Universality and diversity of gene expression patterns in response to cold acclimation in Drosophila albomicans.

Cold acclimation is one of the important factors in temperature adaptation for insects needing to make rapid adjustment to the seasonal temperature changes in their living environment. In a fruit fly species, Drosophila albomicans, which has a tropical origin and currently has a wide geographic distribution extended into Asian temperate regions, cold tolerance in terms of survival time at 1℃ of adult flies reared at 25℃ was substantially improved by a cold acclimation at 20℃ for several days. Examining 29 isofemale lines from widely distributed natural populations, we observed a substantial variation in their acclimation response. However, the acclimation response was not necessarily stronger in the strains from the recently colonized temperate regions. A significantly stronger acclimation response was detected in male flies of the temperate strains when compared to those of the tropical strains. D. albomicans also showed stronger cold tolerance compared to its closely related species belonging to the D. nasuta subgroup. Among these strains, we detected a strong positive correlation between the cold tolerance change and the metabolic rate change upon the cold acclimation, suggesting their strong physiological association regulated by common genetic factors, which may have been the target of natural selection for the temperature adaptation. The response to deacclimation and reacclimation suggested that a systematic change in gene expressions is the main molecular mechanism for the cold acclimation to have effects on the cold tolerance and metabolic rate changes.

Comparative transcriptomics of whole blood can be used to evaluate the systemic host response and its concordance between human and mouse malaria and aid the selection of appropriate models for translational malaria research.

While tau and aging have highly overlapping differential gene expression signatures, they diverge in the affected cell types, with aging having a wide-ranging impact and tau-triggered changes instead polarized to excitatory neurons and glia.

BackgroundThe aim of this study was to identify potential therapeutic target genes for breast cancer (BC) by the investigation of gene expression changes after ionizing radiation (IR) in BC cells. Gene expression profile GSE21748, including BC cell line MCF-7 samples at different time points after IR treatment, were downloaded from Gene Expression Omnibus. Differentially expressed genes (DEGs) were identified in different time points following IR compared with cell samples before IR, respectively. Gene ontology functions and The Kyoto Encyclopedia of Genes and Genomes pathways of the overlapping DEGs were enriched using DAVID. Transcription factor (TFs)-encoding genes were identified from the overlapping DEGs, followed by construction of transcriptional regulatory network and co-expression network.ResultsA total of 864 overlapping DEGs were identified, which were significantly enriched in regulation of cell proliferation and apoptosis, and cell cycle process. We found that FOXD1, STAT6, XBP1, STAT2, LMO2, TFAP4, STAT3, STAT1 were hub nodes in the transcriptional regulatory network of the overlapping DEGs. The co-expression network of target genes regulated by STAT3, STAT1, STAT6 and STAT2 included some key genes such as BCL2L1.ConclusionSTAT1, STAT2, STAT3, STAT6, XBP1, BCL2L1, CYB5D2, ESCO2, and PARP2 were significantly affected by IR and they may be used as therapeutic gene targets in the treatment of BC.

BackgroundCrops are under constant pressure due to global warming, which unfolds at a much faster pace than their ability to adapt through evolution. Agronomic traits are linked to cytoplasmic-nuclear genome interactions. It thus becomes important to understand the influence exerted by the organelles on gene expression under heat stress conditions and profit from the available genetic diversity. Maize (Zea mays) cytolines allow us to investigate how the gene expression changes under heat stress conditions in three different cytoplasmic environments, but each having the same nucleus. Analyzing retrograde signaling in such an experimental set-up has never been done before. Here, we quantified the response of three cytolines to heat stress as differentially expressed genes (DEGs), and studied gene expression patterns in the context of existing polymorphism in their organellar genomes.ResultsOur study unveils a plethora of new genes and GO terms that are differentially expressed or enriched, respectively, in response to heat stress. We report 19,600 DEGs as responding to heat stress (out of 30,331 analyzed), which significantly enrich 164 GO biological processes, 30 GO molecular functions, and 83 GO cell components. Our approach allowed for the discovery of a significant number of DEGs and GO terms that are not common in the three cytolines and could therefore be linked to retrograde signaling. Filtering for DEGs with a fold regulation > 2 (absolute values) that are exclusive to just one of the cytolines, we find a total of 391 up- and down-DEGs. Similarly, there are 19 GO terms with a fold enrichment > 2 that are cytoline-specific. Using GBS data we report contrasting differences in the number of DEGs and GO terms in each cytoline, which correlate with the genetic distances between the mitochondrial genomes (but not chloroplast) and the original nuclei of the cytolines, respectively.ConclusionsThe experimental design used here adds a new facet to the paradigm used to explain how gene expression changes in response to heat stress, capturing the influence exerted by different organelles upon one nucleus rather than investigating the response of several nuclei in their innate cytoplasmic environments.

