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Background Gametogenesis in mammals entails profound re-patterning of the epigenome. In the female germline, DNA methylation is acquired late in oogenesis from an essentially unmethylated baseline and is established largely as a consequence of transcription events. Molecular and functional studies have shown that imprinted genes become methylated at different times during oocyte growth; however, little is known about the kinetics of methylation gain genome wide and the reasons for asynchrony in methylation at imprinted loci. Results Given the predominant role of transcription, we sought to investigate whether transcription timing is rate limiting for de novo methylation and determines the asynchrony of methylation events. Therefore, we generated genome-wide methylation and transcriptome maps of size-selected, growing oocytes to capture the onset and progression of methylation. We find that most sequence elements, including most classes of transposable elements, acquire methylation at similar rates overall. However, methylation of CpG islands (CGIs) is delayed compared with the genome average and there are reproducible differences amongst CGIs in onset of methylation. Although more highly transcribed genes acquire methylation earlier, the major transitions in the oocyte transcriptome occur well before the de novo methylation phase, indicating that transcription is generally not rate limiting in conferring permissiveness to DNA methylation. Instead, CGI methylation timing negatively correlates with enrichment for histone 3 lysine 4 (H3K4) methylation and dependence on the H3K4 demethylases KDM1A and KDM1B, implicating chromatin remodelling as a major determinant of methylation timing. We also identified differential enrichment of transcription factor binding motifs in CGIs acquiring methylation early or late in oocyte growth. By combining these parameters into multiple regression models, we were able to account for about a fifth of the variation in methylation timing of CGIs. Finally, we show that establishment of non-CpG methylation, which is prevalent in fully grown oocytes, and methylation over non-transcribed regions, are later events in oogenesis. Conclusions These results do not support a major role for transcriptional transitions in the time of onset of DNA methylation in the oocyte, but suggest a model in which sequences least dependent on chromatin remodelling are the earliest to become permissive for methylation. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0133-5) contains supplementary material, which is available to authorized users.

2-Ethylamino-1-phenylbutane (EAPB) and 2-amino-1-phenylbutane (APB) were identified by gas chromatography-mass spectrometry in multiple urine samples submitted for stimulant drug testing and screened positive for amphetamines by enzyme immunoassay. Forty-two samples from all over the USA were found, containing both analytes during a 3-month period May-July 2013. A sports dietary supplement 'CRAZE' has been determined to be one of the sources of EAPB supply. EAPB along with its suggested metabolite APB were detected in a urine sample, obtained from a person known to use 'CRAZE'.

Additional file 3: Figure S1. Progression of DNA methylation at transposable elements (TEs) during oocyte growth, complements Fig. 1. Figure S2: Methylation parameters in 60–65 µm oocytes, including comparison of PBAT and RRBS data sets. Figure S3. PCA plots for oocyte mRNA-seq libraries. Figure S4. Differentially expressed genes between consecutive oocyte size populations. Figure S5. GO analysis of genes up-regulated >50-fold between e18.5 and GV oocytes. Figure S6. Graph showing expression levels over oocyte growth of transcripts for Dnmts, Kdm1s and Kdm5s, and SetD2. Figure S7. Methylation level of intragenic CGIs in RRBS datasets in relation to expression level of the corresponding gene. Figure S8. MEME output of search for motifs enriched in late-methylated CGIs.

The study of 34,561 urine specimens, submitted for designer stimulant testing between February 2011 and January 2013, provided an opportunity: to estimate the range of synthetic cathinones (SC) abused in the USA, to observe multiple examples of metabolic profiles for each drug in various stages of excretion in human urine, to evaluate the extent of metabolism of specific SC and to select metabolites or parent drugs for routine testing. Sixteen SC were found in random patient samples: buphedrone; butylone; 3,4-dimethylmethcathinone; ethcathinone; N-ethylbuphedrone; ethylone; flephedrone; mephedrone; 4-methylbuphedrone; 3,4-methylenedioxypyrovalerone (MDPV); 4-methyl-N-ethylcathinone; methylone; pentedrone; pentylone; α-pyrrolidinobutiophenone (PBP) and α-pyrrolidinopentiophenone (PVP). After liquid/liquid extraction and trifluoroacetylation, specimens were screened by gas chromatography–mass spectrometry (GC–MS) for drugs and metabolites excreted free in urine. Each SC exhibited a characteristic metabolic profile, as shown by multiple examples. Metabolites' structures were postulated on the basis of their mass spectra. A large group of SC appears to metabolize extensively by carbonyl reduction into respective substituted ephedrines and further by N-dealkylation into norephedrines. Abundant metabolites in this group are essential markers of the parent drug use. Unchanged drugs are far less abundant or not found at all. SC with methylenedioxy attachment to the aromatic ring, metabolize by carbonyl reduction to a much lesser extent and are best detected as such in free urine fraction. PBP and PVP can be detected either unchanged or as metabolites, resulting from pyrrolidine ring degradation into primary amine followed by carbonyl reduction. MDPV appears in urine as such with no apparent free metabolites.

Ca2+ influxes regulate multiple events in photoreceptor cells including phototransduction and synaptic transmission. An important Ca2+ sensor in Drosophila vision appears to be calmodulin since a reduction in levels of retinal calmodulin causes defects in adaptation and termination of the photoresponse. These functions of calmodulin appear to be mediated, at least in part, by four previously identified calmodulin-binding proteins: the TRP and TRPL ion channels, NINAC and INAD. To identify additional calmodulin-binding proteins that may function in phototransduction and/or synaptic transmission, we conducted a screen for retinal calmodulin-binding proteins. We found eight additional calmodulin-binding proteins that were expressed in the Drosophila retina. These included six targets that were related to proteins implicated in synaptic transmission. Among these six were a homolog of the diacylglycerol-binding protein, UNC13, and a protein, CRAG, related to Rab3 GTPase exchange proteins. Two other calmodulin-binding proteins included Pollux, a protein with similarity to a portion of a yeast Rab GTPase activating protein, and Calossin, an enormous protein of unknown function conserved throughout animal phylogeny. Thus, it appears that calmodulin functions as a Ca2+ sensor for a broad diversity of retinal proteins, some of which are implicated in synaptic transmission.

Building energy simulation has become a useful tool for predicting cooling, heating and electrical loads for facilities. Simulation models have been validated throughout the years by comparing simulation results to actual measured values. The simulations have become more accurate as approaches were changed to be more comprehensive in their ability to model building features. These simulation models tend to require considerable experience in determining input parameters and large amounts of time to construct the models. As a result of the large number of man-hours required, simplified models have been sought and used. Simplified models are particularly useful for conducting preliminary assessments of energy conservation measures. These simplified models often use linear relationships in order to estimate conditions such as infiltration, energy usage, and temperature gradients. Studies have been performed in order to validate popular models such as ASHRAE's Bin or Modified Bin methods. A useful measure would be to determine the accuracy of a simplified model to establish error bounds. Having a simplified model and establishing its error bounds, technical estimations from such models could be used in selected applications with more confidence. The error bound relative to DOE-2 predictions, for a proposed simplified model denoted IEC, for estimating a commercial building's cooling load are presented along with two actual-building test cases for validation purposes. The sensitivity of the error to various building parameters such as minimum make-up air, cooling capacity oversize, and internal equipment load was investigated. The error bound was determined to be within ±15 per cent for both cases and almost all variations. Master of Science