Architecture of succinate dehydrogenase and reactive oxygen species generation

The structure of Escherichia coli succinate dehydrogenase (SQR), analogous to the mitochondrial respiratory complex II, has been determined, revealing the electron transport pathway from the electron donor, succinate, to the terminal electron acceptor, ubiquinone. It was found that the SQR redox centers are arranged in a manner that aids the prevention of reactive oxygen species (ROS) formation at the flavin adenine dinucleotide. This is likely to be the main reason SQR is expressed during aerobic respiration rather than the related enzyme fumarate reductase, which produces high levels of ROS. Furthermore, symptoms of genetic disorders associated with mitochondrial SQR mutations may be a result of ROS formation resulting from impaired electron transport in the enzyme.     

Serine-7 of the RNA polymerase II CTD is specifically required for snRNA gene expression

RNA polymerase II (Pol II) transcribes genes that encode proteins and noncoding small nuclear RNAs (snRNAs). The carboxyl-terminal repeat domain (CTD) of the largest subunit of mammalian RNA Pol II, comprising tandem repeats of the heptapeptide consensus Tyr1-Ser2-Pro3-Thr4-Ser5-Pro6-Ser7, is required for expression of both gene types. We show that mutation of serine-7 to alanine causes a specific defect in snRNA gene expression. We also present evidence that phosphorylation of serine-7 facilitates interaction with the snRNA gene-specific Integrator complex. These findings assign a biological function to this amino acid and highlight a gene type-specific requirement for a residue within the CTD heptapeptide, supporting the existence of a CTD code.     

Over-canopy saline sprinkler irrigation of grapevines during different growth stages

Wetting plant foliage with saline irrigation increases the uptake of toxic ions Na⁺ and Cl⁻. Over three consecutive seasons, Colombard vines grafted on Ramsey rootstock were irrigated with saline water (EC 3.5 dS/m) by over-canopy sprinklers during any one of the first three of the four annual growth stages: bud burst to full bloom (treatment BB-FB), full bloom to veraison (treatment FB-V), and veraison to harvest (treatment V-H). At other times, vines received non-saline water (EC 0.5 dS/m) as did the control. Seasonal average soil salinities remained relatively constant over the trial. In contrast, the concentrations of Na⁺ and Cl⁻ in one-year old wood and grape juice more than doubled. In treatments FB-V and V-H the average yield over the three seasons was reduced by up to 15%. Results were compared with those obtained in an earlier study which was undertaken in the same vineyard with the same treatments applied via dripper. With drippers, the maximum reduction in the average yield over three seasons was 2%. Saline sprinkling caused rises in Na⁺ and Cl⁻ concentrations of fruit, leaf lamina and one-year-old wood that were at least 7-fold, 5-fold and 2-fold greater, respectively, than the rises caused by application of the same treatments with drip. Progressive seasonal rises in the concentrations of Na⁺ and Cl⁻ in these tissues were due in part to carryover of salt added in previous seasons; with saline sprinkling the magnitude of these carryovers was 4-fold greater than those with saline drip irrigation. With saline water, vignerons can reduce losses by using irrigation systems which do not wet the foliage.     

The effect of increased atmospheric carbon dioxide concentration on emissions of nitrous oxide, carbon dioxide and methane from a wheat field in a semi-arid environment in northern China

There are no reports on the effects of elevated carbon dioxide [CO₂] on the fluxes of N₂O, CO₂ and CH₄ from semi-arid wheat cropping systems. These three soil gas fluxes were measured using closed chambers under ambient (420 ± 18 μmol mol⁻¹) and elevated (565 ± 37 μmol mol⁻¹) at the Free-Air Carbon dioxide Enrichment experimental facility in northern China. Measurements were made over five weeks on a wheat crop (Triticum aestivum L. cv. Zhongmai 175). Elevated [CO₂] increased N₂O and CO₂ emission from soil by 60% and 15%, respectively, but had no significant effect on CH₄ flux. There was no significant interaction between [CO₂] and N application rate on these gas fluxes, probably because soil N was not limiting. At least 22% increase in C storage is required to offset the observed increase in greenhouse gas emissions under elevated [CO₂].     

