Expression Profiles Of Genes Research Articles

Immune response and protection efficacy of formalin-killed vaccines against Streptococcus iniae in four-finger threadfin Eleutheronema tetradactylum.

Four-finger threadfin, Eleutheronema tetradactylum farming in southern Taiwan has been facing disease problems caused by Streptococcus iniae since 2018. The development of a vaccine against infectious S. iniae in the cultured threadfin industry is necessary. Thus, this study aimed to examine the efficacy of threadfin immunized formalin-killed cells (FKC) from S. iniae GSI-111 for 42 days post-vaccination (dpv) using two doses of FKC alone (a booster at 14 dpv) as group A, and FKC mixed with ISA763A adjuvant using a single dose as group B or double doses as group C. Immunoglobulin (Ig)-M was purified from threadfin, and rabbit anti-threadfin IgM polyclonal antibodies were used to detect antibody level in immunized fish; the vaccinated group A displayed higher levels at 3 dpv and all vaccinated treatments demonstrated high antibody levels between 14 and 42 dpv. All vaccine groups showed significantly higher values of lysozyme activity at 42 dpv compared with the control group; the vaccinated A group peaked at 14 dpv. The expression profiles of pro-inflammatory and immune-related genes, TNF-α, IL-12A, and C2 were upregulated at 3 dpv, while CD8A and chemokine receptor CXCR4 were upregulated at 42 dpv. Finally, the threadfins were challenged with S. iniae at 42 dpv. The average relative percent survival was 96% for vaccination A and B treatments, and 100% for vaccination C treatment. In summary, this study demonstrated that FKC vaccines whether formulated with an adjuvant could stimulate immune response and effective protect threadfins against S. iniae infection.

Multi-Omics analysis reveals the important role of indole-3-acetic acid homeostasis in male fertility of cotton

Auxin (Indole-3-acetic acid, IAA) is essential for anther development and male fertility, but little is known about its homeostasis in developing anthers due to its complex and diverse synthesis pathways. Here, we employed transcriptomic, targeted metabolomic, and amino acid analyses on a wild type (WT) cotton (Gossypium hirsutum) line SD98–6 and its nearly-isogenic male sterile (MS) line SD98–6A, to delve into the relationship between IAA and anther fertility. In WT anthers, IAA homeostasis was achieved mainly through self-synthesis, conjugate hydrolysis, and polar transport, and accumulation of IAA exhibited an inverted "U" pattern with the highest content observed at the tetrad stage. In MS anthers, no IAA accumulation was observed after the meiosis stage and the IAA content remained constantly low, mainly due to reduction of the substrates (phenylalanine and tryptophan) for IAA synthesis, and significantly decreased expression of the genes involved in IAA synthesis. Meanwhile, carbohydrate metabolism pathways directly contributing to IAA synthesis and synthesis of amino acids were malfunctional in MS anthers based on the expression profile of the metabolic genes and content measurement. These results provide valuable insights into the IAA homeostasis in cotton anthers and imply that genes related to IAA homeostasis are potential targets for development of IAA-sensitive male sterile cotton lines.

A first de novo transcriptome assembly of feijoa (Acca sellowiana [Berg] Burret) reveals key genes involved in flavonoid biosynthesis.

Acca sellowiana [Berg] Burret, a cultivated fruit tree originating from South America, is gaining the attention of the nutraceutical and pharmaceutical industries due to their high content of flavonoids and other phenolic compounds in fruits, leaves, and flowers. Flavonoids are a diverse group of secondary metabolites with antioxidant, anti-inflammatory, and antimicrobial properties. They also play a crucial role in plant immune response. Despite their importance, the lack of research on A. sellowiana genomics and transcriptomics hinders a deeper understanding of the molecular mechanisms behind flavonoid biosynthesis and its regulation. Here, we de novo assembled and benchmarked 11 A. sellowiana transcriptomes from leaves and floral tissues at three developmental stages using high-throughput sequencing. We selected and annotated the best assembly according to commonly used metrics and databases. This reference transcriptome consisted of 221,649 nonredundant transcripts, of which 107,612 were functionally annotated. We then used this reference transcriptome to explore the expression profiling of key secondary metabolite genes. Transcripts from genes involved in the flavonoid and anthocyanin biosynthesis pathways were identified. We also identified 4068 putative transcription factors, with the most abundant families being bHLH, C2H2, NAC, MYB, and MYB-related. Transcript expression profiling revealed distinct patterns of gene expression during flower development. Particularly, we found 71 differentially expressed transcripts representing 14 enzymes of the flavonoid pathway, suggesting major changes in flavonoid accumulation across floral stages. Our findings will contribute to understanding the genetic basis of flavonoids and provide a foundation for further research and exploitation of the economic potential of this species.

Molecular Susceptibility and Treatment Challenges in Melanoma.

Melanoma is the most aggressive subtype of cancer, with a higher propensity to spread compared to most solid tumors. The application of OMICS approaches has revolutionized the field of melanoma research by providing comprehensive insights into the molecular alterations and biological processes underlying melanoma development and progression. This review aims to offer an overview of melanoma biology, covering its transition from primary to malignant melanoma, as well as the key genes and pathways involved in the initiation and progression of this disease. Utilizing online databases, we extensively explored the general expression profile of genes, identified the most frequently altered genes and gene mutations, and examined genetic alterations responsible for drug resistance. Additionally, we studied the mechanisms responsible for immune checkpoint inhibitor resistance in melanoma.

Immune checkpoint gene signature assesses immune infiltration profiles in bladder cancer and identifies KRT23 as an immunotherapeutic target

BackgroundIn the past few decades, researchers have made promising progress, including the development of immune checkpoint inhibitors (ICIs) in the therapy of bladder cancer (BLCA). Existing studies mainly focus on single immune checkpoint inhibitors but lack relevant studies on the gene expression profiles of multiple immune checkpoints.MethodsRNA-sequencing profiling data and clinical information of BLCA patients and normal human bladder samples were acquired from the Cancer Genome Atlas and Gene Expression Omnibus databases and analyzed to identify different expression profiles of immune checkpoint genes (ICGs) after consensus clustering analysis. Based on the 526 intersecting differentially expressed genes, the LASSO Cox regression analysis was utilized to construct the ICG signature.ResultsAccording to the expression of ICGs, BLCA patients were divided into three subtypes with different phenotypic and mechanistic characteristics. Furthermore, the developed ICG signature were independent predictors of outcome in BLCA patients, and was correlated with the immune infiltration, the expression of ICGs and chemotherapeutic effect.ConclusionsThis study systematically and comprehensively analyzed the expression profile of immune checkpoint genes, and established the ICG signature to investigate the differences in ICGs expression and tumor immune microenvironment, which will help risk stratification and accelerate precision medicine. Finally, we identified KRT23 as the most critical model gene, and highlighted KRT23 as a potential target to enhance immunotherapy against BLCA.

Assessment of dietary yeast-based additives for cultured catfish and tilapia health.

Channel catfish (Ictalurus punctatus) and Nile tilapia (Oreochromis niloticus) are two aquaculture species of great importance. Intensive production is often hindered by poor growth performance and disease mortality. The aim of this study was to evaluate the potential of a commercial fermented yeast product, DVAQUA, on channel catfish and Nile tilapia growth performance metrics and disease resistance. Channel catfish and Nile tilapia were fed practical diets supplemented with 0%, 0.1% or 0.4% of DVAQUA over approximately 2-month feeding periods in recirculation aquaculture systems. To assess the potential of the postbiotic against common aquaculture pathogens, juvenile catfish were subsequently challenged by immersion with Edwardsiella ictaluri S97-773 or virulent Aeromonas hydrophila ML09-119. Nile tilapia juveniles were challenged by injection with Streptococcus iniae ARS-98-60. Serum lysozyme activity, blood chemistry and growth metrics were measured at the end of the feeding period, but no differences were observed across the different metrics, except for survival. For the pathogen challenges, there were no differences in endpoint mortality for channel catfish with either pathogen (p > .05). In contrast, Nile tilapia survivability to S. iniae infection increased proportionally to the inclusion of DVAQUA (p = .005). Changes to sera lysozyme activity were also noted in the tilapia trial, with a reduction of activity in the fish fed the 0.4% DVAQUA diet compared to the control diet (p = .031). Expression profiles of proinflammatory genes and antibodies were also found to be modulated in channel catfish fed the postbiotic, indicating some degree of protective response. These results suggest that this postbiotic may be beneficial in protecting Nile tilapia against S. iniae infection by influencing immune parameters and additional research is needed to evaluate the potential of this DVAQUA for improving catfish health and disease control.

Expression profile of IL2RA, FOXP3, PPARG, IL6, IL10, LRRC32 AND GATA3 genes in adipose tissue of patients with obesity and type 2 diabetes mellitus

Expression profile of IL2RA, FOXP3, PPARG, IL6, IL10, LRRC32 AND GATA3 genes in adipose tissue of patients with obesity and type 2 diabetes mellitus

Cross-talk between oxidative stress and lipid metabolism regulators reveals molecular clusters and immunological characterization in polycystic ovarian syndrome

BackgroundChanges in the oxidative stress and lipid metabolism (OSLM) pathways play important roles in polycystic ovarian syndrome (PCOS) pathogenesis and development. Consequently, a systematic analysis of genes related to OSLM was conducted to identify molecular clusters and explore new biomarkers that are helpful for the diagnostic of PCOS.MethodsGene expression and clinical data from 22 PCOS women and 14 normal women were obtained from the GEO database (GSE34526, GSE95728, and GSE106724). Consensus clustering identified OSLM-related molecular clusters, and WGCNA revealed co-expression patterns. The immune microenvironment was quantitatively assessed utilizing the CIBERSORT algorithm. Multiple machine learning models and connectivity map analyses were subsequently applied to explore potential biomarkers for PCOS, and nomograms were employed to develop a predictive multigene model of PCOS. Finally, the OSLM status of PCOS and the hub genes expression profiles were preliminarily verified using TUNEL, qRT‒PCR, western blot, and IHC assays in a PCOS mouse model.Results19 differential expression genes (DEGs) related to OSLM were identified. Based on 19 DEGs that were strongly influenced by OSLM, PCOS patients were stratified into two distinct clusters, designated Cluster 1 and Cluster 2. Distinct differences in the immune cell proportions existed in normal and two PCOS clusters. The random forest showed the best results, with the least cross-entropy and the utmost AUC (cross-entropy: 0.111 AUC: 0.960). Among the 19 OSLM-related genes, CXCR1, ACP5, CEACAM3, S1PR4, and TCF7 were identified by a Bayesian network and had a good fit with PCOS disease risk by the nomogram (AUC: 0.990 CI: 0.968–1.000). TUNEL assays revealed more severe DNA damage within the ovarian granule cells of PCOS mice than in those of normal mice (P < 0.001). The RNA and protein expression levels of the five hub genes were significantly elevated in PCOS mice, which was consistent with the results of the bioinformatics analyses.ConclusionA novel predictive model was constructed for PCOS patients and five hub genes were identified as potential biomarkers to offer novel insights into clinical diagnostic strategies for PCOS.

Cloning and expression profiling of voltage-gated sodium channel gene (VGSC) from Spodoptera frugiperda

Spodoptera frugiperda is a long-distance migratory pest with strong dispersal ability, fast reproduction speed and destructive feeding, so it is difficult to prevent and control. Pyrethroid insecticides are commonly used in pest insects control, And since the voltage-gated sodium channel (VGSC) serves as a major target of pyrethroids, it is important to study this gene for pest control. VGSC is an integral transmembrane protein consisting of approximately 2,000 amino acid residues found in neurons, myocytes, endocrine cells, and ovarian cells and involved in the initiation and propagation of excitable cellular action potentials. In this study, the cDNA sequence of the VGSC was identified from S. frugiperda by rapid amplification of cDNA ends (RACE) which contained an open reading frame of 6,261 bp encoding a protein of 2,086 amino acids. The molecular weight of this protein was predicted to be 236 kDa, and the theoretical isoelectric point was 5.21. A phylogenetic tree constructed based on lepidopteran insects showed that the VGSC of S. frugiperda was most closely relative to that of Spodoptera litura. VGSC is a highly conserved protein with Ion channel conserved structural domains of transmembrane proteins. qPCR showed that the VGSC gene was highly expressed in the epidermis of 2nd instar larvae, and its expression level was low in other tissues, such as the foregut and Malpighian tubules. In addition, VGSC was also detected in the prepupal stage, then gradually increased in abundance after entering the adult stage, peaked at the adult males on the 4th day of pupal stage, and decreased afterwards. The recombinant plasmid of pSumo-mut-VGSC was constructed and induced to express a His tag fused VGSC protein. Polyclonal antibodies were prepared from purified recombinant VGSC protein. The antibody was ELISA-titered, and the western blotting results showed that it specifically recognized VGSC, whether it was recombinant or endogenous protein. These results have laid the foundation for future studies on the physiological function of this gene in the growth and development of S. frugiperda.

Genome-wide identification of SHMT family genes in alfalfa (Medicago sativa) and its functional analyses under various abiotic stresses

BackgroundAlfalfa (Medicago sativa L.) is the most widely planted legume forage and one of the most economically valuable crops in the world. Serine hydroxymethyltransferase (SHMT), a pyridoxal phosphate-dependent enzyme, plays crucial roles in plant growth, development, and stress responses. To date, there has been no comprehensive bioinformatics investigation conducted on the SHMT genes in M. sativa.ResultsHere, we systematically analyzed the phylogenetic relationship, expansion pattern, gene structure, cis-acting elements, and expression profile of the MsSHMT family genes. The result showed that a total of 15 SHMT members were identified from the M. sativa genome database. Phylogenetic analysis demonstrated that the MsSHMTs can be divided into 4 subgroups and conserved with other plant homologues. Gene structure analysis found that the exons of MsSHMTs ranges from 3 to 15. Analysis of cis-acting elements found that each of the MsSHMT genes contained different kinds of hormones and stress-related cis-acting elements in their promoter regions. Expression and function analysis revealed that MsSHMTs expressed in all plant tissues. qRT-PCR analysis showed that MsSHMTs induced by ABA, Salt, and drought stresses.ConclusionsThese results provided definite evidence that MsSHMTs might involve in growth, development and adversity responses in M. sativa, which laid a foundation for future functional studies of MsSHMTs.

Metabolic role of the amino acids in the adaptation of Holstein dairy cows to two contrasting challenging situations

This thesis investigated the role of the amino acids (AA) during the transition period and lactation under grazing conditions, and heat stress (HS) as two contrasting challenging situations for the dairy cow. In the experiment 1, the branched-chain AA (BCAA) metabolism was studied in North American (NAH) vs. New Zealand (NZH) Holstein cows between -45 and 180 days in milk (DIM). Higher plasma concentrations of BCAA were confirmed in NAH vs. NZH in early lactation. The temporal profile of hepatic gene expression of specific BCAA transporters, especially LAT1 and Eeg1, differed between the genetic strains in association with the level of somatotropic axis uncoupling and insulin resistance in the liver. In the experiments 2 and 3, we studied the role of the metabolism of the AA against HS and its amelioration through nutritional strategies under controlled conditions. The plasma and milk metabolomics indicated that the HS triggered skeletal muscle mobilization and enhanced AA catabolism. Dietary supply of vitamin E and Se above requirements seemed to have modulated the skeletal muscle mobilization, while D3 and Ca did not show significant effects (experiment 2). The results of experiment 3 suggested that the partial amelioration of HS effects on productive and physiological parameters through high dietary supply of Met (+70 %), Lys (+65 %) and His (+21 %) were mediated by a recovery of phosphatidylcholines and decreased oxidation of Val, Trp and Leu due to enhanced one-carbon metabolism and Lys oxidation, respectively.

Voltage-gated ion channel’s gene expression in the myocardium of embryo and adult chickens

The functioning of the cardiovascular system is critical for embryo survival. Cardiac contractions depend on the sequential activation of different classes of voltage-gated ion channels. Understanding the fundamental features of these interactions is important for identifying the mechanisms of pathologies development in the myocardium. However, at present there is no consensus on which ion channels are involved in the formation of automaticity in the early embryonic stages. The aim of this study was to elucidate the expression of genes encoding various types of ion channels that are involved in the generation of electrical activity chicken heart at different stages of ontogenesis. We analyzed the expression of 14 genes from different families of ion channels. It was revealed that the expression profiles of ion channel genes change depending on the stages of ontogenesis. The HCN4, CACNA1D, SCN1A, SCN5A, KCNA1 genes have maximum expression at the tubular heart stage. In adult, a switch occurs to the higher expression of CACNA1C, KCNH6, RYR and SLC8A1 genes. This data correlated with the results obtained by the microelectrode method. It can be assumed that the automaticity of the tubular heart is mainly due to the mechanism of the «membrane–clock» (hyperpolarization-activated current (If), Ca2+–current L–type (ICaL), Na+–current (INa) and the slow component of the delayed rectifier K+–current (IKs)). Whereas in adult birds, the mechanism for generating electrical impulses is determined by both « membrane– clock» and «Ca2+–clock».

Interference of skeleton photoperiod in circadian clock and photosynthetic efficiency of tea plant: in-depth analysis of mathematical model.

The circadian system of plants is a complex physiological mechanism, a biological process in which plants can adjust themselves according to the day and night cycle. To understand the effects of different photoperiods on the biological clock of tea plants, we analyzed the expression levels of core clock genes (CCA1, PRR9, TOC1, ELF4) and photosynthesis-related genes (Lhcb, RbcS, atpA) under normal light (light/dark = 12h/12h, 12L12D) and took the cost function defined by cycle and phase errors as the basic model parameter. In the continuous light environment (24h light, 24L), the peak activity and cycle of key genes that control the biological clock and photosynthesis were delayed by 1-2h. Under a skeleton photoperiod (6L6D, 3L3D), the expression profiles of clock genes and photosynthesis-related genes in tea plants were changed and stomatal opening showed a circadian rhythm. These observations suggest that a skeleton photoperiod may have an effect on the circadian rhythm, photosynthetic efficiency and stomatal regulation of tea plants. Our study and model analyzed the components of circadian rhythms under different photoperiodic pathways, and also revealed the underlying mechanisms of circadian regulation of photosynthesis in tea plants.

Transcriptome Profiling of Gene Expression in Atlantic Salmon (Salmo salar) at Early Stage of Development.

For Atlantic salmon development, the most critical phase is the early development stage from egg to fry through alevin. However, the studies investigating the early development of Atlantic salmon based on RNA-seq are scarce and focus only on one stage of development. Therefore, using the RNA-seq technology, the assessment of different gene expressions of various early development stages (egg, alevin, and fry) was performed on a global scale. Over 22GB of clean data was generated from 9 libraries with three replicates for each stage with over 90% mapping efficiency. A total of 5534 genes were differentially expressed, among which 19, 606, and 826 genes were specifically expressed in each stage, respectively. The transcriptome analysis showed that the number of differentially expressed genes (DEGs) increased as the Atlantic salmon progressed in development from egg to fry stage. In addition, gene ontology enrichment demonstrated that egg and alevin stages are characterized by upregulation of genes involved in spinal cord development, neuron projection morphogenesis, axonogenesis, and cytoplasmic translation. At the fry stage, upregulated genes were enriched in the muscle development process (muscle cell development, striated muscle cell differentiation, and muscle tissue development), immune system (defense response and canonical NF-kappaB signal transduction), as well as epidermis development. These results suggest that the early development of Atlantic salmon is characterized by a dynamic shift in gene expression and DEGs between different stages, which provided a solid foundation for the investigation of Atlantic salmon development.

Single-cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer's risk gene mutation.

The R47H missense mutation of the TREM2 gene is a known risk factor for development of Alzheimer's Disease. In this study, we analyze the impact of the Trem2R47H mutation on specific cell types in multiple cortical and subcortical brain regions in the context of wild-type and 5xFAD mouse background. We profile 19 mouse brain sections consisting of wild-type, Trem2R47H, 5xFAD and Trem2R47H; 5xFAD genotypes using MERFISH spatial transcriptomics, a technique that enables subcellular profiling of spatial gene expression. Spatial transcriptomics and neuropathology data are analyzed using our custom pipeline to identify plaque and Trem2R47H-induced transcriptomic dysregulation. We initially analyzecell type-specific transcriptomic alterations induced by plaque proximity. Next, we analyze spatial distributions of disease associated microglia and astrocytes, and how they vary between 5xFAD and Trem2R47H; 5xFAD mouse models. Finally, we analyze the impact of the Trem2R47H mutationon neuronal transcriptomes. The Trem2R47H mutation induces consistent upregulation of Bdnf and Ntrk2 across many cortical excitatory neuron types, independent of amyloid pathology. Spatial investigation of genotype enriched subclusters identified spatially localized neuronal subpopulations reduced in 5xFAD and Trem2R47H; 5xFAD mice. Overall, our MERFISH spatial transcriptomics analysis identifies glial and neuronal transcriptomic alterations induced independently by 5xFAD and Trem2R47H mutations, impacting inflammatory responses in microglia and astrocytes, and activity and BDNF signaling in neurons.

Nitrogen limitation-induced adaptive response and lipogenesis in the Antarctic yeast Rhodotorula mucilaginosa M94C9.

The extremotolerant red yeast Rhodotorula mucilaginosa displays resilience to diverse environmental stressors, including cold, osmolarity, salinity, and oligotrophic conditions. Particularly, this yeast exhibits a remarkable ability to accumulate lipids and carotenoids in response to stress conditions. However, research into lipid biosynthesis has been hampered by limited genetic tools and a scarcity of studies on adaptive responses to nutrient stressors stimulating lipogenesis. This study investigated the impact of nitrogen stress on the adaptive response in Antarctic yeast R. mucilaginosa M94C9. Varied nitrogen availability reveals a nitrogen-dependent modulation of biomass and lipid droplet production, accompanied by significant ultrastructural changes to withstand nitrogen starvation. In silico analysis identifies open reading frames of genes encoding key lipogenesis enzymes, including acetyl-CoA carboxylase (Acc1), fatty acid synthases 1 and 2 (Fas1/Fas2), and acyl-CoA diacylglycerol O-acyltransferase 1 (Dga1). Further investigation into the expression profiles of RmACC1, RmFAS1, RmFAS2, and RmDGA1 genes under nitrogen stress revealed that the prolonged up-regulation of the RmDGA1 gene is a molecular indicator of lipogenesis. Subsequent fatty acid profiling unveiled an accumulation of oleic and palmitic acids under nitrogen limitation during the stationary phase. This investigation enhances our understanding of nitrogen stress adaptation and lipid biosynthesis, offering valuable insights into R. mucilaginosa M94C9 for potential industrial applications in the future.

Insights into immune microenvironment and therapeutic targeting in androgen-associated prostate cancer subtypes

Prostate cancer, one of the most prevalent malignancies among men worldwide, is intricately linked with androgen signaling, a key driver of its pathogenesis and progression. Understanding the diverse expression patterns of androgen-responsive genes holds paramount importance in unraveling the biological intricacies of this disease and prognosticating patient outcomes. In this study, utilizing consensus clustering analysis based on the expression profiles of androgen-responsive genes, prostate cancer patients from the TCGA database were stratified into two distinct subtypes, denoted as C1 and C2. Notably, the C1 subtype demonstrates a significant upregulation of certain genes, such as CGA and HSD17B12, along with a shorter progression-free survival duration, indicating a potentially unfavorable prognosis. Further analyses elucidated the immune infiltration disparities, mutation landscapes, and gene functional pathways characteristic of each subtype. Through integrated bioinformatics approaches and machine learning techniques, key genes such as BIRC5, CENPA, and MMP11 were identified as potential therapeutic targets, providing novel insights into tailored treatment strategies. Additionally, single-cell transcriptome analysis shed light on the heterogeneous expression patterns of these genes across different cell types within the tumor microenvironment. Furthermore, virtual screening identified candidate drugs targeting the BIRC5 receptor, offering promising avenues for drug development. Collectively, these findings deepen our understanding of prostate cancer biology, paving the way for personalized therapeutic interventions and advancing the quest for more effective treatments in prostate cancer management.

Evaluation and Validation of Reference Genes for Gene Expression Analysis Using qRT-PCR in the Sugarcane Stem Borer Chilo sacchariphagus (Lepidoptera: Pyralidae).

Chilo sacchariphagus (Lepidoptera: Pyralidae) is an economically important sugarcane pest. Although numerous studies were conducted on the physiological responses in C. sacchariphagus, little is known regarding the genes regulating these physiological processes. Gene expression analysis by qRT-PCR can offer a significant indication for functional gene studies. To our knowledge, the reference genes of C. sacchariphagus have not been screened or evaluated, which hinders the functional gene study. In the present study, the stability of seven reference genes (β-ACT, GAPDH, BTF3, 28S, RPL7, EF1α, and SDHA) was evaluated in C. sacchariphagus under different experimental conditions, including tissues (antenna, head, thorax, abdomen, leg, and wing), temperatures (4 °C, 25 °C, and 37 °C) and sexes (male and female), through RefFinder, which integrates four algorithms (Normfinder, BestKeeper, ΔCt method, and geNorm). The findings suggested that the combination of β-ACT and RPL7 is ideal to analyze gene expressions in different tissues and at distinct temperatures, and EF1α and SDHA were suitable reference genes for comparing gene expressions between sexes. Finally, the expression profiles of CsacPBP1 gene were evaluated, and the outcomes further confirm the importance of selecting fitting reference genes for normalization of qRT-PCR data. This study represents the first kind in screening out suitable reference genes for gene expression analysis in C. sacchariphagus. Information from this study is poised to galvanize future inquiry into the gene expression of C. sacchariphagus, an economically important pest of sugarcane.

DDX21 functions as a potential novel oncopromoter in pancreatic ductal adenocarcinoma: a comprehensive analysis of the DExD box family

BackgroundPancreatic ductal adenocarcinoma (PDAC) is a highly lethal tumor with an ill-defined pathogenesis. DExD box (DDX) family genes are widely distributed and involved in various RNA metabolism and cellular biogenesis; their dysregulation is associated with aberrant cellular processes and malignancies. However, the prognostic significance and expression patterns of the DDX family in PDAC are not fully understood. The present study aimed to explore the clinical value of DDX genes in PDAC.MethodsDifferentially expressed DDX genes were identified. DDX genes related to prognostic signatures were further investigated using LASSO Cox regression analysis. DDX21 protein expression was analyzed using the UALCAN and human protein atlas (HPA) online tools and confirmed in 40 paired PDAC and normal tissues through Tissue Microarrays (TMA). The independent prognostic significance of DDX21 in PDAC was determined through the construction of nomogram models and calibration curves. The functional roles of DDX21 were investigated using gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). Cell proliferation, invasion, and migration were assessed using Cell Counting Kit-8, colony formation, Transwell, and wound healing assays.ResultsUpregulation of genes related to prognostic signatures (DDX10, DDX21, DDX60, and DDX60L) was significantly associated with poor prognosis of patients with PDAC based on survival and recurrence time. Considering the expression profile and prognostic values of the signature-related genes, DDX21 was finally selected for further exploration. DDX21 was overexpressed significantly at both the mRNA and protein levels in PDAC compared to normal pancreatic tissues. DDX21 expression, pathological stage, and residual tumor were significant independent prognostic indicators in PDAC. Moreover, functional enrichment analysis revealed that Genes co-expressed with DDX21 are predominantly involved in RNA metabolism, helicase activity, ribosome biogenesis, cell cycle, and various cancer-related pathways, such as PI3K/Akt signaling pathway and TGF-β signaling pathway. Furthermore, in vitro experiments confirmed that the knockdown of DDX21 significantly reduced MIA PaCa-2 cell viability, proliferation, migration, and invasion.ConclusionsFour signature-related genes could relatively precisely predict the prognosis of patients with PDAC. Specifically, DDX21 upregulation may signal an unfavorable prognosis by negatively affecting the biological properties of PDAC cells. DDX21 may be considered as a candidate therapeutic target in PDAC.

Role of Rubus chingii BBX gene family in anthocyanin accumulation during fruit ripening.

The B-box (BBX) family, which is a class of zinc finger transcription factors, exhibits special roles in plant growth and development as well as in plants' ability to cope with various stresses. Even though Rubus chingii is an important traditional medicinally edible plant in east Asia, there are no comprehensive studies of BBX members in R. chingii. In this study, 32 RcBBX members were identified, and these were divided into five groups. A collinearity analysis showed that gene duplication events were common, and when combined with a motif analysis of the RcBBX genes, it was concluded that group V genes might have undergone deletion of gene fragments or mutations. Analysis of cis-acting elements revealed that each RcBBX gene contained hormone-, light-, and stress-related elements. Expression patterns of the 32 RcBBX genes during fruit ripening revealed that highest expression occurred at the small green fruit stage. Of note, the expression of several RcBBX genes increased rapidly as fruit developed. These findings, combined with the expression profiles of anthocyanin biosynthetic genes during fruit ripening, allowed us to identify the nuclear-targeted RcBBX26, which positively promoted anthocyanin production in R. chingii. The collective findings of this study shed light on the function of RcBBX genes in different tissues, developmental stages, and in response to two abiotic stresses.