Welcome to EB2012 at entrance to the San Diego Convention Center.

San Diego, CA   APRIL 21-25, 2012

Flags and palm trees outside the San Diego Convention Center.

For the past 12 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 16th Undergraduate Poster Competition in which 18 UD students participated. Since 2001, students from the University have received more awards in this competition than students from any other college or university.  This year was no exception with UD students receiving 20% of the awards. In each of the four judging categories, First Place and four Honorable Mention Awards were given. University of Delaware students, in competition with over 200 students from across the country, received one of the First Place (Michael Brister) and three of the Honorable Mention awards (Lyana Labrada, Soma Jobbagy, and Christopher Wright). In addition the University's Undergraduate Affiliate of the ASBMB received the Outstanding Chapter Award for the Northeast Region. Based on their abstracts, two UD students (Allison McCague and Timothy Gilpatrick) were selected for platform presentations in symposia and recieved NSF-funded undergraduate travel awards from ASBMB. Three students (Erica Boetefuer, Sarah Stamm, and Dylan Lowe) received ASBMB undergraduate travel awards.  UDaily article.

The University of Delaware group included five faculty and 18 undergraduates.

University of Delaware undergraduates receiving the American Society for Biochemistry and Molecular Biology's  2012 Outstanding Northeast Regional Undergraduate Affiliate Award on Sunday, 22 April.

From left to right: Soma Jobbagy, Lauren Gurski, Adam Reese, RamkrishnaPatel, Frank Shen, Dylan Lowe, Sarah Stamm, Chris Wright, Lyana Labrada, Mike Brister, Alicia Liu, Victoria Roop, Ashley Shay, Hamza Bhatti, Hal White (advisor), Allison McCague, and Tim Gilpatrick. (Erica Boetefuer, Seung Hong, Gary Laverty, David Usher, and Erica Selva not shown)
Prof. Hal White, Chem &Biochem
Prof. Dave Usher, Biol. Sci.
Prof. Seung Hong, Biol Sci
Prof. Erica Selva, Biol. Sci.
Prof. Gary Laverty, Biol Sci

Hamza Bhatti
Erica Boetefuer
Michael Brister
Alex D'Angelo
Tim Gilpatrick
Lauren Gurski
Soma Jobbagy
Lyana Labrada
Alicia Liu
Dylan Lowe
Allison McCague
Ramkrishna Patel
Adam Reese
Victoria Roop
Ashley Shay
Frank Shen
Sarah Stamm
Christopher Wright

University of Delaware students and their abstracts.

Hamza Bhatti

Attenuated L1 expression by glioma cells results in
decreased cell migration on monolayer co-cultures

Hamza Bhatti, Deni Galileo

Biological Sciences, University of Delaware, Newark, DE 

L1 is a neural recognition molecule primarily responsible for the invasive quality of glioblastoma multiforme (GBM) cells. It acts by signaling through integrin receptors, and more recently discovered, the fibroblast growth receptor (FGFR). In addition, L1 is abnormally expressed, proteolyzed by ADAM10, and released (shed) by high-grade glioma cell lines. Using short-hairpin RNA (shRNA) and  recombinant DNA techniques, we  used lentiviral vector to shut down L1 expression in a L1 expressing glioma cell line (T98G).   The effect of attenuated L1 expression by glioma cells on cell motility was measured on a substratum of axons and glial cell monolayer isolated from embryonic chick brain tissue. The results show that glioma cells that secrete L1 (T98G-pLKO.1) display greater motility on monolayer co-cultures than glioma cells that  do  not  secrete  L1  (T98G-shL1).    Research  support  was provided by Howard Hughes Medical Insititute.

