Single step genomic evaluation for female fertility in Nordic Red dairy cattle

Joint Nordic (Denmark, Finland, Sweden) genetic evaluation of female fertility is currently based on the multiple trait multilactation animal model (BLUP). Here, single step genomic model (ssGBLUP) was applied for the Nordic Red dairy cattle fertility evaluation. The 11 traits comprised of nonreturn rate and days from first to last insemination in heifers and first three parities, and days from calving to first insemination in the first three parities. Traits had low heritabilities (0.015–0.04), but moderately high genetic correlations between the parities (0.60–0.88). Phenotypic data included 4,226,715 animals with records and pedigree 5,445,392 animals. Unknown parents were assigned into 332 phantom parent groups (PPG). In mixed model equations animals were associated with PPG effects through the pedigree or both the pedigree and genomic information. Genotype information of 46,914 SNPs was available for 33,969 animals in the pedigree. When PPG used pedigree information only, BLUP converged after 2,420 iterations whereas the ssGBLUP evaluation needed over ten thousand iterations. When the PPG effects were solved accounting both the pedigree and the genomic information, the ssGBLUP model converged after 2,406 iterations. Also, with the latter model breeding values by ssGBLUP and BLUP became more consistent and genetic trends followed each other well. Models were validated using forward prediction of the young bulls. Reliabilities and variance inflation of predicted genomic breeding values (values for parent averages in brackets) for the 11 traits ranged 0.22–0.31 (0.10–0.27) and 0.81–0.95 (0.83–1.06), respectively. The ssGBLUP model gave always higher validation reliabilities than BLUP, but largest increases were for the cow fertility traits.     

Protein-lipid interactions during liposome oxidation with added anthocyanin and other phenolic compounds

Oxidation of bovine serum albumin, casein, and lactalbumin and the effect of different procyanidins, anthocyanins, and their aglycons (10 and 20 microM) on lactalbumin oxidation were investigated in a liposome system. Samples were incubated in the dark at 37 degrees C with copper, and the extent of oxidation was measured by determining the loss of tryptophan fluorescence and the formation of protein carbonyls, conjugated diene hydroperoxides, and hexanal. The correlation between different protein and lipid oxidation measurements was good and statistically significant. Casein was the most stable protein in the liposome model, and it was also the best inhibitor of liposome oxidation. All tested anthocyanins and other phenolic compounds inhibited both lipid and protein oxidation. There were no systematic differences with anthocyanins and their aglycons in relation to the concentrations used or glycosylation with either glucose or rutinose. Procyanidins B1 and B2 and ellagic acid were potentially better antioxidants than anthocyanins due to their several hydroxyl groups as measured by both protein and lipid oxidation. In conclusion, oxidative deterioration of liposomes due to protein-lipid interaction is inhibited by anthocyanins, procyanidins, and ellagitannin present, for example, in berries.     

Applicability of a sequential P fractionation procedure to Si in sediment

Purpose  

A sequential phosphorus (P) fractionation procedure for sediments was applied to silicon (Si) to test its applicability. We wanted to know (1) whether it would be used in a cost-efficient way to study the finding of both elements, defining Si pools corresponding to the respective P pools, and in particular, (2) whether it could be shown that redox-sensitive processes affect Si mobility in sediment.     

Linear–threshold animal model for birth weight, gestation length and calving ease in United Kingdom Limousin beef cattle data

Breeding value evaluation for UK Limousin beef cattle data was carried out by multiple-trait linear–threshold animal model with variance components assumed to be known. Polychotomous calving ease with five categories was analysed with two continuous traits: birth weight and gestation length. Field data consisted of 220,799 animals with observations with every possible combination of traits, and 270,035 animals in the pedigree. The threshold model was solved either with Newton Raphson or Expectation Maximisation algorithm, and solutions were compared to evaluation by a linear model with original and normalised scores. There were insignificant differences in solutions between the two algorithms for threshold model analyses. Furthermore, solutions of the continuous traits were similar by the threshold and linear models. For the categorical trait, correlations for random effects from the threshold and linear models were high. In case of normalised scores (original scores case in brackets) correlations with solutions from the threshold and linear model were 0.97 (0.94) and 0.97 (0.93) for direct and maternal genetic effects and 0.95 (0.89) for permanent maternal effects. Even so, at least one third of the top 1% ranking of bulls differed between the linear and the threshold models. Predictive abilities as correlations between estimated breeding values and pedigree indices were almost equal between the linear and threshold models for both continuous and categorical traits. In conclusion, despite the higher computational demand, the linear–threshold animal model can be seen worthwhile in the genetic evaluation of the national UK beef cattle data set.     

The relationship between dissolved organic matter and percolation water chemistry in northern Finland

The aim of this study was to investigate the relationship between dissolved organic matter and chemical constituents of percolation water collected at 5, 20 and 40 cm depths from 13 ionbalance sampling plots located along lines extending through Finnish Lapland from Cu-Ni smelters in the Kola Peninsula, Russia. All the monitoring plots have as uniform as possible stand and site characteristics. The plots were located in Scots pine stands on dry and dryish sites with genetic horizons characteristic of Fe-humus podsols. The soil type on most of the sites was sorted fine sand or sand. Significant positive correlations were found between dissolved organic matter (DOM) and total dissolved Al concentrations at 5 and 20 cm, but not at 40 cm. A significant negative correlation was found between DOM and pH at 5 cm, but not at 20 or 40 cm. The anion deficit was positively correlated with DOM at 5 cm in the percolation water. Organic matter thus plays an important role as an anioh in percolation water, and regulates water pH in the surface soil. A high proportion of dissolved Al was in the form of organic complexes. Total dissolved Al levels were well below the toxic limits for pine.     

Changes in Collembola richness and diversity along a gradient of land-use intensity: A pan European study

Changes in Collembola richness and diversity along a land-use intensity gradient were studied in eight European countries (Portugal, Spain, France, Switzerland, Hungary, UK, Ireland and Finland). In each country a set of six 1 km² land-use units (LUUs) were selected forming a gradient ranging from natural forest to agricultural dominated landscapes, passing through mixed-use ones. In addition to data on Collembola, detailed information regarding landscape diversity and structure was collected for each LUU. A total of 47,774 individuals were identified from 281 species. Collembola reacted not only to changes in the diversity of the landscape, but also to the composition of that diversity and the area occupied by each land-use type at each LUU. Although species richness patterns were not concordant among the different countries, the total number of species per LUU (landscape richness) was generally higher in natural forests and mixed-used landscapes, and lower in agricultural dominated landscapes. Moreover, high richness and diversity of Collembola at each LUU were associated with a diverse landscape structure, both in terms of number of patches and patch richness. Despite this comparable species richness between mixed-use landscapes and those dominated by natural forests, average species richness on forested areas (local richness) decreased along the gradient, showing that forest patches on mixed-use landscapes support a lower richness than in landscapes dominated by forest. This aspect is important when addressing the role of native forests in structuring biodiversity in disturbed and fragmented landscapes. Although a diverse landscape can support a high biodiversity, the results suggest that intensive fragmentation should be avoided with the risk of collapsing local species richness with the consequent result for regional biodiversity.     

Inhibition of protein and lipid oxidation in liposomes by berry phenolics

The antioxidant activity of berry phenolics (at concentrations of 1.4, 4.2, and 8.4 mug of purified extracts/mL of liposome sample) such as anthocyanins, ellagitannins, and proanthocyanidins from raspberry (Rubus idaeus), bilberry (Vaccinium myrtillus), lingonberry (Vaccinium vitis-idaea), and black currant (Ribes nigrum) was investigated in a lactalbumin-liposome system. The extent of protein oxidation was measured by determining the loss of tryptophan fluorescence and formation of protein carbonyl compounds and that of lipid oxidation by conjugated diene hydroperoxides and hexanal analyses. The antioxidant protection toward lipid oxidation was best provided by lingonberry and bilberry phenolics followed by black currant and raspberry phenolics. Bilberry and raspberry phenolics exhibited the best overall antioxidant activity toward protein oxidation. Proanthocyanidins, especially the dimeric and trimeric forms, in lingonberries were among the most active phenolic constituents toward both lipid and protein oxidation. In bilberries and black currants, anthocyanins contributed the most to the antioxidant effect by inhibiting the formation of both hexanal and protein carbonyls. In raspberries, ellagitannins were responsible for the antioxidant activity. While the antioxidant effect of berry proanthocyanidins and anthocyanins was dose-dependent, ellagitannins appeared to be equally active at all concentrations. In conclusion, berries are rich in monomeric and polymeric phenolic compounds providing protection toward both lipid and protein oxidation.     

Cyanobacteria from Terrestrial and Marine Sources Contain Apoptogens Able to Overcome Chemoresistance in Acute Myeloid Leukemia Cells

In this study, we investigated forty cyanobacterial isolates from biofilms, gastropods, brackish water and symbiotic lichen habitats. Their aqueous and organic extracts were used to screen for apoptosis-inducing activity against acute myeloid leukemia cells. A total of 28 extracts showed cytotoxicity against rat acute myeloid leukemia (IPC-81) cells. The design of the screen made it possible to eliminate known toxins, such as microcystins and nodularin, or known metabolites with anti-leukemic activity, such as adenosine and its analogs. A cytotoxicity test on human embryonic kidney (HEK293T) fibroblasts indicated that 21 of the 28 extracts containing anti-acute myeloid leukemia (AML) activity showed selectivity in favor of leukemia cells. Extracts L26-O and L30-O were able to partly overcome the chemotherapy resistance induced by the oncogenic protein Bcl-2, whereas extract L1-O overcame protection from the deletion of the tumor suppressor protein p53. In conclusion, cyanobacteria are a prolific resource for anti-leukemia compounds that have potential for pharmaceutical applications. Based on the variety of cellular responses, we also conclude that the different anti-leukemic compounds in the cyanobacterial extracts target different elements of the death machinery of mammalian cells.     

Genome Reduction and Secondary Metabolism of the Marine Sponge-Associated Cyanobacterium Leptothoe

Sponges form symbiotic relationships with diverse and abundant microbial communities. Cyanobacteria are among the most important members of the microbial communities that are associated with sponges. Here, we performed a genus-wide comparative genomic analysis of the newly described marine benthic cyanobacterial genus Leptothoe (Synechococcales). We obtained draft genomes from Le. kymatousa TAU-MAC 1615 and Le. spongobia TAU-MAC 1115, isolated from marine sponges. We identified five additional Leptothoe genomes, host-associated or free-living, using a phylogenomic approach, and the comparison of all genomes showed that the sponge-associated strains display features of a symbiotic lifestyle. Le. kymatousa and Le. spongobia have undergone genome reduction; they harbored considerably fewer genes encoding for (i) cofactors, vitamins, prosthetic groups, pigments, proteins, and amino acid biosynthesis; (ii) DNA repair; (iii) antioxidant enzymes; and (iv) biosynthesis of capsular and extracellular polysaccharides. They have also lost several genes related to chemotaxis and motility. Eukaryotic-like proteins, such as ankyrin repeats, playing important roles in sponge-symbiont interactions, were identified in sponge-associated Leptothoe genomes. The sponge-associated Leptothoe stains harbored biosynthetic gene clusters encoding novel natural products despite genome reduction. Comparisons of the biosynthetic capacities of Leptothoe with chemically rich cyanobacteria revealed that Leptothoe is another promising marine cyanobacterium for the biosynthesis of novel natural products.     

Effects of earthworms on decomposition and metal availability in contaminated soil: Microcosm studies of populations with different exposure histories

Population-specific differences in the responses of earthworms to simultaneous exposure to Cu and Zn were studied in microcosm experiments. Two populations of Aporrectodea caliginosa tuberculata (Eisen) with different metal exposure histories were chosen for the studies. Microcosms were prepared containing either uncontaminated soil or soils with low or high combined Cu/Zn -concentrations (79/139 or 178/311 mg kg⁻¹ dry mass of soil, respectively). Earthworms from each population were introduced to the microcosm treatments with some microcosms serving as controls without earthworms. One series of microcosms was destructively sampled after 16 weeks incubation in a climate chamber. Survival, growth, reproduction and decomposition by earthworms in each treatment were measured. An additional microcosm series was sampled for soil and earthworm measurements at four weeks intervals to determine temporal changes in the availability of metals in the soils and their accumulation into earthworms. Cu and Zn were sequentially extracted from the soil samples of both microcosm series to estimate mobility and availability of the metals in the soil. Earthworms with long-term exposure history to metal-contaminated soil seemed to tolerate higher soil metal concentrations than earthworms without earlier exposure. Both earthworms and metals affected soil respiration (CO₂ production) and nitrogen mineralization. In addition, earthworms seemed to decrease the mobility and bioavailability of metals in the soil through their burrowing activity.