Mass Spectrometry Informatics in Systems Biology

Mass spectrometry (MS) became a standard tool for identifying metabolites in biological tissues, and metabolomics is slowly acknowledged as a legitimate research discipline for characterizing biological conditions. The computational analyses of metabolomics, however, lag behind compared with the rapid advances in analytical aspects for two reasons. First is the lack of standardized data repository for mass spectra: each research institution is flooded with gigabytes of mass-spectral data from its own analytical groups and cannot host a world-class repository for mass spectra. The second reason is the lack of informatics experts that are fully experienced with spectral analyses. The two barriers must be overcome to establish a publicly free data server for MS analysis in metabolomics as does GenBank in genomics and UniProt in proteomics. The workshop brought together bioinformaticians working on mass spectral analyses in Finland and Japan with the goal to establish a consortium to freely exchange and publicize mass spectra of metabolites measured on various platforms computational tools to analyze spectra spectral knowledge that are computationally predicted from standardized data. This book contains the abstracts of the presentations given in the workshop. The programme of the workshop consisted of oral presentations from Japan and Finland, invited lectures from Steffen Neumann (Leibniz Institute of Plant Biochemistry), Matej Oresic (VTT), Merja Penttila (VTT) and Nicola Zamboni (ETH Zurich) as well as free form discussion among the participants. The event was funded by Academy of Finland (grants 139203 and 118653), Japan Society for the Promotion of Science (JSPS Japan-Finland Bilateral Semi- nar Program 2010) and Department of Computer Science University of Helsinki. We would like to thank all the people contributing to the technical pro- gramme and the sponsors for making the workshop possible. Helsinki, October 2010 Masanori Arita, Markus Heinonen and Juho Rousu

Laminar compressible boundary layer flow at a three-dimensional stagnation point with vectored mass transfer

The effect of surface mass transfer velocities having normal, principal and transverse direction components (�vectored� suction and injection) on the steady, laminar, compressible boundary layer at a three-dimensional stagnation point has been investigated both for nodal and saddle points of attachment. The similarity solutions of the boundary layer equations were obtained numerically by the method of parametric differentiation. The principal and transverse direction surface mass transfer velocities significantly affect the skin friction (both in the principal and transverse directions) and the heat transfer. Also the inadequacy of assuming a linear viscosity-temperature relation at low-wall temperatures is shown.

Spin and mass content of linearized Poincaré gauge theories

A unified gauge theory of massless and massive spin-2 fields is of considerable current interest. The Poincaré gauge theories with quadratic Lagrangian are linearized, and the conditions on the parameters are found which will lead to viable linear theories with massive gauge particles. As well as the 2+ massless gravitons coming from the translational gauge potential, the rotational gauge potentials, in the linearized limit, give rise to 2+ and 2− particles of equal mass, as well as a massive pseudoscalar.

Contraceptive vaccines: current status and problems in mass application

Progress in the development of contraceptive vaccines for males and females is reviewed. Based on the criteria which need to be met with, none of the proposed candidate antigens meets the requirements for use as a contraceptive vaccine for human application. One of the major problems is the need for periodic injections to maintain required titre and use of an alternate method until effective titres are obtained. Some of the problems associated with active immunization approach can be overcome by the use of preformed, highly specific, potent antibodies. Some progress has been achieved in this direction by the use of humanized single chain monoclonal antibodies to human chorionic gonadotropin.

Determinations of MC-LR and [Dha(7)] MC-LR Concentrations and Physicochemical Properties by Liquid Chromatography-Tandem Mass Spectrometry

A liquid chromatography electrospray mass spectrometry (LC/ESI/MS) method working in multiple reactions monitoring mode for the determination of trace amounts of microcystin variants (MC-LR and [Dha(7)] MC-LR) in waters was developed. The limit of quantification was 0.05 mu g/L and the limit of detection was 0.015 mu g/L for MC-LR and [Dha(7)] MC-LR, respectively. Recoveries for MCs were in the range of 68%-81%. MC-LR and [Dha(7)] MC-LR were chemically stable with similar physiochemical behavior.

A pilot experiment for mass measurement at CSRe

A pilot experiment of mass measurement was performed at CSRe with the method of isochronous mass spectrometry. The secondary fragments produced via RIBLL2 with the primary beam of 400 MeV/u, Ar-36 delivered by CSRm were injected into CSRe. The revolution periods of the stored ions, which depend on the mass-to-charge ratios of the stored ions, were measured with a time-of-flight detector system. The results show that the mass resolution around 8 x 10(-6) for Delta m/m is achieved.

High precision mass measurement and LPT

A Penning trap, which can measure the atomic masses with the highest precision, is one of the most important facilities in nuclear physics research nowadays. The precision mass data play an important role in the studies of nuclear models, mass formulas, nuclear synthesis processes in the nuclear astrophysics, symmetries of the weak interaction and the conserved vector current (CVC) hypothesis. The status of high precision mass measurement around the world, the basic principle of Penning trap and the basic information about the LPT (Lanzhou Penning Trap) are introduced.

The impact of 21st century Arctic sea ice decline on the climate and mass balance of the Greenland ice sheet and Svalbard’s glaciers and ice caps

The Arctic is a region particularly susceptible to rapid climate change. General circulation models (GCMs) suggest a polar amplification of any global warming signal by a factor of about 1.5 due, in part, to sea ice feedbacks. The dramatic recent decline in multi-year sea ice cover lies outside the standard deviation of the CMIP3 ensemble GCM predictions. Sea ice acts as a barrier between cold air and warmer oceans during winter, as well as inhibiting evaporation from the ocean surface water during the summer. An ice free Arctic would likely have an altered hydrological cycle with more evaporation from the ocean surface leading to changes in precipitation distribution and amount. Using the U.K. Met Office Regional Climate Model (RCM), HadRM3, the atmospheric effects of the observed and projected reduction in Arctic sea ice are investigated. The RCM is driven by the atmospheric GCM HadAM3. Both models are forced with sea surface temperature and sea ice for the period 2061-2090 from the CMIP3 HadGEM1 experiments. Here we use an RCM at 50km resolution over the Arctic and 25km over Svalbard, which captures well the present-day pattern of precipitation and provides a detailed picture of the projected changes in the behaviour of the oceanic-atmosphere moisture fluxes and how they affect precipitation. These experiments show that the projected 21stCentury sea ice decline alone causes large impacts to the surface mass balance (SMB) on Svalbard. However Greenland’s SMB is not significantly affected by sea ice decline alone, but responds with a strongly negative shift in SMB when changes to SST are incorporated into the experiments. This is the first study to characterise the impact of changes in future sea ice to Arctic terrestrial cryosphere mass balance.

Center of mass energy and system-size dependence of photon production at forward rapidity at RHIC

We present the multiplicity and pseudorapidity distributions of photons produced in Au + Au and Cu + Cu collisions at root(s)NN = 62.4 and 200 GeV. The photons are measured in the region -3.7 < eta < -2.3 using the photon Multiplicity detector in the STAR experiment at RHIC. The number of photons produced per average number of participating nucleon pairs increases with the beam energy and is independent of (lie collision centrality. For collisions with similar average numbers of participating nucleons the photon multiplicities are observed to be similar for An + Au and Cu + Cu collisions at a given beam energy. The ratios of the number of charged particles to photons in the measured pseudorapidity range are found to be 1.4 +/- 0.1 and 1.2 +/- 0.1 for root(s)NN = 62.4 and 200 GeV, respectively. The energy dependence of this ratio could reflect varying contributions from baryons to charged particles, while mesons are the dominant contributors to photon production in the given kinematic region. The photon pseudorapidity distributions normalized by average number of participating nucleon pairs, when plotted as a function of eta-Y(beam), are found to follow a longitudinal scaling independent of centrality and colliding ion species at both beam energies. (C) 2009 Elsevier B.V. All rights reserved.

Position-dependent effective mass Dirac equations with PT-symmetric and non-PT-symmetric potentials

We present a new procedure to construct the one-dimensional non-Hermitian imaginary potential with a real energy spectrum in the context of the position-dependent effective mass Dirac equation with the vector-coupling scheme in 1 + 1 dimensions. In the first example, we consider a case for which the mass distribution combines linear and inversely linear forms, the Dirac problem with a PT-symmetric potential is mapped into the exactly solvable Schrodinger-like equation problem with the isotonic oscillator by using the local scaling of the wavefunction. In the second example, we take a mass distribution with smooth step shape, the Dirac problem with a non-PT-symmetric imaginary potential is mapped into the exactly solvable Schrodinger-like equation problem with the Rosen-Morse potential. The real relativistic energy levels and corresponding wavefunctions for the bound states are obtained in terms of the supersymmetric quantum mechanics approach and the function analysis method.