Genetic recombination is targeted towards gene promoter regions in dogs

The identification of the H3K4 trimethylase, PRDM9, as the gene responsible for recombination hotspot localization has provided considerable insight into the mechanisms by which recombination is initiated in mammals. However, uniquely amongst mammals, canids appear to lack a functional version of PRDM9 and may therefore provide a model for understanding recombination that occurs in the absence of PRDM9, and thus how PRDM9 functions to shape the recombination landscape. We have constructed a fine-scale genetic map from patterns of linkage disequilibrium assessed using high-throughput sequence data from 51 free-ranging dogs, Canis lupus familiaris. While broad-scale properties of recombination appear similar to other mammalian species, our fine-scale estimates indicate that canine highly elevated recombination rates are observed in the vicinity of CpG rich regions including gene promoter regions, but show little association with H3K4 trimethylation marks identified in spermatocytes. By comparison to genomic data from the Andean fox, Lycalopex culpaeus, we show that biased gene conversion is a plausible mechanism by which the high CpG content of the dog genome could have occurred.Comment: Updated version, with significant revision

Cytosine Methylation Dysregulation in Neonates Following Intrauterine Growth Restriction

Perturbations of the intrauterine environment can affect fetal development during critical periods of plasticity, and can increase susceptibility to a number of age-related diseases (e.g., type 2 diabetes mellitus; T2DM), manifesting as late as decades later. We hypothesized that this biological memory is mediated by permanent alterations of the epigenome in stem cell populations, and focused our studies specifically on DNA methylation in CD34+ hematopoietic stem and progenitor cells from cord blood from neonates with intrauterine growth restriction (IUGR) and control subjects.Our epigenomic assays utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. We found that changes in cytosine methylation occur in response to IUGR of moderate degree and involving a restricted number of loci. We also identify specific loci that are targeted for dysregulation of DNA methylation, in particular the hepatocyte nuclear factor 4alpha (HNF4A) gene, a well-known diabetes candidate gene not previously associated with growth restriction in utero, and other loci encoding HNF4A-interacting proteins.Our results give insights into the potential contribution of epigenomic dysregulation in mediating the long-term consequences of IUGR, and demonstrate the value of this approach to studies of the fetal origin of adult disease

Allele-specific transcriptional elongation regulates monoallelic expression of the IGF2BP1 gene

<p>Abstract</p> <p>Background</p> <p>Random monoallelic expression contributes to phenotypic variation of cells and organisms. However, the epigenetic mechanisms by which individual alleles are randomly selected for expression are not known. Taking cues from chromatin signatures at imprinted gene loci such as the insulin-like growth factor 2 gene 2 (<it>IGF2</it>), we evaluated the contribution of CTCF, a zinc finger protein required for parent-of-origin-specific expression of the <it>IGF2 </it>gene, as well as a role for allele-specific association with DNA methylation, histone modification and RNA polymerase II.</p> <p>Results</p> <p>Using array-based chromatin immunoprecipitation, we identified 293 genomic loci that are associated with both CTCF and histone H3 trimethylated at lysine 9 (H3K9me3). A comparison of their genomic positions with those of previously published monoallelically expressed genes revealed no significant overlap between allele-specifically expressed genes and colocalized CTCF/H3K9me3. To analyze the contributions of CTCF and H3K9me3 to gene regulation in more detail, we focused on the monoallelically expressed <it>IGF2BP1 </it>gene. <it>In vitro </it>binding assays using the CTCF target motif at the <it>IGF2BP1 </it>gene, as well as allele-specific analysis of cytosine methylation and CTCF binding, revealed that CTCF does not regulate mono- or biallelic <it>IGF2BP1 </it>expression. Surprisingly, we found that RNA polymerase II is detected on both the maternal and paternal alleles in B lymphoblasts that express <it>IGF2BP1 </it>primarily from one allele. Thus, allele-specific control of RNA polymerase II elongation regulates the allelic bias of <it>IGF2BP1 </it>gene expression.</p> <p>Conclusions</p> <p>Colocalization of CTCF and H3K9me3 does not represent a reliable chromatin signature indicative of monoallelic expression. Moreover, association of individual alleles with both active (H3K4me3) and silent (H3K27me3) chromatin modifications (allelic bivalent chromatin) or with RNA polymerase II also fails to identify monoallelically expressed gene loci. The selection of individual alleles for expression occurs in part during transcription elongation.</p

Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus

We described the study design, detailed analytical methods, and verification results in the supporting information file. (DOCX 21.2 MB

