Sequencing, Mapping, and Analysis of 27,455 Maize Full-Length cDNAs

Full-length cDNA (FLcDNA) sequencing establishes the precise primary structure of individual gene transcripts. From two libraries representing 27 B73 tissues and abiotic stress treatments, 27,455 high-quality FLcDNAs were sequenced. The average transcript length was 1.44 kb including 218 bases and 321 bases of 5′ and 3′ UTR, respectively, with 8.6% of the FLcDNAs encoding predicted proteins of fewer than 100 amino acids. Approximately 94% of the FLcDNAs were stringently mapped to the maize genome. Although nearly two-thirds of this genome is composed of transposable elements (TEs), only 5.6% of the FLcDNAs contained TE sequences in coding or UTR regions. Approximately 7.2% of the FLcDNAs are putative transcription factors, suggesting that rare transcripts are well-enriched in our FLcDNA set. Protein similarity searching identified 1,737 maize transcripts not present in rice, sorghum, Arabidopsis, or poplar annotated genes. A strict FLcDNA assembly generated 24,467 non-redundant sequences, of which 88% have non-maize protein matches. The FLcDNAs were also assembled with 41,759 FLcDNAs in GenBank from other projects, where semi-strict parameters were used to identify 13,368 potentially unique non-redundant sequences from this project. The libraries, ESTs, and FLcDNA sequences produced from this project are publicly available. The annotated EST and FLcDNA assemblies are available through the maize FLcDNA web resource (www.maizecdna.org)

Portable Imaging Polarimeter and Imaging Experiments

Polarimetry is the method of recording the state of polarization of light. Imaging polarimetry extends this method to recording the spatially resolved state of polarization within a scene. Imaging-polarimetry data have the potential to improve the detection of manmade objects in natural backgrounds. We have constructed a midwave infrared complete imaging polarimeter consisting of a fixed wire-grid polarizer and rotating form-birefringent retarder. The retardance and the orientation angles of the retarder were optimized to minimize the sensitivity of the instrument to noise in the measurements. The optimal retardance was found to be 132{degree} rather than the typical 90{degree}. The complete imaging polarimeter utilized a liquid-nitrogen cooled PtSi camera. The fixed wire-grid polarizer was located at the cold stop inside the camera dewar. The complete imaging polarimeter was operated in the 4.42-5 {micro}m spectral range. A series of imaging experiments was performed using as targets a surface of water, an automobile, and an aircraft. Further analysis of the polarization measurements revealed that in all three cases the magnitude of circular polarization was comparable to the noise in the calculated Stokes-vector components

ISIS; An Information-efficient Spectral Imaging System

A specialized hyperspectral imager has been developed that preprocesses the spectra from an image before the light reaches the detectors. This "optical computer" does not allow the flexibility of digital post-processing. However, the processing is done in real time and the system can examine = 2 x 10{sup 6} scene pixels/sec. Therefore, outdoors it could search for pollutants, vegetation types, minerals, or man-made objects. On a high- speed production line it could identify defects in sheet products like plastic wrap or film, or on painted or plastic parts. ISIS is a line scan imager. A spectrally dispersed slit image is projected on a Spatial Light Modulator. The SLM is programmed to take the inner product of the spectral intensity vector and a spectral basis vector. The SLM directs the positive and negative parts of the inner product to different linear detector arrays so the signal difference equals the inner product. We envision a system with one telescope and =4 SLMS

Computed tomography-based spectral imaging for fluorescence microscopy.

The computed tomography imaging spectrometer (CTIS) is a non-scanning instrument capable of simultaneously acquiring full spectral information (450-750 nm) from every position element within its field of view (75 microm x 75 microm). The current spatial and spectral sampling intervals of the spectrometer are 1.0 microm and 10 nm, respectively. This level of resolution is adequate to resolve signal responses from multiple fluorescence probes located within individual cells or different locations within the same cell. Spectral imaging results are presented from the CTIS combined with a commercial inverted fluorescence microscope. Results demonstrate the capability of the CTIS to monitor the spatiotemporal evolution of pH in rat insulinoma cells loaded with SNARF-1. The ability to analyze full spectral information for two-dimensional (x, y) images allows precise evaluation of heterogeneous physiological responses within cell populations. Due to low signal levels, integration times up to 2 s were required. However, reasonable modifications to the instrument design will provide higher system transmission efficiency with increased temporal and spatial resolution. Specifically, a custom optical design including the use of a larger format detector array is under development for a second-generation system

Design and Optimization of a Complete Stokes Polarimeter for the MWIR

A figure of merit for optimization of a complete Stokes polarimeter based on its measurement matrix is described from the standpoint of singular value decomposition and analysis of variance. It is applied to optimize a system featuring a rotatable retarder and fixed polarizer, and to study the effects of non-ideal retarder properties. A retardance of 132{degree} (approximately three-eighths wave) and retarder orientation angles of {+-}51.7{degree} and {+-}15.1{degree} are favorable when four measurements are used. An achromatic, form-birefringent retarder for the 3--5 {micro}m spectral region has been fabricated and characterized. The effects of non-idealities in the form-birefringent retarder are moderate, and performance superior to that of a quarter-wave plate is expected

Mass-producible micro-holographic tags

Microtags are microscopic computer-generated holograms with 130-nm features and are mass-producible with EUVL. This fabrication method renders microtags difficult to counterfeit. Applications includ tagging and tracking of microprocessors, memory chips, currencey, and credit cards