KEGG Enrichment Analysis Research Articles

Modulation of metabolic pathways and EndMT inhibition by a traditional Chinese herbal formula in the treatment of high-risk infections

BackgroundHerbal products have long been utilized as remedies for various disease conditions, including infections. This study investigates the therapeutic mechanism of a traditional Chinese herbal combination in treating high-risk HPV infections.MethodsThe herbal formula was prepared using common herbs: dry Millettia speciosa, Guanzhong (a spermatophyte), Sarsaparilla, White Fruit, and Cockscomb Flower. Eight female patients diagnosed with high-risk HPV were enrolled from January to September 2023 at Shenzhen Hospital of Beijing University of Traditional Chinese Medicine. Cervicovaginal secretions were collected before and after treatment with the herbal remedy and analyzed using non-targeted metabolomics techniques. In vitro studies were conducted using HeLa cells to determine the optimal effective concentration of the remedy, assessed via the CCK8 method. The proliferation and migration of HeLa cells were evaluated using Transwell assays. Quantitative PCR was employed to measure mRNA levels of endothelial-to-mesenchymal transition (EndMT) markers, including VE-Cadherin, eNOS, α-SMA, and Snail.ResultsIn vivo, significant alterations in cervicovaginal secretion metabolites post-treatment were observed through PCA, OPLS-DA, and volcano plot analyses. KEGG enrichment analysis highlighted crucial signaling pathways such as arginine and proline metabolism, purine metabolism, glycerophospholipid metabolism, and phenylalanine metabolism, indicating the herbal combination’s systemic effects on patients. In vitro experiments demonstrated a dose-dependent reduction in HeLa cell proliferation and migration, confirmed by scratch and Transwell assays. Additionally, qPCR analysis revealed down-regulation of α-SMA and Snail, and up-regulation of VE-Cadherin and eNOS, suggesting inhibition of EndMT in HeLa cells.ConclusionThe traditional Chinese herbal combination modulates key metabolic pathways in vivo and inhibits EndMT in vitro, while reducing HeLa cell proliferation and migration. These findings highlight its potential as a therapeutic approach for managing HPV infections, bridging traditional practices with scientific research.

Astragalus polysaccharide ameliorates diabetic retinopathy by inhibiting the SHH-Gli1-AQP1 signaling pathway in streptozotocin-induced type 2 diabetic rats.

This study aims to investigate the effects of astragalus polysaccharide (APS) on diabetic retinopathy through the SHH-Gli1-AQP1 pathway. The anti-type 2 diabetes mellitus (T2DM) targets of APS were identified through comprehensive searches of drug and disease-related databases. A protein-protein interaction network was then constructed, followed by GO and KEGG enrichment analyses. Molecular docking simulations were performed to evaluate the interactions of APS and metformin with Gli1 and AQP1. An in vivo T2DM rat model was established via streptozotocin (STZ) injection and treated with metformin and varying doses of APS for 12 weeks. Histological changes in retinal cells were assessed using H&E and PAS staining. The expression levels of AQP1, Gli1, and SHH in the retina were measured using immunohistochemistry, Western blotting, immunofluorescence, and ELISA. Additionally, mRNA expression of AQP1, Gli1, and SHH was quantified by RT-qPCR. Bioinformatic analyses indicated that Gli1 and AQP1, key components of the SHH-Gli1- AQP1 signaling pathway, may be associated with T2DM. Subsequent experiments demonstrated that the STZ-induced T2DM rats exhibited significant retinal damage, which was notably mitigated by both APS and metformin treatments. Furthermore, the SHH-Gli1-AQP1 signaling pathway was found to be overactivated in STZ-induced T2DM rats. Treatment with APS and metformin significantly reduced the elevated expression levels of SHH, Gli1, and AQP1. APS effectively inhibits retinal damage of STZ-induced T2DM rats by restraining the SHH-Gli1-AQP1 signaling pathway.

Single-cell transcriptomic analysis reveals the developmental trajectory and transcriptional regulatory networks of quinoa salt bladders.

