Opposite Expression Pattern Research Articles

Transcriptomics profiling of Parkinson’s disease progression subtypes reveals distinctive patterns of gene expression

Background Parkinson’s Disease (PD) varies widely among individuals, and Artificial Intelligence (AI) has recently helped to identify three disease progression subtypes. While their clinical features are already known, their gene expression profiles remain unexplored. Objectives The objectives of this study were (1) to describe the transcriptomics characteristics of three PD progression subtypes identified by AI, and (2) to evaluate if gene expression data can be used to predict disease subtype at baseline. Design This is a retrospective longitudinal cohort study utilizing the Parkinson’s Progression Markers Initiative (PPMI) database. Methods Whole blood RNA-Sequencing data underwent differential gene expression analysis, followed by multiple pathway analyses. A Machine Learning (ML) classifier, namely XGBoost, was trained using data from multiple modalities, including gene expression values. Results Our study identified differentially expressed genes (DEGs) that were uniquely associated with Parkinson’s disease (PD) progression subtypes. Importantly, these DEGs had not been previously linked to PD. Gene-pathway analysis revealed both distinct and shared characteristics between the subtypes. Notably, two subtypes displayed opposite expression patterns for pathways involved in immune response alterations. In contrast, the third subtype exhibited a more unique profile characterized by increased expression of genes related to detoxification processes. All three subtypes showed a significant modulation of pathways related to the regulation of gene expression, metabolism, and cell signaling. ML revealed that the progression subtype with the worst prognosis can be predicted at baseline with 0.877 AUROC, yet the contribution of gene expression was marginal for the prediction of the subtypes. Conclusion This study provides novel information regarding the transcriptomics profiles of PD progression subtypes, which may foster precision medicine with relevant indications for a finer-grained diagnosis and prognosis.

Morphological and functional analysis of colorectal cancer cell lines in 2D and 3D culture models

The epithelial and mesenchymal features of colorectal adenocarcinoma (CRAC) cell lines were compared in two-dimensional (2D) and three-dimensional (3D) cultures. In 2D cultures, the three CRAC cell lines exhibited epithelial characteristics with high E-cadherin and low vimentin levels, whereas two exhibited mesenchymal traits with opposite expression patterns. In 3D cultures using low-attachment plates, mesenchymal cells from 2D cultures showed reduced vimentin mRNA levels. Morphologically, the five CRAC cell lines appeared similarly shaped in 2D culture but formed different structures in 3D culture. Epithelial DLD-1 and mesenchymal COLO-320 cells produced large granular spheres, whereas epithelial HCT-15 cells formed small solid spheres. Tubular structures were observed in epithelial CACO-2 and mesenchymal SW480 spheres. Desmosome-like structures developed in epithelial CRAC cells, whereas entosis was observed in CACO-2, HCT-15, and SW480 cells. The Ki-67-positive proliferating cell count varied in 2D and 3D cultures of epithelial cells but remained high and unchanged in mesenchymal cells. These findings suggest that while CRAC cells display distinct epithelial and mesenchymal properties in 2D cultures, they form diverse 3D structures, irrespective of these traits.

Genome-wide identification of WRKY transcription factor genes in Euphorbia lathyris reveals ElWRKY48 as a negative regulator of phosphate uptake and ingenol biosynthesis.

WRKY transcription factors (TFs) play pivotal roles in regulating plant nutrient uptake, particularly phosphate (Pi) acquisition, and biosynthesis of secondary metabolites. Euphorbia lathyris, a significant medicinal plant with diverse pharmacological activities, lacks a systematic analysis of WRKY members and their functional roles. In this study, 58 ElWRKY genes were identified in the E. lathyris genome, classified into seven subgroups through comparative genomics analysis, and distributed on 10 chromosomes. Phylogenetic and expression pattern analyses identified ElWRKY48 as a candidate gene involved in Pi uptake regulation. The transgenic validation assay demonstrated that ElWRKY48 overexpression negatively regulated Pi uptake and led to phosphorus-deficient phenotypes in the hairy roots of E. lathyris. Furthermore, the transcriptome analysis revealed an opposite expression pattern between the Pi transporter gene ElPHT1 (Elat0034050.1) and ElWRKY48 in the transgenic lines overexpressing ElWRKY48. The negative regulation of ElPHT1 expression by ElWRKY48 was validated through qRT-PCR, Y1H, EMSA, gene knockout (CRISPR/Cas9), and LUC assays. Additionally, the overexpression of ElWRKY48 reduced diterpenoid ingenol biosynthesis by suppressing the expression of its biosynthesis-related genes. These findings provide valuable insights into the role of WRKY in Pi uptake and offer potential avenues for genetic improvement in the yield and quality of E. lathyris.

Evaluation of the Effect of Adipokinetic Hormone/Corazonin-Related Peptide (ACP) on Ovarian Development in the Mud Crab, Scylla paramamosain.

In this study, we identified Sp-ACP and its putative receptor from the mud crab S. paramamosain and explored its potential role in ovarian development. RT-PCR results suggested Sp-ACP was extensively expressed in nervous tissues, the ovary, the middle gut, and the Y-organ, while Sp-ACPR was highly expressed in the ovary. The expression level of Sp-ACP in the ovary, eyestalk, and cerebral ganglia gradually increased during ovarian development, whereas its receptor exhibited an opposite expression pattern in the ovary. Immunofluorescence revealed that ACP was specifically localized in the follicle cells of the ovary. In vitro experiments showed that the expression of vitellogenin receptor (Sp-VgR) in the ovary was significantly increased by 4 and 6 h incubation of Sp-ACP (10 nM). In addition, 12 h injection of Sp-ACP significantly induced the levels of Sp-Vg in the hepatopancreas and Sp-VgR in the ovary, and hemolymph 17β-estradiol titer. Finally, it demonstrated that prolonged injection of Sp-ACP significantly increased the level of Vg and VgR expression, hemolymph 17β-estradiol titer, GSI, and the oocyte diameter. In conclusion, our results suggested that ACP is involved in the regulation of ovarian development of S. paramamosain, likely by inducing hepatopancreas Sp-Vg expression through estradiol and promoting the uptake of Vg by oocytes.

Transcriptome and miRNAome analyses uncover the regulatory role of miR6155 in trichome development of tobacco

BackgroundGlandular trichomes, which act as the first barrier against damage induced by insects and disease, can produce specialized metabolites that play important roles during plant development. However, the role played by microRNAs (miRNAs), which regulate many plant physiological processes, during trichome development is not unraveled in detail.ResultsIn this study, we performed RNA sequencing (RNA-Seq) and small RNA sequencing assessments of tobacco trichome, leaf minus trichome (leaf-trichome), and leaf tissue to improve our understanding of the miRNA mechanisms regulating trichome development. Totally, we identified 270 differentially expressed miRNAs (DEMs) and 10,430 differentially expressed genes (DEGs) between trichome and leaf-trichome tissues. DEM targets were mainly associated with plant hormone signal transduction, plant–pathogen interactions, and the biosynthesis of secondary metabolites. Of these, 1233 miRNA–mRNA pairs were identified with reverse expression patterns. Next, we used dual-luciferase reporter (LUC) assays to reveal that several potential targets were significantly inhibited by corresponding miRNAs, including the transcription factors (TF) NAC021, AP2, MYB36, WRKY6 and TIFY10B. Further analysis showed that miR6155-WRKY6 might perform vital roles in trichome development, and that overexpression of miR6155 resulted in decreased trichome density.ConclusionsTaken together, these findings demonstrate that miRNAs may be involved in trichome development in tobacco, and they may advance our understanding of the regulation of trichome development mediated by miRNA and can help to improve genetic engineering of trichome regulation in plants.Graphical

Osteoblast-derived exosomal miR-140-3p targets ACER2 and increases the progression of prostate cancer via the AKT/mTOR pathway-mediated inhibition of autophagy.

Advanced prostate cancer (aPCa) often results in bone metastases (BM). However, the mechanism underlying its progression and metastasis to bones remains unclear. Therefore, we examined whether exosomal miR-140-3p affects prostate cancer (PCa) progression. We obtained from cell lines, clinical data analyses, and animal models consistently provide important evidence. Patients with PCa having BM had higher miR-140-3p expression in their serum exosomes than those without BM. Clinical investigations have manifested that the exosomal miR-140-3p overexpression connects with serum prostate-specific antigen (PSA) levels and Gleason grade in patients with PCa. Osteoblast-derived exosomal miR-140-3p targeting ACER2 activates the AKT/mTOR pathway invitro, inhibits autophagy, and promotes PCa cell proliferation, invasion, and migration. miR-140-3p significantly increased tumorigenesis and metastasis of LNCaP invitro. Bone metastatic PCa tissues exhibited elevated levels of miR-140-3p, p-GSK3, p-mTOR, p62, p-AKT (S473), and p-AKT (T308) contrasted with non-BM tissues. Moreover, their expression was intensified in the metastatic bone tissues. However, ACER2 and LC3 II showed opposite expression patterns. Based on our study outcomes, the evidence suggests that osteoblast-derived miR-140-3p inhibition of autophagy through the AKT/mTOR pathway is involved in PCa progression. Osteoblast-secreted exosomal miR-140-3p activates the AKT/mTOR pathway by targeting ACER2, inhibiting autophagy, and promoting the progression of PCa cells invitro. Moreover, miR-140-3p induces the progression and metastasis of PCa invivo.

