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In experiments, the distributions of mRNA or protein numbers in single cells are often fitted to the random telegraph model which includes synthesis and decay of mRNA or protein, and switching of the gene between active and inactive states. While commonly used, this model does not describe how fluctuations are influenced by crucial biological mechanisms such as feedback regulation, non-exponential gene inactivation durations, and multiple gene activation pathways. Here we investigate the dynamical properties of four relatively complex gene expression models by fitting their steady-state mRNA or protein number distributions to the simple telegraph model. We show that despite the underlying complex biological mechanisms, the telegraph model with three effective parameters can accurately capture the steady-state gene product distributions, as well as the conditional distributions in the active gene state, of the complex models. Some effective parameters are reliable and can reflect realistic dynamic behaviors of the complex models, while others may deviate significantly from their real values in the complex models. The effective parameters can also be applied to characterize the capability for a complex model to exhibit multimodality. Using additional information such as single-cell data at multiple time points, we provide an effective method of distinguishing the complex models from the telegraph model. Furthermore, using measurements under varying experimental conditions, we show that fitting the mRNA or protein number distributions to the telegraph model may even reveal the underlying gene regulation mechanisms of the complex models. The effectiveness of these methods is confirmed by analysis of single-cell data for E. coli and mammalian cells. All these results are robust with respect to cooperative transcriptional regulation and extrinsic noise. In particular, we find that faster relaxation speed to the steady state results in more precise parameter inference under large extrinsic noise., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Jiao et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Cervical cancer, as the second leading cause of death in women malignant tumor, is not optimistic about survival rate and late recurrence rate. RCAN3 has been reported to function in a variety of diseases, but its relationship with cervical cancer has not been reported. This study aimed to investigate whether RCAN3 contributes to the development of cervical cancer and its mechanism. RCAN3 expression was analyzed in 306 cervical cancer tissues and 13 normal healthy tissues from TCGA and GTEX databases. Kaplan-Meier analysis and Cox regression analysis were carried out to assess the potential function of RCAN3. Subsequently, the upstream regulatory miRNA of RCAN3 was predicted by bioinformatics and confirmed using dual luciferase reporter assay. CCK-8, colony formation assay, transwell assay were used for functional analysis of miR-145/RCAN3 axis in vitro. The results showed that RCAN3 was highly expressed in cervical cancer tissues, leading to poor prognosis, and could be used as a prognostic factor for cervical cancer. MiR-145 directly targeted RCAN3, which was lowly expressed in cervical cancer tissues and cell lines, and the higher the miR-145 expression, the longer the survival time of patients. Finally, from the functional experiments results we can see that miR-145 can inhibit the proliferation, migration and invasion of cervical cancer cells, but overexpression of RCAN3 can reverse miR-145-mediated inhibition. To sum up, miR-145/RCAN3 axis may serve as a potential therapeutic target to regulate the progression of cervical cancer., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Society for Biology of Reproduction & the Institute of Animal Reproduction and Food Research of Polish Academy of Sciences in Olsztyn. Published by Elsevier B.V. All rights reserved.)

Background: Saline-alkaline stress is a major abiotic stress that is harmful to plant growth worldwide. Two peach cultivars (GF677 and Maotao) display distinct phenotypes under saline-alkaline stress. The molecular mechanism explaining the differences between the two cultivars is still unclear., Results: In the present study, we systematically analysed the changes in GF677 and Maotao leaves upon saline-alkaline stress by using cytological and biochemical technologies as well as comparative transcriptome analysis. Transmission electron microscopy (TEM) observations showed that the structure of granum was dispersive in Maotao chloroplasts. The biochemical analysis revealed that POD activity and the contents of chlorophyll a and chlorophyll b, as well as iron, were notably decreased in Maotao. Comparative transcriptome analysis detected 881 genes with differential expression (including 294 upregulated and 587 downregulated) under the criteria of |log2 Ratio| ≥ 1 and FDR ≤0.01. Gene ontology (GO) analysis showed that all differentially expressed genes (DEGs) were grouped into 30 groups. MapMan annotation of DEGs showed that photosynthesis, antioxidation, ion metabolism, and WRKY TF were activated in GF677, while cell wall degradation, secondary metabolism, starch degradation, MYB TF, and bHLH TF were activated in Maotao. Several iron and stress-related TFs (ppa024966m, ppa010295m, ppa0271826m, ppa002645m, ppa010846m, ppa009439m, ppa008846m, and ppa007708m) were further discussed from a functional perspective based on the phylogenetic tree integration of other species homologues., Conclusions: According to the cytological and molecular differences between the two cultivars, we suggest that the integrity of chloroplast structure and the activation of photosynthesis as well as stress-related genes are crucial for saline-alkaline resistance in GF677. The results presented in this report provide a theoretical basis for cloning saline-alkaline tolerance genes and molecular breeding to improve saline-alkaline tolerance in peach.

Background: Up to 30-40% of Ewing sarcoma (EwS) patients with non-metastatic disease develop local or metastatic relapse within a time span of 2-10 years. This is in part caused by the absence of prognostic biomarkers that can identify high-risk patients and thus assign them to risk-adapted monitoring and treatment regimens. Since cancer stemness has been associated with tumour relapse and poor patient outcomes, we investigated in the current study the prognostic potential SOX2 (sex determining region Y box 2) - a major transcription factor involved in development and stemness - which was previously described to contribute to the undifferentiated phenotype of EwS., Methods: Two independent patient cohorts, one consisting of 189 retrospectively collected EwS tumours with corresponding mRNA expression data (test-cohort) and the other consisting of 141 prospectively collected formalin-fixed and paraffin-embedded resected tumours (validation and cohort), were employed to analyse SOX2 expression levels through DNA microarrays or immunohistochemistry, respectively, and to compare them with clinical parameters and patient outcomes. Two methods were employed to test the validity of the results at both the mRNA and protein levels., Findings: Both cohorts showed that only a subset of EwS patients (16-20%) expressed high SOX2 mRNA or protein levels, which significantly correlated with poor overall survival. Multivariate analyses of our validation-cohort revealed that high SOX2 expression represents a major risk-factor for poor survival (HR = 3·19; 95%CI 1·74-5·84; p < 0·01) that is independent from metastasis and other known clinical risk-factors at the time of diagnosis. Univariate analyses demonstrated that SOX2-high expression was correlated with tumour relapse (p = 0·002). The median first relapse was at 14·7 months (range: 3·5-180·7)., Interpretation: High SOX2 expression constitutes an independent prognostic biomarker for EwS patients with poor outcomes. This may help to identify patients with localised disease who are at high risk for tumour relapse within the first two years after diagnosis., Funding: The laboratory of T. G. P. Grünewald is supported by grants from the 'Verein zur Förderung von Wissenschaft und Forschung an der Medizinischen Fakultät der LMU München (WiFoMed)', by LMU Munich's Institutional Strategy LMUexcellent within the framework of the German Excellence Initiative, the 'Mehr LEBEN für krebskranke Kinder - Bettina-Bräu-Stiftung', the Walter Schulz Foundation, the Wilhelm Sander-Foundation (2016.167.1), the Friedrich-Baur foundation, the Matthias-Lackas foundation, the Barbara & Hubertus Trettner foundation, the Dr. Leopold & Carmen Ellinger foundation, the Gert & Susanna Mayer foundation, the Deutsche Forschungsgemeinschaft (DFG 391665916), and by the German Cancer Aid (DKH-111886 and DKH-70112257). J. Li was supported by a scholarship of the China Scholarship Council (CSC), J. Musa was supported by a scholarship of the Kind-Philipp foundation, and T. L. B. Hölting by a scholarship of the German Cancer Aid. M. F. Orth and M. M. L. Knott were supported by scholarships of the German National Academic Foundation. G. Sannino was supported by a scholarship from the Fritz-Thyssen Foundation (FTF-40.15.0.030MN). The work of U. Dirksen is supported by grants from the German Cancer Aid (DKH-108128, DKH-70112018, and DKH-70113419), the ERA-Net-TRANSCAN consortium (project number 01KT1310), and Euro Ewing Consortium (EEC, project number EU-FP7 602,856), both funded under the European Commission Seventh Framework Program FP7-HEALTH (http://cordis.europa.eu/), the Barbara & Hubertus Trettner foundation, and the Gert & Susanna Mayer foundation. G. Hardiman was supported by grants from the National Science Foundation (SC EPSCoR) and National Institutes of Health (U01-DA045300). The laboratory of J. Alonso was supported by Instituto de Salud Carlos III (PI12/00816; PI16CIII/00026); Asociación Pablo Ugarte (TPY-M 1149/13; TRPV 205/18), ASION (TVP 141/17), Fundación Sonrisa de Alex & Todos somos Iván (TVP 1324/15)., (Copyright © 2019 The Author(s). Published by Elsevier B.V. All rights reserved.)

Background: More than a dozen of fungal immunomodulatory proteins (FIPs) have been identified to date, most of which are from Ganoderma species. However, little is known about the similarities and differences between different Ganoderma FIPs' bioactivities. In the current study, two FIP genes termed FIP-gap1 and FIP-gap2 from G. applanatum, along with LZ-8 and FIP-gsi, another two representative Ganoderma FIP genes from G. lucidum and G. sinense were functionally expressed in Pichia. Subsequently, bioactivities of four recombinant Ganoderma FIPs were demonstrated and compared., Results: All the four Ganoderma FIP genes could be effectively expressed in P. pastoris GS115 at expression levels ranging from 197.5 to 264.3 mg L - 1 and simply purified by one step chromatography using HisTrap™ FF prepack columns. Amino acid sequence analysis showed that they all possessed the FIP conserved fragments. The homologies of different Ganoderma FIPs were from 72.6 to 86.4%. In vitro haemagglutination exhibited that FIP-gap1, FIP-gsi and LZ-8 could agglutinate human, sheep and mouse red blood cells but FIP-gap2 agglutinated none. Besides, the immunomodulation activities of these Ganoderma FIPs were as: rFIP-gap2 > rFIP-gap1 > rLZ-8 and rFIP-gsi in terms of proliferation stimulation and cytokine induction on murine splenocytes. Additionally, the cytotoxic activity of different FIPs was: rFIP-gap1 > rLZ-8 > rFIP-gsi > rFIP-gap2, examined by their inhibition of three human carcinomas A549, Hela and MCF-7., Conclusions: Taken together, four typical Ganoderma FIP genes could be functionally expressed in P. pastoris, which might supply as feasible efficient resources for further study and application. Both similarities and differences were indeed observed between Ganoderma FIPs in their amino acid sequences and bioactivities. Comprehensively, rFIP-gaps from G. applanatum proved to be more effective in immunomodulation and cytotoxic assays in vitro than rLZ-8 (G. lucidum) and rFIP-gsi (G. sinense).

Strawberries were treated with different concentrations of ethanol vapor and then cut into four wedges and stored at 4 °C for 1 week. It was found that 4 mL/kg of ethanol was the optimal concentration to reduce the decrease of firmness and weight loss. Total phenolics content, total flavonoid and anthocyanin contents, antioxidant enzyme activities, and gene expression related to the antioxidant were elevated using the ethanol treatment. Ethanol vapor also suppressed microbial growth and promoted free radical (hydroxyl and DPPH) scavenging capacities and four kinds of esters and bioactive components in strawberry wedges. Moreover, ethanol enhanced antioxidant enzyme activities including superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX) by activating related gene expression. The results of our research indicate that ethanol vapor has potential application in preserving quality and improving antioxidant capacity of fresh-cut strawberries.

Long noncoding RNAs (lncRNAs) are involved in many aspects of cellular processes, including the antiviral immune response. To identify influenza A virus (IAV)-related lncRNAs, we performed RNA deep sequencing to compare the profiles of lncRNAs in A549 and HEK293T cells with or without IAV infection. We identified an IAV-upregulated lncRNA named lnc-ISG20 because it shares most of its sequence with ISG20. We found that lnc-ISG20 is an interferon-stimulated gene similar to ISG20. Overexpression of lnc-ISG20 inhibited IAV replication, while lnc-ISG20 knockdown favored viral replication, suggesting that lnc-ISG20 is inhibitory to IAV replication. Further study indicated that overexpression of lnc-ISG20 enhances ISG20 protein levels, while knockdown of lnc-ISG20 reduces ISG20 protein levels in A549 cells induced with poly(I·C) and Sendai virus. We demonstrated that lnc-ISG20 inhibits IAV replication in an ISG20-dependent manner. As lnc-ISG20 did not affect the mRNA level of ISG20, we postulated that lnc-ISG20 may function as endogenous RNA competing with ISG20 to enhance its translation. Indeed, we identified that microRNA 326 (miR-326) is a mutual microRNA for both ISG20 and lnc-ISG20 that targets the 3' untranslated region of ISG20 mRNA to inhibit its translation. We confirmed that lnc-ISG20 can bind miR-326, which in turn decreased the amount of miR-326 bound to ISG20 mRNA. In conclusion, we identified that the IAV-upregulated lnc-ISG20 is a novel interferon-stimulated gene that elicits its inhibitory effect on IAV replication by enhancing ISG20 expression. We demonstrated that lnc-ISG20 functions as a competitive endogenous RNA to bind miR-326 to reduce its inhibition of ISG20 translation. Our results revealed the mechanism by which lnc-ISG20 inhibits IAV replication. IMPORTANCE The replication of influenza A virus is regulated by host factors. However, the mechanisms by which lncRNAs regulate IAV infection are not well understood. We identified that lnc-ISG20 is upregulated during IAV infection and is also an interferon-stimulated gene. We demonstrated that lnc-ISG20 can enhance ISG20 expression, which in turn inhibits IAV replication. Our studies indicate that lnc-ISG20 functions as a competing endogenous RNA that binds miR-326 and reduces its inhibitory effect on ISG20. Taken together, our findings reveal the mechanistic details of lnc-ISG20 negatively regulating IAV replication. These findings indicate that lnc-ISG20 plays an important role during the host antiviral immune response., (Copyright © 2018 American Society for Microbiology.)

Estrogens play important roles in autoimmune thyroiditis, but it remains unknown which estrogen receptor (ER) subtype mediates the stimulatory effects. Herein we treated ovariectomized mice with ERα or ERβ selective agonist followed by thyroglobulin-immunization to induce experimental autoimmune thyroiditis (EAT), and observed the aggravation of EAT after diarylpropionitrile (DPN, ERβ selective agonist) administration. The mRNA levels of interleukin(IL)-17A, IL-21 and RORγt and percentages of T helper (Th) 17 cells were up-regulated in the splenocytes of DPN-treated mice. Activated ERβ was found directly binding to IL-17A and IL-21 gene promoters, and also indirectly promoting IL-21 and RORγt gene transcription through interaction with NF-κB. The expressions of co-stimulatory molecules were increased on antigen-presenting cells (APCs) after DPN administration. It suggests that ERβ is the predominant ER subtype responsible for EAT development, and its activation may enhance Th17-type responses through genomic pathways and alteration of APCs' activities., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)

High throughput mRNA expression profiling can be used to characterize the response of cell culture models to perturbations such as pharmacologic modulators and genetic perturbations. As profiling campaigns expand in scope, it is important to homogenize, summarize, and analyze the resulting data in a manner that captures significant biological signals in spite of various noise sources such as batch effects and stochastic variation. We used the L1000 platform for large-scale profiling of 978 representative genes across thousands of compound treatments. Here, a method is described that uses deep learning techniques to convert the expression changes of the landmark genes into a perturbation barcode that reveals important features of the underlying data, performing better than the raw data in revealing important biological insights. The barcode captures compound structure and target information, and predicts a compound's high throughput screening promiscuity, to a higher degree than the original data measurements, indicating that the approach uncovers underlying factors of the expression data that are otherwise entangled or masked by noise. Furthermore, we demonstrate that visualizations derived from the perturbation barcode can be used to more sensitively assign functions to unknown compounds through a guilt-by-association approach, which we use to predict and experimentally validate the activity of compounds on the MAPK pathway. The demonstrated application of deep metric learning to large-scale chemical genetics projects highlights the utility of this and related approaches to the extraction of insights and testable hypotheses from big, sometimes noisy data., Competing Interests: At the time of submission, all of the authors were paid employees of Merck & Co., Inc. (Kenilworth, NJ).

ADMATS-7 is known to play an important role in the pathogenesis of various diseases, including cartilaginous diseases. IL-17A is an inflammatory cytokine detected in degenerative disc tissues. However, the interplay between IL-17A and ADMATS-7 in human disc degeneration is still unknown. Samples collected from 50 patients were divided into three groups according to MRI degeneration grading system score. Immunohistochemistry, RT-PCR and western Blotting were used to investigate the expression of ADAMTS-7 in NP tissues. Furthermore, a rat disc degeneration model was established, and the expression level of ADAMTS-7 was assayed using immunohistochemistry, RT-PCR and western Blotting. The human NP cells were cultured in the presence and absence of IL-17A stimulation. RNA extracts were collected, and real-time PCR was performed to determine the expression of ADAMTS-7. Moreover, ADAMTS-7 concentrations were detected in human NP cell culture supernatants by ELISA. After culturing NP cells with IL-17A (with or without Etanercept), ADAMTS-7 levels were detected in each group. ADAMTS-7 expression was dramatically elevated in both human and rat degenerative NP tissues compared with normal controls. The RT-PCR and ELISA results revealed that IL-17A could enhance the production of ADAMTS-7, while ADAMTS-7 expression dramatically decreased in the IL-17A + Etanercept group in comparison to the IL-17A alone group. Our results indicate the presence of ADAMTS-7 in human NP cells and imply its potential role in disc degeneration. Additionally, our results indicate that IL-17A induced ADAMTS-7 expression via TNF-α, which may form a molecular axis in human NP cells.

Objectives: The prognosis of pancreatic cancer (PC) is poor and the pathogenesis of PC-associated diabetes is unknown. We investigated the possible expression of immunoglobulin G (IgG) in human pancreatic carcinomas and adjacent pancreatic islets to gain a better understanding of these diseases., Methods: We employed immunohistochemistry, Western Blot, real-time polymerase chain reaction, and in situ hybridization to examine IgG expression in PC tissues and adjacent islets with and without cancer-associated diabetes. The IgG mRNA and IgG synthesizing-related enzymes were examined in PC cell lines. The IgG expression and secretion were downregulated with specific small interfering RNA and antibody to IgG followed by flow cytometry to assess its effect on apoptosis of cultured PC cells., Results: The expression of IgG was detected in pancreatic carcinoma and adjacent islets. Small interfering RNA and antibody treatments induced apoptosis in PC cell lines. In the carcinoma tissue, the levels of IgG expression varied depending on the stages of the cancers with more malignant cancers expressing more IgG (P < 0.05). The IgG levels in cancer cells were also increased when the patients had diabetes or hyperglycemia (P < 0.05). In addition, the extent of IgG expression in the seemingly normal islet cells adjacent to the tumor varied in relation to the grade of cancer differentiation and distance to the cancer nests., Conclusions: (1) Immunoglobulin G was locally produced by PC cells and adjacent islet cells. (2) Immunoglobulin G may promote tumor growth by inhibiting cancer cell apoptosis. (3) Locally produced IgG might play a role in PC-associated diabetes.

Objective: To observe the effect of nourishing yin removing fire Chinese herbs (NYRF-CH) on the gene expression of hypothalamic growth hormone secretion peptide (Ghrelin) and its receptor growth hormone secretion peptide receptor 1alpha (GHSR1-alpha) at the puberty onset of danazol induced female precocious rats., Methods: Forty female SD rats were randomly divided into 4 groups, i.e., the normal group (N), the model group (M), the normal saline intervention group (NS), and the NYRFCH intervention group (NI), 10 in each group. 300 microg danazol was subcutaneously injected to all rats except those in the N group to prepare precocious rat model. NYRFCH and normal saline was respectively administered to rats in the NI and the NS group from the 15th day old for 7-10 days. No treatment was given to rats in the N group. Time of rats' vulva opening was recorded. Ovary index and uterus index were calculated. Peripheral blood levels of estradiol (E2), follicle stimulating hormone (FSH), and luteinizing hormone (LH), and hypothalamic contents of gonadotropin releasing hormone (GnRH) as well as the gene expression of hypothalamic Ghrelin and GHSR1-alpha were determined. Results Compared with the N group, the vulva opening time was advanced in the model group; peripheral blood levels of E2 and LH, uterus index, hypothalamic contents of GnRH increased; peripheral blood FSH levels and mRNA levels of hypothalamic Ghrelin and GHSR1-alpha decreased (P < 0.05, P < 0.01). Compared with the M group and the NS group, the vulva opening time was not advanced in the NI group; peripheral blood levels of E2 and LH, uterus index and hypothalamic contents of GnRH obviously decreased (P < 0.05, P < 0.01); mRNA levels of hypothalamic Ghrelin and GHSR1-alpha increased (all P < 0.01). But there was no statistical difference in the hypothalamic contents of Ghrelin, or the number and activity of GHSR1-alpha (P > 0.05)., Conclusion: NYRFCH had regulatory effect on regulating hypothalamic Ghrelin and GHSR1-alpha at gene transcription levels.

Background : Baryscapus dioryctriae (Chalcidodea: Eulophidae) is a parasitic wasp that parasitizes the pupae of many Pyralidae members and has been used as a biological control agent against Dioryctria pests of pinecones. Results: This B. dioryctriae assembly has a genome size of 485.5 Mb with a contig N50 of 2.17 Mb, and scaffolds were assembled onto six chromosomes using Hi-C analysis, significantly increasing the scaffold N50 to 91.17 Mb, with more than 96.13% of the assembled bases located on chromosomes, and an analysis revealed that 94.73% of the BUSCO gene set. A total of 54.82% (279.27 Mb) of the assembly was composed of repetitive sequences and 24,778 protein-coding genes were identified. Comparative genomic analysis demonstrated that the chemosensory perception, genetic material synthesis, and immune response pathways were primarily enriched in the expanded genes. Moreover, the functional characteristics of an odorant-binding protein (BdioOBP45) with ovipositor-biased expression identified from the expanded olfactory gene families were investigated by the fluorescence competitive binding and RNAi assays, revealing that BdioOBP45 primarily binds to the D. abietella-induced volatile compounds, suggesting that this expanded OBP is likely involved in locating female wasp hosts and highlighting a direction for future research. Conclusions: Taken together, this work not only provides new genomic sequences for the Hymenoptera systematics, but also the high-quality chromosome-level genome of B. dioryctriae offers a valuable foundation for studying the molecular, evolutionary, and parasitic processes of parasitic wasps. [ABSTRACT FROM AUTHOR]

Raspberry ketone accounts for the characteristic aroma of the raspberry fruit. In order to explore the genes involved in raspberry ketone synthesis, the transcriptome in fruit tissues of two red raspberry varieties "Polka" and "Orange legend", were sequenced and 24213 single genes were obtained. As the red raspberry fruit ripening, genes involved in flavonoid and anthocyanin synthesis were up-regulated, while those associated with lignin synthesis were down-regulated. A gene (RinPKS4) highly related to raspberry ketone synthesis was identified by transcriptome analysis, and RinPKS4 gene was over-expressed in raspberry in order to further understand the function of RinPKS4 gene in raspberry ketone synthesis. The results showed that the gene expression level of RinPKS4 in the leaf tissues of a transgenic lines increased by about 4-fold and the content of raspberry ketone increased by 42.64% compared with the wide type. This study lays a theoretical foundation for further study on the synthesis and regulation of raspberry ketone in red raspberry. [ABSTRACT FROM AUTHOR]

Background: The activity and number of immune cells in the tumor microenvironment are closely related to the overall survival of patients with hepatocellular carcinoma (HCC). The sex-determining region Y-box 4 (SOX4) gene is abnormally expressed in various tumor tissues and is critical for tumor development. However, the correlation between SOX4 expression in HCC and tumor immunity is unclear. Methods: SOX4 expression was explored using data from The Cancer Genome Atlas, and UALCAN databases. Real-time reverse transcription quantitative and western blotting were used to analyze SOX4 expression in several liver cancer cell lines. Additionally, correlations among SOX4 expression, cancer immune characteristics, and infiltrated immune cell gene marker sets in patients with HCC were analyzed using data from the Tumor Immune Estimation Resource, Gene Expression Profiling Interactive Analysis, and Tumor-Immune System Interactions databases. Moreover, we evaluated SOX4 expression in HCC tissues and the correlation of SOX4 expression with survival rate. Subsequently, noncoding RNAs (ncRNAs) responsible for SOX4 overexpression were identified using expression, correlation, and survival analyses. Results: SOX4 expression was significantly upregulated in HCC and correlated with a poor prognosis. Additionally, SOX4 upregulation in HCC positively correlated with immune cell infiltration, several biomarkers of immune cells, and immune checkpoint expression. Finally, the MCM3AP-AS1/hsa-miR-204-5p axis was identified as the most likely upstream ncRNA-related pathway for SOX4 in HCC. These results indicated that ncRNA-mediated upregulation of SOX4 correlated with the immune infiltration level and poor prognosis in HCC. Our findings provide new directions for the development of novel immunotherapeutic targets for HCC. [ABSTRACT FROM AUTHOR]

The plerocercoid larva of Spirometra mansoni can cause a parasitic zoonosis—sparganosis. Malate dehydrogenase (MDH) plays a very important role in the life activities of parasites. However, little is known about the MDH family in S. mansoni. We identified eight new MDH members in S. mansoni in this study. Clustering analysis divided SmMDHs into two groups and revealed patterns similar to the conserved motif organization. RT–qPCR suggested that five MDHs were highly expressed in the mature proglottid and that three MDHs were highly expressed in the gravid proglottid. Phylogenetic analysis revealed that SmMDHs contain both conserved family members and members in the process of further diversification. rSmMDH has an NAD binding domain, a dimer interface and a substrate binding domain. Natural SmMDH was immunolocalized in the tissues and follicles around the uterus in the mature or gravid proglottid and eggshells. The maximum forward and reverse reaction activities of rSmMDH were observed at pH 8.5 and 9.0, respectively. The optimum temperature for enzyme activity was 37 °C in the forward reaction and 40 °C in the reverse reaction. These results lay the foundation for studying the molecular functions and mechanisms of MDHs in S. mansoni and related taxa. [ABSTRACT FROM AUTHOR]

Simple Summary: Zinc (Zn) is an essential microelement for normal poultry production. This study determined the microbiota, intestinal morphology and immune status after supplementation with two different doses of Zn in pigeons. The results revealed that Zn can increase the average daily gain and ileal gene expression and improve the serum immune indices and feces microbiota profiles. Our findings provides scientific basis for the application of Zn in pigeon production. We aimed to explore the effects of two different doses of Zn on the fecal microbiota in pigeons and the correlation between these effects and intestinal immune status. Zn doses affected pigeon growth performance, and pigeons in the T60 (60 mg/kg Zn) and T90 (90 mg/kg Zn) groups exhibited higher villus height and crypt depth in duodenum and ileum compared to the control group, respectively. Supplementation with Zn increased the expression of the IL8, CD798, TJP and NKTR genes (p < 0.05), while enhancing serum immunoglobulin (Ig) G, IgM, and IgA concentrations compared to the control pigeons (p < 0.05). T60 treatment reduced relative Actinobacteriota abundance, while Lactobacillus spp. abundance was highest in the T90 group compared to the two other groups. The core functional genera significantly associated with immune indices in these pigeons were Rhodococcus erythropolis and Lactobacillus ponti. Our findings will help facilitate the application of dietary Zn intake in pig production. [ABSTRACT FROM AUTHOR]

The prevalence of papillary thyroid cancer (PTC) has been rising in recent years. Despite its relatively low mortality, PTC frequently metastasizes to lymph nodes and often recurs, posing significant health and economic burdens. The role of iodine in the pathogenesis and advancement of thyroid cancer remains poorly understood. Circular RNAs (circRNAs) are recognized to function as competing endogenous RNAs (ceRNAs) that modulate gene expression and play a role in various cancer stages. Consequently, this research aimed to elucidate the mechanism by which circRNA influences the impact of iodine on PTC. Our research indicates that high iodine levels can exacerbate the malignancy of PTC via the circ_0004851/miR-296-3p/FGF11 axis. These insights into iodine's biological role in PTC and the association of circRNA with the disease could pave the way for novel biomarkers and potentially effective therapeutic strategies to mitigate PTC progression. [ABSTRACT FROM AUTHOR]

Background and purpose: Silent information regulator proteins (sirtuins, SIRT) are a class III histone deacetylases with nicotinamide adenine dinucleotide (NAD+) as coenzyme. YME1 like 1 ATPase (YME1L1) is essential for the maintenance of mitochondrial morphology, function and plasticity. Optic atrophy 1 (OPA1) mainly mediates mitochondrial fusion. The aim of this study was to explore the expression of SIRT3 in the endocrine resistance of breast cancer, the relationship between SIRT3 and YME1L1 and OPA1, and the mechanism of SIRT3 in the endocrine resistance of breast cancer. Methods: 4-hydroxytamoxifen was used to induce tamoxifen-resistant MCF-7/TAM cells. cell counting kit-8 (CCK-8) was used to detect cell proliferation and verify drug resistance. The mitochondrial morphology was observed by transmission electron microscopy (TEM) and immunofluorescence staining. The expressions of SIRT3 and OPA1 were detected by real-time fluorescent quantitative polymerase chain reaction (RTFQ-PCR) and Western blot. JC-1 staining was used to detect mitochondrial membrane potential, and dihydroethidium (DHE) staining was used to detect reactive oxygen species (ROS) to verify mitochondrial function. SIRT3 was knocked down in drug-resistant cells by RNA interference, and SIRT3 and YME1L1 wild type (WT), simulated acetylation state mutant (MUT K237Q), and simulated deacetylation state mutant (MUT K237R) were overexpressed in parental cells by overexpression plasmid. Immunoprecipitation assay (IP) and immunofluorescence (IF) were used to verify the interaction between SIRT3 and YME1L1. Results: RTFQ-PCR and Western blot results showed that SIRT3 gene expression and protein level was significantly higher in drug-resistant cells than in parental cells. Overexpression of SIRT3 in parental cells decreased the sensitivity of breast cancer cells to tamoxifen. Knockdown of SIRT3 in drug-resistant cells enhanced the sensitivity of drug-resistant cells to tamoxifen. DHE staining showed that the ROS level was lower in tamoxifen resistant cells than in parental cells at the same concentration. Transmission electron microscopy and fluorescence staining showed that the mitochondria of the drug-resistant cells were elongated compared with the parental cells. Western blot results showed that the expression level of L-OPA1 protein was higher in drug-resistant cells than in parental cells. Overexpression of SIRT3 in the parental cells resulted in enhanced mitochondrial function and longer mitochondrial morphology compared with the control cells. Western blot showed that the expression of L-OPA1 was upregulated. When SIRT3 was knocked down in drug-resistant cells, the opposite result was obtained. We further verified how SIRT3 regulated OPA1 protein, affected the morphology and function of mitochondria, and promoted drug resistance of breast cancer. Overexpression of YME1L1 (wild-type and mutant plasmids) in parental cells showed that overexpression of YME1L1 in the simulated deacetylation state resulted in similar results as overexpression of SIRT3, and overexpression of YME1L1 in the acetylated state resulted in similar results as knockdown of SIRT3. IP assay confirmed the interaction between SIRT3 and YME1L1 in breast cancer cells. The acetylation level of YME1L1 was different at different SIRT3 expression levels. IF assay showed that YME1L1 was co-localized with SIRT3 in MCF-7 cells. Conclusion: SIRT3 is highly expressed in tamoxifen-resistant breast cancer cells. SIRT3 upregulates L-OPA1 expression by deacetylating YME1L1, thereby promoting mitochondrial fusion and enhancing mitochondrial function, and promotes tamoxifen resistance in breast cancer. [ABSTRACT FROM AUTHOR]

