Affiliation: University of Arizona
- High-throughput monitoring of plant nuclear DNA contents via flow cytometryDavid W Galbraith
School of Plant Sciences, University of Arizona, Tucson, AZ, USA
Methods Mol Biol 918:311-25. 2012..This chapter provides a general discussion of flow cytometric methods for measuring plant genome sizes, and detailed methods for carrying out these analyses...
- Development of high-yield autofluorescent protein microarrays using hybrid cell-free expression with combined Escherichia coli S30 and wheat germ extractsXristo Zarate
BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
Proteome Sci 8:32. 2010..A cell-free expression system that synthesizes folded eukaryotic proteins in considerable yields would optimize in vitro translation for protein microarray assembly...
- Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in riceJeremy D Edwards
University of Florida, Gulf Coast Research and Education Center, Wimauma FL, 33598, USA
Plant Methods 4:13. 2008..In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features...
- The construction and use of bacterial DNA microarrays based on an optimized two-stage PCR strategyBradley L Postier
Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078 USA
BMC Genomics 4:23. 2003..g. over-expression of protein). We describe the successful construction and use of DNA microarrays by the two-stage amplification approach and discuss the technical challenges that were met and resolved during the project...
- Comparison of the contributions of the nuclear and cytoplasmic compartments to global gene expression in human cellsRoger A Barthelson
Bio5 Institute for Collaborative Bioresearch and Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
BMC Genomics 8:340. 2007..One technology, based on microarrays, categorizes gene expression in terms of the abundance of RNA transcripts, and typically employs RNA prepared from whole cells, where cytoplasmic RNA predominates...
- Simultaneous flow cytometric quantification of plant nuclear DNA contents over the full range of described angiosperm 2C valuesDavid W Galbraith
Department of Plant Sciences and BIO5 Institute for Collaborative Bioresearch, University of Arizona, Tucson Arizona 85721 0240, USA
Cytometry A 75:692-8. 2009....
- DNA microarray analyses in higher plantsDavid W Galbraith
Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
OMICS 10:455-73. 2006..This article describes, in a necessarily selective manner, the types of platforms currently employed in microarray research and provides an overview of recent activities using these platforms in plant biology...
- Global studies of cell type-specific gene expression in plantsDavid W Galbraith
Department of Plant Sciences and BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
Annu Rev Plant Biol 57:451-75. 2006..The spatial dissection of the transcriptome has also yielded insights into the localized mediators of hormone inputs and promises to provide detail on cell-specific effects of microRNAs...
- Cytometry and plant sciences: a personal retrospectiveDavid W Galbraith
Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
Cytometry A 58:37-44. 2004
- Global characterization of cell-specific gene expression through fluorescence-activated sorting of nucleiChangqing Zhang
Department of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
Plant Physiol 147:30-40. 2008..We demonstrate the validity of the approach through the identification of 12 genes that are selectively expressed in phloem...
- A framework of integrating gene relations from heterogeneous data sources: an experiment on Arabidopsis thalianaJiexun Li
Department of Management Information Systems, University of Arizona Tucson, AZ 85721, USA
Bioinformatics 22:2037-43. 2006..Domain expert judgments on the gene functional clusters in the network confirmed the validity of our approach for relation integration and network inference...
- Temporal progression of gene expression responses to salt shock in maize rootsHong Wang
Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
Plant Mol Biol 52:873-91. 2003..Within this framework, 16 signaling molecules, including six protein kinases, two protein phosphatases and eight transcription factors, were regulated with distinct expression patterns by high salinity...
- High-throughput, high-sensitivity analysis of gene expression in ArabidopsisRichard Martin Kris
NuvoGen Research LLC, Tucson, AZ 85728, USA
Plant Physiol 144:1256-66. 2007....
- Monitoring large-scale changes in transcript abundance in drought- and salt-stressed barleyZ Neslihan Oztur
Department of Biochemistry and Molecular Biophysics, University of Arizona, Biosciences West, Tucson 85721 0088, USA
Plant Mol Biol 48:551-73. 2002....
- Integrative flow cytometric and microarray approaches for use in transcriptional profilingDavid W Galbraith
Department of Plant Sciences, University of Arizona, Tucson, AZ, USA
Methods Mol Biol 263:259-80. 2004....
- Performance analysis of a dual-buffer architecture for digital flow cytometryShiva Murthi
Department of Electrical and Computer Engineering, University of Arizona, Tucson, AZ 85721, USA
Cytometry A 66:109-18. 2005..An improved version of the system is discussed in this paper, focusing on dual-buffering to ensure increased pulse capture. A mathematical model of the system is also presented for performance analysis...
- The rainbow of fluorescent proteinsDavid W Galbraith
University of Arizona, Department of Plant Sciences, Institute for Biomedical Science and Biotechnology, Tucson, Arizona 85721, USA
Methods Cell Biol 75:153-69. 2004
- AtSAP18, an orthologue of human SAP18, is involved in the regulation of salt stress and mediates transcriptional repression in ArabidopsisChun Peng Song
Department of Plant Sciences, University of Arizona, 303 Forbes Building, Tucson, AZ 85721, USA
Plant Mol Biol 60:241-57. 2006....
- The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus OryzaJetty S S Ammiraju
Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721 USA
Genome Res 16:140-7. 2006....
- A probable Na+(K+)/H+ exchanger on the chloroplast envelope functions in pH homeostasis and chloroplast development in Arabidopsis thalianaChun Peng Song
Department of Plant Sciences, University of Arizona, Tucson, 85721, USA
Proc Natl Acad Sci U S A 101:10211-6. 2004..chx23 mutants displayed a high sensitivity to NaCl. Together, these data indicate that CHX23 is a probable chloroplast Na(+)(K(+))/H(+) exchanger important for pH homeostasis and chloroplast development and function...
- Meiotically stable natural epialleles of Sadhu, a novel Arabidopsis retroposonSanjida H Rangwala
Department of Biology, Washington University in St Louis, St Louis, Missouri, USA
PLoS Genet 2:e36. 2006..These findings support the view that an important component of natural variation in retroelements is epigenetic...
- The sfr6 mutant of Arabidopsis is defective in transcriptional activation via CBF/DREB1 and DREB2 and shows sensitivity to osmotic stressJoy M Boyce
Department of Plant Sciences, University of Oxford, South Parks Road, UK
Plant J 34:395-406. 2003..Tolerance of osmotic stress was also found to be reduced in sfr6, consistent with a role in osmotic stress tolerance for the cold-, ABA- and drought-inducible genes whose expression is affected by the sfr6 mutation...
- A gene expression map of the Arabidopsis rootKenneth Birnbaum
Department of Biology, New York University, New York, NY 10003, USA
Science 302:1956-60. 2003..Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics...
- Diurnal and circadian rhythms in the tomato transcriptome and their modulation by cryptochrome photoreceptorsPaolo Facella
ENEA, Trisaia Research Center, Rotondella MT, Italy
PLoS ONE 3:e2798. 2008..There is considerable experimental evidence demonstrating the roles of photoreceptors in providing light input to the clock...
- Methods for transcriptional profiling in plants. Be fruitful and replicateBlake C Meyers
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Plant Physiol 135:637-52. 2004
- Comparison of RNA expression profiles based on maize expressed sequence tag frequency analysis and micro-array hybridizationJohn Fernandes
Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
Plant Physiol 128:896-910. 2002..Reassembly of ESTs at the criterion of 90% identity suggests how cross hybridization among gene family members can overestimate the overlap in genes expressed in micro-array hybridization experiments...
- Salt cress. A halophyte and cryophyte Arabidopsis relative model system and its applicability to molecular genetic analyses of growth and development of extremophilesGunsu Inan
Center for Plant Environmental Stress Physiology, Purdue University, West Lafayette, Indiana 47907 2010, USA
Plant Physiol 135:1718-37. 2004..In addition, the generation of T-DNA-tagged mutant collections of salt cress, already in progress, will open the door to a new era of forward and reverse genetic studies of extremophile plant biology...
- Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expressionMaria Eugenia Zanetti
Department of Botany and Plant Science, Center for Plant Cell Biology, University of California, Riverside, California 92521 0124, USA
Plant Physiol 138:624-35. 2005..This technology can be extended to evaluation of mRNA populations at the cell- or tissue-specific level by regulation of the tagged RP with distinct promoters...
- Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter linesKenneth Birnbaum
Department of Biology, New York University, 100 Washington Square East, New York, New York 10003, USA
Nat Methods 2:615-9. 2005
- Metabolic engineering of dhurrin in transgenic Arabidopsis plants with marginal inadvertent effects on the metabolome and transcriptomeCharlotte Kristensen
Plant Biochemistry Laboratory, Department of Plant Biology, and Center for Molecular Plant Physiology, Royal Veterinary and Agricultural University, 40 Thorvaldsensvej, DK 1871 Frederiksberg C, Copenhagen, Denmark
Proc Natl Acad Sci U S A 102:1779-84. 2005..thaliana plants with marginal inadvertent effects on the transcriptome and metabolome...
- Nanobiotechnology: silica breaks through in plantsDavid W Galbraith
Nat Nanotechnol 2:272-3. 2007
- The daunting process of MIAMEDavid W Galbraith
Nature 444:31. 2006
- Plant systems biology comes of ageJoshua S Yuan
UTIA Genomics Hub, University of Tennessee, Knoxville, TN 37996, USA
Trends Plant Sci 13:165-71. 2008..Applications of systems biology to plant science have been rapid, and have increased our knowledge about circadian rhythms, multigenic traits, stress responses and plant defenses, and have advanced the virtual plant project...
- Functional Genomics of NucleiDavid Galbraith; Fiscal Year: 2005..Moreover, the constructs will be used to develop mouse lines from which investigators can perform the cell specific gene array studies, as well a studies of cell function within sections of living tissue. ..