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PubMed2006

A system for studying evolution of life-like virtual organisms.

BACKGROUND: Fitness landscapes, the dependences of fitness on the genotype, are of critical importance for the evolution of living beings. Unfortunately, fitness landscapes that are relevant to the evolution of complex biological functions are very poorly known. As a result, the existing theory of evolution is mostly based on postulated fitness landscapes, which diminishes its usefulness. Attempts to deduce fitness landscapes from models of actual biological processes led, so far, to only limited success. RESULTS: We present a model system for studying the evolution of biological function, which makes it possible to attribute fitness to genotypes in a natural way. The system mimics a very simple cell and takes into account the basic properties of gene regulation and enzyme kinetics. A virtual cell contains only two small molecules, an organic nutrient A and an energy carrier X, and proteins of five types--two transcription factors, two enzymes, and a membrane transporter. The metabolism of the cell consists of importing A from the environment and utilizing it in order to produce X and an unspecified end product. The genome may carry an arbitrary number of genes, each one encoding a protein of one of the five types. Both major mutations that affect whole genes and minor mutations that affect individual characteristics of genes are possible. Fitness is determined by the ability of the cell to maintain homeostasis when its environment changes. The system has been implemented as a computer program, and several numerical experiments have been performed on it. Evolution of the virtual cells usually involves a rapid initial increase of fitness, which eventually slows down, until a fitness plateau is reached. The origin of a wide variety of genetic networks is routinely observed in independent experiments performed under the same conditions. These networks can have different, including very high, levels of complexity and often include large numbers of non-essential genes. CONCLUSION: The described system displays a rich repertoire of biologically sensible behaviors and, thus, can be useful for investigating a number of unresolved issues in evolutionary biology, including evolution of complexity, modularity and redundancy, as well as for studying the general properties of genotype-to-fitness maps. REVIEWERS: This article was reviewed by Drs. Eugene Koonin, Shamil Sunyaev and Arcady Mushegian.

Journal Article↗
PubMed2005

Tools for building a comprehensive modeling system for virtual screening under real biological conditions: The Computational Titration algorithm.

Computational tools utilizing a unique empirical modeling system based on the hydrophobic effect and the measurement of logP(o/w) (the partition coefficient for solvent transfer between 1-octanol and water) are described. The associated force field, Hydropathic INTeractions (HINT), contains much rich information about non-covalent interactions in the biological environment because of its basis in an experiment that measures interactions in solution. HINT is shown to be the core of an evolving virtual screening system that is capable of taking into account a number of factors often ignored such as entropy, effects of solvent molecules at the active site, and the ionization states of acidic and basic residues and ligand functional groups. The outline of a comprehensive modeling system for virtual screening that incorporates these features is described. In addition, a detailed description of the Computational Titration algorithm is provided. As an example, three complexes of dihydrofolate reductase (DHFR) are analyzed with our system and these results are compared with the experimental free energies of binding.

1-Octanol↗
PubMed2007

Molecular dynamics of rhodopsin and free opsin: computer simulation.

Computer simulation was used to perform a comparative study of the molecular dynamics of rhodopsin containing the chromophore group (11-cis-retinal) and free opsin. The molecular dynamics were followed over a time interval of 3000 psec; a total of 3 x 10(6) discrete conformational states of rhodopsin and opsin. The presence of the chromophore group in the chromophore center of opsin was shown to have significant effects on the immediate protein environment of the chromophore and the conformational state of the cytoplasmic domain, but to have virtually no effect on the conformational state of the intradisk domain. The simulation results are used to discuss the possible intramolecular mechanism by which rhodopsin is maintained as a G-protein-coupled receptor in the inactive state, i.e., the function of the chromophore as an effective antagonist ligand.

Animals↗
PubMed1998

The prevalence and natural history of periodontal disease in Britain from prehistoric to modern times.

