RESUMO
Generalized linear mixed models are commonly used to describe relationships between correlated responses and covariates in medical research. In this paper, we propose a simple and easily implementable regularized estimation approach to select both fixed and random effects in generalized linear mixed model. Specifically, we propose to construct and optimize the objective functions using the confidence distributions of model parameters, as opposed to using the observed data likelihood functions, to perform effect selections. Two estimation methods are developed. The first one is to use the joint confidence distribution of model parameters to perform simultaneous fixed and random effect selections. The second method is to use the marginal confidence distributions of model parameters to perform the selections of fixed and random effects separately. With a proper choice of regularization parameters in the adaptive LASSO framework, we show the consistency and oracle properties of the proposed regularized estimators. Simulation studies have been conducted to assess the performance of the proposed estimators and demonstrate computational efficiency. Our method has also been applied to two longitudinal cancer studies to identify demographic and clinical factors associated with patient health outcomes after cancer therapies.
Assuntos
Neoplasias , Humanos , Modelos Lineares , Funções Verossimilhança , Simulação por Computador , Estudos LongitudinaisRESUMO
A novel osClpD gene, encoding a highly conservative ClpD subfamily member, was first isolated and characterized from Oryza sativa. The full-length cDNA of osClpD gene was 3140 bp and contained a 2884 bp open reading frame encoding a 938 amino acid protein. The phylogenetic tree and blast search showed that OSClpD belonged to the ClpD subfamily of the Hsp100/Clp family, and contained all protein motifs characteristic for the ClpD subfamily of Hsp100/Clp proteins. The real-time quantitative PCR analysis proved that it was inducible by water deficit and temperature stress in vegetative tissues.
Assuntos
Adenosina Trifosfatases/genética , Oryza/genética , Filogenia , Serina Endopeptidases/genética , Sequência de Aminoácidos , Sequência de Bases , Análise por Conglomerados , Primers do DNA , DNA Complementar/genética , Dessecação , Endopeptidase Clp , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , TemperaturaRESUMO
A subtractive cDNA library was constructed using rice (Oryza sativa L.) callus cDNA as driver and differentiating callus cDNA as tester. A novel cDNA fragment encoding RNase L inhibitor (RLI) was isolated by screening the subtractive library, which had a higher expression level in differentiating callus than in callus. The full-length cDNA of rice-RLI was obtained by the method of rapid amplification of cDNA ends, which contained a 1812-bp open reading frame encoding a 604 amino acid polypeptide. Homologous analysis showed that rice-RLI contained the conserved motifs (two repeated P-loops, two ATP-binding boxes and an iron-sulfur binding motif). The fluorescence quantitative PCR analysis showed that it was a constitutive expressed gene but up-regulated in abiotic stress (low temperature and NaCl treatment) and down-regulated under the treatments of NAA and IAA.
Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Chaperoninas/genética , Regulação da Expressão Gênica , Oryza/genética , Motivos de Aminoácidos , Sequência de Aminoácidos , Sequência de Bases , Primers do DNA , DNA Complementar/genética , Fluorescência , Dados de Sequência Molecular , Reação em Cadeia da Polimerase , Análise de Sequência de DNA , Cloreto de Sódio , Temperatura , Fatores de TempoRESUMO
Using Rapid Amplification of cDNA ends (RACE) technique, the full-length cDNA encoding a NaCl-induced fructose-1, 6-diphosphate aldolase (DsALDP) was obtained. It was shown that the DsALDP had a relatively high homology (66%-73%) to chloroplast fructose-1, 6-diphosphate aldolase (AldP) in many plants according to their amino acid sequences. The phylogenetic analysis further confirmed that AldP in alga is the nearest to DsALDP. As to its expression pattern, DsALDP was de novo synthesized by NaCl induction. Its expression level was significantly changed with inducing time. After the selected DsALDP cDNA subcloned into a binary vector pBI121, the new construct was introduced into tobacco by Agrobacterium tumefaciens. The results of Southern blot and RT-PCR analysis of four transgenic T1 plants indicated that DsALDP was integrated into genome of these transgenic plants and effectively expressed. Aldolase activities have been detected in T1-1, T1-2 and T1-3 plants by bioassay under 100-200 mmol/L NaCl. It was also observed that proline contents in them were differentially increased.
Assuntos
Clorófitas/enzimologia , Clorófitas/genética , Frutose-Bifosfato Aldolase/genética , Nicotiana/enzimologia , Nicotiana/genética , Proteínas de Algas/genética , Sequência de Aminoácidos , Sequência de Bases , Clonagem Molecular , DNA de Algas/genética , DNA Complementar/genética , Expressão Gênica , Dados de Sequência Molecular , Plantas Geneticamente Modificadas , Proteínas Recombinantes/genética , Plantas Tolerantes a Sal/enzimologia , Plantas Tolerantes a Sal/genética , Homologia de Sequência de Aminoácidos , Cloreto de Sódio/farmacologia , Equilíbrio Hidroeletrolítico/genética , Equilíbrio Hidroeletrolítico/fisiologiaRESUMO
In silico cloning was a new strategy of gene cloning developed with the development of genome, EST projects and bioinformatics. Using wheat glucose-6-phosphate dehydrogenase cDNA (clone: Tagpdl) sequence as a querying probe, one highly homologous BAC clone sequence was obtained from rice sequence database of GenBank and the putative cDNA sequence of rice glucose-6-phosphate dehydrogenase was assembled according to the wheat clone. Furthermore, the full-length cDNA of rice glucose-6-phosphate dehydrogenase was cloned by RT-PCR with two primers designed based on this assembled cDNA sequence. Since this fragment contained a complete ORF of 1515 bp with a stop codon in its upstream and poly(A) signal in its downstream, it could be concluded that a full-length gene (GenBank accession number AY078072), which was named as OsG6PDH. Homology analysis of OsG6PDH showed a 88% identity with wheat and the deduced amino acid showed 89%, 79% and 80% homology with G6PDH from wheat, tomato and tobacco respectively. OsG6PDH was expressed in inflorescence, embryo, root and leaf of rice, with a slightly higher in inflorescence and root. It was also discussed in this paper that the application of in silico cloning in the isolation of functional genes from rice.