Erica Boetefuer

Recipient of an ASBMB-UAN non-competitive Travel Award
 The role of atg18 in signal transduction pathways 
during Drosophila development 
Erica Lee Boetefuer, David L Raden, Erica M Selva.
Biological Sciences, University of Delaware, Newark, DE

8J16 and 9E6 are allelic mutations that disrupt Wnt/Wingless (Wg) or Hedgehog (Hh) signaling based upon their embryonic ‘lawn of denticles’ phenotype. Goals of this project were to identify the disrupted gene and determine its role in Drosophila developmental signaling. Complementation analysis revealed 8J16/9E6 are alleles of autophagy-specific gene 18, atg18, which plays a role in autophagosome-lysosome fusion.  In yeast, atg18 negatively regulates endosome-lysosome targeting. In Drosophila, endocytic machinery mutations that block lysosome targeting cause continuous signaling. Thus, atg18 mutants should show a buildup of lysosomes at the expense of endosomes and decrease signaling. To the contrary, Distalless, a long-range Wg target, was enhanced in 8J16/9E6 mutant tissue in Drosophila wing discs. Analysis of 8J16/9E6 germline clone (glc) mutant embryos confirmed atg188J16, atg189E6, and atg18KG03090 are allelic. Immunofluorescent staining of glc embryos showed the segmentation defect is due to loss of Wg expression at embryonic stage 9.  8J16/9E6 glc embryos also display severe CNS defects not strictly the result of Wg loss and thus, are pleiotropic effects of these mutations. 8J16/9E6 are intronic point mutations not predicted to disrupt mRNA splicing and are temperature sensitive, yielding lethality at 25ºC, but are viable at 29ºC. Molecular explanations for this phenotype are explored. HHMI.

Michael Brister

For the second year in a row, received First Prize for his poster presentation

President of UD's 2012 outstanding ASBMB UAN Chapter
Glycosylation and phosphorylation induce alternative structural
conformations in tau's proline-rich domain

Michael Angelo Brister, Agata A Bielska, Neal J Zondlo.
University of Delaware, Newark, DE

The microtubule-associated protein tau is the primary constituent of neurofibrillary tangles, a pathological hallmark of Alzheimer's disease. In its diseased state, tau is phosphorylated on over 30 residues, many of which are alternatively modified by glycosylation by N-acetylglucosamine (O-GlcNAc) in tau’s native state. We hypothesized that glycosylation of threonine and serine residues on tau peptides may induce a structural effect different from that of phosphorylation at these locations. We have employed a scheme for the synthesis of glycopeptides incorporating O-GlcNAc and isolated O-GlcNAcylated peptides derived from tau’s proline-rich domain. Furthermore, we have developed a functional group to mimic O-GlcNAc modification (pseudo-glycosylation). Phosphorylated, glycosylated, pseudo-glycosylated and unmodified tau peptides were structurally characterized using circular dichroism and NMR. While phosphorylated sequences exhibited high propensity to form a type II polyproline helix, glycosylated and pseudo-glycosylated peptides exhibited more flexible secondary structures. These findings suggest a structural role for tau modification by O-GlcNAc. MAB was supported in part by the Howard Hughes Medical Institute.

Alex D'Angelo

Bone morphogenetic protein 2 and casein kinase 2
regulate the differentiation of osteoblasts

Alex Michael D'Angelo, Beth Bragdon, Jeremy Bonor, Anja Nohe.
Biological Sciences, University of Delaware, Newark, DE

The objective of this research is to study the shuttling and localization of BMP2 receptors on the cell membrane during signaling leading to osteoblast differentiation.  Signaling is initiated by the binding of bone morphogenetic protein 2 (BMP2) to transmembrane BMP receptors type Ia (BMPRIa) and type II (BMPRII).  Intracellularly, the protein casein kinase II (CK2) is associated with BMPRIa at three binding sites, denoted 2.1, 2.2, and 2.3.  CK2 is a negative regulator of BMP2 signaling.  Its dissociation, in response to BMP2 binding or blockage of CK2 binding sites, leads to signal transduction.  As a location of BMP receptors, the membrane domains caveolae are known to be involved in signaling.  To study the localization of BMP receptors in response to BMP2 and blockage of CK2 binding sites with blocking peptides, mesenchymal stem cells of the mouse cell line C2C12 were labeled for caveolin 1 (marker for caveolae), BMPRIa, and CK2 and imaged.  The technique of image cross correlation spectroscopy determined the spatial similarity (colocalization) of the proteins to establish where BMP receptors were located on the membrane.  The results showed that BMP2 stimulation and blockage of CK2 binding site 2.3, led to increased colocalization of BMPRIa with caveolin 1.  This indicates that BMP receptors are localizing to caveolae with these particular treatments. AMD supported in part by an HHMI Undergraduate Research Award.           

Tim Gilpatrick

Selected for a 10 minute talk in the ASBMB Metabolomics Symposium and an all expense undergraduate travel award
Publicity officer for 2012 outstanding ASBMB UAN Chapter
Examining the Role of Lipoprotein-Associated Phospholipase A2
in Atherosclerosis

Timothy Gilpatrick, Jonathan Tomczak, and Brian J. Bahnson

Interest in the enzyme Lipoprotein Associated Phospholipase A2 (Lp-PLA2) emerged when it was recognized to be elevated in patients at risk for developing atherosclerosis.  Lp-PLA2 exists in human plasma on the membrane of lipoproteins, and preliminary investigations indicate that the physiological effect of Lp-PLA2 is dependent on the lipoprotein to which it is coupled— namely, that the enzyme has a protective effect when it is on the surface of High Density Lipoproteins (HDL) and is atherogenic when on the surface of Low Density Lipoproteins (LDL). This project aims to develop and employ an assay for the investigation of factors that perturb the distribution of Lp-PLA2 between lipoproteins, identifying correlations between its location and its role in human health. To analyze Lp-PLA2 distribution, lipoproteins are separated using electrophoresis in custom designed non-denaturing poly-acrylamide gels. Separation of lipoproteins by native electrophoresis has been done previously, and a modification of this method is employed for a cost-efficient approach that causes LDL and HDL to form discrete bands, allowing for quantification of Lp-PLA2 in each. By increasing our understanding of the function of Lp-PLA2 we have the ability to improve current models, aiding in the future development of improved treatments for atherosclerosis.

Lauren Gurski

Redirection of adipocyte to osteoblast through the alteration of the Casein Kinase 2 interaction with the Bone Morphogenetic Protein 2 Pathway

Lauren Gurski, B. Bragdon, Anje Nohe

Osteoporosis is a degenerative disorder resulting in the loss of bone mass over time with the replacement of fat. Bone Morphogenetic Protein 2 (BMP2) is a growth factor that promotes the differentiation of osteoblasts and adipocytes. Casein Kinase 2 (CK2) interacts with BMP2 receptor Ia (BMPRIa) at three phosphorylation sites. When CK2 is prevented from binding to one of its sites on BMPRIa with the use of a CK2 blocking peptide, the pathway promotes the differentiation of a particular cell. When peptide CK2.2 is used to stimulate cells differentiating the stem cells into both adipocytes and osteoblast then several days later stimulated again with CK2.3 we see a decrease in adipocyte and an increase in osteoblast in comparison to the controls only stimulated with either peptide alone. This difference suggests a redirection from adipocytes to osteoblasts caused by CK2.3. To find further evidence for a redirection, cells were cultured out of three types of mice: a high bone density mouse (1-12), a low bone density mouse (6T), and a control mouse (B6). Each type of cell was stimulated with CK2.3 and a series of controls. The amount of mineralization and adipogenesis was then determined.

Soma Jobbagy

Recipient of an Honorable Mention
Award for his poster presentation

Characterization of Novel Anti-androgens
as Potential Prostate Cancer Therapeutics
Soma Jobbagy1, Pavan Kumar Mantravadi2, Robert Sikes3, John Koh2
1University of Delaware, Newark, DE, 2Chemistry and Biochemistry, 3Biological Sciences, University of Delaware,

Anti-androgens are the gold standard of care for treatment of advanced prostate cancer (PCa). The purpose of this study was to assess novel anti-androgens PLM1, PLM6, and PAN52 designed and synthesized in the Koh laboratory. These compounds are based on the clinical standard bicalutamide, but have expanded aryl sulfonyl moieties. PLM6 and PAN52, but not PLM1, are thought to have unique mechanisms of action based on their ability to evade progression to anti-androgen insensitivity in vitro. Prevention of androgen receptor (AR) nuclear translocation was found to correlate with evasion of anti-androgen resistance in prostate cancer cell lines. Furthermore, these novel anti-androgens were found to down-regulate the androgen receptor, which may contribute to their efficacy. Statistically significant increases in prostatic apoptosis were observed in C57/Bl6 mice treated intraperitoneally with PLM6 and PAN52, indicating that these compounds hold promise as therapy for advanced prostate cancer. Motivated by these findings, we are exploring compounds with increased potency.

