Anaerobic degradation of papermill sludge in a two-phase digester containing rumen microorganisms and colonized polyurethane foam

Summary The use of reticulated polyurethane foam as a support material for the immobilization of methanogenic associations and its application to the anaerobic treatment of fine particulate solid wastes was investigated. The colonization of polyurethane support particles in a continuous upflow reactor fed on a mixture of acetate, propionate and butyrate, was both rapid and dense. The combination of rumen microorganisms and colonized support particles in a two-phase digester resulted in an efficient anaerobic decomposition of papermill sludge.     

Responses of algae, bacteria, Daphnia and natural parasite fauna of Daphnia to nutrient enrichment in mesocosms

Understanding responses of parasites to changes in nutrient regimes is necessary for prediction of their role in aquatic ecosystems under global change in nutrient loading. We studied the response of the natural parasite fauna of Daphnia longispina to nutrient enrichment in mesocosms in a small humic lake. We measured the concentrations of inorganic phosphorus and nitrogen in the water, total nutrients in the seston, algal and bacterial biomass, Daphnia population dynamics, Daphnia stoichiometry, Daphnia stable isotope values and the presence and abundance of parasites in treated mesocosms as compared to three control ones. Incorporation of the nutrient enrichment in the food web was seen as increased nutrient concentrations in the epilimnion and as a decrease in carbon:nutrient ratios and δ¹⁵N values in Daphnia. Nutrient enrichment did not significantly influence algal, bacterial or Daphnia biomass. One of the four parasite species observed, unidentified small gut parasite, had a higher prevalence (percentage of Daphnia infected) in treated mesocosms, but its intensity (number of parasites per infected host) remained the same among treatments. Our results suggest that the effect of nutrient enrichment on host–parasite dynamics is dependent on complex interactions within food webs and on the epidemiological traits of parasites.     

The effect of genomic information on optimal contribution selection in livestock breeding programs

Background

Long-term benefits in animal breeding programs require that increases in genetic merit be balanced with the need to maintain diversity (lost due to inbreeding). This can be achieved by using optimal contribution selection. The availability of high-density DNA marker information enables the incorporation of genomic data into optimal contribution selection but this raises the question about how this information affects the balance between genetic merit and diversity.

Methods

The effect of using genomic information in optimal contribution selection was examined based on simulated and real data on dairy bulls. We compared the genetic merit of selected animals at various levels of co-ancestry restrictions when using estimated breeding values based on parent average, genomic or progeny test information. Furthermore, we estimated the proportion of variation in estimated breeding values that is due to within-family differences.

Results

Optimal selection on genomic estimated breeding values increased genetic gain. Genetic merit was further increased using genomic rather than pedigree-based measures of co-ancestry under an inbreeding restriction policy. Using genomic instead of pedigree relationships to restrict inbreeding had a significant effect only when the population consisted of many large full-sib families; with a half-sib family structure, no difference was observed. In real data from dairy bulls, optimal contribution selection based on genomic estimated breeding values allowed for additional improvements in genetic merit at low to moderate inbreeding levels. Genomic estimated breeding values were more accurate and showed more within-family variation than parent average breeding values; for genomic estimated breeding values, 30 to 40% of the variation was due to within-family differences. Finally, there was no difference between constraining inbreeding via pedigree or genomic relationships in the real data.

Conclusions

The use of genomic estimated breeding values increased genetic gain in optimal contribution selection. Genomic estimated breeding values were more accurate and showed more within-family variation, which led to higher genetic gains for the same restriction on inbreeding. Using genomic relationships to restrict inbreeding provided no additional gain, except in the case of very large full-sib families.     

