sarctrack sarcomere analysis software  (MathWorks Inc)

Journal: Stem Cell Reports

Article Title: Protein-encapsulated doxorubicin reduces cardiotoxicity in hiPSC-cardiomyocytes and cardiac spheroids while maintaining anticancer efficacy

doi: 10.1016/j.stemcr.2023.08.005

Figure Lengend Snippet: SPEDOX-6 induces less functional toxicity than UF DOX in hiPSC-CMs (A) hiPSC-CM beat rate normalized to DMSO after 3 days of UF DOX or SPEDOX-6 treatment. See . ∗ p < 0.05 between DMSO and other groups, determined by one-way ANOVA with Tukey’s post hoc test. n = 4 independent experiments. (B) Representative field potential recordings from contracting hiPSC-CMs in multielectrode arrays treated with DMSO, UF DOX, or SPEDOX-6 for up to 72 h. (C) Average spike amplitude mean and field potential duration (FPD) mean from field potential recordings of contracting hiPSC-CMs in multielectrode arrays treated with DMSO, UF DOX, or SPEDOX-6 for up to 72 h, corresponding with (B). n = 9 technical replicates. Error bars represent SD. (D) Live fluorescence imaging of ACTN2-GFP hiPSC-CMs subjected to DMSO, UF DOX, or SPEDOX-6 for up to 72 h. α-actinin (green) represents a cardiomyocyte-specific protein marking the striated cardiac sarcomeres in live hiPSC-CMs. DOX (red) shows DOX intracellular accumulation. (E) SarcTrack dataset showing representative sarcomere displacement timegraphs of ACTN2-GFP hiPSC-CMs treated with DMSO, UF DOX, or SPEDOX-6 for 72 h. See . (F) SarcTrack-based quantification of sarcomere displacement during the hiPSC-CM contraction cycle in ACTN2-GFP hiPSC-CMs treated with DMSO, UF DOX, or SPEDOX-6 for 72 h. See . n = 10, 29, and 22 sarcomeres were detected for DMSO, UF DOX, and SPEDOX-6 conditions, respectively. (G) Calcium imaging timegraphs of WTC-GCaMP hiPSC-CMs treated with DMSO, UF DOX, or SPEDOX-6 for 72 h. ΔF/F0 compares the change of the fluorescence intensity to the baseline fluorescence intensity before the contraction. See .

Article Snippet: Videos were analyzed in MATLAB R2022 using SarcTrack sarcomere analysis software, as shown previously ( ).

Techniques: Functional Assay, Fluorescence, Imaging

Journal: bioRxiv

Article Title: Mechanisms of Pathogenicity of Hypertrophic Cardiomyopathy-Associated Troponin T (TNNT2) Variant R278C +/− During Development

doi: 10.1101/2023.06.06.542948

Figure Lengend Snippet: Panel A. GFP-tagged α-actinin hiPSC-CMs cultured on 5 kPa PDMS (left) and SarcTrack wavelet fitting (right). Panel B. The relaxation of WT (black, n=9) and R278C +/− (red, n=12) hiPSC-CMs cultured on 5 kPa PDMS, with respect to: B1) time-to-half maximal relaxation (ms). B2) the maximum velocity of relaxation (μm . s −1 ). Panel C. The contractile parameters of WT (black, n=9) and R278C +/− (red, n=12) hiPSC-CMs cultured on 5 kPa PDMS and stimulated at 1 Hz with respect to: C1) percent maximal shortening; C2) time to half maximal contraction; C3) maximum velocity of contraction (μm s −1 ). (* p-value< 0.05, ** p-value <0.005, ***p-value<0.0005)

Article Snippet: To examine the contractile properties of R278C, we employed the newly developed Matlab-based algorithm, SarcTrack, to quantify sarcomeric shortening in α-actinin 2-GFP tagged hiPSC-CMs.

Techniques: Cell Culture

Journal: bioRxiv

Article Title: Mechanisms of Pathogenicity of Hypertrophic Cardiomyopathy-Associated Troponin T (TNNT2) Variant R278C +/− During Development

doi: 10.1101/2023.06.06.542948

Figure Lengend Snippet: Panel A. GFP-tagged α-actinin hiPSC-CMs cultured on 5 kPa PDMS (left) and SarcTrack wavelet fitting (right). Panel B. The relaxation of WT (black, n=9) and R278C +/− (red, n=12) hiPSC-CMs cultured on 5 kPa PDMS, with respect to: B1) time-to-half maximal relaxation (ms). B2) the maximum velocity of relaxation (μm . s −1 ). Panel C. The contractile parameters of WT (black, n=9) and R278C +/− (red, n=12) hiPSC-CMs cultured on 5 kPa PDMS and stimulated at 1 Hz with respect to: C1) percent maximal shortening; C2) time to half maximal contraction; C3) maximum velocity of contraction (μm s −1 ). (* p-value< 0.05, ** p-value <0.005, ***p-value<0.0005)

Article Snippet: Using the MATLAB based algorithm SarcTrack , we found sarcomere shortening, contraction, and relaxation kinetics to be disrupted in R278C +/− hiPSC-CMs, which were alleviated in part by mavacamten.

Techniques: Cell Culture

Journal: bioRxiv

Article Title: Mechanisms of Pathogenicity of Hypertrophic Cardiomyopathy-Associated Troponin T (TNNT2) Variant R278C +/- During Development

doi: 10.1101/2023.06.06.542948

Figure Lengend Snippet: Panel A. GFP-tagged α-actinin hiPSC-CMs cultured on 5 kPa PDMS (left) and SarcTrack wavelet fitting (right). Panel B. The relaxation of WT (black, n=9) and R278C +/- (red, n=12) hiPSC-CMs cultured on 5 kPa PDMS, with respect to: B1) time-to-half maximal relaxation (ms). B2) the maximum velocity of relaxation (µm. s-1). Panel C. The contractile parameters of WT (black, n=9) and R278C +/- (red, n=12) hiPSC-CMs cultured on 5 kPa PDMS and stimulated at 1 Hz with respect to: C1) percent maximal shortening; C2) time to half maximal contraction; C3) maximum velocity of contraction (µm s -1 ). (* p-value< 0.05, ** p-value <0.005, ***p-value<0.0005)

Article Snippet: Therefore, a MATLAB based algorithm SarcTrack was used to assess sarcomere shortening, contraction, and relaxation kinetics of 2D monolayers of hiPSC-CMs.

Techniques: Cell Culture

Journal: PLoS Computational Biology

Article Title: Sarc-Graph: Automated segmentation, tracking, and analysis of sarcomeres in hiPSC-derived cardiomyocytes

doi: 10.1371/journal.pcbi.1009443

Figure Lengend Snippet: Summary of experimental examples included in this paper (E1, E2, E3, E4, and E5). We note that Examples E1 and E2 have already been published and made publicly available at https://github.com/HMS-IDAC/SarcTrack [ 10 ].

Article Snippet: In , the SarcTrack code is implemented in MATLAB and available from https://github.com/HMS-IDAC/SarcTrack .

Techniques: Cell Culture