Intensification of grasslands is necessary to meet the increasing demand of livestock products. The application of nitrogen (N) on grasslands affects the N balance therefore the nitrogen use ...efficiency (NUE). Emissions of nitrous oxide (N2O) are produced due to N fertilisation and low NUE. These emissions depend on the type and rates of N applied. In this study we have compiled data from 5 UK N fertilised grassland sites (Crichton, Drayton, North Wyke, Hillsborough and Pwllpeiran) covering a range of soil types and climates. The experiments evaluated the effect of increasing rates of inorganic N fertiliser provided as ammonium nitrate (AN) or calcium ammonium nitrate (CAN). The following fertiliser strategies were also explored for a rate of 320 kg N ha−1: using the nitrification inhibitor dicyandiamide (DCD), changing to urea as an N source and splitting fertiliser applications. We measured N2O emissions for a full year in each experiment, as well as soil mineral N, climate data, pasture yield and N offtake. N2O emissions were greater at Crichton and North Wyke whereas Drayton, Hillsborough and Pwllpeiran had the smallest emissions. The resulting average emission factor (EF) of 1.12% total N applied showed a range of values for all the sites between 0.6 and 2.08%. NUE depended on the site and for an application rate of 320 kg N ha−1, N surplus was on average higher than 80 kg N ha−1, which is proposed as a maximum by the EU Nitrogen Expert Panel. N2O emissions tended to be lower when urea was applied instead of AN or CAN, and were particularly reduced when using urea with DCD. Finally, correlations between the factors studied showed that total N input was related to Nofftake and Nexcess; while cumulative emissions and EF were related to yield scaled emissions.
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•N2O emissions and NUE were measured at 5 UK grassland sites.•Different fertilisation rates and strategies were tested in all sites.•Average N2O emission factor was 1.12%, but ranged from 0.60% to 2.08%.•Using urea and urea with DCD reduced N2O emission factor.•Yield scaled emissions and emissions relative to herbage N content show similar trend.
Risk stratification of COVID-19 patients upon hospital admission is key for their successful treatment and efficient utilization of hospital resources. We sought to evaluate the risk factors on ...admission (including comorbidities, vital signs, and initial laboratory assessment) associated with ventilation need and in-hospital mortality in COVID-19.
We established a retrospective cohort of COVID-19 patients from Mass General Brigham hospitals. Demographic, clinical, and admission laboratory data were obtained from electronic medical records of patients admitted to the hospital with laboratory-confirmed COVID-19 before May 19, 2020. Multivariable logistic regression analyses were used to construct and validate the Ventilation in COVID Estimator (VICE) and Death in COVID Estimator (DICE) risk scores.
The entire cohort included 1042 patients (median age, 64 years; 56.8% male). The derivation and validation cohorts for the risk scores included 578 and 464 patients, respectively. We found four factors to be independently predictive for mechanical ventilation requirement (diabetes mellitus, SpO2:FiO2 ratio, C-reactive protein, and lactate dehydrogenase), and 10 factors to be predictors of in-hospital mortality (age, male sex, coronary artery disease, diabetes mellitus, chronic statin use, SpO2:FiO2 ratio, body mass index, neutrophil to lymphocyte ratio, platelet count, and procalcitonin). Using these factors, we constructed the VICE and DICE risk scores, which performed with C-statistics of 0.84 and 0.91, respectively. Importantly, the chronic use of a statin was associated with protection against death due to COVID-19. The VICE and DICE score calculators have been placed on an interactive website freely available to healthcare providers and researchers (https://covid-calculator.com/).
The risk scores developed in this study may help clinicians more appropriately determine which COVID-19 patients will need to be managed with greater intensity.
COVID-19 Fast Grant (fastgrants.org).
