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Loyola University Chicago

LUROP

Center for Experiential Learning

Carbon Fellows

David Baltrusaitis

Year: Senior

Major(s):  Bioinformatics, Biology

Mentor(s): Putonti, Catherine and Kelly, John

Department:  Biology

Project Title: CRISPRs: A Hindrance to Viral Conquest

Project Abstract:  CRISPR/Cas systems (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) exist in many bacterial genomes. Genomic comparisons and new studies have found that the CRISPR/Cas system serves as a rudimentary bacterial immune system against viruses. The objective of this study is to determine the importance of CRISPRs for viral protection, and observe how they shape bacterial/microbial communities in nature. I will analyze the genomes of bacteria living in rivers, and inspect the prevalence of CRISPRs and phages in this ecological niche. I will look at bacteria found upstream and downstream from wastewater treatment facilities, which may be affected by phage present in the effluent. This interdisciplinary endeavor will include the development of new computational tools, field sampling, and laboratory experiments in the investigation of CRISPRs and viruses.

 

Jonathon Brenner

Year: Junior

Major(s):  Bioinformatics

Mentor(s): Thiruvathukal, George and Putonti, Catherine

Department:  Biology

Project Title: Unearthing Genomic Fossils of Symbiotic Relationships

Project Abstract:  In the usual sense, transfer of genetic material and evolutionary change is thought as following a path of so called vertical inheritance. Under certain circumstances, however, a process known as horizontal (lateral) gene transfer, the direct transmission of genetic material between species, can occur. While HGT has been found quite frequently amongst bacteria and viruses, HGT between prokaryotes and multicellular eukaryotes, however, has much less frequently been observed. But given the ubiquity of intracellular symbiotic relationships, it stands to reason that HGT should be occurring with regularity in these instances. Existing bioinformatic software is ill-equipped to address the tasks necessitated by searches for HGT. As such, a new tool is needed to extract HGT elements from the genomes of closely-linked organisms. Taking an interdisciplinary approach, we will investigate the prevalence.

 

Mouneeb Choudry

Year: Senior

Major(s):  Biology

Mentor(s): Becker, Daniel and Holz, Richard

Department:  Chemistry & Biochemistry

Project Title: Synthesis of Potential Inhibitors of dapE Enzymes

Project Abstract:  The endpoint of this research is to create, synthesize, and test inhibitors of the dapE enzyme from Haemophilus influenzae with antibiotic activity. The main goal for this project: (I) To construct highly potent small molecule inhibitors of dapE enzymes. It has been proven that DapE¿s are vital for cell growth and proliferation. For this reason, deletion of this gene would cause cell death. The DapE gene has been indentified in several pathogenic Gram-positive and Gram-negative bacteria such as Mycobactrium tuberculosis. In order to define inhibitor binding to the dapE, an interdisciplinary approach will be applied, uniting organic synthetic methods with biochemical, spectroscopic, and X-ray crystallographic methods. Advances are anticipated from the success of this work, since the creation of antibiotics that are effective against antibiotic resistant strains is a major health concern.

 

Emily Cybulla

Year: Junior

Major(s):  Biochemistry

Mentor(s): Becker, Daniel

Department:  Chemistry & Biochemistry

Project Title: Novel GabR Inhibitors as New Antibiotics for Cystic Fibrosis

Project Abstract: Antibiotic development for multi-drug resistant bacterial strains that contribute to recurring infections in Cystic Fibrosis (CF) patients is a critical area of biomedical and medicinal chemistry research. Proposed interdisciplinary studies toward the discovery of inhibitors of GabR and PLP-dependent GABA metabolism in the nonpathogenic species Bacillus Subtilis will enable medical intervention to stall or indefinitely prolong the aminotransferase activity of GabR-related proteins in the pathogens Burkholderia cenocepacia and Bukholderia multivorans. Intervention will enhance the quality of life and prolong the lifespan of CF patients, as these two species belong to the Bcc complex often associated with infections in CF patients, and synthesized inhibitors of GabR in B. Subtilis will likely have similar inhibitory effects in the pathogens.

 

Maxim Maron

Year: Junior

Major(s):  Biology (Molecular emphasis)

Mentor(s): Williamson, Kim

Department:  Biology

Project Title: Screen of LOPAC using Flow Cytometric analysis to identify potential pathways for malaria transmission blocking drug development

Project Abstract:  There is an intimate connection between sexual differentiation and transmission in the life cycle of the malaria parasite Plasmodium falciparum. This link is maintained through the development of gametocytes in a human host which are required for transmission from human to human via a mosquito. Current anti-malarials target the asexual stages of parasites, which are responsible for the physical symptoms seen in patients, and do not affect gametocytes allowing continued transmission of the disease. P. falciparum has a complex life cycle, and the biology of the sexual stages differs from that of the asexual. In order to effectively block malaria transmission inhibitory gametocytocidal compounds are necessary. The Sigma-Aldrich Library of Pharmacologically Active Compounds (LOPAC) contains 1280 compounds that affect a variety of cellular functions. A current technique, flow cytometry, allows for the rapid quantification of individual cells in complex mixtures of populations. Thus, a screen of these compounds on developing gametocytes using flow cytometric analysis will provide useful information regarding stage specific gametocyte cell physiology. This screen will also potentially locate shared pathways between sexual and asexual parasites, which may allow the development of more effective anti-malarial medications. I propose over the course of two years to screen the compounds in the LOPAC and assess which pathways are affected by composites that inhibit gametocyte development.

 

Nicole Minalt

Year: Junior

Major(s):  Biology (Molecular emphasis)

Mentor(s): Kelly, John

Department:  Biology

Project Title: Characterizing the ecology of bacterial biofilms within municipal drinking water distribution systems

Project Abstract:  Biofilms are complex communities of microorganisms attached to solid surfaces that are present in most aquatic habitats, including within municipal drinking water distribution pipes. Very little research has been done on the ecology of biofilms in these pipes, but understanding these communities is important because they contribute to pathogen persistence. I will investigate the ecology of biofilms within drinking water pipes with faculty mentors from the Loyola Biology Department and the Environmental Engineering Department at Northwestern. We have obtained pipe sections from a drinking water utility in Florida and analyzed the biofilms within these pipes using pyrosequencing. My analysis indicated that species composition of biofilms varied seasonally, and that methylotrophic bacteria predominated. Our next step will be to establish a laboratory scale model that will enable us to study these biofilms under more controlled conditions. A Carbon Fellowship would provide me with a tremendous opportunity to continue this important project.

 

Natasha Vyas

Year: Senior

Major(s):  Biology

Mentor(s): Heineke, Amy and Silton, Rebecca

Department:  School of Education, Psychology

Project Title: Neural Correlates Associated with Executive Function Performance in Bilingual Individuals

Project Abstract:  Past research has demonstrated that bilinguals perform very efficiently on executive function measures. EF measures are known to recruit frontocingulate brain regions during tasks that control processing conflicting information, such as inhibition, updating, and shifting. These areas have been linked with resilience, social competence, and school readiness. The proposed study will retroactively examine language brokering skills to study how the ability to rapidly translate between two languages and switch between cultural contexts influences EF and related patterns of brain activity. Frontocingulate brain regions involved in EF will be assessed using electroencephalography methods to illuminate differences between bilingual brokers, bilingual non-brokers, and monolingual individuals. Participants will perform verbal and non-verbal tasks in the three EF domains while we collect EEG data.

 

Paul Wadsworth

Year: Senior

Major(s):  Bioinformatics Biology (Molecular emphasis)

Mentor(s): Liu, Dali and Olsen, Ken

Department:  Chemistry & Biochemistry

Project Title: Simulation Assisted Enzyme Engineering on N-Acyl Homoserine Lactonase, AiiA

Project Abstract:  Vibrio Cholerae, the causative agent of cholera, produces N-acyl homoserine lactones (AHLs) as quorum-sensing signaling molecules to regulate virulence production. The quorum-quenching AHL lactonase (AiiA) can subvert the quorum-sensing pathways of V. Cholerae by hydrolyzing AHLs. Using in silico mutagenesis via Molecular Dynamics simulation, ¿hot spot¿ residues in the active site can be identified and mutated to improve the enzyme potency. The mutant proteins displaying enhanced enzyme specificity and potency in simulations will be experimentally expressed, purified and characterized to validate the results of the simulation assisted enzyme engineering. This project will (1) exploit the anti-virulent potential of AiiA and (2) provide better understanding of the parameter restraints inherent in Molecular Dynamics simulation.

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