Paul J. Marchese

Nucleotide fluctuation of RecA repair gene in Siberian permafrost Psychrobacter cryohalolentis K5

A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the RecA repair gene of Psychrobacter cryohalolentis K5, Psychrobacter arcticus 273-4, and Psychrobacter sp. PRwf-1. The fractal dimension was found to correlate with the genes operating temperature with the highest fractal dimension associated with P. cryohalolentis K5 living at the low temperatures found in Siberian permafrost. The CpG dinucleotide content was found to be about 5% for the three species of Psychrobacters, which is substantially lower than that of Deinococcus radiodurans at about 12%. The average nucleotide pair-wise free energy was found to be lowest for Psychrobacter sp. PRwf-1, the species with the lowest fractal dimension of the three, consistent with the recent finding that Psychrobacter sp. PRw-f1 has a temperature growth maximum of 15-20°C higher than P. arcticus 273-4 and P. cryohaloentis K5. The results suggest that microbial vitality in extreme environments is associated with fractal dimension as well as high CpG dinucleotide content, while the average nucleotide pair-wise free energy is related to the operating environment. Evidence that extreme temperature operation would impose constraints measurable by Shannon entropy is also discussed. A quantitative estimate of an entropy-based measure having the characteristics of a mechanical pressure shows that the Psychrobacter RecA sequence experiences lower pressure than that of the human HAR1 sequence.

Fractal Analysis of Filamentous Actin Fluorescent Speckle Microscope Patterns in Cell Migration

The fluorescent speckle microscope pattern of newt lung epithelial cell filamentous actin during migration was analyzed using the Higuchi fractal method. The public domain datasets of 2004 PNAS Vallotton et al. were studied. The time series data from time lapsed images exhibited similar fractal dimensions (about 1.68 to 1.82) for various cell regions. Computer simulation of random time series data suggested an average fractal dimension of about 2 with a standard deviation of about 0.027. Speckle trend removals revealed pulsation features which were further studied using a sinusoidal signal model commonly used in gene regulatory studies. Gaussian noise models mixed with sinusoidal signal were used to simulate the observed fractal dimensions. The extracted constraints could be interpreted as polymerization and control pathway related. The administration of contractility promotion drug calyculin-A resulted in an increase of the overall image fractal dimension, which is consistent with the loss of correlation due to random direction contractions. It appears that high fractal dimension could be interpreted as being due to further randomization. Two doses of 20 nM calyculin-A increased cell noise by about 45%. Extension of this proof-of-concept fractal analysis to clinical treatment was also discussed.

DNA sequence-based comparative studies between non-extremophile and extremophile organisms with implications in exobiology

We have characterized function related DNA sequences of various organisms using informatics techniques, including fractal dimension calculation, nucleotide and multi-nucleotide statistics, and sequence fluctuation analysis. Our analysis shows trends which differentiate extremophile from non-extremophile organisms, which could be reproduced in extraterrestrial life. Among the systems studied are radiation repair genes, genes involved in thermal shocks, and genes involved in drug resistance. We also evaluate sequence level changes that have occurred during short term evolution (several thousand generations) under extreme conditions.

Remote sensing of ash tree health associated with the emerald ash borer via analyses of fluctuations in land-based and satellite-based data indices

The beetle, Agrilus planipennis Fairmaire, was introduced to Michigan in 2002 and has since spread to many other states. In recent years, it has been reported in parts of New York. The fluctuations in satellite data signal associated with indices describing ash tree health, such as leaf area index (LAI) and Normalized Difference Vegetation Index (NVDI) as reported by the MODIS, have been studied. The fraction of Photosynthetically Active Radiation (FPAR) data was also studied. MODIS hyperspectral data, as calibrated to winged aircraft hyperspectral data, was used for ash tree characterization.

Utilization of Solar Dynamics Observatory space weather digital image data for comparative analysis with applicationto Baryon Oscillation Spectroscopic Survey

Digital solar image data is available to users with access to standard, mass-market software. Many scientific projects utilize the Flexible Image Transport System (FITS) format, which requires specialized software typically used in astrophysical research. Data in the FITS format includes photometric and spatial calibration information, which may not be useful to researchers working with self-calibrated, comparative approaches. This project examines the advantages of using mass-market software with readily downloadable image data from the Solar Dynamics Observatory for comparative analysis over with the use of specialized software capable of reading data in the FITS format. Comparative analyses of brightness statistics that describe the solar disk in the study of magnetic energy using algorithms included in mass-market software have been shown to give results similar to analyses using FITS data. The entanglement of magnetic energy associated with solar eruptions, as well as the development of such eruptions, has been characterized successfully using mass-market software. The proposed algorithm would help to establish a publicly accessible, computing network that could assist in exploratory studies of all FITS data. The advances in computer, cell phone and tablet technology could incorporate such an approach readily for the enhancement of high school and first-year college space weather education on a global scale. Application to ground based data such as that contained in the Baryon Oscillation Spectroscopic Survey is discussed.

Remote sensing of LAI-FPAR fluctuations and Synchrotron EXAFS-XANES studies of metal absorption under stress

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 grids 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.

Deep-water chlorophyll concentration global time series fluctuation

The deep water chlorophyll concentration fluctuation from 2003 to 2007 has been studied using fractal analysis. The SeaWiFS global daily mean chlorophyll concentration time series were used. The Higuchi fractal algorithm was used to calculate fractal dimension, which is given by the slope of an associated length versus the lag. Short range fluctuation investigation using a six point slope gives fractal dimensions from 1.80 to 1.85, suggesting the presence of correlation, which was confirmed by computer simulations. The gradual increase of fractal dimension to 1.9 in about 15 lag-days suggests that a long-range de-correlation mechanism favoring random fluctuation is present. The 2007 times series shows a relatively low overall fractal dimension and exhibits a peculiar multi-fractal behavior. This phenomenon and the observed low accumulated cyclone energy in 2007 support the interpretation that cyclone energy can promote deep-water chlorophyll concentration fluctuation. A regression of fractal dimension at 10 lag-days versus the log of cyclone energy gives an R2 value of 0.75 (N = 5)., which suggests the presence of additional or related de-correlation mechanisms.

Phaeodactylum tricornutum photosynthesis and Thalassiosira pseudonana bio-silica formation genes nucleotide fluctuations

Diatom bioactivity has been reported to be responsible for about 20% of carbon fixation globally and together with other photosynthetic organisms, the bioactivity can be monitored via satellite ocean imaging. The bioinformatics embedded in the nucleotide fluctuations of photosynthesis and bio-silicate genes in diatoms were studied. The recently reported phosphoenolpyruvate carboxylase PEPC1 and PEPC2 C4-like photosynthesis genes in Phaeodactylum tricornutum were found to have similar fractal dimensions of about 2.01. In comparison, the green alga Chlamydomonas reinhardtii PEPC1 and PEPC2 genes have fractal dimensions of about 2.05. The PEPC CpG dinucleotide content is 8% in P. tricornutum and 10% in C. reinhardtii. Further comparison of the cell wall protein gene showed that the VSP1 gene sequence in C. reinhardtii has a fractal dimension of 2.03 and the bio-silica formation silaffin gene in Thalassiosira pseudonana has a fractal dimension of 2.01. The phosphoenolpyruvate carboxylase PPC1 and PPC2 in T. pseudonana were found to have fractal dimensions and CpG dinucleotide content similar to that of P. tricornutum. The fractal dimension of the dnaB replication helicase gene is about 1.98 for both diatoms as well as for the alga Heterosigma akashiwo. In comparison, the E. coli dnaB gene has a fractal dimension of about 2.03. Given that high fractal dimension and CpG dinucleotide content sequences have been associated with the presence of selective pressures, the relatively low fractal dimension gene sequences of the two unique properties of Earth-bound diatoms (photosynthesis and bio-silica cell wall) suggests the potential for the development of high fractal dimension sequences for adaptation in harsh environments.

Imaging through diffusive layers using speckle pattern fractal analysis and application to embedded object detection in tissues

The absorption effect of the back surface boundary of a diffuse layer was studied via laser generated reflection speckle pattern. The spatial speckle intensity provided by a laser beam was measured. The speckle data were analyzed in terms of fractal dimension (computed by NIH ImageJ software via the box counting fractal method) and weak localization theory based on Mie scattering. Bar code imaging was modeled as binary absorption contrast and scanning resolution in millimeter range was achieved for diffusive layers up to thirty transport mean free path thick. Samples included alumina, porous glass and chicken tissue. Computer simulation was used to study the effect of speckle spatial distribution and observed fractal dimension differences were ascribed to variance controlled speckle sizes. Fractal dimension suppressions were observed in samples that had thickness dimensions around ten transport mean free path. Computer simulation suggested a maximum fractal dimension of about 2 and that subtracting information could lower fractal dimension. The fractal dimension was shown to be sensitive to sample thickness up to about fifteen transport mean free paths, and embedded objects which modified 20% or more of the effective thickness was shown to be detectable. The box counting fractal method was supplemented with the Higuchi data series fractal method and application to architectural distortion mammograms was demonstrated. The use of fractals in diffusive analysis would provide a simple language for a dialog between optics experts and mammography radiologists, facilitating the applications of laser diagnostics in tissues.

Fractal analysis of noise buried time series signals with applications to exoplanet spectroscopy and bio-data

The shape of an exoplanet lightcurve is usually obtained by averaging the noise over multiple datasets. Fractal analysis has been demonstrated to be an effective tool for the detection of exoplanet transits using lightcurves summed over all wavelengths sensitive to the detector (G. Tremberger, Jr et. al, 2006 Proc SPIE Vol 6265). The detection of spectral features would depend on the extent to which the signal was buried in the noise. Different noise sources would have different fractal characteristics. Also, the signal strength could be discontinuous in time depending on the exoplanets local atmospheric environment. Such a discontinuity is unlikely to be detected with time integrated data. The lightcurve noise and shape information were characterized with fractal dimension analysis of a noise buried time series signal. Computer simulation revealed that when the noise is three times that of the signal, the fractal algorithm could detect the signal at about the 87% confidence level. Application to noise buried time series datasets (HD 209458b lightcurve, HD149026b lightcurve) detected discontinuities consistent with the results obtained by averaging datasets. Extension to individual wavelength lightcurves would establish a detection limit for the existence of spectral features at wavelengths important for exoplanet study. Other applications such as pre-implantation genetic screening spectroscopy and spatially varied aneuploidy bio-data could use the same analysis principle as well.