Cold temperatures often severely restrict the growth, distribution and productivity of plants. The freezing tolerance of plants from temperate climates can be improved by undergoing periods of cold acclimation (CA). Tobacco is an important economic plant and is sensitive to cold stress. However, the dynamic changes and regulatory mechanisms of gene expression and metabolic processes during CA remain largely unknown. In this study, we performed RNA sequencing and metabolomic profiling analyses to identify the genes and metabolites specifically expressed during CA. Our transcriptomic data revealed 6905 differentially expressed genes (DEGs) during CA. Functional annotation and enrichment analyses revealed that the DEGs were involved mainly in signal transduction, carbohydrate metabolism and phenylpropanoid biosynthesis. Moreover, a total of 35 significantly changed metabolites were identified during CA via an LC-MS platform. Many protective metabolites, such as amino acids, carbohydrates, tricarboxylic acid (TCA) cycle intermediates and phenylpropanoid-related substances, were identified during CA. The gene-metabolite network extensively outlined the biological processes associated with the utilization of sugars, activation of amino acid metabolism, TCA cycle and phenylpropanoid biosynthesis in tobacco under CA. The results of our present study provide a comprehensive view of signal transduction and regulation, gene expression and dynamic changes in metabolites during CA.

Droughts, due to global warming, have become a major abiotic stress for plants. Rhododendron pulchrum is among the top 10 most sought-after flowers in China; however, because of its sensitivity to water, it is often drought-stressed in landscaping practices. This has restricted its promotion in garden landscaping. Thus, we performed transcriptomic analyses of this species under moderate to severe dehydration and rehydration to investigate the dynamics of gene expression. A total of 310, 1452, and 2610 differentially expressed genes (DEGs) were identified under moderate drought stress vs control, moderate drought vs severe drought, and severe drought vs re-watering conditions, respectively. A total of 209 transcription factors (TFs) were shown to be dehydration-responsive. Trend analysis of all the DEGs yielded 26 profiles of dynamic expression patterns. Among them, 6 profiles could be further grouped into cluster 1 (1230 DEGs) and cluster 2 (1164 DEGs) representing drought-induced and drought-repressed conditions, respectively. Transcriptomic changes in the key GO/pathways in this plant were analyzed and have been discussed in relation to hormone signal transduction, metabolic processes, and protein protective activity during drought treatment. This study provides valuable dataset regarding R. pulchrum gene expression changes in response to drought and may facilitate identification of potential genes that could be used to improve drought tolerance via genetic engineering of non-model plant species.

BackgroundIn strawberry cultivation, continuous cropping (CC) obstacles seriously threaten production. A patented soil amendment (SA) can effectively relieve the CC obstacles to strawberry cultivation, but knowledge of the recovery mechanisms underlying this phenomenon is limited.ResultsIn this study, transcriptomic profiling of strawberry roots in soil with and without the SA was conducted using RNA-Seq technology to reveal gene expression changes in response to SA treatment. In total, 188 differentially expressed genes (DEGs), including 144 upregulated and 44 downregulated DEGs, were identified. SA treatment resulted in genotype-dependent responses, and the response pattern, including an overall increase in the expression of nutrient transport genes and a decrease in the expression of defense response genes, may be a possible mechanism underlying recovery strategies in strawberry roots after the application of the SA to CC soil. We also found that 9 Hsp genes involved in plant defense pathways were all downregulated in the SA-treated roots.ConclusionsThis research indicated that strawberry plants reallocated defense resources to development when SA treatment alleviated the stress caused by a CC soil environment. The present study provides an opportunity to reveal the fundamental mechanisms of the tradeoff between growth and defense in strawberry.

The ovarian immune system ages while coping with the two main challenges of the aging ovary before menopause, the inflammatory stimulations due to repeated cycles and the increasing need for clearance of accumulating atretic follicles.

BackgroundAs part of the civil aviation safety program to define the adverse effects of ethanol on flying performance, we performed a DNA microarray analysis of human whole blood samples from a five-time point study of subjects administered ethanol orally, followed by breathalyzer analysis, to monitor blood alcohol concentration (BAC) to discover significant gene expression changes in response to the ethanol exposure.MethodsSubjects were administered either orange juice or orange juice with ethanol. Blood samples were taken based on BAC and total RNA was isolated from PaxGene™ blood tubes. The amplified cDNA was used in microarray and quantitative real-time polymerase chain reaction (RT-qPCR) analyses to evaluate differential gene expression. Microarray data was analyzed in a pipeline fashion to summarize and normalize and the results evaluated for relative expression across time points with multiple methods. Candidate genes showing distinctive expression patterns in response to ethanol were clustered by pattern and further analyzed for related function, pathway membership and common transcription factor binding within and across clusters. RT-qPCR was used with representative genes to confirm relative transcript levels across time to those detected in microarrays.ResultsMicroarray analysis of samples representing 0%, 0.04%, 0.08%, return to 0.04%, and 0.02% wt/vol BAC showed that changes in gene expression could be detected across the time course. The expression changes were verified by qRT-PCR.The candidate genes of interest (GOI) identified from the microarray analysis and clustered by expression pattern across the five BAC points showed seven coordinately expressed groups. Analysis showed function-based networks, shared transcription factor binding sites and signaling pathways for members of the clusters. These include hematological functions, innate immunity and inflammation functions, metabolic functions expected of ethanol metabolism, and pancreatic and hepatic function. Five of the seven clusters showed links to the p38 MAPK pathway.ConclusionsThe results of this study provide a first look at changing gene expression patterns in human blood during an acute rise in blood ethanol concentration and its depletion because of metabolism and excretion, and demonstrate that it is possible to detect changes in gene expression using total RNA isolated from whole blood. The analysis approach for this study serves as a workflow to investigate the biology linked to expression changes across a time course and from these changes, to identify target genes that could serve as biomarkers linked to pilot performance.

BackgroundCucurbit yellow stunting disorder virus (CYSDV; genus Crinivirus, Closteroviridae) is transmitted in a semipersistent manner by the whitefly, Bemisia tabaci, and is efficiently transmitted by the widely prevalent B. tabaci cryptic species, MEAM1. In this study, we compared transcriptome profiles of B. tabaci MEAM1, after 24 h, 72 h and 7 days of acquisition feeding on melon plants infected with CYSDV (CYSDV-whiteflies) with those fed on virus-free melon, using RNA-Seq technology. We also compared transcriptome profiles with whiteflies fed on tomato plants separately infected with Tomato chlorosis virus (ToCV), a crinivirus closely related to CYSDV, and Tomato yellow leaf curl virus (TYLCV), a member of the genus Begomovirus, which has a distinctly different mode of transmission and their respective virus-free controls, to find common gene expression changes among viruliferous whiteflies feeding on different host plants infected with distinct (TYLCV) and related (CYSDV and ToCV) viruses.ResultsA total of 275 differentially expressed genes (DEGs) were identified in CYSDV-whiteflies, with 3 DEGs at 24 h, 221 DEGs at 72 h, and 51 DEGs at 7 days of virus acquisition. Changes in genes encoding orphan genes (54 genes), phosphatidylethanolamine-binding proteins (PEBP) (20 genes), and AAA-ATPase domain containing proteins (10 genes) were associated with the 72 h time point. Several more orphan genes (20 genes) were differentially expressed at 7 days. A total of 59 common DEGs were found between CYSDV-whiteflies and ToCV-whiteflies, which included 20 orphan genes and 6 lysosomal genes. A comparison of DEGs across the three different virus-host systems revealed 14 common DEGs, among which, eight showed similar and significant up-regulation in CYSDV-whiteflies at 72 h and TYLCV-whiteflies at 24 h, while down-regulation of the same genes was observed in ToCV-whiteflies at 72 h.ConclusionsDynamic gene expression changes occurred in CYSDV-whiteflies after 72 h feeding, with decreased gene expression changes associated with 7 days of CYSDV acquisition. Similarities in gene expression changes among CYSDV-whiteflies, ToCV-whiteflies and TYLCV-whiteflies suggest the possible involvement of common genes or pathways for virus acquisition and transmission by whiteflies, even for viruses with distinctly different modes of transmission.

