Cycling of inorganic and organic sulfur in peat from Big Run Bog,West Virginia

Total S concentration in the top 35 cm of Big Run Bog peat averaged 9.7 mol·g — wet mass^–1 (123 mol·g dry mass^–1). Of that total, an average of 80.8% was carbon bonded S, 10.4% was ester sulfate S, 4.5% was FeS₂­S, 2.7% was FeS­S, 1.2% was elemental S, and 0.4% was SO₄ ^2–­S. In peat collected in March 1986, injected with³⁵S­SO₄ ^2– and incubated at 4 °C, mean rates of dissimilatory sulfate reduction (formation of H₂S + S⁰ + FeS + FeS₂), carbon bonded S formation, and ester sulfate S formation averaged 3.22, 0.53, and 0.36 nmol·g wet mass^–1·h^–1, respectively. Measured rates of sulfide oxidation were comparable to rates of sulfate reduction. Although dissolved SO₄ ^2– concentrations in Big Run Bog interstitial water (< 200 µM) are low enough to theoretically limit sulfate reducing bacteria, rates of sulfate reduction integrated throughout the top 30–35 cm of peat of 9 and 34 mmol·m^–2·d^–1 (at 4 °C are greater than or comparable to rates in coastal marine sediments. We suggest that sulfate reduction was supported by a rapid turnover of the dissolved SO₄ ^2– pool (average turnover time of 1.1 days). Although over 90% of the total S in Big Run Bog peat was organic S, cycling of S was dominated by fluxes through the inorganic S pools.     

Experimental removal and addition of leaf litter inputs reduces nitrate production and loss in a lowland tropical forest

Environmental perturbations such as changes in land use, climate, and atmospheric carbon dioxide concentrations may alter organic matter inputs to surface soils. While the carbon (C) cycle response to such perturbations has received considerable attention, potential responses of the soil nitrogen (N) cycle to changing organic matter inputs have been less well characterized. Changing litter inputs to surface to soils may alter the soil N cycle directly, by controlling N substrate availability, or indirectly, via interactions with soil C biogeochemistry. We investigated soil N-cycling responses to a leaf litter manipulation in a lowland tropical forest using isotopic and molecular techniques. Both removing and doubling leaf litter inputs decreased the size of the soil nitrate pool, gross nitrification rates, and the relative abundance of ammonia-oxidizing microorganisms. Gross nitrification rates were correlated with the relative abundance of ammonia-oxidizing archaea, and shifts in the N-cycling microbial community composition correlated with concurrent changes in edaphic properties, notably pH and C:N ratios. These results highlight the importance of understanding coupled biogeochemical cycles in global change scenarios and suggest that environmental perturbations that alter organic matter inputs in tropical forests could reduce inorganic N losses to surface waters and the atmosphere by limiting nitrate production.     

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis

Over-representation analysis (ORA) is one of the commonest pathway analysis approaches used for the functional interpretation of metabolomics datasets. Despite the widespread use of ORA in metabolomics, the community lacks guidelines detailing its best-practice use. Many factors have a pronounced impact on the results, but to date their effects have received little systematic attention. Using five publicly available datasets, we demonstrated that changes in parameters such as the background set, differential metabolite selection methods, and pathway database used can result in profoundly different ORA results. The use of a non-assay-specific background set, for example, resulted in large numbers of false-positive pathways. Pathway database choice, evaluated using three of the most popular metabolic pathway databases (KEGG, Reactome, and BioCyc), led to vastly different results in both the number and function of significantly enriched pathways. Factors that are specific to metabolomics data, such as the reliability of compound identification and the chemical bias of different analytical platforms also impacted ORA results. Simulated metabolite misidentification rates as low as 4% resulted in both gain of false-positive pathways and loss of truly significant pathways across all datasets. Our results have several practical implications for ORA users, as well as those using alternative pathway analysis methods. We offer a set of recommendations for the use of ORA in metabolomics, alongside a set of minimal reporting guidelines, as a first step towards the standardisation of pathway analysis in metabolomics.     

Oxidative stress promotes ligand-independent and enhanced ligand-dependent tumor necrosis factor receptor signaling

