Gene Expression Patterns Research Articles

Identification, validation and candidate gene analysis of major QTL for Supernumerary spikelets in wheat

BackgroundThe number of spikelets per spike is a key trait that affects the yield of bread wheat (Triticum aestivum L.). Identification of the QTL for spikelets per spike and its genetic effects that could be used in molecular assistant breeding in the future.ResultsIn this study, four recombinant inbred line (RIL) populations were generated and used, having YuPi branching wheat (YP), with Supernumerary Spikelets (SS) phenotype, as a common parent. QTL (QSS.sicau-2 A and QSS.sicau-2D) related to SS trait were mapped on chromosomes 2 A and 2D through bulked segregant exome sequencing (BSE-Seq). Fourteen molecular markers were further developed within the localization interval, and QSS.sicau-2 A was narrowed to 3.0 cM covering 7.6 Mb physical region of the reference genome, explaining 13.7 − 15.9% the phenotypic variance. Similarly, the QSS.sicau-2D was narrowed to 1.8 cM covering 2.4 Mb physical region of the reference genome, and it explained 27.4 − 32.9% the phenotypic variance. These two QTL were validated in three different genetic backgrounds using the linked markers. QSS.sicau-2 A was identified as WFZP-A, and QSS.sicau-2D was identified a novel locus, different to the previously identified WFZP-D. Based on the gene expression patterns, gene annotation and sequence analysis, TraesCS2D03G0260700 was predicted to be a potential candidate gene for QSS.sicau-2D.ConclusionTwo significant QTL for SS, namely QSS.sicau-2 A and QSS.sicau-2D were identified in multiple environments were identified and their effect in diverse genetic populations was assessed. QSS.sicau-2D is a novel QTL associated with the SS trait, with TraesCS2D03G0260700 predicted as its candidate gene.

Relationships between nine neuropsychiatric disorders and cervical cancer: insights from genetics, causality and shared gene expression patterns.

Neuropsychiatric disorders and cervical cancer exert substantial influences on women's health. Furthermore, neuropsychiatric disorders frequently manifest as common symptoms in cancer patients, potentially increasing the risk of malignant neoplasms. This study aimed to identify neuropsychiatric disorders that are genetically and causally related to cervical cancer and to investigate the molecular mechanisms underlying these associations. GWAS data related to nine neuropsychiatric disorders, namely, schizophrenia, bipolar disorder, autism spectrum disorder, Parkinson's disease, anxiety, Alzheimer's disease, mood disorders, depression, and alcohol dependence, were obtained to calculate heritability (h2) and genetic correlation (rg) with cervical cancer using linkage disequilibrium score regression (LDSC). Mendelian randomization (MR) analysis of the two cohorts was employed to assess the causal effects. Shared gene expression pattern analysis was subsequently conducted to investigate the molecular mechanism underlying these significant associations. Anxiety, mood disorders, depression, and alcohol dependence were genetically correlated with cervical cancer (all adjusted P < 0.05). Only depression was causally related to cervical cancer in both the discovery (ORIVW: 1.41, PIVW = 0.02) and replication cohorts (ORIVW: 1.80, PIVW = 0.03) in the MR analysis. Gene expression pattern analysis revealed that 270 genes related to depression and cervical cancer, including tumour necrosis factor (TNF), were significantly upregulated in cervical cancer patients, while vascular endothelial growth factor A (VEGFA), transcription factor AP-1 (JUN), and insulin-like growth factor I (IGF-I) were associated with prognosis in cervical cancer patients (all P < 0.05). These overlapping genes implicated the involvement of multiple biological mechanisms, such as neuron death, the PI3K-Akt signalling pathway, and human papillomavirus infection. Genetic, causal and molecular evidence indicates that depression increases the risk of cervical cancer. The TNF, VEGFA, JUN, and IGF-1 genes and the neuron death, PI3K-Akt, and human papillomavirus infection signalling pathways may possibly explain this association.

Metabolomic and Transcriptomic Profiles in Diverse Brassica oleracea Crops Provide Insights into the Genetic Regulation of Glucosinolate Profiles.

