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DNA modifications add another layer of complexity to the eukaryotic genome to regulate gene expression, playing critical roles as epigenetic marks. In eukaryotes, the study of DNA epigenetic modifications has been confined to 5mC and its derivatives for decades. However, rapid developing approaches have witnessed the expansion of DNA modification reservoirs during the past several years, including the identification of 6mA, 5gmC, 4mC, and 4acC in diverse organisms. However, whether these DNA modifications function as epigenetic marks requires careful consideration. In this review, we try to present a panorama of all the DNA epigenetic modifications in eukaryotes, emphasizing recent breakthroughs in the identification of novel DNA modifications. The characterization of their roles in transcriptional regulation as potential epigenetic marks is summarized. More importantly, the pathways for generating or eliminating these DNA modifications, as well as the proteins involved are comprehensively dissected. Furthermore, we briefly discuss the potential challenges and perspectives, which should be taken into account while investigating novel DNA modifications. [ABSTRACT FROM AUTHOR]

Sea cucumber Apostichopus japonicus displays the typical circadian rhythms. This present study investigated the molecular regulation of clock genes, as well as monoamines and melatonin, in multiple tissues of A. japonicus , responding to the photoperiod. In order to determine their pivotal role in circadian rhythms, the crucial clock genes, namely AjClock , AjArnt1 , AjCry1 , and AjTimeless , were identified and a comprehensive analysis of their expressions across various tissues in adult A. japonicus was conducted, revealing the potential existence of central and peripheral oscillators. Results demonstrated that the tissues of polian vesicle and nerve ring exhibited significant clock gene expression associated with the orchestration of circadian regulation, and that environmental light fluctuations exerted influence on the expression of these clock genes. However, a number of genes, such as AjArnt1 and AjCry1 , maintained their circadian rhythmicity even under continuous light conditions. Moreover, we further investigated the circadian patterns of melatonin (MT), serotonin (5-HT), and dopamine (DA) secretion in A. japonicus , data that underscored the tissue-specific regulatory differences and the inherent adaptability to dynamic light environments. Collectively, these findings will provide the molecular mechanisms controlling the circadian rhythm in echinoderms and the candidate tissues playing the role of central oscillators in sea cucumbers. [Display omitted] • The molecular circadian system was identified in Apostichopus japonicus. • The polian vesicle and nerve ring were determined with roles as circadian oscillators. • A. japonicus circadian system exhibits stability. • The rhythmicity of molecular circadian system can be affected by photoperiods. [ABSTRACT FROM AUTHOR]

The sea cucumber Apostichopus japonicus is an economically important marine species in China, and understanding the mechanisms underlying its gonad development is crucial for successful reproduction and breeding. In this study, we performed transcriptome comparisons and analyses of A. japonicus gonadal and non-gonadal tissues to identify genes and molecular pathways associated with gonadal development. We also supplemented the annotation of the A. japonicus genome. Collectively, results revealed a total of 941 ovary-specific genes and 2499 testis-specific genes through different expression analysis and WGCNA analysis. The most enriched pathways in ovary and testis were "DNA replication" and "purine metabolism", respectively. Additionally, we identified key candidate gene modules that control gonad development and germ cell maturation, with CDT1 and DYNC2LI1 serving as hub genes. Our findings provide important insights into the gonadal development system of A. japonicus and offer valuable references for further research on reproductive biology in this marine invertebrate species. [Display omitted] • Comparative analyses of gene expression in sea cucumber gonadal and non-gonadal tissues • Key candidate gene modules specifically expressed by females and males gonad were screened. • The ovarian module with CDT1 as the core gene may affect ovarian development through the pre-replication complex. [ABSTRACT FROM AUTHOR]

Abstract: In this study, an oxidative stress model was first developed in a mouse macrophage cell line (RAW264.7 cells) by infecting the cells with porcine circovirus type 2 (PCV2). The regulatory effect of Sophora subprosrate polysaccharide (SSP) on PCV2-induced oxidative stress was investigated. The results showed that after infection with PCV2, reactive oxygen species (ROS) and nitric oxide (NO) production, myeloperoxidase (MPO) activity, and inducible nitric oxide synthase (iNOS) expression were significantly increased. Meanwhile, the ratio of reduced glutathione to oxidized glutathione (GSH/GSSG) and hydroxyl radical prevention capacity were greatly reduced. These data indicate successful creation of an oxidative stress model in RAW264.7 cells. A dramatic decrease in cell viability was observed in the cells exposed to oxidative stress compared to the control. When the cells were treated with SSP in concentrations of 100, 200 or 400μg/mL post PCV2 infection, an increase in the GSH/GSSG ratio and hydroxyl radical prevention capacity was observed. We also observed decreased ROS and NO production, MPO activity, and iNOS expression in the infected cells. Our results demonstrated that PCV2 infection was able to induce oxidative stress in RAW264.7 cells and that SSP could reduce the negative effects resulting from the PCV2 infection. [Copyright &y& Elsevier]

Zuojin Pill (ZJP) has been a classic prescription for the treatment of gastrointestinal diseases in China since ancient times. But its effect on non-steroidal anti-inflammatory drugs (NSAIDs) induced gastric injury (GI) is still uncharted. This study aims to investigate the therapeutic effect and molecular mechanism of ZJP on indomethacin (IDO) induced gastric injury. GI was induced in rat by oral administration of 5 mg/kg IDO. Then the rats were treated with ZJP (1.26, 2.52, 5.04 g/kg, ig). The changes of food intake, body weight, gastric pH and general state observation were carried out to determine the improvement of ZJP in IDO-induced GI: HE staining and AB-PAS staining was analyzed to characterize the thickness of gastric mucosa and micro mucosal injury; in order to elucidate the effect of ZJP on IDO-induced inflammatory injury, the inflammatory infiltration of gastric tissue was observed by MPO immunohistochemical method, and the contents of TNF-α, IL-6 and IL-10 were measured. Furthermore, the regulatory mechanism of ZJP in treating IDO-induced GI was predicted with the help of network pharmacology, and the expression levels of key proteins ERK, p-ERK, P38, p-P38, JNK, p-JNK were determined to elucidate the molecular mechanism of ZJP. Current data strongly demonstrated that ZJP alleviated food intake reduction, weight loss and gastric injury caused by IDO and made gastric pH and mucosal thickness return to normal. In addition, ZJP could reduce the level of MPO to alleviate the inflammatory infiltration of gastric tissue. Simultaneously, ZJP could down regulate the expression of TNF-α and IL-6 and up regulate the expression of IL-10 to reduce the damage caused by inflammatory, and create a healing environment. Furthermore, ZJP could significantly inhibit the phosphorylation of ERK, p38 and JNK, which leaded to the increase of inflammatory factors and the damage of gastric mucosa. ZJP improved local inflammation by inhibiting MAPK signaling pathway, and had a good therapeutic effect on IDO-induced GI. This study has reference significance for the study of ZJP in the prevention and treatment of NSAID induced gastric injury. In addition, ZJP may be a new treatment option for the prevention and treatment of NSAID induced gastric disease. [Display omitted] [ABSTRACT FROM AUTHOR]

Tumor necrosis factor α (TNFα), an inflammatory cytokine, induces lipolysis and increases circulating concentrations of free fatty acids. In addition, TNFα is the first adipokine produced by adipose tissue in obesity, contributing to obesity-associated metabolic disease. Given that benzyl isothiocyanate (BITC) is a well-known anti-inflammatory agent, we hypothesized that BITC can ameliorate TNFα-induced lipolysis and investigated the working mechanisms involved. We first challenged 3T3-L1 adipocytes with TNFα to induce lipolysis, which was confirmed by increased glycerol release, decreased protein expression of peroxisome proliferator-activated receptor γ (PPARγ) and perilipin 1 (PLIN1), and increased phosphorylation of ERK, protein kinase A (PKA), and hormone-sensitive lipase (HSL). However, inhibition of ERK or PKA significantly attenuated the lipolytic activity of TNFα. Meanwhile, pretreatment with BITC significantly ameliorated the lipolytic activity of TNFα; the TNFα-induced phosphorylation of ERK, PKA, and HSL; the TNFα-induced ubiquitination of PPARγ; the TNFα-induced decrease in PPARγ nuclear protein binding to PPAR response element; and the TNFα-induced decrease in PLIN1 protein expression. Our results indicate that BITC ameliorates TNFα-induced lipolysis by inhibiting the ERK/PKA/HSL signaling pathway, preventing PPARγ proteasomal degradation, and maintaining PLIN1 protein expression. BITC inhibits TNFα-induced ubiquitination of PPARγ and subsequent proteasomal degradation and PPARγ is a critical transcription factor for PLIN1, which acts as a barrier to the breakdown of storage lipids. In addition, TNFα activates the ERK/PKA/HSL signaling pathway participating in lipolysis, which is suppressed by BITC. Abbreviations: BITC, benzyl isothiocyanate; DG, diglyceride; FFA, free fatty acid; HSL, hormone-sensitive lipase; MG, monoglyceride; PKA, protein kinase A; PLIN1, perilipin 1; PPARγ, peroxisome proliferator-activated receptor γ; TG, triglyceride; TNFα, tumor necrosis factor α. [Display omitted] [ABSTRACT FROM AUTHOR]

Glioma, as the most common aggressive malignant tumor in the central nervous system, is still an insurmountable issue in neural diseases. The proliferation and survival mechanism of glioma cells need to be explored further for the development of glioma treatment. Hematopoietic cell-specific protein 1 associated protein X-1 (HAX-1) is well known for its anti-apoptotic effect. It was reported to play an important role in several malignant tumors. However, the effect of HAX-1 in glioma still remains unknown. This study aimed to investigate the expression of HAX-1 in glioma and the correlation between HAX-1 and the clinicopathological characteristics and prognosis of glioma. Quantitative reverse transcription polymerase chain reaction and Western blot analysis showed that HAX-1 was overexpressed in glioma cell lines compared with normal human astrocytes. This trend was confirmed by comparing the expression of HAX-1 in glioma tissues and nontumorous tissues. The study also analyzed the correlation between the expression of HAX-1 and clinicopathological characteristics of glioma and found the expression of HAX-1 to be highly related to the differentiation and World Health Organization stage of glioma tissues. The survival analysis revealed that HAX-1 was an independent prognostic factor. In conclusion, this novel study suggested that the overexpression of HAX-1 might contribute to the malignant progression of glioma. [ABSTRACT FROM AUTHOR]

• GLP-2 ameliorated D-galactose induced muscle atrophy in mice. • GLP-2 promoted protein synthesis and alleviated protein degradation and apoptosis. • The IGF-1/PI3K/Akt/FoxO3 pathway played a role in the protective effect of GLP-2. The study aimed to investigate the effect of Glucagon-like peptide-2 (GLP-2) on muscle aging in vivo and in vitro. Six-week-old C57BL/6J mice were administered with D-galactose (200 mg/kg/day, intraperitoneally) for 8weeks, followed by daily subcutaneous injections of GLP-2 (300 or 600 μg/kg/day) for 4weeks. Skeletal muscle function and mass were evaluated using relative grip strength and muscle weight. The sizes and types of muscle fibers and apoptosis were assessed through histological analysis, immunofluorescence staining, and TUNEL staining, respectively. C2C12 myotubes were treated with D-galactose (40 mg/mL) and GLP-2. Protein expression of differentiation-related myogenic differentiation factor D (MyoD), myogenin (MyoG), and myosin heavy chain (Myhc), degradation-related Muscle RING finger 1 (MuRF-1), and muscle atrophy F-box (MAFbx)/Atrogin-1, and apoptosis-related B-cell leukemia/lymphoma 2 (Bcl-2) and Bax, were assessed using western blots. The Pi3k inhibitor LY294002 was applied to investigate whether GLP-2 regulated myogenesis and myotube aging via IGF-1/Pi3k/Akt/FoxO3a signaling pathway. The results demonstrated that GLP-2 significantly reversed the decline in muscles weight, relative grip strength, diameter, and cross-sectional area of muscle fibers induced by D-galactose in mice. Apart from suppressing the expressions of MuRF-1 and Atrogin-1 in the muscles and C2C12 myotubes, GLP-2 significantly increased the expressions of MyoD, MyoG, and Myhc compared to the D-galactose. GLP-2 significantly suppressed cell apoptosis. Western blot analysis indicated that the regulation of GLP-2 may be attributed to the activation of theIGF-1/Pi3k/Akt/FoxO3a phosphorylation pathway. This study suggested that GLP-2 ameliorated D-galactose induced muscle aging by IGF-1/Pi3k/Akt/FoxO3a pathway. [Display omitted] [ABSTRACT FROM AUTHOR]

• Over-expression of AdBcl-w inhibited the apoptotic process during GSIV infection while RNAi of AdBcl-w promoted this process. • Over-expression of AdBcl-w can effectively reduce the replication of GSIV. • The interaction of AdBcl-w and AdBak reduced after GSIV infection. • Over-expression of AdBcl-w restrained the mRNA expression of molecules in p53 pathway during GSIV infection. B-cell lymphoma-2 (BCL-2) superfamily molecules play crucial roles in mitochondrial apoptosis induced by Chinese giant salamander iridovirus (GSIV). As an anti-apoptotic molecule in the BCL-2 family, the molecular mechanism of Bcl-w during GSIV infection remains unknown. In this study, we characterized for the first time an amphibian Bcl-w from Chinese giant salamander Andrias davidianus (AdBcl-w), and its function and regulatory mechanism during GSIV infection were investigated. AdBcl-w possesses the conserved structural features of Bcl-w and shares 35–54% sequence identities with other Bcl-w. mRNA expression of AdBcl-w was most abundant in liver and muscle. The AdBcl-w mRNA expression was regulated during GSIV infection. Western blotting assays revealed that the level of Bcl-w protein was downregulated markedly as the infection progresses. Confocal microscopy showed that overexpressed AdBcl-w was translocated to the mitochondria after infection with GSIV. Flow cytometry analysis demonstrated that compared with control, the apoptotic progress in cells transfected with AdBcl-w was reduced while that in cells transfected with AdBcl-w siRNA was enhanced. The number of virus major capsid protein gene copies was lower and protein synthesis was reduced in AdBcl-w overexpressing cells. In addition, AdBcl-w could bind directly to the pro-apoptotic molecule AdBak, while this interaction was weakened with GSIV infection. Moreover, p53 level was reduced and the mRNA expression levels of crucial regulatory molecules in the p53 pathway were regulated in AdBcl-w overexpressing cells during GSIV infection. These results suggested that AdBcl-w inhibit GSIV replication by regulating the virus induced mitochondrial apoptosis. [ABSTRACT FROM AUTHOR]

In the present study, effect of Sophora subprosrate polysaccharide on PCV2 infection-induced inflammation and histone acetylation modification in swine alveolar macrophage 3D4/2 cells was described for the first time. The relationship between histone acetylation modifications and inflammation response was investigated. The results showed that PCV2 infection induced inflammation by promoting the secretion of TNF-α, IL-1β, IL-6 and IL-10 in 3D4/2 cells. The production of TNF-α, IL-1β and IL-6 and their mRNA expression levels markedly decreased while the level and mRNA expression of IL-10 were elevated when the cells were treated with Sophora subprosrate polysaccharide. The SSP also decreased the activity of HATs, histone H3 acetylation (Ac-H3) and histone H4 acetylation (Ac-H4), p65 phosphorylation (P-p65) in the cells infected with PCV2 while HDACs activity was down-regulated, which involved in the inhibitory effect of SSP on histone acetylation and NF-κB signaling pathways activation. Down-regulation of HAT1 mRNA expression and up-regulation of HDAC1 mRNA expression further support the inhibitory effect of SSP on histone acetylation. In conclusion, Sophora subprosrate polysaccharide antagonized inflammatory responses induced by PCV2, via mechanisms involved in histone acetylation and NF-κB signaling pathways. [ABSTRACT FROM AUTHOR]

Ethnopharmacological relevance The pathogenesis of thromboangiitis obliterans (TAO) has not been fully elucidated until now. Shenfu injection (SFI), a traditional Chinese formula has been widely used clinically for the treatment of cardiovascular diseases for more than two decade. Our previous results first suggested that SFI can cause a significant therapeutic effect on experimental TAO model rats. This experiment was designed to further investigate the protective effect of SFI on VEC damaged by hydrogen peroxide (H 2 O 2 ) oxidative stress in vitro . Meterials and methods The cell viability was evaluated by the MTT assay, the activities of SOD and GSH-PX and the content of MDA in the supernatants of the cultured ECV304 cells were evaluated by a colorimetry method, cell apoptosis was detected by flow cytometry and an AO/EB double staining method. The protein expressions of Bcl2, Bax and caspase-3 were examined by Western blotting. Results When compared with control group, lower survival rate of ECV304 cells was observed in H 2 O 2 group ( p <0.01) ; 20 μl/ml, 30 μl/ml and 40 μl/ml SFI increased the survival rate of ECV304 cells under H 2 O 2 oxidative stress ( p <0.05 and p <0.01). The activities of SOD and GSH-PX were higher and MDA level was lower in H 2 O 2 group than those in control group. These effects of H 2 O 2 on SOD, GSH-PX activities and MDA content were reversed by SFI in concentration-dependent way ( p <0.05 and p <0.01). Flow cytometry and AO–EB double staining discovered that SFI pretreatment inhibited the ECV304 cells apoptosis. The protein expression of caspase3 in 30 μl/ml and 40 μl/ml SFI groups significantly decreased whereas Bcl2 protein expressions in 20 μl/ml, 30 μl/ml and 40 μl/ml SFI groups were higher than H 2 O 2 group, with Bax protein expression much lower than H 2 O 2 group ( p <0.05 and p <0.01). Conclusions Our findings suggest that SFI could prevent the ECV304 cells against H 2 O 2 oxidative-stress by enhancing antioxidant enzyme activities, reducing the membrane lipid peroxidation, as well as upregulating antiapoptotic and downregulating apoptosis protein expressions. [ABSTRACT FROM AUTHOR]