Biology subjects

Choi, J. H.

Publications and source records attributed to Choi, J. H..

42 records · Page 3Linked to original sources

bioRxiv2020

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to {pound}10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.

genomics↗

bioRxiv2020

Auxetic Two-Dimensional Nanostructures from DNA

Architectured materials exhibit negative Poissons ratios and enhanced mechanical properties compared with regular materials. Their auxetic behaviors should emerge from periodic cellular structures regardless of the materials used. The majority of such metamaterials are constructed by top-down approaches and macroscopic with unit cells of microns or larger. On the other extreme, there are molecular-scale auxetics including naturally-occurring crystals which are not designable. There is a gap from few nanometers to microns, which may be filled by bottom-up biomolecular self-assembly. Here we demonstrate two-dimensional auxetic nanostructures using DNA origami. Structural reconfiguration experiments are performed by strand displacement and complemented by mechanical deformation studies using coarse-grained molecular dynamics (MD) simulations. We find that the auxetic properties of DNA nanostructures are mostly defined by geometrical designs, yet materials chemistry also plays an important role. From elasticity theory, we introduce a set of design principles for auxetic DNA metamaterials, which should find diverse applications.

biophysics↗

bioRxiv2020

Development of a diamide resistance diagnostic method using LAMP based on a resistance-specific indel in ryanodine receptors for Spodoptera exigua (Lepidoptera: Noctuidae)

Recently, resistance to diamide insecticides (IRAC group 28) has been reported in various lepidopteran pests, including Spodoptera exigua. In the present study, susceptibility of six field populations was evaluated to two diamide insecticides: chlorantraniliprole and flubendiamide. The bioassay test for resistance revealed a high level of diamide resistance and helped to select a diamide resistant (Di-R) strain, whose LC50 values against chlorantraniliprole and flubendiamide were 28,950- and 135,286-fold higher, respectively, than those of susceptible strains. In the ryanodine receptor, instead of the G4946E mutation, one of the well-known diamide resistance mechanisms, we found a I4790M mutation and identified the resistance allele-specific indel linked to it. Resistance allele diagnostic primers were designed using this distinct region and applied in loop-mediated isothermal amplification (LAMP) and general PCR. LAMP accurately detected the specific indel when conducted for 2 h at temperature range from 63 {degrees}C to 65 {degrees}C and using four LAMP primers; its efficiency was further amplified by an additional loop primer. A broad range of DNA concentrations was workable in the LAMP assay, with the minimum detectable DNA concentration of 100 pg. The new DNA releasing method used for the LAMP assay consisted of 5 min of incubation of a larva or adult tissue at 95{degrees}C. The entire diagnostic process, which included the DNA releasing technique and LAMP, lasted only 100 min. This simple and accurate LAMP assay can be applied to monitor diamide resistance and for integrated resistance management of S. exigua in the field.

ecology↗

bioRxiv2020

Quantitative Proteomics and Phosphoproteomics Supports a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis

Summary/AbstractProtein phosphorylation is one of the most prevalent post-translational modifications found in eukaryotic systems. It serves as a key molecular mechanism that regulates protein function in response to environmental stimuli. The Mut9-Like Kinases (MLKs) are a plant-specific family of Ser/Thr kinases linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. Proteins involved in light, circadian, and hormone signaling, as well as several chromatin-modifying enzymes and DNA damage response factors, were found to have altered phosphorylation profiles in the absence of MLK family kinases. In addition to altered phosphorylation levels, mlk mutant seedlings have an increase in glucosinolate metabolism enzymes. Subsequently, we show that a functional consequence of the changes to the proteome and phosphoproteome in mlk mutant plants is elevated glucosinolate accumulation, and increased sensitivity to DNA damaging agents. Combined with previous reports, this work supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs serve as key regulators linking environmental inputs to developmental outputs.

plant biology↗

bioRxiv2019

Functional dissociation of theta oscillations in the frontal and visual cortices and their long-range network during sustained attention

Theta-band (4-12 Hz) activities in the frontal cortex have been thought to be a key mechanism of sustained attention and goal-related behaviors, forming a phase-coherent network with task-related sensory cortices for integrated neuronal ensembles. However, recent visual task studies found that selective attention attenuates stimulus-related theta power in the visual cortex, suggesting a functional dissociation of cortical theta oscillations. To investigate this contradictory behavior of cortical theta, a visual Go/No-Go task was performed with electroencephalogram recording in mice. During the No-Go period, transient theta oscillations were observed in both the frontal and visual cortices, but theta oscillations of the two areas were prominent in different trial epochs. By separating trial epochs based on subjects short-term performance, we found that frontal theta was prominent in good-performance epochs, while visual theta was prominent in bad-performance epochs, exhibiting a functional dissociation of cortical theta rhythms. Furthermore, the two theta rhythms also showed a heterogeneous pattern of phase-amplitude coupling with fast oscillations, reflecting their distinct architecture in underlying neuronal circuitry. Interestingly, in good-performance epochs, where visual theta was relatively weak, stronger fronto-visual long-range synchrony and shorter posterior-to-anterior temporal delay were found. These findings highlight a previously overlooked aspect of long-range synchrony between distinct oscillatory entities in the cerebral cortex and provide empirical evidence of a functional dissociation of cortical theta rhythms.\n\nIN BRIEFPrevious literature emphasized the pro-cognitive role of coherent oscillatory networks between distal brain regions, such as the fronto-visual theta synchrony. However, such a conceptual framework has been challenged as recent findings revealed distinct behavioral correlates of theta oscillations found in different cortical regions, especially in the frontal and visual cortices. Here, we show that frontal and visual theta represent distinct cortical processes and that the functional connectivity between them increases during sustained attention, especially when one of the two theta rhythms is relatively suppressed. The data presented here highlight a novel aspect of neural long-range synchrony between distinct cortical oscillators with distinct functional significance in task performance.

neuroscience↗

bioRxiv2019

SCINA: Semi-Supervised Analysis of Single Cells in silico

Advances in single-cell RNA sequencing (scRNA-Seq) have allowed for comprehensive analyses of single cell data. However, current analyses of scRNA-Seq data usually start from unsupervised clustering or visualization. These methods ignore the prior knowledge of transcriptomes and of the probable structures of the data. Moreover, cell identification heavily relies on subjective and inaccurate human inspection afterwards. We reversed this paradigm and developed SCINA, a semi-supervised model, for analyses of scRNA-Seq and flow cytometry/CyTOF data, and other data of similar format, by automatically exploiting previously established gene signatures using an expectation-maximization (EM) algorithm. We applied SCINA on a wide range of datasets, and showed its accuracy, stableness and efficiency exceeded most popular unsupervised approaches. Notably, SCINA discovered an intermediate stage of oligodendrocyte from mouse brain scRNA-Seq data. SCINA also detected immune cell population shifting in Stk4 knock-out mouse cytometry data. Finally, SCINA identified a new kidney tumor clade with similarity to FH-deficient tumors from bulk tumor data. Overall, SCINA provides both methodological advances and biological insights from perspectives different from traditional analytical methods.

bioinformatics↗