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Baland E, Pérez Jimenez L, Mateus A. Teaching protein structure and function through molecular visualization. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2024. [PMID: 39230433 DOI: 10.1002/bmb.21860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 08/15/2024] [Accepted: 08/23/2024] [Indexed: 09/05/2024]
Abstract
The function of proteins is governed by their three-dimensional structure. This structure is determined by the chemical characteristics and atomic interactions of amino acids. Students of biochemistry, with a particular focus on protein chemistry, benefit from looking at protein structures and understanding how proteins are built and fold. Due to their three-dimensional nature, static two-dimensional representations in textbooks can be limiting to student learning. Here, we developed a series of tutorials that introduce students to molecular graphics software. The students are challenged to apply the software to look at proteins and to get a deeper understanding of how amino acid properties are linked to structure. We also familiarize students with some of the latest tools in computational structural biology. Students performed the tutorials with visual enthusiasm and reported general satisfaction in being able to visualize theoretical concepts learned during lectures. We further stimulated student engagement by allowing space for self-exploration. We share the tutorial instructions for other teachers to build on them, and we also offer suggestions for further improvement based on student feedback. In summary, we present a series of tutorials aimed at students of an advanced course in protein biochemistry to enable them to explore the universe of protein structures and how those relate to function.
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Affiliation(s)
| | - Lucía Pérez Jimenez
- Department of Chemistry, Umeå University, Umeå, Sweden
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - André Mateus
- Department of Chemistry, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
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2
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Tandori E, Favilla S. Art, science and inclusion: multisensory Sciart of immunology for blind, low-vision and diverse-needs audiences. Immunol Cell Biol 2024; 102:315-320. [PMID: 38693615 DOI: 10.1111/imcb.12759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Art is a powerful tool for conveying scientific discovery. Despite the perceived gap between art and science, as highlighted by CP Snow and others, examples of art communicating science can be found in the ancient world, the Renaissance and contemporary data visualization, demonstrating an enduring and historic connection. However, much of science relies on visual elements, excluding those with blindness, low vision and diverse needs, resulting in their low representation in STEM discourse. This paper introduces a novel science and art collaboration in the form of an exhibition program exploring the concepts of Immunology and Biomedicine to blind and vision-impaired audiences, capitalizing on the lived experience of a legally blind artist. Employing multisensory design, art and co-creation methodologies, it transcends traditional vision-based science communication, showcasing the potential for multisensory art to bridge the gap at the intersection of science and inclusion.
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Affiliation(s)
- Erica Tandori
- Rossjohn Lab, Monash Sensory Science, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Stuart Favilla
- Rossjohn Lab, Monash Sensory Science, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- Department of Communication Design, Swinburne University of Technology, Hawthorn, VIC, Australia
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3
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Pokojná H, Kozlíková B, Berry D, Kriglstein S, Furmanová K. Seeing the unseen: Comparison study of representation approaches for biochemical processes in education. PLoS One 2023; 18:e0293592. [PMID: 37930950 PMCID: PMC10627439 DOI: 10.1371/journal.pone.0293592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 10/06/2023] [Indexed: 11/08/2023] Open
Abstract
The representations of biochemical processes must balance visual portrayals with descriptive content to be an effective learning tool. To determine what type of representation is the most suitable for education, we designed five different representations of adenosine triphosphate (ATP) synthesis and examined how they are perceived. Our representations consisted of an overview of the process in a detailed and abstract illustrative format, continuous video formats with and without narration, and a combined illustrative overview with dynamic components. The five representations were evaluated by non-experts who were randomly assigned one of them and experts who viewed and compared all five representations. Subsequently, we conducted a focus group on the outcomes of these evaluations, which gave insight into possible explanations of our results, where the non-experts preferred the detailed static representation and found the narrated video least helpful, in contradiction to the experts who favored the narrated video the most.
