Biology subjects

Shin, H.

Publications and source records attributed to Shin, H..

5 recordsLinked to original sources

bioRxiv2018

Developmental fidelity imposed by the RGL-1 balanced switch mediating opposing signals

The six C. elegans vulval precursor cells (VPCs) are induced to form the 30-30-20-{Gamma}-20-3{degrees} pattern of cell fates with high fidelity. In response to EGF signal, the LET-60/Ras-LIN-45/Raf-MEK-2/MEK-MPK-1/ERK canonical MAP kinase cascade is necessary to induce 1{degrees} fate and synthesis of DSL ligands. In turn, LIN-12/Notch signal is necessary to induce neighboring cells to become 2{degrees}. We previously showed that, in response to lower dose of EGF signal, the modulatory LET-60/Ras-RGL-1/RalGEF-RAL-1/Ral signal promotes 2{degrees} fate in support of LIN-12. In this study we identify two key differences between RGL-1 and RAL-1 functions. First, deletion of RGL-1 confers no overt developmental defects, while previous studies showed RAL-1 to be essential for viability and fertility. From this observation we hypothesize that the developmentally essential functions of RAL-1 are independent of upstream activation. Second, RGL-1 plays opposing and genetically separable roles in VPC fate patterning. RGL-1 promotes 2{degrees} fate via canonical GEF-dependent activation of RAL-1 and 1{degrees} fate via a non-canonical GEF-independent activity. Our genetic epistasis experiments are consistent with RGL-1 functioning in the modulatory 1{degrees}-promoting AGE-1/PI3-Kinase-PDK-1-AKT-1 cascade. Additionally, animals without RGL-1 experience 15-fold higher rates of VPC patterning errors compared to the wild type. Yet VPC patterning in RGL-1 deletion mutants is not more sensitive to environmental perturbations. We propose that RGL-1 functions as a \"Balanced Switch\" that orchestrates opposing 1{degrees}- and 2{degrees}-promoting modulatory cascades to decrease inappropriate fate decisions. We speculate that such switches are broadly conserved but mostly masked by paralog redundancy or essential genes.

genetics↗

bioRxiv2018

Ral signals through a MAP4 Kinase-p38 MAP kinase cascade in C. elegans cell fate patterning.

C. elegans vulval precursor cell (VPC) fates are patterned by an EGF gradient. High dose EGF induces 1{degrees} VPC fate, while lower dose EGF contributes to 2{degrees} fate in support of LIN-12/Notch. We previously showed that the EGF 2{degrees}-promoting signal is mediated by LET-60/Ras switching effectors, from the canonical Raf-MEK-ERK MAP kinase cascade that promotes 1{degrees} fate to the non-canonical RalGEF-Ral that promotes 2{degrees} fate. Of oncogenic Ras effectors, RalGEF-Ral is by far the least well-understood. We use genetic analysis to identify an effector cascade downstream of C. elegans RAL-1/Ral, starting with an established Ral binding partner, Exo84 of the exocyst complex. Additionally, RAL-1 signals through GCK-2, a CNH domain-containing MAP4 kinase, and PMK-1/p38 MAP kinase cascade to promote 2{degrees} fate. Our study delineates a Ral-dependent developmental signaling cascade in vivo, thus providing the mechanism by which lower EGF dose is transduced.

developmental biology↗

bioRxiv2018

Persistent Gamma Spiking in Non-Sensory Fast-Spiking Cells Predicts Perceptual Success

Persistent gamma oscillations (30-55Hz) are hypothesized to temporally coordinate stimulus encoding, enabling perception. This prediction poses a conundrum: How can gamma serve as a template when the stimulus itself drives its mediators, presumably perturbing its maintenance? Specifically, fast-spiking interneurons (FS), a key gamma generator, can be highly sensory responsive. Further, the gamma-band local field potential (LFP) shows properties inconsistent with temporal coordination. Combining tetrode recording with controlled psychophysics revealed an FS subtype ({gamma}nsFS) that was not sensory responsive, whose inter-spike intervals peaked at gamma, and that fired with higher periodicity than other FS. Successful detection was predicted by increased regularity in {gamma}nsFS spiking at gamma, persisting from before to after sensory onset. In contrast, gamma LFP power negatively predicted detection, and was negatively related to gamma band spiking by {gamma}nsFS. These results suggest that a distinct interneuron subgroup, not distracted by sensory input, mediates perceptually-relevant oscillations independent of LFP.

neuroscience↗

bioRxiv2017

The rate of transient beta frequency events predicts impaired function across tasks and species

Beta frequency oscillations (15-29Hz) are among the most prominent signatures of brain activity. Beta power is predictive of many healthy and abnormal behaviors, including perception, attention and motor action. Recent evidence shows that in non-averaged signals, beta can emerge as transient high-power \"events\". As such, functionally relevant differences in averaged power across time and trials can reflect accumulated changes in the number, power, duration, and/or frequency span of the events. We show for the first time that functionally relevant differences in averaged prestimulus beta power in human sensory neocortex reflects a difference in the number of high-power beta events per trial, i.e., the rate of events. Further, high power beta events close to the time of the stimulus were more likely to impair perception. This result is consistent across detection and attention tasks in human magnetoencephalography (MEG) and is conserved in local field potential (LFP) recordings of mice performing a detection task. Our findings suggest transient brain rhythms are best viewed as a \"rate metric\" in their impact on function, and provides a new framework for understanding and manipulating functionally relevant rhythmic events.

neuroscience↗

bioRxiv2017

PGS: a dynamic and automated population-based genome structure software

Hi-C technologies are widely used to investigate the spatial organization of genomes. However, the structural variability of the genome is a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range/interchromosomal interactions. We pioneered a probabilistic approach for generating a population of distinct diploid 3D genome structures consistent with all the chromatin-chromatin interaction probabilities from Hi-C experiments. Each structure in the population is a physical model of the genome in 3D. Analysis of these models yields new insights into the causes and the functional properties of the genomes organization in space and time. We provide a user-friendly software package, called PGS, that runs on local machines and high-performance computing platforms. PGS takes a genome-wide Hi-C contact frequency matrix and produces an ensemble of 3D genome structures entirely consistent with the input. The software automatically generates an analysis report, and also provides tools to extract and analyze the 3D coordinates of specific domains.

bioinformatics↗