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Puspita L, Juwono VB, Shim JW. Advances in human pluripotent stem cell reporter systems. iScience 2024; 27:110856. [PMID: 39290832 PMCID: PMC11407076 DOI: 10.1016/j.isci.2024.110856] [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] [Indexed: 09/19/2024] Open
Abstract
The capability of human pluripotent stem cells (hPSCs) to self-renew and differentiate into any cell type has greatly contributed to the advancement of biomedicine. Reporter lines derived from hPSCs have played a crucial role in elucidating the mechanisms underlying human development and diseases by acting as an alternative reporter system that cannot be used in living humans. To bring hPSCs closer to clinical application in transplantation, scientists have generated reporter lines for isolating the desired cell populations, as well as improving graft quality and treatment outcomes. This review presents an overview of the applications of hPSC reporter lines and the important variables in designing a reporter system, including options for gene delivery and editing tools, design of reporter constructs, and selection of reporter genes. It also provides insights into the prospects of hPSC reporter lines and the challenges that must be overcome to maximize the potential of hPSC reporter lines.
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Affiliation(s)
- Lesly Puspita
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si 31151, Korea
| | - Virginia Blessy Juwono
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
| | - Jae-Won Shim
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan-si 31151, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si 31151, Korea
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Lilli G, Sirot C, Campbell H, Hermand F, Brophy D, Flot JF, Graham CT, George IF. Do fish gut microbiotas vary across spatial scales? A case study of Diplodus vulgaris in the Mediterranean Sea. Anim Microbiome 2024; 6:32. [PMID: 38872229 PMCID: PMC11177387 DOI: 10.1186/s42523-024-00319-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024] Open
Abstract
BACKGROUND Biogeography has been linked to differences in gut microbiota in several animals. However, the existence of such a relationship in fish is not clear yet. So far, it seems to depend on the fish species studied. However, most studies of fish gut microbiotas are based on single populations. In this study, we investigated the gut microbiota of fish from three wild populations of the two-banded sea bream Diplodus vulgaris (Geoffroy Saint-Hilaire, 1817) to determine whether its diversity, structure and potential functionality reflect the geographic origin of the fish, at large and small geographical scale. Additionally, we explored the host- and environmental-related factors explaining this relationship. RESULTS We showed that the taxonomy and potential functionality of the mucosa-associated gut microbiota of Diplodus vulgaris differ to varying degrees depending on the spatial scale considered. At large scale, we observed that both the taxonomical structure and the potential functionality of the fish microbiota differed significantly between populations. In contrast, the taxonomical diversity of the microbial community displayed a significant relationship with factors other than the geographic origin of the fish (i.e. sampling date). On the other hand, at small scale, the different composition and diversity of the microbiota differ according to the characteristics of the habitat occupied by the fish. Specifically, we identified the presence of Posidonia oceanica in the benthic habitat as predictor of both the microbiota composition and diversity. Lastly, we reported the enrichment of functions related to the metabolism of xenobiotics (i.e. drugs and 4-aminobenzoate) in a population and we indicated it as a potential target of future monitoring. CONCLUSIONS With this study, we confirmed the importance of investigating the gut microbiota of wild fish species using multiple populations, taking into account the different habitats occupied by the individuals. Furthermore, we underscored the use of the biodegradation potential of the gut microbiota as an alternative means of monitoring emerging contaminants in Mediterranean fish.
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Affiliation(s)
- Ginevra Lilli
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium.
| | - Charlotte Sirot
- Centre de Recherches Insulaires et Observatoire de l'Environnement (CRIOBE), University of Perpignan, Perpignan, France
| | - Hayley Campbell
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Fanny Hermand
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
| | - Deirdre Brophy
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels - (IB)², 1050, Brussels, Belgium
| | - Conor T Graham
- Marine and Freshwater Research Centre, Atlantic Technological University, Dublin Road, Galway, Ireland
| | - Isabelle F George
- Laboratoire d'Ecologie des Systèmes Aquatiques (ESA), Université Libre de Bruxelles (ULB), 1050, Brussels, Belgium
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Claes JM, Haddock SHD, Coubris C, Mallefet J. Systematic Distribution of Bioluminescence in Marine Animals: A Species-Level Inventory. Life (Basel) 2024; 14:432. [PMID: 38672704 PMCID: PMC11051050 DOI: 10.3390/life14040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.
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Affiliation(s)
- Julien M. Claes
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (C.C.); (J.M.)
| | - Steven H. D. Haddock
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Constance Coubris
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (C.C.); (J.M.)
| | - Jérôme Mallefet
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium; (C.C.); (J.M.)
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Azizan A, Alfaro AC, Jaramillo D, Venter L, Young T, Frost E, Lee K, Van Nguyen T, Kitundu E, Archer SDJ, Ericson JA, Foxwell J, Quinn O, Ragg NLC. Pathogenicity and virulence of bacterial strains associated with summer mortality in marine mussels (Perna canaliculus). FEMS Microbiol Ecol 2022; 98:6855225. [PMID: 36449667 DOI: 10.1093/femsec/fiac140] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/09/2022] [Accepted: 11/28/2022] [Indexed: 12/02/2022] Open
Abstract
The occurrence of pathogenic bacteria has emerged as a plausible key component of summer mortalities in mussels. In the current research, four bacterial isolates retrieved from moribund Greenshell࣪ mussels, Perna canaliculus, from a previous summer mortality event, were tentatively identified as Vibrio and Photobacterium species using morpho-biochemical characterization and MALDI-TOF MS and confirmed as V. celticus, P. swingsii, P. rosenbergii, and P. proteolyticum using whole genome sequencing. These isolates were utilized in a laboratory challenge where mussels were injected with cell concentrations ranging from 105 to 109 CFU/mussel. Of the investigated isolates, P. swingsii induced the highest mortality. Additionally, results from quantitative polymerase chain reaction analysis, focusing on known virulence genes were detected in all isolates grown under laboratory conditions. Photobacterium rosenbergii and P. swingsii showed the highest expression levels of these virulence determinants. These results indicate that Photobacterium spp. could be a significant pathogen of P. canaliculus, with possible importance during summer mortality events. By implementing screening methods to detect and monitor Photobacterium concentrations in farmed mussel populations, a better understanding of the host-pathogen relationship can be obtained, aiding the development of a resilient industry in a changing environment.
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Affiliation(s)
- Awanis Azizan
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Andrea C Alfaro
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Diana Jaramillo
- Animal Health Laboratory, Ministry for Primary Industries, New Zealand PO Box 2526, Wellington 6140, New Zealand
| | - Leonie Venter
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Tim Young
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.,Centre for Biomedical & Chemical Sciences, School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Emily Frost
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Kevin Lee
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Thao Van Nguyen
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand.,NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Eileen Kitundu
- Department of Food Sciences and Microbiology, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Stephen D J Archer
- Aquaculture Biotechnology Research Group, Department of Environmental Sciences, School of Science, Auckland University of Technology, Private Bag 92006, Auckland 1142, New Zealand
| | - Jessica A Ericson
- Aquaculture Department, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Jonathan Foxwell
- Animal Health Laboratory, Ministry for Primary Industries, New Zealand PO Box 2526, Wellington 6140, New Zealand
| | - Oliver Quinn
- Animal Health Laboratory, Ministry for Primary Industries, New Zealand PO Box 2526, Wellington 6140, New Zealand
| | - Norman L C Ragg
- Aquaculture Department, Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
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Banchi E, Manna V, Fonti V, Fabbro C, Celussi M. Improving environmental monitoring of Vibrionaceae in coastal ecosystems through 16S rRNA gene amplicon sequencing. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:67466-67482. [PMID: 36056283 PMCID: PMC9492620 DOI: 10.1007/s11356-022-22752-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
The Vibrionaceae family groups genetically and metabolically diverse bacteria thriving in all marine environments. Despite often representing a minor fraction of bacterial assemblages, members of this family can exploit a wide variety of nutritional sources, which makes them important players in biogeochemical dynamics. Furthermore, several Vibrionaceae species are well-known pathogens, posing a threat to human and animal health. Here, we applied the phylogenetic placement coupled with a consensus-based approach using 16S rRNA gene amplicon sequencing, aiming to reach a reliable and fine-level Vibrionaceae characterization and identify the dynamics of blooming, ecologically important, and potentially pathogenic species in different sites of the northern Adriatic Sea. Water samples were collected monthly at a Long-Term Ecological Research network site from 2018 to 2021, and in spring and summer of 2019 and 2020 at two sites affected by depurated sewage discharge. The 41 identified Vibrionaceae species represented generally below 1% of the sampled communities; blooms (up to ~ 11%) mainly formed by Vibrio chagasii and Vibrio owensii occurred in summer, linked to increasing temperature and particulate matter concentration. Pathogenic species such as Vibrio anguilllarum, Vibrio tapetis, and Photobacterium damselae were found in low abundance. Depuration plant samples were characterized by a lower abundance and diversity of Vibrionaceae species compared to seawater, highlighting that Vibrionaceae dynamics at sea are unlikely to be related to wastewater inputs. Our work represents a further step to improve the molecular approach based on short reads, toward a shared, updated, and curated phylogeny of the Vibrionaceae family.
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Affiliation(s)
- Elisa Banchi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy.
| | - Vincenzo Manna
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Viviana Fonti
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Cinzia Fabbro
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
| | - Mauro Celussi
- National Institute of Oceanography and Applied Geophysics - OGS, Via A. Piccard, 54, 34151, Trieste, Italy
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Structure-Function Relationships in Temperature Effects on Bacterial Luciferases: Nothing Is Perfect. Int J Mol Sci 2022; 23:ijms23158119. [PMID: 35897698 PMCID: PMC9332260 DOI: 10.3390/ijms23158119] [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: 07/06/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 12/04/2022] Open
Abstract
The evaluation of temperature effects on the structure and function of enzymes is necessary to understand the mechanisms underlying their adaptation to a constantly changing environment. In the current study, we investigated the influence of temperature variation on the activity, structural dynamics, thermal inactivation and denaturation of Photobacterium leiognathi and Vibrio harveyi luciferases belonging to different subfamilies, as well as the role of sucrose in maintaining the enzymes functioning and stability. We used the stopped-flow technique, differential scanning calorimetry and molecular dynamics to study the activity, inactivation rate, denaturation and structural features of the enzymes under various temperatures. It was found that P. leiognathi luciferase resembles the properties of cold-adapted enzymes with high activity in a narrow temperature range and slightly lower thermal stability than V. harveyi luciferase, which is less active, but more thermostable. Differences in activity at the studied temperatures can be associated with the peculiarities of the mobile loop conformational changes. The presence of sucrose does not provide an advantage in activity but increases the stability of the enzymes. Differential scanning calorimetry experiments showed that luciferases probably follow different denaturation schemes.
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Acquisition of bioluminescent trait by non-luminous organisms from luminous organisms through various origins. Photochem Photobiol Sci 2021; 20:1547-1562. [PMID: 34714534 DOI: 10.1007/s43630-021-00124-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 10/20/2021] [Indexed: 12/20/2022]
Abstract
Bioluminescence is a natural light emitting phenomenon that occurs due to a chemical reaction between luciferin and luciferase. It is primarily an innate and inherited trait in most terrestrial luminous organisms. However, most luminous organisms produce light in the ocean by acquiring luminous symbionts, luciferin (substrate), and/or luciferase (enzyme) through various transmission pathways. For instance, coelenterazine, a well-known luciferin, is obtained by cnidarians, crustaceans, and deep-sea fish through multi-level dietary linkages from coelenterazine producers such as ctenophores, decapods, and copepods. In contrast, some non-luminous Vibrio bacteria became bioluminescent by obtaining lux genes from luminous Vibrio species by horizontal gene transfer. Various examples detailed in this review show how non-luminescent organisms became luminescent by acquiring symbionts, dietary luciferins and luciferases, and genes. This review highlights three modes (symbiosis, ingestion, and horizontal gene transfer) that allow organisms lacking genes for autonomous bioluminescent systems to obtain the ability to produce light. In addition to bioluminescence, this manuscript discusses the acquisition of other traits such as pigments, fluorescence, toxins, and others, to infer the potential processes of acquisition.
