Molecular cloning and mRNA expression analysis of sheep MYL3 and MYL4 genes

Microstripe pattern substrate consisting of alternating planar and nanoprotrusive regions improved hiPSC-derived cardiomyocytes' unidirectional alignment and functional properties

The alignment of each cell in human myocardium is considered critical for the efficient movement of cardiac tissue. We investigated 96-well microstripe-patterned plates to align human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes (CMs), which resemble fetal myocardium. The aligned CMs (ACMs) cultured on the microstripe-patterned plates exhibited pathology, motor function, gene expression, and drug response that more closely resembled those of adult cells than did unaligned CMs cultured on a flat plate (FCMs). We used these ACMs to evaluate drug side effects and efficacy, and to determine whether these were similar to adult-like responses. When CMs from patients with hypertrophic cardiomyopathy (HCMs) were seeded and cultured on the microstripe-patterned plates or layered on top of the ACMs, both sets of HCMs showed increased heart rate and synchronized contractions, indicating improved cardiac function. It is suggested that the ACMs could be used for drug screening as cells representative of adult-like CMs and be transplanted in the form of a cell sheet for regenerative treatment of heart failure.

Genome-wide identification and analysis of TMT-based proteomes in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle

With the gradual completion of the human genome project, proteomes have gained extremely important value in the fields of human disease and biological process research. In our previous research, we performed transcriptomic analyses of longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle and conducted in-depth studies on the muscles of both species through epigenetics. However, it is unclear whether differentially expressed proteins in Kazakh cattle and Xinjiang brown cattle regulate muscle production and development. In this study, a proteomic analysis was performed on Xinjiang brown cattle and Kazakh cattle by using TMT markers, HPLC classification, LC/MS and bioinformatics analysis. A total of 13,078 peptides were identified, including 11,258 unique peptides. We identified a total of 1874 proteins, among which 1565 were quantifiable. Compared to Kazakh cattle, Xinjiang brown cattle exhibited 75 upregulated proteins and 44 downregulated proteins. These differentially expressed proteins were enriched for the functions of adrenergic signaling in cardiomyocytes, fatty acid degradation and glutathione metabolism. In our research, we found differentially expressed proteins in longissimus dorsi tissue between Kazakh cattle and Xinjiang brown cattle. We predict that these proteins regulate muscle production and development through select enriched signaling pathways. This study provides novel insights into the roles of proteomes in cattle genetics and breeding.

Transcriptomic analysis the mechanisms of anti-osteoporosis of desert-living Cistanche herb in ovariectomized rats of postmenopausal osteoporosis

Desert-living Cistanche herb (DC), as a traditional Chinese medicine for tonifying kidney yang, is often used to treat postmenopausal osteoporosis (PMOP). Total phenylethanoid glycosides are instruction ingredients for discrimination and assay according to the China pharmacopoeia for DC. This research aimed to reveal the anti-osteoporosis mechanism of total phenylethanoid glycosides of DC (PGC) by transcriptomic analysis of ovariectomized rats. Serum levels of BGP were evaluated by ELISA, the bone weight was measured, and transmission electron microscopy was used to examine the ultrastructure of osteoblasts in rats. In addition, micro-CT was used to detect the bone volume (Tb.BS/BV), bone mineral density (Tb.BMD), and bone mineral content (Tb.BMC) in trabecular bone, and the ratio of cortical bone area to total area (Ct.ar/Tt.ar), and the level of bone mineral content (Ct.BMC) in cortical bone. Differential expressed genes (DEGs) after PGC treatment were analyzed by transcriptomics. Then, a bioinformatics analysis of DEGs was carried out through GO enrichment, KEGG enrichment, and selection of the nucleus gene through the protein-protein interaction network. Through qRT-PCR analysis, the DEGs were verified. The analysis results indicated that PGC increased the secretion of osteogenic markers, and ultrastructural characterization of osteoblasts and bone morphology were improved in ovariectomized rats. A total of 269 genes were differentially expressed, including 201 genes that were downregulated and 68 genes that were upregulated between the model group and the PGC group. Bioinformation analysis results prompt the conclusion that PGC could promote the bone metabolism by muscle cell development, myofibril assembly, etc. In addition, our study also found that PGC has a good effect on osteoporosis complicated with cardiomyopathy, and it also provided evidence for the correlation between sarcopenia and osteoporosis.

Molecular Mechanism of MYL4 Regulation of Skeletal Muscle Development in Pigs

The processes of muscle growth and development, including myoblast proliferation, migration, differentiation, and fusion, are modified by a variety of regulatory factors. MYL4 plays an important role in atrial development, atrial cardiomyopathy, muscle-fiber size, and muscle development. The structural variation (SV) of MYL4 was found via the de novo sequencing of Ningxiang pigs, and the existence of SV was verified in the experiments. The genotype distribution of Ningxiang pigs and Large White pigs was detected, and it was found that Ningxiang pigs were mainly of the BB genotype and that Large White pigs were mainly of the AB genotype. However, the molecular mechanisms behind the MYL4-mediated regulation of skeletal muscle development need to be deeply explored. Therefore, RT-qPCR, 3'RACE, CCK8, EdU, Western blot, immunofluorescence, flow cytometry, and bioinformation analysis were used to explore the function of MYL4 in myoblast development. The cDNA of MYL4 was successfully cloned from Ningxiang pigs, and its physicochemical properties were predicted. The expression profiles in six tissues and four stages of Ningxiang pigs and Large White pigs were found to be the highest in the lungs and 30 days after birth. The expression of MYL4 increased gradually with the extension of the myogenic differentiation time. The myoblast function test showed that the overexpression of MYL4 inhibited proliferation and promoted apoptosis and differentiation. The knockdown of MYL4 showed the opposite result. These results enhance our understanding of the molecular mechanisms of muscle development and provide a solid theoretical foundation for further exploring the role of the MYL4 gene in muscle development.

Genetic polymorphism of the ovine MAP3K5 gene and its association with body size traits in Hu sheep of China

Abstract. As an excellent local sheep breed in China, Hu sheep have the characteristics of producing more lambs and good motherhood. The purpose of this study was to identify the polymorphism of the mitogen-activated protein kinase 5 (MAP3K5) gene and determine whether it was associated with the body size traits (body height, body length, chest circumference, and cannon circumference) in Hu sheep. The polymorphism of MAP3K5 was identified by using PCR amplification, followed by Sanger sequencing, and KASPar (Kompetitive Allele Specific PCR) technology was used for genotyping subsequently. The results of the association analysis showed that MAP3K5 (g.205261 A > G) was significantly associated with body height at 80, 100, 140, 160, and 180 d; body length at 80 and 160 d; chest circumference at 100, 140, 160, and 180 d; and cannon circumference at 100 and 120 d, respectively. The results of qRT-PCR showed that the expression level of MAP3K5 in the heart was significantly higher (P < 0.05) than in the other 10 tissues. In summary, the MAP3K5 mutation loci may be used as a candidate molecular marker for the body size traits of Hu sheep.

Postmenopausal osteoporosis: a bioinformatics-integrated experimental study the pathogenesis

Postmenopausal osteoporosis (PMOP) is a chronic bone metabolic disease, which often causes fractures and various complications, it causes a great social and economic burden, and it is urgent to use modern research techniques to elucidate the pathogenesis of PMOP. At the same time, because of the complex physiological and pathological interaction mechanism between osteoporosis and sarcopenia, the correlation research has become a hot topic. Ovary removal is a commonly used experimental method to study the endocrine system of female animals, and it is also the best animal model to study PMOP. In this study, the preparation of the ovariectomized rat was confirmed through the detection of vaginal smear, the level of bone formation markers, and the analysis of bone tissue morphology. Transcriptome sequencing was used to analyze the molecular mechanism of PMOP in ovariectomized rats, qRT-PCR was used to verify the key targets. Results of Micro-CT and scanning electron microscopy (SEM) showed that the trabecular structure was disorganized and the symptoms of osteoporosis appeared, this indicating that the ovariectomized rats model was successfully prepared. Transcriptional sequencing results of femur tissue showed that 452 differentially expressed genes (DEGs) were screened. Bioinformatics analysis results showed that the osteoporosis caused by ovariectomized rats was mainly related to muscle contraction, calcium signaling pathway, etc. Results of qRT-PCR were consistent with transcriptome analysis. These results reveal the pathogenesis of PMOP in ovariectomized rats and also offer a possibility for elucidating the relevance of action between PMOP and sarcopenia.

Embryonic transcriptome unravels mechanisms and pathways underlying embryonic development with respect to muscle growth, egg production, and plumage formation in native and broiler chickens

Background: Muscle development, egg production, and plumage colors are different between native and broiler chickens. The study was designed to investigate why improved Aseel (PD4) is colorful, stronger, and grew slowly compared with the control broiler (CB).

Methods: A microarray was conducted using the 7th-day embryo (7EB) and 18th-day thigh muscle (18TM) of improved Aseel and broiler, respectively. Also, we have selected 24 Gallus gallus candidate reference genes from NCBI, and total RNA was isolated from the broiler, improved Aseel embryo tissues, and their expression profiles were studied by real-time quantitative PCR (qPCR). Furthermore, microarray data were validated with qPCR using improved Aseel and broiler embryo tissues.

Results: In the differential transcripts screening, all the transcripts obtained by microarray of slow and fast growth groups were screened by fold change ≥ 1 and false discovery rate (FDR) ≤ 0.05. In total, 8,069 transcripts were differentially expressed between the 7EB and 18TM of PD4 compared to the CB. A further analysis showed that a high number of transcripts are differentially regulated in the 7EB of PD4 (6,896) and fewer transcripts are differentially regulated (1,173) in the 18TM of PD4 compared to the CB. On the 7th^- and 18th-day PD4 embryos, 3,890, 3,006, 745, and 428 transcripts were up- and downregulated, respectively. The commonly up- and downregulated transcripts are 91 and 44 between the 7th- and 18th-day of embryos. In addition, the best housekeeping gene was identified. Furthermore, we validated the differentially expressed genes (DEGs) related to muscle growth, myostatin signaling and development, and fatty acid metabolism genes in PD4 and CB embryo tissues by qPCR, and the results correlated with microarray expression data.

Conclusion: Our study identified DEGs that regulate the myostatin signaling and differentiation pathway; glycolysis and gluconeogenesis; fatty acid metabolism; Jak-STAT, mTOR, and TGF-β signaling pathways; tryptophan metabolism; and PI3K-Akt signaling pathways in PD4. The results revealed that the gene expression architecture is present in the improved Aseel exhibiting embryo growth that will help improve muscle development, differentiation, egg production, protein synthesis, and plumage formation in PD4 native chickens. Our findings may be used as a model for improving the growth in Aseel as well as optimizing the growth in the broiler.

Phosphoproteome Analysis Using Two-Dimensional Electrophoresis Coupled with Chemical Dephosphorylation

Protein phosphorylation is a reversible post-translational modification (PTM) with major regulatory roles in many cellular processes. However, the analysis of phosphoproteins remains the most challenging barrier in the prevailing proteome research. Recent technological advances in two-dimensional electrophoresis (2-DE) coupled to mass spectrometry (MS) have enabled the identification, characterization, and quantification of protein phosphorylation on a global scale. Most research on phosphoproteins with 2-DE has been conducted using phosphostains. Nevertheless, low-abundant and low-phosphorylated phosphoproteins are not necessarily detected using phosphostains and/or MS. In this study, we report a comparative analysis of 2-DE phosphoproteome profiles using Pro-Q Diamond phosphoprotein stain (Pro-Q DPS) and chemical dephosphorylation of proteins with HF-P from longissimus thoracis (LT) muscle samples of the Rubia Gallega cattle breed. We found statistically significant differences in the number of identified phosphoproteins between methods. More specifically, we found a three-fold increase in phosphoprotein detection with the HF-P method. Unlike Pro-Q DPS, phosphoprotein spots with low volume and phosphorylation rate were identified by HF-P technique. This is the first approach to assess meat phosphoproteome maps using HF-P at a global scale. The results open a new window for 2-DE gel-based phosphoproteome analysis.

Identification of differentially expressed genes at different post-natal development stages of longissimus dorsi muscle in Tianzhu white yak

The regulatory mechanisms controlling post-natal muscle development in the yak (Bos grunniens) are still largely unknown, yet the growth and development of muscle is a complex process that plays a crucial role in determining the yield and quality of an animal's meat. In this study, we performed a transcriptome analysis based on the RNA sequencing (RNA-Seq) of yak longissimus dorsi muscle tissue obtained from calves (6 months of age; 6 M), young adults (30 months of age; 30 M) and adult (54 months of age; 54 M) to identify which genes are differentially expressed and to investigate their temporal expression profiles. In total, 1788 differentially expressed genes (DEGs) (|log2FC| ≥ 1, P-adjusted < 0.05) were detected by pairwise comparisons between the different age groups. The expression levels of 10 of the DEGs were confirmed using reverse transcription-quantitative PCR (RT-qPCR), and the results were consistent with the transcriptome profile. A time-series expression profile analysis clustered the DEGs into four groups that could be divided into two classes (P < 0.05): class 1 profiles, which had up-regulated patterns of gene expression and class 2 profiles, which featured down-regulated patterns. Based on that cluster analysis, GO enrichment analysis revealed 1073, 127, and 184 terms as significantly enriched in biological process (BP), cellular component (CC), and molecular function (MF) categories in the class 1 profiles, while 714, 66, and 206 terms were significantly enriched in BP, CC, and MF in the class 2 profiles. A KEGG pathway analysis revealed that DEGs from the class 1 profiles were enriched in 62 pathways, with the most enriched being the phosphoinositide 3-kinase (PI3K) - protein kinase B (Akt)-signaling pathway. The DEGs from the class 2 profiles were enriched in 16 pathways, of which forkhead box protein O (FoxO) - signaling was the most enriched. Taken together, these results provide insight into the mechanisms of skeletal muscle development, as well suggesting some potential genes of importance for yak meat production.

Expression of atrial‑fetal light chains in cultured human cardiomyocytes after chemical ischemia‑reperfusion injury

Atrial light chains (ALC1) are naturally present in adult heart atria, while ventricular light chains (VLC1) are predominant in ventricles. Degradation of VLC1 and re-expression of ALC1 in heart ventricles are associated with heart disorders in response to pressure overload. The aim of the current study was to investigate changes in myosin light chain expression after simulated ischemia and simulated reperfusion (sI/sR). Human cardiomyocytes (HCM) isolated from adult heart ventricles were subjected to chemical ischemia. The control group was maintained under aerobic conditions. Myocyte injury was determined by testing lactate dehydrogenase (LDH) activity. The gene expression of ALC1, VLC1 and MMP-2 were assessed by reverse transcription-quatitive PCR. Additionally, protein synthesis was measured using ELISA kits and MMP-2 activity was measured by zymography. The results revealed that LDH activity was increased in sI/sR cell-conditioned medium (P=0.02), confirming the ischemic damage of HCM. ALC1 gene expression and content in HCM were also increased in the sI/sR group (P=0.03 and P<0.001, respectively), while VLC1 gene expression after sI/sR was decreased (P=0.008). Furthermore, MMP-2 gene expression and synthesis were lower in the sI/sR group when compared with the aerobic control group (P<0.001 and P=0.03, respectively). MMP-2 activity was also increased in sI/sR cell-conditioned medium (P=0.006). In conclusion, sI/sR treatment led to increased ALC1 and decreased VLC1 expression in ventricular cardiomyocytes, which may constitute an adaptive mechanism to altered conditions and contribute to the improvement of heart function.

