Assessing the impact of thermal acclimation on physiological condition in the zebrafish model

The zebrafish has become a valuable vertebrate model organism in a wide range of scientific disciplines, but current information concerning the physiological temperature response of adult zebrafish is rather scarce. In this study, zebrafish were experimentally acclimated for 28 days to 18, 26 or 34 °C and a suite of non-invasive and invasive methods was applied to determine the thermal dependence of zebrafish physiological condition. With decreasing temperature, the metabolic rate of zebrafish decreased, as shown by the decreasing oxygen uptake and ammonia excretion rates, limiting the critical swimming speed, probably due to a decreased muscle fibre power output. In response to exercise, fuel stores were mobilized to the liver as shown by the increased hepatosomatic index, liver total absolute energetic value and liver carbohydrate concentration but due to the low metabolic rate they could not be adequately addressed to power swimming activity at 18 °C. Conversely, the increased metabolic performance at high temperature came with an increased metabolic cost resulting in decreased energy status reflected particularly well by the non-invasive condition factor and invasive measures of carcass protein concentration, carcass total absolute energetic value and liver carbohydrate concentration. We showed that the combined measurement of the relative condition factor and critical swimming speed is a powerful non-invasive tool for long-term follow-up studies. Invasive methods were redundant for measuring general energy status but they provided detailed information concerning metabolic reorganization. With this study we proved that the usefulness of the zebrafish as a model organism can easily be expanded to include physiological studies and we provided a reference dataset for the selection of measures of physiological responses for future studies using the zebrafish.     

Incomplete datasets obscure associations between traits affecting dispersal ability and geographic range size of reef fishes in the Tropical Eastern Pacific

Dispersal is thought to be an important process determining range size, especially for species in highly spatially structured habitats, such as tropical reef fishes. Despite intensive research efforts, there is conflicting evidence about the role of dispersal in determining range size. We hypothesize that traits related to dispersal drive range sizes, but that complete and comprehensive datasets are essential for detecting relationships between species’ dispersal ability and range size. We investigate the roles of six traits affecting several stages of dispersal (adult mobility, spawning mode, pelagic larval duration (PLD), body size, aggregation behavior, and circadian activity), in explaining range size variation of reef fishes in the Tropical Eastern Pacific (TEP). All traits, except for PLD (148 species), had data for all 497 species in the region. Using a series of statistical models, we investigated which traits were associated with large range sizes, when analyzing all TEP species or only species with PLD data. Furthermore, using null models, we analyzed whether the PLD‐subset is representative of the regional species pool. Several traits affecting dispersal ability were strongly associated with range size, although these relationships could not be detected when using the PLD‐subset. Pelagic spawners (allowing for passive egg dispersal) had on average 56% larger range sizes than nonpelagic spawners. Species with medium or high adult mobility had on average a 25% or 33% larger range, respectively, than species with low mobility. Null models showed that the PLD‐subset was nonrepresentative of the regional species pool, explaining why model outcomes using the PLD‐subset differed from the ones based on the complete dataset. Our results show that in the TEP, traits affecting dispersal ability are important in explaining range size variation. Using a regionally complete dataset was crucial for detecting the theoretically expected, but so far empirically unresolved, relationship between dispersal and range size.     

Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference

We investigated the usefulness of a parallel genetic algorithm for phylogenetic inference under the maximum-likelihood (ML) optimality criterion. Parallelization was accomplished by assigning each "individual" in the genetic algorithm "population" to a separate processor so that the number of processors used was equal to the size of the evolving population (plus one additional processor for the control of operations). The genetic algorithm incorporated branch-length and topological mutation, recombination, selection on the ML score, and (in some cases) migration and recombination among subpopulations. We tested this parallel genetic algorithm with large (228 taxa) data sets of both empirically observed DNA sequence data (for angiosperms) as well as simulated DNA sequence data. For both observed and simulated data, search-time improvement was nearly linear with respect to the number of processors, so the parallelization strategy appears to be highly effective at improving computation time for large phylogenetic problems using the genetic algorithm. We also explored various ways of optimizing and tuning the parameters of the genetic algorithm. Under the conditions of our analyses, we did not find the best-known solution using the genetic algorithm approach before terminating each run. We discuss some possible limitations of the current implementation of this genetic algorithm as well as of avenues for its future improvement.     

Transformation and mineralization of benzo[<Emphasis Type="Italic">a</Emphasis>]pyrene by microbial cultures enriched on mixtures of three- and four-ring polycyclic aromatic hydrocarbons

Microorganisms originating from a soil contaminated by low levels of polycyclic aromatic hydrocarbons (PAHs) were enriched with three- and four-ring PAHs as primary substrates in the presence of benzo[a]pyrene (BaP). Most enrichment cultures, isolated in the presence or absence of a sorptive matrix, significantly transformed BaP. Evidence of BaP mineralization was obtained with cultures enriched on phenanthrene and anthracene. Our findings supplement literature data suggesting the wide occurrence of microbial activity against BaP. Journal of Industrial Microbiology & Biotechnology (2002) 28, 70–73 DOI: 10.1038/sj/jim/7000211 Received 11 December 2000/ Accepted in revised form 04 September 2001     

Maturation of mouse primordial follicles by combination of grafting and in vitro culture

Cryopreservation of ovarian cortical tissue and subsequent transplantation or in vitro culture of follicles are technologies under development with the aim to safeguard fertility in patients with gonadal failure. In the present study, we investigated whether primordial follicles could be triggered to full maturation by a combination of in vivo transplantation and in vitro culture in a mouse model. In a first step, newborn mouse ovaries containing only primordial follicles were allotransplanted under the renal capsule of ovariectomized recipient mice. The second step was to mechanically isolate growing preantral follicles from the graft and culture these in vitro to maturity. In our experiment, one newborn mouse ovary was transplanted under the renal capsule of each 8- to 12-wk-old F1 (C57Bl/6j x CBA/Ca) female ovariectomized recipient (n = 26). Two weeks after transplantation, all 26 grafts were recovered. Four grafts were processed for histology and showed that developmental stages of follicles in 14-day-old ovarian grafts were comparable to those in 14-day-old mouse ovaries. The 22 remaining grafts were used for mechanical isolation of preantral follicles. As a control group, preantral follicles isolated from ovaries of 14-day-old mice were used. The mean preantral follicle yield per ovary was 11 in the transplant group versus 33 in the control group. Follicles were cultured individually in 20-microliter droplets of alpha-MEM supplemented with 100 mIU rFSH and 5% fetal bovine serum for 12 days under an atmosphere of 5% CO(2) in air at 37 degrees C. By Day 12 of culture, 66.5% of follicles retained their oocytes in the grafting group versus 97.5% in the control group (P < 0.001). Final oocyte maturation was induced by addition of 2.5 IU/ml hCG. At 14-16 h post-HCG, the percentages of oocytes showing germinal vesicle breakdown and polar body extrusion were significantly higher in the control group (90.6% and 82.8%) compared to the grafting group (60% and 45%). The mean diameter of the mature oocytes of the grafting group (69.9 +/- 4.45 micrometer) was similar to that of oocytes from the control group (70.5 +/- 2.35 micrometer). Our results suggest that maturation of mouse primordial follicles is feasible by combination of in vivo transplantation and in vitro culture. This two-step strategy may be an attractive model for promoting the growth and maturation of primordial follicles from other species.     

High critical temperature above T(g) may contribute to the stability of biological systems

In this study, we characterized the molecular mobility around T(g) in sugars, poly-L-lysine and dry desiccation-tolerant biological systems, using ST-EPR, (1)H-NMR, and FTIR spectroscopy, to understand the nature and composition of biological glasses. Two distinct changes in the temperature dependence of the rotational correlation time (tau(R)) of the spin probe 3-carboxy-proxyl or the second moment (M(2)) were measured in sugars and poly-L-lysine. With heating, the first change was associated with the melting of the glassy state (T(g)). The second change (T(c)), at which tau(R) abruptly decreased over several orders of magnitude, was found to correspond with the so-called cross-over temperature, where the dynamics changed from solid-like to liquid-like. The temperature interval between T(g) and T(c) increased in the order of sucrose < trehalose < raffinose 50 degrees C, implying that the stability above T(g) improved in the same order. These differences in temperature-dependent mobilities above T(g) suggest that proteins rather than sugars play an important role in the intracellular glass formation. The exceptionally high T(c) of intracellular glasses is expected to provide excellent long-term stability to dry organisms, maintaining a slow molecular motion in the cytoplasm even at temperatures far above T(g).     

Flocculation of microalgae using cationic starch

Due to their small size and low concentration in the culture medium, cost-efficient harvesting of microalgae is a major challenge. We evaluated the potential of cationic starch as a flocculant for harvesting microalgae using jar test experiments. Cationic starch was an efficient flocculant for freshwater (Parachlorella, Scenedesmus) but not for marine microalgae (Phaeodactylum, Nannochloropsis). At high cationic starch doses, dispersion restabilization was observed. The required cationic starch dose to induce flocculation increased linearly with the initial algal biomass concentration. Of the two commercial cationic starch flocculants tested, Greenfloc 120 (used in wastewater treatment) was more efficient than Cargill C*Bond HR 35.849 (used in paper manufacturing). For flocculation of Parachlorella using Greenfloc 120, the cationic starch to algal biomass ratio required to flocculate 80% of algal biomass was 0.1. For Scenedesmus, a lower dose was required (ratio 0.03). Flocculation of Parachlorella using Greenfloc 120 was independent of pH in the pH range of 5 to 10. Measurements of the maximum quantum yield of PSII suggest that Greenfloc 120 cationic starch was not toxic to Parachlorella. Cationic starch may be used as an efficient, nontoxic, cost-effective, and widely available flocculant for harvesting microalgal biomass.     

Aerial dispersal plasticity under different wind velocities in a salt marsh wolf spider

Dispersal can be regarded as a process operating both betweenand within patches of suitable habitat. For uncontrolled dispersalprocesses, the risk of crossing the borders of the habitat patchand arriving in the unsuitable landscape matrix will increasewith decreasing patch area, in particular when the distancebetween isolated habitat patches is larger than the species'average dispersal capacity. Ballooning dispersal in spiderscan be considered as a passive dispersal process, in which disperseddistances depend on the prevalent wind velocity. We executeda reaction norm analysis to analyze how dispersal propensityof the salt marsh wolf spider Pardosa purbeckensis dependedon population characteristics (patch size) and the environment(wind velocity). Dispersal propensity was affected by the interactionbetween wind velocity and maternal patch size. Ballooning propensitiesdecreased with decreasing salt marsh size. Interestingly, genotypesfrom large salt marshes show higher ballooning propensitiesunder higher wind velocities, whereas those from small habitatpatches show their highest dispersal propensity under low windvelocities. Crossing reaction norms and subsequently stronggenotype x environment interaction variation was observed inall populations but tended to be lower in genotypes from largesalt marshes. It is likely that this pattern results from differencesin wind velocity–related costs of within-habitat dispersalin salt marshes of different sizes.     

SLIDER: a generic metaheuristic for the discovery of correlated motifs in protein-protein interaction networks

Correlated motif mining (cmm) is the problem of finding overrepresented pairs of patterns, called motifs, in sequences of interacting proteins. Algorithmic solutions for cmm thereby provide a computational method for predicting binding sites for protein interaction. In this paper, we adopt a motif-driven approach where the support of candidate motif pairs is evaluated in the network. We experimentally establish the superiority of the Chi-square-based support measure over other support measures. Furthermore, we obtain that cmm is an np-hard problem for a large class of support measures (including Chi-square) and reformulate the search for correlated motifs as a combinatorial optimization problem. We then present the generic metaheuristic slider which uses steepest ascent with a neighborhood function based on sliding motifs and employs the Chi-square-based support measure. We show that slider outperforms existing motif-driven cmm methods and scales to large protein-protein interaction networks. The slider-implementation and the data used in the experiments are available on http://bioinformatics.uhasselt.be.