CARBON DIOXIDE FIXATION.

DOE Office of Scientific and Technical Information (OSTI.GOV)

FUJITA,E.

2000-01-12

Solar carbon dioxide fixation offers the possibility of a renewable source of chemicals and fuels in the future. Its realization rests on future advances in the efficiency of solar energy collection and development of suitable catalysts for CO{sub 2} conversion. Recent achievements in the efficiency of solar energy conversion and in catalysis suggest that this approach holds a great deal of promise for contributing to future needs for fuels and chemicals.

The impact of environmental factors on carbon dioxide fixation by microalgae.

PubMed

Morales, Marcia; Sánchez, León; Revah, Sergio

2018-02-01

Microalgae are among the most productive biological systems for converting sunlight into chemical energy, which is used to capture and transform inorganic carbon into biomass. The efficiency of carbon dioxide capture depends on the cultivation system configuration (photobioreactors or open systems) and can vary according to the state of the algal physiology, the chemical composition of the nutrient medium, and environmental factors such as irradiance, temperature and pH. This mini-review is focused on some of the most important environmental factors determining photosynthetic activity, carbon dioxide biofixation, cell growth rate and biomass productivity by microalgae. These include carbon dioxide and O2 concentrations, light intensity, cultivation temperature and nutrients. Finally, a review of the operation of microalgal cultivation systems outdoors is presented as an example of the impact of environmental conditions on biomass productivity and carbon dioxide fixation. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

CO(2) fixation through hydrogenation by chemical or enzymatic methods.

PubMed

Beller, Matthias; Bornscheuer, Uwe T

2014-04-25

Two birds with one stone: The simulaneous fixation of the greenhouse gas carbon dioxide and storage of the alternative fuel hydrogen can be accomplished with the formation of formic acid. In principle, this is now possible either with an enzymatic system based on a newly discovered bacterial hydrogen-dependent carbon dioxide reductase or by using organometallic catalysts at room temperature and ambient pressure. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Heterotrophic Carbon Dioxide Fixation Products of Euglena

PubMed Central

Peak, Jennifer G.; Peak, Meyrick J.; Ting, Irwin P.

1980-01-01

The metabolic products of heterotrophic (dark) CO2 fixation by Euglena gracilis Klebs strain Z Pringsheim were separated and identified. They consisted of amino acids, phosphorylated compounds, tricarboxylic acid cycle intermediates, and nucleotides. Exposure of the cells to NH4+ after a period of NH4+ deprivation stimulated heterotrophic CO2 fixation almost 4-fold, modifying the spectrum of the fixation products. In particular, the NH4+ treatment stimulated fixation of CO2 into glutamine, glycine, alanine, and serine. PMID:16661238

Two Iron Complexes as Homogeneous and Heterogeneous Catalysts for the Chemical Fixation of Carbon Dioxide.

PubMed

Karan, Chandan Kumar; Bhattacharjee, Manish

2018-04-16

Two new bimetallic iron-alkali metal complexes of amino acid (serine)-based reduced Schiff base ligand were synthesized and structurally characterized. Their efficacy as catalysts for the chemical fixation of carbon dioxide was explored. The heterogeneous version of the catalytic reaction was developed by the immobilization of these homogeneous bimetallic iron-alkali metal complexes in an anion-exchange resin. The resin-bound complexes can be used as recyclable catalysts up to six cycles.

Fixation of carbon dioxide into dimethyl carbonate over titanium-based zeolitic thiophene-benzimidazolate framework

EPA Science Inventory

A titanium-based zeolitic thiophene-benzimidazolate framework has been designed for the direct synthesis of dimethyl carbonate (DMC) from methanol and carbon dioxide. The developed catalyst activates carbon dioxide and delivers over 16% yield of DMC without the use of any dehydra...

Prebiotic Chemistry and Atmospheric Warming of Early Earth by an Active Young Sun

NASA Technical Reports Server (NTRS)

Airapetian, V. S.; Glocer, A.; Gronoff, G.; Hebrard, E.; Danchi, W.

2016-01-01

Nitrogen is a critical ingredient of complex biological molecules. Molecular nitrogen, however, which was outgassed Into the Earth's early atmosphere, is relatively chemically inert and nitrogen fixation into more chemically reactive compounds requires high temperatures. Possible mechanisms of nitrogen fixation include lightning, atmospheric shock heating by meteorites, and solar ultraviolet radiation. Here we show that nitrogen fixation in the early terrestrial atmosphere can be explained by frequent and powerful coronal mass ejection events from the young Sun -- so-called superflares. Using magnetohydrodynamic simulations constrained by Kepler Space Telescope observations, we find that successive superflare ejections produce shocks that accelerate energetic particles, which would have compressed the early Earth's magnetosphere. The resulting extended polar cap openings provide pathways for energetic particles to penetrate into the atmosphere and, according to our atmospheric chemistry simulations, initiate reactions converting molecular nitrogen, carbon dioxide and methane to the potent greenhouse gas nitrous oxide as well as hydrogen cyanide, an essential compound for life. Furthermore, the destruction of N2, C02 and CH, suggests that these greenhouse gases cannot explain the stability of liquid water on the early Earth. Instead, we propose that the efficient formation of nitrous oxide could explain a warm early Earth.

Titanium-based zeolitic imidazolate framework for chemical fixation of carbon dioxide

EPA Science Inventory

A titanium-based zeolitic imidazolate framework (Ti-ZIF) with high surface area and porous morphology was synthesized and itsefficacy was demonstrated in the synthesis of cyclic carbonates from epoxides and carbon dioxide.

The effects of acid rain on nitrogen fixation in Western Washington coniferous forests

Treesearch

Robert Denison; Bruce Caldwell; Bernard Bormann; Lindell Eldred; Cynthia Swanberg; Steven Anderson

1976-01-01

We investigated both the current status of nitrogen fixation in Western Washington forests, and the potential effects of acid rain on this vital process. Even the low concentrations of sulfur dioxide presently found in the Northwest are thought to have an adverse effect on nitrogen fixation by limiting the distribution of the epiphytic nitrogen-fixing lichen, ...

Integration of metagenomic and stable carbon isotope evidence reveals the extent and mechanisms of carbon dioxide fixation in high-temperature microbial communities

DOE PAGES

Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.; ...

2017-02-03

Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less

Fixation of carbon dioxide into dimethyl carbonate over ...

EPA Pesticide Factsheets

A titanium-based zeolitic thiophene-benzimidazolate framework has been designed for the direct synthesis of dimethyl carbonate (DMC) from methanol and carbon dioxide. The developed catalyst activates carbon dioxide and delivers over 16% yield of DMC without the use of any dehydrating agent or requirement for azeotropic distillation. Prepared for submission to Nature Scientific reports.

Carbon Dioxide Fixation in Isolated Kalanchoe Chloroplasts 1

PubMed Central

Levi, Carolyn; Gibbs, Martin

1975-01-01

Chloroplasts isolated from Kalanchoe diagremontiana leaves were capable of photosynthesizing at a rate of 5.4 μmoles of CO2 per milligram of chlorophyll per hour. The dark rate of fixation was about 1% of the light rate. A high photosynthetic rate was associated with low starch content of the leaves. Ribose 5-phosphate, fructose 1,6-diphosphate, and dithiothreitol stimulated fixation, whereas phosphoenolpyruvate and azide were inhibitors. The products of CO2 fixation were primarily those of the photosynthetic carbon reduction cycle. PMID:16659249

Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide

PubMed Central

Hutchins, David A.; Walworth, Nathan G.; Webb, Eric A.; Saito, Mak A.; Moran, Dawn; McIlvin, Matthew R.; Gale, Jasmine; Fu, Fei-Xue

2015-01-01

Nitrogen fixation rates of the globally distributed, biogeochemically important marine cyanobacterium Trichodesmium increase under high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity. However, its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. Here we show that experimental evolution under extended selection at projected future elevated CO2 levels results in irreversible, large increases in nitrogen fixation and growth rates, even after being moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained after returning to the ancestral environment. Constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, and increased activity of a potentially regulatory DNA methyltransferase enzyme. High CO2-selected cell lines also exhibit increased phosphorus-limited growth rates, suggesting a potential advantage for this keystone organism in a more nutrient-limited, acidified future ocean. PMID:26327191

Irreversibly increased nitrogen fixation in Trichodesmium experimentally adapted to elevated carbon dioxide

NASA Astrophysics Data System (ADS)

Hutchins, David A.; Walworth, Nathan G.; Webb, Eric A.; Saito, Mak A.; Moran, Dawn; McIlvin, Matthew R.; Gale, Jasmine; Fu, Fei-Xue

2015-09-01

Nitrogen fixation rates of the globally distributed, biogeochemically important marine cyanobacterium Trichodesmium increase under high carbon dioxide (CO2) levels in short-term studies due to physiological plasticity. However, its long-term adaptive responses to ongoing anthropogenic CO2 increases are unknown. Here we show that experimental evolution under extended selection at projected future elevated CO2 levels results in irreversible, large increases in nitrogen fixation and growth rates, even after being moved back to lower present day CO2 levels for hundreds of generations. This represents an unprecedented microbial evolutionary response, as reproductive fitness increases acquired in the selection environment are maintained after returning to the ancestral environment. Constitutive rate increases are accompanied by irreversible shifts in diel nitrogen fixation patterns, and increased activity of a potentially regulatory DNA methyltransferase enzyme. High CO2-selected cell lines also exhibit increased phosphorus-limited growth rates, suggesting a potential advantage for this keystone organism in a more nutrient-limited, acidified future ocean.

Characterization of carbon dioxide concentrating chemolithotrophic bacterium Serratia sp. ISTD04 for production of biodiesel.

PubMed

Kumar, Manish; Morya, Raj; Gnansounou, Edgard; Larroche, Christian; Thakur, Indu Shekhar

2017-11-01

Proteomics and metabolomics analysis has become a powerful tool for characterization of microbial ability for fixation of Carbon dioxide. Bacterial community of palaeoproterozoic metasediments was enriched in the shake flask culture in the presence of NaHCO 3 . One of the isolate showed resistance to NaHCO 3 (100mM) and was identified as Serratia sp. ISTD04 by 16S rRNA sequence analysis. Carbon dioxide fixing ability of the bacterium was established by carbonic anhydrase enzyme assay along with proteomic analysis by LC-MS/MS. In proteomic analysis 96 proteins were identified out of these 6 protein involved in carbon dioxide fixation, 11 in fatty acid metabolism, indicating the carbon dioxide fixing potency of bacterium along with production of biofuel. GC-MS analysis revealed that hydrocarbons and FAMEs produced by bacteria within the range of C 13 -C 24 and C 11 -C 19 respectively. Presence of 59% saturated and 41% unsaturated organic compounds, make it a better fuel composition. Copyright © 2017 Elsevier Ltd. All rights reserved.

An efficient copper-based magnetic nanocatalyst for the fixation of carbon dioxide at atmospheric pressure.

PubMed

Sharma, Rakesh Kumar; Gaur, Rashmi; Yadav, Manavi; Goswami, Anandarup; Zbořil, Radek; Gawande, Manoj B

2018-01-30

In the last few decades, the emission of carbon dioxide (CO 2 ) in the environment has caused havoc across the globe. One of the most promising strategies for fixation of CO 2 is the cycloaddition reaction between epoxides and CO 2 to produce cyclic carbonates. For the first time, we have fabricated copper-based magnetic nanocatalyst and have applied for the CO 2 fixation. The prepared catalyst was thoroughly characterized using various techniques including XRD, FT-IR, TEM, FE-SEM, XPS, VSM, ICP-OES and elemental mapping. The reactions proceeded at atmospheric pressure, relatively lower temperature, short reaction time, solvent- less and organic halide free reaction conditions. Additionally, the ease of recovery through an external magnet, reusability of the catalyst and excellent yields of the obtained cyclic carbonates make the present protocol practical and sustainable.

Prebiotic chemistry and atmospheric warming of early Earth by an active young Sun

NASA Astrophysics Data System (ADS)

Airapetian, V. S.; Glocer, A.; Gronoff, G.; Hébrard, E.; Danchi, W.

2016-06-01

Nitrogen is a critical ingredient of complex biological molecules. Molecular nitrogen, however, which was outgassed into the Earth’s early atmosphere, is relatively chemically inert and nitrogen fixation into more chemically reactive compounds requires high temperatures. Possible mechanisms of nitrogen fixation include lightning, atmospheric shock heating by meteorites, and solar ultraviolet radiation. Here we show that nitrogen fixation in the early terrestrial atmosphere can be explained by frequent and powerful coronal mass ejection events from the young Sun--so-called superflares. Using magnetohydrodynamic simulations constrained by Kepler Space Telescope observations, we find that successive superflare ejections produce shocks that accelerate energetic particles, which would have compressed the early Earth’s magnetosphere. The resulting extended polar cap openings provide pathways for energetic particles to penetrate into the atmosphere and, according to our atmospheric chemistry simulations, initiate reactions converting molecular nitrogen, carbon dioxide and methane to the potent greenhouse gas nitrous oxide as well as hydrogen cyanide, an essential compound for life. Furthermore, the destruction of N2, CO2 and CH4 suggests that these greenhouse gases cannot explain the stability of liquid water on the early Earth. Instead, we propose that the efficient formation of nitrous oxide could explain a warm early Earth.

Electrocarboxylation: towards sustainable and efficient synthesis of valuable carboxylic acids

PubMed Central

Matthessen, Roman; Fransaer, Jan; Binnemans, Koen

2014-01-01

Summary The near-unlimited availability of CO2 has stimulated a growing research effort in creating value-added products from this greenhouse gas. This paper presents the trends on the most important methods used in the electrochemical synthesis of carboxylic acids from carbon dioxide. An overview is given of different substrate groups which form carboxylic acids upon CO2 fixation, including mechanistic considerations. While most work focuses on the electrocarboxylation of substrates with sacrificial anodes, this review considers the possibilities and challenges of implementing other synthetic methodologies. In view of potential industrial application, the choice of reactor setup, electrode type and reaction pathway has a large influence on the sustainability and efficiency of the process. PMID:25383120

Effect of air pollution on nitrogen fixation in lichens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kallio, S.; Varheenmaa, T.

1974-01-01

Clear decrease (80-90%) of acetylene reduction in Stereocaulon paschale and Nephroma arcticum was observed in the polluted city area of Turku (SW Finland) within a period of three-four weeks, while nitrogenase activity remained unchanged in the specimens outside the city area. Carbon dioxide fixation in these lichens lowered 20-50%.

The emergence and early evolution of biological carbon-fixation.

PubMed

Braakman, Rogier; Smith, Eric

2012-01-01

The fixation of CO₂ into living matter sustains all life on Earth, and embeds the biosphere within geochemistry. The six known chemical pathways used by extant organisms for this function are recognized to have overlaps, but their evolution is incompletely understood. Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form. We find that innovations in carbon-fixation were the foundation for most major early divergences in the tree of life. These findings are based on a novel method that fully integrates metabolic and phylogenetic constraints. Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. One of these is a linear folate-based pathway of CO₂ reduction previously only recognized as a fixation route in the complete Wood-Ljungdahl pathway, but which more generally may exclude the final step of synthesizing acetyl-CoA. Using metabolic constraints we then reconstruct a "phylometabolic" tree with a high degree of parsimony that traces the evolution of complete carbon-fixation pathways, and has a clear structure down to the root. This tree requires few instances of lateral gene transfer or convergence, and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. Energy optimization and oxygen toxicity are the two strongest forces of selection. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.

Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

PubMed

Bharti, Randhir K; Srivastava, Shaili; Thakur, Indu Shekhar

2014-01-01

A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials.

Proteomic Analysis of Carbon Concentrating Chemolithotrophic Bacteria Serratia sp. for Sequestration of Carbon Dioxide

PubMed Central

Bharti, Randhir K.; Srivastava, Shaili; Thakur, Indu Shekhar

2014-01-01

A chemolithotrophic bacterium enriched in the chemostat in presence of sodium bicarbonate as sole carbon source was identified as Serratia sp. by 16S rRNA sequencing. Carbon dioxide sequestering capacity of bacterium was detected by carbonic anhydrase enzyme and ribulose-1, 5- bisphosphate carboxylase/oxygenase (RuBisCO). The purified carbonic anhydrase showed molecular weight of 29 kDa. Molecular weight of RuBisCO was 550 kDa as determined by fast protein liquid chromatography (FPLC), however, sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) showed presence of two subunits whose molecular weights were 56 and 14 kDa. The Western blot analysis of the crude protein and purified sample cross reacted with RuBisCO large-subunit polypeptides antibodies showed strong band pattern at molecular weight around 56 kDa regions. Whole cell soluble proteins of Serratia sp. grown under autotrophic and heterotrophic conditions were resolved by two-dimensional gel electrophoresis and MALDI-TOF/MS for differential expression of proteins. In proteomic analysis of 63 protein spots, 48 spots were significantly up-regulated in the autotrophically grown cells; seven enzymes showed its utilization in autotrophic carbon fixation pathways and other metabolic activities of bacterium including lipid metabolisms indicated sequestration potency of carbon dioxide and production of biomaterials. PMID:24619032

The Path of Carbon in Photosynthesis IX. Photosynthesis, Photoreduction, and the Hydrogen-Oxygen-Carbon Dioxide Dark Reaction

DOE R&D Accomplishments Database

Badin, E. J.; Calvin, M.

1950-02-01

A comparison of the rates of fixation of Carbon 14 dioxide in algae for the processes of photosynthesis, photoreduction and the hydrogen-oxygen-carbon dioxide dark reaction has been made. For the same series of experiments, rates of incorporation of tracer carbon into the separate soluble components using the radiogram method have been determined. The mechanism of carbon dioxide uptake has been shown to occur via two distinct paths. In all cases studied, essentially the same compounds appear radioactive. The distribution with time, however, differs markedly.

Evolution and Adaptation of Phytoplankton Photosynthetic Pathways to perturbations of the geological carbon system

NASA Astrophysics Data System (ADS)

Rickaby, R. E.; Young, J. N.; Hermoso, M.; Heureux, A.; McCLelland, H.; Lee, R.; Eason Hubbard, M.

2012-12-01

The ocean and atmosphere carbon system has varied greatly over geological history both in response to initial evolutionary innovation, and as a driver of adaptive change. Here we establish that positive selection in Rubisco, the most abundant enzyme on the Earth responsible for all photosynthetic carbon fixation, occurred early in Earth's history, and basal to the radiation of the modern marine algal groups. Our signals of positive selection appear to be triggered by changing intracellular concentrations of carbon dioxide (CO2) due to the emergence of carbon concentrating mechanisms between 1.56 and 0.41 Ba in response to declining atmospheric CO2 . We contend that, at least in terms of carbon, phytoplankton generally were well poised to manage subsequent abrupt carbon cycle perturbations. The physiological pathways for optimising carbon acquisition across a wide range of ambient carbon dioxide concentrations had already been established and were genetically widespread across open ocean phytoplankton groups. We will further investigate some case studies from the Mesozoic and Cenozoic abrupt carbon cycle excursions using isotopic tools to probe the community photosynthetic response and demonstrate the flexibility of phytoplankton photosynthesis in the face of major perturbations. In particular, an unprecedented resolution record across the Toarcian (Early Jurassic) carbon isotope excursion in the Paris Basin reveals a selection and evolution towards a community reliant solely on diffusive carbon dioxide supply for photosynthesis at the height of the excursion at 1500-2500 ppm CO2. The continued flourishing of the phytoplankton biological pump throughout this excursion was able to remove the excess carbon injected into the water column in less than 45 kyrs.

Elucidation of rice rhizosphere metagenome in relation to methane and nitrogen metabolism under elevated carbon dioxide and temperature using whole genome metagenomic approach.

PubMed

Bhattacharyya, P; Roy, K S; Das, M; Ray, S; Balachandar, D; Karthikeyan, S; Nayak, A K; Mohapatra, T

2016-01-15

Carbon (C) and nitrogen (N) mineralization is one of the key processes of biogeochemical cycling in terrestrial ecosystem in general and rice ecology in particular. Rice rhizosphere is a rich niche of microbial diversity influenced by change in atmospheric temperature and concentration of carbon dioxide (CO2). Structural changes in microbial communities in rhizosphere influence the nutrient cycling. In the present study, the bacterial diversity and population dynamics were studied under ambient CO2 (a-CO2) and elevated CO2+temperature (e-CO2T) in lowland rice rhizosphere using whole genome metagenomic approach. The whole genome metagenomic sequence data of lowland rice exhibited the dominance of bacterial communities including Proteobacteria, Firmicutes, Acidobacteria, Actinobacteria and Planctomycetes. Interestingly, four genera related to methane production namely, Methanobacterium, Methanosphaera, Methanothermus and Methanothermococcus were absent in a-CO2 but noticed under e-CO2T. The acetoclastic pathway was found as the predominant pathway for methanogenesis, whereas, the serine pathway was found as the principal metabolic pathway for CH4 oxidation in lowland rice. The abundances of reads of enzymes in the acetoclastic methanogenesis pathway and serine pathways of methanotrophy were much higher in e-CO2T (328 and 182, respectively) as compared with a-CO2 (118 and 98, respectively). Rice rhizosphere showed higher structural diversities and functional activities in relation to N metabolism involving nitrogen fixation, assimilatory and dissimilatory nitrate reduction and denitrification under e-CO2T than that of a-CO2. Among the three pathways of N metabolism, dissimilarity pathways were predominant in lowland rice rhizosphere and more so under e-CO2T. Consequently, under e-CO2T, CH4 emission, microbial biomass nitrogen (MBN) and dehydrogenase activities were 45%, 20% and 35% higher than a-CO2, respectively. Holistically, a high bacterial diversity and abundances of C and N decomposing bacteria in lowland rice rhizosphere were found under e-CO2T, which could be explored further for their specific role in nutrient cycling, sustainable agriculture and environment management. Copyright © 2015 Elsevier B.V. All rights reserved.

Cyanuric Acid-Based Organocatalyst for Utilization of Carbon Dioxide at Atmospheric Pressure.

PubMed

Yu, Bing; Kim, Daeun; Kim, Seoksun; Hong, Soon Hyeok

2017-03-22

A organocatalytic system based on economical and readily available cyanuric acid has been developed for the synthesis of 2-oxazolidinones and quinazoline-2,4(1H,3H)-diones from propargylamines and 2-aminobenzonitriles under atmospheric pressure carbon dioxide. Notably, a low concentration of carbon dioxide in air was directly converted into 2-oxazolidinone in excellent yields without an external base. Through mechanistic investigation by in situ FTIR spectroscopy, cyanuric acid was demonstrated to be an efficient catalyst for carbon dioxide fixation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Emerging model systems for functional genomics analysis of Crassulacean acid metabolism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartwell, James; Dever, Louisa V.; Boxall, Susanna F.

Crassulacean acid metabolism (CAM) is one of three main pathways of photosynthetic carbon dioxide fixation found in higher plants. It stands out for its ability to underpin dramatic improvements in plant water use efficiency, which in turn has led to a recent renaissance in CAM research. The current ease with which candidate CAM-associated genes and proteins can be identified through high-throughput sequencing has opened up a new horizon for the development of diverse model CAM species that are amenable to genetic manipulations. The adoption of these model CAM species is underpinning rapid advances in our understanding of the complete genemore » set for CAM. Here, we highlight recent breakthroughs in the functional characterisation of CAM genes that have been achieved through transgenic approaches.« less

Emerging model systems for functional genomics analysis of Crassulacean acid metabolism

DOE PAGES

Hartwell, James; Dever, Louisa V.; Boxall, Susanna F.

2016-04-12

Crassulacean acid metabolism (CAM) is one of three main pathways of photosynthetic carbon dioxide fixation found in higher plants. It stands out for its ability to underpin dramatic improvements in plant water use efficiency, which in turn has led to a recent renaissance in CAM research. The current ease with which candidate CAM-associated genes and proteins can be identified through high-throughput sequencing has opened up a new horizon for the development of diverse model CAM species that are amenable to genetic manipulations. The adoption of these model CAM species is underpinning rapid advances in our understanding of the complete genemore » set for CAM. Here, we highlight recent breakthroughs in the functional characterisation of CAM genes that have been achieved through transgenic approaches.« less

Direct gas-solid carbonation of serpentinite residues in the absence and presence of water vapor: a feasibility study for carbon dioxide sequestration.

PubMed

Veetil, Sanoopkumar Puthiya; Pasquier, Louis-César; Blais, Jean-François; Cecchi, Emmanuelle; Kentish, Sandra; Mercier, Guy

2015-09-01

Mineral carbonation of serpentinite mining residue offers an environmentally secure and permanent storage of carbon dioxide. The strategy of using readily available mining residue for the direct treatment of flue gas could improve the energy demand and economics of CO2 sequestration by avoiding the mineral extraction and separate CO2 capture steps. The present is a laboratory scale study to assess the possibility of CO2 fixation in serpentinite mining residues via direct gas-solid reaction. The degree of carbonation is measured both in the absence and presence of water vapor in a batch reactor. The gas used is a simulated gas mixture reproducing an average cement flue gas CO2 composition of 18 vol.% CO2. The reaction parameters considered are temperature, total gas pressure, time, and concentration of water vapor. In the absence of water vapor, the gas-solid carbonation of serpentinite mining residues is negligible, but the residues removed CO2 from the feed gas possibly due to reversible adsorption. The presence of small amount of water vapor enhances the gas-solid carbonation, but the measured rates are too low for practical application. The maximum CO2 fixation obtained is 0.07 g CO2 when reacting 1 g of residue at 200 °C and 25 barg (pCO2 ≈ 4.7) in a gas mixture containing 18 vol.% CO2 and 10 vol.% water vapor in 1 h. The fixation is likely surface limited and restricted due to poor gas-solid interaction. It was identified that both the relative humidity and carbon dioxide-water vapor ratio have a role in CO2 fixation regardless of the percentage of water vapor.

Promoting helix pitch and trichome length to improve biomass harvesting efficiency and carbon dioxide fixation rate by Spirulina sp. in 660 m2 raceway ponds under purified carbon dioxide from a coal chemical flue gas.

PubMed

Cheng, Jun; Guo, Wangbiao; Ameer Ali, Kubar; Ye, Qing; Jin, Guiyong; Qiao, Zhanshan

2018-08-01

The helix pitch and trichome length of Spirulina sp. were promoted to improve the biomass harvesting efficiency and CO 2 fixation rate in 660 m 2 raceway ponds aerated with food-grade CO 2 purified from a coal chemical flue gas. The CO 2 fixation rate was improved with increased trichome length of the Spirulina sp. in a raceway pond with double paddlewheels, baffles, and CO 2 aerators (DBA raceway pond). The trichome length has increased by 33.3 μm, and CO 2 fixation rate has increased by 42.3% and peaked to 51.3 g/m 2 /d in a DBA raceway pond. Biomass harvesting efficiency was increased with increased helix pitch. When the day-average greenhouse temperature was 33 °C and day-average sunlight intensity was 72,100 lu×, the helix pitch of Spirulina sp. was increased to 56.2 μm. Hence the biomass harvesting efficiency was maximized to 75.6% and biomass actual yield was increased to 35.9 kg in a DBA raceway pond. Copyright © 2018 Elsevier Ltd. All rights reserved.

Induction of Photosynthetic Carbon Fixation in Anoxia Relies on Hydrogenase Activity and Proton-Gradient Regulation-Like1-Mediated Cyclic Electron Flow in Chlamydomonas reinhardtii.

PubMed

Godaux, Damien; Bailleul, Benjamin; Berne, Nicolas; Cardol, Pierre

2015-06-01

The model green microalga Chlamydomonas reinhardtii is frequently subject to periods of dark and anoxia in its natural environment. Here, by resorting to mutants defective in the maturation of the chloroplastic oxygen-sensitive hydrogenases or in Proton-Gradient Regulation-Like1 (PGRL1)-dependent cyclic electron flow around photosystem I (PSI-CEF), we demonstrate the sequential contribution of these alternative electron flows (AEFs) in the reactivation of photosynthetic carbon fixation during a shift from dark anoxia to light. At light onset, hydrogenase activity sustains a linear electron flow from photosystem II, which is followed by a transient PSI-CEF in the wild type. By promoting ATP synthesis without net generation of photosynthetic reductants, the two AEF are critical for restoration of the capacity for carbon dioxide fixation in the light. Our data also suggest that the decrease in hydrogen evolution with time of illumination might be due to competition for reduced ferredoxins between ferredoxin-NADP(+) oxidoreductase and hydrogenases, rather than due to the sensitivity of hydrogenase activity to oxygen. Finally, the absence of the two alternative pathways in a double mutant pgrl1 hydrogenase maturation factor G-2 is detrimental for photosynthesis and growth and cannot be compensated by any other AEF or anoxic metabolic responses. This highlights the role of hydrogenase activity and PSI-CEF in the ecological success of microalgae in low-oxygen environments. © 2015 American Society of Plant Biologists. All Rights Reserved.

Iodide-Photocatalyzed Reduction of Carbon Dioxide to Formic Acid with Thiols and Hydrogen Sulfide.

PubMed

Berton, Mateo; Mello, Rossella; González-Núñez, María Elena

2016-12-20

The photolysis of iodide anions promotes the reaction of carbon dioxide with hydrogen sulfide or thiols to quantitatively yield formic acid and sulfur or disulfides. The reaction proceeds in acetonitrile and aqueous solutions, at atmospheric pressure and room temperature by irradiation using a low-pressure mercury lamp. This transition-metal-free photocatalytic process for CO 2 capture coupled with H 2 S removal may have been relevant as a prebiotic carbon dioxide fixation. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enantioselective small molecule synthesis by carbon dioxide fixation using a dual Brønsted acid/base organocatalyst.

PubMed

Vara, Brandon A; Struble, Thomas J; Wang, Weiwei; Dobish, Mark C; Johnston, Jeffrey N

2015-06-17

Carbon dioxide exhibits many of the qualities of an ideal reagent: it is nontoxic, plentiful, and inexpensive. Unlike other gaseous reagents, however, it has found limited use in enantioselective synthesis. Moreover, unprecedented is a tool that merges one of the simplest biological approaches to catalysis-Brønsted acid/base activation-with this abundant reagent. We describe a metal-free small molecule catalyst that achieves the three component reaction between a homoallylic alcohol, carbon dioxide, and an electrophilic source of iodine. Cyclic carbonates are formed enantioselectively.

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hawley, Alyse K.; Brewer, Heather M.; Norbeck, Angela D.

2014-08-05

Oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified marine waters. Currently OMZs are expanding due to global climate change. This expansion alters marine ecosystem function and the productivity of fisheries due to habitat compression and changes in biogeochemical cycling leading to fixed nitrogen loss and greenhouse gas production. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally anoxic fjord, Saanich Inlet to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components formore » nitrification, anaerobic ammonium oxidation (anammox), denitrification and inorganic carbon fixation predominantly co-varied with abundance and distribution patterns of Thaumarchaeota, Nitrospira, Planctomycetes and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Within these groups, pathways mediating inorganic carbon fixation and nitrogen and sulfur transformations were differentially expressed across the redoxcline. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters and denitrification, sulfur-oxidation and inorganic carbon fixation pathways affiliated with SUP05 dominated suboxic and anoxic waters. Nitrite-oxidation and anammox pathways affiliated with Nitrospina and Planctomycetes respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The differential expression of these pathways under changing water column redox conditions has quantitative implications for coupled biogeochemical cycling linking different modes of inorganic carbon fixation with distributed nitrogen and sulfur-based energy metabolism extensible to coastal and open ocean OMZs.« less

Design and analysis of synthetic carbon fixation pathways

PubMed Central

Bar-Even, Arren; Noor, Elad; Lewis, Nathan E.; Milo, Ron

2010-01-01

Carbon fixation is the process by which CO2 is incorporated into organic compounds. In modern agriculture in which water, light, and nutrients can be abundant, carbon fixation could become a significant growth-limiting factor. Hence, increasing the fixation rate is of major importance in the road toward sustainability in food and energy production. There have been recent attempts to improve the rate and specificity of Rubisco, the carboxylating enzyme operating in the Calvin–Benson cycle; however, they have achieved only limited success. Nature employs several alternative carbon fixation pathways, which prompted us to ask whether more efficient novel synthetic cycles could be devised. Using the entire repertoire of approximately 5,000 metabolic enzymes known to occur in nature, we computationally identified alternative carbon fixation pathways that combine existing metabolic building blocks from various organisms. We compared the natural and synthetic pathways based on physicochemical criteria that include kinetics, energetics, and topology. Our study suggests that some of the proposed synthetic pathways could have significant quantitative advantages over their natural counterparts, such as the overall kinetic rate. One such cycle, which is predicted to be two to three times faster than the Calvin–Benson cycle, employs the most effective carboxylating enzyme, phosphoenolpyruvate carboxylase, using the core of the naturally evolved C4 cycle. Although implementing such alternative cycles presents daunting challenges related to expression levels, activity, stability, localization, and regulation, we believe our findings suggest exciting avenues of exploration in the grand challenge of enhancing food and renewable fuel production via metabolic engineering and synthetic biology. PMID:20410460

Emerging model systems for functional genomics analysis of Crassulacean acid metabolism.

PubMed

Hartwell, James; Dever, Louisa V; Boxall, Susanna F

2016-06-01

Crassulacean acid metabolism (CAM) is one of three main pathways of photosynthetic carbon dioxide fixation found in higher plants. It stands out for its ability to underpin dramatic improvements in plant water use efficiency, which in turn has led to a recent renaissance in CAM research. The current ease with which candidate CAM-associated genes and proteins can be identified through high-throughput sequencing has opened up a new horizon for the development of diverse model CAM species that are amenable to genetic manipulations. The adoption of these model CAM species is underpinning rapid advances in our understanding of the complete gene set for CAM. We highlight recent breakthroughs in the functional characterisation of CAM genes that have been achieved through transgenic approaches. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

The Biological Deep Sea Hydrothermal Vent as a Model to Study Carbon Dioxide Capturing Enzymes

PubMed Central

Minic, Zoran; Thongbam, Premila D.

2011-01-01

Deep sea hydrothermal vents are located along the mid-ocean ridge system, near volcanically active areas, where tectonic plates are moving away from each other. Sea water penetrates the fissures of the volcanic bed and is heated by magma. This heated sea water rises to the surface dissolving large amounts of minerals which provide a source of energy and nutrients to chemoautotrophic organisms. Although this environment is characterized by extreme conditions (high temperature, high pressure, chemical toxicity, acidic pH and absence of photosynthesis) a diversity of microorganisms and many animal species are specially adapted to this hostile environment. These organisms have developed a very efficient metabolism for the assimilation of inorganic CO2 from the external environment. In order to develop technology for the capture of carbon dioxide to reduce greenhouse gases in the atmosphere, enzymes involved in CO2 fixation and assimilation might be very useful. This review describes some current research concerning CO2 fixation and assimilation in the deep sea environment and possible biotechnological application of enzymes for carbon dioxide capture. PMID:21673885

The biological deep sea hydrothermal vent as a model to study carbon dioxide capturing enzymes.

PubMed

Minic, Zoran; Thongbam, Premila D

2011-01-01

Deep sea hydrothermal vents are located along the mid-ocean ridge system, near volcanically active areas, where tectonic plates are moving away from each other. Sea water penetrates the fissures of the volcanic bed and is heated by magma. This heated sea water rises to the surface dissolving large amounts of minerals which provide a source of energy and nutrients to chemoautotrophic organisms. Although this environment is characterized by extreme conditions (high temperature, high pressure, chemical toxicity, acidic pH and absence of photosynthesis) a diversity of microorganisms and many animal species are specially adapted to this hostile environment. These organisms have developed a very efficient metabolism for the assimilation of inorganic CO₂ from the external environment. In order to develop technology for the capture of carbon dioxide to reduce greenhouse gases in the atmosphere, enzymes involved in CO₂ fixation and assimilation might be very useful. This review describes some current research concerning CO₂ fixation and assimilation in the deep sea environment and possible biotechnological application of enzymes for carbon dioxide capture.

Metabolic flux analysis of Cyanothece sp. ATCC 51142 under mixotrophic conditions.

PubMed

Alagesan, Swathi; Gaudana, Sandeep B; Sinha, Avinash; Wangikar, Pramod P

2013-11-01

Cyanobacteria are a group of photosynthetic prokaryotes capable of utilizing solar energy to fix atmospheric carbon dioxide to biomass. Despite several "proof of principle" studies, low product yield is an impediment in commercialization of cyanobacteria-derived biofuels. Estimation of intracellular reaction rates by (13)C metabolic flux analysis ((13)C-MFA) would be a step toward enhancing biofuel yield via metabolic engineering. We report (13)C-MFA for Cyanothece sp. ATCC 51142, a unicellular nitrogen-fixing cyanobacterium, known for enhanced hydrogen yield under mixotrophic conditions. Rates of reactions in the central carbon metabolism under nitrogen-fixing and -non-fixing conditions were estimated by monitoring the competitive incorporation of (12)C and (13)C from unlabeled CO2 and uniformly labeled glycerol, respectively, into terminal metabolites such as amino acids. The observed labeling patterns suggest mixotrophic growth under both the conditions, with a larger fraction of unlabeled carbon in nitrate-sufficient cultures asserting a greater contribution of carbon fixation by photosynthesis and an anaplerotic pathway. Indeed, flux analysis complements the higher growth observed under nitrate-sufficient conditions. On the other hand, the flux through the oxidative pentose phosphate pathway and tricarboxylic acid cycle was greater in nitrate-deficient conditions, possibly to supply the precursors and reducing equivalents needed for nitrogen fixation. In addition, an enhanced flux through fructose-6-phosphate phosphoketolase possibly suggests the organism's preferred mode under nitrogen-fixing conditions. The (13)C-MFA results complement the reported predictions by flux balance analysis and provide quantitative insight into the organism's distinct metabolic features under nitrogen-fixing and -non-fixing conditions.

Draft genome sequence of Janthinobacterium lividum strain MTR reveals its mechanism of capnophilic behavior.

PubMed

Valdes, Natalia; Soto, Paola; Cottet, Luis; Alarcon, Paula; Gonzalez, Alex; Castillo, Antonio; Corsini, Gino; Tello, Mario

2015-01-01

Janthinobacterium lividum is a Gram-negative bacterium able to produce violacein, a pigment with antimicrobial and antitumor properties. Janthinobacterium lividum colonizes the skin of some amphibians and confers protection against fungal pathogens. The mechanisms underlying this association are not well understood. In order to identify the advantages for the bacterium to colonize amphibian skin we sequenced Janthinobacterium lividum strain MTR, a strain isolated from Cajón del Maipo, Chile. The strain has capnophilic behavior, with growth favored by high concentrations (5 %) of carbon dioxide. Its genome is 6,535,606 bp in size, with 5,362 coding sequences and a G + C content of 62.37 %. The presence of genes encoding for products that participate in the carbon fixation pathways (dark CAM pathways), and the entire set of genes encoding for the enzymes of the glyoxylate cycle may explain the capnophilic behavior and allow us to propose that the CO2 secreted by the skin of amphibians is the signal molecule that guides colonization by Janthinobacterium lividum.

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide

PubMed Central

Nishihara, Arisa; Haruta, Shin; McGlynn, Shawn E.; Thiel, Vera; Matsuura, Katsumi

2018-01-01

The activity of nitrogen fixation measured by acetylene reduction was examined in chemosynthetic microbial mats at 72–75°C in slightly-alkaline sulfidic hot springs in Nakabusa, Japan. Nitrogenase activity markedly varied from sampling to sampling. Nitrogenase activity did not correlate with methane production, but was detected in samples showing methane production levels less than the maximum amount, indicating a possible redox dependency of nitrogenase activity. Nitrogenase activity was not affected by 2-bromo-ethane sulfonate, an inhibitor of methanogenesis. However, it was inhibited by the addition of molybdate, an inhibitor of sulfate reduction and sulfur disproportionation, suggesting the involvement of sulfate-reducing or sulfur-disproportionating organisms. Nitrogenase activity was affected by different O2 concentrations in the gas phase, again supporting the hypothesis of a redox potential dependency, and was decreased by the dispersion of mats with a homogenizer. The loss of activity that occurred from dispersion was partially recovered by the addition of H2, sulfate, and carbon dioxide. These results suggested that the observed activity of nitrogen fixation was related to chemoautotrophic sulfate reducers, and fixation may be active in a limited range of ambient redox potential. Since thermophilic chemosynthetic communities may resemble ancient microbial communities before the appearance of photosynthesis, the present results may be useful when considering the ancient nitrogen cycle on earth. PMID:29367473

Use of the S3 Corridor for Iliosacral Fixation in a Dysmorphic Sacrum: A Case Report.

PubMed

El Dafrawy, Mostafa H; Strike, Sophia A; Osgood, Greg M

2017-01-01

The S1 and S2 corridors are the typical osseous pathways for iliosacral screw fixation of posterior pelvic ring fractures. In dysmorphic sacra, the S1 screw trajectory is often different from that in normal sacra. We present a case of iliosacral screw placement in the third sacral segment for fixation of a complex lateral compression type-3 pelvic fracture in a patient with a dysmorphic sacrum. In patients with dysmorphic sacra and unstable posterior pelvic ring fractures or dislocations, the S3 corridor may be a feasible osseous fixation pathway that can be used in a manner equivalent to the S2 corridor in a normal sacrum.

Metagenomic analysis reveals a green sulfur bacterium as a potential coral symbiont.

PubMed

Cai, Lin; Zhou, Guowei; Tian, Ren-Mao; Tong, Haoya; Zhang, Weipeng; Sun, Jin; Ding, Wei; Wong, Yue Him; Xie, James Y; Qiu, Jian-Wen; Liu, Sheng; Huang, Hui; Qian, Pei-Yuan

2017-08-24

Coral reefs are ecologically significant habitats. Coral-algal symbiosis confers ecological success on coral reefs and coral-microbial symbiosis is also vital to coral reefs. However, current understanding of coral-microbial symbiosis on a genomic scale is largely unknown. Here we report a potential microbial symbiont in corals revealed by metagenomics-based genomic study. Microbial cells in coral were enriched for metagenomic analysis and a high-quality draft genome of "Candidatus Prosthecochloris korallensis" was recovered by metagenome assembly and genome binning. Phylogenetic analysis shows "Ca. P. korallensis" belongs to the Prosthecochloris clade and is clustered with two Prosthecochloris clones derived from Caribbean corals. Genomic analysis reveals "Ca. P. korallensis" has potentially important ecological functions including anoxygenic photosynthesis, carbon fixation via the reductive tricarboxylic acid (rTCA) cycle, nitrogen fixation, and sulfur oxidization. Core metabolic pathway analysis suggests "Ca. P. korallensis" is a green sulfur bacterium capable of photoautotrophy or mixotrophy. Potential host-microbial interaction reveals a symbiotic relationship: "Ca. P. korallensis" might provide organic and nitrogenous nutrients to its host and detoxify sulfide for the host; the host might provide "Ca. P. korallensis" with an anaerobic environment for survival, carbon dioxide and acetate for growth, and hydrogen sulfide as an electron donor for photosynthesis.

Photoactive TiO2 antibacterial coating on surgical external fixation pins for clinical application

PubMed Central

Villatte, Guillaume; Massard, Christophe; Descamps, Stéphane; Sibaud, Yves; Forestier, Christiane; Awitor, Komla-Oscar

2015-01-01

External fixation is a method of osteosynthesis currently used in traumatology and orthopedic surgery. Pin tract infection is a common problem in clinical practice. Infection occurs after bacterial colonization of the pin due to its contact with skin and the local environment. One way to prevent such local contamination is to create a specific coating that could be applied in the medical field. In this work, we developed a surface coating for external fixator pins based on the photocatalytic properties of titanium dioxide, producing a bactericidal effect with sufficient mechanical strength to be compatible with surgical use. The morphology and structure of the sol-gel coating layers were characterized using, respectively, scanning electron microscopy and X-ray diffraction. The resistance properties of the coating were investigated by mechanical testing. Photodegradation of acid orange 7 in aqueous solution was used as a probe to assess the photocatalytic activity of the titanium dioxide layers under ultraviolet irradiation. The bactericidal effect induced by the process was evaluated against two strains, ie, Staphylococcus aureus and multiresistant Staphylococcus epidermidis. The coated pins showed good mechanical strength and an efficient antibacterial effect after 1 hour of ultraviolet irradiation. PMID:26005347

Efficient Hydrogen-Dependent Carbon Dioxide Reduction by Escherichia coli.

PubMed

Roger, Magali; Brown, Fraser; Gabrielli, William; Sargent, Frank

2018-01-08

Hydrogen-dependent reduction of carbon dioxide to formic acid offers a promising route to greenhouse gas sequestration, carbon abatement technologies, hydrogen transport and storage, and the sustainable generation of renewable chemical feedstocks [1]. The most common approach to performing direct hydrogenation of CO 2 to formate is to use chemical catalysts in homogeneous or heterogeneous reactions [2]. An alternative approach is to use the ability of living organisms to perform this reaction biologically. However, although CO 2 fixation pathways are widely distributed in nature, only a few enzymes have been described that have the ability to perform the direct hydrogenation of CO 2 [3-5]. The formate hydrogenlyase (FHL) enzyme from Escherichia coli normally oxidizes formic acid to carbon dioxide and couples that reaction directly to the reduction of protons to molecular hydrogen [6]. In this work, the reverse reaction of FHL is unlocked. It is established that FHL can operate as a highly efficient hydrogen-dependent carbon dioxide reductase when gaseous CO 2 and H 2 are placed under pressure (up to 10 bar). Using intact whole cells, the pressurized system was observed to rapidly convert 100% of gaseous CO 2 to formic acid, and >500 mM formate was observed to accumulate in solution. Harnessing the reverse reaction has the potential to allow the versatile E. coli system to be employed as an exciting new carbon capture technology or as a cell factory dedicated to formic acid production, which is a commodity in itself as well as a feedstock for the synthesis of other valued chemicals. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Augmenting the Calvin-Benson-Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway.

PubMed

Yu, Hong; Li, Xiaoqian; Duchoud, Fabienne; Chuang, Derrick S; Liao, James C

2018-05-22

The Calvin-Benson-Bassham (CBB) cycle is presumably evolved for optimal synthesis of C3 sugars, but not for the production of C2 metabolite acetyl-CoA. The carbon loss in producing acetyl-CoA from decarboxylation of C3 sugar limits the maximum carbon yield of photosynthesis. Here we design a synthetic malyl-CoA-glycerate (MCG) pathway to augment the CBB cycle for efficient acetyl-CoA synthesis. This pathway converts a C3 metabolite to two acetyl-CoA by fixation of one additional CO 2 equivalent, or assimilates glyoxylate, a photorespiration intermediate, to produce acetyl-CoA without net carbon loss. We first functionally demonstrate the design of the MCG pathway in vitro and in Escherichia coli. We then implement the pathway in a photosynthetic organism Synechococcus elongates PCC7942, and show that it increases the intracellular acetyl-CoA pool and enhances bicarbonate assimilation by roughly 2-fold. This work provides a strategy to improve carbon fixation efficiency in photosynthetic organisms.

Toward solar biodiesel production from CO2 using engineered cyanobacteria.

PubMed

Woo, Han Min; Lee, Hyun Jeong

2017-05-01

Metabolic engineering of cyanobacteria has received attention as a sustainable strategy to convert carbon dioxide to various biochemicals including fatty acid-derived biodiesel. Recently, Synechococcus elongatus PCC 7942, a model cyanobacterium, has been engineered to convert CO2 to fatty acid ethyl esters (FAEEs) as biodiesel. Modular pathway has been constructed for FAEE production. Several metabolic engineering strategies were discussed to improve the production levels of FAEEs, including host engineering by improving CO2 fixation rate and photosynthetic efficiency. In addition, protein engineering of key enzyme in S. elongatus PCC 7942 was implemented to address issues on FAEE secretions toward sustainable FAEE production from CO2. Finally, advanced metabolic engineering will promote developing biosolar cell factories to convert CO2 to feasible amount of FAEEs toward solar biodiesel. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Larimer, Frank W; Chain, Patrick S. G.; Hauser, Loren John

Rhodopseudomonas palustris is among the most metabolically versatile bacteria known. It uses light, inorganic compounds, or organic compounds, for energy. It acquires carbon from many types of green plant-derived compounds or by carbon dioxide fixation, and it fixes nitrogen. Here we describe the genome sequence of R. palustris, which consists of a 5,459,213-base-pair (bp) circular chromosome with 4,836 predicted genes and a plasmid of 8,427 bp. The sequence reveals genes that confer a remarkably large number of options within a given type of metabolism, including three nitrogenases, five benzene ring cleavage pathways and four light harvesting 2 systems. R. palustrismore » encodes 63 signal transduction histidine kinases and 79 response regulator receiver domains. Almost 15% of the genome is devoted to transport. This genome sequence is a starting point to use R. palustris as a model to explore how organisms integrate metabolic modules in response to environmental perturbations.« less

Carbon dioxide dynamics of combined crops of wheat, cowpea, pinto beans in the Laboratory Biosphere closed ecological system

NASA Astrophysics Data System (ADS)

Dempster, William F.; Nelson, M.; Silverstone, S.; Allen, J. P.

2009-04-01

A mixed crop consisting of cowpeas, pinto beans and Apogee ultra-dwarf wheat was grown in the Laboratory Biosphere, a 40 m 3 closed life system equipped with 12,000 W of high pressure sodium lamps over planting beds with 5.37 m 2 of soil. Similar to earlier reported experiments, the concentration of carbon dioxide initially increased to 7860 ppm at 10 days after planting due to soil respiration plus CO 2 contributed from researchers breathing while in the chamber for brief periods before plant growth became substantial. Carbon dioxide concentrations then fell rapidly as plant growth increased up to 29 days after planting and subsequently was maintained mostly in the range of about 200-3000 ppm (with a few excursions) by CO 2 injections to feed plant growth. Numerous analyses of rate of change of CO 2 concentration at many different concentrations and at many different days after planting reveal a strong dependence of fixation rates on CO 2 concentration. In the middle period of growth (days 31-61), fixation rates doubled for CO 2 at 450 ppm compared to 270 ppm, doubled again at 1000 ppm and increased a further 50% at 2000 ppm. High productivity from these crops and the increase of fixation rates with elevated CO 2 concentration supports the concept that enhanced CO 2 can be a useful strategy for remote life support systems. The data suggests avenues of investigation to understand the response of plant communities to increasing CO 2 concentrations in the Earth's atmosphere. Carbon balance accounting and evapotranspiration rates are included.

Oxygen and Carbon Dioxide Fluxes from Barley Shoots Depend on Nitrate Assimilation 1

PubMed Central

Bloom, Arnold J.; Caldwell, Richard M.; Finazzo, John; Warner, Robert L.; Weissbart, Joseph

1989-01-01

A custom oxygen analyzer in conjunction with an infrared carbon dioxide analyzer and humidity sensors permitted simultaneous measurements of oxygen, carbon dioxide, and water vapor fluxes from the shoots of intact barley plants (Hordeum vulgare L. cv Steptoe). The oxygen analyzer is based on a calciazirconium sensor and can resolve concentration differences to within 2 microliters per liter against the normal background of 210,000 microliters per liter. In wild-type plants receiving ammonium as their sole nitrogen source or in nitrate reductase-deficient mutants, photosynthetic and respiratory fluxes of oxygen equaled those of carbon dioxide. By contrast, wild-type plants exposed to nitrate had unequal oxygen and carbon dioxide fluxes: oxygen evolution at high light exceeded carbon dioxide consumption by 26% and carbon dioxide evolution in the dark exceeded oxygen consumption by 25%. These results indicate that a substantial portion of photosynthetic electron transport or respiration generates reductant for nitrate assimilation rather than for carbon fixation or mitochondrial electron transport. PMID:16667024

Processing of urushiol (poison ivy) hapten by both endogenous and exogenous pathways for presentation to T cells in vitro.

PubMed

Kalish, R S; Wood, J A; LaPorte, A

1994-05-01

The antigen processing requirements for urushiol, the immunogen of poison ivy (Toxicodendron radicans), were tested by presentation of urushiol to cultured human urushiol-responsive T cells. Urushiol was added to antigen-presenting cells (APC) either before or after fixation with paraformaldehyde. Three distinct routes of antigen processing were detected. CD8+ and CD4+ T cells, which were dependent upon processing, proliferated if urushiol was added to APC before fixation, but did not proliferate when urushiol was added to APC after fixation. Processing of urushiol for presentation to CD8+ T cells was inhibited by azide, monensin, and brefeldin A. This suggests that urushiol was processed by the endogenous pathway. In contrast, presentation of urushiol to CD4+ T cells was inhibited by monensin but not by brefeldin A. This was compatible with antigen processing by the endosomal (exogenous) pathway. Finally, certain CD8+ T cells recognized urushiol in the absence of processing. These cells proliferated in response to APC incubated with urushiol after fixation. Classification of contact allergens by antigen processing pathway may predict the relative roles of CD4+ and CD8+ cells in the immunopathogensis of allergic contact dermatitis.

Processing of urushiol (poison ivy) hapten by both endogenous and exogenous pathways for presentation to T cells in vitro.

PubMed Central

Kalish, R S; Wood, J A; LaPorte, A

1994-01-01

The antigen processing requirements for urushiol, the immunogen of poison ivy (Toxicodendron radicans), were tested by presentation of urushiol to cultured human urushiol-responsive T cells. Urushiol was added to antigen-presenting cells (APC) either before or after fixation with paraformaldehyde. Three distinct routes of antigen processing were detected. CD8+ and CD4+ T cells, which were dependent upon processing, proliferated if urushiol was added to APC before fixation, but did not proliferate when urushiol was added to APC after fixation. Processing of urushiol for presentation to CD8+ T cells was inhibited by azide, monensin, and brefeldin A. This suggests that urushiol was processed by the endogenous pathway. In contrast, presentation of urushiol to CD4+ T cells was inhibited by monensin but not by brefeldin A. This was compatible with antigen processing by the endosomal (exogenous) pathway. Finally, certain CD8+ T cells recognized urushiol in the absence of processing. These cells proliferated in response to APC incubated with urushiol after fixation. Classification of contact allergens by antigen processing pathway may predict the relative roles of CD4+ and CD8+ cells in the immunopathogensis of allergic contact dermatitis. Images PMID:7910172

Microbial fixation of CO2 in water bodies and in drylands to combat climate change, soil loss and desertification.

PubMed

Rossi, Federico; Olguín, Eugenia J; Diels, Ludo; De Philippis, Roberto

2015-01-25

The growing concern for the increase of the global warming effects due to anthropogenic activities raises the challenge of finding novel technological approaches to stabilize CO2 emissions in the atmosphere and counteract impinging interconnected issues such as desertification and loss of biodiversity. Biological-CO2 mitigation, triggered through biological fixation, is considered a promising and eco-sustainable method, mostly owing to its downstream benefits that can be exploited. Microorganisms such as cyanobacteria, green algae and some autotrophic bacteria could potentially fix CO2 more efficiently than higher plants, due to their faster growth. Some examples of the potential of biological-CO2 mitigation are reported and discussed in this paper. In arid and semiarid environments, soil carbon sequestration (CO2 fixation) by cyanobacteria and biological soil crusts is considered an eco-friendly and natural process to increase soil C content and a viable pathway to soil restoration after one disturbance event. Another way for biological-CO2 mitigation intensively studied in the last few years is related to the possibility to perform carbon dioxide sequestration using microalgae, obtaining at the same time bioproducts of industrial interest. Another possibility under study is the exploitation of specific chemotrophic bacteria, such as Ralstonia eutropha (or picketii) and related organisms, for CO2 fixation coupled with the production chemicals such as polyhydroxyalkanoates (PHAs). In spite of the potential of these processes, multiple factors still have to be optimized for maximum rate of CO2 fixation by these microorganisms. The optimization of culture conditions, including the optimal concentration of CO2 in the provided gas, the use of metabolic engineering and of dual purpose systems for the treatment of wastewater and production of biofuels and high value products within a biorefinery concept, the design of photobioreactors in the case of phototrophs are some of the issues that, among others, have to be addressed and tested for cost-effective CO2 sequestration. Copyright © 2013 Elsevier B.V. All rights reserved.

Local strategies to prevent and treat osteoporosis.

PubMed

Torstrick, F Brennan; Guldberg, Robert E

2014-03-01

Despite advances in systemic osteoporosis therapeutic outcomes, management of fragility fractures and implant fixation in osteoporotic bone remain difficult clinical challenges. Low initial bone density and a prolonged healing response can lead to fracture nonunion and aseptic implant loosening. Local treatment strategies could be used to prevent fracture, accelerate healing, and increase implant fixation by locally stimulating anabolic pathways or inhibiting catabolic pathways. Local strategies under investigation include direct drug release from injectable materials or implant surface coatings. Common locally delivered drugs include bisphosphonates, parathyroid hormone, and bone morphogenetic proteins, yet additional compounds targeting novel pathways in bone biology are also being actively explored. Mechanical stimulation via low intensity pulsed ultrasound, alone or in combination with drug therapy, may also prove effective to promote local bone healing and implant fixation within osteoporotic bone.

[Phenotypic properties of Sulfobacillus thermotolerans: comparative aspects].

PubMed

Tsaplina, I A; Krasil'nikova, E N; Zhuravleva, A E; Egorova, M A; Zakharchuk, L M; Suzina, N E; Duda, V I; Bogdanova, T I; Stadnichuk, I N; Kondrat'eva, T F

2008-01-01

The phenotypic characteristics of the species Sulfobacillus thermotolerans Kr1(T), as dependent on the cultivation conditions, are described in detail. High growth rates (0.22-0.30 h(-1)) and high oxidative activity were recorded under optimum mixotrophic conditions at 40 degrees C on medium with inorganic (Fe(II), S(0), or pyrite-arsenopyrite concentrate) and organic (glucose and/or yeast extract) substrates. In cells grown under optimum conditions on medium with iron, hemes a, b, and, most probably, c were present, indicating the presence of the corresponding cytochromes. Peculiar extended structures in the form of cylindrical cords, never observed previously, were revealed; a mucous matrix, likely of polysaccharide nature, occurred around the cells. In the cells of sulfobacilli grown litho-, organo-, and mixotrophically at 40 degrees C, the enzymes of the three main pathways of carbon utilization and some enzymes of the TCA cycle were revealed. The enzyme activity was maximum under mixotrophic growth conditions. The growth rate in the regions of limiting temperatures (55 degrees C and 12-14 degrees C) decreased two- and tenfold, respectively; no activity of 6-phosphogluconate dehydrogenase, one of the key enzymes of the oxidative pentose phosphate pathway, could be revealed; and a decrease in the activity of almost all enzymes of glucose metabolism and of the TCA cycle was observed. The rate of 14CO2 fixation by cells under auto-, mixo-, and heterotrophic conditions constituted 31.8, 23.3, and 10.3 nmol/(h mg protein), respectively. The activities of RuBP carboxylase (it peaked during lithotrophic growth) and of carboxylases of heterotrophic carbon dioxide fixation were recorded. The physiological and biochemical peculiarities of the thermotolerant sulfobacillus are compared versus moderately thermophilic sulfobacilli.

Entrapment of carbon dioxide with chitosan-based core-shell particles containing changeable cores.

PubMed

Dong, Yanrui; Fu, Yinghao; Lin, Xia; Xiao, Congming

2016-08-01

Water-soluble chitosan-based core-shell particles that contained changeable cores were successfully applied to anchor carbon dioxide. The entrapment capacity of the particles for carbon dioxide (EC) depended on the cores. It was found that EC of the particles contained aqueous cores was higher than that of the beads with water-soluble chitosan gel cores, which was confirmed with thermogravimetric analysis. In addition, calcium ions and sodium hydroxide were introduced within the particles to examine their effect on the entrapment. EC of the particles was enhanced with sodium hydroxide when the cores were WSC gel. The incorporation of calcium ions was helpful for stabilizing carbon dioxide through the formation of calcium carbonate, which was verified with Fourier transform infrared spectra and scanning electron microscopy/energy-dispersive spectrometry. This phenomenon meant the role of calcium ions for fixating carbon dioxide was significant. Copyright © 2016 Elsevier B.V. All rights reserved.

Response of Carbon Dioxide Fixation to Water Stress

PubMed Central

Plaut, Z.; Bravdo, B.

1973-01-01

Application of water stress to isolated spinach (Spinacia oleracea) chloroplasts by redutcion of the osmotic potentials of CO2 fixation media below −6 to −8 bars resulted in decreased rates of fixation regardless of solute composition. A decrease in CO2 fixation rate of isolated chloroplasts was also found when leaves were dehydrated in air prior to chloroplast isolation. An inverse response of CO2 fixation to osmotic potential of the fixation medium was found with chloroplasts isolated from dehydrated leaves—namely, fixation rate was inhibited at −8 bars, compared with −16 or −24 bars. Low leaf water potentials were found to inhibit CO2 fixation of intact leaf discs to almost the same degree as they did CO2 fixation by chloroplasts isolated from those leaves. CO2 fixation by intact leaves was decreased by 50 and 80% when water potentials were reduced from −7.1 to −9.6 and from −7.1 to −17.6 bars, respectively. Transpiration was decreased by only 40 and 60%, under the same conditions. However, correction for the increase in leaf temperature indicated transpiration decreases of 57 and 80%, similar to the relative decreases in CO2 fixation. Despite the 4-fold increase in leaf resistance to CO2 diffusion in the gas phase when the water potential of leaves was reduced from −6.5 to −14.0 bars, an additional increase of about 50% in mesophyll resistance was obtained. CO2 concentration at compensation also increased when leaf water potential was reduced. PMID:16658493

Community structure and soil pH determine chemoautotrophic carbon dioxide fixation in drained paddy soils.

PubMed

Long, Xi-En; Yao, Huaiying; Wang, Juan; Huang, Ying; Singh, Brajesh K; Zhu, Yong-Guan

2015-06-16

Previous studies suggested that microbial photosynthesis plays a potential role in paddy fields, but little is known about chemoautotrophic carbon fixers in drained paddy soils. We conducted a microcosm study using soil samples from five paddy fields to determine the environmental factors and quantify key functional microbial taxa involved in chemoautotrophic carbon fixation. We used stable isotope probing in combination with phospholipid fatty acid (PLFA) and molecular approaches. The amount of microbial (13)CO2 fixation was determined by quantification of (13)C-enriched fatty acid methyl esters and ranged from 21.28 to 72.48 ng of (13)C (g of dry soil)(-1), and the corresponding ratio (labeled PLFA-C:total PLFA-C) ranged from 0.06 to 0.49%. The amount of incorporationof (13)CO2 into PLFAs significantly increased with soil pH except at pH 7.8. PLFA and high-throughput sequencing results indicated a dominant role of Gram-negative bacteria or proteobacteria in (13)CO2 fixation. Correlation analysis indicated a significant association between microbial community structure and carbon fixation. We provide direct evidence of chemoautotrophic C fixation in soils with statistical evidence of microbial community structure regulation of inorganic carbon fixation in the paddy soil ecosystem.

Elevated CO2: Impact on diurnal patterns of photosynthesis in natural microbial ecosystems

NASA Technical Reports Server (NTRS)

Rothschild, L. J.

1994-01-01

Algae, including blue-green algae (cyanobacteria), are the major source of fixed carbon in many aquatic ecosystems. Previous work has shown that photosynthetic carbon fixation is often enhanced in the presence of additional carbon dioxide (CO2). This study was undertaken to determine if this CO2 fertilization effect extended to microbial mats, and, if so, at what times during the day might the addition of CO2 affect carbon fixation. Four microbial mats from diverse environments were selected, including mats from a hypersaline pond (area 5, Exportadora de Sal, Mexico), the marine intertidal (Lyngbya, Laguna Ojo de Liebre, Mexico), an acidic hotspring (Cyanidium, Nymph Creek, Yellowstone National Park), and an acidic stream at ambient temperature (Zygogonium, Yellowstone National Park). Carbon fixation in the absence of additional CO2 essentially followed the rising and falling sunlight levels, except that during the middle of the day there was a short dip in carbon fixation rates. The addition of CO2 profoundly enhanced carbon fixation rates during the daylight hours, including during the midday dip. Therefore, it is unlikely that the midday dip was due to photoinhibition. Surprisingly, enhancement of carbon fixation was often greatest in the early morning or late afternoon, times when carbon fixation would be most likely to be light limited.

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes

PubMed Central

Hawley, Alyse K.; Brewer, Heather M.; Norbeck, Angela D.; Paša-Tolić, Ljiljana; Hallam, Steven J.

2014-01-01

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand. PMID:25053816

Metaproteomics reveals differential modes of metabolic coupling among ubiquitous oxygen minimum zone microbes.

PubMed

Hawley, Alyse K; Brewer, Heather M; Norbeck, Angela D; Paša-Tolić, Ljiljana; Hallam, Steven J

2014-08-05

Marine oxygen minimum zones (OMZs) are intrinsic water column features arising from respiratory oxygen demand during organic matter degradation in stratified waters. Currently OMZs are expanding due to global climate change with resulting feedback on marine ecosystem function. Here we use metaproteomics to chart spatial and temporal patterns of gene expression along defined redox gradients in a seasonally stratified fjord to better understand microbial community responses to OMZ expansion. The expression of metabolic pathway components for nitrification, anaerobic ammonium oxidation (anammox), denitrification, and inorganic carbon fixation were differentially expressed across the redoxcline and covaried with distribution patterns of ubiquitous OMZ microbes including Thaumarchaeota, Nitrospina, Nitrospira, Planctomycetes, and SUP05/ARCTIC96BD-19 Gammaproteobacteria. Nitrification and inorganic carbon fixation pathways affiliated with Thaumarchaeota dominated dysoxic waters, and denitrification, sulfur oxidation, and inorganic carbon fixation pathways affiliated with the SUP05 group of nitrate-reducing sulfur oxidizers dominated suboxic and anoxic waters. Nitrifier nitrite oxidation and anammox pathways affiliated with Nirospina, Nitrospira, and Planctomycetes, respectively, also exhibited redox partitioning between dysoxic and suboxic waters. The numerical abundance of SUP05 proteins mediating inorganic carbon fixation under anoxic conditions suggests that SUP05 will become increasingly important in global ocean carbon and nutrient cycling as OMZs expand.

Photoassisted carbon dioxide reduction and formation of twoand three-carbon compounds. [prebiological photosynthesis

NASA Technical Reports Server (NTRS)

Halmann, M.; Aurian-Blajeni, B.; Bloch, S.

1981-01-01

The photoassisted reduction of aqueous carbon dioxide in the presence of naturally occurring minerals is investigated as a possible abiotic precursor of photosynthesis. Aqueous carbon dioxide saturated suspensions or surfaces of the minerals nontronite, bentonite, anatase, wolframite, molybdenite, minium, cinnabar and hematite were irradiated with high-pressure mercury lamps or sunlight. Chemical analyses reveal the production of formic acid, formaldehyde, methanol and methane, and the two and three-carbon compounds glyoxal (CHOCHO) and malonaldehyde (CH2(CHO)2). It is suggested that such photosynthetic reactions with visible light in the presence of semiconducting minerals may provide models for prebiological carbon and nitrogen fixation in both oxidized and reduced atmospheres.

In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways*♦

PubMed Central

Dey, Swati; North, Justin A.; Sriram, Jaya; Evans, Bradley S.; Tabita, F. Robert

2015-01-01

All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO2 as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilation. In addition, sulfur salvage pathways are necessary to ensure that key sulfur-containing compounds are both available and, where necessary, detoxified in the cell. Using knock-out mutations and metabolomics in the bacterium Rhodospirillum rubrum, we show here that Rubisco concurrently catalyzes key and essential reactions for seemingly unrelated but physiologically essential central carbon and sulfur salvage metabolic pathways of the cell. In this study, complementation and mutagenesis studies indicated that representatives of all known extant functional Rubisco forms found in nature are capable of simultaneously catalyzing reactions required for both CO2-dependent growth as well as growth using 5-methylthioadenosine as sole sulfur source under anaerobic photosynthetic conditions. Moreover, specific inactivation of the CO2 fixation reaction did not affect the ability of Rubisco to support anaerobic 5-methylthioadenosine metabolism, suggesting that the active site of Rubisco has evolved to ensure that this enzyme maintains both key functions. Thus, despite the coevolution of both functions, the active site of this protein may be differentially modified to affect only one of its key functions. PMID:26511314

Inhibitory effect of self-generated extracellular dissolved organic carbon on carbon dioxide fixation in sulfur-oxidizing bacteria during a chemoautotrophic cultivation process and its elimination.

PubMed

Wang, Ya-Nan; Tsang, Yiu Fai; Wang, Lei; Fu, Xiaohua; Hu, Jiajun; Li, Huan; Le, Yiquan

2018-03-01

The features of extracellular dissolved organic carbon (EDOC) generation in two typical aerobic sulfur-oxidizing bacteria (Thiobacillus thioparus DSM 505 and Halothiobacillus neapolitanus DSM 15147) and its impact on CO 2 fixation during chemoautotrophic cultivation process were investigated. The results showed that EDOC accumulated in both strains during CO 2 fixation process. Large molecular weight (MW) EDOC derived from cell lysis and decay was dominant during the entire process in DSM 505, whereas small MW EDOC accounted for a large proportion during initial and middle stages of DSM 15147 as its cytoskeleton synthesis rate did not keep up with CO 2 assimilation rate. The self-generated EDOC feedback repressed cbb gene transcription and thus decreased total bacterial cell number and CO 2 fixation yield in both strains, but DSM 505 was more sensitive to this inhibition effect. Moreover, the membrane bioreactor effectively decreased the EDOC/TOC ratio and improved carbon fixation yield of DSM 505. Copyright © 2017 Elsevier Ltd. All rights reserved.

Preparation of 2-hydroxy-5-oxoproline and analogs thereof

DOEpatents

Martinez, Rodolfo A.; Unkefer, Pat J.

2001-01-01

The compound 2-hydroxy-5-oxoproline and analogs thereof may be used to produce an increase in carbon dioxide fixation, growth, dry weight, nutritional value (proteins and amino acids), nodulation and nitrogen fixation and photosynthetically derived chemical energy when applied to plants through their roots and/or through their foliar portions. The present invention includes an essentially quantitative chemical synthesis for this compound which is performed in a single step reaction of Fremy's Salt (potassium nitrosodisulphonate) with either glutamine or 2-pyrrolidone-5-carboxylic acid. Fremy's salt (potassium nitrosodisulphonate) is available commercially, or can be readily synthesized.

Transcriptome-based analysis on carbon metabolism of Haematococcus pluvialis mutant under 15% CO2.

PubMed

Li, Ke; Cheng, Jun; Lu, Hongxiang; Yang, Weijuan; Zhou, Junhu; Cen, Kefa

2017-06-01

To elucidate the mechanism underlying the enhanced growth rate in the Haematococcus pluvialis mutated with 60 Co-γ rays and domesticated with 15% CO 2 , transcriptome sequencing was conducted to clarify the carbon metabolic pathways of mutant cells. The CO 2 fixation rate of mutant cells increased to 2.57gL -1 d -1 under 15% CO 2 due to the enhanced photosynthesis, carbon fixation, glycolysis pathways. The upregulation of PetH, ATPF0A and PetJ related to photosynthetic electron transport, ATP synthase and NADPH generation promoted the photosynthesis. The upregulation of genes related to Calvin cycle and ppdK promoted carbon fixation in both C3 and C4 photosynthetic pathways. The reallocation of carbon was also enhanced under 15% CO 2 . The 19-, 14- and 3.5-fold upregulation of FBA, TPI and PK genes, respectively, remarkably promoted the glycolysis pathways. This accelerated the conversion of photosynthetic carbon to pyruvate, which was an essential precursor for astaxanthin and lipids biosynthesis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Abundance and Distribution of Diagnostic Carbon Fixation Genes in a Deep-Sea Hydrothermal Gradient Ecosystem

NASA Astrophysics Data System (ADS)

Blumenfeld, H. N.; Kelley, D. S.; Girguis, P. R.; Schrenk, M. O.

2010-12-01

The walls of deep-sea hydrothermal vent chimneys sustain steep thermal and chemical gradients resulting from the mixing of hot (350°C+) hydrothermal fluids with cold, oxygenated seawater. The chemical disequilibrium generated from this process has the potential to drive numerous chemolithoautotrophic metabolisms, many of which have been demonstrated to be operative in microbial pure cultures. In addition to the well-known Calvin Cycle, at least five additional pathways have been discovered including the Reverse Tricarboxylic Acid Cycle (rTCA), the Reductive Acetyl-CoA pathway, and the 3-hydroxyproprionate pathway. Most of the newly discovered pathways have been found in thermophilic and hyperthermophilic Bacteria and Archaea, which are the well represented in microbial diversity studies of hydrothermal chimney walls. However, to date, little is known about the environmental controls that impact various carbon fixation pathways. The overlap of limited microbial diversity with distinct habitat conditions in hydrothermal chimney walls provides an ideal setting to explore these relationships. Hydrothermal chimney walls from multiple structures recovered from the Juan de Fuca Ridge in the northeastern Pacific were sub-sampled and analyzed using PCR-based assays. Earlier work showed elevated microbial abundances in the outer portions of mature chimney walls, with varying ratios of Archaea to Bacteria from the outer to inner portions of the chimneys. Common phylotypes identified in these regions included Epsilonproteobacteria, Gammaproteobacteria, and Desulfurococcales. Total genomic DNA was extracted from mineralogically distinct niches within these structures and queried for genes coding key regulatory enzymes for each of the well studied carbon fixation pathways. Preliminary results show the occurrence of genes representing rTCA cycle (aclB) and methyl coenzyme A reductase (mcrA) - a proxy for the Reductive Acetyl-CoA Pathway within interior portion of mature hydrothermal chimneys. Ongoing analyses are aimed at quantifying the abundances of these diagnostic carbon fixation genes within the hydrothermal chimney gradients. These data are being compared to a broad array of contextual data to provide insight into the environmental and biological controls that may impact the distribution of the various carbon fixation pathways. Application of genomic approaches to the hydrothermal chimney ecosystem will provide insight into the microbial ecology of such structures and refine our ability to measure autotrophy in hydrothermal habitats sustained by chemical energy.

Communication: Photoinduced carbon dioxide binding with surface-functionalized silicon quantum dots.

PubMed

Douglas-Gallardo, Oscar A; Sánchez, Cristián Gabriel; Vöhringer-Martinez, Esteban

2018-04-14

Nowadays, the search for efficient methods able to reduce the high atmospheric carbon dioxide concentration has turned into a very dynamic research area. Several environmental problems have been closely associated with the high atmospheric level of this greenhouse gas. Here, a novel system based on the use of surface-functionalized silicon quantum dots (sf-SiQDs) is theoretically proposed as a versatile device to bind carbon dioxide. Within this approach, carbon dioxide trapping is modulated by a photoinduced charge redistribution between the capping molecule and the silicon quantum dots (SiQDs). The chemical and electronic properties of the proposed SiQDs have been studied with a Density Functional Theory and Density Functional Tight-Binding (DFTB) approach along with a time-dependent model based on the DFTB framework. To the best of our knowledge, this is the first report that proposes and explores the potential application of a versatile and friendly device based on the use of sf-SiQDs for photochemically activated carbon dioxide fixation.

Communication: Photoinduced carbon dioxide binding with surface-functionalized silicon quantum dots

NASA Astrophysics Data System (ADS)

Douglas-Gallardo, Oscar A.; Sánchez, Cristián Gabriel; Vöhringer-Martinez, Esteban

2018-04-01

Nowadays, the search for efficient methods able to reduce the high atmospheric carbon dioxide concentration has turned into a very dynamic research area. Several environmental problems have been closely associated with the high atmospheric level of this greenhouse gas. Here, a novel system based on the use of surface-functionalized silicon quantum dots (sf-SiQDs) is theoretically proposed as a versatile device to bind carbon dioxide. Within this approach, carbon dioxide trapping is modulated by a photoinduced charge redistribution between the capping molecule and the silicon quantum dots (SiQDs). The chemical and electronic properties of the proposed SiQDs have been studied with a Density Functional Theory and Density Functional Tight-Binding (DFTB) approach along with a time-dependent model based on the DFTB framework. To the best of our knowledge, this is the first report that proposes and explores the potential application of a versatile and friendly device based on the use of sf-SiQDs for photochemically activated carbon dioxide fixation.

Reactions of Criegee Intermediates with Non-Water Greenhouse Gases: Implications for Metal Free Chemical Fixation of Carbon Dioxide.

PubMed

Kumar, Manoj; Francisco, Joseph S

2017-09-07

High-level theoretical calculations suggest that a Criegee intermediate preferably interacts with carbon dioxide compared to two other greenhouse gases, nitrous oxide and methane. The results also suggest that the interaction between Criegee intermediates and carbon dioxide involves a cycloaddition reaction, which results in the formation of a cyclic carbonate-type adduct with a barrier of 6.0-14.0 kcal/mol. These results are in contrast to a previous assumption that the reaction occurs barrierlessly. The subsequent decomposition of the cyclic adduct into formic acid and carbon dioxide follows both concerted and stepwise mechanisms. The latter mechanism has been overlooked previously. Under formic acid catalysis, the concerted decomposition of the cyclic carbonate may be favored under tropospheric conditions. Considering that there is a strong nexus between carbon dioxide levels in the atmosphere and global warming, the high reactivity of Criegee intermediates could be utilized for designing efficient carbon capture technologies.

Conversion of 4-Hydroxybutyrate to Acetyl Coenzyme A and Its Anapleurosis in the Metallosphaera sedula 3-Hydroxypropionate/4-Hydroxybutyrate Carbon Fixation Pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hawkins, AB; Adams, MWW; Kelly, RM

2014-03-25

The extremely thermoacidophilic archaeon Metallosphaera sedula (optimum growth temperature, 73 degrees C, pH 2.0) grows chemolithoautotrophically on metal sulfides or molecular hydrogen by employing the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) carbon fixation cycle. This cycle adds two CO2 molecules to acetyl coenzyme A (acetyl-CoA) to generate 4HB, which is then rearranged and cleaved to form two acetyl-CoA molecules. Previous metabolic flux analysis showed that two-thirds of central carbon precursor molecules are derived from succinyl-CoA, which is oxidized to malate and oxaloacetate. The remaining one-third is apparently derived from acetyl-CoA. As such, the steps beyond succinyl-CoA are essential for completing the carbon fixation cyclemore » and for anapleurosis of acetyl-CoA. Here, the final four enzymes of the 3HP/4HB cycle, 4-hydroxybutyrate-CoA ligase (AMP forming) (Msed_0406), 4-hydroxybutyryl-CoA dehydratase (Msed_1321), crotonyl-CoA hydratase/(S)-3-hydroxybutyryl-CoA dehydrogenase (Msed_0399), and acetoacetyl-CoA beta-ketothiolase (Msed_0656), were produced recombinantly in Escherichia coli, combined in vitro, and shown to convert 4HB to acetyl-CoA. Metabolic pathways connecting CO2 fixation and central metabolism were examined using a gas-intensive bioreactor system in which M. sedula was grown under autotrophic (CO2-limited) and heterotrophic conditions. Transcriptomic analysis revealed the importance of the 3HP/4HB pathway in supplying acetyl-CoA to anabolic pathways generating intermediates in M. sedula metabolism. The results indicated that flux between the succinate and acetyl-CoA branches in the 3HP/4HB pathway is governed by 4-hydroxybutyrate-CoA ligase, possibly regulated posttranslationally by the protein acetyltransferase (Pat)/Sir2-dependent system. Taken together, this work confirms the final four steps of the 3HP/4HB pathway, thereby providing the framework for examining connections between CO2 fixation and central metabolism in M. sedula.« less

In Vivo Studies in Rhodospirillum rubrum Indicate That Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (Rubisco) Catalyzes Two Obligatorily Required and Physiologically Significant Reactions for Distinct Carbon and Sulfur Metabolic Pathways.

PubMed

Dey, Swati; North, Justin A; Sriram, Jaya; Evans, Bradley S; Tabita, F Robert

2015-12-25

All organisms possess fundamental metabolic pathways to ensure that needed carbon and sulfur compounds are provided to the cell in the proper chemical form and oxidation state. For most organisms capable of using CO2 as sole source of carbon, ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes primary carbon dioxide assimilation. In addition, sulfur salvage pathways are necessary to ensure that key sulfur-containing compounds are both available and, where necessary, detoxified in the cell. Using knock-out mutations and metabolomics in the bacterium Rhodospirillum rubrum, we show here that Rubisco concurrently catalyzes key and essential reactions for seemingly unrelated but physiologically essential central carbon and sulfur salvage metabolic pathways of the cell. In this study, complementation and mutagenesis studies indicated that representatives of all known extant functional Rubisco forms found in nature are capable of simultaneously catalyzing reactions required for both CO2-dependent growth as well as growth using 5-methylthioadenosine as sole sulfur source under anaerobic photosynthetic conditions. Moreover, specific inactivation of the CO2 fixation reaction did not affect the ability of Rubisco to support anaerobic 5-methylthioadenosine metabolism, suggesting that the active site of Rubisco has evolved to ensure that this enzyme maintains both key functions. Thus, despite the coevolution of both functions, the active site of this protein may be differentially modified to affect only one of its key functions. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Acetogenesis and the Wood-Ljungdahl Pathway of CO2 Fixation

PubMed Central

Ragsdale, Stephen W.; Pierce, Elizabeth

2008-01-01

I. Summary Conceptually, the simplest way to synthesize an organic molecule is to construct it one carbon at a time. The Wood-Ljungdahl pathway of CO2 fixation involves this type of stepwise process. The biochemical events that underlie the condensation of two one-carbon units to form the two-carbon compound, acetate, have intrigued chemists, biochemists, and microbiologists for many decades. We begin this review with a description of the biology of acetogenesis. Then, we provide a short history of the important discoveries that have led to the identification of the key components and steps of this usual mechanism of CO and CO2 fixation. In this historical perspective, we have included reflections that hopefully will sketch the landscape of the controversies, hypotheses, and opinions that led to the key experiments and discoveries. We then describe the properties of the genes and enzymes involved in the pathway and conclude with a section describing some major questions that remain unanswered. PMID:18801467

Critical Involvement of Environmental Carbon Dioxide Fixation to Drive Wax Ester Fermentation in Euglena

PubMed Central

Nishio, Kazuki; Nakazawa, Masami; Nakamoto, Masatoshi; Okazawa, Atsushi; Kanaya, Shigehiko; Arita, Masanori

2016-01-01

Accumulation profiles of wax esters in Euglena gracilis Z were studied under several environmental conditions. The highest amount of total wax esters accumulated under hypoxia in the dark, and C28 (myristyl-myristate, C14:0-C14:0) was prevalent among all conditions investigated. The wax ester production was almost completely suppressed under anoxia in the light, and supplying exogenous inorganic carbon sources restored wax ester fermentation, indicating the need for external carbon sources for the wax ester fermentation. 13C-labeling experiments revealed specific isotopic enrichment in the odd-numbered fatty acids derived from wax esters, indicating that the exogenously-supplied CO2 was incorporated into wax esters via the propionyl-CoA pathway through the reverse tricarboxylic acid (TCA) cycle. The addition of 3-mercaptopicolinic acid, a phosphoenolpyruvate carboxykinase (PEPCK) inhibitor, significantly affected the incorporation of 13C into citrate and malate as the biosynthetic intermediates of the odd-numbered fatty acids, suggesting the involvement of PEPCK reaction to drive wax ester fermentation. Additionally, the 13C-enrichment pattern of succinate suggested that the CO2 assimilation might proceed through alternative pathways in addition to the PEPCK reaction. The current results indicate that the mechanisms of anoxic CO2 assimilation are an important target to reinforce wax ester fermentation in Euglena. PMID:27669566

From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources.

PubMed

Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-01-01

At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe(2+) ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD(+) through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats.

From chemolithoautotrophs to electrolithoautotrophs: CO2 fixation by Fe(II)-oxidizing bacteria coupled with direct uptake of electrons from solid electron sources

PubMed Central

Ishii, Takumi; Kawaichi, Satoshi; Nakagawa, Hirotaka; Hashimoto, Kazuhito; Nakamura, Ryuhei

2015-01-01

At deep-sea vent systems, hydrothermal emissions rich in reductive chemicals replace solar energy as fuels to support microbial carbon assimilation. Until recently, all the microbial components at vent systems have been assumed to be fostered by the primary production of chemolithoautotrophs; however, both the laboratory and on-site studies demonstrated electrical current generation at vent systems and have suggested that a portion of microbial carbon assimilation is stimulated by the direct uptake of electrons from electrically conductive minerals. Here we show that chemolithoautotrophic Fe(II)-oxidizing bacterium, Acidithiobacillus ferrooxidans, switches the electron source for carbon assimilation from diffusible Fe2+ ions to an electrode under the condition that electrical current is the only source of energy and electrons. Site-specific marking of a cytochrome aa3 complex (aa3 complex) and a cytochrome bc1 complex (bc1 complex) in viable cells demonstrated that the electrons taken directly from an electrode are used for O2 reduction via a down-hill pathway, which generates proton motive force that is used for pushing the electrons to NAD+ through a bc1 complex. Activation of carbon dioxide fixation by a direct electron uptake was also confirmed by the clear potential dependency of cell growth. These results reveal a previously unknown bioenergetic versatility of Fe(II)-oxidizing bacteria to use solid electron sources and will help with understanding carbon assimilation of microbial components living in electronically conductive chimney habitats. PMID:26500609

Carboxysomes: metabolic modules for CO 2 fixation

DOE PAGES

Turmo, Aiko; Gonzalez-Esquer, Cesar Raul; Kerfeld, Cheryl A.

2017-08-14

The carboxysome is a bacterial microcompartment encapsulating the enzymes carbonic anhydrase and ribulose-1,5-bisphosphate carboxylase/oxygenase. As the site of CO 2 fixation, it serves an essential role in the carbon dioxide concentrating mechanism of many chemoautotrophs and all cyanobacteria. Carboxysomes and other bacterial microcompartments self-assemble through specific protein–protein interactions that are typically mediated by conserved protein domains. In this review, we frame our current understanding of carboxysomes in the context of their component protein domains with their inherent function as the ‘building blocks’ of carboxysomes. These building blocks are organized in genetic modules (conserved chromosomal loci) that encode for carboxysomes andmore » ancillary proteins essential for the integration of the organelle with the rest of cellular metabolism. This conceptual framework provides the foundation for ‘plug-and-play’ engineering of carboxysomes as CO 2 fixation modules in a variety of biotechnological applications.« less

Low oxygen affects photophysiology and the level of expression of two-carbon metabolism genes in the seagrass Zostera muelleri.

PubMed

Kim, Mikael; Brodersen, Kasper Elgetti; Szabó, Milán; Larkum, Anthony W D; Raven, John A; Ralph, Peter J; Pernice, Mathieu

2018-05-01

Seagrasses are a diverse group of angiosperms that evolved to live in shallow coastal waters, an environment regularly subjected to changes in oxygen, carbon dioxide and irradiance. Zostera muelleri is the dominant species in south-eastern Australia, and is critical for healthy coastal ecosystems. Despite its ecological importance, little is known about the pathways of carbon fixation in Z. muelleri and their regulation in response to environmental changes. In this study, the response of Z. muelleri exposed to control and very low oxygen conditions was investigated by using (i) oxygen microsensors combined with a custom-made flow chamber to measure changes in photosynthesis and respiration, and (ii) reverse transcription quantitative real-time PCR to measure changes in expression levels of key genes involved in C 4 metabolism. We found that very low levels of oxygen (i) altered the photophysiology of Z. muelleri, a characteristic of C 3 mechanism of carbon assimilation, and (ii) decreased the expression levels of phosphoenolpyruvate carboxylase and carbonic anhydrase. These molecular-physiological results suggest that regulation of the photophysiology of Z. muelleri might involve a close integration between the C 3 and C 4 , or other CO 2 concentrating mechanisms metabolic pathways. Overall, this study highlights that the photophysiological response of Z. muelleri to changing oxygen in water is capable of rapid acclimation and the dynamic modulation of pathways should be considered when assessing seagrass primary production.

Path of Carbon in Photosynthesis III.

DOE R&D Accomplishments Database

Benson, A. A.; Calvin, M.

1948-06-01

Although the overall reaction of photosynthesis can be specified with some degree of certainty (CO{sub 2} + H{sub 2}O + light {yields} sugars + possibly other reduced substances), the intermediates through which the carbon passes during the course of this reduction have, until now, been largely a matter of conjecture. The availability of isotopic carbon, that is, a method of labeling the carbon dioxide, provides the possibility of some very direct experiments designed to recognize these intermediates and, perhaps, help to understand the complex sequence and interplay of reactions which must constitute the photochemical process itself. The general design of such experiments is an obvious one, namely the exposure of the green plant to radioactive carbon dioxide and light under a variety of conditions and for continually decreasing lengths of time, followed by the identification of the compounds into which the radioactive carbon is incorporated under each condition and time period. From such data it is clear that in principle, at least, it should be possible to establish the sequence of compounds in time through which the carbon passes on its path from carbon dioxide to the final products. In the course of shortening the photosynthetic times, one times, one ultimately arrives at the condition of exposing the plants to the radioactive carbon dioxide with a zero illumination time, that is, in the dark. Actually, in the work the systematic order of events was reversed, and they have begun by studying first the dark fixation and then the shorter photosynthetic times. The results of the beginnings of this sort of a systematic investigation are given in Table I which includes three sets of experiments, namely a dark fixation experiment and two photosynthetic experiments, one of 30 seconds duration and the other of 60 seconds duration.

Transcriptome and key genes expression related to carbon fixation pathways in Chlorella PY-ZU1 cells and their growth under high concentrations of CO2.

PubMed

Huang, Yun; Cheng, Jun; Lu, Hongxiang; He, Yong; Zhou, Junhu; Cen, Kefa

2017-01-01

The biomass yield of Chlorella PY-ZU1 drastically increased when cultivated under high CO 2 condition compared with that cultivated under air condition. However, less attention has been given to the microalgae photosynthetic mechanisms response to different CO 2 concentrations. The genetic reasons for the higher growth rate, CO 2 fixation rate, and photosynthetic efficiency of microalgal cells under higher CO 2 concentration have not been clearly defined yet. In this study, the Illumina sequencing and de novo transcriptome assembly of Chlorella PY-ZU1 cells cultivated under 15% CO 2 were performed and compared with those of cells grown under air. It was found that carbonic anhydrase (CAs, enzyme for interconversion of bicarbonate to CO 2 ) dramatically decreased to near 0 in 15% CO 2 -grown cells, which indicated that CO 2 molecules directly permeated into cells under high CO 2 stress without CO 2 -concentrating mechanism. Extrapolating from the growth conditions and quantitative Real-Time PCR of CCM-related genes, the K m (CO 2 ) (the minimum intracellular CO 2 concentration that rubisco required) of Chlorella PY-ZU1 might be in the range of 80-192 μM. More adenosine triphosphates was saved for carbon fixation-related pathways. The transcript abundance of rubisco (the most important enzyme of CO 2 fixation reaction) was 16.3 times higher in 15% CO 2 -grown cells than that under air. Besides, the transcript abundances of most key genes involved in carbon fixation pathways were also enhanced in 15% CO 2 -grown cells. Carbon fixation and nitrogen metabolism are the two most important metabolisms in the photosynthetic cells. These genes related to the two most metabolisms with significantly differential expressions were beneficial for microalgal growth (2.85 g L -1 ) under 15% CO 2 concentration. Considering the micro and macro growth phenomena of Chlorella PY-ZU1 under different concentrations of CO 2 (0.04-60%), CO 2 transport pathways responses to different CO 2 (0.04-60%) concentrations was reconstructed.

Ocean Fertilization for Sequestration of Carbon Dioxide from the Atmosphere

NASA Astrophysics Data System (ADS)

Boyd, Philip W.

The ocean is a major sink for both preindustrial and anthropogenic carbon dioxide. Both physically and biogeochemically driven pumps, termed the solubility and biological pump, respectively Fig.5.1) are responsible for the majority of carbon sequestration in the ocean's interior [1]. The solubility pump relies on ocean circulation - specifically the impact of cooling of the upper ocean at high latitudes both enhances the solubility of carbon dioxide and the density of the waters which sink to great depth (the so-called deepwater formation) and thereby sequester carbon in the form of dissolved inorganic carbon (Fig.5.1). The biological pump is driven by the availability of preformed plant macronutrients such as nitrate or phosphate which are taken up by phytoplankton during photosynthetic carbon fixation. A small but significant proportion of this fixed carbon sinks into the ocean's interior in the form of settling particles, and in order to maintain equilibrium carbon dioxide from the atmosphere is transferred across the air-sea interface into the ocean (the so-called carbon drawdown) thereby decreasing atmospheric carbon dioxide (Fig.5.1).Fig.5.1

The contribution of changes in P release and CO2 consumption by chemical weathering to the historical trend in land carbon uptake

NASA Astrophysics Data System (ADS)

Goodale, C. L.; Fredriksen, G.; McCalley, C. K.; Sparks, J. P.; Thomas, S. A.

2011-12-01

The atmospheric carbon dioxide (CO2) concentration has increased to a level unprecedented in the last 2 million years, and the concentration is projected to increase further with a rate unseen in geological past. The increase in CO2 cause a rise in surface temperatures and changes in the hydrological cycle through the redistribution of rainfall patterns. All of these changes will impact the weathering of rocks, which in turn affect atmospheric CO2 concentrations via two different pathways. On the one hand, CO2 is consumed by the dissolution reaction of the exposed minerals. And on the other hand, biological CO2 fixation is affected due to changes in phosphorus release from minerals, as biological activity is constrained by phosphorus availability at large scales. The traditional view is that both effects are negligible on a centennial time scale, but recent work on catchment scale challenge this view in favor of a potential high sensitivity of weathering to ongoing climate and land use changes. To globally quantify the contribution of CO2 fixation associated with weathering on the historical trend in terrestrial CO2 uptake, we applied a model of chemical weathering and phosphorus release under climate reconstructions from four Earth System Models. The simulations indicate that changes in weathering could have contributed considerably to the trend in terrestrial CO2 uptake since the pre-industrial revolution, with warming being the main driver of change. The increase in biological CO2 fixation is of comparable magnitude as the increase in CO2 consumption by chemical weathering. Our simulations support the previous findings on catchment scale that weathering can change significantly on a centennial time scale. This finding has implications for 21st century climate projections, which ignore changes in weathering, as well as for long-term airborne fraction of CO2 emissions, whose calculation usually neglects changes in phosphorus availability.

The contribution of changes in P release and CO2 consumption by chemical weathering to the historical trend in land carbon uptake

NASA Astrophysics Data System (ADS)

Goll, D. S.; Moosdorf, N.; Brovkin, V.; Hartmann, J.

2013-12-01

The atmospheric carbon dioxide (CO2) concentration has increased to a level unprecedented in the last 2 million years, and the concentration is projected to increase further with a rate unseen in geological past. The increase in CO2 cause a rise in surface temperatures and changes in the hydrological cycle through the redistribution of rainfall patterns. All of these changes will impact the weathering of rocks, which in turn affect atmospheric CO2 concentrations via two different pathways. On the one hand, CO2 is consumed by the dissolution reaction of the exposed minerals. And on the other hand, biological CO2 fixation is affected due to changes in phosphorus release from minerals, as biological activity is constrained by phosphorus availability at large scales. The traditional view is that both effects are negligible on a centennial time scale, but recent work on catchment scale challenge this view in favor of a potential high sensitivity of weathering to ongoing climate and land use changes. To globally quantify the contribution of CO2 fixation associated with weathering on the historical trend in terrestrial CO2 uptake, we applied a model of chemical weathering and phosphorus release under climate reconstructions from four Earth System Models. The simulations indicate that changes in weathering could have contributed considerably to the trend in terrestrial CO2 uptake since the pre-industrial revolution, with warming being the main driver of change. The increase in biological CO2 fixation is of comparable magnitude as the increase in CO2 consumption by chemical weathering. Our simulations support the previous findings on catchment scale that weathering can change significantly on a centennial time scale. This finding has implications for 21st century climate projections, which ignore changes in weathering, as well as for long-term airborne fraction of CO2 emissions, whose calculation usually neglects changes in phosphorus availability.

Biophotonics for Biofuel Upgradation

NASA Astrophysics Data System (ADS)

Rana, Gopinath; Mandal, Tanusri

2017-12-01

Experimental studies have been made to find out Cyanobacterias' biophotonical response in gaseous-fuelation and carbon dioxide fixation during photo-anaerobic digestion. A new horizontal type photo-bioreactor has been designed by using environment hazard plastic bottles and it works ideally for anoxygenic cyanobacterial growth. Through `V3-metagenomics' of 16S rRNA gene sequencing by paired-end Illumina MiSeq and downstream analysis by QIIME program, we have identified anaerobic cyanobacteria, represent the orders YS2 and Streptophyta. OTUs have been identified by aligning against Greengenes and Silva databases, separately. The flame temperature of the fuel gas is 860°C and the percent-content of carbon dioxide (CO2) is 17.6%.

Elevated Carbon Dioxide Alleviates Aluminum Toxicity by Decreasing Cell Wall Hemicellulose in Rice (Oryza sativa)

PubMed Central

Zhu, Xiao Fang; Zhao, Xu Sheng; Wang, Bin; Wu, Qi; Shen, Ren Fang

2017-01-01

Carbon dioxide (CO2) is involved in plant growth as well as plant responses to abiotic stresses; however, it remains unclear whether CO2 is involved in the response of rice (Oryza sativa) to aluminum (Al) toxicity. In the current study, we discovered that elevated CO2 (600 μL·L−1) significantly alleviated Al-induced inhibition of root elongation that occurred in ambient CO2 (400 μL·L−1). This protective effect was accompanied by a reduced Al accumulation in root apex. Al significantly induced citrate efflux and the expression of OsALS1, but elevated CO2 had no further effect. By contrast, elevated CO2 significantly decreased Al-induced accumulation of hemicellulose, as well as its Al retention. As a result, the amount of Al fixed in the cell wall was reduced, indicating an alleviation of Al-induced damage to cell wall function. Furthermore, elevated CO2 decreased the Al-induced root nitric oxide (NO) accumulation, and the addition of the NO scavenger c-PTIO (2-(4-carboxyphenyl)-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) abolished this alleviation effect, indicating that NO maybe involved in the CO2-alleviated Al toxicity. Taken together, these results demonstrate that the alleviation of Al toxicity in rice by elevated CO2 is mediated by decreasing hemicellulose content and the Al fixation in the cell wall, possibly via the NO pathway. PMID:28769823

Facet-dependent solar ammonia synthesis of BiOCl nanosheets via a proton-assisted electron transfer pathway

NASA Astrophysics Data System (ADS)

Li, Hao; Shang, Jian; Shi, Jingu; Zhao, Kun; Zhang, Lizhi

2016-01-01

Under the pressure of a fossil fuels shortage and global climate change, solar ammonia synthesis and the need to develop N2 fixation under mild conditions is becoming more urgent need; however, their intrinsic mechanisms still remain unclear. Herein, we demonstrate that the kinetic inertia of N2 can be overcome using oxygen vacancies (OVs) of BiOCl as the catalytic centers to create lower energy molecular steps, which are amendable for the solar light driven N-N triple bond cleavage via a proton-assisted electron transfer pathway. Moreover, the distinct structures of OVs on different BiOCl facets strongly determine the N2 fixation pathways by influencing both the adsorption structure and the activation level of N2. The fixation of terminal end-on bound N2 on the OVs of BiOCl {001} facets follows an asymmetric distal mode by selectively generating NH3, while the reduction of side-on bridging N2 on the OVs of BiOCl {010} facets is more energetically favorable in a symmetric alternating mode to produce N2H4 as the main intermediate.Under the pressure of a fossil fuels shortage and global climate change, solar ammonia synthesis and the need to develop N2 fixation under mild conditions is becoming more urgent need; however, their intrinsic mechanisms still remain unclear. Herein, we demonstrate that the kinetic inertia of N2 can be overcome using oxygen vacancies (OVs) of BiOCl as the catalytic centers to create lower energy molecular steps, which are amendable for the solar light driven N-N triple bond cleavage via a proton-assisted electron transfer pathway. Moreover, the distinct structures of OVs on different BiOCl facets strongly determine the N2 fixation pathways by influencing both the adsorption structure and the activation level of N2. The fixation of terminal end-on bound N2 on the OVs of BiOCl {001} facets follows an asymmetric distal mode by selectively generating NH3, while the reduction of side-on bridging N2 on the OVs of BiOCl {010} facets is more energetically favorable in a symmetric alternating mode to produce N2H4 as the main intermediate. Electronic supplementary information (ESI) available: Other experimental details, additional SEM and TEM images, X-ray diffraction patterns (XRD), UV-Vis diffuse reflectance spectra (DRS), and additional data. See DOI: 10.1039/c5nr07380d

The Path of Carbon in Photosynthesis XVII. Phosphorus Compounds as Intermediates in Photosynthesis

DOE R&D Accomplishments Database

Buchanan, J. G.; Bassham, J. A.; Benson, A. A.; Bradley, D. F.; Calvin, M.; Daus, L. L.; Goodman, M.; Hayes, P. M.; Lynch, V. H.; Norris, L. T.; Wilson, A. T.

1952-07-08

Studies of carbon dioxide fixation in green plants using the C{sup 14} isotope have shown that in very short times phosphoglyceric acid contains most of the radioactivity. The tracer is present almost entirely in the carboxyl group. The importance of organic phosphates in the subsequent metabolism of phosphoglyceric acid can be seen from the accompanying photographs.

Carbon Fixation Driven by Molecular Hydrogen Results in Chemolithoautotrophically Enhanced Growth of Helicobacter pylori.

PubMed

Kuhns, Lisa G; Benoit, Stéphane L; Bayyareddy, Krishnareddy; Johnson, Darryl; Orlando, Ron; Evans, Alexandra L; Waldrop, Grover L; Maier, Robert J

2016-05-01

A molecular hydrogen (H2)-stimulated, chemolithoautotrophic growth mode for the gastric pathogen Helicobacter pylori is reported. In a culture medium containing peptides and amino acids, H2-supplied cells consistently achieved 40 to 60% greater growth yield in 16 h and accumulated 3-fold more carbon from [(14)C]bicarbonate (on a per cell basis) in a 10-h period than cells without H2 Global proteomic comparisons of cells supplied with different atmospheric conditions revealed that addition of H2 led to increased amounts of hydrogenase and the biotin carboxylase subunit of acetyl coenzyme A (acetyl-CoA) carboxylase (ACC), as well as other proteins involved in various cellular functions, including amino acid metabolism, heme synthesis, or protein degradation. In agreement with this result, H2-supplied cells contained 3-fold more ACC activity than cells without H2 Other possible carbon dioxide (CO2) fixation enzymes were not up-expressed under the H2-containing atmosphere. As the gastric mucus is limited in carbon and energy sources and the bacterium lacks mucinase, this new growth mode may contribute to the persistence of the pathogen in vivo This is the first time that chemolithoautotrophic growth is described for a pathogen. Many pathogens must survive within host areas that are poorly supplied with carbon and energy sources, and the gastric pathogen Helicobacter pylori resides almost exclusively in the nutritionally stringent mucus barrier of its host. Although this bacterium is already known to be highly adaptable to gastric niches, a new aspect of its metabolic flexibility, whereby molecular hydrogen use (energy) is coupled to carbon dioxide fixation (carbon acquisition) via a described carbon fixation enzyme, is shown here. This growth mode, which supplements heterotrophy, is termed chemolithoautotrophy and has not been previously reported for a pathogen. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Energetics and Application of Heterotrophy in Acetogenic Bacteria.

PubMed

Schuchmann, Kai; Müller, Volker

2016-07-15

Acetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2 fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogen Acetobacterium woodii Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2 reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Energetics and Application of Heterotrophy in Acetogenic Bacteria

PubMed Central

Schuchmann, Kai

2016-01-01

Acetogenic bacteria are a diverse group of strictly anaerobic bacteria that utilize the Wood-Ljungdahl pathway for CO2 fixation and energy conservation. These microorganisms play an important part in the global carbon cycle and are a key component of the anaerobic food web. Their most prominent metabolic feature is autotrophic growth with molecular hydrogen and carbon dioxide as the substrates. However, most members also show an outstanding metabolic flexibility for utilizing a vast variety of different substrates. In contrast to autotrophic growth, which is hardly competitive, metabolic flexibility is seen as a key ability of acetogens to compete in ecosystems and might explain the almost-ubiquitous distribution of acetogenic bacteria in anoxic environments. This review covers the latest findings with respect to the heterotrophic metabolism of acetogenic bacteria, including utilization of carbohydrates, lactate, and different alcohols, especially in the model acetogen Acetobacterium woodii. Modularity of metabolism, a key concept of pathway design in synthetic biology, together with electron bifurcation, to overcome energetic barriers, appears to be the basis for the amazing substrate spectrum. At the same time, acetogens depend on only a relatively small number of enzymes to expand the substrate spectrum. We will discuss the energetic advantages of coupling CO2 reduction to fermentations that exploit otherwise-inaccessible substrates and the ecological advantages, as well as the biotechnological applications of the heterotrophic metabolism of acetogens. PMID:27208103

Influences of Air, Oxygen, Nitrogen, and Carbon Dioxide Nanobubbles on Seed Germination and Plant Growth.

PubMed

Ahmed, Ahmed Khaled Abdella; Shi, Xiaonan; Hua, Likun; Manzueta, Leidy; Qing, Weihua; Marhaba, Taha; Zhang, Wen

2018-05-23

Nanobubbles (NBs) hold promise in green and sustainable engineering applications in diverse fields (e.g., water/wastewater treatment, food processing, medical applications, and agriculture). This study investigated the effects of four types of NBs on seed germination and plant growth. Air, oxygen, nitrogen, and carbon dioxide NBs were generated and dispersed in tap water. Different plants, including lettuce, carrot, fava bean, and tomato, were used in germination and growth tests. The seeds in water-containing NBs exhibited 6-25% higher germination rates. Especially, nitrogen NBs exhibited considerable effects in the seed germination, whereas air and carbon dioxide NBs did not significantly promote germination. The growth of stem length and diameter, leave number, and leave width were promoted by NBs (except air). Furthermore, the promotion effect was primarily ascribed to the generation of exogenous reactive oxygen species by NBs and higher efficiency of nutrient fixation or utilization.

Soil DIC uptake and fixation in Pinus taeda seedlings and its C contribution to plant tissues and ectomycorrhizal fungi

Treesearch

Chelcy R. Ford; Nina Wurzburger; Ronald L. Henderick; Robert O. Teskey

2007-01-01

Plants can aquaire carbon from sources other than atmospheric carbon dioxide (CO2), including soil-dissolved inorganic carbon (DIC). Although the next flux of CO2 is out of the root, soil DIC can be taken up by the root, transported within the plant, and fixed either photosynthetically or anaplerotically by plant tissues....

Two Pathways of Glutamate Fermentation by Anaerobic Bacteria

PubMed Central

Buckel, Wolfgang; Barker, H. A.

1974-01-01

Two pathways are involved in the fermentation of glutamate to acetate, butyrate, carbon dioxide, and ammonia—the methylaspartate and the hydroxyglutarate pathways which are used by Clostridium tetanomorphum and Peptococcus aerogenes, respectively. Although these pathways give rise to the same products, they are easily distinguished by different labeling patterns of the butyrate when [4-14C]glutamate is used as substrate. Schmidt degradation of the radioactive butyrate from C. tetanomorphum yielded equally labeled propionate and carbon dioxide, whereas nearly all the radioactivity of the butyrate from P. aerogenes was recovered in the corresponding propionate. This procedure was used as a test for the pathway of glutamate fermentation by 15 strains (9 species) of anaerobic bacteria. The labeling patterns of the butyrate indicate that glutamate is fermented via the methylaspartate pathway by C. tetani, C. cochlearium, and C. saccarobutyricum, and via the hydroxyglutarate pathway by Acidaminococcus fermentans, C. microsporum, Fusobacterium nucleatum, and F. fusiformis. Enzymes specific for each pathway were assayed in crude extracts of the above organisms. 3-Methylaspartase was found only in clostridia which use the methylaspartate pathway, including Clostridium SB4 and C. sticklandii, which probably degrade glutamate to acetate and carbon dioxide by using a second amino acid as hydrogen acceptor. High levels of 2-hydroxyglutarate dehydrogenase were found exclusively in organisms that use the hydroxyglutarate pathway. The data indicate that only two pathways are involved in the fermentation of glutamate by the bacteria analyzed. The methylaspartate pathway appears to be used only by species of Clostridium, whereas the hydroxyglutarate pathway is used by representatives of several genera. PMID:4813895

Reversibility of citrate synthase allows autotrophic growth of a thermophilic bacterium.

PubMed

Mall, Achim; Sobotta, Jessica; Huber, Claudia; Tschirner, Carolin; Kowarschik, Stefanie; Bačnik, Katarina; Mergelsberg, Mario; Boll, Matthias; Hügler, Michael; Eisenreich, Wolfgang; Berg, Ivan A

2018-02-02

Biological inorganic carbon fixation proceeds through a number of fundamentally different autotrophic pathways that are defined by specific key enzymatic reactions. Detection of the enzymatic genes in (meta)genomes is widely used to estimate the contribution of individual organisms or communities to primary production. Here we show that the sulfur-reducing anaerobic deltaproteobacterium Desulfurella acetivorans is capable of both acetate oxidation and autotrophic carbon fixation, with the tricarboxylic acid cycle operating either in the oxidative or reductive direction, respectively. Under autotrophic conditions, the enzyme citrate synthase cleaves citrate adenosine triphosphate independently into acetyl coenzyme A and oxaloacetate, a reaction that has been regarded as impossible under physiological conditions. Because this overlooked, energetically efficient carbon fixation pathway lacks key enzymes, it may function unnoticed in many organisms, making bioinformatical predictions difficult, if not impossible. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Unique pioneer microbial communities exposed to volcanic sulfur dioxide

PubMed Central

Fujimura, Reiko; Kim, Seok-Won; Sato, Yoshinori; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

2016-01-01

Newly exposed volcanic substrates contain negligible amounts of organic materials. Heterotrophic organisms in newly formed ecosystems require bioavailable carbon and nitrogen that are provided from CO2 and N2 fixation by pioneer microbes. However, the knowledge of initial ecosystem developmental mechanisms, especially the association between microbial succession and environmental change, is still limited. This study reports the unique process of microbial succession in fresh basaltic ash, which was affected by long-term exposure to volcanic sulfur dioxide (SO2). Here we compared the microbial ecosystems among deposits affected by SO2 exposure at different levels. The results of metagenomic analysis suggested the importance of autotrophic iron-oxidizing bacteria, particularly those involved in CO2 and N2 fixation, in the heavily SO2 affected site. Changes in the chemical properties of the deposits after the decline of the SO2 impact led to an apparent decrease in the iron-oxidizer abundance and a possible shift in the microbial community structure. Furthermore, the community structure of the deposits that had experienced lower SO2 gas levels showed higher similarity with that of the control forest soil. Our results implied that the effect of SO2 exposure exerted a selective pressure on the pioneer community structure by changing the surrounding environment of the microbes. PMID:26791101

Fixation of carbon dioxide by a hydrogen-oxidizing bacterium for value-added products.

PubMed

Yu, Jian

2018-06-09

With rapid technology progress and cost reduction, clean hydrogen from water electrolysis driven by renewable powers becomes a potential feedstock for CO 2 fixation by hydrogen-oxidizing bacteria. Cupriavidus necator (formally Ralstonia eutropha), a representative member of the lithoautotrophic prokaryotes, is a promising producer of polyhydroxyalkanoates and single cell proteins. This paper reviews the fundamental properties of the hydrogen-oxidizing bacterium, the metabolic activities under limitation of individual gases and nutrients, and the value-added products from CO 2 , including the products with large potential markets. Gas fermentation and bioreactor safety are discussed for achieving high cell density and high productivity of desired products under chemolithotrophic conditions. The review also updates the recent research activities in metabolic engineering of C. necator to produce novel metabolites from CO 2 .

The complex effects of ocean acidification on the prominent N2-fixing cyanobacterium Trichodesmium.

PubMed

Hong, Haizheng; Shen, Rong; Zhang, Futing; Wen, Zuozhu; Chang, Siwei; Lin, Wenfang; Kranz, Sven A; Luo, Ya-Wei; Kao, Shuh-Ji; Morel, François M M; Shi, Dalin

2017-05-05

Acidification of seawater caused by anthropogenic carbon dioxide (CO 2 ) is anticipated to influence the growth of dinitrogen (N 2 )-fixing phytoplankton, which contribute a large fraction of primary production in the tropical and subtropical ocean. We found that growth and N 2 -fixation of the ubiquitous cyanobacterium Trichodesmium decreased under acidified conditions, notwithstanding a beneficial effect of high CO 2 Acidification resulted in low cytosolic pH and reduced N 2 -fixation rates despite elevated nitrogenase concentrations. Low cytosolic pH required increased proton pumping across the thylakoid membrane and elevated adenosine triphosphate production. These requirements were not satisfied under field or experimental iron-limiting conditions, which greatly amplified the negative effect of acidification. Copyright © 2017, American Association for the Advancement of Science.

Recycling Carbon Dioxide during Xylose Fermentation by Engineered Saccharomyces cerevisiae.

PubMed

Xia, Peng-Fei; Zhang, Guo-Chang; Walker, Berkley; Seo, Seung-Oh; Kwak, Suryang; Liu, Jing-Jing; Kim, Heejin; Ort, Donald R; Wang, Shu-Guang; Jin, Yong-Su

2017-02-17

Global climate change caused by the emission of anthropogenic greenhouse gases (GHGs) is a grand challenge to humanity. To alleviate the trend, the consumption of fossil fuels needs to be largely reduced and alternative energy technologies capable of controlling GHG emissions are anticipated. In this study, we introduced a synthetic reductive pentose phosphate pathway (rPPP) into a xylose-fermenting Saccharomyces cerevisiae strain SR8 to achieve simultaneous lignocellulosic bioethanol production and carbon dioxide recycling. Specifically, ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and phosphoribulokinase from Spinacia oleracea were introduced into the SR8 strain. The resulting strain with the synthetic rPPP was able to exhibit a higher yield of ethanol and lower yields of byproducts (xylitol and glycerol) than a control strain. In addition, the reduced release of carbon dioxide by the engineered strain was observed during xylose fermentation, suggesting that the carbon dioxide generated by pyruvate decarboxylase was partially reassimilated through the synthetic rPPP. These results demonstrated that recycling of carbon dioxide from the ethanol fermentation pathway in yeast can be achieved during lignocellulosic bioethanol production through a synthetic carbon conservative metabolic pathway. This strategy has a great potential to alleviate GHG emissions during the production of second-generation ethanol.

Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves.

PubMed

Feng, Dan; Wang, Yanwei; Lu, Tiegang; Zhang, Zhiguo; Han, Xiao

2017-01-01

Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level.

A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus.

PubMed

Lyu, Xueliang; Shen, Cuicui; Xie, Jiatao; Fu, Yanping; Jiang, Daohong; Hu, Zijin; Tang, Lihua; Tang, Liguang; Ding, Feng; Li, Kunfei; Wu, Song; Hu, Yanping; Luo, Lilian; Li, Yuanhao; Wang, Qihua; Li, Guoqing; Cheng, Jiasen

2015-08-11

Carbon fixation pathway of plants (CFPP) in photosynthesis converts solar energy to biomass, bio-products and biofuel. Intriguingly, a large number of heterotrophic fungi also possess enzymes functionally associated with CFPP, raising the questions about their roles in fungal development and in evolution. Here, we report on the presence of 17 CFPP associated enzymes (ten in Calvin-Benson-Basham reductive pentose phosphate pathway and seven in C4-dicarboxylic acid cycle) in the genome of Sclerotinia sclerotiorum, a heterotrophic phytopathogenic fungus, and only two unique enzymes: ribulose-1, 5-bisphosphate carboxylase-oxygenase (Rubisco) and phosphoribulokinase (PRK) were absent. This data suggested an incomplete CFPP-like pathway (CLP) in fungi. Functional profile analysis demonstrated that the activity of the incomplete CLP was dramatically regulated during different developmental stages of S. sclerotiorum. Subsequent experiments confirmed that many of them were essential to the virulence and/or sclerotial formation. Most of the CLP associated genes are conserved in fungi. Phylogenetic analysis showed that many of them have undergone gene duplication, gene acquisition or loss and functional diversification in evolutionary history. These findings showed an evolutionary links in the carbon fixation processes of autotrophs and heterotrophs and implicated the functions of related genes were in course of continuous change in different organisms in evolution.

Comparative Transcriptional Profiling and Preliminary Study on Heterosis Mechanism of Super-Hybrid Rice

PubMed Central

Song, Gui-Sheng; Zhai, Hong-Li; Peng, Yong-Gang; Zhang, Lei; Wei, Gang; Chen, Xiao-Ying; Xiao, Yu-Guo; Wang, Lili; Wu, Bin; Zhang, Yu; Feng, Xiu-Jing; Gong, Wan-Kui; Liu, Yao; Yin, Zhi-Jie; Wang, Feng; Liu, Guo-Zhen; Xu, Hong-Lin; Wei, Xiao-Li; Zhao, Xiao-Ling; Ouwerkerk, Pieter B.F.; Hankemeier, Thomas; Reijmers, Theo; van der Heijden, Rob; Wang, Mei; van der Greef, Jan; Zhu, Zhen

2010-01-01

Heterosis is a biological phenomenon whereby the offspring from two parents show improved and superior performance than either inbred parental lines. Hybrid rice is one of the most successful apotheoses in crops utilizing heterosis. Transcriptional profiling of F1 super-hybrid rice Liangyou-2186 and its parents by serial analysis of gene expression (SAGE) revealed 1183 differentially expressed genes (DGs), among which DGs were found significantly enriched in pathways such as photosynthesis and carbon-fixation, and most of the key genes involved in the carbon-fixation pathway exhibited up-regulated expression in F1 hybrid rice. Moreover, increased catabolic activity of corresponding enzymes and photosynthetic efficiency were also detected, which combined to indicate that carbon fixation is enhanced in F1 hybrid, and might probably be associated with the yield vigor and heterosis in super-hybrid rice. By correlating DGs with yield-related quantitative trait loci (QTL), a potential relationship between differential gene expression and phenotypic changes was also found. In addition, a regulatory network involving circadian-rhythms and light signaling pathways was also found, as previously reported in Arabidopsis, which suggest that such a network might also be related with heterosis in hybrid rice. Altogether, the present study provides another view for understanding the molecular mechanism underlying heterosis in rice. PMID:20729474

CARBON-14 FIXATION IN POLLEN OF YELLOW LUPINE (LUPINUS LUTEUS LINN.)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schwien, W.G.; Frazier, J.C.; Moser, H.C.

1962-10-31

Carbon-14 fixation studies were made on germinated pollen of yellow lupine to ascertain whether the chlorophyll reported to be in these grains was functional photosynthetically. Light and dark exposures to atmospheres containing 20 and 500 mu c of carbon-14 labeled carbon dioxide were made for 1.5 and 45 minutes, respectively. The exposed pollen was extracted in 80% ethanol, the resulting extract reduced in volume, and chromatographed two dimensionally. When the chromatograms were cut inio numbered small squares and their activity counted in an automatic sample counting system, a marked similarity was observed in the pattern of radioactivity from all exposures.more » Eluting and co- chromatographing this activity from the squares, with known standards, demonstrated labeling to be specific to certain intermediates of the Krebs cycle and their derived amine acids. The labeling in these intermediates and the absence of labeling in photosynthetic metabolites is strong evidence that only respiratory fixation of carbon-14 occurs in the germinated pollen of this variety of yellow lupine under the conditions of the experiment. (auth)« less

Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome

DOE PAGES

Ross, Daniel E.; Gulliver, Djuna

2016-10-06

The draft genome sequence ofPseudomonas stutzeristrain K35 was separated from a metagenome derived from a produced water microbial community of a coalbed methane well. The genome encodes a complete nitrogen fixation pathway and the upper and lower naphthalene degradation pathways.

Reconstruction of a Nearly Complete Pseudomonas Draft Genome Sequence from a Coalbed Methane-Produced Water Metagenome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ross, Daniel E.; Gulliver, Djuna

The draft genome sequence ofPseudomonas stutzeristrain K35 was separated from a metagenome derived from a produced water microbial community of a coalbed methane well. The genome encodes a complete nitrogen fixation pathway and the upper and lower naphthalene degradation pathways.

Methanogenic heterodisulfide reductase (HdrABC-MvhAGD) uses two noncubane [4Fe-4S] clusters for reduction.

PubMed

Wagner, Tristan; Koch, Jürgen; Ermler, Ulrich; Shima, Seigo

2017-08-18

In methanogenic archaea, the carbon dioxide (CO 2 ) fixation and methane-forming steps are linked through the heterodisulfide reductase (HdrABC)-[NiFe]-hydrogenase (MvhAGD) complex that uses flavin-based electron bifurcation to reduce ferredoxin and the heterodisulfide of coenzymes M and B. Here, we present the structure of the native heterododecameric HdrABC-MvhAGD complex at 2.15-angstrom resolution. HdrB contains two noncubane [4Fe-4S] clusters composed of fused [3Fe-4S]-[2Fe-2S] units sharing 1 iron (Fe) and 1 sulfur (S), which were coordinated at the CCG motifs. Soaking experiments showed that the heterodisulfide is clamped between the two noncubane [4Fe-4S] clusters and homolytically cleaved, forming coenzyme M and B bound to each iron. Coenzymes are consecutively released upon one-by-one electron transfer. The HdrABC-MvhAGD atomic model serves as a structural template for numerous HdrABC homologs involved in diverse microbial metabolic pathways. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

N-Heterocyclic Olefins as Robust Organocatalyst for the Chemical Conversion of Carbon Dioxide to Value-Added Chemicals.

PubMed

Saptal, Vitthal B; Bhanage, Bhalchandra M

2016-08-09

In this report, the activity of N-heterocyclic olefins (NHOs) as a newly emerging class of organocatalyst is investigated for the chemical fixation of carbon dioxide through reactions with aziridines to form oxazolidinones and the N-formylation of amines with polymethylhydrosiloxane (PMHS) or 9-borabicyclo[3.3.1]nonane (9-BBN) as the reducing agent under mild conditions. The exocyclic carbon atoms of NHOs are highly nucleophilic owing to the electron-donating ability of the two nitrogen atoms. This high nucleophilicity of the NHOs activates CO2 molecules to form zwitterionic NHO-carboxylate (NHO-CO2 ) adducts, which are active in formylation reactions as well as the carboxylation of aziridines to oxazolidinones. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Acidithiobacillus caldus Sulfur Oxidation Model Based on Transcriptome Analysis between the Wild Type and Sulfur Oxygenase Reductase Defective Mutant

PubMed Central

Chen, Linxu; Ren, Yilin; Lin, Jianqun; Liu, Xiangmei; Pang, Xin; Lin, Jianqiang

2012-01-01

Background Acidithiobacillus caldus (A. caldus) is widely used in bio-leaching. It gains energy and electrons from oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs) for carbon dioxide fixation and growth. Genomic analyses suggest that its sulfur oxidation system involves a truncated sulfur oxidation (Sox) system (omitting SoxCD), non-Sox sulfur oxidation system similar to the sulfur oxidation in A. ferrooxidans, and sulfur oxygenase reductase (SOR). The complexity of the sulfur oxidation system of A. caldus generates a big obstacle on the research of its sulfur oxidation mechanism. However, the development of genetic manipulation method for A. caldus in recent years provides powerful tools for constructing genetic mutants to study the sulfur oxidation system. Results An A. caldus mutant lacking the sulfur oxygenase reductase gene (sor) was created and its growth abilities were measured in media using elemental sulfur (S0) and tetrathionate (K2S4O6) as the substrates, respectively. Then, comparative transcriptome analysis (microarrays and real-time quantitative PCR) of the wild type and the Δsor mutant in S0 and K2S4O6 media were employed to detect the differentially expressed genes involved in sulfur oxidation. SOR was concluded to oxidize the cytoplasmic elemental sulfur, but could not couple the sulfur oxidation with the electron transfer chain or substrate-level phosphorylation. Other elemental sulfur oxidation pathways including sulfur diooxygenase (SDO) and heterodisulfide reductase (HDR), the truncated Sox pathway, and the S4I pathway for hydrolysis of tetrathionate and oxidation of thiosulfate in A. caldus are proposed according to expression patterns of sulfur oxidation genes and growth abilities of the wild type and the mutant in different substrates media. Conclusion An integrated sulfur oxidation model with various sulfur oxidation pathways of A. caldus is proposed and the features of this model are summarized. PMID:22984393

Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii.

PubMed

Boyle, Nanette R; Morgan, John A

2009-01-07

Photosynthetic organisms convert atmospheric carbon dioxide into numerous metabolites along the pathways to make new biomass. Aquatic photosynthetic organisms, which fix almost half of global inorganic carbon, have great potential: as a carbon dioxide fixation method, for the economical production of chemicals, or as a source for lipids and starch which can then be converted to biofuels. To harness this potential through metabolic engineering and to maximize production, a more thorough understanding of photosynthetic metabolism must first be achieved. A model algal species, C. reinhardtii, was chosen and the metabolic network reconstructed. Intracellular fluxes were then calculated using flux balance analysis (FBA). The metabolic network of primary metabolism for a green alga, C. reinhardtii, was reconstructed using genomic and biochemical information. The reconstructed network accounts for the intracellular localization of enzymes to three compartments and includes 484 metabolic reactions and 458 intracellular metabolites. Based on BLAST searches, one newly annotated enzyme (fructose-1,6-bisphosphatase) was added to the Chlamydomonas reinhardtii database. FBA was used to predict metabolic fluxes under three growth conditions, autotrophic, heterotrophic and mixotrophic growth. Biomass yields ranged from 28.9 g per mole C for autotrophic growth to 15 g per mole C for heterotrophic growth. The flux balance analysis model of central and intermediary metabolism in C. reinhardtii is the first such model for algae and the first model to include three metabolically active compartments. In addition to providing estimates of intracellular fluxes, metabolic reconstruction and modelling efforts also provide a comprehensive method for annotation of genome databases. As a result of our reconstruction, one new enzyme was annotated in the database and several others were found to be missing; implying new pathways or non-conserved enzymes. The use of FBA to estimate intracellular fluxes also provides flux values that can be used as a starting point for rational engineering of C. reinhardtii. From these initial estimates, it is clear that aerobic heterotrophic growth on acetate has a low yield on carbon, while mixotrophically and autotrophically grown cells are significantly more carbon efficient.

Timing of definitive fixation of major long bone fractures: Can fat embolism syndrome be prevented?

PubMed

Blokhuis, Taco J; Pape, Hans-Christoph; Frölke, Jan-Paul

2017-06-01

Fat embolism is common in patients with major fractures, but leads to devastating consequences, named fat embolism syndrome (FES) in some. Despite advances in treatment strategies regarding the timing of definitive fixation of major fractures, FES still occurs in patients. In this overview, current literature is reviewed and optimal treatment strategies for patients with multiple traumatic injuries, including major fractures, are discussed. Considering the multifactorial etiology of FES, including mechanical and biochemical pathways, FES cannot be prevented in all patients. However, screening for symptoms of FES should be standard in the pre-operative work-up of these patients, prior to definitive fixation of major fractures. Copyright © 2017. Published by Elsevier Ltd.

Gene Discovery and Expression Profiling in the Toxin-Producing Marine Diatom, Pseudo-nitzschia Multiseries (Hasle) Hasle

DTIC Science & Technology

2004-09-01

carboxylase/oxygenase ( rubisco ) is a another principal carbon fixation enzyme, which is alleged to represent the most abundant enzyme on earth...known to have plastid-encoded rubisco , which would account for why this gene was not identified in the P. multiseries library (Hwang and Tabita, 1989...thought to have evolved in certain plants as an adaptation to the competition of oxygen with carbon dioxide for ribulose- 15-bisphosphate ( rubisco ), a

Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate

PubMed Central

Mahato, Sourav; De, Debojyoti; Dutta, Debajyoti; Kundu, Moloy; Bhattacharya, Sumana; Schiavone, Marc T; Bhattacharya, Sanjoy K

2004-01-01

Sugar binding proteins and binders of intermediate sugar metabolites derived from microbes are increasingly being used as reagents in new and expanding areas of biotechnology. The fixation of carbon dioxide at emission source has recently emerged as a technology with potentially significant implications for environmental biotechnology. Carbon dioxide is fixed onto a five carbon sugar D-ribulose-1,5-bisphosphate. We present a review of enzymatic and non-enzymatic binding proteins, for 3-phosphoglycerate (3PGA), 3-phosphoglyceraldehyde (3PGAL), dihydroxyacetone phosphate (DHAP), xylulose-5-phosphate (X5P) and ribulose-1,5-bisphosphate (RuBP) which could be potentially used in reactors regenerating RuBP from 3PGA. A series of reactors combined in a linear fashion has been previously shown to convert 3-PGA, (the product of fixed CO2 on RuBP as starting material) into RuBP (Bhattacharya et al., 2004; Bhattacharya, 2001). This was the basis for designing reactors harboring enzyme complexes/mixtures instead of linear combination of single-enzyme reactors for conversion of 3PGA into RuBP. Specific sugars in such enzyme-complex harboring reactors requires removal at key steps and fed to different reactors necessitating reversible sugar binders. In this review we present an account of existing microbial sugar binding proteins and their potential utility in these operations. PMID:15175111

Acclimation of photosynthetic parameters is not the icing on the cake. It is the cake.

NASA Astrophysics Data System (ADS)

Prentice, Iain Colin; Wang, Han; Togashi, Henrique; Keenan, Trevor; Davis, Tyler; Wright, Ian

2015-04-01

Photosynthesis and transpiration are tightly coupled through stomatal behaviour and therefore it is impossible to understand and parsimoniously model one without also considering the other. The ratio of leaf-internal to ambient carbon dioxide concentration (ci:ca ratio) is a measure of the "exchange rate" between water and carbon. We have shown that it is possible to predict the observed dependencies of ci:ca on environmental factors (temperature, vapour pressure deficit and atmospheric pressure) based on the "least-cost hypothesis", which states that plants minimize the sum of the unit costs (respiration per unit assimilation) of maintaining the capacities for carbon fixation (Vcmax) and water transport. Moreover, with the help of the "co-ordination hypothesis" (the long-accepted idea that Rubisco capacity and electron transport tend to co-limit photosynthesis) it is possible to predict not only how ci:ca should vary, but also how Vcmax and electron transport capacity (Jmax) should vary, in space and time. We will present empirical support for this idea based on both ecophysiological measurements at the leaf scale, and analysis of carbon dioxide flux measurements at the ecosystem scale. We conclude that acclimation of photosynthetic parameters is pervasive. This is fundamental because it predicts a quite different set of environmental responses than those that are usually applied in models that incorrectly assume constancy of parameter values with time and within plant functional types (PFTs). In addition, acclimation actually simplifies modelling because it describes universal relationships that apply across all PFTs with the C3 photosynthetic pathway, and it removes the need to specify parameters such as Vcmax and Jmax as if they were properties of PFTs.

Carbon-nitrogen interactions in idealized simulations with JSBACH (version 3.10)

NASA Astrophysics Data System (ADS)

Goll, Daniel S.; Winkler, Alexander J.; Raddatz, Thomas; Dong, Ning; Prentice, Ian Colin; Ciais, Philippe; Brovkin, Victor

2017-05-01

Recent advances in the representation of soil carbon decomposition and carbon-nitrogen interactions implemented previously into separate versions of the land surface scheme JSBACH are here combined in a single version, which is set to be used in the upcoming 6th phase of coupled model intercomparison project (CMIP6).Here we demonstrate that the new version of JSBACH is able to reproduce the spatial variability in the reactive nitrogen-loss pathways as derived from a compilation of δ15N data (R = 0. 76, root mean square error (RMSE) = 0. 2, Taylor score = 0. 83). The inclusion of carbon-nitrogen interactions leads to a moderate reduction (-10 %) of the carbon-concentration feedback (βL) and has a negligible effect on the sensitivity of the land carbon cycle to warming (γL) compared to the same version of the model without carbon-nitrogen interactions in idealized simulations (1 % increase in atmospheric carbon dioxide per year). In line with evidence from elevated carbon dioxide manipulation experiments, pronounced nitrogen scarcity is alleviated by (1) the accumulation of nitrogen due to enhanced nitrogen inputs by biological nitrogen fixation and reduced losses by leaching and volatilization. Warming stimulated turnover of organic nitrogen further counteracts scarcity.The strengths of the land carbon feedbacks of the recent version of JSBACH, with βL = 0. 61 Pg ppm-1 and γL = -27. 5 Pg °C-1, are 34 and 53 % less than the averages of CMIP5 models, although the CMIP5 version of JSBACH simulated βL and γL, which are 59 and 42 % higher than multi-model average. These changes are primarily due to the new decomposition model, indicating the importance of soil organic matter decomposition for land carbon feedbacks.

Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria.

PubMed

Kanno, Masahiro; Carroll, Austin L; Atsumi, Shota

2017-03-13

Cyanobacteria have attracted much attention as hosts to recycle CO 2 into valuable chemicals. Although cyanobacteria have been engineered to produce various compounds, production efficiencies are too low for commercialization. Here we engineer the carbon metabolism of Synechococcus elongatus PCC 7942 to improve glucose utilization, enhance CO 2 fixation and increase chemical production. We introduce modifications in glycolytic pathways and the Calvin Benson cycle to increase carbon flux and redirect it towards carbon fixation. The engineered strain efficiently uses both CO 2 and glucose, and produces 12.6 g l -1 of 2,3-butanediol with a rate of 1.1 g l -1  d -1 under continuous light conditions. Removal of native regulation enables carbon fixation and 2,3-butanediol production in the absence of light. This represents a significant step towards industrial viability and an excellent example of carbon metabolism plasticity.

Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria

NASA Astrophysics Data System (ADS)

Kanno, Masahiro; Carroll, Austin L.; Atsumi, Shota

2017-03-01

Cyanobacteria have attracted much attention as hosts to recycle CO2 into valuable chemicals. Although cyanobacteria have been engineered to produce various compounds, production efficiencies are too low for commercialization. Here we engineer the carbon metabolism of Synechococcus elongatus PCC 7942 to improve glucose utilization, enhance CO2 fixation and increase chemical production. We introduce modifications in glycolytic pathways and the Calvin Benson cycle to increase carbon flux and redirect it towards carbon fixation. The engineered strain efficiently uses both CO2 and glucose, and produces 12.6 g l-1 of 2,3-butanediol with a rate of 1.1 g l-1 d-1 under continuous light conditions. Removal of native regulation enables carbon fixation and 2,3-butanediol production in the absence of light. This represents a significant step towards industrial viability and an excellent example of carbon metabolism plasticity.

Enzymology of the Wood–Ljungdahl Pathway of Acetogenesis

PubMed Central

Ragsdale, Stephen W.

2011-01-01

The biochemistry of acetogenesis is reviewed. The microbes that catalyze the reactions that are central to acetogenesis are described and the focus is on the enzymology of the process. These microbes play a key role in the global carbon cycle, producing over 10 trillion kilograms of acetic acid annually. Acetogens have the ability to anaerobically convert carbon dioxide and CO into acetyl-CoA by the Wood–Ljungdahl pathway, which is linked to energy conservation. They also can convert the six carbons of glucose stoichiometrically into 3 mol of acetate using this pathway. Acetogens and other anaerobic microbes (e.g., sulfate reducers and methanogens) use the Wood–Ljungdahl pathway for cell carbon synthesis. Important enzymes in this pathway that are covered in this review are pyruvate ferredoxin oxidoreductase, CO dehydrogenase/acetyl-CoA synthase, a corrinoid iron-sulfur protein, a methyltransferase, and the enzymes involved in the conversion of carbon dioxide to methyl-tetrahydrofolate. PMID:18378591

Proteomics analysis reveals a dynamic diurnal pattern of photosynthesis-related pathways in maize leaves

PubMed Central

Lu, Tiegang; Zhang, Zhiguo

2017-01-01

Plant leaves exhibit differentiated patterns of photosynthesis rates under diurnal light regulation. Maize leaves show a single-peak pattern without photoinhibition at midday when the light intensity is maximized. This mechanism contributes to highly efficient photosynthesis in maize leaves. To understand the molecular basis of this process, an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomics analysis was performed to reveal the dynamic pattern of proteins related to photosynthetic reactions. Steady, single-peak and double-peak protein expression patterns were discovered in maize leaves, and antenna proteins in these leaves displayed a steady pattern. In contrast, the photosystem, carbon fixation and citrate pathways were highly controlled by diurnal light intensity. Most enzymes in the limiting steps of these pathways were major sites of regulation. Thus, maize leaves optimize photosynthesis and carbon fixation outside of light harvesting to adapt to the changes in diurnal light intensity at the protein level. PMID:28732011

Transition metal-catalyzed carboxylation reactions with carbon dioxide.

PubMed

Martin, Ruben; Tortajada, Andreu; Juliá-Hernández, Francisco; Borjesson, Marino; Moragas, Toni

2018-05-03

Driven by the inherent synthetic potential of CO2 as an abundant, inexpensive and renewable C1 chemical feedstock, the recent years have witnessed renewed interest in devising catalytic CO2 fixations into organic matter. Although the formation of C-C bonds via catalytic CO2 fixation remained rather limited for a long period of time, a close look into the recent literature data indicates that catalytic carboxylation reactions have entered a new era of exponential growth, evolving into a mature discipline that allows for streamlining the synthesis of carboxylic acids, building blocks of utmost relevance in industrial endeavours. These strategies have generally proven broadly applicability and convenient to perform. However, substantial challenges still need to be addressed reinforcing the need to cover metal-catalyzed carboxylation arena in a conceptual and concise manner, delineating the underlying new principles that are slowly emerging in this vibrant area of expertise. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hybrid Amine-Functionalized Graphene Oxide as a Robust Bifunctional Catalyst for Atmospheric Pressure Fixation of Carbon Dioxide using Cyclic Carbonates.

PubMed

Saptal, Vitthal B; Sasaki, Takehiko; Harada, Kei; Nishio-Hamane, Daisuke; Bhanage, Bhalchandra M

2016-03-21

An environmentally-benign carbocatalyst based on amine-functionalized graphene oxide (AP-GO) was synthesized and characterized. This catalyst shows superior activity for the chemical fixation of CO2 into cyclic carbonates at the atmospheric pressure. The developed carbocatalyst exhibits superior activity owing to its large surface area with abundant hydrogen bonding donor (HBD) capability and the presence of well-defined amine functional groups. The presence of various HBD and amine functional groups on the graphene oxide (GO) surface yields a synergistic effect for the activation of starting materials. Additionally, this catalyst shows high catalytic activity to synthesize carbonates at 70 °C and at 1 MPa CO2 pressure. The developed AP-GO could be easily recovered and used repetitively in up to seven recycle runs with unchanged catalyst activity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Biochemistry and control of the reductive tricarboxylic acid pathway of CO 2 fixation and physiological role of the Rubis CO-like protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tabita, F. Robert

2008-12-04

During the past years of this project we have made progress relative to the two major goals of the proposal: (1) to study the biochemistry and regulation of the reductive TCA cycle of CO 2 fixation and (2) to probe the physiological role of a RubisCO-like protein (RLP). Both studies primarily employ the green sulfur bacterium Chlorobium tepidum as well as other photosynthetic bacteria including Rhodospirillum rubrum and Rhodopseudomonas palustris.

Response of vegetation to carbon dioxide. Field studies of plant responses to elevated carbon dioxide levels 1984

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-08-01

In the present study, CO{sub 2} enrichment has been applied to sweet potatoes and cowpeas in order to investigate its effect on their growth, physiology, and yield under field condition. Objectives were: (1) to establish at Tuskegee Institute the facilities for growing crops in the field under enriched CO{sub 2} atmospheric conditions; (2) to obtain field data on the morphological, physiological, biochemical, growth and yield responses of sweet potatoes and cowpeas to elevated levels of CO{sub 2}; (3) to determine the effects of elevated CO{sub 2} in the rate of nitrogen fixation of cowpeas; (4) to provide data for amore » generalized crop growth model for predicting yield of both sweet potatoes and cowpeas as a function of atmospheric CO{sub 2} enrichment.« less

Moss-cyanobacteria associations as biogenic sources of nitrogen in boreal forest ecosystems.

PubMed

Rousk, Kathrin; Jones, Davey L; Deluca, Thomas H

2013-01-01

The biological fixation of atmospheric nitrogen (N) is a major pathway for available N entering ecosystems. In N-limited boreal forests, a significant amount of N2 is fixed by cyanobacteria living in association with mosses, contributing up to 50% to the total N input. In this review, we synthesize reports on the drivers of N2 fixation in feather moss-cyanobacteria associations to gain a deeper understanding of their role for ecosystem-N-cycling. Nitrogen fixation in moss-cyanobacteria associations is inhibited by N inputs and therefore, significant fixation occurs only in low N-deposition areas. While it has been shown that artificial N additions in the laboratory as well as in the field inhibit N2 fixation in moss-cyanobacteria associations, the type, as well as the amounts of N that enters the system, affect N2 fixation differently. Another major driver of N2 fixation is the moisture status of the cyanobacteria-hosting moss, wherein moist conditions promote N2 fixation. Mosses experience large fluctuations in their hydrological status, undergoing significant natural drying and rewetting cycles over the course of only a few hours, especially in summer, which likely compromises the N input to the system via N2 fixation. Perhaps the most central question, however, that remains unanswered is the fate of the fixed N2 in mosses. The cyanobacteria are likely to leak N, but whether this N is transferred to the soil and if so, at which rates and timescales, is unknown. Despite our increasing understanding of the drivers of N2 fixation, the role moss-cyanobacteria associations play in ecosystem-N-cycling remains unresolved. Further, the relationship mosses and cyanobacteria share is unknown to date and warrants further investigation.

Assessment of oceanic productivity with the triple-isotope composition of dissolved oxygen.

PubMed

Luz, B; Barkan, E

2000-06-16

Plant production in the sea is a primary mechanism of global oxygen formation and carbon fixation. For this reason, and also because the ocean is a major sink for fossil fuel carbon dioxide, much attention has been given to estimating marine primary production. Here, we describe an approach for estimating production of photosynthetic oxygen, based on the isotopic composition of dissolved oxygen of seawater. This method allows the estimation of integrated oceanic productivity on a time scale of weeks.

Measuring Photosynthetic Response to Drought Stress using Active and Passive Fluorescence

NASA Astrophysics Data System (ADS)

Helm, L.; Lerdau, M.; Wang, W.; Yang, X.

2017-12-01

Photosynthesis, the endothermic reactions involving the absorption of light and fixation and reduction of carbon dioxide by plants, plays important roles in carbon and water cycles, food security, and even weather and climate patterns. Solar radiation provides the energy for photosynthesis, but often plants absorb more solar energy than they can use to reduce carbon dioxide. This excess energy, which is briefly stored as high-energy electrons in the chloroplast, must be removed or damage to the leaf's photosynthetic machinery will occur. One important energy dissipation pathway is for the high energy electrons to return to their lower valance state and, in doing so, release radiation (fluorescence). This fluorescence (known as solar induced fluorescence (SIF) has been found to strongly correlate with gross photosynthesis. Recent advances in the remote sensing of SIF allow for large-scale real-time estimation of photosynthesis. In a warming climate with more frequent stress, remote sensing is necessary for measuring the spatial and temporal variability of photosynthesis. However, the mechanisms that link SIF and photosynthesis are unclear, particularly how the relationship may or may not change under stress. We present data from leaf-level measurements of gas exchange, pulse amplitude modulation (PAM) fluorescence, and SIF in two major tree species in North America. Water-stressed and well-watered plants were compared to determine how SIF and carbon dioxide exchange are modulated by drought diurnally and seasonally. Secondly, photosynthesis and fluorescence under high and low oxygen concentrations were compared to determine how photorespiration alters the relationship between SIF and gross photosynthesis. We find a strong correlation between SIF and steady-state fluorescence measured with conventional PAM fluorometry. Our results also indicate that drought-stress modulates the SIF-photosynthesis relationship, and this may be driven by drought-induced changes in stomatal conductance that change the relationship between photosynthesis and photorespiration. We also show a response to drought stress measured with active and passive fluorescence. Application of these findings will allow remote sensing of SIF to be utilized on a larger scale.

Ischemic time impacts biological integrity of phospho-proteins in PI3K/Akt, Erk/MAPK, and p38 MAPK signaling networks.

PubMed

Holzer, Timothy R; Fulford, Angie D; Arkins, Austin M; Grondin, Janet M; Mundy, Christopher W; Nasir, Aejaz; Schade, Andrew E

2011-06-01

Post-translational modifications of proteins, such as phosphorylation, are labile events dynamically regulated by opposing kinase and phosphatase activities. Preanalytical factors, such as ischemic time before fixation, affect these activities and can have a significant impact on the ability to elucidate signaling pathways in tissue. Immunohistochemical analysis of phosphorylated proteins involved in PI3K/Akt, Erk/MAPK, and p38 MAPK signaling networks was performed in human cell line xenografts from lung, brain, ovary, and prostate tumors. In order to replicate real-world practices, the tissues were subjected to ischemic times of 0 (baseline), 1, 4, and 24 hours before fixation in formalin. Two key concepts emerge from this analysis: (1) the stability of different phospho-epitopes within a given tumor type is variable (e.g. phospho-PRAS40 is more labile than phospho-S6 ribosomal protein) and (2) the stability of a given phospho-epitope (e.g. phospho-MAPKAPK2) varies significantly across different tumor types. These results highlight the importance of proper tissue acquisition and rapid fixation to preserve the biological integrity of signal transduction pathways that may guide therapeutic decision making.

Carbon dioxide fixation in the metabolism of propylene and propylene oxide by Xanthobacter strain Py2.

PubMed Central

Small, F J; Ensign, S A

1995-01-01

Evidence for a requirement for CO2 in the productive metabolism of aliphatic alkenes and epoxides by the propylene-oxidizing bacterium Xanthobacter strain Py2 is presented. In the absence of CO2, whole-cell suspensions of propylene-grown cells catalyzed the isomerization of propylene oxide (epoxypropane) to acetone. In the presence of CO2, no acetone was produced. Acetone was not metabolized by suspensions of propylene-grown cells, in either the absence or presence of CO2. The degradation of propylene and propylene oxide by propylene-grown cells supported the fixation of 14CO2 into cell material, and the time course of 14C fixation correlated with the time course of propylene and propylene oxide degradation. The degradation of glucose and propionaldehyde by propylene-grown or glucose-grown cells did not support significant 14CO2 fixation. With propylene oxide as the substrate, the concentration dependence of 14CO2 fixation exhibited saturation kinetics, and at saturation, 0.9 mol of CO2 was fixed per mol of propylene oxide consumed. Cultures grown with propylene in a nitrogen-deficient medium supplemented with NaH13CO3 specifically incorporated 13C label into the C-1 (major labeled position) and C-3 (minor labeled position) carbon atoms of the endogenous storage compound poly-beta-hydroxybutyrate. No specific label incorporation was observed when cells were cultured with glucose or n-propanol as a carbon source. The depletion of CO2 from cultures grown with propylene, but not glucose or n-propanol, inhibited bacterial growth. We propose that propylene oxide metabolism in Xanthobacter strain Py2 proceeds by terminal carboxylation of an isomerization intermediate, which, in the absence of CO2, is released as acetone. PMID:7592382

Proteome Profiling of BEAS-2B Cells Treated with Titanium Dioxide Reveals Potential Toxicity of and Detoxification Pathways for Nanomaterial

EPA Science Inventory

Oxidative stress is known to play important roles in nanomaterial-induced toxicities. However, the proteins and signaling pathways associated with nanomaterial-mediated oxidative stress and toxicity are largely unknown. To identify oxidative stress-responding toxicity pathways an...

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution

EPA Science Inventory

There are many technological pathways that can lead to reduced carbon dioxide emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessmen...

Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic

PubMed Central

Baltar, Federico; Lundin, Daniel; Palovaara, Joakim; Lekunberri, Itziar; Reinthaler, Thomas; Herndl, Gerhard J.; Pinhassi, Jarone

2016-01-01

To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates—assumed to be related to autotrophic metabolisms—were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention. PMID:27818655

In‐loop flow [11C]CO2 fixation and radiosynthesis of N,N′‐[11C]dibenzylurea

PubMed Central

Downey, Joseph; Bongarzone, Salvatore; Hader, Stefan

2017-01-01

Cyclotron‐produced carbon‐11 is a highly valuable radionuclide for the production of positron emission tomography (PET) radiotracers. It is typically produced as relatively unreactive carbon‐11 carbon dioxide ([11C]CO2), which is most commonly converted into a more reactive precursor for synthesis of PET radiotracers. The development of [11C]CO2 fixation methods has more recently enabled the direct radiolabelling of a diverse array of structures directly from [11C]CO2, and the advantages afforded by the use of a loop‐based system used in 11C‐methylation and 11C‐carboxylation reactions inspired us to apply the [11C]CO2 fixation “in‐loop.” In this work, we developed and investigated a new ethylene tetrafluoroethylene (ETFE) loop‐based [11C]CO2 fixation method, enabling the fast and efficient, direct‐from‐cyclotron, in‐loop trapping of [11C]CO2 using mixed DBU/amine solutions. An optimised protocol was integrated into a proof‐of‐concept in‐loop flow radiosynthesis of N,N′‐[11C]dibenzylurea. This reaction exhibited an average 78% trapping efficiency and a crude radiochemical purity of 83% (determined by radio‐HPLC), giving an overall nonisolated radiochemical yield of 72% (decay‐corrected) within just 3 minutes from end of bombardment. This proof‐of‐concept reaction has demonstrated that efficient [11C]CO2 fixation can be achieved in a low‐volume (150 μL) ETFE loop and that this can be easily integrated into a rapid in‐loop flow radiosynthesis of carbon‐11–labelled products. This new in‐loop methodology will allow fast radiolabelling reactions to be performed using cheap/disposable ETFE tubing setup (ideal for good manufacturing practice production) thereby contributing to the widespread usage of [11C]CO2 trapping/fixation reactions for the production of PET radiotracers. PMID:28977686

In-loop flow [11 C]CO2 fixation and radiosynthesis of N,N'-[11 C]dibenzylurea.

PubMed

Downey, Joseph; Bongarzone, Salvatore; Hader, Stefan; Gee, Antony D

2018-03-01

Cyclotron-produced carbon-11 is a highly valuable radionuclide for the production of positron emission tomography (PET) radiotracers. It is typically produced as relatively unreactive carbon-11 carbon dioxide ([ 11 C]CO 2 ), which is most commonly converted into a more reactive precursor for synthesis of PET radiotracers. The development of [ 11 C]CO 2 fixation methods has more recently enabled the direct radiolabelling of a diverse array of structures directly from [ 11 C]CO 2 , and the advantages afforded by the use of a loop-based system used in 11 C-methylation and 11 C-carboxylation reactions inspired us to apply the [ 11 C]CO 2 fixation "in-loop." In this work, we developed and investigated a new ethylene tetrafluoroethylene (ETFE) loop-based [ 11 C]CO 2 fixation method, enabling the fast and efficient, direct-from-cyclotron, in-loop trapping of [ 11 C]CO 2 using mixed DBU/amine solutions. An optimised protocol was integrated into a proof-of-concept in-loop flow radiosynthesis of N,N'-[ 11 C]dibenzylurea. This reaction exhibited an average 78% trapping efficiency and a crude radiochemical purity of 83% (determined by radio-HPLC), giving an overall nonisolated radiochemical yield of 72% (decay-corrected) within just 3 minutes from end of bombardment. This proof-of-concept reaction has demonstrated that efficient [ 11 C]CO 2 fixation can be achieved in a low-volume (150 μL) ETFE loop and that this can be easily integrated into a rapid in-loop flow radiosynthesis of carbon-11-labelled products. This new in-loop methodology will allow fast radiolabelling reactions to be performed using cheap/disposable ETFE tubing setup (ideal for good manufacturing practice production) thereby contributing to the widespread usage of [ 11 C]CO 2 trapping/fixation reactions for the production of PET radiotracers. © 2017 The Authors. Journal of Labelled Compounds and Radiopharmaceuticals Published by John Wiley & Sons, Ltd.

The effects of environmental physical factors on the microbial communities and the distribution of different CO2 fixation pathways in a limestone landscape

NASA Astrophysics Data System (ADS)

Wun, S. R.; Huang, T. Y.; Hsu, B. M.; Fan, C. W.

2017-12-01

We aimed to study the effects of physical factors on the relative abundance of bacteria and their preferential admissions of autotrophic CO2 fixation pathways after subjected to environmental long-term influence. The Narrow-Sky located in upper part of Takangshan is a small gulch of Pleistocene coralline limestone formation in southern Taiwan. The physical parameters such as illumination, humidity, and temperature were varied largely in habitats around the gulch, namely on the limestone wall at the opening of gulch, on the coordinate ground soil, on the wall inside the gulch, and the water drip from limestone wall. The total organic carbon was measured in solid samples to evaluate the biomass of the habitats. A metagenomic approach was carried out to reveal their microbial community structure. After the metagenomic library of operational taxonomic units (OTUs) was constructed, a BLAST search by "nomenclature of bacteria" instead of sequences between the OTU libraries and KEGG database was carried out to generate libraries of "model microbial communities", which the complete genomes of the entire bacterial populations were available. Our results showed the biomass of habitats in the opening of gulch was twice higher than the inside, suggesting the illumination played an important role in biosynthesis. In quantitative comparison in key enzymes of CO2 fixation pathways by model communities, 70% to 90% of bacteria possessed key enzymes of Fuchs-Holo cycle, while only 5% to 20% of bacteria contained key enzymes of Calvin-Benson cycle. The key enzymes for hydroxypropionate/ hydroxybutyrate and dicarboxylate/ 4-hydroxybutyrate cycles were not found in this study. In the water sample, approximate 10% of bacteria consisted of the key enzyme for Arnon-Buchanan cycle. Less than 2% of bacteria in all habitats take the reductive acetyl-CoA cycle for CO2 fixation. This study provides a novel method to study biosynthetic process of microbial communities in natural habitats.

Carbon dioxide utilisation of Dunaliella tertiolecta for carbon bio-mitigation in a semicontinuous photobioreactor.

