Accuracy of high-density genotype imputation in Japanese Black cattle

Genotype imputation facilitates the identification of missing genotypes on a high-density array using low-density arrays and has great potential for reducing genotyping costs for cattle populations. However, the imputation quality varies across breeds, which have different effective population sizes. Therefore, the accuracy of genotype imputation must be evaluated in each breed. The Japanese Black cattle population has a unique genetic background, and this study aimed to investigate different factors affecting imputation quality in this population. A total of 1368 animals were genotyped using the Illumina BovineHD BeadChip, and the accuracy of imputation was evaluated using information from four lower density arrays. The extent of linkage disequilibrium for this population was relatively higher than that in other beef breeds but lower than that in dairy breeds. The accuracy of arrays with more than 20 000 single nucleotide polymorphisms (SNPs) was similar to or higher than that of lower density arrays. In addition, the minor allele frequency of SNPs in the reference population affected the accuracy. The accuracy increased as the size of the reference population increased, up to 400 animals, beyond which there was little increase. A higher genetic relationship between the reference and test populations increased imputation accuracy. These results indicate that high imputation accuracy can be achieved using high-density arrays, having enough reference animals and including relatives in the reference population.

Ultraviolet-nanoimprinted packaged metasurface thermal emitters for infrared CO2 sensing

Packaged dual-band metasurface thermal emitters integrated with a resistive membrane heater were manufactured by ultraviolet (UV) nanoimprint lithography followed by monolayer lift-off based on a soluble UV resist, which is mass-producible and cost-effective. The emitters were applied to infrared CO2 sensing. In this planar Au/Al2O3/Au metasurface emitter, orthogonal rectangular Au patches are arrayed alternately and exhibit nearly perfect blackbody emission at 4.26 and 3.95 μm necessary for CO2 monitoring at the electric power reduced by 31%. The results demonstrate that metasurface infrared thermal emitters are almost ready for commercialization.

Optical characterization of In-flushed InAs/GaAs quantum dots emitting a broadband spectrum with multiple peaks at ~1 μm

We investigated optical properties of In-flushed InAs quantum dots (QDs) grown on a GaAs substrate by molecular beam epitaxy. By using the In-flush technique for setting the height of self-assembled InAs QDs, we have tuned the emission wavelength of InAs QDs to the ~1 μm regime, which can be utilized as a non-invasive and deeply penetrative probe for biological and medical imaging systems. The controlled emission exhibited a broadband spectrum comprising multiple peaks with an interval of approximately 30 meV. We examined the origin of the multiple peaks using spectral and time-resolved photoluminescence, and concluded that it is attributed to monolayer step fluctuations in the height of the In-flushed QDs. This feature can be advantageous for realizing a broadband light source centered at the ~1 μm regime, which is especially suitable for the non-invasive cross-sectional biological and medical imaging system known as optical coherence tomography.

Overcoming metal-induced fluorescence quenching on plasmo-photonic metasurfaces coated by a self-assembled monolayer

A schematic energy diagram of the present fluorescence (FL)-enhancing process including nonradiative (NR) paths that a self-assembled monolayer (SAM) blocks is presented.

Experimental investigation of double-groove grating satisfying total internal reflection condition

We experimentally demonstrate a TiO(2) double-groove grating coupler with two different groove widths on a SiO(2) substrate in the visible region. Tolerance investigations based on Bloch-mode profiles in the grating and coupling strengths between the Bloch modes and diffraction orders reveal that the transmission performance is robust when one of the paired ridges is narrow enough (60 nm and less) considering a typical nanofabrication accuracy. Moreover, the ridge shape affects weakly the transmission performance due to the non-resonance operation of our dielectric device. Such tolerance investigations together with current nanofabrication technology enable us to accomplish a 70% efficiency for coupling the normal incident light into the + 1st order transmission diffraction satisfying the total internal reflection condition at a 640 nm wavelength of operation.

