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Data analysis 10

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Data Analysis 10.0 software is a comprehensive data analysis tool designed to assist researchers in interpreting and visualizing experimental data. The software provides a range of advanced analytical capabilities, including curve fitting, statistical analysis, and graphical representation of data. Data Analysis 10.0 is a versatile tool suitable for use across various scientific disciplines.

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Lab products found in correlation

Anti mouse igg fc capture amc biosensors, by Molecular Devices (2 mentions) Kinetics buffer, by Molecular Devices (2 mentions) Octet qke system, by Molecular Devices (1 mentions) Octet red96e bio layer interferometry system, by Molecular Devices (1 mentions) Oktet k2 system, by Molecular Devices (1 mentions) Octet red96 system, by Molecular Devices (1 mentions) Octet red bli, by Molecular Devices (1 mentions) Aps biosensor, by Molecular Devices (1 mentions) Sa biosensor, by Molecular Devices (1 mentions) Octet red384, by Molecular Devices (1 mentions) 96 well flat bottom black plate, by Greiner (1 mentions) Anti human igg fc capture sensors, by Molecular Devices (1 mentions) Octet red96e instrument, by Molecular Devices (1 mentions) Octet red system, by Molecular Devices (1 mentions) Anti human igg fc capture biosensors, by Molecular Devices (1 mentions) Octet qke device, by Molecular Devices (1 mentions)

12 protocols using data analysis 10

1

Binding Kinetics of LbCas12a with crRNA

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The BLI Ni-NTA biosensors were purchased from Fortebio to perform the binding kinetic study with polyhistidine-tagged LbCas12a. In detail, the experiment was carried out in a 96-well plate and included five steps: baseline, loading, baseline2, association, and dissociation. The biosensors were dipped into the baseline containing 1× kinetic buffer (1× PBS, 0.1% BSA, and 0.01% Tween 20). They were then transferred into each loading well containing 10 μg/ml of LbCas12a. After processing through loading and baseline2, the protein-tagged biosensor was next allowed to dip into the crRNA sample wells at different dilutions (10, 5, 2.5, 1.25, 0.625, 0.3125, 0.15625, and 0 μg/ml) in the association step. The dissociation step occurred when the biosensors were transferred back to baseline2 at a shaking speed of 1000 rpm. All the samples were read by the Octet QKe system (Fortebio). Kd was determined by software Data Analysis 10.0 (Fortebio), and only Kd with R2 > 0.9 were extracted for comparison between crRNA wild-type and modified crRNAs.
Nguyen L.T., Smith B.M, & Jain P.K. (2020). Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection. Nature Communications, 11, 4906.
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2

Quantifying SARS-CoV-2 Spike-ACE2 Binding

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An Octet RED96e BioLayer Interferometry system (FortéBio, Menlo Park, USA) was used to measure the binding affinities of non-glycosylated spike (ng-spike) extracellular domain (ECD) to ACE2 and a spike monoclonal mouse antibody. Briefly, Anti-Mouse IgG Fc Capture (AMC) biosensors (FortéBio) were pre-equilibrated in PBS-TB binding buffer (1x PBS, pH 7.4, 0.2% BSA, 0.05% Tween-20) for 10 min prior to loading. 200 nM ACE2-Fc and 40 nM spike antibodies were loaded onto the sensor for 240 s and washed by binding buffer for 120 s to reach a stable baseline. The sensors were then subjected to association phase immersion for 180 s in wells containing both 100 nM g-spike and ng-spike ECD-His diluted in binding buffer. After association, the sensors were placed back into the binding buffer to allow the dissociation phase to occur for 600 to 1,800 s. The kinetic constants were calculated via the Data Analysis 10.0 (FortéBio) software and were fitted by using 1:1 and 2:1 binding models for ACE2 and antibodies, respectively. The final equilibrium dissociation constant (KD) was calculated as the dissociation constant divided by the association constant (KD = Kd/Ka).
Huang H.C., Lai Y.J., Liao C.C., Yang W.F., Huang K.B., Lee I.J., Chou W.C., Wang S.H., Wang L.H., Hsu J.M., Sun C.P., Kuo C.T., Wang J., Hsiao T.C., Yang P.J., Lee T.A., Huang W., Li F.A., Shen C.Y., Lin Y.L., Tao M.H, & Li C.W. (2021). Targeting conserved N-glycosylation blocks SARS-CoV-2 variant infection in vitro. EBioMedicine, 74, 103712.
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3

