General formulation of Haldane's laws for competing ligands

Haldane's laws, which apply to situations in which CO and O₂ compete for the four heme sites of hemoglobin, are discussed in general statistical mechanical terms. Necessary and sufficient conditions for the validity of Haldane's laws are presented and discussed for general situations in which two ligands compete for interacting active sites on a molecule. Our considerations therefore apply to a competing substrate-inhibitor-allosteric enzyme system for example, as well as to hemoglobin. A generalization of the Monod-Wyman-Changeux model for competing ligands is briefly discussed.     

Contributions to topological biology: Some considerations on the primordial graph and on some possible transformations

This paper is a continuation of some discussions published previously (Bull. Math. Biophysics,16, 317–347, 1954). A different example of a primordial graph is suggested and discussed. Then six different types of geometric transformations, similar in some respects to the one discussed in the previous paper are proposed. Another set of seven different transformations which emphasize the central role of the circulatory system is described. A theorem about the “lumping” of several points of a graph into one point is proved and possible biological aspects of it are discussed.     

Somatic hybrids of Solanum tuberosum – application to genetics and breeding

Cultivated potato (Solanum tuberosum L.) is one of the first agricultural crops successfully cultured in vitro and used for obtaining of somatic hybrids. The review presents the current state of knowledge of somatic hybridisation involving this and other species from the genus of Solanum. Methods of somatic hybridisation, in particular factors that must be considered during designing the experiments are presented and discussed. The main attention however is focused on processes that are responsible for somatic hybrid formation. Complex interactions between genomes and plasmones lead to formation of symmetric, asymmetric and cytoplasmic recombinants. The concept of alloplasmic incompatibility is presented and discussed in relation to Solanum hybrids. Selected examples of potato somatic hybrids with agronomically important traits derived from wild species are presented in the table and discussed.     

Current status of the role of Cl− ion in the oxygen-evolving complex

This minireview summarizes the current state of knowledge concerning the role of Cl⁻ in the oxygen-evolving complex (OEC) of photosystem II (PSII). The model that proposes that Cl⁻ is a Mn ligand is discussed in light of more recent work. Studies of Cl⁻ specificity, stoichiometry, kinetics, and retention by extrinsic polypeptides are discussed, as are the results that fail to detect Cl⁻ ligation to Mn and results that show a lack of a requirement for Cl⁻ in PSII-catalyzed H₂O oxidation. Mutagenesis experiments in cyanobacteria and higher plants that produce evidence for a correlation between Cl⁻ retention and stable interactions among intrinsic and extrinsic polypeptides are summarized, and spectroscopic data on the interaction between PSII and Cl⁻ are discussed. Lastly, the question of the site of Cl⁻ action in PSII is discussed in connection with the current crystal structures of the enzyme.     

Aspects of the mineral nutrition of some native British plants — inter-site variation

Fifteen common native British plants were each sampled at a range of sites in Great Britain and green tissues analysed for several inorganic nutrients. Sampling criteria are discussed. The inter-site variation of each element within a species is assessed as a frequency distribution of raw data. Sample values of parameters including arithmetic mean, variance (coefficient of variation), skewness and kurtosis are presented. Their stability is assessed from nitrogen in sub-samples of Pteridium. This suggested sample sizes were adequate but some distributions had sufficient kurtosis to affect the variance. These parameters showed distinctions between macro- and micro-elements and between species. Some mean values sharply distinguished between species and may help to assess current theories of strategy and adaptation but a wider range of species is needed to clarify trends. Coefficients of variation are discussed and were relatively low for a nation-wide survey after allowing for sampling constraints. Coefficients of skewness and kurtosis showed two-thirds of the sample distributions were non-normal. Ecological aspects of the distributions are discussed and are relevant to studies along environmental gradients. Published hypotheses linking positive skewness to stress in the field are considered and two other postulates discussed. Distribution bounds such as those confining 95% of the values are discussed in relation to possible critical levels of nutrients.Nomenclature follows Clapham et al. (1981), Excursion flora of the British Isles. 3rd ed. University Press, Cambridge, except Chamaenerion.     

The evolutionary importance of behavioural development: the ontogeny and phylogeny of bird song

It has been proposed that ontogeny may be an important constraint on the evolution of morphological traits. In this paper, ontogeny is discussed as a possible constraint on behavioural evolution. A literature review of the development of song in oscine birds (Passeriformes; Passeres) shows that song development follows von Baer's law; that is, that development proceeds from early, generally distributed stages to later, specialized stages. Song ontogeny is found to parallel phylogeny in a lineage of sparrows (Emberizidae; Emberizinae). Possible cases of paedomorphosis (slowing down or truncation of development) in bird song are discussed, specifically in the family Mimidae and in the reed warbler, Acrocephalus palustris (Muscicapidae; Sylviinae). Finally, the implications of developmental constraints for the study of the adaptive significance of behaviour are discussed.     

