Reference gene selection for expression studies in the reproductive axis tissues of Magang geese at different reproductive stages under light treatment

Effect of active immunization with OPN5 on follicular development and egg production in quail under different photoperiods

OPN5 is one of the main deep brain photoreceptors (DBPs), converting photoperiodic information into neuroendocrine signals to regulate reproduction in birds. This study investigated the mechanism of OPN5-mediated photoperiodic regulation of reproduction by active immunization against OPN5. 96 female quail were divided into OPN5-immunized and control group under the same photoperiod: 16 L:8 D (d 1 to d 35), 8 L:16 D (d 36 to d 70) and 12 L:12 D (d 71 to d 126). OPN5-immunized group was conducted with OPN5 protein vaccination and control group was given a blank vaccine. Samples were collected on d 1, d 30, d 60, and d 126. Results showed switching photoperiod to 8 L:16 D decreased the laying rate, GSI%, numbers of YFs and WFs, serum levels of PRL, P4 and E2, and pituitary PRL and TSHβ protein expressions in both groups (P < 0.05). Whereas the OPN5-immunized group exhibited higher laying rates than the control group (P < 0.05). The control group showed reduced GnRHR and TSHβ gene expressions in the pituitary and increased GnIH and DIO3 transcript and/or protein abundance in the hypothalamus. (P < 0.05). The OPN5-immunized group had lower DIO3 expression at both mRNA and protein levels. (P < 0.05). Switching photoperiod from 8 L:16 D to 12 L:12 D increased the laying rates, GSI%, numbers of YFs and WFs, serum levels of PRL, and PRL protein expression in both groups (P < 0.05), and the responses were more pronounced in OPN5-immunized group (P < 0.05). In contrast to the control group, quail with OPN5-immunization had higher OPN5 and DIO2 transcript and/or protein levels but lower DIO3 expressions in the hypothalamus along the transition photoperiods (P < 0.05). The results revealed that OPN5 responds to photoperiod transition, and its activation mediates related signaling to up-regulate TSH-DIO2/DIO3 pathway and VIP-PRL secretion to prime quail reproductive functions.

The DNA methylation status of the vitamin A signaling associated with testicular degeneration induced by long-day photoperiods in Magang geese

Magang geese are typical short-day breeders whose reproductive behaviors are significantly influenced by photoperiod. Exposure to a long-day photoperiod results in testicular regression and spermatogenesis arrest in Magang geese. To investigate the epigenetic influence of DNA methylation on the seasonal testicular regression in Magang geese, we conducted whole-genome bisulfite sequencing and transcriptome sequencing of testes across 3 reproductive phases during a long-day photoperiod. A total of 250,326 differentially methylated regions (DMR) were identified among the 3 comparison groups, with a significant number showing hypermethylation, especially in intronic regions of the genome. Integrating bisulfite sequencing with transcriptome sequencing data revealed that DMR-associated genes tend to be differentially expressed in the testes, highlighting a potential regulatory role for DNA methylation in gene expression. Furthermore, there was a significant negative correlation between changes in the methylation of CG DMRs and changes in the expression of their associated genes in the testes. A total of 3,359 DMR-associated differentially expressed genes (DEG) were identified; functional enrichment analyses revealed that motor proteins, MAPK signaling pathway, ECM-receptor interaction, phagosome, TGF-beta signaling pathway, and calcium signaling might contribute to the testicular regression process. GSEA revealed that the significantly enriched activated hallmark gene set was associated with apoptosis and estrogen response during testicular regression, while the repressed hallmark gene set was involved in spermatogenesis. Our study also revealed that methylation changes significantly impacted the expression level of vitamin A metabolism-related genes during testicular degeneration, with hypermethylation of STRA6 and increased calmodulin levels indicating vitamin A efflux during the testicular regression. These findings were corroborated by pyrosequencing and real-time qPCR, which revealed that the vitamin A metabolic pathway plays a pivotal role in testicular degeneration under long-day conditions. Additionally, metabolomics analysis revealed an insufficiency of vitamin A and an abnormally high level of oxysterols accumulated in the testes during testicular regression. In conclusion, our study demonstrated that testicular degeneration in Magang geese induced by a long-day photoperiod is linked to vitamin A homeostasis disruption, which manifests as the hypermethylation status of STRA6, vitamin A efflux, and a high level of oxysterol accumulation. These findings offer new insights into the effects of DNA methylation on the seasonal testicular regression that occurs during long-day photoperiods in Magang geese.

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.

Expression of housekeeping genes varies depending on mevalonate pathway inhibition in cancer cells

Statins have anticancer effects and may be used as anticancer agents via drug repositioning. In reverse transcription-quantitative polymerase chain reaction (RT-qPCR) assays, the internal reference gene must not be affected by any experimental conditions. As statins exert a wide range of effects on cells by inhibiting the mevalonate pathway, it is possible that statin treatment might alter the expression of housekeeping genes used as internal reference genes, thereby misleading the assessment of obtained gene expression data. Here, we evaluated the expression stability of internal reference genes in atorvastatin-treated cancer cell lines. We treated both statin-sensitive and statin-resistant cancer cell lines with atorvastatin at seven different concentrations and performed RT-qPCR on 15 housekeeping genes whose expression stability was then assessed using five different algorithms. In both statin-sensitive and statin-resistant cancer cell lines, atorvastatin affected the expression of certain internal reference genes in a dose-dependent and cancer cell line-dependent manner; therefore, caution should be exercised when comparing target gene expression between cells. Our findings emphasize the importance of the validation of internal reference genes in gene expression analyses in drug treatment-based cancer research.

Reliable reference genes and abiotic stress marker genes in Klebsormidium nitens

Microalgae have recently emerged as a key research topic, especially as biological models. Among them, the green alga Klebsormidium nitens, thanks to its particular adaptation to environmental stresses, represents an interesting photosynthetic eukaryote for studying the transition stages leading to the colonization of terrestrial life. The tolerance to different stresses is manifested by changes in gene expression, which can be monitored by quantifying the amounts of transcripts by RT-qPCR. The identification of optimal reference genes for experiment normalization was therefore necessary. In this study, using four statistical algorithms followed by the RankAggreg package, we determined the best reference gene pairs suitable for normalizing RT-qPCR data in K. nitens in response to three abiotic stresses: high salinity, PEG-induced dehydration and heat shock. Based on these reference genes, we were able to identify marker genes in response to the three abiotic stresses in K. nitens.

Evaluation of Reference Genes in the Polyploid Complex Dianthus broteri (Caryophyllaceae) Using qPCR

Dianthus broteri is an endemic complex which is considered the largest polyploid series within the Dianthus genus. This polyploid species involves four cytotypes (2×, 4×, 6× and 12×) with spatial and ecological segregation. The study of gene expression in polyploid species must be very rigorous because of the effects of duplications on gene regulation. In these cases, real-time polymerase chain reaction (qPCR) is the most appropriate technique for determining the gene expression profile because of its high sensitivity. The relative quantification strategy using qPCR requires genes with stable expression, known as reference genes, for normalization. In this work, we evaluated the stability of 13 candidate genes to be considered reference genes in leaf and petal tissues in Dianthus broteri. Several statistical analyses were used to determine the most stable candidate genes: Bayesian analysis, network analysis based on equivalence tests, geNorm and BestKeeper algorithms. In the leaf tissue, the most stable candidate genes were TIP41, TIF5A, PP2A and SAMDC. Similarly, the most adequate reference genes were H3.1, TIP41, TIF5A and ACT7 in the petal tissue. Therefore, we suggest that the best reference genes to compare different ploidy levels for both tissues in D. broteri are TIP41 and TIF5A.

Wood Smoke Extract Promotes Extracellular Matrix Remodeling in Normal Human Lung Fibroblasts

Wood smoke (WS) contains many harmful compounds, including polycyclic aromatic hydrocarbons (PAHs). WS induces inflammation in the airways and lungs and can lead to the development of various acute and chronic respiratory diseases. Pulmonary fibroblasts are the main cells involved in the remodeling of the extracellular matrix (ECM) during the WS-induced inflammatory response. Although fibroblasts remain in a low proliferation state under physiological conditions, they actively participate in ECM remodeling during the inflammatory response in pathophysiological states. Consequently, we used normal human lung fibroblasts (NHLFs) to assess the potential effects of the PAHs-containing wood smoke extract (WSE) on the growth rate, total collagen synthesis, and the expression levels of collagen I and III, matrix metalloproteinase (MMP)-1, MMP-2, MMP-9, tissue inhibitor of metalloproteinase (TIMP)-1, TIMP-2, and the transforming growth factor (TGF)-β1. We also assessed MMPs activity. The results showed that WSE induced a trimodal behavior in the growth rate curves in NHLFs; the growth rate increased with 0.5-1 % WSE and decreased with 2.5% WSE, without causing cell damage; 5-20% WSE inhibited the growth and induced cell damage. After 3 hours of exposure, 2.5% WSE induced an increase in total collagen synthesis and upregulation of TGF-β1, collagen I and III, MMP-1, TIMP-1, and TIMP-2 expression. However, MMP-2 expression was downregulated and MMP-9 was not expressed. The gelatinase activity of MMP-2 was also increased. These results suggest that WSE affects the ECM remodeling in NHLFs and indicate the potential involvement of PAHs in this process.