Complete genome sequence of Halopiger xanaduensis type strain (SH-6(T))

Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.     

PI3Kγ Drives Priming and Survival of Autoreactive CD4+ T Cells during Experimental Autoimmune Encephalomyelitis

The class IB phosphoinositide 3-kinase gamma enzyme complex (PI3Kγ) functions in multiple signaling pathways involved in leukocyte activation and migration, making it an attractive target in complex human inflammatory diseases including MS. Here, using pik3cg ^−/− mice and a selective PI3Kγ inhibitor, we show that PI3Kγ promotes development of experimental autoimmune encephalomyelitis (EAE). In pik3cg^−/− mice, EAE is markedly suppressed and fewer leukocytes including CD4⁺ and CD8⁺ T cells, granulocytes and mononuclear phagocytes infiltrate the CNS. CD4⁺ T cell priming in secondary lymphoid organs is reduced in pik3cg^−/− mice following immunisation. This is attributable to defects in DC migration concomitant with a failure of full T cell activation following TCR ligation in the absence of p110γ. Together, this results in suppressed autoreactive T cell responses in pik3cg^−/− mice, with more CD4⁺ T cells undergoing apoptosis and fewer cytokine-producing Th1 and Th17 cells in lymphoid organs and the CNS. When administered from onset of EAE, the orally active PI3Kγ inhibitor AS605240 caused inhibition and reversal of clinical disease, and demyelination and cellular pathology in the CNS was reduced. These results strongly suggest that inhibitors of PI3Kγ may be useful therapeutics for MS.     

Soluble ST2 Associates with Diabetes but Not Established Cardiovascular Risk Factors: A New Inflammatory Pathway of Relevance to Diabetes?

Preliminary data mostly from animal models suggest the sST2/IL-33 pathway may have causal relevance for vascular disease and diabetes and thus point to a potential novel inflammatory link to cardiometabolic disease. However, the characterisation of sST2 levels in terms of metabolic or vascular risk in man is completely lacking. We sought to address this gap via a comprehensive analysis of risk factor and vascular correlates of sST2 in a cross-sectional study (pSoBid). We measured sST2 in plasma in 639 subjects and comprehensively related it to cardiovascular and diabetes risk factors and imaged atherosclerosis measures. Circulating sST2 levels increased with age, were lower in women and in highest earners. After adjusting for age and gender, sST2 levels associated strongly with markers of diabetes, including triglycerides [effect estimate (EE) per 1 standard deviation increase in sST2∶1.05 [95%CI 1.01,1.10]), liver function (alanine aminotransaminase [ALT] and γ-glutamyl transferase [GGT]: EE 1.05 [1.01,1.09] and 1.13 [1.07,1.19] respectively), glucose (1.02 [1.00,1.03]) and sICAM-1 (1.05 [1.02,1.07]). However, sST2 levels were not related to smoking, cholesterol, blood pressure, or atheroma (carotid intima media thickness, plaque presence). These results suggest that sST2 levels, in individuals largely without vascular disease, are related principally to markers associated with diabetes and ectopic fat and add support for a role of sST2 in diabetes. Further mechanistic studies determining how sST2 is linked to diabetes pathways may offer new insights into the inflammatory paradigm for type 2 diabetes.     

FOXM1 induces a global methylation signature that mimics the cancer epigenome in head and neck squamous cell carcinoma

The oncogene FOXM1 has been implicated in all major types of human cancer. We recently showed that aberrant FOXM1 expression causes stem cell compartment expansion resulting in the initiation of hyperplasia. We have previously shown that FOXM1 regulates HELLS, a SNF2/helicase involved in DNA methylation, implicating FOXM1 in epigenetic regulation. Here, we have demonstrated using primary normal human oral keratinocytes (NOK) that upregulation of FOXM1 suppressed the tumour suppressor gene p16^INK4A (CDKN2A) through promoter hypermethylation. Knockdown of HELLS using siRNA re-activated the mRNA expression of p16^INK4A and concomitant downregulation of two DNA methyltransferases DNMT1 and DNMT3B. The dose-dependent upregulation of endogenous FOXM1 (isoform B) expression during tumour progression across a panel of normal primary NOK strains (n = 8), dysplasias (n = 5) and head and neck squamous cell carcinoma (HNSCC) cell lines (n = 11) correlated positively with endogenous expressions of HELLS, BMI1, DNMT1 and DNMT3B and negatively with p16^INK4A and involucrin. Bisulfite modification and methylation-specific promoter analysis using absolute quantitative PCR (MS-qPCR) showed that upregulation of FOXM1 significantly induced p16^INK4A promoter hypermethylation (10-fold, P<0.05) in primary NOK cells. Using a non-bias genome-wide promoter methylation microarray profiling method, we revealed that aberrant FOXM1 expression in primary NOK induced a global hypomethylation pattern similar to that found in an HNSCC (SCC15) cell line. Following validation experiments using absolute qPCR, we have identified a set of differentially methylated genes, found to be inversely correlated with in vivo mRNA expression levels of clinical HNSCC tumour biopsy samples. This study provided the first evidence, using primary normal human cells and tumour tissues, that aberrant upregulation of FOXM1 orchestrated a DNA methylation signature that mimics the cancer methylome landscape, from which we have identified a unique FOXM1-induced epigenetic signature which may have clinical translational potentials as biomarkers for early cancer screening, diagnostic and/or therapeutic interventions.     

