Harsh Dweep
Medical Research Centre, Medical Faculty Mannheim
University of Heidelberg

Dr. Carsten Sticht
Medical Research Centre, Medical Faculty Mannheim
University of Heidelberg

Prof. Norbert Gretz
Medical Research Centre, Medical Faculty Mannheim
University of Heidelberg

MicroRNAs are small, non-coding RNA molecules that can complementarily bind to the mRNA 3'-UTR region to regulate the gene expression by transcriptional repression or induction of mRNA degradation. Increasing evidences suggest a new mechanism by which miRNAs may regulate target gene expression by binding to promoter and amino acid coding regions. Most of the existing databases on miRNAs are restricted to mRNA 3'-UTR region. To address this issue, we present miRWalk, a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat.

All mRNAs, mitochondrial genes and 10kb upstream flanking regions of all known genes of human, mouse and rat were analysed by using a newly developed algorithm named "miRWalk" as well as with 8 already established programs for putative miRNA binding sites. An automated and extensive text-mining search was performed on PubMed database to extract validated information on miRNAs. Combined information was put into a MySQL database (http://mirwalk.uni-hd.de/).

Area: Biology

Links:

• http://mirwalk.uni-hd.de/

Yang Zhang
Institut für Theoretische Physik
Universität Heidelberg

Prof. Dr. Dieter W. Heermann
Institut für Theoretische Physik
Universität Heidelberg

Despite many years of extensive studies the structure of the mitotic chromosome still remains unclear. The present work introduces a new probabilistic polymer model for mitotic chromosomes. The key assumption of the model is the ability of the chromatin fibre to crosslink to itself due to the dyanmic binding of proteins to the fiber. These protein-chromatin interactions were included by a probabilistic and dynamic mechanism. This is motivated by the observation of high repulsive forces between ring polymers. Computer simulations were performed to examine the validity of the model. Our results show that the presence of loops leads to a tight compaction and contributes significantly to the bending rigidity of chromosomes. Moreover, its qualitative prediction of the force elongation behaviour are close to experimental findings. The dynamic loop model indicates the crucial role of loops in mitotic chromosomes and a strong influence of their number and size on the mechanical properties. This shows that changes of these mechanical characteristics under different conditions can be explained by an altered loop structure.

Area: Physics, Biology

Markus Knodel
Goethe Center for Scientific Computing (GCSC)
Frankfurt University

Daniel Buchner
Department of Neurobiology, IZN
Heidelberg University

Romina Geiger
Department of Neurobiology, IZN
Heidelberg University

Alfio Grillo
Goethe Center for Scientific Computing (GCSC)
Frankfurt University

Guillian Queisser
Goethe Center for Scientific Computing (GCSC)
Frankfurt University

Christoph Schuster
Department of Neurobiology, IZN
Heidelberg University

Gabriel Wittum
Goethe Center for Scientific Computing (GCSC)
Frankfurt University

One aim of the burgeoning field of computational neuroscience is to produce highly realistic, quantitative models which accurately reproduce of the physical processes which underlie synaptic transmission. To truly appreciate the myriad of events which relate synaptic function and vesicle dynamics, simulations must be done in a spatially realistic environment. This holded true in particular in order to explain the rather astonishing motor patterns presented here which we observed within in vivo recordings which underlie peristaltic contractions at a well characterized synapse, the neuromuscular junction (NMJ) of the Drosophila larva. To this end, we have employed a reductionist approach and generated three dimensional models of single presynaptic boutons at the Drosophila larval NMJ. Vesicle dynamics are described by diffusion-like partial differential equations which are solved numerically on unstructured grids using the UG platform. In our model we varied parameters such as bouton-size, vesicle output probability (Po), stimulation frequency and number of synapses, to observe how altering these parameters effected bouton function. Hence we demonstrate that the morphologic and physiologic specialization maybe a convergent evolutionary adaptation to regulate the trade off between sustained, low output, and short term, high output, synaptic signals. There seems to be a biologically meaningful explanation for the co-existence of the two different bouton types as previously observed at the NMJ (characterized especially by the relation between size and Po), the assigning of two different tasks with respect to short- and long-time behaviour could allow for an optimized interplay of different synapse types. As a side product, we demonstrate how advanced methods from numerical mathematics could help in future to resolve also other difficult experimental neurobiological issues.

