Mass transfer limitation of sulfate in methanogenic aggregates

The role of mass transfer limitation of sulfate as a factor governing the competition between sulfate reducing and methane producing bacteria in methanogenic aggregates was theoretically evaluated by the calculation of steady-state sulfate microprofiles using a reference set of parameters obtained from the literature. The shooting method was used as a numerical technique for solving the mathematical model. The effect of the parameters on mass transport limitation was tested by varying each reference value of the parameters with a factor of 3. Sulfate limitation within granules prevailed at moderate (0.1 kg m(-3)) and low sulfate concentrations in the bulk liquid, at high maximum sulfate utilization rates (3.73 x 10(-5) kg SO(4) (2-) kg(-1) VSS S(-1) or biomass concentrations (40 KG VSS m(-3)), and in large aggregates (radius of 7.5 10(-4) m). The effective diffusion coefficient of sulfate and the affinity constant were less determinative for the penetration depth of sulfate within a granule. (c) 1994 John Wiley & Sons, Inc.     

Dynamic approaches to the mechanism of photosynthesis

An account of the author's life and scientific research is presented. Two main lines of research have been pursued: (1) Studies on the physiological aspect of photosynthesis started from experiments with crops under field conditions and then extended to the study of photosynthesis in nature; and (2) studies on the mechanism of photophosphorylation and related problems which began with the measurement of quantum requirement of photophosphorylation. This work led to the discovery of the high energy state of phosphorylation and many other interesting findings. In recent years, efforts have been made to study the operation and regulation of photosynthetic apparatus with a view to link the above-mentioned lines of research together.Written at the invitation of Govindjee.     

Selective disruption of energy flow from phycobilisomes to Photosystem I

Efficient production of ATP and NADPH by the light reactions of oxygen-evolving photosynthesis demands continuous adjustment of transfer of absorbed light energy from antenna complexes to Photosystem I (PS I) and II (PS II) reaction center complexes in response to changes in light quality. Treatment of intact cyanobacterial cells with N-ethylmaleimide appears to disrupt energy transfer from phycobilisomes to Photosystem I (PS I). Energy transfer from phycobilisomes to Photosystem II (PS II) is unperturbed. Spectroscopic analysis indicates that the individual complexes (phycobilisomes, PS II, PS I) remain functionally intact under these conditions. The results are consistent with the presence of connections between phycobiliproteins and both PS II and PS I, but they do not support the existence of direct contacts between the two photosystems.Abbreviations Chl chlorophyll - EPR electron paramagnetic resonance - NEM N-ethylmaleimide - PBS phycobilisome - PS photosystem     

Biomass production in a nitrogen-fertilized,tallgrass prairie ecosystem exposed to ambient and elevated levels of CO2

Increased biomass production in terrestrial ecosystems with elevated atmospheric CO₂ may be constrained by nutrient limitations as a result of increased requirement or reduced availability caused by reduced turnover rates of nutrients. To determine the short-term impact of nitrogen (N) fertilization on plant biomass production under elevated CO₂, we compared the response of N-fertilized tallgrass prairie at ambient and twice-ambient CO₂ levels over a 2-year period. Native tallgrass prairie plots (4.5 m diameter) were exposed continuously (24 h) to ambient and twice-ambient CO₂ from 1 April to 26 October. We compared our results to an unfertilized companion experiment on the same research site. Above- and belowground biomass production and leaf area of fertilized plots were greater with elevated than ambient CO₂ in both years. The increase in biomass at high CO₂ occurred mainly aboveground in 1991, a dry year, and belowground in 1990, a wet year. Nitrogen concentration was lower in plants exposed to elevated CO₂, but total standing crop N was greater at high CO₂. Increased root biomass under elevated CO₂ apparently increased N uptake. The biomass production response to elevated CO₂ was much greater on N-fertilized than unfertilized prairie, particularly in the dry year. We conclude that biomass production response to elevated CO₂ was suppressed by N limitation in years with below-normal precipitation. Reduced N concentration in above- and belowground biomass could slow microbial degradation of soil organic matter and surface litter, thereby exacerbating N limitation in the long term.     

Optimization of the electrostatic interactions in proteins of different functional and folding type

The 3-dimensional optimization of the electrostatic interactions between the charged amino acid residues was studied by Monte Carlo simulations on an extended representative set of 141 protein structures with known atomic coordinates. The proteins were classified by different functional and structural criteria, and the optimization of the electrostatic interactions was analyzed. The optimization parameters were obtained by comparison of the contribution of charge-charge interactions to the free energy of the native protein structures and for a large number of randomly distributed charge constellations obtained by the Monte Carlo technique. On the basis of the results obtained, one can conclude that the charge-charge interactions are better optimized in the enzymes than in the proteins without enzymatic functions. Proteins that belong to the mixed αβ folding type are electrostatically better optimized than pure α-helical or β-strand structures. Proteins that are stabilized by disulfide bonds show a lower degree of electrostatic optimization. The electrostatic interactions in a native protein are effectively optimized by rejection of the conformers that lead to repulsive charge-charge interactions. Particularly, the rejection of the repulsive contacts seems to be a major goal in the protein folding process. The dependence of the optimization parameters on the choice of the potential function was tested. The majority of the potential functions gave practically identical results.     

Resource limitation and the lethal and sublethal effects of a viral pathogen in the Indian meal moth, Plodia interpunctella

Abstract.

• 1 The effects of resource limitation and the lethal and sublethal effects of a granulosis virus on a lepidopteran host, the Indian meal moth, Plodia interpunctella, were examined.
• 2 The food quality was manipulated by the addition of an inert bulking agent (methyl cellulose) which caused the size, development rate and fecundity of the moths to be reduced.
• 3 The resource quality had no effect on the mortality due to the virus. In contrast, sublethal effects of the virus on pupal weight were more apparent under conditions of resource limitation.
• 4 Considerable variation between the sublethal effects after challenge with different doses of the virus was found. The balance between deleterious sublethal effects of the virus and the selection of more robust individuals by the bioassays is proposed as a mechanism to explain this variation.
• 5 Implications for the dynamics of insect hosts and their pathogens are discussed.

     

Is there an energy conservation “system” in brain that protects against the consequences of energy depletion?

A poorly understood marked decrease (circa 50% of control) in local cerebral glucose utilization is caused by sublethal doses of NaCN. The decrease is global, occurring in essentially all brain regions and is entirely reversible within hours, leaving no obvious pathology. This event is not unique to NaCN in so far as a strikingly similar pattern of decreased glucose utilization occus with some other toxins. Nor can it be attributed to a direct action of NaCN since local application by microdialysis to the striatum produces a global depression. These results imply that some widely distributed system or substance is involved. We speculate the existence of a system possibly related to the reticular activating system that senses a fall in energy production and acts globally to make cells quiescent and thus would give some protection from excitotoxic driven damage.Special issue dedicated to Dr. Sidney Ochs.     

Evaluation of the effects of cosmetic or dermo-pharmaceutical products on cutaneous energy metabolism using the Episkin model of reconstructed epidermis

This study was implemented to test the Episkin model of reconstructed epidermis in the evaluation of the efficacy of cosmetic or dermopharmaceutical products on cutaneous energy metabolism. The energy metabolism is evaluated by measuring the concentration of intracellular ATP by a method using an ultrasensitive bioluminescent reaction. The work presented compares results obtained in reconstructed epithelium and monolayer primary cultures of human keratinocytes.After application of a hydrosoluble product, the increase in intracellular ATP is identical in a monolayer culture of keratinocytes (+239±18% versus control) and in Episkin (+248±21% versus control). An emulsion was also tested on the two models. It is only possible to test the emulsion at a dilution of under 0.05% on a keratinocyte culture, and this means that the real efficacy of the product is underestimated (+145±18% versus control). The three-dimensional model enables the application of the undiluted emulsion, and the results show an increase in intracellular ATP of +420±80% versus control: products in final formulation can be tested in normal conditions of use.Abbreviations BPE bovine pituitary extract - DMEM Dulbecco's modified Eagle's medium - EDTA ethylene diamine tetraacetic acid - EGF epidermal growth factor - K-SFM keratinocytes serum free medium - MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide - O/W oil in water - PBS phosphate-buffered saline     

Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry

Globular proteins have high packing densities as a result of residue side chains in the core achieving a tight, complementary packing. The internal packing is considered the main determinant of native protein structure. From that point of view, we present here a method of energy minimization using an automata network to predict a set of amino acid sequences and their side-chain conformations from a desired backbone geometry for de novo design of proteins. Using discrete side-chain conformations, that is, rotamers, the sequence generation problem from a given backbone geometry becomes one of combinatorial problems. We focused on the residues composing the interior core region and predicted a set of amino acid Sequences and their side-chain conformations only from a given backbone geometry. The kinds of residues were restricted to six hydrophobic amino acids (Ala, Ile, Met, Leu, Phe, and Val) because the core regions are almost always composed of hydrophobic residues. The obtained sequences were well packed as was the native sequence. The method can be used for automated sequence generation in the de novo design of proteins. © 1994 Wiley-Liss, Inc.     

Intrinsic pKas of ionizable residues in proteins: An explicit solvent calculation for lysozyme

Molecular dynamics simulations of triclinic hen egg white lysozyme in aqueous solution were performed to calculate the intrinsic pK_as of 14 ionizable residues. An all-atom model was used for both solvent and solute, and a single 180 ps simulation in conjunction with a Gaussian fluctuation analysis method was used. An advantage of the Gaussian fluctuation method is that it only requires a single simulation of the system in a reference state to calculate all the pK_as in the protein, in contrast to multiple simulations for the free energy perturbation method. pK_int shifts with respect to reference titratable residues were evaluated and compared to results obtained using a finite difference Poisson-Boltzmann (FDPB) method with a continuum solvent model; overall agreement with the direction of the shifts was generally observed, though the magnitude of the shifts was typically larger with the explicit solvent model. The contribution of the first solvation shell to the total charging free energies of the titratable groups was explicitly evaluated and found to be significant. Dielectric shielding between pairs of titratable groups was examined and found to be smaller than expected. The effect of the approximations used to treat the long-range interactions on the pK_int shifts is discussed. © 1994 Wiley-Liss, Inc.