RNA-Seq Reveals the Angiogenesis Diversity between the Fetal and Adults Bone Mesenchyme Stem Cell

<div><p>In this research, we used RNA sequencing (RNA-seq) to analyze 23 single cell samples and 2 bulk cells sample from human adult bone mesenchyme stem cell line and human fetal bone mesenchyme stem cell line. The results from the research demonstrated that there were big differences between two cell lines. Adult bone mesenchyme stem cell lines showed a strong trend on the blood vessel differentiation and cell motion, 48/49 vascular related differential expressed genes showed higher expression in adult bone mesenchyme stem cell lines (Abmsc) than fetal bone mesenchyme stem cell lines (Fbmsc). 96/106 cell motion related genes showed the same tendency. Further analysis showed that genes like ANGPT1, VEGFA, FGF2, PDGFB and PDGFRA showed higher expression in Abmsc. This work showed cell heterogeneity between human adult bone mesenchyme stem cell line and human fetal bone mesenchyme stem cell line. Also the work may give an indication that Abmsc had a better potency than Fbmsc in the future vascular related application.</p></div

Aggregation-Induced Emission Fluorophore-Incorporated Curcumin-Based Ratiometric Nanoprobe for Hypochlorite Detection in Food Matrices

The development of efficient, economic, reliable, and accurate monitoring of hypochlorite (ClO–) in food matrices is in great demand for food safety assessment, particularly during its massive use against the COVID-19 epidemic. Here, we prepared an aggregation-induced emission (AIE) fluorophore tetraphenylethylene (TPE)-incorporated curcumin-based hybrid ratiometric fluorescence nanoprobe (Curcumin/TPE@HyNPs) through amphiphilic phospholipid polymer-powered nanoprecipitation, which exhibited a fast, highly sensitive, and selective response to the residual ClO– in real food matrices. Because of the inner filter effect (IFE) from curcumin toward TPE inside the nanoprobe, the bright fluorescence of TPE aggregation at ∼437 nm was effectively quenched, along with an enhanced fluorescence of curcumin at ∼478 nm. Once there was a ClO– residue in food matrices, ClO– triggered the oxidation of o-methoxyphenol inside curcumin and led to the almost complete absorption collapse, thereby terminating curcumin fluorescence at ∼478 nm and the IFE process. Accordingly, the fluorescence of TPE at ∼437 nm was recovered. In this case, a ratiometric fluorescent response of Curcumin/TPE@HyNPs toward the residual ClO– in food matrices (e.g., milk) was proposed with a low detection limit of 0.353 μM and a rapid response time of 140.0 s. Notably, the phospholipid polymer as the protection layer effectively reduced/evaded the nonspecific binding of signal reporters inside the nanoprobe, facilitating it to directly monitor the residual ClO– in real food matrices. This work provided a novel approach to utilize the unconventional AIE luminophors for constructing the efficient and reliable early warning mechanisms toward various food contaminants

The general results of the RNAseq.

<p>a) The distribution of genes in single cell sample and bulk cell sample with the FPKM≥1, red: Fetal bmsc bulk cell, blue: Fetal bmsc, green: Adult bmsc, orange: Adult bmsc bulk cell; b-e) The Pearson and Spearman correlation coefficient were calculated between different groups. b) Abmsc and hESC; c) Abmsc and Fbmsc, d) Fbmsc and hESC; e) Adult bmsc bulk cell and Fetal bmsc bulk cell; e) Unsupervised clustering of the transcriptome of single cell sample. All RefSeq genes expressed in at least one of the samples with FPKM ≥ 1 were used for the analysis, with the order of hESC, Fbmsc and Abmsc.</p

WGCNA analysis on the DEgene datasets.