Salt bladders, specialized structures on the surface of quinoa leaves, secrete Na+ to mitigate the effects of the plant from abiotic stresses, particularly salt exposure. Understanding the development of these structures is crucial for elucidating quinoa's salt tolerance mechanisms. In this study, we employed transmission electron microscopy to detail cellular differentiation across the developmental stages of quinoa salt bladders. To further explore the developmental trajectory and underlying molecular mechanisms, we conducted single-cell RNA sequencing on quinoa protoplasts derived from young leaves. This allowed us to construct a cellular atlas, identifying 13 distinct cell clusters. Through pseudotime analysis, we mapped the developmental pathways of salt bladders and identified regulatory factors involved in cell fate decisions. GO and KEGG enrichment analyses, as well as experimental results, revealed the impacts of salt stress and the deprivation of sulfur and nitrogen on the development of quinoa salt bladders. Analysis of the transcription factor interaction network in pre-stalk cells (pre-SC), stalk cells (SC), and epidermal bladder cells (EBCs) indicated that TCP5, YAB5, NAC078, SCL8, GT-3B, and T1P17.40 play crucial roles in EBC development. Based on our findings, we developed an informative model elucidating salt bladder formation. This study provides a vital resource for mapping quinoa leaf cells and contributes to our understanding of its salt tolerance mechanisms.

Elucidating common biomarkers and pathways of osteoporosis and aortic valve calcification: insights into new therapeutic targets.

Osteoporosis and aortic valve calcification, prevalent in the elderly, have unclear common mechanisms. This study aims to uncover them through bioinformatics analysis. Microarray data from GEO was analyzed for osteoporosis and aortic valve calcification. Differential expression analysis identified co-expressed genes. SVM-RFE and random forest selected key genes. GO and KEGG enrichment analyses were performed. Immunoinfiltration and GSEA analyses were subsequently performed. NetworkAnalyst analyzed microRNAs/TFs. HERB predicted drugs, and molecular docking assessed targeting potential. Thirteen genes linked to osteoporosis and aortic valve calcification were identified. TNFSF11, KYNU, and HLA-DMB emerged as key genes. miRNAs, TFs, and drug predictions offered therapeutic insights. Molecular docking suggested 17-beta-estradiol and vitamin D3 as potential treatments. The study clarifies shared mechanisms of osteoporosis and aortic valve calcification, identifies biomarkers, and highlights TNFSF11, KYNU, and HLA-DMB. It also suggests 17-beta-estradiol and vitamin D3 as potential effective treatments.

Ectopic expression of a truncated NLR gene from wild Arachis enhances resistance to Fusarium oxysporum

Fusarium oxysporum causes devastating vascular wilt diseases in numerous crop species, resulting in substantial yield losses. The Arabidopsis thaliana-F. oxysporum f.sp. conglutinans (FOC) model system enables the identification of meaningful genotype–phenotype correlations and was applied in this study to evaluate the effects of overexpressing an NLR gene (AsTIR19) from Arachis stenosperma against pathogen infection. AsTIR19 overexpression (OE) lines exhibited enhanced resistance to FOC without any discernible phenotype penalties. To elucidate the underlying resistance mechanisms mediated by AsTIR19 overexpression, we conducted whole transcriptome sequencing of an AsTIR19-OE line and non-transgenic wild-type (WT) plants inoculated and non-inoculated with FOC using Illumina HiSeq4000. Comparative analysis revealed 778 differentially expressed genes (DEGs) attributed to transgene overexpression, while fungal inoculation induced 434 DEGs in the OE line, with many falling into defense-related Gene Ontology (GO) categories. GO and KEGG enrichment analysis showed that DEGs were enriched in the phenylpropanoid and flavonoid pathways in the OE plants. This comprehensive transcriptomic analysis underscores how AsTIR19 overexpression reprograms transcriptional networks, modulating the expression of stress-responsive genes across diverse metabolic pathways. These findings provide valuable insights into the molecular mechanisms underlying the role of this NLR gene under stress conditions, highlighting its potential to enhance resistance to Fusarium oxysporum.

Origin tracking of Brucella strain B. melitensis bv.3 ARQ-070 using biochemical and genomic studies.

