Complexome analysis of the nitrite - dependent methanotroph Methylomirabilis lanthanidiphila

The atmospheric concentration of the potent greenhouse gases methane and nitrous oxide (N2O) has increased drastically during the last century. Methylomirabilis bacteria can play an import role in controlling the emission of these two gases from natural ecosystems, by oxidizing methane to CO2 and reducing nitrite to N2 without producing N2O. These bacteria have an anaerobic metabolism, but are proposed to possess an oxygen-dependent pathway for the activation of methane. Methylomirabilis bacteria reduce nitrite to NO, and are proposed to dismutate NO into O2 and N2 by a putative NO dismutase (NO-D). The O2 produced in the cell can then be used for the activation of methane by a particulate methane monooxygenase. So far, the metabolic model of Methylomirabilis bacteria was based mainly on (meta)genomics and physiological experiments. Here we applied a complexome profiling approach to determine which of the proposed enzymes are actually expressed in Methylomirabilis lanthanidiphila. To validate the metabolic model, we focused on enzymes involved in respiration, and nitrogen and C1 transformation. All complexes proposed to be involved in nitrite-dependent methane oxidation, were identified in M. lanthanidiphila, including the putative NO-D. Furthermore, several complexes involved in nitrate reduction/nitrite oxidation and NO reduction were detected, which likely play a role in detoxification and redox homeostasis. In conclusion, complexome profiling validated the expression and composition of enzymes proposed to be involved in the energy, methane and nitrogen metabolism of M. lanthanidiphila, thereby further corroborating the metabolically unique and environmentally relevant process of nitrite-dependent methane oxidation

Management of aneurysmal subarachnoid hemorrhage patients with antiplatelet use before the initial hemorrhage: an international survey

INTRODUCTION The case fatality in aneurysmal subarachnoid hemorrhage (aSAH) is 50% due to the initial hemorrhage or subsequent complications like aneurysmal rebleed or delayed cerebral ischemia (DCI). One factor that might influence the initial brain damage or subsequent complications is the use of antiplatelet medication before the initial hemorrhage. The goal of this survey was to assess the different management options of patients with aSAH with antiplatelet use before the initial hemorrhage. MATERIAL AND METHODS An anonymous survey of 11 multiple-choice questions about management of aSAH patients with antiplatelet use before the initial hemorrhage was distributed to the international panel of attendees of the European Association of Neurosurgical Societies (EANS) annual meeting in Venice, Italy at 1-5 October 2017. RESULTS A total of 258 (54%) completed surveys were returned. In about 80%, the departments of neurosurgery and neurology were responsible for acute management of aSAH patients, whereas in 15% the intensive care unit. Department guidelines were present in 32%. In 65%, the responders always stop the antiplatelet agent at admission and in 4.3% are thrombocytes always transfused. When a guideline is present, the neurospecialists consider thrombocyte transfusion more often (83% vs. 65% p=0.02). CONCLUSION Our survey among mainly European neurosurgeons show that there is a significant variability in the management of aSAH patients who have been using antiplatelets before the initial hemorrhage. These findings emphasize the importance of the development of evidence-based guidelines for management of patients with aSAH and antiplatelet use before the initial hemorrhage

Blood oxygenation-level dependent cerebrovascular reactivity imaging as strategy to monitor CSF-hemoglobin toxicity

Objectives: Cell-free hemoglobin in the cerebrospinal fluid (CSF-Hb) may be one of the main drivers of secondary brain injury after aneurysmal subarachnoid hemorrhage (aSAH). Haptoglobin scavenging of CSF-Hb has been shown to mitigate cerebrovascular disruption. Using digital subtraction angiography (DSA) and blood oxygenation-level dependent cerebrovascular reactivity imaging (BOLD-CVR) the aim was to assess the acute toxic effect of CSF-Hb on cerebral blood flow and autoregulation, as well as to test the protective effects of haptoglobin. Methods: DSA imaging was performed in eight anesthetized and ventilated sheep (mean weight: 80.4 kg) at baseline, 15, 30, 45 and 60 minutes after infusion of hemoglobin (Hb) or co-infusion with haptoglobin (Hb:Haptoglobin) into the left lateral ventricle. Additionally, 10 ventilated sheep (mean weight: 79.8 kg) underwent BOLD-CVR imaging to assess the cerebrovascular reserve capacity. Results: DSA imaging did not show a difference in mean transit time or cerebral blood flow. Whole-brain BOLD-CVR compared to baseline decreased more in the Hb group after 15 minutes (Hb vs Hb:Haptoglobin: -0.03 ± 0.01 vs -0.01 ± 0.02) and remained diminished compared to Hb:Haptoglobin group after 30 minutes (Hb vs Hb:Haptoglobin: -0.03 ± 0.01 vs 0.0 ± 0.01), 45 minutes (Hb vs Hb:Haptoglobin: -0.03 ± 0.01 vs 0.01 ± 0.02) and 60 minutes (Hb vs Hb:Haptoglobin: -0.03 ± 0.02 vs 0.01 ± 0.01). Conclusion: It is demonstrated that CSF-Hb toxicity leads to rapid cerebrovascular reactivity impairment, which is blunted by haptoglobin co-infusion. BOLD-CVR may therefore be further evaluated as a monitoring strategy for CSF-Hb toxicity after aSAH

An intracellular pH gradient in the anammox bacterium Kuenenia stuttgartiensis as evaluated by 31P NMR

The cytoplasm of anaerobic ammonium oxidizing (anammox) bacteria consists of three compartments separated by membranes. It has been suggested that a proton motive force may be generated over the membrane of the innermost compartment, the “anammoxosome”. 31P nuclear magnetic resonance (NMR) spectroscopy was employed to investigate intracellular pH differences in the anammox bacterium Kuenenia stuttgartiensis. With in vivo NMR, spectra were recorded of active, highly concentrated suspensions of K. stuttgartiensis in a wide-bore NMR tube. At different external pH values, two stable and distinct phosphate peaks were apparent in the recorded spectra. These peaks were equivalent with pH values of 7.3 and 6.3 and suggested the presence of a proton motive force over an intracytoplasmic membrane in K. stuttgartiensis. This study provides for the second time—after discovery of acidocalcisome-like compartments in Agrobacterium tumefaciens—evidence for an intracytoplasmic pH gradient in a chemotrophic prokaryotic cell

The polygonal cell shape and surface protein layer of anaerobic methane-oxidizing Methylomirabilis ianthanidiphila bacteria

This is the final version. Available from Frontiers Media via the DOI in this record. The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found below: ProteomeXchange, PXD029319; EMDB, EMD-13672 and EMD-13670; and EMPIAR, EMPIAR-10822 and EMPIAR-10829Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.European CommissionEuropean Research CouncilOCW/NWO Gravitation grantEuropean Research CouncilNetherlands Organisation for Scientific Research (NWO

Rolled-Up Nanotech: Illumination-Controlled Hydrofluoric Acid Etching of AlAs Sacrificial Layers

<p>Abstract</p> <p>The effect of illumination on the hydrofluoric acid etching of AlAs sacrificial layers with systematically varied thicknesses in order to release and roll up InGaAs/GaAs bilayers was studied. For thicknesses of AlAs below 10 nm, there were two etching regimes for the area under illumination: one at low illumination intensities, in which the etching and releasing proceeds as expected and one at higher intensities in which the etching and any releasing are completely suppressed. The &#8220;etch suppression&#8221; area is well defined by the illumination spot, a feature that can be used to create heterogeneously etched regions with a high degree of control, shown here on patterned samples. Together with the studied self-limitation effect, the technique offers a way to determine the position of rolled-up micro- and nanotubes independently from the predefined lithographic pattern.</p

Advances in methods for detection of anaerobic ammonium oxidizing (anammox) bacteria

Anaerobic ammonium oxidation (anammox), the biochemical process oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor, has only been recognized for its significant role in the global nitrogen cycle not long ago, and its ubiquitous distribution in a wide range of environments has changed our knowledge about the contributors to the global nitrogen cycle. Currently, several groups of methods are used in detection of anammox bacteria based on their physiological and biochemical characteristics, cellular chemical composition, and both 16S rRNA gene and selective functional genes as biomarkers, including hydrazine oxidoreductase and nitrite reductase encoding genes hzo and nirS, respectively. Results from these methods coupling with advances in quantitative PCR, reverse transcription of mRNA genes and stable isotope labeling have improved our understanding on the distribution, diversity, and activity of anammox bacteria in different environments both natural and engineered ones. In this review, we summarize these methods used in detection of anammox bacteria from various environments, highlight the strengths and weakness of these methods, and also discuss the new development potentials on the existing and new techniques in the future

Varieties of living things: Life at the intersection of lineage and metabolism

publication-status: Publishedtypes: Articl