CLONING: a microcomputer program for cloning simulations

A comprehensive computational tool is presented that performs cloning simulations using IBM PC/XT/AT or compatible microcomputers. The CLONING program contains a specific data base for restriction sites, gene markers, fragment sources and reference comments. It draws complete linear or circular maps either on the screen or employing conventional dot-matrix printers. The design of new recombinant molecules is a totally interactive process.     

Habituating pigs for in-pen, non-invasive biophysical skin analysis.

The purpose of this study was to develop a method for habituating pigs (Sus scrofa domestica, middle white strain) to enable non-invasive, biophysical measurements of dorsal skin to be obtained on a daily basis over a 7-week period, thus eliminating the need for anaesthesia or restraint. This was accomplished by associating measurements of transepidermal water loss (TEWL) and skin reflectance spectroscopy (SRS) with feeding times, and with positive reinforcement by allowing exercise outside the home pen. During the pig habituation period, a well-defined series of behavioural changes were observed that included dominant/ submissive leadership changes. Values of TEWL (6.29 +/- 1.25g.m(-2) x h(-1)) were in agreement with previous studies (7.56+/-2.90g.m 2 x h(-1)) obtained from unrestrained Yucatan hairless micro-pigs (Gabard et al. 1995). The coefficient of variance of TEWL and SRS measurements were comparable with those reported previously using anaesthetized pigs (Chilcott et al. 2000). These data imply that biophysical skin measurements obtained from unrestrained, conscious animals are comparable to those obtained from anaesthetized pigs and therefore, support the use of unrestrained pigs for non-invasive biophysical skin measurements. Habituating animals for in-pen, non-invasive, biophysical measurements has substantial implications for reducing and refining laboratory animal experiments in dermatological research without compromising animal welfare.     

Inclusion Body Myositis: A View from the <Emphasis Type="Italic">Caenorhabditis elegans</Emphasis> Muscle

Inclusion body myositis (IBM) is the most common myopathy in people over 50 years of age. It involves an inflammatory process that, paradoxically, does not respond to anti-inflammatory drugs. A key feature of IBM is the presence of amyloid-β-peptide aggregates called amyloid deposits, which are also characteristic of Alzheimer’s disease. The use of animals that mimic at least some characteristics of a disease has become very important in the quest to elucidate the molecular mechanisms underlying this and other pathogeneses. Although there are some transgenic mouse strains that recreate some aspects of IBM, in this review, we hypothesize that the great degree of similarity between nematode and human genes known to be involved in IBM as well as the considerable conservation of biological mechanisms across species is an important feature that must be taken into consideration when deciding on the use of this nematode as a model. Straightforward laboratory techniques (culture, transformation, gene knockdown, genetic screenings, etc.) as well as anatomical, physiological, and behavioral characteristics add to the value of this model. In the present work, we review evidence that supports the use of Caenorhabditis elegans as a biological model for IBM.     

Individual-based modeling of phytoplankton: evaluating approaches for applying the cell quota model

Present phytoplankton models typically use a population-level (lumped) modeling (PLM) approach that assumes average properties of a population within a control volume. For modern biogeochemical models that formulate growth as a nonlinear function of the internal nutrient (e.g. Droop kinetics), this averaging assumption can introduce a significant error. Individual-based (agent-based) modeling (IBM) does not make the assumption of average properties and therefore constitutes a promising alternative for biogeochemical modeling. This paper explores the hypothesis that the cell quota (Droop) model, which predicts the population-average specific growth or cell division rate, based on the population-average nutrient cell quota, can be applied to individual algal cells and produce the same population-level results. Three models that translate the growth rate calculated using the cell quota model into discrete cell division events are evaluated, including a stochastic model based on the probability of cell division, a deterministic model based on the maturation velocity and fraction of the cell cycle completed (maturity fraction), and a deterministic model based on biomass (carbon) growth and cell size. The division models are integrated into an IBM framework (iAlgae), which combines a lumped system representation of a nutrient with an individual representation of algae. The IBM models are evaluated against a conventional PLM (because that is the traditional approach) and data from a number of steady and unsteady continuous (chemostat) and batch culture laboratory experiments. The stochastic IBM model fails the steady chemostat culture test, because it produces excessive numerical randomness. The deterministic cell cycle IBM model fails the batch culture test, because it has an abrupt drop in cell quota at division, which allows the cell quota to fall below the subsistence quota. The deterministic cell size IBM model reproduces the data and PLM results for all experiments and the model parameters (e.g. maximum specific growth rate, subsistence quota) are the same as those for the PLM. In addition, the model-predicted cell age, size (carbon) and volume distributions are consistent with those derived analytically and compare well to observations. The paper discusses and illustrates scenarios where intra-population variability in natural systems leads to differences between the IBM and PLM models.     

Kinetic,isotherm and thermodynamic investigations on adsorption of trace elements and pigments from soybean oil using high voltage electric field-assisted bleaching: A comparative study

In this study, the amounts of trace elements (Fe (II) and Cu (II)) and pigments (chlorophyll and carotenoid) in soybean oil were evaluated under high voltage electric field (HVEF) bleaching method at different voltage (10 and 20 kV), temperature (35–65 °C), time (0−30 min) and clay percentage (0.5–2 %) and then were compared to the industrial bleaching method (IBM). The kinetic data of ions and pigments adsorbed on activated bentonite clay under IBM and HVEF at two voltages of 10 and 20 kV followed the mechanism of the pseudo-first-order model (PFOM). The carotenoid and chlorophyll equilibrium data followed a Freundlich isotherm type model, which demonstrated multilayer adsorption under HVEF. The thermodynamic parameters (ΔG°, ΔH°, and ΔS°) displayed that the adsorption of trace metal ions and pigments on bentonite clay under IBM and HVEF were feasible, endothermic and spontaneous between 35 and 65 °C. The results indicated that the HVEF, especially at higher voltage, has a high remarkable capability to remove metal ions and pigments from soybean oil than the IBM. The highest removal capacity for metal and pigments of soybean oil bleaching were obtained in the order of HVEF-20 kV > HVEF-10 kV > IBM.     

Programming for the DNA analysis of FCM data on an IBM microcomputer

The analysis of data generated on a flow cytometer (FCM) is often performed on a computer obtained especially for dedicated use with the flow cytometer. This computer component can be expensive and also presents the FCM user with the added burden of mastering specialized programming language or of accepting the secret analytical processes of protected proprietary program routines. We believe that the evolution of more accurate and efficient FCM analyses that have the power to consider complex signal distributions can be assisted by the availability of analysis programs written in languages common to many users. DNA analysis routines written for a relatively inexpensive microcomputer (IBM PC/XT) in Basic and Pascal are described here. The routines can automatically process multiple FCM data files and can provide high-resolution graphic hardcopy. A foreground/background utilization is also described that allows the computer to be available for other uses in the laboratory.     

Measurement of water transport during freezing in mammalian liver tissue: Part II--The use of differential scanning calorimetry.

There is currently a need for experimental techniques to assay the biophysical response (water transport or intracellular ice formation, IIF) during freezing in the cells of whole tissue slices. These data are important in understanding and optimizing biomedical applications of freezing, particularly in cryosurgery. This study presents a new technique using a Differential Scanning Calorimeter (DSC) to obtain dynamic and quantitative water transport data in whole tissue slices during freezing. Sprague-Dawley rat liver tissue was chosen as our model system. The DSC was used to monitor quantitatively the heat released by water transported from the unfrozen cell cytoplasm to the partially frozen vascular/extracellular space at 5 degrees C/min. This technique was previously described for use in a single cell suspension system (Devireddy, et al. 1998). A model of water transport was fit to the DSC data using a nonlinear regression curve-fitting technique, which assumes that the rat liver tissue behaves as a two-compartment Krogh cylinder model. The biophysical parameters of water transport for rat liver tissue at 5 degrees C/min were obtained as Lpg = 3.16 x 10(-13) m3/Ns (1.9 microns/min-atm), ELp = 265 kJ/mole (63.4 kcal/mole), respectively. These results compare favorably to water transport parameters in whole liver tissue reported in the first part of this study obtained using a freeze substitution (FS) microscopy technique (Pazhayannur and Bischof, 1997). The DSC technique is shown to be a fast, quantitative, and reproducible technique to measure dynamic water transport in tissue systems. However, there are several limitations to the DSC technique: (a) a priori knowledge that the biophysical response is in fact water transport, (b) the technique cannot be used due to machine limitations at cooling rates greater than 40 degrees C/min, and (c) the tissue geometric dimensions (the Krogh model dimensions) and the osmotically inactive cell volumes Vb, must be determined by low-temperature microscopy techniques.     

Sterilization and preservation influence the biophysical properties of human amnion grafts.

The introduction of amniotic membrane (AM) transplantation in ophthalmic surgery holds great promise and in many clinical situations it offers an alternative to existing management options. The purpose of this study was to examine the influence of established sterilization and preservation procedures on biophysical and histological properties of AM grafts. Amnion was sterilized by peracetic acid/ethanol sterilization [PES] and preserved by air-drying (sterile laminar flow) [AD] or in glycerol [GLYC]. Unsterilized AM were preserved at -80 degrees C [-80 degrees C] and served as an experimental control. Amnion allografts were characterized by the determination of their thickness, moisture vapour permeability (MVP), oxygen permeability (OPERM), tensile strength and sulphur content. Immunostaining for tissue-specific and basement membrane-related proteins was performed. Differences in biophysical parameters were found between the unsterilized allografts and the sterilized, air-dried or glycerol-preserved allografts. [PES/AD] showed the highest MVP and OPERM, the highest tensile strength and the lowest sulphur content and thickness. [PES/GLYC] exhibited the lowest OPERM and the highest thickness compared to [-80 degrees C] and [PES/AD]. Collagen types V and VII were preserved the best in the control group. Sterilization and preservation affect biophysical properties important for the use of AM as allogenic grafts. It has to be determined if any change, as noted, has a clinical impact.     

Plotting genetic maps on a microcomputer

Maps of genetic linkage and restriction enzyme cleavage sites can be quickly prepared on an IBM PC microcomputer with the commercially available program Lotus 1-2-3. Data can be entered on the keyboard or imported from other programs. The maps can be displayed on the screen or with a printer or plotter. These procedures should be useful in the research laboratory, in preparing figures for publication and in teaching.     

Microcomputer information systems designed to provide documentation about patients treated with dialysis]

A program specifically designed for PC/XT/AT compatible with IBM was written. This program is intended for collecting data on the patients treated with repeated dialyses. The system collects, edits, and surveys data according certain rules. It may print required data. It may also be extended by inclusion of the additional modules and adopted to other centres of dialysis. It is used for 2 years already and proved quite useful in the center of dialysis.     

Computer program for the IBM personal computer which searches for approximate matches to short oligonucleotide sequences in long target DNA sequences.

We describe a program which may be used to find approximate matches to a short predefined DNA sequence in a larger target DNA sequence. The program predicts the usefulness of specific DNA probes and sequencing primers and finds nearly identical sequences that might represent the same regulatory signal. The program is written in the C programming language and will run on virtually any computer system with a C compiler, such as the IBM/PC and other computers running under the MS/DOS and UNIX operating systems. The program has been integrated into an existing software package for the IBM personal computer (see article by Mount and Conrad, this volume). Some examples of its use are given.     

Bayesian state-space modeling of metapopulation dynamics in the Glanville fritillary butterfly

The complexity of mathematical models of ecological dynamics varies greatly, and it is often difficult to judge what would be the optimal level of complexity in a particular case. Here we compare the parameter estimates, model fits, and predictive abilities of two models of metapopulation dynamics: a detailed individual-based model (IBM) and a population-based stochastic patch occupancy model (SPOM) derived from the IBM. The two models were fitted to a 17-year time series of data for the Glanville fritillary butterfly (Melitaea cinxia) inhabiting a network of 72 small meadows. The data consisted of biannual counts of larval groups (IBM) and the annual presence or absence of local populations (SPOM). The models were fitted using a Bayesian state-space approach with a hierarchical random effect structure to account for observational, demographic, and environmental stochasticities. The detection probability of larval groups (IBM) and the probability of false zeros of local populations (SPOM) in the observation models were simultaneously estimated from the time-series data and independent control data. Prior distributions for dispersal parameters were obtained from a separate analysis of mark–recapture data. Both models fitted the data about equally, but the results were more precise for the IBM than for the SPOM. The two models yielded similar estimates for a random effect parameter describing habitat quality in each patch, which were correlated with independent empirical measures of habitat quality. The modeling results showed that variation in habitat quality influenced patch occupancy more through the effects on movement behavior at patch edges than on carrying capacity, whereas the latter influenced the mean population size in occupied patches. The IBM and the SPOM explained 63% and 45%, respectively, of the observed variation in the fraction of occupied habitat area among 75 independent patch networks not used in parameter estimation. We conclude that, while carefully constructed, detailed models can have better predictive ability than simple models, this advantage comes with the cost of greatly increased data requirements and computational challenges. Our results illustrate how complex models can be helpful in facilitating the construction of effective simpler models.     

Microcomputer simulation of steady-state enzyme kinetics for educational purposes

A BASIC program to assist the instruction of steady-state enzymekinetics has been developed for the IBM PC microcomputer. Itspurpose is to simulate laboratory experiments in order to minimizethe time required to obtain kinetic data from which studentsdeduce kinetic mechanisms and determine kinetic constants ofenzyme-catalyzed reactions. The program randomly selects a kineticscheme from various sequential, ping pong, and iso reactionsequences as well as values for the kinetic constants. The schemeand kinetic constants are unknown to the student at this time;the only thing he or she knows is the stoichiometry of the catalyzedreaction which can have two or three substrates and products.The student is prompted to enter values for concentrations ofsubstrates and products; several different concentrations foreach substrate and product can be entered in a single experiment.The program then calculates, displays and prints (if desired)the corresponding initial steadystate velocities. The studentcan perform as many experiments as desired until enough informationis obtained to determine the kinetic mechanism and to calculatevalues for the kinetic constants. Received on March 10, 1986; accepted on May 6, 1986     

Water transport and IIF parameters for a connective tissue equivalent

Understanding the biophysical processes that govern freezing injury of a tissue equivalent (TE) is an important step in characterizing and improving the cryopreservation of these systems. TEs were formed by entrapping human dermal fibroblasts (HDFs) in collagen or in fibrin gels. Freezing studies were conducted using a Linkam cryostage fitted to an optical microscope allowing observation of the TEs cooled under controlled rates between 5 and 130 degrees C/min. Typically, freezing of cellular systems results in two biophysical processes that are both dependent on the cooling rate: dehydration and/or intracellular ice formation (IIF). Both these processes can potentially be destructive to cells. In this study, the biophysics of freezing cells in collagen and fibrin TEs have been quantified and compared to freezing cells in suspension. Experimental data were fitted in numerical models to extract parameters that governed water permeability, E(Lp) and L(pg), and intracellular ice nucleation, omega(o) and kappa(o). Results indicate that major differences exist between freezing HDFs in suspension and in a tissue equivalent. During freezing, 55% of the HDFs in suspension formed IIF as compared to 100% of HDFs forming IIF in collagen and fibrin TE at a cooling rate of 130 degrees C/min. Also, both the water permeability and the IIF parameters were determined to be higher for HDFs in TEs as compared to cell suspensions. Between the TEs, HDFs in fibrin TE exhibited higher values for the biophysical parameters as compared to HDFs in collagen TE. The observed biophysics seems to indicate that cell-cell and cell-matrix interactions play a major role in ice propagation in TEs.     

