Estimating the fitness effect of an insertion sequence.

Since its discovery, mobile DNA has fascinated researchers. In particular, many researchers have debated why insertion sequences persist in prokaryote genomes and populations. While some authors think that insertion sequences persist only because of occasional beneficial effects they have on their hosts, others argue that horizontal gene transfer is strong enough to overcome their generally detrimental effects.

Mobile DNA can drive lineage extinction in prokaryotic populations.

Natural selection ultimately acts on genes and other DNA sequences. Adaptations that are good for the gene can have adverse effects at higher levels of organization, including the individual or the population. Mobile genetic elements illustrate this principle well, because they can self-replicate within a genome at a cost to their host.

The early phase of a bacterial insertion sequence infection.

Bacterial insertion sequences are the simplest form of autonomous mobile DNA. It is unknown whether they need to have beneficial effects to infect and persist in bacterial populations, or whether horizontal gene transfer suffices for their persistence. We address this question by using branching process models to investigate the critical, early phase of an insertion sequence infection.

A survey of bacterial insertion sequences using IScan.

Bacterial insertion sequences (ISs) are the simplest kinds of bacterial mobile DNA. Evolutionary studies need consistent IS annotation across many different genomes. We have developed an open-source software package, IScan, to identify bacterial ISs and their sequence elements--inverted and target direct repeats--in multiple genomes using multiple flexible search parameters.

Context-dependent stimulus presentation to freely moving animals in 3D.

The presentation of controllable, dynamic sensory stimuli provides a powerful experimental paradigm, which has been extensively applied to explore sensory processing in walking and tethered flying insects. Recent advances in computer hardware and software technology provide the opportunity to track the 3D flight path of free-flying insects and process these data in real-time, opening up the possibility to present dynamic stimuli to free-flying animals. To accommodate for the increased complexity relating to 3D space, we partitioned experimental design, real-time data acquisition and stimulus control into multiple self-contained modules.