An improved arbitrary primed PCR method for rapid characterization of transposon insertion sites

Modifications were made to published arbitrary primed polymerase chain reaction (AP-PCR) procedures that resulted in increased specificity and sensitivity. Several arbitrary primer sequences were also evaluated, resulting in recommendations for primer design.     

Training a new response using conditioned reinforcement

Some of the most frequently used methods in the study of conditioned reinforcement seem to be insufficient to demonstrate the effect. The clearest way to assess this phenomenon is the training of a new response. In the present study, rats were exposed to a situation in which a primary reinforcer and an arbitrary stimulus were paired and subsequently the effect of this arbitrary event was assessed by presenting it following a new response. Subjects under these conditions emitted more responses compared to their own responding before the pairing and to their responding on a similar operandum that was available concurrently that had no programmed consequences. Response rates also were higher compared to responding by subjects in similar conditions in which there was no contingency (a) between the arbitrary stimulus and the reinforcer, (b) between the response and the arbitrary stimulus or (c) both. Results are discussed in terms of necessary and sufficient conditions to study conditioned reinforcement.     

Electrostatic potentials in membrane systems

A membrane with an arbitrary distribution of fixed charges inside and on its surfaces is considered. A procedure for calculating the local electrostatic potential at an arbitrary point of the system is described and its validity discussed. This procedure is based on the linearization of the 3-dimensional Poisson-Boltzmann equation around an exact 1-dimensional solution.     

Selective imitation for a private sign system

A distinctive feature of all human languages is the diverse and arbitrary nature of the sign (signifier). This can be interpreted as stating that the mapping between signals and referents is established by convention rather than by functional constraints. This property of the sign provides for a great deal of linguistic flexibility and is a key component of symbolic communication. Game theoretic models to describe signal imitation are investigated with a view to understanding how non-arbitrary (indexical) animal-style signals might 'evolve' culturally into diverse, arbitrary signs. I explore the evolutionary hypothesis that private, arbitrary signs emerge as a result of selective imitation within a socially structured population. Once arbitrary signs have emerged, they contribute towards greater assortative interactions among individuals using a shared sign system. In natural populations, the models for imitation will very often be close kin. Hence, kinship provides one mechanism for the creation of true symbols. An imitation-structured population can support many more sign systems than an equivalent non-structured population and is one in which symbols become the dominant force in assortative interactions.     

A Model Allowing Continuous Variation in Electrophoretic Mobility of Neutral Alleles

The infinite-sites model with no recombination is extended to include mutations that affect electrophoretic mobility. The model allows the effect of a single-site mutation to have a continuous effect on mobility. Formulae are obtained for the variance of electrophoretic mobility of alleles after an arbitrary lenght of time. A special case of the general model is the case of stepwise production of neutral alleles with an arbitrary number of steps.     

Efficient Boolean implementation of universal sequence maps (bUSM)

Background  

Recently, Almeida and Vinga offered a new approach for the representation of arbitrary discrete sequences, referred to as Universal Sequence Maps (USM), and discussed its applicability to genomic sequence analysis. Their work generalizes and extends Chaos Game Representation (CGR) of DNA for arbitrary discrete sequences.     

Transient Potentials in Dendritic Systems of Arbitrary Geometry

A simple graphical calculus is developed that generates analytic solutions for membrane potential transforms at any point on the dendritic tree of neurons with arbitrary dendritic geometries, in response to synaptic “current” inputs. Such solutions permit the computation of transients in neurons with arbitrary geometry and may facilitate analysis of the role of dendrites in such cells.     

Continuous-genotype models and assortative mating

Feldman and Cavalli-Sforza (1979a,b) have argued that the convergence properties of classical models of assortative mating are not known, and that these models involve arbitrary assumptions which assume rather than derive the achievement of equilibrium. A careful consideration of all models shows that the classical models are well defined and seem to achieve their equilibria. The model used by Feldman and Cavalli-Sforza involves an arbitrary assumption. Consideration of the models of Wright, Fisher, Bulmer, and Lande in the context of assortative mating or of selection versus mutation shows that these models are consistent with each other. The treatment of the balance between mutation and normalizing selection by Cavalli-Sforza and Feldman comes to conclusions sharply different from those of other authors, apparently as a result of this same arbitrary assumption.     