Tunable enhanced 0th-order transmission in a metal-dielectric hole array covered with a subwavelength liquid crystal layer

We demonstrate tunable, enhanced 0th-order transmission through a metal-dielectric nanohole array device with a subwavelength-thick liquid crystal (LC) layer. The LC filled the nanoholes and formed a subwavelength covering layer, which is then capped by a top cover layer. The wavelength where the transmittance dip associated with the LC occurs is determined by the anisotropic refractive-index component of the LC, which is normal to the surface of the hole array. A low-refractive-index cover layer suppresses unwanted higher-order diffraction, which results in an enhancement of the 0th-order transmission, which is closely related to laterally propagating surface plasmon polaritons. The proposed design is expected to help realize tunable plasmonic devices with high optical transmittance.

Impact of molecular mutations on treatment response to DNMT inhibitors in myelodysplasia and related neoplasms

We hypothesized that specific molecular mutations are important biomarkers for response to DNA methyltransferase inhibitors (DNMT inhibitors) and may have prognostic value in patients with myelodysplastic syndromes (MDS). Mutational analysis was performed in 92 patients with MDS and related disorders who received 5-azacytidine (n=55), decitabine (n=26) or both (n=11). Mutational status was correlated with overall response rate (ORR), progression-free survival (PFS) and overall survival (OS) by univariate and multivariate analysis. Risk stratification models were created. TET2, DNMT3A, IDH1/IDH2, ASXL1, CBL, RAS and SF3B1 mutations were found in 18, 9, 8, 26, 3, 2 and 13% of patients, respectively. In multivariate analysis, TET2(MUT) and/or DNMT3A(MUT) (P=0.03), platelets > or = 100 × 10(9)/l (P=0.007) and WBC<3.0 × 10(9)/l (P=0.03) were independent predictors of better response. TET2(MUT) and/or DNMT3A(MUT) (P=0.04) status was also independently prognostic for improved PFS, as were good or intermediate cytogenetic risk (P<0.0001), age<60 (P=0.0001), treatment with both 5-azacytidine and decitabine (P=0.02) and hemoglobin > or = 10 g/dl (P=0.01). Better OS was associated with ASXL1(WT) (P=0.008) and SF3B1(MUT) (P=0.01), and, similar to PFS, cytogenetic risk (P=0.0002), age (P=0.02) and hemoglobin (P=0.04). These data support the role of molecular mutations as predictive biomarkers for response and survival in MDS patients treated with DNMT inhibitors.

Multiple mechanisms deregulate EZH2 and histone H3 lysine 27 epigenetic changes in myeloid malignancies

Polycomb repressive complex 2 (PRC2) is involved in trimethylation of histone H3 lysine 27 (H3K27), chromatin condensation and transcriptional repression. The silencing function of PRC2 complex is mostly attributed to its intrinsic activity for methylating H3K27. Unlike in B-cell lymphomas, enhancer of zeste homolog 2 (EZH2) mutations in myeloid malignancies are inactivating/hypomorphic. When we assessed the mutational status in myeloid malignancies (N=469 cases examined), we found EZH2 and EED/SUZ12 mutations in 8% and 3.3% of cases, respectively. In addition to mutant cases, reduced EZH2 expression was also found in 78% cases with hemizygous deletion (-7/del7q cases involving EZH2 locus) and 41% of cases with diploid chromosome 7, most interestingly cases with spliceosomal mutations (U2AF1/SRSF2 mutations; 63% of cases). EZH2 mutations were characterized by decreased H3K27 trimethylation and increased chromatin relaxation at specific gene loci accompanied by higher transcriptional activity. One of the major downstream target is HOX gene family, involved in the regulation of stem cell self-renewal. HOXA9 was found to be overexpressed in cases with decreased EZH2 expression either by EZH2/spliceosomal mutations or because of -7/del7q. In summary, our results suggest that loss of gene repression through a variety of mutations resulting in reduced H3K27 trimethylation may contribute to leukemogenesis.

