Extraction of antimicrobial peptides from pea protein hydrolysates by sulfonic acid functionalized biochar.

The extraction methods for antimicrobial peptides (AMPs) from plants are varied, but the absence of a standardized and rapid technique remains a challenge. In this study, a functionalized biochar was developed and characterized for the extraction of AMPs from pea protein hydrolysates. The results indicated that the biochar mainly enriched AMPs through electrostatic interaction, hydrogen bonding and pore filling. Then three novel cationic antimicrobial peptides were identified, among which the RDLFK (Arg-Asp-Leu-Phe-Lys) had the greatest inhibitory effect against Staphylococcus aureus and Bacillus subtilis, showcasing IC50 value of 2.372 and 1.000 mg/mL, respectively. Additionally, it was found that RDLFK could damage bacterial cell membranes and penetrate the cells to inhibit DNA synthesis. These results provided that the biochar-based extraction method presents an efficient and promising avenue for isolating AMPs, addressing a critical gap in the current methodologies for their extraction from plant sources.

The antitumor effects of herbal medicine Triphala on oral cancer by inactivating PI3K/Akt signaling pathway: based on the network pharmacology, molecular docking, in vitro and in vivo experimental validation.

BACKGROUND: This research aimed to investigate the anti-tumor effects and underlying genetic mechanisms of herbal medicine Triphala (TRP) in oral squamous cell carcinoma (OSCC). METHODS: The target genes of Triphala (TRP) in oral squamous cell carcinoma (OSCC) were identified, and subsequent functional enrichment analysis was conducted to determine the enriched signaling pathways. Based on these genes, a protein-protein interaction network was constructed to identify the top 10 genes with the highest degree. Genes deregulated in OSCC tumor samples were identified to be hub genes among the top 10 genes. In vitro experiments were performed to investigate the influence of TRP extracts on the cell metabolic activity, migration, invasion, apoptosis, and proliferation of two OSCC cell lines (CAL-27 and SCC-9). The functional rescue assay was conducted to investigate the effect of applying the inhibitor and activator of an enriched pathway on the phenotypes of cancer cells. In addition, the zebrafish xenograft tumor model was established to investigate the influence of TRP extracts on tumor growth and metastasis in vivo. RESULTS: The target genes of TRP in OSCC were prominently enriched in the PI3K-Akt signaling pathway, with the identification of five hub genes (JUN, EGFR, ESR1, RELA, and AKT1). TRP extracts significantly inhibited cell metabolic activity, migration, invasion, and proliferation and promoted cell apoptosis in OSCC cells. Notably, the application of TRP extracts exhibited the capacity to downregulate mRNA and phosphorylated protein levels of AKT1 and ESR1, while concomitantly inducing upregulation of mRNA and phosphorylated protein levels in the remaining three hub genes (EGFR, JUN, and RELA). The functional rescue assay demonstrated that the co-administration of TRP and the PI3K activator 740Y-P effectively reversed the impact of TRP on the phenotypes of OSCC cells. Conversely, the combination of TRP and the PI3K inhibitor LY294002 further enhanced the effect of TRP on the phenotypes of OSCC cells. Remarkably, treatment with TRP in zebrafish xenograft models demonstrated a significant reduction in both tumor growth and metastatic spread. CONCLUSIONS: Triphala exerted significant inhibitory effects on cell metabolic activity, migration, invasion, and proliferation in OSCC cell lines, accompanied by the induction of apoptosis, which was mediated through the inactivation of the PI3K/Akt pathway.

Tibetan medicine Ruyi Zhenbao Pill ameliorates neuropathic pain by inhibiting the CXCL10-CXCR3 pathway in spinal cord of spinal nerve ligation model.

ETHNOPHARMACOLOGICAL RELEVANCE: Ruyi Zhenbao Pill (RYZBP) is a traditional Tibetan medicine that has been used for over 300 years in China to treat neurological diseases, specifically neuropathic pain (NP). However, its characteristics and mechanism of action in treating NP remains unclear. AIM OF THE STUDY: Based on animal experiments and transcriptomics to evaluate the characteristics and mechanism of RYZBP in treating NP. METHODS: Mice were divided into six groups using random assignment: sham-operation group, spinal nerve ligation (SNL) group, RYZBP low (0.65 g kg-1), medium (1.30 g kg-1), high (2.60 g kg-1) doses groups, and positive drug pregabalin (PGB, 0.05 g kg-1) group. Mice received intragastrical administered for 14 consecutive days. SNL and intrathecal injection models were employed. The analgesic effects were assessed using the Von Frey test, Acetone test, and Hot Plate test. L5 spinal dorsal horns were collected for transcriptomics on day 15. The potential signaling pathways and Hub genes of RYZBP to ameliorate NP were obtained through transcriptomics and network pharmacology. Molecular docking was utilized to evaluate the binding ability of candidate active ingredients with the Hub genes. Finally, western blot (WB) and immunofluorescence (IF) were used to validate the predicted targets. RESULTS: RYZBP demonstrated a dose-dependent alleviation of mechanical allodynia, cold and heat stimulus-induced pain in SNL mice. Transcriptomics analysis identified 24 differentially expressed genes, and pathway enrichment analysis revealed that the CXCL10-CXCR3 signal axis may be the primary biological pathway through which RYZBP relieve NP. Molecular docking test indicated that the active ingredient in RYZBP exhibit a strong affinity for the target protein CXCL10. WB and IF tests showed that RYZBP can significantly inhibit CXCL10 and CXCR3 and its downstream molecules expression in the spinal dorsal horn of SNL mice. Additionally, intrathecal injection of rmCXCL10 worsened pain hypersensitivity, while RYZBP was able to suppress the pain hypersensitivity response induced by rmCXCL10 and reduce the expression levels of CXCL10 and CXCR3 and its downstream molecules. CONCLUSION: RYZBP had a significant analgesic effect on NP model, and this effect may be related to inhibiting the CXCL10-CXCR3 pathway in the spinal dorsal horn.

Fate of progesterone and norgestrel in anaerobic/anoxic/oxic (A/A/O) process: Insights from biotransformation and mass flow.

Progesterone (P4) and norgestrel (NGT) are two steroid progestogens that can pose adverse effects on aquatic organisms at ng/L levels. Despite increasing concern on their occurrence and removal in wastewater, their fate in the wastewater treatment process has not been well documented. This study identified the transformation products (TPs) of P4 and NGT in anaerobic/anoxic/oxic (A/A/O) process. Potential functional genes involved in biotransformation of P4 and NGT were explored. The elimination or formation behavior of P4, NGT and convinced TPs along various units of A/A/O process was revealed through the mass flow. Results showed that 12 and 13 TPs were identified in the P4 and NGT groups respectively, wherein 10 identical TPs and C-19 structures transformation pathways were observed in both groups. Six genes were found that may be involved in dehydrogenation and isomerization reactions in the pathways. Mass flow indicated that P4 and NGT were mainly eliminated in anaerobic and anoxic units, while convinced TPs mainly formed in anaerobic and anoxic units and were then eliminated in aerobic unit. Further, the ecological risks of the effluent should not be ignored as residual compounds including P4 or NGT and their TPs in the effluent still posed adverse effects on zebrafish transcript levels.

Mitochondrial impairment and repair in the pathogenesis of systemic lupus erythematosus.

Nucleic acid autoantibodies, increase type I interferon (IFN-α) levels, and immune cell hyperactivation are hallmarks of systemic lupus erythematosus (SLE). Notably, immune cell activation requires high level of cellular energy that is predominately generated by the mitochondria. Mitochondrial reactive oxygen species (mROS), the byproduct of mitochondrial energy generation, serves as an essential mediator to control the activation and differentiation of cells and regulate the antigenicity of oxidized nucleoids within the mitochondria. Recently, clinical trials on normalization of mitochondrial redox imbalance by mROS scavengers and those investigating the recovery of defective mitophagy have provided novel insights into SLE prophylaxis and therapy. However, the precise mechanism underlying the role of oxidative stress-related mitochondrial molecules in skewing the cell fate at the molecular level remains unclear. This review outlines distinctive mitochondrial functions and pathways that are involved in immune responses and systematically delineates how mitochondrial dysfunction contributes to SLE pathogenesis. In addition, we provide a comprehensive overview of damaged mitochondrial function and impaired metabolic pathways in adaptive and innate immune cells and lupus-induced organ tissues. Furthermore, we summarize the potential of current mitochondria-targeting drugs for SLE treatment. Developing novel therapeutic approaches to regulate mitochondrial oxidative stress is a promising endeavor in the search for effective treatments for systemic autoimmune diseases, particularly SLE.

Spatiotemporal variation and removal of selected endocrine-disrupting chemicals in wastewater treatment plants across China: Treatment process comparison.

In this study, the spatiotemporal variation in the occurrence of 19 endocrine-disrupting chemicals (EDCs) spanning four seasons in wastewater treatment plants (WWTPs) located in 17 Chinese cities was investigated. Removal efficiencies for selected EDCs in 17 WWTPs over four seasons were analyzed. Contributions of conventional and advanced process segments to the removal efficiency of EDCs were explored, which compared the removal efficacies of a variety of secondary and advanced processes for EDCs. Results showed that EDCs were extensively detected in WWTPs, with bisphenol A (BPA), dehydroepiandrosterone (DHRD), androstenedione (ADD), and pregnanediol (PD) being dominant in excess sludge and wastewater. Seasonally, the greatest seasonal differences were observed in the influent, with the concentrations of 12 EDCs varying significantly between seasons. Spatially, concentrations of BPA, DHRD, testosterone (TTR), and estriol (E3) in the influent significantly varied between the northern and southern WWTPs. Fourteen EDCs were removed steadily among the four seasons, while most EDCs had considerable removal differences between WWTPs. Contribution of the conventional process segment to the removal of individual EDCs was higher than that of the advanced process segment in WWTPs. Quantitative meta-analysis indicated that the anaerobic-anoxic-anaerobic (AAO) process in the various secondary processes had the highest removal of the target EDCs. Mass balance analysis further suggested that biodegradation in the aerobic tank of the AAO process was the major pathway for most EDCs removal. This study systematically depicts the spatiotemporal distribution of EDCs in WWTPs located across China and deepens the comprehension of EDCs removal in Chinese WWTPs from a treatment process perspective.

Insight into the effect of wastewater-derived dissolved organic matter composition on norgestrel degradation in activated sludge: Coupled bacterial community and molecular characteristics.

Dissolved organic matter (DOM) mediates the microbial transformation of micropollutants, including norgestrel (NGT) in natural waters. However, little is known of the effect of complex and variable wastewater-derived DOM composition on NGT degradation during wastewater treatment. In this study, the relationship between the compositions of initial DOM and NGT removal efficiencies of 17 wastewater treatment plants (WWTPs) in spring and summer were analyzed. The different molecular composition of DOM was selected in the lab to further explore its effect on NGT degradation by activated sludge. Results indicated that the DOM composition was a substantial driver of NGT removal in WWTPs. The discrepancies in the initial DOM composition contributed to the differences in the kinetics of NGT degradation by activated sludge. The larger rapid decay phase rates of NGT are usually accompanied by a large proportion of labile substances in DOM. High-throughput sequencing and ultrahigh-resolution mass spectrometry were used to further analyze the evolution of bacterial communities and DOM molecular composition were combined with network analysis to reveal the intrinsic relationship that how DOM composition affected NGT degradation by regulating core microbes. Eighty-nine core OTUs were significantly associated with NGT degradation, and 73 occurred in the rapid decay phase, implying that NGT degradation was mainly regulated by the initial composition of DOM. Nine major transformation products were identified in different groups with widely varying concentrations or relative abundances of these transformation products. This work provides valuable insights into the effects of wastewater-derived DOM composition on NGT degradation by activated sludge and innovatively explores the influence mechanisms from the bacterial community and molecular characterization perspectives.

Implications of Human Antimicrobial Peptide Defensin Beta-1 in Clinical Oral Squamous Cell Carcinoma Patients via an Integrated Bioinformatics Approach.

BACKGROUND: The human antimicrobial peptide defensin beta 1 (DEFB1) has been found to play antimicrobial and anti-inflammatory roles in oral diseases; however, its tumor-regulating role in oral squamous cell carcinoma (OSCC) has not yet been researched by using an integrative bioinformatics approach. OBJECTIVE: To investigate the regulating mechanisms of the DEFB1 gene in OSCC in terms of its expression patterns, prognostic values, biological functions, and implication for tumor immunity. METHODS: The DEFB1 gene expression pattern and regulatory involvement in OSCC were investigated using publically accessible data from TCGA database. R software tools and public web servers were utilized to conduct statistical analysis of data from cancer and noncancerous samples. RESULTS: DEFB1 was found to be significantly downregulated in OSCC tumor samples compared with healthy control oral samples. The DEFB1 gene was found associated with the prognostic outcomes of OSCC, and its upregulation represented better survival outcome. Gene set enrichment analysis (GSEA) results showed that DEFB1-significantly correlated genes were mainly enriched in four signaling pathways mediating the antitumor role of DEFB1 in OSCC, including extracellular matrix-related pathway, RTK/PI3K/AKT/mTOR pathway, keratinization, and cytokine-related pathway. The gene-gene interaction network showed that DEFB1 was closely correlated with several genes, for example, CCR6 (C-C motif chemokine receptor 6), CXCL1 (C-X-C motif chemokine ligand 1), MAP4K2 (mitogen-activated protein kinase kinase kinase kinase 2), PTGER3 (prostaglandin E receptor 3), and MMP7 (matrix metallopeptidase 7). Moreover, DEFB1 was found to be involved in the tumor immunity of OSCC by regulating the function of tumor macrophage cells, mast cells, T cells, and NK cells. CONCLUSIONS: Given the dysregulation, prognostic value, and tumor progression-related biological pathway alteration, indicating the tumor immune-modulatory role of DEFB1 in OSCC, the DEFB1 gene should be regarded as a potential therapeutic target for treating oral cancer.

Occurrence and removal of progestogens from wastewater treatment plants in China: Spatiotemporal variation and process comparison.

This study investigated the overall occurrence and spatiotemporal variation of 19 progestogens in 608 samples collected from 17 wastewater treatment plants (WWTPs) distributed across China during four seasons. The aqueous removal efficiencies of progestogens were calculated and the efficacies of process segments, secondary and advanced processes, and process units in the removal of progestogens were explored. The results indicated that progestogens were widely detected in investigating WWTPs, with the progesterone, dydrogesterone, dienogest, ethisterone, and norethindrone were always dominant in the influent, secondary effluent, final effluent, and excess sludge. Seasonally, the influent exhibited more variability than the other matrices, that 10 progestogens concentrations varied significantly during the four seasons. Spatially, the influent concentrations of progestogens were generally higher in northern WWTPs than that in southern WWTPs during spring and summer. Eight progestogens were stably removed by the WWTPs across seasons, and most progestogens varied considerably in removal in different WWTPs. The conventional process segment was the dominant contributor to progestogen removal. The anaerobic-anoxic-oxic process and a combined process consisting of densadeg and cloth media filter and ultraviolet disinfection showed the highest removal of progestogens among various secondary and advanced treatment processes, respectively. Mass balance analysis showed that most progestogens were effectively eliminated in the aerobic unit, with biodegradation being the primary removal pathway. This study presents the first picture of the spatiotemporal dynamics of the distribution of progestogens in WWTPs of China and provides valuable information for better understanding of the occurrence and removal of progestogens in WWTPs.

Effects of the Tibetan medicine Byur dMar Nyer lNga Ril Bu on Alzheimer's disease in mice models.

ETHNOPHARMACOLOGICAL RELEVANCE: Byur dMar Nyer lNga Ril Bu (BdNlRB) is a classic Tibetan medicine prescription for treating " white vein disease". Alzheimer's disease (AD) is a chronic degenerative disease of the central nervous system, characterized by distinct "white vein disease". In the absence of effective drugs for AD, BdNlRB may be a possible treatment for AD. AIM OF THE STUDY: To verify the therapeutic effect and possible mechanism of the proved Tibetan medicine BdNlRB on Alzheimer's disease. MATERIALS AND METHODS: 60 APP/PS1 double transgenic AD mice (Mt) and 60 Aß1-40 protein-induced AD mice (Mi) were divided into 3 groups according to the dose of BdNlRB: BdNlRB-100, BdNlRB-200 and BdNlRB-400, with 100, 200 and 400 mg/kg*weight, respectively. The mice were administrated by gavage for 8 weeks. The cognitive ability of mice was detected by Morris Water Maze, the expression of Aß protein, p-tau and microglia was detected by immunofluorescent staining, the protein expression in the hippocampus was detected by proteomics, and the abundance of fecal intestinal flora was detected by 16S RNA. RESULTS: The learning ability and memory ability of Mi mice were significantly improved after BdNlRB administration. The learning ability of Mt mice was significantly improved, while the memory ability was not improved after BdNlRB administration. After the treatment with low and medium doses of BdNlRB, the expression of p-tau decreased significantly (the rate of decrease in BdNlRB-100 and BdNlRB-200 groups was 8.05% and 12.7%, respectively), and the number of microglia increased (39.3% and 31.6%, respectively). BdNlRB significantly affected the protein expression in the hippocampus of Mt mice. 382 proteins in different expression in all three groups mainly involved in amino acid synthesis, fatty acid degradation, glutamine metabolism, synaptic vesicular cycle and oxidative phosphorylation, PPAR signaling pathway and Fc gamma-mediated phagocytosis were activated. Meanwhile, the administration of BdNlRB can regulate the intestinal flora of Mt mice, which reduces the abundance of Muribaculum and uncultured bacteroidales bacterium, and improves the abundance of Ruminococcus-1 and Ruminiclostridium-9. CONCLUSION: The oral administration of BdNlRB significantly improved the cognitive ability of AD mice, and neuroinflammation and intestinal flora regulation were the possible mechanisms.

Identification and Characterization of Antimicrobial Peptides From Butterflies: An Integrated Bioinformatics and Experimental Study.

Butterflies represent one of the largest animal groups on Earth, yet antimicrobial peptides (AMPs) of this group are less studied in comparison with their moth counterparts. This study employed an integrated bioinformatics approach to survey natural AMPs from publicly available genomic datasets. Numerous AMPs, including cecropins, defensins, and moricins, were identified and subsequently used as templates for the design of a series of synthetic AMPs that mimicked the naturally occurring sequences. Despite differing biological effects among the various sequences, the synthetic AMPs exhibited potent antibacterial and antifungal activities in vitro and in vivo, without inducing hemolysis, which implied their therapeutic potential in infectious diseases. Electron and confocal fluorescence microscopies revealed that the AMPs induced distinct morphological and biophysical changes on microbial cell membranes and nuclei, suggesting that the antimicrobial effects were related to a mechanism of membrane penetration and nucleic acid binding by the peptides. In conclusion, this study not only offers insights into butterfly AMPs but also provides a practical strategy for high-throughput natural AMP discoveries that will have implications for future research in this area.

Protective Effect of Triphala against Oxidative Stress-Induced Neurotoxicity.

BACKGROUND: Oxidative stress is implicated in the progression of many neurological diseases, which could be induced by various chemicals, such as hydrogen peroxide (H2O2) and acrylamide. Triphala is a well-recognized Ayurvedic medicine that possesses different therapeutic properties (e.g., antihistamine, antioxidant, anticancer, anti-inflammatory, antibacterial, and anticariogenic effects). However, little information is available regarding the neuroprotective effect of Triphala on oxidative stress. MATERIALS AND METHODS: An in vitro H2O2-induced SH-SY5Y cell model and an in vivo acrylamide-induced zebrafish model were established. Cell viability, apoptosis, and proliferation were examined by MTT assay, ELISA, and flow cytometric analysis, respectively. The molecular mechanism underlying the antioxidant activity of Triphala against H2O2 was investigated dose dependently by Western blotting. The in vivo neuroprotective effect of Triphala on acrylamide-induced oxidative injury in Danio rerio was determined using immunofluorescence staining. RESULTS: The results indicated that Triphala plays a neuroprotective role against H2O2 toxicity in inhibiting cell apoptosis and promoting cell proliferation. Furthermore, Triphala pretreatment suppressed the phosphorylation of the mitogen-activated protein kinase (MARK) signal pathway (p-Erk1/2, p-JNK1/2, and p-p38), whereas it restored the activities of antioxidant enzymes (superoxide dismutase 1 (SOD1) and catalase) in the H2O2-treated SH-SY5Y cells. Consistently, similar protective effects of Triphala were observed in declining neuroapoptosis and scavenging free radicals in the zebrafish central neural system, possessing a critical neuroprotective property against acrylamide-induced oxidative stress. CONCLUSION: In summary, Triphala is a promising neuroprotective agent against oxidative stress in SH-SY5Y cells and zebrafishes with significant antiapoptosis and antioxidant activities.

Deep Learning Reveals Key Immunosuppression Genes and Distinct Immunotypes in Periodontitis.

BACKGROUND: Periodontitis is a chronic immuno-inflammatory disease characterized by inflammatory destruction of tooth-supporting tissues. Its pathogenesis involves a dysregulated local host immune response that is ineffective in combating microbial challenges. An integrated investigation of genes involved in mediating immune response suppression in periodontitis, based on multiple studies, can reveal genes pivotal to periodontitis pathogenesis. Here, we aimed to apply a deep learning (DL)-based autoencoder (AE) for predicting immunosuppression genes involved in periodontitis by integrating multiples omics datasets. METHODS: Two periodontitis-related GEO transcriptomic datasets (GSE16134 and GSE10334) and immunosuppression genes identified from DisGeNET and HisgAtlas were included. Immunosuppression genes related to periodontitis in GSE16134 were used as input to build an AE, to identify the top disease-representative immunosuppression gene features. Using K-means clustering and ANOVA, immune subtype labels were assigned to disease samples and a support vector machine (SVM) classifier was constructed. This classifier was applied to a validation set (Immunosuppression genes related to periodontitis in GSE10334) for predicting sample labels, evaluating the accuracy of the AE. In addition, differentially expressed genes (DEGs), signaling pathways, and transcription factors (TFs) involved in immunosuppression and periodontitis were determined with an array of bioinformatics analysis. Shared DEGs common to DEGs differentiating periodontitis from controls and those differentiating the immune subtypes were considered as the key immunosuppression genes in periodontitis. RESULTS: We produced representative molecular features and identified two immune subtypes in periodontitis using an AE. Two subtypes were also predicted in the validation set with the SVM classifier. Three "master" immunosuppression genes, PECAM1, FCGR3A, and FOS were identified as candidates pivotal to immunosuppressive mechanisms in periodontitis. Six transcription factors, NFKB1, FOS, JUN, HIF1A, STAT5B, and STAT4, were identified as central to the TFs-DEGs interaction network. The two immune subtypes were distinct in terms of their regulating pathways. CONCLUSION: This study applied a DL-based AE for the first time to identify immune subtypes of periodontitis and pivotal immunosuppression genes that discriminated periodontitis from the healthy. Key signaling pathways and TF-target DEGs that putatively mediate immune suppression in periodontitis were identified. PECAM1, FCGR3A, and FOS emerged as high-value biomarkers and candidate therapeutic targets for periodontitis.

The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation.

AIM: To identify the critical genetic and epigenetic biomarkers by constructing the long noncoding RNA- (lncRNA-) related competing endogenous RNA (ceRNA) network involved in irreversible pulp neural inflammation (pulpitis). MATERIALS AND METHODS: The public datasets regarding irreversible pulpitis were downloaded from the gene expression omnibus (GEO) database. The differential expression analysis was performed to identify the differentially expressed genes (DEGs) and DElncRNAs. Functional enrichment analysis was performed to explore the biological processes and signaling pathways enriched by DEGs. By performing a weighted gene coexpression network analysis (WGCNA), the significant gene modules in each dataset were identified. Most importantly, DElncRNA-DEmRNA regulatory network and DElncRNA-associated ceRNA network were constructed. A transcription factor- (TF-) DEmRNA network was built to identify the critical TFs involved in pulpitis. RESULT: Two datasets (GSE92681 and GSE77459) were selected for analysis. DEGs involved in pulpitis were significantly enriched in seven signaling pathways (i.e., NOD-like receptor (NLR), Toll-like receptor (TLR), NF-kappa B, tumor necrosis factor (TNF), cell adhesion molecules (CAMs), chemokine, and cytokine-cytokine receptor interaction pathways). The ceRNA regulatory relationships were established consisting of three genes (i.e., LCP1, EZH2, and NR4A1), five miRNAs (i.e., miR-340-5p, miR-4731-5p, miR-27a-3p, miR-34a-5p, and miR-766-5p), and three lncRNAs (i.e., XIST, MIR155HG, and LINC00630). Six transcription factors (i.e., GATA2, ETS1, FOXP3, STAT1, FOS, and JUN) were identified to play pivotal roles in pulpitis. CONCLUSION: This paper demonstrates the genetic and epigenetic mechanisms of irreversible pulpitis by revealing the ceRNA network. The biomarkers identified could provide research direction for the application of genetically modified stem cells in endodontic regeneration.

Identification of miRNAs as the Crosstalk in the Interaction between Neural Stem/Progenitor Cells and Endothelial Cells.

AIM: This study is aimed at identifying genetic and epigenetic crosstalk molecules and their target drugs involved in the interaction between neural stem/progenitor cells (NSPCs) and endothelial cells (ECs). MATERIALS AND METHODS: Datasets pertaining to reciprocal mRNA and noncoding RNA changes induced by the interaction between NSPCs and ECs were obtained from the GEO database. Differential expression analysis (DEA) was applied to identify NSPC-induced EC alterations by comparing the expression profiles between monoculture of ECs and ECs grown in EC/NSPC cocultures. DEA was also utilized to identify EC-induced NSPC alterations by comparing the expression profiles between monoculture of NSPCs and NSPCs grown in EC/NSPC cocultures. The DEGs and DEmiRNAs shared by NSPC-induced EC alterations and EC-induced NSPC alterations were then identified. Furthermore, miRNA crosstalk analysis and functional enrichment analysis were performed, and the relationship between DEmiRNAs and small molecular drug targets/environment chemical compounds was investigated. RESULTS: One dataset (GSE29759) was included and analyzed in this study. Six genes (i.e., MMP14, TIMP3, LOXL1, CCK, SMAD6, and HSPA2), three miRNAs (i.e., miR-210, miR-230a, and miR-23b), and three pathways (i.e., Akt, ERK1/2, and BMPs) were identified as crosstalk molecules. Six small molecular drugs (i.e., deptropine, fluphenazine, lycorine, quinostatin, resveratrol, and thiamazole) and seven environmental chemical compounds (i.e., folic acid, dexamethasone, choline, doxorubicin, thalidomide, bisphenol A, and titanium dioxide) were identified to be potential target drugs of the identified DEmiRNAs. CONCLUSION: To conclude, three miRNAs (i.e., miR-210, miR-230a, and miR-23b) were identified to be crosstalks linking the interaction between ECs and NSPCs by implicating in both angiogenesis and neurogenesis. These crosstalk molecules might provide a basis for devising novel strategies for fabricating neurovascular models in stem cell tissue engineering.

Dysregulation of antimicrobial peptide expression distinguishes Alzheimer's disease from normal aging.

Alzheimer's disease (AD) is an age-related neurodegenerative disease with unknown mechanism that is characterized by the aggregation of abnormal proteins and dysfunction of immune responses. In this study, an integrative approach employing in silico analysis and wet-lab experiment was conducted to estimate the degrees of innate immune system relevant gene expression, neurotoxic Aß42 generation and neuronal apoptosis in normal Drosophila melanogaster and a transgenic model of AD. Results demonstrated mRNA levels of antimicrobial peptide (AMP) genes gradually increased with age in wild-type flies, while which exhibited a trend for an initial decrease followed by subsequent increase during aging in the AD group. Time series and correlation analysis illustrated indicated a potential relationship between variation in AMP expression and Aß42 concentration. In conclusion, our study provides evidence for abnormal gene expression of AMPs in AD flies with age, which is distinct from the expression profiles in the normal aging process. Aberrant AMP expression may participate in the onset and development of AD by inducing or accelerating Aß deposition. These findings suggest that AMPs may serve as potential diagnostic biomarkers and therapeutic targets. However, further studies are required to elucidate the pathological effects and underlying mechanisms of AMP dysregulation in AD progression.

Effects of exogenous lanthanum(III) exposure on the positive interaction between mutually beneficial populations.

Rare earth elements (REEs) are widely used in various fields, and their accumulation has been reported to pose environmental risks. Most studies confirmed the damage of excessive REE exposure to individual plants; however, little attention has been given to their effects on plant populations. A positive interaction indicates a mutually beneficial relationship between two populations, which is beneficial to the survival and growth of the populations. However, it remains unknown whether exogenous REEs affect the positive interactions between populations. This study investigated the effects of exogenous lanthanum(III) [La(III)] exposure on the positive interaction between soybean (Glycine max L.) and wheat (Triticum aestivum L.) populations by their modules. At normal nutrient level (½-strength Hoagland), the inhibition of excessive La(III) on population modules decreased with increasing population density. Decreases of 39.26 to 1.05% for soybean and 41.45 to 2.41% for wheat indicated the inhibition of La(III) on the positive interaction of both populations weakened with increasing population density. At low nutrient level (»-strength Hoagland), the inhibition of excessive La(III) on population modules increased with increasing population density. Decreases of 5.82-57.14% for soybean and 4.22-59.04% for wheat indicated the inhibition of La(III) on the positive interaction of both population was strengthened with increasing population density. In summary, the inhibitory effects of exogenous La(III) exposure on the positive interaction between populations vary with both nutrient level and population density. This is a new factor that needs to be considered when evaluating the safety risks of REEs in the environment.

The molecular differences between human papillomavirus-positive and -negative oropharyngeal squamous cell carcinoma: A bioinformatics study.

OBJECTIVE: To investigate the genetic and epigenetic differences between human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC) and HPV-negative OPSCC. METHODS: Microarray data of HPV-positive and -negative OPSCC were retrieved from NCBI GEO datasets. Differentially expressed genes (DEGs) and differentially expressed miRNAs (DE-miRNAs) were identified by performing differential expression analysis. A functional enrichment analysis was performed to explore the biological processes and signaling pathways that DEGs and DE-miRNAs were involved in, respectively. A protein-protein interaction (PPI) network of DEGs was constructed to identify hub genes. miRNA-target network and miRNA-miRNA functional synergistic network were each constructed in order to identify risk-marker miRNAs. An miRNA-target-pathway network was constructed in order to explore the function of identified risk-marker miRNAs. RESULTS: Microarray data from 3 datasets (GSE39366, GSE40774, and GSE55550) was included and analyzed. The PPI network identified 3 hub genes (VCAM1, UBD, and RPA2). MiR-107 and miR-142-3p were found to play the most significant role in both the DE-miRNA-target network as well as in the miRNA-miRNA functional synergistic network. MiR-107 was involved in HPV-induced tumorigenesis by targeting many genes (CAV1, CDK6, MYB, and SERPINB5) and regulating the p53 signaling pathway, the PI3K-Akt signaling pathway, and the autophagy pathway. In addition, miR-142-3p was implicated in HPV-induced tumorigenesis by targeting the PPFIA1 gene and regulating transcriptional dysregulation and other cancerous pathways. CONCLUSION: Three genes (VCAM1, UBD, and RPA2), two miRNAs (miR-107 and miR-142-3p), and four pathways (p53, PI3K-Akt, autophagy, and transcription dysregulation in cancer) were identified to play critical roles in distinguishing HPV-positive OPSCC from HPV-negative OPSCC.

Chebulinic acid derived from triphala is a promising antitumour agent in human colorectal carcinoma cell lines.

BACKGROUND: Triphala is an Ayurvedic rasayana formulation reputed for its antitumour activities, and chebulinic acid and chebulagic acid, along with other phenolic acids, have been proposed to be responsible for its effects. METHODS: In this study, the anti-proliferative activities of these agents were evaluated in colorectal carcinoma cell lines with three phenotypes exposed to several batches of triphala samples with different quantities of chebulinic acid and chebulagic acid. The pro-apoptotic and anti-migratory activities and the probable antitumour mechanisms of the more potent anti-proliferative phytochemical were also investigated. RESULTS: The results demonstrated that chebulinic acid, which exerts potent anti-proliferative, pro-apoptotic and anti-migratory effects, is a key molecule for maintaining the antitumour efficacy of triphala. The antitumour mechanism of chebulinic acid is probably related to the PI3K/AKT and MAPK/ERK pathways. CONCLUSIONS: Chebulinic acid is not only a critical component of the anticancer activities of triphala but also a promising natural multi-target antitumour agent with therapeutic potential.

Shared genetic and epigenetic mechanisms between chronic periodontitis and oral squamous cell carcinoma.

OBJECTIVES: To analyze bioinformatic datasets for detecting genetic and epigenetic mechanisms shared by chronic periodontitis (CP) and oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS: Datasets from GEO and TCGA databases reporting mRNAs, miRNAs or methylation expression in human CP and OSCC tissues were analyzed. Differential expression, functional enrichment and protein-protein interaction (PPI) network analyses were performed. Differentially expressed miRNAs (DEmiRNAs) and genes (DEG) in CP and OSCC were determined. DEmiRNA-target and DEmiRNA-DEG networks were constructed. Directly and indirectly interacting cross-talk genes were screened, and their prediction accuracy and association with OSCC prognosis was determined. RESULTS: 3 DE-miRNAs (miR-375, miR-3609 and miR-3652) expressed in both CP and OSCC critically regulated most DEGs. Among 12 directly interacting cross-talk genes, NCAPH was significantly related with the prognosis of OSCC. NR2F2 had highest differential expression in CP and OSCC. Among 4 cross-talk genes (FN1, MPPED1, NDEL1, and NR2F2) differentially expressed in CP, 3 (FN1, MPPED1, NDEL1) were also expressed in OSCC. Among 12 indirectly interacting cross-talk genes differentially expressed in OSCC, 3 genes (CDCA8, HIST1H3J, and RAD51) were significantly related to its prognosis. Significant pathways involved in CP and OSCC included: chemokine receptors, class I PI3K signaling events, epithelial-to-mesenchymal transition and signaling events by VEGFR1 and VEGFR2, EGF receptor (ErbB1). CONCLUSION: Bioinformatic analysis of available datasets implicated 1 directly interacting cross-talk gene (NCAPH), 4 indirectly interacting cross-talk genes (NCAPH, NR2F2, FN1, and MPPED1) and 3 DE-miRNAs (hsa-miR-375, miR-3609 and miR-3652) as shared genetic and epigenetic expression patterns between CP and OSCC.