Comparative systemic analysis of experimental models of chemical hepatic carcinogenesis in the rat

The aim of this work is to compare several experimental protocols inducing hepatocarcinogenesis in the rat. The results show that the experimental protocols using an initiator and a promotor are not equivalent (in term of latency period and premalignant lesions) to experimental protocols using a chronic administration of one carcinogenic compound.     

Relation between calculated amide frequencies and solution structure in Ala-X peptides

Computational techniques have been used to aid interpretation of observed systematic shifts in the amide III frequencies of Ala-X peptides. Optimized structures and frequencies have been calculated for Ala-X peptides using GAUSSIAN86/88 with the 4-31G basis, MOPAC, and normal mode methods based on empirical force fields. We observe the following: (1) Frequencies calculated using scaled GAUSSIAN86 force constants correlate well with the experimental results. (2) Structures of the Ala-X peptides optimized by GAUSSIAN show a clear trend toward lower values of the dihedral angle phi as the X side chain becomes larger, while structures optimized here using semiempirical and empirical force fields do not show trends. (3) Computational changes in peptide conformations from beta-sheet to alpha-helix produce large changes in both amide I and amide III frequencies that are inconsistent with the experimental results. (4) Computational changes in the dihedral angle phi of Ala-Ala produce a change in the amide III frequency consistent with the experimental results. (5) The experimental frequency shifts cannot be attributed directly to the effects of changing mass.     

Weak acid transport across bilayer lipid membrane in the presence of buffers. Theoretical and experimental pH profiles in the unstirred layers.

This paper presents a simple model to describe experimental data on weak acid transport across planar bilayer lipid membrane separating two buffered solutions. The model takes into account multiple proton-transfer reactions occurring in the unstirred layers (ULs) adjacent to the membrane. Differential equations of the model are shown to be reduced to a set of nonlinear algebraic equations. Since the latter equations depend monotonically on unknown variables, they can be easily solved numerically, using bisection method. For the particular system studied experimentally (with acetate as the weak acid and TRIS+MES as the buffer mixture) pH profiles in the ULs are calculated from the model. These results are compared with experimental data obtained using pH microelectrode. The agreement between theoretical and experimental pH profiles is found to be satisfactory. The most pronounced deviations are observed at the UL/bulk solution boundary. To obtain a better correlation between the theoretical and experimental results, two other, less idealized models are considered. They take into account, respectively, (a) the electric field arising in the ULs from ion diffusion and (b) finiteness of the rates of proton-transfer reactions. However, both acetate membrane fluxes and pH profiles in the ULs computed from these models are found to be close to those of the simple model. One can thus conclude that the difference between experimental and theoretical pH profiles is due to the inconsistency of the generally accepted model of the "unstirred layer", assuming the existence of a strict boundary between the regions of "pure diffusion" and "ideal stirring".     

Validation and characterization of uninhibited enzyme kinetics performed in multiwell plates

Several systematic errors may occur during the analysis of uninhibited enzyme kinetic data using commercially available multiwell plate reader software. A MATLAB program is developed to remove these systematic errors from the data analysis process for a single substrate-enzyme system conforming to Michaelis-Menten kinetics. Three experimental designs that may be used to validate a new enzyme preparation or assay methodology and to characterize an enzyme-substrate system, while capitalizing on the ability of multiwell plate readers to perform multiple reactions simultaneously, are also proposed. These experimental designs are used to (i) test for enzyme inactivation and the quality of data obtained from an enzyme assay using Selwyn's test, (ii) calculate the limit of detection of the enzyme assay, and (iii) calculate Km and Vm values. If replicates that reflect the overall error in performing a measurement are used, the latter two experiments may be performed with internal estimation of the error structure. The need to correct for the systematic errors discussed and the utility of the proposed experimental designs were confirmed by numerical simulation. The proposed experiments were conducted using recombinant inducible nitric oxide synthase preparations and the oxyhemoglobin assay.     

Exploratory recruitment plasticity in a social spider (Anelosimus eximius)

Exploratory recruitment was investigated in an artificial experimental set-up on location in French Guyana. Groups of 200 freshly collected spiders of the neotropical social theridiid Anelosimus eximius were released on an open circular surface and offered a choice between two accessible shelters. Results indicated that a clear-cut collective decision was not always reached, unlike what we found using a different set-up in another set of experiments. Simulations were conducted using available information in order to explore the potential causes for this difference. Theoretical projections fit experimental data and strongly suggest that variability in the collective response results from a combination between modifications of the environment's properties and alteration of the recruitment procedure. Multiple variants of the theoretical set-up (including external bias) are investigated and emphasize plasticity in the collective response. New experimental studies are suggested and adaptative value of exploratory recruitment in social spiders is briefly discussed.     

Triethanolammonium acetate as a multifunctional ionic liquid in the palladium-catalyzed green Heck reaction

An efficient green Heck reaction protocol was performed using a triethanolammonium acetate ionic liquid–palladium(II) catalytic system. The ionic liquid used acts as a reaction medium, base, precatalyst-precursor, and mobile support for the active Pd species. Our experimental investigation indicates that performing the Heck reaction in ionic liquid is superior to the same procedure carried out in triethanolamine. The mechanism of the reaction of triethanolammonium acetate with PdCl₂ was examined using density functional theory (M06 method). It was found that two Pd(II) complexes are formed, one of which acts further as a precatalyst yielding catalytically active Pd(0) complex. The calculated activation energies are in agreement with our experimental findings.     

Inter-annual variability of NDVI in response to long-term warming and fertilization in wet sedge and tussock tundra

This study explores the relationship between the normalized difference vegetation index (NDVI) and aboveground plant biomass for tussock tundra vegetation and compares it to a previously established NDVI–biomass relationship for wet sedge tundra vegetation. In addition, we explore inter-annual variation in NDVI in both these contrasting vegetation communities. All measurements were taken across long-term experimental treatments in wet sedge and tussock tundra communities at the Toolik Lake Long Term Ecological Research (LTER) site, in northern Alaska. Over 15 years (for wet sedge tundra) and 14 years (for tussock tundra), N and P were applied in factorial experiments (N, P and N+P), air temperature was increased using greenhouses with and without N+P fertilizer, and light intensity was reduced by 50% using shade cloth. during the peak growing seasons of 2001, 2002, and 2003, NDVI measurements were made in both the wet sedge and tussock tundra experimental treatment plots, creating a 3-year time series of inter-annual variation in NDVI. We found that: (1) across all tussock experimental tundra treatments, NDVI is correlated with aboveground plant biomass (r ²=0.59); (2) NDVI–biomass relationships for tussock and wet sedge tundra communities are community specific, and; (3) NDVI values for tussock tundra communities are typically, but not always, greater than for wet sedge tundra communities across all experimental treatments. We suggest that differences between the response of wet sedge and tussock tundra communities in the same experimental treatments result from the contrasting degree of heterogeneity in species and functional types that characterize each of these Arctic tundra vegetation communities.     

Dark nests and egg colour in birds: a possible functional role of ultraviolet reflectance in egg detectability

Owing to the conspicuousness of ultraviolet (UV) colour in dark environments, natural selection might have selected UV egg coloration because it would enhance egg detectability by parents in murky nests. Here, we tested this hypothesis by using comparative and experimental approaches. First, we studied variation in egg coloration of 98 species of European passerines measured using UV-visible reflectance spectrometry (300-700nm) in relation to nesting habits. Analyses based on raw data and controlling for phylogenetic distances both at the species and the family levels revealed that hole-nester species produced eggs with higher UV reflectance than those nesting in open habitats. The experimental approach consisted of the manipulation of UV reflectance of the experimental eggs introduced outside the nest-cup of the hole-nester spotless starling Sturnus unicolor and the study of the retrieval of these eggs. Ultraviolet-reflecting eggs (controls) were more frequently retrieved to the nest-cup than non-reflecting (-UV) eggs. These results were not due to '-UV' eggs being recognized by starlings as parasitic because when a parasitic egg is detected, starlings removed it from the nest-box. Therefore, these results are consistent with the hypothesis that UV egg colours are designed to provide highly detectable targets for parent birds in dark nest environments.     

How to quantify protein diffusion in the bacterial membrane

Lateral diffusion of proteins in the plane of a biological membrane is important for many vital processes, including energy conversion, signaling, chemotaxis, cell division, protein insertion, and secretion. In bacteria, all these functions are located in a single membrane. Therefore, quantitative measurements of protein diffusion in bacterial membranes can provide insight into many important processes. Diffusion of membrane proteins in eukaryotes has been studied in detail using various experimental techniques, including fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), and particle tracking using single-molecule fluorescence (SMF) microscopy. In case of bacteria, such experiments are intrinsically difficult due to the small size of the cells. Here, we review these experimental approaches to quantify diffusion in general and their strengths and weaknesses when applied to bacteria. In addition, we propose a method to extract multiple diffusion coefficients from trajectories obtained from SMF data, using cumulative probability distributions (CPDs). We demonstrate the power of this approach by quantifying the heterogeneous diffusion of the bacterial membrane protein TatA, which forms a pore for the translocation of folded proteins. Using computer simulations, we study the effect of cell dimensions and membrane curvature on measured CPDs. We find that at least two mobile populations with distinct diffusion coefficients (of 7 and 169 nm(2) ms(-1) , respectively) are necessary to explain the experimental data. The approach described here should be widely applicable for the quantification of membrane-protein diffusion in living bacteria.     

Models of skeletal muscle to explain the increase in passive stiffness in desmin knockout muscle

Absence of desmin in skeletal muscle was found to induce an increase in passive stiffness. The present study aimed at developing rheological models of passive muscle to explain this stiffening. Models were elaborated by using experimental data depicting muscle viscoelastic behaviour. The experimental protocol included stepwise extension tests applied on control and desmin knockout soleus muscles from mice. Linear and non-linear models were composed of elastic and viscous elements. They were constructed with the aim at taking the presence or absence of desmin into account by simulating desmin as an elastic element. Furthermore, associated adaptation of connective tissues in absence of desmin was modelled as an additional elastic element. Differences in passive behaviour induced by absence of desmin were predicted by using a linear model and a non-linear one. The non-linear model was selected because: (1) it is able to predict experimental viscoelastic kinetics accounting for the increase in passive stiffness in muscles lacking desmin, (2) its design is consistent with morphological data, and (3) stiffness characteristics of its elements are in accordance with the literature. Finally, this modelling approach demonstrates that both absence of desmin and adaptation of connective tissue are required to explain the increase in passive stiffness in desmin knockout muscles.     

Unmatched masses in peptide mass fingerprints caused by cross-contamination: an updated statistical result

Unmatched masses are often observed in the experimental peptide mass spectra when database searching is performed with the ProFound program. Comparison between theoretical and experimental mass spectra of standard proteins shows that contamination accounts for most of the unmatched masses. In this retrospective analysis, the top 100 most probable contaminating masses, as listed in order of their probability, are statistically filtered out from 118 different experimental peptide mass fingerprinting (PMF) maps. Most of the interfering masses originate from trypsin autolysis and human keratins. Subtraction of known contaminants from raw data and using cleaner masses for searching can enhance protein identification by PMF.     

On using time-averaging restraints in molecular dynamics simulation

Introducing experimental values as restraints into molecular dynamics (MD) simulations to bias the values of particular molecular properties, such as nuclear Overhauser effect intensities or distances, 3J coupling constants, chemical shifts or crystallographic structure factors, towards experimental values is a widely used structure refinement method. To account for the averaging of experimentally derived quantities inherent in the experimental techniques, time-averaging restraining methods may be used. In the case of structure refinement using 3J coupling constants from NMR experiments, time-averaging methods previously proposed can suffer from large artificially induced structural fluctuations. A modified time-averaged restraining potential energy function is proposed which overcomes this problem. The different possible approaches are compared using stochastic dynamics simulations of antamanide, a cyclic peptide of ten residues.     

An explicit solution for progress curve analysis in systems characterized by endogenous substrate production

The Lambert W function was used to explicitly relate substrate concentration S, to time t, and the kinetic parameters V (m), K (m), and R in the modified Michaelis-Menten equation that accounts for endogenous substrate production. The applicability of this explicit formulation for kinetic parameter estimation by progress curve analysis was demonstrated using a combination of synthetic and experimental substrate depletion data. Synthetic substrate depletion data were generated using S (0) values of 1, 2, and 3 μM and V (m), K (m), and R values of 1.0 μM h(-1), 1.0 μM, and 0.1 μM h(-1), respectively, and contained 5% normally distributed error. Experimental data were obtained from two previously published studies on hydrogen depletion in four experimental systems. In all instances, experimental data were well described by the explicit solution presented in this study. Differential equation solution and iterative S estimation are eliminated with the explicit solution approach, thereby simplifying progress curve analysis in systems characterized by endogenous substrate production.     

Sorption and precipitation of metals in activated sludge

A conceptual model describing the relative roles of sorption and precipitation processes for metals in solid-solution suspensions is presented. The model performance is demonstrated using experimental data on sorption and precipitation of metals in samples of activated sludge mixed liquor. Based on the experimental results presented here, it appears that, at total metal and mixed liquor suspended solids concentrations and pH values generally encountered in full-scale municipal (or combined municipal/industrial) activated sludge systems, metals are primarily removed by sorption processes.     

Assessing Differences in Sperm Competitive Ability in Drosophila

Competition among conspecific males for fertilizing the ova is one of the mechanisms of sexual selection, i.e. selection that operates on maximizing the number of successful mating events rather than on maximizing survival and viability ¹. Sperm competition represents the competition between males after copulating with the same female ², in which their sperm are coincidental in time and space. This phenomenon has been reported in multiple species of plants and animals ³. For example, wild-caught D. melanogaster females usually contain sperm from 2-3 males ⁴. The sperm are stored in specialized organs with limited storage capacity, which might lead to the direct competition of the sperm from different males ^2,5.Comparing sperm competitive ability of different males of interest (experimental male types) has been performed through controlled double-mating experiments in the laboratory ^6,7. Briefly, a single female is exposed to two different males consecutively, one experimental male and one cross-mating reference male. The same mating scheme is then followed using other experimental male types thus facilitating the indirect comparison of the competitive ability of their sperm through a common reference. The fraction of individuals fathered by the experimental and reference males is identified using markers, which allows one to estimate sperm competitive ability using simple mathematical expressions ^7,8. In addition, sperm competitive ability can be estimated in two different scenarios depending on whether the experimental male is second or first to mate (offense and defense assay, respectively) ⁹, which is assumed to be reflective of different competence attributes.Here, we describe an approach that helps to interrogate the role of different genetic factors that putatively underlie the phenomenon of sperm competitive ability in D. melanogaster.     

Use of the photoelastic method and finite element analysis in the assessment of wall strain in abdominal aortic aneurysm models

Abdominal aortic aneurysm (AAA) is a significant health problem. Current clinical rupture-risk relies primarily on the maximum diameter of the AAA and also growth rate. However, AAAs are a patient-specific problem and recently, numerical tools have been employed to estimate rupture-potential. Alternatively, experimental assessment of AAA biomechanics receives less attention, yet, rigorous validation of numerical tools is required prior to clinical acceptance. This paper examines the use of the photoelastic method to assess wall strain and its validation using finite element analysis (FEA) in a small number of patient-specific AAA models. Experimental models were manufactured in-house using the injection-moulding procedure together with a commercially available photoelastic material. The material was mechanically characterised prior to testing, with models examined under three loading regimes (80, 120 and 160mmHg). Each experimental model was imaged using computed tomography (CT) and reconstructed in three dimensions (3D) for numerical analyses. Experimental wall strain was measured and numerical wall strain calculated with finite element analysis (FEA). Results were qualitatively and quantitatively compared. There was good qualitative agreement between the experimental and numerical methods, with similar trends apparent throughout all models at all pressures. Overall, acceptable percentage errors between the techniques were observed for all models. Median errors of -6.5%, -0.4% and 3.9% for the models at 80, 120 and 160mmHg pressures, respectively, were determined. The photoelastic method is a very useful experimental tool that provides instant, easy to interpret, information regarding wall strain. The technique is useful for validation of numerical AAA studies.     

Asbestos and glass fibres in bacterial mutation tests.

Asbestos fibres are carcinogenic in man and experimental animals but fine glass fibres are known, at present, only to be carcinogenic in experimental animals. Asbestos and glass fibres have been studied in mutation tests using auxotrophic strains of Escherichia coli and Salmonella typhimurium. The mutagenic activities of the positive control mutagens ultraviolet light, potassium chromate, ethyl methanesulphonate and benzo(a)pyrene were detected in the experiments. However, no mutagenic activity was found to be associted with any of the asbestos and glass fibres tested over a wide range of concentrations. The implications of these findings for the mode of action of asbestos and glass fibres as carcinogens are discussed.     

Study of the radial distribution of the magnetic field in the wire array plasma at the Angara-5-1 facility

Results are presented from experimental studies of the implosion of wire (tungsten, aluminum, and molybdenum) and fiber (kapron) arrays at the Angara 5-1 facility at currents of up to 4 MA. The radial distributions of the azimuthal magnetic field in the stage of plasma production in such arrays are measured in detail for the first time, and the radial profiles of the current density are evaluated. The data obtained using an optical streak camera are compared with the results of measurements of the current and voltage. Using the obtained experimental results, the rate of plasma production in the arrays made of different materials is estimated.     

Guidelines for the design and statistical analysis of experiments using laboratory animals

For ethical and economic reasons, it is important to design animal experiments well, to analyze the data correctly, and to use the minimum number of animals necessary to achieve the scientific objectives---but not so few as to miss biologically important effects or require unnecessary repetition of experiments. Investigators are urged to consult a statistician at the design stage and are reminded that no experiment should ever be started without a clear idea of how the resulting data are to be analyzed. These guidelines are provided to help biomedical research workers perform their experiments efficiently and analyze their results so that they can extract all useful information from the resulting data. Among the topics discussed are the varying purposes of experiments (e.g., exploratory vs. confirmatory); the experimental unit; the necessity of recording full experimental details (e.g., species, sex, age, microbiological status, strain and source of animals, and husbandry conditions); assigning experimental units to treatments using randomization; other aspects of the experiment (e.g., timing of measurements); using formal experimental designs (e.g., completely randomized and randomized block); estimating the size of the experiment using power and sample size calculations; screening raw data for obvious errors; using the t-test or analysis of variance for parametric analysis; and effective design of graphical data.