Structural model studies for the high-valent intermediate Q of methane monooxygenase from broken-symmetry density functional calculations

Mössbauer isomer shift parameters have been obtained for both density functional theory (DFT) OPBE and OLYP functionals by linear regressions between the measured isomer shifts and calculated electron densities at Fe nuclei for a number of Fe^2+,2.5+ and Fe^{2.5+,3+,3.5+,4+} complexes grouped separately. The calculated isomer shifts and quadrupole splittings on the sample Fe complexes from OPBE and OLYP functionals are similar to those of PW91 calculations [J. Comput. Chem. 27 (2006) 1292], however the fit parameters from the linear regressions differ between PW91 and OPBE, OLYP. Four models for the active site structure of intermediate Q of the hydroxylase component of soluble methane monooxygenase (MMOH) have been studied, using three DFT functionals OPBE, OLYP, and PW91, incorporated with broken-symmetry methodology and the conductor-like screening (COSMO) solvation model. The calculated properties, including optimized geometries, electronic energies, pK_a’s, Fe net spin populations, and Mössbauer isomer shifts and quadrupole splittings, have been reported and compared with available experimental values. The high-spin antiferromagnetically (AF) coupled Fe⁴⁺ sites are correctly predicted by OPBE and OLYP methods for all active site models. PW91 potential overestimates the Fe-ligand covalencies for some of the models because of spin crossover. Our calculations and data analysis support the structure (our current model II shown in Fig. 8) proposed by Friesner and Lippard’s group [J. Am. Chem. Soc. 123 (2001) 3836-3837], which contains an Fe⁴⁺(μ-O)₂Fe⁴⁺ center, one axial water which also H-bonds to both side chains of Glu243 and Glu114, and one bidentate carboxylate group from the side chain of Glu144, which is likely to represent the active site of MMOH-Q. A new model structure (model IV shown in Fig. 9), which has a terminal hydroxo and a protonated His147 which is dissociated from a nearby Fe, is more asymmetric in its Fe(μ-O)₂Fe diamond core, and is another very good candidate for intermediate Q.     

Linking dispersal, immigration and scale in the neutral theory of biodiversity

In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m . A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory.     

Evolution as a cognition process: Towards an evolutionary epistemology

Recently, biologist and philosophers have been much attracted by an evolutionary view of knowledge, so-called evolutionary epistemology. Developing this insight, the present paper argues that our cognitive abilities are the outcome of organic evolution, and that, conversely, evolution itself may be described as a cognition process. Furthermore, it is argued that the key to an adequate evolutionary epistemology lies in a system-theoretical approach to evolution which grows from, but goes beyond, Darwin's theory of natural selection.     

Application of the Percolation Theory to Random Networks of Biochemical Reactions

Percolation Theory is used to get statements about random networks. It can be seen that the probability distribution that vertices belong to a finite cluster in dependence on the mean catalytic activity C = K/N has an analogy to phase transition of second kind.     

Proximal effects in the modulation of nitric oxide synthase reactivity: a QM-MM study

Nitric oxide synthases (NOS) are heme proteins that have a cysteine residue as axial ligand, which generates nitric oxide (NO). The proximal environment, specifically H-bonding between tryptophan (Trp) 178 and thiolate, has been proposed to play a fundamental role in the modulation of NOS activity. We analyzed the molecular basis of this modulation by performing electronic structure calculations on isolated model systems and hybrid quantum-classical computations of the active sites in the protein environment for wild-type and mutant (Trp 178 × Gly) proteins. Our results show that in the ferrous proteins NO exhibits a considerable trans effect. We also showed that in the ferrous (Fe⁺²) mutant NOS the absence of Trp, experimentally associated to a protonated cysteine, weakens the Fe–S bond and yields five coordinate complexes. In the ferric (Fe⁺³) state, the NO dissociation energy is shown to be slightly smaller in the mutant NOS, implying that the Fe⁺³–NO complex has a shorter half-life. We found computational evidence suggesting that ferrous NOS is favored in wild-type NOS when compared to the Trp mutant, consistently with the fact that Trp mutants have been shown to accumulate less Fe⁺²–NO dead end species. We also found that the heme macrocycle showed a significant distortion in the wild-type protein, due to the presence of the nearby Trp 178. This may also play a role in the subtle tuning of the electronic structure of the heme moiety.     

Methodologic Implications of the Precautionary Principle: Causal Criteria

Applying the Precautionary Principle to public health requires a re-evaluation of the methods of inference currently used to make claims about disease causation from epidemiologic and other forms of scientific evidence. In current thinking, a well-established, near-certain causal relationship implies highly consistent statistically significant results across many different studies, large relative risk estimates, extensive understanding of biological mechanisms and dose-response relationships, positive prevention trial results, a clear temporal relationship between cause and effect, and other conditions spelled out in terms of the widely-used causal criteria. The Precautionary Principle, however, states that preventive measures are to be taken when cause and effect relationships are not fully established scientifically. What evidentiary conditions, as reflected in the causal criteria, will be certain enough to warrant precautionary preventive action? This paper argues that minimum evidentiary requirements for causation need to be articulated if the Precautionary Principle is to be successfully incorporated into public health practice. Two precautionary changes to criteria-based methods of causal inference are examined: reducing the number of criteria and weakening the rules of inference accompanying the criteria. Such changes point in the direction of identifying minimum evidentiary conditions, but would be premature without better understanding how well current methods of causal inference work.     

Early stress predicts age at menarche and first birth,adult attachment,and expected lifespan

Life history theory suggests that in risky and uncertain environments the optimal reproductive strategy is to reproduce early in order to maximize the probability of leaving any descendants at all. The fact that early menarche facilitates early reproduction provides an adaptationist rationale for our first two hypotheses: that women who experience more risky and uncertain environments early in life would have (1) earlier menarche and (2) earlier first births than women who experience less stress at an early age. Attachment theory and research provide the rationale for our second two hypotheses: that the subjective early experience of risky and uncertain environments (insecurity) is (3) part of an evolved mechanism for entraining alternative reproductive strategies contingent on environmental risk and uncertainty and (4) reflected in expected lifespan. Evidence from our pilot study of 100 women attending antenatal clinics at a large metropolitan hospital is consistent with all four hypotheses: Women reporting more troubled family relations early in life had earlier menarche, earlier first birth, were more likely to identify with insecure adult attachment styles, and expected shorter lifespans. Multivariate analyses show that early stress directly affected age at menarche and first birth, affected adult attachment in interaction with expected lifespan, but had no effect on expected lifespan, where its original effect was taken over by interactions between age at menarche and adult attachment as well as age at first birth and adult attachment. We discuss our results in terms of the need to combine evolutionary and developmental perspectives and the relation between early stress in general and father absence in particular. This work was supported by The University of Melbourne Department of Obstetrics and Gynaecology. James S. Chisholm is Professor in the School of Anatomy and Human Biology at the University of Western Australia. He is an anthropologist whose interests lie in the fields of human behavioral biology, evolutionary ecology, life history theory, and parental investment theory, where he focuses on infant social-emotional development, the development of reproductive strategies, and the integration of evolutionary, developmental, and cultural psychology and public health. Julie A. Quinlivan is Associate Professor in Obstetrics and Gynaecology at the University of Melbourne and Head of the Maternity Care Program at the Royal Women’s Hospital, Melbourne. Her interests are teenage pregnancy, domestic violence, child abuse prevention, and high-risk pregnancy. Rodney W. Petersen is Senior Lecturer in Obstetrics and Gynaecology at the University of Melbourne and Senior Consultant in Obstetrics and Gynaecology at the Royal Women’s Hospital and Sunshine Hospital in Melbourne. His interests are in psychosocial aspects of women’s health and cancer. David A. Coall is a Ph.D. student in the School of Anatomy and Human Biology at the University of Western Australia. His main interest lies in the application of evolutionary theory within an epidemiological framework. He is currently working on the synthesis of life history theory, parental investment theory, and parent-offspring conflict theory in exploring factors that influence variation in human birth weight and placental weight.     

Modeling Response of N Addition on C and N Allocation in Scandinavian Norway Spruce Stands

Because nitrogen is considered to be the major growth-limiting element in boreal forests, the increasing nitrogen availability from deposition should lead to increasing growth. We have tested this assumption by simulating, with a simple model, carbon and nitrogen development in seven long-term fertilization experiments in three Nordic countries. The only differences between sites in the model are climate, the ambient nitrogen deposition, nitrogen fertilization regimes, and the initial conditions at the start of the experiment. The model simulates the observed stand development well as long as nitrogen remains the limiting factor. The simulated retention of deposited nitrogen is in general low (less than 50%), whereas retention of fertilizer nitrogen is higher. This seems to imply that the higher production in the fertilized stands will not be maintained once the fertilization is stopped. The model results also indicate that the major effect of climate on site productivity is through soil processes, not tree physiology.     

Hubbell's fundamental biodiversity parameter and the Simpson diversity index

Central to Hubbell's neutral theory of biodiversity is a universal, dimensionless fundamental biodiversity parameter that is the product of community size and speciation rate. One of the most important discoveries of Hubbell's theory is that the species‐abundance distribution and the species–area relationship of the neutral metacommunity is completely determined by this fundamental biodiversity parameter, although the diversity patterns of the local community are collectively determined by the biodiversity parameter and migration. Using the relative abundance of species and following the concept of heterozygosity of population genetics, here we developed an analytical relationship between this biodiversity parameter and the well‐known Simpson diversity index. This relationship helps bridge the evolutionary aspect of biodiversity to the ecological and statistical aspect of the diversity. The relationship between these two parameters suggests that diversity patterns of the metacommunity can also be equally described by the Simpson index. This relationship provides an alternative approach to interpret and estimate the fundamental biodiversity parameter for the metacommunity.