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The aim of the current study was to identify the major genes and pathways involved in the process of hypertrophy and skeletal muscle maturation that is common for Bos taurus, Ovis aries, and Sus scrofa species. Gene expression profiles related to Bos taurus, Ovis aries, and Sus scrofa muscle, with accession numbers GSE44030, GSE23563, and GSE38518, respectively, were downloaded from the GEO database. Differentially expressed genes (DEGs) were screened out using the Limma package of R software. Genes with Fold Change > 2 and an adjusted p-value < 0.05 were identified as significantly different between two treatments in each species. Subsequently, gene ontology and pathway enrichment analyses were performed. Moreover, hub genes were detected by creating a protein–protein interaction network (PPI). The results of the analysis in Bos taurus showed that in the period of 280 dpc–3-months old, a total of 1839 genes showed a significant difference. In Ovis aries, however, during the period of 135dpc–2-months old, a total of 486 genes were significantly different. Additionally, in the 91 dpc–adult period, a total of 2949 genes were significantly different in Sus scrofa. The results of the KEGG pathway enrichment analysis and GO function annotation in each species separately revealed that in Bos taurus, DEGs were mainly enriched through skeletal muscle fiber development and skeletal muscle contraction, and the positive regulation of fibroblast proliferation, positive regulation of skeletal muscle fiber development, PPAR signaling pathway, and HIF-1 signaling pathway. In Ovis aries, DEGs were mainly enriched through regulating cell growth, skeletal muscle fiber development, the positive regulation of fibroblast proliferation, skeletal muscle cell differentiation, and the PI3K-Akt signaling, HIF-1 signaling, and Rap1 signaling pathways. In Sus scrofa, DEGs were mainly enriched through regulating striated muscle tissue development, the negative regulation of fibroblast proliferation and myoblast differentiation, and the HIF-1 signaling, AMPK signaling, and PI3K-Akt signaling pathways. Using a Venn diagram, 36 common DEGs were identified between Bos taurus, Ovis aries, and Sus scrofa. A biological pathways analysis of 36 common DEGs in Bos taurus, Ovis aries, and Sus scrofa allowed for the identification of common pathways/biological processes, such as myoblast differentiation, the regulation of muscle cell differentiation, and positive regulation of skeletal muscle fiber development, that orchestrated the development and maturation of skeletal muscle. As a result, hub genes were identified, including PPARGC1A, MYOD1, EPAS1, IGF2, CXCR4, and APOA1, in all examined species. This study provided a better understanding of the relationships between genes and their biological pathways in the skeletal muscle maturation process.

Background Muscle growth post-birth relies on muscle fiber number and size. Myofibre number, metabolic and contractile capacities are established pre-birth during prenatal myogenesis. The aim of this study was to identify genes involved in skeletal muscle development in cattle, sheep, and pigs - livestock. Results The cattle analysis showed significant differences in 5043 genes during the 135–280 dpc period. In sheep, 444 genes differed significantly during the 70–120 dpc period. Pigs had 905 significantly different genes for the 63–91 dpc period.The biological processes and KEGG pathway enrichment results in each species individually indicated that DEGs in cattle were significantly enriched in regulation of cell proliferation, cell division, focal adhesion, ECM-receptor interaction, and signaling pathways (PI3K-Akt, PPAR, MAPK, AMPK, Ras, Rap1); in sheep - positive regulation of fibroblast proliferation, negative regulation of endothelial cell proliferation, focal adhesion, ECM-receptor interaction, insulin resistance, and signaling pathways (PI3K-Akt, HIF-1, prolactin, Rap1, PPAR); in pigs - regulation of striated muscle tissue development, collagen fibril organization, positive regulation of insulin secretion, focal adhesion, ECM-receptor interaction, and signaling pathways (PPAR, FoxO, HIF-1, AMPK). Among the DEGs common for studied animal species, 45 common genes were identified. Based on these, a protein-protein interaction network was created and three significant modules critical for skeletal muscle myogenesis were found, with the most significant module A containing four recognized hub genes - EGFR , VEGFA , CDH1 , and CAV1 . Using the miRWALK and TF2DNA databases, miRNAs (bta-miR-2374 and bta-miR-744) and transcription factors (CEBPB, KLF15, RELA, ZNF143, ZBTB48, and REST) associated with hub genes were detected. Analysis of GO term and KEGG pathways showed that such processes are related to myogenesis and associated with module A: positive regulation of MAP kinase activity, vascular endothelial growth factor receptor, insulin-like growth factor binding, focal adhesion, and signaling pathways (PI3K-Akt, HIF-1, Rap1, Ras, MAPK). Conclusions The identified genes, common to the prenatal developmental period of skeletal muscle in livestock, are critical for later muscle development, including its growth by hypertrophy. They regulate valuable economic characteristics. Enhancing and breeding animals according to the recognized genes seems essential for breeders to achieve superior gains in high-quality muscle mass.

