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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.

Lateral and vertical ordered one-dimensional quantum structures, i.e. InGaAs/GaAs(001) quantum dot chains and quantum wires, have been obtained using molecular beam epitaxy. It was found that the InGaAs wires or dot chains sit on two-dimensional wetting layers and run along the [-110] direction, as the result of anisotropic strain and in-plane adatom diffusion. This anisotropic nature produces a model system for studying the electronic properties of one-, two-, and three-dimensional quantum confinements and related optical responses. The strain anisotropy is of importance in determining the electronic states of the quantum structures and the surrounding strained barrier. The strain-induced effects, such as change of band-gap and splitting of heavy–light hole states, were studied experimentally and theoretically. Optical anisotropy of these quantum structures is also discussed.

Contactless optical electroreflectance measurements at different temperatures are used to study exciton states in a structure involving a periodic system of 36 GaAs quantum wells separated by tunneling-nontransparent AlGaAs barriers with thickness 104 nm. In the structure, the width of 32 of the quantum wells is 15 nm, while the width of the remaining four quantum wells, numbered 5, 14, 23, and 32, is 20 nm. The periodicity of the structure corresponds to the Bragg interference condition at the excitonic frequency in quantum wells at the angle of incidence of light ∼43°. From the quantitative analysis of the shape of the contactless electroreflectance line, the parameters of the exciton ground states and excited states are determined for both types of quantum wells. It is established that, for the system of four 20-nm-wide quantum wells separated by a distance of 830 nm, the size-quantization energy in the ground state is 8.4 ± 0.1 meV, and the parameter of broadening of the excitonic peak is 1.8 ± 0.1 meV at 17 K and increases with temperature up to 2.0 ± 0.1 meV at 80 K. For the system of 32 wells with the width 15 nm, the quantum confinement energy in the ground state is 14.9 ± 0.1 meV, and the parameter of broadening of the excitonic peak is 2.2 ± 0.1 and 2.6 ± 0.1 meV at 17 and 80 K, respectively. The possible causes of radiative and nonradiative broadening of exciton states in the systems are discussed.

We studied optical reflection (OR) and contactless electroreflection (CER) from a periodic system of multiple GaAs/AlGaAs quantum wells (QWs). The QW width was 15 or 20 nm and the barriers were 104 nm thick. In this system the electromagnetic resonance of Bragg reflection occurs at the frequency that coincides or is close to the frequency of the exciton–polariton resonance in the wells. The optical measurements were made at various temperatures, angles of the light incidence and polarization. The optical reflection spectra have been found to be a result of the interplay of three different contributions, namely (i) the reflection from the air/semiconductor interface, (ii) the Bragg reflection due to periodic modulation of the background indices of refraction being different for the wells and barriers and (iii) the resonant reflection from the periodic system of exciton–polaritons in quantum wells. The latter contribution was separately studied by CER technique in the spectral range covering ground states of the heavy-hole and light-hole excitons. A quantitative analysis of the experimental CER line shape has been done along with quantum-mechanical calculations, which revealed the characteristic energies and broadening parameters for different exciton–polariton levels. In particular, the systems of four and 32 QWs exhibit spectral features with the characteristic broadening of 1.8 meV and 2.2 meV at 17 K, respectively. By comparison with theoretical calculations we discuss the radiative and non-radiative contributions to the total broadening.

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 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"]}

Optical reflection and electroreflection for the AlGaAs layers containing the periodically arranged GaAs quantum wells of different thickness are studied at photon energies ranging from 1 to 2 eV. It is established that the spectral dependence of the reflectance involves three different contributions made by (i) the reflection from the medium-air interface; (ii) the interference reflection due to the periodically modulated refractive index, since the materials of the wells and barriers have different refractive indices; and (iii) the reflection produced by the interaction of electromagnetic waves with the excition states in the quantum wells. Analysis of the reflection spectra shows that these contributions are characterized by different behavior with variations in temperature, angle of incidence of light, and polarization; however, quantitative separation of the spectra into individual contributions presents a rather difficult problem. To separate the contribution originating from the interaction of light with the exciton states from the optical spectra, a special approach based on contactless measurements of the optical electroreflectance over a certain spectral region is developed. It is shown that this method provides a means for determining the parameters of the exciton states in the quantum wells.

Detecting, characterizing, and interpreting gene-gene interactions or epistasis in studies of human disease susceptibility is both a mathematical and a computational challenge. To address this problem, we have previously developed a multifactor dimensionality reduction (MDR) method for collapsing high-dimensional genetic data into a single dimension (i.e. constructive induction) thus permitting interactions to be detected in relatively small sample sizes. In this paper, we describe a comprehensive and flexible framework for detecting and interpreting gene-gene interactions that utilizes advances in information theory for selecting interesting single-nucleotide polymorphisms (SNPs), MDR for constructive induction, machine learning methods for classification, and finally graphical models for interpretation. We illustrate the usefulness of this strategy using artificial datasets simulated from several different two-locus and three-locus epistasis models. We show that the accuracy, sensitivity, specificity, and precision of a naïve Bayes classifier are significantly improved when SNPs are selected based on their information gain (i.e. class entropy removed) and reduced to a single attribute using MDR. We then apply this strategy to detecting, characterizing, and interpreting epistatic models in a genetic study (n = 500) of atrial fibrillation and show that both classification and model interpretation are significantly improved.

