Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C

Background

A number of neurodevelopmental syndromes are caused by mutations in genes encoding proteins that normally function in epigenetic regulation. Identification of epigenetic alterations occurring in these disorders could shed light on molecular pathways relevant to neurodevelopment.

Results

Using a genome-wide approach, we identified genes with significant loss of DNA methylation in blood of males with intellectual disability and mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, in comparison to age/sex matched controls. Loss of DNA methylation in such individuals is consistent with known interactions between DNA methylation and H3 lysine 4 methylation. Further, loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP was not observed in more than 900 population controls. We also found that DNA methylation at these three genes in blood correlated with dosage of KDM5C and its Y-linked homologue KDM5D. In addition, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP.

Conclusions

We have, for the first time, identified epigenetic alterations in patient samples carrying a mutation in a gene involved in the regulation of histone modifications. These data support the concept that DNA methylation and H3 lysine 4 methylation are functionally interdependent. The data provide new insights into the molecular pathogenesis of intellectual disability. Further, our data suggest that some DNA methylation marks identified in blood can serve as biomarkers of epigenetic status in the brain.     

The fossil record of Glypturus Stimpson, 1866 (Crustacea,Decapoda, Axiidea,Callianassidae) revisited,with notes on palaeoecology and palaeobiogeography

Abstract: The fossil record of the callianassid genus Glypturus (Decapoda, Axiidea) is re‐evaluated. Our systematic revision, both of extant and fossil taxa, is based on major cheliped morphology only, thus providing an important impetus for palaeontological studies. Both spination and tuberculation of chelipeds are herein considered of great taxonomic importance. Presence of spines on the upper margins of the merus and propodus and the lower margin of the carpus are significant for generic assignment, whereas the extent of tuberculation on lateral surfaces of the propodus is important for assignment at the species level. Altogether, four extant and six exclusively fossil species of Glypturus are recognized. Several extinct callianassid taxa are now transferred to the genus, namely Callianassa berryi, Callianassa fraasi, Callianassa munieri, Callianassa pugnax and Callianassaspinosa; Callianassa pseudofraasi is considered a junior synonym of C. fraasi. Based on a comparison of ecological preferences of extant representatives, the presence of Glypturus in the fossil record is considered to be linked with tropical to subtropical, nearshore carbonate environments of normal salinity. We argue that Glypturus is of Tethyan origin, with a stratigraphical range going as far back as the Eocene. Since then, the genus migrated both westwards and eastwards, establishing present‐day communities in the western Atlantic and Indo‐West Pacific which both comprise several distinct species. In the presumed area of origin, the genus does no longer occur today. The exlusively fossil (middle Eocene) genus Eoglypturus from Italy is considered closely related to Glypturus and is thus assigned to the subfamily Callichirinae as well.     

cDNA cloning of the CEPUS, a secreted type of neural glycoprotein belonging to the immunoglobulin-like opioid binding cell adhesion molecule (OBCAM) subfamily.

GP55 is a family of glycoproteins distributed predominantly in the nervous system, and its previously characterized members, including the GP55A (EMBL Y08170) and E19S (EMBL Y08171) reveal a typical glycosyl phosphatidyl inositol (GPI)-anchored pattern for membrane proteins. CEPUS identified in this study appeared to represent the third member of GP55. This 3.2 kb long complete cDNA clone from the chicken brain exhibited 3 Ig-like domains. The open reading frame of CEPUS contains 313 amino acids, which can encode a 31.7 kDa core protein (pI 5.75) for the mature form. The signal peptide cleavage site was predicted at Gln25. The structural features of the CEPUS cDNA sequence represented a soluble counterpart to the recently identified cerebellar Purkinje cell specific antigen, CEPU-1. The sequence difference between CEPU-1 and CEPUS was only found in the C-terminus in which the CEPUS lacked the GPI-anchored binding site. It displays significant sequence homology to GP55-related molecules, including OBCAM, GP55A, E19S/LAMP, neurotrimin, and CEPU-1, which are all membrane attached types. The absence of the hydrophobic tail sequence in CEPUS may, therefore, suggest that CEPUS would represent the first identified secreted member in this group of genes. We defined that this molecule forms the opioid-binding cell adhesion molecule (OBCAM) subfamily in the molecular phylogeny. Structurally, these molecules represent acidic proteins (pI 5.47-6.09). Six cysteins, as well as 5 Asn-linked potential glycosylation sites were evolutionary-conserved, suggesting that this OBCAM subfamily resembles immunoglobulin-like and highly glycosylated molecules. The presence of CEPUS would probably suggest to us that the spatial/local expression of the CEPU gene may provide a favorable route for migrating CEPU-positive population of neurons to generate a neuron-specific guidance in developing neurons in vivo.     

