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Bajgar A, Krejčová G. On the origin of the functional versatility of macrophages. Front Physiol 2023; 14:1128984. [PMID: 36909237 PMCID: PMC9998073 DOI: 10.3389/fphys.2023.1128984] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Macrophages represent the most functionally versatile cells in the animal body. In addition to recognizing and destroying pathogens, macrophages remove senescent and exhausted cells, promote wound healing, and govern tissue and metabolic homeostasis. In addition, many specialized populations of tissue-resident macrophages exhibit highly specialized functions essential for the function of specific organs. Sometimes, however, macrophages cease to perform their protective function and their seemingly incomprehensible response to certain stimuli leads to pathology. In this study, we address the question of the origin of the functional versatility of macrophages. To this end, we have searched for the evolutionary origin of macrophages themselves and for the emergence of their characteristic properties. We hypothesize that many of the characteristic features of proinflammatory macrophages evolved in the unicellular ancestors of animals, and that the functional repertoire of macrophage-like amoebocytes further expanded with the evolution of multicellularity and the increasing complexity of tissues and organ systems. We suggest that the entire repertoire of macrophage functions evolved by repurposing and diversification of basic functions that evolved early in the evolution of metazoans under conditions barely comparable to that in tissues of multicellular organisms. We believe that by applying this perspective, we may find an explanation for the otherwise counterintuitive behavior of macrophages in many human pathologies.
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Affiliation(s)
- Adam Bajgar
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, Ceske Budejovice, Czechia.,Biology Centre, Institute of Entomology, Academy of Sciences, Ceske Budejovice, Czechia
| | - Gabriela Krejčová
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, Ceske Budejovice, Czechia.,Biology Centre, Institute of Entomology, Academy of Sciences, Ceske Budejovice, Czechia
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2
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Akunuri R, Vadakattu M, Bujji S, Veerareddy V, Madhavi YV, Nanduri S. Fused-azepinones: Emerging scaffolds of medicinal importance. Eur J Med Chem 2021; 220:113445. [PMID: 33901899 DOI: 10.1016/j.ejmech.2021.113445] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/23/2021] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Hymenialdisine an alkaloid of oroidin class has drawn the attention of researchers owing to its unique structural features and interesting biological properties. Hymenialdisine exhibited promising inhibitory activity against a number of therapeutically important kinases viz., CDKs, GSK-3β etc., and showed anti-cancer, anti-inflammatory, anti-HIV, neuroprotective, anti-fouling, anti-plasmodium properties. Hymenialdisine and other structurally related oroidin alkaloids such as dibromo-hymenialdisine, stevensine, hymenin, axinohydantoin, spongicidines A-D, latonduines and callyspongisines contain pyrrolo[2,3-c] azepin-8-one core in common. Keeping in view of the interesting structural and therapeutic features of HMD, several structural modifications were carried around the fused-azepinone core which resulted in a number of diverse structural motifs like indolo-azepinones, paullones, aza-paullones, darpones and 5,7-dihydro-6H-benzo[b]pyrimido[4,5-d] azepin-6-one. In this review, an attempt is made to collate and review the structures of diverse hymenialdisine and related fused-azepinones of synthetic/natural origin and their biological properties.
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Affiliation(s)
- Ravikumar Akunuri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Manasa Vadakattu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Sushmitha Bujji
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Vaishnavi Veerareddy
- Department of Pharmaceutical Technology (Process Chemistry), National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Y V Madhavi
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Srinivas Nanduri
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India.
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Slater LT, Gkoutos GV, Hoehndorf R. Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies. BMC Med Inform Decis Mak 2020; 20:311. [PMID: 33319712 PMCID: PMC7736131 DOI: 10.1186/s12911-020-01336-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/25/2022] Open
Abstract
Background Ontologies are widely used throughout the biomedical domain. These ontologies formally represent the classes and relations assumed to exist within a domain. As scientific domains are deeply interlinked, so too are their representations. While individual ontologies can be tested for consistency and coherency using automated reasoning methods, systematically combining ontologies of multiple domains together may reveal previously hidden contradictions. Methods We developed a method that tests for hidden unsatisfiabilities in an ontology that arise when combined with other ontologies. For this purpose, we combined sets of ontologies and use automated reasoning to determine whether unsatisfiable classes are present. In addition, we designed and implemented a novel algorithm that can determine justifications for contradictions across extremely large and complicated ontologies, and use these justifications to semi-automatically repair ontologies by identifying a small set of axioms that, when removed, result in a consistent and coherent set of ontologies.
Results We tested the mutual consistency of the OBO Foundry and the OBO ontologies and find that the combined OBO Foundry gives rise to at least 636 unsatisfiable classes, while the OBO ontologies give rise to more than 300,000 unsatisfiable classes. We also applied our semi-automatic repair algorithm to each combination of OBO ontologies that resulted in unsatisfiable classes, finding that only 117 axioms could be removed to account for all cases of unsatisfiability across all OBO ontologies. Conclusions We identified a large set of hidden unsatisfiability across a broad range of biomedical ontologies, and we find that this large set of unsatisfiable classes is the result of a relatively small amount of axiomatic disagreements. Our results show that hidden unsatisfiability is a serious problem in ontology interoperability; however, our results also provide a way towards more consistent ontologies by addressing the issues we identified.
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Affiliation(s)
- Luke T Slater
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK. .,Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, Birmingham, B15 2TT, UK.
| | - Georgios V Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, Birmingham, B15 2TT, UK.,NIHR Experimental Cancer Medicine Centre, Birmingham, B15 2TT, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, Birmingham, B15 2TT, UK.,NIHR Biomedical Research Centre, Birmingham, B15 2TT, UK.,MRC Health Data Research UK (HDR UK Midlands, Birmingham, B15 2TT, UK
| | - Robert Hoehndorf
- Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia
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Protein-driven biomineralization: Comparing silica formation in grass silica cells to other biomineralization processes. J Struct Biol 2020; 213:107665. [PMID: 33227416 DOI: 10.1016/j.jsb.2020.107665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/20/2022]
Abstract
Biomineralization is a common strategy adopted by organisms to support their body structure. Plants practice significant silicon and calcium based biomineralization in which silicon is deposited as silica in cell walls and intracellularly in various cell-types, while calcium is deposited mostly as calcium oxalate in vacuoles of specialized cells. In this review, we compare cellular processes leading to protein-dependent mineralization in plants, diatoms and sponges (phylum Porifera). The mechanisms of biomineralization in these organisms are inherently different. The composite silica structure in diatoms forms inside the cytoplasm in a membrane bound vesicle, which after maturation is exocytosed to the cell surface. In sponges, separate vesicles with the mineral precursor (silicic acid), an inorganic template, and organic molecules, fuse together and are extruded to the extracellular space. In plants, calcium oxalate mineral precipitates in vacuolar crystal chambers containing a protein matrix which is never exocytosed. Silica deposition in grass silica cells takes place outside the cell membrane when the cells secrete the mineralizing protein into the apoplasm rich with silicic acid (the mineral precursor molecules). Our review infers that the organism complexity and precursor reactivity (calcium and oxalate versus silicic acid) are main driving forces for the evolution of varied mineralization mechanisms.
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Abstract
In 1882, Elie Metchnikoff identified myeloid-like cells from starfish larvae responding to the invasion by a foreign body (rose thorn). This marked the origins for the study of innate immunity, and an appreciation that cellular immunity was well established even in these "primitive" organisms. This chapter focuses on these myeloid cells as well as the newest members of this family, the dendritic cells, and explores their evolutionary origins. Our goal is to provide evolutionary context for the development of the multilayered immune system of mammals, where myeloid cells now serve as central effectors of innate immunity and regulators of adaptive immunity. Overall, we find that core contributions of myeloid cells to the regulation of inflammation are based on mechanisms that have been honed over hundreds of millions of years of evolution. Using phagocytosis as a platform, we show how fairly simple beginnings have offered a robust foundation onto which additional control features have been integrated, resulting in central regulatory nodes that now manage multifactorial aspects of homeostasis and immunity.
