Desulfuromonas svalbardensis sp nov and Desulfuromusa ferrireducens sp nov., psychrophilic, Fe(III)-reducing bacteria isolated from Arctic sediments, Svalbard

Two psychrophilic, Gram-negative, rod-shaped, motile bacteria (strains 112T and 102T) that conserved energy from dissimilatory Fe(III) reduction concomitant with acetate oxidation were isolated from permanently cold Arctic marine sediments. Both strains grew at temperatures down to -2 degrees C, with respective temperature optima of 14 degrees C and 14-17 degrees C for strains 112T and 102T. The isolated strains reduced Fe(III) using common fermentation products such as acetate, lactate, propionate, formate or hydrogen as electron donors, and they also grew with fumarate as the sole substrate. As alternatives to Fe(III), they reduced fumarate, S0 and Mn(IV). Based on 16S rRNA gene sequence similarity, strain 112T was most closely related to Desulfuromonas acetoxidans (97.0 %) and Desulfuromonas thiophila NZ27T (95.5 %), and strain 102T to Malonomonas rubra Gra Mal 1T (96.3 %) and Desulfuromusa succinoxidans GylacT (95.9 %) within the Deltaproteobacteria. Strains 112T and 102T therefore represent novel species, for which the names Desulfuromonas svalbardensis sp. nov. (type strain 112T=DSM 16958T=JCM 12927T) and Desulfuromusa ferrireducens sp. nov. (type strain 102T=DSM 16956T=JCM 12926T) are proposed

Radiographic signs of acetabular retroversion using a low-dose slot-scanning radiographic system (EOS^®)

Introduction: Acetabular retroversion is assessed using pelvic X-ray. Cross-over-sign (COS), posterior-wall-sign (PWS) and ischial-spine-sign (ISS) are important radiographic signs of the condition. The pelvic area is sensitive to radiation and thus, possibilities to reduce dose should be considered. The purpose was to compare radiographic signs of acetabular retroversion on conventional pelvic anteroposterior (AP) X-rays with a low-dose slot-scanning system (EOS) in a sample of patients with retroversion of the acetabulum and to compare the radiation doses. Methods: 34 participants with radiographic signs of acetabular retroversion in one or both hips on conventional pelvic X-ray were consecutively recruited. Pelvic EOS-images were acquired in each patient and COS, PWS, ISS, COS-ratio and PWS-ratio was assessed. Radiation dose comparison of X-ray vs. EOS was performed using Dose-Area Products. Results: Retroversion was present in 57 out of 68 hips. The absolute agreement was 91%, 84% and 76% for COS, PWS and ISS, respectively. No statistically significant differences were present between COS-ratio and PWS-ratio in either modality and Bland–Altman limits of agreement were narrow. The mean radiation dose was 1053 mGy*cm2 in X-ray and 593 mGy*cm2 in EOS (p = 0.003). Conclusion: The results indicate that pelvic EOS provides diagnostic qualities similar to conventional X-ray using 44% less radiation when radiographic signs of acetabular retroversion are assessed

Local diagnostic reference levels for skeletal surveys in suspected physical child abuse

NoIntroduction: The purpose was to determine if an age based, local diagnostic reference level for paediatric skeletal surveys could be established using retrospective data. Methods: All children below two years of age referred for a primary skeletal survey as a result of suspected physical abuse during 2017 or 2018 (n ¼ 45) were retrospectively included from a large Danish university hospital. The skeletal survey protocol included a total of 33 images. Dose Area Product (DAP) and acquisition parameters for all images were recorded from the Picture Archival and Communication System (PACS) and effective dose was estimated. The 75th percentile for DAP was considered as the diagnostic reference level (DRL). Results: The 75th percentile for DAP was 314 mGy*cm2 , 520 mGy*cm2 and 779 mGy*cm2 for children <1 month, 1e11 months and 12 < 24 months of age respectively. However, only the age group 1e11 months had a sufficient number of children (n ¼ 27) to establish a local DRL. Thus, for the other groups the DAP result must be interpreted with caution. Effective dose was 0.19, 0.26 and 0.18 mSv for children <1, 1e11 months and 12 < 24 months of age respectively. Conclusion: For children between 1 and 11 months of age, a local diagnostic reference level of 520 mGy*cm2 was determined. This may be used as an initial benchmark for primary skeletal surveys as a result of suspected physical abuse for comparison and future discussion. Implications for practice: While the data presented reflects the results of a single department, the suggested diagnostic reference level may be used as a benchmark for other departments when auditing skeletal survey radiation dose

Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud 510 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group I intron also carried a MITE sequence that, like the hupL MITE family, occurs broadly across the genome. The presence of a high degree of mobile elements in genes central to Thiomargarita's core metabolism has not been previously reported in free-living bacteria and suggests a highly mutable genome