To conduct an origin tracking and genomic study of the Brucella strain B. melitensis bv.3 ARQ-070, with the aim of addressing the challenges posed by the highly conserved genome of Brucella to conventional typing methods and to gain an understanding of the geographic distribution and interspecies transmission of this pathogen in China. Differentiation and genotyping were established via biochemical profiles and polymerase chain reaction (AMOS-PCR). Illumina MiSeq® was applied to sequence the Brucella isolates. Using multilocus sequence typing (MLST) multilocus sequence typing and Fisher's exact test was used for the KEGG enrichment analysis of differential genes. Differential gene protein PPI network analysis was conducted using the STRING database and visualisation was performed using. According to the final identification results of an A/M serum agglutination test. ARQ-070 was identified as the No. 3 white spirulina biological variety, and mM was identified as the No. 1 white Spirulina biological variety. The genetic information of this strain is very close to that of the M5 vaccine strain, suggesting possible vaccine-escape infection. In the comparative genomics analysis with B. melitensis bv.1 16M, the main differences between the B. melitensis strains were found to be concentrated in the genes related to amino acid metabolism and environmental perception. A base mutation was found in the Brucella gene virB9, which is associated with the key virulence factor of the type IV secretion system (T4SS), but this mutation did not lead to changes in the protein's tertiary structure, and the strain did not lose its infectivity. The study discovered a base mutation in the virB9 gene of Brucella, which is linked to T4SS but does not affect the protein's structure or the strain's infectivity. This mutation could influence public health approaches to detecting and preventing Brucella transmission. Future research aims to analyse a wider range of Brucella strains for a deeper understanding of their epidemiology.

Predictive Analysis of Yi-Gai-San's Multifaceted Mechanisms for Tremor-dominant Parkinson's Disease via Network Pharmacology and Molecular Docking Validation.

Based on comprehensive network-pharmacology and molecular docking analysis, this study was intended to unveil the multiple mechanisms of Yi- Gai-San (YGS) in treating the tremor-dominant subtype of Parkinson's disease (PD-DT). The compounds of YGS were meticulously analyzed, selected, and standardized with references to their pharmacological attributes. Its components included Gouteng (Uncaria rhynchophylla), Chaihu (Radix Bupleuri), Chuanxiong (Chuanxiong Rhizoma), Danggui (Angelicae sinensis radix), Fuling (Wolfiporia extensa), Baizhu (Atractylodis macrocephalae rhizoma), and Gancao (Licorice, Glycyrrhizae radix). We identified 75 active compounds within YGS. From these, we predicted 110 gene targets, which exhibited a direct association with PD-DT. PPI network results highlighted core target proteins, including TP53, SLC6A3, GAPDH, MAOB, AKT, BAX, IL6, BCL2, PKA, and CASP3. These proteins potentially alleviate PD-DT by targeting inflammation, modulating neuronal cell apoptosis, and regulating the dopamine system. Furthermore, GO and KEGG enrichment analyses emphasized that YGS might influence various mechanisms, such as the apoptotic process, mitochondrial autophagy, Age-Rage signaling, and dopaminergic and serotonergic synapses. The core proteins from the PPI analysis were selected for the docking experiment. The docking results demonstrated that the most stable ligand-receptor conformations were kaempferol with CASP3 (-9.5 kcal/mol), stigmasterol with SLC6A3 (-10.5 kcal/mol), shinpterocarpin with BCL2L1 (-9.6 kcal/mol), hirsutine with MAOB (-9.7 kcal/mol), hederagenin with PRKACA (-9.8 kcal/mol), and yatein with GAPDH (-9.8 kcal/mol). These results provide us with research objectives for future endeavors in extracting single compounds for drug manufacturing or in-depth studies on drug mechanisms. From these computational findings, we suggested that YGS might mitigate PD-DT via "multi-compounds, multi-targets, and multi-pathways."

Molecular mechanisms underlying floral fragrance in Camellia japonica ‘High Fragrance’: a time-course assessment

Camellia japonica ‘High Fragrance’ is a camellia hybrid known for its unique and intense floral scent. The current understanding of the dynamic changes in its fragrance and the underlying mechanisms are still limited. This study employed a combination of metabolomic and transcriptomic approaches to reveal the characteristics of the metabolites involved in the remarkable fragrance of this camellia and their biosynthetic mechanisms along three flower developmental stages (flower bud, initial bloom, and full bloom). Among the 349 detected volatile organic compounds (VOCs), the majority were terpenes (57, 16.33%) and esters (53, 15.19%). Of these, 136 VOCs exhibited differential accumulation over time. Transcriptomic data from floral organs at different flowering stages identified 56,303 genes, with 13,793 showing significant differential expression. KEGG enrichment analysis revealed 57, 91, and 33 candidate differential genes related to the biosynthesis of terpenes, phenylpropanoids, and fatty acid derivatives, respectively. This indicates that terpenes, esters, and their related synthetic genes might play a crucial role in the formation of ‘High Fragrance’ characteristics. During the entire flowering process, the majority of genes exhibited an elevated expression pattern, which correlated with the progressive accumulation of VOCs. Interestingly, the expression patterns of the differentially expressed genes in the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, associated with terpene synthesis, showed opposite trends. A transcriptional-metabolic regulatory network linking terpenoid compounds, related synthetic enzymes, and potential transcription factors could be outlined for ‘High Fragrance’ camellia, thus providing a theoretical basis for further exploring these events and breeding more fragrant camellias.

Bioinformatics analysis and identification of underlying biomarkers potentially linking allergic rhinitis and autophagy.

Allergic rhinitis (AR) resulted in impairing human health and quality of life seriously. There is currently no definitive remedy for AR. Recent studies have shown that autophagy may regulate airway inflammation. Our comprehension of autophagy and its molecular mechanism in the field of AR condition remains incomplete. Our research endeavors to bridge this knowledge deficit by investigating the correlation between AR and autophagy. The AR-related gene expression profile GSE50223 was screened and downloaded. The "limma" package of R software was utilized to identify differentially expressed genes associated with autophagy. GO, KEGG, and Gene set enrichment analyses were conducted. A PPI network of differentially expressed autophagy-related genes were established and further identified through the CytoHubba algorithm. A receiver operating characteristic curve analysis was employed to evaluate the diagnostic effectiveness of the hub genes and to examine the relationship between autophagy-related genes and AR. Finally, qRT-PCR was carried out to confirm the chosen autophagy-related genes using clinical samples. 21 autophagy-related genes in allergic rhinitis were identified. BECN1, PIK3C3, GABARAPL2, ULK2, and UVRAG were considered as significant differentially expressed autophagy-related genes. However, additional molecular biological experiments will be necessary to elucidate the underlying mechanism connecting autophagy and AR.

Effects of L-arginine on gut microbiota and muscle metabolism in fattening pigs based on omics analysis

IntroductionL-arginine is an α-amino acid and a semi-essential nutrient of significant biological interest. It plays a role in influencing various aspects of animal meat traits, gut microbiota composition, and physiological metabolism.MethodsThis study aimed to investigate the combined effects of L-arginine supplementation on gut microbiota composition and the metabolism of the longissimus dorsi muscle in fattening pigs. Eighteen Yorkshire commercial pigs were divided into two groups: a control group that received no supplements and a treatment group that was given 1% L-arginine for 52 days. The diversity and composition of microorganisms in the feces of the control (NC) and L-arginine (Arg) groups were analyzed by sequencing the 16S rRNA V3 -V4 region of the bacterial genome.ResultsThe findings indicated that L-arginine supplementation increased both the abundance and diversity of gut microbiota, particularly affecting the Firmicutes and Bacteroidetes phyla. KEGG enrichment analysis revealed significant changes in several metabolism-related pathways, including amino acid, carbohydrate, and lipid metabolism. Metabolomic analysis identified 85 differential metabolites between the arginine and control groups, with phospholipids ranking among the top 20. Additionally, functional predictions indicated an increased abundance in the glycerophospholipid metabolism pathway. Correlation analysis linked changes in gut microbiota to phospholipid levels, which subsequently influenced post-slaughter meat color and drip loss.DiscussionThese results suggest that L-arginine supplementation positively impacts gut microbiota composition and the metabolic profile of the longissimus dorsi muscle in fattening pigs, with potential implications for meat quality.

Emergence of hypervirulent and carbapenem-resistant Klebsiella pneumoniae from 2014 - 2021 in Central and Eastern China: a molecular, biological, and epidemiological study.

In recent years, the hypervirulent and carbapenem-resistant Klebsiella pneumoniae has been increasingly reported worldwide. The objective of this study was to compare the antibiotic resistance and virulence profiles of carbapenem-resistant hypervirulent K.pneumoniae (CR-hvKP) and hypervirulent carbapenem-resistant K.pneumoniae (hv-CRKP) and identify the prevailing strain in clinical settings. In this study, hv-CRKP or CR-hvKP were identified based on the results of whole-genome analysis (WGS), multilocus sequence typing (MLST) and the antimicrobial susceptibility testing. We then compared antibiotic resistance and virulence profiles between CR-hvKP and hv-CRKP through the antimicrobial susceptibility testing and a series of virulence experiments including biofilm formation ability detection method, the resistance test against human serum, siderophore production test, neutrophil phagocytosis assay and Galleria mellonella infection model. Additionally, pathway enrichment analysis was conducted to assess the effect of SNPs on the phenotype. In this study, we categorized 17.4% of hypervirulent and carbapenem-resistant K. pneumoniae strains as CR-hvKP and 82.6% as hv-CRKP. Among them, 84.2% (16/19) of CR-hvKP strains harboring carbapenemase genes exhibited lower imipenem and meropenem MIC values compared to hv-CRKP strains. The virulence potential of hv-CRKP and CR-hvKP was confirmed by using virulence experiments in vitro and in vivo, showing that virulence of the CR-hvKP strains was comparable to that of hv-CRKP strains. Notably, the 90 hv-CRKP strains were classified into 3 different ST types and 8 capsule types, each showing varying degrees of resistance and virulence. We observed that subclonal replacement was within the predominant hv-CRKP clone, with the ST11-KL64 strain, characterized by high-level resistance and virulence emerging as the currently prevailing subclone, replacing ST11-KL47. KEGG enrichment analysis showed that pathways associated with the citrate cycle (TCA cycle), glycolysis/gluconeogenesis, glutathione metabolism, two-component regulatory system, and folate metabolism were significantly enriched among the group expressing different levels of capsular polysaccharides. The hv-CRKP strains exhibited a greater survival advantage in the hospital environment than CR-hvKP strains. Notably, the ST11-KL64 hv-CRKP strain which displayed a high level of resistance and hypervirulence, warrants the most clinical vigilance. Not applicable.

Network Pharmacology and Molecular Dynamics Simulations Reveal the Mechanism of Total Alkaloid Components in Anisodus Tanguticus (Maxim.) Pascher in Treating Inflammation and Pain.

This study aimed to elucidate the mechanism that total alkaloids in Anisodus tanguticus (AT)(Maxim.) Pascher played anti-inflammatory and analgesic effects. In this paper, the anti-inflammatory effect in the total alkaloids of AT was confirmed via lipopolysaccharide (LPS)-induced inflammation model in RAW 264.7 cells and the main components of AT were immediately analyzed by UPLC/MS. Disease targets were obtained in GeneCards and DisGeNET. Targets of major compounds were searched in ETCM, TCMSP and other databases. The protein-protein interaction (PPI) network was constructed using STRING database, and Cytoscape was used for core targets screening. GO and KEGG enrichment analysis were performed using Daivid database. Sailvina was used for molecular docking. Molecular dynamics simulation analysis was performed using the Amber 20 program. The results showed that the main components in AT were anisodamine, atropine, fabiatrin, scopolamine, scopoletin and scopolin, possibly exerting anti-inflammatory and analgesic effects through pathways such as EGFR tyrosine kinase inhibitor resistance and IL-17 signaling pathway. Fabiatrin and scopolin could be potential drugs with good anti-inflammatory and analgesic effects.

Molecular Mechanisms of Poplar Adaptation to Water–Fertilizer Coupling: Insights from Transcriptomic and Metabolomic Analyses

The aim of this paper was to investigate the transcriptomic and metabolomic differences in Populus cathayana × canadasis ‘Xinlin1’ (P. cathayana × canadasis ‘Xinlin 1’) under varying irrigation and fertilization conditions. Ten-year-old P. cathayana × canadasis ‘Xinlin 1’ was selected as the test subject in this study; different irrigation and fertilization treatments were set up, and DEGs and DAMs in response to water and fertilizer regulation were identified. Transcriptomic and metabolomic profiles were analyzed from both leaves and roots. A total of 22,870 DEGs were identified in response to water and fertilizer treatments, predominantly belonging to 48 transcription factor families, including MYB, ERF, and MYB-related ones. Additionally, 2432 DAMs were detected and categorized into 18 metabolite classes, with flavonoids being the most abundant (342 metabolites), followed by terpenoids, lipids, and others. KEGG enrichment analysis revealed that DEGs and DAMs were significantly associated with pathways such as plant hormone signal transduction and starch and sucrose metabolism pathways. The levels of ABA exhibited an initial decrease followed by an increase, with several key genes, including PYR/PYL, PP2C, SnRK2, and ABF, also differentially expressed in the plant hormone signal transduction pathway. In the starch and sucrose metabolic pathways, sucrose was more hydrolyzed into D-fructose, which gradually translocated from roots to leaves. DEGs were significantly involved in sucrose synthesis and decomposition into D-fructose and 1,3-β-glucose, as well as starch synthesis and starch decomposition into cellulose dextrin, which underwent complete hydrolysis to glucose. In the starch hydrolysis process, 29 DEGs were involved, with 12 down-regulated and 17 up-regulated.

Histone Lysine Lactylation (Kla)-induced BCAM Promotes OSCC Progression and Cis-Platinum Resistance.

Histone lysine lactylation (Kla) plays a vital role in cancer progression. However, the prognostic value of histone Kla in oral squamous cell carcinoma (OSCC) remains unclear. OSCC RNA expression data were obtained from the TCGA and GEO databases. We explored the prognostic value of histone Kla in OSCC via constructing a Cox model and determined the role of Kla in OSCC drug susceptibility and tumor microenvironment (TME). In addition, the biological roles of candidate biomarkers were identified. A total of 1223 Kla-specific genes were obtained, with 228 DEKlaGs in OSCC. GO and KEGG enrichment analyses suggested that DEKlaGs contributed to inflammatory and cancer progression. A Cox model in accordance with BCAM, CGNL1, DGKG, and OLR1 could predict OSCC patient prognosis accurately. Subsequently, Kla-induced prognostic genes were identified to play a crucial role in OSCC drug therapy and TME. Moreover, BCAM was identified as a biomarker that promoted OSCC invasion, angiogenesis, and chemotherapy resistance. Kla was identified to be associated with OSCC prognosis, drug therapy, and TME. Histone Kla-induced BCAM was identified to play a crucial role during OSCC progression, suggesting that Kla is promising to be a novel therapeutic target for OSCC.

Dietary Influence on Growth, Physicochemical Stability, and Antimicrobial Mechanisms of Antimicrobial Peptides in Black Soldier Fly Larvae

Safe antibiotic substitutes are needed given the rise in antimicrobial resistance, environmental contamination, and stringent antibiotic regulations. Insect-derived antimicrobial peptides (AMPs) are promising candidates due to their antimicrobial activity, stability, and safety. This study investigates the antimicrobial mechanism of crude AMP extracts and their physicochemical characteristics in black soldier fly larvae (BSFL). The results indicated that BSFL reared on a wheat bran diet exhibited significantly improved growth performance and AMP production when compared to the other three diets. AMP extracts showed enhanced antimicrobial activity and physicochemical stability, including temperatures and metal ions except Cu+. Moreover, AMP extracts disrupted the cell membrane and inhibited the cell cycle of Staphylococcus aureus (S. aureus), thus exhibiting antimicrobial activity. Furthermore, transcriptomic and KEGG enrichment analyses identified 509 differentially expressed genes (DEGs) related to the Toll and IMD signaling pathways. STRING and GeneMANIA analyses confirmed the association of these pathways with immune response and AMP secretion. qRT-PCR results showed elevated expression of immune genes (GNBP3, NFKBIA, GADD45, and Spz) in BSFL following S. aureus immunization, consistent with RNA-seq findings. These findings offer a valuable reference for using AMPs as antibiotic substitutes in animal feeds and highlight the need for further research on AMP purification and the synergistic regulation of protein synthesis and AMP production in BSFL.

Transcriptome analysis of mammary epithelial cell between Sewa sheep and East FriEsian sheep from different localities.

Mammary epithelial cells, the only milk-producing cell type in the mammary gland, undergo dynamic proliferation and differentiation during pregnancy, culminating in lactation postpartum. The East FriEsian sheep ranks among the world's most prolific dairy breeds, while the Sewa sheep, a unique dual-purpose breed autochthonous to the Qinghai-Tibet Plateau, exhibits significantly lower milk production. Employing tissue culture methods, we successfully established mammary epithelial cell lines from both breeds. Morphological assessment of mammary epithelial cells and immunofluorescence identification of Cytokeratin 7 and Cytokeratin 8 confirmed the epithelial identity of the isolated cells. Subsequent RNA-seq analysis of these in vitro epithelial cell lines revealed 1813 differentially expressed genes (DEGs). Among these, 1108 were significantly up-regulated and 705 were down-regulated in Sewa epithelial sheep cells compared to East FriEsian epithelial cells. KEGG enrichment analysis identified cellular processes, environmental information processing, human diseases, metabolism, and organismal systems as the primary functional categories associated with DEGs. Gene ontology (GO) terms annotation, categorized into molecular function, biological processes, and cellular component, yielded "binding and catalytic activity," "molecular function regulator activity," and "cellular process," "biological regulation," and "regulation of biological process" as the top three terms within each domain, respectively. Clusters of Orthologous Groups of proteins (KOG) classification further revealed that "signal transduction mechanisms" accounted for the largest proportion of DEGs among all KOG categories. Finally, based on these analyses, ATF3 and MPP7 were identified as promising candidate genes for regulating lactation.

Metabolomic profiling of human feces and plasma from extrauterine growth restriction infants.

Extrauterine growth restriction (EUGR) affects a substantial proportion of preterm infants and may influence both short-term complications and long-term sequelae. While many preterm infants with EUGR are secondary to small for gestational age (SGA) or very low birth weight (VLBW), a subset of EUGR infants do not exhibit these conditions. The purpose of this study is to investigate the metabolic profiles and biomarkers of EUGR infants in the absence of SGA and VLBW. A total of 100 feces (n = 50) and plasma samples (n = 50) were collected from participants categorized as either EUGR (EUGR group) or non-EUGR (NonEUGR group) in the absence of SGA and VLBW. Metabolites were characterized via UPLC-MS/MS using the Discovery HD4® platform. Data normalization, partial least squares discriminant analysis (PLSDA), and KEGG enrichment analysis of metabolite profiles were performed using the MetaboAnalyst 6.0. The clinical characteristics of preterm infants differed significantly between the EUGR and NonEUGR groups at discharge, including length of stay, weight Z-score, weight, height Z-score, height, head circumference, and fat-free mass. The PLSDA model exhibited clustering within groups and separation between groups. A total of 58 and 71 differential metabolites were identified in feces and plasma samples, respectively. They were involved in pathways such as caffeine, galactose, glutathione, cysteine, and methionine metabolisms. In the feces sample, 1-palmitoyl-galactosylglycerol exhibited a significant negative correlation with the growth characteristics of preterm infants, while 1-palmitoyl-2-palmitoleoyl-GPC displayed the opposite pattern. In plasma samples, androsterone glucuronide displayed a significant positive correlation with the growth characteristics of preterm infants, whereas 2-methoxyhydroquinone sulfate generated an opposite pattern. Moreover, 2-oleoylglycerol and sphinganine-1-phosphate exhibited the highest area under the curve in feces and plasma samples, respectively, according to diagnostic ROC curves. Preterm infants with EUGR, in the absence of SGA and VLBW, exhibit specific clinical characteristics and metabolomic profiles. Sphinganine-1-phosphate and 2-oleoylglycerol may hold promise as diagnostic markers for EUGR in the absence of SGA and VLBW. The objective of this study is to identify the differential metabolites in preterm infants with extrauterine growth restriction (EUGR) in the absence of small for gestational age (SGA) or very low birth weight (VLBW). Preterm infants with EUGR without SGA and VLBW exhibit specific clinical characteristics and metabolomic profiles. Sphinganine-1-phosphate and 2-oleoylglycerol emerged as potential diagnostic biomarkers for EUGR. This study enhances our understanding of the metabolomic profile in preterm infants with EUGR without SGA or VLBW. Our findings will offer valuable evidence for improving nutritional management and shedding light on the associated pathophysiological mechanisms of EUGR.

Exosomes derived from platelet-rich plasma present a novel potential in repairing knee articular cartilage defect combined with cyclic peptide-modified β-TCP scaffold

