MyoD- and nerve-dependent maintenance of MyoD expression in mature muscle fibres acts through the DRR/PRR element

<p>Abstract</p> <p>Background</p> <p>MyoD is a transcription factor implicated in the regulation of adult muscle gene expression. Distinguishing the expression of <it>MyoD </it>in satellite myoblasts and muscle fibres has proved difficult <it>in vivo </it>leading to controversy over the significance of <it>MyoD </it>expression within adult innervated muscle fibres. Here we employ the <it>MD6.0-lacZ </it>transgenic mouse, in which the 6 kb proximal enhancer/promoter (DRR/PRR) of <it>MyoD </it>drives <it>lacZ</it>, to show that MyoD is present and transcriptionally active in many adult muscle fibres.</p> <p>Results</p> <p>In culture, <it>MD6.0-lacZ </it>expresses in myotubes but not myogenic cells, unlike endogenous <it>MyoD</it>. Reporter expression <it>in vivo </it>is in muscle fibre nuclei and is reduced in <it>MyoD </it>null mice. The <it>MD6.0-lacZ </it>reporter is down-regulated both in adult muscle fibres by denervation or muscle disuse and in cultured myotubes by inhibition of activity. Activity induces and represses <it>MyoD </it>through the DRR and PRR, respectively. During the postnatal period, accumulation of β-galactosidase correlates with maturation of innervation. Strikingly, endogenous <it>MyoD </it>expression is up-regulated in fibres by complete denervation, arguing for a separate activity-dependent suppression of <it>MyoD </it>requiring regulatory elements outside the DRR/PRR.</p> <p>Conclusion</p> <p>The data show that <it>MyoD </it>regulation is more complex than previously supposed. Two factors, MyoD protein itself and fibre activity are required for essentially all expression of the 6 kb proximal enhancer/promoter (DRR/PRR) of <it>MyoD </it>in adult fibres. We propose that modulation of MyoD positive feedback by electrical activity determines the set point of <it>MyoD </it>expression in innervated fibres through the DRR/PRR element.</p

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses

The host innate immune response mediated by type I interferon (IFN) and the resulting up-regulation of hundreds of interferon-stimulated genes (ISGs) provide an immediate barrier to virus infection. Studies of the type I ‘interferome’ have mainly been carried out at a single species level, often lacking the power necessary to understand key evolutionary features of this pathway. Here, using a single experimental platform, we determined the properties of the interferomes of multiple vertebrate species and developed a webserver to mine the dataset. This approach revealed a conserved ‘core’ of 62 ISGs, including genes not previously associated with IFN, underscoring the ancestral functions associated with this antiviral host response. We show that gene expansion contributes to the evolution of the IFN system and that interferomes are shaped by lineage-specific pressures. Consequently, each mammal possesses a unique repertoire of ISGs, including genes common to all mammals and others unique to their specific species or phylogenetic lineages. An analysis of genes commonly down-regulated by IFN suggests that epigenetic regulation of transcription is a fundamental aspect of the IFN response. Our study provides a resource for the scientific community highlighting key paradigms of the type I IFN response

Testing the effectiveness of protocols for removal of common conservation treatments for radiocarbon dating

To achieve a reliable radiocarbon date for an object, any contamination that may be of a different age must be removed prior to dating. Samples that have been conserved with treatments such as adhesives, varnishes or consolidants can pose a particular challenge to radiocarbon dating. At the Oxford Radiocarbon Accelerator Unit (ORAU), common examples of such substances encountered include shellac, the acrylic polymers Paraloid B-67 and B-72, and vinyl acetate-derived polymers (e.g. ‘PVA’). Here, a non-carbon containing absorbent substrate called Chromosorb® was deliberately contaminated with a range of varieties or brands of these conservation treatments, as well as two cellulose nitrate lacquers. A selection of chemical pretreatments was tested for their efficiency at removing them. While the varieties of shellac and Paraloid tested were completely removed with some treatments (water/methanol and acetone/methanol/chloroform sequential washes, respectively), no method was found that was capable of completely removing any of the vinyl acetate-derived materials or the cellulose nitrate lacquers. While Chromosorb is not an exact analogue of archaeological wood or bone, for example, this study suggests that it may be possible to remove aged shellac and Paraloid from archaeological specimens with standard organic-solvent-acid-base-acid pretreatments, but it may be significantly more difficult to remove vinyl acetate-derived polymers and cellulose nitrate lacquers sufficiently to provide reliable radiocarbon dates. The four categories of conservation treatment studied demonstrate characteristic FTIR spectra, while highlighting subtle chemical and molecular differences between different varieties of shellac, Paraloid and cellulose nitrate lacquers, and significant differences between the vinyl acetate derivatives

Effect of body composition methodology on heritability estimation of body fatness

Heritability estimates of human body fatness vary widely and the contribution of body composition methodology to this variability is unknown. The effect of body composition methodology on estimations of genetic and environmental contributions to body fatness variation was examined in 78 adult male and female monozygotic twin pairs reared apart or together. Body composition was assessed by six methods - body mass index (BMI), dual energy x-ray absorptiometry (DXA), underwater weighing (UWW), total body water (TBW), bioelectric impedance (BIA), and skinfold thickness. Body fatness was expressed as percent body fat, fat mass, and fat mass/height2 to assess the effect of body fatness expression on heritability estimates. Model-fitting multivariate analyses were used to assess the genetic and environmental components of variance. Mean BMI was 24.5 kg/m2 (range of 17.8-43.4 kg/m2). There was a significant effect of body composition methodology (p<0.001) on heritability estimates, with UWW giving the highest estimate (69%) and BIA giving the lowest estimate (47%) for fat mass/height2. Expression of body fatness as percent body fat resulted in significantly higher heritability estimates (on average 10.3% higher) compared to expression as fat mass/height2 (p=0.015). DXA and TBW methods expressing body fatness as fat mass/height2 gave the least biased heritability assessments, based on the small contribution of specific genetic factors to their genetic variance. A model combining DXA and TBW methods resulted in a relatively low FM/ht2 heritability estimate of 60%, and significant contributions of common and unique environmental factors (22% and 18%, respectively). The body fatness heritability estimate of 60% indicates a smaller contribution of genetic variance to total variance than many previous studies using less powerful research designs have indicated. The results also highlight the importance of environmental factors and possibly genotype by environmental interactions in the etiology of weight gain and the obesity epidemic.R01 AR046124 - NIAMS NIH HHS; R01 MH065322 - NIMH NIH HHS; T32 HL069772 - NHLBI NIH HHS; R21 DK078867 - NIDDK NIH HHS; R37 DA018673 - NIDA NIH HHS; R01 DK076092 - NIDDK NIH HHS; R01 DK079003 - NIDDK NIH HHS; F32 DK009747 - NIDDK NIH HHS; R01 DA018673 - NIDA NIH HH

Back-to-back coral bleaching events on isolated atolls in the Coral Sea

Severe bleaching events caused by marine heatwaves over the past four decades have now affected almost every coral reef ecosystem in the world. These recurring events have led to major losses of coral cover, with adverse consequences for tropical reef ecosystems and the people who depend on them. Here, we document two consecutive and widespread coral bleaching events on remote atolls in the Coral Sea in 2016 and 2017. In each year, the proportion of colonies that bleached was strongly related to heat exposure (measured as Degree Heating Weeks, DHW, °C-weeks), depth and coral assemblage structure. Bleaching was more severe at higher DHW exposure, and at sites with a higher proportion of susceptible taxa. Bleaching was also lower at 6 m than at 2 m depth. Despite the severe bleaching in 2016 on reefs in the central section of the Coral Sea Marine Park, total coral cover was not significantly reduced by 2017, suggesting that most bleached corals survived. Moreover, bleaching was less severe in 2017 despite a higher exposure to heat stress. These results indicate that while the isolation of these oceanic reefs provides no refuge from bleaching, low nutrient levels, high wave energy and proximity to cooler deeper waters may make coral on these reefs more resistant to bleaching induced mortality

Absorption Properties of a Porous Organic Crystalline Apohost Formed by a Self-Assembled Bis-Urea Macrocycle

We report herein the characterization and binding properties of a microporous crystalline host formed by the self assembly of a bis-urea macrocycle 1. Bis-urea macrocycle 1 has been designed to crystallize into stacked hollow columns. The self-assembly process is guided primarily by hydrogen bonding and aromatic stacking interactions that yield crystals of filled host 1âacetic acid (AcOH). The AcOH guests are bound in the cylindrical cavities of the crystal. The guest AcOH can be removed by heating to form a stable crystalline apohost 1. Apohost 1 displays a type I gas adsorption isotherm with CO2 that is consistent with an open framework microporous material. Apohost 1 binds a range of small molecule guests with specific stoichiometry. The formation of these inclusion complexes does not destroy the crystal framework and therefore apohost 1 can be reused, much like a zeolite. We investigated the structure of apohost 1 and its inclusion complexes by powder X-ray diffraction. The ability of guests to bind and their stoichiometry could be rationalized on the basis of the size, shape, and polarity of the guest molecules. Finally, the shape selectivity of these self-assembled porous materials was demonstrated in competition studies in which apohost 1 preferentially bound p-xylene from a mixture of xylene isomers

Comprehensive Biotransformation Analysis of Phenylalanine-Tyrosine Metabolism Reveals Alternative Routes of Metabolite Clearance in Nitisinone-Treated Alkaptonuria

