A method for estimating the numbers of synonymous and nonsynonymous substitutions per site

A method for estimating the numbers of synonymous (Ks) and nonsynonymous (Ka) substitutions per site is proposed. The method is based on the Li's (J Mol. Evol. 36:96–99, 1993) and Pamilo and Bianchi's (Mol. Biol. Evol. 10:271–281, 1993) method, but a putative source of bias is solved. It is proposed that the number of synonymous substitutions that are actually transitions or transversions should be computed by separating the twofold degenerate sites into two types of sites, 2S-fold and 2V-fold, where only transitional and transversional substitutions are synonymous, respectively. Kimura's (J. Mol. Evol. 16:111–120, 1980) two-parameter correcting method for multiple substitutions at a site is then applied using the overall observed synonymous transversion frequency to estimate both the numbers of synonymous transversional (Bs) and transitional (As) substitutions per site. This approach, therefore, also minimizes stochastic errors. Computer simulations indicate that the method presented gives more accurate Ks and Ka estimates than the aforementioned methods. Furthermore, the obtention of confidence intervals for divergence estimates by computer simulation is proposed.     

A scanning electron microscope study of Craspedella sp. from the branchial chamber of redclaw crayfish,Cherax quadricarinatus,from Queensland,Australia

Epidermal topography was examined, including papillate ridges, grooves and ciliated sensory papillae of Craspedella sp. from the branchial chamber of redclaw crayfish, Cherax quadricarinatus, from Queensland, Australia. Rhandites were observed to discharge from ducts opening mainly in a small distal region of the ventral epidermis of the three central (of five) tentacles. These regions, devoid of ciliated sensory papillae, serve to adhere the anterior end of the worms during locomotion. Secretions from glands associated with the posterior attachment organ were observed to discharge from pores on the outside region of the ventral surface of the disc.A comparison of various scanning electron microscopy (SEM) fixation techniques showed that (1) hot fixatives at 90 °C provide most information on the largest number of epidermal structures and (2) different fixation regimes highlight different epidermal features.     

Flatworms flatten to size up each other

When copulations are costly, fertilization is reciprocal and fecundity is positively related to size, hermaphrodites are expected to favour large partners, leading to size-assortative mating. Size-related mate choice has, however, never been observed in hermaphrodites. In the flatworm Dugesia gonocephala copulations cost time and are reciprocal, and size is a positive predictor of female fecundity. Every copulation is preceded by a phase in which one partner glides on top of the other and both spread out and flatten, suggesting that partners assess each other''s size. A total of 124 copulating pairs collected on four different dates, proved that mating is size-assorted in the field. In experiments with groups, more copulations took place between equally sized individuals than were expected when matings were random. In experiments with pairs, partners of different size exhibited twice as many mating attempts for the first copulation than did partners of the same size. We conclude that D. gonocephala employs a unique kind of pre-copulatory ''flattening'' behaviour as a mechanism to signal as well as to assess relative size. This does not only confirm that hermaphrodites can mate assortatively when certain assumptions are met, it also proves that even lower invertebrates can show active mate choice.     

Responses of benthic macroinvertebrates in small intermittent streams to silvicultural practices

We examined macroinvertebrate communities in small(0.1-1.0 m²) pools of intermittent streams (alwayscontainingsome water but without perennial flow) with small watersheds(2-6 ha) subjected to five types of forest harvest to assesspotential impacts of the different harvest methods. Bufferstrips10 m wide were left on each side of the streams. Each harvesttreatment was coupled with a similar unharvested referencestand.An incomplete block design included three 0.05 m² vacuumsamples from each treatment paired with three from theadjacentreferences. There was a high degree of similarity amongreferencesfor parameters other than taxonomic composition (e.g.macroinvertebrate density, number of species, Shannondiversity,functional groups, etc.). Statistically significantdifferenceswere found between references and treatments and among harvestmethods but the responses varied among response variables(density,Shannon-Weiner diversity, species composition), differentspeciesassemblages (all invertebrates, chironomids,Ephemeroptera-Plecoptera-Trichoptera [EPT], isopods), andfunctional group categories (shredders, collector-gatherers).Wecollected 56 taxa, 7–16 per site, with low communitysimilarity(mean Jaccards=0.18, mean Bray-Curtis percentdissimilarity=81). The most severe harvest treatmentsresultedin the highest diversities of total invertebrates in thesesmallspring pool communities.     

Uncertain branch lengths, taxonomic sampling error, and the egg to body size allometry in temperate butterflies (Lepidoptera)

The allometry of egg to body size in temperate butterflies, and the relationships between egg size and larval host structure, taxonomy, voltinism, and duration of the egg stage, are investigated using cross-species analysis and the comparative analysis of independent contrasts. In addition, the effect of two sources of uncertainty that may affect continuous data when treated under a statistical, comparative, framework, is assessed: (1) unknown evolutionary distances, and (2) taxonomic representativity (proportion of species of a given taxon, from which data are available). It is suggested that the effects of taxonomic under-representation could be important in comparative, quantitative studies, but this problem may be tempered by means of weighted regression. Under the assumption that taxonomy represents butterfly phylogeny, egg and adult body size are related by negative allometry (i.e. the slope of the line fitted to the logarithmically transformed data is lower than 1.0). However, the precise slope (0.2-0.9) depends on the method used, branch lengths, and taxonomic sampling. There is evidence for a relationship between a species' voltinism and the number of days it spends in the egg stage, as well as between adult butterfly size and the gross structure of the plants used as larval hosts (woody plants or herbs). Egg size proves to be related to foodplant taxonomy, voltinism, and duration of the egg stage when the data are analysed using species means, but these relationships become non-significant when the comparative method is employed.     

Production of gliotoxin during the pathogenic state in turkey poults byAspergillus fumigatus Fresenius

Turkey poults were given either of two different dosages of two different gliotoxin-producing strains ofAspergillus fumigatus. Infected lung tissue was examined postmortem for the presence of gliotoxin. Gliotoxin was found in lung tissue of ten poults infected with one strain and in seven of ten poults infected with the other strain. Concentrations of gliotoxin in the tissue exceeded 6 ppm in some of the infected tissues. The concentration of gliotoxin found in infected tissue did not appear to be correlated with the dosage of organism given. Considering the pathologic changes observed in turkey poults with aspergillosis and the production of gliotoxin during the pathogenic state in turkey poults, gliotoxin is considered likely to be involved in avian aspergillosis. Disclaimer: Names are necessary to report factually on available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by USDA implies no approval of the product to the exclusion of others that may also be suitable.     

Development and characterization of monoclonal antibodies specific for the genus Listeria

Abstract Monoclonal antibodies were obtained by the classic hybridoma technique with lymphocytes of BALB/c mice immunized with formalin killed Listeria monocytogenes cells. Among 1000 hybridomas issued from the fusion, four monoclonal antibodies (mAbs A6 A E4, C10 A F7, G4 A D6, G7 A D5) gave interesting results. By Western-blot analysis with various soluble extracts of different Listeria species, the four mAbs reacted with two major antigens of 38 and 41 kDa, with all Listeria species tested. The mAb A6 A E4 is an IgG2b with κ light chains and reacted only with Listeria antigens without any cross reaction with other organisms tested by ELISA, dot-blotting and Western-blotting. With the same conditions, the three other mAbs reacted with Listeria and with other genus extracts, particularly with Streptococcus and Enterococcus . mAb A6 A E4-reactive antigens are proteins, and glycoprotein immunoassay indicated that the epitope is devoid of carbohydrate moiety. This mAb A6 A E4-reactive protein was neither expressed on cell surface nor released outside the bacteria; immunogold electron microscopy showed that these antigens were localized in the cytoplasma area.     

Microscopic contributions to the pressure-volume diagram of the cell-water relations as demonstrated with tissue cells

Summary Continuing microscopic studies on cell-water relations with single cells (Gerdenitsch 1979) based on the relationship between the osmotic potential and the cell water volume, tissue cells were investigated. The experiments were done with inner epidermis of the bulb scale of onion (Allium cepa) which seemed to be most suitable for those investigations. Using a diagram described byRichter (1978) pressure volume curves of cells at the margin of the epidermis pieces neighboured by a various amount of dead cells and of cells in the center of tissue were worked out. They were contributed to one of three groups according to their amount of free surface (group 1: >1/3 free surface, group 2: <1/3 free surface, group 3: cells surrounded only by living-cells). Curves of the mean values of each of the three groups were compared as well as the mean -values, calculated as a measure for the elasticity of the cell wall.It was found that cells surrounded only by living cells had -values less than with both other groups. Assuming from observations during the experiments that all cells had very similar properties, this difference could be attributed to the expression of the effect of tissue counterpressure.     

Effects of temperature and moisture on urease activity in semi-arid tropical soils

Summary Studies of urease activity in an Indian Vertisol and Alfisol using both buffer (THAM pH 9.0) and non-buffer methods for assay of the urease activity showed that activity increased with increase in temperature from 10°C to a maximum at 60°C (Vertisol) and 70°C (Alfisol). Further increase in temperature decreased urease activity which was nearly totally inhibited at 100°C. Urease activity was not detected in soil samples collected in late summer when the soil moisture content was far below — 15 bar pressure. Urease activity increased with increase in moisture content up to field capacity and remained constant with further increase in moisture content. The relevance of these findings to the ICRISAT improved management practices for Vertisols, which involve seeding of crops into dry soil just before the onset of rains is discussed. Approved as Journal Article No. 288 by the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT).