Analysis of peptides from known proteins: Clusterization in sequence space

A combinatorial sequence space (CSS) model was introduced to represent sequences as a set of overlapping k-tuples of some fixed length which correspond to points in the CSS. The aim was to analyze clusterization of protein sequences in the CSS and to test various hypotheses about the possible evolutionary basis of this clusterization. The authors developed an easy-to-use technique which can reveal and analyze such a clusterization in a multidimensional CSS. Application of the technique led to an unexpectedly high clusterization of points in the CSS corresponding to k-tuples from known proteins. The clusterization could not be inferred from nonuniform amino acid frequencies or be explained by the influence of homologous data. None of the tested possible evolutionary and structural factors could explain the clusterization observed either. It looked as if certain protein sequence variations occurred and were fixed in the early course of evolution. Subsequent evolution (predominantly neutral) allowed only a limited number of changes and permitted new variants which led to preservation of certain k-tuples during the course of evolution. This was consistent with the theory of exon shuffling and protein block structure evolution. Possible applications of sequence space features found were also discussed.Correspondence to: H.A. Lim     

Insulin-Like Growth Factor-I-Enhanced Secretion Is Abolished in Protein Kinase C-Deficient Chromaffin Cells

Abstract: Previous studies have demonstrated that bovine chromaffin cells cultured in medium with 10 nM insulin-like growth factor-I (IGF-I) secrete about twofold more catecholamine when exposed to secretory stimuli than do cells cultured without IGF-I. The purpose of this study was to determine whether protein kinase C (PKC) is involved in the effect of IGF-I on secretion from these cells. PKC was down-regulated in the cells by 16–18 h of treatment with β-phorbol didecanoate (β-PDD; 100 nM). Such treatment had no effect on high-K⁺-stimulated secretion from cells cultured without IGF-I; however, secretion from cells cultured with IGF-I was reduced to a level comparable to that in cells cultured without the peptide. The inactive isomer, α-PDD (100 nM), had no effect on secretion from untreated or IGF-I-treated chromaffin cells. The effect of β-PDD was time and concentration dependent, with 100 nM β-PDD producing a maximal effect in 8–10 h. In situ PKC activity measured in permeabilized cells treated with PMA (300 nM) was decreased by～40% by 10 h and was reduced to almost basal levels by 18 h. Immunoblotting experiments demonstrated that both α-and ε-PKC were lost from the cells with time courses similar to that seen in the in situ PKC assay. Overnight treatment with the PKC inhibitor H7 (100 μM) prevented the enhanced secretion normally seen in IGF-l-treated cells, whereas HA1004 had no effect. High-K⁺-stimulated ⁴⁵Ca²⁺ uptake in IGF-I-treated cells was attenuated by long-term treatment with β-PDD (200 nM) or H7 (100 μM). Together these observations suggest that PKC is required for IGF-I-enhanced secretion from chromaffin cells.     

Hormone- and growth factor-stimulated NADH oxidase

An NADH oxidase activity of animal and plant plasma membrane is described that is stimulated by hormones and growth factors. In plasma membranes of cancer cells and tissues, the activity appears to be constitutively activated and no longer hormone responsive. With drugs that inhibit the activity, cells are unable to grow although growth inhibition may be more related to a failure of the cells to enlarge than to a direct inhibition of mitosis. The hormone-stimulated activity in plasma membranes of plants and the constitutively activated NADH oxidase in tumor cell plasma membranes is inhibited by thiol reagents whereas the basal activity is not. These findings point to a thiol involvement in the action of the activated form of the oxidase. NADH oxidase oxidation by Golgi apparatus of rat liver is inhibited by brefeldin A plus GDP. Brefeldin A is a macrolide antibiotic inhibitor of membrane trafficking. A model is presented where the NADH oxidase functions as a thiol-disulfide oxidoreductase activity involved in the formation and breakage of disulfide bonds. The thiol-disulfide interchange is postulated as being associated with physical membrane displacement as encountered in cell enlargement or in vesicle budding. The model, although speculative, does provide a basis for further experimentation to probe a potential function for this enzyme system which, under certain conditions, exhibits a hormone- and growth factor-stimulated oxidation of NADH.     

Accumulation of cesium and radiocesium in forest litter in selected regions of poland and its influence on litter-to-mushroom transfer factor

The aim of this work was to check whether the stable cesium content in forest litter affects the value of radiocesium from litter-to-mushroom transfer factorTf or not. Total cesium in litter, measured by AAS, varied from 0.1–2.7 μg/g. These data, combined with earlier results for mushrooms, showed no simple correlation forTf. More complex relationships provided very high correlation coefficients, but their validity needs further investigation.     

