The cryo-thermal therapy-induced IL-6-rich acute pro-inflammatory response promoted DCs phenotypic maturation as the prerequisite to CD4⁺ T cell differentiation

<p>In our previous studies, a novel tumour therapeutic modality of the cryo-thermal therapy has been developed leading to long-term survival in 4T1 murine mammary carcinoma model. The cryo-thermal therapy induced the strong acute inflammatory response and IL-6 was identified in an acute profile. In this study, we found that the cryo-thermal therapy triggered robust acute inflammatory response with high expression of IL-6 locally and systemically. The phenotypic maturation of dendritic cells (DCs) was induced by acute IL-6 following the treatment. The mature DCs promoted CD4⁺ T cell differentiation. Moreover, the production of interferon γ (IFN γ) in the serum and CD4⁺ T cells were both abrogated by IL-6 neutralisation following the treatment. Our findings revealed that the cryo-thermal therapy-induced acute IL-6 played an important role in initiating the cascading innate and adaptive anti-tumour immune responses, resulting in CD4⁺ T cell differentiation. It would be interesting to investigate acute IL-6 as an early indicator in predicating tumour therapeutic effect.</p

DataSheet_1_Revealing the mechanisms of the bioactive ingredients accumulation in Polygonatum cyrtonema by multiomics analyses.doc

Polygonatum cyrtonema is a medicinal and edible herb rich in polysaccharides, steroidal saponins, and flavonoids that has been widely used as a food, vegetable, and medicine over the years. Although previous studies have preliminarily explored the metabolic and transcriptional regulatory mechanisms of the main secondary metabolites in P. cyrtonema, the complex mechanism of microRNA (miRNA)-mediated posttranscriptional regulation remains unclear. Metabolome analysis showed that iso-ophiopogonanone B, (25S)-pratioside D1, disporopsin, and isodiosgenin-Glc-Glc, which are associated with intermediates in the flavonoids and saponins pathways, were significantly upregulated in the stem and leaf compared with the rhizome, and most saccharides, including arabinose, cellobiose, maltotetraose, and panose, showed the opposite trend, suggesting that they may contribute to the formation and accumulation of the main active ingredients in P. cyrtonema. We found that 4-hydroxymandelonitrile have a relatively good inhibitory effect on α-glucosidase, indicating that it may play a role in hypoglycemic functions. Transcriptome and weighted gene coexpression network analysis (WGCNA) were combined to reveal several candidate genes involved in the accumulation of polysaccharides, saponins, and flavonoids, including PcSQLE, PcCYP71A1, PcSUS, PcFK, and PcMYB102. Integrated analyses of miRNAs and messengerRNAs (mRNAs) showed that novel_miR14, novel_miR49, novel_miR75, and aof_miR164 were negatively correlated with alpha-linolenic acid metabolism and the mitogen activated protein kinase (MAPK) signaling pathway, including PcAOS, PcSPLA2, PcFRK1, and PcDELLA, indicating that these miRNAs may coordinately regulate the biosynthesis of other secondary metabolites in P. cyrtonema. These findings will facilitate in-depth research on the functions of these miRNAs and mRNAs related to the main active substances for pathological and biological regulation, which will be beneficial to provide theoretical guidance for the molecular breeding of P. cyrtonema.</p

DataSheet_2_Revealing the mechanisms of the bioactive ingredients accumulation in Polygonatum cyrtonema by multiomics analyses.doc

Polygonatum cyrtonema is a medicinal and edible herb rich in polysaccharides, steroidal saponins, and flavonoids that has been widely used as a food, vegetable, and medicine over the years. Although previous studies have preliminarily explored the metabolic and transcriptional regulatory mechanisms of the main secondary metabolites in P. cyrtonema, the complex mechanism of microRNA (miRNA)-mediated posttranscriptional regulation remains unclear. Metabolome analysis showed that iso-ophiopogonanone B, (25S)-pratioside D1, disporopsin, and isodiosgenin-Glc-Glc, which are associated with intermediates in the flavonoids and saponins pathways, were significantly upregulated in the stem and leaf compared with the rhizome, and most saccharides, including arabinose, cellobiose, maltotetraose, and panose, showed the opposite trend, suggesting that they may contribute to the formation and accumulation of the main active ingredients in P. cyrtonema. We found that 4-hydroxymandelonitrile have a relatively good inhibitory effect on α-glucosidase, indicating that it may play a role in hypoglycemic functions. Transcriptome and weighted gene coexpression network analysis (WGCNA) were combined to reveal several candidate genes involved in the accumulation of polysaccharides, saponins, and flavonoids, including PcSQLE, PcCYP71A1, PcSUS, PcFK, and PcMYB102. Integrated analyses of miRNAs and messengerRNAs (mRNAs) showed that novel_miR14, novel_miR49, novel_miR75, and aof_miR164 were negatively correlated with alpha-linolenic acid metabolism and the mitogen activated protein kinase (MAPK) signaling pathway, including PcAOS, PcSPLA2, PcFRK1, and PcDELLA, indicating that these miRNAs may coordinately regulate the biosynthesis of other secondary metabolites in P. cyrtonema. These findings will facilitate in-depth research on the functions of these miRNAs and mRNAs related to the main active substances for pathological and biological regulation, which will be beneficial to provide theoretical guidance for the molecular breeding of P. cyrtonema.</p

Table_3_Revealing the mechanisms of the bioactive ingredients accumulation in Polygonatum cyrtonema by multiomics analyses.doc

Polygonatum cyrtonema is a medicinal and edible herb rich in polysaccharides, steroidal saponins, and flavonoids that has been widely used as a food, vegetable, and medicine over the years. Although previous studies have preliminarily explored the metabolic and transcriptional regulatory mechanisms of the main secondary metabolites in P. cyrtonema, the complex mechanism of microRNA (miRNA)-mediated posttranscriptional regulation remains unclear. Metabolome analysis showed that iso-ophiopogonanone B, (25S)-pratioside D1, disporopsin, and isodiosgenin-Glc-Glc, which are associated with intermediates in the flavonoids and saponins pathways, were significantly upregulated in the stem and leaf compared with the rhizome, and most saccharides, including arabinose, cellobiose, maltotetraose, and panose, showed the opposite trend, suggesting that they may contribute to the formation and accumulation of the main active ingredients in P. cyrtonema. We found that 4-hydroxymandelonitrile have a relatively good inhibitory effect on α-glucosidase, indicating that it may play a role in hypoglycemic functions. Transcriptome and weighted gene coexpression network analysis (WGCNA) were combined to reveal several candidate genes involved in the accumulation of polysaccharides, saponins, and flavonoids, including PcSQLE, PcCYP71A1, PcSUS, PcFK, and PcMYB102. Integrated analyses of miRNAs and messengerRNAs (mRNAs) showed that novel_miR14, novel_miR49, novel_miR75, and aof_miR164 were negatively correlated with alpha-linolenic acid metabolism and the mitogen activated protein kinase (MAPK) signaling pathway, including PcAOS, PcSPLA2, PcFRK1, and PcDELLA, indicating that these miRNAs may coordinately regulate the biosynthesis of other secondary metabolites in P. cyrtonema. These findings will facilitate in-depth research on the functions of these miRNAs and mRNAs related to the main active substances for pathological and biological regulation, which will be beneficial to provide theoretical guidance for the molecular breeding of P. cyrtonema.</p

Additional file 4 of Screening lifespan-extending drugs in Caenorhabditis elegans via label propagation on drug-protein networks

The aging-related genes of C. elegans extracted from GenAge database, together with the corresponding transcripts of each aging-related genes. (XLSX 99 kb

The role of the outer membrane protein gene <i>ybjX</i> in the pathogenicity of avian pathogenic <i>Escherichia coli</i>

<p>Avian pathogenic <i>Escherichia coli</i> (APEC) are important pathogens that cause serious economic losses to the poultry industry worldwide. The PhoP/Q system is essential for APEC pathogenicity, and its mutation leads to a decrease in <i>ybjX</i> gene expression, but whether <i>ybjX</i> regulated by PhoP/Q plays a role in pathogenicity remains unclear. The role of <i>ybjX</i> in APEC pathogenicity was investigated using a <i>ybjX</i> mutant strain constructed from APEC strain AE17 by the Red recombination method. The mutant strain displayed significantly reduced adherence to and invasion of chicken embryo fibroblast cell line (DF-1) cells. Moreover, N-phenyl-1-naphthylamine (NPN) assays revealed an increase in outer membrane permeabilization for the <i>ybjX</i> mutant, suggesting <i>ybjX</i> affected susceptibility to avian beta-defensin through this mechanism. The <i>ybjX</i> mutation increased susceptibility to avian beta-defensin 9 (AvBD9), and <i>in vivo</i> LD₅₀ assays revealed reduced bacterial virulence in a chicken model. Taken together, these results indicated that mutation of <i>ybjX</i> may attenuate APEC pathogenicity, not only by affecting bacterial adhesion and invasion, but also via reducing resistance to avian beta-defensin by increasing outer membrane permeabilization of bacteria.</p

Proteomic Analysis of Two Metabolic Proteins with Potential to Translocate to Plasma Membrane Associated with Tumor Metastasis Development and Drug Targets

Metastasis is the main cause for death of breast cancer patients. However, the underlying mechanism is still poorly understood. Plasma membrane (PM) proteins play a key role in various biological processes, especially for cell migration. In this study, we used a set of well-characterized mammary mouse cell lines, 67NR, 168FARN, 4T1, representing the metastatic progression, to study the differentially expressed membrane proteins. These proteins were analyzed by a linear ion trap tandem mass spectrometry (LTQ-MS/MS) following cell surface biotinylation and streptavidin purification. A total of 1667 membrane proteins were identified, out of which 472 were characterized as differentially expressed with at least 2-fold change and <i>p</i>-value < 0.01. Functional clustering of the 472 proteins revealed that 178 of them were metabolic proteins. Finally, we focused on two metabolic proteins, fatty acid synthase (FASN) and NAD­(P)H steroid dehydrogenase-like protein (NSDHL), which were validated by Western blot and immunofluorescence. We found that FASN and NSDHL translocated to the plasma membrane from the intracellular compartment, and their expressions increased from 67NR to 4T1. This alteration of localization along with differential expressions might be necessary for metastasis development. Potentially, FASN and NSDHL could serve as drug targets in new antimetastasis therapy

Additional file 1 of Integration analysis of ATAC-seq and RNA-seq provides insight into fatty acid biosynthesis in Schizochytrium limacinum under nitrogen limitation stress

Additional file 1: Table S1. Evaluation statistics of sample sequencing data. Table S2. Mapping statistical of each sample. Table S3. Distribution statistics of Reads in gene functional elements. Table S4. Motif enrichment analysis showed the potential functions of DARs-associated genes between control and treatment group. Table S5. TFs identification of DEGs between control and treatment group. Table S6. Annotation of up-DEGs in the treatment compared with control group. Table S7. Annotation of down-DEGs in the treatment compared with control group. Table S8. Annotation of shared genes from DEGs and DARs-associated genes by RNA-seq and ATAC-seq

Results of inter-observer reproducibility of OQASII.

<p>Results of inter-observer reproducibility of OQASII.</p

A Supersensitive CTC Analysis System Based on Triangular Silver Nanoprisms and SPION with Function of Capture, Enrichment, Detection, and Release

Detection of circulating tumor cells (CTCs) may be applied for diagnosis of early tumors like a liquid biopsy. However, the sensitivity remains a challenge because CTCs are extremely rare in peripheral blood. In this study, we developed a supersensitive CTC analysis system based on triangular silver nanoprisms (AgNPR) and superparamagnetic iron oxide nanoparticles (SPION) with function of capture, enrichment, detection, and release. The AgNPR was encoded with MBA (i.e., 4-mercaptobenzoic acid) and modified with rBSA (i.e., reductive bovine serum albumin) and FA (i.e., folic acid) generating organic/inorganic composite nanoparticle MBA-AgNPR-rBSA-FA, which has the function of surface-enhanced Raman scattering (SERS). The optimized SERS nanoparticles (i.e., MBA3-AgNPR-rBSA4-FA2) can be utilized for CTC detection in blood samples with high sensitivity and specificity, and the LOD (i.e., limit of detection) reaches to five cells per milliliter. In addition, the SPION was also modified with rBSA and FA generating magnetic nanoparticle SPION-rBSA-FA. Our supersensitive CTC analysis system is composed of MBA3-AgNPR-rBSA4-FA2 and SPION-rBSA-FA nanoparticles, which were applied for capture (via interaction between FA and FRα), enrichment (via magnet), and detection (via SERS) of cancer cells from blood samples. The results demonstrate that our supersensitive CTC analysis system has a better sensitivity and specificity than the SERS nanoparticles alone, and the LOD is up to 1 cell/mL. The flow cytometry and LSCM (i.e., laser scanning confocal microscope) results indicate the CTCs captured, enriched, and isolated by our supersensitive CTC analysis system can also be further released (via adding excessive free FA) for further cell expansion and phenotype identification