Barfly: sculpting membranes at the Drosophila neuromuscular junction

The ability of a cell to change the shape of its membranes is intrinsic to many cellular functions. Proteins that can alter or recognize curved membrane structures and those that can act to recruit other proteins which stabilize the membrane curvature are likely to be essential in cell functions. The BAR (Bin, amphiphysin, RVS167 homology) domain is a protein domain that can either induce lipidic membranes to curve or can sense curved membranes. BAR domains are found in several proteins at neuronal synapses. We will review BAR domain structure and the role that BAR domain containing proteins play in regulating the morphology and function of the Drosophila neuromuscular junction. In flies the BAR domain containing proteins, endophilin and syndapin affect synaptic vesicle endocytosis, whereas CIP4, dRich, nervous wreck and syndapin affect synaptic morphology. We will review the growing evidence implicating mutations in BAR domain containing proteins being the cause of human pathologies.     

Phenotypic Variation in Senescence in Miscanthus: Towards Optimising Biomass Quality and Quantity

Senescence impacts the harvestable biomass yield and quality in Miscanthus. Very early autumn senescence shortens the canopy duration reducing yield potential. When senescence is too late or slow, the crop does not ripen sufficiently before harvest, resulting in high moisture and nutrient offtakes that reduce biomass quality. In this study, variation in senescence was monitored over 3?years in a trial of 244 Miscanthus genotypes planted in four replicate blocks. The experiment comprised 199 genotypes of Miscanthus sinensis, 36 genotypes of Miscanthus sacchariflorus, and 9 genotypes of Miscanthus?×?giganteus. On average, M. sinensis genotypes remained greener for longer than M. sacchariflorus genotypes. There was a strong correlation between senescence and moisture content at harvest in 2007 and 2008 (R ²?=?0.59, R ²?=?0.57, respectively; n?=?244). The senescence rate of M.?×?giganteus, an interspecific hybrid between M. sinensis and M. sacchariflorus, was found to lie between the two parental species groups. Environmental signals likely to be involved in the timing and rate of senescence, such as variation in photoperiod and thermal time that occurred through the growing season were investigated. Interactions between individual environmental signals and senescence were difficult to separate. The majority of plants senesced consistently between replicate blocks, and rank order was mostly consistent across all years suggesting strong genotypic control of senescence. This study provides valuable information for the future optimisation of Miscanthus, and potentially other energy grasses, where new varieties are needed to maximise net energy yields and crop quality for different end uses in different global regions.     

Breeding for Bio-ethanol Production in Lolium perenne L.: Association of Allelic Variation with High Water-Soluble Carbohydrate Content

Increasing the extractable sugar yield from perennial crops is one strategy to generate renewable fuels such as bio-ethanol. Lolium perenne L. (perennial ryegrass) can contain significant (>30% dry matter) water-soluble sugars in the form of polymeric fructan which is readily extracted, broken down and fermented to bio-ethanol. A population of L. perenne generated from four parents which differed in water-soluble carbohydrate (WSC) content was subjected to multiple rounds of selection and recombination on the basis of early spring WSC content to produce a high WSC, and a low WSC population. A control population was generated by selecting the same number of plants at random. The alleles present at six candidate gene loci were analysed before and after selection and correlated to WSC content. Significant differences in the allele frequency of L. perenne soluble-acid invertase1:4 were observed between the three populations with one haplotype significantly associated with the high WSC C2^S+ population (after three rounds of selection and two rounds of recombination). Moreover, WSC content was also associated with biomass accumulation. Thus, in addition to a 2.84-fold increase in WSC yield, the C2^S+ population also had 1.48-fold more biomass per plant, resulting in 3.9-fold higher WSC yield per plant than the control population.     

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.     

Iceberg Scour and Shell Damage in the Antarctic Bivalve Laternula elliptica

We document differences in shell damage and shell thickness in a bivalve mollusc (Laternula elliptica) from seven sites around Antarctica with differing exposures to ice movement. These range from 60% of the sea bed impacted by ice per year (Hangar Cove, Antarctic Peninsula) to those protected by virtually permanent sea ice cover (McMurdo Sound). Patterns of shell damage consistent with blunt force trauma were observed in populations where ice scour frequently occurs; damage repair frequencies and the thickness of shells correlated positively with the frequency of iceberg scour at the different sites with the highest repair rates and thicker shells at Hangar Cove (74.2% of animals damaged) compared to the other less impacted sites (less than 10% at McMurdo Sound). Genetic analysis of population structure using Amplified Fragment Length Polymorphisms (AFLPs) revealed no genetic differences between the two sites showing the greatest difference in shell morphology and repair rates. Taken together, our results suggest that L. elliptica exhibits considerable phenotypic plasticity in response to geographic variation in physical disturbance.     

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.