Beam Performance and Luminosity Limitations in the High-Energy Storage Ring (HESR)

The High-Energy Storage Ring (HESR) of the future International Facility for Antiproton and Ion Research (FAIR) at GSI in Darmstadt is planned as an antiproton synchrotron and storage ring in the momentum range from 1.5 to 15 GeV/c. An important feature of this new facility is the combination of phase space cooled beams with dense internal targets (e.g. pellet targets), resulting in demanding beam parameter of two operation modes: high luminosity mode with peak luminosities up to 2*10^32 cm-2 s-1, and high resolution mode with a momentum spread down to 10^-5, respectively. To reach these beam parameters very powerful phase space cooling is needed, utilizing high-energy electron cooling and high-bandwidth stochastic cooling. The effect of beam-target scattering and intra-beam interaction is investigated in order to study beam equilibria and beam losses for the two different operation modes.Comment: 8 pages, based on a talk presented at COULOMB'05, Accepted for publication by Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipmen

Analysis of Oct4-dependent transcriptional networks regulating self-renewal and pluripotency in human embryonic stem cells

The POU domain transcription factor OCT4 is a key regulator of pluripotency in the early mammalian embryo and is highly expressed in the inner cell mass of the blastocyst. Consistent with its essential role in maintaining pluripotency, Oct4 expression is rapidly downregulated during formation of the trophoblast lineage. To enhance our understanding of the molecular basis of this differentiation event in humans, we used a functional genomics approach involving RNA interference-mediated suppression of OCT4 function in a human ESC line and analysis of the resulting transcriptional profiles to identify OCT4-dependent genes in human cells. We detected altered expression of >1,000 genes, including targets regulated directly by OCT4 either positively (NANOG, SOX2, REX1, LEFTB, LEFTA/EBAF DPPA4, THY1, and TDGF1) or negatively (CDX2, EOMES, BMP4, TBX18, Brachyury [T], DKK1, HLX1, GATA6, ID2, and DLX5), as well as targets for the OCT4-associated stem cell regulators SOX2 and NANOG. Our data set includes regulators of ACTIVIN, BMP, fibroblast growth factor, and WNT signaling. These pathways are implicated in regulating human ESC differentiation and therefore further validate the results of our analysis. In addition, we identified a number of differentially expressed genes that are involved in epigenetics, chromatin remodeling, apoptosis, and metabolism that may point to underlying molecular mechanisms that regulate pluripotency and trophoblast differentiation in humans. Significant concordance between this data set and previous comparisons between inner cell mass and trophectoderm in human embryos indicates that the study of human ESC differentiation in vitro represents a useful model of early embryonic differentiation in humans

Bioinformatics

The analysis of gene regulatory networks (GRNs) is a central goal of bioinformatics highly accelerated by the advent of new experimental techniques, such as RNA interference. A battery of reverse engineering methods has been developed in recent years to reconstruct the underlying GRNs from these and other experimental data. However, the performance of the individual methods is poorly understood and validation of algorithmic performances is still missing to a large extent. To enable such systematic validation, we have developed the web application GeNGe (GEne Network GEnerator), a controlled framework for the automatic generation of GRNs. The theoretical model for a GRN is a non-linear differential equation system. Networks can be user-defined or constructed in a modular way with the option to introduce global and local network perturbations. Resulting data can be used, e.g. as benchmark data for evaluating GRN reconstruction methods or for predicting effects of perturbations as theoretical counterparts of biological experiment

Genetic variation in hippocampal microRNA expression differences in C57BL/6 J X DBA/2 J (BXD) recombinant inbred mouse strains

BACKGROUND: miRNAs are short single-stranded non-coding RNAs involved in post-transcriptional gene regulation that play a major role in normal biological functions and diseases. Little is currently known about how expression of miRNAs is regulated. We surveyed variation in miRNA abundance in the hippocampus of mouse inbred strains, allowing us to take a genetic approach to the study of miRNA regulation, which is novel for miRNAs. The BXD recombinant inbred panel is a very well characterized genetic reference panel which allows quantitative trait locus (QTL) analysis of miRNA abundance and detection of correlates in a large store of brain and behavioural phenotypes. RESULTS: We found five suggestive trans QTLs for the regulation of miRNAs investigated. Further analysis of these QTLs revealed two genes, Tnik and Phf17, under the miR-212 regulatory QTLs, whose expression levels were significantly correlated with miR-212 expression. We found that miR-212 expression is correlated with cocaine-related behaviour, consistent with a reported role for this miRNA in the control of cocaine consumption. miR-31 is correlated with anxiety and alcohol related behaviours. KEGG pathway analysis of each miRNA's expression correlates revealed enrichment of pathways including MAP kinase, cancer, long-term potentiation, axonal guidance and WNT signalling. CONCLUSIONS: The BXD reference panel allowed us to establish genetic regulation and characterize biological function of specific miRNAs. QTL analysis enabled detection of genetic loci that regulate the expression of these miRNAs. eQTLs that regulate miRNA abundance are a new mechanism by which genetic variation influences brain and behaviour. Analysis of one of these QTLs revealed a gene, Tnik, which may regulate the expression of a miRNA, a molecular pathway and a behavioural phenotype. Evidence of genetic covariation of miR-212 abundance and cocaine related behaviours is strongly supported by previous functional studies, demonstrating the value of this approach for discovery of new functional roles and downstream processes regulated by miRNA

