Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 1,135 records · Page 63Linked to original sources

bioRxiv2020

Distribution of ACE2, CD147, cyclophilins, CD26 and other SARS-CoV-2 associated molecules in human tissues and immune cells in health and disease

BackgroundMorbidity and mortality from COVID-19 caused by novel coronavirus SARS-CoV-2 is accelerating worldwide and novel clinical presentations of COVID-19 are often reported. The range of human cells and tissues targeted by SARS-CoV-2, its potential receptors and associated regulating factors are still largely unknown. The aim of our study was to analyze the expression of known and potential SARS-CoV-2 receptors and related molecules in the extensive collection of primary human cells and tissues from healthy subjects of different age and from patients with risk factors and known comorbidities of COVID-19. MethodsWe performed RNA sequencing and explored available RNA-Seq databases to study gene expression and co-expression of ACE2, CD147 (BSG), CD26 (DPP4) and their direct and indirect molecular partners in primary human bronchial epithelial cells, bronchial and skin biopsies, bronchoalveolar lavage fluid, whole blood, peripheral blood mononuclear cells (PBMCs), monocytes, neutrophils, DCs, NK cells, ILC1, ILC2, ILC3, CD4+ and CD8+ T cells, B cells and plasmablasts. We analyzed the material from healthy children and adults, and from adults in relation to their disease or COVID-19 risk factor status. ResultsACE2 and TMPRSS2 were coexpressed at the epithelial sites of the lung and skin, whereas CD147 (BSG), cyclophilins (PPIA and PPIB), CD26 (DPP4) and related molecules were expressed in both, epithelium and in immune cells. We also observed a distinct age-related expression profile of these genes in the PBMCs and T cells from healthy children and adults. Asthma, COPD, hypertension, smoking, obesity, and male gender status generally led to the higher expression of ACE2- and CD147-related genes in the bronchial biopsy, BAL or blood. Additionally, CD147-related genes correlated positively with age and BMI. Interestingly, we also observed higher expression of ACE2- and CD147-related genes in the lesional skin of patients with atopic dermatitis. ConclusionsOur data suggest different receptor repertoire potentially involved in the SARS-CoV-2 infection at the epithelial barriers and in the immune cells. Altered expression of these receptors related with age, gender, obesity and smoking, as well as with the disease status might contribute to COVID-19 morbidity and severity patterns.

immunology↗

bioRxiv2020

Functional Exploration of Heterotrimeric Kinesin-II in IFT and Ciliary Length Control in Chlamydomonas

Heterotrimeric organization of kinesin-II is essential for its function in anterograde IFT in ciliogenesis. However, the molecular basis of forming this complex for its function is not well understood. In addition, the anterograde IFT velocity varies significantly in different organisms, but how motor speed affects ciliary length is not clear. We show that Chlamydomonas kinesin-II (CrKinesin-II) involves distinct mechanisms from mammals and C. elegans in its assembly to necessitate its function in IFT. Furthermore, chimeric CrKinesin-II with human kinesin-II motor domains functioned in vitro and in vivo, leading to a ~2.8-fold reduced anterograde IFT velocity and a similar fold reduction in IFT injection rate that supposedly correlates with ciliary assembly activity. However, the ciliary length was only mildly reduced (~15%). Modelling analyses suggest that such a non-linear scaling relationship between IFT velocity and ciliary length can be accounted for by limitation of the motors and/or its ciliary cargoes, e.g. tubulin.

cell biology↗

bioRxiv2020

Generating Artificial Sensations with Spinal Cord Stimulation in Primates and Rodents

For patients who have lost sensory function due to a neurological injury such as spinal cord injury (SCI), stroke, or amputation, spinal cord stimulation (SCS) may provide a mechanism for restoring somatic sensations via an intuitive, non-visual pathway. Inspired by this vision, here we trained rhesus monkeys and rats to detect and discriminate patterns of epidural SCS. Thereafter, we constructed psychometric curves describing the relationship between different SCS parameters and the animals ability to detect SCS and/or changes in its characteristics. We found that the stimulus detection threshold decreased with higher frequency, longer pulse-width, and increasing duration of SCS. Moreover, we found that monkeys were able to discriminate temporally- and spatially-varying patterns (i.e. variations in frequency and location) of SCS delivered through multiple electrodes. Additionally, sensory discrimination of SCS-induced sensations in rats obeyed Webers law of just noticeable differences. These findings suggest that by varying SCS intensity, temporal pattern, and location different sensory experiences can be evoked. As such, we posit that SCS can provide intuitive sensory feedback in neuroprosthetic devices.

neuroscience↗

bioRxiv2020

Single cell RNA sequencing reveals the landscape of early female germ cell development

Female germ cell development consists of complex events including sex determination, meiosis initiation, retardation and resumption. During early oogenesis, the asynchrony of the transition from mitosis to meiosis results in heterogeneity in the female germ cell populations at a certain embryonic stage, which limits the studies of meiosis initiation and progression at a higher resolution level. Here, we investigated the transcriptional profiles of 19363 single germ cells collected from E12.5, E14.5 and E16.5 mouse fetal ovaries. Clustering analysis identified seven groups and defined dozens of corresponding transcription factors, providing a global view of cellular differentiation from primordial germ cells towards meiocytes. Further, we explored the dynamics of gene expression within the developmental trajectory with special focus on the mechanisms underlying meiotic initiation. We found that Dpy30 may be involved in the regulation of meiosis initiation at the epigenetic level. Our data provide key insights into the transcriptome features of peri-meiotic female germ cells, which offers new information not only on meiosis initiation and progression but also on screening pathogenic mutations in meiosis-associated diseases.

developmental biology↗

bioRxiv2020

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries

Proteolysis is a major post-translational regulator of biology both inside and outside of cells. Broad identification of optimal cleavage sites and natural substrates of proteases is critical for drug discovery and to understand protease biology. Here we present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical 6 to 8 residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases 2, 3, 6, 7 and 8, and the ectodomains of the membrane sheddases, ADAMs 10 and 17. The first library (Lib 10AA) was used to determine substrate cleavage motifs. Lib 10AA contains a highly diverse randomized 10-mer substrate peptide sequences (109 unique members) that was displayed mono-valently on filamentous phage and bound to magnetic beads via an N-terminal biotin. The protease was allowed to cleave the SPD beads, and the released phage subjected to up to three total rounds of positive selection followed by next generation sequencing (NGS). This allowed us to identify from 104 to 105 unique cleavage sites over a 1000-fold dynamic range of NGS counts (ranging from 3-4000), and produced consensus and optimal cleavage motifs based positional sequencing scoring matrices that closely matched synthetic peptide data. A second SPD-NGS library (Lib hP) was constructed that allowed us to identify candidate human proteome sequences. Lib hP displayed virtually the entire human proteome tiled in contiguous 49AA sequences with 25AA overlaps (nearly 1 million members). After three rounds of positive selection we identified up to 104 natural linear cut sites depending on the protease and captured most of the examples previously identified by proteomics (ranging from 30 to 1500) and predicted 10 to 100-fold more. Structural bioinformatics was used to facilitate the identification of candidate natural protein substrates. SPD-NGS is rapid, reproducible, simple to perform and analyze, inexpensive, renewable, with unprecedented depth of coverage for substrate sequences. SPD-NGS is an important tool for protease biologists interested protease specificity for specific assays and inhibitors and to facilitate identification of natural protein substrates.

biochemistry↗

bioRxiv2020

Selective Plane Illumination Microscopy and Computing Reveal Differential Obliteration of Retinal Vascular Plexuses

Murine models of visual impairment provide micro-vascular insights into the 3-D network disarray in retinopathy. Current imaging and analysis tend to be confined to the 2-D retinal vasculature. We hereby integrated selective plane illumination imaging or known as light-sheet fluorescence microscopy (LSFM) with dual-illumination, followed by computational analyses, to reveal the topological network of vertical sprouts bridging the primary and secondary plexuses in a postnatal mouse model of oxygen-induced retinopathy (OIR). We revealed a preferential obliteration of the secondary plexus and bridging vessels despite a relatively unscathed primary plexus. We compared the local versus global vascular connectivity using clustering coefficients and Euler numbers, respectively. The global vascular connectivity in hyperoxia-exposed retinas was significantly reduced (p < 0.05, n = 5 vs. normoxia), whereas the local connectivity was preserved (p > 0.05, n = 5 vs. normoxia). We further applied principal component analysis (PCA) to automatically segment the vertical sprouts, corroborating the preferential obliteration of the interconnection between vertical sprouts and secondary plexuses that were accompanied with impaired vascular branching and connectivity, and reduced vessel volumes and lengths (p < 0.05, n=5 vs. normoxia). Thus, integration of 3-D selective plane illumination with computational analyses allows for early detection of global and spatially-specific vaso-obliteration, but preserved local reticular structure in response to hyperoxia-induced retinopathy.

bioengineering↗

bioRxiv2020

A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes

Over the past decades, optimization of media formulation and feeding strategies have fueled a many-fold improvement in CHO-based biopharmaceutical production. While Design of Experiments (DOE) and media screens have led to many advances, genome editing offers another avenue for enhancing cell metabolism and bioproduction. However the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we developed a comprehensive pooled CRISPR screen for CHO cell metabolism, including [~]16,000 gRNAs against [~]2500 metabolic enzymes and regulators. We demonstrated the value of this screen by identifying a glutamine response network in CHO cells. Glutamine is particularly important since it is often substantially over-fed to drive increased TCA cycle flux but can lead to accumulation of toxic ammonia. Within the glutamine-response network, the deletion of a novel and poorly characterized lipase, Abhd11, was found to substantially increase growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait.

bioengineering↗

bioRxiv2020

Release sites are positioned to activate NMDA receptors

Neurotransmitter is released synchronously and asynchronously following an action potential. The release sites of these two phases are segregated within an active zone, with asynchronous release sites enriched near the center. Here we demonstrate that synchronous and asynchronous release sites are aligned with AMPA receptor and NMDA receptor clusters, respectively. Computational simulations indicate that this spatial and temporal arrangement of release ensures maximal membrane depolarization through AMPA receptors, alleviating the pore-blocking magnesium leading to greater activation of NMDA receptors. Together, these results suggest that release sites are organized to efficiently activate NMDA receptors.

neuroscience↗

bioRxiv2020

Molecular basis for the ATPase-powered substrate translocation by the Lon AAA+ protease

The Lon AAA+ (adenosine triphosphatases associated with diverse cellular activities) protease (LonA) converts ATP-fuelled conformational changes into sufficient mechanical force to drive translocation of the substrate into a hexameric proteolytic chamber. To understand the structural basis for the substrate translocation process, we have determined the cryo-electron microscopy (cryo-EM) structure of Meiothermus taiwanensis LonA (MtaLonA) at 3.6 [A] resolution in a substrate-engaged state. Substrate interactions are mediated by the dual pore-loops of the ATPase domains, organized in spiral staircase arrangement from four consecutive protomers in different ATP-binding and hydrolysis states; a closed AAA+ ring is nevertheless maintained by two disengaged ADP-bound protomers transiting between the lowest and highest position. The structure reveals a processive rotary translocation mechanism mediated by LonA-specific nucleotide-dependent allosteric coordination among the ATPase domains, which is induced by substrate binding.

biophysics↗

bioRxiv2020

What does your cell really do? Model-based assessment of mammalian cells metabolic functionalities using omics data

Large-scale omics experiments have become standard in biological studies, leading to a deluge of data. However, researchers still face the challenge of connecting changes in the omics data to changes in cell functions, due to the complex interdependencies between genes, proteins and metabolites. Here we present a novel framework that begins to overcome this problem by allowing users to infer how metabolic functions change, based on omics data. To enable this, we curated and standardized lists of metabolic tasks that mammalian cells can accomplish. We then used genome-scale metabolic networks to define gene modules responsible for each specific metabolic task. We further developed a framework to overlay omics data on these modules to predict pathway usage for each metabolic task. The proposed approach allows one to directly predict how changes in omics experiments change cell or tissue function. We further demonstrated how this new approach can be used to leverage the metabolic functions of biological entities from the single cell to their organization in tissues and organs using multiple transcriptomic datasets (human and mouse). Finally, we created a web-based CellFie module that has been integrated into the list of tools available in GenePattern (www.genepattern.org) to enable adoption of the approach.