Quantitative proteomic and phosphoproteomic analysis of chicken skeletal muscle during embryonic development

Skeletal muscle also plays a vital role in regulating the movement energy storage and health of metabolism. In order to investigate the expression profile of protein and phosphor-proteins in chicken skeletal muscle during embryonic development, we performed phosphor-proteomics analysis by label-free and TiO₂ enrichment strategy in chicken leg muscle tissues of at embryonic age embryo day 7(E7), E12, E17 and 3-day post-hatch (D3). The study led to the identification of 4332 proteins in the proteome and 1043 phosphorylation modification sites in the phosphorylated proteome, corresponding to 718 proteins (FC ≥ 2 or FC ≤ 0.5 and p < 0.05). The DEP-associated biological processes were involved in Focal adhesion, Glycolysis/gluconeogenesis, Arginine and proline metabolism by KEGG analysis. PPI analyses revealed that these DEPs TNNC1, TNNC2, TNNT2, TNNT3 and phosphorylated DEPs MYLPF interacted with involved pathways. Integrative analysis of proteome and phosphoproteome data found 324 common proteins, corresponding to 521 modification sites and Focal adhesion was the only pathway significantly enriched. These results provide a basis for further understanding the proteome and phosphoproteome and their regulatory biochemical pathways during the development of embryonic chicken skeletal muscle.

Combined transcriptome and proteome analyses reveal differences in the longissimus dorsi muscle between Kazakh cattle and Xinjiang brown cattle

Objective

With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects.

Methods

Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3).

Results

In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results.

Conclusion

Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

Developmental programming: Adipose depot-specific transcriptional regulation by prenatal testosterone excess in a sheep model of PCOS

Prenatal testosterone (T)-treated female sheep manifest adipose depot-specific disruptions in inflammatory/oxidative state, adipocyte differentiation and thermogenic adipocyte distribution. The objective of this study was to identify common and divergent gene pathways underlying prenatal T excess-induced adipose depot-specific disruptions. RNA sequencing and network analyses were undertaken with visceral (VAT), subcutaneous (SAT), epicardiac (ECAT) and perirenal (PRAT) adipose tissues from control and prenatal T-treated (100 mg T propionate twice a week from days 30-90 of gestation) female sheep at 21 months of age. Increased expression of adiposity and inflammation-related genes in VAT and genes that promote differentiation of white adipocytes in SAT were congruous with their metabolic roles with SAT favoring uptake/storage of free fatty acids and triglycerides and VAT favoring higher rate of fatty acid turnover and lipolysis. Selective upregulation of cardiac muscle and renoprotection genes in ECAT and PRAT respectively are suggestive of protective paracrine actions. Expression profile in prenatal T-treated sheep paralleled depot-specific dysfunctions with increased proinflammatory genes in VAT, reduced adipocyte differentiation genes in VAT and SAT and increased vascular related gene expression in PRAT. The high expression of genes involved in cardiomyocyte function in ECAT is suggestive of cardioprotective function being maintained to overcome the prenatal T-induced cardiac dysfunction and hypertension. These findings coupled with changes in gene pathways and networks involved in chromatin modification, extracellular matrix, immune and mitochondrial function, and endoplasmic reticulum to Golgi transport suggest that dysregulation in gene expression underlie prenatal T-treatment induced functional differences among adipose depots and manifestation of metabolic dysfunction.

Tissue Expression of Atrial and Ventricular Myosin Light Chains in the Mechanism of Adaptation to Oxidative Stress

Ischemia/reperfusion (I/R) injury induces post-translational modifications of myosin light chains (MLCs), increasing their susceptibility to degradation by matrix metalloproteinase 2 (MMP-2). This results in the degradation of ventricular light chains (VLC1) in heart ventricles. The aim of the study was to investigate changes in MLCs content in the mechanism of adaptation to oxidative stress during I/R. Rat hearts, perfused using the Langendorff method, were subjected to I/R. The control group was maintained in oxygen conditions. Lactate dehydrogenase (LDH) activity and reactive oxygen/nitrogen species (ROS/RNS) content were measured in coronary effluents. Atrial light chains (ALC1) and ventricular light chains (VLC1) gene expression were examined using RQ-PCR. ALC1 and VLC1 protein content were measured using ELISA tests. MMP-2 activity was assessed by zymography. LDH activity as well as ROS/RNS content in coronary effluents was higher in the I/R group (p = 0.01, p = 0.04, respectively), confirming heart injury due to increased oxidative stress. MMP-2 activity in heart homogenates was also higher in the I/R group (p = 0.04). ALC1 gene expression and protein synthesis were significantly increased in I/R ventricles (p < 0.01, 0.04, respectively). VLC1 content in coronary effluents was increased in the I/R group (p = 0.02), confirming the increased degradation of VLC1 by MMP-2 and probably an adaptive production of ALC1 during I/R. This mechanism of adaptation to oxidative stress led to improved heart mechanical function.

Transcriptome analysis of leg muscles in fast and slow growth Bian chickens

Chicken is popular among consumers in the market, but the mechanism for regulating its growth is still unclear. In this experiment, two groups of Bian chickens of different body weights at 16 weeks of age were studied. The leg muscles were taken for transcriptome sequencing after slaughter. In the differential gene screening, all the genes obtained by sequencing the fast and slow growth groups were screened by Fold Change ≥2 and False Discovery Rate (FDR) <0.05, and 108 differentially expressed genes were obtained. The slow growth group has 17 up-regulated genes and 91 down-regulated genes compared with the fast growing group. Significance analysis of differentially expressed genes in gene ontology (GO) enrichment indicates that there are 65, 16 and 6 significantly enriched entries in the three main categories of biological processes, cellular components and molecular functions (P-value <0.05), respectively. Pathway enrichment analysis yielded three significantly enriched signal pathways: Adrenergic signaling in cardiomyocytes, Cardiac muscle contraction and Tight junction. The experiment would contribute to reveal the molecular mechanism of chicken growth and provide a theoretical basis for improving the performance of Bian chicken.

RNA-Seq transcriptome analysis of breast muscle in Pekin ducks supplemented with the dietary probiotic Clostridium butyricum

BACKGROUND

Increased attention is being paid to breast muscle yield and meat quality in the duck breeding industry. Our previous report has demonstrated that dietary Clostridium butyricum (C. butyricum) can improve meat quality of Pekin ducks. However, the potential biological processes and molecular mechanisms that are modulated by dietary C. butyricum in the breast muscle of Pekin ducks remain unknown.

RESULTS

Supplementation with C. butyricum increased growth performance and meat yield. Therefore, we utilized de novo assembly methods to analyze the RNA-Seq transcriptome profiles in breast muscle to explore the differentially expressed genes between C. butyricum-treated and control Pekin ducks. A total of 1119 differentially expressed candidate genes were found of which 403 genes were significantly up-regulated and 716 genes were significantly down-regulated significantly. qRT-PCR analysis was used to confirm the accuracy of the of RNA-Seq results. GO annotations revealed potential genes, processes and pathways that may participate in meat quality and muscle development. KEGG pathway analysis showed that the differentially expressed genes participated in numerous pathways related to muscle development, including ECM-receptor interaction, the MAPK signaling pathway and the TNF signaling pathway.

CONCLUSIONS

This study suggests that long-time dietary supplementation with C. butyricum can modulate muscle development and meat quality via altering the expression patterns of genes involved in crucial metabolic pathways. The findings presented here provide unique insights into the molecular mechanisms of muscle development in Pekin ducks in response to dietary C. butyricum.