A tool for the morphological analysis of mixtures of lipids and water in computer simulations

When analyzing computer simulations of mixtures of lipids and water, the questions to be answered are often of a morphological nature. They can deal with global properties, like the kind of phase that is adopted or the presence or absence of certain key features like a pore or stalk, or with local properties, like the local curvature present at a particular part of the lipid/water interface. While in principle all of the information relating to the global and local morphological properties of a system can be obtained from the set of atomic coordinates generated by a computer simulation, the extraction of this information is a tedious task that usually involves using a visualization program and performing the analysis by eye. Here we present a tool that employs the technique of morphological image analysis (MIA) to automatically extract the global morphology—as given by Minkowski functionals—from a set of atomic coordinates, and creates an image of the system onto which the local curvatures are mapped as a color code.     

Structural Features of Transiently Modified Beta-Lactoglobulin Relevant to the Stable Binding of Large Hydrophobic Molecules

Binding sites for hydrophobic molecules on bovine β-lactoglobulin, and their susceptibility to temperature, were studied by using various spectroscopic probes. Binding of probes carrying a single fluorophore moiety, a single nitroxide moiety, or both moieties on the same molecule, was followed by EPR and fluorescence. The presence of a fatty acid side chain in the dual probes was found to be required for binding to β-lactoglobulin. Binding occurred only after the protein was heated at temperatures below the threshold for its irreversible denaturation. Binding became extremely tight and stable upon cooling of the protein–probe mixture. Comparison among the various probes suggests that multiple binding sites for hydrophobes are present in the native protein, and in the partially—and reversibly—modified form of β-lactoglobulin present in solution at neutral pH and subdenaturing temperatures. Thus, the specificity of hydrophobes binding to β-lactoglobulin may be modulated by simple physical treatment of the protein.     

A stochastic model for the synthesis and degradation of natural organic matter part II: molecular property distributions

A stochastic biogeochemical model has been developed to simulate the transformation and degradation of natural organic matter (NOM) using an agent-based algorithm which treats each molecule as a separate and potentially unique entity. Molecules react when a pseudo-random number is lower than the calculated reaction probability in a given time step; repeated time steps simulate the transformation of precursor molecules into a complex NOM assemblage. The data for each molecule—elemental and functional group composition—can be used to calculate many properties directly and exactly for each molecule in the assemblage, e.g., molecular weight (MW), fraction of aromatic C (Ar), and charge at pH 7 (Z). Empirical quantitative structure activity relationships (QSARs) are developed which permit the estimation of thermodynamic quantities K _ow (the octanol–water partition coefficient) and pK _a (acidity) for each molecule. Root mean square errors for these QSARs are 0.39 log units for log K _ow and 0.45 log units for pK _a. Distributions of both exactly calculated (MW, Ar, Z) and estimated thermodynamic (K _ow, pK _a) properties are examined and compared with published experimental data. Molecular weight distributions from size exclusion HPLC experiments on aquatic NOM are quantitatively similar to simulation results. pH titrations and polarity distributions from reversed-phase HPLC are qualitatively similar to simulation results. This agreement suggests that the agent-based model can be used to explore hypotheses regarding both compositional and thermodynamic properties of NOM. Robert Wetzel—deceased.     

Simple menaquinones reduce carbon tetrachloride and iron (III)

Cell-free supernatant from Shewanella oneidensis MR-1 reduced carbon tetrachloride to chloroform, a suspension of Fe(III) and solid Fe(III) to iron (II). The putative reducing agent was tentatively identified as menaquinone-1 (MQ-1)—a water-soluble menaquinone with a single isoprenoid residue in the side chain. Synthetic MQ-1 reduced carbon tetrachloride to chloroform and amorphous iron (III) hydroxide to iron (II). To test the generality of this result among menaquinones, the reductive activities of vitamin K₂ (MQ-7)—a lipid-associated menaquinone with 7 or 8 isoprenoid residues—was evaluated. This molecule also reduced carbon tetrachloride to chloroform and iron (III) to iron (II). The results indicate that molecules within the menaquinone family may contribute to both the extracellular and cell-associated reduction of carbon tetrachloride and iron (III).     

Conditions Under Which Nitrogen Can Limit Steady-State Net Primary Production in a General Class of Ecosystem Models

Human activity is drastically altering global nitrogen (N) availability. The extent to which ecosystems absorb additional N—and with it, additional CO₂—depends on whether net primary production (NPP) is N-limited, so it is important to understand conditions under which N can limit NPP. Here I use a general dynamical model to show that N limitation at steady-state—such as in old-growth forests—depends on the balance of biotically controllable versus uncontrollable N inputs and losses. Steady-state N limitation is only possible when uncontrollable inputs (for example, atmospheric deposition) exceed controllable losses (for example, leaching of plant-available soil N), which is the same as when uncontrollable losses (for example, leaching of plant-unavailable soil N) exceed controllable inputs (biological N fixation). These basic results are robust to many model details, such as the number of plant-unavailable soil N pools and the number and type of N fixers. Empirical data from old-growth tropical (Hawai’i) and temperate (Oregon, Washington, Chile) forests support the model insights. Practically, this means that any N fixer—symbiotic or not—could overcome ecosystem N limitation, so understanding N limitation requires understanding controls on all N fixers. Further, comparing losses of plant-available N to abiotic inputs could offer a rapid diagnosis of whether ecosystems can be N-limited, although the applicability of this result is constrained to ecosystems with a steady-state N cycle such as old-growth forests largely devoid of disturbance.     

Theoretical evaluation of the order of reactivity of transfer agents utilized in RAFT polymerization

Density functional theory, DFT, PBE1PBE functional and 6−31+G(d,p) basis set in Gaussian 03 software were used in order to determine the reactivity order of the R group in RAFT agents used in the radical addition-fragmentation tranfer polymerization, through the evaluation of reactivity parameters such as: global and local electronegativity, hardness, softness, and philicity. It was found that the reactivity order is governed by both the number and the composition of the substituent group (primary, secondary or tertiary); that is, the larger those parameters are the larger factors like steric hindrance, polar effects and electronic interchanges are, which favors the breaking of the C−S bond from the adduct radical, permitting the exit of the leaving radical and allowing, as a consequence, the fragmentation step in RAFT polymerization. Trisubstituted dithioesters with structure S = C(Z)S−R, where Z = Phenyl and R = C(CH₃)₂CONH₂, C(CH3)2Ph or (CH₃)₂C₆H₈OCH₃, in accordance with the previously exposed, presented the most favorable reactivity parameters.     

Residue 3 of β2-microglobulin affects binding of class I MHC molecules by the W6/32 antibody

 Previous studies of class I MHC molecules have shown that the owl monkey (Aotus) possesses at least two variants of the β₂-microglobulin (β₂m) protein. These two variants have different isoelectric points, and exhibit differential reactivity with the monoclonal antibody W6/32. We report cDNA sequences of the B2m gene, from W6/32-positive and W6/32-negative Aotus cell lines. The two β₂m variants we identified exhibit a single amino acid difference at position three. An arginine residue at position 3 was correlated with W6/32 reactivity, whereas histidine was associated with non-reactivity. W6/32 reactivity was conferred to a W6/32-negative Aotus cell line when it was transfected with the B2m from the W6/32-positive cell line. Residue 3 of β₂m is located at the surface of the class I molecule. It is also close to position 121 of the MHC class I heavy chain, which has previously been shown to influence W6/32 antibody binding. We conclude that W6/32 binds a compact epitope on the class I molecule that includes both residue 3 of β₂m and residue 121 of the heavy chain. We examined the distribution of the two β₂m motifs in a sample Aotus population using an allele-specific polymerase chain reaction assay. The pattern of β₂m segregation we observed matches that which was defined previously by serology. Additionally, we identified laboratory-born hybrid animals who possess both variants of β₂m. Received: 1 April 1998 / Received: 3 July 1998     

Palaeoproterozoic petrified oil field (Shunga Event)

Significant accumulation of autochthonous organic matter preserved in Palaeoproterozoic rocks is rare. One of the largest and most remarkable occurrences is the deposit at Shunga, in Karelia, northwestern Russia. This enormous accumulation of C-rich rocks is part of the world-wide Shunga Event. The integrated data suggest that the OM was most likely derived from planktonic microorganisms. This remarkable accumulation of OM and inferred generation of giant volume of petroleum took place in the aftermath of the ca 2330–2060 Ma Lomagundi—Jatulian Event—the largest positive excursion of δ¹³C_carb of sedimentary carbonate in the Earth’s history. The formation of shungite carbon and its diagenetic, catagenetic and metamorphic transformation are related to fundamental problems of biological evolution, global carbon cycle and the earliest oil generation.     

Continuity,Collapse or Metamorphosis? Demographic anthropology and the study of change within human populations.Foreword

this first paper introduces the topic of the volume, outcomes of a symposium organised at the 13th ICAES held in Mexico in August 1993. It briefly reminds of the convergence between anthropology and demography up to date and stresses on the need of real transdisciplinary work in this challenging domain. The aim of the symposium was to make a contribution on the central theme chosen by the congress — the cultural and biological dimensions of global change — while examining the place of demographic anthropology in the study of change. The papers presented at the symposium have been organised in three parts which form the present volume: the composition of population, the choice of spouse and mobility, the reproduction and dynamics of populations. The basic mechanisms of change are considered through examples at the level of local populations. This also leads to question the definitions of human groups and to make a “declaration” stressing on the importance of individual heterogeneity and the arbitrariness and reductive nature of any grouping of individuals, stating therefore the misapprehension of the most recent scientific work inherent to the rationale of programs of “ethnic cleasing”. Translated from the french by prof. Derek F. Roberts     

Hierarchies and the Sloshing Bucket: Toward the Unification of Evolutionary Biology

Evolutionary biology presents a bewildering array of phenomena to scientists and students alike—ranging from molecules to species and ecosystems; and embracing 3.8 billion years of life’s history on earth. Biological systems are arranged hierarchically, with smaller units forming the components of larger systems. The evolutionary hierarchy, based on replication of genetic information and reproduction, is a complex of genes/organisms/demes/species and higher taxa. The ecological hierarchy, based on patterns of matter–energy transfer, is a complex of proteins/organisms/avatars/local ecosystems/regional ecosystems. All organisms are simultaneously parts of both hierarchical systems. Darwin’s original formulation of natural selection maps smoothly onto a diagram where the two hierarchical systems are placed side-by-side. The “sloshing bucket” theory of evolution emerges from empirical cases in biological history mapped onto this dual hierarchy scheme: little phenotypically discernible evolution occurs with minor ecological disturbance; conversely, greatest concentrations of change in evolutionary history follow mass extinctions, themselves based on physical perturbations of global extent. Most evolution occurs in intermediate-level regional “turnovers,” when species extinction leads to rapid evolution of new species. Hierarchy theory provides a way of integrating all fields of evolutionary biology into an easily understood—and taught—rubric.

Marker-assisted selection and evaluation of the QTL for stigma exsertion under japonica rice genetic background

Stigma exsertion is one of the important traits which contribute to the efficient improvement of commercial seed production in hybrid rice. In order to understand the genetic factors involved in the stigma exsertion of an indica variety—IR24—a QTL analysis was conducted using the F₂ population between a japonica variety—Koshihikari—and a breeding line showing exserted stigma selected from the backcross population between IR24 as a donor and japonica varieties. As a result, a highly significant QTL (qES3), which had been predicted in the recombinant inbred population of IR24, was confirmed at the centromeric region on chromosome 3. qES3 increases about 20% of the frequency of the exserted stigmas at the IR24 allele and explains about 32% of the total phenotypic variance. A QTL near-isogenic line for qES3 increased the frequency of the exserted stigma by 36% compared to that of Koshihikari in a field evaluation, which suggests that qES3 is a promising QTL for the development of a maternal line for hybrid rice. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users. Maiko Miyata and Toshio Yamamoto contributed equally to this study.