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Bíró P, Novák T, Czvik E, Mihály J, Szikora S, van de Linde S, Erdélyi M. Triggered cagedSTORM microscopy. BIOMEDICAL OPTICS EXPRESS 2024; 15:3715-3726. [PMID: 38867795 PMCID: PMC11166440 DOI: 10.1364/boe.517480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 06/14/2024]
Abstract
In standard SMLM methods, the photoswitching of single fluorescent molecules and the data acquisition processes are independent, which leads to the detection of single molecule blinking events on several consecutive frames. This mismatch results in several data points with reduced localization precision, and it also increases the possibilities of overlapping. Here we discuss how the synchronization of the fluorophores' ON state to the camera exposure time increases the average intensity of the captured point spread functions and hence improves the localization precision. Simulations and theoretical results show that such synchronization leads to fewer localizations with 15% higher sum signal on average, while reducing the probability of overlaps by 10%.
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Affiliation(s)
- Péter Bíró
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
| | - Tibor Novák
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
| | - Elvira Czvik
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
| | - József Mihály
- Institute of Genetics, HUN-REN Biological Research Centre Szeged, Temesvári körút 62, Szeged 6726, Hungary
- Department of Genetics, University of Szeged, Közép fasor 52, Szeged 6726, Hungary
| | - Szilárd Szikora
- Institute of Genetics, HUN-REN Biological Research Centre Szeged, Temesvári körút 62, Szeged 6726, Hungary
| | - Sebastian van de Linde
- Department of Physics, SUPA, University of Strathclyde, Glasgow G4 0NG, Scotland, United Kingdom
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Dóm tér 9, Szeged 6720, Hungary
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Application of Lacunarity for Quantification of Single Molecule Localization Microscopy Images. Cells 2022; 11:cells11193105. [PMID: 36231067 PMCID: PMC9562870 DOI: 10.3390/cells11193105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 09/27/2022] [Accepted: 09/30/2022] [Indexed: 11/23/2022] Open
Abstract
The quantitative analysis of datasets achieved by single molecule localization microscopy is vital for studying the structure of subcellular organizations. Cluster analysis has emerged as a multi-faceted tool in the structural analysis of localization datasets. However, the results it produces greatly depend on the set parameters, and the process can be computationally intensive. Here we present a new approach for structural analysis using lacunarity. Unlike cluster analysis, lacunarity can be calculated quickly while providing definitive information about the structure of the localizations. Using simulated data, we demonstrate how lacunarity results can be interpreted. We use these interpretations to compare our lacunarity analysis with our previous cluster analysis-based results in the field of DNA repair, showing the new algorithm’s efficiency.
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Sinha NR, Tripathi R, Balne PK, Green SL, Sinha PR, Bunyak F, Giuliano EA, Chaurasia SS, Mohan RR. Time-dependent in situ structural and cellular aberrations in rabbit cornea in vivo after mustard gas exposure. Exp Eye Res 2022; 224:109247. [PMID: 36113569 DOI: 10.1016/j.exer.2022.109247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/23/2022] [Accepted: 09/07/2022] [Indexed: 11/19/2022]
Abstract
An array of corneal pathologies collectively called mustard gas keratopathy (MGK) resulting from ocular exposure to sulfur mustard (SM) gas are the most prevalent chemical warfare injury. MGK involves chronic ocular discomfort that results in vision impairment. The etiology of MGK remains unclear and poorly understood primarily due to a lack of scientific data regarding structural and cellular changes in different layers of the cornea altered by mustard vapor exposure in vivo. The goals of this study were to (a) characterize time-dependent changes in different layers of corneal epithelium, stroma, and endothelium in live animals in situ by employing state-of-the-art multimodal clinical ophthalmic imaging techniques and (b) determine if SM-induced acute changes in corneal cells could be rescued by a topical eye drop (TED) treatment using in an established rabbit in vivo model. Forty-five New Zealand White Rabbit eyes were divided into four groups (Naïve, TED, SM, and SM + TED). Only one eye was exposed to SM (200 mg-min/m3 for 8 min), and each group had three time points with six eyes each (Table-1). TED was topically applied twice a day for seven days. Clinical eye examinations and imaging were performed in live rabbits with stereo, Slit-lamp, HRT-RCM3, and Spectralis microscopy system. Fantes grading, fluorescein staining, Schirmer's tests, and applanation tonometry were conducted to measure corneal haze, ocular surface aberrations, tears, and intraocular pressure respectively. H&E and PSR staining were used for histopathological cellular changes in the cornea. In vivo confocal and OCT imaging revealed significant changes in structural and morphological appearance of corneal epithelium, stroma, and endothelium in vivo in SM-exposed rabbit corneas in a time-dependent manner compared to naïve cornea. Also, SM-exposed eyes showed loss of corneal transparency characterized by increased stromal thickness and light-scattering myofibroblasts or activated keratocytes, representing haze formation in the cornea. Neither naive nor TED-alone treated eyes showed any structural, cellular, and functional abnormalities. Topical TED treatment significantly reduced SM-induced abnormalities in primary corneal layers. We conclude that structural and cellular changes in primary corneal layers are early pathological events contributing to MGK in vivo, and efficient targeting of them with suitable agents has the potential to mitigate SM ocular injury.
