Biology subjects

Xu, N.

Publications and source records attributed to Xu, N..

64 records · Page 4Linked to original sources

bioRxiv2020

Revealing the functions of supra-temporal and insular auditory responsive areas in humans

The human auditory sensory area, which includes primary and non-primary auditory cortices, has been considered to locate in the supra-temporal lobe for more than a century. Recently, accumulating evidence shows that the posterior part of insula responses to sounds under non-task states with relevant short latencies. However, whether posterior insula (InsP) contribute to forming auditory sensation remains unclear. Here we addressed this issue by recording and stimulation directly on the supra-temporal and insular areas via intracranial electrodes from 53 epileptic patients. During passive listening to a non-speech sound, the high-{gamma} (60-140 Hz) active rate of InsP (68.8%) was approximate to the non-primary auditory areas (72.4% and 79.0%). Moreover, we could not distinguish InsP from supra-temporal subareas by either activation, latency, temporal pattern or lateral dominance of sound induce high-{gamma}. On the contrary, direct electrical stimulation evoked auditory sensations effectively on supra-temporal subareas (> 65%), while sparsely on InsP (9.49%). The results of cortico-cortical evoked potentials (CCEPs) showed strong bidirectional connectivity within supra-temporal areas, but weak connectivity between supra-temporal areas and InsP. These findings suggest that even the InsP has similar basic auditory response properties to the primary or non-primary cortex, it may not directly participate in the formation of auditory perception.

neuroscience↗

bioRxiv2020

Polar Gini Curve: a Technique to Discover Single-cell Biomarker Using 2D Visual Information

In this work, we design the Polar Gini Curve (PGC) technique, which combines the gene expression and the 2D embedded visual information to detect biomarkers from single-cell data. Theoretically, a Polar Gini Curve characterizes the shape and evenness of cell-point distribution of cell-point set. To quantify whether a gene could be a marker in a cell cluster, we can combine two Polar Gini Curves: one drawn upon the cell-points expressing the gene, and the other drawn upon all cell-points in the cluster. We hypothesize that the closers these two curves are, the more likely the gene would be cluster markers. We demonstrate the framework in several simulation case-studies. Applying our framework in analyzing neonatal mouse heart single-cell data, the detected biomarkers may characterize novel subtypes of cardiac muscle cells. The source code and data for PGC could be found at https://figshare.com/projects/Polar_Gini_Curve/76749.

bioinformatics↗

bioRxiv2020

The origin of domestication genes in goats

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here we analyze the genomes of worldwide domestic goats, wild caprid species and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7,200 and 8,100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanism of animal domestication. One Sentence SummaryGoat domestication mainly focused on immune and neural genes, with adaptive leaps driven by introgression and selection.

genomics↗

bioRxiv2019

BSU1 family phosphatases mediate Flagellin-FLS2 signaling through a specific phosphocode.

Hundreds of leucine-rich repeat receptor kinases (LRR-RKs) have evolved to control diverse processes of growth, development, and immunity in plants; the mechanisms that link LRR-RKs to distinct cellular responses are not understood. Here we show that two LRR-RKs, the brassinosteroid hormone receptor BRI1 (BRASSINOSTEROID INSENSITIVE 1) and the flagellin receptor FLS2 (FLAGELLIN SENSING 2), regulate downstream glycogen synthase kinase 3 (GSK3) and mitogen-activated protein (MAP) kinases, respectively, through phosphocoding of the BRI1-SUPPRESSOR1 (BSU1) phosphatase. BSU1 was previously identified as a component that inactivates GSK3s in the BRI1 pathway. We found surprisingly that loss of the BSU1 family phosphatases activates effector-triggered immunity (ETI) and impairs flagellin-triggered MAP kinase activation and immunity. The flagellin-activated BOTRYTIS-INDUCED KINASE 1 (BIK1) phosphorylates BSU1 at serine-251. Mutation of serine-251 reduces the ability of BSU1 to mediate flagellin-induced MAP kinase activation and immunity, but not its abilities to suppress ETI and interact with GSK3, which is enhanced through the phosphorylation of BSU1 at serine-764 upon brassinosteroid signaling. These results demonstrate that BSU1 plays an essential role in immunity and transduces brassinosteroid-BRI1 and flagellin-FLS2 signals using different phosphorylation sites. Our study illustrates that phosphocoding in shared downstream components provides signaling specificities for diverse plant receptor kinases.

plant biology↗

bioRxiv2019

NEAT1 involves Alzheimer’s Disease (AD) progression via regulation of glycolysis and P-tau

Nuclear paraspeckles assembly transcript 1 (NEAT1) is a well-known long noncoding RNA (LncRNA) with unclear mechanism in Alzheimers disease (AD) progression. Here, we found that NEAT1 down-regulates in the early stage of AD patients and APPswe/PS1dE9 mouse. Moreover, knockdown of NEAT1 induced de-polymerization of microtubule (MT) and axonal retraction of nerve cells by dysregulation of the FZD3/GSK3{beta}/p-tau signaling pathway. Histone acetylation analysis at the Frizzled Class Receptor 3 (FZD3) promoter shows a marked decreased in the levels of the H3K27 acetylation (H3K27Ac) after NEAT1 knockdown. Our data demonstrates that P300/CBP recruited by NEAT1 to the FZD3 promoter and induced its transcription via histone acetylation. In recent years a growing number of evidences have shown an abnormal brain glucose homeostasis in AD. In the present study we also observed an abnormal brain glucose homeostasis and enhanced sirtuin1 (SIRT1) activity after knockdown of NEAT similarly as in AD. Our results provided insight into the role of NEAT1 in the maintenance of MT stability and its effect on glucose metabolism during early stages of AD.

neuroscience↗

bioRxiv2019

Dynamic metabolic profiles of marine macroalga Ulva prolifera during fragmentation-induced proliferation

Ulva prolifera, a type of marine macroalgae, is the causative species behind green tides mainly in the Yellow Sea and adjacent regions, nevertheless, it can be used as food or animal feed in South China. The vegetative fragments of U. prolifera are an important seed source for successive green tide blooms. Fragmentation shortens the transition time from the vegetative state to the reproductive state. However, the translation of the algal metabolites during gametogenesis was far from well understood. In this study, the dynamic metabolic profiles of U. prolifera thallus during fragmentation-induced proliferation were investigated using non-targeted metabolomics approach in a time series of experiments in June 2017. After a 30 min low temperature shock, fragmentation induced a reproductive response of 91.57% of U. prolifera in 48 h, whereas that was only 21.43% in the control group. A total of 156 chromatographic peaks were detected, and 63 metabolites were significantly changed in U. prolifera during reproduction. The results of the Kinetic metabolic pattern showed that the fragments not only induced the formation of sporangium, but also complicated their metabolites accumulation. During fragmentation-induced proliferation, U. prolifera consumed different sugars at different time points. {gamma}-aminobutyric acid (GABA), glutamic acid, gallic acid, and malic acid may play important roles in germ cell formation and release of U. prolifera, whereas n-hexanol, 2-methyl-3-phenylindole, and 3-indoleacetonitrile may be beneficial in biotic stress resistance. Compared with the control group, the metabolites, such as alcohol and organic acid, also showed significant difference with the photoperiod at the initial stage of proliferation (before 60 h). In conclusion, that the metabolites including sugars, organic acids, and alcohol changed with different photoperiod may be the strategy for U. prolifera to cope with adverse environment and rapid proliferation.

physiology↗

bioRxiv2018

Precisely control mitochondrial membrane potential with light to manipulate cell fate decisions

Mitochondrial dysfunction has been implicated in many pathological conditions and diseases. The normal functioning of mitochondria relies on maintaining the inner mitochondrial membrane (IMM) potential (a.k.a. {Delta}{Psi}m) that is essential for ATP synthesis, Ca2+ homeostasis, redox balance and regulation of other key signaling pathways such as mitophagy and apoptosis. However, the detailed mechanisms by which {Delta}{Psi}m regulates cellular function remain incompletely understood, partially due to difficulty of manipulating {Delta}{Psi}m with spatiotemporal resolution, reversibility, or cell type specificity. To address this need, we have developed a next-generation optogenetic-based technique for controllable mitochondrial depolarization with light. We demonstrate successful targeting of the heterologous Channelrhodopsin-2 (ChR2) fusion protein to the IMM and formation of functional cationic channels capable of light-induced selective {Delta}{Psi}m depolarization and mitochondrial autophagy. Importantly, we for the first time show that optogenetic-mediated mitochondrial depolarization can be well-controlled to differentially influence the fate of cells expressing mitochondrial ChR2: while sustained moderate light illumination induces substantial apoptotic cell death, transient mild light illumination elicits cytoprotection via mitochondrial preconditioning. Finally, we show that Parkin overexpression exacerbates, instead of ameliorating, mitochondrial depolarization-mediated cell death in HeLa cells. In summary, we provide evidence that the described mitochondrial-targeted optogenetics may have a broad application for studying the role of mitochondria in regulating cell function and fate decision.

cell biology↗

bioRxiv2018

Kipoi: accelerating the community exchange and reuse of predictive models for genomics

Advanced machine learning models applied to large-scale genomics datasets hold the promise to be major drivers for genome science. Once trained, such models can serve as a tool to probe the relationships between data modalities, including the effect of genetic variants on phenotype. However, lack of standardization and limited accessibility of trained models have hampered their impact in practice. To address this, we present Kipoi, a collaborative initiative to define standards and to foster reuse of trained models in genomics. Already, the Kipoi repository contains over 2,000 trained models that cover canonical prediction tasks in transcriptional and post-transcriptional gene regulation. The Kipoi model standard grants automated software installation and provides unified interfaces to apply and interpret models. We illustrate Kipoi through canonical use cases, including model benchmarking, transfer learning, variant effect prediction, and building new models from existing ones. By providing a unified framework to archive, share, access, use, and build on models developed by the community, Kipoi will foster the dissemination and use of machine learning models in genomics.

bioinformatics↗

bioRxiv2018

Dynamic and causal contribution of parietal cortex to perceptual decisions during category learning

Making perceptual decisions to categorize unknown sensory stimuli is a fundamental cognitive function, known as category learning. The posterior parietal cortex (PPC), although has been intensively studied for its role in decision-making and other cognitive functions, its causal link with behavior remains controversial. Here we combine in vivo two-photon imaging, circuit manipulation and auditory psychophysics behavior in mice to probe the role of PPC and its connectivity with sensory cortex in decision-making during category learning. We show that PPC neuronal populations exhibit coding dynamics characteristic of category learning, showing representations for both new sensory stimuli and prior learned categories. Circuit-specific perturbations of PPC and its projections to auditory cortex impaired decision performance specifically for categorizing new auditory stimuli. These data reveal a dynamic and causal role of the parietal-auditory circuit in decision-making, integrating prior knowledge to guide categorical decisions on new sensory stimuli.

neuroscience↗

bioRxiv2017

Influence of APOA5 locus on the treatment efficacy of three statins: evidence from a randomized pilot study in Chinese subjects

Pharmacogenetics or pharmacogenomics approaches are important for addressing the individual variabilities of drug efficacy especially in the era of precision medicine. One particular interesting gene to investigate is APOA5 which has been repeatedly linked with the inter-individual variations of serum triglycerides. Here, we explored APOA5-statin interactions in 195 Chinese subjects randomized to rosuvastatin (5-10 mg/day), atorvastatin (10-20 mg/day), or simvastatin (40 mg/day) for 12 weeks by performing a targeted genotyping analysis of the APOA5 promoter SNP rs662799 (-1131T>C). There were no significant differences between the treatment arms for any of the statin-induced changes in clinical biomarkers. Reductions in LDL cholesterol were influenced by the APOA5 genotype in all three treatment groups. By contrast, changes in HDL cholesterol and triglycerides were only affected by the APOA5 genotype in the atorvastatin and simvastatin groups and not in the rosuvastatin group. Our results support earlier findings indicating that rosuvastatin is a better treatment option and that future studies should consider stratifying subjects not only by genetic background but also by statin type.\n\nAbbreviations

clinical trials↗