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2. Probing functional polymorphisms in the dengue vector, Aedes aegypti

Author

Bonizzoni, M, Britton, M, Marinotti, O, Dunn, WA, Fass, J, and James, AA

Abstract

Background: Dengue is the most prevalent arboviral disease world-wide and its primary vector is the mosquito Aedes aegypti. The current lack of commercially-available vaccines makes control of vector populations the only effective strategy to prevent dengue transmission. Aedes aegypti geographic populations exhibit great variability in insecticide resistance and susceptibility to dengue infection. The characterization of single nucleotide polymorphisms (SNPs) as molecular markers to study quantitatively this variation is needed greatly because this species has a low abundance of microsatellite markers and limited known restriction fragments length polymorphisms (RFLPs) and single-strand conformation polymorphism (SSCP) markers.Results: We used RNA-seq to characterize SNPs in three Ae. aegypti strains, including the Liverpool (LVP) strain, from which the current genome annotation is derived. We identified 131,764 unique genome locations with at least one alternative nucleotide to what is reported in the reference annotation. These comprised changes in both open-reading frames (ORFs) and untranslated regions (UTRs) of transcripts. An in depth-look at sequence variation in immunity genes revealed that those associated with autophagy, MD2-like receptors and Peptidoglycan Recognition Proteins had more sequence variation in their 3'UTRs than mutations associated with non-synonymous changes. This supports the conclusion that these genes had maintained their functional specificity while being adapted to different regulatory domains. In contrast, a number of peroxidases, serpins and Clip-domain serine proteases exhibited conservation of putative UTR regulatory sequences while displaying diversification of the ORFs. Transcriptome evidence also was found for ~2500 novel transcriptional units (NTUs) not annotated in the reference genome.Conclusions: The transcriptome-wide assessment of within and inter-strain polymorphisms in Ae. aegypti adds considerably to the number of molecular markers available for genetic studies in this mosquito. Additionally, data supporting NTU discovery emphasizes the need for continuous amendments of the reference genome annotation. © 2013 Bonizzoni et al.; licensee BioMed Central Ltd.

Published
2013

15. Editorial: Information Is Ugly

Author

Fass, J, Yamada-Rice, D, James, S, Lewis, M, Pappas, G, Fass, J, Yamada-Rice, D, James, S, Lewis, M, and Pappas, G

Abstract

Design frameworks that outline the benefits of thinking in terms of binaries suggest that, as designers, we can situate ourselves and our work in relation to opposite extremes. Doing so is more likely to bring about innovation and imagine ideological possibilities. This Special Issue creates a binary between ugly and beautiful with a specific focus on the former. The standard dictionary definitions of ugly are in relation to an unpleasant or repulsive appearance or a topic that is likely to involve violence or other unpleasantries. We draw both definitions into our discussion. We have collected articles that have at their heart ugly topics, including the climate crisis, racism and digital surveillance, which reflect contemporary times. As we write, a war has begun in Ukraine. The news shifts the global pandemic to second position and shunts Black Lives Matter, the rising cost of living in the UK, widening social inequality and the climate crisis out of the news headline. Each news package is filled to the brim with infinite amounts of ugly information. We push for a rebellion against the convention of beautifying data, such as became mainstream following the popularity of Information Is Beautiful (McCandless, 2009) and other works emphasizing the sleek graphic design of data visualization. Instead, we seek to engage people in exploring how to research, analyse and present ugly information in other ways. We aim to encourage thinking beyond one mode and focus attention on the complex array of ways in which modes can meet and combine. We suggest that hybrid assemblages of digital and physical materials can reach audiences via their senses in new ways. We seek to encourage readers to find their own connections between modes, materials and senses in order to understand and communicate complex and particularly ugly issues in innovative ways. We shift our emphasis from visual communication towards experience and interaction. In other words, we try to bring about ugly infor

Published
2022

18. Aktueller Stand der Magenchirurgie — zu Ehren von E. Ungeheuer

Author

Hartel, W., Rösch, W., Farthmann, E. H., Eggstein, S., Wiebecke, B., Encke, A., Schmidt-Matthiesen, A., Juhl, H., Schreiber, H.-W., Kremer, B., Hermanek, P., Siewert, J. R., Kirchner, R., Kreutz, F., Marcelja, Z., Seifert, E., Schwarz, A., Usinger, K., Glasbrenner, B., Beger, H. G., Böttcher, K. A., Roder, J. D., Nekarda, H., Faß, J., Riesener, K. P., Schumpelick, V., Hartel, W., editor, and Hierholzer, G.

Published
1995
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48. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

Author

Gill, SC, Lim, NM, Grinaway, PB, Rustenburg, AS, Fass, J, Ross, GA, Chodera, JD, and Mobley, DL

Subjects
Protein Structure, Binding Sites, Water, Molecular Dynamics Simulation, Ligands, Engineering, Physical Sciences, Chemical Sciences, Thermodynamics, Muramidase, Monte Carlo Method, Tertiary, Toluene, Protein Binding
Abstract

Accurately predicting protein-ligand binding affinities and binding modes is a major goal in computational chemistry, but even the prediction of ligand binding modes in proteins poses major challenges. Here, we focus on solving the binding mode prediction problem for rigid fragments. That is, we focus on computing the dominant placement, conformation, and orientations of a relatively rigid, fragment-like ligand in a receptor, and the populations of the multiple binding modes which may be relevant. This problem is important in its own right, but is even more timely given the recent success of alchemical free energy calculations. Alchemical calculations are increasingly used to predict binding free energies of ligands to receptors. However, the accuracy of these calculations is dependent on proper sampling of the relevant ligand binding modes. Unfortunately, ligand binding modes may often be uncertain, hard to predict, and/or slow to interconvert on simulation time scales, so proper sampling with current techniques can require prohibitively long simulations. We need new methods which dramatically improve sampling of ligand binding modes. Here, we develop and apply a nonequilibrium candidate Monte Carlo (NCMC) method to improve sampling of ligand binding modes. In this technique, the ligand is rotated and subsequently allowed to relax in its new position through alchemical perturbation before accepting or rejecting the rotation and relaxation as a nonequilibrium Monte Carlo move. When applied to a T4 lysozyme model binding system, this NCMC method shows over 2 orders of magnitude improvement in binding mode sampling efficiency compared to a brute force molecular dynamics simulation. This is a first step toward applying this methodology to pharmaceutically relevant binding of fragments and, eventually, drug-like molecules. We are making this approach available via our new Binding modes of ligands using enhanced sampling (BLUES) package which is freely available on GitHub.

Published
2018
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