Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila

<p>Abstract</p> <p>Background</p> <p>Speculation regarding the importance of changes in gene regulation in determining major phylogenetic patterns continues to accrue, despite a lack of broad-scale comparative studies examining how patterns of gene expression vary during development. Comparative transcriptional profiling of adult interspecific hybrids and their parental species has uncovered widespread divergence of the mechanisms controlling gene regulation, revealing incompatibilities that are masked in comparisons between the pure species. However, this has prompted the suggestion that misexpression in adult hybrids results from the downstream cascading effects of a subset of genes improperly regulated in early development.</p> <p>Results</p> <p>We sought to determine how gene expression diverges over development, as well as test the cascade hypothesis, by profiling expression in males of <it>Drosophila melanogaster</it>, <it>D. sechellia</it>, and <it>D. simulans</it>, as well as the <it>D. simulans </it>(♀) × <it>D. sechellia </it>(♂) male F1 hybrids, at four different developmental time points (3rd instar larval, early pupal, late pupal, and newly-emerged adult). Contrary to the cascade model of misexpression, we find that there is considerable stage-specific autonomy of regulatory breakdown in hybrids, with the larval and adult stages showing significantly more hybrid misexpression as compared to the pupal stage. However, comparisons between pure species indicate that genes expressed during earlier stages of development tend to be more conserved in terms of their level of expression than those expressed during later stages, suggesting that while Von Baer's famous law applies at both the level of nucleotide sequence and expression, it may not apply necessarily to the underlying overall regulatory network, which appears to diverge over the course of ontogeny and which can only be ascertained by combining divergent genomes in species hybrids.</p> <p>Conclusion</p> <p>Our results suggest that complex integration of regulatory circuits during morphogenesis may lead to it being more refractory to divergence of underlying gene regulatory mechanisms - more than that suggested by the conservation of gene expression levels between species during earlier stages. This provides support for a 'developmental hourglass' model of divergence of gene expression in <it>Drosophila </it>resulting in a highly conserved pupal stage.</p

Spectrum of the Schr\"odinger operator in a perturbed periodically twisted tube

We study Dirichlet Laplacian in a screw-shaped region, i.e. a straight twisted tube of a non-circular cross section. It is shown that a local perturbation which consists of "slowing down" the twisting in the mean gives rise to a non-empty discrete spectrum.Comment: LaTeX2e, 10 page

A Hardy inequality in twisted waveguides

We show that twisting of an infinite straight three-dimensional tube with non-circular cross-section gives rise to a Hardy-type inequality for the associated Dirichlet Laplacian. As an application we prove certain stability of the spectrum of the Dirichlet Laplacian in locally and mildly bent tubes. Namely, it is known that any local bending, no matter how small, generates eigenvalues below the essential spectrum of the Laplacian in the tubes with arbitrary cross-sections rotated along a reference curve in an appropriate way. In the present paper we show that for any other rotation some critical strength of the bending is needed in order to induce a non-empty discrete spectrum.Comment: LaTeX, 20 page

Suppression of quantum oscillations and the dependence on site energies in electronic excitation transfer in the Fenna-Matthews-Olson trimer

Energy transfer in the photosynthetic complex of the Green Sulfur Bacteria known as the Fenna-Matthews-Olson (FMO) complex is studied theoretically taking all three subunits (monomers) of the FMO trimer and the recently found eighth bacteriochlorophyll (BChl) molecule into account. We find that in all considered cases there is very little transfer between the monomers. Since it is believed that the eighth BChl is located near the main light harvesting antenna we look at the differences in transfer between the situation when BChl 8 is initially excited and the usually considered case when BChl 1 or 6 is initially excited. We find strong differences in the transfer dynamics, both qualitatively and quantitatively. When the excited state dynamics is initialized at site eight of the FMO complex, we see a slow exponential-like decay of the excitation. This is in contrast to the oscillations and a relatively fast transfer that occurs when only seven sites or initialization at sites 1 and 6 is considered. Additionally we show that differences in the values of the electronic transition energies found in the literature lead to a large difference in the transfer dynamics

Near-field examination of perovskite-based superlenses and superlens-enhanced probe-object coupling

A planar slab of negative index material works as a superlens with sub-diffraction-limited imaging resolution, since propagating waves are focused and, moreover, evanescent waves are reconstructed in the image plane. Here, we demonstrate a superlens for electric evanescent fields with low losses using perovskites in the mid-infrared regime. The combination of near-field microscopy with a tunable free-electron laser allows us to address precisely the polariton modes, which are critical for super-resolution imaging. We spectrally study the lateral and vertical distributions of evanescent waves around the image plane of such a lens, and achieve imaging resolution of wavelength/14 at the superlensing wavelength. Interestingly, at certain distances between the probe and sample surface, we observe a maximum of these evanescent fields. Comparisons with numerical simulations indicate that this maximum originates from an enhanced coupling between probe and object, which might be applicable for multifunctional circuits, infrared spectroscopy, and thermal sensors.Comment: 20 pages, 6 figures, published as open access article in Nature Communications (see http://www.nature.com/ncomms/

Electronic Coherence Dephasing in Excitonic Molecular Complexes: Role of Markov and Secular Approximations

We compare four different types of equations of motion for reduced density matrix of a system of molecular excitons interacting with thermodynamic bath. All four equations are of second order in the linear system-bath interaction Hamiltonian, with different approximations applied in their derivation. In particular we compare time-nonlocal equations obtained from so-called Nakajima-Zwanzig identity and the time-local equations resulting from the partial ordering prescription of the cummulant expansion. In each of these equations we alternatively apply secular approximation to decouple population and coherence dynamics from each other. We focus on the dynamics of intraband electronic coherences of the excitonic system which can be traced by coherent two-dimensional spectroscopy. We discuss the applicability of the four relaxation theories to simulations of population and coherence dynamics, and identify features of the two-dimensional coherent spectrum that allow us to distinguish time-nonlocal effects.Comment: 14 pages, 8 figure

Electron Transfer from Cyt b559 and Tyrosine-D to the S2 and S3 states of the water oxidizing complex in Photosystem II at Cryogenic Temperatures

The Mn4CaO5 cluster of photosystem II (PSII) catalyzes the oxidation of water to molecular oxygen through the light-driven redox S-cycle. The water oxidizing complex (WOC) forms a triad with Tyrosine(Z) and P-680, which mediates electrons from water towards the acceptor side of PSII. Under certain conditions two other redox-active components, Tyrosine(D) (Y-D) and Cytochrome b (559) (Cyt b (559)) can also interact with the S-states. In the present work we investigate the electron transfer from Cyt b (559) and Y-D to the S-2 and S-3 states at 195 K. First, Y-D (aEuro cent) and Cyt b (559) were chemically reduced. The S-2 and S-3 states were then achieved by application of one or two laser flashes, respectively, on samples stabilized in the S-1 state. EPR signals of the WOC (the S-2-state multiline signal, ML-S-2), Y-D (aEuro cent) and oxidized Cyt b (559) were simultaneously detected during a prolonged dark incubation at 195 K. During 163 days of incubation a large fraction of the S-2 population decayed to S-1 in the S-2 samples by following a single exponential decay. Differently, S-3 samples showed an initial increase in the ML-S-2 intensity (due to S-3 to S-2 conversion) and a subsequent slow decay due to S-2 to S-1 conversion. In both cases, only a minor oxidation of Y-D was observed. In contrast, the signal intensity of the oxidized Cyt b (559) showed a two-fold increase in both the S-2 and S-3 samples. The electron donation from Cyt b (559) was much more efficient to the S-2 state than to the S-3 state

Propagating Quantum Microwaves: Towards Applications in Communication and Sensing

The field of propagating quantum microwaves has started to receive considerable attention in the past few years. Motivated at first by the lack of an efficient microwave-to-optical platform that could solve the issue of secure communication between remote superconducting chips, current efforts are starting to reach other areas, from quantum communications to sensing. Here, we attempt at giving a state-of-the-art view of the two, pointing at some of the technical and theoretical challenges we need to address, and while providing some novel ideas and directions for future research. Hence, the goal of this paper is to provide a bigger picture, and -- we hope -- to inspire new ideas in quantum communications and sensing: from open-air microwave quantum key distribution to direct detection of dark matter, we expect that the recent efforts and results in quantum microwaves will soon attract a wider audience, not only in the academic community, but also in an industrial environment

Is Mn-Bound Substrate Water Protonated in the S2 State of Photosystem II?

In spite of great progress in resolving the geometric structure of the water-splitting Mn4OxCa cluster in photosystem II, the binding sites and modes of the two substrate water molecules are still insufficiently characterized. While time-resolved membrane-inlet mass spectrometry measurements indicate that both substrate water molecules are bound to the oxygen-evolving complex (OEC) in the S2 and S3 states (Hendry and Wydrzynski in Biochemistry 41:13328–13334, 2002), it is not known (1) if they are both Mn-bound, (2) if they are terminal or bridging ligands, and (3) in what protonation state they are bound in the different oxidation states Si (i = 0, 1, 2, 3, 4) of the OEC. By employing 17O hyperfine sublevel correlation (HYSCORE) spectroscopy we recently demonstrated that in the S2 state there is only one (type of) Mn-bound oxygen that is water exchangeable. We therefore tentatively identified this oxygen as one substrate ‘water’ molecule, and on the basis of the finding that it has a hyperfine interaction of about 10 MHz with the electron spin of the Mn4OxCa cluster, we suggest that it is bound as a Mn–O–Mn bridge within a bis-μ2 oxo-bridged unit (Su et al. in J Am Chem Soc 130:786–787, 2008). Employing pulse electron paramagnetic resonance, 1H/2H Mims electron-nuclear double resonance and 2H-HYSCORE spectroscopies together with 1H/2H-exchange here, we test this hypothesis by probing the protonation state of this exchangeable oxygen. We conclude that this oxygen is fully deprotonated. This result is discussed in the light of earlier reports in the literature