San Diego, CA   APRIL 26-30, 2014

For the past 14 years, the University of Delaware Howard Hughes Medical Institute’s (HHMI) Undergraduate Science Education Program has sent undergraduate students to the Experimental Biology Meetings to present their research. As part of this conference, the American Society for Biochemistry and Molecular Biology (ASBMB) sponsored its 18th Undergraduate Poster Competition in which 8 UD students will participate. Since 2001, students from the University have received more awards in this competition than students from any other college or university. 

The University of Delaware group included four faculty and 9 undergraduates.

Front Row, left to right: Seung Hong, Lauren Genova, Fanta Kalli, Ramya Sridharan, Shaili Patel, and Dave Usher.
Back row, left to right: Gary Laverty, Seth Ritter, Doug Kenny, Hal White, Matt Urbam, Christine Dang, and Brooke Palus.

Prof. Hal White, Chem & Biochem
Prof. Dave Usher, Biol. Sci.
Prof. Seung Hong, Biol Sci
Prof. Gary Laverty, Biol Sci

Christine Dang, Biological Sciences
Lauren Genova, Chemistry
Fanta Kalle, Biological Sciences
Douglas Kenny, Chemistry
Brooke Palus, Biological Sciences
Shaili Patel, Biological Sciences
Seth Ritter, Chemical Engineering
Ramya Sridharan, Biochemistry
Matthew Urban, Biochemistry

University of Delaware students and their abstracts.

Christine Dang

Characterization of Celf1 function in mouse lens cell lines
Christine Dang1, Archana D. Siddam1, Salil Lachke1,2

1Biological Sciences, University of Delaware, Newark, DE,2Center for Bioinformatics and Computational Biology,
University of Delaware, Newark, DE

Although the human genome encodes ~1500 RNA binding protein (RBP) encoding genes, mutations in only ~20 are associated with human disease. We used a novel bioinformatics approach iSyTE (integrated Systems Tool for Eye gene discovery) to identify a new RBP, Celf1 (CUGBP Elav (embryonic lethal, abnormal vision)-Like Family member 1), in the lens that is potentially associated with cataract. Celf1 contains three conserved RNA Regulatory Motifs that function in sequence-specific binding to target RNAs. To develop a new resource to study Celf1 function in lens cells, we generated and characterized Celf1-knockdown (KD) mouse lens epithelial cell lines. We first selected the mouse lens epithelial cell line 21EM15 as it expresses several critical lens-expressed genes and thus recapitulates important aspects of lens biology. We infected 21EM15 cells with lentiviral particles carrying inhibitory short hairpin (sh)RNAs against mouse Celf1 mRNA and isolated infected cells based on their acquired resistance to puromycin. Celf1-KD was confirmed by reduced Celf1 expression in Western blotting. We are presently characterizing the effect of Celf1-KD on distinct classes of RNA granules (e.g. Stress granules and Processing bodies) involved in post-transcriptional regulation. In sum, we describe development of a new Celf1-KD lens cell line as a unique resource for gaining novel functional insights of an RBP in lens biology.

Poster: Mon, Apr 28, 1:15 - 2:45 PM 746.1/D62 -

Lauren Genova

The Role of Bacterial Cell Wall Dimers in the Innate Immune Response

Lauren Genova, James Melnyk, Vishnu Mohanan, and Catherine Leimkuhler Grimes

Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716

The innate immune system is the body’s first line of defense against pathogens. The innate immune system is triggered by pathogen associated molecular patterns (PAMPs) that are recognized by pattern recognition receptors (PRRs) such as Toll-like receptors (TLRs) and Nod-like receptors (NLRs). This research project focuses on providing a better understanding of how the innate immune system senses and responds to the presence of bacteria. Specifically, our group is interested in the relationship between Nucleotide-binding oligomerization domain-containing protein 2 (Nod2), an NLR protein found in the cytosol of mammalian host cells, and muramyl dipeptide (MDP), the smallest bacterial cell wall fragment known to elicit an immunological response. When Nod2 is mutated, the signaling pathway becomes disrupted and uncontrollable inflammation arises, leading to chronic inflammatory bowel disorders such as Crohn’s disease. In order to discover how to better treat these diseases, it is imperative to learn more about how Nod2 and MDP interact, a mechanism which is currently unknown. The Grimes Lab has previously shown that Nod2 binds to MDP in vitro; however, research suggests that a heightened immunological response may be elicited in a host if molecules containing multiple MDP’s are used, suggesting multivalency is at play. This project highlights my current research progress to synthesize a variety of novel MDP dimers to test for a multivalent interaction between Nod2 and MDP.

Poster: Tue, Apr 29, 12:15 - 1:45 PM 970.1/D178

Recipient of an ASBMB-UAN $500 Undergraduate Travel Award

Fanta Kalle

Effects of heparin and heparin-binding growth factor on human aortic adventitial fibroblasts

1Biological Sciences, University of Delaware, Newark, DE; 2Biomedical Research, Nemours - Alfred I. duPont Hospital for Children, Wilmington, DE; 3Materials Science & Engineering, University of Delaware, Newark, DE

Cardiovascular diseases are primary treated using bypass graft surgery and angioplasty; unfortunately, these procedures often fail due to maladaptive tissue remodeling leading to stenosis, fibrosis, and vessel failure. Methods to decrease failure rates are needed. We are developing instructive biomaterials for placement along the abluminal surface of at-risk vessels to provide mechanical support and to deliver bioactive molecules and/or stem cells to help attenuate maladaptive responses, encourage healing, and improve clinical outcomes. The present study examines the effects of critical biomaterial components including basic fibroblast growth factor (FGF2), low-molecular weight heparin (LMWH) and desulfated LMWH on vascular cells. Cell morphology, proliferation, and viability are assessed using fluorescence microscopy. Image Pro and SPSS software packages are used to acquire and analyze data. Data indicate that FGF2 and LMWH affect human aortic adventitial fibroblast (AoAF) phenotype. The presence of FGF2 significantly increased proliferation rates and the appearance of filopodia; whereas, the absence of FGF2 was associated with an increase in the prevalence of lamellipodia and stress fibers. Increasing LMWH doses correlated with decreased AoAF proliferation and alterations in cell morphology. Desulfated LMWH did not alter FGF2-mediated effects on cell phenotype. These data suggest that the biomaterial components LMWH and FGF2 can influence the phenotype of cardiovascular cells like AoAFs. Although in vivo, LMWH is thought to potentiate FGF2-induced effects, in our system, LMWH significantly decreased AoAF proliferation, particularly in the absence of FGF2. The sulfation state of LMWH was critical to these effects. Further studies to determine the mechanisms accounting for these effects and to establish combined effects on cell phenotype will be needed to enable development of injectable formulations that may be useful in improving clinical outcome.

Poster: Tue, Apr 29, 1:15 - 2:45 PM  1012.4/D376

Recipient of an ASBMB-UAN $500 Undergraduate Travel Award.

Douglas Kenny

Synthesis of Muramic Acid Derivatives to Investigate the Promiscuity of Bacterial Cell Wall Biosynthetic Enzymes for the Investigation of Nod2

Douglas Kenny, Yu Liu, Catherine L. Grimes
Department of Chemistry and Biochemistry, University of Delaware

Nod2 is an innate immune receptor found in mammalian cells that plays a role in recognizing bacteria.  Specifically, Nod2 detects bacterial cell wall or peptidoglycan.  Recently in vitro studies have shown that Nod2 can bind directly to a small fragment of peptidoglycan called muramyl-dipeptide (MDP). Yet, it is still unclear how the bacterial cell wall fragments are generated and gain access into the cytosol to activate the receptor. In order to observe the cell wall and its interactions with the receptor, a method to label the cell wall of bacteria using fluorescent probes can be used. This method will allow us to track the uptake of the cell wall and observe its interaction with Nod2 in a cellular context. In order to label the cell wall, two derivatives of peptidoglycan precursors, UDP-N-Acetyl-muramic acid, are being synthesized. These derivatives contain an azide on either the 2 or 6 positions, as they are the only positions not used in building the peptidoglycan framework. The azide functionality can act as a chemical handle and undergo quick, bioorthogonal coupling with a fluorescent probe for visualization. The derivative with the azide on the 6 position has been successfully synthesized, and the derivate with the azide on the 2 position is currently being synthesized. Once finished, the ability of the bacteria to incorporate these molecules into their cell wall will be tested through both in vitro, using the purified biosynthetic enzymes, and in vivo studies. With the fluorescently labeled bacterial cell wall, the mode of Nod2 activation can be studied with living cells.

Poster: Tue, Apr 29, 12:15 - 1:45 PM  970.2/D179

Brooke Palus
Examining O-xylosyltransferase shedding in Drosophila

Brooke Palus and Erica Selva
Department of Biological Scences, University of Delaware, Newark, DE

O-xylosyltransferase (Oxt) is a Golgi transmembrane glycosyltransferase that initiates the first step in the heperan and chrondroitin sulfate biosynthesis on core proteoglycans (HSPG and CSPG). HSPGs and CSPGs are abundant extracellular matrix proteins present in virtually all tissues and have critical functions in articular cartilage in vertebrates. In this tissue, HSPGs and CSPGs are essential in regulating signaling and homeostasis. Disrupted homeostasis of articular cartilage leads to its degradation and osteoarthritis (OA). The onset of OA has been shown to result in increased serum levels of Oxt in mouse and humans. While the biosynthetic activity of Oxt has been studied, little is known about its function extracellularly. Understanding how and why Oxt is shed and its role extracellularly may provide further insight into how cell signaling and tissue homeostasis can be disrupted in OA patients. The goal of this study is to determine if Oxt is shed from Drosophila wing imaginal discs and what function extracellular Oxt has in organismal development. As expected, Oxt localizes to the Golgi and the ER the site of HSPG and CSPG biosynthesis. Oxt was also found extrcellularly suggesting it is shed in Drosophila. In loss-of-function and over expression studies the composition of the extracellular matrix and Oxt diffusion from it cell of origin were also examined.

Poster: Sun, Apr 27, 12:15 - 1:45 PM   539.1/B62

Shaili Patel

Identification of differentially expressed transcripts in Tdrd7 null mutant mouse lens

Shaili D. Patel, Carrie Barnum, Salil A. Lachke
Department of Biological Sciences, Universirty of Delaware

Lens is a transparent tissue within the eye that focuses light on the retina and facilitates high-resolution vision. Cataract is an eye disease that results due to the loss of lens transparency and causes severely impaired vision. It can be caused by genetic changes, aging or physiological conditions like diabetes. Treatment depends upon the patient's specific visual needs and often involves cataract surgery. Over 77 million individuals are affected worldwide, and in the United States alone, costs exceed $3 billion annually. Recently, a mutations in the human TDRD7 (Tudor domain containing protein 7) gene were shown to cause congenital/pediatric cataracts in patients. Moreover, it was also demonstrated that Tdrd7 targeted germline knockout or ENU-induced knockout mouse mutants exhibit cataracts that closely resemble the human phenotype. My research goal is to understand the regulatory function of Tdrd7 in the lens. Specifically, I aim to investigate if Tdrd7 deficiency affects the mRNA profiles in the apical and the basal regions of differentiating lens fiber cells. To achieve this I have expanded the Tdrd7 germline knockout mouse mutant colony and collected Tdrd7 mutant and control (Tdrd7+/- mice that do not exhibit cataracts) embryonic lens tissue for analysis. To study the expression of mRNAs in different locations within fiber cells, I have undertaken standardization of an approach using Laser Capture Microdissection (LCM). LCM on embryonic lens sections from Tdrd7 null mutants and control will be used to isolate the apical and the basal fiber cell regions at embryonic stage E10.5, E11.5, and E12.5. Once the specific tissues are collected, expression of mRNAs will be tested by whole genome expression profiling using Gene expression analysis. Comparative analysis of gene expression profiles of the apical and basal tissues from mutant and control will allow the identification of transcripts that are misregulated as a result of Tdrd7 mutation.

Mon, Apr 28, 1:15 - 2:45 PM 747.1/D64

Recipient of a University of Delaware Unbdergraduate Research Travel Award.

Seth Ritter

Development of a fluorescent bar-coding system for cell-based proteomic libraries

Seth C. Ritter, Stefanie Berges, David Colby
University of Delaware, Newark, DE

A major objective for biological scientists is to understand the complex intricacies of cellular maintenance, and environmental response. Proteins constitute a significant fraction of the molecules in biological systems under study; however the tools for proteomic analysis fall short of those that have enabled the thorough cataloging of genes and the quantification of gene transcripts. It is therefore beneficial to produce a technology for high-throughput, quantitative analysis of the proteome. To this aim we are developing a novel heritable surface protein construct. Such surface proteins will protrude out and operate as scaffolds for fluorescently labeled antibodies, or other high-affinity reagents. By varying the number of repeating epitope elements in the scaffold a series of fluorescent signals through multiple channels and levels of intensity are generated. These Unique Identifying Proteins (UIP), allow for identification of multiple cell populations simultaneously using multidimensional flow cytometry. We found that eight unique barcodes were possible utilizing three total epitopes, where in any channel at least 60% of cells of a population could be taken while error rates in population identification remained below 5%. This system will enable the coupling of population identification and various fluorescent readouts of interests, offering insight into population statistics as well as single cell analysis.

Poster: Mon, Apr 28, 12:45 - 3:00 PM   912.13/A616

Ramya Sridharan

Identifying cytokines associated with acute and chronic Lyme arthritis

Ramya Sridharan
1, Victoria L. Maduskie2, Paul T. Fawcett2
1Biology, University of Delaware, Hockessin, DE,
2Immunology Laboratory, Nemours/Alfred I. DuPont Hospital for Children, Wilmington, DE

Symptoms of untreated infection with Borrelia burgdorferi, which is the causative agent of Lyme disease, frequently include arthritis, particularly of large joints. In pediatric patients, symptoms of arthritis typically resolve following treatment with an adequate course of antibiotics. However, in 10 to 20 percent of pediatric patients with Lyme arthritis, symptoms persist despite patients having received adequate treatment with antibiotics. Patients whose symptoms resolve in less than 6 months after initiation of antibiotic therapy are classified as having acute Lyme arthritis. Patients whose symptoms do not resolve within 6 months are classified as having chronic Lyme arthritis. Cells were obtained from the synovial fluid from pediatric patients with both chronic and acute Lyme arthritis. These were analyzed to determine if cytokines produced by synoviocytes could be used to predict the outcome of treatment with antibiotics. Primary cell cultures were cultured in transformation media to change fibroblasts into adipocytes and osteocytes. Culture supernatants were then tested for cytokine concentration changes. Results showed that transformation of synoviocytes caused significant variation of inflammatory cytokine concentrations associated with arthritis inflammation: MCP-1 and IL-6. IL-6 rapidly declined in both adipogenic and osteogenic transformations. MCP-1 also declined. Results confirm that transformation of synoviocytes from synovial fluid samples caused significant variation of inflammatory cytokine concentrations associated with arthritis inflammation.
Poster: Mon, Apr 28, 11:45 AM - 1:45 PM   835.6/B376

Matthew Urban

Novel ubiquitin binding sites of S. cerevisiae polymerase η
identified by a genetically encoded photoreactive probe

Matthew Urban, Kun Yang, Zhihao Zhuang

Dept. of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716

DNA translesion synthesis is carried out by specialized DNA polymerases, called Y-family polymerases, such as Polη. Polη contains a ubiquitin-binding zinc finger (UBZ) domain required for effective recruitment to the stalled replication fork in response to DNA damages. Previous study reported a novel ubiquitin-binding mode of S. cerevisiae Polη in which the C-terminal portion of Polη binds ubiquitin with 30-fold higher binding affinity than the UBZ domain. However, the mechanism of such higher binding affinity is not clear. In this study, a genetically encoded photoreactive probe, p-benzoyl-L-phenylalanine (pBpa), was incorporated at various positions on ubiquitin to map the interaction sites between Polη and ubiquitin. Data suggests that besides the I44-V70 hydrophobic patch which was known to bind UBZ domain of Polη, several other residues at both C-terminus (L73 and R74) and the back surface (I13, T14 and D24) of ubiquitin also bind to Polη in the C-terminus region outside the UBZ domain. These new binding sites increase the binding affinity between ubiquitin and Polη, which could be important for understanding of the role of ubiquitin in the recruitment of Polη during DNA transelsion synthesis. 

Poster: Tue, Apr 29, 1:15 - 2:45 PM   927.4/D14

Selected by the ASBMB organizers of the DNA Replication, Recombination and Repair theme for a short oral presentation at the ASBMB Annual Meeting. Recipient of a $900 ASBMB Undergraduate Travel Award.
Oral Presentation: Mon, Apr 28, 5:10 - 5:25 PM

Harold White
Stimulating Attitudes of Inquiry

Harold B. White
Department of Chemistry and Biochemistry, Univ. of Delaware, Newark, DE

Much of contemporary science education focuses on what we know, but neglects the evidence supporting the conclusions that fill textbooks. Students thus often learn information as abstractions disconnected from their experience. They rarely encounter the observations, clever experiments, and controversies that generate new ideas and refute old. Problem-based learning (PBL) is an approach to education that encourages students to identify what they don’t know, ask questions, and actively pursue knowledge based on their curiosity and through collaboration with other students. Rather than attempt to cover massive amounts of information, PBL seeks to foster life-long habits of learning through in-depth exploration and fundamental understanding of carefully selected problems that reveal basic concepts and interdisciplinary connections. Problems based on the primary literature with emphasis on classic articles expose students not only to the logic of research but introduce them to the history of science, the people who made important discoveries, and the culture science.

Recipient of ASBMB Award for Excemplary Contributions to Education -see pg 27

Award Lecture: Sun, Apr 27, 12:50 - 1:20 PM  100.1
Video recording of award lecture

No wonder we couldn't find your poster.

UD Group in front of UD ASBMB-Undergraduate Affiliate Poster.

Plenary Speakers for ASBMB

Doug marking time before takeoff at PHL.

Dinner at the Fish market in San Diego.

Dinner at the Fish market in San Diego.

Checking cell phones upon arrival in San Diego.

Defiying gravity in San Diego.

Dr. White's Award

Finally, Palms trees again after 10 years!

The tatoos are only temporary.

Experimental Biol;ogy 2014

Selfie. What's Doug contemplating?

At the Zoo

Seth and Ramya on Coranado Island
across from the Conference Center.

With a pool like this,
who wants to go to conference session?

Pretty nice view from Hotel room.

This hippo isn't very soft

Candy Store!

Ticket to Old Town

Lauren and Fanta

The trip to the Experimental Biology 2014 Meetings in San Diego was organized by the University of Delaware HHMI Undergraduate Science Education Program with additional support from travel grants from the American Society for Biochemistry and Molecular Biology. The HHMI Undergradaute Science Education Program, Charles Peter White Fund, Undergraduate Research Program, NIH, NSF, supported research by the students.

Links to previous EB Meetings:
2001 in Orlando
2002 in New Orleans 2003 in San Diego
2004 in Boston
2005 in San Diego
2006 in San Francisco 2007 in Washington, DC 2008 in San Diego 2009 in New Orleans 2010 in Anaheim
2011 in Washington, DC 2012 in San Diego 2013 in Boston

Return to  University of Delaware HHMI Home Page
Created 29 March 2014,  Last revised 10 June 2014 by Hal White [halwhite at udel.edu]
Copyright  2014 Harold B. White, Department of Chemistry and Biochemistry, University of Delaware