Energy-dependent quenching adjusts the excitation diffusion length to regulate photosynthetic light harvesting

An important determinant of crop yields is the regulation of photosystem II (PSII) light harvesting by energy-dependent quenching (qE). However, the molecular details of excitation quenching have not been quantitatively connected to the PSII yield, which only emerges on the 100 nm scale of the grana membrane and determines flux to downstream metabolism. Here, we incorporate excitation dissipation by qE into a pigment-scale model of excitation transfer and trapping for a 200 nm x 200 nm patch of the grana membrane. We demonstrate that single molecule measurements of qE are consistent with a weak-quenching regime. Consequently, excitation transport can be rigorously coarse-grained to a 2D random walk with an excitation diffusion length determined by the extent of quenching. A diffusion-corrected lake model substantially improves the PSII yield determined from variable chlorophyll fluorescence measurements and offers an improved model of PSII for photosynthetic metabolism.Comment: 19 pages, 4 figures, 3 supplementary figure

Mechanisms of light harvesting by photosystem II in plants

Light harvesting by photosystem II (PSII) in plants is highly efficient and acclimates to rapid changes in the intensity of sunlight. However, the mechanisms of PSII light harvesting have remained experimentally inaccessible. Using a structure-based model of excitation energy flow in 200 nanometer (nm) x 200 nm patches of the grana membrane, where PSII is located, we accurately simulated chlorophyll fluorescence decay data with no free parameters. Excitation movement through the light harvesting antenna is diffusive, but becomes subdiffusive in the presence of charge separation at reaction centers. The influence of membrane morphology on light harvesting efficiency is determined by the excitation diffusion length of 50 nm in the antenna. Our model provides the basis for understanding how nonphotochemical quenching mechanisms affect PSII light harvesting in grana membranes.Comment: 23 pages, 3 figure

Baryonic Operators for Lattice Simulations

The construction of baryonic operators for determining the N* excitation spectrum is discussed. The operators are designed with one eye towards maximizing overlaps with the low-lying states of interest, and the other eye towards minimizing the number of sources needed in computing the required quark propagators. Issues related to spin identification are outlined. Although we focus on tri-quark baryon operators, the construction method is applicable to both mesons and penta-quark operators.Comment: 3 pages, poster presented at Lattice2003(spectrum), Tsukuba, Japan, July 15-19, 200

A QTL for osteoporosis detected in an F2 population derived from White Leghorn chicken lines divergently selected for bone index

Osteoporosis, resulting from progressive loss of structural bone during the period of egg-laying in hens, is associated with an increased susceptibility to bone breakage. To study the genetic basis of bone strength, an F cross was produced from lines of hens that had been divergently selected for bone index from a commercial pedigreed White Leghorn population. Quantitative trait loci (QTL) affecting the bone index and component traits of the index (tibiotarsal and humeral strength and keel radiographic density) were mapped using phenotypic data from 372 F individuals in 32 F families. Genotypes for 136 microsatellite markers in 27 linkage groups covering ∼80% of the genome were analysed for association with phenotypes using within-family regression analyses. There was one significant QTL on chromosome 1 for bone index and the component traits of tibiotarsal and humeral breaking strength. Additive effects for tibiotarsal breaking strength represented 34% of the trait standard deviation and 7.6% of the phenotypic variance of the trait. These QTL for bone quality in poultry are directly relevant to commercial populations

Group-theoretical construction of extended baryon operators

The design and implementation of large sets of spatially extended baryon operators for use in lattice simulations are described. The operators are constructed to maximize overlaps with the low-lying states of interest, while minimizing the number of sources needed in computing the required quark propagators.Comment: 3 pages, 3 tables, talk presented at Lattice2004(spectrum), Fermilab, June 21-26, 200

Transdifferentiation of blood-derived human adult endothelial progenitor cells into functionally active cardiomyocytes

Background - Further to promoting angiogenesis, cell therapy may be an approach for cardiac regeneration. Recent studies suggest that progenitor cells can transdifferentiate into other lineages. However, the transdifferentiation potential of endothelial progenitor cells (EPCs) is unknown

The [4+2]‐Cycloaddition of α‐Nitrosoalkenes with Thiochalcones as a Prototype of Periselective Hetero‐Diels–Alder Reactions—Experimental and Computational Studies

The [4+2]‐cycloadditions of α‐nitrosoalkenes with thiochalcones occur with high selectivity at the thioketone moiety of the dienophile providing styryl‐substituted 4H‐1,5,2‐oxathiazines in moderate to good yields. Of the eight conceivable hetero‐Diels–Alder adducts only this isomer was observed, thus a prototype of a highly periselective and regioselective cycloaddition has been identified. Analysis of crude product mixtures revealed that the α‐nitrosoalkene also adds competitively to the thioketone moiety of the thiochalcone dimer affording bis‐heterocyclic [4+2]‐cycloadducts. The experiments are supported by high‐level DFT calculations that were also extended to related hetero‐Diels–Alder reactions of other nitroso compounds and thioketones. These calculations reveal that the title cycloadditions are kinetically controlled processes confirming the role of thioketones as superdienophiles. The computational study was also applied to the experimentally studied thiochalcone dimerization, and showed that the 1,2‐dithiin and 2H‐thiopyran isomers are in equilibrium with the monomer. Again, the DFT calculations indicate kinetic control of this process

Baryonic sources using irreducible representations of the double-covered octahedral group

Irreducible representations (IRs) of the double-covered octahedral group are used to construct lattice source and sink operators for three-quark baryons. The goal is to achieve a good coupling to higher spin states as well as ground states. Complete sets of local and nonlocal straight-link operators are explicitly shown for isospin 1/2 and 3/2 baryons. The orthogonality relations of the IR operators are confirmed in a quenched lattice simulation.Comment: Talk presented at Lattice2004(heavy), Fermilab, June 21-26, 2004, 3 page

Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked Files. This article is open access.Reaction directionality is a key constraint in the modeling of genome-scale metabolic networks. We thermodynamically constrained reaction directionality in a multicompartmental genome-scale model of human metabolism, Recon 1, by calculating, in vivo, standard transformed reaction Gibbs energy as a function of compartment-specific pH, electrical potential, and ionic strength. We show that compartmental pH is an important determinant of thermodynamically determined reaction directionality. The effects of pH on transport reaction thermodynamics are only seen to their full extent when metabolites are represented as pseudoisomer groups of multiple protonated species. We accurately predict the irreversibility of 387 reactions, with detailed propagation of uncertainty in input data, and manually curate the literature to resolve conflicting directionality assignments. In at least half of all cases, a prediction of a reversible reaction directionality is due to the paucity of compartment-specific quantitative metabolomic data, with remaining cases due to uncertainty in estimation of standard reaction Gibbs energy. This study points to the pressing need for 1), quantitative metabolomic data, and 2), experimental measurement of thermochemical properties for human metabolites.Icelandic Research Fund/00406022 eu-repo/grantAgreement/EC/FP7/23281