Elastic priors to dynamically borrow information from historical data in clinical trials

Use of historical data and real-world evidence holds great potential to improve the efficiency of clinical trials. One major challenge is to effectively borrow information from historical data while maintaining a reasonable type I error and minimal bias. We propose the elastic prior approach to address this challenge. Unlike existing approaches, this approach proactively controls the behavior of information borrowing and type I errors by incorporating a well-known concept of clinically significant difference through an elastic function, defined as a monotonic function of a congruence measure between historical data and trial data. The elastic function is constructed to satisfy a set of prespecified criteria such that the resulting prior will strongly borrow information when historical and trial data are congruent, but refrain from information borrowing when historical and trial data are incongruent. The elastic prior approach has a desirable property of being information borrowing consistent, that is, asymptotically controls type I error at the nominal value, no matter that historical data are congruent or not to the trial data. Our simulation study that evaluates the finite sample characteristic confirms that, compared to existing methods, the elastic prior has better type I error control and yields competitive or higher power. The proposed approach is applicable to binary, continuous, and survival endpoints.     

Genome analysis of Elytrigia caespitosa, Lophopyrum nodosum, Pseudoroegneria geniculata ssp. scythica, and Thinopyrum intermedium (Triticeae: Gramineae).

To elucidate the genome constitutions of the tetraploid (2n = 4x = 28) species Elytrigia caespitosa, Lophopyrum nodosum, and Pseudoroegneria geniculata ssp. scythica and the hexaploid (2n = 6x = 42) Thinopyrum intermedium, meiotic pairing was studied in these species as well as 10 hybrids. Karyotype analysis with aceto-orcein stained root-tip cells was performed for the four species and the hybrids of T. bessarabicum with E. caespitosa, P. geniculata ssp. scythica, and T. intermedium. Karyotype analysis by Giemsa C-banding was carried out with the three tetraploid species and the two triploid hybrids involving T. bessarabicum. The species behaved as strict allopolyploids. All hybrids were male sterile with few stainable pollen grains. It is concluded from the results that the three tetraploid species have the genome formula JeJeSS and T. intermedium has the formula JeJeJeJeSS. The chromosomes of the Je and S genomes in these species had C-banding patterns differing from each other and from those of the extant diploid species. Based on these findings, the four species investigated should be placed in the same genus or the same section of a genus. However, new combinations are not proposed at this time pending future taxonomic investigation of the genome constitution of Elytrigia repens (L.) Nevski.     

Effects of compound sodium nitrophenol on microspore embryogenesis and plantlet regeneration in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee)

Isolated microspore culture has been implemented in breeding programs to produce doubled haploid (DH) lines and thus accelerates the breeding process. However, low microspore embryogenesis frequency in flowering Chinese cabbage remains a key obstacle to the practical application of this technique. This study aimed to establish an efficient microspore culture protocol for flowering Chinese cabbage that would be applied for heterosis breeding. Microspores of five genotypes, 19AY05, 19AY06, 19AY10, 19AY12, and 19AY15, were successfully induced to produce embryos in NLN-13 medium. Microspores of two genotypes, 19AY05 and 19AY15, were cultivated in NLN-13 medium supplemented with different concentrations (0, 0.01, 0.05, 0.1, or 0.2 mg·L⁻¹) of compound sodium nitrophenol (sodium nitrophenol, 5-nitrophenol) to enhance microspore embryogenesis and plant regeneration without an intervening callus phase. The results showed that 0.05 ~ 0.1 mg· L⁻¹ sodium nitrophenol and 0.01 ~ 0.2 mg· L⁻¹ of 5-nitrophenol significantly promoted the induction of microspore embryogenesis of two genotypes, and the best concentrations required for different genotypes are different. Moreover, 0.1 mg· L⁻¹ sodium nitrophenol can significantly increase the plant regeneration rate of the two genetypes. The 5-nitrophenol at 0.01 mg·L⁻¹ significantly increased rate of embryos directly convert to plant in 19AY15. In addition, the average doubled haploid rates in the five genotypes were close to 63%. Horticultural traits of DH lines from 19AY05 were identified and all of them were self-incompatible lines. They showed a high uniformity and consistency that can be directly used for hybrid breeding. Furthermore, the hybrid combination was prepared with the selected DH lines and the Guangdong nucleus genic sterile line GMS019 to screen the excellent hybrid combination for the flowering Chinese cabbage breeding program. This method accelerates the application of microspore culture in hybrid breeding of flowering Chinese cabbage.

     

Effects of Allelochemicals on Root Growth and Pod Yield in Response to Continuous Cropping Obstacle of Peanut

Continuous cropping (CC) obstacle is a major threat in legume crops production; however, the underlying mechanisms concerning the roles allelochemicals play in CC obstacle are poorly understood. The current 2-year study was conducted to investigate the effects of different kinds and concentrations of allelochemicals, p-hydroxybenzoic acid (H), cinnamic acid (C), phthalic acid (P), and their mixtures (M) on peanut root growth and productivity in response to CC obstacle. Treatment with H, C, P, and M significantly decreased the plant height, dry weight of the leaves and stems, number of branches, and length of the lateral stem compared with control. Exogenous application of H, C, P, and M inhibited the peanut root growth as indicated by the decreased root morphological characters. The allelochemicals also induced the cell membrane oxidation even though the antioxidant enzymes activities were significantly increased in peanut roots. Meanwhile, treatment with H, C, P, and M reduced the contents of total soluble sugar and total soluble protein. Analysis of ATPase activity, nitrate reductase activity, and root system activity revealed that the inhibition effects of allelochemicals on peanut roots might be due to the decrease in activities of ATPase and NR, and the inhibition of root system. Consequently, allelochemicals significantly decreased the pod yield of peanut compared with control. Our results demonstrate that allelochemicals play a dominant role in CC obstacle-induced peanut growth inhibition and yield reduction through damaging the root antioxidant system, unbalancing the osmolytes accumulation, and decreasing the activities of root-related enzymes.