High resolution genetic mapping by genome sequencing reveals genome duplication and tetraploid genetic structure of the diploid Miscanthus sinensis

We have created a high-resolution linkage map of Miscanthus sinensis, using genotyping-by-sequencing (GBS), identifying all 19 linkage groups for the first time. The result is technically significant since Miscanthus has a very large and highly heterozygous genome, but has no or limited genomics information to date. The composite linkage map containing markers from both parental linkage maps is composed of 3,745 SNP markers spanning 2,396 cM on 19 linkage groups with a 0.64 cM average resolution. Comparative genomics analyses of the M. sinensis composite linkage map to the genomes of sorghum, maize, rice, and Brachypodium distachyon indicate that sorghum has the closest syntenic relationship to Miscanthus compared to other species. The comparative results revealed that each pair of the 19 M. sinensis linkages aligned to one sorghum chromosome, except for LG8, which mapped to two sorghum chromosomes (4 and 7), presumably due to a chromosome fusion event after genome duplication. The data also revealed several other chromosome rearrangements relative to sorghum, including two telomere-centromere inversions of the sorghum syntenic chromosome 7 in LG8 of M. sinensis and two paracentric inversions of sorghum syntenic chromosome 4 in LG7 and LG8 of M. sinensis. The results clearly demonstrate, for the first time, that the diploid M. sinensis is tetraploid origin consisting of two sub-genomes. This complete and high resolution composite linkage map will not only serve as a useful resource for novel QTL discoveries, but also enable informed deployment of the wealth of existing genomics resources of other species to the improvement of Miscanthus as a high biomass energy crop. In addition, it has utility as a reference for genome sequence assembly for the forthcoming whole genome sequencing of the Miscanthus genus.     

Response of blanket bog vegetation to drain‐blocking

Question: Does blocking of moorland drains increase bog vegetation on blanket peat? Location: Two sites with blocked drains and two with unblocked drains on Forsinard Flows National Nature Reserve, Sutherland, UK. Methods: Vegetation cover was recorded from 70 locations, with 12 sampling points at different distances (0.5‐14.5 m) from moorland drains in each location. Gradients in the cover of species indicative of wet and dry conditions, as well as bog recovery and degradation in relation to distance from drain, were compared from a sample of drains at two sites with blocked drains and two with unblocked drains. Results: There was evidence for drain‐blocking having a negative effect on vegetation indicative of drier conditions and bog degradation. One of the blocked sites had the lowest values of these indices near to the drain and increasing at greater distances perpendicular from the drain. The two unblocked sites, and the other blocked site, had a contrasting pattern of highest values of these indices close to the drain declining with distance. Cover of species indicative of bog recovery was greater where the drains had been blocked for the longest time. Conclusions: In some cases drain‐blocking can improve the ecological functioning of blanket bogs by increasing cover of healthy bog vegetation. Further studies into the causes of such variability in restoring vegetation through drain‐blocking are needed to aid targeting of peatland restoration projects to areas or methods most likely to be effective.     

Donating Embryos to Stem Cell Research The “Problem” of Gratitude

This paper is based on linked qualitative studies of the donation of human embryos to stem cell research carried out in the United Kingdom, Switzerland, and China. All three studies used semi-structured interview protocols to allow an in-depth examination of donors’ and non-donors’ rationales for their donation decisions, with the aim of gaining information on contextual and other factors that play a role in donor decisions and identifying how these relate to factors that are more usually included in evaluations made by theoretical ethics. Our findings have implications for one factor that has previously been suggested as being of ethical concern: the role of gratitude. Our empirical work shows no evidence that interpersonal gratitude is an important factor, but it does support the existence of a solidarity-based desire to “give something back” to medical research. Thus, we use empirical data to expand and refine the conceptual basis of bioethically theorizing the IVF–stem cell interface.     

Quantifying small‐scale deforestation and forest degradation in African woodlands using radar imagery

Carbon emissions from tropical land‐use change are a major uncertainty in the global carbon cycle. In African woodlands, small‐scale farming and the need for fuel are thought to be reducing vegetation carbon stocks, but quantification of these processes is hindered by the limitations of optical remote sensing and a lack of ground data. Here, we present a method for mapping vegetation carbon stocks and their changes over a 3‐year period in a > 1000 km² region in central Mozambique at 0.06 ha resolution. L‐band synthetic aperture radar imagery and an inventory of 96 plots are combined using regression and bootstrapping to generate biomass maps with known uncertainties. The resultant maps have sufficient accuracy to be capable of detecting changes in forest carbon stocks of as little as 12 MgC ha^?1 over 3 years with 95% confidence. This allows characterization of biomass loss from deforestation and forest degradation at a new level of detail. Total aboveground biomass in the study area was reduced by 6.9 ± 4.6% over 3 years: from 2.13 ± 0.12 TgC in 2007 to 1.98 ± 0.11 TgC in 2010, a loss of 0.15 ± 0.10 TgC. Degradation probably contributed 67% (96.9 ± 91.0 GgC) of the net loss of biomass, but is associated with high uncertainty. The detailed mapping of carbon stock changes quantifies the nature of small‐scale farming. New clearances were on average small (median 0.2 ha) and were often additions to already cleared land. Deforestation events reduced biomass from 33.5 to 11.9 MgC ha^?1 on average_. Contrary to expectations, we did not find evidence that clearances were targeted towards areas of high biomass. Our method is scalable and suitable for monitoring land cover change and vegetation carbon stocks in woodland ecosystems, and can support policy approaches towards reducing emissions from deforestation and degradation (REDD).     

Effects of acclimation and acute temperature change on specific dynamic action and gastric processing in the green shore crab, Carcinus maenas

The effects of temperature acclimation and acute temperature change were investigated in postprandial green shore crabs, Carcinus maenas. Oxygen uptake, gut contractions and transit rates and digestive efficiencies were measured for crabs acclimated to either 10 °C or 20 °C and subsequently exposed to treatment temperatures of 5, 15, or 25 °C. Temperature acclimation resulted in a partial metabolic compensation in unfed crabs, with higher oxygen uptake rates measured for the 10 °C acclimated group exposed to acute test temperatures. The Q₁₀ values were higher than normal, probably because the acute temperature change prevented crabs from fully adjusting to the new temperature. Both the acclimation and treatment temperature altered the characteristics of the specific dynamic action (SDA). The duration of the response was longer for 20 °C acclimated crabs and was inversely related to the treatment temperature. The scope (peak oxygen consumption) was also higher for 20 °C acclimated crabs with a trend towards an inverse relationship with treatment temperature. Since the overall SDA (energy expenditure) is a function of both duration and scope, it was also higher for 20 °C acclimated crabs, with the highest value measured at the treatment temperature of 15 °C. The decline in total SDA after acute exposure to 5 and 25 °C suggests that both cold stress and limitations to oxygen supply at the temperature extremes could be affecting the SDA response. The contractions of the pyloric sac of the foregut region function to propel digesta through the gut, and contraction rates increased with increasing treatment temperature. This translated into faster transit rates with increasing treatment temperatures. Although pyloric sac contractions were higher for 20 °C acclimated crabs, temperature acclimation had no effect on transit rates. This suggests that a threshold level in pyloric sac contraction rates needs to be reached before it manifests itself on transit rates. Although there was a correlation between faster transit times and the shorter duration of the SDA response with increasing treatment temperature, transit rates do not make a good proxy for calculating the SDA characteristics. The digestive efficiency showed a trend towards a decreasing efficiency with increasing treatment temperature; the slower transit rates at the lower treatment temperatures allowing for more efficient nutrient absorption. Even though metabolic rates of 10 °C acclimated crabs were higher, there was no effect of acclimation temperature on digestive efficiency. This probably occurred because intracellular enzymes and digestive enzymes are modulated through different control pathways. These results give an insight into the metabolic and digestive physiology of Carcinus maenas as it makes feeding excursions between the subtidal and intertidal zones.