Inhibition of sulfate-reducing bacteria with formate.

Despite hostile environmental conditions, microbial communities have been found in µL-sized water droplets enclosed in heavy oil of the Pitch Lake, Trinidad. Some droplets showed high sulfate concentrations and surprisingly low relative abundances of sulfate-reducing bacteria in a previous study. Hence, we investigated here whether sulfate reduction might be inhibited naturally. Ion chromatography revealed very high formate concentrations around 2.37 mM in 21 out of 43 examined droplets. Since these concentrations were unexpectedly high, we performed growth experiments with the three sulfate-reducing type strains Desulfovibrio vulgaris, Desulfobacter curvatus, and Desulfococcus multivorans, and tested the effects of 2.5, 8, or 10 mM formate on sulfate reduction. Experiments demonstrated that 8 or 10 mM formate slowed down the growth rate of D. vulgaris and D. curvatus and the sulfate reduction rate of D. curvatus and D. multivorans. Increasing formate concentrations delayed the onsets of growth and sulfate reduction of D. multivorans, which were even inhibited completely while formate was added constantly. Contrary to previous studies, D. multivorans was the only organism capable of formate consumption. Our study suggests that formate accumulates in the natural environment of the water droplets dispersed in oil and that such levels are very likely inhibiting sulfate-reducing microorganisms.

Aryl Coenzyme A Ligases, a Subfamily of the Adenylate-Forming Enzyme Superfamily.

Aryl coenzyme A (CoA) ligases belong to class I of the adenylate-forming enzyme superfamily (ANL superfamily). They catalyze the formation of thioester bonds between aromatic compounds and CoA and occur in nearly all forms of life. These ligases are involved in various metabolic pathways degrading benzene, toluene, ethylbenzene, and xylene (BTEX) or polycyclic aromatic hydrocarbons (PAHs). They are often necessary to produce the central intermediate benzoyl-CoA that occurs in various anaerobic pathways. The substrate specificity is very diverse between enzymes within the same class, while the dependency on Mg2+, ATP, and CoA as well as oxygen insensitivity are characteristics shared by the whole enzyme class. Some organisms employ the same aryl-CoA ligase when growing aerobically and anaerobically, while others induce different enzymes depending on the environmental conditions. Aryl-CoA ligases can be divided into two major groups, benzoate:CoA ligase-like enzymes and phenylacetate:CoA ligase-like enzymes. They are widely distributed between the phylogenetic clades of the ANL superfamily and show closer relationships within the subfamilies than to other aryl-CoA ligases. This, together with residual CoA ligase activity in various other enzymes of the ANL superfamily, leads to the conclusion that CoA ligases might be the ancestral proteins from which all other ANL superfamily enzymes developed.

Densely Populated Water Droplets in Heavy-Oil Seeps.

Most of the microbial degradation in oil reservoirs is believed to take place at the oil-water transition zone (OWTZ). However, a recent study indicates that there is microbial life enclosed in microliter-sized water droplets dispersed in heavy oil of Pitch Lake in Trinidad and Tobago. This life in oil suggests that microbial degradation of oil also takes place in water pockets in the oil-bearing rock of an oil leg independent of the OWTZ. However, it is unknown whether microbial life in water droplets dispersed in oil is a generic property of oil reservoirs rather than an exotic exception. Hence, we took samples from three heavy-oil seeps, Pitch Lake (Trinidad and Tobago), the La Brea Tar Pits (California, USA), and an oil seep on the McKittrick oil field (California, USA). All three tested oil seeps contained dispersed water droplets. Larger droplets between 1 and 10 µl revealed high cell densities of up to 109 cells ml-1 Testing for ATP content and LIVE/DEAD staining showed that these populations consist of active and viable microbial cells with an average of 60% membrane-intact cells and ATP concentrations comparable to those of other subsurface ecosystems. Microbial community analyses based on 16S rRNA gene amplicon sequencing revealed the presence of known anaerobic oil-degrading microorganisms. Surprisingly, the community analyses showed similarities between all three oil seeps, revealing common OTUs, although the sampling sites were thousands of kilometers apart. Our results indicate that small water inclusions are densely populated microhabitats in heavy oil and possibly a generic trait of degraded-oil reservoirs.IMPORTANCE Our results confirmed that small water droplets in oil are densely populated microhabitats containing active microbial communities. Since these microhabitats occurred in three tested oil seeps which are located thousands of kilometers away from each other, such populated water droplets might be a generic trait of biodegraded oil reservoirs and might be involved in the overall oil degradation process. Microbial degradation might thus also take place in water pockets in the oil-bearing oil legs of the reservoir rock rather than only at the oil-water transition zone.

