Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds.

The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment.     

Seasonal change in photoperiodic response of the larvae of the lacewing Nineta pallida

Larvae of the lacewing Nineta pallida (Schneider), collected in the field during two seasons, from September to July, were reared in the laboratory under short- or long-day light conditions at 21°C. In autumn and winter, artificial short days delayed the first ecdysis. The influence on the duration of the first instar was maximal (3.4 times longer) when the short days began at hatching time, and later regularly diminished. In spring, the second and third instars showed a reversed response so that the long days now increased the duration of development, although development took no more than 1.4 time as long as in short days. A similar effect appeared in field-collected third instars on and after mid June, reaching its maximum (1.8 time until the cocoon spinning) in July. This sort of photoperiodic effect on the larval development is new to the seasonal adaptation of the life cycle in insects.

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Résumé Des formes préimaginales (oeufs, puis larves) de N. pallida sont récoltées sur des conifères de montagne (Pyrénées), chaque mois depuis septembre jusqu'en juillet en deux saisons (1983/84 et 1985/86). Elles sont ensuite élevées au laboratoire à 21°C, soit en jours longs (JL=L16:D8), soit en jours courts (JC=L8:D16).Le développement embryonnaire est légèrement plus long s'il se fait en JC. Pour les larves de premier stade récoltées en automne et en hiver, les JC retardent considérablement la première mue et prolongent aussi le deuxième stade qui en provient. L'influence retardatrice est maximale (3,4 fois) lorsque les JC agissent dès l'éclosion. Elle diminue ensuite progressivement et devient insignificante pour les larves récoltées à artir de février.Au printemps, les larves récoltées au deuxième stade ainsi que les troisièmes stades qui en découlent présentent une réaction inverse: ce sont alors les JL qui augmentent la durée du dévelopement, toutefois, pas plus de 1,4 fois par rapport aux JC. Un effet de même ordre se manifeste sur les larves de troisième stade récoltées à partir de juin, atteignant son maximum (1,8 fois) dans le lot de larves de juillet, c'est-à-dire peu avant la fin de la croissance pondérale larvaire et le coconnage.Un tel retardement du développement larvaire hivernal, prolongé au printemps et au début de l'été par une inversion de la réponse à la photopériode, est nouveau comme élément d'adaptation saisonnière du cycle naturel chez les insectes.

     

Seasonal dynamics of the zoobenthic communities in the mesohaline zone of the Loire estuary (France)

The application of correspondence factorial analysis to four types of sediment in the upper reaches of the Loire estuary enabled the significance of environmental factors in the spatial distribution, abundance and seasonal dynamics of the biotic communities to be determined. In coarse sand, the communities are stable but species are few in number and population densities are low. In muddy sediments (from muddy sand to fluid mud) population densities are high but undergo seasonal fluctuations due to changes in the hydrological regime (especially the dissolved oxygen regime). This is true for the composition of the biotic communities. The oligohaline phase, in which the fluvial element is predominant, is characterized by abundance maxima due to freshwater species. The mesohaline phase, in which the marine element is predominant, exerts a restrictive action on population densities; certain species are supplanted by others, their development being governed by the quality of the environment.     

Observations on egg production rates and seasonal changes in the internal morphology of Mediterranean populations of Acartia clausi and Centropages typicus

Egg production rates in wild populations of Acartia clausi and Centropages typicus, sampled biweekly in the Gulf of Naples from October 1985 to July 1987, showed marked seasonal fluctuations with maximum values in early spring that proceeded the annual maxima for adult female densities in summer. A positive correlation between chlorophyll a concentrations and egg production was evident only during the early spring phytoplankton bloom. A strong diminution in egg deposition occurred later in spring and continued throughout the summer notwithstanding high chlorophyll concentrations. In winter, when population abundances for adult females were lowest, egg production rates were always higher than in summer. Differences in egg production rates coincided with pronounced morphological changes between summer and winter populations of both species. The most striking of these changes consisted, in winter, in the presence of a dark brown fluid-like mass of granular material that seemed to freely bathe the gonads. The presence of this substance only during periods of elevated egg production suggests that it may enhance egg production rates when the adult population reaches minimum annual levels. Such a mechanism of self-regulation may operate to dampen the effects of environmental variability thereby contributing to maintain a conservative structure in coastal copepod communities.     

Developmental rates of heterozygous and homozygous rainbow trout reared at three temperatures

The hatching distributions of rainbow trout (Salmo gairdneri) with different genotypes at eight loci are compared in two experiments with the same strain. Embryos were incubated at temperatures colder (5 and 8°C) and warmer (12°C) than normally experienced by these fish (9.5°C). At hatching, embryos were separated into five hatching groups representing the chronological order of hatching. There is no significant correlation between multilocus heterozygosity and hatching time at any temperature in either experiment. Fish in the middle of the hatching distribution had the highest average heterozygosity. In both experiments, heterozygotes at the majority of loci examined tended to hatch relatively later within the hatching distribution at 12°C than at both 5 and 8°C. Fish with different genotypes atPgm2 andCk1 showed significant differences in hatching time that were consistent between experiments.Ck1 heterozygotes hatched sooner than homozygotes at 8°C but later at 12°C.Pgm2 heterozygotes hatched later than homozygotes at all temperatures and significantly later in four of five cases. At the other loci examined, however, the relative hatching distributions of fish with particular genotypes were not significantly different or repeatable between experiments.This research was supported by National Science Foundation Grant BSR-8300039 awarded to Dr. Fred W. Allendorf. Moira M. Ferguson was supported by a postgraduate scholarship from the Natural Sciences and Engineering Research Council of Canada.     

Primary productivity and related parameters in three different types of inland waters in Sri Lanka

Gross and net primary production together with chlorophyll-a biomass were investigated with respect to depth and diurnal changes in three categories of inland waters (reservoirs, temporary ponds, brackish water lagoons) in Sri Lanka. Ten field sites, in both the dry and wet zones of the island, were investigated. Bimodal productivity profiles were recorded in two of the three reservoirs studied. The diel pattern of net photosynthetic rate varied between sites although peak photosynthetic efficiency occurred at solar noon. Surface photoinhibition was characteristic of the reservoirs and brackish water lagoons but not of the temporary ponds. Mean gross primary production was 3.02 g C m^–2 d^–1 but was higher in the temporary ponds than in the reservoirs. The gross primary production in the brackish water Koggala Lagoon at 0.08 g C m^–2 d^–1 is a record low for tropical lagoons and was 2.5 times less than the two other lagoons investigated. Variability in net primary production between sites was similar to the variation in gross production with a relatively low mean value for tropical inland waters of 0.495 C m^–2 d^–1. Mean maximum photosynthetic rate was 0.30 mg C m^–3 h^–1 but was lower in the reservoirs than in the temporary ponds and lagoons.     

Differential winter mortality and seasonal selection in the polymorphic ladybird Adalia bipunctata (L) in the Netherlands

Seasonal selection acting on the melanic polymorphism in the two-spot ladybird Adalia bipunctata was investigated in The Netherlands. An increase in melanic frequency over the spring-summer reproductive period was quantified. The selective advantage gained by melanics averaged 9%, but significant heterogeneity occurred between populations. Adult hibernation behaviour is described. The beetles when outdoors show a highly clumped distribution both between and within trees. The distribution of the morph classes between aggregations is random. Survivorship in a hibernating cohort (initial n= 1898) on a grid of 70 lime trees near Utrecht was monitored by making three counts over the winter of 1981–1982. Intense selection favouring each melanic morph occurred during December and January. The relative fitness of non-melanics was 0.55 (melanics =1). The discovery of dead beetles in late January (about 5% of total losses) and the absence of spatially density-dependent mortality were consistent with a climatic stress rather than selective predation. The period of selection was associated with very cold temperatures averaging up to 4°C below normal and an overall mortality of nearly 75%. There was no change in morph frequency, near normal temperatures and a lower mortality from February to early April. Examination of groups of nearby trees in late January strongly suggested that similar differential mortality had occurred except on some willows. This difference was probably due to the more protected hibernation sites available on these trees. Samples of hibernating cohorts at three other sites showed no evidence of differential mortality. Laboratory experiments with hibernating beetles found no difference in survivorship or rate of weight loss between starved non-melanics and melanics in temperature regimes with and without periods of adult activity. It is concluded that the intense winter selection on the study limes is probably exceptional. Examination of changes in morph frequency through the annual cycle suggests that at some sites the selection favouring melanics during reproduction is counterbalanced by selection against melanics in late summer or early autumn. The results are discussed in relation to mathematical models of cyclical selection and to other field studies including that of Timoféeff-Ressovsky (1940), who found large decreases in melanic frequency during hibernation in Berlin.     

Temporal dynamics of estuarine phytoplankton: A case study of San Francisco Bay

Detailed surveys throughout San Francisco Bay over an annual cycle (1980) show that seasonal variations of phytoplankton biomass, community composition, and productivity can differ markedly among estuarine habitat types. For example, in the river-dominated northern reach (Suisun Bay) phytoplankton seasonality is characterized by a prolonged summer bloom of netplanktonic diatoms that results from the accumulation of suspended particulates at the convergence of nontidal currents (i.e. where residence time is long). Here turbidity is persistently high such that phytoplankton growth and productivity are severely limited by light availability, the phytoplankton population turns over slowly, and biological processes appear to be less important mechanisms of temporal change than physical processes associated with freshwater inflow and turbulent mixing. The South Bay, in contrast, is a lagoon-type estuary less directly coupled to the influence of river discharge. Residence time is long (months) in this estuary, turbidity is lower and estimated rates of population growth are high (up to 1–2 doublings d^–1), but the rapid production of phytoplankton biomass is presumably balanced by grazing losses to benthic herbivores. Exceptions occur for brief intervals (days to weeks) during spring when the water column stratifies so that algae retained in the surface layer are uncoupled from benthic grazing, and phytoplankton blooms develop. The degree of stratification varies over the neap-spring tidal cycle, so the South Bay represents an estuary where (1) biological processes (growth, grazing) and a physical process (vertical mixing) interact to cause temporal variability of phytoplankton biomass, and (2) temporal variability is highly dynamic because of the short-term variability of tides. Other mechanisms of temporal variability in estuarine phytoplankton include: zooplankton grazing, exchanges of microalgae between the sediment and water column, and horizontal dispersion which transports phytoplankton from regions of high productivity (shallows) to regions of low productivity (deep channels).Multi-year records of phytoplankton biomass show that large deviations from the typical annual cycles observed in 1980 can occur, and that interannual variability is driven by variability of annual precipitation and river discharge. Here, too, the nature of this variability differs among estuary types. Blooms occur only in the northern reach when river discharge falls within a narrow range, and the summer biomass increase was absent during years of extreme drought (1977) or years of exceptionally high discharge (1982). In South Bay, however, there is a direct relationship between phytoplankton biomass and river discharge. As discharge increases so does the buoyancy input required for density stratification, and wet years are characterized by persistent and intense spring blooms.     

Seasonal dynamics of rotifer and crustacean zooplankton populations in a eutrophic,monomictic lake with a note on rotifer sampling techniques

The abundances, biomass, and seasonal succession of rotifer and crustacean zooplankton were examined in a man-made, eutrophic lake, Lake Oglethorpe, over a 13 month period. There was an inverse correlation between the abundance of rotifers and crustaceans. Rotifers were most abundant and dominated (>69%) the rotifer-crustacean biomass during summer months (June–September) while crustacean zooplankton dominated during the remainder of the year (>89%). Peak biomasses of crustaceans were observed in the fall (151 µg dry wt l^–1 in October) and spring (89.66 µg dry wt l^–1 in May). Mean annual biomass levels were 46.99 µg dry wt l^–1 for crustaceans and 19.26 µg dry wt l^–1 for rotifers. Trichocerca rousseleti, Polyarthra sp., Keratella cochlearis and Kellicottia bostoniensis were the most abundant rotifers in the lake. Diaptomus siciloides and Daphnia parvula were the most abundant crustaceans. Lake Oglethorpe is distinct in having an unusually high abundance of rotifers (range 217–7980 l^–1). These high densities can be attributed not only to the eutrophic conditions of the lake but also to the detailed sampling methods employed in this study.The research was supported by National Science Foundation grants DEB 7725354 and DEB 8005582 to Dr. K. G. Porter. It is lake Oglethorpe Limnological Association Contribution No. 25 and Contribution No. 371 of the Harbor Branch Foundation, Inc.