Effect of growth media and washing on the spectral signatures of aerosolized biological simulants

Impact of different classification schemes on discrimination of proteins with noise-contaminated spectra using laboratory-measured fluorescence data

Biological agents are important to detect and identify with respect to environmental contamination and public health. Noise contamination in fluorescent spectra is one of the contributors to the uncertainties of identification. In order to investigate the noise-tolerant capability provided by laboratory-measured excitation-emission matrix (EEM) fluorescence spectra that are used as a database, fluorescence properties of four proteinaceous biotoxin samples and ten harmless protein samples were characterized by EEM fluorescence spectra, and the predicting performance of models trained by laboratory-measured fluorescence data was tested and verified from validation data with noise-contaminated spectra. By means of peak signal of noise (PSNR) as an indicator of noise levels, the potential impact of noise contaminations on the characterization and discrimination of these samples was evaluated quantitatively. Different classification schemes utilizing multivariate analysis techniques of Principal Component Analysis (PCA), Random Forest (RF), and Multi-layer Perceptron (MPL) coupled with feature descriptors of differential transform (DT), Fourier transform (FT) and wavelet transform (WT) were conducted under different PSNR values. We systematically analyzed the performance of classification schemes by the case study at 20 PSNR and by statistical analysis from 1-100 PSNR. The results show that the spectral features with EEM-WT decreased the demanding number of input variables while retaining high performances in sample classification. The spectral features with EEM-FT presented the worst performance although having the largest number of features. The distributions of feature importance and contribution were found sensitive to noise contaminations. The classification scheme of PCA prior to MPL with EEM-WT as input presented an improvement in lower PSNR. These results indicate that robust features extracted by corresponding techniques are critical to enhancing the spectral differentiation capabilities among these samples and play an important role in eliminating the noise effect. The study of classification schemes for discriminating protein samples with noise-contaminated spectra presents tremendous potential for future developments in the rapid detection and identification of proteinaceous biotoxins based on three-dimensional fluorescence spectrometry.

Performance of feature extraction method for classification and identification of proteins based on three-dimensional fluorescence spectrometry

Three-dimensional excitation emission matrix (EEM) fluorescence spectroscopy was employed to discriminate protein samples comprising bovine serum albumin, neurotensin, ovalbumin, ricin, trypsin from bovine pancreas and trypsin from porcine pancreas. Two methods of feature extraction with and without parameterization were applied to the spectral data in order to evaluate their performance of discrimination between protein samples. The discrimination of protein samples was conducted by k-means clustering algorithm and eigenvalue extracting procedure based on principal component analysis (PCA). It was found that the method of feature extraction without parameterization performed best, correctly attributing 100% of the spectral data in the condition of two principal components (PCs) captured. Features extracted with spectral parameterization failed to separate ricin and trypsin from bovine pancreas in same condition. Without spectral parameterization, less dimensionality and unique principal components captured by PCA indicates the spectrally-resolved features of corresponding protein samples. By clustering using each spectrum at fixed excitation wavelength, excitation wavelengths matched with common intrinsic fluorophores were found to be more sensitive to the classification accuracy. Contributions of spectral features extracted from EEM to the principal components were discussed and demonstrated their feature differentiation capabilities among six protein samples. These results reveal that appropriate extraction approach of features in combination with PCA analysis could be used in discrimination of protein samples at species level as a spectroscopic diagnostic tool. Our study provides fundamental references about computational strategies when EEM are used to explore proteins in ambient environment.

Spectrally-resolved fluorescence cross sections of aerosolized biological live agents and simulants using five excitation wavelengths in a BSL-3 laboratory

A system for measuring spectrally-resolved fluorescence cross sections of single bioaerosol particles has been developed and employed in a biological safety level 3 (BSL-3) facility at Edgewood Chemical and Biological Center (ECBC). It is used to aerosolize the slurry or solution of live agents and surrogates into dried micron-size particles, and to measure the fluorescence spectra and sizes of the particles one at a time. Spectrally-resolved fluorescence cross sections were measured for (1) bacterial spores: Bacillus anthracis Ames (BaA), B. atrophaeus var. globigii (BG) (formerly known as Bacillus globigii), B. thuringiensis israelensis (Bti), B. thuringiensis kurstaki (Btk), B. anthracis Sterne (BaS); (2) vegetative bacteria: Escherichia coli (E. coli), Pantoea agglomerans (Eh) (formerly known as Erwinia herbicola), Yersinia rohdei (Yr), Yersinia pestis CO92 (Yp); and (3) virus preparations: Venezuelan equine encephalitis TC83 (VEE) and the bacteriophage MS2. The excitation wavelengths were 266 nm, 273 nm, 280 nm, 365 nm and 405 nm.

Bacillus thuringiensis as a surrogate for Bacillus anthracis in aerosol research

Characterization of candidate surrogate spores prior to experimental use is critical to confirm that the surrogate characteristics are as closely similar as possible to those of the pathogenic agent of interest. This review compares the physical properties inherent to spores of Bacillus anthracis (Ba) and Bacillus thuringiensis (Bt) that impact their movement in air and interaction with surfaces, including size, shape, density, surface morphology, structure and hydrophobicity. Also evaluated is the impact of irradiation on the physical properties of both Bacillus species. Many physical features of Bt and Ba have been found to be similar and, while Bt is considered typically non-pathogenic, it is in the B. cereus group, as is Ba. When cultured and sporulated under similar conditions, both microorganisms share a similar cylindrical pellet shape, an aerodynamic diameter of approximately 1 μm (in the respirable size range), have an exosporium with a hairy nap, and have higher relative hydrophobicities than other Bacillus species. While spore size, morphology, and other physical properties can vary among strains of the same species, the variations can be due to growth/sporulation conditions and may, therefore, be controlled. Growth and sporulation conditions are likely among the most important factors that influence the representativeness of one species, or preparation, to another. All Bt spores may, therefore, not be representative of all Ba spores. Irradiated spores do not appear to be a good surrogate to predict the behavior of non-irradiated spores due to structural damage caused by the irradiation. While the use of Bt as a surrogate for Ba in aerosol testing appears to be well supported, this review does not attempt to narrow selection between Bt strains. Comparative studies should be performed to test the hypothesis that viable Ba and Bt spores will behave similarly when suspended in the air (as an aerosol) and to compare the known microscale characteristics versus the macroscale response.

Fluorescence of bioaerosols: mathematical model including primary fluorescing and absorbing molecules in bacteria

This paper describes a mathematical model of fluorescent biological particles composed of bacteria, viruses, or proteins. The fluorescent and/or light absorbing molecules included in the model are amino acids (tryptophan, etc.); nucleic acids (DNA, RNA, etc.); coenzymes (nicotinamide adenine dinucleotides, flavins, and vitamins B₆ and K and variants of these); and dipicolinates. The concentrations, absorptivities, and fluorescence quantum yields are estimated from the literature, often with large uncertainties. The bioparticles in the model are spherical and homogeneous. Calculated fluorescence cross sections for particles excited at 266, 280, and 355 nm are compared with measured values from the literature for several bacteria, bacterial spores and albumins. The calculated 266- and 280-nm excited fluorescence is within a factor of 3.2 of the measurements for the vegetative cells and proteins, but overestimates the fluorescence of spores by a factor of 10 or more. This is the first reported modeling of the fluorescence of bioaerosols in which the primary fluorophores and absorbing molecules are included.

Standoff detection of biological agents using laser induced fluorescence-a comparison of 294 nm and 355 nm excitation wavelengths

Standoff detection measuring the fluorescence spectra of seven different biological agents excited by 294 nm as well as 355 nm wavelength laser pulses has been undertaken. The biological warfare agent simulants were released in a semi-closed aerosol chamber at 210 m standoff distance and excited by light at either of the two wavelengths using the same instrument. Significant differences in several of the agents' fluorescence response were seen at the two wavelengths. The anthrax simulants' fluorescence responses were almost an order of magnitude stronger at the shorter wavelength excitation. However, most importantly, the fluorescence spectra were significantly more dissimilar at 294 nm than at 355 nm excitation with ~7 nm spectral resolution. This indicates that classification of the substances should be possible with a lower error rate for standoff detection using 294 nm rather than 355 nm excitation wavelength, or even better, utilizing both.