systems biology↗

bioRxiv2020

MpsLDA-ProSVM: predicting multi-label protein subcellular localization by wMLDAe dimensionality reduction and ProSVM classifier

Proteins play a significant part in life processes such as cell growth, development, and reproduction. Exploring protein subcellular localization (SCL) is a direct way to better understand the function of proteins in cells. Studies have found that more and more proteins belong to multiple subcellular locations, and these proteins are called multi-label proteins. They not only play a key role in cell life activities, but also play an indispensable role in medicine and drug development. This article first presents a new prediction model, MpsLDA-ProSVM, to predict the SCL of multi-label proteins. Firstly, the physical and chemical information, evolution information, sequence information and annotation information of protein sequences are fused. Then, for the first time, use a weighted multi-label linear discriminant analysis framework based on entropy weight form (wMLDAe) to refine and purify features, reduce the difficulty of learning. Finally, input the optimal feature subset into the multi-label learning with label-specific features (LIFT) and multi-label k-nearest neighbor (ML-KNN) algorithms to obtain a synthetic ranking of relevant labels, and then use Prediction and Relevance Ordering based SVM (ProSVM) classifier to predict the SCLs. This method can rank and classify related tags at the same time, which greatly improves the efficiency of the model. Tested by jackknife method, the overall actual accuracy (OAA) on virus, plant, Gram-positive bacteria and Gram-negative bacteria datasets are 98.06%, 98.97%, 99.81% and 98.49%, which are 0.56%-9.16%, 5.37%-30.87%, 3.51%-6.91% and 3.99%-8.59% higher than other advanced methods respectively. The source codes and datasets are available at https://github.com/QUST-AIBBDRC/MpsLDA-ProSVM/.

bioinformatics↗

bioRxiv2020

Deciphering cellular transcriptional alterations in Alzheimer's disease brains

Large-scale brain bulk-RNAseq studies identified molecular pathways implicated in Alzheimers disease (AD), however these findings can be confounded by cellular composition changes in bulk-tissue. To identify cell intrinsic gene expression alterations of individual cell types, we designed a bioinformatics pipeline and analyzed three AD and control bulk-RNAseq datasets of temporal and dorsolateral prefrontal cortex from 685 brain samples. We detected cell-proportion changes in AD brains that are robustly replicable across the three independently assessed cohorts. We applied three different algorithms including our in-house algorithm to identify cell intrinsic differentially expressed genes in individual cell types (CI-DEGs). We assessed the performance of all algorithms by comparison to single nucleus RNAseq data. We identified consensus CI-DEGs that are common to multiple brain regions. Despite significant overlap between consensus CI-DEGs and bulk-DEGs, many CI-DEGs were absent from bulk-DEGs. Consensus CI-DEGs and their enriched GO terms include genes and pathways previously implicated in AD or neurodegeneration, as well as novel ones. We demonstrated that the detection of CI-DEGs through computational deconvolution methods is promising and highlight remaining challenges. These findings provide novel insights into cell-intrinsic transcriptional changes of individual cell types in AD and may refine discovery and modeling of molecular targets that drive this complex disease.

neuroscience↗

bioRxiv2020

Consolidated bioprocessing of lignocellulose for production of glucaric acid by an artificial microbial consortium

