Phytoglobins: Elucidation of Structural, Functional and Practical Features of Non-Symbiotic Plant Hemoglobins

Phytoglobins (Pgb) (plant hemoglobins) are heme-containing proteins and less well known in comparison to the mammalian counterparts hemoglobin (Hb) andmyoglobin (Mb). They share the same secondary structure as other globin-related proteins, six to eight α-helices comprising the myoglobin-fold (Mb-fold) with one prosthetic heme moiety per subunit. Pgbs are divided into different classes, where the non-symbiotic Pgbs (nsPgb) are found in vast number of plants. Unlike their mammalian counterparts, nsPgbs usually have an additional coordination site interacting with the iron called the distal histidine, in addition to the proximal histidine below the heme plane. Even though they bind oxygen (O2), the proposed functions of these proteins are linked to nitric oxide (NO) metabolism, redox balance and energy maintenance, especially in hypoxic conditions, to a higher extent than oxygen transport.One aim of this thesis was to generate mutant(s) with altered characteristics using site-directed mutagenesis and investigate the role of these residues. One residue in particular was a conserved cysteine residue located at position 86 (C86A) in sugar beet (Beta vulgaris ssp. vulgaris) nsPgb BvPgb1.2. After crystallization and structure determination, this cysteine-to-alanine substitution had no impact on the tertiary and quaternary structure but major implications regarding functionality were observed. The mutant had faster autoxidation rate and increased thermal stability, while the wild-type (WT) protein showed higher peroxidase activity. Both species appeared as homodimers and did not show any heme loss, unlike human hemoglobin.To gain more information regarding the intra- and intermolecular interactions innsPgbs, triple-labeled BvPgb1.2 was expressed, purified and analyzed using 2DNuclear Magnetic Resonance (NMR). 83% of the expected amide cross-peaks were assigned. The majority of the non-assigned residues were located in G and H αhelices, which are proposed to be an important area of dimer interactions. Hydrogen bonding between specific residues (T53 and E123) and a hydrophobic cluster in opposing monomers were suggested to be important in dimer formation. Structure predictions were conducted to gain knowledge regarding the role of the conserved cysteine in dimerization and mapping the lost residues in the crystal structure. These residues were located at highly flexible regions in the N- and C-termini, as well as in the loops for helices CD/DE. Small angle X-ray scattering (SAXS) confirmed maintained a dimeric quaternary structure at low protein concentrations (~0.15 mg/ml) and physiological salt concentrations for WT and C86A. Different proteindependent oligomerization tendencies were observed for the proteins, where the effects for C86A were most prominent. High degree of dimerization was observed for both proteins, not affected by the imposed cysteine-substitution to great extent.To evaluate the biotechnical applicability of these proteins, encapsulation ofBvPgb1.2 and Mb were carried out using a lipid-based sponge phase system. High protein concentrations were correlated with increased aggregation tendencies, especially for BvPgb1.2. This effect seemed to be reversible upon agitation and the internal sponge phase structure was maintained. When analyzed with size exclusion chromatography (SEC), no protein leakage was detected for the nsPgb. To study toxicological effects of BvPgb1.2 WT, C86A and Mb, these proteins were labeled with fluorescent markers and studied in vivo using a zebrafish model. The globins were injected into brain and lateral muscle tissues to study potential accumulation and toxicity. Granules of C86A and Mb were detected in brain tissue, while all proteins were observed in the muscle tissues. In general, either no/low oxidative stress was observed for the penta- or hexacoordinated globins, except for the most concentrated granules of BvPgb1.2 WT, indicating good tolerance in this model system.The results highlighted in this thesis provide valuable insights in order toimprove/strengthen several areas within biotechnology, including potentialgeneration of resilient crops, iron supplements and oxygen therapeutics

Directional supercontinuum generation: the role of the soliton

In this paper we numerically study supercontinuum generation by pumping a silicon nitride waveguide, with two zero-dispersion wavelengths, with femtosecond pulses. The waveguide dispersion is designed so that the pump pulse is in the normal-dispersion regime. We show that because of self-phase modulation, the initial pulse broadens into the anomalous-dispersion regime, which is sandwiched between the two normal-dispersion regimes, and here a soliton is formed. The interaction of the soliton and the broadened pulse in the normal-dispersion regime causes additional spectral broadening through formation of dispersive waves by non-degenerate four-wave mixing and cross-phase modulation. This broadening occurs mainly towards the second normal-dispersion regime. We show that pumping in either normal-dispersion regime allows broadening towards the other normal-dispersion regime. This ability to steer the continuum extension towards the direction of the other normal-dispersion regime beyond the sandwiched anomalous-dispersion regime underlies the directional supercontinuum notation. We numerically confirm the approach in a standard silica microstructured fiber geometry with two zero-dispersion wavelengths

Influence of clamp-widening on the quality factor of nanomechanical silicon nitride resonators

Nanomechanical resonators based on strained silicon nitride (Si$_3$N$_4$) have received a large amount of attention in fields such as sensing and quantum optomechanics due to their exceptionally high quality factors ($Q$s). Room-temperature $Q$s approaching 1 billion are now in reach by means of phononic crystals (soft-clamping) and strain engineering. Despite great progress in enhancing $Q$s, difficulties in fabrication of soft-clamped samples limits their implementation into actual devices. An alternative means of achieving ultra-high $Q$s was shown using trampoline resonators with engineered clamps, which serves to localize the stress to the center of the resonator, while minimizing stress at the clamping. The effectiveness of this approach has since come into question from recent studies employing string resonators with clamp-tapering. Here, we investigate this idea using nanomechanical string resonators with engineered clampings similar to those presented for trampolines. Importantly, the effect of orienting the strings diagonally or perpendicularly with respect to the silicon frame is investigated. It is found that increasing the clamp width for diagonal strings slightly increases the $Q$s of the fundamental out-of-plane mode at small radii, while perpendicular strings only deteriorate with increasing clamp width. Measured $Q$s agree well with finite element method simulations even for higher-order resonances. The small increase cannot account for previously reported $Q$s of trampoline resonators. Instead, we propose the effect to be intrinsic and related to surface and radiation losses.Comment: 7 pages, 4 figure

The treatment of mixing in core helium burning models - I. Implications for asteroseismology

The detection of mixed oscillation modes offers a unique insight into the internal structure of core helium burning (CHeB) stars. The stellar structure during CHeB is very uncertain because the growth of the convective core, and/or the development of a semiconvection zone, is critically dependent on the treatment of convective boundaries. In this study we calculate a suite of stellar structure models and their non-radial pulsations to investigate why the predicted asymptotic g-mode $\ell = 1$ period spacing $\Delta\Pi_1$ is systematically lower than is inferred from Kepler field stars. We find that only models with large convective cores, such as those calculated with our newly proposed "maximal-overshoot" scheme, can match the average $\Delta\Pi_1$ reported. However, we also find another possible solution that is related to the method used to determine $\Delta\Pi_1$: mode trapping can raise the observationally inferred $\Delta\Pi_1$ well above its true value. Even after accounting for these two proposed resolutions to the discrepancy in average $\Delta\Pi_1$, models still predict more CHeB stars with low $\Delta\Pi_1$ ($< 270$ s) than are observed. We establish two possible remedies for this: i) there may be a difficulty in determining $\Delta\Pi_1$ for early CHeB stars (when $\Delta\Pi_1$ is lowest) because of the effect that the sharp composition profile at the hydrogen burning shell has on the pulsations, or ii) the mass of the helium core at the flash is higher than predicted. Our conclusions highlight the need for the reporting of selection effects in asteroseismic population studies in order to safely use this information to constrain stellar evolution theory.Comment: 24 pages. 24 figures. Published in MNRA

Duplication and diversification of the LEAFY HULL STERILE1 and Oryza sativa MADS5 SEPALLATA lineages in graminoid Poales

<p>Abstract</p> <p>Background</p> <p>Gene duplication and the subsequent divergence in function of the resulting paralogs via subfunctionalization and/or neofunctionalization is hypothesized to have played a major role in the evolution of plant form. The <it>LEAFY HULL STERILE1 (LHS1) SEPALLATA </it>(<it>SEP</it>) genes have been linked with the origin and diversification of the grass spikelet, but it is uncertain 1) when the duplication event that produced the <it>LHS1 </it>clade and its paralogous lineage <it>Oryza sativa MADS5 (OSM5) </it>occurred, and 2) how changes in gene structure and/or expression might have contributed to subfunctionalization and/or neofunctionalization in the two lineages.</p> <p>Methods</p> <p>Phylogenetic relationships among 84 <it>SEP </it>genes were estimated using Bayesian methods. RNA expression patterns were inferred using <it>in situ </it>hybridization. The patterns of protein sequence and RNA expression evolution were reconstructed using maximum parsimony (MP) and maximum likelihood (ML) methods, respectively.</p> <p>Results</p> <p>Phylogenetic analyses mapped the <it>LHS1/OSM5 </it>duplication event to the base of the grass family. MP character reconstructions estimated a change from cytosine to thymine in the first codon position of the first amino acid after the <it>Zea mays MADS3 </it>(<it>ZMM3</it>) domain converted a glutamine to a stop codon in the <it>OSM5 </it>ancestor following the <it>LHS1/OSM5 </it>duplication event. RNA expression analyses of <it>OSM5 </it>co-orthologs in <it>Avena sativa, Chasmanthium latifolium, Hordeum vulgare, Pennisetum glaucum</it>, and <it>Sorghum bicolor </it>followed by ML reconstructions of these data and previously published analyses estimated a complex pattern of gain and loss of <it>LHS1 </it>and <it>OSM5 </it>expression in different floral organs and different flowers within the spikelet or inflorescence.</p> <p>Conclusions</p> <p>Previous authors have reported that rice OSM5 and LHS1 proteins have different interaction partners indicating that the truncation of OSM5 following the <it>LHS1/OSM5 </it>duplication event has resulted in both partitioned and potentially novel gene functions. The complex pattern of <it>OSM5 </it>and <it>LHS1 </it>expression evolution is not consistent with a simple subfunctionalization model following the gene duplication event, but there is evidence of recent partitioning of <it>OSM5 </it>and <it>LHS1 </it>expression within different floral organs of <it>A. sativa, C. latifolium, P. glaucum </it>and <it>S. bicolor</it>, and between the upper and lower florets of the two-flowered maize spikelet.</p

Regioswitchable palladium-catalyzed decarboxylative coupling of 1,3-dicarbonyl compounds

A palladium-catalyzed chemo- and regioselective coupling of 1,3-dicarbonyl compounds via an allylic linker has been developed. This reaction, which displays broad substrate scope, forms two C−C bonds and installs two all-carbon quaternary centers. The regioselectivity of the reaction can be predictably controlled by utilizing an enol carbonate of one of the coupling partners