Loyola University Chicago

The Graduate School

Summer 2015 Research Mentoring Projects

Note about the Biomedical projects at the Maywood campus:  It is typically expected that you will spend 7-8 hours most days in the lab with your mentor.  There is public transportation to Maywood via the Blue line of the El and bus – RMP will help cover commuting costs.

Project Description: My research focuses on the performance of small groups of individuals working together to make decisions and solve problems, and the social processes by which such groups function. Many real-world decisions are entrusted to groups (rather than individuals), often under the assumption that groups are in some ways better at using their knowledge and the information that they have to make good decisions and solve problems effectively and efficiently. Despite being a popular area of research within social psychology and other fields, many questions about how individuals combine their efforts into a group decision remain unanswered. One such topic is the extent to which groups will consider or use information presented from an advisor outside the group, and the factors which may facilitate or inhibit the group members’ consideration of that outside guidance. My dissertation study will investigate this topic utilizing an experimental design in a laboratory setting. Experiment participants will work to solve a complex series of math and logic problems individually or in a group with others. I will be videotaping the sessions to examine group members’ behavior and communication of opinions, ideas, and strategies for sharing information and solving the problems.

Undergraduate Work: During the summer months, I will expect my undergraduate assistant to work 6-8 weeks in my laboratory on the Lake Shore campus. The schedule is somewhat flexible and will be discussed in advance of beginning the work. The assistant’s primary responsibilities will include: (1) entry and analysis of data (including observational video data) collected for the study; (2) assisting with management, storage, and organization of data files, research records, and laboratory equipment; (3) assisting with development of presentations and written reports of results.

Research:

Chicago from 1870 to 1920 represented the quintessential industrial city, a hotbed of Progressive reform and prominent theater where national modes of labor and business relationships were forged.  A bureaucratizing court emerged at the center of the struggle over social order, as self-proclaimed reformers fought for the power to decide which people and what behavior should be designated as criminal. Analyzing the felony court records of women indicted for violent criminal acts will reveal how contested categories of crime and gender changed over time.  The research seeks to understand which acts and which women were considered criminal, and what defense narratives and strategies were effective from one year to the next.  Studying feminine criminality in turn-of-the-century Chicago will provide insight into broader battles over moral, political, and economic power in the United States.

Undergraduate work:

The undergraduate student will be conducting primary source research in the archives of the Cook County Circuit Court.  At least once per week for six weeks, the student will travel to the Richard J. Daley Center to sift through boxes of criminal court cases, identifying and scanning all cases in which a female defendant is indicted for a violent crime, including riot, assault, or murder.  The student will also spend time organizing the digital files, searching for patterns and highlighting any information of interest. Additionally, the student will search online newspaper databases to find and collect articles related to each case.  The student will compile their research into dossiers for each case of violent feminine criminality, including all relevant primary sources and a brief report in which the student summarizes their observations. With introductory training and weekly support from the graduate mentor, the student will gain familiarity with the process of historical research and acquire experience in navigating research tools like Zotero and ProQuest.

Project Description:

My dissertation research examines the strategy shifts from using violent means to nonviolent means in armed conflicts. Even most violent rebel organizations adopt unarmed strategies at times (i.e. Hezbollah, Fatah, Chiapas etc.), yet the reasons of transition from armed movement to nonviolent movement have not been studied systematically. In my dissertation, I analyze the causes that influence shift from armed resistances to unarmed resistances within the same movement. I examine the strategy shifts in the Kurdish movement in Turkey and in Iran. Specifically, I look at the use of nonviolent methods by Kurdish armed groups PKK (Kurdistan Workers` Party), KOMALA (the Organization of Revolutionary Toilers of Iranian Kurdistan) and KDPI (the Kurdish Democratic Party of Iran).

Undergraduate Work:

The undergraduate student will have the opportunity to closely engage with nonviolent methods of political change as well as quantitative and qualitative data collecting techniques. The student will be responsible for assisting me in compiling a large-N dataset on the nonviolent actions of PKK in Turkey for the years between 1984 and 2014. This would include searching newspapers, civil society publications and reports, and reflecting the information found through these means with appropriate coding. I would help the student learn how to code the relevant textual information in a large-N dataset. A student who is fluent in Turkish would be very helpful. If the time permits, the student would also accompany me to conduct in-depth interviews with scholars who are expert in Kurdish movement in Iran.

Project Description

Methicillin-resistant S. aureus (MRSA) infections constitute a serious burden to human health, yet no vaccine is available to prevent these infections. We have generated Adenovirus vaccine vectors expressing proteins from MRSA, and have preliminary data showing that these vectors provide protection from MRSA infections. Our goal is to use these vectors to develop a protective vaccine for MRSA, and to understand the mechanism of vaccine-mediated protection.

Undergraduate Work

The undergraduate research assistant will evaluate the antibody response elicited by our Adenovirus-vector MRSA vaccine. They will perform ELISAs to determine the antibody response to MRSA proteins delivered by our vaccine vector, and compare this to antibody responses elicited by other vaccination strategies. The student will also assess the ability of these antibodies to mediate uptake and killing of the bacteria by immune cells, which are processes critical for clearing MRSA infections.  The student will be expected to work at the Maywood campus Monday – Friday, all day in the lab for 4-6 weeks.

Project Description

I enjoy investigating human motivation and decision-making processes and my recent projects have shown that an individual’s ideal self – the person they most want to be – influences both how they view others and how they behave. For example, if you believe that someone is similar to your ideal self (ideal self similarity), you are more likely to respect them, like them, be romantically attracted to them, want to be their friend, or perform a task with them. On the other hand, if you are similar to your own ideal self (actual:ideal self-discrepancy), you can cope better with the stress of adverse events, such as racial discrimination. This summer, I will be conducting a study of African American romantic couples to determine if similarity to your own ideal self (self-discrepancy) effects how loved and accepted you feel after experiencing negative events. The data for this study has already been collected and the remaining work is primarily conducting literature reviews and running statistical analyses.

Undergraduate Work

During the summer program, you will learn how to conduct empirical research in social psychology which will help you understand how to apply that practical knowledge to your own independent research in the future. This experience can be generalized to other subfields of psychology and to other social sciences. I hope that you will be open to experiencing all the details of the empirical research process and will actively make connections to your own interests. I encourage you to share ideas and communicate openly, rather than just comply with task assignments. When we have a few minutes of free time, we will discuss choosing your post-college career, the graduate school application process, choosing a program that fits you, funding graduate school, balancing academic commitments with social/familial commitments, and planning a successful route through graduate school. At the conclusion of the program, you will be able to independently:

  • conduct journal article searches online and in the library
  • design research projects and develop relevant hypotheses to test
  • prepare data files for analysis using MS Excel and SPSS (statistical software)
  • conduct basic statistical tests using SPSS
  • give and receive constructive feedback in a research setting

https://www.taskstream.com/ts/jeremie-brink/NathanJeremieBrink

Project Description

Most scholarly and popular treatments of African American abolitionists emphasize mid-nineteenth century slave narratives like Frederick Douglass’ Narrative and Solomon Northrup’s Twelve Years a Slave.  But African Americans were reading, writing, editing, printing, and distributing a variety of texts more than half a century before these narratives ever hit the press.  As they distributed pamphlets, newspapers, broadsides, books, lithographs, tracts, almanacs, and manuscript copies of antislavery texts, African Americans took great risks and at times broke laws as they sold, purchased, borrowed, mailed, read, or listened as materials were read aloud.  My research highlights these distribution practices of early African American print culture to recover the social networks involved in these exchanges and to show how these networks and their strategies proved foundational to the growth of the abolitionist movement and essential in securing print access to African American voices for freedom.  This mentored research project involves digital mapping and visualization of the distribution networks of antislavery newspapers.  The project will build upon my own prior experiments in mapping early antislavery print culture, and map the subscription agents for select African American periodicals.

Undergraduate Work

Our mentored research will not only gather data, but explore the use of innovative digital tools for historical research.  The research assistant will closely examine Freedom’s Journal, The Liberator, The Palladium of Liberty, and The Rights of All (accessible through Loyola University Libraries’ digital collections) in order to map the distribution agents of these early African American periodicals.  Exposure to these archived newspapers will include time with extant physical copies held at the Newberry Library.  Tasks involve investigating and collecting data from these sources, basic social history research on agents and subscribers, and the organizing, coding, and mapping of data on Google Fusion Tables.  Fusion Tables will preserve the functionality of our data spreadsheets, and its power as a digital gazetteer will assist us to create graphs and geospatial visualizations with a variety of filters.  We will examine the significance of our preliminary findings and explore the possibility of alternate visualizations through manipulation of variables and experimentation with other types of visualization techniques, such as network analysis.  Students with experience with Gephi, ArcGIS, etc. are more than welcome to use knowledge of alternate platforms.  Our work will explore innovative historical methods, consider the significance of race and slavery in the early US, and investigate the role of early African American print culture on the antislavery movement. 

Research

Although research has attempted to identify risk factors and mechanisms for treating disordered eating, eating disorders remain a significant public and mental health concern associated with devastating mortality rates amongst adolescents and young adults, as well as a host of complications including increased risk for depression, obesity, substance use, and health problems. While numerous intervention programs have been developed to treat disordered eating, a majority of individuals display a chronic course and do not fully recover. Thus, it is important to evaluate treatment effectiveness, comparing and critically examining existing interventions. Over the last few decades, meta-analytic review processes have become the gold standard for conducting comprehensive, systematic reviews and in developing treatment recommendations, guidelines, and evidence-based practices. Meta-analysis involves multiple steps including systematic searching of available research studies, analyzing studies for inclusion in the review, coding studies on content, gathering quantitative data from studies, summarizing study data using effect sizes, and analyzing data using available software. The major goal of this project is to comprehensively examine available treatments of eating disorders for adolescents and emerging adults to identify which treatments will be most effective for which types of people and to identify not just what affects treatment success, but how treatments work and what are the most important elements of treatment.

Undergraduate Work

As part of this project, an undergraduate will be trained in all steps of conducting a meta-analytic review through one-on-one mentoring. This includes learning the following steps: (1) database searching, as well as how to critically analyze articles for whether they meet certain inclusion criteria , (2) evaluating and coding complicated aspects of research studies allowing a greater understanding of procedure involved in research, (3) examining articles and extracting necessary data for computing a statistic known as an effect size, that represents how successful the treatment was for certain outcomes, (4) computing these effect sizes and learning how to analyze data, (5) testing for variables that affect treatment effectiveness, and (6) how to write and discuss the project.

Project Abstract

Transcription is the first step in gene expression, where DNA is converted to RNA by the enzyme RNA polymerase. In bacteria, to understand how gene transcription controls the biological functions of the cell, the regulation mechanisms of transcription regulators need to be studied. My project will focus on studying PdxR, a MocR family protein, which is involved in regulation of genes involved in PLP synthesis in the Vitamin B6 biosynthesis pathway. Vitamin B6 is an essential metabolite and is required as a cofactor for many enzymes catalyzing biochemical reactions, especially those involved in amino acid metabolism. The primary goal of this project is to understand how PdxR regulates transcription in bacteria. This information will give us an insight into the regulation of Vitamin B6 synthesis in bacteria and can potentially be used to develop a therapeutic agent to control the detrimental effects of bacteria. To study transcription regulation of PdxR, we will use x-ray protein crystallography to solve the structure of the protein followed by the development of functional assays.

Undergraduate Work

The first component of this research project involves growth, expression and purification of the target protein. The undergraduate student will have an opportunity to learn protein purification from bacterial cells, including the use of a Fast protein liquid chromatography (FPLC) instrument. This protein will be used to set up crystallization screens using a protein crystallization robot. The student will also be trained to optimize and manually set up crystal screens. Once we obtain crystals of the target protein, I will organize a trip to the Advanced Photon Source at Argonne National labs. Here, the undergraduate student can observe how data is collection and interpreted from these protein crystals. Finally, I will assist the student in scientific writing and summarization of the project. The undergraduate student will also get an opportunity to present this work at our weekly group meeting.

Project Description

Sleep is a critical aspect of adolescent development, and research has increasingly recognized the negative effects of disturbed sleep on adolescent physical, psychological, social, and neurocognitive (i.e., bio-neuropsychosocial) functioning. In particular, adolescents with spina bifida (SB) are at-risk for poor bio-neuropsychsocial functioning (e.g., pain, depressive symptoms, executive dysfunction). Sleep disturbances such as difficulty falling asleep, frequent nighttime awakenings, and excessive daytime fatigue are common in youth with chronic illnesses and medical conditions. However, few studies have explored the potential negative impact of disturbed sleep on key bio-neuropsychosocial outcomes in adolescents with SB. Therefore, the overarching goal of this project is to examine sleep disturbances as possible behavioral factors associated with bio-neuropsychosocial functioning in adolescents with SB. This study will assess sleep patterns in adolescents ages 12 to 17 with SB (N = 40) compared to a matched comparison group of typically developing youth (N = 40). A subjective and objective sleep assessment will be conducted; ambulatory actigraphic recordings will be completed over 10 days, and adolescents will complete several questionnaires and a daily sleep diary. Increasing our understanding of the relationship between sleep disturbances and bio-neuropsychosocial functioning in adolescents with SB will be the first step in determining modifiable behavioral mechanisms to inform the development of interventions to improve overall health and well-being in youth with SB.

Undergraduate Work

The undergraduate mentee working with the applicant will be responsible for a variety of tasks that will include coding of sleep-wake profiles using specialized computer software, data entry/management/analyses, as well as involvement in Dr. Grayson Holmbeck’s larger longitudinal study on psychosocial adjustment in children and adolescents with spina bifida. Caitlin will provide one-on-one guidance and support for the development of the mentee’s own independent research project, which will culminate in the dissemination and presentation of research findings for the Graduate Research Symposium. The student’s independent project may focus on data from the applicant’s sleep project or Dr. Holmbeck’s larger study.

Project Description

Binge drinking is a prevalent habit among adolescents; a recent survey showed almost a quarter of high school seniors had reported binge drinking within the last two weeks, despite the U.S. minimum legal drinking age of 21 years of age.  Adolescence is a critical period of brain maturation. Therefore it is no surprise that binge alcohol consumption during adolescence has long-term impacts on the brain and behavior. Importantly, our laboratory has demonstrated long-term dysfunction of the neuroendocrine stress response in rats exposed to binge alcohol during adolescence.  Furthermore, our laboratory is interested in figuring out the molecular mechanisms that underlie the development of this dysfunction. Since dysfunction of the stress response is associated with many psychiatric disorders, it is important to understand how adolescent binge alcohol consumption exerts its effects on the neuroendocrine system. The overarching hypothesis of this work is that binge alcohol during adolescence alters the proteins that modulate the neuroendocrine system, which contributes to inappropriate neuroendocrine and behavioral responses to psychological stress during adulthood.

Undergraduate Work

My undergraduate mentee will help me with two portions of my research. The first portion pertains to the effect of adolescent binge drinking on anxiety behavior later in life. I am currently acquiring behavioral data using a video camera-based tracking system which will be validated by the undergraduate researcher before he or she is un-blinded to the study design. This will give the mentee hands-on experience analyzing behavioral data which is commonly generated in neuroscience research. The second portion of this research pertains to the alterations to the neuroendocrine stress response as a result of adolescent binge drinking. To measure this stress response, the research assistant will use a variety of molecular biology techniques (such as PCR and Western blotting) to detect important mediators in the HPA-axis. These are very commonly used lab techniques that any student pursuing a career in a biomedical-related field would use in his or her future job. The student will spend about 7-8 hours in lab here, 4-5 days a week.

Abstract of Research

Breast cancer remains the second leading cause of cancer-mortality in women worldwide. A cure for breast cancer has been difficult to obtain due to inherent heterogeneity within the disease. HER2+ breast cancer is one of three major subtypes of breast cancer that is associated with gene amplification or protein overexpression of human epidermal growth factor  receptor 2 (HER2).  Current targeted therapy for treatment of HER2+ patients employs a class of drugs such as the monoclonal antibody, trastuzumab or a tyrosine kinase inhibitor, lapatinib. Initially, women respond well to this therapy. However, drug resistance develops during the course of treatment. Notch signaling is a developmentally conserved pathway that is implicated in drug resistance in HER2+ breast cancer. In simple terms, cell signaling refers to transmission of cascade of complex information for the regulation of basic cell function and is initiated when a substance known as ligand binds to a receptor protein and forms ligand receptor complex. Drug resistance is believed to develop from a population of cells termed, “Cancer Stem Cells” (CSCs). These CSCs are believed to be responsible for tumor recurrence which is one reason for disease progression and death. Notch signaling is important for survival of CSCs. However, the mechanism by which Notch signaling leads to survival of CSCs is unknown. My proposal is to investigate a mechanism of action.  Currently, I am investigating different aspects that could lead to increased surface expression of Jagged1. The study would provide novel biomarkers for targeting CSCs and for preventing drug resistance in HER2+ positive breast cancer with the goal of initiating future clinical trials to prevent tumor recurrence.

Project - Undergraduate Student

Epithelial Mesenchymal Transition (EMT) is a process by which cells lose polarity and adhesion while acquiring migratory and invasive properties to become mesenchymal stem cells. EMT is important for developmental processes and plays a role in cancer metastasis and cancer progression. Moreover, EMT has been implicated in CSC formation and additionally Notch signaling, the topic of this proposal, is known to play a critical role in EMT. Since HER2 inhibition leads to CSC formation by upregulation of surface expression of Jagged1, it would be interesting to investigate the possible role of EMT and EMT transcription factors-regulated by Jagged1-mediated Notch signaling.  EMT leads to downregulation of epithelial marker E-cadherin and upregulation of mesenchymal markers like N-cadherin, vimentin and fibronectin. Commonly involved EMT transcription factors include Snail, Slug, Twist and ZEB1. The project would involve assessment of gene expression and protein levels of EMT markers and EMT transcription factors upon pharmacologic/genetic inhibition of HER2. Gene expression would be measured using quantitative Real Time Polymerase Chain Reaction (qRT-PCR) and protein levels would be measured using Western blot. In the long term, the project would provide an insight for the development of novel biomarkers to target CSCs in order to prevent/revert acquired drug resistance in HER2+ breast cancer. The expectation is that the student will work in the lab at Maywood campus Monday – Friday for 4-6 weeks this summer.

Project Abstract

The development of an effective blood substitute is urgent due to increasingly common blood shortages, the need to type-match donated blood, and blood pathogens (e.g. HIV) posing risks for blood transfusions around the world. There have been many attempts at creating hemoglobin based oxygen carriers (HBOC) using a variety of techniques centered around the use of polyethylene glycol (PEG) conjugated to hemoglobin (Hb) tetramers.  A novel method, “Inside-Out” PEGylation, has been developed by our lab to produce a polyethylene glycol crosslinked hemoglobin (PEG XL Hb) polymer. This method utilizes a single PEG backbone that is surrounded by multiple proteins, instead of covering a protein with multiple PEG chains. Hemoglobin is extracted from bovine red blood cells, followed by a crosslinking modification to prevent the protein from splitting apart (protein dissociation). The newly stabilized product is then further modified to produce a reactive site that is able to react with the eight arm PEG reagent. Post production, characterization of the polymer is preformed to determine the polymer’s size, ability to release oxygen, and stability of the polymer compared to un-reacted Hb. Post product characterization, we intend to do in vivo studies to see our product’s efficacy in living systems, looking at oxygen delivery and immunogenic studies. From preliminary studies, we propose that “Inside-Out” PEGylation may lead to the production of a successful universal, disease free blood substitute derived from non-human sources.

Undergraduate Work

The undergraduate research assistant will be working with me in the production of our hemoglobin polymer. This will include extracting hemoglobin from bovine red blood cells, purification of the hemoglobin, crossliking hemoglobin, and modifying the hemoglobin sample with PEG. Post production, they will assist me in further characterization of the product, and purifying reacted hemoglobin from un-reacted hemoglobin. We will proceed to adjust reaction conditions to optimize product formation. By the end of the program the undergraduate assistant will have learned the basics on hemoglobin functionality, and protein preparation/modification. They will leave with a working knowledge of quintessential biochemical techniques and experimentation procedures used in all of academia and industrial research.