Lyana Labrada

Recipient of an Honorable Mention Award for her poster presentation

Role of Hyaluronidases in Prostate Cancer  Metastasis

na  Labrada,  Lisa  Gurski,  Kenneth  van  Golen

Biological Sciences, University of Delaware, Newark, DE

Prostate cancer (PCa) is the second most common type of cancer in American males.  If caught early, there are several effective therapies   to  treat  this  disease.    However,  once   the   cancer metastasizes to the bone, there is no cure. Therefore, there is a defined clinical need to identify drug targets to treat or prevent bone metastatic PCa.  Here, we study the expression of the hyaluronidases, Hyal1 and Hyal2, in relation to their role in PCa metastasis.    Hyaluronidases    degrade    hyaluronan    (HA),    a glycosaminoglycan present in the extracellular matrix.  By degrading HA, these enzymes may facilitate invasion by clearing a path for cancer cells to spread, thereby facilitating metastasis to the bone.   Using  western  blotting,   Q-PCR   and   substrate   gel electrophoresis, we measured the expression and activity of these enzymes in PCa cell lines of different metastatic abilities.  By looking at differences across the cell lines, we hope to identify whether increased expression and/or activity of any of the hyaluronidases correlates with increased metastatic capability of the  PCa  cells.  Western blotting showed  similar  expression  of hyaluronidases throughout PCa cell lines while Q-PCR showed increased Hyal1 expression in C4-2 cells. A hyaluronidase activity assay   using  substrate   gel  electrophoresis   showed   increased hyaluronidase activity in more aggressive cell lines. Ongoing investigations use the hyaluronidase inhibitors disodium cromoglycate, L-ascorbic acid 6-palmitoyl, and octyl gallate to test the effects of hyaluronidase inhibition on PCa cell invasion in a 3D HA hydrogel. This project is funded by the Milton Stetson Award.

Alicia Liu

The Effects of the O-xylosyltransferase (oxt) Mutation
on Wg, Hh, and Dpp Signaling

Alicia Liu and  Erica M. Selva

  Department of Biological Sciences


The o-xylosyltransferase (oxt) encodes a glycosyltransferase needed for the first step of proteoglycan glycosaminoglycan (GAG) biosynthesis. Disruptions in heparan sulfate proteoglycan (HSPG) biosynthesis change the extracellular environment, which has been shown to block Wingless (Wg)/Wnt, Hedgehog (Hh), and Decapentaplegic (Dpp)/TGF-β intercellular signaling. Therefore, mutations in oxt are predicted to disrupt normal Wg, Hh, and Dpp signaling due to the absence of heparan sulfate (HS) and chondroitan sulfate (CS) modified extracellular proteogl ycans. Characterization of the oxt mutant in Drosophila wing discs shows this mutation has an unexpectedly mild phenotype as compared with other mutants acting further down in the HS biosynthetic pathway, such as sulfateless (sfl), which is responsible for specific downstream sulfation and activation of only HS chains. The double mutant oxt-sfl was made to address why the oxt phenotype is less severe. Clonal analysis shows that the double mutant looks more like sfl, suggesting the oxt null mutation does not yield a fully penetrant phenotype, allowing some xylose addition to the core proteoglycan upon which sfl can act. Because the oxt mutation is a nonsense mutation that eliminates its active site, the lack of penetrance can be attributed to either perdurance of residual Oxt protein or mRNA in mutant cells.

Dylan Lowe

Recipient of a ASBMB-UAN Competitive Travel Award
Chondrocyte Phenotype of Mice Expressing Reduced Levels of
Perlecan/HSPG2, an Essential Component of Cartilage
Dylan A. Lowe, Padma P. Srinivasan, and Catherine B. Kirn-Safran

Perlecan/Hspg2 (PLN) is a heparan sulfate proteoglycan functioning as a modulator of growth factor bioavailability and scaffold in the extracellular matrix (ECM). PLN gene loss-of-function mutations result in severe skeletal defects and embryonic death. In this study, we use a viable PLN mutant mouse model in which PLN expression is reduced. Adult PLN mutant mice display a short stature, early osteoarthritis, and altered bone properties. Immunostaining of developing growth plates revealed an absence of columnar organization and severe reduction of PLN secretion in the cartilage matrix of PLN mutant versus control bones. Furthermore, the majority of PLN in the hypomorphs co-localized with a strong signal for BiP, an endoplasmic reticulum (ER) chaperone involved in the unfolded protein response (UPR). Our data suggest that mutant PLN retained within the ER elevates ER stress, which contributes to the disease phenotype. Furthermore, chondrocyte proliferation is altered in the developing growth plates of PLN mutant mice. Ongoing work further investigates how elevated ER stress and altered fibroblast growth factor signaling in the developing growth plate contribute to the abnormal phenotype in PLN mutant mice. Supported by NIH P20 RR016458 COBRE and HHMI and UD Science and Engineering Scholarship.

Allison McCague

Selected for a 10 minute talk in the ASBMB Symposium on 
Role of Glycoconjugates in Signaling and Development and an all expense undergraduate Travel Award
The role of N-linked glycosylation
during Drosophila embryonic development
Allison McCague
and Erica M. Selva

Dept. of Biological Sciences, Univ. of Delaware, Newark, DE 19716

N-linked glycosylation is a key post-translational modification for many secretory proteins. It has roles in cell recognition and adhesion, protein folding, and cellular signaling. Endoplasmic reticulum glycosyltranferases construct a 14-sugar precursor on a dolichol carrier, which is then transferred en mass to proteins on consensus sites. The function of N-glycosylation during Drosophila embryogenesis was investigated in alg9 and alg10 germ line clone mutant embryos. alg10 encodes the enzyme catalyzing terminal glucose addition to the sugar-substrate prior to protein transfer, while the alg9 encoded enzyme acts five steps earlier in sugar synthesis. alg9 and alg10 displayed severe and pleotrophic defects in cuticle secretion.  Expression of Wingless (Wg), a model secreted glycoprotein of the Wnt pathway, was examined to identify earlier effects of these mutations. Normal Wg secretion was disrupted in alg9 and alg10 glc embryos. However, defects in secretion did not block downstream Wg signaling, as Engrailed (En) was expressed fairly normally in both backgrounds.  The central nervous system (CNS) develops later and is highly dependent on glycosylation, alg10 loss caused severe defects in CNS development, but alg9 glc embryos lack CNS. Hence, alg10 may cause global underglycosylation or is only needed for some glycoproteins, while alg9 may be required for N-glycosylation of most or all protein substrates.

Ramkrishna Patel

Expression of PMCA4a in the Extratesticular Pathway and Accessory Organs of the Mouse 
Ramkrishna Patel1, Deborah L. Stabley2,
Emanuel E. Strehler3, Patricia A. Martin-DeLeon1

1Department of Biological Sciences, University of Delaware, 2A.I. DuPont Hospital for Children, Wilmington , DE,  3Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN.

Plasma Membrane Ca2+ ATPase isoform 4b (PMCA4b) is the primary Ca2+ efflux pump in murine sperm where it regulates motility.  In Pmca4 null sperm hyperactivated motility is lost, resulting in infertility. We have shown that PMCA4b interacts with CASK in regulating Ca2+ homeostasis and motility.  Recently, it has been shown that PMCA4a and 4b are expressed in all bovine epididymal (EPL) regions, with increasing amounts of 4a distally and only 4b in testis. These findings suggest that PMCA4a and b are acquired by sperm during EPL maturation.  Here we show, via RT-PCR, that murine Pmca4b mRNA is expressed uniformly in testis and epididymis (EP) and 4a differentially in the EP. Western confirmed the RT-PCR results showing that PMCA4a is most abundant in testis and cauda EP.  Immunoprecipitation using pan-PMCA4 antibody showed 4b and 4a in caput and corpus EP and 4a in cauda, seminal vesicle (SV), and vas deferens (VD).  Western revealed an ~4 fold increase of 4a in caudal, compared to, caput sperm and confirmed its presence in the VD and SV.  Importantly, PMCA4a was seen in sperm-free EPL luminal fluid, suggesting that it is secreted, and acquired by sperm via epididymosomes.  Since PMCA4a and 4b have different kinetic properties for Ca2+ transport, our study suggests for the first time that murine sperm possess PMCA4a which has a higher Ca2+ turnover, better facilitating capacitation events in the female tract.  Funding: NIH-RO3 HD061637.

