Quantification of cardiac capillarization in basement-membrane-immunostained myocardial slices using Segment Anything Model.

Decreased myocardial capillary density has been reported as an important histopathological feature associated with various heart disorders. Quantitative assessment of cardiac capillarization typically involves double immunostaining of cardiomyocytes (CMs) and capillaries in myocardial slices. In contrast, single immunostaining of basement membrane protein is a straightforward approach to simultaneously label CMs and capillaries, presenting fewer challenges in background staining. However, subsequent image analysis always requires expertise and laborious manual work to identify and segment CMs/capillaries. Here, we developed an image analysis tool, AutoQC, for automatic identification and segmentation of CMs and capillaries in immunofluorescence images of basement membrane. Commonly used capillarization-related measurements can be derived from segmentation results. By leveraging the power of a pre-trained segmentation model (Segment Anything Model, SAM) via prompt engineering, the training of AutoQC required only a small dataset with bounding box annotations instead of pixel-wise annotations. AutoQC outperformed SAM (without prompt engineering) and YOLOv8-Seg, a state-of-the-art instance segmentation model, in both instance segmentation and capillarization assessment. Thus, AutoQC, featuring a weakly supervised algorithm, enables automatic segmentation and high-throughput, high-accuracy capillarization assessment in basement-membrane-immunostained myocardial slices. This approach reduces the training workload and eliminates the need for manual image analysis once AutoQC is trained.

Management of autofluorescence in formaldehyde-fixed myocardium: choosing the right treatment.

Autofluorescence (AF) poses challenges for detecting proteins of interest in situ when employing immunofluorescence (IF) microscopy. This interference is particularly pronounced in strongly autofluorescent tissues such as myocardium, where tissue AF can be comparable to IF. Although various histochemical methods have been developed to achieve effective AF suppression in different types of tissue, their applications on myocardial  samples have not been well validated. Due to inconsistency across different autofluorescent structures in sometypes of tissue, it is unclear if these methods can effectively suppress AF across all autofluorescent structures within the myocardium. Here, we quantitatively evaluated the performance of several commonly used quenching treatments on formaldehyde-fixed myocardial samples, including 0.3 M glycine, 0.3% Sudan Black B (SBB), 0.1% and 1% sodium borohydride (NaBH4), TrueVIEW® and TrueBlack®. We further assessed their quenching performance by employing the pre-treatment and post-treatment protocols, designed to cover two common IF staining scenarios where buffers contained detergents or not. The results suggest that SBB and TrueBlack® outperform other reagents in AF suppression on formaldehyde-fixed myocardial samples in both protocols. Furthermore, we inspected the quenching performance of SBB and TrueBlack® on major autofluorescent myocardial structures and evaluated their influence on IF imaging. The results suggest that SBB outperforms TrueBlack® in quenching major autofluorescent structures, while TrueBlack® excels in preserving IF labeling signal. Surprisingly, we found the treatment of NaBH4 increased AF signal and enhanced the AF contrast of major autofluorescent structures. This finding suggests that NaBH4 has the potential to act as an AF enhancer and may facilitate the interpretation of myocardial structures without the need for counterstaining.

Cooperation between myofibril growth and costamere maturation in human cardiomyocytes.

Costameres, as striated muscle-specific cell adhesions, anchor both M-lines and Z-lines of the sarcomeres to the extracellular matrix. Previous studies have demonstrated that costameres intimately participate in the initial assembly of myofibrils. However, how costamere maturation cooperates with myofibril growth is still underexplored. In this work, we analyzed zyxin (costameres), α-actinin (Z-lines) and myomesin (M-lines) to track the behaviors of costameres and myofibrils within the cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs). We quantified the assembly and maturation of costameres associated with the process of myofibril growth within the hiPSC-CMs in a time-dependent manner. We found that asynchrony existed not only between the maturation of myofibrils and costameres, but also between the formation of Z-costameres and M-costameres that associated with different structural components of the sarcomeres. This study helps us gain more understanding of how costameres assemble and incorporate into the cardiomyocyte sarcomeres, which sheds a light on cardiomyocyte mechanobiology.

Molecular mechanisms of cardiac actomyosin transforming from rigor state to post-rigor state.

