Relative Gene Expression Levels Research Articles

Effect of entecavir on IL-6/STAT3/SOCS3 pathway in patients with chronic hepatitis B-induced liver fibrosis

Purpose: To evaluate the impact of entecavir (ENT) on patients with liver fibrosis resulting from chronic hepatitis B (CHB) and its association with the interleukin (IL)-6/signal transducer and activator of transcription 3 (STAT3)/suppressor of cytokine signaling 3 (SOCS3) pathway.Methods: Thirty-one patients with liver fibrosis received ENT at a dose of 0.5 mg/day for 48 weeks. Relevant protein levels in patient’s serum before and after treatment were assayed using enzyme-linked immunosorbent assay (ELISA). Furthermore, human hepatic stellate cells (HSCs) were cultured in vitro and divided into three groups: control, transforming growth factor beta 1 (TGF-β1) induction (TGF-β1 group), and ENT treatment (TGF-β1 + ENT group). Protein levels in the supernatant were assayed using ELISA, while the expression levels of related genes were determined by quantitative reverse transcription-polymerase chain reaction (qRT-PCR). Expression of α-SMA was visualized using immunofluorescence assay and the relevant protein levels were determined by Western blotting.Results: Treatment with ENT significantly decreased (p < 0.01) IL-6 and STAT3 expression, increased SOCS3 expression and significantly reduced (p < 0.01) the concentrations of hyaluronic acid (HA), type IV collagen (IVC), laminin (LN) and pro-collagen type III (PCIII) in patients with liver fibrosis. TGF-β1 significantly (p < 0.01) elevated IL-6, STAT3 and Col-I expressions and a tissue inhibitor of metalloproteinases-1 (TIMP-1) suppressed the expression of SOCS3 in human HSCs and induced fibrosis. Entecavir mitigated TGF-β1-induced fibrogenesis in HSCs (p < 0.01).Conclusion: Entecavir has a positive effect on liver fibrosis resulting from CHB by regulating IL- 6/STAT3/SOCS3 pathway. Future research will focus on conducting larger clinical trials to further validate these findings and explore the long-term effects of ENT on liver fibrosis progression and patient outcomes.

Comparative analysis of different rice substrates for solid-state fermentation by a citrinin-free Monascus purpureus mutant strain with high pigment production

Monascus pigment (MP) is a safe and natural microbial coloring agent. MP and red yeast rice (RYR) play an important role in the food industry. In this study, a citrinin-free Monascus puprureus MS-12 with high MP production was generated using dual mutagenesis of atmospheric and room-temperature plasma and heavy ion beam irradiation. The fermentation characteristics of eight rice substrates for solid-state fermentation (SSF) were compared to produce a premium RYR. Indica rice was the optimal fermentation substrate (MP = 4526 U/g in RYR), followed by japonica rice (MP = 3556 U/g). The MP value was <1000 U/g using other substrates (red, brown and black rice) for fermentation. RT-qPCR results demonstrated that the expression levels of MP synthesis- and the glycolysis-related genes of the mutant strain were upregulated compared with those of the parental strain, with MpigA exhibiting a 1.70-fold increase, while the relative expression levels of citrinin synthesis-related genes were downregulated; citE was downregulated 7.84-fold. In comparison to M. purpureus MS-12 mRNA levels using indica rice as the fermentation substrate during SSF, genes for MP, citrinin biosynthesis, and glycolysis resulted in the downregulation of other substrates. Our results show that colored and glutinous rice are unsuitable for RYR preparation via SSF. The maximum MP value was obtained using indical rice as the fermentation substrate, resulting from the upregulated expression levels of the pigment biosynthesis gene cluster and glycolytic pathway.

Daqu and environmental microbiota regulate fatty acid biosynthesis via driving the core microbiota in soy sauce aroma type liquor fermentation

Fatty acids are considered as important compounds for the aroma and taste of Chinese liquor. Revealing the core microbiota related with fatty acid biosynthesis and how they are influenced are essential to control fatty acids in spontaneous Chinese liquor fermentation. Herein, we identified the core microbiota related with fatty acid biosynthesis based on their microbial abundance, abundance and expression level of genes related with fatty acid biosynthesis, using high-throughput amplicon sequencing, metagenomic and metatranscriptomic analysis, respectively. Acetilactobacillus, Kroppenstedtia, Saccharomyces, Paecilomyces and Pichia were identified as the core microbiota (the criteria for identifying core microbiota: average relative abundance ≥1 %, average abundance of related genes >400 fragments per kilobase of transcript per million fragments mapped [FPKM], and expression level of related genes >1000 FPKM) related with fatty acid biosynthesis. SourceTracker analysis showed that Daqu mainly provided Kroppenstedtia (34.01 %) and Acetilactobacillus (3.31 %). Ground mainly provided Pichia (47.47 %), Saccharomyces (16.17 %) and Paecilomyces (8.55 %). Structural equation model revealed that Daqu and environmental microbiota drove the core microbiota (P < 0.05), and the core microbiota drove the biosynthesis of fatty acids (P < 0.05). This work revealed the important role of Daqu and environmental microbiota in fatty acid biosynthesis in liquor fermentation. It would benefit controlling fatty acids in liquor fermentation, and improving the liquor quality.

Effect of methanol fixation on single-cell RNA sequencing of the murine dentate gyrus.

Single-cell RNA sequencing (scRNA-seq) provides a powerful tool to evaluate the transcriptomic landscape and heterogeneity of thousands of cells in parallel. However, complex study designs or the unavailability of in-house instruments require the temporal disconnection between sample preparation and library construction, raising the need for efficient sample preservation methods which are compatible with scRNA-seq downstream analysis. Several studies evaluated the effect of methanol fixation as preservation method, yet none of them deeply assessed its effect on adult primary dissociated brain tissue. Here, we evaluated its effect on murine dentate gyrus (DG) single cell suspensions and on subsequent scRNA-seq downstream analysis by performing SOrting and Robot-assisted Transcriptome SEQuencing (SORT-seq), a partially robotized version of the CEL-seq2 protocol. Our results show that MeOH fixation preserves RNA integrity and has no apparent effects on cDNA library construction. They also suggest that fixation protects from sorting-induced cell stress and increases the proportion of high-quality cells. Despite evidence of mRNA leakage in fixed cells, their relative gene expression levels correlate well with those of fresh cells and fixation does not significantly affect the variance of the dataset. Moreover, it allows the identification of all major DG cell populations, including neural precursors, granule neurons and different glial cell types, with a tendency to preserve more neurons that are underrepresented in fresh samples. Overall, our data show that MeOH fixation is suitable for preserving primary neural cells for subsequent single-cell RNA profiling, helping to overcome challenges arising from complex workflows, improve experimental flexibility and facilitate scientific collaboration.

Comparative study of purgative pharmacological effects and mechanisms of Moringa oleifera leaves and Rhei Radix et Rhizoma

Moringa oleifera leaves are known for their &quot;Virechana&quot;(purgative) effect in Ayurvedic medicine in India. This study compared the purgative effects and mechanisms of M. oleifera leaves with the reference Rhei Radix et Rhizoma to establish a foundation for the further application of M. oleifera leaves in traditional Chinese medicine(TCM). Using network pharmacology and molecular docking methods, this study identified the material basis, common targets, and signaling pathways through which Rhei Radix et Rhizoma and M. oleifera leaves exerted their purgative pharmacological effects. A low-fiber diet-induced constipation mouse model was established to measure fecal parameters and small intestinal propulsion rate, and histological changes in the colon were observed using HE staining. Relative expression levels of relevant genes and target proteins were assessed using RT-qPCR and immunohistochemistry, respectively. The results showed that mapping the targets of Rhei Radix et Rhizoma and M. oleifera leaves onto the biological process network of constipation revealed close proximity, indicating that they may exert their therapeutic effects on constipation through similar biological processes. Molecular docking results indicated that compounds such as sennoside C and isoquercitrin could target serine/threonine protein kinases(AKT1) and mitogen-activated protein kinase 3(MAPK3), thereby affecting MAPK and calcium signaling pathways to promote defecation. Animal experiments demonstrated that both M. oleifera leaves and Rhei Radix et Rhizoma increased the number of fecal pellets and water content in constipated mice, improved small intestine motility, colon mucosal thickness, and muscle layer thickness, upregulated the gene expression levels of AKT1 and MAPK3 in the colon, and downregulated the expression of AQP3 protein. These findings suggest that M. oleifera leaves and Rhei Radix et Rhizoma share similarities in their therapeutic efficacy and mechanisms for treating constipation. Using Rhei Radix et Rhizoma as a reference can provide a better understanding of the characteristics of the &quot;Virechana&quot;(purgative) effect of M. oleifera leaves in TCM.

