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Background: Aedes (Stegomyia) albopictus (Skuse) is an invasive and widespread mosquito species that can transmit dengue, chikungunya, yellow fever, and Zika viruses. Its control heavily relies on the use of insecticides. However, the efficacy of the insecticide-based intervention is threatened by the increasing development of resistance to available insecticides. Understanding the current status and potential mechanisms of insecticide resistance is an important prerequisite for devising strategies to maintain the sustainability of vector control programs. In this study, we investigated the current status and probable candidate detoxification genes associated with insecticide resistance in the Asian tiger mosquito in Beijing, the capital city of China. Methods: Bioassays were conducted on three field populations of Ae. albopictus collected from urban communities in Beijing by exposure to diagnostic doses of permethrin, deltamethrin, malathion, and propoxur. Differentially expressed genes (DEGs) associated with insecticide resistance were screened by transcriptomic analysis using Illumina RNA sequencing data (RNA-seq) from 12 independent RNA libraries constructed from female strains of the three field populations and one susceptible strain. Results: The bioassay results indicated that all the three field populations were resistant to propoxur (carbamate), deltamethrin, and permethrin (pyrethroids), but susceptible to malathion (organophosphate). Eighteen (18) cytochrome P450s (P450s), five (5) glutathione S-transferases (GSTs), four (4) carboxy/cholinesterases (CCEs), eight (8) UDP-glycosyltransferases (UGTs), and three (3) ATP-binding cassette transporters (ABCs) were found to be significantly overexpressed in the three field populations relative to the susceptible strain via transcriptomic analysis. Conclusion: This study demonstrates that the Ae. albopictus field populations in Beijing exhibit multiple phenotypic resistance to commonly used pyrethroids and carbamate. The identification of a number of DEGs associated with insecticide resistance indicates that the mechanisms underlying resistance in field populations are complicated, and detoxifying enzymes may play important roles. The multiple resistance status detected in the three field populations suggests that resistance management strategies such as insecticide rotation and non-chemical-based measures should be implemented in order to sustain effective control of the disease vector and vector-borne diseases. [ABSTRACT FROM AUTHOR]

In allotetraploid common carp, protein-coding homoeologs presented divergent expression levels between the two subgenomes. However, whether subgenome dominance occurs in other transcriptional and post-transcriptional events remains unknown. Using Illumina RNA sequencing and PacBio full-length sequencing, we refined the common carp transcriptome annotation and explored differences in four transcriptional and post-transcriptional events between the two subgenomes. The results revealed that the B subgenome presented more alternative splicing events, as did lncRNAs and circRNAs. However, the expression levels, tissue specificity, sequence features, and functions of lncRNAs and circRNAs did not significantly differ between the two subgenomes, suggesting a common regulatory mechanism shared by the two subgenomes. Furthermore, both the number and base substitution frequency of RNA editing events were greater in the B subgenome. Functional analyses of these transcriptional events also revealed subgenome bias. Genes that undergo alternative splicing in the A subgenome participate in more biological processes, and lncRNA targets show a preference between subgenomes. CircRNA host genes in the B subgenome were associated with more biological functions, and RNA editing preferentially occurred in noncoding regions or led to nonsynonymous mutations in the B subgenome. Taken together, the refined transcriptome annotation revealed complicated and imbalanced expression strategies in allotetraploid common carp. Comprehensive transcriptomic analysis revealed distinct patterns in expression, regulation, and function of alternative splicing, lncRNA, circRNA,and RNA editing events between the two subgenomes of allotetraploid common carp. [ABSTRACT FROM AUTHOR]

Faba bean is an important pulse. It provides proteins for the human diet and is used in industrial foodstuffs, such as flours. Drought stress severely reduces the yield of faba bean, and this can be efficiently overcome through the identification and application of key genes in response to drought. In this study, PacBio and Illumina RNA sequencing techniques were used to identify the key pathways and candidate genes involved in drought stress response. During seed germination, a total of 17,927 full-length transcripts and 12,760 protein-coding genes were obtained. There were 1676 and 811 differentially expressed genes (DEGs) between the varieties E1 and C105 at 16 h and 64 h under drought stress, respectively. Six and nine KEGG pathways were significantly enriched at 16 h and 64 h under drought stress, which produced 40 and 184 nodes through protein–protein interaction (PPI) analysis, respectively. The DEGs of the PPI nodes were involved in the ABA (abscisic acid) and MAPK (mitogen-activated protein kinase) pathways, N-glycosylation, sulfur metabolism, and sugar metabolism. Furthermore, the ectopic overexpression of a key gene, AAT, encoding aspartate aminotransferase (AAT), in tobacco, enhanced drought tolerance. The activities of AAT and peroxidase (POD), the contents of cysteine and isoleucine, were increased, and the contents of malonaldehyde (MDA) and water loss decreased in the overexpressed plants. This study provides a novel insight into genetic response to drought stress and some candidate genes for drought tolerance genetic improvements in this plant. [ABSTRACT FROM AUTHOR]

Oxidative stress represents a critical facet of the array of abiotic stresses affecting crop growth and yield. In this paper, we investigated the potential differences in the functions of two highly homologous Arabidopsis DSS1 proteins in terms of maintaining genome integrity and response to oxidative stress. In the context of homologous recombination (HR), it was shown that overexpressing AtDSS1(I) using a functional complementation test increases the resistance of the Δdss1 mutant of Ustilago maydis to genotoxic agents. This indicates its conserved role in DNA repair via HR. To investigate the global transcriptome changes occurring in dss1 plant mutant lines, gene expression analysis was conducted using Illumina RNA sequencing technology. Individual RNA libraries were constructed from three total RNA samples isolated from dss1(I), dss1(V), and wild-type (WT) plants under hydrogen peroxide-induced stress. RNA-Seq data analysis and real-time PCR identification revealed major changes in gene expression between mutant lines and WT, while the dss1(I) and dss1(V) mutant lines exhibited analogous transcription profiles. The Kyoto Encyclopedia of Genes and Genomes enrichment analysis revealed significantly enriched metabolic pathways. Notably, genes associated with HR were upregulated in dss1 mutants compared to the WT. Otherwise, genes of the metabolic pathway responsible for the synthesis of secondary metabolites were downregulated in both dss1 mutant lines. These findings highlight the importance of understanding the molecular mechanisms of plant responses to oxidative stress. [ABSTRACT FROM AUTHOR]

Drought stress can significantly affect plant growth, development, and yield. Fewer comparative studies have been conducted between different species of pines, particularly involving Pinus yunnanensis var. pygmaea (P. pygmaea). In this study, the physiological indices, photosynthetic pigment and related antioxidant enzyme changes in needles from P. pygmaea, P. elliottii and P. massoniana under drought at 0, 7, 14, 21, 28 and 35 d, as well as 7 days after rehydration, were measured. The PacBio single-molecule real-time (SMRT) and Illumina RNA sequencing were used to uncover the gene expression differences in P. pygmaea under drought and rehydration conditions. The results showed that the total antioxidant capacity (TAOC) of P. pygmaea was significantly higher than P. massoniana and P. elliottii. TAOC showed a continuous increase trend across all species. Soluble sugar (SS), starch content and non-structural carbohydrate (NSC) of all three pines displayed a "W" pattern, declining initially, increasing, and then decreasing again. P. pygmaea exhibits stronger drought tolerance and greater recovery ability under prolonged drought conditions. Through the PacBio SMRT-seq, a total of 50,979 high-quality transcripts were generated, and 6,521 SSR and 5,561 long non-coding RNAs (LncRNAs) were identified. A total of 2310, 1849, 5271, 5947, 7710, and 6854 differentially expressed genes (DEGs) were identified compared to the control (Pp0D) in six pair-wise comparisons of treatment versus control. bHLH, NAC, ERF, MYB_related, C3H transcription factors (TFs) play an important role in drought tolerance of P. pygmaea. KEGG enrichment analysis and Gene set enrichment analysis (GSEA) analysis showed that P. pygmaea may respond to drought by enhancing metabolic processes such as ABA signaling pathway, alpha-linolenic acid. Weighted gene co-expression network analysis (WGCNA) revealed GST, CAT, LEC14B, SEC23 were associated with antioxidant enzyme activity and TAOC. This study provides a basis for further research on drought tolerance differences among coniferous species. [ABSTRACT FROM AUTHOR]

The larval waste, exoskeleton shedding, and leftover feed components of the black soldier fly and its larvae make up the by-product known as frass. In this study, we subjected channel catfish (Ictalurus punctatus) to a 10-week feeding trial to assess how different dietary amounts of frass inclusion would affect both systemic and mucosal tissue gene expression, especially in regard to growth and immunerelated genes. Fish were divided in quadruplicate aquaria, and five experimental diets comprising 0, 50, 100, 200, and 300 g of frass per kilogram of feed were fed twice daily. At the end of the trial, liver, head kidney, gill, and intestine samples were collected for gene expression analyses. First, liver and intestine samples from fish fed with a no frass inclusion diet (control), low-frass (50 g/kg) inclusion diet, or a high-frass (300 g/kg) inclusion diet were subjected to Illumina RNA sequencing to determine global differential gene expression among diet groups. Differentially expressed genes (DEGs) included the upregulation of growth-related genes such as glucose-6-phosphatase and myostatin, as well as innate immune receptors and effector molecules such as toll-like receptor 5, apolipoprotein A1, C-type lectin, and lysozyme. Based on the initial screenings of low/high frass using RNA sequencing, a more thorough evaluation of immune gene expression of all tissues sampled, and all levels of frass inclusion, was further conducted. Using targeted quantitative PCR panels for both innate and adaptive immune genes from channel catfish, differential expression of genes was identified, which included innate receptors (TLR1, TLR5, TLR9, and TLR20A), proinflammatory cytokines (IL-1ß type a, IL-1ß type b, IL-17, IFN-1, and TNFa), chemokines (CFC3 and CFD), and hepcidin in both systemic (liver and head kidney) and mucosal (gill and intestine) tissues. Overall, frass from black soldier fly larvae inclusion in formulated diets was found to alter global gene expression and activate innate and adaptive immunity in channel catfish, which has the potential to support disease resistance in this species in addition to demonstrated growth benefits. [ABSTRACT FROM AUTHOR]

