Lucia Brown

An inventory of nitrous oxide emissions from agriculture in the UK using the IPCC methodology: emission estimate, uncertainty and sensitivity analysis

Nitrous oxide emission from UK agriculture was estimated, using the IPCC default values of all emission factors and parameters, to be 87 Gg N2O–N in both 1990 and 1995. This estimate was shown, however, to have an overall uncertainty of 62%. The largest component of the emission (54%) was from the direct (soil) sector. Two of the three emission factors applied within the soil sector, EF1 (direct emission from soil) and EF3PRP (emission from pasture range and paddock) were amongst the most influential on the total estimate, producing a ±31 and +11% to −17% change in emissions, respectively, when varied through the IPCC range from the default value. The indirect sector (from leached N and deposited ammonia) contributed 29% of the total emission, and had the largest uncertainty (126%). The factors determining the fraction of N leached (FracLEACH) and emissions from it (EF5), were the two most influential. These parameters are poorly specified and there is great potential to improve the emission estimate for this component. Use of mathematical models (NCYCLE and SUNDIAL) to predict FracLEACH suggested that the IPCC default value for this parameter may be too high for most situations in the UK. Comparison with other UK-derived inventories suggests that the IPCC methodology may overestimate emission. Although the IPCC approach includes additional components to the other inventories (most notably emission from indirect sources), estimates for the common components (i.e. fertiliser and animals), and emission factors used, are higher than those of other inventories. Whilst it is recognised that the IPCC approach is generalised in order to allow widespread applicability, sufficient data are available to specify at least two of the most influential parameters, i.e. EF1 and FracLEACH, more accurately, and so provide an improved estimate of nitrous oxide emissions from UK agriculture.

Molecular Regulation of the Developing Commissural Plate

Coordinated transfer of information between the brain hemispheres is essential for function and occurs via three axonal commissures in the telencephalon: the corpus callosum (CC), hippocampal commissure (HC), and anterior commissure (AC). Commissural malformations occur in over 50 human congenital syndromes causing mild to severe cognitive impairment. Disruption of multiple commissures in some syndromes suggests that common mechanisms may underpin their development. Diffusion tensor magnetic resonance imaging revealed that forebrain commissures crossed the midline in a highly specific manner within an oblique plane of tissue, referred to as the commissural plate. This specific anatomical positioning suggests that correct patterning of the commissural plate may influence forebrain commissure formation. No analysis of the molecular specification of the commissural plate has been performed in any species; therefore, we utilized specific transcription factor markers to delineate the commissural plate and identify its various subdomains. We found that the mouse commissural plate consists of four domains and tested the hypothesis that disruption of these domains might affect commissure formation. Disruption of the dorsal domains occurred in strains with commissural defects such as Emx2 and Nfia knockout mice but commissural plate patterning was normal in other acallosal strains such as Satb2−/−. Finally, we demonstrate an essential role for the morphogen Fgf8 in establishing the commissural plate at later developmental stages. The results demonstrate that correct patterning of the commissural plate is an important mechanism in forebrain commissure formation. J. Comp. Neurol. 518:3645–3661, 2010.

Microarray assessment of methylation in individual mouse blastocyst stage embryos shows that in vitro culture may have widespread genomic effects

BACKGROUND Although assisted reproductive technology (ART) is reported to result in abnormal genomic imprinting and/or altered genomic methylation, few if any studies have used high-throughput methods to analyze genomic methylation in ART embryos. We hypothesized that a microarray-based assessment of genomic methylation could be used to reveal differences between ART and normal preimplantation embryos. METHODS In this pilot study, we performed methylation-sensitive amplification of genomic DNA from preimplantation mouse blastocysts, obtained by natural mating and either maintained in vivo until E3.5 (n = 4) or cultured in vitro (n = 4) from E0.5 until E3.5. An oligonucleotide microarray was then used to perform comparative hybridization of amplified DNA, allowing us to assess relative methylation at ~16,000 loci on mouse chromosome 7. RESULTS We show that for in vivo derived embryos, the methylation/microarray results were strikingly consistent. In contrast, all four in vitro cultured embryos showed evidence of generalized hypermethylation as well as greater locus-to-locus variability, when compared with in vivo derived embryos. Genomic segments that overlapped exons and CpG islands were most likely to be hypomethylated in both normal and experimental blastocysts. Other sequence features, such as repetitive elements, were not associated with the presence of or the degree of methylation. CONCLUSIONS We conclude that a general assessment of genomic methylation in blastocyst stage embryos is technically feasible. Data from this small sample suggest that in vitro embryo culture is associated with generalized hypermethylation as well as increased locus-to-locus variability in methylation. However, it is premature to conclude that this is a general property of in vitro cultured blastocysts.

Zic2 is expressed in pluripotent cells in the blastocyst and adult brain expression overlaps with makers of neurogenesis.

Members of the zic family of transcription factors are widely understood to act during neural patterning and neural crest development. In particular, studies in mice and humans have shown that Zic2 has a role in forebrain patterning, while studies in Xenopus and zebrafish have shown that Zic2 acts during gastrulation. Expression of Zic2 prior to gastrulation has not been reported in the mouse. In the adult, Zic2 is known to be strongly expressed in cerebellar granule cells, but expression elsewhere in the adult brain has not been reported. We present data showing that Zic2 is expressed in pluripotent cells during very early mouse development. Further, in the adult brain, Zic2 expression is broad and overlaps with markers of neurogenesis. The presence of Zic2 in pluripotent cells of the embryo as well as in dividing neural cells in the adult suggests that this transcription factor may have a role in maintaining pluripotency.

Recurrent pregnancy loss in a woman with NLRP7 mutation: not all molar pregnancies can be easily classified as either "partial" or "complete" hydatidiform moles.

Recurrent hydatidiform moles is an uncommon occurrence. Over the past decade, genetic studies of women with multiple recurrent molar pregnancies have revealed that maternal mutations in two different genes, NLRP7 and C6orf221, result in recurrent moles. We report a 23 year old woman, born of unrelated parents, who has experienced three molar pregnancies in succession. Whilst the first pregnancy was classified as a complete hydatidiform mole, the second and third moles defied classification as complete or partial mole using conventional histology, p57 nuclear staining pattern and ploidy studies. Molecular and cytogenetic studies proved that all three molar pregnancies were diploid and biparental in origin. Gene sequencing analysis showed that the patient is homozygous for a previously described mutation in NLRP7. A SNP microarray ruled out the presence of deletion of the NLRP7 locus. This case draws attention to the fact that recurrent molar pregnancies may be the result of specific, identifiable gene mutations, even in patients from non-consanguineous backgrounds. When pathologists encounter patients with molar pregnancies that are diploid and p57 negative and yet have fetal elements such as nucleated red blood cells or immature fetal tissues, it should heighten their suspicion of a possible genetic basis and appropriate molecular genetic workup performed with counseling offered.

Generalized Disturbance of DNA Methylation in the Uterine Decidua in the CBA/J × DBA/2 Mouse Model of Pregnancy Failure

ABSTRACT Nonchromosomal pregnancy failure is a common but poorly understood phenomenon. Because recent data have suggested that epigenetic abnormalities such as abnormal placental DNA methylation may play a role in human pregnancy failure, we undertook experiments to test whether decidual and/or placental DNA methylation abnormalities are present in a mouse model of pregnancy failure. A large number of studies have shown that crosses between CBA/J female mice and DBA/2 males result in pregnancies with a high rate of failure/resorption, whereas other crosses with CBA/J females produce normal pregnancies. Although the CBA/J × DBA/2 mouse has frequently been used as a model for miscarriage, a detailed explanation for the pregnancy failure phenotype is lacking. We performed timed matings between CBA/J female and DBA/2 male mice as well as between DBA/2 female and CBA/J male mice. Decidual caps were isolated at Embryonic Day (E) 9.5 from both crosses, and a microarray-based method was used to comparatively assess genomic methylation at approximately 16 000 loci on mouse chromosome 7. In comparison with decidual caps from DBA/2 × CBA/J pregnancies, CBA/J × DBA/2 decidual caps were characterized by widely and apparently randomly disturbed methylation. In another set of analogous experiments, genomic methylation of placental DNA from E8.5 pregnancies was assessed using the same microarray-based method. This analysis revealed that in contrast to the decidua, placental DNA methylation from CBA/J × DBA/2 pregnancies was indistinguishable from that of normal controls. We conclude that abnormal DNA methylation in the uterine decidua likely plays a role in the CBA/J × DBA/2 model of pregnancy failure. To our knowledge, these experiments are the first to demonstrate that epigenetic abnormalities of the decidua are associated with pregnancy failure, and they set the stage for future efforts to understand the role of DNA methylation at the maternal-fetal interface.