Nitrous oxide emissions from soil in mango and banana fields: effects of nitrogen rate, fertiliser type, and ground cover practices

Globally, agricultural soils are the dominant source of the greenhouse gas, nitrous oxide (N₂O), and a growing body of evidence indicates that soils in tropical zones may emit disproportionately large amounts to the atmosphere. This is important as N₂O contributes approximately 6% of anthropogenically induced global warming and is also responsible for ozone depletion. These emissions primarily originate from microbial nitrification and denitrification processes in soil, which are driven by soil water content, temperature, available nitrogen (N), organic carbon (OC) and their interactions. This study investigated the effects of N fertiliser application rate and type, and ground cover, on N₂O emissions from soil in mango and banana fields in tropical northern Australia. The fertiliser types were conventional urea and two enhanced efficiency fertilisers (EEFs): urea treated with a nitrification inhibitor (3, 4-dimethylpyrazole phosphate, DMPP) and polymer sulphur-coated (PC) urea mixed with standard urea at a 40/60 ratio (in mangoes only). Ground cover treatments were bare ground versus vegetative ground cover in bananas, and bare ground versus hay mulch in mangoes. A manual chamber technique was used to measure gas emissions from three field experiments with factorial designs (randomised block, four replications of each treatment). The experiments were conducted in 1) a commercial mango orchard on a Yellow Chromosol soil at Mutchilba, 2) a commercial banana farm on a Red Ferrosol soil at East Palmerston, and 3) a banana research farm on a Brown Dermosol soil at South Johnstone. In banana fields (Chapter 3), soil mineral N content, water content, and time since fertiliser application were the primary drivers of N₂O emissions. Low N rate treatments (12 kg N ha⁻¹ mth⁻¹) had consistently lower N₂O emissions than high N rates (18 to 54 kg N ha⁻¹ mth⁻¹), however overall N₂O flux was highest in all treatments when fertiliser was applied during persistently wet conditions (>68% water-filled pore space, WFPS). Urea treated with DMPP had approximately half the N₂O emissions than untreated urea on the Brown Dermosol, but did not significantly reduce emissions on the Red Ferrosol. Vegetative ground cover reduced N₂O emissions compared to bare soil during wet conditions and with higher N rates, presumably due to N uptake by the ground cover decreasing soil mineral N concentrations. In the mango orchard (Chapter 2), N₂O emissions were lower than under bananas at the other sites. The mango site soil had less mineral N, lower water holding capacity and lower OC content. N₂O emissions were not lowered by using EEFs rather than urea at application rates <25 kg N ha⁻¹. However, at a higher fertiliser application rate of 42 kg N ha⁻¹, DMPP approximately halved N₂O emissions. Mulching also lowered N₂O emissions, however sufficient irrigation after fertiliser application to mulch is recommended to reduce potential ammonia volatilisation. Overall, the management factors examined influenced soil mineral N, water content, temperature and possibly OC, all of which played important roles in determining total N₂O emissions in both crops. In banana fields, using lower N rates and DMPP treated urea during wet conditions will reduce N₂O losses. However, vegetative ground covers do not appear to be a reliable or consistent method of N₂O mitigation, as any reduction may be offset by the potential additional N required to compensate for plant competition and to avoid yield decline. In mangoes the most benefit would be gained from mulching, due to the reduction in N₂O and an increase in yield. However, further research is required to substantiate the N₂O reduction of hay mulch over the longer term. There appeared to be little justification for N₂O mitigation measures with EEFs in mangoes, due to generally negotiable N₂O emissions in the Yellow Chromosol, and the additional cost of EEFs. On the whole, more research is required around the mechanisms reducing the efficacy of DMPP-treated urea in Red Ferrosols and during hot conditions (35– 45°C). Finally, the PC urea product in this study needs to be tested in more suitable conditions that favour denitrification (higher N rate and soil water content) in order to more appropriately assess its impact on N₂O production

Necrotic Cell Sensor Clec4e Promotes a Proatherogenic Macrophage Phenotype Through Activation of the Unfolded Protein Response.