Objective To investigate the effect of MAPK on intestinal obstruction during pregnancy. Methods A total of 105 SPF Wistar rats (female = 70 and male = 35) were selected. After placing all the rats in the same cage, 33 female rats were pregnant, and 8 rats were assigned to the control group and the other 25 rats were used to established bowel obstruction model. A total of 24 rats were successfully modelled, which were divided into model group (n = 8), up-regulation group (n = 8), and down-regulation group (n = 8). Results Compared with the model group, MAPK expression, VIP, GAS, TNF-α, IL-6 levels, TLR4, Myd88, NF-κB mRNA were increased and MOT, IL-4, IL-10 levels were decreased in up-regulation group; MAPK expression, VIP, GAS, TNF-α, IL-6 levels, TLR4, Myd88, NF-κB mRNA were decreased and MOT, IL-4, IL-10 levels were increased in down-regulation group (P < 0.05). Conclusion MAPK down-regulation reduced inflammatory response and improved bowel obstruction in pregnancy, and the mechanism may be related to the inhibition of TLR4/Myd88/NF-κB pathway. [ABSTRACT FROM AUTHOR]

Background: The circadian clock, also known as the circadian rhythm, is responsible for predicting daily and seasonal changes in the environment, and adjusting various physiological and developmental processes to the appropriate times during plant growth and development. The circadian clock controls the expression of the Lhcb gene, which encodes the chlorophyll a/b binding protein. However, the roles of the Lhcb gene in tea plant remain unclear. Results: In this study, a total of 16 CsLhcb genes were identified based on the tea plant genome, which were distributed on 8 chromosomes of the tea plant. The promoter regions of CsLhcb genes have a variety of cis-acting elements including hormonal, abiotic stress responses and light response elements. The CsLhcb family genes are involved in the light response process in tea plant. The photosynthetic parameter of tea leaves showed rhythmic changes during the two photoperiod periods (48 h). Stomata are basically open during the day and closed at night. Real-time quantitative PCR results showed that most of the CsLhcb family genes were highly expressed during the day, but were less expressed at night. Conclusions: Results indicated that CsLhcb genes were involved in the circadian clock process of tea plant, it also provided potential references for further understanding of the function of CsLhcb gene family in tea plant. [ABSTRACT FROM AUTHOR]

Post-transcriptional regulation by small RNAs and post-translational modifications (PTM) such as lysine acetylation play fundamental roles in physiological circuits, offering rapid responses to environmental signals with low energy consumption. Yet, the interplay between these regulatory systems remains underexplored. Here, we unveil the cross-talk between sRNAs and lysine acetylation in Streptococcus mutans, a primary cariogenic pathogen known for its potent acidogenic virulence. Through systematic overexpression of sRNAs in S. mutans, we identified sRNA SmsR1 as a critical player in modulating acidogenicity, a key cariogenic virulence feature in S. mutans. Furthermore, combined with the analysis of predicted target mRNA and transcriptome results, potential target genes were identified and experimentally verified. A direct interaction between SmsR1 and 5'-UTR region of pdhC gene was determined by in vitro binding assays. Importantly, we found that overexpression of SmsR1 reduced the expression of pdhC mRNA and increased the intracellular concentration of acetyl-CoA, resulting in global changes in protein acetylation levels. This was verified by acetyl-proteomics in S. mutans, along with an increase in acetylation level and decreased activity of LDH. Our study unravels a novel regulatory paradigm where sRNA bridges post-transcriptional regulation with post-translational modification, underscoring bacterial adeptness in fine-tuning responses to environmental stress. Author summary: Post-transcriptional regulation and post-translational modification are widely present in physiological circuits due to their low energy consumption and rapid response to the environment. sRNA is an important post-transcriptional regulatory factor in bacterial response to environmental stress, and bacteria also use sRNA as a key signal to control multicellular behaviors such as biofilm formation and quorum sensing to regulate virulence. S. mutans is an intractable cariogenic pathogen, but the role of sRNA in S. mutans is poorly understood. Here, we elucidated the virulence regulation and mechanism of sRNA SmsR1 in S. mutans by means of transcriptomics, acetyl-proteomics and animal models, and found its relationship with protein acetylation (post-translational modification), and a new role of sRNA physiological regulatory network was shown. This study presents an innovative perspective that a sRNA in S. mutans is involved in the correlation between post-transcriptional regulation and post-translational modification. [ABSTRACT FROM AUTHOR]

Rheumatoid arthritis (RA) and primary Sjögren's syndrome (pSS) are the most common systemic autoimmune diseases, and they are increasingly being recognized as occurring in the same patient population. These two diseases share several clinical features and laboratory parameters, but the exact mechanism of their co-pathogenesis remains unclear. The intention of this study was to investigate the common molecular mechanisms involved in RA and pSS using integrated bioinformatic analysis. RNA-seq data for RA and pSS were picked up from the Gene Expression Omnibus (GEO) database. Co-expression genes linked with RA and pSS were recognized using weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) analysis. Then, we screened two public disease–gene interaction databases (GeneCards and Comparative Toxicogenomics Database) for common targets associated with RA and pSS. The DGIdb database was used to predict therapeutic drugs for RA and pSS. The Human microRNA Disease Database (HMDD) was used to screen out the common microRNAs associated with RA and pSS. Finally, a common miRNA–gene network was created using Cytoscape. Four hub genes (CXCL10, GZMA, ITGA4, and PSMB9) were obtained from the intersection of common genes from WGCNA, differential gene analysis and public databases. Twenty-four drugs corresponding to hub gene targets were predicted in the DGIdb database. Among the 24 drugs, five drugs had already been reported for the treatment of RA and pSS. Other drugs, such as bortezomib, carfilzomib, oprozomib, cyclosporine and zidovudine, may be ideal drugs for the future treatment of RA patients with pSS. According to the miRNA–gene network, hsa-mir-21 may play a significant role in the mechanisms shared by RA and pSS. In conclusion, we identified commom targets as potential biomarkers in RA and pSS from publicly available databases and predicted potential drugs based on the targets. A new understanding of the molecular mechanisms associated with RA and pSS is provided according to the miRNA–gene network. [ABSTRACT FROM AUTHOR]

Polymerase chain reaction (PCR) is a widely used technique in gene expression analysis, diagnostics, and various molecular biology applications. However, the accuracy and sensitivity of PCR can be compromised by primer–template mismatches, potentially leading to erroneous results. In this study, we strategically designed 111 primer–template combinations with varying numbers, types, and locations of mismatches to meticulously assess their impact on qPCR performance while two distinctly different types of DNA polymerases were used. Notably, when a single-nucleotide mismatch occurred at the 3' end of the primer, we observed significant decreases in the analytical sensitivity (0–4%) with Invitrogen™ Platinum™ Taq DNA Polymerase High Fidelity, while the analytical sensitivity remained unchanged with Takara Ex Taq Hot Start Version DNA Polymerase. Leveraging these findings, we designed a highly specific PCR to amplify Babesia while effectively avoiding the genetically close Theileria. Through elucidating the critical interplay between types of DNA polymerases and primer–template mismatches, this research provides valuable insights for improving PCR accuracy and performance. These findings have important implications for researchers aiming to achieve robust qPCR results in various molecular biology applications. [ABSTRACT FROM AUTHOR]

Macaques (genus Macaca) are the most widely distributed non‐human primates, and their evolutionary history, gene expression profiles, and genetic differences have been extensively studied. However, the DNA methylomes of macaque species are not available in public databases, which hampers understanding of epigenetic differences among macaque species. Epigenetic modifications can potentially affect development, physiology, behavior, and evolution. Here, we investigated the methylation patterns of the Tibetan macaque (M. thibetana; TM), Chinese rhesus macaque (M. mulatta lasiota; CR), and crab‐eating macaque (M. fascicularis; CE) through whole‐genome bisulfite sequencing from peripheral blood. We compared genome‐wide methylation site information for the three species. We identified 12,128 (CR vs. CE), 59,165 (CR vs. TM), and 39,751 (CE vs. TM) differentially methylated regions (DMRs) in the three macaques. Furthermore, we obtained the differentially expressed genes (DEGs) among the three macaque species. The differences between CR and CE were smaller at both the methylome and transcriptome levels than compared with TM (CR vs. TM and CE vs. TM). We also found a change in the density of single nucleotide mutations in DMRs relative to their flanking regions, indicating a potential mechanism through which genomic alterations may modulate methylation landscapes, thereby influencing the transcriptome. Functional enrichment analyses showed the DMR‐related genes were enriched in developmental processes and neurological functions, such as the growth hormone‐related pathway, insulin secretion pathway, thyroid hormone synthesis pathway, morphine addiction, and GABAergic synapses. These differences may be associated with variations in physiology and habitat among the macaques. Our study provides one of the first genome‐wide comparisons of genetic, gene expression, and epigenetic variations across different macaques. Our results should facilitate further research on comparative genomic and genetic differences in macaque species. [ABSTRACT FROM AUTHOR]

Eosinophils are a group of granulocytes well known for their capacity to protect the host from parasites and regulate immune function. Diverse biological roles for eosinophils have been increasingly identified, but the developmental pattern and regulation of the eosinophil lineage remain largely unknown. Herein, we utilize the zebrafish model to analyze eosinophilic cell differentiation, distribution, and regulation. By identifying eslec as an eosinophil lineage-specific marker, we establish a Tg(eslec:eGFP) reporter line, which specifically labeled cells of the eosinophil lineage from early life through adulthood. Spatial-temporal analysis of eslec+ cells demonstrates their organ distribution from larval stage to adulthood. By single-cell RNA-Seq analysis, we decipher the eosinophil lineage cells from lineage-committed progenitors to mature eosinophils. Through further genetic analysis, we demonstrate the role of Cebp1 in balancing neutrophil and eosinophil lineages, and a Cebp1-Cebpβ transcriptional axis that regulates the commitment and differentiation of the eosinophil lineage. Cross-species functional comparisons reveals that zebrafish Cebp1 is the functional orthologue of human C/EBPεP27 in suppressing eosinophilopoiesis. Our study characterizes eosinophil development in multiple dimensions including spatial-temporal patterns, expression profiles, and genetic regulators, providing for a better understanding of eosinophilopoiesis. Eosinophils are innate immune cells critical for protection from parasites, but their developmental origin remains under studied. Here they analyze development of eosinophils in zebrafish and find that eosinophilic lineage commitment and differentiation are regulated by the Cebp1-Cebpβ axis. [ABSTRACT FROM AUTHOR]

SUMMARY: Chromatin in eukaryotes folds into a complex three‐dimensional (3D) structure that is essential for controlling gene expression and cellular function and is dynamically regulated in biological processes. Studies on plant phosphorus signaling have concentrated on single genes and gene interactions. It is critical to expand the existing signaling pathway in terms of its 3D structure. In this study, low‐Pi treatment led to greater chromatin volume. Furthermore, low‐Pi stress increased the insulation score and the number of TAD‐like domains, but the effects on the A/B compartment were not obvious. The methylation levels of target sites (hereafter as RdDM levels) peaked at specific TAD‐like boundaries, whereas RdDM peak levels at conserved TAD‐like boundaries shifted and decreased sharply. The distribution pattern of RdDM sites originating from the Helitron transposons matched that of genome‐wide RdDM sites near TAD‐like boundaries. RdDM pathway genes were upregulated in the middle or early stages and downregulated in the later stages under low‐Pi conditions. The RdDM pathway mutant ddm1a showed increased tolerance to low‐Pi stress, with shortened and thickened roots contributing to higher Pi uptake from the shallow soil layer. ChIP‐seq results revealed that ZmDDM1A could bind to Pi‐ and root development‐related genes. Strong associations were found between interacting genes in significantly different chromatin‐interaction regions and root traits. These findings not only expand the mechanisms by which plants respond to low‐Pi stress through the RdDM pathway but also offer a crucial framework for the analysis of biological issues using 3D genomics. Significance Statement: This study is a pioneering study in the field of plant nutrient utilization. For the first time, this study discovered that the plant's low‐Pi response was closely linked to the RdDM pathway and chromatin spatial structure, and the low‐Pi response was validated by a mutant of chromatin remodeling gene ZmDDM1a (RdDM pathway gene). In addition, the results of ChIP‐seq and multi‐point GWAS for 2 years revealed the interaction of a large number of candidate genes related to Pi and roots with ZmDDM1A. We believe that the results presented in this article will have a great influence in this field and will be concerned and cited by many researchers. [ABSTRACT FROM AUTHOR]

The loquat (Eriobotrya japonica L.) is a special evergreen tree, and its fruit is of high medical and health value as well as having stable market demand around the world. In recent years, research on the accumulation of nutrients in loquat fruit, such as carotenoids, flavonoids, and terpenoids, has become a hotspot. The SBP-box gene family encodes transcription factors involved in plant growth and development. However, there has been no report on the SBP-box gene family in the loquat genome and their functions in carotenoid biosynthesis and fruit ripening. In this study, we identified 28 EjSBP genes in the loquat genome, which were unevenly distributed on 12 chromosomes. We also systematically investigated the phylogenetic relationship, collinearity, gene structure, conserved motifs, and cis-elements of EjSBP proteins. Most EjSBP genes showed high expression in the root, stem, leaf, and inflorescence, while only five EjSBP genes were highly expressed in the fruit. Gene expression analysis revealed eight differentially expressed EjSBP genes between yellow- and white-fleshed fruits, suggesting that the EjSBP genes play important roles in loquat fruit development at the breaker stage. Notably, EjSBP01 and EjSBP19 exhibited completely opposite expression patterns between white- and yellow-fleshed fruits during fruit development, and showed a close relationship with SlCnr involved in carotenoid biosynthesis and fruit ripening, indicating that these two genes may participate in the synthesis and accumulation of carotenoids in loquat fruit. In summary, this study provides comprehensive information about the SBP-box gene family in the loquat, and identified two EjSBP genes as candidates involved in carotenoid synthesis and accumulation during loquat fruit development. [ABSTRACT FROM AUTHOR]

[Objective] Transient gene expression is a rapid and effective cellular and genetic technique. It is particularly valuable for swiftly assessing gene function, with wide-ranging applications in plant research. To fully understand the application of genetic engineering in the field of plant secondary metabolite research and achieve research feedback teaching, a comprehensive experiment concerning transient gene expression and its impacts on the accumulation of secondary metabolites in plants was designed. [Methods]Compared with the model plants used in transient expression assay traditionally, Nelumbo nucifera(lotus), a non-model-horticultural plant, was selected as the research object. Lotus is a perennial aquatic plant that is edible, has extremely important medicinal value and contains a large amount of secondary metabolites such as alkaloids and flavonoids, making it a very suitable material for studying the biosynthesis of secondary metabolites and their regulationin plants. In this study, transcription factors NnWRKY70 and NnMYB5 involved in lotus alkaloid biosynthesis and anthocyan in accumulation were cloned, and the full-length coding sequences of NnWRKY70 and NnMYB5 were inserted into the binary vector pMDC83 to generate pMDC83-NnWRKY70 and pMDC83-NnMYB5 constructs. Transient overexpressions of NnWRKY70 and NnMYB5 were conducted in the lotus petals of the 'Qiuxing' and 'Zhigaowushang' varieties 3 days before blooming. Agrobacterium GV3101 strain carrying the pMDC83- NnWRKY70 and pMDC83-NnMYB5 vectors were infiltrated on the lower side of petals using a needleless syringe. The lotus petals were sampled 2 days after infiltration for subsequent gene expression analysis using real-time quantitative polymerase chain reaction, and the alkaloid content in the petals was quantitatively measured by high-performance liquid chromatography (HPLC). Also, the accumulation of anthocyanins in the petals was qualitatively observed. [Results]The results showed that the expression level of NnWRKY70 in the 'Qiuxing' petals after transient transformation increased significantly, 2.75 times higher than that of the control, indicating the successful transient expression of NnWRKY70 in the petals. The HPLC detection indicated that the overexpression of NnWRKY70 promoted a significant increase in total alkaloids in petals at 2.25 times higher than the control, suggesting that the NnWRKY70 transcription factor might play a positive role in the regulation of alkaloid biosynthesis in lotus. Similarly, the transient expression of NnMYB5 in the 'Zhigaowushang' petals led to the upregulation of this gene and the anthocyanin accumulation in the white lotus petals, demonstrating the role of NnMYB5 transcription factor in the control of petal coloration. [Conclusions]This experiment achieved a breakthrough in transient gene expression on lotus petals and preliminarily verified the function of the transcription factors NnWRKY70 and NnMYB5 in regulating the biosynthesis of secondary metabolites in aquatic plants. The introduction of this experiment to the experimental teaching system for plant biology and physiology courses was successful, enabling students to better understand and master the principle of instantaneous gene expression and its application in plant research and fully stimulating students' enthusiasm for scientific research and higher-order thinking. Moreover, this experimental design is an expansion and improvement of previous experiments in plant physiology, thus effectively improving the quality and effectiveness of experimental teaching and laying the foundation for cultivating comprehensive and high-quality professionals in biology. [ABSTRACT FROM AUTHOR]

Pseudomonas aeruginosa (P. aeruginosa) can cause severe acute infections, including pneumonia and sepsis, and cause chronic infections, commonly in patients with structural respiratory diseases. However, the molecular and pathophysiological mechanisms of P. aeruginosa respiratory infection are largely unknown. Here, we performed assays for transposase-accessible chromatin using sequencing (ATAC-seq), transcriptomics, and quantitative mass spectrometry-based proteomics and ubiquitin-proteomics in P. aeruginosa-infected lung tissues for multi-omics analysis, while ATAC-seq and transcriptomics were also examined in P. aeruginosa-infected mouse macrophages. To identify the pivotal factors that are involved in host immune defense, we integrated chromatin accessibility and gene expression to investigate molecular changes in P. aeruginosa-infected lung tissues combined with proteomics and ubiquitin-proteomics. Our multi-omics investigation discovered a significant concordance for innate immunological and inflammatory responses following P. aeruginosa infection between hosts and alveolar macrophages. Furthermore, we discovered that multi-omics changes in pioneer factors Stat1 and Stat3 play a crucial role in the immunological regulation of P. aeruginosa infection and that their downstream molecules (e.g., Fas) may be implicated in both immunosuppressive and inflammation-promoting processes. Taken together, these findings indicate that transcription factors and their downstream signaling molecules play a critical role in the mobilization and rebalancing of the host immune response against P. aeruginosa infection and may serve as potential targets for bacterial infections and inflammatory diseases, providing insights and resources for omics analyses. Author summary: Pseudomonas aeruginosa (P. aeruginosa) is a gram-negative aerobic pathogenic bacterium that is widespread in the environment, can undergo anaerobic metabolic activity under certain conditions, is particularly pathogenic and is often associated with lung infections and high mortality rates. In recent years, molecular studies of the mechanisms of the host immune response to bacterial infection have been well interpreted, but the multi-omics changes of multiple molecules in P. aeruginosa systematic analysis of the relationship between them has never been uncovered in detail. In this study, we integrated bioinformatics analysis of ATAC-seq, RNA-seq, proteomics and ubiquitinated proteomics to reveal the landscape of molecular and functional changes of P. aeruginosa infected lung tissues in multiple dimensions. Moreover, we reveal a host defense mechanism by which the crucially important transcription factors Stat1 and Stat3 may co-operatively regulate the expression of the downstream inflammatory genes. [ABSTRACT FROM AUTHOR]

(1) Background: Vaccinium vitis-idaea is a nutritionally and economically valuable natural wild plant species that produces berries useful for treating various diseases. There is growing interest in lingonberry, but there is limited information regarding lingonberry reference genes suitable for gene expression analyses of different tissues under various abiotic stress conditions. The objective of this study was to identify stable reference genes suitable for different lingonberry tissues in response to abiotic stress. (2) Methods: The delta Ct method and the GeNorm v3.5 and NormFinder v20 programs were used to comprehensively analyze gene expression stability. (3) Results: Actin Unigene23839 was the best reference gene for analyzing different cultivars, whereas Actin CL5740.Contig2 was the most suitable reference gene for analyzing different tissues and alkali stress. In contrast, 18S rRNA CL5051.Contig1 was the most stable reference gene under drought conditions. (4) Conclusions: These suitable reference genes may be used in future qRT-PCR analyses of different lingonberry tissues and the effects of abiotic stresses. Furthermore, the study data may be useful for functional genomics studies and the molecular breeding of lingonberry. In summary, internal reference genes or internal reference gene combinations should be carefully selected according to the experimental conditions to ensure that the generated gene expression data are accurate. [ABSTRACT FROM AUTHOR]

Background: This study aimed to investigate the neuroanatomical subtypes among early-onset schizophrenia (EOS) patients by exploring the association between structural alterations and molecular mechanisms using a combined analysis of morphometric similarity network (MSN) changes and specific transcriptional expression patterns. Methods: We recruited 206 subjects aged 7 to 17 years, including 100 EOS patients and 106 healthy controls (HC). Heterogeneity through discriminant analysis (HYDRA) was used to identify the EOS subtypes within the MSN strength. The differences in morphometric similarity between each EOS subtype and HC were compared. Furthermore, we examined the link between morphometric changes and brain-wide gene expression in different EOS subtypes using partial least squares regression (PLS) weight mapping, evaluated genetic commonalities with psychiatric disorders, identified functional enrichments of PLS-weighted genes, and assessed cellular transcriptional signatures. Results: Two distinct MSN-based EOS subtypes were identified, each exhibiting different abnormal MSN strength and cognitive functions compared to HC. The PLS1 score mapping demonstrated anterior–posterior gradients of gene expression in EOS1, whereas inverse distributions were observed in EOS2 cohorts. Genetic commonalities were identified in autistic disorder and adult schizophrenia with EOS1 and inflammatory bowel diseases with EOS2 cohorts. The EOS1 PLS1- genes (Z < -5) were significantly enriched in synaptic signaling-related functions, whereas EOS2 demonstrated enrichments in virtual infection-related pathways. Furthermore, the majority of observed associations with EOS1-specific MSN strength differences contributed to specific transcriptional changes in astrocytes and neurons. Conclusions: The findings of this study provide a comprehensive analysis of neuroanatomical subtypes in EOS, shedding light on the intricate relationships between macrostructural and molecular aspects of the EOS disease. [ABSTRACT FROM AUTHOR]

Aeromonas hydrophila and A. veronii are widespread and important critical pathogenic bacteria in the aquaculture industry and cause severe economic damage. At present, magnolol has been proved to be a broad‐spectrum antibacterial activity, such as A. hydrophila, Staphylococcus aureus and Streptococcus mutans. In order to explore the cause of in vivo disease resistance of magnolol and promote its safe application in aquaculture, the pathological detection and changes in immune indicators of fish after feeding with magnolol were conducted in this paper. Results showed that the diets supplemented with magnolol (3 g magnolol/kg commercial feed) significantly increase the expression level of anti‐inflammatory cytokines (IL‐10, TGF‐β and IL‐4) in the liver of goldfish (p <.05). Additionally, the expression levels of proinflammatory cytokines (IL‐1β, IL‐8 and IFN‐γ) did not increase significantly. Subsequently, this study investigated the resistance of goldfish to A. hydrophila and A. veronii infection after feeding with magnolol. The results showed that the survival rates of treatment groups fed 3 g magnolol/kg commercial feed daily increased by 23.1% and 38.5% after 10 days post A. hydrophila and A. veronii (p =.0351) infection, respectively. Meanwhile, growth performance (body weight and length), major internal organs (liver, spleen, kidney and intestine) and the serum biochemistry indicators (ATL and AST) all exhibited no significant adverse effects after the goldfish fed with magnolol for 30 days. TP showed an increasing concentration in the treatment group (p <.05). Results of the mRNA expression of stress response indicated that the expression level of cyp1a and hsp70 was significantly down‐regulated after a 30‐day treatment (p <.05), and the two genes recovered to the similar level as the control group after a commercial feed diet. In brief, the diets supplemented with magnolol protected the host from the excessive immune response caused by A. hydrophila and A. veronii via enhancing its anti‐inflammatory capacity and had no adverse effects with feeding. [ABSTRACT FROM AUTHOR]

Simple Summary: This study explores the role of circTPST2, a circular RNA, in the chemotherapy sensitivity of head and neck squamous cell carcinoma (HNSCC). Elevated levels of circTPST2 were observed in HNSCC tissues, and functional experiments revealed its inhibitory effect on cisplatin sensitivity in HNSCC cells. By interacting with miR-770-5p and the Nucleolin pathway, circTPST2 emerged as a crucial regulator influencing chemotherapy responsiveness. The findings suggest that circTPST2 may serve as a potential marker for chemotherapy regimen selection in HNSCC patients, providing insights to enhance treatment efficacy and patient outcomes. Chemoresistance poses a significant challenge in the treatment of advanced head and neck squamous cell cancer (HNSCC). The role and mechanism of circular RNAs (circRNAs) in HNSCC chemoresistance remain understudied. We conducted circRNA microarray analysis to identify differentially expressed circRNAs in HNSCC. The expression of circRNAs from the tyrosylprotein sulfotransferase 2 (TPST2) gene and miRNAs was evaluated through qPCR, while the circular structure of circTPST2 was verified using Sanger sequencing and RNase R. Through Western blotting, biotin-labeled RNA pulldown, RNA immunoprecipitation, mass spectrometry, and rescue experiments, we discovered miR-770-5p and nucleolin as downstream targets of circTPST2. Functional tests, including CCK8 assays and flow cytometry, assessed the chemoresistance ability of circTPST2, miR-770-5p, and Nucleolin. Additionally, FISH assays determined the subcellular localization of circTPST2, miR-770-5p, and Nucleolin. IHC staining was employed to detect circTPST2 and Nucleolin expression in HNSCC patients. circTPST2 expression was inversely correlated with cisplatin sensitivity in HNSCC cell lines. Remarkably, high circTPST2 expression correlated with lower overall survival rates in chemotherapeutic HNSCC patients. Mechanistically, circTPST2 reduced chemosensitivity through sponge-like adsorption of miR-770-5p and upregulation of the downstream protein Nucleolin in HNSCC cells. The TCGA database revealed improved prognosis for patients with low circTPST2 expression after chemotherapy. Moreover, analysis of HNSCC cohorts demonstrated better prognosis for patients with low Nucleolin protein expression after chemotherapy. We unveil circTPST2 as a circRNA associated with chemoresistance in HNSCC, suggesting its potential as a marker for selecting chemotherapy regimens in HNSCC patients. Further exploration of the downstream targets of circTPST2 advanced our understanding and improved treatment strategies for HNSCC. [ABSTRACT FROM AUTHOR]

Simple Summary: Bladder cancer (BLCA) is one of the most prevalent urinary cancers and novel non-invasive BLCA tumor biomarkers with high sensitivity and specificity are needed to support early diagnosis. Exosomal long non-coding RNAs (lncRNAs) are promising diagnostic biomarkers for BLCA. Our study suggests that the combined evaluation of lncRNA RMRP levels in urinary and plasma exosomes is an excellent potential non-invasive diagnostic biomarker for BLCA patients. Additionally, targeting the RMRP/miR-206/G6PD axis is a promising strategy for BLCA treatment. Bladder cancer (BLCA) is one of the cancers that is highly sensitive to specific non-invasive tumor biomarkers that facilitate early diagnosis. Exosome-derived long non-coding RNAs (lncRNAs) hold promise as diagnostic biomarkers for BLCA. In this study, we employed RNA-sequencing to compare the expression patterns of lncRNAs in urine exosomes from three BLCA patients and three healthy individuals. RMRP displayed the most significant differential expression. Elevated RMRP expression levels were observed in urinary and plasma exosomes from BLCA patients compared with those from healthy individuals. RMRP exhibited significant associations with certain BLCA patient clinicopathological features, including tumor stage, poor prognosis, and tumor grade. Combined diagnosis using RMRP in urine and plasma exosomes demonstrated a superior diagnostic performance with receiver operating characteristic curve analysis. RMRP was found to be related to BLCA tumor progression and the cell migration and invasion processes via the miR-206/G6PD axis both in vitro and in vivo. Mechanistically, RMRP serves as an miR-206 sponge, as suggested by dual-luciferase reporter assays and RNA immunoprecipitation. Our study suggests that the combined diagnosis of RMRP in urinary and plasma exosomes can serve as an excellent non-invasive diagnostic biomarker for BLCA patients. Additionally, targeting the RMRP/miR-206/G6PD axis holds promise as a therapeutic strategy for BLCA. [ABSTRACT FROM AUTHOR]

Omega-3 has been proposed as an antitumor substance that suppresses the growth and metastasis of multiple types of tumor cells, including lung cancer, but the specific mechanisms involved remain obscure. Our previous studies showed that the expression of chemokine ligand 18 was related to the migration and metastasis of non-small cell lung cancer. Here, we aim to explore whether omega-3 inhibits invasion and metastasis of NSCLC by regulating the expression of CCL18. The expression of CCL18, metastasis- and epithelial-mesenchymal transition (EMT)-related genes at mRNA and protein levels in NSCLC cell lines were detected by RT-qPCR and Western blot, respectively. The metastatic and invasive capability of NSCLC cells were evaluated by scratch wound healing and Transwell assays, respectively. Our results showed that the level of CCL18 is positively associated with metastatic ability of NSCLC cells. Docosahexaenoic acid, an important long-chain, polyunsaturated omega-3 (n−3) fatty acid, significantly inhibited invasion and metastasis of NSCLC cells, and concomitantly downregulated the expression of metastasis- and EMT-related genes and p-STAT3 signaling pathway. Additionally, we found that DHA inhibited CCL18 expression in lung cancer cells, while overexpression of CCL18 effectively reversed DHA-mediated downregulation in the expression of metastasis- and EMT-related genes and p-STAT3 signaling as well as DHA-mediated inhibitory effect on metastasis and invasion of NSCLC cells. DHA inhibits NSCLC cell invasion and metastasis possibly through targeted inhibition of CCL18/ STAT3 signaling pathway and EMT process. [ABSTRACT FROM AUTHOR]