The Chromatin of Active Genes Is Not in a Permanently Open Conformation

Quantitative measurements of local chromatin accessibility to DNase I in 15-day chicken embryo erythrocyte nuclei have been performed using a range of nuclease concentrations and real-time TaqMan PCR to monitor the loss of short (∼ 80 bp) amplicons. At the β-globin locus, well-established DNase I hypersensitive sites stand out against a background in which actively transcribed gene sequences (e.g., β-adult and β-hatching) are no more sensitive than the nearby constitutive heterochromatin that has previously been shown to form the 30-nm fibre structure. Similar observations were made at the lysozyme locus containing the active Gas41 gene and also at the GAPDH locus. We conclude that active genes are not continuously held in an open ‘beads-on-a-string’ configuration, but adopt a 30-nm-type structure most of the time. This implies that the compact nucleosomal supercoil re-forms in the wake of the polymerase complex.     

Sea-trial verification of ultrasonic antifouling control

An ultrasonic antifouling treatment was applied to a 96,000 m³ class drill-ship to verify its feasibility through a sea-trial. Soon after the hull cleaning had been performed, six ultrasonic projectors were evenly deployed around the starboard shell plate. Driven by a 23 kHz sinusoidal ultrasound in an intermittent manner, the projectors emitted a high-intensity sound reaching 214 dB at the source level causing cavitation around the adjacent water and eventually deterring the settlement of marine fouling organisms. Underwater photographs acquired after four months showed fairly clean slabs on the starboard side, but heavy fouling on the port side. This experiment revealed that ultrasound treatment is a promising method for inhibiting fouling accumulation, even for large-scale ship applications.     

Fumarate reductase: structural and mechanistic insights from the catalytic reduction of 2-methylfumarate

The soluble fumarate reductase (FR) from Shewanella frigidimarina can catalyse the reduction of 2-methylfumarate with a k(cat) of 9.0 s(-1) and a K(M) of 32 microM. This produces the chiral molecule 2-methylsuccinate. Here, we present the structure of FR to a resolution of 1.5 A with 2-methylfumarate bound at the active site. The mode of binding of 2-methylfumarate allows us to predict the stereochemistry of the product as (S)-2-methylsuccinate. To test this prediction we have analysed the product stereochemistry by circular dichroism spectroscopy and confirmed the production of (S)-2-methylsuccinate.     

Effects of shade on root characters associated with lodging in wheat (Triticum aestivum)

Previous work has shown that as the density of wheat plants increase, the spread of the root plate, root length and root number per plant decrease, leading to reduced anchorage strength and increased lodging susceptibility. The aim of this study was to determine which aspect of mutual plant shading [reduction of photosynthetically active radiation (PAR) or the ratio of red to far red light (R : FR)] is associated with this reduction in anchorage strength. Field experiments were conducted at Sutton Bonington, Leicestershire, UK, in two seasons using a range of plant densities in conjunction with shading materials to manipulate PAR and R : FR independently. The spread of the root plate, which has been linked most strongly with anchorage strength, was almost exclusively influenced by PAR intercepted per plant at the beginning of stem extension. Root number and root length were influenced by both PAR and R : FR. When structural roots (defined as thicker than 0.5 mm) and nonstructural roots were considered separately, it was discovered that increasing plant density and PAR shading reduced the length of both structural and nonstructural roots. However, reducing R : FR only reduced the length of structural roots without affecting the length of nonstructural roots.     

Direct electron transfer from graphite and functionalized gold electrodes to T1 and T2/T3 copper centers of bilirubin oxidase

Direct electron transfer (DET) from bare spectrographic graphite (SPGE) or 3-mercaptopropionic acid-modified gold (MPA-gold) electrodes to Trachyderma tsunodae bilirubin oxidase (BOD) was studied under anaerobic and aerobic conditions by cyclic voltammetry and chronoamperometry. On cyclic voltammograms nonturnover Faradaic signals with midpoint potentials of about 700 mV and 400 mV were clearly observed corresponding to redox transformations of the T1 site and the T2/T3 cluster of the enzyme, respectively. The immobilized BOD was differently oriented on the two electrodes and its catalysis of O₂-electroreduction was also massively different. On SPGE, where most of the enzyme was oriented with the T1 copper site proximal to the carbon with a quite slow ET process, well-pronounced DET-bioelectroreduction of O₂ was observed, starting already at > 700 mV vs. NHE. In contrast, on MPA-gold most of the enzyme was oriented with its T2/T3 copper cluster proximal to the metal. Indeed, there was little DET-based catalysis of O₂-electroreduction, even though the ET between the MPA-gold and the T2/T3 copper cluster of BOD was similar to that observed for the T1 site at SPGE. When BOD actively catalyzes the O₂-electroreduction, the redox potential of its T1 site is 690 mV vs. NHE and that of one of its T2/T3 copper centers is 390 mV vs. NHE. The redox potential of the T2/T3 copper cluster of a resting form of BOD is suggested to be about 360 mV vs. NHE. These values, combined with the observed biocatalytic behavior, strongly suggest an uphill intra-molecular electron transfer from the T1 site to the T2/T3 cluster during the catalytic turnover of the enzyme.     

Plastocyanin redox kinetics in spinach chloroplasts: evidence for disequilibrium in the high potential chain

Reduction kinetics of cytochrome f, plastocyanin (PC) and P₇₀₀ (‘high-potential chain’) in thylakoids from spinach were followed after pre-oxidation by a saturating light pulse. We describe a novel approach to follow PC redox kinetics from deconvolution of 810-860 nm absorption changes. The equilibration between the redox-components was analyzed by plotting the redox state of cytochrome f and PC against that of P₇₀₀. In thylakoids with (1) diminished electron transport rate (adjusted with a cytochrome bf inhibitor) or (2) de-stacked grana, cytochrome f and PC relaxed close to their thermodynamic equilibriums with P₇₀₀. In stacked thylakoids with non-inhibited electron transport, the equilibration plots were complex and non-hyperbolic, suggesting that during fast electron flux, the ‘high-potential chain’ does not homogeneously equilibrate throughout the membrane. Apparent equilibrium constants <5 were calculated, which are below the thermodynamic equilibrium known for the ‘high potential chain’. The disequilibrium found in stacked thylakoids with high electron fluxes is explained by restricted long-range PC diffusion. We develop a model assuming that about 30% of Photosystem I mainly located in grana end-membranes and margins rapidly equilibrate with cytochrome f via short-distance transluminal PC diffusion, while long-range lateral PC migration between grana cores and distant stroma lamellae is restricted. Implications for the electron flux control are discussed.