bioRxiv Science⌕ Search

Biology subjects

Yoon, H.

Publications and source records attributed to Yoon, H..

31 records · Page 2Linked to original sources
bioRxiv2022

Immature Myeloid Cell Deposition in Old Bone Marrow Revealed by Single-Cell Transcriptome Analysis

Aging causes dysfunction of innate immunity, although hematopoietic stem cells of aged bone marrow (BM) show an increased differentiation potential to myeloid lineage cells. The alteration of cellular heterogeneity and intercellular communications between BM immune cells may provide important clues to understanding age-dependent immune dysfunction. Here, we provide a deep single-cell transcriptomic analysis of total immune cell populations of young and old BM. We identified the well-organized differentiation status of 11 myeloid/lymphoid lineage cell populations and age-dependent alterations in the proportions of cells. The neutrophil lineages showed the most prominent alteration by aging, and subclustering of neutrophils indicated that the specific immature neutrophils are increased in old BM. In addition, we identified age-dependent alterations in secretory phenotypes associated with a decline in innate immunity and immune cell differentiation. Among these secretory phenotypes, SPP1 could be suggested as a representative signal that triggers myeloid skewing and immature neutrophil deposition in aged BM. Collectively, these results provide a novel link between the altered immune cell proportions in BM and age-dependent dysregulation of innate immunity.

bioinformatics↗
bioRxiv2022

Ptr1 and ZAR1 immune receptors confer overlapping and distinct bacterial pathogen effector specificities

Nucleotide-binding and leucine-rich repeat receptors (NLRs) detect pathogen effectors inside the plant cell. To identify Nicotiana benthamiana NLRs (NbNLRs) with novel effector recognition specificity, we designed an NbNLR VIGS library and conducted a rapid reverse genetic screen. During the NbNLR VIGS library screening, we identified that N. benthamiana homolog of Ptr1 (PSEUDOMONAS SYRINGAE PV. TOMATO RACE 1 RESISTANCE) recognizes the Pseudomonas effectors AvrRpt2, AvrRpm1, and AvrB. We demonstrated that recognition of the Xanthomonas effector AvrBsT and the Pseudomonas effector HopZ5 in N. benthamiana is conferred independently by N. benthamiana homolog of Ptr1 and ZAR1 (HOPZ-ACTIVATED RESISTANCE 1). In addition, we showed that the RLCK XII family protein JIM2 (XOPJ4 IMMUNITY 2) physically interacts with AvrBsT and HopZ5 and is required for the NbZAR1-dependent recognition of AvrBsT and HopZ5. The recognition of multiple bacterial effectors by Ptr1 and ZAR1 in N. benthamiana demonstrates a convergent evolution of effector recognition across plant species. Identification of key components involved in Ptr1 and ZAR1 mediated immunity would reveal unique mechanisms of expanded effector recognition and be useful for engineering resistance in solanaceous crops.

plant biology↗
bioRxiv2021

Change in protein, oil and fatty acid contents in soybeans (Glycine max (L.) Merr.) of different seed coat colors and seed weight

Soybean seeds are one of the best sources of plant-based high-quality proteins and oils. The contents of these metabolites are affected by both environmental and genetic factors. In this study, 49 soybean germplasms were cultivated in Korea, the contents of total protein, total oil and five fatty acids were determined, and the influences of seed coat color and seed weight on each were assessed. The total protein and total oil contents were evaluated using Kjeldahl and Soxhlet methods and were in the ranges of 36.28-44.19% and 13.45-19.20%, respectively. Moreover, the contents of individual fatty acids were determined as area percentage from acquired gas-chromatography peaks. The contents of palmitic, stearic, oleic, linoleic and linolenic acids were in the ranges of 9.90-12.55, 2.45-4.00, 14.97-38.74, 43.22-60.26, and 5.37-12.33%, respectively and each significantly varied between the soybean germplasms. Unlike total oil and fatty acid contents, total protein content was not significantly affected by both seed coat color and seed weight. Cluster analysis grouped the soybeans into two classes with notable content differences. Fatty acids were the main factors for the variabilities seen between the soybean germplasms as observed in the principal component analysis. Correlation analysis revealed a significant but negative association between total oil and total protein contents (r = -0.714, p < 0.0001). Besides, a trade-off relationship was observed between oleic acid and linoleic acid (r = -0.936, p < 0.0001) which was reflected with respect to both seed coat color and seed weight. Among all colored soybeans, pale-yellow soybeans had the highest and the lowest levels of oleic acid and linoleic acid, respectively each being significantly different from the rest of colored soybeans (p < 0.05). Likewise, oleic acid content increased with seed weight while that of linoleic acid decreased with seed weight (p < 0.05). In general, this study showed the significance of seed coat color and seed weight to discriminate soybean genotypes, mainly in terms of their fatty acid contents. Moreover, the soybean germplasms with distinct characters and fatty acid contents identified in this study could be important genetic resources for cultivar development.

plant biology↗
bioRxiv2021

Recombination and low-diversity confound homoplasy-based methods to detect the effect of SARS-CoV-2 mutations on viral transmissibility

The SARS-CoV-2 variant carrying the Spike protein mutation G614 was first detected in late January 2020 and within a few months became the dominant form globally. In the months that followed, many studies, both in vitro and in animal models, showed that variants carrying this mutation were more infectious and more readily transmitted than the ancestral Wuhan form. Here we investigate why a recently published study by van Dorp et al. failed to detect such higher transmissibility of the G614 variant using homoplasy-based methods. We show that both low diversity and recombination confound the methods utilized by van Dorp et al. and significantly decrease their sensitivity. Furthermore, though they claim no evidence of recombination in their dataset, we and several other studies identify a subset of the sequences as recombinants, possibly enough to affect their statistic adversely.

bioinformatics↗
bioRxiv2021

SARS-CoV-2 variant B.1.1.7 is susceptible to neutralizing antibodies elicited by ancestral Spike vaccines

The SARS-CoV-2 Spike glycoprotein mediates virus entry and is a major target for neutralizing antibodies. All current vaccines are based on the ancestral Spike with the goal of generating a protective neutralizing antibody response. Several novel SARS-CoV-2 variants with multiple Spike mutations have emerged, and their rapid spread and potential for immune escape have raised concerns. One of these variants, first identified in the United Kingdom, B.1.1.7 (also called VUI202012/01), contains eight Spike mutations with potential to impact antibody therapy, vaccine efficacy and risk of reinfection. Here we employed a lentivirus-based pseudovirus assay to show that variant B.1.1.7 remains sensitive to neutralization, albeit at moderately reduced levels (~2-fold), by serum samples from convalescent individuals and recipients of two different vaccines based on ancestral Spike: mRNA-1273 (Moderna), and protein nanoparticle NVX-CoV2373 (Novavax). Some monoclonal antibodies to the receptor binding domain (RBD) of Spike were less effective against the variant while others were largely unaffected. These findings indicate that B.1.1.7 is not a neutralization escape variant that would be a major concern for current vaccines, or for an increased risk of reinfection.

