Grant Description

From Website: "Undergraduate Research Mini-Grants are internal grants available for Drexel faculty and undergraduate student collaborators to support their work together. The goal of these grants is to provide further support for faculty and student collaboration in undergraduate research, scholarship, and creative work at the university while also offering undergraduate students the opportunity to build skills in crafting effective application materials for funding opportunities.Grant applications will open twice annually – in the Fall Term to support work undertaken the following Winter Term and in the Winter Term to support work undertaken the following Spring Term. The number of grants available and funding per grant will be contingent on budgetary constraints and will be announced each academic year."

Taken from the website: "Undergraduate Research Mini-Grants are internal grants available for Drexel faculty and undergraduate student collaborators to support their work together. The goal of these grants is to provide further support for faculty and student collaboration in undergraduate research, scholarship, and creative work at the university while also offering undergraduate students the opportunity to build skills in crafting effective application materials for funding opportunities.Grant applications will open twice annually – in the Fall Term to support work undertaken the following Winter Term and in the Winter Term to support work undertaken the following Spring Term. The number of grants available and funding per grant will be contingent on budgetary constraints and will be announced each academic year."

"Undergraduate Research Mini-Grants are internal grants available for Drexel faculty and undergraduate student collaborators to support their work together. The goal of these grants is to provide further support for faculty and student collaboration in undergraduate research, scholarship, and creative work at the university while also offering undergraduate students the opportunity to build skills in crafting effective application materials for funding opportunities." 

I applied and received the UREP mini grant to work with Dr. Gwen Ottinger on RefineryAirWatch.org. 

(I grabbed this from the UREP website)

Undergraduate Research Mini-Grants are internal grants available for Drexel faculty and undergraduate student collaborators to support their work together. The goal of these grants is to provide further support for faculty and student collaboration in undergraduate research, scholarship, and creative work at the university while also offering undergraduate students the opportunity to build skills in crafting effective application materials for funding opportunities.Grant applications will open twice annually – in the Fall Term to support work undertaken the following Winter Term and in the Winter Term to support work undertaken the following Spring Term. The number of grants available and funding per grant will be contingent on budgetary constraints and will be announced each academic year.

Eligibility

Drexel undergraduate students who are currently working with Drexel University faculty are eligible to apply for this funding. Funding may be put towards hiring the student or toward research expenses, materials, or equipment. Student/faculty pairs awarded funding in previous rounds may reapply, though those who have not previously been awarded a mini-grant will be given priority.

Application Requirements

The student in the student/faculty pair is expected to submit the online application via the online portal. The link to the open application will be made available here when a submission cycle is open. Applications must include:

• research statement,
• a timeline of work,
• a personal statement of interest (from the student’s perspective)
• a faculty letter of support, and
• a budget outlining proposed use of funds.

Grant applications will be reviewed by staff in Undergraduate Research & Enrichment Programs. Funding will be distributed to faculty or departmental accounts for final disbursement.

Undergraduate Research & Enrichment Programs in the Pennoni Honors College is happy to announce our Undergraduate Research Mini-Grants for Winter Term of the 2022/2023 academic year. Undergraduate student and faculty pairs from across the University can apply for $2,000 each term to support their research efforts. At least 10 grants will be awarded for Winter Term. At the end of the term, students who have received a mini-grant will be expected to write a blog post for the UREP Blog and to present their work at a poster session during the 2023 Week of Undergraduate Excellence (to be held in May 2023).

Description

Undergraduate Research & Enrichment Programs in the Pennoni Honors College is happy to announce our Undergraduate Research Mini-Grants for Winter Term of the 2022/2023 academic year. Undergraduate student and faculty pairs from across the University can apply for $2,000 each term to support their research efforts. At least 10 grants will be awarded for Winter Term. At the end of the term, students who have received a mini-grant will be expected to write a blog post for the UREP Blog and to present their work at a poster session during the 2023 Week of Undergraduate Excellence (to be held in May 2023). 


Abstract Submission
Clinician Perspectives on Exercise-Based Pain Interventions for People Living with Dementia
Pain affects 50-80% of people living with dementia (PLWD), and its effective management is critical to sustaining or improving quality of life. Exercise is a recommended first line treatment for pain management in older adults; yet the use of exercise-based programs by clinicians working with those experiencing impaired cognitive processing is unclear. The purpose of this qualitative description study was to explore clinicians’ perceptions in managing chronic musculoskeletal pain in PLWD who are community-dwelling with exercise-based pain interventions. Individual, semi-structured, virtual interviews were conducted with 12 clinicians (physical therapists = 6, occupational therapists = 4, and nurse practitioners = 2, mean age ±SD = 39.9 ±10.7 years, mean clinical experience ±SD = 8.8±6.7 years, female = 10,) from 4 outpatient facilities. Through a conventional content analysis, the key theme thatemerged was that exercise interventions used for pain management among PLWD needed to be “carefully tailored”. The clinicians reported that they consider several factors, including the PLWD’s underlying pain mechanism, cognitive ability, physical function, comorbidities, and preferences when developing their exercise programs to manage chronic pain of PLWD. .Few studies have emphasized these factors in exercise-based pain interventions, which are especially critical and applicable for pain management in PLWD and should be prioritized in future research. 

Faculty Mentor Name: Michael J. Bouchard, Ph.D.
Faculty Mentor Email: mjb93@drexel.edu
Department Administrative Contact: Joshua Stevenson
Department Administrative Email: jds336@drexel.edu
Department Account Code: 130555-5876  

Research Statement: A short description of the project the student will undertake, including the research or create question the student will explore, the experience the student has with this topic/project, the background or significance of this work, and the methods used to explore this topic:  
Hepatocellular carcinoma (HCC) incidence continues to rise and poses an evolving global issue [1-6]. The molecular mechanisms that underlie HCC development are poorly understood, and approved therapies are rarely curative [1-6].    Using publicly available RNAseq data to assess the levels of long noncoding (lnc) RNAs in normal livers and HCCs, the Bouchard research team discovered that the lncRNA – FAM99A – is highly expressed in normal liver but absent in HCCs [7,8,9]. This indicates potential tumor-suppressor capabilities; however, the function of FAM99A in hepatocytes is currently own.  Therefore, our research interest lies in defining FAM99A activities in hepatocytes and determining if FAM99A is a true tumor suppressor. We hypothesize that FAM99A helps maintain the differentiated status of hepatocytes by acting as a tumor suppressor. Our objectives are to define functions of FAM99A, including a role in hepatocyte differentiation; identify interacting partners of FAM99A; and assess the effect of FAM99A on the transformed phenotype of a panel of HCC cell lines.   During the Spring Term, the student will determine if FAM99A expression is required to maintain the differentiated status of human hepatocytes and assess FAM99A tumor-suppressor activity in HCC cell lines. Studies will be conducted in cultured primary human hepatocytes to assess the effect of FAM99A overexpression or knockdown on hepatocyte differentiation. Studies, such as analyzing colony formation in soft agar, will be conducted in a panel of HCC cell lines to assess the effect of over-expressed FAM99A on the transformed phenotype of these cells.   The student has limited experience with mammalian tissue culturing and knowledge of HCC, which permits for a perfect learning opportunity. Furthermore, the student has taken lower and upper biology and chemistry courses with an extensive background in wet-bench experience,  that gives the fundamental skills needed for this project. Techniques and skills from molecular biology and microbiology will be greatly built upon throughout the project.  
References:
1.  Singal, A.G., P. Lampertico, and P. Nahon, Epidemiology and surveillance for hepatocellular carcinoma: New trends. J Hepatol, 2020. 72(2): p. 250-261.
2.  Hou, J., et al., The immunobiology of hepatocellular carcinoma in humans and mice: Basic concepts and therapeutic implications. J Hepatol, 2020. 72(1): p. 167-182.
3.  Zhu, C., et al., The fusion landscape of hepatocellular carcinoma. Mol Oncol, 2019. 13(5): p. 1214-1225.
4.  Yang, J.D., et al., A global view of hepatocellular carcinoma: trends, risk, prevention and management. Nat Rev Gastroenterol Hepatol, 2019. 16(10): p. 589-604.
5.  Keenan, B.P., L. Fong, and R.K. Kelley, Immunotherapy in hepatocellular carcinoma: the complex interface between inflammation, fibrosis, and the immune response. J Immunother Cancer, 2019. 7(1): p. 267.
6.  Hlady, R.A., et al., Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma. Hepatology, 2019. 69(2): p. 639-652.
7.  The GTEx Consortium atlas of genetic regulatory effects across human tissues. Science, 2020. 369(6509): p. 1318-1330.
8.  Zhao, B., et al., HIF-1alpha and HDAC1 mediated regulation of FAM99A-miR92a signaling contributes to hypoxia induced HCC metastasis. Signal Transduct Target Ther, 2020. 5(1): p. 118.
9.  Mo, M., et al., A liver-specific lncRNA, FAM99B, suppresses hepatocellular carcinoma progression through inhibition of cell proliferation, migration, and invasion. J Cancer Res Clin Oncol, 2019. 145(8): p. 2027-2038.              
Timeline of Work: A short description of how the project will progress over the Spring Term, including when and how the student will prepare to participate in the Week of Undergraduate Excellence:  
Preliminary studies showed that while FAM99A expression is absent in HCCs, it is highly expressed in normal primary human hepatocytes (PHHs), but its expression is lost by 24 hours after plating PHHs, which also correlates with de-differentiation of the cultured hepatocytes. This suggests that FAM99A might be required to maintain the differentiated status of hepatocytes and thus acts as a tumor suppressor.  
Therefore, the student will:
1) Knockdown and overexpress FAM99A in plated PHHs and assess effects on PHH differentiation.
2) Overexpress FAM99A in a panel of HCC cell lines and assess effects on colony formation in soft agar (an indicator of a cell’s ability to form a tumor) and cell proliferation and death.  
De-identified PHHs will be purchased from commercial sources and cultured as in our previous studies [1,2]. PHHs will be infected with a recombinant Adenovirus (recAd) expressing green fluorescent protein (GFP), or AdGFP-FAM99A in suspension prior to plating by incubating the cells with the recAds. Cells will then be analyzed at 24, 48, and 72 hours post infection. Albumin and urea levels in the cell-culture supernatant will be analyzed as indicators of hepatocyte function [3-5]. We will also use western blot analysis to assess levels of transferrin, hepatocyte nuclear factor 4a, and transthyretin, markers of differentiated hepatocytes [3-8, 9, 10]. HCC cell lines will also be assessed for effects on colony formation in soft agar. When an effect on colony formation is observed, we will assess cell proliferation and death using well established protocols [11-12].   The student will be conducting full-time research in the Bouchard lab for the Spring Term, thus they will see many facets of this project at whatever capacity 10 weeks may grant. The first ~2 weeks are expected to consist of literature review and laboratory familiarization. Weeks ~2-4 will roughly be focused on lab technique monitoring and development, as well as preliminary project design, development, and implementation. Weeks 4-8 will then consist of semi-independent research and laboratory group work. The last few weeks of the term will be spent on poster development for the Week of Undergraduate Excellence as well as final data analysis.  
References
1.  Lamontagne, J., J.C. Mell, and M.J. Bouchard, Transcriptome-Wide Analysis of Hepatitis B Virus-Mediated Changes to Normal Hepatocyte Gene Expression. PLoS Pathog, 2016. 12(2): p. e1005438.
2.  Arrigoni, A., et al., Analysis RNA-seq and Noncoding RNA. Methods Mol Biol, 2016. 1480: p. 125-35.
3.  Kang, Y.B., Rawat, S., Duchemin, N., Bouchard, MJ., Noh, M., Human liver sinusoid on a chip for hepatitis B viral replication study. Micromachines, 2017. In press.
4.  Kang, Y.B., et al., Liver sinusoid on a chip: Long-term layered co-culture of primary rat hepatocytes and endothelial cells in microfluidic platforms. Biotechnol Bioeng, 2015. 112(12): p. 2571-82.
5.  Kang, Y.B., et al., Layered long-term co-culture of hepatocytes and endothelial cells on a transwell membrane: toward engineering the liver sinusoid. Biofabrication, 2013. 5(4): p. 045008.
6.  Kang, Y.B., et al., Layered long-term co-culture of hepatocytes and endothelial cells on a transwell membrane: toward engineering the liver sinusoid. Biofabrication, 2013. 5(4): p. 045008.
7.  Sodunke, T.R., M.J. Bouchard, and H.M. Noh, Microfluidic platform for hepatitis B viral replication study. Biomed Microdevices, 2008. 10(3): p. 393-402.
8.  Clippinger, A.J. and M.J. Bouchard, The Hepatitis B Virus Hbx Protein Localizes to Mitochondria in Primary Rat Hepatocytes and Modulates Mitochondrial Membrane Potential. J Virol, 2008. 82: p. 6798-6811.
9.  Clippinger, A.J., T.L. Gearhart, and M.J. Bouchard, Hepatitis B virus X protein modulates apoptosis in primary rat hepatocytes by regulating both NF-kappaB and the mitochondrial permeability transition pore. J Virol, 2009. 83(10): p. 4718-31.
10. Casciano, J.C., et al., Hepatitis B virus modulates store-operated calcium entry to enhance viral replication in primary hepatocytes. PLoS One, 2017. 12(2): p. e0168328.
11. Crowley, L.C., et al., Measuring Cell Death by Trypan Blue Uptake and Light Microscopy. Cold Spring Harb Protoc, 2016. 2016(7).
12. Crowley, L.C., et al., Measuring Cell Death by Propidium Iodide Uptake and Flow Cytometry. Cold Spring Harb Protoc, 2016. 2016(7).                            
Personal statement of interest: A short description of the student’s interest in this work, including how this project may fit into the student’s academic plan/goals, what drew them to this work, and/or why they are passionate about this work:  
I have been involved in many research endeavors throughout my time in high school and undergrad; each has propelled me toward biochemical and molecular biological research. In high school, I worked on individual projects and competed internationally three times, including environmental projects which won national awards. Since high school, I have had two experiences with the United States Department of Agriculture – Agricultural Research Services. The first was an internship, focused on enzyme identification and bioinformatic database mining, and the second was with the Molecular Characterization of Foodborne Pathogens unit, developing a rapid identification method using next-generation sequencing. I also participated in the Student Tackling Advanced Research program and worked with a professor to investigate a new polymerization technique. I am currently working in a neuroengineering lab through Vertically Integrated Projects, where I have been the lead in establishing a research records database that is Institutional Review Board and HIPAA (Health Insurance Portability and Accountability) compliant.   Upon looking at my research history, most would say that these topics are varied in field and show no direction or culmination. However, I argue that each experience has allowed me to build an arsenal of skills that could not be developed from one area alone. There is value in these skills, especially as I find myself aiming for a career as a principal investigator with the National Institutes of Health. As I reflect on my time in the laboratory and my contributions towards the advancement of knowledge, I find myself yearning for research that directly reflects the future I want. Furthermore, research that can one day be applied to alleviate health disparities or address disproportions in minority communities is a driving force for why I want to work at the NIH. Although the studies outlined in this proposal are not designed to directly address a specific health disparity, the incidence of HCC is higher in Asian, African Americans, Hispanics, and American Indians/Alaskan Natives populations (REFS). Therefore, any identification of novel biomarkers or treatment methods would be directly applicable to both general health and the higher incidence of HCC in these specific minority groups.   With the Bouchard Lab at the Drexel University College of Medicine, I would gain experience with mammalian cell tissue culturing, molecular biological techniques, and biochemical techniques. I also find the research fascinating – knowing that I’m directly contributing to knowledge that can help my community and many others that face similar issues. I believe that this research will enhance the skills I’ve developed and can show me how research can surpass the fundamental sciences and begin to translate into something that directly benefits humankind. I have aggressively pursued research as a student, but topics similar to this project are what I foresee myself doing for the rest of my career.   Proposal title: Investigating the Tumor-suppressing Potential of Long noncoding RNA FAM99A in Primary Human Hepatocytes    

Background
As an estimated 1 in 3 Americans have a criminal record, the stigmas associated with past deviant behavior inevitably influence employment opportunities for stated individuals (Ciaravolo, 2011). According to labeling theory, the labels we assign people ultimately influence our interactions and perceptions of them. Labeling theory also suggests the social reaction to primary deviance, an individual's first offense, often contributes to secondary deviance, or reoffending, as the individual internalizes the presented stigmas (Breen, 2011). Recidivism, or the act of reoffending, presents a cycle of crime as discrimination, stigmatization, and lack of reintegration support act as contributing factors (Denver, 2020). In response to these factors, as well as other challenges such as poverty and lack of social support, 1 in 4 Americans will be re- incarcerated again within the same year (Sawyer & Wagner, 2020). In recent years, scholars and policymakers have begun to understand and attempt to address these hurdles.
Some of the efforts to assist formerly incarcerated individuals with their return to society have focused on assisting with employment by limiting discrimination in the hiring process. There have been mixed results of the procedures, following and contrasting the intentions of such laws. Although Ban-the-Box laws exist to limit employers’ ability to inquire about a criminal record during an initial application, there have been unintended consequences of the legislation. According to previous studies, employers began to rely on race to avoid hiring individuals with criminal histories (Raphael, 2020). The studies found employers use race as an inferential factor given crime often associates with racial minorities (Nakamura, 2017). Other studies have found the implementation of Ban-the-Box laws relies on the limitations of the social stigma of a criminal record and the failure of ex-offenders to find employment (D’Alessio et al., 2014). Accordingly, studies suggest employers look past the mere presence of a criminal record in the event that they have do not have access to such information (Uggen et al., 2014). The inconsistent results of Ban-the-Box laws encourage a need for an efficient understanding of how employers may label individuals with a criminal record. In turn, this can lead to the development of an effective and fair way to present the job applications of individuals who have been arrested.
Our previous work in this area, completed through the STAR Program, focused on gathering data on how the experiences of formerly incarcerated people are perceived in a community. The survey we developed examined the perspectives of three unique groups of North Philadelphia residents, consisting of university students, church members, and formerly incarcerated individuals. The study recorded their judgements of crime, recidivism, and employment suitability of formerly incarcerated individuals. We found students had positive attitudes toward individuals with criminal histories, church members had the lowest expectationsof recidivism, and previously incarcerated individuals had lower perceptions of employment opportunities for formerly convicted individuals.I have continued to advance this work with Dr. Hyatt through an independent study course, examining employers’ judgments of redemption, attitudes toward a criminal background check, and perceptions of a formerly incarcerated individual’s disclosure of rehabilitative credentials. The unique survey developed for the project will be put into the field in the coming weeks. I hope to learn of employer perceptions regarding formal declarations of redemption and how it may influence their attitudes concerning the utility of criminal background checks. Following the study, Dr. Hyatt and I expect to complete a manuscript using these data in the coming months.

Project Overview
The next phase of this project will build on our current foundation by allowing us to gather qualitative interview data from employers and individuals with a criminal record who have sought a job. In addition, we will better understand the survey data and identify new area of inquiry. The qualitative approach of the proposed project will record the experiences of employers and formerly incarcerated individuals as it pertains to redemption, criminal background checks, and rehabilitative credentials. The Undergraduate Research & Enrichment Programs will contribute to our research efforts as it provides the necessary support to continue my studies with Dr. Hyatt, and eventually establish a community-facing event.

Timeline
During the first three weeks of the term, I will complete an in-depth literature review and begin to draft the interview questions. In addition to regularly meeting with Dr. Hyatt, I will also meet with leading scholars in this area (e.g., Lageson, Uggen). I will revise and finalize the interview questions and protocol during week 4, and I will administer the interviews during weeks 5 through 7. Then, I will analyze the data during weeks 8 through 10. And I will create my preliminary deliverables, including a project report and executive summary, and establish the next steps for my project with Dr. Hyatt during weeks 9 and 10.

Professional Impact
As I hold a professional goal to ameliorate employment opportunities for previously incarcerated individuals, the study will identify the problem based on the experiences and perceptions of both employers and formerly incarcerated individuals in Philadelphia, PA. I will examine the ways employers perceive applicants with criminal histories and the attitudes formerly incarcerated individuals hold toward employment. My goal of the study is to determine and suggest an effective way for individuals with a criminal background to present their applications while disassociating from the stigmas that may often hinder their ability to find employment. The funds from the undergraduate research mini-grant, in addition to my participation in the STAR
program and independent research study, will allow me to continue active research with Dr. Hyatt and, eventually, to produce a project to assist individuals with criminal backgrounds.