Renal stone detection using a low kilo-voltage paediatric CT protocol – A porcine phantom study

yesIntroduction: Reducing tube voltage is an effective dose saving method in computed tomography (CT) assuming tube current is not concurrently increased. Recent innovations in scanner technology now enable CT tube voltage reduction to 70 kV thereby increasing opportunities for dose reduction in paediatric patients, but it is unclear if the increased image noise associated with 70 kV impacts on ability to visualise renal stones accurately. The purpose was to assess detectability of nephrolithiasis using a bespoke paediatric phantom and low kV, non-contrast CT and to assess inter-observer agreement. Methods: Forty-two renal stones of different size and chemical composition were inserted into porcine kidneys and positioned in a bespoke, water-filled phantom mimicking a 9-year-old child weighing approximately 33kg. The phantom was scanned using 120 and 70 kV CT protocols, and the detectability of the stones was assessed by three radiologists. Absolute agreement and Fleiss’ kappa regarding detectability were assessed. Results: The mean diameter of renal stones as measured physically was 4.24 mm ranging from 1 to 11 mm. Four stones were missed by at least one observer. One observer had a sensitivity of 93 and 95% at 70 and 120 kV, respectively, while the sensitivity for observers 2 and 3 was 98% at both kV levels. Specificity was 100% across readers and kV levels. Absolute agreement between the readers at 70 kV was 92% (kappa = 0.86) and 98% (kappa = 0.96) at 120 kV indicating a strong agreement at both kV levels. Conclusions: The results suggest that lowering the kV does not affect the detection rate of renal stones and may be a useful dose reduction strategy for assessment of nephrolithiasis in children

Harvesting Electricity with Geobacter bremensis Isolated from Compost

Electrochemically active (EA) biofilms were formed on metallic dimensionally stable anode-type electrode (DSA), embedded in garden compost and polarized at +0.50 V/SCE. Analysis of 16S rRNA gene libraries revealed that biofilms were heavily enriched in Deltaproteobacteria in comparison to control biofilms formed on non-polarized electrodes, which were preferentially composed of Gammaproteobacteria and Firmicutes. Among Deltaproteobacteria, sequences affiliated with Pelobacter and Geobacter genera were identified. A bacterial consortium was cultivated, in which 25 isolates were identified as Geobacter bremensis. Pure cultures of 4 different G. bremensis isolates gave higher current densities (1400 mA/m2 on DSA, 2490 mA/m2 on graphite) than the original multi-species biofilms (in average 300 mA/m2 on DSA) and the G. bremensis DSM type strain (100–300 A/m2 on DSA; 2485 mA/m2 on graphite). FISH analysis confirmed that G. bremensis represented a minor fraction in the original EA biofilm, in which species related to Pelobacter genus were predominant. The Pelobacter type strain did not show EA capacity, which can explain the lower performance of the multi-species biofilms. These results stressed the great interest of extracting and culturing pure EA strains from wild EA biofilms to improve the current density provided by microbial anodes

Constraint-based modeling analysis of the metabolism of two Pelobacter species

BACKGROUND: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. RESULTS: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models. CONCLUSIONS: We have developed genome-scale metabolic models of P. carbinolicus and P. propionicus. These models of Pelobacter metabolism can now be incorporated into the growing repertoire of genome scale models of the Geobacteraceae family to aid in describing the growth and activity of these organisms in anoxic environments and in the study of their roles and interactions in the subsurface microbial community

Modulation of the surface proteome through multiple ubiquitylation pathways in African Trypanosomes

Recently we identified multiple suramin-sensitivity genes with a genome wide screen in Trypanosoma brucei that includes the invariant surface glycoprotein ISG75, the adaptin-1 (AP-1) complex and two deubiquitylating enzymes (DUBs) orthologous to ScUbp15/HsHAUSP1 and pVHL-interacting DUB1 (type I), designated TbUsp7 and TbVdu1, respectively. Here we have examined the roles of these genes in trafficking of ISG75, which appears key to suramin uptake. We found that, while AP-1 does not influence ISG75 abundance, knockdown of TbUsp7 or TbVdu1 leads to reduced ISG75 abundance. Silencing TbVdu1 also reduced ISG65 abundance. TbVdu1 is a component of an evolutionarily conserved ubiquitylation switch and responsible for rapid receptor modulation, suggesting similar regulation of ISGs in T. brucei. Unexpectedly, TbUsp7 knockdown also blocked endocytosis. To integrate these observations we analysed the impact of TbUsp7 and TbVdu1 knockdown on the global proteome using SILAC. For TbVdu1, ISG65 and ISG75 are the only significantly modulated proteins, but for TbUsp7 a cohort of integral membrane proteins, including the acid phosphatase MBAP1, that is required for endocytosis, and additional ISG-related proteins are down-regulated. Furthermore, we find increased expression of the ESAG6/7 transferrin receptor and ESAG5, likely resulting from decreased endocytic activity. Therefore, multiple ubiquitylation pathways, with a complex interplay with trafficking pathways, control surface proteome expression in trypanosomes

Data for: Local diagnostic reference levels for skeletal surveys in suspected physical child abuse

Exposure data for calculation of diagnostic reference levels in children referred for full skeletal surveyTHIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV