Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

<p>Abstract</p> <p>Background</p> <p>Heterosis is the superior performance of F₁hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.</p> <p>Results</p> <p>We observed that the distributions of better parent heterosis among a series of 25 maize hybrids generally do not exhibit significant correlations between different traits. Expression profiling analyses for six of these hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the six different hybrids exhibited additive expression patterns, and ~25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, ~80% exhibited hybrid expression levels between the parental levels, ~20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range.</p> <p>Conclusion</p> <p>We have found that maize inbred genetic diversity is correlated with transcriptional variation. However, sampling of seedling tissues indicated that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents. The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.</p

A non-Markovian quantum trajectory approach to radiation into structured continuum

We present a non-Markovian quantum trajectory method for treating atoms radiating into a reservoir with a non-flat density of states. The results of an example numerical simulation of the case where the free space modes of the reservoir are altered by the presence of a cavity are presented and compared with those of an extended system approach

Non-Markovian quantum trajectories for spectral detection

We present a formulation of non-Markovian quantum trajectories for open systems from a measurement theory perspective. In our treatment there are three distinct ways in which non-Markovian behavior can arise; a mode dependent coupling between bath (reservoir) and system, a dispersive bath, and by spectral detection of the output into the bath. In the first two cases the non-Markovian behavior is intrinsic to the interaction, in the third case the non-Markovian behavior arises from the method of detection. We focus in detail on the trajectories which simulate real-time spectral detection of the light emitted from a localized system. In this case, the non-Markovian behavior arises from the uncertainty in the time of emission of particles that are later detected. The results of computer simulations of the spectral detection of the spontaneous emission from a strongly driven two-level atom are presented

Non-Markovian stochastic Schr\"odinger equations: Generalization to real-valued noise using quantum measurement theory

Do stochastic Schr\"odinger equations, also known as unravelings, have a physical interpretation? In the Markovian limit, where the system {\em on average} obeys a master equation, the answer is yes. Markovian stochastic Schr\"odinger equations generate quantum trajectories for the system state conditioned on continuously monitoring the bath. For a given master equation, there are many different unravelings, corresponding to different sorts of measurement on the bath. In this paper we address the non-Markovian case, and in particular the sort of stochastic \sch equation introduced by Strunz, Di\' osi, and Gisin [Phys. Rev. Lett. 82, 1801 (1999)]. Using a quantum measurement theory approach, we rederive their unraveling which involves complex-valued Gaussian noise. We also derive an unraveling involving real-valued Gaussian noise. We show that in the Markovian limit, these two unravelings correspond to heterodyne and homodyne detection respectively. Although we use quantum measurement theory to define these unravelings, we conclude that the stochastic evolution of the system state is not a true quantum trajectory, as the identity of the state through time is a fiction.Comment: 17 pages, 3 figure

The Josephson plasmon as a Bogoliubov quasiparticle

We study the Josephson effect in alkali atomic gases within the two-mode approximation and show that there is a correspondence between the Bogoliubov description and the harmonic limit of the phase representation. We demonstrate that the quanta of the Josephson plasmon can be identified with the Bogoliubov excitations of the two-site Bose fluid. We thus establish a mapping between the Bogoliubov approximation for the many-body theory and the linearized pendulum Hamiltonian.Comment: 9 pages, LaTeX, submitted to J. Phys.

Resonance fluorescence in a band gap material: Direct numerical simulation of non-Markovian evolution

A numerical method of calculating the non-Markovian evolution of a driven atom radiating into a structured continuum is developed. The formal solution for the atomic reduced density matrix is written as a Markovian algorithm by introducing a set of additional, virtual density matrices which follow, to the level of approximation of the algorithm, all the possible trajectories of the photons in the electromagnetic field. The technique is perturbative in the sense that more virtual density matrices are required as the product of the effective memory time and the effective coupling strength become larger. The number of density matrices required is given by $3^{M}$ where $M$ is the number of timesteps per memory time. The technique is applied to the problem of a driven two-level atom radiating close to a photonic band gap and the steady-state correlation function of the atom is calculated.Comment: 14 pages, 9 figure

A randomised controlled trial comparing graded exercise treatment and usual physiotherapy for patients with non-specific neck pain (the GET UP neck pain trial).

Evidence supports exercise-based interventions for the management of neck pain, however there is little evidence of its superiority over usual physiotherapy. This study investigated the effectiveness of a group neck and upper limb exercise programme (GET) compared with usual physiotherapy (UP) for patients with non-specific neck pain. A total of 151 adult patients were randomised to either GET or UP. The primary measure was the Northwick Park Neck pain Questionnaire (NPQ) score at six weeks, six months and 12 months. Mixed modelling identified no difference in neck pain and function between patients receiving GET and those receiving UP at any follow-up time point. Both interventions resulted in modest significant and clinically important improvements on the NPQ score with a change score of around 9% between baseline and 12 months. Both GET and UP are appropriate clinical interventions for patients with non-specific neck pain, however preferences for treatment and targeted strategies to address barriers to adherence may need to be considered in order to maximise the effectiveness of these approaches

Absorbing state phase transitions with a non-accessible vacuum

We analyze from the renormalization group perspective a universality class of reaction-diffusion systems with absorbing states. It describes models where the vacuum state is not accessible, as the set of reactions $2 A \to A$ together with creation processes of the form $A \to n A$ with $n \geq 2$. This class includes the (exactly solvable in one-dimension) {\it reversible} model $2 A \leftrightarrow A$ as a particular example, as well as many other {\it non-reversible} reactions, proving that reversibility is not the main feature of this class as previously thought. By using field theoretical techniques we show that the critical point appears at zero creation-rate (in accordance with exact results), and it is controlled by the well known pair-coagulation renormalization group fixed point, with non-trivial exactly computable critical exponents in any dimension. Finally, we report on Monte-Carlo simulations, confirming all field theoretical predictions in one and two dimensions for various reversible and non-reversible models.Comment: 6 pages. 3 Figures. Final version as published in J.Stat.Mec