                 Gene mapping includes methods to identify positions of a gene on a chromosome and physical distances between genes. Genome assembly refers to the process of taking a large number of short DNA sequences and reassembling them to create a representation of the original chromosomes from which the DNA originated. Technologies to map the entire genome of an organism have been developed in recent years. These findings provide scaffolds for structural variation analysis and mutation frequency detection. Structural variations (SVs) are defined as regions of DNA approximately 50bp and larger in size and can include genomic inversions, duplications, insertions, translocations, and deletions. Identifying SVs is important for genome interpretation and determining the relationship to disease. Several short and long-read DNA sequencing methods have been developed. These methods are aimed at determining the nucleic acid sequence in DNA. Optical mapping is a method to linearize single DNA strands in nanochannels and construct DNA maps by imaging fluorescently labeled sequence motifs in single DNA molecules. Optical maps are advantageous over DNA sequencing as they can easily span difficult to read genomic regions for large-scale SV detection.

                  Dr. Xiao’s lab has developed a new sequence-specific DNA labeling approach to complement the traditional enzyme motif-based strategy in optical mapping. This two-color mapping allows targeting the breakpoints of genome structural variations in repetitive regions which are hard to detect by all other methods. The task at hand is to process the molecular data from an optical mapping of two-color labeling in repetitive regions. This data is generated by the optical mapping, which is to assemble single DNA molecules to a reference. SVs are detected by identifying outlier molecule alignments. I will explore different detection strategies and statistical approaches based on the analysis need and the research hypothesis, in hopes of developing a better pipeline for the identification of the second color label signal in specific regions. This task will not only involve understanding algorithms previously formulated by the lab but will also require a solid understanding of the mapping experiments conducted to obtain the data. The biological structure and function of the target gene region will also need to be thoroughly studied to understand the relationship of SVs in that region to gene function or regulations. The findings from these studies have the potential to support pioneering research in cell and gene therapy development.

                     I have previous experience with compiling alignment algorithms to process sequencing data through a project in Dr. Xiao’s Computational Bioengineering class. This project was aimed at aligning sequencing data to a reference sequence to output parameters like the number of aligned bases, the length distribution of aligned sequence reads, and the mapping quality score. Through my other biocomputational classes, I have obtained excellent proficiency with MATLAB programming and its application in a broad range of biomedical fields. My co-ops have allowed me to build a robust skillset in cell and molecular research and manufacturing processes. Above all, I am eager to push myself to new limits by learning new concepts and familiarizing myself with the latest technologies in the field. I will be able to make invaluable connections with my lab members for guidance on future pursuits. This experience will provide me with the training and background I need to achieve my professional goals in a challenging and competitive industry. 

Abstract: 

Image analysis pipeline for DNA linearization methods
Zeal Jinwala, Dharma Varapula , Ming Xiao
Department of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia 19104

Gene mapping includes methods to identify positions of a gene on a chromosome and physical distances between genes. Genome assembly refers to the process of taking short DNA sequences and reassembling them to create a representation of the original chromosomes from which the DNA originated [1]. Structural variations (SVs) are defined as regions of DNA approximately 50bp and larger in size and can include genomic inversions, duplications, insertions, translocations, and deletions [2]. Optical mapping is a method to linearize single DNA strands in nanochannels and constructing DNA maps by imaging fluorescently labelled sequence motifs in single DNA molecules. Mapping of linearized DNA molecules is useful in sequence assembly, large structural variant detection, and diagnostics [3]. The goal of this study is to develop a pipeline for batch processing and digitization of DNA linearization images for the identification of labels, and inter-label distances to provide the basis for DNA mapping.

References
[1] Lam, Ernest T, et al. “Genome Mapping on Nanochannel Arrays for Structural Variation Analysis and Sequence Assembly.” Nature Biotechnology, vol. 30, no. 8, 2012, pp. 771–776., doi:10.1038/nbt.2303.
[2] Ho, Steve S., et al. “Structural Variation in the Sequencing Era.” Nature Reviews Genetics, vol. 21, no. 3, 2019, pp. 171–189., doi:10.1038/s41576-019-0180-9.
[3] Varapula, D.; LaBouff, E.; Raseley, K.; Uppuluri, L.; Ehrlich, G. D.; Noh, M.; Xiao, M. A Micropatterned Substrate for on-Surface Enzymatic Labelling of Linearized Long DNA Molecules. Scientific Reports 2019, 9.