Mice have emerged as a widely employed model for investigating various retinal diseases. However, the availability of comprehensive datasets capturing the entire developmental and aging stages of the mouse retina, particularly during the elderly period, encompassing integrated lncRNA and mRNA expression profiles, is limited. In this study, we assembled a total of 18 retina samples from mice across 6 distinct stages of development and aging (5 days, 3 weeks, 6 weeks, 10 weeks, 6 months, and 15 months) to conduct integrated lncRNA and mRNA sequencing analysis. This invaluable dataset offers a comprehensive transcriptomic resource of mRNA and lncRNA expression profiles during the natural progression of retinal development and aging. The discoveries stemming from this investigation will significantly contribute to the elucidation of the underlying molecular mechanisms associated with various retinal diseases, such as congenital retinal dysplasia and retinal degenerative diseases. Design Type(s) organism development and aging design • transcriptional profiling by RNA sequencing design Measurement Type(s) long noncoding RNA and mRNA profiling assay Technology Type(s) illumina RNA sequencing Factor Type(s) life cycle stage Sample Characteristic(s) Mus musculus • retina [ABSTRACT FROM AUTHOR]

Simple Summary: Diaphorina citri is an important transmission vector of Candidatus Liberibacter asiaticus (CLas), the causal agent of citrus Huanglongbing (HLB). The control of HLB mainly depends on the management of D. citri. The efficiency of D. citri nymphs in acquiring CLas bacteria is significantly higher than that of the adults, while the transmission efficiency of CLas bacteria by adults is significantly higher than that of nymphs. Therefore, it is of great significance to research the functions of key genes during the molting of fifth-instar nymphs. In this study, SMRT and Illumina sequencing were performed on D. citri fifth-instar nymphs and adults. SMRT-Seq-generated full-length transcripts provide valuable information for improving functional gene research in D. citri. Additionally, Illumina sequencing revealed that the Hippo pathway played an important role in regulating the transition of D. citri from fifth-instar nymphs to adults. Our findings provide useful reference information and lay a foundation for controlling D. citri. Huanglongbing (HLB) is a systemic plant disease caused by 'Candidatus Liberibacter asiaticus (CLas)' and transmitted by Diaphorina citri. D. citri acquires the CLas bacteria in the nymph stage and transmits it in the adult stage, indicating that molting from the nymph to adult stages is crucial for HLB transmission. However, the available D. citri reference genomes are incomplete, and gene function studies have been limited to date. In the current research, PacBio single-molecule real-time (SMRT) and Illumina sequencing were performed to investigate the transcriptome of D. citri nymphs and adults. In total, 10,641 full-length, non-redundant transcripts (FLNRTs), 594 alternative splicing (AS) events, 4522 simple sequence repeats (SSRs), 1086 long-coding RNAs (lncRNAs), 281 transcription factors (TFs), and 4459 APA sites were identified. Furthermore, 3746 differentially expressed genes (DEGs) between nymphs and adults were identified, among which 30 DEGs involved in the Hippo signaling pathway were found. Reverse transcription–quantitative PCR (RT-qPCR) further validated the expression levels of 12 DEGs and showed a positive correlation with transcriptome data. Finally, the spatiotemporal expression pattern of genes involved in the Hippo signaling pathway exhibited high expression in the D. citri testis, ovary, and egg. Silencing of the D. citri transcriptional co-activator (DcYki) gene significantly increased D. citri mortality and decreased the cumulative molting. Our results provide useful information and a reliable data resource for gene function research of D. citri. [ABSTRACT FROM AUTHOR]

In termites with a true worker caste, the development pattern splits up from early developmental stages: primary reproductives develop through the nymphal line, whereas workers and soldiers follow the apterous developmental line. In some species, such as Cavitermes tuberosus Emerson (Isoptera: Termitidae, Termitinae), secondary reproductives (or neotenics) may also develop through the nymphal line from a transitional stage called aspirant. Aspirants originate mostly from automictic parthenogenetic reproduction. Therefore, C. tuberosus queens originate from sexual (primary queens) or parthenogenetic (neotenic queens) reproduction. A comparison of these two queen castes offers the possibility to better understand core molecular underpinnings of caste development and plasticity in termites. We investigated these molecular mechanisms by using high‐throughput Illumina RNA sequencing of pooled individuals. We first assembled the de novo reference transcriptome of C. tuberosus, and then identified the transcripts consistently co‐expressed across castes, sexes, and two alternative routes to female reproduction. Cavitermes tuberosus final transcriptome had 130 874 transcripts, N50 of 3398, and total length of 213 549 184 bp. We found that female reproductive maturation was characterized by gene expression down‐regulation: primary queens expressed fewer transcripts overall and had the greatest number of down‐regulated transcripts when compared to all other castes. In both secondary and primary queens, biological processes involved in muscle development and contraction, flight, and olfactory learning were enriched in the down‐regulated gene cluster. In contrast, processes related to reproductive development, insulin receptor signaling pathway, isoprenoid biosynthesis, and multiple metabolic processes were enriched among up‐regulated genes in primary queens. Finally, we found that 17% of all transcripts (21852) were differently co‐expressed when females from sexual and parthenogenetic origins were compared, even though the expression profile of core reproductive‐related gene clusters showed a similar trend in all reproductive females despite their origin. Our findings fit the genomic imprinting model predictions of a maternal effect that commonly regulates the expression of core reproductive genes in females from parthenogenetic and non‐parthenogenetic origins, whereas the expression of non‐reproductive genes varies. [ABSTRACT FROM AUTHOR]

Pinus elliottii , an important coniferous timber species, has recently become one of the most popular sources of resin in China. Resinosis is a common disease that may negatively affect pine tree growth and production. In this study, we used single-molecule real-time sequencing and Illumina RNA sequencing to generate an accurate transcriptome for P. elliottii. The transcriptome included 90,026 transcripts, 5160 long non-coding RNAs and 7710 transcription factors. We then analyzed RNA-sequencing, small RNA-sequencing and degradome data to identify genes, miRNAs and key miRNA–target pairs involved in response to resinosis in P. elliottii. We identified 1305 genes and 1151 miRNAs exhibiting significant differential expression in response to resinosis. According to the degradome sequencing analysis, 318 differentially expressed transcripts were targets of 14 differentially expressed miRNAs. Our study has provided resources for further functional characterization of genes and miRNAs involved in resinosis in P. elliottii , which should aid the future disease-resistance breeding of this species. [ABSTRACT FROM AUTHOR]

Thuja koraiensis Nakai (Cupressaceae) is an endangered and ecologically important conifer endemic to Korea. Previously, we established a protocol for micropropagation in T. koraiensis, which involved somatic embryogenesis from embryogenic callus of T. koraiensis. However, the molecular mechanisms underlying somatic embryogenesis remain unclear. Herein, we performed transcriptomic analysis to identify somatic embryogenesis-related genes of T. koraiensis via Illumina RNA sequencing. We conducted de novo transcriptome assembly using a Trinity assembler, which produced 274,077 transcript contigs clustered into 205,843 transcripts (unigenes), with an average length of 825 base pairs. Of all the unigenes, 14.69%, 18.62%, and 7.4% had homologs in the Gene Ontology, NCBI Non-redundant Protein, and NCBI Nucleotide databases, respectively. Among these mRNA sequences, expression of putative embryogenesis-associated transcription factors, namely BABYBOOM (BBM), WUSCHEL-RELATED HOMEOBOX (WOX), and SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE (SERK), was analyzed during somatic embryogenesis. RT-PCR analysis revealed that TkBBM, TkWOX, and TkSERK were highly expressed in embryogenic callus and seedling roots, whereas their expression was reduced in seedling leaves. Our findings provide new insights into the roles of BBM, WOX, and SERK in somatic embryogenesis. Our results may serve as a reference for comparative transcriptome analysis in related species and further aid functional genomics studies in conifers. [ABSTRACT FROM AUTHOR]

Mikania micrantha is a notorious invasive weed that has caused huge economic loss and negative ecological consequences in invaded areas. This species can adapt well to invasive environments with various stress factors. The identification of gene families and functional pathways related to environmental adaptability is lack in M. micrantha at the multi-organ full-length transcriptome level. In this study, we sequenced the transcriptomes of five M. micrantha organs using PacBio single-molecule real-time sequencing and Illumina RNA sequencing technologies. Based on the transcriptome data, full-length transcripts were captured and gene expression patterns among the five organs were analyzed. KEGG enrichment analysis of genes with higher expression indicated their special roles in environmental stress response and adversity adaptation in the various five organs. The gene families and pathways related to biotic and abiotic factors, including terpene synthases, glutathione S-transferases, antioxidant defense system, and terpenoid biosynthesis pathway, were characterized. The expression levels of most differentially expressed genes in the antioxidant defense system and terpenoid biosynthesis pathway were higher in root, stem, and leaf than in the other two organs, suggesting that root, stem, and leaf have strong ability to respond to adverse stresses and form the important organs of terpenoid synthesis and accumulation. Additionally, a large number of transcription factors and alternative splicing events were predicted. This study provides a comprehensive transcriptome resource for M. micrantha, and our findings facilitate further research on the adaptive evolution and functional genomics of this species. [ABSTRACT FROM AUTHOR]

Glioblastoma multiforme (GBM), the most prevalent primary malignant brain tumor in adults, exhibits a dismal 6.9% five-year survival rate post-diagnosis. Thymoquinone (TQ), the most abundant bioactive compound in Nigella sativa, has been extensively researched for its anticancer properties across various human cancers. However, its specific anti-cancer mechanisms and pathways in glioblastoma remain to be completely elucidated. In this study, we assessed the impact of different TQ concentrations on the viability of A172 cells using WST-8 and Toluidine blue assays, followed by RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs). We confirmed their expression levels through quantitative RT-PCR and performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses for these DEGs. RNA-seq revealed no significant gene expression changes at 2.5 μM and 5 μM TQ concentrations. However, at 25 μM and 50 μM, TQ significantly reduced cell viability dose-dependently. We identified 1548 DEGs at 25 μM TQ (684 up-regulated, 864 down-regulated) and 2797 DEGs at 50 μM TQ (1528 up-regulated, 1269 downregulated), with 1202 DEGs common to both concentrations. TQ inhibited key pathways such as PI3K-Akt signaling, calcium signaling, focal adhesion, and ECM-receptor interaction in A172 cells. It downregulated several potential oncogenes (e.g., AEBP1, MIAT) and genes linked to GBM proliferation and migration (e.g., SOCS2, HCP5) while modulating Wnt signaling and up-regulating tumor suppressor genes (e.g., SPRY4, BEX2). TQ also affected p53 downstream targets, maintaining p53 levels. This study elucidates the anti-cancer mechanisms of TQ in A172 GBM cells, underscoring its effects on multiple signaling pathways and positioning TQ as a promising candidate for innovative glioblastoma treatment strategies. [ABSTRACT FROM AUTHOR]

RNA stability, important for eukaryotic gene expression, is thought to depend on deadenylation rates, with shortened poly(A) tails triggering decapping and 5′ to 3′ degradation. In contrast to this view, recent large-scale studies indicate that the most unstable mRNAs have, on average, long poly(A) tails. To clarify the role of deadenylation in mRNA decay, we first modeled mRNA poly(A) tail kinetics and mRNA stability in yeast. Independent of deadenylation rates, differences in mRNA decapping rates alone were sufficient to explain current large-scale results. To test the hypothesis that deadenylation and decapping are uncoupled, we used rapid depletion of decapping and deadenylation enzymes and measured changes in mRNA levels, poly(A) length and stability, both transcriptome-wide and with individual reporters. These experiments revealed that perturbations in poly(A) tail length did not correlate with variations in mRNA stability. Thus, while deadenylation may be critical for specific regulatory mechanisms, our results suggest that for most yeast mRNAs, it is not critical for mRNA decapping and degradation. Synopsis: Degradation of mRNA is thought to depend on the speed by which poly(A) tails are trimmed in the process of deadenylation. This study shows that decapping, which initiates mRNA degradation in yeast, seems to operate independently of deadenylation, in particular for unstable mRNA. A negative correlation between mRNA stability and poly(A) tail length can be explained by both deadenylation-dependent and -independent kinetic models. Inhibition of decapping leads to accumulation of mRNA with shorter poly(A) tails. Deadenylation inhibition leads to longer average poly(A) tails, without a global mRNA stabilization effect. Degradation kinetics of a short-lived model mRNA are similar for long and short poly(A) tail species and independent of the deadenylation rate. Modeling of mRNA poly(A) tail removal and mRNA stability together with rapid depletion of decapping and deadenylation enzymes reveal that deadenylation speed is not generally correlated with decapping rates in yeast. [ABSTRACT FROM AUTHOR]

Background: Alcoholic hepatitis is a severe inflammatory liver disease. In recent years, the incidence of AH has been on the rise, leading to an increasingly severe disease burden. Currently, there is a lack of specific biomarkers for the diagnosis and prognosis of AH in clinical practice. Therefore, the main objective of this study is to identify biomarkers closely associated with the progression of AH, to address the shortcomings in pathological diagnosis, and to identify potential therapeutic targets. Methods: Bioinformatics and machine learning methods were used to comparatively study the differentially expressed genes (DEGs) between AH patients and healthy individuals by analyzing four mRNA microarray data sets obtained from the GEO database. Subsequently, the role of potential biomarkers in AH and their mechanism of action were further confirmed by AH patients and in vitro and in vivo experiments. Results: Using differential analysis and WGCNA of the data set, a total of 167 key genes that may be related to AH were obtained. Among 167 genes, the LASSO logistic regression algorithm identified four potential biomarkers (KCNJ10, RPL21P23, ADRB2, and AC025279.1). Notably, ADRB2 showed biomarker potential in GSE28619, GSE94397, and E-MTAB-2664 datasets, and clinical liver samples. Furthermore, AH patients and in vivo experiments demonstrated ADRB2 inhibition and suppression of SIRT1/PPARα/PGC-1α signaling pathways, accompanied by elevated inflammatory factors and lipid deposition. In vitro experiments showed that ADRB2 overexpression mitigated the inhibition of the SIRT1/PPARα/PGC-1α signaling pathway, reversing the decrease in mitochondrial membrane potential, cell apoptosis, oxidative stress, and lipid deposition induced by alcohol exposure. Besides, the results also showed that ADRB2 expression in AH was negatively correlated with the levels of inflammatory factors (e.g., CCL2, CXCL8, and CXCL10). Conclusion: This study points to ADRB2 as a promising biomarker with potential diagnostic and prognostic value in clinical cohort data. In addition, in AH patients, in vivo and in vitro experiments confirmed the key role of ADRB2 in the progression of AH. These findings suggest that ADRB2 may alleviate AH by activating the SIRT1/PPARα/PGC-1α pathway. This finding provides a new perspective for the diagnosis and treatment of AH. [ABSTRACT FROM AUTHOR]

Background: TP53 gene mutation is crucial in determining the prognosis of Multiple Myeloma (MM) patients. Understanding metabolic genes linked to TP53 mutation is vital for developing targeted therapies for these patients. Method: We analyzed The Cancer Genome Atlas (TCGA) dataset to identify genes related to TP53 mutation and metabolism. Using univariate Cox regression and protein–protein interaction (PPI) analysis, we identified key genes. We categorized patients into high and low metabolism groups via non-negative matrix factorization (NMF) clustering, which led to the discovery of relevant differential genes. Integrating these with genes from the Gene Expression Omnibus (GEO) datasets and PPI interactions, we pinpointed crucial metabolic genes associated with TP53 mutation in MM. Additionally, we conducted prognostic analyses involving survival curves and receiver operating characteristic (ROC) charts. Results: Our study reveals that the metabolic gene ribonucleotide reductase M2 (RRM2), linked to TP53 mutation, correlates positively with the International Staging System (ISS) stage in MM patients and is an independent prognostic risk factor. In the TCGA dataset, among the 767 patients, the 35 MM patients with TP53 mutation generally had poor survival outcomes. Specifically, the patients with both TP53 mutation and high RRM2 expression had a 2-year survival rate of only 38.87%, whereas those with normal TP53 function and low RRM2 expression had a 2-year survival rate of 86.31% (p < 0.001). Conclusion: RRM2 significantly impacts MM prognosis and is associated with TP53 mutation, presenting itself as a potential therapeutic target and prognostic marker for MM. [ABSTRACT FROM AUTHOR]

Simple Summary: The growth pattern of the Chinese soft-shelled turtle (Pelodiscus sinensis) is remarkably sexually dimorphic. However, the molecular mechanism of this phenomenon has been studied mainly in the gonadal tissues of P. sinensis, and no article has been published on the study of sex differentiation in the brain of P. sinensis. Here, we performed a whole transcriptome analysis of the brains of adult female and male P. sinensis. We obtained a set of differentially expressed genes and transcription factors, which we annotated with GO and KEGG, and screened some genes and pathways related to growth. In addition, through GESA analysis, we screened out two genes, LHX1 and FGF7, which are related to both growth and sex differentiation, and through protein interaction analysis of these genes, we screened out eight genes and verified the expression levels of these eight genes in the brain of P. sinensis by qRT-PCR, which supported the reliability and accuracy of our transcriptome analysis. This study provides a solid foundation for analyzing the growth mechanism of sexual dimorphism in P. sinensis and even other turtles. The Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically important species in aquaculture, and its growth pattern is characterized by significant sexual dimorphism. However, the underlying molecular mechanisms of this phenomenon have mostly been investigated in the gonadal tissues of P. sinensis, and there are no articles on sex differentiation from the brain of P. sinensis. Here, we analyzed transcriptomes of the brains of adult male and female P. sinensis using high-throughput Illumina sequencing technology, establishing a set of differential genes and differential transcription factors. The data showed that there were 908 genes with significant differences in expression, of which 357 genes were up-regulated and 551 genes were down-regulated. We annotated using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), and screened some genes and pathways related to growth. There were 282 growth-related differential genes and 181 sex-related differential genes. We screened the genes' growth hormone receptor (GHR) and vascular endothelial growth factor A (VEGFA), which may be related to the growth of P. sinensis. The pathways related to the growth and development of P. sinensis are the growth hormone synthesis, secretion, and action pathway; the MAPK (mitogen-activated protein kinase) pathway; and the calcium signaling pathway. In addition, through gene set enrichment analysis (GSEA), we screened out two genes, LIM homeobox protein 1 (LHX1) and fibroblast growth factor 7 (FGF7), which are related to both growth and sex differentiation, and through protein interaction analysis of these genes, we screened out eight genes, including LHX1, FGF7, GHR, fibroblast growth factor 4 (FGF4), EGFR, BMP3, GLI family zinc finger 2 (GLI2), and neuronal differentiation 1 (NEUROD1), and verified the expression levels of these eight genes in the brain of the P. sinensis by real-time quantitative PCR (qRT-PCR), which supported the reliability and accuracy of our transcriptome analysis. Our study provides a solid foundation for analyzing the mechanisms of sexual-dimorphic growth of P. sinensis and even other turtles. [ABSTRACT FROM AUTHOR]

Grass carp hemorrhagic disease is caused by the grass carp reovirus (GCRV). The disease spreads rapidly and has a high fatality rate, which seriously affects grass carp culture. Moreover, the molecular mechanisms underlying grass carp hemorrhagic disease remain unclear. To decipher the effects of GCRV on grass carp tissues, resistant grass carp A (GA) and susceptible grass carp B (GB) were selected through GCRV treatment, and control grass carp C (GC) was also established. The gill, liver, and muscle tissues exhibited different onset symptoms under the influence of GCRV by histological observation. We selected muscle samples with significant differences in symptoms for Illumina RNA sequencing. Analyses using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes revealed 3512, 3074, and 1853 differentially expressed genes between "GC vs. GB," "GC vs. GA," and "GA vs. GB," respectively. Additionally, 40 differential immune-related genes and 28 differential interferon-stimulating genes (ISGs) related to the interferon (IFN) pathway were identified. The expression of immunogene-related genes of GB and GA, such as MDA5 , IL-34 , NF-KB , TRIM25 , SOCS3 , CEBPB , and BCL2 , and genes associated with the JAK-STAT signaling pathway, such as IRF4 , STAT1 , STAT3 , JAK 1 , and JAK 2 , was significantly upregulated. The IFN and JAK-STAT signaling pathways were closely related to anti-GCRV infection. The transcriptome data and predicted immune genes and ISGs in this study provide novel insights into the treatment of GCRV. • A large number of DEGs were screened by RNA-Seq of GCRV resistant and susceptible grass carp. • Forty immunity genes and 28 ISGs related to the IFN pathway were identified. • The DDX and CEBP family play important roles in grass carp's resistance to GCRV. [ABSTRACT FROM AUTHOR]

In this paper, we present a comparative analysis of the transcriptomic profile of three different human cell types: hematopoietic stem cells (HSCs), bone marrow-derived mesenchymal stem cells (MSCs) and fibroblasts (FIBs). The work aims to identify unique genes that are differentially expressed as specific markers of bone marrow-derived MSCs, and to achieve this undertakes a detailed analysis of three independent datasets that include quantification of the global gene expression profiles of three primary cell types: HSCs, MSCs and FIBs. A robust bioinformatics method, called GlobalTest, is used to assess the specific association between one or more genes expressed in a sample and the outcome variable, that is, the 'cell type' provided as a single univariate response. This outcome variable is predicted for each sample tested, based on the expression profile of the specific genes that are used as input to the test. The precision of the tests is calculated along with the statistical sensitivity and specificity for each gene in each dataset, yielding four genes that mark MSCs with high accuracy. Among these, the best performer is the protein-coding gene Transgelin (TAGLN, Gene ID: 6876) (with a Positive Predictive Value > 0.96 and FDR < 0.001), which identifies MSCs better than any of the currently used standard markers: ENG (CD105), THY1 (CD90) or NT5E (CD73). The results are validated by RT-qPCR, providing novel gene biomarkers specific for human MSCs. [ABSTRACT FROM AUTHOR]

Background: Codonopsis pilosula (Campanulaceae) is a traditional herbal plant that is widely used in China, and the drought stress during the seedling stage directly affects the quality, ultimately impacting its yield. However, the molecular mechanisms underlying the drought resistance of C. pilosula seedlings remain unclear. Method: Herein, we conducted extensive comparative transcriptome and physiological studies on two distinct C. pilosula cultivar (G1 and W1) seedlings subjected to a 4-day drought treatment. Results: Our findings revealed that cultivar G1 exhibited enhanced retention of proline and chlorophyll, alongside a marked elevation in peroxidase activity, coupled with diminished levels of malondialdehyde and reduced leaf relative electrolyte leakage compared with cultivar W1. This suggested that cultivar G1 had relatively higher protective enzyme activity and ROS quenching capacity. We discerned a total of 21,535 expressed genes and identified 4,192 differentially expressed genes (DEGs) by RNA sequencing (RNA-seq). Our analysis revealed that 1,764 DEGs unique to G1 underwent thorough annotation and functional categorization utilizing diverse databases. Under drought conditions, the DEGs in G1 were predominantly linked to starch and sucrose metabolic pathways, plant hormone signaling, and glutathione metabolism. Notably, the drought-responsive genes in G1 were heavily implicated in hormonal modulation, such as ABA receptor3-like gene (PYL9), regulation by transcription factors (KAN4 , BHLH80 , ERF1B), and orchestration of drought-responsive gene expression. These results suggest that cultivar G1 possesses stronger stress tolerance and can better adapt to drought growing conditions. The congruence between qRT-PCR validation and RNA-seq data for 15 DEGs further substantiated our findings. Conclusion: Our research provides novel insights into the physiological adaptations of C. pilosula to arid conditions and lays the groundwork for the development of new, drought-tolerant C. pilosula cultivars. [ABSTRACT FROM AUTHOR]

Contrast-induced acute kidney injury (CI-AKI) is one of the main causes of hospital-acquired renal failure, and still lacks of effective treatments. Previously, we demonstrated that αKlotho, which is an anti-aging protein that highly expresses in the kidney, has therapeutic activity in CI-AKI through promoting autophagy. However, the specific mechanism underlying αKlotho-mediated autophagy remains unclear. The RNA sequencing analysis of renal cortex revealed that the differentially expressed genes related to autophagy between αKlotho-treated CI-AKI mice and vehicle-treated CI-AKI mice were found to be associated with mitophagy and apoptosis. In the kidney of CI-AKI mice and HK-2 cells exposed to Iohexol, we revealed that αKlotho promoted mitophagy and decreased cell apoptosis. Mechanistically, αKlotho attenuated mitochondria damage, decreased mitochondrial ROS by upregulating BNIP3-mediated mitophagy. BNIP3 deletion abolished the beneficial effects of αKlotho both in vivo and in vitro. Moreover, we further demonstrated that αKlotho upregulated FoxO3 nuclear expression in Iohexol-treated HK-2 cells. Knockdown of FOXO3 gene inhibited αKlotho-promoted BNIP3-mediated mitophagy and subsequently increased the oxidative injury and cell apoptosis. Taken together, our results indicated a critical role of αKlotho in alleviating CI-AKI via mitophagy promotion involving the FoxO3-BNIP3 pathway. [ABSTRACT FROM AUTHOR]

Histone post-translational modifications play pivotal roles in eukaryotic gene expression. To date, most studies have focused on modifications in unstructured histone N-terminal tail domains and their binding proteins. However, transcriptional regulation by chromatin-effector proteins that directly recognize modifications in histone globular domains has yet to be clearly demonstrated, despite the richness of their multiple modifications. Here, we show that the ATP-dependent chromatin-remodeling BAF complex stimulates p53-dependent transcription through direct interaction with H3K56ac located on the lateral surface of the histone globular domain. Mechanistically, the BAF complex recognizes nucleosomal H3K56ac via the DPF domain in the DPF2 subunit and exhibits enhanced nucleosome-remodeling activity in the presence of H3K56ac. We further demonstrate that a defect in H3K56ac–BAF complex interaction leads to impaired p53-dependent gene expression and DNA damage responses. Our study provides direct evidence that histone globular domain modifications participate in the regulation of gene expression. The authors suggest that histone globular domain modifications participate in the regulation of gene expression. The ATP-dependent chromatin-remodeling BAF complex enhances transcription through direct interaction with H3K56ac located on the lateral surface of the histone globular domain. [ABSTRACT FROM AUTHOR]

Background: The study of rodent malaria parasites has significantly advanced our understanding of malaria parasite biology and host responses to parasite infections. There are four well-characterized rodent malaria parasite species (Plasmodium yoelii, P. chabaudi, P. berghei, and P. vinckei). Each species also has multiple strains that cause different disease phenotypes. P. yoelii nigeriensis N67C and N67, two isogenic parasites, are particularly intriguing as they differ in virulence and incite different immune responses in mice. The genome of the N67 parasite has been assembled recently, but not that of N67C. This study used PacBio HiFi sequencing data to assemble the N67C genome, compared the two genomes, and performed RNA sequencing to identify polymorphisms and differentially expressed genes (DEGs). Results: The assembled N67C parasite genome consisted of 16 scaffolds and three contigs of approximately 22.5 Mb with 100% and 96.6% completeness based on well-characterized single-copy orthologs specific to the Apicomplexa phylum and the Plasmodium genus, respectively. A comparison between the annotated N67C and N67 genomes revealed 133 single nucleotide polymorphisms (SNPs) and 75 indels. Among the polymorphic sites, an S (N67) to N (N67C) amino acid substitution at position 114 (S114N) in the dihydrofolate reductase-thymidylate synthase (DHFR-TS) confers resistance to pyrimethamine in mice. Additionally, 60 differentially expressed single-copy genes (DEGs) were detected after comparing mRNA levels between the two parasites. Starting with the predicted and annotated 5,681 N67C and 5,749 N67 genes, we identified 4,641 orthogroups that included at least one gene from the four P. yoelii parasites (N67, N67C, 17X, and YM), whereas 758 orthogroups showed subspecies or strain-specific patterns. Conclusion: The identification of polymorphic sites between the N67 and N67C genomes, along with the detection of the DEGs, may provide crucial insights into the variations in parasite drug responses and disease severity between these two isogenic parasites. The functional characterization of these genetic differences and candidate genes will deepen our understanding of disease mechanisms and pave the way for developing more effective control measures against malaria. [ABSTRACT FROM AUTHOR]

The role of the iron–sulfur [Fe-S] cluster transcriptional regulator IscR in maintaining [Fe-S] homeostasis in bacteria is still poorly characterized in many groups. Caulobacter crescentus and other Alphaproteobacteria have a single operon encoding [Fe-S] cluster biosynthesis enzymes. We showed that the expression of this operon increases in iron starvation, but not in oxidative stress, and is controlled mainly by IscR. Transcriptome analysis comparing an iscR null mutant strain with the wild-type (wt) strain identified 94 differentially expressed genes (DEGs), with 47 upregulated and 47 downregulated genes in the ΔiscR mutant. We determined the IscR binding sites in conditions of sufficient or scarce iron by Chromatin Immunoprecipitation followed by DNA sequencing (ChIP-seq), identifying two distinct putative DNA binding motifs. The estimated IscR regulon comprises 302 genes, and direct binding to several regulatory regions was shown by Electrophoresis Mobility Shift Assay (EMSA). The results showed that the IscR and Fur regulons partially overlap and that IscR represses the expression of the respiration regulator FixK, fine-tuning gene regulation in response to iron and redox balance. [ABSTRACT FROM AUTHOR]

Background: The Leishmania genome harbors formerly active short interspersed degenerated retroposons (SIDERs) representing the largest family of repetitive elements among trypanosomatids. Their substantial expansion in Leishmania is a strong predictor of important biological functions. In this study, we combined multilevel bioinformatic predictions with high-throughput genomic and transcriptomic analyses to gain novel insights into the diversified roles retroposons of the SIDER2 subfamily play in Leishmania genome evolution and expression. Results: We show that SIDER2 retroposons form various evolutionary divergent clusters, each harboring homologous SIDER2 sequences usually located nearby in the linear sequence of chromosomes. This intriguing genomic organization underscores the importance of SIDER2 proximity in shaping chromosome dynamics and co-regulation. Accordingly, we show that transcripts belonging to the same SIDER2 cluster can display similar levels of expression. SIDER2 retroposons are mostly transcribed as part of 3'UTRs and account for 13% of the Leishmania transcriptome. Genome-wide expression profiling studies underscore SIDER2 association generally with low mRNA expression. The remarkable link of SIDER2 retroposons with downregulation of gene expression supports their co-option as major regulators of mRNA abundance. SIDER2 sequences also add to the diversification of the Leishmania gene expression repertoire since ~ 35% of SIDER2-containing transcripts can be differentially regulated throughout the parasite development, with a few encoding key virulence factors. In addition, we provide evidence for a functional bias of SIDER2-containing transcripts with protein kinase and transmembrane transporter activities being most represented. Conclusions: Altogether, these findings provide important conceptual advances into evolutionary innovations of transcribed extinct retroposons acting as major RNA cis-regulators. [ABSTRACT FROM AUTHOR]

Backgroud: Elephant grass (Cenchrus purpureus) is a perennial forage grass characterized by tall plants, high biomass and wide adaptability. Low-temperature stress severely limits elephant grass biomass and geographic distribution. WRKY is one of the largest families of plant-specific transcription factors and plays important roles in plant resistance to low-temperature. However, the understanding of the WRKY family in grasses is limited. In this study, we conducted a genome-wide characterization of WRKY proteins in elephant grass, including gene structure, phylogeny, expression, conserved motif organization, and functional annotation, to identify key CpWRKY candidates involved in cold tolerance. Results: In this study, a total of 176 WRKY genes were identified in elephant grass. It was found that 172 were unevenly distributed across its 14 chromosomes, while the remaining 4 genes were not anchored to any chromosome. The genes were classified into three groups based on their WRKY conserved domains and zinc finger motifs. There were 12, 8, 19, 27, 12, 18 and 80 CpWRKYs belonging to group I, group IIa, group IIb, group IIc, group IId, group IIe and group III, respectively. We hypothesized that the ancient subgroup IIc WRKY gene is the ancestor of all WRKY genes in elephant grass. Most CpWRKYs in the same group have similar structure and motif composition. A total of 169 duplicate gene pairs were identified, suggesting that segmental duplication might have contributed to the expansion of the CpWRKY gene family. Ka/Ks analysis revealed that most of the CpWRKYs were subjected to purifying selection during the evolution. It was also found that six genes (CpWRKY51, CpWRKY81, CpWRKY100, CpWRKY101, CpWRKY140 and CpWRKY143) exhibited higher expression in roots compare to leaves, and were significantly induced by low temperature stress. Among them, CpWRKY81 had the highest expression under low-temperature stress, and its over-expression significantly enhanced the cold tolerance in yeast. Conlusions: In this study, we characterized WRKY genes in elephant grass and further investigated their physicochemical properties, evolution, and expression patterns under low-temperature stress. This research provides valuable resources for identifying key CpWRKY genes that contribute to cold tolerance in elephant grass. [ABSTRACT FROM AUTHOR]

Background : Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity. Methods: We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers. Results: Capture with the Twist CVRP increased sensitivity by at least 10–100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600–6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT. Conclusions: Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context. [ABSTRACT FROM AUTHOR]

Sugarcane holds global promise as a biofuel feedstock, necessitating a deep understanding of factors that influence biomass yield. This study unravels the intricate dynamics of plant hormones that govern growth and development in sugarcane. Transcriptome analysis of F2 introgression hybrids, derived from the cross of Saccharum officinarum "LA Purple" and wild Saccharum robustum "MOL5829", was conducted, utilizing the recently sequenced allele-specific genome of "LA Purple" as a reference. A total of 8059 differentially expressed genes were categorized into gene models (21.5%), alleles (68%), paralogs (10%), and tandemly duplicated genes (0.14%). KEGG analysis highlighted enrichment in auxin (IAA), jasmonic acid (JA), and abscisic acid (ABA) pathways, revealing regulatory roles of hormone repressor gene families (Aux/IAA, PP2C, and JAZ). Signaling pathways indicated that downregulation of AUX/IAA and PP2C and upregulation of JAZ repressor genes in high biomass segregants act as key players in influencing downstream growth regulatory genes. Endogenous hormone levels revealed higher concentrations of IAA and ABA in high biomass, which contrasted with lower levels of JA. Weighted co-expression network analysis demonstrated strong connectivity between hormone-related key genes and cell wall structural genes in high biomass genotypes. Expression analysis confirmed the upregulation of genes involved in the synthesis of structural carbohydrates and the downregulation of inflorescence and senescence-related genes in high biomass, which suggested an extended vegetative growth phase. The study underscores the importance of cumulative gene expression, including gene models, dominant alleles, paralogs, and tandemly duplicated genes and activators and repressors of disparate hormone (IAA, JA, and ABA) signaling pathways are the points of hormone crosstalk in contrasting biomass F2 segregants and could be applied for engineering high biomass acquiring varieties. [ABSTRACT FROM AUTHOR]

Tomato leaf curl New Delhi virus (ToLCNDV) is a begomovirus causing significant melon (Cucumis melo) crop losses globally. This study aims to map the ToLCNDV resistance in the PI 414723 melon accession, previously identified and characterized through phenotypic studies, thereby exploring shared genomic regions with the established resistant source WM-7. In the present study, WM-7 and PI 414723 were crossed with the susceptible accessions 'Rochet' and 'Blanco' respectively, to generate F1 hybrids. These hybrids were self-pollinated to generate the populations for mapping the ToLCNDV resistance region and designing markers for marker-assisted selection. Disease evaluation included visual symptom scoring, viral-load quantification and tissue printing. Genotyping-by-sequencing and SNP markers were used for quantitative trait loci (QTL) mapping. For genetic analysis, qPCR and bulked segregant RNA-seq (BSR-seq) were performed. Gene expression was assessed using RNA-seq, and qRT-PCR was used for confirmation. The research narrows the candidate region for resistance in WM-7 and identifies overlapping QTLs on chromosome 11 in PI 414723, found in the region of the DNA primase large subunit. BSR-seq and expression analyses highlight potential regulatory roles of chromosome 2 in conferring resistance. Differential expression was confirmed for six genes in the candidate region on chromosome 2. This study confirms the existence of common resistance genes in PI 414723 and WM-7. [ABSTRACT FROM AUTHOR]

Southern flounder skin pigmentation is a critical phenotypic characteristic for this species' survival in the natural environment. Normal pigmentation allows rapid changes of color for concealment to capture prey and UV light protection. In contrast, highly visible hypopigmented pseudo-albinos exhibit a compromised immune system and are vulnerable to predation, sensitive to UV exposure, and likely have poor survival in the wild. Skin and brain tissue samples from normally pigmented and hypopigmented individuals were analyzed with next-generation RNA sequencing. A total of 1,589,613 transcripts were used to identify 952,825 genes to assemble a de novo transcriptome, with 99.43% of genes mapped to the assembly. Differential gene expression and gene enrichment analysis of contrasting tissues and phenotypes revealed that pseudo-albino individuals appeared more susceptible to environmental stress, UV light exposure, hypoxia, and osmotic stress. The pseudo-albinos' restricted immune response showed upregulated genes linked to cancer development, signaling and response, skin tissue formation, regeneration, and healing. The data indicate that a modified skin collagen structure likely affects melanocyte differentiation and distribution, generating the pseudo-albino phenotype. In addition, the comparison of the brain transcriptome revealed changes in myelination and melanocyte stem cell activity, which may indicate modified brain function, reduced melanocyte migration, and impaired vision. [ABSTRACT FROM AUTHOR]

Simple Summary: Simple Summary: The loreyi leafworm, Mythimna loreyi (Duponchel), has recently expanded its distribution range to many countries around the world. To understand the molecular response mechanism of this pest to cold stress, a comprehensive transcriptome analysis was carried out in three developmental stages (larvae, pupae, and adults) of M. loreyi. The results indicated that there were significant differences in metabolism-related processes and gene expression when they were exposed to low temperatures. In addition, several differentially expressed genes were identified in these stages after exposure to cold stress. This is the first study to test cold stress-induced transcriptional changes in three developmental stages of M. loreyi and provide basic data for understanding the molecular response mechanisms of moths under cold stress. The loreyi leafworm Mythimna loreyi (Lepidoptera: Noctuidae) is a serious pest of agriculture that causes particular damage to Gramineae crops in Asia, Europe, Australia, Africa, and the Middle East. Low temperature is one of the important environmental factors that limits the survival, distribution, colonization, and abundance of M. loreyi. However, the metabolic synthesis pathways of cold-tolerant substances in M. loreyi and the key genes involved in the regulation under cold stress remain largely unknown. In this study, we sequenced the transcriptomes of three developmental stages (larvae, pupae, and adults) of M. loreyi to discover the molecular mechanisms of their responses to cold stress. In total, sequencing generated 120.64 GB of clean data from 18 samples, of which 19,459 genes and 1740 differentially expressed genes (DEGs) were identified. The enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that many DEGs were mainly enriched in pathways associated with energy metabolism and hormone metabolism. Among these, genes encoding multiple metabolic enzymes, cuticle proteins (CPs), and heat shock proteins (HSPs) were differentially expressed. These results indicate that there are significant differences among the three developmental stages of M. loreyi exposed to cold stress and provide a basis for further studying the molecular mechanisms of cold tolerance in insects. [ABSTRACT FROM AUTHOR]

Platycladus orientalis (P. orientalis) is a common tree used for vegetation restoration in northern China, and its large area propagation helps to improve site conditions. However, under harsh conditions such as poor land, the survival rate of P. orientalis is very low. Numerous studies have shown that root pruning can promote the formation of lateral roots in seedlings, enhancing the roots' capacity to absorb soil nutrients and water, and thereby improving the survival rate of seedlings. In this study, a one-third root pruning treatment was applied to P. orientalis seedlings, and the whole transcriptome of seedlings subjected to both control (CK) and root pruning treatments was sequenced to analyze their gene expression profiles. This study investigated the regulatory mechanisms of lateral root development in response to root pruning damage at the molecular level. Using nine cells, 15.28 Gb of clean data were obtained, which yielded 101,688 high-quality full-length transcript sequences and 22,955 low-quality full-length transcript sequences after clustering. Redundancy was then removed using CD-HIT, and Illumina RNA-seq sequencing produced 139.26 Gb of clean data. A total of 2025 differentially expressed genes (DEGs) were identified at three time points following root pruning treatment. Enrichment analysis revealed that the peroxidase gene family plays a significant role in lateral root proliferation. Furthermore, the expression levels of the peroxidase gene family were notably upregulated in comparison to the control group. Pathway enrichment analysis identified 22 relevant genes, which appeared to be highly associated with root growth and resilience to stress. Through examining the expression patterns and correlations of these genes, five central genes emerged as key players. The findings of this research suggest that the peroxidase gene family plays a crucial role in the stress response and root development of P. orientalis, providing reference and guidance for root development in other plant species. [ABSTRACT FROM AUTHOR]

Purpose: Vibrio parahaemolyticus is a leading seafood borne pathogen worldwide. The aim of this study was to decipher the response mechanism of V. parahaemolyticus isolates of clinical and aquatic animal origins to the hypoxic condition, which challenges the bacterial survival in the host and in the environment. Methods: Growth profiles of V. parahaemolyticus isolates (n = 5) of clinical and aquatic animal origins were examined at different stress conditions (osmolality, acid, temperature, and O2 concentrations). Draft genomes of the V. parahaemolyticus isolates were determined using the Illumina sequencing technique. Comparative genomic analysis were performed to identify and validate the hypoxic tolerance-related genes. Results: The V. parahaemolyticus isolates had an oxygen concentration-dependent growth mode, and the 10% O2 condition strongly inhibited the bacterial growth, when incubated in TSB medium (pH 8.5, 3% NaCl) at 37 °C. Unexpectedly, in marked contrast to the normal 21% O2 condition, the 10% O2 treatment for 24 h significantly increased biofilm formation of V. parahaemolyticus isolates (p < 0.05). Draft genome sequences of four V. parahaemolyticus isolates of aquatic animal origins were determined (4.914–5.3530 Mb), which carried mobile genetic elements (n = 12–29). Genome-wide gene expression changes triggered by the hypoxic condition were further examined. Comparative transcriptomic analyses unveiled multiple molecular strategies employed by the bacterium to mitigate the cell damage caused by the hypoxia. Of note, the pathogenic V. parahaemolyticus ATCC17802 down-regulated and/or shut down ten metabolic pathways to reduce cell viability and maintain cell structure under the hypoxic stress. Conclusions: The results of this study fill prior gaps in the response mechanism of V. parahaemolyticus to the hypoxic condition. Different tolerance to hypoxia contributes to the persistence of pathogenic V. parahaemolyticus in the niches. [ABSTRACT FROM AUTHOR]

Tangeretin (Tan), a citrus flavonoid, possesses a strong anti-tumor efficacy in various human cancers. However, the precise role of Tan in the development of esophageal squamous cell carcinoma (ESCC) remains unclear. RNA sequencing (RNA-seq) analysis was performed to observe the Tan-related genes in Tan-treated TE-1 cells. The direct relationship between GLI family zinc finger 2 (GLI2) and the promoter of glycoprotein non-metastatic melanoma protein B (GPNMB) was predicted by bioinformatics analysis and validated by luciferase reporter and chromatin immunoprecipitation (ChIP) assays. Cell survival after Tan treatment was assessed by CCK8 assay. Gene expression levels were evaluated by a qRT-PCR, western blot, or immunofluorescence method. Cell migration and invasion were detected by wound-healing and transwell assays. The function of Tan in vivo was examined using xenograft studies. Our data indicated anti-migration and anti-invasion functions of Tan in ESCC cells in vitro. Tan also diminished tumor growth in vivo. Mechanistically, Tan diminished the expression and transcriptional activity of GLI2 in ESCC cells. Silencing of GLI2 resulted in decreased expression of GPNMB by inhibiting GPNMB transcription via the binding site at the GPNMB promoter at position +(1539–1550). Moreover, Tan down-regulated GPNMB expression in ESCC cells, and re-expression of GPNMB reversed anti-migration and anti-invasion functions of Tan in ESCC cells. Our findings uncover anti-migration and anti-invasion effects of Tan in ESCC cells by down-regulating GPNMB by suppressing GLI2-mediated GPNMB transcription, providing new evidence that Tan can function as a therapeutic agent against ESCC. [ABSTRACT FROM AUTHOR]

Background: Wild emmer wheat is a great candidate to revitalize domesticated wheat genetic diversity. Recent years have seen intensive investigation into the evolution and domestication of wild emmer wheat, including whole-genome DNA and transcriptome sequencing. However, the impact of intraspecific hybridization on the transcriptome of wild emmer wheat has been poorly studied. In this study, we assessed changes in methylation patterns and transcriptomic variations in two accessions of wild emmer wheat collected from two marginal populations, Mt. Hermon and Mt. Amasa, and in their stable F4 hybrid. Results: Methylation-Sensitive Amplified Polymorphism (MSAP) detected significant cytosine demethylation in F4 hybrids vs. parental lines, suggesting potential transcriptome variation. After a detailed analysis, we examined nine RNA-Seq samples, which included three biological replicates from the F4 hybrid and its parental lines. RNA-Seq databases contained approximately 200 million reads, with each library consisting of 15 to 25 million reads. There are a total of 62,490 well-annotated genes in these databases, with 6,602 genes showing differential expression between F4 hybrid and parental lines Mt. Hermon and Mt. Amasa. The differentially expressed genes were classified into four main categories based on their expression patterns. Gene ontology (GO) analysis revealed that differentially expressed genes are associated with DNA/RNA metabolism, photosynthesis, stress response, phosphorylation and developmental processes. Conclusion: This study highlights the significant transcriptomic changes resulting from intraspecific hybridization within natural plant populations, which might aid the nascent hybrid in adapting to various environmental conditions. [ABSTRACT FROM AUTHOR]

Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the democratization of diverse model systems. They allow for the economical sequencing of an entire genome or transcriptome of interest, and with technical variations can even provide insight into genome organization and the expression and regulation of genes. The analysis and biological interpretation of such large datasets can present significant challenges that depend on the 'scientific status' of the model system. While high-quality genome and transcriptome references are readily available for well-established model systems, the establishment of such references for an emerging model system often requires extensive resources such as finances, expertise and computation capabilities. The de novo assembly of a transcriptome represents an excellent entry point for genetic and molecular studies in emerging model systems as it can efficiently assess gene content while also serving as a reference for differential gene expression studies. However, the process of de novo transcriptome assembly is non-trivial, and as a rule must be empirically optimized for every dataset. For the researcher working with an emerging model system, and with little to no experience with assembling and quantifying short-read data from the Illumina platform, these processes can be daunting. In this guide we outline the major challenges faced when establishing a reference transcriptome de novo and we provide advice on how to approach such an endeavor. We describe the major experimental and bioinformatic steps, provide some broad recommendations and cautions for the newcomer to de novo transcriptome assembly and differential gene expression analyses. Moreover, we provide an initial selection of tools that can assist in the journey from raw short-read data to assembled transcriptome and lists of differentially expressed genes. [ABSTRACT FROM AUTHOR]