Sudden cardiac death contributed to half of all deaths from cardiovascular diseases. The mechanism of the kinetic cycle of cardiac myosin is crucial for heart protection and drug development. The state change in the myosin kinetic cycle from the rigor state to the post-rigor state is fundamental to explain binding and dissociation. Here, we used ß-cardiac myosin in the rigor and post-rigor states to model the actomyosin complexes. Molecular dynamics simulations, electrostatic analysis, and energetic analysis of actomyosin complexes were performed in this work. The results showed that there are fewer interactions and lower electrostatic binding strength in the post-rigor state than in the rigor state. In the post-rigor state, there were higher free binding energy, fewer salt bridges, and fewer hydrogen bonds. The results showed a lower binding affinity in the post-rigor state than in the rigor state. The decrease in the binding affinity provided important conditions for dissociation of the myosin from the actin filament. Although previous studies focused mostly on the binding process, this study provides evidence of dissociation, which is even more important in the myosin kinetic cycle. This research on the mechanism of myosin kinetic cycles provides a novel direction for future genetic disease studies.

High-efficiency 3D reconstruction with a uniaxial MEMS-based fringe projection profilometry.

Micro-Electro-Mechanical System (MEMS) scanning is increasingly popular in 3D surface measurement with the merits of the compact structure and high frame-rate. In this paper, we achieve real-time fringe structured 3D reconstruction by using a uniaxial MEMS-based projector. To overcome the limitations on uniaxial MEMS-based projector of lensless structure and unidirectional fringe projection, a novel isophase plane model is proposed, in which the laser line from MEMS-based projector is regarded as an isophase plane. Our model directly establishes the mapping relationship between phase and spatial 3D coordinates through the intersection point of camera back-projection light ray and isophase plane. Furthermore, a flexible calibration strategy to obtain 3D mapping coefficients is introduced with a specially designed planar target. Experiments demonstrated that our method can achieve high-accuracy and real-time 3D reconstruction.

Hybrid method for representing ions in implicit solvation calculations.

Fast and accurate calculations of the electrostatic features of highly charged biomolecules such as DNA, RNA, and highly charged proteins are crucial and challenging tasks. Traditional implicit solvent methods calculate the electrostatic features quickly, but these methods are not able to balance the high net biomolecular charges effectively. Explicit solvent methods add unbalanced ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which require more expensive computing resources. Here we report developing a novel method, Hybridizing Ions Treatment (HIT), which hybridizes the implicit solvent method with an explicit method to realistically calculate the electrostatic potential for highly charged biomolecules. HIT utilizes the ionic distribution from an explicit method to predict the bound ions. The bound ions are then added in the implicit solvent method to perform the electrostatic potential calculations. In this study, two training sets were developed to optimize parameters for HIT. The performance on the testing set demonstrates that HIT significantly improves the electrostatic calculations. Results on molecular motors myosin and kinesin reveal some mechanisms and explain some previous experimental findings. HIT can be widely used to study highly charged biomolecules, including DNA, RNA, molecular motors, and other highly charged biomolecules. The HIT package is available at http://compbio.utep.edu/static/downloads/download_hit.zip.

Study of the Expression Transition of Cardiac Myosin Using Polarization-Dependent SHG Microscopy.

Detection of the transition between the two myosin isoforms α- and ß-myosin in living cardiomyocytes is essential for understanding cardiac physiology and pathology. In this study, the differences in symmetry of polarization spectra obtained from α- and ß-myosin in various mammalian ventricles and propylthiouracil-treated rats are explored through polarization-dependent second harmonic generation microscopy. Here, we report for the, to our knowledge, first time that α- and ß-myosin, as protein crystals, possess different symmetries: the former has C6 symmetry, and the latter has C3v. A single-sarcomere line scan further demonstrated that the differences in polarization-spectrum symmetry between α- and ß-myosin came from their head regions: the head and neck domains of α- and ß-myosin account for the differences in symmetry. In addition, the dynamic transition of the polarization spectrum from C6 to C3v line profile was observed in a cell culture in which norepinephrine induced an α- to ß-myosin transition.

Changes in the crystallographic structures of cardiac myosin filaments detected by polarization-dependent second harmonic generation microscopy.

Detecting the structural changes caused by volume and pressure overload is critical to comprehending the mechanisms of physiologic and pathologic hypertrophy. This study explores the structural changes at the crystallographic level in myosin filaments in volume- and pressure-overloaded myocardia through polarization-dependent second harmonic generation microscopy. Here, for the first time, we report that the ratio of nonlinear susceptibility tensor components d33/d15 increased significantly in volume- and pressure-overloaded myocardial tissues compared with the ratio in normal mouse myocardial tissues. Through cell stretch experiments, we demonstrated that mechanical tension plays an important role in the increase of d33/d15 in volume- and pressure-overloaded myocardial tissues.

