Modeling capsid self-assembly: design and analysis

A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible and an explicit solvent is optionally included. Model design, simulation methodology and analysis techniques are discussed. The analysis focuses on the growth pathways and the nature of the intermediate states, properties that are hard to access experimentally. Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered.     

Continuing professional development systems for medical physicists: A global survey and analysis

Continuing professional development (CPD) and continuing professional education (CPE) are seen as being necessary for medical physicists to ensure that they are up-to-date with current clinical practice. CPD is more than just continuing professional education, but can include research publication, working group contribution, thesis examination and many other activities. A systematic way of assessing and recording such activities that a medical physicist undertakes is used in a number of countries. This can be used for certification and licensing renewal purposes. Such systems are used in 27 countries, but they should be implemented in all countries where clinical medical physicists are employed.A survey of the CPD systems that are currently operated around the world is presented. In general they are quite similar although there are a few countries that have CPD systems that differ significantly from the others in many respects. Generally they ensure that medical physicists are kept up-to-date, although there are some that clearly will fail to achieve that.An analysis of what is required to construct a useful medical physics CPD system is made. Finally, the need for medical physicist professional organizations to cooperate and share in the production and distribution of CPD and CPE materials is emphasized.     

A search for conceptual congruence between individuals and species

A new argument that species are individuals has recently been presented based on the way species names are used and systemic logic. The alternate idea that species are a categorical item, i.e., collections of individuals, was rejected. We wanted to evaluate this approach by establishing concepts that apply to individuals in order to examine if they are also applicable to a species viewed as a categorical item. It is our thinking that if species are not such, then concepts applicable to individuals will not be applicable to species so viewed. Individuals and species are similar in the presence of conceptual boundaries, unidirectional change and the presence of past and future time. These are all central, and salient, biological phenomena. But, these are concepts that apply also to populations which, for the most part, are not the same as species. Thus, these considerations infer that species, when viewed as a collection of individuals, do not share relevant concepts with individuals. Our conclusion is that a species is a 'unity' rather than an 'individual'.     

RuvABC is required to resolve holliday junctions that accumulate following replication on damaged templates in Escherichia coli

RuvABC is a complex that promotes branch migration and resolution of Holliday junctions. Although ruv mutants are hypersensitive to UV irradiation, the molecular event(s) that necessitate RuvABC processing in vivo are not known. Here, we used a combination of two-dimensional gel analysis and electron microscopy to reveal that although ruvAB and ruvC mutants are able to resume replication following arrest at UV-induced lesions, molecules that replicate in the presence of DNA damage accumulate unresolved Holliday junctions. The failure to resolve the Holliday junctions on the fully replicated molecules correlates with a delayed loss of genomic integrity that is likely to account for the loss of viability in these cells. The strand exchange intermediates that accumulate in ruv mutants are distinct from those observed at arrested replication forks and are not subject to resolution by RecG. These results indicate that the Holliday junctions observed in ruv mutants are intermediates of a repair pathway that is distinct from that of the recovery of arrested replication forks. A model is proposed in which RuvABC is required to resolve junctions that arise during the repair of a subset of nonarresting lesions after replication has passed through the template.     

Model for the feedback control system of bacterial growth. II. Growth in continuous culture

A mathematical model is developed that describes substrate limited bacterial growth in a continuous culture and that is based upon the conceptual framework elaborated in a previous paper for describing the feedback control system of cell growth [S. Bleecken, (1988). J. theor. Biol. 133, 37.] Central to the theory are the ideas that the limiting substrate is converted into low molecular weight building blocks of macromolecular synthesis which again are converted into biomass (RNA and protein) and that the rates of RNA and protein synthesis are controlled by the intracellular concentration of building blocks. It is shown that a continuous culture can be simulated by two interconnected feedback control systems the actuating signals of which are limiting substrate concentration and the intracellular concentration of building blocks, respectively. Three types of steady-states are found to appear in a continuous culture, besides the well-known stable steady-state of the whole culture there exist two batchlike steady-states of the biotic part of the culture which are metastable. The model is used to analyse the steady-states and their stability properties as well as the dynamic responses of biomass, RNA, protein, building block and substrate concentrations to changes in environmental conditions. Especially the inoculation of a continuous culture and the effects of step changes in dilution rate, inlet substrate concentration and growth temperature are studied in detail. Relations between the growth behaviour of a single cell and that of a continuous culture are derived. The RNA to protein ratio is introduced as a rough measure of the physiological state of cells and it is shown that a cell reacts to environmental changes with a simple pattern of basic responses in growth rate and physiological state. There are reasons to assume that the model presented is the minimal version of a structured model of bacterial growth and represents an optimum compromise between biological relevance and mathematical practicability.     

Hypothesis: the rate and scale of dispersal of freshwater diatom species is a function of their global abundance

We have analysed the geographical records of a representative selection of extant diatom species from a freshwater pond. The more often a species is recorded in the ecological literature, the greater is its apparent global distribution. One explanation is that the frequently recorded species are globally abundant, whereas species that are infrequently recorded are globally rare. We suggest a model in which random dispersal is the dominant force driving large-scale distribution of species, with the rate and scale of dispersal largely determined by global population size. Thus species that are locally rare or abundant are likewise rare or abundant worldwide. It is predicted that many of the rarer diatom species will, with additional sampling effort, be shown to have wide geographical distribution, but this requires intensive studies focused on revealing species that are normally cryptic. The argument in favour of endemic diatom species is untenable, because it is not possible to disprove their existence elsewhere in the biosphere.     

The placebo response: an attachment strategy that counteracts the effects of stress-related dysfunction

The placebo response represents an enigmatic element of therapeutics. The potency of placebo effects is highlighted by the fact that the current gold standard for determining therapeutic efficacy, the randomized controlled clinical trial, is based on identifying treatment responses that are statistically superior to those elicited by a placebo. Although much has been written concerning the phenomenology of placebos, little is known concerning how they are elicited, although recent research has demonstrated that placebo effects are mediated via objective physiological pathways. I have previously argued that the placebo response is a developmental achievement, rooted in implicit procedural memories that are linked to background affects of well-being evoked by a relational dynamic with a caregiver. This article develops this idea further, suggesting that placebo response represents a nervous-system response aimed at countering the dysphoric effects attributable to chronic stress, and that it is dependent on developmental attachment dynamics. A range of behaviors by caregivers that mimic those achieved during secure attachment are suggested to promote placebo responses.     

How to eradicate fraudulent statistical methods: statisticians must do science

The two steps necessary for the clinical expression of a mutagenic disease, genetic damage and viability, are countervailing forces and therefore the dosage response curve for mutagens must have a maximum. To illustrate that science is common sense reduced to calculation, a new mathematical derivation of this result and supporting data are given. This example also shows that the term "context-free" is a snare and a delusion. When statistical methods are used in a scientific context where their assumptions are known to fail and where there is a reasonable presumption of intent to deceive, they are fraudulent. Estimation of low-level mutagenic risks by linear extrapolation from high-dose data is one example of such a method that is widely used by Executive Branch agencies. Other examples are given of fraudulent statistical methods that are currently used in biomedical research done by or for U.S. government agencies. In the long run, it is argued, the surest way to eradicate such fraud is for biostatisticians to do their own science.     

ELISA detection of restriction site polymorphisms in the pig ryanodine receptor locus

We compare two strategies for ELISA detection of restriction site polymorphisms (EDRSP) that are suitable for high-throughput genotyping of the pig ryanodine receptor point mutation (RYR1 ^hal ). In both procedures, target DNA is amplified by PCR with one primer that is 5′ biotinylated and a second primer that is 5′ fluoresceinylated. PCR products are captured in duplicate wells on a streptavidin-coated, 96-well plate. The duplicates may be treated in two ways. In a single restriction enzyme assay, one duplicate is exposed to a restriction enzyme that cuts one allele specifically, and the second duplicate is exposed to no restriction enzyme. In a dual restriction enzyme assay, the second replicate is exposed to a second restriction enzyme that cuts the alternate allele specifically. Thereafter, the two procedures are similar; anti-fluorescein antibodies conjugated to peroxidase are allowed to bind to the fluoresceinylated ends, the plate is washed, and a substrate is converted to a colored end product. The ratio of the absorbances in the two wells is used to classify subjects by genotype. When the dual restriction enzyme assay is run, three genotype groups are easily distinguishable. When the single restriction enzyme assay is run, heterozygotes generate values that may overlap with those of the homozygotes that are not cut by the restriction enzyme. Dual restriction enzyme assays are more accurate than single restriction enzyme assays; however, single restriction enzyme assays are sufficient for identifying pigs that carry RYR1 ^hal . Received: 30 December 1997 / Accepted: 20 April 1998     

The challenges facing scientists in the development of foods in Europe using biotechnology

The public's major concern over the introduction of genetic engineering into the food chain focuses on potential health risks. Proving that a food is safe is an impossible goal since there will always be a risk associated with eating food. Diets that are natural in every sense of the word pose risks but the general public believe that they are inherently less risky. The differences in risk between foods that are natural, as opposed to foods that are produced by the application of technology, are likely to be minute. Nor does it follow that they all lie in favour of `natural' food. The fact is that all foods pose a balance of risks and benefits but the scientific method has so far not been applied to its measurement. Only risk is emphasised and estimated, albeit with many conservative assumptions, often resulting in an emphasis on minute risk. Conventional plant products are not subject to the rigorous risk evaluations that apply to genetically modified plants. So the outcome is that the public only receive part of the information and this is the emphasis on risk of the `artificial' food. The only future for foods produced by biotechnology in Europe is if the public are persuaded of the real health benefits that will result from its application. Given the present state of nutritional knowledge, and the limited resources that are given to it, there are only a few clear examples of where nutritional improvement of plant food would bring really significant benefits. The paper highlights these with examples and indicates where further nutritional research will be required before other targets for improvement can be realised.     

The generation of non-linear solute gradients for chromatography by using only simple apparatus.

It is shown that by using only a series of tubes with constant cross-sectional area and a single-channel peristaltic pump, it is possible to produce solute gradients with time profiles that are concave, convex, sigmoid or even with turning points. The general theory for predicting gradients, by using tubes in series that are either open or closed to the atmosphere, is presented, and the equations using three compartments are given. Experiments are described that support the usefulness and accuracy of such a theoretical treatment.     

Phylogeny and Biogeography of the Stapeliads

The stapeliads (Apocynaceae — Asclepiadoideae — Ceropegieae) form a group of highly succulent, practically leafless plants with a very diverse floral morphology. They are found in the drier parts of the Old World from southern Africa eastwards to Burma. 55 characters are selected on which a cladistic analysis is based and these are discussed in detail where necessary. From this a phylogeny is produced for the stapeliads. It is shown that they are monophyletic and that they are nested within a larger group among the tribe Ceropegieae of the subfamily Asclepiadoideae. Several of the important innovations that have led to the diversification of the stapeliads in semidesertic regions are discussed. The stapeliads appear to be mainly fly-pollinated. The methods of attraction of flies are mentioned and it is suggested that there are four basic floral types among the stapeliads.     

The effects of density on the topological structure of the mitochondrial DNA from trypanosomes

Trypanosomatida parasites, such as trypanosoma and lishmania, are the cause of deadly diseases in many third world countries. A distinctive feature of these organisms is the three dimensional organization of their mitochondrial DNA into maxi and minicircles. In some of these organisms minicircles are confined into a small disk volume and are topologically linked, forming a gigantic linked network. The origins of such a network as well as of its topological properties are mostly unknown. In this paper we quantify the effects of the confinement on the topology of such a minicircle network. We introduce a simple mathematical model in which a collection of randomly oriented minicircles are spread over a rectangular grid. We present analytical and computational results showing that a finite positive critical percolation density exists, that the probability of formation of a highly linked network increases exponentially fast when minicircles are confined, and that the mean minicircle valence (the number of minicircles that a particular minicircle is linked to) increases linearly with density. When these results are interpreted in the context of the mitochondrial DNA of the trypanosome they suggest that confinement plays a key role on the formation of the linked network. This hypothesis is supported by the agreement of our simulations with experimental results that show that the valence grows linearly with density. Our model predicts the existence of a percolation density and that the distribution of minicircle valences is more heterogeneous than initially thought.     

Induction of systemic resistance in plants

When a pathogen is perceived by a host plant, a series of defense responses can be activated. One of these are "local" defenses that occur rapidly at the site of pathogen invasion. Another are "systemic" defenses that are induced in uninoculated parts of the plant. Recently, molecular genetic studies have revealed genes that are signaling components of systemic resistance pathways. Cloning of these genes and characterization of the function of their proteins is now providing insights to processes regulating plant defense against pathogens. Evidence that "systemic" defenses are important for resistance is that when the way is blocked in transgenic plants or in mutants, the plant's defense is compromised. When the pathway is stimulated by exogenous compounds or in mutants, the host resistance is strengthened. A detailed understanding of this pathway is important for both practical and theoretical reasons.     

