WGCNA based identification of hub genes associated with cold response and development in Apis mellifera metamorphic pupae

Identification of Key Biomarkers of Growth-Related Traits in the Bay Scallop Argopecten irradians irradians via Multi-omics Analysis Strategies

In an attempt to promote and advance molecular-assisted selective breeding of shellfish, in this study, gills from selected (shell color as the marker trait and growth performance as the target trait) and unselected Argopecten irradians irradians were sampled. 2b-restriction site-associated DNA sequencing, genome-wide association study, comparative transcriptome, comparative small RNA transcriptome, miRNA-mRNA integrated analysis, quantitative real-time reverse transcription-polymerase chain reaction, and weighted gene co-expression network analysis were used to identify candidate SNPs, mRNAs, miRNAs, and miRNA/mRNA pairs with potential selective breeding value at a genomic scale in A. irradians irradians. The results revealed that a total of 6 significant SNPs were correlated closely with at least two examined growth-related traits. In addition, a total of 10 mRNAs and 7 miRNAs were identified to have positive correlations with shell length, shell height, shell width, total weight, and shell color. These candidate mRNAs and miRNAs may form 11 miRNA-mRNA pairs, which have great potential for developing molecular markers for molecular-assisted selective breeding of A. irradians irradians. The findings of this study will benefit the development of molecular-assisted breeding techniques in bay scallop aquaculture.

Comparative Transcriptome Analysis of Cold Tolerance Mechanism in Honeybees (Apis mellifera sinisxinyuan)

Honeybees are important pollinators worldwide that are closely related to agricultural production and ecological balance. The biological activities and geographical distribution of honeybees are strongly influenced by temperature. However, there is not much research on the cold tolerance of honeybees. The Apis mellifera sinisxinyuan, a kind of western honeybee, exhibits strong cold hardiness. Here, we determined that short-term temperature treatment could regulate the honeybee's cold tolerance ability by measuring the supercooling point of A. m. sinisxinyuan treated with different temperatures. Transcriptome data were analyzed between the treated and untreated honeybees. A total of 189 differentially expressed genes were identified. Among them, Abra, Pla1, rGC, Hr38, and Maf were differentially expressed in all comparisons. GO and KEGG analysis showed that the DEGs were enriched in molecular functions related to disease, signal transduction, metabolism, and the endocrine system's function. The main components involved were ribosomes, nucleosomes, proteases, and phosphokinases, among others. This study explored the formation and regulation mechanism of cold tolerance in honeybees, not only providing a theoretical basis for cultivating honeybees with excellent traits but also promoting research and practice on insect stress tolerance.

Bioinformatics-based analysis of the relationship between plasminogen regulatory genes and photoaging

BACKGROUND

Ultraviolet radiation causes skin photoaging by producing a variety of enzymes, which impact both skin health and hinder beauty. Currently, the early diagnosis and treatment of photoaging remain a challenge. Bioinformatics analysis has strong advantages in exploring core genes and the biological pathways of photoaging.

AIMS

To screen and validate key risk genes associated with plasminogen in photoaging and to identify potential target genes for photoaging.

METHODS

Two human transcriptome datasets were obtained by searching the Gene Expression Omnibus (GEO) database, and the mRNAs in the GSE131789 dataset were differentially analyzed, and then the weighted gene co-expression network analysis (WGCNA) was performed to find out the strongest correlations. Template genes, interaction analysis of differentially expressed genes (DEGs), modular genes with the most WGCNA correlations, and genecard database genes related to plasminogen were performed, and further Kyoto genes and Genome Encyclopedia (KEGG) pathway analysis. Two different algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machines-recursive feature elimination (SVM-RFE), were used to find key genes. Then the data set (GSE206495) was validated and analyzed. Real-time PCR was performed to validate the expression of key genes through in vitro cellular experiments.

RESULTS

IFI6, IFI44L, HRSP12, and BMP4 were screened from datasets as key genes for photoaging and further analysis showed that these genes have significant diagnostic value for photoaging.

CONCLUSION

IFI6, IFI44L, HRSP12, and BMP4 play a key role in the pathogenesis of photoaging, and serve as promising potential predictive biomarkers for photoaging.

Transcriptome Analysis Revealed Potential Genes of Skeletal Muscle Thermogenesis in Mashen Pigs and Large White Pigs under Cold Stress

Pigs are susceptible to cold stress due to the absence of brown fat caused by the partial deletion of uncoupling protein 1 during their evolution. Some local pig breeds in China exhibit potential cold adaptability, but research has primarily focused on fat and intestinal tissues. Skeletal muscle plays a key role in adaptive thermogenesis in mammals, yet the molecular mechanism of cold adaptation in porcine skeletal muscle remains poorly understood. This study investigated the cold adaptability of two pig breeds, Mashen pigs (MS) and Large White pigs (LW), in a four-day cold (4 °C) or normal temperature (25 °C) environment. We recorded phenotypic changes and collected blood and longissimus dorsi muscle for transcriptome sequencing. Finally, the PRSS8 gene was randomly selected for functional exploration in porcine skeletal muscle satellite cells. A decrease in body temperature and body weight in both LW and MS pigs under cold stress, accompanied by increased shivering frequency and respiratory frequency, were observed. However, the MS pigs demonstrated stable physiological homeostasis, indicating a certain level of cold adaptability. The LW pigs primarily responded to cold stress by regulating their heat production and glycolipid energy metabolism. The MS pigs exhibited a distinct response to cold stress, involving the regulation of heat production, energy metabolism pathways, and robust mitochondrial activity, as well as a stronger immune response. Furthermore, the functional exploration of PRSS8 in porcine skeletal muscle satellite cells revealed that it affected cellular energy metabolism and thermogenesis by regulating ERK phosphorylation. These findings shed light on the diverse transcriptional responses of skeletal muscle in LW and MS pigs under cold stress, offering valuable insights into the molecular mechanisms underlying cold adaptation in pigs.