The functional form of angular forces around transition metal ions in biomolecules.

A method for generating angular forces around sigma-bonded transition metal ions is generalized to treat pi-bonded configurations. The theoretical approach is based on an analysis of ligand-field and small-cluster Hamiltonians based on the moments of the electron state distribution. The functional forms that are obtained involve a modification of the usual expression of the binding energy as a sum of ligand-ligand interactions, which, however, requires very little increase in CPU time. The angular interactions have simple forms involving sin and cos functions, whose relative weights depend on whether the ligands are sigma- or pi-bonded. They describe the ligand-field stabilization energy to an accuracy of about 10%, and the interaction energy of covalently bonded systems to an accuracy of better than 4%. The resulting functional forms for the force field are used to model the structure of small clusters, including fragments of the copper blue protein structure. Large deviations from the typical square copper coordination are found when pi-bonded ligands are present.     

The study on the interaction between phytosterols and phospholipids in model membranes

Sterols are one of the major components of cellular membranes. Although in mammalian membranes cholesterol is a predominant sterol, in the human organism plant sterols (phytosterols) can also be found. Phytosterols, especially if present in concentrations higher than normal (phytosterolemia), may strongly affect membrane properties. In this work, we studied phytosterol-phospholipid interactions in mixed Langmuir monolayers serving as model membranes. Investigated were two phytosterols, beta-sitosterol and stigmasterol and a variety of phospholipids, both phosphatidylethanolamines and phosphatidylcholines. The phospholipids had different polar heads, different length and saturation of their hydrocarbon chains. The interactions between molecules in mixed sterol/phospholipid films were characterized with the mean area per molecule (A(12)) and the excess free energy of mixing (DeltaG(Exc)). The effect of the sterols on the molecular organization of the phospholipid monolayers was analyzed based on the compression modulus values. It was found that the incorporation of the phytosterols into the phospholipid monolayers increased their condensation. The plant sterols revealed higher affinity towards phosphatidylcholines as compared to phosphatidylethanolamines. The phytosterols interacted more strongly with phospholipids possessing longer and saturated chains. Moreover, both the length and the saturation of the phosphatidylcholines influenced the stoichiometry of the most stable complexes. Our results, compared with those presented previously for cholesterol/phospholipid monolayers, allowed us to draw a conclusion that the structure of sterol (cholesterol, beta-sitosterol, stigmasterol) does not affect the stoichiometry of the most stable complexes formed with particular phospholipids, but influences their stability. Namely, the strongest interactions were found for cholesterol/phospholipids mixtures, while the weakest for mixed systems containing stigmasterol.     

Modeling Colitis-Associated Cancer with Azoxymethane (AOM) and Dextran Sulfate Sodium (DSS)

Individuals with inflammatory bowel disease (IBD), such as Crohn''s disease (CD) or ulcerative colitis (UC) are at increased risk of developing colorectal cancer (CRC) over healthy individuals. This risk is proportional to the duration and extent of disease, with a cumulative incidence as high as 30% in individuals with longstanding UC with widespread colonic involvement.¹ Colonic dysplasia in IBD and colitis associated cancer (CAC) are believed to develop as a result of repeated cycles of epithelial cell injury and repair while these cells are bathed in a chronic inflammatory cytokine milieu.² While spontaneous and colitis-associated cancers share the quality of being adenocarcinomas, the sequence of underlying molecular events is believed to be different.³ This distinction argues the need for specific animal models of CAC.Several mouse models currently exist for the study of CAC. Dextran sulfate sodium (DSS), an agent with direct toxic effects on the colonic epithelium, can be administered in drinking water to mice in multiple cycles to create a chronic inflammatory state. With sufficient duration, some of these mice will develop tumors.⁴ Tumor development is hastened in this model if administered in a pro-carcinogenic setting. These include mice with genetic mutations in tumorigenesis pathways (APC, p53, Msh2), as well as mice pre-treated with genotoxic agents (azoxymethane [AOM], 1,2-dimethylhydrazine [DMH]).⁵ The combination of DSS with AOM as a model for colitis associated cancer has gained popularity for its reproducibility, potency, low price, and ease of use. Though they have a shared mechanism, AOM has been found to be more potent and stable in solution than DMH. While tumor development in other models generally requires several months, mice injected with AOM and subsequently treated with DSS develop adequate tumors in as little as 7-10 weeks.^{6, 7} Finally, AOM and DSS can be administered to mice of any genetic background (knock out, transgenic, etc.) without cross-breeding to a specific tumorigenic strain. Here, we demonstrate a protocol for inflammation-driven colonic tumorigenesis in mice utilizing a single injection of AOM followed by three seven-day cycles of DSS over a 10 week period. This model induces tumors with histological and molecular changes closely resembling those occurring in human CAC and provides a highly valuable model for the study of oncogenesis and chemoprevention in this disease.⁸     

