Biology subjects

Kang, H.

Publications and source records attributed to Kang, H..

At least 91 records · Page 5Linked to original sources

bioRxiv2021

Characteristic core voxels in normal individuals revealed by hyperbolic disc embedding and k-core percolation on resting state fMRI

Hyperbolic disc embedding and k-core percolation reveal the core structure of the functional connectivity on resting-state fMRI (rsfMRI). Inter-voxel relations were visualized on embedded hyperbolic discs, and their core composition was traced using k-core percolation. Using 180 normal adults rsfMRI data from the Human Connectome Project database, scale- free intervoxel connectivity represented by IC-voxels composition, while visualized on hyperbolic discs using [Formula] model, showed the expected change of the largest component decreasing its size on k-core percolation eventually yielding the core structures of individuals. This kmax-core voxels-ICs composition revealed such stereotypes of individuals as visual network dominant, default mode network dominant, and distributed patterns. Characteristic core structures of resting-state brain connectivity of normal subjects disclosed the distributed or asymmetric contribution of voxels to the kmax-core, which suggests the hierarchical dominance of certain IC subnetworks characteristic to subgroups of individuals at rest.

neuroscience↗

bioRxiv2021

Early flowering in oilseed-type Brassica rapa plants results from nonsense-mediated mRNA decay (NMD) of BrFLC2

Many Brassica species require vernalization (long-term winter-like cooling) for transition to the reproductive stage. In the past several decades, scientific efforts have been made to discern the molecular mechanisms underlying vernalization in many species. Thus, to identify the key regulators required for vernalization in Brassica rapa L., we constructed a linkage map composed of 7,833 single nucleotide polymorphism (SNP) markers using the late-flowering Chinese cabbage (B. rapa L. ssp. pekinensis) inbred line Chiifu and the early-flowering yellow sarson (B. rapa L. ssp. trilocularis (Roxb.)) line LP08 and identified a single major QTL on the upper-arm of the chromosome A02. In addition, we compared the transcriptomes of the lines Chiifu and LP08 at five vernalization time points, including both non-vernalized and post-vernalization conditions. We observed that BrFLC2 was significantly downregulated in the early flowering LP08 and had two deletion sites around the BrFLC2 genomic region compared with the BrFLC2 genomic region in Chiifu. In the present study, we also demonstrate that early flowering in LP08 line is attributed to the low expression of BrFLC2, which is caused by nonsense-mediated mRNA decay (NMD). Therefore, this study provides a better understanding of the molecular mechanisms underlying floral transition in B. rapa. One sentence summaryNMD-mediated degradation of BrFLC2 mRNA transcripts is the main cause of rapid flowering of oilseed-type B. rapa LP08 plants.

plant biology↗

bioRxiv2021

Generation of SIV resistant T cells and Macrophages from Nonhuman Primate Induced Pluripotent Stem Cells with Edited CCR5 locus

Adoptive therapies with genetically modified somatic T cells rendered HIV resistant have shown promise for AIDS therapy. A renewable source of HIV resistant human T cells from induced pluripotent stem cells (iPSCs) would further facilitate and broaden the applicability of these therapies. Here, we report successful targeting of the CCR5 locus in iPSCs generated from peripheral blood T cells (T-iPSCs) or fibroblasts (fib-iPSCs) from Mauritian Cynomolgus macaques (MCM), using CRISPR/Cas9 technology. We found that CCR5 editing does not affect pluripotency or hematopoietic and T cell differentiation potentials of fib-iPSCs. However, deletion of CCR5 in T-iPSCs leads to selective loss of their T cell redifferentiation potential without affecting myeloid development. T cells and macrophages produced from CCR5-edited MCM- iPSCs did not support replication of the CCR5-tropic simian immunodeficiency viruses SIVmac239 (T-cell tropic) and SIVmac316 (macrophage-tropic). Overall, these studies provide a platform for further exploration of AIDS therapies based on gene-edited iPSCs in a nonhuman primate preclinical model.

cell biology↗

bioRxiv2021

Hyperbolic disc embedding of functional human brain connectomes using resting state fMRI

