Biology subjects

Jang, J.

Publications and source records attributed to Jang, J..

64 records · Page 4Linked to original sources

bioRxiv2019

Simultaneous development and periodic clustering of simple and complex cells in visual cortex

Neurons in the primary visual cortex (V1) are often classified as simple or complex cells, but it is debated whether they are discrete hierarchical classes of neurons developing sequentially, or if they represent a continuum of variation within a single class of cells developing simultaneously. Herein, we show that simple and complex cells may arise simultaneously from the universal process of retinal development. From analysis of the cortical receptive fields in cats, we show evidence that simple and complex cells originate from the periodic variation of ON-OFF segregation in the feedforward projection of retinal mosaics, by which they organize into periodic clusters in V1. Our key prediction that clusters of simple and complex cells correlate topographically with orientation maps was confirmed by data in cats. Our results suggest that simple and complex cells are not two distinct neural populations but arise from common retinal afferents, simultaneous with orientation tuning.\n\nHighlightsO_LISimple and complex cells arise simultaneously from retinal afferents.\nC_LIO_LISimple/complex cells are organized into periodic clusters across visual cortex.\nC_LIO_LISimple/complex clusters are topographically correlated with orientation maps.\nC_LIO_LIDevelopment of clustered cells in V1 is explained by the Paik-Ringach model.\nC_LI

neuroscience↗

bioRxiv2019

Green, orange, red, and far-red optogenetic tools derived from cyanobacteriochromes

Existing optogenetic tools for controlling protein-protein interactions are available in a limited number of wavelengths thereby limiting opportunities for multiplexing. The cyanobacteriochrome (CBCR) family of photoreceptors responds to an extraordinary range of colors, but light-dependent binding partners for CBCR domains are not currently known. We used a phage-display based approach to develop small (~50-residue) monomeric binders selective for the green absorbing state (Pg), or for the red absorbing state (Pr) of the CBCR Am1_c0023g2 with a phycocyanobilin chromophore and also for the far-red absorbing state (Pfr) of Am1_c0023g2 with a biliverdin chromophore. These bind in a 1:1 mole ratio with KDs for the target state from 0.2 to 2 M and selectivities from 10 to 500-fold. We demonstrate green, orange, red, and far-red light-dependent control of protein-protein interactions in vitro and also in vivo where these multicolor optogenetic tools are used to control transcription in yeast.

synthetic biology↗

bioRxiv2019

Loss of BubR1 Acetylation instigates Replication Stress leading to Complex Chromosomal Rearrangement in tumors

Chromosome number and structure instability is the hallmark of cancer. Equal chromosome segregation is guaranteed by the spindle assembly checkpoint (SAC), thus defective SAC leads to chromosome instability. However, aneuploidy alone is not oncogenic, and whether compromised SAC is associated with structure instability remains elusive. BubR1 is a core component of SAC, which is acetylated at lysine 250 in mitosis. Previously, we showed that deficiency of BubR1 acetylation in mice (K243R/+) leads to spontaneous tumorigenesis via chromosome mis-segregation. Here, we asked whether loss of BubR1 acetylation is associated with chromosome structure instability by examining K243R/+ mice intercrossed to p53-deficient mice. Genome-wide sequencing and spectral karyotyping of the double mutant mouse tumors revealed that BubR1 acetylation deficiency leads to complex chromosome rearrangements, including Robertsonian-like whole-arm translocations and premature sister-chromatid separations (PMSCS). In primary MEFs, replication stress was markedly increased in telomeres and centromeres, suggesting that the replication stress underlies the significant increase of DNA damage and subsequent chromosome rearrangements. Furthermore, defects in BubR1 acetylation at K250 were detected in human cancers as well. Collectively, we propose that chromosome mis-segregation by the loss of BubR1 acetylation causes chromosome structure instability, leading to massive chromosome rearrangements through the induction of replication stress.

cancer biology↗

bioRxiv2019

Classification of columnar and salt-and-pepper organization in mammalian visual cortex

In mammalian visual cortex, neural tuning to stimulus orientation is organized in either columnar1 or salt- and-pepper2 patterns across species. This is often considered to reflect disparate mechanisms of cortical development across mammalian taxa. However, it is unknown whether different cortical architectures are generated by species-specific mechanisms3,4, or simply originate from the variation of biological parameters within a universal principle of development5-8. We analysed neural parameters in eight mammalian species and found that cortical organization is predictable by a single factor: the retino-cortical mapping ratio. We show that a Nyquist sampling model explains parametric division of the patterns with high accuracy and that simulations of controlled mapping conditions reproduce both types of organization. Our results explain the origin of distinct cortical circuits under a universal development process.

neuroscience↗

bioRxiv2019

Holding the arm still through subcortical mathematical integration of cortical commands

A period of holding still follows every movement. It has been assumed that for the arm, moving and holding are functionally independent: movement is via an adaptive, feedback-dependent controller that generates commands to transport the arm, while holding is via setting of reflexes that produce a postural field at movement endpoint. This assumption predicts that commands that move the arm should not affect the postural field at movement termination. Surprisingly, we found that as the reach commands changed, so did the ensuing postural field. The postural commands depended on mathematical integration of the reach commands. Following damage to the corticospinal tract, despite severe reach impairments, the holding system faithfully integrated the imperfect reach commands on a trial-by-trial basis. Together, these findings suggest that holding the arm still is accomplished via a separate, likely subcortical structure that acts as a mathematical integrator of the commands generated by the cortical reach controller.

neuroscience↗

bioRxiv2018

RUNX3 regulates cell cycle-dependent chromatin dynamics by functioning as a pioneer factor of the restriction point

The cellular decision regarding whether to undergo proliferation or death is made at the restriction (R)-point, which is disrupted in nearly all tumors. The identity of the molecular mechanisms that govern the R-point decision is one of the fundamental issues in cell biology. We found that early after mitogenic stimulation, RUNX3 bound to its target loci, where it opened chromatin structure by sequential recruitment of Trithorax group proteins and cell-cycle regulators to drive cells to the R-point. Soon after, RUNX3 closed these loci by recruiting Polycomb repressor complexes, causing the cell to pass through the R-point toward S phase. If the RAS signal was constitutively activated, RUNX3 inhibited cell cycle progression by maintaining R-point-associated genes in an open structure. Our results identify RUNX3 as a pioneer factor for the R-point and reveal the molecular mechanisms by which appropriate chromatin modifiers are selectively recruited to target loci for appropriate R-point decisions.

cell biology↗

bioRxiv2018

Universality of the developmental origins of diverse functional maps in the visual cortex

The primary visual cortex of higher mammals is organized into diverse functional maps of correlated topography, implying an efficient tiling of functional domains. However, no fundamental principle is available on how systematic organization of the maps could develop initially in various species. Here, we propose that diverse functional maps are seeded from a common framework of retinal afferents, and that this universality of development explains the observed topographical correlations among the maps. From the simulation of retinal ganglion cell mosaics, we successfully developed all four cortical maps observed so far. We validated our model prediction of inter-map relationships from analysis of map data in evolutionarily divergent mammalian species. Our key prediction, the hexagonal periodicity of every functional map, was validated from analysis of the map data in diverse mammalian species. Our results provide new insight into a universal mechanism for the development and evolution of the visual cortex.

neuroscience↗

bioRxiv2018

How small-molecule inhibitors of dengue-virus infection interfere with viral membrane fusion

Dengue virus (DV) is a compact, icoshedrally symmetric, enveloped particle, covered by 90 dimers of envelope protein (E), which mediates viral attachment and membrane fusion. Fusion requires a dimer-to-trimer transition and membrane engagement of hydrophobic \"fusion loops\". We previously characterized the steps in membrane fusion for the related West Nile virus (WNV), using recombinant, WNV virus-like particles (VLPs) for single-particle experiments. Trimerization and membrane engagement are rate-limiting; fusion requires at least two adjacent trimers; availability of competent monomers within the contact zone between virus and target membrane creates a trimerization bottleneck. We have extended that work to dengue VLPs, from all four DV serotypes, finding an essentially similar mechanism. Small-molecule inhibitors of DV infection that target E block its fusion-inducing conformation change. We show that [~]15 bound molecules per particle ([~]8.5 % occupancy) completely prevent fusion, in accord with the proposed mechanism and the likely inhibitor binding site on E.\n\nImpact statementSingle-particle studies of dengue-virus membrane fusion and the effect of small-molecule inhibitors of infection clarify the viral fusion mechanism.

biophysics↗

bioRxiv2017

KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses

High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations. Herein, we report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals with an average coverage depth of 31x. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project data when prioritizing disease-causing variants. CNV analyses revealed gene losses related to bone mineral densities and duplicated genes involved in brain development and fat reduction. Finally, KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.

genomics↗

bioRxiv2017

Recording action potential propagation in single axons using multi-electrode arrays

The small caliber of central nervous system (CNS) axons makes routine study of axonal physiology relatively difficult. However, while recording extracellular action potentials from neurons cultured on planer multi-electrode arrays (MEAs) we found activity among groups of electrodes consistent with action potential propagation in single neurons. Action potential propagation was evident as widespread, repetitive cooccurrence of extracellular action potentials (eAPs) among groups of electrodes. These eAPs occurred with invariant sequences and inter-electrode latencies that were consistent with reported measures of action potential propagation in unmyelinated axons. Within co-active electrode groups, the inter-electrode eAP latencies were temperature sensitive, as expected for action potential propagation. Our data are consistent with these signals primarily reflecting axonal action potential propagation, from axons with a high density of voltage-gated sodium channels. Repeated codetection of eAPs by multiple electrodes confirmed these eAPs are from individual neurons and averaging these eAPs revealed sub-threshold events at other electrodes. The sequence of electrodes at which eAPs co-occur uniquely identifies these neurons, allowing us to monitor spiking of single identified neurons within neuronal ensembles. We recorded dynamic changes in single axon physiology such as simultaneous increases and decreases in excitability in different portions of single axonal arbors over several hours. Over several weeks, we measured changes in inter-electrode propagation latencies and ongoing changes in excitability in different regions of single axonal arbors. We recorded action potential propagation signals in human induced pluripotent stem cell-derived neurons which could thus be used to study axonal physiology in human disease models.\n\nSignificance StatementStudying the physiology of central nervous system axons is limited by the technical challenges of recording from axons with pairs of patch or extracellular electrodes at two places along single axons. We studied action potential propagation in single axonal arbors with extracellular recording with multi-electrode arrays. These recordings were non-invasive and were done from several sites of small caliber axons and branches. Unlike conventional extracellular recording, we unambiguously identified and labelled the neuronal source of propagating action potentials. We manipulated and quantified action potential propagation and found a surprisingly high density of axonal voltage-gated sodium channels. Our experiments also demonstrate that the excitability of different portions of axonal arbors can be independently regulated on time scales from hours to weeks.

neuroscience↗