3 results
Sampling the Waterhemp (Amaranthus tuberculatus) Genome Using Pyrosequencing Technology
- Ryan M. Lee, Jyothi Thimmapuram, Kate A. Thinglum, George Gong, Alvaro G. Hernandez, Chris L. Wright, Ryan W. Kim, Mark A. Mikel, Patrick J. Tranel
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- Journal:
- Weed Science / Volume 57 / Issue 5 / October 2009
- Published online by Cambridge University Press:
- 20 January 2017, pp. 463-469
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Recent advances in sequencing technologies (next-generation sequencing) offer dramatically increased sequencing throughput at a lower cost than traditional Sanger sequencing. This technology is changing genomics research by allowing large scale sequencing experiments in nonmodel systems. Waterhemp is an important weed in the midwestern United States with characteristics that makes it an interesting ecological model. However, very few genomic resources are available for this species. One half of a 70 by 75 picotiter plate of 454-pyrosequencing was performed on total DNA isolated from waterhemp, generating 158,015 reads of an average length of 271 bp, or a total of nearly 43 Mbp of sequence. Included in this sequence was a nearly complete sequence of the chloroplast genome, sequences of several important herbicide resistance genes, leads for simple sequence repeat (SSR) markers, and a sampling of the repeated elements (e.g., transposons) present in this species. Here we present the waterhemp genomic data gleaned from this sequencing experiment and illustrate the value of next-generation sequencing technology to weed science research.
Characterization of an EST Database for the Perennial Weed Leafy Spurge: An Important Resource for Weed Biology Research
- James V. Anderson, David P. Horvath, Wun S. Chao, Michael E. Foley, Alvaro G. Hernandez, Jyothi Thimmapuram, Lie Liu, George L. Gong, Mark Band, Ryan Kim, Mark A. Mikel
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- Journal:
- Weed Science / Volume 55 / Issue 3 / June 2007
- Published online by Cambridge University Press:
- 20 January 2017, pp. 193-203
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Genomics programs in the weed science community have not developed as rapidly as that of other crop, horticultural, forestry, and model plant systems. Development of genomic resources for selected model weeds are expected to enhance our understanding of weed biology, just as they have in other plant systems. In this report, we describe the development, characteristics, and information gained from an expressed sequence tag (EST) database for the perennial weed leafy spurge. ESTs were obtained using a normalized cDNA library prepared from a comprehensive collection of tissues. During the EST characterization process, redundancy was minimized by periodic subtractions of the normalized cDNA library. A sequencing success rate of 88% yielded 45,314 ESTs with an average read length of 671 nucleotides. Using bioinformatic analysis, the leafy spurge EST database was assembled into 23,472 unique sequences representing 19,015 unigenes (10,293 clusters and 8,722 singletons). Blast similarity searches to the GenBank nonredundant protein database identified 18,186 total matches, of which 14,205 were nonredundant. These data indicate that 77.4% of the 23,472 unique sequences and 74.7% of the 19,015 unigenes are similar to other known proteins. Further bioinformatics analysis indicated that 2,950, or 15.5%, of the unigenes have previously not been identified suggesting that some may be novel to leafy spurge. Functional classifications assigned to leafy spurge unique sequences using Munich Information Center for Protein or Gene Ontology were proportional to functional classifications for genes of arabidopsis, with the exception of unclassified or unknowns and transposable elements which were significantly reduced in leafy spurge. Although these EST resources have been developed for the purpose of constructing high-density leafy spurge microarrays, they are already providing valuable information related to sugar metabolism, cell cycle regulation, dormancy, terpenoid secondary metabolism, and flowering.
Controlling Magnetism with an Electric Field in Multiferroic Complex Oxide Heterostructures: La0.7Sr0.3MnO3/BiFeO3
- Ying-Hao Chu, Kilho Lee, Lane W. Martin, Mikel Barry, Mark Huijben, Martin Gajek, Jan Seidel, Qian Zhan, Padraic Shafer, Yu Pu, Pei-Ling Yang, Ramamoorthy Ramesh
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- Journal:
- MRS Online Proceedings Library Archive / Volume 1000 / 2007
- Published online by Cambridge University Press:
- 12 July 2019, 1000-L05-09
- Print publication:
- 2007
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Format
This is a copy of the slides presented at the meeting but not formally written up for the volume.
AbstractInteractions at magnetic interfaces are central to the operation of virtually all magnetic heterostructures. When the interface is between two magnetic materials, the exchange interaction between spins at the interface is often a dominant force, and can dramatically change the magnetic response of the overall heterostructure. In ferromagnet (FM)/antiferromagnet (AFM) heterostructures, this interaction is often referred to as exchange anisotropy or bias and it has been widely used over the past decade in a wide array of applications such as magnetic recording heads, MRAMs, etc. The powerful implications of interactions between an AFM and a FM have been realized in a wide range of thin film heterostructure with both metallic and oxide constituents. There is, however, much less work on oxide-oxide FM/AFM systems. On the other hand, the development and understanding of functional oxide materials, especially multifunctional materials like BiFeO3 (BFO), have piqued the interest of researchers worldwide with the promise of coupling between order parameters such as ferroelectricity and antiferromagnetism. Recent research suggests that there is exchange coupling and anisotropy between the metallic ferromagnet Co0.9Fe0.1 (CoFe) and the multiferroic, antiferromagnet BFO, showing the possibility to create highly desirable multifunctional systems with new possibilities for device design. Such a result provides the driving force to create multifunctional oxide-oxide systems where exchange interactions could be much stronger then in metal/oxide structures due the added epitaxial nature of the interface. In this study, we use La0.7Sr0.3MnO3(LSMO)/BFO thin film heterostructures as a model system to explore the exchange interaction at an oxide interface. The heterostructures are grown on various vicinal cuts of SrTiO3 single crystal substrates using laser MBE. Structural analysis using x-ray diffraction, transmission electron microscopy and Rutherford backscattering spectrometry reveals high quality films with the pristine interfaces required for exchange coupling. First results from photoemission electron microscope (PEEM) studies reveal that the magnetic LSMO domain structure mimics underneath ferroelectric BFO domain structure, i..e, it is strongly pinned by the underlying AFM structure. The coupling behavior is being characterized by magnetic measurements (SQUID, VSM), which shows a strong enhancement in the coercivity of the LSMO layer, suggesting the existence of exchange bias coupling. We are probing the strength of this coupling using a combination of careful laser MBE growth experiments and physical property measurements. In this paper, we will report results of experiments in which the LSMO layer has been grown by laser MBE in the thickness range of 2-50nm on a [001] BFO layer.