BackgroundThe aim of this study was to investigate the therapeutic effects and mechanisms of PRP-exos combined with cyclic peptide-modified β-TCP scaffold in the treatment of rabbit knee cartilage defect.MethodsPRP-exos were extracted and characterized by TEM, NTA and WB. The therapeutic effects were evaluated by ICRS score, HE staining, Immunohistochemistry, qRT-PCR and ELISA. The repair mechanism of PRP-exos was estimated and predicted by miRNA sequencing analysis and protein–protein interaction network analysis.ResultsThe results showed that PRP-exos had a reasonable size distribution and exhibited typical exosome morphology. The combination of PRP-exos and cyclic peptide-modified β-TCP scaffold improved ICRS score and the expression level of COL-2, RUNX2, and SOX9. Moreover, this combination therapy reduced the level of MMP-3, TNF-α, IL-1β, and IL-6, while increasing the level of TIMP-1. In PRP-exos miRNA sequencing analysis, the total number of known miRNAs aligned across all samples was 252, and a total of 91 differentially expressed miRNAs were detected. The results of KEGG enrichment analysis and the protein–protein interaction network analysis indicated that the PI3K/AKT signaling pathway could impact the function of chondrocytes by regulating key transcription factors to repair cartilage defect.ConclusionPRP-exos combined with cyclic peptide-modified β-TCP scaffold effectively promoted cartilage repair and improved chondrocyte function in rabbit knee cartilage defect. Based on the analysis and prediction of PRP-exos miRNAs sequencing, PI3K/AKT signaling pathway may contribute to the therapeutic effect. These findings provide experimental evidence for the application of PRP-exos in the treatment of cartilage defect.

Transcriptomic responses to transportation stress in the juvenile Chinese sea bass (Lateolabrax maculatus)

Transportation is a necessary aspect of the aquaculture industry that might induce inevitable stress and compromise product quality. In the present study, the transcriptomic profiles in the brain and liver of Chinese sea bass (Lateolabrax maculatus) were characterized after transportation stress at two different densities (low-density: 20 kg/m3 and high-density: 40 kg/m3). Transcriptome analysis revealed that 485 and 627 differentially expressed genes (DEGs) were determined in the brain and liver from sea bass after transportation stress, respectively. KEGG enrichment analysis demonstrated that the DEGs were significantly enriched in focal adhesion, PI3K-Akt, MAPK signaling pathway, apoptosis, and circadian rhythm under transportation stress. Protein-Protein Interaction (PPI) networks showed that COL1A1, COL1A2, COL5A2, COL10A1, and COL16A1 associated with protein digestion and absorption, together with LUM, SERPINH1, and ADAMTS2 were recognized as hub genes in the brain, while JUN, NFKB1, MAPK14, MAP3K7, HSPA1, HSP90AA1, PIK3CA and PIK3R1 tightly related to MAPK and PI3K-Akt signaling pathway and SMAD3 and PPARGC1A were considered as hub genes in the liver. These results indicated that the alterations in transcripts of sea bass are primarily involved in cell adhesion, signal transduction, immune response, and metabolic regulation in response to transportation stress. Our study provides new perspectives into the molecular mechanism underlying responses to transportation and theoretical support for optimizing transportation in the Chinese sea bass.

Transcriptome Profiling of Two Camellia japonica Cultivars with Different Heat Tolerance Reveals Heat Stress Response Mechanisms.

Camellia (Camellia japonica) is a semi-shaded plant that is highly vulnerable to heat stress. To investigate the mechanisms underlying heat stress in C. japonica, two C. japonica cultivars, "Xiaotaohong" and "Zhuapolian", which exhibit significant differences in heat tolerance, were selected from four common cultivars. The selection methods included phenotypic observations and physiological index detection, including relative electric conductivity (REC), malondialdehyde (MDA) content, superoxide dismutase (SOD) enzyme activity, relative water content (RWC), and chlorophyll content. RNA-seq analysis yielded 980 million reads and identified 68,455 differentially expressed genes (DEGs) in the two C. japonica cultivars during heat stress compared to the control samples. Totals of 12,565 and 16,046 DEGs were differentially expressed at 16 h and 32 h, respectively, in "Xiaotaohong" during heat stress. In "Zhuapolian", 40,280 and 37,539 DEGs were found at 16 h and 32 h, respectively. KEGG enrichment analysis revealed that both cultivars were enriched in the "plant hormone signal transduction" and "circadian rhythm" pathways at two stages, indicating the critical role these pathways play in the heat stress response. The differences in the tolerance between the two cultivars are likely linked to pathways such as "plant hormone signal transduction", "photosynthesis", and "circadian rhythm". Some members of heat shock proteins (HSPs) are associated with the heat stress response. It is speculated that transcription factor families contributing to the tolerance differences include AP2/ERF, C3H, bHLH, bZIP, and MYB-related with a small number of heat shock factors (HSFs) also induced by the stress. In conclusion, these results reveal the changes in the physiological indices and molecular networks of two C. japonica cultivars under heat stress. This study lays the foundation for the breeding of superior heat-resistant C. japonica cultivars and for further molecular research.