Discrimination between different types of low-level luminescence in mammalian cells: The biophysical radiation

Cellular low-level luminescence was measured after various disintegrative processes in brain cell preparations. In addition to known origins of low-level luminescence, e.g. oxygen radical reactions or enzymatic and non-enzymatic redox systems, a further source of photon emission is reported which is independent of external oxygen, oxygen radicals and enzyme activities. Vital cells from rat brain homogenates or pig oligodendrocytes could be kept for hours at 37 °C without any photon emission. Only after disintegrative processes a cellular photon emission could be induced. The maximal intensity of about 400 impulses/s/mg protein and a total radiation of about 6 × 10⁶ I/mg depended on the type of cells. The signal could be retained completely at 4 °C or in frozen samples. Heating (10 min, 90 °C) did not suppress the photon emission. Luminol and lucigenin did not amplify the signal as is usually observed in oxygen radical-producing cells. Non-specific radical scavengers as well as detergents suppressed the cellular photon emission completely. It is suggested that this cellular luminescence represents a biophysical radiation which originates from the interruption of an intermolecular radiationless energy transfer.     

Surface activity of a synthetic lung surfactant containing a phospholipase-resistant phosphonolipid analog of dipalmitoyl phosphatidylcholine

Surface activity and sensitivity to inhibition from phospholipase A2 (PLA2), lysophosphatidylcholine (LPC), and serum albumin were studied for a synthetic C16:0 diether phosphonolipid (DEPN-8) combined with 1.5% by weight of mixed hydrophobic surfactant proteins (SP)-B/C purified from calf lung surfactant extract (CLSE). Pure DEPN-8 had better adsorption and film respreading than the major lung surfactant phospholipid dipalmitoyl phosphatidylcholine and reached minimum surface tensions <1 mN/m under dynamic compression on the Wilhelmy balance and on a pulsating bubble surfactometer (37 degrees C, 20 cycles/min, 50% area compression). DEPN-8 + 1.5% SP-B/C exhibited even greater adsorption and had overall dynamic surface tension lowering equal to CLSE on the bubble. In addition, films of DEPN-8 + 1.5% SP-B/C on the Wilhelmy balance had better respreading than CLSE after seven (but not two) cycles of compression-expansion at 23 degrees C. DEPN-8 is structurally resistant to degradation by PLA2, and DEPN-8 + 1.5% SP-B/C maintained high adsorption and dynamic surface activity in the presence of this enzyme. Incubation of CLSE with PLA2 led to chemical degradation, generation of LPC, and reduced surface activity. DEPN-8 + 1.5% SP-B/C was also more resistant than CLSE to direct biophysical inhibition by LPC, and the two were similar in their sensitivity to biophysical inhibition by serum albumin. These findings indicate that synthetic surfactants containing DEPN-8 combined with surfactant proteins or related synthetic peptides have potential utility for treating surfactant dysfunction in inflammatory lung injury.     

Mechanistic forecasts of species responses to climate change: The promise of biophysical ecology

A core challenge in global change biology is to predict how species will respond to future environmental change and to manage these responses. To make such predictions and management actions robust to novel futures, we need to accurately characterize how organisms experience their environments and the biological mechanisms by which they respond. All organisms are thermodynamically connected to their environments through the exchange of heat and water at fine spatial and temporal scales and this exchange can be captured with biophysical models. Although mechanistic models based on biophysical ecology have a long history of development and application, their use in global change biology remains limited despite their enormous promise and increasingly accessible software. We contend that greater understanding and training in the theory and methods of biophysical ecology is vital to expand their application. Our review shows how biophysical models can be implemented to understand and predict climate change impacts on species' behavior, phenology, survival, distribution, and abundance. It also illustrates the types of outputs that can be generated, and the data inputs required for different implementations. Examples range from simple calculations of body temperature at a particular site and time, to more complex analyses of species' distribution limits based on projected energy and water balances, accounting for behavior and phenology. We outline challenges that currently limit the widespread application of biophysical models relating to data availability, training, and the lack of common software ecosystems. We also discuss progress and future developments that could allow these models to be applied to many species across large spatial extents and timeframes. Finally, we highlight how biophysical models are uniquely suited to solve global change biology problems that involve predicting and interpreting responses to environmental variability and extremes, multiple or shifting constraints, and novel abiotic or biotic environments.     

