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den Bakker, H.

Publications and source records attributed to den Bakker, H..

3 recordsLinked to original sources

Neurons in the medial prefrontal cortex that are not modulated by hippocampal sharp-wave ripples are involved in spatial tuning and signaling upcoming choice.

The hippocampus is known to encode spatial information and reactivate experienced trajectories during sharp-wave ripple events. These events are thought to be key time-points at which information about learned trajectories is transferred to the neocortex for long-term storage. It is unclear, however, how this information may be transferred and integrated in downstream cortical regions. In this study, we performed high-density probe recordings across the full depth of the medial prefrontal cortex and in the hippocampus simultaneously in rats while they were performing a task of spatial navigation. We find that neurons in the medial prefrontal cortex encode spatial information and reliably predict upcoming choice on a maze, and we find that a subset of neurons in the mPFC is modulated by hippocampal sharp-wave ripples. However, sharp-wave ripple modulation does not appear to be the main driving factor in predicting upcoming choice. This indicates that the integration of spatial information requires the collaboration of different specialized populations of neurons.

neuroscience↗

Sharp-wave ripple associated activity in the medial prefrontal cortex supports spatial rule switching

Previous studies have highlighted an important role for hippocampal sharp-wave ripples in spatial alternation learning, as well as modulating activity in the medial prefrontal cortex (mPFC). However, no study so far has investigated the direct influence of hippocampal sharp-wave ripples on mPFC activity during spatial alternation learning. Long Evans rats were trained on a three-arm radial maze to perform a sequence of alternations. Three different alternation sequences needed to be learnt, and while learning a new sequence, the activity in the mPFC was inhibited either directly following sharp-wave ripples in the hippocampus (on-time condition) or with a randomized delay (delayed condition). In the on-time condition the behavioral performance was significantly worse compared to the same animals in the delayed inhibition condition, as measured by a lower correct alternation performance and more perseverative behavior. This indicates that the activity in the mPFC directly following hippocampal sharp-wave ripples is necessary for spatial rule switching.

neuroscience↗

Real-time search of all bacterial and viral genomic data

Genome sequencing of pathogens is now ubiquitous in microbiology, and the sequence archives are effectively no longer searchable for arbitrary sequences. Furthermore, the exponential increase of these archives is likely to be further spurred by automated diagnostics. To unlock their use for scientific research and real-time surveillance we have combined knowledge about bacterial genetic variation with ideas used in web-search, to build a DNA search engine for microbial data that can grow incrementally. We indexed the complete global corpus of bacterial and viral whole genome sequence data (447,833 genomes), using four orders of magnitude less storage than previous methods. The method allows future scaling to millions of genomes. This renders the global archive accessible to sequence search, which we demonstrate with three applications: ultra-fast search for resistance genes MCR1-3, analysis of host-range for 2827 plasmids, and quantification of the rise of antibiotic resistance prevalence in the sequence archives.

bioinformatics↗