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Iskandar M, Ruiz-Houston KM, Bracco SD, Sharkasi SR, Calabi Villarroel CL, Desai MN, Gerges AG, Ortiz Lopez NA, Xiao Barbero M, German AA, Moluguri VS, Walker SM, Silva Higashi J, Palma JM, Medina DZ, Patel M, Patel P, Valentin M, Diaz AC, Karthaka JP, Santiago AD, Skiles RB, Romero Umana LA, Ungrey MD, Wojtkowiak A, Howard DV, Nurge R, Woods KG, Nanjundan M. Deep-Sea Sponges and Corals off the Western Coast of Florida-Intracellular Mechanisms of Action of Bioactive Compounds and Technological Advances Supporting the Drug Discovery Pipeline. Mar Drugs 2023; 21:615. [PMID: 38132936 PMCID: PMC10744787 DOI: 10.3390/md21120615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023] Open
Abstract
The majority of natural products utilized to treat a diverse array of human conditions and diseases are derived from terrestrial sources. In recent years, marine ecosystems have proven to be a valuable resource of diverse natural products that are generated to defend and support their growth. Such marine sources offer a large opportunity for the identification of novel compounds that may guide the future development of new drugs and therapies. Using the National Oceanic and Atmospheric Administration (NOAA) portal, we explore deep-sea coral and sponge species inhabiting a segment of the U.S. Exclusive Economic Zone, specifically off the western coast of Florida. This area spans ~100,000 km2, containing coral and sponge species at sea depths up to 3000 m. Utilizing PubMed, we uncovered current knowledge on and gaps across a subset of these sessile organisms with regards to their natural products and mechanisms of altering cytoskeleton, protein trafficking, and signaling pathways. Since the exploitation of such marine organisms could disrupt the marine ecosystem leading to supply issues that would limit the quantities of bioactive compounds, we surveyed methods and technological advances that are necessary for sustaining the drug discovery pipeline including in vitro aquaculture systems and preserving our natural ecological community in the future. Collectively, our efforts establish the foundation for supporting future research on the identification of marine-based natural products and their mechanism of action to develop novel drugs and therapies for improving treatment regimens of human conditions and diseases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Meera Nanjundan
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, ISA2015, Tampa, FL 33620, USA; (M.I.); (K.M.R.-H.); (S.D.B.); (S.R.S.); (C.L.C.V.); (M.N.D.); (A.G.G.); (N.A.O.L.); (M.X.B.); (A.A.G.); (V.S.M.); (S.M.W.); (J.S.H.); (J.M.P.); (D.Z.M.); (M.P.); (P.P.); (M.V.); (A.C.D.); (J.P.K.); (A.D.S.); (R.B.S.); (L.A.R.U.); (M.D.U.); (A.W.); (D.V.H.); (R.N.); (K.G.W.)
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Li J, Liu F, Ren Z, Fu G, Shi J, Zhao N, Huang Y, Su J. Generation of a monoclonal antibody against duck circovirus capsid protein and its potential application for native viral antigen detection. Front Microbiol 2023; 14:1206038. [PMID: 37426000 PMCID: PMC10326623 DOI: 10.3389/fmicb.2023.1206038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction Duck circovirus (DuCV) infection is currently recognized as an important immunosuppressive disease in commercial duck flocks in China. Specific antibodies against DuCV viral proteins are required to improve diagnostic assays and understand the pathogenesis of DuCV infection. Methods and results To generate DuCV-specific monoclonal antibodies (mAbs), a recombinant DuCV capsid protein without the first 36 N-terminal amino acids was produced in Escherichia coli. Using the recombinant protein as an immunogen, a mAb was developed that reacted specifically with the DuCV capsid protein, expressed in E. coli and baculovirus systems. Using homology modeling and recombinant truncated capsid proteins, the antibody-binding epitope was mapped within the region of 144IDKDGQIV151, which is exposed to solvent in the virion capsid model structure. To assess the applicability of the mAb to probe the native virus antigen, the murine macrophage cell line RAW267.4 was tested for DuCV replicative permissiveness. Immunofluorescence and Western blot analysis revealed that the mAb recognized the virus in infected cells and the viral antigen in tissue samples collected from clinically infected ducks. Discussion This mAb, combined with the in vitro culturing method, would have widespread applications in diagnosing and investigating DuCV pathogenesis.
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Affiliation(s)
- Jinxin Li
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Fengli Liu
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhihao Ren
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Guanghua Fu
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jizhen Shi
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Naiyu Zhao
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Huang
- Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jingliang Su
- Key Laboratory of Animal Epidemiology and Zoonosis of the Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing, China
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Hao Z, Li L, Ning Z, Zhang X, Mayne J, Cheng K, Walker K, Liu H, Figeys D. Metaproteomics Reveals Growth Phase-Dependent Responses of an In Vitro Gut Microbiota to Metformin. J Am Soc Mass Spectrom 2020; 31:1448-1458. [PMID: 32320607 DOI: 10.1021/jasms.0c00054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Metaproteomics has been used in combination with in vitro gut microbiota models to study drug-microbiome interactions. However, it remains unexplored whether the metaproteomics profile of in vitro gut microbiota responds differently to a same stimulus added at different growth phases. In this study, we cultured a human gut microbiota in 96-deep well plates using a previously validated model. Metformin was added during the lag, log, and stationary phases. Microbiome samples, collected at different time points, were analyzed by optical density and function by metaproteomic. The in vitro gut microbiota growth curves, taxonomy, and functional responses were different depending whether metformin was added during the lag, log, or stationary phases. The addition of drugs at the log phase may lead to the greatest decline of bacterial growth. Metaproteomic analysis suggests that the strength of the metformin effect on the gut microbiome functional profile may be ranked as lag phase > log phase > stationary phase. Metformin added at the lag phase may result in a significantly reduced level of the Clostridiales order and an increased level of the Bacteroides genus, which is different from stimulations during the rest of the growth phases. Metformin may also result in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure, and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.
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Affiliation(s)
- Zikai Hao
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing 100083, China
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Leyuan Li
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Zhibin Ning
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Xu Zhang
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Janice Mayne
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Kai Cheng
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Krystal Walker
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Hong Liu
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing 100083, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Daniel Figeys
- Beijing Advanced Innovation Centre for Biomedical Engineering, Beihang University, Beijing 100083, China
- Department of Biochemistry, Microbiology and Immunology, Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, Ottawa K1H 8M5, Canada
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Itsara LS, Zhou Y, Do J, Grieser AM, Vaughan AM, Ghosh AK. The Development of Whole Sporozoite Vaccines for Plasmodium falciparum Malaria. Front Immunol 2018; 9:2748. [PMID: 30619241 PMCID: PMC6297750 DOI: 10.3389/fimmu.2018.02748] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 11/08/2018] [Indexed: 12/20/2022] Open
Abstract
Each year malaria kills hundreds of thousands of people and infects hundreds of millions of people despite current control measures. An effective malaria vaccine will likely be necessary to aid in malaria eradication. Vaccination using whole sporozoites provides an increased repertoire of immunogens compared to subunit vaccines across at least two life cycle stages of the parasite, the extracellular sporozoite, and intracellular liver stage. Three potential whole sporozoite vaccine approaches are under development and include genetically attenuated parasites, radiation attenuated sporozoites, and wild-type sporozoites administered in combination with chemoprophylaxis. Pre-clinical and clinical studies have demonstrated whole sporozoite vaccine immunogenicity, including humoral and cellular immunity and a range of vaccine efficacy that depends on the pre-exposure of vaccinated individuals. While whole sporozoite vaccines can provide protection against malaria in some cases, more recent studies in malaria-endemic regions demonstrate the need for improvements. Moreover, challenges remain in manufacturing large quantities of sporozoites for vaccine commercialization. A promising solution to the whole sporozoite manufacturing challenge is in vitro culturing methodology, which has been described for several Plasmodium species, including the major disease-causing human malaria parasite, Plasmodium falciparum. Here, we review whole sporozoite vaccine immunogenicity and in vitro culturing platforms for sporozoite production.
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Affiliation(s)
| | | | - Julie Do
- MalarVx, Inc., Seattle, WA, United States
| | | | - Ashley M Vaughan
- Seattle Children's Research Institute, Seattle, WA, United States
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Li L, Zhang X, Ning Z, Mayne J, Moore JI, Butcher J, Chiang CK, Mack D, Stintzi A, Figeys D. Evaluating in Vitro Culture Medium of Gut Microbiome with Orthogonal Experimental Design and a Metaproteomics Approach. J Proteome Res 2017; 17:154-163. [PMID: 29130306 DOI: 10.1021/acs.jproteome.7b00461] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In vitro culture based approaches are time- and cost-effective solutions for rapidly evaluating the effects of drugs or natural compounds against microbiomes. The nutritional composition of the culture medium is an important determinant for effectively maintaining the gut microbiome in vitro. This study combines orthogonal experimental design and a metaproteomics approach to obtaining functional insights into the effects of different medium components on the microbiome. Our results show that the metaproteomic profile respond differently to medium components, including inorganic salts, bile salts, mucin, and short-chain fatty acids. Multifactor analysis of variance further revealed significant main and interaction effects of inorganic salts, bile salts, and mucin on the different functional groups of gut microbial proteins. While a broad regulating effect was observed on basic metabolic pathways, different medium components also showed significant modulations on cell wall, membrane, and envelope biogenesis and cell motility related functions. In particular, flagellar assembly related proteins were significantly responsive to the presence of mucin. This study provides information on the functional influences of medium components on the in vitro growth of microbiome communities and gives insight on the key components that must be considered when selecting and optimizing media for culturing ex vivo microbiotas.
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Affiliation(s)
- Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Jasmine I Moore
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - James Butcher
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Cheng-Kang Chiang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - David Mack
- Department of Paediatrics, CHEO Inflammatory Bowel Disease Centre and Research Institute, University of Ottawa , Ottawa, Ontario K1H 8L1, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa , Ottawa, Ontario K1H 8M5, Canada.,Canadian Institute for Advanced Research , Toronto, Ontario M5G 1Z8, Canada
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Hayashi R, Hayashi S, Arai K, Yoshida S, Chikuda M, Machida S. Evaluating the Biostability of Yellow and Clear Intraocular Lenses with a System Simulating Natural Intraocular Environment. Transl Vis Sci Technol 2016; 5:11. [PMID: 27933221 PMCID: PMC5142717 DOI: 10.1167/tvst.5.6.11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/27/2016] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Blue light-filtering intraocular lenses (IOLs) are thought to protect the retina from blue light damage after cataract surgery, and the implantation of yellow-tinted IOLs has been commonly used in cataract surgery. To our knowledge, this is the first investigation measuring the long-term biostability of yellow-tinted IOLs using an in vitro system simulating natural intraocular environment. METHODS Six hydrophobic acrylic IOLs, three clear IOLs, and three yellow-tinted IOLs were included in the study. Each yellow-tinted IOL was a matching counterpart of a clear IOL, with the only difference being the lens color. The IOLs were kept in conditions replicating the intraocular environment using a perfusion culture system for 7 months. Resolution, light transmittance rate, and the modulation transfer function (MTF) were measured before and after culturing. Surface roughness of the anterior and posterior surfaces was also measured. RESULTS After culturing for 7 months, there were no changes in the resolution, the light transmittance rate, and MTF. The surface roughness of the anterior and posterior surfaces increased after culturing; however, this increase was clinically insignificant. There were no differences in surface roughness between the clear and yellow-tinted IOLs, either before or after culturing. CONCLUSIONS A novel in vitro system replicating intraocular environment was used to investigate the biostability of yellow-tinted IOLs. The surface roughness showed no clinically significant increase after culturing for 7 months. TRANSLATIONAL RELEVANCE This system is useful for evaluating the biostability of IOLs.
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Affiliation(s)
- Rijo Hayashi
- Department of Ophthalmology, Koshigaya Hospital, Dokkyo Medical University, Koshigaya, Saitama, Japan
| | - Shimmin Hayashi
- Department of Ophthalmology, Koshigaya Hospital, Dokkyo Medical University, Koshigaya, Saitama, Japan ; Lively Eye Clinic, Soka, Saitama, Japan
| | - Kiyomi Arai
- Department of Ophthalmology, Koshigaya Hospital, Dokkyo Medical University, Koshigaya, Saitama, Japan
| | - Shinichirou Yoshida
- Department of Ophthalmology, Koshigaya Hospital, Dokkyo Medical University, Koshigaya, Saitama, Japan ; Yoshida Eye Hospital, Hokodate, Hokkaido, Japan
| | - Makoto Chikuda
- Department of Ophthalmology, Koshigaya Hospital, Dokkyo Medical University, Koshigaya, Saitama, Japan
| | - Shigeki Machida
- Department of Ophthalmology, Koshigaya Hospital, Dokkyo Medical University, Koshigaya, Saitama, Japan
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