Marginal proportional hazards models for clustered interval-censored data with time-dependent covariates

The Botswana Combination Prevention Project was a cluster-randomized HIV prevention trial whose follow-up period coincided with Botswana's national adoption of a universal test and treat strategy for HIV management. Of interest is whether, and to what extent, this change in policy modified the preventative effects of the study intervention. To address such questions, we adopt a stratified proportional hazards model for clustered interval-censored data with time-dependent covariates and develop a composite expectation maximization algorithm that facilitates estimation of model parameters without placing parametric assumptions on either the baseline hazard functions or the within-cluster dependence structure. We show that the resulting estimators for the regression parameters are consistent and asymptotically normal. We also propose and provide theoretical justification for the use of the profile composite likelihood function to construct a robust sandwich estimator for the variance. We characterize the finite-sample performance and robustness of these estimators through extensive simulation studies. Finally, we conclude by applying this stratified proportional hazards model to a re-analysis of the Botswana Combination Prevention Project, with the national adoption of a universal test and treat strategy now modeled as a time-dependent covariate.     

Identification of a genomic region linked with sex determination of Undaria pinnatifida (Alariaceae) through genomic resequencing and genetic linkage analyses of a segregating gametophyte family

Different from the traditional knowledge about kelp, three sexual phenotypes (female, male, and monoecious) exist in the haploid gametophytes of Undaria pinnatifida. However, the sex-determining mechanisms remain unknown. Genetic linkage mapping is an efficient tool to identify sex-linked regions. In the present study, we resequenced a segregating gametophyte family based on the male genome of U. pinnatifida. A high-density genetic linkage map was constructed using 9887 SNPs, with an average distance of 0.41 cM between adjacent SNPs. On the basis of this genetic map and using the composite interval mapping method, we identified 62 SNPs significantly linked with the sexual phenotype. They were located at a position of 67.67 cM on the linkage group 23, corresponding to a physical range of 14.67 Mbp on the HiC_Scaffold_23 of the genome. Reanalysis of the previous specific length amplified fragment sequencing data according to the reference genome led to the identification of a sex-linked genomic region that encompassed the above-mentioned 14.67 Mbp region. Hence, this overlapped genomic range was likely the sex-determining region. Within this region, 129 genes were retrieved and 39 of them were annotated with explicit function, including the potential male sex-determining gene-encoding high mobility group (HMG) domain protein. Relative expression analysis of the HMG gene showed that its expression was higher in male gametophytes during the vegetative phase and monoecious gametophytes during both the vegetative and gametogenesis phases, but significantly lower in male gametophytes during the gametogenesis phase. These results provide a foundation for deciphering the sex-determining mechanism of U. pinnatifida.     

Effects of Mechanized,Deep Application of Slow-Release Fertilizer on Yield and Nitrogen,Phosphorus, and Potassium Utilization of Direct-Seeded Rice

Compared with the standard method of manual fertilizer broadcasting (MFB), mechanized hill-drilling direct-seeding with deep application of slow-release nitrogen fertilizer (MHDDF) is an efficient method to integrate both fertilization and seeding. However, there are few studies that combine the use of slow-release fertilizer with MHDDF. We sought to explore the combined effect of MHDDF with slow-release fertilizer on rice yield and nitrogen, phosphorus, and potassium utilization, compared to MFB. We compared three different MHDDF methods (D30: 450 kg ha^?1, D40: 600 kg ha^?1, D50: 750 kg ha^?1), with one MFB method (B50: 750 kg ha^?1), and one control (CK: 0 kg ha^?1). We found that the yield of all MHDDF method was higher than that of both the MFB method. Yield was the highest in the D50 treatment and was 14.14–46.03% higher than that in B50 treatment. Biomass accumulation, nutrient accumulation, and nutrient use efficiency were similarly higher in MHDDF method than both MFB and CK. Compared to B50, the D50 treatment increased nitrogen recovery efficiency by 170.53–231.50%, phosphorus recovery efficiency by 480.00–724.25%, and potassium recovery efficiency by 201.55–169.59%. Overall, we found that combining MHDDF with slow-release fertilizer was an effective method to increase rice yield and nutrient use efficiency compared with MFB.

     

异育银鲫及其人工杂合种外源遗传物质的检测分析

采用 DNA 杂交的方法,对异育银鲫及其人工杂合种进行了外源 DNA 的检测分析,发现两个雌核发育系的异育银鲫及其人工杂合种的 DNA 与红鲤 DNA 片段间的分子杂交均有阳性斑点出现,这表明,在异育银鲫及其人工杂合种产生过程中,父本(红鲤)的 DNA 片段的确可以随机地掺入到母本细胞的 DNA 中,从而产生了异精效应,使其子代生长加快,并出现父本性状。     

聚球藻(Synechococcus leopoliensis625)藻胆体-类囊体膜光化学活性和亚显微结构的研究

聚球藻藻胆体-类囊体膜吸收光谱中有五个吸收峰,它们位于420nm,438nm,490nm,624nm 和678nm。放氧速率为161—179mol O2/mg Chl.hr.电镜照片中显示在类囊体膜上有大量藻胆体。     

湿地松木质部和针叶松脂合成基因分析

为挖掘湿地松(Pinus elliottii)松脂合成相关的基因,对不同采脂期的木质部和针叶进行高通量转录组测序,与火炬松(Pinus taeda)参考基因组进行比对,共获得了68 211条unigenes,546 356 450条clean reads,平均比对率达90.21%。将不同时期木质部、木质部与针叶间进行两两对比,以P＜0.05,|log₂FoldChange|＞1.0为标准来筛选差异基因,并进行GO和KEGG富集分析。结果表明,参与萜类物质合成的差异基因有133个,其中大部分富集在MEP途径,从差异基因中挑选8个产脂相关的候选基因进行RT-qPCR验证,确定HMGR、DXS、TPS、ABC转运蛋白基因与产脂存在关联性。通过转录组测序与分析,挖掘出133个参与松脂萜类物质合成相关的差异基因,其中萜烯合酶基因(TPS)和ABC转运基因在正调控萜类物质合成中发挥关键作用。     

Genome-wide identification,classification, and expression profiling of serine esterases and other esterase-related proteins in the tobacco hornworm,Manduca sexta

Serine esterases (SEs) are hydrolases that catalyze the conversion of carboxylic esters into acids and alcohols. Lipases and carboxylesterases constitute two major groups of SEs. Although over a hundred of insect genomes are known, systematic identification and classification of SEs are rarely performed, likely due to large size and complex composition of the gene family in each species. Considering their key roles in lipid metabolism and other physiological processes, we have categorized 144 M. sexta SEs and SE homologs (SEHs), 114 of which contain a motif of GXSXG. Multiple sequence alignment and phylogenetic tree analysis have revealed 39 neutral lipases (NLs), 3 neutral lipase homologs (NLHs), 11 acidic lipases (ALs), 3 acidic lipase homologs (ALHs), a lipase-3, a triglyceride lipase, a monoglyceride lipase, a hormone-sensitive lipase, and a GDSL lipase. Eighty-three carboxylesterase genes encode 29 α-esterases (AEs), 12 AEHs (e.g., SEH4-1–3), 20 feruloyl esterases (FEs), 2 FEHs, 2 β-esterases (BEs), 2 integument esterases (IEs), 1 IEH, 4 juvenile hormone esterases, 2 acetylcholinesterases, gliotactin, 6 neuroligins, neurotactin, and an uncharacteristic esterase homolog. In addition to these GXSXG proteins, we have identified 26 phospholipases and 13 thioesterases. Expression profiling of these genes in specific tissues and stages has provided insights into their functions including digestion, detoxification, hormone processing, neurotransmission, reproduction, and developmental regulation. In summary, we have established a framework of information on SEs and related proteins in M. sexta to stimulate their research in the model species and comparative investigations in agricultural pests or disease vectors.