Flooding-induced N₂O emission bursts controlled by pH and nitrate in agricultural soils

Agricultural soils are a major source of the greenhouse gas nitrous oxide (N₂O) to the atmosphere. Increasing frequency and severity of flooding as predicted for large intensively cropped areas may promote temporary denitrification and N₂O production but the effect of flooding events on N₂O emissions is poorly studied for agricultural systems. The overall N₂O dynamics during flooding of an agricultural soil and the effect of pH and NO₃⁻ concentration has been investigated based on a combination of the use of microsensors, stable isotope techniques, KCl extractions and modelling. This study shows that non-steady state peak N₂O emission events during flooding might potentially be at least in the order of reported annual mean N₂O emissions, which typically do not include flood induced N₂O emissions, and that more than one-third of the produced N₂O in the soil is not emitted but consumed within the soil. The magnitude of the emissions are, not surprisingly, positively correlated with the soil NO₃⁻ concentration but also negatively correlated with liming (neutral pH). The redox potential of the soil is found to influence N₂O accumulation as the production and consumption of N₂O occurs in narrow redox windows where the redox range levels are negatively correlated with the pH. This study highlights the potential importance of N₂O bursts associated with flooding and infers that annual N₂O emission estimates for tilled agricultural soils that are temporarily flooded will be underestimated. Furthermore, this study shows that subsurface N₂O reduction is a key process limiting N₂O emission and that a reduction in N₂O emissions is achievable if highly fertilized N-rich soils are limed

Global Research Alliance N2 O chamber methodology guidelines:Introduction, with health and safety considerations

Non-steady-state (NSS) chamber techniques have been used for decades to measure nitrous oxide (N₂O) fluxes from agricultural soils. These techniques are widely used because they are relatively inexpensive, easy to adopt, versatile, and adaptable to varying conditions. Much of our current understanding of the drivers of N₂O emissions is based on studies using NSS chambers. These chamber techniques require decisions regarding multiple methodological aspects (e.g., chamber materials and geometry, deployment, sample analysis, and data and statistical analysis), each of which may significantly affect the results. Variation in methodological details can lead to challenges in comparing results between studies and assessment of reliability and uncertainty. Therefore, the New Zealand Government, in support of the objectives of the Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gases (GRA), funded two international projects to, first, develop standardized guidelines on the use of NSS chamber techniques and, second, refine them based on the most up to date knowledge and methods. This introductory paper summarizes a collection of papers that represent the revised guidelines. Each article summarizes existing knowledge and provides guidance and minimum requirements on chamber design, deployment, sample collection, storage and analysis, automated chambers, flux calculations, statistical analysis, emission factor estimation and data reporting, modeling, and “gap-filling” approaches. The minimum requirements are not meant to be highly prescriptive but instead provide researchers with clear direction on best practices and factors that need to be considered. Health and safety considerations of NSS chamber techniques are also provided with this introductory paper

Soil respiratory quotient determined via barometric process separation combined with nitrogen-15 labeling

The barometric process separation (BaPS) and ¹⁵N dilution techniques were used to determine gross nitrification rates on the same soil cores from an old grassland soil. The BaPS-technique separates the O₂ consumption into that from nitrification and that from soil organic matter (SOM) respiration. The most sensitive parameter for the calculations via the BaPS technique is the respiratory quotient (RQ = ∆CO₂/∆O₂) for SOM turnover (RQSOM). Combining both methods (BaPS–¹⁵N ) allowed the determination of the RQSOM. The RQ value determined in such a way is adjusted for the influence of nitrification and denitrification, which are both characterized by totally different RQ values. The results for the grassland soil showed that 6 to 10% of O₂ was consumed by nitrification when incubated at 20°C and 0.49 g H₂O g⁻¹ soil. A set of BaPS measurements with the same soil at various temperature and moisture contents showed that up to 49% of the total O₂ consumption was due to nitrification. The calculated RQSOM values via the BaPS–¹⁵N technique presented here are more closely associated with the overall SOM turnover than the usual net RQ reported in the literature. Furthermore, the RQSOM value provides an overall indication of the decomposability and chemical characteristics of the respired organic material. Hence, it has the potential to serve as a single state index for SOM quality and therefore be a useful index for SOM turnover models based on substrate quality

Genetic and chemical characterisation of the cornexistin pathway provides further insight into maleidride biosynthesis

The biosynthetic gene cluster for the selective herbicide cornexistin 1 from the fungus Paecilomyces variotii has been identified and analysed.</p

Effects of human footprint and biophysical factors on the body-size structure of fished marine species

Marine fisheries in coastal ecosystems in many areas of the world have historically removed large-bodied individuals, potentially impairing ecosystem functioning and the long-term sustainability of fish populations. Reporting on size-based indicators that link to food-web structure can contribute to ecosystem-based management, but the application of these indicators over large (cross-ecosystem) geographical scales has been limited to either fisheries-dependent catch data or diver-based methods restricted to shallow waters (<20 m) that can misrepresent the abundance of large-bodied fished species. We obtained data on the body-size structure of 82 recreationally or commercially targeted marine demersal teleosts from 2904 deployments of baited remote underwater stereo-video (stereo-BRUV). Sampling was at up to 50 m depth and covered approximately 10,000 km of the continental shelf of Australia. Seascape relief, water depth, and human gravity (i.e., a proxy of human impacts) were the strongest predictors of the probability of occurrence of large fishes and the abundance of fishes above the minimum legal size of capture. No-take marine reserves had a positive effect on the abundance of fishes above legal size, although the effect varied across species groups. In contrast, sublegal fishes were best predicted by gradients in sea surface temperature (mean and variance). In areas of low human impact, large fishes were about three times more likely to be encountered and fishes of legal size were approximately five times more abundant. For conspicuous species groups with contrasting habitat, environmental, and biogeographic affinities, abundance of legal-size fishes typically declined as human impact increased. Our large-scale quantitative analyses highlight the combined importance of seascape complexity, regions with low human footprint, and no-take marine reserves in protecting large-bodied fishes across a broad range of species and ecosystem configurations.publishedVersio

The MCM-Binding Protein ETG1 Aids Sister Chromatid Cohesion Required for Postreplicative Homologous Recombination Repair

The DNA replication process represents a source of DNA stress that causes potentially spontaneous genome damage. This effect might be strengthened by mutations in crucial replication factors, requiring the activation of DNA damage checkpoints to enable DNA repair before anaphase onset. Here, we demonstrate that depletion of the evolutionarily conserved minichromosome maintenance helicase-binding protein ETG1 of Arabidopsis thaliana resulted in a stringent late G2 cell cycle arrest. This arrest correlated with a partial loss of sister chromatid cohesion. The lack-of-cohesion phenotype was intensified in plants without functional CTF18, a replication fork factor needed for cohesion establishment. The synergistic effect of the etg1 and ctf18 mutants on sister chromatid cohesion strengthened the impact on plant growth of the replication stress caused by ETG1 deficiency because of inefficient DNA repair. We conclude that the ETG1 replication factor is required for efficient cohesion and that cohesion establishment is essential for proper development of plants suffering from endogenous DNA stress. Cohesion defects observed upon knockdown of its human counterpart suggest an equally important developmental role for the orthologous mammalian ETG1 protein

Insulated molecular wires: inhibiting orthogonal contacts in metal complex based molecular junctions

Metal complexes are receiving increased attention as molecular wires in fundamental studies of the transport properties of metal|molecule|metal junctions. In this context we report the single-molecule conductance of a systematic series of d8 square-planar platinum(II) trans-bis(alkynyl) complexes with terminal trimethylsilylethynyl (C[triple bond, length as m-dash]CSiMe3) contacting groups, e.g. trans-Pt{C[triple bond, length as m-dash]CC6H4C[triple bond, length as m-dash]CSiMe3}2(PR3)2 (R = Ph or Et), using a combination of scanning tunneling microscopy (STM) experiments in solution and theoretical calculations using density functional theory and non-equilibrium Green's function formalism. The measured conductance values of the complexes (ca. 3–5 × 10−5G0) are commensurate with similarly structured all-organic oligo(phenylene ethynylene) and oligo(yne) compounds. Based on conductance and break-off distance data, we demonstrate that a PPh3 supporting ligand in the platinum complexes can provide an alternative contact point for the STM tip in the molecular junctions, orthogonal to the terminal C[triple bond, length as m-dash]CSiMe3 group. The attachment of hexyloxy side chains to the diethynylbenzene ligands, e.g. trans-Pt{C[triple bond, length as m-dash]CC6H2(Ohex)2C[triple bond, length as m-dash]CSiMe3}2(PPh3)2 (Ohex = OC6H13), hinders contact of the STM tip to the PPh3 groups and effectively insulates the molecule, allowing the conductance through the full length of the backbone to be reliably measured. The use of trialkylphosphine (PEt3), rather than triarylphosphine (PPh3), ancillary ligands at platinum also eliminates these orthogonal contacts. These results have significant implications for the future design of organometallic complexes for studies in molecular junctions

Direct targets of the transcription factors ABA-Insensitive(ABI)4 and ABI5 reveal synergistic action by ABI4 and several bZIP ABA response factors

The plant hormone abscisic acid (ABA) is a key regulator of seed development. In addition to promoting seed maturation, ABA inhibits seed germination and seedling growth. Many components involved in ABA response have been identified, including the transcription factors ABA insensitive (ABI)4 and ABI5. The genes encoding these factors are expressed predominantly in developing and mature seeds, and are positive regulators of ABA mediated inhibition of seed germination and growth. The direct effects of ABI4 and ABI5 in ABA response remain largely undefined. To address this question, plants over-expressing ABI4 or ABI5 were used to allow identification of direct transcriptional targets. Ectopically expressed ABI4 and ABI5 conferred ABA-dependent induction of slightly over 100 genes in 11 day old plants. In addition to effector genes involved in seed maturation and reserve storage, several signaling proteins and transcription factors were identified as targets of ABI4 and/or ABI5. Although only 12% of the ABA- and ABI-dependent transcriptional targets were induced by both ABI factors in 11 day old plants, 40% of those normally expressed in seeds had reduced transcript levels in both abi4 and abi5 mutants. Surprisingly, many of the ABI4 transcriptional targets do not contain the previously characterized ABI4 binding motifs, the CE1 or S box, in their promoters, but some of these interact with ABI4 in electrophoretic mobility shift assays, suggesting that sequence recognition by ABI4 may be more flexible than known canonical sequences. Yeast one-hybrid assays demonstrated synergistic action of ABI4 with ABI5 or related bZIP factors in regulating these promoters, and mutant analyses showed that ABI4 and these bZIPs share some functions in plants

Land-use effects on local biodiversity in tropical forests vary between continents

The file attached is the Published/publisher’s pdf version of the article

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value &lt; 1 × 10-5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p &lt; 1 × 10-5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10-10, odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression