[Identification of Protein-Coding Gene Markers in Breast Invasive Carcinoma Based on Machine Learning].

Objective To screen out the biomarkers linked to prognosis of breast invasive carcinoma based on the analysis of transcriptome data by random forest (RF),extreme gradient boosting (XGBoost),light gradient boosting machine (LightGBM),and categorical boosting (CatBoost). Methods We obtained the expression data of breast invasive carcinoma from The Cancer Genome Atlas and employed DESeq2,t-test,and Cox univariate analysis to identify the differentially expressed protein-coding genes associated with survival prognosis in human breast invasive carcinoma samples.Furthermore,RF,XGBoost,LightGBM,and CatBoost models were established to mine the protein-coding gene markers related to the prognosis of breast invasive cancer and the model performance was compared.The expression data of breast cancer from the Gene Expression Omnibus was used for validation. Results A total of 151 differentially expressed protein-coding genes related to survival prognosis were screened out.The machine learning model established with C3orf80,UGP2,and SPC25 demonstrated the best performance. Conclusions Three protein-coding genes (UGP2,C3orf80,and SPC25) were screened out to identify breast invasive carcinoma.This study provides a new direction for the treatment and diagnosis of breast invasive carcinoma.

[Role of Eukaryotic Translation Elongation Factor 1 Family Members in the Tumorigenesis and Progression of Lung Adenocarcinoma].

Objective To investigate the role and mechanism of eukaryotic translation elongation factor 1(EEF1) family members (EEF1D,EEF1A1,and EEF1A2) in lung adenocarcinoma (LUAD) based on public databases.Methods We examined EEF1 member expression levels in human LUAD samples via The Cancer Genome Atlas in the UCSC Xena browser and the Clinical Proteomic Tumor Analysis Consortium.We analyzed the mRNA and protein levels of EEF1D,EEF1A1,and EEF1A2 and their correlations with pathological variables via the Mann-Whitney U test.The Kaplan-Meier curves were established to assess the prognostic values of EEF1D,EEF1A1,and EEF1A2.The single-sample gene set enrichment analysis algorithm was employed to explore the relationship between the expression levels of EEF1 members and tumor immune cell infiltration.Spearman and Pearson correlation analyses were performed to examine the relationship between the expression levels of EEF1 members and those of the genes in the phosphatidylinositol 3-kinase/protein kinase B signaling pathway.The immunohistochemical assay was employed to determine the expression levels of EEF1D,EEF1A1,and EEF1A2 in the LUAD tissue (n=75) and paracancer tissue (n=75) samples.Results The mRNA and protein levels of EEF1D,EEF1A1,and EEF1A2 showed significant differences between tumor and paracancer tissues (all P<0.001).The patients with high protein levels of EEF1A1 showed bad prognosis in terms of overall survival (P=0.039),and those with high protein levels of EEF1A2 showed good prognosis in terms of overall survival (P=0.012).The influence of the mRNA level of EEF1D on prognosis was associated with pathological characteristics.The expression levels of EEF1 members were significantly associated with the infiltration of various immune cells and the expression of key molecules in the phosphatidylinositol 3-kinase/protein kinase B signaling pathway.Conclusion EEF1D,EEF1A1,and EEF1A2 are associated with the progression of LUAD,serving as the candidate prognostic markers for LUAD.

Evaluation of ubiquitination and sumoylation of acrosin inhibitor during in vitro capacitation of porcine sperm.

The main objective of this study was to investigate the expression of acrosin inhibitor (AI), ubiquitin (Ub), and small ubiquitin-related modifier 1 (SUMO1) proteins during in vitro capacitation of pig sperm. Duroc pig sperm was divided into fresh sperm and capacitation treatment groups. Protein expression was evaluated using computer-assisted sperm analysis (CASA) systems, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), western blotting, and immunofluorescence. The results showed that the expression of AI (30 kDa) incapacitated sperm was significantly lower than that in fresh sperm (P < 0.05), and that the levels of ubiquitinated and SUMO1-ylated proteins in capacitated sperm were significantly higher than those in fresh sperm (P < 0.05). Immunofluorescence results showed that AI, Ub, and SUMO1 were located in the acrosome region of the fresh and capacitated sperm heads. After capacitation, the fluorescence intensity of AI and SUMO1 decreased, while that of Ub increased. The protein band at 30 kDa represented the AI-Ub-SUMO1 complex, indicating that this complex was involved in sperm capacitation. Furthermore, SUMO1 increased the stability of AI at 30 kDa, preventing its complete decomposition, while at 46 kDa, in the absence of SUMO1, AI is bound to ubiquitin, and was completely degraded.

[Uncovering the molecular mechanisms behind steroidal saponin accumulation in Liriope muscari (Decne.) Baily through transcriptome sequencing and bioinformatics analysis].

The leaves and roots of Liriope muscari (Decne.) Baily were subjected to high-throughput Illumina transcriptome sequencing. Bioinformatics analysis was used to investigate the enzyme genes and key transcription factors involved in regulating the accumulation of steroidal saponins, which are the main active ingredient in L. muscari. These analyses aimed to reveal the molecular mechanism behind steroidal saponin accumulation. The sequencing results of L. muscari revealed 31 enzymes, including AACT, CAS, DXS and DXR, that are involved in the synthesis of steroidal saponins. Among these enzymes, 16 were in the synthesis of terpenoid skeleton, 3 were involved in the synthesis of sesquiterpene and triterpene, and 12 were involved in the synthesis of steroidal compound. Differential gene expression identified 15 metabolic enzymes coded by 34 differentially expressed genes (DEGs) in the leaves and roots, which were associated with steroidal saponin synthesis. Further analysis using gene co-expression patterns showed that 14 metabolic enzymes coded by 31 DEGs were co-expressed. In addition, analysis using gene co-expression analysis and PlantTFDB's transcription factor analysis tool predicted the involvement of 8 transcription factors, including GAI, PIF4, PIL6, ERF8, SVP, LHCA4, NF-YB3 and DOF2.4, in regulating 6 metabolic enzymes such as DXS, DXR, HMGR, DHCR7, DHCR24, and CAS. These eight transcription factors were predicted to play important roles in regulating steroidal saponin accumulation in L. muscari. Promoter analysis of these transcription factors indicated that their main regulatory mechanisms involve processes such as abscisic acid response, drought-induction stress response and light response, especially abscisic acid responsive elements (ABRE) response and MYB binding site involved in drought-inducibility (MBS) response pathway. Furthermore, qRT-PCR analysis of these eight key transcription factors demonstrated their specific differences in the leaves and roots.

Follicular fluid exosome-derived miR-339-5p enhances in vitro maturation of porcine oocytes via targeting SFPQ, a regulator of the ERK1/2 pathway.

In this study, we aimed to investigate cytoplasmic maturation and miRNA expression of mature oocytes cultured in porcine follicular fluid exosomes. We also examined the effect of miR-339-5p on oocyte maturation. Twenty eight differentially expressed miRNAs were detected using miRNA-seq. We then transfected cumulus oocyte complexes with miR-339-5p mimics and inhibitor during culture. The results showed that exosomes increased endoplasmic reticulum levels and the amount of lipid droplets, and decreased ROS levels, lipid droplet size, and percentage of oocytes with abnormal cortical granule distribution. Overexpressing miR-339-5p significantly decreased cumulus expansion genes, oocyte maturation-related genes, target gene proline/glutamine-rich splicing factor (SFPQ), ERK1/2 phosphorylation levels, oocyte maturation rate, blastocyst rate, and lipid droplet number, but increased lipid droplet size and the ratio of oocytes with abnormal cortical granule distribution. Inhibiting miR-339-5p reversed the decrease observed during overexpression. Mitochondrial membrane potential and ROS levels did not differ significantly between groups. In summary, exosomes promote oocyte cytoplasmic maturation and miR-339-5p regulating ERK1/2 activity through SFPQ expression, thereby elevating oocyte maturation and blastocyst formation rate in vitro.

Comparative Metabolome and Transcriptome Analyses of the Regulatory Mechanism of Light Intensity in the Synthesis of Endogenous Hormones and Anthocyanins in Anoectochilus roxburghii (Wall.) Lindl.

To explore the regulatory mechanism of endogenous hormones in the synthesis of anthocyanins in Anoectochilus roxburghii (Wall.) Lindl (A. roxburghii) under different light intensities, this study used metabolomics and transcriptomics techniques to identify the key genes and transcription factors involved in anthocyanin biosynthesis. We also analyzed the changes in and correlations between plant endogenous hormones and anthocyanin metabolites under different light intensities. The results indicate that light intensity significantly affects the levels of anthocyanin glycosides and endogenous hormones in leaves. A total of 38 anthocyanin-related differential metabolites were identified. Under 75% light transmittance (T3 treatment), the leaves exhibited the highest anthocyanin content and differentially expressed genes such as chalcone synthase (CHS), flavonol synthase (FLS), and flavonoid 3'-monooxygenase (F3'H) exhibited the highest expression levels. Additionally, 13 transcription factors were found to have regulatory relationships with 7 enzyme genes, with 11 possessing cis-elements responsive to plant hormones. The expression of six genes and two transcription factors was validated using qRT-PCR, with the results agreeing with those obtained using RNA sequencing. This study revealed that by modulating endogenous hormones and transcription factors, light intensity plays a pivotal role in regulating anthocyanin glycoside synthesis in A. roxburghii leaves. These findings provide insights into the molecular mechanisms underlying light-induced changes in leaf coloration and contribute to our knowledge of plant secondary metabolite regulation caused by environmental factors.

Molecular occurrence and risk factors for Toxoplasma gondii infection in equids in Jilin, China.

Toxoplasma gondii, one of the important zoonotic parasites, has been detected in lots of hosts including humans, with a widespread prevalence. The products of equids, such as meat and milk, have been closely related to humans' life. As the intermediate hosts, little is known about equids toxoplasmosis in Jilin province. Therefore, the present study aimed to evaluate the occurrence and risk factors of Toxoplasma gondii infections in equids from Jilin, northeastern China. In this study, a total of 245 blood samples of equids (192 horses, 25 donkeys and 28 mules) were collected from six localities in Jilin Province from March 2018 to August 2020 and detected by PCR. The occurrence rate of T. gondii B1 gene was analyzed using multivariable logistic regression to evaluate risk factors associated with the positive rates in equids. Among 245equids, T. gondii molecular occurrence was 9.0% (22/245). The highest positive rate was observed in equids from Dongfeng (16.3%) followed by Taonan (10.0%), Wangqing (8.3%), Antu (8.0%), Tonghua (8.0%) and Shulan (2.3%). Statistical analysis revealed that farming model and region may be two main risk factors. Data analysis indicated that the positive rate in captive farm (3.2%, 95% CI: 0.0-6.7%) was significantly lower than those in cage-free farm (P < 0.05), and the region of Shulan was protective factor (OR: 0.063, 95% CI: 0.007-0.559).The results of our study alert people to be aware that the present of equids T. gondii infection in this region, and contribute to a prevention and treatment program for toxoplasmosis in Jilin, China.

Survey of tick species and molecular detection of selected tick-borne pathogens in Yanbian, China.

Ticks and tick-borne diseases pose a significant threat to public health. In this study, we aimed to determine the tick species distribution and pathogens carried by ticks in Yanbian, China. A total of 2673 questing ticks were collected from eight counties and cities in Yanbian and were morphologically identified. The presence of Candidatus Rickettsia tarasevichiae (CRT), spotted fever group Rickettsia (SFGR), severe fever thrombocytopenia syndrome virus (SFTSV), Theileria, and other pathogens was confirmed using polymerase chain reaction (PCR) and real-time quantitative PCR assays, followed by phylogenetic and genotypic analyses. According to the morphological identification, the tick species in Yanbian consisted of Haemaphysalis longicornis, Ixodes persulcatus, Dermacentor silvarum, H. japonica, and H. concinna. In H. longicornis, CRT, SFGR, SFTSV and Theileria orientalis were detected, while CRT, SFGR, and SFTSV were detected in I. persulcatus, H. japonica, and D. silvarum. Only SFTSV was detected in H. concinna. Mixed infection with CRT and SFTSV was observed in I. persulcatus and H. japonica. The gene sequences of all tested pathogens exhibited 95.7%-100% identity with the corresponding sequences deposited in GenBank. Phylogenetic analysis showed that different SFGR and SFTSV genotypes were closely related to the Korean strains. This study is the first to describe the genetic diversity of SFGR Candidatus Rickettsia longicornii in H. longicornis in Yanbian, China, using the ompA, ompB, sca4, and rrs genes. These results provide epidemiological data to support the prevention and control of ticks and tick-borne diseases in the border areas of China, North Korea, and Russia.

Title: Enquête sur les espèces de tiques et détection moléculaire de certains agents pathogènes transmis par les tiques à Yanbian, en Chine. Abstract: Les tiques et les maladies transmises par les tiques constituent une menace importante pour la santé publique. Dans cette étude, nous avons cherché à déterminer la distribution des espèces et les agents pathogènes portés par les tiques à Yanbian, en Chine. Un total de 2 673 tiques errantes ont été collectées dans huit comtés et villes de Yanbian et identifiées morphologiquement. La présence de Candidatus Rickettsia tarasevichiae (CRT), de Rickettsia du groupe de la fièvre boutonneuse (SFGR), du virus du syndrome de la fièvre thrombocytopénique sévère (SFTSV), de Theileria et d'autres agents pathogènes a été confirmée à l'aide d'une réaction en chaîne par polymérase (PCR) et de PCR quantitative en temps réel, suivies par des analyses phylogénétiques et génotypiques. Selon leur identification morphologique, les espèces de tiques à Yanbian se composaient de Haemaphysalis longicornis, Ixodes persulcatus, Dermacentor silvarum, H. japonica et H. concinna. Chez H. longicornis, CRT, SFGR, SFTSV et Theileria orientalis ont été détectés, tandis que CRT, SFGR et SFTSV ont été détectés chez I. persulcatus, H. japonica et D. silvarum. Seul le SFTSV a été détecté chez H. concinna. Une infection mixte par CRT et SFTSV a été observée chez I. persulcatus et H. japonica. Les séquences des gènes de tous les agents pathogènes testés présentaient une identité de 95,7 % à 100 % avec les séquences correspondantes déposées dans GenBank. L'analyse phylogénétique a montré que différents génotypes SFGR et SFTSV étaient étroitement liés aux souches coréennes. Cette étude est la première à décrire la diversité génétique de SFGR Candidatus Rickettsia longicornii chez H. longicornis à Yanbian, en Chine, en utilisant les gènes ompA, ompB, sca4 et rrs. Ces résultats fournissent des données épidémiologiques pour soutenir la prévention et le contrôle des tiques et des maladies transmises par les tiques dans les zones frontalières de la Chine, de la Corée du Nord et de la Russie.

Effects of Taraxacum and Astragalus extracts combined with probiotic Bacillus subtilis and Lactobacillus on Escherichia coli-infected broiler chickens.

Diarrhea caused by Escherichia coli (E. coli) is one of the most common diseases that affects the growth and development of poultry. This study was conducted to investigate the synergistic effects of traditional Chinese medicine (TCM) combined with probiotics against E. coli infection and its mechanism in broiler chickens. The optimal proportion formula TCM and probiotics was screened by orthogonal test and range analysis method; the in vitro antibacterial activity was based on the Oxford cup method. Isolated pathogenic E. coli was injected subcutaneously into the neck of the broilers to establish an E. coli-infected model. The broilers were administrated with drugs in drinking water daily for 7 d before and after E. coli infection. The diarrhea rate, mortality, body weight (BW) gain, feed intake, immune organ index, intestinal and hepatic histopathological changes were monitored. The expression of IL-2, IL-10, and TLR-4 mRNA in the intestinal tissues was measured by RT-PCR. Our results showed that the optimal proportion formula of Taraxacum extracts: total flavonoids of Astragalus: polysaccharides of Astragalus: probiotics was 5: 2: 2: 2; TCM combined with probiotics was highly sensitive to E. coli. TCM combined with probiotics synergistically increased BW gain, decreased the diarrhea rate and mortality of broilers, alleviated intestinal and hepatic pathological changes, accompanied by the increase of IL-2 and IL-10 mRNA expression and the inhibition of TLR-4 mRNA expression. It suggests that the combination of TCM and probiotics may produce a synergistic protective effect against E. coli infection by improving the indicators of diarrhea and regulating the expression of IL-2, IL-10, and TLR-4 mRNA in broiler chickens. The synergistic interactions between TCM and probiotics represent a promising strategy for the treatment of E. coli infection.

Curcumin Activates ROS Signaling to Promote Pyroptosis in Hepatocellular Carcinoma HepG2 Cells.

