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2015 Summer Research Symposium Sponsored by

The Bayer School of Natural and Environmental Sciences

Duquesne University Undergraduate Research

Program

Keynote Address:

Charles Kahle, II, Ph.D.

Vice President, Research and Development, Coatings

Chief Technology Officer

PPG Industries

“The Secret Life of Paint:

What You See and the Science Behind It”

Friday, July 31, 2015 9:00 a.m. – 4:00 p.m. Bayer Learning Center & Mellon Hall of Science Duquesne University

Welcome to the 2015 Summer Undergraduate Research Symposium!

It is a pleasure and privilege to welcome you to today’s 18

th Annual Summer Undergraduate Research

Symposium at Duquesne University. Each year the number of student participants and the quality and breadth of the research presented at this symposium continue to grow. The abstracts in this year’s program highlight the remarkable quality of the student research that we will see and discuss at today’s symposium. In an era in which we hear persistent concerns regarding our nation’s ability to sustain global competitiveness and global pre-eminence in the STEM disciplines, events such as today’s conference should reassure all of us of the superb caliber of the scientific research and training that occurs on a daily basis in our colleges, universities and research centers. Today’s presentations reinforce our conviction and confidence that we are preparing an emerging cadre of future scientific leaders who will possess the creativity, motivation, and intellect to meet and solve the challenges that our society faces. On behalf of the faculty, students, and staff of the Bayer School and Duquesne University, I am pleased to offer my sincerest congratulations to each of the student researchers participating in today’s symposium and to convey our best wishes for continued success in your academic and professional careers! Sincerely,

Philip Reeder, Dean, Bayer School of Natural and Environmental Sciences Schedule:

9:00 AM Registration and Poster Set-Up Mellon Patio, Academic Walk Side Continental Breakfast Rotunda, Bayer Learning Center

10:00 AM Welcome and Keynote Address Pappert Hall, Bayer Learning Center 11:00 AM Plenary Session (Student Presentations) Pappert Hall, Bayer Learning Center 1:00 PM Picnic Lunch Mellon Patio, Bluff Street Side 2 – 4:00 PM Poster Session Mellon Patio, Academic Walk Side Contents:

Map…………………………………………………………………………………..………..………………………….2 Welcome, Keynote Address, Plenary Session Schedule…………………………………………………..….……3 About Dr, Charles Kahle, II…….…………………………………………………………………………….…………4 Index of Authors and Posters………………………………………………………....………………….…..………..5 Colleges and High Schools Represented……………………………………………………………………..………9 Abstracts……………………………………………………………………………….…………………….……..……10

Instructions to Authors:

Authors presenting posters should locate their abstract number in the index of this program and then find the poster board space marked with that number. Authors with even numbered poster assignments must be present from 2 p.m. to 3 p.m. to answer any questions. Authors with odd numbered posters must be present from 3 p.m. to 4 p.m. Authors presenting talks during the Plenary Session should report to Pappert Hall no later than 9:15 a.m. A tech assistant will be available to download your PowerPoint presentation.

_______________________________________________

10 a.m. Welcome, Dr. Philip Reeder, Dean, Bayer School of Natural and

Environmental Sciences, Duquesne University

10:10 a.m. Keynote Address, Dr. Charles Kahle, II Vice President, Research and Development, Coatings and Chief Technology Officer PPG Industries

“The Secret Life of Paint: What you see and the science behind it”.

11:00 AM Student Presentations

Katelyn Dray Diffusivity and loading capacity of doxorubicin in a series of tubular DNA origami nanocarriers Department of Chemical and Petroleum Engineering, University of Pittsburgh

Gage Tiber Part per Million Resolution Optical Wavemeter

Department of Physics, Duquesne University

Amanda Kowalczyk Identifying Genes Associated with Longevity in Mammals by Comparing Rates of Evolution of Orthologous Genes Department of Computational and Systems Biology, University of Pittsburgh

11:45 AM Short Break

Lianna Paul A Genetic Screen for Blood-induced Promoters from Asaia bogorensis,

a Midgut Symbiont of Malaria Vector Mosquitoes Department of Biological Sciences, Duquesne University

Fatima Umanzor Impedimetric Detection of Cardiac Blood Markers Using Platinum Wire-

Based Biosensors Department of Biomedical Engineering, University of Pittsburgh

Joshua Imperatore RNA G-Quadruplex Topology and Stability Department of Chemistry and Biochemistry, Duquesne University

Marc Hazur Detection of metastatic melanoma in the bloodstream using laser

technologies and properties of photoacoustics Biomedical Engineering Program, Duquesne University

Session Moderator Theordore A. Corcovilos, Ph.D.; Assistant Professor, Department of Physics,

Duquesne University

Plenary Session Schedule Pappert Lecture Hall

Bayer Learning Center

Page 3

Charles F. (Chuck) Kahle, II

Chief Technology Officer and

Vice President, Coatings R&D

Chuck Kahle is chief technology officer and vice president, coatings research and development

for PPG Industries, with responsibility for science & technology globally.

He began his career with PPG in 1987 as a research chemist at Allison Park. Chuck progressed

through several research assignments until 1998 when he was appointed associate director for

R&D for silica products. He was appointed associate director R&D for OEM glass in 2002

and director, research coatings & resins in 2004. In 2007, Chuck was appointed vice president

coatings R&D, and in 2008 assumed the additional role of chief technology officer.

Chuck earned a BS degree in chemistry from Bowling Green State University, and a PhD in

organic chemistry from the University of Illinois at Urbana-Champaign.

Chuck is a member of the American Chemical Society and a board member of the Carnegie

Science Center. He is named in 16 U.S. patents.

Name Poster # Page # Name Poster # Page #

Adams, Brian 35 18 Clymer, T. 31 17

Agosto Rivera, Jose 25 16 Coleman, Mary 27 16

Ahmed, Ayan 15, 112 13, 37 Colvin, Amanda 29 17

Aitken, Dr. Jennifer 18, 24, 43 14, 15, 20 Corcoran, Timothy 120, 121 39, 40

Allen, Erika 88 31 Corcovilos, Dr. Theodore 69, 116 27, 38

Altobelli, Ashley 95 33 Cox, Abigail 74 28

Anderson, Dr. Carl 94 33 Cribbs, Marvene 18 14

Andreola, Laura 31 17 Cutteridge, Taylor 64 25

Auron, Dr. Philip 98 34 Cwalina, Caroline 22, 100, 101 15, 34, 35

Bandi, Kathryn 84 30 Davidson, Lance 33 18

Basu, Dr. Partha 51, 55, 67 22, 23, 26 Davies, Isaac 69, 116 27, 38

Baucom, Kierstin 112 37 Davis, Imogene 117 39

Baumgartner, Matthew 108 36 Dean, James 48 21

Bayline, Dr. Ronald 45, 46 21 DeMarco, Andrew 14 13

Begur, Mallik 94 33 Dempsey, Alison 50 22

Behrmann, Marlene 8 11 Devlin, Kasey 18, 24 14, 15

Benmokhtar, Dr. Fatiha 52 22 Diallo, Amadou 22 15

Bennett, Jennifer 44 20 Diaz, Vanessa 96 33

Bergman, Shana 36 18 Dickter, Adam 8 11

Blystone, Ashley 87 31 Dille, Sara 51, 67 22, 26

Bondi, C. 71 27 DiSanti, Domenic 23 15

Bonifacio, Cecile 65 26 Dittrich, Markus 53 23

Boyd, Sunny 107 36 Dove, Lindsey 45, 46 21

Brant, Jacob 62 25 Dray, Kate "OP" 19 14

Broderick, Jennifer 117 39 Drennen, Dr. James 94 33

Brodsky, Jeffrey 50, 66 22, 26 Dubnik, Sarah 104 35

Brooke, Robert 69, 116 27, 38 Eckert, Scott 72 27

Bruchez, Marcel 50 22 Ermentrout, Bard 107 36

Buerk, Stephanie 102 35 Esposito, Emilio 98 34

Buszko, Ethan 71 27 Evans, Dr. Timothy 114 38

Camacho-Flores, Antonio 6 11 Evanseck, Dr. Jeffrey 15, 31, 63, 106, 112, 122 13, 17, 25, 36, 37, 39

Camacho, Carlos 108 36 Federspiel, Dr. William 56 23

Candiello, Sarah 10 12 Ferrara, Lyndsie 119 39

Carlson, Amy 106 36 Ferraro, Nick 14 13

Carnahan-Craig, Sarah 109 37 Fiedor, Jaclyn 113 38

Cascio, Dr. Michael 14, 21, 29, 41, 58 13, 15, 17, 20, 24 Firestine, Dr. Steven 31, 122 17, 40

Castelleno, Holly 20 14 Fucich, Daniel 34 18

Cavanaugh, Dr. Jane 77, 88 29, 31 Gaetano, Christian 89 32

Chennubhotla, Chakra 32 17 Gagliardi, Austin 106 36

Chikina, Maria 118 39 Galbraith, Madeline 76 28

Cho, Nicholas 33 18 Gawalt, Dr. Ellen 26, 47, 87, 106 16, 21, 31, 36

Chowdhury, Tara 96 33 Gillis, Julie 69, 116 27, 38

Clark, Nathan 118 39 Glenn, Jennifer 18, 43 14, 20

Clermont, Dr. Gilles 49 22 Goldschmidt, Benjamin 91, 92, 93 32, 33

Graca, Connor 78 29

Index of Posters and Authors

OP - Oral Presentation Page 5


Hain, Ethan 13 13 Kwiatkowski, Adam 50 22

Harper, James 17 14 Lai, Yi-Tak 45, 46 21

Hazur, Marc "OP" 92, 93 32, 33 Lampe, Dr. David 79 29

Hebert, Sebastien 31 17 Lash, Melissa 54 23

Heinemann, Scott 66 26 Latona, Amber 24 15

Herneisey, Michele 1, 3 10 Latta, Steven 105 36

Hockman, Megan 59 24 Lau, Stephen 83 28

Hoenig, Brandon 105 36 Lax, Neil 74 30

Hogan, Brea 43 20 Leak, Dr. Rehana 66, 115 26, 38

Holland-Minkley, Amanda 4 10 Leonhard, Anne 49 22

Hong, Eun Joo 1 10 Lesuisse, Catherine 110 37

Honick, Anthony 64 25 Lettan, Dr. Robert 10 12

Huber, Alex 120 39 Levine, Dr. Stacey 5, 7 11

Hutchison, Daniel 115 38 Lezon, Timothy 36 18

Imperatore, Joshua "OP" 86, 103 31, 35 Lim, Min Soo 26 16

Ireland, Timothy 61, 69, 116 25, 27, 38 Little, Steven 54 23

Isnata, Kinardi 7 11 Liu, Lu 1, 3 10

Iuliucci, Robbie 80 29 Liu, Tina 8 11

Janecka, Dr. Jan 117 39 Long, Caela 90 32

Janjic, Dr. Jelena 1, 2, 3 10 Lotz, Nicholas 121 40

Jean, Bernandie 10 12 Lutty, Sara 41 20

Jensen-Seaman, Dr. Michael 59, 109 24, 37 Mackie, Timothy 50 22

Jimenez-Ruiz, Ivan 25 16 Madura, Dr. Jeffry D.10, 35, 75, 76, 78, 82, 83,

86, 98, 103

12, 18, 28, 29, 30, 31,

34, 35

Jones, Jeramiah 67 26 Magyan, Andrew 28 16

Jones, Kara 16 13 Malkin, Alex 56 23

Jonik, Benjamin 60 24 Maria, S. 71 27

Kadjo, Josiane 3 10 Markovetz, Matthew 121 40

Kantor, Elyssa 10 12 Martin, Matthew 53 23

Keith, John 48 21 Mason, Daniel 115 38

Kelley, Zachary 58 23 Matuk, James 5 11

Kelly, Allison 112 37 Maxwell, Andrew 97 34

Kim, Hye-Young 33 18 Mazzone, Carly 87 31

Kirk, Sean 44 20 McBride, Michael 119 39

Kochanek, Sarah 31 17 McCarthy, Dr. Joseph 54 23

Kocher, Matthew 39 19 McCormick, Dr. Joseph 34, 39. 44 18, 19, 20

Kodjo, Nadejda 47 21 McCullough, Tyler 17 14

Koes, David Ryan 13 13 McGregor, Sarah 57 24

Kolb, Alex 50 22 McKenzie, Sarine 51 22

Kolber, Dr. Benedict 16, 74, 90 13, 28, 32 McLaughlin, Rebecca 73 28

Kostek, Matthew 40 19 McShea, Hannah 107 36

Kowalczyk, Amanda "OP" 118 39 Mesinere, Sam 80 29

Krasowski, Collin 50 22 Mihailescu, Dr. Mihaela-Rita 84, 89, 111, 114 30, 32, 37, 38

Kuhn, Jenna 70 27 Mills, Sara 65 26

Kumta, Dr. Prashant 42, 85 20, 31 Mogesa, Benjamin 55 23




Moghaddam, Bita 96 33 Robinson, Daniel 12 12

Molina, Ana 45, 46 21 Roffe, Simonseth 11 12

Moore, Carrie Ann 39 19 Rohde, Dr. Jeffrey 15, 112 13, 37

Moore, Colin 93 33 Ropelewski, Alex 25 16

Mraz, Margaret 9 12 Rutter, Nathan 98 34

Mrohs, Kevin 34 18 Sadler, Katelyn 16 13

Murugavel Shanthi, Pavithra 85 31 Saleem, Muzamil 2 10

Neel, Spenser 122 40 Sanders, Ryan 2 10

Nehl, Emily 2 10 Sannerud, Jens 99 34

Neilan, Dr. Rachel 61 25 Santiago-Berríos, Mitk’El 6 11

Nesbitt, Nicole 60, 62 24, 25 Saravanan, Karthikeyan 48 21

Newbury, Dr. Roberta 117 39 Schall, Rachael 86, 103 31, 35

Nguyen, Dr. Linh 23, 30 15, 17 Schultz, Autumn 30 17

Nguyen, Jenna 56 23 Seliman, Youstina 38 19

Ni Chochlain, Aife 32 17 Seybert, Dr. David 22, 100, 101 15, 34, 35

Nicholas, Hugh 6 11 Shaffer, Jacob 114 38

Nuttle, Timothy 38, 105 19, 36 Shaffer, John 72 27

O'Donnell, Dr. Allyson 50 22 Shaik, Sadiq 22, 100, 101 15, 34, 35

Ortiz-Zuazaga, Humberto 25 16 Shane, Jackie 79 29

Oshin, Dr. Kayode 9 12 Siefert, Elizabeth 2 10

Palmer, Abigail 4 10 Simko, Dr. Lynn 113 38

Parker, Dr. Robert 49, 121 22, 40 Simon, Nicholas 96 31

Patterson, Khiry 81 30 Sinagra III, Charles 24, 43 15, 20

Patton-Vogt, Dr. Jana 60, 62 24, 25 Spirik, Kassandra 75 28

Patil, Mitali 42 20 Sprauer, Sarah 117 39

Paul, Lianna "OP" 79 29 Stabile, Nicholas 88 31

Perez, Cheyeanne 21 15 Steinbach, Douglas 94 33

Perez, Elizabeth 21 15 Stevens, Andrea 2 10

Perlman, Susan 102 35 Stolz, Dr. John 12, 70, 95 12, 27, 33

Pestok, Jordan 81 30 Stone, John 35 18

Petrell, Elizabeth 91, 92, 93 32, 33 Suarez, Nicholas 37 19

Pintauer, Dr. Tomislav 9 12 Suehr, Gregory 68 26

Plavchak, Christine 80 29 Sullivan, William 54 23

Pollock, Dr. John 2 10 Sweeney, Matthew 85 31

Pollock, Taylor 109 37 Sweetnich, Rachel 40 19

Porter, Dr. Brady 38, 64, 105 19, 25, 36 Szent-Gyorgyi, Christopher 50 22

Posimo, Jessica 66, 115 26, 38 Szucs, Dr. Kimberly 40 19

Potdar, Sneha 88 31 Tamez, Angel 63 25

Ratvasky, Stephen 55 23 Tang, Pei 97 34

Raybuck, Christopher 77 29 Thomas, Rebekah 26 16

Reger, Nina 47, 87 21, 31 Tian, Xiao-Jun 99 34

Reid, Dr. Pamela 95 33 Tiber, Gage "OP" 69, 116 27, 38

Resko, Zachary 39 19 Trevelline, Brian 38, 105 19, 36

Rhodes, Professor Diane 113 38 Trotta, Richard 52 22




Twigg, Julianna 91, 92 32 Wright, Thomas 77 29

Umanzor, Fatima "OP" 42 18 Xing, Jianhua 99 34

Underwood, Soraya 29 17 Zaccagnini, Chris 69 27

Upadhyay, Shiv 75 28 Zhang, J.H. 43 20

Valenti, Domenic 17 14 Zuckerman, Daniel 104 35

Van Stipdonk, Dr. Michael 55, 73, 81 23, 28, 30

Vázquez-Quiñones, Luis 6 11

Vera, Michael 60 24

Vernier, Brandon 15, 112 13, 37

Viator, Dr. John 91, 92, 93 32, 33

Waddell, Jordan 77 29

Weiland, Nicole 66 26

Weixel, Kelly 4 10

Wells, Marta 97 34

Wendekier, Katy 77 29

West, Brittany 34 18

Wetzel, Dr. Stephanie 20, 27, 57 14, 16, 24

Wheeler, Dr. Ralph 23. 30 15, 17

Wierbowski, Shayne 108 36

Williams, Allison 111 37

Williamson-Wheat, Angel 20 14

Willison, Nicholas 82 30

Wipf, Peter 66 26

Witt-Enderby, P. 71 27

Woodley, Dr. Sarah 28 16

Workman, Riley 75 28



Colleges and High Schools Represented at the 2015 Summer Undergraduate Research Symposium

Carnegie Mellon University

Carrick High School

Chartiers Valley High School

Chatham University

Brown University

Duquesne University

Franciscan University of Steubenville

Georgetown University

Grove City College

Harvard University

Illinois Institute of Technology

McKeesport Area High School

Otterbein University

Roanoke College

Seton Hill University

Slippery Rock University

St. Mary’s College

St. Vincent College

Sto-Rox High School

Swarthmore College

Taylor Allderdice High School

Universidad Metropolitana Main Campus,

San Juan, Puerto Rico

University of Alberta

University of Central Florida

University of Connecticut

University of Illinois at Urbana Champaign

University of Miami

University of Notre Dame

University of Pittsburgh

University of Pittsburgh at Johnstown

University of Puerto Rico, Rio Piedras Campus,

San Juan, Puerto Rico

University of Texas – Pan American

Washington and Jefferson College

Wayne State University

West Mifflin High School

Westminster College

West Texas A&M University

2015 Summer Research Symposium Abstract Index

Page 10

1 Stability Studies for Celecoxib-Loaded Nanoemulsions using Dynamic Light Scattering Technique Eun Joo Hong, Lu Liu, Michele Herneisey, Jelena M. Janjic* Mylan School of Pharmacy, Duquesne University Theranostic (therapeutic and diagnostic) nanomedicine is an emerging field that personalizes medical treatment by combining imaging and drug delivery into one drug delivery system. Our group has developed a nanoemulsion-based anti-inflammatory nanomedicine platform. Nanoemulsions are commonly used to increase the bioavailability of poorly water-soluble drugs. Celecoxib, which is known to reduce inflammation by inhibiting the COX-2 pathway, was used as a model drug. In this study, new nanoemulsions were formulated with significantly increased drug loading (4 and 8 times higher) than previously reported formulations. Celecoxib-loaded nanoemulsions reported here were evaluated for drug loading, storage stability, and stability upon exposure to biological media and mechanical stress. Stability testing was performed using dynamic light scattering technique on ZetaSizer Nano by measuring droplet size, polydispersity, and zeta potential. Drug loading was assessed using UV/Vis spectroscopy. Our data indicate that increased celecoxib loading in theranostic nanoemulsions does not significantly change nanoemulsion colloidal properties.

2 Biodistribution studies of Near-Infrared Labeled Nanoemulsions in a Rat CCI Pain Model Sanders, Ryan

1, 2, Nehl, Emily

1, 2, Siefert, Elizabeth

1,

Saleem, Muzamil1, 2

, Stevens, Andrea1, 2

, Janjic, Jelena2,

3, Pollock, John

1, 2

1Department of Biological Sciences;

2Chronic Pain

Research Consortium; 3Mylan School of Pharmacy

Duquesne University Chronic pain is a commonly misunderstood condition that is accompanied by common mistreatment. Neuropathic pain, a type of chronic pain, is a complex syndrome resulting from peripheral nerve damage and neuroinflammation. In order to understand the underlying mechanisms, chronic constriction injury (CCI) was performed on a rat. The CCI surgery involves exposing the sciatic nerve, and applying constricting sutures to elicit a peripheral neuropathic pain response. In earlier studies we demonstrated that near-infrared (NIR) dye labeled nanoemulsions accumulate in macrophages infiltrating the site of CCI injury (Vasudeva et al, PLOS One 2014). The focus of this study was to utilize NIR imaging supported by histology of excised tissues to assess nanoemulsion distribution in organs and tissues. Deeper understanding of nanoemulsion distribution in organs is needed to further improve overall dosing regiment of these nanoemulsions in live animals with the aim to non-invasively visualize neuronal injury inflammation so that improve pain therapy can be realized.

3 Formulation studies of anti-inflammatory drug and natural products loaded nanoemulsions as new therapeutics for inflammatory pain Josiane Kadjo, Michele Herneisey, Lu Liu, Jelena M. Janjic* Mylan School of Pharmacy Duquesne University Nanoemulsions are small oil-in-water emulsions with an average droplet size of less than 500nm. Nanoemulsions improve the bioavailability, chemical stability, and solubility of poorly water soluble anti-inflammatory drugs (celecoxib) and natural products (resveratrol), thus providing a safer alternative pain treatment to opioids. Traditional methods used to formulate nanoemulsions include ultrasonification and microfluidization. We hypothesize that the formulation of celecoxib- and resveratrol-loaded nanoemulsions using a thin film method can increase nanoemulsion drug loading and therefore provide greater clinical benefits. Nanoemulsions were prepared using both microfluidization and thin film methods. Nanoemulsion colloidal stability was assessed using 72h serum stability and centrifugation stability tests, and nanoemulsion drug loading was assessed with UV/Vis spectroscopy. Formulation method did not appear to have an effect on nanoemulsion colloidal stability. Therefore, the thin film method of nanoemulsion formulation has the potential to increase drug loading of non-opioid anti-inflammatory drugs and natural products without altering nanoemulsion properties.

4 The Limited Accuracy of Fitness Tracking Devices Palmer, Abigail A.; Holland-Minkley, Amanda; Weixel, Kelly Departments of Biology and Computing and Information Studies Washington and Jefferson College Fitness tracking devices offer personalized health information by estimating energy expenditure through motion-based activities. The standard method for measuring energy expenditure is by quantifying the maximum volume of oxygen (VO2 maximum) an individual uses during strenuous activity. Instead of using VO2 maximum, sensory software in popular fitness tracking devices estimates calories burned through motion and customized algorithms. To compare these methods, eight volunteers completed a submaximal cardiorespiratory endurance test on an exercise bicycle while wearing three fitness tracking devices (Argus mobile app, Fitbit One, and MisFit Shine). A significant difference in calories counts was detected between the MisFit Shine and cardiorespiratory endurance test. These results indicate fitness devices convey a level of accuracy they do not possess.


Page 11

5 Image Noise -vs- Curvature Noise: Denoising Isn’t Dead Matuk, James; Levine, Stacey Department of Mathematics and Computer Science Duquesne University Image denoising techniques include tools from a number of fields of mathematics including partial differential equations, probability, linear algebra, and both convex and non-convex optimization. Recent work by Bertalmío and Levine has demonstrated that it might be more effective to denoise the curvature of the level lines of a noisy image function and then use this denoised curvature information to reconstruct an estimate of the original image. The goal of this research is to statistically analyze image curvature data in order to develop denoising methods for this new framework. In this talk I will give a brief description of the problem: image noise. An analysis of the curvature noise distribution which motivates new techniques for denoising will follow. Finally, a variational model for reconstructing a denoised image from this smoothed curvature data will be explained. Our numerical results show this approach can improve upon state-of-the art denoising methods.

6 Bioinformatics characterization of CXCR3 (Chemokine Receptor Type 3) from the Rhodopsin protein family to identify potential candidate regions to build a nano-biosensor for prostate cancer. Camacho-Flores, Antonio.

1, Nicholas, Hugh

2, Santiago-

Berríos, Mitk’El1 and Vázquez-Quiñones, Luis E.

1

1. School of Science and Technology, Universidad

Metropolitana Main Campus, San Juan, Puerto Rico 2. Pittsburgh Supercomputing Center, Carnegie Mellon

University Prostate cancer is one of the most common in the US. In 2011, 209,292 men were diagnosed with prostate cancer from which 27,970 died, according to the National Cancer Institute.

The current detection methods

are Digital Rectal Examination (DRE) and Prostate Specific Antigen (PSA) which provide ambiguous results leading to under-and-over treatments. Therefore, efforts to create more accurate detection procedures are needed for early detection and proper treatment. CXCR3 (Chemokine Receptor Type 3) is a biomarker gene found in aggressive prostate cancer. A bioinformatics characterization using various multiple sequence alignment (MSA) tools was performed on CXCR3. The purpose was to determine the best MSA tool for this set and then identify unique DNA regions that could be used in a nano-biosensor to detect prostate cancer. MSA tools compared were ClustalW, Kalign, MAFFT, MUSCLE, Probcons and T-COFFEE, from which MAFFT was selected as the most accurate in determining conserved amino acids.

7 A Variational Approach for High Dynamic Range Imaging (HDR) Isnata, Kinardi; Levine, Stacey Computer Science and Mathematics Department Duquesne University In this talk, we present a variational approach for fusing information from a stack of image data consisting of short and long exposure images into a High Dynamic Range (HDR) image. The varying range of exposures allow for an HDR that possesses the desired visual information in various regions in the image (e.g. vibrant colors, sharp details, and a greater dynamic range of luminosity), which a regular camera cannot capture. We use a variational approach based on the framework proposed by Bertalmio and Levine (2013) for fusing exposure bracketed images. As this framework is less sensitive to misalignments than comparable techniques, it allows for fusing images that are not completely aligned as well as have spatially varying blur, a very common situation when the image content involves people.

8 Hemispheric Differences in Face Discrimination After Priming Dickter, Adam, Liu, Tina, Behrmann, Marlene Department of Psychology Carnegie Mellon University Studies show that the accuracy of face recognition is correlated with the laterality of processing and that this laterality is mediated by the right hemisphere. This study explores whether one can bias the perceptual processing of faces by introducing information that enhances the global or local precedence of the right hemisphere prior to the onset of a face stimulus. Specifically, we ‘primed’ participants by presenting local or global information to the right or left hemisphere (using a visual half-field paradigm) and then examined the effect of this information on face processing performance. Subsequent analysis revealed local priming enhancement of left hemisphere face discrimination but no performance facilitation for either hemisphere after global priming of facial features. Further exploration of laterality effects may improve the understanding of priming conditions that facilitate selectivity in facial recognition tasks.


Page 12

9 Effect of Methylation and Stereochemistry in Hetero-macrocyclic (CYCLAM) Complexes as Catalysts in Atom Transfer Radical Addition (ATRA) Reactions Mraz, Margaret E.

1; Oshin, Kayode D.

1; Pintauer,

Tomislav.2

1 Department of Chemistry and Physics, Saint Mary’s

College, Notre Dame, IN 2

Department of Chemistry and Biochemistry, Duquesne University The effectiveness of hetero-macrocyclic (CYCLAM) complexes as catalysts in atom transfer radical addiction (ATRA) reactions was investigated. More specifically, the effect of altering methylation and stereochemistry of different positions on the CYCLAM ligands was investigated in relation to the activity produced by the catalyst. Fourteen copper(II) complexes were synthesized, eight copper(II) bromide complexes and six copper(II) chloride complexes. An initial screening showed that the bromide complexes were more effective compared to the chloride complexes. As a result, the copper(II) bromide complexes were utilized in all future reactions. ATRA reactions were conducted with the copper(II) bromide complexes as catalysts utilizing straight-chain terminal alkenes and carbon tetrabromide (CBr4) as the alkyl halide initiator with ascorbic acid as reducing agent. The conversion of alkene to monoadduct was determined using integration obtained in

1H Nuclear

Magnetic Resonance (NMR) spectroscopy experiments.

10 Synthesis of Selective Serotonin Reuptake Inhibitor Analogs Candiello, Sarah; Kantor, Elyssa; Jean, Bernandie; Lettan, Robert; Madura, Jeffry D. Department of Chemistry and Biochemistry Duquesne and Chatham Universities The serotonin transporter, SERT, belongs to a class called the sodium-dependent neurotransmitter symporter (NSS) and transports serotonin from the synapse to the presynapse. Decreased serotonin concentration in the synapse has been hypothesized to cause depression behavior. Inhibition of SERT using a selective serotonin reuptake inhibitor (SSRI) has been proposed to block the transmission of serotonin into the presynapse, increasing serotonin levels in the synapse. The methoxy and dichloro analogs of a tested parent compound, SM-11, proposed by Dr. Jeffry D. Madura et.al. were synthesized, purified, and analyzed. Synthesizing analogs of a computationally derived compound will validate the implementation of a SERT structure-based pharmacophore. Competitive binding assays will corroborate the dichloro analog as having the greatest inhibition of SERT based on the Topliss operational scheme. However, further evaluation of the synthetic process is required to increase the purity greater than 90 % while still yielding 10 mg or greater.

11 Belle II Experiment: FPGA Trigger TOP Electronics Roffé, Simonseth Department of Physics and Astronomy University of Pittsburgh The Belle Experiment is a scientific endeavor conducted by the High Energy Accelerator Research Organization, KEK, in Tsukuba, Japan. Belle II is the upgraded B-factory from the Belle B-factory with two orders of magnitude more luminosity. The main goal of the experiment is to investigate the sources of charge-parity violation. Measuring decays of B-mesons provides an excellent way to indirectly investigate new physics of high energy scales, of up to 100 TeV, at low energy experiments. Separation between kaons and pions aid in distinguishing so-called “penguin” decays from each other. To do this we need novel, high end electronics, and through the use of field programmable gate arrays (FPGAs), we can create trigger and readout electronics to collect data. Consequently, firmware for data readout was written, and the front-end electronics were tested for production quality in this project.

12 Environmental Assessment of Deer Lakes County Park Before Unconventional Shale Gas Drilling Robinson, Daniel and Stolz, John F. Center for Environmental Research and Education Duquesne University Allegheny County, Pennsylvania, has signed a lease to allow unconventional natural gas extraction from the Marcellus Shale beneath Deer Lakes County Park. Plans call for at least eight wells and drilling is currently underway. We report here the initial results of our independent water study establishing a baseline for water quality prior to the drilling. Parameters included conductivity, pH, D.O., anions, and metals. The park is home to three man-made lakes and four waterways that eventually flow into the Allegheny River. Base maps have been created that indicate the location of the pad and the proposed lateral wells, as well as park topology, currently active gas wells, and legacy mines. The latter indicates Deer Lakes Park is located directly over an abandoned coal mine. Visual evidence and water analysis suggest that mine drainage is currently appearing in the park’s waters, posing a potential risk to water quality.


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13 Fragment Oriented Molecular Shape (FOMS) Search: a Novel Shape-Based Virtual Screening Method Hain, Ethan and Koes, David Ryan Department of Computational and Systems Biology University of Pittsburgh Molecular shape is a useful tool for identifying small-molecules for therapeutics. Shape similarity can be found through both alignment methods, a computationally demanding approach, or through feature vector methods, computationally less demanding. Maximization of both volume overlap and various feature points makes alignment methods computationally intensive. The computational burden of alignment can be reduced by pre-aligning shapes. The recently published Volumetric-Aligned Molecular Shapes (VAMS) search pre-aligns the entire molecule, and was shown to be effective as a pre-screen. The introduced method, fragment oriented molecular shape (FOMS) search, pre-aligns shapes to only a part of the shape in detail (i. e. the binding site). This eliminates the burden of aligning shapes, so large libraries consisting of millions of shapes are searched on the scale of a few seconds, at the loss of accuracy. FOMS has outperformed VAMS for simple protein-ligand interactions. FOMS’ performance for complex protein-ligand interactions is also explained.

14 Characterization of the Serotonin Transporter in the Lipid Bilayer DeMarco Andrew; Ferraro, Nick, and Cascio Michael Department of Chemistry and Biochemistry Duquesne University Serotonin (5-HT) is a neurotransmitter and altered serotonin levels contribute to multiple disease states, including but not limited to depression and neuropathic pain. Levels of synaptic serotonin is partially regulated by the serotonin transporter (SERT), making it a potential therapeutic target. Our laboratory seeks to study the structure and function of SERT. Human SERT was expressed by Tetracycline-Regulated Expression (T-REx) Human embryonic kidney cell lines (HEK-293); the product was then purified. Solubilized SERT samples were purified by affinity chromatography and reconstituted. The lipid-accessible structure of the reconstituted transporter in membranes will be studied via photo-crosslinking to derivatized phosphatidylcholine followed by mass spectrometry and laser induced fluorescence. This initial study will determine the lipid-facing portions of SERT in the absence of any ligands, as well as identify any potential cholesterol binding sites. These studies may be extended to examine state-dependent changes in the transporter.

15 Insight into asymmetric catalysis of aqueous asymmetric Mukaiyama aldol reactions by dinuclear zinc semi-crown ligands Ahmed, Ayan; Vernier, Brandon; Rohde, Jeffrey; Evanseck, Jeffrey D. Center for Computational Sciences and Department of Chemistry and Biochemistry Duquesne University and Franciscan University of Steubenville Semi-crown ligands have been utilized in the asymmetric Mukaiyama aldol reactions involving enol silyl ethers; however, the factors that influence the stereoselectivity are not understood. Our previous work suggests that competition between the formyl and alpha hydrogen bonds between a chiral catalyst and the formyl or alpha hydrogen of the aldehyde play a critical role in the overall stereoselectivity. To understand the Mukaiyama aldol reaction, we investigate the Trost dinuclear zinc-based semi-crown ligand and its role in the reaction using the M06-2X functional paired with Dunning basis sets. Our discussion centers upon our energetic findings and consequences of the alpha and formal hydrogen bonds that occur separately for the electrophile and the nucleophile in the Mukaiyama aldol reaction. Our results contribute to the development of a rational strategy for designing catalysts for the Mukaiyama aldol reaction, which may serve to be an excellent template to expand to other asymmetric processes.

16 Analysis of brain mast cells in a model of chronic bladder pain Jones, Kara; Sadler, Katelyn; Kolber, Benedict Department of Biological Sciences and Chronic Pain Research Consortium Duquesne University Mast cells are found in connective tissue and play a vital role in maintaining homeostasis by releasing chemical mediators in response to injury or toxins. These inflammatory mediators act on neurons within the peripheral and central nervous system to change neuronal activity. In the periphery, increased mast cells numbers are observed in chronic pain conditions such as fibromyalgia, rheumatoid arthritis, and painful bladder syndrome. The role of central mast cells in chronic pain however remains unclear. In these studies, changes in brain mast cell populations were observed in a model of visceral pain. Over the course of five days, female mice were treated with cyclophosphamide, an antineoplastic drug that induces bladder pain. Mast cells were stained with Toluidine blue, then analyzed for number and anatomical location in the brain.


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17 Isolation and Characterization of Natural Products from a fungus in a Quercus species through Advanced 2-D NMR Techniques McCullough, Tyler M.

1 ; Valenti, Domenic

2 ; Harper,

James K.2

Department of Chemistry, Washington & Jefferson College

1

Department of Chemistry, University of Central Florida2

Natural products derived from microbes found in living plant tissues (i.e. endophytes), are a viable and relatively unstudied source of novel compounds with medicinal and agricultural applications. Particularly, natural product research is desirable for the production of antibiotics and agrochemicals which are highly effective, yet may produce less environmental impact and possess lower toxicity than similar compounds produced through synthetic methods. Despite the lower cost of drug production through combinatorial chemistry, large drug companies often pursue natural product research as it can produce unusual model compounds for further modification. From a species belonging to the genus Quercus, an unknown compound was isolated and purified through separation chemistry techniques. The structure of the purified compound was characterized through electrospray ionization mass spectrometry and 2-D NMR spectroscopy techniques including COSY, HSQC, HMBC, and INADEQUATE. The resulting spectra reflect the process followed in determining an unknown compound’s structure through NMR spectroscopy.

18

Synthesis and Characterization of Diamond-like Semiconductors with Potential Infrared Nonlinear Optical Applications Cribbs, Marvene; Glenn, Jennifer; Devlin, Kasey; Aitken, Jennifer Department of Chemistry and Biochemistry, Duquesne University Nonlinear optical (NLO) crystals are used to shift the coherent, monochromatic light of lasers to other desirable wavelengths for military, medical, commercial and industrial applications. Current commercially available materials for IR NLO applications are ternary diamond-like semiconductors (DLSs) such as AgGaS2

and AgGaSe2. However, these materials exhibit drawbacks including relatively low laser damage thresholds (LDTs), multiphoton absorption, difficult crystal growth, and limited phase matchability. Quaternary DLSs offer compositional flexibility that allows for the tuning of properties, such as bandgap. Little is known concerning the quaternary DLSs Cu2MnGeS4, Ag2FeSiS4, and Ag2ZnSiS4; no NLO studies have been performed. In preparation for these studies, these compounds were prepared by high-temperature solid-state synthesis and characterized using X-ray powder diffraction and diffuse reflectance UV/Vis/NIR spectroscopy. Scanning electron microscopy was used to study the morphology of the synthesized materials and energy dispersive spectroscopy was used to assess the homogeneity and composition of the samples.

19 Diffusivity and loading capacity of doxorubicin in a series of tubular DNA origami nanocarriers Dray, Kate Chemical Engineering University of Pittsburgh DNA origami, a technique that causes single-stranded DNA to self-assemble into specific three-dimensional shapes using shorter “staple” strands, has shown great promise for designing effective nanocarriers for drug delivery of chemotherapy to tumors. Biocompatible and selectively functionalizable, DNA origami structures take advantage of the specificity of Watson-Crick base-pairing

and can be programmed to perform logic functions to deliver drugs at desired locations. We have used DNA origami to design three tubular nanocarriers with different diameters. Using course-grained models, we performed classical Monte Carlo and molecular dynamics simulations to estimate loading capacity and diffusivity of the known chemotherapy drug doxorubicin. Our investigation demonstrates the potential of DNA origami structures for use as effective drug delivery vehicles for delivery of chemotherapy to tumors and provides a computational method for estimating drug loading and release properties of unique DNA origami structures.

20 Investigation of the Transfer of Gunshot Residue through a Handshake Williamson-Wheat, Angel; Castelleno, Holly; Wetzel, Stephanie J. Department of Chemistry & Biochemistry Duquesne University Gunshot residue (GSR) is used in many court cases to determine the shooter, and any witnesses in the vicinity of a gun being fired. GSR is deposited when a gun is fired due to the high pressure reaction which propels the bullet from the barrel. This reaction releases a mixture of different elements into the resulting smoke plume. Using SEM/EDS the presence of gunshot residue on suspects or witnesses can be determined by analyzing samples for the presence of Lead(Pb), Barium(Ba), and Antimony(Sb); which must be present in a single particle for GSR confirmation. Defense attorneys often argue that the presence of GSR on their client was transferred, for example, from something as simple as a handshake. In this study, a .38 caliber revolver and a .45 caliber automatic handgun were used to determine if GSR is transferred during a handshake.


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21 Probing Serotonin Transporter (SERT) Structure by Mutagenesis Perez, Cheyeanne; Perez, Elizabeth; Cascio, Michael Department of Chemistry and Biochemistry Duquesne University The serotonin transporter (SERT) is a transmembrane protein found in neurons; and is responsible for the re-uptake of monoamine neurotransmitter serotonin from the synapse back to the pre-synaptic neuron, thereby regulating the concentration of serotonin in the synapse. SERT is a target for the development of antidepressants, however little is known about its structure. Dr. Gary Rudnick (Yale University) generously provided rat SERT construct containing no reactive cysteines (X8C rSERT) in a pBlueScript plasmid. In this project, the X8C DNA was cloned into pFastBac and cDNA3 plasmids. Then single cysteine mutations were introduced by PCR mutagenesis. Expressed rSERT may then be selectively crosslinked using a MTS-crosslinker to elucidate SERT structure. Single Cys mutations are currently being introduced in the extracellular loops and the N and C termini of the rSERT allowing the crosslinker to identify amino acids within crosslinking range of the introduced Cys mutations.

22 Enzyme Kinetics in a Crowded Macromolecular Environment Diallo, Amadou; Cwalina, Caroline; Shaik, Sadiq A.; Seybert, David W. Department of Chemistry and Biochemistry Duquesne University A cell's interior is very viscous with high concentrations of macromolecules. Macromolecular crowding describes the phenomenon in which these high concentrations cause changes in the equilibrium and kinetic behavior of other macromolecules. Historically, most enzymes have been characterized in vitro in dilute solutions which ignore macromolecular crowding effects. We wished to study the effects of macromolecular crowding on the enzyme glucose-6-phosphate dehydrogenase (G6PDH), an important enzyme in regulating carbon flow in the pentose phosphate pathway. This pathway produces NADPH (required for metabolic syntheses) and 5-carbon sugars (required for DNA and RNA synthesis). G6PDH catalyzes the oxidation of glucose 6-phosphate, reducing NADP

+ to NADPH. The steady-state rate of

the reaction was followed at 340 nm. Results of our in vitro experiments using Ficoll-70 and bovine serum albumin as model crowding agents will enable us to better describe the in vivo kinetic behavior of this enzyme.

23 Molecular dynamic simulations of hydrophobic peptides from γ-D crystallin and potential protein aggregation leading to cataract formation DiSanti, Domenic. Nguyen, Bao Linh. Wheeler, Ralph A. Department of Chemistry and Biochemistry Duquesne University Amyloid diseases such as Huntington’s, Alzheimer’s, and type II diabetes are becoming increasingly prevalent and are characterized by protein aggregation. Cataracts are suspected to be another amyloid disease caused by aggregation of the protein human γ-D crystallin (HGD) in the lens of the eye leading to decreased vision. The current study uses molecular dynamics (MD) simulations to determine what role hydrophobic residues in the core of the HGD protein play in protein aggregation. Currently, two locations near the N and C termini have been identified to have five consecutive hydrophobic residues. These sequences have been isolated and duplicated to generate two systems of 215 identical hydrophobic peptides in explicit water solvent system. Early results indicate that the hydrophobic peptides do aggregate and that the aggregates contain a variety of structural components.

24 Synthesis and Characterization of Blue Pigments, an Undergraduate Laboratory Module Latona, Amber; Sinagra III, Charles W.; Devlin, Kasey P.; Aitken, Jennifer A. Department of Chemistry and Biochemistry Duquesne University Recently several series of blue pigments have been prepared by substituting Mn

3+ into several oxide

materials, such as YInO3, using the formula YIn1-xMnxO3. These pigments are an ideal case study for a junior/senior level integrated laboratory course due to the introduction of multiple instruments, crucial to the study of solid-state materials, and the resulting pigments being useful industrially. X-ray powder diffraction was used to identify the structure of the compounds and to investigate the phase purity of each sample. X-ray powder diffraction in combination with Rietveld Refinement was used to perform whole pattern fitting and quantify the phase fractions of each phase and any impurity phases. Diffuse reflectance UV/Vis/NIR spectroscopy was utilized to determine the bandgap for each sample. Scanning electron microscopy was utilized to determine morphology and particle size of the powders. Energy dispersive spectroscopy was used to assess homogeneity and provide semi-quantitative elemental analysis of the synthesized materials.


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25 Evaluating quantification and expression methods with D. Melanogaster data Jimenez-Ruiz, Ivan

1 , Ropelewski, Alex

2 , Agosto Rivera,

José1, Ortiz-Zuazaga, Humberto

1

1.University of Puerto Rico, Rio Piedras Campus, San

Juan, Puerto Rico 2.

Pittsburgh Supercomputing Center, Carnegie Mellon University Detection of differential expression in two samples is a recurring problem in bioinformatics. This detection is affected by the accuracy of the quantification methods used in the process, which in turn depend on the techniques used for assembly. Serially diluted RNAseq data from D. melanogaster containing aliquots from both ERCC and S2 cell lines at different percentages were assembled. We used the NCBI SRA database to retrieve four transcriptomic datasets containing a total of 2,049,901,812 nucleotides (nt). The average number of bases per read in each dataset was 36 nt. Quantification results obtained from the assembled transcripts produced by Trinity and RSEM (de-novo) were compared with those from Tophat and Cufflinks (reference based) to determine the validity of these protocols. This approach provides a draft workflow to be used with spike-in data produced from de-novo RNAseq experiments using non-models organisms.

26 Chemical and Tribological Properties of Monolayers and Mixed Monolayers of Nonadecanoic acid and Octacosanoic acid on Sapphire Surfaces Thomas, Rebekah

1; Gawalt, Ellen

2; Lim, Min Soo

1

1 Department of Chemistry, Slippery Rock University 2 Department of Chemistry and Biochemistry, Duquesne University Self-assembled Monolayers (SAMs) are two dimensional molecular arrays that are spontaneously formed by adsorption of surfactant organic molecules onto a solid surface. Each molecule of the monolayer is composed of a head group, which binds to the substrate surface, an alkyl chain that determines the stability and the order of the SAM, and a tail group that determines surface properties. SAMs have been used to alter the properties of the substrate surface such as lubricity, hydrophobicity, friction, etc. This project focused on monolayers and mixed monolayers of nonadecanoic acid (C19) and octacosanoic acid (C28), formed on sapphire surfaces. Single monolayers of C19 and C28 and mixed monolayers with mixing ratios of 75%-25%, 50%-50%, and 25%-75% of C19 and C28 were prepared using solution deposition. They were analyzed via diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), contact angles, and atomic force microscopy (AFM).

27 Method Development and Optimization for the Identification and Quantification of Vitamins A, D3, E and K Coleman, Mary; Wetzel, Stephanie J. Department of Chemistry and Biochemistry Duquesne University Labels of pharmaceuticals list components and quantities of active ingredients. In order to identify the components of a multi-vitamin, the corresponding UV and fluorescent wavelengths for each vitamin must be known. Fluorescence excitation and emission wavelengths were determined for vitamins A, D3, E and K. A solvent system was determined and an accurate method was developed in order to separate and analyze vitamins A, D3, E and K using High Performance Liquid Chromatography (HPLC) with UV and fluorescence detection. The new method was then used to analyze and quantitate an over-the-counter multi-vitamin and the results were compared to the corresponding label.

28 Do Salamander Skin Secretions Act as Primary Defense Mechanism? Magyan, Andrew; Woodley, Sarah. Biology Duquesne University Batrachochytrium dendrobatidis is a fungal pathogen that infects amphibian skin and can cause mortality. Some amphibian species are highly susceptible to the fungus, while others resist or tolerate infection. While it is not fully understood why some animals are more susceptible than others, it is theorized that peptides secreted from the skin act as a primary defense mechanism. I tested the hypothesis that skin peptides would inhibit the growth of Bd in red-legged salamanders (Plethodon Shermani), a species that is fairly resistant to infection by Bd. At a variety of concentrations, the peptides and Bd were grown together on a 96 well plate and absorbance was measured daily. It was found that skin peptides from P. Shermani did not inhibit the growth of Bd at the concentrations tested. Thus, factors other than skin peptides, such as antifungal metabolites from skin microbiota, must confer resistance to Bd in this species.


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29 Baculoviral Expression of Evolutionarily Related Proteins in Sf9 Insect Cells Underwood, Soraya; Colvin, Amanda; Cascio, Michael Department of Chemistry and Biochemistry Duquesne University The goal of this project is to overexpress, purify, and subsequently test the enzymatic activity of evolutionarily related proteins whose functions reflect the mating habits of their respective hosts. The recombinant proteins are human semenogelin 2, an abundant seminal plasma protein, the same protein with mutagenized mutations to match the chimpanzee sequence, chimpanzee kallikrein, rat structural semenogelin 1, which is secreted by seminal vesicles, and human prostate-specific transglutaminase. This research will determine how the function of these proteins changed due to natural selection. The bacmid DNA encoding these proteins were first produced and isolated. Bacmid DNA was transfected into Sf9 insect cells to isolate and amplify the respective baculoviruses. Subsequent baculoviral infection of Sf9 insect cells was conducted to maximize protein expression as visualized by SDS-PAGE and Western blotting. Once the protein is amply produced, it can then be purified and assayed to characterize its function.

30 Mechanisms of aggregation in gammaD-crystallin Schultz, Autumn A.; Nguyen, Bao Linh; Wheeler, Ralph A. Department of Chemistry and Biochemistry Duquesne University Amyloid fibrils are very stable, highly ordered protein aggregates that are characteristic of a large family of diseases, and their stability causes them to be dangerous. When proteins are damaged and misfold they can aggregate into amyloid fibrils. Cataracts are caused by the aggregation of proteins in the lens, specifically gammaD-crystallin, into aggregates proposed to be amyloid fibrils. It has been suggested that at least one of two hydrophobic cores, a sequence of five consecutive hydrophobic residues, is responsible for the nucleation of gammaD-crystallin aggregates. Molecular dynamics simulations were used to determine the propensity of aggregation of the hydrophobic core and its adjacent beta strand. Study of the aggregation of the truncated sequence of the protein was used to gain a greater understanding of protein folding and misfolding.

31 Charge-Assisted Intramolecular Hydrogen Bond of Carboxyphosphate Andreola, Laura; Hebert, Sebastien; Kochanek, Sarah; Clymer, T.; Firestine, Steven, M.;

1 Evanseck, Jeffrey D.

Center for Computational Sciences and Department of Chemistry and Biochemistry Duquesne University, and

1Eugene Applebaum College of

Pharmacy and Health Sciences, Wayne State University Eight analogues designed to modify the hydrogen bond donor and acceptor moieties of monoanionic and dianionic carboxyphosphate have been examined to define the stereoelectronic features that affect the charge-assisted-intramolecular hydrogen bond (CAHB) strength. Natural bond orbital (NBO) analysis was conducted using HF/aug-cc-PVTZ//M06-2X/aug-cc-PVTZ. Second-order perturbation energy, E(2), provided a quantitative description of the delocalization (charge-transfer). Dispelling the notion of a delocalized cyclic (aromatic) structure of carboxyphosphate,

we first observed that the n(O)σ*(O-H) charge-transfer is the only delocalization found to bridge between the

functionalities. The CAHB strengths and the n(O) σ*(O-H) delocalizations were shown to have r

2=0.97 across

carboxyphosphate and analogues. Finally, the n(O)σ*(O-H) delocalizations and Pauli repulsion energies were found to have r

2=0.88, underscoring the attractive and repulsive

nature of the CAHB. Our results provide further insight into controlling the stability of the elusive carboxyphosphate intermediate in purine biosynthesis, which could be instrumental in finding different pathways for anti-bacterial drugs.

32 Network Communication Measures for Protein Dynamics Ní Chochlain, Aífe; Chennubhotla, Chakra Department of Computational and Systems Biology University of Pittsburgh Information theory has been previously applied to descriptions of protein dynamics, particularly either molecular dynamics simulations or elastic network models. The application of information theory to the protein reveals the most central nodes of the protein network and the effects of perturbation on the protein structure, both of which can reveal underlying structural and functional elements of the protein (e.g. allosteric hubs). We used the Python program ProDy’s framework to create a module to analyze protein structure. The module takes advantage of innovations to create increased efficiency, e.g. using a straightforward matrix calculation rather than singular value decomposition to calculate the Moore-Penrose pseudoinverse, and aspects of information theory, such as hit and commute time, perturbation, and frustration scores. Additionally, as the ProDy framework uses an elastic network modelling system, the high efficiency of this module compared to other analytic methods makes it ideal to apply information theory to large proteins.


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33 Exploring the influence of surface tension on mesenchymal-to-epithelial transitionin mesenchymal sheets Cho, Nicholas; Kim, Hye-Young; Davidson, Lance Department of Bioengineering University of Pittsburgh Mesenchymal to Epithelial transition (MET) is a cellular process involved in the transition from motile, spindle-shaped mesenchymal cells to polarized epithelial cells and is central to organogenesis and the formation of various metastatic cancers. While the biochemical signals involved in MET have been studied, the physical cues that influence MET are still not understood. Studies in three-dimensional aggregates of mesenchymal cells isolated from Xenopus embryos have shown that MET progression requires surface tissue tension on the aggregate surface. Further, epithelial transition can be accelerated when tension is increased. There are several challenges when imaging and manipulating the mechanics of these live spherical aggregates that limit the study of this process. Here, we use two-dimensional sheets of mesenchymal cells isolated from early Xenopus embryos to better charactertize the progression of MET over time and to observe how the physical characteristics of mesenchymal cells play a role in the progression of MET.

34 Development of Streptomyces coelicolor Spores for Vaccine Delivery West, Brittany; Mrohs, Kevin; Fucich, Daniel; McCormick, Joseph Department of Biology Duquesne University One type of vaccine production has traditionally been explored using endospores from unicellular bacteria. However, similar use of exospores from filamentous bacteria such as Streptomyces coelicolor has not been investigated thoroughly. Spore-associated protein SapD is believed to be located on the outside of S. coelicolor spores. This project focused on fusing the gene encoding the β subunit of the heat liable toxin (LTB) of E. coli to the 3’end of the sapD gene in order to express and incorporate the LTB antigen on the spore surface. The SapD-LTB encoding fusion gene was inserted into the S. coelicolor chromosome in order to potentially express LTB on the spore coat. Recombinant spores have been characterized using SDS-PAGE and western blot techniques. Because of the durability and longevity of spores and their associated proteins, antigens expressed on exospores could potentially result in an oral, nasal, or inhalation vaccine with extended shelf life.

35 Using the Oculus Rift for Molecular Visualization Adams, Brian

1, Stone, John

2, and Madura, Jeffry D.

1

1Center for Computational Science, Department of

Chemistry and Biochemistry, Duquesne University 2Theoretical and Computational Biophysics Group,

University of Illinois at Urbana-Champaign Molecular visualization software such as VMD and PyMol, have a significant amount of popularity among the computational science community. Each program is simple to use and provides a wide variety of methods to visualize large data sets. However, one of the significant frontiers that they have always lacked in is virtual reality (VR). The methods to properly visualize a molecular structure inside a virtual reality construct are few and often are very expensive. However, with the creation of the Oculus Rift, a VR headset, we have the ability to not only view structures in 3D stereoscopic vision but also manipulate structures, allowing the molecular modeling community to use it to their advantage. The Oculus Rift has been interfaced with VMD which immerses the viewer inside a molecule.

