Carbon Metabolism

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Calcium regulation in chloroplasts and the role of calcium-dependent phosphorylation of transketolase in carbon metabolism

Calcium regulation in chloroplasts and the role of calcium-dependent phosphorylation of transketolase in carbon metabolism

All in all, these results indicate that phosphorylation of AtTKL1 might be an important part of its regulation during a typical light-dark cycle of the plant and Figure 26 represents a proposed model for the TKL regulation mechanism in correlation to its function in carbon metabolism. Nevertheless, it remains unclear whether calcium-dependent phosphorylation of AtTKL1 is limited to a role on enzyme activity exclusively in the diurnal rhythm of the plant. For instance, studies on Populus revealed oscillations in phosphate sugars content throughout the year (Sagisaka 1974) without any evidence how this oscillation is regulated. To really understand the role of calcium-dependent phosphorylation of AtTKL1 for the plant it will be essential to elucidate the in vivo effect of this modification, e.g. by introducing non-phosphorylatable or phospho-mimicking variants of AtTKL1 into Arabidopsis plants.
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Carbon Metabolism of Methylotrophic Methanogens and Asgard Archaea in Marine Sediments

Carbon Metabolism of Methylotrophic Methanogens and Asgard Archaea in Marine Sediments

archaea (Lokiarchaeota) (Chapter 4). By amending organic polymers, i.e., lignin, humic acid and cellulose, activities of Lokiarchaeota were successfully detected in SIP incubations. In combination with metagenomic sequencing, we have shown that Lokiarchaeota might degrade the polymeric sugar part of these organic compounds via Embden–Meyerhof–Parnas pathway or potentially use the products of polymer breakdown (benzoate) as carbon or energy source. Asgard archaea harbor a more complex carbon metabolism than methanogens, which is indicated by the observation of oxidation pathways of both, short- and medium-chain alkanes. The finding of methyl-coenzyme M reductase genes in Asgard archaea widely extends the phylogenetic distribution of microorganisms involved in short-chain alkane oxidation way beyond methane as a substrate. Taken together, the new findings about activities and potential capabilities of Asgard archaea suggest multiple carbon utilization potentials and versatile activities in alkane oxidation, potentially linked to environmental adaption.
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The transcriptome and flux profiling of Crabtree‐negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

The transcriptome and flux profiling of Crabtree‐negative hydroxy acid producing strains of Saccharomyces cerevisiae reveals changes in the central carbon metabolism

Figure 3. 13 C‐based metabolic flux and transcriptomic analyses of central carbon metabolism of the hydroxy acid‐producing strains under batch fermentation conditions with 10 g L −1 initial glucose concentrations. Crabtree‐negative S. cerevisiae strains (TAM—STtam_2803) producing different hydroxy acids: lactate (STlac_7031), malate (STmal_5413), and 3HP (SThpdh_2779 and SThibadh_2780) were analyzed for their relative flux distributions and the differential expression of the genes involved in each reaction. Bar charts next to each reaction show the relative flux values for each strain calculated from a genome‐scale model constrained with data from 13 C‐MFA (normalized over glucose uptake rate). Underneath each graph are heat map plots for the relative transcript levels. Beside each heat map plots are the name of the associated gene. AC, acetate; ACALD, acetaldehyde; ACoAmit, acetyl‐CoA (mitochondrial); AKG, α‐ ketoglutarate; CIT, citrate; DHAP, dihydroxy‐acetone‐phosphate; 13DPG, 1,3‐diphosphateglycerate; E4P, erythrose‐4‐phosphate; EtOH, ethanol; F6P, fructose‐6‐ phosphate; FDP, fructose‐1,6‐diphosphate; FUM, fumarate; GLC, glucose; GLYC, glycerol; GLYC3P, glycerol‐3‐phosphate; G3P, glyceraldehyde‐3‐phosphate; G6P, glucose‐6‐phosphate; ICIT, isocitrate; MAL, malate; OAA, oxaloacetate; PEP, phosphoenolpyruvate; 2PG, 2‐phosphoglycerate; 3PG, 3‐phosphoglycerate; 6PGC, 6‐phospho‐ D ‐gluconate; 6PGL, D ‐6‐phospho‐glucono‐δ‐lactone; PYRcyt, pyruvate (cytosolic); PYRmit, pyruvate (mitochondrial); RU5P, ribulose‐5‐
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Substrate Flow from Photosynthetic Carbon Metabolism to Chloroplast Isoprenoid Synthesis in Spinach Evidence for a Plastidic Phosphoglycerate Mutase 

Substrate Flow from Photosynthetic Carbon Metabolism to Chloroplast Isoprenoid Synthesis in Spinach Evidence for a Plastidic Phosphoglycerate Mutase 

carotene plus PQ but not fatty acids. The high rates of fatty acid synthesis observed elsewhere were only obtained when acetate was used as substrate. A ce­ tate also strongly enhanced sterol synthesis in the cytosol. This finding together with the fact (Table I, see also [1, 4]) that m evalonate only favours sterol synthesis in the cytosol and E R but not of plastidic isoprenoids indicates that the plastidic isoprenoid synthesis is directly supplied by the photosynthetic carbon metabolism. To obtain evidence for such a pathway, it was necessary to re-examine w hether a phosphoglycerate mutase is indeed present in spinach chloroplasts. This was undertaken in the following two ways.
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Impact of the Histidine-Containing Phosphocarrier Protein HPr on Carbon Metabolism and Virulence in Staphylococcus aureus

Impact of the Histidine-Containing Phosphocarrier Protein HPr on Carbon Metabolism and Virulence in Staphylococcus aureus

Numerous genes have been identified to be regulated on the transcriptional level by CcpA in S. aureus [ 15 – 17 ]. In addition to genes/operons involved in carbon catabolism, the synthesis of factors associated with biofilm formation and virulence of S. aureus are also influenced by CcpA [ 6 , 15 – 21 ]. Specifically, CcpA promotes transcription of the ica- operon and cidA [ 19 ], encoding proteins needed for polysaccharide intercellular adhesion (PIA) synthesis and extracellular DNA release, respectively [ 22 , 23 ]. These observations are consistent with the fact that deletion of ccpA abrogates biofilm formation under glucose- rich conditions. [ 19 ]. Furthermore, inactivation of ccpA in S. aureus reduces the formation of liver and skin abscesses in mouse models of infection [ 6 , 24 , 25 ]. Taken together, these observations demonstrate the linkage between CcpA, glucose catabolism, and virulence in S. aureus; however, the function of HPr remains largely unknown. Here, we characterize the function of HPr of S. aureus in the context of carbon metabolism, growth kinetics, biofilm formation, and in vivo infectivity in different murine infection models.
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Anoxygenic photosynthesis and dark carbon metabolism under micro-oxic conditions in the purple sulfur bacterium "Thiodictyon syntrophicum" nov. strain Cad16T

Anoxygenic photosynthesis and dark carbon metabolism under micro-oxic conditions in the purple sulfur bacterium "Thiodictyon syntrophicum" nov. strain Cad16T

anoxygenic phototrophic sulfur bacteria in the chemocline of meromictic Lake Cadagno.. Isolation and characterization of aggregate-forming 846[r]

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Global aspects of the socioeconomic carbon metabolism / Christian Lauk

Global aspects of the socioeconomic carbon metabolism / Christian Lauk

And finally (4) an estimate of global bioenergy potentials in 2050, based on a biomass balance model that integrates food, livestock, agriculture and bioenergy scenarios. T[r]

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Metabolic trafficking between astrocytes and neurons under hyperammonemia and manganism: Nitrogen- and Carbon metabolism

Metabolic trafficking between astrocytes and neurons under hyperammonemia and manganism: Nitrogen- and Carbon metabolism

ATP/mol of glucose. Pyruvate can be converted into lactate, which regenerates nicotinamide adenine dinucleotide (NAD + ), which is required for the maintenance of glycolysis. Alternatively, pyruvate can enter the TCA cycle and produces 30 mol of ATP/mol of glucose via mitochondrial oxidative phosphorylation. Any disorder in these physiological processes, (i.e. glycolysis, the TCA cycle, and oxidative phosphorylation) may cause disturbance in energy metabolism and result in damage of neural cells and/or in neurotransmitter dysfunction. These disorders can be caused by a variety of agents, such as ammonia, manganese, and excitotoxic elevated extracellular glutamate concentrations. Previous studies have shown that cells with dysfunctions in their energy metabolism caused by hypoxia/ischemia, hypoglycemia, and in Hepatic Encephalopathy (HE) are more susceptible to excitotoxic injury or death, i.e. even slight elevations of extracellular concentration of glutamate are toxic to energy-deficient cells (Novelli et al., 1988). This also means that a deprivation of energy substrates in brain, such as glucose, but also any disturbance in the energy producing processes, may result in brain dysfunction (Magistretti et al., 1993; Magistretti and Pellerin, 1999a). In the present study, we investigated the energy metabolism of astrocytes, neurons, and co-cultures under each pathological condition as hyperammonemia, glutamine-deprivation, and hypoglycemia.
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Redox regulation of photosynthetic carbon metabolism in leaves of Arabidopsis thaliana

Redox regulation of photosynthetic carbon metabolism in leaves of Arabidopsis thaliana

pathways of generating NADPH to be up-regulated. Therefore, we checked the activation status of the G6PDH, which is the key enzyme of the oxidative pentose phosphate cycle in the cytosol and plastids ( Kruger and von Schaewen, 2003 ) and that of NADP–ICDH, which produces NADPH in the plastids, cytosol, mitochondria, and peroxisomes ( Hodges et al., 2003 ). Under normal conditions, plastidial G6PDH is activated by oxidation in the dark to ensure production of NADPH when photosynthetic activity ceases and no Trx is reduced, whereas several Calvin cycle enzymes are activated upon reduction in the light ( Schürmann and Buchanan, 2008 ; Née et al., 2009 ). In contrast to our expectations, the activities of both G6PDH and NADP–ICDH were lower in the tic62 trol plants than in WT ( Figure 5 ). This indicates that the oxidative pentose phos- phate pathway as well as NADP–ICDH is not activated to com- pensate for the shortage of NADPH. Rather, it seems that the lower activity of G6PDH in the mutants results from the expe- ditious flow of electrons from Fd to Trx, which agrees with the increased activation state of AGPase ( Figure 6 ). Moreover, as the plants direct NADPH towards carbon fixation, the allocation of reducing power in the form of malate ( Scheibe et al., 1990 ) is likely to be decreased in the tic62 trol plants ( Figure 6 ). Malate is also needed as a counter-ion for the chlo- roplast import of 2-oxoglutarate ( Weber and Flügge, 2002 ), produced by cytosolic NADP–ICDH, and thus it is tempting to speculate that the activities of NADP–MDH and NADP–ICDH may be co-regulated. Additionally, the decreased NADPH/ NADP + ratio might have led to the decreased NADP–MDH
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Trade in Virtual Carbon

Trade in Virtual Carbon

Carbon emissions are a global pollutant and it is important to stabilize global atmospheric concentra- tion of emissions. However, when deciding on global mitigation strategies and debating global climate agree- ments, it is necessary to be aware of the differences between production- and consumption-based emis- sions. In the debate about appropriate policy measures a tax on the carbon contents of final consumption has been proposed. This tax would have substantial distri- butional effects. Atkinson et al. (2011) calculate the effective tax rate that would fall on countries’ exports by adopting a globally uniform consumption-based carbon tax. Such a tax would increase prices of e.g. Chinese products as much as a production-based tax
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Low carbon pathways

Low carbon pathways

Low carbon pathways Himanshu Gupta 1. Introduction The NITI Aayog, (the erstwhile Planning Commission), rolled out an Integrated Energy Policy (IEP) 1 in 2006 that defines the concept of Energy Security for India as providing “lifeline energy to all its citizens irrespective of their ability to pay as well meet their demand for convenient energy for citizens to satisfy their various needs at competitive prices, at all times, considering shocks and disruptions that can be reasonably expected”. It further talks about exploring options for achieving India’s Energy Independence beyond 2050. The concept of Energy Security might seem to be about exploiting domestic resources maximally and delivering energy at the cheapest price to the consumer, but it is often described with the associated implications for food, air quality and water security: in short, sustainability. Because of global and local repercussions, a country cannot simply aim for high levels of growth based on fossil fuels alone. Local effects are a result of carbon intensive fuels used in transport, biomass incineration, etc. Particulate matter emissions from power plants located close to cities have worsened their air quality: Delhi already, is one of the lowest ranking cities in the world with respect to air quality, as per a recent World Health Organization 2 report.
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D-arabitol metabolism of Corynebacterium glutamicum

D-arabitol metabolism of Corynebacterium glutamicum

In order to test whether the P. luminescens luciferase is functional in C. glutamicum, the test strain C. glutamicum (pET2_luxAB_paceA) was cultivated in minimal medium containing 0.5% (w/v) glucose or 1% (w/v) potassium acetate. For determination of the luciferase activity, 200 µl samples were taken from the cultures at different time points. As the test system did not contain the fatty acid reductase complex which regenerates the luciferase substrate, it was important to analyze whether the luciferase reaction can proceed by external addition of n-decanal as a substrate. For this purpose, each sample was measured without and with addition of n-decanal to a final concentration of 8 mM. In Fig. 21, the luminescence levels of C. glutamicum (pET2_luxAB_paceA) grown on glucose and on acetate are shown. Compared to the luciferase activities in glucose-grown cells (Fig. 21A) the acetate-grown cells (Fig. 21B) showed an up to 20-fold increase of luminescence which indicated a carbon source-dependent luciferase activity as it was expected by the acetate inducible aceA promoter. The gray columns display the determinations with addition of n-decanal, showing a 100- to 500-fold higher luminescence levels compared to the determinations (indicated by black columns) without additional n-decanal. This result points out that the omission of the fatty acid reductase complex can be compensated by external addition of the luciferase substrate n-decanal. Furthermore, this result suggests a fast uptake of n-decanal into the cells which is required for saturation of the luciferase with its substrate. Taken together, these first results indicated that the P. luminescens luciferase system is applicable as a reporter gene assay in C. glutamicum due to the fact that the luciferase genes luxA and luxB are expressed in C. glutamicum and that the enzyme is functional in this organism.
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C4-Metabolism in Marine Brown Macrophytic Algae 

C4-Metabolism in Marine Brown Macrophytic Algae 

A ssim ilation o f inorganic carbon by /?-carboxyla- tion via phosphoenolpyruvate carboxykinase is a m etabolic feature particularly occurring in brown macrophytic algae, w hereas its extent is negligible in representatives o f the C hlorophyceae and Rhodo- phyceae. Evidence for the relative efficiency o f this process is derived from a com parison o f photosyn­ thesis and non-photosynthetic carbon fixation in the dark as well as by m easurem ents o f the respective carboxylating enzymes m ediating the entrance o f C 0 2 into organic com pounds. The potential for ß-
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Carbon Tariffs Revisited

Carbon Tariffs Revisited

Figure 7: Percentage change in domestic supply and export supply of EITE goods in the USA Key: EITE – average of all emission-intensive and trade-exposed industries; crp – chemical products; i_s – iron and steel; nfm – non-ferrous metals; nmm – non-metallic minerals; oil – refined oil products; ppp – paper, pulp and print Turning to the results for Switzerland – reported in Figure 8 – yields a very different picture. The Swiss EITE industry as whole decreases in output by 2.6% for the case of domestic emission pricing only, but shrinks by 18% for the case of additional carbon import tariffs. 16 The non-ferrous metals industry stands out for the differential impacts between REF and TRF: while it is barely affected by domestic emission pricing only (REF) – its output declines by less than 1% – the imposition of tariffs leads to a dramatic output loss of more than 40%. The MRIO analysis of Section 2 provides the reasoning behind this initially surprising result as the Swiss non-ferrous metals industry exhibits the most disadvantageous characteristics. Firstly, almost 90% of the embodied carbon stems from imported sources (Figure 2), which gets additionally priced under TRF. Secondly, almost 90% of the output is supplied to the export market (Figure 4), where the carbon import tariffs constitute an additional cost-disadvantage compared to unregulated competitors. Among Swiss EITE industries the iron and steel (i_s), non-metallic minerals (nmm), as well as paper, pulp and print (ppp)
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Crack Microstructure During the Carbonization of Carbon Fibre Reinforced Plastics to Carbon/Carbon Composites

Crack Microstructure During the Carbonization of Carbon Fibre Reinforced Plastics to Carbon/Carbon Composites

Institute of Statics and Dynamics in Aerospace Structures, University of Stuttgart, Pfaffenwaldring 27, D- 70550 Stuttgart SUMMARY: The major process for manufacturing carbon/carbon composites is the carboni- zation of carbon fibre reinforced plastics (CFRP). In this process, the shrinkage of the matrix is hindered by the fibres and leads to a high amount of cracks resulting in a microscopic open porosity. To control this process, it is necessary to gain knowledge about its essential parame- ters, in which the crack microstructure plays an important role. Micrographs (SEM) revealed that the cracks can be distinguished in three different types: fibre-matrix debonding, segmenta- tion cracks and micro-delaminations. Fibre-matrix bonding determines which crack type domi- nates the structure of the final carbon/carbon composite. The evolution of the cracks during pyrolysis (temperature, sequence and importance of the crack types) was investigated by means of acoustic emission and microscopy in combination with a heating stage. By comparing these results with those of thermogravimetric analysis and dilatometer experiments, the devel- opment of the cracks can be explained.
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Targeted carbon tariffs: Carbon leakage and welfare effects

Targeted carbon tariffs: Carbon leakage and welfare effects

more details in the numerical model and, second, by also allowing for flexible carbon tariffs in response to low-carbon choices of electricity input. Our results are more promising with respect to carbon tariffs than previous findings. Firm-targeted tariffs can deliver much stronger leakage reduction and higher global efficiency gains than region- specific tariffs. In particular, because the exporters are able to reduce their carbon tariffs by adjusting to the implicit carbon taxation of the system, both their competitiveness and the overall welfare of their economies will be less adversely affected than with region-specific tariff regimes. This beneficial distributional impact could facilitate a higher degree of legitimacy and legality. We discuss possible practical designs of targeted carbon tariffs in Section 2, then model these systems analytically in Section 3 and within a computable framework in Section 4. The numerical results are discussed in Section 5, and Section 6 concludes.
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Financing Low-Carbon Transitions through Carbon Pricing and Green Bonds

Financing Low-Carbon Transitions through Carbon Pricing and Green Bonds

4 Conclusion In the Paris Agreement, all countries committed to transitioning towards low-carbon, climate- resilient economies. Several policy instruments have been proposed to finance this transition, including green bonds and carbon pricing. Often these instruments are perceived as alternative choices, but this paper finds there are important gains from deploying them jointly, provided countries have sufficient fiscal space. Debt levels are rising in many low-income countries (Essl et al. 2019), and in such circumstances it is preferable for climate policy to be financed by taxation or budget reallocation instead of deficit spending (Forni et al. 2019). However, for advanced econo- mies, Blanchard (2019) observes that sovereign debt is, in contrast to corporate debt, not rising that much, so there may be space for pursuing climate policies by green bonds and carbon pricing. Carbon pricing improves the performance of green bonds, which in turn improve inter-genera- tional equity, political feasibility, and help address multiple market failures. Yet, not all carbon pricing is the same: the synergies with green bonds are greater for carbon taxation than for emissions trading.
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Optimal decisions of countries with carbon tax and carbon tariff

Optimal decisions of countries with carbon tax and carbon tariff

Because of the financial crisis erupted in 2008, countries seek ways to shift the crisis, of which slight trade protectionism mitigates to some extent the economic depression. Tax policy, especially tariff on importers, has been an effective and reasonable way of trade protection. Currently, carbon tax has been a mainly used measure in developed countries due to its simplicity and capability to indicate carbon price immediately (Avi-Yonah & Uhlmann, 2009). Developed countries ask for extending emission-reduction regulations to the whole world, especially to developing countries. Specifically, developed countries with low-emission level declare to implement carbon tariff on imported products from the high-emission countries, which forced developing countries to seek for ways to mitigate the negative effects on international trade.
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Comparing organisms on the level of metabolism

Comparing organisms on the level of metabolism

Fatty Acid Metabolism (KEGG pathway number 00071). As has already been re- ported above, both C. jeikeium and C. urealyticum are able to metabolize fatty acids as they belong to the lipophilic Corynebacteria (Tauch et al., 2005, 2008). That they are nevertheless not grouped together for this pathway is mainly due to the lack of a gene in C. urealyticum coding for a 3-hydroxyacyl-CoA dehydrogenase catalyzing reac- tions R01975, R04737, R04739, R04741, R04743, R04745, and R04748 (all EC 1.1.1.35). It has not been reported in the literature that C. urealyticum lacks this function, so a sequence-based homology search was conducted using the corresponding gene from the close relative C. jeikeium, named jk0159. The best hit is a CDS called cu0178 which is already annotated with the very same function, suggesting that this function is present in C. urealyticum. Searching the KEGG database for this gene reveals that it actually is present in the KEGG annotation, but no EC number has been assigned. This might be the reason that this enzyme is not mapped to the respective reaction in the KEGG pathway. Meanwhile the KEGG database has been updated, and as has been predicted here, in the current version this gene is annotated with the respective function. This example again underlines the capability of the developed comparative approach to assist in improving existing annotation.
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In situ Metabolism and Biogeography of Phototrophic Consortia

In situ Metabolism and Biogeography of Phototrophic Consortia

Biomarkers of green sulfur bacteria, especially those of the brown-colored forms, have been used to detect anoxic states of ancient water bodies, like the Pliocene Eastern Mediterranean Sea (23, 34). Due to the high specific pigment content of green sulfur bacteria, their bacteriochlorophylls are abundant in illuminated chemoclines of freshwater lakes and sediments. Besides the carotenoids of green sulfur bacteria (18, 23, 34), BChl c, d and e, and oxidation products of their porphyrin ring systems, namely methyl iso-butyl maleimide and methyl n-propyl maleimide, have been employed as paleoindicators (16, 17). So far, however, the esterifying alcohols of BChl c, d and e, have not been used extensively in geochemical studies. These long-chain alcohols are not specific for green sulfur bacteria but can also originate from other organisms. While stable carbon isotope analyses indicate that all farnesane (derived from farnesol by catalytic hydrogenation with PtO 2 ) which is present in
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