PubMed

Farrelly, Damien J; Brennan, Liam; Everard, Colm D; McDonnell, Kevin P

2014-04-01

Bio-fixation of carbon dioxide (CO2) by microalgae has been recognised as an attractive approach to offset anthropogenic emissions. Biological carbon mitigation is the process whereby autotrophic organisms, such as microalgae, convert CO2 into organic carbon and O2 through photosynthesis; this process through respiration produces biomass. In this study Dunaliella tertiolecta was cultivated in a semicontinuous culture to investigate the carbon mitigation rate of the system. The algae were produced in 1.2-L Roux bottles with a working volume of 1 L while semicontinuous production commenced on day 4 of cultivation when the carbon mitigation rate was found to be at a maximum for D. tertiolecta. The reduction in CO2 between input and output gases was monitored to predict carbon fixation rates while biomass production and microalgal carbon content are used to calculate the actual carbon mitigation potential of D. tertiolecta. A renewal rate of 45 % of flask volume was utilised to maintain the culture in exponential growth with an average daily productivity of 0.07 g L(-1) day(-1). The results showed that 0.74 g L(-1) of biomass could be achieved after 7 days of semicontinuous production while a total carbon mitigation of 0.37 g L(-1) was achieved. This represented an increase of 0.18 g L(-1) in carbon mitigation rate compared to batch production of D. tertiolecta over the same cultivation period.

Nitrogen Fixation by Anaerobes is Stimulated by Low Oxygen and Insensitive to Combined Nitrogen in Coastal Sediments

NASA Astrophysics Data System (ADS)

Jenkins, B. D.; Spinette, R.; Jones, A.; Puggioni, G.; Ehrlich, A.; Brown, S. M.

2016-02-01

Coastal sediments are typically zones of nitrogen removal via coupled nitrification-denitrification pathways. Increasingly, there are reports of nitrogen fixation in anthropogenically impacted sediments containing ample combined nitrogen. In previous work in the estuarine sediments of Narragansett Bay, we found that anaerobes related to Desulfovibrio spp. and in the Desulfuromonadales express genes for nitrogen fixation (nifH). We also determined that nitrogen fixation rates and gene expression are elevated during periods of seasonal hypoxia. Statistical modeling shows that a combination of elevated phytoplankton biomass as with a duration of hypoxia for a week or longer lead to conditions that promote nitrogen fixation as measured by acetylene reduction. Interestingly, diazotrophs closely related to those identified in Narragansett Bay are present and active in other low oxygen systems, suggesting that expansion of hypoxic events may lead to unanticipated consequences for the benthic nitrogen cycle in many ecosystems. To determine controls on diazotrophy on the organismal level, we isolated and sequenced the genomes of two Narragansett Bay members of the Desulfovibrio. We found that these organisms are insensitive to nitrate and urea, as they are missing the genes to assimilate these nitrogen sources. However, their nitrogen fixation is suppressed by increasing concentrations of ammonium, indicating that they may be sensitive to this nitrogen source in the environment. The paradox of detectable nitrogen fixation in the background of measurable ammonium in estuarine systems is a newly emergent theme and suggests that there are complex microbial interactions and/or structure to the nutrient regimes allowing for fixation.

Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium

PubMed Central

Kuever, Jan; Visser, Michael; Loeffler, Claudia; Boll, Matthias; Worm, Petra; Sousa, Diana Z.; Plugge, Caroline M.; Schaap, Peter J.; Muyzer, Gerard; Pereira, Ines A.C.; Parshina, Sofiya N.; Goodwin, Lynne A.; Kyrpides, Nikos C.; Detter, Janine; Woyke, Tanja; Chain, Patrick; Davenport, Karen W.; Rohde, Manfred; Spring, Stefan; Klenk, Hans-Peter; Stams, Alfons J.M.

2014-01-01

Desulfotomaculum gibsoniae is a mesophilic member of the polyphyletic spore-forming genus Desulfotomaculum within the family Peptococcaceae. This bacterium was isolated from a freshwater ditch and is of interest because it can grow with a large variety of organic substrates, in particular several aromatic compounds, short-chain and medium-chain fatty acids, which are degraded completely to carbon dioxide coupled to the reduction of sulfate. It can grow autotrophically with H2 + CO2 and sulfate and slowly acetogenically with H2 + CO2, formate or methoxylated aromatic compounds in the absence of sulfate. It does not require any vitamins for growth. Here, we describe the features of D. gibsoniae strain GrollT together with the genome sequence and annotation. The chromosome has 4,855,529 bp organized in one circular contig and is the largest genome of all sequenced Desulfotomaculum spp. to date. A total of 4,666 candidate protein-encoding genes and 96 RNA genes were identified. Genes of the acetyl-CoA pathway, possibly involved in heterotrophic growth and in CO2 fixation during autotrophic growth, are present. The genome contains a large set of genes for the anaerobic transformation and degradation of aromatic compounds, which are lacking in the other sequenced Desulfotomaculum genomes. PMID:25197466

Proteome Profiling Reveals Potential Toxicity and Detoxification Pathways Following Exposure of BEAS-2B Cells to Engineered Nanoparticle Titanium Dioxide

EPA Science Inventory

Identification of toxicity pathways linked to chemical -exposure is critical for a better understanding of biological effects of the exposure, toxic mechanisms, and for enhancement of the prediction of chemical toxicity and adverse health outcomes. To identify toxicity pathways a...

Self-repairable polyurethane networks by atmospheric carbon dioxide and water.

PubMed

Yang, Ying; Urban, Marek W

2014-11-03

Sugar moieties were incorporated into cross-linked polyurethane (PUR) networks in an effort to achieve self-repairing in the presence of atmospheric carbon dioxide (CO2) and water (H2O). When methyl-α-D-glucopyranoside (MGP) molecules are reacted with hexamethylene diisocyanate trimer (HDI) and polyethylene glycol (PEG) to form cross-linked MGP-polyurethane (PUR) networks, these materials are capable of self-repairing in air. This process requires atmospheric amounts of CO2 and H2O, thus resembling plant behavior of carbon fixation during the photosynthesis cycle. Molecular processes responsible for this unique self-repair process involve physical diffusion of cleaved network segments as well as the formation of carbonate and urethane linkages. Unlike plants, MGP-PUR networks require no photo-initiated reactions, and they are thus capable of repair in darkness under atmospheric conditions. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metagenomics-guided analysis of microbial chemolithoautotrophic phosphite oxidation yields evidence of a seventh natural CO2 fixation pathway.

PubMed

Figueroa, Israel A; Barnum, Tyler P; Somasekhar, Pranav Y; Carlström, Charlotte I; Engelbrektson, Anna L; Coates, John D

2018-01-02

Dissimilatory phosphite oxidation (DPO), a microbial metabolism by which phosphite (HPO 3 2- ) is oxidized to phosphate (PO 4 3- ), is the most energetically favorable chemotrophic electron-donating process known. Only one DPO organism has been described to date, and little is known about the environmental relevance of this metabolism. In this study, we used 16S rRNA gene community analysis and genome-resolved metagenomics to characterize anaerobic wastewater treatment sludge enrichments performing DPO coupled to CO 2 reduction. We identified an uncultivated DPO bacterium, Candidatus Phosphitivorax ( Ca. P.) anaerolimi strain Phox-21, that belongs to candidate order GW-28 within the Deltaproteobacteria , which has no known cultured isolates. Genes for phosphite oxidation and for CO 2 reduction to formate were found in the genome of Ca. P. anaerolimi, but it appears to lack any of the known natural carbon fixation pathways. These observations led us to propose a metabolic model for autotrophic growth by Ca. P. anaerolimi whereby DPO drives CO 2 reduction to formate, which is then assimilated into biomass via the reductive glycine pathway.

Estimating environmental co-benefits of U.S. low-carbon pathways using an integrated assessment model with state-level resolution.

PubMed

Ou, Yang; Shi, Wenjing; Smith, Steven J; Ledna, Catherine M; West, J Jason; Nolte, Christopher G; Loughlin, Daniel H

2018-04-15

There are many technological pathways that can lead to reduced carbon dioxide emissions. However, these pathways can have substantially different impacts on other environmental endpoints, such as air quality and energy-related water demand. This study uses an integrated assessment model with state-level resolution of the energy system to compare environmental impacts of alternative low-carbon pathways for the United States. One set of pathways emphasizes nuclear energy and carbon capture and storage, while another set emphasizes renewable energy, including wind, solar, geothermal power, and bioenergy. These are compared with pathways in which all technologies are available. Air pollutant emissions, mortality costs attributable to particulate matter smaller than 2.5 μm in diameter, and energy-related water demands are evaluated for 50% and 80% carbon dioxide reduction targets in 2050. The renewable low-carbon pathways require less water withdrawal and consumption than the nuclear and carbon capture pathways. However, the renewable low-carbon pathways modeled in this study produce higher particulate matter-related mortality costs due to greater use of biomass in residential heating. Environmental co-benefits differ among states because of factors such as existing technology stock, resource availability, and environmental and energy policies.

Regulation of Carbon Flow by Nitrogen and Light in the Red Alga, Gelidium coulteri.

PubMed

Macler, B A

1986-09-01

The red alga Gelidium coulteri Harv. photosynthetically fixed [(14)C] bicarbonate at high rates under defined conditions in unialgal laboratory culture. The fixation rate and flow of photosynthate into various end products were dependent on the nitrogen status of the tissue. Plants fed luxury levels of nitrogen (approximately 340 micromolar) showed fixation rates several-fold higher than those seen for plants starved for nitrogen. The addition of NO(3) (-) or NH(4) (+) to such starved plants further inhibited fixation over at least the first several hours after addition. The majority of (14)C after incubations of 30 minutes to 8 hours was found in the compounds floridoside, agar and floridean starch. In addition, amino acids and intermediate compounds of the reductive pentose phosphate pathway, glycolytic pathway and tricarboxylic acid cycle were detected. Nitrogen affected the partitioning of labeled carbon into these compounds. Plants under luxury nitrogen conditions had higher floridoside levels and markedly lower amounts of agar and starch than found in plants limited for nitrogen. Amino acid, phycobiliprotein and chlorophyll levels were also significantly higher in nitrogen-enriched plants. Addition of NO(3) (-) to starved plants led to an increase in floridoside, tricarboxylic acid cycle intermediates and amino acids within 1 hour and inhibited carbon flow into agar and starch. Carbon fixation in the dark was only 1 to 7% of that seen in the light. Dark fixation of [(14)C]bicarbonate yielded label primarily in tricarboxylic acid cycle intermediates, amino acids and polysaccharides. Nitrogen stimulated amino acid synthesis at the expense of agar and starch. Floridoside was only a minor component in the dark. Pulse-chase experiments, designed to show carbon turnover, indicated a 2-fold increase in labeling of agar over 96 hours of chase in the light. No increases were seen in the dark. Low molecular weight pools, including floridoside, decreased 2- to 5-fold over this period under both light and dark conditions. Nitrogen status did not influence turnover. There was little or no organic carbon released into the culture medium over this period. The results are consistent with biosynthetic pathways to floridoside and agar that share the common intermediate UDP-d-galactose. It is hypothesized that synthesis of floridoside is regulated by nitrogen and light at the enzymic level.

Regulation of Carbon Flow by Nitrogen and Light in the Red Alga, Gelidium coulteri1

PubMed Central

Macler, Bruce A.

1986-01-01

The red alga Gelidium coulteri Harv. photosynthetically fixed [14C] bicarbonate at high rates under defined conditions in unialgal laboratory culture. The fixation rate and flow of photosynthate into various end products were dependent on the nitrogen status of the tissue. Plants fed luxury levels of nitrogen (approximately 340 micromolar) showed fixation rates several-fold higher than those seen for plants starved for nitrogen. The addition of NO3− or NH4+ to such starved plants further inhibited fixation over at least the first several hours after addition. The majority of 14C after incubations of 30 minutes to 8 hours was found in the compounds floridoside, agar and floridean starch. In addition, amino acids and intermediate compounds of the reductive pentose phosphate pathway, glycolytic pathway and tricarboxylic acid cycle were detected. Nitrogen affected the partitioning of labeled carbon into these compounds. Plants under luxury nitrogen conditions had higher floridoside levels and markedly lower amounts of agar and starch than found in plants limited for nitrogen. Amino acid, phycobiliprotein and chlorophyll levels were also significantly higher in nitrogen-enriched plants. Addition of NO3− to starved plants led to an increase in floridoside, tricarboxylic acid cycle intermediates and amino acids within 1 hour and inhibited carbon flow into agar and starch. Carbon fixation in the dark was only 1 to 7% of that seen in the light. Dark fixation of [14C]bicarbonate yielded label primarily in tricarboxylic acid cycle intermediates, amino acids and polysaccharides. Nitrogen stimulated amino acid synthesis at the expense of agar and starch. Floridoside was only a minor component in the dark. Pulse-chase experiments, designed to show carbon turnover, indicated a 2-fold increase in labeling of agar over 96 hours of chase in the light. No increases were seen in the dark. Low molecular weight pools, including floridoside, decreased 2- to 5-fold over this period under both light and dark conditions. Nitrogen status did not influence turnover. There was little or no organic carbon released into the culture medium over this period. The results are consistent with biosynthetic pathways to floridoside and agar that share the common intermediate UDP-d-galactose. It is hypothesized that synthesis of floridoside is regulated by nitrogen and light at the enzymic level. PMID:16664980

Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil.

PubMed

Pratscher, Jennifer; Dumont, Marc G; Conrad, Ralf

2011-03-08

Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO(2) fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO(2) fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO(2) using the 3-hydroxypropionate-4-hydroxybutyrate cycle, one of the two pathways recently identified for CO(2) fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO(2) assimilation and that their importance to the overall archaeal community might be larger than previously thought.

Ammonia oxidation coupled to CO2 fixation by archaea and bacteria in an agricultural soil

PubMed Central

Pratscher, Jennifer; Dumont, Marc G.; Conrad, Ralf

2011-01-01

Ammonia oxidation is an essential part of the global nitrogen cycling and was long thought to be driven only by bacteria. Recent findings expanded this pathway also to the archaea. However, most questions concerning the metabolism of ammonia-oxidizing archaea, such as ammonia oxidation and potential CO2 fixation, remain open, especially for terrestrial environments. Here, we investigated the activity of ammonia-oxidizing archaea and bacteria in an agricultural soil by comparison of RNA- and DNA-stable isotope probing (SIP). RNA-SIP demonstrated a highly dynamic and diverse community involved in CO2 fixation and carbon assimilation coupled to ammonia oxidation. DNA-SIP showed growth of the ammonia-oxidizing bacteria but not of archaea. Furthermore, the analysis of labeled RNA found transcripts of the archaeal acetyl-CoA/propionyl-CoA carboxylase (accA/pccB) to be expressed and labeled. These findings strongly suggest that ammonia-oxidizing archaeal groups in soil autotrophically fix CO2 using the 3-hydroxypropionate–4-hydroxybutyrate cycle, one of the two pathways recently identified for CO2 fixation in Crenarchaeota. Catalyzed reporter deposition (CARD)-FISH targeting the gene encoding subunit A of ammonia monooxygenase (amoA) mRNA and 16S rRNA of archaea also revealed ammonia-oxidizing archaea to be numerically relevant among the archaea in this soil. Our results demonstrate a diverse and dynamic contribution of ammonia-oxidizing archaea in soil to nitrification and CO2 assimilation and that their importance to the overall archaeal community might be larger than previously thought. PMID:21368116

Anatomical Evidence that the Superior Colliculus Controls Saccades through Central Mesencephalic Reticular Formation Gating of Omnipause Neuron Activity

PubMed Central

Wang, Niping; Perkins, Eddie; Zhou, Lan; Warren, Susan

2013-01-01

Omnipause neurons (OPNs) within the nucleus raphe interpositus (RIP) help gate the transition between fixation and saccadic eye movements by monosynaptically suppressing activity in premotor burst neurons during fixation, and releasing them during saccades. Premotor neuron activity is initiated by excitatory input from the superior colliculus (SC), but how the tectum's saccade-related activity turns off OPNs is not known. Since the central mesencephalic reticular formation (cMRF) is a major SC target, we explored whether this nucleus has the appropriate connections to support tectal gating of OPN activity. In dual-tracer experiments undertaken in macaque monkeys (Macaca fascicularis), cMRF neurons labeled retrogradely from injections into RIP had numerous anterogradely labeled terminals closely associated with them following SC injections. This suggested the presence of an SC–cMRF–RIP pathway. Furthermore, anterograde tracers injected into the cMRF of other macaques labeled axonal terminals in RIP, confirming this cMRF projection. To determine whether the cMRF projections gate OPN activity, postembedding electron microscopic immunochemistry was performed on anterogradely labeled cMRF terminals with antibody to GABA or glycine. Of the terminals analyzed, 51.4% were GABA positive, 35.5% were GABA negative, and most contacted glycinergic cells. In summary, a trans-cMRF pathway connecting the SC to the RIP is present. This pathway contains inhibitory elements that could help gate omnipause activity and allow other tectal drives to induce the bursts of firing in premotor neurons that are necessary for saccades. The non-GABAergic cMRF terminals may derive from fixation units in the cMRF. PMID:24107960

De Novo Transcriptome Analysis of an Aerial Microalga Trentepohlia jolithus: Pathway Description and Gene Discovery for Carbon Fixation and Carotenoid Biosynthesis

PubMed Central

Li, Qianqian; Liu, Jianguo; Zhang, Litao; Liu, Qian

2014-01-01

Background Algae in the order Trentepohliales have a broad geographic distribution and are generally characterized by the presence of abundant β-carotene. The many monographs published to date have mainly focused on their morphology, taxonomy, phylogeny, distribution and reproduction; molecular studies of this order are still rare. High-throughput RNA sequencing (RNA-Seq) technology provides a powerful and efficient method for transcript analysis and gene discovery in Trentepohlia jolithus. Methods/Principal Findings Illumina HiSeq 2000 sequencing generated 55,007,830 Illumina PE raw reads, which were assembled into 41,328 assembled unigenes. Based on NR annotation, 53.28% of the unigenes (22,018) could be assigned to gene ontology classes with 54 subcategories and 161,451 functional terms. A total of 26,217 (63.44%) assembled unigenes were mapped to 128 KEGG pathways. Furthermore, a set of 5,798 SSRs in 5,206 unigenes and 131,478 putative SNPs were identified. Moreover, the fact that all of the C4 photosynthesis genes exist in T. jolithus suggests a complex carbon acquisition and fixation system. Similarities and differences between T. jolithus and other algae in carotenoid biosynthesis are also described in depth. Conclusions/Significance This is the first broad transcriptome survey for T. jolithus, increasing the amount of molecular data available for the class Ulvophyceae. As well as providing resources for functional genomics studies, the functional genes and putative pathways identified here will contribute to a better understanding of carbon fixation and fatty acid and carotenoid biosynthesis in T. jolithus. PMID:25254555

Anatomical evidence that the superior colliculus controls saccades through central mesencephalic reticular formation gating of omnipause neuron activity.

PubMed

Wang, Niping; Perkins, Eddie; Zhou, Lan; Warren, Susan; May, Paul J

2013-10-09

Omnipause neurons (OPNs) within the nucleus raphe interpositus (RIP) help gate the transition between fixation and saccadic eye movements by monosynaptically suppressing activity in premotor burst neurons during fixation, and releasing them during saccades. Premotor neuron activity is initiated by excitatory input from the superior colliculus (SC), but how the tectum's saccade-related activity turns off OPNs is not known. Since the central mesencephalic reticular formation (cMRF) is a major SC target, we explored whether this nucleus has the appropriate connections to support tectal gating of OPN activity. In dual-tracer experiments undertaken in macaque monkeys (Macaca fascicularis), cMRF neurons labeled retrogradely from injections into RIP had numerous anterogradely labeled terminals closely associated with them following SC injections. This suggested the presence of an SC-cMRF-RIP pathway. Furthermore, anterograde tracers injected into the cMRF of other macaques labeled axonal terminals in RIP, confirming this cMRF projection. To determine whether the cMRF projections gate OPN activity, postembedding electron microscopic immunochemistry was performed on anterogradely labeled cMRF terminals with antibody to GABA or glycine. Of the terminals analyzed, 51.4% were GABA positive, 35.5% were GABA negative, and most contacted glycinergic cells. In summary, a trans-cMRF pathway connecting the SC to the RIP is present. This pathway contains inhibitory elements that could help gate omnipause activity and allow other tectal drives to induce the bursts of firing in premotor neurons that are necessary for saccades. The non-GABAergic cMRF terminals may derive from fixation units in the cMRF.

Carbon fixation in oceanic crust: Does it happen, and is it important?

NASA Astrophysics Data System (ADS)

Orcutt, B.; Sylvan, J. B.; Rogers, D.; Lee, R.; Girguis, P. R.; Carr, S. A.; Jungbluth, S.; Rappe, M. S.

2014-12-01

The carbon sources supporting a deep biosphere in igneous oceanic crust, and furthermore the balance of heterotrophy and autotrophy, are poorly understood. When the large reservoir size of oceanic crust is considered, carbon transformations in this environment have the potential to significantly impact the global carbon cycle. Furthermore, igneous oceanic crust is the most massive potential habitat for life on Earth, so understanding the carbon sources for this potential biosphere are important for understanding life on Earth. Geochemical evidence suggests that warm and anoxic upper basement is net heterotrophic, but the balance of these processes in cooler and potentially oxic oceanic crust are poorly known. Here, we present data from stable carbon isotope tracer incubations to examine carbon fixation in basalts collected from the Loihi Seamount, the Juan de Fuca Ridge, and the western flank of the Mid-Atlantic Ridge, to provide a first order constraint on the rates of carbon fixation on basalts. These data will be compared to recently available assessments of carbon cycling rates in fluids from upper basement to synthesize our current state of understanding of the potential for carbon fixation and respiration in oceanic crust. Moreover, we will present new genomic data of carbon fixation genes observed in the basalt enrichments as well as from the subsurface of the Juan de Fuca Ridge flank, enabling identification of the microbes and metabolic pathways involved in carbon fixation in these systems.

Role of photoexcited nitrogen dioxide chemistry on ozone formation and emission control strategy over the Pearl River Delta, China

EPA Science Inventory

A new hydroxyl radical formation pathway via photo-excited nitrogen dioxide chemistry is incorporated into a chemistry-only box model as well as a 3D air quality model to examine its potential role on ozone formation and emission control strategy over the Pearl River Delta region...

Scanning electron microscopic appearance of rat otocyst of the twelfth postcoital day: elaboration of a method.

PubMed

Marovitz, W F; Khan, K M

1977-01-01

A method for removal, fixation, microdissection, and drying of early rat otocyst for examination by the scanning electron microscope is elaborated. Tissues were dissected, fixed as for conventional transmission electron microscopy and dried by critical point evaporation using amylacetate as the transitional fluid and carbon dioxide as the pressure head. Otocysts were either dissected at the time of initial fixation, or subsequent to drying. The otocyst of the 12th postcoital day was used as a model system in this preliminary report. Critical point drying retained the overall configuration and the fine ultrastructural detail of the otocyst. The interior otocystic surface was visualized and cilia bearing cells of the luminal surface were identified. Most if not all of these cells had a comspicuous, but short kinocillum which terminated in an ovoid bulb. The scanning electron microscopic appearance was correlated to the transmission electron microscopic image seen in the second paper in this Supplement.

A short history of RubisCO: the rise and fall (?) of Nature's predominant CO2 fixing enzyme.

PubMed

Erb, Tobias J; Zarzycki, Jan

2018-02-01

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) is arguably one of the most abundant proteins in the biosphere and a key enzyme in the global carbon cycle. Although RubisCO has been intensively studied, its evolutionary origins and rise as Nature's most dominant carbon dioxide (CO 2 )-fixing enzyme still remain in the dark. In this review we will bring together biochemical, structural, physiological, microbiological, as well as phylogenetic data to speculate on the evolutionary roots of the CO 2 -fixation reaction of RubisCO, the emergence of RubisCO-based autotrophic CO 2 -fixation in the context of the Calvin-Benson-Bassham cycle, and the further evolution of RubisCO into the 'RubisCOsome', a complex of various proteins assembling and interacting with the enzyme to improve its operational capacity (functionality) under different biological and environmental conditions. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Oxidative Stress, Inflammation, and DNA Damage Responses Elicited by Silver, Titanium Dioxide, and Cerium Oxide Nanomaterials

EPA Science Inventory

Previous literature on the biological effects of engineered nanomaterials has focused largely on oxidative stress and inflammation endpoints without further investigating potential pathways. Here we examine time-sensitive biological response pathways affected by engineered nanoma...

Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament.

PubMed

MacGregor, Barbara J; Biddle, Jennifer F; Harbort, Christopher; Matthysse, Ann G; Teske, Andreas

2013-09-01

A near-complete draft genome has been obtained for a single vacuolated orange Beggiatoa (Cand. Maribeggiatoa) filament from a Guaymas Basin seafloor microbial mat, the third relatively complete sequence for the Beggiatoaceae. Possible pathways for sulfide oxidation; nitrate respiration; inorganic carbon fixation by both Type II RuBisCO and the reductive tricarboxylic acid cycle; acetate and possibly formate uptake; and energy-generating electron transport via both oxidative phosphorylation and the Rnf complex are discussed here. A role in nitrite reduction is suggested for an abundant orange cytochrome produced by the Guaymas strain; this has a possible homolog in Beggiatoa (Cand. Isobeggiatoa) sp. PS, isolated from marine harbor sediment, but not Beggiatoa alba B18LD, isolated from a freshwater rice field ditch. Inferred phylogenies for the Calvin-Benson-Bassham (CBB) cycle and the reductive (rTCA) and oxidative (TCA) tricarboxylic acid cycles suggest that genes encoding succinate dehydrogenase and enzymes for carboxylation and/or decarboxylation steps (including RuBisCO) may have been introduced to (or exported from) one or more of the three genomes by horizontal transfer, sometimes by different routes. Sequences from the two marine strains are generally more similar to each other than to sequences from the freshwater strain, except in the case of RuBisCO: only the Guaymas strain encodes a Type II enzyme, which (where studied) discriminates less against oxygen than do Type I RuBisCOs. Genes subject to horizontal transfer may represent key steps for adaptation to factors such as oxygen and carbon dioxide concentration, organic carbon availability, and environmental variability. © 2013.

High Temperature Raman Spectroscopy Study of the Conversion of Formate into Oxalate: Search for the Elusive CO 2 2 - Intermediate

NASA Astrophysics Data System (ADS)

Ryan, Charles; Mead, Anna; Lakkaraju, Prasad; Kaczur, Jerry; Bennett, Christopher; Dobbins, Tabbetha

Research on conversion of carbon dioxide into chemicals and fuels has the potential to address three problems of global relevance. (a) By removing carbon dioxide from the atmosphere, we are able to reduce the amount of greenhouse gases in the atmosphere, (b) by converting carbon dioxide into fuels, we are providing pathways for renewable energy sources, (c) by converting carbon dioxide into C2 and higher order compounds, and we are able to generate valuable precursors for organic synthesis. Formate salts are formed by the electrochemical reduction of carbon dioxide in aqueous media. However, in order to increase the utilization of carbon dioxide, methods need to be developed for the conversion of formate into compounds containing two carbon atoms such as oxalate or oxalic acid. Recently, we examined the thermal conversion of sodium formate into sodium oxalate utilizing a hydride ion catalyst. The proposed mechanism for this reaction involves the carbon dioxide dianion. Currently at NASA Goddard Space Flight Center.

Lanthanide Complexes with Multidentate Oxime Ligands as Single-Molecule Magnets and Atmospheric Carbon Dioxide Fixation Systems.

PubMed

Hołyńska, Małgorzata; Clérac, Rodolphe; Rouzières, Mathieu

2015-09-14

The synthesis, structure, and magnetic properties of five lanthanide complexes with multidentate oxime ligands are described. Complexes 1 and 2 (1: [La2 (pop)2 (acac)4 (CH3 OH)], 2: [Dy2 (pop)(acac)5 ]) are synthesized from the 2-hydroxyimino-N-[1-(2-pyridyl)ethylidene]propanohydrazone (Hpop) ligand, while 3, 4, and 5 (3: [Dy2 (naphthsaoH)2 (acac)4 H(OH)]⋅0.85 CH3 CN⋅1.58 H2 O; 4: [Tb2 (naphthsaoH)2 (acac)4 H(OH)]⋅0.52 CH3 CN⋅1.71 H2 O; 5: [La6 (CO3 )2 (naphthsao)5 (naphthsaoH)0.5 (acac)8 (CO3 )0.5 (CH3 OH)2.76 H5.5 (H2 O)1.24 ]⋅2.39 CH3 CN⋅0.12 H2 O) contain 1-(1-hydroxynaphthalen-2-yl)-ethanone oxime (naphthsaoH2 ). In 1-4, dinuclear [Ln2 ] complexes crystallize, whereas hexanuclear La(III) complex 5 is formed after fixation of atmospheric carbon dioxide. Dy(III) -based complexes 2 and 3 display single-molecule-magnet properties with energy barriers of 27 and 98 K, respectively. The presence of a broad and unsymmetrical relaxation mode observed in the ac susceptibility data for 3 suggest two different dynamics of the magnetization which might be a consequence of independent relaxation processes of the two different Dy(3+) ions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An evaluation of possible mechanisms for conversion of sulfur dioxide to sulfuric acid and sulfate aerosols in the troposphere

Treesearch

Jack G. Calvert

1976-01-01

The mechanisms and rates of conversion of sulfur dioxide to sulfur trioxide, sulfuric acid, and other "sulfate" aerosol precursors are considered in view of current knowledge related to atmospheric reactions and chemical kinetics. Several heterogeneous pathways exist for SO2 oxidation promoted on solid catalyst particles and in aqueous...

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing

PubMed Central

Godwin, Scott; Kang, Alicia; Gulino, Lisa-Maree; Manefield, Mike; Gutierrez-Zamora, Maria-Luisa; Kienzle, Marco; Ouwerkerk, Diane; Dawson, Kerri; Klieve, Athol V

2014-01-01

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. PMID:24621520

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing.

PubMed

Godwin, Scott; Kang, Alicia; Gulino, Lisa-Maree; Manefield, Mike; Gutierrez-Zamora, Maria-Luisa; Kienzle, Marco; Ouwerkerk, Diane; Dawson, Kerri; Klieve, Athol V

2014-09-01

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.

Atmospheric dynamics in Laboratory Biosphere with wheat and sweet potato crops

NASA Astrophysics Data System (ADS)

Dempster, W. F.; Allen, J. P.; Alling, A.; Nelson, M.; Silvertone, S.; van Thillo, M.

Laboratory Biosphere is a 40 m3 closed life system equipped with 12000 watts of high pressure sodium lamps over planting beds with 5.37 m2 of soil. Atmospheric composition changes due to photosynthetic fixation of carbon dioxide and corresponding production of oxygen or the reverse, respiration, are observed in short timeframes, eg. hourly. To focus on inherent characteristics of the crop as distinct from its area or the volume of the chamber, we report fixation and respiration rates in millimoles per hour per square meter of planted area. An 85 day crop of USU Apogee wheat under a 16 hour lighted / 8 hour dark regime peaked in fixation rate at about 100 mmol h-1 m-2 approximately 24 days after planting. Light intensity was about 840 mol m-2 s-1. Dark respiration peaked at about 31 mmol h-1 m-2 at the same time. Thereafter, both fixation and respiration declined toward zero as harvest time approached. A residual soil respiration rate of about 1.9 mmol h-1 m-2 was observed in the dark closed chamber for 100 days after the harvest. A 126 day crop of Tuskegee TU-82-155 sweet potato behaved quite differently. Under a 680 mol m-2 s-1, 18 hour lighted / 6 hour dark regime, fixation during lighted hours rose to a plateau ranging from about 27 to 48 mmol h-1 m-2 after 42 days and respiration settled into a range of 12 to 23 mmol h-1 m-2. These rates continued unabated until the harvest at 126 days, suggesting that tuber biomass production might have continued at about the same rate for some time beyond the harvest time that was exercised in this experiment. In both experiments CO2 levels were allowed to range widely from a few hundred ppm to about 3000 ppm, which permitted observation of fixation rates both at varying CO2 concentrations and at each number of days after planting. This enables plotting the fixation rate as a function of both variables. Understanding the atmospheric dynamics of individual crops will be essential for design and atmospheric management of more complex CES which integrate the simultaneous growth of several crops as in a sustainable remote life support system.

Atmospheric dynamics in the “Laboratory Biosphere” with wheat and sweet potato crops

NASA Astrophysics Data System (ADS)

Dempster, William F.; Allen, J. P.; Alling, A.; Silverstone, S.; Van Thillo, M.

Laboratory Biosphere is a 40-m 3 closed life system equipped with 12,000 W of high pressure sodium lamps over planting beds with 5.37 m 2 of soil. Atmospheric composition changes due to photosynthetic fixation of carbon dioxide and corresponding production of oxygen or the reverse, respiration, are observed in short timeframes, e.g., hourly. To focus on inherent characteristics of the crop as distinct from its area or the volume of the chamber, we report fixation and respiration rates in mmol h -1 m -2 of planted area. An 85-day crop of USU Apogee wheat under a 16-h lighted/8-h dark regime peaked in fixation rate at about 100 mmol h -1 m -2 approximately 24 days after planting. Light intensity was about 840 μmol m -2 s -1. Dark respiration peaked at about 31 mmol h -1 m -2 at the same time. Thereafter, both fixation and respiration declined toward zero as harvest time approached. A residual soil respiration rate of about 1.9 mmol h -1 m -2 was observed in the dark closed chamber for 100 days after the harvest. A 126-day crop of Tuskegee TU-82-155 sweet potato behaved quite differently. Under a 680 μmol m -2 s -1, 18-h lighted/6-h dark regime, fixation during lighted hours rose to a plateau ranging from about 27 to 48 mmol h -1 m -2 after 42 days and dark respiration settled into a range of 12-23 mmol h -1 m -2. These rates continued unabated until the harvest at 126 days, suggesting that tuber biomass production might have continued at about the same rate for some time beyond the harvest time that was exercised in this experiment. In both experiments CO 2 levels were allowed to range widely from a few hundred to about 3000 ppm, which permitted observation of fixation rates both at varying CO 2 concentrations and at each number of days after planting. This enables plotting the fixation rate as a function of both variables. Understanding the atmospheric dynamics of individual crops will be essential for design and atmospheric management of more complex CELSS which integrate the simultaneous growth of several crops as in a sustainable remote life support system.

Arsenic metabolism in high altitude modern stromatolites revealed by metagenomic analysis.

PubMed

Kurth, Daniel; Amadio, Ariel; Ordoñez, Omar F; Albarracín, Virginia H; Gärtner, Wolfgang; Farías, María E

2017-04-21

Modern stromatolites thrive only in selected locations in the world. Socompa Lake, located in the Andean plateau at 3570 masl, is one of the numerous extreme Andean microbial ecosystems described over recent years. Extreme environmental conditions include hypersalinity, high UV incidence, and high arsenic content, among others. After Socompa's stromatolite microbial communities were analysed by metagenomic DNA sequencing, taxonomic classification showed dominance of Proteobacteria, Bacteroidetes and Firmicutes, and a remarkably high number of unclassified sequences. A functional analysis indicated that carbon fixation might occur not only by the Calvin-Benson cycle, but also through alternative pathways such as the reverse TCA cycle, and the reductive acetyl-CoA pathway. Deltaproteobacteria were involved both in sulfate reduction and nitrogen fixation. Significant differences were found when comparing the Socompa stromatolite metagenome to the Shark Bay (Australia) smooth mat metagenome: namely, those involving stress related processes, particularly, arsenic resistance. An in-depth analysis revealed a surprisingly diverse metabolism comprising all known types of As resistance and energy generating pathways. While the ars operon was the main mechanism, an important abundance of arsM genes was observed in selected phyla. The data resulting from this work will prove a cornerstone for further studies on this rare microbial community.

Diurnal variation in the functioning of cowpea nodules.

PubMed

Rainbird, R M; Atkins, C A; Pate, J S

1983-06-01

Nitrogenase (EC 1.7.99.2) activity of nodules of cowpea (Vigna unguiculata [L.] Walp), maintained under conditions of a 12-hour day at 30 degrees C and 800 to 1,000 microeinsteins per square meter per second (photosynthetically active radiation) and a 12-hour night at 20 degrees C, showed a marked diurnal variation with the total electron flux through the enzyme at night being 60% of that in the photoperiod. This diurnal pattern was, however, due to changes in hydrogen evolution. The rate of nitrogen fixation, measured by short-term (15)N(2) assimilation or estimated from the difference in hydrogen evolution in air or Ar:O(2) (80:20; v/v), showed no diurnal variation. Carbon dioxide released from nodules showed a diurnal variation synchronized with that of nitrogenase functioning and, as a consequence, the apparent ;respiratory cost' of nitrogen fixation in the photoperiod was almost double that at night (9.74 +/- 0.38 versus 5.70 +/- 0.90 moles CO(2) evolved per mole N(2) fixed). Separate carbon and nitrogen balances constructed for nodules during the photoperiod and dark period showed that, at night, nodule functioning required up to 40% less carbohydrate to achieve the same level of nitrogen fixation as during the photoperiod (2.4 versus 1.4 moles hexose per mole N(2) fixed).Stored reserves of nonstructural carbohydrate of the nodule only partly satisfied the requirement for carbon at night, and fixation was dependent on continued import of translocated assimilates at all times. Measurements of the soluble nitrogen pools of the nodule together with (15)N studies indicated that, both during the day and night, nitrogenous products of fixation were effectively translocated to all organs of the host plant despite low rates of transpiration at night. Reduced fluxes of water through the plant at night were apparently counteracted by increased concentration of nitrogen, especially as ureides, in the xylem stream.

Medications influencing central cholinergic pathways affect fixation stability, saccadic response time and associated eye movement dynamics during a temporally-cued visual reaction time task.

PubMed

Naicker, Preshanta; Anoopkumar-Dukie, Shailendra; Grant, Gary D; Modenese, Luca; Kavanagh, Justin J

2017-02-01

Anticholinergic medications largely exert their effects due to actions on the muscarinic receptor, which mediates the functions of acetylcholine in the peripheral and central nervous systems. In the central nervous system, acetylcholine plays an important role in the modulation of movement. This study investigated the effects of over-the-counter medications with varying degrees of central anticholinergic properties on fixation stability, saccadic response time and the dynamics associated with this eye movement during a temporally-cued visual reaction time task, in order to establish the significance of central cholinergic pathways in influencing eye movements during reaction time tasks. Twenty-two participants were recruited into the placebo-controlled, human double-blind, four-way crossover investigation. Eye tracking technology recorded eye movements while participants reacted to visual stimuli following temporally informative and uninformative cues. The task was performed pre-ingestion as well as 0.5 and 2 h post-ingestion of promethazine hydrochloride (strong centrally acting anticholinergic), hyoscine hydrobromide (moderate centrally acting anticholinergic), hyoscine butylbromide (anticholinergic devoid of central properties) and a placebo. Promethazine decreased fixation stability during the reaction time task. In addition, promethazine was the only drug to increase saccadic response time during temporally informative and uninformative cued trials, whereby effects on response time were more pronounced following temporally informative cues. Promethazine also decreased saccadic amplitude and increased saccadic duration during the temporally-cued reaction time task. Collectively, the results of the study highlight the significant role that central cholinergic pathways play in the control of eye movements during tasks that involve stimulus identification and motor responses following temporal cues.

Proteome Profiling Reveals Potential Toxicity and Detoxification Pathways Following Exposure of BEAS-2B Cells to Engineered Titanium Dioxide Nanoparticles

EPA Science Inventory

Oxidative stress is known to play important roles in engineered nanomaterial induced cellular toxicity. However, the proteins and signaling pathways associated with the engineered nanomaterial mediated oxidative stress and toxicity are largely unknown. To identify these toxicity ...

Coupled RNA-SIP and metatranscriptomics of active chemolithoautotrophic communities at a deep-sea hydrothermal vent.

PubMed

Fortunato, Caroline S; Huber, Julie A

2016-08-01

The chemolithoautotrophic microbial community of the rocky subseafloor potentially provides a large amount of organic carbon to the deep ocean, yet our understanding of the activity and metabolic complexity of subseafloor organisms remains poorly described. A combination of metagenomic, metatranscriptomic, and RNA stable isotope probing (RNA-SIP) analyses were used to identify the metabolic potential, expression patterns, and active autotrophic bacteria and archaea and their pathways present in low-temperature hydrothermal fluids from Axial Seamount, an active submarine volcano. Metagenomic and metatranscriptomic results showed the presence of genes and transcripts for sulfur, hydrogen, and ammonium oxidation, oxygen respiration, denitrification, and methanogenesis, as well as multiple carbon fixation pathways. In RNA-SIP experiments across a range of temperatures under reducing conditions, the enriched (13)C fractions showed differences in taxonomic and functional diversity. At 30 °C and 55 °C, Epsilonproteobacteria were dominant, oxidizing hydrogen and primarily reducing nitrate. Methanogenic archaea were also present at 55 °C, and were the only autotrophs present at 80 °C. Correspondingly, the predominant CO2 fixation pathways changed from the reductive tricarboxylic acid (rTCA) cycle to the reductive acetyl-CoA pathway with increasing temperature. By coupling RNA-SIP with meta-omics, this study demonstrates the presence and activity of distinct chemolithoautotrophic communities across a thermal gradient of a deep-sea hydrothermal vent.

Atmospheric dynamics of combined crops of wheat, cowpea, pinto beans in the Laboratory Biosphere closed ecological system

NASA Astrophysics Data System (ADS)

Dempster, W.; Nelson, M.; Silverstone, S.; Allen, J.; Alling, A.; van Thillo, M.

A mixed crop consisting of cowpeas pinto beans and Apogee ultra-dwarf wheat was grown in Laboratory Biosphere a 40 m 3 closed life system equipped with 12000 watts of high pressure sodium lamps over planting beds with 5 37 m 2 of soil Similar to earlier reported experiments the concentration of carbon dioxide initially increased to 7860 ppm at 10 days after planting due to soil respiration plus CO 2 contributed from researchers breathing while in the chamber for brief periods before plant growth became substantial fell rapidly as plant growth increased up to 29 days after planting and then was maintained mostly in the range of about 200 -- 3000 ppm with a few excursions by CO 2 injections to feed plant growth Numerous analyses of rate of change of CO 2 concentration at many different concentrations and at many different days after planting reveals a strong dependence of fixation rates on CO 2 concentration In the middle period of growth days 31 -- 61 fixation rates doubled for CO 2 at 450 ppm compared to 270 ppm doubled again at 1000 ppm and increased a further 50 at 2040 ppm High productivity from these crops and the increase of fixation rates with elevated CO 2 concentration supports the concept that enhanced CO2 can be a useful strategy for remote life support systems

Inhibition of the. beta. -carboxylation pathway of CO/sub 2/ fixation by bisulfite compounds. [Leaves of Sedum praealtum and Atriplex spongiosa were used

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osmond, C.B.; Avadhani, P.N.

1970-01-01

Bisulfite compounds are well known as inhibitors of glycolate oxidase in green tissues of higher plants. In an effort to understand the relation between low glycolate oxidase activity and high P-enolpyruvate carboxylase activity in plants with the C/sub 4/ dicarboxylic acid pathway of photosynthesis, the authors have treated leaves of related species of Atriplex with these compounds. In this photosynthetic process, as well as during dark CO/sub 2/ fixation leading to acidification of Sedum leaves, they have found bisulfite compounds to be effective inhibitors of the P-enolpyruvate carboxylation system. This report provides evidence in vivo for this inhibition and describesmore » the inhibition in vitro of P-enolpyruvate carboxylation system. This report provides evidence in vivo for this inhibition and describes the inhibition in vitro of P-enolpyruvate carboxylase and NADH malate dehydrogenase. 16 references, 4 figures, 1 table.« less

Sequestration and utilization of carbon dioxide by chemical and biological methods for biofuels and biomaterials by chemoautotrophs: Opportunities and challenges.

PubMed

Thakur, Indu Shekhar; Kumar, Manish; Varjani, Sunita J; Wu, Yonghong; Gnansounou, Edgard; Ravindran, Sindhu

2018-05-01

To meet the CO 2 emission reduction targets, carbon dioxide capture and utilization (CCU) comes as an evolve technology. CCU concept is turning into a feedstock and technologies have been developed for transformation of CO 2 into useful organic products. At industrial scale, utilization of CO 2 as raw material is not much significant as compare to its abundance. Mechanisms in nature have evolved for carbon concentration, fixation and utilization. Assimilation and subsequent conversion of CO 2 into complex molecules are performed by the photosynthetic and chemolithotrophic organisms. In the last three decades, substantial research is carry out to discover chemical and biological conversion of CO 2 in various synthetic and biological materials, such as carboxylic acids, esters, lactones, polymer biodiesel, bio-plastics, bio-alcohols, exopolysaccharides. This review presents an over view of catalytic transformation of CO 2 into biofuels and biomaterials by chemical and biological methods. Copyright © 2018 Elsevier Ltd. All rights reserved.

Techno-economics of carbon preserving butanol production using a combined fermentative and catalytic approach.

PubMed

Nilsson, Robert; Bauer, Fredric; Mesfun, Sennai; Hulteberg, Christian; Lundgren, Joakim; Wännström, Sune; Rova, Ulrika; Berglund, Kris Arvid

2014-06-01

This paper presents a novel process for n-butanol production which combines a fermentation consuming carbon dioxide (succinic acid fermentation) with subsequent catalytic reduction steps to add hydrogen to form butanol. Process simulations in Aspen Plus have been the basis for the techno-economic analyses performed. The overall economy for the novel process cannot be justified, as production of succinic acid by fermentation is too costly. Though, succinic acid price is expected to drop drastically in a near future. By fully integrating the succinic acid fermentation with the catalytic conversion the need for costly recovery operations could be reduced. The hybrid process would need 22% less raw material than the butanol fermentation at a succinic acid fermentation yield of 0.7g/g substrate. Additionally, a carbon dioxide fixation of up to 13ktonnes could be achieved at a plant with an annual butanol production of 10ktonnes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Polypyrrole membranes as scaffolds for biomolecule immobilization

NASA Astrophysics Data System (ADS)

Hery, Travis M.; Satagopan, Sriram; Northcutt, Robert G.; Tabita, F. Robert; Sundaresan, Vishnu-Baba

2016-12-01

Enzymes have evolved over hundreds of years through changes in ecosystems (climate, atmosphere, hydrology, etc). The evolutionary changes driven by the need to survive has led to enzymes with diverse functionality such as reduction of carbon dioxide and methane to other forms of carbon, fixation of nitrogen, and high temperature biochemical processes. While these enzymes have useful properties, engineering a scalable cell-free system with these enzymes will be useful for stable production of desired products without involving the vagaries of cellular metabolism. This article presents various approaches to incorporate ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) in a conducting polymer (polypyrrole (PPy)) doped with a bulky anion (dodecylbenzenesulfonate (DBS)) in an effort to create functional devices for the conversion of carbon dioxide into precursors for high-value chemicals. We demonstrate that the tailored device creates an environment where the enzyme can retain its function while being protected from denaturing conditions. It is envisioned that the 3-PGA produced by RuBisCO will be converted into value-added products.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir

PubMed Central

Freedman, Adam J.E.; Tan, BoonFei

2017-01-01

Summary Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO2 reservoirs, which serve as analogs for the long‐term fate of sequestered scCO2, harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO2‐water separators at a natural scCO2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO2 and N2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO2 reservoir indicates that potential impacts of the deep biosphere on CO2 fate and transport should be taken into consideration as a component of GCS planning and modelling. PMID:28229521

Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism.

PubMed

Steinbacher, Stefan; Schiffmann, Susanne; Richter, Gerald; Huber, Robert; Bacher, Adelbert; Fischer, Markus

2003-10-24

Skeletal rearrangements of carbohydrates are crucial for many biosynthetic pathways. In riboflavin biosynthesis ribulose 5-phosphate is converted into 3,4-dihydroxy-2-butanone 4-phosphate while its C4 atom is released as formate in a sequence of metal-dependent reactions. Here, we present the crystal structure of Methanococcus jannaschii 3,4-dihydroxy-2-butanone 4-phosphate synthase in complex with the substrate ribulose 5-phosphate at a dimetal center presumably consisting of non-catalytic zinc and calcium ions at 1.7-A resolution. The carbonyl group (O2) and two out of three free hydroxyl groups (OH3 and OH4) of the substrate are metal-coordinated. We correlate previous mutational studies on this enzyme with the present structural results. Residues of the first coordination sphere involved in metal binding are indispensable for catalytic activity. Only Glu-185 of the second coordination sphere cannot be replaced without complete loss of activity. It contacts the C3 hydrogen atom directly and probably initiates enediol formation in concert with both metal ions to start the reaction sequence. Mechanistic similarities to Rubisco acting on the similar substrate ribulose 1,5-diphosphate in carbon dioxide fixation as well as other carbohydrate (reducto-) isomerases are discussed.

‘ Candidatus Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen

DOE PAGES

Ikeda-Ohtsubo, Wakako; Strassert, Jürgen F. H.; Köhler, Tim; ...

2016-02-23

Termite gut flagellates are typically colonized by specific bacterial symbionts. Here we describe the phylogeny, ultrastructure and subcellular location of 'Candidatus Adiutrix intracellularis', an intracellular symbiont of Trichonympha collaris in the termite Zootermopsis nevadensis. It represents a novel, deep-branching clade of uncultured Deltaproteobacteria widely distributed in intestinal tracts of termites and cockroaches. Fluorescence in situ hybridization and transmission electron microscopy localized the endosymbiont near hydrogenosomes in the posterior part and near the ectosymbiont 'Candidatus Desulfovibrio trichonymphae' in the anterior part of the host cell. The draft genome of 'Ca. Adiutrix intracellularis' obtained from a metagenomic library revealed the presence ofmore » a complete gene set encoding the Wood-Ljungdahl pathway, including two homologs of fdhF encoding hydrogenase-linked formate dehydrogenases (FDHH ) and all other components of the recently described hydrogen-dependent carbon dioxide reductase (HDCR) complex, which substantiates previous claims that the symbiont is capable of reductive acetogenesis from CO2 and H2 . The close phylogenetic relationship between the HDCR components and their homologs in homoacetogenic Firmicutes and Spirochaetes suggests that the deltaproteobacterium acquired the capacity for homoacetogenesis via lateral gene transfer. The presence of genes for nitrogen fixation and the biosynthesis of amino acids and cofactors indicate the nutritional nature of the symbiosis.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

‘ Candidatus Adiutrix intracellularis’, an endosymbiont of termite gut flagellates, is the first representative of a deep-branching clade of Deltaproteobacteria and a putative homoacetogen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ikeda-Ohtsubo, Wakako; Strassert, Jürgen F. H.; Köhler, Tim

Termite gut flagellates are typically colonized by specific bacterial symbionts. Here we describe the phylogeny, ultrastructure and subcellular location of 'Candidatus Adiutrix intracellularis', an intracellular symbiont of Trichonympha collaris in the termite Zootermopsis nevadensis. It represents a novel, deep-branching clade of uncultured Deltaproteobacteria widely distributed in intestinal tracts of termites and cockroaches. Fluorescence in situ hybridization and transmission electron microscopy localized the endosymbiont near hydrogenosomes in the posterior part and near the ectosymbiont 'Candidatus Desulfovibrio trichonymphae' in the anterior part of the host cell. The draft genome of 'Ca. Adiutrix intracellularis' obtained from a metagenomic library revealed the presence ofmore » a complete gene set encoding the Wood-Ljungdahl pathway, including two homologs of fdhF encoding hydrogenase-linked formate dehydrogenases (FDHH ) and all other components of the recently described hydrogen-dependent carbon dioxide reductase (HDCR) complex, which substantiates previous claims that the symbiont is capable of reductive acetogenesis from CO2 and H2 . The close phylogenetic relationship between the HDCR components and their homologs in homoacetogenic Firmicutes and Spirochaetes suggests that the deltaproteobacterium acquired the capacity for homoacetogenesis via lateral gene transfer. The presence of genes for nitrogen fixation and the biosynthesis of amino acids and cofactors indicate the nutritional nature of the symbiosis.« less

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir: Microbial life in the deep carbonated biosphere

DOE PAGES

Freedman, Adam J. E.; Tan, BoonFei; Thompson, Janelle R.

2017-05-02

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected super-critical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 harbor a ‘deep carbonated biosphere’ with carbon cycling potential. We sampled subsurface fluids from scCO 2- water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four membersmore » of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. In conclusion, the existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling.« less

Differential Expression of pro-inflammatory and oxidative stress mediators induced by nitrogen dioxide and ozone in primary human bronchial epithelial cells

EPA Science Inventory

CONTEXT: N02 and 03 are ubiquitous air toxicants capable of inducing lung damage to the respiratory epithelium. Due to their oxidizing capabilities, these pollutants have been proposed to target specific biological pathways, but few publications have compared the pathways activat...

The coupling of glycolysis and the Rubisco-based pathway through the non-oxidative pentose phosphate pathway to achieve low carbon dioxide emission fermentation.

PubMed

Li, Ya-Han; Ou-Yang, Fan-Yu; Yang, Cheng-Han; Li, Si-Yu

2015-01-01

In this study, Rubisco-based engineered Escherichia coli, containing two heterologous enzymes of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and phosphoribulokinase (PrkA), has been shown to be capable of the in situ recycling of carbon dioxide (CO2) during glycolysis. Two alternative approaches have been proposed to further enhance the carbon flow from glycolysis to a Rubisco-based pathway through the non-oxidative pentose phosphate pathway (NOPPP). The first is achieved by elevating the expression of transketolase I (TktA) and the second by blocking the native oxidation-decarboxylation reaction of E. coli by deleting the zwf gene from the chromosome (designated as JB/pTA and MZB, respectively). Decreases in the CO2 yield and the CO2 evolution per unit mole of ethanol production by at least 81% and 40% are observed. It is demonstrated in this study that the production of one mole of ethanol using E. coli strain MZB, the upper limit of CO2 emission is 0.052mol. Copyright © 2015 Elsevier Ltd. All rights reserved.

Titanium dioxide nanoparticles activate IL8-related inflammatory pathways in human colonic epithelial Caco-2 cells

NASA Astrophysics Data System (ADS)

Krüger, Kristin; Cossais, François; Neve, Horst; Klempt, Martin

2014-05-01

Nanosized titanium dioxide (TiO2) particles are widely used as food additive or coating material in products of the food and pharmaceutical industry. Studies on various cell lines have shown that TiO2 nanoparticles (NPs) induced the inflammatory response and cytotoxicity. However, the influences of TiO2 NPs' exposure on inflammatory pathways in intestinal epithelial cells and their differentiation have not been investigated so far. This study demonstrates that TiO2 NPs with particle sizes ranging between 5 and 10 nm do not affect enterocyte differentiation but cause an activation of inflammatory pathways in the human colon adenocarcinoma cell line Caco-2. 5 and 10 nm NPs' exposures transiently induce the expression of ICAM1, CCL20, COX2 and IL8, as determined by quantitative PCR, whereas larger particles (490 nm) do not. Further, using nuclear factor (NF)-κB reporter gene assays, we show that NP-induced IL8 mRNA expression occurs, in part, through activation of NF-κB and p38 mitogen-activated protein kinase pathways.

The evolution of photosynthesis...again?

PubMed

Rothschild, Lynn J

2008-08-27

'Replaying the tape' is an intriguing 'would it happen again?' exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis -- although perhaps not oxygenic photosynthesis -- would also have evolved.

Ubiquitous Gammaproteobacteria dominate dark carbon fixation in coastal sediments.

PubMed

Dyksma, Stefan; Bischof, Kerstin; Fuchs, Bernhard M; Hoffmann, Katy; Meier, Dimitri; Meyerdierks, Anke; Pjevac, Petra; Probandt, David; Richter, Michael; Stepanauskas, Ramunas; Mußmann, Marc

2016-08-01

Marine sediments are the largest carbon sink on earth. Nearly half of dark carbon fixation in the oceans occurs in coastal sediments, but the microorganisms responsible are largely unknown. By integrating the 16S rRNA approach, single-cell genomics, metagenomics and transcriptomics with (14)C-carbon assimilation experiments, we show that uncultured Gammaproteobacteria account for 70-86% of dark carbon fixation in coastal sediments. First, we surveyed the bacterial 16S rRNA gene diversity of 13 tidal and sublittoral sediments across Europe and Australia to identify ubiquitous core groups of Gammaproteobacteria mainly affiliating with sulfur-oxidizing bacteria. These also accounted for a substantial fraction of the microbial community in anoxic, 490-cm-deep subsurface sediments. We then quantified dark carbon fixation by scintillography of specific microbial populations extracted and flow-sorted from sediments that were short-term incubated with (14)C-bicarbonate. We identified three distinct gammaproteobacterial clades covering diversity ranges on family to order level (the Acidiferrobacter, JTB255 and SSr clades) that made up >50% of dark carbon fixation in a tidal sediment. Consistent with these activity measurements, environmental transcripts of sulfur oxidation and carbon fixation genes mainly affiliated with those of sulfur-oxidizing Gammaproteobacteria. The co-localization of key genes of sulfur and hydrogen oxidation pathways and their expression in genomes of uncultured Gammaproteobacteria illustrates an unknown metabolic plasticity for sulfur oxidizers in marine sediments. Given their global distribution and high abundance, we propose that a stable assemblage of metabolically flexible Gammaproteobacteria drives important parts of marine carbon and sulfur cycles.

Use of prolines for improving growth and other properties of plants and algae

DOEpatents

Unkefer, Pat J.; Knight, Thomas J.; Martinez, Rodolfo A.

2003-07-15

Increasing the concentration of prolines, such as 2-hydroxy-5-oxoproline, in the foliar portions of plants has been shown to cause an increase in carbon dioxide fixation, growth rate, dry weight, nutritional value (amino acids), nodulation and nitrogen fixation, photosynthetically derived chemical energy, and resistance to insect pests over the same properties for wild type plants. This can be accomplished in four ways: (1) the application of a solution of the proline directly to the foliar portions of the plant by spraying these portions; (2) applying a solution of the proline to the plant roots; (3) genetically engineering the plant and screening to produce lines that over-express glutamine synthetase in the leaves which gives rise to increased concentration of the metabolite, 2-hydroxy-5-oxoproline (this proline is also known as 2-oxoglutaramate); and (4) impairing the glutamine synthetase activity in the plant roots which causes increased glutamine synthetase activity in the leaves which gives rise to increased concentration of 2-hydroxy-5-oxoproline. Prolines have also been found to induce similar effects in algae.

Use of prolines for improving growth and other properties of plants and algae

DOEpatents

Unkefer, Pat J.; Knight, Thomas J.; Martinez, Rodolfo A.

2004-12-14

Increasing the concentration of prolines, such as 2-hydroxy-5-oxoproline, in the foliar portions of plants has been shown to cause an increase in carbon dioxide fixation, growth rate, dry weight, nutritional value (amino acids), nodulation and nitrogen fixation, photosynthetically derived chemical energy, and resistance to insect pests over the same properties for wild type plants. This can be accomplished in four ways: (1) the application of a solution of the proline directly to the foliar portions of the plant by spraying these portions; (2) applying a solution of the proline to the plant roots; (3) genetically engineering the plant and screening to produce lines that over-express glutamine synthetase in the leaves which gives rise to increased concentration of the metabolite, 2-hydroxy-5-oxoproline (this proline is also known as 2-oxoglutaramate); and (4) impairing the glutamine synthetase activity in the plant roots which causes increased glutamine synthetase activity in the leaves which gives rise to increased concentration of 2-hydroxy-5-oxoproline. Prolines have also been found to induce similar effects in algae.

Use of prolines for improving growth and other properties of plants and algae

DOEpatents

Unkefer, Pat J.; Knight, Thomas J.; Martinez, Rodolfo A.

2003-04-29

Increasing the concentration of prolines such as 2-hydroxy-5-oxoproline, in the foliar portions of plants has been shown to cause an increase in carbon dioxide fixation, growth rate, dry weight, nutritional value (amino acids), nodulation and nitrogen fixation, photosynthetically derived chemical energy, and resistance to insect pests over the same properties for wild type plants. This can be accomplished in four ways: (1) the application of a solution of the proline directly to the foliar portions of the plant by spraying these portions; (2) applying a solution of the proline to the plant roots; (3) genetically engineering the plant and screening to produce lines that overexpress glutamine synthetase in the leaves which gives rise to increased concentration of the metabolite, 2-hydroxy-5-oxoproline (this proline is also known as 2-oxoglutaramnate); and (4) impairing the glutamine synthetase activity in the plant roots which causes increased glutamine synthetase activity in the leaves which gives rise to increased concentration of 2-hydroxy-5-oxoproline. Prolines have also been found to induce similar effects in algae.

Tailor-made Molecular Cobalt Catalyst System for the Selective Transformation of Carbon Dioxide to Dialkoxymethane Ethers.

PubMed

Schieweck, Benjamin G; Klankermayer, Jürgen

2017-08-28

Herein a non-precious transition-metal catalyst system for the selective synthesis of dialkoxymethane ethers from carbon dioxide and molecular hydrogen is presented. The development of a tailored catalyst system based on cobalt salts in combination with selected Triphos ligands and acidic co-catalysts enabled a synthetic pathway, avoiding the oxidation of methanol to attain the formaldehyde level of the central CH 2 unit. This unprecedented productivity based on the molecular cobalt catalyst is the first example of a non-precious transition-metal system for this transformation utilizing renewable carbon dioxide sources. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Iron catalysis at the origin of life.

PubMed

Camprubi, Eloi; Jordan, Sean F; Vasiliadou, Rafaela; Lane, Nick

2017-06-01

Iron-sulphur proteins are ancient and drive fundamental processes in cells, notably electron transfer and CO 2 fixation. Iron-sulphur minerals with equivalent structures could have played a key role in the origin of life. However, the 'iron-sulphur world' hypothesis has had a mixed reception, with questions raised especially about the feasibility of a pyrites-pulled reverse Krebs cycle. Phylogenetics suggests that the earliest cells drove carbon and energy metabolism via the acetyl CoA pathway, which is also replete in Fe(Ni)S proteins. Deep differences between bacteria and archaea in this pathway obscure the ancestral state. These differences make sense if early cells depended on natural proton gradients in alkaline hydrothermal vents. If so, the acetyl CoA pathway diverged with the origins of active ion pumping, and ancestral CO 2 fixation might have been equivalent to methanogens, which depend on a membrane-bound NiFe hydrogenase, energy converting hydrogenase. This uses the proton-motive force to reduce ferredoxin, thence CO 2 . The mechanism suggests that pH could modulate reduction potential at the active site of the enzyme, facilitating the difficult reduction of CO 2 by H 2 . This mechanism could be generalised under abiotic conditions so that steep pH differences across semi-conducting Fe(Ni)S barriers drives not just the first steps of CO 2 fixation to C1 and C2 organics such as CO, CH 3 SH and CH 3 COSH, but a series of similar carbonylation and hydrogenation reactions to form longer chain carboxylic acids such as pyruvate, oxaloacetate and α-ketoglutarate, as in the incomplete reverse Krebs cycle found in methanogens. We suggest that the closure of a complete reverse Krebs cycle, by regenerating acetyl CoA directly, displaced the acetyl CoA pathway from many modern groups. A later reliance on acetyl CoA and ATP eliminated the need for the proton-motive force to drive most steps of the reverse Krebs cycle. © 2017 IUBMB Life, 69(6):373-381, 2017. © 2017 The Authors IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

Iron deficiency increases growth and nitrogen-fixation rates of phosphorus-deficient marine cyanobacteria.

PubMed

Garcia, Nathan S; Fu, Feixue; Sedwick, Peter N; Hutchins, David A

2015-01-01

Marine dinitrogen (N2)-fixing cyanobacteria have large impacts on global biogeochemistry as they fix carbon dioxide (CO2) and fertilize oligotrophic ocean waters with new nitrogen. Iron (Fe) and phosphorus (P) are the two most important limiting nutrients for marine biological N2 fixation, and their availabilities vary between major ocean basins and regions. A long-standing question concerns the ability of two globally dominant N2-fixing cyanobacteria, unicellular Crocosphaera and filamentous Trichodesmium, to maintain relatively high N2-fixation rates in these regimes where both Fe and P are typically scarce. We show that under P-deficient conditions, cultures of these two cyanobacteria are able to grow and fix N2 faster when Fe deficient than when Fe replete. In addition, growth affinities relative to P increase while minimum concentrations of P that support growth decrease at low Fe concentrations. In Crocosphaera, this effect is accompanied by a reduction in cell sizes and elemental quotas. Relatively high growth rates of these two biogeochemically critical cyanobacteria in low-P, low-Fe environments such as those that characterize much of the oligotrophic ocean challenge the common assumption that low Fe levels can have only negative effects on marine primary producers. The closely interdependent influence of Fe and P on N2-fixing cyanobacteria suggests that even subtle shifts in their supply ratio in the past, present and future oceans could have large consequences for global carbon and nitrogen cycles.

An Endogenous Carbon-Sensing Pathway Triggers Increased Auxin Flux and Hypocotyl Elongation1[C][W][OA

PubMed Central

Lilley, Jodi L. Stewart; Gee, Christopher W.; Sairanen, Ilkka; Ljung, Karin; Nemhauser, Jennifer L.

2012-01-01

The local environment has a substantial impact on early seedling development. Applying excess carbon in the form of sucrose is known to alter both the timing and duration of seedling growth. Here, we show that sucrose changes growth patterns by increasing auxin levels and rootward auxin transport in Arabidopsis (Arabidopsis thaliana). Sucrose likely interacts with an endogenous carbon-sensing pathway via the PHYTOCHROME-INTERACTING FACTOR (PIF) family of transcription factors, as plants grown in elevated carbon dioxide showed the same PIF-dependent growth promotion. Overexpression of PIF5 was sufficient to suppress photosynthetic rate, enhance response to elevated carbon dioxide, and prolong seedling survival in nitrogen-limiting conditions. Thus, PIF transcription factors integrate growth with metabolic demands and thereby facilitate functional equilibrium during photomorphogenesis. PMID:23073695

Carbon isotopic composition of individual Precambrian microfossils

NASA Technical Reports Server (NTRS)

House, C. H.; Schopf, J. W.; McKeegan, K. D.; Coath, C. D.; Harrison, T. M.; Stetter, K. O.

2000-01-01

Ion microprobe measurements of carbon isotope ratios were made in 30 specimens representing six fossil genera of microorganisms petrified in stromatolitic chert from the approximately 850 Ma Bitter Springs Formation, Australia, and the approximately 2100 Ma Gunflint Formation, Canada. The delta 13C(PDB) values from individual microfossils of the Bitter Springs Formation ranged from -21.3 +/- 1.7% to -31.9 +/- 1.2% and the delta 13C(PDB) values from microfossils of the Gunflint Formation ranged from -32.4 +/- 0.7% to -45.4 +/- 1.2%. With the exception of two highly 13C-depleted Gunflint microfossils, the results generally yield values consistent with carbon fixation via either the Calvin cycle or the acetyl-CoA pathway. However, the isotopic results are not consistent with the degree of fractionation expected from either the 3-hydroxypropionate cycle or the reductive tricarboxylic acid cycle, suggesting that the microfossils studied did not use either of these pathways for carbon fixation. The morphologies of the microfossils suggest an affinity to the cyanobacteria, and our carbon isotopic data are consistent with this assignment.

Exploring stress tolerance mechanism of evolved freshwater strain Chlorella sp. S30 under 30 g/L salt.

PubMed

Li, Xuyang; Yuan, Yizhong; Cheng, Dujia; Gao, Juan; Kong, Lingzhao; Zhao, Quanyu; Wei, Wei; Sun, Yuhan

2018-02-01

Enhancement of stress tolerance to high concentration of salt and CO 2 is beneficial for CO 2 capture by microalgae. Adaptive evolution was performed for improving the tolerance of a freshwater strain, Chlorella sp. AE10, to 30 g/L salt. A resulting strain denoted as Chlorella sp. S30 was obtained after 46 cycles (138 days). The stress tolerance mechanism was analyzed by comparative transcriptomic analysis. Although the evolved strain could tolerate 30 g/L salt, high salinity caused loss to photosynthesis, oxidative phosphorylation, fatty acid biosynthesis and tyrosine metabolism. The related genes of antioxidant enzymes, CO 2 fixation, amino acid biosynthesis, central carbon metabolism and ABC transporter proteins were up-regulated. Besides the up-regulation of several genes in Calvin-Benson cycle, they were also identified in C4 photosynthetic pathway and crassulacean acid metabolism pathway. They were essential for the survival and CO 2 fixation of Chlorella sp. S30 under 30 g/L salt and 10% CO 2 . Copyright © 2017 Elsevier Ltd. All rights reserved.

Connecting biodiversity and potential functional role in modern euxinic environments by microbial metagenomics

PubMed Central

Llorens-Marès, Tomàs; Yooseph, Shibu; Goll, Johannes; Hoffman, Jeff; Vila-Costa, Maria; Borrego, Carles M; Dupont, Chris L; Casamayor, Emilio O

2015-01-01

Stratified sulfurous lakes are appropriate environments for studying the links between composition and functionality in microbial communities and are potentially modern analogs of anoxic conditions prevailing in the ancient ocean. We explored these aspects in the Lake Banyoles karstic area (NE Spain) through metagenomics and in silico reconstruction of carbon, nitrogen and sulfur metabolic pathways that were tightly coupled through a few bacterial groups. The potential for nitrogen fixation and denitrification was detected in both autotrophs and heterotrophs, with a major role for nitrogen and carbon fixations in Chlorobiaceae. Campylobacterales accounted for a large percentage of denitrification genes, while Gallionellales were putatively involved in denitrification, iron oxidation and carbon fixation and may have a major role in the biogeochemistry of the iron cycle. Bacteroidales were also abundant and showed potential for dissimilatory nitrate reduction to ammonium. The very low abundance of genes for nitrification, the minor presence of anammox genes, the high potential for nitrogen fixation and mineralization and the potential for chemotrophic CO2 fixation and CO oxidation all provide potential clues on the anoxic zones functioning. We observed higher gene abundance of ammonia-oxidizing bacteria than ammonia-oxidizing archaea that may have a geochemical and evolutionary link related to the dominance of Fe in these environments. Overall, these results offer a more detailed perspective on the microbial ecology of anoxic environments and may help to develop new geochemical proxies to infer biology and chemistry interactions in ancient ecosystems. PMID:25575307

A Medicago truncatula Tobacco Retrotransposon Insertion Mutant Collection with Defects in Nodule Development and Symbiotic Nitrogen Fixation1[W][OA

PubMed Central

Pislariu, Catalina I.; D. Murray, Jeremy; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; A. Benedito, Vagner; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E.; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S.; Chen, Rujin; Udvardi, Michael K.

2012-01-01

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod−), 51 mutants with totally ineffective nodules (Nod+ Fix−), 17 mutants with partially ineffective nodules (Nod+ Fix+/−), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/− Fix−), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/− Fix+), and 11 supernodulating mutants (Nod++Fix+/−). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN’T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod− lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging. PMID:22679222

A Medicago truncatula tobacco retrotransposon insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation.

PubMed

Pislariu, Catalina I; Murray, Jeremy D; Wen, JiangQi; Cosson, Viviane; Muni, RajaSekhara Reddy Duvvuru; Wang, Mingyi; Benedito, Vagner A; Andriankaja, Andry; Cheng, Xiaofei; Jerez, Ivone Torres; Mondy, Samuel; Zhang, Shulan; Taylor, Mark E; Tadege, Million; Ratet, Pascal; Mysore, Kirankumar S; Chen, Rujin; Udvardi, Michael K

2012-08-01

A Tnt1-insertion mutant population of Medicago truncatula ecotype R108 was screened for defects in nodulation and symbiotic nitrogen fixation. Primary screening of 9,300 mutant lines yielded 317 lines with putative defects in nodule development and/or nitrogen fixation. Of these, 230 lines were rescreened, and 156 lines were confirmed with defective symbiotic nitrogen fixation. Mutants were sorted into six distinct phenotypic categories: 72 nonnodulating mutants (Nod-), 51 mutants with totally ineffective nodules (Nod+ Fix-), 17 mutants with partially ineffective nodules (Nod+ Fix+/-), 27 mutants defective in nodule emergence, elongation, and nitrogen fixation (Nod+/- Fix-), one mutant with delayed and reduced nodulation but effective in nitrogen fixation (dNod+/- Fix+), and 11 supernodulating mutants (Nod++Fix+/-). A total of 2,801 flanking sequence tags were generated from the 156 symbiotic mutant lines. Analysis of flanking sequence tags revealed 14 insertion alleles of the following known symbiotic genes: NODULE INCEPTION (NIN), DOESN'T MAKE INFECTIONS3 (DMI3/CCaMK), ERF REQUIRED FOR NODULATION, and SUPERNUMERARY NODULES (SUNN). In parallel, a polymerase chain reaction-based strategy was used to identify Tnt1 insertions in known symbiotic genes, which revealed 25 additional insertion alleles in the following genes: DMI1, DMI2, DMI3, NIN, NODULATION SIGNALING PATHWAY1 (NSP1), NSP2, SUNN, and SICKLE. Thirty-nine Nod- lines were also screened for arbuscular mycorrhizal symbiosis phenotypes, and 30 mutants exhibited defects in arbuscular mycorrhizal symbiosis. Morphological and developmental features of several new symbiotic mutants are reported. The collection of mutants described here is a source of novel alleles of known symbiotic genes and a resource for cloning novel symbiotic genes via Tnt1 tagging.

Spatial Differences in East Scotia Ridge Hydrothermal Vent Food Webs: Influences of Chemistry, Microbiology and Predation on Trophodynamics

PubMed Central

Reid, William D. K.; Sweeting, Christopher J.; Wigham, Ben D.; Zwirglmaier, Katrin; Hawkes, Jeffrey A.; McGill, Rona A. R.; Linse, Katrin; Polunin, Nicholas V. C.

2013-01-01

The hydrothermal vents on the East Scotia Ridge are the first to be explored in the Antarctic and are dominated by large peltospiroid gastropods, stalked barnacles (Vulcanolepas sp.) and anomuran crabs (Kiwa sp.) but their food webs are unknown. Vent fluid and macroconsumer samples were collected at three vent sites (E2, E9N and E9S) at distances of tens of metres to hundreds of kilometres apart with contrasting vent fluid chemistries to describe trophic interactions and identify potential carbon fixation pathways using stable isotopes. δ13C of dissolved inorganic carbon from vent fluids ranged from −4.6‰ to 0.8‰ at E2 and from −4.4‰ to 1.5‰ at E9. The lowest macroconsumer δ13C was observed in peltospiroid gastropods (−30.0‰ to −31.1‰) and indicated carbon fixation via the Calvin-Benson-Bassham (CBB) cycle by endosymbiotic gamma-Proteobacteria. Highest δ13C occurred in Kiwa sp. (−19.0‰ to −10.5‰), similar to that of the epibionts sampled from their ventral setae. Kiwa sp. δ13C differed among sites, which were attributed to spatial differences in the epibiont community and the relative contribution of carbon fixed via the reductive tricarboxylic acid (rTCA) and CBB cycles assimilated by Kiwa sp. Site differences in carbon fixation pathways were traced into higher trophic levels e.g. a stichasterid asteroid that predates on Kiwa sp. Sponges and anemones at the periphery of E2 assimilated a proportion of epipelagic photosynthetic primary production but this was not observed at E9N. Differences in the δ13C and δ34S values of vent macroconsumers between E2 and E9 sites suggest the relative contributions of photosynthetic and chemoautotrophic carbon fixation (rTCA v CBB) entering the hydrothermal vent food webs vary between the sites. PMID:23762393

Imaging metal-like monoclinic phase stabilized by surface coordination effect in vanadium dioxide nanobeam

PubMed Central

Li, Zejun; Wu, Jiajing; Hu, Zhenpeng; Lin, Yue; Chen, Qi; Guo, Yuqiao; Liu, Yuhua; Zhao, Yingcheng; Peng, Jing; Chu, Wangsheng; Wu, Changzheng; Xie, Yi

2017-01-01

In correlated systems, intermediate states usually appear transiently across phase transitions even at the femtosecond scale. It therefore remains an open question how to determine these intermediate states—a critical issue for understanding the origin of their correlated behaviour. Here we report a surface coordination route to successfully stabilize and directly image an intermediate state in the metal-insulator transition of vanadium dioxide. As a prototype metal-insulator transition material, we capture an unusual metal-like monoclinic phase at room temperature that has long been predicted. Coordinate bonding of L-ascorbic acid molecules with vanadium dioxide nanobeams induces charge-carrier density reorganization and stabilizes metallic monoclinic vanadium dioxide, unravelling orbital-selective Mott correlation for gap opening of the vanadium dioxide metal–insulator transition. Our study contributes to completing phase-evolution pathways in the metal-insulator transition process, and we anticipate that coordination chemistry may be a powerful tool for engineering properties of low-dimensional correlated solids. PMID:28613281

Warming caused by cumulative carbon emissions towards the trillionth tonne.

