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Loyola University Chicago

The Graduate School

Summer 2014 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 uses ultra-high vacuum (UHV) scanning tunneling microscopy (STM) to study chemical reactions on an atomic scale. The reaction I am studying, the synthesis of ethylene oxide by silver catalyzed ethylene epoxidation, has been carried out commercially for 80 years and is now a $22 billion a year industry. Despite this, the fundamental steps in the reaction are still debated. Using UHV-STM, we image individual oxygen and ethylene atoms as they move and interact on a silver surface. The surface is a single crystal of pure silver requiring several weeks of cleaning under vacuum to prepare. The silver crystal is kept at UHV conditions, similar to the pressure in deep space, to ensure that only the materials we want to study are present. Once the surface is properly prepared and characterized, small amounts of oxygen and ethylene are introduced to the UHV chamber. The STM is then used to image the activity on the surface. This is done by moving an atomically sharp metal tip across the surface in picometer sized steps. The current that flows between the tip and sample due to the quantum tunneling of electrons is measured at each point and then plotted, giving an atomic resolution image.

Undergraduate Work: Tips used in scanning tunneling microscopy must be sharpened to a point containing only a single atom. Since there is no easy way to determine whether a tip is sharp other than attempting to image with it, it is important to have a reliable method to produce tips. In our lab we currently use a simple method based on cutting a wire while simultaneously stretching it. Although simple, this method has a fairly low success rate. A common method that has a much higher success rate is to electrochemically etch platinum/iridium or tungsten wire in a strong base. Many factors such as the current used, the length of the wire being etched and the strength of the solution being used are known to impact the sharpness of the tips produced by this approach. Another complication is that platinum/iridium needs to be etched using an alternating current while tungsten is etched using direct current. The project for the summer would be to build an electrochemical etching system and to optimize the etching procedure to reliably produce atomically sharp tips. The overall goal of the project is to have the research assistant make tips that can be used to produce atomically resolved images of oxygen on the silver surface by the end of the summer. The research assistant will also have an opportunity to work with the lab’s scanning tunneling microscope.

Project Description: My project engages a very old topic in philosophy (causation) with a very new method (phenomenology). The essential question “What is causality?” has stumped philosophers for thousands of year. From Plato, to Aristotle, to Aquinas, Hume, Husserl and more, philosophers have had plenty to say about causality, but have rarely found themselves in agreement with one another. Using the methodology of a historical phenomenology, my project investigates the experiential grounds out of which philosophers of causality understood the subject of their investigation. In other words, when Plato or Hume made a statement like “X is the cause of Y”, what sort of experience were they having? How precisely can we describe it? Through a more precise description of the experiences which correspond to causal assertions, I propose that certain paradoxes of causality can be solved or dissolved. The aim of this research is not to defend the position of one or more of the above thinkers, but rather to take a critical and phenomenological perspective on the history of the philosophy of causation in general.

Undergraduate Work:

The undergraduate student will have the opportunity to closely engage the topic of causality through the work of a major philosopher of his or her own choosing. I will help the student come up with an overall plan of research, guide the student through rough spots, and be a general resource on how to pursue advanced level research projects. Together the student and I will progress through a 6-8 week itinerary in which we comb through primary sources on the philosophy of causality, with special attention to passages in which the philosopher illustrates, exemplifies, or otherwise qualitatively describes the experience of cause and effect. Throughout the itinerary, the student will be expected to produce work documenting his or her progress, including (i) an index of relevant passages, (ii) explications of said passages, and (iii) an overarching summary of the philosopher’s philosophy of causation based on said explications. Regular meetings, either in-person or via Skype, will help us stay on course and talk through results. For the final presentation we will compile our collective results into an online chronology app (likely, Timeglider) that will track the evolution of causal experience coordinate with the development of the philosophy of causation. For a sample, see my timeline of Husserl’s influences.

Project Description: My project focuses on cancer research, specifically, the changes in cellular signaling that occur to promote cancer.  Our lab studies a protein called Sprouty2, which acts as a “brake” on a signaling pathway initiated by a group of cell surface receptors called receptor tyrosine kinases.  The other proteins I study are the Hypoxia Inducible Factors or HIFs.  When tumors grow large enough, the oxygen from nearby blood vessels cannot diffuse into the center of the tumor.  This results in the formation of a hypoxic (or lack of oxygen) environment.  Normally, a hypoxic environment would kill cells, however, many cell types, including cancer cells, adapt and survive the hypoxic environment by increasing the HIFs.  HIFs are transcription factors that control the transcription of a variety of genes. Based on previous research and some preliminary data I acquired, I hypothesize that Sprouty2 decreases proteins levels of the HIFs and thereby decreases the transcription of the key genes that the HIFs regulate.

Undergraduate Work: If you choose to work with me, you will be performing a lot of biochemistry experiments.  You would assist me with plating immortalized cell lines, transfecting cells with DNA or siRNA, incubating the cells in a hypoxic incubator, lysing the cells, and performing a western blot.  I would say the major technique that you would need to perform is western blotting.

Project Description: My research focuses on contemporary North American (American, Canadian, and Caribbean) authors – in some cases, extremely contemporary, having first published novels in the last decade. While very different in many respects, all of these authors belong to and/or write about diasporic communities. “Diaspora” refers to populations holding significant political, ethnic, cultural, economic, and religious ties, despite spanning across several nation-states. The social identities of these communities are split between host countries, home countries (real or imagined), and other diasporic clusters. My dissertation asks about the possibility of a “diasporic public sphere” and its relationship to recent diasporic fiction. Briefly, I argue that in an age of globalization, our ideas about what constitutes “the public” are rapidly changing and developing beyond a strictly national community. My project examines the role that diasporic print cultures (including novels, essays, podcasts, graphic novels, promotional websites, Twitter feeds, art books, and original interviews) play in critiquing the nationalist assumptions of previous public sphere theories, and how such cultures shape new transnational publics.

Undergraduate Work: There are three components to your work this summer. The first asks you to gather research on several contemporary authors. Since these authors are so new, you will have to go “off-road and into the wild web to find all extant information on them. JSTOR and other academic databases will not always have much information on them yet; as a result, you will be looking for reviews, interviews, original essays, podcasts, promotional materials, and more. The second component is preparation for a summer institute conference I will be attending at Dartmouth in June. This will entail researching the attendees and gaining information about changes in the discipline of American Studies. The third component is researching publication information: for example academic journals in the field, citation software, and formatting requirements. Together, these three components cover the majority of the independent work conducted by graduate students, and for that reason, should provide you with great experience in all aspects of the field.

Project Description: Depression is one of the most common and devastating psychological disorders. Identifying vulnerability factors for the development, maintenance, and recurrence of depression is an important challenge with clinical relevance, informing treatment and prevention programs. An individual’s capacity to cope with stress and negative life events has been consistently and strongly linked to the likelihood of developing depression. However, the fundamental mechanisms underlying how individuals cope are not well understood. This translational project proposes to extend existing coping and depression research to explore relevant brain circuitry and cognitive processes. Using a combination of self-report measures, behavioral tasks and electroencephalography (EEG) methodologies, the study will investigate the relations between specific cognitive functions and how individuals cope with stress, as well as the subsequent impact on depression symptoms. Self-report measures will be used to assess depression symptoms, coping style, and coping flexibility. Measures of behavioral performance (e.g., reaction time on computer tasks) will be used to assess fundamental cognitive functions, such as set-shifting and inhibition, that likely support coping abilities. Neural activity will be measured by placing an EEG cap on top of the scalp during these tasks, and recording electrical signals that occur naturally within the brain. Based on previous research, it is predicted that individuals’ ability to efficiently inhibit processing of negative information and/or shift attention to different stimuli or tasks will be associated with their ability to effectively cope with stress, which will then predict subsequent levels of depression symptoms.

Undergraduate Work: The undergraduate research assistant (RA) working on this project will have the opportunity to become trained in electroencephalography (EEG) methodology, questionnaire administration, scoring/coding responses, and data entry. He/she will work with a team of graduate students and advanced undergraduate RAs on various aspects of the study. He/she will initially practice administering project tasks and setting up EEG data collection to become comfortable with the project details. He/she will also become familiar with project recruitment materials and computer-administered tasks, and trained on contacting and replying to potential participants. The RA will ultimately be involved with participant recruitment and data collection (administration of questionnaires, computer tasks, and EEG capping). He/she will be invited to attend project meetings, in addition to frequent one-on-one meetings with me. Toward the latter portion of the summer, the RA will work with me on scoring, coding, and entering data into SPSS/PASW (a statistical database). He/she will have the opportunity to observe data entry and simple statistical tests, as well as more complex statistical analyses with preliminary data. We will work together to interpret these findings, and how they support or refute the hypotheses of this study.

Project Description: My dissertation research examines the emergence of support for prosecutions of current and former officials for human rights crimes in three Middle Eastern countries. Specifically, I look at the subject of enforced disappearances in Turkey, Lebanon and Algeria. During fieldwork in these countries I will be collecting data through interviews with human rights activists, legal professionals and relatives of victims of enforced disappearances.

Undergraduate Work: An undergraduate research assistant would be responsible for carrying out online research into media and civil society accounts of enforced disappearances in the three countries. This would include first searching online for journalistic accounts, civil society publications, artistic work and other media relating to enforced disappearances in the three cases. I would work with the student to create a digital database of those sources I have already collected and those found during the students research, with certain information recorded about each source. If time permits the student would also be asked to do library database searches and summaries of relevant work on the phenomenon of enforced disappearances. The work would consist of 10-15 hours of work a week. A student with Arabic, Turkish or French language skills would be beneficial. This research would facilitate my ability to write up the background chapters on my three cases, as well as an additional chapter (to be written later) on the context of disappearances in the Middle East North Africa region.

Project Description: Backlash is a specific type of discrimination that occurs when people discriminate against a person for defying cultural stereotypes. Both working women without children and working mothers often face discrimination in the workplace, but researchers have not yet looked at how backlash against working mothers might be different from backlash against working women without children. Working mothers may face different forms of backlash than working women without children because stereotype of working mothers (generally liked but not seen as very intelligent) is different than the stereotype of working women without children (generally seen as intelligent but not liked). People draw on the content of group stereotypes to inform how they behave towards stereotyped group members, the form of backlash against the two groups might be different. My dissertation project includes a face-to-face lab study to test whether working women are primarily vulnerable to hostile sexist backlash such as hiring discrimination and resentment, whereas working mothers primarily experience benevolent sexist backlash such as patronizing help and unintended ostracism.

Undergraduate Work: Undergraduate students who assist me with my dissertation project will recruit participants, serve as a research assistant and run participants through a psychology experiment, and manage all research data. For participant recruitment, the student will approach students on campus, contact potential participants, and manage the participant schedule. As a research assistant, the student will train on the research protocol, set up materials for the study, and run experimental sessions. Finally, the student will be responsible for backing up all of the data we collect to external hard drives. During our last week, I will sit down with the student to go through preliminary data analysis and discuss our preliminary results and implications. By the end of the program, the student will gain important experience with conducting a face-to-face laboratory study and common experimental social psychology research protocols, as well as learn what it is like to be a graduate student in psychology.

Project Description: Since its early usage in post-Enlightenment philosophy, the concept of ideology has been an enduring problem between theology and politics. This is due primarily to the plurality and ambiguity of its meaning and its usage.  In its classical definition by Marxist critical theory, “ideology” refers, in a pejorative way, to how certain ideas hide or conceal the concrete realities that shape human life, practical activity, and social relations, usually for the benefit of those who possess political power and/or economic privilege. “Ideology” is also most generally understood as a descriptive term for a broad belief system or a rigid set of values. The variety of contexts and meanings in which ‘ideology’ can and is used results in a regrettable and superficial understanding or application, especially when it comes to Political Theology; my dissertation hopes to show that this state of affairs stems in large part from the absence of ‘immanent critique’ within theology itself. Meanwhile, in a surprising reversal, the supporters of contemporary critical theories of ideology have been turning to theology precisely as ideology critique, rather than as its target. They represent a new recognition of the emancipatory potential of theology, not only to diagnose instances of injustice, but also to respond with an acute awareness of our current social crisis and political impasse. It must be said, however, that major representatives of this trajectory also lack substantive accounts of ‘immanent critique’. It is at this point that my dissertation makes its contribution: I sketch a constructive response, namely “a political theology of critique” that retrieves immanence and materialism as truly intrinsic, and even more so, critical concepts in theology. I clarify the role of “ideology critique” in political theologies with recourse to critical theory, and so further illustrate how contemporary theories of ideology continue to mediate theology and politics, a point that is increasingly important in light of the recent “turn to religion” in contemporary politics and culture.

Undergraduate Work: My research is theoretical in focus, but political in orientation. My undergraduate collaborator and I will be practicing a Critical Pedagogy research model that privileges critical thinking and praxis. In this model, research engages in a cycle of theory, application, evaluation, critique, and then a return to theory, with the ultimate aim of producing innovative knowledge for the sake of social transformation. Toward this end, my research collaborator and I will read Paulo Freire’s seminal Pedagogy of the Oppressed together in order to learn more about how to integrate insights from critical education into research methods in theology and philosophy. We will attempt to implement this pattern in tandem, working together closely throughout the summer Research Mentoring Program to produce close readings of primary texts from seminal authors in both philosophy and theology, in consort with relevant secondary literature, specifically on the topic of the relation between political theology and ideology critique. In the first four weeks, my undergraduate collaborator will work from a set of research questions that I will provide and explain in our initial meetings. She/he will be primarily responsible to identify and collect secondary articles from academic journals and reports from research institutes as it relates to those questions. The questions will focus on ‘the theological turn’ in critical theory, specifically concerning the concepts of immanence and materialism, and its impact on various political movements like the global Occupy acts or the Spanish Indignados protests. In the second half of the program, the collaborator will annotate these sources and summarize their contributions to the guiding questions of the dissertation. The student will also actively help me with drafting and editing the initial drafts of chapter 6, the dissertation’s constructive chapter. Throughout this process, I plan to meet weekly with my collaborator to discuss our collective progress and work through various questions we both may have, in addition to more general discussions about our mutual interests. I am very eager to have intentional conversations with the student about her/his own research agenda, and find ways to contribute directly to her/his academic and professional goals. Also, it is very likely that we will find ourselves drinking (a lot of) coffee or tea.

Project Description: The central question of my research project is this: in today’s globalized, networked world, how do people and cultures deal with the overwhelming amount of information and worldviews that surround and influence us? I explore this question by looking at the ways literary authors represent and analyze globalized complexity in contemporary global fiction and, to a lesser extent, new media literatures (web-based narratives and video games). My dissertation uses cultural, narrative, and media theory to analyze how individuals, communities, and globalized networks manage differences among interpretations of history or politics, between the promises of an ideology or nation and the lived experiences, and among multiple cultural and national traditions. I highlight newly prominent composite narrative structures featuring multiple focal points that span diverse times, places, ideologies, identities, and geopolitical situations (as well as complex technological networks). Through this research, I hope to illuminate how we manage overwhelming complexity and what slips through the cracks when we realize we can’t deal with all the information and perspectives that inform our identities and communities.

Undergraduate Work: My undergraduate mentee will assist with research on chapter four of my dissertation, which analyzes the close ties between globalization and technology in a novel of globalization (Hari Kunzru’s Transmission) and a novel commonly labeled (and disregarded) as science fiction (Neal Stephenson’s The Diamond Age). Our research will support a technology and globalization-oriented analysis of these works’ forms and effects to develop new perspectives on the influence of technology and geopolitics on our lives and societies. My mentee’s primary tasks would involve reading the two novels and conducting research in the fields of globalization studies; media, technology, and science fiction studies; and literary criticism of the two novels. Limited additional research work would relate to other chapters of my dissertation to provide my mentee with a productive diversity of tasks and topics. Which research texts and tasks I assign to my research assistant will depend to some extent on his or her own research interests (which we will discuss early on) as well as what I deem likely to be most productive for my assistant as a developing researcher, so that the experience can be of maximal interest and benefit to him or her. My mentee will gain familiarity with multiple fields of specialization and develop effective research practices with both short and long scholarly and literary texts involving different forms of research reading and annotation (reading the whole text thoroughly, reading the introduction and selected chapters, skimming large sections to get a general sense of the contents, etc.).

Project Description: Kathryn’s research explores how new technology influences children’s cognitive development.  She is interested in comparing children’s learning from traditional and contemporary forms of media.  Because no research to date has examined how preschool children learn from electronic books (e.g., e-books on the iPad), Kathryn is utilizing an experimental design to address this issue.  In her project, children are exposed to print or electronic books and listen to a story read by an adult or narrated by an audio device.  Such a design permits her to measure how book type (print vs. electronic) and narration type (live adult reader vs. audio narration) affect learning.  After children hear the story, she tests their learning of words from the story.  She also measures their attention to the books.  Her dissertation will contribute novel findings to the growing field of developmental science.

Undergraduate Work: During the summer months, the undergraduate research assistant will experience many aspects of graduate level research.  Specifically, the primary responsibilities will include: (1) participant and school recruitment, (2) data coding, and (3) data entry.  The majority of the work will be conducted on campus at the Infant and Early Childhood Cognition Laboratory.  In addition, the undergraduate will attend 1-2 testing sessions offsite to experience data collection.  Testing will take place at preschools in the Chicagoland area (Kathryn will provide transportation). Because the project is conducted with preschoolers, the undergraduate should have experience working with children and be able to build rapport with this young population.  The undergraduate is expected to work 8-10 hours per week for 6-8 weeks; a schedule will be created  in advance to accommodate work, holiday, and travel plans.  Because there are several components to the position, there will always be something new and challenging for the assistant to learn.  After the summer, the mentor and mentee will remain in contact in order to prepare for future commitments (i.e., meetings with the Associate Dean, final presentation, and the Research Symposium).

Project Description: To promote their survival in harsh conditions, bacteria often form a complex structure called a biofilm, a community of bacteria encased in an extracellular matrix that can protect the cells from environmental threats, including treatment with antibiotics. As a result, pathogenic bacteria that form biofilms during human colonization pose an increasing threat to human health. One of the few natural model systems used to study biofilm formation in the context of a host is the colonization of the squid, Euprymna scolopes by its symbiotic partner, the bacterium Vibrio fischeri. To successfully colonize the squid, V. fischeri cells must form a biofilm during the initial stages of host-microbe interaction. This model thus serves as a simple but powerful model for asking questions about the regulation of biofilm formation and colonization in the context of a host that may be translated to better understand the pathogenic colonization of humans by related bacteria such as Vibrio cholerae. Recent work has identified a number of genes required for biofilm formation and colonization by V. fischeri, but data from other systems suggest that additional cellular factors are involved. One such factor is the concentration of the signaling molecule cyclic-di-GMP (c-di-GMP). Expression of phosphodiesterase (PDE) genes, which encode proteins that break down c-di-GMP, decrease the overall cellular pools of c-di-GMP. In other bacteria, PDE expression promotes a transition from a biofilm to a non-biofilm state. We hypothesize that one or more of the 20 putative PDEs encoded by V. fischeri will similarly disrupt biofilm formation. To test this hypothesis, we will assess the ability of each of these genes to disrupt biofilm formation in V. fischeri. Through this work, we will gain a broader understanding of how PDEs control biofilm formation in V. fischeri, information that has the potential to contribute insights into the development of methods to treat human infections.

Undergraduate Work: The student will use well-established protocols to isolate and clone various PDE genes hypothesized to disrupt biofilm formation into plasmid vectors. S/he will then introduce those plasmids into biofilm-forming V. fischeri cells. The student will then test whether the PDE genes disrupt biofilm formation by assessing the strains for the ability to form a biofilm.

