Knockdown of Ezrin Suppresses the Migration and Angiogenesis of Human Umbilical Vein Endothelial Cells In Vitro

Progressive tumor growth is dependent on angiogenesis. The mechanisms by which endothelial cells（ECs） are incorporated to develop new blood vessels are not well understood. Recent studies reveal that the ezrin radixin moesin（ERM） family members are key regulators of cellular activities such as adhesion, morphogenetic change, and migration. We hypothesized that ezrin, one of the ERM family members, may play important roles in ECs organization during angiogenesis, and new vessels formation in preexisting tissues. To test this hypothesis, in this study, we investigated the effects of ezrin gene silencing on the migration and angiogenesis of human umbilical vein endothelial cells（HUVECs） in vitro. HUVECs were transfected with plasmids with ezrin-targeting short hairpin RNA by using the lipofectamine-2000 system. Wound assay in vitro and three-dimensional culture were used to detect the migration and angiogenesis capacity of HUVECs. The morphological changes of transfected cells were observed by confocal and phase contrast microscopy. Our results demonstrated that the decreased expression of ezrin in HUVECs significantly induced the morphogenetic changes and cytoskeletal reorganization of the transfected cells, and also reduced cell migration and angiogenesis capacity in vitro, suggesting that ezrin play an important role in the process of HUVECs migration and angiogenesis.

Comprehensive analysis of the potential pathogenesis of COVID-19 infection and liver cancer

BACKGROUND A growing number of clinical examples suggest that coronavirus disease 2019(COVID-19)appears to have an impact on the treatment of patients with liver cancer compared to the normal population,and the prevalence of COVID-19 is significantly higher in patients with liver cancer.However,this mechanism of action has not been clarified.Gene sets for COVID-19(GSE180226)and liver cancer(GSE87630)were obtained from the Gene Expression Omnibus database.After identifying the common differentially expressed genes(DEGs)of COVID-19 and liver cancer,functional enrichment analysis,protein-protein interaction network construction and scree-ning and analysis of hub genes were performed.Subsequently,the validation of the differential expression of hub genes in the disease was performed and the regulatory network of transcription factors and hub genes was constructed.RESULTS Of 518 common DEGs were obtained by screening for functional analysis.Fifteen hub genes including aurora kinase B,cyclin B2,cell division cycle 20,cell division cycle associated 8,nucleolar and spindle associated protein 1,etc.,were further identified from DEGs using the“cytoHubba”plugin.Functional enrichment analysis of hub genes showed that these hub genes are associated with P53 signalling pathway regulation,cell cycle and other functions,and they may serve as potential molecular markers for COVID-19 and liver cancer.Finally,we selected 10 of the hub genes for in vitro expression validation in liver cancer cells.CONCLUSION Our study reveals a common pathogenesis of liver cancer and COVID-19.These common pathways and key genes may provide new ideas for further mechanistic studies.

Ezrin蛋白在幽门螺杆菌感染的结节性胃炎中的研究进展

ERM蛋白家族(包括ezrin、radixin、moesin)在细胞形态、迁移和信号转导中发挥着至关重要的作用。Ezrin是ERM蛋白家族的成员之一,是幽门螺杆菌(Helicobacter pylori)感染宿主所致细胞毒性的重要介质,通过ezrin磷酸化可以调节其与肌动蛋白细胞骨架的相互作用,进而对细胞形态产生显著影响。本文综述了ezrin蛋白在H.pylori感染引发的结节性胃炎中的重要性,探讨了ezrin蛋白的结构及其功能、信号通路及磷酸化与结节性胃炎的关系,为以ezrin蛋白作为潜在的治疗靶点对结节性胃炎的防治提供新思路。

Identification of hub genes associated with Helicobacter pylori infection and type 2 diabetes mellitus:A pilot bioinformatics study