immunology↗
bioRxiv2020

Physiological role of the 3'IgH CBEs super-anchor in antibody class switching

IgH class switch recombination (CSR) replaces C constant region (CH) exons with one of six downstream CHS by joining transcription-targeted DSBs in the C switch (S) region to DSBs in a downstream S region. Chromatin loop extrusion underlies fundamental CSR mechanisms including 3IgH regulatory region (3IgHRR)-mediated S region transcription, CSR center formation, and deletional CSR joining. There are ten consecutive CTCF binding elements (CBEs) downstream of the 3IgHRR, termed the "3IgH CBEs". Prior studies showed that deletion of eight 3IgH CBEs did not detectably affect CSR. Here, we report that deletion of all 3IgH CBEs impacts, to varying degrees, germline transcription and CSR of upstream S regions, except S{gamma}1. Moreover, deletion of all 3IgH CBEs rendered the 6kb region just downstream highly transcribed and caused sequences within to be aligned with S, broken, and joined to form aberrant CSR rearrangements. These findings implicate the 3IgH CBEs as a critical insulator for focusing loop extrusion-mediated 3IgHRR transcriptional and CSR activities on upstream CH locus targets. SignificanceB lymphocytes change antibody heavy chain (IgH) isotypes by a recombination/deletion process called IgH class switch recombination (CSR). CSR involves introduction of DNA breaks into a donor switch (S) region and also into one of six downstream S regions, with joining of the breaks changing antibody isotype. A chromatin super-anchor, of unknown function, is located just downstream of the IgH locus. We show that complete deletion of this super-anchor variably decreases CSR to most S regions and creates an ectopic S region downstream of IgH locus that undergoes aberrant CSR-driven chromosomal rearrangements. Based on these and other findings, we conclude that the super-anchor downstream of IgH is a critical insulator for focusing potentially dangerous CSR rearrangements to the IgH locus.

immunology↗
bioRxiv2020

Decoding spontaneous pain from brain cellular calcium signals using deep learning

We developed AI-bRNN (Average training, Individual test-bidirectional Recurrent Neural Network) to decipher spontaneous pain information from brain cellular calcium signals recorded by two-photon imaging in awake, head-fixed mice. The AI-bRNN determines the intensity and time point of spontaneous pain even during the chronic pain period and evaluates the efficacy of analgesics. Furthermore, it could be applied to different cell types and brain areas, and it distinguished between itch and pain, proving its versatility.

neuroscience↗
bioRxiv2020

CD38 dependent NAD+ depletion contributes to oligodendrocyte loss and inhibition of myelin regeneration

Western-style diets cause disruptions in myelinating cells and astrocytes within the mouse CNS. CD38 has increased expression in the cuprizone and EAE demyelination models and is the main NAD+ depleting enzyme in CNS tissue. Altered NAD+ metabolism has been linked to both high fat consumption and Multiple Sclerosis (MS). We identified increased CD38 expression in the male mouse spinal cord following chronic high fat consumption or focal lysolecithin-induced demyelinating injury as well as in reactive astrocytes within an active MS lesion. CD38-catalytically inactive mice are significantly protected from high fat-induced NAD+ depletion, oligodendrocyte loss, oxidative damage, and astrogliosis. 78c, a CD38 inhibitor, increased NAD+ and attenuated neuroinflammatory changes in astrocytes induced by saturated fat. Conditioned media from saturated fat-treated astrocytes impaired oligodendrocyte differentiation pointing to indirect mechanisms of oligodendrogliopathy. Combined saturated fat and lysolecithin demyelination in cerebellar slices resulted in additional deficits in myelin proteins that were mitigated by concomitant 78c treatment. Importantly, oral 78c increased counts of oligodendrocytes and remyelinated axons after focal demyelination. Our findings suggest high fat diet impairs oligodendrocyte survival and differentiation through astrocyte-linked mechanisms mediated by the NAD+ase CD38, and highlight the use of CD38 inhibitors as potential therapeutic candidates to improve myelin regeneration.

neuroscience↗
bioRxiv2020

Spike mutation pipeline reveals the emergence of a more transmissible form of SARS-CoV-2

We have developed an analysis pipeline to facilitate real-time mutation tracking in SARS-CoV-2, focusing initially on the Spike (S) protein because it mediates infection of human cells and is the target of most vaccine strategies and antibody-based therapeutics. To date we have identified thirteen mutations in Spike that are accumulating. Mutations are considered in a broader phylogenetic context, geographically, and over time, to provide an early warning system to reveal mutations that may confer selective advantages in transmission or resistance to interventions. Each one is evaluated for evidence of positive selection, and the implications of the mutation are explored through structural modeling. The mutation Spike D614G is of urgent concern; it began spreading in Europe in early February, and when introduced to new regions it rapidly becomes the dominant form. Also, we present evidence of recombination between locally circulating strains, indicative of multiple strain infections. These finding have important implications for SARS-CoV-2 transmission, pathogenesis and immune interventions.

