Inhibitors of the heme oxygenase - carbon monoxide system: on the doorstep of the clinic?

The past decade has seen substantial developments in our understanding of the physiology, pathology, and pharmacology of heme oxygenases (HO), to the point that investigators in the field are beginning to contemplate therapies based on administration of HO agonists or HO inhibitors. A significant amount of our current knowledge is based on the judicious application of metalloporphyrin inhibitors of HO, despite their limitations of selectivity. Recently, imidazole-based compounds have been identified as potent and more selective HO inhibitors. This 'next generation' of HO inhibitors offers a number of desirable characteristics, including isozyme selectivity, negligible effects on HO protein expression, and physicochemical properties favourable for in vivo distribution. Some of the applications of HO inhibitors that have been suggested are treatment of hyperbilirubinemia, neurodegenerative disorders, certain types of cancer, and bacterial and fungal infections. In this review, we address various approaches to altering HO activity with a focus on the potential applications of second-generation inhibitors of HO.     

Effect of carbon source on the β-glucosidase system of the thermophilic fungus Humicola grisea

H. grisea produced an extracellular -glucosidase (EC 3.2.1.21) at high activity in media supplemented with carboxymethyl cellulose (CMC) or cellobiose. Cellobiose-induced -glucosidase was insensitive to glucose repression whereas that of CMC-supplemented cultures was partially repressed. Molecular sieving revealed three main active components (M_r 50, 128 and 240 kDa). Glucose competitively inhibited -glucosidase activities with K_i values of 0.9mM and 3.3mM (extracellular) and 10.2mM and 22.6mM (cytosolic), induced in the presence of CMC or cellobiose respectively.The authors are with the Departamento de Biologia, Faculdade de Filosofia. Ciências e Letras de Ribeirão Preto, Universidade de São Paulo-14040-901 Ribeirão Preto, São Paulo, Brasil;     

Does the age of fine root carbon indicate the age of fine roots in boreal forests?

To test the reliability of the radiocarbon method for determining root age, we analyzed fine roots (originating from the years 1985?C1993) from ingrowth cores with known maximum root age (1?C6?years old). For this purpose, three Scots pine (Pinus sylvestris L.) stands were selected from boreal forests in Finland. We analyzed root ¹⁴C age by the radiocarbon method and compared it with the above-mentioned known maximum fine root age. In general, ages determined by the two methods (root ¹⁴C age and ingrowth core root maximum age) were in agreement with each other for roots of small diameter (<0.5?mm). By contrast, in most of the samples of fine roots of larger diameter (1.5?C2?mm), the ¹⁴C age of root samples of 1987?C1989 exceeded the ingrowth core root maximum age by 1?C10?years. This shows that these roots had received a large amount of older stored carbon from unknown sources in addition to atmospheric CO₂ directly from photosynthesis. We conclude that the ¹⁴C signature of fine roots, especially those of larger diameter, may not always be indicative of root age, and that further studies are needed concerning the extent of possible root uptake of older carbon and its residence time in roots.     

Light modulation of the activity of carbon metabolism enzymes in the crassulacean Acid metabolism plant kalanchoë

When intact Kalanchoë plants are illuminated NADP-linked malic dehydrogenase and three enzymes of the reductive pentose phosphate pathway, ribulose-5-phosphate kinase, NADP-linked glyceraldehyde-3-phosphate dehydrogenase, and sedoheptulose-1,7-diphosphate phosphatase, are activated. In crude extracts these enzymes are activated by dithiothreitol treatment. Light or dithiothreitol treatment does not inactivate the oxidative pentose phosphate pathway enzyme glucose-6-phosphate dehydrogenase. Likewise, neither light, in vivo, nor dithiothreitol, in vitro, affects fructose-1,6-diphosphate phosphatase. Apparently the potential for modulation of enzyme activity by the reductively activated light effect mediator system exists in Crassulacean acid metabolism plants, but some enzymes which are light-dark-modulated in the pea plant are not in Kalanchoë.     

Why are estimates of the terrestrial carbon balance so different?

The carbon balance of the world's terrestrial ecosystems is uncertain. Both top‐down (atmospheric) and bottom‐up (forest inventory and land‐use change) approaches have been used to calculate the sign and magnitude of a net terrestrial flux. Different methods often include different processes, however, and comparisons can be misleading. Differences are not necessarily the result of uncertainties or errors, but often result from incomplete accounting inherent in some of the methods. Recent estimates are reviewed here. Overall, a northern mid‐latitude carbon sink of approximately 2 Pg C yr^?1 appears robust, although the mechanisms responsible are uncertain. Several lines of evidence point to environmentally enhanced rates of carbon accumulation. Other lines suggest that recovery from past disturbances is largely responsible for the sink. The tropics appear to be a small net source of carbon or nearly neutral, and the same uncertainties of mechanism exist. In addition, studies in the tropics do not permit an unequivocal choice between two alternatives: large emissions of carbon from deforestation offset by large sinks in undisturbed forests, or moderate emissions from land‐use change with essentially no change in the carbon balance in undisturbed forests. Resolution of these uncertainties is most likely to result from spatially detailed historical reconstructions of land‐use change and disturbance in selected northern mid‐latitude regions where such data are available, and from systematic monitoring of changes in the area of tropical forests with satellite data of high spatial resolution collected over the last decades and into the future.     

How much carbon is stored in the terrestrial ecosystems of the Chilean Patagonia?

We estimated the amount of carbon (C) stored in terrestrial ecosystems of the Chilean Patagonia and the proportion within protected areas. We used existing public databases that provide information on C stocks in biomass and soils. Data were analysed by ecosystem and forest type in the case of native forests. Our results show that some ecosystems have been more extensively studied both for their stocks in biomass and soils (e.g. forests) compared with others (e.g. shrublands). Forests and peatlands store the largest amount of C because of their large stocks per hectare and the large area they cover. The total amount of C stored per unit area varies from 261.7 to 432.8 Mg C ha⁻¹, depending on the published value used for soil organic C stocks in peatlands, highlighting the need to have more precise estimates of the C stored in this and other ecosystems. The mean stock in national parks (508 Mg C ha⁻¹) is almost twice the amount stored in undisturbed forests in the Amazon. State and private protected areas contain 58.9% and 2.1% of the C stock, respectively, playing a key role in protecting ecosystems in this once pristine area.     

Microbial contributions to the evolution of the ‘steady state’ carbon dioxide system

Various processes for the production of carbon dioxide by microorganisms are presented. It is postulated that a microniche developed in a reducing environment; a symbiotic relationship between alga-like organisms and bacterium-like organisms in the microniche governed the production of carbon dioxide resulting in the establishment of the steady state carbon dioxide system in the sea.     

Historical and projected carbon balance of mature black spruce ecosystems across North America: the role of carbon–nitrogen interactions

The role of carbon (C) and nitrogen (N) interactions on sequestration of atmospheric CO₂ in black spruce ecosystems across North America was evaluated with the Terrestrial Ecosystem Model (TEM) by applying parameterizations of the model in which C–N dynamics were either coupled or uncoupled. First, the performance of the parameterizations, which were developed for the dynamics of black spruce ecosystems at the Bonanza Creek Long-Term Ecological Research site in Alaska, were evaluated by simulating C dynamics at eddy correlation tower sites in the Boreal Ecosystem Atmosphere Study (BOREAS) for black spruce ecosystems in the northern study area (northern site) and the southern study area (southern site) with local climate data. We compared simulated monthly growing season (May to September) estimates of gross primary production (GPP), total ecosystem respiration (RESP), and net ecosystem production (NEP) from 1994 to 1997 to available field-based estimates at both sites. At the northern site, monthly growing season estimates of GPP and RESP for the coupled and uncoupled simulations were highly correlated with the field-based estimates (coupled: R ²= 0.77, 0.88 for GPP and RESP; uncoupled: R ² = 0.67, 0.92 for GPP and RESP). Although the simulated seasonal pattern of NEP generally matched the field-based data, the correlations between field-based and simulated monthly growing season NEP were lower (R ² = 0.40, 0.00 for coupled and uncoupled simulations, respectively) in comparison to the correlations between field-based and simulated GPP and RESP. The annual NEP simulated by the coupled parameterization fell within the uncertainty of field-based estimates in two of three years. On the other hand, annual NEP simulated by the uncoupled parameterization only fell within the field-based uncertainty in one of three years. At the southern site, simulated NEP generally matched field-based NEP estimates, and the correlation between monthly growing season field-based and simulated NEP (R ² = 0.36, 0.20 for coupled and uncoupled simulations, respectively) was similar to the correlations at the northern site. To evaluate the role of N dynamics in C balance of black spruce ecosystems across North America, we simulated historical and projected C dynamics from 1900 to 2100 with a global-based climatology at 0.5° resolution (latitude × longitude) with both the coupled and uncoupled parameterizations of TEM. From analyses at the northern site, several consistent patterns emerge. There was greater inter-annual variability in net primary production (NPP) simulated by the uncoupled parameterization as compared to the coupled parameterization, which led to substantial differences in inter-annual variability in NEP between the parameterizations. The divergence between NPP and heterotrophic respiration was greater in the uncoupled simulation, resulting in more C sequestration during the projected period. These responses were the result of fundamentally different responses of the coupled and uncoupled parameterizations to changes in CO₂ and climate.     

Lipogenesis in the brain of suckling rats. Studies on the mechanism of mitochondrial–cytosolic carbon transfer

1. Studies on the incorporation of [3-¹⁴C]pyruvate and d-3-hydroxy[3-¹⁴C]butyrate into the brain lipid fraction by brain homogenates of the suckling (7-day-old) rat have been carried out. 2. Whereas approximately twice as much CO₂ was evolved from pyruvate compared with 3-hydroxybutyrate metabolism, similar amounts of the radioactivity of these two precursors were incorporated into the lipid fraction. Furthermore, in both cases the incorporation into lipid was almost tripled when glucose (10mm) or NADPH (2.5mm) was added to the incubation media. 3. If 5mm-(—)-hydroxycitrate, an ATP–citrate lyase inhibitor, was added to the incubation the incorporation of carbon from pyruvate was inhibited to 39% of the control and from 3-hydroxybutyrate to 73% of the control, whereas CO₂ production from both precursors was not affected. 4. The incorporation from pyruvate or 3-hydroxybutyrate into lipids was not affected by the presence of 10mm-glutamate in the medium (to encourage N-acetylaspartate production). However, incorporation from pyruvate was inhibited by 21% in the presence of 5mm-amino-oxyacetate (a transaminase inhibitor) and by 83% in the presence of both hydroxycitrate (5mm) and amino-oxyacetate. 5. Incorporation from 3-hydroxybutyrate into brain lipids was inhibited by 20% by amino-oxyacetate alone, but by 55% in the presence of both hydroxycitrate and amino-oxyacetate. 6. It is concluded that the mechanism of carbon transfer from pyruvate into lipids across the mitochondrial membrane in the suckling rat brain is mainly via citrate and N-acetylaspartate. 3-Hydroxybutyrate, in addition to using these routes, may also be incorporated via acetoacetate formation and transport to the cytosol.     

Distribution of soil phytolith-occluded carbon in the Chinese Loess Plateau and its implications for silica–carbon cycles

Background and aims

Plants absorb and carry soluble silica from soils and then deposit SiO₂?·?nH₂O within themselves producing amorphous silica particles known as phytoliths. Trace amount of organic carbon is occluded during phytolith formation referred to as phytolith-occluded carbon (PhytOC). This carbon fraction has been recognized as an important way of carbon biosequestration. Previous studies have investigated the PhytOC contents of many crop plants and their contribution to global carbon sink. However, the PhytOC in soil is less focused. In this study, we investigated the distribution of soil PhytOC in the Chinese Loess Plateau (CLP).

Methods

Twenty-six soil profiles were collected in the Chinese Loess Plateau. A wet oxidation method was used for phytolith extraction. Occluded carbon was determined by element analyzer.

Results

Our results showed that the soil PhytOC density (SPCD) ranged from 0.757 to 23.110 g/m² among different soil profiles. The SPCD of profiles in the Southern CLP was generally higher than that in the Northern CLP. It was estimated that 5.35 Mt of PhytOC was stored in the upper soil of the CLP. We also estimated the annual phytolith flux into the Yellow River from the CLP by soil erosion and about 2.5 Mt of phytoliths eroded and transported into rivers per year.

Conclusions

Our study indicated that PhytOC was one of the potential biosequestration way and phytoliths had an important influence on biogeochemical cycle of silica. Our results suggested that the soil PhytOC was mainly influenced by different plant communities.     

Structural and functional reconstruction in situ of the [CuSMoO2] active site of carbon monoxide dehydrogenase from the carbon monoxide oxidizing eubacterium Oligotropha carboxidovorans

Carbon monoxide dehydrogenase from the bacterium Oligotropha carboxidovorans catalyzes the oxidation of CO to CO₂ at a unique [CuSMoO₂] cluster. In the bacteria the cluster is assembled post-translational. The integration of S, and particularly of Cu, is rate limiting in vivo, which leads to CO dehydrogenase preparations containing the mature and fully functional enzyme along with forms of the enzyme deficient in one or both of these elements. The active sites of mature and immature forms of CO dehydrogenase were converted into a [MoO₃] centre by treatment with potassium cyanide. We have established a method, which rescues 50% of the CO dehydrogenase activity by in vitro reconstitution of the active site through the supply of sulphide first and subsequently of Cu(I) under reducing conditions. Immature forms of CO dehydrogenase isolated from the bacterium, which were deficient in S and/or Cu at the active site, were similarly activated. X-ray crystallography and electron paramagnetic resonance spectroscopy indicated that the [CuSMoO₂] cluster was properly reconstructed. However, reconstituted CO dehydrogenase contains mature along with immature forms. The chemical reactions of the reconstitution of CO dehydrogenase are summarized in a model, which assumes resulphuration of the Mo-ion at both equatorial positions at a 1:1 molar ratio. One equatorial Mo–S group reacts with Cu(I) in a productive fashion yielding a mature, functional [CuSMoO₂] cluster. The other Mo–S group reacts with Cu(I), then Cu₂S is released and an oxo group is introduced from water, yielding an inactive [MoO₃] centre.     

Does the threshold of transcutaneous partial pressure of carbon dioxide represent the respiratory compensation point or anaerobic threshold?

On reaching the respiratory compensation point (RCP) during rapidly increasing incremental exercise, the ratio of minute ventilation (V_E) to CO₂ output (VCO₂) rises, which coincides with changes of arterial partial pressure of carbon dioxide (P _aCO₂). Since P _aCO₂ changes can be monitored by transcutaneous partial pressure of carbon dioxide (PCO_2,tc) RCP may be estimated by PCO_2,tc measurement. Few available studies, however, have dealt with comparisons between PCO_2,tc threshold (T _AT) and lactic, ventilatory or gas exchange threshold (V _AT), and the results have been conflicting. This study was designed to examine whether this threshold represents RCP rather than V _AT. A group of 11 male athletes performed incremental excercise (25 W · min^–1) on a cycle ergometer. The PCO_2,tc at (44°C) was continuously measured. Gas exchange was computed breath-by-breath, and hyperaemized capillary blood for lactate concentration ([la^–]_b) and P _aCO₂ measurements was sampled each 2 min. The T _AT was determined at the deflection point of PCO_2,tc curve where PCO_2,tc began to decrease continuously. The V _AT and RCP were evaluated with VCO₂ compared with oxygen uptake (VO₂) and V_E compared with the VCO₂ method, respectively. The PCO_2,tc correlated with P _aCO₂ and end-tidal PCO₂. At T _AT, power output [P, 294 (SD 40) W], VO₂ [4.18 (SD 0.57)l · min^–1] and [la^–] [4.40 (SD 0.64) mmol · l^–1] were significantly higher than those at V _AT[P 242 (SD 26) W, VO₂ 3.56 (SD 0.53) l · min^–1 and [la^–]_b 3.52 (SD 0.75), mmol · l^–1 respectively], but close to those at RCP [P 289 (SD 37) W; VO₂ 3.97 (SD 0.43) l · min^– and [la^–]_b 4.19 (SD 0.62) mmol · l^–1, respectively]. Accordingly, linear correlation and regression analyses showed that P, VO₂ and [la^–]_b at T _AT were closer to those at RCP than at V _AT. In conclusion, the T _AT reflected the RCP rather than V _AT during rapidly increasing incremental exercise.     

Whales in the carbon cycle: can recovery remove carbon dioxide?

The great whales (baleen and sperm whales), through their massive size and wide distribution, influence ecosystem and carbon dynamics. Whales directly store carbon in their biomass and contribute to carbon export through sinking carcasses. Whale excreta may stimulate phytoplankton growth and capture atmospheric CO₂; such indirect pathways represent the greatest potential for whale-carbon sequestration but are poorly understood. We quantify the carbon values of whales while recognizing the numerous ecosystem, cultural, and moral motivations to protect them. We also propose a framework to quantify the economic value of whale carbon as populations change over time. Finally, we suggest research to address key unknowns (e.g., bioavailability of whale-derived nutrients to phytoplankton, species- and region-specific variability in whale carbon contributions).     

Stabilization of carbon in mineral soils from mangroves of the Sinú river delta,Colombia

Mangrove forests of the Sinú river delta in Cispatá bay, Colombia, show large differences in soil carbon storage between fringe (oceanic) and basin (estuarine) mangroves. We were interested in testing whether these differences in soil carbon are associated with sediment transport processes or whether most of the carbon is produced in situ within the mangrove system. Given past sedimentation dynamics of the Sinú river, we hypothesized that a large portion of soil carbon in basin mangroves is due to sedimentation. We determined total organic carbon content (TOC) as 660.93 ± 259.18 MgC ha^?1 for basin soils up to a sampling depth of 1 m, and as 259 ± 42.61 MgC ha^?1 for fringe soils up to 80 cm depth (maximum soil depth for fringe soils). Using analyses of mineralogy (Al- and Fe-oxides, clay minerals) as well as isotopic analyses of carbon (δ¹³C), the origin of the sediments and their carbon was determined. We found that basin soils in Cispatá bay show similar mineralogical composition than those of fluvial sediments, but the carbon concentration of river sediments was close to zero. Given the large capacity of the Fe and Al oxides in clay minerals to store dissolved carbon, and that the isotopic composition of the carbon is mostly of plant origin, we concluded contrary to our initial hypothesis that the carbon stored in basin mangrove soils are produced in situ. The deposited fluvial sediments do play an important role for carbon storage, but mostly in providing binding surfaces for the stabilization of organic carbon.     

Quantitative classification and carbon density of the forest vegetation in Lüliang Mountains of China

Forests play a major role in global carbon (C) cycle, and the carbon density (CD) could reflect its ecological function of C sequestration. Study on the CD of different forest types on a community scale is crucial to characterize in depth the capacity of forest C sequestration. In this study, based on the forest inventory data of 168 field plots in the study area (E 111°30′–113°50′, N 37°30′–39°40′), the forest vegetation was classified by using quantitative method (TWINSPAN); the living biomass of trees was estimated using the volume-derived method; the CD of different forest types was estimated from the biomass of their tree species; and the effects of biotic and abiotic factors on CD were studied using a multiple linear regression analysis. The results show that the forest vegetation in this region could be classified into 9 forest formations. The average CD of the 9 forest formations was 32.09 Mg ha⁻¹ in 2000 and 33.86 Mg ha⁻¹ in 2005. Form. Picea meyeri had the highest CD (56.48 Mg ha⁻¹), and Form. Quercus liaotungensis + Acer mono had the lowest CD (16.14 Mg ha⁻¹). Pre-mature forests and mature forests were very important stages in C sequestration among four age classes in these formations. Forest densities, average age of forest stand, and elevation had positive relationships with forest CD, while slope location had negative correlation with forest CD.     

Influence of sulfate enrichment on the carbon dioxide and phosphate fluxes across the sediment–water interface

Fluxes of CO2 and o-P across the sediment-water interfacewere measured adding different amounts of sulfatein order to quantify the influence in these processes againsta control, and using chloramphenicol as an inhibitor ofbacterial activity. These experiments were performed underoxic and anoxic conditions. Results show that the additionof sulfate stimulated the fluxes of CO2 and o-P, whilethe use of chloramphenicol decreased these fluxes. Theratio of o-P release to Org-C release ranged from 1 to 5 underoxic conditions and from 18 to 42 under anoxicconditions.     

The production of γ-linolenic acid by selected members of the Dikaryomycota grown on different carbon sources

In this study, seven fungal strains, representing different phylogenetic groups within the Dikaryomycota, were tested for the presence of -linolenic acid [18:3(6)], when grown in synthetic liquid media devoid of fatty acids, on a series of 40 different carbon sources. The fungal strains represented the species Dipodascopsis uninucleata, Eurotium rubrum, Galactomyces geotrichum, Neurospora crassa, Saccharomyces cerevisiae, Spongipellis unicolor and Talaromyces flavus. Cultures were periodically harvested during growth and the fatty acids in the total lipids analysed as methyl esters, using gas chromatography and mass spectrometry. It was found that 18:3(6) is present in E. rubrum CBS 350.65, S. unicolor CBS 117.16 and in T. flavus CBS 310.38NT, when these strains were grown on certain carbon sources. No correlation between the growth phase of the organism and the presence of 18:3(6) could be detected. In order to confirm the production of 18:3(6), the lipid metabolism of two unrelated dikaryomycotan fungi (S. unicolor CBS 117.16 and E. rubrum CBS 350.65) grown on two different carbon sources each, was examined. Cultures of E. rubrum CBS 350.65 were grown on glucose and sorbose and cultures of S. unicolor CBS 117.16 on glucose and sucrose in synthetic liquid media with a C:N ratio of 50:1 (w/w). The total lipids of these cultures were fractionated and the fatty acids in the fractions analysed as methyl esters, using gas chromatography and mass spectrometry. The lipid metabolism of both E. rubrum CBS 350.65 and S. unicolor CBS 117.16 differed on the two carbon sources used. The ab initio production of 18:3(6) by E. rubrum CBS 350.65 in synthetic liquid media was confirmed. In contrast, the ab initio production of 18:3(6) by S. unicolor CBS 117.16 in synthetic liquid media could not be confirmed.