Search

Background: Steroid-induced osteonecrosis of femoral head (SONFH) is a severe health risk, and this study aims to identify immune-related biomarkers and pathways associated with the disease through bioinformatics analysis and animal experiments. Method: Using SONFH-related datasets obtained from the GEO database, we performed differential expression analysis and weighted gene co-expression network analysis (WGCNA) to extract SONFH-related genes. A protein-protein interaction (PPI) network was then constructed, and core sub-network genes were identified. Immune cell infiltration and clustering analysis of SONFH samples were performed to assess differences in immune cell populations. WGCNA analysis was used to identify module genes associated with immune cells, and hub genes were identified using machine learning. Internal and external validation along with animal experiments were conducted to confirm the differential expression of hub genes and infiltration of immune cells in SONFH. Results: Differential expression analysis revealed 502 DEGs. WGCNA analysis identified a blue module closely related to SONFH, containing 1928 module genes. Intersection analysis between DEGs and blue module genes resulted in 453 intersecting genes. The PPI network and MCODE module identified 15 key targets enriched in various signaling pathways. Analysis of immune cell infiltration showed statistically significant differences in CD8 + t cells, monocytes, macrophages M2 and neutrophils between SONFH and control samples. Unsupervised clustering classified SONFH samples into two clusters (C1 and C2), which also exhibited significant differences in immune cell infiltration. The hub genes (ICAM1, NR3C1, and IKBKB) were further identified using WGCNA and machine learning analysis. Based on these hub genes, a clinical prediction model was constructed and validated internally and externally. Animal experiments confirmed the upregulation of hub genes in SONFH, with an associated increase in immune cell infiltration. Conclusion: This study identified ICAM1, NR3C1, and IKBKB as potential immune-related biomarkers involved in immune cell infiltration of CD8 + t cells, monocytes, macrophages M2, neutrophils and other immune cells in the pathogenesis of SONFH. These biomarkers act through modulation of the chemokine signaling pathway, Toll-like receptor signaling pathway, and other pathways. These findings provide valuable insights into the disease mechanism of SONFH and may aid in future drug development efforts. [ABSTRACT FROM AUTHOR]

Long noncoding RNAs (lncRNAs) play important roles in immune regulation in humans and animals. The lnc-34015 was discovered to be critical for the development of muscles, based on the muscle transcriptome of pigs; however, the underlying molecular mechanism requires better understanding. Here, the sequence characteristics of lnc-34015 were analyzed and a competitive endogenous RNA regulatory network of lncRNA was predicted. The developmental expression trend and tissue expression profiles of lnc-34015 were investigated using quantitative polymerase chain reaction. The lnc-34015 sequence is overlapped with introns 11 and 12 of CWF19L1, while CWF19L1, PKD2L1, and CHUK were identified as cis-regulatory genes of lnc-34015. Bioinformatics analyses revealed that lnc-34015 binds to 15 microRNAs (miRNAs), including miR-3646, miR-377-3p, and miR-190b-3p, to regulate downstream gene expression. GO and KEGG enrichment results show that lnc-34015 was mainly involved in cell proliferation, stress response, transcriptional regulation, and alternative splicing. The expression trend of lnc-34015 in muscle was similar to that of target genes and opposite to that of miRNAs. The expression of lnc-34015 was significantly higher in the porcine small intestine and IPEC-J2 cells. Our findings suggest that lnc-34015 regulates CHUK, ZBTB20, and XIAP gene expression by competing with endogenous RNAs to regulate porcine inflammatory responses. [ABSTRACT FROM AUTHOR]

