Accuracy of genomic breeding values revisited: Assessment of two established approaches and a novel one to determine the accuracy in two-step genomic prediction.

Selection decisions in genomic selection schemes are made based on genomic breeding values (GBV) of candidates. Thus, the accuracy of GBV is a relevant parameter, as it reflects the stability of prediction and the possibility that the GBV might change when more information becomes available. Accuracy of genomic prediction defined as the correlation between GBV and true breeding values (TBV), however, is difficult to assess, considering TBV of the candidates are not available in reality. In previous studies, several methods were proposed to assess the accuracy of GBV including methods using population parameters or parameters inferred from mixed-model equations. In practice, most approaches tended to overestimate the accuracy of genomic prediction. We thus tested approaches used in previous studies in order to assess the magnitude of bias. Analyses were performed based on simulated data under a variety of scenarios mimicking different livestock breeding programmes. Furthermore, we proposed a novel method and tested it both with simulated data and in a real Holstein data set. The new method provided a better prediction for the accuracy of GBV in the simulated scenarios.

Identification of a haplotype associated with cholesterol deficiency and increased juvenile mortality in Holstein cattle.

Over the last decades, several genetic disorders have been discovered in cattle. However, the genetic background of disorders in calves is less reported. Recently, German cattle farmers reported on calves from specific matings with chronic diarrhea and retarded growth of unknown etiology. Affected calves did not respond to any medical treatment and died within the first months of life. These calves were underdeveloped in weight and showed progressive and severe emaciation despite of normal feed intake. Hallmark findings of the blood biochemical analysis were pronounced hypocholesterolemia and deficiency of fat-soluble vitamins. Results of the clinical and blood biochemical examination had striking similarities with findings reported in human hypobetalipoproteinemia. Postmortem examination revealed near-complete atrophy of the body fat reserves including the spinal canal and bone marrow. To identify the causal region, we performed a genome-wide association study with 9 affected and 21,077 control animals genotyped with the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA), revealing a strong association signal on BTA 11. Subsequent autozygosity mapping identified a disease-associated haplotype encompassing 1.01 Mb. The segment of extended homozygosity contains 6 transcripts, among them the gene APOB, which is causal for cholesterol disorders in humans. However, results from multi-sample variant calling of 1 affected and 47 unaffected animals did not detect any putative causal mutation. The disease-associated haplotype has an important adverse effect on calf mortality in the homozygous state when comparing survival rates of risk matings vs. non-risk matings. Blood cholesterol values of animals are significantly associated with the carrier status indicating a codominant inheritance. The frequency of the haplotype in the current Holstein population was estimated to be 4.2%. This study describes the identification and phenotypic manifestation of a new Holstein haplotype characterized by pronounced hypocholesterolemia, chronic emaciation, growth retardation, and increased mortality in young cattle, denominated as cholesterol deficiency haplotype. Our genomic investigations and phenotypic examinations provide additional evidence for a mutation within the APOB gene causing cholesterol deficiency in Holstein cattle.

First global forum on education on organ donation and transplantation for schools.

The Transplantation Society, in collaboration with the Canadian Society of Transplantation, organized a forum on education on ODT for schools. The forum included participants from around the world, school boards, and representatives from different religions. Participants presented on their countries' experience in the area of education on ODT. Working groups discussed about technologies for education, principles for sharing of resources globally, and relationships between education, and health authorities and non-governmental organizations. The forum concluded with a discussion about how to best help existing programs and those wishing to start educational programs on ODT.

A psoralen-conjugated triplex-forming oligodeoxyribonucleotide containing alternating methylphosphonate-phosphodiester linkages: synthesis and interactions with DNA.

A psoralen-conjugated oligodeoxyribopyrimidine (1443), PS-pTTTTCTTTTCTTCTT, where PS is trimethylpsoralen and C is 5-methyl-2'-deoxycytidine, that contains alternating methylphosphonate-phosphodiester internucleotide linkages was synthesized. The ability of 1443 to form triple-stranded complexes with a purine tract in a synthetic DNA duplex was studied. Irradiation of solutions containing the DNA target and 10 microM 1443 or 0.25 microM of a similar psoralen-conjugated oligodeoxyribonucleotide that contained all phosphodiester linkages, (1193), with long-wavelength UV light resulted in approximately 80% formation of interstrand cross-links at pH 7.0, 37 degrees C, in the presence of 20 mM magnesium chloride. The extent of triplex formation as monitored by photo-cross-linking decreased over the pH range 5.5-8.0, and the apparent pK of the 5-methylcytosines (C) in 1443 was approximately one-half of a pH unit less than that of the 5-methylcytosines in 1193. Oligomer 1443 formed triplexes in the absence of magnesium, and maximum triplex formation was observed in solutions containing 2.5 mM magnesium, whereas maximal triplex formation by the fully charged 1193 was not observed until the magnesium concentration was 10 mM or higher. Unlike the all-phosphodiester backbone of 1193, the alternating methylphosphonate-phosphodiester backbone of 1193 is resistant to hydrolysis by exonucleases in fetal calf serum. The nuclease resistance of 1443 and its ability to form triplexes at very low magnesium concentrations suggests that triplex-forming oligomers with alternating methylphosphonate-phosphodiester backbones may be good candidates for use as antigene reagents in cell culture.

Coupling superheated water extraction with enzyme immunoassay for an efficient and fast PAH screening in soil.

The coupling of an enzyme immunoassay with a superheated water extraction is an attractive technique because of the reduced use of hazardous solvents, due to their hostile impact on the environment. This paper describes the use of superheated water extraction and enzyme immunoassay (EIA) for the determination of polycyclic aromatic hydrocarbons (PAHs) in native (not spiked) surface soil and sediment samples. The extraction recoveries with superheated water were comparable to those achieved with conventional Soxhlet techniques. The benefits of superheated water extraction-EIA includes replacement of harmful organic solvents used in extraction, fast extractions (15-30 min.) with an inexpensive extractant, reduced number of steps in the determination of the target compounds, and the application of sensitive and relatively inexpensive assays. Further advantages of the superheated water extraction are higher extraction efficiencies compared with the methanol based extraction kits associated with the EIA and direct measurement of the extracts with EIA. Both techniques can be used as efficient screening methods in the field since the type of equipment used in superheated water extraction and EIA can be loaded into a van and operated on a car battery or a small generator.

Language maintenance and language shift: community languages in Australia, 1996.

"There is a continuing significant shift to English spoken in the home among Australia's established community language groups. There are also success stories in language maintenance. Factors influencing language use include the distribution of speakers, the age profile of the community, intermarriage patterns and cultural distance from Anglo-Australians. Australia-wide, the shift rates to English spoken at home range between three percent from Macedonian and 62 percent from Dutch in the first generation, and 15 percent from Macedonian and 95 percent from Dutch in the second generation."

Linguistic diversity in Australia.

"This paper explores the changing patterns of language diversity in Australia, Sydney and Melbourne between 1991 and 1996. It shows that there has been a great increasing linguistic diversity, accompanied by an overall decline in the use of ¿older' community languages in favour of ¿newer' languages from Asia and the Middle East."

Triplex formation by a psoralen-conjugated oligodeoxyribonucleotide containing the base analog 8-oxo-adenine.

Oligodeoxyribonucleotides containing thymidine and 8-oxo-2'-deoxyadenosine can form pyr.pur.pyr type triplexes with double-stranded DNA. Unlike triplexes whose third strands contain thymidine and deoxycytidine, the stability of these triplexes is independent of pH. We have prepared d-ps-TAAATAAATTTTTAT-L [I(A)], where A is 8-oxo-2'-deoxyadenosine, ps is 4'-hydroxymethyl-4,5',8- trimethylpsoralen and L is a 6-amino-2-(hydroxymethyl)hexyl linker. The oligomer is designed to interact with a homopurine sequence in the promoter region of the human gene coding for the 92 kDa form of collagenase type IV. Oligomer I(A) and oligomer I(C), which contains 2'-deoxycytidine in place of 8-oxo-2'-deoxycytidine, both form stable triplexes at pH 6.2, but only I(A) forms a stable triplex with a model duplex DNA target at pH 7.5, as determined by UV melting experiments. Triplex formation is stabilized by the presence of the psoralen group. Upon irradiation both I(A) and I(C) form photoadducts with the DNA target at pH 6.2, but only I(A) forms a photoadduct at pH 7.5. In these photoreactions oligomer I(A) appears to selectively form a photoadduct with a C in the purine-rich strand of the duplex target. Although a T residue is present in the pyrimidine-rich strand of the target at the duplex/triplex junction, essentially no adduct formation takes place with this strand, nor is interstrand cross-linking observed. The extent of photoadduct formation decreases with increasing temperature, behavior which is consistent with the UV melting curve of the triplex. A tetramethylrhodamine derivative of I(A) was prepared and found to cross-link less extensively than I(A) itself. Oligomer I(A) is completely resistant to hydrolysis when incubated for 24h in the presence of 10% fetal bovine serum at 37 degree C, although it is hydrolyzed by S1 nuclease. The properties of oligomer I(A) suggest that 8-oxo- containing oligomers may find utility as antigene oligonucleotide reagents.

Inhibition of herpes simplex virus replication by antisense oligo-2'-O-methylribonucleoside methylphosphonates.

Antisense oligonucleoside methylphosphonates complementary to the 12 nucleotides found at the intron/exon junction of the splice acceptor site of herpes simplex virus type 1 (HSV-1) immediate early mRNAs 4 and 5 were synthesized. The methylphosphonate oligomers contained either 2'-deoxyribose nucleosides, d-OMPs, or 2'O-methylribose nucleosides, mr-OMPs. At 37 degrees C, the affinity of the mr-OMP for a complementary 12-mer RNA target was approximately four times higher than that of the corresponding d-OMP as measured by a constant activity gel electrophoresis mobility shift assay. An mr-OMP whose sequence contained two mismatched bases did not bind to the RNA target under these conditions. The mr-OMP also showed improved ability to inhibit HSV-1 replication in HSV-1 infected Vero cells in culture. Thus the IC50 of the mr-OMP was five times less than that of the d-OMP. No inhibition was observed by the mismatched mr-OMP, and no inhibition of herpes simplex virus type 2 (HSV-2) replication was observed with any of the oligomers. These results demonstrate a direct correlation between oligomer binding affinity and antisense activity in cell culture and suggest that oligo-2'-O-methylribonucleoside methylphosphonates are promising candidates for development of effective antisense reagents.

Dietary self-selection following subdiaphragmatic vagotomy in the white rat.

Nineteen female Wistar rats were employed in a self-selection-of-diet study assessing the effects of vagotomy on macronutrient consumption. Nutrients offered were a 30% sucrose solution, a 15% casein hydrolysate solution, and olive oil. In addition, noncaloric bulk, vitamins, and water were allowed. Bilaterally, subdiaphragmatically vagotomized rats showed a significant decrement in carbohydrate ingestion and daily total caloric intake (P less than .05 in both comparisons). Fat and protein intakes were unreliably altered. It is hypothesized that the vagus nerve relays glucose absorption and/or storage information from the periphery to the brain (perhaps lateral hypothalamusy, and hence, vagotomy produces carbohydrate-intake decrements, specifically. The decrement could also be explained as resulting from efferent effects of vagotomy such as decreased gut hormonal release.