Sequenced-based GWAS for linear classification traits in Belgian Blue beef cattle reveals new coding variants in genes regulating body size in mammals

BACKGROUND

Cohorts of individuals that have been genotyped and phenotyped for genomic selection programs offer the opportunity to better understand genetic variation associated with complex traits. Here, we performed an association study for traits related to body size and muscular development in intensively selected beef cattle. We leveraged multiple trait information to refine and interpret the significant associations.

RESULTS

After a multiple-step genotype imputation to the sequence-level for 14,762 Belgian Blue beef (BBB) cows, we performed a genome-wide association study (GWAS) for 11 traits related to muscular development and body size. The 37 identified genome-wide significant quantitative trait loci (QTL) could be condensed in 11 unique QTL regions based on their position. Evidence for pleiotropic effects was found in most of these regions (e.g., correlated association signals, overlap between credible sets (CS) of candidate variants). Thus, we applied a multiple-trait approach to combine information from different traits to refine the CS. In several QTL regions, we identified strong candidate genes known to be related to growth and height in other species such as LCORL-NCAPG or CCND2. For some of these genes, relevant candidate variants were identified in the CS, including three new missense variants in EZH2, PAPPA2 and ADAM12, possibly two additional coding variants in LCORL, and candidate regulatory variants linked to CCND2 and ARMC12. Strikingly, four other QTL regions associated with dimension or muscular development traits were related to five (recessive) deleterious coding variants previously identified.

CONCLUSIONS

Our study further supports that a set of common genes controls body size across mammalian species. In particular, we added new genes to the list of those associated with height in both humans and cattle. We also identified new strong candidate causal variants in some of these genes, strengthening the evidence of their causality. Several breed-specific recessive deleterious variants were identified in our QTL regions, probably as a result of the extreme selection for muscular development in BBB cattle.

An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants

We report the generation of an organism-wide catalog of 976,813 cis-acting regulatory elements for the bovine detected by the assay for transposase accessible chromatin using sequencing (ATAC-seq). We regroup these regulatory elements in 16 components by nonnegative matrix factorization. Correlation between the genome-wide density of peaks and transcription start sites, correlation between peak accessibility and expression of neighboring genes, and enrichment in transcription factor binding motifs support their regulatory potential. Using a previously established catalog of 12,736,643 variants, we show that the proportion of single-nucleotide polymorphisms mapping to ATAC-seq peaks is higher than expected and that this is owing to an approximately 1.3-fold higher mutation rate within peaks. Their site frequency spectrum indicates that variants in ATAC-seq peaks are subject to purifying selection. We generate eQTL data sets for liver and blood and show that variants that drive eQTL fall into liver- and blood-specific ATAC-seq peaks more often than expected by chance. We combine ATAC-seq and eQTL data to estimate that the proportion of regulatory variants mapping to ATAC-seq peaks is approximately one in three and that the proportion of variants mapping to ATAC-seq peaks that are regulatory is approximately one in 25. We discuss the implication of these findings on the utility of ATAC-seq information to improve the accuracy of genomic selection.

Influence of the concentrate inclusion level in a grass silage-based diet on hepatic transcriptomic profiles in Holstein-Friesian dairy cows in early lactation

Excessive negative energy balance in early lactation is linked to an increased disease risk but may be mitigated by appropriate nutrition. The liver plays central roles in both metabolism and immunity. Hepatic transcriptomic profiles were compared between 3 dietary groups in each of 40 multiparous and 18 primiparous Holstein-Friesian cows offered isonitrogenous grass silage-based diets with different proportions of concentrates: (1) low concentrate (LC, 30% concentrate + 70% grass silage); (2) medium concentrate (MC, 50% concentrate + 50% grass silage), or (3) high concentrate (HC, 70% concentrate + 30% grass silage). Liver biopsies were taken from all cows at around 14 d in milk for RNA sequencing, and blood metabolites were measured. The sequencing data were analyzed separately for primiparous and multiparous cows using CLC Genomics Workbench V21 (Qiagen Digital Insights), focusing on comparisons between HC and LC groups. More differentially expressed genes (DEG) were seen between the primiparous cows receiving HC versus LC diets than for multiparous cows (597 vs. 497), with only 73 in common, indicating differential dietary responses. Multiparous cows receiving the HC diet had significantly higher circulating glucose and insulin-like growth factor-1 and lower urea than those receiving the LC diet. In response to HC, only the multiparous cows produced more milk. In these animals, bioinformatic analysis indicated expression changes in genes regulating fatty acid metabolism and biosynthesis (e.g., ACACA, ELOVL6, FADS2), increased cholesterol biosynthesis (e.g., CYP7A1, FDPS, HMGCR), downregulation in hepatic AA synthesis (e.g., GPT, GCLC, PSPH, SHMT2), and decreased expression of acute phase proteins (e.g., HP, LBP, SAA2). The primiparous cows on the HC diet also downregulated genes controlling AA metabolism and synthesis (e.g., CTH, GCLC, GOT1, ODC1, SHMT2) but showed higher expression of genes indicative of inflammation (e.g., CCDC80, IL1B, S100A8) and fibrosis (e.g., LOX, LUM, PLOD2). This potentially adverse response to a HC diet in physically immature animals warrants further investigation.