• Knodel M., Bucher D., Schuster C. and Wittum G. (2008): Mathematical modeling of the Drosophila neuromuscular junction. Frontiers in Computational Neuroscience. Conference Abstract: Bernstein Symposium 2008. online

Area: Biology/Mathematics

Software:

• UG

Links:

• http://www.dmspin.org/

Prof. Dr. Marcus Koch
Centre for Organismal Studies (COS Heidelberg)
Dept. Biodiversity and Plant Systematics
Universität Heidelberg

Dr. Roswitha Schmickl
Centre for Organismal Studies (COS Heidelberg)
Dept. Biodiversity and Plant Systematics
Universität Heidelberg

Crucifers (Brassicaceae) are a large plant family comprising approximately 338 genera and 3700 species. The family includes important crops as well as several model species in various fields of plant research. Meanwhile, there is a nearly complete coverage of a molecular-systematic characterisation of all genera. Additionally, numerous phylogenetic hypotheses, based on various genes from the plastome, nuclear, and mitochondrial DNA, are available and enable us to provide first robust and reliable family-wide phylogenetic trees. The Brassicaceae are characterised by frequently occurring hybridisation and polyploidisation events, which, as a consequence, greatly affect genome size and organisation. Interestingly, it is still unclear if the evolution of the Brassicaceae on the various taxonomic/temporal levels is best explained by multiple radiation events, which could account for the difficulties resolving deep phylogenies within the family. In this study we construct phylogenetic trees for each of the 46 currently recognised tribes within the Brassicaceae using Bayesian MCMC analyses (MrBayes v.3.1.2). We add genome size data and ploidy information across the whole family in order to unravel some principles of crucifer evolution. Another application for bwGRiD regards the field of population genetics within the genus Arabidopsis. This genus includes the plant scientists´ model plant A. thaliana as well as numerous other model and non-model organisms. We apply analyses using nuclear microsatellites to a large sampling of several thousand individuals in order to resolve population substructure and calculate, e.g., effective population size, migration rates, and gene flow with software such as Structure v.2.3.3 and LAMARC v.2.1.6.

Area: Biology

Software:

• MrBayes v.3.1.2, LAMARC v.2.1.6, Structure v.2.3.3

Prof. Dr. Marcus Koch
Centre for Organismal Studies (COS Heidelberg)
Dept. Biodiversity and Plant Systematics
Universität Heidelberg

Robert Karl
Centre for Organismal Studies (COS Heidelberg)
Dept. Biodiversity and Plant Systematics
Universität Heidelberg

As now the Brassicaceae family is structured in 46 monophyletic clades, phylogenetic studies will focus on the infrastructure of the respective clades. We are building up a phylogeny of the tribe Arabideae with a species coverage of over 90%. The Arabideae do not only include Draba L. (appr. 350 sp.), the largest genus within the Brassicaceae, but also Arabis (appr. 80 sp.), which has been notorious for its problematical taxonomical histories. Based mainly on convergent developments in fruit and trichome morphology the genus was an artificial aggregate of morphological more or less similar species with only a distant relationship. Based on molecular and cytological findings several species were excluded from the genus Arabis, and even from the tribe Arabideae. However, Arabis remains a paraphyletic genus and needs comprehensive molecular studies to establish monophyly and delimit its boundaries.

Using two molecular marker set (nrDNA ITS and cpDNA trnL-F) we construct trees with Bayesian MCMC analyses, which were performed with the mpi (message parsing interface) version of MrBayes v.3.1.2. Studies on Arabis' sister species Draba have shown that reconstruction of phylogenetic trees with large-scale data sets use up considerable time when run on a single computer. Therefore we employ the bwGRiD for any larger tree-construction.

Area: Biology

Software:

• MrBayes v.3.1.2

Prof. Dr. Marcus Koch
Centre for Organismal Studies (COS Heidelberg)
Dept. Biodiversity and Plant Systematics
Universität Heidelberg

Florian Michling
Centre for Organismal Studies (COS Heidelberg)
Dept. Biodiversity and Plant Systematics
Universität Heidelberg

Dianthus gratianopolitanus Vill. (Cheddar Pink, Pfingstnelke), a member of the Caryophyllaceae and endemic to Central Europe, grows nearly exclusively in rocky habitats, but is associated with different types of substrate, such as siliceous bedrocks, limestone/dolomite, serpentine, sandstone, and others. A distribution hot spot are the calciferous Jura Mountains in Germany (Baden-Württemberg) and Switzerland. In most other Central European countries few populations or metapopulations still exist.

The rare species is severely protected throughout its distribution range, being at the risk of becoming extinct in several regions, mostly because of the succession of grassland and woodland vegetation is closing the open, rocky habitats. Also, of course, the immediate effects of human leisure activities (hiking, climbing, collecting) pose a threat to the speicies. Metapopulations are widely isolated from each other and the plant is missing in several, potentially suitable locations, which often applies to the immediate vicinity of established populations. Mode and extent of sexual reproduction in this polyploid species (2n=4x/6x=60/90) are unknown.

In this project, we aim to investigate (a) genetic variability within and (b) genetic relationships among European populations using Amplified Fragment Length Polymorphisms (ALFP) and chloroplast-DNA (cpDNA) markers. Understanding the genetic structure on the population level may yield insights into whether there is a regional or general correlation between levels of genetic variation and diversity and population demography and history. We would learn more about the adaptational potential of this species, since it is a rare case that a highly endangered plant species in Central Europe does not prefer one single habitat type as defined by edaphic conditions.

The analyses of population genetic data involves computationally costly methods that will be carried out on the bw-GRiD infrastructure.

Area: Biology

Software:

• Structure 2.3, pritch.bsd.uchicago.edu/software.html

Tomasz Berezniak
Computational Molecular Biophysics
Interdisciplinary Center for Scientific Computing (IWR)
University of Heidelberg

Petra Imhof
Computational Molecular Biophysics
Interdisciplinary Center for Scientific Computing (IWR)
University of Heidelberg

Andres Jäschke
Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg

Jeremy C. Smith
Computational Molecular Biophysics
Interdisciplinary Center for Scientific Computing (IWR)
University of Heidelberg

Ribozymes, that is, ribonucleic acid enzymes, are capable of both catalyzing chemical reactions and storing genetic information. These two features support the hypothesis of a preprotein "RNA world". Ribozymes have been found in nature to mediate phosphodiester bond formation and cleavage and peptide bond formation reactions. Further, artificial ribozymes have been shown to catalyze a broad array of other chemical reactions. These findings suggest that in vitro-selected ribozymes may be regarded as analogues of the missing links in the transition from an RNA world to the present, protein-dominated life. Among the artificial ribozymes, an in vitro-evolved Diels-Alderase ribozyme has been found to accelerate the formation of carbon-carbon bonds between anthracene dienes and maleimide dienophiles, presumably by a [4 + 2] cycloaddition reaction. Catalysis proceeds with multiple-turnover catalytic reactions and high enantioselectivity in a bimolecular fashion. Reactions of this type, that is, creating simultaneously two new C-C bonds and up to four new stereocenters, have broad applications in organic chemistry and may have been essential in preprotein chemistry for a complex metabolism based on RNA.

We have examined the Diels-Alderase ribozyme via molecular dynamics (MD) simulations in both crystalline and aqueous solution environments. Our simulations indicate that the catalytic pocket is highly dynamic. At low magnesium ion concentrations, inactive states with the catalytic pocket closed dominate. Stabilization of the enzymatically active, open state of the catalytic pocket requires a high concentration of magnesium ions (e.g., 54 mM), with cations binding to specific phosphate sites on the backbone of the residues bridging the opposite strands of the pocket. The free energy profile for pocket opening at high magnesium cation concentration exhibits a double minimum, with a barrier to opening of ∼5.5 kJ/mol and the closed state ∼3 kJ/mol lower than the open state. Selection of the open state on substrate binding leads to the catalytic activity of the ribozyme. The simulation results explain structurally the experimental observation that full catalytic activity depends on the magnesium ion concentration.

In the present project we will carry out solution MD simulations of the Diels-Alderase ribozyme using the NAMD package with the CHARMM27 nucleic acids force field as the potential energy function. The four systems of study, that is, with bound substrate or product, each in both possible stereo-conformations, will be prepared using the crystallographic structure of the ribozyme with bound product. Each production run will be up to 100 ns long, thus the number and length of the trajectories will allow to probe stability of the system with either substrate or product bound within the catalytic pocket in different conformations. Ribozyme internal dynamics as well as binding modes of enzyme-ligand interactions will be analyzed with atomic resolution. Furthermore, steered MD simulations will be performed allowing to obtain free energy profile upon binding of reactants, and dissociation of product. These results will be compared with the experimental findings.

• Berezniak, T., Zahran, M., Imhof, P., Jäschke, A., and Smith, J. C., Magnesium-Dependent Active-Site Conformational Selection in the Diels-Alderase Ribozyme, J. Am. Chem. Soc., 132 (2010), 12587-12596; online
• Oak Ridge National Laboratory press release about the article

Area: Biology