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Hoeger, M.

Publications and source records attributed to Hoeger, M..

3 recordsLinked to original sources

The P600 during sentence reading predicts behavioral and neural markers of recognition memory

The P600 ERP component is elicited by a wide range of anomalies and ambiguities during sentence comprehension and remains important for neurocognitive models of language processing. It has been proposed that the P600 is a more domain-general component, signaling phasic norepinephrine release from the locus coeruleus in response to salient stimuli that require attention and behavioral adaptation. Since such norepinephrine release promotes explicit memory formation, we here investigated whether the P600 during sentence reading (encoding) is thus predictive of such explicit memory formation using a subsequent old/new word recognition task. Indeed, the P600 amplitude during our encoding task was related to behavioral recognition effects in the memory task on a trial-by-trial basis, though only for one type of violation. Recognition performance was better for semantically, but not syntactically violated words that had previously elicited a larger P600. However, the P600 to both types of violations during encoding was positively related to a more subtle, neural marker of recognition, namely the amplitude of the recollection ERP component in response to old words. In sum, we find that the P600 predicts later recognition memory both on the behavioral and neural level. Such explicit memory effects further link the late positivity to norepinephrine activity, suggesting a more domain-general nature of the component. The connection between the P600 and later recognition indicates that the neurocognitive processes that deal with salient and anomalous aspects in the linguistic input in the moment will also be involved in keeping this event available for later recognition.

neuroscience↗

Hi-C yields chromosome-length scaffolds for a legume genome, Trifolium subterraneum

We present a chromosome-length assembly of the genome of subterranean clover, Trifolium subterraneum, a key Australian pasture legume. Specifically, in situ Hi-C data (48X) was used to correct misjoins and anchor, order, and orient scaffolds in a previously published genome assembly (TSUd_r1.1; scaffold N50: 287kb). This resulted in an improved genome assembly (TrSub3; scaffold N50: 56Mb) containing eight chromosome-length scaffolds that span 95% of the sequenced bases in the input assembly.

genomics↗

The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000

Hi-C contact maps are valuable for genome assembly (Lieberman-Aiden, van Berkum et al. 2009; Burton et al. 2013; Dudchenko et al. 2017). Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al. 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al. 2017). Here, we introduce \"Assembly Tools,\" a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly. Together, 3D-DNA and the Juicebox Assembly Tools greatly reduce the cost of accurately assembling complex eukaryotic genomes. To illustrate, we generated de novo assemblies with chromosome-length scaffolds for three mammals: the wombat, Vombatus ursinus (3.3Gb), the Virginia opossum, Didelphis virginiana (3.3Gb), and the raccoon, Procyon lotor (2.5Gb). The only inputs for each assembly were Illumina reads from a short insert DNA-Seq library (300 million Illumina reads, maximum length 2x150 bases) and an in situ Hi-C library (100 million Illumina reads, maximum read length 2x150 bases), which cost <$1000.

genomics↗