Expression Profiles Of Genes Research Articles

Comparative genomics and transcriptomics analysis of the bHLH gene family indicate their roles in regulating flavonoid biosynthesis in Sophora flavescens.

The basic helix-loop-helix (bHLH) transcription factors play crucial roles in various processes, such as plant development, secondary metabolism, and response to biotic/abiotic stresses. Sophora flavescens is a widely used traditional herbal medicine in clinical practice, known for its abundant flavonoids as the main active compounds. However, there has been no comprehensive analysis of S. flavescens bHLH (SfbHLH) gene family reported currently. In this study, we identified 167 SfbHLH genes and classified them into 23 subfamilies based on comparative genomics and phylogenetic analysis. Furthermore, widespread duplications significantly contributed to the expansion of SfbHLH family. Notably, SfbHLH042 was found to occupy a central position in the bHLH protein-protein interaction network. Transcriptome analysis of four tissues (leaf, stem, root and flower) revealed that most SfbHLH genes exhibited high expression levels exclusively in specific tissues of S. flavescens. The integrated analysis of transcriptomics and metabolomics during pod development stages revealed that SfbHLH042 may play a central role in connecting SfbHLH genes, flavonoids, and key enzymes involved in the biosynthesis pathway. Moreover, we also checked the expression of 8 SfbHLH genes using RT-qPCR analysis to realize the expression profiles of these genes among various tissues at different cultivated periods and root development. Our study would aid to understand the phylogeny and expression profile of SfbHLH family genes, and provide a promising candidate gene, SfbHLH042, for regulating the biosynthesis of flavonoids in S. flavescens.

Identification of immune infiltration and PANoptosis-related molecular clusters and predictive model in Alzheimer's disease based on transcriptome analysis.

This study aims to explore the expression profile of PANoptosis-related genes (PRGs) and immune infiltration in Alzheimer's disease (AD). Based on the Gene Expression Omnibus database, this study investigated the differentially expressed PRGs and immune cell infiltration in AD and explored related molecular clusters. Gene set variation analysis (GSVA) was used to analyze the expression of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes in different clusters. Weighted gene co-expression network analysis was utilized to find co-expressed gene modules and core genes in the network. By analyzing the intersection genes in random forest, support vector machine, generalized linear model, and extreme gradient boosting (XGB), the XGB model was determined. Eventually, the first five genes (Signal Transducer and Activator of Transcription 3, Tumor Necrosis Factor (TNF) Receptor Superfamily Member 1B, Interleukin 4 Receptor, Chloride Intracellular Channel 1, TNF Receptor Superfamily Member 10B) in XGB model were selected as predictive genes. This research explored the relationship between PANoptosis and AD and established an XGB learning model to evaluate and screen key genes. At the same time, immune infiltration analysis showed that there were different immune infiltration expression profiles in AD.

Novel prognostic model of complement and coagulation cascade-related genes correlates with immune environment and drug sensitivity in hepatocellular carcinoma

IntroductionHepatocellular carcinoma (HCC) is an immunogenic cancer characterized by high morbidity and mortality rates. The complement and coagulation systems are traditionally associated with the incidence of thrombotic complications and complement activation in cancer. However, the prognostic value of complement and coagulation-related factors (CCCR) in HCC remains undetermined. This study aims to construct a prognostic model based on the complement and coagulation cascades to evaluate its potential for immunotherapy and its relationship with drug sensitivity. Materials and methodsWe comprehensively investigated the expression profiles of CCCR genes using the TCGA, ICGC, and GTEx databases. Cox proportional hazards regression models were employed to assess prognostic value. ResultsThis study presents a novel prognostic model derived from the comprehensive analysis of nine CCCR genes (C1S, C6, C7, F11, F13B, F7, SERPINE1, SERPINF2, and SERPING1) to elucidate their correlation with the tumor immune environment and drug sensitivity in patients with HCC. Our model stratified patients into high- and low-risk groups based on distinct survival outcomes. The area under the curve (AUC) values of the risk score for one-, two-, and three-year survival rates were all greater than 0.660. Additionally, we analyzed immune cell infiltration patterns, revealing a strong correlation between CCCR gene expression and the immune microenvironment, including T cell and macrophage activity. Our findings also identified potential therapeutic targets, demonstrating differential drug sensitivity profiles between the risk groups. JAK1_8709_1718 was found to be more suitable for patients with low-risk HCC. ConclusionOur findings provide promising insights into the clinical relevance of CCCR genes as prognostic markers and therapeutic targets. This study underscores the significance of CCCR in HCC and paves the way for improved therapeutic strategies.

