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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 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."]}

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."]}