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Mishra A, Kumar S, Singh A. Biosynthesis and characterization of Ocimum sanctum green silver nanoparticles and unravelling their enhanced anti-filarial activity through a HRAMS proteomics approach. RSC Adv 2024; 14:5893-5906. [PMID: 38362069 PMCID: PMC10866198 DOI: 10.1039/d3ra08702f] [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: 12/20/2023] [Accepted: 02/04/2024] [Indexed: 02/17/2024] Open
Abstract
The available anti-filarial medications are largely ineffective against adult filarial worms. Also, these drugs have several drawbacks such as toxicity and development of resistance owing to long-term usage. Green nanomedicine may offer better solutions for Lymphatic Filariasis treatment due to its tiny size, biocompatibility, and better penetration at considerably lower costs with higher therapeutic efficacy. In the present study, Ocimum sanctum silver nanoparticles (OSAgNPs) were bio-synthesized and their anti-filarial efficacy was evaluated against adult filarial parasites. The green nanoparticles were characterized by UV-VIS spectroscopy, XRD, FTIR, SEM, and TEM analysis. The OSAgNPs significantly affected the motility and viability of adult Setaria cervi parasites after 4 h of incubation at concentrations higher than 0.5 μg ml-1. Proteomics analysis by high resolution accurate mass spectrometry revealed that 213 proteins were differentially expressed following OSAgNP treatment. Mostly these DEPs belonged to the many biochemical and molecular pathways of parasites such as muscle proteins, antioxidant proteins, heat shock proteins, signal recognition proteins, and energy metabolism-related proteins. Undoubtedly, this study will open new avenues for the development of novel anti-filarial drugs based on green nanoparticles.
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Affiliation(s)
- Ayushi Mishra
- Department of Biochemistry, Institute of Science, Banaras Hindu University Varanasi 221005 U.P. India
| | - Sunil Kumar
- Department of Biochemistry, Institute of Science, Banaras Hindu University Varanasi 221005 U.P. India
| | - Anchal Singh
- Department of Biochemistry, Institute of Science, Banaras Hindu University Varanasi 221005 U.P. India
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2
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Rocha JJ, Jayaram SA, Stevens TJ, Muschalik N, Shah RD, Emran S, Robles C, Freeman M, Munro S. Functional unknomics: Systematic screening of conserved genes of unknown function. PLoS Biol 2023; 21:e3002222. [PMID: 37552676 PMCID: PMC10409296 DOI: 10.1371/journal.pbio.3002222] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023] Open
Abstract
The human genome encodes approximately 20,000 proteins, many still uncharacterised. It has become clear that scientific research tends to focus on well-studied proteins, leading to a concern that poorly understood genes are unjustifiably neglected. To address this, we have developed a publicly available and customisable "Unknome database" that ranks proteins based on how little is known about them. We applied RNA interference (RNAi) in Drosophila to 260 unknown genes that are conserved between flies and humans. Knockdown of some genes resulted in loss of viability, and functional screening of the rest revealed hits for fertility, development, locomotion, protein quality control, and resilience to stress. CRISPR/Cas9 gene disruption validated a component of Notch signalling and 2 genes contributing to male fertility. Our work illustrates the importance of poorly understood genes, provides a resource to accelerate future research, and highlights a need to support database curation to ensure that misannotation does not erode our awareness of our own ignorance.
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Affiliation(s)
- João J. Rocha
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Tim J. Stevens
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | | | - Rajen D. Shah
- Centre for Mathematical Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Sahar Emran
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Cristina Robles
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Sean Munro
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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3
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Mackmull MT, Nagel L, Sesterhenn F, Muntel J, Grossbach J, Stalder P, Bruderer R, Reiter L, van de Berg WDJ, de Souza N, Beyer A, Picotti P. Global, in situ analysis of the structural proteome in individuals with Parkinson's disease to identify a new class of biomarker. Nat Struct Mol Biol 2022; 29:978-989. [PMID: 36224378 DOI: 10.1038/s41594-022-00837-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/18/2022] [Indexed: 12/23/2022]
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disease for which robust biomarkers are needed. Because protein structure reflects function, we tested whether global, in situ analysis of protein structural changes provides insight into PD pathophysiology and could inform a new concept of structural disease biomarkers. Using limited proteolysis-mass spectrometry (LiP-MS), we identified 76 structurally altered proteins in cerebrospinal fluid (CSF) of individuals with PD relative to healthy donors. These proteins were enriched in processes misregulated in PD, and some proteins also showed structural changes in PD brain samples. CSF protein structural information outperformed abundance information in discriminating between healthy participants and those with PD and improved the discriminatory performance of CSF measures of the hallmark PD protein α-synuclein. We also present the first analysis of inter-individual variability of a structural proteome in healthy individuals, identifying biophysical features of variable protein regions. Although independent validation is needed, our data suggest that global analyses of the human structural proteome will guide the development of novel structural biomarkers of disease and enable hypothesis generation about underlying disease processes.
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Affiliation(s)
- Marie-Therese Mackmull
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Luise Nagel
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Fabian Sesterhenn
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | - Jan Grossbach
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Patrick Stalder
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | | | | | - Wilma D J van de Berg
- Amsterdam UMC location Vrije Universiteit Amsterdam, Section Clinical Neuroanatomy and Biobanking, Department Anatomy and Neurosciences, Amsterdam, the Netherlands.,Amsterdam Neuroscience, Neurodegeneration, Amsterdam, the Netherlands
| | - Natalie de Souza
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.,Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
| | - Andreas Beyer
- Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany. .,Faculty of Medicine and University Hospital of Cologne, and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Institute for Genetics, Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany.
| | - Paola Picotti
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland.
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Zambom-Ferraresi F, Zambom-Ferraresi F, Fernández-Irigoyen J, Lachén-Montes M, Cartas-Cejudo P, Lasarte JJ, Casares N, Fernández S, Cedeño-Veloz BA, Maraví-Aznar E, Uzcanga-Lacabe MI, Galbete A, Santamaría E, Martínez-Velilla N. Olfactory Characterization and Training in Older Adults: Protocol Study. Front Aging Neurosci 2021; 13:757081. [PMID: 34867284 PMCID: PMC8637846 DOI: 10.3389/fnagi.2021.757081] [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: 08/11/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
The aim of this article is to present the research protocol for a prospective cohort study that will assess the olfactory function and the effect of an intervention based on olfactory training in healthy very old adults (≥75 years old). A convenience sample of 180 older people (50% female) will be recruited in three different environments: hospitalized control group (CH) with stable acute illness (n = 60); ambulatory control group (CA) of community-based living (n = 60); and an experimental odor training group (EOT) from nursing homes (n = 60). The odor training (OT) intervention will last 12 weeks. All the volunteers will be assessed at baseline; CA and EOT groups will also be assessed after 12 weeks. The primary end point will be change in olfactory capacity from baseline to 12 weeks period of intervention or control. The intervention effects will be assessed with the overall score achieved in Sniffin Sticks Test (SST) – Threshold, Discrimination, and Identification (TDI) extended version. Secondary end points will be changes in cognitive tasks, quality of life, mood, immune status, and functional capacity. All these measurements will be complemented with an immune fitness characterization and a deep proteome profiling of the olfactory epithelium (OE) cultured ex vivo. The current study will provide additional evidence to support the implementation of olfactory precision medicine and the development of immunomodulatory nasal therapies based on non-invasive procedures. The proposed intervention will also intend to increase the knowledge about the olfactory function in very elderly people, improve function and quality of life, and promote the recovery of the health.
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Affiliation(s)
- Fabíola Zambom-Ferraresi
- Geriatric Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
| | - Fabricio Zambom-Ferraresi
- Geriatric Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
| | - Paz Cartas-Cejudo
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
| | - Juan José Lasarte
- Immunology and Immunotherapy Program, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IdisNa), Universidad de Navarra, Pamplona, Spain
| | - Noelia Casares
- Immunology and Immunotherapy Program, Centro de Investigación Médica Aplicada, Instituto de Investigación Sanitaria de Navarra (IdisNa), Universidad de Navarra, Pamplona, Spain
| | - Secundino Fernández
- Department of Otolaryngology, Clínica Universidad de Navarra, Facultad de Medicina, Universidad de Navarra, Pamplona, Spain
| | | | - Enrique Maraví-Aznar
- Department of Otolaryngology, Hospital Universitario de Navarra (HUN), Pamplona, Spain
| | | | - Arkaitz Galbete
- Department of Statistics, Computer Science and Mathematics, Universidad Pública de Navarra (UPNA), Pamplona, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
| | - Nicolás Martínez-Velilla
- Geriatric Unit, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain.,Department of Geriatrics, Hospital Universitario de Navarra (HUN), Pamplona, Spain
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5
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Barrera-Conde M, Ausin K, Lachén-Montes M, Fernández-Irigoyen J, Galindo L, Cuenca-Royo A, Fernández-Avilés C, Pérez V, de la Torre R, Santamaría E, Robledo P. Cannabis Use Induces Distinctive Proteomic Alterations in Olfactory Neuroepithelial Cells of Schizophrenia Patients. J Pers Med 2021; 11:jpm11030160. [PMID: 33668817 PMCID: PMC7996288 DOI: 10.3390/jpm11030160] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/17/2021] [Accepted: 02/20/2021] [Indexed: 12/19/2022] Open
Abstract
A close epidemiological link has been reported between cannabis use and schizophrenia (SCZ). However, biochemical markers in living humans related to the impact of cannabis in this disease are still missing. Olfactory neuroepithelium (ON) cells express neural features and offer a unique advantage to study biomarkers of psychiatric diseases. The aim of our study was to find exclusively deregulated proteins in ON cells of SCZ patients with and without a history of cannabis use. Thus, we compared the proteomic profiles of SCZ non-cannabis users (SCZ/nc) and SCZ cannabis users (SCZ/c) with control subjects non-cannabis users (C/nc) and control cannabis users (C/c). The results revealed that the main cascades affected in SCZ/nc were cell cycle, DNA replication, signal transduction and protein localization. Conversely, cannabis use in SCZ patients induced specific alterations in metabolism of RNA and metabolism of proteins. The levels of targeted proteins in each population were then correlated with cognitive performance and clinical scores. In SCZ/c, the expression levels of 2 proteins involved in the metabolism of RNA (MTREX and ZNF326) correlated with several cognitive markers and clinical signs. Moreover, use duration of cannabis negatively correlated with ZNF326 expression. These findings indicate that RNA-related proteins might be relevant to understand the influence of cannabis use on SCZ.
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Affiliation(s)
- Marta Barrera-Conde
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain;
| | - Karina Ausin
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Mercedes Lachén-Montes
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Joaquín Fernández-Irigoyen
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Liliana Galindo
- Department of Psychiatry, University of Cambridge, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge CB2 1TN, UK;
- Neuropsychiatry and Addictions Institute (INAD) of Parc de Salut Mar, 08003 Barcelona and CIBER de Salud Mental, Spain;
| | - Aida Cuenca-Royo
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
| | | | - Víctor Pérez
- Neuropsychiatry and Addictions Institute (INAD) of Parc de Salut Mar, 08003 Barcelona and CIBER de Salud Mental, Spain;
- Department of Psychiatry and Legal Medicine, Autonomous University of Barcelona, 08193 Barcelona, Spain
| | - Rafael de la Torre
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain;
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Enrique Santamaría
- Clinical Neuroproteomics Unit, Proteomics Platform, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdisNA, Proteored-ISCIII, 31006 Pamplona, Spain; (K.A.); (M.L.-M.); (J.F.-I.); (E.S.)
| | - Patricia Robledo
- Integrative Pharmacology and Systems Neuroscience, Neuroscience Research Program, IMIM-Hospital del Mar Research Institute, 08003 Barcelona, Spain; (M.B.-C.); (A.C.-R.); (R.d.l.T.)
- Department of Experimental and Health Sciences, University Pompeu Fabra, 08003 Barcelona, Spain;
- Correspondence: ; Tel.: +34-93-316-0455
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