Distribution of two congeneric charrs in streams of Hokkaido Island,Japan: considering multiple factors across scales

Salvelinus leucomaenis (white-spotted charr) and S. malma (Dolly Varden) are distributed throughout Hokkaido Island, Japan, but sites where they occur in sympatry are rare. In general, S. malma inhabit upstream reaches and S. leucomaenis extend downstream to the ocean. Factors influencing their distribution were analyzed at four spatial scales ranging from the whole island to individual stream pools. At the island scale, S. leucomaenis were found in the warmer south-west region and at lower altitudes elsewhere, whereas S. malma were found in the colder north-east and at higher altitudes. At a regional scale, the downstream limit of S. malma and upstream limit of S. leucomaenis shifted to lower altitude from south-west to north-east across the island, coincident with the decrease in temperature. Further analysis showed that transition points from S. leucomaenis or sympatry to S. malma in individual watersheds were closely related to an index of cumulative mean monthly temperatures exceeding 5°C. However, at the scale of a single watershed, the transition occurred at different altitudes, gradients, and temperatures in two tributaries, apparently because stream discharge, habitat, and disturbances from floods interacted with these abiotic factors to limit distribution. The two charr species developed interspecific dominance hierarchies in individual pools, and there was strong complementary density compensation among stream pools that could be explained by interspecific competition but not by differences in habitat. However, patterns at watershed and regional scales suggested that interspecific competition interacts with temperature in complex ways. We conclude that the importance of various abiotic and biotic factors in shaping Hokkaido charr distributions depends on the scale at which they are viewed.     

On the relationship between food, reproduction and survival of two carabid beetles: Calathus melanocephalus and Pterostichus versicolor

Abstract.

• 1 The relative influences of temperature and availability of food on reproduction, survival and growth of all developmental stages of two carabid beetle species are discussed with special reference to the suggested relationship between availability of food, size of egg production and survival of adults from one breeding season to the next.
• 2 Temperature as well as food supply influence the length of larval growth and adult body size. Beetles grown at low temperatures and low amounts of food are smaller than those grown at higher temperature and with more food.
• 3 The number of eggs laid per female was correlated with the amount of food gathered. There was no inverse relationship (trade-off) between reproductive output and survival in the field until the next breeding season.
• 4 In 1980 no significant relationship was found between winter mortality and the amounts of food gathered by beetles in the period after reproduction and before winter diapause. However, in 1981 in C. melanocephalus a lower number of starved beetles survived the winter than the fed ones and‘field’beetles.
• 5 Only in the first part of the feeding activity period in autumn can enough food be gathered by C.melunocephalus for successful hibernation. In the second part of this period there is not enough food to build up the fat reserves needed to survive the winter.
• 6 Difference in population fluctuations of both species are discussed in relation to their life histories.

     

从睡眠剥夺树鼩（TBC）尿液提取内源性“睡眠因子”（sleep factor）的研究

本研究报道从睡眠剥夺（ＳＤ）４８—７２ｈ的灵长类原宗（ｐｒｉｍｉｔｉｖｅｓｔｏｃｋ）Ｔｕｐａｉａｂｅｌａｎｇｅｒｉｃｈｉｎｅｎｓｉｓ（ＴＢＣ）提取内源性“睡眠因子”（ｓｌｅｅｐｆａｃｔｏｒ）Ｓ２Ｃ和Ｓ４Ｂ。收集的尿液经超滤,清液冻干经ＳｅｐｈａｄｅｘＧ１５分离得到ＦｒａｃｔｉｏｎⅠ－Ⅴ。活性测定发现Ｆｒａｃｔｉｏｎ－Ⅲ（Ｓ２Ｃ）呈现显著δ－增强促眠效应。经ＳｅｐｈａｄｅｘＧ２５和ＳｅｐｈａｄｅｘＬＨ２０进一步净化的Ｓ４Ｂ也呈现显著δ－增强促眠效应。     

Oxidative processes as indicators of chemical stress in marine bivalves

Deleterious effects of environmental contaminants could be due to enhanced prooxidant forces overcoming antioxidant defences. Before practical biomarkers based on free radical biology will be generally accepted and validated in situ, additional research is required concerning normal physiological and environmental influences on the relevant systems. The aims of this study were to evaluate in situ the importance of oxyradical production in the presence and absence of pollutants and to characterize some antioxidant systems in Mytilus edulis L. Specimens of M. edulis L. were transplanted from a reference site (Franquelin) to Baie Comeau (Baie des Anglais), on the North shore of the St. Lawrence maritime estuary, where are found aluminium and pulp and paper plants. An oxidative stress was observed in mussels submitted to a chronic exposure in the polluted environment. Variations of pro-and anti-oxidant molecules involved in oxidative processes were related in part to seasonal and physico-chemical influences. Catalase activity, malondialdehyde and glutathione concentrations will be useful as biomarkers of stress in situ since they react to anthropogenic influence and to abiotic factors such as emersion period and temperature.