The far-infrared c-axis conductivity of flux-grown Y$_{1-x}$Pr$_{x}$Ba$_{2}$Cu$_{3}$O$_{7}$ single crystals with 0.2$\leq $x$\leq $0.5 has been studied by sepectral ellipsometry. We find that the c-axis response exhibits spectral features similar to deoxygenated underdoped YBa$_{2}$Cu$_{3}$O$_{7-\delta}$, i.e., a pseudogap develops in the normal state, the phonon mode at 320 cm$^{-1}$ exhibits an anomalous T-dependence and an additional absorption peak forms at T. This suggests that the T$_{c}$ suppression in flux grown Pr-substituted crystals is caused by a decrease of the hole content and/or by carrier localization rather than by pair breaking.

Pump-probe experiments in GaAs/AlGaAs multiple quantum well samples are described using both picosecond and femtosecond laser pulses in different polarization configurations. The excitonic and free carrier components of exciton absorption saturation were analyzed as a function of well width. The relative importance of phase space filling, Coulomb screening and broadening contributions was determined from polarization and laser bandwidth dependencies via spin-dependent and spin-independent components. A five-level model was used to fit the data and nonlinear coefficients for the individual contributions were determined for each well width. The Coulomb contributions arising from screening and broadening of the excitons was found to dominate the absorption bleaching using picosecond pulses, whereas phase space filling was largest in the femtosecond regime. Exciton phase space filling was found to be four times larger than free carrier phase space filling at narrower well widths. A sublinear dependence of exciton broadening with carrier density was observed.

Degenerately doped (>1019 cm−3) n-type InxGa1−xAs (x∼0.67) and InPyAs1−y (y∼0.65) possess a number of intriguing electrical and optical properties relevant to electro-optic devices and thermophotovoltaic devices in particular. Due to the low electron effective mass of these materials (m*

The quaternary alloy In0.48(Ga1−xAlx)0.52P, lattice-matched to GaAs, has a direct band gap transition in the wavelength range of green-red light and is useful in optoelectronic applications such as visible light emitting diodes and laser diodes. We have investigated a set of six nominal In0.48(Ga1−xAlx)0.52P layers that were grown on GaAs (001) by low pressure metalorganic chemical vapor deposition (MOCVD) turbo disk technology. In order to control and optimize the growth conditions to produce high quality InGaAlP epilayers, a variety of nondestructive techniques, including photoluminescence (PL), Raman scattering, photoreflectance (PR), reflectance anisotropy (RA) spectroscopy, atomic force microscopy (AFM), and high resolution x-ray diffraction (HRXRD) have been applied to evaluate the epitaxial films and growth processes. HRXRD confirmed a good lattice match between the epilayers and the substrate material. The PL and PR spectra showed the variations of the InGaAlP PL peak and the energy band with grow...

We have evaluated the effective surface electric fields, effective depletion widths, and the sign (n-type/upward band bending) of the near-surface electric fields in undoped as well as $n\ensuremath{-}(5\ifmmode\times\else\texttimes\fi{}{10}^{18}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3})$ and $p\ensuremath{-}(5\ifmmode\times\else\texttimes\fi{}{10}^{18}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3}$ and $2\ifmmode\times\else\texttimes\fi{}{10}^{19}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3})$ doped low-temperature grown (LTG) GaAs (001) using the optical method of reflection-anisotropy (RA) spectroscopy in the vicinity of the spin-orbit split ${E}_{1},$ ${E}_{1}+{\ensuremath{\Delta}}_{1}$ optical features. Even for the highest p doping the surface band bending is still n type, indicating the strong influence of the large donor trap densities. Our results are in good agreement with a self-consistent Poisson's calculation of the near-surface electric fields assuming deep donor $(1\ifmmode\times\else\texttimes\fi{}{10}^{20}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3})$ and acceptor $(1\ifmmode\times\else\texttimes\fi{}{10}^{19}{\mathrm{cm}}^{\mathrm{\ensuremath{-}}3})$ trap densities and midgap surface Fermi-level pinning. This experiment provides valuable information about the defect density and position in LTG:GaAs. Our results will be compared to the recent RA spectroscopy experiment and interpretation of Chen et al. [Phys. Rev. B 55, R7379 (1997)].

Spectral ellipsometry at 300 K, in the range 0.8--5.5 eV, has been used to study the bulk and surface oxide properties of a molecular-beam-epitaxy grown ${\mathrm{Zn}}_{0.53}{\mathrm{Cd}}_{0.47}\mathrm{S}\mathrm{e}/\mathrm{I}\mathrm{n}\mathrm{P}$ film ($\ensuremath{\approx}1\ensuremath{\mu}\mathrm{m}$ thick). We have observed the direct gap ${E}_{0},$ which exhibits a well-defined excitonic structure, its spin-orbit split component ${E}_{0}+{\ensuremath{\Delta}}_{0},$ as well as the spin-orbit split ${E}_{1},$ ${E}_{1}+{\ensuremath{\Delta}}_{1}$ doublet. The experimental data over the entire measured spectral range (after oxide removal) have been fit using a model dielectric function based on the electronic energy-band structure near critical points plus excitonic and Coulomb enhancement effects. The influence of a native oxide on the optical properties also was investigated.

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.

Fractal dimension and Shannon entropy were used to analyze the nucleotide fluctuation of dim-light vision rhodopsin gene. The maximal absorption wavelengths of the studied gene sequences span a range of 480 nm to 526 nm. The di-nucleotide Shannon entropy correlates with (a) the mono-nucleotide Shannon entropy with R² of 0.99; (b) the CG+GC content with R² of 0.86 (N = 6). The absorption maximal wavelength correlation with the CG+GC content was found to have an R² of 0.82 for the gene sequence and 0.91 for the mRNA sequence. The fractal dimensions of the gene sequences and mRNA sequences were found to be correlated with R² of 0.78. Selection pressure on the CG+GC content at the gene and mRNA levels would be a consistent observation for phenotype dim-light functionality.

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.

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.