Background 
There is an unmet need to monitor human and natural environments for substances that are intentionally or unintentionally introduced. A long-sought goal is to adapt plants to sense and respond to specific substances for use as environmental monitors. Computationally re-designed periplasmic binding proteins (PBPs) provide a means to design highly sensitive and specific ligand sensing capabilities in receptors. Input from these proteins can be linked to gene expression through histidine kinase (HK) mediated signaling. Components of HK signaling systems are evolutionarily conserved between bacteria and plants. We previously reported that in response to cytokinin-mediated HK activation in plants, the bacterial response regulator PhoB translocates to the nucleus and activates transcription. Also, we previously described a plant visual response system, the de-greening circuit, a threshold sensitive reporter system that produces a visual response which is remotely detectable and quantifiable.


Methodology/Principal Findings 
We describe assembly and function of a complete synthetic signal transduction pathway in plants that links input from computationally re-designed PBPs to a visual response. To sense extracellular ligands, we targeted the computational re-designed PBPs to the apoplast. PBPs bind the ligand and develop affinity for the extracellular domain of a chemotactic protein, Trg. We experimentally developed Trg fusions proteins, which bind the ligand-PBP complex, and activate intracellular PhoR, the HK cognate of PhoB. We then adapted Trg-PhoR fusions for function in plants showing that in the presence of an external ligand PhoB translocates to the nucleus and activates transcription. We linked this input to the de-greening circuit creating a detector plant.


Conclusions/Significance 
Our system is modular and PBPs can theoretically be designed to bind most small molecules. Hence our system, with improvements, may allow plants to serve as a simple and inexpensive means to monitor human surroundings for substances such as pollutants, explosives, or chemical agents.

/pdf/programmable-ligand-detection-system-in-plants-through-a-5cqt8gwvbz.pdf

Programmable ligand detection system in plants through a synthetic signal transduction pathway.

In multiple frequency estimation, the bandwidth and resolution of Fast Fourier Transform (FFT) based frequency estimators are limited by A/D converter sampling rate constraints and also by real-time computational requirements. The disclosed configuration uses a Modified Chinese Remainder Theorem of a paper entitled, "A Noise Insensitive Solution to an Ambiguity Problem in Spectra Estimation" by McCormick et al and a subsampling approach of U.S. Pat. No. 5,099,194 entitled, "Digital Frequency Measurement Receiver With Bandwidth Improvement Through Multiple Sampling of Real Signals" to resolve the frequency ambiguity problem. The configuration extends these ideas to the multiple frequency case. It significantly extends system bandwidth by operating I FFT units in parallel at specific sampling rates chosen to maximize system bandwidth for a fixed level of noise protection. Each FFT unit output is processed by a "peak detecting" algorithm that detects the M remainders of the M frequencies for the sampling frequency, Fi, of that particular FFT unit. Using a multiple frequency ambiguity resolution algorithm, the M frequencies are estimated from the I sets of M remainders. The configuration essentially resolves the 2π or aliasing ambiguity problem for multiple frequencies in a parallel, highly efficient manner. In its current configuration, the system is designed for complex signal inputs.

Frequency measurement receiver with means to resolve an ambiguity in multiple frequency estimation

A three-antenna synthetic aperture radar interferometer (InSAR) with a statistically optimal data processor for three-dimensional (3D) terrain mapping has been proposed recently to reduce the phase ambiguity and data-noise drawbacks of the conventional two-antenna SAR interferometry technique. In this paper, a numerical simulator is developed to assess the achievable performance and various design tradeoffs of the three-antenna InSAR. The most critical conditions for the new reduced-ambiguity system operating on realistic scenes are taken into account. The phase-unwrapping procedure is included in the simulator to compare the new and the conventional technique in terms of both phase and height-estimation accuracy. The performance achievable by a three-antenna airborne InSAR system on a given site are analyzed, and the parameter optimization of the new system is investigated. The results of several case studies show that the new technique can outperform the conventional one significantly for a typical airborne configuration, especially for high-terrain steepness. It provides reduced-phase aliasing and better estimation accuracy. So, the phase unwrapping Is simplified and high-quality maps of terrain height can be obtained. As a limit, absolute phase retrieval can be achieved with good accuracy and the unwrapping procedure can be avoided.

/pdf/simulated-analysis-and-optimization-of-a-three-antenna-39ifntfeix.pdf

Simulated analysis and optimization of a three-antenna airborne InSAR system for topographic mapping

Frequency determination from truly sub-Nyquist samplers based on robust Chinese remainder theorem

An antenna receives an analog waveform and an analog signal indicative of the amplitude and frequency of the analog waveform. The analog signal is processed in a plurality of parallel digital processing channels each arranged to digitize the analog signal at a corresponding sampling frequency f si to produce a plurality of digital signals. A discrete Fourier transform is applied to each of the digital signals output to produce a corresponding plurality of unique Fourier spectra of length m i =(f si )(T Li ) where T Li is the integration time for the discrete Fourier transform for each digital processing channel. The lengths of the Fourier spectra (m i ) are selected to be pairwise relatively prime. The discrete Fourier transform encodes the signals in same form as the symmetrical number system (SNS). A SNS-to-decimal algorithm is then applied to the detected bin values (a i ) to determine the numerical value of the frequency f of the analog waveform. The receiver resolves all undersampling ambiguities exactly, thereby relaxing the speed requirements on the digital section of the receiver.

Wideband undersampling digital receiver

The instantaneous frequency measurement (IFM) receiver is capable of measuring the center frequency of single frequency pulses over a wide range (bandwidth) of center frequencies. Because of various constraints, the frequency resolution requirement results in long correlator delay times that reduce the single correlator bandwidth. A large bandwidth can be achieved only if two or more correlators are used. The problem of estimating frequency is then reduced to the simultaneous congruence problem of number theory. A design procedure is presented for solving the congruence problem for a given amount of noise protection, a stated frequency resolution, a minimum bandwidth, and a fixed level of precision (bits) in the IFM receiver. >

A noise insensitive solution to an ambiguity problem in spectral estimation

An algorithm is proposed to resolve a fundamental 2/spl pi/ ambiguity problem occurring in multiple frequency spectral estimation. Given M frequencies f/sub m/, and I separate frequency estimators with unambiguous bandwidths F/sub i/, the ambiguity problem can be stated as solving for the fm, given the estimator outputs, /spl alphasub mi/, (1/spl les/m/spl les/M;1/spl les/i/spl les/I) where f/sub m/=/spl alphasub mi/+K/sub mi/F/sub i/ and K/sub mi/ is some integer. The proposed algorithm exhaustively resolves all possible /spl alphasub mi/ groupings into single frequency values using a noise insensitive technique that exchanges system bandwidth for noise protection. The correct multiple frequencies are then defined as the single frequencies that repeat a specified number of times. A complete analysis is included. >

Resolution of a 2/spl pi/ ambiguity problem in multiple frequency spectral estimation

A laser-pulse generator for the transfer of continous-wave (cw) absolute radiometric calibrations to high-speed pulse photodetectors is described. The cw input lasers are modulated by a spinning polygon mirror in a ring cavity to produce high-speed, constant-amplitude, constant-shape laser pulses. Constant-amplitude outputs range temporally from cw to 15-ns full-width at half-maximum (FWHM) Gaussian pulses. An all-reflective optical design permits operation of the device from the visible to the far-infrared spectral regions. Design and performance estimates for the pulse generator as well as experimental verification are presented.

High-bandwidth laser-pulse generator using continuous-wave lasers

The primary goal of this paper is to develop Hyperspectral algorithms for early detection of a readout system used in
conjunction with plants designed to de-green or discolor after detection of explosives, harmful chemicals, and
environmental pollutants. Work in progress is aimed to develop a new class of biosensors or Plant Sentinels that can
serve as inexpensive plant-based biological early-warning systems capable of detecting substances that are harmful to
human or the environment [LoHe03]. The de-greening circuits in the laboratory plant, Arabidopsis, have been shown to
induce rapid chlorophyll loss, thereby change color under the influence of synthetic estrogens. However, as of now, the
bio de-greening phenomenon is detectable by human eyes or with a system (chlorophyll fluorescence) that works best in
laboratory conditions. In order to make the plant sentinel system practically viable, we have developed automated
monitoring scheme for early detection of the de-greening phenomenon. The automated detection capability would lead to
practical applicability and wider usage. This paper presents novel and effective HSI-based algorithms for early detection
of de-greening of plants and vegetation due to explosives or chemical agents. The image processing based automated degreening
detector, presented in this paper will be capable of 24/7 monitoring of the plant sentinels and to detect minutest
possible discoloration of the plant-sensors to serve as an early-warning system. We also present preliminary results on
estimating the length of time that the explosive or chemical agent has been present.

Hyperspectral exploitation with plant sentinels

One of the acknowledged lightning threats to aircraft is the induction threat in which a lightning-induced fuselage skin current inductively or capacitively flux couples through small dielectric "holes" or apertures in the fuselage onto intemal avionics cabling. In order to optimize the circuit protection, it is necessary to identify both the nature and location of the flux excitation. Using standard capacitor-bank LTA testing, this paper advances a linear-system-identification technique, based on the impulse response, that will defme both the nature and location of the dominant excitations. The technique is then successfuily applied to the identification of the Yaw Damper Circuit of the USAF F-111.

The Analysis and Identification of Flux-Induced Voltage Transients on Low-Loss Transmission Lines with Application to the Lightning-Transient-Analysis (LTA) Problem

William S. McCormick

Papers

A noise insensitive solution to an ambiguity problem in spectral estimation

Resolution of a 2/spl pi/ ambiguity problem in multiple frequency spectral estimation

High-bandwidth laser-pulse generator using continuous-wave lasers

Hyperspectral exploitation with plant sentinels

The Analysis and Identification of Flux-Induced Voltage Transients on Low-Loss Transmission Lines with Application to the Lightning-Transient-Analysis (LTA) Problem