How can the functional reponse best be determined?

Summary We evaluated three methods for the analysis of functional response data by asking whether a given method could discriminate among functional responses and whether it could accurately identify regions of positive density-dependent predation. We evaluated comparative curve fitting with foraging models, linear least-squares analysis using the angular transformation, and logit analysis. Using data from nature and simulations, we found that the analyses of predation rates with the angular transformation and logit analysis were best at consistently determining the true functional response, i.e. the model used to generate simulated data. These methods also produced the most accurate estimates of the true regions of density dependence. Of these two methods, functional response data best fulfill the assumptions of logit analysis. Angularly transformed predation rates only approximate the assumptions of linear leastsquares analysis for predation rates between 0.1 and 0.9. Lack-of-fit statistics can reveal inadequate fit of a model to a data set where simple regression statistics might erroneously suggest a good match.     

Adenovirus serotype determines association and localization of the large E1B tumor antigen with cellular tumor antigen p53 in transformed cells.

The distribution and stability of the cellular tumor antigen p53 were studied in baby rat kidney cells transformed by region E1 sequences of nononcogenic adenovirus (Ad) type 5 (Ad5) or oncogenic type 12 (Ad12). In transformed cells expressing the large E1B T antigen of Ad5, p53 was associated with this T antigen. The complexed proteins were concentrated in a cytoplasmic body, which has been shown to consist of a cluster of 8-nm filaments (A. Zantema et al., Virology 142:44-58, 1985). In transformed cells expressing the E1B region of Ad12, however, no association between the viral large T antigen and p53 was detectable. In the latter case, both proteins were found almost exclusively in the nucleus. The stability of p53 in both Ad5- and Ad12-transformed cells was increased relative to that in primary cells or cells immortalized by the E1A region only. Thus, the increased stability of p53 in Ad-transformed cells is not caused by association with a viral T antigen, but it correlates with expression of E1B and with morphological transformation.     

PHENOTYPIC PLASTICITY IN THE SAILFIN MOLLY,POECILIA LATIPINNA (PISCES: POECILIIDAE). I. FIELD EXPERIMENTS

Sailfin mollies (Poecilia latipinna) display marked interdemic variation in body size. We employed “common-garden” experiments in field enclosures to explore the potential role of environmental factors in determining the interdemic phenotypic variation in growth rate, age at maturity, and size at maturity. The largest single, consistent source of variation for all traits was family identity within populations. Environmental effects acted predominantly through family x environment interactions. There was little evidence for any intrinsic variation among populations once family heterogeneity had been accounted for. In general, when statistically significant differences existed, fish raised in a saltwater pond grew faster than their broodmates raised in a freshwater pond. Both males and females tended to mature at a smaller size and later in the freshwater pond than in the saltwater pond. The effects of the environmental conditions differed among the three years in which we performed these studies. In only one year was there a substantial difference between fish raised under the two environmental conditions. These results indicate that direct environmental effects are not strong enough to account for the differences in body size among natural populations and that intrinsic differences among natural populations are due to different frequency distributions of genotypes that are present in all populations.     

PHENOTYPIC PLASTICITY IN THE SAILFIN MOLLY,POECILIA LATIPINNA (PISCES: POECILIIDAE). II. LABORATORY EXPERIMENT

Field studies indicate that the influence of environmental factors on growth rate and size and age at maturity in sailfin mollies (Poecilia latipinna) is inconsistent over time and suggest that the marked interdemic variation in male body size in this species is the result of genetic variation. However, the role of specific environmental factors in generating phenotypic variation must be studied under controlled conditions unattainable in nature. We raised newborn sailfin mollies from four populations in laboratory aquaria under all possible combinations of two temperatures, three salinities, and two food levels to examine explicitly the influence of these environmental factors. Males were much less susceptible than females to temperature variation and were generally less plastic than females in terms of all three traits. Members of both sexes matured at larger sizes and at later ages in less saline and in cooler environments. Food levels were not sufficiently different to affect the traits we studied. The effects of temperature and salinity were not synergistic. Males from different populations exhibited different average ages and sizes at maturity, but females did not. The magnitudes of the effects we found were not substantial enough to account for the consistent interdemic differences in male and female body size that have been observed previously. Our results also indicate that no single environmental factor is solely responsible for the environmental effects observed in field experiments on growth and development. These studies, together with other work, indicate that the strongest sources of interdemic variation are genetic differences in males and differences in postmaturation growth and survivorship in females.     

Disturbance regime and limits on benefits of refuge use for fishes in a fluctuating hydroscape

Refuge habitats increase survival rate and recovery time of populations experiencing environmental disturbance, but limits on the ability of refuges to buffer communities are poorly understood. We hypothesized that importance of refuges in preventing population declines and alteration in community structure has a non‐linear relationship with severity of disturbance. In the Florida Everglades, alligator ponds are used as refuge habitat by fishes during seasonal drying of marsh habitats. Using an 11‐year record of hydrological conditions and fish abundance in 10 marshes and 34 alligator ponds from two regions of the Everglades, we sought to characterize patterns of refuge use and temporal dynamics of fish abundance and community structure across changing intensity, duration, and frequency of drought disturbance. Abundance in alligator ponds was positively related to refuge size, distance from alternative refugia (e.g. canals), and abundance in surrounding marsh prior to hydrologic disturbance. Variables negatively related to abundance in alligator ponds included water level in surrounding marsh and abundance of disturbance‐tolerant species. Refuge community structure did not differ between regions because the same subset of species in both regions used alligator ponds during droughts. When time between disturbances was short, fish abundance declined in marshes, and in the region with the most spatially extensive pattern of disturbance, community structure was altered in both marshes and alligator ponds because of an increased proportion of species more resistant to disturbance. These changes in community structure were associated with increases in both duration and frequency of hydrologic disturbance. Use of refuge habitat had a modal relationship with severity of disturbance regime. Spatial patterns of response suggest that decline in refuge use was because of decreased effectiveness of refuge habitat in reducing mortality and providing sufficient time for recovery for fish communities experiencing reduced time between disturbance events.     

Invasion impacts on functions and services of aquatic ecosystems

Hydrobiologia - Non-native species can simultaneously affect ecological structures, functions, and services of the invaded ecosystem. In this paper, we report that the study of non-native...     

STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

Resource allocation in offspring provisioning: an evaluation of the conditions favoring the evolution of matrotrophy

We used analytic and simulation models to determine the ecological conditions favoring evolution of a matrotrophic fish from a lecithotrophic ancestor given a complex set of trade-offs. Matrotrophy is the nourishment of viviparous embryos by resources provided between fertilization and parturition, while lecithotrophy describes embryo nourishment provided before fertilization. In fishes and reptiles, embryo nourishment encompasses a continuum from solely lecithotrophic to primarily matrotrophic. Matrotrophy has evolved independently from lecithotrophic ancestors many times in many groups. We assumed matrotrophy increased the number of offspring a viviparous female could gestate and evaluated conditions of food availability favoring lecithotrophy or matrotrophy. The matrotrophic strategy was superior when food resources exceeded demand during gestation but at a risk of overproduction and reproductive failure if food intake was limited. Matrotrophic females were leaner during gestation than lecithotrophic females, yielding shorter life spans. Our models suggest that matrotrophic embryo nourishment evolved in environments with high food availability, consistently exceeding energy requirements for maintaining relatively large broods. Embryo abortion with some resorption of invested energy is a necessary preadaptation to the evolution of matrotrophy. Future work should explore trade-offs of age-specific mortality and reproductive output for females maintaining different levels of fat storage during gestation.     

Structural characterization of the second TSP1-module of human thrombospondin

The TSP1-module has been first identified as the type 1 repeat of thrombospondin-1. Members of this extracellular module-family have since been shown to be present in several hundred metazoan proteins as well as in proteins of some protists. Despite the widespread occurrence and biological importance of this module-type, relatively little is known about their three-dimensional structure. To define the structural features of this important module-family, we have expressed the second TSP1-domain of human thrombospondin 1 in Escherichia coli. Amino acid sequencing of proteolytic fragments of the recombinant protein have shown that its disulfide bonds connect the six conserved cysteines in a 1-5, 2-6, 3-4 pattern. Circular dichroism studies on the recombinant protein indicate that the disulfide-bonded TSP1-module consists primarily of distorted beta-strands.