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Selectable marker recycling is a basic technique in bioengineering. However, this technique is usually unavailable in non-model microorganisms. In this study, we proposed a simple and efficient method for selectable marker recycling in the astaxanthin-synthesizing yeast Xanthophyllomyces dendrorhous. This method was based on a Cre-loxP system, in which the transient expression of the Cre recombinase was controlled by a genetically unstable vector independent of episomal plasmids and inducible promoters. The selectable markers in single-gene locus and multigene loci were removed along with the loss of the Cre vector with a ratio of 100% and 29%, respectively. The significance of the method was highlighted by the finding that stable autotrophic mutants were not readily obtained in X. dendrorhous. Comparative studies in X. dendrorhous and the non-homologous end joining dominant yeast Yarrowia lipolytica suggested that the method could be universally used in homologous recombination dominant yeasts.

Overlap in morphologic features between malignant and benign myogenic tumors, such as leiomyosarcoma (LMS) vs. leiomyoma as well as rhabdomyosarcoma (RMS) vs. rhabdomyoma, often makes differential diagnosis difficult and challenging. Here the expressions of Enhancer of Zeste Homolog 2 (EZH2), Suppressor of Zeste 12 (SUZ12), retinoblastoma protein associated protein 46 (RbAp46), Embryonic Ectoderm Development (EED) and ki-67 protein were detected by immunohistochemistry to evaluate their values in differential diagnosis. The expression of EZH2 mRNA was investigated by analyzing the Gene Expression Omnibus Datasets. The results demonstrated that EZH2 protein was detected in 81.25% (26/32) of LMS and 70.58% (36/51) of RMS, whereas none of leiomyoma (n = 16), rhabdomyoma (n = 15) and normal tissues (n = 31) showed positive immunostaining (p < 0.05). EZH2 protein was found to have a sensitivity of 91.30% and specificity of 100% in distinguishing well-differentiated LMS from cellular leiomyoma, and a sensitivity of 92.86% and specificity of 100% in distinguishing well-differentiated embryonal rhabdomyosarcoma (ERMS) from fetal rhabdomyoma. Besides, the expression of EZH2 mRNA was higher in LMS and RMS than in benign tumors (p < 0.05). The expressions of SUZ12 and RbAp46 protein were higher in RMS than in rhabdomyoma (p < 0.05). Conclusively, the high expression of EZH2 is a promising marker in distinguishing well-differentiated LMS from cellular leiomyoma, or well-differentiated ERMS from fetal rhabdomyoma, and the upregulation of EZH2 protein expression may occur at transcriptional level.

In this study, the effect of mutations in transcription factor-binding elements was investigated in the human papillomavirus (HPV) 18 P(105) promoter. Site-directed mutagenesis activities, in the AP1/YY1-, KRF-1-, GRE/YY1-, Sp1- and the double mutation (AP1/YY1- and GRE/YY1)-binding sites were assessed in five human cell lines: HeLa (HPV18-positive cervical carcinoma), SiHa (HPV16-positive cervical carcinoma), C33A (HPV-negative cervical carcinoma), H1299 (non-small cell lung carcinoma) and MRC-5 (foetal lung fibroblast). The results indicated that the GRE/YY1 mutation increased the HPV18 P(105) promoter activity in the cervical cell lines by 53-135%. In HeLa and SiHa cells, mutations in the AP1/YY1, KRF-1 and Sp1 transcription factor-binding sites resulted in reduced promoter activity. For C33A, mutations in KRF-1 and Sp1 reduced the promoter activity, while the GRE/YY1 mutation increased the activity. The double mutation, AP1/YY1 and GRE/YY1, appeared to display an additive effect of the two individual mutations in cervical cells. Compared with HeLa cells, HPV18 P(105) promoter activity was more than 80-fold lower in H1299 cells and more than 500-fold lower in MRC-5 cells. Hence in this study, a comprehensive site-directed mutagenesis analysis, of important transcription factor-binding elements, in the HPV18 P(105) promoter was accomplished in a range of human cell lines. In particular, we concluded that HPV-induced factors were extremely important in the transcriptional activity of the HPV18 P(105) promoter.

NHX proteins are transmembrane antiporters belonging to the cation/proton antiporter gene family, with a conserved Na+ (K+)/H+ exchange (PF00999) protein domain. NHXs play a prominent role in plant growth, development, and defense. However, the role of NHX gene family in potato (Solanum tuberosum L.) is yet to be known. In this study, we conducted a genome-wide analysis of the potatoNHX gene family. A total of 25StNHX family memberswere identified to be unevenly distributed on 10 chromosomes. The proteins ranged in length from 252 to 1,153 amino acids, with molecular masses ranging from 27516.32 to 127860.87 kD, and isoelectric points (pI) ranging from 4.96 to 9.3. Analyses of gene structures and conserved motifs indicated that StNHX genes in the same phylogenetic cluster are conserved. Phylogenetic analysis divided the StNHX genes into three subfamilies (Classes I, II, and III). Synteny analysis indicated that StNHX gene family Class III of NHX and all Arabidopsis thaliana NHXs shared a close evolutionary relationship. Analysis of cisacting elements in the upstream 1,500 bp promoter region of potato NHX genes showed that these genes could be regulated by light, stress, and hormones such as abscisic acid and gibberellic acid. Protein-protein interaction network analysis indicated that StNHX proteins may participate in the regulation of potato growth and stress response. Besides, To determine a potential role of these genes in tissue development and drought response, we analyzed the RNA-seq data of different DM potato tissues. The results showed that NHX genes exhibited distinct tissue-specific expression patterns. We further examined the expression patterns of StNHX in different tissues (leaves, roots, shoots, tubers, stolons, and flowers) during the flowering stage in 'Jizhangshu NO.8.' potato. The qRT-PCR results further confirmed the importance of StNHX genes in potato plant growth and development. We further analyzed the RNA-seq data (DM potato) under different abiotic stresses (salt, drought, and heat), and found that the expression of StNHX genes was induced under abiotic stress. qRT-PCR analysis of shoots and roots of 'Jizhangshu NO.8.' potato treated for 0, 6, 12, and 24 hwith 15% PEG6000 confirmed that the 25 StNHX genes are involved in the response to drought stress in potato. The results of this study may be useful for selecting appropriate candidate genes for the breeding of new drought-tolerant potato varieties. Furthermore, this study lays a foundation for prospective analysis of StNHX gene functions. [ABSTRACT FROM AUTHOR]

Coccidiosis, a parasitic disease caused by single or multiple Eimeria species, leads to significant economic losses in the poultry industry. The Eimeria life cycle includes schizogony, gametogony, and sporogony. To investigate the dynamics of gene expression and regulatory networks during the development of Eimeria acervulina, we employed time-course transcriptomics to rigorously compare the gene expression patterns between a precocious line (PL) and the wild type (WT) of E. acervulina. The results revealed that the PL enters into gametogony 12 h earlier than the WT, and both the PL and WT exhibited distinct clustering patterns during the development phase. A weighted gene co-expression network analysis (WGCNA) identified genes specifically expressed at four distinct developmental stages, schizogony, gametogony, sporulated oocysts, and unsporulated oocysts, clarifying the key biological processes at each stage. This study used global transcriptome profiling to elucidate molecular variations throughout the E. acervulina life cycle, providing critical insights into molecular characterization and valuable resources for investigating other apicomplexan parasites of public health importance. [ABSTRACT FROM AUTHOR]

Phytoplasmas manipulate host plant development to benefit insect vector colonization and their own invasion. However, the virulence factors and mechanisms underlying small-leaf formation caused by jujube witches' broom (JWB) phytoplasmas remain largely unknown. Here, effectors SJP1 and SJP2 from JWB phytoplasmas were identified to induce small-leaf formation in jujube (Ziziphus jujuba). In vivo interaction and expression assays showed that SJP1 and SJP2 interacted with and stabilized the transcription factor ZjTCP2. Overexpression of SJP1 and SJP2 in jujube induced ZjTCP2 accumulation. In addition, the abundance of miRNA319f_1 was significantly reduced in leaves of SJP1 and SJP2 transgenic jujube plants and showed the opposite pattern to the expression of its target, ZjTCP2 , which was consistent with the pattern in diseased leaves. Overexpression of ZjTCP2 in Arabidopsis promoted ectopic leaves arising from the adaxial side of cotyledons and reduced leaf size. Constitutive expression of the miRNA319f_1 precursor in the 35S::ZjTCP2 background reduced the abundance of ZjTCP2 mRNA and reversed the cotyledon and leaf defects in Arabidopsis. Therefore, these observations suggest that effectors SJP1 and SJP2 induced small-leaf formation, at least partly, by interacting with and activating ZjTCP2 expression both at the transcriptional and the protein level, providing new insights into small-leaf formation caused by phytoplasmas in woody plants. [ABSTRACT FROM AUTHOR]

