Aquaphotomics: Water Spectral Pattern Reveals UV Induced Changes of DNA and Identifies Bacteria Functionality
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1 Aquaphotomics: Water Spectral Pattern Reveals UV Induced Changes of DNA and Identifies Bacteria Functionality Roumiana Tsenkova Kobe University, Japan Water Conference
2 水 と 光 Water and Light Roumiana Tsenkova Kobe University, Japan Water Conference
3 Contents 1. Near Infrared Spectroscopy 2. Aquaphotomics: introduction 3. Water Spectral Pattern Reveals : - UV Induced Changes of DNA - Bacteria Functionality Water Conference
4 Contents 1. Near Infrared Spectroscopy 2. Aquaphotomics: introduction 3. Water Spectral Pattern Reveals : - UV Induced Changes of DNA - Bacteria Functionality Water Conference
5 Functional NIRS, fnirs: Probing Brain with Light Photon Migration in Tissue Source Detector Metabolic coupling during activation Neuronal-vascular coupling Hemodynamic response Pulse oximetry Water Conference
6 Near infrared light Water Conference
7 X-rays UV VIS 赤外光 NIR IR μwave wavelengths(μm) R Abs T Short NIR small small big big small small Abs R T NIR range Water Conference
8 Bio Fluid Analysis in Test Tubes Water Conference
9 PORTABLE INSTRUMENTS and FIBER PROBES FOR TISSUE MEASUREMENTS BIO MONITORING AND BIO DIAGNOSIS Water Conference
10 Water spectral patterns in bio monitoring and diagnosis Mastitis disease Altered milk components trace signals influence the bonding structure of water measured by NIRS all at once and provide rapid and accurate mastitis diagnosis Aquaphotomics: R. Tsenkova, S. Atanassova, S. Kawano, K. Toyoda, Somatic cell count determination in cow milk by near infrared spectroscopy: A new diagnostic tool, J. Animal Sci : Prion disease consecutive exposure of hydrogen bond network, in the body of mouse, to NIR light allowed successful diagnosis of fatal prion disease Aquaphotomics: Tsenkova, R., Iordanova, I., Toyoda, K and Brown, D., : Prion protein fate governed by metal binding: BBRC. pp , Soybean Mosaic disease Monitoring of Second Overtone of Water Absorbance Bands Reveals Hypersensitive Response from Virus Infected Plants Aquaphotomics: B.M Jinendraa, K. Tamakib R.Tsenkovaa * Use of Near Infrared Spectroscopy for Nondestructive and Rapid Detection of Soybean Plants Infected with Soybean Mosaic Virus. Abstract published at Japanese society of Near Infrared Spectroscopy, Tsukuba, Virus diagnosis - HIV Regression vector coefficients reveals variations in water structures related to functionality of HIV Aqua-Photomics: Sakudo A., Tsenkova R., Onozuka D., Morita K., Li S, Warachit J., Iwabu I., Li G., Onodera T., Ikuta K., A novel diagnostic method for human immunodeficiency virus type-1 in plasma by near-infrared Water Conference spectroscopy Microbiol Immunol, 49 (7), ,
11 Water spectral patterns in micro particle analysis Micro particles in water Better prediction of polystyrene mesoscopic particle concentration is obtained by multivariate analysis (a) based on water absorbance bands than univariate method based on polystyrene absorbance (b) band at 1680nm Aquaphotomics: A NIRS Investigation into the Perturbation of Water Spectrum in an Aqueous Suspension of Mesoscopic Scale Polystyrene Spheres. Asia Near Infrared conference, Tsukuba 2008 Particle size % R2(a) 0.69 R2(b) Heavy metal in water % % Mg/L concentration measurement of Cd, Mg, Mn, Zn in water solution possible because of the interaction with water seen by the NIR light at various water absorbance bands. Cd? Aquaphotomics: Sakudo, A., Tsenkova, R., Tei, K., Onozuka, T., Ikuta, K., Yoshimura, E., and Onodera, T.: Comparison of Vibration Mode of Metals in HNO3 by Partial Least Squares Regression, Wavelength Calibration Wavelength Validation Prediction Calibr Bioscience, Biotechnology and Biochemistry, Factor Factor range (nm) R² SEC range R² (nm) SEV R² SEP R² Inv of N det low aqu Microbial organism detection (bacteria) On going work Water Conference