High-resolution structural variants catalogue in a large-scale whole genome sequenced bovine family cohort data

BACKGROUND

Structural variants (SVs) are chromosomal segments that differ between genomes, such as deletions, duplications, insertions, inversions and translocations. The genomics revolution enabled the discovery of sub-microscopic SVs via array and whole-genome sequencing (WGS) data, paving the way to unravel the functional impact of SVs. Recent human expression QTL mapping studies demonstrated that SVs play a disproportionally large role in altering gene expression, underlining the importance of including SVs in genetic analyses. Therefore, this study aimed to generate and explore a high-quality bovine SV catalogue exploiting a unique cattle family cohort data (total 266 samples, forming 127 trios).

RESULTS

We curated 13,731 SVs segregating in the population, consisting of 12,201 deletions, 1,509 duplications, and 21 multi-allelic CNVs (> 50-bp). Of these, we validated a subset of copy number variants (CNVs) utilising a direct genotyping approach in an independent cohort, indicating that at least 62% of the CNVs are true variants, segregating in the population. Among gene-disrupting SVs, we prioritised two likely high impact duplications, encompassing ORM1 and POPDC3 genes, respectively. Liver expression QTL mapping results revealed that these duplications are likely causing altered gene expression, confirming the functional importance of SVs. Although most of the accurately genotyped CNVs are tagged by single nucleotide polymorphisms (SNPs) ascertained in WGS data, most CNVs were not captured by individual SNPs obtained from a 50K genotyping array.

CONCLUSION

We generated a high-quality SV catalogue exploiting unique whole genome sequenced bovine family cohort data. Two high impact duplications upregulating the ORM1 and POPDC3 are putative candidates for postpartum feed intake and hoof health traits, thus warranting further investigation. Generally, CNVs were in low LD with SNPs on the 50K array. Hence, it remains crucial to incorporate CNVs via means other than tagging SNPs, such as investigation of tagging haplotypes, direct imputation of CNVs, or direct genotyping as done in the current study. The SV catalogue and the custom genotyping array generated in the current study will serve as valuable resources accelerating utilisation of full spectrum of genetic variants in bovine genomes.

Comparing the transcriptome of developing native and iPSC-derived mouse retinae by single cell RNA sequencing

We report the generation and analysis of single-cell RNA-Seq data (> 38,000 cells) from mouse native retinae and induced pluripotent stem cell (iPSC)-derived retinal organoids at four matched stages of development spanning the emergence of the major retinal cell types. We combine information from temporal sampling, visualization of 3D UMAP manifolds, pseudo-time and RNA velocity analyses, to show that iPSC-derived 3D retinal organoids broadly recapitulate the native developmental trajectories. However, we observe relaxation of spatial and temporal transcriptome control, premature emergence and dominance of photoreceptor precursor cells, and susceptibility of dynamically regulated pathways and transcription factors to culture conditions in retinal organoids. We demonstrate that genes causing human retinopathies are enriched in cell-type specifying genes and identify a subset of disease-causing genes with expression profiles that are highly conserved between human retinae and murine retinal organoids. This study provides a resource to the community that will be useful to assess and further improve protocols for ex vivo recapitulation and study of retinal development.

Discovery of ^{39}Na

The new isotope ^{39}Na, the most neutron-rich sodium nucleus observed so far, was discovered at the RIKEN Nishina Center Radioactive Isotope Beam Factory using the projectile fragmentation of an intense ^{48}Ca beam at 345  MeV/nucleon on a beryllium target. Projectile fragments were separated and identified in flight with the large-acceptance two-stage separator BigRIPS. Nine ^{39}Na events have been unambiguously observed in this work and clearly establish the particle stability of ^{39}Na. Furthermore, the lack of observation of ^{35,36}Ne isotopes in this experiment significantly improves the overall confidence that ^{34}Ne is the neutron dripline nucleus of neon. These results provide new key information to understand nuclear binding and nuclear structure under extremely neutron-rich conditions. The newly established stability of ^{39}Na has a significant impact on nuclear models and theories predicting the neutron dripline and also provides a key to understanding the nuclear shell property of ^{39}Na at the neutron number N=28, which is normally a magic number.

β-Delayed One and Two Neutron Emission Probabilities Southeast of ^{132}Sn and the Odd-Even Systematics in r-Process Nuclide Abundances

The β-delayed one- and two-neutron emission probabilities (P_{1n} and P_{2n}) of 20 neutron-rich nuclei with N≥82 have been measured at the RIBF facility of the RIKEN Nishina Center. P_{1n} of ^{130,131}Ag, ^{133,134}Cd, ^{135,136}In, and ^{138,139}Sn were determined for the first time, and stringent upper limits were placed on P_{2n} for nearly all cases. β-delayed two-neutron emission (β2n) was unambiguously identified in ^{133}Cd and ^{135,136}In, and their P_{2n} were measured. Weak β2n was also detected from ^{137,138}Sn. Our results highlight the effect of the N=82 and Z=50 shell closures on β-delayed neutron emission probability and provide stringent benchmarks for newly developed macroscopic-microscopic and self-consistent global models with the inclusion of a statistical treatment of neutron and γ emission. The impact of our measurements on r-process nucleosynthesis was studied in a neutron star merger scenario. Our P_{1n} and P_{2n} have a direct impact on the odd-even staggering of the final abundance, improving the agreement between calculated and observed Solar System abundances. The odd isotope fraction of Ba in r-process-enhanced (r-II) stars is also better reproduced using our new data.