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Affiliation(s)
- Nishant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - Ratnakar Tripathi
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - Praveen K Balne
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - Sydney L Green
- Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - Prashant R Sinha
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - Filiz Bunyak
- Departments of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO, USA
| | - Elizabeth A Giuliano
- Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA
| | - Shyam S Chaurasia
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA; Ocular Immunology and Angiogenesis Lab, Department of Ophthalmology & Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Rajiv R Mohan
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO, USA; Departments of Veterinary Medicine & Surgery and Biomedical Sciences, University of Missouri, Columbia, MO, USA; Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO, USA.
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Bolaños P, Calderón JC. Excitation-contraction coupling in mammalian skeletal muscle: Blending old and last-decade research. Front Physiol 2022; 13:989796. [PMID: 36117698 PMCID: PMC9478590 DOI: 10.3389/fphys.2022.989796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
The excitation–contraction coupling (ECC) in skeletal muscle refers to the Ca2+-mediated link between the membrane excitation and the mechanical contraction. The initiation and propagation of an action potential through the membranous system of the sarcolemma and the tubular network lead to the activation of the Ca2+-release units (CRU): tightly coupled dihydropyridine and ryanodine (RyR) receptors. The RyR gating allows a rapid, massive, and highly regulated release of Ca2+ from the sarcoplasmic reticulum (SR). The release from triadic places generates a sarcomeric gradient of Ca2+ concentrations ([Ca2+]) depending on the distance of a subcellular region from the CRU. Upon release, the diffusing Ca2+ has multiple fates: binds to troponin C thus activating the contractile machinery, binds to classical sarcoplasmic Ca2+ buffers such as parvalbumin, adenosine triphosphate and, experimentally, fluorescent dyes, enters the mitochondria and the SR, or is recycled through the Na+/Ca2+ exchanger and store-operated Ca2+ entry (SOCE) mechanisms. To commemorate the 7th decade after being coined, we comprehensively and critically reviewed “old”, historical landmarks and well-established concepts, and blended them with recent advances to have a complete, quantitative-focused landscape of the ECC. We discuss the: 1) elucidation of the CRU structures at near-atomic resolution and its implications for functional coupling; 2) reliable quantification of peak sarcoplasmic [Ca2+] using fast, low affinity Ca2+ dyes and the relative contributions of the Ca2+-binding mechanisms to the whole concert of Ca2+ fluxes inside the fibre; 3) articulation of this novel quantitative information with the unveiled structural details of the molecular machinery involved in mitochondrial Ca2+ handing to understand how and how much Ca2+ enters the mitochondria; 4) presence of the SOCE machinery and its different modes of activation, which awaits understanding of its magnitude and relevance in situ; 5) pharmacology of the ECC, and 6) emerging topics such as the use and potential applications of super-resolution and induced pluripotent stem cells (iPSC) in ECC. Blending the old with the new works better!
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Affiliation(s)
- Pura Bolaños
- Laboratory of Cellular Physiology, Centre of Biophysics and Biochemistry, Venezuelan Institute for Scientific Research (IVIC), Caracas, Venezuela
| | - Juan C. Calderón
- Physiology and Biochemistry Research Group-PHYSIS, Faculty of Medicine, University of Antioquia, Medellín, Colombia
- *Correspondence: Juan C. Calderón,
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Gupta S, Buyank F, Sinha NR, Grant DG, Sinha PR, Iozzo RV, Chaurasia SS, Mohan RR. Decorin regulates collagen fibrillogenesis during corneal wound healing in mouse in vivo. Exp Eye Res 2022; 216:108933. [PMID: 35031282 PMCID: PMC8885890 DOI: 10.1016/j.exer.2022.108933] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/14/2021] [Accepted: 01/05/2022] [Indexed: 12/22/2022]
Abstract
A characteristic rigid spatial arrangement of collagen fibrils in the stroma is critical for corneal transparency. This unique organization of collagen fibrils in corneal stroma can be impacted by the presence and interactions of proteoglycans and extracellular matrix (ECM) proteins in a corneal microenvironment. Earlier studies revealed that decorin, a leucine-rich proteoglycan in stroma, regulates keratocyte-collagen matrix assembly and wound healing in the cornea. This study investigated the role of decorin in the regulation of stromal fibrillogenesis and corneal transparency in vivo employing a loss-of-function genetic approach using decorin null (dcn-/-) and wild type (dcn+/+) mice and a standard alkali-injury model. A time-dependent ocular examinations with Slit lamp microscope in live animals assessed corneal clarity, haze, and neovascularization levels in normal and injured eyes. Morphometric changes in normal and injured dcn+/+ and dcn-/- corneas, post-euthanasia, were analyzed with Masson's Trichrome and Periodic Acid-Schiff (PAS) histology evaluations. The ultrastructure changes in all corneas were investigated with transmission electron microscopy (TEM). Injury to eye produced clinically relevant corneal haze and neovascularization in dcn-/- and dcn+/+ mice while corneas of uninjured eyes remained clear and avascular. A clinically significant haze and neovascularization appeared in injured dcn-/- corneas compared to the dcn+/+ corneas at day 21 post-injury and not at early tested times. Histological examinations revealed noticeably abnormal morphology and compromised collagen levels in injured dcn-/- corneas compared to the injured/normal dcn+/+ and uninjured dcn-/- corneas. TEM analysis exhibited remarkably uneven collagen fibrils size and distribution in the stroma with asymmetrical organization and loose packing in injured dcn-/- corneas than injured/normal dcn+/+ and uninjured dcn-/- corneas. The minimum and maximum inter-fibril distances were markedly irregular in injured dcn-/- corneas compared to all other corneas. Together, results of clinical, histological, and ultrastructural investigations in a genetic knockout model suggested that decorin influenced stromal fibrillogenesis and transparency in healing cornea.
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Affiliation(s)
- Suneel Gupta
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, USA.,Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Filiz Buyank
- Department of Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Nihant R. Sinha
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, USA.,Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - DeAna G. Grant
- Electron Microscopy Core, University of Missouri, Columbia, Missouri, USA
| | - Prashant R. Sinha
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, USA.,Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Renato V. Iozzo
- Department of Pathology, Anatomy, and Cell Biology, and Translational Cellular Oncology Program, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Shyam S. Chaurasia
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, USA.,Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Rajiv R. Mohan
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, USA.,Departments of Veterinary Medicine & Surgery and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA.,Mason Eye Institute, School of Medicine, University of Missouri, Columbia, Missouri, USA.,Corresponding author: Rajiv R. Mohan, MS, PhD, FARVO, Professor of Ophthalmology & Molecular Medicine, University of Missouri, 1600 E. Rollins Rd, Columbia, MO 65211,
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Sinha NR, Balne PK, Bunyak F, Hofmann AC, Lim RR, Mohan RR, Chaurasia SS. Collagen matrix perturbations in corneal stroma of Ossabaw mini pigs with type 2 diabetes. Mol Vis 2021; 27:666-678. [PMID: 35002212 PMCID: PMC8684810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 12/05/2021] [Indexed: 11/17/2022] Open
Abstract
