Search

Simple Summary: This study aimed to conduct a comprehensive analysis of the factors involved in muscle growth and development, along with their associated biological functions and pathways, in cattle, pigs, and sheep. This was achieved by integrating an interpretable machine learning model with a comparative transcriptomic approach. The findings revealed that the elements closely linked to muscle growth and development across these three species exhibited high repeatability. Specifically, we identified 8 unique factors in cattle, 2 in pigs, and 1 in sheep, thereby providing novel insights into the mechanisms underlying muscle growth and development within these species. The growth and development of muscle tissue play a pivotal role in the economic value and quality of meat in agricultural animals, garnering close attention from breeders and researchers. The quality and palatability of muscle tissue directly determine the market competitiveness of meat products and the satisfaction of consumers. Therefore, a profound understanding and management of muscle growth is essential for enhancing the overall economic efficiency and product quality of the meat industry. Despite this, systematic research on muscle development-related genes across different species still needs to be improved. This study addresses this gap through extensive cross-species muscle transcriptome analysis, combined with interpretable machine learning models. Utilizing a comprehensive dataset of 275 publicly available transcriptomes derived from porcine, bovine, and ovine muscle tissues, encompassing samples from ten distinct muscle types such as the semimembranosus and longissimus dorsi, this study analyzes 113 porcine (n = 113), 94 bovine (n = 94), and 68 ovine (n = 68) specimens. We employed nine machine learning models, such as Support Vector Classifier (SVC) and Support Vector Machine (SVM). Applying the SHapley Additive exPlanations (SHAP) method, we analyzed the muscle transcriptome data of cattle, pigs, and sheep. The optimal model, adaptive boosting (AdaBoost), identified key genes potentially influencing muscle growth and development across the three species, termed SHAP genes. Among these, 41 genes (including NANOG, ADAMTS8, LHX3, and TLR9) were consistently expressed in all three species, designated as homologous genes. Specific candidate genes for cattle included SLC47A1, IGSF1, IRF4, EIF3F, CGAS, ZSWIM9, RROB1, and ABHD18; for pigs, DRP2 and COL12A1; and for sheep, only COL10A1. Through the analysis of SHAP genes utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, relevant pathways such as ether lipid metabolism, cortisol synthesis and secretion, and calcium signaling pathways have been identified, revealing their pivotal roles in muscle growth and development. [ABSTRACT FROM AUTHOR]

The heritability of litter size in sheep is low and controlled by multiple genes, but the research on its related genes is not sufficient. Here, to explore the expression pattern of multi-tissue genes in Chinese native sheep, we selected 10 tissues of the three adult ewes with the highest estimated breeding value in the early study of the prolific Xinggao sheep population. The global gene expression analysis showed that the ovary, uterus, and hypothalamus expressed the most genes. Using the Uniform Manifold Approximation and Projection (UMAP) cluster analysis, these samples were clustered into eight clusters. The functional enrichment analysis showed that the genes expressed in the spleen, uterus, and ovary were significantly enriched in the Ataxia Telangiectasia Mutated Protein (ATM) signaling pathway, and most genes in the liver, spleen, and ovary were enriched in the immune response pathway. Moreover, we focus on the expression genes of the hypothalamic–pituitary–ovarian axis (HPO) and found that 11,016 genes were co-expressed in the three tissues, and different tissues have different functions, but the oxytocin signaling pathway was widely enriched. To further explore the differences in the expression genes (DEGs) of HPO in different sheep breeds, we downloaded the transcriptome data in the public data, and the analysis of DEGs (Xinggao sheep vs. Sunite sheep in Hypothalamus, Xinggao sheep vs. Sunite sheep in Pituitary, and Xinggao sheep vs. Suffolk sheep in Ovary) revealed the neuroactive ligand–receptor interactions. In addition, the gene subsets of the transcription factors (TFs) of DEGs were identified. The results suggest that 51 TF genes and the homeobox TF may play an important role in transcriptional variation across the HPO. Altogether, our study provided the first fundamental resource to investigate the physiological functions and regulation mechanisms in sheep. This important data contributes to improving our understanding of the reproductive biology of sheep and isolating effecting molecular markers that can be used for genetic selection in sheep. [ABSTRACT FROM AUTHOR]

In this work, La1−xSrxNi0.4Fe0.6O3-δ (0 ≤ x ≤ 0.2) oxides were synthesized and employed as the identical electrode of direct methane symmetrical solid oxide fuel cell (SSOFC). In addition, the phase structure, redox stability, electrical conductivity, chemical compatibility, and thermal expansion of La1−xSrxNi0.4Fe0.6O3-δ oxides were evaluated. The La2NiO4 phase occurs when the amount of doped Sr rises to 0.2. The composition of La0.9Sr0.1Ni0.4Fe0.6O3-δ (LSNF9146) boasts the highest conductivity of 463 S cm−1 with lowest activation energy of 0.066 eV as well as a relatively large thermal expansion coefficient. After treatment in methane for 10 h, the LSNF9146 oxide exhibits 33% lower carbon deposition than the LaNi0.4Fe0.6O3-δ (LNF46) oxide. Moreover, the impregnated LSNF9146 electrode demonstrates lower polarization resistance in both air and methane atmospheres. SSOFCs with impregnated LSNF9146 and LNF46 identical composite electrodes have the maximum power densities of 233 and 170 mW cm−2 at 850 °C in methane, respectively. These results prove that LSNF9146 is a promising symmetrical electrode with high catalytic activity, good redox stability, and coking resistance to direct methane SSOFCs. [ABSTRACT FROM AUTHOR]

Abstract: Based on Rhodamine B, two Al3+/Cu2+-selective chemosensors were synthesized, which display a high selectivity for Al3+ and Cu2+ among environmentally and biologically relevant metal ions. A 1,8-Naphthyridine modified rhodamine derivative can detect Al3+ in ethanol with off–on fluorescence behavior, and detect Cu2+ in aqueous solution with colorimetric method. The 8-Hydroxyquinoline-based rhodamine sensor can detect Al3+ in ethanol with both off–on fluorescence and colorimetric methods. The detection mechanism involves a ring-opening process as a consequence of metal complex formation. Job's plots and a time-of-flight mass spectral study indicated that each chemosensor chelated Al3+/Cu2+ with 1:1 stoichiometry. The binding of the chemosensors and Al3+/Cu2+ is chemically reversible by the addition of F−/EDTA solution, respectively. [Copyright &y& Elsevier]

• Leuciscinae was monophyletic group and Leuciscus was paraphyletic group. • A promising potential of comparative mitogenomes in phylogenetics between fishes. • Mitogenomes should be considered in clarifying phylogenetics of fish. Cyprinidae is the largest family in the order of freshwater fish Cypriniformes. Increased subfamily members of Cyprinidae have been suggested to be re-classified for decades. In this study, we sequenced the mitochondrial genomes (mitogenomes) of Leuciscus baicalensis and Rutilus rutilus collected from northwest China and compared with other closely related species to determine their associated family or subfamily. We used Illumina NovaSeq to sequence the entire mitochondrial genomes of Leuciscus baicalensis and Rutilus rutilus and characterized the mitogenomes by the gene structure, gene order, and the secondary structures of the 22 tRNA genes. We compared mitogenome features of Leuciscinae with other subfamilies in Cyprinidae. We used the analytic Bayesian Information and Maximum Likelihood methods to determine phylogenetic trees of 13 PCGs. The mitogenomes of Leuciscus baicalensis and Rutilus rutilus were 16,607 bp and 16,606 bp, respectively. Organization and location of these genes were consistent with already studied Leuciscinae fishes. Synonymous codon usage was conservative in Leuciscinae as compared with other subfamilies in Cyprinidae. Phylogenetic analysis indicated that Leuciscinae was a monophyletic group, and genus Leuciscus was a paraphyletic group. Our approach, for the first time, of studying comparative mitochondrial genomics and phylogenetics together provided a supportive platform to the analysis of population genetics and phylogeny for Leuciscinae. Our results indicated a promising potential of comparative mitochondrial genomics in the manifestation of phylogenetic relationships between fishes, leading us to a suggestion that mitogenomes should be routinely considered in clarifying phylogenetics of family and subfamily members of fish. [ABSTRACT FROM AUTHOR]

The growth and development of muscle tissue play a pivotal role in the economic value and quality of meat in agricultural animals, garnering close attention from breeders and researchers. The quality and palatability of muscle tissue directly determine the market competitiveness of meat products and the satisfaction of consumers. Therefore, a profound understanding and management of muscle growth is essential for enhancing the overall economic efficiency and product quality of the meat industry. Despite this, systematic research on muscle development-related genes across different species still needs to be improved. This study addresses this gap through extensive cross-species muscle transcriptome analysis, combined with interpretable machine learning models. Utilizing a comprehensive dataset of 275 publicly available transcriptomes derived from porcine, bovine, and ovine muscle tissues, encompassing samples from ten distinct muscle types such as the semimembranosus and longissimus dorsi, this study analyzes 113 porcine ( n = 113), 94 bovine ( n = 94), and 68 ovine ( n = 68) specimens. We employed nine machine learning models, such as Support Vector Classifier (SVC) and Support Vector Machine (SVM). Applying the SHapley Additive exPlanations (SHAP) method, we analyzed the muscle transcriptome data of cattle , pigs , and sheep . The optimal model, adaptive boosting (AdaBoost), identified key genes potentially influencing muscle growth and development across the three species, termed SHAP genes. Among these, 41 genes (including NANOG , ADAMTS8 , LHX3 , and TLR9 ) were consistently expressed in all three species, designated as homologous genes. Specific candidate genes for cattle included SLC47A1 , IGSF1 , IRF4 , EIF3F , CGAS , ZSWIM9 , RROB1 , and ABHD18 ; for pigs , DRP2 and COL12A1 ; and for sheep , only COL10A1 . Through the analysis of SHAP genes utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, relevant pathways such as ether lipid metabolism, cortisol synthesis and secretion, and calcium signaling pathways have been identified, revealing their pivotal roles in muscle growth and development.

Introduction: The advancement of high-throughput, high-quality, flexible, and cost-effective genotyping platforms is crucial for the progress of dairy breeding in Bactrian camels. This study focuses on developing and evaluating a 1K functional liquid single nucleotide polymorphism (SNP) array specifically designed for milk performance in Bactrian camels., Methods: We utilized RNA sequencing data from 125 lactating camels to identify and select 1,002 loci associated with milk production traits for inclusion in the SNP array. The array's performance was then assessed using 24 randomly selected camels. Additionally, the array was employed to genotype 398 individuals, which allowed for population validation to assess the polymorphism of SNP sites., Results: The SNP array demonstrated high overall SNP call rates (> 99%) and a remarkable 100% consistency in genotyping. Population validation results indicate that camels from six breeding areas in Northwest China share a similar genetic background regarding lactation functionality., Discussion: This study highlights the potential of the SNP array to accelerate the breeding process of lactating Bactrian camels and provides a robust technical foundation for improving lactation performance., Competing Interests: BL was employed by Inner Mongolia Bionew Technology Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Guo, Dao, Liu, Wang, Liu, Ma, Morigen, Chang, Bai, Guo, Shi, Cao and Zhang.)

Objective: The purpose of this study was to investigate the effects of different doses of Sophora alopecuroides (SA) on the rumen fermentation and microbial diversity of sheep., Methods: A total of 32 healthy Dumont crossbred male lambs weighing 25.73 ± 2.17 kg were randomly assigned to 4 treatment groups with 8 replicates each: a control group (CG) fed a basal diet with a concentrate-to-forage ratio of 7:3 and three experimental groups - the 0.1% group(TG1), 0.3% group (TG2), and 0.5% group (TG3), which were fed the same basal diet but supplemented with increasing doses of SA., Results: (1) Increasing the SA dose led to a significant linear increase ( p -< 0.05) in acetate, propionate, butyrate, and total volatile fatty acid (TVFA) concentrations in the rumen, as well as a significant quadratic effect ( p -< 0.05) on the propionate concentration. In contrast, there was a significant linear decrease ( p -< 0.05) in the NH 3 -N concentration in the rumen. (2) At the level of rumen bacterial phyla, the abundance of Bacteroidetes in the rumen increased, and that of Firmicutes decreased ( p = 0.08). At the genus level, the rumen abundances of Ruminococcus and Phocaeicola of sheep in the three experimental groups were significantly higher than in the control group ( p -< 0.05), and the abundances of Clostridiales and Candidatus-Hepatincola were significantly increased in the 0.1% and 0.3% groups ( p < 0.05). (3) Regarding rumen anaerobic fungi, the differences between the control group and experimental groups at the phylum level and genus level were not significant ( p > 0.05), but the relative abundances of Neocallimastigomycota and Piromyces in the 0.1% group were significantly higher than that in the control group., Conclusion: SA addition to a high grain diet could increase the VFA concentration and pH in the sheep rumen, reduce the NH 3 -N concentration in the rumen and improve rumen fermentation function. Although there was no significant change in rumen bacterial or fungal diversity, SA addition increased the rumen abundances of Bacteroidetes, Ruminococcus , Phocaeicola, Clostridiales, Neocallimastigomycota and Piromyces , decreased the rumen abundance of Firmicutes , and had a positive effect on the rumen microbiota to improve sheep health., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 An, Wang, Zong, Gao, Shi, Li and Khas-Erdene.)

Information regarding the effect of nanoscale titanium dioxide particles (nTiO 2 ) on the environment under dark conditions is scarce, and the effect of nTiO 2 on fungi is largely unknown. Due to its huge size and high sensitivity to external stimuli, the slime mold fungi cell, Physarum polycephalum macroplasmodium, was utilized as a novel subject for the toxicity investigations in the present study, and oxidative stress from nTiO 2 on the macroplasmodium was assessed under dark conditions. Short exposure (2-3 h) caused an intracellular reactive oxygen species (ROS) imbalance, and an anti-oxidative mechanism was activated from intermediate doses of nTiO 2 (5-18 mg/mL). At long exposure times (~3 days), relatively low doses of nTiO 2 (≤9 mg/mL) stimulated the growth of macroplasmodium and oxidative stress without DNA damage, whereas higher doses of nTiO 2 (≥15 mg/mL) led to growth inhibition, significant DNA oxidative damage, and activation of the DNA single-strand repairing system. Although DNA oxidative damage was decreased to the same level as the control group by the supplementation of the anti-oxidant vitamin C, growth of the macroplasmodium failed to be completely restored. We inferred that nTiO 2 induced a complicated toxicity effect on P. polycephalum in addition to DNA oxidative damage. Taken as a whole, the present study implied the probability of using P. polycephalum macroplasmodium for toxicity studies at the single-cell level, indicating that nTiO 2 could induce oxidative stress or damage in P. polycephalum even under dark conditions and suggesting that the release of nTiO 2 could lead to a growth imbalance of slime molds in the environment.

Sanshuibaihu decoction (SSBH) is an anti-arthritic Chinese herbal formula which has been used in the treatment of rheumatoid arthritis (RA) for many years. We herein aimed to confirm its anti-arthritic effect and explore the potential mechanism of action on collagen-induced arthritis (CIA) in rats. CIA was induced by immunizing 50 female Wistar rats with bovine type II collagen. 13 days following the immunization rats with CIA were treated with SSBH (50mg/kg), leflunomide (LEF) (10mg/kg) and physiological saline for 30 days, and rats without CIA were left untreated. After the treatment, paw edema was obviously improved in SSBH-treated rats, with the significant difference of arthritis score (F=6.032, P=0.006) observed between the three treated groups. In pathological observation, SSBH-treated rats showed a significant improvement of inflammatory infiltration, synovial hyperplasia, cartilage and bone destruction and joint fusion. After the treatment of SSBH, radiological score of knee (t=11.504, P=0.000) and ankle joints (t=9.250, P=0.000) was decreased significantly. In situ hybridization on joint tissue section indicated only slight synovial hyperblastosis and expression of NF-kappaB in SSBH-treated rats. Image analysis indicated a significant difference of means of integrated optical density (MIOD) (F=3.956, P=0.040) and means of stained area (MSA) (F=3.867, P=0.032) of NF-kappaB between the three treated groups. MIOD and MSA of SSBH-treated group were significantly lower vs control. Enzyme linked immunosorbent assay (ELISA) showed a significant difference (F=10.167, P=0.000) of the amount of p-p38 MAPKalpha in the three treated groups. The detected amount of p-p38 MAPKalpha in SSBH-treated group was significantly lower vs control. These results show SSBH has an inhibiting effect on CIA, which may be associated with NF-kappaB and p38 MAPKalpha., (Published by Elsevier Ireland Ltd.)