PubMed

Allen, Myles R; Frame, David J; Huntingford, Chris; Jones, Chris D; Lowe, Jason A; Meinshausen, Malte; Meinshausen, Nicolai

2009-04-30

Global efforts to mitigate climate change are guided by projections of future temperatures. But the eventual equilibrium global mean temperature associated with a given stabilization level of atmospheric greenhouse gas concentrations remains uncertain, complicating the setting of stabilization targets to avoid potentially dangerous levels of global warming. Similar problems apply to the carbon cycle: observations currently provide only a weak constraint on the response to future emissions. Here we use ensemble simulations of simple climate-carbon-cycle models constrained by observations and projections from more comprehensive models to simulate the temperature response to a broad range of carbon dioxide emission pathways. We find that the peak warming caused by a given cumulative carbon dioxide emission is better constrained than the warming response to a stabilization scenario. Furthermore, the relationship between cumulative emissions and peak warming is remarkably insensitive to the emission pathway (timing of emissions or peak emission rate). Hence policy targets based on limiting cumulative emissions of carbon dioxide are likely to be more robust to scientific uncertainty than emission-rate or concentration targets. Total anthropogenic emissions of one trillion tonnes of carbon (3.67 trillion tonnes of CO(2)), about half of which has already been emitted since industrialization began, results in a most likely peak carbon-dioxide-induced warming of 2 degrees C above pre-industrial temperatures, with a 5-95% confidence interval of 1.3-3.9 degrees C.

Potential Impacts of two SO2 oxidation pathways on regional sulfate concentrations: acqueous-hase oxidation by NO2 and gas-phase oxidation by Stabilized Criegee Intermediates

EPA Science Inventory

We examine the potential impacts of two additional sulfate production pathways using the Community Multiscale Air Quality modeling system. First we evaluate the impact of the aqueous-phase oxidation of S(IV) by nitrogen dioxide using two published rate constants, differing by 1-2...

Diversity of Total Bacterial Communities and Chemoautotrophic Populations in Sulfur-Rich Sediments of Shallow-Water Hydrothermal Vents off Kueishan Island, Taiwan.

PubMed

Wang, Li; Cheung, Man Kit; Liu, Rulong; Wong, Chong Kim; Kwan, Hoi Shan; Hwang, Jiang-Shiou

2017-04-01

Shallow-water hydrothermal vents (HTVs) are an ecologically important habitat with a geographic origin similar to that of deep-sea HTVs. Studies on shallow-water HTVs have not only facilitated understanding of the influences of vents on local ecosystems but also helped to extend the knowledge on deep-sea vents. In this study, the diversity of bacterial communities in the sediments of shallow-water HTVs off Kueishan Island, Taiwan, was investigated by examining the 16S ribosomal RNA gene as well as key functional genes involved in chemoautotrophic carbon fixation (aclB, cbbL and cbbM). In the vent area, Sulfurovum and Sulfurimonas of Epsilonproteobacteria appeared to dominate the benthic bacterial community. Results of aclB gene analysis also suggested involvement of these bacteria in carbon fixation using the reductive tricarboxylic acid (rTCA) cycle. Analysis of the cbbM gene showed that Alphaproteobacterial members such as the purple non-sulfur bacteria were the major chemoautotrophic bacteria involving in carbon fixation via the Calvin-Benson-Bassham (CBB) cycle. However, they only accounted for <2% of the total bacterial community in the vent area. These findings suggest that the rTCA cycle is the major chemoautotrophic carbon fixation pathway in sediments of the shallow-water HTVs off Kueishan Island.

Biotransformation of carbon dioxide in bioelectrochemical systems: State of the art and future prospects

NASA Astrophysics Data System (ADS)

Bajracharya, Suman; Srikanth, Sandipam; Mohanakrishna, Gunda; Zacharia, Renju; Strik, David PBTB; Pant, Deepak

2017-07-01

Carbon dioxide (CO2) utilization/recycling for the production of chemicals and gaseous/liquid energy-carriers is a way to moderate the rising CO2 in the atmosphere. One of the possible solutions for the CO2 sequestration is the electrochemical reduction of this stable molecule to useful fuel/products. Nevertheless, the surface chemistry of CO2 reduction is a challenge due to the presence of large energy barriers, requiring noticeable catalysis. The recent approach of microbial electrocatalysis of CO2 reduction has promising prospects to reduce the carbon level sustainably, taking full advantage of CO2-derived chemical commodities. We review the currently investigated bioelectrochemical approaches that could possibly be implemented to enable the handling of CO2 emissions. This review covers the most recent advances in the bioelectrochemical approaches of CO2 transformations in terms of biocatalysts development and process design. Furthermore, the extensive research on carbon fixation and conversion to different value added chemicals is reviewed. The review concludes by detailing the key challenges and future prospects that could enable economically feasible microbial electrosynthesis technology.

Chemical Impact of Solar Energetic Particle Event From The Young Sun: Implications for the Origin of Prebiotic Chemistry and the Fain Young Sun Paradox

NASA Astrophysics Data System (ADS)

Airapetian, V.; Gronoff, G.; Hébrard, E.; Danchi, W.

2015-12-01

Understanding how the simple molecules present on the early Earth and possibly Mars may have set a path for complex biological molecules, the building blocks of life, represents one of greatest unsolved questions. Here we present a new model of the rise of the abiotic nitrogen fixation and associated pre-biotic chemistry in the early Earth and Mars atmosphere mediated by solar eruptive events. Our physical models of interaction of magnetic clouds ejected from the young Sun with magnetospheres of the early Earth show significant perturbations of geomagnetic fields that produce extended polar caps. These polar caps provide pathways for energetic particles associated with magnetic clouds to penetrate into the nitrogen-rich weakly reducing atmosphere and initiate the reactive chemistry by breaking molecular nitrogen, carbon dioxide, methane and producing hydrogen cyanide, the essential compound for life. The model also shows that contrary to the current models of warming of early Earth and Mars, major atmospheric constituents, CO2 and CH4 will be destroyed due to collisional dissociation with energetic particles. Instead, efficient formation of the potent greenhouse gas, nitrous oxide, as a by-product of these processes is expected. This mechanism can consistently explain the Faint Young Sun's paradox for the early atmospheres of Earth and Mars. Our new model provides insight into how life may have initiated on Earth and Mars and how to search for the spectral signatures on planets "pregnant" with the potential for life.

Microbial potential for carbon and nutrient cycling in a geogenic supercritical carbon dioxide reservoir.

PubMed

Freedman, Adam J E; Tan, BoonFei; Thompson, Janelle R

2017-06-01

Microorganisms catalyze carbon cycling and biogeochemical reactions in the deep subsurface and thus may be expected to influence the fate of injected supercritical (sc) CO 2 following geological carbon sequestration (GCS). We hypothesized that natural subsurface scCO 2 reservoirs, which serve as analogs for the long-term fate of sequestered scCO 2 , harbor a 'deep carbonated biosphere' with carbon cycling potential. We sampled subsurface fluids from scCO 2 -water separators at a natural scCO 2 reservoir at McElmo Dome, Colorado for analysis of 16S rRNA gene diversity and metagenome content. Sequence annotations indicated dominance of Sulfurospirillum, Rhizobium, Desulfovibrio and four members of the Clostridiales family. Genomes extracted from metagenomes using homology and compositional approaches revealed diverse mechanisms for growth and nutrient cycling, including pathways for CO 2 and N 2 fixation, anaerobic respiration, sulfur oxidation, fermentation and potential for metabolic syntrophy. Differences in biogeochemical potential between two production well communities were consistent with differences in fluid chemical profiles, suggesting a potential link between microbial activity and geochemistry. The existence of a microbial ecosystem associated with the McElmo Dome scCO 2 reservoir indicates that potential impacts of the deep biosphere on CO 2 fate and transport should be taken into consideration as a component of GCS planning and modelling. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Multiple Sensory-Motor Pathways Lead to Coordinated Visual Attention

PubMed Central

Yu, Chen; Smith, Linda B.

2016-01-01

Joint attention has been extensively studied in the developmental literature because of overwhelming evidence that the ability to socially coordinate visual attention to an object is essential to healthy developmental outcomes, including language learning. The goal of the present study is to understand the complex system of sensory-motor behaviors that may underlie the establishment of joint attention between parents and toddlers. In an experimental task, parents and toddlers played together with multiple toys. We objectively measured joint attention – and the sensory-motor behaviors that underlie it – using a dual head-mounted eye-tracking system and frame-by-frame coding of manual actions. By tracking the momentary visual fixations and hand actions of each participant, we precisely determined just how often they fixated on the same object at the same time, the visual behaviors that preceded joint attention, and manual behaviors that preceded and co-occurred with joint attention. We found that multiple sequential sensory-motor patterns lead to joint attention. In addition, there are developmental changes in this multi-pathway system evidenced as variations in strength among multiple routes. We propose that coordinated visual attention between parents and toddlers is primarily a sensory-motor behavior. Skill in achieving coordinated visual attention in social settings – like skills in other sensory-motor domains – emerges from multiple pathways to the same functional end. PMID:27016038

Multiple Sensory-Motor Pathways Lead to Coordinated Visual Attention.

PubMed

Yu, Chen; Smith, Linda B

2017-02-01

Joint attention has been extensively studied in the developmental literature because of overwhelming evidence that the ability to socially coordinate visual attention to an object is essential to healthy developmental outcomes, including language learning. The goal of this study was to understand the complex system of sensory-motor behaviors that may underlie the establishment of joint attention between parents and toddlers. In an experimental task, parents and toddlers played together with multiple toys. We objectively measured joint attention-and the sensory-motor behaviors that underlie it-using a dual head-mounted eye-tracking system and frame-by-frame coding of manual actions. By tracking the momentary visual fixations and hand actions of each participant, we precisely determined just how often they fixated on the same object at the same time, the visual behaviors that preceded joint attention and manual behaviors that preceded and co-occurred with joint attention. We found that multiple sequential sensory-motor patterns lead to joint attention. In addition, there are developmental changes in this multi-pathway system evidenced as variations in strength among multiple routes. We propose that coordinated visual attention between parents and toddlers is primarily a sensory-motor behavior. Skill in achieving coordinated visual attention in social settings-like skills in other sensory-motor domains-emerges from multiple pathways to the same functional end. Copyright © 2016 Cognitive Science Society, Inc.

Pursuit and prediction in the tracking of moving food by a teleost fish (Acanthaluteres spilomelanurus).

PubMed

Lanchester, B S; Mark, R F

1975-12-01

1. The path, eye and body movements of a teleost fish (the leatherjacket Acanthaluteres spilomelanurus) approaching and taking food were measured by cinematography. 2. Fixation of the food by movement of the eyes is an invariable feature of the approach. The eyes then remain aligned with the target while the body moves forward and round to bring the mouth to the food. 3. When pursuing pieces of food moving vertically at constant velocity through the water these fish normally trace out the pathway that can be calculated by assuming the fish aims constantly at the food. Predictive pathways that imply anticipation of the point of intersection with the food are not regularly seen. 4. Deviations from pursuit occur sporadically, usually in the direction of a predictive path, particularly when the fish approach falling food from below. 5. The geometry of the situation suggests that predictive paths may sometimes be generated if the alignment of eye and body during the pursuit of moving food can be delayed. In approaches from below this may be because forward movement of the fish would tend to stabilize the image of the falling food in the retina. 6. We suggest that a simple linked control system using both eye and body movements to fixate retinal images will on occasions generate predictive pathways without any need for the central nervous system to calculate them in advance.

Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi

NASA Astrophysics Data System (ADS)

Shih, Patrick M.; Ward, Lewis M.; Fischer, Woodward W.

2017-10-01

Various lines of evidence from both comparative biology and the geologic record make it clear that the biochemical machinery for anoxygenic photosynthesis was present on early Earth and provided the evolutionary stock from which oxygenic photosynthesis evolved ca. 2.3 billion years ago. However, the taxonomic identity of these early anoxygenic phototrophs is uncertain, including whether or not they remain extant. Several phototrophic bacterial clades are thought to have evolved before oxygenic photosynthesis emerged, including the Chloroflexi, a phylum common across a wide range of modern environments. Although Chloroflexi have traditionally been thought to be an ancient phototrophic lineage, genomics has revealed a much greater metabolic diversity than previously appreciated. Here, using a combination of comparative genomics and molecular clock analyses, we show that phototrophic members of the Chloroflexi phylum are not particularly ancient, having evolved well after the rise of oxygen (ca. 867 million years ago), and thus cannot be progenitors of oxygenic photosynthesis. Similarly, results show that the carbon fixation pathway that defines this clade—the 3-hydroxypropionate bicycle—evolved late in Earth history as a result of a series of horizontal gene transfer events, explaining the lack of geological evidence for this pathway based on the carbon isotope record. These results demonstrate the role of horizontal gene transfer in the recent metabolic innovations expressed within this phylum, including its importance in the development of a novel carbon fixation pathway.

Automated synthesis of a library of triazolated 1,2,5-thiadiazepane 1,1-dioxides via a double aza-Michael strategy.

PubMed

Zang, Qin; Javed, Salim; Hill, David; Ullah, Farman; Bi, Danse; Porubsky, Patrick; Neuenswander, Benjamin; Lushington, Gerald H; Santini, Conrad; Organ, Michael G; Hanson, Paul R

2012-08-13

The construction of a 96-member library of triazolated 1,2,5-thiadiazepane 1,1-dioxides was performed on a Chemspeed Accelerator (SLT-100) automated parallel synthesis platform, culminating in the successful preparation of 94 out of 96 possible products. The key step, a one-pot, sequential elimination, double-aza-Michael reaction, and [3 + 2] Huisgen cycloaddition pathway has been automated and utilized in the production of two sets of triazolated sultam products.

Automated Synthesis of a Library of Triazolated 1,2,5-Thiadiazepane 1,1-Dioxides via a Double aza-Michael Strategy

PubMed Central

Zang, Qin; Javed, Salim; Hill, David; Ullah, Farman; Bi, Danse; Porubsky, Patrick; Neuenswander, Benjamin; Lushington, Gerald H.; Santini, Conrad; Organ, Michael G.; Hanson, Paul R.

2013-01-01

The construction of a 96-member library of triazolated 1,2,5-thiadiazepane 1,1-dioxides was performed on a Chemspeed Accelerator (SLT-100) automated parallel synthesis platform, culminating in the successful preparation of 94 out of 96 possible products. The key step, a one-pot, sequential elimination, double-aza-Michael reaction, and [3+2] Huisgen cycloaddition pathway has been automated and utilized in the production of two sets of triazolated sultam products. PMID:22853708

Carbon dioxide in the atmosphere. [and other research projects

NASA Technical Reports Server (NTRS)

Johnson, F. S.

1974-01-01

Research projects for the period ending September 15, 1973 are reported as follows: (1) the abundances of carbon dioxide in the atmosphere, and the processes by which it is released from carbonate deposits in the earth and then transferred to organic material by photosynthesis; the pathways for movement of carbon and oxygen through the atmosphere; (2) space science computation assistance by PDP computer; the performance characteristics and user instances; (3) OGO-6 data analysis studies of the variations of nighttime ion temperature in the upper atmosphere.

Engineering a synthetic pathway in cyanobacteria for isopropanol production directly from carbon dioxide and light.

PubMed

Kusakabe, Tamami; Tatsuke, Tsuneyuki; Tsuruno, Keigo; Hirokawa, Yasutaka; Atsumi, Shota; Liao, James C; Hanai, Taizo

2013-11-01

Production of alternate fuels or chemicals directly from solar energy and carbon dioxide using engineered cyanobacteria is an attractive method to reduce petroleum dependency and minimize carbon emissions. Here, we constructed a synthetic pathway composed of acetyl-CoA acetyl transferase (encoded by thl), acetoacetyl-CoA transferase (encoded by atoAD), acetoacetate decarboxylase (encoded by adc) and secondary alcohol dehydrogenase (encoded by adh) in Synechococcus elongatus strain PCC 7942 to produce isopropanol. The enzyme-coding genes, heterogeneously originating from Clostridium acetobutylicum ATCC 824 (thl and adc), Escherichia coli K-12 MG1655 (atoAD) and Clostridium beijerinckii (adh), were integrated into the S. elongatus genome. Under the optimized production conditions, the engineered cyanobacteria produced 26.5 mg/L of isopropanol after 9 days. © 2013 Published by Elsevier Inc.

δ15N constraints on long-term nitrogen balances in temperate forests

USGS Publications Warehouse

Perakis, S.S.; Sinkhorn, E.R.; Compton, J.E.

2011-01-01

Biogeochemical theory emphasizes nitrogen (N) limitation and the many factors that can restrict N accumulation in temperate forests, yet lacks a working model of conditions that can promote naturally high N accumulation. We used a dynamic simulation model of ecosystem N and δ15N to evaluate which combination of N input and loss pathways could produce a range of high ecosystem N contents characteristic of forests in the Oregon Coast Range. Total ecosystem N at nine study sites ranged from 8,788 to 22,667 kg ha−1 and carbon (C) ranged from 188 to 460 Mg ha−1, with highest values near the coast. Ecosystem δ15N displayed a curvilinear relationship with ecosystem N content, and largely reflected mineral soil, which accounted for 96–98% of total ecosystem N. Model simulations of ecosystem N balances parameterized with field rates of N leaching required long-term average N inputs that exceed atmospheric deposition and asymbiotic and epiphytic N2-fixation, and that were consistent with cycles of post-fire N2-fixation by early-successional red alder. Soil water δ15NO3 − patterns suggested a shift in relative N losses from denitrification to nitrate leaching as N accumulated, and simulations identified nitrate leaching as the primary N loss pathway that constrains maximum N accumulation. Whereas current theory emphasizes constraints on biological N2-fixation and disturbance-mediated N losses as factors that limit N accumulation in temperate forests, our results suggest that wildfire can foster substantial long-term N accumulation in ecosystems that are colonized by symbiotic N2-fixing vegetation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

James C. Liao

This project is a collaboration with F. R. Tabita of Ohio State. Our major goal is to understand the factors and regulatory mechanisms that influence hydrogen production. The organisms to be utilized in this study, phototrophic microorganisms, in particular nonsulfur purple (NSP) bacteria, catalyze many significant processes including the assimilation of carbon dioxide into organic carbon, nitrogen fixation, sulfur oxidation, aromatic acid degradation, and hydrogen oxidation/evolution. Our part of the project was to develop a modeling technique to investigate the metabolic network in connection to hydrogen production and regulation. Organisms must balance the pathways that generate and consume reducing powermore » in order to maintain redox homeostasis to achieve growth. Maintaining this homeostasis in the nonsulfur purple photosynthetic bacteria is a complex feat with many avenues that can lead to balance, as these organisms possess versatile metabolic capabilities including anoxygenic photosynthesis, aerobic or anaerobic respiration, and fermentation. Growth is achieved by using H{sub 2} as an electron donor and CO{sub 2} as a carbon source during photoautotrophic and chemoautotrophic growth, where CO{sub 2} is fixed via the Calvin-Benson-Bassham (CBB) cycle. Photoheterotrophic growth can also occur when alternative organic carbon compounds are utilized as both the carbon source and electron donor. Regardless of the growth mode, excess reducing equivalents generated as a result of oxidative processes, must be transferred to terminal electron acceptors, thus insuring that redox homeostasis is maintained in the cell. Possible terminal acceptors include O{sub 2}, CO{sub 2}, organic carbon, or various oxyanions. Cells possess regulatory mechanisms to balance the activity of the pathways which supply energy, such as photosynthesis, and those that consume energy, such as CO{sub 2} assimilation or N{sub 2} fixation. The major route for CO{sub 2} assimilation is the CBB reductive pentose phosphate pathway, whose key enzyme is ribulose 1,5-biphosphate carboxylase/oxygenase (RubisCO). In addition to providing virtually all cellular carbon during autotrophic metabolism, RubisCO-mediated CO{sub 2} assimilation is also very important for nonsulfur purple photosynthetic bacteria under photoheterotrophic growth conditions since CO{sub 2} becomes the major electron sink under these conditions. In this work, Ensemble Modeling (EM) was developed to examine the behavior of CBB-compromised RubisCO knockout mutant strains of the nonsulfur purple photosynthetic bacterium Rhodobacter sphaeroides. Mathematical models of metabolism can be a great aid in studying the effects of large perturbations to the system, such as the inactivation of RubisCO. Due to the complex and highly-interconnected nature of these networks, it is not a trivial process to understand what the effect of perturbations to the metabolic network will be, or vice versa, what enzymatic perturbations are necessary to yield a desired effect. Flux distribution is controlled by multiple enzymes in the network, often indirectly linked to the pathways of interest. Further, depending on the state of the cell and the environmental conditions, the effect of a perturbation may center around how it effects the carbon flow in the network, the balancing of cofactors, or both. Thus, it is desirable to develop mathematical models to describe, understand, and predict network behavior. Through the development of such models, one may gain the ability to generate a set of testable hypotheses for system behavior.« less

Functional Metagenomic Investigations of Microbial Communities in a Shallow-Sea Hydrothermal System

PubMed Central

Tang, Kai; Liu, Keshao; Jiao, Nianzhi; Zhang, Yao; Chen, Chen-Tung Arthur

2013-01-01

Little is known about the functional capability of microbial communities in shallow-sea hydrothermal systems (water depth of <200 m). This study analyzed two high-throughput pyrosequencing metagenomic datasets from the vent and the surface water in the shallow-sea hydrothermal system offshore NE Taiwan. This system exhibited distinct geochemical parameters. Metagenomic data revealed that the vent and the surface water were predominated by Epsilonproteobacteria (Nautiliales-like organisms) and Gammaproteobacteria ( Thiomicrospira -like organisms), respectively. A significant difference in microbial carbon fixation and sulfur metabolism was found between the vent and the surface water. The chemoautotrophic microorganisms in the vent and in the surface water might possess the reverse tricarboxylic acid cycle and the Calvin−Bassham−Benson cycle for carbon fixation in response to carbon dioxide highly enriched in the environment, which is possibly fueled by geochemical energy with sulfur and hydrogen. Comparative analyses of metagenomes showed that the shallow-sea metagenomes contained some genes similar to those present in other extreme environments. This study may serve as a basis for deeply understanding the genetic network and functional capability of the microbial members of shallow-sea hydrothermal systems. PMID:23940820

Hydroxyl-Exchanged Nanoporous Ionic Copolymer toward Low-Temperature Cycloaddition of Atmospheric Carbon Dioxide into Carbonates.

PubMed

Guo, Zengjing; Cai, Xiaochun; Xie, Jingyan; Wang, Xiaochen; Zhou, Yu; Wang, Jun

2016-05-25

An ionic copolymer catalyst with nanopores, large surface area, high ionic density, and superior basicity was prepared via the radical copolymerization of amino-functionalized ionic liquid bromide and divinylbenzene, followed with a hydroxyl exchange for removing bromonium. Evaluated in chemical fixation of CO2 with epoxides into cyclic carbonates in the absence of any solvent and basic additive, the nanoporous copolymer catalyst showed high and stable activity, superior to various control catalysts including the halogen-containing analogue. Further, high yields were obtained over a wide scope of substrates including aliphatic long carbon-chain alkyl epoxides and internal epoxide, even under atmospheric pressure and less than 100 °C for the majority of the substrates. On the basis of in situ Fourier transform infrared (FT-IR) investigation and density functional theory (DFT) calculation for the reaction intermediates, we proposed a possible reaction mechanism accounting for the superior catalytic activity of the ionic copolymer. The specifically prepared ionic copolymer material of this work features highly stable, noncorrosive, and sustainable catalysis and, thus, may be a new possibility for efficient chemical fixation of CO2 since it is an environmentally friendly, metal-free solid catalyst.

Engineering self-assembled bioreactors from protein microcompartments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Savage, David

2016-10-12

The goals of this research are to understand how organisms such as bacteria segregate certain metabolic processes inside of specific structures, or “microcompartments,” in the cell and apply this knowledge to develop novel engineered microcompartments for use in nanotechnology and metabolic engineering. For example, in some bacteria, self-assembling protein microcompartments called carboxysomes encapsulate the enzymes involved in carbon fixation, enabling the cell to utilize carbon dioxide more effectively than if the enzymes were free in the cell. The proposed research will determine how structures such as carboxysomes assemble and function in bacteria and develop a means for creating novel, syntheticmore » microcompartments for optimizing production of specific energy-rich compounds.« less

The Structure of Isolated Synechococcus Strain WH8102 Carboxysomes as Revealed by Electron Cryotomography

PubMed Central

Iancu, Cristina V.; Ding, H. Jane; Morris, Dylan M.; Dias, D. Prabha; Gonzales, Arlene D.; Martino, Anthony; Jensen, Grant J.

2007-01-01

Carboxysomes are organelle-like polyhedral bodies found in cyanobacteria and many chemoautotrophic bacteria that are thought to facilitate carbon fixation. Carboxysomes are bounded by a proteinaceous outer shell and filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the first enzyme in the CO2 fixation pathway, but exactly how they enhance carbon fixation is unclear. Here we report the three-dimensional structure of purified carboxysomes from Synechococcus species strain WH8102 as revealed by electron cryotomography. We found that while the sizes of individual carboxysomes in this organism varied from 114 to 137 nm, surprisingly, all were approximately icosahedral. There were on average ∼250 RuBisCOs per carboxysome, organized into 3-4 concentric layers. Some models of carboxysome function depend on specific contacts between individual RuBisCOs and the shell, but no evidence of such contacts was found: no systematic patterns of connecting densities or RuBisCO positions against the shell's presumed hexagonal lattice could be discerned, and simulations showed that packing forces alone could account for the layered organization of RuBisCOs. PMID:17669419

Two MicroRNAs Linked to Nodule Infection and Nitrogen-Fixing Ability in the Legume Lotus japonicus1[W

PubMed Central

De Luis, Ana; Markmann, Katharina; Cognat, Valérie; Holt, Dennis B.; Charpentier, Myriam; Parniske, Martin; Stougaard, Jens; Voinnet, Olivier

2012-01-01

Legumes overcome nitrogen shortage by developing root nodules in which symbiotic bacteria fix atmospheric nitrogen in exchange for host-derived carbohydrates and mineral nutrients. Nodule development involves the distinct processes of nodule organogenesis, bacterial infection, and the onset of nitrogen fixation. These entail profound, dynamic gene expression changes, notably contributed to by microRNAs (miRNAs). Here, we used deep-sequencing, candidate-based expression studies and a selection of Lotus japonicus mutants uncoupling different symbiosis stages to identify miRNAs involved in symbiotic nitrogen fixation. Induction of a noncanonical miR171 isoform, which targets the key nodulation transcription factor Nodulation Signaling Pathway2, correlates with bacterial infection in nodules. A second candidate, miR397, is systemically induced in the presence of active, nitrogen-fixing nodules but not in that of noninfected or inactive nodule organs. It is involved in nitrogen fixation-related copper homeostasis and targets a member of the laccase copper protein family. These findings thus identify two miRNAs specifically responding to symbiotic infection and nodule function in legumes. PMID:23071252

Human antibodies fix complement to inhibit Plasmodium falciparum invasion of erythrocytes and are associated with protection against malaria.

PubMed

Boyle, Michelle J; Reiling, Linda; Feng, Gaoqian; Langer, Christine; Osier, Faith H; Aspeling-Jones, Harvey; Cheng, Yik Sheng; Stubbs, Janine; Tetteh, Kevin K A; Conway, David J; McCarthy, James S; Muller, Ivo; Marsh, Kevin; Anders, Robin F; Beeson, James G

2015-03-17

Antibodies play major roles in immunity to malaria; however, a limited understanding of mechanisms mediating protection is a major barrier to vaccine development. We have demonstrated that acquired human anti-malarial antibodies promote complement deposition on the merozoite to mediate inhibition of erythrocyte invasion through C1q fixation and activation of the classical complement pathway. Antibody-mediated complement-dependent (Ab-C') inhibition was the predominant invasion-inhibitory activity of human antibodies; most antibodies were non-inhibitory without complement. Inhibitory activity was mediated predominately via C1q fixation, and merozoite surface proteins 1 and 2 were identified as major targets. Complement fixation by antibodies was very strongly associated with protection from both clinical malaria and high-density parasitemia in a prospective longitudinal study of children. Ab-C' inhibitory activity could be induced by human immunization with a candidate merozoite surface-protein vaccine. Our findings demonstrate that human anti-malarial antibodies have evolved to function by fixing complement for potent invasion-inhibitory activity and protective immunity. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Conflict between aftereffects of retinal sweep and looming motion.

PubMed

Bridgeman, B; Nardello, C

1994-01-01

Observers looked monocularly into a tunnel, with gratings on the left and right sides drifting toward the head. An exposure period was followed by a test with fixed gratings. With fixation points, left and right retinal fields could be stimulated selectively. When exposure and test were on the same retinal fields, but fixation was on opposite sides of the tunnel during exposure and test periods, aftereffects of retinal sweep and of perceived looming were in opposite directions. The two effects tended to cancel, yielding no perceived aftereffect. When they did occur, aftereffects in the retinal and the looming directions were equally likely. Cancellation was significantly more likely in the experimental conditions than in the control, when fixation always remained on the same side. When areas of retinal stimulation in the exposure and test periods did not overlap, cancellation was less frequent and aftereffects of looming were more frequent. Results were not significantly different for left and right visual fields, indicating that cortical vs. subcortical OKN pathways do not influence the illusion. Vection resulted for 16 of 20 observers under one or another of our conditions.

A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea

PubMed Central

Kono, Takunari; Mehrotra, Sandhya; Endo, Chikako; Kizu, Natsuko; Matusda, Mami; Kimura, Hiroyuki; Mizohata, Eiichi; Inoue, Tsuyoshi; Hasunuma, Tomohisa; Yokota, Akiho; Matsumura, Hiroyoshi; Ashida, Hiroki

2017-01-01

Two enzymes are considered to be unique to the photosynthetic Calvin–Benson cycle: ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), responsible for CO2 fixation, and phosphoribulokinase (PRK). Some archaea possess bona fide RuBisCOs, despite not being photosynthetic organisms, but are thought to lack PRK. Here we demonstrate the existence in methanogenic archaea of a carbon metabolic pathway involving RuBisCO and PRK, which we term ‘reductive hexulose-phosphate' (RHP) pathway. These archaea possess both RuBisCO and a catalytically active PRK whose crystal structure resembles that of photosynthetic bacterial PRK. Capillary electrophoresis-mass spectrometric analysis of metabolites reveals that the RHP pathway, which differs from the Calvin–Benson cycle only in a few steps, is active in vivo. Our work highlights evolutionary and functional links between RuBisCO-mediated carbon metabolic pathways in methanogenic archaea and photosynthetic organisms. Whether the RHP pathway allows for autotrophy (that is, growth exclusively with CO2 as carbon source) remains unknown. PMID:28082747

Nitric oxide-fixation by non-symbiotic haemoglobin proteins in Arabidopsis thaliana under N-limited conditions.

PubMed

Kuruthukulangarakoola, Gitto Thomas; Zhang, Jiangli; Albert, Andreas; Winkler, Barbro; Lang, Hans; Buegger, Franz; Gaupels, Frank; Heller, Werner; Michalke, Bernhard; Sarioglu, Hakan; Schnitzler, Jörg-Peter; Hebelstrup, Kim Henrik; Durner, Jörg; Lindermayr, Christian

2017-01-01

Nitric oxide (NO) is an important signalling molecule that is involved in many different physiological processes in plants. Here, we report about a NO-fixing mechanism in Arabidopsis, which allows the fixation of atmospheric NO into nitrogen metabolism. We fumigated Arabidopsis plants cultivated in soil or as hydroponic cultures during the whole growing period with up to 3 ppmv of NO gas. Transcriptomic, proteomic and metabolomic analyses were used to identify non-symbiotic haemoglobin proteins as key components of the NO-fixing process. Overexpressing non-symbiotic haemoglobin 1 or 2 genes resulted in fourfold higher nitrate levels in these plants compared with NO-treated wild-type. Correspondingly, rosettes size and weight, vegetative shoot thickness and seed yield were 25, 40, 30, and 50% higher, respectively, than in wild-type plants. Fumigation with 250 ppbv 15 NO confirmed the importance of non-symbiotic haemoglobin 1 and 2 for the NO-fixation pathway, and we calculated a daily uptake for non-symbiotic haemoglobin 2 overexpressing plants of 250 mg N/kg dry weight. This mechanism is probably important under conditions with limited N supply via the soil. Moreover, the plant-based NO uptake lowers the concentration of insanitary atmospheric NOx, and in this context, NO-fixation can be beneficial to air quality. © 2016 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heffelfinger, Grant S.; Martino, Anthony; Rintoul, Mark Daniel

This SAND report provides the technical progress through October 2004 of the Sandia-led project, %22Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling,%22 funded by the DOE Office of Science Genomes to Life Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganismsmore » play a key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these - 4 - pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort. More information about this project, including a copy of the original proposal, can be found at www.genomes-to-life.org Acknowledgment We want to gratefully acknowledge the contributions of the GTL Project Team as follows: Grant S. Heffelfinger1*, Anthony Martino2, Andrey Gorin3, Ying Xu10,3, Mark D. Rintoul1, Al Geist3, Matthew Ennis1, Hashimi Al-Hashimi8, Nikita Arnold3, Andrei Borziak3, Bianca Brahamsha6, Andrea Belgrano12, Praveen Chandramohan3, Xin Chen9, Pan Chongle3, Paul Crozier1, PguongAn Dam10, George S. Davidson1, Robert Day3, Jean Loup Faulon2, Damian Gessler12, Arlene Gonzalez2, David Haaland1, William Hart1, Victor Havin3, Tao Jiang9, Howland Jones1, David Jung3, Ramya Krishnamurthy3, Yooli Light2, Shawn Martin1, Rajesh Munavalli3, Vijaya Natarajan3, Victor Olman10, Frank Olken4, Brian Palenik6, Byung Park3, Steven Plimpton1, Diana Roe2, Nagiza Samatova3, Arie Shoshani4, Michael Sinclair1, Alex Slepoy1, Shawn Stevens8, Chris Stork1, Charlie Strauss5, Zhengchang Su10, Edward Thomas1, Jerilyn A. Timlin1, Xiufeng Wan11, HongWei Wu10, Dong Xu11, Gong-Xin Yu3, Grover Yip8, Zhaoduo Zhang2, Erik Zuiderweg8 *Author to whom correspondence should be addressed (gsheffe%40sandia.gov) 1. Sandia National Laboratories, Albuquerque, NM 2. Sandia National Laboratories, Livermore, CA 3. Oak Ridge National Laboratory, Oak Ridge, TN 4. Lawrence Berkeley National Laboratory, Berkeley, CA 5. Los Alamos National Laboratory, Los Alamos, NM 6. University of California, San Diego 7. University of Illinois, Urbana/Champaign 8. University of Michigan, Ann Arbor 9. University of California, Riverside 10. University of Georgia, Athens 11. University of Missouri, Columbia 12. National Center for Genome Resources, Santa Fe, NM Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.« less

Genomes to Life Project Quarterly Report April 2005.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heffelfinger, Grant S.; Martino, Anthony; Rintoul, Mark Daniel

2006-02-01

This SAND report provides the technical progress through April 2005 of the Sandia-led project, "Carbon Sequestration in Synechococcus Sp.: From Molecular Machines to Hierarchical Modeling," funded by the DOE Office of Science Genomics:GTL Program. Understanding, predicting, and perhaps manipulating carbon fixation in the oceans has long been a major focus of biological oceanography and has more recently been of interest to a broader audience of scientists and policy makers. It is clear that the oceanic sinks and sources of CO2 are important terms in the global environmental response to anthropogenic atmospheric inputs of CO2 and that oceanic microorganisms play amore » key role in this response. However, the relationship between this global phenomenon and the biochemical mechanisms of carbon fixation in these microorganisms is poorly understood. In this project, we will investigate the carbon sequestration behavior of Synechococcus Sp., an abundant marine cyanobacteria known to be important to environmental responses to carbon dioxide levels, through experimental and computational methods. This project is a combined experimental and computational effort with emphasis on developing and applying new computational tools and methods. Our experimental effort will provide the biology and data to drive the computational efforts and include significant investment in developing new experimental methods for uncovering protein partners, characterizing protein complexes, identifying new binding domains. We will also develop and apply new data measurement and statistical methods for analyzing microarray experiments. Computational tools will be essential to our efforts to discover and characterize the function of the molecular machines of Synechococcus. To this end, molecular simulation methods will be coupled with knowledge discovery from diverse biological data sets for high-throughput discovery and characterization of protein-protein complexes. In addition, we will develop a set of novel capabilities for inference of regulatory pathways in microbial genomes across multiple sources of information through the integration of computational and experimental technologies. These capabilities will be applied to Synechococcus regulatory pathways to characterize their interaction map and identify component proteins in these - 4 -pathways. We will also investigate methods for combining experimental and computational results with visualization and natural language tools to accelerate discovery of regulatory pathways. The ultimate goal of this effort is develop and apply new experimental and computational methods needed to generate a new level of understanding of how the Synechococcus genome affects carbon fixation at the global scale. Anticipated experimental and computational methods will provide ever-increasing insight about the individual elements and steps in the carbon fixation process, however relating an organism's genome to its cellular response in the presence of varying environments will require systems biology approaches. Thus a primary goal for this effort is to integrate the genomic data generated from experiments and lower level simulations with data from the existing body of literature into a whole cell model. We plan to accomplish this by developing and applying a set of tools for capturing the carbon fixation behavior of complex of Synechococcus at different levels of resolution. Finally, the explosion of data being produced by high-throughput experiments requires data analysis and models which are more computationally complex, more heterogeneous, and require coupling to ever increasing amounts of experimentally obtained data in varying formats. These challenges are unprecedented in high performance scientific computing and necessitate the development of a companion computational infrastructure to support this effort. More information about this project can be found at www.genomes-to-life.org Acknowledgment We want to gratefully acknowledge the contributions of: Grant Heffelfinger1*, Anthony Martino2, Brian Palenik6, Andrey Gorin3, Ying Xu10,3, Mark Daniel Rintoul1, Al Geist3, Matthew Ennis1, with Pratul Agrawal3, Hashim Al-Hashimi8, Andrea Belgrano12, Mike Brown1, Xin Chen9, Paul Crozier1, PguongAn Dam10, Jean-Loup Faulon2, Damian Gessler12, David Haaland1, Victor Havin4, C.F. Huang5, Tao Jiang9, Howland Jones1, David Jung3, Katherine Kang14, Michael Langston15, Shawn Martin1, Shawn Means1, Vijaya Natarajan4, Roy Nielson5, Frank Olken4, Victor Olman10, Ian Paulsen14, Steve Plimpton1, Andreas Reichsteiner5, Nagiza Samatova3, Arie Shoshani4, Michael Sinclair1, Alex Slepoy1, Shawn Stevens8, Charlie Strauss5, Zhengchang Su10, Ed Thomas1, Jerilyn Timlin1, WimVermaas13, Xiufeng Wan11, HongWei Wu10, Dong Xu11, Grover Yip8, Erik Zuiderweg8 *Author to whom correspondence should be addressed (gsheffe@sandia.gov) 1. Sandia National Laboratories, Albuquerque, NM 2. Sandia National Laboratories, Livermore, CA 3. Oak Ridge National Laboratory, Oak Ridge, TN 4. Lawrence Berkeley National Laboratory, Berkeley, CA 5. Los Alamos National Laboratory, Los Alamos, NM 6. University of California, San Diego 7. University of Illinois, Urbana/Champaign 8. University of Michigan, Ann Arbor 9. University of California, Riverside 10. University of Georgia, Athens 11. University of Missouri, Columbia 12. National Center for Genome Resources, Santa Fe, NM 13. Arizona State University 14. The Institute for Genomic Research 15. University of Tennessee 5 Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL8500.« less

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation

NASA Astrophysics Data System (ADS)

Pachiadaki, Maria G.; Sintes, Eva; Bergauer, Kristin; Brown, Julia M.; Record, Nicholas R.; Swan, Brandon K.; Mathyer, Mary Elizabeth; Hallam, Steven J.; Lopez-Garcia, Purificacion; Takaki, Yoshihiro; Nunoura, Takuro; Woyke, Tanja; Herndl, Gerhard J.; Stepanauskas, Ramunas

2017-11-01

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean’s interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed.

Oxygenation of Earth's atmosphere and its impact on the evolution of nitrogen-based metabolisms

NASA Astrophysics Data System (ADS)

Papineau, D.; Mojzsis, S. J.

2002-12-01

The evolution of metabolic pathways is closely linked to the evolution of the redox state of the terrestrial atmosphere. Nitrogen has been an essential biological element since the emergence of life when reduced nitrogen compounds (e.g. ammonia) were utilized in the prebiotic synthesis of proteins and nucleic acids. The nitrogen isotopic composition of sediments has been used to trace the origin of sedimentary organic matter in the rock record. Nitrogen is therefore suitable as a biosignature to trace the emergence of life on Earth or other planetary bodies as well as to follow the subsequent evolution of the biosphere in response to global redox changes. Evidence is strong that biological nitrogen fixation evolved very early in the history of life. The Last Common Ancestor (LCA) on Earth was most likely capable of nitrogen fixation as seen from the phylogenetic distribution of nitrogen-fixing organisms in both the domains of Bacteria and Archaea. Phylogenetic trees plotted with nitrogen-fixing gene (Nif) sequences from lineages of Bacteria and Archaea suggest that the Nif genes originated in a common ancestor of the two domains. Other phylogenetic analyses have also demonstrated that the paralogous duplication of the nifDK and nifEN operons, central to nitrogen fixation, predated the divergence of Archaea from Bacteria and therefore occurred prior to the emergence of the LCA. Although the same may be true for denitrification, this metabolic pathway probably did not become dominant until atmospheric pO2 increased between ~2.4 to 1.9 Ga during the Great Oxygenation Event (GOE). Recent work has shown a general depletion in 15N content of Archean (pre-2.5 Ga) relative to Phanerozoic (<540 Ma) kerogens. Studies have shown that the distribution of the δ15N values in kerogens shift from negative values in the Early Archean (from -6 to +6‰ with an average near 0‰ ) to approximately contemporary positive values (from +2 to +10‰ with an average at +6‰ ) by the Early Proterozoic. In the anoxic Archean atmosphere, the nitrogen cycle must have been different and the instability of oxidized nitrogen species such as NO3- under low pO2 must have limited its availability. Therefore nitrogen fixation probably was the dominant nitrogen-based metabolic pathway during the Archean until the rise of oxygen in the atmosphere in the Early Proterozoic, which resulted in more favorable conditions for denitrification to become the dominant nitrogen-based metabolism. Stable isotopic ratios can be used to detect denitrification (which positively fractionates δ15N) and nitrogen fixation (which negatively fractionates δ15N) in K+-containing minerals such as biotite and muscovite. In an effort to characterize the transition from the essentially anoxic Archean atmosphere to the modern oxidizing atmosphere, we are investigating sedimentary rocks spanning 2.4 to 1.9 Ga from Rovaniemi, Finland. Structural NH4+ in minerals is characterized by μFTIR spectroscopy. Our new μFTIR measurements of Early Proterozoic metasediments spanning the 2.4 - 1.9 Ga time interval (and focused on the well-represented 2.2 - 1.9 Ga time interval from Rovaniemi) provide a high-resolution record of ammonium content during the GOE as a prelude to future detailed δ15N measurements by laser mass spectrometry. This work traces the evolution of nitrogen fixation in the biosphere, its response to changes in global redox and provides a tool for the investigation of biosignatures in samples returned from other ancient planetary surfaces.

Carbon dioxide-sensing in organisms and its implications for human disease

PubMed Central

Cummins, Eoin P.; Selfridge, Andrew C.; Sporn, Peter H.; Sznajder, Jacob I.; Taylor, Cormac T.

2013-01-01

The capacity of organisms to sense changes in the levels of internal and external gases and to respond accordingly is central to a range of physiologic and pathophysiologic processes. Carbon dioxide, a primary product of oxidative metabolism is one such gas that can be sensed by both prokaryotic and eukaryotic cells and in response to altered levels, elicit the activation of multiple adaptive pathways. The outcomes of activating CO2-sensitive pathways in various species include increased virulence of fungal and bacterial pathogens, prey-seeking behavior in insects as well as taste perception, lung function, and the control of immunity in mammals. In this review, we discuss what is known about the mechanisms underpinning CO2 sensing across a range of species and consider the implications of this for physiology, disease progression, and the possibility of developing new therapeutics for inflammatory and infectious disease. PMID:24045706

Photoredox activation of carbon dioxide for amino acid synthesis in continuous flow

NASA Astrophysics Data System (ADS)

Seo, Hyowon; Katcher, Matthew H.; Jamison, Timothy F.

2017-05-01

Although carbon dioxide (CO2) is highly abundant, its low reactivity has limited its use in chemical synthesis. In particular, methods for carbon-carbon bond formation generally rely on two-electron mechanisms for CO2 activation and require highly activated reaction partners. Alternatively, radical pathways accessed via photoredox catalysis could provide new reactivity under milder conditions. Here we demonstrate the direct coupling of CO2 and amines via the single-electron reduction of CO2 for the photoredox-catalysed continuous flow synthesis of α-amino acids. By leveraging the advantages of utilizing gases and photochemistry in flow, a commercially available organic photoredox catalyst effects the selective α-carboxylation of amines that bear various functional groups and heterocycles. The preliminary mechanistic studies support CO2 activation and carbon-carbon bond formation via single-electron pathways, and we expect that this strategy will inspire new perspectives on using this feedstock chemical in organic synthesis.

Metabolic flux analysis of the mixotrophic metabolisms in the green sulfur bacterium Chlorobaculum tepidum.

PubMed

Feng, Xueyang; Tang, Kuo-Hsiang; Blankenship, Robert E; Tang, Yinjie J

2010-12-10

The photosynthetic green sulfur bacterium Chlorobaculum tepidum assimilates CO(2) and organic carbon sources (acetate or pyruvate) during mixotrophic growth conditions through a unique carbon and energy metabolism. Using a (13)C-labeling approach, this study examined biosynthetic pathways and flux distributions in the central metabolism of C. tepidum. The isotopomer patterns of proteinogenic amino acids revealed an alternate pathway for isoleucine synthesis (via citramalate synthase, CimA, CT0612). A (13)C-assisted flux analysis indicated that carbons in biomass were mostly derived from CO(2) fixation via three key routes: the reductive tricarboxylic acid (RTCA) cycle, the pyruvate synthesis pathway via pyruvate:ferredoxin oxidoreductase, and the CO(2)-anaplerotic pathway via phosphoenolpyruvate carboxylase. During mixotrophic growth with acetate or pyruvate as carbon sources, acetyl-CoA was mainly produced from acetate (via acetyl-CoA synthetase) or citrate (via ATP citrate lyase). Pyruvate:ferredoxin oxidoreductase converted acetyl-CoA and CO(2) to pyruvate, and this growth-rate control reaction is driven by reduced ferredoxin generated during phototrophic growth. Most reactions in the RTCA cycle were reversible. The relative fluxes through the RTCA cycle were 80∼100 units for mixotrophic cultures grown on acetate and 200∼230 units for cultures grown on pyruvate. Under the same light conditions, the flux results suggested a trade-off between energy-demanding CO(2) fixation and biomass growth rate; C. tepidum fixed more CO(2) and had a higher biomass yield (Y(X/S), mole carbon in biomass/mole substrate) in pyruvate culture (Y(X/S) = 9.2) than in acetate culture (Y(X/S) = 6.4), but the biomass growth rate was slower in pyruvate culture than in acetate culture.

Regulators of nonsulfur purple phototrophic bacteria and the interactive control of CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy generation.

PubMed

Dubbs, James M; Tabita, F Robert

2004-06-01

For the metabolically diverse nonsulfur purple phototrophic bacteria, maintaining redox homeostasis requires balancing the activities of energy supplying and energy-utilizing pathways, often in the face of drastic changes in environmental conditions. These organisms, members of the class Alphaproteobacteria, primarily use CO2 as an electron sink to achieve redox homeostasis. After noting the consequences of inactivating the capacity for CO2 reduction through the Calvin-Benson-Bassham (CBB) pathway, it was shown that the molecular control of many additional important biological processes catalyzed by nonsulfur purple bacteria is linked to expression of the CBB genes. Several regulator proteins are involved, with the two component Reg/Prr regulatory system playing a major role in maintaining redox poise in these organisms. Reg/Prr was shown to be a global regulator involved in the coordinate control of a number of metabolic processes including CO2 assimilation, nitrogen fixation, hydrogen metabolism and energy-generation pathways. Accumulating evidence suggests that the Reg/Prr system senses the oxidation/reduction state of the cell by monitoring a signal associated with electron transport. The response regulator RegA/PrrA activates or represses gene expression through direct interaction with target gene promoters where it often works in concert with other regulators that can be either global or specific. For the key CO2 reduction pathway, which clearly triggers whether other redox balancing mechanisms are employed, the ability to activate or inactivate the specific regulator CbbR is of paramount importance. From these studies, it is apparent that a detailed understanding of how diverse regulatory elements integrate and control metabolism will eventually be achieved.

Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi

DOE PAGES

Shih, Patrick M.; Ward, Lewis M.; Fischer, Woodward W.

2017-09-18

We report various lines of evidence from both comparative biology and the geologic record make it clear that the biochemical machinery for anoxygenic photosynthesis was present on early Earth and provided the evolutionary stock from which oxygenic photosynthesis evolved ca. 2.3 billion years ago. However, the taxonomic identity of these early anoxygenic phototrophs is uncertain, including whether or not they remain extant. Several phototrophic bacterial clades are thought to have evolved before oxygenic photosynthesis emerged, including the Chloroflexi, a phylum common across a wide range of modern environments. Although Chloroflexi have traditionally been thought to be an ancient phototrophic lineage,more » genomics has revealed a much greater metabolic diversity than previously appreciated. Here, using a combination of comparative genomics and molecular clock analyses, we show that phototrophic members of the Chloroflexi phylum are not particularly ancient, having evolved well after the rise of oxygen (ca. 867 million years ago), and thus cannot be progenitors of oxygenic photosynthesis. Similarly, results show that the carbon fixation pathway that defines this clade—the 3-hydroxypropionate bicycle—evolved late in Earth history as a result of a series of horizontal gene transfer events, explaining the lack of geological evidence for this pathway based on the carbon isotope record. Finally, these results demonstrate the role of horizontal gene transfer in the recent metabolic innovations expressed within this phylum, including its importance in the development of a novel carbon fixation pathway.« less

Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shih, Patrick M.; Ward, Lewis M.; Fischer, Woodward W.

We report various lines of evidence from both comparative biology and the geologic record make it clear that the biochemical machinery for anoxygenic photosynthesis was present on early Earth and provided the evolutionary stock from which oxygenic photosynthesis evolved ca. 2.3 billion years ago. However, the taxonomic identity of these early anoxygenic phototrophs is uncertain, including whether or not they remain extant. Several phototrophic bacterial clades are thought to have evolved before oxygenic photosynthesis emerged, including the Chloroflexi, a phylum common across a wide range of modern environments. Although Chloroflexi have traditionally been thought to be an ancient phototrophic lineage,more » genomics has revealed a much greater metabolic diversity than previously appreciated. Here, using a combination of comparative genomics and molecular clock analyses, we show that phototrophic members of the Chloroflexi phylum are not particularly ancient, having evolved well after the rise of oxygen (ca. 867 million years ago), and thus cannot be progenitors of oxygenic photosynthesis. Similarly, results show that the carbon fixation pathway that defines this clade—the 3-hydroxypropionate bicycle—evolved late in Earth history as a result of a series of horizontal gene transfer events, explaining the lack of geological evidence for this pathway based on the carbon isotope record. Finally, these results demonstrate the role of horizontal gene transfer in the recent metabolic innovations expressed within this phylum, including its importance in the development of a novel carbon fixation pathway.« less

Cloud chemistry in eastern China: Observations from Mt. Tai

NASA Astrophysics Data System (ADS)

Collett, J. L.; Shen, X.; Lee, T.; Wang, X.; Li, Y.; Wang, W.; Wang, T.

2010-07-01

Until recently, studies of fog and cloud chemistry in China have been rare - even though the fate of China’s large sulfur dioxide emissions depends, in part, on the ability of regional clouds to support rapid aqueous oxidation to sulfate. Sulfur dioxide oxidized in regional clouds is more likely to be removed by wet deposition while sulfur dioxide that undergoes slower gas phase oxidation is expected to survive longer in the atmosphere and be transported over a much broader spatial scale. Two 2008 field campaigns conducted at Mt. Tai, an isolated peak on the NE China plain, provide insight into the chemical composition of regional clouds and the importance of various aqueous phase sulfur oxidation pathways. Single and two-stage Caltech Active Strand Cloudwater Collectors were used to collect bulk and drop size-resolved samples of cloudwater. Collected cloudwater was analyzed for key species that influence in-cloud sulfate production, including pH, S(IV), H2O2, Fe and Mn. Other major cloud solutes, including inorganic ions, total organic carbon (TOC), formaldehyde, and organic acids were also analyzed, as were gas phase concentrations of SO2, O3, and H2O2. A wide range of cloud pH was observed, from below 3 to above 6. High concentrations of cloudwater sulfate were consistent with abundant sulfur dioxide emissions in the region. Sampled clouds were also found to contain high concentrations of ammonium, nitrate, and organic carbon. Peak TOC concentrations reached approximately 200 ppmC, among the highest concentrations ever measured in cloudwater. Hydrogen peroxide was found to be the dominant aqueous phase S(IV) oxidant when cloud pH was less than approximately 5.4. Despite its fast reaction with sulfur dioxide in cloud droplets, high concentrations of residual hydrogen peroxide were measured in some clouds implying a substantial additional capacity for sulfate production. Ozone was found to be an important S(IV) oxidant when cloud pH was high. Oxidation of S(IV) by oxygen, catalyzed by Fe (III) and Mn(II) was generally the second or third fastest pathway for sulfate production. Differences between the pH and trace metal concentrations of small and large cloud droplets were observed, giving rise to aqueous phase sulfate production rates that were drop size-dependent for the ozone and metal-catalyzed pathways.

Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus.

PubMed

Zarzycki, Jan; Brecht, Volker; Müller, Michael; Fuchs, Georg

2009-12-15

The phototrophic bacterium Chloroflexus aurantiacus uses a yet unsolved 3-hydroxypropionate cycle for autotrophic CO(2) fixation. It starts from acetyl-CoA, with acetyl-CoA and propionyl-CoA carboxylases acting as carboxylating enzymes. In a first cycle, (S)-malyl-CoA is formed from acetyl-CoA and 2 molecules of bicarbonate. (S)-Malyl-CoA cleavage releases the CO(2) fixation product glyoxylate and regenerates the starting molecule acetyl-CoA. Here we complete the missing steps devoted to glyoxylate assimilation. In a second cycle, glyoxylate is combined with propionyl-CoA, an intermediate of the first cycle, to form beta-methylmalyl-CoA. This condensation is followed by dehydration to mesaconyl-C1-CoA. An unprecedented CoA transferase catalyzes the intramolecular transfer of the CoA moiety to the C4 carboxyl group of mesaconate. Mesaconyl-C4-CoA then is hydrated by an enoyl-CoA hydratase to (S)-citramalyl-CoA. (S)-Citramalyl-CoA is cleaved into acetyl-CoA and pyruvate by a tri-functional lyase, which previously cleaved (S)-malyl-CoA and formed beta-methylmalyl-CoA. Thus, the enigmatic disproportionation of glyoxylate and propionyl-CoA into acetyl-CoA and pyruvate is solved in an elegant and economic way requiring only 3 additional enzymes. The whole bicyclic pathway results in pyruvate formation from 3 molecules of bicarbonate and involves 19 steps but only 13 enzymes. Elements of the 3-hydroxypropionate cycle may be used for the assimilation of small organic molecules. The 3-hydroxypropionate cycle is compared with the Calvin-Benson-Bassham cycle and other autotrophic pathways.

Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in ‘Chlorochromatium aggregatum'.

PubMed Central

Cerqueda-García, Daniel; Martínez-Castilla, León P; Falcón, Luisa I; Delaye, Luis

2014-01-01

A symbiotic association occurs in ‘Chlorochromatium aggregatum', a phototrophic consortium integrated by two species of phylogenetically distant bacteria composed by the green-sulfur Chlorobium chlorochromatii CaD3 epibiont that surrounds a central β-proteobacterium. The non-motile chlorobia can perform nitrogen and carbon fixation, using sulfide as electron donors for anoxygenic photosynthesis. The consortium can move due to the flagella present in the central β-protobacterium. Although Chl. chlorochromatii CaD3 is never found as free-living bacteria in nature, previous transcriptomic and proteomic studies have revealed that there are differential transcription patterns between the symbiotic and free-living status of Chl. chlorocromatii CaD3 when grown in laboratory conditions. The differences occur mainly in genes encoding the enzymatic reactions involved in nitrogen and amino acid metabolism. We performed a metabolic reconstruction of Chl. chlorochromatii CaD3 and an in silico analysis of its amino acid metabolism using an elementary flux modes approach (EFM). Our study suggests that in symbiosis, Chl. chlorochromatii CaD3 is under limited nitrogen conditions where the GS/GOGAT (glutamine synthetase/glutamate synthetase) pathway is actively assimilating ammonia obtained via N2 fixation. In contrast, when free-living, Chl. chlorochromatii CaD3 is in a condition of nitrogen excess and ammonia is assimilated by the alanine dehydrogenase (AlaDH) pathway. We postulate that ‘Chlorochromatium aggregatum' originated from a parasitic interaction where the N2 fixation capacity of the chlorobia would be enhanced by injection of 2-oxoglutarate from the β-proteobacterium via the periplasm. This consortium would have the advantage of motility, which is fundamental to a phototrophic bacterium, and the syntrophy of nitrogen and carbon sources. PMID:24285361

Prebiotic synthesis of phosphoenol pyruvate by α-phosphorylation-controlled triose glycolysis

NASA Astrophysics Data System (ADS)

Coggins, Adam J.; Powner, Matthew W.

2017-04-01

Phosphoenol pyruvate is the highest-energy phosphate found in living organisms and is one of the most versatile molecules in metabolism. Consequently, it is an essential intermediate in a wide variety of biochemical pathways, including carbon fixation, the shikimate pathway, substrate-level phosphorylation, gluconeogenesis and glycolysis. Triose glycolysis (generation of ATP from glyceraldehyde 3-phosphate via phosphoenol pyruvate) is among the most central and highly conserved pathways in metabolism. Here, we demonstrate the efficient and robust synthesis of phosphoenol pyruvate from prebiotic nucleotide precursors, glycolaldehyde and glyceraldehyde. Furthermore, phosphoenol pyruvate is derived within an α-phosphorylation controlled reaction network that gives access to glyceric acid 2-phosphate, glyceric acid 3-phosphate, phosphoserine and pyruvate. Our results demonstrate that the key components of a core metabolic pathway central to energy transduction and amino acid, sugar, nucleotide and lipid biosyntheses can be reconstituted in high yield under mild, prebiotically plausible conditions.

Advances in the study on endogenous sulfur dioxide in the cardiovascular system.

PubMed

Tian, Hong

2014-01-01

This review summarized the current advances in understanding the role of the novel gasotransmitter, sulfur dioxide (SO2), in the cardiovascular system. Articles on the advances in the study of the role of endogenous sulfur dioxide in the cardiovascular system were accessed from PubMed and CNKI from 2003 to 2013, using keywords such as "endogenous sulfur dioxide" and "cardiovascular system". Articles with regard to the role of SO2 in the regulation of cardiovascular system were selected. Recently, scientists discovered that an endogenous SO2 pathway is present in the cardiovascular system and exerts physiologically significant effects, such as regulation of the cardiac function and the pathogenesis of various cardiopulmonary diseases such as hypoxic pulmonary hypertension, hypertension, coronary atherosclerosis, and cardiac ischemia-reperfusion (I/R) injury, in the cardiovascular system. Endogenous SO2 is a novel member of the gasotransmitter family in addition to the nitric oxide (NO), carbon monoxide (CO), and hydrogen sulfide (H2S). Studies indicated that it has a role in regulating the cardiovascular disease.

Single-cell sequencing of Thiomargarita reveals genomic flexibility for adaptation to dynamic redox conditions

DOE PAGES

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja; ...

2016-06-21

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

Life in hot acid: Pathway analyses in extremely thermoacidophilic archaea

PubMed Central

Auernik, Kathryne S.; Cooper, Charlotte R.; Kelly, Robert M.

2013-01-01

SUMMARY The extremely thermoacidophilic archaea are a particularly intriguing group of microorganisms that must simultaneously cope with biologically extreme pHs (≤ 4) and temperatures (Topt ≥ 60°C) in their natural environments. Their expandi ng biotechnological significance relates to their role in biomining of base and precious metals and their unique mechanisms of survival in hot acid, at both the cellular and biomolecular levels. Recent developments, such as advances in understanding of heavy metal tolerance mechanisms, implementation of a genetic system, and discovery of a new carbon fixation pathway, have been facilitated by availability of genome sequence data and molecular genetic systems. As a result, new insights into the metabolic pathways and physiological features that define extreme thermoacidophily have been obtained, in some cases suggesting prospects for biotechnological opportunities. PMID:18760359

Genome-scale modeling of the evolutionary path to C4 photosynthesis

NASA Astrophysics Data System (ADS)

Myers, Christopher R.; Bogart, Eli

In C4 photosynthesis, plants maintain a high carbon dioxide level in specialized bundle sheath cells surrounding leaf veins and restrict CO2 assimilation to those cells, favoring CO2 over O2 in competition for Rubisco active sites. In C3 plants, which do not possess such a carbon concentrating mechanism, CO2 fixation is reduced due to this competition. Despite the complexity of the C4 system, it has evolved convergently from more than 60 independent origins in diverse families of plants around the world over the last 30 million years. We study the evolution of the C4 system in a genome-scale model of plant metabolism that describes interacting mesophyll and bundle sheath cells and enforces key nonlinear kinetic relationships. Adapting the zero-temperature string method for simulating transition paths in physics and chemistry, we find the highest-fitness paths connecting C3 and C4 positions in the model's high-dimensional parameter space, and show that they reproduce known aspects of the C3-C4 transition while making additional predictions about metabolic changes along the path. We explore the relationship between evolutionary history and C4 biochemical subtype, and the effects of atmospheric carbon dioxide levels.

Integrated carbon dioxide/sludge gasification using waste heat from hot slags: syngas production and sulfur dioxide fixation.

PubMed

Sun, Yongqi; Zhang, Zuotai; Liu, Lili; Wang, Xidong

2015-04-01

The integrated CO2/sludge gasification using the waste heat in hot slags, was explored with the aim of syngas production, waste heat recovery and sewage sludge disposal. The results demonstrated that hot slags presented multiple roles on sludge gasification, i.e., not only a good heat carrier (500-950 °C) but also an effective desulfurizer (800-900 °C). The total gas yields increased from 0.022 kg/kgsludge at 500 °C to 0.422 kg/kgsludge at 900 °C; meanwhile, the SO2 concentration at 900 °C remarkably reduced from 164 ppm to 114 ppm by blast furnace slags (BFS) and 93 ppm by steel slags (SS), respectively. A three-stage reaction was clarified including volatile release, char transformation and fixed carbon using Gaussian fittings and the kinetic model was analyzed. Accordingly, a decline process using the integrated method was designed and the optimum slag/sludge ratio was deduced. These deciphered results appealed potential ways of reasonable disposal of sewage sludge and efficient recovery of waste heat from hot slags. Copyright © 2015 Elsevier Ltd. All rights reserved.

Monitoring CO[subscript 2] Fixation Using GC-MS Detection of a [superscript 13]C-Label

ERIC Educational Resources Information Center

Hammond, Daniel G.; Bridgham, April; Reichert, Kara; Magers, Martin

2010-01-01

Much of our understanding of metabolic pathways has resulted from the use of chemical and isotopic labels. In this experiment, a heavy isotope of carbon, [superscript 13]C, is used to label the product of the well-known RuBisCO enzymatic reaction. This is a key reaction in photosynthesis that converts inorganic carbon to organic carbon; a process…

Microbial Ecology of Thermophilic Anaerobic Digestion. Final Report

DOE R&D Accomplishments Database

Zinder, Stephen H.

2000-04-15

This grant supported research on methanogenic archaea. The two major areas that were supported were conversion of acetic acid to methane and nitrogen fixation by Methanosarcina. Among the achievements of this research were the isolation of novel methanogenic cultures, elucidation of the pathways from acetate to methane, description of a specific DNA-binding complex in nitrogen fixing methanogens, and demonstration of an alternative nitrogenase in Methanosarcina.

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feist, AM; Nagarajan, H; Rotaru, AE

2014-04-24

Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically withmore » formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species. Author Summary The ability of microorganisms to exchange electrons directly with their environment has large implications for our knowledge of industrial and environmental processes. For decades, it has been known that microbes can use electrodes as electron acceptors in microbial fuel cell settings. Geobacter metallireducens has been one of the model organisms for characterizing microbe-electrode interactions as well as environmental processes such as bioremediation. Here, we significantly expand the knowledge of metabolism and energetics of this model organism by employing constraint-based metabolic modeling. Through this analysis, we build the metabolic pathways necessary for carbon fixation, a desirable property for industrial chemical production. We further discover a novel growth condition which enables the characterization of autotrophic (i.e., carbon-fixing) metabolism in Geobacter. Importantly, our systems-level modeling approach helped elucidate the key metabolic pathways and the energetic cost associated with extracellular electron transfer. This model can be applied to characterize and engineer the metabolism and electron transfer capabilities of Geobacter for biotechnological applications.« less

Cerebral fat embolism syndrome causing brain death after long-bone fractures and acetazolamide therapy.

PubMed

Walshe, Criona M; Cooper, James D; Kossmann, Thomas; Hayes, Ivan; Iles, Linda

2007-06-01

A 19-year-old woman with multiple fractures and mild brain injury developed severe cerebral fat embolism syndrome after "damage control" orthopaedic surgery. Acetazolamide therapy to manage ocular trauma, in association with hyperchloraemia, caused a profound metabolic acidosis with appropriate compensatory hypocapnia. During ventilator weaning, unexpected brainstem coning followed increased sedation and brief normalisation of arterial carbon dioxide concentration. Autopsy found severe cerebral fat embolism and brain oedema. In patients with multiple trauma, cerebral fat embolism syndrome is difficult to diagnose, and may be more common after delayed fixation of long-bone fractures. Acetazolamide should be used with caution, as sudden restoration of normocapnia during compensated metabolic acidosis in patients with raised intracranial pressure may precipitate coning.

Climate-driven basin-scale decadal oscillations of oceanic phytoplankton.

PubMed

Martinez, Elodie; Antoine, David; D'Ortenzio, Fabrizio; Gentili, Bernard

2009-11-27

Phytoplankton--the microalgae that populate the upper lit layers of the ocean--fuel the oceanic food web and affect oceanic and atmospheric carbon dioxide levels through photosynthetic carbon fixation. Here, we show that multidecadal changes in global phytoplankton abundances are related to basin-scale oscillations of the physical ocean, specifically the Pacific Decadal Oscillation and the Atlantic Multidecadal Oscillation. This relationship is revealed in approximately 20 years of satellite observations of chlorophyll and sea surface temperature. Interaction between the main pycnocline and the upper ocean seasonal mixed layer is one mechanism behind this correlation. Our findings provide a context for the interpretation of contemporary changes in global phytoplankton and should improve predictions of their future evolution with climate change.

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation.

PubMed

Pachiadaki, Maria G; Sintes, Eva; Bergauer, Kristin; Brown, Julia M; Record, Nicholas R; Swan, Brandon K; Mathyer, Mary Elizabeth; Hallam, Steven J; Lopez-Garcia, Purificacion; Takaki, Yoshihiro; Nunoura, Takuro; Woyke, Tanja; Herndl, Gerhard J; Stepanauskas, Ramunas

2017-11-24

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior, but the relevant taxa and energy sources remain enigmatic. We show evidence that nitrite-oxidizing bacteria affiliated with the Nitrospinae phylum are important in dark ocean chemoautotrophy. Single-cell genomics and community metagenomics revealed that Nitrospinae are the most abundant and globally distributed nitrite-oxidizing bacteria in the ocean. Metaproteomics and metatranscriptomics analyses suggest that nitrite oxidation is the main pathway of energy production in Nitrospinae. Microautoradiography, linked with catalyzed reporter deposition fluorescence in situ hybridization, indicated that Nitrospinae fix 15 to 45% of inorganic carbon in the mesopelagic western North Atlantic. Nitrite oxidation may have a greater impact on the carbon cycle than previously assumed. Copyright © 2017, American Association for the Advancement of Science.

Cytochemical Detection of Peroxisomes in Light and Electron Microscopy with 3,3'-diaminobenzidine.

PubMed

Fahimi, H Dariush

2017-01-01

Peroxisomes are ubiquitous dynamic and multifunctional organelles that contribute to numerous anabolic and catabolic pathways, being essential for human health and development. Their best known functions include the oxidation of fatty acids and metabolism of hydrogen peroxide with catalase as a marker enzyme. Indeed, historically, it was the cytochemical staining of catalase in many different cells and tissues that revealed the ubiquitous presence of peroxisomes in almost all animal and plant cells. In this chapter, the method for cytochemical staining of catalase with the alkaline 3, 3'-diaminobenzidine (DAB) is described. Since aldehyde fixation is a prerequisite for staining of catalase with DAB, a method for perfusion fixation of rat liver with glutaraldehyde is presented prior to the cytochemical staining method and the subsequent tissue processing for light and electron microscopy.

Niche specialization of novel Thaumarchaeota to oxic and hypoxic acidic geothermal springs of Yellowstone National Park

PubMed Central

Beam, Jacob P; Jay, Zackary J; Kozubal, Mark A; Inskeep, William P

2014-01-01

Novel lineages of the phylum Thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. The primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65–72 °C), acidic (pH∼3) iron oxide and sulfur sediment environments of Yellowstone National Park (YNP). Metabolic reconstruction was coupled with detailed geochemical measurements of each geothermal habitat and reverse-transcriptase PCR to confirm the in situ activity of these populations. Phylogenetic analyses of ribosomal and housekeeping proteins place these archaea near the root of the thaumarchaeal branch. Metabolic reconstruction suggests that these populations are chemoorganotrophic and couple growth with the reduction of oxygen or nitrate in iron oxide habitats, or sulfur in hypoxic sulfur sediments. The iron oxide population has the potential for growth via the oxidation of sulfide to sulfate using a novel reverse sulfate reduction pathway. Possible carbon sources include aromatic compounds (for example, 4-hydroxyphenylacetate), complex carbohydrates (for example, starch), oligopeptides and amino acids. Both populations contain a type III ribulose bisphosphate carboxylase/oxygenase used for carbon dioxide fixation or adenosine monophosphate salvage. No evidence for the oxidation of ammonia was obtained from de novo sequence assemblies. Our results show that thermoacidophilic Thaumarchaeota from oxic iron mats and hypoxic sulfur sediments exhibit different respiratory machinery depending on the presence of oxygen versus sulfide, represent deeply rooted lineages within the phylum Thaumarchaeota and are endemic to numerous sites in YNP. PMID:24196321

An Examination of the Carbon Isotope Effects Associated with Amino Acid Biosynthesis

NASA Astrophysics Data System (ADS)

Scott, James H.; O'Brien, Diane M.; Emerson, David; Sun, Henry; McDonald, Gene D.; Salgado, Antonio; Fogel, Marilyn L.

2006-12-01

Stable carbon isotope ratios (δ13C) were determined for alanine, proline, phenylalanine, valine, leucine, isoleucine, aspartate (aspartic acid and asparagine), glutamate (glutamic acid and glutamine), lysine, serine, glycine, and threonine from metabolically diverse microorganisms. The microorganisms examined included fermenting bacteria, organotrophic, chemolithotrophic, phototrophic, methylotrophic, methanogenic, acetogenic, acetotrophic, and naturally occurring cryptoendolithic communities from the Dry Valleys of Antarctica. Here we demonstrated that reactions involved in amino acid biosynthesis can be used to distinguish amino acids formed by life from those formed by nonbiological processes. The unique patterns of δ13C imprinted by life on amino acids produced a biological bias. We also showed that, by applying discriminant function analysis to the δ13C value of a pool of amino acids formed by biological activity, it was possible to identify key aspects of intermediary carbon metabolism in the microbial world. In fact, microorganisms examined in this study could be placed within one of three metabolic groups: (1) heterotrophs that grow by oxidizing compounds containing three or more carbon-to-carbon bonds (fermenters and organotrophs), (2) autotrophs that grow by taking up carbon dioxide (chemolitotrophs and phototrophs), and (3) acetoclastic microbes that grow by assimilation of formaldehyde or acetate (methylotrophs, methanogens, acetogens, and acetotrophs). Furthermore, we demonstrated that cryptoendolithic communities from Antarctica grouped most closely with the autotrophs, which indicates that the dominant metabolic pathways in these communities are likely those utilized for CO2 fixation. We propose that this technique can be used to determine the dominant metabolic types in a community and reveal the overall flow of carbon in a complex ecosystem.

Experimental assessment of diazotroph responses to elevated seawater pCO2 in the North Pacific Subtropical Gyre

NASA Astrophysics Data System (ADS)

Böttjer, Daniela; Karl, David M.; Letelier, Ricardo M.; Viviani, Donn A.; Church, Matthew J.

2014-06-01

We examined short-term (24-72 h) responses of naturally occurring marine N2 fixing microorganisms (termed diazotrophs) to abrupt increases in the partial pressure of carbon dioxide (pCO2) in seawater during nine incubation experiments conducted between May 2010 and September 2012 at Station ALOHA (A Long-term Oligotrophic Habitat Assessment) (22°45'N, 158°W) in the North Pacific Subtropical Gyre (NPSG). Rates of N2 fixation, nitrogenase (nifH) gene abundances and transcripts of six major groups of cyanobacterial diazotrophs (including both unicellular and filamentous phylotypes), and rates of primary productivity (as measured by 14C-bicarbonate assimilation into plankton biomass) were determined under contemporary (~390 ppm) and elevated pCO2 conditions (~1100 ppm). Quantitative polymerase chain reaction (QPCR) amplification of planktonic nifH genes revealed that unicellular cyanobacteria phylotypes dominated gene abundances during these experiments. In the majority of experiments (seven out of nine), elevated pCO2 did not significantly influence rates of dinitrogen (N2) fixation or primary productivity (two-way analysis of variance (ANOVA), P > 0.05). During two experiments, rates of N2 fixation and primary productivity were significantly lower (by 79 to 82% and 52 to 72%, respectively) in the elevated pCO2 treatments relative to the ambient controls (two-way ANOVA, P < 0.05). QPCR amplification of nifH genes and gene transcripts revealed that diazotroph abundances and nifH gene expression were largely unchanged by the perturbation of the seawater pCO2. Our results suggest that naturally occurring N2 fixing plankton assemblages in the NPSG are relatively resilient to large, short-term increases in pCO2.

Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem

PubMed Central

He, Zhili; Xiong, Jinbo; Kent, Angela D; Deng, Ye; Xue, Kai; Wang, Gejiao; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2014-01-01

The concentrations of atmospheric carbon dioxide (CO2) and tropospheric ozone (O3) have been rising due to human activities. However, little is known about how such increases influence soil microbial communities. We hypothesized that elevated CO2 (eCO2) and elevated O3 (eO3) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. To test these hypotheses, we analyzed 96 soil samples from a soybean free-air CO2 enrichment (SoyFACE) experimental site using a comprehensive functional gene microarray (GeoChip 3.0). The results showed the overall functional composition and structure of soil microbial communities shifted under eCO2, eO3 or eCO2+eO3. Key functional genes involved in carbon fixation and degradation, nitrogen fixation, denitrification and methane metabolism were stimulated under eCO2, whereas those involved in N fixation, denitrification and N mineralization were suppressed under eO3, resulting in the fact that the abundance of some eO3-supressed genes was promoted to ambient, or eCO2-induced levels by the interaction of eCO2+eO3. Such effects appeared distinct for each treatment and significantly correlated with soil properties and soybean yield. Overall, our analysis suggests possible mechanisms of microbial responses to global atmospheric change factors through the stimulation of C and N cycling by eCO2, the inhibition of N functional processes by eO3 and the interaction by eCO2 and eO3. This study provides new insights into our understanding of microbial functional processes in response to global atmospheric change in soybean agro-ecosystems. PMID:24108327

Chemical approaches to carbon dioxide utilization for manned Mars missions

NASA Technical Reports Server (NTRS)

Hepp, Aloysius F.; Landis, Geoffrey A.; Kubiak, Clifford P.

1991-01-01

Use of resources available in situ is a critical enabling technology for a permanent human presence in space. A permanent presence on Mars, e.g., requires a large infrastructure to sustain life under hostile conditions. As a resource on Mars, atmospheric CO2 is as follows: abundant; available at all points on the surface; of known presence; chemically simple; and can be obtained by simple compression. Many studies focus on obtaining O2 and the various uses for O2 including life support and fuel; discussion of CO, the coproduct from CO2 fixation revolves around its uses as a fuel, being oxidized back to CO2. Several new proposals are studied for CO2 fixation through chemical, photochemical, and photoelectrochemical means. For example, the reduction of CO2 to hydrocarbons such as acetylene (C2H2) can be accomplished with H2. C2H2 has a theoretical vacuum specific impulse of approx. 375 secs. Potential uses were also studied of CO2, as obtained or further reduced to carbon, as a reducing agent in metal oxide processing to form metals or metal carbides for use as structural or power materials; the CO2 can be recycled to generate O2 and CO.

Evolution of a Multidisciplinary Clinical Pathway for the Management of Unstable Patients With Pelvic Fractures

PubMed Central

Biffl, Walter L.; Smith, Wade R.; Moore, Ernest E.; Gonzalez, Ricardo J.; Morgan, Steven J.; Hennessey, Theresa; Offner, Patrick J.; Ray, Charles E.; Franciose, Reginald J.; Burch, Jon M.

2001-01-01

Objective To determine whether the evolution of the authors’ clinical pathway for the treatment of hemodynamically compromised patients with pelvic fractures was associated with improved patient outcome. Summary Background Data Hemodynamically compromised patients with pelvic fractures present a complex challenge. The multidisciplinary trauma team must control hemorrhage, restore hemodynamics, and rapidly identify and treat associated life-threatening injuries. The authors developed a clinical pathway consisting of five primary elements: immediate trauma attending surgeon’s presence in the emergency department, early simultaneous transfusion of blood and coagulation factors, prompt diagnosis and management of associated life-threatening injuries, stabilization of the pelvic girdle, and timely insinuation of pelvic angiography and embolization. The addition of two orthopedic pelvic fracture specialists led to a revision of the pathway, emphasizing immediate emergency department presence of the orthopedic trauma attending to provide joint decision making with the trauma surgeon, closing the pelvic volume in the emergency department, and using alternatives to traditional external fixation devices. Methods Using trauma registry and blood bank records, the authors identified pelvic fracture patients receiving blood transfusions in the emergency department. They analyzed patients treated before versus after the May 1998 revision of the clinical pathway. Results A higher proportion of patients in the late period had blood pressure less than 90 mmHg (52% vs. 35%). In the late period, diagnostic peritoneal lavage was phased out in favor of torso ultrasound as a primary triage tool, and pelvic binding and C-clamp application largely replaced traditional external fixation devices. The overall death rate decreased from 31% in the early period to 15% in the later period, as did the rate of deaths from exsanguination (9% to 1%), multiple organ failure (12% to 1%), and death within 24 hours (16% to 5%). Conclusions The evolution of a multidisciplinary clinical pathway, coordinating the resources of a level 1 trauma center and directed by joint decision making between trauma surgeons and orthopedic traumatologists, has resulted in improved patient survival. The primary benefits appear to be in reducing early deaths from exsanguination and late deaths from multiple organ failure. PMID:11407336

Glycerol Dehydration to Acrolein Catalyzed by ZSM‐5 Zeolite in Supercritical Carbon Dioxide Medium

PubMed Central

Zou, Bin; Ren, Shoujie

2016-01-01

Abstract Supercritical carbon dioxide (SC‐CO2) has been used for the first time as a reaction medium for the dehydration of glycerol to acrolein catalyzed by a solid acid. Unprecedented catalyst stability over 528 hours of time‐on‐stream was achieved and the rate of coke deposition on the zeolite catalyst was the lowest among extensive previous studies, showing potential for industrial application. Coking pathways in SC‐CO2 were also elucidated for future development. The results have potential implications for other dehydration reactions catalyzed by solid acids. PMID:27796088

Ultrafast electron crystallography of the cooperative reaction path in vanadium dioxide

PubMed Central

Yang, Ding-Shyue; Baum, Peter; Zewail, Ahmed H.

2016-01-01

Time-resolved electron diffraction with atomic-scale spatial and temporal resolution was used to unravel the transformation pathway in the photoinduced structural phase transition of vanadium dioxide. Results from bulk crystals and single-crystalline thin-films reveal a common, stepwise mechanism: First, there is a femtosecond V−V bond dilation within 300 fs, second, an intracell adjustment in picoseconds and, third, a nanoscale shear motion within tens of picoseconds. Experiments at different ambient temperatures and pump laser fluences reveal a temperature-dependent excitation threshold required to trigger the transitional reaction path of the atomic motions. PMID:27376103

Theoretical Study of Sodium Effect on the Gasification of Carbonaceous Materials with Carbon Dioxide.

PubMed

Calderón, Lucas A; Garza, Jorge; Espinal, Juan F

2015-12-24

The effect of sodium on the thermodynamics and kinetics of carbon gasification with carbon dioxide was studied by using quantum chemistry methods. Specifically, in the density functional context, two exchange-correlation functionals were used: B3LYP and M06. Some results obtained by these exchange-correlation functionals were contrasted with those obtained by the CCSD(T) method. It was found that density functional theory gives similar conclusions with respect to the coupled-cluster method. As one important conclusion we can mention that the thermodynamics of carbon monoxide desorption is not favored by the sodium presence. However, the presence of this metal induces: (a) an easier formation of one semiquinone group, (b) the dissociation of carbon dioxide, and (c) an increment on the CO desorption rate for one of the proposed pathways.

Draft Genome Sequence of the Novel Thermoacidophilic Archaeon Acidianus copahuensis Strain ALE1, Isolated from the Copahue Volcanic Area in Neuquén, Argentina

PubMed Central

Rascovan, Nicolás; Castro, Camila; Revale, Santiago; Giaveno, M. Alejandra; Vazquez, Martín; Donati, Edgardo R.

2014-01-01

Acidianus copahuensis is a recently characterized thermoacidophilic archaeon isolated from the Copahue volcanic area in Argentina. Here, we present its draft genome sequence, in which we found genes involved in key metabolic pathways for developing under Copahue’s extreme environmental conditions, such as sulfur and iron oxidation, carbon fixation, and metal tolerance. PMID:24812211

A carbon sink pathway increases carbon productivity in cyanobacteria.

PubMed

Oliver, John W K; Atsumi, Shota

2015-05-01

The burning of fossil reserves, and subsequent release of carbon into the atmosphere is depleting the supply of carbon-based molecules used for synthetic materials including plastics, oils, medicines, and glues. To provide for future society, innovations are needed for the conversion of waste carbon (CO2) into organic carbon useful for materials. Chemical production directly from photosynthesis is a nascent technology, with great promise for capture of CO2 using sunlight. To improve low yields, it has been proposed that photosynthetic capacity can be increased by a relaxation of bottlenecks inherent to growth. The limits of carbon partitioning away from growth within the cell and the effect of partitioning on carbon fixation are not well known. Here we show that expressing genes in a pathway between carbon fixation and pyruvate increases partitioning to 2,3-butanediol (23BD) and leads to a 1.8-fold increase in total carbon yield in the cyanobacterium Synechococcus elongatus PCC 7942. Specific 2,3-butanediol production increases 2.4-fold. As partitioning increases beyond 30%, it leads to a steep decline in total carbon yield. The data suggests a local maximum for carbon partitioning from the Calvin Benson cycle that is scalable with light intensity. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilumT.

PubMed

Christel, Stephan; Herold, Malte; Bellenberg, Sören; El Hajjami, Mohamed; Buetti-Dinh, Antoine; Pivkin, Igor V; Sand, Wolfgang; Wilmes, Paul; Poetsch, Ansgar; Dopson, Mark

2017-11-17

Leptospirillum ferriphilum plays a major role in acidic, metal rich environments where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of this model species' type strain is available, limiting the possibilities to investigate the strategies and adaptations Leptospirillum ferriphilum T applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum T DSM 14647 obtained by PacBio SMRT long read sequencing for use as a high quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as substrate and bioleaching cultures containing chalcopyrite (CuFeS 2 ). Leptospirillum ferriphilum T adaptations to growth on chalcopyrite included a possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, expression and translation of genes responsible for chemotaxis and motility were enhanced. IMPORTANCE Leptospirillum ferriphilum is one of the most important iron-oxidizers in the context of acidic and metal rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on Leptospirillum ferriphilum T adaptation strategies to growth on the copper mineral chalcopyrite. This data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction. Copyright © 2017 Christel et al.

Autotrophy of green non-sulphur bacteria in hot spring microbial mats: biological explanations for isotopically heavy organic carbon in the geological record

NASA Technical Reports Server (NTRS)

van der Meer, M. T.; Schouten, S.; de Leeuw, J. W.; Ward, D. M.

2000-01-01

Inferences about the evidence of life recorded in organic compounds within the Earth's ancient rocks have depended on 13C contents low enough to be characteristic of biological debris produced by the well-known CO2 fixation pathway, the Calvin cycle. 'Atypically' high values have been attributed to isotopic alteration of sedimentary organic carbon by thermal metamorphism. We examined the possibility that organic carbon characterized by a relatively high 13C content could have arisen biologically from recently discovered autotrophic pathways. We focused on the green non-sulphur bacterium Chloroflexus aurantiacus that uses the 3-hydroxypropionate pathway for inorganic carbon fixation and is geologically significant as it forms modern mat communities analogous to stromatolites. Organic matter in mats constructed by Chloroflexus spp. alone had relatively high 13C contents (-14.9%) and lipids diagnostic of Chloroflexus that were also isotopically heavy (-8.9% to -18.5%). Organic matter in mats constructed by Chloroflexus in conjunction with cyanobacteria had a more typical Calvin cycle signature (-23.5%). However, lipids diagnostic of Chloroflexus were isotopically enriched (-15.1% to -24.1%) relative to lipids typical of cyanobacteria (-33.9% to -36.3%). This suggests that, in mats formed by both cyanobacteria and Chloroflexus, autotrophy must have a greater effect on Chloroflexus carbon metabolism than the photoheterotrophic consumption of cyanobacterial photosynthate. Chloroflexus cell components were also selectively preserved. Hence, Chloroflexus autotrophy and selective preservation of its products constitute one purely biological mechanism by which isotopically heavy organic carbon could have been introduced into important Precambrian geological features.

Genomic evidence for the Wood-Ljungdahl pathway for carbon fixation in warm basaltic ocean crust

NASA Astrophysics Data System (ADS)

Smith, A. R.; Fisk, M. R.; Mueller, R.; Colwell, F. S.; Mason, O. U.; Popa, R.

2016-12-01

Microbial life in the deep suboceanic aquifer can harness geochemical energy resulting from water-rock reactions and contribute to carbon cycling in the ocean via primary production, or chemosynthesis. Iron-bearing minerals such as olivine in oceanic crust can produce molecular hydrogen, small molecular weight hydrocarbons, and hydrogen sulfide as they react with seawater. Although this generally occurs in serpentinizing systems at very high temperatures deep in the subsurface, it has also been hypothesized to drive the subseafloor microbial ecosystems present in shallower basaltic aquifers. We present genome-based evidence for chemolithoautotrophic microbes present on the surface of olivine incubated in Juan de Fuca Ridge basaltic ocean crust for a 4-year period. These metagenome-derived genomes show dominant taxa capable of using both branches of the Wood-Ljungdahl pathway for carbon fixation and energy generation. This pathway uses molecular hydrogen potentially derived from the olivine surface as it reacts with seawater and CO2 which is inherent to seawater. These taxa were not reported from aquifer fluid samples, but have been found only in association with mineral surfaces in this study location. Most taxa in this simple community are distant relatives of cultured taxa; therefore this genome information is crucial to understanding how the subseafloor aquifer community is structured, how it obtains energy, how it cycles carbon, and gives us keys to help cultivate these organisms in the laboratory. Our findings also support the Subsurface Lithoautotrophic Microbial Ecosystem (SLiME) hypothesis and have implications for understanding life on early Earth and the potential for life in the Martian subsurface.

Exploring How Technology Growth Limits Impact Optimal Carbon dioxide Mitigation Pathways

EPA Science Inventory

Energy system optimization models prescribe the optimal mix of technologies and fuels for meeting energy demands over a time horizon, subject to energy supplies, demands, and other constraints. When optimizing, these models will, to the extent allowed, favor the least cost combin...

Measuring protection of aromatic wine thiols from oxidation by competitive reactions vs wine preservatives with ortho-quinones.

PubMed

Nikolantonaki, Maria; Magiatis, Prokopios; Waterhouse, Andrew L

2014-11-15

Quinones are central intermediates in wine oxidation that can degrade the quality of wine by reactions with varietal thiols, such as 3-sulfanylhexanol, decreasing desirable aroma. Protection by wine preservatives (sulphur dioxide, glutathione, ascorbic acid and model tannin, phloroglucinol) was assessed by competitive sacrificial reactions with 4-methyl-1,2-benzoquinone, quantifying products and ratios by HPLC-UV-MS. Regioselectivity was assessed by product isolation and identification by NMR spectroscopy. Nucleophilic addition reactions compete with two electron reduction of quinones by sulphur dioxide or ascorbic acid, and both routes serve as effective quenching pathways, but minor secondary products from coupled redox reactions between the products and reactants are also observed. The wine preservatives were all highly reactive and thus all very protective against 3-sulfanylhexanol loss to the quinone, but showed only additive antioxidant effects. Confirmation of these reaction rates and pathways in wine is needed to assess the actual protective action of each tested preservative. Copyright © 2014 Elsevier Ltd. All rights reserved.

Angiotensin-converting Enzyme Inhibition Improves the Effectiveness of Transcutaneous Carbon Dioxide Treatment

PubMed Central

NEMETH, BALAZS; KISS, ISTVAN; JENCSIK, TIMEA; PETER, IVAN; KRESKA, ZITA; KOSZEGI, TAMAS; MISETA, ATTILA; KUSTAN, PETER; BONCZ, IMRE; LACZO, ANDREA; AJTAY, ZENO

2017-01-01

Aim: To study the effect of carbon dioxide (CO2) therapy on the nitric oxide (NO) pathway by monitoring plasma asymmetric dimethylarginine (ADMA) concentrations. Patients and Methods: Forty-seven hypertensive patients who underwent transcutaneous CO2 therapy were enrolled. Thirty healthy individuals were recruited for the control group. Blood samples were taken one hour before, as well as one hour, 24 hours and 3 weeks after the first CO2 treatment. Controls did not undergo CO2 treatment. Plasma ADMA levels were measured by ELISA. Results: ADMA levels decreased significantly one hour after the first CO2 treatment compared to the baseline concentrations (p=0.003). Significantly greater reduction was found among patients in whom angiotensin converting enzyme inhibitors (ACEIs) were administered (p=0.019). Conclusion: The short- and long-term decrease of ADMA levels suggests that CO2 is not only a vasodilator, but also has a beneficial effect on the NO pathway. ACE inhibition seems to enhance the effect of CO2 treatment. PMID:28438873

A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea.

PubMed

Berg, Ivan A; Kockelkorn, Daniel; Buckel, Wolfgang; Fuchs, Georg

2007-12-14

The assimilation of carbon dioxide (CO2) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl-coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.

Geochemical roots of autotrophic carbon fixation: hydrothermal experiments in the system citric acid, H 2O-(±FeS)-(±NiS)

NASA Astrophysics Data System (ADS)

Cody, G. D.; Boctor, N. Z.; Hazen, R. M.; Brandes, J. A.; Morowitz, Harold J.; Yoder, H. S.

2001-10-01

Recent theories have proposed that life arose from primitive hydrothermal environments employing chemical reactions analogous to the reductive citrate cycle (RCC) as the primary pathway for carbon fixation. This chemistry is presumed to have developed as a natural consequence of the intrinsic geochemistry of the young, prebiotic, Earth. There has been no experimental evidence, however, demonstrating that there exists a natural pathway into such a cycle. Toward this end, the results of hydrothermal experiments involving citric acid are used as a method of deducing such a pathway. Homocatalytic reactions observed in the citric acid-H2O experiments encompass many of the reactions found in modern metabolic systems, i.e., hydration-dehydration, retro-Aldol, decarboxylation, hydrogenation, and isomerization reactions. Three principal decomposition pathways operate to degrade citric acid under thermal and aquathermal conditions. It is concluded that the acid catalyzed βγ decarboxylation pathway, leading ultimately to propene and CO2, may provide the most promise for reaction network reversal under natural hydrothermal conditions. Increased pressure is shown to accelerate the principal decarboxylation reactions under strictly hydrothermal conditions. The effect of forcing the pH via the addition of NaOH reveals that the βγ decarboxylation pathway operates even up to intermediate pH levels. The potential for network reversal (the conversion of propene and CO2 up to a tricarboxylic acid) is demonstrated via the Koch (hydrocarboxylation) reaction promoted heterocatalytically with NiS in the presence of a source of CO. Specifically, an olefin (1-nonene) is converted to a monocarboxylic acid; methacrylic acid is converted to the dicarboxylic acid, methylsuccinic acid; and the dicarboxylic acid, itaconic acid, is converted into the tricarboxylic acid, hydroaconitic acid. A number of interesting sulfur-containing products are also formed that may provide for additional reaction. The intrinsic catalytic qualities of FeS and NiS are also explored in the absence of CO. It was shown that the addition of NiS has a minimal effect in the product distribution, whereas the addition of FeS leads to the formation of hydrogenated and sulfur-containing products (thioethers). These results point to a simple hydrothermal redox pathway for citric acid synthesis that may have provided a geochemical ignition point for the reductive citrate cycle.

Towards Providing Solutions to the Air Quality Crisis in the Mexico City Metropolitan Area: Carbon Sequestration by Succulent Species in Green Roofs

PubMed Central

Collazo-Ortega, Margarita; Rosas, Ulises; Reyes-Santiago, Jerónimo

2017-01-01

INTRODUCTION: In the first months of 2016, the Mexico City Metropolitan Area experienced the worst air pollution crisis in the last decade, prompting drastic short-term solutions by the Mexico City Government and neighboring States. In order to help further the search for long-term sustainable solutions, we felt obliged to immediately release the results of our research regarding the monitoring of carbon sequestration by green roofs. Large-scale naturation, such as the implementation of green roofs, provides a way to partially mitigate the increased carbon dioxide output in urban areas. METHODS: Here, we quantified the carbon sequestration capabilities of two ornamental succulent plant species, Sedum dendroideum and Sedum rubrotinctum, which require low maintenance, and little or no irrigation. To obtain a detailed picture of these plants’ carbon sequestration capabilities, we measured carbon uptake on the Sedum plants by quantifying carbon dioxide exchange and fixation as organic acids, during the day and across the year, on a green roof located in Southern Mexico City. RESULTS: The species displayed their typical CAM photosynthetic metabolism. Moreover, our quantification allowed us to conservatively estimate that a newly planted green roof of Sedum sequesters approximately 180,000,000 ppm of carbon dioxide per year in a green roof of 100 square meters in the short term. DISCUSSION: The patterns of CAM and carbon dioxide sequestration were highly robust to the fluctuations of temperature and precipitation between seasons, and therefore we speculate that carbon sequestration would be comparable in any given year of a newly planted green roof. Older green roof would require regular trimming to mantain their carbon sink properties, but their carbon sequestration capabilities remain to be quantified. Nevertheless, we propose that Sedum green roofs can be part of the long-term solutions to mitigate the air pollution crisis in the Mexico City Metropolitan area, and other “megacities” with marked seasonal drought. PMID:28480127

Towards Providing Solutions to the Air Quality Crisis in the Mexico City Metropolitan Area: Carbon Sequestration by Succulent Species in Green Roofs.

PubMed

Collazo-Ortega, Margarita; Rosas, Ulises; Reyes-Santiago, Jerónimo

2017-03-31

In the first months of 2016, the Mexico City Metropolitan Area experienced the worst air pollution crisis in the last decade, prompting drastic short-term solutions by the Mexico City Government and neighboring States. In order to help further the search for long-term sustainable solutions, we felt obliged to immediately release the results of our research regarding the monitoring of carbon sequestration by green roofs. Large-scale naturation, such as the implementation of green roofs, provides a way to partially mitigate the increased carbon dioxide output in urban areas. Here, we quantified the carbon sequestration capabilities of two ornamental succulent plant species, Sedum dendroideum and Sedum rubrotinctum, which require low maintenance, and little or no irrigation. To obtain a detailed picture of these plants' carbon sequestration capabilities, we measured carbon uptake on the Sedum plants by quantifying carbon dioxide exchange and fixation as organic acids, during the day and across the year, on a green roof located in Southern Mexico City. The species displayed their typical CAM photosynthetic metabolism. Moreover, our quantification allowed us to conservatively estimate that a newly planted green roof of Sedum sequesters approximately 180,000,000 ppm of carbon dioxide per year in a green roof of 100 square meters in the short term. The patterns of CAM and carbon dioxide sequestration were highly robust to the fluctuations of temperature and precipitation between seasons, and therefore we speculate that carbon sequestration would be comparable in any given year of a newly planted green roof. Older green roof would require regular trimming to mantain their carbon sink properties, but their carbon sequestration capabilities remain to be quantified. Nevertheless, we propose that Sedum green roofs can be part of the long-term solutions to mitigate the air pollution crisis in the Mexico City Metropolitan area, and other "megacities" with marked seasonal drought.

Treatment of organic waste

DOEpatents

Grantham, LeRoy F.

1979-01-01

An organic waste containing at least one element selected from the group consisting of strontium, cesium, iodine and ruthenium is treated to achieve a substantial reduction in the volume of the waste and provide for fixation of the selected element in an inert salt. The method of treatment comprises introducing the organic waste and a source of oxygen into a molten salt bath maintained at an elevated temperature to produce solid and gaseous reaction products. The gaseous reaction products comprise carbon dioxide and water vapor, and the solid reaction products comprise the inorganic ash constituents of the organic waste and the selected element which is retained in the molten salt. The molten salt bath comprises one or more alkali metal carbonates, and may optionally include from 1 to about 25 wt.% of an alkali metal sulfate.

Nitrogenase Reduction of Carbon-Containing Compounds

PubMed Central

Seefeldt, Lance C.; Yang, Zhi-Yong; Duval, Simon; Dean, Dennis R.

2013-01-01

Nitrogenase is an enzyme found in many bacteria and archaea that catalyzes biological dinitrogen fixation, the reduction of N2 to NH3, accounting for the major input of fixed nitrogen into the biogeochemical N cycle. In addition to reducing N2 and protons, nitrogenase can reduce a number of small, non-physiological substrates. Among these alternative substrates are included a wide array of carbon containing compounds. These compounds have provided unique insights into aspects of the nitrogenase mechanism. Recently, it was shown that carbon monoxide (CO) and carbon dioxide (CO2) can also be reduced by nitrogenase to yield hydrocarbons, opening new insights into the mechanism of small molecule activation and reduction by this complex enzyme as well as providing clues for the design of novel molecular catalysts. PMID:23597875

Review of sulfur dioxide to sulfate aerosol chemistry at Kīlauea Volcano, Hawai'i

NASA Astrophysics Data System (ADS)

Pattantyus, Andre K.; Businger, Steven; Howell, Steven G.

2018-07-01

Sulfur dioxide emissions from the Kīlauea Volcano on the island of Hawai'i and the subsequent formation of sulfate aerosols have caused a public health hazard across the state of Hawai'i since the volcano began erupting continuously in 1983. The University of Hawai'i at Mānoa began to forecast the trajectory and dispersion of emissions in 2010 to help mitigate the hazards to public health. In this paper a comprehensive review of potential conversion reactions is presented with the goal of more accurately representing the sulfur dioxide chemistry in the dispersion model. Atmospheric sulfur dioxide chemistry and major process responsible for sulfate formation are well documented in urban and industrial settings. The atmosphere in the vicinity of Kīlauea Volcano on the island of Hawai'i differs from that in previous investigations by virtue of being far removed from both urban and industrial settings in a remote, tropical marine atmosphere. Additionally, the combination of the high rate of sulfur dioxide emissions and trace gases and metals from Kīlauea Volcano creates a unique circumstance that requires a new look at potential conversion pathways to determine the dominant reactions. The theoretical analysis suggests that the dominant reaction in clear air will be between sulfur dioxide and the hydroxyl radical (0.01-5% h-1) and the dominant reaction in cloudy air involves hydrogen peroxide (3-50% s-1). Moreover, given the high SO2 emissions from the Halema'uma'u Crater vent, the oxidation of sulfur dioxide by these reactants is limited by their rate of production.

The Involvement of Hydrogen-producing and ATP-dependent NADPH-consuming Pathways in Setting the Redox Poise in the Chloroplast of Chlamydomonas reinhardtii in Anoxia

PubMed Central

Clowez, Sophie; Godaux, Damien; Cardol, Pierre; Wollman, Francis-André; Rappaport, Fabrice

2015-01-01

Photosynthetic microalgae are exposed to changing environmental conditions. In particular, microbes found in ponds or soils often face hypoxia or even anoxia, and this severely impacts their physiology. Chlamydomonas reinhardtii is one among such photosynthetic microorganisms recognized for its unusual wealth of fermentative pathways and the extensive remodeling of its metabolism upon the switch to anaerobic conditions. As regards the photosynthetic electron transfer, this remodeling encompasses a strong limitation of the electron flow downstream of photosystem I. Here, we further characterize the origin of this limitation. We show that it stems from the strong reducing pressure that builds up upon the onset of anoxia, and this pressure can be relieved either by the light-induced synthesis of ATP, which promotes the consumption of reducing equivalents, or by the progressive activation of the hydrogenase pathway, which provides an electron transfer pathway alternative to the CO2 fixation cycle. PMID:25691575

Structural aspects of denitrifying enzymes.

PubMed

Moura, I; Moura, J J

2001-04-01

The reduction of nitrate to nitrogen gas via nitrite, nitric oxide and nitrous oxide is the metabolic pathway usually known as denitrification, a key step in the nitrogen cycle. As observed for other elemental cycles, a battery of enzymes are utilized, namely the reductases for nitrate, nitrite, nitric oxide and nitrous oxide, as well as multiple electron donors that interact with these enzymes, in order to carry out the stepwise reactions that involve key intermediates. Because of the importance of this pathway (of parallel importance to the nitrogen-fixation pathway), efforts are underway to understand the structures of the participating enzymes and to uncover mechanistic aspects. Three-dimensional structures have been solved for the majority of these enzymes in the past few years, revealing the architecture of the active metal sites as well as global structural aspects, and possible mechanistic aspects. In addition, the recognition of specific electron-transfer partners raises important questions regarding specific electron-transfer pathways, partner recognition and control of metabolism.

Complete Genome Sequence of Sulfuriferula sp. Strain AH1, a Sulfur-Oxidizing Autotroph Isolated from Weathered Mine Tailings from the Duluth Complex in Minnesota

PubMed Central

Roepke, Elizabeth W.; Hua, An An; Flood, Beverly E.; Bailey, Jake V.

2017-01-01

ABSTRACT We report the closed and annotated genome sequence of Sulfuriferula sp. strain AH1. Strain AH1 has a 2,877,007-bp chromosome that includes a partial Sox system for inorganic sulfur oxidation and a complete nitrogen fixation pathway. It also has a single 39,138-bp plasmid with genes for arsenic and mercury resistance. PMID:28798167

Modulating Wnt Signaling Pathway to Enhance Allograft Integration in Orthopedic Trauma Treatment

DTIC Science & Technology

2013-10-01

presented below. Quantitative output provides an extensive set of data but we have chosen to present the most relevant parameters that are reflected in...multiple parameters .  Most samples have been mechanically tested and data extracted for multiple parameters .  Histological evaluation of subset of...Sumner, D. R. Saline Irrigation Does Not Affect Bone Formation or Fixation Strength of Hydroxyapatite /Tricalcium Phosphate-Coated Implants in a Rat Model

Acute carbon dioxide avoidance in Caenorhabditis elegans

PubMed Central

Hallem, Elissa A.; Sternberg, Paul W.

2008-01-01

Carbon dioxide is produced as a by-product of cellular respiration by all aerobic organisms and thus serves for many animals as an important indicator of food, mates, and predators. However, whether free-living terrestrial nematodes such as Caenorhabditis elegans respond to CO2 was unclear. We have demonstrated that adult C. elegans display an acute avoidance response upon exposure to CO2 that is characterized by the cessation of forward movement and the rapid initiation of backward movement. This response is mediated by a cGMP signaling pathway that includes the cGMP-gated heteromeric channel TAX-2/TAX-4. CO2 avoidance is modulated by multiple signaling molecules, including the neuropeptide Y receptor NPR-1 and the calcineurin subunits TAX-6 and CNB-1. Nutritional status also modulates CO2 responsiveness via the insulin and TGFβ signaling pathways. CO2 response is mediated by a neural circuit that includes the BAG neurons, a pair of sensory neurons of previously unknown function. TAX-2/TAX-4 function in the BAG neurons to mediate acute CO2 avoidance. Our results demonstrate that C. elegans senses and responds to CO2 using multiple signaling pathways and a neural network that includes the BAG neurons and that this response is modulated by the physiological state of the worm. PMID:18524955

Acute carbon dioxide avoidance in Caenorhabditis elegans.

PubMed

Hallem, Elissa A; Sternberg, Paul W

2008-06-10

Carbon dioxide is produced as a by-product of cellular respiration by all aerobic organisms and thus serves for many animals as an important indicator of food, mates, and predators. However, whether free-living terrestrial nematodes such as Caenorhabditis elegans respond to CO2 was unclear. We have demonstrated that adult C. elegans display an acute avoidance response upon exposure to CO2 that is characterized by the cessation of forward movement and the rapid initiation of backward movement. This response is mediated by a cGMP signaling pathway that includes the cGMP-gated heteromeric channel TAX-2/TAX-4. CO2 avoidance is modulated by multiple signaling molecules, including the neuropeptide Y receptor NPR-1 and the calcineurin subunits TAX-6 and CNB-1. Nutritional status also modulates CO2 responsiveness via the insulin and TGFbeta signaling pathways. CO2 response is mediated by a neural circuit that includes the BAG neurons, a pair of sensory neurons of previously unknown function. TAX-2/TAX-4 function in the BAG neurons to mediate acute CO2 avoidance. Our results demonstrate that C. elegans senses and responds to CO2 using multiple signaling pathways and a neural network that includes the BAG neurons and that this response is modulated by the physiological state of the worm.

Understanding the Effectiveness of Carbon Dioxide Removal to Reduce the Impacts of Climate Change.

NASA Astrophysics Data System (ADS)

Scott, V.; Tett, S. F.; Brander, M.

2017-12-01

The current Nationally Determined Contributions to the Paris Agreement suggest exceeding the emissions budgets corresponding to the below 2°C and 1.5°C temperature targets. To address this the future application of Carbon Dioxide Removal (CDR) is proposed to recapture excess emissions at a later time, so keeping the total net emissions within budget. This assumes that the climate change impact of CO2 emitted now can be fully compensated by a matched CO2 removal in the future. However, the impacts from this pathway of emissions budget overshoot and subsequent recapture may differ from those resulting from a pathway where emissions are held within budget with no temporary overshoot. These pathway dependent impacts could give rise to different climatic and societal futures despite the total net emissions being the same. Using a low resolution fully coupled Earth System Model with an interactive carbon cycle, we present an investigation into the pathway dependence of climate change impacts and how these relate to the scale and duration of the emissions budget overshoot and subsequent recapture. From this we discuss the effectiveness of CDR in avoiding climate change impacts relative to more immediate emissions reductions. We consider how this relative effectiveness might be reflected in GHG accounting methods and national GHG accounts, and explore the implications for Article 2 of the Paris Agreement, where holding temperatures to the targets is recognised to "significantly reduce the risks and impacts of climate change".

Glycerol Dehydration to Acrolein Catalyzed by ZSM-5 Zeolite in Supercritical Carbon Dioxide Medium.

PubMed

Zou, Bin; Ren, Shoujie; Ye, X Philip

2016-12-08

Supercritical carbon dioxide (SC-CO 2 ) has been used for the first time as a reaction medium for the dehydration of glycerol to acrolein catalyzed by a solid acid. Unprecedented catalyst stability over 528 hours of time-on-stream was achieved and the rate of coke deposition on the zeolite catalyst was the lowest among extensive previous studies, showing potential for industrial application. Coking pathways in SC-CO 2 were also elucidated for future development. The results have potential implications for other dehydration reactions catalyzed by solid acids. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Postmortem changes in the neuroanatomical characteristics of the primate brain: the hippocampal formation

PubMed Central

Lavenex, Pierre; Lavenex, Pamela Banta; Bennett, Jeffrey L.; Amaral, David G.

2009-01-01

Comparative studies of the structural organization of the brain are fundamental to our understanding of human brain function. However, whereas brains of experimental animals are fixed by perfusion of a fixative through the vasculature, human or ape brains are fixed by immersion after varying postmortem intervals. Although differential treatments might affect the fundamental characteristics of the tissue, this question has not been evaluated empirically in primate brains. Monkey brains were either perfused, or acquired after varying postmortem intervals before immersion-fixation in 4% paraformaldehyde. We found that the fixation method affected the neuroanatomical characteristics of the monkey hippocampal formation. Soma size was smaller in Nissl-stained, immersion-fixed tissue, although overall brain volume was larger, as compared to perfusion-fixed tissue. Non-phosphorylated high-molecular-weight neurofilament immunoreactivity was lower in CA3 pyramidal neurons, dentate mossy cells and the entorhinal cortex, whereas it was higher in the mossy fiber pathway in immersion-fixed tissue. Serotonin-immunoreactive fibers were well-stained in perfused tissue but were undetectable in immersion-fixed tissue. Although regional immunoreactivity patterns for calcium-binding proteins were not affected, intracellular staining degraded with increasing postmortem intervals. Somatostatin-immunoreactive clusters of large axonal varicosities, previously reported only in humans, were observed in immersion-fixed monkey tissue. In addition, calretinin-immunoreactive multipolar neurons, previously observed only in rodents, were found in the rostral dentate gyrus in both perfused and immersion-fixed brains. In conclusion, comparative studies of the brain must evaluate the effects of fixation on the staining pattern of each marker in every structure of interest before drawing conclusions about species differences. PMID:18972553

Does It Really Matter Where You Look When Walking on Stairs? Insights from a Dual-Task Study

PubMed Central

Miyasike-daSilva, Veronica; McIlroy, William E.

2012-01-01

Although the visual system is known to provide relevant information to guide stair locomotion, there is less understanding of the specific contributions of foveal and peripheral visual field information. The present study investigated the specific role of foveal vision during stair locomotion and ground-stairs transitions by using a dual-task paradigm to influence the ability to rely on foveal vision. Fifteen healthy adults (26.9±3.3 years; 8 females) ascended a 7-step staircase under four conditions: no secondary tasks (CONTROL); gaze fixation on a fixed target located at the end of the pathway (TARGET); visual reaction time task (VRT); and auditory reaction time task (ART). Gaze fixations towards stair features were significantly reduced in TARGET and VRT compared to CONTROL and ART. Despite the reduced fixations, participants were able to successfully ascend stairs and rarely used the handrail. Step time was increased during VRT compared to CONTROL in most stair steps. Navigating on the transition steps did not require more gaze fixations than the middle steps. However, reaction time tended to increase during locomotion on transitions suggesting additional executive demands during this phase. These findings suggest that foveal vision may not be an essential source of visual information regarding stair features to guide stair walking, despite the unique control challenges at transition phases as highlighted by phase-specific challenges in dual-tasking. Instead, the tendency to look at the steps in usual conditions likely provides a stable reference frame for extraction of visual information regarding step features from the entire visual field. PMID:22970297

Postmortem changes in the neuroanatomical characteristics of the primate brain: hippocampal formation.

PubMed

Lavenex, Pierre; Lavenex, Pamela Banta; Bennett, Jeffrey L; Amaral, David G

2009-01-01

Comparative studies of the structural organization of the brain are fundamental to our understanding of human brain function. However, whereas brains of experimental animals are fixed by perfusion of a fixative through the vasculature, human or ape brains are fixed by immersion after varying postmortem intervals. Although differential treatments might affect the fundamental characteristics of the tissue, this question has not been evaluated empirically in primate brains. Monkey brains were either perfused or acquired after varying postmortem intervals before immersion-fixation in 4% paraformaldehyde. We found that the fixation method affected the neuroanatomical characteristics of the monkey hippocampal formation. Soma size was smaller in Nissl-stained, immersion-fixed tissue, although overall brain volume was larger as compared to perfusion-fixed tissue. Nonphosphorylated high-molecular-weight neurofilament immunoreactivity was lower in CA3 pyramidal neurons, dentate mossy cells, and the entorhinal cortex, whereas it was higher in the mossy fiber pathway in immersion-fixed tissue. Serotonin-immunoreactive fibers were well stained in perfused tissue but were undetectable in immersion-fixed tissue. Although regional immunoreactivity patterns for calcium-binding proteins were not affected, intracellular staining degraded with increasing postmortem intervals. Somatostatin-immunoreactive clusters of large axonal varicosities, previously reported only in humans, were observed in immersion-fixed monkey tissue. In addition, calretinin-immunoreactive multipolar neurons, previously observed only in rodents, were found in the rostral dentate gyrus in both perfused and immersion-fixed brains. In conclusion, comparative studies of the brain must evaluate the effects of fixation on the staining pattern of each marker in every structure of interest before drawing conclusions about species differences.

[CAM in Tillandsia usneoides: Studies on the pathway of carbon and the dependency of CO2-exchange on light intensity, temperature and water content of the plant].

PubMed

Kluge, M; Lange, O L; Eichmann, M V; Schmid, R

1973-12-01

Tillandsia usneoides, in the common sense a non-succulent plant, exhibits CO2 exchange characterized by net CO2 dark fixation during the night and depression of CO2 exchange during the day. Malate has been demonstrated to accumulate during CO2 dark fixation and to be converted to carbohydrates in light. Thus, T. usneoides exhibits CAM like typical succulents.Net CO2 uptake during the day is increased with net CO2 output being suppressed in duration of time and extent when light intensity increases. Furthermore, a slight increase in CO2 fixation during the following night can be observed if the plants were treated with high light intensity during the previous day.Curves of CO2 exchange typical for CAM are obtained if T. usneoides is kept at 15°C and 20°C. Lower temperature tend to increase CO2 uptake during the day and to inhibit CO2 dark fixation. Temperatures higher than 20°C favour loss of CO2 by respiration, which becomes apparent during the whole day and night at 30°C and higher temperatures. Thus, T. usneoides gains carbon only at temperatures well below 25°C.Net CO2 uptake during the day occurs only in moist plant material and is inhibited in plants cept under water stress conditions. However, CO2 uptake during the night is clearly favoured if the plants dry out. Therefore dry plants gain more carbon than moist ones.Curves of CO2 exchange typical for CAM were also obtained with 13 other species of the genus Tillandsia.The exhibition of CAM by the non-succulent T. usneoides calls for a new definition of the term "succulence" if it is to remain useful in characterizing this metabolic pathway. Because CO2-fixing cells of T. usneoides possess relatively large vacuoles and are relatively poor in chloroplasts, they resembles the assimilatory cells of typical CAM-exhibiting succulents. Therefore, if "succulence" only means the capacity of big vacuoles to store malate, the assimilatory cells in T. usneoides are succulent. It seems to be useful to investigate parameters which would allow a definition of the term "succulence" on the level of the cell rather than on the level of the whole plant or plant organs.

Space experiment "Cellular Responses to Radiation in Space (CELLRAD)": Hardware and biological system tests

NASA Astrophysics Data System (ADS)

Hellweg, Christine E.; Dilruba, Shahana; Adrian, Astrid; Feles, Sebastian; Schmitz, Claudia; Berger, Thomas; Przybyla, Bartos; Briganti, Luca; Franz, Markus; Segerer, Jürgen; Spitta, Luis F.; Henschenmacher, Bernd; Konda, Bikash; Diegeler, Sebastian; Baumstark-Khan, Christa; Panitz, Corinna; Reitz, Günther

2015-11-01

One factor contributing to the high uncertainty in radiation risk assessment for long-term space missions is the insufficient knowledge about possible interactions of radiation with other spaceflight environmental factors. Such factors, e.g. microgravity, have to be considered as possibly additive or even synergistic factors in cancerogenesis. Regarding the effects of microgravity on signal transduction, it cannot be excluded that microgravity alters the cellular response to cosmic radiation, which comprises a complex network of signaling pathways. The purpose of the experiment ;Cellular Responses to Radiation in Space; (CELLRAD, formerly CERASP) is to study the effects of combined exposure to microgravity, radiation and general space flight conditions on mammalian cells, in particular Human Embryonic Kidney (HEK) cells that are stably transfected with different plasmids allowing monitoring of proliferation and the Nuclear Factor κB (NF-κB) pathway by means of fluorescent proteins. The cells will be seeded on ground in multiwell plate units (MPUs), transported to the ISS, and irradiated by an artificial radiation source after an adaptation period at 0 × g and 1 × g. After different incubation periods, the cells will be fixed by pumping a formaldehyde solution into the MPUs. Ground control samples will be treated in the same way. For implementation of CELLRAD in the Biolab on the International Space Station (ISS), tests of the hardware and the biological systems were performed. The sequence of different steps in MPU fabrication (cutting, drilling, cleaning, growth surface coating, and sterilization) was optimized in order to reach full biocompatibility. Different coatings of the foil used as growth surface revealed that coating with 0.1 mg/ml poly-D-lysine supports cell attachment better than collagen type I. The tests of prototype hardware (Science Model) proved its full functionality for automated medium change, irradiation and fixation of cells. Exposure of HEK cells to the β-rays emitted by the radiation source dose-dependently decreased cell growth and increased NF-κB activation. The signal of the fluorescent proteins after formaldehyde fixation was stable for at least six months after fixation, allowing storage of the MPUs after fixation for several months before the transport back to Earth and evaluation of the fluorescence intensity. In conclusion, these tests show the feasibility of CELLRAD on the ISS with the currently available transport mechanisms.

Ecohydrological Responses of Dense Canopies to Environmental Variability Part 1: Interplay Between Vertical Structure and Photosynthetic Pathway

USDA-ARS?s Scientific Manuscript database

Vegetation acclimation to changing climate, in particular elevated atmospheric concentrations of carbon dioxide (CO2), has been observed to include modifications to the biochemical and eco physiological functioning of leaves and the structural components of the canopy. These responses have the poten...

Evaluation of photosynthetic efficacy and CO2 removal of microalgae grown in an enriched bicarbonate medium.

PubMed

Abinandan, S; Shanthakumar, S

2016-06-01

Bicarbonate species in the aqueous phase is the primary source for CO 2 for the growth of microalgae. The potential of carbon dioxide (CO 2 ) fixation by Chlorella pyrenoidosa in enriched bicarbonate medium was evaluated. In the present study, effects of parameters such as pH, sodium bicarbonate concentration and inoculum size were assessed for the removal of CO 2 by C. pyrenoidosa under mixotrophic condition. Central composite design tool from response surface methodology was used to validate statistical methods in order to study the influence of these parameters. The obtained results reveal that the maximum removal of CO 2 was attained at pH 8 with sodium bicarbonate concentration of 3.33 g/l, and inoculum size of 30 %. The experimental results were statistically significant with R 2 value of 0.9527 and 0.960 for CO 2 removal and accumulation of chlorophyll content, respectively. Among the various interactions, interactive effects between the parameters pH and inoculum size was statistically significant (P < 0.05) for CO 2 removal and chlorophyll accumulation. Based on the studies, the application of C. pyrenoidosa as a potential source for carbon dioxide removal at alkaline pH from bicarbonate source is highlighted.

Coordinated regulation of growth, activity and transcription in natural populations of the unicellular nitrogen-fixing cyanobacterium Crocosphaera.

PubMed

Wilson, Samuel T; Aylward, Frank O; Ribalet, Francois; Barone, Benedetto; Casey, John R; Connell, Paige E; Eppley, John M; Ferrón, Sara; Fitzsimmons, Jessica N; Hayes, Christopher T; Romano, Anna E; Turk-Kubo, Kendra A; Vislova, Alice; Armbrust, E Virginia; Caron, David A; Church, Matthew J; Zehr, Jonathan P; Karl, David M; DeLong, Edward F

2017-07-31

The temporal dynamics of phytoplankton growth and activity have large impacts on fluxes of matter and energy, yet obtaining in situ metabolic measurements of sufficient resolution for even dominant microorganisms remains a considerable challenge. We performed Lagrangian diel sampling with synoptic measurements of population abundances, dinitrogen (N 2 ) fixation, mortality, productivity, export and transcription in a bloom of Crocosphaera over eight days in the North Pacific Subtropical Gyre (NPSG). Quantitative transcriptomic analyses revealed clear diel oscillations in transcript abundances for 34% of Crocosphaera genes identified, reflecting a systematic progression of gene expression in diverse metabolic pathways. Significant time-lagged correspondence was evident between nifH transcript abundance and maximal N 2 fixation, as well as sepF transcript abundance and cell division, demonstrating the utility of transcriptomics to predict the occurrence and timing of physiological and biogeochemical processes in natural populations. Indirect estimates of carbon fixation by Crocosphaera were equivalent to 11% of net community production, suggesting that under bloom conditions this diazotroph has a considerable impact on the wider carbon cycle. Our cross-scale synthesis of molecular, population and community-wide data underscores the tightly coordinated in situ metabolism of the keystone N 2 -fixing cyanobacterium Crocosphaera, as well as the broader ecosystem-wide implications of its activities.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jennings, Ryan de Montmollin; Moran, James J.; Jay, Zackary J.

Biological fixation of CO 2 is the primary mechanism of C reduction in natural systems, and provides a diverse suite of organic compounds utilized by chemoorganoheterotrophs. The extent and mechanisms of CO 2 fixation were evaluated across a comprehensive set of high-temperature, chemotrophic microbial communities in Yellowstone National Park by combining metagenomic and stable 13C isotope analyses. Fifteen geothermal sites representing three distinct habitat types (iron-oxide mats, anoxic sulfur sediments, and filamentous ‘streamer’ communities) were investigated. Genes of the 3-hydroxypropionate/4-hydroxybutyrate, dicarboxylate/4-hydroxybutyrate, and reverse tricarboxylic acid CO 2 fixation pathways were identified in assembled genome sequence corresponding to the predominant Crenarchaeotamore » and Aquificales observed across this habitat range. Stable 13C analyses of dissolved inorganic and organic C (DIC, DOC), and possible landscape C sources were used to interpret the 13C content of microbial community samples. Isotope mixing models showed that the minimum amounts of autotrophic C in microbial biomass were > 50 % in the majority of communities analyzed, but were also dependent on the amounts of heterotrophy and/or accumulation of landscape C. Furthermore, the significance of CO 2 as a C source in these communities provides a foundation for understanding metabolic linkages among autotrophs and heterotrophs, community assembly and succession, and the likely coevolution of deeply-branching thermophiles.« less

Effect of light on N2 fixation and net nitrogen release of Trichodesmium in a field study

NASA Astrophysics Data System (ADS)

Lu, Yangyang; Wen, Zuozhu; Shi, Dalin; Chen, Mingming; Zhang, Yao; Bonnet, Sophie; Li, Yuhang; Tian, Jiwei; Kao, Shuh-Ji

2018-01-01

Dinitrogen fixation (NF) by marine cyanobacteria is an important pathway to replenish the oceanic bioavailable nitrogen inventory. Light is the key to modulating NF; however, field studies investigating the light response curve (NF-I curve) of NF rate and the effect of light on diazotroph-derived nitrogen (DDN) net release are relatively sparse in the literature, hampering prediction using models. A dissolution method was applied using uncontaminated 15N2 gas to examine how the light changes may influence the NF intensity and DDN net release in the oligotrophic ocean. Experiments were conducted at stations with diazotrophs dominated by filamentous cyanobacterium Trichodesmium spp. in the western Pacific and the South China Sea. The effect of light on carbon fixation (CF) was measured in parallel using the 13C tracer method specifically for a station characterized by Trichodesmium bloom. Both NF-I and CF-I curves showed a Ik (light saturation coefficient) range of 193 to 315 µE m-2 s-1, with light saturation at around 400 µE m-2 s-1. The proportion of DDN net release ranged from ˜ 6 to ˜ 50 %, suggesting an increasing trend as the light intensity decreased. At the Trichodesmium bloom station, we found that the CF / NF ratio was light-dependent and the ratio started to increase as light was lower than the carbon compensation point of 200 µE m-2 s-1. Under low-light stress, Trichodesmium physiologically preferred to allocate more energy for CF to alleviate the intensive carbon consumption by respiration; thus, there is a metabolism tradeoff between CF and NF pathways. Results showed that short-term ( < 24 h) light change modulates the physiological state, which subsequently determined the C / N metabolism and DDN net release by Trichodesmium. Reallocation of energy associated with the variation in light intensity would be helpful for prediction of the global biogeochemical cycle of N by models involving Trichodesmium blooms.

Catabolism of α-Ketoglutarate by a sucA Mutant of Bradyrhizobium japonicum: Evidence for an Alternative Tricarboxylic Acid Cycle

PubMed Central

Green, Laura S.; Li, Youzhong; Emerich, David W.; Bergersen, Fraser J.; Day, David A.

2000-01-01

A complete tricarboxylic acid (TCA) cycle is generally considered necessary for energy production from the dicarboxylic acid substrates malate, succinate, and fumarate. However, a Bradyrhizobium japonicum sucA mutant that is missing α-ketoglutarate dehydrogenase is able to grow on malate as its sole source of carbon. This mutant also fixes nitrogen in symbiosis with soybean, where dicarboxylic acids are its principal carbon substrate. Using a flow chamber system to make direct measurements of oxygen consumption and ammonium excretion, we confirmed that bacteroids formed by the sucA mutant displayed wild-type rates of respiration and nitrogen fixation. Despite the absence of α-ketoglutarate dehydrogenase activity, whole cells of the mutant were able to decarboxylate α-[U-14C]ketoglutarate and [U-14C]glutamate at rates similar to those of wild-type B. japonicum, indicating that there was an alternative route for α-ketoglutarate catabolism. Because cell extracts from B. japonicum decarboxylated [U-14C]glutamate very slowly, the γ-aminobutyrate shunt is unlikely to be the pathway responsible for α-ketoglutarate catabolism in the mutant. In contrast, cell extracts from both the wild type and mutant showed a coenzyme A (CoA)-independent α-ketoglutarate decarboxylation activity. This activity was independent of pyridine nucleotides and was stimulated by thiamine PPi. Thin-layer chromatography showed that the product of α-ketoglutarate decarboxylation was succinic semialdehyde. The CoA-independent α-ketoglutarate decarboxylase, along with succinate semialdehyde dehydrogenase, may form an alternative pathway for α-ketoglutarate catabolism, and this pathway may enhance TCA cycle function during symbiotic nitrogen fixation. PMID:10781553

Reservoir-Scale Biological Community Response to Trace Element Additions in a Northern Montana Oil Field

NASA Astrophysics Data System (ADS)

Connors, D. E.; Bradfish, J.; DeBruyn, R. P.; Zemetra, J.; Mitchell, H.

2017-12-01

In subsurface oil bearing formations, microbial growth and metabolism is restricted due to a lack of elements other than carbon, hydrogen, and oxygen required for cell structure and as cofactors. A chemical treatment that adds these elements back into the formation was deployed into an oil reservoir in Northern Montana, with the intent of increasing biogenic methane generation. Samples of water from producing wells in the reservoir were collected anaerobically, and analyzed for geochemical content, and cells from the water were collected and analyzed via 16S rRNA gene DNA sequencing to determine the makeup of the microbial community over the course of twelve months of treatment, and for two years after. Prior to chemical treatment, this reservoir was depleted in elements required for enzyme co-factors in the methanogenesis metabolic pathway (Co, Mo, Ni, W, Zn) as well as nitrogen and phosphorus. Most the microbial community was composed of chemoheterotrophic bacteria associated with the biodegradation of large carbon molecules, with a small community of acetoclastic methanogens. During and after additions of the depleted elements, the metabolism of the community in the reservoir shifted towards chemoautotrophs and hydrogenotrophic methanogens, and the cell density increased. After treatment was ended, cell counts stabilized at a new equilibrium concentration, and the autotrophic metabolism was maintained. The pre-treatment community was dependent on energy input from solubilized oil molecules, whereas the post-treatment community more effectively utilized dissolved organics and carbon dioxide as carbon sources for fixation and respiration. This study demonstrates the capability of microbial communities to rapidly reorganize in the environment when provided with an influx of the elements required for growth and metabolism.

Processes regulating progressive nitrogen limitation under elevated carbon dioxide: a meta-analysis

NASA Astrophysics Data System (ADS)

Liang, J.; Qi, X.; Souza, L.; Luo, Y.

2015-10-01

Nitrogen (N) cycle has the potential to regulate climate change through its influence on carbon (C) sequestration. Although extensive researches have been done to explore whether or not progressive N limitation (PNL) occurs under CO2 enrichment, a comprehensive assessment of the processes that regulate PNL is still lacking. Here, we quantitatively synthesized the responses of all major processes and pools in terrestrial N cycle with meta-analysis of CO2 experimental data available in the literature. The results showed that CO2 enrichment significantly increased N sequestration in plant and litter pools but not in soil pool. Thus, the basis of PNL occurrence partially exists. However, CO2 enrichment also significantly increased the N influx via biological N fixation, but decreased the N efflux via leaching. In addition, no general diminished CO2 fertilization effect on plant growth over time was observed. Overall, our analyses suggest that the extra N supply by the increased biological N fixation and decreased leaching may potentially alleviate PNL under elevated CO2 conditions. Moreover, our synthesis showed that CO2 enrichment increased soil ammonium (NH4+) but decreased nitrate (NO3-). The different responses of NH4+ and NO3-, and the consequent biological processes, may result in changes in soil microenvironment, community structures and above-belowground interactions, which could potentially affect the terrestrial biogeochemical cycles and the feedback to climate change.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tabita, Fred Robert

The overall objective of this project is to determine the mechanism by which a transcriptional activator protein affects CO 2 fixation (cbb) gene expression in nonsulfur purple photosynthetic bacteria, with special emphasis to Rhodobacter sphaeroides and with comparison to Rhodopseudomonas palustris. These studies culminated in several publications which indicated that additional regulators interact with the master regulator CbbR in both R. sphaeroides and R. palustris. In addition, the interactive control of the carbon and nitrogen assimilatory pathways was studied and unique regulatory signals were discovered.

Concerted changes in N and C primary metabolism in alfalfa (Medicago sativa) under water restriction.

PubMed

Aranjuelo, Iker; Tcherkez, Guillaume; Molero, Gemma; Gilard, Françoise; Avice, Jean-Christophe; Nogués, Salvador

2013-02-01

Although the mechanisms of nodule N(2) fixation in legumes are now well documented, some uncertainty remains on the metabolic consequences of water deficit. In most cases, little consideration is given to other organs and, therefore, the coordinated changes in metabolism in leaves, roots, and nodules are not well known. Here, the effect of water restriction on exclusively N(2)-fixing alfalfa (Medicago sativa L.) plants was investigated, and proteomic, metabolomic, and physiological analyses were carried out. It is shown that the inhibition of nitrogenase activity caused by water restriction was accompanied by concerted alterations in metabolic pathways in nodules, leaves, and roots. The data suggest that nodule metabolism and metabolic exchange between plant organs nearly reached homeostasis in asparagine synthesis and partitioning, as well as the N demand from leaves. Typically, there was (i) a stimulation of the anaplerotic pathway to sustain the provision of C skeletons for amino acid (e.g. glutamate and proline) synthesis; (ii) re-allocation of glycolytic products to alanine and serine/glycine; and (iii) subtle changes in redox metabolites suggesting the implication of a slight oxidative stress. Furthermore, water restriction caused little change in both photosynthetic efficiency and respiratory cost of N(2) fixation by nodules. In other words, the results suggest that under water stress, nodule metabolism follows a compromise between physiological imperatives (N demand, oxidative stress) and the lower input to sustain catabolism.

OXALOACETATE DECARBOXYLATION AND OXALOACETATE-CARBON DIOXIDE EXCHANGE IN ACETOBACTER XYLINUM

PubMed Central

Benziman, Moshe; Heller, N.

1964-01-01

Benziman, Moshe (The Hebrew University of Jerusalem, Jerusalem, Israel), and N. Heller. Oxaloacetate decarboxylation and oxaloacetate-carbon dioxide exchange in Acetobacter xylinum. J. Bacteriol. 88:1678–1687. 1964.—Extracts of Acetobacter xylinum, prepared by sonic treatment, were shown to catalyze the decarboxylation of oxaloacetate (OAA) to pyruvate and CO2, and the exchange of C14-carbon dioxide into the β-carboxyl of OAA. Fractionation of the extracts with ammonium sulfate resulted in a 10-fold increase of the specific activity of the enzyme system catalyzing the CO2 exchange and OAA decarboxylation reactions. The purified preparation catalyzed the exchange of pyruvate-3-C14 into OAA. Similar pH curves with a pH optimum of 5.6 were obtained for the CO2 exchange and OAA decarboxylation reactions. Both reactions require the presence of Mn2+ or Mg2+ ions. OAA decarboxylation was more strongly inhibited than the exchange of CO2 by dialysis or metal-chelating agents. Avidin did not inhibit either reaction. Adenosine triphosphate (ATP), adenosine diphosphate (ADP), guanosine triphosphate (GTP), guanosine diphosphate (GDP), pyrophosphate, or inorganic phosphate did not promote OAA decarboxylation and the CO2-exchange reaction catalyzed by the purified preparation. The purified preparation failed to catalyze the carboxylation of phosphoenolpyruvate in the presence of GDP, ADP, or inorganic phosphate, and that of pyruvate in the presence of ATP or GTP, even when supplemented with an OAA-trapping system. A scheme for OAA decarboxylation which could account for the observed exchange reactions and for the failure to obtain net fixation of CO2 is proposed. The relation between the exchange reaction and the synthesis of cellulose from pyruvate by A. xylinum is discussed. PMID:14240957

Effects of Elevated Carbon Dioxide on Photosynthesis and Carbon Partitioning: A Perspective on Root Sugar Sensing and Hormonal Crosstalk

PubMed Central

Thompson, Michael; Gamage, Dananjali; Hirotsu, Naoki; Martin, Anke; Seneweera, Saman

2017-01-01

Plant responses to atmospheric carbon dioxide will be of great concern in the future, as carbon dioxide concentrations ([CO2]) are predicted to continue to rise. Elevated [CO2] causes increased photosynthesis in plants, which leads to greater production of carbohydrates and biomass. Which organ the extra carbohydrates are allocated to varies between species, but also within species. These carbohydrates are a major energy source for plant growth, but they also act as signaling molecules and have a range of uses beyond being a source of carbon and energy. Currently, there is a lack of information on how the sugar sensing and signaling pathways of plants are affected by the higher content of carbohydrates produced under elevated [CO2]. Particularly, the sugar signaling pathways of roots are not well understood, along with how they are affected by elevated [CO2]. At elevated [CO2], some plants allocate greater amounts of sugars to roots where they are likely to act on gene regulation and therefore modify nutrient uptake and transport. Glucose and sucrose also promote root growth, an effect similar to what occurs under elevated [CO2]. Sugars also crosstalk with hormones to regulate root growth, but also affect hormone biosynthesis. This review provides an update on the role of sugars as signaling molecules in plant roots and thus explores the currently known functions that may be affected by elevated [CO2]. PMID:28848452

Effects of Elevated Carbon Dioxide on Photosynthesis and Carbon Partitioning: A Perspective on Root Sugar Sensing and Hormonal Crosstalk.

PubMed

Thompson, Michael; Gamage, Dananjali; Hirotsu, Naoki; Martin, Anke; Seneweera, Saman

2017-01-01

Plant responses to atmospheric carbon dioxide will be of great concern in the future, as carbon dioxide concentrations ([CO 2 ]) are predicted to continue to rise. Elevated [CO 2 ] causes increased photosynthesis in plants, which leads to greater production of carbohydrates and biomass. Which organ the extra carbohydrates are allocated to varies between species, but also within species. These carbohydrates are a major energy source for plant growth, but they also act as signaling molecules and have a range of uses beyond being a source of carbon and energy. Currently, there is a lack of information on how the sugar sensing and signaling pathways of plants are affected by the higher content of carbohydrates produced under elevated [CO 2 ]. Particularly, the sugar signaling pathways of roots are not well understood, along with how they are affected by elevated [CO 2 ]. At elevated [CO 2 ], some plants allocate greater amounts of sugars to roots where they are likely to act on gene regulation and therefore modify nutrient uptake and transport. Glucose and sucrose also promote root growth, an effect similar to what occurs under elevated [CO 2 ]. Sugars also crosstalk with hormones to regulate root growth, but also affect hormone biosynthesis. This review provides an update on the role of sugars as signaling molecules in plant roots and thus explores the currently known functions that may be affected by elevated [CO 2 ].

High solubility pathway for the carbon dioxide free production of iron.

PubMed

Licht, Stuart; Wang, Baohui

2010-10-07

We report a fundamental change in the understanding of iron oxide thermochemistry, opening a facile, new CO(2)-free route to iron production. The resultant process can eliminate a major global source of greenhouse gas emission, producing the staple iron in molten media at high rate and low electrolysis energy.

Selection of Sustainable Processes using Sustainability Footprint Method: A Case Study of Methanol Production from Carbon Dioxide

EPA Science Inventory

Chemical products can be obtained by process pathways involving varying amounts and types of resources, utilities, and byproduct formation. When such competing process options such as six processes for making methanol as are considered in this study, it is necessary to identify t...

Recycling carbon dioxide during xylose fermentation by engineered Saccharomyces cerevisiae

USDA-ARS?s Scientific Manuscript database

In this study, we introduced the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and phosphoribulokinase (PRK) into an engineered S. cerevisiae (SR8) harboring the XR/XDH pathway and up-regulated PPP 10, to enable CO2 recycling through a synthetic rPPP during xylose fermentation (Fig. 1). ...

Partitioning evapotranspiration using long-term carbon dioxide and water vapor fluxes: New approach to ET partitioning

USDA-ARS?s Scientific Manuscript database

The separate components of evapotranspiration (ET) provide critical information about the pathways and time scales over which water is returned to the atmosphere, but ecosystem-scale measurements of transpiration (T) and evaporation (E) remain elusive. We propose a novel determination of average E a...

Titanium dioxide nanoparticles stimulate sea urchin immune cell phagocytic activity involving TLR/p38 MAPK-mediated signalling pathway

PubMed Central

Pinsino, Annalisa; Russo, Roberta; Bonaventura, Rosa; Brunelli, Andrea; Marcomini, Antonio; Matranga, Valeria

2015-01-01

Titanium dioxide nanoparticles (TiO2NPs) are one of the most widespread-engineered particles in use for drug delivery, cosmetics, and electronics. However, TiO2NP safety is still an open issue, even for ethical reasons. In this work, we investigated the sea urchin Paracentrotus lividus immune cell model as a proxy to humans, to elucidate a potential pathway that can be involved in the persistent TiO2NP-immune cell interaction in vivo. Morphology, phagocytic ability, changes in activation/inactivation of a few mitogen-activated protein kinases (p38 MAPK, ERK), variations of other key proteins triggering immune response (Toll-like receptor 4-like, Heat shock protein 70, Interleukin-6) and modifications in the expression of related immune response genes were investigated. Our findings indicate that TiO2NPs influence the signal transduction downstream targets of p38 MAPK without eliciting an inflammatory response or other harmful effects on biological functions. We strongly recommend sea urchin immune cells as a new powerful model for nano-safety/nano-toxicity investigations without the ethical normative issue. PMID:26412401

Angiotensin-converting Enzyme Inhibition Improves the Effectiveness of Transcutaneous Carbon Dioxide Treatment.

PubMed

Nemeth, Balazs; Kiss, Istvan; Jencsik, Timea; Peter, Ivan; Kreska, Zita; Koszegi, Tamas; Miseta, Attila; Kustan, Peter; Boncz, Imre; Laczo, Andrea; Ajtay, Zeno

2017-01-01

To study the effect of carbon dioxide (CO 2 ) therapy on the nitric oxide (NO) pathway by monitoring plasma asymmetric dimethylarginine (ADMA) concentrations. Forty-seven hypertensive patients who underwent transcutaneous CO 2 therapy were enrolled. Thirty healthy individuals were recruited for the control group. Blood samples were taken one hour before, as well as one hour, 24 hours and 3 weeks after the first CO 2 treatment. Controls did not undergo CO 2 treatment. Plasma ADMA levels were measured by ELISA. ADMA levels decreased significantly one hour after the first CO2 treatment compared to the baseline concentrations (p=0.003). Significantly greater reduction was found among patients in whom angiotensin converting enzyme inhibitors (ACEIs) were administered (p=0.019). The short- and long-term decrease of ADMA levels suggests that CO 2 is not only a vasodilator, but also has a beneficial effect on the NO pathway. ACE inhibition seems to enhance the effect of CO 2 treatment. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

Induced Infiltration of Hole-Transporting Polymer into Photocatalyst for Staunch Polymer-Metal Oxide Hybrid Solar Cells.

PubMed

Park, Jong Hwan; Jung, Youngsuk; Yang, Yooseong; Shin, Hyun Suk; Kwon, Soonchul

2016-10-05

For efficient solar cells based on organic semiconductors, a good mixture of photoactive materials in the bulk heterojunction on the length scale of several tens of nanometers is an important requirement to prevent exciton recombination. Herein, we demonstrate that nanoporous titanium dioxide inverse opal structures fabricated using a self-assembled monolayer method and with enhanced infiltration of electron-donating polymers is an efficient electron-extracting layer, which enhances the photovoltaic performance. A calcination process generates an inverse opal structure of titanium dioxide (<70 nm of pore diameters) providing three-dimensional (3D) electron transport pathways. Hole-transporting polymers was successfully infiltrated into the pores of the surface-modified titanium dioxide under vacuum conditions at 200 °C. The resulting geometry expands the interfacial area between hole- and electron-transport materials, increasing the thickness of the active layer. The controlled polymer-coating process over titanium dioxide materials enhanced photocurrent of the solar cell device. Density functional theory calculations show improved interfacial adhesion between the self-assembled monolayer-modified surface and polymer molecules, supporting the experimental result of enhanced polymer infiltration into the voids. These results suggest that the 3D inverse opal structure of the surface-modified titanium dioxide can serve as a favorable electron-extracting layer in further enhancing optoelectronic performance based on organic or organic-inorganic hybrid solar cell.

Highly Efficient Catalytic Cyclic Carbonate Formation by Pyridyl Salicylimines.

PubMed

Subramanian, Saravanan; Park, Joonho; Byun, Jeehye; Jung, Yousung; Yavuz, Cafer T

2018-03-21

Cyclic carbonates as industrial commodities offer a viable nonredox carbon dioxide fixation, and suitable heterogeneous catalysts are vital for their widespread implementation. Here, we report a highly efficient heterogeneous catalyst for CO 2 addition to epoxides based on a newly identified active catalytic pocket consisting of pyridine, imine, and phenol moieties. The polymeric, metal-free catalyst derived from this active site converts less-reactive styrene oxide under atmospheric pressure in quantitative yield and selectivity to the corresponding carbonate. The catalyst does not need additives, solvents, metals, or co-catalysts, can be reused at least 10 cycles without the loss of activity, and scaled up easily to a kilogram scale. Density functional theory calculations reveal that the nucleophilicity of pyridine base gets stronger due to the conjugated imines and H-bonding from phenol accelerates the reaction forward by stabilizing the intermediate.

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

PubMed

Karl, David M

2014-01-01

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

Contribution and pathways of diazotroph-derived nitrogen to zooplankton during the VAHINE mesocosm experiment in the oligotrophic New Caledonia lagoon

NASA Astrophysics Data System (ADS)

Hunt, Brian P. V.; Bonnet, Sophie; Berthelot, Hugo; Conroy, Brandon J.; Foster, Rachel A.; Pagano, Marc

2016-05-01

In oligotrophic tropical and subtropical oceans, where strong stratification can limit the replenishment of surface nitrate, dinitrogen (N2) fixation by diazotrophs can represent a significant source of nitrogen (N) for primary production. The VAHINE (VAriability of vertical and tropHIc transfer of fixed N2 in the south-wEst Pacific) experiment was designed to examine the fate of diazotroph-derived nitrogen (DDN) in such ecosystems. In austral summer 2013, three large ( ˜ 50 m3) in situ mesocosms were deployed for 23 days in the New Caledonia lagoon, an ecosystem that typifies the low-nutrient, low-chlorophyll environment, to stimulate diazotroph production. The zooplankton component of the study aimed to measure the incorporation of DDN into zooplankton biomass, and assess the role of direct diazotroph grazing by zooplankton as a DDN uptake pathway. Inside the mesocosms, the diatom-diazotroph association (DDA) het-1 predominated during days 5-15 while the unicellular diazotrophic cyanobacteria UCYN-C predominated during days 15-23. A Trichodesmium bloom was observed in the lagoon (outside the mesocosms) towards the end of the experiment. The zooplankton community was dominated by copepods (63 % of total abundance) for the duration of the experiment. Using two-source N isotope mixing models we estimated a mean ˜ 28 % contribution of DDN to zooplankton nitrogen biomass at the start of the experiment, indicating that the natural summer peak of N2 fixation in the lagoon was already contributing significantly to the zooplankton. Stimulation of N2 fixation in the mesocosms corresponded with a generally low-level enhancement of DDN contribution to zooplankton nitrogen biomass, but with a peak of ˜ 73 % in mesocosm 1 following the UCYN-C bloom. qPCR analysis targeting four of the common diazotroph groups present in the mesocosms (Trichodesmium, het-1, het-2, UCYN-C) demonstrated that all four were ingested by copepod grazers, and that their abundance in copepod stomachs generally corresponded with their in situ abundance. 15N2 labelled grazing experiments therefore provided evidence for direct ingestion and assimilation of UCYN-C-derived N by the zooplankton, but not for het-1 and Trichodesmium, supporting an important role of secondary pathways of DDN to the zooplankton for the latter groups, i.e. DDN contributions to the dissolved N pool and uptake by nondiazotrophs. This study appears to provide the first evidence of direct UCYN-C grazing by zooplankton, and indicates that UCYN-C-derived N contributes significantly to the zooplankton food web in the New Caledonia lagoon through a combination of direct grazing and secondary pathways.

Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

NASA Astrophysics Data System (ADS)

Davis, R.; Tebo, B. M.

2013-12-01

Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn oxidases McoA and MopA. The greater diversity of Mn oxidase pathways in this metagenome suggests a more diverse Mn oxidizing microbial community in the cold pumice sample. Key enzymes for four of the six known carbon fixation pathways (the Calvin Cycle, the reductive TCA cycle, the Wood-Ljungdahl pathway, and the 3-hydroxypropionate/4-hydroxybutyrate Cycle) were also identified in both samples indicating primary production occurs via a diverse community of carbon fixing organisms. Together, these samples contain active, diverse populations of Mn oxidizing bacteria living in association with microbial communities supported by chemoautotrophic carbon fixation.

Nitrogen cycling in Sandusky Bay, Lake Erie: oscillations between strong and weak export and implications for harmful algal blooms

NASA Astrophysics Data System (ADS)

Salk, Kateri R.; Bullerjahn, George S.; McKay, Robert Michael L.; Chaffin, Justin D.; Ostrom, Nathaniel E.

2018-05-01

Recent global water quality crises point to an urgent need for greater understanding of cyanobacterial harmful algal blooms (cHABs) and their drivers. Nearshore areas of Lake Erie such as Sandusky Bay may become seasonally limited by nitrogen (N) and are characterized by distinct cHAB compositions (i.e., Planktothrix over Microcystis). This study investigated phytoplankton N uptake pathways, determined drivers of N depletion, and characterized the N budget in Sandusky Bay. Nitrate (NO3-) and ammonium (NH4+) uptake, N fixation, and N removal processes were quantified by stable isotopic approaches. Dissimilatory N reduction was a relatively modest N sink, with denitrification, anammox, and N2O production accounting for 84, 14, and 2 % of sediment N removal, respectively. Phytoplankton assimilation was the dominant N uptake mechanism, and NO3- uptake rates were higher than NH4+ uptake rates. Riverine N loading was sometimes insufficient to meet assimilatory and dissimilatory demands, but N fixation alleviated this deficit. N fixation made up 23.7-85.4 % of total phytoplankton N acquisition and indirectly supports Planktothrix blooms. However, N fixation rates were surprisingly uncorrelated with NO3- or NH4+ concentrations. Owing to temporal separation in sources and sinks of N to Lake Erie, Sandusky Bay oscillates between a conduit and a filter of downstream N loading to Lake Erie, delivering extensively recycled forms of N during periods of low export. Drowned river mouths such as Sandusky Bay are mediators of downstream N loading, but climate-change-induced increases in precipitation and N loading will likely intensify N export from these systems.

Evidence of carbon fixation pathway in a bacterium from candidate phylum SBR1093 revealed with genomic analysis.

PubMed

Wang, Zhiping; Guo, Feng; Liu, Lili; Zhang, Tong

2014-01-01

Autotrophic CO2 fixation is the most important biotransformation process in the biosphere. Research focusing on the diversity and distribution of relevant autotrophs is significant to our comprehension of the biosphere. In this study, a draft genome of a bacterium from candidate phylum SBR1093 was reconstructed with the metagenome of an industrial activated sludge. Based on comparative genomics, this autotrophy may occur via a newly discovered carbon fixation path, the hydroxypropionate-hydroxybutyrate (HPHB) cycle, which was demonstrated in a previous work to be uniquely possessed by some genera from Archaea. This bacterium possesses all of the thirteen enzymes required for the HPHB cycle; these enzymes share 30∼50% identity with those in the autotrophic species of Archaea that undergo the HPHB cycle and 30∼80% identity with the corresponding enzymes of the mixotrophic species within Bradyrhizobiaceae. Thus, this bacterium might have an autotrophic growth mode in certain conditions. A phylogenetic analysis based on the 16S rRNA gene reveals that the phylotypes within candidate phylum SBR1093 are primarily clustered into 5 clades with a shallow branching pattern. This bacterium is clustered with phylotypes from organically contaminated environments, implying a demand for organics in heterotrophic metabolism. Considering the types of regulators, such as FnR, Fur, and ArsR, this bacterium might be a facultative aerobic mixotroph with potential multi-antibiotic and heavy metal resistances. This is the first report on Bacteria that may perform potential carbon fixation via the HPHB cycle, thus may expand our knowledge of the distribution and importance of the HPHB cycle in the biosphere.

CO2 Injection Into CH4 Hydrate Reservoirs: Quantifying Controls of Micro-Scale Processes

NASA Astrophysics Data System (ADS)

Bigalke, N. K.; Deusner, C.; Kossel, E.; Haeckel, M.

2014-12-01

The exchangeability of methane for carbon dioxide in gas hydrates opens the possibility of producing emission-neutral hydrocarbon energy. Recent field tests have shown that the production of natural gas from gas hydrates is feasible via injection of carbon dioxide into sandy, methane-hydrate-bearing sediment strata. Industrial-scale application of this method requires identification of thermo- and fluid-dynamic as well as kinetic controls on methane yield from and carbon dioxide retention within the reservoir. Extraction of gas via injection of carbon dioxide into the hydrate reservoir triggers a number of macroscopic effects, which are revealed for example by changes of the hydraulic conductivity and geomechanical stability. Thus far, due to analytical limitations, localized reactions and fluid-flow phenomena held responsible for these effects remain unresolved on the microscale (1 µm - 1 mm) and at near-natural reservoir conditions. We address this deficit by showing results from high-resolution, two-dimensional Raman spectroscopy mappings of an artificial hydrate reservoir during carbon dioxide injection under realistic reservoir conditions. The experiments allow us to resolve hydrate conversion rate and efficiency as well as activation of fluid pathways in space and time and their effect on methane yield, carbon-dioxide retention and hydraulic conductivity of the reservoir. We hypothesize that the conversion of single hydrate grains is a diffusion-controlled process which starts at the grain surface before continuing into the grain interior and show that the conversion can be modeled simply by using published permeation coefficients for CO2 and CH4 in hydrate and grain size as only input parameters.

Biological nitrogen fixation in sugar cane: A key to energetically viable biofuel production

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boddey, R.M.

1995-05-01

The advantages of producing biofuels to replace fossil energy sources are derived from the fact that the energy accumulated in the biomass in captured directly from photosynthesis and is thus renewable, and that the cycle of carbon dioxide fixation by the crop, followed by burning of the fuel makes no overall contribution to atmospheric CO{sub 2} or, consequently, to global warming. However, these advantages are negated if large quantities of fossil fuels need to be used to grow or process the biofuel crop. In this regard, the Brazilian bioethanol program, based on the fermentation/distillation of sugar cane juice, is particularlymore » favorable, not only because the crop is principally hand harvested, but also because of the low nitrogen fertilizer use on sugar cane in Brazil. Recent {sup 15}N and N balance studies have shown that in some Brazilian cane varieties, high yields are possible without N fertilization because the plants are able to obtain large contributions of nitrogen from plant-associated biological N{sub 2} fixation (BNF). The N{sub 2}-fixing acid-tolerant bacterium Acetobacter diazotrophicus was first found to occur within roots, stems, and leaves of sugar cane. Subsequently, two species of Herbaspirillum also have been found to occur within the interior of all sugar cane tissues. The discovery of these, and other N{sub 2}-fixing bacteria that survive poorly in soil but thrive within plant tissue (endophytic bacteria), may account for the high BNF contributions observed in sugar cane. Further study of this system should allow the gradual elimination of N fertilizer use on sugar cane, at least in Brazil, and opens up the possibility of the extension of this efficient N{sub 2}-fixing system to cereal and other crops with consequent immense potential benefits to tropical agriculture. 44 refs., 9 figs., 4 tabs.« less

Accelerated carbonation using municipal solid waste incinerator bottom ash and cold-rolling wastewater: Performance evaluation and reaction kinetics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, E-E; Pan, Shu-Yuan; Yang, Liuhanzi

2015-09-15

Highlights: • Carbonation was performed using CO{sub 2}, wastewater and bottom ash in a slurry reactor. • A maximum capture capacity of 102 g CO{sub 2} per kg BA was achieved at mild conditions. • A maximum carbonation conversion of MSWI-BA was predicted to be 95% by RSM. • The CO{sub 2} emission from Bali incinerator could be expected to reduce by 6480 ton/y. • The process energy consumption per ton CO{sub 2} captured was estimated to be 180 kW h. - Abstract: Accelerated carbonation of alkaline wastes including municipal solid waste incinerator bottom ash (MSWI-BA) and the cold-rolling wastewatermore » (CRW) was investigated for carbon dioxide (CO{sub 2}) fixation under different operating conditions, i.e., reaction time, CO{sub 2} concentration, liquid-to-solid ratio, particle size, and CO{sub 2} flow rate. The MSWI-BA before and after carbonation process were analyzed by the thermogravimetry and differential scanning calorimetry, X-ray diffraction, and scanning electron microscopy equipped with energy dispersive X-ray spectroscopy. The MSWI-BA exhibits a high carbonation conversion of 90.7%, corresponding to a CO{sub 2} fixation capacity of 102 g per kg of ash. Meanwhile, the carbonation kinetics was evaluated by the shrinking core model. In addition, the effect of different operating parameters on carbonation conversion of MSWI-BA was statistically evaluated by response surface methodology (RSM) using experimental data to predict the maximum carbonation conversion. Furthermore, the amount of CO{sub 2} reduction and energy consumption for operating the proposed process in refuse incinerator were estimated. Capsule abstract: CO{sub 2} fixation process by alkaline wastes including bottom ash and cold-rolling wastewater was developed, which should be a viable method due to high conversion.« less

Engineering photorespiration: current state and future possibilities.

