Gene Expression Levels Research Articles

The Impact of Selenium Deficiency and T-2 Toxin on Zip6 Expression in Kashin-Beck Disease.

This study investigated the expression of Zip6, a gene predominantly located in the placenta, breast, and prostate tissues, in patients with Kashin-Beck disease (KBD). Environmental risk factor models for KBD were developed using low selenium (Se) feeding (with a Se content of 0.02mg Se/kg in the feed) and exposure to T-2 toxin (200ng/g*BW/D). Additionally, the study examined the alterations in Se and Zn2+ levels, along with the mRNA and protein expression levels of Zip6 and KBD related genes, including Mtf1, Mmp3, Mmp13, Adamts5, and Col2a1. Differentially expressed genes (DEGs) were examined by transcriptome sequencing to elucidate the mechanism by which Zip6 induces metabolic disorder of the extracellular matrix (ECM), subsequently leading to cartilage injury under the influence of Se deficiency and T-2 toxin. The findings indicated that the expression levels of Zip6 in adult and pediatric KBD chondrocytes were not synchronized. In the animal study, there was a notable increase in the Zn2+ level in the comprehensive exposure (CE) group. Moreover, in both the T-2 exposure (T-2) and CE groups, there was a significant decrease in the expression of Zip6 in each zone, and the expression of Adamts5 in the middle zone exhibited a significant increase (P < 0.05) correlating with varying degrees of cartilage tissue damage in each group. Sequencing results revealed that the significantly up-regulated DEGs in the CE group included Zimz2. This study suggested that Se and T-2 toxin may influence the expression of Zip6, and it investigated the role of Zn2+ in the pathogenesis of KBD, thereby providing a novel scientific foundation for understanding the pathogenesis of KBD.

Alterations in expression of TLR2 and TLR4 during successful and pathological aging

The generally accepted theory of aging is the theory of inflammaging. The leading role in its development is played by the mechanisms of innate immunity. Key receptors of innate immunity are TLRs. The patterns of age-related changes in the functioning of the TLR system remain the subject of study. The purpose of the work is to study the expression of TLR2 and TLR4 receptors in peripheral blood cells of centenarians and elderly people at the level of genes and surface molecules. The study analyzed the expression of genes and molecules TLR2 and TLR4 in young donors (n = 50), elderly people (n = 50) and centenarians (n = 100). Analysis of TLR2 and TLR4 gene expression was carried out using RT-PCR. Determination of surface expression of TLR2 and TLR4 was carried out using flow cytofluorimetry. This study is the first to analyze the age-related dynamics of expression of genes and molecules TLR2 and TLR4. It was revealed that in groups of elderly patients and long-livers, TLR2 expression is increased both at the gene and on the cell surface, compared to young donors. In contrast, TLR4 expression decreased with age. Studied groups of patients were divided depending on the aging phenotype into two subgroups: successful and pathological aging. In elderly individuals, TLR2 is increased in both phenotypes, while TLR4 is decreased in the pathological aging. In the group of centenarians with a pathological aging, a decrease in both TLR2 and TLR4 is observed, compared with young. In long-livers with successful aging, an increase in TLR2 expression was observed at the gene and protein level and TLR4 expression was comparable to the group of young individuals. Identified changes in the expression of TLR2 and TLR4, observed in different age groups, can be considered as markers of various aging phenotypes.

Investigation of the efficacy of different cryoprotectants in the freezing of testicular tissue and epididymal sperm: Spermatological parameters, tissue viability and PARP-1 gene expression

The presented study covers testicular tissue and epididymal spermatozoa cryopreservation processes in bulls and aims to investigate the effects of these applications on spermatological parameters, cell viability in testicular tissue, and the expression of the PARP-1 gene, a DNA repair enzyme. Testes of 20 bulls over 2 years old, slaughtered in a slaughterhouse, were used in the study. After spermatological evaluations, the semen obtained from the cauda epididymis was frozen in liquid nitrogen vapor according to the straw method and stored in liquid nitrogen (−196 °C). Testicular tissue pieces obtained from the testicles were frozen by the slow freezing method in cryotubes in diluents containing Dimethylsulfoxide (DMSO) and Ethylene Glycol (EG) cryoprotectants and stored in liquid nitrogen (−196 °C). The total motility (TM) (85.89 ± 12.83 %), progressive motility (PM) (54.02 ± 15.77 %), and kinematic parameter values of fresh sperm were significantly higher compared to the TM (57.62 ± 13.13 %), PM (29.60 ± 10.76 %), and kinematic parameter values after thawing (P < 0.05). Significant decreases in plasma membrane integrity (PMI) and viability and an increase in chromatin condensation and morphological disorders in the head, middle part, and tail regions were observed in post-thaw semen samples (P < 0.05). When the effects of DMSO and EG on cell viability after thaw in frozen testicular tissue were evaluated, it was observed that the cell viability values of testicular tissues frozen with EG (45.70 ± 10.00) were statistically significantly lower than those frozen with DMSO (51.20 ± 7.70) (P < 0.05). When the effects of both cryoprotectants on gene expression in tissue and semen samples were examined, it was determined that gene expression increased on average 0.19 ± 0.27 times in the tissue samples in the DMSO group compared to fresh tissue samples and 0.17 ± 0.19 times in the tissue samples in the EG group. It was determined that gene expression levels increased by an average of 1.20 ± 1.08 times in post-thaw epididymal spermatozoa samples compared to fresh semen samples. The results show that cryopreservation can activate cellular repair mechanisms by stimulating PARP-1 gene expression and affect gene expression by activating specific pathways in tissues and cells.

Role of C-C chemokine receptor type 5 in pathogenesis of malaria and its severe forms.

Malaria is a mosquito-borne disease caused by Plasmodium parasites, responsible for a significant impact on public health in several tropical and sub-tropical countries. The majority of infection cases are classified as uncomplicated malaria, causing mild symptoms such as fever and headache. However, the disease may progress to severe malaria and death if the infection is not properly treated. Furthermore, malaria poses a major concern for children, pregnant women and immunosuppressed individuals. Exacerbated inflammation is characteristic of severe malaria cases. The C-C chemokine receptor type 5 (CCR5) is an important molecule for leukocyte migration and regulation of inflammation. Although widely known as an HIV-1 co-receptor, CCR5 also affects the susceptibility and progression of autoimmune and inflammatory diseases. There is evidence supporting the participation of CCR5 in malaria manifestations, with the evaluation of CCR5 gene expression levels suggested as a marker to monitor malaria severity. Certain genetic variants in the CCR5 gene affect CCR5 expression, potentially altering CCR5-mediated inflammatory responses during malaria infection. However, the complex influences of CCR5 on malaria remain underexplored. Therefore, this review examines and updates the role of CCR5 in various contexts of malaria infection, including uncomplicated malaria, Plasmodium/HIV co-infection, pregnancy and severe (cerebral) malaria.

Oregano essential oil and Bacillus subtilis role in enhancing broiler’s growth, stress indicators, intestinal integrity, and gene expression under high stocking density

This study investigates the role of dietary Bacillus subtilis and oregano essential oil in mitigating the effects of high stocking density on growth performance, carcass traits, physiological stress indicators, gene expression, and intestinal integrity in broiler chickens. A total of, 1250 one-day-old Ross 308 male broiler chicks were randomly allocated to five experimental groups, where each group had five replicates of 50 chicks. Group 1 (control, LSD): 15 chicks/m2 fed a basal diet without feed additive, group 2 (HSD): 20 chicks/m2 fed a basal diet without feed additive, group 3 (BHSD): 20 chicks/m2 fed a basal diet supplemented with B. subtilis (500 mg/kg diet), group 4 (OHSD): 20 chicks/m2 fed a basal diet supplemented with oregano essential oil (300 mg/kg diet), group 5 (CHSD): 20 chicks/m2 fed a basal diet supplemented with oregano essential oil and B. subtilis. At 35 days of age, there was a noticeable improvement in the growth performance of broilers fed CHSD under high stocking density through the increase in body weight gain, dressing percentage, and crude protein digestibility with a decrease in feed conversion rate compared to other groups. Adding CHSD enhanced the state of oxidation and immunity through increasing superoxide dismutase, glutathione peroxidase, and the relative weight of bursa of Fabricius, while decreasing malondialdehyde, in addition to increasing plasma triiodothyronine levels. The microbial structure and morphometric parameters improved in the group that received the CHSD compared to the other groups, where villus height and Lactobacillus population increased, whereas Escherichia coli and Clostridium perfringens population decreased. Glucose transporter 2 (GLUT2), fatty acid transporter 1 (FABP1), and amino acid transferase 1 (CAT1) gene expression levels significantly increased when feeding on oregano essential oil with B. subtilis. In conclusion, combining oregano essential oil and B. subtilis supplements mitigated the effects of high stocking density by enhancing growth performance, antioxidative status, and intestinal integrity, in addition to modifying the genetic expression of genes related to nutrient absorption.

The Potential Role of Toxoplasma Gondii Infection in Breast Cancer Through Affecting Programmed Death-1 Genes

Background: This study aimed to evaluate the possible effects of Toxoplasma gondii infection on breast cancer through affecting the serum and expression gene level of programmed death-1 (PD-1) and programmed death-ligand 1 (PD-L1) in breast cancer patients from Thi-qar province, Iraq. Methods: This case-control study was involved 150 patients suffering from breast cancer (BC) who were referring to general hospitals of Thi-Qar province between July to September 2023 and 150 healthy patients (non-BC). Enzyme-linked immunosorbent test (ELISA) kit was used to evaluate the anti-Toxoplasma IgG and the serum level of PD-1 and PDL-1. Furthermore, the expression level of PD-1 and PDL-1 was measured through Real-time PCR. Results: Among 150 breast cancer patients, 71 patients (47.3%) and 25 (16.6%) of healthy subjects exhibited seropositivity for anti-T. gondii IgG antibodies, resepectively. We found that the serum level and the gene expression level of PD-1 and PDL-1 were significantly higher among BC patients seropositive for T. gondii compared with BC patients who were seronegative for T. gondii antibodies (p&lt;0.05). Conclusion: These results indicated that T. gondii may play a role in the occurrence and even progression of cancer probably by elevating levels of PD-1 and PDL-1 genes. However, further studies are required to confirm these findings.

Effects of ensemble-forecasted key environmental factors on the distribution, active constituents, and transcription regulation in Ligusticum chuanxiong Hort.

Ligusticum chuanxiong Hort., with over 2000 years of medicinal use and cultivation history, is extensively used in clinical settings for treating heart disease, headache, dysmenorrhea, and amenorrhea. Constructing the geographic distribution pattern of L. chuanxiong and identifying the environmental factors limiting its range, as well as clarifying the effects of key environmental factors on the content of major active constituents and transcription regulation, could provide a scientific foundation for the conservation and effective management of this valuable medicinal resource. The results reveal that the predominant environmental factors influencing the distribution were the minimum temperature of the coldest month (Bio6) and solar radiation (Srad), with cumulative account for 87.46% of the importance. Correlation analysis further reveals significant negative correlations between Bio6 and the content of major active constituents in L. chuanxiong, with Srad exhibiting a negative correlation with these constituents. The gene differential expression analysis indicated that the expression levels of some genes associated with growth and active constituent biosynthesis pathways, such as RPT2_13888, UVR8_16871, CLPB3_3155, and 4CLL5_116, varied significantly among locations influenced by differing key environmental factors. Consequently, alterations in the environment were found to influence the gene expression levels within these pathways, resulting in variations in the content of active constituents. These findings contribute to an enhanced understanding of how environmental factors impact the distribution and quality of medicinal plants and offer a theoretical reference for the introduction, cultivation, quality improvement, resource utilization and management of L. chuanxiong. © 2024 Society of Chemical Industry.

PbAGL7-PbNAC47-PbMYB73 complex coordinately regulates PbC3H1 and PbHCT17 to promote the lignin biosynthesis in stone cells of pear fruit.

Lignification of the cell wall in pear (Pyrus) fruit results in the formation of stone cells, which affects the texture and quality of the fruit. However, it is still unclear that how different transcription factors (TFs) work together to coordinate the synthesis and deposition of lignin. Here, we examined the transcriptome of pear varieties with different stone cell contents and found a key TF (PbAGL7) that can promote the increase of stone cell contents and secondary cell wall thicknesses. In addition, PbAGL7 can facilitate the expression level of lignin biosynthesis-related genes and accelerate the lignin biosynthesis in pear fruit and Arabidopsis. However, PbAGL7 did not directly bind to the promoters of PbC3H1 and PbHCT17 which are crucial genes involved in lignin biosynthesis. On the other hand, yeast two-hybrid (Y2H) library showed that PbNAC47 and PbMYB73 interacted with PbAGL7 in the nucleus. PbNAC47 and PbMYB73 also increased the stone cell and lignin contents, and upregulated the expressions of PbC3H1 and PbHCT17 by binding to the SNBE and AC elements, respectively. Moreover, PbNAC47 also interacted with PbMYB73 to form PbAGL7-PbNAC47-PbMYB73 complex. This complex significantly activated the expression levels of PbC3H1 and PbHCT17 and promoted lignin biosynthesis to form stone cells in pear fruit. Overall, our study provides new insights into the molecular mechanism of TFs that coordinately regulate the stone cell formation in pear fruit and extend our knowledge to understand cell wall lignification in plants.

