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  Data associated with "Understanding the antimicrobial activity of selected disinfectants against methicillin-resistant Staphylococcus aureus (MRSA)"

  Ebrahim Aboualizadeh, Violet V. Bumah, Daniela S. Masson-Meyers, Janis T. Eells, Carol J. Hirschmugl, and Chukuka S. Enwemeka

  This data folder is associated with the following publication in the Journal of Plos One:

  Understanding the antimicrobial activity of selected disinfectants against methicillin-resistant Staphylococcus aureus (MRSA)

  The paper has been published by E. Aboualizadeh, et al. in October 2017. You can access the paper via the following link:

  https://doi.org/10.1371/journal.pone.0186375

  When using the data, please cite the publication. Here is the abstract of the publication:

  “Disinfectants and biocidal products have been widely used to combat Methicillin-resistant Staphylococcus aureus (MRSA) infections in homes and healthcare environments. Although disruption of cytoplasmic membrane integrity has been documented as the main bactericidal effect of biocides, little is known about the biochemical alterations induced by these chemical agents. In this study, we used Fourier transform infrared (FT-IR) spectroscopy and chemometric tools as an alternative non-destructive technique to determine the bactericidal effects of commonly used disinfectants against MRSA USA-300. FTIR spectroscopy permits a detailed characterization of bacterial reactivity, allowing an understanding of the fundamental mechanism of action involved in the interaction between bacteria and disinfectants. The disinfectants studied were ethanol 70% (N = 5), isopropanol (N = 5), sodium hypochlorite (N = 5), triclosan (N = 5) and triclocarban (N = 5). Results showed less than 5% colony forming units growth of MRSA treated with triclocarban and no growth in the other groups. Nearly 70,000 mid-infrared spectra from the five treatments and the two control (untreated; N = 4) groups of MRSA (bacteria grown in TSB and incubated at 37°C (Control I) / at ambient temperature (Control II), for 24h) were pre-processed and analyzed using principal component analysis followed by linear discriminant analysis (PCA-LDA). Clustering of strains of MRSA belonging to five treatments and the discrimination between each treatment and two control groups in MRSA (untreated) were investigated. PCA-LDA discriminatory frequencies suggested that ethanol-treated spectra are the most similar to isopropanol-treated spectra biochemically. Also reported here are the biochemical alterations in the structure of proteins, lipid membranes, and phosphate groups of MRSA produced by sodium hypochlorite, triclosan, and triclocarban treatments. These findings provide mechanistic information involved in the interaction between MRSA strains and hygiene products; thereby demonstrating the potential of spectroscopic analysis as an objective, robust, and label-free tool for evaluating the macromolecular changes involved in disinfectant-treated MRSA."

  The data folder contains all the data that has been included in this publication. The data files are stored as .dpt files in the order of dates that we collected data. Dpt files contain FT-IR spectra from alive and five different disinfectant-treated MRSA as well as FT-IR spectra from pure disinfectants studied in this publication. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. All relevant data are within the paper.

  Please feel free to contact either Dr. Carol Hirschmugl (cjhirsch@uwm.edu) or Dr. Ebrahim Aboualizadeh (eabouali@ur.rochester.edu) for any question or concerns regarding this data.

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  Data associated with "Quantifying Biochemical Alterations in Brown and Subcutaneous White Adipose Tissues of Mice Using Fourier Transform Infrared Widefield Imaging"

  Ebrahim Aboualizadeh, Owen T. Carmichael, Diana C. Albarado, Christopher D. Morrison, Carol J. Hirschmugl, and Ping He

  This data folder is associated with the following publication in the Journal of Frontiers in Endocrinology, obesity section:

  Quantifying Biochemical Alterations in Brown and Subcutaneous White Adipose Tissues of Mice Using Fourier Transform Infrared Widefield Imaging

  The paper has been published by E. Aboualizadeh, et al. in May 2017. You can access the paper via the following link:

  https://doi.org/10.3389/fendo.2017.00121

  When using the data, please cite the publication. Here is the abstract of the publication:

  “Stimulating increased thermogenic activity in adipose tissue is an important biological target for obesity treatment, and label-free imaging techniques with the potential to quantify stimulation-associated biochemical changes to the adipose tissue are highly sought after. In this study, we used spatially resolved Fourier transform infrared (FTIR) imaging to quantify biochemical changes caused by cold exposure in the brown and subcutaneous white adipose tissues (BAT and s-WAT) of 6 week-old C57BL6 mice exposed to 30°C (N = 5), 24°C (N = 5), and 10°C (N = 5) conditions for 10 days. Fat exposed to colder temperatures demonstrated greater thermogenic activity as indicated by increased messenger RNA expression levels of a panel of thermogenic marker genes including uncoupling protein 1 (UCP-1) and Dio2. Protein to lipid ratio, calculated from the ratio of the integrated area from 1,600 to 1,700 cm⁻¹ (amide I) to the integrated area from 2,830 to 2,980 cm⁻¹ (saturated lipids), was elevated in 10°C BAT and s-WAT compared to 24°C (p = 0.004 and p < 0.0001) and 30°C (p = 0.0033 and p < 0.0001). Greater protein to lipid ratio was associated with greater UCP-1 expression level in the BAT (p = 0.021) and s-WAT (p = 0.032) and greater Dio2 expression in s-WAT (p = 0.033). The degree of unsaturation, calculated from the ratio of the integrated area from 2,992 to 3,020 cm⁻¹ (unsaturated lipids) to the integrated area from 2,830 to 2,980 cm−1 (saturated lipids), showed stepwise decreases going from colder-exposed to warmer-exposed BAT. Complementary ¹H NMR measurements confirmed the findings from this ratio in BAT. Principal component analysis applied to FTIR spectra revealed pronounced differences in overall spectral characteristics between 30, 24, and 10°C BAT and s-WAT. Spatially resolved FTIR imaging is a promising technique to quantify cold-induced biochemical changes in BAT and s-WAT in a label-free manner. “

  The data folder contains all the data that has been included in this publication. The data files are stored as OPUS files and DPT files in the order of dates that we collected data. The DPT data are FTIR spectra that were collected via MCT data and the opus data are the hyperspectral data that has been used for showing images in the paper. Files contain FT-IR spectra from 10C, 24C, and 30C brown, subcutaneous, and visceral mouse adipose tissues as well as some ratiometric studies to calculate the protein:lipid ratios in FT-IR spectra in each tissue.

  Please feel free to contact either Dr. Carol Hirschmugl (cjhirsch@uwm.edu) or Dr. Ebrahim Aboualizadeh (eabouali@ur.rochester.edu) for any questions or concerns regarding this data.

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  Data associated with "Spectrally resolved infrared microscopy and chemometric tools to reveal the interaction between blue light (470 nm) and methicillin-resistant Staphylococcus aureus"

  Violet V. Bumah, Ebrahim Aboualizadeh, Daniela S. Masson-Meyers, Janis T. Eells, Chukuka S. Enwemeka, and Carol J. Hirschmugl

  This data folder is associated with the following publication in the Journal of Photochemistry and Photobbiology: Biology B:

  Spectrally resolved infrared microscopy and chemometric tools to reveal the interaction between blue light (470 nm) and methicillin-resistant Staphylococcus aureus

  The paper has been published by E. Aboualizadeh, et al. in February 2017. You can acess the paper via the following link:

  https://doi.org/10.1016/j.jphotobiol.2016.12.030

  When using the data, please cite the publication. Here is the abstract of the publication:

  “Blue light inactivates methicillin-resistant Staphylococcus aureus (MRSA), a Gram-positive antibiotic resistant bacterium that leads to fatal infections; however, the mechanism of bacterial death remains unclear. In this paper, to uncover the mechanism underlying the bactericidal effect of blue light, a combination of Fourier transform infrared (FTIR) spectroscopy and chemometric tools is employed to detect the photoreactivity of MRSA and its distinctive pathway toward apoptosis after treatment. The mechanism of action of UV light and vancomycin against MRSA is also investigated to support the findings. Principal component analysis followed by linear discriminant analysis (PCA- LDA) is employed to reveal clustering of five groups of MRSA samples, namely untreated (control I), untreated and incubated at ambient air (control II), irradiated with 470 nm blue light, irradiated with 253.5 UV light, and vancomycin-treated MRSA. Loadings plot from PCA-LDA analysis reveals important functional groups in proteins (1683, 1656, 1596, 1542 cm⁻¹), lipids (1743, 1409 cm⁻¹), and nucleic acids region of the spectrum (1060, 1087 cm⁻¹) that are responsible for the classification of blue light irradiated spectra and control spectra. Cluster vector plots and scores plot reveals that UV light-irradiated spectra are the most biochemically similar to blue light- irradiated spectra; however, some wavenumbers experience a shift. The shifts between blue light and UV light irradiated loadings plot at ν_asym PO²⁻ band (from 1228 to 1238 cm⁻¹), DNA backbone (from 970 to 966 cm⁻¹) and base pairing vibration of DNA (from 1717 to 1712 cm⁻¹) suggest distinctive changes in DNA conformation in response to irradiation. Our findings indicate that irradiation of MRSA with 470 nm light induces A-DNA cleavage and that B-DNA is more resistant to damage by blue light. Blue light and UV light treatment of MRSA are complementary and distinct from the known antimicrobial effect of vancomycin. Moreover, it is known that UV-induced cleavage of DNA predominantly targets B-DNA, which is in agreement with the FTIR findings. Overall the results suggest that the combination of light and vancomycin could be a more robust approach in treating MRSA infections. “

  The data folder contains all the data that has been included in this publication. The data files are stored as .dpt files, which contain FT-IR spectra from alive, blue-light irradiated, UV-irradiated, and vancomycin-treated MRSA.

  Please feel free to contact either Dr. Carol Hirschmugl (cjhirsch@uwm.edu) or Dr. Ebrahim Aboualizadeh (eabouali@ur.rochester.edu) for any question or concerns regarding this data.

