Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression

Additional file 3: Figure S2. Changes in methylation levels by genomic element. (A) Protein levels in knockdown lines by western blotting. As a control HCT116 colon cancer cells which are WT or have a homozygous mutation in DNMT1 (KO) are shown: the DNMT1-specific top band is indicated by the arrowhead at right. (B) Median levels of methylation are shown for each genomic element (listed at top). The positions of medians are also indicated at right (arrowheads). The differences between WT and KD medians were used to plot Fig. 1d. (C) Density distribution of methylation at the three main elements involved in gene regulation, shown by cell line. Demethylation seems most marked at gene bodies (Genes), indicated by increased density of probes at low methylation (β) values

High-level inhibition of mitochondrial complexes III and IV is required to increase glutamate release from the nerve terminal

<p>Abstract</p> <p>Background</p> <p>The activities of mitochondrial complex III (ubiquinol-cytochrome <it>c </it>reductase, EC 1.10.2.2) and complex IV (cytochrome <it>c </it>oxidase EC 1.9.3.1) are reduced by 30-70% in Huntington's disease and Alzheimer's disease, respectively, and are associated with excitotoxic cell death in these disorders. In this study, we investigated the control that complexes III and complex IV exert on glutamate release from the isolated nerve terminal.</p> <p>Results</p> <p>Inhibition of complex III activity by 60-90% was necessary for a major increase in the rate of Ca²⁺-independent glutamate release to occur from isolated nerve terminals (synaptosomes) depolarized with 4-aminopyridine or KCl. Similarly, an 85-90% inhibition of complex IV activity was required before a major increase in the rate of Ca²⁺-independent glutamate release from depolarized synaptosomes was observed. Inhibition of complex III and IV activities by ~ 60% and above was required before rates of glutamate efflux from polarized synaptosomes were increased.</p> <p>Conclusions</p> <p>These results suggest that nerve terminal mitochondria possess high reserves of complex III and IV activity and that high inhibition thresholds must be reached before excess glutamate is released from the nerve terminal. The implications of the results in the context of the relationship between electron transport chain enzyme deficiencies and excitotoxicity in neurodegenerative disorders are discussed.</p

Activated mesothelial cells produce heparin-binding growth factors: implications for tumour metastases

Curative surgery for gastrointestinal malignancy is commonly thwarted by local tumour recurrence. The heparin-binding growth factors, basic fibroblast growth factor (bFGF), heparin-binding epidermal growth factor-like growth factor (HB-EGF) and vascular epidermal growth factor (VEGF) are all implicated in the metastatic process, but whether or not these essential growth factors are produced by the activated peritoneum is unknown. This study reveals that peritoneal mesothelial cells constitutively express mRNA for bFGF, HB-EGF and two VEGF spliced variants, VEGF121and VEGF165. Mesothelial activation with interleukin (IL)-1b or tumour necrosis factor (TNF)-a produced an up-regulation of mRNA for HB-EGF and VEGF, but not bFGF expression. IL-6 failed to stimulate growth factor expression, whereas IL-2 produced a marked suppression in HB-EGF and bFGF, but not VEGF expression. Mesothelial cells were shown to predominantly express mRNA for the intermediate affinity (bgc) IL-2 receptor. Cytokine-induced growth factor up-regulation was confirmed at the protein level using Western blotting of mesothelial cell lysates for HB-EGF and culture supernatant enzyme-linked immunosorbent assay for VEGF. The production of these growth factors by human mesothelial cells may play a significant role in post-operative peritoneal tumour recurrence. Their common heparin-binding property offers a potential therapeutic target for manipulating the growth factor environment of the human peritoneum. © 2000 Cancer Research Campaig

Stepwise investigation of the influences of steric groups versus counter ions to target Cu/Dy complexes

From an investigation of varying the steric bulk of a flexible ligand, we have produced a family of structures using similar reaction conditions. Even small changes from a hydrogen atom to a methyl to an ethyl group on the ligand influences the structural outcome, which can also be steered by the nature of the metal source. We employed Schiff base ligands by combining o-vanillin and three different 2-amino-1,3-propandiol units, leading to H3L1 (R=hydrogen), H3L2 (R=methyl) and H3L3 (R=ethyl). The differing nuclearities of the three clusters, 1 to 3, originate mainly from the steric influence, while this effect is not seen in complex 4 to 6, where the general butterfly motif is maintained. We present here the synthesis, crystal structures and magnetic properties of six new CuII-LnIII complexes, providing valuable insight into future synthetic directions. The topological part includes a table of all CuII-DyIII complexes with nuclearities higher than four and their topological motif. The investigation of the magnetic behaviors reveal that all six complexes show frequency dependent signals in the out-of phase ac susceptibility, which is indicative for SMM behavior

'Mine's a Pint of Bitter': Performativity, gender, class and representations of authenticity in real-ale tourism