Gene profiling methods have been widely useful for delineating changes in gene expression as an approach for gaining insight into the mechanism of rejection or disease pathology. Herein, we use gene profiling to compare changes in gene expression associated with different orthotopic cardiac xenotransplantation (OCXTx) outcomes and to identify potential effects of OCXTx on cardiac physiology. We used the Affymetrix GeneChip Porcine Genomic Array to characterize three types of orthotopic cardiac xenograft outcomes: 1) rejected hearts that underwent delayed xenograft rejection (DXR); 2) survivor hearts in which the xenograft was not rejected and recipient death was due to model complications; and 3) hearts which failed to provide sufficient circulatory support within the first 48 h of transplant, termed "perioperative cardiac xenograft dysfunction" (PCXD). Gene expression in each group was compared to control, not transplanted pig hearts, and changes in gene expression > 3 standard deviations (±3SD) from the control samples were analyzed. A bioinformatics analysis was used to identify enrichments in genes involved in Kyoto Encyclopedia of Genes and Genomes pathways and gene ontogeny molecular functions. Changes in gene expression were confirmed by quantitative RT-PCR. The ±3SD data set contained 260 probes, which minimally exhibited a 3.5-fold change in gene expression compared to control pig hearts. Hierarchical cluster analysis segregated rejected, survivor and PCXD samples, indicating a unique change in gene expression for each group. All transplant outcomes shared a set of 21 probes with similarly altered expression, which were indicative of ongoing myocardial inflammation and injury. Some outcome-specific changes in gene expression were identified. Bioinformatics analysis detected an enrichment of genes involved in protein, carbohydrate and branched amino acid metabolism, extracellular matrix-receptor interactions, focal adhesion, and cell communication. This is the first genome wide assessment of changes in cardiac gene expression after OCXTx. Hierarchical cluster analysis indicates a unique gene profile for each transplant outcome but additional samples will be required to define the unique classifier probe sets. Quantitative RT-PCR confirmed that all transplants exhibited strong evidence of ongoing inflammation and myocardial injury consistent with the effects of cytokines and vascular antibody-mediated inflammation. This was also consistent with bioinformatic analysis suggesting ongoing tissue repair in survivor and PCXD samples. Bioinformatics analysis suggests for the first time that xenotransplantation may affect cardiac metabolism in survivor and rejected samples. This study highlights the potential utility of molecular analysis to monitor xenograft function, to identify new molecular markers and to understand processes, which may contribute to DXR.

Simple SummaryThe fat body is one of the most important tissues in the body of insects due to its number of functions. Nowadays the new physiological function of H2S has gained attention as a novel signaling molecule. H2S performs crucial regulatory functions involving growth, the cardiovascular system, oxidative stress, and inflammation in many organisms. In this study, RNA-seq technology was used to investigate the fat body of the silkworm at the transcriptional level after H2S exposure during the 5th larvae stage. A total of 1200 (DEGs) was identified after 7.5 µM H2S treatment, of which 977 DEGs were up-regulated and 223 DEGs were down-regulated. DEGs were mainly involved in the transport pathway, cellular community, carbohydrate metabolism, and immune-associated signal transduction. Present research provides new insights on the gene expression changes in the fat body of silkworms after H2S exposure.Hydrogen sulfide (H2S) has been recognized for its beneficial influence on physiological alterations. The development (body weight) and economic characteristics (cocoon weight, cocoon shell ratio, and cocoon shell weight) of silkworms were increased after continuous 7.5 µM H2S treatment. In the present study, gene expression changes in the fat body of silkworms at the 5th instar larvae in response to the H2S were investigated through comparative transcriptome analysis. Moreover, the expression pattern of significant differentially expressed genes (DEGs) at the 5th instar larvae was confirmed by quantitative real-time PCR (qRT-PCR) after H2S exposure. A total of 1200 (DEGs) was identified, of which 977 DEGs were up-regulated and 223 DEGs were down-regulated. Most of the DEGs were involved in the transport pathway, cellular community, carbohydrate metabolism, and immune-associated signal transduction. The up regulated genes under H2S exposure were involved in endocytosis, glycolysis/gluconeogenesis, the citrate cycle (TCA cycle), and the synthesis of fibroin, while genes related to inflammation were down-regulated, indicating that H2S could promote energy metabolism, the transport pathway, silk synthesis, and inhibit inflammation in the silkworm. In addition, the expression levels of these genes were increased or decreased in a time-dependent manner during the 5th instar larvae. These results provided insight into the effects of H2S on silkworms at the transcriptional level and a substantial foundation for understanding H2S function.

Aims/hypothesisRepeated exposures to insulin-induced hypoglycaemia in people with diabetes progressively impairs the counterregulatory response (CRR) that restores normoglycaemia. This defect is characterised by reduced secretion of glucagon and other counterregulatory hormones. Evidence indicates that glucose-responsive neurons located in the hypothalamus orchestrate the CRR. Here, we aimed to identify the changes in hypothalamic gene and protein expression that underlie impaired CRR in a mouse model of defective CRR.MethodsHigh-fat-diet fed and low-dose streptozocin-treated C57BL/6N mice were exposed to one (acute hypoglycaemia [AH]) or multiple (recurrent hypoglycaemia [RH]) insulin-induced hypoglycaemic episodes and plasma glucagon levels were measured. Single-nuclei RNA-seq (snRNA-seq) data were obtained from the hypothalamus and cortex of mice exposed to AH and RH. Proteomic data were obtained from hypothalamic synaptosomal fractions.ResultsThe final insulin injection resulted in similar plasma glucose levels in the RH group and AH groups, but glucagon secretion was significantly lower in the RH group (AH: 94.5±9.2 ng/l [n=33]; RH: 59.0±4.8 ng/l [n=37]; p<0.001). Analysis of snRNA-seq data revealed similar proportions of hypothalamic cell subpopulations in the AH- and RH-exposed mice. Changes in transcriptional profiles were found in all cell types analysed. In neurons from RH-exposed mice, we observed a significant decrease in expression of Avp, Pmch and Pcsk1n, and the most overexpressed gene was Kcnq1ot1, as compared with AH-exposed mice. Gene ontology analysis of differentially expressed genes (DEGs) indicated a coordinated decrease in many oxidative phosphorylation genes and reduced expression of vacuolar H+- and Na+/K+-ATPases; these observations were in large part confirmed in the proteomic analysis of synaptosomal fractions. Compared with AH-exposed mice, oligodendrocytes from RH-exposed mice had major changes in gene expression that suggested reduced myelin formation. In astrocytes from RH-exposed mice, DEGs indicated reduced capacity for neurotransmitters scavenging in tripartite synapses as compared with astrocytes from AH-exposed mice. In addition, in neurons and astrocytes, multiple changes in gene expression suggested increased amyloid beta (Aβ) production and stability. The snRNA-seq analysis of the cortex showed that the adaptation to RH involved different biological processes from those seen in the hypothalamus.Conclusions/interpretationThe present study provides a model of defective counterregulation in a mouse model of type 2 diabetes. It shows that repeated hypoglycaemic episodes induce multiple defects affecting all hypothalamic cell types and their interactions, indicative of impaired neuronal network signalling and dysegulated hypoglycaemia sensing, and displaying features of neurodegenerative diseases. It also shows that repeated hypoglycaemia leads to specific molecular adaptation in the hypothalamus when compared with the cortex.Data availabilityThe transcriptomic dataset is available via the GEO (http://www.ncbi.nlm.nih.gov/geo/), using the accession no. GSE226277. The proteomic dataset is available via the ProteomeXchange data repository (http://www.proteomexchange.org), using the accession no. PXD040183.Graphical

Eucalyptus nitens (H. Deane & Maiden) is a fast-growing species used principally for pulpwood and solid-wood production. Due to its cold tolerance, it is preferred over other Eucalyptus species at high elevations. To get a deeper insight in the molecular mechanisms of cold acclimation, the transcriptome profiling by RNA-Seq in plants of E. nitens under cold acclimation and deacclimation process was compared in order to identify differentially expressed genes (DEGs). Transcriptomes from control, cold acclimated to chilling temperature, cold acclimated at freezing temperature, and deacclimation condition were compared using Eucalyptus grandis as reference genome. The differential expression analysis allowed the identification of a total of 1600 DEGs out of which 1088 and 1071 were identified in response to cold acclimation and deacclimation, respectively. The gene ontology analysis revealed that DEGs were significantly enriched in response to stimulus, response to abiotic stimulus, membrane, catalytic activity, and cell periphery. Furthermore, the biochemical pathways analysis revealed a large number of DEGs represented in the biosynthesis of phenylpropanoids, specifically flavonoid biosynthesis likely to support ROS scarvening, genes related to photosynthesis, genes that take part in glycolysis/gluconeogenesis related to starch biosynthesis pathway, and genes represented in carotenoid biosynthesis pathway suggesting a role in the regulation of ABA synthesis, which has been previously involved in stress tolerance. A total of 115 DEGs corresponding to transcription factors were identified, being the most represented families AP2, MYB, and WRKY. Expression of six DEGs was validated using qRT-PCR that further supported the in silico results. The present study provides a comprehensive view of global gene expression and revealed valuable information about the dynamic and complex nature of gene expression occurring during cold acclimation and deacclimation process in E. nitens.