Wavefront control by stacked metal-dielectric hole array with variable hole shapes

A stacked metal-dielectric hole array (SHA) containing rectangular holes whose shape gradually varies in-plane is proposed as a means of achieving wavefront control. The dependence of the transmitted phase on the frequency can be tuned by the hole shape, in particular the length of the sides that are normal to the incident polarization. The combination of periodic holes along the polarization direction and the gradual change in hole shape normal to the polarization direction produce an inclined wavefront for 1-dimensional beam steering. An in-plane phase difference of 0.6π using an SHA with a thickness of one-sixth of the wavelength has been experimentally demonstrated.

Optical rectification effect due to surface plasmon polaritons at normal incidence in a nondiffraction regime

We carried out an experimental and numerical investigation of photoinduced voltage at normal incidence in the nondiffraction regime, which was not predicted to occur by the simple momentum conservation model. We prepared two samples: one having space inversion symmetry and the other without this feature. At normal incidence in the nondiffraction regime, we observed a finite signal only for the asymmetric structure. We found that surface plasmon polaritons (SPPs) are excited by the signal and are attributed to the origin of the voltage. We also evaluated the radiation force of light by using the Maxwell stress tensor and found that pressure of light and not shear force is mainly induced in the structure due to the asymmetric excitation of SPPs.

Transmission phase control by stacked metal-dielectric hole array with two-dimensional geometric design

Transmission phase control is experimentally demonstrated using stacked metal-dielectric hole arrays with a two-dimensional geometric design. The transmission phase varies drastically with small frequency shifts due to structural resonances. Laterally propagating surface plasmon polaritons excited by the periodic hole array roughly determine the resonance frequency, whereas localized resonances in each hole determine the dispersion. The transmission phase at various frequencies is directly evaluated using interferometric microscopy, and the formation of an inclined wavefront is demonstrated using a beam steering element in which the hole shapes gradually change in-plane from square to circular.

Intracerebral microinjection of interleukin-4/interleukin-13 reduces β-amyloid accumulation in the ipsilateral side and improves cognitive deficits in young amyloid precursor protein 23 mice

We previously reported that the anti-inflammatory cytokine interleukin (IL)-4 induced selective clearance of oligomeric β-amyloid (Aβ(1-42)) in rat primary type 2 microglial cells. For the present study, we investigated whether IL-4 and IL-13 could activate microglial cells to induce Aβ clearance in vivo and improve cognitive deficits in APP23 mice, which are amyloid precursor protein transgenic mice. We administered an intracerebral microinjection of a mixture of IL-4 and IL-13 or of saline vehicle into one hemisphere of APP23 mice and their wild-type littermates, 4.5 and 9 months old, after which we evaluated the effects of these treatments on spatial learning and memory by Morris Water Maze test and on accumulated amounts of Aβ. The cytokine injection significantly improved memory deficits of 4.5-month-old APP23 mice, but did not do so in 9-month-old APP23 mice, even though similar Aβ reductions were observed in both age groups of APP23 mice in the ipsilateral neocortex. The cytokine injection improved memory impairment of 9-month-old wild-type (WT) mice in the probe trial. Immunohistochemical analysis of the 4.5-month-old APP23 mice revealed the presence of increased numbers of microglial cells at 2 days after the cytokine injection. In addition to induced CD36 expression in the activated microglia, increased expression of neprilysin, mainly in neurons, suggested that the cytokines improved the cognitive deficits via degradation and clearance of intra- and extraneuronal Aβ peptides, of buffer-extractable nonplaque form. Double immunostaining also revealed that most of the activated microglia had the M2-like phenotype. This unique mechanism of IL-4/IL-13-induced clearance of Aβ may provide an additional strategy to prevent and/or cure Alzheimer's disease at early stage.

CBL mutation-related patterns of phosphorylation and sensitivity to tyrosine kinase inhibitors

Recurrent homozygous CBL-inactivating mutations in myeloid malignancies decrease ubiquitin ligase activity that inactivates SRC family kinases (SFK) and receptor tyrosine kinases (RTK). However, the most important SFK and RTK affected by these mutations, and hence, the most important therapeutic targets, have not been clearly characterized. We compared SFK and RTK pathway activity and inhibitors in acute myeloid leukemia cell lines containing homozygous R420Q mutation (GDM-1), heterozygous deletion (MOLM13) and wild-type (WT) CBL (THP1, U937). As expected with CBL loss, GDM-1 displayed high KIT expression and granulocyte-macrophage colony-stimulating factor (GM-CSF) hypersensitivity. Ectopic expression of WT CBL decreased GDM-1 proliferation but not cell lines with WT CBL. GDM-1, but not the other cell lines, was highly sensitive to growth inhibition by dasatinib (dual SFK and RTK inhibitor, LD50 50 nM); there was less or no selective inhibition of GDM-1 growth by sunitinib (RTK inhibitor), imatinib (ABL, KIT inhibitor), or PP2 (SFK inhibitor). Phosphoprotein analysis identified phosphorylation targets uniquely inhibited by dasatinib treatment of GDM-1, including a number of proteins in the KIT and GM-CSF receptor pathways (for example, KIT Tyr721, STAT3 Tyr705). In conclusion, the promiscuous effects of CBL loss on SFK and RTK signaling appear to be best targeted by dual SFK and RTK inhibition.

Influence of micro-joints formed between spheres in coupled-resonator optical waveguide

Light propagation is simulated through coupled-resonator optical waveguides (CROWs) composed of seven transparent polystyrene microspheres, including micro-joints formed between the spheres. In nanojet-induced mode (NIM) light propagation, the micro-joints increased the optical coupling between microspheres drastically, and the light confinement by individual microspheres weakened as the micro-joint diameter increases. These results suggest that we can control NIM light propagation by changing the micro-joint diameter; this amounts to a nanojet throttle valve.

Nano/microstructural effect of hydroxyapatite nanocrystals on hepatocyte cell aggregation and adhesion

Hepatocyte cell aggregation and adhesion to HAp nanocrystals covered with SU-8 polymer micropatterns by nano/microfabrication techniques is demonstrated. The surface roughness and wettability of the HAp nanocrystals are significantly different from those of the SU-8 polymer. QCM-D and microscopic observation clearly reveal that the cells realize the surface properties to form aggregation and preferentially adhere to the HAp nanocrystals at 2 h after seeding, indicating the importance of the microstructures as well as the interfacial phenomena at a nanometer scale.

Cavity formation on an optical nanofiber using focused ion beam milling technique

We present the experimental realization of nanofiber Bragg grating (NFBG) by drilling periodic nano-grooves on a subwavelength-diameter silica fiber using focused ion beam milling technique. Using such NFBG structures we have realized nanofiber cavity systems. The typical finesse of such nanofiber cavity is F ∼ 20 - 120 and the on-resonance transmission is ∼ 30 - 80%. Moreover the structural symmetry of such NFBGs results in polarization-selective modes in the nanofiber cavity. Due to the strong confinement of the field in the guided mode, such a nanofiber cavity can become a promising workbench for cavity QED.

Enhanced clinical mastitis resistance in Holsteins with a FEZL p.Gly105(12_13) polymorphism

