Methamphetamine effects in zebrafish (Danio rerio) depend on behavioral endpoint, dose and test session duration

Research using zebrafish (Danio rerio) has begun to provide novel information in many fields, including the behavioral pharmacology of drug use and misuse. There have been limited studies on the effects of methamphetamine in adult zebrafish and the parameters of exposure (dose, test session length) have not been well-documented. Behavior following drug exposure is generally measured during relatively short sessions (6-10 min is common) in a novel tank environment. Many procedural variables (isolation, netting, novel tank) elicit anxiety-like behavior that is most apparent during the initial portion of a test session. This anxiety-like behavior might mask the initial effects of methamphetamine. During longer test sessions, these anxiety-like responses would be expected to habituate and drug effects should become more apparent. To test this idea, we measured several locomotor activity responses for 50-min following a range of methamphetamine doses (0.1-3.0 mg/L via immersion in methamphetamine solution). Methamphetamine failed to alter swimming velocity, distance travelled, or freezing time. In contrast, methamphetamine produced a dose-dependent decrease in time spent in the bottom of the tank, an increase in the number of visits to the top of the tank, and an increase in the number of transitions along the sides of the tank. The effects of methamphetamine were apparent 10-20 min following exposure and generally persisted throughout the session. These findings indicate that longer test sessions are required to measure methamphetamine-induced changes in behavior in zebrafish, as has been shown in other laboratory animals. The results also suggest that anxiety-like responses associated with various procedural aspects (netting, isolation, novel test apparatus) likely interfere with the ability to observe many behavioral effects of methamphetamine in zebrafish. Based on the current results, habituation to testing procedures to reduce anxiety-like behaviors is recommended in determining the effects of methamphetamine in zebrafish.

Integrative Analysis of Differentially Expressed Genes in Time-Course Multi-Omics Data with MINT-DE

Background

Time-course multi-omics experiments have been highly informative for obtaining a comprehensive understanding of the dynamic relationships between molecules in a biological process, especially if the different profiles are obtained from the same samples. A fundamental step in analyzing time-course multi-omics data involves selecting a short list of genes or gene regions ("sites") that warrant further study. Two important criteria for site selection are the magnitude of change and the temporal dynamic consistency. However, existing methods only consider one of these criteria, while neglecting the other.

Results

In our study, we propose a framework called MINT-DE (Multi-omics INtegration of Time-course for Diffierential Expression analysis) to address this limitation. MINT-DE is capable of selecting sites based on summarized measures of both aforementioned aspects. We calculate evidence measures assessing the extent of differential expression for each assay and for the dynamical similarity across assays. Then based on the summary of the evidence assessment measures, sites are ranked. To evaluate the performance of MINT-DE, we apply it to analyze a time-course multi-omics dataset of Drosophila development. We compare the selection obtained from MINT-DE with those obtained from other existing methods. The analysis reveal that MINT-DE is able to identify differentially expressed time-course pairs with the highest correlations. Their corresponding genes are significantly enriched for known biological functions, as measured by gene-gene interaction networks and the Gene Ontology enrichment.

Conclusions

These findings suggest the effectiveness of MINT-DE in selecting sites that are both differentially expressed within at least one assay and temporally related across assays. This highlights the potential of MINT-DE to identify biologically important sites for downstream analysis and provide a complementarity of sites that is neglected by existing methods.

Age differences in the neural correlates of recollection: transient versus sustained fMRI effects

Prior functional magnetic resonance imaging findings in young adults indicate that recollection-sensitive neural regions dissociate according to the time courses of their respective recollection effects. Here, we examined whether such dissociations are also evident in older adults. Young and older participants encoded a series of word-image pairs, judging which of the denoted objects was the smaller. At the test, participants judged whether each of a series of test words was old or new. If a word was old, the requirement was to recall the associated image and maintain it over a variable delay period. Older adults demonstrated significantly lower associative memory performance than young adults. Transient recollection effects were identified in the left hippocampus, medial prefrontal cortex, and posterior cingulate, while sustained effects were widespread across left lateral cortex and were also evident in the bilateral striatum. Except for those in the left insula, all effects were age-invariant. These findings suggest that both transient and sustained recollection effects are largely stable across much of the healthy adult life span.

Metabolism of hydrogen peroxide by Lactobacillus plantarum NJAU-01: A proteomics study

This study aimed to investigate the time-course effect of Lactobacillus plantarum NJAU-01 in scavenging exogenous hydrogen peroxide (H₂O₂). The results showed that L. plantarum NJAU-01 at 10⁷ CFU/mL was able to eliminate a maximum of 4 mM H₂O₂ within a prolonged lag phase and resume to proliferate during the following culture. Redox state in the start-lag phase (0 h, without the addition of H₂O₂), indicated by glutathione and protein sulfhydryl, was impaired in the lag phase (3 h and 12 h) and then gradually recovered during subsequent growing stages (20 h and 30 h). By using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and proteomics analysis, a total of 163 proteins such as PhoP family transcriptional regulator, glutamine synthetase, peptide methionine sulfoxide reductase, thioredoxin reductase, ribosomal proteins, acetolactate synthase, ATP binding subunit ClpX, phosphoglycerate kinase, UvrABC system protein A and UvrABC system protein B were identified as differential proteins across the entire growth phase. Those proteins were mainly involved in H₂O₂ sensing, protein synthesis, repairing proteins and DNA lesions, amino sugar and nucleotide sugar metabolism. Our data suggest that biomolecules of L. plantarum NJAU-01 are oxidized to passively consume H₂O₂ and are restored by the enhanced protein and/or gene repair systems.

Toxicity of perfluorobutanesulfonate on gill functions of marine medaka (Oryzias melastigma): A time course and hypoxia co-exposure study

Perfluorobutanesulfonate (PFBS) is found in hypoxia regions. Results of previous studies have shown that hypoxia was capable of altering the inherent toxicity of PFBS. However, regarding gill functions, hypoxic influences and time course progression of toxic effects of PFBS remain unclear. In this study, with the aim to reveal the interaction behavior between PFBS and hypoxia, adult marine medaka Oryzias melastigma were exposed for 7 days to 0 or 10 μg PFBS/L under normoxic or hypoxic conditions. Subsequently, to explore the time-course transition in gill toxicity, medaka were exposed to PFBS for 21 days. The results showed that hypoxia dramatically increased the respiratory rate of medaka gill, which was further enhanced by exposure to PFBS; although exposure to PFBS under normoxic conditions for 7 days did not alter respiration, exposure to PFBS for 21 days significantly accelerated the respiration rate of female medaka. Concurrently, both hypoxia and PFBS were potent to interrupt the gene transcriptions and Na⁺, K⁺-ATPase enzymatic activity that play pivotal roles in the osmoregulation in gills of marine medaka, consequently disrupting homeostasis of major ions in blood, such as Na⁺, Cl^-, and Ca²⁺. In addition, composition and diversity of the microbiome residing on surfaces of the gill were profiled by using amplicon sequencing. Acute exposure to hypoxia for only 7 days caused a significant decrease in diversity of the bacterial community of gill whatever the presence of PFBS, while PFBS exposure for 21 days increased the diversity of gill microbial community. Principal component analysis revealed that, compared with PFBS, hypoxia was the predominant driver of gill microbiome dysbiosis. Depending on duration of exposure, a divergence was caused in the microbial community of gill. Overall, the current findings underline the interaction between hypoxia and PFBS on gill function and demonstrate the temporal variation in PFBS toxicity.

Temporal dynamics of brain BDNF expression following a single bout of exercise: A bioluminescence imaging study

Physical exercise increases brain-derived neurotrophic factor (BDNF) expression in the brain. However, the absence of non-invasive and repetitive monitoring of BDNF expression in the brains of living animals has limited the understanding of how BDNF expression changes after exercise. This study aimed to elucidate the temporal dynamics of BDNF expression in the brain after a single bout of exercise, using in vivo bioluminescence imaging. This study included Bdnf-Luc mice with a firefly Luciferase gene inserted at the translation start site of the mouse Bdnf gene. BDNF expression was evaluated based on the luminescence signal of the luciferase substrate administered to mice. Bioluminescence imaging was performed at 0, 1, 3, 6, 12, and 24 h after treadmill exercise (15 m/min for 1 h). Compared to the sedentary condition of each mouse, the luminescence signal increased by approximately 60 % between 1 and 3 h after exercise. The luminescence signal remained slightly increased by approximately 20 % even 6-24 h after exercise. This study is the first to demonstrate exercise-enhanced BDNF expression in the brains of living animals. These results provide evidence that a single bout of exercise transiently increases BDNF expression in the brain within a limited time window.

Data on cardiac lncRNA STX18-AS1 expression in developing human hearts and function during in vitro hESC-cardiomyocyte differentiation

This article presents data concerning STX18-AS1, a long noncoding RNA gene identified from a Genome-wide association study of Atrial Septal Defect (ASD). The data describes its expression patterns in human tissues and functions in regulating cardiomyocyte differentiation in vitro. STX18-AS1 is a lncRNA with a higher abundance in developing tissues, including hearts. Its transcription distribution within the embryonic hearts during key heart septation stages supports STX18-AS1's association with risk SNPs for ASD. The CRISPR stem cell pool in which STX18-AS1 was knocked down, showed reduced CM differentiation efficiency and lower expression of key cardiac transcriptional factors. This indicated its regulative role in supporting the lineage specification from cardiac mesoderm into cardiac progenitors and cardiomyocytes. These data can benefit the understanding of human embryonic heart developmental biology, and the time-course changes of cardiac transcriptional factors during in vitro cardiomyocyte differentiation from human embryonic stem cells.

Interpretation of exercise-induced changes in human skeletal muscle mRNA expression depends on the timing of the post-exercise biopsies

BACKGROUND

Exercise elicits a range of adaptive responses in skeletal muscle, which include changes in mRNA expression. To better understand the health benefits of exercise training, it is important to investigate the underlying molecular mechanisms of skeletal muscle adaptation to exercise. However, most studies have assessed the molecular events at only a few time-points within a short time frame post-exercise, and the variations of gene expression kinetics have not been addressed systematically.

METHODS

We assessed the mRNA expression of 23 gene isoforms implicated in the adaptive response to exercise at six time-points (0, 3, 9, 24, 48, and 72 h post exercise) over a 3-day period following a single session of high-intensity interval exercise.

RESULTS

The temporal patterns of target gene expression were highly variable and the expression of mRNA transcripts detected was largely dependent on the timing of muscle sampling. The largest fold change in mRNA expression of each tested target gene was observed between 3 and 72 h post-exercise.

DISCUSSION AND CONCLUSIONS

Our findings highlight an important gap in knowledge regarding the molecular response to exercise, where the use of limited time-points within a short period post-exercise has led to an incomplete understanding of the molecular response to exercise. Muscle sampling timing for individual studies needs to be carefully chosen based on existing literature and preliminary analysis of the molecular targets of interest. We propose that a comprehensive time-course analysis on the exercise-induced transcriptional response in humans will significantly benefit the field of exercise molecular biology.

The processing characteristics of bodily expressions under the odor context: An ERP study

The recognition of facial expressions has been shown to be influenced by contextual odors. The aims of this study were (1) to investigate whether odor has a similar effect on the recognition of bodily expressions, and (2) to analyze the time-course of such effects. Sixty-nine adults were randomized into three groups to identify bodily expressions (happy, fearful, and neutral) in three odor environments (pleasant odor, unpleasant odor, and no odor). Event-related potentials (ERPs) induced by the viewing bodily expressions were analyzed. Behaviorally, the unpleasant odor context promoted the recognition of bodily expressions. The ERP results showed odor influences on bodily expression recognition in two phases. In a middle stage phase (150-200 ms post-stimulus onset), VPP amplitudes induced by bodily expressions were greater in an unpleasant odor context than in a pleasant odor context. In a mid-late stage phase (beyond 200 ms), an interaction between contextual odor and bodily expression type was observed. When exposed to an unpleasant contextual odor, N2 and LPP amplitudes related to fearful bodily expressions were smaller than when exposed to other odor contexts, showing the promoting effect of mood coherence effect. Behavioral and ERP evidence confirmed that contextual odor can modulate the visual processing of bodily expressions, with an overall promoting effect of an unpleasant odor on bodily expression processing (phase one) and a specific modulating influence of odors on affectively congruent/incongruent bodily expressions (phase two).

Transcriptome analysis reveals a complex response to the RGNNV/SJNNV reassortant Nervous Necrosis Virus strain in sea bream larvae

The gilthead sea bream (Sparus aurata) is a marine fish of great importance for Mediterranean aquaculture. This species has long been considered resistant to Nervous Necrosis Virus (NNV), an RNA virus that causes massive mortalities in several farmed fish animals. However, the recent appearance of RGNNV/SJNNV reassortant strains started to pose a serious threat to sea bream hatcheries, as it is able to infect larvae and juveniles of this species. While host response to NNV has been extensively studied in adult fish, little attention has been devoted to early life history stages, which are generally the most sensitive ones. Here we report for the first time a time-course RNA-seq analysis on 21-day old fish gilthead sea bream larvae experimentally infected with a RGNNV/SJNNV strain. NNV-infected and mock-infected samples were collected at four time points (6 h, 12 h, 24 h, and 48 h post infection). Four biological replicates, each consisting of five pooled larvae, were analysed for each time point and group. A large set of genes were found to be significantly regulated, especially at early time points (6 h and 12 h), with several heat shock protein encoding transcripts being up-regulated (e.g. hspa5, dnaj4, hspa9, hsc70), while many immune genes were down-regulated (e.g. myd88 and irf5 at T06, pik3r1, stat3, jak1, il12b and il6st at T12). A gene set enrichment analysis (GSEA) identified several altered pathways/processes. For instance, the formation of peroxisomes, which are important anti-viral components as well as essential for nervous system homeostasis, and the autophagy pathway were down-regulated at 6 h and 24 h post infection (hpi). Finally, two custom "reactomes" (i.e. significant gene sets observed in other studies) were defined and used. The first reactome integrated the transcriptomic response to NNV in different fish species, while the second one included all genes found to be stimulated either by interferon (IFN) or by IFN and Chikungunya virus in zebrafish. Genes in both reactomes showed predominant up-regulation at 6hpi and 12hpi and a general down-regulation at 24hpi. Such evidence suggest a certain degree of similarity between the response of sea bream and that of other fish species to NNV, while the observed down-regulation of IFN- and viral-stimulated pathways argues for a possible interference of NNV against the host response.

Time-course analysis of Streptococcus sanguinis after manganese depletion reveals changes in glycolytic and nucleic acid metabolites

INTRODUCTION

Manganese is important for the endocarditis pathogen Streptococcus sanguinis. Little is known about why manganese is required for virulence or how it impacts the metabolome of streptococci.

OBJECTIVES

We applied untargeted metabolomics to cells and media to understand temporal changes resulting from manganese depletion.

METHODS

EDTA was added to a S. sanguinis manganese-transporter mutant in aerobic fermentor conditions. Cell and media samples were collected pre- and post-EDTA treatment. Metabolomics data were generated using positive and negative modes of data acquisition on an LC-MS/MS system. Data were subjected to statistical processing using MetaboAnalyst and time-course analysis using Short Time series Expression Miner (STEM). Recombinant enzymes were assayed for metal dependence.

RESULTS

We observed quantitative changes in 534 and 422 metabolites in cells and media, respectively, after EDTA addition. The 173 cellular metabolites identified as significantly different indicated enrichment of purine and pyrimidine metabolism. Further multivariate analysis revealed that the top 15 cellular metabolites belonged primarily to lipids and redox metabolites. The STEM analysis revealed global changes in cells and media in comparable metabolic pathways. Glycolytic intermediates such as fructose-1,6-bisphosphate increased, suggesting that enzymes that utilize them require manganese for activity or expression. Recombinant enzymes were confirmed to utilize manganese in vitro. Nucleosides accumulated, possibly due to a blockage in conversion to nucleobases resulting from manganese-dependent regulation.

CONCLUSION

Differential analysis of metabolites revealed the activation of a number of metabolic pathways in response to manganese depletion, many of which are connected to carbon catabolite repression.

Short-term effects of the allelochemical umbelliferone on Triticum durum L. metabolism through GC-MS based untargeted metabolomics

The present study used untargeted metabolomics to investigate the short-term metabolic changes induced in wheat seedlings by the specialized metabolite umbelliferone, an allelochemical. We used 10 day-old wheat seedlings treated with 104 μM umbelliferone over a time course experiment covering 6 time points (0 h, 6 h, 12 h, 24 h, 48 h, and 96 h), and compared the metabolomic changes to control (mock-treated) plants. Using gas chromatography mass spectrometry (GCMS)-based metabolomics, we obtained quantitative data on 177 metabolites that were derivatized (either derivatized singly or multiple times) or not, representing 139 non-redundant (unique) metabolites. Of these 139 metabolites, 118 were associated with a unique Human Metabolome Database (HMDB) identifier, while 113 were associated with a Kyoto Encyclopedia of Genes and Genomes (KEGG) identifier. Relative quantification of these metabolites across the time-course of umbelliferone treatment revealed 22 compounds (sugars, fatty acids, secondary metabolites, organic acids, and amino acids) that changed significantly (repeated measures ANOVA, P-value < 0.05) over time. Using multivariate partial least squares discriminant analysis (PLS-DA), we showed the grouping of samples based on time-course across the control and umbelliferone-treated plants, whereas the metabolite-metabolite Pearson correlations revealed tightly formed clusters of umbelliferone-derived metabolites, fatty acids, amino acids, and carbohydrates. Also, the time-course umbelliferone treatment revealed that phospho-l-serine, maltose, and dehydroquinic acid were the top three metabolites showing highest importance in discrimination among the time-points. Overall, the biochemical changes converge towards a mechanistic explanation of the plant metabolic responses induced by umbelliferone. In particular, the perturbation of metabolites involved in tryptophan metabolism, as well as the imbalance of the shikimate pathways, which are strictly interconnected, were significantly altered by the treatment, suggesting a possible mechanism of action of this natural compound.

Creativity is associated with a characteristic U-shaped function of alpha power changes accompanied by an early increase in functional coupling

Although there exists increasing knowledge about brain correlates underlying creative ideation in general, the specific neurocognitive mechanisms implicated in different stages of the creative thinking process are still under-researched. Some recent EEG studies suggested that alpha power during creative ideation varies as a function of time, with the highest levels of alpha power after stimulus onset and at the end of the creative thinking process. The main aim of the present study was to replicate and extend this finding by applying an individual differences approach, and by investigating functional coupling between long distance cortical sites during the process of creative ideation. Eighty-six participants performed the Alternate Uses (AU) task during EEG assessment. Results revealed that more original people showed increased alpha power after stimulus onset and before finalizing the process of idea generation. This U-shaped alpha power pattern was accompanied by an early increase in functional communication between frontal and parietal-occipital sites during the creative thinking process, putatively indicating activation of top-down executive control processes. Participants with lower originality showed no significant time-related variation in alpha power and a delayed increase in long distance functional communication. These findings are in line with dual process models of creative ideation and support the idea that increased alpha power at the beginning of the creative ideation process may indicate more associative modes of thinking and memory processes, while the alpha increases at later stages may indicate executive control processes, associated with idea elaboration/evaluation.

Identifying temporal molecular signatures underlying cardiovascular diseases: A data science platform

OBJECTIVE

During cardiovascular disease progression, molecular systems of myocardium (e.g., a proteome) undergo diverse and distinct changes. Dynamic, temporally-regulated alterations of individual molecules underlie the collective response of the heart to pathological drivers and the ultimate development of pathogenesis. Advances in high-throughput omics technologies have enabled cost-effective, temporal profiling of targeted systems in animal models of human diseases. However, computational analysis of temporal patterns from omics data remains challenging. In particular, bioinformatic pipelines involving unsupervised statistical approaches to support cardiovascular investigations are lacking, which hinders one's ability to extract biomedical insights from these complex datasets.

APPROACH AND RESULTS

We developed a non-parametric data analysis platform to resolve computational challenges unique to temporal omics datasets. Our platform consists of three modules. Module I preprocesses the temporal data using either cubic splines or principal component analysis (PCA), and it simultaneously accomplishes the tasks on missing data imputation and denoising. Module II performs an unsupervised classification by K-means or hierarchical clustering. Module III evaluates and identifies biological entities (e.g., molecular events) that exhibit strong associations to specific temporal patterns. The jackstraw method for cluster membership has been applied to estimate p-values and posterior inclusion probabilities (PIPs), both of which guided feature selection. To demonstrate the utility of the analysis platform, we employed a temporal proteomics dataset that captured the proteome-wide dynamics of oxidative stress induced post-translational modifications (O-PTMs) in mouse hearts undergoing isoproterenol (ISO)-induced hypertrophy.

CONCLUSION

We have created a platform, CV.Signature.TCP, to identify distinct temporal clusters in omics datasets. We presented a cardiovascular use case to demonstrate its utility in unveiling biological insights underlying O-PTM regulations in cardiac remodeling. This platform is implemented in an open source R package (https://github.com/UCLA-BD2K/CV.Signature.TCP).

Time and sex dependency of hemodynamic, renal, and survivability effects of endotoxemia in rats

Widely different exposure times to endotoxic insults have been employed in reported studies. The current experimental study systematically evaluated the time-course and sex influences of endotoxic insult on survivability and cardiovascular and renal functions. Rats received i.p. lipopolysaccharide (LPS, 5 mg/kg) once or twice (over 2 successive days). Systolic blood pressure (SBP), biomarkers of renal function and inflammation, and vasodilator responsiveness of isolated perfused kidneys to acetylcholine (ACh) or N-ethylcarboxamidoadenosine (NECA) were evaluated 6 hr after first LPS injection or 1, 2, or 6 days later. A single 6-hr LPS challenge caused (i) sex-unrelated elevations in serum urea and creatinine and reductions in NECA, but not ACh, vasodilations, (ii) more increases in renal NF-κB/iNOS expressions in male than in female rats, and (iii) hypotension and tachycardia only in male rats. These parameters, except for hemodynamic changes, were restored to near-control levels 1 day after single LPS dosing. The 2-days dosing with LPS had no effects on renal function biomarkers, but caused hypotension, tachycardia, and increases in renal NF-κB/iNOS expression and NECA and ACh vasodilations in both rat sexes. None of these parameters were different from control values when measured 6 days after the endotoxic insult. Alternatively, the rat mortality was observed during first 2 days of the study and was notably higher in male than in female rats. Our data suggest that the frequency and time elapsed after LPS exposure as well as rat sex are important determinants of the magnitude and direction of detrimental effects of endotoxemia.

Efficacy of triptans for the treatment of acute migraines: a quantitative comparison based on the dose-effect and time-course characteristics

OBJECTIVES

This study aimed to establish a pharmacodynamic model to quantitatively compare the efficacy characteristics of seven kinds of triptans and their different dosage forms in the treatment of acute migraines.

METHODS

Clinical studies of triptans in the treatment of acute migraines were comprehensively searched in the public databases. Pharmacodynamic models were established to describe the dose-effect and time-course of each kind of triptan for the proportion of patients who became pain free or had pain relief.

RESULTS

A total of 92 articles involving 47,376 subjects were included in the analysis. After eliminating the placebo effect, oral eletriptan (40 mg) had the highest efficacy among all oral drugs at the maximum approved dose, and the proportion of patients who became pain free and had pain relief were 30.9% and 37.9% at 2 h, respectively. However, oral naratriptan (2.5 mg) had the lowest efficacy, and the proportion of patients who became pain free and had pain relief was 10.3% and 21.6% at 2 h, respectively. The efficacy of subcutaneous administration was significantly higher than that of oral administration, and the efficacy of nasal spray administration was comparable to that of oral administration. Regarding the dose-effect, the efficacy of the sumatriptan nasal spray significantly increased within the FDA (Food and Drug Administration)-approved dose range. When the dose was increased from 5 to 20 mg of sumatriptan nasal spray, the proportion of patients who became pain free and had pain relief increased by 16.8% and 18.3% at 2 h, respectively. Regarding the time-course, the time of onset of subcutaneous sumatriptan (6 mg) was the fastest, and the fraction of patients who were pain free at 2 h accounted for 90.6% of that at 4 h.

CONCLUSIONS

This study evaluated the efficacy characteristics of seven kinds of triptans and their different dosage forms. The present findings provide necessary quantitative information for migraine medication guidelines.

Using metabolomics to assess the sub-lethal effects of zinc and boscalid on an estuarine polychaete worm over time

INTRODUCTION

Zinc is a heavy metal commonly detected in urban estuaries around Australia. Boscalid is a fungicide found in estuaries, both in water and sediment, it enters the system predominantly through agricultural run-off. Zinc is persistent while boscalid breaks down, with a half-life of 108 days. Both contaminants are widely distributed and their effects on ecosystems are not well understood.

OBJECTIVES

The aim of this study was to determine the metabolite changes in Simplisetia aequisetis (an estuarine polychaete) following laboratory exposure to a sub-lethal concentration of zinc or boscalid over a 2-week period.

METHODS

Individuals were collected at six time points over a 2-week period. Whole polychaete metabolites were extracted and quantified using a multi-platform approach. Polar metabolites were detected using a semi-targeted GC-MS analysis and amine containing compounds were analysed using a targeted LC-MS analysis. Total lipid energy content was also analysed for Simplisetia aequisetis.

RESULTS

The pathways that responded to zinc and boscalid exposure were alanine, aspartate and glutamate metabolism (AAG); glycine, serine and threonine metabolism (GST) and metabolites associated with the tricarboxylic acid cycle (TCA). Results showed that changes in total abundance of some metabolites could be detected as early as 24-h exposure. Changes were detected in the metabolites before commonly used total lipid energy assays identified effects.

CONCLUSION

A multi-platform approach provided a holistic overview of the metabolomic response to contaminants in polychaetes. This approach shows promise to be used in biomonitoring programs to provide early diagnostic indicators of contamination and exposure.

Sex differences in the expression of morphine withdrawal symptoms and associated activity in the tail of the ventral tegmental area

Recent studies, in male rodents, have begun to elucidate a role for the GABAergic neurons in the tail of the ventral tegmental area (tVTA) in morphine withdrawal. To date, the mechanisms underlying morphine withdrawal have been studied almost exclusively in male animals. As a result, there is a considerable gap in our current understanding of the processes underlying sex differences in morphine withdrawal behaviors and its effects on cellular activity in the tVTA in females. The purpose of the present study was to investigate the influence of sex on the expression and duration of spontaneous somatic morphine withdrawal syndrome, and to characterize the relationship between spontaneous somatic withdrawal symptoms and cellular activation (measured as phosphorylated CREB; pCREB), in the GABAergic tVTA in male and female rats. Morphine-dependent adult male and female Long Evans rats underwent 72 h of spontaneous withdrawal, and somatic withdrawal symptoms were assessed every 12 h. Male morphine-dependent rats expressed more severe symptoms during the early phases of withdrawal compared to females. Although, females demonstrated lower overall symptom severity, their symptoms persisted for a longer period of time, thus demonstrating higher withdrawal-symptom severity than males during late withdrawal. pCREB activity in the tVTA was elevated in morphine-withdrawn rats and was positively correlated with the severity of withdrawal symptoms. These results demonstrate sex differences in the timing of the expression of somatic withdrawal. Our data add to the growing body of evidence demonstrating a role for the tVTA in morphine withdrawal and begin to establish a sex-dependent behavioral and molecular profile within this brain region.

Mucosal and systemic immune responses in Senegalese sole (Solea senegalensis Kaup) bath challenged with Tenacibaculum maritimum: A time-course study

Tenacibaculosis, caused by Tenacibaculum maritimum, continues to inflict substantial losses among cultured marine species, particularly in the Senegalese sole. However, the immune mechanisms in fish involved in fighting against this disease are still poorly understood. Thus, the present study aimed to investigate the skin mucus's terminal carbohydrate composition, several immune-related enzymes (i.e. lysozyme, peroxidase, proteases and antiproteases), the haemolytic activity of complement and the bactericidal activity in the skin mucus and plasma of the Senegalese sole in a time-course study following a bath challenge with T. maritimum. The haematological profile and the kinetics of cell migration post-infection were also considered. The bath challenge induced slight variations in the terminal carbohydrate composition of Senegalese sole skin mucus. In general, results from this study showed a delay in the mucosal immune response compared to that found at the systemic level (i.e. blood and plasma). For instance, a significant increase in the skin mucus's lysozyme, complement, protease and antiprotease activities were observed at the end of the experiment (14 d post-challenge). Interestingly, the higher activity of these enzymes could be related to the skin mucus's bactericidal capacity and haemolytic complement activity, suggesting that these enzymes play an important role in the defence against Gram-negative bacteria. The haematological profile revealed a significant increase in circulating neutrophils in challenged fish after 48 and 72 h, which was positively correlated to the increments observed in peroxidase and lysozyme activities, respectively, in the plasma of challenged fish at the same time. Although the route of entry and the survival strategy of T. maritimum are still not fully elucidated, results from the present study will contribute to this endeavour through the study of the mucosal immune responses of fish against this particular pathogen.

Trendy: segmented regression analysis of expression dynamics in high-throughput ordered profiling experiments

BACKGROUND

High-throughput expression profiling experiments with ordered conditions (e.g. time-course or spatial-course) are becoming more common for studying detailed differentiation processes or spatial patterns. Identifying dynamic changes at both the individual gene and whole transcriptome level can provide important insights about genes, pathways, and critical time points.

RESULTS

We present an R package, Trendy, which utilizes segmented regression models to simultaneously characterize each gene's expression pattern and summarize overall dynamic activity in ordered condition experiments. For each gene, Trendy finds the optimal segmented regression model and provides the location and direction of dynamic changes in expression. We demonstrate the utility of Trendy to provide biologically relevant results on both microarray and RNA-sequencing (RNA-seq) datasets.

CONCLUSIONS

Trendy is a flexible R package which characterizes gene-specific expression patterns and summarizes changes of global dynamics over ordered conditions. Trendy is freely available on Bioconductor with a full vignette at https://bioconductor.org/packages/release/bioc/html/Trendy.html .

Transcriptional profiling of human bronchial epithelial cell BEAS-2B exposed to diesel and biomass ultrafine particles

BACKGROUND

Emissions from diesel vehicles and biomass burning are the principal sources of primary ultrafine particles (UFP). The exposure to UFP has been associated to cardiovascular and pulmonary diseases, including lung cancer. Although many aspects of the toxicology of ambient particulate matter (PM) have been unraveled, the molecular mechanisms activated in human cells by the exposure to UFP are still poorly understood. Here, we present an RNA-seq time-course experiment (five time point after single dose exposure) used to investigate the differential and temporal changes induced in the gene expression of human bronchial epithelial cells (BEAS-2B) by the exposure to UFP generated from diesel and biomass combustion. A combination of different bioinformatics tools (EdgeR, next-maSigPro and reactome FI app-Cytoscape and prioritization strategies) facilitated the analyses the temporal transcriptional pattern, functional gene set enrichment and gene networks related to cellular response to UFP particles.

RESULTS

The bioinformatics analysis of transcriptional data reveals that the two different UFP induce, since the earliest time points, different transcriptional dynamics resulting in the activation of specific genes. The functional enrichment of differentially expressed genes indicates that the exposure to diesel UFP induces the activation of genes involved in TNFα signaling via NF-kB and inflammatory response, and hypoxia. Conversely, the exposure to ultrafine particles from biomass determines less distinct modifications of the gene expression profiles. Diesel UFP exposure induces the secretion of biomarkers associated to inflammation (CCXL2, EPGN, GREM1, IL1A, IL1B, IL6, IL24, EREG, VEGF) and transcription factors (as NFE2L2, MAFF, HES1, FOSL1, TGIF1) relevant for cardiovascular and lung disease. By means of network reconstruction, four genes (STAT3, HIF1a, NFKB1, KRAS) have emerged as major regulators of transcriptional response of bronchial epithelial cells exposed to diesel exhaust.

CONCLUSIONS

Overall, this work highlights modifications of the transcriptional landscape in human bronchial cells exposed to UFP and sheds new lights on possible mechanisms by means of which UFP acts as a carcinogen and harmful factor for human health.

Time course study of the response to LPS targeting the pig immune gene networks

Background

Stress is a generic term used to describe non-specific responses of the body to all kinds of challenges. A very large variability in the response can be observed across individuals, depending on numerous conditioning factors like genetics, early influences and life history. As a result, there is a wide range of individual vulnerability and resilience to stress, also called robustness. The importance of robustness-related traits in breeding strategies is increasing progressively towards the production of animals with a high level of production under a wide range of climatic conditions and management systems, together with a lower environmental impact and a high level of animal welfare. The present study aims at describing blood transcriptomic, hormonal, and metabolic responses of pigs to a systemic challenge using lipopolysaccharide (LPS). The objective is to analyze the individual variation of the biological responses in relation to the activity of the HPA axis measured by the levels of plasma cortisol after LPS and ACTH in 120 juvenile Large White (LW) pigs. The kinetics of the response was measured with biological variables and whole blood gene expression at 4 time points. A multilevel statistical analysis was used to take into account the longitudinal aspect of the data.

Results

Cortisol level reaches its peak 4 h after LPS injection. The characteristic changes of white blood cell count to LPS were observed, with a decrease of total count, maximal at t=+4 h, and the mirror changes in the respective proportions of lymphocytes and granulocytes. The lymphocytes / granulocytes ratio was maximal at t=+1 h. An integrative statistical approach was used and provided a set of candidate genes for kinetic studies and ongoing complementary studies focused on the LPS-stimulated inflammatory response.

Conclusions

The present study demonstrates the specific biomarkers indicative of an inflammation in swine. Furthermore, these stress responses persist for prolonged periods of time and at significant expression levels, making them good candidate markers for evaluating the efficacy of anti-inflammatory drugs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-4363-5) contains supplementary material, which is available to authorized users.

Cell-type-specific gene expression patterns in the knee cartilage in an osteoarthritis rat model

Osteoarthritis (OA) is a chronic degenerative disease that leads to joint failure, pain, and disability. Gene regulation is implicated as a driver of the imbalance between the expression of catabolic and anabolic factors that eventually leads to the degeneration of osteoarthritic cartilage. In our model, knee-joint OA was induced in male Wistar rats by intra-articular sodium monoiodoacetate (MIA) injections. Whole-genome microarrays were used to analyse the alterations in gene expression during the time-course of OA development (at 2, 14, and 28 days post-injection) in rat knee joints. The identified co-expressed groups of genes were analysed for enriched regulatory mechanisms, functional classes, and cell-type-specific expression. This analysis revealed 272 regulated transcripts (ANOVA FDR < 0.1% and fold > 2). Functionally, the five major gene expression patterns (A–E) were connected to PPAR signalling and adipogenesis (in cluster A), WNT signalling (in cluster B), endochondral ossification (in cluster C), matrix metalloproteinases and the ACE/RAGE pathway (in cluster D), and the Toll-like receptor, and IL-1 signalling pathways (in cluster E). Moreover, the dynamic profiles of these transcriptional changes were assigned to cellular compartments of the knee joint. Classifying the molecular processes associated with the development of cartilage degeneration provides novel insight into the OA disease process. Our study identified groups of co-regulated genes that share functional relationships and that may play an important role in the early and intermediate stages of OA.

CXCR4 expression is associated with time-course permanent and temporary myocardial infarction in rats

Objective(s):

Experimental myocardial infarction triggers secretion of Stromal cell-derived factor1 and lead to increase in the expression of its receptor “CXCR4” on the surface of various cells. The aim of this study was to evaluate the expression pattern of CXCR4 in peripheral blood cells following time-course permanent and temporary ischemia in rats.

Materials and Methods:

Fourteen male Wistar rats were divided into two groups of seven and were placed under permanent and transient ischemia. Peripheral blood mononuclear cells were isolated at different time points, RNAs extracted and applied to qRT-PCR analysis of the CXCR4 gene.

Results:

Based on repeated measures analysis of variance, the differences in the expression levels of the gene in each of the groups were statistically significant over time (the effect of time) (P<0.001). Additionally, the difference in gene expression between the two groups was statistically significant (the effect of group), such that at all times, the expression levels of the gene were significantly higher in the permanent ischemia than in the transient ischemia group (P<0.001). Moreover, the interactive effect of time-group on gene expression was statistically significant (P<0.001).

Conclusion:

CXCR4 is modulated in an induced ischemia context implying a possible association with myocardial infarction. Checking of CXCR4 expression in the ischemic changes shows that damage to the heart tissue trigger the secretion of inflammatory chemokine SDF, Followed by it CXCR4 expression in blood cells. These observations suggest that changes in the expression of CXCR4 may be considered a valuable marker for monitoring myocardial infarction.

Time-course of serotonin transporter occupancy by single dose of three SSRIs in human brain: A positron emission tomography study with [(11)C]DASB

Sixteen healthy volunteers were enrolled and divided into four groups according to the single administration of 10mg or 20mg escitalopram, 50mg sertraline, or 20mg paroxetine. Four positron emission tomography scans with [(11)C]DASB were performed on each subject, the first prior to taking the drug, followed by the others at 4, 24, and 48h after. Serotonin transporter occupancies of the drugs at each time point were calculated. All drugs showed maximum occupancy at 4h after dosing and then decreasing occupancies with time. Escitalopram and sertraline showed high occupancies of 69.1-77.9% at 4h, remaining at 52.8-57.8% after 48h. On the other hand, paroxetine showed relatively low occupancy of 44.6%, then decreasing to 10.3% at 48h. Escitalopram (both 10mg and 20mg) and sertraline (50mg) showed high and sustained occupancy. Paroxetine (20mg) showed relatively low and rapidly decreasing occupancy, possibly due to the low plasma concentration by single dosing schedule. Applying the reported concentration of multiple dosing, 20mg paroxetine will induce over 80% occupancy. The present study suggested that these drugs and doses would be sufficient for the treatment of depression.

Time-course and molecular mechanism of hepatotoxicity induced by 1,3-dichloro-2-propanol in rats

This study investigated the time-course of 1,3-dichloro-2-propanol (1,3-DCP)-induced hepatotoxicity and the molecular mechanism of its oxidative stress and apoptotic changes in rats. Thirty-six male rats were randomly assigned to six groups of six rats each and were administered a single oral dose of 1,3-DCP (90 mg/kg) or its vehicle. 1,3-DCP caused acute hepatic damage, as evidenced by marked increases in serum aminotransferase, alkaline phosphatase, and histopathological alterations. These functional and histopathological changes in the liver peaked at 12h after administration and then decreased progressively. Oxidative stress indices were increased significantly at 6h, peaked at 12h, and then decreased progressively. The number of terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL)- and caspase-3-positive cells increased after 6h, peaked at 12 and 24h, and then decreased. The protein levels of phosphorylated mitogen-activated protein kinases (MAPKs) including p-Erk1/2 and p-JNK showed a similar trend to the numbers of TUNEL- and caspase-3-positive cells. These results indicate that 1,3-DCP increases oxidative stress, nuclear translocation of Nrf2, and expression of Nrf2-targeted genes, followed by increased functional and histopathological alterations in the liver. The increase in hepatocellular apoptosis induced by 1,3-DCP may be related to oxidative stress-mediated MAPK activation.

Balance maintenance as an acquired motor skill: Delayed gains and robust retention after a single session of training in a virtual environment

Does the learning of a balance and stability skill exhibit time-course phases and transfer limitations characteristic of the acquisition and consolidation of voluntary movement sequences? Here we followed the performance of young adults trained in maintaining balance while standing on a moving platform synchronized with a virtual reality road travel scene. The training protocol included eight 3 min long iterations of the road scene. Center of Pressure (CoP) displacements were analyzed for each task iteration within the training session, as well as during tests at 24h, 4 weeks and 12 weeks post-training to test for consolidation phase ("offline") gains and assess retention. In addition, CoP displacements in reaction to external perturbations were assessed before and after the training session and in the 3 subsequent post-training assessments (stability tests). There were significant reductions in CoP displacements as experience accumulated within session, with performance stabilizing by the end of the session. However, CoP displacements were further reduced at 24h post-training (delayed "offline" gains) and these gains were robustly retained. There was no transfer of the practice-related gains to performance in the stability tests. The time-course of learning the balance maintenance task, as well as the limitation on generalizing the gains to untrained conditions, are in line with the results of studies of manual movement skill learning. The current results support the conjecture that a similar repertoire of basic neuronal mechanisms of plasticity may underlay skill (procedural, "how to" knowledge) acquisition and skill memory consolidation in voluntary and balance maintenance tasks.

The time-course of cortico-limbic neural responses to air hunger

Several studies have mapped brain regions associated with acute dyspnea perception. However, the time-course of brain activity during sustained dyspnea is unknown. Our objective was to determine the time-course of neural activity when dyspnea is sustained. Eight healthy subjects underwent brain blood oxygen level dependent functional magnetic imaging (BOLD-fMRI) during mechanical ventilation with constant mild hypercapnia (∼ 45 mm Hg). Subjects rated dyspnea (air hunger) via visual analog scale (VAS). Tidal volume (V(T)) was alternated every 90 s between high VT (0.96 ± 0.23 L) that provided respiratory comfort (12 ± 6% full scale) and low V(T) (0.48 ± 0.08 L) which evoked air hunger (56 ± 11% full scale). BOLD signal was extracted from a priori brain regions and combined with VAS data to determine air hunger related neural time-course. Air hunger onset was associated with BOLD signal increases that followed two distinct temporal profiles within sub-regions of the anterior insula, anterior cingulate and prefrontal cortices (cortico-limbic circuitry): (1) fast, BOLD signal peak <30s and (2) slow, BOLD signal peak >40s. BOLD signal during air hunger offset followed fast and slow temporal profiles symmetrical, but inverse (signal decreases) to the time-courses of air hunger onset. We conclude that differential cortico-limbic circuit elements have unique contributions to dyspnea sensation over time. We suggest that previously unidentified sub-regions are responsible for either the acute awareness or maintenance of dyspnea. These data enhance interpretation of previous studies and inform hypotheses for future dyspnea research.

Effects of water accommodated fractions of crude oils and diesel on a suite of biomarkers in Atlantic cod (Gadus morhua)

The aim of this study was to characterize concentration- and time-dependent responses in juvenile Atlantic cod (Gadus morhua) following exposure for one and three weeks to the water-soluble fraction (WAF) of three weathered oils: Arabian Light crude oil (ALC), North Sea crude oil (NSC) and ship-diesel. The sum of polycyclic aromatic hydrocarbons (PAH) in water was highest after one week of exposure and within environmentally relevant concentrations. PAH metabolites in bile confirmed exposure to and uptake of PAHs. Hepatic cytochrome P450 1A (CYP1A) gene expression (mRNA quantification) increased dramatically following exposure to all three oil types (fold-change up to 165) and there was a time lag between gene and protein expression. Hepatic CYP1A protein concentration and ethoxyresorufin-O-deethylase (EROD) activity were more variable among individuals and treatments than gene expression. EROD activity in liver and gills increased in fish exposed to WAF from the two crude oils, but not in fish exposed to WAF from diesel. Exposure to diesel appeared to induce oxidative stress to a greater extent than exposure to crude oils. Other biomarkers (glutathione S-transferases, acetylcholine esterase, vitellogenin) did not appear to respond to the exposure and hence did not discriminate among oils. Biomarker responses in cod after exposure to weathered crude oils and diesel suggested that the CYP1A system and oxidative stress markers have the highest potential for discriminating among different oil types and to monitor the environmental consequences of spills.

Approach-avoidance pattern of visual attention in hazardous drinkers with ambivalence

Ambivalence toward alcohol often develops when hazardous drinkers try to quit or to control their drinking. The purpose of this study was to investigate the differences between hazardous drinkers with and without ambivalence toward alcohol in terms of their visual attention to alcohol-related pictures over time using an eye-tracker. The study included 20 hazardous drinkers with ambivalence and 21 hazardous drinkers without ambivalence. The eye movements of the participants were monitored while the participants conducted a free-viewing task in which 20 pairs of alcohol-related pictures and matched control pictures were presented. The results showed that the hazardous drinkers with ambivalence were more attentive to the alcohol-related pictures at first and were more attentive to the control pictures toward the end of the task. On the other hand, the hazardous drinkers without ambivalence were more attentive to the alcohol-related pictures from beginning to end. The findings of this study indicated that ambivalence toward alcohol resulted in the inclination to approach and then avoid alcohol in a consecutive sequence. The present results could be helpful in distinguishing hazardous drinkers who may have ambivalence toward alcohol and identifying the pattern of ambivalence more concretely. Additionally, further studies need to consider the time that is important to measure ambivalence toward alcohol.

Combining fMRI and behavioral measures to examine the process of human learning

Prior to the advent of fMRI, the primary means of examining the mechanisms underlying learning were restricted to studying human behavior and non-human neural systems. However, recent advances in neuroimaging technology have enabled the concurrent study of human behavior and neural activity. We propose that the integration of behavioral response with brain activity provides a powerful method of investigating the process through which internal representations are formed or changed. Nevertheless, a review of the literature reveals that many fMRI studies of learning either (1) focus on outcome rather than process or (2) are built on the untested assumption that learning unfolds uniformly over time. We discuss here various challenges faced by the field and highlight studies that have begun to address them. In doing so, we aim to encourage more research that examines the process of learning by considering the interrelation of behavioral measures and fMRI recording during learning.

Time-course profiling of molecular stress responses to silver nanoparticles in the earthworm Eisenia fetida

The molecular mechanism of silver nanoparticle (AgNP) toxicity, particularly its temporal aspect, is currently limited in the literature. This study seeks to identify and profile changes in molecular response patterns over time during soil exposure of the earthworm Eisenia fetida to AgNPs (82±27 nm) with reference to dissolved silver salt (AgNO₃). Principal component analysis of selected gene and enzyme response profiles revealed dissimilar patterns between AgNO₃ and AgNP treatments and also over time. Despite the observed difference in molecular profiles, the body burdens of total Ag were within the same range (10-40 mg/kg dry weight worm) for both treatments with apparent correlation to the induction pattern of metallothionein. AgNO₃ induced the genes and enzymes related to oxidative stress at day 1, after which markers of energy metabolism were all suppressed at day 2. Exposure to AgNPs likewise led to induction of oxidative stress genes at day 2, but with a temporal pattern shift to immune genes at day 14 following metabolic upregulation at day 7. The involvement of oxidative stress and subsequent alterations in immune gene regulation were as predicted by our in vitro study reported previously, highlighting the importance of immunological endpoints in nanosilver toxicity.