New methods for estimating the numbers of synonymous and nonsynonymous substitutions

New methods for estimating the numbers of synonymous and nonsynonymous substitutions per site were developed. The methods are unweighted pathway methods based on Kimura's two-parameter model. Computer simulations were conducted to evaluate the accuracies of the new methods, Nei and Gojobori's (NG) method, Miyata and Yasunaga's (MY) method, Li, Wu, and Luo's (LWL) method, and Pamilo, Bianchi, and Li's (PBL) method. The following results were obtained: (1) The NG, MY, and LWL methods give overestimates of the number of synonymous substitutions and underestimates of the number of nonsynonymous substitutions. The major cause for the biased estimation is that these three methods underestimate the number of synonymous sites and overestimate the number of nonsynonymous sites. (2) The PBL method gives better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. (3) The new methods also give better estimates of the numbers of synonymous and nonsynonymous substitutions than those obtained by the NG, MY, and LWL methods. In addition, estimates of the numbers of synonymous and nonsynonymous sites obtained by the new methods are reasonably accurate. (4) In some cases, the new methods and the PBL method give biased estimates of substitution numbers. However, from the number of nucleotide substitutions at the third position of codons, we can examine whether estimates obtained by the new methods are good or not, whereas we cannot make an examination of estimates obtained by the PBL method. (5) When there are strong transition/transversion and nucleotide-frequency biases like mitochondrial genes, all of the above methods give biased estimates of substitution numbers. In such cases, Kondo et al.'s method is recommended to be used for estimating the number of synonymous substitutions, although their method cannot estimate the number of nonsynonymous substitutions and is time-consuming. These results, particularly result (1), call for reexaminations of some genes. This is because evolutionary pictures of genes have often been discussed on the basis of results obtained by the NG, MY, and LWL methods, which are favorable for the neutral theory of molecular evolution.     

Regulation of Phenylethanolamine N-Methyltransferase Gene Expression by Imidazoline Receptors in Adrenal Chromaffin Cells

Abstract: As adrenal medullary chromaffin cells express imidazoline binding sites in the absence of α₂-adrenergic receptors, these cells provide an ideal system in which to determine whether imidazolines can influence catecholamine gene expression through nonadrenergic receptors. This study evaluates the ability of clonidine and related drugs to regulate expression of the gene for the epinephrine-synthesizing enzyme phenylethanolamine N -methyltransferase (PNMT) in the rat adrenal gland and in bovine adrenal chromaffin cell cultures. In vivo, PNMT and tyrosine hydroxylase (TH) mRNA levels increase in rat adrenal medulla after a single injection of clonidine. Clonidine also dose-dependently stimulates PNMT mRNA expression in vitro in primary cultures of bovine chromaffin cells, with a threshold dose of 0.1 μ M . Other putative imidazoline receptor agonists, including cimetidine, rilmenidine, and imidazole-4-acetic acid, likewise enhance PNMT mRNA production showing relative potencies that correlate with their binding affinities at chromaffin cell I₁-imidazoline binding sites. The effects of clonidine on PNMT mRNA appear to be distinct from and additive with those exerted by nicotine. Moreover, neither nicotinic antagonists nor calcium channel blockers, which attenuate nicotine's influence on PNMT mRNA production, diminish clonidine's effects on PNMT mRNA. Although 100 μ M clonidine diminishes nicotine-stimulated release of epinephrine and norepinephrine in chromaffin cells, this effect appears unrelated to stimulation of imidazoline receptor subtypes. This is the first report to link imidazoline receptors to neurotransmitter gene expression.     

Opposing Actions of Thrombin and Protease Nexin-1 on Amyloid β-Peptide Toxicity and on Accumulation of Peroxides and Calcium in Hippocampal Neurons

Abstract: Amyloid β-peptide (Aβ) is the principal component of neuritic plaques in the brain in Alzheimer's disease (AD). Recent studies revealed that Aβ can be neurotoxic by a mechanism involving free radical production and loss of cellular ion homeostasis, thus implicating Aβ as a key factor in the pathogenesis of AD. However, other proteins are present in plaques in AD, including the protease thrombin and protease nexin-1 (PN1), a thrombin inhibitor. We therefore tested the hypothesis that thrombin and PN1 modify neuronal vulnerability to Aβ toxicity. In dissociated rat hippocampal cell cultures the toxicity of Aβ was significantly enhanced by coincubation with thrombin, whereas PN1 protected neurons against Aβ toxicity. Aβ induced an increase in levels of intracellular peroxides and calcium. Thrombin enhanced, and PN1 attenuated, the accumulation of peroxides and calcium induced by Aβ. Taken together, these data demonstrate that thrombin and PN1 have opposing effects on neuronal vulnerability to Aβ and suggest that thrombin and PN1 play roles in the pathogenesis of neuronal injury in AD.     

Elimination of heparan sulfate by heparitinases induces abnormal mesodermal and neural formation in Xenopus embryos

The expression of heparan sulfate glycosaminoglycan (HS-GAG) was examined in Xenopus embryos during the developmental stages. Chemical analysis showed the existence of HS-GAG in the ³⁵S-labeled embryos. By western blot analysis using a specific anti-HS monoclonal antibody, HS-GAG related epitope was found after the neurulation on two protein bands, whose molecular weights were approximately 90 kDa and 100 kDa, respectively. Immunohistochemistry revealed that HS-GAG occurred exclusively in the animal hemisphere in early gastrulae, and then appeared predominantly on the sheath of the neural tube, the notochord and epithelium. To address whether HS-GAG chains contribute to Xenopus embryonic development, we eliminated the embryonic HS-GAG by injecting purified Flavobacterium heparitinases (HSase) into their blastocoels. Most of the injected embryos were aberrant in mesodermal and neural formation, and became acephalic. Histological examination showed that these embryos were completely devoid of the central nervous system and the mesodermal tissues. Neither heat-inactivated heparitinase nor chondroitinase showed such abnormality. The HS-GAG-eliminated embryos showed decreased expression of both muscular and neural-specific markers. These results suggest that HS-GAG plays an indispensable role in establishing the fundamental body plan during early Xenopus development.     

Spatial and Temporal variations of mangrove fish assemblages in Martinique (French West Indies)

A study of the mangrove fish fauna in a bay of Martinique Island (French West Indies) was carried out at different seasons during two consecutive years. fishes were sampled with specific hoop-nets in the coastal areas at 8 stations.A total of 87 species was collected in the bay. Most individuals were represented by small-size specimens and juveniles. The overall species richness varied according to the stations and the sampling periods. The biomass and number of individuals were variable according to the location but remained stable in time. A factor correspondence analysis and a hierarchical clustering with median links were used to follow the evolution of the stations in space and time. Two types of stations were differentiated: the stations characterized by the mangrove and those under the influence of seagrass beds. A seasonal cycle, opposing the dry periods to the others, was observed.Thus, it seems that the use of the mangrove habitat by the fishes is optimized through a complete reorganization of communities in terms of species composition whereas the overall number and biomass remain stable. This model remains valid even for the most constraining biota of the mangrove ecosystem inhabited by a small number of well adapted species.     

Environmental and macroinvertebrate dynamics in the Lower Rhône River and a lateral dike field: a study matching two functioning descriptors

Environmental variables and macroinvertebrate communities are studied in two sites of the Lower Rhône River, the main channel and a lateral, occasionally connected dike field. Environmental variables and faunistic communities allow discrimination the two compartments. The environmental and faunistic differences the two sites change over time. The physical and chemical differences are significantly correlated with water discharge of the main channel. The faunistic ones are significantly correlated with the temperature of the dike field water. The connections between the main channel and the dike field could be very important to maintain a high heterogeneity of the habitat, and for recolonization of the main channel after a perturbation.     

On the Modeling of Some Anti-inflammatory and Anti-thrombotic Drugs by AM1

Two families of autacoids from cell membrane phospholipids have been identified. The first, the icosanoids, which are formed from arachidonic acid, include prostaglandins and leukotrienes. The other includes modified phospholipids, as the platelet aggregating factor (PAF). These compounds are related to inflammatory and cardiovascular diseases. We review in this paper some of the work that has been done in our laboratories in the last few years relating to the modeling of new potential thromboxane synthase (TXS) and 5-lipoxygenase (5-LO) and cyclooxygenase (COX) inhibitors, and TXA₂ receptor antagonists derived from nitrogenated heterocycles. We include the results of the modeling of a group of proposed PAF antagonists, and compare their structures with PAF itself and with a recently proposed PAF antagonist model. This revised version was published online in June 2006 with corrections to the Cover Date.     

Rehabilitating degraded forests in Central Europe into self–sustaining forest ecosystems

There is a need for a consistent forest restoration strategy for the `Black Triangle', Central Europe. In the past 50 years, forests in this area have been heavily affected by industrial pollution. Recently, the amount of pollutants has decreased. This means that effective forest restoration programmes can be started. Forest decline must be seen as an ecological disturbance which cannot be solved by applying technical measures only. An ecosystem approach to forest restoration must be introduced into restoration policy and management. Basic principles and working methods of such an approach are briefly described and proposals are made for forest restoration policy, management and research in the area.     

Dendroecological reconstruction and interpretation of larch budmoth (Zeiraphera diniana) outbreaks in two central alpine valleys of Switzerland from 1470 – 1990

 Outbreaks of the larch budmoth (LBM) (Zeiraphera diniana) recur cyclically approximately every 7 to 10 years in subalpine larch-cembran pine and montane to subalpine larch-Norway spruce forests of the relatively dry valleys of the European Alps. By dendroecologically analyzing increment cores from 570 host (European larch –Larix decidua) and non-host trees (cembran pine –Pinus cembra, Norway spruce –Picea abies) through the use of skeleton plots, at least 57 (59) outbreaks could be reconstructed in the optimum Upper Engadine Valley (suboptimum Goms Valley), Switzerland, during the time period 1503 (1472) to 1990. The average interval between initial years of successive outbreaks was 8.58 (8.95) years, SD 1.66 (2.13) years. Over the centuries spatial shifts of LBM activity between the two study areas occurred, probably due to climatic changes. Clear, site-specific differences in LBM attack could only be found in the suboptimum area where high-lying (>1800 m) and/or south-facing stands were infested most. LBM-afflicted trees proved to be unsuitable for climate reconstructions because the impact of the persistently recurring outbreaks on tree growth is dominant. In order to provide sufficient information for a detailed ecological interpretation of the course of an outbreak, latewood widths and/or densities have to be analyzed in addition to the ring-widths. Received: 11 February 1995 / Accepted: 19 July 1996