Light-field-based absolute phase unwrapping.

Ambiguity caused by a wrapped phase is an intrinsic problem in fringe projection-based 3D shape measurement. Among traditional methods for avoiding phase ambiguity, spatial phase unwrapping is sensitive to sensor noise and depth discontinuity, and temporal phase unwrapping requires additional encoding information that leads to an increase of image sequence acquisition time or a reduction of fringe contrast. Here, to the best of our knowledge, we report a novel method of absolute phase unwrapping based on light field imaging. In a recorded light field under structured illumination, i.e., a structured light field, a wrapped phase-encoded field can be retrieved and resampled in diverse image planes associated with several possible fringe orders in a measurement volume. Then, by leveraging phase consistency constraint in the resampled wrapped phase-encoded field, correct fringe orders can be determined to unwrap the wrapped phase without any additional encoding information. Experimental results demonstrated that the proposed method was suitable for accurate and robust absolute phase unwrapping.

Ray calibration and phase mapping for structured-light-field 3D reconstruction.

In previous work, we presented a structured light field (SLF) method combining light field imaging with structured illumination to perform multi-view depth measurement. However, the previous work just accomplishes depth rather than 3D reconstruction. In this paper, we propose a novel active method involving ray calibration and phase mapping, to achieve SLF 3D reconstruction. We performed the ray calibration for the first time to determine each light field ray with metric spatio-angular parameters, making the SLF realize multi-view 3D reconstruction. Based on the ray parametric equation, we further derived the phase mapping in the SLF that spatial coordinates can be directly mapped from phase. A flexible calibration strategy was correspondently designed to determine mapping coefficients for each light field ray, achieving high-efficiency SLF 3D reconstruction. Experimental results demonstrated that the proposed method was suitable for high-efficiency multi-view 3D reconstruction in the SLF.

Universal phase-depth mapping in a structured light field.

Technologies and devices for light field imaging have recently been developed for both industrial applications and scientific research to achieve excellent imaging properties. In our previous work, we combined light field imaging with structured illumination to propose a structured light field method in which multidirectional depth estimation can be performed for high-quality 3D imaging. However, the projection axis was implicitly assumed to be perpendicular to the reference plane, which is hard to meet in practice. In this paper, we derive a universal phase-depth mapping in a structured light field by relaxing this implicit condition. Both nonlinear and linear models were proposed based on this universal relationship. To test the model's practical performance, we simulated experiments by adding errors to the real measured values to evaluate the deviation in depth estimation. By comparing the root-mean-square distributions of the depth deviations with respect to the depth positions, we demonstrated that the nonlinear model was precise and consistent in a wide range of depth, and we employed this model to realize high-quality multidirectional scene reconstruction.

Phase-3D mapping method developed from back-projection stereovision model for fringe projection profilometry.

Two major methods for 3D reconstruction in fringe projection profilometry, phase-height mapping and stereovision, have their respective problems: the former has low-flexibility in practical application due to system restrictions and the latter requires time-consuming homogenous points searching. Given these limitations, we propose a phase-3D mapping method developed from back-projection stereovision model to achieve flexible and high-efficient 3D reconstruction for fringe projection profilometry. We showed that all dimensional coordinates (X, Y, and Z), but not just the height coordinate (Z), of a measured point can be mapped from phase through corresponding rational functions directly and independently. To determine the phase-3D mapping coefficients, we designed a flexible two-step calibration strategy. The first step, ray reprojection calibration, is to determine the stereovision system parameters; the second step, sampling-mapping calibration, is to fit the mapping coefficients using the calibrated stereovision system parameters. Experimental results demonstrated that the proposed method was suitable for flexible and high-efficient 3D reconstruction that eliminates practical restrictions and dispenses with the time-consuming homogenous point searching.

Structured light field 3D imaging.

In this paper, we propose a method by means of light field imaging under structured illumination to deal with high dynamic range 3D imaging. Fringe patterns are projected onto a scene and modulated by the scene depth then a structured light field is detected using light field recording devices. The structured light field contains information about ray direction and phase-encoded depth, via which the scene depth can be estimated from different directions. The multidirectional depth estimation can achieve high dynamic 3D imaging effectively. We analyzed and derived the phase-depth mapping in the structured light field and then proposed a flexible ray-based calibration approach to determine the independent mapping coefficients for each ray. Experimental results demonstrated the validity of the proposed method to perform high-quality 3D imaging for highly and lowly reflective surfaces.