PubMed

Peterhansel, C; Krause, K; Braun, H-P; Espie, G S; Fernie, A R; Hanson, D T; Keech, O; Maurino, V G; Mielewczik, M; Sage, R F

2013-07-01

Reduction of flux through photorespiration has been viewed as a major way to improve crop carbon fixation and yield since the energy-consuming reactions associated with this pathway were discovered. This view has been supported by the biomasses increases observed in model species that expressed artificial bypass reactions to photorespiration. Here, we present an overview about the major current attempts to reduce photorespiratory losses in crop species and provide suggestions for future research priorities. © 2012 German Botanical Society and The Royal Botanical Society of the Netherlands.

Effect of Engineered Nanoparticles on Exopolymeric Substances Release from Marine Phytoplankton

NASA Astrophysics Data System (ADS)

Chiu, Meng-Hsuen; Khan, Zafir A.; Garcia, Santiago G.; Le, Andre D.; Kagiri, Agnes; Ramos, Javier; Tsai, Shih-Ming; Drobenaire, Hunter W.; Santschi, Peter H.; Quigg, Antonietta; Chin, Wei-Chun

2017-12-01

Engineered nanoparticles (ENPs), products from modern nanotechnologies, can potentially impact the marine environment to pose serious threats to marine ecosystems. However, the cellular responses of marine phytoplankton to ENPs are still not well established. Here, we investigate four different diatom species ( Odontella mobiliensis, Skeletonema grethae, Phaeodactylum tricornutum, Thalassiosira pseudonana) and one green algae ( Dunaliella tertiolecta) for their extracellular polymeric substances (EPS) release under model ENP treatments: 25 nm titanium dioxide (TiO2), 10-20 nm silicon dioxide (SiO2), and 15-30 nm cerium dioxide (CeO2). We found SiO2 ENPs can significantly stimulate EPS release from these algae (200-800%), while TiO2 ENP exposure induced the lowest release. Furthermore, the increase of intracellular Ca2+ concentration can be triggered by ENPs, suggesting that the EPS release process is mediated through Ca2+ signal pathways. With better understanding of the cellular mechanism mediated ENP-induced EPS release, potential preventative and safety measures can be developed to mitigate negative impact on the marine ecosystem.

FINE STRUCTURAL LOCALIZATION OF ACYLTRANSFERASES

PubMed Central

Higgins, Joan A.; Barrnett, Russell J.

1971-01-01

A study of the fine structural localization of the acyltransferases of the monoglyceride and α-glycerophosphate pathways for triglyceride synthesis in the intestinal absorptive cell is reported. Glutaraldehyde-fixed tissue was found to synthesize diglyceride and triglyceride from monopalmitin and palmityl CoA, and parallel morphological studies showed the appearance of lipid droplets in the smooth endoplasmic reticulum of the absorptive cell. Glutaraldehyde-fixed tissue also synthesized triglyceride from α-glycerophosphate, although this enzyme system was more susceptible to fixation than the monoglyceride pathway acyltransferases. Cytochemical methods for the localization of free CoA were based (a) on the formation of the insoluble lanthanium mercaptide of CoA and (b) on the reduction of ferricyanide by CoA to yield ferrocyanide which forms an insoluble precipitate with manganous ions. By these methods the monoglyceride pathway acyltransferases were found to be located mainly on the inner surface of the smooth endoplasmic reticulum. The α-glycerophosphate pathway acyltransferases were localized mainly on the rough endoplasmic reticulum. Activity limited to the outer cisternae of the Golgi membranes occurred with both pathways. The possible organization of triglyceride absorption and chylomicron synthesis is discussed in view of these results. PMID:5563442

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT

PubMed Central

2017-01-01

ABSTRACT Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647T (here referred to as Leptospirillum ferriphilumT) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilumT obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS2). Adaptations of Leptospirillum ferriphilumT to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced. IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilumT coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilumT for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction. PMID:29150517

Effects of model structural uncertainty on carbon cycle projections: biological nitrogen fixation as a case study

NASA Astrophysics Data System (ADS)

Wieder, William R.; Cleveland, Cory C.; Lawrence, David M.; Bonan, Gordon B.

2015-04-01

Uncertainties in terrestrial carbon (C) cycle projections increase uncertainty of potential climate feedbacks. Efforts to improve model performance often include increased representation of biogeochemical processes, such as coupled carbon-nitrogen (N) cycles. In doing so, models are becoming more complex, generating structural uncertainties in model form that reflect incomplete knowledge of how to represent underlying processes. Here, we explore structural uncertainties associated with biological nitrogen fixation (BNF) and quantify their effects on C cycle projections. We find that alternative plausible structures to represent BNF result in nearly equivalent terrestrial C fluxes and pools through the twentieth century, but the strength of the terrestrial C sink varies by nearly a third (50 Pg C) by the end of the twenty-first century under a business-as-usual climate change scenario representative concentration pathway 8.5. These results indicate that actual uncertainty in future C cycle projections may be larger than previously estimated, and this uncertainty will limit C cycle projections until model structures can be evaluated and refined.

Ammonia formation by a thiolate-bridged diiron amide complex as a nitrogenase mimic

NASA Astrophysics Data System (ADS)

Li, Yang; Li, Ying; Wang, Baomin; Luo, Yi; Yang, Dawei; Tong, Peng; Zhao, Jinfeng; Luo, Lun; Zhou, Yuhan; Chen, Si; Cheng, Fang; Qu, Jingping

2013-04-01

Although nitrogenase enzymes routinely convert molecular nitrogen into ammonia under ambient temperature and pressure, this reaction is currently carried out industrially using the Haber-Bosch process, which requires extreme temperatures and pressures to activate dinitrogen. Biological fixation occurs through dinitrogen and reduced NxHy species at multi-iron centres of compounds bearing sulfur ligands, but it is difficult to elucidate the mechanistic details and to obtain stable model intermediate complexes for further investigation. Metal-based synthetic models have been applied to reveal partial details, although most models involve a mononuclear system. Here, we report a diiron complex bridged by a bidentate thiolate ligand that can accommodate HN=NH. Following reductions and protonations, HN=NH is converted to NH3 through pivotal intermediate complexes bridged by N2H3- and NH2- species. Notably, the final ammonia release was effected with water as the proton source. Density functional theory calculations were carried out, and a pathway of biological nitrogen fixation is proposed.

A Deeply Branching Thermophilic Bacterium with an Ancient Acetyl-CoA Pathway Dominates a Subsurface Ecosystem

PubMed Central

Takami, Hideto; Noguchi, Hideki; Takaki, Yoshihiro; Uchiyama, Ikuo; Toyoda, Atsushi; Nishi, Shinro; Chee, Gab-Joo; Arai, Wataru; Nunoura, Takuro; Itoh, Takehiko; Hattori, Masahira; Takai, Ken

2012-01-01

A nearly complete genome sequence of Candidatus ‘Acetothermum autotrophicum’, a presently uncultivated bacterium in candidate division OP1, was revealed by metagenomic analysis of a subsurface thermophilic microbial mat community. Phylogenetic analysis based on the concatenated sequences of proteins common among 367 prokaryotes suggests that Ca. ‘A. autotrophicum’ is one of the earliest diverging bacterial lineages. It possesses a folate-dependent Wood-Ljungdahl (acetyl-CoA) pathway of CO2 fixation, is predicted to have an acetogenic lifestyle, and possesses the newly discovered archaeal-autotrophic type of bifunctional fructose 1,6-bisphosphate aldolase/phosphatase. A phylogenetic analysis of the core gene cluster of the acethyl-CoA pathway, shared by acetogens, methanogens, some sulfur- and iron-reducers and dechlorinators, supports the hypothesis that the core gene cluster of Ca. ‘A. autotrophicum’ is a particularly ancient bacterial pathway. The habitat, physiology and phylogenetic position of Ca. ‘A. autotrophicum’ support the view that the first bacterial and archaeal lineages were H2-dependent acetogens and methanogenes living in hydrothermal environments. PMID:22303444

Effects of the biosynthesis and signaling pathway of ecdysterone on silkworm (Bombyx mori) following exposure to titanium dioxide nanoparticles.

PubMed

Li, Fanchi; Gu, Zhiya; Wang, Binbin; Xie, Yi; Ma, Lie; Xu, Kaizun; Ni, Min; Zhang, Hua; Shen, Weide; Li, Bing

2014-08-01

Silkworm (Bombyx mori), a model Lepidoptera insect, is economically important. Its growth and development are regulated by endogenous hormones. During the process of transition from larvae to pupae, 20-hydroxyecdysone (20E) plays an important role. The recent surge in consumer products and applications using metallic nanoparticles has increased the possibility of human or ecosystem exposure due to their unintentional release into the environment. We investigated the effects of exposure to titanium dioxide nanoparticles (TiO2 NPs) on the action of 20E in B. mori. Titanium dioxide nanoparticle treatment shortened the molting duration by 8 hr and prolonged the molting peak period by 10 %. Solexa sequencing profiled the changes in gene expression in the brain of fifth-instar B. mori in response to TiO2NPS exposure for 72 hr, to address the effects on hormone metabolism and regulation. Thirty one genes were differentially expressed. The transcriptional levels of pi3k and P70S6K, which are involved in the target of the rapamycin (TOR) signaling pathway, were up-regulated. Transcriptional levels of four cytochrome P450 genes, which are involved in 20E biosynthesis, at different developmental stages (48, 96, 144, and 192 hr) at 5th instars of all displayed trends of increasing expression. Simultaneously, the ecdysterone receptors, also displayed increasing trends. The 20E titers at four developmental stages during the 5th instar were 1.26, 1.23, 1.72, and 2.16 fold higher, respectively, than the control group. These results indicate that feeding B. mori with TiO2 NPs stimulates 20E biosynthesis, shortens the developmental progression, and reduces the duration of molting. Thus, application of TiO2 NPs is of high significance for saving the labor force in sericulture, and our research provides a reference for the ecological problems in the field of Lepidoptera exposured to titanium dioxide nanoparticles.

RNA-Seq analysis of nodule development at five different developmental stages of soybean (Glycine max) inoculated with Bradyrhizobium japonicum strain 113-2

PubMed Central

Yuan, Song L.; Li, Rong; Chen, Hai F.; Zhang, Chan J.; Chen, Li M.; Hao, Qing N.; Chen, Shui L.; Shan, Zhi H.; Yang, Zhong L.; Zhang, Xiao J.; Qiu, De Z.; Zhou, Xin A.

2017-01-01

Nodule development directly affects nitrogen fixation efficiency during soybean growth. Although abundant genome-based information related to nodule development has been released and some studies have reported the molecular mechanisms that regulate nodule development, information on the way nodule genes operate in nodule development at different developmental stages of soybean is limited. In this report, notably different nodulation phenotypes in soybean roots inoculated with Bradyrhizobium japonicum strain 113-2 at five developmental stages (branching stage, flowering stage, fruiting stage, pod stage and harvest stage) were shown, and the expression of nodule genes at these five stages was assessed quantitatively using RNA-Seq. Ten comparisons were made between these developmental periods, and their differentially expressed genes were analysed. Some important genes were identified, primarily encoding symbiotic nitrogen fixation-related proteins, cysteine proteases, cystatins and cysteine-rich proteins, as well as proteins involving plant-pathogen interactions. There were no significant shifts in the distribution of most GO functional annotation terms and KEGG pathway enrichment terms between these five development stages. A cystatin Glyma18g12240 was firstly identified from our RNA-seq, and was likely to promote nodulation and delay nodule senescence. This study provides molecular material for further investigations into the mechanisms of nitrogen fixation at different soybean developmental stages. PMID:28169364

Combination of Open Subtotal Calcanectomy and Stabilization With External Fixation as Limb Salvage Procedure in Hindfoot-Infected Diabetic Foot Ulcers.

PubMed

Dalla Paola, Luca; Carone, Anna; Boscarino, Giulio; Scavone, Giuseppe; Vasilache, Lucian

2016-12-01

Diabetic hindfoot ulcers, complicated by osteomyelitis, are associated with a high risk of major amputation. Partial calcanectomy, preceded by an effective management of the infection and of the eventual peripheral artery disease, can be considered as valid therapeutic option. We have evaluated a therapeutic protocol for diabetic hindfoot ulcers complicated by osteomyelitis, which, besides an adequate surgical debridement, considers a reconstructive pathway assisted by the positioning of a circular external fixator. We made a prospective study of a cohort of diabetic patients affected by heel ulcer complicated by osteomyelitis. All patients underwent open partial calcanectomy associated with the positioning of a circular external frame specifically designed for hindfoot stabilization and offloading. A reconstructive procedure was implemented starting with the application of negative pressure wound therapy and coverage with dermal substitute and split thickness skin grafting. From November 2014 to November 2015, 18 consecutive patients were enrolled. Mean follow-up period was 212.3 ± 64.0 days. Healing was achieved in 18 (100%) patients. The mean healing time was 69.0 ± 64.0 days. No major amputation had to be performed during the follow-up. Open partial calcanectomy associated with external fixation and skin reconstruction was as efficient as limb salvage in patients with infected lesions of the hindfoot complicated by calcaneal osteomyelitis.

Cyanobacterial-based approaches to improving photosynthesis in plants.

PubMed

Zarzycki, Jan; Axen, Seth D; Kinney, James N; Kerfeld, Cheryl A

2013-01-01

Plants rely on the Calvin-Benson (CB) cycle for CO(2) fixation. The key carboxylase of the CB cycle is ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). Efforts to enhance carbon fixation in plants have traditionally focused on RubisCO or on approaches that can help to remedy RubisCO's undesirable traits: its low catalytic efficiency and photorespiration. Towards reaching the goal of improving plant photosynthesis, cyanobacteria may be instrumental. Because of their evolutionary relationship to chloroplasts, they represent ideal model organisms for photosynthesis research. Furthermore, the molecular understanding of cyanobacterial carbon fixation provides a rich source of strategies that can be exploited for the bioengineering of chloroplasts. These strategies include the cyanobacterial carbon concentrating mechanism (CCM), which consists of active and passive transporter systems for inorganic carbon and a specialized organelle, the carboxysome. The carboxysome encapsulates RubisCO together with carbonic anhydrase in a protein shell, resulting in an elevated CO(2) concentration around RubisCO. Moreover, cyanobacteria differ from plants in the isoenzymes involved in the CB cycle and the photorespiratory pathways as well as in mechanisms that can affect the activity of RubisCO. In addition, newly available cyanobacterial genome sequence data from the CyanoGEBA project, which has more than doubled the amount of genomic information available for cyanobacteria, increases our knowledge on the CCM and the occurrence and distribution of genes of interest.

The challenge to keep global warming below 2 °C

NASA Astrophysics Data System (ADS)

Peters, Glen P.; Andrew, Robbie M.; Boden, Tom; Canadell, Josep G.; Ciais, Philippe; Le Quéré, Corinne; Marland, Gregg; Raupach, Michael R.; Wilson, Charlie

2013-01-01

The latest carbon dioxide emissions continue to track the high end of emission scenarios, making it even less likely global warming will stay below 2 °C. A shift to a 2 °C pathway requires immediate significant and sustained global mitigation, with a probable reliance on net negative emissions in the longer term.

Negative Emissions: Where Will the Carbon Come From?

NASA Astrophysics Data System (ADS)

Aines, R. D.; McCoy, S. T.

2017-12-01

The need for energy technologies that remove carbon dioxide from the air grows with each year of delay in acting to address climate change. The most commonly mentioned approach for achieving that, bioenergy with carbon capture and storage (BECCS), today is largely a modeler's concept, not a technology. Thus, in the near term how can we confidently discuss the scale of biomass for energy with a net reduction in CO2 concentrations in the absence of examples? As a first step toward achieving that research objective, this talk frames the likely ways in which net reductions in CO2 concentrations can be achieved from a lifecycle perspective, and the pathways through which biomass can be converted to fuels and materials while removing CO2 from the atmosphere. We will address questions such as: What pathways exist for converting biomass into transportation fuels, electricity, and materials? How can we capture and manage the carbon dioxide emissions from these kinds of activities? And, what are the tradeoffs between pathways? We have conducted preliminary analyses of some of the common biofuel production pathways, such as ethanol from corn with and without carbon capture. These pathways are still uniformly carbon positive, that is to say, they do not achieve the goal of reducing atmospheric CO2, even if they result in lower emissions than do petroleum-based fuels. More advanced pathways appear to have the capacity for minor atmospheric reductions, including those for drop-in replacement transportation fuels and some long-lived materials. Targets and options for improving these technologies to the point that they can, in fact, be carbon negative will be discussed, including pre-processing of the biomass near the production site to reduce transportation emissions, finding ways to manage small CO2 sources associated with processing, and uses of biochar. We will end with a summary of near-term RD&D needs to advance carbon-negative pathways and the associated technologies. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Response of Respiration of Soybean Leaves Grown at Ambient and Elevated Carbon Dioxide Concentrations to Day-to-day Variation in Light and Temperature under Field Conditions

PubMed Central

BUNCE, JAMES A.

2005-01-01

• Background and Aims Respiration is an important component of plant carbon balance, but it remains uncertain how respiration will respond to increases in atmospheric carbon dioxide concentration, and there are few measurements of respiration for crop plants grown at elevated [CO2] under field conditions. The hypothesis that respiration of leaves of soybeans grown at elevated [CO2] is increased is tested; and the effects of photosynthesis and acclimation to temperature examined. • Methods Net rates of carbon dioxide exchange were recorded every 10 min, 24 h per day for mature upper canopy leaves of soybeans grown in field plots at the current ambient [CO2] and at ambient plus 350 µmol mol−1 [CO2] in open top chambers. Measurements were made on pairs of leaves from both [CO2] treatments on a total of 16 d during the middle of the growing seasons of two years. • Key Results Elevated [CO2] increased daytime net carbon dioxide fixation rates per unit of leaf area by an average of 48 %, but had no effect on night-time respiration expressed per unit of area, which averaged 53 mmol m−2 d−1 (1·4 µmol m−2 s−1) for both the ambient and elevated [CO2] treatments. Leaf dry mass per unit of area was increased on average by 23 % by elevated [CO2], and respiration per unit of mass was significantly lower at elevated [CO2]. Respiration increased by a factor of 2·5 between 18 and 26 °C average night temperature, for both [CO2] treatments. • Conclusions These results do not support predictions that elevated [CO2] would increase respiration per unit of area by increasing photosynthesis or by increasing leaf mass per unit of area, nor the idea that acclimation of respiration to temperature would be rapid enough to make dark respiration insensitive to variation in temperature between nights. PMID:15781437

A reverse glyoxylate shunt to build a non-native route from C-4 to C-2 in Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mainguet, SE; Gronenberg, LS; Wong, SS

2013-09-01

Most central metabolic pathways such as glycolysis, fatty acid synthesis, and the TCA cycle have complementary pathways that run in the reverse direction to allow flexible storage and utilization of resources. However, the glyoxylate shunt, which allows for the synthesis of four-carbon TCA cycle intermediates from acetyl-CoA, has not been found to be reversible to date. As a result, glucose can only be converted to acetyl-CoA via the decarboxylation of the three-carbon molecule pyruvate in heterotrophs. A reverse glyoxylate shunt (rGS) could be extended into a pathway that converts C-4 carboxylates into two molecules of acetyl-CoA without loss of CO2.more » Here, as a proof of concept, we engineered in Escherichia coli such a pathway to convert malate and succinate to oxaloacetate and two molecules of acetyl-CoA. We introduced ATP-coupled heterologous enzymes at the thermodynamically unfavorable steps to drive the pathway in the desired direction. This synthetic pathway in essence reverses the glyoxylate shunt at the expense of ATP. When integrated with central metabolism, this pathway has the potential to increase the carbon yield of acetate and biofuels from many carbon sources in heterotrophic microorganisms, and could be the basis of novel carbon fixation cycles. (C) 2013 Elsevier Inc. All rights reserved.« less

A reverse glyoxylate shunt to build a non-native route from C4 to C2 in Escherichia coli.

PubMed

Mainguet, Samuel E; Gronenberg, Luisa S; Wong, Sio Si; Liao, James C

2013-09-01

Most central metabolic pathways such as glycolysis, fatty acid synthesis, and the TCA cycle have complementary pathways that run in the reverse direction to allow flexible storage and utilization of resources. However, the glyoxylate shunt, which allows for the synthesis of four-carbon TCA cycle intermediates from acetyl-CoA, has not been found to be reversible to date. As a result, glucose can only be converted to acetyl-CoA via the decarboxylation of the three-carbon molecule pyruvate in heterotrophs. A reverse glyoxylate shunt (rGS) could be extended into a pathway that converts C4 carboxylates into two molecules of acetyl-CoA without loss of CO2. Here, as a proof of concept, we engineered in Escherichia coli such a pathway to convert malate and succinate to oxaloacetate and two molecules of acetyl-CoA. We introduced ATP-coupled heterologous enzymes at the thermodynamically unfavorable steps to drive the pathway in the desired direction. This synthetic pathway in essence reverses the glyoxylate shunt at the expense of ATP. When integrated with central metabolism, this pathway has the potential to increase the carbon yield of acetate and biofuels from many carbon sources in heterotrophic microorganisms, and could be the basis of novel carbon fixation cycles. © 2013 Elsevier Inc. All rights reserved.

Space experiment "Cellular Responses to Radiation in Space (CellRad)": Hardware and biological system tests.

PubMed

Hellweg, Christine E; Dilruba, Shahana; Adrian, Astrid; Feles, Sebastian; Schmitz, Claudia; Berger, Thomas; Przybyla, Bartos; Briganti, Luca; Franz, Markus; Segerer, Jürgen; Spitta, Luis F; Henschenmacher, Bernd; Konda, Bikash; Diegeler, Sebastian; Baumstark-Khan, Christa; Panitz, Corinna; Reitz, Günther

2015-11-01

One factor contributing to the high uncertainty in radiation risk assessment for long-term space missions is the insufficient knowledge about possible interactions of radiation with other spaceflight environmental factors. Such factors, e.g. microgravity, have to be considered as possibly additive or even synergistic factors in cancerogenesis. Regarding the effects of microgravity on signal transduction, it cannot be excluded that microgravity alters the cellular response to cosmic radiation, which comprises a complex network of signaling pathways. The purpose of the experiment "Cellular Responses to Radiation in Space" (CellRad, formerly CERASP) is to study the effects of combined exposure to microgravity, radiation and general space flight conditions on mammalian cells, in particular Human Embryonic Kidney (HEK) cells that are stably transfected with different plasmids allowing monitoring of proliferation and the Nuclear Factor κB (NF-κB) pathway by means of fluorescent proteins. The cells will be seeded on ground in multiwell plate units (MPUs), transported to the ISS, and irradiated by an artificial radiation source after an adaptation period at 0 × g and 1 × g. After different incubation periods, the cells will be fixed by pumping a formaldehyde solution into the MPUs. Ground control samples will be treated in the same way. For implementation of CellRad in the Biolab on the International Space Station (ISS), tests of the hardware and the biological systems were performed. The sequence of different steps in MPU fabrication (cutting, drilling, cleaning, growth surface coating, and sterilization) was optimized in order to reach full biocompatibility. Different coatings of the foil used as growth surface revealed that coating with 0.1 mg/ml poly-D-lysine supports cell attachment better than collagen type I. The tests of prototype hardware (Science Model) proved its full functionality for automated medium change, irradiation and fixation of cells. Exposure of HEK cells to the β-rays emitted by the radiation source dose-dependently decreased cell growth and increased NF-κB activation. The signal of the fluorescent proteins after formaldehyde fixation was stable for at least six months after fixation, allowing storage of the MPUs after fixation for several months before the transport back to Earth and evaluation of the fluorescence intensity. In conclusion, these tests show the feasibility of CellRad on the ISS with the currently available transport mechanisms. Copyright © 2015 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide.

PubMed

Young, J N; Rickaby, R E M; Kapralov, M V; Filatov, D A

2012-02-19

Rubisco, the most abundant enzyme on the Earth and responsible for all photosynthetic carbon fixation, is often thought of as a highly conserved and sluggish enzyme. Yet, different algal Rubiscos demonstrate a range of kinetic properties hinting at a history of evolution and adaptation. Here, we show that algal Rubisco has indeed evolved adaptively during ancient and distinct geological periods. Using DNA sequences of extant marine algae of the red and Chromista lineage, we define positive selection within the large subunit of Rubisco, encoded by rbcL, to occur basal to the radiation of modern marine groups. This signal of positive selection appears to be responding to changing intracellular concentrations of carbon dioxide (CO(2)) triggered by physiological adaptations to declining atmospheric CO(2). Within the ecologically important Haptophyta (including coccolithophores) and Bacillariophyta (diatoms), positive selection occurred consistently during periods of falling Phanerozoic CO(2) and suggests emergence of carbon-concentrating mechanisms. During the Proterozoic, a strong signal of positive selection after secondary endosymbiosis occurs at the origin of the Chromista lineage (approx. 1.1 Ga), with further positive selection events until 0.41 Ga, implying a significant and continuous decrease in atmospheric CO(2) encompassing the Cryogenian Snowball Earth events. We surmise that positive selection in Rubisco has been caused by declines in atmospheric CO(2) and hence acts as a proxy for ancient atmospheric CO(2).

Preparation of graphene oxide-manganese dioxide for highly efficient adsorption and separation of Th(IV)/U(VI).

PubMed

Pan, Ning; Li, Long; Ding, Jie; Li, Shengke; Wang, Ruibing; Jin, Yongdong; Wang, Xiangke; Xia, Chuanqin

2016-05-15

Manganese dioxide decorated graphene oxide (GOM) was prepared via fixation of crystallographic MnO2 (α, γ) on the surface of graphene oxide (GO) and was explored as an adsorbent material for simultaneous removal of thorium/uranium ions from aqueous solutions. In single component systems (Th(IV) or U(VI)), the α-GOM2 (the weight ratio of GO/α-MnO2 of 2) exhibited higher maximum adsorption capacities toward both Th(IV) (497.5mg/g) and U(VI) (185.2 mg/g) than those of GO. In the binary component system (Th(IV)/U(VI)), the saturated adsorption capacity of Th(IV) (408.8 mg/g)/U(VI) (66.8 mg/g) on α-GOM2 was also higher than those on GO. Based on the analysis of various data, it was proposed that the adsorption process may involve four types of molecular interactions including coordination, electrostatic interaction, cation-pi interaction, and Lewis acid-base interaction between Th(IV)/U(VI) and α-GOM2. Finally, the Th(IV)/U(VI) ions on α-GOM2 can be separated by a two-stage desorption process with Na2CO3/EDTA. Those results displayed that the α-GOM2 may be utilized as an potential adsorbent for removing and separating Th(IV)/U(VI) ions from aqueous solutions. Copyright © 2016 Elsevier B.V. All rights reserved.

Adaptive signals in algal Rubisco reveal a history of ancient atmospheric carbon dioxide

PubMed Central

Young, J. N.; Rickaby, R. E. M.; Kapralov, M. V.; Filatov, D. A.

2012-01-01

Rubisco, the most abundant enzyme on the Earth and responsible for all photosynthetic carbon fixation, is often thought of as a highly conserved and sluggish enzyme. Yet, different algal Rubiscos demonstrate a range of kinetic properties hinting at a history of evolution and adaptation. Here, we show that algal Rubisco has indeed evolved adaptively during ancient and distinct geological periods. Using DNA sequences of extant marine algae of the red and Chromista lineage, we define positive selection within the large subunit of Rubisco, encoded by rbcL, to occur basal to the radiation of modern marine groups. This signal of positive selection appears to be responding to changing intracellular concentrations of carbon dioxide (CO2) triggered by physiological adaptations to declining atmospheric CO2. Within the ecologically important Haptophyta (including coccolithophores) and Bacillariophyta (diatoms), positive selection occurred consistently during periods of falling Phanerozoic CO2 and suggests emergence of carbon-concentrating mechanisms. During the Proterozoic, a strong signal of positive selection after secondary endosymbiosis occurs at the origin of the Chromista lineage (approx. 1.1 Ga), with further positive selection events until 0.41 Ga, implying a significant and continuous decrease in atmospheric CO2 encompassing the Cryogenian Snowball Earth events. We surmise that positive selection in Rubisco has been caused by declines in atmospheric CO2 and hence acts as a proxy for ancient atmospheric CO2. PMID:22232761

Features of CO2 fracturing deduced from acoustic emission and microscopy in laboratory experiments

NASA Astrophysics Data System (ADS)

Ishida, Tsuyoshi; Chen, Youqing; Bennour, Ziad; Yamashita, Hiroto; Inui, Shuhei; Nagaya, Yuya; Naoi, Makoto; Chen, Qu; Nakayama, Yoshiki; Nagano, Yu

2016-11-01

We conducted hydraulic fracturing (HF) experiments on 170 mm cubic granite specimens with a 20 mm diameter central hole to investigate how fluid viscosity affects HF process and crack properties. In experiments using supercritical carbon dioxide (SC-CO2), liquid carbon dioxide (L-CO2), water, and viscous oil with viscosity of 0.051-336.6 mPa · s, we compared the results for breakdown pressure, the distribution and fracturing mechanism of acoustic emission, and the microstructure of induced cracks revealed by using an acrylic resin containing a fluorescent compound. Fracturing with low-viscosity fluid induced three-dimensionally sinuous cracks with many secondary branches, which seem to be desirable pathways for enhanced geothermal system, shale gas recovery, and other processes.

Unprecedented Carbonato Intermediates in Cyclic Carbonate Synthesis Catalysed by Bimetallic Aluminium(Salen) Complexes.

PubMed

Castro-Osma, José A; North, Michael; Offermans, Willem K; Leitner, Walter; Müller, Thomas E

2016-04-21

The mechanism by which [Al(salen)]2 O complexes catalyse the synthesis of cyclic carbonates from epoxides and carbon dioxide in the absence of a halide cocatalyst has been investigated. Density functional theory (DFT) studies, mass spectrometry and (1) H NMR, (13) C NMR and infrared spectroscopies provide evidence for the formation of an unprecedented carbonato bridged bimetallic aluminium complex which is shown to be a key intermediate for the halide-free synthesis of cyclic carbonates from epoxides and carbon dioxide. Deuterated and enantiomerically-pure epoxides were used to study the reaction pathway. Based on the experimental and theoretical results, a catalytic cycle is proposed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Concerted changes in N and C primary metabolism in alfalfa (Medicago sativa) under water restriction

PubMed Central

Aranjuelo, Iker

2013-01-01

Although the mechanisms of nodule N2 fixation in legumes are now well documented, some uncertainty remains on the metabolic consequences of water deficit. In most cases, little consideration is given to other organs and, therefore, the coordinated changes in metabolism in leaves, roots, and nodules are not well known. Here, the effect of water restriction on exclusively N2-fixing alfalfa (Medicago sativa L.) plants was investigated, and proteomic, metabolomic, and physiological analyses were carried out. It is shown that the inhibition of nitrogenase activity caused by water restriction was accompanied by concerted alterations in metabolic pathways in nodules, leaves, and roots. The data suggest that nodule metabolism and metabolic exchange between plant organs nearly reached homeostasis in asparagine synthesis and partitioning, as well as the N demand from leaves. Typically, there was (i) a stimulation of the anaplerotic pathway to sustain the provision of C skeletons for amino acid (e.g. glutamate and proline) synthesis; (ii) re-allocation of glycolytic products to alanine and serine/glycine; and (iii) subtle changes in redox metabolites suggesting the implication of a slight oxidative stress. Furthermore, water restriction caused little change in both photosynthetic efficiency and respiratory cost of N2 fixation by nodules. In other words, the results suggest that under water stress, nodule metabolism follows a compromise between physiological imperatives (N demand, oxidative stress) and the lower input to sustain catabolism. PMID:23440170

Many-molecule encapsulation by an icosahedral shell

PubMed Central

Perlmutter, Jason D; Mohajerani, Farzaneh; Hagan, Michael F

2016-01-01

We computationally study how an icosahedral shell assembles around hundreds of molecules. Such a process occurs during the formation of the carboxysome, a bacterial microcompartment that assembles around many copies of the enzymes ribulose 1,5-bisphosphate carboxylase/ oxygenase and carbonic anhydrase to facilitate carbon fixation in cyanobacteria. Our simulations identify two classes of assembly pathways leading to encapsulation of many-molecule cargoes. In one, shell assembly proceeds concomitantly with cargo condensation. In the other, the cargo first forms a dense globule; then, shell proteins assemble around and bud from the condensed cargo complex. Although the model is simplified, the simulations predict intermediates and closure mechanisms not accessible in experiments, and show how assembly can be tuned between these two pathways by modulating protein interactions. In addition to elucidating assembly pathways and critical control parameters for microcompartment assembly, our results may guide the reengineering of viruses as nanoreactors that self-assemble around their reactants. DOI: http://dx.doi.org/10.7554/eLife.14078.001 PMID:27166515

Maintenance of Segmental Lordosis and Disk Height in Stand-alone and Instrumented Extreme Lateral Interbody Fusion (XLIF).

PubMed

Malham, Gregory M; Ellis, Ngaire J; Parker, Rhiannon M; Blecher, Carl M; White, Rohan; Goss, Ben; Seex, Kevin A

2017-03-01

A prospective single-surgeon nonrandomized clinical study. To evaluate the radiographic and clinical outcomes, by fixation type, in extreme lateral interbody fusion (XLIF) patients and provide an algorithm for determining patients suitable for stand-alone XLIF. XLIF may be supplemented with pedicle screw fixation, however, since stabilizing structures remain intact, it is suggested that stand-alone XLIF can be used for certain indications. This eliminates the associated morbidity, though subsidence rates may be elevated, potentially minimizing the clinical benefits. A fixation algorithm was developed after evaluation of patient outcomes from the surgeon's first 30 cases. This algorithm was used prospectively for 40 subsequent patients to determine the requirement for supplemental fixation. Preoperative, postoperative, and 12-month follow-up computed tomography scans were measured for segmental and global lumbar lordosis and posterior disk height. Clinical outcome measures included back and leg pain (visual analogue scale), Oswestry Disability Index (ODI), and SF-36 physical and mental component scores (PCS and MCS). Preoperatively to 12-month follow-up there were increases in segmental lordosis (7.9-9.4 degrees, P=0.0497), lumbar lordosis (48.8-55.2 degrees, P=0.0328), and disk height (3.7-5.5 mm, P=0.0018); there were also improvements in back (58.6%) and leg pain (60.0%), ODI (44.4%), PCS (56.7%), and MCS (16.1%) for stand-alone XLIF. For instrumented XLIF, segmental lordosis (7.6-10.5 degrees, P=0.0120) and disk height (3.5-5.6 mm, P<0.001) increased, while lumbar lordosis decreased (51.1-45.8 degrees, P=0.2560). Back (49.8%) and leg pain (30.8%), ODI (32.3%), PCS (37.4%), and MCS (2.0%) were all improved. Subsidence occurred in 3 (7.5%) stand-alone patients. The XLIF treatment fixation algorithm provided a clinical pathway to select suitable patients for stand-alone XLIF. These patients achieved positive clinical outcomes, satisfactory fusion rates, with sustained correction of lordosis and restoration of disk height.

Chemical microenvironments and single-cell carbon and nitrogen uptake in field-collected colonies of Trichodesmium under different pCO2

PubMed Central

Eichner, Meri J; Klawonn, Isabell; Wilson, Samuel T; Littmann, Sten; Whitehouse, Martin J; Church, Matthew J; Kuypers, Marcel MM; Karl, David M; Ploug, Helle

2017-01-01

Gradients of oxygen (O2) and pH, as well as small-scale fluxes of carbon (C), nitrogen (N) and O2 were investigated under different partial pressures of carbon dioxide (pCO2) in field-collected colonies of the marine dinitrogen (N2)-fixing cyanobacterium Trichodesmium. Microsensor measurements indicated that cells within colonies experienced large fluctuations in O2, pH and CO2 concentrations over a day–night cycle. O2 concentrations varied with light intensity and time of day, yet colonies exposed to light were supersaturated with O2 (up to ~200%) throughout the light period and anoxia was not detected. Alternating between light and dark conditions caused a variation in pH levels by on average 0.5 units (equivalent to 15 nmol l−1 proton concentration). Single-cell analyses of C and N assimilation using secondary ion mass spectrometry (SIMS; large geometry SIMS and nanoscale SIMS) revealed high variability in metabolic activity of single cells and trichomes of Trichodesmium, and indicated transfer of C and N to colony-associated non-photosynthetic bacteria. Neither O2 fluxes nor C fixation by Trichodesmium were significantly influenced by short-term incubations under different pCO2 levels, whereas N2 fixation increased with increasing pCO2. The large range of metabolic rates observed at the single-cell level may reflect a response by colony-forming microbial populations to highly variable microenvironments. PMID:28398346

Effects of nutrient ratios and carbon dioxide bio-sequestration on biomass growth of Chlorella sp. in bubble column photobioreactor.

PubMed

Vo, Hoang-Nhat-Phong; Bui, Xuan-Thanh; Nguyen, Thanh-Tin; Nguyen, Dinh Duc; Dao, Thanh-Son; Cao, Ngoc-Dan-Thanh; Vo, Thi-Kim-Quyen

2018-08-01

Photobioreactor technology, especially bubble column configuration, employing microalgae cultivation (e.g., Chlorella sp.), is an ideal man-made environment to achieve sufficient microalgae biomass through its strictly operational control. Nutrients, typically N and P, are necessary elements in the cultivation process, which determine biomass yield and productivity. Specifically, N:P ratios have certain effects on microalgae's biomass growth. It is also attractive that microalgae can sequester CO 2 by using that carbon source for photosynthesis and, subsequently, reducing CO 2 emission. Therefore, this study aims to investigate the effect of N:P ratios on Chlorella sp.'s growth, and to study the dynamic of CO 2 fixation in the bubble column photobioreactor. According to our results, N:P ratio of 15:1 could produce the highest biomass yield (3568 ± 158 mg L -1 ). The maximum algae concentration was 105 × 10 6  cells mL -1 , receiving after 92 h. Chlorella sp. was also able to sequester CO 2 at 28 ± 1.2%, while the specific growth rate and carbon fixation rate were observed at 0.064 h -1 and 68.9 ± 1.91 mg L -1  h -1 , respectively. The types of carbon sources (e.g., organic and inorganic carbon) possessed potential impact on microalgae's cultivation. Copyright © 2018 Elsevier Ltd. All rights reserved.

Supramolecular Porphyrin Cages Assembled at Molecular–Materials Interfaces for Electrocatalytic CO Reduction

PubMed Central

2017-01-01

Conversion of carbon monoxide (CO), a major one-carbon product of carbon dioxide (CO2) reduction, into value-added multicarbon species is a challenge to addressing global energy demands and climate change. Here we report a modular synthetic approach for aqueous electrochemical CO reduction to carbon–carbon coupled products via self-assembly of supramolecular cages at molecular–materials interfaces. Heterobimetallic cavities formed by face-to-face coordination of thiol-terminated metalloporphyrins to copper electrodes through varying organic struts convert CO to C2 products with high faradaic efficiency (FE = 83% total with 57% to ethanol) and current density (1.34 mA/cm2) at a potential of −0.40 V vs RHE. The cage-functionalized electrodes offer an order of magnitude improvement in both selectivity and activity for electrocatalytic carbon fixation compared to parent copper surfaces or copper functionalized with porphyrins in an edge-on orientation. PMID:28979945

Identification and characterization of multiple rubisco activases in chemoautotrophic bacteria

PubMed Central

Tsai, Yi-Chin Candace; Lapina, Maria Claribel; Bhushan, Shashi; Mueller-Cajar, Oliver

2015-01-01

Ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco) is responsible for almost all biological CO2 assimilation, but forms inhibited complexes with its substrate ribulose-1,5-bisphosphate (RuBP) and other sugar phosphates. The distantly related AAA+ proteins rubisco activase and CbbX remodel inhibited rubisco complexes to effect inhibitor release in plants and α-proteobacteria, respectively. Here we characterize a third class of rubisco activase in the chemolithoautotroph Acidithiobacillus ferrooxidans. Two sets of isoforms of CbbQ and CbbO form hetero-oligomers that function as specific activases for two structurally diverse rubisco forms. Mutational analysis supports a model wherein the AAA+ protein CbbQ functions as motor and CbbO is a substrate adaptor that binds rubisco via a von Willebrand factor A domain. Understanding the mechanisms employed by nature to overcome rubisco's shortcomings will increase our toolbox for engineering photosynthetic carbon dioxide fixation. PMID:26567524

Supramolecular Porphyrin Cages Assembled at Molecular–Materials Interfaces for Electrocatalytic CO Reduction

DOE PAGES

Gong, Ming; Cao, Zhi; Liu, Wei; ...

2017-09-13

Conversion of carbon monoxide (CO), a major one-carbon product of carbon dioxide (CO 2) reduction, into value-added multicarbon species is a challenge to addressing global energy demands and climate change. Here in this paper, we report a modular synthetic approach for aqueous electrochemical CO reduction to carbon-carbon coupled products via self-assembly of supramolecular cages at molecular-materials interfaces. Heterobimetallic cavities formed by face-to-face coordination of thiol-terminated metalloporphyrins to copper electrodes through varying organic struts convert CO to C2 products with high faradaic efficiency (FE = 83% total with 57% to ethanol) and current density (1.34 mA/cm 2) at a potential ofmore » -0.40 V vs RHE. The cage-functionalized electrodes offer an order of magnitude improvement in both selectivity and activity for electrocatalytic carbon fixation compared to parent copper surfaces or copper functionalized with porphyrins in an edge-on orientation.« less

Image analysis supported moss cell disruption in photo-bioreactors.

PubMed

Lucumi, A; Posten, C; Pons, M-N

2005-05-01

Diverse methods for the disruption of cell entanglements and pellets of the moss Physcomitrella patens were tested in order to improve the homogeneity of suspension cultures. The morphological characterization of the moss was carried out by means of image analysis. Selected morphological parameters were defined and compared to the reduction of the carbon dioxide fixation, and the released pigments after cell disruption. The size control of the moss entanglements based on the rotor stator principle allowed a focused shear stress, avoiding a severe reduction in the photosynthesis. Batch cultures of P. patens in a 30.0-l pilot tubular photo-bioreactor with cell disruption showed no significant variation in growth rate and a delayed cell differentiation, when compared to undisrupted cultures. A highly controlled photoautotrophic culture of P. patens in a scalable photo-bioreactor was established, contributing to the development required for the future use of mosses as producers of relevant heterologous proteins.

Formate production through carbon dioxide hydrogenation with recombinant whole cell biocatalysts.

PubMed

Alissandratos, Apostolos; Kim, Hye-Kyung; Easton, Christopher J

2014-07-01

The biological conversion of CO2 and H2 into formate offers a sustainable route to a valuable commodity chemical through CO2 fixation, and a chemical form of hydrogen fuel storage. Here we report the first example of CO2 hydrogenation utilising engineered whole-cell biocatalysts. Escherichia coli JM109(DE3) cells transformed for overexpression of either native formate dehydrogenase (FDH), the FDH from Clostridium carboxidivorans, or genes from Pyrococcus furiosus and Methanobacterium thermoformicicum predicted to express FDH based on their similarity to known FDH genes were all able to produce levels of formate well above the background, when presented with H2 and CO2, the latter in the form of bicarbonate. In the case of the FDH from P. furiosus the yield was highest, reaching more than 1 g L(-1)h(-1) when a hydrogen-sparging reactor design was used. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular Signatures of Microbial Metabolism in an Actively Growing, Silicified, Microbial Structure from Yellowstone National Park

NASA Astrophysics Data System (ADS)

Ferreira, M.; Creveling, J.; Hilburn, I.; Karlsson, E.; Pepe-Ranney, C.; Spear, J.; Dawson, S.; Geobio2008, I.

2008-12-01

Silicified structures that exhibit a putative biologic component in their formation permeate the rock record as stromatolites. We have studied a silicified microbial structure from a hot spring in Yellowstone National Park using phenotypic, phylogenetic, and metagenomic analyses to determine microbial carbon metabolic pathways and the phylogenetic affiliations of microbes present in this unique structure. In this multi-faceted approach, dominant physiologies, specifically with regards to anaerobic and aerobic metabolisms, were inferred from 16S rRNA gene sequences and 454 sequencing data from bulk DNA samples of the structure. Carbon utilization as indicated by ECO Biolog plates showed abundant heterotrophy and heterotrophic diversity throughout the microbial structure. Microbes within the structure are able to utilize all tested sources of carbohydrates, lipids/fatty acids, and protein/amino acids as carbon sources. ECO plate testing of the hot spring water yielded considerable less carbohydrate consumption (only 4 out of 13 tested carbohydrates) and similar lipids/fatty acids and protein/amino acids consumption (2 out of 3 and 5 out of 5 tested sources respectively). Full length 16S rRNA gene sequences and metagenomic 454 pyrosequencing of community DNA showed limited diversity among primary producers. From the 16S data, the majority of the autotrophs are inferred to utilize the Calvin cycle for CO2 fixation, followed by 3-hydroxypropionate/4- hydroxybutyrate CO2 fixation. However, an analysis of the metagenomic data compared to the KEGG database does not show genes directly involved with Calvin cycle carbon fixation. Further BLAST searches of our data failed to find significant matches within our 6514 metagenomic sequences to known RuBisCo sequences taken from the NCBI database. This is likely due to a far under-sampled dataset of metagenomic sequences, and the low number (958) that had matches to the KEGG pathways database. Anaerobic versus aerobic physiology also can be estimated from the 16S clone libraries. Phylogenetic analysis of recovered 16S sequences suggests that 15% of the 16S sequences can be attributed to anaerobic microbes while 42% likely come from aerobes. The remaining 43% of 16S rRNA gene sequences belong to metabolically unassigned phyla both known and novel. This preliminary study demonstrates that the small spatially stratified silicified microbial structure present on the margins of a hot spring contains a rich and complex microbial community with different trophic levels and enzymatic pathways.

Variations in microbial carbon sources and cycling in the deep continental subsurface

NASA Astrophysics Data System (ADS)

Simkus, Danielle N.; Slater, Greg F.; Lollar, Barbara Sherwood; Wilkie, Kenna; Kieft, Thomas L.; Magnabosco, Cara; Lau, Maggie C. Y.; Pullin, Michael J.; Hendrickson, Sarah B.; Wommack, K. Eric; Sakowski, Eric G.; van Heerden, Esta; Kuloyo, Olukayode; Linage, Borja; Borgonie, Gaetan; Onstott, Tullis C.

2016-01-01

Deep continental subsurface fracture water systems, ranging from 1.1 to 3.3 km below land surface (kmbls), were investigated to characterize the indigenous microorganisms and elucidate microbial carbon sources and their cycling. Analysis of phospholipid fatty acid (PLFA) abundances and direct cell counts detected varying biomass that was not correlated with depth. Compound-specific carbon isotope analyses (δ13C and Δ14C) of the phospholipid fatty acids (PLFAs) and carbon substrates combined with genomic analyses did identify, however, distinct carbon sources and cycles between the two depth ranges studied. In the shallower boreholes at circa 1 kmbls, isotopic evidence indicated microbial incorporation of biogenic CH4 by the in situ microbial community. At the shallowest site, 1.05 kmbls in Driefontein mine, this process clearly dominated the isotopic signal. At slightly deeper depths, 1.34 kmbls in Beatrix mine, the isotopic data indicated the incorporation of both biogenic CH4 and dissolved inorganic carbon (DIC) derived from CH4 oxidation. In both of these cases, molecular genetic analysis indicated that methanogenic and methanotrophic organisms together comprised a small component (<5%) of the microbial community. Thus, it appears that a relatively minor component of the prokaryotic community is supporting a much larger overall bacterial community in these samples. In the samples collected from >3 kmbls in Tau Tona mine (TT107, TT109 Bh2), the CH4 had an isotopic signature suggesting a predominantly abiogenic origin with minor inputs from microbial methanogenesis. In these samples, the isotopic enrichments (δ13C and Δ14C) of the PLFAs relative to CH4 were consistent with little incorporation of CH4 into the biomass. The most 13C-enriched PLFAs were observed in TT107 where the dominant CO2-fixation pathway was the acetyl-CoA pathway by non-acetogenic bacteria. The differences in the δ13C of the PLFAs and the DIC and DOC for TT109 Bh2 were ∼-24‰ and 0‰, respectively. The dominant CO2-fixation pathways were 3-HP/4-HB cycle > acetyl-CoA pathway > reductive pentose phosphate cycle.

The preparation of large surface area lanthanum based perovskite supports for AuPt nanoparticles: tuning the glycerol oxidation reaction pathway by switching the perovskite B site

PubMed Central

Evans, Christopher D.; Smith, Paul J.; Manning, Troy D.; Miedziak, Peter J.; Brett, Gemma L.; Armstrong, Robert D.; Bartley, Jonathan K.; Taylor, Stuart H.; Rosseinsky, Matthew J.; Hutchings, Graham J.

2016-01-01

Gold and gold alloys, in the form of supported nanoparticles, have been shown over the last three decades to be highly effective oxidation catalysts. Mixed metal oxide perovskites, with their high structural tolerance, are ideal for investigating how changes in the chemical composition of supports affect the catalysts' properties, while retaining similar surface areas, morphologies and metal co-ordinations. However, a significant disadvantage of using perovskites as supports is their high crystallinity and small surface area. We report the use of a supercritical carbon dioxide anti-solvent precipitation methodology to prepare large surface area lanthanum based perovskites, making the deposition of 1 wt% AuPt nanoparticles feasible. These catalysts were used for the selective oxidation of glycerol. By changing the elemental composition of the perovskite B site, we dramatically altered the reaction pathway between a sequential oxidation route to glyceric or tartronic acid and a dehydration reaction pathway to lactic acid. Selectivity profiles were correlated to reported oxygen adsorption capacities of the perovskite supports and also to changes in the AuPt nanoparticle morphologies. Extended time on line analysis using the best oxidation catalyst (AuPt/LaMnO3) produced an exceptionally high tartronic acid yield. LaMnO3 produced from alternative preparation methods was found to have lower activities, but gave comparable selectivity profiles to that produced using the supercritical carbon dioxide anti-solvent precipitation methodology. PMID:27074316

The preparation of large surface area lanthanum based perovskite supports for AuPt nanoparticles: tuning the glycerol oxidation reaction pathway by switching the perovskite B site.

PubMed

Evans, Christopher D; Kondrat, Simon A; Smith, Paul J; Manning, Troy D; Miedziak, Peter J; Brett, Gemma L; Armstrong, Robert D; Bartley, Jonathan K; Taylor, Stuart H; Rosseinsky, Matthew J; Hutchings, Graham J

2016-07-04

Gold and gold alloys, in the form of supported nanoparticles, have been shown over the last three decades to be highly effective oxidation catalysts. Mixed metal oxide perovskites, with their high structural tolerance, are ideal for investigating how changes in the chemical composition of supports affect the catalysts' properties, while retaining similar surface areas, morphologies and metal co-ordinations. However, a significant disadvantage of using perovskites as supports is their high crystallinity and small surface area. We report the use of a supercritical carbon dioxide anti-solvent precipitation methodology to prepare large surface area lanthanum based perovskites, making the deposition of 1 wt% AuPt nanoparticles feasible. These catalysts were used for the selective oxidation of glycerol. By changing the elemental composition of the perovskite B site, we dramatically altered the reaction pathway between a sequential oxidation route to glyceric or tartronic acid and a dehydration reaction pathway to lactic acid. Selectivity profiles were correlated to reported oxygen adsorption capacities of the perovskite supports and also to changes in the AuPt nanoparticle morphologies. Extended time on line analysis using the best oxidation catalyst (AuPt/LaMnO3) produced an exceptionally high tartronic acid yield. LaMnO3 produced from alternative preparation methods was found to have lower activities, but gave comparable selectivity profiles to that produced using the supercritical carbon dioxide anti-solvent precipitation methodology.

Revising Estimates of the Methane Production Pathway in Peatland Porewater Using Intramolecular Isotopic Analyses of Acetate

NASA Astrophysics Data System (ADS)

Thomas, B.; Arthur, M. A.; Freeman, K. H.

2007-12-01

Stable isotopic measurements of methane and carbon dioxide are routinely applied to environmental samples to assess the relative importance of methane production by either aceticlastic or hydrogenotrophic methanogenesis. Such estimates rely upon assumptions about isotopic fractionation during methane production and oxidation. Rigorous isotope-based pathway estimates require knowledge of the carbon isotopic composition of both carbon dioxide and acetate. In practice, technical barriers have limited measurements of the isotopic composition of whole acetate in natural samples. Yet, the estimate of whole acetate isotopic values, even when available, may not represent accurately the composition of the methyl carbon, which is, in fact, the precursor to methane. It is exceedingly rare to find carbon isotopic measurements of acetate-methyl in the literature, and, to our knowledge, the d13C of the acetate-methyl precursor to methane has never before been reported from peatland porewater samples. Extremely 13C-depleted methane, -70 permil VPDB, and 13C-enriched carbon dioxide from acidic northern peat bogs are typically interpreted as signatures of hydrogenotrophic methanogenesis. The hypothesized dominance of methane production from hydrogen in acidic bogs contrasts with the vast majority of freshwater wetlands in which aceticlastic methanogenesis dominates. Using a new technique for the online analysis of the intramolecular carbon isotopic composition of acetate in natural samples, we find the acetate-methyl in peat porewaters can be significantly depleted relative to bulk organic matter. In porewater profiles from both winter and summer, acetate is as much as 15 permil depleted relative to bulk carbon. We hypothesize that acetate- methyl isotopic depletion results from conditions that favor autotrophic acetogenesis and subsequent acetate consumption by aceticlastic methanogens. Porewater depth profiles during winter and summer illustrate depth- dependent increases in the fraction of methane derived from carbon dioxide, with deeper peat dominated by hydrogenotrophic methanogenesis, but shallow peat dominated by aceticlastic methanogens. Significant aceticlastic methane production from autotrophically produced acetate challenges the ability of hydrogen isotopic measurements of methane to represent the pathway of methanogenesis. Supplementing our field observations, intramolecular acetate measurements of incubation experiments confirm that an aceticlastic methanogen can facilitate significant acetate-carboxyl exchange with DIC. This novel technique confirms two caveats associated with whole acetate carbon isotopic data: 1, the carboxyl carbon isotopic composition may not accurately reflect the composition of the parent molecule, and 2, the acetate methyl may be derived from inorganic carbon or the fractionation effect of fermentation in acidic porewaters may be significant.

Optimal Treatment of Malignant Long Bone Fracture: Influence of Method of Repair and External Beam Irradiation on the Pathway and Efficacy of Fracture Healing

DTIC Science & Technology

2015-10-01

stiffness, or a partial snap with lower yield force and stiffness (Figure 4). Three dimensional micro CT analysis around fracture Figure 3. (a-b... fractures with plate fixation on both sides and irradiation on the left while the contralateral limb serves as a non-radiated internal control. The...AWARD NUMBER: W81XWH-13-1-0430 TITLE: Optimal Treatment of Malignant Long Bone Fracture : Influence of Method of Repair and External Beam

Effect of Engineered Nanoparticles on Exopolymeric Substances Release from Marine Phytoplankton.

PubMed

Chiu, Meng-Hsuen; Khan, Zafir A; Garcia, Santiago G; Le, Andre D; Kagiri, Agnes; Ramos, Javier; Tsai, Shih-Ming; Drobenaire, Hunter W; Santschi, Peter H; Quigg, Antonietta; Chin, Wei-Chun

2017-12-13

Engineered nanoparticles (ENPs), products from modern nanotechnologies, can potentially impact the marine environment to pose serious threats to marine ecosystems. However, the cellular responses of marine phytoplankton to ENPs are still not well established. Here, we investigate four different diatom species (Odontella mobiliensis, Skeletonema grethae, Phaeodactylum tricornutum, Thalassiosira pseudonana) and one green algae (Dunaliella tertiolecta) for their extracellular polymeric substances (EPS) release under model ENP treatments: 25 nm titanium dioxide (TiO 2 ), 10-20 nm silicon dioxide (SiO 2 ), and 15-30 nm cerium dioxide (CeO 2 ). We found SiO 2 ENPs can significantly stimulate EPS release from these algae (200-800%), while TiO 2 ENP exposure induced the lowest release. Furthermore, the increase of intracellular Ca 2+ concentration can be triggered by ENPs, suggesting that the EPS release process is mediated through Ca 2+ signal pathways. With better understanding of the cellular mechanism mediated ENP-induced EPS release, potential preventative and safety measures can be developed to mitigate negative impact on the marine ecosystem.

Clinical comparison between the retromandibular approach for reduction and fixation and endoscope-assisted open reduction and internal fixation for mandibular condyle fractures.

PubMed

Nogami, Shinnosuke; Takahashi, Tetsu; Yamauchi, Kensuke; Miyamoto, Ikuya; Kaneuji, Takeshi; Yamamoto, Noriaki; Yoshiga, Daigo; Yamashita, Yoshihiro

2012-11-01

Endoscope-assisted transoral open reduction and internal fixation (EAORIF) for mandibular condyle fractures has recently become popular because it is minimally invasive, provides excellent visibility without a large incision, and reduces surgical scarring and the risk of facial nerve injury. This report describes a retrospective clinical study that compared certain clinical parameters, including postoperative function, between the retromandibular (RM) approach and EAORIF. Fifteen patients were treated by the RM approach, whereas 15 underwent EAORIF between July 2006 and September 2011 at Kyushu Dental College, Japan. Clinical indices comprised fracture line, fracture type, number of plates used, surgical duration, bleeding amount, and functional items, including maximum interincisal opening, mandibular deviation on the opening pathway, malocclusion, facial paresthesia, and temporomandibular joint pain and clicking. The areas subjected to either approach included lower neck and subcondyle. The RM approach was used for mandibular condyle fractures with dislocation of a small bone segment. Both groups used 2 plates in all cases. Surgical duration, maximum interincisal opening, mandibular deviation, occlusion, and temporomandibular joint function at 6 months after surgery were comparable between groups. The average bleeding amount in the EAORIF group was greater than in the RM group. One patient from the RM group developed facial paresthesia that persisted for 6 months after surgery. It was concluded that surgical treatment was suitable for fractures of the lower neck and subcondylar. Both procedures showed good results in the functional items of this study.

Engineering chloroplasts to improve Rubisco catalysis: prospects for translating improvements into food and fiber crops.

PubMed

Sharwood, Robert E

2017-01-01

494 I. 495 II. 496 III. 496 IV. 499 V. 499 VI. 501 VII. 501 VIII. 502 IX. 505 X. 506 507 References 507 SUMMARY: The uncertainty of future climate change is placing pressure on cropping systems to continue to provide stable increases in productive yields. To mitigate future climates and the increasing threats against global food security, new solutions to manipulate photosynthesis are required. This review explores the current efforts available to improve carbon assimilation within plant chloroplasts by engineering Rubisco, which catalyzes the rate-limiting step of CO 2 fixation. Fixation of CO 2 and subsequent cycling of 3-phosphoglycerate through the Calvin cycle provides the necessary carbohydrate building blocks for maintaining plant growth and yield, but has to compete with Rubisco oxygenation, which results in photorespiration that is energetically wasteful for plants. Engineering improvements in Rubisco is a complex challenge and requires an understanding of chloroplast gene regulatory pathways, and the intricate nature of Rubisco catalysis and biogenesis, to transplant more efficient forms of Rubisco into crops. In recent times, major advances in Rubisco engineering have been achieved through improvement of our knowledge of Rubisco synthesis and assembly, and identifying amino acid catalytic switches in the L-subunit responsible for improvements in catalysis. Improving the capacity of CO 2 fixation in crops such as rice will require further advances in chloroplast bioengineering and Rubisco biogenesis. © 2016 The Author. New Phytologist © 2016 New Phytologist Trust.

Investigating patterns of symbiotic nitrogen fixation during vegetation change from grassland to woodland using fine scale δ(15) N measurements.

PubMed

Soper, Fiona M; Boutton, Thomas W; Sparks, Jed P

2015-01-01

Biological nitrogen fixation (BNF) in woody plants is often investigated using foliar measurements of δ(15) N and is of particular interest in ecosystems experiencing increases in BNF due to woody plant encroachment. We sampled δ(15) N along the entire N uptake pathway including soil solution, xylem sap and foliage to (1) test assumptions inherent to the use of foliar δ(15) N as a proxy for BNF; (2) determine whether seasonal divergences occur between δ(15) Nxylem sap and δ(15) Nsoil inorganic N that could be used to infer variation in BNF; and (3) assess patterns of δ(15) N with tree age as indicators of shifting BNF or N cycling. Measurements of woody N-fixing Prosopis glandulosa and paired reference non-fixing Zanthoxylum fagara at three seasonal time points showed that δ(15) Nsoil inorganic N varied temporally and spatially between species. Fractionation between xylem and foliar δ(15) N was consistently opposite in direction between species and varied on average by 2.4‰. Accounting for these sources of variation caused percent nitrogen derived from fixation values for Prosopis to vary by up to ∼70%. Soil-xylem δ(15) N separation varied temporally and increased with Prosopis age, suggesting seasonal variation in N cycling and BNF and potential long-term increases in BNF not apparent through foliar sampling alone. © 2014 John Wiley & Sons Ltd.

Investigating the hydrological origins of Blood Falls - geomicrobiological insights into a briny subglacial Antarctic aquifer

NASA Astrophysics Data System (ADS)

Mikucki, J.; Tulaczyk, S. M.; Purcell, A. M.; Dachwald, B.; Lyons, W. B.; Welch, K. A.; Auken, E.; Dugan, H. A.; Walter, J. I.; Pettit, E. C.; Doran, P. T.; Virginia, R. A.; Schamper, C.; Foley, N.; Feldmann, M.; Espe, C.; Ghosh, D.; Francke, G.

2015-12-01

Subglacial waters tend to accumulate solutes from extensive rock-water interactions, which, when released to the surface, can provide nutrients to surface ecosystems providing a 'hot spot' for microbial communities. Blood Falls, an iron-rich, saline feature at the terminus of Taylor Glacier in the McMurdo Dry Valleys, Antarctica is a well-studied subglacial discharge. Here we present an overview of geophysical surveys, thermomechanical drilling exploration and geomicrobiological analyses of the Blood Falls system. A helicopter-borne transient electromagnetic system (SkyTEM) flown over the Taylor Glacier revealed a surprisingly extensive subglacial aquifer and indicates that Blood Falls may be the only surface manifestation of this extensive briny groundwater. Ground-based temperature sensing and GPR data combined with the helicopter-borne TEM data enabled targeted drilling into the englacial conduit that delivers brine to the surface. During the 2014-15 austral summer field season, we used a novel ice-melting drill (the IceMole) to collect englacial brine for geomicrobiological analyses. Results from previously collected outflow and more recent samples indicate that the brine harbors a metabolically active microbial community that persists, despite cold, dark isolation. Isotope geochemistry and molecular analysis of functional genes from BF suggested that a catalytic or 'cryptic' sulfur cycle was linked to iron reduction. Recent metagenomic analysis confirms the presence of numerous genes involved in oxidative and reductive sulfur transformations. Metagenomic and metabolic activity data also indicate that subglacial dark CO2 fixation occurs via various pathways. Genes encoding key steps in CO2 fixation pathways including the Calvin Benson Basham and Wood Ljungdahl pathway were present and brine samples showed measureable uptake of 14C-labeled bicarbonate. These results support the notion that, like the deep subsurface, subglacial environments are chemosynthetic, deriving energy in part by cycling iron and sulfur compounds. Collectively our interdisciplinary dataset indicates that subsurface brines are widespread in the Taylor Valley polar desert and this previously unknown groundwater network likely supports unique microbial life.

Following the electroreduction of uranium dioxide to uranium in LiCl-KCl eutectic in situ using synchrotron radiation

NASA Astrophysics Data System (ADS)

Brown, L. D.; Abdulaziz, R.; Jervis, R.; Bharath, V. J.; Atwood, R. C.; Reinhard, C.; Connor, L. D.; Simons, S. J. R.; Inman, D.; Brett, D. J. L.; Shearing, P. R.

2015-09-01

The electrochemical reduction of uranium dioxide to metallic uranium has been investigated in lithium chloride-potassium chloride eutectic molten salt. Laboratory based electrochemical studies have been coupled with in situ energy dispersive X-ray diffraction, for the first time, to deduce the reduction pathway. No intermediate phases were identified using the X-ray diffraction before, during or after electroreduction to form α-uranium. This suggests that the electrochemical reduction occurs via a single, 4-electron-step, process. The rate of formation of α-uranium is seen to decrease during electrolysis and could be a result of a build-up of oxygen anions in the molten salt. Slow transport of O2- ions away from the UO2 working electrode could impede the electrochemical reduction.

Oxygen Consumption of Tilapia and Preliminary Mass Flows through a Prototype Closed Aquaculture System

NASA Technical Reports Server (NTRS)

Muller, Matthew S.; Bauer, Clarence F.

1994-01-01

Performance of NASA's prototype CELSS Breadboard Project Closed Aquaculture System was evaluated by estimating gas exchange quantification and preliminary carbon and nitrogen balances. The total system oxygen consumption rate was 535 mg/hr kg/fish (cv = 30%) when stocked with Tilapia aurea populations (fresh weights of 97 +/- 19 to 147 +/- 36 g/fish for various trials). Oxygen consumption by T. aurea (260 mg/hr kg/fish) contributed to approximately one-half of total system demand. Continuous carbon dioxide quantification methods were analyzed using the,relation of carbon dioxide to oxygen consumption. Overall food conversion rates averaged 18.2 +/- 3.2%. Major pathways for nitrogen and carbon in the system were described with preliminary mass closure of 60-80% and 60% for nitrogen and carbon.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steinberg, Daniel; Bielen, Dave; Eichman, Josh

Electrification of end-use services in the transportation, buildings, and industrial sectors coupled with decarbonization of electricity generation has been identified as one of the key pathways to achieving a low-carbon future in the United States. By lowering the carbon intensity of the electricity generation and substituting electricity for higher-emissions fossil fuels in end-use sectors, significant reductions in carbon dioxide emissions can be achieved. This report describes a preliminary analysis that examines the potential impacts of widespread electrification on the U.S. energy sector. We develop a set of exploratory scenarios under which electrification is aggressively pursued across all end-use sectors andmore » examine the impacts of achieving these electrification levels on electricity load patterns, total fossil energy consumption, carbon dioxide emissions, and the evolution of the U.S. power system.« less

Biomechanical stability of a supra-acetabular pedicle screw internal fixation device (INFIX) vs external fixation and plates for vertically unstable pelvic fractures.

PubMed

Vigdorchik, Jonathan M; Esquivel, Amanda O; Jin, Xin; Yang, King H; Onwudiwe, Ndidi A; Vaidya, Rahul

2012-09-27

We have recently developed a subcutaneous anterior pelvic fixation technique (INFIX). This internal fixator permits patients to sit, roll over in bed and lie on their sides without the cumbersome external appliances or their complications. The purpose of this study was to evaluate the biomechanical stability of this novel supraacetabular pedicle screw internal fixation construct (INFIX) and compare it to standard internal fixation and external fixation techniques in a single stance pelvic fracture model. Nine synthetic pelves with a simulated anterior posterior compression type III injury were placed into three groups (External Fixator, INFIX and Internal Fixation). Displacement, total axial stiffness, and the stiffness at the pubic symphysis and SI joint were calculated. Displacement and stiffness were compared by ANOVA with a Bonferroni adjustment for multiple comparisons The mean displacement at the pubic symphysis was 20, 9 and 0.8 mm for external fixation, INFIX and internal fixation, respectively. Plate fixation was significantly stiffer than the INFIX and external Fixator (P = 0.01) at the symphysis pubis. The INFIX device was significantly stiffer than external fixation (P = 0.017) at the symphysis pubis. There was no significant difference in SI joint displacement between any of the groups. Anterior plate fixation is stiffer than both the INFIX and external fixation in single stance pelvic fracture model. The INFIX was stiffer than external fixation for both overall axial stiffness, and stiffness at the pubic symphysis. Combined with the presumed benefit of minimizing the complications associated with external fixation, the INFIX may be a more preferable option for temporary anterior pelvic fixation in situations where external fixation may have otherwise been used.

Biomechanical Evaluation of All-Polyethylene Pegged Bony Ingrowth Glenoid Fixation Techniques on Implant Micromotion.

PubMed

Wiater, Brett P; Moravek, James E; Kurdziel, Michael D; Baker, Kevin C; Wiater, J Michael

2016-01-01

Newer glenoid components that allow for hybrid cement fixation via traditional cementation of peripheral pegs and bony ingrowth into an interference-fit central peg introduce the possibility of long-term biological fixation. However, little biomechanical work has been done on the initial stability of these components and the various fixation options. We conducted a study in which all-polyethylene glenoid components with a centrally fluted peg were implanted in polyurethane blocks with interference-fit, hybrid cement, and fully cemented fixation (5 per fixation group). Biomechanical evaluation of glenoid loosening, according to ASTM Standard F-2028-12, subjected the glenoids to 50,000 cycles of rim loading, and glenoid component motion was recorded with 2 differential variable reluctance transducers fixed to each glenoid prosthesis. Fully cemented fixation exhibited significantly less mean distraction in comparison with interference-fit fixation (P < .001) and hybrid cement fixation (P < .001). Hybrid cement fixation exhibited significantly less distraction (P < .001), more compression (P < .001), and no significant difference in glenoid translation (P = .793) in comparison with interference-fit fixation. Fully cemented fixation exhibited the most resistance to glenoid motion in comparison with hybrid cement fixation and interference-fit fixation. However, hybrid cement fixation and interference-fit fixation exhibited equivocal motion. Given these results, cementation of peripheral pegs may confer no additional initial stability over that provided by uncemented interference-fit fixation.

Comparative Proteomic Analysis of the Molecular Responses of Mouse Macrophages to Titanium Dioxide and Copper Oxide Nanoparticles Unravels Some Toxic Mechanisms for Copper Oxide Nanoparticles in Macrophages

PubMed Central

Triboulet, Sarah; Aude-Garcia, Catherine; Armand, Lucie; Collin-Faure, Véronique; Chevallet, Mireille; Diemer, Hélène; Gerdil, Adèle; Proamer, Fabienne; Strub, Jean-Marc; Habert, Aurélie; Herlin, Nathalie; Van Dorsselaer, Alain; Carrière, Marie; Rabilloud, Thierry

2015-01-01

Titanium dioxide and copper oxide nanoparticles are more and more widely used because of their catalytic properties, of their light absorbing properties (titanium dioxide) or of their biocidal properties (copper oxide), increasing the risk of adverse health effects. In this frame, the responses of mouse macrophages were studied. Both proteomic and targeted analyses were performed to investigate several parameters, such as phagocytic capacity, cytokine release, copper release, and response at sub toxic doses. Besides titanium dioxide and copper oxide nanoparticles, copper ions were used as controls. We also showed that the overall copper release in the cell does not explain per se the toxicity observed with copper oxide nanoparticles. In addition, both copper ion and copper oxide nanoparticles, but not titanium oxide, induced DNA strands breaks in macrophages. As to functional responses, the phagocytic capacity was not hampered by any of the treatments at non-toxic doses, while copper ion decreased the lipopolysaccharide-induced cytokine and nitric oxide productions. The proteomic analyses highlighted very few changes induced by titanium dioxide nanoparticles, but an induction of heme oxygenase, an increase of glutathione synthesis and a decrease of tetrahydrobiopterin in response to copper oxide nanoparticles. Subsequent targeted analyses demonstrated that the increase in glutathione biosynthesis and the induction of heme oxygenase (e.g. by lovastatin/monacolin K) are critical for macrophages to survive a copper challenge, and that the intermediates of the catecholamine pathway induce a strong cross toxicity with copper oxide nanoparticles and copper ions. PMID:25902355

Establishment of a Vaporous Hydrogen Peroxide Bio-Decontamination Capability

DTIC Science & Technology

2007-02-01

of Colorado at Denver and Health Sciences Center. There he utilised mass spectrometry to investigate the biochemical pathways involved in lipid... techniques (NMR, GC). Since then she has worked in a variety of areas including: (a) computer simulation of vapour dispersion for early warning to...to inactivate biological agents such as B. anthracis and these include beta-propiolactone, chlorine dioxide, ethylene oxide, propylene oxide, ozone

Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle.

PubMed

Detman, Anna; Mielecki, Damian; Pleśniak, Łukasz; Bucha, Michał; Janiga, Marek; Matyasik, Irena; Chojnacka, Aleksandra; Jędrysek, Mariusz-Orion; Błaszczyk, Mieczysław K; Sikora, Anna

2018-01-01

Anaerobic digestion, whose final products are methane and carbon dioxide, ensures energy flow and circulation of matter in ecosystems. This naturally occurring process is used for the production of renewable energy from biomass. Lactate, a common product of acidic fermentation, is a key intermediate in anaerobic digestion of biomass in the environment and biogas plants. Effective utilization of lactate has been observed in many experimental approaches used to study anaerobic digestion. Interestingly, anaerobic lactate oxidation and lactate oxidizers as a physiological group in methane-yielding microbial communities have not received enough attention in the context of the acetogenic step of anaerobic digestion. This study focuses on metabolic transformation of lactate during the acetogenic and methanogenic steps of anaerobic digestion in methane-yielding bioreactors. Methane-yielding microbial communities instead of pure cultures of acetate producers were used to process artificial lactate-rich media to methane and carbon dioxide in up-flow anaerobic sludge blanket reactors. The media imitated the mixture of acidic products found in anaerobic environments/digesters where lactate fermentation dominates in acidogenesis. Effective utilization of lactate and biogas production was observed. 16S rRNA profiling was used to examine the selected methane-yielding communities. Among Archaea present in the bioreactors, the order Methanosarcinales predominated. The acetoclastic pathway of methane formation was further confirmed by analysis of the stable carbon isotope composition of methane and carbon dioxide. The domain Bacteria was represented by Bacteroidetes , Firmicutes , Proteobacteria , Synergistetes , Actinobacteria , Spirochaetes , Tenericutes , Caldithrix , Verrucomicrobia , Thermotogae , Chloroflexi , Nitrospirae, and Cyanobacteria. Available genome sequences of species and/or genera identified in the microbial communities were searched for genes encoding the lactate-oxidizing metabolic machinery homologous to those of Acetobacterium woodii and Desulfovibrio vulgaris . Furthermore, genes for enzymes of the reductive acetyl-CoA pathway were present in the microbial communities. The results indicate that lactate is oxidized mainly to acetate during the acetogenic step of AD and this comprises the acetotrophic pathway of methanogenesis. The genes for lactate utilization under anaerobic conditions are widespread in the domain Bacteria. Lactate oxidation to the substrates for methanogens is the most energetically attractive process in comparison to butyrate, propionate, or ethanol oxidation.

Alnus peptides modify membrane porosity and induce the release of nitrogen-rich metabolites from nitrogen-fixing Frankia.

PubMed

Carro, Lorena; Pujic, Petar; Alloisio, Nicole; Fournier, Pascale; Boubakri, Hasna; Hay, Anne E; Poly, Franck; François, Philippe; Hocher, Valerie; Mergaert, Peter; Balmand, Severine; Rey, Marjolaine; Heddi, Abdelaziz; Normand, Philippe

2015-08-01

Actinorhizal plant growth in pioneer ecosystems depends on the symbiosis with the nitrogen-fixing actinobacterium Frankia cells that are housed in special root organs called nodules. Nitrogen fixation occurs in differentiated Frankia cells known as vesicles. Vesicles lack a pathway for assimilating ammonia beyond the glutamine stage and are supposed to transfer reduced nitrogen to the plant host cells. However, a mechanism for the transfer of nitrogen-fixation products to the plant cells remains elusive. Here, new elements for this metabolic exchange are described. We show that Alnus glutinosa nodules express defensin-like peptides, and one of these, Ag5, was found to target Frankia vesicles. In vitro and in vivo analyses showed that Ag5 induces drastic physiological changes in Frankia, including an increased permeability of vesicle membranes. A significant release of nitrogen-containing metabolites, mainly glutamine and glutamate, was found in N2-fixing cultures treated with Ag5. This work demonstrates that the Ag5 peptide is central for Frankia physiology in nodules and uncovers a novel cellular function for this large and widespread defensin peptide family.

Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.

PubMed

Feist, Adam M; Nagarajan, Harish; Rotaru, Amelia-Elena; Tremblay, Pier-Luc; Zhang, Tian; Nevin, Kelly P; Lovley, Derek R; Zengler, Karsten

2014-04-01

Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.

Glucose metabolism in batch and continuous cultures of Gluconacetobacter diazotrophicus PAL 3.

PubMed

Luna, María F; Bernardelli, Cecilia E; Galar, María L; Boiardi, José L

2006-03-01

Periplasmic glucose oxidation (by way of a pyrrolo-quinoline-quinone [PQQ]-linked glucose dehydrogenase [GDH]) was observed in continuous cultures of Gluconacetobacter diazotrophicus regardless of the carbon source (glucose or gluconate) and the nitrogen source (N(2) or NH(3)). Its synthesis was stimulated by conditions of high energetic demand (i.e., N(2)-fixation) and/or C-limitation. Under C-excess conditions, PQQ-GDH synthesis increased with the glucose concentration in the culture medium. In batch cultures, PQQ-GDH was actively expressed in very early stages with higher activities under conditions of N(2)-fixation. Hexokinase activity was almost absent under any culture condition. Cytoplasmic nicotinamide adenine dinucleotide (NAD)-linked glucose dehydrogenase (GDH) was expressed in continuous cultures under all tested conditions, and its synthesis increased with the glucose concentration. In contrast, low activities of this enzyme were detected in batch cultures. Periplasmic oxidation, by way of PQQ-GDH, seems to be the principal pathway for metabolism of glucose in G. Diazotrophicus, and NAD-GDH is an alternative route under certain environmental conditions.

Preanalytical variables and phosphoepitope expression in FFPE tissue: quantitative epitope assessment after variable cold ischemic time.

PubMed

Vassilakopoulou, Maria; Parisi, Fabio; Siddiqui, Summar; England, Allison M; Zarella, Elizabeth R; Anagnostou, Valsamo; Kluger, Yuval; Hicks, David G; Rimm, David L; Neumeister, Veronique M

2015-03-01

Individualized targeted therapies for cancer patients require accurate and reproducible assessment of biomarkers to be able to plan treatment accordingly. Recent studies have shown highly variable effects of preanalytical variables on gene expression profiling and protein levels of different tissue types. Several publications have described protein degradation of tissue samples as a direct result of delay of formalin fixation of the tissue. Phosphorylated proteins are more labile and epitope degradation can happen within 30 min of cold ischemic time. To address this issue, we evaluated the change in antigenicity of a series of phosphoproteins in paraffin-embedded samples from breast tumors as a function of time to formalin fixation. A tissue microarray consisting of 93 breast cancer specimens with documented time-to-fixation was used to evaluate changes in antigenicity of 12 phosphoepitopes frequently used in research settings as a function of cold ischemic time. Analysis was performed in a quantitative manner using the AQUA technology for quantitative immunofluorescence. For each marker, least squares univariate linear regression was performed and confidence intervals were computed using bootstrapping. The majority of the epitopes tested revealed changes in expression levels with increasing time to formalin fixation. Some phosphorylated proteins, such as phospho-HSP27 and phospho-S6 RP, involved in post-translational modification and stress response pathways increased in expression or phosphorylation levels. Others (like phospho-AKT, phosphor-ERK1/2, phospho-Tyrosine, phospho-MET, and others) are quite labile and loss of antigenicity can be reported within 1-2 h of cold ischemic time. Therefore specimen collection should be closely monitored and subjected to quality control measures to ensure accurate measurement of these epitopes. However, a few phosphoepitopes (like phospho-JAK2 and phospho-ER) are sufficiently robust for routine usage in companion diagnostic testing.

Gaze shifts and fixations dominate gaze behavior of walking cats

PubMed Central

Rivers, Trevor J.; Sirota, Mikhail G.; Guttentag, Andrew I.; Ogorodnikov, Dmitri A.; Shah, Neet A.; Beloozerova, Irina N.

2014-01-01

Vision is important for locomotion in complex environments. How it is used to guide stepping is not well understood. We used an eye search coil technique combined with an active marker-based head recording system to characterize the gaze patterns of cats walking over terrains of different complexity: (1) on a flat surface in the dark when no visual information was available, (2) on the flat surface in light when visual information was available but not required, (3) along the highly structured but regular and familiar surface of a horizontal ladder, a task for which visual guidance of stepping was required, and (4) along a pathway cluttered with many small stones, an irregularly structured surface that was new each day. Three cats walked in a 2.5 m corridor, and 958 passages were analyzed. Gaze activity during the time when the gaze was directed at the walking surface was subdivided into four behaviors based on speed of gaze movement along the surface: gaze shift (fast movement), gaze fixation (no movement), constant gaze (movement at the body’s speed), and slow gaze (the remainder). We found that gaze shifts and fixations dominated the cats’ gaze behavior during all locomotor tasks, jointly occupying 62–84% of the time when the gaze was directed at the surface. As visual complexity of the surface and demand on visual guidance of stepping increased, cats spent more time looking at the surface, looked closer to them, and switched between gaze behaviors more often. During both visually guided locomotor tasks, gaze behaviors predominantly followed a repeated cycle of forward gaze shift followed by fixation. We call this behavior “gaze stepping”. Each gaze shift took gaze to a site approximately 75–80 cm in front of the cat, which the cat reached in 0.7–1.2 s and 1.1–1.6 strides. Constant gaze occupied only 5–21% of the time cats spent looking at the walking surface. PMID:24973656

Dogs Evaluate Threatening Facial Expressions by Their Biological Validity – Evidence from Gazing Patterns

PubMed Central

Somppi, Sanni; Törnqvist, Heini; Kujala, Miiamaaria V.; Hänninen, Laura; Krause, Christina M.; Vainio, Outi

2016-01-01

Appropriate response to companions’ emotional signals is important for all social creatures. The emotional expressions of humans and non-human animals have analogies in their form and function, suggesting shared evolutionary roots, but very little is known about how animals other than primates view and process facial expressions. In primates, threat-related facial expressions evoke exceptional viewing patterns compared with neutral or positive stimuli. Here, we explore if domestic dogs (Canis familiaris) have such an attentional bias toward threatening social stimuli and whether observed emotional expressions affect dogs’ gaze fixation distribution among the facial features (eyes, midface and mouth). We recorded the voluntary eye gaze of 31 domestic dogs during viewing of facial photographs of humans and dogs with three emotional expressions (threatening, pleasant and neutral). We found that dogs’ gaze fixations spread systematically among facial features. The distribution of fixations was altered by the seen expression, but eyes were the most probable targets of the first fixations and gathered longer looking durations than mouth regardless of the viewed expression. The examination of the inner facial features as a whole revealed more pronounced scanning differences among expressions. This suggests that dogs do not base their perception of facial expressions on the viewing of single structures, but the interpretation of the composition formed by eyes, midface and mouth. Dogs evaluated social threat rapidly and this evaluation led to attentional bias, which was dependent on the depicted species: threatening conspecifics’ faces evoked heightened attention but threatening human faces instead an avoidance response. We propose that threatening signals carrying differential biological validity are processed via distinctive neurocognitive pathways. Both of these mechanisms may have an adaptive significance for domestic dogs. The findings provide a novel perspective on understanding the processing of emotional expressions and sensitivity to social threat in non-primates. PMID:26761433

Sulfur dioxide inhibits vascular smooth muscle cell proliferation via suppressing the Erk/MAP kinase pathway mediated by cAMP/PKA signaling

PubMed Central

Liu, D; Huang, Y; Bu, D; Liu, A D; Holmberg, L; Jia, Y; Tang, C; Du, J; Jin, H

2014-01-01

The present study was designed to investigate the role of endogenous sulfur dioxide (SO2) in vascular smooth muscle cell (VSMC) proliferation, and explore the possible role of cross-talk between cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) and extracellular signal-regulated kinase (Erk)/mitogen-activated protein kinase (MAPK) pathways in this action. By cell counting, growth curve depict, flow cytometry and bromodeoxyuridine (BrdU) labeling assays, we found that SO2 inhibited VSMC proliferation by preventing cell cycle progression from G1 to S phase and by reducing DNA synthesis. SO2 synthase aspartate aminotransferase (AAT1 and AAT2) overexpression significantly inhibited serum-induced proliferating cell nuclear antigen (PCNA) protein expression in VSMCs, demonstrated by western blot analysis. Moreover, overexpression of AAT1 or AAT2 markedly reduced incorporation of BrdU in serum-treated VSMCs. By contrast, either AAT1 or AAT2 knockdown significantly exacerbated serum-stimulated VSMC proliferation. Thus, both exogenous- and endogenous-derived SO2 suppressed serum-induced VSMC proliferation. However, annexin V-propidium iodide (PI) staining and cell cycle analysis demonstrated that SO2 did not influence VSMC apoptosis in the serum-induced proliferation model. In a platelet-derived growth factor (PDGF)-BB-stimulated VSMC proliferation model, SO2 dephosphorylated the active sites of Erk1/2, MAPK kinase 1/2 and RAF proto-oncogene serine/threonine-protein kinase (c-Raf) induced by PDGF-BB. However, the inactivation of the three kinases of the Erk/MAPK pathway was not due to the separate interferences on them by SO2 simultaneously, but a consequence of the influence on the upstream activity of the c-Raf molecule. Hence, we examined the cAMP/PKA pathway, which could inhibit Erk/MAPK transduction in VSMCs. The results showed that SO2 could stimulate the cAMP/PKA pathway to block c-Raf activation, whereas the Ser259 site on c-Raf had an important role in SO2-induced suppression of Erk/MAPK pathway. The present study firstly demonstrated that SO2 exerted a negative regulation of VSMC proliferation via suppressing the Erk/MAPK pathway mediated by cAMP/PKA signaling. PMID:24853429

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

PubMed Central

Badhai, Jhasketan; Ghosh, Tarini S.; Das, Subrata K.

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria. PMID:26579081

Anaerobic Carbon Metabolism by the Tricarboxylic Acid Cycle : Evidence for Partial Oxidative and Reductive Pathways during Dark Ammonium Assimilation.

PubMed

Vanlerberghe, G C; Horsey, A K; Weger, H G; Turpin, D H

1989-12-01

Nitrogen-limited cells of Selenastrum minutum (Naeg.) Collins are able to assimilate NH(4) (+) in the dark under anaerobic conditions. Addition of NH(4) (+) to anaerobic cells results in a threefold increase in tricarboxylic acid cycle (TCAC) CO(2) efflux and an eightfold increase in the rate of anaplerotic carbon fixation via phosphoenolpyruvate carboxylase. Both of these observations are consistent with increased TCAC carbon flow to supply intermediates for amino acid biosynthesis. Addition of H(14)CO(3) (-) to anaerobic cells assimilating NH(4) (+) results in the incorporation of radiolabel into the alpha-carboxyl carbon of glutamic acid. Incorporation of radiolabel into glutamic acid is not simply a short-term phenomenon following NH(4) (+) addition as the specific activity of glutamic acid increases over time. This indicates that this alga is able to maintain partial oxidative TCAC carbon flow while under anoxia to supply alpha-ketoglutarate for glutamate production. During dark aerobic NH(4) (+) assimilation, no radiolabel appears in fumarate or succinate and only a small amount occurs in malate. During anaerobic NH(4) (+) assimilation, these metabolites contain a large proportion of the total radiolabel and radiolabel accumulates in succinate over time. Also, the ratio of dark carbon fixation to NH(4) (+) assimilation is much higher under anaerobic than aerobic conditions. These observations suggest the operation of a partial reductive TCAC from oxaloacetic acid to malate, fumarate, and succinate. Such a pathway might contribute to redox balance in an anaerobic cell maintaining partial oxidative TCAC activity.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India.

PubMed

Badhai, Jhasketan; Ghosh, Tarini S; Das, Subrata K

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58°C; pH: 7.2-7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

Modeling pathways of riverine nitrogen and phosphorus in the Baltic Sea

NASA Astrophysics Data System (ADS)

Radtke, H.; Neumann, T.; Voss, M.; Fennel, W.

2012-09-01

A better understanding of the fate of nutrients entering the Baltic Sea ecosystem is an important issue with implications for environmental management. There are two sources of nitrogen and phosphorus: riverine input and atmospheric deposition. In the case of nitrogen, the fixation of dinitrogen by diazotrophic bacteria represents a third source. From an analysis of stable nitrogen isotope ratios it was suggested that most of the riverine nitrogen is sequestered in the coastal rim, specifically along the southern Baltic Sea coast with its coarse sediments, whereas nitrogen from fixation dominates the central basins. However, pathways of nutrients and timescales between the input of the nutrients and their arrival in different basins are difficult to obtain from direct measurements. To elucidate this problem, we use a source attribution technique in a three-dimensional ecosystem model, ERGOM, to track nutrients originating from various rivers. An “age” variable is attributed to the marked elements to indicate their propagation speeds and residence times. In this paper, we specifically investigate the spreading of nitrogen and phosphorus from the riverine discharges of the Oder, Vistula, Neman and Daugava. We demonstrate which regions they are transported to and for how long they remain in the ecosystem. The model results show good agreement with source estimations from observed δ15N values in sediments. The model results suggest that 95% of nitrogen is lost by denitrification in sediments, after an average time of 1.4 years for riverine nitrogen. The residence time of riverine phosphorus is much longer and exceeds our simulated period of 35 years.

Sodium fluoride and sulfur dioxide affected male reproduction by disturbing blood-testis barrier in mice.

PubMed

Zhang, Jianhai; Li, Zhihui; Qie, Mingli; Zheng, Ruibo; Shetty, Jagathpala; Wang, Jundong

2016-08-01

Fluoride and sulfur dioxide (SO2), two well-known environmental toxicants, have been implicated to have adverse effects on male reproductive health in humans and animals. The objective of this study to investigate if the BTB is one of the pathways that lead to reproductive toxicity of sodium fluoride and sulfur dioxide alone or in combination, in view of the key role of blood testis barrier (BTB) in testis. The results showed that a marked decrease in sperm quality, and altered morphology and ultrastructure of BTB in testis of mice exposure to fluoride (100 mg NaF/L in drinking water) or/and sulfur dioxide (28 mg SO2/m(3), 3 h/day). Meanwhile, the mRNA expression levels of some vital BTB-associated proteins, including occluding, claudin-11, ZO-1, Ncadherin, α-catenin, and connexin-43 were all strikingly reduced after NaF exposure, although only the reduction of DSG-2 was statistically significant in all treatment groups. Moreover, the proteins expressions also decreased significantly in claudin-11, N-cadherin, α-catenin, connexin-43 and desmoglein-2 in mice treated with fluoride and/or SO2. These changes in BTB structure and constitutive proteins may therefore be connected with the low sperm quality in these mice. The role of fluoride should deserves more attention in this process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Biomechanical characteristics of fixation methods for floating pubic symphysis.

PubMed

Song, Wenhao; Zhou, Dongsheng; He, Yu

2017-03-07

Floating pubic symphysis (FPS) is a relatively rare injury caused by high-energy mechanisms. There are several fixation methods used to treat FPS, including external fixation, subcutaneous fixation, internal fixation, and percutaneous cannulated screw fixation. To choose the appropriate fixation, it is necessary to study the biomechanical performance of these different methods. The goal of this study was to compare the biomechanical characteristics of six methods by finite element analysis. A three-dimensional finite element model of FPS was simulated. Six methods were used in the FPS model, including external fixation (Ext), subcutaneous rod fixation (Sub-rod), subcutaneous plate fixation (Sub-plate), superior pectineal plate fixation (Int-sup), infrapectineal plate fixation (Int-ifa), and cannulated screw fixation (Int-scr). Compressive and rotational loads were then applied in all models. Biomechanical characteristics that were recorded and analyzed included construct stiffness, micromotion of the fracture gaps, von Mises stress, and stress distribution. The construct stiffness of the anterior pelvic ring was decreased dramatically when FPS occurred. Compressive stiffness was restored by the three internal fixation and Sub-rod methods. Unfortunately, rotational stiffness was not restored satisfactorily by the six methods. For micromotion of the fracture gaps, the displacement was reduced significantly by the Int-sup and Int-ifa methods under compression. The internal fixation methods and Sub-plate method performed well under rotation. The maximum von Mises stress of the implants was not large. For the plate-screw system, the maximum von Mises stress occurred over the region of the fracture and plate-screw joints. The maximum von Mises stress appeared on the rod-screw and screw-bone interfaces for the rod-screw system. The present study showed the biomechanical advantages of internal fixation methods for FPS from a finite element view. Superior stabilization of the anterior pelvic ring and fracture gaps was obtained by internal fixation. Subcutaneous fixation had satisfactory outcomes as well. Sub-rod fixation offered good anti-compression, while the Sub-plate fixation provided favorable anti-rotational capacity.

The effect of hubs and shortcuts on fixation time in evolutionary graphs

NASA Astrophysics Data System (ADS)

Askari, Marziyeh; Moradi Miraghaei, Zeinab; Aghababaei Samani, Keivan

2017-07-01

How can a new species (like a gene, an idea, or a strategy) take over the whole of a population? This process, which is called fixation, is considerably affected by the structure of the population. There are two key quantities to quantify the fixation process, namely fixation probability and fixation time. Fixation probability has been vastly studied in recent years, but fixation time has not been completely explored, yet. This is because the discovery of a relationship between fixation time and network structure is quite challenging. In this paper we investigate this relationship for a number of well-known complex networks. We show that the existence of a few high-degree nodes (hubs) in the network results in a longer fixation time, while the existence of a few short-cuts decreases the fixation time. Furthermore we investigate the effect of network parameters, such as connection probability, on fixation time. We show that by increasing the density of edges, fixation time decreases for all types of studied networks. Finally, we survey the effect of rewiring probability in a Watts-Strogatz network on fixation time.

Comparison of Tibiofemoral Contact Mechanics After Various Transtibial and All-Inside Fixation Techniques for Medial Meniscus Posterior Root Radial Tears in a Porcine Model.

PubMed

Chung, Kyu Sung; Choi, Choong Hyeok; Bae, Tae Soo; Ha, Jeong Ku; Jun, Dal Jae; Wang, Joon Ho; Kim, Jin Goo

2018-04-01

To compare tibiofemoral contact mechanics after fixation for medial meniscus posterior root radial tears (MMPRTs). Seven fresh knees from mature pigs were used. Each knee was tested under 5 conditions: normal knee, MMPRT, pullout fixation with simple sutures, fixation with modified Mason-Allen sutures, and all-inside fixation using Fastfix 360. The peak contact pressure and contact surface area were evaluated using a capacitive sensor positioned between the meniscus and tibial plateau, under a 1,000-N compression force, at different flexion angles (0°, 30°, 60°, and 90°). The peak contact pressure was significantly higher in MMPRTs than in normal knees (P = .018). Although the peak contact pressure decreased significantly after fixation at all flexion angles (P = .031), it never recovered to the values noted in the normal meniscus. No difference was observed among fixation groups (P = .054). The contact surface area was significantly lower in MMPRTs than in the normal meniscus (P = .018) and increased significantly after fixation at all flexion angles (P = .018) but did not recover to within normal limits. For all flexion angles except 60°, the contact surface area was significantly higher for fixation with Mason-Allen sutures than for fixation with simple sutures or all-inside fixation (P = .027). At 90° of flexion, the contact surface area was significantly better for fixation with simple sutures than for all-inside fixation (P = .031). The peak contact pressure and contact surface area improved significantly after fixation, regardless of the fixation method, but did not recover to the levels noted in the normal meniscus after any type of fixation. Among the fixation methods evaluated in this time 0 study, fixation using modified Mason-Allen sutures provided a superior contact surface area compared with that noted after fixation using simple sutures or all-inside fixation, except at 60° of flexion. However, this study had insufficient power to accurately detect the differences between the outcomes of various fixation methods. Our results in a porcine model suggest that fixation can restore tibiofemoral contact mechanics in MMPRT and that fixation with a locking mechanism leads to superior biomechanical properties. Copyright © 2017 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

BIOSYNTHESIS OF CHLORAMPHENICOL IV.

PubMed Central

Gottlieb, David; Carter, H. E.; Robbins, P. W.; Burg, R. W.

1962-01-01

Gottlieb, David (University of Illinois, Urbana), H. E. Carter, P. W. Robbins, and R. W. Burg. Biosynthesis of chloramphenicol. IV. Incorporation of carbon14-labeled precursors. J. Bacteriol. 84:888–895. 1962.—Metabolism of dl-phenylalanine stimulated antibiotic synthesis by Streptomyces venezuelae, and resulted in the fixation of carbons 1 and 2 into the carbonyl group of chloramphenicol. It probably occurs by the oxidation of these carbons to carbon dioxide, followed by incorporation. Carbon 3 and the adjacent ring carbon were found in the dichloromethyl and the carbonyl carbons, respectively, of the dichloroacetyl portion of the molecule. The phenyl group of the amino acid is not transferred to the ring in chloramphenicol. Another stimulatory amino acid, dl-norleucine, contributed carbon 2 only as the carbonyl carbon. dl-Leucine is metabolized so that two adjacent carbons appear as the carbons in the dichloroacetyl moiety of the antibiotic. From acetic acid, carbon 1 is found only in the carbonyl group of chloramphenicol; carbon 2 of the acid is more generally distributed among the ring and side chain of the p-nitrophenylserinol part of the antibiotic, but is in greatest concentration in the dichloroacetyl fraction. Formic acid and carbon dioxide also are transformed only to the carbonyl group. Glycerol, the main source of metabolized carbon in the medium, has a general role and contributes to all parts of the molecule. In addition, it has a specific role in supplying an intact three-carbon fragment which enters into the molecule of chloramphenicol as a unit. PMID:13949488

Eighth international congress on nitrogen fixation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1990-01-01

This volume contains the proceedings of the Eighth International Congress on Nitrogen Fixation held May 20--26, 1990 in Knoxville, Tennessee. The volume contains abstracts of individual presentations. Sessions were entitled Recent Advances in the Chemistry of Nitrogen Fixation, Plant-microbe Interactions, Limiting Factors of Nitrogen Fixation, Nitrogen Fixation and the Environment, Bacterial Systems, Nitrogen Fixation in Agriculture and Industry, Plant Function, and Nitrogen Fixation and Evolution.

Eighth international congress on nitrogen fixation. Final program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Not Available

1990-12-31

This volume contains the proceedings of the Eighth International Congress on Nitrogen Fixation held May 20--26, 1990 in Knoxville, Tennessee. The volume contains abstracts of individual presentations. Sessions were entitled Recent Advances in the Chemistry of Nitrogen Fixation, Plant-microbe Interactions, Limiting Factors of Nitrogen Fixation, Nitrogen Fixation and the Environment, Bacterial Systems, Nitrogen Fixation in Agriculture and Industry, Plant Function, and Nitrogen Fixation and Evolution.

Alternative pathways to the 1.5 °C target reduce the need for negative emission technologies

NASA Astrophysics Data System (ADS)

van Vuuren, Detlef P.; Stehfest, Elke; Gernaat, David E. H. J.; van den Berg, Maarten; Bijl, David L.; de Boer, Harmen Sytze; Daioglou, Vassilis; Doelman, Jonathan C.; Edelenbosch, Oreane Y.; Harmsen, Mathijs; Hof, Andries F.; van Sluisveld, Mariësse A. E.

2018-05-01

Mitigation scenarios that achieve the ambitious targets included in the Paris Agreement typically rely on greenhouse gas emission reductions combined with net carbon dioxide removal (CDR) from the atmosphere, mostly accomplished through large-scale application of bioenergy with carbon capture and storage, and afforestation. However, CDR strategies face several difficulties such as reliance on underground CO2 storage and competition for land with food production and biodiversity protection. The question arises whether alternative deep mitigation pathways exist. Here, using an integrated assessment model, we explore the impact of alternative pathways that include lifestyle change, additional reduction of non-CO2 greenhouse gases and more rapid electrification of energy demand based on renewable energy. Although these alternatives also face specific difficulties, they are found to significantly reduce the need for CDR, but not fully eliminate it. The alternatives offer a means to diversify transition pathways to meet the Paris Agreement targets, while simultaneously benefiting other sustainability goals.

Building carbon–carbon bonds using a biocatalytic methanol condensation cycle

PubMed Central

Bogorad, Igor W.; Chen, Chang-Ting; Theisen, Matthew K.; Wu, Tung-Yun; Schlenz, Alicia R.; Lam, Albert T.; Liao, James C.

2014-01-01

Methanol is an important intermediate in the utilization of natural gas for synthesizing other feedstock chemicals. Typically, chemical approaches for building C–C bonds from methanol require high temperature and pressure. Biological conversion of methanol to longer carbon chain compounds is feasible; however, the natural biological pathways for methanol utilization involve carbon dioxide loss or ATP expenditure. Here we demonstrated a biocatalytic pathway, termed the methanol condensation cycle (MCC), by combining the nonoxidative glycolysis with the ribulose monophosphate pathway to convert methanol to higher-chain alcohols or other acetyl-CoA derivatives using enzymatic reactions in a carbon-conserved and ATP-independent system. We investigated the robustness of MCC and identified operational regions. We confirmed that the pathway forms a catalytic cycle through 13C-carbon labeling. With a cell-free system, we demonstrated the conversion of methanol to ethanol or n-butanol. The high carbon efficiency and low operating temperature are attractive for transforming natural gas-derived methanol to longer-chain liquid fuels and other chemical derivatives. PMID:25355907

Comparison of clinical outcomes of iris fixation and scleral fixation as treatment for intraocular lens dislocation.

PubMed

Kim, Kyeong Hwan; Kim, Wan Soo

2015-09-01

To compare the efficacy and safety of iris fixation with scleral fixation in surgical repositioning of dislocated intraocular lenses (IOLs). Retrospective, consecutive, comparative interventional case series. setting: Referral hospital. Seventy-eight consecutive patients who underwent surgical repositioning of dislocated intraocular lenses using suturing to the sclera or iris. Forty-four eyes of 44 patients underwent scleral fixation and 35 eyes of 34 patients underwent iris fixation of dislocated intraocular lenses. Visual acuity, refractive stability, operation time, and perioperative complications, including recurrence of IOL dislocation. Corrected distance visual acuity (CDVA) improved significantly 1 month postoperatively in both groups (P < .01 each), and remained stable for 12 months. One week postoperatively, however, CDVA improved significantly in the scleral fixation (P = .040) but not in the iris fixation (P = .058) group. The amount of refractive error significantly diminished 1 day after surgery (P = .028 in the scleral fixation and P = .046 in the iris fixation group). For the astigmatic components, Jackson crossed cylinders equivalent to conventional cylinders of positive power at axes of 0 degrees (J0) and 45 degrees (J45), J45 differed significantly in the scleral fixation and iris fixation groups (P = .009), whereas J0 was similar (P > .05). Operation time was significantly shorter (P = .0007), while immediate postoperative inflammation was significantly more severe (P = .001), in the iris fixation than in the scleral fixation group. Recurrence rates were similar (P > .05), but the mean time to recurrence was significantly shorter in the iris fixation than in the scleral fixation group (P = .031). Iris fixation and scleral fixation techniques had similar efficacy in the repositioning of dislocated intraocular lenses. Although operation time was shorter for iris fixation, it had several disadvantages, including induced astigmatism, immediate postoperative inflammation, earlier recurrence, and less stable refraction. Copyright © 2015 Elsevier Inc. All rights reserved.

Reverse Anterior Cruciate Ligament Reconstruction Fixation: A Biomechanical Comparison Study of Tibial Cross-Pin and Femoral Interference Screw Fixation.

PubMed

Lawley, Richard J; Klein, Samuel E; Chudik, Steven C

2017-03-01

To evaluate the biomechanical performance of tibial cross-pin (TCP) fixation relative to femoral cross-pin (FCP), femoral interference screw (FIS), and tibial interference screw (TIS) fixation. We randomized 40 porcine specimens (20 tibias and 20 femurs) to TIS fixation (group 1, n = 10), FIS fixation (group 2, n = 10), TCP fixation (group 3, n = 10), or FCP fixation (group 4, n = 10) and performed biomechanical testing to compare ultimate load, stiffness, yield load, cyclic displacement, and load at 5-mm displacement. We performed cross-pin fixation of the looped end and interference screw fixation of the free ends of 9-mm-diameter bovine extensor digitorum communis tendon grafts. Graft fixation constructs were cyclically loaded and then loaded to failure in line with the tunnels. Regarding yield load, FIS was superior to TIS (704 ± 125 N vs 504 ± 118 N, P = .002), TCP was superior to TIS (1,449 ± 265 N vs 504 ± 118 N, P < .001), and TCP was superior to FCP (1,449 ± 265 N vs 792 ± 397 N, P < .001). Cyclic displacement for FCP was superior to TCP. Cyclic displacement for TIS versus FIS showed no statistically significant difference (2.5 ± 1.0 mm vs 2.2 ± 0.6 mm, P = .298). Interference screw fixation consistently failed by graft slippage, whereas TCP fixation failed by tibial bone failure. FCP fixation failed by either femoral bone failure or failure elsewhere in the testing apparatus. Regarding yield load, TCP fixation performed biomechanically superior to the clinically proven FCP at time zero. Because TIS fixation shows the lowest yield strength, it represents the weak link, and combined TCP-FIS fixation theoretically would be biomechanically superior relative to combined FCP-TIS fixation with regard to yield load. Cyclic displacement showed a small difference in favor of FCP over TCP fixation and no difference between TIS and FIS. Time-zero biomechanics of TCP fixation paired with FIS fixation show that this method of fixation can be considered a potential alternative to current practice and may pose clinical benefits in different clinical scenarios of anterior cruciate ligament reconstruction. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Chemosynthetic microbial activity at Mid-Atlantic Ridge hydrothermal vent sites

NASA Astrophysics Data System (ADS)

Wirsen, Carl O.; Jannasch, Holger W.; Molyneaux, Stephen J.

1993-06-01

Chemosynthetic production of microbial biomass, determined by 14CO2 fixation and enzymatic (RuBisCo) activity, at the Mid-Atlantic Ridge (MAR) 23° and 26°N vent sites was found in various niches: warm water emissions, loosely rock-attached flocculent material, dense morphologically diverse bacterial mats covering the surfaces of polymetal sulfide deposits, and filamentous microbes on the carapaces of shrimp (Rimicaris exoculata). The bacterial mats on polymetal sulfide surfaces contained unicellular and filamentous bacteria which appeared to use as their chemolithotrophic electron or energy source either dissolved reduced minerals from vent emissions, mainly sulfur compounds, or solid metal sulfide deposits, mainly pyrite. Moderately thermophilic Chemosynthetic activity was observed in carbon dioxide fixation experiments and in enrichments, but no thermophilic aerobic sulfur oxidizers could be isolated. Both obligate and facultative chemoautotrophs growing at mesophilic temperatures were isolated from all chemosynthetically active surface scrapings. The obligate autotrophs could oxidize sterilized MAR natural sulfide deposits as well as technical pyrite at near neutral pH, in addition to dissolved reduced sulfur compounds. While the grazing by shrimp on the surface mats of MAR metal sulfide deposits was observed and deemed important, the animals' primary occurrence in dense swarms near vent emissions suggests that they were feeding at these sites, where conditions for Chemosynthetic growth of their filamentous microbial epiflora were optimal. The data show that the transformation of geothermal energy at the massive polymetal sulfide deposits of the MAR is based on the lithoautotrophic oxidation of soluble sulfides and pyrites into microbial biomass.

Irrigation management and phosphorus addition alter the abundance of carbon dioxide-fixing autotrophs in phosphorus-limited paddy soil.

PubMed

Wu, Xiaohong; Ge, Tida; Yan, Wende; Zhou, Juan; Wei, Xiaomeng; Chen, Liang; Chen, Xiangbi; Nannipieri, Paolo; Wu, Jinshui

2017-12-01

In this study, we assessed the interactive effects of phosphorus (P) application and irrigation methods on the abundances of marker genes (cbbL, cbbM, accA and aclB) of CO2-fixing autotrophs. We conducted rice-microcosm experiments using a P-limited paddy soil, with and without the addition of P fertiliser (P-treated-pot (P) versus control pot (CK)), and using two irrigation methods, namely alternate wetting and drying (AWD) and continuous flooding (CF). The abundances of bacterial 16S rRNA, archaeal 16S rRNA, cbbL, cbbM, accA and aclB genes in the rhizosphere soil (RS) and bulk soil (BS) were quantified. The application of P significantly altered the soil properties and stimulated the abundances of Bacteria, Archaea and CO2-fixation genes under CF treatment, but negatively influenced the abundances of Bacteria and marker genes of CO2-fixing autotrophs in BS soils under AWD treatment. The response of CO2-fixing autotrophs to P fertiliser depended on the irrigation management method. The redundancy analysis revealed that 54% of the variation in the functional marker gene abundances could be explained by the irrigation method, P fertiliser and the Olsen-P content; however, the rhizosphere effect did not have any significant influence. P fertiliser application under CF was more beneficial in improving the abundance of CO2-fixing autotrophs compared to the AWD treatment; thus, it is an ideal irrigation management method to increase soil carbon fixation. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Comparison of Risk of Carpal Tunnel Syndrome in Patients with Distal Radius Fractures After 7 Treatments

PubMed Central

Zhao, Huan-Li; Wang, Gui-Bin; Jia, Yue-Qing; Zhu, Shi-Cai; Zhang, Feng-Fang; Liu, Hong-Mei

2015-01-01

Background To compare risk of carpal tunnel syndrome (CTS) in distal radius fracture (DRF) patients after 7 treatments using bridging external fixation (BrEF), non-bridging external fixation (non-BrEF), plaster fixation, K-wire fixation, dorsal plating fixation, volar plating fixation, and dorsal and volar plating by performing a network meta-analysis. Material/Methods An exhaustive search of electronic databases identified randomized controlled trails (RCTs) closely related to our study topic. The published articles were screened, based on predefined inclusion and exclusion criteria, to select high-quality studies for the present network meta-analysis. Data extracted from the selected studies were analyzed using STATA version 12.0 software. Results The literature search and selection process identified 12 eligible RCTs that contained a total of 1370 DRF patients (394 patients with BrEF, 377 patients with non-BrEF, 89 patients with K-wire fixation, 192 patients with plaster fixation, 42 patients with dorsal plating fixation, 152 patients with volar plating fixation, and 124 patients with dorsal and volar plating fixation). Our network meta-analysis results demonstrated no significant differences in CTS risk among the 7 treatments (P>0.05). The value of surface under the cumulative ranking curve (SUCRA), however, suggested that dorsal plating fixation is the optimal treatment, with the lowest risk of CTS in DRF patients (dorsal plating fixation: 89.2%; dorsal and volar plating: 57.8%; plaster fixation: 50.9%; non-BrEF: 50.6%; volar plating fixation: 39.6%; BrEF: 38.4%; K-wire fixation: 23.6%). Conclusions Our network meta-analysis provides evidence that dorsal plating fixation significantly decreases the risk of CTS and could be the method of choice in DRF patients. PMID:26391617

Single-screw Fixation of Adolescent Salter-II Proximal Humeral Fractures: Biomechanical Analysis of the "One Pass Door Lock" Technique.

PubMed

Miller, Mark Carl; Redman, Christopher N; Mistovich, R Justin; Muriuki, Muturi; Sangimino, Mark J

2017-09-01

Pin fixation of Salter-II proximal humeral fractures in adolescents approaching skeletal maturity has potential complications that can be avoided with single-screw fixation. However, the strength of screw fixation relative to parallel and diverging pin fixation is unknown. To compare the biomechanical fixation strength between these fixation modalities, we used synthetic composite humeri, and then compared these results in composite bone with cadaveric humeri specimens. Parallel pinning, divergent pinning, and single-screw fixation repairs were performed on synthetic composite humeri with simulated fractures. Six specimens of each type were tested in axial loading and other 6 were tested in torsion. Five pair of cadaveric humeri were tested with diverging pins and single screws for comparison. Single-screw fixation was statistically stronger than pin fixation in axial and torsional loading in both composite and actual bone. There was no statistical difference between composite and cadaveric bone specimens. Single-screw fixation can offer greater stability to adolescent Salter-II fractures than traditional pinning. Single-screw fixation should be considered as a viable alternative to percutaneous pin fixation in transitional patients with little expected remaining growth.

Signal processing related to the vestibulo-ocular reflex during combined angular rotation and linear translation of the head

NASA Technical Reports Server (NTRS)

McCrea, R. A.; Chen-Huang, C.; Peterson, B. W. (Principal Investigator)

1999-01-01

The contributions of vestibular nerve afferents and central vestibular pathways to the angular (AVOR) and linear (LVOR) vestibulo-ocular reflex were studied in squirrel monkeys during fixation of near and far targets. Irregular vestibular afferents did not appear to be necessary for the LVOR, since when they were selectively silenced with galvanic currents the LVOR was essentially unaffected during both far- and near-target viewing. The linear translation signals generated by secondary AVOR neurons in the vestibular nuclei were, on average, in phase with head velocity, inversely related to viewing distance, and were nearly as strong as AVOR-related signals. We suggest that spatial-temporal transformation of linear head translation signals to angular eye velocity commands is accomplished primarily by the addition of viewing distance multiplied, centrally integrated, otolith regular afferent signals to angular VOR pathways.

Steps Toward Understanding Mitochondrial Fe/S Cluster Biogenesis.

PubMed

Melber, Andrew; Winge, Dennis R

2018-01-01

Iron-sulfur clusters (Fe/S clusters) are essential cofactors required throughout the clades of biology for performing a myriad of unique functions including nitrogen fixation, ribosome assembly, DNA repair, mitochondrial respiration, and metabolite catabolism. Although Fe/S clusters can be synthesized in vitro and transferred to a client protein without enzymatic assistance, biology has evolved intricate mechanisms to assemble and transfer Fe/S clusters within the cellular environment. In eukaryotes, the foundation of all cellular clusters starts within the mitochondria. The focus of this review is to detail the mitochondrial Fe/S biogenesis (ISC) pathway along with the Fe/S cluster transfer steps necessary to mature Fe/S proteins. New advances in our understanding of the mitochondrial Fe/S biogenesis machinery will be highlighted. Additionally, we will address various experimental approaches that have been successful in the identification and characterization of components of the ISC pathway. © 2018 Elsevier Inc. All rights reserved.

Models of glycolysis: Glyceraldehyde as a source of energy and monomers for prebiotic condensation reactions

NASA Technical Reports Server (NTRS)

Weber, A. L.

1986-01-01

All organisms require energy in a chemical form for maintenance and growth. In contemporary life this chemical energy is obtained by the synthesis of the phosphoanhydride bonds of ATP. Among the biological processes that yield ATP, fermentation is generally considered primitive, because it operates under anaerobic conditions by substrate-level phosphorylation which does not require compartmentation by membranes. Fermentation by the glycolytic pathway, which is found in almost every living cell, is an especially attractive energy source for primitive life. Glycolysis not only produces useful chemical energy (ATP), but intermediates of this pathway are also involved in amino acid synthesis and photosynthetic carbon-fixation. It is believed that energy and substrates needed for the origin of life were provided by nonenzymatic chemical reactions that resemble the enzyme-mediated reactions of glycolysis. These nonenzymatic reactions would have provided a starting point for the evolutionary development of glycolysis.

Open reduction and internal fixation compared to closed reduction and external fixation in distal radial fractures

PubMed Central

Kopylov, Philippe; Geijer, Mats; Tägil, Magnus

2009-01-01

Background and purpose In unstable distal radial fractures that are impossible to reduce or to maintain in reduced position, the treatment of choice is operation. The type of operation and the choice of implant, however, is a matter of discussion. Our aim was to investigate whether open reduction and internal fixation would produce a better result than traditional external fixation. Methods 50 patients with an unstable or comminute distal radius fracture were randomized to either closed reduction and bridging external fixation, or open reduction and internal fixation using the TriMed system. The primary outcome parameter was grip strength, but the patients were followed for 1 year with objective clinical assessment, subjective outcome using DASH, and radiographic examination. Results At 1 year postoperatively, grip strength was 90% (SD 16) of the uninjured side in the internal fixation group and 78% (17) in the external fixation group. Pronation/supination was 150° (15) in the internal fixation group and 136° (20) in the external fixation group at 1 year. There were no differences in DASH scores or in radiographic parameters. 5 patients in the external fixation group were reoperated due to malunion, as compared to 1 in the internal fixation group. 7 other cases were classified as radiographic malunion: 5 in the external fixation group and 2 in the internal fixation group. Interpretation Internal fixation gave better grip strength and a better range of motion at 1 year, and tended to have less malunions than external fixation. No difference could be found regarding subjective outcome. PMID:19857180

[Comparison of external fixation with or without limited internal fixation for open knee fractures].

PubMed

Li, K N; Lan, H; He, Z Y; Wang, X J; Yuan, J; Zhao, P; Mu, J S

2018-03-01

Objective: To explore the characteristics and methods of different fixation methods and prevention of open knee joint fracture. Methods: The data of 86 cases of open knee joint fracture admitted from January 2002 to December 2015 in Department of Orthopaedics, Affiliated Hospital of Chengdu University were analyzed retrospectively.There were 65 males and 21 females aged of 38.6 years. There were 38 cases treated with trans articular external fixation alone, 48 cases were in the trans articular external fixation plus auxiliary limited internal fixation group. All the patients were treated according to the same three stages except for different fixation methods. Observation of external fixation and fracture fixation, fracture healing, wound healing and treatment, treatment and related factors of infection control and knee function recovery. χ(2) test was used to analyze data. Results: Eleven patients had primary wound healing, accounting for 12.8%. Seventy-five patients had two wounds healed, accounting for 87.2%. Only 38 cases of trans articular external fixator group had 31 cases of articular surface reduction, accounting for 81.6%; Five cases of trans articular external fixator assisted limited internal fixation group had 5 cases of poor reduction, accounting for 10.4%; There was significant difference between the two groups (χ(2)=44.132, P <0.05). Take a single cross joint external fixation group, a total of 23 cases of patients with infection, accounted for 60.5% of external fixation group; trans articular external fixation assisted limited internal fixation group there were 30 cases of patients with infection, accounting for the assistance of external fixator and limited internal fixation group 62.5%; There was significant difference between the two groups(χ(2)=0.035, P >0.05). Five cases of fracture nonunion cases of serious infection, patients voluntarily underwent amputation. The Lysholm Knee Scale: In the external fixation group, 23 cases were less than 50 points, accounting for 60.5%, 15 cases were more than 50 points, accounting for 39.5%, external fixation and limited internal fixation group 20 cases were less than 50 points, accounting for 41.7%, 28 cases were more than 50 points, accounting for 58.3%; There was significant difference between the two groups(χ(2)=1.279, P >0.05). Conclusions: Prevention and control of infection is a central link in the treatment of open fracture of the knee. Trans articular external fixator plus limited internal fixation is an important measure to treat open fracture of the knee-joint.

Metabolism of mequindox in liver microsomes of rats, chicken and pigs.

PubMed

Liu, Zhao-Ying; Huang, Ling-Li; Chen, Dong-Mei; Yuan, Zong-Hui

2010-04-15

Mequindox, 3-methyl-2-quinoxalinacetyl-1,4-dioxide, is a quinoxaline-N,N-dioxide used in veterinary medicine as a antibacterial in China. To gain an understanding of the interspecies differences in the metabolism of mequindox, comparative metabolite profiles were qualitatively and quantitatively carried out for the first time in rat, chicken and pig liver microsomes by high-performance liquid chromatography combined with hybrid ion trap/time-of-flight mass spectrometry. A total of 14 metabolites were characterized based on their accurate MS(2) spectra and known structure of mequindox. The in vitro metabolic pathways of mequindox in three species were proposed as N-->O group reduction, carbonyl reduction, N-->O group reduction followed by carbonyl reduction or methyl mono-hydroxylation. A metabolic pathway involving N-->O group reduction followed by acetyl group mono-hydroxylation in only chicken was also proposed. There was also quantitative species difference for mequindox metabolism in three species. 1-Desoxymequindox was the main metabolite in all species, but otherwise there were some qualitative interspecies differences in mequindox major metabolites. This work has revealed biotransformation characteristics of mequindox among different species, and moreover will further facilitate the explanations of the biological activities of mequindox in animals. 2010 John Wiley & Sons, Ltd.

Analysis of usage and associated cost of external fixators at an urban level 1 trauma centre.

PubMed

Chaus, George W; Dukes, Chase; Hak, David J; Mauffrey, Cyril; Mark Hammerberg, E

2014-10-01

To determine the usage, indication, duration, and cost associated with external fixation usage. Additionally, to show the significant cost associated with external fixator use and reinvigorate discussions on external fixator reuse. A retrospective review of a prospectively gathered trauma database was undertaken to identify all patients treated with external fixation frames for pelvic and lower extremity injuries between September 2007 and July 2010. We noted the indications for frame use, and we determined the average duration of external fixation for each indication. The cost of each frame was calculated from implant records. 341 lower extremity and pelvic fractures were treated with external fixation frames during the study period. Of these, 92% were used as temporary external fixation. The average duration of temporary external fixation was 10.5 days. The cost of external fixation frame components was $670,805 per year. The average cost per external fixation frame was $5900. The majority of external fixators are intended as temporary frames, in place for a limited period of time prior to definitive fixation of skeletal injuries. As such, most frames are not intended to withstand physiologic loads, nor are they expected provide a precise maintenance of reduction. Given the considerable expense associated with external fixation frame components, the practice of purchasing external fixation frame components as disposable "single-use" items appears to be somewhat wasteful. Level II. Copyright © 2014 Elsevier Ltd. All rights reserved.

Fixation distance and fixation duration to vertical road signs.

PubMed

Costa, Marco; Simone, Andrea; Vignali, Valeria; Lantieri, Claudio; Palena, Nicola

2018-05-01

The distance of first-fixation to vertical road signs was assessed in 22 participants while driving a route of 8.34 km. Fixations to road signs were recorded by a mobile eye-movement-tracking device synchronized to GPS and kinematic data. The route included 75 road signs. First-fixation distance and fixation duration distributions were positively skewed. Median distance of first-fixation was 51 m. Median fixation duration was 137 ms with a modal value of 66 ms. First-fixation distance was linearly related to speed and fixation duration. Road signs were gazed at a much closer distance than their visibility distance. In a second study a staircase procedure was used to test the presentation-time threshold that lead to a 75% accuracy in road sign identification. The threshold was 35 ms, showing that short fixations to a road signs could lead to a correct identification. Copyright © 2018 Elsevier Ltd. All rights reserved.

An in-vitro biomechanical study of different fixation techniques for the extended trochanteric osteotomy in revision THA.

PubMed

Zhu, Zhonglin; Ding, Hui; Shao, Hongyi; Zhou, Yixin; Wang, Guangzhi

2013-04-09

The wire fixation and the cable grip fixation have been developed for the extended trochanteric osteotomy (ETO) in the revision of total hip arthroplasty (THA). Many studies reported the postoperative performance of the patients, but with little quantitative biomechanical comparison of the two fixation systems. An in-vitro testing approach was designed to record the loosening between the femoral bed and the greater trochanter after fixations. Ten cadaveric femurs were chosen in this study. Each femur underwent the THA, revision by ETO and fixations. The tension to the greater trochanter was from 0 to 500N in vertical and lateral direction, respectively. The translation and rotation of the greater trochanter with respect to the bony bed were captured by an optical tracking system. In the vertical tension tests, the overall translation of the greater trochanter was observed 0.4 mm in the cable fixations and 7.0 mm in the wire fixations. In the lateral tension tests, the overall motion of the greater trochanter was 2.0 mm and 1.2° in the cable fixations, while it was 6.2 mm and 5.3° in the wire fixations. The result was significantly different between the two fixation systems. The stability of the proximal femur after ETO using different fixations in the revision THA was investigated. The cable grip fixation was significantly more stable than the wire fixation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burnum, Kristin E.; Callister, Stephen J.; Nicora, Carrie D.

Termites degrade and thrive on lignocellulose with help from the bacterial microbiome harbored within their guts. Because most of the diverse microorganisms within the gut microcobial community have yet to be cultivated, the proteomics details of the symbiotic mechanism remain unclear. In a metaproteomics study, we analyzed the bacterial community resident in the hindgut paunch of the wood-feeding ‘higher’ Nasutitermes species and identified 886 proteins, 197 of which have known enzymatic function. Using these enzymes, we reconstructed known metabolic pathways to gain a better understanding of carbohydrate transport and metabolism, nitrogen fixation and assimilation, energy production, and amino acid synthesismore » in these bacterial microbiomes.« less

Tendon transfer fixation: comparing a tendon to tendon technique vs. bioabsorbable interference-fit screw fixation.

PubMed

Sabonghy, Eric Peter; Wood, Robert Michael; Ambrose, Catherine Glauber; McGarvey, William Christopher; Clanton, Thomas Oscar

2003-03-01

Tendon transfer techniques in the foot and ankle are used for tendon ruptures, deformities, and instabilities. This fresh cadaver study compares the tendon fixation strength in 10 paired specimens by performing a tendon to tendon fixation technique or using 7 x 20-25 mm bioabsorbable interference-fit screw tendon fixation technique. Load at failure of the tendon to tendon fixation method averaged 279N (Standard Deviation 81N) and the bioabsorbable screw 148N (Standard Deviation 72N) [p = 0.0008]. Bioabsorbable interference-fit screws in these specimens show decreased fixation strength relative to the traditional fixation technique. However, the mean bioabsorbable screw fixation strength of 148N provides physiologic strength at the tendon-bone interface.

A Novel Fixation System for Acetabular Quadrilateral Plate Fracture: A Comparative Biomechanical Study

PubMed Central

Zha, Guo-Chun; Sun, Jun-Ying; Dong, Sheng-Jie; Zhang, Wen; Luo, Zong-Ping

2015-01-01

This study aims to assess the biomechanical properties of a novel fixation system (named AFRIF) and to compare it with other five different fixation techniques for quadrilateral plate fractures. This in vitro biomechanical experiment has shown that the multidirectional titanium fixation (MTF) and pelvic brim long screws fixation (PBSF) provided the strongest fixation for quadrilateral plate fracture; the better biomechanical performance of the AFRIF compared with the T-shaped plate fixation (TPF), L-shaped plate fixation (LPF), and H-shaped plate fixation (HPF); AFRIF gives reasonable stability of treatment for quadrilateral plate fracture and may offer a better solution for comminuted quadrilateral plate fractures or free floating medial wall fracture and be reliable in preventing protrusion of femoral head. PMID:25802849

SULFATE PRODUCTION IN CLOUDS IN EASTERN CHINA: OBSERVATIONS FROM MT. TAI

NASA Astrophysics Data System (ADS)

Collett, J. L.; Shen, X.; Lee, T.; Wang, X.; Wang, W.; Wang, T.

2009-12-01

The fate of China’s sulfur dioxide emissions depends, in part, on the ability of regional clouds to support rapid aqueous oxidation of these emissions to sulfate. Sulfur dioxide oxidized in regional clouds is more likely to be removed by wet deposition while sulfur dioxide that undergoes slower gas phase oxidation is expected to survive longer in the atmosphere and exert a radiative forcing impact over a broader spatial scale. Two 2008 field campaigns conducted at Mt. Tai, an isolated peak on the NE China plain, provide insight into the importance of various aqueous phase sulfur oxidation pathways in the region. Single and two-stage cloudwater collectors were used to collect bulk and drop size-resolved samples of cloudwater. Collected cloudwater was analyzed for key species that influence in-cloud sulfate production, including pH, S(IV), H2O2, Fe and Mn. Other major cloud solutes, including inorganic ions, total organic carbon, formaldehyde, and organic acids were also analyzed, as were gas phase concentrations of SO2, O3, and H2O2. A wide range of cloud pH was observed, from below 3 to above 6. High concentrations of cloudwater sulfate were consistent with abundant sulfur dioxide emissions in the region. Despite its fast aqueous reaction with sulfur dioxide, high concentrations of residual hydrogen peroxide were measured in some clouds implying a substantial capacity for additional sulfate production. Ozone was found to be an important S(IV) oxidant in some periods when cloud pH was high. This presentation will examine the importance of different oxidants (H2O2, O3, and O2 catalyzed by trace metals) for sulfur oxidation and the overall capacity of regional clouds to support rapid aqueous phase sulfate production.

Calibration and standardization of microwave ovens for fixation of brain and peripheral nerve tissue.

PubMed

Login, G R; Leonard, J B; Dvorak, A M

1998-06-01

Rapid and reproducible fixation of brain and peripheral nerve tissue for light and electron microscopy studies can be done in a microwave oven. In this review we report a standardized nomenclature for diverse fixation techniques that use microwave heating: (1) microwave stabilization, (2) fast and ultrafast primary microwave-chemical fixation, (3) microwave irradiation followed by chemical fixation, (4) primary chemical fixation followed by microwave irradiation, and (5) microwave fixation used in various combinations with freeze fixation. All of these methods are well suited to fix brain tissue for light microscopy. Fast primary microwave-chemical fixation is best for immunoelectron microscopy studies. We also review how the physical characteristics of the microwave frequency and the dimensions of microwave oven cavities can compromise microwave fixation results. A microwave oven can be calibrated for fixation when the following parameters are standardized: irradiation time; water load volume, initial temperature, and placement within the oven; fixative composition, volume, and initial temperature; and specimen container shape and placement within the oven. Using two recently developed calibration tools, the neon bulb array and the agar-saline-Giemsa tissue phantom, we report a simple calibration protocol that identifies regions within a microwave oven for uniform microwave fixation. Copyright 1998 Academic Press.

Insights into mechanisms governing forest carbon response to nitrogen deposition: a model-data comparison using observed responses to nitrogen addition

NASA Astrophysics Data System (ADS)

Thomas, R. Q.; Bonan, G. B.; Goodale, C. L.

2013-01-01

In many forest ecosystems, nitrogen (N) deposition enhances plant uptake of carbon dioxide, thus reducing climate warming from fossil fuel emissions. Therefore, accurately modeling how forest carbon (C) sequestration responds to N deposition is critical for understanding how future changes in N availability will influence climate. Here, we use observations of forest C response to N inputs along N deposition gradients and at five temperate forest sites with fertilization experiments to test and improve a~global biogeochemical model (CLM-CN 4.0). We show that the CLM-CN plant C growth response to N deposition was smaller than observed and the modeled response to N fertilization was larger than observed. A set of modifications to the CLM-CN improved the correspondence between model predictions and observational data (1) by increasing the aboveground C storage in response to historical N deposition (1850-2004) from 14 to 34 kg C per additional kg N added through deposition and (2) by decreasing the aboveground net primary productivity response to N fertilization experiments from 91 to 57 g C m-2 yr-1. Modeled growth response to N deposition was most sensitive to altering the processes that control plant N uptake and the pathways of N loss. The response to N deposition also increased with a more closed N cycle (reduced N fixation and N gas loss) and decreased when prioritizing microbial over plant uptake of soil inorganic N. The net effect of all the modifications to the CLM-CN resulted in greater retention of N deposition and a greater role of synergy between N deposition and rising atmospheric CO2 as a mechanism governing increases in temperate forest primary production over the 20th century. Overall, testing models with both the response to gradual increases in N inputs over decades (N deposition) and N pulse additions of N over multiple years (N fertilization) allows for greater understanding of the mechanisms governing C-N coupling.

Insights into mechanisms governing forest carbon response to nitrogen deposition: a model-data comparison using observed responses to nitrogen addition

NASA Astrophysics Data System (ADS)

Thomas, R. Q.; Bonan, G. B.; Goodale, C. L.

2013-06-01

In many forest ecosystems, nitrogen (N) deposition enhances plant uptake of carbon dioxide, thus reducing climate warming from fossil fuel emissions. Therefore, accurately modeling how forest carbon (C) sequestration responds to N deposition is critical for understanding how future changes in N availability will influence climate. Here, we use observations of forest C response to N inputs along N deposition gradients and at five temperate forest sites with fertilization experiments to test and improve a global biogeochemical model (CLM-CN 4.0). We show that the CLM-CN plant C growth response to N deposition was smaller than observed and the modeled response to N fertilization was larger than observed. A set of modifications to the CLM-CN improved the correspondence between model predictions and observational data (1) by increasing the aboveground C storage in response to historical N deposition (1850-2004) from 14 to 34 kg C per additional kg N added through deposition and (2) by decreasing the aboveground net primary productivity response to N fertilization experiments from 91 to 57 g C m-2 yr-1. Modeled growth response to N deposition was most sensitive to altering the processes that control plant N uptake and the pathways of N loss. The response to N deposition also increased with a more closed N cycle (reduced N fixation and N gas loss) and decreased when prioritizing microbial over plant uptake of soil inorganic N. The net effect of all the modifications to the CLM-CN resulted in greater retention of N deposition and a greater role of synergy between N deposition and rising atmospheric CO2 as a mechanism governing increases in temperate forest primary production over the 20th century. Overall, testing models with both the response to gradual increases in N inputs over decades (N deposition) and N pulse additions of N over multiple years (N fertilization) allows for greater understanding of the mechanisms governing C-N coupling.

Distribution and geochemical characterization of coalbed gases at excavation fields at natural analogue site area Velenje Basin, Slovenia

NASA Astrophysics Data System (ADS)

Kanduč, Tjaša; Žigon, Stojan; Grassa, Fausto; Sedlar, Jerneja; Zadnik, Ivo; Zavšek, Simon

2016-04-01

Unconventional gas resources, including coal bed methane and shale gas, are a growing part of the global energy mix, which has changed the economic and strategic picture for gas consuming and producing countries, including the USA, China and Australia that, together are responsible for around half the currently recoverable unconventional gas resources. However, CBM production was often hindered by low permeability and mineralization in cleats and fractures, necessitating the development of cost effective horizontal drilling and completion techniques. Geochemical and isotopic monitoring of coalbed gases at excavation fields in Velenje Basin started in year 2000, with the aim to obtain better insights into the origin of coalbed gases. Results from active excavation fields in the mining areas Pesje and Preloge in the year period 2014-2015 are presented in this study. Composition and isotopic composition of coalbed gases were determined with mass - spectrometric methods. The chemical (methane, carbon dioxide, nitrogen) and isotopic composition of carbon in methane and carbon dioxide in the Velenje Basin vary and depend on the composition of the source of coalbed gas before excavation, advancement of the working face, depth of the longwall face, pre-mining activity and newly mined activity. The basic gas components determined in excavation fields are carbon dioxide and methane. Knowledge of the stable isotope geochemistry of coal bed and shale gas and the related production water is essential to determine not only gas origins but also the dominant methanogenic pathway in the case of microbial gas. Concentrations of methane at active excavation fields are changing from 1.8 to 63.9 %, concentrations of carbon dioxide are changing from 36.1 to 98.2% and CDMI (Carbon Dioxide Methane Index) index from 0.2 to 100 %. Isotopic composition of carbon dioxide is changing from -11.0 to -1.9‰ , isotopic composition of methane from -71.8 to -43.3‰ , isotopic composition of deuterium in methane from -343.9 to -223.1‰ , respectively. Further, these characteristics of methane have been compared with those observed in other coal sedimentary basins worldwide. The isotopic compositions of carbon and hydrogen in methane in the excavation fields show its biogenic origin, while a high Carbon Dioxide Methane Index (CDMI index) indicates the bacterial and endogenic origin of carbon dioxide.

Isobutanol production as an alternative metabolic sink to rescue the growth deficiency of the glycogen mutant of Synechococcus elongatus PCC 7942

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, XQ; Shen, CR; Liao, JC

2014-03-04

Glycogen synthesis initiated by glucose-1-phosphate adenylyltransferase (glgC) represents a major carbon storage route in cyanobacteria which could divert a significant portion of assimilated carbon. Significant growth retardation in cyanobacteria with glgC knocked out (Delta glgC) has been reported in high light conditions. Here, we knocked out the glgC gene and analyzed its effects on carbon distribution in an isobutanol-producing strain of Synechococcus elongatus PCC7942 and its parental wild-type strain. We showed that isobutanol production was able to partially rescue the growth of Delta glgC mutant where the growth rescue effect positively correlated with the rate of isobutanol production. Using (NaHCO3)-C-14more » incorporation analysis, we observed a 28 % loss of total carbon fixation rate in the Delta glgC mutant compared to the wild-type. Upon expression of the isobutanol production pathway in Delta glgC mutant, the total carbon fixation rate was restored to the wild-type level. Furthermore, we showed that 52 % of the total carbon fixed was redirected into isobutanol biosynthesis in the Delta glgC mutant expressing enzymes for isobutanol production, which is 2.5 times higher than that of the wild-type expressing the same enzymes. These results suggest that biosynthesis of non-native product such as isobutanol can serve as a metabolic sink for replacing glycogen to rescue growth and restore carbon fixation rate. The rescue effect may further serve as a platform for cyanobacteria energy and carbon metabolism study.« less

A spatially nonselective baseline signal in parietal cortex reflects the probability of a monkey’s success on the current trial

PubMed Central

Zhang, Mingsha; Wang, Xiaolan; Goldberg, Michael E.

2014-01-01

We recorded the activity of neurons in the lateral intraparietal area of two monkeys while they performed two similar visual search tasks, one difficult, one easy. Each task began with a period of fixation followed by an array consisting of a single capital T and a number of lowercase t’s. The monkey had to find the capital T and report its orientation, upright or inverted, with a hand movement. In the easy task the monkey could explore the array with saccades. In the difficult task the monkey had to continue fixating and find the capital T in the visual periphery. The baseline activity measured during the fixation period, at a time in which the monkey could not know if the impending task would be difficult or easy or where the target would appear, predicted the monkey’s probability of success or failure on the task. The baseline activity correlated inversely with the monkey's recent history of success and directly with the intensity of the response to the search array on the current trial. The baseline activity was unrelated to the monkey’s spatial locus of attention as determined by the location of the cue in a cued visual reaction time task. We suggest that rather than merely reflecting the noise in the system, the baseline signal reflects the cortical manifestation of modulatory state, motivational, or arousal pathways, which determine the efficiency of cortical sensorimotor processing and the quality of the monkey’s performance. PMID:24889623

Regional constraints to biological nitrogen fixation in post-fire forest communities

USGS Publications Warehouse

Yelenik, Stephanie; Perakis, Steven S.; Hibbs, David

2013-01-01

Biological nitrogen fixation (BNF) is a key ecological process that can restore nitrogen (N) lost in wildfire and shape the pace and pattern of post-fire forest recovery. To date, there is limited information on how climate and soil fertility interact to influence different pathways of BNF in early forest succession. We studied asymbiotic (forest floor and soil) and symbiotic (the shrub Ceanothus integerrimus) BNF rates across six sites in the Klamath National Forest, California, USA. We used combined gradient and experimental phosphorus (P) fertilization studies to explore cross-site variation in BNF rates and then related these rates to abiotic and biotic variables. We estimate that our measured BNF rates 22 years after wildfire (6.1–12.1 kg N·ha-1·yr-1) are unlikely to fully replace wildfire N losses. We found that asymbiotic BNF is P limited, although this is not the case for symbiotic BNF in Ceanothus. In contrast, Ceanothus BNF is largely driven by competition from other vegetation: in high-productivity sites with high potential evapotranspiration (Et), shrub biomass is suppressed as tree biomass increases. Because shrub biomass governed cross-site variation in Ceanothus BNF, this competitive interaction led to lower BNF in sites with high productivity and Et. Overall, these results suggest that the effects of nutrients play a larger role in driving asymbiotic than symbiotic fixation across our post-fire sites. However, because symbiotic BNF is 8–90x greater than asymbiotic BNF, it is interspecific plant competition that governs overall BNF inputs in these forests.

Application of alternative fixatives to formalin in diagnostic pathology

PubMed Central

Gatta, L. Benerini; Cadei, M.; Balzarini, P.; Castriciano, S.; Paroni, R.; Verzeletti, A.; Cortellini, V.; De Ferrari, F.; Grigolato, P.

2012-01-01

Fixation is a critical step in the preparation of tissues for histopathology. The aim of this study was to investigate the effects of different fixatives vs formalin on proteins and DNA, and to evaluate alternative fixation for morphological diagnosis and nucleic acid preservation for molecular methods. Forty tissues were fixed for 24 h with six different fixatives: the gold standard fixative formalin, the historical fixatives Bouin and Hollande, and the alternative fixatives Greenfix, UPM and CyMol. Tissues were stained (Haematoxylin-Eosin, Periodic Acid Schiff, Trichromic, Alcian-blue, High Iron Diamine stainings), and their antigenicity was determined by immunohistochemistry (performed with PAN-CK, CD31, Ki-67, S100, CD68, AML antibodies). DNA extraction, KRAS sequencing, FISH for CEP-17, and flow cytometry analysis of nuclear DNA content were applied. For cell morphology the alternative fixatives (Greenfix, UPM, CyMol) were equivalent to formalin. As expected, Hollande proved to be the best fixative for morphology. The morphology obtained with Bouin was comparable to the one with formalin. Hollande was the best fixative for histochemistry. Bouin proved to be equivalent to formalin. The alternative fixatives were equivalent to formalin, although with greater variability in haematoxylin-eosin staining. It proved the possibility to obtain immunohistochemical staining largely equivalent to that following formalin-fixation with the following fixatives: Greenfix, Hollande, UPM and CyMol. The tissues fixed in Bouin did not provide results comparable to those obtained with formalin. The DNA extracted from samples fixed with alternative fixatives was found to be suitable for molecular analysis. PMID:22688293

[Tibial press-fit fixation of flexor tendons for reconstruction of the anterior cruciate ligament].

PubMed

Ettinger, M; Liodakis, E; Haasper, C; Hurschler, C; Breitmeier, D; Krettek, C; Jagodzinski, M

2012-09-01

Press-fit fixation of hamstring tendon autografts for anterior cruciate ligament reconstruction is an interesting technique because no hardware is necessary. This study compares the biomechanical properties of press-fit fixations to an interference screw fixation. Twenty-eight human cadaveric knees were used for hamstring tendon explantation. An additional bone block was harvested from the tibia. We used 28 porcine femora for graft fixation. Constructs were cyclically stretched and then loaded until failure. Maximum load to failure, stiffness and elongation during failure testing and cyclic loading were investigated. The maximum load to failure was 970±83 N for the press-fit tape fixation (T), 572±151 N for the bone bridge fixation (TS), 544±109 N for the interference screw fixation (I), 402±77 N for the press-fit suture fixation (S) and 290±74 N for the bone block fixation technique (F). The T fixation had a significantly better maximum load to failure compared to all other techniques (p<0.001). This study demonstrates that a tibial press-fit technique which uses an additional bone block has better maximum load to failure results compared to a simple interference screw fixation.

Porcine Intestinal Mast Cells. Evaluation of Different Fixatives for Histochemical Staining Techniques Considering Tissue Shrinkage

PubMed Central

Rieger, J.; Twardziok, S.; Huenigen, H.; Hirschberg, R.M.; Plendl, J.

2013-01-01

Staining of mast cells (MCs), including porcine ones, is critically dependent upon the fixation and staining technique. In the pig, mucosal and submucosal MCs do not stain or stain only faintly after formalin fixation. Some fixation methods are particularly recommended for MC staining, for example the fixation with Carnoy or lead salts. Zinc salt fixation (ZSF) has been reported to work excellently for the preservation of fixation-sensitive antigens. The aim of this study was to establish a reliable histological method for counting of MCs in the porcine intestinum. For this purpose, different tissue fixation and staining methods that also allow potential subsequent immunohistochemical investigations were evaluated in the porcine mucosa, as well as submucosa of small and large intestine. Tissues were fixed in Carnoy, lead acetate, lead nitrate, Zamboni and ZSF and stained subsequently with either polychromatic methylene blue, alcian blue or toluidine blue. For the first time our study reveals that ZSF, a heavy metal fixative, preserves metachromatic staining of porcine MCs. Zamboni fixation was not suitable for histochemical visualization of MCs in the pig intestine. All other tested fixatives were suitable. Alcian blue and toluidine blue co-stained intestinal goblet cells which made a prima facie identification of MCs difficult. The polychromatic methylene blue proved to be the optimal staining. In order to compare MC counting results of the different fixation methods, tissue shrinkage was taken into account. As even the same fixation caused shrinkagedifferences between tissue from small and large intestine, different factors for each single fixation and intestinal localization had to be calculated. Tissue shrinkage varied between 19% and 57%, the highest tissue shrinkage was found after fixation with ZSF in the large intestine, the lowest one in the small intestine after lead acetate fixation. Our study emphasizes that MC counting results from data using different fixation techniques can only be compared if the respective studyimmanent shrinkage factor has been determined and quantification results are adjusted accordingly. PMID:24085270

[Effectiveness comparison of flexible fixation and rigid fixation in treatment of ankle pronation-external rotation fractures with distal tibiofibular syndesmosis].

PubMed

Li, Yuewei; Zhang, Minghui; Li, Xiaorong; Chen, Xiaoyong; Deng, Jianlong

2017-07-01

To compare the effectiveness of flexible fixation and rigid fixation in the treatment of ankle pronation-external rotation fractures with distal tibiofibular syndesmosis. A retrospective analysis was made on the clinical data of 50 patients with ankle pronation-external rotation fractures and distal tibiofibular syndesmosis treated between January 2013 and December 2015. Suture-button fixation was used in 23 patients (flexible fixation group) and cortical screw fixation in 27 patients (rigid fixation group). There was no significant difference in age, gender, weight, side, fracture type, and time from trauma to surgery between 2 groups ( P >0.05). The operation time, medial clear space (MCS), tibiofibular clear space (TFCS), tibiofibular overlap (TFO), American Orthopaedic Foot and Ankle Society (AOFAS) score, and Foot and Ankle Disability Index (FADI) score were compared between 2 groups. The operation time was (83.0±9.1) minutes in the flexible fixation group and was (79.6±13.1) minutes in the rigid fixation group, showing no significant difference ( t =1.052, P =0.265). All patients achieved healing of incision by first intention. The patients were followed up 12-20 months (mean, 14 months). The X-ray films showed good healing of fracture in 2 groups. There was no screw fracture, delayed union or nounion. The fracture healing time was (12.1±2.5) months in the flexible fixation group and was (11.3±3.2) months in the rigid fixation group, showing no significant difference between 2 groups ( t =1.024, P =0.192). Reduction loss occurred after removal of screw in 2 cases of the rigid fixation group. At last follow-up, there was no significant difference in MCS, TFCS, TFO, AOFAS score and FADI score between 2 groups ( P >0.05). Suture-button fixation has similar effectiveness to screw fixation in ankle function and imaging findings, and flexible fixation has lower risk of reduction loss of distal tibiofibular syndesmosis than rigid fixation.

Comparison of Monolateral External Fixation and Internal Fixation for Skeletal Stabilisation in the Management of Small Tibial Bone Defects following Successful Treatment of Chronic Osteomyelitis.

PubMed

Wang, Yicun; Jiang, Hui; Deng, Zhantao; Jin, Jiewen; Meng, Jia; Wang, Jun; Zhao, Jianning; Sun, Guojing; Qian, Hongbo

2017-01-01

To compare the salvage rate and complication between internal fixation and external fixation in patients with small bone defects caused by chronic infectious osteomyelitis debridement. 125 patients with chronic infectious osteomyelitis of tibia fracture who underwent multiple irrigation, debridement procedure, and local/systemic antibiotics were enrolled. Bone defects, which were less than 4 cm, were treated with bone grafting using either internal fixation or monolateral external fixation. 12-month follow-up was conducted with an interval of 3 months to evaluate union of bone defect. Patients who underwent monolateral external fixation had higher body mass index and fasting blood glucose, longer time since injury, and larger bone defect compared with internal fixation. No significant difference was observed in incidence of complications (23.5% versus 19.3%), surgery time (156 ± 23 minutes versus 162 ± 21 minutes), and time to union (11.1 ± 3.0 months versus 10.9 ± 3.1 months) between external fixation and internal fixation. Internal fixation had no significant influence on the occurrence of postoperation complications after multivariate adjustment when compared with external fixation. Furthermore, patients who underwent internal fixation experienced higher level of daily living scales and lower level of anxiety. It was relatively safe to use internal fixation for stabilization in osteomyelitis patients whose bone defects were less than 4 cm and infection was well controlled.

Comparison of Monolateral External Fixation and Internal Fixation for Skeletal Stabilisation in the Management of Small Tibial Bone Defects following Successful Treatment of Chronic Osteomyelitis

PubMed Central

Wang, Yicun; Jiang, Hui; Deng, Zhantao; Meng, Jia; Wang, Jun

2017-01-01

Background To compare the salvage rate and complication between internal fixation and external fixation in patients with small bone defects caused by chronic infectious osteomyelitis debridement. Methods 125 patients with chronic infectious osteomyelitis of tibia fracture who underwent multiple irrigation, debridement procedure, and local/systemic antibiotics were enrolled. Bone defects, which were less than 4 cm, were treated with bone grafting using either internal fixation or monolateral external fixation. 12-month follow-up was conducted with an interval of 3 months to evaluate union of bone defect. Results Patients who underwent monolateral external fixation had higher body mass index and fasting blood glucose, longer time since injury, and larger bone defect compared with internal fixation. No significant difference was observed in incidence of complications (23.5% versus 19.3%), surgery time (156 ± 23 minutes versus 162 ± 21 minutes), and time to union (11.1 ± 3.0 months versus 10.9 ± 3.1 months) between external fixation and internal fixation. Internal fixation had no significant influence on the occurrence of postoperation complications after multivariate adjustment when compared with external fixation. Furthermore, patients who underwent internal fixation experienced higher level of daily living scales and lower level of anxiety. Conclusions It was relatively safe to use internal fixation for stabilization in osteomyelitis patients whose bone defects were less than 4 cm and infection was well controlled. PMID:29333448

Comparison of screw fixation with elastic fixation methods in the treatment of syndesmosis injuries in ankle fractures.

PubMed

Seyhan, Mustafa; Donmez, Ferdi; Mahirogullari, Mahir; Cakmak, Selami; Mutlu, Serhat; Guler, Olcay

2015-07-01

17 patients with ankle syndesmosic injury were treated with a 4.5mm single cortical screw fixation (passage of screw 4 cortices) and 15 patients were treated with single-level elastic fixation material. All patients were evaluated according to the AOFAS ankle and posterior foot scale at the third, sixth and twelfth months after the fixation. The ankle range of movement was recorded together with the healthy side. The Student's t test was used for statistical comparisons. No statistical significant difference was observed between the AOFAS scores (p>0.05). The range of dorsiflexion and plantar flexion motion of the elastic fixation group at the 6th and 12th months were significantly better compared to the screw fixation group (p<0.01). Elastic fixation is as functional as screw fixation in the treatment of ankle syndesmosis injuries. The unnecessary need of a second surgical intervention for removal of the fixation material is another advantageous aspect of this method of fixation. Copyright © 2015. Published by Elsevier Ltd.

A Subconscious Interaction between Fixation and Anticipatory Pursuit

PubMed Central

Bal, Japjot; Heinen, Stephen J.

2017-01-01

Ocular smooth pursuit and fixation are typically viewed as separate systems, yet there is evidence that the brainstem fixation system inhibits pursuit. Here we present behavioral evidence that the fixation system modulates pursuit behavior outside of conscious awareness. Human observers (male and female) either pursued a small spot that translated across a screen, or fixated it as it remained stationary. As shown previously, pursuit trials potentiated the oculomotor system, producing anticipatory eye velocity on the next trial before the target moved that mimicked the stimulus-driven velocity. Randomly interleaving fixation trials reduced anticipatory pursuit, suggesting that a potentiated fixation system interacted with pursuit to suppress eye velocity in upcoming pursuit trials. The reduction was not due to passive decay of the potentiated pursuit signal because interleaving “blank” trials in which no target appeared did not reduce anticipatory pursuit. Interspersed short fixation trials reduced anticipation on long pursuit trials, suggesting that fixation potentiation was stronger than pursuit potentiation. Furthermore, adding more pursuit trials to a block did not restore anticipatory pursuit, suggesting that fixation potentiation was not overridden by certainty of an imminent pursuit trial but rather was immune to conscious intervention. To directly test whether cognition can override fixation suppression, we alternated pursuit and fixation trials to perfectly specify trial identity. Still, anticipatory pursuit did not rise above that observed with an equal number of random fixation trials. The results suggest that potentiated fixation circuitry interacts with pursuit circuitry at a subconscious level to inhibit pursuit. SIGNIFICANCE STATEMENT When an object moves, we view it with smooth pursuit eye movements. When an object is stationary, we view it with fixational eye movements. Pursuit and fixation are historically regarded as controlled by different neural circuitry, and alternating between invoking them is thought to be guided by a conscious decision. However, our results show that pursuit is actively suppressed by prior fixation of a stationary object. This suppression is involuntary, and cannot be avoided even if observers are certain that the object will move. The results suggest that the neural fixation circuitry is potentiated by engaging stationary objects, and interacts with pursuit outside of conscious awareness. PMID:29061701

A Subconscious Interaction between Fixation and Anticipatory Pursuit.

PubMed

Watamaniuk, Scott N J; Bal, Japjot; Heinen, Stephen J

2017-11-22

Ocular smooth pursuit and fixation are typically viewed as separate systems, yet there is evidence that the brainstem fixation system inhibits pursuit. Here we present behavioral evidence that the fixation system modulates pursuit behavior outside of conscious awareness. Human observers (male and female) either pursued a small spot that translated across a screen, or fixated it as it remained stationary. As shown previously, pursuit trials potentiated the oculomotor system, producing anticipatory eye velocity on the next trial before the target moved that mimicked the stimulus-driven velocity. Randomly interleaving fixation trials reduced anticipatory pursuit, suggesting that a potentiated fixation system interacted with pursuit to suppress eye velocity in upcoming pursuit trials. The reduction was not due to passive decay of the potentiated pursuit signal because interleaving "blank" trials in which no target appeared did not reduce anticipatory pursuit. Interspersed short fixation trials reduced anticipation on long pursuit trials, suggesting that fixation potentiation was stronger than pursuit potentiation. Furthermore, adding more pursuit trials to a block did not restore anticipatory pursuit, suggesting that fixation potentiation was not overridden by certainty of an imminent pursuit trial but rather was immune to conscious intervention. To directly test whether cognition can override fixation suppression, we alternated pursuit and fixation trials to perfectly specify trial identity. Still, anticipatory pursuit did not rise above that observed with an equal number of random fixation trials. The results suggest that potentiated fixation circuitry interacts with pursuit circuitry at a subconscious level to inhibit pursuit. SIGNIFICANCE STATEMENT When an object moves, we view it with smooth pursuit eye movements. When an object is stationary, we view it with fixational eye movements. Pursuit and fixation are historically regarded as controlled by different neural circuitry, and alternating between invoking them is thought to be guided by a conscious decision. However, our results show that pursuit is actively suppressed by prior fixation of a stationary object. This suppression is involuntary, and cannot be avoided even if observers are certain that the object will move. The results suggest that the neural fixation circuitry is potentiated by engaging stationary objects, and interacts with pursuit outside of conscious awareness. Copyright © 2017 the authors 0270-6474/17/3711424-07$15.00/0.

Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans

DOE PAGES

Nazem-Bokaee, Hadi; Gopalakrishnan, Saratram; Ferry, James G.; ...

2016-01-17

Methanosarcina acetivorans is a model archaeon with renewed interest due to its unique reversible methane production pathways. However, the mechanism and relevant pathways implicated in (co)utilizing novel carbon substrates in this organism are still not fully understood. This paper provides a comprehensive inventory of thermodynamically feasible routes for anaerobic methane oxidation, co-reactant utilization, and maximum carbon yields of major biofuel candidates by M. acetivorans. Here, an updated genome-scale metabolic model of M. acetivorans is introduced (iMAC868 containing 868 genes, 845 reactions, and 718 metabolites) by integrating information from two previously reconstructed metabolic models (i.e., iVS941 and iMB745), modifying 17 reactions,more » adding 24 new reactions, and revising 64 gene-proteinreaction associations based on newly available information. The new model establishes improved predictions of growth yields on native substrates and is capable of correctly predicting the knockout outcomes for 27 out of 28 gene deletion mutants. By tracing a bifurcated electron flow mechanism, the iMAC868 model predicts thermodynamically feasible (co)utilization pathway of methane and bicarbonate using various terminal electron acceptors through the reversal of the aceticlastic pathway. In conclusion, this effort paves the way in informing the search for thermodynamically feasible ways of (co)utilizing novel carbon substrates in the domain Archaea.« less

Metagenomic Insights into Effects of Chemical Pollutants on Microbial Community Composition and Function in Estuarine Sediments Receiving Polluted River Water.

PubMed

Lu, Xiao-Ming; Chen, Chang; Zheng, Tian-Ling

2017-05-01

Pyrosequencing and metagenomic profiling were used to assess the phylogenetic and functional characteristics of microbial communities residing in sediments collected from the estuaries of Rivers Oujiang (OS) and Jiaojiang (JS) in the western region of the East China Sea. Another sediment sample was obtained from near the shore far from estuaries, used for contrast (CS). Characterization of estuary sediment bacterial communities showed that toxic chemicals potentially reduced the natural variability in microbial communities, while they increased the microbial metabolic enzymes and pathways. Polycyclic aromatic hydrocarbons (PAHs) and nitrobenzene were negatively correlated with the bacterial community variation. The dominant class in the sediments was Gammaproteobacteria. According to Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme profiles, dominant enzymes were found in estuarine sediments, which increased greatly, such as 2-oxoglutarate synthase, acetolactate synthase, inorganic diphosphatase, and aconitate hydratase. In KEGG pathway profiles, most of the pathways were also dominated by specific metabolism in these sediments and showed a marked increase, for instance alanine, aspartate, and glutamate metabolism, carbon fixation pathways in prokaryotes, and aminoacyl-tRNA biosynthesis. The estuarine sediment bacterial diversity varied with the polluted river water inputs. In the estuary receiving river water from the more seriously polluted River Oujiang, the sediment bacterial community function was more severely affected.

The restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus: lessons from tiered functional genomics

PubMed Central

Rupakula, Aamani; Kruse, Thomas; Boeren, Sjef; Holliger, Christof; Smidt, Hauke; Maillard, Julien

2013-01-01

Dehalobacter restrictus strain PER-K23 is an obligate organohalide respiring bacterium, which displays extremely narrow metabolic capabilities. It grows only via coupling energy conservation to anaerobic respiration of tetra- and trichloroethene with hydrogen as sole electron donor. Dehalobacter restrictus represents the paradigmatic member of the genus Dehalobacter, which in recent years has turned out to be a major player in the bioremediation of an increasing number of organohalides, both in situ and in laboratory studies. The recent elucidation of the D. restrictus genome revealed a rather elaborate genome with predicted pathways that were not suspected from its restricted metabolism, such as a complete corrinoid biosynthetic pathway, the Wood–Ljungdahl (WL) pathway for CO2 fixation, abundant transcriptional regulators and several types of hydrogenases. However, one important feature of the genome is the presence of 25 reductive dehalogenase genes, from which so far only one, pceA, has been characterized on genetic and biochemical levels. This study describes a multi-level functional genomics approach on D. restrictus across three different growth phases. A global proteomic analysis allowed consideration of general metabolic pathways relevant to organohalide respiration, whereas the dedicated genomic and transcriptomic analysis focused on the diversity, composition and expression of genes associated with reductive dehalogenases. PMID:23479754

Stress and stability of plate-screw fixation and screw fixation in the treatment of Schatzker type IV medial tibial plateau fracture: a comparative finite element study.

PubMed

Huang, Xiaowei; Zhi, Zhongzheng; Yu, Baoqing; Chen, Fancheng

2015-11-25

The purpose of this study is to compare the stress and stability of plate-screw fixation and screw fixation in the treatment of Schatzker type IV medial tibial plateau fracture. A three-dimensional (3D) finite element model of the medial tibial plateau fracture (Schatzker type IV fracture) was created. An axial force of 2500 N with a distribution of 60% to the medial compartment was applied to simulate the axial compressive load on an adult knee during single-limb stance. The equivalent von Mises stress, displacement of the model relative to the distal tibia, and displacement of the implants were used as the output measures. The mean stress value of the plate-screw fixation system was 18.78 MPa, which was significantly (P < 0.001) smaller than that of the screw fixation system. The maximal value of displacement (sum) in the plate-screw fixation system was 2.46 mm, which was lower than that in the screw fixation system (3.91 mm). The peak stress value of the triangular fragment in the plate-screw fixation system model was 42.04 MPa, which was higher than that in the screw fixation model (24.18 MPa). But the mean stress of the triangular fractured fragment in the screw fixation model was significantly higher in terms of equivalent von Mises stress (EVMS), x-axis, and z-axis (P < 0.001). This study demonstrated that the load transmission mechanism between plate-screw fixation system and screw fixation system was different and the stability provided by the plate-screw fixation system was superior to the screw fixation system.

Comparison of effects of seven treatment methods for distal radius fracture on minimizing complex regional pain syndrome

PubMed Central

Sun, Tao

2016-01-01

Introduction Using network meta-analysis, we evaluated the adverse effects of the seven most common treatment methods, i.e., bridging external fixation, non-bridging external fixation, K-wire fixation, plaster fixation, dorsal plating, volar plating, and dorsal and volar plating, by their associated risk of developing complex regional pain syndrome (CRPS) in distal radius fracture (DRF) patients. Material and methods Following an exhaustive search of scientific literature databases for high quality studies, randomized controlled trials (RCTs) related to our study topic were screened and selected based on stringent predefined inclusion and exclusion criteria. Data extracted from the selected studies were used for statistical analyses using Stata 12.0 software. Results A total of 17 RCTs, including 1658 DRF patients, were enrolled in this network meta-analysis. Among the 1658 DRF patients, 452 received bridging external fixation, 525 received non-bridging external fixation, 154 received K-wire fixation, 84 received plaster fixation, 132 received dorsal plating, 123 received volar plating, and 188 received dorsal and volar plating. When compared to bridging external fixation patients, there was no marked difference in the CRPS risk in DRF patients receiving different treatments (all p > 0.05). However, the surface under the cumulative ranking curves (SUCRA) for plaster fixation (77.0%) and non-bridging external fixation (71.3%) were significantly higher compared with the other five methods. Conclusions Our findings suggest that compared with bridging external fixation, K-wire fixation, dorsal plating, volar plating, dorsal and volar plating, plaster fixation and non-bridging external fixation might be the better treatment methods to reduce the risk of CRPS in DRF patients. PMID:28144268

Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro

PubMed Central

Yacoby, Iftach; Pochekailov, Sergii; Toporik, Hila; Ghirardi, Maria L.; King, Paul W.; Zhang, Shuguang

2011-01-01

Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the main limitations for its commercialization. Here we provide evidence that, under the anaerobic conditions that support hydrogen production, there is a significant loss of photosynthetic electrons toward NADPH production in vitro. To elucidate the basis for competition, we bioengineered a ferredoxin-hydrogenase fusion and characterized hydrogen production kinetics in the presence of Fd, ferredoxin:NADP+-oxidoreductase (FNR), and NADP+. Replacing the hydrogenase with a ferredoxin-hydrogenase fusion switched the bias of electron transfer from FNR to hydrogenase and resulted in an increased rate of hydrogen photoproduction. These results suggest a new direction for improvement of biohydrogen production and a means to further resolve the mechanisms that control partitioning of photosynthetic electron transport. PMID:21606330

The Viking mission search for life on Mars

NASA Technical Reports Server (NTRS)

Klein, H. P.; Lederberg, J.; Rich, A.; Horowitz, N. H.; Oyama, V. I.; Levin, G. V.

1976-01-01

The scientific payload on the Viking Mars landers is described. Shortly after landing, two facsimile cameras capable of stereoscopic imaging will scan the landing site area in black and white, color, and infrared to reveal gross evidence of past or present living systems. A wide range mass spectrometer will record a complete mass spectrum for soil samples from mass 12 to mass 200 every 10.3 sec. Three experiments based on different assumptions on the nature of life on Mars, if it exists, will be carried out by the bio-lab. A pyrolytic release experiment is designed to measure photosynthetic or dark fixation of carbon dioxide or carbon monoxide into organic compounds. A labelled release experiment will test for metabolic activity during incubation of a surface sample moistened with a solution of radioactively labelled simple organic compounds. A gas exchange experiment will detect changes in the gaseous medium surrounding a soil sample as the result of metabolic activity. The hardware, function, and terrestrial test results of the bio-lab experiments are discussed.

Physiological effects of the Mexico City atmosphere on lichen transplants on oaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zambrano, A.; Nash, T.H. III; Gries, C.

1999-10-01

Two lichen species, Usnea ceratina Ach. and Everniastrum neocirrhatum (Hale M. Wirth) Hale ex Sipman, were transplanted for 54 d into an oak forest (Quercus rugosa) in the vicinity of Mexico City to assess their ability to survive near a highly polluted urban environment. Net photosynthesis based on dry weight and chlorophyll b decreased respectively ca. 30 and 25% compared with control samples in a less polluted site, ca. 100 km north of Mexico City. There was no interspecific difference in the response of carbon fixation, but E. neocirrhatum was more sensitive to chlorophyll b degradation near Mexico City thanmore » U. ceratina. Chlorophyll a was also degradated (ca. 15%) near Mexico City. Changes in total carotenes were mostly dependent on species and time rather than on location. High concurrent levels of ozone and sulfur dioxide in the air are discussed as possible causes of the decline in the lichen photosynthesis and chlorophyll content.« less

Hybrid bioinorganic approach to solar-to-chemical conversion.

PubMed

Nichols, Eva M; Gallagher, Joseph J; Liu, Chong; Su, Yude; Resasco, Joaquin; Yu, Yi; Sun, Yujie; Yang, Peidong; Chang, Michelle C Y; Chang, Christopher J

2015-09-15

Natural photosynthesis harnesses solar energy to convert CO2 and water to value-added chemical products for sustaining life. We present a hybrid bioinorganic approach to solar-to-chemical conversion in which sustainable electrical and/or solar input drives production of hydrogen from water splitting using biocompatible inorganic catalysts. The hydrogen is then used by living cells as a source of reducing equivalents for conversion of CO2 to the value-added chemical product methane. Using platinum or an earth-abundant substitute, α-NiS, as biocompatible hydrogen evolution reaction (HER) electrocatalysts and Methanosarcina barkeri as a biocatalyst for CO2 fixation, we demonstrate robust and efficient electrochemical CO2 to CH4 conversion at up to 86% overall Faradaic efficiency for ≥ 7 d. Introduction of indium phosphide photocathodes and titanium dioxide photoanodes affords a fully solar-driven system for methane generation from water and CO2, establishing that compatible inorganic and biological components can synergistically couple light-harvesting and catalytic functions for solar-to-chemical conversion.

Ocean acidification: the other CO2 problem.

PubMed

Doney, Scott C; Fabry, Victoria J; Feely, Richard A; Kleypas, Joan A

2009-01-01

Rising atmospheric carbon dioxide (CO2), primarily from human fossil fuel combustion, reduces ocean pH and causes wholesale shifts in seawater carbonate chemistry. The process of ocean acidification is well documented in field data, and the rate will accelerate over this century unless future CO2 emissions are curbed dramatically. Acidification alters seawater chemical speciation and biogeochemical cycles of many elements and compounds. One well-known effect is the lowering of calcium carbonate saturation states, which impacts shell-forming marine organisms from plankton to benthic molluscs, echinoderms, and corals. Many calcifying species exhibit reduced calcification and growth rates in laboratory experiments under high-CO2 conditions. Ocean acidification also causes an increase in carbon fixation rates in some photosynthetic organisms (both calcifying and noncalcifying). The potential for marine organisms to adapt to increasing CO2 and broader implications for ocean ecosystems are not well known; both are high priorities for future research. Although ocean pH has varied in the geological past, paleo-events may be only imperfect analogs to current conditions.

N2-fixing tropical legume evolution: a contributor to enhanced weathering through the Cenozoic?

PubMed Central

Hedin, Lars O.; Leake, Jonathan R.

2017-01-01

Fossil and phylogenetic evidence indicates legume-rich modern tropical forests replaced Late Cretaceous palm-dominated tropical forests across four continents during the early Cenozoic (58–42 Ma). Tropical legume trees can transform ecosystems via their ability to fix dinitrogen (N2) and higher leaf N compared with non-legumes (35–65%), but it is unclear how their evolutionary rise contributed to silicate weathering, the long-term sink for atmospheric carbon dioxide (CO2). Here we hypothesize that the increasing abundance of N2-fixing legumes in tropical forests amplified silicate weathering rates by increased input of fixed nitrogen (N) to terrestrial ecosystems via interrelated mechanisms including increasing microbial respiration and soil acidification, and stimulating forest net primary productivity. We suggest the high CO2 early Cenozoic atmosphere further amplified legume weathering. Evolution of legumes with high weathering rates was probably driven by their high demand for phosphorus and micronutrients required for N2-fixation and nodule formation. PMID:28814651

Ecology and ecophysiology of tree stems: corticular and wood photosynthesis.

PubMed

Pfanz, H; Aschan, G; Langenfeld-Heyser, R; Wittmann, C; Loose, M

2002-04-01

Below the outer peridermal or rhytidomal layers, most stems of woody plants possess greenish tissues. These chlorophyll-containing tissues (the chlorenchymes) within the stems are able to use the stem internal CO2 and the light penetrating the rhytidome to photoassimilate and produce sugars and starch. Although net photosynthetic uptake of CO2 is rarely found, stem internal re-fixation of CO2 in young twigs and branches may compensate for 60-90% of the potential respiratory carbon loss. Isolated chlorenchymal tissues reveal rather high rates of net photosynthesis (being up to 75% of the respective rates for leaf photosynthesis). Corticular photosynthesis is thus thought to be an effective mechanism for recapturing respiratory carbon dioxide before it diffuses out of the stem. Furthermore, chloroplasts of the proper wood or pith fraction also take part in stem internal photosynthesis. Although there has been no strong experimental evidence until now, we suggest that the oxygen evolved during wood or pith photosynthesis may play a decisive role in avoiding/reducing stem internal anaerobiosis.

Ecology and ecophysiology of tree stems: corticular and wood photosynthesis

NASA Astrophysics Data System (ADS)

Pfanz, H.; Aschan, G.; Langenfeld-Heyser, R.; Wittmann, C.; Loose, M.

2002-03-01

Below the outer peridermal or rhytidomal layers, most stems of woody plants possess greenish tissues. These chlorophyll-containing tissues (the chlorenchymes) within the stems are able to use the stem internal CO2 and the light penetrating the rhytidome to photoassimilate and produce sugars and starch. Although net photosynthetic uptake of CO2 is rarely found, stem internal re-fixation of CO2 in young twigs and branches may compensate for 60-90% of the potential respiratory carbon loss. Isolated chlorenchymal tissues reveal rather high rates of net photosynthesis (being up to 75% of the respective rates for leaf photosynthesis). Corticular photosynthesis is thus thought to be an effective mechanism for recapturing respiratory carbon dioxide before it diffuses out of the stem. Furthermore, chloroplasts of the proper wood or pith fraction also take part in stem internal photosynthesis. Although there has been no strong experimental evidence until now, we suggest that the oxygen evolved during wood or pith photosynthesis may play a decisive role in avoiding/reducing stem internal anaerobiosis.

N2-fixing tropical legume evolution: a contributor to enhanced weathering through the Cenozoic?

PubMed

Epihov, Dimitar Z; Batterman, Sarah A; Hedin, Lars O; Leake, Jonathan R; Smith, Lisa M; Beerling, David J

2017-08-16

Fossil and phylogenetic evidence indicates legume-rich modern tropical forests replaced Late Cretaceous palm-dominated tropical forests across four continents during the early Cenozoic (58-42 Ma). Tropical legume trees can transform ecosystems via their ability to fix dinitrogen (N 2 ) and higher leaf N compared with non-legumes (35-65%), but it is unclear how their evolutionary rise contributed to silicate weathering, the long-term sink for atmospheric carbon dioxide (CO 2 ). Here we hypothesize that the increasing abundance of N 2 -fixing legumes in tropical forests amplified silicate weathering rates by increased input of fixed nitrogen (N) to terrestrial ecosystems via interrelated mechanisms including increasing microbial respiration and soil acidification, and stimulating forest net primary productivity. We suggest the high CO 2 early Cenozoic atmosphere further amplified legume weathering. Evolution of legumes with high weathering rates was probably driven by their high demand for phosphorus and micronutrients required for N 2 -fixation and nodule formation. © 2017 The Author(s).

Hybrid bioinorganic approach to solar-to-chemical conversion

PubMed Central

Nichols, Eva M.; Gallagher, Joseph J.; Liu, Chong; Su, Yude; Resasco, Joaquin; Yu, Yi; Sun, Yujie; Yang, Peidong; Chang, Michelle C. Y.; Chang, Christopher J.

2015-01-01

Natural photosynthesis harnesses solar energy to convert CO2 and water to value-added chemical products for sustaining life. We present a hybrid bioinorganic approach to solar-to-chemical conversion in which sustainable electrical and/or solar input drives production of hydrogen from water splitting using biocompatible inorganic catalysts. The hydrogen is then used by living cells as a source of reducing equivalents for conversion of CO2 to the value-added chemical product methane. Using platinum or an earth-abundant substitute, α-NiS, as biocompatible hydrogen evolution reaction (HER) electrocatalysts and Methanosarcina barkeri as a biocatalyst for CO2 fixation, we demonstrate robust and efficient electrochemical CO2 to CH4 conversion at up to 86% overall Faradaic efficiency for ≥7 d. Introduction of indium phosphide photocathodes and titanium dioxide photoanodes affords a fully solar-driven system for methane generation from water and CO2, establishing that compatible inorganic and biological components can synergistically couple light-harvesting and catalytic functions for solar-to-chemical conversion. PMID:26305947

Bioethanol production from the nutrient stress-induced microalga Chlorella vulgaris by enzymatic hydrolysis and immobilized yeast fermentation.

PubMed

Kim, Kyoung Hyoun; Choi, In Seong; Kim, Ho Myeong; Wi, Seung Gon; Bae, Hyeun-Jong

2014-02-01

The microalga Chlorella vulgaris is a potential feedstock for bioenergy due to its rapid growth, carbon dioxide fixation efficiency, and high accumulation of lipids and carbohydrates. In particular, the carbohydrates in microalgae make them a candidate for bioethanol feedstock. In this study, nutrient stress cultivation was employed to enhance the carbohydrate content of C. vulgaris. Nitrogen limitation increased the carbohydrate content to 22.4% from the normal content of 16.0% on dry weight basis. In addition, several pretreatment methods and enzymes were investigated to increase saccharification yields. Bead-beating pretreatment increased hydrolysis by 25% compared with the processes lacking pretreatment. In the enzymatic hydrolysis process, the pectinase enzyme group was superior for releasing fermentable sugars from carbohydrates in microalgae. In particular, pectinase from Aspergillus aculeatus displayed a 79% saccharification yield after 72h at 50°C. Using continuous immobilized yeast fermentation, microalgal hydrolysate was converted into ethanol at a yield of 89%. Copyright © 2013 Elsevier Ltd. All rights reserved.

Recent advances in fixation of the craniomaxillofacial skeleton.

PubMed

Meslemani, Danny; Kellman, Robert M

2012-08-01

Fixation of the craniomaxillofacial skeleton is an evolving aspect for facial plastic, oral and maxillofacial, and plastic surgery. This review looks at the recent advances that aid in reduction and fixation of the craniomaxillofacial skeleton. More surgeons are using resorbable plates for craniomaxillofacial fixation. A single miniplate on the inferior border of the mandible may be sufficient to reduce and fixate an angle fracture. Percutaneous K-wires may assist in plating angle fractures. Intraoperative computed tomography (CT) may prove to be useful for assessing reduction and fixation. Resorbable plates are becoming increasingly popular in orthognathic surgery and facial trauma surgery. There are newer operative techniques for fixating the angle of the mandible. Also, the utilization of the intraoperative CT provides immediate feedback for accurate reduction and fixation. Prebent surgical plates save operative time, decrease errors, and provide more accurate fixation.

Biomechanical Comparison of External Fixation and Compression Screws for Transverse Tarsal Joint Arthrodesis.

PubMed

Latt, L Daniel; Glisson, Richard R; Adams, Samuel B; Schuh, Reinhard; Narron, John A; Easley, Mark E

2015-10-01

Transverse tarsal joint arthrodesis is commonly performed in the operative treatment of hindfoot arthritis and acquired flatfoot deformity. While fixation is typically achieved using screws, failure to obtain and maintain joint compression sometimes occurs, potentially leading to nonunion. External fixation is an alternate method of achieving arthrodesis site compression and has the advantage of allowing postoperative compression adjustment when necessary. However, its performance relative to standard screw fixation has not been quantified in this application. We hypothesized that external fixation could provide transverse tarsal joint compression exceeding that possible with screw fixation. Transverse tarsal joint fixation was performed sequentially, first with a circular external fixator and then with compression screws, on 9 fresh-frozen cadaveric legs. The external fixator was attached in abutting rings fixed to the tibia and the hindfoot and a third anterior ring parallel to the hindfoot ring using transverse wires and half-pins in the tibial diaphysis, calcaneus, and metatarsals. Screw fixation comprised two 4.3 mm headless compression screws traversing the talonavicular joint and 1 across the calcaneocuboid joint. Compressive forces generated during incremental fixator foot ring displacement to 20 mm and incremental screw tightening were measured using a custom-fabricated instrumented miniature external fixator spanning the transverse tarsal joint. The maximum compressive force generated by the external fixator averaged 186% of that produced by the screws (range, 104%-391%). Fixator compression surpassed that obtainable with screws at 12 mm of ring displacement and decreased when the tibial ring was detached. No correlation was found between bone density and the compressive force achievable by either fusion method. The compression across the transverse tarsal joint that can be obtained with a circular external fixator including a tibial ring exceeds that which can be obtained with 3 headless compression screws. Screw and external fixator performance did not correlate with bone mineral density. This study supports the use of external fixation as an alternative method of generating compression to help stimulate fusion across the transverse tarsal joints. The findings provide biomechanical evidence to support the use of external fixation as a viable option in transverse tarsal joint fusion cases in which screw fixation has failed or is anticipated to be inadequate due to suboptimal bone quality. © The Author(s) 2015.

The carbon dioxide chaperon efficiency for the reaction H + O2 + M yields HO2 + M from ignition delay times behind reflected shock waves

NASA Technical Reports Server (NTRS)

Brabbs, Theodore A.; Robertson, Thomas F.

1987-01-01

Ignition delay times for stoichiometric hydrogen-oxygen in argon with and without carbon dioxide were measured behind reflected shock waves. A 20-reaction kinetic mechanism models the measured hydrogen-oxygen delay times over the temperature range 950 to 1300 K. The chaperon efficiency for carbon dioxide determined for the hydrogen-oxygen carbon dioxide mixture was 7.0. This value is in agreement with literature values but much less than a recent value obtained from flow tube experiments. Delay times measured behind a reflected shock wave were about 20% longer than those measured behind incident shock waves. The kinetic mechanism successfully modeled the high-pressure data of Skinner and the hydrogen-air data of Stack. It is suggested that the lowest temperature points for the hydrogen-air data of Slack are unreliable and that the 0.27-atm data may illustrate a case where vibrational relaxation of nitrogen is important. The reaction pathway HO2 yields H2O2 yields OH yields H was required to model the high-pressure data of Skinner. The successful modeling of the stoichiometric hydrogen-air data demonstrates the appropriateness of deriving kinetic models from data for gas mixtures highly diluted with argon. The technique of reducing a detailed kinetic mechanism to only the important reactions for a limited range of experimental data may render the mechanism useless for other test conditions.

Time Savings and Surgery Task Load Reduction in Open Intraperitoneal Onlay Mesh Fixation Procedure.

PubMed

Roy, Sanjoy; Hammond, Jeffrey; Panish, Jessica; Shnoda, Pullen; Savidge, Sandy; Wilson, Mark

2015-01-01

This study assessed the reduction in surgeon stress associated with savings in procedure time for mechanical fixation of an intraperitoneal onlay mesh (IPOM) compared to a traditional suture fixation in open ventral hernia repair. Nine general surgeons performed 36 open IPOM fixation procedures in porcine model. Each surgeon conducted two mechanical (using ETHICON SECURESTRAP ™ Open) and two suture fixation procedures. Fixation time was measured using a stopwatch, and related surgeon stress was assessed using the validated SURG-TLX questionnaire. T-tests were used to compare between-group differences, and a two-sided 95% confidence interval for the difference in stress levels was established using nonparametric methodology. The mechanical fixation group demonstrated an 89.1% mean reduction in fixation time, as compared to the suture group (p < 0.00001). Surgeon stress scores measured using SURG-TLX were 55.5% lower in the mechanical compared to the suture fixation group (p < 0.001). Scores in five of the six sources of stress were significantly lower for mechanical fixation. Mechanical fixation with ETHICON SECURESTRAP ™ Open demonstrated a significant reduction in fixation time and surgeon stress, which may translate into improved operating efficiency, improved performance, improved surgeon quality of life, and reduced overall costs of the procedure.

Time Savings and Surgery Task Load Reduction in Open Intraperitoneal Onlay Mesh Fixation Procedure

PubMed Central

Roy, Sanjoy; Hammond, Jeffrey; Panish, Jessica; Shnoda, Pullen; Savidge, Sandy; Wilson, Mark

2015-01-01

Background. This study assessed the reduction in surgeon stress associated with savings in procedure time for mechanical fixation of an intraperitoneal onlay mesh (IPOM) compared to a traditional suture fixation in open ventral hernia repair. Study Design. Nine general surgeons performed 36 open IPOM fixation procedures in porcine model. Each surgeon conducted two mechanical (using ETHICON SECURESTRAPTM Open) and two suture fixation procedures. Fixation time was measured using a stopwatch, and related surgeon stress was assessed using the validated SURG-TLX questionnaire. T-tests were used to compare between-group differences, and a two-sided 95% confidence interval for the difference in stress levels was established using nonparametric methodology. Results. The mechanical fixation group demonstrated an 89.1% mean reduction in fixation time, as compared to the suture group (p < 0.00001). Surgeon stress scores measured using SURG-TLX were 55.5% lower in the mechanical compared to the suture fixation group (p < 0.001). Scores in five of the six sources of stress were significantly lower for mechanical fixation. Conclusions. Mechanical fixation with ETHICON SECURESTRAPTM Open demonstrated a significant reduction in fixation time and surgeon stress, which may translate into improved operating efficiency, improved performance, improved surgeon quality of life, and reduced overall costs of the procedure. PMID:26240834

Salient in space, salient in time: Fixation probability predicts fixation duration during natural scene viewing.

PubMed

Einhäuser, Wolfgang; Nuthmann, Antje

2016-09-01

During natural scene viewing, humans typically attend and fixate selected locations for about 200-400 ms. Two variables characterize such "overt" attention: the probability of a location being fixated, and the fixation's duration. Both variables have been widely researched, but little is known about their relation. We use a two-step approach to investigate the relation between fixation probability and duration. In the first step, we use a large corpus of fixation data. We demonstrate that fixation probability (empirical salience) predicts fixation duration across different observers and tasks. Linear mixed-effects modeling shows that this relation is explained neither by joint dependencies on simple image features (luminance, contrast, edge density) nor by spatial biases (central bias). In the second step, we experimentally manipulate some of these features. We find that fixation probability from the corpus data still predicts fixation duration for this new set of experimental data. This holds even if stimuli are deprived of low-level images features, as long as higher level scene structure remains intact. Together, this shows a robust relation between fixation duration and probability, which does not depend on simple image features. Moreover, the study exemplifies the combination of empirical research on a large corpus of data with targeted experimental manipulations.

The comparative risk of developing postoperative complications in patients with distal radius fractures following different treatment modalities

PubMed Central

Qiu, Wen-Jun; Li, Yi-Fan; Ji, Yun-Han; Xu, Wei; Zhu, Xiao-Dong; Tang, Xian-Zhong; Zhao, Huan-Li; Wang, Gui-Bin; Jia, Yue-Qing; Zhu, Shi-Cai; Zhang, Feng-Fang; Liu, Hong-Mei

2015-01-01

In this study, we performed a network meta-analysis to compare the outcomes of seven most common surgical procedures to fix DRF, including bridging external fixation, non-bridging external fixation, K-wire fixation, plaster fixation, dorsal plating, volar plating, and dorsal and volar plating. Published studies were retrieved through PubMed, Embase and Cochrane Library databases. The database search terms used were the following keywords and MeSH terms: DRF, bridging external fixation, non-bridging external fixation, K-wire fixation, plaster fixation, dorsal plating, volar plating, and dorsal and volar plating. The network meta-analysis was performed to rank the probabilities of postoperative complication risks for the seven surgical modalities in DRF patients. This network meta-analysis included data obtained from a total of 19 RCTs. Our results revealed that compared to DRF patients treated with bridging external fixation, marked differences in pin-track infection (PTI) rate were found in patients treated with plaster fixation, volar plating, and dorsal and volar plating. Cluster analysis showed that plaster fixation is associated with the lowest probability of postoperative complication in DRF patients. Plaster fixation is associated with the lowest risk for postoperative complications in DRF patients, when compared to six other common DRF surgical methods examined. PMID:26549312

When do anterior external or internal fixators provide additional stability in an unstable (Tile C) pelvic fracture? A biomechanical study.

PubMed

Mcdonald, E; Theologis, A A; Horst, P; Kandemir, U; Pekmezci, M

2015-12-01

This study aimed at evaluating the additional stability that is provided by anterior external and internal fixators in an unstable pelvic fracture model (OTA 61-C). An unstable pelvic fracture (OTA 61-C) was created in 27 synthetic pelves by making a 5-mm gap through the sacral foramina (posterior injury) and an ipsilateral pubic rami fracture (anterior injury). The posterior injury was fixed with either a single iliosacral (IS) screw, a single trans-iliac, trans-sacral (TS) screw, or two iliosacral screws (S1S2). Two anterior fixation techniques were utilized: external fixation (Ex-Fix) and supra-acetabular external fixation and internal fixation (In-Fix); supra-acetabular pedicle screws connected with a single subcutaneous spinal rod. The specimens were tested using a nondestructive single-leg stance model. Peak-to-peak (P2P) displacement and rotation and conditioning displacement (CD) were calculated. The Ex-Fix group failed in 83.3 % of specimens with concomitant single-level posterior fixation (Total: 15/18-7 of 9 IS fixation, 8 of 9 TS fixation), and 0 % (0/9) of specimens with concomitant two-level (S1S2) posterior fixation. All specimens with the In-Fix survived testing except for two specimens treated with In-Fix combined with IS fixation. Trans-sacral fixation had higher pubic rotation and greater sacral and pubic displacement than S1S2 (p < 0.05). Rotation of the pubis and sacrum was not different between In-Fix constructs combined with single-level IS and TS fixation. In this model of an unstable pelvic fracture (OTA 61-C), anterior fixation with an In-Fix was biomechanically superior to an anterior Ex-Fix in the setting of single-level posterior fixation. There was no biomechanical difference between the In-Fix and Ex-Fix when each was combined with two levels of posterior sacral fixation.

Comparison of stability of different types of external fixation.

PubMed

Grubor, Predrag; Grubor, Milan; Asotic, Mithat

2011-01-01

Stabilization of fractures by external fixator is based on the mechanical connecting of the pins, screwed into the proximal and distal bone fragment. Site of fracture is left without any foreign materials, which is essential for prevention of infections. Aim of this work is to compare stability of constructs bone model-external fixators of different types (Ortofix, Mitković, Charneley and Ilizarov). Stability is estimated under compression and bending (vertical and horizontal forces of 100 kg magnitudes, with distances between pins of4 cm). The mathematical-computer software (Tower, Planet and Planet Pro) was used in the laboratory for accurate measurements of MDP "Jelsingrad" company, Banjaluka. Interfragmental motions in millimeters at the appliance of vertical and horizontal forces were 2.80/2.56 at Ortofix (uniplanar fixator), 1.57/1.56 and fixator by Mitković-M20 (uniplanar fixator with convergent oriented pins), 0.16/0.28 at Charnely's external fixator (biplanar fixator), and 4.49/0.114 mm at Ilizarov's external fixator (fixator with two proximal and two distal rings, each attached on the 6 Kirschner wires). It has confirmed that uniplanar fixation is easier and provides sufficient biomechanics circumstances in the site of fracture for bone healing, especially if the pins are oriented convergently. Ilizarov's fixator is multiplanar fixator, but its stability is dependent of tightness of wires, and provides adequate stability only in transversal plane. By other words, each fixator has its indications; selection of the fixator should be based on theirs mechanic characteristics, fracture geometry, and potential of bone healing, with permanent simplification of treatment, which has to be safe and acceptable for the patient. The main advantage of this study is Sits nature-the comparison of four most used external fixators, by the only one possible way-on the bone model. Each other way of comparison would result with much more questions than answers, due to unacceptable high bias of other parameters, which significantly influences on the results of the study.

Ocular Fixation Abnormality in Patients with Autism Spectrum Disorder

ERIC Educational Resources Information Center

Shirama, Aya; Kanai, Chieko; Kato, Nobumasa; Kashino, Makio

2016-01-01

We examined the factors that influence ocular fixation control in adults with autism spectrum disorder (ASD) including sensory information, individuals' motor characteristics, and inhibitory control. The ASD group showed difficulty in maintaining fixation especially when there was no fixation target. The fixational eye movement characteristics of…

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave.

PubMed

Ortiz, Marianyoly; Legatzki, Antje; Neilson, Julia W; Fryslie, Brandon; Nelson, William M; Wing, Rod A; Soderlund, Carol A; Pryor, Barry M; Maier, Raina M

2014-02-01

Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.

Synthetic CO2-fixation enzyme cascades immobilized on self-assembled nanostructures that enhance CO2/O2 selectivity of RubisCO.

PubMed

Satagopan, Sriram; Sun, Yuan; Parquette, Jon R; Tabita, F Robert

2017-01-01

With increasing concerns over global warming and depletion of fossil-fuel reserves, it is attractive to develop innovative strategies to assimilate CO 2 , a greenhouse gas, into usable organic carbon. Cell-free systems can be designed to operate as catalytic platforms with enzymes that offer exceptional selectivity and efficiency, without the need to support ancillary reactions of metabolic pathways operating in intact cells. Such systems are yet to be exploited for applications involving CO 2 utilization and subsequent conversion to valuable products, including biofuels. The Calvin-Benson-Bassham (CBB) cycle and the enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) play a pivotal role in global CO 2 fixation. We hereby demonstrate the co-assembly of two RubisCO-associated multienzyme cascades with self-assembled synthetic amphiphilic peptide nanostructures. The immobilized enzyme cascades sequentially convert either ribose-5-phosphate (R-5-P) or glucose, a simpler substrate, to ribulose 1,5-bisphosphate (RuBP), the acceptor for incoming CO 2 in the carboxylation reaction catalyzed by RubisCO. Protection from proteolytic degradation was observed in nanostructures associated with the small dimeric form of RubisCO and ancillary enzymes. Furthermore, nanostructures associated with a larger variant of RubisCO resulted in a significant enhancement of the enzyme's selectivity towards CO 2 , without adversely affecting the catalytic activity. The ability to assemble a cascade of enzymes for CO 2 capture using self-assembling nanostructure scaffolds with functional enhancements show promise for potentially engineering entire pathways (with RubisCO or other CO 2 -fixing enzymes) to redirect carbon from industrial effluents into useful bioproducts.

Detection of diazotrophy in the acetylene-fermenting anaerobe Pelobacter sp. strain SFB93

USGS Publications Warehouse

Akob, Denise M.; Baesman, Shaun; Sutton, John M.; Fierst, Janna L.; Mumford, Adam; Shrestha, Yesha; Poret-Peterson, Amisha T.; Bennett, Stacy; Dunlap, Darren S.; Haase, Karl B.; Oremland, Ronald S.

2017-01-01

Acetylene (C2H2) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C2H2 block assays of N2O reductase, and Pelobacter acetylenicus was shown to grow on C2H2 via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N2ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N2ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N2ase. Diazotrophic growth was observed under N2 but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N2ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days.

Hot topics and controversies in arthroplasty: cementless femoral fixation in elderly patients.

PubMed

Dutton, Andrew; Rubash, Harry E

2008-01-01

Cementless femoral fixation has been established as the gold standard for hip arthroplasty in young patients because of its exceptional longevity. Because older Americans are living longer and staying active, cementless femoral fixation for hip arthroplasty should be considered in all patients who have good bone quality. Numerous studies have shown excellent results using cementless fixation for hip arthroplasty in elderly patients. Histologic analysis, radiographic review, and dual-energy x-ray absorptiometry have shown solid osseointegration for biologic fixation and minimal bone loss. Cementless fixation provides superb functional outcomes with results comparable to those achieved using cemented fixation for hip arthroplasty. Additional advantages of cementless femoral fixation include shorter surgical times and substantial savings in health care costs.

Fixation Characteristics of Severe Amblyopia Subtypes: Which One is Worse?

PubMed

Koylu, Mehmet Talay; Ozge, Gokhan; Kucukevcilioglu, Murat; Mutlu, Fatih Mehmet; Ceylan, Osman Melih; Akıncıoglu, Dorukcan; Ayyıldız, Onder

2017-01-01

To determine differences in macular sensitivity and fixation patterns in different subtypes of severe amblyopia. This case-control study enrolled a total of 73 male adults, including 18 with pure strabismic severe amblyopia, 19 with pure anisometropic severe amblyopia, 18 with mixed (strabismic plus anizometropic) severe amblyopia, and 18 healthy controls. MP-1 microperimetry was used to evaluate macular sensitivity, location of fixation, and stability of fixation. Mean macular sensitivity, stability of fixation, and location of fixation were significantly worse in all amblyopia subtypes when compared with healthy controls. Intergroup comparisons between amblyopia subtypes revealed that mean macular sensitivity, stability of fixation, and location of fixation were significantly worse in pure strabismic and mixed amblyopic eyes when compared with pure anisometropic amblyopic eyes. Strabismus seems to be a worse prognostic factor in severe amblyopia than anisometropia in terms of fixation characteristics and retinal sensitivity.

An oculomotor continuum from exploration to fixation

PubMed Central

Otero-Millan, Jorge; Macknik, Stephen L.; Langston, Rachel E.; Martinez-Conde, Susana

2013-01-01

During visual exploration, saccadic eye movements scan the scene for objects of interest. During attempted fixation, the eyes are relatively still but often produce microsaccades. Saccadic rates during exploration are higher than those of microsaccades during fixation, reinforcing the classic view that exploration and fixation are two distinct oculomotor behaviors. An alternative model is that fixation and exploration are not dichotomous, but are instead two extremes of a functional continuum. Here, we measured the eye movements of human observers as they either fixed their gaze on a small spot or scanned natural scenes of varying sizes. As scene size diminished, so did saccade rates, until they were continuous with microsaccadic rates during fixation. Other saccadic properties varied as function of image size as well, forming a continuum with microsaccadic parameters during fixation. This saccadic continuum extended to nonrestrictive, ecological viewing conditions that allowed all types of saccades and fixation positions. Eye movement simulations moreover showed that a single model of oculomotor behavior can explain the saccadic continuum from exploration to fixation, for images of all sizes. These findings challenge the view that exploration and fixation are dichotomous, suggesting instead that visual fixation is functionally equivalent to visual exploration on a spatially focused scale. PMID:23533278

Effectiveness of external fixator combined with T-plate internal fixation for the treatment of comminuted distal radius fractures.

PubMed

Han, L R; Jin, C X; Yan, J; Han, S Z; He, X B; Yang, X F

2015-03-31

This study compared the efficacy between external fixator combined with palmar T-plate internal fixation and simple plate internal fixation for the treatment of comminuted distal radius fractures. A total of 61 patients classified as type C according to the AO/ASIF classification underwent surgery for comminuted distal radius fractures. There were 54 and 7 cases of closed and open fractures, respectively. Moreover, 19 patients received an external fixator combined with T-plate internal fixation, and 42 received simple plate internal fixation. All patients were treated successfully during 12-month postoperative follow-up. The follow-up results show that the palmar flexion and dorsiflexion of the wrist, radial height, and palmar angle were significantly better in those treated with the external fixator combined with T-plate compared to those treated with the simple plate only (P < 0.05); however, there were no significant differences in radial-ulnar deviation, wrist range of motion, or wrist function score between groups (P > 0.05). Hence, the effectiveness of external fixator combined with T-plate internal fixation for the treatment of comminuted distal radius fractures was satisfactory. Patients sufficiently recovered wrist, forearm, and hand function. In conclusion, compared to the simple T-plate, the external fixator combined with T-plate internal fixation can reduce the possibility of the postoperative re-shifting of broken bones and keep the distraction of fractures to maintain radial height and prevent radial shortening.

[Complications of open reduction and internal fixation versus external fixation for unstable distal radius fractures: a meta-analysis].

PubMed

Yang, Z; Yuan, Z Z; Ma, J X; Ma, X L

2016-12-20

Objective: To make a systematic assessment of the complications of open reduction and internal fixation versus external fixation for unstable distal radius fractures. Method: A computer-based online search of PubMed, ScienceDirect, EMBASE, BIOSIS, Springer and Cochrane Library were performed.The randomized and controlled trials of open reduction and internal fixation versus external fixation for unstable distal radius fractures were collected.The included trials were screened out strictly based on the criterion of inclusion and exclusion.The quality of included trials was evaluated.RevMan 5.0 was used for data analysis. Result: A total of 17 studies involving 1 402 patients were included.There were 687 patients with open reduction and internal fixation and 715 with external fixation.The results of Meta-analysis indicated that there were statistically significant differences with regard to the postoperatively total complications, infection, malunion, tendon rupture ( I 2 =8%, RR =0.77(95% CI 0.65-0.91, Z =3.10, P <0.05). There were no statistically significant differences observed between two approaches with respect to nounion, re-operation, complex regional pain syndrome, carpal tunnel syndrome, neurapraxia, tendonitis, painful hardware, scar( P >0.05). Conclusion: Postoperative complications are present in both open reduction and internal fixation and external fixation.Compared with external fixation, open reduction and internal fixation is lower in total complications postoperatively, infection and malunion, but external fixation has lower tendon rupture incidence.

An ex vivo mechanical evaluation of single versus double semitubular plate fixation of a transverse distal-third scapular osteotomy in the dog.

PubMed

Mair, Jacqueline J; Belkoff, Stephen M; Boudrieau, Randy J

2003-01-01

To compare single versus double semitubular plate fixation for scapular body fractures. Ex vivo mechanical study. Eighteen paired cadaveric canine scapulae. Transverse scapular body osteotomies were created in the distal third of 18 pairs of scapulae. One scapula of each pair was repaired with a single plate, whereas the contralateral scapula was repaired with 2 plates. Initial strength and stiffness of the constructs were measured in 10 pairs of scapulae. Eight pairs of scapulae underwent cyclic loading and then were subjected to failure testing. Double-plate fixation was significantly stronger (3,899 +/- 632 N) but not stiffer (614 +/- 130 N/mm) than the single-plate fixation (3,238 +/- 935 N and 537 +/- 202 N/mm, respectively). Cyclic loading variables were not significantly different between the 2 methods of fixation. After cyclic loading, double-plate fixation was significantly stronger (2,916 +/- 618 N) than single-plate fixation (2,347 +/- 495 N). There was no significant difference (P =.11) in stiffness between double- versus single-plate fixations: 734 +/- 247 N/mm and 595 +/- 139 N/mm, respectively. Double-plate fixation was generally stronger and stiffer than single-plate fixation. Because all constructs failed at loads that greatly exceeded those estimated to occur clinically, any difference between the 2 methods of fixation probably is not clinically relevant. Single-plate fixation may be of sufficient strength for fixation of scapular body fractures. Copyright 2003 by The American College of Veterinary Surgeons

Screw fixation versus arthroplasty versus plate fixation for 3-part radial head fractures.

PubMed

Wu, P H; Shen, L; Chee, Y H

2016-04-01

To compare the outcome following headless compression screw fixation versus radial head arthroplasty versus plate fixation for 3-part Mason types III or IV radial head fracture. Records of 25 men and 16 women aged 21 to 80 (mean, 43.3) years who underwent fixation using 2 to 3 2-mm cannulated headless compression screws (n=16), radial head arthroplasty (n=13), or fixation with a 2-mm Synthes plate (n=12) for 3-part Mason types III or IV radial head and neck fracture were reviewed. Treatment option was decided by the surgeon based on the presence of associated injury, neurovascular deficit, and the Mason classification. Bone union, callus formation, and complications (such as heterotopic ossification, malunion, and nonunion) were assessed by an independent registrar or consultant using radiographs. The Mayo Elbow Performance Score and range of motion were assessed by an independent physiotherapist. The median age of the 3 groups were comparable. Associated injuries were most common in patients with arthroplasty, followed by screw fixation and plate fixation (61.5% vs. 50% vs. 33%, p=0.54). The median time to bone union was shorter after screw fixation than plate fixation (55 vs. 86 days, p=0.05). No patient with screw fixation had nonunion, but 4 patients with plate fixation had nonunion. The 3 groups were comparable in terms of the mean Mayo Elbow Performance Score (p=0.56) and the mean range of motion (p=0.45). The complication rate was highest after plate fixation, followed by screw fixation and arthroplasty (50% vs. 18.8% vs. 15.4%, p=0.048). Excluding 20 patients with associated injuries (8 in screw fixation, 8 in arthroplasty, and 4 in plate fixation), the 3 groups were comparable in terms of the median time to bone union (p=0.109), mean Mayo Elbow Performance Score (p=0.260), mean range of motion (p=0.162), and complication rate (p=0.096). Headless compression screw fixation is a viable option for 3-part radial head fracture. It achieves earlier bone union with fewer complications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

M. D. White; B. P. McGrail; S. K. Wurstner

Displacing natural gas and petroleum with carbon dioxide is a proven technology for producing conventional geologic hydrocarbon reservoirs, and producing additional yields from abandoned or partially produced petroleum reservoirs. Extending this concept to natural gas hydrate production offers the potential to enhance gas hydrate recovery with concomitant permanent geologic sequestration. Numerical simulation was used to assess a suite of carbon dioxide injection techniques for producing gas hydrates from a variety of geologic deposit types. Secondary hydrate formation was found to inhibit contact of the injected CO{sub 2} regardless of injectate phase state, thus diminishing the exchange rate due to poremore » clogging and hydrate zone bypass of the injected fluids. Additional work is needed to develop methods of artificially introducing high-permeability pathways in gas hydrate zones if injection of CO{sub 2} in either gas, liquid, or micro-emulsion form is to be more effective in enhancing gas hydrate production rates.« less

Microbial methane in the shallow Paleozoic sediments and glacial deposits of Illinois, U.S.A.

USGS Publications Warehouse

Coleman, D.D.; Liu, Chao-Li; Riley, K.M.

1988-01-01

Methane formed by the microbial decomposition of buried organic matter is virtually ubiquitous in the groundwaters of Illinois. Chemical and carbon isotopic compositions are reported for gas samples collected from over 200 private and municipal water wells and from 39 small gas wells completed in glacial deposits (drift-gas wells). Carbon and hydrogen isotopic data for methane, carbon dioxide and water show that these gases were formed by the carbon dioxide reduction pathway, the same mechanism which has been previously shown to be responsible for microbial methane formation in the marine environment. The isotopic composition of methane in these samples can be closely correlated with the chemical composition of the gas and with water chemistry. The data are interpreted as indicating that isotopically very light methane is found in waters where the residence time of groundwater in the methanogenesis zone was very short relative to the methane production rate. ?? 1988.

Ultrafast fragmentation dynamics of triply charged carbon dioxide: Vibrational-mode-dependent molecular bond breakage

NASA Astrophysics Data System (ADS)

Yang, HongJiang; Wang, Enliang; Dong, WenXiu; Gong, Maomao; Shen, Zhenjie; Tang, Yaguo; Shan, Xu; Chen, Xiangjun

2018-05-01

The a b i n i t i o molecular dynamics (MD) simulations using an atom-centered density matrix propagation method have been carried out to investigate the fragmentation of the ground-state triply charged carbon dioxide, CO23 +→C+ + Oa+ + Ob+ . Ten thousands of trajectories have been simulated. By analyzing the momentum correlation of the final fragments, it is demonstrated that the sequential fragmentation dominates in the three-body dissociation, consistent with our experimental observations which were performed by electron collision at impact energy of 1500 eV. Furthermore, the MD simulations allow us to have detailed insight into the ultrafast evolution of the molecular bond breakage at a very early stage, within several tens of femtoseconds, and the result shows that the initial nuclear vibrational mode plays a decisive role in switching the dissociation pathways.

Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

PubMed Central

Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C.; Mackie, Roderick I.

2014-01-01

Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds. PMID:25383887

The involvement of the nif-associated ferredoxin-like genes fdxA and fdxN of Herbaspirillum seropedicae in nitrogen fixation.

PubMed

Souza, André L F; Invitti, Adriana L; Rego, Fabiane G M; Monteiro, Rose A; Klassen, Giseli; Souza, Emanuel M; Chubatsu, Leda S; Pedrosa, Fábio O; Rigo, Liu U

2010-02-01

The pathway of electron transport to nitrogenase in the endophytic beta-Proteobacterium Herbaspirillum seropedicae has not been characterized. We have generated mutants in two nif-associated genes encoding putative ferredoxins, fdxA and fdxN. The fdxA gene is part of the operon nifHDKENXorf1orf2fdxAnifQmodABC and is transcribed from the nifH promoter, as revealed by lacZ gene fusion. The fdxN gene is probably cotranscribed with the nifB gene. Mutational analysis suggests that the FdxA protein is essential for maximum nitrogenase activity, since the nitrogenase activity of the fdxA mutant strain was reduced to about 30% of that of the wild-type strain. In addition, the fdxA mutation had no effect on the nitrogenase switch-off in response to ammonium. Nitrogenase activity of a mutant strain lacking the fdxN gene was completely abolished. This phenotype was reverted by complementation with fdxN expressed under lacZ promoter control. The results suggest that the products of both the fdxA and fdxN genes are probably involved in electron transfer during nitrogen fixation.

Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds.

PubMed

Finster, Kai Waldemar; Kjeldsen, Kasper Urup; Kube, Michael; Reinhardt, Richard; Mussmann, Marc; Amann, Rudolf; Schreiber, Lars

2013-04-15

Desulfocapsa sulfexigens SB164P1 (DSM 10523) belongs to the deltaproteobacterial family Desulfobulbaceae and is one of two validly described members of its genus. This strain was selected for genome sequencing, because it is the first marine bacterium reported to thrive on the disproportionation of elemental sulfur, a process with a unresolved enzymatic pathway in which elemental sulfur serves both as electron donor and electron acceptor. Furthermore, in contrast to its phylogenetically closest relatives, which are dissimilatory sulfate-reducers, D. sulfexigens is unable to grow by sulfate reduction and appears metabolically specialized in growing by disproportionating elemental sulfur, sulfite or thiosulfate with CO2 as the sole carbon source. The genome of D. sulfexigens contains the set of genes that is required for nitrogen fixation. In an acetylene assay it could be shown that the strain reduces acetylene to ethylene, which is indicative for N-fixation. The circular chromosome of D. sulfexigens SB164P1 comprises 3,986,761 bp and harbors 3,551 protein-coding genes of which 78% have a predicted function based on auto-annotation. The chromosome furthermore encodes 46 tRNA genes and 3 rRNA operons.

Complete genome sequence of Desulfocapsa sulfexigens, a marine deltaproteobacterium specialized in disproportionating inorganic sulfur compounds

PubMed Central

Finster, Kai Waldemar; Kjeldsen, Kasper Urup; Kube, Michael; Reinhardt, Richard; Mussmann, Marc; Amann, Rudolf; Schreiber, Lars

2013-01-01

Desulfocapsa sulfexigens SB164P1 (DSM 10523) belongs to the deltaproteobacterial family Desulfobulbaceae and is one of two validly described members of its genus. This strain was selected for genome sequencing, because it is the first marine bacterium reported to thrive on the disproportionation of elemental sulfur, a process with a unresolved enzymatic pathway in which elemental sulfur serves both as electron donor and electron acceptor. Furthermore, in contrast to its phylogenetically closest relatives, which are dissimilatory sulfate-reducers, D. sulfexigens is unable to grow by sulfate reduction and appears metabolically specialized in growing by disproportionating elemental sulfur, sulfite or thiosulfate with CO2 as the sole carbon source. The genome of D. sulfexigens contains the set of genes that is required for nitrogen fixation. In an acetylene assay it could be shown that the strain reduces acetylene to ethylene, which is indicative for N-fixation. The circular chromosome of D. sulfexigens SB164P1 comprises 3,986,761 bp and harbors 3,551 protein-coding genes of which 78% have a predicted function based on auto-annotation. The chromosome furthermore encodes 46 tRNA genes and 3 rRNA operons. PMID:23961312

Plate versus intramedullary fixation of two-part and multifragmentary displaced midshaft clavicle fractures - a long-term analysis.

PubMed

Chan, Gareth; Korac, Zelimir; Miletic, Matija; Vidovic, Dinko; Phadnis, Joideep; Bakota, Bore

2017-11-01

Surgical fixation of displaced midshaft clavicle fractures is predominantly achieved with intramedullary (IM) or plate fixation. Both techniques have potential pitfalls: plate fixation involves greater periosteal stripping and protuberance of the implant, whereas IM fixation may be associated with implant-related complications, such as migration or skin irritation, which may lead to further surgery for implant removal. The aim of this study was to compare these two methods in simple (Robinson 2b.1) and multifragmentary (Robinson 2b.2) displaced midshaft clavicle fractures. A total of 133 consecutive patients who underwent surgical fixation for a displaced midshaft clavicle fracture with either IM fixation using a 2.5-mm Kirschner wire or plate fixation using an 8-hole Dynamic Compression Plate (DCP) were retrospectively reviewed. Follow-up was a minimum of 1 year. The patients were allocated into two injury groups: displaced simple 2-part fractures (64 IM vs. 16 DCP) and displaced multifragmentary fractures (27 IM vs. 26 DCP). The major observed outcome measures were: infection rate, non-union rate, reoperation rate and postoperative range of motion (ROM). Rates of non-union for displaced 2-part fractures were 2/64 (3.13%) with IM fixation and 0/16 (0.00%) with plate fixation (p = 0.477). For displaced multifragmentary fractures, rates of non-union were 2/27 (7.41%) with IM fixation and 0/26 (0.00%) with plate fixation (p = 0.161). No significant difference was observed between the two fixation modalities in patient-reported time to regain ROM on the injured side for displaced 2-part fractures (p = 0.129) and displaced multifragmentary fractures (p = 0.070). Deep infection rate was zero (p = 1.000) overall in the study, and reoperation rate for IM and plate fixation, respectively, was 3.13% and 6.25% in the Robinson 2b.1 group (p = 0.559) and 7.41% and 7.69% in the Robinson 2b.2 group (p = 0.969). IM fixation of displaced midshaft clavicle fractures (Robinson 2b.1) has an equivalent non-union rate to plate fixation and similarly low complication and reoperation rates. For displaced midshaft multifragmentary clavicle fractures (Robinson 2b.2), the higher non-union rates observed with IM fixation leads us to recommend consideration of plate fixation for Robinson 2b.2 fractures. © 2017 Elsevier Ltd. All rights reserved.

Petit-High Pressure Carbon Dioxide stress increases synthesis of S-Adenosylmethionine and phosphatidylcholine in yeast Saccharomyces cerevisiae.

PubMed

Niu, Liyuan; Nomura, Kazuki; Iwahashi, Hitoshi; Matsuoka, Hiroyuki; Kawachi, Satoshi; Suzuki, Yoshihisa; Tamura, Katsuhiro

2017-12-01

Petit-High Pressure Carbon Dioxide (p-HPCD) is a promising nonthermal technology for foods pasteurization. Cluster analysis of gene expression profiles of Saccharomyces cerevisiae exposed to various stresses exhibited that gene expression profile for p-HPCD stress (0.5MPa, 25°C) was grouped into a cluster including profiles for Sodium Dodecyl Sulfate and Roundup herbicide. Both are detergents that can disorder membrane structurally and functionally, which suggests that cell membrane may be a target of p-HPCD stress to cause cell growth inhibition. Through metabolomic analysis, amount of S-Adenosylmethionine (AdoMet) that is used as methyl donor to participate in phosphatidylcholine synthesis via phosphatidylethanolamine (PE) methylation pathway, was increased after p-HPCD treatment for 2h. The key gene OPI3 encoding phospholipid methyltransferase that catalyzes the last two steps in PE methylation pathway was confirmed significantly induced by RT-PCR. Transcriptional expression of genes (MET13, MET16, MET10, MET17, MET6 and SAM2) related to AdoMet biosynthesis was also significantly induced. Choline as the PC precursor and ethanolamine as PE precursor in Kennedy pathway were also found increased under p-HPCD condition. We also found that amounts of most of amino acids involving protein synthesis were found decreased after p-HPCD treatment for 2h. Moreover, morphological changes on cell surface were observed by scanning electron microscope. In conclusion, the effects of p-HPCD stress on cell membrane appear to be a very likely cause of yeast growth inhibition and the enhancement of PC synthesis could contribute to maintain optimum structure and functions of cell membrane and improve cell resistance to inactivation. Copyright © 2017 Elsevier B.V. All rights reserved.

A comparative analysis of the effectiveness of active versus passive atrial lead fixation in Chinese patients with cardiac implantable electrical devices: a long term, retrospective, observational, single-center study.

PubMed

Hao, Yinglu; Li, Yanping; Liao, Derong; Yang, Ling; Liu, Fangyan

2017-03-01

Data comparing active atrial lead fixation with passive atrial lead fixation in Chinese patients with cardiovascular implantable electronic devices (CIEDs) for atrial pacing is limited. Our study evaluated the effectiveness of active fixation versus passive fixation of atrial leads by observing the lead performance parameters. This retrospective, long-term, single-center study included a cohort of Chinese patients who underwent CIED implantation at the Department of Cardiology of People's Hospital of Yuxi City, China, from 1 March 2010 to 1 March 2015. Efficacy was determined by comparing implantation time, threshold values, incidence of lead dislocation/failure, and lead-related complications between the two groups. Of the 1217 patients, active and passive atrial lead fixation were performed in 530 (mean age, 69.37 ± 11.44 years) and 497 (mean age, 68.33 ± 10.96 years). The active fixation group reported significantly lower mean atrial implantation times (P = .0001) and threshold values (P = .044) compared with the passive atrial lead fixation group. In addition, threshold values in the active atrial lead fixation group were stable throughout the observation period. No instances of myocardial perforation, cardiac tamponade, implantation failure, or electrode dislocation/re-fixation were reported in the active atrial lead fixation group. A favorable decrease in patient comfort parameters such as bed rest time (P = .027) and duration of hospital stay (P = .038) were also observed in the active lead fixation group. Active atrial lead fixation demonstrated greater stability, steady long-term thresholds and minimal lead-related complications compared to passive lead fixation in Chinese patients with CIEDs.

Relocatable fixation systems in intracranial stereotactic radiotherapy. Accuracy of serial CT scans and patient acceptance in a randomized design.

PubMed

Theelen, A; Martens, J; Bosmans, G; Houben, R; Jager, J J; Rutten, I; Lambin, P; Minken, A W; Baumert, B G

2012-01-01

The goal was to provide a quantitative evaluation of the accuracy of three different fixation systems for stereotactic radiotherapy and to evaluate patients' acceptance for all fixations. A total of 16 consecutive patients with brain tumours undergoing fractionated stereotactic radiotherapy (SCRT) were enrolled after informed consent (Clinical trials.gov: NCT00181350). Fixation systems evaluated were the BrainLAB® mask, with and without custom made bite-block (fixations S and A) and a homemade neck support with bite-block (fixation B) based on the BrainLAB® frame. The sequence of measurements was evaluated in a randomized manner with a cross-over design and patients' acceptance by a questionnaire. The mean three-dimensional (3D) displacement and standard deviations were 1.16 ± 0.68 mm for fixation S, 1.92 ± 1.28 and 1.70 ± 0.83 mm for fixations A and B, respectively. There was a significant improvement of the overall alignment (3D vector) when using the standard fixation instead of fixation A or B in the craniocaudal direction (p = 0.037). Rotational deviations were significantly less for the standard fixation S in relation to fixations A (p = 0.005) and B (p = 0.03). EPI imaging with off-line correction further improved reproducibility. Five out of 8 patients preferred the neck support with the bite-block. The mask fixation system in conjunction with a bite-block is the most accurate fixation for SCRT reducing craniocaudal and rotational movements. Patients favoured the more comfortable but less accurate neck support. To optimize the accuracy of SCRT, additional regular portal imaging is warranted.

Nutrient feedbacks to soil heterotrophic nitrogen fixation in forests

USGS Publications Warehouse

Perakis, Steven; Pett-Ridge, Julie C.; Catricala, Christina E.

2017-01-01

Multiple nutrient cycles regulate biological nitrogen (N) fixation in forests, yet long-term feedbacks between N-fixation and coupled element cycles remain largely unexplored. We examined soil nutrients and heterotrophic N-fixation across a gradient of 24 temperate conifer forests shaped by legacies of symbiotic N-fixing trees. We observed positive relationships among mineral soil pools of N, carbon (C), organic molybdenum (Mo), and organic phosphorus (P) across sites, evidence that legacies of symbiotic N-fixing trees can increase the abundance of multiple elements important to heterotrophic N-fixation. Soil N accumulation lowered rates of heterotrophic N-fixation in organic horizons due to both N inhibition of nitrogenase enzymes and declines in soil organic matter quality. Experimental fertilization of organic horizon soil revealed widespread Mo limitation of heterotrophic N-fixation, especially at sites where soil Mo was scarce relative to C. Fertilization also revealed widespread absence of P limitation, consistent with high soil P:Mo ratios. Responses of heterotrophic N-fixation to added Mo (positive) and N (negative) were correlated across sites, evidence that multiple nutrient controls of heterotrophic N-fixation were more common than single-nutrient effects. We propose a conceptual model where symbiotic N-fixation promotes coupled N, C, P, and Mo accumulation in soil, leading to positive feedback that relaxes nutrient limitation of overall N-fixation, though heterotrophic N-fixation is primarily suppressed by strong negative feedback from long-term soil N accumulation.

21 CFR 888.3040 - Smooth or threaded metallic bone fixation fastener.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Smooth or threaded metallic bone fixation fastener... metallic bone fixation fastener. (a) Identification. A smooth or threaded metallic bone fixation fastener..., slotted head on the end. It may be used for fixation of bone fractures, for bone reconstructions, as a...

21 CFR 888.3040 - Smooth or threaded metallic bone fixation fastener.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Smooth or threaded metallic bone fixation fastener... metallic bone fixation fastener. (a) Identification. A smooth or threaded metallic bone fixation fastener..., slotted head on the end. It may be used for fixation of bone fractures, for bone reconstructions, as a...

21 CFR 888.3040 - Smooth or threaded metallic bone fixation fastener.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Smooth or threaded metallic bone fixation fastener... metallic bone fixation fastener. (a) Identification. A smooth or threaded metallic bone fixation fastener..., slotted head on the end. It may be used for fixation of bone fractures, for bone reconstructions, as a...

21 CFR 888.3040 - Smooth or threaded metallic bone fixation fastener.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Smooth or threaded metallic bone fixation fastener... metallic bone fixation fastener. (a) Identification. A smooth or threaded metallic bone fixation fastener..., slotted head on the end. It may be used for fixation of bone fractures, for bone reconstructions, as a...

21 CFR 888.3040 - Smooth or threaded metallic bone fixation fastener.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Smooth or threaded metallic bone fixation fastener... metallic bone fixation fastener. (a) Identification. A smooth or threaded metallic bone fixation fastener..., slotted head on the end. It may be used for fixation of bone fractures, for bone reconstructions, as a...

High-nitrogen fixation rates in the particulate and dissolved pools in the Western Tropical Pacific (Solomon and Bismarck Seas)

NASA Astrophysics Data System (ADS)

Berthelot, H.; Benavides, M.; Moisander, P. H.; Grosso, O.; Bonnet, S.

2017-08-01

Dinitrogen (N2) fixation rates were investigated in the euphotic layer of the Bismarck and Solomon Seas using 15N2 incubation assays taking into account both the particulate and the dissolved pools. Average depth-integrated particulate N2 fixation rates were 203 (range 43-399) and 1396 (range 176-3132) μmol N m-2 d-1 in the Bismarck and Solomon Seas, respectively. In both seas, N2 fixation measured in the dissolved pool was similar to particulate N2 fixation, highlighting the potentially substantial underestimation of N2 fixation in oceanic budgets when only particulate N2 fixation is considered. Among the diazotroph phylotypes targeted using quantitative polymerase chain reaction amplification of nifH genes, Trichodesmium was the most abundant. Regression analyses suggest that it accounted for the major proportion of N2 fixation. However, unicellular cyanobacterial and non-cyanobacterial diazotrophs were also occasionally abundant. This study reports high pelagic N2 fixation rates and confirms that the Western Tropical South Pacific is a hot spot for marine N2 fixation.

Complement fixation test to C burnetii

MedlinePlus

... complement fixation test; Coxiella burnetii - complement fixation test; C burnetii - complement fixation test ... a specific foreign substance ( antigen ), in this case, C burnetii . Antibodies defend the body against bacteria, viruses, ...

Oxidation in Enceladus' Ocean

NASA Astrophysics Data System (ADS)

Ray, C.; Waite, J. H., Jr.; Glein, C.; Teolis, B. D.

2017-12-01

The detection of molecular hydrogen in the plume of Saturn's icy moon Enceladus reports that there is positive chemical affinity for methanogenesis, the reaction of hydrogen with carbon dioxide to form methane and water [Waite et al., 2017]. Methanogenesis, however, is just one of many possible metabolic pathways that could be utilized. While some of the oxidants involved in these metabolic pathways have already been detected in the plume (i.e. carbon dioxide), sulfate, which could play an important role in several of these reactions, has not yet been observed. To constrain the amount of sulfate and other oxidants that could be present to support these metabolisms, we present a geochemical model of Enceladus' ocean based on detections made by the Cassini INMS instrument [Waite et. al, 2017]. We use a model of radiolysis on the surface of Enceladus to estimate the amount of molecular oxygen (O2) contained in the ice. We calculate the delivery rate of O2 from the surface ice to the ocean using previous estimates of the rate of ice deposition on the south polar region [Kempf et al., 2010], and the meteoritic gardening rate for the older surface of the moon. Assuming this activity has occurred over 4.5 billion years, we obtain an upper limit of > 1020 moles of O2 delivered to the ocean over Enceladus' lifetime. This large amount of oxygen could react with sulfides, reduced iron, or organic materials to produce sulfate, ferric oxyhydroxides, or carbon dioxide/carboxylic acids, respectively. We calculate upper limits on the amounts of these materials using a mineralogical model of Enceladus' core [Waite et al., 2017]. We find that the abiotic oxidation of pyrrhotite, which is the most likely pathway for sulfate production, could yield a sulfate concentration > 4 mol/(kg H2O). We suggest that oxidants should be abundant in the ocean and plume unless they are being consumed by life, the rate of ice deposition on the surface is much smaller than what has been predicted, or the duration of activity delivering O2 to the ocean is much shorter than the age of the solar system. References: [1] J. H. Waite, et al., Cassini finds molecular hydrogen in the Enceladus plume: Evidence for hydrothermal processes, Science 357, 6349 (2017). [2] S. Kempf, et al., How the Enceladus dust plume feeds Saturn's E ring, Icarus 206, 2 (2010)

Fixation Patterns and Reading Rates in Eyes with Central Scotomas from Advanced Atrophic Age-related Macular Degeneration and Stargardt Disease

PubMed Central

Sunness, Janet S.; Applegate, Carol A.; Haselwood, David; Rubin, Gary S.

2009-01-01

Purpose To study fixation patterns and reading rates in eyes with central scotomas from geographic atrophy (GA) of age-related macular degeneration and to compare fixation patterns with those of patients with Stargardt disease. Methods Scanning laser ophthalmoscope analysis of fixation patterns in eyes with 20/80 to 20/200 visual acuity. Included were 41 eyes of 35 patients with GA and 10 eyes of 5 patients with Stargardt disease. The patients with GA also were tested for maximum reading rate, and the size of the areas of atrophy were measured by fundus photograph analysis. Results Sixty-three percent of GA eyes fixating outside the atrophy placed the scotoma to the right of fixation in visual field space, 22% placed the scotoma above fixation, and 15% placed it to the left, regardless of the laterality of the GA eye. Fixation was stable in subsequent years of testing for scotoma placement to the right of or above fixation. All GA eyes fixated immediately adjacent to the atrophy. In contrast, seven of ten eyes with Stargardt disease fixated at a considerable distance from the scotoma border, with the dense scotoma far above the fixation site in visual field space. For the patients with GA, the maximum reading rate was highly correlated with size of the atrophic area, but not with age or visual acuity within the limited visual acuity range tested. There was a trend to more rapid reading with the scotoma above fixation and slower reading with the scotoma to the left. Conclusion There is a preference for fixation with the scotoma to the right in eyes with GA. Patients with Stargardt disease use different strategies for fixation, perhaps due to subclinical pathology adjacent to the atrophic regions. The size of the atrophic area in GA plays the predominant role in reading rate for eyes that have already lost foveal vision. PMID:8841306

Biomechanical comparison of four C1 to C2 rigid fixative techniques: anterior transarticular, posterior transarticular, C1 to C2 pedicle, and C1 to C2 intralaminar screws.

PubMed

Lapsiwala, Samir B; Anderson, Paul A; Oza, Ashish; Resnick, Daniel K

2006-03-01

We performed a biomechanical comparison of several C1 to C2 fixation techniques including crossed laminar (intralaminar) screw fixation, anterior C1 to C2 transarticular screw fixation, C1 to 2 pedicle screw fixation, and posterior C1 to C2 transarticular screw fixation. Eight cadaveric cervical spines were tested intact and after dens fracture. Four different C1 to C2 screw fixation techniques were tested. Posterior transarticular and pedicle screw constructs were tested twice, once with supplemental sublaminar cables and once without cables. The specimens were tested in three modes of loading: flexion-extension, lateral bending, and axial rotation. All tests were performed in load and torque control. Pure bending moments of 2 nm were applied in flexion-extension and lateral bending, whereas a 1 nm moment was applied in axial rotation. Linear displacements were recorded from extensometers rigidly affixed to the C1 and C2 vertebrae. Linear displacements were reduced to angular displacements using trigonometry. Adding cable fixation results in a stiffer construct for posterior transarticular screws. The addition of cables did not affect the stiffness of C1 to C2 pedicle screw constructs. There were no significant differences in stiffness between anterior and posterior transarticular screw techniques, unless cable fixation was added to the posterior construct. All three posterior screw constructs with supplemental cable fixation provide equal stiffness with regard to flexion-extension and axial rotation. C1 lateral mass-C2 intralaminar screw fixation restored resistance to lateral bending but not to the same degree as the other screw fixation techniques. All four screw fixation techniques limit motion at the C1 to 2 articulation. The addition of cable fixation improves resistance to flexion and extension for posterior transarticular screw fixation.

Differential vergence movements in reading Chinese and English: Greater fixation-initial binocular disparity is advantageous in reading the denser orthography.

PubMed

Hsiao, Yi-Ting; Shillcock, Richard; Obregón, Mateo; Kreiner, Hamutal; Roberts, Matthew A J; McDonald, Scott

2017-07-11

We explore two aspects of exovergence: we test whether smaller binocular fixation disparities accompany the shorter saccades and longer fixations observed in reading Chinese; we test whether potentially advantageous psychophysical effects of exovergence (cf. Arnold & Schindel, 2010; Kersten & Murray, 2010) transfer to text reading. We report differential exovergence in reading Chinese and English: Chinese readers begin fixations with more binocular disparity, but end fixations with a disparity closely similar to that of the English readers. We conclude that greater fixation-initial binocular fixation disparity can be adaptive in the reading of visually and cognitively denser text.

Using decision pathway surveys to inform climate engineering policy choices

PubMed Central

Gregory, Robin; Satterfield, Terre; Hasell, Ariel

2016-01-01

Over the coming decades citizens living in North America and Europe will be asked about a variety of new technological and behavioral initiatives intended to mitigate the worst impacts of climate change. A common approach to public input has been surveys whereby respondents’ attitudes about climate change are explained by individuals’ demographic background, values, and beliefs. In parallel, recent deliberative research seeks to more fully address the complex value tradeoffs linked to novel technologies and difficult ethical questions that characterize leading climate mitigation alternatives. New methods such as decision pathway surveys may offer important insights for policy makers by capturing much of the depth and reasoning of small-group deliberations while meeting standard survey goals including large-sample stakeholder engagement. Pathway surveys also can help participants to deepen their factual knowledge base and arrive at a more complete understanding of their own values as they apply to proposed policy alternatives. The pathway results indicate more fully the conditional and context-specific nature of support for several “upstream” climate interventions, including solar radiation management techniques and carbon dioxide removal technologies. PMID:26729883

Designing overall stoichiometric conversions and intervening metabolic reactions

DOE PAGES

Chowdhury, Anupam; Maranas, Costas D.

2015-11-04

Existing computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e.,more » minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C 2+ metabolites with higher carbon efficiency.« less

Using decision pathway surveys to inform climate engineering policy choices.

PubMed

Gregory, Robin; Satterfield, Terre; Hasell, Ariel

2016-01-19

Over the coming decades citizens living in North America and Europe will be asked about a variety of new technological and behavioral initiatives intended to mitigate the worst impacts of climate change. A common approach to public input has been surveys whereby respondents' attitudes about climate change are explained by individuals' demographic background, values, and beliefs. In parallel, recent deliberative research seeks to more fully address the complex value tradeoffs linked to novel technologies and difficult ethical questions that characterize leading climate mitigation alternatives. New methods such as decision pathway surveys may offer important insights for policy makers by capturing much of the depth and reasoning of small-group deliberations while meeting standard survey goals including large-sample stakeholder engagement. Pathway surveys also can help participants to deepen their factual knowledge base and arrive at a more complete understanding of their own values as they apply to proposed policy alternatives. The pathway results indicate more fully the conditional and context-specific nature of support for several "upstream" climate interventions, including solar radiation management techniques and carbon dioxide removal technologies.