The transcription factor TaFDL2-1A functions in auxin metabolism mediated by abscisic acid to regulate shoot growth in wheat.

Genetic strategies can be effective in improving wheat (Triticum aestivum L.) drought stress tolerance, but accumulating evidence suggests that overexpressing drought-resistance genes, especially genes related to the abscisic acid (ABA) signaling pathway, can retard plant growth. We previously characterized the positive roles of the wheat bZIP transcription factor TaFD-Like2-1A (TaFDL2-1A) in drought stress tolerance and ABA biosynthesis and response, whereas a dwarfing shoot exhibited under normal conditions. This study determined the underlying mechanisms that allow TaFDL2-1A to affect shoot growth. Overexpressing TaFDL2-1A decreased cell length, cell width, leaf size, shoot length, and biomass in wheat. The results of RNA-seq showed that multiple differently expressed transcripts are enriched in the auxin signaling pathway. Further analysis indicated higher expression levels of Gretchen Hagen3 (GH3) genes and lower indole-3-acetic acid (IAA) concentrations in the TaFDL2-1A overexpression lines. Exogenous IAA treatment restored the phenotypes of the TaFDL2-1A overexpression lines to wild-type levels. Transcriptional regulation analysis suggested that TaFDL2-1A enhances the expression of auxin metabolism genes, such as TaGH3.2-3A, TaGH3.2-3B, TaGH3.8-2A, and TaGH3.8-2D, by directly binding to ACGT core cis-elements. Furthermore, tafdl2 knock-out plants had lower expression levels of these GH3 genes and higher IAA levels than Fielder wheat. These GH3 gene expression and IAA levels were induced and reduced in Fielder wheat and tafdl2 knock-out plants treated with exogenous ABA. Our findings elucidate mechanisms underlying the functional redundancy of TaFDL2-1A in the crosstalk between ABA and IAA to affect shoot growth and provide insights into the balance between drought resistance and yield in wheat.

Predicting the role of β-GAL genes in bean under abiotic stress and genome-wide characterization of β-GAL gene family members.

Β-Gals are a subgroup of the glycoside hydrolase (GH) family of enzymes, which possess the Glyco_hydro_35 (GH35) domain. Although studies have been conducted on the β-Gal gene family in numerous plant species, no such research has been conducted on beans. The purpose of this study was to determine the gene expression levels of β-Gal genes in the leaf tissue of P. vulgaris under salt and drought stress using quantitative real-time polymerase chain reaction (qRT-PCR) and to perform a comprehensive analysis of β-Gal gene family members using bioinformatics tools. In the bean genome, 25 Pvul-βGAL proteins with amino acid numbers ranging from 291 to 1119, molecular weights from 32.94 to 126.56kDa, and isoelectric points from 5.46 to 9.08 were identified. Both segmental and tandem duplication have occurred in β-Gal genes in the bean genome, and Pvul-BGAL genes have been subject to negative selection in the evolutionary process. For a deeper comprehension of the evolutionary proximity of Pvul-BGAL genes, a phylogenetic tree and synteny map were drawn together with Arabidopsis thaliana and Glycine max β-Gal genes. The expression profiles of β-Gal genes in different tissues of the bean were determined in silico. In addition, the expression profiles of β-Gal genes in the leaves of bean plants subjected to drought and salt stress were analyzed, and the role of β-Gal genes in salt and drought stress was estimated. In this study, the role of β-Gal gene family in abiotic stress response and the characterization of β-Gal genes in beans were determined for the first time and will provide a basis for future functional genomics studies.

Characteristics of Nitrogen Removal from an Integrated Fixed-Film Activated Sludge (IFAS) System and the Relationship Between Activated Sludge and Biofilm Interactions