Impacts of climate change on the transcriptional dynamics and timing of bud dormancy release in Yoshino‐cherry tree

Societal Impact StatementThe iconic Yoshino cherry tree in Japan is experiencing shifts in its blossom timing due to climate warming. To develop a genetically informed predictive model for bud dormancy release, we examined seasonal gene expression in Yoshino cherry trees at three different locations. Our experiments, coupled with the analysis of DORMANCY‐ASSOCIATED MADS‐box (DAM) genes, highlighted DAM4 as the most reliable indicator for the rate of bud dormancy release. Our study demonstrated that seasonal gene expression profiles serve as a valuable indicator for forecasting the timing of dormancy release, benefiting Japanese traditions and providing insights into the biological impacts of climate change.Summary The Yoshino cherry tree Cerasus × yedoensis ‘Somei‐yoshino’ stands out as an iconic springtime symbol in Japan. For the Yoshino cherry trees to bloom in the spring, dormant buds must undergo a period of exposure to low temperatures, allowing them to break dormancy. Key genes related to dormancy release, known as DORMANCY‐ASSOCIATED MADS‐box (DAM), have been extensively studied. However, it remains unclear how these genes function in natural environments to regulate the timing of bud dormancy release. To develop a genetically informed predictive model for bud dormancy release, we explored seasonal changes in genome‐wide gene expression profiles in the Yoshino cherry trees at three distinct sites in Japan. Five distinct genome‐wide transcription profiles, subjectively named as modes—early summer, summer, autumn, winter, and spring—were identified, with the winter and spring modes observed when the daily mean temperature was below approximately 10°C. Our experiments of bud dormancy release, along with the assessment of expression profiles of DAM genes, have revealed that among the six DAM genes, DAM4 expression profile is the most indicative of the rate of bud dormancy break. Our estimates suggest that, on average, the tree needs to be exposed to temperatures below 10.1°C for 61.1 days to suppress DAM4 expression to the threshold required for bud dormancy release. Our projections for the timing of bud dormancy release indicated a delay of approximately 2.3 days per decade from 1990 to 2020. Our study demonstrated that gene expression serves as a valuable indicator for forecasting the timing of dormancy release.

Plant miR6262 Modulates the Expression of Metabolic and Thermogenic Genes in Human Hepatocytes and Adipocytes.

Edible plants have been linked to the mitigation of metabolic disturbances in liver and adipose tissue, including the decrease of lipogenesis and the enhancement of lipolysis and adipocyte browning. In this context, plant microRNAs could be key bioactive molecules underlying the cross-kingdom beneficial effects of plants. This study sought to explore the impact of plant-derived microRNAs on the modulation of adipocyte and hepatocyte genes involved in metabolism and thermogenesis. Plant miR6262 was selected as a candidate from miRBase for the predicted effect on the regulation of human metabolic genes. Functional validation was conducted after transfection with plant miRNA mimics in HepG2 hepatocytes exposed to free fatty acids to mimic liver steatosis and hMADs cells differentiated into brown-like adipocytes. miR6262 decreases the expression of the predicted target RXRA in the fatty acids-treated hepatocytes and in brown-like adipocytes and affects the expression profile of critical genes involved in metabolism and thermogenesis, including PPARA, G6PC, SREBF1 (hepatocytes) and CIDEA, CPT1M and PLIN1 (adipocytes). Nevertheless, plant miR6262 mimic transfections did not decrease hepatocyte lipid accumulation or stimulate adipocyte browning. these findings suggest that plant miR6262 could have a cross-kingdom regulation relevance through the modulation of human genes involved in lipid and glucose metabolism and thermogenesis in adipocytes and hepatocytes.

