Transport,anoxia and end-product accumulation control carbon dioxide and methane production and release in peat soils

Anaerobic respiration and methanogenesis have been found to slow-down in water saturated peat soils with accumulation of metabolic end-products, i.e. dissolved inorganic carbon (DIC) and methane (CH₄), due to a lack of solute and gas transport. So far it is not well understood how solute and gas transport may control this effect. We conducted a column experiment with homogenized ombrotrophic peat over a period of 300 days at 20 °C. We specifically evaluated the effects of diffusive flux as control, downward advective water flux, intensified ebullition by conduit gas transport and diffusive oxygen supply on controlling anaerobic decomposition rates and carbon (C) turnover. To simulate advective flux, water and solutes were recirculated downward through the column after stripping of dissolved gases. We analyzed DIC and CH₄ concentrations, production rates and fluxes, gas filled porosity, oxygen profiles (O₂) and microbial C biomass over time. DIC residence time thereby served as proxy to characterize transport. A slowdown of anaerobic respiration and methanogenesis evolved with the accumulation of the end-products DIC and CH₄ and set in after 150 days. This slow-down was accompanied by a decrease in the distribution of microbial biomass C with depths. Anaerobic DIC and CH₄ production rates were fastest close to the water table and sharply slowed with depth. Accumulation of DIC and CH₄ in the homogeneous peat material throughout the column decreased decomposition constants from about 10^?5 near the surface to 10^?9 year^?1 deeper in the profile. Advective water transport extended the zone of active methanogenesis compared to a diffusive system; experimental enhancement of ebullition had little or no effect as well as strictly anoxic conditions. DIC residence time was negatively correlated to anaerobic respiration suggesting this parameter to be a predictor of anaerobic peat decomposition in peatlands. Overall, this study suggests that burial of peat and accumulation of metabolic end-products effectively slows decomposition and that this effect needs to be considered to explain peat accumulation and the response of peat mineralization rates to changes in environmental conditions.     

Carbon flux from decomposing wood and its dependency on temperature,wood N2 fixation rate,moisture and fungal composition in a Norway spruce forest

Globally 40–70 Pg of carbon (C) are stored in coarse woody debris on the forest floor. Climate change may reduce the function of this stock as a C sink in the future due to increasing temperature. However, current knowledge on the drivers of wood decomposition is inadequate for detailed predictions. To define the factors that control wood respiration rate of Norway spruce and to produce a model that adequately describes the decomposition process of this species as a function of time, we used an unprecedentedly diverse analytical approach, which included measurements of respiration, fungal community sequencing, N₂ fixation rate, nifH copy number, ¹⁴C‐dating as well as N%, δ¹³C and C% values of wood. Our results suggest that climate change will accelerate C flux from deadwood in boreal conditions, due to the observed strong temperature dependency of deadwood respiration. At the research site, the annual C flux from deadwood would increase by 27% from the current 117 g C/kg wood with the projected climate warming (RCP4.5). The second most important control on respiration rate was the stage of wood decomposition; at early stages of decomposition low nitrogen content and low wood moisture limited fungal activity while reduced wood resource quality decreased the respiration rate at the final stages of decomposition. Wood decomposition process was best described by a Sigmoidal model, where after 116 years of wood decomposition mass loss of 95% was reached. Our results on deadwood decomposition are important for C budget calculations in ecosystem and climate change models. We observed for the first time that the temperature dependency of N₂ fixation, which has a major role at providing N for wood‐inhabiting fungi, was not constant but varied between wood density classes due to source supply and wood quality. This has significant consequences on projecting N₂ fixation rates for deadwood in changing climate.     

Studies in the stability theory of complex homogeneous kinetics

Summary The results of an investigation of the formal stability behavior of equivalent classes of asymptotically stable kinetic equations (generated by well-posed stability constraint specifications), general enough so as to include non-polynomial kinetics, are presented in detail. The qualitative properties of such equivalent classes — especially with respect to physical admissibility and fluctuation regression, including bounds on generalized relaxation times—are deduced without resorting to an explicit solution. The immediate motivation for the study arose from the need for a comprehensive theory when steric interactions in biosynthetic networks are explicitly taken into account. It is known that such interactions result in non-polynomial kinetics.     

Analysis of receptor binding displacement curves by a nonhomologous ligand, on the basis of an equivalent competition principle

An exact method for the analysis of receptor-ligand binding data when labeled bound ligand is displaced by a nonhomologous ligand with a different dissociation constant is described. The present method, which is based on an equivalent competition principle for the homologous and the nonhomologous ligand, converts displacement curves into a linear form and is also applicable to situations in which free concentrations of ligand are significantly smaller than the added concentrations as a result of ligand binding. It is shown that the dissociation constant of the nonhomologous ligand is given directly by the concentration of this nonhomologous ligand added and the free concentration of unlabeled homologous ligand required to give the same level of displacement of labeled bound ligand. On the basis of these displacement characteristics, all binding parameters for receptor interaction of the nonhomologous ligand can be obtained and expressed, for example, in a Scatchard plot. The present method, which is referred to as the equivalent competition method, is also evaluated in this study with respect to the effects of nonspecific ligand binding and the presence of multiple receptor classes.     

Plant identity influences decomposition through more than one mechanism

Plant litter decomposition is a critical ecosystem process representing a major pathway for carbon flux, but little is known about how it is affected by changes in plant composition and diversity. Single plant functional groups (graminoids, legumes, non-leguminous forbs) were removed from a grassland in northern Canada to examine the impacts of functional group identity on decomposition. Removals were conducted within two different environmental contexts (fertilization and fungicide application) to examine the context-dependency of these identity effects. We examined two different mechanisms by which the loss of plant functional groups may impact decomposition: effects of the living plant community on the decomposition microenvironment, and changes in the species composition of the decomposing litter, as well as the interaction between these mechanisms. We show that the identity of the plant functional group removed affects decomposition through both mechanisms. Removal of both graminoids and forbs slowed decomposition through changes in the decomposition microenvironment. We found non-additive effects of litter mixing, with both the direction and identity of the functional group responsible depending on year; in 2004 graminoids positively influenced decomposition whereas in 2006 forbs negatively influenced decomposition rate. Although these two mechanisms act independently, their effects may be additive if both mechanisms are considered simultaneously. It is essential to understand the variety of mechanisms through which even a single ecosystem property is affected if we are to predict the future consequences of biodiversity loss.     

ACoM: A classification method for elementary flux modes based on motif finding

Elementary flux mode analysis is a powerful tool for the theoretical study of metabolic networks. However, when the networks are complex, the determination of elementary flux modes leads to combinatorial explosion of their number which prevents from drawing simple conclusions from their analysis. To deal with this problem we have developed a method based on the Agglomeration of Common Motifs (ACoM) for classifying elementary flux modes. We applied this algorithm to describe the decomposition into elementary flux modes of the central carbon metabolism in Bacillus subtilis and of the yeast mitochondrial energy metabolism. ACoM helps to give biological meaning to the different elementary flux modes and to the relatedness between reactions. ACoM, which can be viewed as a bi-clustering method, can be of general use for sets of vectors with values 0, +1 or −1.     

Leaf Decomposition in a Dry Season Irrigation Experiment in Eastern Amazonian Forest Regrowth

Leaf-litter decomposition is a major component of carbon and nutrient dynamics in tropical forest ecosystems, and moisture availability is widely considered to be a major influence on decomposition rates. Here, we report the results of a study of leaf-litter decomposition of five tree species in response to dry-season irrigation in a tropical forest regrowth stand in the Brazilian Amazon; three experiments differing in the timing of installation and duration allowed for an improved resolution of irrigation effects on decomposition. We hypothesized that decomposition rates would be faster under higher moisture availability in the wet season and during dry-season irrigation periods in the treatment plots, and that decomposition rates would be faster for species with higher quality leaves, independent of treatment. The rates of decomposition ( k ) were up to 2.4 times higher in irrigated plots than in control plots. The highest k values were shown by Annona paludosa (0.97 to 1.26/yr) while Ocotea guianensis (0.73 to 0.85/yr) had the lowest values; intermediate rates were found for Lacistema pubescens (0.91 to 1.02/yr) and Vismia guianensis (0.91 to 1.08/yr). These four tree species differed significantly in leaf-litter quality parameters (nitrogen, phosphorus, lignin, and cellulose concentrations, as well as lignin:nitrogen and carbon:nitrogen ratios), but differences in decomposition rates among tree species were not strictly correlated with leaf-litter quality. Overall, our results show that dry-season moisture deficits limit decomposition in Amazonian forest regrowth.     

Auxin transport in roots

Summary The movement of IAA has been investigated in roots of dark-grown seedlings of Zea mays using IAA-I-¹⁴C.With 6-mm segments excised 1 mm below the apex of the root it has been shown that: (a) There is a strictly acropetal flux of IAA through the tissues, the amount of IAA found in an apical receiving block increasing almost linearly with increasing transport period up to about 6–7 hours, but thereafter declining for at least a further 18 hours. The onset of this decline appears to be dependent upon the concentration of IAA in the donor block. (b) The amount of IAA recovered in the apical receiving block increases with increasing concentration of IAA in the donor block over the range from 0.1–10 M, with transport periods of both 4 and 9 hours. (c) The radioactivity in the receiving block is confined to the IAA molecule. (d) The orientation of the segment with respect to gravity did not significantly affect the acropetal polar flux of IAA in the tissue.With non-decapitated 7-mm root apices it has been found that the presence of the apex has no effect on the strictly acropetal flux of IAA in the tissues, but that it entirely prevented the emergence of IAA into an apical receiving block.     

A role for the Saccharomyces cerevisiae RENT complex protein Net1 in HMR silencing

Silencing in the yeast Saccharomyces cerevisiae is known in three classes of loci: in the silent mating-type loci HML and HMR, in subtelomeric regions, and in the highly repetitive rDNA locus, which resides in the nucleolus. rDNA silencing differs markedly from the other two classes of silencing in that it requires a DNA-associated protein complex termed RENT. The Net1 protein, a central component of RENT, is required for nucleolar integrity and the control of exit from mitosis. Another RENT component is the NAD(+)-dependent histone deacetylase Sir2, which is the only silencing factor known to be shared among the three classes of silencing. Here, we investigated the role of Net1 in HMR silencing. The mutation net1-1, as well as NET1 expression from a 2micro-plasmid, restored repression at silencing-defective HMR loci. Both effects were strictly dependent on the Sir proteins. We found overexpressed Net1 protein to be directly associated with the HMR-E silencer, suggesting that Net1 could interact with silencer binding proteins and recruit other silencing factors to the silencer. In agreement with this, Net1 provided ORC-dependent, Sir1-independent silencing when artificially tethered to the silencer. In contrast, our data suggested that net1-1 acted indirectly in HMR silencing by releasing Sir2 from the nucleolus, thus shifting the internal competition for Sir2 from the silenced loci toward HMR.     

Crystal structure of a theta-class glutathione transferase.

Glutathione S-transferases (GSTs) are a family of enzymes involved in the cellular detoxification of xenotoxins. Cytosolic GSTs have been grouped into four evolutionary classes for which there are representative crystal structures of three of them. Here we report the first crystal structure of a theta-class GST. So far, all available GST crystal structures suggest that a strictly conserved tyrosine near the N-terminus plays a critical role in the reaction mechanism and such a role has been convincingly demonstrated by site-directed mutagenesis. Surprisingly, the equivalent residue in the theta-class structure is not in the active site, but its role appears to have been replaced by either a nearby serine or by another tyrosine residue located in the C-terminal domain of the enzyme.     

On the robustness of update schedules in Boolean networks

Deterministic Boolean networks have been used as models of gene regulation and other biological networks. One key element in these models is the update schedule, which indicates the order in which states are to be updated. We study the robustness of the dynamical behavior of a Boolean network with respect to different update schedules (synchronous, block-sequential, sequential), which can provide modelers with a better understanding of the consequences of changes in this aspect of the model. For a given Boolean network, we define equivalence classes of update schedules with the same dynamical behavior, introducing a labeled graph which helps to understand the dependence of the dynamics with respect to the update, and to identify interactions whose timing may be crucial for the presence of a particular attractor of the system. Several other results on the robustness of update schedules and of dynamical cycles with respect to update schedules are presented. Finally, we prove that our equivalence classes generalize those found in sequential dynamical systems.     

Specificity and non-specificity of synaptic connections within mammalian visual cortex

It is clear from reviewing the findings of our own studies and those of others that the cerebral cortex has combined two very different strategies of organisation. Firstly it has a strictly defined genetically determined substrate of specific neurons classes, specific rules for which kinds of cells interconnect, a laminar architecture where efferent and afferent relays and interlaminar links are predetermined. But, as well, a second strategy allows great developmental lability in the precise spatial patterns of intralaminar circuits of the excitatory neurons and in the actual weights of excitatory and inhibitory synapses that are contributed to each neuron. This second strategy presumably allows the cortex to be tailor-made to the early experience of each individual and, as well, allow for lability of responses to different conditions of stimulation and adjustment of the system to compensate to some degree for injuries affecting afferents and circuitry in the adult system.     

Do fatal infectious diseases eradicate host species?

In simple SI epidemic and endemic models, three classes of incidence functions are identified for their potential to be associated with host extinction: weakly upper density-dependent incidences are never associated with host extinction. Power incidences that depend on the number of susceptibles and infectives by powers strictly between 0 and 1 are associated with initial-constellation-dependent host extinction for all parameter values. Homogeneous incidences, of which frequency-dependent incidence is a very particular case, and power incidences are associated with global host extinction for certain parameter constellations and with host survival for others. Laboratory infection experiments with salamander larvae are equally well fitted by power incidences and certain upper density-dependent incidences such as the negative binomial incidence and do not rule out homogeneous incidences such as an asymmetric frequency-dependent incidence either.

     

Phenomenological definition of response times with application to metabolic reactions

The metabolic response time, i.e. the delay the system introduces in the response to an input flux, is considered. A novel phenomenological definition is presented, which is valid for any kind of behavior, including transitory or permanent oscillatory responses. In order to calculate the response time of single-input systems, output fluxes have to be deconvoluted with the input flux. The bases for this are established. The resulting function (unit impulse response in time-invariant linear systems) is transformed by subtracting its final state, taking the absolute value and normalizing by the resulting area, so that a norm can be applied that weights the response at every time. This response time can also be interpreted as an average. It coincides with the transition (characteristic) time of an output flux, provided that the input is performed instantaneously (step function). A strictly non-negative response function is needed for the response time to be interpreted as a mass balance. A simple example is used to study the deviation otherwise. The method is advantageous in that it provides clues on the phenomenological behavior of biochemical systems. For example, deconvolution reveals the intrinsic oscillation-generating mechanism of an allosteric enzyme, which becomes hidden when the input flux increases in a slow way. This is illustrated by means of a model.     

Cytochrome c involved in the reductive decomposition of organic mercurials. Purification of cytochrome c-I from mercury-resistant Pseudomonas and reactivity of cytochromes c from various kinds of bacteria

Cytochrome c-I which was involved in the decomposition of organic mercurials as an electron carrier was purified from the cell-free extract of the mercury-resistant strain, Pseudomonas K62, by means of (NH₄)₂SO₄ precipitation and column chromatography on Sephadex G-150, DEAE-Sephadex and Sephadex G-75. The cytochrome was crystallized in a needle-like form. It showed absorption maxima at 550, 521, and 416.5 nm in the reduced form, and the pyridine ferrohemochrome had absorption maxima at 549, 520, and 413 nm, suggesting it to be a c-type cytochrome.

Cytochromes c prepared from type cultures of bacteria belonging to the genera Aeromonas, Micrococcus, Bacillus, Corynebacterium, Staphylococcus, Aerobacter, and Pseudomonas were all inactive with respect to the decomposition of phenylmercuric acetate. However, cytochrome c prepared from Pseudomonas CF, which was isolated from the activated sludge acclimatized with HgCl₂ and phenylmercuric acetate, as well as the cytochrome c-I of Pseudomonas K62, were active in this respect.     

Rational design of 13C-labeling experiments for metabolic flux analysis in mammalian cells

ABSTRACT: BACKGROUND: 13C-Metabolic flux analysis (13C-MFA) is a standard technique to probe cellular metabolism and elucidate in vivo metabolic fluxes. 13C-Tracer selection is an important step in conducting 13C-MFA, however, current methods are restricted to trial-and-error approaches, which commonly focus on an arbitrary subset of the tracer design space. To systematically probe the complete tracer design space, especially for complex systems such as mammalian cells, there is a pressing need for new rational approaches to identify optimal tracers. RESULTS: Recently, we introduced a new framework for optimal 13C-tracer design based on elementary metabolite units (EMU) decomposition, in which a measured metabolite is decomposed into a linear combination of so-called EMU basis vectors. In this contribution, we applied the EMU method to a realistic network model of mammalian metabolism with lactate as the measured metabolite. The method was used to select optimal tracers for the two free fluxes in the system, the oxidative pentose phosphate pathway (oxPPP) flux and anaplerosis by pyruvate carboxylase (PC). Our approach was based on sensitivity analysis of EMU basis vector coefficients with respect to free fluxes. Through efficient grouping of coefficient sensitivities, simple tracer selection rules were derived for high-resolution quantification of the fluxes in the mammalian network model. The approach resulted in a significant reduction of the number of possible tracers and the feasible tracers were evaluated using numerical simulations. Two optimal, novel tracers were identified that have not been previously considered for 13C-MFA of mammalian cells, specifically [2,3,4,5,6-13C]glucose for elucidating oxPPP flux and [3,4-13C]glucose for elucidating PC flux. We demonstrate that 13C-glutamine tracers perform poorly in this system in comparison to the optimal glucose tracers. CONCLUSIONS: In this work, we have demonstrated that optimal tracer design does not need to be a pure simulation-based trial-and-error process; rather, rational insights into tracer design can be gained through the application of the EMU basis vector methodology. Using this approach, rational labeling rules can be established a priori to guide the selection of optimal 13C-tracers for high-resolution flux elucidation in complex metabolic network models.     

On the analysis of linear binding effects associated with curved Scatchard plots.

First the question is examined as to which binding data, especially if given as Scatchard plots, can be described in terms of a basic model mechanism. This referes to a linear lattice of equivalent binding sites (as for example located on a linear biopolymer) which can exert cooperative interaction between nearest neighbors. It is shown that the effect of overlapping of potential site (so-called "multiple-contact"binding), as may occur with larger ligands, will largely be compensated by a higher degree of cooperativity. Therefore, in practice such properties can scarcely be separated by means of oridnary binding experiments. A pronounced inflection point in the Scatchard plot turns out to be clearly indicating a more complex mechanism involving at least two rather antagonistic cooperative interactions which may, however, occur even between equivalent binding sites. Finally some consequences of different classes of bindings sites are considered. In particular a simple approach is introduced by which the binding to mutually exclusive classes of sites may be described. Such a model is of interest for multiple-mode binding of ionic ligands to oppositely charged polymers.     

Histone synthesis during infection of monkey kidney cells with Simian Virus 40.

The synthesis of histones during lytic infection of BSC-1 (African Green Monkey kidney) cells with SV40 has been investigated. The synthesis of all five classes of histones was stimulated, and all classes appeared to be stimulated to the same extent. The increase in rate of histone synthesis in response to SV40 infection was detectable several hours before SV40 DNA synthesis was measureable, and the rate of histone synthesis decreased at a time when SV40 DNA synthesis was occuring at a maximal or relatively high rate. In addition, the changes in rates of histone synthesis did not correlate well with the rates of host DNA synthesis during infection. Thus it appears that DNA synthesis and histone synthesis may not be strictly coupled in SV40 infected cells.     

Effect of salinity and plant species on CO2 flux and leaching of dissolved organic carbon during decomposition of plant residue

Mitigation of increased concentrations of CO₂ in the atmosphere by plants may be more efficient in saline systems with soils lower in organic matter than in other freshwater systems. In saline systems, decomposition rates may be lower and potential soil carbon storage higher than in fresh water systems. The effects of salinity, plant species and time on CO₂ surface flux and dissolved organic carbon (DOC) leached during irrigation were determined in the laboratory in microcosms containing sand amended with residues of two halophytes, Atriplex nummularia and Salicornia bigelovii, and one glycophyte, Triticum aestivum. Surface flux of CO₂ and DOC leached during decomposition were monitored for 133 days at 24 °C in microcosms containing different plant residue (5% w/w). Microcosms were irrigated every 14 days with distilled water or seawater adjusted to 10, 20, or 40 g L^-1 salts. CO₂ flux and DOC leached were significantly higher from microcosms amended with A. nummularia residue compared to S. bigelovii or T. aestivum at all salinities and decreased significantly over time for all plant species. Irrigating with water of high salinity, 40 g L^-1, compared to distilled water resulted in a decrease in CO₂ surface flux and DOC in leachate, but differences were not significant at all sampling dates. Results indicate that plant residue composition, as well as increased salinity, affect CO₂ surface flux and DOC in leachate during plant residue decomposition and may be an important consideration for C storage in saline systems.     

Equivalence of branched and unbranched Michaelian pathways concerning periodic signal transmission

Sinusoidal oscillation transmission through branched metabolic pathways is studied. Two systems are analyzed, which are composed of two convergent reaction branches and differ in the length of one of them. Linear kinetics is assumed first. Michaelis-Menten enzymes are then considered by using previous results that suggest their behavior with respect to propagation of oscillations is close to linearity around the mean input flux. As a result, there exist ways to modulate the activity of the enzymes so that propagation is equivalent for branched and specific unbranched pathways. Cells may have taken advantage of such a possibility in cases where oscillations have a biological role.