12 A b s o r b a n c e Water Conference Wavelengths, nm
13 WATER DYNAMIC SPECTRA 2D and 3D Synchronous Correlation Maps represent negative correlation represent positive correlation Water Conference
14 WATER DYNAMIC SPECTRA Power Spectra at 1530nm Water Conference
15 Water Conference
16 WATER SPECTRUM IR range fundamental frequencies NIR range overtone region Water Conference
17 NIR and H 2 O Vibration frequency of hydrogen bonds in water are highly influenced by nearby molecules & environment Changes in these bonds may be used to gain information on the changing environments causing them (e.g. Presence of solutes, changing temperature) Water Conference
18 Contents 1. Near Infrared Spectroscopy 2. Aquaphotomics: introduction 3. Water Spectral Pattern Reveals : - UV Induced Changes of DNA - Bacteria Functionality Water Conference
19 Aquaphotomics concept Water as molecular mirror Water Conference
20 AQUAPHOTOMICS Aqua - : water Photo - : light Omics - : all about, complement of something Water Conference
21 Paracelsus in the 16th century said that water was the matrix of the world and of all its creatures. The properties of liquid water that govern processes such as aqueous solvation and the transport of protons arise from the motions of water molecules within a constantly changing network of hydrogen bonds. Water Conference
22 Albert Szent-Gyorgyi suggested that biology did not succeed in understanding basic living functions because it focused its attention to a substance in the form of particles dissecting them from two matrixes: water and electromagnetic field Szent-Gyorgyi, A. Bioenergetics. Academic Press, New York. Water Conference
23 AQUAPHOTOMICS: THE CONCEPT AQUAPHOTOMICS: WATER as a MOLECULAR MIRROR Perturbations water Spectral Data Base WAMACS Activated Water Absorbance Bands Bio Aqueous System NIR spectrum Water Absorbance Spectral Pattern, WASP WAMACS = Water Matrix Coordinates, i.e. water absorbance bands in VIS-NIR range Water Conference
24 AQUAPHOTOME is the entire complements of water matrix coodinates found under various perturbations Water Conference
25 WAMACS Water Matrix Coordinates: Water absorbance bands corresponding to pools of water molecules with the same vibration frequency Water Conference
26 Water Illumination Water Temperature Water Time (Vapor) HSA(Concentration High) HSA(Concentration Low) Globulin Prion protein PrP Prion protein PrP (Cu) Prion protein PrP (Mn) Prion protein Water (Mn) Milk Protein (Healthy) Milk Protein (Mastitis) Milk Cell count (Mastitis) Quarter milk(healthy) Quarter milk(mastitis) Milk Healthy Milk Mastitis Blood Healthy Blood Mastitis Urine Healthy Urine Mastitis Particle Polystyrene Wheat Protein Wheat PSI (Kernel texture) Wheat MTI (Kernel texture) Wheat Water (Kernel texture) C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C ~ ~ ~ ~1430 Water Conference 1448~ ~ ~ ~ ~ ~ ~ ~1495
27 Assignment C (1342)nm ν nm H2O - 2* ν 3 (Siesler, Ozaki, Kawata, & Heise, 2001) 1340nm liquid water/moisture (Williams, 2009) C (1364)nm OH-(H 2 O) 1, OH-(H 2 O) 2, OH-(H 2 O) nm 1st overtone free OH stretch (OH-(H2O)4) cm -1 (Robertson, Diken, Price, Shin, & Johnson, 2003) 1366nm 1st overtone OH- stretch (OH-(H2O)2) cm -1 (Robertson et al., 2003) C (1374)nm ν 1 + ν nm H2O - ν1 + ν3 7250cm -1 (Siesler et al., 2001) nm overtone of stretching vibration 7250cm -1 (Kuroda, Hamano, Mori, Yoshikawa, & Nagao, 2000) 1373 nm first overtone of 2ν OH (Lakshmi Reddy, Padma Suvarna, Udayabhaska Reddy, Endo, & Frost, 2014) C (1384)nm OH-(H 2 O) 1, OH-(H 2 O) 4, O 2 -(H 2 O) nm 1st overtone interwater / DD stretch (OH-(H2O)4) cm -1 (Robertson et al., 2003) 1381nm H2O-ν 1+ ν 3 (Cattaneo, Cabassi, Profaizer, & Giangiacomo, 2009) Water Conference
28 Water Absorbance Pattern, WAP AQUAGRAM Aquagram was devised to visualize the WASP. The aquagram displays normalized absorbance values at specific water bands on the axes originating from the center of the graph. Absorbance values at the WAMACs are placed on the respective radial axes. Water Conference
29 WATER and VAPOR SPECTRA and AQUGRAM Absorbance VAPOR WATER MPA 1474nm (S3) 1492nm (S4) 1518nm (V1, V2) 1344nm (V3) nm (water shell) 1372nm (V1+V3) 1382nm (water shell) 1464nm (S2) 1398nm (free OH) Wavelength (nm) 1444nm (S1) 1438nm (H5O2) 1410nm (S0, free water) moisture water A' A A : Absorbance after EMSC ( nm) μ:mean of Averaged spectra σ:sd of absorbance each wave length Water Conference
30 AQUAPHOTOMICS Perturbations Experiments Water Sun UV VIS IR NIRS Bio Aqueous System Medical Science, Pharmacy. Data Analysis Spectral Data Base Multivariate Analysis WAMACS: Activated Water Absorbance Bands Database AQUAPHOTOME: Database of water absorbance bands and patterns WAPS: Database of water absorbance patterns according to change perturbation GOAL Building bio-system HOLISTIC MODELS through analyzing spectral changes of WATER MOLECULAR SYSTEM Engineering Biotechnology Basic Science Analyzing of aqueous system Interaction of water with DNA Interaction of water with organic and non-organic molecules Aqueous systems in cells Aqueous systems in tissue Aqueous systems in organs Aqueous systems in whole body Applying in various fields Water Conference
31 WATER NANOSTRUCTURE Water Conference
32 WATER Change in temperature Absorbance MPA 1474nm (S3) 1492nm (S4) 1518nm (V1, V2) 1344nm (V3) nm (OH-H2O) 1372nm (V1+V3) 1382nm (O2-(H2O) nm (S2) 1398nm (free OH) Wavelength (nm) 1444nm (S1) 1410nm (S0, free water ) 1438nm (H5O2) Water Conference
33 nm Plants 2D spectra Nafion in water 1409nm nm 1386nm 1344nm DNA solutions 2D spectra 1414nm 1446nm 1462nm Water Conference
34 Contents 1. Near Infrared Spectroscopy 2. Aquaphotomics: introduction 3. Water Spectral Pattern Reveals : - UV Induced Changes of DNA - Bacteria Functionality Water Conference
35 Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics Noriko Goto, Gyorgy Bazar, Zoltan Kovacs, Makoto Kunisada, Hiroyuki Morita, Seiichiro Kizaki, Hiroshi Sugiyama, Roumiana Tsenkova*, Chikako Nishigori* 2015/7/2 Scientific reports Volume 5 Publisher Nature Publishing Group Water Conference
36 Differential Near Infrared Spectra DNA mq water puc18: Circular double stranded DNA and has 2686 base pairs. Lambda DNA : Lambda is a medium size E.coli bacteriophage. The DNA molecule of basepairs is linear and except for the extreme ends double-stranded. Water Conference
37 Arbitrary units Lambda DNA puc18 DNA phsg298 DNA phsg396 DNA Wavelength (nm) Water Matrics Coordinates, WAMACS C2: nm - aqueous proton [H+ (H2O)2] - H2O asymmetric stretch, 1st overt. C2: 1368nm - H15O7+, 1st overt. C6: 1420nm - aquesous proton, 3rd overt. C8: 1454nm - H2O - 2*n2+n3 C12: 1506nm - aqueous proton [H+ (H2O)6] - H2O in H5O2+ asymmetric stretch, 1st overt. 1532nm - 1st overtone IHB stretch (OH-(H2O)4) 1543nm - HOH intermolecular bend dangling, 3rd overt. Arbitrary units Deference between straight and circular structure of DNA 1368 D1. λdna: Straight chain of bp D2. puc18: Circular chain of 2686 bp D3. phsg298: Circular chain of 2675 bp D4. phsg398: Circular chain of 2238 bp Discriminating Power Plot Wavelength (nm)
38 DNA Dilutions The conventional ways of measuring DNA density Spectroscope using 260 nm & 280 nm Electrophoresis etc. However the accuracy is not enough, and the final determination of DNA density depends on professional experiences. Objective 1) Estimating DNA density using the NIR spectrophotometer 2) Comparing the results between the conventional way and NIR Materials DNA 1) puc18 Dilution Level: 10-1, 10-2, 10-3, 10-4, ) Lambda Dilution Level: 1/2, 1/5, 10-1, 1/50, 10-2, 10-3 mq water was used for dilution. Water Conference
39 The Conventional Instrument for measuring DNA Density Device: NanoDrop (ND-1000) Measurement range: ng/ μl Sample volume: 1 μl 260 nm and 280 nm wavelengths 260 nm: DNA 280 nm: Protein (contamination) puc18 D2 D3 D4 D5 Dilution Level Original Density (ng / μl) ND ND 1.4 ND Theoretical Value Lambda L5 L50 L100 L1000 Dilution Level Original 1/2 1/ / Density (ng / μl) Theoretical Value Water Conference
40 Measurement with NIR spectroscopy NIR instrument: NIRSystems 6500 Sample: puc18 D2, D3, D4, D5 Wavelength: nm Consecutive Time: 3 times Path length: 1 mm Condition: Room temperature Water Conference
41 Absorbance (-) Raw Spectra (NIRECO, puc-18) Water Conference 2015 Wavelength (nm) 41
42 Different Spectra (-) Different Spectra (-mqwater) ( nm, puc-18) D2 D3 D4 D Water Conference 2015 Wavelength (nm) 42
43 Different Spectra (-) Different Spectra (-D2) ( nm, puc-18) C3,1374 C9, 1462 C4, 1382 C12, 1500 C2,1362 C6, 1426 C10, 1472 D3 D4 D5 C5, 1416 Water Conference 2015 Wavelength (nm) 43
44 Different Spectra (-) Different Spectra (-Water) ( nm, MPA, Lambda) L5 L50 L100 L1000 Wavelength (nm) 44
45 Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics Noriko Goto, Gyorgy Bazar, Zoltan Kovacs, Makoto Kunisada, Hiroyuki Morita, Seiichiro Kizaki, Hiroshi Sugiyama, Roumiana Tsenkova*, Chikako Nishigori* 2015/7/2 Scientific reports Volume 5 Publisher Nature Publishing Group Water Conference
46 NIRS regression model according to DNA concentration. (A) Y-fit for DNA concentration of partial least squares regression (PLSR) with pretreatment by mean centering, smoothing (21 points), OSC (one component), and active class validation. N = 32, number of applied latent variables = 2, r Cal = , SEC = , r Val = , SECV = (B) Regression vector of the PLSR calibration model for DNA concentration showing characteristic water peaks at the nm spectral interval. Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics N Goto, G Bazar, Z Kovacs, M Kunisada, H Morita - Scientific reports, 2015 Water Conference
47 NIRS based discrimination of Milli-Q water and cis-syn T<>Ts solutions. SIMCA using nm interval of NIR spectra with mean-centering and smoothing (45 points). Factor # =2: samples of Milli-Q water and isolated cis-syn T<>Ts solutions form separate groups (ratio of correctly classified samples = 94.9 %). C) PLS-DA using nm interval of NIR spectra : 94.9 % of samples were classified correctly in cross-validation. Factor # =1. Detection of UV-induced cyclobutane pyrimidine dimers by Water near-infrared Conference spectroscopy 2015 and aquaphotomics N Goto, G Bazar, Z Kovacs, 47 M Kunisada, H Morita - Scientific reports, 2015
48 Results of NIRS regression models dependent on the irradiated UVC doses show close correlation between the actually irradiated doses of UVC and the levels determined by the NIRS calibration model when DNA samples irradiated with UVC at doses of 0, 5, 10, 15 and 20 kj/m 2 were measured in 20 μm aqueous solutions. Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics N Goto, G Bazar, Z Kovacs, M Kunisada, H Morita - Scientific reports, 2015 Water Conference
49 Quantitative analysis of isolated cis-syn T<>Ts using NIRS and HPLC data showing high correlation between cis-syn T<>Ts concentrations determined by the NIR calibration model and the laboratory reference values (0.77 μm -3.0 μm) determined by HPLC. A) Y-fit for cis-syn T<>Ts concentration of PLSR with pretreatment of mean centering, smoothing (21 points), OSC (one component) and leave-one-out cross validation: N = 24, number of applied latent variables = 2, r Cal = , SEC = , r Val = , SECV = B) Regression vector of PLSR calibration model on cis-syn T<>Ts concentration revealed characteristic water peaks in 1400 nm-1500 nm spectral interval. Detection of UV-induced cyclobutane pyrimidine dimers by near-infrared spectroscopy and aquaphotomics N Goto, G Bazar, Z Kovacs, M Kunisada, H Morita - Scientific Water Conference reports,
50 Contents 1. Near Infrared Spectroscopy 2. Aquaphotomics: introduction 3. Water Spectral Pattern Reveals : - UV Induced Changes of DNA - Bacteria Functionality Water Conference
