Excision of a selectable marker in transgenic rice (Oryza sativa L.) using a chemically regulated Cre/loxP system

Removal of a selectable marker gene from genetically modified (GM) crops alleviates the risk of its release into the environment and hastens the public acceptance of GM crops. Here we report the production of marker-free transgenic rice by using a chemically regulated, Cre/loxP-mediated site-specific DNA recombination in a single transformation. Among 86 independent transgenic lines, ten were found to be marker-free in the T₀ generation and an additional 17 lines segregated marker-free transgenic plants in the T₁ generation. Molecular and genetic analyses indicated that the DNA recombination and excision in transgenic rice were precise and the marker-free recombinant T-DNA was stable and heritable.The first two authors contributed equally to the work     

The comparison of the confidence regions in phylogeny

In this paper, several different procedures for constructing confidence regions for the true evolutionary tree are evaluated both in terms of coverage and size without considering model misspecification. The regions are constructed on the basis of tests of hypothesis using six existing tests: Shimodaira Hasegawa (SH), SOWH, star form of SOWH (SSOWH), approximately unbiased (AU), likelihood weight (LW), generalized least squares, plus two new tests proposed in this paper: single distribution nonparametric bootstrap (SDNB) and single distribution parametric bootstrap (SDPB). The procedures are evaluated on simulated trees both with small and large number of taxa. Overall, the SH, SSOWH, AU, and LW tests led to regions with higher coverage than the nominal level at the price of including large numbers of trees. Under the specified model, the SOWH test gives accurate coverage and relatively small regions. The SDNB and SDPB tests led to the small regions with occasional undercoverage. These two procedures have a substantial computational advantage over the SOWH test. Finally, the cutoff levels for the SDNB test are shown to be more variable than those for the SDPB test.     

Identification of Self-Incompatibility Genotypes of Apricot (<Emphasis Type="Italic">Prunus armeniaca</Emphasis> L.) by S-Allele-Specific PCR Analysis

A cDNA of 417 bp encoding an S-RNase gene, named PA S3, was isolated from apricot, Prunus aremeniaca. Nine S-alleles, S₁–S₉, were recognized by S-allele-specific PCR and confirmed by Southern blot analysis using PA S3 as probe. The S-genotypes of the six cultivars were determined and the results of self- and cross-pollination tests among the six cultivars were consistent with the predicted S-haplotypes by PCR analysis.     

Molecular mechanisms of the 2,3,7,8-tetrachlorodibenzo-p-dioxin-induced inverted U-shaped dose responsiveness in anchorage independent growth and cell proliferation of human breast epithelial cells with stem cell characteristics

Although 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) has a variety of carcinogenic and noncarcinogenic effects in experimental animals, its role in human carcinogenicity remain controversial. A simian virus 40-immortalized cell line from normal human breast epithelial cells with stem cells and luminal characteristics (M13SV1) was used to study whether TCDD can induce AIG positive colony formation and cause increased cell numbers in a inverted U-shaped dose–response manner. TCDD activated Akt, ERK2, and increased the expression of CYP1A1, PAI-2, IL-lb mRNA, and ERK2 protein levels. TCDD was able to increased phosphorylation and expression of ERK2 in same dose–response manner as AIG positive colony formation. Thus, TCDD induced tumorigenicity in M13SV1, possibly through the phosphorylation of ERK2 and/or Akt. Further, cDNA microarray with 7448 sequence-verified clones was used to profile various gene expression patterns after treatment of TCDD. Three clear patterns could be delineated: genes that were dose-dependently up-regulated, genes expressed in either U-shape and/or inverted U-shape. The fact that these genes are intrinsically related to breast epithelial cell proliferation and survival clearly suggests that they may be involved in the TCDD-induced breast tumorigenesis.     

Analysis of the plant architecture via tree-structured statistical models: the hidden Markov tree models

Plant architecture is the result of repetitions that occur through growth and branching processes. During plant ontogeny, changes in the morphological characteristics of plant entities are interpreted as the indirect translation of different physiological states of the meristems. Thus connected entities can exhibit either similar or very contrasted characteristics. We propose a statistical model to reveal and characterize homogeneous zones and transitions between zones within tree-structured data: the hidden Markov tree (HMT) model. This model leads to a clustering of the entities into classes sharing the same 'hidden state'. The application of the HMT model to two plant sets (apple trees and bush willows), measured at annual shoot scale, highlights ordered states defined by different morphological characteristics. The model provides a synthetic overview of state locations, pointing out homogeneous zones or ruptures. It also illustrates where within branching structures, and when during plant ontogeny, morphological changes occur. However, the labelling exhibits some patterns that cannot be described by the model parameters. Some of these limitations are addressed by two alternative HMT families.     

How rainfall, relative humidity and temperature influence volatile emissions from apple trees in situ

Headspace volatiles from apple-bearing twigs were collected in the field with a Radiello sampler during three different diurnal periods over the complete fruit growing season. Analyses by thermal desorption-GC-MS identified a total of 62 compounds in changing quantities, including the terpenoids alpha-pinene, camphene, beta-pinene, limonene, beta-caryophyllene and (E,E)-alpha-farnesene, the aldehydes (E)-2-hexenal, benzaldehyde and nonanal, and the alcohol (Z)-3-hexen-1-ol. The variations in emission of these plant odours were statistically related to temperature, humidity and rainfall in the field. Remarkably, rainfall had a significant positive influence on changes in volatile release during all three diurnal periods, and further factors of significance were temperature and relative humidity around noon, relative humidity in the late afternoon, and temperature and relative humidity during the night. Rainfall was associated consistently with an increase in the late afternoon in terpene and aldehyde volatiles with a known repellent effect on the codling moth, one of the key pests of apple fruit. During the summer of 2003, a season characterized by below-average rainfall, some postulated effects of drought on trees were tested by establishing correlations with rainfall. Emissions of the wood terpenes alpha-pinene, beta-pinene and limonene were negatively correlated with rainfall. Another monoterpene, camphene, was only detected in this summer but not in the previous years, and its emissions were negatively correlated with rainfall, further supporting the theory that drought can result in higher formation of secondary metabolites. Finally, the two green leaf volatiles (E)-2-hexenal and (Z)-3-hexen-1-ol were negatively correlated with rainfall, coinciding well with the expectation that water deficit stress increases activity of lipoxygenase. To our knowledge, this work represents the first empirical study concerning the influence of abiotic factors on volatile emissions from apple trees in situ.     

Calmodulin regulates the post-anaphase reposition of centrioles during cytokinesis

INTRODUCTIONCytokinesis is a very complicated and carefully orches-trated process. During the last step of this process, anintercellular bridge is formed between the two daughtercells. A number of studies suggest that this intercellularbridge is not merel…     

Fundamental significance of specific phosphodiesterases in the control of spontaneous meiotic resumption in porcine oocytes

The meiosis of mammalian oocytes begins during the fetal life and stops at the dictyate stage. This study has assessed the role of specific phosphodiesterase (PDE) inhibitors on the control of meiotic resumption in porcine oocytes investigating the influence of PMSG-hCG and cAMP stimulation. Cumulus-oocytes complexes (COCs) and denuded oocytes (DOs) were collected from gilt ovaries obtained at a local slaughterhouse. Oocytes were cultured in NCSU23 with different PDE inhibitors. The EC(50) for oocytes maintained in germinal vesicle (GV) stage was evaluated using different doses of both cilostamide (CIL), PDE3 inhibitor and 3-isobutyl-1-methylxanthine (IBMX), a nonspecific PDE inhibitor. In presence of PMSG-hCG, meiotic resumption is observed after 24 hr of culture. Both CIL and IBMX reversibly blocked meiotic resumption. In absence of PMSG-hCG, meiotic resumption is reduced after 24 hr of culture. After 48 hr of culture, only CIL significantly blocked meiotic resumption. Still in absence of PMSG-hCG, significant effect of treatment was only observed in COCs using the combination of CIL and rolipram (PDE3 and PDE4 inhibitor, respectively) compared to the use of IBMX. To assess the contribution of cAMP synthesis, a low dose of an adenylyl cyclase (AC) stimulator, forskolin, has been used in combination with CIL showing a significant effect of this combination. In CIL-treated COCs and DOs, significant higher percentages of oocytes were maintained in GV stage when cultured in combination with forskolin instead of PMSG-hCG. In conclusion, these results demonstrate that the control of meiotic resumption in porcine oocytes is highly regulated by cAMP. Both the degradation by specific PDE3 enzyme and the synthesis by an active AC are highly involved.     

Estimation of the extent of linkage disequilibrium in seven regions of the porcine genome

Linkage disequilibrium (LD) refers to the correlation among neighboring alleles, reflecting non-random patterns of association between alleles at (nearby) loci. A better understanding of LD in the porcine genome is of direct relevance for identification of genes and mutations with a certain effect on the traits of interest. Here, 215 SNPs in seven genomic regions were genotyped in individuals of three breeds. Pairwise linkage disequilibrium was calculated for all marker pairs. To estimate the extent of LD, all pairwise LD values were plotted against the distance between the markers. Based on SNP markers in four genomic regions analyzed in three panels from populations of Large White, Dutch Landrace, and Meishan origin, useful LD is estimated to extend for approximately 40 to 60 kb in the porcine genome.     

A comprehensive study of optimal conditions for naked plasmid DNA transfer into skeletal muscle by electroporation

Efficient gene transfer is a key factor in gene therapy. Reducing the damage caused by gene transfer to muscle by electroporation is very important for its clinical application. Extensive investigation of optimal conditions for gene transfer by electroporation is required. The parameters used for electroporation, including plasmid concentration; injection volume; the plasmid dose of the injection; the concentration of saline media; the size of plasmid DNA; the age of the mice; the lag time between plasmid injection and electroporation; and the effect of repeated gene transfer by electroporation, were systematically investigated in the present study. The efficiencies of gene transfer by electroporation in normal and rodent models of diabetes were also evaluated. We found that electroporation used for non-viral gene transfer could be repeated in the same place in the muscle, but the expression efficiency was closely related to the muscle damage. Increasing pulse times could enhance the efficiency of gene transfer with a lower strength of electric field. It was better to use a higher plasmid concentration than to use a larger dose of plasmid and repeated injection to achieve a high level of transgene expression. Optimal conditions varied in different animal models, being milder for diabetic mice than for normal mice, and it was also shown that the conditions that worked well on these small rodents were not necessarily suitable for larger animals. Our results provide a comprehensive view of the factors that affect the efficiency of gene transfer into skeletal muscle by electroporation.