ABPL

Computer analysis of biological systems, using approaches such as metabolic control analysis is common. A typical example is a language like Herbert Sauro's SCAMP (Sauro & Fell, 1991), which allows simulations of enzyme systems, and calculation of control coefficients and elasticities. However such systems are motivated by the underlying biochemical theory and often have limitations as programming languages which mean that they can only be applied to particular classes of problems. ABPL (a biochemical programming language) extends these ideas by adding all the facilities of a fully-fledged programming language, together with some of the capabilities of a modern computer algebra system. Syntactically it derives from the programming language LISP, while the underlying functionality is that of iMAP, the successor to SCAMP. This provides us with a computer system capable of performing most of the tasks undertaken by existing packages, but more importantly, a system which can be easily extended into new areas. Key features of the work are:

- Ability to use the language both interactively and as a batch programming language

- Ability to work both symbolically and numerically

- Ability to handle matrices and vectors

- Ability to define and manipulate reaction schemes

- Common techniques are built in to the language

- Ability to add new operations to the language

The implementation is in ANSI standard C for portability.     

Composition chimique elementaire des populations naturelles de Sphaeroma hookeri (Crustace: Isopode Flabellifere). Aspect spatio-temporel

1. Elemental chemical composition of Sphaeroma hookeri Leach of different natural populations from Camargue (Rhône delta) and from the Bassin de Berre (near Marseilles), was studied on samples taken the same day in different populations and on samples collected at different seasons in the same population.
2. Individual analyses of carbon, hydrogen and nitrogen were performed with a Perkin Elmer elemental analyzer. Total inorganic content was obtained for each specimen by weighing the residue after the output of the analyzer.
3. Relative growth in ash, carbon, hydrogen and nitrogen content of the different populations samples was compared by means of Reeve's statistical method.
4. Chemical allometry lines of each population are given. Variability of growth coefficients or mean values in a given population appears from several samples taken in the course of the year.
5. The differences in slope and position have been tested and their significance stated.
6. Growth coefficients of ash, carbon, hydrogen and nitrogen contents show a certain variability among the different populations. But these differences are not always significant owing to the dispersion of the data, a result of the wide individual variation within a population.
7. Much greater significant differences appear from relative positions of the growth lines, and these seem to be due to some ecological factors, among which, for instance, nutriment can lead to a large difference in carbon content.
8. Within a given population no significant difference appears in the growth coefficients of ash, carbon, hydrogen or nitrogen content and therefore the obtained values characterize each population.

     

EPR characterization of oxide supported transition metal ions: Relevance to catalysis

EPR spectroscopy is a powerful tool to identify at a molecular level, the different steps of catalyst preparation, and of catalytic reactions:

1. Deposition of paramagnetic transition metal ions onto a support is monitored, and the coordination sphere of the metallic center is characterized by EPR.
2. The catalyst is also characterized after activation (thermal oxidation or reduction):

- the distribution among the different sites in zeolites can be determined;

- the dispersion of the active phase may be appreciated;

- the unsaturation degree of the active site may be evaluated using probe molecules such as water or¹³C enriched carbon monoxide.

1. The catalytic mechanisms can be investigated by studying the elementary steps of the catalytic reaction, as illustrated for methanol oxidation over Mo/SiO₂ catalysts whose EPR results have extended the reaction mechanism proposed on the basis of kinetic data. In addition, reaction intermediates may be isolated inquasi-in situ conditions as in the case of olefin oligomerization catalyzed by Ni/SiO₂ systems.

     

The anaerobic metabolism of malate of Saccharomyces bailii and the partial purification and characterization of malic enzyme

1. The main pathway of the anaerobic metabolism of l-malate in Saccharomyces bailii is catalyzed by a l-malic enzyme.
2. The enzyme was purified more than 300-fold. During the purification procedure fumarase and pyruvate decarboxylase were removed completely, and malate dehydrogenase and oxalacetate decarboxylase were removed to a very large extent.
3. Manganese ions are not required for the reaction of malic enzyme of Saccharomyces bailii, but the activity of the enzyme is increased by manganese.
4. The reaction of l-malic enzyme proceeds with the coenzymes NAD and (to a lesser extent) NADP.
5. The K _m-values of the malic enzyme of Saccharomyces bailii were 10 mM for l-malate and 0.1 mM for NAD.
6. A model based on the activity and substrate affinity of malic enzyme, the intracellular concentration of malate and phosphate, and its action on fumarase, is proposed to explain the complete anaerobic degradation of malate in Saccharomyces bailii as compared with the partial decomposition of malate in Saccharomyces cerevisiae.