The RNase III enzyme DICER generates both microRNAs (miRNAs) and endogenous short interfering RNAs (endo-siRNAs). Both small RNA species silence gene expression post-transcriptionally in association ...with the ARGONAUTE (AGO) family of proteins. In mammals, there are four AGO proteins (AGO1-4), of which only AGO2 possesses endonucleolytic activity. siRNAs trigger endonucleolytic cleavage of target mRNAs, mediated by AGO2, whereas miRNAs cause translational repression and mRNA decay through association with any of the four AGO proteins. Dicer deletion in mouse oocytes leads to female infertility due to defects during meiosis I. Because mouse oocytes express both miRNAs and endo-siRNAs, this phenotype could be due to the absence of either class of small RNA, or both. However, we and others demonstrated that miRNA function is suppressed in mouse oocytes, which suggested that endo-siRNAs, not miRNAs, are essential for female meiosis. To determine if this was the case we generated mice that express a catalytically inactive knock-in allele of Ago2 (Ago2ADH) exclusively in oocytes and thereby disrupted the function of siRNAs. Oogenesis and hormonal response are normal in Ago2ADH oocytes, but meiotic maturation is impaired, with severe defects in spindle formation and chromosome alignment that lead to meiotic catastrophe. The transcriptome of these oocytes is widely perturbed and shows a highly significant correlation with the transcriptome of Dicer null and Ago2 null oocytes. Expression of the mouse transcript (MT), the most abundant transposable element in mouse oocytes, is increased. This study reveals that endo-siRNAs are essential during meiosis I in mouse females, demonstrating a role for endo-siRNAs in mammals.
Aging is characterized by functional impairment and reduced capacity to respond appropriately to environmental stimuli and injury. With age, there is an increase in the incidence and severity of ...chronic and acute lung diseases. However, the relationship between age and the lung's reduced ability to repair is far from established and necessitates further research in the field.
Little is currently known about age-related phenomena in mesenchymal stem cells (MSCs). On account of their ability to protect the endothelium and the alveolar epithelium through multiple paracrine mechanisms, we looked for adverse effects that aging might cause in MSC biology. Such age-related changes might partly account for the increased susceptibility of the aging lung to injury.
We demonstrated that old mice have more inflammation in response to acute lung injury. To investigate the causes, we compared the global gene expression of aged and young bone marrow-derived MSCs (B-MSCs). Our results revealed that the expression levels of inflammatory response genes depended on the age of the B-MSCs. We demonstrated that the age-dependent decrease in expression of several cytokine and chemokine receptors is important for the migration and activation of B-MSCs. Finally, we showed by adoptive transfer of aged B-MSCs to young endotoxemic mice that aged cells lacked the antiinflammatory protective effect of their young counterparts.
Taken together, the decreased expression of cytokine and chemokine receptors in aged B-MSCs compromises their protective role by perturbing the potential of B-MSCs to become activated and mobilize to the site of injury.
Thoracic aortic aneurysm (TAA) can lead to fatal complications such as aortic dissection. Since aneurysm dimension poorly predicts dissection risk, microRNAs (miRNAs) may be useful to diagnose or ...risk stratify TAA patients. We aim to identify miRNAs associated with TAA pathogenesis and that are possibly able to improve TAA diagnosis. MiRNA microarray experiments of aortic media tissue samples from 19 TAA patients and 19 controls allowed identifying 232 differentially expressed miRNAs. Using interaction networks between these miRNAs and 690 genes associated with TAA, we identified miR-574-5p as a potential contributor of TAA pathogenesis. Interestingly, miR-574-5p was significantly down-regulated in the TAA tissue compared to the controls, but was up-regulated in serum samples from a separate group of 28 TAA patients compared to 20 controls (
< 0.001). MiR-574-5p serum levels discriminated TAA patients from controls with an area under the receiver operating characteristic curve of 0.87. In the
mouse model, miR-574-5p was down-regulated in aortic tissue compared to wild-type (
< 0.05), and up-regulated in plasma extracellular vesicles from
mice compared to wild-type mice (
< 0.05). Furthermore, in vascular smooth muscle cells, angiotensin II appears to induce miR-574-5p secretion in extracellular vesicles. In conclusion, miR-574-5p is associated with TAA pathogenesis and may help in diagnosing this disease.
A trial was conducted consisting of 14 experiments across sites in England of contrasting soil type and annual rainfall to assess the effectiveness of nitrification inhibitors (predominantly ...dicyandiamide (DCD) but limited assessment also of 3, 4-dimethylpyrazole phosphate (DMPP) and a commercial product containing two pyrazole derivatives) in reducing direct nitrous oxide (N2O) emissions from fertilizer nitrogen (N), cattle urine and cattle slurry applications to land. Measurements were also made of the impact on ammonia (NH3) volatilization, nitrate (NO3−) leaching, crop yield and crop N offtake. DCD proved to be very effective in reducing direct N2O emissions following fertilizer and cattle urine applications, with mean reduction efficiencies of 39, 69 and 70% for ammonium nitrate, urea and cattle urine, respectively. When included with cattle slurry a mean, non-significant reduction of 56% was observed. There were no N2O emission reductions observed from the limited assessments of the other nitrification inhibitors. Generally, there were no impacts of the nitrification inhibitors on NH3 volatilization, NO3− leaching, crop yield or crop N offtake. Use of DCD could give up to 20% reduction in N2O emissions from UK agriculture, but cost-effective delivery mechanisms are required to encourage adoption by the sector. Direct N2O emissions from the studied sources were substantially lower than IPCC default values and development of UK country-specific emission factors for use in inventory compilation is warranted.
Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more ...accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis. This tool offers a user-friendly interface, and leads clinicians through simple steps by limiting the number of candidates to achieve a final diagnosis of a medical genetics case. A useful innovation is the "1-click" method, which enables listing all the relevant variants in genes present at OMIM for perusal by clinicians. Mendel,MD was experimentally validated using clinical cases from the literature and was tested by students at the Universidade Federal de Minas Gerais, at GENE-Núcleo de Genética Médica in Brazil and at the Children's University Hospital in Dublin, Ireland. We show in this article how it can simplify and increase the speed of identifying the culprit mutation in each of the clinical cases that were received for further investigation. Mendel,MD proved to be a reliable web-based tool, being open-source and time efficient for identifying the culprit mutation in different clinical cases of patients with Mendelian Disorders. It is also freely accessible for academic users on the following URL: https://mendelmd.org.
Genome-wide association studies have identified hundreds of loci associated with common vascular diseases, such as coronary artery disease, myocardial infarction, and hypertension. However, the lack ...of mechanistic insights for many GWAS loci limits their translation into the clinic. Among these loci with unknown functions is
-four-and-a-half LIM (LIN-11, Isl-1, MEC-3) domain 5 (
; chr6q16.1), which reached genome-wide significance in a recent coronary artery disease/ myocardial infarction GWAS meta-analysis.
is also associated with several vascular diseases, consistent with the widespread pleiotropy observed for GWAS loci.
We apply a multimodal approach leveraging statistical fine-mapping, epigenomic profiling, and ex vivo analysis of human coronary artery tissues to implicate
as the top candidate causal gene. We unravel the molecular mechanisms of the cross-phenotype genetic associations through in vitro functional analyses and epigenomic profiling experiments in coronary artery smooth muscle cells.
We prioritized
as the top candidate causal gene at the
locus through expression quantitative trait locus colocalization methods.
gene expression was enriched in the smooth muscle cells and pericyte population in human artery tissues with coexpression network analyses supporting a functional role in regulating smooth muscle cell contraction. Unexpectedly, under procalcifying conditions, FHL5 overexpression promoted vascular calcification and dysregulated processes related to extracellular matrix organization and calcium handling. Lastly, by mapping FHL5 binding sites and inferring FHL5 target gene function using artery tissue gene regulatory network analyses, we highlight regulatory interactions between FHL5 and downstream coronary artery disease/myocardial infarction loci, such as
and
that have roles in vascular remodeling.
Taken together, these studies provide mechanistic insights into the pleiotropic genetic associations of
We show that FHL5 mediates vascular disease risk through transcriptional regulation of downstream vascular remodeling gene programs. These transacting mechanisms may explain a portion of the heritable risk for complex vascular diseases.
Idiopathic pulmonary fibrosis (IPF) is a chronic fatal lung disease with dismal prognosis and no cure. The potential role of the ubiquitously expressed SH2 domain-containing tyrosine phosphatase-2 ...(SHP2) as a therapeutic target has not been studied in IPF.
To determine the expression, mechanistic role, and potential therapeutic usefulness of SHP2 in pulmonary fibrosis.
The effects of SHP2 overexpression and inhibition on fibroblast response to profibrotic stimuli were analyzed in vitro in primary human and mouse lung fibroblasts. In vivo therapeutic effects were assessed in the bleomycin model of lung fibrosis by SHP2-lentiviral administration and transgenic mice carrying a constitutively active SHP2 mutation.