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Affiliation(s)
- Hana Pokojná
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
| | - Barbora Kozlíková
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
| | - Drew Berry
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Simone Kriglstein
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
- AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | - Katarína Furmanová
- Department of Visual Computing, Masaryk University, Brno, Czech Republic
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Shao Y, Wang Z, Wu J, Lu Y, Chen Y, Zhang H, Huang C, Shen H, Xu L, Fu Z. Unveiling immunogenic cell death-related genes in colorectal cancer: an integrated study incorporating transcriptome and Mendelian randomization analyses. Funct Integr Genomics 2023; 23:316. [PMID: 37789099 DOI: 10.1007/s10142-023-01238-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/06/2023] [Accepted: 09/18/2023] [Indexed: 10/05/2023]
Abstract
Immunogenic cell death (ICD), a type of cell death that activates the tumor-specific immune response and thus exerts anti-tumor effects, is an emerging target in tumor therapy, but research on ICD-related genes (ICDGs) in colorectal cancer (CRC) remains limited. This study aimed to identify the CRC-specific ICDGs and explore their potential roles. Through RNA sequencing for tissue samples from CRC patients and integration with The Cancer Genome Atlas (TCGA) data, we identified 33 differentially expressed ICDGs in CRC. We defined the ICD score based on these genes in single-cell data, where a high score indicated an immune-active microenvironment. Additionally, molecular subtypes identified in bulk RNA data showed distinct immune landscapes. The ICD-related signature constructed with machine learning effectively distinguished patients' prognosis. The summary data-based Mendelian randomization (SMR) and colocalization analysis prioritized CFLAR for its positive association with CRC risk. Molecular docking revealed its stable binding with chemotherapeutic drugs like irinotecan. Furthermore, experimental validation confirmed CFLAR overexpression in CRC samples, and its knockdown inhibited tumor cell proliferation. Overall, this study expands the understanding of the potential roles and mechanisms of ICDGs in CRC and highlights CFLAR as a promising target for CRC.
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Affiliation(s)
- Yu Shao
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhenling Wang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jingyu Wu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yunfei Lu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yang Chen
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongqiang Zhang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Changzhi Huang
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hengyang Shen
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lei Xu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zan Fu
- The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China.
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
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5
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Rosignoli S, Paiardini A. Boosting the Full Potential of PyMOL with Structural Biology Plugins. Biomolecules 2022; 12:biom12121764. [PMID: 36551192 PMCID: PMC9775141 DOI: 10.3390/biom12121764] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022] Open
Abstract
Over the past few decades, the number of available structural bioinformatics pipelines, libraries, plugins, web resources and software has increased exponentially and become accessible to the broad realm of life scientists. This expansion has shaped the field as a tangled network of methods, algorithms and user interfaces. In recent years PyMOL, widely used software for biomolecules visualization and analysis, has started to play a key role in providing an open platform for the successful implementation of expert knowledge into an easy-to-use molecular graphics tool. This review outlines the plugins and features that make PyMOL an eligible environment for supporting structural bioinformatics analyses.
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Spalvieri D, Mauviel AM, Lambert M, Férey N, Sacquin-Mora S, Chavent M, Baaden M. Design - a new way to look at old molecules. J Integr Bioinform 2022; 19:jib-2022-0020. [PMID: 35776840 PMCID: PMC9377703 DOI: 10.1515/jib-2022-0020] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/13/2022] [Indexed: 12/25/2022] Open
Abstract
We discuss how design enriches molecular science, particularly structural biology and bioinformatics. We present two use cases, one in academic practice and the other to design for outreach. The first case targets the representation of ion channels and their dynamic properties. In the second, we document a transition process from a research environment to general-purpose designs. Several testimonials from practitioners are given. By describing the design process of abstracted shapes, exploded views of molecular structures, motion-averaged slices, 360-degree panoramic projections, and experiments with lit sphere shading, we document how designers help make scientific data accessible without betraying its meaning, and how a creative mind adds value over purely data-driven visualizations. A similar conclusion was drawn for public outreach, as we found that comic-book-style drawings are better suited for communicating science to a broad audience.
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Affiliation(s)
- Davide Spalvieri
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, UPR 9080, 13 rue Pierre et Marie Curie, F-75005, Paris, France
- Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, Paris, France
| | - Anne-Marine Mauviel
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, UPR 9080, 13 rue Pierre et Marie Curie, F-75005, Paris, France
- Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, Paris, France
| | | | - Nicolas Férey
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, UPR 9080, 13 rue Pierre et Marie Curie, F-75005, Paris, France
- Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, Paris, France
- Université Paris-Saclay, CNRS, Laboratoire Interdisciplinaire des Sciences du Numérique, 91405, Orsay, France
| | - Sophie Sacquin-Mora
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, UPR 9080, 13 rue Pierre et Marie Curie, F-75005, Paris, France
- Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, Paris, France
| | - Matthieu Chavent
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, Université Paul Sabatier, 31400, Toulouse, France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, Université Paris Cité, UPR 9080, 13 rue Pierre et Marie Curie, F-75005, Paris, France
- Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, Paris, France
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7
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Werner E. Strategies for the Production of Molecular Animations. FRONTIERS IN BIOINFORMATICS 2022; 2:793914. [PMID: 36304328 PMCID: PMC9580893 DOI: 10.3389/fbinf.2022.793914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 04/14/2022] [Indexed: 09/06/2024] Open
Abstract
Molecular animations play an increasing role in scientific visualisation and science communication. They engage viewers through non-fictional, documentary type storytelling and aim at advancing the audience. Every scene of a molecular animation is to be designed to secure clarity. To achieve this, knowledge on design principles from various design fields is essential. The relevant principles help to draw attention, guide the eye, establish relationships, convey dynamics and/or trigger a reaction. The tools of general graphic design are used to compose a signature frame, those of cinematic storytelling and user interface design to choreograph the relative movement of characters and cameras. Clarity in a scientific visualisation is reached by simplification and abstraction where the choice of the adequate representation is of great importance. A large set of illustration styles is available to chose the appropriate detail level but they are constrained by the availability of experimental data. For a high-quality molecular animation, data from different sources can be integrated, even filling the structural gaps to show a complete picture of the native biological situation. For maintaining scientific authenticity it is good practice to mark use of artistic licence which ensures transparency and accountability. The design of motion requires knowledge from molecule kinetics and kinematics. With biological macromolecules, four types of motion are most relevant: thermal motion, small and large conformational changes and Brownian motion. The principles of dynamic realism should be respected as well as the circumstances given in the crowded cellular environment. Ultimately, consistent complexity is proposed as overarching principle for the production of molecular animations and should be achieved between communication objective and abstraction/simplification, audience expertise and scientific complexity, experiment and representation, characters and environment as well as structure and motion representation.
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8
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Patterson K, Terrill B, Dorfman BS, Blonder R, Yarden A. Molecular animations in genomics education: designing for whom? Trends Genet 2022; 38:517-520. [DOI: 10.1016/j.tig.2022.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
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9
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Online tools to easily build virtual molecular models for display in augmented and virtual reality on the web. J Mol Graph Model 2022; 114:108164. [PMID: 35325844 DOI: 10.1016/j.jmgm.2022.108164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 11/20/2022]
Abstract
Several groups developed in the last years augmented and virtual reality (AR/VR) software to visualize 3D molecules, most rather static, limited in content, and requiring software installs, some even requiring expensive hardware. We launched in 2020 moleculARweb (https://molecularweb.epfl.ch), a website that offers interactive content for chemistry and structural biology education through commodity web-based AR that works on consumer devices like smartphones, tablets and laptops. Among thousands of users, teachers increasingly request more biological macromolecules to be available, a demand that we cannot address individually. Therefore, to allow users to build their own material, we built a web interface where they can create online AR experiences in few steps starting from Protein Data Bank, AlphaFold or custom uploaded structures, or from virtual objects/scenes exported from the Visual Molecular Dynamics program, without any programming knowledge. The web tool also returns WebXR sessions for viewing and manipulating the models in WebXR-compatible devices including smartphones, tablets, and also immersive VR headsets with WebXR-capable browsers, where models can be manipulated even with bare hands when supported by the device. The tool is accessible for free at https://molecularweb.epfl.ch/pages/pdb2ar.html.
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10
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Kadir SR, Lilja A, Gunn N, Strong C, Hughes RT, Bailey BJ, Rae J, Parton RG, McGhee J. Nanoscape, a data-driven 3D real-time interactive virtual cell environment. eLife 2021; 10:64047. [PMID: 34191720 PMCID: PMC8245131 DOI: 10.7554/elife.64047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Our understanding of cellular and structural biology has reached unprecedented levels of detail, and computer visualisation techniques can be used to create three-dimensional (3D) representations of cells and their environment that are useful in both teaching and research. However, extracting and integrating the relevant scientific data, and then presenting them in an effective way, can pose substantial computational and aesthetic challenges. Here we report how computer artists, experts in computer graphics and cell biologists have collaborated to produce a tool called Nanoscape that allows users to explore and interact with 3D representations of cells and their environment that are both scientifically accurate and visually appealing. We believe that using Nanoscape as an immersive learning application will lead to an improved understanding of the complexities of cellular scales, densities and interactions compared with traditional learning modalities.
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Affiliation(s)
- Shereen R Kadir
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Andrew Lilja
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Nick Gunn
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Campbell Strong
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Rowan T Hughes
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - Benjamin J Bailey
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
| | - James Rae
- Institute for Molecular Bioscience, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Australia
| | - John McGhee
- 3D Visualisation Aesthetics Lab, School of Art and Design, and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney, Australia
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Rachmawati E, Sargowo D, Rohman MS, Widodo N, Kalsum U. miR-155-5p predictive role to decelerate foam cell atherosclerosis through CD36, VAV3, and SOCS1 pathway. Noncoding RNA Res 2021; 6:59-69. [PMID: 33869908 PMCID: PMC8027696 DOI: 10.1016/j.ncrna.2021.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 01/22/2023] Open
Abstract
MicroRNAs (miRNAs) are noncoding RNA molecules that play a significant role in atherosclerosis pathogenesis through post-transcriptional regulation. In the present work, a bioinformatic analysis using TargetScan and miRdB databases was performed to identify the miRNAs targeting three genes involved in foam cell atherosclerosis (CD36, Vav3, and SOCS1). A total number of three hundred and sixty-seven miRNAs were recognized and only miR-155-5p was selected for further evaluation based on Venn analysis. Another objective of this study was to evaluate the biological process and regulatory network of miR-155-5p associated with foam cell atherosclerosis using DIANA, DAVID, Cytoscape, and STRING tools. Additionally, the comprehensive literature review was performed to prove the miR-155-5p function in foam cell atherosclerosis. miR-155-5p might be related with ox-LDL uptake and endocytosis in macrophage cell by targeting CD36 and Vav3 genes which was showed from the KEGG pathways hsa04979, hsa04666, hsa04145 H, hsa04810, and GO:0099632, GO:0060100, GO:0010743, GO:001745. Furthermore, miR-155-5p was also predicted to increase the cholesterol efflux from macrophage by inhibit SOCS1 expression based on KEGG pathway hsa04120. Eleven original studies were included in the review and strongly suggest the role of miR-155-5p in foam cell atherosclerosis inhibition.
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Affiliation(s)
- Ermin Rachmawati
- Doctoral Program of Medical Science, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
- Faculty of Medicine and Health Sciences UIN Maulana Malik Ibrahim Malang
| | - Djanggan Sargowo
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
| | - M. Saifur Rohman
- Department of Cardiology and Vascular Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
- Brawijaya Cardiovascular Research Center
| | - Nashi Widodo
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Brawijaya, Malang, Indonesia
| | - Umi Kalsum
- Department of Pharmacology, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
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Sánchez-Angulo M, López-Goñi I, Cid VJ. Teaching microbiology in times of plague. Int Microbiol 2021; 24:665-670. [PMID: 33942184 PMCID: PMC8092966 DOI: 10.1007/s10123-021-00179-9] [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: 03/30/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 11/30/2022]
Abstract
The COVID-19 pandemic has imposed several challenges and strains at all levels of the educational system, especially as a consequence of lockdown and social distance measures. After a period of exclusive use of the online educational environment, educators have adapted to the new circumstances and, by a combination of different strategies, have fought to overcome the limitations and deficiencies of virtual learning. Student motivation, productivity, and creativity continue to be the main pedagogical issues that have to be reached with the new didactic tools developed during the pandemic. At the same time, this pandemic has shown the importance of the inclusion of microbiology as a core element of the educational curriculum and the opportunity to raise public awareness of the importance of microbes to everyday life.
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Affiliation(s)
- Manuel Sánchez-Angulo
- Departamento de Producción Vegetal y Microbiología, Edificio Torrepinet, Universidad Miguel Hernández, 03202, Elche, Spain.
| | - Ignacio López-Goñi
- Departamento de Microbiología y Parasitología, Universidad de Navarra, 31008, Pamplona, Spain
| | - Víctor J Cid
- Departamento de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid, & Instituto Ramón y Cajal de Investigaciones Sanitarias (IRyCIS), Pza. Ramón y Cajal s/n 28040, Madrid, Spain
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13
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Visualizing protein structures - tools and trends. Biochem Soc Trans 2021; 48:499-506. [PMID: 32196545 DOI: 10.1042/bst20190621] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/01/2020] [Accepted: 03/04/2020] [Indexed: 02/06/2023]
Abstract
Molecular visualization is fundamental in the current scientific literature, textbooks and dissemination materials. It provides an essential support for presenting results, reasoning on and formulating hypotheses related to molecular structure. Tools for visual exploration of structural data have become easily accessible on a broad variety of platforms thanks to advanced software tools that render a great service to the scientific community. These tools are often developed across disciplines bridging computer science, biology and chemistry. This mini-review was written as a short and compact overview for scientists who need to visualize protein structures and want to make an informed decision which tool they should use. Here, we first describe a few 'Swiss Army knives' geared towards protein visualization for everyday use with an existing large user base, then focus on more specialized tools for peculiar needs that are not yet as broadly known. Our selection is by no means exhaustive, but reflects a diverse snapshot of scenarios that we consider informative for the reader. We end with an account of future trends and perspectives.
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14
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Feng G, Jun H, Elaine G, Haitao S. Powdered Activated Charcoal Tracing in Hand Hygiene Training and Compliance Assessment During the COVID-19 Pandemic. Risk Manag Healthc Policy 2021; 14:675-683. [PMID: 33623457 PMCID: PMC7896769 DOI: 10.2147/rmhp.s295551] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/18/2021] [Indexed: 11/23/2022] Open
Abstract
Objective Because of the COVID-19 pandemic there has been a significant increase in the prevalence of nosocomial infections. As a result, we sought to find an effective, efficient and safe way to train healthcare workers on proper hand washing techniques. We used powdered activated carbon (PAC) as a tracer to visually display hand washing defects after the hand washing process. The real-time visual assessment of the efficacy of the hand washing technique aided in the immediate correction of errors, and this definitively improved hand hygiene techniques of the interns. Methods Clinical interns at the emergency department of Shengjing Hospital were included in this study and received training in relation to the six-step hand-washing technique developed by the World Health Organization (WHO). The subjects’ hand-washing defects or faults were traced using PAC and corrected accordingly. Acceptance of the PAC tracing method by the interns, and its safety, were both assessed using a questionnaire survey. Results The results indicated that the back of the hands, fingers, and the wrists were prone to hand-washing defects. The hand-washing defects were significantly reduced after targeted corrections by the trainers. Subjects reported satisfactory acceptance toward the PAC tracing method and the method was relatively safe for subjects. Conclusion The PAC tracing method can visually display hand-washing defects and significantly improve the effectiveness of hand-washing training.
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Affiliation(s)
- Guo Feng
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Han Jun
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Gitonga Elaine
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
| | - Shen Haitao
- Department of Emergency Medicine, Shengjing Hospital of China Medical University, Shenyang, 110004, People's Republic of China
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Mooers BHM, Brown ME. Templates for writing PyMOL scripts. Protein Sci 2021; 30:262-269. [PMID: 33179363 PMCID: PMC7737772 DOI: 10.1002/pro.3997] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/06/2020] [Accepted: 11/10/2020] [Indexed: 11/10/2022]
Abstract
PyMOL commands are used to exert exquisite control over the appearance of a molecular model. This control has made PyMOL popular for making images of protein structures for publications and presentations. However, many users have poor recall of the commands due to infrequent use of PyMOL. This poor recall hinders the writing of new code in scripts. One solution is to build the new script by using code fragments as templates for modular parts of the task at hand. The code fragments can be accessed from a library while writing the code from inside a text editor (e.g., Visual Studio Code, Vim, and Emacs). We developed a library of PyMOL code templates or snippets called pymolsnips to ease the writing of PyMOL code in scripts. We made pymolsnips available on GitHub in formats for 18 popular text editors. Most of the supported text editors are available for Mac, Windows, and Linux operating systems. The GitHub site includes animations that complement the instructions for installing the library for each text editor. We expect that the library will help many PyMOL users to be more productive when writing PyMOL script files.
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Affiliation(s)
- Blaine H. M. Mooers
- Department of Biochemistry and Molecular BiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Stephenson Cancer CenterUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
- Laboratory of Biomolecular Structure and FunctionUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
| | - Marina E. Brown
- Department of Biochemistry and Molecular BiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahomaUSA
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16
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Richardson JS, Richardson DC, Goodsell DS. Seeing the PDB. J Biol Chem 2021; 296:100742. [PMID: 33957126 PMCID: PMC8167287 DOI: 10.1016/j.jbc.2021.100742] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 01/21/2023] Open
Abstract
Ever since the first structures of proteins were determined in the 1960s, structural biologists have required methods to visualize biomolecular structures, both as an essential tool for their research and also to promote 3D comprehension of structural results by a wide audience of researchers, students, and the general public. In this review to celebrate the 50th anniversary of the Protein Data Bank, we present our own experiences in developing and applying methods of visualization and analysis to the ever-expanding archive of protein and nucleic acid structures in the worldwide Protein Data Bank. Across that timespan, Jane and David Richardson have concentrated on the organization inside and between the macromolecules, with ribbons to show the overall backbone "fold" and contact dots to show how the all-atom details fit together locally. David Goodsell has explored surface-based representations to present and explore biological subjects that range from molecules to cells. This review concludes with some ideas about the current challenges being addressed by the field of biomolecular visualization.
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Affiliation(s)
- Jane S Richardson
- Department of Biochemistry, Duke University, Durham, North Carolina, USA.
| | - David C Richardson
- Department of Biochemistry, Duke University, Durham, North Carolina, USA
| | - David S Goodsell
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, California, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, New Jersey, USA.
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17
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Poronnik P, Sellwood MJ. Bioscience education 2030 and beyond: Where will technology take the curriculum? BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:563-567. [PMID: 32745335 DOI: 10.1002/bmb.21393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
This brief review explores the ever-increasing role that technological affordances may play in the 21C biochemistry and molecular biology curriculum. We consider the need to develop digital and creative fluencies in our students and the importance of creativity and visualization in learning science. The potential of virtual reality (VR) platforms to complement these goals are discussed with a number of examples. Finally, we look into the future where to see how VR might fit into a future curriculum.
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Affiliation(s)
- Philip Poronnik
- Discipline of Physiology, School of Medical Sciences, The University of Sydney, Camperdown, New South Wales, Australia
| | - Matthew J Sellwood
- Discipline of Physiology, School of Medical Sciences, The University of Sydney, Camperdown, New South Wales, Australia
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18
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Wang J, Youkharibache P, Zhang D, Lanczycki CJ, Geer RC, Madej T, Phan L, Ward M, Lu S, Marchler GH, Wang Y, Bryant SH, Geer LY, Marchler-Bauer A. iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures. Bioinformatics 2020; 36:131-135. [PMID: 31218344 DOI: 10.1093/bioinformatics/btz502] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/03/2019] [Accepted: 06/13/2019] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Build a web-based 3D molecular structure viewer focusing on interactive structural analysis. RESULTS iCn3D (I-see-in-3D) can simultaneously show 3D structure, 2D molecular contacts and 1D protein and nucleotide sequences through an integrated sequence/annotation browser. Pre-defined and arbitrary molecular features can be selected in any of the 1D/2D/3D windows as sets of residues and these selections are synchronized dynamically in all displays. Biological annotations such as protein domains, single nucleotide variations, etc. can be shown as tracks in the 1D sequence/annotation browser. These customized displays can be shared with colleagues or publishers via a simple URL. iCn3D can display structure-structure alignments obtained from NCBI's VAST+ service. It can also display the alignment of a sequence with a structure as identified by BLAST, and thus relate 3D structure to a large fraction of all known proteins. iCn3D can also display electron density maps or electron microscopy (EM) density maps, and export files for 3D printing. The following example URL exemplifies some of the 1D/2D/3D representations: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html?mmdbid=1TUP&showanno=1&show2d=1&showsets=1. AVAILABILITY AND IMPLEMENTATION iCn3D is freely available to the public. Its source code is available at https://github.com/ncbi/icn3d. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Philippe Youkharibache
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.,National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dachuan Zhang
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Christopher J Lanczycki
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Renata C Geer
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA.,National Cancer Institute, National Institutes of Health, Bethesda, MD 20894, USA
| | - Lon Phan
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Minghong Ward
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Shennan Lu
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Gabriele H Marchler
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yanli Wang
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Stephen H Bryant
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Lewis Y Geer
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Aron Marchler-Bauer
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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Goodsell DS, Olson AJ, Forli S. Art and Science of the Cellular Mesoscale. Trends Biochem Sci 2020; 45:472-483. [PMID: 32413324 PMCID: PMC7230070 DOI: 10.1016/j.tibs.2020.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/12/2020] [Accepted: 02/27/2020] [Indexed: 12/22/2022]
Abstract
Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.
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Affiliation(s)
- David S Goodsell
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Mooers BHM. Shortcuts for faster image creation in PyMOL. Protein Sci 2020; 29:268-276. [PMID: 31710740 PMCID: PMC6933860 DOI: 10.1002/pro.3781] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022]
Abstract
PyMOL is often used to generate images of biomolecular structures. Hundreds of parameters in PyMOL provide precise control over the appearance of structures. We developed 241 Python functions-called "shortcuts"-that extend and ease the use of PyMOL. A user runs a shortcut by entering its name at the PyMOL prompt. We clustered the shortcuts by functionality into 25 groups for faster look-up. One set of shortcuts generates new styles of molecular representation. Another group saves files with time stamps in the file names; the unique filenames avoid overwriting files that have already been developed. A third group submits search terms in the user's web browser. The help function prints the function's documentation to the command history window. This documentation includes the PyMOL commands that the user can reuse by copying and pasting onto the command line or into a script file. The shortcuts should save the average PyMOL user many hours per year searching for code fragments in their computer or on-line. STATEMENT FOR LAY PUBLIC: Computer-generated images of protein structures are vital to the interpretation of and communication about the molecular structure of proteins. PyMOL is a popular computer program for generating such images. We made a large collection of macros or shortcuts that save time by executing complex operations with a few keystrokes.
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Affiliation(s)
- Blaine H. M. Mooers
- Department of Biochemistry and Molecular BiologyUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahoma
- Stephenson Cancer CenterUniversity of Oklahoma Health Sciences CenterOklahoma CityOklahoma
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21
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Seeing Your Way to New Insights in Biology. J Mol Biol 2019; 431:2485-2486. [PMID: 31034886 DOI: 10.1016/j.jmb.2019.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Provost JJ, Bell JK, Bell JE. Development and Use of CUREs in Biochemistry. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1337.ch007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joseph J. Provost
- Department Chemistry and Biochemistry, University of San Diego, San Diego, California 91977, United States
| | - Jessica K. Bell
- Department Chemistry and Biochemistry, University of San Diego, San Diego, California 91977, United States
| | - John E. Bell
- Department Chemistry and Biochemistry, University of San Diego, San Diego, California 91977, United States
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23
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Kopecki-Fjetland MA. Vignette #1: Introducing Active Learning to Improve Student Performance on Threshold Concepts in Biochemistry. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1337.ch012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Mary A. Kopecki-Fjetland
- Department of Chemistry, St. Edward’s University, 3001 South Congress Avenue, Austin, Texas 78704, United States
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24
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Loertscher J, Minderhout V. Implementing Guided Inquiry in Biochemistry: Challenges and Opportunities. ACS SYMPOSIUM SERIES 2019. [DOI: 10.1021/bk-2019-1337.ch005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jennifer Loertscher
- Department of Chemistry, Seattle University, 901 12th Avenue, Seattle, Washington 98122, United States
| | - Vicky Minderhout
- Department of Chemistry, Seattle University, 901 12th Avenue, Seattle, Washington 98122, United States
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25
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Goodstadt MN, Marti-Renom MA. Communicating Genome Architecture: Biovisualization of the Genome, from Data Analysis and Hypothesis Generation to Communication and Learning. J Mol Biol 2018; 431:1071-1087. [PMID: 30419242 DOI: 10.1016/j.jmb.2018.11.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/29/2018] [Accepted: 11/01/2018] [Indexed: 01/07/2023]
Abstract
Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the experimental and visualization techniques that have been developed recently which capture the three-dimensional interactions regulating how genes are expressed. We detail the challenges faced in integration of the data to portray the components and organization and their dynamic landscape. The goal is more than a single data-driven representation as interactive visualization for de novo research is paramount to decipher insights on genome organization in space.
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Affiliation(s)
- Mike N Goodstadt
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain; Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, Barcelona 08010, Spain.
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