Collective Response of Zebrafish Shoals to a Free-Swimming Robotic Fish

In this work, we explore the feasibility of regulating the collective behavior of zebrafish with a free-swimming robotic fish. The visual cues elicited by the robot are inspired by salient features of attraction in zebrafish and include enhanced coloration, aspect ratio of a fertile female, and carangiform/subcarangiform locomotion. The robot is autonomously controlled with an online multi-target tracking system and swims in circular trajectories in the presence of groups of zebrafish. We investigate the collective response of zebrafish to changes in robot speed, achieved by varying its tail-beat frequency. Our results show that the speed of the robot is a determinant of group cohesion, quantified through zebrafish nearest-neighbor distance, which increases with the speed of the robot until it reaches . We also find that the presence of the robot causes a significant decrease in the group speed, which is not accompanied by an increase in the freezing response of the subjects. Findings of this study are expected to inform the design of experimental protocols that leverage the use of robots to study the zebrafish animal model.     

The Response of Three Bacterial Populations to Pollution in a Stream

Abstract Practical methods for biomonitoring of natural systems are still under development. Bacteria are potentially useful indicators of water quality because of their species diversity and ability to rapidly respond to changing environmental conditions. In this study, bacterial populations from unpolluted and polluted stream sites in two watersheds were compared to determine their suitability for use as environmental indicators. Upper Three Runs Creek and Four Mile Creek headwaters have had little anthropogenic disturbance, as opposed to lower Four Mile Creek which received thermal, radioactive, and chemical perturbations. Chemical and physical measurements provided evidence that seepage from holding ponds polluted Four Mile Creek. Polluted sites did not have altered total bacterial numbers but had decreased numbers of colony-forming units. Abundances of three bacterial species, Acinetobacter calcoaceticus, Burkholderia cepacia, and Pseudomonas putida, were determined by colony hybridization with species-specific rDNA probes. Contribution of A. calcoaceticus to the assemblage was higher at polluted sites, which indicated either tolerance of polluted conditions or the ability to utilize compounds existing at these sites to reach larger populations. No differences in B. cepacia populations were detected, and differences in P. putida populations could not be attributed solely to disturbance. The pollution of Four Mile Creek induced differences in bacterial populations that could be monitored using the described approach. Received: 24 September 1996; Accepted: 20 December 1996     

Comparative Response of Alfalfa to Pratylenchus penetrans Populations

Four populations of Pratylenchus penetrans did not differ (P > 0.05) in their virulence or reproductive capability on Lahontan alfalfa. There was a negative relationship (r = -0 .7 9 ) between plant survival and nematode inocula densities at 26 ± 3 C in the greenhouse. All plants survived at an inoculum level (Pi) of 1 nematode/cm³ soil, whereas survival rates were 50 to 55% at 20 nematodes/cm³ soil. Alfalfa shoot and root weights were negatively correlated (r = - 0.87; P < 0.05) with nematode inoculum densities. Plant shoot weight reductions ranged from 13 % at Pi 1 nematode/cm³ soil to 69% for Pi 20 nematodes/cm³ soil, whereas root weight reductions ranged from 17% for Pi 1 nematode/cm³ soil to 75% for Pi 20 nematodes/cm³ soil. Maximum and minimum nematode reproduction (Pf/Pi) for the P. penetrans populations were 26.7 and 6.2 for Pi 1 and 20 nematodes/cm³ soil, respectively. There were negative correlations between nematode inoculum densities and plant survival (r = 0.84), and soil temperature and plant survival (r = -0 .7 8 ). Nematode reproduction was positively correlated to root weight (r = 0.89).     

Barn Owl Productivity Response to Variability of Vole Populations

We studied the response of the barn owl annual productivity to the common vole population numbers and variability to test the effects of environmental stochasticity on their life histories. Current theory predicts that temporal environmental variability can affect long-term nonlinear responses (e.g., production of young) both positively and negatively, depending on the shape of the relationship between the response and environmental variables. At the level of the Czech Republic, we examined the shape of the relationship between the annual sum of fledglings (annual productivity) and vole numbers in both non-detrended and detrended data. At the districts’ level, we explored whether the degree of synchrony (measured by the correlation coefficient) and the strength of the productivity response increase (measured by the regression coefficient) in areas with higher vole population variability measured by the s-index. We found that the owls’ annual productivity increased linearly with vole numbers in the Czech Republic. Furthermore, based on district data, we also found that synchrony between dynamics in owls’ reproductive output and vole numbers increased with vole population variability. However, the strength of the response was not affected by the vole population variability. Additionally, we have shown that detrending remarkably increases the Taylor’s exponent b relating variance to mean in vole time series, thereby reversing the relationship between the coefficient of variation and the mean. This shift was not responsible for the increased synchrony with vole population variability. Instead, we suggest that higher synchrony could result from high food specialization of owls on the common vole in areas with highly fluctuating vole populations.     

Effects of Spearfishing on Reef Fish Populations in a Multi-Use Conservation Area

Although spearfishing is a popular method of capturing fish, its ecological effects on fish populations are poorly understood, which makes it difficult to assess the legitimacy and desirability of spearfishing in multi-use marine reserves. Recent management changes within the Great Barrier Reef Marine Park (GBRMP) fortuitously created a unique scenario by which to quantify the effects of spearfishing on fish populations. As such, we employed underwater visual surveys and a before-after-control-impact experimental design to investigate the effects of spearfishing on the density and size structure of target and non-target fishes in a multi-use conservation park zone (CPZ) within the GBRMP. Three years after spearfishing was first allowed in the CPZ, there was a 54% reduction in density and a 27% reduction in mean size of coral trout (Plectropomus spp.), the primary target species. These changes were attributed to spearfishing because benthic habitat characteristics and the density of non-target fishes were stable through time, and the density and mean size of coral trout in a nearby control zone (where spearfishing was prohibited) remained unchanged. We conclude that spearfishing, like other forms of fishing, can have rapid and substantial negative effects on target fish populations. Careful management of spearfishing is therefore needed to ensure that conservation obligations are achieved and that fishery resources are harvested sustainably. This is particularly important both for the GBRMP, due to its extraordinarily high conservation value and world heritage status, and for tropical island nations where people depend on spearfishing for food and income. To minimize the effects of spearfishing on target species and to enhance protection of functionally important fishes (herbivores), we recommend that fishery managers adjust output controls such as size- and catch-limits, rather than prohibit spearfishing altogether. This will preserve the cultural and social importance of spearfishing in coastal communities where it is practised.     

Feeding and Refuge Use by Small Fish in the Presence of Cyanobacteria Blooms

We studied the effect of cyanobacteria on foraging and refuge use in small fish. We measured pike larval feeding in the presence of cyanobacteria by counting leftover prey. Our results showed that feeding by pike larvae on zooplankton prey decreased significantly in the presence of non-toxic cyanobacteria. The behaviour can be due to lowered vision caused by turbidity or clogging of the gills. Further, we tested whether the three-spined stickleback use toxic cyanobacteria as a refuge against predators in a choice experiment. The choice experiment was performed in a Y-maze fluviarum, where the fish could select between two different environments. Our results support the refuge use hypothesis because the three-spined stickleback clearly preferred toxic cyanobacteria to the chemical predator signal. To conclude, cyanobacteria decrease feeding rates in fish larvae, but may function as important refuge for e.g. sticklebacks, during predation pressure in pelagic algal blooms.     

生境破碎化后濒危植物缙云卫矛种群的数量动态

运用种群静态生命表、生殖力表和Leslie矩阵模型,研究了重庆特有濒危植物缙云卫矛在北温泉、鸡公山和东温泉3个片断生境中种群的数量动态。静态生命表结果显示3个种群的最大龄级分别为14、13、9龄;相对于其它两个种群,北温泉种群表现出数量较多的幼苗,但同时该样地幼苗种群表现出较高的种群消失率（K_x）。种群生殖力表显示3个种群的净增殖率（R₀）均大于1,内禀增长率（r_m）均大于0,表明缙云卫矛种群可以完成自我更新,种群表现出正增长。Leslie矩阵模型对缙云卫矛种群进行的数量预测结果显示缙云卫矛3个种群20年后均表现出数量的增长,这与生殖力表显示的结果一致。缙云卫矛的濒危可能是其生境破碎化引起的。     

Effect of Non-normality on Response to Selection in small Populations

The expressions for the r-th largest standardised deviate have been derived for beta, gamma, exponential and log-normal distributions. Using these expressions the intensities of selection have been computed for different parametric values of the distributions and of p, the proportion saved for samples of size upto 10 and compared with the corresponding values for normal distribution. The normal approximation to beta and gamma distributions is seen to be quite robust in predicting response to selection under moderately heavy and low cullings.     

Differential Response of Fish Assemblages to Coral Reef-Based Seaweed Farming

As the global demand for seaweed-derived products drives the expansion of seaweed farming onto shallow coral ecosystems, the effects of farms on fish assemblages remain largely unexplored. Shallow coral reefs provide food and shelter for highly diverse fish assemblages but are increasingly modified by anthropogenic activities. We hypothesized that the introduction of seaweed farms into degraded shallow coral reefs had potential to generate ecological benefits for fish by adding structural complexity and a possible food source. We conducted 210 transects at 14 locations, with sampling stratified across seaweed farms and sites adjacent to and distant from farms. At a seascape scale, locations were classified by their level of exposure to human disturbance. We compared sites where (1) marine protected areas (MPAs) were established, (2) neither MPAs nor blast fishing was present (hence “unprotected”), and (3) blast fishing occurred. We observed 80,186 fish representing 148 species from 38 families. The negative effects of seaweed farms on fish assemblages appeared stronger in the absence of blast fishing and were strongest when MPAs were present, likely reflecting the positive influence of the MPAs on fish within them. Species differentiating fish assemblages with respect to seaweed farming and disturbance were typically small but also included two key target species. The propensity for seaweed farms to increase fish diversity, abundance, and biomass is limited and may reduce MPA benefits. We suggest that careful consideration be given to the placement of seaweed farms relative to MPAs.     

Genetic Structure Within and Among Populations of Saruma henryi, an Endangered Plant Endemic to China

The endangered perennial plant Saruma henryi Oliv. is endemic to China and has phylogenetic, ecological, and medicinal value. We used 10 microsatellite (SSR) loci to investigate genetic diversity and differentiation in 16 natural populations. Genetic diversity was high at the species level (H(E) = 0.9427, h = 0.9410, I = 3.0213) and low at the population level (H(E) = 0.4441, h = 0.4307, I = 0.6822). Pronounced genetic differentiation was detected among populations (G(ST) = 0.5428, F(ST) = 0.5524), in line with the limited among-population gene flow (Nm = 0.21). The significant isolation-by-distance pattern revealed by a Mantel test (r = 0.311, P = 0.001) suggested a clear geographic tendency in the distribution of genetic variability. Bayesian assignment and principal coordinates analyses supported the clustering of 16 populations into three groups. The present SSR results were also compared with previously published ISSR results. These results have significant implications for conservation of the species.     

Cytogenetic Approach to Estimation of Developmental Stability of the Natural Populations of Coregonid Fish

A comparative cytogenetic analysis of Coregonid fish was carried out in the river and lake ecosystems of the northern Tyumen' District. The occurrence of chromosomal aberrations in embryonic cells of fish steadily increased during the period from 1989 until 2001. Possible causes of this dynamic are discussed.     

A Note on Response to Selection in Non-Random Mating Populations

The selection theory proposed by Muralidharan and Jain (1992a, b; Biom. J. 34 , 147–152, 633–637) was re-examined. Although they concluded that the theory is appropriate for any system of mating, the author showed that it is not applicable to inbreeding populations, which is the most important type of non-random mating.     

ShapeR: An R Package to Study Otolith Shape Variation among Fish Populations

ShapeR is an open source software package that runs on the R platform and is specifically designed to study otolith shape variation among fish populations. The package extends previously described software used for otolith shape analysis by allowing the user to automatically extract closed contour outlines from a large number of images, perform smoothing to eliminate pixel noise, choose from conducting either a Fourier or Wavelet transform to the outlines and visualize the mean shape. The output of the package are independent Fourier or Wavelet coefficients which can be directly imported into a wide range of statistical packages in R. The package might prove useful in studies of any two dimensional objects.     

