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Dual daughter strand incision is processive and increases the efficiency of DNA mismatch repair
(2016)Nucleic Acids ResearchDNA mismatch repair (MMR) is an evolutionarily-conserved process responsible for the repair of replication errors. In Escherichia coli, MMR is initiated by MutS and MutL, which activate MutH to incise transiently-hemimethylated GATC sites. MMR efficiency depends on the distribution of these GATC sites. To understand which molecular events determine repair efficiency, we quantitatively studied the effect of strand incision on unwinding and ...Journal Article -
Analysis of neural crest-derived clones reveals novel aspects of facial development
(2016)Science AdvancesCranial neural crest cells populate the future facial region and produce ectomesenchyme-derived tissues, such as cartilage, bone, dermis, smooth muscle, adipocytes, and many others. However, the contribution of individual neural crest cells to certain facial locations and the general spatial clonal organization of the ectomesenchyme have not been determined. We investigated how neural crest cells give rise to clonally organized ectomesenchyme ...Journal Article -
Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data
(2016)Molecular Biology and EvolutionWhen viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of ...Journal Article -
SEX-DETector: A Probabilistic Approach to Study Sex Chromosomes in Non-Model Organisms
(2016)Genome Biology and EvolutionWe propose a probabilistic framework to infer autosomal and sex-linked genes from RNA-seq data of a cross for any sex chromosome type (XY, ZW, and UV). Sex chromosomes (especially the non-recombining and repeat-dense Y, W, U, and V) are notoriously difficult to sequence. Strategies have been developed to obtain partially assembled sex chromosome sequences. Most of them remain difficult to apply to numerous non-model organisms, either ...Journal Article -
SBtab: a flexible table format for data exchange in systems biology
(2016)BioinformaticsSummary: SBtab is a table-based data format for Systems Biology, designed to support automated data integration and model building. It uses the structure of spreadsheets and defines conventions for table structure, controlled vocabularies and semantic annotations. The format comes with predefined table types for experimental data and SBML-compliant model structures and can easily be customized to cover new types of data. Availability and ...Journal Article -
Synergy between NMR measurements and MD simulations of protein/RNA complexes: Application to the RRMs, the most common RNA recognition motifs
(2016)Nucleic Acids ResearchRNA recognition motif (RRM) proteins represent an abundant class of proteins playing key roles in RNA biology. We present a joint atomistic molecular dynamics (MD) and experimental study of two RRM-containing proteins bound with their single-stranded target RNAs, namely the Fox-1 and SRSF1 complexes. The simulations are used in conjunction with NMR spectroscopy to interpret and expand the available structural data. We accumulate more than ...Journal Article -
Domain morphology, boundaries, and topological defects in biophotonic gyroid nanostructures of butterfly wing scales
(2016)Science AdvancesMany organisms in nature have evolved sophisticated cellular mechanisms to produce photonic nanostructures and, in recent years, diverse crystalline symmetries have been identified and related to macroscopic optical properties. However, because we know little about the distributions of domain sizes, the orientations of photonic crystals, and the nature of defects in these structures, we are unable to make the connection between the ...Journal Article -
Engineering a ribozyme cleavage-induced split fluorescent aptamer complementation assay
(2016)Nucleic Acids ResearchHammerhead ribozymes are self-cleaving RNA molecules capable of regulating gene expression in living cells. Their cleavage performance is strongly influenced by intra-molecular loop–loop interactions, a feature not readily accessible through modern prediction algorithms. Ribozyme engineering and efficient implementation of ribozyme-based genetic switches requires detailed knowledge of individual self-cleavage performances. By rational ...Journal Article -
Motivational state, reward value, and Pavlovian cues differentially affect skilled forelimb grasping in rats
(2016)Learning and MemoryMotor skills represent high-precision movements performed at optimal speed and accuracy. Such motor skills are learned with practice over time. Besides practice, effects of motivation have also been shown to influence speed and accuracy of movements, suggesting that fast movements are performed to maximize gained reward over time as noted in previous studies. In rodents, skilled motor performance has been successfully modeled with the ...Journal Article -
The Effects of Coloured LED Light on Behaviour and Physiology in Healthy Horses
(2016)Open Biological Sciences JournalThe use of colour light therapy to treat diseases and disorders in animals is increasingly common but only very little research has been conducted on the effects of illumination with coloured light. The present study examined to which extent coloured light causes behavioural and physiological responses in horses. Red, green, blue and yellow as well as white as a control colour were tested in 20 healthy stallions of the breed Freiberger. ...Journal Article