Neuronal activity: from in vitro preparation to behaving animals.

The knowledge of the mechanisms regulating electric neuronal activity is fragmented by the wide variety of techniques and experimental models currently used in neurophysiological research. The interest and importance of the results obtained in any research is improved when interpreted in the perspective of the organism functioning as a whole in physiological conditions. Such interpretation, freed of the constraints imposed by the different techniques and experimental conditions used, is especially important when discussing together results obtained at the behavioral, cellular, and molecular level. This article outlines some of the key factors to consider when experiments from different models are interpreted together.     

Neuronal activity: from in vitro preparation to behaving animals

The knowledge of the mechanisms regulating electric neuronal activity is fragmented by the wide variety of techniques and experimental models currently used in neurophysiological research. The interest and importance of the results obtained in any research is improved when interpreted in the perspective of the organism functioning as a whole in physiological conditions. Such interpretation, freed of the constraints imposed by the different techniques and experimental conditions used, is especially important when discussing together results obtained at the behavioral, cellular, and molecular level. This article outlines some of the key factors to consider when experiments from different models are interpreted together.     

Studies of inclusion complexes of natural and modified cyclodextrin with (+)catechin by NMR and molecular modeling

The aim of this paper is to describe the inclusion properties and the factors affecting the complexation selectivity and stabilization of catechin (CA) into beta-cyclodextrin (beta-CD) and two of its derivatives, namely Heptakis 2,6-di-O-methyl-beta-cyclodextrin (DM-beta-CD) and 2 hydroxypropyl-beta-cyclodextrin (HP-beta-CD). Analysis of the proton shift change using the continuous variation method confirm the formation of a 1:1 stoichiometric complex for catechin and the different CDs in aqueous medium. The formations constant obtained by diffusion-ordered spectroscopy (DOSY) techniques indicated the following trend upon complex formation: beta-CD>HP-beta-CD>DM-beta-CD. The detailed spatial configuration is proposed based on 2D NMR methods. These results are further interpreted using molecular modeling studies. The latter results are in good agreement with the experimental data. The models confirm that when CA-beta-CD is formed, the catechol moiety in the complex is oriented toward the primary rim; however when CD is derivatized to HP-beta-CD and DM-beta-CD this ring is oriented toward the secondary rim.     

Cytotoxicity of copper ions released from metal

The aim of this work is to contribute to the elucidation of the cytotoxic process caused by the copper ions released from the biomaterials. Clonal cell lines UMR106 were used in the experiments. Copper ions were obtained from two different sources: copper salts and metal dissolution. Experiments carried out with constant ion concentrations (copper salts) were compared with those with concentrations that vary with time and location (dissolution of the metal). Present results and others previously reported could be interpreted through mathematical models that describe: (1) the variation of concentration of copper ions with time and location within a biofilm and (2) the variation of the killing rate with the concentration of the toxic ion and time. The large number of dead cells found near the copper sample with an average ion concentration below the toxic limit could be interpreted bearing in mind that these cells should be exposed to a local concentration higher than this limit. A logarithmic dependence between the number of cells and exposure time was found for nearly constant ion concentrations. Apparent discrepancies, observed when these results and those of different researchers were contrasted, could be explained considering the dissimilar experimental conditions such as the source of the ions and their local concentration at real time.     

Growth Curves of Anaerobic Bacteria in Solid Media

Simple pour plate and spectrophotometric techniques for the evaluation of growth curves of several anaerobic bacteria on solid media are described. Three basic patterns of anaerobic growth were observed. The curves obtained were very reproducible when studied on separate occasions. The curves obtained by spectrophotometric measurement were comparable to those obtained by the pour plate method, especially when a large bacterial inoculum was used. Limitations in the interpretation of the results are discussed. The methods and principles reported could provide the basis for the determination of bacterial growth on solid media using other organisms and different experimental conditions.     

A comparison of absolute performance of different correlative and mechanistic species distribution models in an independent area

To investigate the comparative abilities of six different bioclimatic models in an independent area, utilizing the distribution of eight different species available at a global scale and in Australia. Global scale and Australia. We tested a variety of bioclimatic models for eight different plant species employing five discriminatory correlative species distribution models (SDMs) including Generalized Linear Model (GLM), MaxEnt, Random Forest (RF), Boosted Regression Tree (BRT), Bioclim, together with CLIMEX (CL) as a mechanistic niche model. These models were fitted using a training dataset of available global data, but with the exclusion of Australian locations. The capabilities of these techniques in projecting suitable climate, based on independent records for these species in Australia, were compared. Thus, Australia is not used to calibrate the models and therefore it is as an independent area regarding geographic locations. To assess and compare performance, we utilized the area under the receiver operating characteristic (ROC) curves (AUC), true skill statistic (TSS), and fractional predicted areas for all SDMs. In addition, we assessed satisfactory agreements between the outputs of the six different bioclimatic models, for all eight species in Australia. The modeling method impacted on potential distribution predictions under current climate. However, the utilization of sensitivity and the fractional predicted areas showed that GLM, MaxEnt, Bioclim, and CL had the highest sensitivity for Australian climate conditions. Bioclim calculated the highest fractional predicted area of an independent area, while RF and BRT were poor. For many applications, it is difficult to decide which bioclimatic model to use. This research shows that variable results are obtained using different SDMs in an independent area. This research also shows that the SDMs produce different results for different species; for example, Bioclim may not be good for one species but works better for other species. Also, when projecting a “large” number of species into novel environments or in an independent area, the selection of the “best” model/technique is often less reliable than an ensemble modeling approach. In addition, it is vital to understand the accuracy of SDMs' predictions. Further, while TSS, together with fractional predicted areas, are appropriate tools for the measurement of accuracy between model results, particularly when undertaking projections on an independent area, AUC has been proved not to be. Our study highlights that each one of these models (CL, Bioclim, GLM, MaxEnt, BRT, and RF) provides slightly different results on projections and that it may be safer to use an ensemble of models.     

Membrane vesicles in the study of transport processes: a critical analysis of the experimental procedure

A critical analysis of the use of membrane vesicles in the study of cotransport processes is presented. Transport experiments were simulated according to two different models, stressing those conditions that seemed more relevant in affecting the measurements. In particular, we observed that the experimental Vmax values were underestimated. This underevaluation depended on the incubation time employed to measure the initial uptake rate and on the time necessary to wash the vesicles. Also the temperature and the composition of the washing solution, together with the Q10 of the transport process taken into consideration, had a consistent influence on the uptake. All the above mentioned effects were affected by the vesicle volume: the smaller the volume, the greater the underestimate of the uptake. This theoretical analysis underlines, on the one side, that the experimental data should be interpreted with some caution, on the other, that the examined procedure allows an internal check of its validity by adopting suitable simulations of the experiments. The use of the presented models as a tool for the planning and the critical analysis of the experimental results is suggested.     

Empirical validation of SAR values predicted by FDTD modeling.

Rapid increase in the use of numerical techniques to predict current density or specific absorption rate (SAR) in sophisticated three dimensional anatomical computer models of man and animals has resulted in the need to understand how numerical solutions of the complex electrodynamics equations match with empirical measurements. This aspect is particularly important because different numerical codes and computer models are used in research settings as a guide in designing clinical devices, telecommunication systems, and safety standards. To ensure compliance with safety guidelines during equipment design, manufacturing and maintenance, realistic and accurate models could be used as a bridge between empirical data and actual exposure conditions. Before these tools are transitioned into the hands of health safety officers and system designers, their accuracy and limitations must be verified under a variety of exposure conditions using available analytical and empirical dosimetry techniques. In this paper, empirical validation of SAR values predicted by finite difference time domain (FDTD) numerical code on sphere and rat is presented. The results of this study show a good agreement between empirical and theoretical methods and, thus, offer a relatively high confidence in SAR predictions obtained from digital anatomical models based on the FDTD numerical code.     

Method of determination of three dimensional index finger moment arms and tendon lines of action using high resolution MRI scans

High-resolution MRI scans, in conjunction with CAD software, were used to determine the three-dimensional moment arms and force vector direction cosines for 11 structures passing the interphalangeal and metacarpophalangeal joints of the index finger. The results are presented for five different angles of joint flexion for a single subject. The moment arm data obtained differ from previous studies, where results have been derived from tendon excursion techniques or geometrical models. These dissimilarities have been accounted for by the differences in experimental techniques.     

Deformability of red blood cells from different species studied by resistive pulse shape analysis technique

The Cell Transit Analyzer (CTA) is now being used widely in clinical hemorheology. Most of the data obtained by CTA are limited to human blood, although the CTA has an important potential to be used in experimental studies on animal models. However, behavior of red blood cells (RBC) from various species might be different in CTA. Eight parameters reflecting different aspects of cell passage through pores with 5 μm diameter and 15 μm length were determined or human, guinea pig, dog, rabbit, rat, mouse and sheep RBC, together with instrument precision and biological variation. These parameters have a wide range when measured in different species and correlate with cell volume. Sensitivity of these parameters to the glutaraldehyde-induced alterations in RBC deformability was not same for different laboratory mammals. The main reason for this difference seems to be related to the cell size and thus sensitivity might be significantly limited if 5 μm pore-size filters are used to test the smaller RBC. The results of this study may help in designing experimental studies on laboratory mammals using the CTA.     

From components to regulatory motifs in signalling networks.

