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141 protocols using opus 7

1

FTIR Spectroscopy of Mycelial Powder

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The mycelial powder was suspended in 200 μl of sterile distilled water, mixed well, and applied drop-wise onto a 13 mm diameter, 2 mm thick Barium Fluoride (BaF2) window (Pike Technologies, U.S) for infrared spectroscopy. The drops were then dried overnight in a desiccator. Spectral data were collected from an infrared spectroscopy beamline (BL4.1 IR Spectroscopy and Imaging) at the Synchrotron Light Research Institute (SLRI; https://www.slri.or.th), Nakhon Ratchasima, Thailand. Spectra were acquired using a Vertex 70 FTIR spectrometer (Bruker Optics, Ettlingen, Germany) coupled with an IR microscope (Hyperion 2000, Bruker) over the measurement range 4000–400 cm−1 at 6 cm−1 spectral resolution with 64 scans per sample and an aperture set to 10 × 10 μm2. Spectral acquisition and instrument control operations were performed using OPUS 7.2 software (Bruker, Germany). The FTIR spectra were preprocessed (normalization and atmospheric compensation) using OPUS 7.5 software (Bruker, Germany). The cleaned FTIR data over the spectral range 3700–800 cm−1 were selected and saved in comma-separated value (CSV) file format.
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2

FT-IR Characterization of Oil Samples

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An Agilent 5500t FT-IR spectrometer (Agilent Technologies Inc., Santa Clara, USA) equipped with a detector of deuterated triglycine sulfate was used to obtain FT-IR spectra. An oil droplet was placed on a zinc selenide window, and absorbance spectra were recorded in transmittance mode over a path length of 100 μm. The samples were scanned at room temperature at a resolution of 4 cm−1 in the wavenumber range 4001–649 cm−1, whereby 898 data points were generated. The spectra were averaged over 32 scans and ratioed against an air background spectrum which was also averaged over 32 scans. A new background spectrum was obtained after each measurement. The zinc selenide window was cleaned with toluol before a new sample was applied. OPUS 7.2 (Bruker Optik GmbH, Ettlingen, Germany) was used to acquire data and to perform a rubberband baseline correction with 100 baseline points. Average spectra of duplicate measurements were used for statistical analysis.
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FTIR Spectroscopy of Protein Samples

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The measurements were performed using a Vertex 80v FTIR spectrometer (Bruker Corp., Ettlingen, Germany) equipped with a liquid nitrogen cooled MCT-detector (D* = 4 × 1010 cm Hz0.5 W−1 at 9.2 μm). The custom-made temperature-controlled cell was equipped with a 53 μm-thick PTFE spacer. The sample compartment of the spectrometer was continuously flushed with dry air during IR measurements. IR spectra were acquired with a spectral resolution of 2 cm−1 in double-sided acquisition mode using a Blackman-Harris 3-term apodization function and a zero filling factor of 2. For PLL measurements, a total of 450 scans were averaged per spectrum (total measurement time = 100 s), acquired in a temperature range of 20–50 °C (ΔT = 2 °C). After setting the temperature, the cell was allowed to equilibrate for 240 s prior to spectrum acquisition. Following this procedure, the heating rate was the same as for QCL-IR measurements. Protein measurements were carried out at 25.0 °C and a total of 64 scans were averaged per spectrum. Spectra analysis was performed by using the software package OPUS 7.2 (Bruker Corp., Ettlingen, Germany). If necessary, absorption bands of water vapour in the atmosphere were subtracted.
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4

Photochemical Experiments in Ultraviolet

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All photochemical experiments in UHV were performed with a home-built high-intensity UV source in the vicinity of the sample. In brief, we used a high-power LED (Seoul Viosys, CUN6AF4A, 2.35 W), which yields a photon flux density of 1.68 × 10−18 cm−2.s−1 at a wavelength of 365 nm, corresponding to a power density of 910 mW.cm−2. Further information can be found in the literature32 (link). During all photoconversion experiments, the sample was cooled to 110 K. The UV source was operated by an external power supply (TDK Lambda Z + 200) triggered by the IR spectrometer (Bruker OPUS 7.2) or manually. For each sample, nine illumination steps were applied, such that the total illumination time was increasing exponentially (0.01 s, 0.04 s, 0.16 s, 0.64 s, 2.56 s, 10.24 s, 40.96 s, 163.84 s, 655.36 s). After each illumination step, an IR spectrum was recorded with an acquisition time of 10 min.
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5

ATR-FTIR Spectroscopic Analysis of Mucosa Interactions

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ATR-FTIR spectra were recorded by an ATR-FTIR spectrometer (Agilent technologies 4500 series FTIR, Kuala Lumpur, Malaysia). The spectra were obtained in the range of 4000–650 cm−1 and at 4 cm−1 resolution with 256 co-added scans per spectrum. Each spectrum was normalized and integrated by OPUS 7.2 (Bruker, Hanau, Germany). The absorption intensities under the spectra were integrated at wavenumbers of 1695–1596, 1596–1493, and 1189–973 cm−1, which represent the regions of amide I, amide II, and carbohydrate, respectively.
Absorption unit ratios of the integrated results were evaluated for amide I/amide II and carbohydrate/amide II ratios from F1- or F2-treated mucosa with or without niosomes in comparison to the relevant blanks.
From interaction and non-interacted mucosa, samples were analyzed by principal component analysis (PCA). Spectral pre-processing was conducted by taking the second derivative, smoothing with a Savitzky–Golay function (3 polynomials and 15 smoothing points), and correcting the spectral scattering at fingerprint (1780–980 cm−1) by using Extended Multiplicative Scatter Correction of a computer software (Unscrambler X 10.5, (CAMO Software AS, Oslo, Norway).
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6

FTIR Spectroscopy of Material Samples

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The Fourier transform infrared spectra were recorded in ATR mode using a Brucker ALPHA (Platinum ATR) FTIR spectrometer (Bruker Optics GmbH, Ettlingen, Germany) equipped with a diamond crystal in the 3100–800 cm−1 region, with a resolution of 4 cm−1, using air as background, and with all spectra representing an average of 30 scans. Three recordings were performed for each sample, and an evaluation was made using the average spectrum obtained from these recordings. The processing of the spectra was carried out with the Bruker software OPUS 7.2 (Bruker Optics GmbH, Germany). Prior to each test, a background spectrum was obtained to compensate for the effect of humidity and the presence of carbon dioxide by spectra subtraction.
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7

Spectroscopic Data Analysis Protocol

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IR data was analyzed using OPUS 7.2 (Bruker Corporation) and Matlab R2017b (The MathWorks, Inc.) software. UV/VIS data were analyzed using Matlab R2017b.
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8

Fourier-Transform Infrared Spectroscopy

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A Bruker Vertex 80v FT-IR spectrometer
(Ettlingen, Germany) equipped with a Globar (power levels of <15
μW for 1 cm–1 spectral range25 (link)) and a liquid nitrogen cooled MCT detector (D* = 4 × 1010 cm Hz0.5 W–1 at 9.2 μm) was used to perform all FT-IR measurements. The
samples were manually injected into a flow cell, equipped with two
CaF2 windows and an 8 μm-thick spacer. During measurements,
the spectrometer was constantly flushed with dry air for at least
10 min prior to data acquisition until water vapor absorption was
sufficiently constant. Measurements were performed with a spectral
resolution of 2.6 cm–1 in double-sided acquisition
mode. A Blackman-Harris 3-term apodization function and a zero-filling
factor of 2 were used to calculate the final spectra. In total, 266
scans were averaged per spectrum, leading to an acquisition time of
45 s. All measurements were performed at 25 °C. The software
package OPUS 7.2 (Bruker, Ettlingen, Germany) was used for evaluation
of spectral data. Water vapor absorption bands were subtracted, if
required.
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9

ATR-FT-IR Spectroscopic Analysis of Milk Fat

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ATR–FT–IR measurements were performed using a Bruker Tensor 37 FT-IR spectrometer (Ettlingen, Germany) equipped with a mercury cadmium telluride (MCT) detector (D* = 4 × 1010 cm Hz0.5 W−1 at 9.2 μm). The spectrometer was constantly flushed with dry air in order to reduce the influence of water vapor from the atmosphere. One drop of pure milk fat extract was manually placed onto a Platinum ATR single-bounce element (Bruker, Ettlingen, Germany). Measurements were performed with a spectral resolution of 2 cm−1, between 600 and 4000 cm−1 in double-sided, forward–backward acquisition mode. A Blackman–Harris 3-term apodization function and a zero-filling factor of 2 were used to calculate the final spectra. One hundred and twenty-eight scans were averaged per spectrum, leading to an acquisition time of fifty-two seconds. After each spectral acquisition, the ATR surface was cleaned with isopropanol and dichloromethane consecutively until recovery of the baseline signal. Transmission measurements were performed using the same instrument parameters, by injecting homogenized whole milk into a flow cell equipped with two CaF2 windows and a 37 µm-thick spacer. The software package OPUS 7.2 (Bruker, Ettlingen, Germany) was used for evaluation of the spectral data.
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10

SR-FTIR Analysis of Meat Samples

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The biochemical composition of the samples was analyzed using SR-FTIR spectroscopy [38 (link)]. Spectral data were collected using the infrared microspectroscopy beamline BL4.1 IR Spectroscopy and Imaging at the Synchrotron Light Research Institute (SLRI, Nakhon Ratchasima, Thailand). Spectra were obtained using a Vertex 70 FTIR spectrometer (Bruker Optics, Ettlingen, Germany) coupled to an IR microscope (Hypersion 2000, Bruker), equipped with a liquid nitrogen cooled MCT detector. The data were collected over the 4000 to 800 cm−1 measurement range. The measurement was performed in mapping mode with an aperture size of 10 µm × 10 µm and acquisition of 64 scans with a spectral resolution of 4 cm−1. The software OPUS 7.2 (Bruker Optics Ltd, Ettilngen, Germany) was used for the derivation of the spectra and instrument control, and the results were analyzed with the CytoSpec software.
Samples from CO and OR (12 samples per group) were used to investigate the changes in the biochemical composition of meat. First, the original spectra were averaged to obtain a total of five spectra, followed by the second derivation at 13 smoothing points, and the vector was normalized using the Savitzky–Golay method in Unscrambler X software (version 10.1, Camo Analytics, Oslo, Norway) to account for the effects of varying sample thickness.
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