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Comparison of continuous Raman (red – CW-SERS) and time-gated Raman with SERS (green – TG-SERS) at λ exc = 532 nm ( A ) of E. coli cells in media expressing h CNTF (1 hour after induction) and ( B ) eGFP in buffer. The image was created with <t>OriginPro</t> (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).
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Images

1) Product Images from "Assessment of recombinant protein production in E. coli with Time-Gated Surface Enhanced Raman Spectroscopy (TG-SERS)"

Article Title: Assessment of recombinant protein production in E. coli with Time-Gated Surface Enhanced Raman Spectroscopy (TG-SERS)

Journal: Scientific Reports

doi: 10.1038/s41598-020-59091-3

Comparison of continuous Raman (red – CW-SERS) and time-gated Raman with SERS (green – TG-SERS) at λ exc = 532 nm ( A ) of E. coli cells in media expressing h CNTF (1 hour after induction) and ( B ) eGFP in buffer. The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).
Figure Legend Snippet: Comparison of continuous Raman (red – CW-SERS) and time-gated Raman with SERS (green – TG-SERS) at λ exc = 532 nm ( A ) of E. coli cells in media expressing h CNTF (1 hour after induction) and ( B ) eGFP in buffer. The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).

Techniques Used: Expressing

h CNTF old batch (red curve) and new batch (black curve). The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).
Figure Legend Snippet: h CNTF old batch (red curve) and new batch (black curve). The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).

Techniques Used:

Overlapping TG-SERS spectra at different time points. ( A ) HspA1 at 1 h (black), 4 h (red) and 6 h (blue), ( B ) h CNTF at 1 h (black), 3 h (yellow) and 4 h (red) and ( C ) EnBase cultivated (EN): h CNTF (magenta) compared to blank EN BL (green) after 24 h. ( D – F ) Shows corresponding Raman intensities (detector counts) and A-C the normalized arbitrary Raman intensities, respectively. The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).
Figure Legend Snippet: Overlapping TG-SERS spectra at different time points. ( A ) HspA1 at 1 h (black), 4 h (red) and 6 h (blue), ( B ) h CNTF at 1 h (black), 3 h (yellow) and 4 h (red) and ( C ) EnBase cultivated (EN): h CNTF (magenta) compared to blank EN BL (green) after 24 h. ( D – F ) Shows corresponding Raman intensities (detector counts) and A-C the normalized arbitrary Raman intensities, respectively. The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).

Techniques Used:

Suppression of NC background with TG-SERS (red curve) and without background suppression using only NC (black curve). The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).
Figure Legend Snippet: Suppression of NC background with TG-SERS (red curve) and without background suppression using only NC (black curve). The image was created with OriginPro (V. 2016b and 2018b; https://www.originlab.com/index.aspx?go=Products/Origin ).

Techniques Used:

2) Product Images from "Incineration of Nanoclay Composites Leads to Byproducts with Reduced Cellular Reactivity"

Article Title: Incineration of Nanoclay Composites Leads to Byproducts with Reduced Cellular Reactivity

Journal: Scientific Reports

doi: 10.1038/s41598-018-28884-y

( a ) Dose response curve (based on live cell counts) for BEAS-2B cells exposed to PLACC900 from 0–750 µg/ml (n = 5). The data was fit via a sigmoidal curve using OriginPro (OriginLab Corporation) software. ( b ) Cellular viability (based on WST assay) for cells exposed to PLACC900 (n = 6). The symbol * indicates a significant difference between the control cells and exposed cells. The values are normalized relative to the controls. ( c ) Extracellular ROS of cells exposed to varying doses of PLACC900 (n = 4). The symbol * indicates a significant difference between the control cells and exposed cells. Significance was determined by one-way analysis of variance ANOVA with p
Figure Legend Snippet: ( a ) Dose response curve (based on live cell counts) for BEAS-2B cells exposed to PLACC900 from 0–750 µg/ml (n = 5). The data was fit via a sigmoidal curve using OriginPro (OriginLab Corporation) software. ( b ) Cellular viability (based on WST assay) for cells exposed to PLACC900 (n = 6). The symbol * indicates a significant difference between the control cells and exposed cells. The values are normalized relative to the controls. ( c ) Extracellular ROS of cells exposed to varying doses of PLACC900 (n = 4). The symbol * indicates a significant difference between the control cells and exposed cells. Significance was determined by one-way analysis of variance ANOVA with p

Techniques Used: Software, WST Assay

3) Product Images from "An integrated systems-level model of ochratoxin A toxicity in the zebrafish (Danio rerio) embryo based on NMR metabolic profiling"

Article Title: An integrated systems-level model of ochratoxin A toxicity in the zebrafish (Danio rerio) embryo based on NMR metabolic profiling