This study explored the significance of long non-coding RNAs (lncRNAs), particularly their role in maintaining dystrophin protein stability and regulating myocyte proliferation and differentiation. The investigation focused on DMD/mdx mouse skeletal muscle primary myoblasts, aiming to identify lncRNAs potential as biomarkers and therapeutic targets for Duchenne muscular dystrophy (DMD). Utilizing CLC Genomics Workbench software, 554 differentially expressed lncRNAs were identified in DMD/mdx mice compared to wild-type (WT) control. Among them, 373 were upregulated, and 181 were downregulated. The study highlighted specific lncRNAs (e.g., 5930430L01Rik, Gm10143, LncRNA1490, LncRNA580) and their potential regulatory roles in DMD key genes like IGF1 , FN1 , TNNI1 , and MYOD1 . By predicting miRNA and their connections with lncRNA and mRNA (ceRNA network) using tools such as miRNet, miRSYSTEM and miRCARTA, the study revealed potential indirect regulation of Dystrophin , IGF1R and UTRN genes by identified lncRNAs (e.g. 2310001H17Rik-203, C130073E24Rik-202, LncRNA2767, 5930430L01Rik and LncRNA580). These findings suggest that the identified lncRNAs may play crucial roles in the development and progression of DMD through their regulatory influence on key gene expression, providing valuable insights for potential therapeutic interventions.

Camels are increasingly recognized for their potential to meet future nutritional and medical needs due to their unique qualities. This study aims to advance our understanding of the genetic basis of body size in dromedaries by employing confirmatory factor analysis (CFA) and genome-wide association studies (GWAS). We used phenotypic data from 9 body measurements of 96 Iranian male camels to develop a latent variable model for body size. The CFA model demonstrated excellent fit (CFI = 0.99, TLI = 0.99, RMSEA = 0.05, SRMR = 0.02), confirming that the selected biometric traits effectively capture the body size latent variable. Subsequent GWAS, utilizing 14,522 SNPs, identified 13 significant SNPs associated with body size across several chromosomes. The candidate genes linked to these SNPs, including UBE3D , REPS1 , SLC4A1AP , EFR3B , PRR11 , and VMP1 , were further examined through Gene Ontology (GO) enrichment analysis, revealing their involvement in crucial biological processes such as catabolic and metabolic activities, developmental processes, and protein and lipid transport. These findings provide valuable insights into the genetic mechanisms underpinning body size in dromedaries, offering a foundation for future research and potential applications in breeding and genetic improvement strategies.

Cutaneous leishmaniasis (CL) is the most common form of the disease which can cause malignant lesions on the skin. Vaccination for the prevention and treatment of leishmaniasis can be the most effective way to combat this disease. In this study, we designed a novel multi-epitope vaccine against Leishmania major ( L . major ) using immunoinformatics tools to assess its efficacy in silico . Sequences of Leish-F1 protein (TSA, Leif, and LMSTI1) of L . major were taken from GenBank. The helper T (Th) and cytotoxic T (Tc) epitopes of the protein were predicted. The final multi-epitope consisted of 18 CTL epitopes joined by AAY linker. There were also nine HTL epitopes in the structure of the vaccine construct, joined by GPGPG linker. The profilin adjuvant (the toll-like receptor 11 agonist) was also added into the construct by AAY Linker. There were 613 residues in the structure of the vaccine construct. The multi-epitope vaccine candidate was stable and non-allergic. The data obtained from the binding of final multi-epitope vaccine-TLR11 residues (band lengths and weighted scores) unveiled the ligand and the receptor high score of binding affinity. Moreover, in silico assessment of the vaccine construct cloning achieved its suitable expression in E . coli host. Based on these results, the current multi-epitope vaccine prevents L . major infection in silico , while further confirmatory assessments are required.

Duchenne muscular dystrophy (DMD) manifests as a hereditary condition that diminishes muscular strength through the progressive degeneration of structural muscle tissue, which is brought about by deficiencies in the dystrophin protein required for the integrity of muscle cells. DMD is among four different types of dystrophinopathy disorders. Current studies have established that long non-coding RNAs (lncRNAs) play a significant role in determining the trajectory and overall prognosis of chronic musculoskeletal conditions. LncRNAs are different in terms of their lengths, production mechanisms, and operational modes, but they do not produce proteins, as their primary activity is the regulation of gene expression. This research synthesizes current literature on the role of lncRNAs in the regulation of myogenesis with a specific focus on certain lncRNAs leading to DMD increments or suppressing muscle biological functions. LncRNAs modulate skeletal myogenesis gene expression, yet pathological lncRNA function is linked to various muscular diseases. Some lncRNAs directly control genes or indirectly control miRNAs with positive or negative effects on muscle cells or the development of DMD. The research findings have significantly advanced our knowledge about the regulatory function of lncRNAs on muscle growth and regeneration processes and DMD diseases.

Background: Intramuscular fat (IMF) enhances marbling, improving meat quality and value. Transcriptome analysis enables the identification of genes and pathways involved in IMF deposition, supporting targeted breeding and nutritional strategies to improve beef quality. Methods: This study used RNA-Seq to compare gene expression in high- (Hereford; Her), moderate- (Holstein Friesian; Hf), and low-marbling (Limousine; Lim) Semitendinosus muscle. Using Illumina’s NovaSeqX Plus, sequencing data underwent quality control with FastQC to remove low-quality reads and adapters, followed by alignment to the bovine genome using HISAT2. Differential expression analysis was performed using DESeq2, and genes were filtered based on a threshold of p-value < 0.05 and |log2FC| > 0.5 to identify significantly regulated genes. Results: A total of 21,881 expressed genes were detected, with 3025 and 7407 significantly differentially expressed in Her and Hf vs. Lim, respectively (|log2FC| > 0.5, p < 0.05). Protein–protein interaction analysis revealed 20 hub genes, including SMAD3, SCD, PLIN2, SHH, SQLE, RXRA, NPPA, NR1H4, PRKCA, and IL10. Gene ontology and KEGG pathway analyses linked these genes to lipid metabolism and IMF-associated pathways, such as PPAR signaling, fatty acid metabolism, and PI3K–Akt signaling. Conclusions: These findings highlight RNA-Seq’s utility in uncovering the genetic basis of marbling and the importance of aligning beef production with consumer demands through genetic improvements. This study aimed to identify breed-independent molecular mechanisms of intramuscular fat deposition and shared metabolic processes in the Semitendinosus muscle to improve beef quality.

Background Nowadays, the prevention of parasitic diseases including leishmaniasis, particularly cutaneous leishmaniasis as the smost common type of the disease, has increased health concerns around the world. Although some drugs such as Glucantim and Amphotericin B are approved, they have side effects. Therefore, treatment without side effects is a priority. Methodology In this study, the recombinant lentiviral vaccine containing a novel multi-epitope of KMP11 and HASPB of Leishmania major ( L. major ) was synthesized. The multi-epitope construct was previously designed in silico, subcloned into the pCDH513 lentiviral vector, and the recombinant lentiviral multi-epitope vaccine (rLV-multi-epitope) was synthesized in HEK293T cells using the packaging vectors. The Western Blotting method was used to confirm the gene expression. Then, the rLV-multi-epitope vaccine was injected twice, along with two control groups: phosphate buffered saline (PBS) and rLV-empty to immunize the BALB/c mice. Twenty-one days after the second injection, the splenocytes of the mice were isolated and stimulated with the L. major lysate. Also, the serum level of IgG1 and IgG2a, and gamma interfron (IFN-γ) and interleukin-4 (IL-4) were assessed using enzyme-linked immunoassay (ELISA) test. Results The results of the enzyme-linked immunoassay ELISA showed that the titer of IFN-γ and IL-4 were increased in the immunized group. Also, the level of IFN-γ was higher significantly and as compared to IL-4, and as a result, the Th1 response was generated in the main group. Additionally, the humoral immune response was assessed, indicating that the titer of IgG2a and IgG1 antibodies in the sera of the immunized mice was increased compared to the control groups. Moreover, the serum level of IgG2a to IgG1 was increased in the main group. Therefore, the humoral immune response was increased, which can also have a positive effect on increasing the Th1 response. Conclusions Our results revealed that immunization with the novel rLV-multi-epitope vaccine could stimulate the immune system toward Th1 by increasing the production of IFN-γ and IgG2a opsonin antibody.

Duchenne muscular dystrophy (DMD) is a severe X-linked recessive disorder caused by a mutation in the Dmd gene, leading to progressive muscle degradation, increasing weakness, and typically resulting in death before the third decade of life. To investigate the pathobiology of DMD, this study employed the Sprague-Dawley Dmd-mutated rat model (DMD ) and analyzed gene expression profiles and pathological molecular pathways. The methods used included histopathological, biochemical, and transcriptomic analyses of dystrophic skeletal muscle from DMD and wild-type (WT) individuals. Histological analysis of skeletal muscle tissue from DMD rats revealed multifocal necrosis, fibrosis, and inflammation, whereas WT rats displayed normal muscle architecture. Biochemical analysis revealed significant alterations in plasma markers of muscle damage and metabolism in DMD rats compared to WT controls, including elevated AST, ALT, ALP, CPK, and LDH levels. Additionally, oxidative status measurements showed reduced antioxidant capacity and increased lipid peroxidation in dystrophic skeletal muscle, as evidenced by lower TAS, GR, GPx, and SOD activities and higher TBARS levels. RNA-seq analysis identified 3,615 differentially expressed genes between the two groups, associated with muscle contraction, extracellular matrix (ECM) organization, and cytoskeleton organization. Notably, Dmd, Actc1, Col6a1, and Mmp2 were significantly downregulated. Gene ontology and pathway enrichment analyses indicated dystrophic changes in skeletal muscle, disruptions in calcium homeostasis, and alterations in actin cytoskeleton regulation. KEGG and Reactome pathway analyses revealed upregulation of the MAPK signaling and immune system pathways and downregulation of the ECM organization pathway. These findings support the hypothesis that targeting complex intracellular signaling pathways in DMD may represent a promising therapeutic strategy. Given that the DMD rat model closely mimics human DMD pathology compared to other animal models, it offers a more realistic platform for studying the molecular mechanisms of the disease and improving the translational potential of therapeutic approaches.

Investigating genomic regions associated with morphometric traits in camels is valuable, because it allows a better understanding of adaptive and productive features to implement a sustainable management and a customised breeding program for dromedaries. With a genome-wide association study (GWAS) including 96 Iranian dromedaries phenotyped for 12 morphometric traits and genotyped-by-sequencing (GBS) with 14,522 SNPs, we aimed at identifying associated candidate genes. The association between SNPs and morphometric traits was investigated using a linear mixed model with principal component analysis (PCA) and kinship matrix. With this approach, we detected 59 SNPs located in 37 candidate genes potentially associated to morphometric traits in dromedaries. The top associated SNPs were related to pin width, whither to pin length, height at whither, muzzle girth, and tail length. Interestingly, the results highlight the association between whither height, muzzle circumference, tail length, whither to pin length. The identified candidate genes were associated with growth, body size, and immune system in other species. We identified three key hub genes in the gene network analysis including ACTB, SOCS1 and ARFGEF1. In the central position of gene network, ACTB was detected as the most important gene related to muscle function. With this initial GWAS using GBS on dromedary camels for morphometric traits, we show that this SNP panel can be effective for genetic evaluation of growth in dromedaries. However, we suggest a higher-density SNP array may greatly improve the reliability of the results.