Soil moisture variability on a steep slope near a ridge in a forested mountain range, Shikoku, Japan: a model study

Variability in soil moisture on a steep slope near a ridge in a forested mountain range, Shikoku, Japan, was studied observationally and numerically. Vertically integrated soil moisture, from a depth of ?60 cm to the surface, W, was introduced as a key indicator, and its seasonal variation was analysed on a daily basis from August 2011 to August 2012. The “bucket with a bottom hole” (BBH) model of Teshima et al. (2006) was improved to consider the forest environment in simulating the variation in W. A “big-leaf” model was incorporated into the modified BBH model to estimate transpiration and interception by trees. The simulated soil moisture agreed reasonably with observed values on a daily to inter-seasonal timescale.     

The analysis of disease biomarker data using a mixed hidden Markov model (Open Access publication)

A mixed hidden Markov model (HMM) was developed for predicting breeding values of a biomarker (here, somatic cell score) and the individual probabilities of health and disease (here, mastitis) based upon the measurements of the biomarker. At a first level, the unobserved disease process (Markov model) was introduced and at a second level, the measurement process was modeled, making the link between the unobserved disease states and the observed biomarker values. This hierarchical formulation allows joint estimation of the parameters of both processes. The flexibility of this approach is illustrated on the simulated data. Firstly, lactation curves for the biomarker were generated based upon published parameters (mean, variance, and probabilities of infection) for cows with known clinical conditions (health or mastitis due to Escherichia coli or Staphylococcus aureus). Next, estimation of the parameters was performed via Gibbs sampling, assuming the health status was unknown. Results from the simulations and mathematics show that the mixed HMM is appropriate to estimate the quantities of interest although the accuracy of the estimates is moderate when the prevalence of the disease is low. The paper ends with some indications for further developments of the methodology.     

Possible roles of two quinone molecules in direct and indirect proton pumps of bovine heart NADH-quinone oxidoreductase (complex I)

In many energy transducing systems which couple electron and proton transport, for example, bacterial photosynthetic reaction center, cytochrome bc₁-complex (complex III) and E. coli quinol oxidase (cytochrome bo₃ complex), two protein-associated quinone molecules are known to work together. T. Ohnishi and her collaborators reported that two distinct semiquinone species also play important roles in NADH-ubiquinone oxidoreductase (complex I). They were called SQ_Nf (fast relaxing semiquinone) and SQ_Ns (slow relaxing semiquinone). It was proposed that Q_Nf serves as a “direct” proton carrier in the semiquinone-gated proton pump (Ohnishi and Salerno, FEBS Letters 579 (2005) 4555), while Q_Ns works as a converter between one-electron and two-electron transport processes. This communication presents a revised hypothesis in which Q_Nf plays a role in a “direct” redox-driven proton pump, while Q_Ns triggers an “indirect” conformation-driven proton pump. Q_Nf and Q_Ns together serve as (1e^?/2e^?) converter, for the transfer of reducing equivalent to the Q-pool.     

Co-operative response of chemically excitable membrane III. Three-state model

The general three-state model is formulated first, which is the direct extension of the unified two-state model previously formulated (Kijima & Kijima, 1978). In this model, each protomer in a symmetrically interacting system (oligomers or lattices) can take three states, S, R and Q, where S and R states are the same as in the two-state model and Q state is another state either corresponding to a different open-state of ionophore from R open-state or corresponding to another closed state of ionophore. The model has no restriction on the value of Hill coefficient at the midpoint of the dose-response curves in contrast to two-state models. It is applied on GABA sensitive inhibitory synapse of crayfish muscle to account for anomalous behaviour of the membrane in I^? solution.The simplified versions of the above general three-state model are also formulated (simplified three-state model), in which it is assumed that R and Q state are equivalent in regard to the nearest neighbor interaction. By this assumption, R and Q state are collectively treated as state A and mathematical formula obtained on Ising model are applicable on this model. This model is applied on the insect sugar receptor which was shown to be incompatible with the two-state models (Kijima & Kijima, 1980). Further simplification of the above simplified model results in two convenient models: three-state KNF model and three-state MWC model, which have minimum parameters but sufficient to account for most experiments. They give plausible physico-chemical base on the “classical model” in which the existence of both inactive and active ligand-receptor complex is assumed.     

The theoretical possibility of reverse translation of proteins into genes

It is shown on a theoretical basis that the existence of a “power law” relationship between body mass M and total metabolic heat generation rate Q of the form Q = kM^α does not uniquely determine the dependence of metabolic rate on body temperature. However, it is shown that a particular assumption for this temperature dependence, successful in other problems, does predict a “power law” similar to the empirical one. At the same time it also accounts satisfactorily for the linear dependence of metabolic rate on ambient temperature.     

Construction of various bacteriophage λ mutants for stable and efficient production of recombinant protein in Escherichia coli

Three λ mutants were constructed based on the Q⁻ mutant in order to enhance their productivity and stability in an Escherichia coli/bacteriophage λ system. The newly constructed bacteriophage mutants named λSNU1, λSNU2, and λSNU3 were Q⁻S⁻, Q⁻W⁻E⁻, and Q⁻S⁻W⁻E⁻ mutants, respectively. Compared to all of the mutants, λSNU1 turned out to be the best with regards to higher protein expression and better genetic stability. Mechanisms by which these attributes are achieved have been discussed. The high productivity of P90c/λSNU1 for the recombinant protein was due to the high copy number of λ DNA and high translational efficiency. This mutant phage λSNU1 can be used to provide a high level of stability and productivity of the cloned gene particularly for long-term continuous operation.     

Genetic diversity and parentage of Tunisian wild and cultivated grapevines (Vitis vinifera L.) as revealed by single nucleotide polymorphism (SNP) markers

Based on 261 single nucleotide polymorphism (SNP) markers, we analyzed 57 grapevine genotypes, consisting of 29 wild grapevines (Vitis vinifera subsp. sylvestris) prospected from the northwest part of Tunisia and 28 cultivated accessions (V. vinifera subsp. vinifera) maintained in the repository of the Arid Land Institute of Medenine (Tunisia). Pair-wise multilocus comparison with the ICVV SNP database allowed the identification of 13 cultivated genotypes, including ten synonymous groups with known Mediterranean or international varieties, three cases of color sports, and two misnomers. Genotypic analysis showed a high level of genetic diversity for both wild and cultivated groups. Multivariate and structure analyses clearly differentiated wild from cultivated grapevines and showed high average posterior probabilities of assignment to their group of origin. The clustering results largely supported the perceived classification and reflect that most of the present Tunisian cultivated varieties do not derive directly from the local wild populations but could correspond to materials introduced from different locations during historical times. Parentage analysis allowed the determination of the genetic origin of four Tunisian cultivars, “Garai”, “Jerbi” (from Kerkennah), “Mahdoui”, and “Reine de Vignes faux”, and showed that “Heptakilo” and “Planta Fina”, two old and widely distributed varieties in the Mediterranean basin, had an important role in the origin of Tunisian grapevines. The present study demonstrates the efficacy of SNP makers for germplasm characterization and genetic studies in grapevine.     

What is hierarchical selection?

It has been proposed that natural selection occurs on a hierarchy of levels, of which the organismic level is neither the top nor the bottom. This hypothesis leads to the following practical problem: in general, how does one tell if a given phenomenon is a result of selection on level X or level Y. How does one tell what the units of selection actually are? It is convenient to assume that a unit of selection may be defined as a type of entity for which there exists, among all entities on the same “level” as that entity, an additive component of variance for some specific component F of fitness which does not appear as an additive component of variance in any decomposition of this F among entities at any lower level. But such a definition implicitly assumes that if f(x, y) depends nonadditively on its arguments, there must be interaction between the quantities which x and y represent. This assumption is incorrect. And one cannot avoid this error by speaking of “transformability to additivity” instead of merely “additivity”. A general mathematical formulation of the concepts of interaction and non-interaction is proposed, followed by a correspondingly modified approach to the definition of a unit of selection. The practical difficulty of verifying the presence of hierarchical selection is discussed.     

The Guadalupian–Lopingian boundary (Permian) in a pelagic sequence from Panthalassa recognized by integrated conodont and radiolarian biostratigraphy

Guadalupian–Lopingian sedimentary rocks are widely distributed in accretionary complexes in Japan, but the Guadalupian–Lopingian boundary (G–LB) is not well documented from these pelagic sediments. To identify the G–LB and to better correlate an extinction event that occurred around the Guadalupian–Lopingian boundary, we examined the conodont biostratigraphy from a Permian pelagic chert sequence in the Gujo-hachiman section, Gifu, southwest Japan. Age-diagnostic conodonts, including Clarkina postbitteri postbitteri, were found in this section. The biostratigraphic occurrences of these age-diagnostic conodonts can pinpoint the “G–L transitional zone” in the Gujo-hachiman section by comparison with well-studied sections from south China, including the GSSP section. The transitional zone was recognized by the first occurrence horizons of both Clarkina postbitteri hongshuiensis and C. p. postbitteri. The G–LB has been placed at or above the first occurrence horizon of the radiolarians Albaillella yamakitai or Albaillella cavitata in previous studies from China and Japan. We detected the first occurrence horizon of A. yamakitai below the base of the “G–L transitional zone,” in the Upper Capitanian. The conodont biostratigraphy is consistent with the radiolarian biostratigraphy in this section, which can be correlated to relevant sections in China.     

Structure and Stability of the Insulin Dimer Investigated by Molecular Dynamics Simulation

Abstract

Molecular dynamics simulation indicates that the dynamical behaviour of the insulin dimer is asymmetric. Atomic level knowledge of the interaction modes and protein conformation in the solvation state identifies dynamical structures, held by hydrogen bonds that stabilize, mainly in one monomer, the interaction between the chains. Dynamic cross-correlation analysis shows that the two insulin monomers behave asymmetrically and are almost independent. Solvation energy, calculated to evaluate the contribute of each interface residue to the dimer association pattern, well compares with the experimental association state found in protein mutants indicating that this parameter is an important factor to explain the association properties of mutated insulin dimers.     

Aerobic scaling and resting metabolism in oviferous and post-spawning Barents Sea capelin Mallotus villosus villosus (Müller, 1776)

As part of the quantitative investigations into the bioenergetic relationships of the Barents Sea capelin, Mallotus villosus villosus (Müller, 1776), resting metabolic rates were examined in the oviferous and post-spawning fish in order to provide insights to aerobic scaling and the basal energetic costs associated with reproduction. Aerobic scaling of the different categories of sexually mature fish (body weight, W=13-54 g) could be expressed as: Q_O2=0.106W^1.049 (oviferous fish; N=11), Q_O2=0.411W^0.430 (post-spawning females; N=9), and Q_O2=0.075W^1.012 (post-spawning males; N=14), where Q_O2 is the oxygen consumption (ml O₂ h⁻¹) per fish. The weight specific oxygen consumption of oviferous capelin was about 30% higher (∼125 ml O₂ kg⁻¹ h⁻¹) compared to those of the post-spawning fish (79-87 ml O₂ kg⁻¹ h⁻¹). The results are discussed in context with other empirical studies on the aerobic scaling and metabolic costs involved with the build-up of roe in the fish.     

Natural selection under population regulation

The dynamical behavior of multi-allele, one-locus systems is analyzed under population regulation. Weak selection is assumed. It is shown that for sufficiently large times, t, the nth time derivative of the population number N(t) is of order n}+1 in the selection coefficients. These order relations imply there is an asymptotic “quasi-equilibrium” in which population size and mean fitness change slowly relative to changes in gene frequencies. Consistent with the results of other authors, in quasi-equilibrium the mean fitness is second-order in the selection coefficients. In an effort to understand dynamic behavior beyond the immediate neighborhood of equilibrium, the topology of mean fitness surfaces is explored. In general, population regulation leads to regions of decreasing mean fitness in which there are important changes in gene frequencies. To illustrate this and other related phenomena, I analyze models in which there is logarithmic population control, and in which genotypic fitnesses W_i(x) are linear in the allele frequencies x. Exact solutions for mean fitness W(x) are obtained for two- and three-allele systems with symmetric fertilities and mortalities.     

Ecological Stability: Reality,Misconceptions, and Implications for Risk Assessment

Over a long time frame, an ecological system may not exhibit constancy due to successional and evolutionary changes in the species composing the system. However, over shorter time frames an ecological system exhibits a certain degree of constancy (i.e., varies within defined bounds). Traditionally, ecologists considered this short-term constancy to reflect a “balance of nature,” which was viewed akin to the simple homeostatic dynamics of physiological systems. This is an appealing perspective because the disruption of the system's “balance” (i.e., its ”health“) can be ascertained by comparing the system's current state after the imposition of a perturbation with the societally desired state (i.e., baseline). Recently, ecologists have started to develop a much more complex, and perhaps more realistic, perspective regarding ecosystem dynamics, which does not depend upon homeostasis with a single baseline state. This new view includes stochastic variation, nonlinear dynamics and alternative states, and poses a challenge for assessing environmental “health” and the risk of creating “unhealthy” ecological systems     

An ecological indicator to evaluate the effect of chemical insecticide pollution management on complex ecosystems

The extensive input of chemical insecticides for pest control is considered as a serious risk to the environment, and the ecological disturbance of chemical insecticides has both positive and negative effects on complex agro-ecosystems. This paper proposed an indicator based on ecological two-sidedness theory and Shannon entropy, which is intended for analyzing informational complexity in a decision network of the chemical insecticide pollution management. The results indicated that the order of the value of R_CC/CP index (where the R_CC/CP index matrix W_CC/CP is defined as the index optimization matrix of comprehensive cost divided by the index optimization matrix of comprehensive profit) for three insect pest-controlling strategies in scallion fields was “applying frequency vibration lamps and environment-friendly insecticides 8 times” (0.8714) < “applying trap devices and environment-friendly insecticides 9 times” (0.8858) < “applying common insecticides 15 times” (0.9077). The treatment “applying frequency vibration lamps and environment-friendly insecticides 8 times” was recognized as the optimal strategy for chemical insecticide pollution management in scallion fields in Shanghai, China. The results demonstrate that our proposed ecological indicator might arouse the interest of policy makers and eco-environmentalists who seek to minimize the use of chemicals, and the farmers who hope to optimize pest-controlling strategies in practice.     

Influence of environmental,geographic, and seasonal variations in the chemical composition of Miconia species from Cerrado

Miconia albicans (Sw.) Triana and Miconia chamissois Naudin, commonly known as “pixirica” and “pixirica-açu”, two Melastomataceae species, are commonly found in Cerrado areas. M. albicans species grows in dry and humid habitats, so it has adapted to both conditions and M. chamissois species grows in humid environment only. In this work, we have investigated the content of triterpenes, flavonols and flavanones in three different Cerrado fragments of São Paulo State, involving distinct environments (dry and humid) and seasons (dry and rainy) to comprehend the complex interactions among plants and the seasonal, environmental conditions and geographic locations. The leaves plants materials were harvest in August 2016 (dry season) and November/December 2016 (rainy season) in Pirassununga, Pedregulho and Luíz Antônio in dry and humid environments. The contents of the standards rutin (R), quercetin (Q), miconioside B (B), matteucinol 7-O-β-apiofuranosyl(1 → 6)-β-glucopyranoside (matt), ursolic acid (AU), and oleanolic acid (AO) were determined by HPLC-DAD. The data were analyzed using nonparametric tests, Pearson's linear correlation, principal component analysis and hierarchical cluster analysis. The results demonstrated similar flavanone and triterpene production during the dry period, and similar flavonol and flavanone production in the rainy season, thus confirming a seasonal variation in the content of the compounds in the evaluated specimens. Our results also demonstrated intra- and inter-population variations in compounds patterns, M. albicans contained major amounts of the flavonols R and Q; their concentrations were higher in the rainy season. B and matt were the major compounds in M. chamissois; the matt concentration decreased in the rainy season. The triterpenes AU and AO occurred in both M. albicans and M. chamissois, but their production dropped during the rainy periods. Thus corroborating the adaptation of M. albicans and M. chamissonis to the high stress and low levels of resources presented in Cerrado.     

Realtime kinetics of the light driven steps of photosynthetic water oxidation in living organisms by “stroboscopic” fluorometry

We develop a rapid “stroboscopic” fluorescence induction method, using the fast repetition rate fluorometry (FRRF) technique, to measure changes in the quantum yield of light emission from chlorophyll in oxygenic photosynthesis arising from competition with primary photochemical charge separation (P₆₈₀* ➔ P₆₈₀⁺Q_A⁻). This method determines the transit times of electrons that pass through PSII during the successive steps in the catalytic cycle of water oxidation/O₂ formation (S states) and plastoquinone reduction in any oxygenic phototroph (in vivo or in vitro). We report the first measurements from intact living cells, illustrated by a eukaryotic alga (Nannochloropsis oceanica). We demonstrate that S state transition times depend strongly on the redox state of the PSII acceptor side, at both Q_B and the plastoquinone pool which serve as the major locus of regulation of PSII electron flux. We provide evidence for a kinetic intermediate S3′ state (lifetime 220 μs) following formation of S3 and prior to the release of O₂. We compare the FRRF-detected kinetics to other previous spectroscopic methods (optical absorbance, EPR, and XES) that are applicable only to in vitro samples.     

On the “cytosociology” of enzyme action in vivo: A novel thermodynamic correlate of biological evolution

The evolution of enzyme action in vivo is examined, in the light of established thermodynamic correlates of biological evolution. Adopting a “process” view of matter in the “living state,” the authors focus the analysis on the transition-state theory of reaction rates. Thus, the free-energy change associated with the transition-state barrier is seen as a primary target in the evolution of cellular metabolism. The utility and limitations of reductionistic approaches to enzyme evolution, based on the single enzyme, are explored first. Then, canvassing the wealth of evidence on the role of enzyme organization in vivo, the authors synthesize a “cytosociological” view of enzyme evolution. In this view, a composite (resultant) of individual transition-state barriers is deemed a more appropriate “potential function” for modification in the higher evolution of cell metabolism. The suggested direction of evolutionary changes in this function, dictated by the increasing “socialization” of enzyme action in vivo, stands as a novel postulate. This approach is shown to be completely consonant with current thinking on the thermodynamics of biological evolution, and to provide further insight into the nature of material transformations in the “living state”.