scholarly journals Imaging of Cellular Oxidoreductase Activity Suggests Mixotrophic Metabolisms in Thiomargarita spp

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Jake V. Bailey ◽  
Beverly E. Flood ◽  
Elizabeth Ricci ◽  
Nathalie Delherbe
Keyword(s):  
Organic Carbon ◽  
Time Course ◽  
Genomic Data ◽  
Metabolic Potential ◽  
Oxidoreductase Activity ◽  
Metabolic Plasticity ◽  
Hypoxic Conditions ◽  
Genomic Studies ◽  
Genomic Results ◽  
Carbon Degradation

ABSTRACT The largest known bacteria, Thiomargarita spp., have yet to be isolated in pure culture, but their large size allows for individual cells to be monitored in time course experiments or to be individually sorted for omics-based investigations. Here we investigated the metabolism of individual cells of Thiomargarita spp. by using a novel application of a tetrazolium-based dye that measures oxidoreductase activity. When coupled with microscopy, staining of the cells with a tetrazolium-formazan dye allows metabolic responses in Thiomargarita spp. to be to be tracked in the absence of observable cell division. Additionally, the metabolic activity of Thiomargarita sp. cells can be differentiated from the metabolism of other microbes in specimens that contain adherent bacteria. The results of our redox dye-based assay suggest that Thiomargarita is the most metabolically versatile under anoxic conditions, where it appears to express cellular oxidoreductase activity in response to the electron donors succinate, acetate, citrate, formate, thiosulfate, H2, and H2S. Under hypoxic conditions, formazan staining results suggest the metabolism of succinate and likely acetate, citrate, and H2S. Cells incubated under oxic conditions showed the weakest formazan staining response, and then only to H2S, citrate, and perhaps succinate. These results provide experimental validation of recent genomic studies of Candidatus Thiomargarita nelsonii that suggest metabolic plasticity and mixotrophic metabolism. The cellular oxidoreductase response of bacteria attached to the exterior of Thiomargarita also supports the possibility of trophic interactions between these largest of known bacteria and attached epibionts. IMPORTANCE The metabolic potential of many microorganisms that cannot be grown in the laboratory is known only from genomic data. Genomes of Thiomargarita spp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolism with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity of Thiomargarita observed in recently produced genomes. Finding new cultivation-independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms. IMPORTANCE The metabolic potential of many microorganisms that cannot be grown in the laboratory is known only from genomic data. Genomes of Thiomargarita spp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolism with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity of Thiomargarita observed in recently produced genomes. Finding new cultivation-independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms.

scholarly journals Cellular reductase activity in uncultivatedThiomargarita spp. assayed using a redox-sensitive dye

2017 ◽  
Author(s):  
Jake V. Bailey ◽  
Beverly E. Flood ◽  
Elizabeth Ricci ◽  
Nathalie Delherbe
Keyword(s):  
Metabolic Activity ◽  
Time Course ◽  
Experimental Validation ◽  
Reductase Activity ◽  
Electron Donors ◽  
Metabolic Plasticity ◽  
Hypoxic Conditions ◽  
Large Size ◽  
Genomic Studies ◽  
Genomic Results

ABSTRACTThe largest known bacteria,Thiomargarita spp.,have yet to be isolated in pure culture, but their large size allows for individual cells to be followed in time course experiments, or to be individually sorted for ‘omics-based investigations. Here we report a novel application of a tetrazolium-based dye that measures the flux of reductase production from catabolic pathways to investigate the metabolic activity of individual cells ofThiomargaritaspp. When coupled to microscopy, staining of the cells with a tetrazolium-formazan dye allows for metabolic responses inThiomargaritaspp. to be to be tracked in the absence of observable cell division. Additionally, the metabolic activity ofThiomargaritaspp. cells can be differentiated from the metabolism of other microbes in specimens that contain adherent bacteria. The results of our redox-dye-based assay suggests thatThiomargaritais the most metabolically versatile under anoxic conditions where it appears to express cellular reductase activity in response to the electron donors succinate, acetate, citrate, formate, thiosulfate, H2, and H2S. Under hypoxic conditions, formazan staining results suggest the metabolism of succinate, and likely acetate, citrate, and H2S. Cells incubated under oxic conditions showed the weakest formazan staining response, and then only to H2S, citrate, and perhaps succinate. These results provide experimental validation of recent genomic studies ofCa.Thiomargarita nelsonii that suggest metabolic plasticity and mixotrophic metabolism. The cellular reductase response of bacteria attached to the exteriors ofThiomargaritaalso supports the possibility of trophic interactions between these largest of known bacteria and attached epibionts.IMPORTANCEThe metabolic potentials of many microorganisms that cannot be grown in the laboratory are known only from genomic data. Genomes ofThiomargaritaspp. suggest that these largest of known bacteria are mixotrophs, combining lithotrophic metabolisms with organic carbon degradation. Our use of a redox-sensitive tetrazolium dye to query the metabolism of these bacteria provides an independent line of evidence that corroborates the apparent metabolic plasticity ofThiomargaritaobserved in recently produced genomes. Finding new cultivation- independent means of testing genomic results is critical to testing genome-derived hypotheses on the metabolic potentials of uncultivated microorganisms.

scholarly journals Global budgets of organic carbon degradation pathways in marine sediments

2021 ◽  
Author(s):  
Dominik Hülse ◽  
James Bradley ◽  
Sebastiaan van de Velde ◽  
Andy Dale ◽  
Sandra Arndt ◽  
...  
Keyword(s):  
Organic Carbon ◽  
Marine Sediments ◽  
Degradation Pathways ◽  
Global Budgets ◽  
Carbon Degradation

scholarly journals Clinical Value of NGS Genomic Studies for Clinical Management of Pediatric and Young Adult Bone Sarcomas

Cancers ◽  
2021 ◽  
Vol 13 (21) ◽  
pp. 5436
Author(s):  
Miriam Gutiérrez-Jimeno ◽  
Piedad Alba-Pavón ◽  
Itziar Astigarraga ◽  
Teresa Imízcoz ◽  
Elena Panizo-Morgado ◽  
...  
Keyword(s):  
Targeted Therapy ◽  
Young Adult ◽  
Clinical Management ◽  
Genomic Data ◽  
Myxoid Liposarcoma ◽  
Genetic Alteration ◽  
Clinical Value ◽  
Genomic Studies ◽  
Risk Patients ◽  
Genomic Characterization

Genomic techniques enable diagnosis and management of children and young adults with sarcomas by identifying high-risk patients and those who may benefit from targeted therapy or participation in clinical trials. Objective: to analyze the performance of an NGS gene panel for the clinical management of pediatric sarcoma patients. We studied 53 pediatric and young adult patients diagnosed with sarcoma, from two Spanish centers. Genomic data were obtained using the Oncomine Childhood Cancer Research Assay, and categorized according to their diagnostic, predictive, or prognostic value. In 44 (83%) of the 53 patients, at least one genetic alteration was identified. In 80% of these patients, the diagnosis was obtained (n = 11) or changed (n = 9), and thus genomic data affected therapy. The most frequent initial misdiagnosis was Ewing’s sarcoma, instead of myxoid liposarcoma (FUS-DDDIT3), rhabdoid soft tissue tumor (SMARCB1), or angiomatoid fibrous histiocytoma (EWSR1-CREB1). In our series, two patients had a genetic alteration with an FDA-approved targeted therapy, and 30% had at least one potentially actionable alteration. NGS-based genomic studies are useful and feasible in diagnosis and clinical management of pediatric sarcomas. Genomic characterization of these rare and heterogeneous tumors also helps in the search for prognostic biomarkers and therapeutic opportunities.

Pattern Differentiations and Formulations for Heterogeneous Genomic Data through Hybrid Approaches

2011 ◽  
pp. 136-154
Author(s):  
Arpad Kelemen ◽  
Yulan Liang
Keyword(s):  
Time Course ◽  
Hybrid Methods ◽  
Function Analysis ◽  
Genomic Data ◽  
Clustering Methods ◽  
Main Research ◽  
Hybrid Approaches ◽  
Differential Gene ◽  
Value Decomposition ◽  
Multiple Sclerosis Patients

Pattern differentiations and formulations are two main research tracks for heterogeneous genomic data pattern analysis. In this chapter, we develop hybrid methods to tackle the major challenges of power and reproducibility of the dynamic differential gene temporal patterns. The significant differentially expressed genes are selected not only from significant statistical analysis of microarrays but also supergenes resulting from singular value decomposition for extracting the gene components which can maximize the total predictor variability. Furthermore, hybrid clustering methods are developed based on resulting profiles from several clustering methods. We demonstrate the developed hybrid analysis through an application to a time course gene expression data from interferon-b-1a treated multiple sclerosis patients. The resulting integrated-condensed clusters and overrepresented gene lists demonstrate that the hybrid methods can successfully be applied. The post analysis includes function analysis and pathway discovery to validate the findings of the hybrid methods.

Coupled Manganese Redox Cycling and Organic Carbon Degradation on Mineral Surfaces

2020 ◽  
Vol 54 (14) ◽  
pp. 8801-8810 ◽  
Author(s):  
Dong Ma ◽  
Juan Wu ◽  
Peng Yang ◽  
Mengqiang Zhu
Keyword(s):  
Organic Carbon ◽  
Redox Cycling ◽  
Mineral Surfaces ◽  
Carbon Degradation

Impaired oxidative phosphorylation in hepatic mitochondria in growth-retarded rats

2003 ◽  
Vol 285 (6) ◽  
pp. E1258-E1266 ◽  
Author(s):  
Iyalla E. Peterside ◽  
Mary A. Selak ◽  
Rebecca A. Simmons
Keyword(s):  
Oxidative Phosphorylation ◽  
Time Course ◽  
Manganese Superoxide Dismutase ◽  
Hepatic Glucose Production ◽  
Acute Hypoxia ◽  
Glucose Production ◽  
Oxidoreductase Activity ◽  
Oxidation Rates ◽  
Hepatic Glucose ◽  
And Control

Intrauterine growth retardation (IUGR) has been linked to the development of type 2 diabetes in adulthood. We have developed an IUGR model in the rat whereby the animals develop diabetes between 3 and 6 mo of age that is associated with insulin resistance. Alterations in hepatic glucose metabolism are known to contribute to the hyperglycemia of diabetes; however, the mechanisms underlying this phenomenon have not been fully explained. To address this issue, intact liver mitochondria were isolated from IUGR and control offspring at different ages to examine the nature and time course of possible defects in oxidative metabolism. Phospho enolpyruvate carboxykinase (PEPCK) expression was also measured in livers of IUGR and control offspring. Rates of ADP-stimulated (state 3) oxygen consumption were increased for succinate in the fetus and for α-ketoglutarate and glutamate at day 1, reflecting possible compensatory metabolic adaptations to acute hypoxia and acidosis in IUGR rats. By day 14, oxidation of glutamate and α-ketoglutarate had returned to normal, and by day 28, oxidation rates of pyruvate, glutamate, succinate, and α-ketoglutarate were significantly lower than those of controls. Rotenone-sensitive NADH-O2 oxidoreductase activity was similar in control and IUGR mitochondria at all ages, showing that the defect responsible for decreased pyruvate, glutamate, and α-ketoglutarate oxidation in IUGR liver precedes the electron transport chain and involves pyruvate and α-ketoglutarate dehydrogenases. Increased levels of manganese superoxide dismutase suggest that an antioxidant response has been mounted, and hydroxynonenal (HNE) modification of pyruvate dehydrogenase E2-(catalytic) and E3-binding protein subunits suggests that HNE-induced inactivation of this key enzyme may play a role in the mechanism of injury. The level of PEPCK mRNA was increased 250% in day 28 IUGR liver, indicating altered gene expression of the gluconeogenic enzyme that precedes overt hyperglycemia. These results indicate that uteroplacental insufficiency impairs mitochondrial oxidative phosphorylation in the liver and that this derangement predisposes the IUGR rat to increased hepatic glucose production by suppressing pyruvate oxidation and increasing gluconeogenesis.

Biofilm increases permeate quality by organic carbon degradation in low pressure ultrafiltration

2015 ◽  
Vol 85 ◽  
pp. 512-520 ◽  
Author(s):  
A. Chomiak ◽  
J. Traber ◽  
E. Morgenroth ◽  
N. Derlon
Keyword(s):  
Organic Carbon ◽  
Low Pressure ◽  
Carbon Degradation

In vitro and in vivo kinetic handling of nitrite in blood: effects of varying hemoglobin oxygen saturation

2007 ◽  
Vol 293 (3) ◽  
pp. H1508-H1517 ◽  
Author(s):  
Arlin B. Blood ◽  
Gordon G. Power
Keyword(s):  
Nitric Oxide ◽  
Time Course ◽  
Kinetic Properties ◽  
Hemoglobin Oxygen Saturation ◽  
Hypoxic Conditions ◽  
Oxygenation Condition ◽  
Plasma Nitrite ◽  
Kinetics Of

Growing evidence suggests that nitrite, acting via reduction to nitric oxide by deoxyhemoglobin, may play an important role in local control of blood flow during hypoxia. To investigate the effect of hypoxia (65 Torr arterial Po2) on the kinetic properties of nitrite, a bolus injection of sodium nitrite (10 mg/kg iv) was given to normoxic or hypoxic newborn lambs, and the time course of plasma nitrite and methemoglobin (MetHb) concentrations was measured. The in vivo kinetics of nitrite disappearance from plasma were biphasic and were not affected by hypoxia. Changes in MetHb, a product of the nitrite-hemoglobin reaction, also did not differ with the level of oxygenation. Hypoxia potentiated the hypotensive effects of nitrite on pulmonary and systemic arterial pressures. The disappearance of nitrite from plasma was equivalent to the increase in MetHb on a molar basis. In contrast, nitrite metabolism in sheep blood in vitro resulted in more than one MetHb per nitrite equivalent under mid- and high-oxygenation conditions: oxyhemoglobin (HbO2) saturation = 50.3 ± 1.7% and 97.0 ± 1.3%, respectively. Under the low-oxygenation condition (HbO2 saturation = 5.2 ± 0.9%), significantly less than 1 mol of MetHb was produced per nitrite equivalent, indicating that a significant portion of nitrite is metabolized through pathways that do not produce MetHb. These data support the idea that the vasodilating effects of nitrite are potentiated under hypoxic conditions due to the reduction of nitrite to nitric oxide by deoxyhemoglobin.

scholarly journals The Effect and Mechanism of Celecoxib in Hypoxia-Induced Survivin Up-Regulation in HUVECs

2015 ◽  
Vol 37 (3) ◽  
pp. 991-1001 ◽  
Author(s):  
Ning-ning Liu ◽  
Ning Zhao ◽  
Na Cai
Keyword(s):  
Western Blot ◽  
Blot Analysis ◽  
Western Blot Analysis ◽  
Time Course ◽  
Umbilical Vein ◽  
Survivin Expression ◽  
Mrna Levels ◽  
Cytoplasmic Staining ◽  
Hypoxic Conditions ◽  
Cox 2

Background/Aims: To investigate the roles of hypoxia-inducible factor 1α (HIF-1α), cyclooxygenase-2 (Cox-2) and its product, Prostaglandin E2 (PGE2), in the mechanisms underlying hypoxia-induced survivin expression in human umbilical vein endothelial cells (HUVECs) and to examine the effect of celecoxib, a selective Cox-2 inhibitor, on survivin expression. Methods: HUVECs were exposed to a normal (95% O2) or hypoxic (3% O2) environment for 24 hrs. We observed the localized expression of survivin, Cox-2 and HIF-1α in HUVECs using immunocytochemistry and detected the inhibitory effects of celecoxib on the growth of HUVECs using an MTT assay. mRNA and protein levels of Cox-2, HIF-1α and survivin were determined by real-time PCR and Western blot analysis under hypoxic conditions for 0, 6, 12, or 24 hrs. The time course changes of HIF-1α and survivin protein expression induced by cobalt chloride (CoCl2) were studied using Western blot analysis. We then treated HUVECs under hypoxia for 24 hrs with celecoxib (a Cox-2 selective inhibitor), genistein (a HIF-1α inhibitor) or exogenous PGE2 to further investigate the changes in hypoxia-induced survivin expression. Results: Following 24 hrs of hypoxic treatment, cells exhibited strongly positive survivin, HIF-1α and Cox-2 cytoplasmic staining. Celecoxib (65 μM) effectively inhibited cell proliferation under hypoxic conditions. The protein and mRNA levels of Cox-2, HIF-1α and survivin were increased under hypoxia. The patterns of HIF-1α and survivin expression induced by CoCl2 were similar to those induced by exposure to hypoxia. Genistein partially blocked survivin expression. Celecoxib reversed the hypoxia-induced survivin expression, whereas the addition of PGE2 partially restored this effect. Conclusions: Hypoxia-induced survivin expression in HUVECs may be mediated by dual interdependent mechanisms directly involving HIF-1α and indirectly involving the Cox-2/PGE2 pathways. Celecoxib may offset hypoxia-induced survivin expression.

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