Art and Science Exhibition


ISMB/ECCB 2015 brings together scientists from a wide range of disciplines, including biology, medicine, computer science, mathematics and statistics. In these fields people are constantly dealing with information in visual form: from microscope images and photographs of gels to scatter plots, network graphs and phylogenetic trees, structural formulae and protein models to flow diagrams; visual aids for problem-solving are omnipresent. Some of the works of the first such exhibition at the ISMB 2008 in Toronto combine outstanding beauty and aesthetics with deep insight that perfectly proves the validity of our approach or goes beyond the problem's solution. Others were surprising and inspiring through the transition from science to art, opening our eyes and minds to reflect on the work that we are undertaking.

The Art & Science Exhibition 2015 presents the artworks that have been generated as part of research projects. They are also soliciting images resulting from creative efforts that involve scientific concepts or employ scientific tools and methods.

 


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Art & Science Images

A&S01
ALAA ABI Haidar
University of Pierre and Marie Curie, France
Discipline
Wormlike Light Reflections encapsulated in Soap Bubbles
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A&S02
ALAA ABI Haidar
University of Pierre and Marie Curie, France
Smilies
Soap + fats + water = smiling faces in Macro
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A&S03
Moshe Dessau
Bar-Ilan University, Israel
An artistic presentation of the glycoprotein C dimer
An artistic presentation of the glycoprotein C dimer from Rift valley fever virus. The two promotes (Red and Yellow) are in a molecular surface representation.
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A&S04
Moshe Dessau
Bar-Ilan University, Israel
An assembly model of Rift valley fever virus (RVFV)
The crystal structure of RVFV Gc, one of the virus' two envelope glycoproteins, fitted into a cryo-EM 3D reconstruction. (Dessau & Modis, PNAS 2013)
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A&S05
Boris Fichtman
Bar-Ilan University, Israel
SEM image of fruit fly (Drosophila melanogaster) hind foot.
SEM image of fruit fly (Drosophila melanogaster) hind foot.
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A&S06
Amnon Harel
Bar-Ilan University, Israel
Erythrocyte on placenta (human)
Erythrocyte on placenta (human)
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A&S07
Boris Fichtman
Bar-Ilan University, Israel
Glial cell from mice brain
Glial cell from mice brain
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A&S08
Amnon Harel
Bar-Ilan University, Israel
cellular nuclei with nuclear pore complex
cellular nuclei with nuclear pore complex.
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A&S09
Avraham Samson
Bar-Ilan University, Israel
Normal modes dynamics of multibody proteins: The acetylcholine receptor and its complex with snake toxins
Calculating protein dynamics is essential for a better understanding of many biological processes. To better understand the motion involved in channel opening of the acetylcholine receptor (AChR), I calculated the normal mode dynamics of the AChR (1). The normal modes calculations reveal a twist like gating motion responsible for channel opening. This motion is shown in the movie on the right. Throughout this twist motion, the ion channel diameter is shown to increase. Strikingly, the twist motion and the increase in channel diameter are not observed for the acetylcholine receptor in complex with two α-bungarotoxin (αBTX) molecules. The toxins seem to lock together neighboring receptor subunits thereby inhibiting channel opening. Interestingly, one αBTX molecule is sufficient to prevent the twist motion. These results shed light on the gating mechanism of the acetylcholine receptor, and present a complementary inhibition mechanism by snake venom derived α-neurotoxins.
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A&S10
Avraham Samson
Bar-Ilan University, Israel
Elastic network normal mode dynamics reveal the GPCR activation mechanism
G-protein-coupled receptors (GPCR) are a family of membrane-embedded metabotropic receptors which translate extracellular ligand binding into an intracellular response. Here, we calculate the motion of several GPCR family members such as the M2 and M3 muscarinic acetylcholine receptors, the A2A adenosine receptor, the β2 -adrenergic receptor, and the CXCR4 chemokine receptor using elastic network normal modes. The normal modes reveal a dilation and a contraction of the GPCR vestibule associated with ligand passage, and activation, respectively. Contraction of the vestibule on the extracellular side is correlated with cavity formation of the G-protein binding pocket on the intracellular side, which initiates intracellular signaling. Interestingly, the normal modes of rhodopsin do not correlate well with the motion of other GPCR family members. Electrostatic potential calculation of the GPCRs reveal a negatively charged field around the ligand binding site acting as a siphon to draw-in positively charged ligands on the membrane surface. Altogether, these results expose the GPCR activation mechanism and show how conformational changes on the cell surface side of the receptor are allosterically translated into structural changes on the inside
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A&S11
Luke Wilson
University of Dundee, United Kingdom
Jim  Procter, University of Dundee, United Kingdom
Geoff Barton, University of Dundee, United Kingdom
Analogue Alignment
“Multiple sequence alignments were once performed manually, and even today, we still examine automatically computed alignments to check that we can't do better.” –Jim Procter
This is an image of the Jalview Abacus, a sculptural attempt to visually represent the function of the Jalview protein alignment program. The program can be used to find alignments of amino acids in similar proteins. These alignments are then used to find similarities and differences between these proteins.
This object expresses the core process of Jalview in a physical space, and plays on the relationship between high tech and low tech solutions. It is a functioning abacus built by hand from wood and steel. Each row is an extract from different similar proteins (cysteine proteases) and an alignment can be found by lining up the beads of like amino acids in the columns. If it was long enough it could be used to align the entire sequence manually.

Photography: Luke Wilson
Design and Construction: Luke Wilson in collaboration w. Jim Procter and Geoff Barton
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A&S12
Ryuta Nakajima
University of Minnesota Duluth, United States
Amburghese di cuore (no. 6)
Considering the salutations of contemporary visual culture, it is essential to investigate its’ effect and implication by asking such existential questions as Why do we make images, where do they come from and what is their primary function? In order to answer these rather difficult questions, this study focused on Sepia Pharaonis’s adaptive coloration as a empirical and biological model that codes and remaps visual information such as paintings, photographs, and video. More specifically, their adaptive coloration is triggered by both lateral and longitudinal visual stimuli replacing natural elements with various types of digital images. A LED flat-screen monitor controlled by a computer was placed directory under or next to a starphire-glass aquarium as a projection device. Through this study, we observed that basic camouflage tactics of uniform, mottled and disruptive pattern (Hanlon and Messenger 1996) are also applicable and viable methods in categorizing avant-garde paintings and photographs. In short, the body pattern produced by Sepia pharaonis can accurately reproduce culturally driven and highly conceptual images. The collected data from these experiments are used to create a series of photographs and videos installations. The genetically and evolutionally pure empirical may not only uncover certain key information needed to understand the origin of visual communication but also function as a catalyst that will redirect our culture away from the ever simulated hyper-reality. This, in tern, may create a truly valuable interdisciplinary platform to discuss the current trends in both art and science.
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A&S13
Shailesh Tripathi
Queens University Belfast, United Kingdom
Ricardo de Matos Simoes, Queens University Belfast, United Kingdom
Salissou Moutari, Queens University Belfast, United Kingdom
Frank Emmert-Streib, Tampere University of Technology, Finland
Modular layout visualization of an urothelial cancer gene regulatory
The network shows a modular visualization of an urothelial cancer gene regulatory network using the NetBioV Bioconductor R package. The modules were generated by a fast greedy algorithm and are based on structural properties of the network. We inferred the network from a large-scale Illumina bead urothelial cancer microarray dataset using the Bc3net CRAN R Package. In total, 2,405 genes and 2,591 associations are shown that were selected based on a Bc3net threshold of 0.28.
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A&S14
Shailesh Tripathi
Queens University Belfast, United Kingdom
Ricardo de Matos Simoes, Queens University Belfast, United Kingdom
Salissou Moutari, Queens University Belfast, United Kingdom
Frank Emmert-Streib, Tampere University of Technology, Finland
Radial layout visualization of an urothelial cancer gene regulatory network
The network shows a layered visualization of an urothelial cancer gene regulatory network inferred using the BC3NET R Package. For the visualization the layout is initialized based on a random set of nodes that define the first layer. The following layers are defined by the immediate gene neighbors of the previous layer. The layers are plotted successively in a radial configuration. The shown network consists of a total of 10,593 genes and 12,282 associations.
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A&S15
Ricardo de Matos Simoes
Queens University Belfast, United Kingdom
Urothelial cancer associated chromosomal gene subnetworks inferred from large-scale gene expression data
Gene expression profiles that are influenced by genomic and epigenetic alterations can elucidate dependency structures of co-located genes and link to novel genomic target regions which are associated to urothelial cancer. We inferred gene regulatory from three large scale RNAseq, Bead and Oligo gene expression datasets networks by the application of the BC3NET R package. We defined gene sets from 1Mb sliding windows that mimic the extend of co-expressed gene clusters along the human chromosomes with a 500Kb (kilo bases) overlap between adjacent windows. Significant subnetworks were identified by a gene pair enrichment analysis that is based on a hypergeometric test. In total 471 (RNAseq), 117 (Bead) and 58 (Oligo) significant 1Mb regions were identified. A total of 40 significant 1Mb regions were common across the three GRN.
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