On the Three-Taxon Approach to Parsimony Analysis

The following three basic defects for which three-taxon analysis has been rejected as a method for biological systematics are reviewed: (1) character evolution is a priori assumed to be irreversible; (2) basic statements that are not logically independent are treated as if they are; (3) three-taxon statements that are considered as independent support for a given tree may be mutually exclusive on that tree. It is argued that these criticisms only relate to the particular way the three-taxon approach was originally implemented. Four-taxon analysis, an alternative implementation that circumvents these problems, is derived. Four-taxon analysis is identical to standard parsimony analysis except for an unnatural restriction on the maximum amount of homoplasy that may be concentrated in a single character state. This restriction follows directly from the basic tenet of the three-taxon approach, that character state distributions should be decomposed into basic statements that are, in themselves, still informative with respect to relationships. A reconsideration of what constitutes an elementary relevant statement in systematics leads to a reformulation of standard parsimony as two-taxon analysis and to a rejection of four-taxon analysis as a method for biological systematics.     

The importance of subjectivity in perceptual errors on the emergence of indirect reciprocity

Indirect reciprocity is one mechanism that allows for unilateral resource giving among n-persons. Using analytical methods and computer simulations, previous studies have examined a number of strategies that make indirect reciprocity possible. In particular, previous investigations have concentrated on whether differentiating between justified and unjustified not-giving is important. However, whether or not a given strategy is ESS depends on the type of perceptual errors that are assumed. When errors are objective, regarding those who do not give to "bad" as "good" is critical. When perceptual errors are subjective, however, regarding those who give to "bad" as "bad" is critical. Since we believe that there is no guarantee that perceptual errors are shared among all individuals in a society, we argue that the latter moral principle may play a more important role in human interactions.     

Analysis of intracellular receptor/ligand sorting. Calculation of mean surface and bulk diffusion times within a sphere.

Cell surface receptors bind extracellular ligand molecules and transport those ligands into the cell by a process termed receptor-mediated endocytosis. Receptor and ligand molecules are sorted from one another after endocytosis, apparently within a structure consisting of intracellular vesicles and connected thin tubules. The experimental observation is that most free (unbound) ligand molecules are found in the lumen of the vesicles and receptors are located primarily within the tubules. Because equilibrium and geometric considerations do not explain this segregation, a kinetic scheme involving the passive diffusion of molecules from a vesicle into a tubule is investigated. Two possible sorting mechanisms are considered: first, that receptors are able to move into tubules more rapidly than ligand molecules due to an advantage in dimensionality and, second, that receptors diffusing into tubules are trapped there while ligands are not. Mean diffusion times for receptor and ligand movement into a tubule are calculated by solving Poisson's equation in two and three dimensions, respectively, on the surface of and within a sphere. Using estimated parameter values, we found that only the second scheme is able to account for the experimentally observed sorting. An estimate is obtained for the length of time a tubule and vesicle must be connected in order to remove a significant number of receptors into a tubule. The fraction of free ligand that is "mis-sorted" with the recycling receptor population and thus exocytosed is also determined.     

Relating Single-Molecule Measurements to Thermodynamics

Measurements made on large ensembles of molecules are routinely interpreted using thermodynamics, but the normal rules of thermodynamics may not apply to measurements made on single molecules. Using a polymer stretching experiment as an example, it is shown that in the limit of a single, short molecule the outcome of experimental measurements may depend on which variables are held fixed and which are allowed to fluctuate. Thus an experiment in which the end-to-end distance of the polymer molecule is fixed and the tension fluctuates yields a different result than an experiment where the force is fixed and the end-to-end distance fluctuates. It is further shown that this difference is due to asymmetry in the distribution of end-to-end distances for a single molecule, and that the difference vanishes in the appropriate thermodynamic limit; that is, as the polymer molecule becomes long compared to its persistence length. Despite these differences, much of the thermodynamic formalism still applies on the single-molecule level if the thermodynamic free energies are replaced with appropriate potentials of mean force. The primary remaining differences are consequences of the fact that unlike the free energies, the potentials of mean force are not in general homogeneous functions of their variables. The basic thermodynamic concepts of an intensive or extensive quantity, and the thermodynamic relationships that follow from them, are therefore less useful for interpreting single-molecule experiments.