Proteome-wide mapping of short-lived proteins in human cells

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Quantitative Structure-Activity Relationship Study on Some Dihydropteridine Reductase Inhibitors

Abstract

The dihydropteridine reductase (DHPR) inhibitory potencies of some 4-phenyltetrahydropyridines, 4-phenylpiperidines, and 4-phenylpyridines, are analyzed in relation to their physicochemical and molecular properties. They are found to have significant correlation with Hammett constant s and the van der Waals volume V_w. The correlation is linear with s and parabolic with V_w. Hence, it is argued that DHPR inhibition involves dispersion interaction and is enhanced by electron donation from the substituents but hindered by steric effects produced by large substituents. It is also found that these electronic and steric effects are significant only when they are produced by substituents being at specific position in the molecules.     

PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY

The problem of complex adaptations is studied in two largely disconnected research traditions: evolutionary biology and evolutionary computer science. This paper summarizes the results from both areas and compares their implications. In evolutionary computer science it was found that the Darwinian process of mutation, recombination and selection is not universally effective in improving complex systems like computer programs or chip designs. For adaptation to occur, these systems must possess “evolvability,” i.e., the ability of random variations to sometimes produce improvement. It was found that evolvability critically depends on the way genetic variation maps onto phenotypic variation, an issue known as the representation problem. The genotype-phenotype map determines the variability of characters, which is the propensity to vary. Variability needs to be distinguished from variations, which are the actually realized differences between individuals. The genotype-phenotype map is the common theme underlying such varied biological phenomena as genetic canalization, developmental constraints, biological versatility, developmental dissociability, and morphological integration. For evolutionary biology the representation problem has important implications: how is it that extant species acquired a genotype-phenotype map which allows improvement by mutation and selection? Is the genotype-phenotype map able to change in evolution? What are the selective forces, if any, that shape the genotype-phenotype map? We propose that the genotype-phenotype map can evolve by two main routes: epistatic mutations, or the creation of new genes. A common result for organismic design is modularity. By modularity we mean a genotype-phenotype map in which there are few pleiotropic effects among characters serving different functions, with pleiotropic effects falling mainly among characters that are part of a single functional complex. Such a design is expected to improve evolvability by limiting the interference between the adaptation of different functions. Several population genetic models are reviewed that are intended to explain the evolutionary origin of a modular design. While our current knowledge is insufficient to assess the plausibility of these models, they form the beginning of a framework for understanding the evolution of the genotype-phenotype map.     

Minimum area requirements of breeding birds in fragmented woodland of Central Argentina

The breeding avifauna of 25 woodland fragments (0.85–280 ha) was studied between 1996 and 2004 in Córdoba, Argentina. A distinctive feature of the avifauna of the fragments studied is the low area requirement of most of the species. Of the 54 woodland species recorded, 32 (59.3%) require c . 1 ha and 43 (79.6%) needed no more than 3 ha. Also noticeable is the relatively high number of individuals of most of the species. Both characteristics suggest a good tolerance to fragmentation. However, nine species (16.7%), the area-sensitive species, need fragments of 80 ha or larger. Moreover, eight resident species have apparently become extinct in the fragments that were studied, including the five large species that originally inhabited the area. Proportional odds and log linear models were fitted to relate the minimum area requirements of these species to various ecological characteristics (body size, diet, habitat use, migratory status, and nest type). Closed nesters, resident, woodland exterior, and medium-size species were the groups requiring larger areas. No apparent pattern was observed between area requirements and diet. A recent law prohibits woodland removal, which is a positive step towards the conservation of the fragments. The results suggest that as long as the present amount of woodland is maintained, the situation of the avifauna of the fragments is relatively secure, at least in the short term.     

Power of QTL detection by either fixed or random models in half-sib designs

The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses) included the number of sires (5) and sons per sire (80), ratio of QTL variance to total genetic variance (λ = 0.1), marker spacing (10 cM), and QTL allele frequency (0.5). A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (λ) of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log₁₀ of type I error profiles were quite flat at close marker spacing (1 cM), confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.     

Effects of scale on interpreting life-history characteristics of ungulates and carnivores

Many life-history characteristics of large mammals are scale sensitive. We provide examples where varying temporal and spatial scales can affect interpretation of data concerning life-history characteristics in large herbivores and carnivores and offer recommendations for selecting the most appropriate sampling scale or scales. We also document that some animals make decisions concerning their spatial distribution at scales well beyond the size of the home range. Conversely, other decisions involving sexual segregation of sexes, or where to give birth, may be made at scales below the level of the habitat patch. Such differences in behaviour affect our understanding of habitat selection in large herbivores, and interpreting tradeoffs between acquiring essential resources and avoiding predators. Moreover, some landscape attributes may be selected at one scale, whereas other characteristics of the environment may be selected at another. We argue that even sophisticated models for explaining the ecology and behaviour of mammals benefit from framing specific hypotheses that are related to the to the life-history characteristics of those animals. We also believe that the failure to consider and select the most appropriate scale, or suite of scales, may lead to the mismanagement of critical natural resources. We forge relationships among scale, life-history characteristics of mammals, and biodiversity. Finally, we synthesize the literature on scale for large mammals and make recommendations for future research.     

Feeding Characteristics of Three Species of Intertidal Sea Anemones of the South Kuril Islands

We examined the content of the coelenteron of Oulactis orientalis, Cnidopus japonicus, and Aulactinia sp. (family Actiniidae) inhabiting the intertidal area of Shikotan and Kunashir Islands (South Kuril Islands). The feeding characteristics (food spectrum, the index of filling of the coelenteron, the index of food similarity of the species, occurrence frequency, the index of trophic importance, and the proportions of certain components in the food pellet) allowed us to determine that the examined species are euryphagous.     

Method for the appraisal of anthropogenic disturbance of macrozoobenthic communities of soft substrata

A method for quantitative appraisal of disturbances of macrobenthic communities of soft substrata caused by anthropogenic pollution is proposed. This method is based on the establishment of the dependence of various parameters characterizing the abundance and structure of communities (biomass, population density, number of species, Shannon-Weaver and Pielou indices, etc.) on the level of total contamination of bottom sediments. Using the percentage of deviation of abundance parameters and ecological indices from the norm (the initial horizontal segment of model curves), as well as ERL _q and ERM _q values, which limit the area of progressive degradation of bottom communities (an almost linear drop in abundance and structure characters), is suggested as a numerical characteristic of such deformations. Mapping of aqueous areas on the basis of these characteristics enabled us to obtain a synoptic view of the extent and spatial scale of anthropogenic impacts. An example of the application of this method for assessment of the state of benthic communities in the Peter the Great Bay (Sea of Japan) is shown for the end of the 1980s. The method is verified on the basis of comparison with the results obtained by standard methods of appraisal of the ecological status of macrozoobenthic communities.