Two-fluid and magnetohydrodynamic modelling of magnetic reconnection in the MAST spherical tokamak and the solar corona

Twisted magnetic flux ropes are ubiquitous in space and laboratory plasmas, and the merging of such flux ropes through magnetic reconnection is an important mechanism for restructuring magnetic fields and releasing free magnetic energy. The merging-compression scenario is one possible start up scheme for spherical tokamaks, which has been used on the Mega Amp Spherical Tokamak MAST. Two current-carrying plasma rings, or flux ropes, approach each other through the mutual attraction of their like currents, and merge, through magnetic reconnection, into a single plasma torus, with substantial plasma heating. 2D resistive MHD and Hall MHD simulations of this process are reported, and new results for the temperature distribution of ions and electrons are presented. A model of the based on relaxation theory is also described, which is now extended to tight aspect ratio geometry. This model allows prediction of the final merged state and the heating. The implications of the relaxation model for heating of the solar corona are also discussed, and a model of the merger of two or more twisted coronal flux ropes is presented, allowing for different senses of twist

Rheology of Active-Particle Suspensions

We study the interplay of activity, order and flow through a set of coarse-grained equations governing the hydrodynamic velocity, concentration and stress fields in a suspension of active, energy-dissipating particles. We make several predictions for the rheology of such systems, which can be tested on bacterial suspensions, cell extracts with motors and filaments, or artificial machines in a fluid. The phenomena of cytoplasmic streaming, elastotaxis and active mechanosensing find natural explanations within our model.Comment: 3 eps figures, submitted to Phys Rev Let

Enrichment of Clinically Relevant Organisms in Spontaneous Preterm-Delivered Placentas and Reagent Contamination across All Clinical Groups in a Large Pregnancy Cohort in the United Kingdom.

In this study, differences in the placental microbiota from term and preterm deliveries in a large pregnancy cohort in the United Kingdom were studied by using 16S-targeted amplicon sequencing. The impacts of contamination from DNA extraction, PCR reagents, and the delivery itself were also examined. A total of 400 placental samples from 256 singleton pregnancies were analyzed, and differences between spontaneous preterm-, nonspontaneous preterm-, and term-delivered placentas were investigated. DNA from recently delivered placentas was extracted, and screening for bacterial DNA was carried out by using targeted sequencing of the 16S rRNA gene on the Illumina MiSeq platform. Sequenced reads were analyzed for the presence of contaminating operational taxonomic units (OTUs) identified via sequencing of negative extraction and PCR-blank samples. Differential abundances and between-sample (beta) diversity metrics were then compared. A large proportion of the reads sequenced from the extracted placental samples mapped to OTUs that were also found for negative extractions. Striking differences in the compositions of samples were also observed, according to whether the placenta was delivered abdominally or vaginally, providing strong circumstantial evidence for delivery contamination as an important contributor to observed microbial profiles. When OTU- and genus-level abundances were compared between the groups of interest, a number of organisms were enriched in the spontaneous preterm-delivery cohort, including organisms that have been associated previously with adverse pregnancy outcomes, specifically Mycoplasma spp. and Ureaplasma spp. However, analyses of the overall community structure did not reveal convincing evidence for the existence of a reproducible "preterm placental microbiome."IMPORTANCE Preterm birth is associated with both psychological and physical disabilities and is the leading cause of infant morbidity and mortality worldwide. Infection is known to be an important cause of spontaneous preterm birth, and recent research has implicated variation in the "placental microbiome" in the risk of preterm birth. Consistent with data from previous studies, the abundances of certain clinically relevant species differed between spontaneous preterm- and nonspontaneous preterm- or term-delivered placentas. These results support the view that a proportion of spontaneous preterm births have an intrauterine-infection component. However, an additional observation from this study was that a substantial proportion of sequenced reads were contaminating reads rather than DNA from endogenous, clinically relevant species. This observation warrants caution in the interpretation of sequencing outputs from low-biomass samples such as the placenta

FLUORESCENCE AND CIRCULAR DICHROISM STUDIES ON THE PHYCOERYTHROCYANINS FROM THE CYANOBACTERIUM

Two phycoerythrocyanin (PEC) fractions have been obtained from the phycobilisomes of the cyanobac-terium Westiellopsis prolifica ARM 365. They have been characterized by absorption, fluorescence and circular dichroism spectroscopy. One of them is spectroscopically similar to a PEC trimer known from other organisms. Whereas efficient energy transfer from its violin (α-84) to the cyanin (β-84, 155) chromophores is efficient in the trimer (αβ it is impeded after dissociation to the monomer (α,β). A second fraction of PEC which we earlier termed PEC(X) (Maruthi Sai et al., Photochem. Photobiol. 55,119–124, 1992), exhibited the spectral properties similar to that of the α-subunit of PEC from Mastigocladus laminosus. With this highly photoactive fraction, the circular dichroism spectra of the violobilin chromophore in both photoreversible states were obtained

Control of primary productivity and the significance of photosynthetic bacteria in a meromictic kettle lake.

During 1986 planktonic primary production and controlling factors were investigated in a small (A0 = 11.8 · 103 m2, Zmax = 11.5 m) meromictic kettle lake (Mittlerer Buchensee). Annual phytoplankton productivity was estimated to ca 120 gC · m–2 · a–1 (1,42 tC · lake–1 · a–1). The marked thermal stratification of the lake led to irregular vertical distributions of chlorophylla concentrations (Chla) and, to a minor extent, of photosynthesis (Az). Between the depths of 0 to 6 m low Chla concentrations (< 7 mg · m–3) and comparatively high background light attenuation (kw = 0,525 m–1, 77% of total attenuation due to gelbstoff and abioseston) was found. As a consequence, light absorption by algae was low (mean value 17,4%) and self-shading was absent. Because of the small seasonal variation of Chla concentrations, no significant correlation between Chla and areal photosynthesis (A) was observed. Only in early summer (June–July) biomass appears to influence the vertical distribution of photosynthesis on a bigger scale. Around 8 m depth, low-light adapted algae and phototrophic bacteria formed dense layers. Due to low ambient irradiances, the contribution of these organisms to total primary productivity was small. Primary production and incident irradiance were significantly correlated with each other (r2 = 0.68). Although the maximum assimilation number (Popt) showed a clear dependence upon water temperature (Q10 = 2.31), the latter was of minor importance to areal photosynthesis

The state of peer-to-peer network simulators

Networking research often relies on simulation in order to test and evaluate new ideas. An important requirement of this process is that results must be reproducible so that other researchers can replicate, validate and extend existing work. We look at the landscape of simulators for research in peer-to-peer (P2P) networks by conducting a survey of a combined total of over 280 papers from before and after 2007 (the year of the last survey in this area), and comment on the large quantity of research using bespoke, closed-source simulators. We propose a set of criteria that P2P simulators should meet, and poll the P2P research community for their agreement. We aim to drive the community towards performing their experiments on simulators that allow for others to validate their results

High-throughput analysis of candidate imprinted genes and allele-specific gene expression in the human term placenta.

BACKGROUND: Imprinted genes show expression from one parental allele only and are important for development and behaviour. This extreme mode of allelic imbalance has been described for approximately 56 human genes. Imprinting status is often disrupted in cancer and dysmorphic syndromes. More subtle variation of gene expression, that is not parent-of-origin specific, termed 'allele-specific gene expression' (ASE) is more common and may give rise to milder phenotypic differences. Using two allele-specific high-throughput technologies alongside bioinformatics predictions, normal term human placenta was screened to find new imprinted genes and to ascertain the extent of ASE in this tissue. RESULTS: Twenty-three family trios of placental cDNA, placental genomic DNA (gDNA) and gDNA from both parents were tested for 130 candidate genes with the Sequenom MassArray system. Six genes were found differentially expressed but none imprinted. The Illumina ASE BeadArray platform was then used to test 1536 SNPs in 932 genes. The array was enriched for the human orthologues of 124 mouse candidate genes from bioinformatics predictions and 10 human candidate imprinted genes from EST database mining. After quality control pruning, a total of 261 informative SNPs (214 genes) remained for analysis. Imprinting with maternal expression was demonstrated for the lymphocyte imprinted gene ZNF331 in human placenta. Two potential differentially methylated regions (DMRs) were found in the vicinity of ZNF331. None of the bioinformatically predicted candidates tested showed imprinting except for a skewed allelic expression in a parent-specific manner observed for PHACTR2, a neighbour of the imprinted PLAGL1 gene. ASE was detected for two or more individuals in 39 candidate genes (18%). CONCLUSIONS: Both Sequenom and Illumina assays were sensitive enough to study imprinting and strong allelic bias. Previous bioinformatics approaches were not predictive of new imprinted genes in the human term placenta. ZNF331 is imprinted in human term placenta and might be a new ubiquitously imprinted gene, part of a primate-specific locus. Demonstration of partial imprinting of PHACTR2 calls for re-evaluation of the allelic pattern of expression for the PHACTR2-PLAGL1 locus. ASE was common in human term placenta.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Over-expression of Grainyhead-like 3 causes spina bifida and interacts genetically with mutant alleles of Grhl2 and Vangl2 in mice.