OBJECTIVE: To investigate the prevalence of periodontitis in British populations during the past 3000 years. To discuss the relevance of these findings to modern populations denied access to modern dental treatment. DESIGN: Observation and assessment of periodontal status of skeletal material using a recently developed method of assessment. SETTING: Archaeological material from various collections throughout UK covering prehistoric, mediaeval and seventeenth to nineteenth century. SUBJECTS: 504 individuals. MAIN OUTCOME MEASURES: The periodontal status of individual septa was recorded as to whether they were healthy, had gingivitis or periodontitis. The prevalence of periodontitis among individuals and populations was assessed. RESULTS: The prevalence of periodontitis appears to have remained virtually constant during the past 3000 years in Britain, despite considerable changes in the oral environment. CONCLUSIONS: The significance of these findings in respect of untreated populations in underdeveloped countries today is considerable. It is considered essential that clinical and field studies record and report on oral environmental factors that may mimic or, by themselves, be responsible for periodontal attachment loss.

Disease Progression↗
PubMed1991

Poliomyelitis in France: epidemiology and vaccination status.

In France, infants are immunized against paralytic poliomyelitis with enhanced-potency inactivated poliovirus vaccine (eIPV) combined with the diphtheria-tetanus-pertussis vaccine (DTP). Ninety-five percent of all infants in France have received four doses of DTP-eIPV by 24 months of age. No cases of vaccine-associated paralysis, among either recipients or those in contact with recipients, have been reported since 1983, when eIPV became the vaccine of choice. Only three wild indigenous cases have been reported among unvaccinated children in 1988 and 1989, with no cases reported in 1990. Although paralytic poliomyelitis has been virtually eliminated in France, vaccination programs as well as active surveillance of the community and environment for poliovirus circulation should be reinforced to reach the goal of wild poliovirus eradication.

France↗
PubMed2001

Military medical modeling and simulation in the 21st century.

As we enter the 21st century, military medicine struggles with critical issues. One of the most important issues is how to train medical personnel in peace for the realities of war. In April, 1998, The General Accounting Office (GAO) reported, "Military medical personnel have almost no chance during peacetime to practice battlefield trauma care skills. As a result, physicians both within and outside the Department of Defense (DOD) believe that military medical personnel are not prepared to provide trauma care to the severely injured soldiers in wartime. With some of today's training methods disappearing, the challenge of providing both initial; and sustainment training for almost 100,000 military medical personnel is becoming insurmountable. The "training gap" is huge and impediments to training are mounting. For example, restrictions on animal use are increasing and the cost of conducting live mass casualty exercises is prohibitive. Many medical simulation visionaries believe that four categories of medical simulation are emerging to address these challenges. These categories include PC-based multimedia, digital mannequins, virtual workbenches, and total immersion virtual reality (TIVR). The use of simulation training can provide a risk = free realistic learning environment for the spectrum of medical skills training, from buddy-aid to trauma surgery procedures. This will, in turn, enhance limited hands on training opportunities and revolutionize the way we train in peace to deliver medicine in war. High-fidelity modeling will permit manufacturers to prototype new devices before manufacture. Also, engineers will be able to test a device for themselves in a variety of simulated anatomical representations, permitting them to "practice medicine".

Computer Simulation↗
PubMed2002

Host plant resistance to insects: an eco-friendly approach for pest management and environment conservation.

Host plant resistance (HPR) to insects is an effective, economical, and environment friendly method of pest control. The most attractive feature of HPR is that farmers virtually do not need any skill in application techniques, and there is no cash investment by the resource poor farmers. Considerable progress has been made in identification and development of crop cultivars with resistance to the major pests in different crops. There is a need to transfer resistance genes into high-yielding cultivars with adaptation to different agro-ecosystems. Resistance to insects should form one of the criteria to release varieties and hybrids for cultivation by the farmers. Genes from the wild relatives of crops, and novel genes, such as those from Bacillus thuringiensis can also be deployed in different crops to make HPR an effective weapon to minimize the losses due to insect pests. HPR will not only cause a major reduction in pesticide use and slowdown the rate of development of resistance to insecticides in insect populations, but also lead to increased activity of beneficial organisms and reduction in pesticide residues in food and food products.

Adaptation, Physiological↗
PubMedDate not supplied

Elimination of poliomyelitis in France: epidemiology and vaccine status.

In France, both inactivated poliovirus vaccine (IPV) and oral poliovirus vaccine (OPV) were used until 1983. By that time a new enhanced-potency IPV (eIPV) was licensed and recommended by the French Ministry of Health as the vaccine of choice. Ninety-five per cent of infants have received four doses of eIPV by 24 months of age. No cases of vaccine-associated paralysis among either recipients or those in contact with recipients have been reported since 1983. Only four wild indigenous cases of paralytic poliomyelitis have been reported among unvaccinated children in the past five years and none since 1990. Although paralytic poliomyelitis has been virtually eliminated in France, vaccination programs as well as active surveillance of the community and environment for poliovirus circulation should be reinforced to reach the goal of wild poliovirus eradication.

Child↗
PubMed2001

Navigating without vision: basic and applied research.

We describe some of the results of our program of basic and applied research on navigating without vision. One basic research topic that we have studied extensively is path integration, a form of navigation in which perceived self-motion is integrated over time to obtain an estimate of current position and orientation. In experiments on pathway completion, one test of path integration ability, we have found that subjects who are passively guided over the outbound path without vision exhibit significant errors when attempting to return to the origin but are nevertheless sensitive to turns and segment lengths in the stimulus path. We have also found no major differences in path integration ability among blind and sighted populations. A model we have developed that attributes errors in path integration to errors in encoding the stimulus path is a good beginning toward understanding path integration performance. In other research on path integration, in which optic flow information was manipulated in addition to the proprioceptive and vestibular information of nonvisual locomotion, we have found that optic flow is a weak input to the path integration process. In other basic research, our studies of auditory distance perception in outdoor environments show systematic underestimation of sound source distance. Our applied research has been concerned with developing and evaluating a navigation system for the visually impaired that uses three recent technologies: the Global Positioning System, Geographic Information Systems, and virtual acoustics. Our work shows that there is considerable promise of these three technologies in allowing visually impaired individuals to navigate and learn about unfamiliar environments without the assistance of human guides.

Animals↗
PubMed2000

Spatial information transfer from virtual to real versions of the Kiel locomotor maze.

The Kiel locomotor maze requires participants to choose five targets from among 20 locations marked by small red lights on the floor of a dimly lit circular environment having four wall-mounted extramaze cues and two intramaze cues at floor level. In the present study, acquisition of the real task was examined in 11-year-old children following prior accurate training in a virtual version, following misleading virtual training, or following no training. The virtual version was displayed on a desk-top computer monitor. Acquisition testing in the real maze was either locomotor or non-locomotor. Good transfer was achieved from virtual to real versions. Children's exploration of the real maze prior to real maze acquisition training revealed a clear transfer of spatial information previously learned in the virtual version. Children taught the correct target configuration in the simulation made fewer errors and more rapid, confident responses to targets in the real maze than children given no training. However, acquisition was also better following misleading training than no training, suggesting that a non-specific components of performance also transferred. Male superiority was only seen following misleading training, which was interpreted in terms of male superiority in mental rotation. After acquisition, a single probe trial was performed, in which proximal cues and participants' starting position were rotated, but this had equivalent effects on all groups' performance. It is clear that transfer of spatial information occurs from the simulated Kiel maze to the real version. This has implications for its use in diagnosis and training.

Child↗
PubMed2000

Exploration of a novel environment leads to the expression of inducible transcription factors in barrel-related columns.

Tactile information acquired through the vibrissae is of high behavioral relevance for rodents. Numerous physiological studies have shown adaptive plasticity of cortical receptive field properties due to stimulation and/or manipulation of the whiskers. However, the cellular mechanisms leading to these plastic processes remain largely unknown. Although genomic responses are anticipated to take place in this sequel, virtually no data so far exist for freely behaving animals concerning this issue. Thus, adult rats were placed overnight in an enriched environment and most of them were also subjected to clipping of different sets of whiskers. This type of stimulation led to a specific and statistically significant increase in the expression of the protein products of the inducible transcription factors c-Fos, JunB, inducible cyclic-AMP early repressor and Krox-24 (also frequently named Zif268 or Egr-1), but not c-Jun. The response was found in columns of the barrel cortex corresponding to the stimulated vibrissae; it displayed a layer-specific pattern. However, no induction of transcription factors was observed in the subcortical relay stations of the whisker-to-barrel pathway, i.e. the trigeminal nuclei and the ventrobasal complex. These results strongly suggest that a coordinated transcriptional response is initiated in the barrel cortex as a consequence of processing of novel environmental stimuli.