Project Description: The media is saturated with violence and aggression. Decades of research on the effects of media violence exposure have shown a clear association between violent media exposure and increased aggression. Media violence exposure is known to increase pro-violence normative beliefs, hostile attributions, and decrease empathetic responding. However, the cognitive and biological processes underlying these changes in behavior are less well understood. The proposed study will integrate cognitive neuroscience and experimental psychology to study the influence of media violence exposure on the cognitive processes associated with empathetic responding. In particular, the proposed study will examine the influence of media violence exposure on the neural correlates of emotional facial processing and emotional regulation using Electroencephalography (EEG) methodologies. These effects will be examined in habitual violent video gamers and non-habitual gamers. Insight into the effect of media violence exposure on emotional processing will help decrease aggression in society by helping researchers understand the cognitive processes underlying empathetic responding. Abnormalities in these processes place people at increased risk of aggressive behavior and can be used as an early screening tool to identify people at risk for aggressive behavior. Developing a better understanding regarding how media violence exposure modulates neural and cognitive processes will help parents, policy makers, and media makers more accurately evaluate the effects of media violence exposure on aggression, empathy, and society.

Undergraduate Work: It is anticipated that 1-2 participants will be run per week for the 8 week period, resulting in approximately 18 participants. Each participant will take approximately 2.5 hours to run, not including data reduction and cleaning. The undergraduate student will also be responsible for data cleaning, which takes approximately 30 minutes per participant and recruitment and scheduling. The undergraduate student will also be expected to help with manuscript preparation from pilot data collected during the Winter 2014 semester. This pilot project includes EEG recording for approximately 95 participants and survey data. The undergraduate student will be expected to help with manuscript revisions, tables and figures, and writing of the methods section of the manuscript.

Project Description: Charter schools were initially created with the intention of empowering teachers as educational experts.  It would seem, then, that charter schools should be committed to teacher professionalization. Sociologists of Education have identified indicators of teacher professionalization including teacher credentials, mentoring programs, professional development opportunities, teacher specialization, teacher authority over classroom and school decisions, compensation, and prestige.  Using these indicators, this qualitative case study seeks to determine whether a charter school has lived up to its promise for teacher professionalization. Through teacher and administrator interviews, teacher shadowing/observation, school meeting observations, professional development observations, and school document analysis, this study will try to determine how teachers and administrators view teacher expertise as it relates to indicators of professionalization.

Undergraduate Work: This summer, my research mentee will learn about qualitative research techniques in a school context.  The summer work will include interview transcription (typing an audio interview into a word document), school document collection, and some qualitative coding (finding themes in qualitative data). The student will accompany me in observing school meetings and teacher professional development sessions.  As needed, the mentee may conduct an observation independently.

Project Description: Cystic Fibrosis (CF) is a genetic disorder that causes the body to produce thick and sticky mucus in the lungs and pancreas, leaves chronic lung infection and loss of lung function. Approximately 1 in every 29 Caucasian Americans carries the cystic fibrosis gene. Nearly, 1,000 CF diagnoses are reported every year, and their survival age is 37.4. With 70,000 people across the world, antibiotic development presents the opportunity for treatment of bacterial infections. Our research involved in the Burkholderia cepacia Complex (Bcc), the pathogen that related to the respiratory infections among CF patients. Importantly, the strain is related to Bacillus Subtilis by their metabolism of gamma-amino butyric acid (GABA) to produce glutamate, which is an essential metabolite in bacterial nitrogen metabolism. This similar glutamate metabolism makes B. Subtilis an ideal, non-pathogenic model to study the mechanism on the inhibition of GABA/ glutamate metabolism. We are trying to identify the substrate specificity of GabR form the B. subtilis by using X-Ray Crystallography and some enzymology approaches.

Undergraduate Work: During the first two weeks, at the end of May, I will train the student in protein purification and protein crystallization technique, so that he/she will be capable of setting up the crystallization for the target protein and the protein/substrate complex. For the next three/four weeks, we will work with the circular dichroism, trying to identify how the protein secondary structure change while binding with different substrates/ inhibitors. At the end of the June, I will arrange a trip to APS (Advanced Photon Source) @ Argonne National Laboratory; student will be able to visit the APS and observe how we collect the data for the protein crystals. At the last week, I will assist the student in completing a full story of the substrate specificity for the target protein, GabR.


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