Uncoupling protein 3 (Ucp3) is an important transporter within mitochondria and is mainly expressed in skeletal muscle, brown adipose tissue and the myocardium. However, the effects of Ucp3 on myogenic differentiation are still unclear. This study evaluated the effects of Ucp3 on myogenic differentiation, myofiber type and energy metabolism in C2C12 cells. Gain- and loss-of-function studies revealed that Ucp3 could increase the number of myotubes and promote the myogenic differentiation of C2C12 cells. Furthermore, Ucp3 promoted the expression of the type IIb myofiber marker gene myosin heavy chain 4 (Myh4) and decreased the expression of the type I myofiber marker gene myosin heavy chain 7 (Myh7). In addition, energy metabolism related to the expression of PPARG coactivator 1 alpha (Pgc1-α), ATP synthase, H+ transportation, mitochondrial F1 complex, alpha subunit 1 (Atp5a1), lactate dehydrogenase A (Ldha) and lactate dehydrogenase B (Ldhb) increased with Ucp3 overexpression. Ucp3 could promote the myogenic differentiation of type IIb myotubes and accelerate energy metabolism in C2C12 cells. This study can provide the theoretical basis for understanding the role of Ucp3 in energy metabolism. [ABSTRACT FROM AUTHOR]

Inflammation accompanies hepatic dysfunction resulting from tissue oxidative damage. Naringenin (Nar), a natural flavanone, has known antioxidant and anti-inflammatory activities, but its mechanism of action in the regulation of liver dysfunction requires further investigation. In this study, the role of naringenin in lipopolysaccharide (LPS)-induced hepatic oxidative stress and inflammation was explored, as well as its mechanism by transcriptome sequencing. The results indicated that compared with the LPS group, Nar treatment caused a significant increase in the mRNA levels of antioxidant factors glutamate-cysteine ligase catalytic subunit (GCLC) and glutamate-cysteine ligase modifier subunit (GCLM), yet the expression of related inflammatory factors (MCP1, TNFα, IL-1β and IL-6) showed less of an increase. RNA sequencing identified 36 differentially expressed lncRNAs and 603 differentially expressed mRNAs. KEGG enrichment analysis indicated that oxidative stress and inflammation pathways are meticulously linked with naringenin treatment. The Co-lncRNA-mRNA network was also constructed. Tissue expression profiles showed that lncRNA played a higher role in the liver. Subsequently, expression levels of inflammatory factors indicated that lncRNAs and target mRNAs were significantly reduced after naringenin treatment in mouse liver AML12 cells and obese mouse. These results suggest that naringenin helps to prevent liver dysfunction through the regulation of lncRNA-mRNA axis to reduce oxidative stress and inflammatory factors. [ABSTRACT FROM AUTHOR]

This study was designed to investigate the effect of 650-nm low-level laser irradiation (LLLI) as an adjunctive treatment of experimental periodontitis. To investigate possible LLLI-mediated anti-inflammatory effects, we utilized an experimental periodontitis (EP) rat model and analyzed c-Jun, c-Fos, ICAM-1, and CCL2 gene expressions on PB leukocytes and in the gingival tissue. Total RNA was isolated from the gingivae and peripheral blood (PB) leukocytes of normal, EP, scaling, and root planing (SRP)-treated EP and LLLI + SRP-treated EP rats, and gene expressions were analyzed by real-time PCR. The productions of c-Jun, c-Fos, ICAM-1, and CCL2 in gingivae were analyzed immunohistochemically. Tartrate-resistant acid phosphatase (TRAP) staining was used to determine osteoclast activity in alveolar bone. The c-Jun and ICAM-1 messenger RNA (mRNA) levels were significantly decreased in the EP rat gingival tissue treated by SRP + LLLI than by SRP, the c-Jun, ICAM-1, and c-Fos mRNA levels on PB leukocytes reduced after LLLI treatment but did not show any significant differences in both groups. There was no significant difference in CCL2 mRNA levels on PB leukocytes and in gingivae between the SRP + LLLI and the SRP groups. The c-Fos mRNA levels in gingivae did not show significant difference in both groups. Immunohistochemistry showed that the CCL2, ICAM-1, c-Jun, and c-Fos productions were significantly reduced in rats of the SRP + LLLI group compared with the only SRP group. LLLI significantly decreased the number of osteoclasts as demonstrated by TRAP staining. The 650-nm LLLI might be a useful treatment modality for periodontitis. [ABSTRACT FROM AUTHOR]

To determine the optimal activity region of the dopachrome tautomerase gene (DCT) promoter in sheep skin melanocytes, five eukaryotic expression vectors were constructed containing DCT promoter fragments of different lengths (441 bp, 652 bp, 834 bp, 1155 bp, and 1504 bp) ligated to the pLV.ExSi.P/Puro-mouse DCT-eGFP vector. These constructs were transiently transfected into sheep skin melanocytes using liposome transfection technology. GFP (Green Fluorescent Protein) expression varied among the groups transfected with different constructs as follows: 652 bp > 834 bp > 441 bp > 1504 bp > 1155 bp. GFP expression was significantly higher in the 652 bp and 834 bp groups than in the 1155 bp group (p < 0.01), while expression in the 652 bp group was significantly higher than in the 1504 bp group (p < 0.05). Additionally, we identified elements participating in the initiation of gene transcription (a CAAT box), cell type-specific expression (M-box), and the regulation of gene expression (E-box) in the sheep DCT promoter. In conclusion, the optimal active region of the sheep DCT promoter is located between -593 bp and + 41 bp. [ABSTRACT FROM AUTHOR]

Chemosensory genes play a central role in sensing chemical signals and guiding insect behavior. The Chinese honeybee, Apis cerana cerana, is one of the most important insect species in China in terms of resource production, and providing high-quality products for human consumption, and also serves as an important pollinator. Communication and foraging behavior of worker bees is likely linked to a complex chemosensory system. Here, we used transcriptome sequencing on adult A. c. cerana workers of different ages to identify the major chemosensory gene families and the differentially expressed genes(DEGs), and to investigate their expression profiles. A total of 109 candidate chemosensory genes in five gene families were identified from the antennal transcriptome assemblies, including 17 OBPs, 6 CSPs, 74 ORs, 10 IRs, and 2SNMPs, in which nineteen DEGs were screened and their expression values at different developmental stages were determined in silico. No chemosensory transcript was specific to a certain developmental period. Thirteen DEGs were upregulated and 6were downregulated. We created extensive expression profiles in six major body tissues using qRT-PCR and found that most DEGs were exclusively or primarily expressed in antennae. Others were abundantly expressed in the other tissues, such as head, thorax, abdomen, legs, and wings. Interestingly, when a DEG was highly expressed in the thorax, it also had a high level of expression in legs, but showed a lowlevel in antennae. This study explored five chemoreceptor superfamily genes using RNA-Seq coupled with extensive expression profiling of DEGs. Our results provide new insights into the molecular mechanism of odorant detection in the Asian honeybee and also serve as an extensive novel resource for comparing and investigating olfactory functionality in hymenopterans. [ABSTRACT FROM AUTHOR]

In the present study we investigated the developmental expression patterns of Lbx1 gene in skeletal muscle of different genetic profile pigs after birth. A total of 28 Mashen pigs and 28 Large White pigs from seven development stages of 1, 30, 60, 90, 120, 150, 180 d were used and the expression patterns in longissimus dorsi were studied by quantitative real time-polymerase chain reaction and western blot in this study. The results showed that the breed, age, and the interaction of breed and age significantly affected the Lbx1 mRNA and protein expressions in longissimus dorsi (P<0.05). In Large White, the amount of Lbx1 protein was increased from new birth to 30 d, and decreased after 30 d to the lowest level at 180 d. In Mashen pig, Lbx1 protein level showed an increase trend with the age increase before 90 d, then decreased to the lowest level at 120 d, and then gradually increased upwards to the expression peak at 180 d. Before 120 d, the Lbx1 protein content in Large White was higher than that in Mashen pig, except for at 60 d. Afterwards, the protein level in Mashen was higher than that in Large White. The Lbx1 expression pattern was related to the age and genetic profiles of Mashen and Large White pigs, which indicates that Lbx1 could participate in the muscle development through activating the satellite cells of skeletal muscle after birth. [ABSTRACT FROM AUTHOR]