BACKGROUND Helicobacter pylori(H.pylori)infection is related to various extragastric diseases including type 2 diabetes mellitus(T2DM).However,the possible mechanisms connecting H.pylori infection and T2DM remain unknown.AIM To explore potential molecular connections between H.pylori infection and T2DM.METHODS We extracted gene expression arrays from three online datasets(GSE60427,GSE27411 and GSE115601).Differentially expressed genes(DEGs)commonly present in patients with H.pylori infection and T2DM were identified.Hub genes were validated using human gastric biopsy samples.Correlations between hub genes and immune cell infiltration,miRNAs,and transcription factors(TFs)were further analyzed.RESULTS A total of 67 DEGs were commonly presented in patients with H.pylori infection and T2DM.Five significantly upregulated hub genes,including TLR4,ITGAM,C5AR1,FCER1G,and FCGR2A,were finally identified,all of which are closely related to immune cell infiltration.The gene-miRNA analysis detected 13 miRNAs with at least two gene cross-links.TF-gene interaction networks showed that TLR4 was coregulated by 26 TFs,the largest number of TFs among the 5 hub genes.CONCLUSION We identified five hub genes that may have molecular connections between H.pylori infection and T2DM.This study provides new insights into the pathogenesis of H.pylori-induced onset of T2DM.

支气管哮喘婴幼儿血清Ezrin蛋白水平及临床意义

目的探讨Ezrin蛋白在支气管哮喘婴幼儿血清中的表达水平及临床意义。方法61例支气管哮喘婴幼儿按哮喘轻重分级标准分为轻度组(=34)和重度组(=27),并同时纳入同期于儿童保健科门诊体检的健康婴幼儿35例作为对照组。采用酶联免疫吸附测定法检测各组血清中Ezrin蛋白及白介素-13(IL-13)水平。结果对照组血清Ezrin蛋白水平均高于轻度组、重度组(均<0.05);轻度组Ezrin蛋白高于重度组(<0.05)。重度组IL-13水平均高于轻度组、对照组(均<0.05),轻度组与对照组差异无统计学意义(>0.05)。Ezrin蛋白水平与IL-13在血清中的表达呈负相关(=–0.61,<0.05)。当血清Ezrin蛋白截断水平为1.38 ng/ml时,其诊断哮喘的敏感度为98.50%,特异度为91.30%,受试者工作特征曲线下面积为0.998(95%:0.946~1.000)。结论血清Ezrin蛋白水平可用于辅助诊断婴幼儿支气管哮喘并评估病情的严重程度。

Key genes and regulatory networks for diabetic retinopathy based on hypoxia-related genes:a bioinformatics analysis

AIM:To prevent neovascularization in diabetic retinopathy(DR)patients and partially control disease progression.METHODS:Hypoxia-related differentially expressed genes(DEGs)were identified from the GSE60436 and GSE102485 datasets,followed by gene ontology(GO)functional annotation and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis.Potential candidate drugs were screened using the CMap database.Subsequently,a protein-protein interaction(PPI)network was constructed to identify hypoxia-related hub genes.A nomogram was generated using the rms R package,and the correlation of hub genes was analyzed using the Hmisc R package.The clinical significance of hub genes was validated by comparing their expression levels between disease and normal groups and constructing receiver operating characteristic curve(ROC)curves.Finally,a hypoxia-related miRNA-transcription factor(TF)-Hub gene network was constructed using the NetworkAnalyst online tool.RESULTS:Totally 48 hypoxia-related DEGs and screened 10 potential candidate drugs with interaction relationships to upregulated hypoxia-related genes were identified,such as ruxolitinib,meprylcaine,and deferiprone.In addition,8 hub genes were also identified:glycogen phosphorylase muscle associated(PYGM),glyceraldehyde-3-phosphate dehydrogenase spermatogenic(GAPDHS),enolase 3(ENO3),aldolase fructose-bisphosphate C(ALDOC),phosphoglucomutase 2(PGM2),enolase 2(ENO2),phosphoglycerate mutase 2(PGAM2),and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3(PFKFB3).Based on hub gene predictions,the miRNA-TF-Hub gene network revealed complex interactions between 163 miRNAs,77 TFs,and hub genes.The results of ROC showed that the except for GAPDHS,the area under curve(AUC)values of the other 7 hub genes were greater than 0.758,indicating their favorable diagnostic performance.CONCLUSION:PYGM,GAPDHS,ENO3,ALDOC,PGM2,ENO2,PGAM2,and PFKFB3 are hub genes in DR,and hypoxia-related hub genes exhibited favorable diagnostic performance.

Identification and Validation of Vascular-Associated Biomarkers for the Prognosis and Potential Pathogenesis of Hypertension Using Comprehensive Bioinformatics Methods

Background: Hypertension, also known as increased blood pressure, is a phenomenon in which blood flows in blood vessels and causes persistently higher-than-normal pressure on the vessel wall. The identification of novel prognostic and pathogenesis biomarkers plays a key role in the management of hypertension. Methods: The GSE7483 and GSE75815 datasets from the gene expression omnibus (GEO) database were used to identify the genes associated with hypertension that were differentially expressed genes (DEGs). The functional role of the DEGs was elucidated by gene body (GO) enrichment analysis. In addition, we performed an immune infiltration assay and GSEA on the DEGs of hypertensive patients and verified the expression of novel DEGs in the blood of hypertensive patients by RT-qPCR. Results: A total of 267 DEGs were identified from the GEO database. GO analysis revealed that these genes were associated mainly with biological processes such as fibroblast proliferation, cell structural organization, extracellular matrix organization, vasculature development regulation, and angiogenesis. We identified five possible biomarkers, Ecm1, Sparc, Sphk1, Thbsl, and Mecp2, which correlate with vascular development and angiogenesis characteristic of hypertension by bioinformatics, and explored the clinical expression levels of these genes by RT-qPCR, and found that Sparc, Sphk1, and Thbs1 showed significant up-regulation, in agreement with the results of the bioinformatics analysis. Conclusion: Our study suggested that Sparc, Sphk1 and Thbs1 may be potential novel biomarkers for the diagnosis, treatment and prognosis of hypertension and that they are involved in the regulation of vascular development and angiogenesis in hypertension.

Ezrin对小鼠卵母细胞成熟及早期胚胎发育的影响

旨在探究Ezrin对小鼠卵母细胞成熟、受精及早期胚胎发育的影响,揭示其可能作用机制。分别向小鼠GV期卵母细胞和原核期胚胎注射Ezrin的siRNA(si-Ez)或阴性对照siRNA(si-NC),观察对小鼠卵母细胞成熟、受精和早期胚胎发育的影响,并分别通过扫描电镜和免疫荧光染色的方法观察GV期注射si-Ez对小鼠成熟卵母细胞表面微绒毛生长、纺锤体定位和皮质颗粒迁移的影响。结果显示,GV期敲低Ezrin可显著降低小鼠卵母细胞成熟率,极显著降低受精后早期胚胎的囊胚率,虽可降低成熟卵母细胞的受精率,但差异不显著;在原核期敲低Ezrin,可极显著降低小鼠囊胚细胞数,桑椹胚存活率和囊胚率虽有下降趋势,但与对照组无显著差异;扫描电镜观察发现,敲低小鼠GV期卵母细胞Ezrin后显著降低了MⅡ期卵母细胞表面微绒毛的长度和密度;免疫荧光结果显示,敲低小鼠GV期卵母细胞Ezrin影响了纺锤体和皮质颗粒的迁移。结果表明,Ezrin通过影响微绒毛形成、纺锤体定位和皮质颗粒的正常迁移阻滞了小鼠卵母细胞成熟,进而影响了受精和早期胚胎发育。

Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton(Gossypium hirsutum L.)

Root system architecture plays an essential role in water and nutrient acquisition in plants,and it is significantly involved in plant adaptations to various environmental stresses.In this study,a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage,including main root length(MRL),root fresh weight(RFW),total root length(TRL),root surface area(RSA),root volume(RV),and root average diameter(AvgD).The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA,as well as RV with RSA and AvgD,whereas a significant negative correlation was found between TRL and AvgD.Subsequently,a genome-wide association study(GWAS)was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms(SNPs)from the CottonSNP80K array.A total of 41 quantitative trait loci(QTLs)were identified,including nine for MRL,six for RFW,nine for TRL,12 for RSA,12 for RV and two for AvgD.Among them,eight QTLs were repeatedly detected in two or more traits.Integrating these results with a transcriptome analysis,we identified 17 candidate genes with high transcript values of transcripts per million(TPM)≥30 in the roots.Furthermore,we functionally verified the candidate gene GH_D05G2106,which encodes a WPP domain protein 2in root development.A virus-induced gene silencing(VIGS)assay showed that knocking down GH_D05G2106significantly inhibited root development in cotton,indicating its positive role in root system architecture formation.Collectively,these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.

雷公藤红素通过调控Ezrin的活化改善特应性皮炎

目的探究雷公藤红素(Celastrol)对DNCB致敏诱导特应性皮炎(atopic dermatitis,AD)小鼠组织及HaCaT细胞中Ezrin表达的影响。方法取BALB/c小鼠,随机分为Control、DNCB组、Celastrol 25μg、50μg、75μg治疗组、Dex组,每组8只;HaCaT细胞用TNF-α诱导,并用1μmol·L^(-1)Celastrol及Ezrin siRNA治疗。测厚仪测量小鼠耳部及背部皮肤厚度,取小鼠脾及淋巴结观察其变化。采用HE及甲苯胺蓝染色法观察小鼠炎症细胞浸润及肥大细胞脱颗粒情况。利用流式细胞仪检测小鼠淋巴结中IL-4及TNF-α水平,酶联免疫吸附剂测定小鼠血清中IL-4、TNF-α、IgE水平,HaCaT细胞上清液中IL-4、IL-5及IL-13的表达。Western blot检测皮肤组织P-Ezrin、Ezrin的表达。结果Celastrol明显抑制小鼠耳部及背部皮肤组织肿胀程度,减轻炎症细胞浸润及肥大细胞脱颗粒情况,降低小鼠血清中IgE及血清、淋巴结中IL-4、TNF-α含量并减少的Ezrin活化。Ezrin siRNA治疗后,HaCaT细胞上清液中IL-4、IL-5及IL-13的表达得到恢复。结论Celastrol可能是通过调节Ezrin的活化实现可改善AD。

壶腹癌组织中HHLA2、Ezrin、Bcl-2的表达特点

目的探讨壶腹癌组织中人内源性逆转录病毒H长末端重复缔合蛋白2抗体(HHLA2)、埃滋蛋白(Ezrin)、人B细胞淋巴瘤因子2(Bcl-2)的表达特点。方法选取壶腹癌患者52例。从胰十二指肠切除术后的标本中取适量的壶腹癌组织和距离肿瘤病灶约2 cm处的癌旁组织,免疫组化法检测组织标本中HHLA2、Ezrin、Bcl-2表达情况。收集患者的人口学特征及肿瘤分化程度、肿瘤大小、肿瘤病理分期、淋巴结转移、十二指肠浸润、胰腺浸润;出院后对患者进行3 a随访,记录生存情况。结果壶腹癌组织中HHLA2、Ezrin、Bcl-2蛋白表达阳性率明显高于癌旁组织(P<0.01)。HHLA2阳性率在不同分化程度、肿瘤病理分期、淋巴结转移、十二指肠浸润、胰腺浸润情况的壶腹癌患者中比较差异具有统计学意义(P<0.05);HHLA2阳性率在不同性别、年龄、肿瘤大小的壶腹癌患者中比较差异无统计学意义(P>0.05)。Ezrin、Bcl-2阳性率在不同淋巴结转移、十二指肠浸润、胰腺浸润的壶腹癌患者中比较差异具有统计学意义(P<0.01);Ezrin、Bcl-2阳性率在不同性别、年龄、分化程度、肿瘤大小、肿瘤病理分期的壶腹癌患者中比较差异无统计学意义(P>0.05)。52例壶腹癌患者3 a生存率为71.15%(37/52)。HHLA2、Ezrin、Bcl-2阳性的壶腹癌患者3 a生存率明显低于HHLA2、Ezrin、Bcl-2阴性的胃癌患者(log-rank χ^(2)分别为13.528、16.705、12.911,均P<0.01)。ROC曲线分析显示,HHLA2、Ezrin、Bcl-2在预测壶腹癌患者生存情况中具有较高的应用价值(P<0.05),其中,各指标联合检测对壶腹癌患者生存情况的预测价值最高(AUC=0.950,95%CI:0.895~0.983,P<0.001)。结论壶腹癌组织中HHLA2、Ezrin、Bcl-2高表达,且与病理参数和生存情况相关,联合检测对患者生存情况具有较高的预测价值。

Fate and Behavior of Tetracycline Resistance Genes in Activated Carbon Adsorption

The accessibility of tetracycline resistance gene (tetG) into the pores of activated carbon (AC), as well as the impact of the pore size distribution (PSD) of AC on the uptake capacity of tetG, were investigated using eight types of AC (four coal-based and four wood-based). AC showed the capability to admit tetG and the average reduction of tetG for coal-based and wood-based ACs at the AC dose of 1 g·L-1 was 3.12 log and 3.65 log, respectively. The uptake kinetic analysis showed that the uptake of the gene followed the pseudo-second-order kinetics reaction, and the uptake rate constant for the coal-based and wood-based ACs was in the range of 5.97 × 10-12 - 4.64 × 10-9 and 7.02 × 10-11 - 1.59 × 10-8 copies·mg-1·min-1, respectively. The uptake capacity analysis by fitting the obtained experiment data with the Freundlich isotherm model indicated that the uptake constant (KF) values were 1.71 × 103 - 8.00 × 109 (copies·g-1)1-1/n for coal-based ACs and 7.00 × 108 - 3.00 × 1010 (copies·g-1)1-1/n for wood-based ones. In addition, the correlation analysis between KF values and pore volume as well as pore surface at different pore size regions of ACs showed that relatively higher positive correlation was found for pores of 50 - 100 Å, suggesting ACs with more pores in this size region can uptake more tetG. The findings of this study are valuable as reference for optimizing the adsorption process regarding antibiotic resistance-related concerns in drinking water treatment.

The Application of Nicotiana benthamiana as a Transient Expression Host to Clone the Coding Sequences of Plant Genes

Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes.

Dissemination of Resistance Integrons and Genes Coding for Blse and Cabapenemases in the Urban Drainage Network in Cote d’Ivoire

Antibiotic resistance has become a major threat to human health worldwide. Environment, particularly the water environment, has long been overlooked as a player in the antibiotic resistance cycle, although its role remains unclear. These can provide an ideal setting for the acquisition and dissemination of antibiotic resistance, as they are frequently affected by anthropogenic activities. The objective of this study was to establish a diffusion map of resistance integrons used as genetic markers of resistance associated with antibiotic resistance conferring genes (ARGs). Total DNA extracts from non-cultivable bacterial communities were used for the analyses. These communities were obtained from wastewater samples from 14 sites upstream and downstream of drainage channels or effluents in the cities of Abidjan, Bouaké, and Yamoussoukro. The results obtained correspond to the number of positives among the treated samples (n = 39). Among the genetic markers of dissemination, class 1 integrons were the most evident in 94.8% of samples in Abidjan (93.3%), Bouaké (100%) and Yamoussoukro (91.6%). Class 2 integrons and class 3 integrons were found respectively in 41% and 51% of all samples. Genes coding for β-lactamases and blaTEM was identified in almost all samples at a rate of 97.4%. A co-presence of the three genes blaTEM, blaSHV and blaCTX-M is also remarkable in the sites of the city of Yamoussoukro. Among the genes coding for carbapenemases, only blaKPC 17.94%, blaNDM 30.76% and blaOXA48 38.46% were detected in the samples.

J-family genes redundantly regulate flowering time and increase yield in soybean

Soybean(Glycine max)is a short-day crop whose flowering time is regulated by photoperiod.The longjuvenile trait extends its vegetative phase and increases yield under short-day conditions.Natural variation in J,the major locus controlling this trait,modulates flowering time.We report that the three J-family genes influence soybean flowering time,with the triple mutant Guangzhou Mammoth-2 flowering late under short days by inhibiting transcription of E1-family genes.J-family genes offer promising allelic combinations for breeding.

胃癌患者组织中XPNPEP2、EZRIN的表达及意义

目的通过对胃癌及癌旁正常组织氨肽酶P2(XPNPEP2)、埃兹蛋白(EZRIN)的表达情况,探讨二者在胃癌发生、发展时的表达情况及临床意义。方法选取2020年2月至2022年12月于枣庄市立医院胃肠外科就诊的患者,就诊前无任何治疗措施,经组织病理诊断胃癌组96例及正常对照组64例。应用免疫组织化学方法检测胃癌及癌旁正常组织中的XPNPEP2和EZRIN的表达水平。结合临床资料分析其表达情况与患者年龄、性别、肿瘤大小、TNM分期、浸润转移情况的关系。结果病例组XPNPEP2、EZRIN阳性表达率分别为67.71%、63.54%,均高于对照组的26.56%、29.69%,差异有统计学意义(P<0.05);在不同TNM分期、是否发生浸润转移的患者中XPNPEP2阳性表达率组间比较,差异有统计学意义(P<0.05);XPNPEP2、EZRIN阳性表达率与患者年龄、性别、肿瘤大小无关,差异无统计学意义(P>0.05)。结论胃癌组织中XPNPEP2、EZRIN蛋表达水平升高,二者高表达与胃癌TNM分期、肿瘤浸润转移显著相关,在胃癌发生、侵袭、转移过程中发挥了重要作用,可能提示预后不良。

Functional investigation and two-sample Mendelian randomization study of primary biliary cholangitis hub genes

BACKGROUND The identification of specific gene expression patterns is crucial for understanding the mechanisms underlying primary biliary cholangitis(PBC)and finding relevant biomarkers for diagnosis and therapeutic evaluation.AIM To determine PBC-associated hub genes and assess their clinical utility for disease prediction.METHODS PBC expression data were obtained from the Gene Expression Omnibus database.Overlapping genes from differential expression analysis and weighted gene coexpression network analysis(WGCNA)were identified as key genes for PBC.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses were performed to explore the potential roles of key genes.Hub genes were identified in protein-protein interaction(PPI)networks using the Degree algorithm in Cytoscape software.The relationship between hub genes and immune cells was investigated.Finally,a Mendelian randomization study was conducted to determine the causal effects of hub genes on PBC.RESULTS We identified 71 overlapping key genes using differential expression analysis and WGCNA.These genes were primarily enriched in pathways related to cytokinecytokine receptor interaction,and Th1,Th2,and Th17 cell differentiation.We utilized Cytoscape software and identified five hub genes(CD247,IL10,CCL5,CCL3,and STAT3)in PPI networks.These hub genes showed a strong correlation with immune cell infiltration in PBC.However,inverse variance weighting analysis did not indicate the causal effects of hub genes on PBC risk.CONCLUSION Hub genes can potentially serve as valuable biomarkers for PBC prediction and treatment,thereby offering significant clinical utility.

Direct somatic embryogenesis and related gene expression networks in leaf explants of Hippeastrum ‘Bangkok Rose’