Methyl sulfides as intermediates in the anaerobic oxidation of methane

While it is clear that microbial consortia containing Archaea and sulfate-reducing bacteria (SRB) can mediate the anaerobic oxidation of methane (AOM), the interplay between these microorganisms remains unknown. The leading explanation of the AOM metabolism is 'reverse methanogenesis' by which a methanogenesis substrate is produced and transferred between species. Conceptually, the reversal of methanogenesis requires low H₂ concentrations for energetic favourability. We used ¹³C-labelled CH₄ as a tracer to test the effects of elevated H₂ pressures on incubations of active AOM sediments from both the Eel River basin and Hydrate Ridge. In the presence of H₂, we observed a minimal reduction in the rate of CH₄ oxidation, and conclude H₂ does not play an interspecies role in AOM. Based on these results, as well as previous work, we propose a new model for substrate transfer in AOM. In this model, methyl sulfides produced by the Archaea from both CH₄ oxidation and CO₂ reduction are transferred to the SRB. Metabolically, CH₄ oxidation provides electrons for the energy-yielding reduction of CO₂ to a methyl group ('methylogenesis'). Methylogenesis is a dominantly reductive pathway utilizing most methanogenesis enzymes in their forward direction. Incubations of seep sediments demonstrate, as would be expected from this model, that methanethiol inhibits AOM and that CO can be substituted for CH₄ as the electron donor for methylogenesis.     

Scale-up on basis of structured mixing models: A new concept

A new scale-up concept based upon mixing models for bioreactors equipped with Rushton turbines using the tanks-in-series concept is presented. The physical mixing model includes four adjustable parameters, i.e., radial and axial circulation time, number of ideally mixed elements in one cascade, and the volume of the ideally mixed turbine region. The values of the model parameters were adjusted with the application of a modified Monte-Carlo optimization method, which fitted the simulated response function to the experimental curve. The number of cascade elements turned out to be constant (N = 4). The model parameter radial circulation time is in good agreement with the one obtained by the pumping capacity. In case of remaining parameters a first or second order formal equation was developed, including four operational parameters (stirring and aeration intensity, scale, viscosity). This concept can be extended to several other types of bioreactors as well, and it seems to be a suitable tool to compare the bioprocess performance of different types of bioreactors. (c) 1994 John Wiley & Sons, Inc.     

AOM／DSS模型与炎症相关癌变研究进展

氧化偶氮甲烷（azoxymethane,AOM）／葡聚糖硫酸钠（dextran sodium sulfate,DSS）小鼠模型是一种在致癌剂AOM和致炎剂DSS协同作用基础上,由炎症性肠病（inflammatory bowel disease,IBD）逐步发展为结直肠癌的炎症相关性癌症的研究模型。AOM／DSS模型能很好地模拟慢性肠道炎症诱发癌症的生理病理过程,近年来被广泛用于炎症相关性癌症形成机制的研究。简要综述AOM／DSS模型与炎症相关性癌症癌变机理的研究进展。     

A novel, multi-layered methanotrophic microbial mat system growing on the sediment of the Black Sea

A novel microbially diverse type of 1- to 5-cm-thick mat performing anaerobic oxidation of methane (AOM) and covering several square metres of the seafloor was discovered in the Black Sea at 180 m water depth. Contrary to other AOM-mat systems of the Black Sea these floating mats are not associated to free gas and are not stabilized by authigenic carbonates. However, supply of methane is ensured by the horizontal orientation of the mats acting as a cover of methane enriched fluids ascending from the underlying sediments. Thorough investigation of their community composition by molecular microbiology and lipid biomarkers, metabolic activities and elemental composition showed that the mats provide a clearly structured system with extracellular polymeric substances (EPS) building the framework of the mats. The top black zone, showing high rates of AOM (15 μmol  g_dw⁻¹ day⁻¹), was dominated by ANME-2, while the following equally active pink layer was dominated by ANME-1 Archaea . The lowest AOM activity (2 μmol  g_dw⁻¹ day⁻¹) and cell numbers were found in the greyish middle part delimited towards the sediment by a second pink, ANME-1-dominated and sometimes a black outer layer (ANME-2). Our work clearly shows that the different microbial populations are established along defined chemical gradients such as methane, sulfate or sulfide.     