Over the last several years, there has been increased interest in cannabidiol (CBD) to treat various ailments such as pain, anxiety, insomnia, and inflammation. The potential for CBD as an anti-inflammatory therapy has come, in part, from its demonstrated ability to suppress neuroinflammation in autoimmune diseases, such as the mouse model of multiple sclerosis, experimental autoimmune encephalomyelitis (EAE). The increased use of CBD strongly suggests that more research is necessary to elucidate its safety and efficacy and determine the mechanisms by which it acts. Thus, we conducted two separate studies. In the first, RNA sequencing (RNA-Seq) analysis of brains of female mice undergoing EAE in the presence and absence of CBD was conducted to identify potential genes that mediated its neuroprotective effects when efficacious. In the second, we assessed some of the same genes in male and female mice treated with CBD in the absence of an immune stimulus. Together, these data showed that CBD modestly increased oxytocin (Oxt) and arginine vasopressin (vasopressin, Avp) gene expression in the brains of mice, regardless of whether there was active inflammation. Overall, these data suggest that Oxt and Avp might act as biomarkers for CBD exposure. [ABSTRACT FROM AUTHOR]

Suaeda glauca L. is leaf succulent halophyte. Its seed oil content is high and rich in unsaturated fatty acids with high edible and medicinal value. Shoot length and dry weight of S. glauca from saline soils (SS) are higher than that from non-saline soils (NSS). However, the mechanism has not been elucidated. In this work, high-throughput Illumina RNA-sequencing (RNA-seq) was used and photosynthetic traits were evaluated in the species from different habitats, one occurs in SS, and another has been cultivated in NSS for over two decades. There were 1824 DEGs between S. glauca from NSS and SS. Some DEGs were mapped to photosynthesis and photosynthesis-antenna proteins. Notably, genes associated with subunits of photosynthesis and light-capturing complexes (LHCs) showed higher expression levels in the species from SS compared to plants from NSS. This was accompanied by higher potential efficiency of PSII photochemistry (Fv/Fm), actual PSII efficiency (ΦPSII), electron transport rate (ETR), enzyme activity and gene expression of GAPDH and Rubisco in SS seedlings. This study provides evidence that seedlings of S. glauca from SS had higher photosynthetic efficiency compared with that from NSS, thus facilitating their photosynthate accumulation and growth in the SS population, i.e., this characteristic in SS population may be weakened when the species is cultivated in NSS for long time. [Display omitted] • The photoreaction of Suaeda glauca from saline soils (SS) was higher than that from non-saline soils (NSS). • Activity of certain enzymes during carbon assimilation in S. glauca from SS was higher than NSS. • Gene expression of photosynthesis subunits in S. glauca from SS was higher than NSS. • Gene expression of light-harvesting complex in S. glauca from SS was higher than NSS. • S. glauca from SS had higher photosynthetic efficiency compared with that from NSS. [ABSTRACT FROM AUTHOR]

The RE1-silencing transcription factor (REST) acts either as a repressor or activator of transcription depending on the genomic and cellular context. REST is a key player in brain cell differentiation by inducing chromatin modifications, including DNA methylation, in a proximity of its binding sites. Its dysfunction may contribute to oncogenesis. Mutations in IDH1/2 significantly change the epigenome contributing to blockade of cell differentiation and glioma development. We aimed at defining how REST modulates gene activation and repression in the context of the IDH mutation-related phenotype in gliomas. We studied the effects of REST knockdown, genome wide occurrence of REST binding sites, and DNA methylation of REST motifs in IDH wild type and IDH mutant gliomas. We found that REST target genes, REST binding patterns, and TF motif occurrence proximal to REST binding sites differed in IDH wild-type and mutant gliomas. Among differentially expressed REST targets were genes involved in glial cell differentiation and extracellular matrix organization, some of which were differentially methylated at promoters or gene bodies. REST knockdown differently impacted invasion of the parental or IDH1 mutant glioma cells. The canonical REST-repressed gene targets showed significant correlation with the GBM NPC-like cellular state. Interestingly, results of REST or KAISO silencing suggested the interplay between these TFs in regulation of REST-activated and repressed targets. The identified gene regulatory networks and putative REST cooperativity with other TFs, such as KAISO, show distinct REST target regulatory networks in IDH-WT and IDH-MUT gliomas, without concomitant DNA methylation changes. We conclude that REST could be an important therapeutic target in gliomas. [ABSTRACT FROM AUTHOR]

Global warming causes frequent high temperatures in summer; which negatively impacts herbaceous peonies (Paeonia lactiflora Pall.) by accelerating leaf senescence and reducing biomass accumulation, leading to reduced flower quality in the subsequent year. Our findings revealed that as heat stress progressed, the high-temperature-sensitive cultivar 'Meigui Zi' (MGZ) exhibited a higher rate of chlorophyll content reduction and more pronounced premature aging symptoms than the high-temperature-tolerant cultivar 'Chi Fen' (CF). To investigate gene expression differences between CF and MGZ under high-temperature stress, we combined PacBio Iso-Seq sequencing (Iso-Seq) with next-generation sequencing (RNA-seq). Iso-seq yielded 352,891 full-length transcripts ranging from 61 bp to 49,022 bp in length. RNA-seq generated 257,562 transcripts across all samples. Further analysis revealed that differentially expressed genes (DEGs) between CF and MGZ were primarily enriched in "Photosynthesis", with most photosynthesis-related DEGs highly expressed in CF. This indicates that CF has higher stability in its photosystem compared with MGZ, which is crucial for mitigating leaf senescence caused by high temperatures. Additionally, the highly expressed chlorophyll degradation genes stay-green (SGR) and stay-green-like (SGRL) in MGZ may be involved in chlorophyll content reduction induced by high temperature. This study preliminarily revealed the molecular mechanism of high-temperature-induced leaf senescence of in herbaceous peony and provided candidate genes for further studies of the regulation mechanism of high -temperature-induced leaf senescence. [ABSTRACT FROM AUTHOR]

The resurrection plant Selaginella pulvinata possesses an extraordinary ability to survive longterm desiccation, with the capacity to recover to normal growth after four years in a desiccated state. To understand the phenomenon, we investigated morphology, cytology, physiology, and performed PacBio single-molecule, real-time (SMRT) sequencing and Illumina RNA-sequencing of S. pulvinata during dehydration and rehydration. The full-length transcriptome dataset of S. puvinata consisted of 78,914 isoforms, and 75,819 isoforms (96.07%) were functionally annotated. The mapping rate of RNA-seq was 86.83–93.46% when utilizing the full-length transcriptome dataset as a reference. A total of 17,934 differentially expressed genes (DEGs) were identified during dehydration and rehydration. During dehydration, swollen chloroplasts and mitochondria, as well as vacuolation occupied space in desiccated cells, which cooperated with dense cytoplasm to inhibit the collapse and folding of desiccated cells. Accumulation and up-regulated gene expressions of osmotic agent and protective proteins contributed to the formation of vacuolation and dense cytoplasm. To reduce ROS damage during dehydration, two strategies were employed in S. pulvinata , i.e., reducing ROS production and scavenging ROS. Reducing exposure area, inactive PSII and down-regulated gene expression in photosynthesis decreased ROS production caused by excessive light absorption. Increased activities and up-regulated gene expressions in antioxidant enzyme system promoted ROS scavenging. ABA signaling pathway was hypothesized to play an important regulatory role in the desiccation tolerance of S. pulvinata due to significant ABA accumulation and up-regulated expressions of related genes during dehydration. Moreover, the comparative transcriptome analysis revealed that the pathways involved in dehydration and rehydration of the resurrection species S. pulvinata , S. lepidophylla and S. sellowii were consistent, indicating the similar desiccation tolerance mechanisms existing in the different resurrection species of Selaginella. Our study preliminarily revealed the desiccation tolerance mechanisms of S. pulvinata , which holds significant potential for inspiring biotechnological strategies aimed at enhancing drought tolerance in crops. • Changes of morphology, physiology, cytology and transcriptome level were observed in S. pulvinata during dehydration and rehydration. • Desiccation tolerance of S. pulvinata was an intricate process orchestrated by many genes and metabolic pathways. • The different resurrection species of Selaginella possessed the similar desiccation tolerance mechanism. [ABSTRACT FROM AUTHOR]

Harmful substances like the cyanotoxin microcystin-leucine-arginine (MC-LR) are commonly found in eutrophic freshwater environments, posing risks to aquatic organisms. The water flea, Daphnia, is a well-established model organism for environmental toxicology research. Nevertheless, there is currently insufficient research on the genes that respond to MC-LR in Daphnia galeata. This study aimed to gain insights into the notable genes that react significantly to MC-LR. In this study, we generated an extensive RNA-Seq sequences isolated from the D. galeata HK strain, Han River in Korea. This strain was nourished with a diet of the green microalga Chlorella vulgaris and treated with pure MC-LR at a concentration of 36 ug/L. The transcriptome profile in response to the MC-LR treatment was obtained and 336 differentially expressed genes were subjected to Gene Ontology (GO) and euKaryotic Orthologous Groups of proteins analyses. GO enrichment analysis showed that chemical stimulus, amino sugar metabolic and catabolic process, oxidative stress, and detoxification were highly enriched, in reverse, proteolysis and fucosylation were underpresented. Detoxification process related genes such as peroxidase-like, chorion, and thyroid peroxidase-like were enriched for eliminating or neutralizing MC_LR from an organism's body. Furthermore, functional protein classification revealed an upregulation of lipid and inorganic ion transport processes, while amino acid and carbohydrate transport processes were found to be downregulated. These findings offer insights into how organisms respond to ecotoxic stimuli, providing valuable information for understanding adaptation or defense pathways. [ABSTRACT FROM AUTHOR]

