Moderate alcohol consumption alters both leucocyte gene expression profiles and circulating proteins related to immune response and lipid metabolism in men

Moderate alcohol consumption has various effects on immune and inflammatory processes, which could accumulatively modulate chronic disease risk. So far, no comprehensive, integrative profiling has been performed to investigate the effects of longer-term alcohol consumption. Therefore, we studied the effects of alcohol consumption on gene expression patterns using large-scale profiling of whole-genome transcriptomics in blood cells and on a number of proteins in blood. In a randomised, open-label, cross-over trial, twenty-four young, normal-weight men consumed 100 ml vodka (30 g alcohol) with 200 ml orange juice or only orange juice daily during dinner for 4 weeks. After each period, blood was sampled for measuring gene expression and selected proteins. Pathway analysis of 345 down-regulated and 455 up-regulated genes revealed effects of alcohol consumption on various signalling responses, immune processes and lipid metabolism. Among the signalling processes, the most prominently changed was glucocorticoid receptor signalling. A network on immune response showed a down-regulated NF-¿B gene expression together with increased plasma adiponectin and decreased pro-inflammatory IL-1 receptor antagonist and IL-18, and acute-phase proteins ferritin and a1-antitrypsin concentrations (all P <0·05) after alcohol consumption. Furthermore, a network of gene expression changes related to lipid metabolism was observed, with a central role for PPARa which was supported by increased HDL-cholesterol and several apo concentrations (all P <0·05) after alcohol consumption. In conclusion, an integrated approach of profiling both genes and proteins in blood showed that 4 weeks of moderate alcohol consumption altered immune responses and lipid metabolis

Effects of mediated social touch on affective experiences and trust

This study investigated whether communication via mediated hand pressure during a remotely shared experience (watching an amusing video) can (1) enhance recovery from sadness, (2) enhance the affective quality of the experience, and (3) increase trust towards the communication partner. Thereto participants first watched a sad movie clip to elicit sadness, followed by a funny one to stimulate recovery from sadness. While watching the funny clip they signaled a hypothetical fellow participant every time they felt amused. In the experimental condition the participants responded by pressing a hand-held two-way mediated touch device (a Frebble), which also provided haptic feedback via simulated hand squeezes. In the control condition they responded by pressing a button and they received abstract visual feedback. Objective (heart rate, galvanic skin conductance, number and duration of joystick or Frebble presses) and subjective (questionnaires) data were collected to assess the emotional reactions of the participants. The subjective measurements confirmed that the sad movie successfully induced sadness while the funny movie indeed evoked more positive feelings. Although their ranking agreed with the subjective measurements, the physiological measurements confirmed this conclusion only for the funny movie. The results show that recovery from movie induced sadness, the affective experience of the amusing movie, and trust towards the communication partner did not differ between both experimental conditions. Hence, feedback via mediated hand touching did not enhance either of these factors compared to visual feedback. Further analysis of the data showed that participants scoring low on Extraversion (i.e., persons that are more introvert) or low on Touch Receptivity (i.e., persons who do not like to be touched by others) felt better understood by their communication partner when receiving mediated touch feedback instead of visual feedback, while the opposite was found for participants scoring high on these factors. The implications of these results for further research are discussed, and some suggestions for follow-up experiments are presented

To err is human, to give feedback divine? : a study of corrective feedback practices used in Finnish EFL writing classes

Palautteenanto on tärkeä ja väistämätön osa yläkoulun englannin kielen opetusta. Tässä tutkielmassa tarkastellaan englantia yläkoulussa opettavien ajatuksia ja käytänteitä palautteenantoon liittyen. Tutkielma käsittelee tapoja, joilla opettajat antavat palautetta oppilaiden teksteistä yläkoulun englanti vieraana kielenä -opetuksessa. Tutkielmassa verrataan viiden opettajan palautteenantostrategioita ja -konventioita. Tavoitteena on selvittää, mitä palautteenantostrategioita opettajat käyttävät ja saada selville, ovatko opettajien uskomukset ja palautteenantokonventiot keskenään yhteneväiset. Tavoitteena on myös saada selville, millaisia eroja palautteenantomenetelmissä ja -tavoissa on eri opettajien välillä. Tutkielman teoreettinen viitekehys koostuu sekä palautteenantoon liittyvistä käsitteistä että useiden eri tutkijoiden näkökulmista palautteenantotapoihin ja niiden hyödyllisyyteen. Tutkielmassa esitellään debattia, jossa tuodaan esille mielipiteitä sekä virheidenkorjaamisen puolesta että virheidenkorjaamista vastaan. Tutkimuksen aineistona ovat englanninopettajien yksilöhaastattelut sekä englanninopettajien korjaamat kirjoitelmat. Haastattelumenetelmänä käytettiin semi-strukturoitua haastattelua. Tutkimuksessa selviää, että opettajat antavat oppilaille palautetta sekä kirjallisesti että suullisesti. Palautteessa opettajat eivät keskity vain kirjallisissa tuotoksissa esiintyviin virheisiin, vaan heidän oppilaille antamansa palaute on monipuolista. Osa opettajista keskittyy enemmän itse virheisiin ja sisältöön, kun taas osa opettajista antaa myös palautetta kirjoitetusta tekstistä kokonaisuutena. Jotta tulosten pohjalta voitaisiin tehdä päätelmiä yleistettävyyden näkökulmasta, tutkimuksen tulisi olla laajempi. Tutkimuksen tulokset kuitenkin osoittavat, että opettajien oppilaille antama palaute on sekä monipuolista että kannustavaa

An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions

Omics technology used for large-scale measurements of gene expression is rapidly evolving. This work pointed out the need of an extensive bioinformatics analyses for array quality assessment before and after gene expression clustering and pathway analysis. A study focused on the effect of red wine polyphenols on rat colon mucosa was used to test the impact of quality control and normalisation steps on the biological conclusions. The integration of data visualization, pathway analysis and clustering revealed an artifact problem that was solved with an adapted normalisation. We propose a possible point to point standard analysis procedure, based on a combination of clustering and data visualization for the analysis of microarray data

Conspicuous Smooth and White Egg-Shaped Sulfur Structures on a Deep-Sea Hydrothermal Vent Formed by Sulfide-Oxidizing Bacteria

Conspicuous egg-shaped, white, and smooth structures were observed at a hydrothermal vent site in the Guaymas Basin, Gulf of California. The gelatinous structures decomposed within hours after sampling. Scanning electron microscopy (SEM) and light microscopy showed that the structure consisted of filaments of less than 0.1 mm thickness, similar to those observed for "Candidatus Arcobacter sulfidicus." SEM-energy-dispersive X-ray spectroscopy (EDS) showed that the filaments were sulfur rich. According to 16S rRNA gene amplicon and fluorescence in situ hybridization (FISH) analyses, Arcobacter, a sulfide oxidizer that is known to produce filamentous elemental sulfur, was among the dominant species in the structure and was likely responsible for its formation. Arcobacter normally produces woolly snowflake like structures in opposed gradients of sulfide and oxygen. In the laboratory, we observed sulfide consumption in the anoxic zone of the structure, suggesting an anaerobic conversion. The sulfide oxidation and decomposition of the structure in the laboratory may be explained by dissolution of the sulfur filaments by reaction with sulfide under formation of polysulfides. IMPORTANCE At the deep-sea Guaymas Basin hydrothermal vent system, sulfide-rich hydrothermal fluids mix with oxygenated seawater, thereby providing a habitat for microbial sulfur oxidation. Microbial sulfur oxidation in the deep sea involves a variety of organisms and processes and can result in the excretion of elemental sulfur. Here, we report on conspicuous white and smooth gelatinous structures found on hot vents. These strange egg-shaped structures were often observed on previous occasions in the Guaymas Basin, but their composition and formation process were unknown. Our data suggest that the notable and highly ephemeral structure was likely formed by the well-known sulfide-oxidizing Arcobacter. While normally Arcobacter produces loose flocs or woolly layers, here smooth gel-like structures were found

Exploring pathway interactions in insulin resistant mouse liver

<p>Abstract</p> <p>Background</p> <p>Complex phenotypes such as insulin resistance involve different biological pathways that may interact and influence each other. Interpretation of related experimental data would be facilitated by identifying relevant pathway interactions in the context of the dataset.</p> <p>Results</p> <p>We developed an analysis approach to study interactions between pathways by integrating gene and protein interaction networks, biological pathway information and high-throughput data. This approach was applied to a transcriptomics dataset to investigate pathway interactions in insulin resistant mouse liver in response to a glucose challenge. We identified regulated pathway interactions at different time points following the glucose challenge and also studied the underlying protein interactions to find possible mechanisms and key proteins involved in pathway cross-talk. A large number of pathway interactions were found for the comparison between the two diet groups at t = 0. The initial response to the glucose challenge (t = 0.6) was typed by an acute stress response and pathway interactions showed large overlap between the two diet groups, while the pathway interaction networks for the late response were more dissimilar.</p> <p>Conclusions</p> <p>Studying pathway interactions provides a new perspective on the data that complements established pathway analysis methods such as enrichment analysis. This study provided new insights in how interactions between pathways may be affected by insulin resistance. In addition, the analysis approach described here can be generally applied to different types of high-throughput data and will therefore be useful for analysis of other complex datasets as well.</p

Time- and dose-dependent effects of curcumin on gene expression in human colon cancer cells

BACKGROUND: Curcumin is a spice and a coloring food compound with a promising role in colon cancer prevention. Curcumin protects against development of colon tumors in rats treated with a colon carcinogen, in colon cancer cells curcumin can inhibit cell proliferation and induce apoptosis, it is an anti-oxidant and it can act as an anti-inflammatory agent. The aim of this study was to elucidate mechanisms and effect of curcumin in colon cancer cells using gene expression profiling. METHODS: Gene expression changes in response to curcumin exposure were studied in two human colon cancer cell lines, using cDNA microarrays with four thousand human genes. HT29 cells were exposed to two different concentrations of curcumin and gene expression changes were followed in time (3, 6, 12, 24 and 48 hours). Gene expression changes after short-term exposure (3 or 6 hours) to curcumin were also studied in a second cell type, Caco-2 cells. RESULTS: Gene expression changes (>1.5-fold) were found at all time points. HT29 cells were more sensitive to curcumin than Caco-2 cells. Early response genes were involved in cell cycle, signal transduction, DNA repair, gene transcription, cell adhesion and xenobiotic metabolism. In HT29 cells curcumin modulated a number of cell cycle genes of which several have a role in transition through the G2/M phase. This corresponded to a cell cycle arrest in the G2/M phase as was observed by flow cytometry. Functional groups with a similar expression profile included genes involved in phase-II metabolism that were induced by curcumin after 12 and 24 hours. Expression of some cytochrome P450 genes was downregulated by curcumin in HT29 and Caco-2 cells. In addition, curcumin affected expression of metallothionein genes, tubulin genes, p53 and other genes involved in colon carcinogenesis. CONCLUSIONS: This study has extended knowledge on pathways or processes already reported to be affected by curcumin (cell cycle arrest, phase-II genes). Moreover, potential new leads to genes and pathways that could play a role in colon cancer prevention by curcumin were identified