Experimental and theoretical study of energetics of complex formation between nucleic acid bases and the bases with amide group.

A number of nucleic acid base pairs and complexes between the bases and the amide group of acrylamide have been studied experimentally by using mass spectrometry and theoretically by the method of atom-atom potential function calculations. It has been found from temperature dependencies of peak intensities in mass spectra of m2.2.9(3) Gua.m1Ura, m9 Ade.m1Cyt, m2.2.9(3) Gua.m1Gua.m1Cyt pairs that enthalpy values, delta H, of the complex formation are equal to 14.2 +/- 1.1, 13.5 +/- 1.3 and 16.4 +/- 1.4 kcal/M, respectively, and those of acrylamide with m1.3(2) Ura and m1Thy corresponds to 9.7 +/- 1.0 and 6.8 +/- 0.6 kcal/M. There is a good agreement of the experimental data with calculations when taking into account both the amino-oxo and the amino-hydroxy tautomeric forms of guanine. A combined use of the data allows us to determine the energy, the modes of interaction and the structure of the complexes. The results are discussed in connection with the modelling of molecular structure of biopolymers by the method of classical potential functions, protein-nucleic acids recognition and fidelity of nucleic acids biosynthesis.     

Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the michaelis constant

[This corrects the article on p. 2037 in vol. 57.].     

Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the michaelis constant

Formulations are presented that describe the concentration dependency of nutrient-limited transport and growth in molecular terms. They relate the rate of transport at steady state through a two-sequence process, transport and metabolism, to ambient concentrations according to the amounts and kinetic characteristics of the two rate-limiting proteins in these sequences. Sequences are separated by a metabolic pool. A novel feature of these formulations is the translation coefficient, which relates the transport rate attained at given ambient nutrient concentrations and membrane transporter characteristics to the nutrient concentrations sustained in the metabolic pools. The formulations, termed janusian kinetics, show that hyperbolic kinetics are retained during independent changes in transporter and enzyme contents or characteristics. Specific affinity (a degrees (A)) depends strongly on the amount and kinetic characteristics of the transporters; it is also mildly affected by the amount and characteristics of the rate-limiting enzyme. This kinetic constant best describes the ability to accumulate substrate from limiting concentrations. Maximal velocity (V(max)) describes uptake from concentrated solutions and can depend strongly on either limiting enzyme content or the associated content of transporters. The whole-cell Michaelis constant (K(T)), which depends on the ratio of rate-limiting enzyme to transporter, can be relatively independent of change in a degrees (A) and is best used to describe the concentration at which saturation begins to occur. Theory specifies that good oligotrophs have a large a degrees (A) for nutrient collection and a small V(max) for economy of enzyme, giving a small K(T). The product of the two constants is universally rather constant so that oligotrophy is scaled on a plot of a degrees (A) versus K(T), with better oligotrophs toward one end. This idea is borne out by experimental data, and therefore typical small difficult-to-culture aquatic bacteria may be classified as oligobacteria.     

Mechanistic clues to the mutagenicity of alkylated DNA bases: a theoretical study

Experiment indicates that the N7-guanine site in DNA is not "promutagenic" (mutation-inducing) on alkylation, while the O6-guanine and O4-thymine sites are so. These differences in nucleic acid template activity are attributed to corresponding differences in acidity of the Watson-Crick hydrogen bonding protons. Mechanistic indicators for ease of Watson-Crick proton loss are calculated using molecular orbital theory for DNA bases alkylated at the N7-guanine, O6-guanine and O4-thymine sites. Their values point to a definite favouring of the proton loss for the O-alkylated bases compared to the N7-alkylguanines. This may suggest the possibility that, at biological pH, the O-alkylated bases deprotonate readily while the N7-alkylguanines do not, thus accounting for observed differences in promutagenicity and nucleic acid template activity.     

Analysis of the parameter constraints for a proposed antibody affinity distribution

The problem of recovering the affinity distribution in the immune response from experimental binding data is considered. Starting from a previously proposed analytical expression for this distribution the study of the parameter constraints has been completed in order to guarantee the physical meaning of the results.     