Simple Summary: Glioblastoma (GB) is the most common primary brain tumor in adults, but it remains incurable due to its high degree of therapy resistance. Glioblastoma stem-like cells (GSCs) are believed to drive the initiation, progression, and therapy resistance of GB, making them an ideal therapeutic target to improve patient outcomes. However, due to their heterogeneity, there are no universal markers to identify GSCs. We evaluated GARP as a novel marker for GSCs and found that GARP is more stably and uniformly expressed by human GSCs, across cellular states and disease stages, than the commonly used GSC marker, CD133. Additionally, we showed that GARP is intranuclearly localized in GSCs, and we are the first to show that nuclear GARP levels (GARPNU+) are associated with poor patient survival. Our findings indicate that GARP/GARPNU+ expression is an improved marker for GSCs and suggest a potential application of GARP as a prognostic biomarker for GB. Glioblastoma (GB) is notoriously resistant to therapy. GB genesis and progression are driven by glioblastoma stem-like cells (GSCs). One goal for improving treatment efficacy and patient outcomes is targeting GSCs. Currently, there are no universal markers for GSCs. Glycoprotein A repetitions predominant (GARP), an anti-inflammatory protein expressed by activated regulatory T cells, was identified as a possible marker for GSCs. This study evaluated GARP for the detection of human GSCs utilizing a multidimensional experimental design that replicated several features of GB: (1) intratumoral heterogeneity, (2) cellular hierarchy (GSCs with varied degrees of self-renewal and differentiation), and (3) longitudinal GSC evolution during GB recurrence (GSCs from patient-matched newly diagnosed and recurrent GB). Our results indicate that GARP is expressed by GSCs across various cellular states and disease stages. GSCs with an increased GARP expression had reduced self-renewal but no alterations in proliferative capacity or differentiation commitment. Rather, GARP correlated inversely with the expression of GFAP and PDGFR-α, markers of astrocyte or oligodendrocyte differentiation. GARP had an abnormal nuclear localization (GARPNU+) in GSCs and was negatively associated with patient survival. The uniformity of GARP/GARPNU+ expression across different types of GSCs suggests a potential use of GARP as a marker to identify GSCs. [ABSTRACT FROM AUTHOR]

Purpose: Emergent cancer cells likely secrete factors that inhibit anti-tumor immunity. To identify such factors, we applied a functional assay with proteomics to an immunotherapy resistant syngeneic mouse melanoma model. Four secreted factors were identified that potentially mediate immunosuppression and could become targets for novel immunotherapies. We tested for consistent clinical correlates in existing human data and verified in vivo whether knocking out tumor cell production of these factors improved immune-mediated control of tumor growth. Methods: Existing human data was analyzed for clinical correlates. A CRISPR/Cas9 approach to generate knockout cell lines and a kinetic analysis leveraging a Markov Chain Monte Carlo (MCMC) approach quantified the various knockouts' effect on cells' intrinsic growth rate. Flow cytometry was used to characterize differences in immune infiltration. Results: While all four gene products were produced by malignant melanocytes, only increased CCN4 expression was associated with reduced survival in primary melanoma patients. In immunocompetent C57BL/6 mice the CCN4 knockout increased survival while the other knockouts had no effect. This survival advantage was lost when the CCN4 knockout cells were injected into immunocompromised hosts, indicating that the effect of CCN4 may be immune mediated. Parameter estimation from the MCMC analysis shows that CCN4 was the only knockout tested that decreased the net tumor growth rate in immunocompetent mice. Flow cytometry showed an increase in NK cell infiltration in CCN4 knockout tumors. Conclusions: The results suggest that CCN4 is a mediator of immunosuppression in the melanoma tumor microenvironment and a potential collateral immunotherapy target. [ABSTRACT FROM AUTHOR]

In the realm of agriculture, a pressing concern remains the abiotic stresses, such as temperature fluctuation, drought, soil salinity, and heavy metal contamination. These adverse growth conditions hamper crop yields and global food security. In this review, we present a comprehensive examination of the recent advancements in utilizing genomics and transcriptomics, tools to enhance crop resilience against these stress factors. Genomics aids in the identification of genes responsive to stress, unravels regulatory networks, and pinpoints genetic variations linked to stress tolerance. Concurrently, transcriptomics sheds light on the intricate dynamics of gene expression during stress conditions, unearthing novel stress-responsive genes and signaling pathways. This wealth of knowledge shapes the development of stress-tolerant crop varieties, achieved through conventional breeding programs and state-of-the-art genetic engineering and gene editing techniques like CRISPR-Cas9. Moreover, the integration of diverse omics data and functional genomics tools empowers precise manipulation of crop genomes to fortify their stress resilience. In summary, the integration of genomics and transcriptomics holds substantial promise in elucidating the molecular mechanisms behind crop stress tolerance, offering a path towards sustainable agriculture and safeguarding food security amidst shifting environmental challenges. [ABSTRACT FROM AUTHOR]

Translation initiation is a complex and highly regulated process that represents an important mechanism, controlling gene expression. eIF2A was proposed as an alternative initiation factor, however, its role and biological targets remain to be discovered. To further gain insight into the function of eIF2A in Saccharomyces cerevisiae, we identified mRNAs associated with the eIF2A complex and showed that 24% of the most enriched mRNAs encode proteins related to cell wall biogenesis and maintenance. In agreement with this result, we showed that an eIF2A deletion sensitized cells to cell wall damage induced by calcofluor white. eIF2A overexpression led to a growth defect, correlated with decreased synthesis of several cell wall proteins. In contrast, no changes were observed in the transcriptome, suggesting that eIF2A controls the expression of cell wall-related proteins at a translational level. The biochemical characterization of the eIF2A complex revealed that it strongly interacts with the RNA binding protein, Ssd1, which is a negative translational regulator, controlling the expression of cell wall-related genes. Interestingly, eIF2A and Ssd1 bind several common mRNA targets and we found that the binding of eIF2A to some targets was mediated by Ssd1. Surprisingly, we further showed that eIF2A is physically and functionally associated with the exonuclease Xrn1 and other mRNA degradation factors, suggesting an additional level of regulation. Altogether, our results highlight new aspects of this complex and redundant fine-tuned regulation of proteins expression related to the cell wall, a structure required to maintain cell shape and rigidity, providing protection against harmful environmental stress. [ABSTRACT FROM AUTHOR]

The apicomplexan parasite Theileria annulata is transmitted by Hyalomma ticks and causes an acute lymphoproliferative disease that is invariably lethal in exotic cattle breeds. The unique ability of the schizont stage of T. annulata to transform infected leukocytes to a cancer-like phenotype and the simplicity of culturing and passaging T. annulata-transformed cells in vitro have been explored for live vaccine development by attenuating the transformed cells using lengthy serial propagation in vitro. The empirical in vivo evaluation of attenuation required for each batch of long-term cultured cells is a major constraint since it is resource intensive and raises ethical issues regarding animal welfare. As yet, the molecular mechanisms underlying attenuation are not well understood. Characteristic changes in gene expression brought about by attenuation are likely to aid in the identification of novel biomarkers for attenuation. We set out to undertake a comparative transcriptome analysis of attenuated (passage 296) and virulent (passage 26) bovine leukocytes infected with a Tunisian strain of T. annulata termed Beja. RNA-seq was used to analyse gene expression profiles and the relative expression levels of selected genes were verified by real-time quantitative PCR (RT-qPCR) analysis. Among the 3538 T. annulata genes analysed, 214 were significantly differentially expressed, of which 149 genes were up-regulated and 65 down-regulated. Functional annotation of differentially expressed T. annulata genes revealed four broad categories of metabolic pathways: carbon metabolism, oxidative phosphorylation, protein processing in the endoplasmic reticulum and biosynthesis of secondary metabolites. It is interesting to note that of the top 40 genes that showed altered expression, 13 were predicted to contain a signal peptide and/or at least one transmembrane domain, suggesting possible involvement in host-parasite interaction. Of the 16,514 bovine transcripts, 284 and 277 showed up-regulated and down-regulated expression, respectively. These were assigned to functional categories relevant to cell surface, tissue morphogenesis and regulation of cell adhesion, regulation of leucocyte, lymphocyte and cell activation. The genetic alterations acquired during attenuation that we have catalogued herein, as well as the accompanying in silico functional characterization, do not only improve understanding of the attenuation process, but can also be exploited by studies aimed at identifying attenuation biomarkers across different cell lines focusing on some host and parasite genes that have been highlighted in this study, such as bovine genes (CD69, ZNF618, LPAR3, and APOL3) and parasite genes such as TA03875. [ABSTRACT FROM AUTHOR]

Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up‐regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS‐like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up‐regulated within a day of treatment, their predicted targets being the up‐regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS‐like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up‐regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition. [ABSTRACT FROM AUTHOR]

Modulation of odorant receptors mRNA induced by prolonged odor exposure is highly correlated with ligand-receptor interactions in Drosophila as well as mammals of the Muridae family. If this response feature is conserved in other organisms, this presents an intriguing initial screening tool when searching for novel receptor-ligand interactions in species with predominantly orphan olfactory receptors. We demonstrate that mRNA modulation in response to 1-octen-3-ol odor exposure occurs in a time- and concentration-dependent manner in Aedes aegypti mosquitoes. To investigate gene expression patterns at a global level, we generated an odor-evoked transcriptome associated with 1-octen-3-ol odor exposure. Transcriptomic data revealed that ORs and OBPs were transcriptionally responsive whereas other chemosensory gene families showed little to no differential expression. Alongside chemosensory gene expression changes, transcriptomic analysis found that prolonged exposure to 1-octen-3-ol modulated xenobiotic response genes, primarily members of the cytochrome P450, insect cuticle proteins, and glucuronosyltransferases families. Together, these findings suggest that mRNA transcriptional modulation of olfactory receptors caused by prolonged odor exposure is pervasive across taxa and can be accompanied by the activation of xenobiotic responses. [ABSTRACT FROM AUTHOR]