Tumor necrosis factor (TNF) receptor 1 (TNFR1, p55) and 2 (TNFR2, p75) are characterized by several cysteine-rich modules in the extracellular domain, raising the possibility that redox-induced modifications of these cysteine residues might alter TNFR function. To test this possibility, we examined fluorescence resonance energy transfer (FRET) in 293T cells transfected with CFP- and YFP-tagged TNFRs exposed to the thiol oxidant diamide. Treatment with high concentrations of diamide (1 mm) resulted in an increase in the FRET signal that was sensitive to inhibition with the reducing agent dithiothreitol, suggesting that oxidative stress resulted in TNFR self-association. Treatment of cells with low concentrations of diamide (1 mum) that was not sufficient to provoke TNFR self-association resulted in increased TNF-induced FRET signals relative to the untreated cells, suggesting that oxidative stress enhanced ligand-dependent TNFR signaling. Similar findings were obtained when the TNFR1- and TNFR2-transfected cells were pretreated with a cell-impermeable oxidase, DsbA, that catalyzes disulfide bond formation between thiol groups on cysteine residues. The changes in TNFR self-association were functionally significant, because pretreating the HeLa cells and 293T cells resulted in increased TNF-induced NF-kappaB activation and TNF-induced expression of IkappaB and syndecan-4 mRNA levels. Although pretreatment with DsbA did not result in an increase in TNF binding to TNFRs, it resulted in increased TNF-induced activation of NF-kappaB, consistent with an allosteric modification of the TNFRs. Taken together, these results suggest that oxidative stress promotes TNFR receptor self-interaction and ligand-independent and enhanced ligand-dependent TNF signaling.     

Organic Matter Accumulation and Community Change at the Peatland–Upland Interface: Inferences from 14C and 210Pb Dated Profiles

Peatland-margin habitats with organic matter accumulation of 40–150 cm make up a significant but poorly quantified portion of Canada’s boreal forest region. Spanning the transition between non-wetland forest and fen proper, these ecosystems represent a zone of complex environmental and vegetation change, yet little is known about their ecological function or development. We here use vegetation and macrofossil analysis, traditional ¹⁴C, bomb-spike ¹⁴C, and ²¹⁰Pb dating to investigate the development, organic matter accumulation, and recent vegetation history of peat margin communities at two sites in central Saskatchewan, Canada. Although similar in general shape, bomb-spike ¹⁴C and ²¹⁰Pb chronologies show limited agreement in three of the four profiles examined, with ²¹⁰Pb generally producing younger ages than ¹⁴C. Peat initiation and long-term organic matter accumulation at the Old Black Spruce (OBS) transect were probably driven mainly by the dynamics of Sphagnum, whereas at the Sandhill Fen (SF) transect, they were controlled by water level fluctuations in the neighboring fen. Bryophyte macrofossils suggest a recent drying of the vegetation surface at both sites, most likely triggered by regional drought in the late 1950s and 1960s. At OBS, the shift from Sphagnum- to feather moss-dominated communities continued in the 1990s, possibly reflecting effects of direct disturbance on local drainage patterns. Overall, our results suggest that community composition and C dynamics of peat-margin swamps respond dynamically to climatic and hydrologic fluctuations. However, uncertainties regarding the reliability of different chronologies limit our ability to link observed community changes to specific causal events. Author Contributions  IEB conceived/designed study, performed research, analyzed data, wrote paper. JSB conceived/designed study, wrote paper. CS performed research, analyzed data, wrote paper. RKW performed research and analyzed data. CMP performed research and wrote paper.     

Role of Ca2+-activated K+ channels in human erythrocyte apoptosis

Exposure of erythrocytes to the Ca²⁺ ionophore ionomycin has recently been shown to induce cell shrinkage, cell membrane blebbing, and breakdown of phosphatidylserine asymmetry, all features typical of apoptosis of nucleated cells. Although breakdown of phosphatidylserine asymmetry is thought to result from activation of a Ca²⁺-sensitive scramblase, the mechanism and role of cell shrinkage have not been explored. The present study was performed to test whether ionomycin-induced activation of Ca²⁺-sensitive Gardos K⁺ channels and subsequent cell shrinkage participate in ionomycin-induced breakdown of phosphatidylserine asymmetry of human erythrocytes. According to on-cell patch-clamp experiments, ionomycin (1 µM) induces activation of inwardly rectifying K⁺-selective channels in the erythrocyte membrane. Fluorescence-activated cell sorter analysis reveals that ionomycin leads to a significant decrease of forward scatter, reflecting cell volume, an effect blunted by an increase of extracellular K⁺ concentration to 25 mM and exposure to the Gardos K⁺ channel blockers charybdotoxin (230 nM) and clotrimazole (5 µM). As reflected by annexin binding, breakdown of phosphatidylserine asymmetry is triggered by ionomycin, an effect again blunted, but not abolished, by an increase of extracellular K⁺ concentration and exposure to charybdotoxin (230 nM) and clotrimazole (5 µM). Similar to ionomycin, glucose depletion leads (within 55 h) to annexin binding of erythrocytes, an effect again partially reversed by an increase of extracellular K⁺ concentration and exposure to charybdotoxin. K-562 human erythroleukemia cells similarly respond to ionomycin with cell shrinkage and annexin binding, effects blunted by antisense, but not sense, oligonucleotides against the small-conductance Ca²⁺-activated K⁺ channel isoform hSK4 (KCNN4). The experiments disclose a novel functional role of Ca²⁺-sensitive K⁺ channels in erythrocytes, i.e., their participation in regulation of erythrocyte apoptosis. cell volume; charybdotoxin; osmolarity; phosphatidylserine; annexin     

Mechanisms of suicidal erythrocyte death.

Erythrocyte injury such as osmotic shock, oxidative stress or energy depletion stimulates the formation of prostaglandin E2 through activation of cyclooxygenase which in turn activates a Ca2+ permeable cation channel. Increasing cytosolic Ca2+ concentrations activate Ca2+ sensitive K+ channels leading to hyperpolarization, subsequent loss of KCl and (further) cell shrinkage. Ca2+ further stimulates a scramblase shifting phosphatidylserine from the inner to the outer cell membrane. The scramblase is sensitized for the effects of Ca2+ by ceramide which is formed by a sphingomyelinase following several stressors including osmotic shock. The sphingomyelinase is activated by platelet activating factor PAF which is released by activation of phospholipase A2. Phosphatidylserine at the erythrocyte surface is recognised by macrophages which engulf and degrade the affected cells. Moreover, phosphatidylserine exposing erythrocytes may adhere to the vascular wall and thus interfere with microcirculation. Erythrocyte shrinkage and phosphatidylserine exposure ('eryptosis') mimic features of apoptosis in nucleated cells which however, involves several mechanisms lacking in erythrocytes. In kidney medulla, exposure time is usually too short to induce eryptosis despite high osmolarity. Beyond that high Cl- concentrations inhibit the cation channel and high urea concentrations the sphingomyelinase. Eryptosis is inhibited by erythropoietin which thus extends the life span of circulating erythrocytes. Several conditions trigger premature eryptosis thus favouring the development of anemia. On the other hand, eryptosis may be a mechanism of defective erythrocytes to escape hemolysis. Beyond their significance for erythrocyte survival and death the mechanisms involved in 'eryptosis' may similarly contribute to apoptosis of nucleated cells.     

Structure-dependent effects of glucose-containing analogs of platelet activating factor (PAF) on membrane integrity

Synthetic choline-containing phospholipids comprise a new class of compounds with antineoplastic properties. We have investigated the effect of recently synthesized glucose-containing analogs of lysophosphatidylcholine (glyceroglucophospholipid, Glc-PC) and of lysoplatelet activating factor (Glc-PAF) and its C16, C14 and C12 derivatives (ET-16, ET-14, and ET-12) on proliferation of immortalized human keratinocyte (HaCaT) cells. The data were compared to the ability of the compounds to intercalate into phosphatidylserine liposomes and to form lesions in planar bilayer membranes. A correlation between bioactivity and membrane activity was found. The number of molecules that intercalated into phosphatidylserine liposomes depended on the chemical structure of the compounds and was in the order Glc-PAF approximately ET-16 approximately ET-14 > Glc-PC > ET-12. All compounds induced membrane lesions, and the lesion forming activity was in the same order. Similar activity rankings were found for the release of lactate dehydrogenase from HaCaT cells as a measure of lytic activity and for the influence on cell number as a measure of proliferation. In the latter test, however, proliferation was already inhibited at non-toxic concentrations. From these findings, it may be concluded that the intercalation of the compounds at toxic concentrations leads to the formation of membrane lesions and finally results in membrane rupture leading to cell death.     

PGE(2) in the regulation of programmed erythrocyte death

Hyperosmotic shock, energy depletion, or removal of extracellular Cl(-) activates Ca(2+)-permeable cation channels in erythrocyte membranes. Subsequent Ca(2+) entry induces erythrocyte shrinkage and exposure of phosphatidylserine (PS) at the erythrocyte surface. PS-exposing cells are engulfed by macrophages. The present study explored the signalling involved. Hyperosmotic shock and Cl(-) removal triggered the release of prostaglandin E(2) (PGE(2)). In whole-cell recording, activation of the cation channels by Cl(-) removal was abolished by the cyclooxygenase inhibitor diclophenac. In FACS analysis, phospholipase-A(2) inhibitors quinacrine and palmitoyltrifluoromethyl-ketone, and cyclooxygenase inhibitors acetylsalicylic acid and diclophenac, blunted the increase of PS exposure following Cl(-) removal. PGE(2) (but not thromboxane) induced cation channel activation, increase in cytosolic Ca(2+) concentration, cell shrinkage, PS exposure, calpain activation, and ankyrin-R degradation. The latter was attenuated by calpain inhibitors-I/II, while PGE(2)-induced PS exposure was not. In conclusion, hyperosmotic shock or Cl(-) removal stimulates erythrocyte PS exposure through PGE(2) formation and subsequent activation of Ca(2+)-permeable cation channels.