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Petrzik K, Brázdová S, Krawczyk K. Novel Viruses That Lyse Plant and Human Strains of Kosakonia cowanii. Viruses 2021; 13:1418. [PMID: 34452284 PMCID: PMC8402661 DOI: 10.3390/v13081418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/18/2021] [Indexed: 12/02/2022] Open
Abstract
Kosakonia cowanii (syn. Enterobacter cowanii) is a highly competitive bacterium that lives with plant, insect, fish, bird, and human organisms. It is pathogenic on some plants and an opportunistic pathogen of human. Nine novel viruses that lyse plant pathogenic strains and/or human strains of K. cowanii were isolated, sequenced, and characterized. Kc166A is a novel kayfunavirus, Kc261 is a novel bonnellvirus, and Kc318 is a new cronosvirus (all Autographiviridae). Kc237 is a new sortsnevirus, but Kc166B and Kc283 are members of new genera within Podoviridae. Kc304 is a new winklervirus, and Kc263 and Kc305 are new myoviruses. The viruses differ in host specificity, plaque phenotype, and lysis kinetics. Some of them should be suitable also as pathogen control agents.
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Affiliation(s)
- Karel Petrzik
- Biology Centre, Department of Plant Virology, Institute of Plant Molecular Biology, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Sára Brázdová
- Biology Centre, Department of Plant Virology, Institute of Plant Molecular Biology, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic;
| | - Krzysztof Krawczyk
- Department of Molecular Biology and Biotechnology, Institute of Plant Protection-National Research Institute, Władislawa Węgorka 20, 60-318 Poznań, Poland;
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Burtseva O, Baulina O, Zaytseva A, Fedorenko T, Chekanov K, Lobakova E. In vitro Biofilm Formation by Bioluminescent Bacteria Isolated from the Marine Fish Gut. MICROBIAL ECOLOGY 2021; 81:932-940. [PMID: 33247364 DOI: 10.1007/s00248-020-01652-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
The internal surface of the animal gastrointestinal tract is covered by microbial biofilms. They play an important role in the development and functioning of the host organism and protect it against pathogens. Microbial communities of gastrointestinal biofilms are less elucidated than luminal microbiota. Therefore, the studies of biofilm formation by gastrointestinal microorganisms are a topical issue. For the first time, we report the formation of a biofilm in vitro by the strains of bioluminescent bacteria isolated from the intestines of marine fish. These bacteria exhibit co-aggregation and tend to attach to solid surfaces. The attachment of cells is accompanied by appearance of the pili. Then, we observed the formation of microcolonies and the production of extracellular polymer substances (EPSs) connecting bacterial cells into an integrated system. The presence of acidic polysaccharides is shown in the EPS when using the ruthenium red staining. Acidic polysaccharides in this matrix is a biochemical evidence of microbial biofilms. On the fibers of the polymer matrix, these bacteria form the "mushroom body"-type structures. Matured biofilms exhibit a specific three-dimensional architecture with pores and channels formed by cells and EPS. We also demonstrated the formation of a biofilm by binary culture of the luminous enterobacterium Kosakonia cowanii and a Gram-positive Macrococcus sp. The data obtained help to understand the role of these bacteria in the intestines of fish. They lead to a new study in the field of investigation of the intestinal microbiome of fish.
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Affiliation(s)
- Olga Burtseva
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Olga Baulina
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna Zaytseva
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana Fedorenko
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Konstantin Chekanov
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
- National Research Nuclear University MEPhi, Centre for Humanities Research and Technology, Moscow, Russia.
| | - Elena Lobakova
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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