Background: Cancer-associated fibroblasts (CAFs) drive cancer progression and treatment failure on one hand, while their tumor-restraining functions are also observed on the other. Recent single cell RNA sequencing (scRNA-seq) analyses demonstrates heterogeneity of CAFs and defines molecular subtypes of CAFs, which help explain their different functions. However, it remains unclear whether these CAF subtypes have the same or different biological/clinical implications in prostate cancer (PCa) or other malignancies. Methods: PCa cells were incubated with supernatant from normal fibroblasts and CAFs to assess their effects on cell behaviors. Sequencing, genomic, and clinical data were collected from TCGA, MSKCC, CPGEA and GEO databases. CAF molecular subtypes and total CAF scores were constructed and grouped into low and high groups based on CAF-specific gene expression. Progression free interval (PFI), clinicopathological features, telomere length, immune cell infiltration, drug treatment and somatic mutations were compared among CAF molecular subtypes and low/high score groups. Results: The PCa CAF-derived supernatant promoted PCa cell proliferation and invasion. Based on differentially expressed genes identified by scRNA-seq analyses, we classified CAFs into 6 molecular subtypes in PCa tumors, and each subtype was then categorized into score-high and low groups according to the subtype-specific gene expression level. Such score models in 6 CAF subtypes all predicted PFI. Telomeres were significantly shorter in high-score tumors. The total CAF score from 6 CAF subtypes was also associated with PFI in PCa patients inversely, which was consistent with results from cellular experiments. Immunosuppressive microenvironment occurred more frequently in tumors with a high CAF score, which was characterized by increased CTLA4 expression and indicated better responses to CTLA4 inhibitors. Moreover, this model can also serve as a useful PFI predictor in pan-cancers. Conclusion: By combining scRNA-seq and bulk RNA-seq data analyses, we develop a CAF subtype score system as a prognostic factor for PCa and other cancer types. This model system also helps distinguish different immune-suppressive mechanisms in PCa, suggesting its implications in predicting response to immunotherapy. Thus, the present findings should contribute to personalized PCa intervention. [ABSTRACT FROM AUTHOR]

MAPKKs, as one of the main members of the mitogen-activated protein kinase (MAPK) cascade pathway, are located in the middle of the cascade and are involved in many physiological processes of plant growth and development, as well as stress tolerance. Previous studies have found that StMAPKK5 is responsive to drought and salt stress. To further investigate the function and regulatory mechanism of StMAPKK5 in potato stress response, potato variety 'Atlantic' was subjected to drought and NaCl treatments, and the expression of the StMAPKK5 gene was detected by qRT-PCR. StMAPKK5 overexpression and RNA interference-mediated StMAPKK5 knockdown potato plants were constructed. The relative water content, superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) activities, as well as proline (Pro) and malondialdehyde (MDA) contents of plant leaves, were also assayed under drought and NaCl stress. The StMAPKK5 interacting proteins were identified and validated by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). The results showed that the expression of StMAPKK5 was significantly up-regulated under drought and NaCl stress conditions. The StMAPKK5 protein was localized in the nucleus, cytoplasm, and cell membrane. The expression of StMAPKK5 affected the relative water content, the enzymatic activities of SOD, CAT, and POD, and the proline and MDA contents of potatoes under drought and salt stress conditions. These results suggest that StMAPKK5 plays a significant role in regulating drought and salt tolerance in potato crop. Yeast two-hybrid (Y2H) screening identified four interacting proteins: StMYB19, StZFP8, StPUB-like, and StSKIP19. BiFC confirmed the authenticity of the interactions. These findings suggest that StMAPKK5 is crucial for potato growth, development, and response to adversity. [ABSTRACT FROM AUTHOR]

The phytochrome-interacting factor (PIF) proteins are part of a subfamily of basic helix–loop–helix (bHLH) transcription factors that integrate with phytochromes (PHYs) and are known to play important roles in adaptive changes in plant architecture. However, the characterization and function of PIFs in potatoes are currently poorly understood. In this study, we identified seven PIF members in potatoes and named them StPIF01-1, StPIF01-2, StPIF03, StPIF06-1, StPIF06-2, StPIF07, and StPIF09 based on their location in potato chromosomes. The chromosomal location, gene structures, physicochemical characteristics, phylogenetic tree, and tissue-specific expression of StPIFs were also analyzed. RT-qPCR analysis revealed that the StPIF3 gene was highly induced by shade and may play a crucial regulatory role in potato responses to shade stress. Also, multiple cis-regulatory elements involved in light response were detected in the promoter of the StPIF genes. Subcellular localization analysis indicated that the StPIF3-encoding protein is mainly localized in the nucleus. Transgenic overexpression of StPIF3 in potatoes increased stem length, chlorophyll accumulation, and enhanced shade-avoidance symptoms, whereas the StPIF3-interfering lines had a lower plant height and more chlorophyll accumulation. These findings enhance our comprehension of StPIF gene roles, potentially advancing potato yield and quality research. This study provides detailed information about StPIFs and identifies the function of StPIF3, which is involved in shade-avoidance syndrome. [ABSTRACT FROM AUTHOR]

Mutations in the ABCA4 gene are a common cause of autosomal recessive retinal degeneration. All mouse models to date are based on knockouts of Abca4, even though the disease is often caused by missense mutations such as the complex allele L541P;A1038V (PV). We now show that the PV mutation causes severe human disease whereas the V mutation alone causes mild disease. Mutant ABCA4 proteins expressed heterologously in mammalian cells retained normal cellular localization. However, basal and all-trans-retinal-stimulated ATPase activities were reduced substantially for P and PV but only mildly for V. Electron microscopy revealed marked structural changes and misfolding for the P and PV mutants but few changes for the V mutant, consistent with the disease severity difference in patients. We generated Abca4(PV/PV) knock-in mice homozygous for the complex PV allele to investigate the effects of this misfolding mutation in vivo. Mutant ABCA4 RNA levels approximated WT ABCA4 RNA levels but, surprisingly, only trace amounts of mutant ABCA4 protein were noted in the retina. RNA sequencing of WT, Abca4(-/-) and Abca4(PV/PV) mice revealed mild gene expression alterations in the retina and RPE. Similar to Abca4(-/-) mice, Abca4(PV/PV) mice showed substantial A2E and lipofuscin accumulation in their RPE cells but no retinal degeneration up to 12 months of age. Thus, rapid degradation of this large misfolded mutant protein in mouse retina caused little detectable photoreceptor degeneration. These findings suggest likely differences in the unfolded protein response between murine and human photoreceptors and support development of therapies directed at increasing this capability in patients.

Genetic mapping was recently used to identify the underlying cause for a previously uncharacterized cohort of autosomal recessive retinitis pigmentosa cases. Genetic mapping of affected individuals resulted in the identification of an uncharacterized gene, C2Orf71, as the causative locus. However, initial homology searches failed to reveal similarities to any previously characterized protein or domain. To address this issue, we characterized the mouse homolog, BC027072. Immunohistochemistry with a custom polyclonal antibody showed staining localized to the inner segments (IS) of photoreceptor cells, as well as the outer segments (OS) of cone cells. A knockout mouse line (BC(-/-)) was generated and demonstrated that loss of this gene results in a severe, early-onset retinal degeneration. Histology and electron microscopy (EM) revealed disorganized OS as early as 3 weeks with complete loss by 24 weeks of age. EM micrographs displayed packets of cellular material containing OS discs or IS organelles in the OS region and abnormal retinal pigmented epithelium cells. Analyses of retinoids and rhodopsin levels showed

MicroRNAs (miRNAs) are a class of endogenous, non-coding small-molecule RNAs that usually regulate the expression of target genes at the post-transcriptional level. miR156 is one of a class of evolutionarily highly conserved miRNA families. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factor is one of the target genes that is regulated by miR156. SPL transcription factors are involved in regulating plant growth and development, hormone response, stress response, and photosynthesis. In the present study, transgenic potato plants with overexpressed miR156 were obtained via the Agrobacterium-mediated transformation method. The results showed that the expression levels of the target gene, StSPL9, were all downregulated in the transgenic plants with overexpressed Stu-miR156. Compared with those of the control plants, the plant height and root length of the transgenic plants were significantly decreased, while the number of lateral roots was significantly increased. These results revealed that the miR156/SPLs module was involved in regulating potato plant height and root growth. [ABSTRACT FROM AUTHOR]

As a synthetic androgen, 17α‐methyltestosterone (MT) is widely used in aquaculture to induce sex reversal and may pose a potential risk to aquatic organisms. This ecological risk has attracted the attention of many scholars, but it is not comprehensive enough. Thus, the adverse effects of MT on zebrafish (Danio rerio) were comprehensively evaluated from gonadal histology, as well as the mRNA expression levels of 47 genes related to hypothalamic‐pituitary‐gonadal (HPG) axis, germ cell differentiation, sex determination, and hypothalamus‐pituitary‐thyroid (HPT) axis. Adult zebrafish with a female/male ratio of 5:7 were exposed to a solvent control (0.001% dimethyl sulfoxide) and three measured concentrations of MT (5, 51 and 583 ng/L) for 50 days. The results showed that MT had no significant histological effects on the ovaries of females, but the frequency of late‐mature oocytes (LMO) showed a downward trend, indicating that MT could induce ovarian suppression to a certain extent. The transcriptional expression of activating transcription factor 4b1 (atf4b1), activating transcription factor 4b2 (atf4b2), calcium/calmodulin‐dependent protein kinase II delta 1 (camk2d1), calcium/calmodulin‐dependent protein kinase II delta 2 (camk2d2) and calcium/calmodulin‐dependent protein kinase II inhibitor 2 (camk2n2) genes in the brain of females increased significantly at all treatment groups of MT, and the mRNA expression of forkhead box L2a (foxl2) and ovarian cytochrome P450 aromatase (cyp19a1a) genes in the ovaries were down‐regulated by 5 and 583 ng/L group, which would translate into inhibition of oocyte development. As compared to females, MT had relatively little effects on the reproductive system of males, and only the transcriptional alterations of synaptonemal complex protein 3 (sycp3) and 17‐alpha‐hydroxylase/17,20‐lyase (cyp17) genes were observed in the testes, not enough to affect testicular histology. In addition, MT at all treatments strongly increased corticotropin‐releasing hormone (crh) transcript in the brain of females, as well as deiodinase 2 (dio2) transcript in the brain of males. The paired box protein 8 (pax8) gene was significantly decreased at 51 or 583 ng/L of MT in both female and male brains. The above results suggest that MT can pose potential adverse effects on the reproductive and thyroid endocrine system of fish. [ABSTRACT FROM AUTHOR]

Background: Several studies suggest that Proteasome 26S Subunit, ATPase (PSMC) family genes are of great importance in tumor progression and spreading, but the study for systematic evaluation of the function of PSMC genes in hepatocellular carcinoma (HCC) is currently lacking. Methods: The functions of PSMC genes in HCC were analyzed using multiple online databases, including the TCGA database, GEO database, HPA database, cBioPortal database, DAVID, and KEGG pathway. Experiments were later conducted to verify PSMC expression. Results: High levels of PSMC gene expression were detected in HCC tissues and PSMCs exhibited potentially powerful abilities in diagnosing HCC patients. All PSMC proteins are expressed to varying degrees in HCC tissues and high expression of the PSMC genes lead to poor prognosis in patients with HCC. Moreover, DNA methylation involves the regulation of the expression of PSMC2 and PSMC5 in HCC, and the levels of methylation of PSMC2 or PSMC5 correlate positively with patient overall survival in HCC patients. The copy number alteration and mutation of PSMC genes were observed and related to the expression of PSMCs in HCC. Functional enrichment analysis showed that many highly co-expressed genes of PSMCs had a potential role in tumor progression and metastasis, which merited further in-depth study. Functional network analysis also suggests that the primary biological function of PSMC genes is the regulation of protein homeostasis and energy metabolism in HCC. Moreover, the expression levels of PSMCs are related to immune cell infiltrates and immunomodulatory factors in HCC. Conclusion: Our study indicates that PSMC genes are the potential target for precision immunotherapy and novel prognostic biomarkers for HCC. [ABSTRACT FROM AUTHOR]

Simple Summary: Bisphenol AF (BPAF) is a common environmental endocrine-disrupting chemical (EDC) that can potentially affect the growth and development of aquatic organisms. EDCs in the aqueous environment can be deposited in estuaries through runoff or diffused into the marine environment. The toxicity of the EDCs is related to exposure dose and duration. In this study, we used marine medaka as the experimental subject to dynamically observe the response of fish in terms of growth, reproduction and antioxidant immune system during BPAF exposure, providing new insights into understanding the marine ecological risk of BPAF. In recent years, bisphenol AF (BPAF) in aquatic environments has drawn attention to its ecological risks. This study aims to investigate the toxic effects of BPAF (188.33 μg/L) exposure for 30 days on female marine medaka (Oryzias melastigma). On the 10th and 30th day of exposure, the toxicity was evaluated using histological analysis of the liver and ovaries and the transcription levels of genes related to the antioxidant system, immune system, and hypothalamic-pituitary-gonadal (HPG) axis. Findings revealed that (1) BPAF exposure caused vacuolation, karyopyknosis and karyolysis in the liver of marine medaka, and the toxic impact augmented with duration; (2) exposure to BPAF for 10 days facilitated the growth and maturation of primary ova, and this exposure had a comparatively inhibitory effect after 30 days; (3) exposure to BPAF resulted in a biphasic regulation of the transcriptional abundance of genes involved in antioxidant and inflammatory response (e.g., il-8, cat), with an initial up-regulation followed by down-regulation. Additionally, it disrupted the transcriptional pattern of HPG axis-related genes (e.g., 3βhsd, arα). In conclusion, 188.33 μg/L BPAF can alter the expression levels of functionally related genes, impair the structural integrity of marine organisms, and pose a threat to their overall health. [ABSTRACT FROM AUTHOR]

N6-methyladenosine (m6A) RNA methylation is the predominant epigenetic modification for mRNAs that regulates various cancer-related pathways. However, the prognostic significance of m6A modification regulators remains unclear in glioma. By integrating the TCGA lower-grade glioma (LGG) and glioblastoma multiforme (GBM) gene expression data, we demonstrated that both the m6A regulators and m6A-target genes were associated with glioma prognosis and activated various cancer-related pathways. Then, we paired m6A regulators and their target genes as m6A-related gene pairs (MGPs) using the iPAGE algorithm, among which 122 MGPs were significantly reversed in expression between LGG and GBM. Subsequently, we employed LASSO Cox regression analysis to construct an MGP signature (MrGPS) to evaluate glioma prognosis. MrGPS was independently validated in CGGA and GEO glioma cohorts with high accuracy in predicting overall survival. The average area under the receiver operating characteristic curve (AUC) at 1-, 3- and 5-year intervals were 0.752, 0.853 and 0.831, respectively. Combining clinical factors of age and radiotherapy, the AUC of MrGPS was much improved to around 0.90. Furthermore, CIBERSORT and TIDE algorithms revealed that MrGPS is indicative for the immune infiltration level and the response to immune checkpoint inhibitor therapy in glioma patients. In conclusion, our study demonstrated that m6A methylation is a prognostic factor for glioma and the developed prognostic model MrGPS holds potential as a valuable tool for enhancing patient management and facilitating accurate prognosis assessment in cases of glioma. [ABSTRACT FROM AUTHOR]

MicroRNAs are a class of endogenous, non-coding, small-RNA molecules with important functions in plant development and stress response processes. Root systems are important because they allow plants to absorb nutrients and water from the soil and are fundamental for anchoring the plant and responding to environmental signals. However, the roles of miRNAs underlying root development remain poorly investigated in potato. In this research, small-RNA sequencing was performed to thoroughly detect underlying miRNAs and their roles in regulating root development between the early root (ER) stage and the mature root (MR) stage of potato roots. A total of 203 known and 137 novel miRNAs were obtained, and 64 differentially expressed miRNAs (DEMs) were identified between the ER and MR stages. The expression patterns of 12 DEMs were also determined via qRT-PCR. In addition, a mixed degradome library was constructed from the ER and the MR stages to identify the targets of the identified miRNAs, and 2400 target genes were verified to be the targets of 131 miRNAs. Based on target annotation, we identified that nine target genes of six DEMs were probably involved in potato root development, and eight targets of six DEMs were validated via 5'-RLM-RACE assays. These targets may participate in root development by regulating cell proliferation, root cultures (PGSC0003DMT400013837), root meristem growth (PGSC0003DMT400079970), root morphogenesis (PGSC0003DMT400040282), post-embryonic root development (PGSC0003DMT400021612), root hair elongation (PGSC0003DMT400034518), cell wall repair (PGSC0003DMT400074930), and auxin polar transport (PGSC0003DMT400079970), and by negatively regulating cell proliferation (PGSC0003DMT400009997) and cell growth (PGSC0003DMT400003464). The qRT-PCR analysis indicated that most miRNAs have opposing expression patterns to their targets. It is widely accepted that potato root development is regulated by miRNAs, among which stu-miR8006-p5-1ss9AT is substantially down-regulated during root development. We show here that the suppression of stu-miR8006-p5-1ss9AT led to an alteration in the potato root architecture and that it targeted auxin induction in the root culture protein 12-encoding gene that is potentially involved in the regulation of root development. In addition, the suppression of stu-miR8006-p5-1ss9AT led to a significant alteration in the potato root architecture. Altogether, our results might provide some useful insights into stu-miR8006-p5-1ss9AT and the crucial role that it plays in potato root development; they could also facilitate the molecular genetic breeding of potato. [ABSTRACT FROM AUTHOR]

Objective: Population studies have shown that vitamin D (VitD) deficiency is associated with an increased incidence of type 2 diabetes mellitus (T2DM), VitD deficiency is a potential risk factor for T2DM, and the proportion of M1-type macrophages and M2-type macrophages in T2DM patients is imbalanced. Another study reported that VitD can affect the differentiation of macrophages into M1 and M2 types. However, there is no definitive result about the correlation between plasma VitD levels and macrophage typing in patients with T2DM. Whether VitD affects the progression of T2DM by regulating the polarization type of macrophages and the specific regulatory mechanism is not very clear. Therefore, we carried out the following research. Methods: We first used flow cytometry to detect the proportions of M1 and M2 macrophages in peripheral blood of T2DM patients with different VitD levels. Furthermore, we used ELISA to detect the inflammatory factors affecting macrophage differentiation in patients' plasma, including IL-6 secreted by M1-type macrophages and TGF-β secreted by M2-type macrophages. Mononuclear cells were separated from human peripheral blood with immunomagnetic beads, cultured in vitro, and treated with different concentrations of VitD, and the ratio of differentiation into M1 and M2 macrophages was detected by flow cytometry. Results: With the increase of serum 25(OH)D levels in patients with T2DM, the proportion of M1 and M2 macrophages in peripheral blood decreased, that is, the polarized phenotype of macrophages was more inclined to M2 type, while plasma IL-6 gradually decreased, and TGF-β gradually increased. In addition, VitD can promote the differentiation of CD14-positive monocytes cultured in vitro into M2 macrophages. Conclusions: When the level of VitD in T2DM patients is low, there are more M1-type macrophages in peripheral blood, and when the level of VitD is increased, M2-type macrophages are increased. Changes in related inflammatory factors were also consistent. In vitro culture of monocytes further confirmed that VitD can promote the differentiation of macrophages to M2 type in T2DM patients. [ABSTRACT FROM AUTHOR]

Background: Autopolyploidy is a valuable model for studying whole-genome duplication (WGD) without hybridization, yet little is known about the genomic structural and functional changes that occur in autopolyploids after WGD. Cyclocarya paliurus (Juglandaceae) is a natural diploid–autotetraploid species. We generated an allele-aware autotetraploid genome, a chimeric chromosome-level diploid genome, and whole-genome resequencing data for 106 autotetraploid individuals at an average depth of 60 × per individual, along with 12 diploid individuals at an average depth of 90 × per individual. Results: Autotetraploid C. paliurus had 64 chromosomes clustered into 16 homologous groups, and the majority of homologous chromosomes demonstrated similar chromosome length, gene numbers, and expression. The regions of synteny, structural variation and nonalignment to the diploid genome accounted for 81.3%, 8.8% and 9.9% of the autotetraploid genome, respectively. Our analyses identified 20,626 genes (69.18%) with four alleles and 9191 genes (30.82%) with one, two, or three alleles, suggesting post-polyploid allelic loss. Genes with allelic loss were found to occur more often in proximity to or within structural variations and exhibited a marked overlap with transposable elements. Additionally, such genes showed a reduced tendency to interact with other genes. We also found 102 genes with more than four copies in the autotetraploid genome, and their expression levels were significantly higher than their diploid counterparts. These genes were enriched in enzymes involved in stress response and plant defense, potentially contributing to the evolutionary success of autotetraploids. Our population genomic analyses suggested a single origin of autotetraploids and recent divergence (~ 0.57 Mya) from diploids, with minimal interploidy admixture. Conclusions: Our results indicate the potential for genomic and functional reorganization, which may contribute to evolutionary success in autotetraploid C. paliurus. [ABSTRACT FROM AUTHOR]

Flag leaf senescence is a critical factor affecting the yield and quality of wheat. The aim of this study was to identify QTLs associated with flag leaf senescence in an F10 recombinant inbred line population derived from durum wheats UC1113 and Kofa. Bulked segregant analysis using the wheat 660K SNP array identified 3225 SNPs between extreme-phenotype bulks, and the differential SNPs were mainly clustered on chromosomes 1A, 1B, 3B, 5A, 5B, and 7A. BSR-Seq indicated that the significant SNPs were mainly located in two intervals of 354.0–389.0 Mb and 8.0–15.0 Mb on 1B and 3B, respectively. Based on the distribution of significant SNPs on chromosomes 1B and 3B, a total of 109 insertion/deletion (InDel) markers were developed, and 8 of them were finally used to map QTL in UC1113/Kofa population for flag leaf senescence. Inclusive composite interval mapping identified two major QTL in marker intervals Mar2005–Mar2116 and Mar207–Mar289, explaining 14.2–15.4% and 31.4–68.6% of the phenotypic variances across environments, respectively. Using BSR-Seq, gene expression and sequence analysis, the TraesCS1B02G211600 and TraesCS3B02G023000 were identified as candidate senescence-associated genes. This study has potential to be used in cloning key genes for flag leaf senescence and provides available molecular markers for genotyping and marker-assisted selection breeding. [ABSTRACT FROM AUTHOR]

Background: The apicomplexan parasites Eimeria spp. are the causative agents of coccidiosis, a disease with a significant global impact on the poultry industry. The complex life cycle of Eimeria spp. involves exogenous (sporogony) and endogenous (schizogony and gametogony) stages. Unfortunately, the genetic regulation of these highly dynamic processes, particularly for genes involved in specific developmental phases, is not well understood. Methods: In this study, we used RNA sequencing (RNA-Seq) analysis to identify expressed genes and differentially expressed genes (DEGs) at seven time points representing different developmental stages of Eimeria tenella. We then performed K-means clustering along with co-expression analysis to identify functionally enriched gene clusters. Additionally, we predicted apicomplexan AP2 transcription factors in E. tenella using bioinformatics methods. Finally, we generated overexpression and knockout strains of ETH2_0411800 to observe its impact on E. tenella development. Results: In total, we identified 7329 genes that are expressed during various developmental stages, with 3342 genes exhibiting differential expression during development. Using K-means clustering along with co-expression analysis, we identified clusters functionally enriched for oocyte meiosis, cell cycle, and signaling pathway. Among the 53 predicted ApiAP2 transcription factors, ETH2_0411800 was found to be exclusively expressed during sporogony. The ETH2_0411800 overexpression and knockout strains did not exhibit significant differences in oocyst size or output compared to the parental strain, while the resulting ETH2_0411800 knockout parasite showed a relatively small oocyst output. Conclusions: The findings of our research suggest that ETH2_0411800 is not essential for the growth and development of E. tenella. Our study provides insights into the gene expression dynamics and is a valuable resource for exploring the roles of transcription factor genes in regulating the development of Eimeria parasites. [ABSTRACT FROM AUTHOR]

Triple‐negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer that is suggested to be associated with hypoxia. This study is the first to identify a novel circular RNA (circRNA), circTBC1D14, whose expression is significantly upregulated in TNBC. The authors confirm that high circTBC1D14 expression is associated with a poor prognosis in patients with breast cancer. circTBC1D14‐associated mass spectrometry and RNA‐binding protein‐related bioinformatics strategies indicate that FUS can interact with circTBC1D14, which can bind to the downstream flanking sequence of circTBC1D14 to induce cyclization. FUS is an essential biomarker associated with stress granules (SGs), and the authors find that hypoxic conditions can induce FUS–circTBC1D14‐associated SG formation in the cytoplasm after modification by protein PRMT1. Subsequently, circTBC1D14 increases the stability of PRMT1 by inhibiting its K48‐regulated polyubiquitination, leading to the upregulation of PRMT1 expression. In addition, FUS–circTBC1D14 SGs can initiate a cascade of SG‐linked proteins to recognize and control the elimination of SGs by recruiting LAMP1 and enhancing lysosome‐associated autophagy flux, thus contributing to the maintenance of cellular homeostasis and promoting tumor progression in TNBC. Overall, these findings reveal that circTBC1D14 is a potential prognostic indicator that can serve as a therapeutic target for TNBC treatment. [ABSTRACT FROM AUTHOR]

Glucagon-like peptide-1 (GLP-1), one of the expression products of the proglucagon (pg) gene, is an incretin mainly secreted by the gastrointestinal system. In mammals, GLP-1 has hypoglycemic and food-inhibiting effects; while in some fish species, it has been confirmed to increase blood glucose by promoting gluconeogenesis and stimulating glycogenolysis. In order to more deeply understand the role of GLP-1 in the process of glycometabolism in herbivorous fish, the pg gene was cloned from Spinibarbus denticulatus to obtain its sequence characteristics, and the changes in blood glucose level and pg gene expression in S. denticulatus were further explored by feeding with three kinds of carbohydrates and intraperitoneal injection of GLP-1. Basal and temporal blood glucose levels and pg gene expression of S. denticulatus (91.68 ± 10.79 g) were measured at 0, 1, 3, 5, 7, and 12 h after oral administration (n = 4). Then, the changes of blood glucose levels and pg and glucokinase (gk) gene expressions of S. denticulatus (94.29 ± 10.82 g) were determined at 0, 30, 60, and 120 min after intraperitoneal injection (n = 4). It was shown that polysaccharides could induce the upregulation of pg gene expression faster than monosaccharides and stimulate the secretion of GLP-1 in the intestine. Intraperitoneal injection of GLP-1 peptide rapidly raised blood glucose levels, and pg gene expression in the anterior intestine, whole brain, and hepatopancreas decreased continuously after 30 minutes. These results showed that S. denticulatus might inhibit the excessive accumulation of blood glucose by reducing the expression of the pg gene and increasing the expression of gk gene in a short time. It was speculated that GLP-1 of S. denticulatus might have a "gut-brain-liver" pathway similar to mammals in glycemia regulation. Therefore, this study provided a novel perspective for explaining the functional differences of GLP-1 in herbivorous fish and mammals. [ABSTRACT FROM AUTHOR]

