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Paclitaxel (PTX) is one of the most commonly used chemotherapeutic agents for various cancer diseases. Despite its advantages, PTX also causes behavioral deficits related to nervous-system dysfunction, such as neuropathic pain, depression, anxiety, and cognitive impairments. The prefrontal cortex (PFC) is one of the areas that is susceptible to adverse effects of chemotherapeutic agents. Therefore, the present study was designed to examine sex-biased behavioral deficits and whole-transcriptome changes in gene expression in the PFC of mice treated with vehicle or PTX. In this study, PTX (4 mg/kg) was injected intraperitoneally four times in mice every other day. Three weeks later, both PTX-treated male and female mice developed mechanical pain hypersensitivities, as indicated by increased paw withdrawal responses to 0.16-g von Frey filaments. Additionally, PTX-treated mice exhibited depression-like symptoms, as they exhibited increased immobility times in the forced swim test. PTX also induced cognitive impairment, as demonstrated via results of a novel object recognition (NOR) test and anxiety-like behavior in an elevated plus-maze test in male mice, but not in female mice. RNA sequencing and in-depth gene expression analysis of the PFC in paired vehicle and PTX-treated mice showed that PTX induced 1755 differentially expressed genes in the PFCs of male and female mice. Quantitative real-time RT-PCR verified that some gene expressions in the medial PFC (mPFC) were related to neurotransmission. In conclusion, this study identified a sex-biased effect of PTX on PFC function and gene expression, which provides a foundation for future studies to explore the precise mechanisms of PTX-induced behavioral deficits., (Copyright © 2019 IBRO. Published by Elsevier Ltd. All rights reserved.)

In insects, the ecdysteroid 20-hydroxyecdysone coordinates with juvenile hormone (JH) to regulate the process of molting, development and metamorphosis; however, this interaction is still unclear in the mites. In this study, we investigated the gene related to ecdysteroid and JH biosynthesis pathways, including four ecdysteroid and 11 JH biosynthesis genes. We examined their expression patterns during molting of different developmental stages of the two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), an important agricultural pest that feeds on more than 1100 plant species. The expression of ecdysteroid biosynthesis Halloween genes exhibited a positive zigzag-like pattern, with a peak after 8 h of molting and a drop 8 h after entering each quiescent stage. In contrast, JH biosynthesis genes expression displayed a negative zigzag-like pattern, with a peak at 8 h after entering each quiescent stage and a drop after 8 h of each molting. These opposite patterns imply that ecdysteroid and JH expression is coordinated during the developmental transition. Our data provide an initial perspective on the co-expression of ecdysteroid and JH biosynthesis genes to regulate this important developmental process in the two-spotted spider mite.

Class 1 integrons accumulate antibiotic resistance genes by site-specific recombination at aatI-1 sites. Captured genes are transcribed from a promoter located within the integron; for class 1 integrons, the first gene to be transcribed and translated normally encodes an aminoglycoside antibiotic resistance protein (either an acetyltransferase [AAC] or adenyltransferase [AAD]). The leader RNA from the Pseudomonas fluorescens class 1 integron contains an aminoglycoside-sensing riboswitch RNA that controls the expression of the downstream aminoglycoside resistance gene. Here, we explore the relationship between integron-dependent DNA recombination and potential aminoglycoside-sensing riboswitch products of recombination derived from a series of aminoglycoside-resistant clinical strains. Sequence analysis of the clinical strains identified a series of sequence variants that were associated with class I integron-derived aminoglycoside-resistant (both aac and aad ) recombinants. For the aac recombinants, representative sequences showed up to 6-fold aminoglycoside-dependent regulation of reporter gene expression. Microscale thermophoresis (MST) confirmed RNA binding. Covariance analysis generated a secondary-structure model for the RNA that is an independent verification of previous models that were derived from mutagenesis and chemical probing data and that was similar to that of the P. fluorescens riboswitch RNA. The aminoglycosides were among the first antibiotics to be used clinically, and the data suggest that in an aminoglycoside-rich environment, functional riboswitch recombinants were selected during integron-mediated recombination to regulate aminoglycoside resistance. The incorporation of a functional aminoglycoside-sensing riboswitch by integron recombination confers a selective advantage for the expression of resistance genes of diverse origins., (Copyright © 2019 American Society for Microbiology.)

Hepatitis E virus (HEV) is associated with acute hepatitis disease. Numerous truncated HEV capsid proteins have been successfully expressed using different expression systems. Among these, p495, a protein truncated at its N- and C-termini by 111 and 54 amino acids (aa), respectively (HEV ORF2 aa 112-606) can self-assemble into T = 1 virus-like particles (VLPs) when expressed by insect cells. A shorter p239 (aa 368-606) protein is a particulate antigen that we have previously used in our commercialized HEV vaccine, Hecolin. Here, we sought to express p495 in its soluble form (named Ep495) in E. coli and in baculovirus-infected Tn5 insect cells (named BTp495) as a back-to-back control. Characterization of p495 particles derived from these two expression systems showed similarities in particle size, morphology, and sedimentation coefficient. Antigenicity assays using a panel of anti-HEV monoclonal antibodies also showed similar strong reactivities for Ep495 and BTp495, as well as similar binding profiles that were congruent with p239. Mouse immunization results showed that Ep495 particles had comparable immunogenicity with that of BTp495 VLPs, as well as p239. Overall, our findings suggest that p495 particles produced in E. coli are ideal for the development of next-generation prophylactic vaccines against hepatitis E., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

MicroRNA-122 (miR-122), a completely conserved, liver-specific miRNA in vertebrates, is essential for the maintenance of liver homeostasis. This 22-nucleotide-length RNA regulates diverse functions such as cholesterol, glucose, and lipid metabolism as well as iron homeostasis and infection of hepatitis C virus (HCV). Landes goose, which has a good, fatty liver, has important significance for us in studying miR-122 function in goose fatty liver. In the current study, we identified miR-122 in goose liver and its expression pattern and target genes. We found that miR-122 was highly expressed in goose liver and its expression was down-regulated after overfeeding; some genes related to lipid metabolism, including prolyl 4-hydroxylase subunit alpha 1 (P4HA1); aldolase, fructose-bisphosphate B (ALDOB); and pyruvate kinase, muscle (PKM2), were predicted and validated as target genes of goose miR-122. After overexpression or inhibition of miR-122 in primary goose hepatocytes, the expression of ALDOB and PKM2 was changed, but not that of P4HA1, indicating miR-122 regulates ALDOB and PKM2 expression at the mRNA level. These findings suggest miR-122 play important roles in goose fatty liver by targeting some of the genes related to lipid metabolism., (© 2017 Poultry Science Association Inc.)

Background: Liver biopsy is the gold standard to assess pathological features (eg inflammation grades) for hepatitis B virus-infected patients although it is invasive and traumatic; meanwhile, several gene profiles of chronic hepatitis B (CHB) have been separately described in relatively small hepatitis B virus (HBV)-infected samples. We aimed to analyse correlations among inflammation grades, gene expressions and clinical parameters (serum alanine amino transaminase, aspartate amino transaminase and HBV-DNA) in large-scale CHB samples and to predict inflammation grades by using clinical parameters and/or gene expressions., Methods: We analysed gene expressions with three clinical parameters in 122 CHB samples by an improved regression model. Principal component analysis and machine-learning methods including Random Forest, K-nearest neighbour and support vector machine were used for analysis and further diagnosis models. Six normal samples were conducted to validate the predictive model., Results: Significant genes related to clinical parameters were found enriching in the immune system, interferon-stimulated, regulation of cytokine production, anti-apoptosis, and etc. A panel of these genes with clinical parameters can effectively predict binary classifications of inflammation grade (area under the ROC curve [AUC]: 0.88, 95% confidence interval [CI]: 0.77-0.93), validated by normal samples. A panel with only clinical parameters was also valuable (AUC: 0.78, 95% CI: 0.65-0.86), indicating that liquid biopsy method for detecting the pathology of CHB is possible., Conclusions: This is the first study to systematically elucidate the relationships among gene expressions, clinical parameters and pathological inflammation grades in CHB, and to build models predicting inflammation grades by gene expressions and/or clinical parameters as well., (© 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.)

Pharmacological doses of fibroblast growth factor (FGF) 21 effectively normalize glucose, lipid and energy homeostasis in multiple animal models with many benefits translating to obese humans with type 2 diabetes. However, a role for FGF21 in the regulation of bile acid metabolism has not been reported. Herein, we demonstrate AAV-mediated FGF21 overexpression in mice increases liver expression of the key bile acid producing enzyme, Cyp7a1, resulting in an increased bile acid pool. Furthermore, in cholecystectomized mice, FGF21-mediated bile acid pool increase led to increased transit of bile acids into colon. We elucidate that the mechanism of FGF21 induced bile acid changes is mainly through antagonizing FGF15/19 function on liver βKlotho/FGFR4 receptor complex; thus inhibiting FGF15/19-mediated suppression of Cyp7a1 expression. In conclusion, these data reveal a previously unidentified role for FGF21 on bile acid metabolism and may be relevant to understand the effects of FGF21 analogs in clinical studies., (Copyright © 2016. Published by Elsevier B.V.)

This study investigated the effects of the sequence arrangement and orientation of a target gene expression cassette in vectors on expression levels to determine the optimal combination for highly efficient multi-gene expression. Five plant transformation vectors were constructed using dual Bt genes, Cry1Ac and Cry3A, which differed in the sequence arrangement and orientation of the target gene expression cassette. Through an Agrobacterium-mediated method, 5 vectors were used for the genetic transformation of tobacco to obtain transgenic lines. Fluorescence quantitative PCR showed that the target genes were expressed at the transcriptional level, which did not differ significantly among the different vectors. However, an enzyme-linked immunosorbent assay showed that there were significant differences in the toxin expression levels of the different vectors. In vectors N12 and N19, the Cry1Ac gene, located upstream, showed lower average expression than the Cry3A gene, located downstream. Similarly, in vectors N13 and N18, the Cry3A gene, located upstream, had lower expression than the downstream Cry1Ac gene. For vector N21, with the expression cassette containing the Cry1Ac gene located upstream in a trans-arrangement and that of the Cry3A gene located downstream in a cis-arrangement, the Cry1Ac and Cry3A toxin levels were the highest, at 7.41 and 13.24μg·g -1 , respectively. The insect resistance of transgenic lines transformed by the different vectors was related to the Bt toxin level. Resistance to H. armigera, Lepidoptera, and Cry1Ac toxin level were positively correlated; resistance to A. germari larvae, Coleoptera, and Cry3A toxin content were also positively correlated. This study showed that the sequence arrangement of 2 expression cassettes with target genes may be the key to the target gene expression. Two expression cassettes in the same orientation had little influence on gene expression; however, when the 2 expression cassettes were in the reverse arrangement, the expression of both of the target genes was promoted to a certain extent., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxymethylcytosine in DNA. However, the role of TET enzymes in human gastric cancer remains unknown. Here, we show that TET2 mRNA and protein levels are downregulated in human gastric cancer tissues when compared with normal gastric mucosa. Low expression of TET2 predicts poor overall and disease-free survival. Furthermore, we demonstrate that TET2 inhibits the proliferation and colony formation of human gastric cancer cells by using loss-of-function and gain-of-function strategies. Overexpression of TET2 induces apoptosis in human gastric cancer cells. The mechanism study shows that TET2 binds to the promoter region of the oncogenic long noncoding RNA (lncRNA-ANRIL) and regulates the expression of ANRIL and its downstream genes (INK4a, INK4b, and ARF). Finally, we demonstrate that ANRIL knockdown blocks the effects of TET2 on gastric cancer cell proliferation and colony formation. © 2016 IUBMB Life 68(5):355-364, 2016., (© 2016 International Union of Biochemistry and Molecular Biology.)

Members of the interleukin-1 (IL-1) family play important roles in inflammation and host defense against pathogens. Here, we describe a novel member of the IL-1 family, interleukin-38 (IL-38, IL-1F10, or IL-1HY2), which was discovered in 2001. Although the functional role of IL-38 remains unclear, recent reports show that IL-38 binds to the IL-36 receptor (IL-36R) which is also targeted by the IL-36 receptor antagonist (IL-36Ra). Consequently, these two molecules have similar effects on immune cells. Here, we describe the expression of soluble and active recombinant IL-38 in Escherichia coli (E. coli). The IL-38 gene sequence was optimized for expression in E. coli and then cloned into a pEHISTEV expression vector, which has an N-terminal 6-His affinity tag under control of the T7 lac strong promoter. Optimization of culture conditions allowed induction of the recombinant fusion protein with 0.1 mM isopropyl β-D-1-thio galactoside (IPTG) at 37°C for 4h. The recombinant fusion protein was purified using an Ni affinity column and was further digested with TEV protease; the cleaved protein was purified by molecular-exclusion chromatography. Next, we measured IL-38 binding ability using functional ELISA. The purified proteins were used to immunize a New Zealand white rabbit four times to enable the production of polyclonal antibodies. The specificity of the prepared polyclonal antibodies was determined using Western blot, and the results showed they have high specificity against IL-38. Here, we describe the development of an effective and reliable method to express and purify IL-38 and anti-IL-38 antibodies. This will enable the function and structure of IL-38 to be determined., (Copyright © 2014 Elsevier Inc. All rights reserved.)

The β-globin matrix attachment regions (MARs) were inserted into the 5'-site of the eukaryotic expression vector cassette and DNA fragments 350 and 750 bp in length were inserted into the site to generate expression vectors with varying distances between the expression cassette and MAR. The vectors containing MARs increased chloramphenicol acetyltransferase (CAT) expression levels compared to the negative control vector lacking the MAR; the highest expression increase was 3.8-fold. A greater MAR-transgene distance (750 bp) correlated with a greater increase in transgene expression when compared to the control vector that lacked separation between the MAR and transgene. CAT gene copy numbers were higher in cells transformed with the vector possessing a smaller MAR-transgene distance (350 bp) than in cells belonging to the other three groups. However, MAR-induced transgene expression levels did not exhibit a direct relationship with gene copy number.

Matrix metalloproteinase-9 (MMP-9) is a protein involved in diabetes-associated wound healing. The present study aimed to determine whether pioglitazone, an agonist of peroxisome proliferator-activated receptor‑γ (PPAR-γ), inhibits the expression of MMP-9. HaCaT cells at a density of 6x105 cells/well were seeded into 6-well plates in medium and were cultured for 24 h. The cells were then treated with bovine serum albumin (BSA) only or advanced glycation end‑product (AGE)-BSA (50, 100, 200, 300 or 400 µg/ml), with or without pioglitazone (0.5 or 1 µM). The effects of AGE-BSA on cell viability were determined by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. The levels of MMP-9 secreted into the medium were detected by an enzyme-linked immunosorbent assay. The mRNA and protein levels were analyzed by quantitative polymerase chain reaction (qPCR) and western blot analysis, respectively. AGEs are able to increase the level of MMP-9 mRNA in HaCaT cells and the levels of MMP-9 protein secreted into the medium. Pioglitazone (0.5 or 1 µΜ) significantly inhibited the levels of MMP-9 in the treated HaCaT cells. Pioglitazone (0.5 or 1 µΜ) also suppressed the levels of MMP-9 in the cell culture medium. Pioglitazone at concentrations of 0.5 and 1 µΜ significantly suppressed the levels of MMP-9 mRNA to 20 or 8%, respectively. These results suggest that pioglitazone is able to effectively suppress the expression of MMP-9 via a transcriptional mechanism.

Objective: To investigate the effect of Antrodia cinnamomea on gene expression related to aortal endothelial injury of rats with hyperlipidemia., Method: Fifty SD rats were randomly divided into five groups: the normal control group (NG), the model group (MG), the antrodia cinnamomea groups of low, middle and high doses (AC-LG, AC-MG, AC-HG, 250, 500, 1 000 mg x kg(-1)). The rats were fed with high-fat diets to establish the hyperlipidemia model. After the drug administration for 10 weeks, their serum lipid, SOD, MDA and ox-LDL, LOX-1, P38 MAPK and NF-kappaB mRNA and protein expression were respectively determined, and the aortal endothelial injury was observed under electron microscope., Result: In the model group, the contents of TC, TG and LDL-C significant increased (P < 0.01), whereas the content of HDL-C significant decreased (P < 0.01). Compared with the model group, both the AC-M group and the AC-H group showed reduction in endothelial injury and significant decrease in the content of TC, TG and LDL-C (P < 0.05 or P < 0.01). The content of HDL-C increased, but with no significant difference. SOD activity in serum remarkably increased (P < 0.05 or P < 0.01), MDA and ox-LDL levels dramatically decreased (P < 0.05 or P < 0.01)., Conclusion: A. cinnamomea can alleviate endothelial lipid injury by inhibiting the expressions of LOX-1, P38MAPK and NF-kappaB in aorta and better protect aortal endothelial cells from oxidative lipid injury.

Metastasis associated in colon cancer 1 (MACC1) has been regarded as a novel potential therapeutic target for multiple cancers. However, the impact of MACC1 in glioma remains unclear. The aim of this study was to analyze the correlation of MACC1 expression with the clinicopathological features of glioma. MACC1 mRNA and protein expression levels in human glioma tissues were detected by quantitative real-time polymerase chain reaction and immunohistochemistry assays, respectively. MACC1 mRNA and protein expression were both significantly higher in glioma tissues than in corresponding noncancerous brain tissues (both P < 0.001). In addition, statistical analysis suggested that high MACC1 expression was significantly correlated with advanced pathological grade (P = 0.004) and that patients with high expression of MACC1 protein exhibited a poorer prognosis than those with low MACC1 expression. Furthermore, Cox multivariate analysis showed that MACC1 overexpression was an independent prognostic factor for predicting the overall survival of glioma patients. In conclusion, expression of MACC1 in glioma could be adopted as a candidate biomarker for the diagnosis of clinical stage and for assessing prognosis, indicating for the first time that MACC1 may play an important role in the tumor development and progression in glioma. MACC1 might be considered as a novel therapeutic target against this cancer.

Netrin-1, a known axon guidance molecule, being a secreted laminin-related molecule, has been suggested to be involved in multiple physiological and pathological conditions, such as organogenesis, angiogenesis, tumorigenesis, and inflammation-mediated tissue injury. However, its function in thymocyte development is still unknown. Here, we demonstrate that Netrin-1 is expressed in mouse thymus tissue and is primarily expressed in thymic stromal cells, and the expression of Netrin-1 in thymocytes can be induced by anti-CD3 antibody or IL-7 treatment. Importantly, Netrin-1 mediates the adhesion of thymocytes, and this effect is comparable to or greater than that of fibronectin. Furthermore, Netrin-1 specifically promotes the chemotaxis of CXCL12. These suggest that Netrin-1 may play an important role in thymocyte development.

A metagenomic fosmid library containing 1 × 10(5) clones was constructed from a biogas digester fed with pig ordure and rice straw. In total, 121 clones with activity of 4-methylumbelliferyl-cellobiosidase were screened from the metagenomic library. A novel GH5 cellulase gene exo2b was identified from a sequenced clone EXO02C10 and expressed in Escherichia coli BL21. The corresponding recombinant Exo2b protein showed high specific activity toward both carboxymethylcellulose (CMC; 260 U/mg protein) and β-D-glucan from barley (849 U/mg), with an optimal pH and temperature of 7.5 and 58 °C, respectively. Exo2b showed stable activity at a wide pH range from 5.5 to 9.0 and was highly thermostable at 60 °C in the presence of 60 mM cysteine. Residual activity was maintained at nearly 100% when Exo2b was incubated at 60 °C for 15 h. A thin-layer chromatography analysis of the hydrolysis products confirmed that Exo2b was an endo-β-1,4-glucanase and it could also produce oligosaccharide smaller than cellotetraose. The fragment encoding the Exo2b catalytic domain was then fused with the cbh1 gene from Trichoderma reesei, and the fused gene was successfully expressed in T. reesei Rut-C30. Compared to that of the parent strain, the filter paper activity and CMCase activity of the secreted proteins of a selected transformant A1 increased by 24% and 18%, respectively. Besides, the glucose concentration from the hydrolysis of pretreated corn stover by the A1 secreted proteins increased by 19.8%. The present study demonstrated the potential application of metagenome originated cellulase genes to modify cellulase producing fungi.

Senescent cells exhibit altered expression of numerous genes. Identifying the significance of the changes in gene expression may help advance our understanding of the senescence biology. Here, we report on the consistent and strong upregulation of CST1 expression during cellular senescence, independent of the initial trigger. CST1 expression at both the messenger RNA and protein levels was barely detected in control cells, which included early passage proliferating, quiescent, or immortal human fibroblasts and various human tumor cell lines. Immunoblotting and immunofluorescence cytochemical studies further suggest that CST1 accumulates intracellularly, within vesicular structures. We discuss these results in light of the known function of CST1 as a potent inhibitor of lysosomal cysteine proteases.

Aim: To construct the prokaryotic expression vector of UNC5CL, purify the fusion protein of GST-UNC5CL, prepare the polyclonal antibody of UNC5CL and characterize the reactivity and specificity of the polyclonal antibody., Methods: The human UNC5CL nucleotide sequence encoding amino acid from 280 to 518 was amplified and cloned into pGEX-4T-2 vector, then transformed into E.coli BL21, in which the fusion protein GST-UNC5CL (aa280-518) was induced and purified by Glutathione Sepharose-4B. Then the purified protein immunized the rabbits and anti-serum was collected. The anti-serum was further detected by ELISA, Western blot and immunohistochemistry., Results: The prokaryotic expression vector of pGEX-4T-2-UNC5CL(aa280-518) was constructed successfully. It can be induced by IPTG and express a fusion protein of GST-UNC5CL (aa280-518) with M(r); 5 2000. The ELISA, Western blot and Immunohistochemistry demonstrated the rabbit antiserum obtained by immunized by the purified fusion protein can detect the target protein., Conclusion: The rabbit polyclonal antibody against human UNC5CL is prepared. It can react with UNC5CL specifically and provide basis for further function study of UNC5CL.

Proximal spinal muscular atrophy (SMA), one of the most common genetic causes of infant death, results from the selective loss of motor neurons in the spinal cord. SMA is a consequence of low levels of survival motor neuron (SMN) protein. In humans, the SMN gene is duplicated; SMA results from the loss of SMN1 but SMN2 remains intact. SMA severity is related to the copy number of SMN2. Compounds which increase the expression of SMN2 could, therefore, be potential therapeutics for SMA. Ultrahigh-throughput screening recently identified substituted quinazolines as potent SMN2 inducers. A series of C5-quinazoline derivatives were tested for their ability to increase SMN expression in vivo. Oral administration of three compounds (D152344, D153249 and D156844) to neonatal mice resulted in a dose-dependent increase in Smn promoter activity in the central nervous system. We then examined the effect of these compounds on the progression of disease in SMN lacking exon 7 (SMNDelta7) SMA mice. Oral administration of D156844 significantly increased the mean lifespan of SMNDelta7 SMA mice by approximately 21-30% when given prior to motor neuron loss. In summary, the C5-quinazoline derivative D156844 increases SMN expression in neonatal mouse neural tissues, delays motor neuron loss at PND11 and ameliorates the motor phenotype of SMNDelta7 SMA mice.