The brain presents a real complex network of modular, small-world, and hierarchical nature, which are features of non-Euclidean geometry. Using resting-state functional magnetic resonance imaging (rs-fMRI), we constructed a scale-free binary graph for each subject, using internodal time-series correlation of regions-of-interest (ROIs) as a proximity measure. The resulted network could be embedded onto manifolds of various curvature and dimensions. While maintaining the fidelity of embedding (low distortion, high mean average precision), functional brain networks were found to be best represented in the hyperbolic disc. Using [Formula] model, we reduced the dimension of the network into 2-D hyperbolic space and were able to efficiently visualize the internodal connections of the brain, preserving proximity as distances and angles on the hyperbolic discs. Each individual disc revealed decentralized nature of information flow and anatomic relevance. Using the hyperbolic distance on the [Formula] model, we could detect the anomaly of network in autistic spectrum disorder (ASD) subjects. This procedure of embedding grants us a reliable new framework for studying functional brain networks and the possibility of detecting anomalies of the network in the hyperbolic disc on an individual scale.

neuroscience↗

bioRxiv2021

Astrocytes render memory flexible

Cognitive flexibility is an essential ability to adapt to changing environment and circumstances. NMDAR has long been implicated in cognitive flexibility, but the precise molecular and cellular mechanism is not well understood. Here, we report that astrocytes regulate NMDAR tone through Best1-mediated glutamate and D-serine release, which is critical for cognitive flexibility. Co-release of D-serine and glutamate is required for not only homosynaptic LTD but also heterosynaptic LTD, which is induced at unstimulated synapses upon release of norepinephrine and activation of astrocytic 1-AR during homosynaptic LTP. Remarkably, heterosynaptic LTD at unstimulated synapses during memory acquisition is required for later repotentiation LTP during reversal learning, laying a foundation for flexible memory and cognitive flexibility. Our study sheds light on the pivotal role of astrocytes in orchestrating multiple synapses during memory formation and determining the fate of consolidated memory to be retained as a flexible memory. HighlightsO_LIAstrocytes regulate NMDAR tone via Best1-mediated glutamate and D-serine release C_LIO_LIActivation of astrocytic 1-AR induces heterosynaptic LTD via NMDAR tone C_LIO_LIHeterosynaptic LTD is required for repotentiation LTP and spatial reversal learning C_LIO_LIAstrocytic regulation of NMDAR tone is critical for metaplasticity and flexible memory C_LI

neuroscience↗

bioRxiv2021

α1-COP delivers sphingolipid modifiers and controls plasmodesmal callose deposition in Arabidopsis

Callose is a plant cell wall polymer in the form of {beta}-1,3-glucan, which regulates symplasmic channel size at plasmodesmata (PD). It plays a crucial role in a variety of processes in plants through the regulation of intercelluar symplasmic continuity. However, how to maintain callose homeostasis at PD in the molecular levels is poorly understood. To further elucidate the mechanism of PD callose homeostasis, we screened and identified an Arabidopsis mutant plant that exhibited excessive callose deposition at PD. Based on the Next-generation sequencing (NGS)-based mapping, other mutant allele analysis, and complementation assay, the mutated gene was shown to be 1-COP, which encodes a member of the COPI coatomer complex comprised of , {beta}, {beta}', {gamma}, {delta}, {varepsilon}, and {zeta} subunits. Since there is no report on the link between COPI and callose/PD, it was extremely curious to know the roles of 1-COP or COPI in PD regulation through callose deposition. Here, we report that loss-of-function of 1-COP directly elevates the callose accumulation at PD by affecting subcellular protein localization of callose degradation enzyme PdBG2. This process is linked to ERH1, an inositol phosphoryl ceramide synthase (IPCS), and glucosylceramide synthase (GCS) functions through physical interactions with the 1-COP protein. In addition, the loss-of-function of 1-COP also alters the subcellular localization of ERH1 and GCS proteins, results in a reduction of GlcCers and GlcHCers molecules, which are the key SL species for lipid raft formation. According to our findings, we propose that 1-COP protein, together with the SL modifiers controlling lipid raft compositions, regulates the function of GPI-anchored PD proteins and hence the callose turnover at PD and symplastic movement of biomolecules. Our findings provide the first key clue to link the COPI-mediated intracellular trafficking pathway to the callose-mediated intercellular signaling pathway through PD. One-sentence summaryPlant-specific coatomer protein functions as a negative regulator of callose accumulation by regulating the translocation of sphingolipid enzymes.

cell biology↗

bioRxiv2021

Genome Warehouse: A Public Repository Housing Genome-scale Data

The Genome Warehouse (GWH) is a public repository housing genome assembly data for a wide range of species and delivering a series of web services for genome data submission, storage, release, and sharing. As one of the core resources in the National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB, https://bigd.big.ac.cn/), GWH accepts both full genome and partial genome (chloroplast, mitochondrion, and plasmid) sequences with different assembly levels, as well as an update of existing genome assemblies. For each assembly, GWH collects detailed genome-related metadata including biological project and sample, and genome assembly information, in addition to genome sequence and annotation. To archive high-quality genome sequences and annotations, GWH is equipped with a uniform and standardized procedure for quality control. Besides basic browse and search functionalities, all released genome sequences and annotations can be visualized with JBrowse. By December 2020, GWH has received 17,264 direct submissions covering a diversity of 949 species, and has released 3370 of them. Collectively, GWH serves as an important resource for genome-scale data management and provides free and publicly accessible data to support research activities throughout the world. GWH is publicly accessible at https://bigd.big.ac.cn/gwh/.

bioinformatics↗

bioRxiv2021

Physiological underpinning of default-mode network emergence in the human infant brain

Human infancy is characterized by most rapid cerebral blood flow (rCBF) increases across lifespan and emergence of a fundamental brain system default-mode network (DMN). However, how infant rCBF change spatiotemporally across the brain and how the rCBF dynamics support emergence of vital functional networks such as DMN remains unknown. Here, by acquiring cutting-edge multi-modal MRI including pseudo-continuous arterial-spin-labeled perfusion MRI and resting-state functional MRI of infants aged 0 to 24 months, we elucidated unprecedented 4D spatiotemporal infant rCBF framework and region-specific physiology-function coupling across infancy. We found faster rCBF increases in the DMN than other regions. We also found strongly coupled increases of rCBF and network strength specifically in the DMN, suggesting faster local blood flow increase to meet extra neuronal metabolic demands in the DMN maturation. These results offer insights into physiological mechanism of brain functional network emergence and have important implications in altered network maturation in brain disorders.

neuroscience↗

bioRxiv2021

Competitive outcomes between native and invasive plants are linked to shifts in the bacterial rhizosphere microbiome

Rhizosphere microbiomes have received growing attention in recent years for their role in plant health, stress tolerance, soil nutrition, and invasion. Still, relatively little is known about how these microbial communities are altered under plant competition, and even less about whether these shifts are tied to competitive outcomes between native and invasive plants. We investigated the structure and diversity of rhizosphere bacterial and fungal microbiomes of native annual forbs and invasive annual grasses individually and in competition using high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal ITS region. We assessed how differentially abundant microbial families correlate to plant biomass under competition We find that bacterial diversity and structure differ between native forbs and invasive grasses, but fungal diversity and structure do not. Further, bacterial community structures under competition are distinct from individual bacterial community structures. We also identified five bacterial families that varied in normalized abundance between treatments and that were correlated with plant biomass under competition. We speculate that invasive grass dominance over these natives may be partially due to effects on the rhizosphere community, with changes in specific bacterial families potentially benefiting invaders at the expense of natives.

microbiology↗

bioRxiv2020

MASiVar: Multisite, Multiscanner, and Multisubject Acquisitions for Studying Variability in Diffusion Weighted Magnetic Resonance Imaging

PurposeDiffusion weighted imaging (DWI) allows investigators to identify structural, microstructural, and connectivitybased differences between subjects, but variability due to session and scanner biases is a challenge. MethodsTo investigate DWI variability, we present MASiVar, a multisite dataset consisting of 319 diffusion scans acquired at 3T from b = 1000 to 3000 s/mm2 across 14 healthy adults, 83 healthy children (5 to 8 years), three sites, and four scanners as a publicly available, preprocessed, and de-identified dataset. With the adult data, we demonstrate the capacity of MASiVar to simultaneously quantify the intrasession, intersession, interscanner, and intersubject variability of four common DWI processing approaches: (1) a tensor signal representation, (2) a multi-compartment neurite orientation dispersion and density model, (3) white matter bundle segmentation, and (4) structural connectomics. Respectively, we evaluate region-wise fractional anisotropy (FA), mean diffusivity, and principal eigenvector; region-wise cerebral spinal fluid volume fraction, intracellular volume fraction, and orientation dispersion index; bundle-wise shape, volume, FA, and length; and whole connectome correlation and maximized modularity, global efficiency, and characteristic path length. ResultsWe plot the variability in these measures at each level and find that it consistently increases with intrasession to intersession to interscanner to intersubject effects across all processing approaches and that sometimes interscanner variability can approach intersubject variability. ConclusionsThis study demonstrates the potential of MASiVar to more globally investigate DWI variability across multiple levels and processing approaches simultaneously and suggests harmonization between scanners for multisite analyses should be considered prior to inference of group differences on subjects.

bioengineering↗

bioRxiv2020

CTCF-mediated Genomic Effects of BART Region on Epstein-Barr Virus Chromatin 3D Structure in Gastric Carcinoma Cells

EBV latent infection in gastric carcinoma (GC) cells is characterized by distinct viral gene expression programs. CCCTC-binding factor (CTCF) is a chromatin structural factor that has been involved in coordinated chromatin interactions between multiple loci of Epstein-Barr virus (EBV) genes. Here, we investigate the role of CTCF in regulating EBV gene expression and chromosome conformation in model of EBV-associated gastric carcinoma (EBVaGC). Chromatin immunoprecipitation followed by sequencing (ChIP-seq) against CTCF revealed 16 CTCF binding sites (BS) in EBV genome of EBVaGC, SNU719 cells. Among the CTCF BSs, one site named as BARTp (BamHI A right transcript promoter) CTCF BS is located at upstream of 11.8-kb BART region (EBV genome: 139724-151554) and was not yet defined its biological functions in EBV life cycle. EBV BART encodes a complex miRNA cluster of highly spliced transcripts that is implicated in EBV cancer pathogenesis. This present study investigated the functional role of the CTCF binding site at BARTp (BARTp CTCF BS) in regulating EBV gene transcription and EBV three-dimensional (3D) genome structure as DNA loop maker. Circular chromatin confirmation capture (4C)-seq and chromatin confirmation capture (3C)-semi-quantitative(sq)PCR assays using SNU719 cells revealed that BARTp CTCF BS interacts with CTCF BSs of LMP1/2, Cp/OriP, and Qp in EBV genome. We generated mutations in BARTp CTCF BS (S13) in bacmids with (BART+) or without (BART-) the 11.8-kb BART transcript unit (B(+/-)). ChIP-qPCR assay demonstrated that CTCF binding was ablated from BARTp in EBV B(+/-) S13- genomes (mutant S13), elevated at several other sites such as LMP1, OriP, and Cp in EBV B(-) (BART-) S13- genome, and decreased at the same sites in EBV B(+) S13- genome. Infection assay showed that BARTp CTCF BS mutation reduced infectivity, while BART transcript deletion has no detectable effects. Gene expression tests showed that EBNA1 was highly downregulated in B(+/-) S13- EBVs related to B(+/-) S13+ EBVs (wild-type S13). LMP1 and BZLF1 were more downregulated in B(-) S13- EBV than B(+) S13- EBV. Taken together, these findings suggest that the CTCF binding and BART region contribute to EBV 3D genome structure via a cluster of DNA loops formed by BARTp CTCF BS (S13) and are important for coordinated viral gene expression and EBV infectivity.

microbiology↗

bioRxiv2020

Memory Transfer of Random Time Patterns Across Modalities

Perception is sensitive to statistical regularities in the environment, including temporal characteristics of sensory inputs. Interestingly, temporal patterns implicitly learned within one modality can also be recognised in another modality. However, it is unclear how cross-modal learning transfer affects neural responses to sensory stimuli. Here, we recorded neural activity of human volunteers (N=24, 12 females, 12 males) using electroencephalography (EEG), while participants were exposed to brief sequences of randomly-timed auditory or visual pulses. Some trials consisted of a repetition of the temporal pattern within the sequence, and subjects were tasked with detecting these trials. Unknown to the participants, some trials reappeared throughout the experiment, enabling implicit learning. Replicating previous behavioural findings, we showed that participants benefit from temporal information learned in audition, and that they can apply this information to stimuli presented in vision. Such memory transfer was not observed from vision to audition. However, using an analysis of EEG response learning curves, we showed that learning temporal structures both within and across modalities modulates single-trial EEG response amplitudes in both conditions (audition to vision and vision to audition). Interestingly, the neural correlates of temporal learning within modalities relied on modality-specific brain regions, while learning transfer affected activity in frontal regions, suggesting distinct mechanisms. The cross-modal effect could be linked to frontal beta-band activity. The neural effects of learning transfer were similar both when temporal information learned in audition was transferred to visual stimuli and vice versa. Thus, both modality-specific mechanisms for learning of temporal information, and general mechanisms which mediate learning transfer across modalities, have distinct physiological signatures that are observable in the EEG.

neuroscience↗

bioRxiv2020

Neural correlates of auditory pattern learning in the auditory cortex

Learning of new auditory stimuli requires repetitive exposure to the stimulus. Fast and implicit learning of sounds presented at random times enables efficient auditory perception. However, it is unclear how such sensory encoding is processed on a neural level. We investigated neural responses that are developed from a passive, repetitive exposure to a specific sound in the auditory cortex of anesthetized rats, using electrocorticography. We presented a series of random sequences that are generated afresh each time, except for a specific reference sequence that remains constant and re-appears at random times across trials. We compared induced activity amplitudes between reference and fresh sequences. Neural responses from both primary and non-primary auditory cortical regions showed significantly decreased induced activity amplitudes for reference sequences compared to fresh sequences, especially in the beta band. This is the first study showing that neural correlates of auditory pattern learning can be evoked even in anesthetized, passive listening animal models.

neuroscience↗

bioRxiv2020

Further evidence that CP-AMPARs are critically involved in synaptic tag and capture at hippocampal CA1 synapses

The synaptic tag and capture (STC) hypothesis provides an important theoretical basis for understanding the synaptic basis of associative learning. We recently provided pharmacological evidence that calcium-permeable AMPA receptors (CP-AMPARs) are a crucial component of this process. Here we have investigated two predictions that arise on the basis of CP-AMPARs serving as a trigger of the STC effect. Firstly, we compared the effects of the order in which we delivered a strong theta burst stimulation (TBS) protocol (75 pulses) and a weak TBS protocol (15 pulses) to two independent inputs. We only observed a significant STC effect when the strong preceded the weak TBS. Second, we found that pausing stimulation following either the sTBS or the wTBS for [~]20 min largely eliminates the STC effect. These observations are exactly as predicted for a process that is triggered by the synaptic insertion of CP-AMPARs and provide a framework for establishing the underlying molecular mechanism.

neuroscience↗

bioRxiv2020

PKA drives an increase in AMPA receptor unitary conductance during LTP in the hippocampus

Long-term potentiation (LTP) at hippocampal CA1 synapses can be expressed by an increase either in the number (N) of AMPA (-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors or in their single channel conductance ({gamma}). Here we have established how these distinct synaptic processes contribute to the expression of LTP in hippocampal slices obtained from young adult rodents. LTP induced by compressed theta burst stimulation (TBS), with a 10 s inter-episode interval, involved purely an increase in N (LTPN). In contrast, either a spaced TBS, with a 10 min inter-episode interval, or a single TBS, delivered when PKA was activated, resulted in LTP that was associated with a transient increase in {gamma} (LTP{gamma}). This {gamma} increase was due to the insertion of calcium-permeable (CP)-AMPA receptors. Activation of CaMKII was necessary and sufficient for LTPN whilst PKA was additionally required for LTP{gamma}. Thus, two mechanistically distinct forms of LTP co-exist at these synapses.

neuroscience↗

bioRxiv2020

Seminal plasma exosomes evoke calcium signal via CatSper channel to regulate human sperm function

Seminal plasma exosomes (SPE) have been proposed to regulate intracellular calcium concentration ([Ca2+]i) and sperm function. However, neither the underlying mechanisms by which [Ca2+]i is regulated by SPE nor the physiological and pathological significance of the SPE-evoked calcium signal are fully understood. Here, we successfully isolated and characterized SPE by several methods, including transmission electron microscopy, nanoparticle tracking and nanoflow cytometry analysis. Application of SPE dose-dependently increased human sperm [Ca2+]i via extracellular Ca2+ influx. The Ca2+ influx was mediated by the sperm-specific CatSper channel, because the SPE-elevated [Ca2+]i was suppressed by a CatSper inhibitor, and SPE potentiated the CatSper current in human sperm. The role of CatSper in the SPE-induced elevation of [Ca2+]i was further confirmed by the absence of the SPE-induced [Ca2+]i increase and CatSper current in a CatSper-deficient sample. Furthermore, both protein and no-protein components in SPE were shown to contribute to the elevated [Ca2+]i, as well as the hyperactivated motility of human sperm. Interestingly, when sperm were stimulated with exosomes derived from asthenozoospermic semen, the elevation of [Ca2+]i was significantly lower than that by exosomes isolated from normal seminal plasma. The SPE from normal seminal plasma improved the motility of sperm from asthenozoospermic samples. Taken together, these findings demonstrated that SPE modulates Ca2+ signaling and human sperm function by activating a CatSper channel. The application of SPE to enhance sperm motility may provide a new clinical avenue for asthenozoospermic men.

physiology↗

bioRxiv2020

TAZ inhibits GR and coordinates hepatic glucose homeostasis in normal physiologic states

The elucidation of the mechanisms whereby the liver maintains glucose homeostasis is crucial for the understanding of physiologic and pathologic states. Here, we show a novel role of hepatic transcriptional co-activator with PDZ-binding motif (TAZ) in the inhibition of glucocorticoid receptor (GR). TAZ interacts via its WW domain with the ligand-binding domain of GR to limit the binding of GR to gluconeogenic gene promoters. Therefore, liver-specific TAZ knockout mice show increases in glucose production and blood glucose concentration. Conversely, the overexpression of TAZ in mouse liver reduces the binding of GR to gluconeogenic gene promoters and glucose production. Thus, our findings demonstrate distinct roles of the hippo pathway effector proteins yes-associated protein 1 (YAP) and TAZ in liver physiology: while deletion of hepatic YAP has little effect on glucose homeostasis, hepatic TAZ protein expression decreases upon fasting and coordinates gluconeogenesis in response to physiologic fasting and feeding.

biochemistry↗

bioRxiv2020

Two-Step Mixed Model Approach to Analyzing Differential Alternative RNA Splicing

Changes in gene expression can correlate with poor disease outcomes in two ways: through changes in relative transcript levels or through alternative RNA splicing leading to changes in relative abundance of individual transcript isoforms. The objective of this research is to develop new statistical methods in detecting and analyzing both differentially expressed and spliced isoforms, which appropriately account for the dependence between isoforms and multiple testing corrections for the multi-dimensional structure of at both the gene- and isoform-level. We developed a linear mixed effects model-based approach for analyzing the complex alternative RNA splicing regulation patterns detected by whole-transcriptome RNA-sequencing technologies. This approach thoroughly characterizes and differentiates three types of genes related to alternative RNA splicing events with distinct differential expression/splicing patterns. We applied the concept of appropriately controlling for the gene-level overall false discovery rate (OFDR) in this multi-dimensional alternative RNA splicing analysis utilizing a two-step hierarchical hypothesis testing framework. In the initial screening test we identify genes that have differentially expressed or spliced isoforms; in the subsequent confirmatory testing stage we examine only the isoforms for genes that have passed the screening tests. Comparisons with other methods through application to a whole transcriptome RNA-Seq study of adenoid cystic carcinoma and extensive simulation studies have demonstrated the advantages and improved performances of our method. Our proposed method appropriately controls the gene-level OFDR, maintains statistical power, and is flexible to incorporate advanced experimental designs.

bioinformatics↗