     

Metabolic roles of carnitine expressed through the carnitine acetyltransferase system in Candida pintolopesii

• 1.1. The carnitine-responsive mutant yeast, Candida pintolopesii ATCC 26014 and the wild type strain (ATCC 22987) were used to investigate the role of carnitine and the carnitine acetyltransferase system.
• 2.2. [³H]l-Carnitine, supplied to the cells, was incorporated into acetylcamitine and [¹⁴C]pantothenate was incorporated into CoA and its derivatives.
• 3.3. Both bioautography and quantitative assays indicated that the relative amounts of CoA and acetylCoA were very different in the mutant and wild type cells.
• 4.4. The wild type yeast maintained an acetylCoA/CoA ratio of 0.33 ± 0.09 indicating that most of the CoA in the cell is in the free CoA form. Carnitine was not required to establish this ratio nor did its presence lower it further.
• 5.5. In contrast, the mutant cells contained a high acetylCoA/CoA ratio (12.8 ± 3.0).
• 6.6. In the mutant cells, carnitine lowered the ratio by decreasing the intracellular acetylCoA concentration and releasing free CoA.
• 7.7. These data indicated that wild type yeast possess an effective mechanism that is not related to the CAT system for regulating the acetylCoA/CoA ratio.
• 8.8. This mechanism appears to be lacking in the mutant. The CAT system decreased the acetylCoA/CoA ratio in the mutant cells but not to the value which is found in the wild type strain.
• 9.9. In both stains of Candida pintolopesii, in the presence of carnitine, an acetylcamitine pool can be created whose concentration exceeds that of acetylCoA.
• 10.10. The intracellular apparent equilibrium constant (K_app) for carnitine acetyltransferase for wild type Candida pintolopesii ATCC 22987 was 0.73 ± 0.12, close to the established value of 0.6, indicating that the CAT system ran close to equilibrium.
• 11.11. The K_app for the CAT system of the carnitine-responsive mutant yeast was 7.7 ± 1.7 indicating that this reaction was not at equilibrium.

     

Effect of feeding on the respiration rate of the rotifer Brachionus plicatilis

The effect of feeding on the respiration rate of Brachionus plicatilis was studied. Oxygen consumption was determined under two feeding regimes, duplicate feeding and constant feeding. Oxygen consumption rate increased during feeding. The oxygen consumption profile is discussed in relation to the following processes:

1. filtration, mastication, and locomotion during feeding
2. specific dynamic action (SDA)
3. egg formation and routine metabolism.

     

Water balance of small lactating rodents —III. Estimates of milk production and water recycling in lactating Mus musculus under various water regimes

1. The exchanges of water between lactating female and young Mus musculus were modelled on the computer.
2. The model was used to estimate rates of milk production and water recycling in various litter sizes under various water regimes by following the time course of injected tritiated water.
3. The high correlation between estimated rates of milk production and actual growth rates of young was taken to indicate that the method gave if not the actual rates of milk production a very constant proportion of it.
4. Approximately 50% of the water secreted in milk is returned to the mother by recycling.

     

A study on the rate of water transport of the clam katelysia opima in relation to environmental conditions

1. The neutral red technique was employed to study the rate of filtration in Katelysia opima.
2. The weight specific water filtration was found to be greater for younger clams compared to the older ones.
3. The rate of water filtration increased with decreasing salinity.
4. Water filtration was found to increase as temperature increased, reaching a maximum at 35°C. but then sharply decreasing at 39°C.
5. Light had no significant effect on the rate of filtration.
6. Suspended matter was found to affect the rate of water filtration.
7. The rate of filtration was low at high pH and high in low pH.
8. The rate of water filtration was found to be faster during high tide than during low tide.
9. The presence of the parasitic crab, Pennotheris sp., in the mantle cavity of clams had a marked effect on the particle filtration.
10. Accidental cut of the siphon tips had no effect on the rate of filtration.

     

Metabolic products of microorganisms

1. The total nitrogen content of spores of Penicillium notatum increased during swelling and reached a maximum before germ-tubes were formed. It subsequently decreased during germ-tube formation until a constant value in hyphae was reached.
2. An increase in the protein content of the spores was found during swelling, followed by a decrease when germ-tubes were formed. After germination, the protein content increased again to a constant level in hyphae.
3. The content of total lipids steadily decreased during swelling of spores. It reached a minimum value in germinating spores, followed by a net accumulation during hyphal growth. Similar changes occurred in free lipids, phospholipids and the acetone-soluble lipids but not in bound lipids.
4. After an initial decrease during swelling, no further change took place in the neutral carbohydrates content of the spores at the time of germ-tube formation. An accumulation of neutral carbohydrates occurred during late hyphal extension.
5. The nucleic acid content increased sharply during swelling, and reached the highest value in swollen spores just prior to the initiation of germ-tube formation. Afterwards, its content steadily decreased during germ-tube formation and hyphae elongation.

     

Seasonal variations in biochemical constituents of the clam,Paphia laterisulca

1. The total protein, fat and glycogen contents were estimated from the edible clam, P. laterisulca. Seasonal variations in these constituents along with the water content were studied.
2. The gonad index in P. laterisulca was found to increase during the ripe condition and in winter (December–January) and decrease on spawning.
3. A relatively high water content was obtained during monsoon (June to September). This might be due to the loss of salts and gain of water in low salinities.
4. Protein content varied with the reproductive cycle of the clam. The level reached its peak in the mature stage and declined on spawning. Immature clams showed less protein content than gravid ones.
5. Lipid content started to increase as the gametogenesis commenced, reached its peak in fully mature condition (August) and sharply declined due to the shedding of gametes during spawning.
6. Glycogen content was high during the period of active gameto-genesis (May–June). A sharp decrease took place when the clams were fully ripe (July). The glycogen might have been utilized in the formation of active ripe gametes.
7. After starvation for twelve days, total protein and fat contents remained constant, while glycogen content decreased by 66.82%. The water content increased by 4.67%.
8. Seasonal variation in the organic constituents are discussed in relation to the reproductive cycle of the clam.

     

The effect of inhibitors on the electron flow triggering photo-phobic reactions in cyanophyceae

1. Since photo-phobic reactions in the blue green alga Phormidium uncinatum seem to be triggered by changes of electron flow rates into or out of an electron pool situated in the electron transport chain between photosystem II and I, the effect of inhibitors affecting the electron transport chain has been studied.
2. Dose response curves of the phobic reaction have been measured by varying the trap energy in double beam light trap experiments with constant pairs of monochromatic light. From these dose response curves the effects of the inhibitors on both types of phobic reactions, i.e. exit reactions and entrance reactions, have been calculated.
3. Dibromothymoquinone (DBMIB) inhibits the electron transport between the electron pool and photosystem I by preventing the reoxidation of plastoquinone. The phobic entrance reaction, which results in an emptying of the light trap, is triggered by changes in the electron flow out of the pool; thus it is more effected by DBMIB than the exit reaction, which is mediated by the electron transport into the pool.
4. The phobic exit reaction, which results in accumulations in the light trap, is triggered by changes in the electron flow into the electron pool via photosystem II. 3-[3,4-dichlorophenyl]-1,1-dimethylurea (DCMU) inhibits the electron transport near photosystem II; thus it affects the exit reaction more than the entrance reaction.

     

The use of toxicokinetics for the safety assessment of drugs acting in the brain

Pharmacological and toxicological studies undertaken on drugs that affect the brain are frequently performed in disparate species under various experimental conditions, at doses often greatly in excess of those expected to be administered to humans, and the findings are extrapolated implicitly or explicitly with scant regard to differences in the biodisposition of the drugs. Such considerations are necessary since:

1. Species;
2. Strain;
3. Gender;
4. Route;
5. Dose;
6. Frequency and time of administration;
7. Temperature;
8. Coadministration of drugs; and
9. Surgical manipulation

are but some of the factors that have been shown to influence the kinetics and metabolism of drugs. This article, using MDMA and other phenylethylamines as examples, provides evidence for the need to measure the exoosure of the drugs and their active metabolites in blood and brain (toxicokinetics) in order that conclusions based only on dynamic, biochemical, or histological evidence are more pertinent. Further, the combined use of toxicokinetic-dynamic modeling can lead to a better appreciation of the mechanisms involved and a more useful approach to the calculation of safety margins.     

The use of a continuous assay system to show the stimulation of phosphoenolpyruvate production in intact mitochondria by valinomycin and by Mn2+

1. A method for the direct recording of the PEP efflux from isolated mitochondria is described.
2. This method has been used to show the stimulation of PEP efflux by externally added Mn⁺⁺ ions.
3. Valinomycin, uncoupler and oleate were also shown to stimulate PEP efflux.
4. Valinomycin caused an increase in the internal concentration of both PEP and citrate.
5. The results indicate that the major pathway of PEP synthesis in isolated mitochondria is via PEP carboxykinase and the results do not call for an unknown pathway of metabolism.
6. Two interactions between PEP and citrate are described; competition for the mitochondrial interior and the stimulation of PEP production by citrate.

     

Numerical integration of a stochastic model for the Volterra-Lotka reaction

Time-integration of the master equation governing the birth-and-death model of the Volterra-Lotka reaction is carried out for three different initial conditions, with the results:

1. Fluctuations destroy the deterministic steady state in a manner quantitatively predicted from a cumulant expansion;
2. The sustained oscillatory behavior predicted by the deterministic model degenerated after 1/4 cycle in the stochastic model;
3. It is possible to select initial distributions such that the asymptotic distribution is a spike at the origin of the plane of reactants.

     

Seasonal variation in the biochemical composition of Mytilus viridis at Ratnagiri on the West Coast of India

1. The seasonal variation in the water, protein, fat and glycogen contents of the mussel, Mytilus viridis has been studied for the year March, 1974 to March, 1975.
2. The water level increased during the monsoon season and decreased in summer.
3. The level of protein, fat and glycogen showed correlation with the reproductive cycle of the mussel.
4. The protein level was high when the mussels were mature and dropped during the breeding period.
5. During sex change from male to female in May the protein level remained high whereas during sex change from female to male in October and November it was low.
6. The fat level was high in mature mussels and declined on spawning.
7. The glycogen level was at its peak in immature mussels and low in mature.

     

A study of the relationship between mechanical characteristics and the coastal vegetation among several broad-leaf trees in Miura Peninsula in Japan

The mechanical properties of broad-leaf tree species in a maritime-wind exposed habitat in central Japan were examined. The broad-leaf trees studied were Celtis sinensis var. japonica, Ilex integra, Eurya japonica, Pittosporum tobira, Euonymus japonicus and Cinnamomum japonicum. The results obtained can be summarized briefly as follows:

1. At places with weaker wind, the number of species increased and the height of the canopy increased.
2. The fracture strength σ_m showed no dependence on tree part or branch thickness, but was constant.
3. The order of strength was Celtis sinensis var. japonica > Ilex integra > Eurya japonica > Pittosporum tobira > Euonymus japonicus > Cinnamomum japonicum, and these six species could best adapt to the wind pressure in the study area.
4. Within species, fracture strength varied directly with wind strength.
5. The strain ε_m decreased as the trunk became thicker.
6. Within species, strain energy U_m varied directly with wind strength.

     

Experimental problems using electronic particle counters

The following scheme lists the problems which have been and will continue to be encountered in grazing experiments on natural particle assemblages. In some cases there are solutions, but many of the problems listed below remain intractable. To solve them will require innovative approaches, most probably combining the use of particle counters with other techniques to approach the problem to be solved from several angles at once. Variance between samples due to

- statistical causes (especially caused by large particles) and

- differences between experimental bottles and between experimentals and controls at start of experiment. Shifts in particle distribution during experiment due to

- increase in small particles

- growth of bacteria and other organisms due to excretion of grazers and

- breakage during handling by grazers into fragments. Processes, independent of grazing, leading to changes in particle size distribution due to

- primary production

- grazing by additional components and

- bacterial growth on detrital particles and the formation of detrital flocs.

     

Effet des androgènes sur l’activité sportive

Androgenic hormones seem to be of beneficial effects on sports performance:

- they increase motivation, will, aggressiveness, resistance to the stress and to the fatigue, leading to an increase of the training quantity,

- they increase bone mineralization and probably mechanical resistance,

- they stimulate the bone marrow and so, with the erythropoietin, the erythropoiesis,

- they increase the tendancy to hyperglycemia, but with a decrease of the tolerance to the glucose,

- they stimulate the fatty acids mobilization from the adipose tissue, for their utilization in the muscle during the exercise,

- they participate, for the trained sportmen, to a better gestion of the muscle glycogen storage: their utilization during exercise is decreased,

- they increase the lean body mass, with an increase of the protein synthesis and a decrease of the protein catabolism, leading also to an increase of the muscle force under training. There is no beneficial effect upon the tendons,

- they have an immunomodulation action.

     

Les brisures de symetrie du temps

Introduction

Atoms theory and symmetry theory dominated physics. Symmetry propagation and interactions verify the Curie principle. But its violation by symmetry breaking is spontaneous.Fragility is creative. An information breaks a generalized symmetry. Results on symmetry breakings are not valid for fuzzy symmetries. The breaking of a fuzzy symmetry leads only to a pour symmetry (Fig.1). Homogeneity breaking, and atom of time are not usual concepts. We examine in this work symmetry breakings which generate the living time.

Relativistic Time-Space Breaking

1. Medium and environment of living define ordinary referential of space and referential of time. Astronomical phenomena following classical mechanics and microphysical phenomena following quantum mechanics can be written with the same t coordinate.
2. Relativity corrections. Schrödinger's Quantum mechanics (Eq.0) approximately governs molecular systems (Relativity corrections can be expressed as physical effects in the above defined referential).
3. Time reversal symmetry. The well-known Wigner's transformation determines the microscopic reversibility.
4. The three essential particle-vacancy equilibria. This transformation is verified by all particle-vacancy reciprocity. Vacancy moves like particle but with negative moment and positive kinetic energies. Only three biochemical equilibria admit this time reversal symmetry, namely: oxydo-reduction, acido-basicity, fluidity-viscosity. In these case, reacting electron, solvated proton, water molecule are respectively antagonist of the corresponding vacancy.
5. Fuzzy character of time reversal symmetry. Dirac's equation does not admit this symmetry which only appears at the “non relativistic” limit of quantum phenomena. Hence particle-vacancy reciprocity is fuzzy according to the experimental evidence. (Laforgue et al., 1988).

Oriented Time

1. From the universal reversible time, an additional breaking generates the oriented time, both in the astronomical and in the living matter.
2. Irreversibility for the environment. We refer to Prigogine and Stengers (1988).
3. Irreversibility for the living matter. We refer to Lochak (1986). Because equation (0), above discussed, is “microreversible” the second breaking could come from an additional term vanishing in the stationary states but increasing with time in evolutionary processes.
4. Negative times. Taking into account the fuzzy character of the time reversed symmetry, the third breaking cannot suppress completely the occurrence of negative times. Reversed time is controlled by direct time. Except in the three above reported cases, time reversal symmetry is not verified by the medium. Free motion of the particle following eg.(0) or of the vacancy following time reversal reciprocal equation takes place only during short jumps from an interaction site to an other. Fig. 2 schematizes the law of motion of the electric charge corresponding to the transport by proton or by proton vacancy in an unitary field (fluctuations are neglected). The reserved jumps are estimated in the range of 10^?12s. It is not excluded that such a jump can control a direct phenomenon.
5. The living time. Biological phenomenon appears as an oriented set of events. Nevertheless latency or exaltation phases could be perceived. This modulation could be described by positive and negative times additional to the basic time. (Negative can be interpreted as above)

Living produces Time

1. That were not understandable, if time was only a frame, in which change occurs. Taking chance as frame and time as effect, we regard biological activity as integrating reversible and irreversible time. Living synchronizes internal and external time by its own effort as it results (Lestienne, 1990) from Chronobiology.
2. Time modulation. Let us consider the dy₁...dy_i...dy_p changes in the variables of the systems, dy={dy_i} has produced dt. We proof (eq.(1) to (4)) that time is modulated by a φ_(y) speed coefficient depending on the medium. t_modulated=tφ _(y) ^?1
3. The production of reversible time (e.g.acido-basicity) determines time modulation. As above reported it remains some reversibility effects (jumps of negative time) which modulate time. E.G., if an important amount of reagent is necessary to modify an acid-base equilibrium, φ_(y) is small.
4. Time modulation and activation-repression reciprocity. As well-known, long t_modulated means repression, short t_modulated means exaltation. Extrema of ? are symmetrical because particle and vacancy are reciprocal. Nevertheless reciprocity is not perfect. E.g., on fig. 3, the wet receptor determines the cell increasing, the dry receptor the cell senescence of a certain alga (Lück, 1962).
5. Irreversible time production. Medium accepts entropy. Hence it acts in the second breaking of time. Living extracts the free energy from the medium, like a dissipative structure. That insures an operative point far from the thermodynamical equilibrium.

Consumption of Time

1. The three followings correspond to the more trivial time consumption.
2. Rhythmical time. Free energy flux is favourable to the arising of order in space or time. This later gives a structure to the living time.
3. Mutual dependence of reversible time and rhythms. Time irreversible structure can be controlled by the above considered particle-vacancy equilibrium. Consequently the living time (modulated and structured) is a chemical time connected to molecular properties and to statistical thermodynamics. Practically, the connection between chronobiology and chemistry is important. The use of drugs could be interpreted as a response to an aggression against biorhythms.
4. Lifetime. The dead-birth rythm can be broken in two ways: evolution or indefinite life. This later is non exceptional for the living matter, e.g. in the vegetals where it is connected with the chlorophyllic assimilation; the time reversal significance of which is evident.
5. The plan of the alchemist. Indefinitely life has fascinated individuals. Do the human species becomes better adapted by a longer life?

Conclusions

1. Atoms of time could exist.
2. Biological time is defined by the breaking of five generalized symmetries, namely: Minkovski's space symmetry, reversibility, homogeneity, rhythmicity, generations reproduction.
3. Environment and medium determine non relativistic, oriented, structured time.
4. At the microphysical scale, a fuzzy time reversal symmetry takes place, the breaking of which is not complete. Reversible time and dominating irreversible time are integrated in living phenomena.
5. Three fundamental particle-vacancy reciprocities admit a part of reversibity. Irreversibility governs the all others phenomena.
6. Time is produced chemically.
7. A new perspective is the connection between chemical equilibria and rhythms including the time of the life.

     

Field studies on the variability of populations of Aster tripolium L. in relation to saltmarsh zonation

1. Aster tripolium is a very variable species of which a number of types have been described both on a morphological and ecological level.
2. In permanent plots along the height gradient in the salt marsh it appeared that differences in the A. tripolium subpopulations occur.
3. In the lowest zone of the marsh, dominated by Spartina anglica (Spartinion), the mean life expectancy of individual adult plants is relatively high but it is relatively low for seedlings.
4. In the higher zones of the marsh the mean life expectancy is relatively lower, but for the seedlings it is higher (Puccinellion maritimae).
5. In the Spartina-zone individual A. tripolium plants have about twice the number of shoots as the plants from the other zones.
6. The plants from the Spartina zone produce per individual more generative shoots (absolute) but these have less capitula than elsewhere in the marsh. The number of ripe seeds per head is almost constant everywhere in the marsh.