BACKGROUND: Atherosclerotic lesion expansion is characterized by the development of a lipid-rich necrotic core known to be associated with the occurrence of complications. Abnormal lipid handling, inflammation, and alteration of cell survival or proliferation contribute to necrotic core formation, but the molecular mechanisms involved in this process are not properly understood. C-type lectin receptor 4e (Clec4e) recognizes the cord factor of Mycobacterium tuberculosis but also senses molecular patterns released by necrotic cells and drives inflammation. METHODS: We hypothesized that activation of Clec4e signaling by necrosis is causally involved in atherogenesis. We addressed the impact of Clec4e activation on macrophage functions in vitro and on the development of atherosclerosis using low-density lipoprotein receptor-deficient (Ldlr-/-) mice in vivo. RESULTS: We show that Clec4e is expressed within human and mouse atherosclerotic lesions and is activated by necrotic lesion extracts. Clec4e signaling in macrophages inhibits cholesterol efflux and induces a Syk-mediated endoplasmic reticulum stress response, leading to the induction of proinflammatory mediators and growth factors. Chop and Ire1a deficiencies significantly limit Clec4e-dependent effects, whereas Atf3 deficiency aggravates Clec4e-mediated inflammation and alteration of cholesterol efflux. Repopulation of Ldlr-/- mice with Clec4e-/- bone marrow reduces lipid accumulation, endoplasmic reticulum stress, and macrophage inflammation and proliferation within the developing arterial lesions and significantly limits atherosclerosis. CONCLUSIONS: Our results identify a nonredundant role for Clec4e in coordinating major biological pathways involved in atherosclerosis and suggest that it may play similar roles in other chronic inflammatory diseases.This work was supported by a European Research Council grant (to Z.M.), and by the British Heart Foundation (Z. M.).This is the author accepted manuscript. The final version is available from the American Heart Association via https://doi.org/10.1161/CIRCULATIONAHA.116.02266

Necrotic Cell Sensor Clec4e Promotes a Proatherogenic Macrophage Phenotype Through Activation of the Unfolded Protein Response

$\textbf{Background}$: Atherosclerotic lesion expansion is characterized by the development of a lipid-rich necrotic core known to be associated with the occurrence of complications. Abnormal lipid handling, inflammation, and alteration of cell survival or proliferation contribute to necrotic core formation, but the molecular mechanisms involved in this process are not properly understood. C-type lectin receptor 4e (Clec4e) recognizes the cord factor of Mycobacterium $\textit{tuberculosis}$ but also senses molecular patterns released by necrotic cells and drives inflammation. $\textbf{Methods}$: We hypothesized that activation of Clec4e signaling by necrosis is causally involved in atherogenesis. We addressed the impact of Clec4e activation on macrophage functions in vitro and on the development of atherosclerosis using low-density lipoprotein receptor–deficient ($\textit{Ldlr}$$^{−/−}$) mice in vivo. $\textbf{Results}$: We show that Clec4e is expressed within human and mouse atherosclerotic lesions and is activated by necrotic lesion extracts. Clec4e signaling in macrophages inhibits cholesterol efflux and induces a Syk-mediated endoplasmic reticulum stress response, leading to the induction of proinflammatory mediators and growth factors. $\textit{Chop }$and $\textit{Ire1a}$ deficiencies significantly limit Clec4e-dependent effects, whereas $\textit{Atf}$3 deficiency aggravates Clec4e-mediated inflammation and alteration of cholesterol efflux. Repopulation of $\textit{Ldlr}$$^{−/−}$ mice with $\textit{Clec4e}$$^{−/−}$ bone marrow reduces lipid accumulation, endoplasmic reticulum stress, and macrophage inflammation and proliferation within the developing arterial lesions and significantly limits atherosclerosis. $\textbf{Conclusions}$: Our results identify a nonredundant role for Clec4e in coordinating major biological pathways involved in atherosclerosis and suggest that it may play similar roles in other chronic inflammatory diseases.This work was supported by a European Research Council grant (to Z.M.), and by the British Heart Foundation (Z. M.).This is the author accepted manuscript. The final version is available from the American Heart Association via https://doi.org/10.1161/CIRCULATIONAHA.116.02266

MHC class II-restricted antigen presentation by plasmacytoid dendritic cells drives proatherogenic T cell immunity

Background—Plasmacytoid dendritic cells (pDCs) bridge innate and adaptive immune responses and are important regulators of immuno-inflammatory diseases. However, their role in atherosclerosis remains elusive. Methods and Results—Here, we used genetic approaches to investigate the role of pDCs in atherosclerosis. Selective pDC deficiency in vivo was achieved using CD11c-Cre × Tcf4–/flox bone marrow transplanted into Ldlr–/– mice. Compared with control Ldlr–/– chimeric mice, CD11c-Cre × Tcf4–/flox mice had reduced atherosclerosis levels. To begin to understand the mechanisms by which pDCs regulate atherosclerosis, we studied chimeric Ldlr–/– mice with selective MHCII deficiency on pDCs. Significantly, these mice also developed reduced atherosclerosis compared with controls without reductions in pDC numbers or changes in conventional DCs. MHCII-deficient pDCs showed defective stimulation of apolipoprotein B100–specific CD4+ T cells in response to native low-density lipoprotein, whereas production of interferon-α was not affected. Finally, the atheroprotective effect of selective MHCII deficiency in pDCs was associated with significant reductions of proatherogenic T cell–derived interferon-γ and lesional T cell infiltration, and was abrogated in CD4+ T cell–depleted animals. Conclusions—This study supports a proatherogenic role for pDCs in murine atherosclerosis and identifies a critical role for MHCII-restricted antigen presentation by pDCs in driving proatherogenic T cell immunity

Regulatory B cell-specific interleukin-10 is dispensable for atherosclerosis development in mice

Objective: To determine the role of regulatory B cell derived interleukin (Il)-10 in atherosclerosis. Approach and Results: We created chimeric Ldlr-/- mice with a B cell-specific deficiency in Il-10, and confirmed that purified B cells stimulated with LPS failed to produce IL-10 compared to control Ldlr-/- chimeras. Mice lacking B cell Il-10 demonstrated enhanced splenic B cell numbers but no major differences in B cell subsets, T cell or monocyte distribution, and unchanged body weights or serum cholesterol levels compared to control mice. After 8 weeks on high fat diet, there were no differences in aortic root or aortic arch atherosclerosis. In addition to plaque size, plaque composition (macrophages, T cells, smooth muscle cells and collagen) was similar between groups. Conclusions: In contrast to its prominent regulatory role in many immune-mediated diseases and its proposed modulatory role in atherosclerosis, B cell derived Il-10 does not alter atherosclerosis in mice.This work was funded by the British Heart Foundation (to Z.M.). M. N. has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° 608765.This is the author accepted manuscript. The final version is available from American Heart Association at http://dx.doi.org/10.1161/ATVBAHA.115.305568

Regulatory B cell-specific interleukin-10 is dispensable for atherosclerosis development in mice.

OBJECTIVE: To determine the role of regulatory B cell-derived interleukin (IL)-10 in atherosclerosis. APPROACH AND RESULTS: We created chimeric Ldlr(-/-) mice with a B cell-specific deficiency in IL-10, and confirmed that purified B cells stimulated with lipopolysaccharide failed to produce IL-10 compared with control Ldlr(-/-) chimeras. Mice lacking B-cell IL-10 demonstrated enhanced splenic B-cell numbers but no major differences in B-cell subsets, T cell or monocyte distribution, and unchanged body weights or serum cholesterol levels compared with control mice. After 8 weeks on high-fat diet, there were no differences in aortic root or aortic arch atherosclerosis. In addition to plaque size, plaque composition (macrophages, T cells, smooth muscle cells, and collagen) was similar between groups. CONCLUSIONS: In contrast to its prominent regulatory role in many immune-mediated diseases and its proposed modulatory role in atherosclerosis, B cell-derived IL-10 does not alter atherosclerosis in mice.This work was funded by the British Heart Foundation (to Z.M.). M. N. has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° 608765.This is the author accepted manuscript. The final version is available from American Heart Association at http://dx.doi.org/10.1161/ATVBAHA.115.305568

BAFF receptor deficiency reduces the development of atherosclerosis in mice--brief report.

OBJECTIVE: The goal of this study was to assess the role of B-cell activating factor (BAFF) receptor in B-cell regulation of atherosclerosis. METHODS AND RESULTS: Male LDL receptor-deficient mice (Ldlr(-/-)) were lethally irradiated and reconstituted with either wild type or BAFF receptor (BAFF-R)-deficient bone marrow. After 4 weeks of recovery, mice were put on a high-fat diet for 6 or 8 weeks. BAFF-R deficiency in bone marrow cells led to a marked reduction of conventional mature B2 cells but did not affect the B1a cell subtype. This was associated with a significant reduction of dendritic cell activation and T-cell proliferation along with a reduction of IgG antibodies against malondialdehyde-modified low-density lipoprotein. In contrast, serum IgM type antibodies were preserved. Interestingly, BAFF-R deficiency was associated with a significant reduction in atherosclerotic lesion development and reduced numbers of plaque T cells. Selective BAFF-R deficiency on B cells led to a similar reduction in lesion size and T-cell infiltration but in contrast did not affect dendritic cell activation. CONCLUSIONS: BAFF-R deficiency in mice selectively alters mature B2 cell-dependent cellular and humoral immune responses and limits the development of atherosclerosis.British Heart Foundation, Fondation Leducq.This is the author accepted manuscript. The final version is available from the American Heart Association at http://dx.doi.org/10.1161/ATVBAHA.111.244731

Impaired Autophagy in CD11b+ Dendritic Cells Expands CD4+ Regulatory T Cells And Limits Atherosclerosis in Mice.

Rationale: Atherosclerosis is a chronic inflammatory disease. Recent studies have shown that dysfunctional autophagy in endothelial cells, smooth muscle cells and macrophages, plays a detrimental role during atherogenesis, leading to the suggestion that autophagy-stimulating approaches may provide benefit. Objective: Dendritic cells (DCs) are at the crossroad of innate and adaptive immune responses and profoundly modulate the development of atherosclerosis. Intriguingly, the role of autophagy in DC function during atherosclerosis and how the autophagy process would impact disease development has not been addressed. Methods and Results: Here, we show that the autophagic flux in atherosclerosis-susceptible low-density lipoprotein receptor deficient (Ldlr-/-) mice is substantially higher in splenic and aortic DCs compared to macrophages, and is further activated under hypercholesterolemic conditions. RNA sequencing and functional studies on selective cell populations reveal that disruption of autophagy through deletion of Atg16l1 differentially affects the biology and functions of DC subsets in Ldlr-/- mice under high fat diet. Atg16l1 deficient CD11b+ DCs develop a TGF-beta-dependent tolerogenic phenotype and promote the expansion of regulatory T cells (Tregs), whereas no such effects are seen with Atg16l1 deficient CD8alpha+ DCs. Atg16l1 deletion in DCs (all CD11c-expressing cells) expands aortic Tregs in vivo, limits the accumulation of T helper cells type 1 (Th1), and reduces the development of atherosclerosis in Ldlr-/- mice. In contrast, no such effects are seen when Atg16l1 is deleted selectively in conventional CD8alpha+ DCs and CD103+ DCs. Total T cell or selective Treg cell depletion abrogates the atheroprotective effect of Atg16l1 deficient DCs. Conclusions: In contrast to its pro-atherogenic role in macrophages, autophagy disruption in DCs induces a counter-regulatory response that maintains immune homeostasis in Ldlr-/- mice under high fat diet and limits atherogenesis. Selective modulation of autophagy in DCs could constitute an interesting therapeutic target in atherosclerosis.This study was supported by the British Heart Foundation (CH/10/001/27642 and Grant No. 1659), and the European HEALTH 2013.1.3-3 programm

Adjunctive rifampicin for Staphylococcus aureus bacteraemia (ARREST): a multicentre, randomised, double-blind, placebo-controlled trial.

