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Shilpashree PS, Ravi T, Thanuja MY, Anupama C, Ranganath SH, Suresh KV, Srinivas SP. Grading the Severity of Damage to the Perijunctional Actomyosin Ring and Zonula Occludens-1 of the Corneal Endothelium by Ensemble Learning Methods. J Ocul Pharmacol Ther 2023. [PMID: 36930844 DOI: 10.1089/jop.2022.0154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
Purpose: In many epithelia, including the corneal endothelium, intracellular/extracellular stresses break down the perijunctional actomyosin ring (PAMR) and zonula occludens-1 (ZO-1) at the apical junctions. This study aims to grade the severity of damage to PAMR and ZO-1 through machine learning. Methods: Immunocytochemical images of PAMR and ZO-1 were drawn from recent studies on the corneal endothelium subjected to hypothermia and oxidative stress. The images were analyzed for their morphological (e.g., Hu moments) and textural features (based on gray-level co-occurrence matrix [GLCM] and Gabor filters). The extracted features were ranked by SHapley analysis and analysis of variance. Then top features were used to grade the severity of damage using a suite of ensemble classifiers, including random forest, bagging classifier (BC), AdaBoost, extreme gradient boosting, and stacking classifier. Results: A partial set of features from GLCM, along with Hu moments and the number of hexagons, enabled the classification of damage to PAMR into Control, Mild, Moderate, and Severe with the area under the receiver operating characteristics curve (AUC) = 0.92 and F1 score = 0.77 with BC. In contrast, a bank of Gabor filters provided a partial set of features that could be combined with Hu moments, branch length, and sharpness for the classification of ZO-1 images into four levels with AUC = 0.95 and F1 score of 0.8 with BC. Conclusions: We have developed a workflow that enables the stratification of damage to PAMR and ZO-1. The approach can be applied to similar data during drug discovery or pathophysiological studies of epithelia.
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Affiliation(s)
- Palanahalli S Shilpashree
- Department of Electronics and Communication, Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Tapanmitra Ravi
- School of Optometry, Indiana University, Bloomington, Indiana, USA
| | - M Y Thanuja
- Department of Chemical Engineering, and Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Chalimeswamy Anupama
- Department of Biotechnology, Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Sudhir H Ranganath
- Department of Chemical Engineering, and Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
| | - Kaggere V Suresh
- Department of Electronics and Communication, Siddaganga Institute of Technology (Affiliated to VTU, Belagavi), Tumakuru, India
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Moreno-Mármol T, Ledesma-Terrón M, Tabanera N, Martin-Bermejo MJ, Cardozo MJ, Cavodeassi F, Bovolenta P. Stretching of the retinal pigment epithelium contributes to zebrafish optic cup morphogenesis. eLife 2021; 10:63396. [PMID: 34545806 PMCID: PMC8530511 DOI: 10.7554/elife.63396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 09/20/2021] [Indexed: 12/15/2022] Open
Abstract
The vertebrate eye primordium consists of a pseudostratified neuroepithelium, the optic vesicle (OV), in which cells acquire neural retina or retinal pigment epithelium (RPE) fates. As these fates arise, the OV assumes a cup shape, influenced by mechanical forces generated within the neural retina. Whether the RPE passively adapts to retinal changes or actively contributes to OV morphogenesis remains unexplored. We generated a zebrafish Tg(E1-bhlhe40:GFP) line to track RPE morphogenesis and interrogate its participation in OV folding. We show that, in virtual absence of proliferation, RPE cells stretch and flatten, thereby matching the retinal curvature and promoting OV folding. Localized interference with the RPE cytoskeleton disrupts tissue stretching and OV folding. Thus, extreme RPE flattening and accelerated differentiation are efficient solutions adopted by fast-developing species to enable timely optic cup formation. This mechanism differs in amniotes, in which proliferation drives RPE expansion with a much-reduced need of cell flattening. Rounded eyeballs help to optimize vision – but how do they acquire their distinctive shape? In animals with backbones, including humans, the eye begins to form early in development. A single layer of embryonic tissue called the optic vesicle reorganizes itself into a two-layered structure: a thin outer layer of cells, known as the retinal pigmented epithelium (RPE for short), and a thicker inner layer called the neural retina. If this process fails, the animal may be born blind or visually impaired. How this flat two-layered structure becomes round is still being investigated. In fish, studies have shown that the inner cell layer – the neural retina – generates mechanical forces that cause the developing tissue to curve inwards to form a cup-like shape. But it was unclear whether the outer layer of cells (the RPE) also contributed to this process. Moreno-Marmol et al. were able to investigate this question by genetically modifying zebrafish to make all new RPE cells fluoresce. Following the early development of the zebrafish eye under a microscope revealed that RPE cells flattened themselves into long thin structures that stretched to cover the entire neural retina. This change was made possible by the cell’s internal skeleton reorganizing. In fact, preventing this reorganization stopped the RPE cells from flattening, and precluded the optic cup from acquiring its curved shape. The results thus confirmed a direct role for the RPE in generating curvature. The entire process did not require the RPE to produce new cells, allowing the curved shape to emerge in just a few hours. This is a major advantage for fast-developing species such as zebrafish. In species whose embryos develop more slowly, such as mice and humans, the RPE instead grows by producing additional cells – a process that takes many days. The development of the eye thus shows how various species use different evolutionary approaches to achieve a common goal.