Adam Reese

See UDaily article and  video of Adam describling his reasearch.

Endoglin is a key mediator of BMP2 mediated Adipogenesis

Adam Reese, Joyita Dutta, and Anja Nohe

About 1.5 million fractures occur annually due to osteoporosis, which affects nearly 20% of all women. Osteoporosis is the thinning of bone tissue and loss of bone density over time in which the accrual of fat within the bone results in decreased bone density. Bone turnover relies on a dynamic balance between bone forming cells (osteoblasts) and fat cells (adipocytes). Redirecting these fat cells would allow for new development in treatments for osteoporosis. Bone Morphogenetic Protein 2 (BMP2) initiates osteoblast and adipocyte differentiation. Casein Kinase 2 (CK2) interacts with the Bone Morphogenetic Protein receptor type Ia (BMPRIa) during BMP2 signaling and controls the key regulatory mechanism for osteogenesis; however the mechanism is yet to be determined. Endoglin, a TGF-β binding protein, plays a part in BMP2 signaling by associating with BMPRIa, but the effect is unclear. Since CK2 release of BMPRIa induces endoglin expression, the effect of endoglin expression on stimulated C2C12 cells was investigated. Our data suggest that endoglin is up-regulated during BMP2 stimulation and affects differentiation. We postulate that endoglin co-localizes with the BMPRIa receptor to different membrane areas causing adipogenesis. Data analysis supports that endoglin induces adipogenesis and reduces mineralization through the DeltaC and PP domains. Research support provided by Charles Peter White Fellowship.

Victoria Roop

Characterization of the EMT response in Crybb2Phil mutants

Victoria H. Roop, Fahmy A. Mamuya, Melinda K. Duncan

The most abundant protein in the adult lens fiber cells is βB2-crystallin (Crybb2). Mutations in the Crybb2 gene cause cataracts in mice and humans. A twelve nucleotide deletion in mouse lens epithelial cells (LEC), known as the Crybb2Phil mutation, leads to cataracts associated with lens fiber cell defects as well as epithelial to mesenchymal transition (EMT) of the LEC in adulthood. However, the mechanism behind this phenotype is poorly understood. The aim of this project is to characterize the EMT response caused by the Crybb2Phil mutation. Tissues obtained from Crybb2Phil mutants were immunostained for alpha and beta integrin subunits, phospo-SMAD3 (p-SMAD3), transforming growth factor β-induced (BIGH3), and EMT the markers E-cadherin, vimentin, follistatin, and α-smooth muscle actin (α-SMA).  Compared to the wildtype lens, β1, αV, and α5 integrins, vimentin, α-SMA, and p-SMAD3 were upregulated in the Crybb2Phil mice. No changes were seen in α2, α3, and α6 integrin subunits or follistatin. Consistent with EMT, E-cadherin was downregulated in the Crybb2Phil mice. Upregulation of α-SMA signifies that Crybb2Phil mice undergo EMT around two months of age. Furthermore, over expression of β1 and αV integrins along with p-SMAD3 in the Crybb2Phil mutant suggests that the EMT seen in Crybb2Phil mice may be occurring via the TGFβ-SMAD interacting pathway. This project is funded by National Eye Institute grant EY015279.