Glucosinolates (GSLs) are plant secondary metabolites commonly found in the cruciferous vegetables of the Brassicaceae family, offering health benefits to humans and defense against pathogens and pests to plants. In this study, we investigated 23 GSL compounds' relative abundance in four tissues of five different Brassica oleracea morphotypes. Using the five corresponding high-quality B. oleracea genome assemblies, we identified 183 GSL-related genes and analyzed their expression with mRNA-Seq data. GSL abundance and composition varied strongly, among both tissues and morphotypes, accompanied by different gene expression patterns. Interestingly, broccoli exhibited a nonfunctional AOP2 gene due to a conserved 2OG-FeII_Oxy domain loss, explaining the unique accumulation of two health-promoting GSLs. Additionally, transposable element (TE) insertions were found to affect the gene structure of MAM3 genes. Our findings deepen the understanding of GSL variation and genetic regulation in B. oleracea morphotypes, providing valuable insights for breeding with tailored GSL profiles in these crops.

A pan-cancer analysis unveiling the function of NR4A family genes in tumor immune microenvironment, prognosis, and drug response.

NR4A family genes play crucial roles in cancers. However, the role of NR4A family genes in cancers remains paradoxical as they promote or suppress tumorigenesis. We aimed to conduct comprehensive analyses of the association between the expression of NR4A family genes and tumor microenvironment (TME) based on bioinformatics methods. We collected RNA-seq data from 33 cancer types and 20 normal tissue sites from the TCGA and GTEx databases. Expression patterns of NR4A family genes and their associations with DNA methylation, miRNA, overall survival, drug responses, and tumor microenvironment were investigated. Significant downregulation of all NR4A family genes was observed in 15 cancer types. DNA promoter methylation and expression of NR4A family genes were negatively correlated in five cancers. The expression of 10 miRNAs targeting NR4A family genes was negatively correlated with the expression of NR4A family genes. High expression of all NR4A family genes was associated with poor prognosis in stomach adenocarcinoma and increased expressions of NR4A2 and NR4A3 were associated with poor prognosis in adrenocortical carcinoma. In addition, we found an elevated expression of NR4A2, which enhances the response to various chemotherapeutic drugs, whereas NR4A3 decreases drug sensitivity. Interestingly, in breast cancer, NR4A3 was significantly associated with C2 (IFN-γ dominant), C3 (inflammatory), and C6 (TGF-β dominant) immune subtypes and infiltrated immune cell types, implying both oncogenic and tumor-suppressive functions of NR4A3 in breast cancer. The NR4A family genes have the potential to serve as a diagnostic, prognostic, and immunological marker of human cancers.

Single-cell RNA sequencing uncovers cellular heterogeneity and the progression of heterotopic ossification of the elbow

Heterotopic ossification of the elbow (HOE) is a complicated pathologic process characterized by extra bone formation in the elbow. Bone formation is a complex developmental process involving the differentiation of mesenchymal stem cells into osteoblasts. The aim of this study was to explore the cellular origin and progression of HOE by single-cell RNA sequencing. We identified 13 clusters of cells in HOE and further analyzed the subclusters for 4 of the main cell types. Six subclusters of osteoblasts, nine subclusters of chondrocytes, six subclusters of fibroblasts, and five subclusters of mononuclear phagocytes (MPs) were identified and analyzed. The new findings on osterix (OSX) and SOX9 expression in osteoblast subclusters and chondrocyte subclusters indicate that HOE is mediated through endochondral ossification. Further identification of the corresponding signature gene sets of distinct subclusters indicated that subclusters of osteoblasts_3, osteoblasts_4, osteoblasts_5, and osteoblasts_6 are relatively more mature during the osteoblastic progression of HOE. The trajectory analysis of the osteoblasts demonstrated that some genes were gradually downregulated, such as CRYAB, CCL3, SFRP4, WIF1, and IGFBP3, while other critical genes were upregulated, such as VCAN, IGFBP4, FSTL1, POSTN, MDK, THBS2, and ALPL, suggesting that these factors may participate in HOE progression. Cell–cell communication networks revealed extensive molecular interactions among the 13 HOE clusters. Ligand–receptor pairs for IL6, COL24A1, COL22A1, VWF, FZD6, FGF2, and NOTCH1 were identified, suggesting that multiple signaling pathways may be involved in HOE. In conclusion, this study provided the cellular atlas for HOE. We have established a greater extent of the heterogeneity of HOE cells than previously known through transcriptomic analysis at the single-cell level. We have observed gradual patterns of signature gene expression during the differentiation and maturation progression of osteoblasts from stem cells in HOE with higher resolution. The cell heterogeneity of HOE deserves further investigation to pave the way for identification of potential targets for HOE early diagnosis and therapeutic treatment.

