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排序方式: 共有59条查询结果,搜索用时 15 毫秒
21.
Background
Using haplotype blocks as predictors rather than individual single nucleotide polymorphisms (SNPs) may improve genomic predictions, since haplotypes are in stronger linkage disequilibrium with the quantitative trait loci than are individual SNPs. It has also been hypothesized that an appropriate selection of a subset of haplotype blocks can result in similar or better predictive ability than when using the whole set of haplotype blocks. This study investigated genomic prediction using a set of haplotype blocks that contained the SNPs with large effects estimated from an individual SNP prediction model. We analyzed protein yield, fertility and mastitis of Nordic Holstein cattle, and used high-density markers (about 770k SNPs). To reach an optimum number of haplotype variables for genomic prediction, predictions were performed using subsets of haplotype blocks that contained a range of 1000 to 50 000 main SNPs.Results
The use of haplotype blocks improved the prediction reliabilities, even when selection focused on only a group of haplotype blocks. In this case, the use of haplotype blocks that contained the 20 000 to 50 000 SNPs with the highest effect was sufficient to outperform the model that used all individual SNPs as predictors (up to 1.3 % improvement in prediction reliability for mastitis, compared to individual SNP approach), and the achieved reliabilities were similar to those using all haplotype blocks available in the genome data (from 0.6 % lower to 0.8 % higher reliability).Conclusions
Haplotype blocks used as predictors can improve the reliability of genomic prediction compared to the individual SNP model. Furthermore, the use of a subset of haplotype blocks that contains the main SNP effects from genomic data could be a feasible approach to genomic prediction in dairy cattle, given an increase in density of genotype data available. The predictive ability of the models that use a subset of haplotype blocks was similar to that obtained using either all haplotype blocks or all individual SNPs, with the benefit of having a much lower computational demand. 相似文献22.
Background
A haplotype approach to genomic prediction using high density data in dairy cattle as an alternative to single-marker methods is presented. With the assumption that haplotypes are in stronger linkage disequilibrium (LD) with quantitative trait loci (QTL) than single markers, this study focuses on the use of haplotype blocks (haploblocks) as explanatory variables for genomic prediction. Haploblocks were built based on the LD between markers, which allowed variable reduction. The haploblocks were then used to predict three economically important traits (milk protein, fertility and mastitis) in the Nordic Holstein population.Results
The haploblock approach improved prediction accuracy compared with the commonly used individual single nucleotide polymorphism (SNP) approach. Furthermore, using an average LD threshold to define the haploblocks (LD≥0.45 between any two markers) increased the prediction accuracies for all three traits, although the improvement was most significant for milk protein (up to 3.1 % improvement in prediction accuracy, compared with the individual SNP approach). Hotelling’s t-tests were performed, confirming the improvement in prediction accuracy for milk protein. Because the phenotypic values were in the form of de-regressed proofs, the improved accuracy for milk protein may be due to higher reliability of the data for this trait compared with the reliability of the mastitis and fertility data. Comparisons between best linear unbiased prediction (BLUP) and Bayesian mixture models also indicated that the Bayesian model produced the most accurate predictions in every scenario for the milk protein trait, and in some scenarios for fertility.Conclusions
The haploblock approach to genomic prediction is a promising method for genomic selection in animal breeding. Building haploblocks based on LD reduced the number of variables without the loss of information. This method may play an important role in the future genomic prediction involving while genome sequences. 相似文献23.
Y Deng J Zhao D Sakurai KM Kaufman JC Edberg RP Kimberly DL Kamen GS Gilkeson CO Jacob RH Scofield CD Langefeld JA Kelly ME Alarcón-Riquelme BIOLUPUS GENLES Networks JB Harley TJ Vyse BI Freedman PM Gaffney KM Sivils JA James TB Niewold RM Cantor W Chen BH Hahn EE Brown PROFILE BP Tsao 《Arthritis research & therapy》2012,14(Z3):A5
24.
Use of an Intergenic Region in Pseudomonas syringae pv. Syringae B728a for Site-Directed Genomic Marking of Bacterial Strains for Field Experiments 下载免费PDF全文
Susan S. Hirano David K. Willis Murray K. Clayton Christen D. Upper 《Applied microbiology》2001,67(8):3735-3738
To construct differentially-marked derivatives of our model wild-type strain, Pseudomonas syringae pv. syringae B728a (a causal agent of bacterial brown spot disease in snap bean plants), for field experiments, we selected a site in the gacS-cysM intergenic region for site-directed insertion of antibiotic resistance marker cassettes. In each of three field experiments, population sizes of the site-directed chromosomally marked B728a derivatives in association with snap bean plants were not significantly different from that of the wild-type strain. Inserts of up to 7 kb of DNA in the intergenic region did not measurably affect fitness of B728a in the field. The site is useful for site-directed genomic insertions of single copies of genes of interest. 相似文献
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27.
Factors That Influence the Activity of 2,4-Dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one on Erwinia Species in Growth Assays 总被引:2,自引:2,他引:0
Factors affecting the inhibitory activity of 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) against Erwinia carotovora, a nonpathogen of Zea mays L., and against a maize pathovar of Erwinia chrysanthemi (ECZ) were examined. Most experiments were performed with DIMBOA dissolved in a bacterial growth medium containing 10 g/liter of sucrose, inorganic salts, and 1 g/liter of casamino acids at pH 6.75. When temperature and pH were held constant, inhibition of E. carotovora varied linearly with the logarithm of the initial cell population. By altering temperatures, assays with constant pH and initial cell populations were performed under conditions of varying DIMBOA stability. When E. carotovora was grown at 24, 28, 32, and 36 C in the presence of 0.1 to 0.5 mm DIMBOA, the inhibition of bacterial growth was maintained long after DIMBOA had decomposed in the medium to levels which, if added initially, would not have been inhibitory. When assays were performed at pH 5.5, the pH of aqueous maize extracts, E. carotovora was more inhibited than at pH 6.75; however, ECZ was substantially less inhibited at the lower pH. 相似文献
28.
The Hypersensitivity Reaction of Tomatoes Resistant to Meloidogyne incognita: Reversal by Cytokinins
Initiation of larval growth, induction of cell necrosis, and gall formation in the host were measured as criteria of resistance or susceptibility of tomato seedlings to the root-knot nematode, Meloidogyne incognita (Kofoid &White) Chitwood. Seedlings grown at 27 C on water agar containing additions were scored 3 or 4 days after infection.In the absence of exogenous plant growth regulatory substances, approximately 73% of larvae that entered roots of susceptible plants showed growth, none induced necrosis and nearly all induced gall formation. In roots of a resistant variety, only 4% of the larvae grew, 88% induced necrosis of host cells, and only 29% induced galls. Exogenously supplied cytokinins shifted the response of the resistant plants toward the susceptible reaction. Exogenous kinetin at 0.4 and 0.8 µmolar allowed 55 and 57% of the nematodes to grow, reduced the incidence of necrosis to 32 and 31%, and increased gall formation to 73 and 65%. Three additional cytokinins, Zeatin, 6-(γ,γ-dimethylallylamino)purine, and 6-benzylaminopurine produced effects similar to kinetin. Exogenous indoleacetic acid, gibberellic acid, adenine, guanine, uracil, thymine, cytidine, and 6-methylaminopurine neither increased the percentage of larvae which grew nor decreased the extent of host cell necrosis. 相似文献
29.
Bacteria in the Leaf Ecosystem with Emphasis on Pseudomonas syringae—a Pathogen, Ice Nucleus, and Epiphyte 下载免费PDF全文
The extremely large number of leaves produced by terrestrial and aquatic plants provide habitats for colonization by a diversity of microorganisms. This review focuses on the bacterial component of leaf microbial communities, with emphasis on Pseudomonas syringae—a species that participates in leaf ecosystems as a pathogen, ice nucleus, and epiphyte. Among the diversity of bacteria that colonize leaves, none has received wider attention than P. syringae, as it gained notoriety for being the first recombinant organism (Ice− P. syringae) to be deliberately introduced into the environment. We focus on P. syringae to illustrate the attractiveness and somewhat unique opportunities provided by leaf ecosystems for addressing fundamental questions of microbial population dynamics and mechanisms of plant-bacterium interactions. Leaf ecosystems are dynamic and ephemeral. The physical environment surrounding phyllosphere microbes changes continuously with daily cycles in temperature, radiation, relative humidity, wind velocity, and leaf wetness. Slightly longer-term changes occur as weather systems pass. Seasonal climatic changes impose still a longer cycle. The physical and physiological characteristics of leaves change as they expand, mature, and senesce and as host phenology changes. Many of these factors influence the development of populations of P. syringae upon populations of leaves. P. syringae was first studied for its ability to cause disease on plants. However, disease causation is but one aspect of its life strategy. The bacterium can be found in association with healthy leaves, growing and surviving for many generations on the surfaces of leaves as an epiphyte. A number of genes and traits have been identified that contribute to the fitness of P. syringae in the phyllosphere. While still in their infancy, such research efforts demonstrate that the P. syringae-leaf ecosystem is a particularly attractive system with which to bridge the gap between what is known about the molecular biology of genes linked to pathogenicity and the ecology and epidemiology of associated diseases as they occur in natural settings, the field. 相似文献
30.
Mário C BarrosoJúnior Guilherme P Esteves Thiago P Nunes Lucia MG Silva Alvaro CD Faria Pedro L Melo 《Biomedical engineering online》2011,10(1):14