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Affiliation(s)
- Tania Moreno-Mármol
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Mario Ledesma-Terrón
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain
| | - Noemi Tabanera
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Maria Jesús Martin-Bermejo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Marcos J Cardozo
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Florencia Cavodeassi
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Paola Bovolenta
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, c/ Nicolás Cabrera, 1, Campus de la Universidad Autónoma de Madrid, Madrid, Spain.,CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
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Ul-Hasan S, Rodríguez-Román E, Reitzel AM, Adams RMM, Herzig V, Nobile CJ, Saviola AJ, Trim SA, Stiers EE, Moschos SA, Keiser CN, Petras D, Moran Y, Colston TJ. The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP). Toxicon X 2019; 4:100016. [PMID: 32550573 PMCID: PMC7286055 DOI: 10.1016/j.toxcx.2019.100016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date with the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remaining largely unknown. We highlight the potential for the discovery of venom microbiomes within the adaptive landscape of venom systems. The considerable number of convergently evolved venomous animals, juxtaposed with the comparatively few known studies to identify microbial communities in venom, provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics (i.e., venom-microbiomics) and introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing collaborative consortium. We express commitment to the diversity, inclusion and scientific collaboration among researchers interested in this emerging subdiscipline through expansion of the iVAMP consortium. Venom-microbiome studies as an integrative field of venomics and microbiology. Argument for multi-omics-based discovery through a microenvironment framework. Introduction of a venom-microbiome research consortium (iVAMP).
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Affiliation(s)
- Sabah Ul-Hasan
- Quantitative and Systems Biology Graduate Program, University of California Merced, Merced, CA, 95343, USA.,Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Eduardo Rodríguez-Román
- Center for Microbiology and Cell Biology, Venezuelan Institute for Scientific Research. Caracas, 1020A, Venezuela
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Rachelle M M Adams
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, 43212, USA
| | - Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Clarissa J Nobile
- Department of Molecular and Cell Biology, School of Natural Sciences, University of California Merced, Merced, CA, 95343, USA
| | - Anthony J Saviola
- Department of Molecular Medicine and Neurobiology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Steven A Trim
- Venomtech Ltd, Discovery Park, Sandwich, Kent, CT13 9ND, UK
| | - Erin E Stiers
- Department of Biological Science, Clemson University, Clemson, SC, 29634, USA
| | - Sterghios A Moschos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, NE1 8ST, UK
| | - Carl N Keiser
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, USA.,Scripps Institution of Oceanography, University of California, San Diego, USA
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Timothy J Colston
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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Wu Q, Kumar N, Velagala V, Zartman JJ. Tools to reverse-engineer multicellular systems: case studies using the fruit fly. J Biol Eng 2019; 13:33. [PMID: 31049075 PMCID: PMC6480878 DOI: 10.1186/s13036-019-0161-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/07/2019] [Indexed: 01/08/2023] Open
Abstract
Reverse-engineering how complex multicellular systems develop and function is a grand challenge for systems bioengineers. This challenge has motivated the creation of a suite of bioengineering tools to develop increasingly quantitative descriptions of multicellular systems. Here, we survey a selection of these tools including microfluidic devices, imaging and computer vision techniques. We provide a selected overview of the emerging cross-talk between engineering methods and quantitative investigations within developmental biology. In particular, the review highlights selected recent examples from the Drosophila system, an excellent platform for understanding the interplay between genetics and biophysics. In sum, the integrative approaches that combine multiple advances in these fields are increasingly necessary to enable a deeper understanding of how to analyze both natural and synthetic multicellular systems.
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Affiliation(s)
- Qinfeng Wu
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Nilay Kumar
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Vijay Velagala
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
| | - Jeremiah J. Zartman
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556 USA
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