     

Effects of Ultrasonic Seed Treatment on Rice Performances under the Seawater Irrigation

Irrigation with desalinated seawater is an effective way to use ocean resources and save freshwater resources. However, seawater irrigation would cause yield loss of rice. In order to explore the effects of ultrasonic seed treatment on rice performances under seawater irrigation, the present study was conducted with three irrigation treatments (fresh water (SW0), ten times diluted seawater (SW1%, 0.34% salinity), and five times diluted seawater (SW2%, 0.68% salinity)) and two seed treatments (ultrasonic treated seeds (UT) and untreated seeds (CK)). Compared with SW0 + CK treatment, SW1 + CK and SW2 + CK treatments significantly decreased grain yield by 56.19% and 66.69%, spikelets per panicle by 30.11% and 55.80%, seed-setting rate by 23.05% and 18.87%, and 1000-grain weight by 4.55% and 14.50%, respectively. Seawater irrigation also significantly increased malonaldehyde (MDA) and proline contents and the activities of superoxide dismutase (SOD) and peroxidase (POD). Ultrasonic seed treatment significantly increased the grain number per panicle, seed-setting rate, and grain yield of rice under seawater irrigation. Compared with CK, UT treatment substantially reduced MDA content, SOD activity, and POD activity in SW1 and SW2 conditions. Furthermore, UT treatment significantly increased proline content and down-regulated proline dehydrogenase activity under seawater irrigation. We deduced that ultrasonic seed treatment enhanced the salinity tolerance of rice by inducing the proline accmulation. Our findings indicated that ultrasonic seed treatment could an effective strategy to promote rice productivity under seawater irrigation.     

Arbuscular Mycorrhizal Fungal Colonization at Different Succession Stages in Songnen Saline-Alkali Grassland

Arbuscular mycorrhizal (AM) fungi can form symbiosis with 90% of the vascular plants and play important roles in ecosystem. To realize the AM fungal colonization at different succession stages in saline-alkali land and screen AM fungi species with great functions, roots and soil samples were collected from the three succession stages of Songnen saline-alkali grassland. The soil properties and AM fungal colonization were measured, and the fungus distributed extensively in three stages was annotated by sequencing for AML1/AML2 target, subsequently, maize was selected as the host to verify its colonization. The results showed that the soil properties improved with the succession of saline-alkali grassland. The plants’ communities of the three stages could be colonized by AM fungi, and the colonization rate of Leymus chinensis (the third stage) ranged from 66.67% to 100%, Puccinellia tenuiflora (the second stage) ranged from 50% to 80%, while the Suaeda glauca (the first stage) was only 35%–60%. Glomeraceae sp1 was identified as the dominant AM fungi species which occurred frequently in the succession of saline-alkali land with the isolation frequency, relative abundance, and importance value of 100%, 18.1%, and 59.1%, respectively. The colonization rate of Glomeraceae sp1 in maize ranged from 80% to 87% and similar mycorrhizal characteristics were detected in the roots of P. tenuiflora, S. glauca, and L. chinensis, indicating that Glomeraceae sp1 colonized the samples in the field. The correlation matrix indicated that colonization rate, colonization intensity, and vesicle abundance were closely related to soil conditions most, and they were related significantly to all the soil properties except cellulase activity. Besides, redundancy analysis (RDA) showed that soil properties drove the changes of AM fungal colonization and sporulation. These results will provide theoretical support for realizing the relationship between AM fungal colonization and soil conditions, and also for the exploration of AM fungi species with great functions.

     

Investigation of <i>GhFAT</i> Genes Related to Seed Oil Content and Fatty Acid Composition in <i>Gossypium hirsutum</i> L.

Fatty Acyl-ACP thioesterase (FAT) is a key enzyme controlling oil biosynthesis in plant seeds. FATs can be divided into two subfamilies, FATA and FATB according to their amino acid sequences and substrate specificity. The Upland cotton genome contains 20 GhFAT genes, amongst which 6 genes were of the GhFATA subfamily and 14 of the GhFATB subfamily. The 20 GhFAT genes are unevenly distributed on 14 chromosomes. The GhFATA genes have 5 or 7 exons and the GhFATB genes have 6 or 7 exons. All GhFAT proteins have the conserved Acyl-ACP_TE domain and PLN02370 super family, the typical characteristics of plant thioesterases. Analyses of the expression level of GhFATs and the compositions of fatty acid in 5–60 days-post-anthesis seeds showed that the ratio of saturated fatty acids to unsaturated fatty acids was consistent with the expression profile of GhFATB12, GhFATB3, and GhFATB10; the ratio of monounsaturated fatty acid to polyunsaturated fatty acids was consistent with the expression profile of GhFATA3. The oil contents of mature cottonseeds were positively correlated with the contents of palmitic acid and linolenic acid as well as seed vigor. These results provide essential information for further exploring the role(s) of the specific GhFATs in determining oil biosynthesis and cottonseed compositions.     

Successful application of microspore culture in pakchoi (Brassica campestris L. ssp. chinensis Makino var. communis Tsen et Lee) for hybrid breeding

Protoplasma - Microspore embryogenesis is an effective method of obtaining double haploid (DH) lines in only 1&nbsp;year. However, the microspore embryogenesis protocol was not efficient in...