Magnetic resonance tomography of the sellar region in patients with endocrine diseases]

The authors discuss the present-day problems of radiotherapy. They show the major prospective trends in this field and describe the OS3Dplan system, made in this country, that represents a working place of a radiologist and serves for the development, analysis and storage of the schemes of long-distance gamma-beam therapy of oncologic patients. The OS3Dplan system is realized via the IBM PC/AT-286/287 computer but can operate with any of the IBM PC/XT/AT/PS-2--8086/80486 computers, made before 1986 with the videoadapter EGA/VGA, and functioning under MS-DOS, Microsoft (version 3.3 or older). The mathematical provision of the videodigitizer (distance control and videocamera) permit the introduction of videoinformation into the personal computer in the 256 x 256 format, 512 x 512 pixels. The mathematical provision of the OS3Dplan proper permits a volume planning of long-distance gamma-beam therapy. This module type system will be of interest for various specialists (radiologists, roentgenologists, oncologists, students, etc.), for it permits a collection and maintenance of a data bank on patients with imaging of roentgenograms, CT, NM tomography, ultrasonic data on the computer display and printing these data, perform metric analyses and reconstruct the volume.     

The effect of dimethylsulfoxide on the water transport response of rat hepatocytes during freezing.

Successful improvement of cryopreservation protocols for cells in suspension requires knowledge of how such cells respond to the biophysical stresses of freezing (intracellular ice formation, water transport) while in the presence of a cryoprotective agent (CPA). This work investigates the biophysical water transport response in a clinically important cell type--isolated hepatocytes--during freezing in the presence of dimethylsulfoxide (DMSO). Sprague-Dawley rat liver hepatocytes were frozen in Williams E media supplemented with 0, 1, and 2 M DMSO, at rates of 5, 10, and 50 degrees C/min. The water transport was measured by cell volumetric changes as assessed by cryomicroscopy and image analysis. Assuming that water is the only species transported under these conditions, a water transport model of the form dV/dT = f(Lpg([CPA]), ELp([CPA]), T(t)) was curve-fit to the experimental data to obtain the biophysical parameters of water transport--the reference hydraulic permeability (Lpg) and activation energy of water transport (ELp)--for each DMSO concentration. These parameters were estimated two ways: (1) by curve-fitting the model to the average volume of the pooled cell data, and (2) by curve-fitting individual cell volume data and averaging the resulting parameters. The experimental data showed that less dehydration occurs during freezing at a given rate in the presence of DMSO at temperatures between 0 and -10 degrees C. However, dehydration was able to continue at lower temperatures (< -10 degrees C) in the presence of DMSO. The values of Lpg and ELp obtained using the individual cell volume data both decreased from their non-CPA values--4.33 x 10(-13) m3/N-s (2.69 microns/min-atm) and 317 kJ/mol (75.9 kcal/mol), respectively--to 0.873 x 10(-13) m3/N-s (0.542 micron/min-atm) and 137 kJ/mol (32.8 kcal/mol), respectively, in 1 M DMSO and 0.715 x 10(-13) m3/N-s (0.444 micron/min-atm) and 107 kJ/mol (25.7 kcal/mol), respectively, in 2 M DMSO. The trends in the pooled volume values for Lpg and ELp were very similar, but the overall fit was considered worse than for the individual volume parameters. A unique way of presenting the curve-fitting results supports a clear trend of reduction of both biophysical parameters in the presence of DMSO, and no clear trend in cooling rate dependence of the biophysical parameters. In addition, these results suggest that close proximity of the experimental cell volume data to the equilibrium volume curve may significantly reduce the efficiency of the curve-fitting process.