Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16(INK4A) promoter in colon carcinoma cell lines

Aberrant DNA methylation at CpG dinucleotides can result in epigenetic silencing of tumour suppressor genes and represents one of the earliest events in tumourigenesis. To date, however, high-throughput tools that are capable of surveying the methylation status of multiple gene promoters have been restricted to a limited number of cytosines. Here, we present an oligonucleotide microarray that permits the parallel analysis of the methylation status of individual cytosines, thus combining high throughput and high resolution. The approach was used to study the CpG island in the promoter region of the tumour suppressor gene p16(INK4A). In total, 876 oligonucleotide probes of 21 nt in length were used to inspect the methylation status of 53 CpG dinucleotides, producing correct signals in colorectal cancer cell lines as well as control samples with a defined methylation status. The information was validated by established alternative methods. The overall methylation pattern was consistent for each cell line, while different between them. At the level of individual cytosines, however, significant variations between individual cells of the same type were found, but also consistencies across the panel of cancer cell lines were observed

Direct photons ~basis for characterizing heavy ion collisions~

After years of experimental and theoretical efforts, direct photons become a strong and reliable tool to establish the basic characteristics of a hot and dense matter produced in heavy ion collisions. The recent direct photon measurements are reviewed and a future prospect is given.Comment: 8 pages, 8 figures, Invited plenary talk at Quark Matter 200

Overview of experimental results in PbPb collisions at sqrt{s_NN} = 2.76 TeV by the CMS Collaboration

The CMS experiment at the LHC is a general-purpose apparatus with a set of large acceptance and high granularity detectors for hadrons, electrons, photons and muons, providing unique capabilities for both proton-proton and ion-ion collisions. The data collected during the November 2010 PbPb run at sqrt{s_NN} = 2.76 TeV was analyzed and multiple measurements of the properties of the hot and dense matter were obtained. Global event properties, detailed study of jet production and jet properties, isolated photons, quarkonia and weak bosons were measured and compared to pp data and Monte Carlo simulations.Comment: 8 pages, 10 figures, proceedings for Quark Matter 2011, Annecy, France, May 23-28, 201

Loss of synchronization in complex neuronal networks with delay

We investigate the stability of synchronization in networks of delay-coupled excitable neural oscillators. On the basis of the master stability function formalism, we demonstrate that synchronization is always stable for excitatory coupling independently of the delay and coupling strength. Superimposing inhibitory links randomly on top of a regular ring of excitatory coupling, which yields a small-world-like network topology, we find a phase transition to desynchronization as the probability of inhibitory links exceeds a critical value. We explore the scaling of the critical value in dependence on network properties. Compared to random networks, we find that small-world topologies are more susceptible to desynchronization via inhibition.Comment: 6 pages, 4 figure

Dynamics of fully coupled rotators with unimodal and bimodal frequency distribution

We analyze the synchronization transition of a globally coupled network of N phase oscillators with inertia (rotators) whose natural frequencies are unimodally or bimodally distributed. In the unimodal case, the system exhibits a discontinuous hysteretic transition from an incoherent to a partially synchronized (PS) state. For sufficiently large inertia, the system reveals the coexistence of a PS state and of a standing wave (SW) solution. In the bimodal case, the hysteretic synchronization transition involves several states. Namely, the system becomes coherent passing through traveling waves (TWs), SWs and finally arriving to a PS regime. The transition to the PS state from the SW occurs always at the same coupling, independently of the system size, while its value increases linearly with the inertia. On the other hand the critical coupling required to observe TWs and SWs increases with N suggesting that in the thermodynamic limit the transition from incoherence to PS will occur without any intermediate states. Finally a linear stability analysis reveals that the system is hysteretic not only at the level of macroscopic indicators, but also microscopically as verified by measuring the maximal Lyapunov exponent.Comment: 22 pages, 11 figures, contribution for the book: Control of Self-Organizing Nonlinear Systems, Springer Series in Energetics, eds E. Schoell, S.H.L. Klapp, P. Hoeve

e+e- Pairs: a clock and a thermometer of heavy ion collisions

Recently, there is growing evidence that a new state of matter is formed in sqrt(s_NN)= 200 GeV Au+Au collisions at RHIC: a strongly coupled Quark Gluon Plasma of partonic degrees of freedom which develops a collective motion. Dilepton spectra are not affected by strong interaction and can therefore probe the whole time evolution of the collision. Thus they may be sensitive to onset of deconfinement, chiral symmetry restoration, as well as the production of thermal photons. The PHENIX experiment measured the production of e+e- pairs in p+p and Au+Au collisions at sqrt(s_NN)= 200 GeV. An enhanced dilepton yield in the mass range 150<m_ee<750 MeV/c^2 is measured. The excess increases faster with centrality than the number of participating nucleons and is concentrated at p_T<1GeV/c. At higher p_T the excess below 300 MeV/c^2 has been related to an enhanced production of direct photons possibly of thermal origin.Comment: Proceedings of Quark Matter 2008, 8 pages, 7 figure

Unraveling biogeochemical phosphorus dynamics in hyperarid Mars‐analogue soils using stable oxygen isotopes in phosphate

With annual precipitation less than 20 mm and extreme UV intensity, the Atacama Desert in northern Chile has long been utilized as an analogue for recent Mars. In these hyperarid environments, water and biomass are extremely limited, and thus, it becomes difficult to generate a full picture of biogeochemical phosphate‐water dynamics. To address this problem, we sampled soils from five Atacama study sites and conducted three main analyses—stable oxygen isotopes in phosphate, enzyme pathway predictions, and cell culture experiments. We found that high sedimentation rates decrease the relative size of the organic phosphorus pool, which appears to hinder extremophiles. Phosphoenzyme and pathway prediction analyses imply that inorganic pyrophosphatase is the most likely catalytic agent to cycle P in these environments, and this process will rapidly overtake other P utilization strategies. In these soils, the biogenic δ18O signatures of the soil phosphate (δ18OPO4) can slowly overprint lithogenic δ18OPO4 values over a timescale of tens to hundreds of millions of years when annual precipitation is more than 10 mm. The δ18OPO4 of calcium‐bound phosphate minerals seems to preserve the δ18O signature of the water used for biogeochemical P cycling, pointing toward sporadic rainfall and gypsum hydration water as key moisture sources. Where precipitation is less than 2 mm, biological cycling is restricted and bedrock δ18OPO4 values are preserved. This study demonstrates the utility of δ18OPO4 values as indicative of biogeochemical cycling and hydrodynamics in an extremely dry Mars‐analogue environment

The emergence of international food safety standards and guidelines: understanding the current landscape through a historical approach

Following the Second World War, the Food and Agriculture Organization (FAO) and the World Health Organization (WHO) teamed up to construct an International Codex Alimentarius (or 'food code') which emerged in 1963. The Codex Committee on Food Hygiene (CCFH) was charged with the task of developing microbial hygiene standards, although it found itself embroiled in debate with the WHO over the nature these standards should take. The WHO was increasingly relying upon the input of biometricians and especially the International Commission on Microbial Specifications for Foods (ICMSF) which had developed statistical sampling plans for determining the microbial counts in the final end products. The CCFH, however, was initially more focused on a qualitative approach which looked at the entire food production system and developed codes of practice as well as more descriptive end-product specifications which the WHO argued were 'not scientifically correct'. Drawing upon historical archival material (correspondence and reports) from the WHO and FAO, this article examines this debate over microbial hygiene standards and suggests that there are many lessons from history which could shed light upon current debates and efforts in international food safety management systems and approaches