Purpose Diabetes mellitus (DM) is a metabolic disorder that affects over 450 million people worldwide. DM is characterized by hyperglycemia, causing severe systemic damage to the heart, kidneys, skin, vasculature, nerves, and eye. Type 2 diabetes (T2DM) constitutes 90% of clinical cases and is the most common cause of blindness in working adults. Also, about 70% of T2DM patients show corneal complications including delayed wound healing, often described as diabetic keratopathy (DK). Despite the increasing severity of DM, the research on DK is bleak. This study investigated cellular morphology and collagen matrix alterations of the diabetic and non-diabetic corneas collected from Ossabaw mini pigs, a T2DM animal model with a "thrifty genotype." Methods Pig corneas were collected from six-month-old Ossabaw miniature pigs fed on a western diet (WD) for ten weeks. The tissues were processed for immunohistochemistry and analyzed using hematoxylin and eosin staining, Mason Trichrome staining, Picrosirus Red staining, Collage I staining, and TUNEL assay. mRNA was prepared to quantify fibrotic gene expression using quantitative reverse-transcriptase PCR (qRT-PCR). Transmission electron microscopy (TEM) was performed to evaluate stromal fibril arrangements to compare collagen dynamics in WD vs. standard diet (SD) fed Ossabaw pig corneas. Results Ossabaw mini pigs fed on a WD for 10 weeks exhibit classic symptoms of metabolic syndrome and hyperglycemia seen in T2DM patients. We observed significant disarray in cornea stromal collagen matrix in Ossabaw mini pigs fed on WD compared to the age-matched mini pigs fed on a standard chow diet using Masson Trichome and Picrosirius Red staining. Furthermore, ultrastructure evaluation using TEM showed alterations in stromal collagen fibril size and organization in diabetic corneas compared to healthy age-matched corneas. These changes were accompanied by significantly decreased levels of Collagen IV and increased expression of matrix metallopeptidase 9 in WD-fed pigs. Conclusions This pilot study indicates that Ossabaw mini pigs fed on WD showed collagen disarray and altered gene expression involved in wound healing, suggesting that corneal stromal collagens are vulnerable to diabetic conditions.
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Affiliation(s)
- Nishant R. Sinha
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Departments of Ophthalmology and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Praveen K. Balne
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Departments of Ophthalmology and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Filiz Bunyak
- Department of Computer Science, University of Missouri, Columbia, MO
| | - Alexandria C. Hofmann
- One-Health Vision Research Program, Departments of Ophthalmology and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
| | - Rayne R. Lim
- Department of Ophthalmology, University of Washington, Seattle, WA
| | - Rajiv R. Mohan
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO
- One-Health Vision Research Program, Departments of Ophthalmology and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
- Mason Eye Institute, School of Medicine, University of Missouri, Columbia, MO
| | - Shyam S. Chaurasia
- One-Health Vision Research Program, Departments of Ophthalmology and Biomedical Sciences, College of Veterinary Medicine, University of Missouri, Columbia, MO
- Department of Ophthalmology and Visual Sciences, The Eye Institute, Medical College of Wisconsin, Milwaukee, WI
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Sun Y. Potential quality improvement of stochastic optical localization nanoscopy images obtained by frame by frame localization algorithms. Sci Rep 2020; 10:11844. [PMID: 32678167 PMCID: PMC7367355 DOI: 10.1038/s41598-020-68564-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022] Open
Abstract
A data movie of stochastic optical localization nanoscopy contains spatial and temporal correlations, both providing information of emitter locations. The majority of localization algorithms in the literature estimate emitter locations by frame-by-frame localization (FFL), which exploit only the spatial correlation and leave the temporal correlation into the FFL nanoscopy images. The temporal correlation contained in the FFL images, if exploited, can improve the localization accuracy and the image quality. In this paper, we analyze the properties of the FFL images in terms of root mean square minimum distance (RMSMD) and root mean square error (RMSE). It is shown that RMSMD and RMSE can be potentially reduced by a maximum fold equal to the square root of the average number of activations per emitter. Analyzed and revealed are also several statistical properties of RMSMD and RMSE and their relationship with respect to a large number of data frames, bias and variance of localization errors, small localization errors, sample drift, and the worst FFL image. Numerical examples are taken and the results confirm the prediction of analysis. The ideas about how to develop an algorithm to exploit the temporal correlation of FFL images are also briefly discussed. The results suggest development of two kinds of localization algorithms: the algorithms that can exploit the temporal correlation of FFL images and the unbiased localization algorithms.
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Affiliation(s)
- Yi Sun
- Electrical Engineering Department, Nanoscopy Laboratory, The City College of City University of New York, New York, NY, 10031, USA.
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Wu J, Li S, Zhang S, Lin D, Yu B, Qu J. Fast analysis method for stochastic optical reconstruction microscopy using multiple measurement vector model sparse Bayesian learning. OPTICS LETTERS 2018; 43:3977-3980. [PMID: 30106931 DOI: 10.1364/ol.43.003977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 07/09/2018] [Indexed: 06/08/2023]
Abstract
Compressed sensing (CS) can be used in fluorescence microscopy to improve the temporal resolution of stochastic optical reconstruction microscopy (STORM). Currently, most algorithms used in CS-STORM belong to the single measurement vector (SMV) model, where each super-resolution image is recovered individually from a raw frame, thereby prolonging the computational time. Here, we apply the multiple measurement vector (MMV) model CS algorithm to STORM, wherein all raw images are converted into a matrix and recovered by solving the simultaneous sparse recovery problem. We use the MMV model-based sparse Bayesian learning (SBL) algorithm to reconstitute the raw images of STORM, then compare its imaging resolution and run time with the SMV model CS algorithms. The simulated and experimentally recovered super-resolution images prove that the resolution of MMV model SBL (M-SBL) is comparable with the SMV model algorithm, while the run time is far less and decreases from several hours to several minutes. The high resolution and shorter reconstitution time make M-SBL a promising real-time image reconstruction method for CS-STORM.
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Bunyak F, Shiraishi N, Palaniappan K, Lever TE, Avivi-Arber L, Takahashi K. Development of semi-automatic procedure for detection and tracking of fiducial markers for orofacial kinematics during natural feeding. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017; 2017:580-583. [PMID: 29059939 PMCID: PMC5787344 DOI: 10.1109/embc.2017.8036891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Feeding is a highly complex, essential behavior for survival in all species. Characterization of feeding behaviors has implications in basic science and translational medicine. We have been developing methods to study feeding behaviors using high speed videofluoroscopy (XROMM) in rats while self-feeding radiopaque flavored kibble. The rat is a popular model in translational medicine; however, it has not been studied using this methodology. Towards this goal, we surgically implanted radiopaque fiducial markers into the skull, mandible, and tongue of rats to enable motion tracking. We are developing computer vision tools to extract kinematics and behavioral features from XROMM videos to overcome barriers of current analysis methods. By understanding feeding dynamics, we will gain basic scientific knowledge and translational insights for feeding disorders caused by neurological conditions such as ALS, Parkinson's disease, and stroke.
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10
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Gronkiewicz KM, Giuliano EA, Kuroki K, Bunyak F, Sharma A, Teixeira LBC, Hamm CW, Mohan RR. Development of a novel in vivo corneal fibrosis model in the dog. Exp Eye Res 2015; 143:75-88. [PMID: 26450656 DOI: 10.1016/j.exer.2015.09.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 09/09/2015] [Accepted: 09/16/2015] [Indexed: 12/11/2022]
Abstract
The aim of this study was to develop a novel in vivo corneal model of fibrosis in dogs utilizing alkali burn and determine the ability of suberanilohydroxamic acid (SAHA) to inhibit corneal fibrosis using this large animal model. To accomplish this, we used seven research Beagle dogs. An axial corneal alkali burn in dogs was created using 1 N NaOH topically. Six dogs were randomly and equally assigned into 2 groups: A) vehicle (DMSO, 2 μL/mL); B) anti-fibrotic treatment (50 μM SAHA). The degree of corneal opacity, ocular health, and anti-fibrotic effects of SAHA were determined utilizing the Fantes grading scale, modified McDonald-Shadduck (mMS) scoring system, optical coherence tomography (OCT), corneal histopathology, immunohistochemistry (IHC), and transmission electron microscopy (TEM). The used alkali burn dose to produce corneal fibrosis was well tolerated as no significant difference in mMS scores between control and treatment groups (p = 0.89) were detected. The corneas of alkali burned dogs showed significantly greater levels of α-smooth muscle actin, the fibrotic marker, than the controls (p = 0.018). Total corneal thickness of all dogs post-burn was significantly greater than baseline OCT images irrespective of treatment (p = 0.004); TEM showed that alkali burned corneas had significantly greater minimum and maximum interfibrillar distances than the controls (p = 0.026, p = 0.018). The tested topical corneal alkali burn dose generated significant opacity and fibrosis in dog corneas without damaging the limbus as evidenced by histopathology, IHC, TEM, and OCT findings, and represents a viable large animal corneal fibrosis in vivo model. Additional in vivo SAHA dosing studies with larger sample size are warranted.
