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.     

A simple vertical gill net system for variable current conditions

A new technique for suspending vertical gill nets is described. The system is designed to minimize the effects of currents, which otherwise could lift the lead line off the bottom or pull the floating line down.For more than two years, 30 m deep gill nets have been used in a Baltic Sea coastal region and have been found to work well in current, wave and wind conditions characteristic of this area. Setting a net takes about 5 minutes and retrieving it 10 minutes, even under relatively windy conditions (10–15 ms^–1). No special equipment is required to set or to haul a net, and we have used a variety of boats, from a small rowing boat to a 16 m long research vessel. The total material cost per net is about US $100.     

Seasonal variation in the diel vertical distribution of the migratory alga Cryptomonas marssonii (Cryptophyceae) in a small,highly humic lake

The diel vertical distribution patterns of a migratory alga Cryptomonas marssonii in a small, steeply stratified humic lake were investigated during a summer season (10 diurnal experiments between May and September) using a close-interval Blakar-type sampler. The results indicate that the cells were phototactic; they were typically concentrated at the surface or subsurface during daylight, while in darkness the highest densities were recorded in deeper water, usually near the upper limit of anoxia. During a dense blue-green bloom in August the cells of C. marssonii were also concentrated by day into the same water layer, where oxygen was depleted. However, the cells seemed to avoid totally anoxic water. Because the vertical distribution pattern of C. marssonii had special diurnal and seasonal characteristics, care is needed when designing a sampling programme for a phytoplankton population dominated by this species.     

Pelagic rotifers of Lake Glubokoe from 1897 to 1984

After alteration in the pattern of drainage of run-off from the surrounding swamps and changes in the colour and transparency of the Lake Glubokoe water, the previously epilimnial Trichocerca similis, Conochilus unicornis and Keratella cochlearis showed a shift of their maximum numbers to deeper layers. Pompholyx sp. and Trichocerca capucina, which are regarded as indicators of eutrophic waters, have disappeared from the pelagic zone of the lake and Conochilus hippocrepis, Synchaeta pectinata, Gastropus stylifer, Asplanchna herricki, Ascomorpha ecaudis, Ascomorpha saltans, Euchlanis dilatata and Trichocerca porcellus have made their appearance. Most of the new species are considered to be indicators of oligotrophic conditions. However the total density of pelagic rotifers remained at the same level. Apparently the establishment of the new species of rotifers was possible due to some ‘rarefaction’ of the epilimnion, the disappearance of predaceous Mesocyclops leuckarti and the invasion of the pelagic zone by Peridinium cinctum.     

Synchronous division and the pattern of diel vertical migration of Heterosigma akashiwo (Hada) Hada (Raphidophyceae) in a laboratory culture tank

Heterosigma akashiwo (Hada) Hada (Raphidophyceae) causes red tides in Osaka Bay (Japan). A clonal culture of the alga was grown in a 2 m tall culture tank on a 12: 12 LD cycle to determine patterns of vertical migration and cell division. A specific growth rate of 0.43 ln unit · day⁻¹ was obtained during complete mixing conditions. Under weakly stratified conditions (≈ΔT = 3–4°C/1.5 m), H. akashiwo in the tank grew and showed a similar pattern of vertical migration to that observed in the field for at least 6 days. Cell concentration, mean cell volume, and photosynthetic capacity, estimated by DCMU-induced fluorescence increase of H. akashiwo, were monitored in the stratified tank at 2-h intervals over 24 h at three levels in the water column. Cell ascent began shortly before the light period and vertically swimming cells were smaller in size than those sampled near the bottom of the tank. The cell division cycle and the pattern of vertical migration were phased individually by the light regime and were well synchronized with each other. This synchrony must be due to the interrelation between these two processes or the existence of a clock which controlled endogenous rhythms of both processes and was entrained by a light: dark cycle. The relative increase of fluorescence with DCMU was higher for migrating cells than for non-migrating cells.     

Vertical distributions of zooplankton and population dynamics of Daphnia in a meromictic lake

Vertical distributions of zooplankton were studied in relation to profiles of temperature, oxygen and chlorophyll a in Roi Lake, a small meromictic lake in central Alberta. Zooplankton were distributed fairly evenly through the oxygenated part of the water column in early summer, but a gradual descent of several species became evident in June. The vertical distribution of chlorophyll was dominated by a huge peak at the 8- to 9-m-deep chemocline. the location of a plate of photosynthetic sulfur bacteria. Ambient concentration of chlorophyll was a poor predictor of the numbers of zooplankton and the fecundity of Daphnia pulicaria at different depths, and per capita birth rates of Daphnia were usually highest in the surface waters. The reproductively disadvantageous restriction of daphnids to deep water by late summer and their catastrophic decline in the face of high ambient concentrations of chlorophyll suggest that factors other than temperature and food supply are important in influencing the dynamics and distribution of zooplankton in this lake.     