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  Data associated with "Retinal oxidative stress at the onset of diabetes determined by synchrotron FTIR widefield imaging: towards diabetes pathogenesis" and "Temporal diabetes-induced biochemical changes in distinctive layers of mouse retina"

  Masha Ranji, Ebrahim Aboualizadeh, Christine M. Sorenson, Reyhaneh Sepehr, Nader Sheibani, Carol J. Hirschmugl, Alex J. Schofield, and Miriam Unger

  This data folder is associated with the following publications in the Analyst journal and the Scientific Reports:

  1. Retinal oxidative stress at the onset of diabetes determined by synchrotron FTIR widefield imaging: towards diabetes pathogenesis. (E. Aboualizadeh, et al. February 2017)

  DOI: 10.1039/C6AN02603F

  Citation: Aboualizadeh, E., Ranji, M., Sorenson, C. M., Sepehr, R., Sheibani, N., & Hirschmugl, C. J. (2017). Retinal oxidative stress at the onset of diabetes determined by synchrotron FTIR widefield imaging: towards diabetes pathogenesis. Analyst, 142(7), 1061-1072.

  AND

  2. Temporal diabetes-induced biochemical changes in distinctive layers of mouse retina. (E. Aboualizadeh, et al. January 2018)

  DOI: 10.1038/s41598-018-19425-8

  Citation: Aboualizadeh, E., Sorenson, C. M., Schofield, A. J., Unger, M., Sheibani, N., & Hirschmugl, C. J. (2018). Temporal diabetes-induced biochemical changes in distinctive layers of mouse retina. Scientific reports, 8(1), 1096.

  Abstract of paper 1:

  Diabetic retinopathy is a microvascular complication of diabetes that can lead to blindness. In the present study, we aimed to determine the nature of diabetes-induced, highly localized biochemical changes in the neuroretina at the onset of diabetes. High-resolution synchrotron Fourier transform infrared (s-FTIR) wide field microscopy coupled with multivariate analysis (PCA–LDA) was employed to identify biomarkers of diabetic retinopathy with spatial resolution at the cellular level. We compared the retinal tissue prepared from 6-week-old Ins2^Akita/+ heterozygous (Akita/+, N = 6; a model of diabetes) male mice with the wild-type (control, N = 6) mice. Male Akita/+ mice become diabetic at 4-weeks of age. Significant differences (P < 0.001) in the presence of biomarkers associated with diabetes and segregation of spectra were achieved. Differentiating IR bands attributed to nucleic acids (964, 1051, 1087, 1226 and 1710 cm⁻¹), proteins (1662 and 1608 cm⁻¹) and fatty acids (2854, 2923, 2956 and 3012 cm⁻¹) were observed between the Akita/+ and the WT samples. A comparison between distinctive layers of the retina, namely the photoreceptor retinal layer (PRL), outer plexiform layer (OPL), inner nucleus layer (INL) and inner plexiform layer (IPL) suggested that the photoreceptor layer is the most susceptible layer to oxidative stress in short-term diabetes. Spatially-resolved chemical images indicated heterogeneities and oxidative-stress induced alterations in the diabetic retina tissue morphology compared with the WT retina. In this study, the spectral biomarkers and the spatial biochemical alterations in the diabetic retina and in specific layers were identified for the first time. We believe that the conclusions drawn from these studies will help to bridge the gap in our understanding of the molecular and cellular mechanisms that contribute to the pathobiology of diabetic retinopathy.

  Abstract of paper 2:

  "To discover the mechanisms underlying the progression of diabetic retinopathy (DR), a more comprehensive understanding of the biomolecular processes in individual retinal cells subjected to hyperglycemia is required. Despite extensive studies, the changes in the biochemistry of retinal layers during the development of DR are not well known. In this study, we aimed to determine a more detailed understanding of the natural history of DR in Akita/+ (type 1 diabetes model) male mice with different duration of diabetes. Employing label-free spatially resolved Fourier transform infrared (FT-IR) chemical imaging engaged with multivariate analysis enabled us to identify temporal-dependent reproducible biomarkers of the individual retinal layers from mice with 6 weeks,12 weeks, 6 months, and 10 months of age. We report, for the first time, the nature of the biochemical alterations over time in the biochemistry of distinctive retinal layers namely photoreceptor retinal layer (PRL), inner nuclear layer (INL), and plexiform layers (OPL, IPL). Moreover, we present the molecular factors associated with the changes in the protein structure and cellular lipids of retinal layers induced by different duration of diabetes. Our paradigm provides a new conceptual framework for a better understanding of the temporal cellular changes underlying the progression of DR."

  The data folder contains all the data that has been included in this publication. The data files are stored as OPUS files and DPT files. There are files based on the age of mice ranging from 6-weeks to 10 months old diabetic and wild-type mice. The bright field images are also stored in the data folder. The tables contain FT-IR spectra from diabetic and control retina at different duration of diabetes, where each column is one spectrum and the first column in each table shows the wavenumber range. The processed data in this folder are the processed OPUS data in Irydis software and they are saved as PXP file. We included all these data in these 2 mentioned publications. Please feel free to contact either Dr. Carol Hirschmugl (cjhirsch@uwm.edu) or Dr. Ebrahim Aboualizadeh (eabouali@ur.rochester.edu) for any questions or concerns regarding this data. This second article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder.