The biology ofAzospirillum-sugarcane association II. Ultrastructure

Summary Tissue cultures of sugarcane support abundant growth ofAzospirillum brasilense (SP 7). Visible after 1–2 weeks as a white or pink slime, this growth reaches 2×10⁸ bacteria/mm² on the surface of callus. Growth of the bacterium is strictly extracellular in viable callus, and instances of intracellular growth result from rupture of the cell wall during senescence of callus tissue. A significant proportion of the bacterial population on callus is pleomorphic. Varying the nitrogen source in the nutrient medium caused no obvious effect on callus cell structure. The presence of the bacterium caused structural alterations in callus cells which did not inhibit overall growth of the bacterium. Growth of callus as tight groups of cells lacking intercellular spaces may be important for the establishment of a long-term association withAzospirillum. The interface of bacteria and live callus tissue is at the surface of tight cell groups. Browning of the surface cell layers of these groups in the presence ofAzospirillum is not of the rapid nature known for hypersensitivity reactions. Rather, this production of phenolics appears to be due to the accumulation of extracellular bacterial metabolites. The ultrastructure of this and other callus reactions is described. As evidenced by organogenesis, the associated cultures have remained viable for at least 18–20 months.Florida Agricultural Experiment Station Journal Series No. 1695.     

Dimensional analysis in mathematical biology. II

The application of dimensional analysis in biology is further illustrated by functional equations composed of dimensionless numbers and dealing with renal physiology, lung physiology and plant leaf shape. Dimensional variables and dimensionless numbers are examined from the viewpoint of numerical invariant properties of a certain physical system. Utilization of the method for problems such as design of an artificial kidney is considered briefly. A tabulation of variables useful in biology is given, with suggestions for a number of new dimensional entities. A continuation of the list of dimensionless invariants from Part I (Bull. Math. Biophysics,23, 355–376, 1961) is provided and includes terms pertaining to general physiology, geometric growth, metabolism, ecological interactions, muscle kinetics and other areas. It is pointed out that use of dimensionless ratios (similarity criteria) makes possible a direct comparison of form or shape factors and relative growth ratios with a variety of physical ratios, through the use of functional equations containing only dimensionless entities. Organismal similarity during growth and development, and between genetically related species, may be analyzed in terms of “automodel” or “self-similar” systems governed by certain dimensionless invariants. Tables of biological variables and dimensionless groupings are included.     

The next step in systems biology: simulating the temporospatial dynamics of molecular network

As a result of the time- and context-dependency of gene expression, gene regulatory and signaling pathways undergo dynamic changes during development. Creating a model of the dynamics of molecular interaction networks offers enormous potential for understanding how a genome orchestrates the developmental processes of an organism. The dynamic nature of pathway topology calls for new modeling strategies that can capture transient molecular links at the runtime. The aim of this paper is to present a brief and informative, but not all-inclusive, viewpoint on the computational aspects of modeling and simulation of a non-static molecular network.     

Decomposition of protein tryptophan fluorescence spectra into log-normal components. II. The statistical proof of discreteness of tryptophan classes in proteins

The physical causes for wide variation of Stokes shift values in emission spectra of tryptophan fluorophores in proteins have been proposed in the model of discrete states (Burstein, E. A., N. S. Vedenkina, and M. N. Ivkova. 1973. Photochem. Photobiol. 18:263-279; Burstein, E. A. 1977a. Intrinsic Protein Luminescence (The Nature and Application). In Advances in Science and Technology (Itogi Nauki i Tekhniki), Biophysics Vol. 7. VINITI, Moscow [In Russian]; Burstein, E. A. 1983. Molecular Biology (Moscow) 17:455-467 [In Russian; English translation]). It was assumed that the existence of the five most probable spectral classes of emitting tryptophan residues and differences among the classes were analyzed in terms of various combinations of specific and universal interactions of excited fluorophores with their environment. The development of stable algorithms of decomposition of tryptophan fluorescence spectra into log-normal components gave us an opportunity to apply two mathematically different algorithms, SImple fitting with Mean-Square criterion (SIMS) and PHase-plot-based REsolving with Quenchers (PHREQ) for the decomposition of a representative set of emission spectra of proteins. Here we present the results of decomposition of tryptophan emission spectra of >100 different proteins, some in various structural states (native and denatured, in complexes with ions or organic ligands, in various pH-induced conformations, etc.). Analysis of the histograms of occurrence of >300 spectral log-normal components with various maximum positions confirmed the statistical discreteness of several states of emitting tryptophan fluorophores in proteins.     

Reproductive biology of the Pteridophyta. II. Theoretical considerations

Because of the homothallic nature of many pteridophytes, two categories of mating are possible: intragametophytic selling (the origin of both gametes from a single gametophyte) and inter-gametophytic mating (the origin of each gamete from a different gametophyte).Various morphological and genetical criteria (placement of the gametangia on the thallus, their sequence of ontogeny, the capacity for simple polyembryony and genetic self-incompatibility) can be used to indicate the relative probability of intragametophytic selfing or intergametophytic mating. Only the former has genetic significance (i.e.complete homozygosity); if the latter is evidenced, then detailed studies of population variability are required to ascertain the breeding system. Three types of reproductive systems involve the gametophyte generation: intragametophytic selfing, intergametophytic mating and apogamy. Apogamy generally offers the shortest gametophyte generation and the least evolutionary potential, intergametophytic mating systems generally have the longest gametophyte generation and the greatest evolutionary potential, and intragametophytic mating systems are intermediate in both respectS. It is envisioned that the interaction between gametophyte ecology and evolutionary potential is important in the evolution of a taxon's reproductive system.     

Herbivores and the Spatial Distributions of the Phytoplankton. II. Estimating Grazing in Planktonic Environments

Large errors are made when laboratory measurements of the ingestion rate of herbivorous zoo-plankton are used to estimate grazing in planktonic environments. The errors arise because the spatial heterogeneity in natural plankton distributions is greater than the heterogeneity present in laboratory experiments. Two probability models are developed for extrapolating laboratory measurements of ingestion to planktonic environments. Both models require sample statistics of the plankton distributions, and these are estimated from sampling studies of the small scale distribution of marine plankton. One model predicts laboratory measurements overestimate the ration obtained by an individual copepod by 30 %. A second model predicts errors exceeding ±50 % are possible when laboratory measurements are used to estimate the grazing by a population of cope-pods.     

The biology of cartilage. II. Invertebrate cartilages: squid head cartilage

In both light and electron microscopes, head cartilage from the squid Loligo pealii strongly resembles vertebrate hyaline cartilage. The tissue is characterized by the presence of irregularly-shaped cells suspended in an abundant matrix. Cell and matrix contents stain metachromatically with cationic dyes such as toluidin blue. Each cell gives off extensions which ramify via a network of channels throughout the matrix. Thereby, a system of inter-connecting canaliculi is established, with many similarities to the intercanalicular systems seen in vertebrate bone and cartilage tissues. In the electron microscope, the squid cartilage cells are seen to have very abundant endoplasmic reticulum and Golgi complex material. Mitochondrial transformations involving loss of cristae, the appearance of filaments in the mitochondrial matrix, and figures suggesting budding, also occur. Nuclear pores are numerous and easily detected. The matrix is characterized by the presence of a system of decussating fibrils which form polygonal figures, with granules usually evident at the points of intersection of fibrils. By chemical analysis the tissue contains 3- and 4-hydroxyproline and hydroxylysine. Preliminary wide single x-ray diffractions show a pattern characteristic for unoriented collagens, with 12 Å (intermolecular) and 2.86 Å (helix) reflections.     

The role of log-normal dynamics in the evolution of biochemical pathways

The study of the scale-free topology in non-biological and biological networks and the dynamics that can explain this fascinating property of complex systems have captured the attention of the scientific community in the last years. Here, we analyze the biochemical pathways of three organisms (Methanococcus jannaschii, Escherichia coli, Saccharomyces cerevisiae) which are representatives of the main kingdoms Archaea, Bacteria and Eukaryotes during the course of the biological evolution. We can consider two complementary representations of the biochemical pathways: the enzymes network and the chemical compounds network. In this article, we propose a stochastic model that explains that the scale-free topology with exponent in the vicinity of gamma approximately 3/2 found across these three organisms is governed by the log-normal dynamics in the evolution of the enzymes network. Precisely, the fluctuations of the connectivity degree of enzymes in the biochemical pathways between evolutionary distant organisms follow the same conserved dynamical principle, which in the end is the origin of the stationary scale-free distribution observed among species, from Archaea to Eukaryotes. In particular, the log-normal dynamics guarantees the conservation of the scale-free distribution in evolving networks. Furthermore, the log-normal dynamics also gives a possible explanation for the restricted range of observed exponents gamma in the scale-free networks (i.e., gamma > or = 3/2). Finally, our model is also applied to the chemical compounds network of biochemical pathways and the Internet network.     

Notes on the biology of Trypanosoma ambystomae Lehmann, 1954. II. The Life Cycle in the Invertebrate Host.

SYNOPSIS. The leech, Erpobdella sp., is a suitable invertebrate host for Trypanosoma ambystomae. The developmental cycle involves a mononucleate, rounded body derived from the bloodstream form; this body then transforms into a large plump crithidia. Subsequent divisions yield medium crithidia, small crithidia, and ultimately, metacyclic trypanosomes.     

On simulating strongly interacting, stochastic population models. II. Multiple compartments

In Wick and Stelf [Math. Biosci. 187 (2004) 1], we showed how to simulate a pair of strongly interacting biological populations evolving stochastically over many orders-of-magnitude. Here we generalize the method to any (finite) number of compartments; transitions including births, deaths, progression through life-stages, and mitoses; and arbitrary rate functions. We illustrate the technique for a seven-compartment model of the cellular immune response to a viral infection.