Dr. Todd Holden Profile

Dr. Todd Holden

Full Time Faculty at Queensborough Community College

SPIE Involvement:

Author

Publications (32)

Proceedings Article | 11 September 2015 Paper

The bioinformatics of nucleotide sequence coding for proteins requiring metal coenzymes and proteins embedded with metals

G. Tremberger, Sunil Dehipawala, E. Cheung, T. Holden, R. Sullivan, A. Nguyen, D. Lieberman, T. Cheung

Proceedings Volume 9606, 96060E (2015) https://doi.org/10.1117/12.2186563

KEYWORDS: Fractal analysis, Metals, Mode conditioning cables, Proteins, Bioinformatics, Switches, Zinc, Clocks, Biological research, Iron

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All metallo-proteins need post-translation metal incorporation. In fact, the isotope ratio of Fe, Cu, and Zn in physiology and oncology have emerged as an important tool. The nickel containing F430 is the prosthetic group of the enzyme methyl coenzyme M reductase which catalyzes the release of methane in the final step of methano-genesis, a prime energy metabolism candidate for life exploration space mission in the solar system. The 3.5 Gyr early life sulfite reductase as a life switch energy metabolism had Fe-Mo clusters. The nitrogenase for nitrogen fixation 3 billion years ago had Mo. The early life arsenite oxidase needed for anoxygenic photosynthesis energy metabolism 2.8 billion years ago had Mo and Fe. The selection pressure in metal incorporation inside a protein would be quantifiable in terms of the related nucleotide sequence complexity with fractal dimension and entropy values. Simulation model showed that the studied metal-required energy metabolism sequences had at least ten times more selection pressure relatively in comparison to the horizontal transferred sequences in Mealybug, guided by the outcome histogram of the correlation R-sq values. The metal energy metabolism sequence group was compared to the circadian clock KaiC sequence group using magnesium atomic level bond shifting mechanism in the protein, and the simulation model would suggest a much higher selection pressure for the energy life switch sequence group. The possibility of using Kepler 444 as an example of ancient life in Galaxy with the associated exoplanets has been proposed and is further discussed in this report. Examples of arsenic metal bonding shift probed by Synchrotron-based X-ray spectroscopy data and Zn controlled FOXP2 regulated pathways in human and chimp brain studied tissue samples are studied in relationship to the sequence bioinformatics. The analysis results suggest that relatively large metal bonding shift amount is associated with low probability correlation R-sq outcome in the bioinformatics simulation.

Proceedings Article | 11 September 2015 Paper

Bioinformatics comparison of sulfate-reducing metabolism nucleotide sequences

G. Tremberger, Sunil Dehipawala, A. Nguyen, E. Cheung, R. Sullivan, T. Holden, D. Lieberman, T. Cheung

Proceedings Volume 9606, 960610 (2015) https://doi.org/10.1117/12.2188390

KEYWORDS: Fractal analysis, Bacteria, Sulfur, Mode conditioning cables, Thermodynamics, Bioinformatics, Proteins, Calibration, Biological research, Cadmium sulfide

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Proceedings Article | 11 September 2015 Paper

Complexity of genetic sequences modified by horizontal gene transfer and degraded-DNA uptake

George Tremberger, S. Dehipawala, A. Nguyen, E. Cheung, R. Sullivan, T. Holden, D. Lieberman, T. Cheung

Proceedings Volume 9606, 96060H (2015) https://doi.org/10.1117/12.2186550

KEYWORDS: Fractal analysis, Microorganisms, Toxicity, Proteins, Genetics, Transform theory, Calibration, Cadmium sulfide, Iron, Resistance

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Proceedings Article | 26 September 2013 Paper

Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences

Sunil Dehipawala, A. Nguyen, G. Tremberger, E. Cheung, T. Holden, D. Lieberman, T. Cheung

Proceedings Volume 8865, 88650H (2013) https://doi.org/10.1117/12.2024633

KEYWORDS: Fractal analysis, Yeast, Proteins, Astrobiology, Bioinformatics, Medical research, Genetics, Biomedical optics, Analytical research, Image information entropy

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The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, clinical trial targeted cancer gene CD47, SIRT6 in spermatogenesis, and HLA-C in mosquito bite immunology demonstrate the diagram classification methodology. Comparisons to the SEPT4-XIAP pair in stem cell apoptosis, testesexpressed taste genes TAS1R3-GNAT3 pair, and amyloid beta APLP1-APLP2 pair with the yeast-mammal DNA sequences for meiotic proteins RAD50-MRE11 pair and NCAPD2-ICK pair have accounted for the observed fluctuating evolutionary pressure systematically. Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook’s distance, consistent with a non-Earth source for this radiation resistant bacterium. Convergent and divergent fluctuating evolutionary pressure could be studied with extension to genetic sequences in organisms in possible astrobiology conditions, with the assumption that the continuation of a book of life would require meiotic proteins everywhere in the universe.

Proceedings Article | 26 September 2013 Paper

Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction

Sunil Dehipawala, A. Nguyen, G. Tremberger, E. Cheung, P. Schneider, D. Lieberman, T. Holden, T. Cheung

Proceedings Volume 8865, 88650G (2013) https://doi.org/10.1117/12.2024627

KEYWORDS: Fractal analysis, Proteins, Computer simulations, Astrobiology, Calibration, Dichroic materials, Biomedical optics, Bioinformatics, Analytical research, Image information entropy

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A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene reconstruction studies in astrobiology and also be applicable to the study of point mutation in conformational thermostabilization research with Synchrotron based X-ray data for drug applications such as Parkinson’s disease.

Proceedings Article | 24 October 2012 Paper

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

George Tremberger, Sunil Dehipawala, Todd Holden, Paul Marchese, Tak Cheung

Proceedings Volume 8513, 851304 (2012) https://doi.org/10.1117/12.929786

KEYWORDS: Fractal analysis, MODIS, Calibration, Remote sensing, Satellites, Data modeling, Statistical analysis, Biological research, Vegetation, Satellite communications

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Proceedings Article | 15 October 2012 Paper

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

V. Shekoyan, S. Dehipawala, Ernest Liu, Vivek Tulsee, R. Armendariz, G. Tremberger, T. Holden, P. Marchese, T. Cheung

Proceedings Volume 8499, 84991Y (2012) https://doi.org/10.1117/12.929747

KEYWORDS: Fractal analysis, Solar energy, Statistical analysis, Calibration, Magnetism, Observatories, Spectroscopy, Digital imaging, Analytical research, Imaging spectroscopy

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Proceedings Article | 15 October 2012 Paper

Kepler mission exoplanet transit data analysis using fractal imaging

S. Dehipawala, G. Tremberger, Y. Majid, T. Holden, D. Lieberman, T. Cheung

Proceedings Volume 8500, 85000T (2012) https://doi.org/10.1117/12.930004

KEYWORDS: Fractal analysis, Exoplanets, Image compression, Stars, Image analysis, Fourier transforms, Space telescopes, Telescopes, Image resolution, Data analysis

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Proceedings Article | 15 October 2012 Paper

Nucleotide fluctuation in extremophilic cold-adapted sequences and their degradation codes

George Tremberger, S. Dehipawala, E. Cheung, Jesaiah Prayor, Rafael Duran, P. Schneider, D. Lieberman, T. Holden, T. Cheung

Proceedings Volume 8521, 85210J (2012) https://doi.org/10.1117/12.929653

KEYWORDS: Fractal analysis, Image information entropy, Data modeling, Bioinformatics, Calibration, Biological research, Astrobiology, Factor analysis, Mode conditioning cables, Atomic layer deposition

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Proceedings Article | 10 March 2012 Paper

Effect of non-homogenous thermal stress during sub-lethal photodynamic antimicrobial chemotherapy

N. Gadura, D. Kokkinos, S. Dehipawala, E. Cheung, R. Sullivan, R. Subramaniam, P. Schneider, G. Tremberger, T. Holden, D. Lieberman, T. Cheung

Proceedings Volume 8211, 82110O (2012) https://doi.org/10.1117/12.909486

KEYWORDS: Fractal analysis, Light sources, Photoacoustic tomography, Thermal effects, Photodynamic therapy, Pathogens, Microscopy, Iron, Oxides, Doping

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Proceedings Article | 23 February 2012 Paper

Optical diffusion property of cerumen from ear canal and correlation to metal content measured by synchrotron x-ray absorption

Todd Holden, Sumudu Dehipawala, E. Cheung, U. Golebiewska, P. Schneider, G. Tremberger, D. Kokkinos, D. Lieberman, Sunil Dehipawala, T. Cheung

Proceedings Volume 8221, 82211L (2012) https://doi.org/10.1117/12.909896

KEYWORDS: Metals, Absorption, Synchrotrons, Pathogens, Microorganisms, Diffusion, Zinc, Ear, Near field optics, Light sources

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Proceedings Article | 9 February 2012 Paper

Optical speckles of blood proteins embedded in porous glassy substrate

T. Holden, S. Dehipawala, D. Kokkinos, A. Berisha, E. Cheung, A. Nguyen, U. Golebiewska, P. Schneider, G. Tremberger, D. Lieberman, T. Cheung

Proceedings Volume 8222, 822207 (2012) https://doi.org/10.1117/12.909503

KEYWORDS: Proteins, Blood, Molecules, Speckle, Speckle pattern, Calibration, Iron, Doping, Diffusion, Molecular interactions

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Proceedings Article | 2 February 2012 Paper

Single mode and sub-cellular fiber probes for cell scattering and density variation measurements

D. Kokkinos, T. Holden, S. Dehipawala, L. Mora, W. Huazhco, N. Gadura, U. Golebiewska, P. Schneider, G. Tremberger, D. Lieberman, T. Cheung

Proceedings Volume 8230, 82301G (2012) https://doi.org/10.1117/12.909911

KEYWORDS: Scattering, Fourier transforms, Refractive index, Single mode fibers, Monte Carlo methods, Correlation function, Microscopy, Yeast, Calibration, Optical testing

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Proceedings Article | 30 January 2012 Paper

Fiber optic based heart-rate and pulse pressure shape monitor

D. Kokkinos, S. Dehipawala, T. Holden, E. Cheung, M. Musa, G. Tremberger, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 8218, 82180V (2012) https://doi.org/10.1117/12.909582

KEYWORDS: Fiber optics sensors, Sensors, Electrocardiography, Fractal analysis, Heart, Fiber optics, Arteries, Single mode fibers, Optical fabrication, Photonic crystal fibers

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Proceedings Article | 23 September 2011 Paper

Technologically important extremophile 16S rRNA sequence Shannon entropy and fractal property comparison with long term dormant microbes

Todd Holden, N. Gadura, S. Dehipawala, E. Cheung, M. Tuffour, P. Schneider, G. Tremberger, D. Lieberman, T. Cheung

Proceedings Volume 8152, 81520T (2011) https://doi.org/10.1117/12.893450

KEYWORDS: Fractal analysis, Microorganisms, Image information entropy, Biology, Uranium, Proteins, Rockets, Statistical analysis, Electrodes, Data modeling

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Proceedings Article | 23 September 2011 Paper

Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes

Todd Holden, S. Dehipawala, E. Cheung, R. Bienaime, J. Ye, G. Tremberger, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 8152, 81520S (2011) https://doi.org/10.1117/12.893434

KEYWORDS: Fractal analysis, Proteins, Microorganisms, Image information entropy, Sulfur, Biology, Photosynthesis, Metals, Mars, Biological research

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Proceedings Article | 16 September 2011 Paper

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

T. Holden, S. Dehipawala, E. Cheung, R. Regan, G. Tremberger, U. Golebiewska, P. Marchese, T. Cheung

Proceedings Volume 8156, 81560O (2011) https://doi.org/10.1117/12.893887

KEYWORDS: Fractal analysis, Absorption, Remote sensing, Synchrotrons, Metals, Zinc, Iron, MODIS, Calibration, Environmental sensing

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Proceedings Article | 7 September 2010 Paper

Zn-metalloprotease sequences in extremophiles

T. Holden, S. Dehipawala, U. Golebiewska, E. Cheung, G. Tremberger, E. Williams, P. Schneider, N. Gadura, D. Lieberman, T. Cheung

