Biology subjects

Jung, D.

Publications and source records attributed to Jung, D..

23 records · Page 2Linked to original sources

bioRxiv2019

Place cell map genesis via competitive learning and conjunctive coding in the dentate gyrus

Place cells exhibit spatially selective firing fields and collectively map the continuum of positions in environments; how such network pattern develops with experience remains unclear. Here, we recorded putative granule (GC) and mossy (MC) cells from the dentate gyrus (DG) over 27 days as mice repetitively ran through a sequence of objects fixed onto a treadmill belt. We observed a progressive transformation of GC spatial representations, from a sparse encoding of object locations and periodic spatial intervals to increasingly more single, evenly dispersed place fields, while MCs showed little transformation and preferentially encoded object locations. A competitive learning model of the DG reproduced GC transformations via the progressive integration of landmark-vector cells and grid cell inputs and required MC-mediated feedforward inhibition to evenly distribute GC representations, suggesting that GCs progressively encode conjunctions of objects and spatial information via competitive learning, while MCs help homogenize GC spatial representations.

neuroscience↗

bioRxiv2019

SpCas9 activity prediction by DeepCas9, a deep learning-based model with unparalleled generalization performance

We evaluated SpCas9 activities at 12,832 target sequences using a high-throughput approach based on a human cell library containing sgRNA-encoding and target sequence pairs. Deep learning-based training on this large data set of SpCas9-induced indel frequencies led to the development of a SpCas9-activity predicting model named DeepSpCas9. When tested against independently generated data sets (our own and those published by other groups), DeepSpCas9 showed unprecedentedly high generalization performance. DeepSpCas9 is available at http://deepcrispr.info/DeepCas9.

genetics↗

bioRxiv2019

Scopolamine and medial frontal stimulus-processing during interval timing

Neurodegenerative diseases such as Parkinsons disease (PD), dementia with Lewy Bodies (DLB), and Alzheimers disease (AD) involve loss of cholinergic neurons in the basal forebrain. Here, we investigate how cholinergic dysfunction impacts the frontal cortex during interval timing, a process that can be impaired in PD and AD patients. Interval timing requires participants to estimate an interval of several seconds by making a motor response, and depends on the medial frontal cortex (MFC), which is richly innervated by basal forebrain cholinergic projections. Past work has shown that scopolamine, a muscarinic cholinergic receptor antagonist, reliably impairs interval timing. We tested the hypothesis that scopolamine would attenuate time-related ramping, a key form of temporal processing in the MFC. We recorded neuronal ensembles from 8 mice during performance of a 12-s fixed-interval timing task, which was impaired by the administration of scopolamine. Consistent with past work, scopolamine impaired timing. To our surprise, we found that time-related ramping was unchanged, but stimulus-related activity was enhanced in the MFC. Principal component analyses revealed no consistent changes in time-related ramping components, but did reveal changes in higher components. Taken together, these data indicate that scopolamine changes stimulus-processing rather than temporal processing in the MFC. These data could help understand how cholinergic dysfunction affects cortical circuits in diseases such as PD, DLB, and AD.\n\nHighlightsO_LIThe cholinergic muscarinic inhibitor scopolamine impairs interval timing behavior.\nC_LIO_LIScopolamine does not change time-related ramping activity in the medial frontal cortex.\nC_LIO_LIMedial prefrontal stimulus-related modulation increased\nC_LI

neuroscience↗

bioRxiv2019

Cultivating in situ triggers growth of previously uncultivated microorganisms via a growth initiation factor in nature

Most microorganisms resist cultivation under standard laboratory conditions. On the other hand, to cultivate microbes in a membrane-bound device incubated in nature (in situ cultivation) is an effective approach. In the present study, we applied in situ cultivation to isolate diverse previously uncultivated marine sponge-associated microbes and comparatively analyzed this methods efficiencies with those of the conventional method. Then, we attempted to clarify the key and unknown mechanism of in situ cultivation by focusing on growth triggering via growth initiation factor. We hypothesized that majority of environmental microorganisms are in nongrowing state and requiring \"growth initiation factor\" for the recovery and that can be provided from environments. Consequently, significantly more novel and diverse microbial types were isolated via in situ cultivation than by standard direct plating (SDP). Next, the effect of the sponge extract on starvation recovery was compared between strains derived from in situ and SDP cultivation. Adding small amounts of the sponge extracts to the medium elevated the colony-formation efficiencies of the in situ strains at the starvation recovery step, while it showed no positive effect on that of SDP strains. Conversely, specific growth rates or carrying capacities of all tested strains were not positively affected. These results indicate that, 1) the sponge extract contains chemical compounds that facilitate starvation recovery, these substances selectively worked on the in situ strains, and 2) growth initiation factor in the sponge extract did not continuously promote growth activity but worked as triggers for regrowth (resuscitation from dormancy).\n\nImportanceMost microbial species resist cultivation under laboratory condition. This is critical impediment for both academic and applied microbiology, and thus clarification of the mechanism of microbial uncultivability is highly demanded. Several evidences have been reported that to cultivate microbes in a membrane-bound device incubated in nature (in situ cultivation) is an effective approach. However, the mechanism behind this approach has not been clarified. The present study shows the evidence that 1) initiating growth is a key for cultivating previously uncultivated microbes rather than simple growth promotion, and 2) growth initiation factor (signaling-like compounds) in natural environments stimulate microbial resuscitation from a nongrowing state. Since no study has focused on growth initiation for cultivation of previously uncultivated microorganisms, the discovery shown in the present study provides a new insight into microorganisms previously considered uncultivable and a microbial growth controlling system in nature.

microbiology↗

bioRxiv2018

ShinyGO: a graphical enrichment tool for animals and plants

MotivationGene lists are routinely produced from various genome-wide studies. Enrichment analysis can link these gene lists with underlying molecular pathways by using functional categories such as gene ontology (GO).\n\nResultsTo complement existing tools, we developed ShinyGO with several features: (1) large annotation database from GO and many other sources for over 200 plant and animal species, (2) graphical visualization of enrichment results and gene characteristics, and (3) application program interface (API) access to KEGG and STRING for the retrieval of pathway diagrams and protein-protein interaction networks. ShinyGO is an intuitive, graphical web application that can help researchers gain actionable insights from gene lists.\n\nAvailabilityhttp://ge-lab.org/go/\n\nContactgexijin@gmail.com\n\nSupplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