Animals↗
PubMed2004

Determination of solid-liquid partition coefficients (K(d)) for diazinon, propetamphos and cis-permethrin: implications for sheep dip disposal.

Two groups of chemicals are currently licensed for use in sheep dip products in the UK. These are organophosphate (OP) insecticides and synthetic pyrethroid (SP) insecticides. SPs are deemed to be less toxic to human health than OPs, although they are approximately 100 times more toxic to some elements of the aquatic environment. Three insecticides were selected for experimental investigation: diazinon, propetamphos (OPs) and cis-permethrin (SP), representative of the active ingredients used in sheep dip formulations, with additional uses in insect control in crops, and for domestic control of flies, mosquitoes, cockroaches, lice, ticks and spiders. The UK Government has recently reviewed agricultural practices relating to the disposal of used sheep dip, because the constituent insecticides are frequently detected in UK watercourses and the presence of these compounds is a severe hazard to the aquatic environment. Standard batch sorption experiments were carried out to investigate insecticide partitioning from water to soil, and the relationship between sorption and soil organic carbon content is discussed. Sorption isotherms and K(d) values showed that cis-permethrin adsorption was fastest on all five soils investigated, exhibiting the greatest total partitioning to the soil phase (83.8-94.8%) and high resistance to desorption. In comparison, the OP insecticides exhibited moderately strong soil adsorption as evidenced by their K(d) coefficients (diazinon K(d) 12-35 and propetamphos K(d) 9-60), with low sorption reversibility (< 15%). Calculation of a hydrological retardation factor in a scenario representative of a typical UK environment suggested that SP insecticides such as cis-permethrin will not migrate in the soil profile due to their virtual immobility and strong soil retention, and thus waste sheep dip disposal to agricultural land should not pose a risk to aquatic life if applied with appropriate controls.

Agriculture↗
PubMed2004

Effects of an embryonic repair graft on recovery from spinal cord injury.

It is widely believed that mammalian CNS axons have little regenerative capacity because their environment is non-permissive to regrowth. This viewpoint is based, in large part, on the fact that in virtually all previous studies on regeneration following spinal cord injury, regenerated axonal projections have been few in number, quite short, and considered to be mostly aberrant. As a result, motor recovery has been very limited in both experimental preparations and the human. In this chapter, we describe use of a neonatal, spinally transected animal model in which selected spinal cord segments were carefully replaced with equivalent tissue from embryonic tissue of the same species. We demonstrate that the new spinal environment is indeed permissive, and reconstruction is possible of neural connections, which are similar to the pre-injury, normal projections. Moreover, the distribution and number of regenerated axons are closely related to the extent of functional motor recovery. Our results suggest that contrary to doctrinaire thought, the mammalian CNS possesses a remarkable capacity for regrowth. For this to be efficacious, however, regenerating axons must contact the inherent, pre-injury guidance system, whose cues were used for establishing appropriate neural connections in the developing animal, and are retained in the adult. It is argued that by use of these guidance cues, regenerating axons that traverse the site of a spinal cord injury, can project on to locate their pre-injury pathways and targets, and thereby restore function.

Animals↗
PubMed2005

Interactive simulation of needle insertion models.

A novel interactive virtual needle insertion simulation is presented. The simulation models are based on measured planar tissue deformations and needle insertion forces. Since the force-displacement relationship is only of interest along the needle shaft, a condensation technique is shown to reduce the computational complexity of linear simulation models significantly. As the needle penetrates or is withdrawn from the tissue model, the boundary conditions that determine the tissue and needle motion change. Boundary condition and local material coordinate changes are facilitated by fast low-rank matrix updates. A large-strain elastic needle model is coupled to the tissue models to account for needle deflection and bending during simulated insertion. A haptic environment, based on these novel interactive simulation techniques, allows users to manipulate a three-degree-of-freedom virtual needle as it penetrates virtual tissue models, while experiencing steering torques and lateral needle forces through a planar haptic interface.

