Neural Network Analyses of Infrared Spectra for Classifying Cell Wall Architectures

• Published in: Plant physiology (Bethesda) 2007-03, Vol.143 (3), p.1314-1326
• Main Authors: McCann, Maureen C, Defernez, Marianne, Urbanowicz, Breeanna R, Tewari, Jagdish C, Langewisch, Tiffany, Olek, Anna, Wells, Brian, Wilson, Reginald H, Carpita, Nicholas C
• Format: Article
• Language: English
• Subjects: Algorithms; Architecture; Biological and medical sciences; Cell biochemistry; Cell Enlargement; Cell growth; Cell physiology; Cell Wall - classification; Cell Wall - genetics; Cell Wall - ultrastructure; Cell wall components; Cell walls; Coleoptiles; Corn; Cotyledon - genetics; Cotyledon - growth & development; Cotyledon - ultrastructure; Fourier Analysis; Fundamental and applied biological sciences. Psychology; Genome, Plant; Hybridity; Hybridization, Genetic; Linear Models; Mutation; Neural Networks, Computer; Phenotype; Plant physiology and development; Plants; Principal components analysis; Spectrophotometry, Infrared; Spectroscopic analysis; Systems Biology, Molecular Biology, and Gene Regulation; Zea mays; Zea mays - genetics; Zea mays - growth & development; Zea mays - ultrastructure
• ISSN: 0032-0889; 1532-2548; 1532-2548
• DOI: 10.1104/pp.106.093054

About 10% of plant genomes are devoted to cell wall biogenesis. Our goal is to establish methodologies that identify and classify cell wall phenotypes of mutants on a genome-wide scale. Toward this goal, we have used a model system, the elongating maize (Zea mays) coleoptile system, in which cell wall changes are well characterized, to develop a paradigm for classification of a comprehensive range of cell wall architectures altered during development, by environmental perturbation, or by mutation. Dynamic changes in cell walls of etiolated maize coleoptiles, sampled at one-half-d intervals of growth, were analyzed by chemical and enzymatic assays and Fourier transform infrared spectroscopy. The primary walls of grasses are composed of cellulose microfibrils, glucuronoarabinoxylans, and mixed-linkage (1 [rightward arrow] 3),(1 [rightward arrow] 4)-β-D-glucans, together with smaller amounts of glucomannans, xyloglucans, pectins, and a network of polyphenolic substances. During coleoptile development, changes in cell wall composition included a transient appearance of the (1 [rightward arrow] 3),(1 [rightward arrow] 4)-β-D-glucans, a gradual loss of arabinose from glucuronoarabinoxylans, and an increase in the relative proportion of cellulose. Infrared spectra reflected these dynamic changes in composition. Although infrared spectra of walls from embryonic, elongating, and senescent coleoptiles were broadly discriminated from each other by exploratory principal components analysis, neural network algorithms (both genetic and Kohonen) could correctly classify infrared spectra from cell walls harvested from individuals differing at one-half-d interval of growth. We tested the predictive capabilities of the model with a maize inbred line, Wisconsin 22, and found it to be accurate in classifying cell walls representing developmental stage. The ability of artificial neural networks to classify infrared spectra from cell walls provides a means to identify many possible classes of cell wall phenotypes. This classification can be broadened to phenotypes resulting from mutations in genes encoding proteins for which a function is yet to be described.