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Masuda Y, Fukumori R, Tomoshige M, Sarentonglaga B, Sugino T, Nagao Y. Effect of feeding calf starter with calcium salts of medium-chain fatty acids on the growth and metabolic hormones in calves. J Anim Sci 2024; 102:skae166. [PMID: 38875129 PMCID: PMC11221069 DOI: 10.1093/jas/skae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 06/13/2024] [Indexed: 06/16/2024] Open
Abstract
We investigated the effects of a calf starter supplemented with calcium salts of medium-chain fatty acids (MCFA-Ca) on growth and plasma hormone concentration in calves. Twelve Holstein calves were randomly assigned to two dietary groups (without supplementation [CON] and supplemented with MCFA-Ca [MCFA]) from 4 d of age. Calves were fed 1.0 kg/d of milk replacer until 5 wk of age and were completely weaned at 7 wk of age. Calves in the MCFA group received a calf starter containing 1% MCFA-Ca. dry matter intake (DMI) was measured daily, and body weight was measured weekly. Rumen fluid was collected at 13 wk of age to measure pH and volatile fatty acid concentration. Preprandial blood samples were collected weekly to measure the basal plasma hormone and metabolite concentrations. At 4, 8, and 13 wk of age, peri-prandial blood samples were collected every 30 min, from 60 min before feeding to 120 min after feeding, to observe metabolic responses to feeding. In addition, insulin sensitivity was assessed using euglycemic-hyperinsulinemic clamps at 4, 8, and 13 wk of age in three calves from each treatment. There were no differences in starter and hay DMI between the treatments. However, the average daily gain (ADG) after weaning was higher in the MCFA group than in the CON group. Weekly changes in plasma parameters did not differ between the treatments. Plasma concentrations of preprandial ghrelin and postprandial total ketone bodies at 13 wk of age were higher in the MCFA group than in the CON group. At 8 wk of age, peri-prandial plasma insulin concentrations were lower in the MCFA group than in the CON group. There were no differences between the treatments in terms of insulin sensitivity. The present study suggested that feeding weaning calves MCFA-Ca increases the ADG during the postweaning period, which may be mediated by endocrine signals, such as enhanced ghrelin secretion and decreased insulin secretion, without altering insulin sensitivity.
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Ijuin T, Iuchi T, Tawaratsumida H, Masuda Y, Tokushige A, Maeda S, Taniguchi N. Development of a novel animal model of rotator cuff tear arthropathy replicating clinical features of progressive osteoarthritis with subchondral bone collapse. OSTEOARTHRITIS AND CARTILAGE OPEN 2023; 5:100389. [PMID: 37560389 PMCID: PMC10407568 DOI: 10.1016/j.ocarto.2023.100389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/11/2023] Open
Abstract
OBJECTIVE To establish an animal model of modified cuff tear arthropathy (mCTA) in order to better replicate the pathophysiology associated with rotator cuff tear-induced humeral head collapse. DESIGN mCTA was induced by transection of the rotator cuff, the long head of the biceps brachii (LHB), and superior half of the joint capsule in the right shoulder of 12-week-old rats; the left shoulder underwent sham surgery. The severity of CTA was quantitated using the Murine Shoulder Arthritis Score (MSAS). The trabecular bone of the humeral head and metaphysis was analyzed using bone histomorphometry. The expression of proinflammatory cytokines and catabolic enzymes was evaluated immunohistochemically. RESULTS In the mCTA model, the MSAS increased starting from 2 weeks after induction, and there was notable subchondral bone collapse with fibrous cells at 4 weeks. The mCTA cartilage exhibited positive staining for TNF-α, IL-1β/6, MMP-3/13, and ADAMTS5. The trabecular bone volume was reduced not only in the subchondral bone but also in the metaphysis of the humeri, and bone resorption was enhanced in these areas. In the collapsed subchondral bone, both bone formation and resorption were increased. The fibrous cells showed expression of TNF-α, IL-6, and MMP-13, along with specific markers of mesenchymal stem cells. Furthermore, the fibrous cells showed osteoblastic characteristics (RUNX2-positive) and expressed RANKL. CONCLUSIONS The LHB and the capsuloligamentous complex are critical stabilizers of the glenohumeral joint, serving to prevent the advancement of CTA following massive rotator cuff tears. Fibrous cells appear to play a role in the humeral head bone resorption.
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Steyn Y, Lawlor T, Masuda Y, Tsuruta S, Legarra A, Lourenco D, Misztal I. Nonparallel genome changes within subpopulations over time contributed to genetic diversity within the US Holstein population. J Dairy Sci 2023; 106:2551-2572. [PMID: 36797192 DOI: 10.3168/jds.2022-21914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 10/03/2022] [Indexed: 02/16/2023]
Abstract
Maintaining genetic variation in a population is important for long-term genetic gain. The existence of subpopulations within a breed helps maintain genetic variation and diversity. The 20,990 genotyped animals, representing the breeding animals in the year 2014, were identified as the sires of animals born after 2010 with at least 25 progenies, and females measured for type traits within the last 2 yr of data. K-means clustering with 5 clusters (C1, C2, C3, C4, and C5) was applied to the genomic relationship matrix based on 58,990 SNP markers to stratify the selected candidates into subpopulations. The general higher inbreeding resulting from within-cluster mating than across-cluster mating suggests the successful stratification into genetically different groups. The largest cluster (C4) contained animals that were less related to each animal within and across clusters. The average fixation index was 0.03, indicating that the populations were differentiated, and allele differences across the subpopulations were not due to drift alone. Starting with the selected candidates within each cluster, a family unit was identified by tracing back through the pedigree, identifying the genotyped ancestors, and assigning them to a pseudogeneration. Each of the 5 families (F1, F2, F3, F4, and F5) was traced back for 10 generations, allowing for changes in frequency of individual SNPs over time to be observed, which we call allele frequencies change. Alternative procedures were used to identify SNPs changing in a parallel or nonparallel way across families. For example, markers that have changed the most in the whole population, markers that have changed differently across families, and genes previously identified as those that have changed in allele frequency. The genomic trajectory taken by each family involves selective sweeps, polygenic changes, hitchhiking, and epistasis. The replicate frequency spectrum was used to measure the similarity of change across families and showed that populations have changed differently. The proportion of markers that reversed direction in allele frequency change varied from 0.00 to 0.02 if the rate of change was greater than 0.02 per generation, or from 0.14 to 0.24 if the rate of change was greater than 0.005 per generation within each family. Cluster-specific SNP effects for stature were estimated using only females and applied to obtain indirect genomic predictions for males. Reranking occurs depending on SNP effects used. Additive genetic correlations between clusters show possible differences in populations. Further research is required to determine how this knowledge can be applied to maintain diversity and optimize selection decisions in the future.
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Ikeda K, Maezawa Y, Yonezawa T, Shimizu Y, Tashiro T, Kanai S, Sugaya N, Masuda Y, Inoue N, Niimi T, Masuya K, Mizuguchi K, Furuya T, Osawa M. DLiP-PPI library: An integrated chemical database of small-to-medium-sized molecules targeting protein-protein interactions. Front Chem 2023; 10:1090643. [PMID: 36700083 PMCID: PMC9868583 DOI: 10.3389/fchem.2022.1090643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/09/2022] [Indexed: 01/11/2023] Open
Abstract
Protein-protein interactions (PPIs) are recognized as important targets in drug discovery. The characteristics of molecules that inhibit PPIs differ from those of small-molecule compounds. We developed a novel chemical library database system (DLiP) to design PPI inhibitors. A total of 32,647 PPI-related compounds are registered in the DLiP. It contains 15,214 newly synthesized compounds, with molecular weight ranging from 450 to 650, and 17,433 active and inactive compounds registered by extracting and integrating known compound data related to 105 PPI targets from public databases and published literature. Our analysis revealed that the compounds in this database contain unique chemical structures and have physicochemical properties suitable for binding to the protein-protein interface. In addition, advanced functions have been integrated with the web interface, which allows users to search for potential PPI inhibitor compounds based on types of protein-protein interfaces, filter results by drug-likeness indicators important for PPI targeting such as rule-of-4, and display known active and inactive compounds for each PPI target. The DLiP aids the search for new candidate molecules for PPI drug discovery and is available online (https://skb-insilico.com/dlip).
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Hidaka R, Masuda Y, Ogawa K, Tanaka T, Kanazawa M, Suzuki K, Stading M, Iijima K, Matsuo K. Impact of the Comprehensive Awareness Modification of Mouth, Chewing and Meal (CAMCAM) Program on the Attitude and Behavior Towards Oral Health and Eating Habits as Well as the Condition of Oral Frailty: A Pilot Study. J Nutr Health Aging 2023; 27:340-347. [PMID: 37248757 DOI: 10.1007/s12603-023-1913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 03/29/2023] [Indexed: 05/31/2023]
Abstract
OBJECTIVES Preserving sufficient oral function and maintaining aadequate nutrition are essential for preventing physical frailty and the following long-term care. We recently developed the 6-month Comprehensive Awareness Modification of Mouth, Chewing And Meal (CAMCAM) program, in which participants gather monthly to learn about oral health and nutrition while eating a textured lunch together. This study examined whether the CAMCAM program could improve attitude and behavior towards oral health, mastication, and diet as well as ameliorate oral frailty in community-dwelling older adults. DESIGN Single-arm pre-post comparison study. SETTING AND PARTICIPANTS A total of 271 community-dwelling adults (72.3 ± 5.7 years of age; 159 women [58.7%]) in 4 Japanese municipalities were recruited, of which 249 participants (92%) were assessed at the final evaluation. INTERVENTION Participants gathered once a month at community centers to learn about oral health and nutrition while eating a "munchy" textured lunch containing proper nutrition. MEASUREMENTS Oral frailty, frailty, and eating behavior were evaluated with the Oral Frailty Index-8 (OFI-8), Kihon checklist (KCL), and CAMCAM checklist, respectively. Participants were divided into Oral frailty (OF) and Robust groups according to OFI-8 scores. The differences in KCL and CAMCAM checklist results between the OF and Robust groups were statistically tested along with changes in scores after the program. RESULTS KCL and CAMCAM checklist scores were significantly lower in the OF group at the initial assessment. OFI-8 and KCL findings were significantly improved in the OF group after completing the program (all P <0.05). Regarding the CAMCAM checklist, awareness of chewing improved significantly in the Robust group (P=0.009), with a similar tendency in the OF group (P=0.080). CONCLUSION The findings of this pilot study suggest that the CAMCAM program may improve both oral and systemic frailty in addition to attitudes towards chewing, oral health, and meals, especially in individuals with oral frailty. The CAMCAM program merits expansion as a community-based frailty prevention program.
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Steyn Y, Masuda Y, Tsuruta S, Lourenco D, Misztal I, Lawlor T. Identifying influential sires and distinct clusters of selection candidates based on genomic relationships to reduce inbreeding in the US Holstein. J Dairy Sci 2022; 105:9810-9821. [DOI: 10.3168/jds.2022-22143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/19/2022] [Indexed: 11/05/2022]
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Shimokawa K, Matsumoto K, Yokota H, Kobayashi E, Hirano Y, Masuda Y, Uno T. Anxiety relaxation during MRI with a patient-friendly audiovisual system. Radiography (Lond) 2022; 28:725-731. [PMID: 35428571 DOI: 10.1016/j.radi.2022.03.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 03/19/2022] [Accepted: 03/24/2022] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Many patients experience anxiety, not limited to claustrophobia, before magnetic resonance imaging (MRI) examination. We performed a non-randomized controlled trial to evaluate whether a patient-friendly audiovisual (AV) system in the MR scanner room reduces patient anxiety. METHODS We randomly selected 61 participants from outpatients who required brain MRI examination. Patients were informed that they could choose to undergo an MRI examination with a patient-friendly AV system (Ambient Experience, Philips Healthcare, Best, The Netherlands) or the standard system. To complete the MRI examination without affecting clinical practice, all patients who preferred the patient-friendly AV system were assigned to the preferring AV group. Patients who indicated that either system was acceptable were randomly assigned to the no preference but allocated AV group or control (using the standard system) groups. In both groups, state anxiety using the State-Trait Anxiety Inventory (STAI) was assessed before and after the MRI examination (A-State-before and A-State-after MRI, respectively). The changes in A-State-before and A-State-after MRI were categorized as follows: relieved high-state anxiety, no change in high-state anxiety, stable easiness, and intensified anxiety. RESULTS Among the 61 included patients, 19 were assigned to the preferring AV group, 20 to the no preference but allocated AV group, and 22 to the control group. There were no significant differences between the group. However, in patients with high-state anxiety before MRI, the preferring AV group and the no preference but allocated AV group, which used the patient-friendly AV system, relieved high-state anxiety by 63.6% (7 of 11 patients) and 81.8% (9 of 11 patients), respectively. In contrast, the control group using the standard system relieved high-level anxiety by only 42.9% (three out of seven patients). CONCLUSION The patient-friendly AV system may reduce anxiety in patients undergoing MRI examinations. IMPLICATIONS FOR PRACTICE The patient-friendly AV system may reduce anxiety in patients undergoing MRI examination by providing a more patient-centered MRI examination environment. These findings may help ameliorate negative perceptions associated with MRI examination.
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Tsuruta S, Lourenco D, Masuda Y, Lawlor T, Misztal I. Reducing computational cost of large-scale genomic evaluation by using indirect genomic prediction. JDS COMMUNICATIONS 2021; 2:356-360. [PMID: 36337117 PMCID: PMC9623783 DOI: 10.3168/jdsc.2021-0097] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/27/2021] [Indexed: 06/10/2023]
Abstract
Over half a million Holsteins are being genotyped annually in the United States. The computational cost of including all genotypes in single-step genomic (ssG)BLUP is high, although it is feasible to conduct large-scale genomic prediction using an efficient algorithm such as APY (algorithm for proven and young). An effective method to further reduce the computing cost could be the use of indirect genomic predictions (IGP) for genotyped animals when they have neither progeny nor phenotypes. These young genotyped animals have no effect on the other genotyped animals and could have their genomic prediction done indirectly. The main objective of this study was to calculate IGP for various groups of genotyped animals and investigate the reduction in computing time as well as bias and accuracy of the IGP. We compared IGP with genomic (G)EBV for 18 linear type traits in US Holsteins, including 2.3 million (M) genotyped animals. The full data set consisted of 10.9M records for 18 linear type traits up to 2018 calving, 13.6M animals in the pedigree, and 2.3M animals genotyped for 79K SNP. For IGP, ssGBLUP included all genotyped animals except those with neither progeny nor phenotypes by year from 2014 to 2018 (i.e., the target animals). The SNP marker effects were computed based on GEBV for genotyped animals that had progeny, or phenotypes, or both. Further, IGP were calculated for target genotyped animals in each year group. For all genotyped animal groups from 2014 to 2018, the coefficients of determination (R2) of a linear regression of GEBV on IGP were 0.960 for males and 0.954 for females for 18 traits on average. To reduce computing costs, the SNP marker effects were calculated based on GEBV from randomly selected genotyped animals from 15K to 60K. By randomly selecting a small number of genotyped animals, the computing time was dramatically reduced. As more genotyped animals were randomly selected to calculate SNP effects, R2 was higher (more accurate) and the regression coefficient was lower (more inflated IGP). In a practical genomic evaluation in US Holsteins, to get sufficient contributions from GEBV, 25K to 35K is a rational number of genotyped animals that can be randomly selected to compute SNP effects and obtain accurate and unbiased IGP. Considering the computing time and both unbiasedness and accuracy of IGP, genomic evaluation can be conducted separately in GEBV for genotyped animals with phenotypes or progeny and in IGP for young genotyped animals. This can be a practical solution when conducting a large-scale genomic evaluation and would enable more frequent evaluation at lower cost, especially when many genotyped animals have neither phenotypes nor progeny.
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Buaban S, Prempree S, Sumreddee P, Duangjinda M, Masuda Y. Genomic prediction of milk-production traits and somatic cell score using single-step genomic best linear unbiased predictor with random regression test-day model in Thai dairy cattle. J Dairy Sci 2021; 104:12713-12723. [PMID: 34538484 DOI: 10.3168/jds.2021-20263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 08/04/2021] [Indexed: 12/15/2022]
Abstract
Cow genotypes are expected to improve the accuracy of genomic estimated breeding values (GEBV) for young bulls in relatively small populations such as Thai Holstein-Friesian crossbred dairy cattle in Thailand. The objective of this study was to investigate the effect of cow genotypes on the predictive ability and individual accuracies of GEBV for young dairy bulls in Thailand. Test-day data included milk yield (n = 170,666), milk component traits (fat yield, protein yield, total solids yield, fat percentage, protein percentage, and total solids percentage; n = 160,526), and somatic cell score (n = 82,378) from 23,201, 82,378, and 13,737 (for milk yield, milk component traits, and SCS, respectively) cows calving between 1993 and 2017, respectively. Pedigree information included 51,128; 48,834; and 32,743 animals for milk yield, milk component traits, and somatic cell score, respectively. Additionally, 876, 868, and 632 pedigreed animals (for milk yield, milk component traits, and SCS, respectively) were genotyped (152 bulls and 724 cows), respectively, using Illumina Bovine SNP50 BeadChip. We cut off the data in the last 6 yr, and the validation animals were defined as genotyped bulls with no daughters in the truncated set. We calculated GEBV using a single-step random regression test-day model (SS-RR-TDM), in comparison with estimated breed value (EBV) based on the pedigree-based model used as the official method in Thailand (RR-TDM). Individual accuracies of GEBV were obtained by inverting the coefficient matrix of the mixed model equations, whereas validation accuracies were measured by the Pearson correlation between deregressed EBV from the full data set and (G)EBV predicted with the reduced data set. When only bull genotypes were used, on average, SS-RR-TDM increased individual accuracies by 0.22 and validation accuracies by 0.07, compared with RR-TDM. With cow genotypes, the additional increase was 0.02 for individual accuracies and 0.06 for validation accuracies. The inflation of GEBV tended to be reduced using cow genotypes. Genomic evaluation by SS-RR-TDM is feasible to select young bulls for the longitudinal traits in Thai dairy cattle, and the accuracy of selection is expected to be increased with more genotypes. Genomic selection using the SS-RR-TDM should be implemented in the routine genetic evaluation of the Thai dairy cattle population. The genetic evaluation should consider including genotypes of both sires and cows.
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Cesarani A, Masuda Y, Tsuruta S, Nicolazzi EL, VanRaden PM, Lourenco D, Misztal I. Genomic predictions for yield traits in US Holsteins with unknown parent groups. J Dairy Sci 2021; 104:5843-5853. [PMID: 33663836 DOI: 10.3168/jds.2020-19789] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/18/2020] [Indexed: 11/19/2022]
Abstract
The objective of this study was to assess the reliability and bias of estimated breeding values (EBV) from traditional BLUP with unknown parent groups (UPG), genomic EBV (GEBV) from single-step genomic BLUP (ssGBLUP) with UPG for the pedigree relationship matrix (A) only (SS_UPG), and GEBV from ssGBLUP with UPG for both A and the relationship matrix among genotyped animals (A22; SS_UPG2) using 6 large phenotype-pedigree truncated Holstein data sets. The complete data included 80 million records for milk, fat, and protein yields from 31 million cows recorded since 1980. Phenotype-pedigree truncation scenarios included truncation of phenotypes for cows recorded before 1990 and 2000 combined with truncation of pedigree information after 2 or 3 ancestral generations. A total of 861,525 genotyped bulls with progeny and cows with phenotypic records were used in the analyses. Reliability and bias (inflation/deflation) of GEBV were obtained for 2,710 bulls based on deregressed proofs, and on 381,779 cows born after 2014 based on predictivity (adjusted cow phenotypes). The BLUP reliabilities for young bulls varied from 0.29 to 0.30 across traits and were unaffected by data truncation and number of generations in the pedigree. Reliabilities ranged from 0.54 to 0.69 for SS_UPG and were slightly affected by phenotype-pedigree truncation. Reliabilities ranged from 0.69 to 0.73 for SS_UPG2 and were unaffected by phenotype-pedigree truncation. The regression coefficient of bull deregressed proofs on (G)EBV (i.e., GEBV and EBV) ranged from 0.86 to 0.90 for BLUP, from 0.77 to 0.94 for SS_UPG, and was 1.00 ± 0.03 for SS_UPG2. Cow predictivity ranged from 0.22 to 0.28 for BLUP, 0.48 to 0.51 for SS_UPG, and 0.51 to 0.54 for SS_UPG2. The highest cow predictivities for BLUP were obtained with the most extreme truncation, whereas for SS_UPG2, cow predictivities were also unaffected by phenotype-pedigree truncations. The regression coefficient of cow predictivities on (G)EBV was 1.02 ± 0.02 for SS_UPG2 with the most extreme truncation, which indicated the least biased predictions. Computations with the complete data set took 17 h with BLUP, 58 h with SS_UPG, and 23 h with SS_UPG2. The same computations with the most extreme phenotype-pedigree truncation took 7, 36, and 15 h, respectively. The SS_UPG2 converged in fewer rounds than BLUP, whereas SS_UPG took up to twice as many rounds. Thus, the ssGBLUP with UPG assigned to both A and A22 provided accurate and unbiased evaluations, regardless of phenotype-pedigree truncation scenario. Old phenotypes (before 2000 in this data set) did not affect the reliability of predictions for young selection candidates, especially in SS_UPG2.
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Tsuruta S, Lourenco DAL, Masuda Y, Misztal I, Lawlor TJ. Controlling bias in genomic breeding values for young genotyped bulls. J Dairy Sci 2019; 102:9956-9970. [PMID: 31495630 DOI: 10.3168/jds.2019-16789] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/16/2019] [Indexed: 11/19/2022]
Abstract
The objectives of this study were to investigate bias in genomic predictions for dairy cattle and to find a practical approach to reduce the bias. The simulated data included phenotypes, pedigrees, and genotypes, mimicking a dairy cattle population (i.e., cows with phenotypes and bulls with no phenotypes) and assuming selection by breeding values or no selection. With the simulated data, genomic estimated breeding values (GEBV) were calculated with a single-step genomic BLUP and compared with true breeding values. Phenotypes and genotypes were simulated in 10 generations and in the last 4 generations, respectively. Phenotypes in the last generation were removed to predict breeding values for those individuals using only genomic and pedigree information. Complete pedigrees and incomplete pedigrees with 50% missing dams were created to construct the pedigree-based relationship matrix with and without inbreeding. With missing dams, unknown parent groups (UPG) were assigned in relationship matrices. Regression coefficients (b1) and coefficients of determination (R2) of true breeding values on (G)EBV were calculated to investigate inflation and accuracy in GEBV for genotyped animals, respectively. In addition to the simulation study, 18 linear type traits of US Holsteins were examined. For the 18 type traits, b1 and R2 of GEBV with full data sets on GEBV with partial data sets for young genotyped bulls were calculated. The results from the simulation study indicated inflation in GEBV for genotyped males that were evaluated with only pedigree and genomic information under BLUP selection. However, when UPG for only pedigree-based relationships were included, the inflation was reduced, accuracy was highest, and genetic trends had no bias. For the linear type traits, when UPG for only pedigree-based relationships were included, the results were generally in agreement with those from the simulation study, implying less bias in genetic trends. However, when including no UPG, UPG in pedigree-based relationships, or UPG in genomic relationships, inflation and accuracy in GEBV were similar. The results from the simulation and type traits suggest that UPG must be defined accurately to be estimable and inbreeding should be included in pedigree-based relationships. In dairy cattle, known pedigree information with inbreeding and estimable UPG plays an important role in improving compatibility between pedigree-based and genomic relationship matrices, resulting in more reliable genomic predictions.
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Oliveira HR, Lourenco DAL, Masuda Y, Misztal I, Tsuruta S, Jamrozik J, Brito LF, Silva FF, Cant JP, Schenkel FS. Single-step genome-wide association for longitudinal traits of Canadian Ayrshire, Holstein, and Jersey dairy cattle. J Dairy Sci 2019; 102:9995-10011. [PMID: 31477296 DOI: 10.3168/jds.2019-16821] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 07/08/2019] [Indexed: 11/19/2022]
Abstract
Estimating single nucleotide polymorphism (SNP) effects over time is essential to identify and validate candidate genes (or quantitative trait loci) associated with time-dependent variation of economically important traits and to better understand the underlying mechanisms of lactation biology. Therefore, in this study, we aimed to estimate time-dependent effects of SNP and identifying candidate genes associated with milk (MY), fat (FY), and protein (PY) yields, and somatic cell score (SCS) in the first 3 lactations of Canadian Ayrshire, Holstein, and Jersey breeds, as well as suggest their potential pattern of phenotypic effect over time. Random regression coefficients for the additive direct genetic effect were estimated for each animal using single-step genomic BLUP, based on 2 random regression models: one considering MY, FY, and PY in the first 3 lactations and the other considering SCS in the first 3 lactations. Thereafter, SNP solutions were obtained for random regression coefficients, which were used to estimate the SNP effects over time (from 5 to 305 d in lactation). The top 1% of SNP that showed a high magnitude of SNP effect in at least 1 d in lactation were selected as relevant SNP for further analyses of candidate genes, and clustered according to the trajectory of their SNP effects over time. The majority of SNP selected for MY, FY, and PY increased the magnitude of their effects over time, for all breeds. In contrast, for SCS, most selected SNP decreased the magnitude of their effects over time, especially for the Holstein and Jersey breeds. In general, we identified a different set of candidate genes for each breed, and similar genes were found across different lactations for the same trait in the same breed. For some of the candidate genes, the suggested pattern of phenotypic effect changed among lactations. Among the lactations, candidate genes (and their suggested phenotypic effect over time) identified for the second and third lactations were more similar to each other than for the first lactation. Well-known candidate genes with major effects on milk production traits presented different suggested patterns of phenotypic effect across breeds, traits, and lactations in which they were identified. The candidate genes identified in this study can be used as target genes in studies of gene expression.
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Koseki T, Suehiro N, Masuda Y, Miyoshi N, Muraoka D, Ogo N, Asai A. Discovery of a New STAT3 Inhibitor Acting on the Linker Domain. Biol Pharm Bull 2019; 42:792-800. [DOI: 10.1248/bpb.b18-00992] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bradford H, Masuda Y, Cole J, Misztal I, VanRaden P. Modeling pedigree accuracy and uncertain parentage in single-step genomic evaluations of simulated and US Holstein datasets. J Dairy Sci 2019; 102:2308-2318. [DOI: 10.3168/jds.2018-15419] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 11/14/2018] [Indexed: 11/19/2022]
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Oliveira H, Lourenco D, Masuda Y, Misztal I, Tsuruta S, Jamrozik J, Brito L, Silva F, Schenkel F. Application of single-step genomic evaluation using multiple-trait random regression test-day models in dairy cattle. J Dairy Sci 2019; 102:2365-2377. [DOI: 10.3168/jds.2018-15466] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 11/20/2018] [Indexed: 01/30/2023]
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Bradford H, Masuda Y, VanRaden P, Legarra A, Misztal I. Modeling missing pedigree in single-step genomic BLUP. J Dairy Sci 2019; 102:2336-2346. [DOI: 10.3168/jds.2018-15434] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 11/12/2018] [Indexed: 11/19/2022]
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Fragomeni B, Masuda Y, Bradford HL, Lourenco DAL, Misztal I. International bull evaluations by genomic BLUP with a prediction population. J Dairy Sci 2019; 102:2330-2335. [PMID: 30639016 DOI: 10.3168/jds.2018-15554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/08/2018] [Indexed: 11/19/2022]
Abstract