SHP2 was down-regulated in lungs and lung fibroblasts obtained from patients with IPF. Immunolocalization studies revealed that SHP2 was absent within fibroblastic foci. Loss of SHP2 expression or activity was sufficient to induce fibroblast-to-myofibroblast differentiation in primary human lung fibroblasts. Overexpression of constitutively active SHP2 reduced the responsiveness of fibroblasts to profibrotic stimuli, including significant reductions in cell survival and myofibroblast differentiation. SHP2 effects were mediated through deactivation of fibrosis-relevant tyrosine kinase and serine/threonine kinase signaling pathways. Mice carrying the Noonan syndrome-associated gain-of-function SHP2 mutation (SHP2
) were resistant to bleomycin-induced pulmonary fibrosis. Restoration of SHP2 levels in vivo through lentiviral delivery blunted bleomycin-induced pulmonary fibrosis.
Our data suggest that SHP2 is an important regulator of fibroblast differentiation, and its loss as observed in IPF facilitates profibrotic phenotypic changes. Augmentation of SHP2 activity or expression should be investigated as a novel therapeutic strategy for IPF.
► N
2O emissions were significantly higher in top soils than subsoils. ► Total denitrification (N
2O+N
2) was significantly lower in subsoils. ► N
2O mole fraction decreased significantly with soil ...depth. ► Subsoil denitrification ranged from 4 to 29% of applied nitrate. ► Carbon amendment significantly increased total denitrification and subsoil N
2 emission
Understanding subsurface denitrification potential will give greater insights into landscape nitrate (NO
3
−) delivery to groundwater and indirect nitrous oxide (N
2O) emissions to the atmosphere. Potential denitrification rates and ratios of N
2O/(N
2O
+
N
2) were investigated in intact soil cores collected from 0–0.10, 0.45–0.55 and 1.20–1.30
m depths representing A, B and C soil horizons, respectively from three randomly selected locations within a single intensively managed grazed grassland plot in south eastern Ireland. The soil was moderately well drained with textures ranging from loam to clay loam (gleysol) in the A to C horizon. An experiment was carried out by amending soils from each horizon with (i) 90
mg NO
3
−–N as KNO
3, (ii) 90
mg NO
3
−–N
+
150
mg glucose-C, (iii) 90
mg NO
3
−–N
+
150
mg DOC (dissolved organic carbon, prepared using top soil of intensively managed grassland) kg
−1 dry soil. An automated laboratory incubation system was used to measure simultaneously N
2O and N
2, at 15
°C, with the moisture content raised by 3% (by weight) above the moisture content at field capacity (FC), giving a water-filled pore space (WFPS) of 80, 85 and 88% in the A, B and C horizons, respectively. There was a significant effect (
p
<
0.01) of soil horizon and added carbon on cumulative N
2O emissions. N
2O emissions were higher from the A than the B and C horizons and were significantly lower from soils that received only nitrate than soils that received NO
3
−
+
either of the C sources. The two C sources gave similar N
2O emissions. The N
2 fluxes differed significantly (
p
<
0.05) only between the A and C horizons. During a 17-day incubation, total denitrification losses of the added N decreased significantly (
p
<
0.01) with soil depth and were increased by the addition of either C source. The fraction of the added N lost from each horizon were A: 25, 61, 45%; B: 12, 29, 28.5% and C: 4, 20, 18% for nitrate, nitrate
+
glucose-C and nitrate
+
DOC, respectively. The ratios of N
2O to N
2O
+
N
2 differed significantly (
p
<
0.05) only between soil horizons, being higher in the A (0.58–0.75) than in the deeper horizons (0.10–0.36 in B and 0.06–0.24 in C), clearly indicating the potential of subsoils for a more complete reduction of N
2O to N
2. Stepwise multiple regression analysis revealed that N
2O flux increased with total organic C and total N but decreased with NO
3
−–N which together explained 88% of the variance (
p
<
0.001). The N
2 flux was best explained (
R
2
=
0.45,
p
<
0.01) by soluble organic nitrogen (SON) (positive) and with NO
3
−–N (negative). Stepwise multiple regression revealed a best fit for total denitrification rates which were positive for total C and negative for NO
3
−–N with the determination coefficient of 0.76 (
p
<
0.001). The results suggest that without C addition, potential denitrification rate below the root zone was low. Therefore, the added C sources in subsoils can satisfactorily increase nitrate depletion via denitrification where the mole fraction of N
2O would be further reduced to N
2 during diffusional transport through the soil profile to the atmosphere and/or to groundwater. Subsoil denitrification can be accelerated either through introducing C directly into permeable reactive barriers and/or indirectly, by irrigating dirty water and manipulating agricultural plant composition and diversity.
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