36 Computational Analysis of the Uncoating of the HIV-1 Viral Capsid Bergman, Shana; Lezon, Timothy Department of Computational & Systems Biology Drug Discovery Institute University of Pittsburgh HIV is a lentivirus that causes acquired immunodeficiency syndrome (AIDS), which is responsible for millions of deaths annually and has a high resilience to treatment. The HIV capsid, composed of approximately 1300 identical capsid proteins, houses the viral genome. If the capsid cannot dissociate properly or prematurely uncoats, the released viral genome will be unable to infect the cell. This study focuses on isolating structural factors that are critical to the proper uncoating of the capsid. We use an elastic network model to predict the dynamics of the capsid and then, through systematic perturbations, study each residue’s contribution to the overall motion of the capsid. We study the inferred dynamics of the capsomer to determine co-moving structures, which provide the foundation for creating a scheme to coarse-grain the structure while preserving its global motions. We find that perturbation scanning of the coarse-grained model agrees with known influences on capsid stability.


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37 Neutrinos: Reconciling Theoretical Prediction with Experimental Data Suarez, Nicholas Department of Physics & Astronomy University of Pittsburgh The GENIE Neutrino Mote-Carlo Generator seeks to provide high energy particle physicists with a powerful tool for researching neutrinos. As such, it is crucial that the experimental models implemented by the GENIE software are validated against actual experimental results, such as the data sets produced by the Mini-Booster Neutrino Experiment (MiniBooNE) and Main Injector Experiment for v-A (MINERvA), both of which provide information concerning single pion production in neutrino/nucleon interactions. While the corresponding simulations given by the GENIE simulations currently are not in satisfactory agreement with the results of MiniBooNE and MINERvA, by adjusting the parameters of the Monte-Carlo generator, the simulation results have been modified in attempts to obtain a closer fit to the experimental data sets. Work is now underway to examine the results of these modifications of parameters, comparing the new simulations against data in order determine which best accounts for experimental results.

38 The Effect of Mayfly Development on Nesting Duration of the Louisiana Waterthrush Seliman, Youstina

1, Brian K. Trevelline

1, Timothy J.

Nuttle 2 and Brady A. Porter

1.

1 Department of Biological Sciences, Duquesne University. 2 Powdermill Nature Reserve, Carnegie Museum of Natural History. The Louisiana Waterthrush (LOWA) is a neotropical migratory bird that specializes in feeding on larval aquatic insects especially those in the order Ephemeroptera (Mayflies). In a related study, a molecular dietary analysis was performed on fecal sacs of LOWA nestlings facilitated by DNA min-barcodes of CO1. This supporting study created a DNA reference library of aquatic insects from streams at Powdermill and tested a hypothesis: the phenology of LOWA nesting is determined by larval aquatic mayfly availability. Our prediction was that as the mayflies transform into adults, the amount of active LOWA nests would be reduced. To test this prediction, biweekly monitoring of larval insects (surber samples) and mature aquatic terrestrial insects (sticky traps) were conducted and LOWA nests were observed daily along these streams. Some support for our hypothesis was seen; LOWA nesting subsided at the same time as certain genera of mayflies transformed to their terrestrial stage.

39 Using Bacterial Spores for Vaccine Delivery Resko, Zachary J.; Kocher, Matthew; Moore, Carrie Ann; McCormick, Joseph R. Exospores produced from filamentous bacteria, such as Streptomyces coelicolor, might have great potential to be used for vaccine delivery. Spore-associated protein SapC does not contain a normal secretion signal nor is the mechanism of secretion known. In past studies, fusions of antigens such as the β subunit of the E. coli heat labile toxin (LTB) have been made to the C-terminus of SapC and did not affect the secretion and assembly on the spore coat. A goal of this project was to analyze previously constructed C-terminal truncations of SapC fused to LTB to locate the secretion and/or assembly signals of SapC. To further characterize SapC protein secretion, a previously initiated N-terminal fusion of LTB to SapC was further advanced in construction. Once constructed, more information will be gathered to determine the sequences for secretion and assembly. There is potential for this to lead to a new viable method for vaccine delivery.

40 “Managing Pain: Testing the dosing of exercise therapy using a multi-school collaborative approach with human participants.” Sweetnich, Rachel; Szucs, Kimberly; Kostek, Matthew Occupational Therapy/Physical Therapy Duquesne University While it is widely accepted that exercise reduces sensitivity to chronic pain, the effectiveness of exercise dose is unclear. The purpose of the proceeding experiment was to determine the effect of exercise dose on the ability of exercise to reduce acute pain in healthy human participants. After screening, participants were randomly assigned to one of three groups: control (no exercise), low dose (three times per week), and moderate dose (five times per week). Over seven days, participants performed 30 minutes of moderate intensity walking on a treadmill during assigned exercise days. Participants then completed testing to determine sensitivity thresholds for innocuous cutaneous stimulation, painful thermal stimulation, and painful pressure stimulation. Participants also rated the quality and unpleasantness of both thermal and pressure pain. Data has yet to be analyzed, but it was hypothesized that therapy done at a low dose will produce the best cost-to-risk rate for patients with pain.


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41 Structural Analysis of the Serotonin Transporter via Site-Directed Mutagenesis, Crosslinking, and Mass Fingerprinting Lutty, Sara and Cascio, Michael Department of Chemistry and Biochemistry Duquesne University Though the transmembrane domain of the serotonin transporter (SERT) may be modeled based on homologous transporters whose structures are resolved, little is known about the structure of the less conserved extracellular loops and interactions in the binding pockets. Structural determination of SERT’s accessible extracellular domain will initiate improved drug design to help many illnesses and disorders. To characterize SERT, we utilize rat SERT (rSERT) X8C which has been modified to replace eight endogenous cysteines and subcloned into pFastBac for baculoviral overexpression. Systematically introduced single cysteines will be targeted with methanethiosulfate benzophenone. Subsequent non-specific crosslinks will be formed via photoactivation and identified through mass fingerprinting. While optimizing this system for analysis, TREX cells provide a stable cell line to generate smaller amounts of human SERT (hSERT) via tetracycline induction for crosslinking of a fluoxetine analog in the binding pocket. These parallel studies will determine which binding pocket fluoxetine favors in SERT.

42 Impedimetric Detection of Cardiac Blood Markers Using Platinum Wire-Based Biosensors Umanzor, Fatima

1, Patil, Mitali

2, Kumta, Prashant N.

1,2,3

1Department of Chemical and Petroleum Engineering,

2Department of Bioengineering,

3Department of

Mechanical Engineering and Materials Science

University of Pittsburgh Detection of cardiac blood markers, Troponin T (TnT) and Brain Natriuretic Peptide (BNP), is critical for cardiovascular disease (CVD) state diagnosis. This project is focused on developing a biosensor utilizing electrochemical impedance spectroscopy to detect different protein levels. Platinum wire electrodes of different diameters and surface roughness were functionalized with controlled amounts of cysteamine, glutaraldehyde, Avidin, and either of the respective aptamers for TnT and BNP (to create independent binding sites for the two proteins) to determine the optimal surface roughness and diameter for biosensor preparation. The benchtop model was tested for assessing charge transfer resistance changes at multiple stages of functionalization and antigen detection to formulate a calibration curve for determining binding of a protein/antigen to the biosensor. This will potentially, in the future, be translated to a clinical model for testing critical marker concentrations present in the blood samples thus serving as an indicator for the CVD condition.

43 Synthesis and physicochemical characterization of narrow-bandgap tellurides composed of earth-abundant elements Hogan, Brea; Sinagra, Charles W. III; Zhang, J.H.; Glenn, Jennifer R.; Aitken, Jennifer A. Department of Chemistry and Biochemistry, Duquesne University The crystal structures of several quaternary diamond-like semiconductors (DLSs) with the general formula of Cu2-II-IV-Te4 have been reported in the literature; however, these materials have not been completely characterized. Information regarding the applications of these materials, in particular thermoelectrics, can only be acquired from systematic and thorough assessments of the physicochemical properties. Numerous samples of these compounds were prepared by high-temperature, solid-state synthesis using stoichiometric mixtures of the elemental starting materials. The crystal structures and phase purity were then investigated using X-ray powder diffraction and compared with experimental analyses found in the literature. In the course of these investigations, a new ternary compounds in the Cu-Ge-Te system was discovered. Optical diffuse reflectance UV-Vis-NIR spectroscopy was used to estimate the bandgaps. Morphological and compositional characterizations were performed using scanning electron microscopy and energy dispersive spectroscopy, respectively.

44 Characterization of Random Transposon Insertion Mutants Defective for Development in a Filamentous Sporulating Bacterium. Kirk, Sean G.

1; Bennett, Jennifer A.

1; McCormick, Joseph

2

1 Department of Biology and Earth Sciences, Biochemistry

and Molecular Biology. 2

Department of Biological Sciences. 1

Otterbein University, Westerville OH. 2

Duquesne University, Pittsburgh PA. Streptomyces coelicolor is a filamentous, sporulating bacterium commonly found in soil and is a model system to study for microbial cell biology and development. Streptomycetes produce many of the commonly medically utilized antibiotics. Preliminary characterization of four random transposon insertion mutants was done by microscopy and visual analysis on solid media. Using Inverse PCR and DNA sequencing, the transposon insertion sites were identified to further analyze the mutants. One of the insertion mutants, with a spore shape defect, has a transposon insertion in a gene that codes for protein of unknown function. Another mutant has a segregation defect as judged by DNA staining using confocal microscopy. This strain has yet to be sequenced to identify the transposon insertion location. Transformations into wild type Streptomyces are currently being done to determine if the mutant visual and microscopic phenotypes are linked to the insertion mutation.


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45 RNA sequences analysis of muscle development in Manduca sexta Molina, Ana E.; Dove, Lindsey; Lai, Yi-Tak; Bayline, Ronald J. Department of Biology Washington & Jefferson College During muscle development in the fruit fly Drosophila melanogaster, founder myoblasts are specified to form individual muscles. Following specification, the founder cells recruit and fuse with fusion-competent myoblasts, and in Drosophila melanogaster, the genes kirre, sticks and stones, hibris, and roughest promote this fusion. The function of these genes in muscle development in other insects is unknown. Thus, to understand their role in lepidopterans, we extracted the RNA from tobacco hornworm (Manduca sexta) and isolated those muscle development genes from the cDNA. Using the software R, we created phylogenetic trees for these genes to understand their evolution. The genes kirre and roughest may be paralogous genes that arose from a gene duplication event following the dipteran-lepidopteran split. Only one homolog of kirre and roughest exists in lepidopterans and other holometabolous insects. Likewise, hibris and sticks and stones may have arisen from a similar duplication within the dipteran lineage.

46 Studying hedgehog gene expression during muscle development in Manduca sexta Dove, Lindsey J.; Molina, Ana E.; Lai, Yi-Tak; Bayline, Ronald J. Department of Biology Washington & Jefferson College The hedgehog signaling pathway is conserved in all bilaterians and plays a key role in many areas of development, such as in Drosophila brain development. Insect muscles also require a neuronal signal in order for proper myoblast fusion and growth, and the hedgehog pathway may be involved in this process as well. The goal of this study is to determine if the hedgehog signaling pathway is involved in myoblast accumulation and fusion in Tobacco hornworms (Manduca sexta). Smoothened (Smo) and Cubis Interruptis (Ci) DNA sequences have been isolated and riboprobes will be generated from these sequences. In situ hybridizations will be carried out in order to identify the expression patterns of Smo and Ci in embryonic tissue in Manduca sexta. This characterization allows for a better understanding of the evolutionary divergence of the hedgehog pathway for muscle development by comparing expression patterns to other insects, such as Drosophila.

47 Stability of Self-Assembled Monolayers of Organic Acids on Cobalt Kodjo, Nadejda; Reger, Nina; Gawalt, Ellen Department of Chemistry and Biochemistry Duquesne University

Self-assembled monolayers, SAMs, are formed when surfactant molecules spontaneously adsorb in a monomolecular layer on surfaces. SAMs are created by the chemisorption of head groups onto a substrate from either the vapor or liquid phase followed by a slow organization of tail groups. This project is focused on determining the feasibility and conditions for forming self-assembled monolayers of phosphonic acid on cobalt oxide. Samples were prepared using solution deposition. The concentration for the solution was 0.017 M of ODPA. The time of deposition for success was 24 hours. The surfaces were analyzed with infrared spectroscopy, which indicated that the monolayers formed. To determine the stability of the monolayers, the cobalt coupons went through a rinse in THF, sonication in THF, and a tape test. The hydrophobicity of the SAM-modified surface was determined by using contact angle measurement.

48 Toward ab initio modeling of CO2 electroreduction on α-Sn, ß-Sn, and SnO2 particles. Dean, James; Saravanan, Karthikeyan; Keith, John A Department of Chemical and Petroleum Engineeering University of Pittsburgh The ever-increasing global production of greenhouse gases prompts the urgent need for conversion into less-harmful substances. Energetically efficient electrochemical conversion of CO2 into other, more useful products has been a hot topic of recent research. Previous investigations by Bocarsly et al. reported noticeably low overpotentials for CO2 conversions to formate on polycrystalline tin electrodes. Interestingly, electrochemical conditions were found to promote the formation of tin oxide overlayers on the electrode surface, and these surfaces have been attributed to the catalysis of CO2. As a starting point toward in situ computational modeling of this system, we carried out density functional theory calculations to determine various tin and tin oxide structures that would be energetically accessible at electrochemical reaction conditions via Pourbaix diagrams. We report convergence criteria necessary for ab initio modeling of electrochemical reactions on these surfaces. Future work will address the adsorption energies of CO2 reduction reaction intermediates and mechanisms.


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49 A Mathematical Model of Heparin-induced

Thrombocytopenia

Leonhard, Anne C.1; Parker, Robert S.

2; Clermont, Gilles

3

1 Department of Chemical Engineering, Rose-Hulman

Institute of Technology 2 Department of Chemical and Petroleum Engineering,

University of Pittsburgh 3 Department of Critical Care Medicine, University of

Pittsburgh

Heparin-induced thrombocytopenia (HIT) is characterized by platelet destruction as a result of irreversible binding of heparin-triggered antibodies to the platelet surface. While HIT is uncommon, the condition results in increased risk of bleeding and potentially deadly thromboses. A mathematical model was constructed to describe changes in platelet count in response to heparin administration. The key components of the ordinary differential equation model include multi-compartment representations for platelet and antibody dynamics, as well as a biologically-motivated platelet reserve compartment. Platelet count and heparin administration data from clinical patients diagnosed with heparin-induced thrombocytopenia were used to fit model parameters to individual patient profiles. Parameter estimation was performed using Markov chain Monte Carlo sampling and quality of fit was calculated using least squares regression between patient data and the model simulation. This model has the potential to aid clinicians in the early diagnosis of heparin-induced thrombocytopenia.

50 Alpha-arrestin regulation of potassium channel Kir 2.1 trafficking Allyson F. O’Donnell

1, Collin Krasowski

1, Timothy

Mackie3, Alex Kolb

3, Alison Dempsey

4, Christopher

Szent-Gyorgyi4, Marcel Bruchez

4, Adam Kwiatkowski

2,

and Jeffrey L. Brodsky3.

1Dept. of Biological Sciences, Duquesne Univ.;

2Depts.

of Cell Biology; 3Biological Sciences, Univ. of Pittsburgh;

4Molecular Biosensors & Imaging Center, Carnegie

Mellon Univ. Kir2.1 is an inward rectifying potassium channel found at the surface of mammalian cardiomyocytes. Though Kir2.1 is critical for maintaining potassium homeostasis, regulation of Kir2.1 trafficking and abundance at the cell surface is poorly understood. We recently found that a family of trafficking adaptors, the α-arrestins, regulates Kir2.1 localization at the cell surface. Our yeast model has shown that three α-arrestins (Ldb19/Art1, Aly1/Art6, Aly2/Art3) control intracellular sorting of Kir 2.1. We sought to determine how α-arrestin mutants alter Kir2.1 trafficking to identify signaling pathways important for Kir2.1 regulation. To do this, we engineered yeast that express the mammalian Kir2.1 channel in place of the endogenous yeast potassium channels. We then expressed mutant α-arrestins and assessed Kir2.1 localization and protein abundance using fluorescence microscopy and immunoblot analyses. These studies help define the requirements for Kir2.1 trafficking in mammalian cells as the α-arrestins and signaling regulators examined are conserved in humans.

51 Synthesis and characterization of dithione ligands and mixed ligand molybdenum complexes McKenzie, Sarine; Dille, Sara; Basu, Partha Department of Chemistry and Biochemistry Duquesne University Coordination complexes of 1,2-dithiolenes are fascinating molecules that exhibit unique structural and spectroscopic properties. 1,2-dithiolenes have uses in various materials science applications and are also important for the development of mimics for biological metal centers. This project will focus on the synthesis of such ligands and these ligands will used to synthesize mixed ligand molybdenum complexes that may act as a mimic for certain biological metal centers. Both anaerobic and aerobic reaction conditions will be employed and all complexes will be characterized using various spectroscopic techniques such as 1H NMR, IR, and UV-Vis spectroscopy.

52 Implementation of a Ring Imaging Cerenkov Detector in CLAS12 Trotta, Richard; Benmokhtar, Fatiha Undergraduate Program of Natural and Environmental Science Duquesne University Jefferson Lab (Jlab) is performing a large-scale upgrade to its Continuous Electron Beam Accelerator Facility (CEBAF) up to 12GeV beams. The Large Acceptance Spectrometer (CLAS12) in Hall B is being upgraded and a new hybrid Ring Imaging Cherenkov (RICH) detector is being developed to provide better sub-atomic particles separation throughout the 3 to 8 GeV/c momentum range. Cherenkov light can be accurately be detected by a large array of sophisticated Multi-Anode Photomultiplier Tubes (MA-PMT), these MA-PMTs are the active material in this detector. We are presenting our work on implementing the geometry of the RICH in the CLAS12 main Analysis package.


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53 Understanding Effects of Active Zone Material on Synapses using Computer Simulation Martin, Matthew

1; Dittrich, Markus

2

1 Department of Computational and Systems Biology University of Pittsburgh 2 Pittsburgh Supercomputing Center Carnegie Mellon University Understanding how synapses function is integral to neuroscience, and their understanding has great implications to the field. The frog neuromuscular junction is used as a model system for synapses. It has previously been simulated using spatially realistic diffusion-reaction based Monte-Carlo computer simulations. A class of macromolecules called active zone material within the frog neuromuscular junction was recently described in detail. An existing model of the frog active zone was improved by adding active zone material. Using CellBlender, spatially realistic three-dimensional models of active zone material were constructed using descriptions in the literature. After adding active zone material to the existing model, Monte-Carlo Cell (MCell) was used for simulation. Active zone material was demonstrated to have a significant impact on vesicle release in this model. A more realistic model of the frog neuromuscular junction was created, and valuable insight into the behavior of the system was gained.

54 Lubrication Collapse: A Novel Mechanism for Micro-particle Self-assembly Sullivan, William; Lash, Melissa; McCarthy, Joseph; Little, Steven Department of Chemical and Petroleum Engineering, Bioengineering University of Pittsburgh Self-assembly is a “bottom up” materials fabrication method often seen in nature, which is responsible for some of the most elegant and functional structures known. Self-assembly will naturally occur amongst nanoparticles, where Brownian motion drives the nanoparticles to find the most thermodynamically favorable configuration. However, Brownian motion does not induce self-assembly among larger particles, such as microparticles or granular particles, on an experimentally relevant time scale. We have developed a method to organize microparticles using sonication to artificially thermalize particles and induce self-assembly even in highly dilute, untemplated systems. Our hypothesis is that a novel phenomenon we call “lubrication collapse” is responsible for this observed organization. Lubrication collapse arises from the spike in energy dissipation caused by lubrication forces between particles as they pass closely to one another. This poster describes our work in characterizing lubrication collapse using microscopy to observe the effects of sonication on solutions of dilute microparticles.

55 Synthesis, Characterization, and DFT Modeling of Novel Mixed-Ligand Donor/Acceptor (Dithiolato/Dithione) Zinc Coordination Complexes Ratvasky, Stephen; Mogesa, Benjamin; Van Stipdonk, Michael; Basu, Partha Department of Chemistry and Biochemistry Duquesne University Coordination complexes of redox-active dithiolene ligands are known for their multiple well-defined redox states, as well as for their relevance in both biology and materials science. In most cases, the coordination chemistry of these ligands is focused on the reduced state. In this study we examine neutral mixed-ligand complexes of simultaneously coordinated fully oxidized and fully reduced dithiolene ligands about a Zn2+ metal center. Similar literature donor/acceptor (dithiolate/dithione) complexes exhibit intriguing non-linear optical properties. N,N’-diisopropylpiperazine-2,3-dithione (iPr2Dt0) and N,N’-dimethylpiperazine-2,3-dithione (Me2Dt0) were chosen to represent the fully oxidized state, while maleonitriledithiolate (mnt2-) was chosen to represent the fully reduced state. Complexes were characterized using 1H and 13C NMR, FT-IR spectroscopy, UV-vis spectroscopy, cyclic voltammetry, mass spectrometry, and X-ray crystallography. Gas-phase optimized structures and vibrational frequencies of target complexes were calculated using DFT.

56 Microbubble oscillation via ultrasound and immobilization on hollow fiber surfaces to improve gas exchange in respiratory devices Nguyen, Jenna T.; Malkin, Alex; Federspiel, Dr. William Swanson School of Engineering University of Pittsburgh McGowan Center for Regenerative Medicine There are few solutions to patients who suffer from chronic lung disease. Lung transplantation and positive pressure mechanical ventilation seem to be less than ideal for the complications that result from long waiting lists or contraction of other diseases during treatment. Extracorporeal membrane oxygenation (ECMO) incorporates hollow fiber membranes to complete oxygen/carbon dioxide gas exchange as the lungs would on their own. This study aims to optimize the gas exchange abilities of ECMO devices by infusion and ultimately immobilization of lipid microbubbles onto the surface of hollow fiber membranes that pulsate when exposed to ultrasound. The results from this proof of concept device are analyzed to determine the efficiency of gas exchange performance when the bubbles are pulsed with ultrasound, and to develop different techniques to chemically conjugate microbubbles to a hollow fiber surface.


Page 24

57 Gas Chromatography Mass Spectrometry Detection of Ignitable Liquids on Cloth After Washing McGregor, Sarah; Wetzel, Stephanie Forensic Science and Law Program Duquesne University The detection of ignitable liquids is of value to forensic scientists in the investigation of arson cases. In the act of arson the perpetrator may have traces of ignitable fluids on their pants and shoes. The goal of this research was to determine if ignitable liquids could be detected on cloth after it had been washed. Diesel fuel was the ignitable liquid of choice due to its low volatility and its enduring capability when exposed to the environment. Different evaporation times and water temperatures were examined, while the volume of diesel fuel applied to the sample was kept constant. During this research Passive Headspace Extraction and Gas Chromatography Mass Spectrometry (GC-MS) were used for analysis.

58 Baculoviral overexpression of Rat Serotonin Transporter Kelley, Zachary and Cascio Research Group Department of Chemistry and Biochemistry Duquesne University The serotonin transporter (SERT), an integral transmembrane protein involved in reuptake of serotonin from the synaptic cleft to the presynaptic neuron, is the target of many antidepressants due to its involvement in regulating synaptic serotonin levels. In order to understand and improve SERT’s drug binding affinity and characterize the extracellular portions, it is essential that an overexpression system be developed to provide sufficient quantities of recombinant SERT for subsequent characterization. In this work, mutated rat SERT was sub-cloned into pFastBac, transposed into DH10Bac cells, and the resulting recombinant bacmid DNA was isolated. Transfection of the bacmid into Sf9 insect cells produced viable baculovirus that were then amplified and titered. This virus can be used to infect Sf9 cells to produce relatively high quantities of rSERT. Each mutated rSERT protein is then purified and characterized via crosslinking and mass fingerprinting to understand the structure and function of the transporter.

59 Expression and detection of hominoid semen peptides for the investigation of amyloid fibril formation Hockman, Megan; Jensen-Seaman, Michael I. Department of Biological Sciences Duquesne University The semenogelin proteins (SEMG1 and SEMG2), and the prostatic acid phosphatase (ACPP) enzyme, are major components of human and chimpanzee semen, and show differences in length within and between species due to variable numbers of tandem repeats. After ejaculation, these proteins are cleaved into small peptide fragments which form amyloid fibrils, greatly increasing HIV infectivity. Evolutionary differences among primate species could result in varying degrees of infectivity. To study this further, I grew human prostate cells in culture and quantified the endogenous expression of ACPP using an optimized fluorometric assay. To express peptides derived from the semenogelin proteins, I PCR-amplified and cloned portions of the human and chimpanzee coding regions into an expression vector, which I then transformed into Rosetta E. coli cells. I successfully expressed and purified proteins from E. coli. Future research involves expression of ACPP fragments in E. coli cells, and investigation of amyloid fibril formation.

60 PLB1 overexpression upregulates the expression of UASINO regulated genes in Saccharomyces cerevisiae Jonik, Benjamin; Nesbitt, Nicole; Vera, Michael; Patton-Vogt, Jana Biology Department Duquesne University Ypk1 is a protein kinase that affects multiple processes in S. cerevisiae. Our lab has shown that deletion of YPK1 results in upregulation of a phospholipase, Plb1, an enzyme that acts on phosphatidylcholine. In addition, overexpression of PLB1 rescues growth phenotypes associated with loss of YPK1. The loss of YPK1 is known to result in abrogated sphingolipid biosynthesis. Many glycerophospholipid biosynthetic genes contain the UASINO sequence in their promoters and are co-regulated by the presence of inositol in the medium. This study tests the hypothesis that loss of YPK1 effects the expression of UASINO containing genes, and that PLB1 overexpression modulates that activity. An INO1-LacZ reporter construct and a multi-copy plasmid containing PLB1 were employed for our studies. Our results indicate that PLB1 overexpression upregulates UASINO containing genes. These findings provide further information regarding the complex interplay between membrane synthesis and turnover in S. cerevisiae.


Page 25

61

An AgentBased Model of Interacting Feral Cat Colonies and Analysis of Population Control Measures Neilan, Dr. Rachel, Ireland, Timothy Department of Mathematics and Computer Science Duquesne University Freeroaming feral cat populations are common in nearly all areas of concentrated human habitation, and can pose considerable threats of nuisance and damage to native ecosystems. We built a stochastic, agentbased computational model for simulating the behavior and growth of feral cat colonies, as well as the interactions between these colonies. Model replicates are used to examine and compare the ability of trapneuterreturn (TNR) and trapvasectomyhysterectomyreturn (TVHR) methods to control the size and behavior of isolated feral cat colonies, as well as systems of interacting colonies. Results provide inferences regarding the most effective methods for applying population control to feral cat colonies with various spatial configurations and environmental parameters. This research is done in collaboration with Frankie’s Friends, a local nonprofit spay and neuter animal clinic.

62 Overexpression of PLB1 upregulates the Unfolded Protein Response (UPR) in Saccharomyces cerevisiae Brant, Jacob; Nesbitt, Nicole; Patton-Vogt, Jana Biology Department Duquesne University The protein kinase Ypk1 has several physiological roles in Saccharomyces Cerevisiae. Previous research has shown that deletion of YPK1 results in upregulation of phospholipase B1 (plb1), an enzyme involved in phosphatidylcholine turnover. PLB1 overexpression is also known to rescue growth phenotypes associated with the loss of YPK1. Loss of YPK1 results in aberrant sphingolipid biosynthesis, which effects ER function. ER homeostasis is maintained by the Unfolded Protein Response (UPR), which is a transcriptional program induced in response to unfolded luminal proteins of the ER, secretory stress, or inositol starvation. Under inositol poor conditions, sphingolipid biosynthesis decreases and the UPR is activated. The goal of this study was to evaluate how PLB1 overexpression affects induction of the UPR in wildtype and ypk1Δ yeast by evaluating the expression of a UPRE-LacZ construct. Our results showed that PLB1 overexpression increases UPR activity.

63 Ground State Stabilization of Non-enzymatic β-Keto Acid Decarboxylation in Aqueous Solution Tamez, Angel

1 and. Evanseck, Jeffrey D

1Department of Chemistry, University of Texas–Pan

America; Center for Computational Sciences and Department of Chemistry and Biochemistry, Duquesne University Thermodynamic parameters of activation for the uncatalyzed decarboxylation of malonate have been computed in aqueous solution and compared to experimental observation. A mechanism is proposed indicating a tri-membered cyclic arrangement of waters participating in the selective stabilization of the ground state structure. The M06-2X functional with the 6-31+G* basis set was used with a discrete-continuum model, where three explicit waters are defined along with Tomasi’s polarizable continuum model (PCM). The cyclic water structure was computed to form a strong hydrogen bond network with the non-decarboxylating moiety of malonate in the ground state. However, in the decarboxylation transition structure, the hydrogen bond network broke and lost stability. The experimental enthalpy of activation, ΔH

‡, of malonate is 30.0 kcal•mol

-

1, whereas the computed ΔH

‡ is 33.4 kcal•mol

-1. The

novel, non-enzymatic model provides an understanding of the non-enzymatic behavior of similar compounds, and potential in describing the decarboxylation mechanisms in decarboxylases.

64 Optimizing Microsatellite Loci to Study the Genetic Structure of Two Geographically Isolated Populations of the Bluebreast Darter. Cutteridge, Taylor F.; Honick, Anthony S.; Porter, Brady A. Department of Biological Sciences Duquesne University. The bluebreast darter, Etheostoma camurum, is an imperiled fish that lives in small isolated populations of the Ohio River watershed with historically high water quality. Pennsylvania surveys in 2005 revealed a new population in Deer Creek, PA; over 200 river miles from the closest downstream population in central Ohio (Big Darby Creek). As water quality improved, the geographic range of this species has increased to where these populations are now in contact with one another. In this study we used PCR to cross-amplify several microsatellite loci and optimized them for fragment analysis to study the genetic structure of these two bluebreast darter populations. We hypothesized that the historical isolation of these populations has caused differences in microsatellite allele composition or frequency due to genetic drift and inbreeding. If this is true, we could apply these loci to new samples and genetically track the range expansion of this recovering species.


Page 26

65 Development of a Data Fitting Protocol to Determine the Valence States of Evolving Transition Metal Oxides During In Situ TEM Oxidation-Reduction Reactions Mills, Sara and Bonifacio, Cecile Chemical Engineering University of Pittsburgh In this study, the valence states of cobalt from bimetallic nickel-cobalt core shell nanoparticles were analyzed from electron energy loss spectroscopy (EELS) acquired during in situ environmental transmission electron microscopy (ETEM) oxidation-reduction gas reactions. Obtaining the ratio of the areas under the Co L3 and L2 (L3/L2 ratio) gives the valence states of Co. A comparison between fitting two versus three Gaussian curves per L peak is presented to obtain a protocol applicable for EELS analysis of other transition metal oxides. After analysis, the three Gaussian fit resulted in a more precise fitting protocol. Interpolation from literature values shows a valence change from +2.48 to +2.83, and +2.57 to +2.70, through two oxidation-reduction cycles, respectively; the increasing valence states of Co upon reduction are consistent with literature. This study presents an accurate identification of the valence states of the evolving cobalt oxide structures during in situ TEM oxidation-reduction reactions.

66 Hippocampal proteotoxicity is mitigated by N-acetyl cysteine Heinemann, Scott

1, Posimo, Jessica

1, Weiland, Nicole

1,

Brodsky, Jeffrey2, Wipf, Peter

3, and Leak, Rehana

1

1Division of Pharmaceutical Sciences, Duquesne

University 2Department of Biological Sciences, University of

Pittsburgh 3Departments of Chemistry and Pharmaceutical

Sciences, University of Pittsburgh Neurodegenerative diseases such as Alzheimer’s disease are characterized by proteotoxic stress from misfolded proteins and oxidative stress from free radical injury. One of the most vulnerable brain regions in this disorder is the hippocampus of the forebrain. Here we studied the impact of dual hits of proteotoxic and oxidative stress on primary hippocampal neurons. The dual hit hypothesis of neurodegeneration states that stressed cells are more vulnerable to subsequent stress exposures. Consistent with this hypothesis, the proteasome inhibitor MG132 exacerbated the toxic response to the oxidative toxin paraquat according to the three independent, unbiased viability assays. In contrast, dual hits of MG132 were only mildly synergistic. N-acetyl cysteine (NAC) prevented the toxicity of MG132 but had no impact on paraquat toxicity and did not raise glutathione levels. These results suggest that NAC can prevent protein-misfolding stress but not oxidative stress in hippocampal neurons.

67 Adsorption of Arsenic by Activated Carbon Jones, Jeramiah; Dille,Sara; Basu, Partha Department of Chemistry and Biochemistry Duquesne University Arsenic is a toxic element that has the potential to enter ground water sources of drinking water either by erosion or from runoff of agricultural or industrial sites. Arsenic has been linked to non-carcinogenic effects such as nausea, vomiting, partial paralysis, blindness, and cancers of the bladder, lung. Skin, kidney, and liver. The project focuses on the removal of sodium arsenate from aqueous media using an activated carbon filter that has been doped with iron(lll) hydroxide. The filtrate will be analyzed using ion chromatography to test for removal of the sodium arsenate from the initial aqueous solution.

68 Design of Analysis Tools for the iTOP Detector Suehr, Gregory Department of Physics and Astronomy University of Pittsburgh The Belle-II experiment at the superKEKB accelerator will perform high-statistics investigations into the flavor sector of the standard model. The precision measurements that will be made are possible due in part to the particle identification capabilities of the imaging Time-of-Propagation (iTOP) detector. Although the iTOP detector already provides excellent spatial and timing resolution for single photon detection, its development is ongoing at the Cosmic Ray Telescope (CRT) experimental apparatus. During this development, access to information from all parts of the system’s operation is critical. A system to produce standard, summarized information for each data-collecting run was developed using the object-oriented data analysis software ROOT and bash. Low level diagnostic plots and specific timing distributions produced allow for easy data quality monitoring and will inform analysis efforts as more data is collected at the CRT.


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69 Part per Million Resolution Optical Wavemeter Tiber, Gage; Brooke, Robert; Ireland, Timothy; Davies, Isaac; Gillis, Julie; Zaccagnini, Chris; Corcovilos, Theodore Department of Physics, Duquesne University A wavemeter measures the wavelength of a laser. Our design is a Michaelson Interferometer with mirrors that travel along the beams by 26 cm, causing the optical path length of the interferometer arms to change, and creating about 1 million interference fringe oscillations. These oscillations are detected with a photodiode and counted using digital circuitry. Using a temperature-stabilized Helium-Neon reference laser with accurately known wavelength, an unknown laser’s wavelength can be determined with part-permillion resolution by comparing the number of fringes of the two lasers. We control the wavemeter using an Arduino microcontroller which runs the mirror motor, calculates the wavelength from the fringe measurement, and displays the results. We also use digital temperature, pressure, and humidity sensors to correct for the index of refraction of air, giving us the true vacuum wavelength of the unknown laser. Here, we describe the optical, electronic, and mechanical aspects of the wavemeter design.

70 Isolation and Characterization of an Antibiotic Resistant Bacterium from Produced Water Jenna Kuhn and John F Stolz Department of Biological Sciences, Duquesne University Development of natural gas through unconventional drilling and hydraulic fracking well fluid generates production fluids as well as releases formation water. These fluids are not sterile and microbial activity can result in potentially harmful compounds as well as well deterioration and decreased gas production. Produced water from hydraulically fracked wells contains a variety of microbes able to withstand a high total dissolved salt concentration (TDS) environment. This study focused on isolating a single strain by growing cultures in high TDS liquid media and streak plating, analyzing microbial morphology using light microscopy, and identifying the strain through 16S rRNA gene analysis. Antibiotic resistance testing found the strain to be sensitive to erythromycin, but resistant to oxacillin and nalidixic acid. The microbe grew optimally at 10.0 % NaCl, pH of 6, and 24

oC.

71 A Study of the Morphological and Genomic Effect of Melatonin and/or 17 -Estradiol (E2)/Progesterone (P4) Hormone Therapy (HT) in HER2/neu Mouse Mammary Tissue Buszko E, Bondi C, Maria S, Witt-Enderby P Duquesne University, Division of Pharmaceutical Sciences Prempro,

TM which contains conjugated equine estrogens

(CEE) and medroxy progesterone acetate (MPA), but not Premarin (contains CEE only) increased breast cancer incidence and mortality; however, the underlying mechanisms of this are not clear, but may involve MPA effects on mammary ductal differentiation and tumorigenesis. Ten different treatment groups containing E2 and varying doses of P4, CEE/MPA, alone or in combination with melatonin, were tested in 2-3 month old female HER2/neu mice, a transgenic mammary cancer mouse model. Our data demonstrate that mammary ductal differentiation that is associated with cancer protection (decrease in ductal elongation and increase in tertiary branching) was paralleled by temporal changes in pERK 1/2, pERK5, and Runx2 expression. Although the overexpression of any of these proteins may lead to tumorigenesis, the protein signature exhibited in the presence of melatonin induced changes that are theorized to be the most protective against cancer, offering menopausal women a safe HT alternative.

72 Genetic Association of PKD2 with Dental Caries Eckert, Scott

1; Shaffer, John R.

2

1Department of Computational Biology, University of

Pittsburgh; 2Department of Human Genetics, University

of Pittsburgh Dental caries (decay), the most common disease worldwide, costs over $50 billion annually in the US. Though heritable, few genes for dental caries have been identified and replicated. A genome-wide association study of dental caries implicated the genomic region containing the dentin/bone extracellular matrix genes and two adjacent genes (PKD2, ABCG2). As a follow-up study, we analyzed the effects of 49 genetic polymorphisms chosen to tag the genetic variation in this region, while adjusting for age, sex, and ancestry using samples from 6 studies (n=4000). Age- and race-stratified analyses were performed and results were combined using meta-analysis. In black adults, a polymorphism in PKD2 was significantly associated with dental caries (p<0.003). Variants in PKD2, ABCG2, and MEPE were significantly associated with dental caries in individual studies. These results lend additional support to the hypothesis that variation in this genomic region influences risk of dental caries.


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73 Computational and experimental study of peptide fragmentation using small model systems McLaughlin, Rebecca; Van Stipdonk, Michael Center for Computational Sciences; Department of Chemistry and Biochemistry Duquesne University

Tandem mass spectrometry (MS/MS) and collision-induced dissociation (CID) are widely used for peptide/protein identification in proteomics. To gain a better understanding of the “rules” for predicting peptide fragmentation patterns, MS/MS, time and energy resolved CID, and density functional theory were used to study the mechanistic and energetic details of the fragmentation of model protonated peptides in the gas-phase. Specifically, the b2 pathways of AG, GA, GA-OMe, and GA-NH2 were examined. Comparison of the energetics produced from CID experiments of the dipeptides revealed that the formation of the b2

+ ion was

more energetically favored for the amide. While, the formation of the b2

+ ion for the acid showed to have the

highest barrier energy. The experimental data can then be used as a benchmark to access the accuracy of the computational models.

74 The improved solubility of fenobam sulfate and its analgesic properties Cox, Abigail

1,2, Lax, Neil C.

1,2, Kolber, Benedict

1,2

Department of Biological Sciences, and Chronic Pain Research Consortium Duquesne University, Pittsburgh, PA Fenobam is a known analgesic drug that is a specific antagonist to mGluR5. However, the compound has poor solubility and a short half-life. A new salt formulation of the drug, fenobam sulfate, has a longer half-life and better bioavailability than fenobam free base. We tested whether fenobam sulfate shares the same analgesic properties as traditional fenobam in a formalin model of spontaneous and mechanical pain. We found that the analgesic properties of fenobam and fenobam sulfate differed based on the vehicle used to dissolve the compounds. Overall, fenobam sulfate decreased pain-like behaviors in the spontaneous formalin test in both male and female mice. Neither compound, however, blocked formalin-induced hypersensitivity two and three hours post formalin. Fenobam sulfate therefore has the capability of becoming a treatment for pain, but more work must be done to improve its bioavailability so that it can provide longer-lasting analgesia.

75

Free energy changes of Mg2+

/Mg+ in water clusters

using quantum molecular dynamic simulations Spirik, Kassandra; Workman, Riley; Upadhyay, Shiv; Madura, Jeffry D. Center for Computational Science, Department of Chemistry and Biochemistry, Duquesne University, Pittsburgh, PA. Free energy changes can be used to calculate standard reduction potentials and free energy changes for a single ion in solution can then be used to establish an absolute standard reduction potential scale. The preexisting scale is not absolute, but rather the values are defined relative to the standard hydrogen electrode (SHE). This study aimed to find exact free energy changes through the use of accurate molecular dynamic simulations that matched experimental findings. The simulations were run using the B3LYP functional with the 6-31G* and 6-311++G** basis sets implemented in Terachem. Using each basis set, four different systems were run containing a Mg

+ or

Mg2+

ion in a water cluster of both 42 or 65 water molecules. Free energy values were obtained from evaluating the difference in energies of Mg

2+ from the

energies of Mg+ in the water cluster. These results will be

compared against the experimental mass spectrometry data.

76 Examining the LCST and hydration properties of PNIPAM and its substituents Galbraith, Madeline L., Madura, Jeffry D. Department of Chemistry & Biochemistry and Center for Computational Sciences, Bayer School of Natural & Environmental Sciences, Duquesne University The stimuli-responsive polymer, or smart polymer, poly(n-isopropylacrylamide) (PNIPAM) undergoes a conformational change at the lower critical solution temperature (LCST) making it ideal for applications involving volume changes dependent upon temperature, for instance drug delivery. Below the LCST the extended polymer is dominated by enthalpic contributions, while above the LCST the collapsed polymer is dominated by entropic contributions. The hydrophobic isopropyl groups are the main entropic contributor and replacing these groups with bulkier alkyl groups allows the LCST and hydration properties (e.g. volume) to be modified. The molecular-level interactions responsible for the behavior of PNIPAM and its substituents were studied using molecular dynamics simulations. The hydration properties were analyzed and volumes were calculated using geometric algorithms, like Voronoi polyhedra. Above the LCST, PNIPAM and its substituents were less hydrated than below the LCST. Further, the decrease in LCST and changes in other physical properties for PNIPAM and its substituents were calculated.


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77 The effect of kinase inhibition on survival of breast cancer cells Jordan Waddell, Thomas Wright, Katy Wendekier, Christopher Raybuck, and Jane E. Cavanaugh Duquesne University According to the American Cancer Society there will be 1.6 million new cases of breast cancer this year. Specific targets for breast cancer include the MEK1/2 and PI3K pathways, which are both involved in cell survival. Inhibitors of MEK1/2 and PI3K have been used clinically but with limited efficacy. It has been suggested that crosstalk with other parallel pathways may limit their effectiveness. In our study, we used known inhibitors of MEK1/2 (U0126) and PI3K (LY294002) to determine the effect of kinase blockade in MDA-MB-231 and BT474 breast cancer cells. Our results indicate that in the presence of the MEK1/2 inhibitor, U0126, phosphorylation of Akt (an upstream component in the PI3K pathway) increases. In addition, cells treated with U0126 proliferated more than those treated with LY294002. Our data suggest that crosstalk is present between the MEK1/2 and PI3K pathways and perhaps a dual inhibitor may be more efficacious.

78 Solvation and Vibrational Analysis of Propanamide Graça, Connor J*, Madura, Jeffry D. *Duquesne University, Bayer School of Natural and Environmental Science, The Cyril H. Wecht Institute of Forensic Science and Law +Duquesne University, Bayer School of Natural and

Environmental Science, Department of Chemistry and Biochemistry, Center for Computational Sciences Recently it has been shown that ultraviolet resonance Raman (UVRR) spectroscopy can be used to determine peptide structure. In UVRR, one is measuring a shift in the amide III vibration due to hydrogen bonding with the solvent. Propanamide is a small molecule that can be used to study the role of solvent in the amide III vibration. Computational experiments were conducted using the software IQmol and QChem. The molecules used in simulations were calculated for their lowest energy conformation before the frequencies were calculated. Geometry and frequency calculations were conducted using the M06-2X functional and the 6-31G** basis set. The results of the calculations showed that the amide I frequencies of propanamide decreased, while the amide II and III frequencies increased with increased hydrogen bonding.

79 A Genetic Screen for Blood-induced Promoters from Asaia bogorensis, a Midgut Symbiont of Malaria Vector Mosquitoes Paul, Lianna; Shane, Jackie; Lampe, David Department of Biological Sciences Duquesne University With over 3.4 billion people spanning 106 countries and territories at risk, malaria is a global concern. Paratransgenesis, or the genetic modification of symbiotic bacteria to change host phenotype, offers one of the most promising preventative tactics. Asaia, a prevalent bacterium within mosquito microbiota, has previously been engineered with native secretion signals fused to antimalarial effector molecules. However, expressing these molecules constitutively would hinder bacterial survival in the wild. With this in mind, we created a genetic screen to detect blood-induced promoters from Asaia bogorensis SF2.1. Insertion of genomic fragments into the plasmid GLR1 5’ to the coding sequence of GFP allowed for visualization on iron-enhanced and deplete media, a representation of conditions preceding and following a blood meal. Isolates with possible conditionality were then given to blood-fed Anopheles mosquitoes and fluorescent imaging used to determine their presence within target organs. Finally, sequencing allowed for identification of these genomic fragments.

80 Examination of Hydrogen Bond Dynamics in Triphenylsilanol through Variable Temperature Solid-state NMR Spectroscopy Mesinere, Sam, Plavchak, Christine, and Iuliucci, Robbie Environmental Molecular Sciences Laboratory Pacific Northwest National Laboratory Various advancements in energy applications such as batteries are of importance due to their storage capacity and efficiency. Silica species such as silica nanoparticles largely influence the proficiency of these energy storage devices. Silanol groups impact the functionalization of surfaces through their hydrogen bond dynamics. The properties of triphenylsilanol’s crystalline structure are examined through solid-state nuclear magnetic resonance (NMR) spectroscopy at variable temperatures ranging from -150° to 120°C. In particular, the

29Si chemical shift anisotropy (CSA) and

1H T1 spin-lattice relaxation times are studied. CSA,

observed in the intensities of spinning sidebands, is estimated via Herzfeld-Berger Analysis. The accuracy of the CSA values was improved by using Simpson, a numerical simulation program. Three principal components of the CSA (δ11, δ22, and δ33) can be related to molecular structure through quantum mechanical calculations. Such CSA calculations were performed using the density functional theory (DFT) program Quantum Espresso for available crystal structures.


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81 Peptide Sequencing by Tandem Mass Spectrometry Pestok, Jordan

1; Patterson, Khiry

2; Van Stipdonk,

Michael2

1; Sto-Rox High School 2; Dept. Chemistry and Biochemistry, Duquesne University Tandem mass spectrometry (MS/MS) and collision-induced dissociation (CID) are the most widely used tools for identifying peptides and proteins. These tools allow for rapid and accurate sequencing of peptides, and identification of proteins, by probing of ion fragmentation in the gas phase. The goal of this project is to develop and optimize a laboratory module for use in undergraduate laboratory settings that provides experience with (a) use of electrospray ionization to generate gas-phase peptide ions (protonated and metal cationized) and (b) linear ion trap mass spectrometry and multiple-stage collision induced dissociation to probe ion fragmentation. In the module, students “calibrate” themselves using the fragmentation of peptides of known sequence, and apply “rules’ for interpreting fragmentation patterns to determine the sequence of two “unknown” peptides.

82 Markov State Models of the Dopamine Transporter Willison, Nicholas F.

1; Madura, Jeffry D.

2

Department of Chemistry, Washington & Jefferson College

1; Center for Computational Sciences,

Department of Chemistry and Biochemistry, Duquesne University

2

The dopamine transporter (DAT) is a major neurotransmitter transporter in the regulation of dopamine levels in the body. Visualizing the transport mechanism is crucial to understanding its function. The drosophila melanogaster dopamine transporter (dDAT) is used as the model system whose own conformation states are unknown. Markov state model (MSM) analysis is a powerful tool for visualizing conformation states of proteins by grouping together conformations of similar kinetics. We present a method for constructing a MSM of the dDAT to invoke various conformations of the structure and calculating the kinetics between the states. Adaptive sampling techniques were instrumental in generating simulations to build a MSM. Simulations were carried out using high-throughput molecular dynamics (HTMD) and ACEMD at temperatures of 300K and 500K. The MSM generated macrostates of the dDAT and the analysis of these macrostates presented here lay the foundation for obtaining new conformation states of the dDAT.

83 VDR/Substrate Interactions Identified Through Alanine Scanning Lau, Stephen K.; Madura, Jeffry D. Department of Chemistry and Biochemistry, Center for Computational Sciences Duquesne University The vitamin D receptor (VDR) regulates a variety of metabolic pathways, such as those involved in the immune response and cancer. VDR is a ligand-dependent transcription factor that belongs to the nuclear receptor superfamily. Key interactions between a ligand and receptor will influence the strength of binding. Alanine substitution results in a change in affinity between the receptor and ligand, which is used to determine whether or not that residue was important. Molecular Operating Environment (MOE) was used to observe VDR bound to 2MD and TEI-9647 and evaluate the properties of agonist and antagonist binding. Computationally determining the necessary residues for VDR using alanine scanning mutational analysis is validated against experimental mutagenesis of VDR.

84 BIOPHYSICAL CHARACTERIZATION of a G-QUADRUPLEX STRUCTURE IN HUMAN CYCLIN DEPENDENT KINASE 5 REGULATORY SUBUNIT 2 MESSENGER RNA Bandi, Kathryn J.; Mihailescu, Mihaela-Rita Department of Chemistry and Biochemistry Duquesne University Messenger RNA sequences rich in guanine bases have the ability to form a specific secondary structure known as a G-quadruplex. G-quadruplex structures form by the stacking of multiple G-quartets which are produced by the Hoogsteen base pairing of several guanine residues. The human CDK5R2 messenger RNA contains multiple guanine bases and has been predicted to form a G-quadruplex. G-quadruplex structures have been shown to have a high binding affinity to fragile X mental retardation protein (FMRP) associated with fragile X syndrome. This binding affinity to FMRP can be analyzed by characterizing the G-quadruplex structure formed by the CDK5R2 mRNA, therefore determining its role in fragile X syndrome. To characterize the secondary structure of this mRNA strand, biophysical techniques were utilized including circular dichroism spectroscopy,

1H nuclear magnetic resonance

spectroscopy, UV spectroscopy, and native polyacrylamide gel electrophoresis (PAGE).


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85 Metal Organic Frameworks (MOF) – Effective Sulfur Encapsulant in Lithium Sulfur Batteries Sweeney, Matthew

1; Murugavel Shanthi, Pavithra

2; Kumta,

Prashant N.1,2,3

1Department of Chemical and Petroleum Engineering,

2Department of Bioengineering,

3Department of Mechanical

Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA Department of Chemical and Petroleum Engineering University of Pittsburgh Lithium Sulfur batteries are known for having high theoretical capacities, approximately 5-6 fold greater than current lithium batteries. However, the cycling-stability of these batteries is limited due to dissolution of lithium polysulfide compounds into the organic liquid electrolyte. This process leads to large decay in capacity of the battery per cycle with the formation of Lithium Sulfide (Li2S) below the expected theoretical predictions. To prevent this, metal organic frameworks (MOFS) were used to restrain the polysulfide from the electrolyte environment. Different variants of MOF-5 with Zn(II) and Mg(II) cages linked by terephthalic acid molecules were synthesized. Because the pore volume of MOF structures are well known, the amount of sulfur was back calculated to provide sufficient volume in the porous structure for lithium ions to infiltrate and react, while preventing dissolution into the electrolyte. This methodology will likely prevent degradation of the battery and lead to improved cycling performance.

86 Stability of RNA conformations using metadynamics Schall, Rachael M.

1, Imperatore, Joshua A.

2, Madura,

Jeffry D.3

1Roanoke College: Department of Chemistry and

Biochemistry; Salem, VA 2Washington & Jefferson College: Department of

Chemistry; Washington, PA 3Duquesne University: Center for Computational

Sciences; Pittsburgh, PA RNA associated with the replication of the C9orf72 gene is correlated with neurological disorders, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The structure of the RNA is implicative in these diseases. The (G4C2)n sequence expands and affects protein production of the gene. The RNA (G4C2)n sequence can form both hairpin and G-quadruplex conformations. It has been observed that ions can stabilize RNA structures. The hairpin conformation is stabilized by a magnesium ion concentration and the G-quadruplex stabilized by a potassium ion concentration. A 24 nucleotide RNA was studied, (G4C2)4. The free energy landscapes of the nucleic acid under different ion concentrations were calculated using well-tempered metadynamics simulations to determine the relative stability of the conformations. Results will be presented in the poster.

87 Formation of Mixed Carboxylic Acid and Phosphonic

Acid Head Group Self-Assembled Monolayers on a

Titanium Oxide Surface

Mazzone, Carly; Blystone, Ashley; Reger, Nina; Gawalt,

Ellen S.;

Department of Chemistry and Biochemistry

Duquesne University

Applications for titanium metal and its alloys in the medical

and aerospace industries are expanding to greater variety.

The usage of self-assembled monolayers (SAMs) on

titanium metal allows for advancements in corrosion

resistance and specific wettability. SAMs are single layered

organic coatings that are deposited onto metal surfaces to

alter the metal’s surface properties. In this study, a mixed

SAM composed of octadecylphosphonic acid and 16-

hydroxyhexadecanoic acid was attempted to be formed on

titanium metal oxide to observe the effects of the mixed

head groups and tail groups on the properties of the

monolayer. The mixing the head groups in the SAMs allows

for the utilization of the chemical variety of carboxylic acid as

well as the strong binding nature of phosphonic acid. Diffuse

reflectance infrared Fourier transform spectroscopy, contact

angle analysis, and surface energy analysis was used to

characterize the presence, order, and wettability of the thin

films.

88 Resveratrol induced neuroprotective and anti-cancer effects: Investigating the role of kinase signaling pathways Stabile, Nicholas, Potdar, Sneha, Allen, Erika and Cavanaugh, Jane E. Department of Pharmacology and Toxicology Duquesne University Resveratrol, a naturally occurring polyphenol found in grapes and blueberries, exhibits both neuroprotective and anti-cancer effects. However, the mechanisms underlying these contradictory effects are not yet fully known. To address this, we investigated the effects of resveratrol on cell viability and signaling cascades in neuronal-like SH-SY5Y cells and triple negative breast cancer (TNBC) cells (MDA-MB-231). Our data suggest that resveratrol protects SH-SY5Y cells from oxidative stress and may increase cell death in TNBC cells. We also examined the effect of resveratrol on the extracellular signal-regulated protein kinases 1, 2, and 5 (ERK1/2 and ERK5) and protein kinase B (Akt) as these pathways play important roles in cell survival and proliferation. The results of this study will increase our understanding of the mechanisms by which resveratrol enhances survival of neuronal cells, while at the same time, decreases viability of cancer cells.


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89

A BIOPHYSICAL ANALYSIS OF G-QUADRUPLEX STRUCTURES IN THE MOUSE CYCLIN-DEPENDENT KINASE 5, REGULATORY SUBUNIT 2 MESSENGER RNA Gaetano, Christian M.; Mihailescu, Mihaela Rita Department of Chemistry and Biochemistry Duquesne University In silico energy modeling and biophysical characterization experiments have shown that guanine-rich regions of certain nucleic acids are capable of forming secondary structures classified as G-quadruplexes. These structures are subject to targeted protein binding and subsequently act as essential points of regulation. The cyclin-dependent kinase 5, regulatory subunit 2 (CDK5R2) mRNA is of particular interest for the study of these structures due to the presence of several guanine-rich regions in its 3’ untranslated region (3’ UTR). Biophysical characterization techniques such as 1H-nuclear magnetic resonance (NMR) spectroscopy,

circular dichroism (CD) spectroscopy, UV/Vis spectroscopy and polyacrylamide gel electrophoresis (PAGE) were used to probe the structure and stability of the third predicted G-quadruplex (Q3) in the mouse CDK5R2 3’ UTR. Additionally, electromobility shift assays (EMSA) were used to elucidate the binding partnership of this G-quadruplex and fragile X mental retardation protein (FMRP), the principal component of pathogenesis of the genetic disorder fragile X syndrome (FXS).

90 Analysis of Sex-Based Differences in a Mouse Model of Stress-Induced Analgesia Long, Caela

1,2,3, Kolber, Benedict

1,2

1Department of Biological Sciences and

2Chronic Pain

Research Consortium, Duquesne University; 3Swarthmore College

Although pain has evolved as a protective response to noxious stimuli, the suppression of pain during acute stress is evolutionarily advantageous and is known as stress-induced analgesia (SIA). Recent studies have drawn attention to unresolved sex differences in mammalian physiology, including differences in pain modulation. Here, we investigated sex-based differences in a mouse model of SIA. Male and female mice were restrained to induce stress before receiving a formalin paw injection, a common inflammatory pain model. Restrained male mice demonstrated decreased mechanical hypersensitivity and increased corticosterone blood concentrations compared to control males three hours post formalin paw injections. Stress, however, did not have the same effect on pain-like behavior or corticosterone levels in females. Overall, our findings show biological differences between female and male mammals in the context of pain and stress and highlight the need to simultaneously test both sexes in molecular and behavioral models of disease and stress.

91 Photoacoustic and Optical Spectroscopic Analysis of Cerebral Spinal Fluid Twigg, Julianna M; Goldschmidt, Benjamin S; Petrell, Elizabeth A; Viator, John A Biomedical Engineering Duquesne University Cerebral spinal fluid (CSF) has been tested as a less invasive diagnostic method for glioblastoma multiforme using photoacoustics. When performing a photoacoustic test, a laser is pulsed at a sample, and energy is either absorbed or emitted based on the samples optical properties. A LabView program then displays a spectrum of the sample. CSF was tested between the wavelengths of 410 and 710 nm in increments of 10 nm. This resulted in a spectrum that showed no absorption, confirming that the CSF was translucent. The CSF was then tested with a sample of HS936 melanoma cells using the same wavelength parameters. The melanoma-spiked CSF was used in order to determine the limits of the detection method. Melanoma was first used because it is a convenient, similar substitute for the glioblastoma multiforme. Future work will focus on finding glioblastoma cells in CSF, as an early detection system for metastatic brain cancer.

92 Total Internal Reflection Photoacoustic Spectroscopy (TIRPAS) Microscope Petrell, Elizabeth A.; Goldschmidt, Benjamin S.; Twigg, Julianna M.; Hazur, Marc A.J.; Viator, John A. Biomedical Engineering Duquesne University We have designed and fabricated the world’s first total internal reflection photoacoustic microscope that will be capable of imaging nanostructures and cellular interfaces. We modified a Leitz Labovert FS microscope to use a pulsed Nd:YAG laser for a photoacoustic effect. Photoacoustic detection uses laser pulses to generate pressure waves, which may then be picked up by a device known as an ultrasonic transducer, which transmits these waves into electrical impulses that can be used to identify absorbing materials. A relatively unexplored aspect of photoacoustics is a method known as Total Internal Reflection Photoacoustic Spectroscopy, or TIRPAS. TIRPAS uses light reflected at an interface to generate an evanescent field to acquire noninvasive surface images of optically absorbing substances such as the surface of tumor cells. We used different dyes, including Coomassie blue and direct red, to determine image quality and resolution with the TIRPAS microscope.


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93 Detection of metastatic melanoma in the bloodstream using laser technologies and properties of photoacoustics Hazur, Marc A.J.; Goldschmidt, Benjamin S.; Moore, Colin B.; Petrell, Elizabeth A.; Viator, John A. Biomedical Engineering Duquesne University The phenomenon of photoacoustics, laser-induced ultrasound, can be used to detect metastatic melanoma sooner than the methods currently being used. When irradiating samples of hemoglobin and melanoma with pulsed laser light, an acoustic wave is created. At various wavelengths of light the acoustic response of hemoglobin and melanoma differ greatly due to differences in optical absorption, or color. Therefore, we tested 50 samples of melanoma and 50 samples of hemoglobin to determine the Gaussian curves for each, in order to develop a statistical classifier to test unknown samples of blood for the presence of melanoma. Using the Matlab computing language we created a program to run the statistical classification algorithm on inputted samples, determining if they fall within the acoustic wave range of melanoma, and the results were outputted to the user. In order to validate this method, five blind samples were tested for the presence of metastatic melanoma.

94 Effect of Crospovidone on the Dissolution of Carbamazepine Using Various Process Tableting Parameters Begur, Mallik

1; Steinbach, Douglas

2; Anderson, Carl

2;

Drennen, James K. III2

1Department of Chemical and Biological Engineering,

Illinois Institute of Technology 2Graduate School of Pharmaceutical Sciences,

Duquesne University Dissolution is an important in-vitro quality/performance test in the pharmaceutical industry. Crospovidone is an excipient in tablet formulations and is classified as a disintegrant by facilitating tablet fragmentation when exposed to solvent. The granulation of raw materials and subsequent milling are steps commonly employed to facilitate tablet manufacturing and can ultimately affect product dissolution. The purpose of this study was to examine what effect dry granulation (i.e. slugging) parameters and granule milling parameters imparted on the ultimate API dissolution performance of a tablet formulation that contained, among other excipients, crospovidone. Carbamazepine (BCS class II: high permeability and low solubility) was the API. Using dry granulation and direct compression to formulate the tablets, crushing force, milling speed, and compression force were the process parameters studied. UV-Vis was used to determine dissolution profiles of Carbamazepine. Results suggest that crospovidone mitigated the effect of processing parameters on drug release.

95 Imaging Carbonate Precipitation and Chromatic Adaptation in Microbial Communities from Shark Bay, Australia and Little Darby Cay, Bahamas Altobelli, Ashley

1, Reid, Pamela R.

2, and Stolz, John F.

3

1 Department Biological Sciences, University of Pittsburgh

2 Marine Geology and Geophysics, University of Miami

3 Department of Biological Sciences, Duquesne University

Light and confocal microscopy were used to study microbe-mineral interactions and pigment composition in microbialite-forming communities from Shark Bay, Australia and Little Darby Cay, Bahamas. Carbonate precipitation was imaged using reflectance while cyanobacteria were imaged using excitation at both 488 nm and 633 nm. Fluorescence emission spectral scans of individual colonies within different microbial mat samples revealed that pigment composition varied with species in both locals, and putatively identified chlorophyll f, a newly discovered, red-shifted chlorophyll pigment. Lyngbya mats from the intertidal zone at Shark Bay were shown to be excited by the 633 nm laser while emitting in the near infra red (e.g., 720 nm) indicating the presence of chlorophyll f and chromatic adaptation. Evidence for chlorophyll f was also found in Microcoleus dominated mats from the Bahamas, but was not as prevalent. The results suggest that chlorophyll f is widely occurring and may be important in microbialite biogenesis.

96 Behavioral Effects of An Experimental Model of Anxiety on Male and Female Rats Diaz, Vanessa

1,2 ; Chowdhury, Tara

2; Simon, Nicholas

2;

Moghaddam, Bita2

1 Department of Neuroscience, Carnegie Mellon University 2 Department of Neuroscience, University of Pittsburgh The purpose of this study was to identify behavioral changes between male and female rats after an experimental model of anxiety induced by the anxiogenic drug (FG7142). 11 male and 11 female rats were trained in an operant task that simultaneously measures reward-seeking and punishment-avoiding behavior. The rats were presented with two cues, a light or a tone, that indicated to either press a lever or nose poke to avoid the shock or receive a reward. The cues and actions for reward and avoidance were balanced across animals. Males acquired reward-based learning faster than females while females acquired punishment-based learning faster than males. Once behavior in these tasks was stable, performance was measured after the rats were given FG7142 at three different doses. In response to FG7142, males showed decreased performance in both reward and punishment trials while females showed a greater effect of drug on reward trials than punishment trials.


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97 Ensemble-Based Virtual Screening of the Human Glycine Receptor α3 for Novel Cannabinoid-Like Analgesics Maxwell, Andrew*; Wells, Marta

†‡§; Tang, Pei

†‡∥§ Departments of

†Anesthesiology,

‡Computational and

Systems Biology, §Structural Biology, and

∥Pharmacology and Chemical Biology *University of Connecticut,

§University of Pittsburgh

The human glycine receptors (hGlyRs) are critical regulators of inflammatory pain in the adult spinal cord dorsal horn. These receptors induce an analgesic response when exposed to Δ9-tetrahydrocannabinol (THC) that is independent from its psychoactive effects. The α3 subtype of hGlyR (hGlyR-α3) may serve as a target to relieve chronic pain via novel analgesics. Ensemble-based virtual screening was performed on multiple conformations of the hGlyR-α3 transmembrane domain that were generated from molecular dynamics simulations. Virtual screening was run on over 2 million drug-like compounds that were filtered from the ZINC database. These compounds have molecular properties predicted to maximize their likelihood of acting on the central nervous system. Functional validation of the top ranked compounds from virtual screening was performed via electrophysiology experiments on Xenopus laevis oocytes expressing hGlyR-α3.

98 Inhibitor Discovery and Protein-protein Interaction Modeling of the Spi-1•C/EBPβ Complex Rutter, Nathan W.; Esposito, Emilio X.; Auron, Philip E.; Madura, Jeffry D. Department of Chemistry and Biochemistry Duquesne University Disruption of a critical interaction between two transcription factors (Spi-1 and C/EBPβ), required for gene expression of Interleukin-1β, may lead to reduced inflammation in gout, diabetes, and other chronic inflammatory disorders. Protein-protein docking was performed using the applications HADDOCK and ZDOCK, demonstrating that the mutual DNA-binding domain (DBD) interaction involves the carboxylterminus (C-ter) of the C/EBPβ leucine zipper with the Spi-1 β-sheet wing. Computational small molecule docking was employed to isolate a set of lead inhibitors of pockets near Arg232 on Spi-1, a residue experimentally critical for the Spi-1 interaction with C/EBPβ. Additionally, two 9-residue peptide strands from the C/EBPβ C-ter tail that may wrap around the Spi-1 DBD and interact with the Arg232 pockets were modeled with FloppyTail and FlexPepDock. Initial results suggest that small molecule drugs such as L-arginine and bethanidine may have adequate binding affinity to inhibit formation of the complex in an in vitro test system.

99

Reverse-Engineering the Activation of Olfactory Receptor Alleles Jens Sannerud

1, Xiao-Jun Tian

2, Jianhua Xing

2

1Division of Applied Mathematics, Brown University

2Department of Computational and Systems Biology,

University of Pittsburgh Despite the fundamental importance of olfaction, little is known about the activation of odorant receptors by olfactory neurons – a crucial step in the development of a sense of smell. A Nobel-prize winning study observed that each neuron only activates a single olfactory receptor allele, chosen stochastically from a large family of genes, but the study lacks an understanding of the mechanism for this process. By rephrasing the question as a reverse-engineering problem, we formulated mathematical models for an ensemble of possible regulation mechanisms and proceeded to test the efficacy of each of the models against biological constraints through stochastic simulations. The goal of this investigation is twofold: first, to test our hypothesis that, from an engineering perspective, there are only a few viable regulatory schemes, and that natural selection has chosen the optimal one; and second, to characterize that optimal scheme with a formal mechanism.

100 Effect of Macromolecular Crowding on Malate Dehydrogenase Kinetics Cwalina, Caroline; Shaik, Sadiq A.; Seybert, David W. Department of Chemistry and Biochemistry Duquesne University To date, the effects of macromolecular crowding on enzyme function have received minimal attention by the enzymology research community. To better understand the detailed impact of macromolecular crowding on enzymes, we have undertaken a systematic study of crowding effects on the mitochondrial enzyme malate dehydrogenase (MDH). MDH catalyzes the reversible reaction of oxaloacetate (OAA) and NADH to form malate and NAD

+. The kinetics of change in [NADH] can

be monitored at 340 nm. We are studying the effects of the model macromolecular crowders Ficoll-70 and bovine serum albumin (BSA) on the steady-state kinetic behavior of MDH. MDH is also subject to complex allosteric regulation, and we have experimentally confirmed that citrate is an inhibitor of the OAA to malate reaction with an IC50 of approximately 200 μM. Crowding effects on this citrate inhibition of MDH provide valuable mechanistic information on the general sensitivity of allosteric regulation to macromolecular crowding.


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101 Macromolecular Crowding Effects on Lactate Dehydrogenase Shaik, Sadiq A.; Cwalina, Caroline; Seybert, David W. Department of Chemistry and Biochemistry Duquesne University Historically, steady-state enzyme kinetics has been studied in vitro using dilute solutions. In reality, enzymatic reactions occur within high concentrations of macromolecules and metabolites. These “crowders” stimulate effects on enzyme kinetics that have yet to be fully examined. To better understand these effects, our group is examining the kinetic behavior of mammalian lactate dehydrogenase (LDH), a cytosolic enzyme that catalyzes the conversion of pyruvate to lactate and the oxidation of NADH to NAD

+ as the final step in

homolactic fermentation. Flux through this enzyme is significantly increased during the Warburg effect associated with elevated aerobic glycolysis rates in rapidly dividing cells, which include cancerous cells. LDH activity was measured under varying concentrations of Ficoll-70 and bovine serum albumin (BSA) as model crowders. An 8-14% decrease in activity was observed relative to control from 0.1-4.0% Ficoll. Above 4.0% Ficoll, activity increased (at 7.0-10.0% Ficoll), but never exceeded the control.

102 Neural Mechanisms in the Prefrontal Cortex that Correlate to Irritability in Preschool-Aged Children Buerk, Stephanie; Perlman, Susan Department of Psychiatry University of Pittsburgh Compromised development of the neural mechanisms in the lateral prefrontal cortex (LPFC) in preschool–aged children can lead to increased irritability that may correspond to a psychopathological diagnosis. Deficits in psychological executive functioning, such as increased frustration and decreased inhibitory control, have been hypothesized to be correlates of irritability. By using Functional Near-Infrared Spectroscopy (fNIRS), a non-invasive neuro-imaging technique that studies hemodynamic changes in the brain, we have been able to study specific regions of the LPFC in control and clinical groups of preschool-aged children. Results have shown a positive correlation between parent-reported anger/frustration scores and changes in oxygenated hemoglobin [r(15) = 0.72, p < .001], specifically in Brodmann areas 10 and 46 in the LPFC.

103 RNA G-Quadruplex Topology and Stability Imperatore, Joshua A.

1; Schall, Rachael M

2; Madura, Jeffry

D.3

Department of Biochemistry, Washington & Jefferson College

1

Department of Chemistry and Biochemistry, Roanoke College

2

Center for Computational Sciences, Department of Chemistry and Biochemistry, Duquesne University

3

Experimental research on nucleic acids has shown that guanine-rich regions have the capability of folding into secondary structures known as G-quadruplexes. When found in mass quantities, these structures have the potential to disrupt many important interactions between proteins and nucleic acids, leading to gene expression miss-regulation. In particular, a repeated hexanucleotide ((G4C2)n) expansion of RNA has been linked to neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), Alzheimer's disease and Parkinson's disease. The aim of this study was to determine a stable, low-energy, parallel conformation of an RNA G-quadruplex with the sequence (G4C2)n. Molecular Operating Environment (MOE) and Visual Molecular Dynamics (VMD) were used in creating the first computational model of the RNA G-quadruplex. Further molecular dynamics and metadynamic simulations were performed using NAnoscale Molecular Dynamics (NAMD) in order to equilibrate the system and determine free-energy landscapes between the G-quadruplex, hairpin, and random coil.

104 Computational Study of FOF1-ATPase Mechanism Dubnik, Sarah; Zuckerman, Daniel Department of Computational and Systems Biology University of Pittsburgh The FOF1-ATPase enzyme supplies cells with energy by coupling proton transport to ATP synthesis. Rotation driven by a proton gradient in one domain produces conformational changes catalyzing synthesis in the other. Beyond this overall process, experimental observations lack the detail to establish a highly resolved mechanism. Structural computational models, conversely, cannot probe sufficiently long timescales. Discrete-state mass-action models will offer a new approach, focusing on identifying the mechanism’s most important states and the order in which they occur. A script was thus developed to automatically encode models with over 100 states into the rule-based BioNetGen language. To generate reaction rules, the script converts experimentally known rate constants into state and barrier free energies, adding an elastic energy term to account for coupling between the FO and F1 domains. Various versions of these models will be able to expand and modify the proposed mechanisms, serving as useful tools for future study.


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105 Nest Site Selection of Louisiana Waterthrush on Three Pennsylvania Streams Hoenig Brandon D., Latta Steven C., Nuttle Timothy J., Porter Brady A., Trevelline Brian K. Department of Biological Sciences Duquesne University The Louisiana waterthrush (Parkesia motacilla) is a stream-obligate songbird that breeds throughout the Eastern United States. Because of their dependence on aquatic insects as a primary source of prey, waterthrush are considered a biological indicator for overall stream quality. Despite a large body of research on waterthrush as an important indicator of water quality, little is understood regarding waterthrush habitat and nest site selection. We investigated this by characterizing 15 waterthrush nest sites and 200 random reference sites across three Pennsylvania streams. The nest metrics were analyzed to determine the most important factors in waterthrush nest site selection. Nest site metrics included stream bank characterization, tree canopy measurements, and vegetation surveys for a 5 meter and 11.3 meter radius around the nest site. Understanding the nesting preferences of this important bioindicator could help to further identify the causes for waterthrush’s dependence on riparian areas.

106 Computational Determination of the Surface Energy and Relaxed State of the (110) Surface of Rutile TiO2 Gagliardi, Austin L.; Carlson, Amy N.; Gawalt, Ellen S.; Evanseck, Jeffrey D. Center for Computational Sciences; Department of Chemistry and Biochemistry Duquesne University Modification of the titanium oxide surface presents many possible uses in new materials and engineering applications. However, accurate and realistic models must be first developed. Increasing the depth of rutile (110) slab models results in increased model accuracy, as compared to experiment. Prior hurdles in achieving SCF convergence have been overcome by utilizing an all-electron basis set specifically designed for use in solid-state (pob-TZVP) combined with the PW1PW functional. Slab models ranging from 1 to 14 repeating layers deep were generated and optimized, using two-dimensional boundary conditions. The surface energy and displacement of select surface atoms (five-fold titaniums, six-fold titaniums, and bridging oxygens) was determined in order to judge the accuracy of the slab models. Accurate slab models open the door to future computational work in adsorbing molecules to the rutile (110) surface, which can lead to advancements in various fields, especially biomedical implants and bone replacement.

107

Agent-based modeling of the role of oscillatory calling in spatial cluster formation in an Anuran mating chorus McShea, Hannah, Ermentrout, Bard*, and Boyd, Sunny** *Department of Computational and Systems Biology, University of Pittsburgh **Department of Biological Sciences, University of Notre Dame The Anuran mating chorus is a complex system of biological coupled oscillators. In choruses of the gray tree frog Hyla versicolor, it is advantageous for males to call in antiphase with close neighbors, although this is often imperfectly possible in dense clustered choruses. This study expands previous models to consider the feedback between temporal calling and spatial positioning patterns. Two agent-based models were constructed; in one, if frogs adjust their calling in response to dominant callers according to a phase resetting curve (PRC) and increase intra-neighbor spacing if local antiphase is not achieved, dominant agents maintain larger territories and others form clusters. Another model represented calling space physically, allowing agents to jostle according to a PRC for control of calling space. The threshold for stability in this model was similar to that for intra-chorus cluster size as observed in the field.

108 Improving the Accuracy of Molecular Docking Results through Implementation of Punitive Scoring to Prune High Rank High RMSD Docked Poses Wierbowski Shayne, Baumgartner Matthew, and Camacho Carlos Department of Computational & Systems Biology The University of Pittsburgh Vital to computational drug discovery and virtual screening is the ability to accurately predict and score protein-ligand binding interactions. Although molecular docking algorithms have been developed, their success is limited by simplified and hence imperfect scoring functions that cannot reliably sample and rank poses with low (< 2.0 Å) root-mean-square deviation (RMSD) to experimental co-crystals. We show that for test cases, the Vina scoring function only selects a low RMSD pose as the top-ranked pose in 50-75% of cases where a low RMSD pose is sampled. We present here a novel pipeline to enrich molecular docking results. Filtering by Vina score and solvent-accessible surface area (SASA) eliminates up to 50% of high RMSD docked poses. We also trained a novel scoring function to better classify low RMSD poses and prune high rank, high RMSD docked poses based on evaluation of mismatched hydrogen bonding which are largely ignored by Vina.


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109 Relaxin promoter analysis Pollock, Taylor; Carnahan-Craig, Sarah; Jensen-Seaman, Michael Bayer School of Natural and Environmental Science- Biology Department Duquesne University The relaxin hormone is produced by the relaxin genes, primarily relaxin 2 (RLN2) in humans, in the corpus luteum and placenta. This hormone regulates many aspects of pregnancy and childbirth, including uterine muscle relaxation and cervical ripening through collagenase activation. Elevated amounts of the relaxin hormone in late-term pregnancy increase the likelihood of preterm birth. In this study, a single nucleotide polymorphism (rs3758239) was genotyped in the RLN2 promoter in DNA samples from 44 humans (2n=88 chromosomes) around the world, using nested PCR and unidirectional DNA sequencing. These results were combined with previous genotyping data from our lab of a dinucleotide microsatellite repeat of the RLN2 promoter. The promoter from several of these humans was then cloned into a luciferase reporter vector, and future studies will measure luciferase in JAR trophoblast cells transfected with these clones to determine whether varying genotypes at the relaxin promoter affect transcription levels.

110 A Distributed Algorithm for Computing Large-Scale Graph Laplacian to Study Protein Dynamics Catherine Lesuisse University of Pittsburgh For this project I am developing a tool to efficiently compute a large scale graph Laplacian for large proteins such as viral protein assemblies using distributed computing via Apache Spark framework. A Graph Laplacian is a matrix representation of a graph, using spanning trees in it's computation. Laplacian matrices are used in describing the dynamics of many biological systems by computing the normal modes of their collective motions. We first partition the viral proteins in to different cartesian pairs composed of protein chains, and then create a sub-graph for each chain-pair using Apache Spark, a cluster computing framework. These sub-subgraphs are then compiled together to get a complete graph Laplacian. Using this method, the time and memory complexity of Laplacian computation is significantly smaller.

111

Cyclin Dependent Kinase 5 Regulatory Subunit 2 Q1 G quadruplex Messenger RNA Characterization Williams, Allison; Mihailescu, M. Rita Department of Chemistry and Biochemistry Duquesne University Cyclin-dependent kinase 5 regulatory subunit 2 (CKD5R2) mRNA encodes for a cyclin dependent kinase 5 (CDK5) activator in neurons. CDK5 is essential for neuronal development post-natally, and without it, in vivo mice are not viable. CDK5R2 mRNA is a proposed target of the fragile X mental retardation protein (FMRP), a protein whose absence leads to the fragile X syndrome. FMRP binds to secondary messenger RNA structures called G-quadruplexes. The analysis of the CDK5R2 mRNA revealed three highly probable potential G-quadruplex forming sequences. In this project, the first predicted G-quadruplex region (Q1) was analyzed. Structural information about the G-quadruplex was obtain using biophysical methods such as

1H-nuclear magnetic

resonance (NMR), UV-Vis spectroscopy, circular dichroism spectroscopy (CD spectroscopy), and native polyacrylamide gels. Additionally the interactions of the CDK5R2 mRNA G quadruplex with the FMRP RGG box were analyzed by electromobility shift assay.

112 Solvation Effects and Distortion/Interaction Analysis on the Concerted and Stepwise Bimolecular Diels Alder Cycloaddition Pathways of Cyclopentadiene Baucom, Kierstin; Kelly, Allison; Vernier, Brandon; Ahmed, Ayan; Rohde, Jeffrey; Evanseck, Jeffrey D. Center for Computational Sciences, Department of Chemistry and Biochemistry Duquesne University, and Franciscan University of Steubenville Solvation effects upon the asynchronous concerted and stepwise bimolecular Diels-Alder cycloadditions of cyclopentadiene were studied with a quantum discrete-continuum model and compared with experimental activation enthalpies in seven different solvents. Truhlar’s M06-2X density functional with Dunning’s cc-pVTZ basis set and Tomasi’s polarizable continuum model (PCM) method was used to estimate solvation effects. A single solvent molecule was included in the discrete-continuum model. The distortion/interaction model was used to explore the relationship between solvent effects (implicit and explicit), distortion energies (diene and dienophile), interaction energies, and reactivity (activation enthalpy). The influence of solvent upon the energetics (and distortions) of the asynchronous concerted and stepwise reaction pathways are evaluated and compared back to experimental observations. A complete understanding of solvation effects upon the reactivities of cyclopentadienes in Diels-Alder reactions has the potential to reshape protocols in organic synthesis, and result in innovative applications and functionalization of new materials.


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113 Pain empathy kit builds better healthcare and interprofessional practices Fiedor, Jaclyn; Simko, Dr. Lynn, Rhodes, Prof. Diane School of Nursing and Mylan School of Pharmacy Duquesne University Chronic pain is not as easy to empathize with as compared to acute pain. When dealing with chronic pain patients, medical professionals often work independently to manage or treat the pain. Through Etiology, Assessment and Treatment of Pain for Health Professionals, a class at Duquesne University taught by Dr. Lynn Simko and Professor Diane Rhodes, students in the nursing and pharmacy programs worked using interprofessional (IP) collaboration to create tools to better empathize with chronic pain patients. The tools of this kit include everyday household items, but are used in ways that cause a temporary pain simulation to experience the lives of those living with the chronic condition. Students gained better insight into the daily lives of those exhibiting pain and learned empathy was a useful skill to acquire for better healthcare practices.

114 Characterization of G-quadruplex structure formed by a guanine rich fragment within the 5’-UTR of MRP3 mRNA Shaffer, Jacob M.; Evans, Timothy L.; Mihailescu, Mihaela Rita Department of Biochemistry University of Pittsburgh at Johnstown Multidrug-resistance associated protein 3 (MRP3) acts as a transporter of molecules across cellular membranes. Specifically, drugs with anticancer properties are targeted and transported out of cancerous cells by MRP3, thus diminishing drug efficacy. Bioinformatics analysis has predicted that a certain guanine-rich segment in the mRNA 5’-untranslated region (5’-UTR) forms the G-quadruplex structure. This structure is stabilized by cellular K

+ and

can adopt multiple conformations, and its presence typically results in translation inhibition. The mRNA target was in vitro transcribed and purified on a large scale. The presence of a G-quadruplex structure was demonstrated in a 21 nucleotide tract from the MRP3 mRNA 5’-UTR, and the unique structural and thermodynamic properties were characterized using biochemical and biophysical methods. It was determined that the G-quadruplex formed even without the addition of K

+. Furthermore, both intermolecular and

intramolecular conformations existed wherein the increase of [K

+] had little effect on the structural stability.

115 Impact of N-acetyl cysteine on alpha-synuclein pathology in experimental Parkinson’s disease Daniel Hutchison

1, Daniel Mason

1, Jessica Posimo

1, and

Rehana Leak1

1Division of Pharmaceutical Sciences, Duquesne University

2Depts of Chemistry and Pharmaceutical Sciences,

University of Pittsburgh Parkinson’s disease is characterized by hallmark Lewy bodies and Lewy neurites that are partially composed of aggregated and phosphorylated alpha-synuclein. One of the first brain regions to be affected by Lewy pathology in Parkinson’s disease is the olfactory bulb. Here we modeled Lewy pathology in the olfactory bulb by administering alpha-synuclein fibrils to primary olfactory bulb neurons in vitro. Second, we tested the hypothesis that the antioxidant N-acetyl cysteine would protect against Lewy-like pathology, because oxidative and protein misfolding stress are known to propel and propagate each other. As expected, alpha-synuclein fibrils elicit Lewy-like neurites containing phosphorylated alpha-synuclein in this model of olfactory bulb pathology. Furthermore, preliminary data show that N-acetyl cysteine reduced the number of alpha-synuclein+ Lewy-like inclusions. These studies support the view that alpha-synuclein pathology can be mitigated by therapies that reduce levels of oxidative stress.

116 Arduino-based Laboratory Instruments for an Undergraduate Laser Cooling Experiment Robert W.A. Brooke, Isaac Davies, Timothy Ireland, Gage Tiber, Julie M. Gillis, Theodore A. Corcovilos Department of Physics, Duquesne University Arduino is an inexpensive open-source micro-controller platform designed for quick development and easy interfacing, making it ideal for novice programmers and instrument designers. Arduino boards have analog inputs, digital I/O pins, pulse width modulated outputs, and serial communication capabilities. The boards are programmed with standard C/C++ code. The Arduino streamlines the design of both analog and digital data acquisition and control when compared to circuits using discrete components and is powerful enough to run complex algorithms and control routines. Most importantly, Arduino is flexible enough with its versatile inputs and outputs for a wide variety of instrument designs, is fast enough and has a high enough resolution for research-quality instruments, and allows instruments to be built well below their commercial cost. We present several instruments that showcase the versatility of the Arduino platform: a temperature controller, a laser stabilizer, an optical wavelength meter, and an UV fluorometer.


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117 Exploring the Adaptations of Bobcats to Diverse Ecosystems by Identifying Genomic Regions under Selection Sarah E. Sprauer

1, Jennifer C. Broderick

1, Imogene

Davis2, Roberta K. Newbury, Ph.D.

3, and Jan E. Janecka,

Ph.D.1

1Department of Biological Sciences, Duquesne University

2West Texas A&M University

3Department of Biological Sciences, University of Alberta

Our objective is to examine local adaptations of bobcats in diverse regions of the US through genomic analysis and comparison with a specialist, the Canada lynx. Restriction-site associated DNA sequencing (RADseq) libraries were prepared in 19 samples from 3 populations (New Mexico, Montana, Vermont) for sequencing on a MiSeq using modified methods of Elshire et al. (2011) and Peterson et al. (2012). Reads were mapped to the domestic cat genome with mean coverage of 15,506.26 reads/chromosome and used to construct a catalog of 200,865 unique stacks. Of these, 17,196 were shared across >50% of the samples. The mean gene diversity was 0.339. Preliminary results revealed Vermont harbored the most divergent bobcat populations. Loci were used to reconstruct haplotypes, and outlier Fst and gene diversity values were identified as potentially located on chromosomal regions that have been under strong selection pressures.

118 Identifying Genes Associated with Longevity in Mammals by Comparing Rates of Evolution of Orthologous Genes Kowalczyk, Amanda, Chikina, Maria, and Clark, Nathan Department of Computational and Systems Biology University of Pittsburgh The molecular mechanisms behind aging are of considerable interest due to the prevalence of age-related ailments such as cancer and cardiovascular diseases in human populations. Although research has revealed techniques to delay aging and increase lifespan that provide clues to how aging occurs, our general knowledge of genetic pathways that affect aging and age-related diseases is still incomplete. We used a novel method to scan the genomes of 61 mammal species to find genes whose rates of evolution are associated with longevity to identify potential aging pathways. We have discovered that in long-lived species, genes associated with reproduction and the insulin receptor signaling cascade evolve more rapidly, and, in the opposite case, pathways associated with immune responses and DNA repair evolve more slowly. These insights into genetic influences on longevity could eventually be used to develop personalized therapies to mitigate the effects of aging or potentially extend lifespan itself.

119

Method Comparison for Developing Latent Prints on Glass Surfaces McBride, Michael; Ferrara, Lyndsie Forensic Science & Law Program Duquesne University Multiple methods exist for developing latent prints from glass surfaces with no literature supporting one method over another. This research examined four different methods to determine if any differences exist and if one is superior. The development techniques included dusting with black powder as well as cyanoacrylate (superglue) fuming followed by black powder. This study tested the efficiency of each of the methods by comparing the developed prints to inked prints. For this baseline study freshly deposited fingerprints were immediately processed to remove the degradation factor. A statistical analysis was conducted to compare the accuracy of the two fingerprint development methods to determine the most effective method. A cost benefit analysis also provided additional information regarding the cost and time compared to effectiveness for each method. Based on preliminary results no major differences in terms of the quality of developed prints exists.

120 The Effect of Gaming Applications on Treatment of Pediatric Patients with Cystic Fibrosis Huber, Alex; Corcoran, Timothy Department of Pulmonary, Allergy, and Critical Care Medicine University of Pittsburgh Treatment of Cystic Fibrosis heavily relies on the use of inhaled medications, typically hypertonic saline and antibiotics, which are delivered to the patient through a nebulizer in sessions which typically last 10-30 minutes. It is critical that during those 10-30 minutes, patients practice a sustainable breath rate and volume in order for the medication to reach the smaller airways deep in the lungs; otherwise most of the medication will be deposited in the throat and the mouth, not treating the disease. Children with CF typically exercise poor breathing patterns during treatment which commonly involve shallow breaths or erratic breathing patterns. Introducing gaming applications which measure and regulate the children’s breathing pattern is predicted to decrease erratic breathing and shallow breaths using a reward-based system, therefore increasing the effectiveness of treatment. These applications could also be pertinent to children with asthma and other respiratory ailments.


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121 A Cell-Scale, Compartmental Model of Ion Transport and Volume Regulation in Pulmonary Epithelia Lotz, Nicholas W.,

1 Markovetz, Matthew R.,

1 Corcoran,

Timothy E.,1,2,3,

Parker, Robert S.1,3,4,5

1Dept of Chemical and Petroleum Engineering,

2Division of

Pulmonary, Allergy, and Critical Care Medicine,

3Dept of Bioengineering,

4McGowan

Institute of Regenerative Medicine, 5Critical Care Medicine, University of Pittsburgh

Novel computational methods, when coupled with physiologically mechanistic understanding of biological systems, drive the development of improved in silico models that assist scientists and clinicians with disease research and treatment design. A cell-scale, compartmental model was constructed to capture transport dynamics and volume regulation in pulmonary epithelia. Species balances in each compartment were expressed through systems of ordinary differential equations, with the inclusion of potassium and calcium activated channels serving as noteworthy additions to the model scheme. Distributions for channel permeabilities and other parameters were identified using an affine parallel-tempering Markov Chain Monte Carlo (APT-MCMC) algorithm. Estimated parameter sets characterize cell homeostasis, paracellular DTPA transport and apical volume regulation under experimental conditions, lending validity to the model structure. Future work will focus on furthering the mechanistic understanding of model dynamics, incorporating new species and pathways, and implementing predictive control to facilitate treatment design and improve patient outcomes in cystic fibrosis.

122 Water Cluster Catalysis of Carboxyphosphate Decarboxylation Neel, Spenser; Firestine, Steven, M.;

1 Evanseck, Jeffrey D.

Center for Computational Sciences and Department of Chemistry and Biochemistry Duquesne University, and

1Eugene Applebaum College of

Pharmacy and Health Sciences, Wayne State University Carboxyphosphate has yet to be synthesized or observed as an intermediate; however, all indirect evidence suggests that it is a critical intermediate in ATP-dependent carboxylases. Solvation effects upon the nonenzymatic decarboxylation activation energy of carboxyphosphate was studied with a quantum discrete-continuum model. Intrinsic reaction path following was used to connect the transition structure to the reactants and products corresponding to the mechanism of decarboxylation. Truhlar’s M06-2X density functional with Dunning’s cc-pVTZ basis set and Tomasi’s polarizable continuum model (PCM) was used to estimate solvation effects, geometry optimization and frequency analysis. Four waters on the phosphate and two on the carboxylic acid were included in the model. The activation energy of 7.5 kcal/mol in vacuum is reduced to 4.6 kcal/mol with PCM. The impact of the explicit waters will be discussed. Development a mechanistic understanding of carboxyphosphate's reactivity in water clusters has the potential to explain its instability in aqueous solution.

2015 summer research symposium - duquesne … symposium/2015-sum… · 2015 summer research...

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