Other developments regarding the concept of energy in biological systems

In order to recognize the realizability of inputs with different physical natures through a component, Yoneda's Lemma is applied. The major utility of this Lemma is when the components produce only energy. From this, it is assumed that a new material input must exist which was not recognized in the original developments in biological systems representation. Moreover, simple transfers of energy, between objects, components, and among both objects and components are developed under the generic name; energetical evolution. Thus, energetical evolution appears as anew element in the abstract representation of biological systems. These new concepts are incorporated into a new abstract diagram and a newM _β category. This paper was made possible by a Fellowship from the Consejo Nacional de Investigaciones Científicas y Técnicas of the República Argentina.     

The bio-environmental system and the realizability of pre-biological systems

A set of axioms is given which embed theM _γ E andT categories developed previously (Leguizamón 1975a, b; 1976, 1977) into a new categoryK. The categoryK represents a bioenvironmental system with the properties of the three previous developments. This bioenvironmental system is believed to be useful in order to study the realization of prebiological systems. The categorical structure of most simple biological system of “zero life” is given, on the basis of two specific biological conditions. This system is proposed as starting point for study of the organization of living systems. This paper was made possible by a Fellowship from the Consejo Nacional de Investigaciones Cientificas y Técnicas of the República Argentina.     

Theory of transport in linear biological systems: II. Multiflux problems

If in a multiflux system theith flux is given by the integral equation, , the corresponding equation in the Laplace transforms is Γ _i = Σ _j W _ij Γ _j +M _i -the entire system having the matrix formulaion, [I−W]Γ=M. The general solution of this equation and its physical interpretation are discussed. Explicit solutions are given for the general mammillary and catenary systems and for some capillary exchange problems. The theory is applied to the integrated from of the fundamental continuity equation to give equations for total quantity of material in the various “compartments.” If the compartments are uniformly mixed, the integral equation treatment is shown to be mathematically equivalent to the usual differential equation formulation.     

Contributions to relational biology

The principle of biotopological mapping (Rashevsky, 1954,Bull. Math. Biophysics,16, 317–48) is given a generalized formulation, as the principle of relational epimorphism in biology. The connection between this principle and Robert Rosen’s representation of organisms by means of categories (1958,Bull. Math. Biophysics,20, 317–41) is studied. Rosen’s theory of (M,R)-systems, (1958,Bull. Math. Biophysics,20, 245–60) is generalized by dropping the assumption that only terminalM _i components are sending inputs into theR _i components. It is shown that, if the primordial organism is an (M,R)-system, then the higher organisms, obtained by a construction well discussed previously (1958,Bull. Math. Biophysics,20, 71–93), are also (M,R)-systems. Several theorems about such derived (M,R)-systems are demonstrated. It is shown that Rosen’s concept of an organism as a set of mappings throws light on phenomena of synesthesia and also leads to the conclusion that Gestalt phenomena must occur not only in the fields of visual and auditory perception but in perceptions of any modality.     

Expression Optimization and Biochemical Characterization of a Recombinant γ-Glutamyltranspeptidase from Escherichia coli Novablue

A truncated Escherichia coli Novablue γ-glutamyltranspeptidase (EcGGT) gene lacking the first 48-bp coding sequence for part of the signal sequence was amplified by polymerase chain reaction and cloned into expression vector pQE-30 to generate pQE-EcGGT. The maximum production of His₆-tagged enzyme by E. coli M15 (pQE-EcGGT) was achieved with 0.1 mM IPTG induction for 12 h at 20 °C. The overexpressed enzyme was purified to homogeneity by nickel-chelate chromatography to a specific transpeptidase activity of 4.25 U/mg protein and a final yield of 83%. The molecular masses of the subunits of the purified enzyme were estimated to be 41 and 21 kDa respectively by SDS-PAGE, indicating EcGGT still undergoes the post-translational cleavage even in the truncation of signal sequence. The optimum temperature and pH for the recombinant enzyme were 40 °C and 9, respectively. The apparent K _m and V _max values for γ-glutamyl-p-nitroanilide as γ-glutamyl donor in the transpeptidation reaction were 37.9 μM and 53.7 × 10⁻³ mM min⁻¹, respectively. The synthesis of L-theanine was performed in a reaction mixture containing 10 mM L-Gln, 40 mM ethylamine, and 1.04 U His₆-tagged EcGGT/ml, pH 10, and a conversion rate of 45% was obtained.     

Characterization of urease from Sporosarcina ureae

Alkaline stable (pH 7.75–12.5) urease from Sporosarcina ureae was purified over 400-fold by ion exchange and hydrophobic interaction chromatography. The cytoplasmic enzyme was remarkably active with a specific activity of greater than 9300 μmol urea degraded min^-1 mg protein^-1 at pH 7.5, where it has optimal activity. Although S. ureae is closely related to Bacillus pasteurii, known to posses a homopolymeric urease containing 1 nickel per subunit [M _r=65000], the S. ureae enzyme is comprised of three subunits [apparent M _r=63100 (α), 14500 (β), and 8500 (γ)] in an estimated ∝βγ stoichiometry and contains 2.1±0.6 nickel ions per ∝βγ unit as measured by atomic absorption spectrometry. Stationary phase cultures sometimes possessed low levels of urease activity, but the specific activity of cell extracts of partially purified urease preparations from such cultures could be elevated by heat treatment, dilution, or dialysis to values comparable to those observed in samples from exponentially grown cells.     

A generalized theory of particulate electron conduction enzymes applied to cytochrome oxidase. A theory of coupled electron and/or ion transport applied to pyruvate carboxylase

A previously developed theory of particulate electron conduction enzymes was based on a model of an enzyme particle catalyzing the oxidation-reduction of two different substrates at two different enzymatic sites on the same particle with conduction of electrons between the two sites through the enzyme particle. Using the simplifying assumption that the percent reduction of the second substrate is held constant, there was previously shown to be a hyperbolic relationship between the first order rate constant (k′) and the sum (C _x ) of oxidized plus reduced substrate, of the formk′=α/(C _x +β), where α and β are positive constants. It is shown here that if this simplifying assumption is omitted, a positive constant is added to the right hand side of this equation, which describes exactly the experimental data of Smith and conrad on cytochrome oxidase. If electron transport is assumed to be coupled to ion transport, this equation becomesk′=(α/C _x )−γ (where γ is a positive constant) which describes the experimental data of Eadie and Gale on pyruvic carboxylase of yeast. It seems probable that the same theory is applicable to coupled ion-ion transport and coupled electron-electron transport in both membranous systems, and in particulate preparations consisting of membrane fragments.     

Theory of transport in linear biological systems: I. Fundamental integral equation

The conditions under which the output,γ _b (t), of a biological system is related to the input,γ _a (t), by an integral equation of the typeγ _b (t) = ∫ ₀ ^t γ _a (ω)w(t−ω)dω, where ω(t) is a transport functioncharacteristic of the system, are analyzed in detail. Methods of solving this type of integral equation are briefly discussed. The theory is then applied to problems in tracer kinetics in which input and output are sums of exponentials, and explicit formulae, which are applicable whether or not the pool is uniformly mixed, are derived for “turnover time” and “pool” size.     

Density functional study of closed-shell attraction on X(ML)<Subscript>3</Subscript><Superscript>+</Superscript>(<Emphasis Type="Italic">X</Emphasis> = O,S, Se; <Emphasis Type="Italic">M</Emphasis> = Au,Ag, Cu) systems

With the help of quantum mechanical calculations, we have examined the series of central system X(ML)₃ ⁺(X = O, S, Se; M = Au, Ag, Cu). Using a scalar–relativistic density functional approach, we studied the geometry structures, Mulliken populations and charges of the systems. Structure parameters of the experimental systems are reproduced well with Xα method. The metallophilic interaction energy is analyzed and decomposed. For the systems with different central atoms and different metal atoms, the nature of the metallophilic attraction interaction is analyzed.     

Identification of mouse selenomethionine α, γ-elimination enzyme

The purpose of this study was to identify the seleno-l-methionine (l-SeMet) α,γ-elimination enzyme that catalyzes l-SeMet to generate methylselenol (CH₃SeH), a notable intermediate for the metabolism of selenium compounds, in mammalian tissues. The enzyme purified from ICR mouse liver was separated by one-dimensional gel electrophoresis, and the specific band was subjected to in-gel trypsin digestion followed by matrix-assisted laser desorption/ionization-time-of-flight mass spectrometric analysis. In the peptide mass fingerprinting search, the mass numbers of 14 peptides produced by tryptic digestion of the enzyme were consistent with the theoretical mass numbers calculated from the amino acid sequence of murine cystathionine γ-lyase (E.C. 4.4.1.1). The peptide sequence tags search was also performed to obtain the amino acid sequence data of five tryptic peptides. These peptides were significantly identical to the partial amino acid sequences of cystathionine γ-lyase. This enzyme was clearly shown to catalyze the α, γ-elimination reaction of l-cystathionine by the enzymological research. The K _m value for the catalysis of l-cystathionine was 0.81 mM and V _max was. 0.0013 unit/mg protein. These results suggested that cystathionine γ-lyase catalyzes l-SeMet to generate CH₃SeH by its α,γ-elimination reaction.     

Divergence of the F1-ATP Synthase Complex in the Ice Worm, Mesenchytraeus solifugus (Annelida, Clitellata, Enchytraeidae)

The F₁-ATP synthase complex constitutes the catalytic component of F₁F₀-ATP synthase, the primary ATP synthetic enzyme in the cell. Previous studies indicate that the glacier ice worm, Mesenchytraeus solifugus, maintains unusually high ATP levels that continue to rise as temperatures decline, suggesting that molecular changes within ice worm F₁-ATP synthase subunits may contribute to this energetic anomaly. In this report, we compared ice worm F₁-ATP synthase subunits (α, β, γ) with homologues across metazoan phyla (arthropod, chordate, nematode) and among a group of clitellate annelids (Enchytraeus albidus, Enchytraeus buchholzi, Lumbriculus variegatus, Theromyzon tessulatum). Amino acid alignments indicated that ice worm F₁-ATP α and F₁-ATP β subunits share strong sequence homology with their mesophilic counterparts, respectively, but that ATP γ has diverged more rapidly. Moreover, F₁-ATP α and F₁-ATP β displayed amino acid compositional changes consistent with trends observed in other cold adapted proteins, while F₁-ATP γ diverged in unexpected directions (e.g., gains in size, charged residues). Several ice worm-specific amino acid substitutions map to positions near the F₁-ATP β catalytic site while others occur near subunit contact sites.     

Structural and dynamical studies of all-trans and all-cis cyclo[(1R,3S)-γ-Acc-Gly]<Subscript>3</Subscript> peptides

The quantum chemical and molecular dynamics studies have been performed to infer the structural changes of all-trans and all-cis forms of cyclo[(1R,3S)-3-aminocyclohexanecarboxylicacid(γ-Acc)-α-Glycine(Gly)]₃ hexapeptide. The backbone conformations of the above peptide have been analyzed using the valence and peptide deformation angles applying B3LYP/6–311G** level of theory. The conformational preference of the backbone of all-trans and all-cis cyclo[(1R,3S)-γ-Acc-Gly]₃ hexapeptides is found to depend on the puckering of cyclohexane rings. The non-uniform distribution of water inside the cavity is observed, where sometimes water molecules formed a chain like conformation through hydrogen bond networks while traversing the pore of all-cis cyclo[(1R,3S)-γ-Acc-Gly]₃ peptide. Larger relaxation times of the order of a hundred to two hundred pico seconds for active site…water hydrogen bond interactions were noticed. The hydrophobic nature of the cavity of all-trans cyclo[(1R,3S)-γ-Acc-Gly]₃ due to the presence of cyclohexane moiety has been analyzed. Further this investigation emphasized on the non-transport of molecules through the pore of all-trans cyclo[(1R,3S)-γ-Acc-Gly]₃ peptide due to the obstruction produced by cyclohexane groups.     

Influences of cultural medium component on the production of poly(γ-glutamic acid) byBacillus sp. RKY3

In this study, the cultural medium used for the efficient production of γ-PGA with a newly isolatedBacillus sp. RKY3 was optimized. It was necessary to supplement the culture medium withl-glutamic acid and an additional carbon source in order to induce the effective production of γ-PGA. The amount of γ-PGA increased with the addition ofl-glutamic acid to the medium. The addition of 90 g/Ll-glutamic acid to the medium resulted in the maximal yield of γ-PGA (83.2 g/L). The optimum nitrogen source was determined to be peptone, but corn steep liquor, a cheap nutrient, was also found to be effective for γ-PGA production. Both the γ-PGA production and cell growth increased rapidly with the addition of small amounts of K₂HPO₄ and MgSO₄·7H₂O.Bacillus sp. RKY3 appears to require Mg²⁺, rather than Mn²⁺, for γ-PGA production, which is distinct from the production protocols associated with other, previously reported bacteria.Bacillus sp. RKY3 may also have contributed some minor γ-PGA depolymerase activity, resulting in the reduction of the molecular weight of the produced γ-PGA at the end of fermentation.     

Micropropagation of Ceratopetalum gummiferum, an important Australian cut flower corp

Summary Ceratopetalum gummiferum Sm. ‘Albery's Red’ (NSW Christmas Bush), a native to eastern Australia, has become an important commercial plant in both the export and domestic markets. A protocol for in vitro culture was investigated for rapid clonal propagation of selected cultivars. Murashige and Skoog medium, supplemented with various concentrations of 6-benzylaminopurine, kinetin, 6(γ,γ-dimethylallylamino)-purine or zeatin were examined for their effects on multiplication. The most successful treatments were 2.2 μM 6-benzylaminopurine and 11.6 μM kinetin which increased shoot number and explant weight. Although zeatin and 6(γ,γ-dimethylallylamino)-purine increased shoot length, both failed to increase multiplication rates. However, hyperhydricity was found to be a serious physiological disorder in tissue culture of C. gummiferum ‘Albery's Red’. Rooting in vitro was also examined with indole-3-butyric acid and naphthalene acetic acid, the most successful being 4.9 mM indole-3-butyric acid. The development of an in vivo rooting protocol, however, may prove to be essential for the commercial production of this plant.     

Using the water signal to detect invisible exchanging protons in the catalytic triad of a serine protease

Chemical Exchange Saturation Transfer (CEST) is an MRI approach that can indirectly detect exchange broadened protons that are invisible in traditional NMR spectra. We modified the CEST pulse sequence for use on high-resolution spectrometers and developed a quantitative approach for measuring exchange rates based upon CEST spectra. This new methodology was applied to the rapidly exchanging Hδ1 and Hε2 protons of His57 in the catalytic triad of bovine chymotrypsinogen-A (bCT-A). CEST enabled observation of Hε2 at neutral pH values, and also allowed measurement of solvent exchange rates for His57-Hδ1 and His57-Hε2 across a wide pH range (3–10). Hδ1 exchange was only dependent upon the charge state of the His57 (k _ex,Im+ = 470 s⁻¹, k _ex,Im = 50 s⁻¹), while Hε2 exchange was found to be catalyzed by hydroxide ion and phosphate base ( k_{\textOH ^-} k_{{{\text{OH}}^{ - } }}  = 1.7 × 10¹⁰ M⁻¹ s⁻¹, k_{\textHPO4^{2 -}} k_{{{\text{HPO}}_{4}^{2 - } }}  = 1.7 × 10⁶ M⁻¹ s⁻¹), reflecting its greater exposure to solute catalysts. Concomitant with the disappearance of the Hε2 signal as the pH was increased above its pK _a, was the appearance of a novel signal (δ = 12 ppm), which we assigned to Hγ of the nearby Ser195 nucleophile, that is hydrogen bonded to Nε2 of neutral His57. The chemical shift of Hγ is about 7 ppm downfield from a typical hydroxyl proton, suggesting a highly polarized O–Hγ bond. The significant alkoxide character of Oγ indicates that Ser195 is preactivated for nucleophilic attack before substrate binding. CEST should be generally useful for mechanistic investigations of many enzymes with labile protons involved in active site chemistry.     

Contributions to the theory of organismic sets: Leadership

The theory of organismic sets (Bull. Math. Biophysics,31, 159–189, 1969) is applied to the theory of leadership in human society. The ability of making decisions, required for leadership, is a product of the activities of the cells of the cerebral cortex, which are elements of the subsetS ₀₂ of the organismic set “man” (loc. cit.). Products of the activities of the elements of an organismic set do not need to be of a material nature. Such things as thoughts, feelings, attitudes, etc., are also products of the activitiesa ₁ of the elements. An individual can makeall necessary decisions for adaptation in a changing environment, when his subsetS ₀₂ contains as a proper subset a set {a ₁₂ ^′ ∼ ⊂S ₀₂ of activities. It is shown that such individuals are rare. If none exist, then the one who possesses a subset {a ₁₂ ^* ∼ ⊂ {a ₁₂ ^′ ∼ of higher cardinalityc _m than any other individual, will be the leader. The possibility is discussed that fromN individualsN′ 〈N possess subsets {a ₁₂ ^* ∼ ⊂ {a ₁₂ ^′ ∼ all of the same cardinalityc _m but differing in the type of their elements, thus resulting in several leaders. It is then discussed what determines which of theN −N′ individuals will choose a particular oneN′ individuals as leader. Cooperation and competition between leaders is discussed.     

Degradation of chlorinated hydrocarbons by Clostridium sp. isolated from lindane-amended,flooded soil

Summary A Clostridium sp., isolated from flooded soil amended with lindane (γ-BHC), decomposed methoxychlor, γ-BHC and heptachlor in that order under anaerobic condition. During the bacterial degradation of ring-labelled C¹⁴-γ-BHC, there was a net loss of radioactivity from the reaction mixture. Release of C¹⁴O₂ during the degradation of C¹⁴-γ-BHC was negligible. Methane was not detected as an end product of γ-BHC breakdown. re]19720406     

Concept of energy in biological systems

Beside the concept of material inputs and outputs of components of the representation of biological systems given to us by Rosen, the concept of energy is incorporated. The interaction of material and energy is represented by a cartesian product; and separate material and energetical mappings are considered as the new representation of components. These developments generate aMα category, and it is shown thatMα is isomorphic to theM category of previous developments.     

The representation of biological systems from the standpoint of the theory of categories

A mathematical framework for a rigorous theory of general systems is constructed, using the notions of the theory of Categories and Functors introduced by Eilenberg and MacLane (1945,Trans. Am. Math. Soc.,58, 231–94). A short discussion of the basic ideas is given, and their possible application to the theory of biological systems is discussed. On the basis of these considerations, a number of results are proved, including the possibility of selecting a unique representative (a “canonical form”) from a family of mathematical objects, all of which represent the same system. As an example, the representation of the neural net and the finite automaton is constructed in terms of our general theory.     

The smallest value of the axon density for which ‘ignition’ can occur in a random net

As shown by A. Rapoport (1952), when a very brief stimulation or “instantaneous input” is applied to a random net, the subsequent events are determined by the parameters of the net as follows: If the axon densitya is sufficiently large and the fraction γ of the neurons initially stimulated exceeds a certain value γ₁ (theover-all threshold of the net for instantaneous stimulation), excitation will spread through the net until a steady state is reached in which a fraction γ₂ ⩾ γ₁ of the neurons is firing (“ignition phenomenon”). If γ < γ₁ the activity in the net dies out. However, if the axon density is too small, the activity will ultimately die out, no matter how large the fraction of initially stimulated neurons. Thus there exists a limiting valueA of the axon density below which the net cannot “ignite”. ThisA is a function ofh, theindividual threshold of the neurons constituting the net (we assume hereh≥2, since forh=1 the situation is essentially different). Geometrically γ₁ and γ₂ are determined as the two intersection points of a straight line with a sigmoid curve. Whena<A the two curves do not intersect and fora=A they are tangent. In this paper the “tangency case” is investigated and the general features of the functionA(h) are determined. It is shown thatA increases monotonically withh (as one would expect). For all values ofh>1 we haveA(h)>h, but the fractionA(h)/h and the derivativedA(h)/dh approach unity ash increases. An analytical expression of the functionA(h) valid for very large values ofh is derived.