
- Other Affiliation:
- and Honors Carolina
- Person:
- Lorenzo, Damaris and Choi, Grace
- Rights Statement Label:
- In Copyright
7. Light Yield of New Quantum Dot-Doped Liquid Scintillators
- Title Tesim:
- Light Yield of New Quantum Dot-Doped Liquid Scintillators
- Creator:
- Vickers, Sarah
- Date of publication:
- August 29, 2022
- Abstract Tesim:
- Collaborations all around the world are working to prove the Majorana nature of the neutrino by detecting a process called neutrinoless double beta decay. This decay process is only possible for a handful of atomic isotopes, all with extremely long double beta decay half-lives of up to 10^26 years. Consequently, these experiments need huge amounts of decay material to have a chance at seeing a neutrinoless double beta decay event. One way to increase isotope quantity would be to replace the traditional liquid scintillators currently being used with quantum dot-doped liquid scintillators loaded with one of the decay isotopes. This project is a light yield test of new quantum dot-doped scintillators to determine whether they generate light well enough to replace traditional scintillator in upcoming kiloton-scale experiments.
- Affiliation Label Tesim:
- Department of Physics and Astronomy
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/pkdg-6h87
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Vickers, Sarah
- Rights Statement Label:
- In Copyright
8. Daily Lives of Samburu Pastoralist Children in Northern Kenya: Working, Herding and Food Consumption
- Title Tesim:
- Daily Lives of Samburu Pastoralist Children in Northern Kenya: Working, Herding and Food Consumption
- Creator:
- Jackson Plemmons and Charles Hilton
- Date of publication:
- August 28, 2022
- Abstract Tesim:
- While the daily activities, including school, household economic activities, and food consumption patterns of East African pastoralist kids are generally known, few quantitative studies examining the impact of these activities have been conducted. The current study sought to provide greater documentation of time allocation and food consumption patterns seen in Samburu pastoralist kids (ages 6-14 years) of northern Kenya in order to assess their daily levels of energetic intake and energetic expenditure [via heart rate & movement patterns].
- Affiliation Label Tesim:
- Department of Anthropology
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/qrv4-3w48
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Jackson Plemmons and Charles Hilton
- Rights Statement Label:
- In Copyright
9. Concurrent Impacts of Parenting Behaviors on Child Psychopathology
- Title Tesim:
- Concurrent Impacts of Parenting Behaviors on Child Psychopathology
- Creator:
- Li, Tianyi
- Date of publication:
- August 20, 2022
- Abstract Tesim:
- Parenting behaviors have been found to be concurrently associated with children’s psychological disorders. However, many previous studies relied on a single informant to measure both parenting behaviors and child psychopathology, which may have inflated the strength of the established association. Therefore, in order to fill this gap, the study employed data where the two constructs were measured from different informants and aimed to generate more valid results.
- Affiliation Label Tesim:
- Department of Psychology and Neuroscience
- Type:
- http://purl.org/dc/dcmitype/Text
- DOI:
- https://doi.org/10.17615/e94y-g727
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Li, Tianyi
- Rights Statement Label:
- In Copyright
10. The Evolution of Fear-Acquisition Strategies during Predation
- Title Tesim:
- The Evolution of Fear-Acquisition Strategies during Predation
- Creator:
- Bishop,Megan
- Date of publication:
- August 22, 2022
- Abstract Tesim:
- People are born both with a general fear response for threatening stimuli (Ohman 2009) and an ability to learn from experience (Olsson 2007) and from others (Bossan et al 2015). Here, I describe a population genetic model I created during my SURF fellowship in 2022 that considers a trade-off between these two fear-acquisition strategies (innate vs learned) when considering to what degree each strategy evolves: while innate fear does not carry the risk of requiring a predator-prey interaction, it may be too easily triggered because this response is less specific. I ask, how does this trade-off affect the evolution of innate and learned fear-acquisition strategies, and how is the evolution influenced by factors such as predator density, predator threat level, and environmental stability? This presentation describes the empirical justification and beginnings of this model. The data collection and analysis will be conducted during my honors thesis.
- Resource type:
- Presentation
- Affiliation Label Tesim:
- Biological and Biomedical Sciences Program
- DOI:
- https://doi.org/10.17615/m7sz-kw41
- Language Label:
- English
- ORCID:
- Other Affiliation:
- Person:
- Bishop,Megan
- Rights Statement Label:
- In Copyright
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Collection Details
- Total items
-
45
- Size
-
unknown
- Date created
-
August 5, 2022