Functional data analysis with covariate-dependent mean and covariance structures

Functional data analysis has emerged as a powerful tool in response to the ever-increasing resources and efforts devoted to collecting information about response curves or anything that varies over a continuum. However, limited progress has been made with regard to linking the covariance structures of response curves to external covariates, as most functional models assume a common covariance structure. We propose a new functional regression model with covariate-dependent mean and covariance structures. Particularly, by allowing variances of random scores to be covariate-dependent, we identify eigenfunctions for each individual from the set of eigenfunctions that govern the variation patterns across all individuals, resulting in high interpretability and prediction power. We further propose a new penalized quasi-likelihood procedure that combines regularization and B-spline smoothing for model selection and estimation and establish the convergence rate and asymptotic normality of the proposed estimators. The utility of the developed method is demonstrated via simulations, as well as an analysis of the Avon Longitudinal Study of Parents and Children concerning parental effects on the growth curves of their offspring, which yields biologically interesting results.     

Surface imprinted bio-nanocomposites for affinity separation of a cellular DNA repair protein

Apurinic/apyrimidinic endonuclease 1 (APE1) is a multifunctional DNA repair protein localized in different subcellular compartments. The mechanisms responsible for the highly regulated subcellular localization and “interactomes” of this protein are not fully understood but have been closely correlated to the posttranslational modifications in different biological context. In this work, we attempted to develop a bio-nanocomposite with antibody-like properties that could capture APE1 from cellular matrices to enable the comprehensive study of this protein. By fixing the template APE1 on the avidin-modified surface of silica-coated magnetic nanoparticles, we first added 3-aminophenylboronic acid to react with the glycosyl residues of avidin, followed by addition of 2-acrylamido-2-methylpropane sulfonic acid as the second functional monomer to perform the first step imprinting reaction. To further enhance the affinity and selectivity of the binding sites, we carried out the second step imprinting reaction with dopamine as the functional monomer. After the polymerization, we modified the nonimprinted sites with methoxypoly (ethylene glycol) amine (mPEG-NH₂). The resulting molecularly imprinted polymer-based bio-nanocomposite showed high affinity, specificity, and capacity for template APE1. It allowed for the extraction of APE1 from the cell lysates with high recovery and purity. Moreover, the bound protein could be effectively released from the bio-nanocomposite with high activity. The bio-nanocomposite offers a very useful tool for the separation of APE1 from various complex biological samples.     

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.

     

<i>VvAGAMOUS</i> Affect Development of Four Different Grape Species Ovary

Grape pistil has an important influence on fruit size and quality. However, there were few studies on grape ovary, and the development process of the ovary is still unclear. Therefore, in this paper, four different grape varieties with different lengths of small inflorescences, namely ‘Musct Hambourg’ grape (Vitis vinifera), ‘Concord’ grape (Vitis labrusca), ‘ShanPuTao’ grape (Vitis amurensis) and ‘GongNiang2Hao’ grape (Vitis amurensis × Vitis vinifera) were used as test materials. Four varieties ovary were significant differences by means of stereomicroscope, paraffin section. The expression of ovary determining gene VvAGAMOUS (VvAG) and its development related genes VvCRABS CLAW (VvCRC) andVvAGAMOUS-LIKE 11 (VvAGL11) with similar functions during the development of different grape varieties were preliminarily explored using fluorescence quantitative test. The relationship between VvAG and VvCRC, VvAG and VvAGL11 were analyzed using Y1H assay. Our results showed that there were obvious abdominal sutures on the surface of expect for ‘Musct Hambourg’ grape, and existing poly carpels. The ovary development of ‘ShanPuTao’ and ‘GongNiang2Hao’ grape was completed when the inflorescence length was less than 1 cm, while the ‘Concord’ and ‘Musct Hambourg’ grape were fully developed when the length of inflorescence was 3–4 and 4–5 cm, respectively. VvAG and VvCRC began to express in large quantities after the formation of stamen primordia, while VvAGL11 during the forming of ovule primordia. Therefore, VvAG and VvCRC mainly regulated the development of stamens and carpels and also promote the development of ovules, while VvAGL11 major regulated the development of ovules. The promoters of VvCRC and VvAGL11 were bound by VvAG. This study provides an important theoretical basis for further research on the molecular mechanism of grape ovary development.     

Comparative Transcriptome Analyses Reveal Genes Related to Spine Development in Cucumber (<i>Cucumis sativus</i>)

Fruit spine is an important quality trait of cucumber. To better understand the molecular basis of cucumber spine development and function, RNA-Seq was performed to identify differentially expressed genes (DEGs) in fruit spines of different development stages, namely, 8 days before anthesis (SpBA8), anthesis (SpA) and 8 days after anthesis (SpAA8). Stage-wise comparisons obtained 2,259 (SpBA8 vs. SpA), 4,551 (SpA vs. SpAA8), and 5,290 (SpBA8 vs. SpAA8) DEGs. All the DEGs were classified into eight expression clusters by trend analysis. Among these DEGs, in addition to the Mict, Tril, CsTTG1, CsMYB6, NS, and Tu genes that have been reported to regulate fruit spine formation, we found that the CsHDG11, CsSCL8, CsSPL8, CsZFP6 and CsZFP8 may also be involved in spine development in cucumber. Our study provides a theoretical basis for further research on molecular mechanisms of spine development in cucumber.     

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.     

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.