Area estimations of cultivated organic soils in Ireland: reducing GHG reporting uncertainties

peer-reviewed Cultivated organic soils, which are a large source of CO2 emissions, are of particular interest in the Republic of Ireland where peatlands cover 20 % of the landscape. For accurate accounting and national reporting of greenhouse gas (GHG) emissions, there is a need to calculate the total land area used for cultivation activity on drained organic soils. Peatlands (organic soils) in Ireland are also used for arable farming, which results in particularly high greenhouse gas emissions per unit area. However, the Irish National Inventory Report to the United Nations Framework Convention on Climate Change lacks mention of this type of land use. The actual area of organic soils under arable land use (cropland) in Ireland has, thus far, not been quantified. Here we provide a first estimate of the area of organic soil that is used for arable farming in Ireland. Through map overlay analysis using GIS in combination with probability sampling and ground truthing, we estimate the area of organic soils under arable cropping at 1,235 ha, which is considerably lower than the estimate of 3,688 ha based on map overlays alone. This research provides information to support improved accounting of organic soils under cultivation and may contribute to reducing uncertainty in national reporting of GHG emissions, thus providing a more reliable basis for strategies aimed at reducing GHG emissions in Ireland in the future.PUBLISHEDpeer-reviewe

Characterization of elemental ratios and oxidative ratio of horticultural peat

peer-reviewedPeatlands occupy 20% of the land area of Ireland and store over half of soil carbon stocks. Over 80% of these peatlands have been disturbed by human activity such as drainage for peat extraction, afforestation and agriculture. In this study, peat samples were collected from 12 horticultural peat extraction sites in the Irish midlands. The carbon (C), nitrogen (N), hydrogen, and sulphur content were determined, and from these the carbon oxidation state (Cox) and oxidative ratio (OR) were calculated. The carbon oxidation ratio reflects organic matter synthesis and degradation, and is thus an important parameter in understanding terrestrial carbon cycling, whilst OR represents the molar ratio of oxygen (O2) and carbon dioxide (CO2) fluxes associated with net ecosystem exchange. Elemental concentrations and ratios were typical for Irish horticultural peat (e.g. carbon concentrations 54 – 57%), though showed site to site variability. Cox and OR values varied between -0.22 and -0.11, and 1.04 and 1.07 respectively and were comparable to United Kingdom peat soils. All values for OR were lower than 1.1, the value commonly used in global CO2 partitioning studies. Further research should investigate OR values in peatland which has not been studied to date. Across all sites, measures of increased decomposition (i.e. C/N ratios) significantly correlated with increasing OR reflecting more reduced organic matter. This study provides data in temperate peat soils that increases the coverage of Cox and OR values and will inform global CO2 partitioning studies

Transcriptional response to lactic acid stress in the hybrid yeast Zygosaccharomyces parabailii

Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH, and a fermentative metabolism with a fast growth rate. Here we used RNA-seq to analyze Z. parabailii's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than in control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/2, previously described as lactic acid-responsive in Saccharomyces cerevisiae. Furthermore, formate dehydrogenase (FDH) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii as compared to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production.Importance Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression in conditions of interest, and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains

Graphene Nanoflake Uptake Mediated by Scavenger Receptors

The biological interactions of graphene have been extensively investigated over the last 10 years. However, very little is known about graphene interactions with the cell surface and how the graphene internalization process is driven and mediated by specific recognition sites at the interface with the cell. In this work, we propose a methodology to investigate direct molecular correlations between the biomolecular corona of graphene and specific cell receptors, showing that key protein recognition motifs, presented on the nanomaterial surface, can engage selectively with specific cell receptors. We consider the case of apolipoprotein A-I, found to be very abundant in the graphene protein corona, and observe that the uptake of graphene nanoflakes is somewhat increased in cells with greatly elevated expression of scavenger receptors B1, suggesting a possible mechanism of endogenous interaction. The uptake results, obtained by flow cytometry, have been confirmed using Raman microspectroscopic mapping, exploiting the strong Raman signature of graphene

Argonne National Laboratory Reports

This is a sequel to the paper ''A comparison of two ODE codes: GEAR and EPISODE,'' and is concerned with the testing of two superficially similar ODE packages, GEAR and EPISODE. Fourteen basic test problems, some with several cases, are the basis for the testing. These problems represent several types-nonlinear systems with real and complex eigenvalues, linear systems with varied diagonal dominance, linear scalar problems, stiff and non-stiff problems, chemical kinetics with and without diurnal effect, and systems arising from the use of the numerical method of lines. Some problems are included in order to examine the options and error returns. The test results are presented in two forms: raw output and a comparative display of operation counts and of timings for the best method in the GEAR package and the best method in the EPISODE package. This approach allows a comparison of the consequences of the fixed-step interpolate strategy (GEAR) for changing step size against the truly variable step size strategy (EPISODE). It is concluded that EPISODE is generally faster than GEAR for problems involving wave fronts or transients on the interior of the interval of integration. For linear or simply decaying problems, these roles are usually reversed

P352 A propensity score-matched, real-world comparison of ustekinumab vs vedolizumab as a second-line treatment for Crohn's disease. The Cross Pennine study II

Abstract Background The best choice of biological agents after failure to an anti-tumour necrosis factor (TNF)α agent in patients with Crohn's disease (CD) is yet to be defined. Real-world data dealing with this issue are still emerging. Methods This is a multicentre retrospective study including eight UK hospitals (August 2014-April 2020). We retrospectively collected data of patients treated with ustekinumab. Clinical response and remission at 14 and 52 weeks evaluated through Physician Global Assessment (PGA) and adverse events were recorded. Predictors of clinical response were examined, and a propensity score-matched analysis with a cohort of patients treated with vedolizumab was performed. Results Overall, 282 patients (mean age 40±15, F:M ratio 1.7:1) treated with ustekinumab were included. Clinical response or remission was reached by 200/282 patients (70.9%) at 14 weeks, and by 162/259 patients (62.5%) at 52 weeks. The most common reason for discontinuation was either primary failure or loss of response, followed by the occurrence of adverse events and by the need for surgery. The rate of non-adherence was rather low (1.4%). Current smoking (OR 2.48, 95% CI 1.13-5.44; p=0.02), baseline PGA (OR 2.4, 95% CI 1.55-3.69, p<0.001), and use of steroids (OR 2.42, 95% CI 1.26-4.65, p=0.008) were associated with 52-week treatment failure. Overall, 74 adverse events occurred, of which 26 were labelled as serious (8.3 per 100 person-year). After exclusion of patients without anti-TNFα exposure prior to starting ustekinumab or vedolizumab and exclusion of patients previously exposed to vedolizumab or ustekinumab, we analysed 275/282 patients (97.5%) from the ustekinumab cohort and 118/135 patients (87.4%) from the vedolizumab cohort. Propensity score analysis revealed that at 14 weeks, patients treated with ustekinumab were 38% (95% CI 25-50%; p<0.001) more likely to achieve a clinical remission, while at 52 weeks, the difference of 9% (95% CI -15-33%; p=0.462) was not significant. Conclusion Ustekinumab was effective and well tolerated in this real-world cohort. While ustekinumab proved more effective at 14-week follow-up, we found no statistically significant differences in outcomes at 52 weeks

Mountain building in Taiwan: A thermokinematic model

The Taiwan mountain belt is classically viewed as a case example of a critical wedge growing essentially by frontal accretion and therefore submitted to distributed shortening. However, a number of observations call for a significant contribution of underplating to the growth of the orogenic wedge. We propose here a new thermokinematic model of the Taiwan mountain belt reconciling existing kinematic, thermometric and thermochronological constraints. In this model, shortening across the orogen is absorbed by slip on the most frontal faults of the foothills. Crustal thickening and exhumation are sustained by underplating beneath the easternmost portion of the wedge (Tananao Complex, TC), where the uplift rate is estimated to ~6.3 mm a^(−1), and beneath the westernmost internal region of the orogen (Hsueshan Range units, HR), where the uplift rate is estimated to ~4.2 mm a^(−1). Our model suggests that the TC units experienced a synchronous evolution along strike despite the southward propagation of the collision. It also indicates that they have reached a steady state in terms of cooling ages but not in terms of peak metamorphic temperatures. Exhumation of the HR units increases northward but has not yet reached an exhumational steady state. Presently, frontal accretion accounts for less than ~10% of the incoming flux of material into the orogen, although there is indication that it was contributing substantially more (~80%) before 4 Ma. The incoming flux of material accreted beneath the TC significantly increased 1.5 Ma ago. Our results also suggest that the flux of material accreted to the orogen corresponds to the top ~7 km of the upper crust of the underthrust Chinese margin. This indicates that a significant amount (~76%) of the underthrust material has been subducted into the mantle, probably because of the increase in density associated with metamorphism. We also show that the density distribution resulting from metamorphism within the orogenic wedge explains well the topography and the gravity field. By combining available geological data on the thermal and kinematic evolution of the wedge, our study sheds new light onto mountain building processes in Taiwan and allows for reappraising the initial structural architecture of the passive margin

Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres

Centromeres are the chromosomal regions promoting kinetochore assembly for chromosome segregation. In many eukaryotes, the centromere consists of up to mega base pairs of DNA. On such "regional centromeres," kinetochore assembly is mainly defined by epigenetic regulation [1]. By contrast, a clade of budding yeasts (Saccharomycetaceae) has a "point centromere" of 120-200 base pairs of DNA, on which kinetochore assembly is defined by the consensus DNA sequence [2, 3]. During evolution, budding yeasts acquired point centromeres, which replaced ancestral, regional centromeres [4]. All known point centromeres among different yeast species share common consensus DNA elements (CDEs) [5, 6], implying that they evolved only once and stayed essentially unchanged throughout evolution. Here, we identify a yeast centromere that challenges this view: that of the budding yeast Naumovozyma castellii is the first unconventional point centromere with unique CDEs. The N. castellii centromere CDEs are essential for centromere function but have different DNA sequences from CDEs in other point centromeres. Gene order analyses around N. castellii centromeres indicate their unique, and separate, evolutionary origin. Nevertheless, they are still bound by the ortholog of the CBF3 complex, which recognizes CDEs in other point centromeres. The new type of point centromere originated prior to the divergence between N. castellii and its close relative Naumovozyma dairenensis and disseminated to all N. castellii chromosomes through extensive genome rearrangement. Thus, contrary to the conventional view, point centromeres can undergo rapid evolutionary changes. These findings give new insights into the evolution of point centromeres

The genetic architecture of breast papillary lesions as a predictor of progression to carcinoma

Intra-ductal papillomas (IDP) are challenging breast findings because of their variable risk of progression to malignancy. The molecular events driving IDP development and genomic features of malignant progression are poorly understood. In this study, genome-wide CNA and/or targeted mutation analysis was performed on 44 cases of IDP, of which 20 cases had co-existing ductal carcinoma in situ (DCIS), papillary DCIS or invasive ductal carcinoma (IDC). CNA were rare in pure IDP, but 69% carried an activating PIK3CA mutation. Among the synchronous IDP cases, 55% (11/20) were clonally related to the synchronous DCIS and/ or IDC, only one of which had papillary histology. In contrast to pure IDP, PIK3CA mutations were absent from clonal cases. CNAs in any of chromosomes 1, 16 or 11 were significantly enriched in clonal IDP lesions compared to pure and non-clonal IDP. The observation that 55% of IDP are clonal to DCIS/IDC indicates that IDP can be a direct precursor for breast carcinoma, not limited to the papillary type. The absence of PIK3CA mutations and presence of CNAs in IDP could be used clinically to identify patients at high risk of progression to carcinoma

Soil organic carbon stocks by soil group for afforested soils in Ireland

Forest ecosystems are recognised as Natural Climate Solutions because forest soils are such important carbon stores, containing almost half of the total soil organic carbon of terrestrial ecosystems. Here we present the results of a synthesis of soil carbon stocks by World Reference Base soil group, and forest litter carbon stocks for afforested soils in the Republic of Ireland. We report soil carbon stocks of mineral soils separately from organo-mineral soils. We estimated mean soil carbon stocks in a 100 cm deep mineral soil to be between 162 ± 87 t C/ha (Gleysols) and 416 ± 0 t C/ha (Umbrisols, n = 1), and between 173 ± 65 t C/ha (Phaeozems) and 602 ± 226 t C/ha (Regosols) in a 100 cm deep organo-mineral soil; both less than the estimated soil carbon stocks in organic soils (Histosols): 645 ± 222 t C/ha. The entire soil carbon stocks in mineral Leptosols (100 ± 0 t C/ha, n = 1), Stagnosols (144 ± 39 t C/ha), Luvisols (159 ± 52 t C/ha) and Fluvisols (231 ± 0 t C/ha, n = 1) was contained in the upper 50 cm of soil. Based on a 100 cm deep soil, Histosols hold 1.6–4 times the amount of soil C than mineral soils and 1.1–3.7 times the amount in organo-mineral soils for the same profile depth. Certain mineral (e.g. Umbrisols) and organo-mineral soils (e.g Gleysols, Regosols) contain substantial soil carbon stocks relative to Histosols. We found considerable soil carbon stocks below 30 cm depth, which highlights the importance of depth extent for cumulative soil carbon stocks estimates. The upper third of the 100 cm profile contained 33% (Histosols) to 70% (Luvisols) of the soil carbon stocks and the upper half of a 100 cm profile contained the entire soil carbon stocks for Leptosols, Stagnosols, Luvisols and Fluvisols and organo-mineral Leptosols. Unfortunately, there were few samples available for mineral Leptosols, Umbrisols, Luvisols and Fluvisols, and the organo-mineral Stagnosols and Regosols, which precludes the drawing of conclusions for these groups. Relative to the soil carbon stocks, we found low mean forest litter stocks: 4.1 ± 5.5 t C/ha, 4.8 ± 3.3 t C/ha and 2.7 ± 2.9 t C/ha for broadleaf, coniferous and mixed forests respectively. Few exceptions existed for individual sites: 22.7 and 131.3 t C/ha for broadleaf forests. Our results are evidence that soil carbon stocks in mineral, organo-mineral and organic soils need to be protected, appropriately managed, and enhanced to be beneficial for greenhouse gas mitigation. Assessments are needed to identify which soil-site-management practice combinations risk soil carbon stock depletion. The large range observed in soil and litter carbon stocks stresses the importance of adequately accounting for soil group differences when GHG inventories are compiled. The synthesised dataset will contribute to improved SCS estimation for afforested lands in Ireland