Expression patterns of Mal genes and association with differential maltose and maltotriose transport rate of two Saccharomyces pastorianus yeasts.

Beer brewing is a well-known process that still faces great challenges, such as the total consumption of sugars present in the fermentation media. Lager-style beer, a major worldwide beer type, is elaborated by Saccharomyces pastorianus (Sp) yeast, which must ferment high maltotriose content worts, but its consumption represents a notable problem, especially among Sp strains belonging to group I. Factors, such as fermentation conditions, presence of maltotriose transporters, transporter copy number variation, and genetic regulation variations contribute to this issue. We assess the factors affecting fermentation in two Sp yeast strains: SpIB1, with limited maltotriose uptake, and SpIB2, known for efficient maltotriose transport. Here, SpIB2 transported significantly more maltose (28%) and maltotriose (32%) compared with SpIB1. Furthermore, SpIB2 expressed all MAL transporters (ScMALx1, SeMALx1, ScAGT1, SeAGT1, MTT1, and MPHx) on the first day of fermentation, whereas SpIB1 only exhibited ScMalx1, ScAGT1, and MPH2/3 genes. Some SpIB2 transporters had polymorphic transmembrane domains (TMD) resembling MTT1, accompanied by higher expression of these transporters and its positive regulator genes, such as MAL63. These findings suggest that, in addition to the factors mentioned above, positive regulators of Mal transporters contribute significantly to phenotypic diversity in maltose and maltotriose consumption among the studied lager yeast strains.IMPORTANCEBeer, the third most popular beverage globally with a 90% market share in the alcoholic beverage industry, relies on Saccharomyces pastorianus (Sp) strains for lager beer production. These strains exhibit phenotypic diversity in maltotriose consumption, a crucial process for the acceptable organoleptic profile in lager beer. This diversity ranges from Sp group II strains with a notable maltotriose-consuming ability to Sp group I strains with limited capacity. Our study highlights that differential gene expression of maltose and maltotriose transporters and its upstream trans-elements, such as MAL gene-positive regulators, adds complexity to this variation. This insight can contribute to a more comprehensive analysis needed to the development of controlled and efficient biotechnological processes in the beer brewing industry.

Single-cell RNA sequencing uncovers cellular heterogeneity and the progression of heterotopic ossification of the elbow

Heterotopic ossification of the elbow (HOE) is a complicated pathologic process characterized by extra bone formation in the elbow. Bone formation is a complex developmental process involving the differentiation of mesenchymal stem cells into osteoblasts. The aim of this study was to explore the cellular origin and progression of HOE by single-cell RNA sequencing. We identified 13 clusters of cells in HOE and further analyzed the subclusters for 4 of the main cell types. Six subclusters of osteoblasts, nine subclusters of chondrocytes, six subclusters of fibroblasts, and five subclusters of mononuclear phagocytes (MPs) were identified and analyzed. The new findings on osterix (OSX) and SOX9 expression in osteoblast subclusters and chondrocyte subclusters indicate that HOE is mediated through endochondral ossification. Further identification of the corresponding signature gene sets of distinct subclusters indicated that subclusters of osteoblasts_3, osteoblasts_4, osteoblasts_5, and osteoblasts_6 are relatively more mature during the osteoblastic progression of HOE. The trajectory analysis of the osteoblasts demonstrated that some genes were gradually downregulated, such as CRYAB, CCL3, SFRP4, WIF1, and IGFBP3, while other critical genes were upregulated, such as VCAN, IGFBP4, FSTL1, POSTN, MDK, THBS2, and ALPL, suggesting that these factors may participate in HOE progression. Cell–cell communication networks revealed extensive molecular interactions among the 13 HOE clusters. Ligand–receptor pairs for IL6, COL24A1, COL22A1, VWF, FZD6, FGF2, and NOTCH1 were identified, suggesting that multiple signaling pathways may be involved in HOE. In conclusion, this study provided the cellular atlas for HOE. We have established a greater extent of the heterogeneity of HOE cells than previously known through transcriptomic analysis at the single-cell level. We have observed gradual patterns of signature gene expression during the differentiation and maturation progression of osteoblasts from stem cells in HOE with higher resolution. The cell heterogeneity of HOE deserves further investigation to pave the way for identification of potential targets for HOE early diagnosis and therapeutic treatment.

ScMaSigPro: Differential Expression Analysis along Single-Cell Trajectories.

Understanding the dynamics of gene expression across different cellular states is crucial for discerning the mechanisms underneath cellular differentiation. Genes that exhibit variation in mean expression as a function of Pseudotime and between branching trajectories are expected to govern cell fate decisions. We introduce scMaSigPro, a method for the identification of differential gene expression patterns along Pseudotime and branching paths simultaneously. We assessed the performance of scMaSigPro using synthetic and public datasets. Our evaluation shows that scMaSigPro outperforms existing methods in controlling the False Positive Rate and is computationally efficient. scMaSigPro is available as a free R package (version 4.0 or higher) under the GPL(≥2) license on GitHub at 'github.com/BioBam/scMaSigPro' and archived with version 0.03 on Zenodo at 'zenodo.org/records/12568922'.

Tumor Necrosis Factor-Alpha Modulates Expression of Genes Involved in Cytokines and Chemokine Pathways in Proliferative Myoblast Cells.

Skeletal muscle regeneration after injury is a complex process involving inflammatory signaling and myoblast activation. Pro-inflammatory cytokines like tumor necrosis factor-alpha (TNF-α) are key mediators, but their effects on gene expression in proliferating myoblasts are unclear. We performed the RNA sequencing of TNF-α treated C2C12 myoblasts to elucidate the signaling pathways and gene networks regulated by TNF-α during myoblast proliferation. The TNF-α (10 ng/mL) treatment of C2C12 cells led to 958 differentially expressed genes compared to the controls. Pathway analysis revealed significant regulation of TNF-α signaling, along with the chemokine and IL-17 pathways. Key upregulated genes included cytokines (e.g., IL-6), chemokines (e.g., CCL7), and matrix metalloproteinases (MMPs). TNF-α increased myogenic factor 5 (Myf5) but decreased MyoD protein levels and stimulated the release of MMP-9, MMP-10, and MMP-13. TNF-α also upregulates versican and myostatin mRNA. Overall, our study demonstrates the TNF-α modulation of distinct gene expression patterns and signaling pathways that likely contribute to enhanced myoblast proliferation while suppressing premature differentiation after muscle injury. Elucidating the mechanisms involved in skeletal muscle regeneration can aid in the development of regeneration-enhancing therapeutics.

A Modeling Approach to Studying the Influence of Grafting on the Anatomical Features and SAUR Gene Expression in Watermelons

Grafting alters the genetic and anatomical features of plants. Although grafting has been widely applied in plant propagation, the underlying processes that govern the effects of the procedure are not fully understood. Samples were collected to study the long-term influence of grafting on the leaf-shoot morphology, leaf-shoot anatomy, and genetic signature of the grafted plants. Citrulus lanatus (Thunb.) Matsum. &amp; Nakai (cv. Lady) was used as the scion, and Lagenaria siceraria (Molina) Standl (cv. Argentario) as a rootstock. In grafted plants, leaf blades and petioles were 20.92% and 12.82% longer, respectively, while the midrib collenchyma was 35.68% thicker, and the diameter of the vessel member was 11.17% larger than in ungrafted plants. In the stem, grafting affected the arrangement and number of vascular bundles (from 1 to 2 rings). The thickness of the epidermis decreased by 69.79%, and the size of the external fascicular phloem decreased by 23.56%. The diameter of the vessel member of the grafted plants increased by 28.94%. Eight out of ten evaluated primers met the requirements (stability in both watermelons and bottle gourd, tissue-specific). In the genetic tests, we examined whether this change in the gene expression pattern is due to the grafting and, if so, to what extent. Seven out of eight tested Small Auxin Up-Regulated RNA (SAUR) genes were expressed in the ungrafted and grafted C. lanatus lines in four cases; the expression increased by more than 10% after grafting. The morpho-anatomical changes and genetic variation reported in this study for grafted lines of C. lanatus contribute to the understanding of the underlying mechanisms of plant growth observations resulting from grafting.

A Modeling Approach to Studying the Influence of Grafting on the Anatomical Features and SAUR Gene Expression in Watermelons

Grafting alters the genetic and anatomical features of plants. Although grafting has been widely applied in plant propagation, the underlying processes that govern the effects of the procedure are not fully understood. Samples were collected to study the long-term influence of grafting on the leaf-shoot morphology, leaf-shoot anatomy, and genetic signature of the grafted plants. Citrulus lanatus (Thunb.) Matsum. &amp; Nakai (cv. Lady) was used as the scion, and Lagenaria siceraria (Molina) Standl (cv. Argentario) as a rootstock. In grafted plants, leaf blades and petioles were 20.92% and 12.82% longer, respectively, while the midrib collenchyma was 35.68% thicker, and the diameter of the vessel member was 11.17% larger than in ungrafted plants. In the stem, grafting affected the arrangement and number of vascular bundles (from 1 to 2 rings). The thickness of the epidermis decreased by 69.79%, and the size of the external fascicular phloem decreased by 23.56%. The diameter of the vessel member of the grafted plants increased by 28.94%. Eight out of ten evaluated primers met the requirements (stability in both watermelons and bottle gourd, tissue-specific). In the genetic tests, we examined whether this change in the gene expression pattern is due to the grafting and, if so, to what extent. Seven out of eight tested Small Auxin Up-Regulated RNA (SAUR) genes were expressed in the ungrafted and grafted C. lanatus lines in four cases; the expression increased by more than 10% after grafting. The morpho-anatomical changes and genetic variation reported in this study for grafted lines of C. lanatus contribute to the understanding of the underlying mechanisms of plant growth observations resulting from grafting.

Genome-Wide Identification and Characterization of RdHSP Genes Related to High Temperature in Rhododendron delavayi.

Heat shock proteins (HSPs) are molecular chaperones that play essential roles in plant development and in response to various environmental stresses. Understanding R. delavayi HSP genes is of great importance since R. delavayi is severely affected by heat stress. In the present study, a total of 76 RdHSP genes were identified in the R. delavayi genome, which were divided into five subfamilies based on molecular weight and domain composition. Analyses of the chromosome distribution, gene structure, and conserved motif of the RdHSP family genes were conducted using bioinformatics analysis methods. Gene duplication analysis showed that 15 and 8 RdHSP genes were obtained and retained from the WGD/segmental duplication and tandem duplication, respectively. Cis-element analysis revealed the importance of RdHSP genes in plant adaptations to the environment. Moreover, the expression patterns of RdHSP family genes were investigated in R. delavayi treated with high temperature based on our RNA-seq data, which were further verified by qRT-PCR. Further analysis revealed that nine candidate genes, including six RdHSP20 subfamily genes (RdHSP20.4, RdHSP20.8, RdHSP20.6, RdHSP20.3, RdHSP20.10, and RdHSP20.15) and three RdHSP70 subfamily genes (RdHSP70.15, RdHSP70.21, and RdHSP70.16), might be involved in enhancing the heat stress tolerance. The subcellular localization of two candidate RdHSP genes (RdHSP20.8 and RdHSP20.6) showed that two candidate RdHSPs were expressed and function in the chloroplast and nucleus, respectively. These results provide a basis for the functional characterization of HSP genes and investigations on the molecular mechanisms of heat stress response in R. delavayi.

Genome-Wide Identification and Characterization of RdHSP Genes Related to High Temperature in Rhododendron delavayi

Heat shock proteins (HSPs) are molecular chaperones that play essential roles in plant development and in response to various environmental stresses. Understanding R. delavayi HSP genes is of great importance since R. delavayi is severely affected by heat stress. In the present study, a total of 76 RdHSP genes were identified in the R. delavayi genome, which were divided into five subfamilies based on molecular weight and domain composition. Analyses of the chromosome distribution, gene structure, and conserved motif of the RdHSP family genes were conducted using bioinformatics analysis methods. Gene duplication analysis showed that 15 and 8 RdHSP genes were obtained and retained from the WGD/segmental duplication and tandem duplication, respectively. Cis-element analysis revealed the importance of RdHSP genes in plant adaptations to the environment. Moreover, the expression patterns of RdHSP family genes were investigated in R. delavayi treated with high temperature based on our RNA-seq data, which were further verified by qRT-PCR. Further analysis revealed that nine candidate genes, including six RdHSP20 subfamily genes (RdHSP20.4, RdHSP20.8, RdHSP20.6, RdHSP20.3, RdHSP20.10, and RdHSP20.15) and three RdHSP70 subfamily genes (RdHSP70.15, RdHSP70.21, and RdHSP70.16), might be involved in enhancing the heat stress tolerance. The subcellular localization of two candidate RdHSP genes (RdHSP20.8 and RdHSP20.6) showed that two candidate RdHSPs were expressed and function in the chloroplast and nucleus, respectively. These results provide a basis for the functional characterization of HSP genes and investigations on the molecular mechanisms of heat stress response in R. delavayi.

Genome-Wide Identification and Expression Pattern of Sugar Transporter Genes in the Brown Planthopper, Nilaparvata lugens (Stål)

Sugar transporters play important roles in controlling carbohydrate transport and are responsible for mediating the movement of sugars into cells in numerous organisms. In insects, sugar transporters not only play a role in sugar transport but may also act as receptors for virus entry and the accumulation of plant defense compounds. The brown planthopper, Nilaparvata lugens, inflicts damage on rice plants by feeding on their phloem sap, which is rich in sugars. In the present study, we identified 34 sugar transporters in N. lugens, which were classified into three subfamilies based on phylogenetic analysis. The motif numbers varied from seven to eleven, and motifs 2, 3, and 4 were identified in the functional domains of all 34 NlST proteins. Chromosome 1 was found to possess the highest number of NlST genes, harboring 15. The gut, salivary glands, fat body, and ovary were the different tissues enriched with NlST gene expression. The expression levels of NlST2, 3, 4, 7, 20, 27, 28, and 31 were higher in the gut than in the other tissues. When expressed in a Saccharomyces cerevisiae hexose transporter deletion mutant (strain EBY.VW4000), only ApST4 (previously characterized) and NlST4, 28, and 31 were found to transport glucose and fructose, resulting in functional rescue of the yeast mutant. These results provide valuable data for further studies on sugar transporters in N. lugens and lay a foundation for finding potential targets to control N. lugens.

Genome-Wide Identification and Expression Pattern of Sugar Transporter Genes in the Brown Planthopper, Nilaparvata lugens (Stål)

Sugar transporters play important roles in controlling carbohydrate transport and are responsible for mediating the movement of sugars into cells in numerous organisms. In insects, sugar transporters not only play a role in sugar transport but may also act as receptors for virus entry and the accumulation of plant defense compounds. The brown planthopper, Nilaparvata lugens, inflicts damage on rice plants by feeding on their phloem sap, which is rich in sugars. In the present study, we identified 34 sugar transporters in N. lugens, which were classified into three subfamilies based on phylogenetic analysis. The motif numbers varied from seven to eleven, and motifs 2, 3, and 4 were identified in the functional domains of all 34 NlST proteins. Chromosome 1 was found to possess the highest number of NlST genes, harboring 15. The gut, salivary glands, fat body, and ovary were the different tissues enriched with NlST gene expression. The expression levels of NlST2, 3, 4, 7, 20, 27, 28, and 31 were higher in the gut than in the other tissues. When expressed in a Saccharomyces cerevisiae hexose transporter deletion mutant (strain EBY.VW4000), only ApST4 (previously characterized) and NlST4, 28, and 31 were found to transport glucose and fructose, resulting in functional rescue of the yeast mutant. These results provide valuable data for further studies on sugar transporters in N. lugens and lay a foundation for finding potential targets to control N. lugens.

Gene expression and characterization of clonally derived murine embryonic brown and brite adipocytes.

White adipocytes store energy, while brown and brite adipocytes release heat via nonshivering thermogenesis. In this study, we characterized two murine embryonic clonal preadipocyte lines, EB5 and EB7, each displaying unique gene marker expression profiles. EB5 cells differentiate into brown adipocytes, whereas EB7 cells into brite (also known as beige) adipocytes. To draw a comprehensive comparison, we contrasted the gene expression patterns, adipogenic capacity, as well as carbohydrate and lipid metabolism of these cells to that of F442A, a well-known white preadipocyte and adipocyte model. We found that commitment to differentiation in both EB5 and EB7 cells can be induced by 3-Isobutyl-1-methylxanthine/dexamethasone (Mix/Dex) and staurosporine/dexamethasone (St/Dex) treatments. Additionally, the administration of rosiglitazone significantly enhances the brown and brite adipocyte phenotypes. Our data also reveal the involvement of a series of genes in the transcriptional cascade guiding adipogenesis, pinpointing GSK3β as a critical regulator for both EB5 and EB7 adipogenesis. In a developmental context, we observe that, akin to brown fat progenitors, brite fat progenitors make their appearance in murine development by 11-12 days of gestation or potentially earlier. This result contributes to our understanding of adipocyte lineage specification during embryonic development. In conclusion, EB5 and EB7 cell lines are valuable for research into adipocyte biology, providing insights into the differentiation and development of brown and beige adipocytes. Furthermore, they could be useful for the characterization of drugs targeting energy balance for the treatment of obesity and metabolic diseases.

Screening of Reference Genes for Quantitative Real-Time PCR Analysis in Tissues and during Testis Development, and Application to Analyze the Expression of kifc1 in Hemibarbus labeo (Teleostei, Cypriniformes, Cyprinidae).

The selection of proper reference genes is vital for ensuring precise quantitative real-time PCR (qPCR) assays. This study evaluates the stability of the expression of nine candidate reference genes in different tissues and during testicular development in H. labeo. The results show that eef1a is recommended as a reference gene for qPCR analysis in tissues and during testicular development. Furthermore, we evaluated the optimal number of reference genes needed when calculating gene expression levels using the geomean method, revealing that two reference genes are sufficient. Specifically, eef1a and rps27 are recommended for analysis of gene expression in tissues, whereas eef1a and actb are advised for evaluating gene expression during testicular development. In addition, we examined the expression pattern of kifc1, a kinesin involved in the reshaping of spermatids. We detected peak expression levels of kifc1 in testes, with its expression initially increasing before decreasing throughout testicular development. The highest expression of kifc1 was observed in stage IV testes, the active period of spermiogenesis, suggesting a possible role for kifc1 in the regulation of the reshaping of spermatids and hence testicular development. This study represents the first investigation of reference genes for H. labeo, providing a foundation for studying gene expression patterns and investigating gene expression regulation during testicular development.

Genome-wide analysis of wheat xyloglucan endotransglucosylase/hydrolase (XTH) gene family revealed TaXTH17 involved in abiotic stress responses

BackgroundEnvironmental stresses, including high salinity and drought, severely diminish wheat yield and quality globally. The xyloglucan endotransglucosylase/hydrolase (XTH) family represents a class of cell wall-modifying enzymes and plays important roles in plants growth, development and stress adaptation. However, systematic analyses of XTH family genes and their functions under salt and drought stresses have not been undertaken in wheat.ResultsIn this study, we identified a total of 135 XTH genes in wheat, which were clustered into three evolutionary groups. These TaXTHs were unevenly distributed on 21 chromosomes of wheat with a majority of TaXTHs located on homelogous groups 2, 3 and 7. Gene duplication analysis revealed that segmental and tandem duplication were the main reasons for the expansion of XTH family in wheat. Interaction network predictions indicated that TaXTHs could interact with multiple proteins, including three kinases, one methyltransferase and one gibberellin-regulated protein. The promoters of the TaXTH genes harbored various cis-acting elements related to stress and hormone responses. RNA-seq data analyses showed that some TaXTH genes were induced by salt and drought stresses. Furthermore, we verified that TaXTH17 was induced by abiotic stresses and phytohormone treatments, and demonstrated that TaXTH17 was localized in the secretory pathway and cell wall. Functional analyses conducted in heterologous expression systems and in wheat established that TaXTH17 plays a negative role in plant resistance to salt and drought.ConclusionsWe identified 135 XTH genes in wheat and conducted comprehensive analyses of their phylogenetic relationships, gene structures, conserved motifs, gene duplication events, chromosome locations, interaction networks, cis-acting elements and gene expression patterns. Furthermore, we provided solid evidence supporting the notion that TaXTH17 plays a negative role in plant resistance to salt and drought stresses. Collectively, our results provide valuable insights into understanding wheat XTHs, particularly their involvement in plant stress responses, and establish a foundation for further functional and mechanistic studies of TaXTHs.

Effects of Foliar Dressing with Chemical Nano-Selenum and Na2SeO3 on the Antioxidant System and Accumulation of Se and Bioactive Components in Cyclocarya paliurus (Sweet Tea Tree)

Selenium (Se)-rich Cyclocarya paliurus is popular for its bioactive components, and exogenous Se fortification is the most effective means of enrichment. However, the effects of exogenous Se fortification on the nutritional quality of C. paliurus are not well known. To investigate the nutrient contents and antioxidant properties of C. paliurus following Se treatment, we used a foliar spray to apply Se in two forms—chemical nano-Se (Che-SeNPs) and sodium selenite (Na2SeO3). Sampling began 10 days after spraying and was conducted every 5 days until day 30. The Se, secondary metabolite, malondialdehyde contents, antioxidant enzyme activity, Se speciation, and Se-metabolism-related gene expression patterns were analyzed in the collected samples. Exogenous Se enhancement effectively increased the Se content of leaves, reaching a maximum on days 10 and 15 of sampling, while the contents of flavonoids, triterpenes, and polyphenols increased significantly during the same period. In addition, the application of Se significantly enhanced total antioxidant activity, especially the activity of the antioxidant enzyme peroxidase. Furthermore, a positive correlation between the alleviation of lipid peroxidation and Se content was observed, while methylselenocysteine formation was an effective means of alleviating Se stress. Finally, Na2SeO3 exhibited better absorption and conversion efficiency than Che-SeNPs in C. paliurus.

Effects of Foliar Dressing with Chemical Nano-Selenum and Na2SeO3 on the Antioxidant System and Accumulation of Se and Bioactive Components in Cyclocarya paliurus (Sweet Tea Tree).

Selenium (Se)-rich Cyclocarya paliurus is popular for its bioactive components, and exogenous Se fortification is the most effective means of enrichment. However, the effects of exogenous Se fortification on the nutritional quality of C. paliurus are not well known. To investigate the nutrient contents and antioxidant properties of C. paliurus following Se treatment, we used a foliar spray to apply Se in two forms-chemical nano-Se (Che-SeNPs) and sodium selenite (Na2SeO3). Sampling began 10 days after spraying and was conducted every 5 days until day 30. The Se, secondary metabolite, malondialdehyde contents, antioxidant enzyme activity, Se speciation, and Se-metabolism-related gene expression patterns were analyzed in the collected samples. Exogenous Se enhancement effectively increased the Se content of leaves, reaching a maximum on days 10 and 15 of sampling, while the contents of flavonoids, triterpenes, and polyphenols increased significantly during the same period. In addition, the application of Se significantly enhanced total antioxidant activity, especially the activity of the antioxidant enzyme peroxidase. Furthermore, a positive correlation between the alleviation of lipid peroxidation and Se content was observed, while methylselenocysteine formation was an effective means of alleviating Se stress. Finally, Na2SeO3 exhibited better absorption and conversion efficiency than Che-SeNPs in C. paliurus.