Parasite infection alters host stable‐isotope composition under controlled feeding

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Factors affecting abundance of Triaenophorus infection in Cyclops strenuus, and parasite-induced changes in host fitness

Factors affecting the abundance of Triaenophorus crassus and Triaenophorus nodulosus procercoids in their copepod first intermediate host, Cyclops strenuus, and effects of infection on feeding behaviour, reproduction and survival of the host were studied experimentally. When exposed to the same number of coracidia, copepods harboured considerably less procercoids in the trials where ciliates or Artemia salina nauplii were given as alternative food items. The prevalence of infection was higher in adult copepods as compared with copepodite stage IV and stage V, and higher in stage V than in stage IV. The prevalences in adult females and males did not differ significantly from each other. The frequency of females carrying egg sacs was lower among infected than among exposed uninfected and unexposed copepods. The rate of feeding on Artemia nauplii remained at the same level in uninfected copepods, but decreased strongly in infected copepods during 7 days p.i. The survival of unexposed, exposed uninfected and infected copepods did not differ significantly from each other for the first 11 days post-exposure, but the mortality of infected copepods increased significantly after 3 weeks post-exposure. However, the rate of development and mortality of copepods might have been affected by the apparently arrested development of stage IV copepodites found in the experiment. Some of the contradictions between these results and earlier observations are suggested to be caused by the differences in the duration of exposure, intensity of infection and duration of observation post-exposure in the present study as compared with other experiments.     

The IIIb isoform of fibroblast growth factor receptor 2 is required for proper growth and branching of pancreatic ductal epithelium but not for differentiation of exocrine or endocrine cells

Fibroblast growth factors (Fgfs) and their receptors have been implicated in embryonic pancreas development. Recently it was shown that Fgf10, a major ligand for the IIIb isoform of fibroblast growth factor receptor 2 (Fgfr2b), has an important regulatory role in early pancreas development. The aim of our study was to define the role of Fgfr2b in pancreas development by analyzing the phenotype of Fgfr2b (-/-) mice. Pancreases of Fgfr2b (-/-) embryos were noticeably smaller than the wild type littermates during embryogenesis, and pancreatic ductal branching as well as duct cell proliferation was significantly reduced. However, both exocrine and endocrine pancreatic differentiation occurred relatively normally. Exogenous addition of Fgfr2b ligands (Fgf7 and Fgf10) stimulated duct cell proliferation and inhibited endocrine cell differentiation in the ex vivo embryonic organ cultures of wild type pancreas. Our results thus suggest that Fgfr2b-mediated signaling plays a major role in pancreatic ductal proliferation and branching morphogenesis, but has little effect on endocrine and exocrine differentiation.     

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

Background  

Gene loss, inversions, translocations, and other chromosomal rearrangements vary among species, resulting in different rates of structural genome evolution. Major chromosomal rearrangements are rare in most eukaryotes, giving large regions with the same genes in the same order and orientation across species. These regions of macrosynteny have been very useful for locating homologous genes in different species and to guide the assembly of genome sequences. Previous analyses in the fungi have indicated that macrosynteny is rare; instead, comparisons across species show no synteny or only microsyntenic regions encompassing usually five or fewer genes. To test the hypothesis that chromosomal evolution is different in the fungi compared to other eukaryotes, synteny was compared between species of the major fungal taxa.     

Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits

Background

In the analysis of complex traits, genetic effects can be confounded with non-genetic effects, especially when using full-sib families. Dominance and epistatic effects are typically confounded with additive genetic and non-genetic effects. This confounding may cause the estimated genetic variance components to be inaccurate and biased.

Methods

In this study, we constructed genetic covariance structures from whole-genome marker data, and thus used realized relationship matrices to estimate variance components in a heterogenous population of ~ 2200 mice for which four complex traits were investigated. These mice were genotyped for more than 10,000 single nucleotide polymorphisms (SNP) and the variances due to family, cage and genetic effects were estimated by models based on pedigree information only, aggregate SNP information, and model selection for specific SNP effects.

Results and conclusions

We show that the use of genome-wide SNP information can disentangle confounding factors to estimate genetic variances by separating genetic and non-genetic effects. The estimated variance components using realized relationship were more accurate and less biased, compared to those based on pedigree information only. Models that allow the selection of individual SNP in addition to fitting a relationship matrix are more efficient for traits with a significant dominance variance.