Comparison of triclosan and triclocarban in triggering immunotoxicity in larval zebrafish

As two efficient broad-spectrum sterilizing agents, triclosan (TCS) and triclocarban (TCC) are widely used, especially during the COVID-19 pandemic. The health risks caused by secondary pollution of TCS and TCC have aroused wide concern. Because of the similar mother nucleus structure and high lipophilicity, it remains unknown about the differences in the effect and mechanism of the toxicity (especially immunotoxicity) between TCS and TCC in organisms in the environment. In this study, we used zebrafish as a model to compare the immunotoxicity and mechanisms between the two pollutants at the same exposure concentration (0.6 µmol/L). The results showed that both TCS and TCC led to a hatching rate below 60% at the time point of 72 hours post fertilization (hpf) and the mortality rates of 40% and 50% at 120 hpf in larval zebrafish, respectively. The zebrafish exposed to TCS and TCC displayed malformations, such as shortened body, swimming sac closure, pericardial edema, yolk cyst deposition, and absorption disorder. Moreover, the developmental abnormalities caused by TCC were significantly severer than those caused by TCS. TCS exposure increased the proliferation rate of innate immune cells to 20% and decreased the number of mature T cells by 35%, while TCC exposure inhibited the differentiation of both innate immune cells and T cells, with the inhibition rates of 25% and 60%, respectively. The results of real-time quantitative PCR (RT-qPCR) and ELISA showed that TCS and TCC exposure up-regulated the expression levels of il-1β, il-6, and tnf-α, while il-10 and IgM exhibited opposite expression patterns. Additionally, both compounds slightly decreased C3 expression. The Pearson correlation analysis showed that the developmental toxicity induced by TCS and TCC had positive and negative correlations with the differentiation of immune cells, respectively. However, the toxicity induced by either TCS or TCC was positively correlated with the expression of pro-inflammatory cytokines. GO function and KEGG pathway enrichment analyses demonstrated that the target molecules of TCS and TCC were enriched in different signaling pathways, and the key network hub genes and the enriched regulatory pathways differed between TCS and TCC. The findings provide compelling evidence that TCS and TCC adopt different mechanisms in triggering immunotoxicity and offer a theoretical reference for the recognition, warning, and management of TCS and TCC-induced health risks.

Aging affects the mouse brain in a region-specific manner

Aging-related cognitive decline is emerging as a health concern during the aging process of the global population. Hahn and colleagues found that glial aging was particularly accelerated in white matter compared to cortical regions. Specialized neuronal populations showed region-specific changes in gene expression. Acute dietary restriction triggers a reprogramming of genes associated with the circadian clock in glial cells, whereas injections of young mouse plasma selectively reverse age-related expression patterns. The discovery of region-specific aging could enhance our understanding of the aging process and offer new possibilities for innovative treatment strategies and interventions for cognitive impairments related to aging.

Differential salt stress resistance in male and female Salix linearistipularis plants: insights from transcriptome profiling and the identification of the 4-hydroxy-tetrahydrodipicolinate synthase gene.