<p>a,b) With the function of ClueGo in Cytoscape, graphic depiction of blue module (the vasculature development, regulation of cellular component movement) was shown. Before each viewing modules, parameters of P<10⁻⁵, %associated gene >8, and kappa = 0.5 were used to decrease the genes and Go terms in the module. The colors in the network showed the different cell lines expression. Red mean Abmsc showed the highest expression among the cell lines; while green mean Fbmsc and purple mean hESC. c) The relative expression of ANGPT1, VEGFA, FGF2, PDGFB and PDGFRA between Abmsc and Fbmsc.</p

The DEgenes among the three cell lines

<p>, a) Principal-component analysis (PCA) of the transcriptome of three different cells. The different color circles indicated the three different cell lines. PCA1, PCA2 and PCA3 represent the top three dimensions of the genes showing differential expression among these cells, which accounts for 16.69%, 9.37% and 4.17% of the expressed RefSeq genes, respectively. b) Volcano plot of genes differentially expressed in Abmsc and Fbmsc samples. The log2 fold change difference between the samples was represented on the x-axis, and negative log of q-values is represented on the y-axis. Each point represents one gene, which had detectable expression in both samples. The genes differentially expressed in Abmsc compared with Fbmsc were plotted in blue for down-regulated genes and red for up-regulated genes, and non-significant genes are shown as green points. c) Clusters of genes showing representative expression patterns during three cell lines. We selected all of the genes that were differentially expressed between any two samples (fold change > 2 or <0.5, P < 0.01).</p

Data_Sheet_1_Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer.docx

Colorectal cancer (CRC) is the second leading cause of cancer deaths and continuously increases new cancer cases globally. Accumulating evidence links risks of CRC to antibiotic use. Long-term use and abuse of antibiotics increase the resistance of the gut microbiota; however, whether CRC is associated with antibiotic resistance in gut microbiota is still unclear. In this study, we performed a de novo assembly to metagenomic sequences in 382 CRC patients and 387 healthy controls to obtain representative species-level genome bins (rSGBs) and plasmids and analyzed the abundance variation of species and antibiotic resistance genes (ARGs). Twenty-five species and 65 ARGs were significantly enriched in the CRC patients, and among these ARGs, 12 were multidrug-resistant genes (MRGs), which mainly included acrB, TolC, marA, H-NS, Escherichia coli acrR mutation, and AcrS. These MRGs could confer resistance to fluoroquinolones, tetracyclines, cephalosporins, and rifamycin antibiotics by antibiotic efflux and inactivation. A classification model was built using the abundance of species and ARGs and achieved areas under the curve of 0.831 and 0.715, respectively. Our investigation has identified the antibiotic resistance types of ARGs and suggested that E. coli is the primary antibiotic resistance reservoir of ARGs in CRC patients, providing valuable evidence for selecting appropriate antibiotics in the CRC treatment.</p

Engineering an Enzymatic Cascade Catalytic Smartphone-Based Sensor for Onsite Visual Ratiometric Fluorescence–Colorimetric Dual-Mode Detection of Methyl Mercaptan

Precise and reliable onsite detection of methyl mercaptan (CH3SH) is of great significance for environmental surveillance. Here, we synthesized a novel blue fluorescence nanozyme CeO2@TPE with high peroxidase-like activity by employing aggregation-induced emission (AIE) tetraphenylethene (TPE) to embed into hollow CeO2 nanospheres. In the presence of ethanol oxidase (AOX) and o-phenylenediamine (OPD), we engineered an enzymatic cascade activation ratiometric fluorescence–colorimetric dual-mode system AOX/CeO2@TPE + OPD toward CH3SH. In this design, CH3SH initiated AOX catalytic activity to convert it into H2O2 for activating the peroxidase-like activity of CeO2@TPE, producing •OH for oxidizing the naked-eye colorless OPD into deep yellow 2,3-diaminophenazine (DAP) with an absorption enhancement at ∼425 nm, companied by a new emission peak at ∼550 nm to match with the intrinsic emission at ∼441 nm for observing ratiometric fluorescence response, enabling a ratiometric fluorescence–colorimetric dual-mode analysis. Interestingly, both the ratiometric fluorescence and colorimetric signals could be gathered for being converted into the hue parameter on a smartphone-based sensor, achieving the onsite visual fluorescence–colorimetric dual-mode detection of CH3SH in real environmental media with acceptable results. This study gave a novel insight into designing target-responsive enzymatic cascade activation system-based efficient and reliable dual-mode point-of-care sensors for safeguarding environmental health

Data_Sheet_2_Species-Level Analysis of the Human Gut Microbiome Shows Antibiotic Resistance Genes Associated With Colorectal Cancer.xlsx

Colorectal cancer (CRC) is the second leading cause of cancer deaths and continuously increases new cancer cases globally. Accumulating evidence links risks of CRC to antibiotic use. Long-term use and abuse of antibiotics increase the resistance of the gut microbiota; however, whether CRC is associated with antibiotic resistance in gut microbiota is still unclear. In this study, we performed a de novo assembly to metagenomic sequences in 382 CRC patients and 387 healthy controls to obtain representative species-level genome bins (rSGBs) and plasmids and analyzed the abundance variation of species and antibiotic resistance genes (ARGs). Twenty-five species and 65 ARGs were significantly enriched in the CRC patients, and among these ARGs, 12 were multidrug-resistant genes (MRGs), which mainly included acrB, TolC, marA, H-NS, Escherichia coli acrR mutation, and AcrS. These MRGs could confer resistance to fluoroquinolones, tetracyclines, cephalosporins, and rifamycin antibiotics by antibiotic efflux and inactivation. A classification model was built using the abundance of species and ARGs and achieved areas under the curve of 0.831 and 0.715, respectively. Our investigation has identified the antibiotic resistance types of ARGs and suggested that E. coli is the primary antibiotic resistance reservoir of ARGs in CRC patients, providing valuable evidence for selecting appropriate antibiotics in the CRC treatment.</p

Direct Oxidative Amination of the Methyl C–H Bond in N‑Heterocycles over Metal-Free Mesoporous Carbon

Direct oxidative amination of the sp3 C–H bond is an attractive synthesis route to obtain amides. Conventional catalytic systems for this transformation are based on transition metals and complicated synthesis processes. Herein, direct and efficient oxidative amination of the methyl C–H bond in a wide range of N-heterocycles to access the corresponding amides over metal-free porous carbon is successfully developed. To understand the fundamental structure–activity relationships of carbon catalysts, the surface functional groups and the graphitization degree of porous carbon have been purposefully tailored through doping with nitrogen or phosphorus. The results of characterization, kinetic studies, liquid-phase adsorption experiments, and theoretical calculations indicate that the high activity of the carbon catalyst is attributed to the synergistic effect of surface acidic functional groups (hydroxyl/carboxylic acid/phosphate) and more graphene edge structures exposed on the surface of carbon materials with a high graphitization degree, in which the role of acidic functional groups is to adsorb the substrate molecule and the role of the graphene edge structure is to activate O2

Blocking Oxidase-Mimicking Activity-Driven Label-Free Photothermal and Colorimetric Synergistic Sensing for Intelligent Onsite Detection of Tetracycline Residues in Milk

Considering the potential misuse of antibiotics to improve the yield and economic benefits in the production of animal-derived foods such as milk, the development of a simple, label-free, precise, reliable, low-cost, and onsite assay for antibiotic residues is highly desirable to ensure food safety. In this scenario, we here proposed a hybrid oxidase-mimicking nanozyme of the Ru@g-C3N4 nanosheet that combines with 3,3′,5,5′-tetramethylbenzidine (TMB) to develop a blocking oxidase-mimicking activity-driven photothermal and colorimetric synergistic sensing platform for intelligent onsite detection of tetracycline antibiotics (TCs). In the absence of TCs, the prominent oxidase-mimicking activity of Ru@g-C3N4 rapidly catalyzed colorless TMB to dark-blue oxTMB, accompanied by the appearance of an obvious absorbance enhancement at 655 nm and a remarkable photothermal signal upon 660 nm laser irradiation. Conversely, the remaining TCs effectively blocked this chromogenic reaction because of the π–π stacking of its tetraphenyl skeleton with the Ru@g-C3N4 nanozyme to block the affinity of TMB to the catalytic active site inside Ru@g-C3N4. Based on this, a TCs residual level-dependent photothermal and colorimetric signal synergistic decrease sensing platform was developed with the assistance of a 660 nm laser-assisted hand-held thermal imager and a Color Picker APP-inbuilt smartphone, which demonstrated the intelligent onsite label-free, reliable, and precise detection of TCs in real milk samples with acceptable results. Notably, this oxidase-mimicking nanozyme-based dual-mode sensing platform provided a built-in cross-reference correction to improve not only the accuracy but also the reliability for TC detection in milk, which showed a vast promise in the further development of commercial point-of-care testing to achieve early warning of antibiotic residues to ensure the quality and safety of animal-derived foodstuffs