Determination of the collection efficiency of a microbial air sampler

The Biotest RCS Plus air sampler was compared with the well-established Casella slit sampler for the quantitative analysis of the microbiological content of air. The results of the tests reported here show that the RCS Plus sampling efficiency is similar to that of the Casella sampler over the range of particles likely to be encountered in the environment. For particles less than 4 μm down to the sub-micronic sizes the efficiency of sampling falls off only gradually so that the efficiency of sampling for 1·0 μm particles is only reduced to about 50%. The ability to pre-select 10 different volumes (from 1 to 1000 1) enables the samplers to be used for measuring a wide range of concentrations of airborne micro-organisms in a variety of locations.     

Quasi-steady-state kinetics at enzyme and substrate concentrations in excess of the Michaelis-Menten constant

In vitro enzyme reactions are traditionally conducted under conditions of pronounced substrate excess since this guarantees that the bound enzyme is at quasi-steady-state (QSS) with respect to the free substrate, thereby justifying the Briggs-Haldane approximation (BHA). In contrast, intracellular reactions, amplification assays, allergen digestion assays and industrial applications span a range of enzyme-to-substrate ratios for which the BHA is invalid, including the extreme of enzyme excess. The quasi-equilibrium approximation (QEA) is valid for a subset of enzyme excess states. Previously, we showed that the total QSSA (tQSSA) overlaps and extends the validity of the BHA and the QEA, and that it is at least roughly valid for any total substrate and enzyme concentrations. The analysis of the tQSSA is hampered by square root nonlinearity. Previous simplifications of the tQSSA rate law are valid in a parameter domain that overlaps the validity domains of the BHA and the QEA and only slightly extends them. We now integrate the tQSSA rate equation in closed form, without resorting to further approximations. Moreover, we introduce a complimentary simplification of the tQSSA rate law that is valid in states of enzyme excess when the absolute difference between total enzyme and substrate concentrations greatly exceeds the Michaelis-Menten constant. This includes a wide range of enzyme and substrate concentrations where both the BHA and the QEA are invalid and allows us to define precisely the conditions for zero-order and first-order product formation. Remarkably, analytical approximations provided by the tQSSA closely match the expected stochastic kinetics for as few as 15 reactant molecules, suggesting that the conditions for the validity of the tQSSA and for its various simplifications are also of relevance at low molecule numbers.     

Experimental and theoretical studies of rate constant evaluation for the solute-matrix interaction in affinity chromatography.

In an investigation of the problem of determining kinetic parameters for the interaction of a solute with immobilized ligand sites on an affinity matrix, a combination of experimental studies and numerical simulations of frontal chromatography of methyl orange on Sephadex G-25 has yielded a simpler method than existing procedures for characterizing solute-matrix kinetics. A significant change in approach has entailed the direct evaluation of the kinetic contribution to boundary spreading from the flow-rate dependence of boundary variance under conditions of concentration-independent chromatographic migration (linear kinetics). This kinetic contribution is then interpreted in terms of an experimentally more appropriate form of a quantitative relationship for diffusion-free chromatographic migration (H. W. Hethcote and C. DeLisi, 1982, J. Chromatogr. 240, 269-281). Finally, the results of numerical simulations of concentration-dependent chromatographic migration (Langmuir kinetics) have indicated that rate constants should also be determinable under these conditions by extrapolation of their apparent values obtained by the above procedure to infinite dilution.     

Autumn colours and the nutrient retranslocation hypothesis: a theoretical assessment

The adaptive value of the bright colours of leaves in autumn is still debated. It is possible that autumn colours are an adaptation to protect the tree against photoinibition and photooxidation, which allows a more efficient recovery of nutrients. It has been proposed that the preference of aphids for trees that retranslocate nitrogen more efficiently can explain the high diversity of aphids on tree species with bright autumn colours. This scenario however does not take into account the impact of insects on the fitness of the trees and has not been analysed theoretically. Its assumptions and predictions, therefore, remain uncertain. I show with a model of insect-tree interaction that the system can actually evolve under particular conditions. I discuss the differences with the coevolution theory of autumn colours, available evidence and possible tests.     

A numerical study of oxygen diffusion in a spherical cell with the Michaelis-Menten oxygen uptake kinetics

A numerical method is presented for the solution of reaction diffusion systems in biology. The method is used to re-examine the oxygen diffusion in a spherical cell with the Michaelis-Menten oxygen uptake kinetics.     

Oscillatory kinetics of the peroxidase-oxidase reaction in an open system. Experimental and theoretical studies.

1. The oscillations in the peroxidase (donor: hydrogen-peroxide oxidoreductase, EC 1.11.1.7)-catalyzed reaction between NADH and O2 are undamped when the reaction is carried out in a system open to both substrates and when 2,4-dichlorophenol and methylene blue are present in the solution. 2. The waveform of the oscillations changes when the concentration of peroxidase is varied. 3. The waveforms obtained experimentally can be simulated by a branched chain reaction model in which the branching is quadratic. 4. A correlation between the present knowledge of the reaction and the model can be made by combining well established and hypothetical reaction steps into a few reaction schemes. A selection among schemes however, is not possible at the present time. 5. Compound III participates in the reaction as an active intermediate. This is possible because dichlorophenol stimulates the break down of compound III.     

Footprinting: a method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands

Footprinting is a simple method for assessing the sequence selectivity of DNA-binding ligands. The method is based on the ability of the ligand to protect DNA from cleavage at its binding site. This review describes the use of DNase I and hydroxyl radicals, the most commonly used footprinting probes, in footprinting experiments. The success of a footprinting experiment depends on using an appropriate DNA substrate and we describe how these can best be chosen or designed. Although footprinting was originally developed for assessing a ligand's sequence selectivity, it can also be employed to estimate the binding strength (quantitative footprinting) and to assess the association and dissociation rate constants for slow binding reactions.     

Experimental and theoretical investigations of rotating algae biofilm reactors (RABRs): Areal productivity,nutrient recovery,and energy efficiency

Microalgae biofilms have been demonstrated to recover nutrients from wastewater and serve as biomass feedstock for bioproducts. However, there is a need to develop a platform to quantitatively describe microalgae biofilm production, which can provide guidance and insights for improving biomass areal productivity and nutrient uptake efficiency. This paper proposes a unified experimental and theoretical framework to investigate algae biofilm growth on a rotating algae biofilm reactor (RABR). Experimental laboratory setups are used to conduct controlled experiments on testing environmental and operational factors for RABRs. We propose a differential–integral equation-based mathematical model for microalgae biofilm cultivation guided by laboratory experimental findings. The predictive mathematical model development is coordinated with laboratory experiments of biofilm areal productivity associated with ammonia and inorganic phosphorus uptake by RABRs. The unified experimental and theoretical tool is used to investigate the effects of RABR rotating velocity, duty cycle (DC), and light intensity on algae biofilm growth, areal productivity, nutrient uptake efficiency, and energy efficiency in wastewater treatment. Our framework indicates that maintaining a reasonable light intensity range improves biomass areal productivity and nutrient uptake efficiency. Our framework also indicates that faster RABR rotation benefits biomass areal productivity. However, maximizing the nutrient uptake efficiency requires a reasonably low RABR rotating speed. Energy efficiency is strongly correlated with RABR rotating speed and DC.     

Persistence and functional impact of a microbial inoculant on native microbial community structure,nutrient digestion and fermentation characteristics in a rumen model

Small sub-unit (SSU) rRNA-targeted oligonucleotide probes were used to monitor the persistence of a genetically engineered bacterium inoculated in model rumens. Eight dual flow continuous culture fermenters were operated with either standard artificial saliva buffer or buffer with chondroitin sulfate (0.5 g/l) added. After 168 h of operation, fermenters were inoculated with Bacteroides thetaiotaomicron BTX (BTX), at approximately 1% of total bacteria. B. thetaiotaomicron was quantified using a species-specific probe and shown to persist in fermenters 144 h after inoculation (relative abundance 0.48% and 1.42% of total SSU rRNA with standard and chondroitin sulfate buffers, respectively). No B. thetaiotaomicron SSU rRNA was detected in fermenter samples prior to inoculation with strain BTX. Relative abundances of Bacteria, Eucarya and Archaea were not affected by either inoculation or buffer type. Fiber digestion, in particular the hemicellulose fraction, increased after strain BTX addition. Chondroitin sulfate addition to the buffer increased bacterial nitrogen flow in fermenters, but did not alter fiber digestion. Neither inoculum nor buffer type altered total short chain fatty acid (VFA) concentrations but proportions of individual VFA differed. In model rumens, B. thetaiotaomicron BTX increased fiber digestion when added to mixed ruminal microbes, independent of chondroitin sulfate addition; but further study is needed to determine effects on other fiber-digesting bacteria.     

Poly(U)-agarose affinity chromatography: specific, sensitivity selectivity, and affinity of binding

These studies were done to determine four basic intrinsic properties of poly(U)-agarose affinity columns. Specificity of binding studies demonstrated that binding to these columns is highly specific with greater than 90% complementary binding and less than or equal to 3% noncomplementary binding. Sensitivity of binding studies indicated that a minimum sequence of 10 adenylates is required for detectable complementary binding. Selectivity of binding studies revealed that nonsequential adenylates in native RNAs and randomly distributed adenylates in synthetic poly(A)-poly(C) co-polymers did not bind to poly(U)-agarose affinity columns. Whereas, affinity of binding studies demonstrated that A=U complementary base pairing is independent of chain-lengths of greater than or equal to 25 adenylates and dependent of chain-lengths of less than 25 adenylates. Thus the data demonstrates that poly(U)-agarose affinity chromatography is scientifically sound and expedient for the detection and isolation of poly(A)-containing cellular and viral RNAs.     

Experimental manipulations of water and nutrient input to a Norway spruce plantation at Klosterhede,Denmark

At Klosterhede, Denmark experimental manipulations of water and nutrient inputs to a forest stand were carried out under a 1200 m² roof simulating i) summer drought, ii) removal of N and S input, and iii) optimal nutrition and water availability. In practise, manipulation of element fluxes in a complex system like a forest may cause unintended changes such as climatic effects from the roof which may interfere with the results of the intended manipulation. This paper illustrates the extent and effects of such unintended changes.The most important climatic change under the roof was a 50% reduction of photosynthetic light which caused a decrease in moss cover on the ground floor. Soil temperatures under the roof were decreased 0.3°C during summer and increased 0.2°C during winter. Air humidity was not changed. Throughfall water amount decreased close to the stems whereas element concentrations in throughfall increased close to the stems and with tree size on the ambient plots. This distinct spatial pattern was changed under the roof to a more variable water distribution from the sprinkling system and to constant element concentrations in the sprinkling water. This loss/change of spatial variability in the input was reflected in the soil solution. The concentration patterns found in soil water (increasing close to the stem and with tree size) in the ambient plots were no longer observed under the roof.Exclusion of throughfall by the roof disturbed the internal cycle of nutrients leached from the canopy. The removal of canopy leached Ca and K by the roof caused a decline in soil water concentrations, even on the drought plot where natural throughfall was only cut off during two summer months. The internal cycle of Ca and K had to be restored by addition of Ca and K under the roof. Further, leachable elements and soluble compounds may be washed out from litterfall during the collection period on the roof, and thus lost from the internal cycle by by exclusion of throughfall.It is important to consider these problems in the design of new manipulation experiments and in the interpretation of the results. Some recommendations are given.     

Experimental manipulation of water and nutrient input to a Norway spruce plantation at Klosterhede,Denmark

Water and nutrient supply to forest trees are major factors controlling tree growth and forest vitality. Therefore, changes in the supply of water and nutrients to the trees may be important contributing reasons to the forest damages observed in Europe. Such changes may be caused by several factors, e.g. air pollution, soil acidification and climate change. The present study investigates possible effects on tree growth, growth related parameters and nutrition related to changes in the water and nutrient supply. Water and nutrient supply to the forest soil was manipulated in three roof covered plots. The treatments consisted of 1) summer drought, 2) irrigation and 3) combined irrigation and fertilizer application (fertigation). The results from the roof covered treatment plots were compared to a control plot without roof. Increased supply of water during the spring and early summer increased the diameter growth, whereas application of nutrients in addition to irrigation had no additional effect on tree growth. Addition of nutrients increased the needle content of P, Mn, Ca and Mg. Extended summer drought for 2 months had no effect on the tree growth or other growth parameters, but drought reduced the root development in the upper soil layer. Furthermore, drought induced significant stress symptoms by increasing the cone shredding substantially.