expression profiling of all protein-coding genes in wild-type and three DNA repair-deficient substrains of Escherichia coli K-12

Gene chips or cDNA arrays of the entire set of Escherichia coli (E. coli) K12 genes were used to measure the expression, at the mRNA level, of all 4290 protein-coding genes in wild-type (WT) and three DNA repair-deficient derivative strains: (i) AB1157 (WT), (ii) LR39 (ada, ogt), (iii) MV1932 (alkA1, tag-1) and (iv) GM5555 (mutS). The aim was to investigate whether disruption of a single gene would result in significant deviation in the expression of other genes in these organisms. We describe here a simple approach for a stringent statistical evaluation of cDNA array data. This includes: (i) determination of intra- and interassay variation coefficients for different expression levels, (ii) rejection of biased duplicates, (iii) mathematical background determination, and (iv) comparison of expression levels of identical copies of a gene. The results demonstrated a highly significant correlation of gene expression when the mutants were individually compared with the wildtype. Altogether, 81 deviations of the expression of 59 genes were noted, out of 12,870, when 3-fold or greater up- or down-regulation was used as a criterion of differential expression. In the light of current knowledge of E. coli biology, the differential expression did not follow any logical pattern. In fact, the deviations may simply represent inter-assay variation. The results obtained here with a simple model organism are different from those obtained with most mammalian knockouts: disruption of the function of a single gene does not, under good growth conditions, necessarily result in great changes in the expression of other genes.     

Premature prostaglandin F2alpha secretion causes luteal regression in GnRH-induced short estrous cycles in cyclic dairy heifers

This study aimed to confirm that the luteolysis in normal-cycling dairy heifers seen during short estrous cycles induced with cloprostenol (Clp) and GnRH administered 24h apart is caused by a premature release of prostaglandin F(2alpha) (PGF(2alpha)). A further aim was to study the PGF(2alpha) release pattern more closely to determine whether it resembles the spontaneous release occurring during normal regression of the corpus luteum (CL) or whether PGF(2alpha) is continuously secreted after the induced ovulations, leading to short estrous cycles. Twenty-four Ayrshire heifers were allotted to four equally sized groups. After estrus synchronization with 0.5mg of Clp, a new luteolysis was induced with 0.5mg of Clp on Day 6 (groups T-d6 and C-d6) or Day 7 (groups T-d7 and C-d7) after ovulation. Gonadorelin (0.1mg i.m.) was given to groups T-d6 and T-d7 to induce premature ovulation 24h later. Groups C-d6 and C-d7 served as controls. Ovaries were examined daily by transrectal ultrasonography, while blood samples (for progesterone and 15-ketodihydro-PGF(2alpha) analyses) were obtained via a jugular catheter every 3h, starting from the second Clp treatment and continuing for 9 days postovulation. Unresponsiveness to Clp or anovulation resulted in 4 C-d6 heifers being excluded. Four heifers in group T-d6 and three in group T-d7 had a short estrous cycle of 8-12 days, while all others had a cycle of normal length. Significant elevations in 15-ketodihydro-PGF(2alpha) concentrations with recurrent high peaks coincided with a decrease in progesterone concentration and were detected in all heifers that showed a short estrous cycle, but not in any heifers with normal estrous cycles in groups T and C. In conclusion, a premature release of PGF(2alpha), which closely resembles its release during spontaneous luteolysis, causes luteal regression in these short cycles.     

Sandwich hybridisation assay for quantitative detection of yeast RNAs in crude cell lysates

Background  

A rapid microtiter plate based sandwich hybridization assay was developed for detection and quantification of single RNA species using magnetic beads. Following solution hybridization target RNA molecules were collected by biotin-streptavidin affinity binding and detected by fluorescence signal generated by alkaline phosphatase. The 18S rRNA and SUC2 mRNA of Saccharomyces cerevisiae were used as model RNA target molecules.     

Chronic Ethanol Exposure Increases Cytochrome P‐450 and Decreases Activated in Blocked Unfolded Protein Response Gene Family Transcripts in Caenorhabditis elegans

Ethanol is a widely consumed and rapidly absorbed toxin. While the physiological effects of ethanol consumption are well known, the underlying biochemical and molecular changes at the gene expression level in whole animals remain obscure. We exposed the model organism Caenorhabditis elegans to 0.2 M ethanol from the embryo to L4 larva stage and assayed gene expression changes in whole animals using RNA‐Seq and quantitative real‐time PCR. We observed gene expression changes in 1122 genes (411 up, 711 down). Cytochrome P‐450 (CYP) gene family members (12 of 78) were upregulated, whereas activated in blocked unfolded protein response (ABU) (7 of 15) were downregulated. Other detoxification gene family members were also regulated including four glutathione‐S‐transferases and three flavin monooxygenases. The results presented show specific gene expression changes following chronic ethanol exposure in C. elegans that indicate both persistent upregulation of detoxification response genes and downregulation of endoplasmic reticulum stress pathway genes.     

Narrow-band ultraviolet B (NB UV-B) exposures improve mood in healthy individuals differently depending on chronotype

ABSTRACT

The evening chronotype is associated with psychological symptoms such as depressed mood, while skin exposure to ultraviolet radiation (UVR) may affect mood and behavior through neural and humoral routes. This pilot study aimed to investigate the impact of whole-body narrow-band (NB) UV-B exposure on current mood state and circulating 25-hydroxyvitamin D3 (25(OH)D₃), interleukin-6 (IL-6), cortisol and β-endorphin (β-END) levels in healthy participants. Here, eleven healthy women received full-body NB UV-B exposures on four afternoons, and the chronotype was assessed with a shortened version of Horne and Östberg’s Morningness-Eveningness Questionnaire (MEQ). Perceived mood was evaluated using the Visual Analogue Scale (VAS), and serum 25(OH)D₃, IL-6, cortisol and β-END concentrations were monitored daily. Decreasing VAS values showed mood to improve significantly over the five days after the four suberythematous NB UV-B exposures (p = .038), and the more the circadian preference was inclined toward eveningness, the greater the improvement in the mood dimension of wellbeing (p = .021). Baseline mood state was correlated with baseline 25(OH)D₃ (r = ?0.54, 95% CI: ?0.86 to ?0.09) and with baseline cortisol (r = ?0.57, 95% CI: ?0.87 to ?0.04). During the NB UV-B exposures, 25(OH)D₃ increased significantly, as expected, and IL-6 declined significantly by ?0.35 (95% CI: ?0.69 to ?0.07) pg/mL from the initial values of 1.12 ± 0.66 pg/mL (p = .025). In conclusion, in our pilot study, NB UV-B exposure improved mood, especially among those with evening preference for their daily activities, as well as circulating 25(OH)D₃ levels, whereas circulating IL-6 levels decreased.

Abbreviations: UVR: Ultraviolet radiation; NB UV-B: narrow-band UV-B; VAS: Visual Analogue Scales; β-END: β-endorphin; IL-6: Interleukin-6     

Ethanol Inhibits Activation of NLRP3 and AIM2 Inflammasomes in Human Macrophages–A Novel Anti-Inflammatory Action of Alcohol

Objective

In the pathogenesis of coronary atherosclerosis, local macrophage-driven inflammation and secretion of proinflammatory cytokines, interleukin-1β (IL-1β) in particular, are recognized as key factors. Moderate alcohol consumption is associated with a reduced risk of coronary artery disease mortality. Here we examined in cultured human macrophages whether ethanol modulates the intracellular processes involved in the secretion of IL-1β.

Results

Ethanol decreased dose-dependently the production of mature IL-1β induced by activators of the NLRP3 inflammasome, i.e. ATP, cholesterol crystals, serum amyloid A and nigericin. Ethanol had no significant effect on the expression of NLRP3 or IL1B mRNA in LPS-primed macrophages. Moreover, secretion of IL-1β was decreased in parallel with reduction of caspase-1 activation, demonstrating that ethanol inhibits inflammasome activation instead of synthesis of pro-IL-1β. Acetaldehyde, a highly reactive metabolite of ethanol, had no effect on the ATP-induced IL-1β secretion. Ethanol also attenuated the secretion of IL-1β triggered by synthetic double-stranded DNA, an activator of the AIM2 inflammasome. Ethanol conferred the inhibitory functions by attenuating the disruption of lysosomal integrity and ensuing leakage of the lysosomal protease cathepsin B and by reducing oligomerization of ASC.

Conclusion

Ethanol-induced inhibition of the NLRP3 inflammasome activation in macrophages may represent a biological pathway underlying the protective effect of moderate alcohol consumption on coronary heart disease.     