In order to investigate the enhancement mechanism of modified three-dimensional elastic filler (MTEF) on the nitrogen removal performance of the integrated fixed-film activated sludge (IFAS) process, and to clarify the interactions between competition and synergy between activated sludge and biofilm in the IFAS system, an IFAS reactor (T2) filled with MTEF was employed for the study, while a sequencing batch reactor activated sludge process (SBR) reactor (T1) was utilized for comparison. IFAS and SBR reactors were operated over an extended period at ambient temperature to assess the enhancement of pollutant removal performance with the addition of the filler to investigate the competitive dynamics between activated sludge and biofilm under varying influent water qualities (C/N, N/P, and organic loading), and to analyze the synergistic relationship between activated sludge and biofilm at the microbial level using high-throughput sequencing technology. The results demonstrate that throughout the entire operational phase, reactor T2 exhibited superior pollutant removal efficiency. Compared to reactor T1, reactor T2 achieved an average increase in the removal rates of COD, ammonia nitrogen, and total nitrogen by 13.07%, 12.26%, and 28.96%, respectively. The findings on the competitive dynamics between activated sludge and biofilm indicate that the nitrification volumetric load of the IFAS system is significantly higher than that of a pure activated sludge system, suggesting that the IFAS system possesses enhanced nitrification capabilities. Furthermore, when dealing with wastewater characterized by low C/N ratios and high phosphorus pollution, or under substantial organic loads, the biofilm holds a competitive edge and the IFAS system exhibits improved stability. High-throughput sequencing data reveal that the microbial community structures in activated sludge and biofilm can influence each other, thereby enabling the IFAS system to effectively enrich denitrification-related functional microbial populations. Additionally, the biofilm has a certain enhancing effect on the expression levels of nitrogen metabolism-related functional genes in the activated sludge phase microorganisms, indicating that, in addition to competitive interactions, there is also a synergistic effect between the biofilm and activated sludge.

Evaluation of IL 12 gene expression and serum levels of OxPL / apoB in patients with coronary artery disease

Background: Atherosclerotic lesions are formed as a result of low-density lipoprotein (LDL) accumulation, which is produced by oxidizing enzymes and oxidized phospholipids (OxPL). Phospholipid oxide causes inflammation-inducing activation genes and hyper-inflammation in addition to the initiation of inflammation and expression of Th1 cytokines. Interleukin 12 (IL-12) is one of the most significant stimulants of inflammation and immune responses, among the Th1cytokines. Therefore, it may play a significant role in contributing to atherosclerosis. The quantitative expression of IL-12 mRNA, along with serum OxPL levels, has been analyzed in patients with coronary artery disease (CAD). Methods: Coronary angiography patients, aged 45 to 65 years and referred with chest pain, were examined. The patients were classified into normal coronary arteries (N = 38) and severe three-vessel involvement coronary arteries (N = 41). Molecular testing was performed using real-time PCR. Also, an ELISA test was used to check the OxPl level. Results: Expression of IL12 in Individuals with coronary artery disease was increased but was not statistically significant.

Propionibacterium freudenreichii MJ2-derived extracellular vesicles inhibit RANKL-induced osteoclastogenesis and improve collagen-induced rheumatoid arthritis

Rheumatoid arthritis causes excessive bone loss by stimulating osteoclast differentiation. Extracellular vesicles are valuable disease markers, conveyors of distant cell-to-cell communication, and carriers for drug delivery. The aim of this study was to investigate the anti-osteoclastogenic effects of extracellular vesicles derived from dairy Propionibacterium freudenreichii MJ2 (PFEVs) and the improvement effect of PFEVs on collagen-induced arthritis (CIA) animal model. PFEVs were observed by scanning electron microscopy, transmission electron microscopy, nanoparticle tracking analysis, and LC–MS/MS. The inhibitory activity of PFEVs against receptor activator of nuclear factor kappa-B ligand (RANKL)-induced osteoclast differentiation was investigated in RAW 264.7 cells. PFEVs significantly decreased the expression levels of genes and proteins related to osteoclast differentiation. PFEVs decreased RANK–RANKL binding. In a CIA mouse model, PFEVs treatment significantly reduced arthritis scores and collagen-specific immunoglobulins. PFEVs treatment also reduced pro-inflammatory cytokines and increased anti-inflammatory cytokines. The anti-inflammatory effects were confirmed by H&E staining, and PFEVs treatment inhibited osteoclastogenesis in the CIA mouse model. In conclusion, PFEVs inhibited osteoclast differentiation by inhibiting RANK–RANKL signaling, thereby decreasing the expression of osteoclast differentiation-related genes. PFEVs also improved collagen-induced arthritis by inhibiting inflammation and osteoclastogenesis.