Ferulic Acid Enhances Oocyte Maturation and the Subsequent Development of Bovine Oocytes.

Improving the quality of oocytes matured in vitro is integral to enhancing the efficacy of in vitro embryo production. Oxidative stress is one of the primary causes of quality decline in oocytes matured in vitro. In this study, ferulic acid (FA), a natural antioxidant found in plant cell walls, was investigated to evaluate its impact on bovine oocyte maturation and subsequent embryonic development. Bovine cumulus-oocyte complexes (COCs) were treated with different concentrations of FA (0, 2.5, 5, 10, 20 μM) during in vitro maturation (IVM). Compared to the control group, supplementation with 5 μM FA significantly enhanced the maturation rates of bovine oocytes and the expansion of the cumulus cells area, as well as the subsequent cleavage and blastocyst formation rates after in vitro fertilization (IVF) and somatic cell nuclear transfer (SCNT). Furthermore, FA supplementation was observed to effectively decrease the levels of ROS in bovine oocytes and improve their mitochondrial function. Our experiments demonstrate that FA can maintain the levels of antioxidants (GSH, SOD, CAT) in oocytes, thereby alleviating the oxidative stress induced by H2O2. RT-qPCR results revealed that, after FA treatment, the relative mRNA expression levels of genes related to oocyte maturation (GDF-9 and BMP-15), cumulus cell expansion (HAS2, PTX3, CX37, and CX43), and embryo pluripotency (OCT4, SOX2, and CDX2) were significantly increased. In conclusion, these findings demonstrate that FA supplementation during bovine oocyte IVM can enhance oocyte quality and the developmental potential of subsequent embryos.

Enhancement of Triterpenoid Synthesis in Antrodia cinnamomea through Homologous Expression of the Key Synthetic Pathway Genes AcLSS and AcERG4

Antrodia cinnamomea (AC), a rare fungus endemic to Taiwan, contains high levels of various secondary metabolites, notably triterpenoids, having useful medicinal and pharmacological properties. Techniques for increasing the production of AC triterpenoids (ACT) for medicinal purposes are a high research priority. We measured and compared the biomass and ACT content of AC mycelia under various liquid fermentation culture conditions. Relative gene expression levels of ten enzymes involved in the mevalonate (MVA) pathway and “subsequent group modification pathway” were determined, and correlation analysis was performed to evaluate the roles of these enzyme genes in ACT synthesis. Two representative genes encoding the enzymes lanosterol synthase (AcLSS) and sterol C-24 reductase (AcERG4), whose activity is closely associated with ACT content, were selected for homologous expression. AcLSS and AcERG4 were separately linked to plasmid pCT74, and transformed into prepared AC protoplasts to obtain two recombinant strains, termed RpLSS and RpERG4, by polyethylene glycol (PEG)-CaCl2-mediated protoplast transformation. Upregulated expression levels of AcLSS and AcERG4 (1.78- and 1.41-fold, respectively) were associated with significantly higher (1.82- and 1.37-fold, respectively) ACT content in the recombinant strains in comparison with the wild-type. Our findings provide a theoretical and practical basis for the enhancement of ACT production using homologous expression techniques.

Selenium-molybdenum interactions reduce chromium toxicity in Nicotiana tabacum L. by promoting chromium chelation on the cell wall

Chromium (Cr) is a hazardous heavy metal that negatively affects animals and plants. The micronutrients selenium (Se) and molybdenum (Mo) have been widely shown to alleviate heavy metal toxicity in plants. However, the molecular mechanism of Cr chelation on the cell wall by combined treatment with Se and Mo has not been reported. Therefore, this study aimed to explore the effects of Se-Mo interactions on the subcellular distribution of Cr (50 µM) and on cell wall composition, structure, functional groups and Cr content, in addition to performing a comprehensive analysis of the transcriptome. Our results showed that the cell walls of shoots and roots accumulated 51.0% and 65.0% of the Cr, respectively. Furthermore, pectin in the cell wall bound 69.5%/90.2% of the Cr in the shoots/roots. Se-Mo interactions upregulated the expression levels of related genes encoding galacturonosyltransferase (GAUT), UTP-glucose-1-phosphate uridylyltransferase (UGP), and UDP-glucose-4-epimerase (GALE), involved in polysaccharide biosynthesis, thereby increasing pectin and cellulose levels. Moreover, combined treatment with Se and Mo increased the lignin content and cell wall thickness by upregulating the expression levels of genes encoding cinnamyl alcohol dehydrogenase (CAD), peroxidase (POX) and phenylalanine amino-lyase (PAL), involved in lignin biosynthesis. Fourier-transform infrared (FTIR) spectroscopy results showed that Se + Mo treatment (in combination) increased the number of carboxylic acid groups (-COOH) groups, thereby enhancing the Cr chelation ability. The results not only elucidate the molecular mechanism of action of Se-Mo interactions in mitigating Cr toxicity but also provide new insights for phytoremediation and food safety.

Gut microbiota-driven regulation of queen bee ovarian metabolism.

With the global prevalence of Varroa mites, more and more beekeepers resort to confining the queen bee in a queen cage to control mite infestation or to breed superior and robust queen bees. However, the impact of such practices on the queen bee remains largely unknown. Therefore, we subjected the queen bees to a 21-day egg-laying restriction treatment (from the egg stage to the emergence of adult worker bees) and analyzed the queen bees' ovarian metabolites and gut microbiota after 21 days, aiming to assess the queen bees' quality and assist beekeepers in better hive management. Our findings revealed a significant reduction in the relative expression levels of Vg and Hex110 genes in the ovaries of egg laying-restricted queen bees compared to unrestricted egg-laying queens. The diversity of gut microbiota in the queen bee exhibited a notable decrease, accompanied by corresponding changes in the core bacteria of the microbial community, the relative abundance of Lactobacillus and Bifidobacterium increased from 22.34% to 53.14% (P = 0.01) and from 0.053% to 0.580% (P = 0.04), respectively. The relative abundance of Bombella decreased from 25.85% to 1.720% (P = 0.002). Following egg-laying restriction, the activity of the queen bee's ovaries decreased, while the metabolism of glycerophospholipids remained or stored more lipid molecules, awaiting environmental changes for the queen bee to resume egg laying promptly. Furthermore, we observed that Bombella in the queen bee's gut may regulate the queen's ovarian metabolism through tryptophan metabolism. These findings provide novel insights into the interplay among queen egg laying, gut microbiota, and ovarian metabolism. IMPORTANCE With Varroa mite infestation, beekeepers often confine the queen bee in cages for control or breeding. However, the impact on the queen bee is largely unknown. We evaluated queen bee quality by restricting egg laying and analyzing ovarian metabolites and gut microbiota. In this study, we provided a comprehensive explanation of the expression of ovarian genes, the diversity of gut microbiota, and changes in ovarian metabolism in the queen bee. Through integrated analysis of the queen bee's gut microbiota and ovarian metabolism, we discovered that the gut microbiota can regulate the queen bee's ovarian metabolism. These findings provide valuable insights into the interplay among egg laying, gut microbiota, and the reproductive health of the queen bee. Understanding these relationships can contribute to the development of better strategies for Varroa mite control and queen bee breeding.

Metabolomic response to high light from pgrl1 and pgr5 mutants of Chlamydomonas reinhardtii.

Chlamydomonas(C.) reinhardtii metabolomic changes in cyclic electron flow-dependent mutants are still unknown. Here, we used mass spectrometric analysis to monitor the changes in metabolite levels in wild-type, cyclic electron-deficient mutants pgrl1 and pgr5 grown under high-light stress. A total of 55 metabolites were detected using GC-MS analysis. High-light stress-induced selective anaplerotic amino acids in pgr5. In addition, pgr5 showed enhancement in carbohydrate,polyamine,andpolyolmetabolism by 2.5-fold under high light.In response to high light, pgr5 triggers an increase in several metabolites involved in regulating osmotic pressure. Among these metabolites are glycerol pathway compounds such as glycerol-3-phosphate and glyceryl-glycoside, which increase significantly by 1.55 and 3.07 times, respectively. In addition, pgr5 also enhanced proline and putrescine levels by 2.6- and 1.36-fold under high light. On the other hand, pgrl1-induced metabolites, such as alanine and serine, are crucial for photorespiration when subjected to high-light stress. We also observed a significant increase in levels of polyols and glycerol by 1.37- and 2.97-fold in pgrl1 under high-light stress. Both correlation network studies and KEGG pathway enrichment analysis revealed that metabolites related to several biological pathways, such as amino acid, carbohydrate, TCA cycle, and fatty acid metabolism, were positively correlated in pgrl1 and pgr5 under high-light stress conditions. The relative mRNA expression levels of genes related to the TCA cycle, including PDC3, ACH1, OGD2, OGD3, IDH3, and MDH4, were significantly upregulated in pgrl1 and pgr5 under HL. In pgr5, the MDH1 level was significantly increased, while ACS1, ACS3, IDH2, and IDH3 levels were reduced considerably in pgrl1 under high-light stress. The current study demonstrates both pgr5 and prgl1 showed a differential defense response to high-light stress at the primary metabolites and mRNA expression level, which can be added to the existing knowledge to explore molecular regulatory responses of prg5 and pgrl1 to high-light stress.

Streptococcus mitis and Prevotella melaninogenica Influence Gene Expression Changes in Oral Mucosal Lesions in Periodontitis Patients.

Oral microbiome disruptions in periodontitis are related to the chronic inflammatory reactions that could in turn lead to the development of multiple oral diseases. The objective of the study was to assess the frequencies of Streptococcus mitis, Prevotella melaninogenica, and Prevotella intermedia in oral benign lesions, oral potentially malignant disorders (OPMDs), and oral squamous cell carcinomas (OSCCs) and investigate the impact of these bacteria on the expression patterns of the selected (potential) target genes (PI3CA/AKT2/mTOR, DUSP16/MAPK14, and COX2). After sample collection (25 benign lesions, 30 OPMDs, and 35 OSCCs) and DNA/RNA extraction, quantitative real-time polymerase chain reaction (qPCR) was performed to detect bacterial presence and assess relative gene expression levels in different lesion groups. Prevotella melaninogenica was the most prevalent of the three analyzed bacteria, with the frequency being 60% in benign lesions, 87% in OPMDs (p = 0.024), and 77% in OSCC. The OPMD tissues in which Prevotella melaninogenica was present exhibited a higher expression level of AKT2 (p = 0.042). Significantly lower expression of DUSP16 was observed in OSCC tissues containing Streptococcus mitis (p = 0.011). The obtained results indicate a substantial contribution of P. melaninogenica and Str. mitis in the pathogenesis of oral mucosal lesions, possibly via AKT2 upregulation and DUSP16 downregulation.

The pathway of Edwardsiella piscicida infecting Lateolabrax maculatus via the immersion bath.

Edwardsiella piscicida, an infectious bacterium, causes great economic losses to the aquaculture industry. Immersion bath which is the closest way to how the fish infect bacterial pathogens in the natural environment is an effective route of artificial infection. In this study, the dynamic process of E. piscicida infection, in the spotted sea bass (Lateolabrax maculatus) was evaluated via the immersion bath. The results showed that soaking the spotted sea bass with 3 × 106 CFU mL-1 E. piscicida for 30 min could artificially induce edwardsiellosis. The higher culture temperature (28.5 ± 0.5°C) or the longer bath time (30 min) would lead to higher mortality of fish. E.piscicida first invaded the gill, then entered the blood circulation to infect the spleen and kidney, where it is colonized, and gradually multiplied in the liver and brain. Meanwhile, the fluorescence in situ hybridization showed that the localization of E. piscicida in the gill and foregut after the immersion challenge proceeded from the exterior to the interior. The invasion of pathogens triggers the immune response of fish and causes tissue damage to the host. The quantitative real-time PCR results displayed an increase in the relative expression level of immune genes (NK-lysin, LZM, IgM and IgD). Otherwise, the most notable histopathological changes of the infected spotted sea bass were multifocal necrosis. Findings in this study broaden our understanding of the infection conditions of E. piscicida and its pathogenicity to the spotted sea bass.

Cypermethrin induces apoptosis, autophagy and inflammation via ERS-ROS-NF-κB axis in hepatocytes of carp (Cyprinus carpio)

Cypermethrin (CYP, IUPAC name: [cyano-(3-phenoxyphenyl)methyl] 3-(2,2-dichloroethenyl)-2,2-dimethylcyclopropane-1-carboxylate) is a pyrethroid insecticide that poses a threat to the health of humans and aquatic animals due to its widespread use and environmental contamination. However, the mechanism of CYP on apoptosis, autophagy and inflammation in hepatocytes of carp (Cyprinus carpio) is unknown. We hypothesized that CYP caused damage to hepatocytes through the endoplasmic reticulum stress (ERS) pathway, CCK-8 was used to detect the toxic effects of different doses of CYP on hepatocytes, and finally low (L, 10 μM), medium (M, 40 μM), and high (H, 80 μM) doses of CYP was selected to construct the model. ROS staining, oxidative stress-related indices (MDA, CAT, T-AOC, SOD), AO/EB staining, MDC staining, and the expression levels of related genes were detected using qRT-PCR and western blot. Our results showed that CYP exposure resulted in an increase in ROS production, an increase in MDA content, and a decrease in the activity of CAT, SOD, and T-AOC in hepatocytes; the proportion of apoptotic, necrotic, and autophagic cells increased significantly in a dose-dependent manner. We also found that CYP exposure increased the expression levels of endoplasmic reticulum-related genes (GRP78, PERK, IRE-1, ATF-6 and CHOP), apoptosis (Bcl-2, Bax, Caspase-3, Caspase-9 and Cyt-c) and autophagy-related genes (LC3b, Beclin1 and P62) also showed dose-dependent changes, and the expression levels of inflammation-related genes (NF-κB, TNF-α, IL-1β, IL-6) were also significantly elevated. Thus, we demonstrated that CYP exposure caused apoptosis, autophagy and inflammation in hepatocytes via ERS-ROS-NF-κB axis. This research contributes to our understanding of the molecular mechanisms underlying CYP-induced damage in hepatocytes of carp (Cyprinus carpio).

NLG1, encoding a mitochondrial membrane protein, controls leaf and grain development in rice

BackgroundMitochondrion is the key respiratory organ and participate in multiple anabolism and catabolism pathways in eukaryote. However, the underlying mechanism of how mitochondrial membrane proteins regulate leaf and grain development remains to be further elucidated.ResultsHere, a mitochondria-defective mutant narrow leaf and slender grain 1 (nlg1) was identified from an EMS-treated mutant population, which exhibits narrow leaves and slender grains. Moreover, nlg1 also presents abnormal mitochondria structure and was sensitive to the inhibitors of mitochondrial electron transport chain. Map-based cloning and transgenic functional confirmation revealed that NLG1 encodes a mitochondrial import inner membrane translocase containing a subunit Tim21. GUS staining assay and RT-qPCR suggested that NLG1 was mainly expressed in leaves and panicles. The expression level of respiratory function and auxin response related genes were significantly down-regulated in nlg1, which may be responsible for the declination of ATP production and auxin content.ConclusionsThese results suggested that NLG1 plays an important role in the regulation of leaf and grain size development by maintaining mitochondrial homeostasis. Our finding provides a novel insight into the effects of mitochondria development on leaf and grain morphogenesis in rice.

Activation of the DNA damage response pathway in the infected gastric tissue with Helicobacter pylori: a case-control study.

Gastritis is among the most common human diseases worldwide. Although the involvement of Helicobacter pylori infection as a class I human carcinogen for gastric cancer progression is accepted, it is not well known how gastritis progression to atrophy and stomach cancer occurs. In this case-control study, the potential link of H. pylori infection with alteration in the transcription of genes involved in DNA Damage Response pathways was investigated among the patients with gastritis. To measure the difference in the relative mRNA expression level of ATM, CHEK2, TP53, DCLRE1C, POLM, and XRCC4 genes between H. pylori-infected and non-infected patients, gastric biopsies of 30 H. pylori infected patients with moderate chronic gastritis and 30 non-infected patients with mild chronic gastritis were analyzed. Up-regulation of genes linked to non-homologous end joining (NHEJ) pathway (DCLRE1C, POLM, and XRCC) was shown in 40% (8.44 fold ± 13.91), 63.33% (15.72 fold ± 33.08) and 50% (9.99 fold ± 21.55), respectively, and also to DDR pathway (ATM, CHEK2, and TP53) in 33% (2.42 fold ± 3.17), 40% (2.86 fold ± 3.61) and 50% (5.00 fold ± 6.52), respectively. No correlation was detected between alteration in the transcription level of the studied genes and age or gender. Our results provide new data that may support the potential involvement of H. pylori infection in the activation of genes involved in DNA damage response, mainly through a non-homologous end-joining DNA repair system that might be linked to mutagenesis in the pre-cancerous gastric tissue.

Machine learning and single-cell sequencing reveal the potential regulatory factors of mitochondrial autophagy in the progression of gastric cancer.

As an important regulatory mechanism to remove damaged mitochondria and maintain the balance between internal and external cells, mitochondrial autophagy plays a key role in the progression and treatment of cancer Onishi (EMBO J 40(3): e104705, 2021). The purpose of this study is to comprehensively analyze the role of mitochondrial autophagy-related genes in the progression of gastric cancer (GC) by RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq). GSE26942, GSE54129,GSE66229,GSE183904 and other data sets were obtained by GEO databases. Using support vector machine recursive feature elimination (SVM-RVF) algorithm and random forest algorithm, the mitochondrial autophagy-related genes related to gastric cancer were obtained, respectively. After that, the model was constructed and the inflammatory factors, immune score and immune cell infiltration were analyzed. Furthermore, according to the scRNA-seq data of 28,836 cells from 13 GC samples, 18 cell clusters and 7 cell types were identified by scRNA-seq analysis. The expression level and signal pathway of related genes were verified by cell communication analysis. Finally, the regulatory network of cells was analyzed by SCENIC. MAP1LC3B, PGAW5, PINK1, TOMM40 and UBC are identified as key genes through machine learning algorithms. CXCL12-CXCR4, LGALS9-CD44, LGALS9-CD45 and MIF (CD74 + CD44) pathways may play an important role in endothelial cells with high score scores of T cells and monocytes in tumor environment. CEBPB, ETS1, GATA2, MATB, SPl1 and XBP1 were identified as candidate TF with specific regulatory expression in the GC cell cluster. The results of this study will provide implications for the study of the mechanism, diagnosis and treatment of mitochondrial autophagy in GC.

Immune response of silver pomfret (Pampus argenteus) to Photobacterium damselae subsp. Damselae: Virulence factors might induce immune escape by damaging phagosome

Photobacterium damselae subsp. damselae (PDD) is a dangerous bacterial disease that affects silver pomfret (Pampus argenteus) and its main virulence factors are pore-forming toxins. In this study, a highly pathogenic strain was obtained from naturally infected silver pomfret and was introduced into healthy fish for experimentation. Liver, gill, kidney and spleen samples were collected at 0, 24, 48, 72 and 96 h. Histopathological evaluations of these tissues, via HE staining, showed multi-organ bleeding, inflammatory infiltration and histopathocyte vacuolation as the main pathological changes. The levels of AKP, ACP, LZM, SOD, GSH and CAT in serum also displayed an increase following infection. Transcriptome sequencing of liver, kidney and spleen was performed using samples 96 h post-infection. The analysis of the resulting 770,878,120 clean reads collectively assembled into 89,310 unigenes. The WGCNA analysis demonstrated enrichment of phagosome and cytokine-cytokine receptor interaction in the liver, drug metabolism-cytochrome P450 in the kidney, and MAPK signaling pathway and other signaling pathways in the spleen. DEGs related to immune and immune-related pathways, such as Phagosome, Autophagy-animal and Glycerolipid metabolism, were significantly enriched. Selected key genes from these KEGG pathways were examined using RT-qPCR. The expression level of autophagy related genes (pi3k, bcl2) increased after infection, while the gene associated with MAPK and apoptosis (Caspase 9, mapk4) significantly increased after 72 h infection. The expression of phagosome related genes (atp6v1f, ctsl) increased initially, but later decreased. The genes related to innate immunity (ccl4, il15) were up-regulated, while those related to acquired immunity (mhc2a, mhc2b) showed a downward trend. Lysosome-related genes (gilta, giltb, cftr, c-type lectin, m6pra and m6prb) were up-regulated in liver and spleen and down-regulated in kidney and gill. The data obtained illustrated that PDD activated the immune defenses of the fish, increasing metabolic expenditure, but that the pore-forming toxins released by PDD could destroy the phagosome membrane and help the bacteria escape, which could disturb antigen presentation and inhibit the activation of the acquired immunity. This study reveals the potential immune escape mechanism of PDD in the host for the first time and has the potential to aid in the development of anti-PDD drugs.

Molecular characterization and effects of the TGIF1 gene on proliferation and steroidogenesis in yak (Bos grunniens) granulosa cells

TG interaction factor 1 (TGIF1) plays a major role in transcriptional inhibition and suppression of TGF-β signaling, but its functional roles in granulosa cells (GCs) have not been elucidated; in particular, there is no information about the yak (Bos grunniens) TGIF1 gene. Therefore, the objectives of this study were to clone yak TGIF1 and investigate TGIF1 functions in yak GCs. RT‒PCR results showed that the coding region of yak TGIF1 is 759 bp and encodes 252 amino acids. Its nucleotide sequence showed 85.24–99.74% similarity to mouse, human, pig, goat and cattle homologous genes. To explore the functional roles of TGIF1, we studied proliferation, apoptosis, cell cycle progression, steroidogenesis and the expression levels of related genes in yak GCs transfected with small interfering RNA specific to TGIF1. The results showed that TGIF1 knockdown promoted proliferation and cell cycle progression and inhibited apoptosis and estradiol (E2) and progesterone (P4) production in cultured yak GCs. Conversely, TGIF1 overexpression inhibited proliferation and cell cycle progression and stimulated apoptosis and E2 and P4 production. In addition, these functional changes in yak GCs were observed parallel to the expression changes in genes involved in the cell cycle (PCNA, CDK2, CCND1, CCNE1, CDK4 and P53), apoptosis (BCL2, BAX and CASPASE3), and steroidogenesis (CYP11A1, 3β-HSD and StAR). In conclusion, TGIF1 was relatively conserved in the course of animal evolution. TGIF1 inhibited GC viability and stimulated apoptosis and the secretion of E2 and P4 by yak GCs. Our results will help to reveal the mechanism underlying yak follicular development and improve the reproductive efficiency of female yaks.

Functional Identification of ANR Gene in Apple (Malus halliana) Demonstrates It Reduces Saline-alkali Stress Tolerance.

As one of the major abiotic stresses restricting the development of global agriculture, saline-alkali stress can cause osmotic stress, ion poisoning, reactive oxygen species damage and high pH value damage, which seriously restricts the sustainable development of fruit industry. Therefore, it is of great significance to cultivate saline-alkali resistant apple rootstocks to improve the yield and quality of apple in China. Based on transcriptome data, MhANR (LOC114827797), which was significantly induced by saline-alkali stress, was cloned from Malus halliana. The physicochemical properties, evolutionary relationships and cis-acting elements were analyzed. Subsequently, the tolerance of MhANR overexpression in Arabidopsis thaliana, tobacco and apple calli to saline-alkali stress was verified by genetic transformation. Transgenic plants presented lower chla, chlb and proline contents, lower Superoxide dismutase (SOD), Peroxidase enzyme (POD) and Catalase enzyme (CAT) activities, and higher relative electrical conductivity (REC) compared to those in WT plants under saline-alkali stress. In addition, the expression levels of saline-alkali stress related genes in overexpressed apple calli also diaplayed lower values compared to WT calli, including antioxidant genes MhSOD and MhCAT, Na+ transporter genes MhCAX5, MhCAX5, MhSOS1, MhALT1, and H+ -ATPase genes MhAHA2 and MhAHA8, while the expression levels of K+ transporter genes MhSKOR and MhNHX4 displayed higher values. In conclusion, MhANR reduced the tolerance of Arabidopsis thaliana, tobacco and apple calli under saline-alkali stress by regulating osmoregulatory substances, Chlorophyll content, antioxidant enzyme activity and expression of saline-alkali stress-related genes, which provided a theoretical basis for cultivating apple rootstocks with effective saline-alkali stress tolerance.

Aquaporins Transcripts with Potential Prognostic Value in Pancreatic Cancer.

Pancreatic cancer is anticipated to be the second leading cause of cancer-related death by 2030. Aquaporins (AQPs), a family of water channel proteins, have been linked to carcinogenesis. The aim of this study was to determine AQP gene expression in pancreatic cancer tissues and to validate aquaporins as possible diagnosis and/or prognosis genes. The relative gene expression levels of AQP1, AQP3, AQP5, and AQP9 were analyzed using real-time quantitative PCR (RT-qPCR) in 24 paired pancreatic tumors and adjacent healthy tissues according to variables such as age, gender, and tumor invasiveness and aggressiveness. AQPs transcripts were detected in both healthy and tumor tissues. While AQP1 was downregulated in the tumor samples, AQP3 was particularly overexpressed in low-grade invasive tumors. Interestingly, most of the strong positive Pearson correlation coefficients found between AQPs in healthy tissues were lost when analyzing the tumor tissues, suggesting disruption of the coordinated AQP-gene expression in pancreatic cancer.