Applying reverse stable isotope labeling analysis by mid-infrared laser spectroscopy to monitor BDOC in recycled wastewater.

Biological stability of treated wastewater is currently determined by methods such as biological oxygen demand, ATP-quantification, or flow-cytometric cell counting. However, the continuous increase in water reclamation for wastewater reuse requires new methods for quantifying degradation of biodegradable dissolved organic carbon (BDOC) ranging from very small to high concentrations of dissolved organic carbon (DOC). Furthermore, direct activity measures or absolute concentrations of BDOC are needed that produce comparable and reproducible results in all laboratories. Measuring carbon mineralization by CO2 evolution presents a suitable approach for directly measuring the microbial degradation activity. In this work, we investigated the extent of BDOC in water samples from effluent of a wastewater treatment plant and after purification by ultrafiltration over 204 days. BDOC monitoring was performed with the recently introduced reverse stable isotope labeling (RIL) analysis using mid-infrared spectroscopy for the monitoring of microbial CO2 production. Average BDOC degradation rates ranged from 0.11 to 0.32 mg L-1 d-1 for wastewater treatment plant effluent and from 0.03 to 0.22 mg L-1 d-1 after ultrafiltration. BDOC was degraded over >90 days indicating the long-term instability of the DOC. Degradation experiments over 88 days revealed first order kinetic rate constants for BDOC which corresponded to 12.7 ·â€¯10-3 d-1 for wastewater treatment plant effluent and 2.7 ·â€¯10-3 d-1 after ultrafiltration, respectively. A thorough sensitivity analysis of the RIL showed that the method is very accurate and sensitive with method detection limits down to 10 µg·â€¯L-1 of measured CO2.

Identification of naphthalene carboxylase subunits of the sulfate-reducing culture N47.

Expanding industrialization and the associated usage and production of mineral oil products has caused a worldwide spread of polycyclic aromatic hydrocarbons. These pollutants accumulate and persist under anoxic conditions but little is known about the biochemical reactions catalyzing their anaerobic degradation. Recently, carboxylation of naphthalene was demonstrated for the sulfate-reducing culture N47. Proteogenomic studies on N47 allowed the identification of a gene cluster with products suggested to be involved in the initial reaction of naphthalene degradation. Here, we performed comparative proteomic studies with N47 proteins extracted from naphthalene versus 2-methylnapththalene-grown cells on blue native PAGE. The analysis led to the identification of subunits of the naphthalene carboxylase of N47. Moreover, we show that the identified subunits are encoded in an operon structure within the previously mentioned naphthalene carboxylase gene cluster. These findings were supported by a pull-down experiment revealing in vitro interaction partners of a heterologously produced GST-tagged naphthalene carboxylase subunit. Based on these lines of evidence, naphthalene carboxylase is proposed to be a complex of about 750 kDa. Naphthalene carboxylase can be seen as a prototype of a new enzyme family of UbiD like de-/carboxylases catalyzing the anaerobic activation of non-substituted polycyclic aromatic hydrocarbons.

[Medication reconciliation in a department of internal medicine and infectious and tropical diseases: Feedback after one year practice]. / Conciliation médicamenteuse d'entrée en service de médecine interne : retour d'expérience après un an de pratique.

Since April 2015, medication reconciliation is performed in our Department. The objective of this study is to assess the impact of this activity on patients' care after one year of practice. METHODS: All patients who received medication reconciliation between April-October 2015 and June-December 2016 were included in this retrospective study. Undocumented unintentional discrepancies (DNIND) which result from the comparison between the patient's usual treatments and the medication prescribed at admission were collected. Then, a multidisciplinary discussion was initiated to correct them. The gravity of each DNIND was determined a posteriori. RESULTS: A statistical comparison between the two studies (2015 vs. 2016) showed the following significant results: decrease in DNIND (0.9 vs. 0.43), in percentage of patients with at least one DNIND (43% vs 31% P <5.10-6), in reconciliation time (43min vs. 23min) and no significant difference in the distribution of DNIND typology. The main therapeutic classes are: metabolism-diabetes-nutrition (21%), cardiology (18%), pneumology (17%) and neurology-psychiatry (15%). Drugs mainly concerned with DNIND are inhaled anti-asthmatics (13% of the medicines with DNIND), vitamins (8% of DNIND) and the levetiracetam antiepileptic drug (5% of DNIND). CONCLUSION: The implementation of the reconciliation medication allowed a significant reduction of the DNIND that permits to improve the patient healthcare pathway.

The combination of micro-resonators with spatially resolved ferromagnetic resonance.

We present two new and complementary approaches to realize spatial resolution for ferromagnetic resonance (FMR) on the 100 nm-scale. Both experimental setups utilize lithographically fabricated micro-resonators. They offer a detection sensitivity that is increased by four orders of magnitude compared with resonator-based FMR. In the first setup, the magnetic properties are thermally modulated via the thermal near-field effect generated by the thermal probe of an atomic force microscope. In combination with lock-in detection of the absorbed microwave power in the micro-resonator, a spatial resolution of less than 100 nm is achieved. The second setup is a combination of a micro-resonator with a scanning transmission x-ray microscope (STXM). Here a conventional FMR is excited by the micro-resonator while focused x-rays are used for a time-resolved snap-shot detection of the FMR excitations via the x-ray magnetic circular dichroism effect. This technique allows a lateral resolution of nominally 35 nm given by the STXM. Both experimental setups combine the advantage of low-power FMR excitation in the linear regime with high spatial resolution to study single and coupled nanomagnets. As proof-of-principle experiments, two perpendicular magnetic micro-stripes (5 µm × 1 µm) were grown and their FMR excitations were investigated using both setups.

[Modifications of immunity in obesity: The impact on the risk of infection]. / Modifications de l'immunité dans l'obésité: impact sur le risque infectieux.

Incidence of obesity is constantly rising all over the world; obesity has developed into an important problem of public health. Clinical experience, supported by many clinical trials, shows that obesity constitutes a risk factor for numerous cardiovascular, metabolic, cancer and even infectious diseases. In this revue we summarize the present knowledge on immunological properties and functions of adipose tissue and their modifications in obese subjects, with a bending to a potentially deleterious chronic inflammatory state. We will discuss the negative impact of this chronic inflammation on physiological acute inflammatory reaction during infectious episodes. However, the modifications of anti-infectious immune response in obese subjects are not well known at present and need further investigations.

Prevalence and pathogenicity of binary toxin-positive Clostridium difficile strains that do not produce toxins A and B.

Clostridium difficile causes antibiotic-associated diarrhoea and pseudomembranous colitis. The main virulence factors of C. difficile are the toxins A (TcdA) and B (TcdB). A third toxin, called binary toxin (CDT), can be detected in 17% to 23% of strains, but its role in human disease has not been clearly defined. We report six independent cases of patients with diarrhoea suspected of having C. difficile infection due to strains from toxinotype XI/PCR ribotype 033 or 033-like, an unusual toxinotype/PCR ribotype positive for CDT but negative for TcdA and TcdB. Four patients were considered truly infected by clinicians and were specifically treated with oral metronidazole. One of the cases was identified during a prevalence study of A(-)B(-)CDT(+) strains. In this study, we screened a French collection of 220 nontoxigenic strains and found only one (0.5%) toxinotype XI/PCR ribotype 033 or 033-like strain. The description of such strains raises the question of the role of binary toxin as a virulence factor and could have implications for laboratory diagnostics that currently rarely include testing for binary toxin.

[Cannabinoid hyperemesis syndrome: about 6 cases]. / Syndrome d'hyperémèse cannabique : à propos de 6 cas.

INTRODUCTION: The cannabinoid hyperemesis syndrome (CHS) is characterized by cyclic episodes of nausea, vomiting, and abdominal pain, and occurs in young adults with long-term cannabis use. The feature of this syndrome is the relief of symptoms with hot showers. We report here six cases report. CASE REPORTS: Three women and 3 men, chronic consumers of cannabis, presented with typical features of the CHS, but the syndrome remained undiagnosed until then: nausea, vomiting, abdominal pain with morning ascendancy and loss of weight occurring in adult's of less than 50 years. The symptoms were improved by taking repeated hot showers. The medical investigations were negative. After addictologist care and cannabis weaning, digestive symptoms disappeared. CONCLUSION: The CHS is based on a clinical diagnosis. When undiagnosed, clinical presentation leads to a medical wandering and to the realization of repeated, expensive, and sometimes invasive exams. The physiopathology is not clear. The treatment relies on the definitive cannabis weaning.

Model selection for microbial nutrient uptake using a cost-benefit approach.

We consider the uptake of various carbon sources by microorganisms based on four fundamental assumptions: (1) the uptake of nutrient follows a saturation characteristics (2) substrate processing has a benefit but comes at costs of maintaining the process chain (3) substrate uptake is controlled and (4) evolution optimized the control of substrate uptake. These assumptions result in relatively simple mathematical models. In case of two substrates, our main finding is the following: Depending on the overall topology of the metabolic pathway, three different behavioral patterns can be identified. (1) both substrates are consumed at a time, (2) one substrate is preferred and represses the uptake of the other (catabolite repression), or (3) a cell feeds exclusively on one or the other substrate, possibly leading to a population that splits in two sub-populations, each of them specialized on one substrate only. Batch-culture and retentostat data of toluene, benzoate, and acetate uptake by Geobacter metallireducens are used to demonstrate that the model structure is suited for a quantitative description of uptake dynamics.

[Thymic hyperplasia and Graves' disease: a non-fortuitous association. case report and review of literature]. / Hyperplasie thymique et maladie de Basedow : une association non fortuite. Cas clinique et revue de la littérature.

Thymus hyperplasia and Graves' disease association is not well known and is probably not incidental. We report the case of a young woman affected with Graves' disease in which a retrosternal mass was disclosed during a neck ultrasonographic-examination and confirmed by chest CT-examination. Follow-up ultrasound survey showed a decrease in the thymic mass size. Because of various antithyroid drugs allergy, a surgical procedure was performed, during which both her thyroid and thymic mass were removed. The histopathologic examination of this mass confirmed the hyperplasic nature of the thymic bulging. Ninety-one cases of thymus hyperplasia and Graves' disease association have been reported in literature, of which 20 were histologically confirmed. Among these cases 35 showed a thymic mass regression under medical treatment alone. Accordingly, surgical procedures are most frequently unnecessary in such associations because of the thymic mass decrease incurred by antithyroid drug treatment.

Visualization of spin dynamics in single nanosized magnetic elements.

The design of future spintronic devices requires a quantitative understanding of the microscopic linear and nonlinear spin relaxation processes governing the magnetization reversal in nanometer-scale ferromagnetic systems. Ferromagnetic resonance is the method of choice for a quantitative analysis of relaxation rates, magnetic anisotropy and susceptibility in a single experiment. The approach offers the possibility of coherent control and manipulation of nanoscaled structures by microwave irradiation. Here, we analyze the different excitation modes in a single nanometer-sized ferromagnetic stripe. Measurements are performed using a microresonator set-up which offers a sensitivity to quantitatively analyze the dynamic and static magnetic properties of single nanomagnets with volumes of (100 nm)(3). Uniform as well as non-uniform volume modes of the spin wave excitation spectrum are identified and found to be in excellent agreement with the results of micromagnetic simulations which allow the visualization of the spatial distribution of these modes in the nanostructures.

[Hypokalemia induced quadriparesis as the presenting manifestation of Gougerot-Sjögren's syndrome]. / Tétraparésie hypokaliémique révélant un syndrome de Gougerot-Sjögren.

We report a 30-year-old woman who presented with a hypokaliemia-related subacute quadriparesis. The various causes of hypokalemia induced paresis were discussed but the association of hypokalemia with metabolic acidosis and normal anion gap was diagnostic of distal renal tubular acidosis. The renal tubulopathy was the presenting manifestation of a primary Sjogren's syndrome. Distal renal tubular acidosis concerns a third of the patients affected by this auto-immune disease.