Sequence signatures from DNA amplification fingerprints reveal fine population structure of the dogwood pathogen Discula destructiva

Abstract Isolates of Discula destructiva Redlin and an undescribed species of Discula , the filamentous fungi that cause anthracnose of flowering ( Cornus florida L.) and Pacific ( Cornus nuttalli Aud.) dogwoods, were analyzed for genetic variation by nucleic acid scanning with arbitrary mini-hairpin oligonucleotide primers. While the fungal population was highly homogeneous throughout the disease range in eastern and western North America, the generation of arbitrary signatures from amplification profiles (ASAP) distinguished isolates from the northeast, middle and southern Appalachian mountain range, and western United States and Canada. ASAP involves a dual-step arbitrary primer-based amplification procedure that generates a large number of informative allelic characters by amplification of monomorphic DNA fingerprints. ASAP analyses showed a fine fungal population structure consistent with the recent and separate introduction of the pathogen on the west and east coasts of North America.     

Scaffold-free cartilage by rotational culture for tissue engineering

Our objective was to investigate the hypothesis that tissue-engineered cartilage with promising biochemical, mechanical properties can be formed by loading mechanical stress under existing cell-cell interactions analogous to those that occur in condensation during embryonic development. By loading dedifferentiated chondrocytes with mechanical stress under existing cell-cell interactions, we could first form a scaffold-free cartilage tissue with arbitrary shapes and a large size with promising biological, mechanical properties. The cartilage tissue which constituted of chondrocytes and ECM produced by inoculated dedifferentiated chondrocytes to a high porous simple mold has arbitrary shapes, and did not need any biodegradable scaffold to control the shape. In contrast, scaffold-free cartilage tissue cultured under static conditions could not keep their shapes; it was fragile tissue. The possibility of scaffold-free organ design was suggested because the cartilage tissue increases steadily in size with culture time; indeed, the growth of cartilage tissue starting from an arbitrary shape might be predictable by mathematical expression. For tissue-engineered cartilage formation with arbitrary shapes, biochemical and mechanical properties, loading dedifferentiated chondrocytes with mechanical stress under existing cell-cell interactions has prominent effects. Therefore, our scaffold-free cartilage model loaded mechanical stress based on a simple mold system may be applicable for tissue-engineered cartilage.     

Remarks on the Evolutionary Effect of Natural Selection

The so-called "Fundamental Theorem of Natural Selection", that the mean fitness of a population increases with time under natural selection, is known not to be true, as a mathematical theorem, when fitnesses depend on more than one locus. Although this observation may not have particular biological relevance, (so that mean fitness may well increase in the great majority of interesting situations), it does suggest that it is of interest to find an evolutionary result which is correct as a mathematical theorem, no matter how many loci are involved. The aim of the present note is to prove an evolutionary theorem relating to the variance in fitness, rather than the mean: this theorem is true for an arbitrary number of loci, as well as for arbitrary (fixed) fitness parameters and arbitrary linkage between loci. Connections are briefly discussed between this theorem and the principle of quasi-linkage equilibrium.     

On optimal Bayesian classification and risk estimation under multiple classes

A recently proposed optimal Bayesian classification paradigm addresses optimal error rate analysis for small-sample discrimination, including optimal classifiers, optimal error estimators, and error estimation analysis tools with respect to the probability of misclassification under binary classes. Here, we address multi-class problems and optimal expected risk with respect to a given risk function, which are common settings in bioinformatics. We present Bayesian risk estimators (BRE) under arbitrary classifiers, the mean-square error (MSE) of arbitrary risk estimators under arbitrary classifiers, and optimal Bayesian risk classifiers (OBRC). We provide analytic expressions for these tools under several discrete and Gaussian models and present a new methodology to approximate the BRE and MSE when analytic expressions are not available. Of particular note, we present analytic forms for the MSE under Gaussian models with homoscedastic covariances, which are new even in binary classification.     

Sedimentation equilibrium in macromolecular solutions of arbitrary concentration. II. Two protein components

Relations describing sedimentation equilibrium in solutions containing two macromolecular solute components are derived for the following cases: (1) two nonassociating proteins at arbitrary concentration, (2) one dilute self-associating protein in the presence of a second inert protein at arbitrary concentration, and (3) two proteins at arbitrary concentration that can associate to form a single heterocomplex of arbitrary composition. As in earlier work (R. C. Chatelier and A. P. Minton (1987) Biopolymers, 26, 507–524), the relations are obtained by using scaled particle theory to calculate the thermodynamic activity of each species present at a given radial distance in the centrifuge. The results of numerical simulations of sedimentation equilibrium are presented as the dependence of apparent molecular weights, or apparent weight-average molecular weights, upon solution composition. Semiempirical methods are presented, by means of which the weight-average molecular weights of self- and heteroassociating proteins in highly nonideal solutions may be estimated from experimental data. It is found that the semiempirical methods yield reasonably accurate estimates of the true weight-average molecular weight over a broad range of experimental conditions, providing that the partial specific volumes of two components in a heteroassociating system do not differ by more than about 0.05 mL/g.     

Global analysis of gene expression by differential display

Differential display (DD) is one of the most commonly used approaches for identifying differentially expressed genes. However, there has been lack of an accurate guidance on how many DD polymerase chain reaction (PCR) primer combinations are needed to display most of the genes expressed in a eukaryotic cell. This study critically evaluated the gene coverage by DD as a function of the number of arbitrary primers, the number of 3′ bases of an arbitrary primer required to completely match an mRNA target sequence, the additional 5′ base match(s) of arbitrary primers in first-strand cDNA recognition, and the length of mRNA tails being analyzed. The resulting new DD mathematical model predicts that 80 to 160 arbitrary 13mers, when used in combinations with 3 one-base anchored oligo-dT primers, would allow any given mRNA within a eukaryotic cell to be detected with a 74% to 93% probability, respectively. The prediction was supported by both computer simulation of the DD process and experimental data from a comprehensive fluorescent DD screening for target genes of tumor-suppressor p53. Thus, this work provides a theoretical foundation upon which global analysis of gene expression by DD can be pursued.     

Residency effects in animal contests

The question of why territorial residents usually win asymmetrical owner-intruder contests is critical to our understanding of animal contest evolution. Game theory suggests that, under certain conditions, residency could be used as an arbitrary means of contest settlement in a manner analogous to tossing a coin. Key empirical support for this idea is provided by a study on the speckled wood butterfly (Pararge aegeria); however, this result has proven controversial. We show conclusively that residency does not serve as an arbitrary cue for contest settlement in this species. By means of a series of manipulative experiments, conducted on two phenotypically divergent populations of P. aegeria, we also rule out the recently presented alternative that contests are settled due to resource-correlated asymmetries in thoracic temperature. Our results instead suggest that more intrinsically aggressive males accumulate as residents and continue to win due to the self-reinforcing effect of prior winning experience. Truly arbitrary contest settlement may be rare or non-existent in the wild.     

Foundations of a mathematical theory of darwinism

This paper pursues the ‘formal darwinism’ project of Grafen, whose aim is to construct formal links between dynamics of gene frequencies and optimization programmes, in very abstract settings with general implications for biologically relevant situations. A major outcome is the definition, within wide assumptions, of the ubiquitous but problematic concept of ‘fitness’. This paper is the first to present the project for mathematicians. Within the framework of overlapping generations in discrete time and no social interactions, the current model shows links between fitness maximization and gene frequency change in a class-structured population, with individual-level uncertainty but no uncertainty in the class projection operator, where individuals are permitted to observe and condition their behaviour on arbitrary parts of the uncertainty. The results hold with arbitrary numbers of loci and alleles, arbitrary dominance and epistasis, and make no assumptions about linkage, linkage disequilibrium or mating system. An explicit derivation is given of Fisher’s Fundamental Theorem of Natural Selection in its full generality.     

Exact solution of the Boltzmann kinetic equation for a Lorentzian gas

The classical methods of mathematical physics are applied to construct an integral solution to the Chapman-Cowling-Davydov equation, which is derived from the kinetic Boltzmann equation with a collision term in the Lorentzian-gas approximation. For a particular initial distribution, the solution is obtained in an explicit form in terms of a Whittaker function. It is shown that, on long (macroscopic) time scales, the evolving distribution function with an arbitrary initial shape approaches a Maxwellian distribution. This result agrees with the accepted views regarding the overall temporal evolution of an arbitrary unsteady isolated system.     

The Statistical Mechanics for an Extended Nonlinear Epigenetic Dynamics. I

An extension of the control equations discussed by Goodwin is proposed which allows for arbitrary strong coupling and for arbitrary parallel coupling of metabolic pools and genetic loci. It is demonstrated that these generalized control equations can be put into canonical form and further that Liouville's theorem applies. In addition, it is demonstrated that after a suitable canonical transformation the resulting partition function can be solved in closed form, and this result, as well as that for the mean energy, is exhibited. Some remarks appropriate to additional extensions are presented.     

Enzymatic labeling of arbitrary proteins.

This paper describes an enzymatic labeling technique (ELT), using transglutaminases. On the basis of the ELT, isotopic nuclei are easily incorporated into the gamma-carboxyamide groups of glutamine residues in arbitrary proteins, without changing their chemical structures. We have also shown that, by using ELT, protein aggregation was easily checked for NMR studies and that it can be applicable for the screening of weakly bound ligands for proteins. Owing to the simple preparation of the isotope-labeled proteins, ELT should be useful for speeding up various structural and functional analyses of arbitrary proteins.