Lysine plays an essential role in the growth differences between male and female S. linearistipularis plants under salt stress. Furthermore, SlDHDPS is identified as a vital gene contributing to the differences in saline-alkali tolerance between male and female plants of S. linearistipularis. Soil salinization is a significant problem that severely restricts agricultural production worldwide. High salinity and low nutrient concentrations consequently prevent the growth of most plant species. Salix linearistipularis is the only woody plant (shrub) naturally distributed in the saline-alkali lands of the Songnen Plain in Northeast China, and it is one of the few plants capable of thriving in soils with extremely high salt and alkaline pH (>9.0) levels. However, insufficient attention has been given to the interplay between salt and nitrogen in the growth and development of S. linearistipularis. Here, the male and female plants of S. linearistipularis were subjected to salt stress with nitrogen-starvation or nitrogen-supplement treatments, and it was found that nitrogen significantly affects the difference in salt tolerance between male and female plants, with nitrogen-starvation significantly enhancing the salt stress tolerance of female plants compared to male plants. Transcriptional analyses showed 66 differentially expressed nitrogen-responsive genes in female and male roots, with most of them showing sexual differences in expression patterns under salinity stress. RNA-seq and RT-qPCR analysis demonstrated that six genes had an opposite salt-induced expression pattern in female and male roots. The expression of the 4-hydroxy-tetrahydrodipicolinate synthase encoding gene (SlDHDPS) in female roots was higher than that in male roots. Further treatment with exogenous lysine could significantly alleviate the inhibitory effect of salt stress on the growth of female and male plants. These results indicate that the SlDHDPS in the nitrogen metabolism pathway is involved in the resistance of S. linearistipularis to salt stress, which lays a foundation for further exploring the mechanism of nitrogen on salt tolerance of S. linearistipularis, and has a significant reference value for saline-alkali land management and sustainable agricultural development.

Probiotics relieve growth retardation and stress by upgrading immunity in Nile tilapia (Oreochromis niloticus) during high temperature events

Global warming is disastrous to aquatic animals and supplementation of probiotics might mitigate its adverse effects. Therefore, to mitigate the effects of high temperature on growth retardation, stress and immunity, multi-species probiotics consisting of Bacillus subtilis (5×109 cfu/ml), B. thuringiencis (4×109 cfu/ml), Lactobacillus plantarum (5.8×109 cfu/ml), and L. buchneri (6.5×109 cfu/ml) were added in rearing water (1.0 ml/L) of Nile tilapia (Oreochromis niloticus). Fingerlings (1.08 ± 0.13 g) were reared at normal (31ºC) and elevated (34ºC and 37ºC) temperatures with or without probiotics for 6 weeks in triplicates. At the end of the experimental period, weight gain (WG) and specific growth rate (SGR) decreased significantly at 37ºC in fish supplemented with or without probiotics relative to normal temperature (31ºC). Importantly, at the high temperature (37ºC), WG and SGR were improved in fish supplemented with probiotics in contrast to fish reared without probiotics. The physiological status was improved by increasing the hemoglobin level and number of red blood cells and lowering white blood cells and glucose levels in the probiotics-treated high-temperature group. Frequencies of cellular and nuclear abnormalities of erythrocytes were significantly lowered in probiotics-supplemented fish. Histological observation demonstrated that multi-probiotics mitigated the high-temperature stress through increasing mucosal fold fattening, goblet cells, and the size of lamina propria and enterocytes in the intestine. Fish under higher temperatures (34 and 37ºC) showed up-regulated expression of the stress-related heat shock protein 70 (hsp70) gene, while its expression was decreased after probiotics addition. In contrast, two antioxidant-related genes (superoxide dismutase; SOD) and catalase; CAT) showed opposite expression patterns. The expression of three immune response-related genes (tumor necrosis factor alpha; TNF-α, interleukin 1 beta; IL-1β, and interferon gamma; IFN-γ) down-regulated with increase of temperature, while their expressions were increased after probiotics addition. Therefore, addition of probiotics in aquatic environment improved hemato-biochemical properties, blood cell structure, and immunity which ultimately relieve the growth retardation and stress in extreme temperatures in Nile tilapia.

A dual RNA-seq analyses revealed dynamic arms race during the invasion of walnut by Colletotrichum gloeosporioides

BackgroundWalnut anthracnose caused by Colletotrichum gloeosporioides seriously endangers the yield and quality of walnut, and has now become a catastrophic disease in the walnut industry. Therefore, understanding both pathogen invasion mechanisms and host response processes is crucial to defense against C. gloeosporioides infection.ResultsHere, we investigated the mechanisms of interaction between walnut fruits (anthracnose-resistant F26 fruit bracts and anthracnose-susceptible F423 fruit bracts) and C. gloeosporioides at three infection time points (24hpi, 48hpi, and 72hpi) using a high-resolution time series dual transcriptomic analysis, characterizing the arms race between walnut and C. gloeosporioides. A total of 20,780 and 6670 differentially expressed genes (DEGs) were identified in walnut and C. gloeosporioides against 24hpi, respectively. Generous DEGs in walnut exhibited opposite expression patterns between F26 and F423, which indicated that different resistant materials exhibited different transcriptional responses to C. gloeosporioides during the infection process. KEGG functional enrichment analysis indicated that F26 displayed a broader response to C. gloeosporioides than F423. Meanwhile, the functional analysis of the C. gloeosporioides transcriptome was conducted and found that PHI, SignalP, CAZy, TCDB genes, the Fungal Zn (2)-Cys (6) binuclear cluster domain (PF00172.19) and the Cytochrome P450 (PF00067.23) were largely prominent in F26 fruit. These results suggested that C. gloeosporioides secreted some type of effector proteins in walnut fruit and appeared a different behavior based on the developmental stage of the walnut.ConclusionsOur present results shed light on the arms race process by which C. gloeosporioides attacked host and walnut against pathogen infection, laying the foundation for the green prevention of walnut anthracnose.

Constructing lncRNA-miRNA-mRNA networks specific to individual cancer patients and finding prognostic biomarkers

BackgroundThe competitive endogenous RNA (ceRNA) hypothesis suggests that microRNAs (miRNAs) mediate a regulatory relation between long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) which share similar miRNA response elements (MREs) to bind to the same miRNA. Since the ceRNA hypothesis was proposed, several studies have been conducted to construct a network of lncRNAs, miRNAs and mRNAs in cancer. However, most cancer-related ceRNA networks are intended for representing a general relation of RNAs in cancer rather than for a patient-specific relation. Due to the heterogeneous nature of cancer, lncRNA-miRNA-mRNA interactions can vary in different patients.ResultsWe have developed a new method for constructing a ceRNA network of lncRNAs, miRNAs and mRNAs, which is specific to an individual cancer patient and for finding prognostic biomarkers consisting of lncRNA-miRNA-mRNA triplets. We tested our method on extensive data sets of three types of cancer (breast cancer, liver cancer, and lung cancer) and obtained potential prognostic lncRNA-miRNA-mRNA triplets for each type of cancer.ConclusionsAnalysis of expression patterns of the RNAs involved in the triplets and survival rates of cancer patients revealed several interesting findings. First, even for the same cancer type, prognostic lncRNA-miRNA-mRNA triplets can be different depending on whether lncRNA and mRNA show opposite or similar expression patterns. Second, prognostic lncRNA-miRNA-mRNA triplets are often more predictive of survival rates than RNA pairs or individual RNAs. Our approach will be useful for constructing patient-specific lncRNA-miRNA-mRNA networks and for finding prognostic biomarkers from the networks.

Characterization of sciatic nerve myelin sheath during development in C57BL/6 mice.

Myelin sheath plays important roles in information conduction and nerve injury repair in the peripheral nerve system (PNS). Enhancing comprehension of the structure and components of the myelin sheath in the PNS during development would contribute to a more comprehensive understanding of the developmental and regenerative processes. In this research, the structure of sciatic nerve myelin sheath in C57BL/6 mice from embryonic day 14 (E14) to postnatal 12 months (12M) was observed with transmission electron microscopy. Myelin structure appeared in the sciatic nerve as early as E14, and the number and thickness of myelin lamellar gradually increased with the development until 12M. Transcriptome analysis was performed to show the expressions of myelin-associated genes and transcriptional factors involved in myelin formation. The genes encoding myelin proteins (Mag, Pmp22, Mpz, Mbp, Cnp and Prx) showed the same expression pattern, peaking at postnatal day 7 (P7) and P28 after birth, whereas the negative regulators of myelination (c-Jun, Tgfb1, Tnc, Cyr61, Ngf, Egr1, Hgf and Bcl11a) showed an opposite expression pattern. In addition, the expression of myelin-associated proteins and transcriptional factors was measured by Western blot and immunofluorescence staining. The protein expressions of MAG, PMP22, MPZ, CNPase and PRX increased from E20 to P14. The key transcriptional factor c-Jun co-localized with the Schwann cells Marker S100β and decreased after birth, whereas Krox20/Egr2 increased during development. Our data characterized the structure and components of myelin sheath during the early developmental stages, providing insights for further understanding of PNS development.