Objective: To produce human papillomavirus type 11 virus-like particles (HPV11 VLPs) from Escherichia coli and to investigate its immunogenicity and type cross neutralization nature., Methods: We expressed the major capsid protein of HPV11 (HPV11-L1) in Escherichia coli ER2566 in non fusion fashion and purified by amino sulfate precipitation, ion-exchange chromatography and hydrophobic interaction chromatography, sequentially. Then we removed the reductant DTT to have the purified HPV11-L1 self-assemble into VLPs in vitro. We investigated the morphology of these VLPs with dynamic light scattering and transmission electron microscopy. We assayed the immunogenicity of the resultant HPV11 VLPs by vaccinations on mice and evaluated by HPV6/11/16/18 pseudovirion neutralization cell models., Results: We expressed HPV11 L1 in Escherichia coli with two forms, soluble and inclusion body. The soluble HPV11 L1 with over 95% purity can self assemble to VLPs in high efficiency. Morphologically, these VLPs were globular, homogeneous and with a diameter of - 50 nm, which is quite similar with native HPV11 virions. The half effective dosage (ED50) of HPV11 VLPs is 0.031 microg, and the maximum titer of neutralizing antibody elicited is averaged to 10(6). The cross neutralization activity (against HPV6/16/18) of the anti-HPV11 serum was found to have exact correlation to the inter-type homology in amino acid alignment., Conclusion: We can provide HPV11 VLPs with highly immunogenicity from prokaryote expression system, which may pave a new way for research and development of prophylactic vaccine for HPV11.

Aim: To observe the variation in expression of AP-1 and TGF-beta1 in rat kidney of iodine deficiency, to explore the nosogenesis of renal damage in the region of iodine deficiency., Methods: The models of deficient iodine rats were established by treatment with low iodine diet, wistar rats were divided into gentle low iodine group(GLIG), dense low iodine group(DLIG) and control group(CL). Serum levels of thyroid humone were determined by chemiluminescent immunoassay. To observe the gene expression of c-Jun by using RT-PCR, observe the expression of TGF-beta1 by using immunohistochemistry., Results: Compared with CL, the FT3, FT4 of DLIG were significantly decreased(P<0.01), the FT3 of GLIG were significantly decreased(P<0.01), the FT4 of GLIG were not significantly decreased(P>0.05). Compared with GLIG, the FT3, FT4 of DLIG were significantly decreased(P<0.01). Compared with CL, GLIG group, the gene expression of c-Jun was significantly increased(P<0.01) in DLIG group. Compared with CL group, the level of c-Jun was slightly increased(P>0.05)in GLIG group. Compared with CL, the TGF-beta1 of DLIG was significantly increased, the TGF-beta1 of GLIG was significantly increased. Compared with GLIG, the TGF-beta1 of DLIG was significantly increased., Conclusion: Iodine deficiency can decrease the secretion of thyroid humone, can lead the activation of c-Jun and TGF-beta1 in kidney. This finding suggest that AP-1 signal transduction pathway participate in the nosogenesis of renal damage.

Aim: To prepare a soluble human Era(hEra) protein and to measure its bioactivity., Methods: Human era cDNA gene from pUC19 plasmid was subcloned into the expression plasmid pMAL-p2x. pMAL-hEra was transducted to E.coli TB1 and the strain was induced by isopropyl beta-D-thiogalactopyranoside (IPTG)., Results: The expressed MBP-fused protein existed in a soluble form. The fused protein made up 23.9% of the total cell lysate. It was purified by amylose affinity chromotography and digested with Factor X. Although the fused segment was dissected, the remained hEra protein was unstable in the solution with the passage of time. The activity assay showed that hEra was a GTPase that could bind GTP and hydrolyze GTP to GDP., Conclusion: Human Era protein can be expressed in a soluble form and it has been proved to be a kind of G protein by the experiments in vitro. The study is important to further research into the function of human era gene.

BACKGROUND: 2,4,6-Trichlorophenol (TCP), 2,4,6-tribromophenol (TBP) and 2,4,6- triiodophenol (TIP) are three widely detected trihalophenolic disinfection by-products (DBPs). Previous studies have mainly focused on the carcinogenic risk and developmental toxicity of 2,4,6-trihalophenols. Very little is known about their immunotoxicity in mammals. OBJECTIVES: We investigated the effects of 2,4,6-trihalophenols on mammalian immunity using a mouse macrophage model infected with bacteria or intracellular parasites and aimed to elucidate the underlying mechanisms from an epitranscriptomic perspective. The identified mechanisms were further validated in human peripheral blood mononuclear cells (PBMCs). METHODS: The mouse macrophage cell line RAW264.7 and primary mouse peritoneal macrophages were exposed to different concentrations of TCP, TBP, and TIP. The pro-inflammatory marker Ly6C, the survival of the bacterium Escherichia coli (E. coli), and the parasite burden of Toxoplasma gondii (T. gondii) were assessed. Furthermore, the global gene expression profiling of macrophages following exposure to 2,4,6-trihalophenols was obtained through RNA-sequencing (RNA-seq). The effects of 2,4,6-trihalophenols on RNA [N.sup.6]-methyladenosine ([m.sup.6]A) methyltransferases and total RNA [m.sup.6]A levels were evaluated using Western blotting and dot blot, respectively. Transcriptome-wide [m.sup.6]A methylome was analyzed by [m.sup.6]A-seq. In addition, expression of [m.sup.6]A regulators and total RNA [m.sup.6]A levels in human PBMCs exposed to 2,4,6- trihalophenols were detected using quantitative reverse transcriptase polymerase chain reaction and dot blot, respectively. RESULTS: Mouse macrophages exposed to TCP, TBP, or TIP had lower expression of the pro-inflammatory marker Ly6C, with a greater difference from control observed for TIP-exposed cells. Consistently, macrophages exposed to such DBPs, especially TIP, were susceptible to infection with the bacterium E. coli and the intracellular parasite T. gondii, indicating a compromised ability of macrophages to defend against pathogens. Intriguingly, macrophages exposed to TIP had significantly greater [m.sup.6]A levels, which correlated with the greater expression levels of [m.sup.6]A methyltransferases. Macrophages exposed to each of the three 2,4,6-trihalophenols exhibited transcriptome-wide redistribution of [m.sup.6]A. In particular, the [m.sup.6]A peaks in genes associated with immune-related pathways were altered after exposure. In addition, differences in [m.sup.6]A were also observed in human PBMCs after exposure to 2,4,6-trihalophenols. DISCUSSION: These findings suggest that 2,4,6-trihalophenol exposure impaired the ability of macrophages to defend against pathogens. This response might be associated with notable differences in [m.sup.6]A after exposure. To the best of our knowledge, this study presents the first [m.sup.6]A landscape across the transcriptome of immune cells exposed to pollutants. However, significant challenges remain in elucidating the mechanisms by which [m.sup.6]A mediates immune dysregulation in infected macrophages after 2,4,6-trihalophenol exposure. https://doi.org/10.1289/EHP11329, Introduction Disinfection is indispensable in water treatment to inactivate harmful pathogens and protect public health. However, during the disinfection process, disinfectants, such as chlorine and monochloramine, can react with natural [...]

Corneal neovascularization (CNV) is a common clinical finding seen in a range of eye diseases. Current therapeutic approaches to treat corneal angiogenesis, in which vascular endothelial growth factor (VEGF) A plays a central role, can cause a variety of adverse side effects. The technology of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 can edit VEGFA gene to suppress its expression. CRISPR offers a novel opportunity to treat CNV. This study shows that depletion of VEGFA with a novel CRISPR/Cas9 system inhibits proliferation, migration, and tube formation of human umbilical vein endothelial cells (HUVECs) in vitro. Importantly, subconjunctival injection of this dual AAV‐SpCas9/sgRNA‐VEGFA system is demonstrated which blocks suture‐induced expression of VEGFA, CD31, and α‐smooth muscle actin as well as corneal neovascularization in mice. This study has established a strong foundation for the treatment of corneal neovascularization via a gene editing approach for the first time. [ABSTRACT FROM AUTHOR]

DNA methylation, an epigenetic mechanism that alters gene expression without changing DNA sequence, is essential for organism development and key biological processes like genomic imprinting and X‐chromosome inactivation. Despite tremendous efforts in DNA methylation research, accurate quantification of cytosine methylation remains a challenge. Here, a single‐base methylation quantification approach is introduced by weighting methylation of consecutive CpG sites (Wemics) in genomic regions. Wemics quantification of DNA methylation better predicts its regulatory impact on gene transcription and identifies differentially methylated regions (DMRs) with more biological relevance. Most Wemics‐quantified DMRs in lung cancer are epigenetically conserved and recurrently occurred in other primary cancers from The Cancer Genome Atlas (TCGA), and their aberrant alterations can serve as promising pan‐cancer diagnostic markers. It is further revealed that these detected DMRs are enriched in transcription factor (TF) binding motifs, and methylation of these TF binding motifs and TF expression synergistically regulate target gene expression. Using Wemics on epigenomic‐transcriptomic data from the large lung cancer cohort, a dozen novel genes with oncogenic potential are discovered that are upregulated by hypomethylation but overlooked by other quantification methods. These findings increase the understanding of the epigenetic mechanism by which DNA methylation regulates gene expression. [ABSTRACT FROM AUTHOR]

This study examines the prognostic role and immunological relevance of EMP1 (epithelial membrane protein-1) in a pan-cancer analysis, with a focus on ovarian cancer. Utilizing data from TCGA, CCLE, and GTEx databases, we assessed EMP1 mRNA expression and its correlation with tumor progression, prognosis, and immune microenvironment across various cancers. Our results indicate that EMP1 expression is significantly associated with poor prognosis in multiple cancer types, including ovarian, bladder, testicular, pancreatic, breast, brain, and uveal melanoma. Immune-related analyses reveal a positive correlation between EMP1 and immune cell infiltration, particularly neutrophils, macrophages, and dendritic cells, as well as high expression of immune checkpoint such as CD274, HAVCR2, IL10, PDCD1LG2, and TGFB1 in most tumors. In vivo experiments confirm that EMP1 promotes ovarian cancer cell proliferation, metastasis, and invasion. In conclusion, EMP1 emerges as a potential prognostic biomarker and therapeutic target in various cancers, particularly ovarian cancer, due to its influence on tumor progression and immune cell dynamics. Further research is warranted to elucidate the precise mechanisms of EMP1 in cancer biology and to translate these findings into clinical applications. [ABSTRACT FROM AUTHOR]

BACKGROUND: Angiotensin-converting enzyme inhibitors (ACEIs) were reported to protect from hypoxia-induced oxidative stress in coronary endothelial cells (CECs) after acute myocardial infarction (AMI). Nrf2 shows a protective effect in hypoxia-induced CECs after AMI. Plasmalemma vesicle-associated protein (PLVAP) plays a pivotal role in angiogenesis after AMI. AIM: To explore the protective effect of ACEIs and the involved mechanisms under hypoxia challenge. METHODS: Human coronary endothelial cells (HCAECs) were used to establish hypoxia-induced oxidative stress injury in vitro. Flow cytometry was used to evaluate the protective effect of ACEI on hypoxia conditions.ET-1, NO, ROS, and VEGF were detected by ELISA. HO-1, Nrf2, and Keap-1, the pivotal member in the Nrf2 signaling pathway, eNOS and PLVAP were detected in HEAECs treated with ACEI by immunofluorescence, qPCR, and western blotting. RESULTS: The hypoxia ACEI or Nrf2 agonist groups showed higher cell viability compared with the hypoxia control group at 24 (61.75±1.16 or 61.23±0.59 vs. 44.24±0.58, both P < 0.05) and 48 h (41.85±1.19 or 59.64±1.13 vs. 22.98±0.25, both P < 0.05). ACEI decreased the levels of ET-1 and ROS under hypoxia challenge at 24 and 48 h (all P < 0.05); ACEI increased the VEGF and NO levels (all P < 0.05). ACEI promoted the expression level of eNOS, HO-1, Nrf2 and PLVAP but inhibited Keap-1 expression at the mRNA and protein levels (all P < 0.05). Blockade of the Nrf2 signaling pathway significantly decreased the expression level of PLVAP. CONCLUSION: ACEI protects hypoxia-treated HEAECs by activating the Nrf2 signaling pathway and upregulating the expression of PLVAP. [ABSTRACT FROM AUTHOR]

With the rapid development of intensive animal husbandry in the livestock industry, large quantities of manure waste containing phytate phosphorus are being generated. Phytase can effectively solve the problem of high phosphorus pollution in the feces of monogastric animals. Enviropig, which produces phytase in the salivary glands and secretes the enzyme in the saliva, were first generated in 1999. However, phytase is easily inactivated during digestion. To address this problem, cleavage-resistant phytase transgenic pigs were generated using handmade cloning in this study. Transgene construction was improved and three cell lines carrying Cafp were obtained. In total, 810 blastocysts were generated and 712 good-quality were transferred into six recipients. Fourteen piglets were born, of which six survived after weaning. Polymerase chain reaction and sequencing results showed that seven (three live and four dead) of the fourteen piglets carried Cafp. Phytase activity in the saliva of the six live cloned pigs was tested at four months of age, and only one pig had 0.155 FTU/mL enzyme activity. The other five pigs may not have been activated in the transgenic parotid gland. Among all the transgenic pigs, the highest phosphorus digestion rate was 59.2% of intake, representing a 25.4% decrease in fecal emission compared to the average of controls. Immunohistochemical results on the three Cafp- positive pigs that died after six months of age showed that the transgene was only expressed in parotid glands, confirming tissue-specific gene expression. In conclusion, cleavage-resistant phytase transgenic pigs were successfully produced through handmade cloning. The cloned pigs offer a unique biological approach to managing phosphorus nutrition and environmental pollution in animal husbandry. • New phytase with good tolerance to pepsin and trypsin was obtained and verified. • A transgene vector with the cleavage-resistant phytase gene was firstly produced. • Cleavage-resistant phytase transgenic pigs was firstly generated by HMC. • The function of PSP promoter was confirmed by tissue-specific expression. • The study offers a unique biological approach to solving phosphorus pollution. [ABSTRACT FROM AUTHOR]

Data-driven discovery of governing equations is of great significance for helping us understand intrinsic mechanisms and build physical models. Recently, numerous highly innovative algorithms have emerged, aimed at inversely discovering the underlying governing equations from data, such as sparse regression-based methods and symbolic regression-based methods. Along this direction, a novel dimensional homogeneity constrained gene expression programming (DHC-GEP) method is proposed in this work. The DHC-GEP simultaneously discovers the forms and coefficients of functions using basic mathematical operators and physical variables, without requiring preassumed candidate functions. The constraint of dimensional homogeneity is capable of filtering out the overfitting equations effectively. The key advantages of DHC-GEP compared with the original gene expression programming, including being more robust to hyperparameters, the noise level and the size of datasets, are demonstrated on two benchmark studies. Furthermore, DHC-GEP is employed to discover the unknown constitutive relations of two representative non-equilibrium flows. Galilean invariance and the second law of thermodynamics are imposed as constraints to enhance the reliability of the discovered constitutive relations. Comparisons, both quantitative and qualitative, indicate that the derived constitutive relations are more accurate than the conventional Burnett equations in a wide range of Knudsen numbers and Mach numbers, and are also applicable to the cases beyond the parameter space of the training data. [ABSTRACT FROM AUTHOR]

Recent studies have revealed the involvement of RNA m6A modification in embryonic development; however, the relationship between aberrant RNA m6A modification and unexplained recurrent spontaneous abortion (URSA) remains unclear. In this study, we analysed the level of RNA m6A modification in trophoblasts using dot blot, RNA m6A quantification, and MeRIP assays. By integrating data from the GEO database, RNA‐Seq, and MeRIP‐Seq, we examined the aberrant expression of m6A methyltransferases and their downstream molecules in chorionic villus (placental) tissues. RNA pull‐down, RIP, and electrophoretic mobility shift assay were used to analyse the binding relationship between the YTHDC1 protein and MEG3. Additionally, RNA stability and BrU immunoprecipitation chase assays were utilised to elucidate the regulation of MEG3 stability by YTHDC1. ChIP and DNA pull‐down RNA experiments were performed to elucidate the mechanism by which MEG3 targets EZH2 to the TGF‐β1 promoter. The results showed that the expression of the m6A demethylase FTO protein was significantly increased in URSA trophoblasts, leading to inhibition of the MEG3 m6A modification and weakening of the stabilising effect of the m6A binding protein YTHDC1 on MEG3. Furthermore, MEG3 was found to bind simultaneously with the EZH2 protein and the TGF‐β1 gene promoter, enabling the localisation of EZH2 protein to the TGF‐β1 gene promoter and subsequent inhibition of TGF‐β1 gene expression. In summary, our findings elucidate the mechanism by which FTO protein regulates the MEG3‐TGF‐β signalling pathway, thereby suppressing trophoblast invasion and proliferation in URSA trophoblast cells. These findings provide new insights for the treatment of URSA. [ABSTRACT FROM AUTHOR]

Acyl-CoA:lysocardiolipin acyltransferase 1 (ALCAT1) is an enzyme that promotes mitochondrial dysfunction by catalyzing pathological remodeling of cardiolipin. Upregulation of ALCAT1 protein expression by oxidative stress is implicated in the pathogenesis of age-related metabolic diseases, but the underlying molecular mechanisms remain elusive. In this study, we identified a highly conserved upstream open reading frame (uORF) at the 5′-untranslated region (5′-UTR) of ALCAT1 mRNA as a key regulator of ALCAT1 expression in response to oxidative stress. We show that the uORF serves as a decoy that prevents translation initiation of ALCAT1 under homeostatic condition. The inhibitory activity of the uORF on ALCAT1 mRNA translation is mitigated by oxidative stress but not ER stress, which requires the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α). Consequently, ablation of uORF or eIF2α phosphorylation at Ser51 renders ALCAT1 protein expression unresponsive to induction by oxidative stress. Taken together, our data show that the uORF links oxidative stress to translation control of ALCAT1 mRNAs through phosphorylation of eIF2α at Ser51. [Display omitted] • A conserved upstream open reading frame (uORF) is located at the 5′-untranslated region of ALCAT1 mRNA. • The uORF inhibits the translation initiation of ALCAT1 mRNA under homeostatic condition. • The inhibitory activity of the uORF on ALCAT1 mRNA translation is mitigated by oxidative stress, but not ER stress. • Phosphorylation of eIF2α at Ser51 is required for ALCAT1 mRNA translation by oxidative stress. [ABSTRACT FROM AUTHOR]

While single-cell RNA sequencing (scRNA-seq) allows researchers to analyze gene expression in individual cells, its unique characteristics like over-dispersion, zero-inflation, high gene-gene correlation, and large data volume with many features pose challenges for most existing feature selection methods. In this paper, we present a feature selection method based on neural network (scFSNN) to solve classification problem for the scRNA-seq data. scFSNN is an embedded method that can automatically select features (genes) during model training, control the false discovery rate of selected features and adaptively determine the number of features to be eliminated. Extensive simulation and real data studies demonstrate its excellent feature selection ability and predictive performance. [ABSTRACT FROM AUTHOR]

Scald is a common skin injury in daily life. It is well known that skin burns are associated with inflammation and oxidative stress. In our previous study, we found that Abelmoschus manihot (L.) medik had excellent therapeutic effects on scald‐induced inflammation, but its effect on scald‐induced oxidative stress was not reported. In this study, a deep second‐degree scald model in mice was established, and the wound healing rate, healing time, malondialdehyde (MDA) and total superoxide dismutase (T‐SOD) levels, and nuclear factor erythroid 2‐related Factor 2 (Nrf2) expression in wound tissue were measured to evaluate the scald wound healing performance of extraction from A. manihot (L.) medik (EAM). Scalding activity in mice was examined in vivo by hot water‐induced finger swelling. The treatment scald activities were also examined in vivo by subjecting mice to thermal water‐induced digit swelling. Additionally, the antioxidant effect of EAM on fibroblasts was also used to determine the mechanism in vitro. The results showed that EAM not only decreased the wound healing time but also effectively regulated the levels of oxidising, MDA and T‐SOD in wound tissue. Concurrently, EAM suppressed digit swelling and hyperalgesia. Furthermore, EAM had a significant protective effect on NIH‐3T3 cells after H2O2 injury by regulating the Nrf2 signalling pathway against oxidative injury. Therefore, EAM is a promising drug for the treatment of scald‐induced inflammation. [ABSTRACT FROM AUTHOR]

Objective of this study is to identify a set of internal control genes for the analysis of gene expression. Methods: This study employs reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) to assess gene expression in bone tissue. We selected fourteen housekeeping genes and assessed their stability in the cortical bone of mouse models for obesity and diabetes using four well-established algorithms (GeNorm, BestKeeper, NormFinder, and the comparative Delta Ct method). Results and Conclusion: We identified Rpl13a as the mostly stably expressed reference gene in cortical bone tissue from mouse models of obesity and diabetes (db/db), while Gapdh was found to be the most stable reference gene in another diabetes model, KKAy mice. Additionally, Ef1a, Ppia, Rplp0, and Rpl22 were identified as alternative genes suitable for normalizing gene expression in cortical bone from obesity and diabetes mouse models. These findings enhance RT-qPCR accuracy and reliability, offering a strategic guide to select reference gene for studying bone tissue gene expression in metabolic disorders. [ABSTRACT FROM AUTHOR]

Approximately 50% of colorectal cancer (CRC) patients would develop metastasis with poor prognosis, therefore, it is necessary to effectively predict metastasis in clinical treatment. In this study, we aimed to establish a machine-learning model for predicting metastasis in CRC patients by considering radiomics and transcriptomics simultaneously. Here, 1023 patients with CRC from three centers were collected and divided into five queues (Dazhou Central Hospital n  = 517, Nanchong Central Hospital n  = 120 and the Cancer Genome Atlas (TCGA) n  = 386). A total of 854 radiomics features were extracted from tumor lesions on CT images, and 217 differentially expressed genes were obtained from non-metastasis and metastasis tumor tissues using RNA sequencing. Based on radiotranscriptomic (RT) analysis, a novel RT model was developed and verified through genetic algorithms (GA). Interleukin (IL)-26, a biomarker in RT model, was verified for its biological function in CRC metastasis. Furthermore, 15 radiomics variables were screened through stepwise regression, which was highly correlated with the IL26 expression level. Finally, a radiomics model (RA) was established by combining GA and stepwise regression analysis with radiomics features. The RA model exhibited favorable discriminatory ability and accuracy for metastasis prediction in two independent verification cohorts. We designed multicenter, multi-scale cohorts to construct and verify novel combined radiomics and genomics models for predicting metastasis in CRC. Overall, RT model and RA model might help clinicians in directing personalized diagnosis and therapeutic regimen selection for patients with CRC. [ABSTRACT FROM AUTHOR]

AS602801 has been reported as a potential drug candidate against brain metastasis by suppressing the gap‐junction communication between lung cancer stem cells and astrocytes. In this study, we aimed to study the molecular mechanism underlying the role of AS602801 in the treatment of brain metastasis in breast cancer. We utilized female athymic BALB/c nude mice and MDA‐MB‐231/BT‐474BR cells to establish experimental models. Polymerase chain reaction assays were performed to observe changes in the connexin 43 (Cx43) messenger RNA (mRNA) and c‐Jun N‐terminal kinase (JNK) mRNA levels. Dye transfer assay was used to observe the effect of AS602801 on cell–cell communication. An organotypic blood–brain barrier (BBB) model was utilized to observe the effect of AS602801 on transmigration through the BBB barrier. MTT (3‐[4,5‐dimethylthiazol‐2‐yl]‐2,5 diphenyl tetrazolium bromide) assay and flow cytometry were performed to evaluate the proliferation and apoptosis of breast cancer cells co‐cultivated with astrocytes. AS602801 inhibited the upregulation of Cx43 and JNK in brain metastasized breast cancer cells in a dose‐dependent manner. Also, AS602801 significantly decreased the dye transfer rate from astrocytes to breast cancer cells, indicating the inhibitory effect of AS602801 on cell–cell communication. The transmigration ability of breast cancer cells co‐cultured with astrocytes was decreased by AS602801. Furthermore, AS602801 reduced the elevated Cx43/JNK mRNA expression in the co‐astrocyte group while suppressing the increased proliferation and promoting the decreased apoptosis of breast cancer cells co‐cultivated with astrocytes. AS602801 also suppressed the brain metastasis of breast cancer cells and increased mouse survival. AS602801 downregulates the expressions of JNK and Cx43 to suppress the gap‐junction activity. AS602801 also inhibits the communication between breast cancer cells and astrocytes, thus contributing to the treatment of brain metastasis in breast cancer. [ABSTRACT FROM AUTHOR]

Background and Objectives: The utilization of natural products to enhance the function of periodontal ligament cells (PDLCs) has emerged as a popular area of research. Recent investigations have demonstrated that sappanchalcone (SC) possesses pharmacological properties such as anti‐inflammatory and osteoprotective effects. This study aims to explore the impact of SC on the in vivo and in vitro osteogenic differentiation ability of PDLCs. Materials: Cell proliferation was quantified using the CCK‐8 assay, while gene expression levels were assessed through qRT–PCR analysis. Osteoblast differentiation capacity was evaluated by employing Alizarin red staining (ARS), alkaline phosphatase (ALP) staining and western blot (WB) analysis. A rat model of periodontitis was established utilizing the tether‐wire method. Micro‐CT imaging and hematoxylin and eosin (HE) staining were employed to evaluate alveolar bone resorption. Masson's trichrome staining was utilized to observe fiber alignment, whereas immunohistochemistry (IHC) techniques were applied for detecting osteogenic and inflammatory factors. Results: The results from the CCK‐8 assay indicate no observed cytotoxicity for concentrations of 1, 5, or 10 nM for SC treatment (p <.05), while qRT–PCR analysis demonstrates a significant decrease in inflammatory factors such as MMP‐1 and IL‐6 with treatment by SC (p <.05). Additionally, western blotting reveals an increase in protein expression levels of Runx2 and OPN within PDLCs treated with SC compared to control groups (p <.05), which is further supported by ARS and ALP staining indicating an increase in mineralized nodules formation along with elevated ALP content within these cells following treatment with this compound (p <.05). Finally, both HE staining as well as micro‐CT imaging suggest potential benefits associated with using this compound including slowing alveolar bone resorption while simultaneously promoting junctional epithelium proliferation. Conclusions: Our in vitro and in vivo findings suggest that SC can effectively enhance the inflammatory response of PDLCs and promote their osteogenic differentiation ability under inflammatory conditions, indicating its potential as a promising therapeutic agent for improving periodontal inflammation and bone formation. [ABSTRACT FROM AUTHOR]

Background: Temperature is an important environment factor that is critical to the survival and growth of crustaceans. However, the mechanisms by which crustaceans detect changes in temperature are still unclear. The transient receptor potential (TRP) channels are non-selective cation channels well known for properties in temperature sensation. However, comprehensive understandings on TRP channels as well as their temperature sensing functions are still lacking in crustaceans. Results: In this study, a total of 26 TRP genes were identified in the swimming crab, Portunus trituberculatus, which can be classified into TRPA, TRPC, TRPP, TRPM, TRPML, TRPN and TRPV. Tissue expression analysis revealed a wide distribution of these TRP genes in P. trituberculatus, and antennules, neural tissues, and ovaries were the most commonly expressed tissues. To investigate the responsiveness of TRP genes to the temperature change, 18 TRPs were selected to detect their expression after high and low temperature stress. The results showed that 12 TRPs showed induced gene expression in both high and low temperature groups, while 3 were down-regulated in the low temperature group, and 3 showed no change in expression in either group. Conclusions: This study characterized the TRP family genes in P. trituberculatus, and explored their involvement in response to temperature stress. Our results will enhance overall understanding of crustacean TRP channels and their possible functions. [ABSTRACT FROM AUTHOR]

Background: Artemisia annua is the major source for artemisinin production. The artemisinin content in A. annua is affected by different types of light especially the UV light. UVR8, a member of RCC1 gene family was found to be the UV-B receptor in plants. The gene structures, evolutionary history and expression profile of UVR8 or RCC1 genes remain undiscovered in A. annua. Results: Twenty-two RCC1 genes (AaRCC1) were identified in each haplotype genome of two diploid strains of A. annua, LQ-9 and HAN1. Varied gene structures and sequences among paralogs were observed. The divergence of most RCC1 genes occurred at 46.7 – 51 MYA which overlapped with species divergence of core Asteraceae during the Eocene, while no recent novel RCC1 members were found in A. annua genome. The number of RCC1 genes remained stable among eudicots and RCC1 genes underwent purifying selection. The expression profile of AaRCC1 is analogous to that of Arabidopsis thaliana (AtRCC1) when responding to environmental stress. Conclusions: This study provided a comprehensive characterization of the AaRCC1 gene family and suggested that RCC1 genes were conserved in gene number, structures, constitution of amino acids and expression profiles among eudicots. [ABSTRACT FROM AUTHOR]

PUF proteins are characterized by globular RNA-binding domains. They also interact with partner proteins that modulate their RNA-binding activities. Caenorhabditis elegans PUF protein fem-3 binding factor-2 (FBF-2) partners with intrinsically disordered Lateral Signaling Target-1 (LST-1) to regulate target mRNAs in germline stem cells. Here, we report that an intrinsically disordered region (IDR) at the C-terminus of FBF-2 autoinhibits its RNA-binding affinity by increasing the off rate for RNA binding. Moreover, the FBF-2 C-terminal region interacts with its globular RNA-binding domain at the same site where LST-1 binds. This intramolecular interaction restrains an electronegative cluster of amino acid residues near the 5′ end of the bound RNA to inhibit RNA binding. LST-1 binding in place of the FBF-2 C-terminus therefore releases autoinhibition and increases RNA-binding affinity. This regulatory mechanism, driven by IDRs, provides a biochemical and biophysical explanation for the interdependence of FBF-2 and LST-1 in germline stem cell self-renewal. FBF-2 and LST-1 repress gld-1 mRNA expression to maintain C. elegans germline stem cells. The authors show that an intrinsically-disordered region of FBF-2 autoinhibits its RNA binding. LST-1 antagonizes this interaction to promote RNA binding. [ABSTRACT FROM AUTHOR]

The emergence of fungicide resistance severely threatens crop production by limiting the availability and application of established fungicides. Therefore, it is urgent to identify new fungicidal targets for controlling plant diseases. Here, we characterized the function of a conserved homoserine O-acetyltransferase (HOA) from the rice blast fungus Magnaporthe oryzae that could serve as the candidate antifungal target. Deletion of the MoMET2 and MoCYS2 genes encoding HOAs perturbed the biosynthesis of methionine and S-adenyl methionine, a methyl group donor for epigenetic modifications, and severely attenuated the development and virulence of M. oryzae. The ∆Momet2 mutant is significantly increased in 5-methylcytosine (5mC) modification that represses the expression of genes required for pathogenicity, including MoGLIK and MoCDH-CYT. We further showed that host-induced gene silencing (HIGS) targeting MoMET2 and MoCYS2 effectively controls rice blasts. Our studies revealed the importance of HOA in the development and virulence of M. oryzae, which suggests the potential feasibility of HOA as new targets for novel anti-rice blast measurements. Author summary: Despite the effectiveness of available antifungal agents in combating rice blasts, the emergence of resistance to these agents requires the reexamination of fungal pathogens, plant-fungi interactions, and virulence factors. Characterization of virulence factors is expected to improve the understanding of fungus pathogenesis and to help exploration for an antifungal drug target. We here reported that HOAs of the fungal original could serve as a potential target for antifungal agents. Specifically, we found that homoserine O-acetyltransferases MoMet2 and MoCys2 are important in the biosynthesis of methionine and S-adenyl methionine that are critical for the growth, development, and virulence of M. oryzae. We further demonstrated that MoMet2-mediated 5mC modification regulates gene expression and is required for infection by the rice blast fungus. Additionally, using host-induced gene silencing (HIGS) targeting MoMET2 and MoCYS2 genes provided protection against rice blasts. In all, the studies shed significant new insights in understanding the role of methionine synthesis in fungal pathogenicity and in identifying potential antifungal targets. [ABSTRACT FROM AUTHOR]

Flax (Linum usitatissimum L.) is an important oilseed crop widely cultivated for its oil and fiber. This study conducted transcriptome analysis to analyze the gene expression profiles of roots, leaves, stamens, pistils, and fruits in the flax cultivar Longya10. A total of 43,471 genes were detected in the RNA-seq data, with 34,497 genes showing differential expression levels between different organs. Gene expression patterns varied across different organs, with differences observed in expression-regulating genes within specific organs. However, 23,448 genes were found to be commonly expressed across all organs. Further analysis revealed organ-specific gene expressions, with 236, 690, 544, 909, and 1212 genes identified in pistils, fruits, leaves, roots, and stamens, respectively. Gene Ontology (GO) enrichment analysis was performed on these organ-specific genes, and significant enrichment was observed in various biological processes, cellular components, and molecular functions, providing new insights for the specific growth patterns of flax organs. Furthermore, we investigated the expression differences of AP2 transcription factors in various tissues and organs of Longya10. We identified 96 AP2 genes that were differentially expressed in different organs and annotated them into various biological pathways. Our results suggest that AP2 transcription factors may play important roles in regulating the growth and development of flax organs including stress response. In summary, our study provides a comprehensive analysis of gene expression patterns in different organs and tissues of flax plant and identifies potential critical regulators of flax organ growth and development. These findings contribute to a better understanding of the molecular mechanisms underlying flax organ development and may have important implications for the genetic improvement of flax crops. [ABSTRACT FROM AUTHOR]

DNA methylation (5mC) and N6-methyladenosine (m6A) are two important epigenetics regulators, which have a profound impact on plant growth development. Phyllostachys edulis (P. edulis) is one of the fastest spreading plants due to its well-developed root system. However, the association between 5mC and m6A has seldom been reported in P. edulis. In particular, the connection between m6A and several post-transcriptional regulators remains uncharacterized in P. edulis. Here, our morphological and electron microscope observations showed the phenotype of increased lateral root under RNA methylation inhibitor (DZnepA) and DNA methylation inhibitor (5-azaC) treatment. RNA epitranscriptome based on Nanopore direct RNA sequencing revealed that DZnepA treatment exhibits significantly decreased m6A level in the 3′-untranslated region (3′-UTR), which was accompanied by increased gene expression, full-length ratio, higher proximal poly(A) site usage and shorter poly(A) tail length. DNA methylation levels of CG and CHG were reduced in both coding sequencing and transposable element upon 5-azaC treatment. Cell wall synthesis was impaired under methylation inhibition. In particular, differentially expressed genes showed a high percentage of overlap between DZnepA and 5-azaC treatment, which suggested a potential correlation between two methylations. This study provides preliminary information for a better understanding of the link between m6A and 5mC in root development of moso bamboo. [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]

Sucrose non-fermenting-1 (SNF1)-related protein kinase2s (SnRK2s) were reported to be one of the critical factors in abscisic acid (ABA) signaling, playing important roles in response to biotic and abiotic stresses in plants. Common bean (Phaseolus vulgaris L.) is one of the most important protein crops, but little is known about SnRK2s (PvSnRK2s) in common bean. In this study, we identified and characterized PvSnRk2s at the genome-wide level. We identified 10 PvSnRK2 genes, which were divided into 4 groups by phylogenetic analysis. Stress response element (TC-rich repeats), MYB binding site involved in drought-inducibility (MBS), and low-temperature responsiveness element (LTR) were identified in the promoter regions of PvSnRK2s. Real-time fluorescence quantitative RT-PCR (RT-qPCR) was used to verify the expression profiles of 10 genes at 5 time points under high salt, drought and low temperature stresses. Results showed that the expression levels of PvSnRK2.2/2.9 of group II were much higher than that of the other groups' members under drought stress, implying these genes might play an important role in the response of common bean to water deficiency. Furthermore, PvSnRK2.4 was significantly up-regulated under NaCl, Mnt (mannitol) and low-temperature stresses, indicating the gene may be one of the essential regulatory genes of common bean in response to the adverse external environment. This is the first comprehensive analysis of the SnRK2 genes in the common bean, which provided a basis for further elucidating the function of PvSnRK2 genes in the common bean. [ABSTRACT FROM AUTHOR]

Background: Intervertebral disc degeneration (IDD) naturally occurs during the aging process. Its occurrence is closely related to chronic inflammation; however, the causal relationship between them is controversial. This study aimed to investigate if inflammation would promote IDD incidence and explore the underlying mechanism. Methods: A chronic inflammation mouse model was established by intraperitoneal injection of lipopolysaccharide (LPS). Enzyme-linked immunosorbent assay was performed to determine proinflammatory cytokines in serum. Histological staining was used to evaluate the degeneration of IVDs. Immunoblots and RT-qPCR analyses were performed to measure protein and mRNA expression levels. Immunoprecipitation, mass spectrometry, and co-immunoprecipitation assays were used to determine the assembly of protein complex. Results: We found that an inflammatory microenvironment activated p38 kinase, which phosphorylated the Runx2 transcription factor at the Ser28 site. The phosphorylated Runx2 (pRunx2) then recruited a deubiquitinase, ubiquitin-specific peptidase 24 (USP24), which stabilized pRunx2 and protected it from ubiquitin-dependent proteasomal degradation. The stabilized pRunx2 recruited histone acetyltransferase p300 and nuclear receptor coactivator 3 (NCOA3) to assemble a complex. This NCOA3-p300-pRunx2 complex then transactivated the expression of 13 ADAMTS (a disintegrin and metalloproteinase with thrombospondin motif) genes, thereby promoting the degradation of extracellular matrix (ECM) in intervertebral discs (IVDs) and causing IDD. Administration of either a p38 inhibitor (doramapimod), a NCOA3 inhibitor (bufalin), or a p300 inhibitor (EML425) significantly decreased the expression of the 13 ADAMTS genes and slowed the degeneration of IVDs. Conclusion: In summary, our results demonstrate that USP24 protects pRunx2 from proteasomal degradation under chronic inflammation conditions, enabling pRunx2 to transactivate ADAMTS genes and degrade ECM. Our findings provide direct evidence that chronic inflammation triggers IDD and offer a therapeutic strategy for retarding IDD in patients with chronic inflammation. [ABSTRACT FROM AUTHOR]

The brown planthopper Nilaparvata lugens (Stål) (BPH) is a typical monophagous sucking rice pest. Over the course of their evolution, BPH and its symbionts have established an interdependent and mutually beneficial relationship, with the symbionts being important to the growth, development, reproduction, and variation in virulence of BPH. Yeast-like symbionts (YLS), harbored in the abdomen fat body cells of BPH, are vital to the growth and reproduction of the host. In recent research, the symbionts in BPH have mainly been detected using blood cell counting, PCR, real-time quantitative PCR, and other methods. These methods are vulnerable to external interference, cumbersome, time consuming and laborious. Droplet digital PCR (ddPCR) does not need a standard curve, can achieve absolute quantification, does not rely on Cq values, and is more useful for analyzing copy number variation, gene mutations, and relative gene expression. A rapid detection method for the YLS of BPH based on ddPCR was established and optimized in this study. The results showed that the method's limits of detection for the two species of YLS (Ascomycetes symbionts and Pichia guilliermondii) were 1.3 copies/μL and 1.2 copies/μL, respectively. The coefficient of variation of the sample repetition was less than 5%; therefore, the ddPCR method established in this study had good sensitivity, specificity, and repeatability. It can be used to detect the YLS of BPH rapidly and accurately. [ABSTRACT FROM AUTHOR]