Philip N Benfey

..Arabidopsis thaliana, a versatile model organism, represents an opportunity to evaluate the predictive power of biological network inference for plant functional genomics...

..These insights need to be more widely applied to systems biology. Another challenge is to incorporate real-time imaging and develop computational approaches to model biological phenomena in four dimensions...

..Here we review examples of the ways in which availability of the Arabidopsis genome sequence has enhanced progress in understanding root biology...

..Mapping genes to their function is called the "genotype-to-phenotype problem," where phenotype is whatever is changed in the organism when a gene's function is altered...

..Our studies with SHR and SCR homologs from rice suggest that this mechanism is evolutionarily conserved, providing a plausible explanation why nearly all plants have a single layer of endodermis...

..By performing a similar analysis using iron deprivation, we identified common cell-type-specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions...

..Methods that combine these profiles demonstrate transcriptionally rich and complex programs that define Arabidopsis root development in both space and time...

..These results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide data sets to elucidate biological processes...

..This molecular mechanism has characteristics that resemble molecular clock-driven activities in animal species...

..Regulation of expression of the Arabidopsis COB gene family members has highly diversified in comparison to that of the maize COB gene superfamily members. We also identify BRITTLE STALK 2-LIKE 3 as a putative ortholog of AtCOB...

..Together, these results suggest that epigenetic regulation is probably the common basis for SCR and GA activity in cortex cell proliferation...

..Mutations in all enriched transcription factor genes including AGL42 exhibited no detectable root phenotype, raising the possibility of a high degree of functional redundancy in the QC...

..Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway...

..Using these new methods we can begin to understand the biological information contained within large-scale expression data sets...

..This study provides a systematic overview of regulation of TF expression at a cellular level...

..This work lays the foundation for future identification of important genetic components of RSA traits under nutrient limitation using a mapping population derived from these two accessions...

..Finally, among our root hair-specific proteins we identified two unique regulators of root hair development...

..Finally, we provide evidence that movement requires both cytoplasmic and nuclear localization, strongly suggesting a mechanistic link between nuclear transport and cell-to-cell movement...

..Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed...

..Finally, a novel temporal mechanism for lateral root positioning and the implications for intercellular signaling are considered...

..The spatial distribution of competence to respond to SHR highlights the importance of tightly regulated movement in generating the root radial pattern...

..In addition to gene expression, downstream applications of FACS include proteomic and metabolite analysis. This is a powerful method to examine biological functions of specific cell types and tissues with a systems biology approach...

..This pathway functions independently of auxin and cytokinin plant hormonal signaling. Comparison to ROS-regulated growth control in animals suggests that a similar mechanism is used in plants and animals...

..Approaches like this will be useful to lay the groundwork to reconstruct regulatory networks on the level of tissues or even individual cells. AVAILABILITY: Upon request from the authors...

..Future refinement of these models will lead to a more complete description of the complex molecular interactions that give rise to a simple growing root...

..Advancements in the isolation of single-cell populations will be highlighted, and the potential application towards generating detailed metabolic profiles will be discussed...

..Thus, in contrast to proteins that move by a process resembling diffusion, a cytoplasmic pool of SHR is not sufficient for movement...

..Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming that novel miRNAs predicted by PIPmiR have functional relevance...

..This issue is particularly relevant to developmental biologists, who are interested in processes such as growth, segmentation and differentiation, which can all take place simultaneously, but on different time scales...

..Our observations suggest that COB, through its involvement in cellulose microfibril orientation, is an essential factor in highly anisotropic expansion during plant morphogenesis...

..PYE and BTS expression is also tightly coregulated. We propose that interactions among PYE, PYE homologs, and BTS are important for maintaining iron homeostasis under low iron conditions...

..Together, these mechanisms coherently coordinate developmental decisions with resource allocation and growth...

..Several recent studies provide new insight into how transcription factors and phytohormones interact within meristems to control cell proliferation and differentiation...

..This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes...

..Finally, a dynamic transcriptional mechanism for lateral organ positioning that integrates spatial and temporal information into a repeating pattern is summarized...

..Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics...

..These examples occur in early embryogenesis, stomatal development, and ground tissue formation in the root...

..Ultimately, the integration of diverse and massive datasets into coherent models will improve our understanding of the molecular networks that underlie biological processes...

..Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered...

..These findings could shed light on the role and influence of noncoding sequences on gene expression...

..This work enables the automatic phenotyping of RSA of individuals within mapping populations, providing an integrative framework for quantitative trait loci analysis of RSA...

..Recent work using computer modeling and live imaging is helping to elucidate some of the mechanisms responsible for the specification and maintenance of stem cells in the root and shoot...

..In this review we propose that 'triangulation' among transcriptomics, proteomics and metabolomics is a meaningful approach for beginning this integrative analysis and uncovering a systems level perspective of Arabidopsis biology...

..We tracked hundreds of roots to capture detailed expression patterns of 12 transgenic reporter lines under different conditions...

..Improvements in phenotyping will facilitate the genetic analysis of RSA and aid in the identification of the genetic loci underlying useful agronomic traits...

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..In this issue of Cell, it is revealed that a canonical retinoblastoma pathway plays a crucial role in regulating the balance between differentiation and renewal of plant root stem cells...

..Further investigation of plant systems will require data gathering from specific cells and tissues, continued improvement in metabolic technologies, and novel computational methods for data visualization and modeling...

..As a result, future research advances in this field will require tissue-specific information at both the single gene and global level...

..Here we review recent developments in cell-to-cell trafficking of macromolecules in plants and animals...

..We observed a motility phenotype for two of these three genes. Thus, these algorithms allow for high-throughput functional prediction of genes beyond that provided by simple orthology-based annotation endeavors...

..The discovery that a kinase of the MAPKK class plays a key role in cell specification at the first division of the Arabidopsis embryo suggests that there may be similarities based on a common logic...

..The platform is relatively inexpensive, high-throughput, and is ideally suited for researchers aiming to understand the genetic control of root architecture. Here we describe the application of this method to rice and maize root systems...

..Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks...

..Here we highlight promising technologies for 'phenome-scale' analyses in multicellular organisms...

..Availability: BSD-licensed Python code at http://grassrootsbio.com/papers/powrs/...

..Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface...

..A new, high resolution root expression map detailing the transciptome of nearly all cell types in the Arabidopsis root across developmental timepoints will provide a framework for understanding these networks...

..We describe recent regulatory network reconstructions in a variety of organisms, and discuss the success they share in identifying new regulatory components, shared relationships and phenotypic outcomes...

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..We found SCL23 to be the most closely related to SCR in both eudicots and monocots, suggesting that a gene duplication resulting in SCR and SCL23 predates the divergence of dicots and monocots...

..hya/hya seedlings and double mutants point to a role of PLE and HYA in the same process. These mutants provide tools to elucidate the regulation of nuclear cytoskeletal interactions during cell division and cytokinesis...

..The possibility of applying comparative genomics approaches to Arabidopsis and related species promises profound new insights into the interplay of evolution and development...

..Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation...

..A map of gene expression in the Arabidopsis root has identified many new candidate genes that feed into and out of these transcriptional controls...