Spectroscopic evidence for an all-ferrous [4Fe–4S]0 cluster in the superreduced activator of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans

The key enzyme of the fermentation of glutamate by Acidaminococcus fermentans, 2-hydroxyglutarylcoenzyme A dehydratase, catalyzes the reversible syn-elimination of water from (R)-2-hydroxyglutaryl-coenzyme A, resulting in (E)-glutaconylcoenzyme A. The dehydratase system consists of two oxygen-sensitive protein components, the activator (HgdC) and the actual dehydratase (HgdAB). Previous biochemical and spectroscopic studies revealed that the reduced [4Fe–4S]+ cluster containing activator transfers one electron to the dehydratase driven by ATP hydrolysis, which activates the enzyme. With a tenfold excess of titanium(III) citrate at pH 8.0 the activator can be further reduced, yielding about 50% of a superreduced [4Fe–4S]0 cluster in the all-ferrous state. This is inferred from the appearance of a new Mössbauer spectrum with parameters δ = 0.65 mm/s and ΔEQ = 1.51–2.19 mm/s at 140 K, which are typical of Fe(II)S4 sites. Parallel-mode electron paramagnetic resonance (EPR) spectroscopy performed at temperatures between 3 and 20 K showed two sharp signals at g = 16 and 12, indicating an integer-spin system. The X-band EPR spectra and magnetic Mössbauer spectra could be consistently simulated by adopting a total spin St = 4 for the all-ferrous cluster with weak zero-field splitting parameters D = −0.66 cm−1 and E/D = 0.17. The superreduced cluster has apparent spectroscopic similarities with the corresponding [4Fe–4S]0 cluster described for the nitrogenase Fe-protein, but in detail their properties differ. While the all-ferrous Fe-protein is capable of transferring electrons to the MoFe-protein for dinitrogen reduction, a similar physiological role is elusive for the superreduced activator. This finding supports our model that only one-electron transfer steps are involved in dehydratase catalysis. Nevertheless we discuss a common basic mechanism of the two diverse systems, which are so far the only described examples of the all-ferrous [4Fe–4S]0 cluster found in biology

How to Formulate Scientific Realism and Antirealism

The wider the gap between rivaling positions, the more there can be debates between rivaling interlocutors. The gap between the respective formulations of scientific realism and antirealism that invoke the Prussian conception of rationality is wider than the gap between the respective formulations of scientific realism and antirealism that invoke the English conception of rationality. Therefore, scientific realists and antirealists should choose the former over the latter as the framework of their debate

Why Should We Be Pessimistic about Antirealists and Pessimists?

The pessimistic induction over scientific theories (Poincar, in Science and hypothesis, Dover, New York, 1905/1952) holds that present theories will be overthrown as were past theories. The pessimistic induction over scientists (Stanford in Exceeding our grasp: science, history, and the problem of unconceived alternatives, Oxford University Press, Oxford, 2006) holds that present scientists cannot conceive of future theories just as past scientists could not conceive of present theories. The pessimistic induction over realists (Wray in Synthese 190(18):4321-4330, 2013) holds that present realists are wrong about present theories just as past realists were wrong about past theories. The pessimistic induction over antirealist theories (Park in Organon F 21(1):3-21, 2014) holds that the latest antirealist explanation of the success of science (Lyons in Philos Sci 70(5):891-901, 2003) has hidden problems just as its eight predecessors did. In this paper, I (1) criticize the pessimistic inductions over scientific theories, scientists, and realists, (2) introduce a pessimistic induction over antirealist theories, and then (3) construct two new pessimistic inductions. One is a pessimistic induction over antirealists according to which the author of the latest antirealist proposal cannot see hidden problems with his proposal just as his antirealist predecessors could not see hidden problems with their proposals. The other is the pessimistic induction over pessimists according to which since past pessimists have been wrong about their present scientific theories from the early twentieth century to the early twenty-first century, future pessimists will also be wrong about their present scientific theories from the early twenty-first century to the early twenty-second century.clos

Hypoxia shapes the immune landscape in lung injury and promotes the persistence of inflammation.

Hypoxemia is a defining feature of acute respiratory distress syndrome (ARDS), an often-fatal complication of pulmonary or systemic inflammation, yet the resulting tissue hypoxia, and its impact on immune responses, is often neglected. In the present study, we have shown that ARDS patients were hypoxemic and monocytopenic within the first 48 h of ventilation. Monocytopenia was also observed in mouse models of hypoxic acute lung injury, in which hypoxemia drove the suppression of type I interferon signaling in the bone marrow. This impaired monopoiesis resulted in reduced accumulation of monocyte-derived macrophages and enhanced neutrophil-mediated inflammation in the lung. Administration of colony-stimulating factor 1 in mice with hypoxic lung injury rescued the monocytopenia, altered the phenotype of circulating monocytes, increased monocyte-derived macrophages in the lung and limited injury. Thus, tissue hypoxia altered the dynamics of the immune response to the detriment of the host and interventions to address the aberrant response offer new therapeutic strategies for ARDS