BACKGROUND/AIM: Curcumin is a polyphenol that exerts a variety of pharmacological activities and plays an anti-cancer role in many cancer cells. It was recently reported that gasdermin E (GSDME) is involved in the progression of pyroptosis. MATERIALS AND METHODS: HepG2 cells were treated with various concentrations of curcumin and cell viability was examined using MTT assay, apoptosis was analysed using flow cytometry, reactive oxygen species (ROS) levels using dihydroethidium, LDH release using an LDH cytotoxicity assay, and protein expression using western blot. RESULTS: Curcumin increased the expression of the GSDME N-terminus and proteins involved in pyrolysis, promoted HspG2 cell pyrolysis and increased intracellular ROS levels. Moreover, inhibition of the production of intracellular ROS with n-acetylcysteine (NAC) improved the degree of apoptosis and pyrolysis induced by curcumin. CONCLUSION: Curcumin induces HspG2 cell death by increasing apoptosis and pyroptosis, and ROS play a key role in this process. This study improves our understanding of the potential anti-cancer properties of curcumin in liver cancer.

Effects of Arsenic (+3 Oxidation State) Methyltransferase Gene Polymorphisms and Expression on Bladder Cancer: Evidence from a Systematic Review, Meta-analysis and TCGA Dataset.

Inorganic arsenic (iAs) is a recognized environment-related factor for bladder cancer (BCa). Arsenic (+3 oxidation state) methyltransferase (AS3MT) gene might influence BCa by regulating iAs metabolism. The aim of the present study was to explore whether AS3MT polymorphisms could affect BCa susceptibility. We systematically reviewed eligible case-control studies about AS3MT polymorphisms and BCa and to further compare the genotype distribution and allele distribution between BCa patients and controls by meta-analysis for humans. Besides, to clarify the effects of AS3MT expression on BCa clinical outcomes and survival time, we also conducted a series of analyses based on The Cancer Genome Atlas dataset. Databases were systematically retrieved and we applied Stata software to perform meta-analysis. The registration of this study protocol is at PROSPERO and ID is CRD42019133947. Five articles were recruited and pooled results demonstrated that rs3740393 and rs11191438 polymorphisms were related to BCa risk in overall population (p < .05) in the overall population. In addition, GG and GC genotypes in rs3740393 and GG genotype in rs11191438 might be the susceptibility genotypes for BCa. Results based on 168 BCa samples from TGCA indicated that patients with higher expression of AS3MT had poor overall survival time and AS3MT expression is an independent indicator for BCa survival. This study identified that AS3MT polymorphisms could affect BCa risk and AS3MT expression was pivotal in prognosis of BCa.

Relationship Between the ApaI (rs7975232), BsmI (rs1544410), FokI (rs2228570), and TaqI (rs731236) Variants in the Vitamin D Receptor Gene and Urolithiasis Susceptibility: An Updated Meta-Analysis and Trial Sequential Analysis.

The relationship between urolithiasis and vitamin D receptor (VDR) gene variants is still under debate according to the available published literature. To assess correlations between VDR gene variants ApaI (rs7975232), BsmI (rs1544410), FokI (rs2228570), and TaqI (rs731236) and urolithiasis susceptibility, we performed the present study through meta-analysis. The PubMed, Cochrane Library, China National Knowledge Infrastructure, EMBASE, Web of Science, and Wanfang databases were searched to retrieve qualified case-control studies. Finally, 31 reports were selected for the present meta-analysis. The results demonstrated that the VDR gene TaqI TT genotype was related to decreased risk of urolithiasis in the overall population (TT vs. Tt+tt: P = 0.011, OR = 0.824, 95% CI = 0.709-0.957). In ethnicity subgroup analysis, we found that the TaqI variant was obviously correlated to urolithiasis risk among Asians and Caucasians (P < 0.05). Additionally, significant urolithiasis risk was identified in adults. However, the FokI, BsmI, and ApaI variants did not have an increased risk of developing urolithiasis. Trial sequential analysis results were on a sufficiently large number of participants and did not require more research to confirm associations. Our research suggested that the VDR gene variant TaqI was correlated with urolithiasis susceptibility and that the t-allele might be the risk gene and T-allele the protective gene in VDR TaqI variant.

Epidemiological survey of Theileria parasite infection of cattle in Northeast China by allele-specific PCR.

An epidemiological survey on a Theileria parasite infection of cattle in Northeast China was carried out using allele-specific PCR and DNA sequence analysis of the major piroplasm surface protein (MPSP) gene. The results showed that 14 of 104 blood samples were positive for Theileria by PCR. Among the positive cases, co-infection with various combinations of C- and I-type parasites was detected in 12 samples; no B- and Thai-type parasites were detected by allele-specific PCR. Phylogenetic analysis based on the MPSP gene sequences revealed that Theileria parasites with the MPSP types 1, 2, and 4 were distributed in Northeast China.