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Chen, X.

Publications and source records attributed to Chen, X..

At least 1,513 records · Page 84Linked to original sources
bioRxiv2018

A fluorescent reporter enables instantaneous measurement of cell cycle speed in live cells

Cell proliferation changes concomitantly with fate transitions during reprogramming, differentiation, regeneration, and oncogenesis. Methods to resolve cell cycle length heterogeneity in real-time are currently lacking. Here, we describe a genetically encoded fluorescent reporter that captures live cell cycle speed using a single measurement. This reporter is based on the color-changing Fluorescent Timer (FT) protein, which emits blue fluorescence when newly synthesized before maturing into a red fluorescent protein. We generated a mouse strain expressing an H2B-FT fusion reporter from a universally active locus, and demonstrate that faster-cycling cells can be distinguished from slower-cycling ones based on the intracellular fluorescence ratio between the FTs blue and red states. Using this reporter, we reveal the native cell cycle speed distributions of fresh hematopoietic cells, and demonstrate its utility in analyzing cell proliferation in solid tissues. This system is broadly applicable for dissecting functional heterogeneity associated with cell cycle dynamics in complex tissues.

cell biology↗
bioRxiv2018

Molecular mechanism of the Orai channel activation

The Orai channel is characterized by voltage independence, low conductance and high Ca2+ selectivity and plays an important role in Ca2+ influx through the plasma membrane. How the channel is activated and promotes Ca2+ permeation are not well understood. Here, we report the crystal structure and cryo-electron microscopy reconstruction of a Drosophila melanogaster Orai mutant (P288L) channel that is constitutively active according to electrophysiology. The open state of the Orai channel showed a hexameric assembly in which six TM1 helices in the center form the ion-conducting pore, and six TM4 helices in the periphery form extended long helices. Orai channel activation requires conformational transduction from TM4 to TM1 and eventually causes the basic section of TM1 to twist outward. The wider pore on the cytosolic side aggregates anions to increase the potential gradient across the membrane and thus facilitate Ca2+ permeation. The open-state structure of the Orai channel offers insights into channel assembly, channel activation and Ca2+ permeation.

biochemistry↗
bioRxiv2018

MLL-AF9 Initiates Transformation From Fast-Proliferating Myeloid Progenitors

Cancer is a hyper-proliferative clonal disease. Whether the proliferative state originates from the cell-of-origin or emerges later remains elusive. By tracking de novo transformation from normal hematopoietic progenitors expressing an acute myeloid leukemia (AML) oncogene MLL-AF9, we reveal that the cell cycle rate heterogeneity among granulocyte-macrophage progenitors (GMPs) determines their probability of transformation. An intrinsic fast cell cycle kinetics at the time of oncogene expression provide permissiveness for transformation, with the fastest cycling 3% of GMPs ([~]0.006% of bone marrow nucleated cells) acquiring malignancy with nearly 100% efficiency. Molecularly, we propose that MLL-AF9 preserves the gene expression of the cellular states in which it is expressed. As such, when expressed in the naturally-existing, rapidly-cycling myeloid progenitors, this cell state is perpetuated, yielding malignancy. Our work elucidates one of the earliest steps toward malignancy and suggests that modifying the cycling state of the cell-of-origin could be an effective approach to prevent malignancy.

cancer biology↗
bioRxiv2018

Non-cell-autonomous promotion of pluripotency induction mediated by YAP

While Yes-associated protein (YAP) antagonizes pluripotency during early embryogenesis, it has also been shown to promote stemness of multiple stem cell types, including pluripotent stem cells. Whether cellular context underlies these distinct functions of YAP in pluripotency remains unclear. Here, we establish that depending on the specific cells in which it is expressed, YAP exhibits opposing effects on pluripotency induction from somatic cells. Specifically, YAP inhibits pluripotency induction cell-autonomously but promotes it non-cell-autonomously. For its non-cell-autonomous role, YAP alters the expression of many secreted and matricellular proteins including CYR61, which recapitulates the promotional effect when added as a recombinant protein. Thus, we define a unique YAP-driven non-cell-autonomous process that enhances pluripotency induction. Our work highlights the importance of considering the distinct contributions from heterologous cell types in deciphering the mechanism of cell fate control and calls for careful re-examination of the co-existing bystander cells in complex cultures or tissues.

cell biology↗
bioRxiv2018

Generative adversarial network (GAN) enabled on-chip contact microscopy

We demonstrate a deep learning based contact imaging on a CMOS chip to achieve [~]1 m spatial resolution over a large field of view of [~]24 mm2. By using regular LED illumination, we acquire the single lower-resolution image of the objects placed approximate to the sensor with unit fringe magnification. For the raw contact-mode lens-free image, the pixel size of the sensor chip limits the spatial resolution. We apply a generative and adversarial network (GAN), a type of deep learning algorithm, to circumvent this limitation and effectively recover much higher resolution image of the objects, permitting sub-micron spatial resolution to be achieved across the entire sensor chip active area, which is also equivalent to the imaging field-of-view (24 mm2) due to unit magnification. This GAN-contact imaging approach eliminates the need of either lens or multi-frame acquisition, being very handy and cost-effective. We demonstrate the success of this approach by imaging the proliferation dynamics of cells directly cultured on the chip.

biophysics↗
bioRxiv2018

Disordered breathing in a mouse model of Dravet syndrome

Dravet syndrome (DS) is a form of epilepsy with a high incidence of sudden unexpected death in epilepsy (SUDEP). Respiratory failure is a leading cause of SUDEP, and DS patients frequently exhibit disordered breathing. Despite this, mechanisms underlying respiratory dysfunction in DS are entirely unknown. We found that mice expressing a recurrent SCN1a missense mutation (A1783V) conditionally in inhibitory neurons (SCN1aA1783V/+; mixed C57B/6 background) exhibit spontaneous seizures, die prematurely and present a respiratory phenotype similar to DS patients including hypoventilation, apnea and a diminished ventilatory response to CO2. At the cellular level in the retrotrapezoid nucleus (RTN), we found inhibitory neurons expressing the SCN1a A1783V variant are less excitable, whereas chemosensitive RTN neurons, which are a key source of the CO2/H+-dependent drive to breathe, are hyper-excitable in slices from SCN1aA1783V/+ mice. These results show loss of SCN1a function can disrupt brainstem respiratory control including at the level of the RTN.

neuroscience↗
bioRxiv2018

Levels of histidine-rich glycoprotein in human blood predict accelerated aging

1.Despite recognizing aging as risk factor of human diseases, little is still known about the molecular traits of biological age and mortality risk. To identify age-associated proteins circulating human blood, we screened 156 subjects aged 50-92 years using an exploratory and multiplexed affinity proteomics approach. We corroborated the top age-associated protein profile (adjusted P < 0.001) in eight additional study sets (N = 4,044 individuals), and confirmed a consistent age-associated increase (P = 6.61 x 10-6) by meta-analysis. Applying antibody validation determined circulating histidine-rich glycoprotein (HRG) as the target, and we observed that sequence variants influenced the antibodies ability to bind to the protein. Profiles of circulating HRG were associated to several clinical traits and predicted the risk of mortality during a follow-up period of 8.5 years (IQR = 7.7-9.3 years) after blood sampling (HR = 1.25 per SD; 95% CI = 1.12-1.39; P = 7.41 x 10-5). In conclusion, our affinity proteomics analysis found associations between the molecular traits of circulating HRG with age and all-cause mortality. This suggests that the profiles of multi-purpose protein HRG could serve as an accessible indicator of physiological processes related to aging.

epidemiology↗
bioRxiv2018

Single-cell RNA sequencing reveals a dynamic stromal niche within the evolving tumour microenvironment

Non-cancerous stromal cells represent a highly diverse compartment of the tumour, yet their role across tumour evolution remains unclear. We employed single-cell RNA sequencing to determine stromal adaptations in murine melanoma at different points of tumour development. Naive lymphocytes recruited from lymph nodes underwent activation and clonal expansion within the tumour, prior to PD1 and Lag3 expression, while tumour-associated myeloid cells promoted the formation of a suppressive niche through cytokine secretion and inhibitory T cell interactions. We identified three temporally distinct cancer-associated fibroblast (CAF) populations displaying unique signatures, and verified these in human datasets. In early tumours, immune CXCL12/CSF1 and complement-expressing CAFs supported recruitment of macrophages, whereas contractile CAFs became more prevalent in later tumours. This study highlights the complex interplay and increasing diversity among cells that co-evolve with the tumour, indicating that from early stages of development, stromal cells acquire the capacity to modulate the immune landscape towards suppression.

cancer biology↗
bioRxiv2018

Accurate loop calling for 3D genomic data with cLoops

Sequencing-based 3D genome mapping technologies can identify loops formed by interactions between regulatory elements hundreds of kilobases apart. Existing loop-calling tools are mostly restricted to a single data type, with accuracy dependent on a pre-defined resolution contact matrix or called peaks, and can have prohibitive hardware costs. Here we introduce cLoops ( see loops) to address these limitations. cLoops is based on the clustering algorithm cDBSCAN that directly analyzes the paired-end tags (PETs) to find candidate loops and uses a permuted local background to estimate statistical significance. These two data-type-independent processes enable loops to be reliably identified for both sharp and broad peak data, including but not limited to ChIA-PET, Hi-C, HiChIP and Trac-looping data. Loops identified by cLoops showed much less distance-dependent bias and higher enrichment relative to local regions than existing tools. Altogether, cLoops improves accuracy of detecting of 3D-genomic loops from sequencing data, is versatile, flexible, efficient, and has modest hardware requirements, and is freely available at: https://github.com/YaqiangCao/cLoops.

bioinformatics↗
bioRxiv2018

The Human Hippocampus Contributes to Egocentric Coding of Distance to a Local Landmark

Spatial navigation can depend on path integration or environmental cues (e.g., landmarks), which are thought to be integrated in hippocampal and entorhinal circuits. This study investigates the anatomical basis of path integration and navigation based on a single local landmark using an individual differences approach, since people vary substantially in their ability to navigate with path integration cues and landmarks. In two experiments, we dissociated the use of path integration and a local landmark in the same navigation task, and investigated whether morphological variability in the hippocampus and entorhinal cortex could explain behavioral variability in young healthy humans. In Experiment 1, participants navigated in a fully immersive virtual reality environment, with body-based cues available for path integration. The participants first walked through a series of posts before attempting to walk back to the remembered location of the first post. We found that gray matter volume of the hippocampus positively predicted behavioral accuracy of retrieving the targets distance in relation to the local landmark. Hippocampus also positively predicted path integration performance in terms of walking-distance to the target location. Experiment 2 was conducted in a desktop virtual environment, with no body-based cues available. Optic flow served as path integration cues, and participants were tested on their memory of a learned target location along a linear track. Consistent with Experiment 1, the results showed that hippocampal volume positively predicted performance on the targets distance in relation to the local landmark. In contrast to Experiment 1, there was no correlation between hippocampal volume and path integration performance. Together, our two experiments provide novel and converging evidence that the hippocampus plays an important role in encoding egocentric distance to a single local landmark during navigation, and they suggest a stronger hippocampal involvement when path integration is based on body-based compared to optic flow cues.

neuroscience↗
bioRxiv2018

Hypothalamic transcriptome analysis reveals the neuroendocrine mechanisms in controlling broodiness of Muscovy duck (Cairina moschata)

Broodiness, one of the maternal behaviors and instincts for natural breeding in birds, is an interesting topic in reproductive biology. Broodiness in poultry is characterized by persistent nesting, usually associated with cessation of egg laying. The study of avian broodiness is essential for bird conservation breeding and commercial poultry industry. In this study, we examined the hypothalamus transcriptome of Muscovy duck in three reproductive stages, including egg-laying anaphase (LA), brooding prophase (BP) and brooding metaphase (BM). Differences in gene expression during the transition from egg-laying to broodiness were examined, and 155, 379, 292 differently expressed genes (DEGs) were obtained by pairwise comparisons of LA-vs-BP, LA-vs-BM and BP-vs-BM, respectively (fold change[&ge;] 1.5, P < 0.05). Gene Ontology Term (GO) enrichment analysis suggested a possible role of oxidative stress in the hypothalamus might invoke reproductive costs that potentially change genes expression. KEGG analysis revealed glutamatergic synapse, dopaminergic synapse, serotonergic synapse and GABAergic synapse pathway were significantly enriched, and regulator genes were identified. Eight gene expression patterns were illustrated by trend analysis and further clustered into three clusters. Additional six hub genes were identified through combining trend analysis and protein-protein interaction (PPI) analysis. Our results suggested that the cyclical mechanisms of reproductive function conversion include effects of oxidative stress, biosynthesis of neurotransmitters or their receptors, and interactions between glucocorticoids and thyroid hormones and regulatory genes. These candidate genes and biological pathways may be used as targets for artificial manipulation and marker-assisted breeding in the reproductive behavior.

animal behavior and cognition↗
bioRxiv2018

Effects of age on the green autofluorescence of the skin and fingernails of healthy persons

Our recent studies have suggested that altered Pattern of Autofluorescence (AF) of skin and fingernails are novel biomarkers of multiple major diseases. The age of all of the subjects in these studies ranges from 50 to 80 years of old. For future studies on the potential diagnostic value of green AF for age-independent diseases, it is required to answer the following question: Are there differences in the green AF of healthy persons of various age populations? In our current study, we determined the green AF of the skin and fingernails of healthy persons in several age populations, showing significant age dependence of the AF: First, the green AF intensity of the age group between 15 to 20 years of old is significantly higher than that of the age group between 50 to 80 years of old at both right and left Centremetacarpus, right Dorsal Centremetacarpus, and right Dorsal Index Finger. Second, for the green AF intensity of the age groups of 15 to 20 years of old, 60 to 70 years of old, 70 to 80 years of old, and 81 to 85 years of old, the green AF intensity is negatively correlated with the age at both right and left Centremetacarpus and right Dorsal Centremetacarpus. Collectively, our study has provided first evidence indicating the age dependence of the AF intensity of humans skin, which has established essential basis for the studies that determine the diagnostic value of the green AF for the age-independent diseases.

physiology↗
bioRxiv2018

HiAlc Klebsiella pneumonia, one of potential chief culprits of non-alcoholic fatty liver disease: through generation of endogenous ethanol

Non-alcoholic fatty liver disease (NAFLD), a prelude of cirrhosis and hepatocellular carcinoma, is the most common chronic liver disease worldwide. NAFLD has been considerated to be associated with the composition of gut microbiota. However, causal relationship between change of gut microbiome and NAFLD remains unclear. Here we show that Klebsiella pneumoniae was significantly associated with NAFLD through inducing generation of endogenous ethanol. A strain of high alcohol-producing Klebsiella pneumoniae (HiAlc Kpn) was initially isolated from fecal samples of patient with non-alcoholic steatohepatitis (NASH) accompanied with auto-brewery syndrome (ABS). Gavage of HiAlc Kpn was capable of inducing murine model of fatty liver disease (FLD) in which had typical pathological changes of hepatic steatosis and similar liver gene expression profiles to those of alcohol intake in mice. Data derived from germ-free mice by gnotobiotic gavage further demonstrated that the HiAlc Kpn is the major cause of the changes in FLD mice. Furthermore, using proteomic and metabolitic analysis, we found that HiAlc Kpn induced generation of endogenous alcohol through the 2,3-butanediol fermentation pathway. More interestingly, the blood alcohol concentration was elevated in FLD mice induced by HiAlc Kpn after glucose intake. Clinical analysis showed that HiAlc Kpn were observed in up to 60% of patients with NAFLD. Our results suggested that HiAlc Kpn make important contribution to NAFLD, possibly through generation of the endogenous alcohol. Thus, targeting these bacteria might provide a novel therapeutic for clinical treatment of NAFLD.\n\nIn BriefFatty liver disease induced by high alcohol-producing Klebsiella pneumoniae\n\nCompeting Financial Interest StatementThe authors declare no conflicts of interest.

microbiology↗
bioRxiv2018

Specificity of RNA folding and its association with evolutionarily adaptive mRNA secondary structure

Secondary structure is a fundamental feature for both noncoding and messenger RNA. However, our understandings about the secondary structure of mRNA, especially for the coding regions, remain elusive, likely due to translation and the lack of RNA binding proteins that sustain the consensus structure, such as those bind to noncoding RNA. Indeed, mRNA has recently been found to bear pervasive alternative structures, whose overall evolutionary and functional significance remained untested. We hereby approached this problem by estimating folding specificity, the probability that a fragment of RNA folds back to the same partner once re-folded. We showed that folding specificity for mRNA is lower than noncoding RNA, and displays moderate evolutionary conservation between orthologs and between paralogs. More importantly, we found that specific rather than alternative folding is more likely evolutionarily adaptive, since it is more frequently associated with functionally important genes or sites within a gene. Additional analysis in combination with ribosome density suggests the capability of modulating ribosome movement as one potential functional advantage provided by specific folding. Our findings revealed a novel facet of RNA structome with important functional and evolutionary implications, and points to a potential way of disentangling mRNA secondary structures maintained by natural selection from molecular noise.

evolutionary biology↗
bioRxiv2018

Gating TrkB switch by methylglyoxal enables GLO1 as a target for depression

The endogenous metabolite methylglyoxal (MGO) has recently emerged as a potential mediator of psychiatric disorders, such as anxiety and depression, but its precise mechanism of action remains poorly understood. Here, we find that MGO concentrations are decreased in the prefrontal cortex and hippocampus in rats subjected to chronic stress, and low-dose MGO treatment remarkedly enhances resilience to stress and alleviates depression-like symptoms. This effect is achieved by MGOs promotion on the synaptic plasticity in prefrontal cortex and hippocampus. Both in vitro and in vivo experiments show that MGO provokes the dimerization and autophosphorylation of TrkB and the subsequent activation of downstream Akt/CREB signaling, which leads to a rapid and sustained expression of brain-derived neurotrophic factor (BDNF). We further demonstrate that MGO directly binds to the extracellular domain of TrkB, but not its intracellular domain. In addition, we also identify a natural product luteolin and its derivative lutD as potent inhibitors of Glyoxalase 1 and validate their antidepressant effects in chronic stress rat models. The antidepressant role of endogenous MGO provides a new basis for the understanding and therapeutic intervention design for stress-associated mental disorders.

neuroscience↗
bioRxiv2018

Phosphorylation of the alpha2 glycine receptor induces an extracellular conformational change and slows the rise and decay rates of glycinergic synaptic currents

The 2 glycine receptor (GlyR) is a pentameric ligand-gated anion channel that plays a key role in cortical interneuron migration and in the differentiation of cortical progenitor cells into functional neurons. It also mediates tonic inhibitory chloride currents in adult forebrain neurons. Disruption of 2 GlyR gene expression or receptor function results in the aberrant functioning of neuronal circuits which contributes to the pathophysiology of schizophrenia, autism and epilepsy. This implicates the 2 GlyR as a possible therapeutic target for a range of neurological disorders. However, despite its therapeutic potential, little is known about the mechanisms by which 2 GlyRs are functionally modulated. To address this, we investigated whether the 2 GlyR is modulated by phosphorylation at a serine residue (S341) within the same PKA consensus sequence (R-E-S-R) that houses the 3 GlyR S346 residue that is known to be phosphorylated by PKA. Resolving this question might uncover a novel means of physiologically, pathologically or therapeutically modulating 2 GlyRs. We show using voltage-clamp fluorometry that forskolin-induced phosphorylation of S341 induces a conformational change in the glycine binding site. We also employed glycinergic artificial synapses to demonstrate that the S341E phospho-mimetic mutation slows the rise and decay rates of 2-mediated glycinergic inhibitory postsynaptic currents. These results suggest that PKA phosphorylation alters the structural and functional properties of the 2 GlyR. This information may help to identify new mechanisms by which 2 GlyRs may be pathologically modified or therapeutically targeted for the treatment of neurological disorders.

neuroscience↗
bioRxiv2018

Relationship between ecological stoichiometry and community diversity of plant ecosystems in the upper reaches of the Tarim River, China

AimAlthough it is commonly proposed that nutrient cycling can impact plant community diversity, this relationship has not been fully examined in arid and semi-arid zones. Here, we expand on the framework for evaluating the relationship between biodiversity and ecological stoichiometry by scaling up from the level of the community.\n\nLocationThe upper reaches of the Tarim River (Northwest China, 80{degrees}10-84{degrees}36E, 0{degrees}25-41{degrees}10N).\n\nMethodsWe used multivariate analysis of variance to compare the stoichiometric characteristics and species diversity indices of sampled plant communities. We also measured carbon (C), nitrogen (N), and phosphorous (P) content of plants. We then assessed correlations between community stoichiometry and species diversity through structural equation models (SEM) and redundancy analysis (RDA).\n\nResultsWe found that the differences between stoichiometric characteristics and community diversity indices were highly significant. The Margalef index was strongly related to C and P content. The Simpsons index and Shannon-Weaner index were most strongly correlated with C content. Pielous index was closely related to C and N contents, and the C:N and C:P ratios were important at driving ecological dominance.\n\nMain ConclusionsOur study highlights the importance of ecological stoichiometry in driving community assembly and diversity within a desert ecosystems in northwestern China. The relationship between eclogical stoichiometry in the desert plant community had an effect on species diversity, and it was a good indicator of plant community diversity.

ecology↗