Although heterosis is commonly used in Chinese cabbage, its molecular basis is poorly understood. In this study, 16Chinese cabbage hybrids were utilized as test subjects to explore the potential molecular mechanism of heterosis. RNA sequencing revealed 5815–10,252 differentially expressed genes (DEGs) (female parent vs. male parent), 1796–5990 DEGs (female parent-vs-hybrid), and 2244–7063 DEGs (male parent vs. hybrid) in 16 cross combinations at the middle stage of heading. Among of them, 72.83–84.20% DEGs conformed to the dominant expression pattern, which is the predominant expression pattern in hybrids. There were 13 pathways in which DEGs were significantly enriched in most cross combinations. Among them, the plant–pathogen interaction (ko04626) and circadian rhythm-plant (ko04712)were significantly enriched by DEGs in strong heterosis hybrids. WGCNA also proved that the two pathways were significantly related to heterosis in Chinese cabbage. [ABSTRACT FROM AUTHOR]

Sensor—responder complexes comprising calcineurin B-like (CBL) proteins and CBL-interacting protein kinases (CIPKs) are plant-specific Ca2+ receptors, and the CBL-CIPK module is widely involved in plant growth and development and a large number of abiotic stress response signaling pathways. In this study, the potato cv. "Atlantic" was subjected to a water deficiency treatment and the expression of StCIPK18 gene was detected by qRT-PCR. The subcellular localization of StCIPK18 protein was observed by a confocal laser scanning microscope. The StCIPK18 interacting protein was identified and verified by yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC). StCIPK18 overexpression and StCIPK18 knockout plants were constructed. The phenotypic changes under drought stress were indicated by water loss rate, relative water content, MDA and proline contents, and CAT, SOD and POD activities. The results showed that StCIPK18 expression was upregulated under drought stress. StCIPK18 is localized in the cell membrane and cytoplasm. Y2H shows the interaction between StCIPK18 and StCBL1, StCBL4, StCBL6 and StCBL8. BiFC further verifies the reliability of the interaction between StCIPK18 and StCBL4. Under drought stress, StCIPK18 overexpression decreased the water loss rate and MDA, and increased RWC, proline contents and CAT, SOD and POD activities; however, StCIPK18 knockout showed opposite results, compared with the wild type, in response to drought stress. The results can provide information for the molecular mechanism of the StCIPK18 regulating potato response to drought stress. [ABSTRACT FROM AUTHOR]

Ubiquitin-conjugating enzymes (E2s/UBC) are components of the ubiquitin proteasome system (UPS), and the ubiquitin-conjugating enzyme variant (UEV) is one of E2s (ubiquitin-conjugating enzymes, UBC) subfamily. The UEVs and UBC13 play an auxiliary role in mediating Lys63-linked polyUb chain assembly, which is correlated with target protein non-proteolytic functions, such as DNA repair or response to stress. However, the collaborative mechanism of StUBC13 (homologue of AtUBC13) and StUEVs (the UEVs in potato) involved in potato are not fully understood understood. Here, we identified two StUBC13 and seven StUEVs from potato genome. We analyzed protein motif and conserved domain, gene structure, phylogenetic features, cis-acting elements of StUBC13 and StUEVs. Subsequently, we screened StUBC13 partners protein and verified interaction between StUBC13 and StUEVs using yeast two-hybrid, split luciferase complementation (SLC) and bimolecular fluorescence complementation (BiFC) approach. The expression profile and qRT-PCR analysis suggested that StUBC13 and StUEVs gene exhibited a tissue-specific expression and were induced by different stress. Overall, this investigative study provides a comprehensive reference and view for further functional research on StUBC13 and StUEV1s in potato. [ABSTRACT FROM AUTHOR]

Background. QiHuangYiShen granules (QHYS), a traditional Chinese herbal medicine formula, have been used in clinical practice for treating diabetic kidney disease for several years by our team. The efficacy of reducing proteinuria and delaying the decline of renal function of QHYS has been proved by our previous studies. However, the exact mechanism by which QHYS exerts its renoprotection remains largely unknown. Emerging evidence suggests that lncRNA MALAT1 is abnormally expressed in diabetic nephropathy (DN) and can attenuate renal fibrosis by modulating podocyte epithelial-mesenchymal transition (EMT). Objective. In the present study, we aimed to explore whether QHYS could modulate lncRNA MALAT1 expression and attenuate the podocyte EMT as well as the potential mechanism related to the Wnt/β-catenin signal pathway. Methods. SD rats were fed with the high-fat-high-sucrose diet for 8 weeks and thereafter administered with 30 mg/kg streptozotocin intraperitoneally to replicate the DN model. Quality control of QHYS was performed using high-performance liquid chromatography. QHYS were orally administered at 1.25, 2.5, and 5 g/kg doses, respectively, to the DN model rats for 12 weeks. Body weight, glycated haemoglobin, blood urea nitrogen, serum creatinine, 24-h proteinuria, and kidney index were measured. The morphologic pathology of the kidney was evaluated by Hematoxylin-eosin and Masson's trichrome staining. The expression level of lncRNA MALAT1 was determined by quantitative real-time polymerase chain reaction. In addition, the expression levels of podocyte EMT protein markers and Wnt/β-catenin pathway proteins in renal tissues were evaluated by Western blotting and immunohistochemistry. Results. The results showed that QHYS significantly reduced 24-h proteinuria, blood urea nitrogen, kidney index, and ameliorated glomerular hypertrophy and collagen fiber deposition in the kidney of DN rats. Importantly, QHYS significantly downregulated the expression level of lncRNA MALAT1, upregulated the expression of nephrin, the podocyte marker protein, downregulated the expression of desmin and FSP-1, and mesenchymal cell markers. Furthermore, QHYS significantly downregulated the expression levels of Wnt1, β-catenin, and active β-catenin. Conclusion. Conclusively, our study revealed that QHYS significantly reduced proteinuria, alleviated renal fibrosis, and attenuated the podocyte EMT in DN rats, which may be associated with the downregulation of lncRNA MALAT1 expression and inhibition of the Wnt/β-catenin pathway. [ABSTRACT FROM AUTHOR]

Stomata are specialized portals in plant leaves to modulate water loss from plants to the atmosphere by control of the transpiration, thereby determining the water-use efficiency and drought resistance of plants. Despite that the stomata developmental progression is well-understood at the molecular level, the experimental evidence that miRNA regulates stomata development is still lacking, and the underlying mechanism remains elusive. This study demonstrates the involvement of stu-miR827 in regulating the drought tolerance of potato due to its control over the leaf stomatal density. The expression analysis showed that stu-miR827 was obviously repressed by drought stresses and then rapidly increased after rewatering. Suppressing the expression of stu-miR827 transgenic potato lines showed an increase in stomatal density, correlating with a weaker drought resistance compared with wildtype potato lines. In addition, StWRKY48 was identified as the target gene of stu-miR827, and the expression of StWRKY48 was obviously induced by drought stresses and was greatly upregulated in stu-miR827 knockdown transgenic potato lines, suggesting its involvement in the drought stress response. Importantly, the expression of genes associated with stomata development, such as SDD (stomatal density and distribution) and TMM (too many mouths), was seriously suppressed in transgenic lines. Altogether, these observations demonstrated that suppression of stu-miR827 might lead to overexpression of StWRKY48, which may contribute to negatively regulating the drought adaptation of potato by increasing the stomatal density. The results may facilitate functional studies of miRNAs in the process of drought tolerance in plants. [ABSTRACT FROM AUTHOR]

The heading date and grain size are two essential traits affecting rice yield. Here, we found that OsMOS1 promotes rice heading and affects its grain size. Knocking out OsMOS1 delayed heading, while the overexpression of OsMOS1 promoted heading in rice under long-day conditions. The transcriptions of the heading activators Ehd1, Hd3a, and RFT1 were decreased and the heading repressor Hd1 was increased in the osmos1 mutant. Conversely, the overexpression of OsMOS1 promoted the expressions of Ehd1, Hd3a, and RFT1, but inhibited the expression of Hd1. This suggests that OsMOS1 may control heading in rice by modulating the transcriptions of Ehd1, Hd3a, RFT1, and Hd1. In addition, knocking out OsMOS1 led to larger grains with longer grain lengths and higher grain weights. The seed cell size measurement showed that the cell lengths and cell widths of the outer glume epidermal cells of the osmos1 mutant were greater than those of the wild type. Furthermore, we also found that the overexpression of OsMOS1 in the Arabidopsis mos1 mutant background could suppress its phenotypes of late flowering and increased seed size. Thus, our study shows a conserved function of MOS1 in rice and Arabidopsis, and these findings shed light on the heading and seed size regulation in rice and suggest that OsMOS1 is a promising target for rice yield improvement. [ABSTRACT FROM AUTHOR]

Background: Telomerase is a ribonucleoprotein complex consisting of a catalytic component telomerase reverse transcriptase (TERT), internal RNA template and other co‐factors, and its essential function is to synthesize telomeric DNA, repetitive TTAGGG sequences at the termini of linear chromosomes. Telomerase is silent in normal human follicular thyroid cells, primarily due to the TERT gene being tightly repressed. During the development and progression of thyroid carcinomas (TCs), TERT induction and telomerase activation is in general required to maintain telomere length, thereby conferring TC cells with immortal and aggressive phenotypes. Methods: The genomic alterations of the TERT loci including TERT promoter's gain‐of‐function mutations, copy number gain, fusion and rearrangements, have recently been identified in TCs as mechanisms to induce TERT expression and to activate telomerase. Importantly, numerous studies have consistently shown that TERT promoter mutations and TERT expression occur in all TC subtypes, and are robustly associated with TC malignancy, aggressiveness, treatment failure and poor outcomes. Therefore, the assessment of TERT promoter mutations and TERT expression is highly valuable in TC diagnostics, prognosis, treatment decision, and follow‐up design. In addition, the TERT promoter is frequently hypermethylated in TC cells and tumors, which is required to activate TERT transcription and telomerase. Dysregulation of other components in the telomerase complex similarly upregulate telomerase. Moreover, shortened telomeres lead to altered gene expression and metabolism, thereby actively promoting TC aggressiveness. Here we summarize recent findings in TCs to provide the landscape of TC‐featured telomere/telomerase biology and discuss underlying implications in TC precision medicine. Conclusion: Mechanistic insights into telomerase activation and TERT induction in TCs are important both biologically and clinically. The TERT gene aberration and expression‐based molecular classification of TCs is proposed, and for such a purpose, the standardization of the assay and evaluation system is required. Moreover, the TERT‐based system and 2022 WHO TC classification may be combined to improve TC care. [ABSTRACT FROM AUTHOR]

Compared to advanced understanding of intrinsic programs of embryonic hematopoiesis, our knowledge on the niche in the aorta-gonad-mesonephros (AGM) region essential for stagewise hematopoietic stem cell (HSC) development remains limited. Here we conducted spatial transcriptomics analysis using Slide-seq and Curio-seq on mouse E10.5, E11.5 and E12.5 trunk tissues to explore the dynamic and spatial-resolved cells and signals in the AGM region. By integrating the corresponding scRNA-seq data, the Curio-seq data profiled spatial-revolved (at 10 µm resolution) cell identity and gene expression in the AGM region. Next, we utilized CellphoneDB, CellChat and StringDB to predict potential niche signals essential for embryonic hematopoiesis. We then customized RNA probes for 140 genes of interest (including cell markers and signals) and conducted MERFISH (a spatially resolved single-cell transcriptome profiling technology) on E11.5 trunk sections, which well corroborated the cellular and transcriptomic profiles as well as their location in the AGM region revealed by the Curio-seq data. We revealed that a mesenchymal stromal cell (MSC) population co-expressing Cdh2 (encodes N-cadherin or N-cad) and Pdgfra (N-cad+ MSCs) was exclusively at the ventral part of the aorta as a single cell layer between aortic endothelial cells and mesonephric cells. These N-cad+ MSCs are in direct cell-cell contact and exhibited enhanced JAG1-NOTCH1 interaction with pre-HSCs from E10.5 to E12.5. We are conducting transplantation experiments to quantify the repopulating HSCs with or without conditional knockout of N-cad+ MSC derived JAG1 using NcadCreER;Jag1flox/flox mouse model. In summary, our study employed sequencing-based and imaging-based spatial transcriptomics technologies to reveal the dynamic and polarized cellular and transcriptomic profiles in the AGM region at single-cell level. [ABSTRACT FROM AUTHOR]

Norethindrone (NET) is a widely used synthetic progestin, which appears in water environments and threatens aquatic organisms. In this study, marine medaka (Oryzias melastigma) larvae were exposed to 7.6 and 80.1 ng/L NET for 190 days. The effects of NET on growth, sex differentiation, gonad histology and transcriptional expression profiles of hypothalamic‐pituitary‐gonadal (HPG) axis‐related genes were determined. The results showed that exposure to 80.1 ng/L NET caused an all‐male marine medaka population and significantly decreased the growth of males. Exposure to 7.6 ng/L NET increased the ratio of males/females in the marine medaka population, decreased the growth of males and delayed the ovary maturation in females. However, the sperm maturation was accelerated by 7.6 or 80.1 ng/L NET. In females, the transcription levels of cytochrome P450 aromatase (cyp19a1a) and progesterone receptor (pgr) in ovaries, glucocorticoid receptor (gr) and vitellogenin (vtg) in livers were suppressed after exposure to 7.6 ng/L NET, which may cause delayed ovary maturation. In males, NET significantly decreased the transcription levels of follicle stimulating hormone β (fshβ) and Luteinizing hormone β (lhβ)in the brain, Estrogen receptor β (erβ)，gr and pgr in the liver, and vitellogenin receptor (vtgr) in the testes, while NET of 80.1 ng/L led to a significant up‐regulation of steroidogenic acute regulatory protein (star) in the testes of males. These results showed that NET could influence growth, sex differentiation and gonadal maturation and significantly alter the transcriptional expression levels of HPG axis‐related genes. [ABSTRACT FROM AUTHOR]

Pulmonary tuberculosis (TB) is a chronic infectious disease that is caused by respiratory infections, principally Mycobacterium tuberculosis. Increasingly, studies have shown that circular (circ)RNAs play regulatory roles in different diseases through different mechanisms. However, their roles and potential regulatory mechanisms in pulmonary TB remain unclear. In this study, we analyzed circRNA sequencing data from adjacent normal and diseased tissues from pulmonary TB patients and analyzed the differentially expressed genes. We then constructed machine learning models and used single-factor analysis to identify hub circRNAs. We downloaded the pulmonary TB micro (mi)RNA (GSE29190) and mRNA (GSE83456) gene expression datasets from the Gene Expression Omnibus database and performed differential expression analysis to determine the differentially expressed miRNAs and mRNAs. We also constructed a circRNA–miRNA–mRNA interaction network using Cytoscape. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used to predict the biological functions of the identified RNAs and determine hub genes. Then, the STRING database and cytoHubba were used to construct protein-protein interaction networks. The results showed 125 differentially expressed circRNAs in the adjacent normal and diseased tissues of pulmonary TB patients. Among them, we identified three hub genes associated with the development of pulmonary TB: hsa_circ_0007919 (upregulated), hsa_circ_0002419 (downregulated), and hsa_circ_0005521 (downregulated). Through further screening, we determined 16 mRNAs of potential downstream genes for hsa-miR-409-5p and hsa_circ_0005521 and established an interaction network. This network may have important roles in the occurrence and development of pulmonary TB. We constructed a model with 100% prediction accuracy by machine learning and single-factor analysis. We constructed a protein-protein interaction network among the top 50 hub mRNAs, with FBXW7 scoring the highest and SOCS3 the second highest. These results may provide a new reference for the identification of candidate markers for the early diagnosis and treatment of pulmonary TB. [ABSTRACT FROM AUTHOR]

• StSnRK1.1 gene was cloned from potato. • Overexpression of StSnRK1.1 accelerated release of potato tuber dormancy. • Interfering expression of StSnRK1.1 prolonged tuber dormancy time of potato. • Interaction of StSnRK1.1 with StCAT3 and StFBA1 was preliminarily verified. SnRK1 is a plant-specific serine/threonine protein kinase, that plays a vital role in maintaining the energy balance, nutrient distribution, growth, and development of organisms for survival. The period of tuber dormancy seriously affects potato production. To elucidate the effect of the StSnRK1.1 gene on dormancy release, the gene was cloned from the potato cultivar 'Desiree', and the overexpression and interfering expression lines were obtained through genetic transformation. StSnRK1.1 promoted early dormancy release and sprouting of potato tubers in the overexpression line, while it delayed tuber sprouting in the StSnRK1.1- interfering expression line. In addition, it was discovered that abscisic acid (ABA) in the StSnRK1.1 overexpression line was significantly reduced compared with the wild type plants, while the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) were increased. Conversely, the opposite result was found in the StSnRK1.1 gene interference expression line, which indicated that the dormancy release was accelerated, the reactive oxygen species metabolism efficiency was high, and the reactive oxygen species could be quickly removed and the accumulation of reactive oxygen species could be avoided during the dormancy release process. The positive regulatory genes StSnRK2.2 and StABI5 of ABA signal transduction were lower than those of wild type in the overexpression line and higher than that of the wild type in the interfering expression line, while the negative regulatory genes StPP2CA1 and StPP2CA3 of ABA signal transduction were higher than those of the wild type in the overexpression line and lower than that of the wild type in the interfering expression line. In summary, StSnRK1.1 affects ABA signaling by mediating the expression of StSnRK2.2, StABI5, StPP2CA1 and StPP2CA3 , which provides a theoretical basis for the molecular mechanism of StSnRK1.1 to positively regulate the release of potato tuber dormancy. Through yeast two-hybrid (YH2) screening, two interacting proteins, StCAT3 and StFBA1, were identified. The interaction between StCAT3, StFBA1 and StSnRK1.1 was confirmed through bimolecular fluorescence complementation. These results provide novel information for further study on the molecular mechanism of StSnRK1.1 regulating dormancy and germination of potato tubers. [ABSTRACT FROM AUTHOR]

Live anticoccidial vaccines, either formulated with unattenuated or attenuated Eimeria parasites, are powerful stimulators of chicken intestinal immunity. Little is known about the dynamics of gene expression and the corresponding biological processes of chicken responses against infection with precocious line (PL) of Eimeria parasites. In the present study, we performed a time-series transcriptomic analysis of chicken duodenum across 15 time points from 6 to 156 hours post-infection (p.i.) with PL of E. acervulina. A high-quality profile showing two distinct changes in chicken duodenum mRNA expression was generated during the infection of Eimeria. Early response revealed that activation of the chicken immune response was detectable from 6 h.p.i., prominent genes triggered during the initiation of asexual and sexual parasite growth encompass immune regulatory effects, such as interferon gamma (IFN-γ), interferon regulatory factor 1 (IRF1), and interleukin-10 (IL10). The late response was identified significantly associating with maintaining cellular structure and activating lipid metabolic pathways. These analyses provide a detailed depiction of the biological response landscape in chickens infected by the PL of E. acervulina , contributing significant insights for the investigation of the host-parasite interactions and the management of parasitic diseases. • A high-quality profile of gene expression was first demonstrated in chicken duodenal tissues in response to the infection of the PL of E. acervulina. • Transcriptomic dynamics in chicken duodenum reveal two distinct responses to the endogenous development in PL of E. avervulina. • Significant immune responses were observed in the chicken duodenum at the early stages of infection with the PL of E. acervulina. • Late stages of PL E. acervulina infection upregulates expression of genes linked to lipid metabolic process and cellular structural activity. [ABSTRACT FROM AUTHOR]

Date palm regards as a valuable genomic resource for exploring the tolerance genes due to its ability to survive under the sever condition. Although a large number of differentiated genes were identified in date palm responding to salt stress, the genome-wide study of alternative splicing (AS) landscape under salt stress conditions remains unknown. In the current study, we identified the stress-related genes through transcriptomic analysis to characterize their function under salt. A total of 17,169 genes were differentially expressed under salt stress conditions. Gene expression analysis confirmed that the salt overly sensitive (SOS) pathway genes, such as PdSOS2;1 , PdSOS2;2 , PdSOS4 , PdSOS5 , and PdCIPK11 were involved in the regulation of salt response in date palm, which is consistent with the physiological analysis that high salinity affected the Na+/K+ homeostasis and amino acid profile of date palm resulted in the inhibition of plant growth. Interestingly, the pathway of "spliceosome" was enriched in the category of upregulation, indicating their potential role of AS in date palm response to salt stress. Expectedly, many differentially alternative splicing (DAS) events were found under salt stress conditions, and some splicing factors, such as PdRS40 , PdRSZ21 , PdSR45a , and PdU2Af genes were abnormally spliced under salt, suggesting that AS-related proteins might participated in regulating the salt stress pathway. Moreover, the number of differentially DAS-specific genes was gradually decreased, while the number of differentially expressed gene (DEG)-specific genes was increased with prolonged salt stress treatment, suggesting that AS and gene expression could be distinctively regulated in response to salt stress. Therefore, our study highlighted the pivotal role of AS in the regulation of salt stress and provided novel insights for enhancing the resistance to salt in date palm. [ABSTRACT FROM AUTHOR]

Background: Odorant-binding proteins (OBPs) play important roles in many physiological processes of mosquitoes. Previous high-throughput sequencing studies have revealed that some OBPs of Culex quinquefasciatus might be involved in the development of resistance to insecticides. Methods: Based on the results of sequencing analyses, the OBP28 gene was selected for evaluation in this study. Three laboratory strains of Cx. quinquefasciatus [susceptible strain (SS), deltamethrin-resistant strain 1 (HN) and deltamethrin-resistant strain 2 (RR)] were first examined by using the Centers for Disease Control and Prevention bottle bioassay, after which the expression level of the OBP28 gene in the susceptible and deltamethrin-resistant strains was determined by real-time quantitative polymerase chain reaction. The OBP28 gene in deltamethrin-resistant strain RR was silenced using RNA interference technology. The expression level of OBP28 and the resistance level were tested in the silenced strain and control strain after microinjection of double-stranded RNA for a 48-h interference period. Four field-collected strains (henceforth 'field strains') of Cx. quinquefasciatus were also examined for their resistance to deltamethrin and levels of OBP28 expression. Finally, a correlation analysis between deltamethrin resistance and gene expression was carried out for all seven strains, i.e. the four field strains and the three laboratory strains. Results: In the bioassay, the mortality of SS, HN and RR was 100%, 21.33% and 1.67%, respectively. The relative expression levels of OBP28 in strains HN and RR were 6.30- and 6.86-fold higher, respectively, than that of strain SS. After silencing of the OBP28 gene, the mortality of strain RR was 72.20% and that of the control strain 26.32%. The mortality of strain RR increased significantly after interference compared to that of the control strain. There was a negative correlation between OBP28 gene expression and mortality in adult mosquitoes after exposure to deltamethrin. Conclusions: To our knowledge, this study shows for the first time a correlation between the expression of a gene coding for OBP and insecticide resistance in mosquitoes. The potential resistance mechanism that was elucidated provides a new target gene for the surveillance of resistance in mosquitoes. Highlights: RNA sequencing showed that OBP28 gene expression was higher in the deltamethrin-resistant strains. The qPCR results verified that OBP28 gene expression was higher in the resistant strains. RNA interference silenced the OBP28 gene at an efficiency of more than 50%. The sensitivity of Cx. quinquefasciatus to deltamethrin increased after OBP28 had been silenced. [ABSTRACT FROM AUTHOR]

A high-carbohydrate diet could achieve a protein-sparing effect, but it may cause negative impacts on the growth condition of fish due to their poor utilisation ability of carbohydrate. How to reduce the adverse effects caused by a high-carbohydrate diet is important for the development of aquaculture. In the present study, we aimed to identify whether inulin could attenuate the metabolic syndrome caused by a high-carbohydrate diet in fish. Nile tilapia (Oreochromis niloticus) (1·19 (sd 0·01) g) were supplied with 35 % carbohydrate (CON), 45 % carbohydrate (HC) and 45 % carbohydrate + 5 g/kg inulin (HCI) diets for 10 weeks. The results showed that addition of inulin improved the survival rate when fish were challenged with Aeromonas hydrophila, indicating that inulin had an immunostimulatory effect. Compared with the HC group, the HCI group had lower lipid accumulation in liver and the gene expression analyses indicated that addition of inulin down-regulated genes related to lipogenesis and up-regulated genes relevant to β-oxidation significantly (P < 0·05). Higher liver glycogen and glucose tolerance were found in the HCI group compared with the HC group (P < 0·05). These results indicated that inulin could alleviate the metabolic syndrome induced by a high-carbohydrate diet. Furthermore, addition of inulin to a high-carbohydrate diet changed the intestinal bacterial composition and significantly increased the concentration of acetic acid and propionic acid in fish gut which have the potential to increase pathogen resistance and regulate metabolic characteristics in fish. Collectively, our results demonstrated a possible causal role for the gut microbiome in metabolic improvements induced by inulin in fish. [ABSTRACT FROM AUTHOR]

Summary: The SAUR26 subfamily genes play an important role in conferring variations of thermo‐responsiveness of growth architecture among natural accessions of Arabidopsis thaliana. The expression variations are critical for their activity variations, but how expression variations are generated is unknown.We identified genetic loci for gene expression variations through expression genome‐wide association study (eGWAS) and investigated their mechanisms through molecular analyses.We found that cis elements are the major determinants for expression variations of SAUR26, SAUR27, and SAUR28. Polymorphisms in the promoter region likely impact PIF4 regulation while those at the 3′UTR affect mRNA stability to generate variations in SAUR26 expression levels. These polymorphisms also differentially affect the mRNA stability of SAUR26 at two temperatures.This study reveals two mechanisms involving cis elements in generating gene expression diversity, which is likely important for local adaptations in Arabidopsis natural accessions. [ABSTRACT FROM AUTHOR]

