A trade-off relationship between energetic cost and entropic cost for in vitro evolution

In this paper, we consider two complementary cost functions for the landscape exploring processes to obtain the global optimum sequence through in vitro evolution protocol: one is the entropic cost C_etp, which is based on the deviation from the uniformity of a mutant distribution in sequence space, and the other is the energetic cost C_eng, which is based on the total number of sequences to be generated and evaluated. Based on a prior knowledge about the structure of a given fitness landscapes, the conductor of the experiment can think up the efficient search algorithm (ESA), which requires the minimum number of points (=sequences) to be searched up to the global optimum. For five typical fitness landscapes, we considered their respective (putative) ESA, and based on the ESA. As a result, we found a trade-off relationship between and for every case, that is, is approximately equal to the logarithm of the volume of the sequence space. and are interpreted in terms of the information-theoretic concepts.     

The R* rule and energy flux in a plant-nutrient ecosystem

The R* rule predicts that the species that can survive in steady state at the lowest level of limiting resource, R*, excludes all other species. Simple models indicate that this concept is not necessarily consistent with Lotka's conjecture that an ecological system should evolve towards a state of maximum power, Max(G), where G is the power, or rate of biomass production of the system. To explore the relationship in detail, we used a published model of a plant-nutrient system in which a plant can use various strategies, S, of allocation of energy between foliage, roots, and wood. We found that the allocation strategy, S_MinR*, that leads to , where is a limiting nutrient in soil pore water in our model (and equivalent to R* in Tilman's notation), is the same as the strategy, S_{MaxG_root}, for which energy flux to roots is maximized. However, that allocation strategy is different from the strategy, S_MaxG, that produces maximum power, or maximum photosynthetic rate, for the plant system, Max(G). Hence, we conclude that and Max(G) should not necessarily co-occur in an ecological system. We also examined which strategy, S_fit, was fittest; that is, eliminated any other strategies, when allowed to compete. The strategy S_fit differed from S_MinR*, S_MaxG, and S_{MaxG_root}, which we demonstrated mathematically. We also considered the feasible situation in which a plant is able to positively influence external nutrient input to the system. Under such conditions, the strategy, S_{MaxG_root}, that maximizes energy flux to roots was the same as the strategy, S_MaxR*, that leads to maximum concentration of available nutrient in soil pore water, , and not same as S_MinR*, for .     

The BK channel accessory β1 subunit determines alcohol-induced cerebrovascular constriction

Ethanol-induced inhibition of myocyte large conductance, calcium- and voltage-gated potassium (BK) current causes cerebrovascular constriction, yet the molecular targets mediating EtOH action remain unknown. Using BK channel-forming (cbv1) subunits from cerebral artery myocytes, we demonstrate that EtOH potentiates and inhibits current at lower and higher than ∼15 μM, respectively. By increasing cbv1’s apparent -sensitivity, accessory BK β₁ subunits shift the activation-to-inhibition crossover of EtOH action to <3 μM , with consequent inhibition of current under conditions found during myocyte contraction. Knocking-down KCNMB1 suppresses EtOH-reduction of arterial myocyte BK current and vessel diameter. Therefore, BK β₁ is the molecular effector of alcohol-induced BK current inhibition and cerebrovascular constriction.     

Trypanosoma cruzi: Immunological predictors of benznidazole efficacy during experimental infection

C3H/HeN male mice were infected with a lethal population of Trypanosoma cruzi and treated with benznidazole (Bz). Parasitemia, body weight and survival rate were registered during the therapy with significant improvement for T. cruzi-infected Bz-treated animals. Besides, flow cytometry resulted a useful method to discriminate between cured animals from those not cured by monitoring IgG₁ bound to live trypomastigotes levels. At the end of Bz therapy, the LT splenocyte compartment was studied for activation/memory cell surface markers ( and ). Cytofluorometric analysis showed that T. cruzi-infected untreated mice increased their activated LT numbers and this effect was completely abolished only in cured mice at the end of Bz administration. The same behavior was observed for the memory LT subpopulation correlating to an effector memory () displayed by T. cruzi infection. Bz treatment was able to modulate the immunological response by reducing the deleterious effect of the acute phase in all T. cruzi-infected mice.     

Jumping ability: A theoretical integrative approach

A theoretical integrative approach is proposed to understand the overall mechanical characteristics of lower extremities determining jumping ability. This approach considers that external force production during push-off is limited by mechanical constraints imposed by both movement dynamics and force generator properties, i.e. lower extremities characteristics. While the velocity of the body depends on the amount of external force produced over the push-off, the capabilities of force production decrease with increasing movement velocity, notably for force generators driven by muscular contraction, such as lower extremities of large animals during jumping from a resting position. Considering the circular interaction between these two mechanical constraints, and using simple mathematical and physical principles, the proposed approach leads to a mathematical expression of the maximal jump height an individual can reach as a function of only three integrative mechanical characteristics of his lower extremities: the maximal force they can produce (), the maximal velocity at which they can extend under muscles action () and the distance of force production determined by their usual extension range (h_PO). These three integrative variables positively influence maximal jump height. For instance in humans, a 10% variation in , or h_PO induces a change in jump height of about 10-15%, 6-11% and 4-8%, respectively. The proposed theoretical approach allowed to isolate the basic mechanical entities through which all physiological and morphological specificities influence jumping performance, and may be used to separate the very first macroscopic effects of these three mechanical characteristics on jumping performance variability.     

Theoretical investigation of the dissociative interchange (Id) mechanism for water exchange on magnesium(II) in aqueous solution

A dissociative (D) and a solvent-assisted dissociative interchange (I_d) water-exchange pathways for magnesium(II) in aqueous solution were simulated with density functional theory calculations. The D mechanism of includes a five-coordinated intermediate, while the I_d water-exchange pathway of proceeds with the assistance of a solvent water molecule, which supports the experimental assignment of the reaction mechanism. The intrinsic activation volume was used to differentiate between I_d and I_a mechanisms despite of the exclusion of the contribution of transmission coefficient. The calculated intrinsic activation volume for the I_d mechanism is consistent with the experimental data, and is closer to the experimental data than that for D mechanism. The I_d mechanism is suggested as the dominate water-exchange pathway of depending on the intrinsic activation volume with the assistance of the activation entropy. The calculations also showed that the influences of the explicit and bulk waters on energy barriers for D and I_d mechanisms are obviously different.     

New applications of ruthenium solar cell sensitizers N3 and N719 as luminescence turn-on anion sensors

Optical sensing of F⁻, Cl⁻, Br⁻, I⁻, OAc⁻, , , and by cis-dithiocyanatobis(2,2′-bipyridyl-4,4′-dicarboxylic acid)ruthenium(II) (N3) and bis(tetrabutylammonium) cis-dithiocyanatobis(2,2′-bipyridine-4-COOH,4′-COO⁻)ruthenium(II) (N719) have been investigated in dimethyl sulfoxide (DMSO), by means of UV-Vis absorption and emission spectrophotometric titrations. Additions of F⁻, OAc⁻, and in DMSO solution caused obvious UV-Vis spectral changes with appearance of several isosbestic points, and remarkable emission enhancements along with large blue shifts in emission bands. The values of F⁻-induced emission intensity enhancement factor (emission quantum yield enhancement factor), I/I₀ (φ/φ₀), were found to be 40 (86) and 38 (58) for N3 and N719, respectively. No obvious spectral changes were observed upon addition of Cl⁻, Br⁻, I⁻, and in DMSO solutions. Luminescent F⁻ sensing in DMSO/H₂O (4:1, v/v) has also been demonstrated to be operative with a luminescence enhancement factor of 12, indicating that N3 is very potential for practical application as fluorescent anion sensor in aqueous solution. An interaction mechanism of anion-induced deprotonation of N3 and N719 was confirmed, and the deprotonation reaction equilibrium constants of N3 and N719 were derived as well.     

Density-functional analysis of the electronic structure of tris-bipyridyl Ru(II) sensitisers

Excited state transitions and energies of a series of [Ru(bpy)₃]²⁺ type complexes incorporating the ligand, 4,4′-bis-phosphonato(methyl)-2,2′-bipyridine (dmpbpy) was investigated, and the influence of this organometallic ligand on the electronic structure of the complexes was examined using Time-Dependent Density Functional Theory (TD-DFT). Experimental data and the theoretical TD-DFT calculations were presented to support the effect of non-equivalent ligand substitution on spectral and molecular orbital (MO) energy properties on this class of tris-chelate surface sensitisers. For the series of complexes studied, it was identified that the lowest lying LUMO states were consistently found to reside on the ligand 2,2′-bipyridine (bpy) for gas phase calculations. As an implication of this, it was suggested that this could impact the effectiveness of these complexes as surface sensitisers in PEC cell applications such as the dye-sensitised solar cell (DSC) due to the lower probability of the excited state electron residing on a ligand anchored to the semiconductor substrate. However, further calculations in a solvation medium showed that the electron withdrawing nature of PO₃H₂ on dmpbpy saw the lowest lying LUMO states are populated on dmpbpy. This inhomogeneous distribution of electron density across non-equivalent ligands may have implications for further ‘spectral tuning’ of surface sensitisers. Despite the TD-DFT gas phase calculations not being corrected for solvent/media effects, the three longest wavelength bands associated with known charge transfer phenomena were identified. The symmetry allowed _MLCT in the visible region was assigned as a  ← dπ transition, the mid-UV spectrum _LC was assigned  ← π in origin. Whilst the near-UV shoulder on the blue side of _MLCT showed dσ ← dπ and π∗ ← dπ transitional character and was tentatively described as _MC/MLCT. UV-Vis absorption spectra calculated for solvated analogues containing dmpbpy indicated that the low energy transitions associated with the MLCT are subject to bathochromic shift due to solvent polarity by 0.062 eV (500 cm⁻¹) compared with the gas phase calculations, which is more highly correlated to the observed experimental transitions.     

Synthesis and characterization of a family of binuclear non-heme iron monooxygenase model compounds: Evidence for a “phenolate/amide carbonyl (PAC) shift” upon oxidation

A series of binuclear iron compounds has been synthesized using diamide, bis-phenolate ligands in which the carbon-linker between the amide nitrogen atoms has been varied. Two diferrous compounds in the series, along with their two-electron oxidized, di-μ-methoxy-bridged counterparts, have been crystallographically characterized, as have the di-μ-methoxy compounds (H₂Hbab = 1,2-bis(2-hydroxybenzamido) benzene, H₂Hbach = trans-1,2-bis(2-hydroxybenzamido) cyclohexane, H₂Hbame = 1,2-bis(2-hydroxybenzamido) ethane, H₂Hbap = 1,3-bis(2-hydroxybenzamido) propane, H₂Hbabn = 1,4-bis(2-hydroxybenzamido) butane, H₂Hbapen = 1,5-bis(2-hydroxybenzamido) pentane, N-MeIM = N-methylimidazole and OMe = methoxide). are structurally very similar to previously reported diferrous compounds of this family of ligands that have been shown to be active as oxygen atom transfer catalysts. Flexibility in the carbon-linker allows some variability in the orientation of the phenolate arms of the ligands in the diferric di-μ-methoxy compounds, but the Fe₂O₂ core remains largely unchanged across the series. Two-electron oxidation of the ferrous compounds in methanol shows a substantial ligand rearrangement that is consistent with other spectroscopic, electrochemical and kinetic investigations. The loss of both phenolate bridges upon oxidation is reminiscent of the “carboxylate shift” observed in binuclear non-heme enzymes and could provide insight into the driving force behind this family of compounds’ function as a catalyst.     

Dinuclear gold(III) pyrazolato complexes - Synthesis, structural characterization and transformation to their trinuclear gold(I) and gold(I/III) analogues

The reaction of AuCl₃py with Na(pz∗) (pz∗ = pyrazolato, or substituted pyrazolato anion) yields stable dinuclear [cis-Au^IIICl₂(μ-pz∗)]₂ complexes. In the presence of a base, the latter undergo reduction with concomitant transformation of the dinuclear -structure to trinuclear Au^I, Au^III (containing trans Au^IIICl₂-centres) and species.     

NAD(P)H- and superoxide-dependent nitric oxide degradation by rat liver mitochondria

Mitochondria consume nitric oxide (NO) mainly through reaction with superoxide anion (). Here, we analyzed the sources for NO degradation by isolated rat liver mitochondria. Electron leakage from complex III and reverse electron transport to complex I accounted for -dependent NO degradation by mitochondria in the presence of a protonmotive force. Mitochondria incubated with NAD(P)H also presented intense generation and NO degradation rates that were insensitive to respiratory inhibitors and abolished after proteinase treatment. These results suggest that an outer membrane-localized NAD(P)H oxidase activity, in addition to the electron leakage from the respiratory chain, promotes -dependent NO degradation in rat liver mitochondria.     

Alkyl dehydrogenation in iridium tri-cyclopentyl phosphines

The iridium cyclooctadiene complex incorporating a tricyclopentyl phosphine ligand (PCyp₃), Ir(η²:η²-C₈H₁₂)(PCyp₃)Cl, has been prepared. Removal of the chloride from this complex using in CH₂Cl₂/arene solvent results in dehydrogenation (C-H activation followed by β-H transfer) of one of the alkyl phosphine rings and formation of the complexes (X = H, F) which contain a hybrid phosphine-alkene ligand. These complexes are formed alongside another product (5-20% yield) that has been identified as , which can be prepared in high yield by an alternative, and slightly modified, route. This complex is with a minor isomer that has been tentatively identified as , which results from allylic C-H activation of cyclooctadiene. Addition of H₂ to and its isomer in arene solvent (C₆H₅X, X = F, H) forms the dihydrido η⁶-arene Ir(III) complexes . In contrast, hydrogenation in CH₂Cl₂ alone results in the formation of in which the anion is now acting as a ligand through one of its aryl rings. The fluorobenzene complex can be cleanly converted to by addition of the hydrogen acceptor tert-butylethene (tbe).     

Synthesis, structure and magnetic characterization of decamethylmetallocenium ethyl tricyanoethylenecarboxylate charge-transfer salts

Ethyl tricyanoethylenecarboxylate (ETCE) is a one-electron acceptor related to tetracyanoethylene that can serve as a building block for the construction of molecule-based magnets. The reactions of ETCE with decamethylmetallocenes, (M = Cr, Mn, Fe) give three new charge-transfer salt magnets, [ETCE] 1, [ETCE] 2 and [ETCE] 3. The expected mixed pi stacking of anions and cations is obtained, with the ETCE radical anion exhibiting typical disorder over two nearly equivalent footprints. Powder diffraction supports the belief that all three compounds are isomorphous. Magnetic measurements indicate that 1 is a soft ferromagnet, ordering below a critical temperature, T_c, of 3.8 K. Compound 2 exhibits complex magnetic behavior consisting of two frequency-dependent peaks in the ac susceptibility, the first at about 11.2 K and the second at about 7 K. At 1.8 K, the compound is hysteretic and exhibits a coercive field of 10 kG. Compound 3 is a glassy, apparently canted, ferromagnet displaying an out-of-phase ac susceptibility signal below about 3 K.     

Light and nutrient availability affect the size-scaling of growth in phytoplankton

Communities of marine phytoplankton consist of cells of many different sizes. The size-structure of these communities often varies predictably with environmental conditions in aquatic systems. It has been hypothesized that physiological differences in nutrient and light requirements and acquisition efficiencies contribute to commonly observed correlations between phytoplankton community size structure and resource availability. Using physiological models we assess how light and nutrient availability can alter the relative growth rates of phytoplankton species of different cell sizes. Our models predict a change in the size dependence of growth rate depending on the severity of limitation by light and nutrient availability. Under conditions of growth-saturated resource supply, phytoplankton growth rate (mol C ) scales with cell volume with a size-scaling exponent of ; light limitation reduces the size-scaling exponent to approximately , and nutrient limitation decreases the exponent to as a consequence of the size-scaling of resource acquisition. Exponents intermediate between and occur under intermediate availability of light and nutrients and depend on the size-scaling of pigment photoacclimation and the size range examined.     

On invariant property in population statistics

Concept of aging is developed to yield a relationship between life spans and the velocity of aging. The mathematical analysis shows that the mean extent of the advancement of aging throughout one’s life is conserved, or equivalently, the product of the mean life span, T, and the mean rate of aging, , is constant, . The result is in harmony with our experiences: it accounts for the unlimited replicability of tumor cells, and predicts the prolonged life spans of hibernating hamsters according to the equation, (T_χ=0 is a constant and χ denotes the total fraction of hibernation periods), in accordance with the Lyman and co-workers experiment. Comparing the present result and the empirical relationship between life spans of various mammals and basal metabolic rates, it is suggested that the mean rate of aging is intimately connected with the mean basal metabolic rate. With the help of this information, we inquire the reason of the difference in mean life spans between women and men, the result showing that the relative mean life span of women to men is T_women/T_men ≅ 1.08 for various nations, which is close to the corresponding relative value of the basal metabolic rate. The present analysis suggests, however, that this relationship between life spans and basal metabolic rates must be treated with caution.     

Brief exposure to carbon monoxide preconditions cardiomyogenic cells against apoptosis in ischemia-reperfusion

We examined whether and how pretreatment with carbon monoxide (CO) prevents apoptosis of cardioblastic H9c2 cells in ischemia-reperfusion. Reperfusion (6 h) following brief ischemia (10 min) induced cytochrome c release, activation of caspase-9 and caspase-3, and apoptotic nuclear condensation. Brief CO pretreatment (10 min) or a caspase-9 inhibitor (Z-LEHD-FMK) attenuated these apoptotic changes. Ischemia-reperfusion increased phosphorylation of Akt at Ser472/473/474, and this was enhanced by CO pretreatment. A specific Akt inhibitor (API-2) blunted the anti-apoptotic effects of CO in reperfusion. In normoxic cells, CO enhanced generation, which was inhibited by a mitochondrial complex III inhibitor (antimycin A) but not by a NADH oxidase inhibitor (apocynin). The CO-enhanced Akt phosphorylation was suppressed by an scavenger (Tiron), catalase or a superoxide dismutase (SOD) inhibitor (DETC). These results suggest that CO pretreatment induces mitochondrial generation of , which is then converted by SOD to H₂O₂, and subsequent Akt activation by H₂O₂ attenuates apoptosis in ischemia-reperfusion.     

Photocatalysis of chloroform degradation by μ-dichlorotetrachlorodipalladate(II)

Unlike other chlorometallate complexes that catalyze the photodecomposition of haloalkanes through photodissociation of a chlorine atom, both and catalyze chloroform decomposition through a process that appears to involve C-H bond breakage from an excited state association complex with chloroform. This would account for the greatly retarded rate of decomposition in CDCl₃ and for the generation of CCl₄ as a side product. In chloroform, and are in slow equilibrium with each other. The rate for the conversion of - in chloroform at 23 °C obeys the expression (0.03 M⁻¹ s⁻¹) [][Cl⁻]. The equilibrium constant, K = [][Cl⁻]²/[]², was estimated to be 3 × 10⁻³ M in CHCl₃.     

In situ spectroelectrochemical investigation of Pt(II/IV) oxidation in aqueous solution using X-ray absorption spectroscopy

The oxidation from to in HCl aq. was studied in situ by combining electrochemistry with XAFS spectroscopy. During the oxidation of , isosbestic points were observed in Pt L_III and L_II XANES spectra as a function of time, indicating that the Pt(II/IV) redox equilibrium is the only reaction in the system. The Pt L_III and L_II X-ray absorption edge energies of the initial Pt^IICl₄²⁻ are 11562.9 and 13271.8 eV, respectively, while those of the electrolyzed species are 11564.6 and 13273.7 eV which are identical with those of a reference sample. The coordination of the electrolyzed species was characterized by structural parameters derived from the EXAFS curve fit, and identified to .