InCoB2013 introduces Systems Biology as a major conference theme

10.1186/1752-0509-7-S3-S1BMC Systems Biology7SUPPL.3

The infection of primary avian tracheal epithelial cells with infectious bronchitis virus

Here we introduce a culture system for the isolation, passaging and amplification of avian tracheal epithelial (ATE) cells. The ATE medium, which contains chicken embryo extract and fetal bovine serum, supports the growth of ciliated cells, goblet cells and basal cells from chicken tracheas on fibronectin- or matrigel-coated dishes. Non-epithelial cells make up less than 10% of the total population. We further show that ATE cells support the replication and spread of infectious bronchitis virus (IBV). Interestingly, immunocytostaining revealed that basal cells are resistant to IBV infection. We also demonstrate that glycosaminoglycan had no effect on infection of the cells by IBV. Taken together, these findings suggest that primary ATE cells provide a novel cell culture system for the amplification of IBV and the in vitro characterization of viral cytopathogenesis

Genome-wide scan using DArT markers for selection footprints in six-rowed naked barley from the Tibetan Plateau

As one of the world’s earliest domesticated crops, barley is a model species for the study of evolution and domestication. Domestication is an evolutionary process whereby a population adapts, through selection; to new environments created by human cultivation. We describe the genome-scanning of molecular diversity to assess the evolution of barley in the Tibetan Plateau. We used 667 Diversity Arrays Technology (DArT) markers to genotype 185 barley landraces and wild barley accessions from the Tibetan Plateau. Genetic diversity in wild barley was greater than in landraces at both genome and chromosome levels, except for chromosome 3H. Landraces and wild barley accessions were clearly differentiated genetically, but a limited degree of introgression was still evident. Significant differences in diversity between barley subspecies at the chromosome level were observed for genes known to be related to physiological and phenotypical traits, disease resistance, abiotic stress tolerance, malting quality and agronomic traits. Selection on the genome of six-rowed naked barley has shown clear multiple targets related to both its specific end-use and the extreme environment in Tibet. Our data provide a platform to identify the genes and genetic mechanisms that underlie phenotypic changes, and provide lists of candidate domestication genes for modified breeding strategies

Reversible Band Gap Engineering in Carbon Nanotubes by Radial Deformation

We present a systematic analysis of the effect of radial deformation on the atomic and electronic structure of zigzag and armchair single wall carbon nanotubes using the first principle plane wave method. The nanotubes were deformed by applying a radial strain, which distorts the circular cross section to an elliptical one. The atomic structure of the nanotubes under this strain are fully optimized, and the electronic structure is calculated self-consistently to determine the response of individual bands to the radial deformation. The band gap of the insulating tube is closed and eventually an insulator-metal transition sets in by the radial strain which is in the elastic range. Using this property a multiple quantum well structure with tunable and reversible electronic structure is formed on an individual nanotube and its band-lineup is determined from first-principles. The elastic energy due to the radial deformation and elastic constants are calculated and compared with classical theories.Comment: To be appear in Phys. Rev. B, Apr 15, 200

Quantum superchemistry: Role of trapping profile and quantum statistics

The process of Raman photoassociation of a trapped atomic condensate to form condensed molecules has been labeled superchemistry because it can occur at 0 K and experiences coherent bosonic stimulation. We show here that the differences from ordinary chemical processes go even deeper, with the conversion rates depending on the quantum state of the reactants, as expressed by the Wigner function. We consider different initial quantum states of the trapped atomic condensate and different forms of the confining potentials, demonstrating the importance of the quantum statistics and the extra degrees of freedom which massive particles and trapping potentials make available over the analogous optical process of second-harmonic generation. We show that both mean-field analyses and quantum calculations using an inappropriate initial condition can make inaccurate predictions for a given system. This is possible whether using a spatially dependent analysis or a zero-dimensional approach as commonly used in quantum optics

Azimuthal anisotropy and correlations in p+p, d+Au and Au+Au collisions at 200 GeV

We present the first measurement of directed flow ($v_1$) at RHIC. $v_1$ is found to be consistent with zero at pseudorapidities $\eta$ from -1.2 to 1.2, then rises to the level of a couple of percent over the range $2.4 < |\eta| < 4$. The latter observation is similar to data from NA49 if the SPS rapidities are shifted by the difference in beam rapidity between RHIC and SPS. Back-to-back jets emitted out-of-plane are found to be suppressed more if compared to those emitted in-plane, which is consistent with {\it jet quenching}. Using the scalar product method, we systematically compared azimuthal correlations from p+p, d+Au and Au+Au collisions. Flow and non-flow from these three different collision systems are discussed.Comment: Quark Matter 2004 proceeding, 4 pages, 3 figure

Azimuthal anisotropy: the higher harmonics

We report the first observations of the fourth harmonic (v_4) in the azimuthal distribution of particles at RHIC. The measurement was done taking advantage of the large elliptic flow generated at RHIC. The integrated v_4 is about a factor of 10 smaller than v_2. For the sixth (v_6) and eighth (v_8) harmonics upper limits on the magnitudes are reported.Comment: 4 pages, 6 figures, contribution to the Quark Matter 2004 proceeding

Partonic flow and ϕ\phi-meson production in Au+Au collisions at sNN\sqrt{s_{NN}} = 200 GeV

We present first measurements of the $\phi$-meson elliptic flow ($v_{2}(p_{T})$) and high statistics $p_{T}$ distributions for different centralities from $\sqrt{s_{NN}}$ = 200 GeV Au+Au collisions at RHIC. In minimum bias collisions the $v_{2}$ of the $\phi$ meson is consistent with the trend observed for mesons. The ratio of the yields of the $\Omega$ to those of the $\phi$ as a function of transverse momentum is consistent with a model based on the recombination of thermal $s$ quarks up to $p_{T}\sim 4$ GeV/$c$, but disagrees at higher momenta. The nuclear modification factor ($R_{CP}$) of $\phi$ follows the trend observed in the $K^{0}_{S}$ mesons rather than in $\Lambda$ baryons, supporting baryon-meson scaling. Since $\phi$-mesons are made via coalescence of seemingly thermalized $s$ quarks in central Au+Au collisions, the observations imply hot and dense matter with partonic collectivity has been formed at RHIC.Comment: 6 pages, 4 figures, submit to PR

Plasma Wakefield Acceleration with a Modulated Proton Bunch

The plasma wakefield amplitudes which could be achieved via the modulation of a long proton bunch are investigated. We find that in the limit of long bunches compared to the plasma wavelength, the strength of the accelerating fields is directly proportional to the number of particles in the drive bunch and inversely proportional to the square of the transverse bunch size. The scaling laws were tested and verified in detailed simulations using parameters of existing proton accelerators, and large electric fields were achieved, reaching 1 GV/m for LHC bunches. Energy gains for test electrons beyond 6 TeV were found in this case.Comment: 9 pages, 7 figure

The energy dependence of ptp_t angular correlations inferred from mean-ptp_{t} fluctuation scale dependence in heavy ion collisions at the SPS and RHIC

We present the first study of the energy dependence of $p_t$ angular correlations inferred from event-wise mean transverse momentum fluctuations in heavy ion collisions. We compare our large-acceptance measurements at CM energies $\sqrt{s_{NN}} =$ 19.6, 62.4, 130 and 200 GeV to SPS measurements at 12.3 and 17.3 GeV. $p_t$ angular correlation structure suggests that the principal source of $p_t$ correlations and fluctuations is minijets (minimum-bias parton fragments). We observe a dramatic increase in correlations and fluctuations from SPS to RHIC energies, increasing linearly with $\ln \sqrt{s_{NN}}$ from the onset of observable jet-related fluctuations near 10 GeV.Comment: 10 pages, 4 figure