Suppressing Multi-Channel Ultra-Low-Field MRI Measurement Noise Using Data Consistency and Image Sparsity

Ultra-low-field (ULF) MRI (B ₀ = 10–100 µT) typically suffers from a low signal-to-noise ratio (SNR). While SNR can be improved by pre-polarization and signal detection using highly sensitive superconducting quantum interference device (SQUID) sensors, we propose to use the inter-dependency of the k-space data from highly parallel detection with up to tens of sensors readily available in the ULF MRI in order to suppress the noise. Furthermore, the prior information that an image can be sparsely represented can be integrated with this data consistency constraint to further improve the SNR. Simulations and experimental data using 47 SQUID sensors demonstrate the effectiveness of this data consistency constraint and sparsity prior in ULF-MRI reconstruction.     

Enhanced polyamine catabolism alters homeostatic control of white adipose tissue mass, energy expenditure, and glucose metabolism

Peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1 alpha) is an attractive candidate gene for type 2 diabetes, as genes of the oxidative phosphorylation (OXPHOS) pathway are coordinatively downregulated by reduced expression of PGC-1 alpha in skeletal muscle and adipose tissue of patients with type 2 diabetes. Here we demonstrate that transgenic mice with activated polyamine catabolism due to overexpression of spermidine/spermine N(1)-acetyltransferase (SSAT) had reduced white adipose tissue (WAT) mass, high basal metabolic rate, improved glucose tolerance, high insulin sensitivity, and enhanced expression of the OXPHOS genes, coordinated by increased levels of PGC-1 alpha and 5'-AMP-activated protein kinase (AMPK) in WAT. As accelerated polyamine flux caused by SSAT overexpression depleted the ATP pool in adipocytes of SSAT mice and N(1),N(11)-diethylnorspermine-treated wild-type fetal fibroblasts, we propose that low ATP levels lead to the induction of AMPK, which in turn activates PGC-1 alpha in WAT of SSAT mice. Our hypothesis is supported by the finding that the phenotype of SSAT mice was reversed when the accelerated polyamine flux was reduced by the inhibition of polyamine biosynthesis in WAT. The involvement of polyamine catabolism in the regulation of energy and glucose metabolism may offer a novel target for drug development for obesity and type 2 diabetes.     

Dispersal and clonal diversity of North-European parthenogenetic earthworms

At least 15 earthworm species are known to reproduce parthenogenetically. Most of these retain meiosis but the chromosome set is duplicated before meiosis; alternatively there is mitosis instead of meiosis. In both cases the offspring are genetic copies of the parent worm. Parthenogens are always polyploid. Parthenogenesis is associated with a dispersal advantage: a single propagule suffices to establish a new population. We have studied the clone pool structure and dispersal of ecologically dissimilar polyploid parthenogenetic lumbricids in northern Europe using enzyme electrophoresis. The anthropochorous Octolasion cyaneum has a very low number of clones in populations that are located far away from each other. The opposite is the eurytopic Dendrobaena octaedra that has a wide array of clones in each population. The ripicolous Eiseniella tetraedra disperses with flowing water and possibly also through zoochory. On subarctic North-European mountains its clone pool decreases with increasing elevation. At the top there are a few but persistent clones. Small brooks carry propagules downstream, so that at the mouths of brooks clone pools are more diverse than higher up; again larger rivers carry clones downstream. Clone dispersal is relatively free in a freely flowing river, while dams stop propagules in harnessed rivers. The mouths of rivers have high E. tetraedra clone diversity. Clones disperse from these clone centers to islands formed through land uplift along the northern Baltic Sea. The annual turnover of clones is high on these islands. A survey of epigeic and endogeic parthenogens on the Åland islands which serve as stepping stones between Estonia, Finland and Sweden shows an invasion route of clones across the Baltic Sea. Anthropochory (Aporrectodea rosea and Octolasion cyaneum) and hydrochory (E.tetraedra and Dendrobaena octaedra) seem to play important roles in the clone pool formation on the Åland islands. Quite recently an exotic parthenogen Dichogaster bolaui has found a curious habitat in human settlements viz., the sewer pipe system. Many clonal earthworms show significant morphological and morphometric diversity in and between sample localities but we have failed to associate this variation with the clonal variability. It seems that local factors modify the morphometrics and morphology ultimately determined by the genotype of parthenogenetic earthworms.