Algorithms↗
PubMed1997

Influence of dietary lysine levels and arginine:lysine ratios on performance of broilers exposed to heat or cold stress during the period of three to six weeks of age.

Four trials of identical experimental design were conducted to determine the effects of temperature, dietary Lys level, and dietary Arg:Lys ratios on performance and carcass yield of male broilers. Birds of a commercial strain were grown from 21 to 42 d of age in wire-floored finishing batteries placed in environmental chambers. The chambers were programmed to provide either a constant thermoneutral temperature (21.1 C), a constant cold temperature (15.5 C), or a cycling hot diurnal temperature (25.5 to 33.3 C). Within each environment there was a factorial arrangement of three Lys levels (1.0, 1.1, and 1.2%) with four Arg:Lys ratios (1.1:1, 1.2:1, 1.3:1, and 1.4:1). Environmental temperature significantly influenced virtually every characteristic examined. Hot cyclic temperatures reduced weight gain, feed intake, and breast meat yield, and increased feed conversion, dressing percentage, leg quarter yield, and abdominal fat content. The cold environment promoted increased feed intake and mortality. Ascites and cardiomyopathy were the leading causes of death under cold exposure and thermoneutral conditions, whereas complications arising from heat exposure were the main cause of death under hot cyclic conditions. Levels of Lys affected leg quarter yield and abdominal fat content over all environments but increased breast meat yield only under cold conditions. Increasing Arg:Lys ratios improved feed conversion and dressing percentage and reduced abdominal fat content; it could not be determined whether these responses were consistent with Arg per se or were due to a nonspecific N response. As increasing Lys levels or Arg:Lys ratios did not improve weight gain, increase breast meat yield, or attenuate adverse effects due to heat or cold exposure, it is concluded that the levels of Lys and Arg suggested for 21 to 42 d by the NRC are adequate for birds of this age under the environmental conditions encountered.

Aging↗
PubMed1996

The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation.

A system containing the globular protein ubiquitin and 4,197 water molecules has been used for the analysis of the influence exerted by a protein on solvent dynamics in its vicinity. Using Voronoi polyhedra, the solvent has been divided into three subsets, i.e., the first and second hydration shell, and the remaining bulk, which is hardly affected by the protein. Translational motion in the first shell is retarded by a factor of 3 in comparison to bulk. Several molecules in the first shell do not reach the diffusive regime within 100 ps. Shell-averaged orientational autocorrelation functions, which are also subject to a retardation effect, cannot be modeled by a single exponential time law, but are instead well-described by a Kohlrausch-Williams-Watts (KWW) function. The underlying distribution of single-molecule rotational correlation times is both obtained directly from the simulation and derived theoretically. The temperature dependence of reorientation is characterized by a strongly varying correlation time, but a virtually temperature-independent KWW exponent. Thus, the coupling of water structure relaxation with the respective environment, which is characteristic of each solvation shell, is hardly affected by temperature. In other words, the functional form of the distributions of single-molecule rotational correlation times is not subject to a temperature effect. On average, a correlation between reorientation and lifetimes of neighborhood relations is observed.

Proteins↗
PubMed2004

Heavy metal levels and esterase variations between metal-exposed and unexposed duckweed Lemna minor: field and laboratory studies.

Environmental homogeneity is being continuously disturbed and affected by artificially introduced loads of chemical toxicants that also include heavy metals. The Tiljala wetlands of the eastern fringe of Calcutta, West Bengal (India) are a virtual sink for the deposition of urban and industrial wastes that get admixed with the aquatic environment. We have selected Lemna minor (duckweed), as a representative of the biota surviving therein for the present study. Concentrations of lead, cadmium, chromium, zinc, copper and mercury in the fronds of Lemna were measured to peep into the range of input of heavy metals in the duckweed subjects. Natural unexposed population of duckweed from a domestic pond in Batanagar area, 24 Parganas, West Bengal (India) was also found to accumulate similar concentrations of these metals when cultured in artificially contaminated water in the laboratory. The exposed individuals also exhibited polymorphism with respect to the loci of esterase, as compared to an unexposed control plants. Therefore, the present study suggests EST variations of L. minor to be a potential biomarker of heavy metal pollution.

Araceae↗