First Application of Mass Measurements with the Rare-RI Ring Reveals the Solar r-Process Abundance Trend at A=122 and A=123

The Rare-RI Ring (R3) is a recently commissioned cyclotronlike storage ring mass spectrometer dedicated to mass measurements of exotic nuclei far from stability at Radioactive Isotope Beam Factory (RIBF) in RIKEN. The first application of mass measurement using the R3 mass spectrometer at RIBF is reported. Rare isotopes produced at RIBF-^{127}Sn, ^{126}In, ^{125}Cd, ^{124}Ag, ^{123}Pd-were injected in R3. Masses of ^{126}In, ^{125}Cd, and ^{123}Pd were measured whereby the mass uncertainty of ^{123}Pd was improved. This is the first reported measurement with a new storage ring mass spectrometry technique realized at a heavy-ion cyclotron and employing individual injection of the preidentified rare nuclei. The latter is essential for the future mass measurements of the rarest isotopes produced at RIBF. The impact of the new ^{123}Pd result on the solar r-process abundances in a neutron star merger event is investigated by performing reaction network calculations of 20 trajectories with varying electron fraction Y_{e}. It is found that the neutron capture cross section on ^{123}Pd increases by a factor of 2.2 and β-delayed neutron emission probability, P_{1  n}, of ^{123}Rh increases by 14%. The neutron capture cross section on ^{122}Pd decreases by a factor of 2.6 leading to pileup of material at A=122, thus reproducing the trend of the solar r-process abundances. The trend of the two-neutron separation energies (S_{2n}) was investigated for the Pd isotopic chain. The new mass measurement with improved uncertainty excludes large changes of the S_{2n} value at N=77. Such large increase of the S_{2n} values before N=82 was proposed as an alternative to the quenching of the N=82 shell gap to reproduce r-process abundances in the mass region of A=112-124.

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle

Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a prominent CM resistance QTL located on chromosome 6 was reported in various dairy cattle breeds. Nevertheless, the biological mechanism underpinning this QTL has been lacking. Herein, we mapped, fine-mapped, and discovered the putative causal variant underlying this CM resistance QTL in the Dutch dairy cattle population. We identified a ~12 kb multi-allelic copy number variant (CNV), that is in perfect linkage disequilibrium with a lead SNP, as a promising candidate variant. By implementing a fine-mapping and through expression QTL mapping, we showed that the group-specific component gene (GC), a gene encoding a vitamin D binding protein, is an excellent candidate causal gene for the QTL. The multiplicated alleles are associated with increased GC expression and low CM resistance. Ample evidence from functional genomics data supports the presence of an enhancer within this CNV, which would exert cis-regulatory effect on GC. We observed that strong positive selection swept the region near the CNV, and haplotypes associated with the multiplicated allele were strongly selected for. Moreover, the multiplicated allele showed pleiotropic effects for increased milk yield and reduced fertility, hinting that a shared underlying biology for these effects may revolve around the vitamin D pathway. These findings together suggest a putative causal variant of a CM resistance QTL, where a cis-regulatory element located within a CNV can alter gene expression and affect multiple economically important traits.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO-Virgo Observing Run

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO-Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10^{-15}. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

Probing the Symmetry Energy with the Spectral Pion Ratio

Many neutron star properties, such as the proton fraction, reflect the symmetry energy contributions to the equation of state that dominate when neutron and proton densities differ strongly. To constrain these contributions at suprasaturation densities, we measure the spectra of charged pions produced by colliding rare isotope tin (Sn) beams with isotopically enriched Sn targets. Using ratios of the charged pion spectra measured at high transverse momenta, we deduce the slope of the symmetry energy to be 42<L<117  MeV. This value is slightly lower but consistent with the L values deduced from a recent measurement of the neutron skin thickness of ^{208}Pb.

Relationships between metabolic profiles and gene expression in liver and leukocytes of dairy cows in early lactation

Homeorhetic mechanisms assist dairy cows in the transition from pregnancy to lactation. Less successful cows develop severe negative energy balance (NEB), placing them at risk of metabolic and infectious diseases and reduced fertility. We have previously placed multiparous Holstein Friesian cows from 4 herds into metabolic clusters, using as biomarkers measurements of plasma nonesterified fatty acids, β-hydroxybutyrate, glucose and IGF-1 collected at 14 and 35 d in milk (DIM). This study characterized the global transcriptomic profiles of liver and circulating leukocytes from the same animals to determine underlying mechanisms associated with their metabolic and immune function. Liver biopsy and whole-blood samples were collected around 14 DIM for RNA sequencing. All cows with available RNA sequencing data were placed into balanced (BAL, n = 44), intermediate (n = 44), or imbalanced (IMBAL, n = 19) metabolic cluster groups. Differential gene expression was compared between the 3 groups using ANOVA, but only the comparison between BAL and IMBAL cows is reported. Pathway analysis was undertaken using DAVID Bioinformatic Resources (https://david.ncifcrf.gov/). Milk yields did not differ between BAL and IMBAL cows but dry matter intake was less in IMBAL cows and they were in greater energy deficit at 14 DIM (-4.48 v -11.70 MJ/d for BAL and IMBAL cows). Significantly differentially expressed pathways in hepatic tissue included AMPK signaling, glucagon signaling, adipocytokine signaling, and insulin resistance. Genes involved in lipid metabolism and cholesterol transport were more highly expressed in IMBAL cows but IGF1 and IGFALS were downregulated. Leukocytes from BAL cows had greater expression of histones and genes involved in nucleosomes and cell division. Leukocyte expression of heat shock proteins increased in IMBAL cows, suggesting an unfolded protein response, and several key genes involved in immune responses to pathogens were upregulated (e.g., DEFB13, HP, OAS1Z, PTX3, and TLR4). Differentially expressed genes upregulated in IMBAL cows in both tissues included CD36, CPT1, KFL11, and PDK4, all central regulators of energy metabolism. The IMBAL cows therefore had greater difficulty maintaining glucose homeostasis and had dysregulated hepatic lipid metabolism. Their energy deficit was associated with a reduced capacity for cell division and greater evidence of stress responses in the leukocyte population, likely contributing to an increased risk of infectious disease.

Mapping of a New Deformation Region around ^{62}Ti

We performed the first direct mass measurements of neutron-rich scandium, titanium, and vanadium isotopes around the neutron number 40 at the RIKEN RI Beam Factory using the time-of-flight magnetic-rigidity technique. The atomic mass excesses of ^{58-60}Sc, ^{60-62}Ti, and ^{62-64}V were measured for the first time. The experimental results show that the two-neutron separation energies in the vicinity of ^{62}Ti increase compared to neighboring nuclei. This shows that the masses of Ti isotopes near N=40 are affected by the Jahn-Teller effect. Therefore, a development of Jahn-Teller stabilization appears below the Cr isotopes, and the systematics in Sc, Ti, and V isotopes suggest that ^{62}Ti is located close to the peak of the Jahn-Teller effect.

Genetic parameters for conception rate and milk production traits within and across Holstein herds with different housing types and feeding systems during the first 3 lactations

The housing types (HST) in which dairy cows are kept and the feeding systems (FDS) used differ among farmers in Japan. Here, we investigated the genetic relationships among conception rate at first insemination (CR) and milk production traits (PROD) during the first 3 lactations of Holstein cows by using a multiple-trait model that considered the trait values of herds with different HST [tiestall (TSL) barn, freestall (FS) barn, or grazing (GZ)] and FDS as separate traits. Milk production and conception records of Holstein cows in the Hokkaido region of Japan (283,611 records for first lactation, 253,902 for second, and 181,197 for third) were analyzed. We categorized herds with TSL or FS into 2 types of FDS for cows: separate feeding (SF) of roughage plus concentrate or feeding of total mixed ration, in which roughage and concentrates were mixed before feeding. The PROD analyzed were cumulative milk, fat, and protein yields within 305 d and lactation persistency, which we defined as the difference between milk yields at 240 and 60 d in milk. We estimated the heritabilities for CR or PROD within each HST or HST × FDS group and the genetic correlations between these traits within each group or across different groups within each lactation by using a 3-HST (TSL, FS, and GZ) × 2-trait (CR and each PROD) or 2-HST (TSL and FS) × 2-FDS × 2-trait animal model. Heritability estimates for CR in GZ were higher than those in TSL or FS, and genetic correlations for CR between GZ and TSL or FS barns were weaker than those between TSL and FS barns. In addition, genetic correlations between CR and PROD in GZ were weaker than those in TSL and FS barns. In the comparison among the 4 HST × FDS except GZ, heritability estimates for CR in FS × SF were higher than those in the others, and genetic correlations for CR between FS × SF and the other systems were relatively weak. These results indicated that differences in the production system for Holstein cows influence genotypic effects in terms of the cows' ability to conceive and the genetic relationships between fertility traits and milk production traits.

Two-Neutron Halo is Unveiled in ^{29}F

We report the measurement of reaction cross sections (σ_{R}^{ex}) of ^{27,29}F with a carbon target at RIKEN. The unexpectedly large σ_{R}^{ex} and derived matter radius identify ^{29}F as the heaviest two-neutron Borromean halo to date. The halo is attributed to neutrons occupying the 2p_{3/2} orbital, thereby vanishing the shell closure associated with the neutron number N=20. The results are explained by state-of-the-art shell model calculations. Coupled-cluster computations based on effective field theories of the strong nuclear force describe the matter radius of ^{27}F but are challenged for ^{29}F.

How Different is the Core of ^{25}F from ^{24}O_{g.s.} ?

The structure of a neutron-rich ^{25}F nucleus is investigated by a quasifree (p,2p) knockout reaction at 270A  MeV in inverse kinematics. The sum of spectroscopic factors of π0d_{5/2} orbital is found to be 1.0±0.3. However, the spectroscopic factor with residual ^{24}O nucleus being in the ground state is found to be only 0.36±0.13, while those in the excited state is 0.65±0.25. The result shows that the ^{24}O core of ^{25}F nucleus significantly differs from a free ^{24}O nucleus, and the core consists of ∼35% ^{24}O_{g.s.}. and ∼65% excited ^{24}O. The result may infer that the addition of the 0d_{5/2} proton considerably changes neutron structure in ^{25}F from that in ^{24}O, which could be a possible mechanism responsible for the oxygen dripline anomaly.

Halo Structure of the Neutron-Dripline Nucleus ^{19}B

The heaviest bound isotope of boron ^{19}B has been investigated using exclusive measurements of its Coulomb dissociation, into ^{17}B and two neutrons, in collisions with Pb at 220  MeV/nucleon. Enhanced electric dipole (E1) strength is observed just above the two-neutron decay threshold with an integrated E1 strength of B(E1)=1.64±0.06(stat)±0.12(sys)  e^{2} fm^{2} for relative energies below 6 MeV. This feature, known as a soft E1 excitation, provides the first firm evidence that ^{19}B has a prominent two-neutron halo. Three-body calculations that reproduce the energy spectrum indicate that the valence neutrons have a significant s-wave configuration and exhibit a dineutronlike correlation.

g Factor of the ^{99}Zr (7/2^{+}) Isomer: Monopole Evolution in the Shape-Coexisting Region

The gyromagnetic factor of the low-lying E=251.96(9)  keV isomeric state of the nucleus ^{99}Zr was measured using the time-dependent perturbed angular distribution technique. This level is assigned a spin and parity of J^{π}=7/2^{+}, with a half-life of T_{1/2}=336(5)  ns. The isomer was produced and spin aligned via the abrasion-fission of a ^{238}U primary beam at RIKEN RIBF. A magnetic moment |μ|=2.31(14)μ_{N} was deduced showing that this isomer is not single particle in nature. A comparison of the experimental values with interacting boson-fermion model IBFM-1 results shows that this state is strongly mixed with a main νd_{5/2} composition. Furthermore, it was found that monopole single-particle evolution changes significantly with the appearance of collective modes, likely due to type-II shell evolution.

Swelling of Doubly Magic ^{48}Ca Core in Ca Isotopes beyond N=28

Interaction cross sections for ^{42-51}Ca on a carbon target at 280  MeV/nucleon have been measured for the first time. The neutron number dependence of derived root-mean-square matter radii shows a significant increase beyond the neutron magic number N=28. Furthermore, this enhancement of matter radii is much larger than that of the previously measured charge radii, indicating a novel growth in neutron skin thickness. A simple examination based on the Fermi-type distribution, and mean field calculations point out that this anomalous enhancement of the nuclear size beyond N=28 results from an enlargement of the core by a sudden increase in the surface diffuseness of the neutron density distribution, which implies the swelling of the bare ^{48}Ca core in Ca isotopes beyond N=28.

Fragmentation of Single-Particle Strength around the Doubly Magic Nucleus ^{132}Sn and the Position of the 0f_{5/2} Proton-Hole State in ^{131}In

Spectroscopic factors of neutron-hole and proton-hole states in ^{131}Sn and ^{131}In, respectively, were measured using one-nucleon removal reactions from doubly magic ^{132}Sn at relativistic energies. For ^{131}In, a 2910(50)-keV γ ray was observed for the first time and tentatively assigned to a decay from a 5/2^{-} state at 3275(50) keV to the known 1/2^{-} level at 365 keV. The spectroscopic factors determined for this new excited state and three other single-hole states provide first evidence for a strong fragmentation of single-hole strength in ^{131}Sn and ^{131}In. The experimental results are compared to theoretical calculations based on the relativistic particle-vibration coupling model and to experimental information for single-hole states in the stable doubly magic nucleus ^{208}Pb.

Prospects for observing and localizing gravitational-wave transients with Advanced LIGO, Advanced Virgo and KAGRA

We present our current best estimate of the plausible observing scenarios for the Advanced LIGO, Advanced Virgo and KAGRA gravitational-wave detectors over the next several years, with the intention of providing information to facilitate planning for multi-messenger astronomy with gravitational waves. We estimate the sensitivity of the network to transient gravitational-wave signals for the third (O3), fourth (O4) and fifth observing (O5) runs, including the planned upgrades of the Advanced LIGO and Advanced Virgo detectors. We study the capability of the network to determine the sky location of the source for gravitational-wave signals from the inspiral of binary systems of compact objects, that is binary neutron star, neutron star-black hole, and binary black hole systems. The ability to localize the sources is given as a sky-area probability, luminosity distance, and comoving volume. The median sky localization area (90% credible region) is expected to be a few hundreds of square degrees for all types of binary systems during O3 with the Advanced LIGO and Virgo (HLV) network. The median sky localization area will improve to a few tens of square degrees during O4 with the Advanced LIGO, Virgo, and KAGRA (HLVK) network. During O3, the median localization volume (90% credible region) is expected to be on the order of 10 5 , 10 6 , 10 7 Mpc 3 for binary neutron star, neutron star-black hole, and binary black hole systems, respectively. The localization volume in O4 is expected to be about a factor two smaller than in O3. We predict a detection count of 1 - 1 + 12 ( 10 - 10 + 52 ) for binary neutron star mergers, of 0 - 0 + 19 ( 1 - 1 + 91 ) for neutron star-black hole mergers, and 17 - 11 + 22 ( 79 - 44 + 89 ) for binary black hole mergers in a one-calendar-year observing run of the HLV network during O3 (HLVK network during O4). We evaluate sensitivity and localization expectations for unmodeled signal searches, including the search for intermediate mass black hole binary mergers.

Cross-section measurement in the reactions of 136Xe on proton, deuteron and carbon

The isotopic production cross sections for the reactions of 136Xe induced by proton, deuteron and carbon at 168 MeV/u were obtained by using the inverse kinematics technique at RIKEN Radioactive Isotope Beam Factory. The target dependence of the cross sections was investigated systematically. It was found that for the light-mass products, the cross sections on carbon are larger than those on deuteron and proton. The measured cross sections on proton were compared with the previous data at higher reaction energies to study the energy dependence. The experimental results were compared with the theoretical calculations including both the intranuclear cascade and evaporation processes using PHITS and with the EPAX and SPACS empirical parameterizations.

