New approaches to an age-old problem

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New approaches to the problem of generating coherent,reproducible phenotypes

Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. Both competitive coherence and life on the scales deal with the problem of reconciling conflicting constraints. Here, we bring together these concepts in the common framework of hyperstructures and make predictions that may be tested using a learning program, Coco, and secondary ion mass spectrometry.     

Cytochemical studies on the problem of macronuclear subnuclei in tetrahymena

DNA amounts in macronuclei and micronuclei of Tetrahymena pyriformis were measured by Feulgen microspectrophotometry. Assuming that the unreplicated micronucleus is diploid, the unreplicated macronucleus was found to contain approximately 45 times the haploid DNA amount. The relationship of these findings to the 45 independently assorting genetic subunits characterized by Allen and Nanney and their collaborators is discussed. The pattern of DNA synthesis in macro- and micronuclei during the cell cycle is also described.     

Numerical approaches to the species problem

The use of numbers by systematists is not new. Measurements to describe individuals and formal taxa have been used since the beginnings of our science. But the advent of electronic computers now permits a much more accurate understanding of the phenotypic relationships within and among populations and taxa. Furthermore, estimates of cladistic relationship also are being attempted with the help of computers. Computers can increase our understanding of speciation, but this requires us to think intelligently about the meaning of their results.Presented at the symposium Speciation and the Species Concept during the XIIth International Botanical Congress, Leningrad, July 8, 1975.     

Hypothesis testing approaches to the exon prediction problem

MOTIVATION: Many gene identification methods assign scores to gene elements prior to their assembly into predicted genes. The scoring system is often based on log-likelihood ratios. These methods usually perform well but it is difficult to interpret how significant a score is. RESULTS: We have developed several tests of significance for the scores: (1) a sum-of-scores test (SST), (2) an intersection-union test (IUT), based on a multiple hypothesis testing interpretation of an exon's score and (3) a meta-analytical approach (MA), which combines several P-values, corresponding to the exon's parts, to yield a global P-value. We performed simulation studies, which show that the MA has better sensitivity and specificity than other methods and is easier to interpret by non-expert users. This is an improvement over other methods and is especially relevant for users who would like to predict incomplete gene sequences.     

Mathematical approaches to the problem of generating immunoglobulin diversity

The frequency of mutations necessary for maintenance in the organism of the existing diversity of immunoglobulin for specificity of active centres is estimated using a mathematical model. The calculation shows the mutation frequency to be approx. 10(-2) per cell in a generation.     

New approaches to the treatment of osteoporosis

Under physiological conditions, maintenance of skeletal mass is the result of a tightly coupled process of bone formation and bone resorption. Disease states, osteoporosis included, arise when this delicate balance is disrupted such as in menopause, when estrogen levels decrease dramatically corresponding with the cessation of ovarian function. Current therapies for the treatment of osteoporosis, including estrogen replacement therapy, selective estrogen receptor modulators and bisphosphonates, are primarily based on blunting the resorption component of bone homeostasis. Although selective estrogen receptor modulators offer bone protection without the side effects of estrogen replacement therapy, there are some areas of improvement for the current generation of selective estrogen receptor modulators; particularly in reducing their antagonistic properties in the central nervous system that lead to vasomotor symptoms. There are few therapies that are focused on increasing bone formation, but they offer promising avenues in which to expand the repertoire of drugs to restore bone mass. Selective androgen receptor modulators, parathyroid hormone analogs, oxytocin analogs and statins, all with improved pharmacological properties in bone, are among the potential approaches to eliciting anabolic effects in the skeleton.     

Comparison of heuristic approaches to the generalized tree alignment problem

Two commonly used heuristic approaches to the generalized tree alignment problem are compared in the context of phylogenetic analysis of DNA sequence data. These approaches, multiple sequence alignment + phylogenetic tree reconstruction (MSA+TR) and direct optimization (DO), are alternative heuristic procedures used to approach the nested NP‐Hard optimizations presented by the phylogenetic analysis of unaligned sequences under maximum parsimony. Multiple MSA+TR implementations and DO were compared in terms of optimality score (phylogenetic tree cost) over multiple empirical and simulated datasets with differing levels of heuristic intensity. In all cases examined, DO outperformed MSA+TR with average improvement in parsimony score of 14.78% (5.64–52.59%).     

Two new collaborative filtering approaches to solve the sparsity problem

Cluster Computing - Collaborative filtering which is the most successful technique of the Recommender System, has recently attracted great attention, especially in the field of e-commerce. CF is...     

New approaches to high-throughput phasing

Recent progress in macromolecular phasing, in part stimulated by the high-throughput structural biology initiatives, has made this crucial stage of the elucidation of crystal structures easier and more automatic. A quick soak in various salts leads to the rapid incorporation of the anomalously scattering ions, suitable for phasing by MAD (multiwavelength anomalous dispersion), SAD (single-wavelength anomalous dispersion) or MIR (multiple isomorphous replacement) methods. The availability of stable synchrotron beam lines equipped with elaborate hardware control and sophisticated data processing programs makes it possible to collect very accurate diffraction data and to solve structures from the very weak anomalous signal of such atoms as sulfur or phosphorus, inherently present in macromolecules. The current progress in phasing, coupled with the parallel advances in protein crystallization, diffraction data collection and so on, suggests that, in the near future, the process of macromolecular crystal structure elucidation may become fully automatic.     

New approaches to transillumination imaging

A review of the current state of transillumination imaging for the detection and diagnosis of breast cancer and the difficulties that impede more widespread acceptance of the methods is presented. An outline is given of the physical models that may be used to describe the propagation and scattering of light in a tissue matrix and how these models might be valuable in identifying imaging improvements. Some of the proposals for future imaging arrangements are described and the preliminary work on a system for light transmission computed tomography is presented.