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.     

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.     

Snowpack quality as an indicator of air pollution in Finnish Lapland and the Kola Peninsula,NW Russia

Bulk snow samples were collected from the snowpack in open areas along two sampling lines running to the west from the Cu-Ni smelters at Nikel and Monchegorsk, NW Russia, during 1991–1993. The aim of the study was to estimate the area affected by sulphur and heavy metal deposition from the smelters. Snowpack quality was used as an indicator of deposition during winter time. The total sulphur, copper and nickel concentrations in the snowpack decreased significantly (p<0.001) with=" increasing=" distance=" from=" the=" smelters=" along=" the=" sampling=" line=" running=" directly=" to=" the=" west=" from=" monchegorsk.=" the=" deposition=" pattern=" was=" similar=" each=" winter=" during=" 1991–1993.=" the=" ph=" values=" did=" not=" correlate=" with=" the=" corresponding=" sulphur=" concentrations,=" and=" there=" was=" no=" decreasing=" ph=" gradient=" in=" the=" snowpack=" on=" moving=" towards=" monchegorsk.=" the=" effects=" of=" sulphur=" emissions=" from=" monchegorsk=" on=" snowpack=" chemistry=" were=" not=" detectable=" on=" the=" finnish=" side=" of=" the=" border.=" the=" 3-year=" mean=" of=" the=" total=" sulphur=" concentration=" was=" 0.27=" mg/kg,=" and=" of=" the=" ph=" values=" 4.92,=" along=" the=" sampling=" line=" running=" to=" the=" west=" of=" monchegorsk.=" the=" total=" sulphur=" concentrations=" near=" the=" smelters=">< 20=" km)=" varied=" between=" 0.37=" and=" 0.95=" mg/kg.=" the=" effect=" of=" the=" cu-ni=" smelters=" at=" nikel=" on=" snowpack=" quality=" was=" not=" detectable=" in=" northern=" finnish=" lapland.=" the=" 3-year=" mean=" for=" total=" sulphur=" was=" 0.20=" mg/kg=" and=" for=" ph=" 4.96=" along=" the=" sampling=" line=" running=" to=" the=" west=" of=">     

Efficient Monte Carlo algorithm for restricted maximum likelihood estimation of genetic parameters

Monte Carlo (MC) methods have been found useful in estimation of variance parameters for large data and complex models with many variance components (VC), with respect to both computer memory and computing time. A disadvantage has been a fluctuation in round‐to‐round values of estimates that makes the estimation of convergence challenging. Furthermore, with Newton‐type algorithms, the approximate Hessian matrix might have sufficient accuracy, but the inaccuracy in the gradient vector exaggerates the round‐to‐round fluctuation to intolerable. In this study, the reuse of the same random numbers within each MC sample was used to remove the MC fluctuation. Simulated data with six VC parameters were analysed by four different MC REML methods: expectation‐maximization (EM), Newton–Raphson (NR), average information (AI) and Broyden's method (BM). In addition, field data with 96 VC parameters were analysed by MC EM REML. In all the analyses with reused samples, the MC fluctuations disappeared, but the final estimates by the MC REML methods differed from the analytically calculated values more than expected especially when the number of MC samples was small. The difference depended on the random numbers generated, and based on repeated MC AI REML analyses, the VC estimates were on average non‐biased. The advantage of reusing MC samples is more apparent in the NR‐type algorithms. Smooth convergence opens the possibility to use the fast converging Newton‐type algorithms. However, a disadvantage from reusing MC samples is a possible “bias” in the estimates. To attain acceptable accuracy, sufficient number of MC samples need to be generated.