Spectrum software

In order to confirm the presence of particular chemical moieties in MRSA^MupS as well as MRSA^MupRL cells, FTIR and Raman spectroscopy analyses were carried out. After the cultivation of these strains for 18 h at 37 °C on Columbia agar with 5% sheep blood, the cells were washed three times by 5 mL of PBS, centrifuged at 5000 for 5 min, and dried for 24 h at 37 °C. The FTIR spectra of bacterial cells dry samples were obtained at room temperature by attenuated total reflection with a FTIR spectrometer (Perkin Elmer Spectrophotometer 100, Waltham, MA, USA). The samples (100 mg) were then scanned at a range between 650 cm⁻¹ and 4000 cm⁻¹ (64 scans and 1 cm⁻¹ resolution). The obtained spectra were normalized, baseline corrected, and analyzed using SPECTRUM software (v10, Perkin Elmer Spectrophotometer, Waltham, MA, USA).
To obtain Raman spectra, the samples were analyzed using a Raman spectrometer (RamanStation 400F, Perkin Elmer, USA) with point and shot capability using an excitation laser source at 785 nm (to avoid fluorescence excitation), 100 micron spot size, 4 shots, and 8 s exposition time. The obtained spectra were normalized, baseline corrected, and analyzed using SPECTRUM software (v10, Perkin Elmer, Waltham, MA, USA).

In order to confirm the presence of particular chemical moieties in K. pneumoniae^Col-S and K. pneumoniae^Col-R, as well as in their LPS, FTIR and Raman spectroscopic analyses, were performed [18 (link)]. After 18 h cultivation of each strain at 37 °C on Columbia agar with 5% sheep blood, bacterial colonies were harvested, transferred to an Eppendorf tube, and washed three times using saline. Then, the samples were centrifuged at 5000× g for 5 min and dried for 24 h at 37 °C. The FTIR spectra of dried bacterial cell samples and freeze-dried LPS were obtained at room temperature by an attenuated total reflection FTIR spectrometer (Perkin Elmer Spectrophotometer 100, Waltham, MA, USA). The samples (100 mg) were then scanned at a range between 650 cm⁻¹ and 4000 cm⁻¹ (64 scans and 1 cm⁻¹ resolution). The obtained spectra were normalised, baseline corrected, and analysed using SPECTRUM software (v10, Perkin Elmer Spectrophotometer, Waltham, MA, USA).
To obtain Raman spectra, the samples were analysed using the Raman spectrometer (RamanStation 400F, Perkin Elmer, Waltham, MA, USA) with point and shot capability and excitation laser source at 785 nm (to avoid fluorescence excitation), 100-micron spot size, and 4 scans (8 s exposition time). The obtained spectra were normalised, baseline corrected and analysed using SPECTRUM software (v10, Perkin Elmer, Waltham, MA, USA).

Chemical and secondary structural changes associated with collagen denaturation and biomodification were detected with FTIR. The crosslinker-treated and untreated dentin collagen films (n = 5 per treatment group) from the 3 main groups were spread on a cover slip and were allowed to dry in vacuum for 24 h. The FTIR spectra of the films were collected at a resolution of 4 cm⁻¹ with 64 scans using FTIR spectrometer in transmission mode on a barium fluoride disk using the Perkin Elmer FTIR Spectrum Spotlight system (Spectrum one, Spotlight 300, Perkin Elmer, Waltham, MA, USA). The attenuated total reflection (ATR) mode was used to get the spectra of the crosslinker powders used. The spectra were analyzed using Spectrum Software (version 5.3, Perkin Elmer). Two-point baseline correction and normalization to amide I band was undertaken, and band ratios were calculated. For DD CTs the band height ratios A1235/A1445 were measured, while the band ratios (A1400/A1450 and A1550/1450) of spectra of all specimens were calculated. The ratios of band area of the two crosslinkers (~1145 for TF, ~1120 for CR) and Amide I band height were also quantified to evaluate the extent of interactions with dentin collagen. Amide I band height was chosen as it was not affected by heat or acid denaturation.