A central unanswered question in stem cell biology, both in plants and in animals, is how the spatial organization of stem cell niches are maintained as cells move through them. We address this question for the shoot apical meristem (SAM) which harbors pluripotent stem cells responsible for growth of above-ground tissues in flowering plants. We find that localized perception of the plant hormone cytokinin establishes a spatial domain in which cell fate is respecified through induction of the master regulator WUSCHEL as cells are displaced during growth. Cytokinin-induced WUSCHEL expression occurs through both CLAVATA-dependent and CLAVATA-independent pathways. Computational analysis shows that feedback between cytokinin response and genetic regulators predicts their relative patterning, which we confirm experimentally. Our results also may explain how increasing cytokinin concentration leads to the first steps in reestablishing the shoot stem cell niche in vitro.clavata ͉ wuschel ͉ computational modeling P lants ranging from the small weed Arabidopsis to the giant sequoia tree, maintain growth of stems, leaves, flowers, and branches through the action of stem cells. In the model plant Arabidopsis, as in other flowering plants, stem cells which give rise to above-ground tissues reside in a structure termed the shoot apical meristem (SAM) (1, 2). The Arabidopsis SAM is composed of three functionally distinct zones. The central zone (CZ) at the tip of the SAM harbors pluripotent stem cells which are necessary for the indeterminate growth and development of the plant. As the plant grows, CZ cells become either multipotent peripheral zone (PZ) cells on the sides of the meristem, capable of differentiating to leaf and flower primordia, or multipotent rib meristem (RM) cells beneath, which can differentiate to the cell types of the stem (3). Positions of zones within the meristem are maintained even as individual cells are displaced from the CZ through the PZ and RM into differentiating tissues. Molecular mechanisms by which meristematic zones are maintained as cells comprising these domains change remains a fundamental question in plant biology (1, 4). One mechanism involves the transmembrane receptor kinase CLAVATA1 (CLV1), expressed in cells of the RM (5). Its ligand, the extracellular peptide product of the CLAVATA3 (CLV3) gene, is produced in the CZ (6), and when it signals the RM cells, they reduce the activity of the WUSCHEL (WUS) gene, which codes for a homeodomain transcription factor also expressed in the RM (7,8). WUS activity is nonautonomously necessary for the maintenance of the CZ cells as pluripotent stem cells, and therefore for persistence of the SAM (9). Loss of CLV3 activity causes enlargement of the CZ by conversion of PZ cells on the PZ-CZ border to CZ cells within hours, followed by enlargement of the SAM through increased cell division or reduced differentiation, or both, over days (10).Multiple lines of evidence show that the plant hormone cytokinin is involved in the CLV/WUS circuit, as well a...

We demonstrate a computational network model that integrates 18 in vitro, high-throughput screening assays measuring estrogen receptor (ER) binding, dimerization, chromatin binding, transcriptional activation, and ER-dependent cell proliferation. The network model uses activity patterns across the in vitro assays to predict whether a chemical is an ER agonist or antagonist, or is otherwise influencing the assays through a manner dependent on the physics and chemistry of the technology platform ("assay interference"). The method is applied to a library of 1812 commercial and environmental chemicals, including 45 ER positive and negative reference chemicals. Among the reference chemicals, the network model correctly identified the agonists and antagonists with the exception of very weak compounds whose activity was outside the concentration range tested. The model agonist score also correlated with the expected potency class of the active reference chemicals. Of the 1812 chemicals evaluated, 111 (6.1%) were predicted to be strongly ER active in agonist or antagonist mode. This dataset and model were also used to begin a systematic investigation of assay interference. The most prominent cause of false-positive activity (activity in an assay that is likely not due to interaction of the chemical with ER) is cytotoxicity. The model provides the ability to prioritize a large set of important environmental chemicals with human exposure potential for additional in vivo endocrine testing. Finally, this model is generalizable to any molecular pathway for which there are multiple upstream and downstream assays available.

Live cell imaging and computational modeling explains how variability in the timing of cell division generates a characteristic pattern of cell sizes during development.

The transcription factor WUSCHEL (WUS) acts from a well-defined domain within the Arabidopsis thaliana shoot apical meristem (SAM) to maintain a stem cell niche. A negative-feedback loop involving the CLAVATA (CLV) signaling pathway regulates the number of WUS-expressing cells and provides the current paradigm for the homeostatic maintenance of stem cell numbers. Despite the continual turnover of cells in the SAM during development, the WUS domain remains patterned at a fixed distance below the shoot apex. Recent work has uncovered a positive-feedback loop between WUS function and the plant hormone cytokinin. Furthermore, loss of function of the cytokinin biosynthetic gene, LONELY GUY (LOG), results in a wus-like phenotype in rice. Herein, we find the Arabidopsis LOG4 gene is expressed in the SAM epidermis. We use this to develop a computational model representing a growing SAM to suggest the plausibility that apically derived cytokinin and CLV signaling, together, act as positional cues for patterning the WUS domain within the stem cell niche. Furthermore, model simulations backed by experimental data suggest a previously unknown negative feedback between WUS function and cytokinin biosynthesis in the Arabidopsis SAM epidermis. These results suggest a plausible dynamic feedback principle by which the SAM stem cell niche is patterned. A central player in the maintenance of CZ stem cells is the transcription factor WUSCHEL (WUS). WUS-expressing cells reside in the rib meristem (RM) domain of the SAM, just below the CZ, and originate from a central group of multipotent stem cells in the corpus (L3 and lower layers below the anticlinally dividing L1 and L2 layers). WUS is required for the production of a non-cell autonomous proliferative signal to determine the number of overlying pluripotent stem cells in the CZ (3, 4). The CZ cells express the CLAVATA3 gene product, which is processed into a signaling peptide that activates a set of receptor kinases, which, in turn, repress WUS expression in the RM (5-8). Thus, the CLV3-expressing CZ stem cells regulate the strength of the non-cell autonomous proliferative signal produced by WUS in the RM of the SAM (1, 9). Through this feedback loop, the size of the apical pluripotent stem cell population and WUSexpressing cell population are mutually regulated. Although this paradigm adequately explains how the numbers of stem cells are maintained in the SAM, it fails to explain how the relative position of the WUS domain is maintained.Crosstalk exists between WUS function and the action of the plant hormone cytokinin in the SAM. WUS has been found to repress members of the type A ARABIDOPSIS RESPONSE REGULATOR (ARR) family, which negatively regulate cytokinin signaling (10). In addition, cytokinin was shown to induce expression of WUS (11). The expression domains for WUS and the cytokinin receptor ARABIDOPSIS HISTIDINE KINASE 4 (AHK4) overlap in the SAM (11). These data support a model whereby AHK4 and WUS function within the RM to establish a group of cytokinin sensitized cel...

For 17 days in August and September 2002, the LIGO and GEO interferometer gravitational wave detectors were operated in coincidence to produce their first data for scientific analysis. Although the detectors were still far from their design sensitivity levels, the data can be used to place better upper limits on the flux of gravitational waves incident on the earth than previous direct measurements. This paper describes the instruments and the data in some detail, as a companion to analysis papers based on the first data. r