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Development of organisms is a very complex process in that a lot of gene networks of different cell types are to be integrated. Development of cellular automata that model the morphodynamics of different cell types is the first step in understanding and analyzing the regulatory mechanisms that underlie the developmental gene networks. We have developed a model of a cellular automaton that simulates the embryonic development of the shoot meristem in Arabidopsis thaliana. The model adequately describes the basic stages in the development of this organ in wild type and mutants.
相似文献Background
Recent experimental work has uncovered some of the genetic components required to maintain the Arabidopsis thaliana root stem cell niche (SCN) and its structure. Two main pathways are involved. One pathway depends on the genes SHORTROOT and SCARECROW and the other depends on the PLETHORA genes, which have been proposed to constitute the auxin readouts. Recent evidence suggests that a regulatory circuit, composed of WOX5 and CLE40, also contributes to the SCN maintenance. Yet, we still do not understand how the niche is dynamically maintained and patterned or if the uncovered molecular components are sufficient to recover the observed gene expression configurations that characterize the cell types within the root SCN. Mathematical and computational tools have proven useful in understanding the dynamics of cell differentiation. Hence, to further explore root SCN patterning, we integrated available experimental data into dynamic Gene Regulatory Network (GRN) models and addressed if these are sufficient to attain observed gene expression configurations in the root SCN in a robust and autonomous manner.Results
We found that an SCN GRN model based only on experimental data did not reproduce the configurations observed within the root SCN. We developed several alternative GRN models that recover these expected stable gene configurations. Such models incorporate a few additional components and interactions in addition to those that have been uncovered. The recovered configurations are stable to perturbations, and the models are able to recover the observed gene expression profiles of almost all the mutants described so far. However, the robustness of the postulated GRNs is not as high as that of other previously studied networks.Conclusions
These models are the first published approximations for a dynamic mechanism of the A. thaliana root SCN cellular pattering. Our model is useful to formally show that the data now available are not sufficient to fully reproduce root SCN organization and genetic profiles. We then highlight some experimental holes that remain to be studied and postulate some novel gene interactions. Finally, we suggest the existence of a generic dynamical motif that can be involved in both plant and animal SCN maintenance. 相似文献MicroRNA (miRNA), short single-stranded RNA, can bind to eukaryotic mRNA and cause its degradation or inhibit its translation. We have analyzed the correlation between context characteristics of Arabidopsis thaliana mature miRNA sequences and the experimental data on miRNA abundance in the main types of plant tissue. Two correlations between the context pattern and miRNA abundance have been found: (i) concurrent presence of dinucleotides CA at positions 14–16 and CC at 18–19 relative to the miRNA 5′-end is characteristic of miRNA with low abundance in seedling and inflorescence tissues, whereas the absence of both dinucleotides correlates with high miRNA abundance; (ii) presence of UG at positions 5–10 combined with the absence of CC at positions 18–19 correlates with high miRNA abundance in the inflorescence, whereas the absence of UG and presence of CC correlates with miRNA low abundance.
相似文献