Location of the Neutron Dripline at Fluorine and Neon

A search for the heaviest isotopes of fluorine, neon, and sodium was conducted by fragmentation of an intense ^{48}Ca beam at 345  MeV/nucleon with a 20-mm-thick beryllium target and identification of isotopes in the large-acceptance separator BigRIPS at the RIKEN Radioactive Isotope Beam Factory. No events were observed for ^{32,33}F, ^{35,36}Ne, and ^{38}Na and only one event for ^{39}Na after extensive running. Comparison with predicted yields excludes the existence of bound states of these unobserved isotopes with high confidence levels. The present work indicates that ^{31}F and ^{34}Ne are the heaviest bound isotopes of fluorine and neon, respectively. The neutron dripline has thus been experimentally confirmed up to neon for the first time since ^{24}O was confirmed to be the dripline nucleus nearly 20 years ago. These data provide new keys to understanding the nuclear stability at extremely neutron-rich conditions.

Improved Value for the Gamow-Teller Strength of the ^{100}Sn Beta Decay

A record number of ^{100}Sn nuclei was detected and new isotopic species toward the proton dripline were discovered at the RIKEN Nishina Center. Decay spectroscopy was performed with the high-efficiency detector arrays WAS3ABi and EURICA. Both the half-life and the β-decay end point energy of ^{100}Sn were measured more precisely than the literature values. The value and the uncertainty of the resulting strength for the pure 0^{+}→1^{+} Gamow-Teller decay was improved to B_{GT}=4.4_{-0.7}^{+0.9}. A discrimination between different model calculations was possible for the first time, and the level scheme of ^{100}In is investigated further.

Proton Shell Evolution below ^{132}Sn: First Measurement of Low-Lying β-Emitting Isomers in ^{123,125}Ag

The β-delayed γ-ray spectroscopy of neutron-rich ^{123,125}Ag isotopes is investigated at the Radioactive Isotope Beam Factory of RIKEN, and the long-predicted 1/2^{-} β-emitting isomers in ^{123,125}Ag are identified for the first time. With the new experimental results, the systematic trend of energy spacing between the lowest 9/2^{+} and 1/2^{-} levels is extended in Ag isotopes up to N=78, providing a clear signal for the reduction of the Z=40 subshell gap in Ag towards N=82. Shell-model calculations with the state-of-the-art V_{MU} plus M3Y spin-orbit interaction give a satisfactory description of the low-lying states in ^{123,125}Ag. The tensor force is found to play a crucial role in the evolution of the size of the Z=40 subshell gap. The observed inversion of the single-particle levels around ^{123}Ag can be well interpreted in terms of the monopole shift of the π1g_{9/2} orbitals mainly caused by the increasing occupation of ν1h_{11/2} orbitals.

First Observation of ^{20}B and ^{21}B

The most neutron-rich boron isotopes ^{20}B and ^{21}B have been observed for the first time following proton removal from ^{22}N and ^{22}C at energies around 230  MeV/nucleon. Both nuclei were found to exist as resonances which were detected through their decay into ^{19}B and one or two neutrons. Two-proton removal from ^{22}N populated a prominent resonancelike structure in ^{20}B at around 2.5 MeV above the one-neutron decay threshold, which is interpreted as arising from the closely spaced 1^{-},2^{-} ground-state doublet predicted by the shell model. In the case of proton removal from ^{22}C, the ^{19}B plus one- and two-neutron channels were consistent with the population of a resonance in ^{21}B 2.47±0.19  MeV above the two-neutron decay threshold, which is found to exhibit direct two-neutron decay. The ground-state mass excesses determined for ^{20,21}B are found to be in agreement with mass surface extrapolations derived within the latest atomic-mass evaluations.

Extraction of the Landau-Migdal Parameter from the Gamow-Teller Giant Resonance in ^{132}Sn

The key parameter to discuss the possibility of the pion condensation in nuclear matter, i.e., the so-called Landau-Migdal parameter g^{'}, was extracted by measuring the double-differential cross sections for the (p,n) reaction at 216  MeV/u on a neutron-rich doubly magic unstable nucleus, ^{132}Sn with the quality comparable to data taken with stable nuclei. The extracted strengths for Gamow-Teller (GT) transitions from ^{132}Sn leading to ^{132}Sb exhibit the GT giant resonance (GTR) at the excitation energy of 16.3±0.4(stat)±0.4(syst)  MeV with the width of Γ=4.7±0.8  MeV. The integrated GT strength up to E_{x}=25  MeV is S_{GT}^{-}=53±5(stat)_{-10}^{+11}(syst), corresponding to 56% of Ikeda's sum rule of 3(N-Z)=96. The present result accurately constrains the Landau-Migdal parameter as g^{'}=0.68±0.07, thanks to the high sensitivity of the GTR energy to g^{'}. In combination with previous studies on the GTR for ^{90}Zr and ^{208}Pb, the result of this work shows the constancy of this parameter in the nuclear chart region with (N-Z)/A=0.11 to 0.24 and A=90 to 208.

Magic Nature of Neutrons in ^{54}Ca: First Mass Measurements of ^{55-57}Ca

We perform the first direct mass measurements of neutron-rich calcium isotopes beyond neutron number 34 at the RIKEN Radioactive Isotope Beam Factory by using the time-of-flight magnetic-rigidity technique. The atomic mass excesses of ^{55-57}Ca are determined for the first time to be -18650(160), -13510(250), and -7370(990)  keV, respectively. We examine the emergence of neutron magicity at N=34 based on the new atomic masses. The new masses provide experimental evidence for the appearance of a sizable energy gap between the neutron 2p_{1/2} and 1f_{5/2} orbitals in ^{54}Ca, comparable to the gap between the neutron 2p_{3/2} and 2p_{1/2} orbitals in ^{52}Ca. For the ^{56}Ca nucleus, an open-shell property in neutrons is suggested.

Discovery of ^{60}Ca and Implications For the Stability of ^{70}Ca

The discovery of the important neutron-rich nucleus _{20}^{60}Ca_{40} and seven others near the limits of nuclear stability is reported from the fragmentation of a 345  MeV/u ^{70}Zn projectile beam on ^{9}Be targets at the radioactive ion-beam factory of the RIKEN Nishina Center. The produced fragments were analyzed and unambiguously identified using the BigRIPS two-stage in-flight separator. The eight new neutron-rich nuclei discovered, ^{47}P, ^{49}S, ^{52}Cl, ^{54}Ar, ^{57}K, ^{59,60}Ca, and ^{62}Sc, are the most neutron-rich isotopes of the respective elements. In addition, one event consistent with ^{59}K was registered. The results are compared with the drip lines predicted by a variety of mass models and it is found that the models in best agreement with the observed limits of existence in the explored region tend to predict the even-mass Ca isotopes to be bound out to at least ^{70}Ca.

Universal geometric frustration in pyrochlores

Materials with the pyrochlore/fluorite structure have diverse technological applications, from magnetism to nuclear waste disposal. Here we report the observation of structural instability present in the pyrochlores A₂Zr₂O₆Oʹ (A = Pr, La) and Yb₂Ti₂O₆Oʹ, that exists despite ideal stoichiometry, ideal cation-ordering, the absence of lone pair effects, and a lack of magnetic order. Though these materials appear to have good long-range order, local structure probes find displacements, of the order of 0.01 nm, within the pyrochlore framework. The pattern of displacements of the A₂Oʹ sublattice mimics the entropically-driven fluxional motions characteristic of and well-known in the silica mineral β-cristobalite. The universality of such displacements within the pyrochlore structure adds to the known structural diversity and explains the extreme sensitivity to composition found in quantum spin ices and the lack of ferroelectric behavior in pyrochlores.

The family of pyrochlore complex oxides includes many materials of fundamental or practical interest, such as spin ices and dielectrics. Trump et al. show that flexibility of the pyrochlores’ structure leads to local displacements that explain some of their unusual physical properties.

Excitation of the Isovector Spin Monopole Resonance via the Exothermic ^{90}Zr(^{12}N,^{12}C) Reaction at 175 MeV/u

The (^{12}N, ^{12}C) charge-exchange reaction at 175  MeV/u was developed as a novel probe for studying the isovector spin giant monopole resonance (IVSMR), whose properties are important for better understanding the bulk properties of nuclei and asymmetric nuclear matter. This probe, now available through the production of ^{12}N as a secondary rare-isotope beam, is exothermic, is strongly absorbed at the surface of the target nucleus, and provides selectivity for spin-transfer excitations. All three properties enhance the excitation of the IVSMR compared to other, primarily light-ion, probes, which have been used to study the IVSMR thus far. The ^{90}Zr(^{12}N,^{12}C) reaction was measured and the excitation energy spectra up to about 70 MeV for both the spin-transfer and non-spin-transfer channels were deduced separately by tagging the decay by γ emission from the ^{12}C ejectile. Besides the well-known Gamow-Teller and isobaric analog transitions, a clear signature of the IVSMR was identified. By comparing with the results from light-ion reactions on the same target nucleus and theoretical predictions, the suitability of this new probe for studying the IVSMR was confirmed.

Spectroscopy of Pionic Atoms in ^{122}Sn(d,^{3}He) Reaction and Angular Dependence of the Formation Cross Sections

We observed the atomic 1s and 2p states of π^{-} bound to ^{121}Sn nuclei as distinct peak structures in the missing mass spectra of the ^{122}Sn(d,^{3}He) nuclear reaction. A very intense deuteron beam and a spectrometer with a large angular acceptance let us achieve a potential of discovery, which includes the capability of determining the angle-dependent cross sections with high statistics. The 2p state in a Sn nucleus was observed for the first time. The binding energies and widths of the pionic states are determined and found to be consistent with previous experimental results of other Sn isotopes. The spectrum is measured at finite reaction angles for the first time. The formation cross sections at the reaction angles between 0° and 2° are determined. The observed reaction-angle dependence of each state is reproduced by theoretical calculations. However, the quantitative comparison with our high-precision data reveals a significant discrepancy between the measured and calculated formation cross sections of the pionic 1s state.

Effect of Left Ventricular Assistance on Sympathetic Tone

To determine the effect of left ventricular assist device (LVAD) pumping on sympathetic tone, renal sympathetic nerve activity (RSNA) was detected in acute animal experiments.

Our TH-7B pneumatically driven, sac-type ventricular assist device was used in 7 adult mongrel dogs. RSNA was detected by the use of bipolar electrodes attached to the left renal sympathetic nerve. RSNA was amplified and integrated by use of an R-C integrator circuit. The area of the integrated nerve discharge per unit time was calculated in the computer system and expressed as RSNA per unit time.

During LVAD pumping, RSNA decreased with increase in blood pressure, with an increase in pulmonary artery flow, and with a decrease in left atrial pressure. These data suggest that LVAD has an effect on the sympathetic nervous system which is mediated by the aortic and cardiopulmonary baroreflex system.

Effects of a high-fat diet on superoxide anion generation and membrane fluidity in liver mitochondria in rats

Background

Obesity is a primary factor of lifestyle-related diseases, and the age of its onset has decreased. The reactive oxygen species (ROS), the superoxide anion, is generated in the mitochondrial electron transport chain and the damage it induces in cells may be a contributing factor to obesity-related lifestyle diseases. In the present study, the influence of the ingestion of a high-fat diet (HFD) on superoxide anion generation in rat liver mitochondria (Mt) and membrane fluidity was investigated.

Methods

Male Wistar rats were fed a normal diet (ND, n = 6) or HFD (n = 6). Liver Mt were isolated and oxygen consumption, superoxide anion production (the adrenaline method), and membrane fluidity (the spin label method) were measured.

Results

After 11 weeks, body weights and abdominal circumferences were higher in the HFD group than in the ND group. Mt oxygen consumption was higher in the HFD group than in the ND group. Superoxide anion production was significantly lower in the HFD group than in the ND group, while no significant changes were observed in membrane fluidity.

Conclusion

Although rats developed diet-induced obesity, it did not reach the level of disease development. The promotion of lipid metabolism appeared to reduce superoxide anion production, but did not influence membrane fluidity. While superoxide anion damages cells as an oxidative stress, ROS and superoxide dismutase are essential signaling molecules in the body. The present results suggest that the continuous ingestion of a HFD impairs Mt and induces disease development.

Estimation of the following Cardiac Output Using Sympathetic Tone and Hemodynamics for the Control of a Total Artificial Heart

A sympathetic neurogram is potentially useful for the development of a real time total artificial heart (TAH) control system. We used sympathetic tone and hemodynamic derivatives to estimate the following cardiac output in acute animal experiments using adult mongrel dogs. Moving averages of the mean left atrial pressure and mean aortic pressure were used as parameters of the preload and afterload, respectively. Renal sympathetic nerve activity (RSNA) was employed as a parameter of sympathetic tone. Equations for the following cardiac output were calculated using multiple linear regression analysis of the time series data. A significant correlation was observed between the estimated and following measured cardiac output. These results suggest the potential usefulness of the sympathetic neurogram for the real time TAH automatic control system.

Vagal Nerve Activity and the High Frequency Peak of the Heart Rate Variability

For the Quality of life (QOL) of patients with an artificial heart system, monitoring an information of the cardiovascular control system may be important. We have been evaluating the autonomic nervous system for that purpose. Recently, fluctuations in hemodynamic parameters including heart rate variability (HRV) were evaluated by means of spectral analysis and nonlinear mathematical analysis. Respiratory wavers in HRV were thought ro reflect ongoing information of the parasympathetic nerve activity. Is it true? In order to confirm this hypothesis, we recorded vagal nerve activity directly in the chronic animal experiments. Six healthy adult goats were anesthetized with Halothene inhalation and thoracotomy were performed by the fourth lib resection during mechanical ventilation. Arterial blood pressure, right and left atrial pressures were continuously monitored with the catheter insertion. Cardiac output was measured by the electromagnetic flowmeter attached to the ascending aorta. After the chest was closed, incision was made to the left neck and left vagal nerve was separated. Stainless steel electrodes were inserted into the vagal nerve and fixed by the plasticizer. After the incision was closed, the goats were transferred to the cage and extubated after waking. Hemodynamic parameters and vagal nerve activity were measured in the awake condition. The results showed that clear observation of the autonomic nerve discharges were embodied by this experimental system. The vagal nerve discharges were synchronized with heart beat and respiration. The vagal nerve tonus was significantly influenced by the hemodynamic alteration. However in some condition, the respiratory wave was not always consistent with tonus of the vagal nerve activity, thus suggesting that we should check another information to evaluate the parasympathetic tone. We must continue this study to evaluate an autonomic nerve during artifical heart circulation.

Mayer Waves in Dogs with Total Artificial Heart

To assess the effect of a total artificial heart (TAH) on the autonomic nervous system a power spectral analysis of the hemodynamics in a TAH animal was done by the maximum entropy method. Two pneumatically driven sac-type ventricular assist devices were implanted as total biventricular bypass (BVB) in adult mongrel dogs to compare the differences between natural heart and TAH. Once the BVB was pumping, the natural heart was electrically fibrillated to constitute the BVB-type TAH model. In the arterial pressure waveform in animals with TAH, respiratory waves were not changed (97.7±24.6%) though Mayer waves were significantly decreased (47.5 ± 22.6%) compared with the animal with a natural heart. These results suggest that prosthetic hemodynamics in the TAH animal affect fluctuations in the cardiovascular system.

Monitoring System for the Totally Implantable Ventricular Assist System by Use of Sensors for Virtual Reality

For the development of the totally implantable artificial organs, it is an important problem to monitor the conditions of the implantable devices, especially when used in clinical cases. In this study, we used position sensors for the 3-dimensional (3-D) virtual reality (VR) system monitor an implantable artificial heart. The sensors used in the experiments were 3-space Fastrak (Polhemus, USA). The position sensors using electro-magnetic forces were attached to the inner actuating zone. Sensitivity of the position sensors was in the order of around 0.8 mm. By use of these VR position sensors, we could easily detect the six degrees of freedom as x,y,z, and pitch, yaw, roll of these sensors. Experimental evaluation using a model circulation loop and healthy adult goats was performed. Experimental results suggest that our newly developed implantable sensors for monitoring the implantable artificial heart system were useful for sensing driving condition, thus possibly useful for the implantable devices for clinical usage.