Integration of metabolomics and transcriptomics reveals the toxicological mechanism of deltamethrin exposure in Chinese mitten crab Eriocheir sinensis

This study investigated the toxicological mechanism of deltamethrin on Chinese mitten crab Eriocheir sinensis juveniles in fresh water. We first conducted an acute toxicity test, followed by laboratory methods to detect changes in immune-related indices in terms of antioxidant enzyme markers, lipid metabolism-related genes, and autophagy-related and apoptosis genes. The acute toxicity (96-h LC50) of deltamethrin to E. sinensis was 7.195 μg/L. After 48 h of exposure, serum showed elevated immune-related indices (P < 0.05) for alkaline phosphatase (AKP), acid phosphatase (ACP), aspartate aminotransferase (AST), alanine aminotransferase (ALT), complement components C3 and C4, and the key pro-inflammatory cytokines interleukin-6, interleukin-1β, and tumor necrosis factor alpha (TNF-α). In hepatopancreas at 48 h, indicators related to the antioxidant system, namely superoxide dismutase (SOD) and glutathione (GSH), were significantly elevated, whereas nitric oxide and total antioxidant capacity (T-AOC) were decreased (P < 0.05). In contrast, lipid metabolism indices for triglyceride (TG), total cholesterol (TC), and malondialdehyde (MDA) were increased (P < 0.05). Transcriptomics and metabolomics revealed that exposure to deltamethrin disrupted the lipid metabolic process in the hepatopancreas mainly by altering fatty acid synthesis, amino acid metabolism, immune signaling, and autophagy activation, while the exposure increased the content of phospholipids and cholesterol but decreased the levels of amino acids and palmitoleic acid. Quantitative genetics revealed significantly aberrantly expressed (P < 0.05) lipid metabolism-related genes, including acc1, fasn, scd1, and pnpla2, all key genes involved in lipid accumulation. Deltamethrin exposure also significantly altered (P < 0.05) gene expression levels for Toll-like receptor (tlr), myeloid differentiation factor 88 (myd88), crustin1, anti-lipopolysaccharide factor isoform 3 (alf3), tumor necrosis factor alpha (tnf-α), and NF-κB transcription factor relish. Furthermore, deltamethrin activated the toll-like receptor/major myeloid differentiation response gene 88/nuclear factor kappa-light-chain-enhancer of activated B cells (TLR/MyD88/NF-kB) signaling pathway, which activates a nonspecific immune response in E. sinensis. Additionally, carnitine palmitoyltransferase 1 A (cpt1a), cytochrome c (cyt-c), adenosine 5′-monophosphate (amp)-activated protein kinase (ampk), the autophagosomal protein microtubule-associated protein 1 light chain 3c (lc3c), and the autophagy-related proteins beclin1, atg5, atg12 were significantly induced (P < 0.05) in the adenosine monophosphate-activated protein kinase/rapamycin (AMPK/mTOR) signaling pathway. These changes resulted in excess free radicals, causing oxidative stress in the mitochondrial membrane, promoting mitochondrial autophagy. The results confirm that deltamethrin exposure can induce hepatopancreatic injury by promoting mitochondrial autophagy, activating an immune response, and inhibiting lipid metabolism. Overall, this study provides multi-level information to reveal the toxic effects of deltamethrin on E. sinensis.

Identification and Validation of Garlic (Allium sativum) Metabolites as Quorum Sensing Inhibitors of Bacillus cereus Targeting the PlcR Receptor: An In Silico and In Vitro Study.

This study aimed to investigate the influence of garlic metabolites on the quorum sensing (QS) of Bacillus cereus, a foodborne pathogen that controls its main virulence factor through QS. The QS signal receptor PlcR of B. cereus was targeted by molecular docking with 82 garlic metabolites to identify the most potent QS inhibitors. Five metabolites, quercetin, kaempferol, luteolin, flavone, and rutin, were selected for further evaluation of their impacts on the growth, toxin production, and virulence of B. cereus in vitro. The expression levels of key QS genes were also measured to verify their anti-QS ability. The results revealed that quercetin reduced enterotoxin production by B. cereus but did not affect the QS process at the transcriptional level; flavone and rutin in garlic interfered with the QS of B. cereus by competing with the autoinducing peptide (AIP) PapR7 for the PlcR binding site, resulting in decreased enterotoxin secretion and hemolysis without altering the bacterial growth. Interestingly, luteolin and kaempferol in garlic acted as AIP analogs and bound to PlcR to stimulate the QS process and virulence. Furthermore, kaempferol, luteolin, flavone, and rutin had distinct or opposite interactions with PapR7 at the Gln237 or Tyr275 residues of PlcR, which determined the suppression or enhancement of the QS process. The findings suggested that flavone and rutin were effective compounds to inhibit the QS process in garlic and could be used as alternative methods to control B. cereus.

Ustekinumab affects myofibroblast metabolism to alleviate intestinal fibrosis by targeting KDELC1 in Crohn’s disease through multi-machine learning combined with single-cell sequencing analysis

BackgroundUstekinumab (UST), a biologic against interleukin (IL)-12/23, is commonly used to treat Crohn’s disease (CD). Myofibroblast (MF) is known as one of the most important factors causing intestinal fibrosis, and UST has been reported to alleviate this condition. However, the genetic mechanisms underlying UST’s effects on CD remain unclear. This study uses bioinformatics tools to analyze the genes and potential pathways affected by UST in CD, with a focus on its anti-fibrosis effects, providing insights into new therapeutic targets.MethodsThe data downloaded from the Gene Expression Omnibus (GEO) database were analyzed to screen for differentially expressed genes (DEGs). Various machine learning strategies, including the least absolute shrinkage and selection operator (LASSO), support vector machine (SVM), and random forest (RF), were employed to screen for key genes among the DEGs. Functional and pathway enrichment analyses were conducted, and key genes associated with myofibroblast (MF) activity were screened. Finally, endoscopic surgical specimens from CD patients and healthy participants were collected to assess the expression levels of collagen and key genes in intestinal tissues using hematoxylin–eosin (H&amp;amp;E), Masson staining, and immunohistochemistry.ResultsA total of 1,341 DEGs associated with CD were identified. Among them, 738 genes showed low expression in healthy populations but high expression in patients with CD, reduced expression after the treatment of UST. In contrast, 603 genes exhibited high expression in healthy individuals, showed low expression in CD patients, and increased expression after UST treatment. Functional and pathway analysis showed that DEGs were mainly concentrated in response to foreign biological stimuli and bacterial-derived molecules. DEGs are mainly enriched in chemokines, TNF, IL-17, and other signaling pathways. Seven key genes were identified: NCRNA00236, LOC730101, ORP3, XG, UBFD1, KDELC1, and RBP7. Single-cell analysis revealed that KDELC1 was closely related to MF activity. MFs with high KDELC1 expression were significantly enriched in biological functions, signaling pathways, and metabolic processes that promote fibrosis. The experiment showed that UST treatment helped maintain the integrity of intestinal tissue structure, reducing the expression levels of collagen I, KDELC1, and the severity of intestinal fibrosis. The functional and pathway analysis reiterated that DEGs were largely focused on responses to foreign biological stimuli and bacterial-derived molecules, as well as signaling pathways such as chemokines, TNF, and IL-17. Of the identified genes, KDELC1 showed a particularly strong correlation with MF activity in single-cell analysis (R = 0.33, p = 3.2e-07). MFs with high KDELC1 expression were closely linked to pathways promoting fibrosis progression, including TGF-β, epithelial-mesenchymal transformation, TNF/NF-κB, and related metabolic pathways such as vitamin B6 and arginine.ConclusionKDELC1 plays a key role in regulating multiple biological functions, including signaling pathways related to MF. UST alleviates intestinal fibrosis by targeting KDELC1, thereby influencing intramuscular fat metabolism and intercellular communication.

Orexin A protects against cerebral ischemia-reperfusion injury by enhancing reperfusion in ischemic cortex via HIF-1α-ET-1/eNOS pathway

The purpose of this study was to investigate the protective effect and underlying mechanism of orexin A on cerebral ischemia-reperfusion injury, specifically through vasodilation mediated by the hypoxia inducible factor-1α (HIF-1α)-Endothelin-1(ET-1)/endothelial nitric oxide synthase (eNOS) pathway. A model of middle cerebral artery occlusion was established in both wild-type SD rats with exogenous orexin A intervention and in orexin A transgenic rats. Neurological deficit scores and cerebral infarction areas were assessed, and ischemic cortical blood flow was monitored. Gene and protein expression levels of HIF-1α, HIF-2α, ET-1, and three types of NOS were detected using real-time RT-qPCR and Western blot analysis, respectively. Additionally, nitric oxide (NO) levels in the cortex were analyzed through biochemical detection methods. Orexin A demonstrated a protective effect by reducing cerebral infarction and improving neurological deficits, which was achieved by increasing cortical blood flow during reperfusion. This protective mechanism was associated with upregulated HIF-1α expression, downregulated ET-1 expression, upregulated eNOS expression, and increased NO production. This study demonstrates the protective effect of orexin A on cerebral ischemia-reperfusion injury, achieved by regulating the release of vasomotor substances to enhance cortical blood flow during reperfusion. These findings suggest that orexin A may represent a potential therapeutic strategy for ischemic stroke.

Epigenome Mapping in Quiescent Cells Reveals a Key Role for H3K4me3 in Regulation of RNA Polymerase II Activity.

(1) Background: Quiescent cells are those that have stopped dividing and show strongly reduced levels of gene expression during dormancy. In response to appropriate signals, the cells can wake up and start growing again. Many histone modifications are regulated in quiescence, but their exact functions remain to be determined. (2) Methods: Here, we map the different histone modifications, H3K4me3, H3K9ac, H3K9me2, and H3K9me3, and the histone variant H2A.Z, comparing vegetative and quiescent fission yeast (S. pombe) cells. We also map histone H3 as a control and RNA polymerase II (phosphorylated at S2 and S5) to enable comparisons of their occupancies within genes. We use ChIP-seq methodology and several different bioinformatics tools. (3) Results: The histone modification mapping data show that H3K4me3 changes stand out as being the most significant. Changes in occupancy of histone variant H2A.Z were also significant, consistent with earlier studies. Regarding gene expression changes in quiescence, we found that changes in mRNA levels were associated with changes in occupancy of RNA polymerase II (S2 and S5). Analysis of quiescence genes showed that increased H3K4me3 levels and RNA polymerase II occupancy were super-significant in a small set of core quiescence genes that are continuously upregulated during dormancy. We demonstrate that several of these genes were require Set1C/COMPASS activity for their strong induction during quiescence. (4) Conclusions: Our results imply that regulation of gene expression in quiescent cells involves epigenome changes with a key role for H3K4me3 in regulation of RNA polymerase II activity, and that different gene activation mechanisms control early and core quiescence genes. Thus, our data give further insights into important epigenome changes in quiescence using fission yeast as an experimental model.

Evaluation the Impressionability of Acellular Scaffolds in Presence of Different Combination of Umbilical Cord Blood Stem Cells and Platelet Rich Fibrin in Repair of Knee Defects in Rabbit (Novel Method with Xeno-Material Elements

Background: Currently, the use of xenogeneic and allogeneic compounds in the treatment of musculoskeletal diseases is common. Repairing bone and cartilage remains a significant challenge for orthopedic surgeons. One of the principal goals of tissue engineering is the development of appropriate scaffolds that can promote tissue regeneration. Various cells and genes are involved in bone and cartilage regeneration, and new scaffolds can induce these processes during osteoregeneration. Objectives: The aim of this study is to evaluate the effects of umbilical cord blood stem cells (USCs) and platelet-rich fibrin (PRF) using acellular scaffolds in the repair of knee defects in rabbits. Methods: In this study, the femoral patella of 12 male New Zealand rabbits was drilled, and they were divided into four groups: (1) control (rabbits with femoral defects), (2) acellular osteochondral (AO), (3) AO + PRF, and (4) AO + USCs / platelet-rich fibrin. Different scaffolds were implanted into their knees, and after six months, histological evaluations were conducted. To further investigate the effects of scaffolds on bone and cartilage, gene expression levels of Col 1, Col X, Runx2, SOX9, and ALP were measured using real-time PCR. Results: All the implanted materials contributed to knee repair. In terms of statistical analysis, the use of USCs and platelet-rich fibrin with natural scaffolds such as Acellular Osteochondral provided better results for repairing bone and cartilage. The evaluation of specific bone regeneration genes (COLI, RUNX2) and the histological results from the implanted site in experimental osteochondral defects indicated that the most effective knee repair occurred in the group treated with cell-free osteochondral scaffolds, USCs, and platelet-rich fibrin. Conclusions: This study demonstrates that the combination of biomaterials and xenografts can accelerate the regeneration process.

The Role of miR-155 in Modulating Gene Expression in CD4+ T Cells: Insights into Alternative Immune Pathways in Autoimmune Encephalomyelitis

CD4+ T cells are considered the main orchestrators of autoimmune diseases. Their disruptive effect on CD4+ T cell differentiation and the imbalance between T helper cell populations can be most accurately determined using experimental autoimmune encephalomyelitis (EAE) as an animal model of multiple sclerosis (MS). One epigenetic factor known to promote autoimmune inflammation is miRNA-155 (miR-155), which is significantly upregulated in inflammatory T cells. The aim of the present study was to profile the transcriptome of immunized mice and determine their gene expression levels based on mRNA and miRNA sequencing. No statistically significant differences in miRNA profile were observed; however, substantial changes in gene expression between miRNA-155 knockout (KO) mice and WT were noted. In miR-155 KO mice, mRNA expression in CD4+ T cells changed in response to immunization with the myeloid antigen MOG35-55. After restimulation with MOG35-55, increased Ffar1 (free fatty acid receptor 1) and Scg2 (secretogranin-2) expression were noted in the CD4+ T cells of miR-155-deficient mice; this is an example of an alternative response to antigen stimulation.