Revealing the aromatic sonata through terpenoid profiling and gene expression analysis of aromatic and non-aromatic coconut varieties

Aromatic coconut represents an exceptional variety of coconut known for its distinct and delightful flavor and aroma, both of which are highly cherished by consumers. Despite its popularity, there has been a lack of systematic research on aroma components and the associated synthetic genes. In this report, we developed the metabolite profiles of terpenoids by targeted metabolomics and obtained the expression profile of genes related to terpenoid biosynthesis by RNA-seq during different coconut fruit developmental stages. Totally, we separated 26 different terpenoids in aromatic coconut pulp, among which, geranyl acetate and (−)-isosyngene emerged as the most abundant. The integrated analysis of metabolism and RNA-seq data showed that HMGS2, HMGS3, IPI/IDI1, HMGR1, HMGR3, and CMK2 as potentially key genes involved in the synthesis of terpenoids in aromatic coconut. To validate these findings, qRT-PCR was conducted on terpenoid-related genes. These findings lay a foundation for understanding aroma formation and the molecular mechanism of terpenoids in coconut fruit.

Full genomic profiling of gene expression in selected muscle tissue biopsy specimens from myofascial pain syndrome (pilot comparison of muscle biopsy transcriptomes)

Introduction. Myofascial pain syndrome (MFPS) is one of the most frequent musculoskeletal pathologies causing chronic pain. This type of pain reaches the peak of prevalence in middle-aged individuals, women are affected 2,5 times more often than men. The disease leads to significant disability and is not only a medical but also a social problem. At the same time, a number of authors still note the low clinical efficacy of the applied therapy schemes. In this situation, further study of the pathogenesis of MFPS, in particular, genetic aspects of realization of this condition.The aim of the study was to perform full genomic profiling of gene expression (transcriptome study) in selected muscle tissue biopsy specimens of individual patients and control individuals.Materials and methods. To study the genetic aspects of MFPS realization, gene expression profiling in muscle tissue samples by full genome RNA sequencing (RNA-Seq) was performed in 5 patients suffering from myofascial brachial pain syndrome (2 patients with active form of MFPS, 3 — with latent form).Results. The transcriptome analysis of muscle tissue samples from the MFPS area revealed a statistically significant 6-10-fold increase in the expression of the ENSG00000148677:ANKRD1 (ankyrin repeat domain 1) gene in the subgroup of patients with latent form of MFPS compared to active form of MFPS.Conclusion. The results of the studies allowed to suggest that one of the factors of the latent form of MFPS realization may be adaptive hyperexpression of the gene encoding ANKRD1 protein, which regulates myofibrils tension, myoblasts differentiation, lipid metabolism, affects the development of neuronal connections.

Combined Metabolome and Transcriptome Analyses of Maize Leaves Reveal Global Effect of Biochar on Mechanisms Involved in Anti-Herbivory to Spodoptera frugiperda.

Fall armyworm (FAW, Spodoptera frugiperda) has now spread to more than 26 Chinese provinces. The government is working with farmers and researchers to find ways to prevent and control this pest. The use of biochar is one of the economic and environmentally friendly strategies to increase plant growth and improve pest resistance. We tested four v/v combinations of bamboo charcoal with coconut bran [BC1 (10:1), BC2(30:1), BC3(50:1)] against a control (CK) in maize. We found that plant height, stem thickness, fresh weight and chlorophyll content were significantly higher in BC2, in addition to the lowest FAW survival %. We then compared the metabolome and transcriptome profiles of BC2 and CK maize plants under FAW herbivory. Our results show that the levels of flavonoids, amino acids and derivatives, nucleotides and derivatives and most phenolic acids decreased, while terpenoids, organic acids, lipids and defense-related hormones increased in BC-grown maize leaves. Transcriptome sequencing revealed consistent expression profiles of genes enriched in these pathways. We also observed the increased expression of genes related to abscisic acid, jasmonic acid, auxin and MAPK signaling. Based on these observations, we discussed the possible pathways involved in maize against FAW herbivory. We conclude that bamboo charcoal induces anti-herbivory responses in maize leaves.

Whole exome sequencing analysis of 167 men with primary infertility

BackgroundSpermatogenic failure is one of the leading causes of male infertility and its genetic etiology has not yet been fully understood.MethodsThe study screened a cohort of patients (n = 167) with primary male infertility in contrast to 210 normally fertile men using whole exome sequencing (WES). The expression analysis of the candidate genes based on public single cell sequencing data was performed using the R language Seurat package.ResultsNo pathogenic copy number variations (CNVs) related to male infertility were identified using the the GATK-gCNV tool. Accordingly, variants of 17 known causative (five X-linked and twelve autosomal) genes, including ACTRT1, ADAD2, AR, BCORL1, CFAP47, CFAP54, DNAH17, DNAH6, DNAH7, DNAH8, DNAH9, FSIP2, MSH4, SLC9C1, TDRD9, TTC21A, and WNK3, were identified in 23 patients. Variants of 12 candidate (seven X-linked and five autosomal) genes were identified, among which CHTF18, DDB1, DNAH12, FANCB, GALNT3, OPHN1, SCML2, UPF3A, and ZMYM3 had altered fertility and semen characteristics in previously described knockout mouse models, whereas MAGEC1,RBMXL3, and ZNF185 were recurrently detected in patients with male factor infertility. The human testis single cell-sequencing database reveals that CHTF18, DDB1 and MAGEC1 are preferentially expressed in spermatogonial stem cells. DNAH12 and GALNT3 are found primarily in spermatocytes and early spermatids. UPF3A is present at a high level throughout spermatogenesis except in elongating spermatids. The testicular expression profiles of these candidate genes underlie their potential roles in spermatogenesis and the pathogenesis of male infertility.ConclusionWES is an effective tool in the genetic diagnosis of primary male infertility. Our findings provide useful information on precise treatment, genetic counseling, and birth defect prevention for male factor infertility.

Identification and expression profiles of granzyme genes in immune response from Nile tilapia (Oreochromis niloticus)

Granzymes (Gzms) are crucial cytotoxic molecules involved in cell-mediated immunity in mammals. However, their roles in teleost fish, such as Nile tilapia, were less understood. In this study, we focused on the identification of granzyme genes (OnGzms) from Nile tilapia (Oreochromis niloticus) and the potential functions in anti-infectious immunity, as well as their expression patterns in response to interleukin-2 stimulation. Eleven Gzm genes were identified in tilapia, including GzmA-1, GzmA-2, GzmK, GzmB-1, GzmB-2, GzmB-3, GzmH-1, GzmH-2, GzmG, GzmF, and GzmE, which contain conserved serine protease active sites. OnGzms were categorized into four groups through homology analysis at a shared locus. Gene replication processes, such as whole-genome replication specific to teleost and unequal crossing over of tandem genes, may lead to multigene copies of OnGzm genes. It appeared that the vertebrate GzmA/K originated from a common ancestor in terms of evolution. After Streptococcus agalactiae, Aeromonas hydrophila, Edwardsiella piscicida and Poly (I:C) challenges, expression of OnGzms was significantly up-regulated only in response to E. piscicida (an intracellular bacterium) infection, indicating potential functions of OnGzms involving in combating intracellular infection by the bacterium E. piscicida. Stimulation with rOnIL-2 led to increased expression of OnGzms in leukocytes, suggesting involvement in cell-mediated cytotoxicity. These findings enriched the knowledge of potential roles in resisting E. piscicida intracellular infection of granzyme genes in teleost fish.

Genome-wide identification, characterization, and expression analysis of the transient receptor potential gene family in mandarin fish Siniperca chuatsi

BackgroundTemperature is a crucial environmental determinant for the vitality and development of teleost fish, yet the underlying mechanisms by which they sense temperature fluctuations remain largely unexplored. Transient receptor potential (TRP) proteins, renowned for their involvement in temperature sensing, have not been characterized in teleost fish, especially regarding their temperature-sensing capabilities.ResultsIn this study, a genome-wide analysis was conducted, identifying a total of 28 TRP genes in the mandarin fish Siniperca chuatsi. These genes were categorized into the families of TRPA, TRPC, TRPP, TRPM, TRPML, and TRPV. Despite notable variations in conserved motifs across different subfamilies, TRP family members shared common structural features, including ankyrin repeats and the TRP domain. Tissue expression analysis showed that each of these TRP genes exhibited a unique expression pattern. Furthermore, examination of the tissue expression patterns of ten selected TRP genes following exposure to both high and low temperature stress indicated the expression of TRP genes were responsive to temperatures changes. Moreover, the expression profiles of TRP genes in response to mandarin fish virus infections showed significant upregulation for most genes after Siniperca chuatsi rhabdovirus, mandarin fish iridovirus and infectious spleen and kidney necrosis virus infection.ConclusionsThis study characterized the TRP family genes in mandarin fish genome-wide, and explored their expression patterns in response to temperature stress and virus infections. Our work will enhance the overall understanding of fish TRP channels and their possible functions.