Ashley Shay

Publicity officer for 2012 outstanding ASBMB UAN Chapter

Hypoplastic Left Heart Syndrome: Molecular Consequences of Transcription Factor Mutations
Ashley Elizabeth Shay1, Susan Kirwin2, Carol Prospero3,
Christian Pizarro,3, Vicky Funanage, 2

1Biological Sciences, University  of  Delaware,  Newark,  DE,  2Biomedical  Research, 3Nemours  Cardiac  Center,  Nemours  A.I.  duPont  Hospital  for Children, Wilmington, DE

Hypoplastic left heart syndrome (HLHS; OMIM #241550) is characterized by  abnormal hypoplasia of  the  left  ventricle and aorta, stenosis or atresia of the aortic arch and mitral valve, an atrial septal defect, and a patent ductus arteriosus. The incidence of this rare disorder is about 1 in every 5,000 live births. These abnormalities lead to a decrease in proper blood flow from the left ventricle to the systemic circulatory system. Failure of the systemic circulation leads  to   profound  cyanosis  in   patients.  Without intervention, this condition is fatal within the first days of life. Studies have indicated that HLHS has a strong genetic basis when compared to other congenital heart defects. We are examining the role of several genes associated with cardiac development by screening exons and partial intronic regions for mutations by direct screening of genomic DNA from HLHS patients. Candidate genes for this study include TBX5, NKX2.5, GATA4, and GJA1 due to the correlation between mutations in these genes and cardiac defects. These results will be compared within a cohort of HLHS patients to determine if there is a genetic basis for their abnormal cardiovascular development. We have identified three mutations in exon 8 of TBX5: Val263Met, Ser276Asn, and Arg279Gln, as well as three variations within intronic regions: c. 148 -19 A/T (Intron 2), c.755 -29 C/T (Intron 7), and c.983 -8 C/T (Intron 8). Funding: Nemours Research Programs and NIH-INBRE (Delaware)

Frank Shen
Development of Pattern Recognition Algorithms  to Identify Gut Microorganisms using Fatty Acid Signatures
Frank Shen1, Dora Ballesteros2, Myran Sasser4, Len Cimini2, Prasad Dhurjati3
Department    of    Mathematical    Sciences,2Department of Electrical and Computer Engineering, 3Department of Chemical Engineering, University of Delaware, 4MIDI Inc, Newark, DE

A pattern recognition algorithm was developed that was capable of accurately identifying the presence of specific microbial species in gut samples from the sample’s composite fatty acid signature.  We focused on 51 different species found in the human gut and 61 different fatty acids produced by those species. The unique fatty acid signatures of the individual microorganisms were obtained by gas chromatography (provided by MIDI Inc). Several algorithms were developed in Matlab to differentiate individual species using the fatty acid composition data of the simulated mixtures. These algorithms utilized Hamming distance, least-squares optimization, and  combinatorics  methods  to  identify  the  presence  of  each species. The algorithms were tested against myriad virtual samples to analyze their ability to detect the presence of selected species. While more complex mixtures of species decreased the probability of detection, we found that utilizing a constrained least-squares method with Hamming-based filters provided high probabilities of detection for all tested samples.   This algorithm was capable of detecting the presence of a selected species over 90% of the time for instrument tolerances as high as 15%.

Sarah Stamm

Recipient of an ASBMB-UAN non-competitive travel Award

Treasurer for UD's 2012 outstanding

 Mechanisms of resistance to quaternary ammonium compounds 
and other antimicrobials in
Salmonella enterica

Sarah Stamm and Diane Herson
Biological Sciences, University of Delaware, Newark, DE

Each year nearly 1.4 million people in the United States are infected with Salmonella as a result of food poisoning.  Antimicrobials are used for both the prevention and treatment of salmonellosis, and a major concern is that resistance to these agents will develop.  Salmonella enterica Strains with Reduced Susceptibility (SRS) to Quaternary Ammonium Compounds (QAC) were generated by repeatedly passaging strains in increasing concentrations until a Minimum Inhibitory Concentration (MIC) of 400 ppm was obtained.  DSRS strains were generated by culturing SRS stains in the absence of the agent until their MIC returned to that of the parent strain.  Parent, SRS, and DSRS strains were tested for cross resistance to four antibiotics.  Strains were then tested for efflux pump activity by qPCR analysis of the acrB and marA genes.  Unlike DSRS, SRS strains showed cross resistance to all four antibiotics.  These strains showed upregulation of the acrB gene while DSRS showed expression similar to the parent strains.  For marA gene expression, both SRS and DSRS strains showed upregulation compared to the parent strain.  This project was funded by Howard Hughes Medical Institute.        

