Mn(II)-oxidizing Bacteria are Abundant and Environmentally Relevant Members of Ferromanganese Deposits in Caves of the Upper Tennessee River Basin

The upper Tennessee River Basin contains the highest density of our nation's caves; yet, little is known regarding speleogenesis or Fe and Mn biomineralization in these predominantly epigenic systems. Mn:Fe ratios of Mn and Fe oxide-rich biofilms, coatings, and mineral crusts that were abundant in several different caves ranged from ca. 0.1 to 1.0 as measured using ICP-OES. At sites where the Mn:Fe ratio approached 1.0 this represented an order of magnitude increase above the bulk bedrock ratio, suggesting that biomineralization processes play an important role in the formation of these cave ferromanganese deposits. Estimates of total bacterial SSU rRNA genes in ferromanganese biofilms, coatings, and crusts measured approximately 7×107–9×109 cells/g wet weight sample. A SSU-rRNA based molecular survey of biofilm material revealed that 21% of the 34 recovered dominant (non-singleton) OTUs were closely related to known metal-oxidizing bacteria or clones isolated from oxidized metal deposits. Several different isolates that promote the oxidation of Mn(II) compounds were obtained in this study, some from high dilutions (10–8–10–10) of deposit material. In contrast to studies of caves in other regions, SSU rRNA sequences of Mn-oxidizing bacterial isolates in this study most closely matched those of Pseudomonas, Leptothrix, Flavobacterium, and Janthinobacterium. Combined data from geochemical analyses, molecular surveys, and culture-based experiments suggest that a unique consortia of Mn(II)-oxidizing bacteria are abundant and promoting biomineralization processes within the caves of the upper Tennessee River Basin

Sustained Anthropogenic Impact in Carter Saltpeter Cave, Carter County, Tennessee and the Potential Effects On Manganese Cycling

Anthropogenic impact is a pervasive problem in heavily trafficked cave systems and fecal contamination is equally problematic in many cave and karst waters worldwide. Carter Saltpeter Cave in Carter County, Tennessee exhibits Mn(III/IV) oxide coatings associated with groundwater seeps, as well as manganese oxide growth on litter. Culturing results revealed that Mn(III/IV) oxide production on litter was associated with Mn(II)-oxidizing fungi. Immediately prior to this study, a massive Mn(II)-oxidizing biofilm bloomed at a cave seep. During the course of this study from 2009–2011, the seep exhibited a dramatic visual reduction in Mn(III/IV) oxide production, which was hypothesized to correlate with a decrease in fecal nutrient input. Molecular methods (16S rRNA gene sequencing) confirmed the presence of Bacteroides-Prevotella human fecal indicators in this seep, and most probable number assays and ion chromatography of the associated seep water confirmed nutrient loading at the site. Further, phylogenetic analysis from clone sequences suggested a strong initial human-specific fecal signature (50% of the sequences clustering with human feces sequences) in July 2009, and a weaker human signature (20% clustering) by June 2011. Most Probable Number (MPN) analyses of heterotrophic bacteria at this site suggested that Mn(II) oxidation was correlated with heterotrophic activity, due to point source exogenous nutrient loading

Mn(II)-Oxidizing Bacteria Are Abundant And Environmentally Relevant Members Of Ferromanganese Deposits In Caves Of The Upper Tennessee River Basin

The upper Tennessee River Basin contains the highest density of our nation’s caves; yet, little is known regarding speleogenesis or Fe and Mn biomineralization in these predominantly epigenic systems. Mn:Fe ratios of Mn and Fe oxide-rich bio?lms, coatings, and mineral crusts that were abundant in several different caves ranged from ca. 0.1 to 1.0 as measured using ICP-OES. At sites where the Mn:Fe ratio approached 1.0 this represented an order of magnitude increase above the bulk bedrock ratio, suggesting that biomineralization processes play an important role in the formation of these cave ferromanganese deposits. Estimates of total bacterial SSU rRNA genes in ferromanganese bio?lms, coatings, and crusts measured approximately 7×107–9×109 cells/g wet weight sample. A SSU-rRNA based molecular survey of bio?lm material revealed that 21% of the 34 recovered dominant (non-singleton) OTUs were closely related to known metal-oxidizing bacteria or clones isolated from oxidized metal deposits. Several different isolates that promote the oxidation of Mn(II) compounds were obtained in this study, some from high dilutions (10–8–10–10) of deposit material. In contrast to studies of caves in other regions, SSU rRNA sequences of Mn-oxidizing bacterial isolates in this study most closely matched those of Pseudomonas, Leptothrix, Flavobacterium, and Janthinobacterium. Combined data from geochemical analyses, molecular surveys, and culture-based experiments suggest that a unique consortia of Mn(II)-oxidizing bacteria are abundant and promoting biomineralization processes within the caves of the upper Tennessee River Basin

Early ultrasound surveillance of newly-created haemodialysis arteriovenous fistula

IntroductionWe assess if ultrasound surveillance of newly-created arteriovenous fistulas (AVFs) can predict nonmaturation sufficiently reliably to justify randomized controlled trial (RCT) evaluation of ultrasound-directed salvage intervention.MethodsConsenting adults underwent blinded fortnightly ultrasound scanning of their AVF after creation, with scan characteristics that predicted AVF nonmaturation identified by logistic regression modeling.ResultsOf 333 AVFs created, 65.8% matured by 10 weeks. Serial scanning revealed that maturation occurred rapidly, whereas consistently lower fistula flow rates and venous diameters were observed in those that did not mature. Wrist and elbow AVF nonmaturation could be optimally modeled from week 4 ultrasound parameters alone, but with only moderate positive predictive values (PPVs) (wrist, 60.6% [95% confidence interval, CI: 43.9–77.3]; elbow, 66.7% [48.9–84.4]). Moreover, 40 (70.2%) of the 57 AVFs that thrombosed by week 10 had already failed by the week 4 scan, thus limiting the potential of salvage procedures initiated by that scan’s findings to alter overall maturation rates. Modeling of the early ultrasound characteristics could also predict primary patency failure at 6 months; however, that model performed poorly at predicting assisted primary failure (those AVFs that failed despite a salvage attempt), partly because patency of at-risk AVFs was maintained by successful salvage performed without recourse to the early scan data.ConclusionEarly ultrasound surveillance may predict fistula maturation, but is likely, at best, to result in only very modest improvements in fistula patency. Power calculations suggest that an impractically large number of participants (>1700) would be required for formal RCT evaluation

Risk factors for chronic ulceration in patients with varicose veins: A case control study

Background/ObjectiveIdentifying which patients with varicose veins are at risk of progressing to more severe forms of chronic venous disease could help in assigning clinical priorities and targeting appropriate treatments. The aim of this study was to determine, in subjects with varicose veins, the characteristics of venous disease and other factors associated with an increased risk of ulceration.MethodsOne hundred twenty subjects with varicose veins and an open or healed venous leg ulcer were compared with 120 controls with varicose veins and no history of venous ulcer on this case control study. Subjects were recruited from hospital settings and primary care. Each subject completed a questionnaire on lifestyle and medical history and underwent an examination comprising of clinical classification of venous disease (CEAP), duplex scanning, quantitative digital photoplethysmography, and measurement of dorsiflexion. Multiple logistic regression analyses and calculation of receiver operating characteristic (ROC) curves were performed to identify the combination of factors which most accurately predicted which patients with varicose veins will develop leg ulcers.ResultsAn increased risk of ulceration was associated with the severity of clinical venous disease, especially with the presence of skin changes (P < .0001). Other significant risk factors included history of deep vein thrombosis (DVT) (P = .001), higher body mass index (BMI) (P = .006), smoking (P = .009), and reflux in the deep veins (P = .0001). Ulceration was associated with reduced volume of blood displaced as reflected by photoplethysmography and a limited range of ankle movement (not wholly due to the effects of an active ulcer) (both P < .05). Multivariate analyses showed that skin changes including lipodermatosclerosis (odds ratio [OR] 8.90, 95% confidence interval [CI] 1.44-54.8), corona phlebectatica (OR 4.52, 95% CI 1.81-11.3) and eczema (OR 2.87, 95% CI 1.12-7.07), higher BMI (OR 1.08, 95% CI 1.01-1.15), and popliteal vein reflux (OR 2.82, 95% CI 1.03-7.75) remained independently associated with increased risk of ulceration while good dorsiflexion of the ankle (OR 0.88, 95% CI 0.81-0.97) and an effective calf muscle pump (OR 0.96, 95% CI 0.92-0.99) remained protective factors. ROC curve analyses indicated that a model based on clinical observation of skin changes, duplex scanning for popliteal reflux, and calf muscle pump tests would be the most accurate in determining which patients with varicose veins develop leg ulcers.ConclusionsThe results of this study confirm that, in patients with varicose veins, those with skin changes of chronic venous insufficiency and deep vein incompetence are at greatly increased risk of ulceration. However, the risks may also be increased in those who smoke, are obese, and have restricted ankle movement and reduced calf muscle pump power

