Spectrasuite software

Light intensity at the canopy level was set at 100 μmol m⁻² s⁻¹ by adjusting the distance of the light source and a photoperiod of 16 h per day was given. Light treatment sections were separated with curtains, four treatments were applied using different light qualities equipped with LED lighting, which were B (100% blue, peak at 460 nm), R (100% red, 660 nm), and W [white, 7% blue (400–500 nm), 16% green (500–600 nm), 75% red (600–700 nm), and 2% far red (700–800 nm)] (Philips Inc., Eindhoven, The Netherlands) as well as RB (75% R and 25% B, peak at 460 and 660 nm) by a CID-800 programmable LED lighting system (CID Bio-Science, USA), respectively. Light distribution was recorded using JAZ-ULM-200 spectrometer (Ocean Optics, FL, USA) and converted with Spectrasuite software (Ocean Optics) to μmol m⁻² s⁻¹ (Figure 1) and uniformity was verified by measuring the light intensity at five points of each light treatment at the canopy level (Table 1).
The plants were grown for 8 weeks and then the second or third leaf counting from the apex (fully expanded leaves that developed entirely under the given light quality) were selected for the measurements. All measurements were performed in four replications per treatment and per plant species.

The instruments for LSPR namely, reflection probe (R400-7UV-VIS), halogen light source (LS-1-LL) and the spectroscope (USB4000-UV-VIS-ES) were purchased from Ocean Optics. Before taking any signal from the scope, the system was calibrated for dark and light spectrum modes. The LSPR signal was then recorded in absorption mode by observing the wavelength dependence of the light absorbed through by nanoparticles via the SpectraSuite software (cross-platform spectroscopy operating software from Ocean Optics). Transmission electron microscopy (TEM) was done at 200,000× with JEOL JEM1200EXII transmission electron microscope with high contrast pole pieces. For TEM, 300-mesh nickel grids, coated with a fine layer of carbon, were used as substrates for the protein fractions in the microscope. MBP was immobilized in the same way as described in the above sections. The Fourier Transform Infrared Spectroscopy (FTIR) was done directly over the surface of Si₃N₄ using a Perkin Elmer Frontier FTIR instrument in reflection mode and a high resolution Mercury Cadmium Telluride (MCT) detector.

For calibration purposes, unconjugated gold nanoparticles of 20, 40, 50, 60, 80, 100, and 200 nm (Ted Pella Inc., Redding, CA, USA) were diluted 1:10 in distilled deionized water and analyzed for light scattering and extinction using three separate detection methods. Each gold particle size sample contained the same overall molar concentration of gold. Light extinction spectra acquisition were taken with an Ocean Optics Fiber Optic Spectrometer (Ocean Optics, Dunedin, FL, USA, http://oceanoptics.com) specifically a USB4000 spectrometer and SpectraSuite software (Ocean Optics, Dunedin, FL, USA, http://oceanoptics.com) for control and data acquisition. A quartz cuvette of 1 cm path length was used to acquire samples. Spectra for ultraviolet-visible (UV-VIS) data was generally collected between 10 and 100 ms integration time and 20 and 100 spectra were averaged for each sample.

Spectrum of kernel specimens weighing almost 5 g was recorded using a NIR spectrometer (Ocean Optics NIR Quest 256, American) in the Laboratory of Optic Physics located in the Research Institute of Color Science and Technology. A rotating cup was used for all of samples, that is, rice grains and its flour. Spectrometer is equipped with the InGaA (Indium Gallium Arsenide) detector, and inflammatory lamps (incandescent lamps) were used as a light source. The samples were subjected to the spectrometer by contacting the inner part of a cylindrical probe with the lamps̓ radiation, so that the light was reflected through the probe by an optical fiber. Reflected light from the surface of the samples was displayed by the Ocean Optics Spectra Suite software in different measurement modes. Reflectance (R) readings at 6.5‐nm increments (Siriphollakul et al., 2017) were gathered over a NIR wavelength range of 870–2,450 nm and were recorded as log (1/R). For the chemometric analysis, three repeats for each specimen were accomplished and averaged, along with sample repacking.

Neat bacteriophage variants labelled with Cy3 and Cy5 in 50 mM potassium phosphate buffer, pH 8.0 were loaded into a DIOP-0002 Ultra Low Volume Flow Linear Dichroism Accessory (non-thermostatted) (Dioptica Scientific, Rugby, UK) in a 0.5 mm path length homemade quartz Couette cell either stationary or rotating at 3000 rpm. Samples were illuminated using a Jasco J-1500 Circular Dichroism Spectrometer set at 540 nm with a 9 nm bandwidth. Fluorescence in the range of 250–700 nm was collected using an Ocean Optics HR2000 + CCD detector with a 1000 μm fibre optic cable attachment. The fibre optic cable was positioned to collect light at 100° from the incident light at the front face of the Couette cell. Spectra were recorded using Ocean Optics SpectraSuite software with an integration time of 6 s and a total accumulation of 24 scans. Spinning and non-spinning samples were baseline subtracted and are presented with a 4 nm 0th order Savitzky–Golay smoothing window. Error bars correspond to the standard deviation of measurements made in triplicate.