Eosinophil-Associated Genes are Potential Biomarkers for Hepatocellular Carcinoma Prognosis.

Background: Eosinophils, a type of white blood cell originating from the bone marrow, are widely believed to play a crucial role in inflammatory processes, including allergic reactions and parasitic infections. However, the relationship between eosinophils and liver cancer is not well understood. Methods: Tumor immune infiltration scores were calculated using single-sample Gene Set Enrichment Analysis (ssGSEA). Key modules and hub genes associated with eosinophils were screened using Weighted Gene Co-expression Network Analysis (WGCNA). Univariate and multivariate Cox analyses, along with LASSO regression, were used to identify prognostic genes and create a risk model. The Tumor Immune Dysfunction and Exclusion (TIDE) score was used to evaluate the immunotherapeutic significance of the eosinophil-associated gene risk score (ERS) model. Experiments such as flow cytometry, immunohistochemical analysis, real-time quantitative PCR (RT-qPCR), and Western blotting were used to determine gene expression levels and the status of eosinophil infiltration in tumors. Results: A risk trait model including 4 eosinophil-associated genes (RAMP3, G6PD, SSRP1, PLOD2) was developed by univariate Cox analysis and Lasso screening. Pathologic grading (p < 0.001) and model risk scores (p < 0.001) were found to be independent predictors of hepatocellular carcinoma (HCC) patient survival. Western blotting revealed higher levels of eosinophil peroxidase (EPX) in HCC tissues compared to adjacent normal tissues. Immunohistochemistry showed that eosinophils mainly infiltrated the connective tissue around HCC. The HCC samples showed low expression of RAMP3 and high expression of G6PD, SSRP1, and PLOD2, as detected by IHC and RT-qPCR analysis. The in vivo mouse experiments showed that IL-33 treatment induced the recruitment of eosinophils and reduced the number of intrahepatic tumor nodules. Conclusion: Overall, eosinophil infiltration in HCC is significantly correlated with patient survival. The risk assessment model based on eosinophil-related genes serves as a reliable clinical prognostic indicator and provides insights for precise treatment of HCC.

Ferritin Heavy-like subunit is involved in the innate immune defense of the red swamp crayfish Procambarus clarkii.

Iron-binding proteins, known as ferritins, play pivotal roles in immunological response, detoxification, and iron storage. Despite their significance to organisms, little is known about how they affect the immunological system of the red swamp crayfish (Procambarus clarkii). In our previous research, one ferritin subunit was completely discovered as an H-like subunit (PcFeH) from P. clarkii. The full-length cDNA of PcFerH is 1779 bp, including a 5'-UTR (untranslated region, UTR) of 89 bp, 3'-UTR (untranslated region, UTR) of 1180 bp and an ORF (open reading frame, ORF) of 510 bp encoding a polypeptide of 169 amino acids that contains a signal peptide and a Ferritin domain. The deduced PcFerH protein sequence has highly identity with other crayfish. PcFerH protein's estimated tertiary structure is quite comparable to animal structure. The PcFerH is close to Cherax quadricarinatus, according to phylogenetic analysis. All the organs examined showed widespread expression of PcFerH mRNA, with the ovary exhibiting the highest levels of expression. Additionally, in crayfish muscles, intestines, and gills, the mRNA transcript of PcFerH was noticeably up-regulated, after LPS and Poly I:C challenge. The expression of downstream genes in the immunological signaling system was suppressed when the PcFerH gene was knocked down. All of these findings suggested that PcFerH played a vital role in regulating the expression of downstream effectors in the immunological signaling pathway of crayfish.

Complete mitochondrial genome of Parasa sinica: New insights into the phylogeny of Limacodidae.

In this study, the whole mitochondrial genome (mitogenome) of Parasa sinica was sequenced. It contains 15,306 base pairs (bp), 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and one non-coding regulatory area (CR), all of which are shared by other lepidopterans. It follows the same gene order as ordinary lepidopterans. Further, out of these 37 genes, 23 are present on the heavy strand whereas the remaining 14 are located on the light strand. The A + T composition of the mitogenome is relatively high. Although P. sinica has a negative AT-skew and GC-skew, the GC-skew value is significantly lower than the AT-skew value. All PCGs, with the exception of CO1, carry the same start codon (ATN). All tRNAs exhibit the usual cloverleaf secondary structure. We identified the conserved motif "ATAGA + poly-T″ found in other lepidopteran insects at the beginning of the CR. We collected the concatenated PCGs sequences in the mitochondrial genome of 15 species of Zygaenoidea, with the sequences of Geometridae as outgroups, including P. sinica, and constructed phylogenetic trees using Bayesian inference (BI) and maximum likelihood (ML) methods. The monolineage of each superfamily is usually well supported. Based on phylogenetic analysis, P. sinica is a member of family Limacodidae, strongly supporting the monophyly of the Zygaenoidea groups.

Epigenetically modified AP-2α by DNA methyltransferase facilitates glioma immune evasion by upregulating PD-L1 expression.

Programmed death-ligand 1 (PD-L1) ensures that tumor cells escape T-cell-mediated tumor immune surveillance. However, gliomas are characteristic of the low immune response and high-resistance therapy, it is necessary to understand molecular regulatory mechanisms in glioblastoma, especially the limited regulation of PD-L1 expression. Herein, we show that low expression of AP-2α is correlated with high expression of PD-L1 in high-grade glioma tissues. AP-2α binds directly to the promoter of the CD274 gene, not only inhibits the transcriptional activity of PD-L1 but enhances endocytosis and degradation of PD-L1 proteins. Overexpression of AP-2α in gliomas enhances CD8+ T cell-mediated proliferation, effector cytokine secretion, and cytotoxicity in vitro. Tfap2a could increase the cytotoxic effect of Cd8+ T cells in CT26, B16F10, and GL261 tumor-immune models, improve anti-tumor immunity, and promote the efficacy of anti-PD-1 therapy. Finally, the EZH2/H3K27Me3/DNMT1 complex mediates the methylation modification of AP-2α gene and maintains low expression of AP-2α in gliomas. 5-Aza-dC (Decitabine) treatment combines with anti-PD-1 immunotherapy to efficiently suppress the progression of GL261 gliomas. Overall, these data support a mechanism of epigenetic modification of AP-2α that contributes to tumor immune evasion, and reactivation of AP-2α synergizes with anti-PD-1 antibodies to increase antitumor efficacy, which may be a broadly applicable strategy in solid tumors.

The Complete Mitochondrial Genome of Box Tree Moth Cydalima perspectalis and Insights into Phylogenetics in Pyraloidea.

To resolve and reconstruct phylogenetic relationships within Pyraloidea based on molecular data, the mitochondrial genome (mitogenome) was widely applied to understand phylogenetic relations at different taxonomic levels. In this research, a complete mitogenome of Cydalima perspectalis was recorded, and the phylogenetic position of C. perspectalis was inferred based on the sequence in combination with other available sequence data. According to the research, the circular mitochondrial genome is 15,180 bp in length. It contains 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), 13 typical protein-coding genes (PCGs), and a non-coding control region. The arrangement of a gene of the C. perspectalis mitogenome is not the same as the putative ancestral arthropod mitogenome. All of the PCGs are initiated by ATN codons, except for the cytochrome c oxidase subunit 1 (cox1) gene, which is undertaken by CGA. Five genes have incomplete stop codons that contain only 'T'. All tRNA genes display a typical clover-leaf structure of mitochondrial tRNA, except for trnS1 (AGN). The control region contained an 'ATAGG(A)'-like motif followed by a poly-T stretch. Based on the mitochondrial data, phylogenetic analysis within Pyraloidea was carried out using Bayesian inference (BI) and maximum likelihood (ML) analyses. Phylogenetic analysis showed that C. perspectalis is more closely related to Pygospila tyres within Spilomelinae than those of Crambidae and Pyraloidea.

Preliminary Study on the Formation Mechanism of Malformed Sweet Cherry (Prunus avium L.) Fruits in Southern China Using Transcriptome and Metabolome Data.

Gibberellin (GA) is an important plant hormone that is involved in various physiological processes during plant development. Sweet cherries planted in southern China have always encountered difficulty in bearing fruit. In recent years, gibberellin has successfully solved this problem, but there has also been an increase in malformed fruits. This study mainly explores the mechanism of malformed fruit formation in sweet cherries. By analyzing the synthesis pathway of gibberellin using metabolomics and transcriptomics, the relationship between gibberellin and the formation mechanism of deformed fruit was preliminarily determined. The results showed that the content of GA3 in malformed fruits was significantly higher than in normal fruits. The differentially expressed genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were mainly enriched in pathways such as "plant hormone signal transduction", "diterpenoid biosynthesis", and "carotenoid biosynthesis". Using Quantitative Real-Time Reverse Transcription PCR (qRT-PCR) analysis, the gibberellin hydrolase gene GA2ox and gibberellin synthase genes GA20ox and GA3ox were found to be significantly up-regulated. Therefore, we speculate that the formation of malformed fruits in sweet cherries may be related to the accumulation of GA3. This lays the foundation for further research on the mechanism of malformed sweet cherry fruits.

Development of an underwater networking system using bio-inspired electrocommunication.

Current underwater communication typically includes acoustic, optical, radio frequency, and magneto-inductive channels. Wireless sensor networks are usually built on these four channels. However, these underwater networks are vulnerable to complex aquatic environments. In nature, weakly electric fish are able to communicate electrically (called electrocommunication), which is 'invisible' to most other animals, to convey information such as species, courtship, and environmental conditions. Inspired by the electrocommunication of weakly electric fish, an artificial electrocommunication system that uses an electric induction (EI) channel has been developed recently. This paper further develops an underwater networking system using the EI channel, which addresses the solutions to collision avoidance and routing problems during electrocommunication networking. In particular, a CSMA/CA-based electrocommunication mechanism was used to solve the collision problem. Then, a single-hop underwater electrocommunication network (UEN) was established. Furthermore, a complex multi-hop UEN was implemented on the basis of the ad hoc on-demand distance vector routing protocol. Theoretical analysis, simulations, and experiments were conducted to demonstrate the effectiveness of the developed UEN. Extensive results show that the UEN holds the potential to serve as a complement to future underwater wireless sensor networks.

Long non-coding RNA TUG1/microRNA-187-3p/TESC axis modulates progression of pituitary adenoma via regulating the NF-κB signaling pathway.

The molecule mechanisms of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in human diseases have been broadly studied recently, therefore, our research aimed to assess the effect of lncRNA taurine upregulated gene 1 (TUG1)/miR-187-3p/tescalcin (TESC) axis in pituitary adenoma (PA) by regulating the nuclear factor-kappa B (NF-κB) signaling pathway. We observed that TUG1 was upregulated in PA tissues and was associated with invasion, knosp grade and tumor size. TUG1 particularly bound to miR-187-3p. TUG1 knockdown inhibited cell proliferation, invasion, migration, and epithelial-mesenchymal transition, promoted apoptosis, and regulated the expression of NF-κB p65 and inhibitor of κB (IκB)-α in PA cells lines in vitro, and also inhibited tumor growth in vivo, and these effects were reversed by miR-187-3p reduction. Similarly, miR-187-3p elevation inhibited PA cell malignant behaviors and modulated the expression of NF-κB p65 and IκB-α in PA cells, and reduced in vivo tumor growth as well. TUG1 inhibition downregulated TESC, which was targeted by miR-187-3p. In conclusion, this study suggests that TUG1 sponges miR-187-3p to affect PA development by elevating TESC and regulating the NF-κB signaling pathway.

Literature-Based Phenotype Survey and In Silico Genotype Investigation of Antibiotic Resistance in the Genus Bifidobacterium.

Bifidobacteria are typical commensals inhabiting the human intestine and are beneficial to the host because of their probiotic properties. One of the risks concerning probiotics is the potential of introducing antibiotic resistance genes (ARGs) to the host gut pathogens. This study was aimed to depict the general antibiotic resistance characteristics of the genus Bifidobacterium by combining the reported phenotype dataset and in silico genotype prediction. Bifidobacteria were mostly reported to be sensitive to beta-lactams, glycopeptides, chloramphenicol, and rifampicin, but resistant to aminoglycosides, polypeptides, quinolones, and mupirocin. Generally, the resistance phenotypes to erythromycin, tetracycline, fusidic acid, metronidazole, clindamycin, and trimethoprim were variable. Besides cmX and tetQ, characterized in bifidobacterial resident plasmids, 3520 putative ARGs were identified from 831 bifidobacterial genomes through BLASTP search. The identified ARGs matched thirty-eight reference ARGs, four of which seemed to be mutant housekeeping genes. The two high-abundant ARGs, tetW and ermX, were found to have different distribution traits. The predicted ARGs reasonably explained most of the corresponding resistant phenotypes in the published literature.

[Establishment of extraction method for Gardeniae Fructus extract and its application in evaluating different Gardeniae Fructus decoction pieces].

In this experiment,the gradation analysis method was used to evaluate the quality of different pieces of Gardeniae Fructus through the extraction rate difference and the difference analysis of the main components in the extract. In this experiment cold-dip and hot-dip methods were used to compare the yield of Gardeniae Fructus extract and the content of chemical constituents with water,25%,50%,75% and 95% ethanol fractions. By weighted calculation,the optimal extraction method of Gardeniae Fructus was determined,and this was verified by practical application. RESULTS:: showed that for the water-soluble extract,cold dip method was better than the hot dip method; and for alcohol-soluble extract,75% ethanol under cold dip method was best. The verification results showed that water-soluble extracts under cold dip methods could be used to significantly distinguish the raw Gardeniae Fructus( GF) and processed( stir-baked) GF( GFP) collected from the market. Meanwhile,this method could be also used to distinguish the same batch of GF,GFP and carbonized GF( GFC) with significant differences,respectively( P<0. 05). Ethanol-soluble extract can be used to clearly distinguish GFP and GFC pieces in the same batch( P<0. 05). The results of content determination showed that the variation coefficient of components in GF processed products was higher than that in extracts,and the content of hydroxygeniposide was the most significant component between GF and its processed products. It is suggested that the method of water-soluble extract of GF and the determination of the content of gardoside should be combined together to evaluate the quality of GF and its heat processed products.

Treatment Mechanism of Gardeniae Fructus and Its Carbonized Product Against Ethanol-Induced Gastric Lesions in Rats.

Gardeniae Fructus (GF) and carbonized GF (GFC) have been shown to exert a gastrointestinal protective effect and are frequently used in clinical practice for the treatment of hemorrhage and brown stool. In this study, we employed a combination of pharmacological methods and metabolomics in a rat model of ethanol-induced acute stomach ulcer to investigate the gastroprotective effect of GF and GFC water extracts and the potential mechanism involved in this process. The levels of nitric oxide (NO) and interleukin 6 (IL-6) in the plasma of rats were determined. The results showed that both GF and GFC reduced the ethanol-induced gastric lesions and expression of NO and IL-6 in these rats. Of note, 16 and 11 feature metabolites were filtered and identified in the GF and GFC groups, respectively. Both GF and GFC act by restoring the biosynthesis of valine, leucine, and isoleucine, and the metabolism of glycerophospholipids. Moreover, histological evaluation revealed that heat processing of GF to create GFC enhanced the gastric mucosa protective effect. Furthermore, heat processing converted the main pathway from alanine, aspartate, and glutamate metabolism, associated with GF, to histidine metabolism, associated with GFC. GF and GFC ameliorated gastric mucosa lesions in rats via reductions in NO production and inflammatory cytokine secretion, and the induction of prostaglandin E2.

[Study on quality standard of rice as excipients during rice stir-frying method].

Commercially available japonica rice and indica rice with different trade names were collected,and then based on the method of rice stir-frying,their many indexes were evaluated,for example the physical and chemical properties such as appearance color,grain type,broken kernel ratio,length-width ratio,1 000-grain weight,specific heat capacity,moisture content,amylose content,and protein content. The discriminant function analysis was used to determine the effective factors affecting the quality of rice as excipients. The results showed that two types of rice could be distinguished by rice color parameter a*,grain parameter circularity,1 000-grain weight and amylose content. These four effective factors can be used as the quality evaluation indexes for fried rice as excipients.Protein is one of the main components of rice,and its content affects the quality of rice. There is a significant difference in the protein content between japonica rice and indica rice. Therefore,protein content should be used as one of the evaluation indexes for rice quality. After comprehensive consideration,it is suggested that the red-green value a*shall not be less than 0. 50; the circularity not less than 53. 0,the 1 000-grain weight not less than 16. 0 g,the amylose content not less than 12. 0% and the protein content not less than4. 0% in the japonica rice; the red-green value a*shall not be lower than-1. 0,the circularity not less than 41. 0,the 1 000-grain weight not less than 13. 0 g,the amylose content not less than 9. 0% and the protein content not less than 3. 5% in the indica rice. In this study,the quality evaluation standards for rice as excipients( japonica rice,indica rice) were supplemented and improved,laying foundation for the development of quality standards for rice as excipients with the rice stir-frying method.

The Potential Antipyretic Mechanism of Gardeniae Fructus and Its Heat-Processed Products With Plasma Metabolomics Using Rats With Yeast-Induced Fever.

Gardeniae Fructus (GF), prepared GF (GFP), and carbonized GF (GFC) are widely used in China for the treatment of fever. However, the involved antipyretic mechanism has not been fully elucidated. In this study, rectal temperature and pyrogenic cytokines were used to evaluate the antipyretic effect of raw and processed GF in rats with dry-yeast-induced pyrexia. Reverse phase and hydrophilic interaction liquid chromatography and ultra-high-performance liquid chromatography/mass spectrometry were used to acquire the metabolomics profile of GF, GFP, and GFC in rats with pyrexia. The results showed that the rectal temperature of rats treated with GF, GFP, and GFC was suppressed after 6 h (P < 0.05), compared with that observed in pyrexia model rats. The enzyme-linked immunosorbent assay showed that the expression of tumor necrosis factor α and interleukin 6 were suppressed by GF, GFP, and GFC. Moreover, GFC suppressed the expression of interleukin 6 significantly (P < 0.01). Of note, 11, 15, and 25 feature metabolites were identified in the GF, GFP, and GFC groups. Pathway analysis showed that GF mainly regulated the biosynthesis of valine, leucine, and isoleucine. Notably, GFP was involved in glycerophospholipid metabolism, while GFC was linked to glycerophospholipid and sphingolipid metabolism. These results suggested that GF, GFP, and GFC maintained their antipyretic effect despite heat processing. However, heat processing altered endogenous feature metabolites and certain pathways of GF, GFP, and GFC in rats with yeast-induced pyrexia to exert an antipyretic effect.

Analysis on genetic diversity of 51 Grape germplasm resources / Análise da diversidade genética da videira 51

ABSTRACT: The objective of this study is to research the genetic diversity of the ' Zuijinxiang ' grape and its mutant breeding F1 plants, we screened the excellent mutant plants with potential breeding value. 50 mutated single plants obtained from 137Cs-γ irradiated 'Zuijinxiang' grape seeds were used as research objects, and SCoT molecular marker technology was used for genetic diversity and variation analysis, and clustering research was carried out. The results showed that: (1) 36 SCoT primers produced abundant polymorphisms, and the amplification results showed obvious bright bands, and the amplification efficiency and polymorphism rate were 100%. (2) A total of 221 bands were amplified by 36 primers, of which 175 were rich in polymorphism, the average polymorphic percentage was 80.3%, and the average genetic similarity coefficient was 0.916. (3) The number of observed alleles (Na) ranged from 4 to 8, with an average of 6.1389; the number of effective alleles (Ne) ranged from 1.2772 to 5.6322 with an average of 3.5968; the desired heterozygosity (He) The range is from 0.2192 to 0.8344, the average is 0.6965; the observed heterozygosity (Ho) ranges from 0.1656 to 0.7808 with an average of 0.3035; the Nei's gene diversity index (H) ranges from 0.2170 to 0.8224 with an average of 0.6863; Shannon-Wiener The index (I) ranges from 0.5186 to 1.8597 with an average of 1.4517. (4) UPGMA clustering of 51 materials showed that the test materials could be divided into three groups when the genetic distance was 0.856. The experiment shows that the genetic diversity of the 'Zuijinxiang' radiation variation germplasm resources is rich. In addition, SCoT molecular marker technology can distinguish the materials with close genetic distance, and can be used for early identification techniques of grape mutant materials. This study provides a theoretical basis for the development of excellent mutant germplasm of 'Zuijinxiang' grapes.

RESUMO: O objetivo deste estudo é investigar a diversidade genética da uva 'Zuijinxiang' e de suas plantas F1 reprodutoras mutantes. Foram selecionadas as melhores plantas mutantes com potencial e valor genético. Utilizaram-se como objeto de pesquisa 50 plantas individuais mutantes obtidas de sementes de uva irradiadas com 137Cs-γ 'Zuijinxiang', e a tecnologia de marcadores moleculares SCoT para análise de diversidade genética e variação, e foi realizada uma pesquisa de agrupamento. Os resultados mostraram que: (1) 36 iniciadores de SCoT produziram polimorfismos abundantes, e os resultados de amplificação mostraram bandas claras óbvias, e a eficiência de amplificação e taxa de polimorfismo foram de 100%. (2) Um total de 221 bandas foi amplificado por 36 iniciadores, dos quais 175 eram ricos em polimorfismo, a porcentagem polimórfica média foi de 80,3% e o coeficiente médio de similaridade genética foi de 0,916. (3) O número de alelos observados (Na) variou de 4 a 8, com uma média de 6,1389; o número de alelos efetivos (Ne) variou de 1,2772 a 5,6322 com uma média de 3,5968; a heterozigosidade desejada (He), o intervalo é de 0,2192 a 0,8344, a média é de 0,6965; a heterozigosidade observada (Ho) varia de 0,1656 a 0,7808 com uma média de 0,3035; o índice de diversidade genética (H) de Nei varia de 0,2170 a 0,8224 com uma média de 0,6863; Shannon-Wiener o índice (I) varia de 0,5186 a 1,8597 com uma média de 1,4517. (4) O agrupamento de 51 materiais da UPGMA mostrou que os materiais de teste poderiam ser divididos em três grupos quando a distância genética era de 0,856. O experimento mostra que a diversidade genética dos recursos de germoplasma de variação de radiação "Zuijinxiang" é rica. Além disso, a tecnologia de marcadores moleculares da SCoT pode distinguir os materiais com uma distância genética próxima, e pode ser usada para técnicas de identificação precoce de materiais mutantes da uva. Este estudo fornece uma base teórica para o desenvolvimento de germoplasma mutante excelente de uvas "Zuijinxiang".

[TRAP analysis of Salvia miltiorrhiza Bge from different places of production].

The molecular maker system TRAP was utilized to develop a novel more accurate tool to identify the variety and establish the evolutionary relationship of different kind of Salvia miltiorrhiza Bge. PopGene 32 software was applied to conduct the cluster analysis and genetic dendrogram establishment. The results showed that 203 different fragments were amplified with 6 pair primers using the TRAP marker system. The polymorphic fragments number is 43, which takes up to 21.1%. The cluster analysis shows that the 4 materials we used in this study can be classified into 2 main groups and 3 subgroups. The genetic identity is 0.0788 and the average genetic distance is 0.9245 among the four materials in this study. A new tool using the TRAP marker system is more accurate and can be used to identify different kind of Salvia miltiorrhiza Bge at molecular level.

[Progress in the study of application of modern instrument to investigation of gallstones].

The analyses of chemical composition and elements in gallstones can provide significant reference to the treatment and prevention of recurrence of gallstones. In the present paper, the progess in the study of the application of modern instrument to the analyse of gallstones was reviewed. These techniques include Raman spectrum, energy-dispersive X-ray microanalysis, Fourier transform infrared spectroscopy and its derivative spectrum, thermogravimetry, differential scanning calorimetry, atomic absorption spectrum, inductively coupled plasma atomic emission spectrometry, high performance liquid chromatography, scanning electronic microscopy, transmission electron microscopy, etc.