How Microelectrode Array-Based Chick Forebrain Neuron Biosensors Respond to Glutamate NMDA Receptor Antagonist AP5 and GABAA Receptor Antagonist Musimol.

We have established a long-term, stable primary chick forebrain neuron (FBN) culture on a microelectrode array platform as a biosensor system for neurotoxicant screening and for neuroelectrophysiological studies for multiple purposes. This paper reports some of our results, which characterize the biosensor pharmacologically. Dose-response experiments were conducted using NMDA receptor antagonist AP5 and GABAA receptor agonist musimol (MUS). The chick FBN biosensor (C-FBN-biosensor) responds to the two agents in a pattern similar to that of rodent counterparts; the estimated EC50s (the effective concentration that causes 50% inhibition of the maximal effect) are 2.3 µM and 0.25 µM, respectively. Intercultural and intracultural reproducibility and long-term reusability of the C-FBN-biosensor are addressed and discussed. A phenomenon of sensitization of the biosensor that accompanies intracultural reproducibility in paired dose-response experiments for the same agent (AP5 or MUS) is reported. The potential application of the C-FBN-biosensor as an alternative to rodent biosensors in shared sensing domains (NMDA receptor and GABAA receptor) is suggested.

Characterizing relationship between optical microangiography signals and capillary flow using microfluidic channels.

Optical microangiography (OMAG) is a powerful optical angio-graphic tool to visualize micro-vascular flow in vivo. Despite numerous demonstrations for the past several years of the qualitative relationship between OMAG and flow, no convincing quantitative relationship has been proven. In this paper, we attempt to quantitatively correlate the OMAG signal with flow. Specifically, we develop a simplified analytical model of the complex OMAG, suggesting that the OMAG signal is a product of the number of particles in an imaging voxel and the decorrelation of OCT (optical coherence tomography) signal, determined by flow velocity, inter-frame time interval, and wavelength of the light source. Numerical simulation with the proposed model reveals that if the OCT amplitudes are correlated, the OMAG signal is related to a total number of particles across the imaging voxel cross-section per unit time (flux); otherwise it would be saturated but its strength is proportional to the number of particles in the imaging voxel (concentration). The relationship is validated using microfluidic flow phantoms with various preset flow metrics. This work suggests OMAG is a promising quantitative tool for the assessment of vascular flow.

Disassembly of myofibrils and potential imbalanced forces on Z-discs in cultured adult cardiomyocytes.

Myofibrils are the main protein structures that generate force in the beating heart. Myofibril disassembly is related to many physiological and pathological processes. This study investigated, in a cultured rat adult cardiomyocyte model, the effect of force imbalance on myofibril disassembly. The imbalance of forces that were exerted on Z-discs was induced by the synergistic effect of broken intercalated discs and actin-myosin interaction. Cardiomyocytes with well-preserved intercalated discs were isolated from adult rat ventricles. The ultrastructure of cardiomyocyte was observed using a customized two-photon excitation fluorescence and second harmonic generation imaging system. The contraction of cardiomyocytes was recorded with a high-speed CCD camera, and the movement of cellular components was analyzed using a contractile imaging assay technique. The cardiomyocyte dynamic remodeling process was recorded using a time-lapse imaging system. The role of actin-myosin interaction in myofibril disassembly was investigated by incubating cardiomyocytes with blebbistatin (25 µM). Results demonstrated that the hierarchical disassembly process of myofibrils was initiated from cardiomyocyte free ends where intercalated discs had broken, during which the desmin network near the free cell ends was destroyed to release single myofibrils. Analysis of force (based on a schematic model of cardiomyocytes connected at intercalated discs) suggests that breaking of intercalated discs caused force imbalance on both sides of the Z-discs adjacent to the cell ends due to actin-myosin interaction. The damaged intercalated discs and actin-myosin interaction induced force imbalance on both sides of the Z-discs, which played an important role in the hierarchical disassembly of myofibrils. © 2016 Wiley Periodicals, Inc.

Microelectrode Array-evaluation of Neurotoxic Effects of Magnesium as an Implantable Biomaterial.

Magnesium (Mg)-based biomaterials have shown great potential in clinical applications. However, the cytotoxic effects of excessive Mg2+ and the corrosion products from Mg-based biomaterials, particularly their effects on neurons, have been little studied. Although viability tests are most commonly used, a functional evaluation is critically needed. Here, both methyl thiazolyl tetrazolium (MTT) and lactate dehydrogenase (LDH) assays were used to test the effect of Mg2+ and Mg-extract solution on neuronal viability. Microelectrode arrays (MEAs), which provide long-term, real-time recording of extracellular electrophysiological signals of in vitro neuronal networks, were used to test for toxic effects. The minimum effective concentrations (ECmin) of Mg2+ from the MTT and LDH assays were 3 mmol/L and 100 mmol/L, respectively, while the ECmin obtained from the MEA assay was 0.1 mmol/L. MEA data revealed significant loss of neuronal network activity when the culture was exposed to 25% Mg-extract solution, a concentration that did not affect neuronal viability. For evaluating the biocompatibility of Mg-based biomaterials with neurons, MEA electrophysiological testing is a more precise method than basic cell-viability testing.

Biochip-based study of unidirectional mitochondrial transfer from stem cells to myocytes via tunneling nanotubes.

Tunneling nanotubes (TNTs) are small membranous tubes of 50-1000 nm diameter observed to connect cells in culture. Transfer of subcellular organelles through TNTs was observed in vitro and in vivo, but the formation and significance of these structures is not well understood. A polydimethylsiloxane biochip-based coculture model was devised to constrain TNT orientation and explore both TNT-formation and TNT-mediated mitochondrial transfer. Two parallel microfluidic channels connected by an array of smaller microchannels enabled localization of stem cell and cardiomyocyte populations while allowing connections to form between them. Stem cells and cardiomyocytes were deposited in their respective microfluidic channels, and stem cell-cardiomyocyte pairs were formed via the microchannels. Formation of TNTs and transfer of stained mitochondria through TNTs was observed by 24 h real-time video recording. The data show that stem cells are 7.7 times more likely to initiate contact by initial extension of filopodia. By 24 h, 67% of nanotube connections through the microchannels are composed of cardiomyocyte membrane. Filopodial extension and retraction by stem cells draws an extension of TNTs from cardiomyocytes. MitoTracker staining shows that unidirectional transfer of mitochondria between stem cell-cardiomyocyte pairs invariably originates from stem cells. Control experiments with cardiac fibroblasts and cardiomyocytes show little nanotube formation between homotypic or mixed cell pairs and no mitochondrial transfer. These data identify a novel biological process, unidirectional mitochondrial transfer, mediated by heterotypic TNT connections. This suggests that the enhancement of cardiomyocyte function seen after stem-cell injection may be due to a bioenergetic stimulus provided by mitochondrial transfer.

Dynamic Myofibrillar Remodeling in Live Cardiomyocytes under Static Stretch.

An increase in mechanical load in the heart causes cardiac hypertrophy, either physiologically (heart development, exercise and pregnancy) or pathologically (high blood pressure and heart-valve regurgitation). Understanding cardiac hypertrophy is critical to comprehending the mechanisms of heart development and treatment of heart disease. However, the major molecular event that occurs during physiological or pathological hypertrophy is the dynamic process of sarcomeric addition, and it has not been observed. In this study, a custom-built second harmonic generation (SHG) confocal microscope was used to study dynamic sarcomeric addition in single neonatal CMs in a 3D culture system under acute, uniaxial, static, sustained stretch. Here we report, for the first time, live-cell observations of various modes of dynamic sarcomeric addition (and how these real-time images compare to static images from hypertrophic hearts reported in the literature): 1) Insertion in the mid-region or addition at the end of a myofibril; 2) Sequential addition with an existing myofibril as a template; and 3) Longitudinal splitting of an existing myofibril. The 3D cell culture system developed on a deformable substrate affixed to a stretcher and the SHG live-cell imaging technique are unique tools for real-time analysis of cultured models of hypertrophy.

Fringe projection 3D microscopy with the general imaging model.

Three-dimensional (3D) imaging and metrology of microstructures is a critical task for the design, fabrication, and inspection of microelements. Newly developed fringe projection 3D microscopy is presented in this paper. The system is configured according to camera-projector layout and long working distance lenses. The Scheimpflug principle is employed to make full use of the limited depth of field. For such a specific system, the general imaging model is introduced to reach a full 3D reconstruction. A dedicated calibration procedure is developed to realize quantitative 3D imaging. Experiments with a prototype demonstrate the accessibility of the proposed configuration, model, and calibration approach.