QSAR models of quail dietary toxicity based on the graph of atomic orbitals

Graphs of atomic orbitals (GAOs) have been used to represent molecular structures. We describe rules to convert the labelled hydrogen-filled graphs (LHFGs) into GAOs. The GAO is one possible way of taking account of the structure of atoms (i.e., atomic orbitals, such as 1s(1), 2p(2) and 3d(10)) for QSPR/QSAR analyses. Optimization of correlation weights of local invariants (OCWLI) of the LHFGs and the GAOs was used to obtain a method of quail dietary toxicity modelling. Statistical characteristics of the models based on the OCWLI of GAO are better than those based on the OCWLI of the LHFGs.     

Analysis of membrane fusion as a two-state sequential process: evaluation of the stalk model

We propose a model that accounts for the time courses of PEG-induced fusion of membrane vesicles of varying lipid compositions and sizes. The model assumes that fusion proceeds from an initial, aggregated vesicle state ((A) membrane contact) through two sequential intermediate states (I(1) and I(2)) and then on to a fusion pore state (FP). Using this model, we interpreted data on the fusion of seven different vesicle systems. We found that the initial aggregated state involved no lipid or content mixing but did produce leakage. The final state (FP) was not leaky. Lipid mixing normally dominated the first intermediate state (I(1)), but content mixing signal was also observed in this state for most systems. The second intermediate state (I(2)) exhibited both lipid and content mixing signals and leakage, and was sometimes the only leaky state. In some systems, the first and second intermediates were indistinguishable and converted directly to the FP state. Having also tested a parallel, two-intermediate model subject to different assumptions about the nature of the intermediates, we conclude that a sequential, two-intermediate model is the simplest model sufficient to describe PEG-mediated fusion in all vesicle systems studied. We conclude as well that a fusion intermediate "state" should not be thought of as a fixed structure (e.g., "stalk" or "transmembrane contact") of uniform properties. Rather, a fusion "state" describes an ensemble of similar structures that can have different mechanical properties. Thus, a "state" can have varying probabilities of having a given functional property such as content mixing, lipid mixing, or leakage. Our data show that the content mixing signal may occur through two processes, one correlated and one not correlated with leakage. Finally, we consider the implications of our results in terms of the "modified stalk" hypothesis for the mechanism of lipid pore formation. We conclude that our results not only support this hypothesis but also provide a means of analyzing fusion time courses so as to test it and gauge the mechanism of action of fusion proteins in the context of the lipidic hypothesis of fusion.     

An inducible mouse model of colon carcinogenesis for the analysis of sporadic and inflammation-driven tumor progression

Colorectal cancer is a life-threatening disease that can develop spontaneously or as a complication of inflammatory bowel diseases. Mouse models are essential tools for the preclinical testing of novel therapeutic options in vivo. Here, we provide a highly reliable protocol for an experimental mouse model to study the development of colon cancers. It is based on the mutagenic agent azoxymethane (AOM), which exerts colonotropic carcinogenicity. Repeated intraperitoneal administration of AOM results in the development of spontaneous tumors within 30 weeks. As an alternative option, inflammation-dependent tumor growth can be investigated by combining the administration of AOM with the inflammatory agent dextran sodium sulfate in drinking water, which causes rapid growth of multiple colon tumors per mouse within 10 weeks. Different scoring systems including number of tumors and tumor size identify factors promoting or inhibiting tumor initiation and/or tumor progression, respectively.     

Measurement of axial diffusivities in a model of the bronchial airways.

Values for the effective axial diffusivity D for laminar flow of a gas species in the bronchial airways have been obtained as a function of the mean axial gas velocity u by experiment measurements of benzene vapor dispersion in a five generation glass tube model of the bronchial tree. For both inspiration and expiration D is seen to be approximately a linear function of u over the range of Reynolds' numbers 30-2,000 corresponding to peak flows in bronchial generations 0-13 under resting breathing conditions. The diffusivity for expiration is seen to be approximately one-third that for inspiration due presumably to increased radial mixing at bifurcations during expiration. The effective diffusivities relative to the molecular diffusivity can be expressed by the formulas D/Dmol = 1 + 1.08 NPe for inspiration and D/Dmol = 1 + .37 N-Pe for expiration. These velocity dependent diffusivities help to explain the short transit times of gas boluses from mouth to alveoli and will aid in the analysis of airway gas mixing by mathematical transport equations.     

A simple method to display molecular orbitals with computer graphics

A computer program named LOBE was developed to draw molecular orbitals as lobes on a graphic display. With this program, any molecular orbital of large molecules can be displayed quickly. This program is suitable not only for general-purpose computers but also for microcomputers. A sample application is used to illustrate the program.     

QSAR of the testosterone binding globulin affinity by means of correlation weighting of local invariants of the graph of atomic orbitals

Numerical values of the testosterone binding globulin affinity have been modeled as a mathematical function of molecular structure in two versions of molecular structure elucidation: first, by hydrogen-filled molecular graphs (HFG); second, by the so-called graphs of atomic orbitals (GAO). Increased orders of Morgan extended connectivity in the HFG and GAO have been examined as local invariants. Using optimisation of the correlation weights of the above-mentioned invariants, quantitative structure–activity relationships (QSAR) have been obtained. Best statistical characteristics of these QSARs are derived in the case of the Morgan extended connectivity of first order in the GAO. They are as follows: n = 11, r² = 0.6540, s = 0.824, F = 17 (training set); n = 9, r² = 0.8791, s = 0.388, F = 51 (test set).     

Distributed Gaussian orbitals for the description of electrons in an external potential

In this work, we demonstrate the viability of using distributed Gaussian orbitals as a basis set for the calculation of the properties of electrons subjected to an external potential. We validate our method by studying one-electron systems for which we can compare to exact analytical results. We highlight numerical aspects that require particular care when using a distributedGaussian basis set. In particular, we discuss the optimal choice for the distance between two neighboring Gaussian orbitals. Finally, we show how our approach can be applied to many-electron problems.     

Population mixing promotes arms race host–parasite coevolution

The consequences of host–parasite coevolution are highly contingent on the qualitative coevolutionary dynamics: whether selection fluctuates (fluctuating selection dynamic; FSD), or is directional towards increasing infectivity/resistance (arms race dynamic; ARD). Both genetics and ecology can play an important role in determining whether coevolution follows FSD or ARD, but the ecological conditions under which FSD shifts to ARD, and vice versa, are not well understood. The degree of population mixing is thought to increase host exposure to parasites, hence selecting for greater resistance and infectivity ranges, and we hypothesize this promotes ARD. We tested this by coevolving bacteria and viruses in soil microcosms and found that population mixing shifted bacteria–virus coevolution from FSD to ARD. A simple theoretical model produced qualitatively similar results, showing that mechanisms that increase host exposure to parasites tend to push dynamics towards ARD. The shift from FSD to ARD with increased population mixing may help to explain variation in coevolutionary dynamics between different host–parasite systems, and more specifically the observed discrepancies between laboratory and field bacteria–virus coevolutionary studies.     

Three-dimensional simulation of grain mixing in three different rotating drum designs for solid-state fermentation

A previously published two-dimensional discrete particle simulation model for radial mixing behavior of various slowly rotating drums for solid-state fermentation (SSF) has been extended to a three-dimensional model that also predicts axial mixing. Radial and axial mixing characteristics were predicted for three different drum designs: (1) without baffles; (2) with straight baffles; and (3) with curved baffles. The axial mixing behavior was studied experimentally with video- and image-analysis techniques. In the drum without baffles and with curved baffles the predicted mixing behavior matched the observed behavior adequately. The predicted axial mixing behavior in the drum with straight baffles was predicted less accurately, and it appeared to be strongly dependent on particle rotation, which was in contrast to the other drum designs. In the drum with curved baffles complete mixing in the radial and axial direction was achieved much faster than in the other designs; that is, it was already achieved after three to four rotations. This drum design may therefore be very well suited to SSF. It is concluded that discrete particle simulations provide valuable detailed knowledge about particle transport processes, and this may help to understand and optimize related heat and mass transfer processes in SSF.     

Discrete particle simulations predicting mixing behavior of solid substrate particles in a rotating drum fermenter.

A soft-sphere discrete particle model was used to simulate mixing behavior of solid substrate particles in a slow rotating drum for solid-state fermentation. In this approach, forces acting on and subsequent motion of individual particles can be predicted. The (2D) simulations were qualitatively and quantitatively validated by mixing experiments using video and image analysis techniques. It was found that the simulations successfully predicted the mixing progress as a function of the degree of filling and size of the drum. It is shown that only relatively large, straight baffles perpendicular to the drum wall (67% of the drum radius) increase the mixing performance of the rotating drum. Considering the different aspects of mixing dealt with in this work, it is concluded that the soft sphere discrete particle model can serve as a valuable tool for investigating mixing of solid substrate particles. Finally, it is expected that this model may evolve into a potential tool for design and scale-up of mixed solid-state fermenters.     

A simple model of the eco-hydrodynamics of the epilimnion of Lake Tanganyika

1. The ecosystem response of Lake Tanganyika was studied using a four-component, nutrient–phytoplankton–zooplankton–detritus, phosphorus-based ecosystem model coupled to a nonlinear, reduced-gravity, circulation model. The ecosystem model, an improved version of the earlier eco-hydrodynamics model developed for Lake Tanganyika, was used to estimate the annual primary production of Lake Tanganyika and its spatial and temporal variability. The simulations were driven with the National Centres for Environmental Protection (NCEP) records for winds and solar radiation forcing.
2. The simulated annual cycles of the four ecosystem variables and the daily net primary production were compared with the observations. The comparison showed that simulations reproduced realistically the general features of the annual cycles of epilimnial phosphate, net primary production and plankton dynamics.
3. The climatic simulations for the years 1970–2006 yielded a daily averaged integrated upper layer net production ranging from 0.11 to 1.78 g C m⁻² day⁻¹ and daily averaged chlorophyll- a (chl- a ) from 0.16 to 4.3 mg m⁻³. Although the nutrient concentrations in the epilimnion during the strong wind years were high, the net production was low, which is partly because of the greater vertical mixing, produced by strong winds, exposing the phytoplankton to low light conditions in deeper waters. The simulated annual net production and chl- a agreed quite well with observed production available in the literature.
4. We envisage using this model to predict the future scenarios of primary productivity in the lake.     

Stable isotopes indicate the extent of freshwater feeding by cormorants Phalacrocorax carbo shot at inland fisheries in England

1. The numbers of cormorants Phalacrocorax carbo feeding at English freshwater fisheries during winter have increased rapidly over the last 20 years, causing concern among fishery managers and anglers.
2. In order to assess the extent of freshwater feeding, stable isotope ratios of carbon and nitrogen (δ¹³C and δ¹⁵N) in feathers of wild cormorants from inland freshwater fisheries were compared with those in the feathers of piscivorous birds with marine diets (captive 'marine-fed' cormorants, free-ranging shags Phalacrocorax aristotelis ) and freshwater diets (juvenile goosanders Mergus merganser ).
3. Isotope signatures of feathers represent the diet at the time of growth. Feathers grown at different times of the year were taken from wild cormorants; each feather type therefore represented the diet over a different temporal scale.
4. Isotopic analyses of feathers indicated that, when shot, nearly all of the cormorants had been feeding entirely on freshwater prey. The mean δ¹³C value of primary feathers growing when birds were shot was –22·2‰, indicative of an entirely freshwater diet.
5. The move to freshwater habitats from coastal breeding grounds occurred over several months, but once established cormorants appear to have fed at freshwater sites throughout the autumn and winter.
6. The suitability of using a two-source isotopic mixing model in order to quantify the extent of freshwater feeding in piscivorous birds is discussed.
7. Although the results indicate long-term residency and feeding in freshwater systems, they do not indicate whether birds were feeding regularly at the sites at which they were shot, or the composition of the diet. It is recommended that further studies using telemetry and multiple isotope analyses be carried out in order to address these issues.