Characteristics of the response of animals of different typological groups to the action of electromagnetic irradiation in the high and superhigh frequency ranges

Peculiarities in the response of male rats of various typological (e.g. high- and low-entropy) groups to the effect of electromagnetic radiation of high and superhigh frequencies have been investigated. Radiation intensity was 500 microW/cm2 and 500 V/m respectively. Animals of different entropy groups exhibited variations in the radiation response of their CNS and endocrine system as well as in the state of their offspring during the antenatal development.     

The backbone conformational entropy of protein folding: experimental measures from atomic force microscopy

The energy dissipated during the atomic force microscopy-based mechanical unfolding and extension of proteins is typically an order of magnitude greater than their folding free energy. The vast majority of the "excess" energy dissipated is thought to arise due to backbone conformational entropy losses as the solvated, random-coil unfolded state is stretched into an extended, low-entropy conformation. We have investigated this hypothesis in light of recent measurements of the energy dissipated during the mechanical unfolding of "polyproteins" comprised of multiple, homogeneous domains. Given the assumption that backbone conformational entropy losses account for the vast majority of the energy dissipated (an assumption supported by numerous lines of experimental evidence), we estimate that approximately 19(+/-2)J/(mol K residue) of entropy is lost during the extension of three mechanically stable beta-sheet polyproteins. If, as suggested by measured peak-to-peak extension distances, pulling proceeds to near completion, this estimate corresponds to the absolute backbone conformational entropy of the unfolded state. As such, it is exceedingly close to previous theoretical and semi-empirical estimates that place this value at approximately 20J/(mol K residue). The estimated backbone conformational entropy lost during the extension of two helical polyproteins, which, in contrast to the mechanically stable beta-sheet polyproteins, rupture at very low applied forces, is three- to sixfold less. Either previous estimates of the backbone conformational entropy are significantly in error, or the reduced mechanical strength of the helical proteins leads to the rupture of a subsequent domain before full extension (and thus complete entropy loss) is achieved.     

The strategy of ecosystem development: specific dissipation as an indicator of ecosystem maturity

The ratio of entropy generation rate to entropy embodied in structures relatively to the surroundings can be considered as an indicator of the ability of a self-organizing dissipative system to maintain itself far from equilibrium by pumping out entropy. The higher the ratio (which may be called the specific entropy production or the specific dissipation of a system), the lower the capacity of a system to convert the incoming low-entropy energy into internal organization. It appears that the ratio attains special significance for interpreting the evolution of biological systems, as the maximum expression of self-organizing systems, from the sub-cellular to the ecosystem scale. This paper proposes specific dissipation, written as the ratio of biological entropy production to exergy stored in the living biomass, as a thermodynamic orientor as well as an indicator of the development state of ecological systems. After having presented a method for estimating the specific dissipation in lakes, the adequacy of the proposed indicator is discussed and also tested by comparing its response to those of some classical ecological attributes (successional sequences of species, biodiversity, individual body size, structural organization and generation time of organisms) throughout the seasonal progression of the plankton community in Lake Trasimeno (Umbria, Italy). The results support the hypothesis that the minimization of specific dissipation is a primary criterion of evolution of ecological systems and also sustain the use of specific dissipation as an indicator of ecological maturity.     

Photosynthesis and negative entropy production

The widely held view that the maximum efficiency of a photosynthetic pigment system is given by the Carnot cycle expression (1-T/Tr) for energy transfer from a hot bath (radiation at temperature Tr) to a cold bath (pigment system at temperature T) is critically examined and demonstrated to be inaccurate when the entropy changes associated with the microscopic process of photon absorption and photochemistry at the level of single photosystems are considered. This is because entropy losses due to excited state generation and relaxation are extremely small (DeltaS < T/Tr) and are essentially associated with the absorption-fluorescence Stokes shift. Total entropy changes associated with primary photochemistry for single photosystems are shown to depend critically on the thermodynamic efficiency of the process. This principle is applied to the case of primary photochemistry of the isolated core of higher plant photosystem I and photosystem II, which are demonstrated to have maximal thermodynamic efficiencies of xi > 0.98 and xi > 0.92 respectively, and which, in principle, function with negative entropy production. It is demonstrated that for the case of xi > (1-T/Tr) entropy production is always negative and only becomes positive when xi < (1-T/Tr).     

