Biology subjects

Pan, S.

Publications and source records attributed to Pan, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

Accelerated Bone Healing in Calvarial and Femoral Defects with Injectable Microcarriers that Mimic the Osteogenic Niche

Osteo-enhanced human mesenchymal stem cells (OEhMSCs) secrete an osteogenic cell matrix (OCM) that mimics the composition of anabolic bone tissue and strongly enhances OEhMSC retention and subsequent bone repair in vivo. Here we demonstrate a system for rapid production of gelatin methacrylate microcarriers coated with decellularized OCM (OCM-GelMA) to serve as an injectable bone graft material with high osteogenic potential comparable to a clinically utilized gold standard, bone morphogenic protein 2 (BMP-2). OEhMSCs seeded onto OCM-GelMA secreted high levels of osteogenic and angiogenic cytokines and expressed higher levels of BMP-2 relative to OEhMSCs on bare GelMA microcarriers. OEhMSCs co-administered with OCM-GelMA microcarriers resulted in enhanced healing of murine critical-sized calvarial defects, which was comparable to that achieved with a BMP-2-laden gelatin sponge control. When tested in a murine femoral defect model, OCM-GelMA co-administered with OEhMSCs also induced profound bone growth within the defect. We submit that OCM-GelMA promotes OEhMSC paracrine release to accelerate bone repair, indicating their potential as a bone graft for use in minimally invasive surgery.

bioengineering↗

bioRxiv2021

Bicolor angelfish (Centropyge bicolor) provides the first chromosome-level genome of the Pomacanthidae family

The Bicolor Angelfish, Centropyge bicolor, is a tropical coral reef fish. It is named for its striking two-color body. However, a lack of high-quality genomic data means little is known about the genome of this species. Here, we present a chromosome-level C. bicolor genome constructed using Hi-C data. The assembled genome is 650 Mbp in size, with a scaffold N50 value of 4.4 Mbp, and a contig N50 value of 114 Kbp. Protein-coding genes numbering 21,774 were annotated. Our analysis will help others to choose the most appropriate de novo genome sequencing strategy based on resources and target applications. To the best of our knowledge, this is the first chromosome-level genome for the Pomacanthidae family, which might contribute to further studies exploring coral reef fish evolution, diversity and conservation.

genomics↗

bioRxiv2021

SemiBin: Incorporating information from reference genomes with semi-supervised deep learning leads to better metagenomic assembled genomes (MAGs)

Metagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and allow the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we propose SemiBin, an open source tool that uses neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of binning genomes that are outside the reference dataset. SemiBin outperforms existing state-of-the-art binning methods in simulated and real microbiome datasets across three different environments (human gut, dog gut, and marine microbiomes). SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species. SemiBin is available as open source software at https://github.com/BigDataBiology/SemiBin/.

bioinformatics↗

bioRxiv2021

metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies

Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC (https://github.com/ZhaoXM-Lab/metaMIC), a machine-learning based tool for identifying and correcting misassemblies in metagenomic assemblies. Benchmarking results on both simulated and real datasets demonstrate that metaMIC outperforms existing tools when identifying misassembled contigs. Furthermore, metaMIC is able to localize the misassembly breakpoints, and the correction of misassemblies by splitting at misassembly breakpoints can improve downstream scaffolding and binning results.

bioinformatics↗

bioRxiv2021

Clinical Strains of Pseudomonas aeruginosa secret LasB protease to induce hemorrhagic diffused alveolar damage and acute lung injury in mice