BACKGROUND: Staphylococcus aureus bacteraemia is a common cause of severe community-acquired and hospital-acquired infection worldwide. We tested the hypothesis that adjunctive rifampicin would reduce bacteriologically confirmed treatment failure or disease recurrence, or death, by enhancing early S aureus killing, sterilising infected foci and blood faster, and reducing risks of dissemination and metastatic infection. METHODS: In this multicentre, randomised, double-blind, placebo-controlled trial, adults (≥18 years) with S aureus bacteraemia who had received ≤96 h of active antibiotic therapy were recruited from 29 UK hospitals. Patients were randomly assigned (1:1) via a computer-generated sequential randomisation list to receive 2 weeks of adjunctive rifampicin (600 mg or 900 mg per day according to weight, oral or intravenous) versus identical placebo, together with standard antibiotic therapy. Randomisation was stratified by centre. Patients, investigators, and those caring for the patients were masked to group allocation. The primary outcome was time to bacteriologically confirmed treatment failure or disease recurrence, or death (all-cause), from randomisation to 12 weeks, adjudicated by an independent review committee masked to the treatment. Analysis was intention to treat. This trial was registered, number ISRCTN37666216, and is closed to new participants. FINDINGS: Between Dec 10, 2012, and Oct 25, 2016, 758 eligible participants were randomly assigned: 370 to rifampicin and 388 to placebo. 485 (64%) participants had community-acquired S aureus infections, and 132 (17%) had nosocomial S aureus infections. 47 (6%) had meticillin-resistant infections. 301 (40%) participants had an initial deep infection focus. Standard antibiotics were given for 29 (IQR 18-45) days; 619 (82%) participants received flucloxacillin. By week 12, 62 (17%) of participants who received rifampicin versus 71 (18%) who received placebo experienced treatment failure or disease recurrence, or died (absolute risk difference -1·4%, 95% CI -7·0 to 4·3; hazard ratio 0·96, 0·68-1·35, p=0·81). From randomisation to 12 weeks, no evidence of differences in serious (p=0·17) or grade 3-4 (p=0·36) adverse events were observed; however, 63 (17%) participants in the rifampicin group versus 39 (10%) in the placebo group had antibiotic or trial drug-modifying adverse events (p=0·004), and 24 (6%) versus six (2%) had drug interactions (p=0·0005). INTERPRETATION: Adjunctive rifampicin provided no overall benefit over standard antibiotic therapy in adults with S aureus bacteraemia. FUNDING: UK National Institute for Health Research Health Technology Assessment

Marginal zone B cells control the response of follicular helper T cells to a high-cholesterol diet

Splenic marginal zone B (MZB) cells, positioned at the interface between circulating blood and lymphoid tissue, detect and respond to blood-borne antigens. Here we show that MZB cells in mice activate a homeostatic program in response to a high-cholesterol diet (HCD) and regulate both the differentiation and accumulation of T follicular helper (TFH) cells. Feeding mice an HCD resulted in upregulated MZB cell surface expression of the immunoregulatory ligand PDL1 in an ATF3-dependent manner and increased the interaction between MZB cells and pre-TFH cells, leading to PDL1-mediated suppression of TFH cell motility, alteration of TFH cell differentiation, reduced TFH abundance and suppression of the proatherogenic TFH response. Our findings reveal a previously unsuspected role for MZB cells in controlling the TFH–germinal center response to a cholesterol-rich diet and uncover a PDL1-dependent mechanism through which MZB cells use their innate immune properties to limit an exaggerated adaptive immune response.This work was supported by BHF grant no. PG/15/76/31756, BHF grant no. PG/13/73/30466, ERC grant no. 2891164 and EC FP7 VIA grant no. HEALTH-F4- 2013-603131 to Z.M. and by SAF2013-45543-R from the Spanish Ministry of Economy and Competitiveness (MINECO) to J.L.d.l.P. M.N. was first supported by a Sara Borrell grant (CD09/00452) from the Instituto Nacional de Salud Carlos III (Spain) and then by a 2-year BHF Project Grant. M.N. has also received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 608765. The Wellcome Trust supported the Cambridge Mouse Biochemistry Laboratory