Kinetic Analysis of EsaG-EsaD Interaction

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An OKTET K2 system (ForteBio Inc., Menlo Park, CA, USA) and streptavidin (SA)-coated biosensors were used to measure association and dissociation kinetics for Avi-tagged EsaG in relation to EsaDC. Before the experiment, the biosensors were equilibrated in a buffer (300 mM NaCl, 30 mM NaH2PO4, 27 mM KCl, pH7.2) for 10 min, then the biotinylated EsaG was immobilized on streptavidin biosensors. The biosensors were then exposed to different concentrations of EsaDc. Data were analyzed and the binding curves were fit using the Data Analysis 10.0 software package (ForteBio). Association and dissociation curves were exported using Excel format and imported into Prism (GraphPad software) for visualization of the sensorgram.
Wang Y., Zhou Y., Shi C., Liu J., Lv G., Huang H., Li S., Duan L., Zheng X., Liu Y., Zhou H., Wang Y., Li Z., Ding K., Sun P., Huang Y., Lu X, & Zhang Z.M. (2022). A toxin-deformation dependent inhibition mechanism in the T7SS toxin-antitoxin system of Gram-positive bacteria. Nature Communications, 13, 6434.
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4

Kinetic Characterization of Antibody-Antigen Interactions

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BLI-based measurements were determined using an OctetRED96 System (ForteBio, Fremont CA). Antibodies were diluted in kinetic buffer to 10 μg/ml and immobilized onto anti-human IgG Fc capture biosensors (AHC, ForteBio). Kinetics assays were carried out at 30°C using standard kinetics acquisition rate settings (5.0 Hz, averaging by 20) at a sample plate shake speed of 1,000 rpm. The kinetic experiments included five steps: (a) baseline (180 s); (b) antibody loading (300 s); (c) second baseline (180 s); (d) association of antigen (300 s), and (e) dissociation of antigen (300 s). Fitting curves were constructed using ForteBio Data Analysis 10.0 software using a 1:1 binding model, and double reference subtraction was used for correction.
Poumbourios P., Langer C., Boo I., Zakir T., Center R.J., Akerman A., Milogiannakis V., Aggarwal A., Johnstone B.A., Ha J., Coulibaly F., Turville S.G, & Drummer H.E. (2023). Enhanced stability of the SARS CoV-2 spike glycoprotein following modification of an alanine cavity in the protein core. PLOS Pathogens, 19(5), e1010981.
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5

Actin Binding Affinity Measurement

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The binding of rWLP with actin was measured by Bio-Layer Interferometry (BLI) on an Octet RED BLI (Pall ForteBio) at 25°C [31 (link)]. The rWLP (1 mM) was dissolved in PBS buffer (pH 7.4) containing 0.05% (v/v) Tween 20 and 0.1% (v/v) BSA and then loaded onto an APS biosensor (Pall ForteBio) coated with actin. The procedure was as follows: 60 s for the baseline 1, 900 s for loading, 300 s for the baseline 2, 300 s for association, and 120 s for dissociation. The raw data were processed by subtraction and alignment, and the affinity constant (KD) was determined using ForteBio Data Analysis 10.0 software [32 (link)].
Jiang Y., Sun Q., Fan M., Zhang X., Shen W., Xu H, & Liao Z. (2020). Molecular characterization of a whirlin-like protein with biomineralization-related functions from the shell of Mytilus coruscus. PLoS ONE, 15(4), e0231414.
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6

Kinetic Analysis of gp120 Nanofiber Conjugates

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Kinetics measurements of unconjugated 1086.C gp120 and gp120-Q11 nanofiber conjugates were performed on the OctetRED96 BLI platform using an orbital flow rate of 500 rpm (ForteBio, New York). Anti-hIgG Fc Capture (AHC) biosensors were equilibrated in phosphate-buffered saline (PBS; 1.06 mM potassium phosphate monobasic, 2.97 mM sodium phosphate dibasic, 155 mM sodium chloride) (60 s), loaded with CH65, VRC01, B12, CH58, or CH22 antibodies by submersion in 10 µg/mL solutions (300 s), and washed in PBS (60 s). An initial baseline was established in PBS (120 s) followed by an association phase in 0, 12.5, 25, 50, 100, 150, 200, 250 µg/mL 1086.C gp120 or gp120-Q11 nanofiber conjugate (400 s) and a dissociation phase in PBS (600 s). Kinetic analysis was performed using the ForteBio Data Analysis 10.0 software. Experimental curves were double-reference-subtracted using PBS buffer blanks and the CH65 reference sensors. The resultant curves were fit to a 2:1 (heterogeneous ligand) binding model and the reported dissociation rate constants (koff) represent the fast components of the model fit.
Fries C.N., Chen J.L., Dennis M.L., Votaw N.L., Eudailey J., Watts B.E., Hainline K.M., Cain D.W., Barfield R., Chan C., Moody M.A., Haynes B.F., Saunders K.O., Permar S.R., Fouda G.G, & Collier J.H. (2021). HIV envelope antigen valency on peptide nanofibers modulates antibody magnitude and binding breadth. Scientific Reports, 11, 14494.
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7

Plexin-B1 Interaction Profiling

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Cross-reactivity and capability of anti–Plexin-B1 antibodies to block the interaction between Plexin-B1 and Sema4D was analyzed by biolayer interferometry using OctetRED384 (ForteBio). Briefly, an SA biosensor (ForteBio) was used to capture 5 μg/ml of biotinylated human or mouse Plexin-B1 (20–535)-Avi-6xHis in 1xKinetics buffer (ForteBio). In the next step, the binding response was measured to 50 nM of the antibody or buffer, followed by 50 nM of human Sema4D (7470-S4, R&D). Qualitative analysis of individual binding association curves was performed using the Data Analysis 10.0 software (ForteBio).
Vogler M., Oleksy A., Schulze S., Fedorova M., Kojonazarov B., Nijjar S., Patel S., Jossi S., Sawmynaden K., Henry M., Brown R., Matthews D., Offermanns S, & Worzfeld T. (2022). An antagonistic monoclonal anti–Plexin-B1 antibody exerts therapeutic effects in mouse models of postmenopausal osteoporosis and multiple sclerosis. The Journal of Biological Chemistry, 298(9), 102265.
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8

MPER Peptide Liposome Binding Assay

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VRC antibodies were tested for MPER656-GTH1 liposome and blank
liposome binding by BLI using the ForteBio OcteRed96. Liposomes were
prepared at a 1:20 dilution in PBS and captured on APS
(aminopropysilane) sensor tips to a level of approximately 1.0-1.5nm.The
duration of liposome capture was 600s. The liposome loaded sensor tips
were then coated with 0.01% BSA for 600s to block any non-specific
interaction of the antibody with the sensor tips. The sensor tips were
then washed with PBS for 120s. After washing with 1xPBS, the sensor tips
were dipped into the antibodies diluted down to 20 μg/mL and 1
well of the MPER mAb 13H11(Alam et al.,
2007) also diluted to 20 μg/mL for an association
length of 600s. 13H11 was used as a negative control mAb for MPER
peptide liposomes since it does not bind to MPER peptide in the context
of lipids or to peptide-free liposomes (Alam et al. 2007 (link)). After antibody binding, the sensors were
placed back into PBS for a dissociation length of 600s. Antibody binding
analysis was performed using the ForteBio Data Analysis 10.0 software.
The Y-axis was aligned to the baseline from 175s to 179.8s and the
inter-step correction was aligned to dissociation. 13H11 mAb (Alam et al., 2007 (link)) binding was
subtracted from the binding of each antibody to exclude background and
signal drift.
Krebs S.J., Kwon Y.D., Schramm C.A., Law W.H., Donofrio G., Zhou K.H., Gift S., Dussupt V., Georgiev I.S., Schätzle S., McDaniel J.R., Lai Y.T., Sastry M., Zhang B., Jarosinski M., Ransier A., Chenine A.L., Asokan M., Bailer R.T., Bose M., Cagigi A., Cale E.M., Chuang G.Y., Darko S., Driscoll J.I., Druz A., Gorman J., Laboune F., Louder M.K., McKee K., Mendez L., Moody M.A., O’Sullivan A.M., Owen C., Peng D., Rawi R., Sanders-Buell E., Shen C.H., Shiakolas A.R., Stephens T., Tsybovsky Y., Tucker C., Veradi R., Wang K., Zhou J., Zhou T., Georgiou G., Alam S.M., Haynes B.F., Rolland M., Matyas G.R., Polonis V.R., McDermott A., Douek D.C., Shapiro L., Tovanabutra S., Michael N.L., Mascola J.R., Robb M.L., Kwong P.D, & Doria-Rose N.A. (2019). Longitudinal Analysis Reveals Early Development of Three MPER-Directed Neutralizing Antibody Lineages from an HIV-1-Infected Individual. Immunity, 50(3), 677-691.e13.
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9

Biophysical Characterization of RSV F Variants

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A Pall ForteBio Octet Red96e instrument was used to assess association between RSV F variants, sDS-Cav1 and sF, and antibodies against various RSV F conformations. A non-RSV soluble protein was included as a negative control. All assays were completed with agitation at 1000 rpm. Assays were performed at 25 °C in flat bottom black 96-well plates (Greiner Bio-One) with evaporation covers. All antibodies and proteins were diluted in 1X Kinetics Buffer (1X KB: 10X Kinetics Buffer (Pall ForteBio) diluted 1:10 in phosphate-buffered saline (PBS)). The final volume for all solutions in the plate was 200 μl/well. Anti-human IgG Fc Capture sensors (AHC: Pall ForteBio) were stabilized with 5 s alternating pulses of 10 mM glycine pH 1.75 and 1X KB for three cycles, baselined for 60 s in 1X KB and then loaded with antibodies at a concentration of 5 μg/ml for 200 s. Biosensor tips were equilibrated for 300 s in 1X KB before measurement of association with RSV F and non-RSV soluble proteins (25 nM) for 600 sec. Proteins were allowed to dissociate for 600 s. Data analysis and curve generation were completed using ForteBio Data Analysis 10.0 software. To account for systemic baseline drift, all data were background subtracted with the measurement of a reference well, an antibody-loaded sensor incubated in 1X KB buffer alone. All processed data was y-axis aligned to baseline.
Espeseth A.S., Cejas P.J., Citron M.P., Wang D., DiStefano D.J., Callahan C., Donnell G.O., Galli J.D., Swoyer R., Touch S., Wen Z., Antonello J., Zhang L., Flynn J.A., Cox K.S., Freed D.C., Vora K.A., Bahl K., Latham A.H., Smith J.S., Gindy M.E., Ciaramella G., Hazuda D., Shaw C.A, & Bett A.J. (2020). Modified mRNA/lipid nanoparticle-based vaccines expressing respiratory syncytial virus F protein variants are immunogenic and protective in rodent models of RSV infection. NPJ Vaccines, 5, 16.
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10

Antibody Kinetics Characterization by BLI

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BLI-based measurements were determined using an Octet RED System (ForteBio, Fremont CA). Antibodies were diluted in 1× kinetic buffer to 10 μg/ml and immobilized onto anti-human IgG Fc capture biosensors (ForteBio). Kinetics assays were carried out at 30 °C using standard kinetics acquisition rate settings (5.0 Hz, averaging by 20) at a sample plate shake speed of 1,000 rpm. The kinetic experiments included five steps: (a) baseline (180 s); (b) antibody loading (300 s); (c) second baseline (180 s); (d) association of antigen (600 s), and (e) dissociation of antigen (900 s). Fitting curves were constructed using ForteBio Data Analysis 10.0 software using a 1:1 binding model, and double reference subtraction was used for correction.
Center R.J., Boo I., Phu L., McGregor J., Poumbourios P, & Drummer H.E. (2020). Enhancing the antigenicity and immunogenicity of monomeric forms of hepatitis C virus E2 for use as a preventive vaccine. The Journal of Biological Chemistry, 295(21), 7179-7192.
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