Hydrogen sulfide potentiates interleukin-1beta-induced nitric oxide production via enhancement of extracellular signal-regulated kinase activation in rat vascular smooth muscle cells

Hydrogen sulfide (H(2)S) and nitric oxide (NO) are endogenously synthesized from l-cysteine and l-arginine, respectively. They might constitute a cooperative network to regulate their effects. In this study, we investigated whether H(2)S could affect NO production in rat vascular smooth muscle cells (VSMCs) stimulated with interleukin-1beta (IL-1beta). Although H(2)S by itself showed no effect on NO production, it augmented IL-beta-induced NO production and this effect was associated with increased expression of inducible NO synthase (iNOS) and activation of nuclear factor (NF)-kappaB. IL-1Beta activated the extracellular signal-regulated kinase 1/2 (ERK1/2), and this activation was also enhanced by H(2)S. Inhibition of ERK1/2 activation by the selective inhibitor U0126 inhibited IL-1beta-induced NF-kappaB activation, iNOS expression, and NO production either in the absence or presence of H(2)S. Our findings suggest that H(2)S enhances NO production and iNOS expression by potentiating IL-1beta-induced NF-kappaB activation through a mechanism involving ERK1/2 signaling cascade in rat VSMCs.     

Genetic control of methyl halide production in Arabidopsis

Methyl chloride (CH(3)Cl) and methyl bromide (CH(3)Br) are the primary carriers of natural chlorine and bromine, respectively, to the stratosphere, where they catalyze the destruction of ozone, whereas methyl iodide (CH(3)I) influences aerosol formation and ozone loss in the boundary layer. CH(3)Br is also an agricultural pesticide whose use is regulated by international agreement. Despite the economic and environmental importance of these methyl halides, their natural sources and biological production mechanisms are poorly understood. Besides CH(3)Br fumigation, important sources include oceans, biomass burning, tropical plants, salt marshes, and certain crops and fungi. Here, we demonstrate that the model plant Arabidopsis thaliana produces and emits methyl halides and that the enzyme primarily responsible for the production is encoded by the HARMLESS TO OZONE LAYER (HOL) gene. The encoded protein belongs to a group of methyltransferases capable of catalyzing the S-adenosyl-L-methionine (SAM)-dependent methylation of chloride (Cl(-)), bromide (Br(-)), and iodide (I(-)) to produce methyl halides. In mutant plants with the HOL gene disrupted, methyl halide production is largely eliminated. A phylogenetic analysis with the HOL gene suggests that the ability to produce methyl halides is widespread among vascular plants. This approach provides a genetic basis for understanding and predicting patterns of methyl halide production by plants.     

Spatial Patterns in Autotrophic Picoplankton Abundance in a Reservoir Examined Using Microcosm Experiments