Mastitis is a common infectious disease of the mammary gland and a major problem in the dairy industry. We previously reported that forebrain embryonic zinc finger-like (FEZL) encoding a stretch of 12 glycines (p.Gly105[12]) instead of 13 glycines (p.Gly105[13]) is associated with a lower somatic cell score (SCS) in a family derived from Walkway Chief Mark. Here we report that the p.Gly105[12] allele is associated with a significantly decreased incidence of clinical mastitis in a large Holstein population. We genotyped the FEZL polymorphism in 918 randomly collected Holstein sires, and investigated the effect of the polymorphism on the estimated breeding value (EBV) for SCS and milk, fat, solids-not-fat, and protein yield, and on the number of cattle with clinical mastitis among daughters derived from these sires. The average EBV for SCS among sires carrying the heterozygous p.Gly105[12] was significantly lower than that among sires carrying the homozygous p.Gly105[13], whereas we found no unfavorable effects of this polymorphism on EBV for milk, fat, solids-not-fat, and protein yield. The proportion of cows with clinical mastitis derived from sires carrying heterozygous p.Gly105[12] was significantly lower than that of daughters derived from sires carrying the homozygous p.Gly105[13]. Thus, selection of sires carrying p.Gly105[12] could be beneficial in the dairy industry by reducing the incidence of mastitis.

Identification of an FBN1 mutation in bovine Marfan syndrome-like disease

Mutations in the gene encoding fibrillin-1 (FBN1), a component of the extracellular microfibril, cause Marfan syndrome (MFS). Frequent observation of cattle with a normal withers height, but lower body weight than age-matched normal cattle, was recently reported among cattle sired by phenotypically normal Bull A, in Japanese Black cattle. These cattle also showed other characteristic features similar to the clinical phenotype of human MFS, such as a long phalanx proximalis, oval face and crystalline lens cloudiness. We first screened a paternal half-sib family comprising 36 affected and 10 normal offspring of Bull A using the BovineSNP50 BeadChip (illumina). Twenty-two microsatellite markers mapped to a significant region on BTA10 were subsequently genotyped on the family. The bovine Marfan syndrome-like disease (MFSL) was mapped onto BTA10. As FBN1 is located in the significant region, FBN1 was sequenced in Bull A, and three affected and one normal cattle. A G>A mutation at the intron64 splicing accepter site (c.8227-1G>A) was detected in 31 of 36 affected animals (84.7%). The c.8227-1G>A polymorphism was not found in 20 normal offspring of Bull A or in 93 normal cattle unrelated to Bull A. The mutation caused a 1-base shift of the intron64 splicing accepter site to the 3' direction, and a 1-base deletion in processed mRNA. This 1-base deletion creates a premature termination codon, and a 125-amino acid shorter Fibrillin-1 protein is produced from the mutant mRNA. We therefore conclude that the c.8227-1G>A mutation is causative for MFSL. Furthermore, it was suggested that Bull A exhibited germline mosaicism for the mutation, and that the frequency of the mutant sperm was 14.9%.

The SNP c.1326T>G in the non-SMC condensin I complex, subunit G (NCAPG) gene encoding a p.Ile442Met variant is associated with an increase in body frame size at puberty in cattle

Recently, we had located a bovine carcass weight QTL, CW-2, to a 591-kb interval on BTA6 and have identified the SNP c.1326T>G in the NCAPG (non-SMC condensin I complex, subunit G) gene that leads to the amino acid change p.Ile442Met in the NCAPG protein, which is a candidate causative variation. Here, we examined the association of the NCAPG:c.1326T>G locus with linear skeletal measurements of growth-associated traits during adolescence, which is a period of intensive growth, using two historically and geographically distant cattle populations: 792 Japanese Black steers and 161 F(2) bulls of an experimental cross from Charolais and German Holstein. In both populations, the SNP NCAPG:c.1326T>G was associated with each component of body frame size: height, length and width at puberty. The associations of CW-2 with height- and length-associated traits were observed at an earlier growth period compared to the associations with thickness- and width-associated traits, indicating that the primary effect of the CW-2 QTL may possibly be exerted on skeletal growth. The significant associations of the NCAPG:c.1326T>G locus with growth-associated skeletal measurements are similar to the effects of the syntenic region on human chromosome 4 that are associated with adult height in humans, supporting the hypothesis that CW-2 is analogous to the human locus and pointing to a conserved growth-associated locus or chromosomal region present in both species.