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Xu C, Wei Z, Gao H, Bai Y, Liu H, Yang H, Lai Y, Yang L. Bioinspired Mechano-Sensitive Macroporous Ceramic Sponge for Logical Drug and Cell Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2017; 4:1600410. [PMID: 28638781 PMCID: PMC5473326 DOI: 10.1002/advs.201600410] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/18/2017] [Indexed: 05/13/2023]
Abstract
On-demand, ultrahigh precision delivery of molecules and cells assisted by scaffold is a pivotal theme in the field of controlled release, but it remains extremely challenging for ceramic-based macroporous scaffolds that are prevalently used in regenerative medicine. Sea sponges (Phylum Porifera), whose bodies possess hierarchical pores or channels and organic/inorganic composite structures, can delicately control water intake/circulation and therefore achieve high precision mass transportation of food, oxygen, and wastes. Inspired by leuconoid sponge, in this study, the authors design and fabricate a biomimetic macroporous ceramic composite sponge (CCS) for high precision logic delivery of molecules and cells regulated by mechanical stimulus. The CCS reveals unique on-demand AND logic release behaviors in response to dual-gates of moisture and pressure (or strain) and, more importantly, 1 cm3 volume of CCS achieves unprecedentedly delivery precision of ≈100 ng per cycle for hydrophobic or hydrophilic molecules and ≈1400 cells per cycle for fibroblasts, respectively.
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Affiliation(s)
- Changlu Xu
- Orthopaedic InstituteDepartment of OrthopaedicsThe First Affiliated HospitalSoochow UniversitySuzhouJiangsu215006P. R. China
| | - Zhihao Wei
- Orthopaedic InstituteDepartment of OrthopaedicsThe First Affiliated HospitalSoochow UniversitySuzhouJiangsu215006P. R. China
| | - Huajian Gao
- School of EngineeringBrown UniversityProvidenceRI02912USA
- International Research Center for Translational Orthopaedics (IRCTO)Soochow UniversitySuzhouJiangsu215006P. R. China
| | - Yanjie Bai
- School of Public HealthMedical CollegeSoochow UniversitySuzhouJiangsu215123P. R. China
| | - Huiling Liu
- Orthopaedic InstituteDepartment of OrthopaedicsThe First Affiliated HospitalSoochow UniversitySuzhouJiangsu215006P. R. China
| | - Huilin Yang
- Orthopaedic InstituteDepartment of OrthopaedicsThe First Affiliated HospitalSoochow UniversitySuzhouJiangsu215006P. R. China
- International Research Center for Translational Orthopaedics (IRCTO)Soochow UniversitySuzhouJiangsu215006P. R. China
| | - Yuekun Lai
- National Engineering Laboratory for Modern SilkCollege of Textile and Clothing EngineeringSoochow UniversitySuzhouJiangsu215123P. R. China
- International Research Center for Translational Orthopaedics (IRCTO)Soochow UniversitySuzhouJiangsu215006P. R. China
| | - Lei Yang
- Orthopaedic InstituteDepartment of OrthopaedicsThe First Affiliated HospitalSoochow UniversitySuzhouJiangsu215006P. R. China
- International Research Center for Translational Orthopaedics (IRCTO)Soochow UniversitySuzhouJiangsu215006P. R. China
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Collin R, Fredericq S, Freshwater DW, Gilbert E, Madrid M, Maslakova S, Miglietta MP, Rocha RM, Rodríguez E, Thacker RW. TaxaGloss - A Glossary and Translation Tool for Biodiversity Studies. Biodivers Data J 2017:e10732. [PMID: 28174506 PMCID: PMC5267532 DOI: 10.3897/bdj.4.e10732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/12/2016] [Indexed: 11/21/2022] Open
Abstract
Background Correctly identifying organisms is key to most biological research, and is especially critical in areas of biodiversity and conservation. Yet it remains one of the greatest challenges when studying all but the few well-established model systems. The challenge is in part due to the fact that most species have yet to be described, vanishing taxonomic expertise and the relative inaccessibility of taxonomic information. Furthermore, identification keys and other taxonomic resources are based on complex, taxon-specific vocabularies used to describe important morphological characters. Using these resources is made difficult by the fact that taxonomic documentation of the world's biodiversity is an international endeavour, and keys and field guides are not always available in the practitioner's native language. New information To address this challenge, we have developed a publicly available on-line illustrated multilingual glossary and translation tool for technical taxonomic terms using the Symbiota Software Project biodiversity platform. Illustrations, photographs and translations have been sourced from the global community of taxonomists working with marine invertebrates and seaweeds. These can be used as single-language illustrated glossaries or to make customized translation tables. The glossary has been launched with terms and illustrations of seaweeds, tunicates, sponges, hydrozoans, sea anemones, and nemerteans, and already includes translations into seven languages for some groups. Additional translations and development of terms for more taxa are underway, but the ultimate utility of this tool depends on active participation of the international taxonomic community.
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Affiliation(s)
- Rachel Collin
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Suzanne Fredericq
- Department of Biology, University of Louisiana at Lafayette, Lafayette, United States of America
| | - D Wilson Freshwater
- Center for Marine Science, University of North Carolina at Wilmington, Wilmington, United States of America
| | - Edward Gilbert
- School of Life Science, Arizona State University, Tempe, United States of America
| | - Maycol Madrid
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Svetlana Maslakova
- Oregon Institute of Marine Biology, University of Oregon, Charleston, United States of America
| | - Maria Pia Miglietta
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, United States of America
| | - Rosana M Rocha
- Department of Zoology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Estefanía Rodríguez
- Division of Invertebrate Zoology, American Museum of Natural History, New York, United States of America
| | - Robert W Thacker
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, United States of America
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Thessen AE, Bunker DE, Buttigieg PL, Cooper LD, Dahdul WM, Domisch S, Franz NM, Jaiswal P, Lawrence-Dill CJ, Midford PE, Mungall CJ, Ramírez MJ, Specht CD, Vogt L, Vos RA, Walls RL, White JW, Zhang G, Deans AR, Huala E, Lewis SE, Mabee PM. Emerging semantics to link phenotype and environment. PeerJ 2015; 3:e1470. [PMID: 26713234 PMCID: PMC4690371 DOI: 10.7717/peerj.1470] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 11/12/2015] [Indexed: 11/20/2022] Open
Abstract
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.
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Affiliation(s)
- Anne E. Thessen
- Ronin Institute for Independent Scholarship, Monclair, NJ, United States
- The Data Detektiv, Waltham, MA, United States
| | - Daniel E. Bunker
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, United States
| | - Pier Luigi Buttigieg
- HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar-und Meeresforschung, Bremerhaven, Germany
| | - Laurel D. Cooper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wasila M. Dahdul
- Department of Biology, University of South Dakota, Vermillion, SD, United States
| | - Sami Domisch
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Nico M. Franz
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Carolyn J. Lawrence-Dill
- Departments of Genetics, Development and Cell Biology and Agronomy, Iowa State University, Ames, IA, United States
| | | | | | - Martín J. Ramírez
- Division of Arachnology, Museo Argentino de Ciencias Naturales–CONICET, Buenos Aires, Argentina
| | - Chelsea D. Specht
- Departments of Plant and Microbial Biology & Integrative Biology, University of California, Berkeley, CA, United States
| | - Lars Vogt
- Institut für Evolutionsbiologie und Ökologie, Universität Bonn, Bonn, Germany
| | | | - Ramona L. Walls
- iPlant Collaborative, University of Arizona, Tucson, AZ, United States
| | - Jeffrey W. White
- US Arid Land Agricultural Research Center, United States Department of Agriculture—ARS, Maricopa, AZ, United States
| | - Guanyang Zhang
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
| | - Andrew R. Deans
- Department of Entomology, Pennsylvania State University, University Park, PA, United States
| | - Eva Huala
- Phoenix Bioinformatics, Redwood City, CA, United States
| | - Suzanna E. Lewis
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Paula M. Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, United States
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