Symposium MAGAZINE 2021 - Marion County School District
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Symposium MAGAZINE 2021 2021 SC INBRE Science Symposium | 1
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2 | 2021 SC INBRE Science Symposium
S•C •I•E•N•C •E
8:15 am Opening Remarks: Dr. Edie Goldsmith, USC SOMC,
SC INBRE Program Director
202I
Session 1: Developmental Research Project Program Recorded
Presentations and LIVE Q&A
8:30 to 10:15 am DRP Recorded Presentations (up to
15 minutes each) viewable on link provided
to Symposium registrants.
Presenters:
Brian Booth, Clemson University
Sri Chandrasekaran, Furman University
Jessica Larsen, Clemson University
Chang Liu, University of South Carolina
Austin Shull, Presbyterian College 3 Welcome from the
Chris Varnon, Converse College Program Director
10:15 to 10:30 am LIVE Q&A with presenters via Zoom link provided
to registrants. 4 Posters list
Session 2: Bioinformatics Pilot Project Program Recorded Presentations
and LIVE Q&A 10 Student abstracts
10:30 am to 11:45 am BIPP Recorded Presentations (up to
15 minutes each) viewable on link provided to 49 Research Experiences for
Symposium registrants. Presenters are 2019 Teachers (RET) overview
BIPP Recipients: and abstracts
Jennifer Grier (with Steven Fiester), USC SOMG
Nathan Hancock, USC Aiken
Doug Pittman, University of South Carolina
54 Bioinformatics Pilot
Project Program (BIPP)
Mark Sarzynski, University of South Carolina
and Developmental
11:45 am to 12 noon LIVE Q&A with presenters via Zoom link provided to Research Project
registrants. Program (DRP) overview
and abstracts
12 noon to 1 pm Lunch Break
Session 3: LIVE Student Poster Presentations with Q&A 60 Embargoed abstracts
LIVE Selected student presentions (up to 10 minutes each).
1 to 2 pm Bioengineering/Biomedical Engineering:
Marigordon Varner, Poster BE-02
Bioinformatics: Paris Rizzo, BI-07
Chemistry/Biochemistry: Yevgeniy Gerassimovich,
CB-01
2 to 2:15 pm Break
2:15 to 3:30 pm Molecular/Cell Biology: Braxton Hill, MCB-22
Neuroscience: Victoria Miles, NEU-05
Public Health: Brendan Odigwe, PH-02
Research Experiences for Teachers:
Michael Bailey, RET-02
3:30 pm Closing Remarks and Invitation to Network:
Dr. Edie Goldsmith
Session 4: Networking and Poster Questions
3:30 to 4 pm Moderated Zoom Rooms by research category and
Exhibit Hall
2021 SC INBRE Science Symposium | 3
SC INBRE is pleased to announce that a team of Drs. Chandrasekaran and Kowbowski met in graduate
South Carolina biomedical researchers has received school in 2001 and began collaborating in 2014.
an NIH NIGMS P20 collaboration award. The goal of Chandrasekaran says, “My contributions to collaborative
this one-year funding opportunity is to encourage projects with Dr. Kozubowski are based on my expertise
collaborations between IDeA programs investigators in stress response in human cells, while he was exploring
while providing students a broad continuum of research the contribution of cell division to drug resistance in
opportunities. The team of Dr. Srikripa Chandrasekaran Cryptococcus neoformans. Hsp 90 has been shown to
from Furman University and Dr. Lukasz Kozubowski play an important role in drug resistance in the human
from Clemson University were awarded $147,340 pathogen, Candida albicans, but its role in regulating
for their project entitled, “SC INBRE Collaborative drug resistance in Cryptococcus remains unclear.
Administrative Supplement – Role of Hsp90 in Resistance Our preliminary results encouraged us to explore this
of Cryptococcus neoformans to Fluconazole.” Dr. possibility, which led to this project. We are thankful for
Chandrasekaran is a current recipient of an SC INBRE the ability to engage students in this exciting project
Developmental Research Project Program (DRP) award; and thanks to the NIGMS INBRE-COBRE Administrative
Dr. Kozubowski is a member of EPIC (COBRE Eukaryotic Supplement grant opportunity, we can further contribute
Pathogens Innovation Center). to scientific collaborations between Furman University
and Clemson University.”
“This project explores mechanisms that allow a fungal
pathogen, Cryptococcus neoformans, to become resistant Said Dr. Edie Goldsmith, SC INBRE Program Director, “This
to anti-fungal therapy,” explained Dr. Chandrasekaran. is the second consecutive year NIGMS has offered this
“Fungal pathogens are eukaryotes and therefore it is award and the second consecutive year a research team
difficult to design a drug, which is both effective against from South Carolina has been chosen as a recipient. It
the fungus yet not toxic to humans. The antifungal drug, has been said that we are stronger together. This award
fluconazole, is less toxic to humans, but unfortunately shows how strong biomedical research has grown in
resistance to this drug is common, which makes the South Carolina – not only through our program, but also
therapy less effective. Our preliminary study reveals that in collaborations with other IDeA-funded programs. We
Hsp90 chaperone plays a role in the development of look forward to future collaborations with other programs
anti-fungal drug resistance in Cryptococcus neoformans and receiving additional awards.”
and our goal is to unearth specific mechanisms through
which Hsp90 influences drug resistance.”
4 | 2021 SC INBRE Science Symposium
2020 was a very different kind of year. Not only was it the year of the funding
of SC INBRE’s fourth INBRE funding cycle and the first year the Program
offered a Student-Initiated Research Program grant, it was the year that we all
had to learn to do things a different way; masks, social distancing, incessant
hand washing, remote learning and virtual meetings became a way of life. We
originally thought that we would not be able to have research programs this
year – after all, how can you do research if you can’t be at the bench? Our very
resilient and resourceful faculty found a way as you will see from the over 80
abstracts included in this year’s Symposium magazine and during the 12th
Annual Science Symposium, all virtual this year (a first for us).
SC INBRE PROGRAM OFFICE
The purpose of our annual Science Symposium is to bring together those Dr. Edie Goldsmith
who have been funded by SC INBRE to share the work of our grants programs Program Director
recipients. Presenting during the Symposium are representatives of most edie.goldsmith@uscmed.sc.edu
of our 14 network and four outreach/alumni institutions. As always, we also
welcome most of the teachers who participated in the Research Experiences
for Teachers (RET). These middle and high school STEM teachers were directed
in carrying out unique, individualized research projects by faculty mentors
matched from the teacher’s own local area.
Dr. Holly LaVoie
SC INBRE would not exist without the hard work and contributions of many Program Coordinator
people across the state: the Institutional PIs our network institutions, our holly.lavoie@uscmed.sc.edu
Core Facilities Directors and staff, and our faculty and students. We’d like to
especially recognize the members of our External Advisory Committee, Drs.
Clifford Houston, Merry Lindsey, George Littleton, Nancy Mills (EAC Chair) and
introduce our newest member Dr. Laura Furge who replaces Dr. Kathy Parson
who retired this year, for virtual attending our Symposium today and giving their
valuable feedback to our program. Many thanks to the volunteers who serve John G. Clarkson, IV, MPH
as Zoom moderators. And a thank you to the families of the students for their Program Manager
support of their student’s research. We’d also like to thank representatives from john.clarkson@uscmed.sc.edu
NIH’s other IDeA programs, especially COBRE, for attending and participating in
our virtual Exhibit Hall today.
And last, but not least, a big thank you to the members of the SC INBRE
Program Office. Their tireless dedication, not only this Symposium, but also to
the day-to-day operations of SC INBRE has no parallel: Dr. Holly LaVoie, John
Cyndy Buckhaults
Clarkson, and Cyndy Buckhaults. Communications Manager
cyndy.buckhaults@uscmed.sc.edu
Thank you, again, for attending today and your support of SC INBRE!
