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.     

Projecting the suitability of global and local habitats for myrtle rust (Austropuccinia psidii) using model consensus

Myrtle rust (caused by Austropuccinia psidii) affects more than 500 known host species in the Myrtaceae family. Three different modelling approaches (CLIMEX, MaxEnt and Multi-Model Framework) were used to project the habitat suitability for myrtle rust at both global and local scales. Current data on the global occurrence of myrtle rust were collected from online literature and expert solicitation. Long-term averages of climate data (1960–1990) were sourced from WorldClim and CliMond websites. Recent reports of myrtle rust in New Zealand were used for validation of model outputs but not in model training and testing. The model outputs were combined into a consensus model to identify localities projected to be suitable for myrtle rust according to two or three models (hotspots). In addition to the locations where the pathogen is currently present, all models successfully projected independent occurrence data in New Zealand suitable for establishment of the pathogen. Climate suitability for the pathogen was primarily related to temperature followed by rainfall in MaxEnt and the CLIMEX model. The results confirmed the optimum temperature range of this pathogen in the literature (15–25 °C). Additional analysis of the precipitation variables indicated that excessive rain (more than 2000 mm in warmest quarter of the year) combined with high temperatures (>30 °C) constrain pathogen establishment. The results of the current study can be useful for countries such as New Zealand, China, South Africa and Singapore where the pathogen has not fully spread or established.     

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.     

CEREBRAL GLUCOSE UTILIZATION MEASURED WITH HIGH RESOLUTION POSITRON EMISSION TOMOGRAPHY IN EPILEPTIC FINNISH SPITZ DOGS AND HEALTHY DOGS

In human epileptic patients, changes in cerebral glucose utilization can be detected 2‐deoxy‐2‐[¹⁸F] fluoro‐d ‐glucose positron emission tomography (FDG‐PET). The purpose of this prospective study was to determine whether epileptic dogs might show similar findings. Eleven Finnish Spitz dogs with focal idiopathic epilepsy and six healthy dogs were included. Dogs were examined using electroencephalography (EEG) and FDG‐PET, with epileptic dogs being evaluated during the interictal period. Visual and semi‐quantitative assessment methods of FDG‐PET were compared and contrasted with EEG findings. Three independent observers, unaware of dog clinical status, detected FDG‐PET uptake abnormalities in 9/11 epileptic (82%), and 4/8 healthy dogs (50%). Occipital cortex findings were significantly associated with epileptic status (P = 0.013). Epileptic dogs had significantly lower standardized uptake values (SUVs) in numerous cortical regions, the cerebellum, and the hippocampus compared to the control dogs. The lowest SUVs were found in the occipital lobe. White matter normalized and left‐right asymmetry index values for all pairs of homologous regions did not differ between groups. Visual evaluation of the EEGs was less sensitive (36%) than FDG‐PET. Both diagnostic tests were consensual and specific (100%) for occipital findings, but EEG had a lower sensitivity for detecting lateralized foci than FDG‐PET. Findings supported the use of FDG‐PET as a diagnostic test for dogs with suspected idiopathic epilepsy. Visual and semiquantitative analyses of FDG‐PET scans provided complementary information. Findings also supported the theory that epileptogenesis may occur in multiple brain regions in Finnish Spitz dogs with idiopathic epilepsy.     

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.     

A mycobacterium isolated from tissue cultures of mature Pinus sylvestris interferes with growth of Scots pine seedlings

We isolated a rapidly growing, pigment-producing mycobacterium from senescent tissue cultures derived from mature Scots pine (Pinus sylvestris L.). The bacterium was found in three senescent suspension cultures and in a senescent protoplast culture. Growth of Scots pine cells had ceased in all of these cultures. Exogenous contamination was eliminated by rigorous surface sterilization of the buds with hypochlorite before aseptic removal of the bud scales. Based on biochemical and physiological properties and DNA sequence comparisons, the isolated mycobacterium did not belong to any known species. Its sequence most closely resembled those of Mycobacterium obuense (97%) and M. aichiense (96%). Tissue browning was frequently observed in callus or suspension culture of Scots pine. Because the effect of the mycobacterium on growth of undifferentiated tissues that were browning was difficult to evaluate, we applied the bacterium to Scots pine seeds in aseptic conditions. Seedlings grown in the presence of the mycobacterium had shorter hypocotyls than control seedlings and seedlings cocultivated with a Pseudomonas strain known to be harmless to plants. However, hypocotyl growth of seedlings cocultivated with another mycobacterium, M. chlorophenolicum, was similar to that observed in the presence of the isolated mycobacterium. Phenylalanine ammonia-lyase activity of seedlings cocultivated with the mycobacterium isolate was significantly higher than that of control seedlings or seedlings cocultivated with M. chlorophenolicum or Pseudomotnas fluorescens. We believe that this is the first report of the isolation of mycobacteria from tissue cultures of a tree. Our finding that the mycobacterium may interfere with the growth of Scots pine in vitro warrants further study.     

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.