Transient Response of Continuously Cultured Heterogeneous Populations to Changes in Temperature

Completely mixed, once-through continuous culture systems of heterogeneous microbial populations of sewage origin were systematically examined for response to changes in reactor temperature. Systems were operated at two dilution rates of 0.125 and 0.25 per h. "Steady state" conditions of the systems were assessed with the reactors operating at 25 C. From this base line, temperature was decreased to as low as 8 C and increased to as high as 57.5 C. Response was assessed in the ensuing transient phase as the system approached a new "steady state." The response was measured by changes in amount and type of carbon source in the reactor effluent as determined by the chemical oxygen demand test, the anthrone test, and gas chromatography. Biological solids concentration and cell composition (protein, carbohydrate, ribonucleic acid and deoxyribonucleic acid) were also determined. These systems responded more favorably to increases than to decreases in temperature. Regardless of the direction of change, the system with the lowest dilution rate (D = 0.125 per h) responded more successfully; i.e., there was less leakage of carbon source in the effluent and less dilute-out of cells during the transient phase.     

Genome-Wide Association of Lipid-Lowering Response to Statins in Combined Study Populations

Background

Statins effectively lower total and plasma LDL-cholesterol, but the magnitude of decrease varies among individuals. To identify single nucleotide polymorphisms (SNPs) contributing to this variation, we performed a combined analysis of genome-wide association (GWA) results from three trials of statin efficacy.

Methods and Principal Findings

Bayesian and standard frequentist association analyses were performed on untreated and statin-mediated changes in LDL-cholesterol, total cholesterol, HDL-cholesterol, and triglyceride on a total of 3932 subjects using data from three studies: Cholesterol and Pharmacogenetics (40 mg/day simvastatin, 6 weeks), Pravastatin/Inflammation CRP Evaluation (40 mg/day pravastatin, 24 weeks), and Treating to New Targets (10 mg/day atorvastatin, 8 weeks). Genotype imputation was used to maximize genomic coverage and to combine information across studies. Phenotypes were normalized within each study to account for systematic differences among studies, and fixed-effects combined analysis of the combined sample were performed to detect consistent effects across studies. Two SNP associations were assessed as having posterior probability greater than 50%, indicating that they were more likely than not to be genuinely associated with statin-mediated lipid response. SNP rs8014194, located within the CLMN gene on chromosome 14, was strongly associated with statin-mediated change in total cholesterol with an 84% probability by Bayesian analysis, and a p-value exceeding conventional levels of genome-wide significance by frequentist analysis (P = 1.8×10⁻⁸). This SNP was less significantly associated with change in LDL-cholesterol (posterior probability = 0.16, P = 4.0×10⁻⁶). Bayesian analysis also assigned a 51% probability that rs4420638, located in APOC1 and near APOE, was associated with change in LDL-cholesterol.

Conclusions and Significance

Using combined GWA analysis from three clinical trials involving nearly 4,000 individuals treated with simvastatin, pravastatin, or atorvastatin, we have identified SNPs that may be associated with variation in the magnitude of statin-mediated reduction in total and LDL-cholesterol, including one in the CLMN gene for which statistical evidence for association exceeds conventional levels of genome-wide significance.

Trial Registration

PRINCE and TNT are not registered. CAP is registered at Clinicaltrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00451828","term_id":"NCT00451828"}}NCT00451828     

Predicting the Effects of Endocrine Disrupting Chemicals on Fish Populations

This study evaluates the applicability and sensitivity of fish population dynamics modeling in assessing the potential effects of individual chemicals on population sustainability and recovery. Fish reproductive health is an increasingly important issue for ecological risk assessment following international concern over endocrine disruption. Life-history data from natural brook trout and fathead minnow populations were combined with effects data from laboratory-based studies, mainly concerning species other than brook trout and fathead minnows, to assess the likely impact of nonylphenol (NP) and methoxychlor (MXC) on brook trout (Salvelinus fontinalis) and fathead minnow (Pimephales promelas) population size. A delay differential equation (DDE) model with a 1-day timestep was used to predict the population dynamics of the brook trout and fathead minnows. The model predicts that NP, could enhance populations by up to 17% at a concentration of 30?µg l^?1 based on the results of reduction in survival and increased fecundity from life-cycle toxicity tests, however attempting to allow for growth reduction and its effect on fecundity results in a prediction of a 28% reduction in population numbers. For fathead minnows the DDE model predicts that the same concentration of NP could cause a population reduction of 21%. The differences in these predictions are related to these two species having different life history strategies, which are considered in the parameterization of the model. Post-application concentrations of MXC may peak around 300?µg l^?1 and then decline rapidly with time. Predictions show that such applications could cause a reduction of up to 30% in brook trout populations if the application occurs at the peak of the spawning season on successive years but that the effect would be less than 1% if the spawning season is avoided. Effects on the fathead minnow population size are predicted to be smaller (<4%) even if application occurs during the spawning period. Risk based statistics generated by the population dynamics models, such as interval decline risk or quasiextinction risk and predicted time to recovery complement traditional effects parameters such as LC50 and LOEC and may ultimately prove to be more useful in risk assessment.     

Response of Rhizobial Populations to Moderate Copper Stress Applied to an Agricultural Soil

The use of pesticides in agricultural soils may affect the soil microbiota. The effect of repeated application of copper sulfate in soil on indigenous populations of rhizobia was assessed in a medium-term field experiment. Copper sulfate was applied over 8 years at two different rates, 12.5 and 50 kg of CuSO₄ ha^–1 year^–1, in the field. The concentrations of total copper in soil varied between 14.0 (control plots that did not receive copper sulfate) and 91.0 mg kg^–1 (the most contaminated plots) at the time of sampling, 3 years after the end of the copper treatments. All the other physicochemical parameters were similar among the plots that also shared the same cropping history. The target rhizobia were monospecific populations of Rhizobium leguminosarum bv. viciae nodulating Vicia sativa and communities of rhizobial species nodulating Phaseolus vulgaris. The size of the vetch rhizobial populations was significantly reduced in the soils with the higher Cu content, whereas the size of the Phaseolus rhizobial populations was not significantly affected. However, the number of nodules formed on both vetches and common beans were reduced for the plants grown in the most contaminated soils, suggesting an additional toxic effect of copper on plant physiology. The diversity (Simpson's indices) of rhizobial genotypes, as characterized by polymerase chain reaction restriction fragment length polymorphism of 16S–23S rDNA intergenic spacer (IGS), was not influenced by copper application. Also, the genetic structure of the R. leguminosarum bv. viciae populations was not modified by copper treatments. By contrast, a shift was observed in the composition of the Phaseolus-nodulating communities in relation to soil copper content. The communities were composed of three 16S rDNA haplotypes: one corresponding to the R. leguminosarum (biovar phaseoli) species, the two others forming a new lineage of Phaseolus rhizobia based on 16S rDNA sequence analysis. The reduced frequency of the R. leguminosarum species in the Phaseolus-nodulating communities from the copper-treated soils was linked to its higher sensitivity to copper as compared to the higher tolerance of isolates belonging to the other rhizobial lineage. The new lineage was functionally efficient for symbiotic nitrogen fixation with P. vulgaris. Our results suggest that functional redundancy among species exhibiting variability for copper tolerance preserved the size of Phaseolus-nodulating communities. In contrast, the abundance of the vetch-nodulating rhizobia, which was a monospecific functional group mainly constituted by copper-sensitive genotypes, was adversely affected by repeated application of copper sulfate.     

Role of Aerobic Microbial Populations in Cellulose Digestion by Desert Millipedes

I examined the role of aerobic microbial populations in cellulose digestion by two sympatric species of desert millipedes, Orthoporus ornatus and Comanchelus sp. High numbers of bacteria able to grow on media containing cellulose, carboxymethyl cellulose, or cellobiose as the substrate were found in the alimentary tracts of the millipedes. Enzyme assays indicated that most cellulose and hemicellulose degradation occurred in the midgut, whereas the hindgut was an important site for pectin degradation. Hemicellulase and β-glucosidase in both species and possibly C_x-cellulase and pectinase in O. ornatus were of possible microbial origin. Degradation of [¹⁴C]cellulose by millipedes whose gut floras were reduced by antibiotic treatment and starvation demonstrated a reduction in ¹⁴CO₂ release and ¹⁴C assimilation and an increase in ¹⁴C excretion over values for controls. It appears that the millipede-bacterium association is mutualistic and makes available to millipedes an otherwise mostly unutilizable substrate. Such an association may be an important pathway for decomposition in desert ecosystems.     

Response of four species of Sonoran Desert trees to buffel grass removal treatments

Plant Ecology - Buffel grass (Cenchrus ciliaris L.) is an African grass used as forage for livestock that is also invasive. Several methods have been evaluated to remove invasive buffel grass, but...