Radiation entropy and its role in the process of photosynthesis

The paper deals with the following problems: 1) radiation entropy and the value of maximum performance coefficient of photosynthesizing systems eta m; 2) problem of physical meaning of eta m and on its association with real processes in photosynthesis. It has been shown that for calculating entropy of nonequilibrium radiation its origin should be known and that the value eta m does not practically limit the processes which proceed in photosynthesis.     

Conformational Entropy of the RNA Phosphate Backbone and Its Contribution to the Folding Free Energy

While major contributors to the free energy of RNA tertiary structures such as basepairing, base-stacking, and charge and counterion interactions have been studied extensively, little is known about the intrinsic free energy of the backbone. To assess the magnitude of the entropic strains along the phosphate backbone and their impact on the folding free energy, we have formulated a mathematical treatment for computing the volume of the main-chain torsion-angle conformation space between every pair of nucleobases along any sequence to compute the corresponding backbone entropy. To validate this method, we have compared the computed conformational entropies against a statistical free energy analysis of structures in the crystallographic database from several-thousand backbone conformations between nearest-neighbor nucleobases as well as against extensive computer simulations. Using this calculation, we analyzed the backbone entropy of several ribozymes and riboswitches and found that their entropic strains are highly localized along their sequences. The total entropic penalty due to steric congestions in the backbone for the native fold can be as high as 2.4 cal/K/mol per nucleotide for these medium and large RNAs, producing a contribution to the overall free energy of up to 0.72 kcal/mol per nucleotide. For these RNAs, we found that low-entropy high-strain residues are predominantly located at loops with tight turns and at tertiary interaction platforms with unusual structural motifs.     

Conformational Entropy of the RNA Phosphate Backbone and Its Contribution to the Folding Free Energy

While major contributors to the free energy of RNA tertiary structures such as basepairing, base-stacking, and charge and counterion interactions have been studied extensively, little is known about the intrinsic free energy of the backbone. To assess the magnitude of the entropic strains along the phosphate backbone and their impact on the folding free energy, we have formulated a mathematical treatment for computing the volume of the main-chain torsion-angle conformation space between every pair of nucleobases along any sequence to compute the corresponding backbone entropy. To validate this method, we have compared the computed conformational entropies against a statistical free energy analysis of structures in the crystallographic database from several-thousand backbone conformations between nearest-neighbor nucleobases as well as against extensive computer simulations. Using this calculation, we analyzed the backbone entropy of several ribozymes and riboswitches and found that their entropic strains are highly localized along their sequences. The total entropic penalty due to steric congestions in the backbone for the native fold can be as high as 2.4 cal/K/mol per nucleotide for these medium and large RNAs, producing a contribution to the overall free energy of up to 0.72 kcal/mol per nucleotide. For these RNAs, we found that low-entropy high-strain residues are predominantly located at loops with tight turns and at tertiary interaction platforms with unusual structural motifs.     

Statistical Mechanics of the Human Placenta: A Stationary State of a Near-Equilibrium System in a Linear Regime

All near-equilibrium systems under linear regime evolve to stationary states in which there is constant entropy production rate. In an open chemical system that exchanges matter and energy with the exterior, we can identify both the energy and entropy flows associated with the exchange of matter and energy. This can be achieved by applying statistical mechanics (SM), which links the microscopic properties of a system to its bulk properties. In the case of contractile tissues such as human placenta, Huxley’s equations offer a phenomenological formalism for applying SM. SM was investigated in human placental stem villi (PSV) (n = 40). PSV were stimulated by means of KCl exposure (n = 20) and tetanic electrical stimulation (n = 20). This made it possible to determine statistical entropy (S), internal energy (E), affinity (A), thermodynamic force (A / T) (T: temperature), thermodynamic flow (v) and entropy production rate (A / T x v). We found that PSV operated near equilibrium, i.e., A ≺≺ 2500 J/mol and in a stationary linear regime, i.e., (A / T) varied linearly with v. As v was dramatically low, entropy production rate which quantified irreversibility of chemical processes appeared to be the lowest ever observed in any contractile system.     

In vivo studies of gross photosynthesis in attached leaves by means of photothermal radiometry

In photothermal radiometry, heat radiation from an illuminated object, in synchronism with incident chopped light, is observed using an infrared detector with suitable electronics. By thus measuring the heat released during pulse-wise irradiation of leaves, conclusions can be drawn as to the gross efficiency of photosynthesis: More heat means less photochemically stored energy. Saturation of photosynthesis, by employing additional strong continuous-wave background light, affords an internal photothermal radiometry signal reference corresponding to the photochemical zero efficiency level, against which the signal in the absence of saturation can be compared. Through such means, gross energy storage efficiencies approaching 30% have been observed in Caragana arborescens Lam. at low light intensities. Several other examples are given, including measurements on dark-adapted leaves and leaves infiltrated with 3-(3,4-dichlorophenyl)-1,1-dimethylurea, to support our conclusion that photothermal radiometry provides a powerful new method for in vivo studies of photosynthesis in whole, attached leaves.     

p-Toluenesulfonyldiazoacetates: Reagents for photoaffinity labeling

p-Toluenesulfonyldiazoacetyl chloride and p-nitrophenyl p-toluenesulfonyldiazoacetate have been prepared and offer potential advantages as reagents for photoaffinity labeling. (i) The extinction coefficient for the sulfonyldiazo compounds at 370 nm is about 10 times that for the long wavelength absorption of other diazoesters; this absorption permits reasonably rapid photolysis in the presence of compounds that are destroyed by short wavelength uv radiation. (ii) The two derivatives named above are stable thermally; furthermore, since sulfonyldiazoesters are stable to acid and to weak base, photoaffinity labeling can be conducted over a wide range of pH. (iii) Photolysis of ordinary (i.e., oxygen) esters of sulfonyldiazo compounds in methanol or cyclohexane leads to insertion into the solvent to the exclusion of Wolff rearrangement; photolysis of thioesters at 350 nm in methanol gives about 25% insertion into solvent, accompanied by about 75% Wolff rearrangement; in contrast, photolysis of most thioesters of diazo derivatives leads exclusively to Wolff rearrangement     

用光合-蒸散耦合模型模拟冬小麦CO2通量的日变化

根据SPAC理论建立了一个冬小麦光合和蒸散的耦合模型.冬小麦CO2通量包括冠层光合、呼吸和土壤呼吸.冠层光合采用了Farquhar光合作用生化模型,并通过冠层阻力的参数化将光合作用与蒸腾作用耦合起来.用涡度相关方法观测了CO2通量,对模型进行了验证,结果显示模型可以较好地模拟CO2通量日变化过程.对模型的敏感性分析发现日间CO2通量最敏感的参数是初始量子效率.其次,CO2通量对光响应曲线凸度、CO2补偿点、凋萎点和叶面积指数的变化也有着较强的敏感性;夜间CO2通量敏感的参数是最适温度下Rubisco催化能力和暗呼吸参数.     

Surface photochemistry of the herbicide napropamide. The role of the media and environmental factors in directing the fates of intermediates.

The photochemical behaviour of the herbicide napropamide is studied on cellulose and silica surfaces, using steady-state and laser-flash diffuse reflectance techniques. The results are used to probe how the reaction sites of the host matrices influence the photo-reactive pathways. Napropamide undergoes reaction when irradiated with UV (lamps) or visible (sunlight) radiation on both solid supports. The nature of the intermediates and final products depend strongly on the presence or absence of molecular oxygen. The triplet state of napropamide adsorbed on cellulose is detected by both time-resolved luminescence and transient absorption spectroscopies. The triplet sate was not observed on silica, but transients which include the participation of molecular oxygen are detected during flash photolysis studies. The keto intermediates of the photo-Claisen rearrangement products are observed on both solids. Substituted 1-naphthols from photo-Claisen reactions and 1-naphthol are among the main reaction products. 1,4-Naphthoquinone is a major photoproduct in the presence of molecular oxygen and is expected to be prevalent when napropamide undergoes photodegradation in the environment (i.e., after being applied to plants and fields).     

