Life at the Frozen Limit: Microbial Carbon Metabolism Across a Late Pleistocene Permafrost Chronosequence.

Permafrost is an extreme habitat yet it hosts microbial populations that remain active over millennia. Using permafrost collected from a Pleistocene chronosequence (19 to 33 ka), we hypothesized that the functional genetic potential of microbial communities in permafrost would reflect microbial strategies to metabolize permafrost soluble organic matter (OM) in situ over geologic time. We also hypothesized that changes in the metagenome across the chronosequence would correlate with shifts in carbon chemistry, permafrost age, and paleoclimate at the time of permafrost formation. We combined high-resolution characterization of water-soluble OM by Fourier-transform ion-cyclotron-resonance mass spectrometry (FT-ICR MS), quantification of organic anions in permafrost water extracts, and metagenomic sequencing to better understand the relationships between the molecular-level composition of potentially bioavailable OM, the microbial community, and permafrost age. Both age and paleoclimate had marked effects on both the molecular composition of dissolved OM and the microbial community. The relative abundance of genes associated with hydrogenotrophic methanogenesis, carbohydrate active enzyme families, nominal oxidation state of carbon (NOSC), and number of identifiable molecular formulae significantly decreased with increasing age. In contrast, genes associated with fermentation of short chain fatty acids (SCFAs), the concentration of SCFAs and ammonium all significantly increased with age. We present a conceptual model of microbial metabolism in permafrost based on fermentation of OM and the buildup of organic acids that helps to explain the unique chemistry of ancient permafrost soils. These findings imply long-term in situ microbial turnover of ancient permafrost OM and that this pooled biolabile OM could prime ancient permafrost soils for a larger and more rapid microbial response to thaw compared to younger permafrost soils.

Perioperative Coagulation Management of a Hemophilia A Patient During Cardiac Surgery.

Perioperative management of cardiovascular surgical procedures requiring cardiopulmonary bypass (CPB) in patients with hemophilia A poses a clinical challenge in coagulation management. Use of CPB requires the administration of an anticoagulant, usually unfractionated heparin, and also causes dilutional coagulopathy, platelet dysfunction or platelet consumption coagulopathy. Hypothermia and activation of the inflammatory cascade also affect coagulation. The effects of CPB on circulating levels of factor VIII have not been clearly defined. In this review, the effects of CPB and hemodilution on FVIII are shown in a case presentation, and perioperative laboratory testing in patients with hemophilia A having cardiac surgery is discussed along with perioperative and postoperative coagulation management.

Does computed tomography-based muscle density predict muscle function and health-related quality of life in patients with idiopathic inflammatory myopathies?

OBJECTIVE: To investigate the association of low-density (lipid-rich) muscle measured by computed tomography (CT) with skeletal muscle function and health-related quality of life in idiopathic inflammatory myopathies (IIMs). METHODS: Seventeen patients and 10 healthy controls underwent CT of the midthigh to quantify high- (30-100 HU) and low-density (0-29 HU) skeletal muscle areas. Anthropometric measures, body composition, physical activity level, health-related quality of life, skeletal muscle strength, endurance, and fatigue were assessed. Patients were compared against controls. The relationship of anthropometric, body composition, and disease variables with measures of muscle function were examined using Spearman's test on the patient group. Linear regression was used to assess the age- and disease-adjusted relationship of muscle quality to physical function and muscle strength. RESULTS: Patients had higher body fat percentage (P = 0.042), trunk fat mass (P = 0.042), android:gynoid fat (P = 0.033), and midthigh low-density muscle/total muscle area (P < 0.001) compared to controls. Midthigh low-density muscle/total muscle area was negatively correlated with self-reported physical function, strength, and endurance (the Short Form 36 [SF-36] health survey physical functioning [P = 0.004], manual muscle testing [P = 0.020], knee maximal voluntary isometric contraction/thigh mineral-free lean mass [P < 0.001], and the endurance step test [P < 0.001]), suggesting that muscle quality impacts function in IIM. Using multiple linear regression adjusted for age, global disease damage, and total fat mass, poor muscle quality as measured by midthigh low-density muscle/total muscle area was negatively associated with SF-36 physical functioning (P = 0.009). CONCLUSION: Midthigh low-density muscle/total muscle area is a good predictor of muscle strength, endurance, and health-related quality of life as it pertains to physical functioning in patients with IIMs.

Physical impairment in patients with idiopathic inflammatory myopathies is associated with the American College of Rheumatology functional status measure.

The goals of this study were to assess the predictive value of chart-abstracted American College of Rheumatology functional status (ACR-FS) with patient-reported ACR-FS and to relate it with measures of muscle function in a single-institution cohort of patients with idiopathic inflammatory myopathies (IIMs). Demographic and clinical data of 102 patients with IIMs regularly followed in the Rheumatology and Neurology Clinics at the University of Kentucky Medical Center between 2006 and 2012 were obtained through retrospective chart review. Clinical and functional status evaluation, muscle performance testing, and body composition measures were performed on a subset of 21 patients. ACR-FS was obtained by both chart abstraction and direct patient report. Spearman's correlations were used to examine the relationship of ACR-FS derived from chart abstraction with direct patient report, as well as the relationship of measures of physical function and body composition with ACR-FS. ACR-FS derived from chart abstraction was significantly correlated with ACR-FS derived from direct patient report (ρ = 0.78, p < 0.001). ACR-FS derived from chart abstraction was also significantly correlated with patient-reported physical function (ρ = -0.71, p < 0.001) and physical activity (ρ = -0.58, p < 0.05), manual muscle testing (ρ = -0.66, p < 0.01), and skeletal muscle endurance as measured by the functional index-2 test (shoulder flexion ρ = -0.62, p < 0.01; hip flexion ρ = -0.65, p < 0.0; heel lift ρ = -0.67, p < 0.01; and toe lift ρ = -0.68, p < 0.01). The ACR-FS is a simple measure of disability that can be used in chart abstraction studies involving IIM patients. We have demonstrated that ACR-FS correlates well with muscle performance tests of strength and endurance.

Metagenomic insights into anaerobic metabolism along an Arctic peat soil profile.

A metagenomic analysis was performed on a soil profile from a wet tundra site in northern Alaska. The goal was to link existing biogeochemical knowledge of the system with the organisms and genes responsible for the relevant metabolic pathways. We specifically investigated how the importance of iron (Fe) oxides and humic substances (HS) as terminal electron acceptors in this ecosystem is expressed genetically, and how respiratory and fermentative processes varied with soil depth into the active layer and into the upper permafrost. Overall, the metagenomes reflected a microbial community enriched in a diverse range of anaerobic pathways, with a preponderance of known Fe reducing species at all depths in the profile. The abundance of sequences associated with anaerobic metabolic processes generally increased with depth, while aerobic cytochrome c oxidases decreased. Methanogenesis genes and methanogen genomes followed the pattern of CH4 fluxes: they increased steeply with depth into the active layer, but declined somewhat over the transition zone between the lower active layer and the upper permafrost. The latter was relatively enriched in fermentative and anaerobic respiratory pathways. A survey of decaheme cytochromes (MtrA, MtrC and their homologs) revealed that this is a promising approach to identifying potential reducers of Fe(III) or HS, and indicated a possible role for Acidobacteria as Fe reducers in these soils. Methanogens appear to coexist in the same layers, though in lower abundance, with Fe reducing bacteria and other potential competitors, including acetogens. These observations provide a rich set of hypotheses for further targeted study.

BRAF kinase in melanoma development and progression.

Cutaneous melanoma is increasing in incidence at one of the highest rates for any form of cancer in the USA, with a current lifetime incidence of 1 in 68. Although early-stage disease is often curable, the survival rate for advanced disease is low, with an average life expectancy of 6-10 months. Knowledge of the molecular alterations associated with melanoma development and progression is expected to lead to improved therapies and outcomes. Major progress in defining the molecular alterations associated with the evolution of melanoma came in 2002, through a systematic genome-wide assessment of cancer-associated pathways. Large-scale sequencing of growth-associated genes in a variety of cancers identified a high frequency (>60%) of activating mutations of the BRAF kinase gene in human melanomas. This discovery has prompted a large number of studies evaluating the biological significance of BRAF kinase mutations in the initiation and progression of melanoma, and their importance for the development of novel melanoma therapies. Here we review the most recent studies of BRAF kinase in the pathogenesis of melanoma and their implications for defining BRAF kinase as a therapeutic point of interest in melanoma.