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Zhang X, Liew KJ, Cao L, Wang J, Chang Z, Tan MCY, Chong KL, Chong CS. Transcriptome analysis of Candida albicans planktonic cells in response to plasma medicine. J Med Microbiol 2024; 73. [PMID: 38967406 DOI: 10.1099/jmm.0.001841] [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] [Indexed: 07/06/2024] Open
Abstract
Introduction. Cold plasma is frequently utilized for the purpose of eliminating microbial contaminants. Under optimal conditions, it can function as plasma medicine for treating various diseases, including infections caused by Candida albicans, an opportunistic pathogen that can overgrow in individuals with weakened immune system.Gap Statement. To date, there has been less molecular study on cold plasma-treated C. albicans.Research Aim. The study aims to fill the gap in understanding the molecular response of C. albicans to cold plasma treatment.Methodology. This project involved testing a cold plasma generator to determine its antimicrobial effectiveness on C. albicans' planktonic cells. Additionally, the cells' transcriptomics responses were investigated using RNA sequencing at various treatment durations (1, 3 and 5 min).Results. The results show that our cold plasma effectively eliminates C. albicans. Cold plasma treatment resulted in substantial downregulation of important pathways, such as 'nucleotide metabolism', 'DNA replication and repair', 'cell growth', 'carbohydrate metabolism' and 'amino acid metabolism'. This was an indication of cell cycle arrest of C. albicans to preserve energy consumption under unfavourable conditions. Nevertheless, C. albicans adapted its GSH antioxidant system to cope with the oxidative stress induced by reactive oxygen species, reactive nitrogen species and other free radicals. The treatment likely led to a decrease in cell pathogenicity as many virulence factors were downregulated.Conclusion. The study demonstrated the major affected pathways in cold plasma-treated C. albicans, providing valuable insights into the molecular response of C. albicans to cold plasma treatment. The findings contribute to the understanding of the antimicrobial efficiency of cold plasma and its potential applications in the field of microbiology.
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Affiliation(s)
- Xinhua Zhang
- School of Photoelectric Engineering, Changzhou Institute of Technology, Changzhou 213028, PR China
- Suzhou Amazing Grace Medical Equipment Co., Ltd, Suzhou 215101, PR China
- Jiangsu Huayu Printing & Coating Equipment Co. Ltd, Nantong 226300, PR China
| | - Kok Jun Liew
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia
| | - Li Cao
- Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou 215153, PR China
| | - Jie Wang
- Suzhou Hospital, Affiliated Hospital of Medical School, Nanjing University, Suzhou 215153, PR China
| | - Zhidong Chang
- Suzhou Amazing Grace Medical Equipment Co., Ltd, Suzhou 215101, PR China
| | - Melvin Chun Yun Tan
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia
| | - Kheng Loong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia
| | - Chun Shiong Chong
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Skudai 81310, Johor, Malaysia
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iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death. Cells 2022; 11:cells11132018. [PMID: 35805101 PMCID: PMC9265749 DOI: 10.3390/cells11132018] [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: 04/30/2022] [Revised: 06/19/2022] [Accepted: 06/22/2022] [Indexed: 02/05/2023] Open
Abstract
Programmed cell death (PCD) is an essential biological process involved in many human pathologies. According to the continuous discovery of new PCD forms, a large number of proteins have been found to regulate PCD. Notably, post-translational modifications play critical roles in PCD process and the rapid advances in proteomics have facilitated the discovery of new PCD proteins. However, an integrative resource has yet to be established for maintaining these regulatory proteins. Here, we briefly summarize the mainstream PCD forms, as well as the current progress in the development of public databases to collect, curate and annotate PCD proteins. Further, we developed a comprehensive database, with integrated annotations for programmed cell death (iPCD), which contained 1,091,014 regulatory proteins involved in 30 PCD forms across 562 eukaryotic species. From the scientific literature, we manually collected 6493 experimentally identified PCD proteins, and an orthologous search was then conducted to computationally identify more potential PCD proteins. Additionally, we provided an in-depth annotation of PCD proteins in eight model organisms, by integrating the knowledge from 102 additional resources that covered 16 aspects, including post-translational modification, protein expression/proteomics, genetic variation and mutation, functional annotation, structural annotation, physicochemical property, functional domain, disease-associated information, protein–protein interaction, drug–target relation, orthologous information, biological pathway, transcriptional regulator, mRNA expression, subcellular localization and DNA and RNA element. With a data volume of 125 GB, we anticipate that iPCD can serve as a highly useful resource for further analysis of PCD in eukaryotes.
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Ravel JM, Monraz Gomez LC, Sompairac N, Calzone L, Zhivotovsky B, Kroemer G, Barillot E, Zinovyev A, Kuperstein I. Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. Cancers (Basel) 2020; 12:E990. [PMID: 32316560 PMCID: PMC7226067 DOI: 10.3390/cancers12040990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 12/25/2022] Open
Abstract
The processes leading to, or avoiding cell death are widely studied, because of their frequent perturbation in various diseases. Cell death occurs in three highly interconnected steps: Initiation, signaling and execution. We used a systems biology approach to gather information about all known modes of regulated cell death (RCD). Based on the experimental data retrieved from literature by manual curation, we graphically depicted the biological processes involved in RCD in the form of a seamless comprehensive signaling network map. The molecular mechanisms of each RCD mode are represented in detail. The RCD network map is divided into 26 functional modules that can be visualized contextually in the whole seamless network, as well as in individual diagrams. The resource is freely available and accessible via several web platforms for map navigation, data integration, and analysis. The RCD network map was employed for interpreting the functional differences in cell death regulation between Alzheimer's disease and non-small cell lung cancer based on gene expression data that allowed emphasizing the molecular mechanisms underlying the inverse comorbidity between the two pathologies. In addition, the map was used for the analysis of genomic and transcriptomic data from ovarian cancer patients that provided RCD map-based signatures of four distinct tumor subtypes and highlighted the difference in regulations of cell death molecular mechanisms.
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Affiliation(s)
- Jean-Marie Ravel
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
- Laboratoire de génétique médicale, CHRU-Nancy, F-54000 Nancy, France
- Inserm, NGERE, Université de Lorraine, F-54000 Nancy, France
| | - L. Cristobal Monraz Gomez
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Nicolas Sompairac
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
- Centre de Recherches Interdisciplinaires, Université Paris Descartes, 75006 Paris, France
| | - Laurence Calzone
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Boris Zhivotovsky
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Division of Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 210, 17177 Stockholm, Sweden
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université de Paris, Sorbonne Université, Inserm U1138, Institut Universitaire de France, 75006 Paris, France;
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, 94805 Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou 215163, China
- Karolinska Institute, Department of Women’s and Children’s Health, Karolinska University Hospital, 171 77 Stockholm, Sweden
| | - Emmanuel Barillot
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Andrei Zinovyev
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
| | - Inna Kuperstein
- Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, 75005 Paris, France; (J.-M.R.); (L.C.M.G.); (N.S.); (L.C.); (E.B.); (A.Z.)
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Deng W, Ma L, Zhang Y, Zhou J, Wang Y, Liu Z, Xue Y. THANATOS: an integrative data resource of proteins and post-translational modifications in the regulation of autophagy. Autophagy 2019; 14:296-310. [PMID: 29157087 DOI: 10.1080/15548627.2017.1402990] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Macroautophagy/autophagy is a highly conserved process for degrading cytoplasmic contents, determines cell survival or death, and regulates the cellular homeostasis. Besides ATG proteins, numerous regulators together with various post-translational modifications (PTMs) are also involved in autophagy. In this work, we collected 4,237 experimentally identified proteins regulated in autophagy and cell death pathways from the literature. Then we computationally identified potential orthologs of known proteins, and developed a comprehensive database of The Autophagy, Necrosis, ApopTosis OrchestratorS (THANATOS, http://thanatos.biocuckoo.org ), containing 191,543 proteins potentially associated with autophagy and cell death pathways in 164 eukaryotes. We performed an evolutionary analysis of ATG genes, and observed that ATGs required for the autophagosome formation are highly conserved across eukaryotes. Further analyses revealed that known cancer genes and drug targets were overrepresented in human autophagy proteins, which were significantly associated in a number of signaling pathways and human diseases. By reconstructing a human kinase-substrate phosphorylation network for ATG proteins, our results confirmed that phosphorylation play a critical role in regulating autophagy. In total, we mapped 65,015 known sites of 11 types of PTMs to collected proteins, and revealed that all types of PTM substrates were enriched in human autophagy. In addition, we observed multiple types of PTM regulators such as protein kinases and ubiquitin E3 ligases or adaptors were significantly associated with human autophagy, and again the results emphasized the importance of PTM regulations in autophagy. We anticipated THANATOS can be a useful resource for further studies.
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Affiliation(s)
- Wankun Deng
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Lili Ma
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Ying Zhang
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Jiaqi Zhou
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Yongbo Wang
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
| | - Zexian Liu
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China.,b State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine , Sun Yat-sen University Cancer Center , 651 Dongfeng Road East, 510060 , Guangzhou , Guangdong , P. R. China
| | - Yu Xue
- a Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Biomedical Engineering , Huazhong University of Science and Technology , Wuhan , Hubei 430074 , China
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Time-resolved, single-cell analysis of induced and programmed cell death via non-invasive propidium iodide and counterstain perfusion. Sci Rep 2016; 6:32104. [PMID: 27580964 PMCID: PMC5007472 DOI: 10.1038/srep32104] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 08/03/2016] [Indexed: 01/02/2023] Open
Abstract
Conventional propidium iodide (PI) staining requires the execution of multiple steps prior to analysis, potentially affecting assay results as well as cell vitality. In this study, this multistep analysis method has been transformed into a single-step, non-toxic, real-time method via live-cell imaging during perfusion with 0.1 μM PI inside a microfluidic cultivation device. Dynamic PI staining was an effective live/dead analytical tool and demonstrated consistent results for single-cell death initiated by direct or indirect triggers. Application of this method for the first time revealed the apparent antibiotic tolerance of wild-type Corynebacterium glutamicum cells, as indicated by the conversion of violet fluorogenic calcein acetoxymethyl ester (CvAM). Additional implementation of this method provided insight into the induced cell lysis of Escherichia coli cells expressing a lytic toxin-antitoxin module, providing evidence for non-lytic cell death and cell resistance to toxin production. Finally, our dynamic PI staining method distinguished necrotic-like and apoptotic-like cell death phenotypes in Saccharomyces cerevisiae among predisposed descendants of nutrient-deprived ancestor cells using PO-PRO-1 or green fluorogenic calcein acetoxymethyl ester (CgAM) as counterstains. The combination of single-cell cultivation, fluorescent time-lapse imaging, and PI perfusion facilitates spatiotemporally resolved observations that deliver new insights into the dynamics of cellular behaviour.
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Petitjean M, Teste MA, Léger-Silvestre I, François JM, Parrou JL. RETRACTED:A new function for the yeast trehalose-6P synthase (Tps1) protein, as key pro-survival factor during growth, chronological ageing, and apoptotic stress. Mech Ageing Dev 2016; 161:234-246. [PMID: 27507670 DOI: 10.1016/j.mad.2016.07.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 07/20/2016] [Accepted: 07/25/2016] [Indexed: 12/20/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/our-business/policies/article-withdrawal).
This article has been retracted at the request of Marie-Ange Teste, Isabelle Léger-Silvestre, Jean M François and Jean-Luc Parrou. Marjorie Petitjean could not be reached.
The corresponding author identified major issues and brought them to the attention of the Journal.
These issues span from significant errors in the Material and Methods section of the article and major flaws in cytometry data analysis to data fabrication on the part of one of the authors.
Given these errors, the retracting authors state that the only responsible course of action would be to retract the article, to respect scientific integrity and maintain the standards and rigor of literature from the retracting authors' group as well as the Journal.
The retracting authors sincerely apologize to the readers and editors.
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Affiliation(s)
| | - Marie-Ange Teste
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Isabelle Léger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, CNRS, Université de Toulouse, 118 route de Narbonne, F-31000 Toulouse, France
| | - Jean M François
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Jean-Luc Parrou
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France.
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Wanichthanarak K, Nookaew I, Petranovic D. yStreX: yeast stress expression database. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau068. [PMID: 25024351 PMCID: PMC4095678 DOI: 10.1093/database/bau068] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Over the past decade genome-wide expression analyses have been often used to study how expression of genes changes in response to various environmental stresses. Many of these studies (such as effects of oxygen concentration, temperature stress, low pH stress, osmotic stress, depletion or limitation of nutrients, addition of different chemical compounds, etc.) have been conducted in the unicellular Eukaryal model, yeast Saccharomyces cerevisiae. However, the lack of a unifying or integrated, bioinformatics platform that would permit efficient and rapid use of all these existing data remain an important issue. To facilitate research by exploiting existing transcription data in the field of yeast physiology, we have developed the yStreX database. It is an online repository of analyzed gene expression data from curated data sets from different studies that capture genome-wide transcriptional changes in response to diverse environmental transitions. The first aim of this online database is to facilitate comparison of cross-platform and cross-laboratory gene expression data. Additionally, we performed different expression analyses, meta-analyses and gene set enrichment analyses; and the results are also deposited in this database. Lastly, we constructed a user-friendly Web interface with interactive visualization to provide intuitive access and to display the queried data for users with no background in bioinformatics. Database URL:http://www.ystrexdb.com
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Affiliation(s)
- Kwanjeera Wanichthanarak
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden and Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Intawat Nookaew
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden and Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USADepartment of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden and Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dina Petranovic
- Department of Chemical and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden and Comparative Genomics Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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