The purpose of this study was to determine whether multi-country genomic evaluation can be accomplished by multiple-trait genomic best linear unbiased predictor (GBLUP) without sharing genotypes of important animals. Phenotypes and genotypes with 40k SNP were simulated for 25,000 animals, each with 4 traits assuming the same genetic variance and 0.8 genetic correlations. The population was split into 4 subpopulations corresponding to 4 countries, one for each trait. Additionally, a prediction population was created from genotyped animals that were not present in the individual countries but were related to each country's population. Genomic estimated breeding values were computed for each country and subsequently converted to SNP effects. Phenotypes were reconstructed for the prediction population based on the SNP effects of a country and the prediction animals' genotypes. The prediction population was used as the basis for the international evaluation, enabling bull comparisons without sharing genotypes and only sharing SNP effects. The computations were such that SNP effects computed within-country or in the prediction population were the same. Genomic estimated breeding values were calculated by single-trait GBLUP for within-country and multiple-trait GBLUP for multi-country predictions. The true accuracy for the prediction population with reconstructed phenotypes was at most 0.02 less than the accuracy with the original data. The differences increased when countries were assumed unequally sized. However, accuracies by multiple-trait GBLUP with the prediction population were always greater than accuracies from any single within-country prediction. Multi-country genomic evaluations by multiple-trait GBLUP are possible without using original genotypes at a cost of lower accuracy compared with explicitly combining countries' data.
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Kito N, Matsuo K, Ogawa K, Izumi A, Kishima M, Itoda M, Masuda Y. Positive Effects of "Textured Lunches" Gatherings and Oral Exercises Combined with Physical Exercises on Oral and Physical Function in Older Individuals: A Cluster Randomized Controlled Trial. J Nutr Health Aging 2019; 23:669-676. [PMID: 31367733 DOI: 10.1007/s12603-019-1216-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
OBJECTIVES Proper nutrition and physical exercises are essential to prevent frailty in older adults. Proper masticatory performance and oral function may influence on physical activities as well since the mouth is the entrance of nutrition and digestion. Thus, the present study aimed to test the combined program of specially devised lunch gatherings containing textured foods with oral and physical exercises on the improvement of oral and physical function in community-dwelling older adults. DESIGN A Cluster randomized controlled trial; Setting and Participants: Eighty-six community-dwelling older adults in Daito city, Japan, were randomly assigned into control (n = 43) or intervention (n = 43) groups. INTERVENTION The control group performed the physical exercise regimen only. The intervention group participated in a 12-week physical and oral exercise program and ate a so-called "munchy lunch" that introduced textured foods with proper nutrients together after performing the physical exercise twice a week following brief dietary instruction at the intervention onset. Physical training and lunch gatherings were held at local public centers. MEASUREMENTS The differences in measured variables for physical and oral function between baseline and 12 weeks of intervention were statistically tested. RESULTS Oral function as measured by tongue pressure increased significantly in the intervention group (p=0.031), but not in the control group. Physical properties and activities, including body fat percentage and results of the timed up and go test, decreased more significantly in the intervention group than in controls (p<0.05). CONCLUSIONS Our findings suggest that a combined program of textured lunch gatherings with oral and physical exercises may improve physical and oral function as a preventative approach for frailty in community-dwelling older adults.
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Blyth D, Fry J, Fomin N, Alarcon R, Alonzi L, Askanazi E, Baeßler S, Balascuta S, Barrón-Palos L, Barzilov A, Bowman JD, Birge N, Calarco JR, Chupp TE, Cianciolo V, Coppola CE, Crawford CB, Craycraft K, Evans D, Fieseler C, Frlež E, Garishvili I, Gericke MTW, Gillis RC, Grammer KB, Greene GL, Hall J, Hamblen J, Hayes C, Iverson EB, Kabir ML, Kucuker S, Lauss B, Mahurin R, McCrea M, Maldonado-Velázquez M, Masuda Y, Mei J, Milburn R, Mueller PE, Musgrave M, Nann H, Novikov I, Parsons D, Penttilä SI, Počanić D, Ramirez-Morales A, Root M, Salas-Bacci A, Santra S, Schröder S, Scott E, Seo PN, Sharapov EI, Simmons F, Snow WM, Sprow A, Stewart J, Tang E, Tang Z, Tong X, Turkoglu DJ, Whitehead R, Wilburn WS. First Observation of P-odd γ Asymmetry in Polarized Neutron Capture on Hydrogen. PHYSICAL REVIEW LETTERS 2018; 121:242002. [PMID: 30608729 DOI: 10.1103/physrevlett.121.242002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 10/22/2018] [Indexed: 06/09/2023]
Abstract
We report the first observation of the parity-violating gamma-ray asymmetry A_{γ}^{np} in neutron-proton capture using polarized cold neutrons incident on a liquid parahydrogen target at the Spallation Neutron Source at Oak Ridge National Laboratory. A_{γ}^{np} isolates the ΔI=1, ^{3}S_{1}→^{3}P_{1} component of the weak nucleon-nucleon interaction, which is dominated by pion exchange and can be directly related to a single coupling constant in either the DDH meson exchange model or pionless effective field theory. We measured A_{γ}^{np}=[-3.0±1.4(stat)±0.2(syst)]×10^{-8}, which implies a DDH weak πNN coupling of h_{π}^{1}=[2.6±1.2(stat)±0.2(syst)]×10^{-7} and a pionless EFT constant of C^{^{3}S_{1}→^{3}P_{1}}/C_{0}=[-7.4±3.5(stat)±0.5(syst)]×10^{-11} MeV^{-1}. We describe the experiment, data analysis, systematic uncertainties, and implications of the result.
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Noor Mohammadi T, Maung A, Sato J, Sonoda T, Masuda Y, Honjoh K, Miyamoto T. Mechanism for antibacterial action of epigallocatechin gallate and theaflavin-3,3′-digallate on Clostridium perfringens. J Appl Microbiol 2018; 126:633-640. [DOI: 10.1111/jam.14134] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/12/2018] [Accepted: 10/16/2018] [Indexed: 12/31/2022]
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Harada D, Hata A, Okuda C, Kaji R, Masuda Y, Takechi Y, Kozuki T, Nogami N, Katakami N. Docetaxel plus ramucirumab with primary prophylactic pegylated-granulocyte-colony stimulating factor for pretreated non-small cell lung cancer. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy292.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Masuda Y, VanRaden P, Misztal I, Lawlor T. Differing genetic trend estimates from traditional and genomic evaluations of genotyped animals as evidence of preselection bias in US Holsteins. J Dairy Sci 2018; 101:5194-5206. [DOI: 10.3168/jds.2017-13310] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 12/10/2017] [Indexed: 11/19/2022]
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Masuda Y, Tatsuno K, Kitano S, Miyazawa H, Ishibe J, Aoshima M, Shimauchi T, Fujiyama T, Ito T, Tokura Y. Mogamulizumab-induced photosensitivity in patients with mycosis fungoides and other T-cell neoplasms. J Eur Acad Dermatol Venereol 2018; 32:1456-1460. [PMID: 29341283 DOI: 10.1111/jdv.14797] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/03/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Mogamulizumab (Mog) is a defucosylated, therapeutic monoclonal antibody, targeting CCR4 and was first approved in Japan for the treatment of adult T-cell leukaemia/lymphoma (ATLL), followed by cutaneous T-cell lymphoma and peripheral T-cell lymphoma. OBJECTIVE To retrospectively investigate development of photosensitivity in patients with mycosis fungoides and other T-cell neoplasms after treatment with Mog. METHODS We treated seven cutaneous lymphoma patients with Mog. Upon combination treatment with narrow-band UVB, we noticed that four patients developed photosensitivity dermatitis following Mog therapy, including two cases of mycosis fungoides, one case of adult T-cell leukaemia/lymphoma and one case of EB virus-associated T-cell lymphoproliferative disorder. Phototest was performed with UVA and UVB, and immunohistochemical staining for CD4, CD8 and Foxp3 was conducted in both photosensitivity and lymphoma lesions. RESULTS Phototest revealed that the action spectrum of the photosensitivity was UVB in three cases and both UVB and UVA in one case. Histopathologically, the photosensitive lesions were characterized by a lichenoid tissue reaction with a CD8+ T cell-dominant infiltrate, sharing the feature with chronic actinic dermatitis, an autoreactive photodermatosis with a cytotoxic T-cell response. Foxp3+ regulatory T cells (Tregs) were decreased in the photosensitivity lesions compared with the lymphoma lesions. CONCLUSION Increased incidence of photosensitivity reaction was observed during Mog treatment. Decreased number of Tregs in the lesional skin suggests that this reaction is possibly induced by autoreactive cytotoxic T cells.
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Masuda Y, Ogura Y, Inagaki Y, Yasui T, Aizu Y. Analysis of the influence of collagen fibres in the dermis on skin optical reflectance by Monte Carlo simulation in a nine-layered skin model. Skin Res Technol 2017; 24:248-255. [DOI: 10.1111/srt.12421] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2017] [Indexed: 11/29/2022]
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Kuwata Y, Yoshinaga K, Matsuhashi M, Murase N, Ohtani R, Sainouchi M, Takata M, Masuda Y, Nakamura M. Disorganization of alpha-band networks in the hemisphere of the seizure FOCI revealed by functional connectivity analysis. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.3754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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