51 a) PCA Bi-plot calculated on the reference data (strains growth rates, maximal optical densities, bile MIC and the yield of biomass after three hours stay at ph 1.80 in presence of pepsin (9000 U/ml), reference data in Table 1); b) MW-PCA analyses using the nm wavelength interval Score plot calculated on spectral data (n = 150) at the cultivation time of h. Slavchev A, Kovacs Z, Koshiba H, Nagai A, Bázár G, et al. (2015) Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection. PLoSONE 10(7): e doi: /journal.pone Water Conference
52 OPLS-DA model built on the spectral data of the 15 strains in the monitoring time between h (n = 150) using the nm wavelength interval to classify the probiotic, moderate and non-probiotic groups a) score plot and b) loadings plots. Slavchev A, Kovacs Z, Koshiba H, Nagai A, Bázár G, et al. (2015) Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection. PLoSONE 10(7): e doi: /journal.pone Water Conference
53 Aquagram on the spectra of culture media of groups of probiotic, moderate and non-probiotic strains Slavchev A, Kovacs Z, Koshiba H, Nagai A, Bázár G, et al. (2015) Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection. PLoS ONE 10(7): e doi: /journal.pone Water Conference
54 Measured wavelength and calculated wavenumbers of the bands found with PCA, SIMCA, OPLS-DA and PLSR methods and their assignment based on the corresponding references. Slavchev A, Kovacs Z, Koshiba H, Nagai A, Bázár G, et al. (2015) Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection. PLoS ONE 10(7): e doi: /journal.pone Water Conference
55 CELLS: Oxidative Stress NIRS Real Time Monitoring Oxidized cells: in blue 2016/1/3 55
56 Aquagram of DNA EMS Sample ES DNA-HIV-Patient 2 DNA-HIV-104bp 2 DNA-HIV-137bp (1st) 2 DNA-HIV-137bp (2nd) 2 DNA-HIV-194bp 2 DNA-HIV-300bp 1 DNA-E.Coli (1st) 2 DNA-E.Coli (2nd) 2 Sample ES Water-DW 1 Water-MilliQ 1 Water-Kobe 1 Wave-HIV-104bp 2 Wave-Borr 1 Wave-DW 1 DNA-Borr 2 Spectra data of each sample are divided into two groups depending on amplitudes of electromagnetic signal (EMS). 1) Higher ES higher or normal EMS, 2) Lower ES lower EMS In collaboration with the group of Luc Montagnier
57 Predicted EMS (db / Hz) Prediction of EMS by PLS (None) (All samples) Factor: 20 R: 0.77 SEV: 178 db / Hz Measured EMS (db / Hz) Higher ES Lower ES Mean-center Transform: None 1 st, 2 nd, and 3 rd Step 3 All Data-set Sample ES DNA-HIV-Patient 2 DNA-HIV-104bp 2 DNA-HIV-137bp (1st) 2 DNA-HIV-137bp (2nd) 2 DNA-HIV-194bp 2 DNA-HIV-300bp 1 DNA-E.Coli (1st) 2 DNA-E.Coli (2nd) 2 DNA-Borr 2 Water-DW 1 Water-MilliQ 1 Water-Kobe 1 Wave-HIV-104bp 2 Wave-Borr 1 Wave-DW 1 Cross Check 1 LB 1 57
58 Class distance from Lower ES (-) Discrimination between Higher and Lower ES by SIMCA (Smooth[13]) (DNA samples) Class distance from Higher ES (-) Interclass Distance: Higher ES Lower ES Mean-center Smooth[13] 1 st, 2 nd, and 3 rd Step 3 Sample ES DNA-HIV-Patient 2 DNA-HIV-104bp 2 DNA-HIV-137bp (1st) 2 DNA-HIV-137bp (2nd) 2 DNA-HIV-194bp 2 DNA-HIV-300bp 1 DNA-E.Coli (1st) 2 DNA-E.Coli (2nd) 2 DNA-Borr 2 Water-DW 1 Water-MilliQ 1 Water-Kobe 1 Wave-HIV-104bp 2 Wave-Borr 1 Wave-DW 1 Cross Check 1 LB 1 58
59 Discriminating Power (-) Discrimination between Higher and Lower ES by SIMCA (Smooth[13]) (DNA samples) Discriminating Power Wavelength (nm) Mean-center Smooth[13] 1 st, 2 nd, and 3 rd Step 3 Sample ES DNA-HIV-Patient 2 DNA-HIV-104bp 2 DNA-HIV-137bp (1st) 2 DNA-HIV-137bp (2nd) 2 DNA-HIV-194bp 2 DNA-HIV-300bp 1 DNA-E.Coli (1st) 2 DNA-E.Coli (2nd) 2 DNA-Borr 2 Water-DW 1 Water-MilliQ 1 Water-Kobe 1 Wave-HIV-104bp 2 Wave-Borr 1 Wave-DW 1 Cross Check 1 LB 1 59
60 Nafion consecutive spectra: first spectrum subtracted 1414nm nm Water Conference
61 Water Conference
62 Water Conference
63 生きている 光の遊び 水の音 Water Conference
64 Water Conference
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