The biomanufacturing of D-glucaric acid has been attracted increasing interest and the industrial yeast Saccharomyces cerevisiae is regarded as an excellent host for D-glucaric acid production. Here we constructed the biosynthetic pathway of D-glucaric acid in S. cerevisiae INVSc1 whose opi1 was knocked out and obtained two engineered strains, LGA-1 and LGA-C, producing record breaking titers of D-glucaric acid, 9.53 {+/-} 0.46 g/L and 11.21 {+/-} 0.63 g/L D-glucaric acid from 30 g/L glucose and 10.8 g/L myo-inositol in the mode of fed-batch fermentation, respectively. Due to the genetic stability and the outperformance in subsequent applications, however, LGA-1 was a preferable strain. As one of the top chemicals from biomass, there have been no reports on D-glucaric acid production from lignocellulose, which is the most abundant renewable on earth. Therefore, the biorefinery processes of lignocellulose for D-glucaric acid production including separated hydrolysis and fermentation (SHF), simultaneous saccharification and fermentation (SSF) and consolidated bioprocessing (CBP) were investigated in this work and CBP by an artificial microbial consortium composed of Trichoderma reesei Rut-C30 and S. cerevisiae LGA-1 was found to have relatively high D-glucaric acid titers and yields after 7 d fermentation, 0.54 {+/-} 0.12 g/L D-glucaric acid from 15 g/L Avicel, and 0.45 {+/-} 0.06 g/L D-glucaric acid from 15 g/L steam exploded corn stover (SECS), respectively. In attempts to design the microbial consortium for more efficient CBP the team consisted of the two members, T. reesei Rut-C30 and S. cerevisiae LGA-1, was found to be the best with excellent work distribution and collaboration. This desirable and promising approach for direction production of D-glucaric acid from lignocellulose deserves extensive and in-depth research.

synthetic biology↗

bioRxiv2020

Plasmodium falciparum-specific IgM B cells dominate in children, expand with malaria and produce parasite inhibitory IgM

IgG antibodies are known to play a central role in naturally acquired immunity to blood-stage malaria in humans, but little is known about the IgM response to blood-stage malaria, the mechanisms by which IgM may protect, or the underlying biology of Plasmodium falciparum (Pf)-specific IgM B cells. In a Mali cohort spanning infants to adults we conducted a longitudinal analysis of B cells specific for the Pf blood-stage antigens AMA1 and MSP1, as well as the comparator antigen influenza hemagglutinin (HA). At the uninfected baseline, before the malaria season, Pf-specific memory B cells (MBCs) in children are disproportionally IgM+ and only gradually shift to IgG+ with age, in contrast to HA-specific MBCs that are predominantly IgG+ from infancy to adulthood. In response to acute febrile malaria, Pf-specific IgM B cells increase in frequency and upregulate activation and co-stimulatory markers. B cell receptor (BCR) analysis showed that Pf-specific IgM B cells are somatically hypermutated at levels comparable to HA-specific IgG B cells. Finally, IgM antibodies from the plasma of malaria-exposed individuals were comparable to IgG in inhibiting Pf blood-stage growth in vitro, and significantly better at enhancing phagocytosis of Pf merozoites, suggesting that IgM may protect through both direct neutralization and opsonization. Thus, somatically hypermutated Pf-specific IgM MBCs dominate in early life, are activated and expand during acute malaria and are associated with plasma IgM that inhibits parasite growth in vitro.

immunology↗

bioRxiv2020

Quantify the requirements to achieve grain Zn biofortification of high-yield wheat on calcareous soils

The solution to address global human Zn deficiency is Zn biofortification of staple food crops, aimed at high grain Zn concentration as well as high yield. However, the desired high grain Zn concentration above 40 mg kg-1 is rarely observed for high-yield wheat on worldwide calcareous soils, due to inadequate Zn uptake or Zn distribution to grain. The present study aims to investigate how much Zn uptake or distribution is adequate to achieve the Zn.t of high-yield wheat on calcareous soils with low available Zn ([~] 0.5 mg kg-1). Of the 123 cultivars tested in a three-year field experiment, 19 high-yield cultivars were identified with similar yields around 7.0 t ha-1 and various grain Zn concentrations from 9.3 to 26.7 mg kg-1. The adequate Zn distribution to grain was defined from the view of Zn biofortification, as the situation where the Zn distribution to grain (Zn harvest index) increased to the observed maximum of [~] 91.0% and the Zn concentration of vegetative parts (straw Zn concentration) decreased to the observed minimum of [~] 1.5 mg kg-1 (Zn.m). Under the assumed condition of adequate Zn distribution to grain ([~] 91.0%), all the extra Zn above Zn.m was remobilized from straw to grain and the grain Zn concentration would be increased to its highest attainable level, which was 14.5 [~] 31.3 mg kg-1 for the 19 high-yield cultivars but still lower than 40 mg kg-1. Thus, even with the adequate Zn distribution to grain, the current Zn uptake is still not adequate and needs to be increased to 308 g ha-1 or higher to achieve Zn.t for high-yield wheat (7.0 t ha-1) on low-Zn calcareous soils. Besides, the established method here can also provide the priority measures and quantitative guidelines to achieve Zn biofortification in other wheat production regions.

plant biology↗

bioRxiv2020

Hybrid origin of Populus tomentosa Carr. identified through genome sequencing and phylogenomic analysis

Populus tomentosa is widely distributed and cultivated in the Northern and Central China, where it is of great economic and ecological importance. However, the origin of P. tomentosa remains controversial. Here, we used a PacBio+Hi-C+Illumina strategy to sequence and assemble its 740.2 Mb (2n) genome. The assembly accounts for greater than 92.1% of the 800-megabase genome, comprises 38 chromosomes, and contains 59,124 annotated protein-coding genes. Phylogenomic analyses elucidated dynamic genome evolution events among its closely related white poplars, and revealed that tomentosa is comprised of two subgenomes, which we deomonstrate is likely to have resulted from hybridization between Populus adenopoda as the female, and Populus alba var. pyramidalis as the male, around 3.93 Mya. We also detected structural variations and allele-indels across genome. Our study presents a high quality and well assembled genome, unveils the origin of the widely distributed and planted P. tomentosa, and provides a powerful resource for comparative plant biology, breeding, and biotechnology.

genomics↗

bioRxiv2020

CBRPP: a new RNA-centric method to study RNA-protein interactions

RNA-protein interactions play essential roles in tuning gene expression at RNA level and modulating the function of proteins. Abnormal RNA-protein interactions lead to cell dysfunction and human diseases. Therefore, mapping networks of RNA-protein interactions is crucial for understanding cellular mechanism and pathogenesis of diseases. Different practical protein-centric methods for studying RNA-protein interactions has been reported, but few RNA-centric methods exist. Here, we developed CRISPR-based RNA proximity proteomics (CBRPP), a new RNA-centric method to identify proteins associated with the target RNA in native cellular context without cross-linking or RNA manipulation in vitro. CBRPP is based on a fusion of dCas13 and proximity-based labeling (PBL) enzyme. dCas13 can deliver PBL enzyme to the target RNA with high specificity, while PBL enzyme labels the surrounding proteins of the target RNA, which are then identified by mass spectrometry.

molecular biology↗

bioRxiv2020

Insulin/IGF signaling and TOR promote vitellogenesis via inducing juvenile hormone biosynthesis

Vitellogenesis, including vitellogenin (Vg) production in the fat body and Vg uptake by maturing oocytes, is of great importance for the successful reproduction of adult females. The endocrinal and nutritional regulation of vitellogenesis differs distinctly in insects. Here, the complex crosstalk between juvenile hormone (JH) and the two nutrient sensors, insulin/IGF signaling (IIS) and target of rapamycin (TOR), was investigated to elucidate the molecular mechanisms regulating vitellogenesis in the American cockroach, Periplaneta americana. Our data showed that a block of JH biosynthesis or JH action arrested vitellogenesis, partially by inhibiting the expression of doublesex (Dsx), a key transcription factor gene involved in the sex determination cascade. Depletion of IIS and TOR blocked both JH biosynthesis and vitellogenesis. Importantly, the JH analog methoprene, but not bovine insulin (to restore IIS) and amino acids (to restore TOR activity), restored vitellogenesis in the neck-ligated (both nutrient- and JH-deficient) cockroaches. Combining classic physiology with modern molecular techniques, we have demonstrated that JH signaling alone is able to induce vitellogenesis and thus ovarian maturation. By contrast, IIS and TOR do not induce vitellogenesis independent of JH, the nutrient sensors promote vitellogenesis in an indirect manner via activating JH biosynthesis.

developmental biology↗