Distinct Variations in Gene Expression and Cell Composition across Lichen Planus Subtypes.

Lichen planus (LP) is a highly prevalent inflammatory skin disease. While various clinical subtypes have been defined, detailed comparisons of these variants are lacking. This study aimed to elucidate differences in gene expression and cellular composition across LP subtypes. Lesional skin biopsies from 28 LP patients (classical, oral, genital, and lichen planopilaris) and seven non-diseased skin controls (NDC) were analyzed. Gene expression profiling of 730 inflammation-related genes was conducted using NanoString. Immune cell compositions were assessed by multiplex immunohistochemistry. Gene expression profiles revealed unique inflammatory signatures for each LP subtype. Lichen planopilaris exhibited the most divergence, with downregulated gene expression and upregulation of complement pathway genes (C5-7), along with elevated M2 macrophages. Oral and genital LP demonstrated similar profiles with strong upregulation of TNF-related and Toll-like receptor-associated genes. Oral LP showed the highest upregulation of cytotoxicity-associated genes, as well as high numbers of CD8+ IL-17A+ (Tc17) cells (8.02%). Interferon gene signatures were strongly upregulated in oral and classical LP. The study highlights distinct differences in inflammatory gene expression and cell composition across LP subtypes, emphasizing the need for tailored therapeutic approaches.

Genomic Organization and Expression Profiling of GOLDEN2-like Transcription Factor Genes in Eggplant and Their Role in Heat Stresses

GOLDEN2-like (GLK) transcription factor genes are involved in chloroplast biogenesis during all stages of plant growth and development, as well as in the response to biotic and abiotic stresses. However, little is known about this transcription factor family in eggplant. In this study, we identified 54 GLK genes in the eggplant genome (S. melongena L.) and classified them into seven groups (G1–G7). Structural analysis illustrated that the SmGLK proteins of specific groups are relatively conserved. Cis-acting elements indicated that these genes are likely to be involved in multiple responses stimulated by light, phytohormones, and abiotic stress. Collinear analysis indicated that expansion of the SmGLK gene family primarily occurred through segmental duplication. Tissue-specific expression analysis revealed that SmGLKs were preferentially expressed in leaves, fruits, and seeds. Further screening of SmGLK genes revealed their differential expression under various treatments. Notably, SmGLK18 was significantly responsive to multiple phytohormones and stress treatments, whereas SmGLK3 and SmGLK12 were highly induced by ABA, IAA, SA, and drought treatments. Our study provides new information on the eggplant GLK family systematically and comprehensively. For the first time, we propose that SmGLK18 may play a key role in improving heat resistance. This study provides valuable candidate gene resources for further functional research and will benefit eggplant molecular breeding.

Genome-wide investigation of the TIFY transcription factors in alfalfa (Medicago sativa L.): identification, analysis, and expression

BackgroundAlfalfa (Medicago sativa L.) is an essential leguminous forage with high nutrition and strong adaptability. The TIFY family is a plant-specific transcription factor identified in many plants. However, few reports have been reported on the phylogenetic analysis and gene expression profiling of TIFY family genes in alfalfa.ResultA total of 84 TIFY genes belonging to 4 categories were identified in alfalfa, including 58 MsJAZs, 18 MsZMLs, 4 MsTIFYs and 4 MsPPDs, respectively. qRT-PCR data from 8 genes in different tissues revealed that most MsTIFY genes were highly expressed in roots. The expression of MsTIFY14 was up-regulated after different times in both thrips-resistant and susceptible alfalfa after thrips feeding, and the expression of the remaining MsTIFYs had a strong correlation with the time of thrips feeding. Different abiotic stresses, including drought, salt, and cold, could induce or inhibit the expression of MsTIFY genes to varying degrees. In addition, the eight genes were all significantly up-regulated by JA and/or SA. Interestingly, MsTIFY77 was induced considerably by all the biotic, abiotic, or plant hormones (JA or SA) except ABA.ConclusionOur study identified members of the TIFY gene family in alfalfa and analyzed their structures and possible functions. It laid the foundation for further research on the molecular functions of TIFYs in alfalfa.

