Investigating the persistence of accuracy of genomic predictions over time in broilers     

Jorge Hidalgo  Daniela Lourenco  Shogo Tsuruta  Yutaka Masuda  Vivian Breen  Rachel Hawken  Matias Bermann  Ignacy Misztal 《Journal of animal science》2021,99(9)

Accuracy of genomic predictions is an important component of the selection response. The objectives of this research were: 1) to investigate trends for prediction accuracies over time in a broiler population of accumulated phenotypes, genotypes, and pedigrees and 2) to test if data from distant generations are useful to maintain prediction accuracies in selection candidates. The data contained 820K phenotypes for a growth trait (GT), 200K for two feed efficiency traits (FE1 and FE2), and 42K for a carcass yield trait (CY). The pedigree included 1,252,619 birds hatched over 7 years, of which 154,318 from the last 4 years were genotyped. Training populations were constructed adding 1 year of data sequentially, persistency of accuracy over time was evaluated using predictions from birds hatched in the three generations following or in the years after the training populations. In the first generation, before genotypes became available for the training populations (first 3 years of data), accuracies remained almost stable with successive additions of phenotypes and pedigree to the accumulated dataset. The inclusion of 1 year of genotypes in addition to 4 years of phenotypes and pedigree in the training population led to increases in accuracy of 54% for GT, 76% for FE1, 110% for CY, and 38% for FE2; on average, 74% of the increase was due to genomics. Prediction accuracies declined faster without than with genomic information in the training populations. When genotypes were unavailable, the average decline in prediction accuracy across traits was 41% from the first to the second generation of validation, and 51% from the second to the third generation of validation. When genotypes were available, the average decline across traits was 14% from the first to the second generation of validation, and 3% from the second to the third generation of validation. Prediction accuracies in the last three generations were the same when the training population included 5 or 2 years of data, and a decrease of ~7% was observed when the training population included only 1 year of data. Training sets including genomic information provided an increase in accuracy and persistence of genomic predictions compared with training sets without genomic data. The two most recent years of pedigree, phenotypic, and genomic data were sufficient to maintain prediction accuracies in selection candidates. Similar conclusions were obtained using validation populations per year.  相似文献   

Changes in Retrogradation Properties of Rice Starches with Amylose Content and Molecular Properties     

Cheng‐yi Lii  Vivian M.‐F. Lai  Mei‐Ching Shen 《Cereal Chemistry》2004,81(3):392-398

The increases in storage modulus (G′), retrogradation enthalpy change (ΔH) and ΔH‐related Avrami kinetic parameters of gelatinized rice starch dispersions at 25% (w/w) were investigated with respect to storage period, amylose content (AC), and molecular properties. Three high‐AC and five low‐AC rice cultivars were compared for understanding the multiple influences of AC and molecular properties involved. After refining the results of correlation analysis, the G′ of just‐cooled samples changed positively, mainly with AC and additionally with the average chain length of amylose (CL_AM) and the weight ratio of extra‐long plus long chains to short chains of amylopectin (AP) (r_APchain). The developed ΔH on short‐term storage (10 days) elevated with increasing AC and CL_AM and decreasing degree of polymerization of AP (DP_AP), but after long‐term aging for one to three months with increasing r_APchain, especially for the low‐AC cultivars examined. Greater Avrami rate constants for retrogradation could be attributed to the combination of a lower DP_AP and r_APchain or AP chain length and a greater CL_AM. The polynomials using these critical factors to describe the retrogradation parameters were elucidated and could account for 85–99.6% of data deviations.  相似文献   

The sharks of South East Asia – unknown,unmonitored and unmanaged     

Vivian Y Y Lam  Yvonne Sadovy de Mitcheson 《Fish and Fisheries》2011,12(1):51-74

Sharks fisheries have declined globally due to over‐ and unregulated fishing. As with many collapsed and unmonitored coastal fisheries, information is difficult to obtain, yet it is important to understand the historical changes determining population trends and evaluate the current status of sharks in order to conserve these vulnerable species. Here, we document for the first time the history and general condition of the shark fisheries of Southern China, specifically Hong Kong, and Guangdong, Fujian and Hainan Provinces. This study shows, through the use of historical literature and anecdotal accounts, including fisher interviews, that all known shark fisheries in the region collapsed between the 1970s and the 1990s. Of the 109 species present historically in the South China Sea, only 18 species were recorded in current market surveys, of which all were landed as bycatch and 65% were below the size of sexual maturity. Markets are dominated by smaller species, including the spadenose shark (Scoliodon laticaudus) and the whitespotted bambooshark (Chiloscyllium plagiosum). Marketed large shark species are almost all below the size of sexual maturation, evidence of growth overfishing and a factor in recruitment overfishing. Some species, like the whale (Rhincodon typus) and basking sharks (Cetorhinus maximus), are clearly vulnerable to local extinction without intervention. Given the inherent vulnerability of sharks and the overfished states of many sharks, there is clearly an urgent need to formulate impacting conservation and management plans for these rapidly declining species in a region that has the highest demand for shark products globally.  相似文献   

Dilution of digestive fish proteases with protein-free blocking reagents prevents loss of catalytic activity during microquantification     

Andoh  Tadashi 《Fisheries Science》2020,86(3):543-550

Fisheries Science - The activity of proteases may be lost during microquantification because of their nonspecific binding to tubes and pipette tips. In this study, the effects of blocking reagents...  相似文献   

Modeling genetic differences of combined broiler chicken populations in single-step GBLUP     

Matias Bermann  Daniela Lourenco  Vivian Breen  Rachel Hawken  Fernando Brito Lopes  Ignacy Misztal 《Journal of animal science》2021,99(4)

The introduction of animals from a different environment or population is a common practice in commercial livestock populations. In this study, we modeled the inclusion of a group of external birds into a local broiler chicken population for the purpose of genomic evaluations. The pedigree was composed of 242,413 birds and genotypes were available for 107,216 birds. A five-trait model that included one growth, two yield, and two efficiency traits was used for the analyses. The strategies to model the introduction of external birds were to include a fixed effect representing the origin of parents and to use unknown parent groups (UPG) or metafounders (MF). Genomic estimated breeding values (GEBV) were obtained with single-step GBLUP using the Algorithm for Proven and Young. Bias, dispersion, and accuracy of GEBV for the validation birds, that is, from the most recent generation, were computed. The bias and dispersion were estimated with the linear regression (LR) method,whereas accuracy was estimated by the LR method and predictive ability. When fixed UPG were fit without estimated inbreeding, the model did not converge. In contrast, models with fixed UPG and estimated inbreeding or random UPG converged and resulted in similar GEBV. The inclusion of an extra fixed effect in the model made the GEBV unbiased and reduced the inflation. Genomic predictions with MF were slightly biased and inflated due to the unbalanced number of observations assigned to each metafounder. When combining local and external populations, the greatest accuracy can be obtained by adding an extra fixed effect to account for the origin of parents plus UPG with estimated inbreeding or random UPG. To estimate the accuracy, the LR method is more consistent among scenarios, whereas the predictive ability greatly depends on the model specification.  相似文献   

Catching sharks: recreational saltwater angler behaviours and attitudes regarding shark encounters and conservation          下载免费PDF全文

Kate Mcclellan Press  John Mandelman  Elizabeth Burgess  Steven J. Cooke  Vivian M. Nguyen  Andy J. Danylchuk 《水产资源保护:海洋与淡水生态系统》2016,26(4):689-702

Structural identification of novel oligosaccharides produced by Lactobacillus bulgaricus and Lactobacillus plantarum     

Black BA  Lee VS  Zhao YY  Hu Y  Curtis JM  Gänzle MG 《Journal of agricultural and food chemistry》2012,60(19):4886-4894

β-Galactosidases (β-Gal) of lactic acid bacteria produce oligosaccharides from lactose when suitable acceptor carbohydrates are present. This study aimed to elucidate the structure of oligosaccharides formed by galactosylation of N-acetylglucosamine (GlcNAc) and fucose. Crude cellular extract of Lactobacillus bulgaricus and LacLM of Lactobacillus plantarum were used as sources of β-Gal activity. Disaccharides obtained by galactosylation of GlcNAc were identified as Gal-β-(1→4)-GlcNAc or Gal-β-(1→6)-GlcNAc by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and comparison with external standards. Trisaccharides were identified as Gal-β-(1→6)-Gal-β-(1→[4 or 6])-GlcNAc by LC-MS, analysis of the MS/MS spectra of selected in-source fragment ions, and their relative retention times. LC-MS analysis revealed the presence of five galactosylated fucosides, but their linkage type could not be identified, partly due to the lack of reference compounds. β-Gal of lactic acid bacteria may serve as suitable tools for the chemoenzymatic synthesis of therapeutic oligosaccharides.  相似文献   

Antigenotoxicity and Antioxidant Activity of Acerola Fruit (Malpighia glabra L.) at Two Stages of Ripeness     

Nunes Rda S  Kahl VF  Sarmento Mda S  Richter MF  Costa-Lotufo LV  Rodrigues FA  Abin-Carriquiry JA  Martinez MM  Ferronatto S  Ferraz Ade B  da Silva J 《Plant foods for human nutrition (Dordrecht, Netherlands)》2011,66(2):129-135

Genotoxic and antigenotoxic effects of acerola fruit at two stages of ripeness were investigated using mice blood cells. The results show that no ripeness stage of acerola extracts presented any genotoxic potential to damage DNA (Comet assay) or cytotoxicity (MTT assay). When antigenotoxic activity was analyzed, unripe fruit presented higher DNA protection than ripe fruit (red color) extract. The antioxidant capacity of substances also showed that unripe samples inhibit the free radical DPPH more significantly than the ripe ones. The results about determination of compounds made using HPLC showed that unripe acerola presents higher levels of vitamin C as compared to ripe acerola. Thus, vitamin C and the complex mixture of nutrients of Malpighia glabra L., and especially its ripeness stages, influenced the interaction of the fruit extract with the DNA. Acerola is usually consumed when ripe (red fruit), although it is the green fruit (unripe) that has higher potential as beneficial to DNA, protecting it against oxidative stress.  相似文献   

冷却猪肉中假单胞菌生长预测模型的建立与验证   总被引：4，自引：0，他引：4  

唐晓阳  赵勇  孙晓红  吴启华  潘迎捷 《湖南农业科学》2010,(1):128-131,134

以从腐败猪肉中分离得到的假单胞菌P1,P2,P3,P4,P5,P6的混合培养物为受试菌液,应用Origin7．5软件拟合假单胞菌0-10℃下的生长情况。经比较发现,修正的Gompertz模型对假单胞菌生长曲线的拟合效果优于线性模型,R2均在0．96以上。应用平方根模型和Arrhenius模型对由修正的Gompertz模型得出的最大比生长速率进行拟合,所得Arrhenius模型的R2为0．9716,拟合效果优于平方根模型（R2为0．9326）。结果表明,所建二级模型,能真实快速有效地预测0-10℃冷藏条件下假单胞菌的生长。  相似文献   

Mechanism of action of the 1,2,4-triazolo[1,5-a] pyrimidines     

B. Clifford Gerwick  Mani V. Subramanian  Vivian I. Loney-Gallant  Darrell P. Chandler 《Pest management science》1990,29(3):357-364

The substituted 1,2,4-triazolo[1,5-a]pyrimidines are a new class of highly active herbicides. Protection of Arabidopsis thaliana seedlings from triazolopyrimidine-induced injury by the branched-chain amino acids was observed. Acetolactate synthase (EC 4.1.3.18) was isolated and found to be quite sensitive to inhibition. I₅₀ values for inhibition of the enzyme from a number of plant sources show little variation and no correlation to whole-plant response, suggesting uptake, translocation and metabolism play key roles in modulating herbicidal activity. Further studies indicate that these chemicals are slow, tight-binding inhibitors that are readily dissociated by gel filtration. Some correlations between in-vitro activity and in-vivo activity were observed for ortho-substituted analogs on selected broadleaf species.  相似文献