The developments in biochemistry and molecular biology over the past 30 years have produced an impressive parts list of cellular components. It has become increasingly clear that we need to understand how components come together to form systems. One area where this approach has been growing is cell signalling research. Here, instead of focusing on individual or small groups of signalling proteins, researchers are now using a more holistic perspective. This approach attempts to view how many components are working together in concert to process information and to orchestrate cellular phenotypic changes. Additionally, the advancements in experimental techniques to measure and visualize many cellular components at once gradually grow in diversity and accuracy. The multivariate data, produced by experiments, introduce new and exciting challenges for computational biologists, who develop models of cellular systems made up of interacting cellular components. The integration of high-throughput experimental results and information from legacy literature is expected to produce computational models that would rapidly enhance our understanding of the detail workings of mammalian cells.     

Improving prediction of chickpea wilt severity using machine learning coupled with model combination techniques under field conditions

Accurate estimation of disease severity in the field is a key to minimize the yield losses in agriculture. Existing disease severity assessment methods have poor accuracy under field conditions. To overcome this limitation, this study used thermal and visible imaging with machine learning (ML) and model combination (MC) techniques to estimate plant disease severity under field conditions. Field experiments were conducted during 2017–18, 2018–19 and 2021–22 to obtain RGB and thermal images of chickpea cultivars with different levels of wilt resistance grown in wilt sick plots. ML models were constructed using four different datasets created using the wilt severity and image derived indices. ML models were also combined using MC techniques to assess the best predictor of the disease severity. Results indicated that the Cubist was the best ML model, while the KNN model was the poorest predictor of chickpea wilt severity under field conditions. MC techniques improved the prediction accuracy of wilt severity over individual ML models. Combining ML models using the least absolute deviation technique gave the best predictions of wilt severity. The results obtained in the present study showed the MC techniques coupled with ML models improved the prediction accuracies of plant disease severity under field conditions.     

Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models

Decades after the prion protein was implicated in transmissible spongiform encephalopathies, the structure of its toxic isoform and its mechanism of toxicity remain unknown. By gathering available experimental data, albeit low resolution, a few pieces of the prion puzzle can be put in place. Currently, there are two fundamentally different models of a prion protofibril. One has its building blocks derived from a molecular dynamics simulation of the prion protein under amyloidogenic conditions, termed the spiral model. The other model was constructed by threading a portion of the prion sequence through a beta-helical structure from the Protein Data Bank. Here we compare and contrast these models with respect to all of the available experimental information, including electron micrographs, symmetries, secondary structure, oligomerization interfaces, enzymatic digestion, epitope exposure, and disaggregation profiles. Much of this information was not available when the two models were introduced. Overall, we find that the spiral model is consistent with all of the experimental results. In contrast, it is difficult to reconcile several of the experimental observables with the beta-helix model. While the experimental constraints are of low resolution, in bringing together the previously disconnected experiments, we have developed a clearer picture of prion aggregates. Both the improved characterization of prion aggregates and the existing atomic models can be used to devise further experiments to better elucidate the misfolding pathway and the structure of prion protofibrils.     

Electrotonic transmission in the mammalian central nervous system (author's transl]

The aim of this review is to present the electrophysiological data, obtained in the mammalian central nervous system, which show that depolarisations recorded intracellularly, under certain experimental conditions can be interpreted in terms of electrotonic coupling. The results were obtained from very different structures: primary sensory nuclei, sensori-motor integration centres and motor nuclei. The association of the phenomenon of electrotonic transmission with a known ultrastructural substrate--the "gap junction"--has been defined by the term electrotonic coupling. In the cases where it has not been possible to link depolarisations with the presence of gap junctions, other possible morphological correlates have been envisaged. The functional significance of electrotonic interactions are discussed on the basis of information obtained from different experimental approaches.     

The Entry of Sodium into Human Red Blood Cells in Vivo

The kinetics of sodium, movement into human red blood cells has been studied in vivo with ²⁴Na. When human serum albumin^-131I is used to measure the percentage of plasma trapped in the packed red blood cells after centrifugation, approximately 30 % of red blood cell sodium is found to equilibrate immediately with plasma. It is concluded that this immediately exchangeable compartment of red blood cell sodium is an experimental artefact, associated with the use of labeled albumin for measuring plasma trapping. This immediately exchangeable fraction disappears when sucrose-¹⁴C is used to measure plasma trapping. The experimental results were examined by compartmental analysis, using an analogue computer. The results obtained, when plasma trapping was measured with sucrose-¹⁴C could be simulated by the use of models containing two compartments, arranged in series or in parallel. The errors of the techniques used and the possible physical basis for the results are discussed.     

Qualitative holographic study of hemi-pelvic deformation caused by loading different hip prostheses

The dynamic biological response of bone can materially influence the longevity of artificial implants. This paper presents a series of in vitro experiments conducted on epoxy resin models of human hemi-pelves. Different commercially available acetabular components were implanted and used for the construction of simplified three-dimensional models of the artificial hip joint. Boundary conditions included simulation of muscle groups and femoral loading. Real-time holographic interferometry, a stress analysis technique permitting whole-field simultaneous inspection of deformation patterns, was used as the experimental method. The holographic interferograms were interpreted qualitatively rather than quantitatively. High stresses were identified in the hemi-pelvis and it is postulated that these stresses may be implicated in the mechanical pathogenesis of loosening. The obser ed changes in the detected stress levels could influence both future design of acetabular prostheses and surgical techniques.     

Recognition of errors in three-dimensional structures of proteins

A major problem in the determination of the three-dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. New developments in X-ray crystallography and nuclear magnetic resonance spectroscopy have acceleratedd the process of structure determination and the biological community is confronted with a steadily increasing number of experimentally determined protein folds. However, in the recent past several experimentally determined protein structures have been proven to contain major errors, indicating that in some cases the interpretation of experimental data is difficult and may yield incorrect models. Such problems can be avoided when computational methods are employed which complement experimental structure determinations. A prerequisite of such computational tools is that they are independent of the parameters obtained from a particular experiment. In addition such techniques are able to support and accelerate experimental structure determinations. Here we present techniques based on knowledge based mean fields which can be used to judge the quality of protein folds. The methods can be used to identify misfolded structures as well as faulty parts of structural models. The techniques are even applicable in cases where only the C_α trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds. © 1993 Wiley-Liss, Inc.     

Inheritance of body size in the Barnacle Goose under different environmental conditions

Heritabilities, genetic variances and covariances for body size traits, i.e. tarsus length, head length and body mass, were estimated under different environmental conditions in a Barnacle Goose (Branta leucopsis) population. Under poor growth conditions, that is, when average body size of fully grown offspring in a given cohort was small, the offspring-parent regressions and full-sib analyses yielded heritability estimates not significantly different from zero. By contrast, when growth conditions were normal or good the heritability estimates were generally significantly positive. Comparisons of genetic covariance estimates indicated that they also differed across the analysed environmental conditions. This result, together with similar results obtained in studies of passerine birds, suggests that genotype-environment interactions might be frequent within the range of environments normally encountered by birds in natural populations. If general, such results might question the validity of assuming approximate constancy of additive genetic variances and covariances over time and environments in evolutionary models.     

Epithelial transport parameters: an analysis of experimental strategies

A set of experiments was simulated on a computer version of the Koefoed-Johnsen & Ussing model for high-resistance epithelia. The results obtained were analysed according to procedures commonly applied to the analyses of experimental data and interpreted in terms of the model parameters. Although the computer model encodes a stoichiometry of 3:2 for Na-K exchange through the Na pump, the simulation of published experimental procedures yields different figures in almost every case. We show that ENa as originally defined by Ussing & Zerahn (Acta physiol. scand. 23, 110-127 (1951)) and as obtained from flux-ratio experiments has different values under different experimental conditions with unchanged system parameters and that it is distinct from ENa measured by other methods. We also show that unless the pump is saturated with internal Na an increase in the rate of pumping cannot cause a substantial increase in the rate of transepithelial Na transport.     

Applied models to biodegradation kinetics of lubricant and vegetable oils in wastewater

Bioremediation technologies are used in order to remove pollutants from the environment in a safe, economical and harmless way during the treatment of waste, especially with the use of techniques such as biodegradation. A lubricant and vegetable oil contaminated water sample was studied in order to evaluate the biodegradability of different types of oils, considering the relevance of the obtained data in the bioremediation procedures. The objective of this paper is to use respirometry technique as a biodegradation process data source, and then apply to the obtained data the experimental design of mathematical models to characterize and determinate how the different types of oils are capable of affecting the parameters in biodegradation kinetics. The kinetics was then evaluated through selected models with a reasonable fit to experimental data. The Bartha and Pramer respirometer is used as a method to accurately measure the CO₂ formation in the organic compounds degradation by microorganisms. Therefore, the difference in biodegradation efficiency process is compared in the different groups of oils using mathematical models fitting the obtained data for the kinetics of biodegradation. The results demonstrated that used lubricant automotive oils are more susceptible to the biodegradation process, since their molecular structures had already been altered after use. In general, automotive lubricant oils shown better performance in biodegradation than vegetable oils. The models proposed for the obtained data in each of these assays demonstrated that vegetable oils biodegradation rate tends to decrease faster and end sooner than the automotive oils. Also, the modeling predicted that higher rates of biodegradation and total CO₂ production are to be expected in automotive lubricant oils rather than vegetable oils.