BackgroundAcute lung injury and acute respiratory distress syndrome are most often caused by bacterial pneumonia, characterized by severe dyspnea and high mortality. Knowledge about the lung injury effects of current clinical bacteria strains is lacking. The aim of this study was to investigate the ability of representative pathogenic bacteria isolated from patients to cause ALI/ARDS in mice and identify the virulent factors. Method7 major bacteria species were isolated from clinical sputum and instilled in to mice airway unilaterally. Histology study was used to judge the lung injury effect. Virulence genes were examined by PCR. Sequence type of P. aeruginosa strains were identified by MLST. LC-MS/MS was used to identify the suspicious protein bands. LasB was purified through DEAE-cellulose column and its toxicity was tested both in vitro and in vivo. ResultsStaphylococcus aureus, Streptococcus pneumoniae, Streptococcus agalactiae, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Escherichia coli were randomly separated and tested 3 times. Among them, gram-negative bacteria are more potential than gram-positive bacteria to cause acute lung injury. However, P. aeruginosa is the only pathogen which induced diffused alveolar damage, hemorrhage and hyaline membrane in the lung of mice. The lung injury effect is associated to the excreted matrix metalloproteinase LasB of P. aeruginosa. Purified LasB recapitulated hemorrhagic acute lung injury identical to P. aeruginosa infection in vivo. We found this was due to the powerful degradation effect of LasB on both lung extracellular matrix and key proteins in coagulation cascade without inducing cellular apoptosis. ConclusionP. aeruginosa strains are most capable to induce ALI/ARDS among major clinical pathogenic bacteria, this ability is specifically attributed to their LasB production.

microbiology↗

bioRxiv2021

HNF4α isoforms regulate the circadian balance between carbohydrate and lipid metabolism in the liver

Hepatocyte Nuclear Factor 4 (HNF4), a master regulator of hepatocyte differentiation, is regulated by two promoters (P1 and P2). P1-HNF4 is the major isoform in the adult liver while P2-HNF4 is thought to be expressed only in fetal liver and liver cancer. Here, we show that P2- HNF4 is expressed at ZT9 and ZT21 in the normal adult liver and orchestrates a distinct transcriptome and metabolome via unique chromatin and protein-protein interactions. We demonstrate that while P1-HNF4 drives gluconeogenesis, P2-HNF4 drives ketogenesis and is required for elevated levels of ketone bodies in females. Exon swap mice expressing only P2- HNF4 exhibit subtle differences in circadian gene regulation and disruption of the clock increases expression of P2-HNF4. Taken together, we propose that the highly conserved two-promoter structure of the Hnfa gene is an evolutionarily conserved mechanism to maintain the balance between gluconeogenesis and ketogenesis in the liver in a circadian fashion.

genomics↗

bioRxiv2021

An ultrasensitive GRAB sensor for detecting extracellular ATP in vitro and in vivo

The purinergic transmitter ATP (adenosine 5-triphosphate) plays an essential role in both the central and peripheral nervous systems, and the ability to directly measure extracellular ATP in real time will increase our understanding of its physiological functions. We developed an ultrasensitive GPCR Activation-Based ATP sensor called GRABATP1.0, with a robust fluorescence response to extracellular ATP when expressed in several cell types. This sensor has sub-second kinetics, ATP affinity in the range of tens of nanomolar, and can be used to localize ATP release with subcellular resolution. Using this sensor, we monitored ATP release under a variety of in vitro and in vivo conditions, including primary hippocampal neurons, a zebrafish model of injury-induced ATP release, and LPS-induced ATP-release events in individual astrocytes in the mouse cortex measured using in vivo two-photon imaging. Thus, the GRABATP1.0 sensor is a sensitive, versatile tool for monitoring ATP release and dynamics under both physiological and pathophysiological conditions.

neuroscience↗

bioRxiv2020

Acute unilateral emphysema induced by Pseudomonas aeruginosa in mice

Pulmonary emphysema is the major pathological feature of chronic obstructive pulmonary disease (COPD). Although the pathogenesis of emphysema is still not completely understood, but until now a bacterial cause has not really been considered. Recently, we found that the secretion from Pseudomonas aeruginosa could cause severe lung emphysema in mice rapidly. Since the bacterium is ubiquitous and secrets proteases, we hypothesized that direct P. aeruginosa airway infection would have a similar effect. To address this issue, we applied a unilateral lung injury model. First, we observed the dynamic pathophysiology change of acute emphysema. P. aeruginosa secretion was extracted and instilled intratracheally into the left lungs of C57BL/6 and C3H/HeJ mice, while the right lungs were saved as self-control. Alveolar diameter and lung compliance were measured. Later, we tested the effect of P. aeruginosa inoculation in normal C57BL/6 mice, immunosuppressed C57BL/6 mice, and C3H/HeJ (TLR4 deficient) mice. P. aeruginosa secretion extract caused acute panacinar emphysema and decreased dynamic lung compliance. Different types of emphysema are transformable. However, the P. aeruginosa infection could only elicit emphysema in immunosuppressed C57BL/6 mice and C3H/HeJ mice, indicating that normal immunity is essential to protect the hosts from emphysema. Emphysema induced by P. aeruginosa in mice recapitulates all the main features of human emphysema and COPD. Our finding filled a major gap in COPD pathogenesis. We believe P. aeruginosa is the underlying cause of COPD.

pathology↗

bioRxiv2020

Plant DNA polymerases alpha and delta mediate replication of geminiviruses

Geminiviruses are causal agents of devastating diseases in crops. Geminiviruses have circular single-stranded (ss)DNA genomes that are replicated in the nucleus of the infected plant cell through double-stranded (ds)DNA intermediates by the plants DNA replication machinery; which host DNA polymerase mediates geminiviral multiplication, however, has so far remained elusive. Here, we show that subunits of the nuclear replicative DNA polymerases and {delta} physically interact with the geminivirus-encoded replication enhancer protein, C3, and are required for viral replication. Our results suggest that while DNA polymerase is essential to generate the viral dsDNA intermediate, DNA polymerase {delta} mediates the synthesis of new copies of the geminiviral ssDNA genome, and that the virus-encoded C3 acts selectively recruiting DNA polymerase {delta} over {varepsilon} to favour a productive replication.

plant biology↗

bioRxiv2020

An Antioxidant Enzyme Therapeutic for COVID-19

The COVID-19 pandemic has taken a significant toll on people worldwide, and there are currently no specific antivirus drugs or vaccines. We report herein a therapeutic based on catalase, an antioxidant enzyme that can effectively breakdown hydrogen peroxide and minimize the downstream reactive oxygen species, which are excessively produced resulting from the infection and inflammatory process. Catalase assists to regulate production of cytokines, protect oxidative injury, and repress replication of SARS-CoV-2, as demonstrated in human leukocytes and alveolar epithelial cells, and rhesus macaques, without noticeable toxicity. Such a therapeutic can be readily manufactured at low cost as a potential treatment for COVID-19.

biochemistry↗

bioRxiv2020

A GRAB sensor reveals activity-dependent non-vesicular somatodendritic adenosine release

The purinergic signaling molecule adenosine (Ado) modulates many physiological and pathological brain functions,but its spatiotemporal release dynamics in the brain remains largely unknown. We developed a genetically encoded GPCR-Activation-Based Ado sensor (GRABAdo) in which Ado-induced changes in the human A2A receptor are reflected by fluorescence increases. This GRABAdo revealed that neuronal activity-induced extracellular Ado elevation was due to direct Ado release from somatodendritic regions of the neuron, requiring calcium influx through L-type calcium channels, rather than the degradation of extracellular ATP. The Ado release was slow ([~]30 s) and depended on equilibrative nucleoside transporters (ENTs) rather than conventional vesicular release mechanisms. Thus, GRABAdo reveals an activity-dependent slow Ado release from somatodendritic region of the neuron, potentially serving modulating functions as a retrograde signal.

neuroscience↗

bioRxiv2020

High affinity of Skp to OmpC revealed by single-molecule detection

Outer membrane proteins (OMPs) are essential to Gram-negative bacteria, and they need molecular chaperones to prevent from aggregation in periplasm during the OMPs biogenesis. Seventeen kilodalton protein (Skp) is the major protein for this purpose. Here we used singlemolecule detection (SMD) to study the stoichiometry modulation of Skp in binding with outer membrane protein C (OmpC) from Escherichia coli. To accomplish our task, we developed the tool of portion selectively chosen fluorescence correlation spectroscopy (pscFCS). We found that Skp binds OmpC with high affinity. The half concentration for Skp to form homotrimer Skp3 (C1/2) was measured to be 250 nM. Under the Skp concentrations far below C1/2 OmpC can recruit Skp monomers to form OmpC{middle dot}Skp3. The affinity of the process is in picomolar range, indicating that the trimerization of Skp in OmpC{middle dot}Skp3 complex is induced by OmpC-Skp interaction even though free Skp3 is rarely present. In the concentration range that Skp3 is the predominant form, OmpC may directly interact with Skp3. Under micro-molar concentrations of Skp, the formation of OmpC{middle dot}(Skp3)2 was observed. Our results suggest that the fine-tuned modulation of Skp composition stoichiometry plays an important role in the safe-guarding and quality control mechanism of OMPs in the periplasm.

biophysics↗

bioRxiv2020

Menthol in Electronic Cigarettes: A Contributor to Respiratory Disease?

Menthol is widely used in tobacco products. This study compared the effects of menthol on human bronchial epithelium using submerged cultures, a VITROCELL(R) cloud chamber that provides air liquid interface (ALI) exposure without solvents or heating, and a Cultex ALI system that delivers aerosol equivalent to that inhaled during vaping. In submerged culture, menthol significantly increased calcium influx and mitochondrial reactive oxygen species (ROS) via the TRPM8 receptor, responses that were inhibited by a TRPM8 antagonist. VITROCELL(R) cloud chamber exposure of BEAS-2B monolayers increased mitochondrial protein oxidation, expression of the antioxidant enzyme SOD2, activation of NF-{kappa}B, and secretion of inflammatory cytokines (IL-6 and IL-8). Proteomics data collected following ALI exposure of 3D EpiAirway tissue in the Cultex showed upregulation of NRF-2-mediated oxidative stress, oxidative phosphorylation, and IL-8 signaling. Across the three platforms, menthol adversely effected human bronchial epithelium in a manner that could lead to respiratory disease. O_FIG O_LINKSMALLFIG WIDTH=115 HEIGHT=200 SRC="FIGDIR/small/988006v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@b86c96org.highwire.dtl.DTLVardef@1e12bd2org.highwire.dtl.DTLVardef@4008corg.highwire.dtl.DTLVardef@c01cad_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract. Mechanism of action of menthol on human bronchial epithelium.Three in vitro platforms were used to study the effect of menthol on bronchial epithelium. In submerged culture (using BEAS-2B cells), menthol produced rapid calcium influx followed by an increase in oxidative stress and inflammatory cytokines. ALI exposure of BEAS-2B cells to unheated menthol in a cloud chamber caused activation of an inflammatory transcription factor (NF-{kappa}B) and oxidative stress. Proteomics analysis of human EpiAirway tissues exposed at the ALI to heated menthol EC aerosols identified changes in the expression of proteins involved in oxidative stress and in an inflammatory response. C_FIG

cell biology↗

bioRxiv2020

Relatively semi-conservative replication and a folded slippage model for simple repeat sequences

Simple sequence repeats (SSRs) are found ubiquitously in almost all genome, and their formation mechanism is ambiguous yet. Here, the SSRs were analyzed in 55 randomly selected segments of genomes from a fairly wide range of species, with introducing more open standard for extensively mining repeats. A high percentage of repeats were discovered in these segments, which is inconsistent with the current theory suggested that repeats tend to disappear over long-term evolution. Therefore, a mechanism is most probably responsible for continually producing repeats during replication to balance continuous repeat disappearance, which may makes the replicating process relatively semi-conservative. To improve the current straight-line slippage model, we proposed a folded slippage model involving the geometric space of nucleotides and hydrogen bond stability to explain the high-percent SSR occurrence, which can describe SSR expansion and contraction more reasonably. And analysis of external forces in the folding template strands suggested that the microsatellites tend to expand than contract. Our research may provide implements for contributions of microsatellites to genome evolution and complement semi-conservative replication.

molecular biology↗

bioRxiv2020

A genetically encoded GRAB sensor for measuring serotonin dynamics in vivo

Serotonin (5-HT) is a phylogenetically conserved monoamine neurotransmitter modulating a variety of processes in the brain. To directly visualize the dynamics of 5-HT, we developed a genetically encoded GPCR-Activation-Based 5-HT (GRAB5-HT) sensor with high sensitivity, selectivity, and spatiotemporal resolution. GRAB5-HT, detected 5-HT release in multiple physiological and pathological conditions in both flies and mice, and thus provides new insights into the dynamics and mechanisms of 5-HT signaling.

