Gene Expression Response Patterns Research Articles

Acute Inflammation Induces Neuroendocrine and Opioid Receptor Genes Responses in the Seabass Dicentrarchus labrax Brain.

Simple SummaryIt is generally accepted (in mammals and in teleost fish, too) that stressful conditions affect the performance of an immune response. What is still far from being known is at what extend does an immune process affects the neuroendocrine system. Vaccination for instance, is nowadays a common practice in aquaculture and little is known about its physiological implications other than immunization. Here is a first approach to the study of the European seabass’ brain gene expression patterns in response to a peripheral inflammatory process. Genes related to the stress response were focused, along with those related to the opioid system. Increased expression of certain genes suggests the activation of a stress response triggered by inflammatory signals. Additionally, contrasting expression patterns of the same gene (increased vs decreased) in the different brain regions (as well as the time needed for changes to happen) point at different functions. These results clearly show the reactivity of different brain responses to an immune response, highlighting the importance of further studies on downstream implications (behavior, feeding, welfare, reproduction). In fish, as observed in mammals, any stressful event affects the immune system to a larger or shorter extent. The neuroendocrine-immune axis is a bi-directional network of mobile compounds and their receptors that are shared between both systems (neuroendocrine and immune) and that regulate their respective responses. However, how and to what extent immunity modulates the neuroendocrine system is not yet fully elucidated. This study was carried out to understand better central gene expression response patterns in a high-valued farmed fish species to an acute peripheral inflammation, focusing on genes related to the hypothalamus-pituitary-interrenal axis and the opioid system. European seabass, Dicentrarchus labrax, were intra-peritoneally injected with either Freund’s Incomplete Adjuvant to induce a local inflammatory response or Hanks Balances Salt Solution to serve as the control. An undisturbed group was also included to take into account the effects due to handling procedures. To evaluate the outcomes of an acute immune response, fish were sampled at 4, 24, 48, and 72 h post-injection. The brain was sampled and dissected for isolation of different regions: telencephalon, optic tectum, hypothalamus, and pituitary gland. The expression of several genes related to the neuroendocrine response was measured by real-time PCR. Data were statistically analyzed by ANOVA and discriminant analyses to obtain these genes’ responsiveness for the different brain regions. Serotonergic receptors were upregulated in the telencephalon, whereas the optic tectum inhibited these transcription genes. The hypothalamus showed a somewhat delayed response in which serotonin and glucocorticoid receptors were concerned. Still, the hypothalamic corticotropin-releasing hormone played an important role in differentiating fish undergoing an inflammatory response from those not under such conditions. Opioid receptors gene expression increased in both the hypothalamus and the telencephalon, while in the optic tectum, most were downregulated. However, no changes in the pituitary gland were observed. The different brain regions under immune stimulation demonstrated clear, distinct responses regarding gene transcription rates as well as the time period needed for the effect to occur. Further, more integrative studies are required to associate functions to the evaluated genes more safely and better understand the triggering mechanisms.

Oxidative stress-related gene expression in diploid and triploid rainbow trout (Oncorhynchus mykiss) fed diets with organic and inorganic zinc

In rainbow trout, zinc is among the most important essential micro-minerals involved in many biological processes such as oxidative stress, bone mineralization, and growth. Organic minerals are often reported to be more bioavailable to fish, thus requiring lower amounts to meet the zinc requirement. Rainbow trout are commonly reared as both diploids and triploids, but it is unknown if ploidy status affects how the fish responds to dietary zinc supplementation. This study examined gene expression response patterns in both diploid and triploid rainbow trout fed to satiation for 9 weeks with either inorganic (ZnSO4) or organic (amino acid chelated) zinc supplemented in incremental levels (Zn63, Zn123, Zn183) to an otherwise sufficient basal diet (Zn33). Hepatic expression of genes related to oxidative stress were analyzed and included superoxide dismutase (SOD1; SOD2), glutathione peroxidase (GPX1a; GPX1b1; GPX1b2), catalase (CAT), glutathione reductase (GSR), glutathione S-transferase (GST), liver X receptor (LXR), and the zinc storage protein, metallothionein-A (MTA). Expression of all genes, except MTA, was significantly elevated with organic zinc supplementation (all with a p-value < 0.001). There was also a zinc dose-dependent increase in SOD1 (p = 0.002) and SOD2 (p = 0.020) expression (organic zinc only) and CAT (p < 0.001) expression. Dose-dependent reductions in gene expression were detected for GSR (p < 0.001), GST (p = 0.002), and MTA (p = 0.004). There were also gene expression differences between diploids and triploids, suggesting that triploids were more sensitive to potential improvements in zinc bioavailability in the organic zinc-containing diets. Findings support that zinc supplementation, particularly organic zinc, beyond the dietary requirement may enhance the antioxidant defense system and improve fish health by reducing oxidative stress. However, more research is required for better comprehension of all subsequent effects.

Gracilaria tenuistipitata (Rhodophyta) tolerance to cadmium and copper exposure observed through gene expression and photosynthesis analyses

Heavy metals are toxic to all organisms and their presence can have great impact on ecosystems. The study of strategies to remove contaminants is thus important, as is increased understanding of the resistance mechanisms of candidate organisms to be used as phytoremediators. The present study evaluate the genes involved in chronic stress using two different expression techniques to profile the transcriptome of the marine macroalga Gracilaria tenuistipitata after exposure to the EC50 of cadmium (Cd) and copper (Cu). Some known molecular markers for chronic pollution were observed, indicating that resistance mechanisms are induced within the first hour of treatment. Differences in gene expression response patterns between the two metals were found, where Cd up-regulated the expressions of superoxide dismutase and the nitrate transporter NRT even after 6 days of exposure. Expressions of both nuclear and chloroplast-encoded proteins were affected, and a stronger tolerance mechanism involving proteins of unknown function is certainly connected to the tolerance of the alga, warranting further studies. After 6 days of exposure to Cd or Cu, a slower acclimation was detected for the latter. Analysis of the photosynthetic rate revealed acclimation over time, corroborating a previous study where G. tenuistipitata was able to accumulate these metals and tolerate their negative effects, reinforcing the potential use of this macroalga in integrated bioremediation processes.

Cycle training modulates satellite cell and transcriptional responses to a bout of resistance exercise.

This investigation evaluated whether moderate‐intensity cycle ergometer training affects satellite cell and molecular responses to acute maximal concentric/eccentric resistance exercise in middle‐aged women. Baseline and 72 h postresistance exercise vastus lateralis biopsies were obtained from seven healthy middle‐aged women (56 ± 5 years, BMI 26 ± 1, VO 2max 27 ± 4) before and after 12 weeks of cycle training. Myosin heavy chain (MyHC) I‐ and II‐associated satellite cell density and cross‐sectional area was determined via immunohistochemistry. Expression of 93 genes representative of the muscle‐remodeling environment was also measured via NanoString. Overall fiber size increased ~20% with cycle training (P = 0.052). MyHC I satellite cell density increased 29% in response to acute resistance exercise before endurance training and 50% with endurance training (P < 0.05). Following endurance training, MyHC I satellite cell density decreased by 13% in response to acute resistance exercise (acute resistance × training interaction, P < 0.05). Genes with an interaction effect tracked with satellite cell behavior, increasing in the untrained state and decreasing in the endurance trained state in response to resistance exercise. Similar satellite cell and gene expression response patterns indicate coordinated regulation of the muscle environment to promote adaptation. Moderate‐intensity endurance cycle training modulates the response to acute resistance exercise, potentially conditioning the muscle for more intense concentric/eccentric activity. These results suggest that cycle training is an effective endurance exercise modality for promoting growth in middle‐aged women, who are susceptible to muscle mass loss with progressing age.

Identification and expression analysis of cytokinin response regulators in Fragaria vesca

Cytokinin response regulators (RRs) are important components of the two component signal systems, which are involved in the regulation of plant growth and development, and in the response to abiotic stress. In this study, 18 cytokinin RR genes were identified in Fragaria vesca through the genome-wide search. They were further classified into three types: type-A (FvRR1–7), type-B (FvRR8–14) and type-C (FvRR15–18) according to the domain architecture and the phylogeny. Phylogenetic analysis demonstrated that most cytokinin response regulators of F. vesca and Arabidopsis formed clear orthologous pairs. Expression patterns of the cytokinin FvRR genes in various tissues and organs at reproductive stages were detected in this study. Additionally, gene expression response patterns to ABA and abiotic stresses including high temperature and osmotic stress were investigated. The results showed that different types of cytokinin FvRRs have different expression patterns, suggesting the functional differentiation of cytokinin FvRRs during the evolution. This systematic study provides insights into possible functions of the cytokinin FvRR genes and a basis for further functional analysis.

Shade-Inducible Gene Expression Change in &amp;lt;i&amp;gt;Arabidopsis thaliana&amp;lt;/i&amp;gt; at Different Temperatures

We tested whether the plant response to an environmental factor could be affected by the context of another factor by using shade avoidance response at different temperatures. Depleting the red light (R; λmax = 660 nm) and/or enriching the far-red light (FR; λmax = 730 nm) results in a low R:FR ratio in the environment, which induces shade avoidance response such as elongation of petioles and reduction of plant pigments. On the other hand, warmer environmental temperature is known to mimic shade avoidance response under normal light condition, suggesting a potential crosstalk between the temperature and the light quality signals. Therefore, we investigated the patterns of gene expression responses to low R:FR ratio in different temperature contexts (22°C and 26°C) through microarray analyses. Similar, yet distinct patterns between the two responses were implicated by the levels of correlation in the commonly affected MapMan bins. However, the induction levels of typical shade genes such as ATHB2, IAA29, IAA19, HFR1, YUC8, and FT were very similar at both temperatures. Moreover, petiole length, chlorophylls, carotenoids, and anthocyanins contents did not support any statistically significant interaction between the light quality and the high temperature responses despite the obvious independent effect of each signal, which suggests cumulative effects of two independent responses. Nevertheless, other types of low R: FR-responsive genes with differential expression patterns at different temperatures were identified. They are overrepresented in secondary metabolism, lipid transport, oxidative stress, jasmonic acid, ethylene, light, pathogen defense responses, and extracellular region.

Polynomial equation models for yeast cell-cycle time series microarray data by analysing fidelity matrices of gene expression values

Identifying the various gene expression response patterns in microarray time-course experiments is a very challenging issue. It is impossible to manually characterise a parametric form for each of the time point values in gene microarray in a gene by gene manner. The difficulty arises due to heterogeneity in the regulatory reactions among thousands of genes. In this paper, we develop two polynomial equation models to automatically define the time-dependent expression patterns for gene expression time series microarray data. Our developed polynomial equations with power terms from a set of fixed values offer a wide range of curve shapes. The generated polynomial equations suggest the best fitting model of gene microarray time series data values. It also measures the level of mRNA expression of thousands of genes. The effectiveness of the proposed models is first demonstrated for artificial data sets. We then identify the best suited polynomial equation of our specimen real-life gene microarray time series data of yeast cell cycle.

Interferon-Beta Induces Distinct Gene Expression Response Patterns in Human Monocytes versus T cells

BackgroundMonocytes, which are key players in innate immunity, are outnumbered by neutrophils and lymphocytes among peripheral white blood cells. The cytokine interferon-β (IFN-β) is widely used as an immunomodulatory drug for multiple sclerosis and its functional pathways in peripheral blood mononuclear cells (PBMCs) have been previously described. The aim of the present study was to identify novel, cell-specific IFN-β functions and pathways in tumor necrosis factor (TNF)-α-activated monocytes that may have been missed in studies using PBMCs.Methodology/Principal FindingsWhole genome gene expression profiles of human monocytes and T cells were compared following in vitro priming to TNF-α and overnight exposure to IFN-β. Statistical analyses of the gene expression data revealed a cell-type-specific change of 699 transcripts, 667 monocyte-specific transcripts, 21 T cell-specific transcripts and 11 transcripts with either a difference in the response direction or a difference in the magnitude of response. RT-PCR revealed a set of differentially expressed genes (DEGs), exhibiting responses to IFN-β that are modulated by TNF-α in monocytes, such as RIPK2 and CD83, but not in T cells or PBMCs. Known IFN-β promoter response elements, such as ISRE, were enriched in T cell DEGs but not in monocyte DEGs. The overall directionality of the gene expression regulation by IFN-β was different in T cells and monocytes, with up-regulation more prevalent in T cells, and a similar extent of up and down-regulation recorded in monocytes.ConclusionsBy focusing on the response of distinct cell types and by evaluating the combined effects of two cytokines with pro and anti-inflammatory activities, we were able to present two new findings First, new IFN-β response pathways and genes, some of which were monocytes specific; second, a cell-specific modulation of the IFN-β response transcriptome by TNF-α.

Prerequisites, performance and profits of transcriptional profiling the abiotic stress response

During the last decade, microarrays became a routine tool for the analysis of transcripts in the model plant Arabidopsis thaliana and the crop plant species rice, poplar or barley. The overwhelming amount of data generated by gene expression studies is a valuable resource for every scientist. Here, we summarize the most important findings about the abiotic stress responses in plants. Interestingly, conserved patterns of gene expression responses have been found that are common between different abiotic stresses or that are conserved between different plant species. However, the individual histories of each plant affect the inter-comparability between experiments already before the onset of the actual stress treatment. This review outlines multiple aspects of microarray technology and highlights some of the benefits, limitations and also pitfalls of the technique. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.

A Growth Curve Model with Fractional Polynomials for Analysing Incomplete Time-Course Data in Microarray Gene Expression Studies

Identifying the various gene expression response patterns is a challenging issue in expression microarray time-course experiments. Due to heterogeneity in the regulatory reaction among thousands of genes tested, it is impossible to manually characterize a parametric form for each of the time-course pattern in a gene by gene manner. We introduce a growth curve model with fractional polynomials to automatically capture the various time-dependent expression patterns and meanwhile efficiently handle missing values due to incomplete observations. For each gene, our procedure compares the performances among fractional polynomial models with power terms from a set of fixed values that offer a wide range of curve shapes and suggests a best fitting model. After a limited simulation study, the model has been applied to our human in vivo irritated epidermis data with missing observations to investigate time-dependent transcriptional responses to a chemical irritant. Our method was able to identify the various nonlinear time-course expression trajectories. The integration of growth curves with fractional polynomials provides a flexible way to model different time-course patterns together with model selection and significant gene identification strategies that can be applied in microarray-based time-course gene expression experiments with missing observations.

Differential Global Gene Expression Response Patterns of Human Endothelium Exposed to Shear Stress and Intraluminal Pressure

We investigated the global gene expression response of endothelium exposed to shear stress and intraluminal pressure and tested the hypothesis that the two biomechanical forces induce a differential gene expression response pattern. Intact living human conduit vessels (umbilical veins) were exposed to normal or high intraluminal pressure, or to low or high shear stress in combination with a physiological level of the other force in a unique vascular ex vivo perfusion system. Gene expression profiling was performed by the Affymetrix microarray technology on endothelial cells isolated from stimulated vessels. Biomechanical forces were found to regulate a very large number of genes in the vascular endothelium. In this study, 1,825 genes were responsive to mechanical forces, which corresponds to 17% of the expressed genes. Among pressure-responsive genes, 647 genes were upregulated and 519 genes were downregulated, and of shear stress-responsive genes, 133 genes were upregulated and 771 downregulated. The fraction of genes that responded to both pressure and shear stimulation was surprisingly low, only 13% of the regulated genes. Our results indicate that the two different stimuli induce distinct gene expression response patterns, which can also be observed when studying functional groups. Considering the low number of overlapping genes, we suggest that the endothelial cells can distinguish between shear stress and pressure stimulation.

Control of endothelial cell gene expression by flow

The vessel wall is constantly subjected to, and affected by, the stresses resulting from the hemodynamic stimuli of transmural pressure and flow. At the interface between blood and the vessel wall, the endothelial cell plays a crucial role in controlling vessel structure and function in response to changes in hemodynamic conditions. Using bovine aortic endothelium monolayers, we show that fluid shear stress causes simultaneous differential regulation of endothelial-derived products. We also report that the downregulation of endothelin-1 mRNA by flow is a reversible process, and through the use of uncharged dextran supplementation demonstrate it to be shear stress-rather than shear rate-dependent. Recent work on the effect of fluid shear stress on endothelial cell gene expression of a number of potent endothelial products is reviewed, including vasoactive substances, autocrine and paracrine growth factors, thrombosis/fibrinolysis modulators, chemotactic factors, surface receptors and immediate-early genes. The encountered patterns of gene expression responses are classified into three categories: a transient increase with return to baseline (type I), a sustained increase (type II) and a biphasic response consisting of an early transient increase of varying extent followed by a pronounced and sustained decrease (type III). The importance of the dynamic character of the flow stimulus and the magnitude dependence of the response are presented. Potential molecular mechanisms of shear-induced gene regulation, including putative shear stress response elements (SSRE), are discussed. These results suggest exquisite modulation of endothelial cell phenotype by local fluid shear stress and may offer insight into the mechanism of flow-dependent vascular remodeling and the observed propensity of atherosclerosis formation around bifurcations and areas of low shear stress.