Autotrophic picoplankton (APP) are critically important in the production of organic matter in plankton food webs. A number of obvious environmental factors, including light, temperature, nutrient concentrations, and predation, have been identified as influencing APP abundance and growth rates. However, few experiments have investigated more than one factor at a time for their relationships to APP abundance or growth rate. We conducted a series of single and multi‐factor experiments to examine the relative importance of several biotic and abiotic variables, and their interactions, for their effects on APP abundance and growth rates. Experiments were conducted using APP samples collected during summer from the riverine and lacustrine zones of a southeastern U.S. reservoir. Growth rates of APP responded rapidly to nutrient addition, but the magnitude of the response was dependent on location of collection, and on the presence of grazers and other phytoplankton. Growth rates of APP from the riverine zone were limited by nitrogen, whereas lacustrine zone APP responded positively to both phosphorus and nitrogen addition. Regulation of APP population size by heterotrophic nanoflagellates appeared to be most effective when APP growth rates were relatively slow. APP cell chlorophyll concentrations varied inversely with the percentage of surface light in the mixed layer of the reservoir. We suggest that due to spatial differences in the rate and depth of vertical mixing, lacustrine zone APP receive less light on average, or light at less frequent intervals, than APP in the more turbid but shallower riverine zone. Longitudinal declines in both nutrient and light availability during summer may reduce APP growth rates and population size in the lacustrine zone compared to the more productive riverine zone of this reservoir.     

Nebulized perflubron and carbon dioxide rapidly dilate constricted airways in an ovine model of allergic asthma

Background

The low toxicity of perfluorocarbons (PFCs), their high affinity for respiratory gases and their compatibility with lung surfactant have made them useful candidates for treating respiratory diseases such as adult respiratory distress syndrome. We report results for treating acute allergic and non-allergic bronchoconstriction in sheep using S-1226 (a gas mixture containing carbon dioxide and small volumes of nebulized perflubron). The carbon dioxide, which is highly soluble in perflubron, was used to relax airway smooth muscle.

Methods

Sheep previously sensitized to house dust mite (HDM) were challenged with HDM aerosols to induce early asthmatic responses. At the maximal responses (characterised by an increase in lung resistance), the sheep were either not treated or treated with one of the following; nebulized S-1226 (perflubron + 12% CO₂), nebulized perflubron + medical air, 12% CO₂, salbutamol or medical air. Lung resistance was monitored for up to 20 minutes after cessation of treatment.In additional naïve sheep, a segmental bronchus was pre-contracted with methacholine (MCh) and treated with nebulized S-1226 administered via a bronchoscope catheter. Subsequent bronchodilatation was monitored by real time digital video recording.

Results

Treatment with S-1226 for 2 minutes following HDM challenge resulted in a more rapid, more profound and more prolonged decline in lung resistance compared with the other treatment interventions. Video bronchoscopy showed an immediate and complete (within 5 seconds) re-opening of MCh-constricted airways following treatment with S-1226.

Conclusions

S-1226 is a potent and rapid formulation for re-opening constricted airways. Its mechanism(s) of action are unknown. The formulation has potential as a rescue treatment for acute severe asthma.

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-014-0098-x) contains supplementary material, which is available to authorized users.     

Environmental and biological controls on methyl halide emissions from southern California coastal salt marshes

Methyl bromide (CH₃Br) and methyl chloride(CH₃Cl) emission rates from southernCalifornia coastal salt marshes show largespatial and temporal variabilities that arestrongly linked to biological and environmentalfactors. Here we discuss biogeochemical linesof evidence pointing to vegetation as theprimary source of CH₃Br and CH₃Clemissions from salt marshes. Sediments andmacroalgae do not appear to be major producersof these compounds, based on observations thatthe highest fluxes are not inhibited by soilinundation; their emissions are not correlatedwith those of certain gases produced in soils;and emissions from mudflat- andmacroalgae-dominated sites are relativelysmall. In contrast, the seasonal and spatialvariabilities of methyl halide fluxes in thesesalt marshes are consistent with the productionof these compounds by vascular plants, althoughthe possibility of production by microflora orfungi associated with the salt marsh vegetationis not ruled out. Flux chamber measurements ofemission rates are largely correlated to theoverall plant biomass enclosed in the chamber,but appear also to be highly dependent on thepredominant plant species. Emission ratesfollow a diurnal trend similar to the trends ofambient air temperature and photosyntheticallyactive radiation, but not surface soiltemperature. Diurnal variabilities in thecarbon isotope compositions of CH₃Cl andCH₃Br and their relative ratios ofemissions are consistent with simultaneouslycompeting mechanisms of uptake andproduction.