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Affiliation(s)
- K M Gronkiewicz
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Columbia, MO, USA; Harry S. Truman Memorial Veteran Hospital, Columbia, MO, USA
| | - E A Giuliano
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Columbia, MO, USA; Harry S. Truman Memorial Veteran Hospital, Columbia, MO, USA
| | - K Kuroki
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Columbia, MO, USA
| | - F Bunyak
- Department of Computer Science, University of Missouri, Columbia, MO, USA
| | - A Sharma
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Columbia, MO, USA; Harry S. Truman Memorial Veteran Hospital, Columbia, MO, USA
| | - L B C Teixeira
- Department of Pathological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, WI, USA
| | - C W Hamm
- Mason Eye Institute, University of Missouri, Columbia, MO, USA
| | - R R Mohan
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, Columbia, MO, USA; Harry S. Truman Memorial Veteran Hospital, Columbia, MO, USA; Mason Eye Institute, University of Missouri, Columbia, MO, USA.
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11
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Huang J, Gumpper K, Chi Y, Sun M, Ma J. Fast two-dimensional super-resolution image reconstruction algorithm for ultra-high emitter density. OPTICS LETTERS 2015; 40:2989-92. [PMID: 26125349 PMCID: PMC4727250 DOI: 10.1364/ol.40.002989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Single-molecule localization microscopy achieves sub-diffraction-limit resolution by localizing a sparse subset of stochastically activated emitters in each frame. Its temporal resolution is limited by the maximal emitter density that can be handled by the image reconstruction algorithms. Multiple algorithms have been developed to accurately locate the emitters even when they have significant overlaps. Currently, compressive-sensing-based algorithm (CSSTORM) achieves the highest emitter density. However, CSSTORM is extremely computationally expensive, which limits its practical application. Here, we develop a new algorithm (MempSTORM) based on two-dimensional spectrum analysis. With the same localization accuracy and recall rate, MempSTORM is 100 times faster than CSSTORM with ℓ(1)-homotopy. In addition, MempSTORM can be implemented on a GPU for parallelism, which can further increase its computational speed and make it possible for online super-resolution reconstruction of high-density emitters.
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Affiliation(s)
- Jiaqing Huang
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, Ohio 43210, USA
| | - Kristyn Gumpper
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
| | - Yuejie Chi
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, Ohio 43210, USA
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, USA
| | - Mingzhai Sun
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
- Corresponding author:
| | - Jianjie Ma
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
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12
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Jayasinghe ID, Clowsley AH, Munro M, Hou Y, Crossman DJ, Soeller C. Revealing T-Tubules in Striated Muscle with New Optical Super-Resolution Microscopy Techniquess. Eur J Transl Myol 2014; 25:4747. [PMID: 26913143 PMCID: PMC4748971 DOI: 10.4081/ejtm.2015.4747] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/18/2014] [Indexed: 01/03/2023] Open
Abstract
The t-tubular system plays a central role in the synchronisation of calcium signalling and excitation-contraction coupling in most striated muscle cells. Light microscopy has been used for imaging t-tubules for well over 100 years and together with electron microscopy (EM), has revealed the three-dimensional complexities of the t-system topology within cardiomyocytes and skeletal muscle fibres from a range of species. The emerging super-resolution single molecule localisation microscopy (SMLM) techniques are offering a near 10-fold improvement over the resolution of conventional fluorescence light microscopy methods, with the ability to spectrally resolve nanometre scale distributions of multiple molecular targets. In conjunction with the next generation of electron microscopy, SMLM has allowed the visualisation and quantification of intricate t-tubule morphologies within large areas of muscle cells at an unprecedented level of detail. In this paper, we review recent advancements in the t-tubule structural biology with the utility of various microscopy techniques. We outline the technical considerations in adapting SMLM to study t-tubules and its potential to further our understanding of the molecular processes that underlie the sub-micron scale structural alterations observed in a range of muscle pathologies.
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Affiliation(s)
| | | | - Michelle Munro
- Department of Physiology, The University of Auckland , New Zealand
| | - Yufeng Hou
- Department of Physiology, The University of Auckland , New Zealand
| | - David J Crossman
- Department of Physiology, The University of Auckland , New Zealand
| | - Christian Soeller
- Biomedical Physics, University of Exeter, UK, New Zealand; Biomedical Physics, University of Exeter, UK, New Zealand
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