Urea production and turnover following the addition of AMP, CMP, RNA and a protein mixture to a marine sediment

The potential of adenosine 5′-monophosphate (AMP), cytidine 5′-monophosphate (CMP), 16S ribosomal RNA, and a protein (bovine serum albumin) to serve as substrates for bacterial urea production was evaluated in a defaunated, anoxic marine sediment. AMP, CMP and RNA stimulated urea production and urea turnover, but CMP to a lesser degree than AMP and RNA. The increase in urea production and turnover rates took place immediately after AMP, CMP, and RNA were added to the sediment. The rapid response in urea production and turnover rates suggests that the necessary uptake mechanisms and enzymes to utilize the substrates were present constitutively. Addition of the protein mixture did not result in any measurable changes in the urea pool size, urea turnover rate, or urea production rate during the 165 h of incubation. However, an increased and continuous net NH4+ production in the protein-amended sediment relative to the control sediment indicated that the added protein mixture was accessible for bacterial degradation. The results showed that purines and pyrimidines were substrates for the bacterial urea production in the marine sediment, whereas protein was not important for urea production

Identity, abundance and reactivation kinetics of thermophilic fermentative endospores in cold marine sediment and seawater

Cold marine sediments harbor endospores of fermentative and sulfate-reducing, thermophilic bacteria. These dormant populations of endospores are believed to accumulate in the seabed via passive dispersal by ocean currents followed by sedimentation from the water column. However, the magnitude of this process is poorly understood because the endospores present in seawater were so far not identified, and only the abundance of thermophilic sulfate-reducing endospores in the seabed has been quantified. We investigated the distribution of thermophilic fermentative endospores (TFEs) in water column and sediment of Aarhus Bay, Denmark, to test the role of suspended dispersal and determine the rate of endospore deposition and the endospore abundance in the sediment. We furthermore aimed to determine the time course of reactivation of the germinating TFEs. TFEs were induced to germinate and grow by incubating pasteurized sediment and water samples anaerobically at 50 degrees C. We observed a sudden release of the endospore component dipicolinic acid immediately upon incubation suggesting fast endospore reactivation in response to heating. Volatile fatty acids (VFAs) and H-2 began to accumulate exponentially after 3.5 h of incubation showing that reactivation was followed by a short phase of outgrowth before germinated cells began to divide. Thermophilic fermenters were mainly present in the sediment as endospores because the rate of VFA accumulation was identical in pasteurized and non-pasteurized samples. Germinating TFEs were identified taxonomically by reverse transcription, PCR amplification and sequencing of 16S rRNA. The water column and sediment shared the same phylotypes, thereby confirming the potential for seawater dispersal. The abundance of TFEs was estimated by most probable number enumeration, rates of VFA production, and released amounts of dipicolinic acid during germination. The surface sediment contained similar to 105-106 inducible TFEs cm(-3). TFEs thus outnumber thermophilic sulfate-reducing endospores by an order of magnitude. The abundance of cultivable TFEs decreased exponentially with sediment depth with a half-life of 350 years. We estimate that 6 X 109 anaerobic thermophilic endospores are deposited on the seafloor per m2 per year in Aarhus Bay, and that these thermophiles represent >10% of the total endospore community in the surface sediment

Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases

Biological nitrate transport in sediments on the Peruvian margin mitigates benthic sulfide emissions and drives pelagic N loss during stagnation events

Highlights • Very high rates of dissimilatory nitrate reduction to ammonium by Thioploca. • Non-steady state model predicts Thioploca survival on intracellular nitrate reservoir. • Ammonium release by Thioploca may be coupled to pelagic N loss by anammox. • Thioploca may contribute to anammox long after bottom water nitrate disappearance. • Model indicates that benthic foraminifera account for 90% of benthic N2 production. Abstract Benthic N cycling in the Peruvian oxygen minimum zone (OMZ) was investigated at ten stations along 12oS from the middle shelf (74 m) to the upper slope (1024 m) using in situ flux measurements, sediment biogeochemistry and modelling. Middle shelf sediments were covered by mats of the filamentous bacteria Thioploca spp. and contained a large ‘hidden’ pool of nitrate that was not detectable in the porewater. This was attributed to a biological nitrate reservoir stored within the bacteria to oxidize sulfide to sulfate during ‘dissimilatory nitrate reduction to ammonium’ (DNRA). The extremely high rates of DNRA on the shelf (15.6 mmol m-2 d-1 of N), determined using an empirical steady-state model, could easily supply all the ammonium requirements for anammox in the water column. The model further showed that denitrification by foraminifera may account for 90% of N2 production at the lower edge of the OMZ. At the time of sampling, dissolved oxygen was below detection limit down to 400 m and the water body overlying the shelf had stagnated, resulting in complete depletion of nitrate and nitrite. A decrease in the biological nitrate pool was observed on the shelf during fieldwork concomitant with a rise in porewater sulfide levels in surface sediments to 2 mM. Using a non-steady state model to simulate this natural anoxia experiment, these observations were shown to be consistent with Thioploca surviving on a dwindling intracellular nitrate reservoir to survive the stagnation period. The model shows that sediments hosting Thioploca are able to maintain high ammonium fluxes for many weeks following stagnation, potentially sustaining pelagic N loss by anammox. In contrast, sulfide emissions remain low, reducing the economic risk to the Peruvian fishery by toxic sulfide plume development

Neurophysiology and muscle histopathology in ICU-acquired muscle weakness:Lessons learned from COVID-19

Objective: To describe different electrophysiological, histopathological, and ultrastructural patterns of muscle pathology in COVID-19-associated intensive care unit acquired weakness (ICUAW) and raise the question of whether COVID-19-associated critical illness myopathy (CIM) is a distinct entity or is similar to CIM of other causes. Methods: A series of three patients with COVID-19-associated ICUAW were presented. Clinical examination, electrophysiological testing, and muscle pathology with light and electron microscopy were reported systematically. Results: All three patients were clinically affected with severe proximal and distal weakness of upper and lower extremities, increased plasma levels of muscle enzymes, and had myopathic electromyography. Furthermore, in two patients, electrophysiological signs of inflammatory myopathy with profuse denervation activity were present. Muscle pathologies were prominent but very diverse. One patient had signs of CIM, another showed severe inflammatory myopathy, and the main finding in the third patient was mitochondrial changes. Conclusion: Although the three cases showed similar clinical and electrophysiological patterns, muscle pathology revealed distinct underlying features. This spectrum of muscle disease among patients with severe COVID-19 includes CIM, autoimmune response to the COVID-19 infection, and mitochondrial dysfunction. Significance: Electrophysiology and histopathology complement each other and are important for determining the etiology, as well as guiding treatment and prognosis.</p

Development and validation of a porcine artificial colonic mucus model reflecting the properties of native colonic mucus in pigs

Colonic mucus plays a key role in colonic drug absorption. Mucus permeation assays could therefore provide useful insights and support rational formulation development in the early stages of drug development. However, the collection of native colonic mucus from animal sources is labor-intensive, does not yield amounts that allow for routine experimentation, and raises ethical concerns. In the present study, we developed an in vitro porcine artificial colonic mucus model based on the characterization of native colonic mucus. The structural properties of the artificial colonic mucus were validated against the native secretion for their ability to capture key diffusion patterns of macromolecules in native mucus. Moreover, the artificial colonic mucus could be stored under common laboratory conditions, without compromising its barrier properties. In conclusion, the porcine artificial colonic mucus model can be considered a biorelevant way to study the diffusion behavior of drug candidates in colonic mucus. It is a cost-efficient screening tool easily incorporated into the early stages of drug development and it contributes to the implementation of the 3Rs (refinement, reduction, and replacement of animals) in the drug development process

Is there a common water-activity limit for the three domains of life?

Archaea and Bacteria constitute a majority of life systems on Earth but have long been considered inferior to Eukarya in terms of solute tolerance. Whereas the most halophilic prokaryotes are known for an ability to multiply at saturated NaCl (water activity (a w) 0.755) some xerophilic fungi can germinate, usually at high-sugar concentrations, at values as low as 0.650-0.605 a w. Here, we present evidence that halophilic prokayotes can grow down to water activities of <0.755 for Halanaerobium lacusrosei (0.748), Halobacterium strain 004.1 (0.728), Halobacterium sp. NRC-1 and Halococcus morrhuae (0.717), Haloquadratum walsbyi (0.709), Halococcus salifodinae (0.693), Halobacterium noricense (0.687), Natrinema pallidum (0.681) and haloarchaeal strains GN-2 and GN-5 (0.635 a w). Furthermore, extrapolation of growth curves (prone to giving conservative estimates) indicated theoretical minima down to 0.611 a w for extreme, obligately halophilic Archaea and Bacteria. These were compared with minima for the most solute-tolerant Bacteria in high-sugar (or other non-saline) media (Mycobacterium spp., Tetragenococcus halophilus, Saccharibacter floricola, Staphylococcus aureus and so on) and eukaryotic microbes in saline (Wallemia spp., Basipetospora halophila, Dunaliella spp. and so on) and high-sugar substrates (for example, Xeromyces bisporus, Zygosaccharomyces rouxii, Aspergillus and Eurotium spp.). We also manipulated the balance of chaotropic and kosmotropic stressors for the extreme, xerophilic fungi Aspergillus penicilloides and X. bisporus and, via this approach, their established water-activity limits for mycelial growth (∼0.65) were reduced to 0.640. Furthermore, extrapolations indicated theoretical limits of 0.632 and 0.636 a w for A. penicilloides and X. bisporus, respectively. Collectively, these findings suggest that there is a common water-activity limit that is determined by physicochemical constraints for the three domains of life

La messe est dite

Auteur d’une thèse remarquable et remarquée sur La conversion des intellectuels au catholicisme en France, 1885-1935 (Paris, CNRS Éditions, 1998, réédition en 2010), Frédéric Gugelot s’est intéressé plus particulièrement depuis à la figure de l’écrivain catholique. Il a dirigé notamment, avec Alain Dierkens, Fabrice Preyat et Cécile Vanderpelen-Diagre, le précieux ouvrage collectif La Croix et la bannière. L’écrivain catholique en francophonie (xviie-xxie siècles), paru en 2007 aux Éditions d..