A model of photosynthetic CO2 assimilation in C-3 leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway

circle Recently, we reported estimates of anaplerotic carbon flux through the oxidative pentose phosphate pathway (OPPP) in chloroplasts into the Calvin- Benson cycle. These estimates were based on intramolecular hydrogen isotope analysis of sunflower leaf starch. However, the isotope method is believed to underestimate the actual flux at low atmospheric CO2 concentration (C-a).circle Since the OPPP releases CO2 and reduces NADP(+), it can be expected to affect leaf gas exchange under both rubisco- and RuBP-regeneration-limited conditions. Therefore, we expanded Farquhar-von Caemmerer-Berry models to account for OPPP metabolism. Based on model parameterisation with values from the literature, we estimated OPPP-related effects on leaf carbon and energy metabolism in the sunflowers analysed previously.circle We found that flux through the plastidial OPPP increases both above and below C-a approximate to 450 ppm (the condition the plants were acclimated to). This is qualitatively consistent with our previous isotope-based estimates, yet gas-exchange-based estimates are larger at low Ca.circle We discuss our results in relation to regulatory properties of the plastidial and cytosolic OPPP, the proposed variability of CO2 mesophyll conductance, and the contribution of day respiration to the A/C-i curve drop at high Ca. Furthermore, we critically examine the models and parameterisation and derive recommendations for follow-up studies

Organochemical Characterization of Peat Reveals Decomposition of Specific Hemicellulose Structures as the Main Cause of Organic Matter Loss in the Acrotelm

Peatlands store carbon in the form of dead organic residues. Climate change and human impact impose risks on the sustainability of the peatlands carbon balance due to increased peat decomposition. Here, we investigated molecular changes in the upper peat layers (0-40 cm), inferred from high-resolution vertical depth profiles, from a boreal peatland using two-dimensional H-1-C-13 nuclear magnetic resonance (NMR) spectroscopy, and comparison to delta C-13, delta N-15, and carbon and nitrogen content. Effects of hydrological conditions were investigated at respective sites: natural moist, drainage ditch, and natural dry. The molecular characterization revealed preferential degradation of specific side-chain linkages of xylan-type hemicelluloses within 0-14 cm at all sites, indicating organic matter losses up to 25%. In contrast, the xylan backbone, galactomannan-type hemicelluloses, and cellulose were more resistant to degradation and accumulated at the natural moist and drainage site. delta C-13, delta N-15, and carbon and nitrogen content did not correlate with specific hemicellulose structures but reflected changes in total carbohydrates. Our analysis provides novel insights into peat carbohydrate decomposition and indicates substantial organic matter losses in the acrotelm due to the degradation of specific hemicellulose structures. This suggests that variations in hemicellulose content and structure influence peat stability, which may have important implications with respect to climate change

Conserved nucleotides in an RNA essential for hepatitis B virus replication show distinct mobility patterns

The number of regulatory RNAs with identified non-canonical structures is increasing, and structural transitions often play a role in their biological function. This stimulates interest in internal motions of RNA, which can underlie structural transitions. Heteronuclear NMR relaxation measurements, which are commonly used to study internal motion, only report on local motions of few sites within the molecule. Here we have studied a 27-nt segment of the human hepatitis B virus (HBV) pregenomic RNA, which is essential for viral replication. We combined heteronuclear relaxation with the new off-resonance ROESY technique, which reports on internal motions of H,H contacts. Using off-resonance ROESY, we could for the first time detect motion of through-space H,H contacts, such as in intra-residue base-ribose contacts or inter-nucleotide contacts, both essential for NMR structure determination. Motions in non-canonical structure elements were found primarily on the sub-nanosecond timescale. Different patterns of mobility were observed among several mobile nucleotides. The most mobile nucleotides are highly conserved among different HBV strains, suggesting that their mobility patterns may be necessary for the RNA’s biological function

The Fantastic Four: A plug 'n' play set of optimal control pulses for enhancing nmr spectroscopy

We present highly robust, optimal control-based shaped pulses designed to replace all 90{\deg} and 180{\deg} hard pulses in a given pulse sequence for improved performance. Special attention was devoted to ensuring that the pulses can be simply substituted in a one-to-one fashion for the original hard pulses without any additional modification of the existing sequence. The set of four pulses for each nucleus therefore consists of 90{\deg} and 180{\deg} point-to-point (PP) and universal rotation (UR) pulses of identical duration. These 1 ms pulses provide uniform performance over resonance offsets of 20 kHz (1H) and 35 kHz (13C) and tolerate reasonably large radio frequency (RF) inhomogeneity/miscalibration of (+/-)15% (1H) and (+/-)10% (13C), making them especially suitable for NMR of small-to-medium-sized molecules (for which relaxation effects during the pulse are negligible) at an accessible and widely utilized spectrometer field strength of 600 MHz. The experimental performance of conventional hard-pulse sequences is shown to be greatly improved by incorporating the new pulses, each set referred to as the Fantastic Four (Fanta4).Comment: 28 pages, 19 figure

Time Optimal Control in Spin Systems

In this paper, we study the design of pulse sequences for NMR spectroscopy as a problem of time optimal control of the unitary propagator. Radio frequency pulses are used in coherent spectroscopy to implement a unitary transfer of state. Pulse sequences that accomplish a desired transfer should be as short as possible in order to minimize the effects of relaxation and to optimize the sensitivity of the experiments. Here, we give an analytical characterization of such time optimal pulse sequences applicable to coherence transfer experiments in multiple-spin systems. We have adopted a general mathematical formulation, and present many of our results in this setting, mindful of the fact that new structures in optimal pulse design are constantly arising. Moreover, the general proofs are no more difficult than the specific problems of current interest. From a general control theory perspective, the problems we want to study have the following character. Suppose we are given a controllable right invariant system on a compact Lie group, what is the minimum time required to steer the system from some initial point to a specified final point? In NMR spectroscopy and quantum computing, this translates to, what is the minimum time required to produce a unitary propagator? We also give an analytical characterization of maximum achievable transfer in a given time for the two spin system.Comment: 20 Pages, 3 figure