Regional Sediment Deficits in the Dutch Lowlands: Implications for Long-Term Land-Use Options (8 pp)

Background, Aim and Scope   Coastal and river plains are the surfaces of depositional systems, to which sediment input is a parameter of key-importance. Their habitation and economic development usually requires protection with dikes, quays, etc., which are effective in retaining floods but have the side effect of retarding sedimentation in their hinterlands. The flood-protected Dutch lowlands (so-called dike-ring areas) have been sediment-starved for up to about a millennium. In addition to this, peat decomposition and soil compaction, brought about by land drainage, have caused significant land subsidence. Sediment deficiency, defined as the combined effect of sediment-starvation and drainage-induced volume losses, has already been substantial in this area, and it is expected to become urgent in view of the forecasted effects of climate change (sea-level rise, intensified precipitation and run-off). We therefore explore this deficiency, compare it with natural (Holocene) and current human sediment inputs, and discuss it in terms of long-term land-use options. Materials and Methods: We use available 3D geological models to define natural sediment inputs to our study area. Recent progress in large-scale modelling of peat oxidation and compaction enables us to address volume loss associated with these processes. Human sediment inputs are based on published minerals statistics. All results are given as first-order approximations. Results: The current sediment deficit in the diked lowlands of the Netherlands is estimated at 136 ± 67 million m3/a. About 85% of this volume is the hypothetical amount of sediment required to keep up with sea-level rise, and 15% is the effect of land drainage (peat decomposition and compaction). The average Holocene sediment input to our study area (based on a total of 145 km3) is ~14 million m3/a, and the maximum (millennium-averaged) input ~26 million m3/a. Historical sediment deficiency has resulted in an unused sediment accommodation space of about 13.3 km3. Net human input of sediment material currently amounts to ~23 million m3/a. Discussion: As sedimentary processes in the Dutch lowlands have been retarded, the depositional system's natural resilience to sea-level rise is low, and all that is left to cope is human countermeasure. Preserving some sort of status quo with water management solutions may reach its limits in the foreseeable future. The most viable long-term solutions therefore seem a combination of allowing for more water in open country (anything from flood-buffer zones to open water) and raising lands that are to be built up (enabling their lasting protection). As to the latter, doubling or tripling the use of filling sand in a planned and sustained effort may resolve up to one half of the Dutch sediment deficiency problems in about a century. Conclusions: Conclusions, Recommendations and Perspectives. We conclude that sediment deficiency – past, present and future – challenges the sustainable habitation of the Dutch lowlands. In order to explore possible solutions, we recommend the development of long-term scenarios for the changing lowland physiography, that include the effects of Global Change, compensation measures, costs and benefits, and the implications for long-term land-use options. Recommendations and Perspectives: -     

Extracellular prolyl endoprotease from Aspergillus niger and its use in the debittering of protein hydrolysates

The observation that the bitterest peptides from casein hydrolysates contain several proline residues led us to hypothesize that a proline-specific protease would be instrumental in debittering such peptides. To identify the desired proline-specific activity, a microbiological screening was carried out in which the chromogenic peptide benzyloxycarbonyl-glycine-proline-p-nitroanilide (Z-Gly-Pro-pNA) was used as the substrate. An Aspergillus niger (A. niger) strain was identified that produces an extracellular proline-specific protease with an acidic pH optimum. On the basis of sequence similarities, we conclude that the A. niger-derived enzyme probably belongs to the S28 family of clan SC of serine proteases rather than the S9 family to which prolyl oligopeptidases belong. Incubating the overexpressed and purified enzyme with bitter casein hydrolysates showed a major debittering effect. Reversed phase HPLC analysis revealed that this debittering effect is accompanied by a significant reduction of the number of hydrophobic peptides present.     

Identification of intra-accession genetic diversity in selfing crops using AFLP markers: implications for collection management

Germplasm conserved as seeds in genebanks requires regular regeneration. In this process, selection and genetic drift may cause loss of genetic diversity from accessions. In the case of selfing crops, separation of distinct lines into different accessions may be an efficient strategy to avoid these negative effects. In order to evaluate the applicability of this method for collection management, knowledge about the level of intra-accession genetic diversity is required. By means of AFLP analysis intra-accession variation was investigated in two cultivars, two landraces and two wild populations of ex situ conserved barley germplasm. In the total sample of 216 individuals analysed (36 per accession), 22 genotypes were observed based on 104 polymorphic loci. The number of genotypes detected ranged from 1 to 3 per accession, except for a Nepalese landrace that revealed 12 genotypes. An UPGMA cluster analysis grouped the genotypes unambiguously into the accession they belonged to and genotypes within accessions were generally found to be closely related. In order to determine the repeatability of the results obtained, 11 individuals belonging to 4 genotypes from the Nepalese landrace were scored for a second set of AFLP markers. Matrices of genetic distances calculated for the two AFLP datasets were found to be highly correlated (r = 0.9346, P < 0.001). Separation of genotypes into different accessions was considered a relevant option only for the Nepalese landrace. Analysis of molecular variance indicated that this accession could be well divided into 8 distinct lines. Further implications of the results for genebank practices are discussed.