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Odyssey application software version 3

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Odyssey Application Software Version 3.0 is a software package designed for the analysis and management of data acquired from LI-COR Odyssey imaging systems. The software provides tools for image capture, processing, and quantification of fluorescent signals.

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Lab products found in correlation

Odyssey infrared imaging system, by LI COR (3 mentions) Cyclin d1, by Cell Signaling Technology (3 mentions) Odyssey infrared imager, by LI COR (2 mentions) Nitrocellulose membrane, by Bio-Rad (2 mentions) Irdye 800cw goat anti rabbit igg, by LI COR (2 mentions) Odyssey image station, by LI COR (2 mentions) Aprotinin protease inhibitor cocktail, by Roche (2 mentions) Odyssey infrared imaging detection system, by LI COR (2 mentions) Ser1177, by Cell Signaling Technology (1 mentions) Novex tis glycine gel, by Thermo Fisher Scientific (1 mentions) Irdye680 800 conjugated anti mouse rabbit secondary antibody, by LI COR (1 mentions) Anti β actin, by Abcam (1 mentions) Rabbit anti phospho akt ser473, by Cell Signaling Technology (1 mentions) Mouse anti α tubulin, by Merck Group (1 mentions) Prps6 ser235 236, by Cell Signaling Technology (1 mentions) Donkey anti mouse irdye 680lt, by LI COR (1 mentions) Hpv16 e7, by Santa Cruz Biotechnology (1 mentions) β tubulin, by Merck Group (1 mentions) Irdye 800cw goat anti mouse igg, by LI COR (1 mentions) Flag tag (flag), by Merck Group (1 mentions)

Close spelling variants of this product

Odyssey software (152 citations) Odyssey 3.0 software (37 citations) Odyssey software version 3.0 (25 citations) Odyssey application software (23 citations) Odyssey version 3.0 software (6 citations) Odyssey Infrared Imaging System Application Software Version 3.0 (6 citations) Odyssey Application Software 3.1 (2 citations)

13 protocols using odyssey application software version 3

1

Quantifying Myocardial NOS Phosphorylation

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The phosphorylation of myocardial eNOS and nNOS was quantified by western blot (Ibrahim et al., 2014 (link); Yao and Abdel-Rahman, 2016 (link), 2017b (link)). Briefly, 80 μg of protein was separated in a 4–12% gel electrophoresis (Novex Tis-Glycine gel, Life Technologies, CA), and transferred to nitrocellulose membrane (Bio-Rad Laboratories, Hercules, CA). The membranes were incubated with mouse/rabbit anti phosphor-eNOS (Ser1177, Cell Signaling, #9571,1:200) and eNOS (M221, Abcam, #ab76198, 1:500), and phosphor-nNOS (Ser1417, Thermo Fisher Scientific, Waltham, MA, #PA1–032,1:200,) and nNOS (BD Biosciences, San Jose, CA, #6100308, 1:200), the Recombinant Anti-SOD 1 (Abcam, Ann Arbor, MI, ab51254, 1:1000) and Anti- β-actin (Abcam, Ann Arbor, MI, ab8226, 1:2000) primary antibody, overnight at 4°C, and then incubated with IRDye680/800-conjugated anti-mouse/rabbit secondary antibody (LI-COR Biosciences, Lincoln,NE). To determine the monomer/dimer eNOS ratio (indicative of NOS uncoupling), the protein was separated under undenatured condition (no heating, without reducing in the sample and no antioxidant in the running buffer, running the gel under cold temperature). Odyssey Infrared Imager and Odyssey application software version 3 (LI-COR Biosciences, Lincoln, NE) were used to detect and quantify the protein bands.
Yao F, & Abdel-Rahman A.A. (2021). Tetrahydrobiopterin paradoxically mediates cardiac oxidative stress and mitigates ethanol-evoked cardiac dysfunction in conscious female rats. European journal of pharmacology, 909, 174406.
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2

Embryonic Protein Western Blotting

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Embryo protein preparation and Western blotting was performed as described previously [1 (link)]. Membranes were probed with primary antibodies using 1:500 rabbit anti-phospho-Akt (Ser473) (Cell Signalling, Danvers, MA, USA, #4058), 1:100 p-RPS6 (Ser235/236) (Cell Signalling #4856S) or 1:1000 mouse anti-α-tubulin (Sigma-Aldrich, #T9026). Membranes were washed in Tris-buffered saline + Tween 20 (TBST; 10 mM Tris–HCl, pH 7.6, 150 mM NaCl and 0.1% Tween 20) and subsequently incubated for 2 h with either 1:4000 Donkey anti-Rabbit IRDye 800CWLI-COR Biosciences, Lincoln, NE, USA) or 1:4000 Donkey anti-Mouse IRDye 680LT (LI-COR Biosciences). Proteins were visualized using the Odyssey infrared imager and Odyssey application software, version 3 (LI-COR Biosciences). Densitometry was performed using Image-J software v1.53c (National Institute of Health, Bethesda, MD, USA).
Green C.J., Span M., Rayhanna M.H., Perera M, & Day M.L. (2022). Insulin-like Growth Factor Binding Protein 3 Increases Mouse Preimplantation Embryo Cleavage Rate by Activation of IGF1R and EGFR Independent of IGF1 Signalling. Cells, 11(23), 3762.
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3

Western Blot Analysis of Cellular Proteins

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For Western blot analysis, protein were analyzed as described [36 (link)]. The following antibodies were used: Dyrk1B (Cell Signaling Technology), β-Tubulin (Sigma, T5168), p27 (Santa Cruz, sc-528), p27 phospho S10 (Abcam, ab62364), p27 phospho T198 (R&D Systems, AF3994), FLAG (Sigma, F1804), HA (Santa Cruz, sc-7392), HPV16 E7 (Santa Cruz, sc-6981), IRDye 800CW goat anti-mouse IgG (Licor, 926-32210), IRDye 800CW goat anti-rabbit IgG (Licor, 926-32211). The bound complex was detected using the Odyssey Infrared Imaging System (Li-Cor Lincoln, NE). The images were analyzed and quantified using the Odyssey Application Software, version 3.0 (Li-Cor). Intensity of bands was normalized in relative to tubulin signals.
Subcellular fractions were prepared using the ProteoExtract subcellular proteome extraction kit (Calbiochem) according to the manufacturer's instructions. Briefly, cytoplasmic, soluble, and insoluble nuclear extracts were prepared using the hypotonic buffer, hypertonic buffer, and insoluble buffer, respectively. Equal volume of cytoplasm and nuclear extracts was obtained. SP1 and β-Tubulin were used as loading controls for the nuclear and cytoplasmic fractions, respectively.
Zhou N., Yuan S., Wang R., Zhang W, & Chen J.J. (2015). Role of dual specificity tyrosine-phosphorylation-regulated kinase 1B (Dyrk1B) in S-phase entry of HPV E7 expressing cells from quiescence. Oncotarget, 6(31), 30745-30761.
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4

Quantitative Western Blot Analysis of Metabolic Proteins

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Tissues were collected immediately following euthanasia and flash frozen in liquid nitrogen. Homogenates were prepared by Polytron homogenization in RIPA buffer containing protease inhibitor and phosphatase inhibitor cocktails (Sigma, St. Louis, MO). Protein content was quantified by bicinchoninic acid (BCA) assay (Thermo Fisher Scientific). 15–25 μg of protein was run on a 10% SDS-PAGE gel (Bio-Rad) and transferred to a PVDF membrane (Millipore, Billerica, MA). Membranes were incubated overnight with antibodies to NAMPT (A300-372; Bethyl, Montgomery, TX), complex III (MS304, MitoSciences, Eugene, OR), and α-tubulin (ab7291, Abcam) and then probed with IRDye 680 goat anti-mouse IgG or IRDye 800CW goat anti-rabbit IgG (926-32220 and 92632211, respectively; LI-COR, Lincoln, NE). Bands were visualized using an Odyssey Digital Infrared Imaging System (LI-COR) and quantified using Odyssey Application Software version 3.0 (LI-COR).
Costford S.R., Brouwers B., Hopf M.E., Sparks L.M., Dispagna M., Gomes A.P., Cornnell H.H., Petucci C., Phelan P., Xie H., Yi F., Walter G.A., Osborne T.F., Sinclair D.A., Mynatt R.L., Ayala J.E., Gardell S.J, & Smith S.R. (2017). Skeletal muscle overexpression of nicotinamide phosphoribosyl transferase in mice coupled with voluntary exercise augments exercise endurance. Molecular Metabolism, 7, 1-11.
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5

HNE-His ELISA and Western Blot Analysis

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All chemicals used in this study were purchased from Sigma (St. Louis, MO) unless otherwise noted. A SpectraMax 340 from Molecular Devices (Sunnyvale, CA) was used for HNE-His ELISA assay. A protein electrophoresis system from BioRad (Hercules, CA), and an Odyssey Infrared Imaging System and an Odyssey Application Software Version 3.0 (Li-Cor Biosciences, Lincoln, NE) were used in western blot. A Lightcycler 480 II (Roche Applied Science, Indianapolis, IN) was used in Real-time PCR.
Pang X, & Panee J. (2016). Anti-inflammatory Function of Phyllostachys Edulis Extract in the Hippocampus of HIV-1 Transgenic Rats. Journal of HIV and AIDS, 2(3), 10.16966/2380-5536.126.
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6

Quantitative Western Blot Analysis of Angiotensin II

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The protein concentration in cell lysates was determined using a Bio-Rad Protein Assay kit (Bio-Rad, Hercules, CA). Samples containing 20 μg of protein were separated on 10% SDS-PAGE gel, transferred to nitrocellulose membranes (Bio-Rad Laboratories, Hercules, CA). After saturation with 5% (w/v) non-fat dry milk in TBS and 0.1% (w/v) Tween 20 (TBST), the membranes were incubated with mouse anti-ANG II monoclonal antibody (Santa Cruz, Paso Robles, CA). After three washes with TBST, membranes were incubated with secondary immunoglobulins conjugated to IRDye 800CW Infrared Dye (LI-COR, Lincoln, NE). Blots were visualized by the Odyssey Infrared Imaging System (LI-COR Biotechnology, Lincoln, NE). Signals were densitometrically assessed (Odyssey Application Software version 3.0; LI-COR Biotechnology, Lincoln, NE) and normalized to β-actin signal using the mouse monoclonal anti-β-actin antibody (Sigma, St. Louis, MO).
Zhang J., Cai Z., Yang M., Tong L, & Zhang Y. (2020). Inhibition of tanshinone IIA on renin activity protected against osteoporosis in diabetic mice. Pharmaceutical Biology, 58(1), 219-224.
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7

Quantifying Nascent Protein Synthesis

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Isogenic cell lines used to assess nascent protein synthetic rate were
grown in 60-mm dishes until ~70% confluent. Prior to labeling cells were
incubated with methionine-free media containing 2% FBS for 1h, followed by
addition of 50 μm AHA (Life Technologies, C10102) for 20min. Cells were
then washed in cold PBS and immediately lysed in buffer containing 50 mM Tris
HCl, pH 8.0, and 1% SDS. Complete lysis was achieved by sonication. Comparable
amounts of lysates were then subjected to Click-iT reaction for switching
azido-modified nascent proteins to alkyne-biotin (Life Technologies, B10185)
using the Click-iT™ Protein Reaction Buffer Kit (Life Technologies,
C10276) following the manufacturer’s protocol. Biotinylated nascent
proteins were subjected to immunoblotting using either anti-biotin, EIF1AX or
β-actin primary antibodies and the corresponding
IRDye-fluoropore-conjugated secondary antibodies. Images were captured by the
LICOR Odyssey imaging system. Biotinylated proteins on the entire lane was
quantified using Odyssey application software version 3.0 (LICOR
Biosciences).
Krishnamoorthy G.P., Davidson N.R., Leach S.D., Zhao Z., Lowe S.W., Lee G., Landa I., Nagarajah J., Saqcena M., Singh K., Wendel H.G., Dogan S., Tamarapu P.P., Blenis J., Ghossein R.A., Knauf J.A., Rätsch G, & Fagin J.A. (2018). EIF1AX and RAS mutations cooperate to drive thyroid tumorigenesis through ATF4 and c-MYC. Cancer discovery, 9(2), 264-281.
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8

Postmortem Brain Tissue Preparation and Immunoblot Analysis

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Postmortem human brain tissue samples were provided by the University of Washington Alzheimer’s Disease Research Center (ADRC) and its Adult Changes in Thought Study and the Johns Hopkins ADRC and the Baltimore Longitudinal Study of Aging (Table 1). The soluble (S2) fraction was prepared from each case as previously described (Donovan et al. 2012 (link)). Mouse tissue and cells were lysed in PBS plus protease inhibitor cocktail (PIC; Roche Diagnostics), Halt phosphatase inhibitor cocktail (Pierce), and lysis buffer containing 0.5% Nonidet P-40, 0.5% deoxycholate, 150 mM sodium chloride, and 50 mM Tris, pH 7.4. Tissue was homogenized (dounce homogenizer) in the PIC Halt lysis buffer. All lysates were subjected to a 13,000-rpm spin to remove nuclei and debris. Protein concentration was determined by bicinchoninic acid method (Pierce). Immunoblots were performed using standard procedures as described previously (Herskowitz et al. 2011 (link)). 50 μg protein per sample was used per lane. Actin or MUNC18 was used as a loading control. Images were captured using an Odyssey Image Station (LiCor), and band intensities were quantified using Odyssey Application Software Version 3.0 (LiCor).
Henderson B.W., Gentry E.G., Rush T., Troncoso J.C., Thambisetty M., Montine T.J, & Herskowitz J.H. (2016). Rho-associated protein kinase 1 (ROCK1) is increased in Alzheimer’s disease and ROCK1 depletion reduces amyloid-β levels in brain. Journal of neurochemistry, 138(4), 525-531.
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9

Western Blot Analysis of Tight Junction Proteins

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The protein expression of tight junctions including ZO-1, Occludin, and Claudin-1 in the colon tissue was detected via Western blot analysis as described previously (Peng et al., 2009 (link)). The primary and fluorescence-tagged secondary antibodies were summarized in Supplementary Table 4. The fluorescent signal of target protein was obtained via scanning the membranes by Odyssey quantitative Western blot near-infrared system (LI-COR Biosciences, NE, USA), and the intensity of target band was calculated by using Odyssey application software version 3.0 (LI-COR Biosciences, NE, USA) and corrected with the intensity of β-actin. Data were represented as the fold changes relative to control.
Leng J., Tian H.J., Fang Y., Hu Y.Y, & Peng J.H. (2022). Amelioration of Non-Alcoholic Steatohepatitis by Atractylodes macrocephala Polysaccharide, Chlorogenic Acid, and Geniposide Combination Is Associated With Reducing Endotoxin Gut Leakage. Frontiers in Cellular and Infection Microbiology, 12, 827516.
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10

Western Blot Analysis of ROCK, LIMK, and Cofilin

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Cells were lysed in phosphate-buffered saline (PBS) plus protease inhibitor cocktail (PIC; Roche Diagnostics, Risch-Rotkreuz, Switzerland), Halt phosphatase inhibitor cocktail (Pierce, Rockford, IL, USA), and lysis buffer containing 0.5% Nonidet P-40, 0.5% deoxycholate, 150 mM sodium chloride, and 50 mM Tris, pH 7.4. All lysates were subjected to a 15,871 × g spin for 5 minutes to remove nuclei and debris. Protein concentration was determined by bicinchoninic acid method (Pierce). Immunoblots were performed using standard procedures as described previously (74 (link)). A quantity of 50 μg protein per sample was loaded per lane. Tubulin was used as a loading control. Images were captured using an Odyssey Image Station (LiCor), and band intensities were quantified using Odyssey Application Software Version 3.0 (LiCor). Primary antibodies were incubated overnight at 4°C. Primary antibodies include: ROCK1 (Abcam 45171), ROCK2 (Santa Cruz 5561), LIMK (Cell Signaling 3842S), Phospho-LIMK (Cell Signaling 3841), Phospho-Cofilin (Cell Signaling 3313), Cofilin (Cell Signaling 3318), and Tubulin (Iowa Hybridoma Bank). Secondary antibodies include: AlexaFluor 680 goat anti-rabbit (Life Technologies A21109) and goat anti-mouse (Li-Cor 926-32210).
Henderson B.W., Greathouse K.M., Ramdas R., Walker C.K., Rao T.C., Bach S.V., Curtis K.A., Day J.J., Mattheyses A.L, & Herskowitz J.H. (2019). Pharmacologic inhibition of LIMK1 provides dendritic spine resilience against amyloid-β. Science signaling, 12(587), eaaw9318.
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