Epigenetic signature of birth weight discordance in adult twins

Background

A low birth weight has been extensively related to poor adult health outcomes. Birth weight can be seen as a proxy for environmental conditions during prenatal development. Identical twin pairs discordant for birth weight provide an extraordinary model for investigating the association between birth weight and adult life health while controlling for not only genetics but also postnatal rearing environment. We performed an epigenome-wide profiling on blood samples from 150 pairs of adult monozygotic twins discordant for birth weight to look for molecular evidence of epigenetic signatures in association with birth weight discordance.

Results

Our association analysis revealed no CpG site with genome-wide statistical significance (FDR < 0.05) for either qualitative (larger or smaller) or quantitative discordance in birth weight. Even with selected samples of extremely birth weight discordant twin pairs, no significant site was found except for 3 CpGs that displayed age-dependent intra-pair differential methylation with FDRs 0.014 (cg26856578, p = 3.42e-08), 0.0256 (cg15122603, p = 1.25e-07) and 0.0258 (cg16636641, p = 2.05e-07). Among the three sites, intra-pair differential methylation increased with age for cg26856578 but decreased with age for cg15122603 and cg16636641. There was no genome-wide statistical significance for sex-dependent effects on intra-pair differential methylation in either the whole samples or the extremely discordant twins.

Conclusions

Genome-wide DNA methylation profiling did not reveal epigenetic signatures of birth weight discordance although some sites displayed age-dependent intra-pair differential methylation in the extremely discordant twin pairs.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1062) contains supplementary material, which is available to authorized users.     

Alterations in Nitric Oxide Activity and Sensitivity in Early Streptozotocin-Induced Diabetes Depend on Arteriolar Size

Changes in NO activity may play an important role in the early increase in microvascular flow that has been implicated in the pathogenesis of diabetic microangiopathy. We assessed, in the in situ spinotrapezius muscle preparation of 6 weeks'' streptozotocin-diabetic rats (n = 6) and of agematched controls (n = 8), basal inside diameters of A2–A4 arterioles and the reactivity to topically applied acetylcholine and nitroprusside, before and after N^G-nitro-L-arginine. In diabetic rats, cholinergic vasodilatation in A2–A4 arterioles was intact. Basal diameter in A3 and A4 arterioles was significantly higher in streptozotocin-diabetic rats. The increased basal diameter in A3 arterioles was partially due to an increased contribution of NO to basal diameter. The response to nitroprusside was impaired in streptozotocin-diabetic rats in A2, but not in A3 and A4 arterioles. Thus, this study shows that NO activity and sensitivity are altered after 6 weeks of streptozotocin-induced diabetes. These streptozotocin-induced changes are anatomically specific and, for arterioles, depend on their position within the vascular tree.     

Double-strand break toxicity is chromatin context independent

Cells respond to double-strand breaks (DSBs) by activating DNA damage response pathways, including cell cycle arrest. We have previously shown that a single double-strand break generated via CRISPR/Cas9 is sufficient to delay cell cycle progression and compromise cell viability. However, we also found that the cellular response to DSBs can vary, independent of the number of lesions. This implies that not all DSBs are equally toxic, and raises the question if the location of a single double-strand break could influence its toxicity. To systematically investigate if DSB-location is a determinant of toxicity we performed a CRISPR/Cas9 screen targeting 6237 single sites in the human genome. Next, we developed a data-driven framework to design CRISPR/Cas9 sgRNA (crRNA) pools targeting specific chromatin features. The chromatin context was defined using ChromHMM states, Lamin-B1 DAM-iD, DNAseI hypersensitivity, and RNA-sequencing data. We computationally designed 6 distinct crRNA pools, each containing 10 crRNAs targeting the same chromatin state. We show that the toxicity of a DSB is highly similar across the different ChromHMM states. Rather, we find that the major determinants of toxicity of a sgRNA are cutting efficiency and off-target effects. Thus, chromatin features have little to no effect on the toxicity of a single CRISPR/Cas9-induced DSB.     

Induction of indole synthesis in the appendix of Sauromatum guttatum Schott

Induction of indole synthesis in young appendix sections ofSauromatum guttatum Schott was studied. The inducer, known ascalorigen, a compound synthesized in the mature staminate flowerbuds, is capable of triggering a rapid metabolic spurt in theappendix of the inflorescence. The induced indole-formationlasts for only a short period of time, and is similar to thenormal pattern of indole synthesis. Under the experimental conditions,indole was detectable after 7 to 8 hr of calorigen treatmentbut had disappeared about 35 hr later. The moment when indoleis present in maximal amount coincides with that of maximalheat production, i.e., about 27 hr after the application ofcalorigen. A simple and sensitive bioassay for detection ofcalorigen, based on the formation of indole, could be devised. Calorigen also causes, to a lesser extent, a temperature-riseof those young floral parts (male, female and sterile tissues)where indole is not detectable at any time. The time sequenceof the induced production of heat for the various floral partsmimics that of a natural metabolic flare-up. Extracts prepared from the mature staminate flowers of Arummaculatum L., Arum dioscoridis Sibth and Sm., and Dracunculusvulgaris Schott were all able to induce the formation of indolein the appendix of Sauromatum in a fashion similar to that causedby the staminate flower extract of this plant. (Received February 12, 1972; )     

Resurrecting complexity: the interplay of plasticity and rapid evolution in the multiple trait response to strong changes in predation pressure in the water flea Daphnia magna

A resurrection ecology reconstruction of 14 morphological, life history and behavioural traits revealed that a natural Daphnia magna population rapidly tracked changes in fish predation by integrating phenotypic plasticity and widespread evolutionary changes both in mean trait values and in trait plasticity. Increased fish predation mainly generated rapid adaptive evolution of plasticity (especially in the presence of maladaptive ancestral plasticity) resulting in an important change in the magnitude and direction of the multivariate reaction norm. Subsequent relaxation of the fish predation pressure resulted in reversed phenotypic plasticity and mainly caused evolution of the trait means towards the ancestral pre‐fish means. Relaxation from fish predation did, however, not result in a complete reversal to the ancestral fishless multivariate phenotype. Our study emphasises that the study population rapidly tracked environmental changes through a mosaic of plasticity, evolution of trait means and evolution of plasticity to generate integrated phenotypic changes in multiple traits.     

DNA and nuclear protein measurement in columnar epithelial cells of human endometrium

Propidium iodide DNA flow cytometry, Feulgen-DNA, and nuclear light green protein scanning cytometry were performed in columnar epithelial cells of normal, nonmalignant human endometrium and endometrial adenocarcinomas. Columnar cells were identified by immunohistochemical staining for cytokeratin 18, an intermediate filament protein specifically present in columnar cell epithelium. DNA measurements derived from flow and scanning cytometry showed comparable results. The DNA content of the G0/G1 fraction of the adenocarcinomas had a considerable overlap with that of normal endometrium, with that of the carcinomas shifted toward higher values. For the carcinomas, no correlation was found with the histological grade, with the exception of the adenosquamous carcinomas. Most of the clinical stage I tumors showed a DNA content in the normal diploid region. Three of the four carcinomas of clinical stage II and higher had an increased DNA content. For the carcinomas, the percentage of cells in the proliferative fraction, as determined from scanning cytometric derived DNA histograms, was comparable to that of normal endometrium, or higher. No correlation was found with the histological grade. Tumors of clinical stage II and higher had intermediate values compared to carcinomas of lower stages. The nuclear protein/DNA ratio of malignant endometrium completely overlapped that of normal endometrium. Within the tumor population, no correlation was found with the histological grade, with the exception of the adenosquamous carcinomas, and clinical stage. Based on the aforementioned parameters, no discrimination could be obtained between normal and malignant endometrium. However, when the DNA content of the G0/G1 fraction was combined with the coefficient of variation of the nuclear protein/DNA ratio, a clear discrimination could be obtained with only two false-positive cases.     

Quantitative description of classic and variant small cell lung cancer cell lines by nuclear image cytometry

Six small cell lung cancer (SCLC) cell lines were examined using nuclear image analysis to find features characteristic of the classic and the variant type of SCLC. On the basis of their biochemical and biological properties three of these cell lines have been shown to represent the classic types, and three represent the variant type of SCLC. Using a combination of the image-derived run length, density, and geometric features, it was possible to distinguish between the classic and variant SCLC cell lines. The results of this study may be of help in assessing photometric features for the separation of the classic and variant subtypes of SCLC in solid tumors. Because of differences in treatment and prognosis between these two subtypes, such a separation may be of clinical value.     

Sexual reproduction in the arum lily family,with emphasis on thermogenicity

Summary Floral thermogenicity, which is found in several representatives of half a dozen angiosperm families, is most pronounced in the Araceae. It is based on the operation of an alternative, cyanide-resistant electron transport chain which, in contrast to the classic cytochrome oxidase system, produces little ATP; most of the energy originally locked up in the respiratory substrate usually starch — is therefore liberated in the form of heat. The biological function of this (biochemically wasteful) system is to release the heat to serve as a volatilizer for the floral odors (often containing aliphatic amines, indole and skatole) that attract the insect pollinators. This makes the survival value of thermogenesis (for the plant species) immediately clear. Thermogenicity is under tight biological control, as demonstrated by the fact that the same ceiling temperature is always reached, regardless of ambient temperature. In Eastern skunk cabbage (Symplocarpus foetidus), which flowers very early in spring, that ceiling is about 20° C, in tropical forms such as Xanthosoma robustum and Philodendron selloum, it lies in the 42°–44° C range. In several instances, e.g., in Arum and in Sauromatum, the voodoo lily, thermogenicity manifests itself as a flare-up of only a few hours' duration, a respiratory explosion that can lead to rates of metabolism that compare favorably with those of a hovering hummingbird. The metabolic peak is always reached at a particular time of day, which is different for the different arum lily species, and thus reduces competition for pollinators. The odors that accompany the heat are also very characteristic, appealing to different pollinator classes and further reducing such competition. In the voodoo lily and in Arum, the primary site for the production of both heat and odor is the naked appendix of the inflorescence, which acts as a specialized osmophore or odor carrier. The first explosion may be followed by another one several hours later, which manifests itself in the floral chamber of the inflorescence and is under strict photoperiodic control. In Sauromatum, the first metabolic explosion is triggered by a plant hormone, originally referred to as calorigen, which originates in the primordia of the staminate flowers and moves from there into the appendix where it exerts its action after a lag-time of about a day — an indication that synthesis of new enzymatic protein (through unblocking of certain genes?) may well be involved. In 1987, calorigen was shown to be identical with salicylic acid. This compound was already known to induce flowering in certain duck-weeds, Lemnaceae, which until recently were regarded as belonging to the same family as arum lilies. In certain water lilies (Nymphaeaceae), thermogenicity is combined with a pollination syndrome very similar to that of Arum and Sauromatum but involving temporary trap flowers.Dedicated to the memory of A.W.H. van Herk, pioneer in the study of arum lilies, superb lecturer, and unselfish human being     

Bioanalysis of aplidine, a new marine antitumoral depsipeptide, in plasma by high-performance liquid chromatography after derivatization with trans-4′-hydrazino-2-stilbazole

A sensitive bio-analytical assay in plasma of the depsipeptide aplidine is reported, based on reversed-phase liquid chromatography and fluorescence detection of the trans-4′-hydrazino-2-stilbazole (4′H2S) derivative of the analyte. At ambient temperature, two conformations of the depsipeptide are observed in solution due to cis–trans isomerism at the proline–pyruvoyl peptide bond. Aplidine is isolated from the matrix by solid-phase extraction on an octadecyl modified silica stationary phase. After evaporation of the acetone eluate, a derivatization with 4′H2S is performed in a water–acetonitrile mixture at pH 4. The reaction mixture is injected directly into the chromatograph and the analyte is quantified by fluorescence detection at 410 and 560 nm for excitation and emission, respectively. The method has been validated in the 2–100 ng/ml-range, 2 ng/ml being the lower limit of quantification. Precision and accuracy both meet the current requirements for a bioanalytical assay. The identity of the 4′H2S reaction products of aplidine have been confirmed by mass spectrometric analysis. Finally, the method has been employed for a pilot pharmacokinetic study of aplidine in mice which demonstrated its usefulness for pharmacological research.