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Li, C.

Publications and source records attributed to Li, C..

At least 865 records · Page 48Linked to original sources

Decreased KATP channel activity contributes to the low glucose threshold for insulinsecretion in the early postnatal period

Transitional hypoglycemia in normal newborns occurs in the first 3 days of life and has clinical features consistent with hyperinsulinism. We found a lower threshold for glucose-stimulated insulin secretion from freshly isolated embryonic day (E)22 rat islets, which persisted into the first postnatal days. The threshold reached the adult level by postnatal day (P)14. Culturing P14 islets also decreased the glucose threshold. Freshly isolated P1 rat islets had a lower threshold for insulin secretion in response to BCH (2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid), a non-metabolizable leucine analog, and diminished insulin release in response to tolbutamide, an inhibitor of {beta}-cell KATP channels. These findings suggested that decreased KATP channel function could be responsible for the lower glucose threshold for insulin secretion. Single-cell transcriptomic analysis did not reveal a lower expression of KATP subunit genes in E22 compared to P14 {beta}-cells. The investigation of electrophysiological characteristics of dispersed {beta}-cells showed that early neonatal and cultured cells had fewer functional KATP channels per unit membrane area. Our findings suggest that decreased surface density of KATP channels may contribute to the observed differences in glucose threshold for insulin release.

developmental biology↗

Preoptic BRS3 neurons increase body temperature and heart rate via multiple pathways

The preoptic area (POA) is a key region controlling body temperature (Tb), dictating thermogenic, cardiovascular, and behavioral responses to regulate Tb. Known POA neuronal populations reduce Tb when activated; a population that increases Tb upon activation has not yet been reported. We now identify bombesin-like receptor 3 (BRS3)-expressing POA (POABRS3) neurons as having this missing functionality. BRS3 is an orphan receptor that regulates energy and cardiovascular homeostasis, but the relevant neural circuits are incompletely understood. In mice, we demonstrate that POABRS3 neuronal activation increases Tb, heart rate, and blood pressure sympathetically, via projections to the paraventricular nucleus of the hypothalamus and dorsomedial hypothalamus. Acute POABRS3 inhibition reduces Tb. Long-term inactivation of POABRS3 neurons increased Tb variability with exaggerated Tb changes, overshooting both increases and decreases in Tb set point. BRS3 marks preoptic populations that regulate Tb and heart rate, contribute to cold-defense and fine-tune feedback control of Tb. These findings advance understanding of homeothermy, a defining feature of mammalian biology. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/433948v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@121b5a8org.highwire.dtl.DTLVardef@1d67bforg.highwire.dtl.DTLVardef@865eeborg.highwire.dtl.DTLVardef@1c1d41e_HPS_FORMAT_FIGEXP M_FIG Graphical abstract C_FIG

neuroscience↗

The landscape of accessible chromatin in quiescent and post-myocardial infarction cardiac fibroblasts

After myocardial infarction, quiescent cardiac fibroblasts are activated and undergo multiple proliferation and differentiation events, which contribute to the extracellular matrix remodeling of the infarcted myocardium. We recently found that cardiac fibroblasts of different differentiation states had distinct expression profiles closely related to their functions. Gene expression is directly regulated by chromatin state. However, the role of chromatin reorganization in the drastic gene expression changes during post-MI differentiation of cardiac fibroblast has not been revealed. In this study, the gene expression profiling and genome-wide mapping of accessible chromatin in mouse cardiac fibroblasts isolated from uninjured hearts and the infarcts at different time points were performed by RNA sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), respectively. ATAC-seq peaks were highly enriched in the promoter area and distal areas where enhancers might be located. A positive correlation was identified between the transcription level and promoter accessibility for many dynamically expressed genes. In addition, it was found that DNA methylation may contribute to the post-MI chromatin remodeling and gene expression in cardiac fibroblasts. Integrated analysis of ATAC-seq and RNA-seq datasets also identified transcription factors that possibly contributed to the differential gene expression between cardiac fibroblasts of different states.

genomics↗

PDX1 directs a core developmentally and evolutionarily conserved gene program in the pancreatic islet

Pancreatic and duodenal homeobox 1 (PDX1) is crucial for pancreas organogenesis, yet the dynamic changes in PDX1 targets in mouse or human pancreas development have not been examined. We integrated the PDX1 cistrome with cell lineage-specific gene expression in both mouse and human developing pancreas. We identified a core set of developmentally and evolutionarily conserved PDX1 bound genes that reveal the broad multifaceted role of PDX1 in pancreas development. Despite the well-known, dramatic changes in PDX1 function and expression, we showed that PDX1 binding is largely stable from embryonic pancreas to adult islet. This may point towards a dual role of PDX1, activating or repressing the expression of its targets at different ages, dependent on other functionally-congruent or directly-interacting partners. Our work also suggests that PDX1 functions not only in initiating pancreas differentiation, but also as a potential keepsake of the progenitor program in the adult beta cells.

developmental biology↗

Towards a systematic characterization of protein complex function: a natural language processing and machine-learning framework

It is a general assumption of molecular biology that the ensemble of expressed molecules, their activities and interactions determine biological processes, cellular states and phenotypes. Quantitative abundance of transcripts, proteins and metabolites are now routinely measured with considerable depth via an array of "OMICS" technologies, and recently a number of methods have also been introduced for the parallel analysis of the abundance, subunit composition and cell state specific changes of protein complexes. In comparison to the measurement of the molecular entities in a cell, the determination of their function remains experimentally challenging and labor-intensive. This holds particularly true for determining the function of protein complexes, which constitute the core functional assemblies of the cell. Therefore, the tremendous progress in multi-layer molecular profiling has been slow to translate into increased functional understanding of biological processes, cellular states and phenotypes. In this study we describe PCfun, a computational framework for the systematic annotation of protein complex function using Gene Ontology (GO) terms. This work is built upon the use of word embedding-- natural language text embedded into continuous vector space that preserves semantic relationships-- generated from the machine reading of 1 million open access PubMed Central articles. PCfun leverages the embedding for rapid annotation of protein complex function by integrating two approaches: (1) an unsupervised approach that obtains the nearest neighbor (NN) GO term word vectors for a protein complex query vector, and (2) a supervised approach using Random Forest (RF) models trained specifically for recovering the GO terms of protein complex queries described in the CORUM protein complex database. PCfun consolidates both approaches by performing the statistical test for the enrichment of the top NN GO terms within the child terms of the predicted GO terms by RF models. Thus, PCfun amalgamates information learned from the gold-standard protein-complex database, CORUM, with the unbiased predictions obtained directly from the word embedding, thereby enabling PCfun to identify the potential functions of putative protein complexes. The documentation and examples of the PCfun package are available at https://github.com/sharmavaruns/PCfun. We anticipate that PCfun will serve as a useful tool and novel paradigm for the large-scale characterization of protein complex function.

bioinformatics↗

Adjuvanting a subunit SARS-CoV-2 nanoparticle vaccine to induce protective immunity in non-human primates

The development of a portfolio of SARS-CoV-2 vaccines to vaccinate the global population remains an urgent public health imperative. Here, we demonstrate the capacity of a subunit vaccine under clinical development, comprising the SARS-CoV-2 Spike protein receptor binding domain displayed on a two-component protein nanoparticle (RBD-NP), to stimulate robust and durable neutralizing antibody (nAb) responses and protection against SARS-CoV-2 in non-human primates. We evaluated five different adjuvants combined with RBD-NP including Essai O/W 1849101, a squalene-in-water emulsion; AS03, an alpha-tocopherol-containing squalene-based oil-in-water emulsion used in pandemic influenza vaccines; AS37, a TLR-7 agonist adsorbed to Alum; CpG 1018-Alum (CpG-Alum), a TLR-9 agonist formulated in Alum; or Alum, the most widely used adjuvant. All five adjuvants induced substantial nAb and CD4 T cell responses after two consecutive immunizations. Durable nAb responses were evaluated for RBD-NP/AS03 immunization and the live-virus nAb response was durably maintained up to 154 days post-vaccination. AS03, CpG-Alum, AS37 and Alum groups conferred significant protection against SARS-CoV-2 infection in the pharynges, nares and in the bronchoalveolar lavage. The nAb titers were highly correlated with protection against infection. Furthermore, RBD-NP when used in conjunction with AS03 was as potent as the prefusion stabilized Spike immunogen, HexaPro. Taken together, these data highlight the efficacy of the RBD-NP formulated with clinically relevant adjuvants in promoting robust immunity against SARS-CoV-2 in non-human primates.

immunology↗

Focused X-ray Luminescence Computed Tomography using a Continuous Scanning Scheme

X-ray luminescence computed tomography (XLCT) imaging is a hybrid molecular imaging modality combining the merits of both conventional x-ray imaging (high spatial resolution) and optical imaging (high measurement sensitivity). The narrow x-ray beam based XLCT imaging has been shown to be promising. However due to the selective excitation scheme, the imaging speed is slow thus limiting its practical applications for in vivo imaging. In this work, we have introduced a continuous scanning scheme to acquire data for each angular projection in one motion, eliminating the previous stepping scheme and reducing the data acquisition time, which makes it feasible for multiple transverse scans for three-dimensional (3D) imaging. We have introduced a high accuracy vertical stage to our focused x-ray beam based XLCT imaging system to perform high-resolution and 3D XLCT imaging. We have also included a scintillator crystal coupled to a PMT to act as a single-pixel detector for boundary detection purposes to replace our previous flat panel x-ray detector. We have verified the feasibility of our proposed scanning scheme and imaging system by performing phantom experimental studies. A phantom was embedded with a set of cylindrical targets with 200 {micro}m edge-to-edge distance and was scanned in our imaging system with the proposed method. To test the feasibility for 3D scanning, we took measurements from 4 transverse slices with a vertical step size of 1 mm. The results of the experiments verified the feasibility of our proposed method to perform 3D XLCT imaging using a narrow x-ray beam in a reasonable time.

bioengineering↗

ESD1 Affects Seed Setting Rate in Rice by Controlling Embryo Sac Development

Seed setting rate is one of the critical factors that determine rice yield. Grain formation is a complex biological process, whose molecular mechanism is yet to be improved. Here we investigated the function of an OVATE family protein, Embryo Sac Development 1 (ESD1), in the regulation of seed setting rate in rice (Oryza sativa) by examining its loss-of-function mutants generated via CRISPR/Cas9 technology. ESD1 was predominantly expressed at stage 6 of panicle development, especially in the ovules. esd1 mutants displayed reduced seed setting rates with normal stamen development and pollen tube growth but abnormal pistil group. Investigation of embryo sacs revealed that during the mitosis of functional megaspores, some egg cells degraded during differentiation in esd1 mutants, thereby hindering subsequent fertilization process and reducing seed setting rate. In addition, the transcriptional level of OsAPC6, a reported embryo sac developing gene, was found to be significantly reduced in esd1 mutants. These results support that ESD1 is an important modulator of embryo sac development and seed setting rate in rice. Together, this finding demonstrates that ESD1 positively regulates the seed setting rate by controlling embryo sac development in rice, and has implications for the improvement of rice yield.

plant biology↗

An engineered multifunctional protein tag for advanced fluorescence imaging

Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we present the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of live-cell compatible fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. We showed that the ability to tune the fluorescence color and properties through simple molecular modulation provides an unprecedent experimental versatility for imaging proteins in live cells, including delicate cultured hippocampal neurons, and in multicellular organisms. The ability to tune the spectral properties and fluorescence performance enables to match the spectral specifications and requirements of the most advanced imaging techniques, and allowed us to achieve efficient stimulated emission depletion (STED) nanoscopy of fusion proteins in live cells and live primary cultured neurons.

molecular biology↗

Spike mutations decrease SARS-CoV-2 sensitivity to neutralizing antibodies but not ACE2-Ig in vitro

The emergence of SARS-CoV-2 variants poses greater challenges to the control of COVID-19 pandemic. Here, we parallelly investigated three important characteristics of seven SARS-CoV-2 variants, including two mink-associated variants, the B.1.617.1 variant, and the four WHO-designated variants of concerns (B.1.1.7, B.1.351, P.1, and B.1.617.2). We first investigated the ability of these variants to bind and use animal ACE2 orthologs as entry receptor. We found that, in contrast to a prototype variant, the B.1.1.7, B.1.351, and P.1 variants had significantly enhanced affinities to cattle, pig, and mouse ACE2 proteins, suggesting increased susceptibility of these species to these SARS-CoV-2 variants. We then evaluated in vitro neutralization sensitivity of these variants to four monoclonal antibodies in clinical use. We observed that all the variants were partially or completely resistant against at least one of the four tested antibodies, with B.1.351 and P.1 showing significant resistance to three of them. As ACE2-Ig is a broad-spectrum anti-SARS-CoV-2 drug candidate, we then evaluated in vitro neutralization sensitivity of these variants to eight ACE2-Ig constructs previously described in three different studies. All the SARS-CoV-2 variants were efficiently neutralized by these ACE2-Ig constructs. Interestingly, compared to the prototype variant, most tested variants including the variants of concern B.1.1.7, B.1.351, P.1, and B.1.617.2 showed significantly increased (up to [~]15-fold) neutralization sensitivity to ACE2-Ig constructs that are not heavily mutated in the spike-binding interface of the soluble ACE2 domain, suggesting that SARS-CoV-2 evolves toward better utilizing ACE2, and that ACE2-Ig is an attractive drug candidate for coping with SARS-CoV-2 mutations.

microbiology↗

tTARGIT AAVs: A sensitive and flexible method to manipulate intersectional neuronal populations

While Cre-dependent viral systems permit the manipulation of many neuron types, some cell populations cannot be targeted by a single DNA recombinase. Although the combined use of Flp and Cre recombinases can overcome this limitation, insufficient recombinase activity can reduce the efficacy of existing Cre+Flp-dependent viral systems. We developed a sensitive dual recombinase-activated viral approach: tTA-driven Recombinase-Guided Intersectional Targeting (tTARGIT) AAVs. tTARGIT AAVs utilize a Flp-dependent tetracycline transactivator (tTA) "Driver" AAV and a tetracycline response element (TRE)-driven, Cre-dependent "Payload" AAV to express the transgene of interest. We employed this system in Slc17a6FlpO;LeprCre mice to manipulate LepRb neurons of the ventromedial hypothalamus (VMH; LepRbVMH neurons) while omitting neighboring LepRb populations. We defined the circuitry of LepRbVMH neurons and roles for these cells in the control of food intake and energy expenditure. Thus, the tTARGIT system mediates robust recombinase-sensitive transgene expression, permitting the precise manipulation of previously intractable neural populations.

physiology↗

Analysis of Spleen Histopathology, Splenocyte composition and Hematological Parameters in Mice Infected with Plasmodium berghei K173

Malaria is a fatal disease that presents clinically as a continuum of symptoms and severity, which are determined by complex host-parasite interactions. Clearance of infection is believed to be accomplished by the spleen and mononuclear phagocytic system (MPS), both in the presence and absence of artemisinin treatment. The spleen filters infected RBCs from circulation through immune-mediated recognition of the infected RBCs followed by phagocytosis. Using different strains of mice infected with P. berghei K173 (PbK173), the mechanisms leading to splenomegaly, histopathology, splenocyte activation and proliferation, and their relationship to control of parasitemia and host mortality were examined. Survival time of mice infected with PbK173 varied, although the infection was uniformly lethal. Mice of the C57BL/6 strain were the most resistant, while mice of the strain ICR were the most susceptible. BALB/c and KM mice were intermediate. In the course of PbK173 infection, both strains of mice experienced significant splenomegaly. Parasites were observed in the red pulp at 3 days post infection in all animals. All spleens retained late trophozoite stages as well as a fraction of earlier ring-stage parasites. The percentages of macrophages in infected C57BL/6 and KM mice were higher than uninfected mice on 8 dpi. Spleens of infected ICR and KM mice exhibited structural disorganization and remodeling. Furthermore, parasitemia was significantly higher in KM versus C57BL/6 mice at 8 dpi. The percentages of macrophages in ICR infected mice were lower than uninfected mice, and the parasitemia was higher than other strains. The results presented here demonstrate the rate of splenic mechanical filtration and the splenic macrophages likely contribute to an individuals total parasite burden. This in turn can influence the pathogenesis of malaria. Finally, different genetic backgrounds of mice have different splenic mechanisms for controlling malaria infection.

microbiology↗

Brassinosteroid signaling component SlBES1 promotes tomato fruit softening through transcriptional repression of PMEU1

Firmness is one of the most important factors that affect postharvest properties of tomato fruit. However, the regulatory mechanism underlying firmness formation in tomato fruit is poorly understood. Here, we report a novel role of SlBES1, a transcriptional factor (TF) mediating brassinosteroid (BR) signaling, in tomato fruit softening. We first found that SlBES1 promotes fruit softening during tomato fruit ripening and postharvest storage. RNA-seq analysis suggested that PMEU1, which encodes a pectin de-methylesterification protein, might participate in SlBES1-mediated fruit softening. Biochemical and immunofluorescence assays in SlBES1 transgenic fruits indicated that SlBES1 inhibited PMEU1-related pectin de-methylesterification. Further molecular and genetic evidence verified that SlBES1 directly binds to the E-box in the promoter of PMEU1 to repress its expression, leading to the softening of the tomato fruits. Loss-of-function SlBES1 mutant generated by CRISPR/cas9 showed firmer fruits and longer shelf life during postharvest storage without the color, size and nutritional quality alteration. Collectively, our results indicated the potential of manipulating SlBES1 to regulate fruit firmness via transcriptional inhibition of PMEU1 without negative consequence on visual and nutrition quality.

plant biology↗

MolRep: A Deep Representation Learning Library for Molecular Property Prediction

SummaryRecently, novel representation learning algorithms have shown potential for predicting molecular properties. However, unified frameworks have not yet emerged for fairly measuring algorithmic progress, and experimental procedures of different representation models often lack rigorousness and are hardly reproducible. Herein, we have developed MolRep by unifying 16 state-of-the-art models across 4 popular molecular representations for application and comparison. Furthermore, we ran more than 12.5 million experiments to optimize hyperparameters for each method on 12 common benchmark data sets. As a result, CMPNN achieves the best results ranked the 1st in 5 out of 12 tasks with an average rank of 1.75. Relatively, ECC has good performance in classification tasks and MAT good for regression (both ranked 1st for 3 tasks) with an average rank of 2.71 and 2.6, respectively. AvailabilityThe source code is available at: https://github.com/biomed-AI/MolRep Supplementary informationSupplementary data are available online.

bioinformatics↗

Nuclear m6A reader Ythdc1 regulates the scaffold function of LINE1 in mouse ESCs

N6-methyladenosine (m6A) on chromosome-associated regulatory RNAs (carRNAs), including repeat RNAs, play important roles in tuning the chromatin state and transcription1. Among diverse RNA-chromatin interacting modes, the nuclear RNA scaffold is considered important for trans-interactions2,3 but has not yet been connected with m6A yet. Here, we found that Ythdc1 played indispensable roles in the embryonic stem cell (ESC) self-renewal and differentiation potency, and these roles highly depended on its m6A-binding ability. Ythdc1 deficiency in ESCs resulted in decreased rRNA synthesis and the activation of 2-cell (2C) embryo-specific transcriptional program, and these observations recapitulated the transcriptome defects induced by dysfunction of the long interspersed nuclear element-1 (LINE1)-scaffold, which were unrelated to the direct targeting of Ythdc1. A detailed analysis revealed that Ythdc1 recognized m6A on LINE1 and was physically involved in the formation of the LINE1-Nucleolin partnership and the chromatin recruitment of Kap1. In summary, our study reveals a new link between m6A and the RNA scaffold and thus provides a new regulatory model for the crosstalk between RNA and the chromatin epigenome.

cell biology↗

Image-based Quality Assessment of Middle Cerebral Artery Occlusion using SIFT Descriptor and Support Vector Machine

BackgroundThe association between brain metabolic change and ischemic stroke has attracted a lot of attention in the research community. 18F-fluorodeoxyglucose (FDG) positron emission tomography (PET) imaging is widely used to measure the metabolism. In experiments, ischemic stroke is usually induced through middle cerebral artery occlusion (MCAO), and quality assessment of this procedure is of vital importance. However, an assessment method based on FDG PET images is still lacking. Herein, we propose an image feature-based protocol to assess the quality of the procedure. MethodsWe performed permanent MCAO to a total of 161 Sprague-Dawley rats. FDG micro-PET images were acquired both before and after the MCAO procedure. Triphenyl tetrazolium chloride (TTC) staining was also conducted to obtain ground truth of the infarct volume. After preprocessing of the PET images, a combination of 3D scale invariant feature transform (SIFT) and support vector machine (SVM) was applied to extract features and train a classifier that can assess the quality of the MCAO procedure. Results106 rats and 212 images were used as training data to construct the classification model. The SVM classifier achieved over 98% accuracy in cross validation. 10 rats with TTC results showing infarction in the ipsilateral brain region served as validation data. Their images were tested by the classifier and all of them were categorized into the correct group. Finally, the remaining 45 rats from a separate experiment were treated as independent test data. The prediction accuracy for these 90 images reached the level of 91%. An online interface was constructed for users to upload their images and obtain the assessment results. ConclusionThis feature-based protocol provides a convenient, accurate and reliable tool to assess the quality of the MCAO procedure in FDG PET study.

neuroscience↗

FAM72A antagonizes UNG2 to promote mutagenic uracil repair during antibody maturation

Activation-induced cytidine deaminase (AID) catalyzes the deamination of deoxycytidines within Immunoglobulin (Ig) genes to induce somatic hypermutation (SHM) and class switch recombination (CSR) 1,2. AID-induced deoxyuracils within Ig loci are recognized and processed by subverted base excision and mismatch repair pathways that ensure a mutagenic outcome in B lymphocytes 3-8. However, it is unclear why DNA repair pathways that remove deoxyuracil from DNA are not efficient at faithfully repairing AID-induced lesions. Here, we identified through a genome-wide CRISPR screen that FAM72A, a protein with no ascribed function, is a major determinant for the error-prone processing of deoxyuracil. Fam72a-deficient CH12F3-2 B cells and primary B cells from Fam72a-/- mice have reduced CSR and SHM frequencies. The SHM spectrum in B cells from Fam72a-/- mice is opposite to that observed in Ung2-/- mice 9, suggesting that UNG2 is hyperactive in FAM72A-deficient cells. Indeed, FAM72A binds to UNG2 resulting in reduced UNG2 activity, and significantly reduced protein levels in the G1 phase, coinciding with peak AID activity. This effect leads to increased genome-wide deoxyuracils in B cells. By antagonizing UNG2, FAM72A therefore increases U*G mispairs that engage mutagenic mismatch repair promoting error-prone processing of AID-induced deoxyuracils. This work shows that FAM72A bridges base-excision repair and mismatch repair to modulate antibody maturation.

immunology↗

De novo assembly of 64 haplotype-resolved human genomes of diverse ancestry and integrated analysis of structural variation

Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average contig N50: 26 Mbp) integrate all forms of genetic variation across even complex loci such as the major histocompatibility complex. We focus on 107,590 structural variants (SVs), of which 68% are inaccessible by short-read sequencing. We identify new SV hotspots (spanning megabases of gene-rich sequence), characterize 130 of the most active mobile element source elements, and find that 63% of all SVs arise by homology-mediated mechanisms--a twofold increase from previous studies. Our resource now enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1,525 expression quantitative trait loci (SV-eQTLs) as well as SV candidates for adaptive selection within the human population.

genetics↗