A Method to Polarize Stored Antiprotons to a High Degree

Polarized antiprotons can be produced in a storage ring by spin--dependent interaction in a purely electron--polarized hydrogen gas target. The polarizing process is based on spin transfer from the polarized electrons of the target atoms to the orbiting antiprotons. After spin filtering for about two beam lifetimes at energies $T\approx 40-170$ MeV using a dedicated large acceptance ring, the antiproton beam polarization would reach $P=0.2-0.4$. Polarized antiprotons would open new and unique research opportunities for spin--physics experiments in $\bar{p}p$ interactions

Creation and application of immortalized bait libraries for targeted enrichment and next-generation sequencing

Since the introduction of next-generation sequencing, several techniques have been developed to selectively enrich and sequence specific parts of the genome at high coverage. These techniques include enzymatic methods employing molecular inversion probes, PCR based approaches, hybrid capture, and in-solution capture. In-solution capture employs RNA probes transcribed from a pool of DNA template oligos designed to match regions of interest to specifically bind and enrich genomic DNA fragments. This method is highly efficient, especially if genomic target regions are large in size or quantity. Diverse in-solution capture kits are available, but are costly when large sample numbers need to be analyzed. Here we present a cost-effective strategy for the design of custom DNA libraries, their transcription into RNA libraries, and application for in-solution capture. We show the efficacy by comparing the method to a commercial kit and further demonstrate that emulsion PCR can be used for bias free amplification and virtual immortalization of DNA template libraries

IT Future of Medicine: from molecular analysis to clinical diagnosis and improved treatment

The IT Future of Medicine (ITFoM, http://www.itfom.eu/) initiative will produce computational models of individuals to enable the prediction of their future health risks, progression of diseases and selection and efficacy of treatments while minimising side effects. To be able to move our health care system to treat patients as individuals rather than as members of larger, divergent groups, the ITFoM initiative, proposes to integrate molecular, physiological and anatomical data of every person in 'virtual patient' models. The establishment of such 'virtual patient' models is now possible due to the enormous progress in analytical techniques, particularly in the '-omics' technology areas and in imaging, as well as in sensor technologies, but also due to the immense developments in the ICT field. As one of six Future and Emerging Technologies (FET) Flagship Pilot Projects funded by the European Commission, ITFoM with more than 150 academic and industrial partners from 34 countries, will foster the development in functional genomics and computer technologies to generate 'virtual patient' models to make them available for clinical application. The increase in the capacity of next generation sequencing systems will enable the high-throughput analysis of a large number of individuals generating huge amounts of genome, epigenome and transcriptome data, but making it feasible to apply deep sequencing in the clinic to characterise not only the patient's genome, but also individual samples, for example, from tumours. The genome profile will be integrated with proteome and metabolome information generated via new powerful chromatography, mass spectrometry and nuclear magnetic resonance techniques. The individualised model will not only enable the analysis of the current situation, but will allow the prediction of the response of the patient to different therapy options or intolerance for certain drugs

Electromagnetic Simulation and Design of a Novel Waveguide RF Wien Filter for Electric Dipole Moment Measurements of Protons and Deuterons

The conventional Wien filter is a device with orthogonal static magnetic and electric fields, often used for velocity separation of charged particles. Here we describe the electromagnetic design calculations for a novel waveguide RF Wien filter that will be employed to solely manipulate the spins of protons or deuterons at frequencies of about 0.1 to 2 MHz at the COoler SYnchrotron COSY at J\"ulich. The device will be used in a future experiment that aims at measuring the proton and deuteron electric dipole moments, which are expected to be very small. Their determination, however, would have a huge impact on our understanding of the universe.Comment: 10 pages, 10 figures, 4 table

Polarized Proton Beams from Laser-induced Plasmas

We report on the concept of an innovative source to produce polarized proton/deuteron beams of a kinetic energy up to several GeV from a laser-driven plasma accelerator. Spin effects have been implemented into the PIC simulation code VLPL to make theoretical predictions about the behavior of proton spins in laser-induced plasmas. Simulations of spin-polarized targets show that the polarization is conserved during the acceleration process. For the experimental realization, a polarized HCl gas-jet target is under construction using the fundamental wavelength of a Nd:YAG laser system to align the HCl bonds and simultaneously circular polarized light of the fifth harmonic to photo-dissociate, yielding nuclear polarized H atoms. Subsequently, their degree of polarization is measured with a Lamb-shift polarimeter. The final experiments, aiming at the first observation of a polarized particle beam from laser-generated plasmas, will be carried out at the 10 PW laser system SULF at SIOM/Shanghai.Comment: 7 pages, 7 figure