A case study of linear versus non-linear modelling

Theories for the facilitation of neurotransmitter release are discussed in a case study of the properties of linear and non-linear models for a phenomenon whose time course can be represented by a sum of decaying exponentials. Particular attention is paid to the effects of a "key factor" on the slopes and amplitudes of the exponentials that can be derived from semilog plots of the data. It is shown that the presence of such effects can give strong evidence for the inappropriateness of linear models. A non-linear model is demonstrated to be capable of describing the changes with extracellular Ca concentration of straight line segments that fit data in semilog plots of facilitation as a function of time. The conclusion is reached that even if data seems to be representable by several independently alterable exponentials one must be cautious in drawing inferences concerning the number, linearity, or independence of the underlying processes.     

Bacteriorhodopsin in a bloom of halobacteria in the Dead Sea

A dense bloom of red halobacteria developed in the Dead Sea in the summer 1980, bacterial densities of up to 1.9 x10⁷ cells ml^-1 were observed. The population consisted of two types: pleomorphic, cup-shaped cells and rod-shaped cells. A high content of bacteriorhodopsin was found in the bloom (up to 0.4 nmol per mg protein). The rod-shaped Halobacterium was isolated and was shown to contain bacteriorhodopsin.Abbreviations 20 specific gravity at 20°C - Tris Tris-(hydroxymethyl)-aminomethane     

A theoretical study of calcium entry in nerve terminals, with application to neurotransmitter release

In his study of a kin selection model for the evolution of workers' behavior in an incipiently social insect, Craig (1979) found that the haplodiploid mode of sex determination, combined with a female-biased sex ratio, cannot accelerate an evolutionary trend toward eusociality. This seems to contradict to Hamilton's (1964) theory. It is my intention to prove that Craig's result is due to the dependence of relative reproductive success in each sex on the sex ratio of a population. The oviposition of unfertilized eggs by workers is indispensable, in primitive stages in the evolution of eusociality, for maintaining the relative reproductive success of a female. Assuming that workers control the sex ratios, we can distinguish the following three evolutionary phases in accordance with the ratio $\text{N}{}_2\text{N}{}_{10}$ (the ratio of the number of the queen's second brood to that of the progeny laid by workers derived from the same nest). During Phase 1 in which $\text{N}{}_2\text{N}{}_{10}$ < $\text{1}\text{2}$, the reproductive successes of a male and a female are equal, and Hamilton's rule holds. In Phase 2 in which $\text{1}\text{2 <}\text{N}{}_2\text{N}{}_{10}\text{<}\text{3}\text{2}$, the queen produces females, and workers oviposit males. As $\text{N}{}_2\text{N}{}_{10}$ increases, the sex ratio in the whole population becomes female-biased and relative reproductive success of a male increases. In Phase 3 in which N₂/N₁₀ >$\text{3}\text{2}$, the queen lays some male eggs in addition to female eggs. The sociality threshold ($\text{B}\text{C}$)_crit the minimum value of the benefit/cost ratio leading to the evolution of altruism, is $\text{2}\text{3}$on Phase 1. It rises threefold as N₂/N₁₀ increases in Phase 2, and, in Phase 3, it is twice as high as that in a diploid species. The anatomical and physiological characteristics of workers must have been so developed that they are efficient in helping activities after the beginning of eusociality. The evolutionary process before the beginning of helping behavior is also discussed. The egg laying by unmated females, which stay their mother's nest, seems to have been an important preadaptation for the evolution of eusociality in Hymenoptera.     

Diversity of halophilic microorganisms: Environments,phylogeny, physiology,and applications

The phylogenetic diversity of microorganisms living at high salt concentrations is surprising. Halophiles are found in each of the three domains: Archaea, Bacteria, and Eucarya. The metabolic diversity of halophiles is great as well: they include oxygenic and anoxygenic phototrophs, aerobic heterotrophs, fermenters, denitrifiers, sulfate reducers, and methanogens. The diversity of metabolic types encountered decreases with salinity. The upper salinity limit at which each dissimilatory process takes place is correlated with the amount of energy generated and the energetic cost of osmotic adaptation. Our understanding of the biodiversity in salt-saturated environments has increased greatly in recent years. Using a combination of culture techniques, molecular biological methods, and chemotaxonomic studies, we have obtained information on the nature of the halophilic Archaea as well as the halophilic Bacteria that inhabit saltern crystallizer ponds. Several halophilic microorganisms are being exploited in biotechnology. In some cases, such as the production of ectoine, the product is directly related to the halophilic behavior of the producing microorganism. In other cases, such as the extraction of β-carotene from Dunaliella or the potential use of Haloferax species for the production of poly-β-hydroxyalkanoate or extracellular polysaccharides, similar products can be obtained from non-halophiles, but halophilic microorganisms may present advantages over the use of non-halophilic counterparts. Journal of Industrial Microbiology & Biotechnology (2002) 28, 56–63 DOI: 10.1038/sj/jim/7000176 Received 20 May 2001/ Accepted in revised form 20 June 2001     

The putative bioactive surface of insect-selective scorpion excitatory neurotoxins

Scorpion neurotoxins of the excitatory group show total specificity for insects and serve as invaluable probes for insect sodium channels. However, despite their significance and potential for application in insect-pest control, the structural basis for their bioactivity is still unknown. We isolated, characterized, and expressed an atypically long excitatory toxin, Bj-xtrIT, whose bioactive features resembled those of classical excitatory toxins, despite only 49% sequence identity. With the objective of clarifying the toxic site of this unique pharmacological group, Bj-xtrIT was employed in a genetic approach using point mutagenesis and biological and structural assays of the mutant products. A primary target for modification was the structurally unique C-terminal region. Sequential deletions of C-terminal residues suggested an inevitable significance of Ile73 and Ile74 for toxicity. Based on the bioactive role of the C-terminal region and a comparison of Bj-xtrIT with a Bj-xtrIT-based model of a classical excitatory toxin, AaHIT, a conserved surface comprising the C terminus is suggested to form the site of recognition with the sodium channel receptor.     

Gene proximity analysis across whole genomes via PQ trees.

Permutations on strings representing gene clusters on genomes have been studied earlier by Uno and Yagiura (2000), Heber and Stoye (2001), Bergeron et al. (2002), Eres et al. (2003), and Schmidt and Stoye (2004) and the idea of a maximal permutation pattern was introduced by Eres et al. (2003). In this paper, we present a new tool for representation and detection of gene clusters in multiple genomes, using PQ trees (Booth and Leuker, 1976): this describes the inner structure and the relations between clusters succinctly, aids in filtering meaningful from apparently meaningless clusters, and also gives a natural and meaningful way of visualizing complex clusters. We identify a minimal consensus PQ tree and prove that it is equivalent to a maximal pi pattern (Eres et al., 2003) and each subgraph of the PQ tree corresponds to a nonmaximal permutation pattern. We present a general scheme to handle multiplicity in permutations and also give a linear time algorithm to construct the minimal consensus PQ tree. Further, we demonstrate the results on whole genome datasets. In our analysis of the whole genomes of human and rat, we found about 1.5 million common gene clusters but only about 500 minimal consensus PQ trees, with E. Coli K-12 and B. Subtilis genomes, we found only about 450 minimal consensus PQ trees out of about 15,000 gene clusters, and when comparing eight different Chloroplast genomes, we found only 77 minimal consensus PQ trees out of about 6,700 gene clusters. Further, we show specific instances of functionally related genes in two of the cases.     

Cyril Dean Darlington: the man who 'invented' the chromosome

Cyril Darlington (1903-1981) was the most famous cytologist in the world in the decades preceding the molecular revolution of the 1950s. He crossed disciplinary boundaries to create a synthesis of cytology, genetics and evolution by revealing the mechanics of chromosomal recombination and the importance of its evolution. Always controversial during his lifetime, obituaries ultimately referred to him as the 'Copernicus' or 'Newton' of cytology. This article reviews Darlington's scientific contributions, the reasons for their difficult reception at the time and their continuing relevance.     

Lead accumulation in the aquatic fern Azolla filiculoides.

In this study, we characterized lead (Pb2+) accumulation and storage by the aquatic fern Azolla filiculoides. Lead precipitates were detected in the vacuoles of mesophyll cells of Azolla plants cultured for 6 d in rich growth medium containing 20 mg l(-1) Pb2+. Energy dispersive spectroscopy (EDS) analysis of the relative element content of leaves collected from these plants revealed a 100% increase in the levels of P, S, Na and Ca and a 40% decrease in Mg and Cl compared to the untreated plants. Both Azolla whole plants and isolated apoplasts were incubated for 6 d in 20 mg l(-1) Pb2+. Lead content in the whole plant composed 0.37%, 2.3% and 1.8% of the dry weight after 2, 4 and 6 d of growth, respectively, while the isolated Azolla apoplast contained 0.125%, 1.22% and 1.4% Pb2+, respectively. Lead content in Azolla whole plant increase by 200%, 100% and 22% after 2, 4 and 6 d of growth, respectively, when compared to Azolla apoplast. Dark, electron dense deposits of lead were observed in light and transmission electron microscope in leaf cells treated with lead. All the observed lead deposits were localized in vacuoles while larger lead deposits were found in mature leaves than in young leaves. No lead deposits were found in cells of the cyanobiont Anabaena when the plants were exposed to similar conditions. Activity and content of V-H+-ATPase were studied in Azolla plants grown in the presence of 20, 40 and 80 mg l(-1) of lead for a period of 4 d. Activity of V-H+-ATPase was increased by 190%, 210% and 220%, respectively, but the content of V-H+-ATPase was reduced by all lead concentrations.