Leisure choices are expressive of individual agency around the maintenance of taste, boundaries, identity and community. This research paper is part of a wider project designed to assess the social and cultural value of real ale to tourism in the north of England. This paper explores the performativity of real-ale tourism and debates about belonging in northern English real-ale communities. The research combines an ethnographic case study of a real-ale festival with semi-structured interviews with organisers and volunteers, northern English real-ale brewers and real-ale tourists visiting the festival. It is argued that real-ale tourism, despite its origins in the logic of capitalism, becomes a space where people can perform Habermasian, communicative leisure, and despite the contradictions of preferring some capitalist industries over others on the basis of their perceived smaller size and older age, real-ale fans demonstrate agency in their performativity

Precipitation of Mn Oxides in Quaternary microbially induced sedimentary structures (MISS), Cape Vani Paleo-Hydrothermal Vent Field, Milos, Greece

Understanding microbial mediation in sediment-hosted Mn deposition has gained importance in low-temperature ore genesis research. Here we report Mn oxide ores dominated by todorokite, vernadite, hollandite, and manjiroite, which cement Quaternary microbially induced sedimentary structures (MISS) developed along bedding planes of shallow-marine to tidal-flat volcaniclastic sandstones/sandy tuffs, Cape Vani paleo-hydrothermal vent field, Milos, Greece. This work aims to decipher the link between biological Mn oxide formation, low-T hydrothermalism, and, growth and preservation of Mn-bearing MISS (MnMISS). Geobiological processes, identified by microtexture petrography, scanning and transmission electron microscopy, lipid biomarkers, bulk- and lipid-specific δ13Corganic composition, and field data, and, low-temperature hydrothermal venting of aqueous Mn2+ in sunlit shallow waters, cooperatively enabled microbially-mediated Mn (II) oxidation and biomineralization. The MnMISS biomarker content and δ13Corg signatures strongly resemble those of modern Mn-rich hydrothermal sediments, Milos coast. Biogenic and syngenetic Mn oxide precipitation established by electron paramagnetic resonance (EPR) spectroscopy and petrography, combined with hydrothermal fluid flow-induced pre-burial curing/diagenesis, may account for today’s crystalline Mn oxide resource. Our data suggests that MISS are not unique to cyanobacteria mats. Furthermore, microbial mats inhabited by aerobic methanotrophs may have contributed significantly to the formation of the MnMISS, thus widening the spectrum of environments responsible for marine Mn biometallogenesi

The experience of enchantment in human-computer interaction

Improving user experience is becoming something of a rallying call in human–computer interaction but experience is not a unitary thing. There are varieties of experiences, good and bad, and we need to characterise these varieties if we are to improve user experience. In this paper we argue that enchantment is a useful concept to facilitate closer relationships between people and technology. But enchantment is a complex concept in need of some clarification. So we explore how enchantment has been used in the discussions of technology and examine experiences of film and cell phones to see how enchantment with technology is possible. Based on these cases, we identify the sensibilities that help designers design for enchantment, including the specific sensuousness of a thing, senses of play, paradox and openness, and the potential for transformation. We use these to analyse digital jewellery in order to suggest how it can be made more enchanting. We conclude by relating enchantment to varieties of experience.</p

Evaluation of the diagnostic accuracy of prototype rapid tests for human African trypanosomiasis

Peer reviewedPublisher PD

Comprehensive Investigation of the Caveolin 2 Gene: Resequencing and Association for Kidney Transplant Outcomes

Caveolae are plasma membrane structures formed from a complex of the proteins caveolin-1 and caveolin-2. Caveolae interact with pro-inflammatory cytokines and are dysregulated in fibrotic disease. Although caveolae are present infrequently in healthy kidneys, they are abundant during kidney injury. An association has been identified between a CAV1 gene variant and long term kidney transplant survival. Chronic, gradual decline in transplant function is a persistent problem in kidney transplantation. The aetiology of this is diverse but fibrosis within the transplanted organ is the common end point. This study is the first to investigate the association of CAV2 gene variants with kidney transplant outcomes. Genomic DNA from donors and recipients of 575 kidney transplants performed in Belfast was investigated for common variation in CAV2 using a tag SNP approach. The CAV2 SNP rs13221869 was nominally significant for kidney transplant failure. Validation was sought in an independent group of kidney transplant donors and recipients from Dublin, Ireland using a second genotyping technology. Due to the unexpected absence of rs13221869 from this cohort, the CAV2 gene was resequenced. One novel SNP and a novel insertion/deletion in CAV2 were identified; rs13221869 is located in a repetitive region and was not a true variant in resequenced populations. CAV2 is a plausible candidate gene for association with kidney transplant outcomes given its proximity to CAV1 and its role in attenuating fibrosis. This study does not support an association between CAV2 variation and kidney transplant survival. Further analysis of CAV2 should be undertaken with an awareness of the sequence complexities and genetic variants highlighted by this study