SC INBRE Office
USC School of Medicine
6439 Garners Ferry Rd.
Bldg. 1, Rm. B53
Edie C. Goldsmith, Ph.D. Columbia, SC 29209
SC INBRE Program Director
Find and follow us on Facebook, Twitter, LinkedIn, Instagram and Pinterest. Post
and tweet today using #scinbre and/or #IamSCINBRE http://scinbre.org
2021 SC INBRE Science Symposium | 5
Underlined = presenter. Bold = mentor. BI-05 (Embargoed): FEEDING BIOLOGY OF GASTROTRICHA:
RELATING PHARYNGEAL STRUCTURE TO DIET, Mikhail Anfinson1,
Rick Hochberg2, Julian P.S. Smith III1, 1Winthrop University,
2
University of Massachusetts
BI-06 (page 18): THE EFFECTS OF DIETARY IRON ON THE
FUNCTIONAL COMPOSITION OF THE GUT MICROBIOME IN
BE-01 (page 10): ENGRAFTMENT OF HEPATOCYTES GENE EDITED ZEBRAFISH, Danio rerio, Kobie Kirven, Marharyta Petukh, Stuart
EX VIVO FOR THE TREATMENT OF INHERITED METABOLIC LIVER Gordon, Presbyterian College
DISEASE, Ilayda Ates, Tanner Rathbone, Renee Cottle, Clemson
BI-07 (page 18): CANCER STEM CELL-SPECIFIC DNA METHYLATION
BE-02 (page 10): INTERPRETING MYOELECTRIC SIGNALS VIA CHANGES CORRESPOND WITH WORSE CLINICAL PROGNOSIS IN
MACHINE LEARING ALGORITHMS, Marigordon R. Varner1, Preston BREAST CANCER, Paris L. Rizzo, Austin Y. Shull, Presbyterian
K. Robinette2, Eli T. Owens1, Presbyterian College, 2Vanderbilt
BI-08 (page 19): ESTABLISH AN IN-SILICO APTAMER SELECTION FOR
BE-03 (page 11): N‑TERMINAL DERIVATIZATION-ASSISTED EFFICIENT IDENTIFICATION OF APATAMERS FOR HUMAN CORONA
IDENTIFICATION OF INDIVIDUAL AMINO ACIDS WITH NANOPORE, VIRUS FAMILY SPIKE PROTEINS TO DEVELOP A TIME EFFECTIVE
Xiaojun Wei, Leon Y. Wang, Qian Wang, Chang Liu, UofSC DETECTION TOOL, Na’Kia Hannah1, Ja’Niya Sheppard1, Lanaih
Thomas1, Mauri Hilbourn2, Tianna Kidd2, Ankita Menon2, Sachin
BE-04 (page 12): ADVANCING LOW COST, ALL-FOCUS, 3D IMAGING Rustgi3, Prasanna V. Shekar4, Habibunnisa Begum5, 1Marion High
TECHNOLOGIES, USING SHAPE-FROM-FOCUS TECHNIQUES, Joe School, 2SC Governor’s School for Science and Math, 3Clemson
Carson1,2, Stanley McAfee2,1, Kevin Gainey2,1 and Yu-Tsueng Liu3,2, University & Adjunct, Washington State U, 4Marlboro County
1
College of Charleston, 2Pensievision Inc, 3UC San Diego School, Intern at Clemson University, 5Marion High School
BE-05 (page 13): A PRELIMINARY INVESTIGATION IN THE BI-09 (page 19): VIRTUAL MOUSE USING SMARTWATCH, Alaleh
Torkjazi, Homayoun Valafar, UofSC
MOLECULAR BASIS OF HOST SHUTOFF MECHANISM IN SEVERE
ACUTE RESPIRATORY SYNDROME-CORONAVIRUS, Niharika BI-10 (page 20): GENOMIC VARIATION IN CAPTIVE DEER
Pandala1, Casey A. Cole1, Devaun McFarland1, Anita Nag2 , MOUSE (PEROMYSCUS MANICULATUS) POPULATIONS,
Homayoun Valafar1, 1UofSC, 2USC Upstate Matthew D. Lucius, H. Ji, D. Altomare, R. Doran, B. Torkian, A.
Havighorst, Vimala Kaza, Alex Gasparian, Michael Shtutman,
BE-06 (page 13): CHEMICAL PROPERTIES ASSOCIATED WITH Hippokratis Kiaris, UofSC
WHISKER GROWTH PHENOMENON, Reid Haigler, Chad Rodekohr,
Presbyterian College
BE-07 (page 14): A COMPUTATIONAL STUDY OF THE BINDING OF
SARS-CoV-2 Nsp1 TO HUMAN RIBOSOME SUBUNIT, Linkel Boateng, CB-01 (Embargoed): THE IMPACT OF MUTATIONS ON THE
Homayoun Valafar, UofSC FUNCTIONS OF NONSTRUCTURAL PROTEIN 1 OF SARS
CORONAVIRUS, Yevgeniy Gerassimovich1, Samantha Joseph
BE-08 (page 14): COMPARISON OF NON-VIRAL DELIVERY OF Miladinovski-Bengall1, Homayoun Valafar2, Anita Nag1, 1USC
CAS9 REAGENTS INTO HEPATOCYTES FOR THERAPEUTIC GENE Upstate, 2UofSC
EDITING, Tanner Rathbone, Ilayda Ates, Callie Stuary, Renee Cottle,
Clemson University CB-02 (page 20): DEVELOPMENT OF FIRST AND SECOND GENERATION
XEROGEL-BASED AMPEROMETRIC BIOSENSORS FOR THE DETECTION
BE-09 (page 15): THE EFFECTS OF BUFFER COMPOSITION ON THE OF FREE CHOLESTEROL, Abigail Jolley, Tradezha Apkins, William
VIABILITY AND EFFICIENCY OF ELECTROPORATION ON HUH7 CELLS, Case, Converse College
Will Betsill, Tanner Rathbone, Scott Lynn, Renee Cottle, Clemson
CB-03 (page 21): SYNTHESIS OF A 1,3-OXAZOLE PHIDIANIDINE
ANALOG, James D. Heldmann, Brooke Dunnery, Bryan Wakefield,
Coastal Carolina University
CB-04 (page 21): INITIAL INVESTINGATION OF WILDFLOWER HONEY
BI-01 (page 16): INVESTIGATION OF THE CHROMATIN USING HEADSPACE SOLID-PHASE MICROEXTRACTION COUPLED WITH
ARCHITECTURE AT STAT5 TARGET GENE LOCI IN LYMPHOCYTES, GAS CHROMATOGRAPHY-MASS SPECTROMETRY FOR GEOGRAPHICAL
Charles W. Hudson, Rorie M. Vander Ploeg, Haegen L. Nelson, INFORMATION, Tyra Countiss, Drew Budner, Coastal Carolina Univ
Elias M. Wheibe, Jason S. Rawlings, Furman University
CB-05 (page 22): SYNTHESIS OF A PHIDIANIDINE ANALOGUE
BI-02 (page 17): EMPIRICAL MODE DECOMPOSITION OF LONG- CONTAINING A 2,4-DISUBSTITUTED OXAZOLE RING IN PLACE OF A
TERM PHYSIOLOGICAL DATA, Germaine Cornelissen1, Grace 1,2,4-OXADIAZOLE RING, Brooke Dunnery, James Heldmann, Bryan
Wanliss2, James Wanliss2,1U of Minnesota, 2Presbyterian College Wakefield, Coastal Carolina University
BI-03 (Embargoed): INVESTIGATION OF HOMOLOGOUS METALLO- CB-06 (Embargoed): INTRODUCTION OF BENZONITRILES INTO
BETA-LACTAMASE PROTEINS WITH BIOINFORMATICS TOOLS, Dana PROTEINS AND MEMBRANES BY NUCLEOPHILIC AROMATIC
Mae Salvador, Abigail Reeves, Jennifer Fox, Marcello Forconi, SUBSTITUTION: A COMPUTATIONAL STUDY, Kimberly Sok, Michael
College of Charleston Giuliano, Marcello Forconi, College of Charleston
BI-04 (page 17): COMPARATIVE ANALYSIS OF FUNCTIONAL CB-07 (page 22): SYNTHESIZING THE ARM COMPONENT OF A
ACTIVITY OF STEROL-SENSING DOMAIN IN NIEMANN-PICK C1 MOLECULAR TORSIONAL BALANCE FOR MEASURING LONDON
AND NIEMANN-PICK C1-LIKE PROTEIN, Noah Burkett, Marharyta DISPERSION FORCES, Kimberly Leone1, Sharon Strickland1, Alex
Petukh, Presbyterian College Manzewitsch2 and Ken Shimizu2, 1Converse College, 2UofSC
6 | 2021 SC INBRE Science Symposium
CB-08 (Embargoed): CARBON-CARBON COUPLING BETWEEN MCB-07 (page 32): CLONING AND TESTING THE EFFECTS OF
BENZYLBORONIC ESTERS AND ALKYL BROMIDES, Richard W. Russell A SHORT INTERFERING RNA ON THE HIV TRANSACTIVATOR OF
and Timothy J. Barker, College of Charleston TRANSCRIPTION, Q’May Qourters and William H. Jackson, UofSC
Aiken
CB-09 (page 23): SYNTHESIS OF PHIDIANIDINE ANALOGUE THAT
REPLACE THE 1,2,4-OXADIAZOLE RING WITH A BENZENE, Dustin MCB-08 (Embargoed): IMPACT OF TIMP4 GENE DELETION ON
Lowe, Kwesi Jackson, Bryan Wakefield, Coastal Carolina CARDIAC FUNCTION IN PREGNANT AND LACTATING MICE, Allison
Egeli1, Brittney Gentile2, Ashley Thurstin2, Holly LaVoie2, 1UofSC,
CB-10 (page 24): XANTHINE DETECTION USING FIRST GENERATION 2
UofSC School of Medicine
AMPEROMETRIC BIOSENSORS FOR FOOD QUALITY ASSURANCE
AND CLINICAL USE, Tradezha Apkins, Abigail Jolley, William Case, MCB-09 (page 33): ANALYZING THE FUNCTION OF A HIV-
Converse College DEPENDENT EXPRESSION SYSTEM, Madison Carelock and William
H. Jackson, UofSC Aiken
CB-11 (page 24): EXAMINATION OF STEREOCHEMISTRY IN THE
COPPER-CATALYZED BENZYLATION OF EPOXIDES, Sophia G. MCB-10 (page 34): INVESTIGATING THE ROLE OF ZINC FINGER
Gierszal, Timothy J. Barker, College of Charleston PROTEIN, ZF30C IN EPIGENETIC REPRESSION OF DROSOPHILA
ENGRAILED GENE, Jessica Escobar and Payal Ray, Presbyterian
CB-12 (Embargoed): KEMP ELIMINATION IN HEME SYSTEMS,
College
Elizabeth Smolenski, Marcello Forconi, College of Charleston
MCB-11 (Embargoed): EFFECTS OF ANTIOXIDANTS ON
CB-13 (page 25): ORGANIC VS. INORGANIC FOODS, Shanari
FLUCONAZOLE RESISTANCE IN Cryptococcus neoformans, Amari Hill
Buckner1, Luke Alsup1, Justin Dewees2, Azima Kalsum3, 1Calhoun
and Srikripa Chandrasekaran, Furman University
County High School, 2Summerville High School, 3Claflin University
MCB-12 (page 34): PRODUCTION OF ANTIBIOTICS BY SOIL BACTERIA,
CB-14 (page 26): CONFORMATIONAL ANALYSIS OF AGONISTS TO
Rebecca Kigwana1, Elon Tullock2, Randall Harris3, 1New Century
THE µ OPIOID RECEPTOR, Lauren Jones1, Togo Odbadrakh1, Brenna
Outten1, Noah Garrison2, Amy Deveau2, George Shields1, 1Furman Technology High School, 2Calhoun County High School, 3Claflin U
University, 2University of New England MCB-13 (page 35): BIOINFORMATICS-INFORMED
CB-15 (page 26): CONFORMATIONAL ANALYSIS OF ANTAGONISTS CHARACTERIZATION OF PDR5 DRUG PUMP INDUCTION BY THE
AT THE µ OPIOID RECEPTOR, Brenna Outten1, Togo Odbadrakh1, ANTICANCER RUTHENIUM COMPLEX KP1019 IN YEAST, Ben Meyer1,
Lauren Jones1, Noah Garrison2, Amy Deveau2, George Shields1, Christopher Groark2, Pamela Hanson1, 1Furman University,
1
Furman University, 2University of New England
2
Birmingham-Southern College
CB-16 (page 27): SYNTHESIS OF STIMULI-RESPONSIVE, MCB-14 (page 36): A METABOLIC ARRAY SHOWING BASAL-LIKE
PROGRAMMABLE POLYMERS THROUGH RING-OPENING BREAST CANCER CELLS’ ABILITY TO DIFFERENTIALLY METABOLIZE
METATHESIS – CROSS-METATHESIS, Courtney Dziewior1, Sharon SUGAR ALCOHOLS, Layne M. Benson, Paris L. Rizzo, and Austin Y.
Strickland1, Ping Li2, Ken Shimizu2, 1Converse College, 2UofSC Shull, Presbyterian College
CB-17 (page 28): AN INTEGRATED EXPERIMENTAL AND MCB-15 (page 36): DOES EXPOSURE TO SUBLETHAL
COMPUTATIONAL APPROACH TO SIMULATE PROTEIN ADSORPTION CONCENTRATIONS OF GLYPHOSATE, 2,4-D, AND THEIR COMBINED
AT THE BIOTIC/ABIOTIC INTERFACE, Omotola Shode, Makayla F. FORMULATION INDUCE OXIDATIVE STRESS IN EISENIA FETIDA?, Mary
Turner, Derrick Swinton, Claflin University Davidson, Phylicia Allen, Edna Steele, Converse College
CB-18 (page 27): CRYSTAL GROWTH USING HYDROTHERMAL AND MCB-16 (Embargoed): CADHERIN COMPLEXES RECRUIT
EVAPORATION SYNTHESIS, Marlee Cleckley1, Kennedi Graham2 and PIWIL2 TO SUPPRESS TRANSPOSONS AND PRO-TUMORIGENIC
Jie Ling3, 1David W. Butler High School, 2High School for Health TRANSORMATION, Alyssa Risner, Joyce Nair-Menon, Colin
Professions, 3Claflin University McDowell, Vamsi Gangaraju, Antonis Kourtidis, Medical University
of South Carolina
MCB-17 (page 37): CRISPR-CAS9 MEDIATED KNOCKDOWN OF
INTERFERON INDUCED PROTEIN 35 (IFI35) IN A HUMAN LUNG EPITHELIAL
CELL LINE FOR INVESTIGATION OF THE RESPIRATORY ANTIVIRAL RESPONSE,
Adam Okinaga1, Katie McCoy2, and Jennifer T. Grier, 1UofSC,
MCB-01 (page 29): DESIGN, CLONING, AND TESTING OF AN 2
Wofford College, 3UofSC School of Medicine, Greenville
ANTI-HIV REV SIRNA, R. Kylie Tager and William H. Jackson,
UofSC Aiken MCB-18 (page 38): INVESTIGATING CYTOTOXICITY AND
DEFENSE FUNCTIONS OF BACTERIOPHAGE LARVA GENES IN HOST
MCB-02 (page 29): CREATING A HIV-DEPENDENT TBID EXPRESSION MYCOBACTERIUM SMEGMATIS, Dallas K. Nivens, Laela A. Walker,
PLASMID, Nina Adams and William H. Jackson, Uof SC Aiken Victoria J. Frost, Winthrop University
MCB-03 (page 30): DOES THE NUCLEAR EXPORT SIGNAL AFFECT MCB-19 (page 38): THE ROLE OF GALECTIN-3 AND LAMININ IN
HARBINGER TRANSPOSITION IN HUMAN CELLS?, Dania Hailat, TAMOXIFEN INDUCED GROWTH SUPPRESSION OF MCF-7 HUMAN
Priscilla Redd, C. Nathan Hancock, UofSC Aiken BREAST CANCER CELLS, Shakira Flemming, Anuli Segree, Ayoub
Zouaoui, Jerrika Scott, William McAmis, Samir Raychoudhury,
MCB-04 (page 30): THE PREVALENCE OF STREPTOCOCCUS Benedict College
PYOGENES, STAPHYLOCOCCUS AUREUS, AND METHICILLIN-
RESISTANT STAPHYLOCOCCUS AUREUS IN HIGH TRAFFIC AREAS, MCB-20 (page 39): CELL FATE MAPPING OF VASCULAR SMOOTH
Carlie Fusco and Jennifer K. Lyles, Francis Marion MUSCLE CELLS IN MEDIAL ARTERIAL CALCIFICATION, Mengistu
Gebere1, Nazli Gharraee1, John Johnson1, Naren Vyavahare2, Susan
MCB-05 (page 31): EXAMINING THE ROLE OF ADIPOCYTE AMINO Lessner1, Mohamad Azhar1, 1UofSC School of Medicine Columbia,
ACID SENSING CONTROL OF OVARIAN FUNCTION, Subhshri Sahu 2
Clemson University
and Alissa Richmond Armstrong, UofSC
MCB-21 (Embargoed): UNDERSTANDING THE ROLES OF HDAC1
MCB-06 (page 32): MODELING INFLAMMATORY BOWEL DISEASE AND HDAC4 IN ZEBRAFISH CRANIOFACIAL DEVELOPMENT, April
USING P-GLYCOPROTEIN DEFICIENT CAENORHABDITIS ELEGANS, DeLaurier, Alec Jones, Terence Willoner, Maureen Kamanga, Lacie
Brittany Salciccioli and Scott Tanner, UofSC Upstate Mishoe Hernandez, Uof SC Aiken
2021 SC INBRE Science Symposium | 7
MCB-22 (page 39): THE EFFECTIVENESS OF VARIOUS BLEACH PH-05 (page 47): MEDICATION ADHERENCE MONITORING USING
CONCENTRATIONS ON THE GROWTH OF ACINETOBACTER NEURAL NETWORKS ON SMARTWATCH ACCELEROMETER
BAYLYI AND PSEUDOMONA PUTIDA, Braxton Hill1 and Keyana SENSOR DATA, Chrisogonas Odhiambo, Pamela Wright, Cindy
Tyree2, 1Heathwood Hall Episcopal School, 2Claflin University Corbett, Homayoun Valafar, UofSC
MCB-23 (page 40): DEVELOPMENT OF MULTIPLEX PCR PRIMERS PH-06 (page 48): BUILD TRUST, BUILD HEALTH | FOMENTAR
FOR THE DETECTIONS OF M. INCOGNITA, H. GLYCINES, and R. LA CONFIANZA, FOMENTAR LA SALUD – A COMMUNITY-BASED
RENIFORMIS IN SOIL METAGENOMIC POOL, Ny’Kera Hall, Alyia PARTICIPATORY RESEARCH APPROACH TO COMBATTING CHILDHOOD
Bryant, C. Taylor Bright, Abreeota Williams, Converse College OBESITY IN THE HISPANIC COMMUNITY, Rachel Knight, Gabrielle
Maiolo, Gina Kim, Shaniece Criss, Furman University
MCB-24 (page 41): INHIBITION OF DEAD-BOX RNA HELICASE 3
ATTENUATES STRESS GRANULE ASSEMBLY, B. Celia Cui, Vitali
Sikirzhytski, Marina Aksenova, Matthew D. Lucius, Gabrielle H.
Levon, Zachary T. Mack, Charlotte Pollack, Diana Odhiambo,
Eugenia Broude, Sofia B. Lizarraga, Michael D. Wyatt, Michael
Shtutman, UofSC RET-01 (page 50): DYNAMIC NETWORK ACTIVATION OF HYPOTHA‑
LAMIC MCH NEURONS IN REM SLEEP AND EXPLORATORY BEHAVIOR,
MCB-25 (page 41): THE EFFECT OF COMMERCIAL CORDYCEPS
Monica Yvette Hughey1, Carlos Blanco-Centurion3, Priyattam J.
SINENSIS AND CORDYCEPS MILITARIS ON OXIDATIVE STRESS
Shiromani3 and Sorinel A. Oprisan2, 1Greer Middle School, 2College
ENZYMES IN RAT LIVER, Yuting Wang, Weijin Ding, Wenxin He,
of Charleston, 3 Medical University of South Carolina
Jingfei Li, Shurui Tao, H. Neval Erturk, Converse College
RET-02 (page 51): NEURAL NETWORK RESOURCE ALLOCATION
DURING INTERVAL TIMING TASKS, Michael Eric Bailey1, Mona
Buhusi3 and Catalan Buhusi3, Sorinel A. Oprisan2, 1Greenville High
School, 2College of Charleston, 3Utah State University
NEU-01 (page 42): ESTROGEN SIGNALING AND SYNAPTIC RET-03 (page 51): SOUNSCAPES: APPLICATIONS OF SOUND ACROSS
REORGANIZATION AROUND MOTONEURONS AFTER PERIPHERAL THE CURRICULUM, Amber Birden1, Bianca Bryant2, Kayce Looper3,
NERVE INJURY, Shynese Wilson, Vernon Kennedy, Jr., Jennifer Paul Johnson4, Nathan Harness5, John Quinn6 , 1C.C. Pinckney
Wilhelm, College of Charleston Elementary School, 2Swansea High School, 3Eastside High School,
4
Saluda High School, 5Francis Marion Univ, 6Furman Univ
NEU-02 (Embargoed): BLOCKING THE ACQUISITION OF POST
TRAUMATIC STRESS DISORDER USING DOPAMINE D3 ANTAGONISTS, RET-04 (page 52): BIODIVERSITY OF MICROINVERTEBRATES IN
Elizabeth Nethercoat, Ashley Snyder, and Onarae Rice, Furman RIVER SOIL AS BASED ON PROXIMITY TO RIVER, Melissa Dissinger2
and Julian Smith III1, 1Winthrop Univ, 2Spring Valley High School
NEU-03 (page 42): NETWORK-BASED STATISTICAL ANALYSIS OF
FUNCTIONAL MAGNETIC RESONANCE IMAGING DATA IN POST- RET-05 (page 53): BIODIVERSITY OF SOIL FAUNA IN RESPONSE
STROKE APHASIA, Xingpei Zhao, Yuan Wang, Alexander C McLain, TO WEED TREATMENT, Jill Kelsey1 and Julian Smith III2, 1Wade
Roozbeh Behroozmand, Chris Rorden, Julius Fridriksson, UofSC Hampton High School, 2Winthrop University
NEU-04 (page 43): INFERING HYPOTHALAMIC NETWORK ACTIVITY
FROM CALCIUM IMAGING DATA DURING REM SLEEP, Xandre
Clementsmith1, Carlos Blanco-Centurion2, Priyattam J. Shiromani2
and Sorinel A Oprisan3, 1College of Charleston, 2Medical University
of South Carolina, 3College of Charleston
(page 57) REDIRECTION OF HER2-POSITIVE BREAST CANCER CELLS
NEU-05 (page 44): HEAT SHOCK PROTEIN 90 INHIBITION REDUCES RESULTS IN PHENOTYPIC AND GENOTYPIC CHANGES, Anastasia
MORPHINE TOLERANCE, Victoria Miles1, Amanda Smith1, Yapei Frank-Kamenetskii1, Julia Mook2, Meredith Reeves1, Corinne
Huang2, Ryan McCall1, John Streicher2, Wei Lei1, 1Presbyterian A. Boulanger3, Thomas J. Meyer4,5, Lauren Ragle3, H. Caroline
College School of Pharmacy, 2U of Arizona College of Medicine Jordan1, Gilbert H. Smith3, Brian W. Booth1, 1Clemson University,
2
Clemson University, 3National Cancer Institute, 4National Cancer
Institute, 5Frederick National Laboratory for Cancer Research
(page 57) EFFECTS OF ENVIRONMENT ON ANTI-FUNGAL DRUG
RESISTANCE IN Cryptococcus neoformans, Srikripa Chandrasekaran,
Furman University
PH-01 (page 44): MATHEMATICAL MODELS FOR COVID-19, Ernest
James, V and Mei Chen, The Citadel (page 58) TOWARDS THERANOSTIC TECHNOLOGY: ELUCIDATION
AND UTILIZATION OF NEURAL ENZYME UPREGULATION, Sarah Smith,
PH-02 (page 45): APPLICATION OF MACHINE LEARNING IN EARLY Chloe Champion, and Jessica Larsen, Clemson University
RECOMMENDATION OF CARDIAC RESYNCHRONIZATION THERAPY (Embargoed) ULTRASENSITIVE DETECTION OF HIV-1 P24 IN HUMAN
TO HEART FAILURE PATIENTS, Brendan Odigwe1, Frank Spinale2, SERUM SAMPLES BY A CLICK CHEMISTRY AMPLIFICATION-COUPLED
Alaleh Torkjazi1, Celestine Odigwe3, Homayoun Valafar1, 1UofSC, NANOPORE STRATEGY, Xiaojun Wei1,2, Helmut Albrecht3,4, and
2
UofSC School of Medicine, 3Thomas Hospital, Fairhope, AL Chang Liu1,2, 1UofSC, 2UofSC, 3UofSC, 4Palmetto Health USC
Medical Group
PH-03 (page 45): STATE TRANSITION MODELING OF THE SMOKING
BEHAVIOR USING LONG SHORT-TERM MEMORY RECURRENT NEURAL (page 59) AN EPIGENETIC PREDISPOSITION TOWARD INFLAMMATION
NETWORKS, Chrisogonas Odhiambo and Homayoun Valafar, IN BREAST CANCER STEM CELLS, Austin Y. Shull, Presbyterian
UofSC
(Embargoed) DEVELOPING A NEW INVERTEBRATE MODEL OF
PH-04 (page 46): THE EFFECTS OF PRESENTATION SCHEDULE OF ALCOHOLISM, Christopher Varnon, Converse College
SACCHARINE ON WEIGHT GAIN IN RATS, Maria Martinez1, Ilan Falcon2,
Richard Keen1, 1Converse College, 2Spartanburg High School
8 | 2021 SC INBRE Science Symposium
(Embargoed) MUTATIONAL SIGNATURES FOLLOWING THIOPURINE
TREATMENT IN HOMOLOGOUS RECOMBINATION DEFECTIVE CELLS,
Manli Yang, Michael D. Wyatt, Michael Shtutman, Diego Altomare,
(Embargoed) DEVELOPMENT OF MODELS FOR STUDY OF HOST- Hao “Emily” Ji, and Douglas L. Pittman, UofSC
PATHOGEN INTERACTIONS DURING HUMAN ACINETOBACTER
BAUMANNII INFECTION VIA NOVEL DUAL RNA-SEQUENCING (Embargoed) BIOINFORMATIC ANALYSIS IDENTIFIES PROTEOMIC
TECHNOLOGY, Lauren A. Bracken1, Elizabeth Hogue1, Steven E. PREDICTORS OF HIGH-DENSITY LIPOPROTEIN CHOLESTEROL
Fiester2,3, Jennifer T. Grier2, 1Furman University, 2UofSC School of RESPONSE TO REGULAR EXERCISE, Jacob L. Barber1, Guoshuai
Medicine Greenville, 3Prisma Health Cai2, Jeremy M. Robbins3,4, Prashant Rao3, Robert E. Gerszten3,4,
Claude Bouchard5, Mark A. Sarzynski1, 1UofSC, 2UofSC, 3Beth
(page 59) GENOMIC ANALYSIS OF AN RNA SILENCING MUTANT, C. Israel Deaconess Medical Center, 4Beth Israel Deaconess Medical
Nathan Hancock, UofSC Aiken Center, 5Pennington Biomedical Research Center
COVID-19 has changed the way we live our entire lives – students since many professional meetings moved online.
from wearing masks and social distancing in public places, ... our students will be well prepared after giving a virtual
to the way classes and research are conducted. A typical oral and poster presentations. If and when it is safe to meet
summer for SC INBRE’s network institutions consists of in person, I think we might still continue with this style at
students in labs located throughout South Carolina, at the least for some presentations. The online platform allows
bench, at the computer, gathering together for presentations students to give their presentations from their lab and show
and career development, etc. With COVID restrictions, our us their specimens, equipment, methods in real-time and
agile investigators found new ways to keep the research space. For example, two students who conduct research
running. Below are highlights from some of our institutions. with cockroaches were able to show us how they handle
them without causing discomfort to those who have
BENEDICT COLLEGE conducted online katsaridaphobia. Online meetings helped us to create a
research with over 45 students and 13 faculty sense of summer research community which would not
participating in their eight-week Benedict have been possible if we did not conduct any meetings.”
College Summer Undergraduate Institute.
Students participated in faculty-driven Dr. Jeremy Rentsch from FRANCIS MARION
group meeting four days (Monday through UNIVERSITY worked with two students
Thursday), with a Friday research presentation from the this summer. They did a journal club and
students. They also collaborated by routine use of Google developed other methods so that “we can
Drive to share documents, data, and slides. sprint in the fall when we are able to to be
back together.” Journal club was flexible –
Said Dr. Samir Raychoudhury, SC INBRE Institutional PI, allowing the students to upload their journal entries to
“I consider that our undergraduates are future graduate Dropbox. They Zoomed if they had any questions.
students, scientists, or faculty. They must learn the
background of any methods, techniques, or processes, Says Rentsch, “It has actually been quite nice, if not a bit
including RCR. Meeting online only is challenging without unusual. It was a bit of a happy accident, but I think having
the hands-on lab work, however, I found it an excellent my students upload journal entities for the papers they read
platform for undergraduates in understanding and is enlightening. I think my students are spending more time
designing research. From our ongoing project, we discuss truly working to understand the articles they are reading. In
the data, statistics, and presentation tools. ... We have the fall, we'll do face-to-face journal club, but couple it with
learned together.” physical writing journals.”
This summer, CONVERSE COLLEGE did Twelve students and nine faculty worked this
virtual research and met online every Monday, summer at FURMAN UNIVERSITY – eight of
meetings which included presentations the 12 students were funded through Furman’s
followed by a Q&A session. The last day of SC INBRE institutional award and four
presentations on July 27 had virtual poster students through SC INBRE Developmental
presentations for all research groups. A Research Project Program funding. All of the
typical meeting attendance was seven faculty and 21 research this summer was online. Faculty stayed in contact
students (two high schoolers, 19 college). regularly through Zoom.
Said Dr. Neval Erturk, SC INBRE Institutional PI, “We have Said Dr. John Kaup, “Things are going well this summer.
excellent participation from students and faculty during There has been a surge in grant
the Q&A section. More than we had during face to face proposals submitted, as well as an continued on
meetings. I think this is a very valuable experience for our increase in manuscript preparation and page 28
2021 SC INBRE Science Symposium | 9
BE-01 BE-02
ENGRAFTMENT OF HEPATOCYTES INTERPRETING
GENE EDITED EX VIVO FOR THE MYOELECTRIC SIGNALS
TREATMENT OF INHERITED VIA MACHINE LEARING
METABOLIC LIVER DISEASE ALGORITHMS
Ilayda Ates, Tanner Rathbone, and Renee Cottle Marigordon R. Varner1, Preston K. Robinette2, and
Department of Bioengineering, Clemson University, Clemson, SC Eli T. Owens1
1
Department of Physics, Presbyterian College,
introduction/background. Inherited metabolic diseases Clinton, SC, 2Department of Computer Science,
(IMDs) of the liver occur once in 800 live births and are typically Vanderbilt University, Nashville, TN
caused by autosomal recessive single gene mutations resulting in
organ intoxication and premature death if untreated. An example
of an IMD of the liver is hereditary tyrosinemia type I caused
introduction/background. As
technological advancements continue to be
by non-functional mutations in the gene encoding the enzyme
incorporated into the medical field, there is a
fumarylacetoacetate hydrolase (FAH). Liver transplantation
gap that is created by the quality/cost ratio
represents the only curative option, however, the limitations
including severe organ shortages, the life-long requirement for associated with using technologically advanced
immunosuppressant drugs and high risk of mortality, highlight medical solutions. Prosthetics are no different, in
the urgent need for novel therapies. A novel therapeutic approach the sense that many low-cost and open source
consists of ex vivo gene editing using CRISPR-Cas9 nucleases to prosthetics often sacrifice much of the natural
disrupt the gene encoding 4-hydroxyphenylpyruvate dioxygenase mobility that a more expensive prosthetic
(Hpd), an enzyme upstream in the metabolic pathway, in could provide.
hepatocytes isolated from the patient’s resected liver. The gene
edited hepatocytes would be subsequently transplanted into the hypothesis/goal of study. The primary
liver to correct the disease phenotype. Although a promising tool goal of this project is to bridge the gap by
for treating IMDs of the liver, the major challenge of CRISPR-Cas9 developing upper prosthetics that are both
is its delivery into target cells. The standard delivery method for low-cost and provide a natural control
CRISPR-Cas9 reagents is adeno-associated virus vectors that are functionality for the user. Our approach uses
associated with severe safety and efficacy concerns having the an open source 3D printed prosthetic hand
potential to hamper the advancement of gene editing therapies to combined with electronics of our own design to
the clinic. measure and interpret the myoelectric signals
generated by the user. These myoelectric signals
hypothesis/goal of study. The overall objective of this are used to control the prosthetic giving the user
project is to optimize the engraftment of hepatocytes in the liver intuitive operation.
following ex vivo gene editing in a Fah-deficient mouse model of
hereditary tyrosinemia type I. methods and results. As we studied
the myoelectric signals, we observed that flicker
methods and results. In preliminary studies, we optimized noise (1/f noise) was dominating the myoelectric
the delivery of CRISPR-Cas9 nucleases targeting hpd and
signals. However, this noise is easily removed in
observed up to 70% on-target activity in primary hepatocytes.
Fourier space leaving a cleaner data set from
Here, we determine the extent that wild type hepatocytes
which we extract machine learning features. Once
nucleofected ex vivo using our Hpd-aiming CRISPR-Cas9 engraft
in the liver in Fah-/- mouse model. In ongoing studies, we will the noise is removed, several machine learning
examine whether CRISPR-Cas9-mediated disruption of the Hpd in algorithms were investigated, and it was found
donor hepatocytes from a disease mouse protects Fah-/- recipient that the decision tree algorithm had the highest
mice from liver failure. Moreover, we will quantify CRISPR-Cas9 predictive power.
on- and off-target activity and determine the persistence of
genetic alterations in hepatocytes after proliferation in vivo. conclusions. By working to create a
lightweight and reliable system for our 3D printed
conclusions. To our knowledge, this study is the first to prosthetic, we move towards the creation of a
evaluate the feasibility of nucleofection mediated delivery of gene- low-cost but high functioning upper prosthetic
editing tools into hepatocytes as part of a therapeutic strategy for that will enable many children and other
inherited metabolic liver disease. amputees to live a life of confidence and mobility.
10 | 2021 SC INBRE Science SymposiumBall photos credit to Presbyterian College
When Preston Robinette was not on the soccer field
as #4 midfielder for the PC Blue Hose women's soccer
team, you could find her in Dr. Eli Owens’ research lab.
Owens is working on a NASA-funded project involving
a prosthetic hand and 3D printer. Robinette, with Owens
and other students, are developing an affordable
3D-printed myoelectric prosthetic hand that will respond
to the voltage difference across the muscles of the arm.
Robinette received a NASA Undergraduate Student
Research Fellowship (USRF) award which gave funding
towards her research project from August 15, 2019 to
May 15, 2020.
BE-03
N‑TERMINAL DERIVATIZATION-ASSISTED IDENTIFICATION OF
INDIVIDUAL AMINO ACIDS WITH NANOPORE
Xiaojun Wei1, Leon Y. Wang2, Qian Wang2, and Chang Liu1
Biomedical Engineering Program, Department of Chemical Engineering, University of South
1
Carolina, Columbia, SC; 2Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC
introduction/background. Nanopore technology has been employed as a powerful tool for DNA sequencing and
analysis. To extend this method to protein and peptide sequencing, a necessary step is to profile individual amino acids
through their nanopore stochastic signals, which remains a great challenge because of the subtle molecular differences
among all twenty amino acids along with their low signal-tonoise ratio and unpredictable conformational changes of amino
acids during their translocation through nanopores.
hypothesis/goal of study. TWe hypothesize that the combination of an N-terminal derivatization strategy of
amino acids with nanopore technology could lead to effective in situ differentiation of amino acids. Aims to develop an
effective derivatization strategy for the identification of single amino acids through α-hemolysin nanopore.
methods and results. Four series of amino acid derivatives were assessed for their translocation behaviors in
α-hemolysin nanopores, including PITC-derivatives, OPA-derivatives, NITC-derivatives, and NDA-derivatives of five
different amino acids (Ala, Phe, Tyr, His, and Asp) with various polarity, charge, and size, representing different classes
of 20 amino acids. Results showed that NITC-derivatization of five typical amino acids afforded significantly enhanced
distinguishability between their translocation signals.Indicating that using derivatized amino acids as detection surrogates
not only prolongs their interactions with the sensing region, but also improves their conformational variation. Furthermore,
we showed that distinct characteristics including current blockades and dwell times can also be observed among all three
classes ( polar, charged, and non-polar) of amino acids after NDA- and NITC-derivatization, respectively. These observable
characteristics were further applied towards the identification and differentiation of 9 of the 20 natural amino acids using
their NITC derivatives. Making this strategy a promising way for the identification of all amino acids and further protein and
peptide sequencing.
conclusions. BWe demonstrated that N-terminus derivatization is an effective way to differentiate individual
amion acidss using α-Hemolysion nanopore technology. Among four derivatization reagents applied in our work, NITC-
derivatization of five typical amino acids afforded significantly enhanced distinguishability based on the translocation
signals. Furthermore, 3 groups (a total of 9) of similar amino acids can also be effectively identified with improved
discriminatory power by NITC derivatization, making this derivatization method an efficient candidate method for identifying
all 20 amino acids. While we are working on derivatization of more other amino acids and optimizing the strategy, more
advanced data analysis technology is in urgent need to improve resolution through novel characteristics. Finally, further
simulation work is undergoing to better model the conformational changes of each derivative inside the nanopore and to
understand the complexity of the interactions between each amino acid derivative and the lumen of the α-Hemolysin protein.
2021 SC INBRE Science Symposium | 11BE-04
ADVANCING LOW COST, ALL-FOCUS, 3D IMAGING
TECHNOLOGIES, USING SHAPE-FROM-FOCUS TECHNIQUES
Joe Carson1,2, Stanley McAfee2,1, Kevin Gainey2,1 and Yu-Tsueng Liu3,2
1
Department of Physics & Astronomy, College of Charleston, Charleston, SC, 2Pensievision Inc, Charleston, SC, 3School of
Health Sciences, University of California San Diego, San Diego, CA
introduction/background. Three dimensional imaging has become an industry standard for the diagnosis and
clinical management of potentially dangerous tumors. However, the high cost of procuring such instrumentation (i.e. MRI,
3D Ultrasound, etcetera), and the infrastructure needed to safely host and operate them, severely limit their utility. While
alternative, multi-perspective (stereoscopic) imaging can generate 3D images at lower costs, their use is impractical in
confined spaces such as inside the human body. ‘Shape-from-focus’ imaging however offers a solution for generating high-
resolution 3D images at low cost, and in confined spaces typically explored by fiber optic 2D imagers. But while the benefits
are clear, its utility has been limited by the associated large fluctuations in depth accuracy for different parts of the target
surface. An opportunity exists to use calibration procedures combined with machine-learning based confidence algorithms
to improve shape-from-focus 3D imaging to a point where it is powerful and reliable enough for clinical use.
hypothesis/goal of study. We aim to implement calibration procedures combined with machine-learning based
confidence algorithms to enable shape-from-focus 3D imaging that is accurate enough for practical clinical use.
methods and results. The accompanying figure represents a 3D image of
an ex vivo cervix, generated by our homegrown shape-from-focus software applied
to standard 2D images collected with different focus settings. We are implementing
an alternative iterative procedure to replace the manual tuning of code optimizations,
which was required to generate the 3D image. To help evaluate the accuracy of our 3D
imaging technique, and to improve our depth calibration and uncertainty evaluation,
we are testing our shape-from-focus method on model tissue and lesions. To obtain
true patient data, we submitted a largescale grant proposal to the National Institutes
of Health, requesting support for a 20-patient pilot study of cervix imaging.
conclusions. Our INBRE grant activities are ongoing. Our submitted NIH proposal received a rare perfect score. The
associated 20-patient pilot study is expected to begin April 2021.
Dr. Anita Nag (shown far right, formerly
at Furman, now at USC Upstate) and
four students from Furman University
(three of which are shown in the photo),
Garret Gomez, Fareeha Abrar, Maya
Dodhia and Fabiola Gonzalez, published a
paper in Biochemistry and Cell Biology in
December 2019. Research for this paper,
SARS Coronavirus Protein nsp1 Disrupts
Localization of Nup93 From the Nuclear
Pore Complex (https://pubmed.ncbi.nlm.
I9 nih.gov/30943371/), was funded by Anita’s
SC INBRE Bioinformatics Pilot Project
Program grant.
See recording of Anita's recent TIGERTalks
(formerly Science on Tap) at https://www.
youtube.com/watch?v=wGwzpW-AF2Y
12 | 2021 SC INBRE Science SymposiumBE-05 BE-06
A PRELIMINARY INVESTIGATION IN CHEMICAL
THE MOLECULAR BASIS OF HOST PROPERTIES
SHUTOFF MECHANISM IN SEVERE ASSOCIATED WITH
ACUTE RESPIRATORY SYNDROME- WHISKER GROWTH
CORONAVIRUS PHENOMENON
Niharika Pandala1, Casey A. Cole1, Devaun McFarland1, Reid Haigler and Chad Rodekohr
Anita Nag2 and Homayoun Valafar1 Department of Physics, Presbyterian
1
Department of Computer Science and Engineering, University of South College, Clinton, SC
Carolina, Columbia, SC, 2Division of Natural Sciences and Engineering,
USC Upstate, Spartanburg, SC introduction/background.
Tin whiskers are small single crystalline
introduction/background. Severe Acute Respiratory Syndrome filaments that spontaneously grow
(SARS) encoded nonstructural protein 1 (nsp1) causes severe translational from tin surfaces. Many circuit boards
shutoff activities leading to suppression in host gene expression. Nsp1 is use tin solder, and over time these tin
a 180 residue protein that consists of two domains. Residues 1-116 of this whiskers can grow and cause short
protein form a well-defined structure that has been previously studied by circuits resulting in equipment failure of
NMR spectroscopy. The structure of the C-terminus (residues 117-180) is
heart pacemakers and other compact
poorly characterized by traditional methods due to its dynamical properties.
circuit devices.
Laboratory-based mutation of this protein has demonstrated attenuated
activities. Therefore, the structural implication of these mutations may
hypothesis/goal of study.
provide a better understanding of this protein's activity.
This paper explores the relationship
between an element’s chemical
hypothesis/goal of study. Evaluation of two potential binding sites; properties and its ability to whisker.
residues 55-59 (Region 1) and 73-80 (Region 2) speculated to participate in
host shutoff by nsp1. The investigation is a combination of computational
methods validated by biochemistry results to find the region that potentially
methods and results. We use
the R packages “Periodic Table”and
facilitates the critical initial steps in the function of nsp1.
“tidyverse” to explore a logistic
regression model. We also employ
methods and results. Computational modeling software I-TASSER
t-tests and Chi-square tests. The goal
(Iterative Threading ASSEmbly Refinement) has been used to develop
structural models of the wildtype and various mutants of nsp1. Combined is to provide a chemical view of why
results from computed models of nsp1, with deep mining of all existing some elements whisker and others do
protein structures (using PDBMine) and binding site recognition (using not whisker.
msTALI) to examine the two regions. Further studied using VMD and NAMD
software suit; explored the structure-function relation by investigating conclusions. We do not know for
energetics. Both mutations function by distinctly different mechanisms; certain why certain elements whisker
Region 1 stabilized the protein while Region 2 destabilized it. Charge and and others do not whisker. We do
surface perturbation showed both the mutations amplify the host shutoff know that the elements that whisker
function of nsp1. Side-chain interactions in mutated nsp1 expressed are denser and more electronegative
flexibility, which is the key feature of nsp1; it is essential to note that each than elements that don’t whisker.
mutation functions differently in the presence of host factors (RNA and We also know that whiskering is only
proteins). seen in transition metals, metals,
metalloids, and alkaline earth metals.
conclusions. Based on our preliminary results, we conclude that the Furthermore, whiskering is only seen in
residues 73-80 appear as the regions that facilitate the critical initial steps the crystalline phases: body centered
in the function of nsp1. Given the 90% sequence identity between nsp1 from cubic (bcc), face centered cubic (fcc),
SARS-CoV-1 and SARS-CoV-2, we conjecture the same critical initiation step hexagonal (hex), rhombohedral (rho),
in the function of SARS-CoV-2 nsp1. and tetragonal (tet).
2021 SC INBRE Science Symposium | 13BE-07 BE-08
A COMPUTATIONAL COMPARISON OF
STUDY OF THE BINDING NON-VIRAL DELIVERY
OF SARS-CoV-2 Nsp1 TO OF CAS9 REAGENTS
HUMAN RIBOSOME SUBUNIT INTO HEPATOCYTES FOR
THERAPEUTIC GENE EDITING
Linkel Boateng and Homayoun Valafar
Department of Computer Science and Engineering, Tanner Rathbone, Ilayda Ates, Callie Stuary
University of South Carolina, Columbia, SC and Renee Cottle
Department of Bioengineering, Clemson University,
Clemson, SC
The recent worldwide COVID-19 pandemic has sparked
considerable interest in the study of SARS CoV-2 introduction/background. Inherited metabolic
nonstructural protein 1 (nsp1) and its interactions diseases (IMDs) of the liver are a group of genetic
with human ribosome unit. Most research studies disorders that are typically characterized by an enzyme
have however focused on the use of cryo-electron deficiency in a critical metabolic pathway. In the absence
microscopy to study the binding mechanisms. The use of an essential enzyme, substrates can accumulate
leading to toxicity. IMDs occur in roughly 1 in 800 births
of computational approach is vital for understanding the
and can lead to organ failure or premature death if
molecular basis of this infection rapidly. not treated. Hereditary tyrosinemia type 1 (HT1) is an
IMD where patients with HT1 have a loss-of-function
The active site of SARS CoV-2 nsp1 binds to human mutation in the gene encoding fumarylacetoacetate
ribosome subunit at the RNA entrance channel, thereby hydrolase (FAH), an enzyme that plays a role in the
blocking mRNA entry to the ribosome and inhibiting tyrosine catabolism pathway by converting toxic
host protein translation. The C-terminal and N-terminal fumarylacetoacetic acid into non-toxic metabolites.
Without treatment, patients with HT1 suffer from liver
domains of nsp1 play a critical role in the binding
toxicity and have an increased risk for developing
mechanism. The goal of the current study is to adopt
hepatocellular carcinomas (HCCs) in infancy. The only
a computational approach to evaluate the potential curative option for patients with HT1 is orthotopic liver
binding sites of SARS CoV-2 nsp1 and understand its transplantation, but it is limited by donor shortages and
molecular interactions with human ribosome. complications from life-long immunosuppressive therapy.
Therapeutic gene editing via CRISPR-Cas9 offers an
We initially conducted molecular docking to obtain alternative therapy for patients with IMDs.
optimum conformations of the nsp1-ribosome
hypothesis/goal of study. The objective
complexes. To further explore the binding mechanism, of our study is to optimize non-viral methods for
molecular dynamics (MD) simulations of the solvated delivering CRISPR-Cas9 nucleases into hepatocytes as
complex were conducted. Targeted MD simulations were an alternative therapeutic strategy for HT1 and other
performed using nsp1-ribosome reference structure inherited metabolic liver diseases. We seek to evaluate two
to simulate the entry of the C-terminal domain of nsp1 methods for non-viral delivery of Cas9 into hepatocytes:
into the 40S RNA channel. We further evaluated the electroporation and lipid nanoparticles (LNPs).
energetics of the system to determine if the nsp1-
ribosome configurations were energetically favorable in
methods and results. Different forms of Cas9
were delivered into Hepa 1-6 cells, a murine liver-
its bound state. derived cell line, and primary mouse hepatocytes by
electroporation. We compared delivery of Cas9 as a
Results of the simulations indicated favorable plasmid DNA, mRNA, and purified protein along with
interactions between nsp1 and the 40S ribosome, with synthetic sgRNA targeting Hpd. Transfection efficiency
the C-terminus of nsp1 approaching the mRNA channel was measured by transfecting some cells with eGFP
mRNA and counting the percentage of GFP positive cells
during the targeted MD simulations. The simulations
24 hours later. The on-target activity of CRISPR-Cas9
provided insight on the binding mechanisms of nsp1 to
was analyzed using Tracking of Indels by Decomposition
human ribosome and can potentially explain how the at 72 hours post nucleofection. Off-target activity at
binding influences host protein expression which will be three potential off-target sites was measured by next-
critical in the development of therapeutics for COVID-19. generation sequencing (NGS). We observed high activity
14 | 2021 SC INBRE Science Symposiumin Hepa 1-6 cells nucleofected with Cas9 mRNA and ribonucleoprotein (RNP) compared to plasmid DNA. In primary
hepatocytes, we observed high levels of on-target indels for the Hpd-aiming CRISPR-Cas9 with 60.2% using mRNA, 70.3%
with wild-type RNP Cas9, and 61.5% with HiFi Cas9 RNP. NGS showed a large decrease in off-target editing when using the
HiFi Cas9 RNP.
conclusions. Our research indicates that electroporation is capable of delivering Cas9 into hepatocytes for efficient
gene editing. NGS analysis suggests that the HiFi Cas9 is capable of reducing off-target effects when compared to the wild
type. Future work will evaluate gene editing activity of Cas9 in hepatocytes when delivered with lipid nanoparticles.
BE-09
THE EFFECTS OF BUFFER COMPOSITION ON THE VIABILITY
AND EFFICIENCY OF ELECTROPORATION ON HUH7 CELLS
Will Betsill, Tanner Rathbone, Scott Lynn, and Renee Cottle
Department of Bioengineering, Clemson University, Clemson, SC
introduction. Electroporation is a technique that applies an electric current to the desired cells to increase the
membrane permeability. The purpose of our research is to optimize this method to be the most effective by creating a buffer
solution containing varying concentrations of potassium and magnesium ions, and testing the ideal voltage for this process.
We expect that if the voltage is moderate, around 450V, then the cells will be efficiently transfected while remaining viable.
There should be an inverse relationship, where as the voltage is higher, the transfection rate should be higher but the cell
viability will be lower.
methods. Huh7 cells will be transfected with a Celetrix electroporation device. Electroporation parameters will be
optimized by testing different voltages used to deliver eGFP plasmid DNA to cells. Transfected cells will then be measured in
a flow cytometer to determine the percentage of GFP positive cells and nonviable cells. The cells will also be incubated with
propidium iodide, and cells stained red will be considered nonviable. After determining the ideal voltage for electroporation
of huh7 cells, different buffers will be tested with the electroporation device. The buffers will be composed with the
compositions shown in table 1.
results. Preliminary data from our early experiments indicates that of the six voltages tested, 450V is most suitable
for electroporation with the huh7 cells. About 65% of cells electroporated at 450V were GFP%, much higher than cells
electroporated at lower or higher voltages. Increased voltage beyond 450V also decreased the viability from ~90% of cells to
~54% at 475V and ~38% at 500V. Future experiments will test if the addition of cations to the buffer will enhance cell viability
and transfection efficiencies.
2021 SC INBRE Science Symposium | 15NIH describes bioinformatics as the field “that
deals with the application of computers to the
collection, organization, analysis, manipulation,
presentation, and sharing of biologic data. A
central component of bioinformatics is the
study of the best ways to design and operate
biologic databases. This is in contrast with the
field of computational biology, where specific
research questions are the primary focus."
SC INBRE recognizes the importance of
bioinformatics to biomedical research in our
State. We have a commitment to assist South
Carolina’s biomedical research community. We
not only support a Bioinformatics Core which
provides bioinformatics support to faculty,
postdocs, grad and undergrad students of
our lead and partner institutions, but we
also offer competitive Bioinformatics Pilot
Project Program and new Student-Initiated
Research Program funding. Additionally, our
Core offers free workshops and recordings
of workshops are on our website under the
Learning tab for anyone to view.
BI-01
INVESTIGATION OF THE CHROMATIN ARCHITECTURE AT STAT5
TARGET GENE LOCI IN LYMPHOCYTES
Charles W. Hudson, Rorie M. Vander Ploeg, Haegen L. Nelson, Elias M. Wheibe and Jason S. Rawlings
Department of Biology, Furman University, Greenville, SC
introduction/background. Lymphocyte proliferation during development and during an immune response is
controlled by the transcription factor STAT5. Previous work demonstrated that chromatin condensation state influences the
expression of STAT5 target genes. Specifically, signaling via IP 3 (inositol trisphosphate) and DAG (diacyglycerol) is known to
cause chromatin to decondense, permitting STAT5-DNA engagement and subsequent target gene expression.
hypothesis/goal of study. We determined the status of chromatin condensation at known STAT5 loci during T cell
development in the thymus and during activation of naïve B cells in the periphery. Additionally, we assessed the signaling
pathways responsible for changes in chromatin at these loci in Jurkat T cells.
methods and results. DNAse-seq and ATAC-seq datasets were downloaded from the GEO database at NCBI and
displayed on the UCSC Genome Browser. Chromatin accessibility was determined in the proximity of consensus STAT5
DNA binding sites in promoters of known STAT5 target genes. Throughout thymocyte development and B cell activation,
chromatin at known STAT5 target gene loci was generally in a decondensed configuration during known periods of
proliferation and in a condensed configuration during known quiescent periods. Generally, while either IP 3 or DAG signaling
induce changes in chromatin architecture, both signaling pathways are required for maximal effect at the loci examined.
conclusions. Our study shows that chromatin architecture at STAT5 target gene loci dynamically changes during T
cell development in the thymus and in activation of B cells in the periphery during an immune response. Understanding the
mechanism(s) that control these changes is instrumental in our understanding of how T cells proliferate during the immune
response to pathogen and in pathologies affecting lymphocytes such as autoimmune disease, immunodeficiency, and
immunological cancers.
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