Spectra manager 2

Manufactured by Jasco

Sourced in Japan, United States, Germany

Spectra Manager II is a software application that allows users to manage and analyze spectral data. It provides a user-friendly interface for visualization, processing, and data management of spectral information.

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Lab products found in correlation

26 protocols using spectra manager 2

Analyzing Protein Structure Changes after Defatting

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Changes in the G. bimaculatus protein secondary structure after defatting with the different solvents were analyzed using a circular dichroism (CD) spectropolarimeter (J-1500, JASCO, Dunmow, UK). Each sample was diluted to 1 mg/mL in 5 mM potassium phosphate buffer (pH 7.0). The mixtures were centrifuged at 10,000× g for 5 min after extraction with stirring for 1 h. The supernatants (200 μL) in a 0.1 cm path-length quartz cell were recorded by the CD spectropolarimeter with a scan rate of 100 nm/min from 190 nm to 260 nm. The scan results were used to estimate the secondary structure of the soluble proteins using the program Spectra Manager 2 (JASCO).

Jeong M.S., Lee S.D, & Cho S.J. (2021). Effect of Three Defatting Solvents on the Techno-Functional Properties of an Edible Insect (Gryllus bimaculatus) Protein Concentrate. Molecules, 26(17), 5307.

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Measuring α-Synuclein Conformation

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We measure the far-UV CD spectrum of 10 μM wild type α-syn in HEPES buffer (pH 7) at 25 °C in a CD spectrometer (J-1100ST, Jasco, Japan). We perform secondary structure estimation using Spectra Manager 2 (Jasco, Japan) in triplicate.

Chen J., Zaer S., Drori P., Zamel J., Joron K., Kalisman N., Lerner E, & Dokholyan N.V. (2021). The structural heterogeneity of α-synuclein is governed by several distinct subpopulations with interconversion times slower than milliseconds. Structure (London, England : 1993), 29(9), 1048-1064.e6.

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Thermal Unfolding Dynamics of Proteins

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Circular Dichroism experiments were performed in 10 mM Tris-SO₄ pH 7.0 with 2 mM CaSO₄ buffer. Samples were analyzed on a J-815 Circular Dichroism Spectrometer (Jasco) using a 1 mm path-length Spectrosil quartz cuvette (Starna Scientific). The temperature was controlled using a CDF-426S Peltier unit (Jasco). Far-UV CD spectra were obtained by incubating 0.15 mg/mL protein at 10 °C, before ramping at 12 °C/min to 55, 75 or 90 °C. Samples were held at that temperature for 3 minutes before starting a read (the “During heating” trace). The scanning speed of the instrument was set to 50 nm/min and scans were performed from 260 to 185 nm. After the read, samples were cooled to 10 °C. Samples were kept at 10 °C for 3 minutes before taking another read (the “After cooling” trace). Four scans were recorded from each independent sample, the recorded spectra were averaged, and then subtracted by the averaged baseline spectrum (buffer alone). Spectra were smoothened using the Savitzky-Golay method44 on the SpectraManager 2 software (Jasco). Ellipticity was converted to molar ellipticity using the SpectraManager 2 software.

Schoene C., Bennett S.P, & Howarth M. (2016). SpyRing interrogation: analyzing how enzyme resilience can be achieved with phytase and distinct cyclization chemistries. Scientific Reports, 6, 21151.

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ETF Reduction Assay Protocol

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The ETF reduction assay was performed using a Jasco FP-6300 spectrofluorometer (Easton, MD) with a cuvette holder heated with circulating water at 32°C. The assay was otherwise performed as described (68 (link)), at the indicated substrate concentrations. The enzyme was diluted 1200-fold into a buffer containing 50 mM Tris, pH 8.0, 5 mM EDTA and 50% glycerol, and 10 μL were used for each assay. The ETF concentration in the reaction mixture was 2 μM. Spectra Manager 2 software (Jasco, Inc.) was used to collect data and calculate reaction rate and Microsoft Excel was used to calculate the kinetic parameters.

Seminotti B., Leipnitz G., Karunanidhi A., Kochersperger C., Roginskaya V.Y., Basu S., Wang Y., Wipf P., Van Houten B., Mohsen A.W, & Vockley J. (2018). Mitochondrial energetics is impaired in very long-chain acyl-CoA dehydrogenase deficiency and can be rescued by treatment with mitochondria-targeted electron scavengers. Human Molecular Genetics, 28(6), 928-941.

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Electron Transfer Flavoprotein Fluorescence Assay

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The electron transfer flavoprotein (ETF) fluorescence reduction assay was performed using a Jasco FP-6300 spectrofluorometer (Jasco, Inc., Easton, MD) with cuvette holder heated with circulating water at 32 °C, as previously described [20 (link), 21 (link)]. ETF was diluted 1200-fold into a buffer containing 50 mM Tris, pH 8.0, 5 mM EDTA and 50% glycerol, and 10 μl were used for each assay. The ETF concentration in the reaction mixture was 2 μM. 30 μM of isovaleryl-CoA lithium salt hydrate (iC5-CoA; Sigma-Aldrich Co., St. Louis, MO) or octanoyl-CoA lithium salt hydrate (C8-CoA; Sigma Aldrich Co.) were used to measure IVDH and medium chain acyl-CoA dehydrogenase (MCAD) activity, respectively. Spectra Manager 2 software (Jasco, Inc.) was used to collect data and calculate reaction rate and Microsoft Excel was used to calculate kinetic parameters.

D’Annibale O.M., Koppes E.A., Alodaib A.N., Kochersperger C., Karunanidhi A., Mohsen A.W, & Vockley J. (2021). Characterization of variants of uncertain significance in isovaleryl-CoA dehydrogenase identified through newborn screening: An approach for faster analysis. Molecular genetics and metabolism, 134(1-2), 29-36.

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Spectrofluorometric Assay for ETF-Dependent Dehydrogenases

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The electron transfer flavoprotein (ETF) fluorescence reduction assay was performed using a Jasco FP-6300 spectrofluorometer (Easton, MD) with cuvette holder heated with circulating water at 32°C, as previously described [18 (link), 19 (link)]. ETF was diluted 1200-fold into a buffer containing 50 mM Tris, pH 8.0, 5 mM EDTA and 50% glycerol, and 10 μl were used for each assay. The ETF concentration in the reaction mixture was 2 μM. 30 μM of palmitoyl-CoA lithium salt hydrate (C16-CoA; Sigma-Aldrich Co., St. Louis, MO) or heneicosanoyl-CoA ammonium salt (C21-CoA; Avanti Polar Lipids, Alabaster, AL) were used to measure VLCAD activity. 30 μM of octanoyl-CoA lithium salt hydrate (C8-CoA; Sigma Aldrich Co.) was used to measure medium chain acyl-CoA dehydrogenase (MCAD) activity. Spectra Manager 2 software (Jasco, Inc.) was used to collect data and calculate reaction rate and Microsoft Excel was used to calculate kinetic parameters.

D’Annibale O.M., Koppes E.A., Sethuraman M., Bloom K., Mohsen A.W, & Vockley J. (2022). Characterization of exonic variants of uncertain significance in very long-chain acyl-CoA dehydrogenase identified through newborn screening. Journal of inherited metabolic disease, 45(3), 529-540.

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Physicochemical Characterization of Insulin Release

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Physicochemical characterization of samples containing insulin released in vitro from optimized formulation, CS (5 kDa)-zinc-insulin complexes incorporated in thermosensitive copolymeric depot, was performed at specific time points. All samples were centrifuged, filtered and degassed prior to analysis. Thermal transition of released insulin was recorded using nano DSC as specified earlier. Conformational stability analysis was performed using CD spectroscopy by scanning the samples in near-UV region (250-300 nm) and far-UV region (200-250 nm) to investigate the changes in tertiary and secondary structure, respectively. All spectra were recorded at a scan rate of 5 nm/min at 20 °C with a quartz cuvette (0.1 cm path length). Background interference was removed by subtracting scan of fresh PBS (10 mM, pH 7.4) in the same range. Freshly prepared insulin solution was used as standard. Spectra manager®2 software (Jasco, Tokyo, Japan) was used for spectrum analysis.

Sharma D., Arora S, & Singh J. (2019). Smart Thermosensitive Copolymer Incorporating Chitosan-Zinc-Insulin Electrostatic Complexes for Controlled Delivery of Insulin: Effect of Chitosan Chain Length. International journal of polymeric materials, 69(16), 1054-1068.

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Conformational Stability of sCT Analyzed

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Conformational stability of
sCT released in vitro from thermosensitive copolymer formulation mPEG–PL_3.5GA₁–mPEG (LA/GA, 3.5:1) 40% (w/v) at 37
°C was analyzed at specific time intervals using circular CD
spectroscopy. Samples were centrifuged, filtered, and degassed prior
to analysis. PBS (10 mM, pH 7.4) was used as reference buffer. CD
spectra were scanned in the far-UV region (190–230 nm) to investigate
the changes in the secondary structure of sCT. All spectra were recorded
at a scan rate of 50 nm/min at 20 °C using a quartz cuvette (0.1
cm path length). Freshly prepared sCT solution in PBS (10 mM, pH 7.4)
was used as the standard. Spectra Manager2 software (Jasco, Tokyo,
Japan) was used for spectrum analysis.

Lipp L., Sharma D., Banerjee A, & Singh J. (2019). Controlled Delivery of Salmon Calcitonin Using Thermosensitive Triblock Copolymer Depot for Treatment of Osteoporosis. ACS Omega, 4(1), 1157-1166.

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Circular Dichroism Spectroscopy of Proteins

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The CD spectra were recorded using a Jasco J-815 spectropolarimeter (Tokyo, Japan), with a cylindrical cuvette of a 0.1 cm thickness. The light source system was protected by nitrogen (flow rate: 5 L·min⁻¹). Proteins were obtained from cell lysate using a lysis kit (C2978, Sigma-Aldrich) following the manufacturer’s protocol. The protein contents in samples were quantified by absorption at 280 nm measured with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and diluted to 0.2 mg/ml before CD scan at 200 nm/min in the wavelength region of 200–260 nm. Three scans were averaged for each CD spectrum. Data were analyzed and processed using the Jasco Spectra Manager 2 software package. CD measurements of the amino acids are summarized in Fig. S5.

Bauer A., Elamurugan S., Selim S.T., F.a.t.i.m.a., Nega E., Lima IT J.r., Xia W, & Sun D. (2022). A Portable Elliptical Dichroism Spectrometer Targeting Secondary Structural Features of Tumorous Protein for Pancreatic Cancer Detection. Biosensors & bioelectronics, 222, 114934.

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Spectrofluorometric Assay for ETF Activity

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The ETF reduction assay was performed using a Jasco FP-6300 spectrofluorometer (Easton, Talbot County, MD, USA) with a cuvette holder heated with circulating water at 32 °C, as previously described [44 (link)]. Briefly, treated cell pellets were lysed using 50 mM Tris, pH 8.0 buffer, and 0.1 × protease inhibitor EDTA-free and sonicated twice in an ice-cold water bath sonicator at amplitude 45 for 1.5 min with 15 sec intervals. The assay was otherwise performed as described, at the indicated substrate concentrations [44 (link)]. The enzyme was diluted 1200-fold into buffer containing 50 mM Tris, pH 8.0, 5 mM EDTA, and 50% glycerol, and 10 μL was used for each assay. The ETF concentration was 2 µM. Spectra Manager 2 software (Jasco, Inc., Talbot County, MD, USA) was used to collect data and calculate reaction rates, and Microsoft Excel was used to calculate the kinetic parameters.

D’Annibale O.M., Phua Y.L., Van’t Land C., Karunanidhi A., Dorenbaum A., Mohsen A.W, & Vockley J. (2022). Treatment of VLCAD-Deficient Patient Fibroblasts with Peroxisome Proliferator-Activated Receptor δ Agonist Improves Cellular Bioenergetics. Cells, 11(17), 2635.

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