Detection and assessment of copy number variation using PacBio long-read and Illumina sequencing in New Zealand dairy cattle.

Single nucleotide polymorphisms have been the DNA variant of choice for genomic prediction, largely because of the ease of single nucleotide polymorphism genotype collection. In contrast, structural variants (SV), which include copy number variants (CNV), translocations, insertions, and inversions, have eluded easy detection and characterization, particularly in nonhuman species. However, evidence increasingly shows that SV not only contribute a substantial proportion of genetic variation but also have significant influence on phenotypes. Here we present the discovery of CNV in a prominent New Zealand dairy bull using long-read PacBio (Pacific Biosciences, Menlo Park, CA) sequencing technology and the Sniffles SV discovery tool (version 0.0.1; https://github.com/fritzsedlazeck/Sniffles). The CNV identified from long reads were compared with CNV discovered in the same bull from Illumina sequencing using CNVnator (read depth-based tool; Illumina Inc., San Diego, CA) as a means of validation. Subsequently, further validation was undertaken using whole-genome Illumina sequencing of 556 cattle representing the wider New Zealand dairy cattle population. Very limited overlap was observed in CNV discovered from the 2 sequencing platforms, in part because of the differences in size of CNV detected. Only a few CNV were therefore able to be validated using this approach. However, the ability to use CNVnator to genotype the 557 cattle for copy number across all regions identified as putative CNV allowed a genome-wide assessment of transmission level of copy number based on pedigree. The more highly transmissible a putative CNV region was observed to be, the more likely the distribution of copy number was multimodal across the 557 sequenced animals. Furthermore, visual assessment of highly transmissible CNV regions provided evidence supporting the presence of CNV across the sequenced animals. This transmission-based approach was able to confirm a subset of CNV that segregates in the New Zealand dairy cattle population. Genome-wide identification and validation of CNV is an important step toward their inclusion in genomic selection strategies.

Application of genomic evaluation to dairy cattle in New Zealand.

A hybrid method of estimating genomically enhanced breeding values (GEBV) that uses features of a single-step approach and traditional national estimated breeding value (EBV), based on pedigree, as the starting point was developed and assessed. The method uses deregressed EBV from the traditional EBV estimation procedures and a pedigree matrix that is augmented by a genomic relationship matrix based on a Euclidean distance (EDM) in a Gaussian kernel. Genotypes were obtained using the Illumina BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). The pedigree information is restricted to animals with genotypes, as well as all of their ancestors, resulting in a system of equations that is considerably smaller than that of the national evaluation. Genome-wide association studies were used to identify regions of the genome that had high association with the traits in the New Zealand national breeding objective. The EDM were created for each selected region. The amount of variance accounted for by each region was estimated, and the variances, relative to the EDM excluding these areas, were used to create trait-specific weighted EDM that were used for the evaluations. The evaluation is done on the restricted data set and is a reversal of the deregression procedure using the augmented pedigree-based relationship matrix. The method was tested using data on 7,204 progeny-tested sires, in which the daughter records for the 3 youngest cohorts (i.e., validation data; n=1,410) were excluded. Evaluations were done for the 7 traits (3 production, 4 nonproduction) in the New Zealand national breeding objective. Regression of the traditional EBV based on daughter information on the GEBV for validation sires had an average slope of 0.99 (range 0.93 to 1.06); the average correlation between the EBV was 0.79 (range 0.56 to 0.84). The average slope and correlation for the previously used blended GEBV were 0.64 and 0.61, respectively. The method was applied to all genotyped animals that included approximately 13,000 genotyped males and 47,000 genotyped females and their ancestors. The correlation between the traditional EBV and GEBV of the proven bulls was 0.99; the correlations obtained from the previously used blended GEBV were 0.88 (no inflation adjustment) and 0.94 (following inflation adjustment). The values for the unproven bulls were 0.95 (parent average EBV and GEBV), 0.56 (blended GEBV, no inflation adjustment), and 0.88 (blended GEBV, following inflation adjustment). The use of trait-specific weighted EDM provided a 1 to 2% improvement in the accuracy of the genomic evaluations of the production traits and no improvement in the nonproduction traits. The hybrid method of estimating GEBV was found to be considerably less biased and generally more accurate than the previously used blended genomic breeding value.

Photoneutrons from a beryllium reflector: a potential source of problems with Zr-Au flux monitors in k0 standardization based neutron activation analysis.

The assumption that the shape of the epithermal neutron spectrum can be described, in any research reactor, by the 1/E1+α function is a fundamental starting point of the k0 standardization. This assumption may be questioned from a reactor physics viewpoint. The type of moderator, the existence of neutron reflectors, the additional production of (γ, n) neutrons and resonance capture by construction materials may be different for each reactor, with consequences for the shape of the neutron spectrum. This dependency may explain that various practitioners reported contradicting experiences with the use of Zr-Au flux monitors for the determination of the α-parameter. An objective view on the influence of the design of the reactor and irradiation facility on the shape of the neutron spectrum can be obtained by modeling. This has been applied in the Reactor Institute Delft for reactor configurations in which the irradiation facilities face the fuel elements with the presence of beryllium reflector elements. The Monte Carlo calculations indicate a distortion of the 1/E1+α relationship at the higher energy edge of the epithermal neutron spectrum. This distortion is attributed to the formation and thermalisation of both photoneutrons and (n, 2n) produced fast neutrons in the beryllium, and has a direct impact on the resonance activation of 95Zr, other than represented by the 1/E1+α function. The obtained relationship between neutron flux and neutron energy was also used for estimating the f-value and compared with the value obtained by the Delft Cr-Mo-Au flux monitor.

Phenotypic associations between traits other than production and longevity in New Zealand dairy cattle.

A proportional hazards model was used to investigate the phenotypic effect of traits other than production (TOP) on true and functional longevity across purebred and crossbred Holstein-Friesian and Jersey dairy cattle in registered and commercial herds in New Zealand. The hazard function was described as the product of a baseline hazard function and the time-independent effects of age at first calving, heterosis, proportion of breed, period of last calving relative to herdmates, and TOP; a time-dependent effect of herd-year was also included. The influence of TOP on functional longevity was assessed by adjusting true longevity for the time-independent effects of production values as well as the time-dependent effects of deviation of milk, fat, and protein yield within contemporary group. All analyses were stratified by breed, and separate analyses were carried out for registered or commercial herds. All TOP were significantly related to true and functional longevity. Obvious differences existed in the relative influence of individual TOP on longevity in registered or commercial herds. Of the individual TOP describing the physical characteristics of the cow, the udder-related TOP exhibited the largest influence on functional longevity. Farmer opinion explained the largest proportion of variation in true and functional longevity among cows. In commercial herds, the risk of culling in cows with very low farmer opinion was 1.5 to 2.0 times that in cows with average or high farmer opinion.

Niemann-Pick type C disease in two affected sisters: ocular motor recordings and brain-stem neuropathology.

Two sisters with Niemann-Pick disease type C were examined: the brain in one sister, who had died, was examined, and eye movements in the other, surviving sister were recorded. Ocular motor recordings showed marked slowing of vertical saccades with relative sparing of horizontal saccades, pursuit, and the vestibulo-ocular reflex. Neuropathological findings included glial fibrillary lesions in the area of the posterior commissure and neuronal loss in the rostral interstitial nucleus of the MLF with preservation of the interstitial nucleus of Cajal and ocular motor complex. These neuropathologic findings correlate well with our current understanding of the anatomy and physiology of the supranuclear control of vertical gaze.

A TL/OSL emission spectrometer extension of the Risø reader.