Metabolomic analyses in alkaptonuria (AKU) have recently revealed alternative pathways in phenylalanine-tyrosine (phe-tyr) metabolism from biotransformation of homogentisic acid (HGA), the active molecule in this disease. The aim of this research was to study the phe-tyr metabolic pathway and whether the metabolites upstream of HGA, increased in nitisinone-treated patients, also undergo phase 1 and 2 biotransformation reactions. Metabolomic analyses were performed on serum and urine from patients partaking in the SONIA 2 phase 3 international randomised-controlled trial of nitisinone in AKU (EudraCT no. 2013-001633-41). Serum and urine samples were taken from the same patients at baseline (pre-nitisinone) then at 24 and 48 months on nitisinone treatment (patients N = 47 serum; 53 urine) or no treatment (patients N = 45 serum; 50 urine). Targeted feature extraction was performed to specifically mine data for the entire complement of theoretically predicted phase 1 and 2 biotransformation products derived from phenylalanine, tyrosine, 4-hydroxyphenylpyruvic acid and 4-hydroxyphenyllactic acid, in addition to phenylalanine-derived metabolites with known increases in phenylketonuria. In total, we observed 13 phase 1 and 2 biotransformation products from phenylalanine through to HGA. Each of these products were observed in urine and two were detected in serum. The derivatives of the metabolites upstream of HGA were markedly increased in urine of nitisinone-treated patients (fold change 1.2–16.2) and increases in 12 of these compounds were directly proportional to the degree of nitisinone-induced hypertyrosinaemia (correlation coefficient with serum tyrosine = 0.2–0.7). Increases in the urinary phenylalanine metabolites were also observed across consecutive visits in the treated group. Nitisinone treatment results in marked increases in a wider network of phe-tyr metabolites than shown before. This network comprises alternative biotransformation products from the major metabolites of this pathway, produced by reactions including hydration (phase 1) and bioconjugation (phase 2) of acetyl, methyl, acetylcysteine, glucuronide, glycine and sulfate groups. We propose that these alternative routes of phe-tyr metabolism, predominantly in urine, minimise tyrosinaemia as well as phenylalanaemia

Metabolomic studies in the inborn error of metabolism alkaptonuria reveal new biotransformations in tyrosine metabolism

Alkaptonuria (AKU) is an inherited disorder of tyrosine metabolism caused by lack of active enzyme homogentisate 1,2-dioxygenase (HGD). The primary consequence of HGD deficiency is increased circulating homogentisic acid (HGA), the main agent in the pathology of AKU disease. Here we report the first metabolomic analysis of AKU homozygous Hgd knockout (Hgd(−/−)) mice to model the wider metabolic effects of Hgd deletion and the implication for AKU in humans. Untargeted metabolic profiling was performed on urine from Hgd(−/−) AKU (n = 15) and Hgd(+/−) non-AKU control (n = 14) mice by liquid chromatography high-resolution time-of-flight mass spectrometry (Experiment 1). The metabolites showing alteration in Hgd(−/−) were further investigated in AKU mice (n = 18) and patients from the UK National AKU Centre (n = 25) at baseline and after treatment with the HGA-lowering agent nitisinone (Experiment 2). A metabolic flux experiment was carried out after administration of (13)C-labelled HGA to Hgd(−/−)(n = 4) and Hgd(+/−)(n = 4) mice (Experiment 3) to confirm direct association with HGA. Hgd(−/−) mice showed the expected increase in HGA, together with unexpected alterations in tyrosine, purine and TCA-cycle pathways. Metabolites with the greatest abundance increases in Hgd(−/−) were HGA and previously unreported sulfate and glucuronide HGA conjugates, these were decreased in mice and patients on nitisinone and shown to be products from HGA by the (13)C-labelled HGA tracer. Our findings reveal that increased HGA in AKU undergoes further metabolism by mainly phase II biotransformations. The data advance our understanding of overall tyrosine metabolism, demonstrating how specific metabolic conditions can elucidate hitherto undiscovered pathways in biochemistry and metabolism

Are coastal habitats important nurseries? A meta-analysis

Nearshore‐structured habitats—including underwater grasses, mangroves, coral, and other biogenic reefs, marshes, and complex abiotic substrates—have long been postulated to function as important nurseries for juvenile fishes and invertebrates. Here, we review the evolution of the “nursery habitat hypothesis” and use \u3e11,000 comparisons from 160 peer‐reviewed studies to test whether and which structured habitats increase juvenile density, growth, and survival. In general, almost all structured habitats significantly enhanced juvenile density—and in some cases growth and survival—relative to unstructured habitats. Underwater grasses and mangroves also promoted juvenile density and growth beyond what was observed in other structured habitats. These conclusions were robust to variation among studies, although there were significant differences with latitude and among some phyla. Our results confirm the basic nursery function of certain structured habitats, which lends further support to their conservation, restoration, and management at a time when our coastal environments are becoming increasingly impacted. They also reveal a dearth of evidence from many other systems (e.g., kelp forests) and for responses other than density. Although recent studies have advocated for increasingly complex approaches to evaluating nurseries, we recommend a renewed emphasis on more straightforward assessments of juvenile growth, survival, reproduction, and recruitment