Structured Mixture of Continuation-ratio Logits Models for Ordinal Regression

We develop a nonparametric Bayesian modeling approach to ordinal regression based on priors placed directly on the discrete distribution of the ordinal responses. The prior probability models are built from a structured mixture of multinomial distributions. We leverage a continuation-ratio logits representation to formulate the mixture kernel, with mixture weights defined through the logit stick-breaking process that incorporates the covariates through a linear function. The implied regression functions for the response probabilities can be expressed as weighted sums of parametric regression functions, with covariate-dependent weights. Thus, the modeling approach achieves flexible ordinal regression relationships, avoiding linearity or additivity assumptions in the covariate effects. A key model feature is that the parameters for both the mixture kernel and the mixture weights can be associated with a continuation-ratio logits regression structure. Hence, an efficient and relatively easy to implement posterior simulation method can be designed, using P\'olya-Gamma data augmentation. Moreover, the model is built from a conditional independence structure for category-specific parameters, which results in additional computational efficiency gains through partial parallel sampling. In addition to the general mixture structure, we study simplified model versions that incorporate covariate dependence only in the mixture kernel parameters or only in the mixture weights. For all proposed models, we discuss approaches to prior specification and develop Markov chain Monte Carlo methods for posterior simulation. The methodology is illustrated with several synthetic and real data examples

Overexpression of RAN1 in Rice and Arabidopsis Alters Primordial Meristem, Mitotic Progress, and Sensitivity to Auxin

Ran is an evolutionarily conserved eukaryotic GTPase. We previously identified a cDNA of TaRAN1, a novel Ran GTPase homologous gene in wheat (Triticum aestivum) and demonstrated that TaRAN1 is associated with regulation of genome integrity and cell division in yeast (Saccharomyces cerevisiae) systems. However, much less is known about the function of RAN in plant development. To analyze the possible biological roles of Ran GTPase, we overexpressed TaRAN1 in transgenic Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). TaRAN1 overexpression increased the proportion of cells in the G2 phase of the cell cycle, which resulted in an elevated mitotic index and prolonged life cycle. Furthermore, it led to increased primordial tissue, reduced number of lateral roots, and stimulated hypersensitivity to exogenous auxin. The results suggest that Ran protein was involved in the regulation of mitotic progress, either in the shoot apical meristem or the root meristem zone in plants, where auxin signaling is involved. This article determines the function of RAN in plant development mediated by the cell cycle and its novel role in meristem initiation mediated by auxin signaling

Rice ROOT ARCHITECTURE ASSOCIATED1 Binds the Proteasome Subunit RPT4 and Is Degraded in a D-Box and Proteasome-Dependent Manner1[W][OA]

Root growth is mainly determined by cell division and subsequent elongation in the root apical area. Components regulating cell division in root meristematic cells are largely unknown. Previous studies have identified rice (Oryza sativa) ROOT ARCHITECTURE ASSOCIATED1 (OsRAA1) as a regulator in root development. Yet, the function of OsRAA1 at the cellular and molecular levels is unclear. Here, we show that OsRAA1-overexpressed transgenic rice showed reduced primary root growth, increased numbers of cells in metaphase, and reduced numbers of cells in anaphase, which suggests that OsRAA1 is responsible for limiting root growth by inhibiting the onset of anaphase. The expression of OsRAA1 in fission yeast also induced metaphase arrest, which is consistent with the fact that OsRAA1 functions through a conserved mechanism of cell cycle regulation. Moreover, a colocalization assay has shown that OsRAA1 is expressed predominantly at spindles during cell division. Yeast two-hybrid and pull-down assays, as well as a bimolecular fluorescence complementation assay, all have revealed that OsRAA1 interacts with a rice homolog of REGULATORY PARTICLE TRIPLE-A ATPASE4, a component that is involved in the ubiquitin pathway. Treating transgenic rice with specific inhibitors of the 26S proteasome blocked the degradation of OsRAA1 and increased the number of cells in metaphase. Mutation of a putative ubiquitination-targeting D-box (RGSLDLISL) in OsRAA1 interrupted the destruction of OsRAA1 in transgenic yeast. These results suggest that ubiquitination and proteasomic proteolysis are involved in OsRAA1 degradation, which is essential for the onset of anaphase, and that OsRAA1 may modulate root development mediated by the ubiquitin-proteasome pathway as a novel regulatory factor of the cell cycle