neuroscience↗

bioRxiv2019

FACS: antimicrobial peptide screening in genomes and metagenomes

MotivationAntimicrobial peptides (AMPs) have the potential to tackle multidrug-resistant pathogens in both clinical and non-clinical contexts. The recent growth in the availability of genomes and metagenomes provides an opportunity for in silico prediction of novel AMP molecules. However, due to the small size of these peptides, standard gene prospection methods cannot be applied in this domain and alternative approaches are necessary. In particular, standard gene prediction methods have low precision for short peptides, and functional classification by homology results in low recall. ResultsHere, we present Macrel (for metagenomic AMP classification and retrieval), which is an end-to-end pipeline for the prospection of high-quality AMP candidates from (meta)genomes. For this, we introduce a novel set of 22 peptide features. These were used to build classifiers which perform similarly to the state-of-the-art in the prediction of both antimicrobial and hemolytic activity of peptides, but with enhanced precision (using standard benchmarks as well as a stricter testing regime). We demonstrate that Macrel recovers high-quality AMP candidates using realistic simulations and real data. AvailabilityMacrel is implemented in Python 3. It is available as open source at https://github.com/BigDataBiology/macrel and through bioconda. Classification of peptides or prediction of AMPs in contigs can also be performed on the webserver: http://big-data-biology.org/software/macrel.

bioinformatics↗

bioRxiv2019

An optimized acetylcholine sensor for monitoring in vivo cholinergic activity

The ability to directly measure acetylcholine (ACh) release is an essential first step towards understanding its physiological function. Here we optimized the GRABACh (GPCR-Activation-Based-ACh) sensor with significantly improved sensitivity and minimal downstream coupling. Using this sensor, we measured in-vivo cholinergic activity in both Drosophila and mice, revealing compartmental ACh signals in fly olfactory center and single-trial ACh dynamics in multiple regions of the mice brain under a variety of different behaviors

neuroscience↗

bioRxiv2019

Clinicopathological characteristics and survival of lymphoepithelial carcinoma of the oral cavity and pharynx: a population-based study

Lymphoepithelial carcinoma (LEC) of the oral cavity and pharynx is uncommon, and the characteristics and survival remains unclear. The present study aims to describe the clinicopathological characteristics and determine the factors associated with survival of this uncommon cancer. A population-based study was carried out to investigate clinical characteristics and prognosis of LEC of the oral cavity and pharynx using the data from Surveillance, Epidemiology and End Results (SEER) database between 1988 and 2013. The propensity-matched analysis was conducted for prognostic analysis, and a prognostic nomogram was also constructed. Totally, 1025 patients with LEC of the oral cavity and pharynx were identified, including 769 nasopharyngeal LEC patients and 256 non-nasopharyngeal LEC patients. The median OS of all LEC patients was 232.0m (95% CI 169.0-258.0). The 1-, 5-, 10- and 20-year survival rates were 92.9%, 72.9%, 59.3%, and 46.8%, respectively. Surgery could significantly prolong the survival time of LEC patients (P<0.01, mOS: 190m vs. 255m). Radiotherapy, as well as radiotherapy after surgery, could prolong the mOS (P<0.01 for both). The survival analysis demonstrated that old age (>60 years), lymph node (N3) and distant metastases were independent factors for poor survival, whereas radiotherapy and surgery were independent factors for favorable survival. No significant differences in survival time between nasopharyngeal LEC and non-nasopharyngeal LEC patients were observed. The prognostic nomogram was established base on five independent prognostic factors (C-index=0.70; 95% CI 0.66-0.74). In conclusion, LEC of the oral cavity and pharynx is a rare disease, and old age, lymph node and distant metastases, surgery and radiotherapy were significantly associated with prognosis. The prognostic nomogram could be used to make individual predictions of OS.

genetics↗