Engineering N-linked protein glycosylation with diverse O antigen lipopolysaccharide structures in Escherichia coli

Campylobacter jejuni has a general N-linked protein glycosylation system that can be functionally transferred to Escherichia coli. In this study, we engineered E. coli cells in a way that two different pathways, protein N-glycosylation and lipopolysaccharide (LPS) biosynthesis, converge at the step in which PglB, the key enzyme of the C. jejuni N-glycosylation system, transfers O polysaccharide from a lipid carrier (undecaprenyl pyrophosphate) to an acceptor protein. PglB was the only protein of the bacterial N-glycosylation machinery both necessary and sufficient for the transfer. The relaxed specificity of the PglB oligosaccharyltransferase toward the glycan structure was exploited to create novel N-glycan structures containing two distinct E. coli or Pseudomonas aeruginosa O antigens. PglB-mediated transfer of polysaccharides might be valuable for in vivo production of O polysaccharides-protein conjugates for use as antibacterial vaccines.

Understanding the socio-economic distribution of multiple deprivation: An application of self-organising maps

In this paper we seek to contribute to recent efforts to develop and implement multi-dimensional approaches to social exclusion by applying self-organising maps (SOMs) to a set of material deprivation indicators from the Irish component of EU-SILC. The first stage of our analysis involves the identification of sixteen clusters that confirm the multi-dimensional nature of deprivation in contemporary Ireland and the limitations of focusing solely on income. In going beyond this mapping stage, we consider both patterns of socio-economic differentiation in relation to cluster membership and the extent to which such membership contributes to our understanding of economic stress. Our analysis makes clear the continuing importance of traditional forms of stratification relating to factors such as income, social class and housing tenure in accounting for patterns of multiple deprivation. However, it also confirms the role of acute life events and life cycle and location influences. Most importantly, it demonstrates that conclusions relating to the relative impact of different kinds of socio-economic influences are highly dependent on the form of deprivation being considered. Our analysis suggests that debates relating to the extent to which poverty and social exclusion have become individualized should take particular care to distinguish between different kinds of outcomes. Further analysis demonstrates that the SOM approach is considerably more successful than a comparable latent class analysis in identifying those exposed to subjective economic stress. (C) 2010 International Sociological Association Research Committee 28 on Social Stratification and Mobility. Published by Elsevier Ltd. All rights reserved.

Mapping patterns of multiple deprivation using self-organising maps: An application to EU-SILC data for Ireland

The development of conceptual frameworks for the analysis of social exclusion has somewhat out-stripped related methodological developments. This paper seeks to contribute to filling this gap through the application of self-organising maps (SOMs) to the analysis of a detailed set of material deprivation indicators relating to the Irish case. The SOM approach allows us to offer a differentiated and interpretable picture of the structure of multiple deprivation in contemporary Ireland. Employing this approach, we identify 16 clusters characterised by distinct profiles across 42 deprivation indicators. Exploratory analyses demonstrate that, controlling for equivalised household income, SOM cluster membership adds substantially to our ability to predict subjective economic stress. Moreover, in comparison with an analogous latent class approach, the SOM analysis offers considerable additional discriminatory power in relation to individuals' experience of their economic circumstances. The results suggest that the SOM approach could prove a valuable addition to a 'methodological platform' for analysing the shape and form of social exclusion. (c) 2009 Elsevier Inc. All rights reserved.

Altered Long-Range Phase Synchronization and Cortical Activation in Children Born Very Preterm

Children born very preterm, even with broadly normal IQ, commonly show selective difficulties in visuospatial processing and executive functioning. Very little, however, is known what alterations in cortical processing underlie these deficits. We recorded MEG while eight children born very preterm (=32 weeks gestational age) and eight full-term controls performed a visual short-term memory task at mean age 7.5 years (range 6.4 - 8.4). Previously, we demonstrated increased long-range alpha and beta band phase synchronization between MEG sensors during STM retention in a group of 17 full-term children age 6-10 years. Here we present preliminary evidence that long-range phase synchronization in very preterm children, relative to controls, is reduced in the alpha-band but increased in the theta-band. In addition, we investigated cortical activation during STM retention employing synthetic aperture magnetometry (SAM) beamformer to localize changes in gamma-band power. Preliminary results indicate sequential activation of occipital, parietal and frontal cortex in control children, as well as reduced activation in very preterm children relative to controls. These preliminary results suggest that children born very preterm exhibit altered inter-regional functional connectivity and cortical activation during cognitive processing.

Long-range synchronization and local desynchronization of alpha oscillations during visual short-term memory retention in children

Local alpha-band synchronization has been associated with both cortical idling and active inhibition. Recent evidence, however, suggests that long-range alpha synchronization increases functional coupling between cortical regions. We demonstrate increased long-range alpha and beta band phase synchronization during short-term memory retention in children 6-10 years of age. Furthermore, whereas alpha-band synchronization between posterior cortex and other regions is increased during retention, local alpha-band synchronization over posterior cortex is reduced. This constitutes a functional dissociation for alpha synchronization across local and long-range cortical scales. We interpret long-range synchronization as reflecting functional integration within a network of frontal and visual cortical regions. Local desynchronization of alpha rhythms over posterior cortex, conversely, likely arises because of increased engagement of visual cortex during retention.

Human mesenchymal stem cells reduce mortality and bacteremia in gram-negative sepsis in mice in part by enhancing the phagocytic activity of blood monocytes

The potential therapeutic value of cell-based therapy with mesenchymal stem cells (MSC) has been reported in mouse models of polymicrobial peritoneal sepsis. However, the mechanisms responsible for the beneficial effects of MSC have not been well defined. Therefore, we tested the therapeutic effect of intravenous bone marrow-derived human MSC in peritoneal sepsis induced by gram-negative bacteria. At 48 h, survival was significantly increased in mice treated with intravenous MSC compared with control mice treated with intravenous fibroblasts (3T3) or intravenous PBS. There were no significant differences in the levels of TNF-a, macrophage inflammatory protein 2, or IL-10 in the plasma. However, there was a marked reduction in the number of bacterial colony-forming units of Pseudomonas aeruginosa in the blood of MSC-treated mice compared with the 3T3 and PBS control groups. In addition, phagocytic activity was increased in blood monocytes isolated from mice treated with MSC compared with the 3T3 and PBS groups. Furthermore, levels of C5a anaphylotoxin were elevated in the blood of mice treated with MSC, a finding that was associated with upregulation of the phagocytosis receptor CD11b on monocytes. The phagocytic activity of neutrophils was not different among the groups. There was also an increase in alternately activated monocytes/macrophages (CD163- and CD206-positive) in the spleen of the MSC-treated mice compared with the two controls. Thus intravenous MSC increased survival from gram-negative peritoneal sepsis, in part by a monocyte-dependent increase in bacterial phagocytosis.

MicroRNA-34c inversely couples the biological functions of the runt-related transcription factor RUNX2 and the tumor suppressor p53 in osteosarcoma

Osteosarcoma (OS) is a primary bone tumor that is most prevalent during adolescence. RUNX2, which stimulates differentiation and suppresses proliferation of osteoblasts, is deregulated in OS. Here, we define pathological roles of RUNX2 in the etiology of OS and mechanisms by which RUNX2 expression is stimulated. RUNX2 is often highly expressed in human OS biopsies and cell lines. Small interference RNA (siRNA)-mediated depletion of RUNX2 inhibits growth of U2OS OS cells. RUNX2 levels are inversely linked to loss of p53 (which predisposes to OS) in distinct OS cell lines and osteoblasts. RUNX2 protein levels decrease upon stabilization of p53 with the MDM2 inhibitor Nutlin-3. Elevated RUNX2 protein expression is post-transcriptionally regulated and directly linked to diminished expression of several validated RUNX2 targeting microRNAs (miRNAs) in human OS cells compared to mesenchymal progenitor cells. The p53-dependent miR-34c is the most significantly down-regulated RUNX2 targeting miRNA in OS. Exogenous supplementation of miR-34c markedly decreases RUNX2 protein levels, while 3UTR reporter assays establish RUNX2 as a direct target of miR-34c in OS cells. Importantly, Nutlin-3 mediated stabilization of p53 increases expression of miR-34c and decreases RUNX2. Thus, a novel RUNX2-p53-miR34 network controls cell growth of osseous cells and is compromised in OS.

Alkylated organic cages: from porous crystals to neat liquids

Rigid organic iminospherand cages are rendered meltable by multiple alkylation; below their melting points they can take the form of permanently porous crystals, crystals unstable to desolvation or nonporous glassy solids depending on chain length and branching; melting points as low as 50 degrees C are observed and a fully Newtonian liquid phase is obtained above 80 degrees C. Thin glassy fibres can be drawn out from a molten phase.

Strain dependent microstructural modifications of BiCrO3 epitaxial thin films

Strain-dependent microstructural modifications were observed in epitaxial BiCrO3 (BCO) thin films fabricated on single crystalline substrates, utilizing pulsed laser deposition. The following conditions were employed to modify the epitaxial-strain: (i) in-plane tensile strain, BCOSTO [BCO grown on buffered SrTiO3 (001)] and in-plane compressive strain, BCONGO [BCO grown on buffered NdGaO3 (110)] and (ii) varying BCO film thickness. A combination of techniques like X-ray diffraction, X-ray photoelectron spectroscopy (XPS) and high resolution transmission electron microscopy (TEM) was used to analyse the epitaxial growth quality and the microstructure of BCO. Our studies revealed that in the case of BCOSTO, a coherent interface with homogeneous orthorhombic phase is obtained only for BCO film with thicknesses, d < 50 nm. All the BCOSTO films with d = 50 nm were found to be strain-relaxed with an orthorhombic phase showing 1/2 <100> and 1/4 <101> satellite reflections, the latter oriented at 45° from orthorhombic diffraction spots. High angle annular dark field scanning TEM of these films strongly suggested that the satellite reflections, 1/2 <100> and 1/4 <101>, originate from the atomic stacking sequence changes (or “modulated structure”) as reported for polytypes, without altering the chemical composition. The unaltered stoichiometry was confirmed by estimating both valency of Bi and Cr cations by surface and in-depth XPS analysis as well as the stoichiometric ratio (1 Bi:1 Cr) using scanning TEM–energy dispersive X-ray analysis. In contrast, compressively strained BCONGO films exhibited monoclinic symmetry without any structural modulations or interfacial defects, up to d ~ 200 nm. Our results indicate that both the substrate-induced in-plane epitaxial strain and the BCO film thickness are the crucial parameters to stabilise a homogeneous BCO phase in an epitaxially grown film.

Identification of Gene Expression-Based Prognostic Markers in the Hematopoietic Stem Cells of Patients With Myelodysplastic Syndromes

The diagnosis of patients with myelodysplastic syndromes (MDS) is largely dependent on morphologic examination of bone marrow aspirates. Several criteria that form the basis of the classifications and scoring systems most commonly used in clinical practice are affected by operator-dependent variation. To identify standardized molecular markers that would allow prediction of prognosis, we have used gene expression profiling (GEP) data on CD34+ cells from patients with MDS to determine the relationship between gene expression levels and prognosis.

Comment on "On the Uniqueness of Stable Marriage Matchings" [Economic Letters 69(1):1-8, 2000]

We prove with the help of a counterexample that Lemma 6 and Corollary 7 from Eeckhout [1] are incorrect.

Designing and understanding permanent microporosity in liquids

Standard microporous materials are typically crystalline solids that exhibit a regular array of cavities of uniform size and shape. Packing and directional bonding between molecular building blocks give rise to interstitial pores that confer size and shape-specific sorption properties to the material. In the liquid state interstitial cavities are transient. However, permanent and intrinsic "pores'' can potentially be built into the structure of the molecules that constitute the liquid. With the aid of computer simulations we have designed, synthesised and characterised a series of liquids composed of hollow cage-like molecules, which are functionalised with hydrocarbon chains to make them liquid at accessible temperatures. Experiments and simulations demonstrate that chain length and size of terminal chain substituents can be used to tune, within certain margins, the permanence of intramolecular cavities in such neat liquids. Simulations identify a candidate "porous liquid'' in which 30% of the cages remain empty in the liquid state. Absorbed methane molecules selectively occupy these empty cavities.

Defining the role of common variation in the genomic and biological architecture of adult human height

Using genome-wide data from 253,288 individuals, we identified 697 variants at genome-wide significance that together explained one-fifth of the heritability for adult height. By testing different numbers of variants in independent studies, we show that the most strongly associated 1/42,000, 1/43,700 and 1/49,500 SNPs explained 1/421%, 1/424% and 1/429% of phenotypic variance. Furthermore, all common variants together captured 60% of heritability. The 697 variants clustered in 423 loci were enriched for genes, pathways and tissue types known to be involved in growth and together implicated genes and pathways not highlighted in earlier efforts, such as signaling by fibroblast growth factors, WNT/I 2-catenin and chondroitin sulfate-related genes. We identified several genes and pathways not previously connected with human skeletal growth, including mTOR, osteoglycin and binding of hyaluronic acid. Our results indicate a genetic architecture for human height that is characterized by a very large but finite number (thousands) of causal variants.