SUMMARY: Autophagy is a self‐degradative process that is crucial for maintaining cellular homeostasis by removing damaged cytoplasmic components and recycling nutrients. Such an evolutionary conserved proteolysis process is regulated by the autophagy‐related (Atg) proteins. The incomplete understanding of plant autophagy proteome and the importance of a proteome‐wide understanding of the autophagy pathway prompted us to predict Atg proteins and regulators in Arabidopsis. Here, we developed a systems‐level algorithm to identify autophagy‐related modules (ARMs) based on protein subcellular localization, protein–protein interactions, and known Atg proteins. This generates a detailed landscape of the autophagic modules in Arabidopsis. We found that the newly identified genes in each ARM tend to be upregulated and coexpressed during the senescence stage of Arabidopsis. We also demonstrated that the Golgi apparatus ARM, ARM13, functions in the autophagy process by module clustering and functional analysis. To verify the in silico analysis, the Atg candidates in ARM13 that are functionally similar to the core Atg proteins were selected for experimental validation. Interestingly, two of the previously uncharacterized proteins identified from the ARM analysis, AGD1 and Sec14, exhibited bona fide association with the autophagy protein complex in plant cells, which provides evidence for a cross‐talk between intracellular pathways and autophagy. Thus, the computational framework has facilitated the identification and characterization of plant‐specific autophagy‐related proteins and novel autophagy proteins/regulators in higher eukaryotes. Significance Statement: We used a network‐based algorithm to identify autophagy protein modules in Arabidopsis by integrating the text‐mined autophagy proteins and the protein–protein interactions. According to functional importance, four proteins in a module were detected as the candidates in the regulation of autophagy. Two of them are known autophagy proteins and the other two candidates, AGD1 and Sec14, were experimentally validated. [ABSTRACT FROM AUTHOR]

The regulatory effect of luteolin on the progression of Alzheimer's disease (AD) remains unclear from the perspective of apoptosis. The present study aimed to investigate the protective effects of luteolin against Aβ25-35-induced cell apoptosis in pheochromocytoma (PC-12) cells. Aβ25-35 was used to induce an in vitro model of AD. Estradiol was used as a positive control. The PC-12 cells were incubated with luteolin alone or in combination with fulvestrant or U0126. The results showed that luteolin treatment significantly prevents Aβ25-35-induced decrease in cell viability and inhibits Aβ25-35-induced cell apoptosis. After the addition of fulvestrant and U0126, the apoptosis rate of PC-12 cells increased significantly. In addition, luteolin treatment significantly upregulated the expression of Bcl-2 and downregulated the expression of Bax and caspase-3, whereas fulvestrant and U0126 partially reversed the effects of luteolin. Moreover, luteolin treatment upregulated the expression of ERβ and p-ERK1/2, whereas fulvestrant blocked the expression of p-ERK1/2. The study showed that luteolin could activate the ER/ERK/MAPK signalling pathway to protect PC-12 cells against Aβ25-35-induced cell apoptosis via selectively acting on ERβ. Thus, luteolin may be considered as a potential novel therapeutic strategy for AD. [ABSTRACT FROM AUTHOR]

Objectives. To study how thermal energy is converted after moxibustion at local skin from the view of mitochondrial respiratory chain and its key regulatory elements of sirtuins 1 (SIRT1) and sirtuins 3 (SIRT3). Methods. Two moxibustion temperatures usually used in clinical practice (38°C and 46°C) were applied to Zusanli (ST36) acupoint for 30 minutes in C57BL/6J mice. Local skin samples were harvested at 30 min and 72 h after moxibustion intervention, respectively. The activity of mitochondrial respiratory chain complexes I–V was detected by spectrophotometry. The expression of SIRT1 and SIRT3 protein was detected by immunofluorescence staining or western blot. Results. Moxibustion at 38°C triggered more significant increase of mitochondrial respiratory chain complexes I–V expression. However, the protein expression of SIRT1 and SIRT3 at 46°C showed more obvious enhancement. In addition, the effect of mitochondrial respiratory chain complexes I–V activity on local skin of ST36 acupoint was more obvious at 30 min after moxibustion, while the expression of SIRT1 and SIRT3 protein was more significant at 72 h after moxibustion. Conclusion. Mitochondrial respiratory chain and its key regulatory element proteins SIRT1 and SIRT3 play important role in the initial process of thermal energy conversion stimulated by different moxibustion temperatures in local skin. [ABSTRACT FROM AUTHOR]

This study aimed to investigate whether chronic unpredictable mild stress (CUMS) affects follicular development in ovaries through the nerve growth factor (NGF)/high affinity nerve growth factor receptor, the Tropomyosin-related kinase A (TrkA) receptor, mediated signaling pathway and to reveal the relationship between chronic stress and premature ovarian insufficiency (POI) development. In this experiment, a CUMS rat model was constructed. It was found that serum estradiol (E2), anti-Mullerian hormone (AMH), and gonadotropin-releasing hormone (GnRH) levels decreased, while follicle-stimulating hormone (FSH) levels increased. The expression of NGF, TrkA, p75, and FSHR in ovarian tissue decreased significantly. The expression levels of TrkA and p75 protein in ovarian stroma and small follicles were observed by an immunofluorescence assay. In addition, the numbers of small follicles were significantly reduced. The expression of TrkA, p75, and FSHR in CUMS ovarian tissue was upregulated by exogenous NGF in vitro. Furthermore, after treatment with NGF combined with FSH, E2 secretion in ovarian tissue culture supernatant of CUMS rats also increased significantly. Therefore, CUMS downregulates NGF and TrkA and promotes the occurrence of POI in rats. Exogenous NGF and FSH can upregulate the NGF receptor, E2, and AMH in vitro, and improve the rat ovarian function. Future studies may associate these results with female population. [ABSTRACT FROM AUTHOR]

Intervertebral disc (IVD) degeneration is associated with local inflammation and increased expression of neurotrophins. Acidic microenvironment is believed to cause the progression of IVD degeneration. However, there is a paucity of information regarding the relationship between acidic microenvironment and the inflammation and expression of neurotrophins in IVD. G-protein-coupled receptor 4 (GPR4) is a pH-sensing receptor, which can activate the inflammation and increase the expression levels of nerve growth factor in acidic microenvironment. In this study, culture media with pH 7.2 (representing the normal IVD-like acidic condition) and pH 6.5 (degenerated IVD-like acidic condition) were prepared. The gene and protein expression levels of GPR4 in SD rat nucleus pulposus cells were determined under the acidic conditions. And cyclic AMP (cAMP), the second messenger of GPR4, was assayed. Furthermore, the expression levels of receptor activator of nuclear factor κ B (RANK), RANKL ligand (RANKL), osteoprotegerin (OPG), nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and neurotrophin-3 (NT-3) were also determined. To clarify the involvement of GPR4 in the upregulation of the expression of RANK/RANKL/OPG system and neurotrophins, gene knockdown and forced expression of GPR4 and inhibiting its downstream cAMP accumulation and Ca2+ mobilization were performed. The alternation of the expression levels of matrix metalloproteinase-3 (MMP-3), MMP-13, and aggrecanase-2 (ADAMTS-5) were evaluated by RT-PCR and western blot. The results showed that GPR4 was expressed in rat nucleus pulposus cells, and the expression was upregulated under the degenerated IVD-like acidic microenvironment. cAMP accumulation levels were increased under the degenerated IVD-like acidic culture conditions. The expression levels of RANK, RANKL, OPG, NGF, and BNDF were significantly upregulated under the degenerated IVD-like acidic microenvironment. GPR4 knockdown and reduction of cAMP by the inhibitor SQ22536 abolished the upregulation of the expression of RANK, RANKL, OPG, NGF, and BNDF under the degenerated IVD-like acidic microenvironment. On the opposite, acidosis-induced cAMP accumulation and upregulation of RANK, RANKL, OPG, NGF, and BNDF were further promoted by GPR4 overexpression. The expression levels of MMP-3, MMP-13, and ADAMTS-5 were upregulated under the degenerated IVD-like acidic condition, which can be promoted or attenuated by GPR4 overexpression or knockdown, respectively. We concluded that GPR4-mediated cAMP accumulation was involved in the increased expression of RANK/RANKL/OPG system and neurotrophins by nucleus pulposus cells under the degenerated IVD-like acidic microenvironment. [ABSTRACT FROM AUTHOR]

Proline is a multifunctional molecule, which especially is associated with response to abiotic stress. The proline dehydrogenase (ProDH) is the rate‐limiting enzyme in the process of proline catabolism. In the present study, two potato ProDH genes, StProDH1 and StProDH2, were cloned from potato (Solanum tuberosum L.) cultivar 'Favorita'. Gene expression analysis indicated that these two genes exhibited tissue‐specific expression and responded differently to various stress conditions, and that the StProDH1 plays a predominant role in most of these conditions. An artificial microRNA expression vector, under the control of CaMV 35S promoter, was constructed to generate transgenic potato plants by Agrobacterium‐mediated transformation, thereby silencing the StProDH1 gene. The result showed that the artificial microRNA caused a decline in StProDH1 expression, which was accompanied by a concomitant increase in proline content in transgenic plants under drought stress. The transgenic potato plants showed normal phenotypes under drought stress, while the non‐transgenic plants appeared withered. Results of physiological parameters assays showed that malondialdehyde, relative water content, and chlorophyll content in the transgenic potato plants were higher than that of non‐transgenic plants. Upon rehydration after two weeks of drought, proline and soluble sugar contents of the transgenic potato plants were significantly higher than those of non‐transgenic plants. These results combined demonstrate that the StProDH1 is a key player in the process of potato response to drought stress. [ABSTRACT FROM AUTHOR]