Comprehensive Rare Variant Analysis via Whole-Genome Sequencing to Determine the Molecular Pathology of Inherited Retinal Disease

Inherited retinal disease is a common cause of visual impairment and represents a highly heterogeneous group of conditions. Here, we present findings from a cohort of 722 individuals with inherited retinal disease, who have had whole-genome sequencing (n = 605), whole-exome sequencing (n = 72), or both (n = 45) performed, as part of the NIHR-BioResource Rare Diseases research study. We identified pathogenic variants (single-nucleotide variants, indels, or structural variants) for 404/722 (56%) individuals. Whole-genome sequencing gives unprecedented power to detect three categories of pathogenic variants in particular: structural variants, variants in GC-rich regions, which have significantly improved coverage compared to whole-exome sequencing, and variants in non-coding regulatory regions. In addition to previously reported pathogenic regulatory variants, we have identified a previously unreported pathogenic intronic variant in $\textit{CHM}$ in two males with choroideremia. We have also identified 19 genes not previously known to be associated with inherited retinal disease, which harbor biallelic predicted protein-truncating variants in unsolved cases. Whole-genome sequencing is an increasingly important comprehensive method with which to investigate the genetic causes of inherited retinal disease.This work was supported by The National Institute for Health Research England (NIHR) for the NIHR BioResource – Rare Diseases project (grant number RG65966). The Moorfields Eye Hospital cohort of patients and clinical and imaging data were ascertained and collected with the support of grants from the National Institute for Health Research Biomedical Research Centre at Moorfields Eye Hospital, National Health Service Foundation Trust, and UCL Institute of Ophthalmology, Moorfields Eye Hospital Special Trustees, Moorfields Eye Charity, the Foundation Fighting Blindness (USA), and Retinitis Pigmentosa Fighting Blindness. M.M. is a recipient of an FFB Career Development Award. E.M. is supported by UCLH/UCL NIHR Biomedical Research Centre. F.L.R. and D.G. are supported by Cambridge NIHR Biomedical Research Centre

Phenotypic Characterization of EIF2AK4 Mutation Carriers in a Large Cohort of Patients Diagnosed Clinically With Pulmonary Arterial Hypertension.

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease with an emerging genetic basis. Heterozygous mutations in the gene encoding the bone morphogenetic protein receptor type 2 (BMPR2) are the commonest genetic cause of PAH, whereas biallelic mutations in the eukaryotic translation initiation factor 2 alpha kinase 4 gene (EIF2AK4) are described in pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Here, we determine the frequency of these mutations and define the genotype-phenotype characteristics in a large cohort of patients diagnosed clinically with PAH. METHODS: Whole-genome sequencing was performed on DNA from patients with idiopathic and heritable PAH and with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis recruited to the National Institute of Health Research BioResource-Rare Diseases study. Heterozygous variants in BMPR2 and biallelic EIF2AK4 variants with a minor allele frequency of <1:10 000 in control data sets and predicted to be deleterious (by combined annotation-dependent depletion, PolyPhen-2, and sorting intolerant from tolerant predictions) were identified as potentially causal. Phenotype data from the time of diagnosis were also captured. RESULTS: Eight hundred sixty-four patients with idiopathic or heritable PAH and 16 with pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis were recruited. Mutations in BMPR2 were identified in 130 patients (14.8%). Biallelic mutations in EIF2AK4 were identified in 5 patients with a clinical diagnosis of pulmonary veno-occlusive disease/pulmonary capillary hemangiomatosis. Furthermore, 9 patients with a clinical diagnosis of PAH carried biallelic EIF2AK4 mutations. These patients had a reduced transfer coefficient for carbon monoxide (Kco; 33% [interquartile range, 30%-35%] predicted) and younger age at diagnosis (29 years; interquartile range, 23-38 years) and more interlobular septal thickening and mediastinal lymphadenopathy on computed tomography of the chest compared with patients with PAH without EIF2AK4 mutations. However, radiological assessment alone could not accurately identify biallelic EIF2AK4 mutation carriers. Patients with PAH with biallelic EIF2AK4 mutations had a shorter survival. CONCLUSIONS: Biallelic EIF2AK4 mutations are found in patients classified clinically as having idiopathic and heritable PAH. These patients cannot be identified reliably by computed tomography, but a low Kco and a young age at diagnosis suggests the underlying molecular diagnosis. Genetic testing can identify these misclassified patients, allowing appropriate management and early referral for lung transplantation

Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity.

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant