Search

Human (and other mammals) would secrete cerumen (ear wax) to protect the skin of the ear canal against pathogens and insects. The studies of biodiversity of pathogen in human include intestine microbe colony, belly button microbe colony, etc. Metals such as zinc and iron are essentials to bio-molecular pathways and would be related to the underlying pathogen vitality. This project studies the biodiversity of cerumen via its metal content and aims to develop an optical probe for metal content characterization. The optical diffusion mean free path and absorption of human cerumen samples dissolved in solvent have been measured in standard transmission measurements. EXFAS and XANES have been measured at Brookhaven Synchrotron Light Source for the determination of metal contents, presumably embedded within microbes/insects/skin cells. The results show that a calibration procedure can be used to correlate the optical diffusion parameters to the metal content, thus expanding the diagnostic of cerumen in the study of human pathogen biodiversity without the regular use of a synchrotron light source. Although biodiversity measurements would not be seriously affected by dead microbes and absorption based method would do well, the scattering mean free path method would have potential to further study the cell based scattering centers (dead or live) via the information embedded in the speckle pattern in the deep-Fresnel zone.

Blood protein molecules could be embedded in porous glassy substrate with 10-nm pores. The embedding principle is based on blood cell dehydration with the destruction of the cell membrane, and reconstitution and centrifuge could yield a suitable solution for doping into a porous glassy medium. The doped glassy substrate speckle pattern under laser illumination could be used to characterize the protein size distribution. Calibration with known protein embedded samples would result in an optical procedure for the characterization of a blood sample. Samples embedded with larger kilo-Dalton protein molecule show more variation in the speckle patterns, consistent with protein folding interaction inside a pore cavity. A regression model has been used to correlate the protein molecule sizes with speckle sizes. The use of diffusion mean free path information to study protein folding in the embedding process is briefly discussed.

Cell density is an important parameter in the question of bio-variation and the studying of cell scattering could be a viable tool. The development of spatially resolved optical fiber probe would enable the characterization of optical scattering from cells within a colony. Single mode fiber probe would be budget friendly as compared to a 50-nm sub-cellular fiber probe. This project develops a calibration procedure to correlate the optical scattering measured by a single mode fiber probe to that of a 50-nm sub-cellular fiber probe in the context of cell density variation. The Fourier transform of intensity angular transmission would give correlation information in the Efield in the spatial coordinate. Monte Carlo simulation could be used to constrain the input intensity function spatial content resembling microscopy. The use of a 50-nm sub-cellular fiber probe for detailed study of biological samples would give sub-micron scale length information.

The fluctuations of leaf area index (LAI) and Fraction of Photosynthetically Active Radiation (FPAR) as reported by the MODIS 8-day product MOD15A2 over a section of Harriman State Park, New York were studied with reference to another nearby local park. The area selected for study, a seven km square grid with one km resolution, is known for its biodiversity. Time series data points were generated using the sums of the grid's 49 pixel measurements for each of the 46 entries that make up the annual time series. A quadratic relation has been observed that suggests that LAI/FPAR is proportional to FPAR if FPAR is considered as the forcing parameter via chlorophyll (a, b, c, d and f), in an application model for the study of biodiversity. The LAI annual time series from 2000 to 2009 follows the corresponding FPAR annual time series as expected, but with different proportionality ratios in different seasons. The fractal analysis results of the time series data suggest that the LAI sequences have a lower fractal dimension (~1.35) than those of the FPAR sequences (~1.55), consistent with the idea that biological systems are capable of regulating fluctuation. The regression of LAI sequence fractal dimension versus FPAR sequence fractal dimension exhibits an R-square of about 0.7 (N =10). The observed regression outlier for the year 2009 could be indicative of the presence of additional factors. Synchrotron EXAFS and XANES investigations of leaf samples reveal data consistent with metal absorption under stress. Further studies of absorption under stress using remote sensing data are warranted.

The Zn-metalloprotease family contains conserved amino acid structures such that the nucleotide fluctuation at the DNA level would exhibit correlated randomness as described by fractal dimension. A nucleotide sequence fractal dimension can be calculated from a numerical series consisting of the atomic numbers of each nucleotide. The structure's vibration modes can also be studied using a Gaussian Network Model. The vibration measure and fractal dimension values form a two-dimensional plot with a standard vector metric that can be used for comparison of structures. The preference for amino acid usage in extremophiles may suppress nucleotide fluctuations that could be analyzed in terms of fractal dimension and Shannon entropy. A protein level cold adaptation study of the thermolysin Zn-metalloprotease family using molecular dynamics simulation was reported recently and our results show that the associated nucleotide fluctuation suppression is consistent with a regression pattern generated from the sequences's fractal dimension and entropy values (R-square ~ 0.98, N =5). It was observed that cold adaptation selected for high entropy and low fractal dimension values. Extension to the Archaemetzincin M54 family in extremophiles reveals a similar regression pattern (R-square = 0.98, N = 6). It was observed that the metalloprotease sequences of extremely halophilic organisms possess high fractal dimension and low entropy values as compared with non-halophiles. The zinc atom is usually bonded to the histidine residue, which shows limited levels of vibration in the Gaussian Network Model. The variability of the fractal dimension and entropy for a given protein structure suggests that extremophiles would have evolved after mesophiles, consistent with the bias usage of non-prebiotic amino acids by extremophiles. It may be argued that extremophiles have the capacity to offer extinction protection during drastic changes in astrobiological environments.