CG dinucleotide clustering is a species-specific property of the genome

Cytosines at cytosine-guanine (CG) dinucleotides are the near-exclusive target of DNA methyltransferases in mammalian genomes. Spontaneous deamination of methylcytosine to thymine makes methylated cytosines unusually susceptible to mutation and consequent depletion. The loci where CG dinucleotides remain relatively enriched, presumably due to their unmethylated status during the germ cell cycle, have been referred to as CpG islands. Currently, CpG islands are solely defined by base compositional criteria, allowing annotation of any sequenced genome. Using a novel bioinformatic approach, we show that CG clusters can be identified as an inherent property of genomic sequence without imposing a base compositional a priori assumption. We also show that the CG clusters co-localize in the human genome with hypomethylated loci and annotated transcription start sites to a greater extent than annotations produced by prior CpG island definitions. Moreover, this new approach allows CG clusters to be identified in a species-specific manner, revealing a degree of orthologous conservation that is not revealed by current base compositional approaches. Finally, our approach is able to identify methylating genomes (such as Takifugu rubripes) that lack CG clustering entirely, in which it is inappropriate to annotate CpG islands or CG clusters

Child Health Care in Ireland

The Irish health care system is based on a complex and costly mix of private, statutory, and voluntary provisions. The majority of health care expenditure comes from the state, with a significant proportion of acute hospital care funded from private insurance, but there are relatively high out-of-pocket costs for most service users. There is free access to acute hospital care, but not for primary care, for all children. About 40% of the population have free access to primary care. Universal preventive public health services, including vaccination and immunization, newborn blood spot screening, and universal neonatal hearing screening are free. Major health challenges include poverty, obesity, drug and alcohol use, and mental health. The health care system has been dominated for the last 5 years by the impact of the current recession, which has led to very sharp cuts in health care expenditure. It is unclear if the necessary substantial reform of the system will happen. Government policy calls for a move toward a patient-centered, primary care-led system, but without very substantial transfers of resources and investment in Information and Communication Technology, this is unlikely to occur

Emissions of ozone-depleting halocarbons from China

National emission inventories of ozone-depleting substances (ODS) play a key role in the control mechanisms of the Montreal Protocol's emission reduction plans. New quasi-continuous ground-based atmospheric measurements allow us to estimate China's current emissions of the most effective ODS. This serves as an independent validation of China's ODS consumption data reported to the United Nations Environment Programme (UNEP). Emissions of most first-generation ODS have declined in recent years, suggesting compliance with the regulations of China's advanced phase-out program. In contrast the emissions of some second-generation ODS have increased. Because China is currently one of the largest consumers of first generation ODS, the country's upcoming complete phase-out will be crucial for the rate of decline of atmospheric ODS hence the eventual recovery of the stratospheric ozone. Citation: Vollmer, M. K., et al. (2009), Emissions of ozone-depleting halocarbons from China, Geophys. Res. Lett., 36, L15823, doi:10.1029/2009GL038659

Heterogeneous abnormalities of in-vivo left ventricular calcium influx and function in mouse models of muscular dystrophy cardiomyopathy

BACKGROUND: Manganese-enhanced cardiovascular magnetic resonance (MECMR) can non-invasively assess myocardial calcium influx, and calcium levels are known to be elevated in muscular dystrophy cardiomyopathy based on cellular studies. METHODS: Left ventricular functional studies and MECMR were performed in mdx mice (model of Duchenne Muscular Dystrophy, 24 and 40 weeks) and Sgcd−/− mice (Limb Girdle Muscular Dystrophy 2 F, 16 and 32 weeks), compared to wild type controls (C57Bl/10, WT). RESULTS: Both models had left ventricular hypertrophy at the later age compared to WT, though the mdx mice had reduced stroke volumes and the Sgcd−/− mice increased heart rate and cardiac index. Especially at the younger ages, MECMR was significantly elevated in both models (both P<0.05 versus WT). The L-type calcium channel inhibitor diltiazem (5 mg/kg i.p.) significantly reduced MECMR in the mdx mice (P<0.01), though only with a higher dose (10 mg/kg i.p.) in the Sgcd−/− mice (P<0.05). As the Sgcd−/− mice had increased heart rates, to determine the role of heart rate in MECMR we studied the hyperpolarization-activated cyclic nucleotide-gated channel inhibitor ZD 7288 which selectively reduces heart rate. This reduced heart rate and MECMR in all mouse groups. However, when looking at the time course of reduction of MECMR in the Sgcd−/− mice at up to 5 minutes of the manganese infusion when heart rates were matched to the WT mice, MECMR was still significantly elevated in the Sgcd−/− mice (P<0.01) indicating that heart rate alone could not account for all the increased MECMR. CONCLUSIONS: Despite both mouse models exhibiting increased in-vivo calcium influx at an early stage in the development of the cardiomyopathy before left ventricular hypertrophy, there are distinct phenotypical differences between the 2 models in terms of heart rates, hemodynamics and responses to calcium channel inhibitors

HFC-23 (CHF3) emission trend response to HCFC-22 (CHClF2) production and recent HFC-23 emission abatement measures

HFC-23 (also known as CHF3 [CHF subscript 3], fluoroform or trifluoromethane) is a potent greenhouse gas (GHG), with a global warming potential (GWP) of 14 800 for a 100-year time horizon. It is an unavoidable by-product of HCFC-22 (CHClF2 [CHCIF subscript 2], chlorodifluoromethane) production. HCFC-22, an ozone depleting substance (ODS), is used extensively in commercial refrigeration and air conditioning, in the extruded polystyrene (XPS) foam industries (dispersive applications) and also as a feedstock in fluoropolymer manufacture (a non-dispersive use). Aside from small markets in specialty uses, HFC-23 has historically been considered a waste gas that was, and often still is, simply vented to the atmosphere. Efforts have been made in the past two decades to reduce HFC-23 emissions, including destruction (incineration) in facilities in developing countries under the United Nations Framework Convention on Climate Change's (UNFCCC) Clean Development Mechanism (CDM), and by process optimization and/or voluntary incineration by most producers in developed countries. We present observations of lower-tropospheric mole fractions of HFC-23 measured by "Medusa" GC/MSD instruments from ambient air sampled in situ at the Advanced Global Atmospheric Gases Experiment (AGAGE) network of five remote sites (2007–2009) and in Cape Grim air archive (CGAA) samples (1978–2009) from Tasmania, Australia. These observations are used with the AGAGE 2-D atmospheric 12-box model and an inverse method to produce model mole fractions and a "top-down" HFC-23 emission history. The model 2009 annual mean global lower-tropospheric background abundance is 22.6 (±0.2) pmol mol−1 [mol superscript -1]. The derived HFC-23 emissions show a "plateau" during 1997–2003, followed by a rapid ~50% increase to a peak of 15.0 (+1.3/−1.2) Gg/yr in 2006. Following this peak, emissions of HFC-23 declined rapidly to 8.6 (+0.9/−1.0) Gg/yr in 2009, the lowest annual emission of the past 15 years. We derive a 1990–2008 "bottom-up" HFC-23 emission history using data from the United Nations Environment Programme and the UNFCCC. Comparison with the top-down HFC-23 emission history shows agreement within the stated uncertainties. In the 1990s, HFC-23 emissions from developed countries dominated all other sources, then began to decline and eventually became fairly constant during 2003–2008. By this point, with developed countries' emissions essentially at a plateau, the major factor controlling the annual dynamics of global HFC-23 emissions became the historical rise of developing countries' HCFC-22 dispersive use production, which peaked in 2007. Thereafter in 2007–2009, incineration through CDM projects became a larger factor, reducing global HFC-23 emissions despite rapidly rising HCFC-22 feedstock production in developing countries.NASA Upper Atmospheric Research Program (Grant NNX07AE89G)NASA Upper Atmospheric Research Program (Grant NNX07AF09G)NASA Upper Atmospheric Research Program (Grant NNX07AE87G

An analytical inversion method for determining regional and global emissions of greenhouse gases: Sensitivity studies and application to halocarbons

A new analytical inversion method has been developed to determine the regional and global emissions of long-lived atmospheric trace gases. It exploits in situ measurement data from three global networks and builds on backward simulations with a Lagrangian particle dispersion model. The emission information is extracted from the observed concentration increases over a baseline that is itself objectively determined by the inversion algorithm. The method was applied to two hydrofluorocarbons (HFC-134a, HFC-152a) and a hydrochlorofluorocarbon (HCFC-22) for the period January 2005 until March 2007. Detailed sensitivity studies with synthetic as well as with real measurement data were done to quantify the influence on the results of the a priori emissions and their uncertainties as well as of the observation and model errors. It was found that the global a posteriori emissions of HFC-134a, HFC-152a and HCFC-22 all increased from 2005 to 2006. Large increases (21%, 16%, 18%, respectively) from 2005 to 2006 were found for China, whereas the emission changes in North America (−9%, 23%, 17%, respectively) and Europe (11%, 11%, −4%, respectively) were mostly smaller and less systematic. For Europe, the a posteriori emissions of HFC-134a and HFC-152a were slightly higher than the a priori emissions reported to the United Nations Framework Convention on Climate Change (UNFCCC). For HCFC-22, the a posteriori emissions for Europe were substantially (by almost a factor 2) higher than the a priori emissions used, which were based on HCFC consumption data reported to the United Nations Environment Programme (UNEP). Combined with the reported strongly decreasing HCFC consumption in Europe, this suggests a substantial time lag between the reported time of the HCFC-22 consumption and the actual time of the HCFC-22 emission. Conversely, in China where HCFC consumption is increasing rapidly according to the UNEP data, the a posteriori emissions are only about 40% of the a priori emissions. This reveals a substantial storage of HCFC-22 and potential for future emissions in China. Deficiencies in the geographical distribution of stations measuring halocarbons in relation to estimating regional emissions are also discussed in the paper. Applications of the inversion algorithm to other greenhouse gases such as methane, nitrous oxide or carbon dioxide are foreseen for the future