Journal: Scientific Reports

doi: 10.1038/s41598-022-09726-4

Effect of OTA treatment on the metabolic profile of intact zebrafish embryos. Zebrafish embryos (72 hpf) were exposed to 1 µM OTA or solvent vehicle (“Control”), for 24 h. Concentrations of metabolites relative to total creatine (tCr) are shown, and include ( A ) amino acids and related metabolites ( B ) polar head-groups of membrane phospholipids; ( C ) metabolites associated with energy metabolism; and ( D ) lipids, i.e., fatty acids and cholesterol. For statistical analysis, one-way ANOVA with a Tukey post-hoc correction for multiple comparisons were performed using OriginPro v. 8 (Northampton, MA, USA). Values shown are the mean ± standard deviation (n = 6). ## P
Figure Legend Snippet: Effect of OTA treatment on the metabolic profile of intact zebrafish embryos. Zebrafish embryos (72 hpf) were exposed to 1 µM OTA or solvent vehicle (“Control”), for 24 h. Concentrations of metabolites relative to total creatine (tCr) are shown, and include ( A ) amino acids and related metabolites ( B ) polar head-groups of membrane phospholipids; ( C ) metabolites associated with energy metabolism; and ( D ) lipids, i.e., fatty acids and cholesterol. For statistical analysis, one-way ANOVA with a Tukey post-hoc correction for multiple comparisons were performed using OriginPro v. 8 (Northampton, MA, USA). Values shown are the mean ± standard deviation (n = 6). ## P

Techniques Used: Standard Deviation

4) Product Images from "Nematode CDC-37 and DNJ-13 form complexes and can interact with HSP-90"

Article Title: Nematode CDC-37 and DNJ-13 form complexes and can interact with HSP-90

Journal: Scientific Reports

doi: 10.1038/s41598-021-00885-4

Interaction of HSP-90 with the CDC-37·DNJ-13 complex. (a) Sedimentation analysis of the binary complex, consisting of the either *CDC-37 and DNJ-13 (orange), *CDC-37 and HSP-90 (grey) or the ternary CDC-37·DNJ-13·HSP-90 complex (dashed green). ( b) Effect of ATPγS addition to both binary and ternary complex, similar to (a) . Graphs were generated in OriginPro (Version 2018b).
Figure Legend Snippet: Interaction of HSP-90 with the CDC-37·DNJ-13 complex. (a) Sedimentation analysis of the binary complex, consisting of the either *CDC-37 and DNJ-13 (orange), *CDC-37 and HSP-90 (grey) or the ternary CDC-37·DNJ-13·HSP-90 complex (dashed green). ( b) Effect of ATPγS addition to both binary and ternary complex, similar to (a) . Graphs were generated in OriginPro (Version 2018b).

Techniques Used: Sedimentation, Generated

KD and stoichiometry determination. (a) Absorbance sedimentation velocity analysis of CDC-37 titration to 10 µM DNJ-13 in substoichiometric, equal and excess concentrations, as indicated. CDC-37 (purple) and DNJ-13 (green) serve both as control, as well as assistance for the indication of unbound protein used in the titration. ( b) Titration of varying DNJ-13 concentrations in AUC experiments to 100 nM *CDC-37, as indicated. ( c) Kinetics of CDC-37/DNJ-13 binding based on titrated DNJ-13 concentrations and measured sedimentation coefficient. Graphs were generated in OriginPro (Version 2018b).
Figure Legend Snippet: KD and stoichiometry determination. (a) Absorbance sedimentation velocity analysis of CDC-37 titration to 10 µM DNJ-13 in substoichiometric, equal and excess concentrations, as indicated. CDC-37 (purple) and DNJ-13 (green) serve both as control, as well as assistance for the indication of unbound protein used in the titration. ( b) Titration of varying DNJ-13 concentrations in AUC experiments to 100 nM *CDC-37, as indicated. ( c) Kinetics of CDC-37/DNJ-13 binding based on titrated DNJ-13 concentrations and measured sedimentation coefficient. Graphs were generated in OriginPro (Version 2018b).

Techniques Used: Sedimentation, Titration, Binding Assay, Generated

CDC-37 fragment interaction with DNJ-13. (a) SDS-PAGE of crosslinked DNJ-13 (D) together with CDC-37ΔN (ΔN), CDC-37ΔC (ΔC) or full-length CDC-37 (FL). Arrowheads indicate the observed complexes. ( b) Sedimentation analysis of DNJ-13 with either CDC-37ΔN, CDC-37ΔC or full-length CDC-37 as indicated. Shifting sedimentation coefficients are put into perspective by both controls, DNJ-13 (dashed grey) and CDC-37 (dashed yellow) respectively. OriginPro (Version 2018b) was utilized for generating the graph.
Figure Legend Snippet: CDC-37 fragment interaction with DNJ-13. (a) SDS-PAGE of crosslinked DNJ-13 (D) together with CDC-37ΔN (ΔN), CDC-37ΔC (ΔC) or full-length CDC-37 (FL). Arrowheads indicate the observed complexes. ( b) Sedimentation analysis of DNJ-13 with either CDC-37ΔN, CDC-37ΔC or full-length CDC-37 as indicated. Shifting sedimentation coefficients are put into perspective by both controls, DNJ-13 (dashed grey) and CDC-37 (dashed yellow) respectively. OriginPro (Version 2018b) was utilized for generating the graph.

Techniques Used: SDS Page, Sedimentation

Systematic cofactor CDC-37 interactions. (a) Interaction of CDC-37 (C) with and without the crosslinking reagent BS3, as indicated together with the cofactors Sti1, PPH-5, HSP-90, DNJ-12 and DNJ-13. The upper arrowhead indicates the observed crosslinked CDC-37 monomer ·DNJ-13 dimer complex, whereas the lower arrowhead indicates a CDC-37 monomer ·DNJ-13 monomer complex. ( b) Sedimentation analysis of labeled CDC-37 (*CDC-37) together with the J domain-containing proteins DNJ-12 and DNJ-13. OriginPro (Version 2018b) was utilized for generating the graph.
Figure Legend Snippet: Systematic cofactor CDC-37 interactions. (a) Interaction of CDC-37 (C) with and without the crosslinking reagent BS3, as indicated together with the cofactors Sti1, PPH-5, HSP-90, DNJ-12 and DNJ-13. The upper arrowhead indicates the observed crosslinked CDC-37 monomer ·DNJ-13 dimer complex, whereas the lower arrowhead indicates a CDC-37 monomer ·DNJ-13 monomer complex. ( b) Sedimentation analysis of labeled CDC-37 (*CDC-37) together with the J domain-containing proteins DNJ-12 and DNJ-13. OriginPro (Version 2018b) was utilized for generating the graph.

Techniques Used: Sedimentation, Labeling

5) Product Images from "Incineration of Nanoclay Composites Leads to Byproducts with Reduced Cellular Reactivity"

Article Title: Incineration of Nanoclay Composites Leads to Byproducts with Reduced Cellular Reactivity

Journal: Scientific Reports

doi: 10.1038/s41598-018-28884-y

( a ) Dose response curve (based on live cell counts) for BEAS-2B cells exposed to PLACC900 from 0–750 µg/ml (n = 5). The data was fit via a sigmoidal curve using OriginPro (OriginLab Corporation) software. ( b ) Cellular viability (based on WST assay) for cells exposed to PLACC900 (n = 6). The symbol * indicates a significant difference between the control cells and exposed cells. The values are normalized relative to the controls. ( c ) Extracellular ROS of cells exposed to varying doses of PLACC900 (n = 4). The symbol * indicates a significant difference between the control cells and exposed cells. Significance was determined by one-way analysis of variance ANOVA with p
Figure Legend Snippet: ( a ) Dose response curve (based on live cell counts) for BEAS-2B cells exposed to PLACC900 from 0–750 µg/ml (n = 5). The data was fit via a sigmoidal curve using OriginPro (OriginLab Corporation) software. ( b ) Cellular viability (based on WST assay) for cells exposed to PLACC900 (n = 6). The symbol * indicates a significant difference between the control cells and exposed cells. The values are normalized relative to the controls. ( c ) Extracellular ROS of cells exposed to varying doses of PLACC900 (n = 4). The symbol * indicates a significant difference between the control cells and exposed cells. Significance was determined by one-way analysis of variance ANOVA with p

Techniques Used: Software, WST Assay

6) Product Images from "The CLIP-170 N-terminal domain binds directly to both F-actin and microtubules in a mutually exclusive manner"

Article Title: The CLIP-170 N-terminal domain binds directly to both F-actin and microtubules in a mutually exclusive manner

Journal: The Journal of Biological Chemistry

doi: 10.1016/j.jbc.2022.101820

CLIP-170 binds to F-actin directly via CG2 and the surrounding serine-rich regions. A , summary of CLIP-170 fragments used in this study. B and C , determining the K D of CLIP-170 fragments. High-speed cosedimentation assays with CLIP-170 fragments (4 μM), phalloidin (0.8 μM), and F-actin (0, 1, 2, 4, 8, 12, 16, 24, and 28 μM) in PEM50 buffer generated the binding curves in ( B ). Curves were fitted to the data by OriginPro (simple binding equation with assumption of a 1:1 binding ratio with B max = 1). Error bars are standard deviation with n = 3. The apparent K D values of CLIP-170 fragments were extracted from the curve fits and are listed in the table ( C ). D , summary of the CLIP-170 regions involved in binding to F-actin and MTs. This diagram shows that the CLIP-170 F-actin-binding and MT-binding regions overlap. In addition, the data indicate that CLIP-170 dimerization is not required for the CLIP-170–F-actin interactions because the coiled-coil region is not included in the F-actin-binding region. F-actin, filamentous actin; MT, microtubule; ND, binding not detected; PEM50: 50 mM PIPES, 2 mM MgCl, 1 mM EGTA, pH 6.8.
Figure Legend Snippet: CLIP-170 binds to F-actin directly via CG2 and the surrounding serine-rich regions. A , summary of CLIP-170 fragments used in this study. B and C , determining the K D of CLIP-170 fragments. High-speed cosedimentation assays with CLIP-170 fragments (4 μM), phalloidin (0.8 μM), and F-actin (0, 1, 2, 4, 8, 12, 16, 24, and 28 μM) in PEM50 buffer generated the binding curves in ( B ). Curves were fitted to the data by OriginPro (simple binding equation with assumption of a 1:1 binding ratio with B max = 1). Error bars are standard deviation with n = 3. The apparent K D values of CLIP-170 fragments were extracted from the curve fits and are listed in the table ( C ). D , summary of the CLIP-170 regions involved in binding to F-actin and MTs. This diagram shows that the CLIP-170 F-actin-binding and MT-binding regions overlap. In addition, the data indicate that CLIP-170 dimerization is not required for the CLIP-170–F-actin interactions because the coiled-coil region is not included in the F-actin-binding region. F-actin, filamentous actin; MT, microtubule; ND, binding not detected; PEM50: 50 mM PIPES, 2 mM MgCl, 1 mM EGTA, pH 6.8.

Techniques Used: Cross-linking Immunoprecipitation, Generated, Binding Assay, Standard Deviation

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    OriginLab statistical ana lysis two sample t tests
    MET and epidermal growth factor receptor (EGFR) densities in the cell membrane of HeLa and BT-20 cells. ( a ) Concept of super-resolution microscopy by Exchange-PAINT of MET and EGFR (top). A super-resolved image is obtained from transient binding events of short, fluorescently labeled DNA oligonucleotides to DNA-labeled antibodies. The image (bottom) shows MET visualized by widefield microscopy versus DNA-PAINT (scale bar 5 µm). ( b ) Exchange-PAINT images of MET (cyan) and EGFR (magenta) immunostained with secondary antibodies carrying P5 and P1 DNA docking strands and labeled with complementary DNA imager strands labeled with ATTO 655. Total internal reflection fluorescence (TIRF) images of the plasma membrane of HeLa and BT-20 cells were recorded either in the unstimulated state, after hepatocycte growth factor (HGF) stimulation, or after activation with epidermal growth factor (EGF) (scale bar 5 µm, insets 5 µm × 5 µm). Receptor cluster densities of MET (cyan) and EGFR (magenta) in ( c ) HeLa and ( d ) BT-20 cells were determined from DNA-PAINT images ( n  = 6–7 cells/condition from at least three independent experiments) and plotted in the histogram (left). (Note that receptor clusters refer to both monomers and dimers.) Error bars represent standard deviations. Results of two-sample t-tests for comparison of activated samples with the respective unstimulated sample are depicted as arrows ( p >  0.05 no significant difference between populations (n.s.),  p
    Statistical Ana Lysis Two Sample T Tests, supplied by OriginLab, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    OriginLab pro 8 software
    Preparation of the biosensor for measurements. (a) Electrical contacts to the prepared devices are made with copper tape, platinum foil (as the counter electrode) and alligator pins. (b) Measurements were performed using a PalmSens3 analyzer controlled by PS-Trace 4.8. Data was processed with GNU Octave, Igor Pro, and OriginLab Pro 8.
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    OriginLab originpro 8 software
    Unfolding and refolding kinetics of MsEis protein. Intrinsic tryptophan fluorescence spectra of either unfolded or refolded MsEis protein in the presence or absence of GdmCl and urea at different time intervals. 0 h  (Panel A) , 2 h  (Panel B) , 4 h  (panel C) , 6 h  (Panel D) , 8 h  (Panel E) , 10 h  (Panel F)  and 12 h  (Panel G) . The values corresponding to native MsEis without treatment were considered as 100% in each case of unfolding or refolding. The values obtained from emission maxima were fitted using OriginPro 8.0 software.
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    97
    OriginLab originpro 9 0
    3D multi-modal imaging and quantification. A. Representative maximum intensity projection of 60 µm deep stack of WKY and SHR ventricles showing from the left: capillaries labelled with BSA-FITC gel, negative image of cells traced with WGA-Alexa Fluor 594, collagen deposition imaged by second-harmonic generation, and merge of the three different channels (vessels in green, cells in red, collagen in blue). Maximum intensity projections were created using ImageJ 2.0.0-rc-71/1.52p ( https://fiji.sc ). B. Heat Map summarizing vascular, cellular and collagen parameters in all the experimental classes. Five different ventricular regions are shown for each experimental class. All the parameters have been normalized on the same scale. RV is right ventricle (above) and LV is left ventricle (below). Heat Maps were created using OriginPro 9.0 ( https://www.originlab.com ).
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    MET and epidermal growth factor receptor (EGFR) densities in the cell membrane of HeLa and BT-20 cells. ( a ) Concept of super-resolution microscopy by Exchange-PAINT of MET and EGFR (top). A super-resolved image is obtained from transient binding events of short, fluorescently labeled DNA oligonucleotides to DNA-labeled antibodies. The image (bottom) shows MET visualized by widefield microscopy versus DNA-PAINT (scale bar 5 µm). ( b ) Exchange-PAINT images of MET (cyan) and EGFR (magenta) immunostained with secondary antibodies carrying P5 and P1 DNA docking strands and labeled with complementary DNA imager strands labeled with ATTO 655. Total internal reflection fluorescence (TIRF) images of the plasma membrane of HeLa and BT-20 cells were recorded either in the unstimulated state, after hepatocycte growth factor (HGF) stimulation, or after activation with epidermal growth factor (EGF) (scale bar 5 µm, insets 5 µm × 5 µm). Receptor cluster densities of MET (cyan) and EGFR (magenta) in ( c ) HeLa and ( d ) BT-20 cells were determined from DNA-PAINT images ( n  = 6–7 cells/condition from at least three independent experiments) and plotted in the histogram (left). (Note that receptor clusters refer to both monomers and dimers.) Error bars represent standard deviations. Results of two-sample t-tests for comparison of activated samples with the respective unstimulated sample are depicted as arrows ( p >  0.05 no significant difference between populations (n.s.),  p

    Journal: International Journal of Molecular Sciences

    Article Title: Single-Molecule Super-Resolution Microscopy Reveals Heteromeric Complexes of MET and EGFR upon Ligand Activation

    doi: 10.3390/ijms21082803

    Figure Lengend Snippet: MET and epidermal growth factor receptor (EGFR) densities in the cell membrane of HeLa and BT-20 cells. ( a ) Concept of super-resolution microscopy by Exchange-PAINT of MET and EGFR (top). A super-resolved image is obtained from transient binding events of short, fluorescently labeled DNA oligonucleotides to DNA-labeled antibodies. The image (bottom) shows MET visualized by widefield microscopy versus DNA-PAINT (scale bar 5 µm). ( b ) Exchange-PAINT images of MET (cyan) and EGFR (magenta) immunostained with secondary antibodies carrying P5 and P1 DNA docking strands and labeled with complementary DNA imager strands labeled with ATTO 655. Total internal reflection fluorescence (TIRF) images of the plasma membrane of HeLa and BT-20 cells were recorded either in the unstimulated state, after hepatocycte growth factor (HGF) stimulation, or after activation with epidermal growth factor (EGF) (scale bar 5 µm, insets 5 µm × 5 µm). Receptor cluster densities of MET (cyan) and EGFR (magenta) in ( c ) HeLa and ( d ) BT-20 cells were determined from DNA-PAINT images ( n = 6–7 cells/condition from at least three independent experiments) and plotted in the histogram (left). (Note that receptor clusters refer to both monomers and dimers.) Error bars represent standard deviations. Results of two-sample t-tests for comparison of activated samples with the respective unstimulated sample are depicted as arrows ( p > 0.05 no significant difference between populations (n.s.), p

    Article Snippet: Statistical Ana lysis Two-sample t-tests were performed in OriginPro (version 2016G, Origin Lab Corporation, Northampton, MA, USA) to test the significance of differences between the chosen conditions for receptor densities determined from DNA-PAINT data ( c,d) and for normalized diffusion coefficients ( b,e).

    Techniques: Microscopy, Binding Assay, Labeling, Fluorescence, Activation Assay

    Diffusion dynamics of MET and EGFR in HeLa and BT-20 cells after stimulation with HGF and EGF studied by SPT indicate receptor cross-interactions. ( a , d ) MET was tracked by adding Fab-ATTO 647N. EGFR was tracked by adding EGFR-SOMAmer reagent modified with a P1-docking strand and P1-Cy3B for PAINT imaging. The Fab fragment and the SOMAmer reagent bind to the respective receptor but do not activate them. For observations of direct activation or possible cross-interaction, unlabeled HGF (light blue) or EGF (purple) were added to the samples. Diffusion coefficients of MET and EGFR in resting and activated cells (each  n  = 50 from at least three independent experiments) were determined in ( b , e ) HeLa and ( c , f ) BT-20 cells. All diffusion coefficients were normalized against reference measurements of ligand-untreated cells for all types of treatment. The box plots of diffusion coefficients display the 5th percentile, 25th percentile, median (line), mean (square), 75th percentile, and 95th percentile. Results of two-sample t-tests for comparison of ligand-treated cells with the reference are depicted above the box plots ( p >  0.05 no significant difference betw een populations (n.s.),  p

    Journal: International Journal of Molecular Sciences

    Article Title: Single-Molecule Super-Resolution Microscopy Reveals Heteromeric Complexes of MET and EGFR upon Ligand Activation

    doi: 10.3390/ijms21082803

    Figure Lengend Snippet: Diffusion dynamics of MET and EGFR in HeLa and BT-20 cells after stimulation with HGF and EGF studied by SPT indicate receptor cross-interactions. ( a , d ) MET was tracked by adding Fab-ATTO 647N. EGFR was tracked by adding EGFR-SOMAmer reagent modified with a P1-docking strand and P1-Cy3B for PAINT imaging. The Fab fragment and the SOMAmer reagent bind to the respective receptor but do not activate them. For observations of direct activation or possible cross-interaction, unlabeled HGF (light blue) or EGF (purple) were added to the samples. Diffusion coefficients of MET and EGFR in resting and activated cells (each n = 50 from at least three independent experiments) were determined in ( b , e ) HeLa and ( c , f ) BT-20 cells. All diffusion coefficients were normalized against reference measurements of ligand-untreated cells for all types of treatment. The box plots of diffusion coefficients display the 5th percentile, 25th percentile, median (line), mean (square), 75th percentile, and 95th percentile. Results of two-sample t-tests for comparison of ligand-treated cells with the reference are depicted above the box plots ( p > 0.05 no significant difference betw een populations (n.s.), p

    Article Snippet: Statistical Ana lysis Two-sample t-tests were performed in OriginPro (version 2016G, Origin Lab Corporation, Northampton, MA, USA) to test the significance of differences between the chosen conditions for receptor densities determined from DNA-PAINT data ( c,d) and for normalized diffusion coefficients ( b,e).

    Techniques: Diffusion-based Assay, Single-particle Tracking, Modification, Imaging, Activation Assay

    Preparation of the biosensor for measurements. (a) Electrical contacts to the prepared devices are made with copper tape, platinum foil (as the counter electrode) and alligator pins. (b) Measurements were performed using a PalmSens3 analyzer controlled by PS-Trace 4.8. Data was processed with GNU Octave, Igor Pro, and OriginLab Pro 8.

    Journal: ACS applied materials & interfaces

    Article Title: Electrochemical quantification of glycated and non-glycated human serum albumin in synthetic urine

    doi: 10.1021/acsami.8b16071

    Figure Lengend Snippet: Preparation of the biosensor for measurements. (a) Electrical contacts to the prepared devices are made with copper tape, platinum foil (as the counter electrode) and alligator pins. (b) Measurements were performed using a PalmSens3 analyzer controlled by PS-Trace 4.8. Data was processed with GNU Octave, Igor Pro, and OriginLab Pro 8.

    Article Snippet: All electrochemical data was processed on GNU Octave, Igor Pro and OriginLab Pro 8 software.

    Techniques:

    Unfolding and refolding kinetics of MsEis protein. Intrinsic tryptophan fluorescence spectra of either unfolded or refolded MsEis protein in the presence or absence of GdmCl and urea at different time intervals. 0 h  (Panel A) , 2 h  (Panel B) , 4 h  (panel C) , 6 h  (Panel D) , 8 h  (Panel E) , 10 h  (Panel F)  and 12 h  (Panel G) . The values corresponding to native MsEis without treatment were considered as 100% in each case of unfolding or refolding. The values obtained from emission maxima were fitted using OriginPro 8.0 software.

    Journal: PLoS ONE

    Article Title: Differential thermal stability, conformational stability and unfolding behavior of Eis proteins from Mycobacterium smegmatis and Mycobacterium tuberculosis

    doi: 10.1371/journal.pone.0213933

    Figure Lengend Snippet: Unfolding and refolding kinetics of MsEis protein. Intrinsic tryptophan fluorescence spectra of either unfolded or refolded MsEis protein in the presence or absence of GdmCl and urea at different time intervals. 0 h (Panel A) , 2 h (Panel B) , 4 h (panel C) , 6 h (Panel D) , 8 h (Panel E) , 10 h (Panel F) and 12 h (Panel G) . The values corresponding to native MsEis without treatment were considered as 100% in each case of unfolding or refolding. The values obtained from emission maxima were fitted using OriginPro 8.0 software.

    Article Snippet: The obtained data points were fitted to three-state model (biDose-response curve of nonlinear regression analysis) using OriginPro 8 software (Origin Lab, Northampton, USA).

    Techniques: Fluorescence, Software

    Time kinetics, temperature stability and steady-state kinetic parameters of KAN acetylation by MsEis and RvEis. Time course of changes in the absorbance at 412 nm of NTB -  ions formed as a result of acetyltransferase activity of MsEis and RvEis proteins  (Panel A) . The effect of temperature on the catalytic activity of MsEis and RvEis was determined after incubating the Eis proteins at different temperatures ranging from 20°C to 80°C  (Panel B) . Kinetic parameters were calculated for the acetylation of KAN by MsEis and RvEis at fixed concentration of acetyl CoA and increasing concentration of KAN antibiotic  (Panel C) . The experimental values were fitted to Michaelis-Menten equation using OriginPro 8.0 software (Origin Labs, Northampton, USA).

    Journal: PLoS ONE

    Article Title: Differential thermal stability, conformational stability and unfolding behavior of Eis proteins from Mycobacterium smegmatis and Mycobacterium tuberculosis

    doi: 10.1371/journal.pone.0213933

    Figure Lengend Snippet: Time kinetics, temperature stability and steady-state kinetic parameters of KAN acetylation by MsEis and RvEis. Time course of changes in the absorbance at 412 nm of NTB - ions formed as a result of acetyltransferase activity of MsEis and RvEis proteins (Panel A) . The effect of temperature on the catalytic activity of MsEis and RvEis was determined after incubating the Eis proteins at different temperatures ranging from 20°C to 80°C (Panel B) . Kinetic parameters were calculated for the acetylation of KAN by MsEis and RvEis at fixed concentration of acetyl CoA and increasing concentration of KAN antibiotic (Panel C) . The experimental values were fitted to Michaelis-Menten equation using OriginPro 8.0 software (Origin Labs, Northampton, USA).

    Article Snippet: The obtained data points were fitted to three-state model (biDose-response curve of nonlinear regression analysis) using OriginPro 8 software (Origin Lab, Northampton, USA).

    Techniques: Activity Assay, Impedance Spectroscopy, Concentration Assay, Software

    Comparison of conformational stability of MsEis and RvEis proteins in the presence of different denaturants. Intrinsic tryptophan fluorescence spectra of MsEis and RvEis proteins in the presence of increasing concentration of GdmCl  (Panel A),  urea  (Panel C)  and at increasing temperature from 25°C to 100°C  (Panel E) . Unfolding of MsEis and RvEis proteins measured in terms of changes in emission wavelength maxima in the presence of GdmCl  (Panel B),  urea  (panel D)  and temperature  (Panel F) . The values corresponding to native Eis without treatment were considered as 100%. Fitting of the values obtained from emission maxima were done by using equations with OriginPro 8.0 software.

    Journal: PLoS ONE

    Article Title: Differential thermal stability, conformational stability and unfolding behavior of Eis proteins from Mycobacterium smegmatis and Mycobacterium tuberculosis

    doi: 10.1371/journal.pone.0213933

    Figure Lengend Snippet: Comparison of conformational stability of MsEis and RvEis proteins in the presence of different denaturants. Intrinsic tryptophan fluorescence spectra of MsEis and RvEis proteins in the presence of increasing concentration of GdmCl (Panel A), urea (Panel C) and at increasing temperature from 25°C to 100°C (Panel E) . Unfolding of MsEis and RvEis proteins measured in terms of changes in emission wavelength maxima in the presence of GdmCl (Panel B), urea (panel D) and temperature (Panel F) . The values corresponding to native Eis without treatment were considered as 100%. Fitting of the values obtained from emission maxima were done by using equations with OriginPro 8.0 software.

    Article Snippet: The obtained data points were fitted to three-state model (biDose-response curve of nonlinear regression analysis) using OriginPro 8 software (Origin Lab, Northampton, USA).

    Techniques: Fluorescence, Concentration Assay, Impedance Spectroscopy, Software

    3D multi-modal imaging and quantification. A. Representative maximum intensity projection of 60 µm deep stack of WKY and SHR ventricles showing from the left: capillaries labelled with BSA-FITC gel, negative image of cells traced with WGA-Alexa Fluor 594, collagen deposition imaged by second-harmonic generation, and merge of the three different channels (vessels in green, cells in red, collagen in blue). Maximum intensity projections were created using ImageJ 2.0.0-rc-71/1.52p ( https://fiji.sc ). B. Heat Map summarizing vascular, cellular and collagen parameters in all the experimental classes. Five different ventricular regions are shown for each experimental class. All the parameters have been normalized on the same scale. RV is right ventricle (above) and LV is left ventricle (below). Heat Maps were created using OriginPro 9.0 ( https://www.originlab.com ).

    Journal: bioRxiv

    Article Title: 3D imaging and morphometry of the heart capillary system in spontaneously hypertensive rats and normotensive controls

    doi: 10.1101/2020.08.05.237487

    Figure Lengend Snippet: 3D multi-modal imaging and quantification. A. Representative maximum intensity projection of 60 µm deep stack of WKY and SHR ventricles showing from the left: capillaries labelled with BSA-FITC gel, negative image of cells traced with WGA-Alexa Fluor 594, collagen deposition imaged by second-harmonic generation, and merge of the three different channels (vessels in green, cells in red, collagen in blue). Maximum intensity projections were created using ImageJ 2.0.0-rc-71/1.52p ( https://fiji.sc ). B. Heat Map summarizing vascular, cellular and collagen parameters in all the experimental classes. Five different ventricular regions are shown for each experimental class. All the parameters have been normalized on the same scale. RV is right ventricle (above) and LV is left ventricle (below). Heat Maps were created using OriginPro 9.0 ( https://www.originlab.com ).

    Article Snippet: Data analysisGraphs and data statistical analyses were achieved using OriginPro 9.0 (OriginLab Corporation).

    Techniques: Imaging, Whole Genome Amplification

    Vascular disorganization correlate with myocardial disarray. Correlation analysis between vascular morphometries and tissue cytoarchitecture in WKY and SHR ventricles. A. angular dispersion and cellular disarray, B. vasculature density and cellular disarray, C. angular dispersion and collagen percentage, and D vasculature density and collagen content (%). Plots were created using OriginPro 9.0 ( https://www.originlab.com ).

    Journal: bioRxiv

    Article Title: 3D imaging and morphometry of the heart capillary system in spontaneously hypertensive rats and normotensive controls

    doi: 10.1101/2020.08.05.237487

    Figure Lengend Snippet: Vascular disorganization correlate with myocardial disarray. Correlation analysis between vascular morphometries and tissue cytoarchitecture in WKY and SHR ventricles. A. angular dispersion and cellular disarray, B. vasculature density and cellular disarray, C. angular dispersion and collagen percentage, and D vasculature density and collagen content (%). Plots were created using OriginPro 9.0 ( https://www.originlab.com ).

    Article Snippet: Data analysisGraphs and data statistical analyses were achieved using OriginPro 9.0 (OriginLab Corporation).

    Techniques:

    3D imaging of the coronary microcirculation of clarified hearts. A. Diagram showing the main steps of the BSA-FITC/CLARITY protocol. Heart is rapidly isolated, cannulated through the proximal aorta and perfused with fixative solution. Coronaries are stained with BSA-FITC gel and the organ is subjected to modified CLARITY protocol. B. Section of a right ventricle after fixative solution perfusion in PBS (left) and after TDE clearing (right). C. Representative 3D reconstruction of a stack of 450 × 450 × 300 µm 3  acquired with a custom-made Two Photon Fluorescence Microscope. 3D reconstruction was created using ImageJ 2.0.0-rc-71/1.52p ( https://fiji.sc ). D. Validation of the sample preparation protocol: morphometric parameters obtained in acute experiment of ex-vivo hearts (Ex-Vivo) and in BSA-FITC cleared samples (CLARITY). Student T-test applied, p-value = 0.30; 0.31; 0.39. Plots were created using OriginPro 9.0 ( https://www.originlab.com ).

    Journal: bioRxiv

    Article Title: 3D imaging and morphometry of the heart capillary system in spontaneously hypertensive rats and normotensive controls

    doi: 10.1101/2020.08.05.237487

    Figure Lengend Snippet: 3D imaging of the coronary microcirculation of clarified hearts. A. Diagram showing the main steps of the BSA-FITC/CLARITY protocol. Heart is rapidly isolated, cannulated through the proximal aorta and perfused with fixative solution. Coronaries are stained with BSA-FITC gel and the organ is subjected to modified CLARITY protocol. B. Section of a right ventricle after fixative solution perfusion in PBS (left) and after TDE clearing (right). C. Representative 3D reconstruction of a stack of 450 × 450 × 300 µm 3 acquired with a custom-made Two Photon Fluorescence Microscope. 3D reconstruction was created using ImageJ 2.0.0-rc-71/1.52p ( https://fiji.sc ). D. Validation of the sample preparation protocol: morphometric parameters obtained in acute experiment of ex-vivo hearts (Ex-Vivo) and in BSA-FITC cleared samples (CLARITY). Student T-test applied, p-value = 0.30; 0.31; 0.39. Plots were created using OriginPro 9.0 ( https://www.originlab.com ).

    Article Snippet: Data analysisGraphs and data statistical analyses were achieved using OriginPro 9.0 (OriginLab Corporation).

    Techniques: Imaging, Isolation, Staining, Modification, Fluorescence, Microscopy, Sample Prep, Ex Vivo