Genome-wide analysis of the passion fruit invertase gene family reveals involvement of PeCWINV5 in hexose accumulation

BackgroundInvertases (INVs) are key enzymes in sugar metabolism, cleaving sucrose into glucose and fructose and playing an important role in plant development and the stress response, however, the INV gene family in passion fruit has not been systematically reported.ResultsIn this study, a total of 16 PeINV genes were identified from the passion fruit genome and named according to their subcellular location and chromosome position. These include six cell wall invertase (CWINV) genes, two vacuolar invertase (VINV) genes, and eight neutral/alkaline invertase (N/AINV) genes. The gene structures, phylogenetic tree, and cis-acting elements of PeINV gene family were predicted using bioinformatics methods. Results showed that the upstream promoter region of the PeINV genes contained various response elements; particularly, PeVINV2, PeN/AINV3, PeN/AINV5, PeN/AINV6, PeN/AINV7, and PeN/AINV8 had more response elements. Additionally, the expression profiles of PeINV genes under different abiotic stresses (drought, salt, cold temperature, and high temperature) indicated that PeCWINV5, PeCWINV6, PeVINV1, PeVINV2, PeN/AINV2, PeN/AINV3, PeN/AINV6, and PeN/AINV7 responded significantly to these abiotic stresses, which was consistent with cis-acting element prediction results. Sucrose, glucose, and fructose are main soluble components in passion fruit pulp. The contents of total soluble sugar, hexoses, and sweetness index increased significantly at early stages during fruit ripening. Transcriptome data showed that with an increase in fruit development and maturity, the expression levels of PeCWINV2, PeCWINV5, and PeN/AINV3 exhibited an up-regulated trend, especially for PeCWINV5 which showed highest abundance, this correlated with the accumulation of soluble sugar and sweetness index. Transient overexpression results demonstrated that the contents of fructose, glucose and sucrose increased in the pulp of PeCWINV5 overexpressing fruit. It is speculated that this cell wall invertase gene, PeCWINV5, may play an important role in sucrose unloading and hexose accumulation.ConclusionIn this study, we systematically identified INV genes in passion fruit for the first time and further investigated their physicochemical properties, evolution, and expression patterns. Furthermore, we screened out a key candidate gene involved in hexose accumulation. This study lays a foundation for further study on INV genes and will be beneficial on the genetic improvement of passion fruit breeding.

Comprehensive genomic analysis and expression profiling of the cytochrome P450 genes during abiotic stress and flavonoid biosynthesis in potato (Solanum tuberosum)

The research focused on the cytochrome P450 (CYP) superfamily, a prominent enzyme family involved in plant metabolism. A total of 253 StCYP genes from the potato genome were investigated and characterized through various methods, including phylogentic analysis, physical and chemical characterization, chromosome localization, gene structure and conserved protein domain classification, gene duplication occurrences, collinearity and expression pattern analysis. The 253 StCYPs were classified into seven clans and 33 families, distributed unevenly across 12 chromosomes. Collinearity analysis revealed 28 pairs of orthologous genes between potato StCYPs and Arabidopsis AtCYPs. Moreover, the expression of the StCYPs in various tissue parts of doubled haploid (DM) potatoes under abiotic stress and exogenous hormone treatment was investigated by using RNA-seq data from the PGSC database. It was discovered that one StCYP gene likely contributes to drought stress response through the ABA-dependent pathway. Furthermore, RNA-seq analysis of pigmented tuber flesh from three potato clones at three developmental stages enabled the identification of StCYPs potentially implicated in the flavonoid biosynthesis in potato tubers. In particular, StCYP705A-like was further validated for its potential role in this process. Employing Gfanno software in conjunction with RNA-seq data, seven StCYP genes (Two StC4H, three StF3′H, one StFNS Ⅱ and one StF3′5′H) were identified as flavonoid biosynthetic pathway genes in potato. Additionally, five StCYPs in CYP 71 clan demonstrated a strong association with flavonoid biosynthesis. These findings lay a groundwork for a more comprehensive understanding of the StCYP gene family and further exploration of the functions of StCYP genes in potato abiotic stress tolerance and flavonoids biosynthesis.

Decoding 11-Oxygenated Androgen Synthesis: Insights from Enzyme Gene Expression and LC‒MS/MS Quantification.

Adrenal-origin and peripheral tissue-transformed 11-oxygenated androgens are recognized as significant androgens. However, our current understanding of the synthesis of 11-oxygenated androgens, including the organs and cell types involved, remains limited. We performed comprehensive analyses on an extensive dataset of normal human tissues, which included bulk RNA data from 30 tissues, single-cell RNA sequencing (scRNA) data from 16 tissues and proteomics data from 29 tissues, to characterize the expression profiles of enzyme-encoding genes. To validate the findings, immunohistochemical and liquid chromatography-tandem mass spectrometry (LC‒MS/MS) techniques were employed. Our investigation revealed that the gene expression levels of the enzymes HSD11B2 and AKR1C3 were notably elevated in the kidney and intestines. Intriguingly, within these organs, we observed an increasing trend in enzyme expression with age in women, while a decreasing trend was apparent in men. Sc-RNA analysis revealed that HSD11B2 was predominantly expressed in collecting duct principal cells in the kidney, while AKR1C3 was primarily expressed in the proximal tubules. Intriguingly, nearly all epithelial cells in the intestine expressed these key enzymes. Further analysis using LC‒MS/MS revealed that the kidney exhibited the highest levels of 11-ketoandrostenedione (11KA4) and 11-ketotestosterone (11KT) among the seven tissues examined, and substantial synthesis of 11KA4 and 11KT was also observed in the intestine. Finally, we developed the TransMap website (http://gxmujyzmolab.cn:16245/TransMap/) to provide comprehensive visualization of all currently available transcriptome data. This study offers an overarching perspective on tracing the synthesis of 11-oxygenated androgens in peripheral tissues, thereby providing valuable insights into the potential role of these androgens in humans.

Selection of Reference Genes in Siraitia siamensis and Expression Patterns of Genes Involved in Mogrosides Biosynthesis.

Siraitia siamensis is a traditional Chinese medicinal herb. In this study, using S. siamensis cultivated in vitro, twelve candidate reference genes under various treatments were analyzed for their expression stability by using algorithms such as GeNorm, NormFinder, BestKeeper, Delta CT, and RefFinder. The selected reference genes were then used to characterize the gene expression of cucurbitadienol synthase, which is a rate-limiting enzyme for mogroside biosynthesis. The results showed that CDC6 and NCBP2 expression was the most stable across all treatments and are the best reference genes under the tested conditions. Utilizing the validated reference genes, we analyzed the expression profiles of genes related to the synthesis pathway of mogroside in S. siamensis in response to a range of abiotic stresses. The findings of this study provide clear standards for gene expression normalization in Siraitia plants and exploring the rationale behind differential gene expression related to mogroside synthesis pathways.

Profile of gene expression at the berry enlargement phase of the large berry mutant of ‘Delaware’ grape

Profile of gene expression at the berry enlargement phase of the large berry mutant of ‘Delaware’ grape

Arbuscular mycorrhizal fungi alter carbon metabolism and invertase genes expressions of Populus simonii × P. nigra under drought stress.

Arbuscular mycorrhizal fungi (AMF) play a crucial role in regulating the allocation of carbon between source and sink tissues in plants and in regulating their stress responses by changing the sucrose biosynthesis, transportation, and catabolism in plants. Invertase, a key enzyme for plant development, participates in the response of plants to drought stress by regulating sucrose metabolism. However, the detailed mechanisms by which INV genes respond to drought stress in mycorrhizal plants remain unclear. This study examined the sugar content, enzyme activity, and expression profiles of INV genes of Populus simonii × P. nigra (PsnINVs) under two inoculation treatments (inoculation or non-inoculation) and two water conditions (well-watered or drought stress). Results showed that under drought stress, AMF up-regulated the expressions of PsnA/NINV1, PsnA/NINV2, PsnA/NINV3, and PsnA/NINV5 in leaves, which may be related to the enhancement of photosynthetic capacity. Additionally, AMF up-regulated the expressions of PsnA/NINV6, PsnA/NINV10, and PsnA/NINV12 in leaves, which may be related to enhancing osmotic regulation ability and drought tolerance.