Christopher Wright

Recipient of an Honorable Mention
Award for his poster presentation

Analysis of Small RNAs Associated with Plant Senescence
Christopher Wright a, Shawn R. Thatcher a, Shaul Burdb, Amnon Lers b, Pamela J. Green a
 Department of Plant and SoilSciences, Delaware Biotechnology Institute, University of Delaware, b  Department of Postharvest Science of Fresh Produce, Volcani Center, Bet Dagan, Israel.

Since their discovery in 1993, small RNAs have been shown to have an increasingly important role in post-transcriptional gene regulation. MicroRNAs (miRNAs) are of particular interest because they are often conserved across many different species. This allows research on model organisms to be more easily extended to help solve problems in commercial sectors. One major problem in the agricultural sector is the decline in health during plant aging, or senescence. This process is of key importance commercially, where it can cause decreases in crop yield and postharvest quality. If the onset of senescence could be delayed or halted, based on knowledge of the mechanisms involved, this could prove very beneficial for agricultural improvement. To test the hypothesis that miRNAs participate in senescence, we constructed and sequenced a series of small RNA libraries from Arabidopsis leaf tissue at varying stages of senescence. A comparison of miRNA expression changes in these libraries provided evidence for novel senescence regulation. Using northern blots as a confirmation, we have reproduced the regulation of previously published senescence-dependent miRNAs, as well as identified several new candidates. We have also constructed Parallel Analysis of RNA Ends (PARE) libraries  to search for mRNA cleavage products due to specific miRNA-guided cleavage, as well as discover general senescence-related RNA decay patterns. Initial analysis of PARE data has revealed regulated cleavage of a target of one of the senescence-regulated miRNAs at the expected site during senescence. Further analysis and validation of both small RNA as well as PARE library data will help us gain a deeper understanding of the fundamental processes involved in senescence. Supported by BARD, NIH, and HHMI.

Chris, Mike, and Soma killing time until takeoff at PHL.

The rest of the group doing the same thing.

Tory and Allison are glad to be on their way to San Diego

Coming down between the buildings flying into San Diego.

The San Diego Marriott, our home for five days.

Half of the San Diego Convention Hall Floor where posters were presented and vendors displayed.

ASBMB-UAN officers (Tim, Ashley, Sarah, and Mike) tending the poster describing the why the UD chapter was selected best in the Northeast.

Lyana receivening her Honorable Mention Award.

Chris receiving his Honorable Mention Award.

Mike reciving his second First Place Awards in two years.

Tim presenting his invited talk in a symposium session.

Allison presenting her invited talk in a symposium session.

Doctors Selva and Usher chowing down seafood with students at Fin Fish across from the Convention Center.

Allison, Soma, and Sarah ready for the ASBMB "5.5K" fun run.

Sarah waits for the start, Soma halfway, and Soma recouperating
after finishing 10th overall. 

Mike and Chris showoff their complimentary DNA inking courtesy of ASBMB and urge Dr. White to have a DNA strand inked around his neck or across his forehead.

Alicia, Erica, Lyana, Ashley, and Dylan at the Fin Fish Restaurant.

Next Gens breakfast Group

Headed for the morning sessions.

The UD group after the Awards presentation flanked by Dr. Don and Judy Voet, biochemistry textbook authors and recipients of the ASBMB Award for Outstanding Contributions to Education. (Dr. Judy Voet was a sabbatical replacement for Dr. White at UD in 1978.)

Dinner time. Dr. Usher takes the check.

Count the flopflops of this group who made it to the Pacifica Ocean.

Leaving San Diego after a great trip.

The trip to the Experimental Biology 2012 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

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Created 23 November 2011,  Last revised 4 May 2012 by Hal White [halwhite at udel.edu]
Copyright  2012 Harold B. White, Department of Chemistry and Biochemistry, University of Delaware