Studies on ciliated protozoa in eutrophic lakes: 2. Field and laboratory studies on the effects of oxygen and other chemical gradients on ciliate distribution

An investigation into the spatial distribution of hypolimnetic ciliates in three small eutrophic lakes during the period of summer stratification was carried out. Peak ciliate densities were found to occur at the oxic/anoxic boundary, ciliate numbers declining with increasing depth within the hypolimnion. The ciliates only occurred in aerobic water where oxygen levels were less than about 0.5 mgl^–1 Laboratory experiments demonstrated that the ciliates swim upwards under anaerobic conditions but swim rapidly downwards under aerobic conditions. Further laboratory experiments showed that although the bulk of the population occured within anaerobic water, the hypolimnetic ciliates are aerobes and cannot survive indefinite anoxia. Despite the demonstrable toxicity of high levels of ammonia and sulphide, it was probably excesive distance from an available source of oxygen that excluded the ciliates from the lowest levels of the hypolimnion. Possible mechanisms which allowed these aerobic ciliates to colonise anaerobic water are considered.     

Diel migration and vertical distribution of Cladocera in Lake D. Helvecio (Minas Gerais,Brazil)

Six genera of Clad ocera (Diaphanosoma, Daphnia, Ceriodaphnia, Moina, Bosmina, Bosminopsis), each of them usually with only one species were found in Lake D. Helvecio, a natural valley lake located in the eastern part of Brazil. Diurnal migratory movements of the organisms observed in this lake showed a different pattern in different species. Closely related species, which explore the same food source, live in different layers, thus avoiding interspecific competition. The migratory behaviour of the species was studied mainly in relation to temperature and oxygen distribution in the lake. Thus, analyses were made in the summer (January, 1978) when a strong stratification occurs with the establishment of a thermocline and an oxycline. Comparisons were made also with the data obtained in winter (July, 1978), when a complete mixing of water occurs.     

Vertical community structure and resource utilization in neotropical forest cockroaches

ABSTRACT.

• 1 Patterns of vertical habitat use of ten species of cockroaches are examined. Three assemblages of cockroaches are recognized on the basis of morphology, foraging behaviour, foraging heights, and overlaps and breadths of vertical distributions.
• 2 Three apterous and brachypterous species occur near the ground and comprise one assemblage. They feed mainly on material in the leaf-litter.
• 3 Species that perch higher either migrate into the leaf-litter on a diel basis and feed on both leaf-litter and epiphyllic materials, or some are strictly arboreal and forage on algae, liverworts, lichens, spores, pollen and trichomes on the surfaces of leaves.
• 4 Trophic and behavioural correlations with perch height are described and the functions of perching are examined.
• 5 We conclude that studies of interactions among species are confounded by our lack of understanding of stage- and sex-specific interactions of coexisting species. A simplistic ‘species’approach to such interactions is inadequate because it does not recognize intraspecific variation.

     

PHYSIOLOGICAL AND OPTICAL PROPERTIES OF RHIZOSOLENIA FORMOSA (BACILLARIOPHYCEAE) IN THE CONTEXT OF OPEN-OCEAN VERTICAL MIGRATION1

Cultures of Rhizosolenia formosa H. Peragallo were studied to assess whether or not physiological and optical characteristics of this large diatom were consistent with the ability to migrate vertically in the open ocean. Time-course experiments examined changes in chemical composition and buoyancy of R. formosa during nitrate (N)–replete growth, N starvation, and recovery. Cells could maintain unbalanced growth for at least 53 h after depletion of ambient nitrate. Increases in C:N and carbohydrate: protein ratios observed during N starvation reversed within 24 h of reintroduction of nitrate to culture medium. Buoyancy was related to nutrition: Upon N depletion, the percentage of positively buoyant cells decreased to 4% from 11% but reverted to 9% within 12 h of nitrate readdition. Cells took up nitrate in the dark. Nitrogen-specific uptake rates averaged 0.48 d^?1; these rates were higher than N-specific growth rates (0. 15 d^?1), indicating the potential for luxury consumption of nitrate, which can be stored for later use. Measurements of photosynthesis vs. irradiance, chlorophyll-specific absorption (a_ph*(λ)), and pigment composition showed that cells may be adapted for growth under a wide range of irradiances. Values of a_ph*(λ) were lower for N-depleted cells than for N-replete cells, and N-depleted cells had higher ratios of total carotenoids to chlorophyll a. Aggregation of chloroplasts was more pronounced in N-depleted cells. These are possibly photoprotective mechanisms that would be an advantage to N-depleted cells in surface waters. Compounds that absorb in the ultraviolet region were detected in N-replete cells but were absent in N-depleted cultures. Overall, these results have important implications for migrations of Rhizosolenia in nature. Cells may survive fairly long periods in N-depleted surface waters and will continue to take up carbon; then they can resume nitrate uptake and revert to positive buoyancy upon returning to deep, N-rich water. Uncoupled uptake of carbon and nitrogen during migrations of Rhizosolenia is a form of new production that may result in the net removal of carbon from oceanic surface waters.