Lactobacillus casei Zhang, a potential probiotic strain isolated from homemade koumiss in Inner Mongolia of China, has been sequenced and deposited in GenBank. Real-time quantitative PCR is one of the most widely used methods to study related gene expression levels of Lactobacillus casei Zhang. For accurate and reliable gene expression analysis, normalization of gene expression data using one or more appropriate reference genes is essential. We used three statistical methods (geNorm, NormFinder, and BestKeeper) to evaluate the expression levels of five candidate reference genes ( GAPD, gyrB, LDH, 16s rRNA, and recA) under different culture conditions and different growth phases to find a suitable housekeeping gene which can be used as internal standard. The results showed that the best reference gene was GAPD, and a set of two genes, GAPD and gyrB (which were the most stable reference genes), is recommended for normalization of real-time quantitative PCR experiments under all the different experimental conditions tested. The systematic validation of candidate reference genes is important for obtaining reliable analysis results of real-time quantitative PCR studies in gene expression levels of Lactobacillus casei Zhang. [ABSTRACT FROM AUTHOR]

Summary: Soybean is a typical short-day crop, and its photoperiodic response of flowering is critical to its yield. This phenomenon was well studied during the last century, but the molecular mechanism governing it is unknown. The clock-gene homologs, GmLCL1 and GmLCL2 (Glycine max LHY/CCA1 Like 1 and 2) and GmTOC1 (Glycine max TOC1) were cloned from Glycine max L. KN18, and their expression patterns were analyzed using a system developed in this study. We employed 8h light/16h dark and 18h light/6h dark as short- and long-day conditions, respectively, because in these conditions soybean plants had significant indexes of flowering time. We also used unifoliolates, not the whole plant as Arabidopsis, as target organs for gene expression analysis. GmLCL1 and GmLCL2 had similar circadian expression patterns and both were morning genes, while GmTOC1 was an evening gene and peaked in the evening. The expressions of GmLCL1 and GmLCL2 were obviously antiphase to that of GmTOC1.Our study provided a system that simplified the experiments without compromising the quality of data obtained and was suitable for analyzing the molecular mechanism of flowering in soybean. GmLCL1, GmLCL2 and GmTOC1 may be the components of central clock in soybean. [Copyright &y& Elsevier]

Moso bamboo (Phyllostachys edulis), typically a monopodial scattering bamboo, is famous for its rapid growth. The rhizome-root system of Moso bamboo plays a crucial role in its clonal growth and spatial distribution. However, few studies have focused on rhizome-root systems. Here we collected LBs, RTs, and RGFNSs, the most important parts of the rhizome-root system, to study the molecular basis of the rapid growth of Moso bamboo due to epigenetic changes, such as DNA modifications and small RNAs. The angle of the shoot apical meristem of LB gradually decreased with increasing distance from the mother plant, and the methylation levels of LB were much higher than those of RT and RGFNS. 24 nt small RNAs and mCHH exhibited similar distribution patterns in transposable elements, suggesting a potential association between these components. The miRNA abundance of LB gradually increased with increasing distance from the mother plant, and a negative correlation was observed between gene expression levels and mCG and mCHG levels in the gene body. This study paves the way for further exploring the effects of epigenetic factors on the physiology of Moso bamboo. • The angle of SAM of lateral bud was gradually decreased with an increase of the distance from the mother bamboo. • A negative correlation between gene expression levels and mCG and mCHG levels in gene body was found. • In the rhizome-root system, the distribution of 24-nt small RNA was consistent with the DNA methylation patterns on TEs. [ABSTRACT FROM AUTHOR]