evolutionary biology↗
bioRxiv2019

Unusual genome expansion and transcription suppression in ectomycorrhizal Tricholoma matsutake by repetitive insertions of transposable elements

Genome sequence of Tricholoma matsutake was revealed as the one of the large fungal genomes published up to date at 189.0 Mbp with 15,305 predicted genes. The unusual size of this fungal genome contained frequent colonization of transposable elements (TEs) occupying more than half of the entire genome. We identified that 702 genes were surrounded by TEs and 83.2% of those genes were never transcribed at any development stage. This observation corroborated that the insertion of transposable elements alters the transcription of the genes neighboring TEs.\n\nRepeat-induced point mutation such as C to T hypermutation with a bias over CpG dinucleotides was also recognized in this genome, representing a typical defense mechanism against TEs during evolution. Many transcription factor genes were activated in both primordia and fruiting body, which indicates that many regulatory processes are shared during developmental stages. Small secreted protein genes (<300 aa) were dominantly transcribed in hyphae, where symbiotic interactions occur with hosts. Comparative analysis with 37 Agaricomycetes genomes revealed that IstB-like domain (PF01695) was conserved in taxonomically diverse mycorrhizal genomes, where the T. matsutake genome contained four copies of this domain. Three of the IstB-like genes were overexpressed in hyphae. In the CAZyme analysis, reduced CAZyme genes were found as other ectomycorrhizal genomes including a lot of loss of glycoside hydrolase genes. Also, auxiliary activity genes were dominantly transcribed in primordia. The T. matsutake genome sequence provides insight into the large genome size and clues to understand unusual fungal genome expansion.

genomics↗
bioRxiv2019

Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15

The investigational drugs E7820, indisulam and tasisulam (aryl-sulfonamides) promote the degradation of the splicing factor RBM39 in a proteasome-dependent mechanism. While the activity critically depends on the Cullin RING ligase substrate receptor DCAF15, the molecular details remain elusive. Here we present the cryo-EM structure of the DDB1-DCAF15-DDA1 core ligase complex bound to RBM39 and E7820 at 4.4 [A] resolution, together with crystal structures of engineered subcomplexes. We show that DCAF15 adopts a novel fold stabilized by DDA1, and that extensive protein-protein contacts between the ligase and substrate mitigate low affinity interactions between aryl-sulfonamides and DCAF15. Our data demonstrates how aryl-sulfonamides neo-functionalize a shallow, non-conserved pocket on DCAF15 to selectively bind and degrade RBM39 and the closely related splicing factor RBM23 without the requirement for a high affinity ligand, which has broad implications for the de novo discovery of molecular glue degraders.

biochemistry↗
bioRxiv2019

Development of group-specific nosZ quantification method targeting active nitrous oxide reducing population in complex environmental samples

Substantial N2O emission results from activated sludge nitrogen removal processes. The importance of N2O-reducers possessing NosZ-type N2O reductases have been recognized as the only N2O sink in situ key to determination of the net N2O emissions; however, reliable quantification methods for nosZ genes and transcripts have yet to be developed. Here, nosZ genes and transcripts in activated sludge tank microbiomes were analyzed with the group-specific qPCR assays designed de novo combining culture-based and computational approach. A sewage sample was enriched in a batch reactor fed continuous stream of N2 containing 20-10,000 ppmv N2O, where 14 genera of potential N2O-reducers were identified. All available amino acid sequences of NosZ affiliated to these taxa were grouped into five subgroups (two clade I and three clade II groups), and primer/probe sets exclusively and comprehensively targeting the subgroups were designed and validated with in silico PCR. Four distinct activated sludge samples from three different wastewater treatment plants in Korea were analyzed with the qPCR assays and the results were validated by comparison with the shotgun metagenome analysis results. With the validated qPCR assays, the nosZ genes and transcripts of six additional activated sludge samples were analyzed and the results of the analyses clearly indicated the dominance of two clade II nosZ subgroups (Flavobacterium-like and Dechloromonas-like) among both nosZ gene and transcript pools.

microbiology↗