[Ovarian and peritoneal sarcoidosis mimicking an ovarian cancer]. / Sarcoïdose péritonéale et ovarienne simulant un cancer de l'ovaire.

Ovarian and peritoneal sarcoidosis is a very rare condition, with an atypical clinical presentation close to that of ovarian cancer. An erroneous diagnosis could induce a definitive castration. A 38-year-old woman was admitted because of ascites and weight loss. A computerized tomography scan revealed multiple soft tissue nodules in the pelvis, on the ovaries as well as peritoneal deposits. Histological examination after laparoscopic biopsy was indicative of sarcoidosis. Corticosteroids were given to the patient and the symptoms quickly subsided. This case with its clinical presentation is discussed in comparison with previously reported cases.

Combined application of conservative transport modelling and compound-specific carbon isotope analyses to assess in situ attenuation of benzene, toluene, and o-xylene.

In recent years, compound specific isotope analyses (CSIA) have developed into one of the most powerful tools for the quantification of in situ biodegradation of organic contaminants. In this approach, the calculation of the extent of biodegradation of organic contaminants in aquifers is usually based on the Rayleigh equation, and thus neglects physical transport processes such as dispersion that contribute to contaminant dilution in aquifers. Here we combine compound specific isotope analyses with a conservative transport model to study the attenuation of aromatic hydrocarbons at a former gasworks site. The conservative transport model was first used to simulate concentration reductions caused by dilution at wells downgradient of a BTEX source. In a second step, the diluted concentrations, together with the available stable carbon isotope ratios and carbon fractionation factors for benzene, toluene and o-xylene were applied in the Rayleigh equation to quantify the degree of biodegradation at each of those wells. At the investigated site, where other attenuation processes such as sorption and volatilisation were proven to be negligible, the combined approach is recommended for benzene, which represents a compound for which the effect of biodegradation is comparable to or less than the effect of dilution. As demonstrated for toluene and o-xylene, the application of the Rayleigh equation alone is sufficient if dilution can be proved to be insignificant in comparison to biodegradation. The analysis also suggests that the source width and the position of the observation wells relative to the plume center line are significantly related to the degree of dilution.

Stable carbon isotope fractionation during aerobic and anaerobic transformation of trichlorobenzene.

Fractionation of stable carbon isotopes upon degradation of trichlorobenzenes was studied under aerobic and anaerobic conditions. Mineralization of 1,2,4-trichlorobenzene by the aerobic strain Pseudomonas sp. P51 which uses a dioxygenase for the initial enzymatic reaction was not accompanied by a significant isotope fractionation. In contrast, reductive dehalogenation by the anaerobic strain Dehalococcoides sp. strain CBDB1 revealed average isotope enrichment factors (eta) between -3.1 and -3.7 for 1,2,3- and 1,2,4-trichlorobenzene, respectively. The significant isotope fractionation during reductive dehalogenation would allow tracing the in situ biodegradation of halogenated benzenes in contaminated anoxic aquifers, whereas the lack of isotope fractionation during aerobic transformation limits the use of this approach in oxic environments.

In-situ biodegradation of tetrachloroethene and trichloroethene in contaminated aquifers monitored by stable isotope fractionation.

Stable carbon isotope analysis of tetrachloroethene (PCE) and trichloroethene (TCE) was applied to evaluatenatural attenuation processes in the upper Quaternary and lower Tertiary aquifer in the area of a former dry-cleaning plant located in Leipzig, Germany. Groundwater samples were taken during one monitoring campaign in 2001. The 13C enrichment in contaminants along the water flow path suggested that both, PCE and TCE were degraded in the Quaternary aquifer. The enrichment of 13C in the residual PCE fraction and an isotope fractionation factor from laboratory experiments were used to calculate the extent of biodegradation in the Quatemary aquifer. These calculations indicated that a major portion of PCE was biodegraded in the course of the plume. In the Tertiary aquifer the carbon isotope ratios of PCE and TCE indicated that the decreasing concentrations of these contaminants were probably not caused by microbial processes.