Hippeastrum, a highly diverse genus in the Amaryllidaceae family, is a valuable ornamental bulbous flowering plant. Somatic embryogenesis(SE) is an efficient method for mass production of Hippeastrum plantlets. Previous studies have been devoted to the in vitro propagation of Hippeastrum, but the SE and its regulatory networks are rarely reported. In this study, we established a direct SE method of Hippeastrum Bangkok Rose' using leaf bases as explants. MS supplemented with 1.00 mg·L^(-1)NAA +1.00 mg·L^(-1)KT + 0.25 mg·L^(-1)TDZ was the optimal medium for SE. Histological observations showed that the bipolar somatic embryo originated from the epidermal cell layer and underwent initiation,globular, scutellar and coleoptile stages. During SE, endogenous hormones of IAA, CTK, ABA, and SA were highly accumulated. Transcriptomic analysis revealed the genes encoding auxin biosynthesis/metabolic enzymes and efflux carriers were induced, while the auxin receptor of TIR1 and ARF transcriptional repressor of Aux/IAA were down-regulated and up-regulated, respectively, leading to suppression of auxin signaling. In contrast, cytokine signaling was promoted at the early stage of SE, as biosynthesis, transport, and signaling components were up-regulated.Various stress-related genes were up-regulated at the early or late stages of SE. Chromatin remodeling could also be dynamically regulated via distinct expression enzymes that control histone methylation and acetylation during SE. Moreover, key SE regulators, including WOXs and SERKs were highly expressed along with SE. Overall, the present study provides insights into the SE regulatory mechanisms of the Hippeastrum.

Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs

Monitoring the prevalence of antimicrobial resistance genes(ARGs)is vital for addressing the global crisis of antibiotic-resistant bacterial infections.Despite its importance,the characterization of ARGs and microbiome structures,as well as the identification of indicators for routine ARG monitoring in pig farms,are still lacking,particularly concerning variations in antimicrobial exposure in different countries or regions.Here,metagenomics and random forest machine learning were used to elucidate the ARG profiles,microbiome structures,and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe.Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs(P<0.05).ANT(6)-Ib,APH(3')-IIIa,and tet(40)were identified as shared core ARGs between the two pig populations.Furthermore,the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions.Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs,respectively.Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100%and 98.7%,respectively.Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy(r=0.72-0.88).Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs.The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.

Identification of Prognosis-Related Genes and Key Target Genes for Pancreatic Cancer: A Bioinformatics Analysis

Objective: The mortality and morbidity rates associated with pancreatic cancer (PaCa) are extremely high. Various studies have demonstrated that pancreatic cancer will be the fourth cancer-related death by 2030, raising more concern for scholars to find effective methods to prevent and treat in order to improve the pancreatic cancer outcome. Using bioinformatic analysis, this study aims to pinpoint key genes that could impact PaCa patients’ prognosis and could be used as therapeutic targets. Methods: The TCGA and GEO datasets were integratively analyzed to identify prognosis-related differentially expressed genes. Next, the STRING database was used to develop PPI networks, and the MCODE and CytoNCA Cytoscape in Cytoscape were used to screen for critical genes. Through CytoNCA, three kinds of topology analysis were considered (degree, betweenness, and eigenvector). Essential genes were confirmed as potential target treatment through Go function and pathways enrichment analysis, a developed predictive risk model based on multivariate analysis, and the establishment of nomograms using the clinical information. Results: Overall, the GSE183795 and TCGA datasets associated 1311 and 2244 genes with pancreatic cancer prognosis, respectively. We identified 132 genes that were present in both datasets. The PPI network analysis using, the centrality analysis approach with the CytoNCA plug-in, showed that CDK2, PLK1, CCNB1, and TOP2A ranked in the top 5% across all three metrics. The independent analysis of a risk model revealed that the four key genes had a Hazard Ratio (HR) > 1. The monogram showed the predictive risk model and individual patient survival predictions were accurate. The results indicate that the effect of the selected vital genes was significant and that they could be used as biomarkers to predict a patient’s outcome and as possible target therapy in patients with pancreatic cancer. GO function and pathway analysis demonstrated that crucial genes might affect the P53 signaling pathway and FoxO signaling pathway, through which Meiotic nuclear division and cell cycle may have a significant function in essential genes affecting the outcome of patients who have pancreatic cancer. Conclusions: This study suggests that CDK2, CCNB1, PLK1 and TOP2A are four key genes that have a significant influence on PaCa migration and proliferation. CDK2, CCNB1, PLK1, and TOP2A can be used as potential PaCa prognostic biomarkers and therapeutic targets. However, experimental validation is necessary to confirm these predictions. Our study comes into contributions to the development of personalized target therapy for pancreatic cancer patients.