The integration of a low cost, compact sized spectrometer with the Risø reader is described. The luminescence light emitted by the sample is transmitted by an optical fibre onto a fixed entrance slit of a spectrograph. The light is measured with a high sensitivity 2048-element CCD-linear array detector (Avantes PC2000) sensitive in the UV-VIS region. The CCD array has a low readout noise and a photon sensitivity of 86 photons per count. Examples are given of both thermally and optically stimulated 3-D spectra showing the luminescence spectra as a function of temperature and time respectively. Spectra from CaF2:Tm (TLD-300) chips could be distinguished from the background (2 SD) at a 0.7 Gy dose level.

High-dose cyclophosphamide without stem-cell rescue for refractory CIDP.

Four patients with chronic inflammatory demyelinating polyneuropathy (CIDP) who were refractory to conventional treatment were treated with high-dose cyclophosphamide (200 mg/kg over 4 days). All improved in functional status and muscle strength. Nerve conduction studies improved in three of four. Other immunomodulatory medications have been discontinued. High-dose cyclophosphamide can be given safely to patients with CIDP and patients with disease persistence after standard therapy may have a response that lasts for over 3 years and results in long-term disease remission.

Inferior division third nerve paresis from an orbital dural arteriovenous malformation.

Isolated inferior division third nerve palsies are rare. The authors report a patient with an isolated, pupil-involving inferior division third cranial nerve palsy from an intraorbital dural arteriovenous malformation. Despite spontaneous thrombosis of the malformation, the third nerve palsy persisted. To the authors' knowledge, this is the first case report of an inferior division third nerve palsy caused by an orbital dural arteriovenous malformation.

Estimation of heritabilities and correlations associated with milk color traits.

The objective of this study was to estimate the genetic parameters associated with milk color traits of dairy cattle. The data consisted of test day records of 9516 first lactation dairy cows and the records of 6358 of these cows that went on to produce a second lactation. Friesians, Jerseys, and crossbred cows were included in the data. Test day records included measures of milk, fat, and protein as well as milk color measured as absorbance at 450 nm. From these measurements, fat color and beta-carotene yield were calculated. Analyses were performed both within and across breeds. Jerseys produced more beta-carotene than did Friesians, and milk and fat from Jerseys had more intense color. Lactation model estimates for the heritabilities of milk color traits ranged from 0.33 to 0.44 (across breed), 0.40 to 0.49 (Friesians), and 0.17 to 0.31 (Jerseys). In all analyses, the heritability estimates associated with beta-carotene yield were lower than the estimates associated with the color of milk or fat. Genetic correlations between beta-carotene yield and the production traits were positive, but genetic correlations between fat color and production traits were generally negative. Genetic correlations between milk color and milk and protein yields were negative, and the correlations with fat yield were close to zero.

Simultaneous and consecutive administration of nutrients in parenteral nutrition.

In seven patients, six with Crohn's disease and one with pancreatitis, two methods of parenteral nutrition were compared: the partial consecutive administration of the components of a parenteral nutrition regimen versus the administration of all nutrients simultaneously. With respect to the consecutive regimen, the simultaneous infusion regimen gave an improvement in the nitrogen balance of 13% and a decrease in urinary lactic acid of about 50%. Urinary excretion of alpha-amino nitrogen, glucose, and fructose was very small in both cases but was slightly lower during the simultaneous infusion regimen. The improvement in the nitrogen balance attained with the simultaneous infusion regimen can be explained by the fact that infused nutrients, especially carbohydrates, cause fewer metabolic disturbances. The simultaneous infusion regimen has three other advantages. The patients rarely complain of headache and nausea, the infusion regimen is markedly simplified and the risk of contamination when nutrients are added to the infusion bottles in the ward is considerably diminished.

Cerebellar form of progressive multifocal leukoencephalopathy (PML).

A case of progressive multifocal leukoencephalopathy (PML) with selective involvement of cerebellum and brain stem is compared with nine other published cases. Recognition of PML presenting with ataxia before cerebral manifestations is stressed especially, since promising results with some antiviral drugs have been claimed.