Proceedings Volume 7819, 78190V (2010) https://doi.org/10.1117/12.860091

KEYWORDS: Fractal analysis, Proteins, Organisms, Zinc, Biology, Image information entropy, Calibration, Chemical species, Cadmium sulfide, Astrobiology

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Proceedings Article | 7 September 2010 Paper

Cyanobacteria gene and protein sequences in diurnal oscillation metabolic processes

George Tremberger, T. Holden, E. Cheung, S. Dehipawala, N. Gadura, U. Golebiewska, K. Valentin, M. Smulczeski, W. Satizabal, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 7819, 78190U (2010) https://doi.org/10.1117/12.860093

KEYWORDS: Fractal analysis, Proteins, Iron, Biology, Photosynthesis, Organisms, Image information entropy, Nitrogen, Astrobiology, Oxygen

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Proceedings Article | 7 September 2010 Paper

Archaeon and archaeal virus diversity classification via sequence entropy and fractal dimension

George Tremberger, Victor Gallardo, Carola Espinoza, Todd Holden, N. Gadura, E. Cheung, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 7819, 78190T (2010) https://doi.org/10.1117/12.860097

KEYWORDS: Fractal analysis, Oceanography, Proteins, Biology, Image information entropy, Organisms, Ecosystems, Databases, Astrobiology, Solar energy

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Proceedings Article | 11 September 2009 Paper

Nucleotide fluctuation of radiation-resistant Halobacterium sp. NRC-1 single-stranded DNA-binding protein (RPA) genes

Todd Holden, G. Tremberger, E. Cheung, R. Subramaniam, N. Gadura, P. Schneider, R. Sullivan, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 7441, 74410R (2009) https://doi.org/10.1117/12.825827

KEYWORDS: Fractal analysis, Image information entropy, Proteins, Mars, Silver, Bacteria, Resistance, Statistical analysis, Calibration, Gamma radiation

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Proceedings Article | 4 September 2009 Paper

Multi-fractal property of perchlorate reductase gene sequences and DNA photonics application to UV fluorescence detection on Mars-like surfaces

George Tremberger, Eric Cheung, N. Gadura, Todd Holden, Raji Subramaniam, Regina Sullivan, Pat Schneider, Alex Flamholz, David Lieberman, Tak Cheung

Proceedings Volume 7441, 74410G (2009) https://doi.org/10.1117/12.825819

KEYWORDS: Fractal analysis, Image information entropy, Microorganisms, Ultraviolet radiation, Mars, Chemical analysis, Luminescence, DNA photonics, Proteins, Distance measurement

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The discovery of perchlorate on Mars raises the possibility of the existence of perchlorate reduction microbes on that planet. The perchlorate reductase gene sequence fractal dimensions of two Dechloromonas species were compared with five other sequences in the microbial dimethyl sulfoxide (DMSO) reductase family. A nucleotide sequence can be expressed as a numerical sequence where each nucleotide is assigned its proton number. The resulting numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. Analysis of the fractal dimensions for the DMSO reductase family supports phylogenetic analyses that show that the perchlorate reductase gene sequences are members of the same family. A sub-family with roughly the same nucleotide length emerges having the property that the gene fractal dimension is negatively correlated with the Shannon di-nucleotide entropy (R² ~ 0.95, N =5). The gene sequence fractal dimension is found to be positively correlated with the neighbor joining distances reported in a published protein phylogeny tree (R²~ 0.92, N = 5). The multi-fractal property associated with these genes shows that perchlorate reductase has lower dimensionality as compared to the relatively higher dimensionality DNA-break repair genes Rec-A and Rad-A observed in the Dechloromonas aromatica and Deinococcus radiodurans genomes. The studied perchlorate gene sequences show a higher Shannon di-nucleotide entropy (~3.97 bits) relative to Dechloromonas aromatica DNA repair sequences (~3.87 bits Rec-A, ~3.92 bits Rad-A), suggesting that there are fewer constraints on nucleotide variety in the perchorlate sequences . These observations thus allow for the existence of perchlorate reducing microbes on Mars now or in the past. Timeresolved UV fluorescence study near the emission bands of nucleotide sequences could be used for bio-detection on Mars-like surfaces and the results may further constrain the proposed conjectures.

Proceedings Article | 19 August 2009 Paper

Deep-water chlorophyll concentration global time series fluctuation

T. Holden, D. Sunil, E. Cheung, D. Cotten, D. Klarberg, G. Tremberger, T. Nasar, J. Taylor, P. Marchese, T. Cheung

Proceedings Volume 7459, 74590O (2009) https://doi.org/10.1117/12.825807

KEYWORDS: Fractal analysis, Calibration, Wind energy, Satellites, Computer simulations, Climatology, Satellite imaging, Data modeling, Autoregressive models, Remote sensing

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Proceedings Article | 28 August 2008 Paper

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

George Tremberger, T. Holden, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, P. Marchese, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970U (2008) https://doi.org/10.1117/12.794390

KEYWORDS: Fractal analysis, Image information entropy, Astrobiology, Calibration, Proteins, Genetics, Chemical analysis, Microorganisms, Thermodynamics, Biology

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Proceedings Article | 28 August 2008 Paper

Methanosarcina acetivorans 16S rRNA and transcription factor nucleotide fluctuation with implications in exobiology and pathology

Todd Holden, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, P. Marchese, O. Hiciano, H. Yao, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970V (2008) https://doi.org/10.1117/12.794398

KEYWORDS: Fractal analysis, Mars, Pathology, Chemical analysis, Proteins, Biological research, Environmental sensing, Bioinformatics, Calibration, Astrobiology

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Cultures of the methane-producing archaea Methanosarcina, have recently been isolated from Alaskan sediments. It has been proposed that methanogens are strong candidates for exobiological life in extreme conditions. The spatial environmental gradients, such as those associated with the polygons on Mars' surface, could have been produced by past methanogenesis activity. The 16S rRNA gene has been used routinely to classify phenotypes. Using the fractal dimension of nucleotide fluctuation, a comparative study of the 16S rRNA nucleotide fluctuation in Methanosarcina acetivorans C2A, Deinococcus radiodurans, and E. coli was conducted. The results suggest that Methanosarcina acetivorans has the lowest fractal dimension, consistent with its ancestral position in evolution. Variation in fluctuation complexity was also detected in the transcription factors. The transcription factor B (TFB) was found to have a higher fractal dimension as compared to transcription factor E (TFE), consistent with the fact that a single TFB in Methanosarcina acetivorans can code three different TATA box proteins. The average nucleotide pair-wise free energy of the DNA repair genes was found to be highest for Methanosarcina acetivorans, suggesting a relatively weak bonding, which is consistent with its low prevalence in pathology. Multitasking capacity comparison of type-I and type-II topoisomerases has been shown to correlate with fractal dimension using the methicillin-resistant strain MRSA 252. The analysis suggests that gene adaptation in a changing chemical environment can be measured in terms of bioinformatics. Given that the radiation resistant Deinococcus radiodurans is a strong candidate for an extraterrestrial origin and that the cold temperature Psychrobacter cryohalolentis K5 can function in Siberian permafrost, the fractal dimension comparison in this study suggests that a chemical resistant methanogen could exist in extremely cold conditions (such as that which existed on early Mars) where demands on gene activity are low. In addition, the comparative study of the Methanococcoides burtonii cold shock domain sequence has provided further support for the correlation between multitasking capacity and fractal dimension.

Proceedings Article | 28 August 2008 Paper

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

Todd Holden, P. Marchese, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970Q (2008) https://doi.org/10.1117/12.801269

KEYWORDS: Fractal analysis, Organisms, Monte Carlo methods, Statistical analysis, Proteins, Image information entropy, Resistance, Biological research, Information science, Genetics

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Proceedings Article | 28 August 2008 Paper

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

Todd Holden, P. Marchese, G. Tremberger, E. Cheung, R. Subramaniam, R. Sullivan, P. Schneider, A. Flamholz, M. Huerta, D. Lieberman, T. Cheung

Proceedings Volume 7097, 70970R (2008) https://doi.org/10.1117/12.794414

KEYWORDS: Fractal analysis, Photosynthesis, Proteins, Organisms, Calibration, Carbon, Satellite imaging, Satellites, Bioinformatics, Cadmium sulfide

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Proceedings Article | 30 October 2007 Paper

Intensity fluctuation analysis of cell scattering/imaging with clinical application

Raji Subramaniam, R. Sullivan, P. Schneider, T. Holden, G. Tremberger, E. Cheung, A. Flamholz, D. Lieberman, T. Cheung, F. Garcia, N. Bewry, N. Pennie

Proceedings Volume 6796, 67960N (2007) https://doi.org/10.1117/12.778063

KEYWORDS: Fractal analysis, Breast, Biological research, Video, Speckle pattern, Mammography, Magnetic resonance imaging, Microscopes, Speckle, Microscopy

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Proceedings Article | 15 October 2007 Paper

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

George Tremberger, A. Flamholz, E. Cheung, R. Sullivan, R. Subramaniam, P. Schneider, G. Brathwaite, J. Boteju, P. Marchese, D. Lieberman, T. Cheung, Todd Holden

Proceedings Volume 6771, 677117 (2007) https://doi.org/10.1117/12.732302

KEYWORDS: Fractal analysis, Speckle pattern, Speckle, Tissues, Computer simulations, Mammography, Binary data, Absorption, Glasses, Architectural distortion

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Proceedings Article | 1 October 2007 Paper

ATCG nucleotide fluctuation of Deinococcus radiodurans radiation genes

Todd Holden, R. Subramaniam, R. Sullivan, E. Cheung, C. Schneider, G. Tremberger, A. Flamholz, D. Lieberman, T. Cheung

Proceedings Volume 6694, 669417 (2007) https://doi.org/10.1117/12.732283

KEYWORDS: Fractal analysis, Gamma radiation, Statistical analysis, Proteins, Monte Carlo methods, Calibration, Analytical research, Biological research, Computer simulations, Brain

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The radiation resistance-repair genes in Deinococcus radiodurans (DR) and E-coli were analyzed in terms of the A, T, C, G nucleotide fluctuations. The studied genes were Rec-A, Rec-Q, and the unique DR PprA gene. In an ATCG sequence, each base was assigned a number equal to its atomic number. The resulting numerical sequence was the basis of the statistical analysis. Fractal analysis using the Higuchi method gave a fractal dimension increase of the Deinococcus radiodurans genes as compared to E-coli, which is comparable to the enhancement observed in the human HAR1 region (HAR1F gene) over that of the chimpanzee. Near neighbor fluctuation was also studied via the Black-Scholes model where the increment sequence was treated as a random walk series. The Deinococcus radiodurans radiation gene standard deviations were consistently higher than that of the E-coli deviations, and agree with the fractal analysis results. The sequence stacking interaction was studied using the published nucleotide-pair melting free energy values and Deinococcus radiodurans radiation genes were shown to possess larger negative free energies. The high sensitivity of the fractal dimension as a biomarker was tested with correlation analysis of the gamma ray dose versus fractal dimension, and the R square values were found to be above 0.9 (N=5). When compared with other nucleotide sequences such as the rRNA sequences, HAR1 and its chimpanzee counterpart, the higher fluctuation (correlated randomness) and larger negative free energy of a DR radiation gene suggested that a radiation resistance-repair sequence exhibited higher complexity. As the HAR1 nucleotide sequence complexity and its transcription activity of co-expressing cortex protein reelin supported a positive selection event in humans, a similar inference of positive selection of coding genes could be drawn for Deinococcus radiodurans when compared to E-coli. The origin of such a positive selection would be consistent with that of a Martian environment.

Proceedings Article | 19 September 2007 Paper

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

George Tremberger, T. Holden, E. Cheung, A. Flamholz, P. Marchese, H. Yao, P. Schneider, D. Lieberman, T. Cheung

Proceedings Volume 6693, 66931D (2007) https://doi.org/10.1117/12.732987

KEYWORDS: Fractal analysis, Interference (communication), Exoplanets, Signal detection, Stars, Spectroscopy, Computer simulations, Calibration, Detection and tracking algorithms, Genetics

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