Thermal dissipation during photosynthetic induction and subsequent dark recovery as measured by photoacoustic signals

The thermal photoacoustic signal (279 Hz) and the chlorophyll (Chl) fluorescence of radish cotyledons (Raphanus sativus L.) were measured simultaneously. The signals were recorded during a photosynthetic induction with actinic radiation of different quantum fluence rates [20, 200, and 1200 μmol(PAR-quantum) m^-2 s^-1]. The rise of these signals upon irradiation saturating photosynthesis was followed in the steady state of the induction and during the subsequent dark-recovery (i.e., in dark periods of 1, 5, 15, and 45 min after the induction). From these values various parameters (e.g., quantum yield, photochemical loss, different types of quenching coefficients) were calculated. The results show that heat dissipation detected by photoacoustic measurements is neither low, constant, nor always parallel to Chl fluorescence. Therefore, the thermal signal should always be measured in order to fully understand the way leaves convert energy taken up by PAR absorption. This helps in the interpretation of photosynthesis under different natural and anthropogenic conditions (stress and damage effects). This revised version was published online in September 2006 with corrections to the Cover Date.     

用光合-蒸散耦合模型模拟冬小麦CO2通量的日变化

根据 SPAC理论建立了一个冬小麦光合和蒸散的耦合模型。冬小麦 CO2 通量包括冠层光合、呼吸和土壤呼吸。冠层光合采用了 Farquhar光合作用生化模型 ,并通过冠层阻力的参数化将光合作用与蒸腾作用耦合起来。用涡度相关方法观测了 CO2通量 ,对模型进行了验证 ,结果显示模型可以较好地模拟 CO2 通量日变化过程。对模型的敏感性分析发现日间 CO2 通量最敏感的参数是初始量子效率。其次 ,CO2 通量对光响应曲线凸度、CO2 补偿点、凋萎点和叶面积指数的变化也有着较强的敏感性 ;夜间 CO2 通量敏感的参数是最适温度下 Rubisco催化能力和暗呼吸参数     

Minimum entropy production in photosynthesis

In this paper a flux-coupling model of photosynthesis is presented. By requiring minimum entropy production, it is found that the photosynthetic efficiency is essentially given by the square root of D/λ. D and λ are the diffusion coefficient and thermal conductivity of the rate-limiting processes in the chloroplast, respectively. For experimental values of D and λ, the efficiency is found to be 2.4–7.5%, with a likely value of 6.1%, whereas C4-plants are known to have an efficiency of 6.2%. We conclude that the process of photosynthesis is in quantitative agreement with the principle of minimum entropy production.     

Is a constant low-entropy process at the root of glycolytic oscillations?

We measured temporal oscillations in thermodynamic variables such as temperature, heat flux, and cellular volume in suspensions of non-dividing yeast cells which exhibit temporal glycolytic oscillations. Oscillations in these variables have the same frequency as oscillations in the activity of intracellular metabolites, suggesting strong coupling between them. These results can be interpreted in light of a recently proposed theoretical formalism in which isentropic thermodynamic systems can display coupled oscillations in all extensive and intensive variables, reminiscent of adiabatic waves. This interpretation suggests that oscillations may be a consequence of the requirement of living cells for a constant low-entropy state while simultaneously performing biochemical transformations, i.e., remaining metabolically active. This hypothesis, which is in line with the view of the cellular interior as a highly structured and near equilibrium system where energy inputs can be low and sustain regular oscillatory regimes, calls into question the notion that metabolic processes are essentially dissipative.     

The cost of photoinhibition

Photoinhibition is an inevitable consequence of oxygenic photosynthesis. However, the concept of a 'photoinhibition-proof' plant in which photosystem II (PSII) is immune to photodamage is useful as a benchmark for considering the performances of plants with varying mixes of mechanisms which limit the extent of photodamage and which repair photodamage. Some photodamage is bound to occur, and the energy costs of repair are the direct costs of repair plus the photosynthesis foregone during repair. One mechanism permitting partial avoidance of photodamage is restriction of the number of photons incident on the photosynthetic apparatus per unit time, achieved by phototactic movement of motile algae to places with lower incident photosynthetically active radiation (PAR), by phototactic movement of plastids within cells to positions that minimize the incident PAR and by photonastic relative movements of parts of photolithotrophs attached to a substrate. The other means of avoiding photodamage is dissipating excitation of photosynthetic pigments including state transitions, non-photochemical quenching by one of the xanthophyll cycles or some other process and photochemical quenching by increased electron flow through PSII involving CO? and other acceptors, including the engagement of additional electron transport pathways. These mechanisms inevitably have the potential to decrease the rate of growth. As well as the decreased photosynthetic rates as a result of photodamage and the restrictions on photosynthesis imposed by the repair, avoidance, quenching and scavenging mechanisms, there are also additional energy, nitrogen and phosphorus costs of producing and operating repair, avoidance, quenching and scavenging mechanisms. A comparison is also made between the costs of photoinhibition and those of other plant functions impeded by the occurrence of oxygenic photosynthesis, i.e. the competitive inhibition of the carboxylase activity of ribulose bisphosphate carboxylase-oxygenase by oxygen via the oxygenase activity, and oxygen damage to nitrogenase in diazotrophic organisms.     

Evolution of proton pumping ATPases: Rooting the tree of life

Proton pumping ATPases are found in all groups of present day organisms. The F-ATPases of eubacteria, mitochondria and chloroplasts also function as ATP synthases, i.e., they catalyze the final step that transforms the energy available from reduction/oxidation reactions (e.g., in photosynthesis) into ATP, the usual energy currency of modern cells. The primary structure of these ATPases/ATP synthases was found to be much more conserved between different groups of bacteria than other parts of the photosynthetic machinery, e.g., reaction center proteins and redox carrier complexes.These F-ATPases and the vacuolar type ATPase, which is found on many of the endomembranes of eukaryotic cells, were shown to be homologous to each other; i.e., these two groups of ATPases evolved from the same enzyme present in the common ancestor. (The term eubacteria is used here to denote the phylogenetic group containing all bacteria except the archaebacteria.) Sequences obtained for the plasmamembrane ATPase of various archaebacteria revealed that this ATPase is much more similar to the eukaryotic than to the eubacterial counterpart. The eukaryotic cell of higher organisms evolved from a symbiosis between eubacteria (that evolved into mitochondria and chloroplasts) and a host organism. Using the vacuolar type ATPase as a molecular marker for the cytoplasmic component of the eukaryotic cell reveals that this host organism was a close relative of the archaebacteria.A unique feature of the evolution of the ATPases is the presence of a non-catalytic subunit that is paralogous to the catalytic subunit, i.e., the two types of subunits evolved from a common ancestral gene. Since the gene duplication that gave rise to these two types of subunits had already occurred in the last common ancestor of all living organisms, this non-catalytic subunit can be used to root the tree of life by means of an outgroup; that is, the location of the last common ancestor of the major domains of living organisms (archaebacteria, eubacteria and eukaryotes) can be located in the tree of life without assuming constant or equal rates of change in the different branches.A correlation between structure and function of ATPases has been established for present day organisms. Implications resulting from this correlation for biochemical pathways, especially photosynthesis, that were operative in the last common ancestor and preceding life forms are discussed.     

Photolysis of total histone and pBr-322 plasmid DNA in the ultraviolet vacuum region of the spectrum

The action of VUV and far UV (lambda greater than 240 nm) radiation of aqueous solutions of total histone by means of electrophoresis method is compared. By VUV photolysis the more effective destruction of HI and HIA histone fractions is determined. It may be explained by interaction of total histone with water radicals (H, OH) formed by VUV photodissociation (indirect mechanism). By VUV irradiation of plasmid pBR-322 DNA in aqueous solutions the indirect action mechanism of single strand breaks in DNA is established.     

Asymmetric Photolysis with Elliptically Polarized Light

Previous investigations have shown the efficacyof right-(RCPL) and left-(LCPL) circularly polarized light inpromoting the asymmetric photolysis of racemic organic substratesand producing measurable enantiomeric excesses (e.e.s) whenphotolysis is incomplete. Synchrotron radiation, polychromaticand having out-of-plane components which are elliptically andultimately circularly polarized, has been suggested as auniversal source of RCPL and LCPL on a cosmic scale. The moreprevalent right-(REPL) and left-(LEPL) elliptically polarizedcomponents have never been investigated for similar capabilities.The present study, using a 212.8 nm laser beam to mimic thesynchtrotron radiation, explores the potential of REPL and LEPLin this context and finds a qualitative trend indicating thateach induces asymmetric photolysis in the same sense as RCPL andLCPL, but to a lesser degree.