The potential role of hippo pathway effector yap1/yap1b in female-biased sexual size dimorphism of Chinese tongue sole (Cynoglossus semilaevis)

One fundamental question in biology is how animals control their proper body size. Hippo signaling pathway has emerged as an evolutionarily conserved network to regulate organ size from Drosophila to mammals. Interestingly, our previous study has also implied the roles of hippo signaling in Chinese tongue sole (Cynoglossus semilaevis), a flatfish exhibiting female-biased sexual size dimorphism (SSD). Specifically, two yes-associated protein 1 (yap1) homologs, key effectors within hippo signaling, exhibited the opposite expression pattern in the female and male gonads of C. semilaevis. Whether and how these two yap1 genes participate in female-biased SSD is unknown. In the present study, phylogenetic tree analysis firstly designated these two yap1 genes as yap1 and yap1b, with no taz gene available in C. semilaevis. Subsequent quantitative PCR analysis demonstrated that yap1 exhibited the highest expression levels within the male gonad at three-month-old, while the predominant expression of yap1b was detected in the female gonad at two-year-old. The co-localization of yap1 and yap1b was observed in the cytoplasm of oocyte and sperm. Cebpα, a negative regulator for dmrt1, exhibited positive and negative regulation on the yap1 and yap1b, respectively. Myog, a crucial transcription factor for myogenesis, specifically binded and activated yap1b promoter, not yap1. Furthermore, DAP-seq revealed the regulatory networks of yap1 and yap1b in C. semilaevis. Importantly, many growth and reproduction-related pathways, including the JAK-STAT signaling pathway, prolactin signaling pathway, axonal regeneration, and steroid hormone synthesis, were included in the common peaks of yap1 and yap1b. Moreover, the application of verteporfin reagents into testis and ovary cells resulted in a decrease in yap1 and yap1b levels. Consequently, the expression of growth hormone receptor (ghr), growth hormone actin α (smtla), estrogen receptor (esr2b), and 17β-hydroxysteroid dehydrogenase type 7 (hsd17b7), were also affected. In addition, the administration of verteporfin on C. semilaevis caused a significant reduction in growth rate. These findings provided insights into the role of the hippo signaling pathway in regulating SSD of C. semilaevis.

Cytological Observation and RNA-Seq Analyses Reveal miR9564 and Its Target Associated with Pollen Sterility in Autotetraploid Rice.

Understanding the regulation of autotetraploid sterility is essential for harnessing the strong advantages in genomic buffer capacity, biodiversity, and heterosis of autotetraploid rice. miRNAs play crucial roles in fertility regulation, yet information about their reproductive roles and target genes in tetraploid rice remains limited. Here, we used three tetraploid lines, H1 (fertile), HF (fertile), and LF (sterile), to investigate cytological features and identify factors associated with autotetraploid sterility. LF showed abnormal meiosis, resulting in low pollen fertility and viability, ultimately leading to scarce fertilization and a low-seed setting compared to H1 and HF. RNA-seq revealed 30 miRNA-candidate target pairs related to autotetraploid pollen sterility. These pairs showed opposite expression patterns, with differential expression between fertile lines (H1 and HF) and the sterile line (LF). qRT-PCR confirmed that miR9564, miR528, and miR27874 were highly expressed in the anthers of H1 and HF but not in LF, while opposite results were obtained in their targets (ARPS, M2T, and OsRPC53). Haplotype and expression pattern analyses revealed that ARPS was specifically expressed in lines with the same haplotype of MIR9564 (the precursor of miR9564) as LF. Furthermore, the Dual-GFP assay verified that miR9564 inhibited the fluorescence signal of ARPS-GFP. The over-expression of ARPS significantly decreased the seed setting rate (59.10%) and pollen fertility (50.44%) of neo-tetraploid rice, suggesting that ARPS plays important roles in autotetraploid pollen sterility. This study provides insights into the cytological characteristic and miRNA expression profiles of tetraploid lines with different fertility, shedding light on the role of miRNAs in polyploid rice.

Two FT genes synergistically regulate the reproductive transition of loquat

Unlike annual flowering plants that exhibit a single reproductive cycle encompassing vegetative growth, flowering, and senescence within a single year, perennial woody trees undergo a transition between vegetative and reproductive growth every year after a long juvenile phase. Most woody fruit trees bloom when it turns warm in spring, and the fruit ripens in summer or autumn. However, as a member of the Maloideae subfamily, the loquat tree blooms in the cold autumn and winter, and the fruit matures in the spring. To explore the regulatory mechanism of loquat flowering, we characterized two FLOWERING LOCUS T homologous genes in loquat, EjFT1 and EjFT2. qRT-PCR results revealed that EjFT1 and EjFT2 exhibited nearly opposite expression patterns in various tissues. EjFT1 was mainly expressed in young tissues; EjFT2 was mainly expressed in mature leaves, open flowers, and fruits. EjFT2 exhibited an obvious circadian rhythm and was regulated by EjCO. After the trees were exposed to short-day conditions or sprayed with exogenous GA3, the expression of EjFT2 was strongly inhibited, and the loquat tree did not produce floral buds. Furthermore, the yeast two-hybrid, bimolecular fluorescence complementation, and Dual-luciferase assay experiments revealed that both EjFT1 and EjFT2 interacted with EjFD, with the EjFT2-EjFD protein complex enhancing the activity of EjAP1-1 and EjAP1-2 promoters, while EjFT1-EjFD inhibited the activity of the EjAP1-1 promoter. Protein structural analysis of EjFT1 and EjFT2 suggested that differences in amino acid residues at Val123/Leu123, Ser157/Ala157, and Val158/Ala158 may be the reason for their functional differences. Our results showed that EjFT1 and EjFT2 may cooperatively regulate the floral bud differentiation of loquat by competitively binding with EjFD. EjFT2 regulates the onset of loquat floral bud differentiation by responding to photoperiod and gibberellin signals, while EjFT1 is involved in the vegetative growth of loquat. These findings provide important clues for the investigation of the regulatory mechanism of loquat flowering and advance the exploration into the multiple roles of FT homologous genes in regulating the reproductive transformation and vegetative growth of flowering plants.

Type B thymomas in patients with myasthenia gravis display a distinctive pattern of αβ TCR and IL-7 receptor α expression on CD4+CD8+ thymocytes

Thymoma is closely associated with myasthenia gravis (MG). However, due to the heterogeneity of thymoma and the intricate pathogenesis of MG, it remains unclear why some patients with thymoma develop MG and others do not. In this study, we conducted a comparative phenotype analysis of thymocytes in type B thymomas in patients with MG (MG (+) thymomas) and without MG (MG (−) thymomas) via fluorescence-activated cell sorting (FACS). Our results show that the developmental stages defined by the expression of CD3, CD4, and CD8 were largely maintained in both MG (+) and MG (−) thymomas, with CD4+CD8+ cells constituting the majority of thymocytes in type B thymoma, and no significant difference between this cell population was observed in MG (+) and MG (−) thymomas.We discovered that CD4+CD8+ thymocytes in MG (+) thymomas expressed low levels of αβ TCR and high levels of IL-7 receptor α (IL-7Rα), whereas in MG (−) thymomas, CD4+CD8+ thymocytes exhibited the opposite pattern of αβ TCR and IL-7Rα expression. These results suggest that the positive and negative selection processes of CD4+CD8+ thymocytes might differ between MG (+) thymomas and MG (−) thymomas. The expression of the Helios transcription factor is induced during negative selection and marks a group of T cells that have undergone negative selection and are likely to be deleted due to strong TCR binding with self-peptides/MHC ligands. We observed that the percentage of Helios-positive CD4SP T cells was greater in MG (−) than in MG (+) thymomas. Thus, the differentially regulated selection process of CD4+CD8+ thymocytes, which involves TCR and IL-7/IL-7Rα signaling, is associated with the presence of MG in type B thymomas.

A Genome-Wide Comparative Analysis of AUX1/LAX, PIN, and ABCB Genes Reveals Their Roles in Cucumber Fruit Curving

Auxin transport is regulated by the AUX1/LAX, PIN, and ABCB gene families, controlling the distribution of auxin and ultimately fruit curving in cucumbers. However, studies on the differential expression of these auxin transporters and their roles in fruit curving are limited. In this study, we identified 36 auxin transporters from cucumber, including CsLAX1–7, CsPIN1–10, and CsABCB1–19. Basic characteristic analysis revealed that all CsLAX proteins were conservative, and a C-terminal NPNTY motif was found in CsPIN1–4/7–10. CsABCB1/5/11/14/17 were categorized as half-size transporters. Phylogenetic analysis revealed a genetic relationship between auxin transporters in Arabidopsis and cucumber. Exogenous auxin treatment on fruits and qPCR analysis indicated that differential expression patterns of auxin transporters control cucumber fruit curving. Co-expression analysis indicated that CsPIN1 and CsLAX2 were substantially negatively correlated, and they displayed opposite expression patterns in curved fruits. A proposed model suggested that CsLAX2 transports extracellular auxin to the convex side of the fruit; however, CsPIN1 inhibits auxin efflux at the same location. This leads to uneven auxin distribution that results in cucumber fruit curving.

AAV2-PDE6B restores retinal structure and function in the retinal degeneration 10 mouse model of retinitis pigmentosa by promoting phototransduction and inhibiting apoptosis.

JOURNAL/nrgr/04.03/01300535-202508000-00030/figure1/v/2024-09-30T120553Z/r/image-tiff Retinitis pigmentosa is a group of inherited diseases that lead to retinal degeneration and photoreceptor cell death. However, there is no effective treatment for retinitis pigmentosa caused by PDE6B mutation. Adeno-associated virus (AAV)-mediated gene therapy is a promising strategy for treating retinitis pigmentosa. The aim of this study was to explore the molecular mechanisms by which AAV2-PDE6B rescues retinal function. To do this, we injected retinal degeneration 10 (rd10) mice subretinally with AAV2-PDE6B and assessed the therapeutic effects on retinal function and structure using dark- and light-adapted electroretinogram, optical coherence tomography, and immunofluorescence. Data-independent acquisition-mass spectrometry-based proteomic analysis was conducted to investigate protein expression levels and pathway enrichment, and the results from this analysis were verified by real-time polymerase chain reaction and western blotting. AAV2-PDE6B injection significantly upregulated PDE6β expression, preserved electroretinogram responses, and preserved outer nuclear layer thickness in rd10 mice. Differentially expressed proteins between wild-type and rd10 mice were closely related to visual perception, and treating rd10 mice with AAV2-PDE6B restored differentially expressed protein expression to levels similar to those seen in wild-type mice. Kyoto Encyclopedia of Genes and Genome analysis showed that the differentially expressed proteins whose expression was most significantly altered by AAV2-PDE6B injection were enriched in phototransduction pathways. Furthermore, the phototransduction-related proteins Pde6α, Rom1, Rho, Aldh1a1, and Rbp1 exhibited opposite expression patterns in rd10 mice with or without AAV2-PDE6B treatment. Finally, Bax/Bcl-2, p-ERK/ERK, and p-c-Fos/c-Fos expression levels decreased in rd10 mice following AAV2-PDE6B treatment. Our data suggest that AAV2-PDE6B-mediated gene therapy promotes phototransduction and inhibits apoptosis by inhibiting the ERK signaling pathway and upregulating Bcl-2/Bax expression in retinitis pigmentosa.

Comparative Screening of the Liver Gene Expression Profiles from Type 1 and Type 2 Diabetes Rat Models.

Experimental animal models of diabetes can be useful for identifying novel targets related to disease, for understanding its physiopathology, and for evaluating emerging antidiabetic treatments. This study aimed to characterize two rat diabetes models: HFD + STZ, a high-fat diet (60% fat) combined with streptozotocin administration (STZ, 35 mg/kg BW), and a model with a single STZ dose (65 mg/kg BW) in comparison with healthy rats. HFD + STZ- induced animals demonstrated a stable hyperglycemia range (350-450 mg/dL), whereas in the STZ-induced rats, we found glucose concentration values with a greater dispersion, ranging from 270 to 510 mg/dL. Moreover, in the HFD + STZ group, the AUC value of the insulin tolerance test (ITT) was found to be remarkably augmented by 6.2-fold higher than in healthy animals (33,687.0 ± 1705.7 mg/dL/min vs. 5469.0 ± 267.6, respectively), indicating insulin resistance (IR). In contrast, a more moderate AUC value was observed in the STZ group (19,059.0 ± 3037.4 mg/dL/min) resulting in a value 2.5-fold higher than the average exhibited by the control group. After microarray experiments on liver tissue from all animals, we analyzed genes exhibiting a fold change value in gene expression <-2 or >2 (p-value <0.05). We found 27,686 differentially expressed genes (DEG), identified the top 10 DEGs and detected 849 coding genes that exhibited opposite expression patterns between both diabetes models (491 upregulated genes in the STZ model and 358 upregulated genes in HFD + STZ animals). Finally, we performed an enrichment analysis of the 849 selected genes. Whereas in the STZ model we found cellular pathways related to lipid biosynthesis and metabolism, in the HFD + STZ model we identified pathways related to immunometabolism. Some phenotypic differences observed in the models could be explained by transcriptomic results; however, further studies are needed to corroborate these findings. Our data confirm that the STZ and the HFD + STZ models are reliable experimental models for human T1D and T2D, respectively. These results also provide insight into alterations in the expression of specific liver genes and could be utilized in future studies focusing on diabetes complications associated with impaired liver function.