Davydov Soliton Dynamics in Proteins: III. Applications and Calculation of Vibrational Spectra

The mechanism for energy and signal transport in proteins as suggested by Davydov is discussed. The idea is based on a coupling of amide-I oscillators to acoustic phonons in a hydrogen bonded chain. Results as obtained with the usually used ansätze are discussed. The quality of these states for an approximate solution of the time-dependent Schrödinger equation is investigated. It is found that the semiclassical ansatz is a poor approximation, while the more sophisticated |D₁> state seems to represent the exact dynamics quite well. This was shown by extensive calculations, both analytically and numerically in the two preceding papers. Calculations at a temperature of 300K for one chain, as well as for three coupled ones (as they are present in an α-helix) are presented and discussed. From the calculations it is evident, that Davydov solitons are stable for reasonable parameter values at 300K for special initial excitations close to the terminal sites of the chain. Further vibrational spectra are presented and discussed. Our results suggest, that due to their strong dependence on the initial state, the Davydov |D₁> model system might be a (quantum) chaotic one.     

Some highlights in the history of fungi in medicine – A personal journey

The history of the role of fungi in the development of medicine has largely been neglected. Here the early recognition of the germ theory will be discussed in relation to surface infections, the “cholera fungus theory” and recognition of the phenomenon of microbial antagonism. This leads to a short review of the history of those antibiotics produced by fungi, notably penicillin. Finally, the history of the recognition of the potential role fungi play as casual agents of cancer will be discussed; although currently neglected, this work may prove to be of future significance. This history of medical mycology is discussed from the standpoint of my own interest and research into this fascinating, and often overlooked area of medical history.     

Local Order in Some Aprotic Dipolar Liquids

Abstract

Analysis of the local order in four aprotic, dipolar liquids (acetonitrile, acetone, N,N- dimethylformamide, and pyridine) has been carried out by computer simulation methods. The effect of the dipole-dipole-as well as of the Lennard-Jones interactions on the pair distribution functions and some orientational characteristics are discussed. A general observation for this group of liquids is that the local order is accompanied by a favorable orientation of the nearest neighbor molecules with dipole vectors anti-parallel to the central one. This orientation decays rapidly and extends to slightly more than to the first neighbor molecules only. Differences in local order due to the differences in shapes and symmetries of the molecules are discussed.

The present study partly employs the recently developed Reverse Monte Carlo method, special features of which in contrast to the traditional simulation methods are also discussed.     

Studies on skeleton formation in reptiles, v. Patterns of ossification in the skeleton of Alligator mississippiensis DAUDIN (Reptilia, Grocodylia)

Patterns of ossification are described in the endo-and exoskeleton of Alligator mississippiensis. The occurrence of a dermo-supraoccipital is discussed in light of the independence of dermal and endochondral bone. The development of the bony secondary palate is discussed in light of Haeckelian recapitulation. The sequence of ossification in the limb skeleton is shown to differ from the sequence of chondrification of the cartilaginous precursors. Patterns of ossification in Alligator are compared to lepidosaurs in terms of sequence and timing. Important differences relate to ossification patterns in the limb skeleton: lepidosaurs show a dominance of digit III > IV > II > I > V, whereas Alligator shows a dominance of digits III > II> IV > I > V in the ossification process. Ontogenetic repatterning in the ossification of the axial skeleton is discussed as it bears on the serial homology of dorsal ribs, sacral ribs and caudal ribs (transverse processes).     

Rhodopseudomonas palustris and Rh. viridis—Photosynthetic budding bacteria

Summary Rhodopseudomonas palustris and Rh. viridis were found to reproduce by budding. The differences between budding reproduction and binary fission were discussed, and it was concluded that there was a lack of evidence to indicate a fundamental difference between the two processes in bacteria. Taxonomic and nomenclatural changes were discussed.Dedicated to Prof. C. B. van Niel on the occasion of his 70th birthday.     

Nature and natural classification

The contribution ofJohn Gilmour to the philosophy of taxonomy, particularly regarding the concept of natural classification, is discussed. The use of the term by the main schools of taxonomy—phenetic, evolutionary and cladistic—is discussed. It is suggested that classification should be related to the way in which the human brain perceives pattern in nature, and recent developments in optical components, neural computers and random problem solving are considered.Dedicated to the memory of JohnS. L. Gilmour.     

