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Autumn M, Hu Y, Zeng J, McMenamin SK. Growth patterns of caudal fin rays are informed by both external signals from the regenerating organ and remembered identity autonomous to the local tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.586899. [PMID: 38585773 PMCID: PMC10996721 DOI: 10.1101/2024.03.29.586899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Regenerating tissues must remember or interpret their spatial position, using this information to restore original size and patterning. The external skeleton of the zebrafish caudal fin is composed of 18 rays; after any portion of the fin is amputated, position-dependent regenerative growth restores each ray to its original length. We tested for transcriptional differences during regeneration of proximal versus distal tissues and identified 489 genes that differed in proximodistal expression. Thyroid hormone directs multiple aspects of ray patterning along the proximodistal axis, and we identified 364 transcripts showing a proximodistal expression pattern that was dependent on thyroid hormone context. To test what aspects of ray positional identity are directed by extrinsic cues versus remembered identity autonomous to the tissue itself, we transplanted distal portions of rays to proximal environments and evaluated regeneration within the new location. While neighboring proximal tissue showed robust expression of scpp7, a transcript with thyroid-regulated proximal enrichment, regenerating rays originating from transplanted distal tissue showed reduced (distal-like) expression during outgrowth. These distal-to-proximal transplants regenerated far beyond the length of the graft itself, indicating that cues from the proximal environment promoted additional growth. Nonetheless, these transplants initially regenerated at a much slower rate compared to controls, suggesting retained memory of distal identity. This early growth retardation caused rays that originated from transplants to become noticeably shorter than their native neighboring rays. While several aspects of fin ray morphology (bifurcation, segment length) were found to be determined by the environment, regeneration speed and ray length are remembered autonomously by tissues, persisting across multiple rounds of amputation and regeneration.
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Affiliation(s)
- Melody Autumn
- Biology Department, Boston College, Chestnut Hill, MA 02467
| | - Yinan Hu
- Biology Department, Boston College, Chestnut Hill, MA 02467
| | - Jenny Zeng
- Biology Department, Boston College, Chestnut Hill, MA 02467
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Chauhan NR, Kundu S, Bal R, Chattopadhyay D, Sahu R, Mehto S, Yadav R, Krishna S, Jena KK, Satapathy S, Pv A, Murmu KC, Singh B, Patnaik S, Jena S, Harshan KH, Syed GH, Idris MM, Prasad P, Chauhan S. Transgenic mouse models support a protective role of type I IFN response in SARS-CoV-2 infection-related lung immunopathology and neuroinvasion. Cell Rep 2023; 42:113275. [PMID: 37874678 DOI: 10.1016/j.celrep.2023.113275] [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: 04/07/2023] [Revised: 08/14/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
Type I interferon (IFN-I) response is the first line of host defense against invading viruses. In the absence of definite mouse models, the role of IFN-I in SARS-CoV-2 infection remains perplexing. Here, we develop two mouse models, one with constitutively high IFN-I response (hACE2; Irgm1-/-) and the other with dampened IFN-I response (hACE2; Ifnar1-/-), to comprehend the role of IFN-I response. We report that hACE2; Irgm1-/- mice are resistant to lethal SARS-CoV-2 infection. In contrast, a severe SARS-CoV-2 infection along with immune cell infiltration, cytokine storm, and enhanced pathology is observed in the lungs and brain of hACE2; Ifnar1-/- mice. The hACE2; Irgm1-/-Ifnar1-/- double-knockout mice display loss of the protective phenotype observed in hACE2; Irgm1-/- mice, suggesting that heightened IFN-I response accounts for the observed immunity. Taking the results together, we demonstrate that IFN-I protects from lethal SARS-CoV-2 infection, and Irgm1 (IRGM) could be an excellent therapeutic target against SARS-CoV-2.
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Affiliation(s)
- Nishant Ranjan Chauhan
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India.
| | - Soumya Kundu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Ramyasingh Bal
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Diya Chattopadhyay
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Rinku Sahu
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Subhash Mehto
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Rina Yadav
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Sivaram Krishna
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Kautilya Kumar Jena
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Sameekshya Satapathy
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Anusha Pv
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Krushna C Murmu
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Bharati Singh
- Virus-Host Interactions Lab, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | | | - Sarita Jena
- Experimental Animal Facility, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Krishnan H Harshan
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Gulam Hussain Syed
- Virus-Host Interactions Lab, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, Odisha, India
| | - Mohammed M Idris
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India
| | - Punit Prasad
- Epigenetic and Chromatin Biology Unit, Institute of Life Sciences, Bhubaneswar 751023, India
| | - Santosh Chauhan
- Cell Biology and Infectious Diseases Unit, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar 751023, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana 500007, India.
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Banu S, Nagaraj R, Idris MM. A proteomic perspective and involvement of cytokines in SARS-CoV-2 infection. PLoS One 2023; 18:e0279998. [PMID: 36608055 PMCID: PMC9821788 DOI: 10.1371/journal.pone.0279998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Infection with the SARS-CoV-2 virus results in manifestation of several clinical observations from asymptomatic to multi-organ failure. Biochemically, the serious effects are due to what is described as cytokine storm. The initial infection region for COVID-19 is the nasopharyngeal/oropharyngeal region which is the site where samples are taken to examine the presence of virus. We have now carried out detailed proteomic analysis of the nasopharyngeal/oropharyngeal swab samples collected from normal individuals and those tested positive for SARS-CoV-2, in India, during the early days of the pandemic in 2020, by RTPCR, involving high throughput quantitative proteomics analysis. Several proteins like annexins, cytokines and histones were found differentially regulated in the host human cells following SARS-CoV-2 infection. Genes for these proteins were also observed to be differentially regulated when their expression was analyzed. Majority of the cytokine proteins were found to be up regulated in the infected individuals. Cell to Cell signaling interaction, Immune cell trafficking and inflammatory response pathways were found associated with the differentially regulated proteins based on network pathway analysis.
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Affiliation(s)
- Sarena Banu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- * E-mail: (RN); (MMI)
| | - Mohammed M. Idris
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- * E-mail: (RN); (MMI)
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Zhu WQ, Li K, Su S, Chen W, Liu Y, Qiu J. Effects of Zinc Ions Released From Ti-NW-Zn Surface on Osteogenesis and Angiogenesis In Vitro and in an In Vivo Zebrafish Model. Front Bioeng Biotechnol 2022; 10:848769. [PMID: 35528211 PMCID: PMC9068938 DOI: 10.3389/fbioe.2022.848769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/16/2022] [Indexed: 11/25/2022] Open
Abstract
Zinc-modified titanium materials have been widely applied in oral implants. Among them, our previous studies have also successfully prepared a novel acid-etched microstructured titanium surface modified with zinc-containing nanowires (Ti-NW-Zn) and proved its excellent biocompatibility. It is well known that the functional regulation between angiogenesis and osteogenesis is of great importance for bone remodeling around implants. However, there are few reports concerning the biological safety of zinc ions released from materials and the appropriate concentration of released zinc ions which was more conducive to angiogenesis and bone regeneration. In this study, we investigated the effects of zinc ions released from Ti-NW-Zn surfaces on angiogenesis and osteogenesis using the zebrafish model and revealed the relationship between angiogenesis and osteogenesis via HUVECs and MC3T3-E1s in vitro. We found that the zinc ions released from Ti-NW-Zn surfaces, with a concentration lower than median lethal concentrations (LCs) of zebrafish, were biologically safe and promote osteogenesis and angiogenesis in vivo. Moreover, the proper concentration of zinc ions could induce the proliferation of HUVECs and osteogenic differentiation. The positive effects of the appropriate concentration of zinc ions on osteoblast behaviors might be regulated by activating the MAPK/ERK signaling pathway. These aspects may provide new sights into the mechanisms underlying zinc-modified titanium surfaces between osteogenesis and angiogenesis, to lay the foundation for further improving the materials, meanwhile, promoting the applications in dentistry.
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Affiliation(s)
- Wen-Qing Zhu
- Department of Oral Implantology, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, China
| | - Kang Li
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, China
| | - Shan Su
- Department of Oral Implantology, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, China
| | - Wei Chen
- Department of Oral Implantology, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, China
| | - Yao Liu
- Department of Oral Implantology, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, China
| | - Jing Qiu
- Department of Oral Implantology, Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
- Jiangsu Province Key Laboratory of Oral Diseases, Nanjing, China
- Jiangsu Province Engineering Research Center of Stomatological Translational Medicine, Nanjing, China
- *Correspondence: Jing Qiu,
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Enayathullah MG, Parekh Y, Banu S, Ram S, Nagaraj R, Kumar BK, Idris MM. Gramicidin S and melittin: potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection. Sci Rep 2022; 12:3446. [PMID: 35236909 PMCID: PMC8891299 DOI: 10.1038/s41598-022-07341-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 01/02/2023] Open
Abstract
The COVID19 pandemic has led to multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of the well-studied antibacterial peptides gramicidin S and melittin obtained from Bacillus brevis and bee venom respectively. The EC50 values for gramicidin S and melittin were 1.571 µg and 0.656 µg respectively based on in vitro antiviral assay. Significant decrease in the viral load as compared to the untreated group with no/very less cytotoxicity was observed. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 h onwards with a maximal viral clearance after 24 h post infection. Proteomics analysis indicated that more than 250 proteins were differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 h post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.
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Affiliation(s)
| | - Yash Parekh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Sarena Banu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Sushma Ram
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Bokara Kiran Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
| | - Mohammed M Idris
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
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