The genetic basis of human neural tube defects (NTDs), such as anencephaly and spina bifida, is complex and heterogeneous. Grainyhead-like genes represent candidates for involvement in NTDs based on the presence of spina bifida and exencephaly in mice carrying loss-of-function alleles of Grhl2 or Grhl3. We found that reinstatement of Grhl3 expression, by BAC-mediated transgenesis, prevents spina bifida in Grhl3 null embryos, as in the Grhl3 hypomorphic curly tail strain. Notably however, further increase in expression of Grhl3 causes highly penetrant spina bifida. Grhl3 over-expression recapitulates the spinal NTD phenotype of loss-of-function embryos, although the underlying mechanism differs. However, it does not phenocopy other defects of Grhl3 null embryos such as abnormal axial curvature, cranial NTDs (exencephaly) or skin barrier defects, the latter being rescued by the Grhl3-transgene. Grhl2 and Grhl3 can form homo- and heterodimers, suggesting a possible model in which defects arising from over-expression of Grhl3 result from sequestration of Grhl2 in heterodimers, mimicking Grhl2 loss of function. This hypothesis predicts that increased abundance of Grhl2 would have an ameliorating effect in Grhl3 over-expressing embryo. Instead we observed a striking additive genetic interaction between Grhl2 and Grhl3 gain-of-function alleles. Severe spina bifida arose in embryos in which both genes were expressed at moderately elevated levels that individually do not cause NTDs. Furthermore, moderate Grhl3 over-expression also interacted with the Vangl2Lp allele to cause spina bifida, demonstrating genetic interaction with the planar cell polarity signalling pathway that is implicated in mouse and human NTDs

Diverse species-specific phenotypic consequences of loss of function sorting nexin 14 mutations

Mutations in the SNX14 gene cause spinocerebellar ataxia, autosomal recessive 20 (SCAR20) in both humans and dogs. Studies implicating the phenotypic consequences of SNX14 mutations to be consequences of subcellular disruption to autophagy and lipid metabolism have been limited to in vitro investigation of patient-derived dermal fibroblasts, laboratory engineered cell lines and developmental analysis of zebrafish morphants. SNX14 homologues Snz (Drosophila) and Mdm1 (yeast) have also been conducted, demonstrated an important biochemical role during lipid biogenesis. In this study we report the effect of loss of SNX14 in mice, which resulted in embryonic lethality around mid-gestation due to placental pathology that involves severe disruption to syncytiotrophoblast cell differentiation. In contrast to other vertebrates, zebrafish carrying a homozygous, maternal zygotic snx14 genetic loss-of-function mutation were both viable and anatomically normal. Whilst no obvious behavioural effects were observed, elevated levels of neutral lipids and phospholipids resemble previously reported effects on lipid homeostasis in other species. The biochemical role of SNX14 therefore appears largely conserved through evolution while the consequences of loss of function varies between species. Mouse and zebrafish models therefore provide valuable insights into the functional importance of SNX14 with distinct opportunities for investigating its cellular and metabolic function in vivo