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A college outreach engineering education program designed for high school students was implemented in a community college using the three principles of K-12 engineering education, namely, product design, science knowledge, and mindset development. The means of transforming a science question into a design driven one was illustrated using examples and projects from the fields of astronomy and bio-optics. The relevant scientific principles were presented by introducing various iterated designs in an interactive learning environment. A high school level research component using astronomy and bio-optics-related public data was also implemented to enrich the students’ exposure to numerical processing techniques accessible in Microsoft Excel. Examples including solar events driven by magnetic field topology, cosmological images generated by IllustrisTNG Project, muon flux data, Killer T-cell motion, and wound assay cell migration are used in the teaching of iterated designs. A Path Diagram assessment model based on a LISREL computation scheme with learning intent and engineering mindset as latent variables was used to gauge the effectiveness of an implementation, the results of which would be used in the subsequent semester’s implementation of the research component. The materials developed in a College Now course, where high school students take a research course at a community college, would be readily adaptable to other four-year college programs. The possible future incorporation of an introductory engineering course for high school student education, using the MIT low-cost $100 muon detector and Fermi Lab QuarkNet muon scintillation detector, is discussed.

DNA informatics represented by Shannon entropy and fractal dimension have been used to form 2D maps of related genes in various mammals. The distance between points on these maps for corresponding mRNA sequences in different species is used to study evolution. By quantifying the similarity of genes between species, this distance might be indicated when studies on one species (mouse) would tend to be valid in the other (human). The hypothesis that a small distance from mouse to human could facilitate mouse to human translational medicine success is supported by the studied ESR-1, LMNA, Myc, and RNF4 sequences. ID1 and PLCZ1 have larger separation. The collinearity of displacement vectors is further analyzed with a regression model, and the ID1 result suggests a mouse-chimp-human translational medicine approach. Further inference was found in the tumor suppression gene, p53, with a new hypothesis of including the bovine PKM2 pathways for targeting the glycolysis preference in many types of cancerous cells, consistent with quantum metabolism models. The distance between mRNA and protein coding CDS is proposed as a measure of the pressure associated with noncoding processes. The Y-chromosome DYS14 in fetal micro chimerism that could offer protection from Alzheimer's disease is given as an example.

The CYP2E1 CpG methylation sites in the first intron (site +626 to +742 from the starting ATG) as reported in a 2015 epigenetics psychiatry study were analyzed from a bioinformatics perspective. The studied sequences for human, monkey, dog and cow showed a high correlation (R-sq > 0.99) between CpG content and mononucleotide entropy. A comparably high correlation (R-sq > 0.95) was also found between the first exon sequences and mononucleotide entropy. These findings lend support to the hypothesis that CpG content is proportional to nucleotide availability when the latter quantity is computed as information entropy. To probe the nature of CpG sites in HAR1, a comparative study was conducted using the known promoter methylation regions in RELN and EGFR sequences. The observed high correlation (R-sq = 0.999) suggests that the eight CpG sites in HAR1 may function as human-specific gene expression controller sites since the equivalent chimp sequence has no CpG sites. A general scheme using randomly selected CpG methylation sites that precede the starting ATG codon is discussed with regard to fractal dimension modeling. Furthermore, an analysis of the studied RELN homolog CDS sequences for human, bovine, mouse and rat showed a high correlation of dinucleotide entropy with free energy (R > 0.9), consistent with the high correlation (R > 0.9) observed in a similar analysis of the studied pro-BDNF homolog CDS sequences for human, chimp, mouse and rat.

The sulfate-reducing bacteria can be traced back to 3.5 billion years ago. The thermodynamics details of the sulfur cycle have been well documented. A recent sulfate-reducing bacteria report (Robator, Jungbluth, et al , 2015 Jan, Front. Microbiol) with Genbank nucleotide data has been analyzed in terms of the sulfite reductase (dsrAB) via fractal dimension and entropy values. Comparison to oil field sulfate-reducing sequences was included. The AUCG translational mass fractal dimension versus ATCG transcriptional mass fractal dimension for the low temperature dsrB and dsrA sequences reported in Reference Thirteen shows correlation R-sq ~ 0.79 , with a probably of about 3% in simulation. A recent report of using Cystathionine gamma-lyase sequence to produce CdS quantum dot in a biological method, where the sulfur is reduced just like in the H2S production process, was included for comparison. The AUCG mass fractal dimension versus ATCG mass fractal dimension for the Cystathionine gamma-lyase sequences was found to have R-sq of 0.72, similar to the low temperature dissimilatory sulfite reductase dsr group with 3% probability, in contrary to the oil field group having R-sq ~ 0.94, a high probable outcome in the simulation. The other two simulation histograms, namely, fractal dimension versus entropy R-sq outcome values, and di-nucleotide entropy versus mono-nucleotide entropy R-sq outcome values are also discussed in the data analysis focusing on low probability outcomes.

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.

Horizontal gene transfer has been a major vehicle for efficient transfer of genetic materials among living species and could be one of the sources for noncoding DNA incorporation into a genome. Our previous study of lnc- RNA sequence complexity in terms of fractal dimension and information entropy shows a tight regulation among the studied genes in numerous diseases. The role of sequence complexity in horizontal transferred genes was investigated with Mealybug in symbiotic relation with a 139K genome microbe and Deinococcus radiodurans as examples. The fractal dimension and entropy showed correlation R-sq of 0.82 (N = 6) for the studied Deinococcus radiodurans sequences. For comparison the Deinococcus radiodurans oxidative stress tolerant catalase and superoxide dismutase genes under extracellular dGMP growth condition showed R-sq ~ 0.42 (N = 6); and the studied arsenate reductase horizontal transferred genes for toxicity survival in several microorganisms showed no correlation. Simulation results showed that R-sq < 0.4 would be improbable at less than one percent chance, suggestive of additional selection pressure when compared to the R-sq ~ 0.29 (N = 21) in the studied transferred genes in Mealybug. The mild correlation of R-sq ~ 0.5 for fractal dimension versus transcription level in the studied Deinococcus radiodurans sequences upon extracellular dGMP growth condition would suggest that lower fractal dimension with less electron density fluctuation favors higher transcription level.

The iron environment in Fe-doped Vycor Anode was investigated with EXAFS using Brookhaven Synchrotron Light Source. The iron-reducing Shewanella oneidensis culture was grown in a microbial fuel cell under anaerobic respiration. The Fe bond length was found to decrease and correlate with the amount of biofilm growth on the Fe-doped Vycor Anode. The data suggests that Fe-doped Vycor Anode would be a good substrate to study the Shewanella oneidensis nanowire structure using EXAFS., {"references":["Generation of Electricity and Analysis of Microbial Communities in\nWheat Straw Biomass-Powered Microbial Fuel Cells. Yifeng Zhang,\nBooki Min, Liping Huang, and Irini Angelidaki. Applied and\nEnvironmental Microbiology, June 2009, p. 3389–3395","Anode Biofilm Transcriptomics Reveals Outer Surface Components\nEssential for High Density Current Production in Geobacter\nsulfurreducens Fuel Cells. Nevin KP, Kim B-C, Glaven RH, Johnson JP,\nWoodard TL, et al. (2009) PLoS ONE 4(5): e5628\ndoi:10.1371/journal.pone.0005628","Biofilm and Nanowire Production Leads to Increased Current in\nGeobacter sulfurreducens Fuel Cells. Gemma Reguera, Kelly P. Nevin,\nJulie S. Nicoll, Sean F. Covalla, Trevor L. Woodard, and Derek R.\nLovley. Applied and Environmental Microbiology, Nov. 2006, p. 7345–\n7348","Purification and Characterization of OmcZ, an Outer-Surface,\nOctaheme c-Type Cytochrome Essential for Optimal Current Production\nby Geobacter sulfurreducens. Kengo Inoue, Xinlei Qian, Leonor\nMorgado, Byoung-Chan Kim, Tünde Mester, Mounir Izallalen, Carlos\nA. Salgueiro, and Derek R. Lovley. Applied and Environmental\nMicrobiology, June 2010, p. 3999–4007","Enhancement of Survival and Electricity Production in an Engineered\nBacterium by Light Driven Proton Pumping. Ethan T. Johnson, Daniel\nB. Baron, Bele´n Naranjo, Daniel R. Bond, Claudia Schmidt-Dannert, 1\nand Jeffrey A. Gralnick. Applied and Environmental Microbiology, July\n2010, p. 4123–4129","Substrate-Level Phosphorylation Is the Primary Source of Energy\nConservation during Anaerobic Respiration of Shewanella oneidensis\nStrain MR-1. Kristopher A. Hunt, Jeffrey M. Flynn, Bele´n Naranjo,\nIndraneel D. Shikhare, and Jeffrey A. Gralnick Journal of Bacteriology,\nJuly 2010, p. 3345–3351","Electrically conductive bacterial nanowires produced by Shewanella\noneidensis strain MR-1 and other microorganisms. Yuri A. Gorby,\nSvetlana Yanina, Jeffrey S. McLean, Kevin M. Rosso, Dianne Moyles,\nAlice Dohnalkova, Terry J. Beveridge, In Seop Chang, Byung Hong\nKim, Kyung Shik Kim, David E. Culley, Samantha B. Reed, Margaret\nF. Romine, Daad A. Saffarini, Eric A. Hill, Liang Shi, Dwayne A. Elias,\nDavid W. Kennedy, Grigoriy Pinchuk, Kazuya Watanabe, Shun'ichi\nIshii, Bruce Logan, Kenneth H. Nealson, and Jim K. Fredrickson.\nPNAS, July 25, 2006, vol. 103, p.11358-11363","Lower BH1, Shi L, Yongsunthon R, Droubay TC, McCready DE, Lower\nSK. Specific bonds between an iron oxide surface and outer membrane\ncytochromes MtrC and OmcA from Shewanella oneidensis MR-1. J\nBacteriol. 2007 Jul; 189(13):4944-52. Epub 2007 Apr 27.\nhttp://www.ncbi.nlm.nih.gov/pubmed/17468239","Mitchell AC1, Peterson L, Reardon CL, Reed SB, Culley DE, Romine\nMR, Geesey GG. Role of outer membrane c-type cytochromes MtrC and\nOmcA in Shewanella oneidensis MR-1 cell production, accumulation,\nand detachment during respiration on hematite.. Geobiology. 2012 Jul;\n10(4):355-70. doi: 10.1111/j.1472-4669.2012.00321.x. Epub 2012 Feb\n23. http://www.ncbi.nlm.nih.gov/pubmed/22360295\n[10] A gold-sputtered carbon paper as an anode for improved electricity\ngeneration from a microbial fuel cell inoculated with Shewanella\noneidensis MR-1. Sun M, Zhang F, Tong ZH, Sheng GP, Chen YZ,\nZhao Y, Chen YP, Zhou SY, Liu G, Tian YC, Yu HQ. Biosens\nBioelectron. 2010 Oct 15; 26(2):338-43. Epub 2010 Aug 11\n[11] Jian Ding, Tongxiang Fan, Di Zhang, Katsuhiko Saito, Qixin Guo.\nStructural and optical properties of porous iron oxide. Solid State\nCommunications Volume 151, Issue 10, May 2011, Pages 802–805\nhttp://www.sciencedirect.com/science/article/pii/S0038109811001104\n[12] Photochemistry of Fe(CO)5 adsorbed onto porous Vycor glass. Michael\nS. Darsillo, Harry D. Gafney, Michael S. Paquette J. Am. Chem. Soc.,\n1987, 109 (11), pp 3275–3286\n[13] Iron and iron oxide particle growth in porous Vycor glass; correlation\nwith optical and magnetic properties. Sunil, D.; Gafney, H. D.;\nRafailovich, M. H.; Sokolov, J.; Gambino, R. J.; Huang, D. M. Journal\nof Non-Crystalline Solids (2003), 319(1,2), 154-162.\n[14] Jinquan Don, Sunil, D., Harry Gafney. Influence of Amorphous Silicon\nMatrices on the Formation, Structure, and Chemistry of iron, iron oxide\nnanoparticles. Journal of the American Chemical Society 131(41)\n14768-14777 (2009).\n[15] James M. Byrne, Nicole Klueglein, Carolyn Pearce, Kevin M. Rosso,\nErwin Appel, Andreas Kappler. Redox cycling of Fe(II) and Fe(III) in\nmagnetite by Fe-metabolizing bacteria. Science 27 March 2015: Vol.\n347 no. 6229 pp. 1473-1476\n[16] Pirbadian S, El-Naggar MY. Multistep hopping and extracellular charge\ntransfer in microbial redox chains. Phys Chem Chem Phys. 2012 Oct\n28; 14(40):13802-8. http://www.ncbi.nlm.nih.gov/pubmed/22797729\n[17] Pirbadian S, Barchinger SE, Leung KM, Byun HS, Jangir Y, Bouhenni\nRA, Reed SB, Romine MF, Saffarini DA, Shi L, Gorby YA, Golbeck\nJH, El-Naggar MY. Shewanella oneidensis MR-1 nanowires are outer\nmembrane and periplasmic extensions of the extracellular electron\ntransport components. Proc Natl Acad Sci U S A. 2014 Sep 2;\n111(35):12883-8. http://www.ncbi.nlm.nih.gov/pubmed/25143589\n[18] Gorgel M, Ulstrup JJ, Bøggild A, Jones NC, Hoffmann SV, Nissen P,\nBoesen T. High-resolution structure of a type IV pilin from the metalreducing\nbacterium Shewanella oneidensis. BMC Struct Biol. 2015 Feb\n27; 15(1):4. http://www.ncbi.nlm.nih.gov/pubmed/25886849\n[19] Malvankar NS, Lovley DR. Microbial nanowires for bioenergy\napplications. Curr Opin Biotechnol. 2014 Jun; 27:88-95.\nhttp://www.ncbi.nlm.nih.gov/pubmed/24863901\n[20] Polizzi NF, Skourtis SS, Beratan DN. Physical constraints on charge\ntransport through bacterial nanowires. Faraday Discuss. 2012; 155:43-\n62; discussion 103-14. http://www.ncbi.nlm.nih.gov/pubmed/22470966"]}

The arsenic and iron environments in different growth stages have been studied with EXAFS and XANES using Brookhaven Synchrotron Light Source. Collard Greens plants were grown and tissue samples were harvested. The project studied the EXAFS and XANES of tissue samples using As and Fe K-edges. The Fe absorption and the Fourier transform bond length information were used as a control comparison. The Fourier transform of the XAFS data revealed the coexistence of As (III) and As (V) in the As bonding environment inside the studied plant tissue samples, although the soil only had As (III). The data suggests that Collard Greens has a novel pathway to handle arsenic absorption in soil., {"references":["P. L. Smedley and D. G. Kinniburgh, Appl. Geochem. 17, 517-568\n(2002).","World Health Organization, Arsenic in Drinking Water. Fact Sheet No.\n210, Revised May 2001. (http://www.who.int/inf-fs/en/fact210.html)","P. J. Potts, M. H. Ramsey, J. Carlisle, Portable X-ray fluorescence in the\ncharacterization of Arsenic contamination associated with industrial\nbuildings at a heritage Arsenic works near Redruth, Cornwall, UK. J.\nEnviron. Monit, 4, 1017-1024, 2002.","Canche-Tello J, Vargas MC, Hérnandez-Cobos J, Ortega-Blake I,\nLeclercq A, Solari PL, Den Auwer C, Mustre de Leon J. Interpretation\nof X-ray absorption spectra of As(III) in solution using Monte Carlo\nsimulations. J Phys Chem A. 2014 Nov 20; 118(46):10967-73.","Canche-Tello J, Vargas MC, Hérnandez-Cobos J, Ortega-Blake I,\nLeclercq A, Solari PL, Lezama-Pacheco J, Den Auwer C, Mustre de\nLeon X-ray Accelerated Photo-Oxidation of As(III) in Solution. J Phys\nChem A. 2015 Mar 17. (Epub ahead of print)\nhttp://www.ncbi.nlm.nih.gov/pubmed/ 25730736","Zhang G, Liu F, Liu H, Qu J, Liu R. Respective role of Fe and Mn oxide\ncontents for arsenic sorption in iron and manganese binary oxide: an Xray\nabsorption spectroscopy investigation Environ Sci Technol. 2014\nSep 2; 48(17):10316-22.","Zhao Z, Wang X, Zhang Z, Zhang H, Liu H, Zhu X, Li H, Chi X, Yin Z,\nGao J. Real-Time Monitoring of Arsenic Trioxide Release and Delivery\nby Activatable T1 Imaging. ACS Nano. 2015 Feb 18. (Epub ahead of\nprint) http://www.ncbi.nlm.nih.gov/pubmed/25688714","Kahlon TS, Chiu MC, Chapman MH. Steam cooking significantly\nimproves in vitro bile acid binding of collard greens, kale, mustard\ngreens, broccoli, green bell pepper, and cabbage. Nutr Res. 2008 Jun;\n28(6):351-7.","Lin LZ, Harnly JM. Identification of the phenolic components of collard\ngreens, kale, and Chinese broccoli. J Agric Food Chem. 2009 Aug\n26;57(16):7401-8\n[10] Santos J, Oliveira MB, Ibáñez E, Herrero M. Phenolic profile evolution\nof different ready-to-eat baby-leaf vegetables during storage. J\nChromatogr A. 2014 Jan 31;1327:118-31\n[11] M. Azizur Rahman, H. Hasegawa, K. Ueda, T. Maki, M. Mahfuzur\nRahman. Influence of phosphate and iron ions in selective uptake of\narsenic species by water fern (Salvinia natans L.). Chemical\nEngineering Journal Volume 145, Issue 2, 15 December 2008, Pages\n179–184\n[12] United States Department of Agriculture Agricultural Research Service\nNational Nutrient Database for Standard Reference Release 27\nhttp://ndb.nal.usda.gov/ndb/foods (Brassica oleracea)\n[13] Newcomb M, Halgrimson JA, Horner JH, Wasinger EC, Chen LX,\nSligar SG. (2008) X-ray absorption spectroscopic characterization of a\ncytochrome P450 compound II derivative. Proc Natl Acad Sci U S A.\nJun 17; 105(24):8179-84.\n[14] Schlebusch CM, Gattepaille LM, Engström K, Vahter M, Jakobsson M,\nBroberg K. Human Adaptation to Arsenic-Rich Environments.. Mol\nBiol Evol. 2015 Mar 3. pii: msv046.\nhttp://www.ncbi.nlm.nih.gov/pubmed/25739736\n[15] http://www.uniprot.org/uniprot/Q9HBK9\n[16] http://www.uniprot.org/uniprot/B0RA90\n[17] Kumar S, Dubey RS, Tripathi RD, Chakrabarty D, Trivedi PK. Omics\nand biotechnology of arsenic stress and detoxification in plants: current\nupdates and prospective. Environ Int. 2015 Jan; 74:221-30..\nhttp://www.ncbi.nlm.nih.gov/pubmed/25454239\n[18] Zhang J, Zhou W, Liu B, He J, Shen Q, Zhao FJ. Anaerobic arsenite\noxidation by an autotrophic arsenite-oxidizing bacterium from an\narsenic-contaminated paddy soil. Environ Sci Technol. 2015 Apr 2\nhttp://www.ncbi.nlm.nih.gov/pubmed/25905768\n[19] Tong D, Ortega J, Kim C, Huang J, Gu L, Li GM. Arsenic Inhibits DNA\nMismatch Repair by Promoting EGFR Expression and PCNA\nPhosphorylation. J Biol Chem. 2015 Apr 23.\nhttp://www.ncbi.nlm.nih.gov/pubmed/25907674\n[20] Li X & Sun WJ. The clinical activity of arsenic trioxide, ascorbic acid,\nifosfamide and prednisone combination therapy in patients with\nrelapsed and refractory multiple myeloma.. Onco Targets Ther. 2015\nApr 9; 8:775-81. http://www.ncbi.nlm.nih.gov/pubmed/25914547\n[21] Yunxian Liu, Leena Hilakivi-Clarke, Yukun Zhang, Xiao Wang, Yuan-\nXiang Pan, Jianhua Xuan, Stefanie C. Fleck, Daniel R. Doerge and\nWilliam G. Helferich. Isoflavones in soy flour diet have different effects\non whole-genome expression patterns than purified isoflavone mix in\nhuman MCF-7 breast tumors in ovariectomized athymic nude mice.\nMolecular Nutrition & Food Research, forth coming in press.\nhttp://onlinelibrary.wiley.com/doi/10.1002/mnfr.201500028/abstract.\n[22] Juan E. Andrade, Young H. Ju, Chandra Baker, Daniel R. Doerge and\nWilliam G. Helferich. Long-term exposure to dietary sources of\ngenistein induces estrogen-independence in the human breast cancer\n(MCF-7) xenograft model. Molecular Nutrition & Food Research\nVolume 59, Issue 3, pages 413–423, March 2015.\nhttp://onlinelibrary.wiley.com/doi/10.1002/mnfr.201300780/abstract\n[23] Salvo A, Cicero N, Vadalà R, Mottese AF, Bua D, Mallamace D,\nGiannetto C, Dugo G. Toxic and essential metals determination in\ncommercial seafood: Paracentrotus lividus by ICP-MS. Nat Prod Res.\n2015 Apr 28:1-8 http://www.ncbi.nlm.nih.gov/pubmed/25919907"]}

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.

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.

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.

The Kepler mission is designed to survey a fist-sized patch of the sky within the Milky Way galaxy for the discovery of exoplanets, with emphasis on near Earth-size exoplanets in or near the habitable zone. The Kepler space telescope would detect the brightness fluctuation of a host star and extract periodic dimming in the lightcurve caused by exoplanets that cross in front of their host star. The photometric data of a host star could be interpreted as an image where fractal imaging would be applicable. Fractal analysis could elucidate the incomplete data limitation posed by the data integration window. The fractal dimension difference between the lower and upper halves of the image could be used to identify anomalies associated with transits and stellar activity as the buried signals are expected to be in the lower half of such an image. Using an image fractal dimension resolution of 0.04 and defining the whole image fractal dimension as the Chi-square expected value of the fractal dimension, a p-value can be computed and used to establish a numerical threshold for decision making that may be useful in further studies of lightcurves of stars with candidate exoplanets. Similar fractal dimension difference approaches would be applicable to the study of photometric time series data via the Higuchi method. The correlated randomness of the brightness data series could be used to support inferences based on image fractal dimension differences. Fractal compression techniques could be used to transform a lightcurve image, resulting in a new image with a new fractal dimension value, but this method has been found to be ineffective for images with high information capacity. The three studied criteria could be used together to further constrain the Kepler list of candidate lightcurves of stars with possible exoplanets that may be planned for ground-based telescope confirmation.

Extremophilic cold-adapted sequences and their degradation codes have been studied using fractal dimension and Shannon entropy. The nucleotide fluctuation of a DNA and/or RNA sequence can be studied as a random series using the nucleotide atomic number differences between A, T, C, G, and U. Studies of degradation codes suggest a positive correlation of Shannon entropy with mRNA stability, and a negative correlation of fractal dimension with mRNA stability.

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.

The zinc and iron environments in different growth stages have been studied with EXAFS and XANES with Brookhaven Synchrotron Light Source. Tissue samples included meat, organ, vegetable, leaf, and yeast. The project studied the EXAFS and XANES of tissue samples using Zn and Fe K-edges. Duck embryo samples show that brain and intestine would contain shorter EXFAS determined Zn-N/O bond; as with the cases of fresh yeast versus reconstituted live yeast and green leaf versus yellow leaf. The XANES Fourier transform characteristic-length would be useful as a functionality index for selected types of tissue samples in various physical states. The extension to the development of functional synchrotron imaging for tissue engineering application based on spectroscopic technique is discussed., {"references":["Shi W, Chance MR. (2011) Metalloproteomics: forward and reverse\napproaches in metalloprotein structural and functional characterization\nCurr Opin Chem Biol. Feb;15(1):144-8.","Ascone I & Strange R. (2009) Biological X-ray absorption spectroscopy\nand metalloproteomics. J Synchrotron Radiat. 2009 May;16(Pt 3):413-\n21.","Newcomb M, Halgrimson JA, Horner JH, Wasinger EC, Chen LX,\nSligar SG. (2008) X-ray absorption spectroscopic characterization of a\ncytochrome P450 compound II derivative. Proc Natl Acad Sci U S A.\nJun 17;105(24):8179-84.","Liu C, Hong FS, Tao Y, Liu T, Xie YN, Xu JH, Li ZR (2011). The\nmechanism of the molecular interaction between cerium (III) and\nribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). Biol Trace\nElem Res. Nov;143(2):1110-20. Epub 2010 Oct 30.","Meharenna, Y.T.; Doukov, T.; Li, H.; Soltis, S.M.; Poulos, T.L.\n\"Crystallographic and single-crystal spectral analysis of the peroxidase\nferryl intermediate,\" (2010) Biochemistry 49, 2984-2986.","Corbett, M. C., Latimer, M. J., Poulos, T. L., Sevrioukova, I. F.,\nHodgson, K. O., and Hedman, B. (2007) Photoreduction of the active\nsite of the metalloprotein putidaredoxin by synchrotron radiation. Acta\nCrystallogr D Biol Crystallogr 63, 951-960.","Sarret G, Willems G, Isaure MP, Marcus MA, Fakra SC, Frérot H, Pairis\nS, Geoffroy N, Manceau A, Saumitou-Laprade P. (2009) Zinc\ndistribution and speciation in Arabidopsis halleri x Arabidopsis lyrata\nprogenies presenting various zinc accumulation capacities. New Phytol.\nNov;184(3):581-95.","Giachini L, Veronesi G, Francia F, Venturoli G, Boscherini F. (2010)\nSynergic approach to XAFS analysis for the identification of most\nprobable binding motifs for mononuclear zinc sites in metalloproteins. J\nSynchrotron Radiat. Jan;17(1):41-52.","Wang C, Vernon R, Lange O, Tyka M, Baker D. (2010) Prediction of\nstructures of zinc-binding proteins through explicit modeling of metal\ncoordination geometry. Protein Sci. Mar;19(3):494-506.\n[10] Chen J, Zhang H, Tomov IV, Ding X, Rentzepis PM. (2008)\nPhotochemistry and electron-transfer mechanism of transition metal\noxalato complexes excited in the charge transfer band. Proc Natl Acad\nSci U S A. Oct 7;105(40):15235-40.\n[11] Bugaev L, Farges F, Rusakova E, Sokolenko A, Latokha Y, Avakyan L.\n(2005) Fe coordination environment in Fe(II)- and Fe(III)-silicate glasses\nvia the Fourier-transform analysis of Fe K-XANES. Physica Scripta. Vol.\nT115, 215-217.\n[12] Colangelo CM, Lewis LM, Cosper NJ, Scott RA. (2000) Structural\nevidence for a common zinc binding domain in archaeal and eukaryal\ntranscription factor IIB proteins J Biol Inorg Chem. Apr; 5(2):276-83.\n[13] Wellenreuther G, Parthasarathy V, Meyer-Klaucke W.(2010) Towards a\nblack-box for biological EXAFS data analysis. II. Automatic BioXAS\nRefinement and Analysis (ABRA). J Synchrotron Radiat. Jan; 17(1):25-\n35.\n[14] Lancaster WA, Praissman JL, Poole FL 2nd, Cvetkovic A, Menon AL,\nScott JW, Jenney FE Jr, Thorgersen MP, Kalisiak E, Apon JV, Trauger\nSA, Siuzdak G, Tainer JA, Adams MW. (2011) A computational\nframework for proteome-wide pursuit and prediction of metalloproteins\nusing ICP-MS and MS/MS data. BMC Bioinformatics. Feb 28;12:64.\n[15] Shi W, Punta M, Bohon J, Sauder JM, D'Mello R, Sullivan M, Toomey J,\nAbel D, Lippi M, Passerini A, Frasconi P, Burley SK, Rost B, Chance\nMR. (2011) Characterization of metalloproteins by high-throughput Xray\nabsorption spectroscopy. Genome Res. Jun;21(6):898-907."]}

Pathogens could be inactivated via a light source coupled with a photosensitizing agent in photodynamic antimicrobial chemotherapy (PACT). This project studied the effect of non-homogenous substrate on cell colony. The non-homogeneity could be controlled by iron oxide nano-particles doping in porous glassy substrates such that each cell would experience tens of hot spots when illuminated with additional light source. The substrate non-homogeneity was characterized by Atomic Force Microscopy, Transmission Electron Microscopy and Extended X-Ray Absorption Fine Structure at Brookhaven Synchrotron Light Source. Microscopy images of cell motion were used to study the motility. Laboratory cell colonies on non-homogenous substrates exhibit reduced motility similar to those observed with sub-lethal PCAT treatment. Such motility reduction on non-homogenous substrate is interpreted as the presence of thermal stress. The studied pathogens included E. coli and Pseudomonas aeruginosa. Non-pathogenic microbes Bacillus subtilis was also studied for comparison. The results show that sub-lethal PACT could be effective with additional non-homogenous thermal stress. The use of non-uniform illumination on a homogeneous substrate to create thermal stress in sub-micron length scale is discussed via light correlation in propagation through random medium. Extension to sub-lethal PACT application complemented with thermal stress would be an appropriate application.

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.

Macro-bending fiber optic based heart-rate and pulse pressure shape monitors have been fabricated and tested for non-invasive measurement. Study of fiber bending loss and its stability and variations are very important especially for sensor designs based on optical fiber bending. Wavelengths from 1300 nm to 1550 nm have been used with fabrication based on multimode fiber, single mode fiber, and photonic crystal fiber. The smallest studied curvature would demand the use of single mode standard fibers. The collected data series show high quality suitable for random series analysis. Fractal property of optically measured pulse pressure data has been observed to correlate with physical activity. Correlation to EKG signal suggests that the fabricated monitors are capable of measuring the differential time delays at wrist and leg locations. The difference in time delay could be used to formulate a velocity parameter for diagnostics. The pulse shape information collected by the fiber sensor provides additional parameters for the analysis of the fractal nature of the heart. The application to real time measurement of blood vessel stiffness with this optical non-invasive fiber sensor is discussed.

The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.

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.

Archaea are important potential candidates in astrobiology as their metabolism includes solar, inorganic and organic energy sources. Archaeal viruses would also be expected to be present in a sustainable archaeal exobiological community. Genetic sequence Shannon entropy and fractal dimension can be used to establish a two-dimensional measure for classification and phylogenetic study of these organisms. A sequence fractal dimension can be calculated from a numerical series consisting of the atomic numbers of each nucleotide. Archaeal 16S and 23S ribosomal RNA sequences were studied. Outliers in the 16S rRNA fractal dimension and entropy plot were found to be halophilic archaea. Positive correlation (R-square ~ 0.75, N = 18) was observed between fractal dimension and entropy across the studied species. The 16S ribosomal RNA sequence entropy correlates with the 23S ribosomal RNA sequence entropy across species with R-square 0.93, N = 18. Entropy values correspond positively with branch lengths of a published phylogeny. The studied archaeal virus sequences have high fractal dimensions of 2.02 or more. A comparison of selected extremophile sequences with archaeal sequences from the Humboldt Marine Ecosystem database (Wood-Hull Oceanography Institute, MIT) suggests the presence of continuous sequence expression as inferred from distributions of entropy and fractal dimension, consistent with the diversity expected in an exobiological archaeal community.

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.

Nipah virus glycoprotein and nucleoprotein sequences were studied using fractal dimension and Shannon entropy. The nucleotide atomic number fluctuation forms the basis of the phylogeny study. The classification reproduces the main results of traditional phylogeny analysis, but with better ability to distinguish closely related strains. The fractal dimension correlation with the GC pair content in the glycoprotein sequence and di-nucleotide entropy in the nucleoprotein suggests different evolutionary mechanisms or strategies. Extension to other flu virus suggests that low fractal dimensionality in the nucleoprotein sequence could be a marker for the Nipah and Spanish-flu-like viruses.

The Single-Stranded DNA-Binding Protein (RPA) Genes in gamma ray radiation-resistant halophilic archaeon Halobacterium sp. NRC-1 were analyzed in terms of their nucleotide fluctuations. 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 in this study. Fractal analysis using the Higuchi method gave fractal dimensions of 2.04 and 2.06 for the gene sequences VNG2160 and VNG2162, respectively. The 16S rRNA sequence has a fractal dimension of 1.99. The di-nucleotide Shannon entropy values were found to be negatively correlated with the observed fractal dimensions (R 2 ~ 0.992, N=3). Inclusion of Deinococcus radiodurans Rad-A in the regression analysis decreases the R 2 slightly to 0.98 (N=4). A third VNG2163 RPA gene of unknown function but with upregulation activity under irradiation was found to have a fractal dimension of 2.05 and a Shannon entropy of 3.77 bits. The above results are similar to those found in bacterial Deinococcus radiodurans and suggest that their high radiation resistance property would have favored selection of CG di-nucleotide pairs. The two transcription factors TbpD (VNG7114) and TfbA (VNG 2184) were also studied. Using VNG7114, VNG2184, and VNG2163; the regression analysis of fractal dimension versus Shannon entropy shows that R 2 ~ 0.997 for N =3. The VNG2163 unknown function may be related to the pathways with transcriptions closely regulated to sequences VNG7114 and VNG2184.

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.

The Higuchi fractal method on a random series was applied to the study of the brightness fluctuation of Creutzfeld-Jakob disease (CJD) brain magnetic resonance (MR) frontal horn images. The brightness fluctuation along either a horizontal or vertical direction across an image formed a random series suitable for the Higuchi method. The average fractal dimension was found to decrease for the CJD frontal horn images (1.95) when compared to normal frontal horn images (1.97). The t-test gave a probability of about 7% that the CJD fractal dimension values would be a subset of a normal frontal horn dataset. Another MRI dataset taken later was also analyzed. The fractal dimension had increased to be about 1.99. Since the theoretical maximum fractal dimension for a line object is 2, a one-tailed t- test was used. The probability that the near expiration fractal dimension values coming from sampling from a normal dataset is about 15%. Extension to Parkinson MR images is discussed. The Higuchi fractal method could be used as a supplemental tool for extracting additional information and progress monitoring.

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.

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 gene's 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.

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.

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.

Migration in breast cancer cell wound healing assay had been studied using image fractal dimension analysis. The migration of MDA-MB-231 cells (highly motile) in a wound healing assay was captured using time-lapse phase contrast video microscopy and compared to MDA-MB-468 cell migration (moderately motile). The Higuchi fractal method was used to compute the fractal dimension of the image intensity fluctuation along a single pixel width region parallel to the wound. The near-wound region fractal dimension was found to decrease three times faster in the MDA-MB- 231 cells initially as compared to the less cancerous MDA-MB-468 cells. The inner region fractal dimension was found to be fairly constant for both cell types in time and suggests a wound influence range of about 15 cell layer. The box-counting fractal dimension method was also used to study region of interest (ROI). The MDAMB- 468 ROI area fractal dimension was found to decrease continuously up to 7 hours. The MDA-MB-231 ROI area fractal dimension was found to increase and is consistent with the behavior of a HGF-treated MDA-MB-231 wound healing assay posted in the public domain. A fractal dimension based capacity index has been formulated to quantify the invasiveness of the MDA-MB-231 cells in the perpendicular-to-wound direction. Our results suggest that image intensity fluctuation fractal dimension analysis can be used as a tool to quantify cell migration in terms of cancer severity and treatment responses., {"references":["Teri L Larkins, Marchele Nowell, Shailesh Singh and Gary L Sanford,\n\"Inhibition of cyclooxygenase-2 decreases breast cancer cell motility,\ninvasion and matrix metalloproteinase expression\" BMC Cancer, Vol 6,\np181-193, doi:10.1186/1471-2407-6-181, 2006.","Gargi D Basu, Latha B Pathangey, Teresa L Tinder, Sandra J Gendler\nand Pinku Mukherjee, \"Mechanisms underlying the growth inhibitory\neffects of the cyclo-oxygenase-2 inhibitor celecoxib in human breast\ncancer cells\" Breast Cancer Research, Vol. 7, R422-R435, 2005.","George Tzircotis, Rick F. Thorne and Clare M. Isacke, \"Chemotaxis\ntowards hyaluronan is dependent on CD44 expression and modulated by\ncell type variation in CD44 hyaluronan binding\" Journal of Cell Science\nVol. 118, p5119-5128, 2005.","Jin Pu, Colin D. McCaig, Lin Cao, Zhiqiang Zhao, Jeffrey E. Segall and\nMin Zhao, \"EGF receptor signalling is essential for electric-field\ndirected migration of breast cancer cells\" Journal of Cell Science Vol.\n120, p3395-3403, 2007","Zoe N. Demou, Michael Awad, Trevor McKee, Jean Yannis Perentes,\nXiaoye Wang, Lance L. Munn, Rakesh K. Jain, and Yves Boucher,\n\"Lack of Telopeptides in Fibrillar Collagen I Promotes the Invasion of a\nMetastatic Breast Tumor Cell Line\" Cancer Research Vol. 65: p5674-\n5682, 2005.","Masahiro Yanagisawa and Panos Z. Anastasiadis, \"p120 catenin is\nessential for mesenchymal cadherin-mediated regulation of cell motility\nand invasiveness\" The Journal of Cell Biology, Vol. 174, p1087-1096,\n2006.","A. Bru, S. Albertos, J. Subiza, J. Garcia-Asenjo, and I. Bru , \"The\nUniversal Dynamics of Tumor Growth\" Biophysical Journal, vol-85,\n2948-2961, 2003.","Allison Pledgie-Tracy, Michele D. Sobolewski, and Nancy E. Davidson,\n\"Sulforaphane induces cell type-specific apoptosis in human breast\ncancer cell lines\" Mol Cancer Ther Vol. 6, p1013-1021, 2007.","Liang C. et al., \"In vitro scratch assay: a convenient and inexpensive\nmethod for analysis of cell migration in vitro Nature protocols 2;\n(http://www.nature.com/nature protocol), 2007.\n[10] W. Klonowski \"From conformons to human brains: an informal\noverview of nonlinear dynamics and its applications in\nbiomedicine\".Nonlinear Biomed Phys. 2007 Jul 5; 1(1):5.\n[11] T. Higuchi, \"Approach to an irregular time series on the basis of fractal\ntheory\", Physica D, vol 31, 277-283, 1998.\n[12] Xinmin Yang, Haluk Beyenal, Gary Harkin, Zbigniew Lewandowski,\"\nQuantifying biofilm structure using image analysis\", Journal of\nMicrobiological Methods, Vol 39, Pages 109-119, 2000.\n[13] T. Sungkaworn, W. Triampo, P. Nalakarn, D. Triampo, I. M. Tang, Y.\nLenbury, and P. Picha,\" The Effects of TiO2 Nanoparticles on Tumor\nCell Colonies: Fractal Dimension and Morphological Properties\"\nInternational Journal of Biomedical Sciences Vol. 2, p67-74, 2007.\n[14] http://mayoresearch.mayo.edu/mayo/research/anastasiadis_lab/cellmigration.\ncfm (last assessed September 12 2008).\n[15] E.W. Weisstein, \"Capacity Dimension.\" From MathWorld--A Wolfram\nWeb Resource. http://mathworld.wolfram.com/"]}

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 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences., {"references":["Todd Holden, R. Subramaniam, R. Sullivan, E. Cheung, C. Schneider,\nG. Tremberger, Jr., A. Flamholz, D. H. Lieberman, and T. D. Cheung,\n\"ATCG nucleotide fluctuation of Deinococcus radiodurans radiation\ngenes\", Proc. SPIE 6694, 669417, 2007","N. N. Oiwa and J. A. Glazier, \"The fractal structure of the mitochondrial\ngenomes\", Physica A, vol 311, pp221 - 230, 2002.","Z.G. Yu, A. Vo, Z.M. Gong and S.C. Long, \"Fractals in DNA sequence\nanalysis\", Chinese Physics, vol 11, pp1313-1318, 2002.","H.D. Liu, Z.H. Liu, X. Sun, \"Studies of Hurst Index for Different\nRegions of Genes\", ICBBE 2007, pp238-240, 2007.","C.Y. Lee, \"Mass Fractal Dimension of the Ribosome and Implication of\nits Dynamic Characteristics\", Physical Review E, vol 73, 042901 (3\npages), 2006.","Pollard KS, Salama SR, Lambert N, Coppens S, Pedersen JS, et al., \"An\nRNA gene expressed during cortical development evolved rapidly in\nhumans\". Nature 443, 167-172 , 2006.","Pollard KS, Salama SR, King B, Kern AD, Dreszer T, et al.,\"Forces\nshaping the fastest evolving regions in the human genome\", PLoS Genet\n2(10): e168. DOI: 10. 1371/journal.pgen.0020168, 2006","E.W. Weisstein, \"Capacity Dimension.\" From MathWorld--A Wolfram\nWeb Resource. http://mathworld.wolfram.com/","Huai-chun Wang & Donal A. Hickey,\"Evidence for strong selective\nconstraint acting on the nucleotide composition of 16S ribosomal RNA\ngenes\", Nucleic Acid Research, vol 30, 2501-2507, 2002.\n[10] W. Klonowski \"From conformons to human brains: an informal\noverview of nonlinear dynamics and its applications in\nbiomedicine\".Nonlinear Biomed Phys. 2007 Jul 5; 1(1):5.\n[11] M.J. Berryman, A. Allison, and D. Abbott, \"Mutual Information for\nexamining correlations in DNA-, Fluctuation & Noise Letters, vol 4,\nppL237-L246, 2004.\n[12] T. Higuchi, \"Approach to an irregular time series on the basis of fractal\ntheory\", Physica D, vol 31, 277-283, 1998.\n[13] Xinmin Yang, Haluk Beyenal, Gary Harkin, Zbigniew Lewandowski,\"\nQuantifying biofilm structure using image analysis\", Journal of\nMicrobiological Methods, Vol 39, Pages 109-119, 2000\n[14] Todd Holden, G. Tremberger, Jr., P. Marchese, E. Cheung, R.\nSubramaniam, R. Sullivan, P. Schneider, A. Flamholz, D. Lieberman, &\nT. Cheung, \"DNA sequance based comparative studies of between nonextremophile\nand extremophile organisms with implications in\nexobiology\", SPIE Astrobiology Conference Proceedings, 7097-30,,\ninvited, in press, 2008.\n[15] Stoyan Milev, Alemayehu A. Gorfe, Andrey Karshikoff, Robert T.\nClubb, Hans Rudolf Bosshard, and Ilian Jelesarov, \"Energetics of\nSequence-Specific Protein-DNA Association: Binding of Integrase\nTn916 to Its Target DNA\" Biochemistry vol 42, 3481-3491, 2003.\n[16] Stoyan Milev, Alemayehu A. Gorfe, Andrey Karshikoff, Robert T.\nClubb, Hans Rudolf Bosshard, and Ilian Jelesarov, \"Energetics of\nSequence-Specific Protein-DNA Association: Conformational Stability\nof the DNA Binding Domain of Integrase Tn916 and Its Cognate DNA\nDuplex\" Biochemistry vol 42, 3492-3502 , 2003."]}

We have developed a simple algorithm of counting the probability of each possible type of di-nucleotide occurring in a DNA sequence to determining homologs and phylogeny between mammals. A 2-dimensional representation was developed for visualization. This method does not require any DNA alignment or for the DNA sequences to be of the same length. We applied our tools to determining homologs between related zinc finger structures, as well as determining mammalian phylogeny. We also demonstrate this method's ability to classifying dissimilar DNA sequences. Likely future work along these lines will be to increase our vector to include dimensions for other variables such as fractal dimension, large automated DNA searches, and segmenting the DNA sequence before calculating our vector in order to keep some position data.

A C2H2 zinc finger nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting zinc finger numerical sequence could be investigated for its fractal dimension in terms of evolution, multiple finger structure flexibility, and 3-finger structure specificity. The ZNF714 sequence was found to have a fractal dimension higher than its evolutionary ancestor ZNF431, consistent with the recently reported evolutionary direction using traditional analysis. The ZNF91 sequence has 36 zinc fingers and their fractal dimensions form a Gaussian-like histogram, suggesting a maximal flexibility for capacity dimension. The CpG di-nucleotide percentage in the three zinc fingers of EGR1 is found to correlate with the fractal dimension while the five zinc fingers in ZFP91 separated into human-chimp and mouse-rat-dog groups. Extension of the fractal investigation to short genetic sequences is discussed.

We have developed a fractal algorithm to supplement the current analysis in lung-CT scans on non-solid pulmonary nodule. The Cornell University Lung-CT Scans database and the US National Institute of Health ImageJ software were used. We found that the inner core average intensity could be a marker for the fractal dimension of a non-solid nodule. Z-scan image analysis of the adjacent boundaries showed that the fractal dimension has a range of about 0.1 in the studied cases. Extension of this proof-of-concept fractal analysis to growth rate estimation is also discussed.

The CpG di-nucleotide percentage and exon fractal dimension fluctuation were investigated with respect to the recently identified Marfan syndrome exons in the FBN1 gene. The CpG di-nucleotide percentage was found to rank high in exon 1 (9%), exon 44 (6.5%), exon 24 (5.3%) and exon 27 (4.8%). The most significant Marfan exon group was reported to be exon 24- 32. An exon nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. The resulting exon nucleotide numerical sequence could be investigated for its fractal dimension. The fractal dimension exhibited fluctuation across the 65 FBN1 exons and the values formed a Gaussian-like distribution (N = 65). The moving average fractal dimension was found to exhibit a broad peak around exons 24 to 32, consistent with the reported Marfan syndrome exon group.

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.

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.

The Pacific Ocean deep sea height data around latitude 20 N from Jason-1 satellite was analyzed in terms of standard deviation (std) and fractal dimension during a 90-day period that included the coronal mass ejection event of 2003 Oct 29 where a peak solar energetic particles of about 30,000 pfu was measured. The surface height standard deviation series was observed to have two peaks that corresponded to two typhoon events of Oct 25 and Nov 26, 2003. The cross correlation of the height-std series and average-height series showed a positive correlation with time delay. The fractal dimension of the height series peaked on Nov 1 (fractal dimension ~1.96 with a background 90-day average of ~ 1.81) and no corresponding peak was observed in the other time series data. Computer simulation of the fractal dimension of a finite random series suggested a standard deviation of about 0.071. Annual and long-term trends of the fractal dimensions were also found and investigated. The possible contribution of coronal mass ejection to the surface height series fractal dimension and the height correlation to chlorophyll were discussed.

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.

Cell scattering produces a speckle pattern, while imaging produces a contrast pattern. This family of fluctuation signals can be studied by analysis techniques such as correlation and fractal dimension. Human breast cell (normal and cancerous) samples were investigated using laser speckle and imaging microscopy. Image data from tetraploid human cell motion and quorum sensing biofilm growth were studied as well, and we found that the signal fluctuations could be interpreted as gene expression fluctuations occurring during inter-cell communication. We have mapped nucleotide sequences as images and studied the fluctuation. We showed that the fractal dimension and correlation can be used for the description of bio-information from the DNA (nanometer) scale to the tissue (millimeter) level. Fluctuations of the HAR1 nucleotide sequence and IRF-6 single-mutation cases in the van der Woude syndrome were discussed. Sub-cell structures such as the 40S ribosome, GroEL, and lysozyme, were shown to carry texture fractal dimension information in their images consistent with their biological states. Clinical applications to X-ray mammography and Parkinson disease MRI data were discussed.© (2007) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.

Images of packaged raw chicken purchased in neighborhood supermarkets were captured via a digital camera in laboratory and home settings. Each image contained the surface reflectivity information of the chicken tissue. The camera's red, green and blue light signals fluctuated and each spectral signal exhibited a random series across the surface. The Higuchi method, where the length of each increment in time (or spatial) lag is plotted against the lag, was used to explore the fractal property of the random series. (Higuchi, T., "Approach to an irregular time series on the basis of fractal theory", Physica D, vol 31, 277-283, 1988). The fractal calculation algorithm was calibrated with the Weierstrass function. The standard deviation and fractal dimension were shown to correlate with the time duration that a package was left at room temperature within a 24-hour period. Comparison to packaged beef results suggested that the time dependence could be due microbial spoilage. The fractal dimension results in this study were consistent with those obtained from yeast cell, mammalian cell and bacterial cell studies. This analysis method can be used to detect the re-refrigeration of a "left-out" package of chicken. The extension to public health issues such as consumer shopping is also discussed.

Breast cancer cells and normal cells were grown on glass substrates and investigated via laser generated speckles. The optical speckle pattern of a layer was investigated via angular correlation and fractal dimension analysis. A porous silicate slab with various water contents was used as calibration. The angular correlation and its associated Fourier transform results were consistent with the property of the cells. The speckle intensity data can be treated as a random series and the Higuchi method was used to explore the fractal property of the random series. The fractal dimension results differentiated the cancer cells (fractal dimension about 1.5) from the normal cells (fractal dimension about 1.8). The Fourier transformed series showed fractal dimension results consistent with cell functions. A composite of breast cancer/normal cell matrix was built with cancer cell layers embedded within normal cell layers. The optical speckle pattern of a composite was investigated and computer modeling was used to extract the embedded cancer cell fractal dimension information. The measurement of the efficacy of a drug was simulated with the monitoring of the effect of added chemicals in the growth media. Laboratory optical speckle pattern monitoring of the effect of added chemicals was discussed. The extension for early cancer detection in mammography was also discussed and an example of the application of the anisotropic spatial variation of the fractal dimension via the Higuchi fractal method was presented.

The behavior of the point spread function could be analyzed in images of stars with known exoplanets. A transform plot of the log intensity versus the Gaussian or sinc function value was used in the analysis. The intercept was extrapolated for brightness information and the slope or adjacent log intensity difference was also fitted. The robustness of the algorithm was evaluated using a bootstrap statistical method that does not require the error to follow a Gaussian distribution. The bootstrap confidence interval was used to assess the changes in the signal before and during transit with simulations that include Gaussian errors as well as non-Gaussian ones. Simulations using Gaussian noise suggested that transit signal changes at about 1-sigma noise level are detectable with a 90% confidence interval, while non-Gaussian noise simulations suggested a lower confidence level. This bootstrap method and the standard Chi-square method used in the analysis of the point spread function of data taken with space telescopes such as Spitzer was compared. The impact of using under-sampled CCD observations with super-sampled point spread functions on the bootstrap analysis is discussed. The analysis of images such as HD 209548 (captured by our 16-inch telescope) suggested that the point spread function approach is comparable to the photometric approach but requires fewer images. The application to other images from telescopes such as Hubble is also discussed.

Exoplanet transit time series photometric data usually contain noise levels that are comparable to the transit signal jumps. The analysis that assumes Gaussian noise and extensive data averaging calibrated to a reference star has been the traditionally used algorithm. This paper studied the fractal property of the time series and found that the fractal dimension changes for time series data that contain transits. The Higuchi fractal method, where the length of the increment in various time lags is plotted against the lags, was used in this study. (Higuchi, T., "Approach to an irregular time series on the basis of fractal theory", Physica D, vol 31, 277-283, 1988). The fractal algorithm was calibrated with the Weierstrass function. Simulations using Gaussian noise suggested that a transit jump signal at about 1-sigma noise level would produce changes in fractal dimension, while non-Gaussian noise simulations suggested a higher transit jump signal. The fractal algorithm was applied to data collected on HD 209458 as well as on published data. The transit caused a fractal dimension change of about 0.06. An over-exposed CCD dataset with much noise was also analyzed and a fractal dimension change of about 0.02 was obtained. The result suggests that fractal dimension analysis, without the assumption of error normality, is an alternative method for identifying transits in time series photometric data.