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Durham, NC, United States

Ingram P.,University of Chicago | Ingram P.,GrassRoots Biotechnology | Dettmer J.,University of Helsinki | Dettmer J.,Vlaams Institute for Biotechnology | And 2 more authors.
Plant Journal | Year: 2011

We have identified a gene, Lateral Root Development 3 (LRD3), that is important for maintaining a balance between primary and lateral root growth. The lrd3 mutant has decreased primary root growth and increased lateral root growth. We determined that the LRD3 gene encodes a LIM-domain protein of unknown function. LRD3 is expressed only in the phloem companion cells, which suggested a role in phloem function. Indeed, while phloem loading and export from the shoot appear to be normal, delivery of phloem to the primary root tip is limited severely in young seedlings. Abnormalities in phloem morphology in these seedlings indicate that LRD3 is essential for correct early phloem development. There is a subsequent spontaneous recovery of normal phloem morphology, which is correlated tightly with increased phloem delivery and growth of the primary root. The LRD3 gene is one of very few genes described to affect phloem development, and the only one that is specific to early phloem development. Continuous growth on auxin also leads to recovery of phloem development and function in lrd3, which demonstrates that auxin plays a key role in early phloem development. The root system architecture and the pattern of phloem allocation in the lrd3 root system suggested that there may be regulated mechanisms for selectively supporting certain lateral roots when the primary root is compromised. Therefore, this study provides new insights into phloem-mediated resource allocation and its effects on plant root system architecture. © 2011 Blackwell Publishing Ltd.

Busch W.,Duke University | Busch W.,Gregor Mendel Institute of Molecular Plant Biology | Moore B.T.,Duke University | Martsberger B.,Duke University | And 12 more authors.
Nature Methods | Year: 2012

To fully describe gene expression dynamics requires the ability to quantitatively capture expression in individual cells over time. Automated systems for acquiring and analyzing real-time images are needed to obtain unbiased data across many samples and conditions. We developed a microfluidics device, the RootArray, in which 64 Arabidopsis thaliana seedlings can be grown and their roots imaged by confocal microscopy over several days without manual intervention. To achieve high throughput, we decoupled acquisition from analysis. In the acquisition phase, we obtain images at low resolution and segment to identify regions of interest. Coordinates are communicated to the microscope to record the regions of interest at high resolution. In the analysis phase, we reconstruct three-dimensional objects from stitched high-resolution images and extract quantitative measurements from a virtual medial section of the root. We tracked hundreds of roots to capture detailed expression patterns of 12 transgenic reporter lines under different conditions. © 2012 Nature America, Inc. All rights reserved.

Adams P.D.,Lawrence Berkeley National Laboratory | Adams P.D.,University of California at Berkeley | Afonine P.V.,Lawrence Berkeley National Laboratory | Bunkoczi G.,University of Cambridge | And 16 more authors.
Acta Crystallographica Section D: Biological Crystallography | Year: 2010

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. How-ever, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallo-graphic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

A plant growth array device includes an aerial growth chamber configured to receive aerial shoot portions of a plurality of plants and a root growth chamber configured to receive root portions of the plurality of plants. A dividing member is between the aerial growth chamber and the root chamber and has a plurality of apertures for receiving the plurality of plants therein. The plurality of apertures are configured so that the root portions grow substantially in a common orientation.

Agency: National Science Foundation | Branch: | Program: STTR | Phase: Phase I | Award Amount: 150.00K | Year: 2008

This Small Business Technology Transfer (STTR) Phase I develops better gene promoters in order to allow the creation of improved genetically modified crops for food and biofuels. Gene promoters are a critical element of all transgenic crops, precisely controlling when and where within the plant a transgene is expressed. This project utilizes the proprietary root analysis system, the RootArray platform, to identify and characterize these enhanced promoters. The RootArray provides an unprecedented ability to monitor gene expression within developing plant roots. The broader impacts of this research are the development of better genetically modified crop varieties. The next generation of genetically modified food crops will more easily withstand environmental stresses, like drought and pests, while producing higher yields and more nutritional value. These crops will play an important role in guaranteeing food security. Moreover, genetically modified crops hold tremendous promise to produce better biofuel crops to help meet the nation's growing demand for energy. Genetically modified plants have the potential to play a key role in reducing our dependence on fossil fuels and cutting greenhouse emissions. Innovations in plant biotechnology - including the development of enhanced gene promoters - will help bring these enormous benefits to society.

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