Some remarks on the boolean algebra of nervous nets in mathematical biophysics

Recent demonstration by the author has shown that the fundamental equations of the mathematical biophysics of the central nervous system can be considered as describing the behavior of very large numbers of neurons, of which each one follows discontinuous laws, such as discussed by W. S. McCulloch and W. Pitts. In that light some of the old problems are discussed. The comparative merits of the “microscopic” and “macroscopic” approaches are discussed for the problem of the point to point correspondence between the retina and the cortex, with the number of connecting fibers much less than the number of cells. Some aspects of discrimination of intensities are also discussed. Finally, a few generalizations of the McCulloch-Pitts treatment are suggested, and a nervous network is constructed which illustrates some aspects of the perception of numbers.     

Ligand and metal X-ray absorption in transition metal complexes

The ligand K edges and metal L edges of transition metal complexes are discussed within the perspective of recent progress in calculations on bulk transition metal oxides. Similarities and differences between bulk transition metal systems and coordination complexes are discussed. It is argued that the core hole effect reduces the amount of ligand p-states in the 3d-band (the β² value) by approximately 10-20%. It is suggested that matrix elements do not have to be included in XAS calculations if one calculates the projected DOS in the area of the core state radius. In case of metal L edge spectra, the additional effects of multiplets and charge transfer are discussed and compared with DFT calculations.     

Monte Carlo Simulation of Hydration of the Nucleic Acid Fragments

Abstract

Systems containing a base or a base pair and 25 water molecules, as well as a helical stack and 30 water molecules per base pair, have been simulated. Changes in the base hydration shell structure, after the bases have been included into the pair and then into the base pair stack are discussed. Hydration shells of several configurations of the base pair stacks are discussed. Probabilities of formation of the hydrogen-bonded bridges of 1, 2 and 3 water molecules between hydrophilic centres have been estimated. The hydration shell structure was shown to depend on the nature of the base pair and on the stack configuration, while dependence of the global hydration shell characteristics on the stack configuration has been proved to be rather slight. The most typical structural elements of hydration shells, in the glycosidic (minor in B-like conformation) and non-glycosidic (major) grooves, for different configurations of AU and GC stacks, have been found and discussed. The number of hydrogen bonds between water molecules and bases per water molecule was shown to change upon transformation of the stack from A to B configuration. This result is discussed in connection with the reasons for B to A conformational transition and the concept of “water economy”. Hydration shell patterns of NH₂-groups of AU and GC helical stacks differ significantly.     

Davydov Soliton Dynamics in Proteins: III. Applications and Calculation of Vibrational Spectra

The mechanism for energy and signal transport in proteins as suggested by Davydov is discussed. The idea is based on a coupling of amide-I oscillators to acoustic phonons in a hydrogen bonded chain. Results as obtained with the usually used ansätze are discussed. The quality of these states for an approximate solution of the time-dependent Schrödinger equation is investigated. It is found that the semiclassical ansatz is a poor approximation, while the more sophisticated |D₁> state seems to represent the exact dynamics quite well. This was shown by extensive calculations, both analytically and numerically in the two preceding papers. Calculations at a temperature of 300K for one chain, as well as for three coupled ones (as they are present in an -helix) are presented and discussed. From the calculations it is evident, that Davydov solitons are stable for reasonable parameter values at 300K for special initial excitations close to the terminal sites of the chain. Further vibrational spectra are presented and discussed. Our results suggest, that due to their strong dependence on the initial state, the Davydov |D₁> model system might be a (quantum) chaotic one.     

Effects of Environmental Stressors and Immunosuppressants on Immunity in Fundulus heteroclitus

Environmental stressors have been shown to alter immunocompetencein mammals. Similar effects have been reported in fish. Thepurpose of this paper is to review the literature concerningthe white blood cells and immunity in Fundulus heteroclitus.Evidence for immunosuppression following prolonged captivity,handling, hypophysectomy, radiation, changes in temperatureand salinity, and exposure to chemicals including environmentalpollutants is discussed. New evidence for immunosuppressionfollowing exposure to benzo-a-pyrene, pentachlorophenol, andhexachlorobenzene is presented. Possible mechanisms of immunealteration and the consequences to F. heteroclitus are discussed.     

Clinical significance and perspectives of gastrointestinal peptide hormones.

Present knowledge about gastrointestinal peptide hormones is discussed from three points of view: (a) diagnostic significance of these hormones; (b) states characterized by over-production or deficiency of peptide hormones; (c) clinical application and perspectives of gastrointestinal hormones. The data in the literature are subjected to a critical analysis; in addition, the author's own experiments are discussed.