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2013 CIRC Poster Session Abstracts 3rd Annual Center for Integrated Research Computing Poster Session! May 10, 2013 2013 Annual Poster Session ! 1 3rd Annual Center for Integrated Research Computing Poster Session! May 10, 2013 Computational Design and Characterization of 2-D tendency to cross- and self-hybridize. These features are observed in Photonic Crystal Geometries for Biosensing RNA sequences with known structure. We demonstrate that pre- James E. Baker and Benjamin L. Miller selected sequences accelerate the design of structures that are mimics Physics and Astronomy of biologically relevant structures. This is implemented as a new Dermatology structure design component of RNAstructure (http:// Biochemistry and Biophysics rna.urmc.rochester.edu/RNAstructure.html). This work is a Biomedical Engineering collaboration with Celadon Laboratories, Inc. (http:// The importance of early disease diagnosis both for initiating www.celadonlabs.com/). successful clinical treatment and preventing disease transmission continues to drive the development of rapid, ultrasensitive, label-free Next Generation Sequence Analysis of the Transcriptional biosensors. Sensors based on two-dimensional photonic bandgap Response to Neonatal Hyperoxia crystal structures, in particular, have the potential for single- Soumyaroop Bhattacharya, Chin-Yi Chu, Zhongyang Zhou, Min Yee, pathogen detection capabilities. In order to achieve such high Ashley M. Lopez, Valerie A. Lunger, Bradley Buczynski, Gloria S. sensitivity, the geometric structure of the photonic crystal must be Pryhuber, Michael A. O’Reilly, and Thomas J. Mariani designed in a way that pathogen binding is evident in the optical Pediatrics transmission spectrum of the crystal. Computational modeling methods allow us to simulate the electric field profiles and Rationale: Bronchopulmonary Dysplasia (BPD) is a major transmission spectra that we expect to observe for different photonic complication of preterm birth associated with significant morbidity. crystal designs. Ongoing computational characterization of photonic Due to the complexity of risk factors and limited availability of crystal designs are presented. clinical samples, an understanding of this disease, potential biomarkers and causal mechanisms are limited. BPD is a debilitating condition characterized by inflammation, enlarged airspaces, Accelerating Nucleic Acid Design Using Pre-Selected vascular dysmorphia and aberrant extracellular matrix accumulation Sequences that is typically described as arrested lung development. This is in Stanislav Bellaousov and David Mathews part due to oxidative stress, resulting from therapeutic oxygen Biochemistry and Biophysics supplementation, that disrupts critical pathways of lung development. Rodent models involving neonatal exposure to Nanoscale nucleic acids could potentially be designed to be catalysts, excessive oxygen concentrations (hyperoxia) have been used to study pharmaceuticals, or probes for detecting pathogens. We hypothesize the mechanisms contributing to BPD pathology. Transcriptomic that designing nucleic acid molecules from pre-selected sequences, assessment of the effects of hyperoxia in neonatal mouse lungs using rather than from random sequences, would increase the speed of RNASeq will help to identify genes and pathways associated with designing large molecules and also increase the accuracy of design. BPD. Helices should be formed in the optimal folding free energy change range, have maximal structure probability and minimal ensemble Methods: Whole lung tissue from newborn C57BL/6 mice exposed to defect. Loops should be composed of sequences with the lowest 100% oxygen for 10 days (n=8) and room air-exposed age matched ensemble free energy change. All sequences should have low controls (n=6) were compared. Total RNA was isolated from ! 2 3rd Annual Center for Integrated Research Computing Poster Session! May 10, 2013 individual whole lung tissues (n=14) and pooled in duplicates to Further analysis of these data will enhance our current knowledge of perform transcriptome Sequencing (RNA-seq) using the Illumina BPD, and may be useful for developing novel therapeutic strategies. Genome Analyzer II platform. Alignments were generated using multiple algorithms (ELAND v1.8 algorithm using Illumina CASAVA software; TopHat; and Shrimp2). Raw counts obtained from The Effects of Inhomogeneities within Colliding Flows on each alignment algorithm were further normalized using trimmed- the Formation and Evolution of Molecular Clouds mean and reads per million bases. Normalized gene expression data Jonathan Carroll-Nellenback, Adam Frank, and Fabian Heitsch were filtered to remove undetected genes. Differentially expressed Center for Integrated Research Computing genes were detected using Significance Analysis of Microarrays Physics and Astronomy (SAM) and CuffDiff2, on each version of mapped and normalized Observational evidence from local star-forming regions mandates data. Ingenuity Pathway Analysis (IPA) was used for pathway and that star formation occurs shortly after, or even during, molecular network analyses. Expression patterns for selected genes were cloud formation. Models of the formation of molecular clouds in examined by quantitative polymerase chain reaction (qPCR). Results: large-scale converging flows have identified the physical A total of 248 genes were identified as differentially expressed mechanisms driving the necessary rapid fragmentation. They also between hyperoxia and control samples by both SAM (at median point to global gravitational collapse driving supersonic turbulence FDR = 0) and CuffDiff2 (at p < 0.05) and had a magnitude of change in molecular clouds. Previous cloud formation models have focused greater than or equal to two-fold (fold change > 2). We successfully on turbulence generation, gravitational collapse, magnetic fields, and validated 36 of 51 genes by qPCR. There was a clear association feedback. Here, we explore the effect of structure in the flow on the between the magnitude change identified by RNASeq and resulting clouds and the ensuing gravitational collapse. We compare subsequent qPCR validation. There were also differences in the rate two extreme cases, one with a collision between two smooth streams, of validation dependent upon the mapping and gene selection and one with streams containing small clumps. We find that approaches used. Canonical pathways significantly dysregulated in structured converging flows lead to a delay of local gravitational hyperoxia lungs included Nrf2-mediated oxidative stress signaling, collapse ("star formation"). Thus, more gas has time to accumulate, p53 signaling, hepatic fibrosis and sildenafil pathways. Interestingly eventually leading to a strong global collapse, and thus to a high star most genes significantly affected (~70%) showed a pattern of formation rate. Uniform converging flows fragment hydro- expression consistent with an arrest in lung development following dynamically early on, leading to the rapid onset of local gravitational hyperoxia. A subset of the genes dysregulated in hyperoxic neonatal collapse and an overall low sink formation rate. mouse lungs (13%) were also differentially expressed (as defined by t-test p<0.05) in human BPD lung tissue (Bhattacharya et al., 2012, AJRCCM). Summary: We have generated genome-wide expression data from hyperoxia-exposed neonatal mouse lung tissue using RNA-Seq. We have identified and validated genes dysregulated in this model of BPD-like pathology. This model captures some aspects of BPD. ! 3 3rd Annual Center for Integrated Research Computing Poster Session! May 10, 2013 Prediction of Nucleic Acid α and ζ Torsions From 31P NMR disperse fengycin about the membrane eliminating radical pockets of Chemical Shifts curvature. David E. Condon, Brendan C. Mort, Scott D. Kennedy, and Douglas H. Turner Chemistry Discovery of Novel ncRNA by Scanning Multiple Genome Alignments Structural databases were searched for nucleic acids that had both Yinghan Fu, Zhenjiang Xu, Zhi J. Lu, Shan Zhao, and David H. 31P NMR chemical shifts assigned and known ! and " torsion angles, Mathews specifically structures that had non-A-form characteristics, e.g. a Biochemistry and Biophysics hairpin. Quantum mechanics data was used to predict NMR chemical shift using the GIAO method. Hartree-Fock and the DFT Recently, non-coding RNAs (ncRNAs) have been discovered with functionals wB97X-D, SSB-D, B3LYP, and a mean functional of all five novel functions, and it has been appreciated that there is pervasive were tested to see which would give the best agreement with the transcription. Therefore, de novo computational ncRNA detection empirical data. Here, the NMR 31P chemical shifts estimated with that are accurate and efficient are desirable. The purpose of this study B3LYP are recommended as a guide for future structural studies. is to develop a ncRNA detection method based on structural conservation. A new method called Multifind, based on Multilign (Xu & Mathews 2011), was developed. It uses an algorithm that Interactions of the Antifungal Fengycin with Model predicts common structures among multiple sequences and estimates Biomembranes Characterized using Molecular Simulation the probability the input sequences are ncRNA using a classification Aaron Cravens, Joshua N. Horn, and Alan Grossfield support vector machine (SVM). Multilign uses Dynalign (Mathews & Biochemistry and Biophysics Turner 2002), which folds and aligns two sequences simultaneously without requiring any sequence identity; its structure prediction With the advent of
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