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Aghaieabiane N, Koutis I. SGCP: a spectral self-learning method for clustering genes in co-expression networks. BMC Bioinformatics 2024; 25:230. [PMID: 38956463 PMCID: PMC11221046 DOI: 10.1186/s12859-024-05848-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/18/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND A widely used approach for extracting information from gene expression data employs the construction of a gene co-expression network and the subsequent computational detection of gene clusters, called modules. WGCNA and related methods are the de facto standard for module detection. The purpose of this work is to investigate the applicability of more sophisticated algorithms toward the design of an alternative method with enhanced potential for extracting biologically meaningful modules. RESULTS We present self-learning gene clustering pipeline (SGCP), a spectral method for detecting modules in gene co-expression networks. SGCP incorporates multiple features that differentiate it from previous work, including a novel step that leverages gene ontology (GO) information in a self-leaning step. Compared with widely used existing frameworks on 12 real gene expression datasets, we show that SGCP yields modules with higher GO enrichment. Moreover, SGCP assigns highest statistical importance to GO terms that are mostly different from those reported by the baselines. CONCLUSION Existing frameworks for discovering clusters of genes in gene co-expression networks are based on relatively simple algorithmic components. SGCP relies on newer algorithmic techniques that enable the computation of highly enriched modules with distinctive characteristics, thus contributing a novel alternative tool for gene co-expression analysis.
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Affiliation(s)
- Niloofar Aghaieabiane
- Computer Science Department, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Ioannis Koutis
- Computer Science Department, New Jersey Institute of Technology, Newark, NJ, 07102, USA.
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Deane CS, da Silveira WA, Herranz R. Space omics research in Europe: Contributions, geographical distribution and ESA member state funding schemes. iScience 2022; 25:103920. [PMID: 35265808 PMCID: PMC8898910 DOI: 10.1016/j.isci.2022.103920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The European research community, via European Space Agency (ESA) spaceflight opportunities, has significantly contributed toward our current understanding of spaceflight biology. Recent molecular biology experiments include "omic" analysis, which provides a holistic and systems level understanding of the mechanisms underlying phenotypic adaptation. Despite vast interest in, and the immense quantity of biological information gained from space omics research, the knowledge of ESA-related space omics works as a collective remains poorly defined due to the recent exponential application of omics approaches in space and the limited search capabilities of pre-existing records. Thus, a review of such contributions is necessary to clarify and promote the development of space omics among ESA and ESA state members. To address this gap, in this review, we i) identified and summarized omics works led by European researchers, ii) geographically described these omics works, and iii) highlighted potential caveats in complex funding scenarios among ESA member states.
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Affiliation(s)
- Colleen S Deane
- Department of Sport and Health Science, College of Life and Environmental Sciences, University of Exeter, Exeter EX1 2LU, UK.,Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | | | - Willian A da Silveira
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida MSD, 2080, Malta
| | - Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), 28040 Madrid, Spain
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Salvetti A, Degl'Innocenti A, Gambino G, van Loon JJ, Ippolito C, Ghelardoni S, Ghigo E, Leoncino L, Prato M, Rossi L, Ciofani G. Artificially altered gravity elicits cell homeostasis imbalance in planarian worms, and cerium oxide nanoparticles counteract this effect. J Biomed Mater Res A 2021; 109:2322-2333. [PMID: 33960131 PMCID: PMC8518838 DOI: 10.1002/jbm.a.37215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/12/2021] [Accepted: 04/26/2021] [Indexed: 01/17/2023]
Abstract
Gravity alterations elicit complex and mostly detrimental effects on biological systems. Among these, a prominent role is occupied by oxidative stress, with consequences for tissue homeostasis and development. Studies in altered gravity are relevant for both Earth and space biomedicine, but their implementation using whole organisms is often troublesome. Here we utilize planarians, simple worm model for stem cell and regeneration biology, to characterize the pathogenic mechanisms brought by artificial gravity alterations. In particular, we provide a comprehensive evaluation of molecular responses in intact and regenerating specimens, and demonstrate a protective action from the space-apt for nanotechnological antioxidant cerium oxide nanoparticles.
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Affiliation(s)
- Alessandra Salvetti
- Università di Pisa, Department of Clinical and Experimental MedicineBiology and Genetics unitPisaItaly
| | - Andrea Degl'Innocenti
- Istituto Italiano di TecnologiaCenter for Materials Interfaces, Smart Bio‐InterfacesPisaItaly
| | - Gaetana Gambino
- Università di Pisa, Department of Clinical and Experimental MedicineBiology and Genetics unitPisaItaly
| | - Jack J.W.A. van Loon
- Dutch Experiment Support Center (DESC), Department of Oral and Maxillofacial Surgery/Oral PathologyAmsterdam UMC location VU University Medical Center & Academic Centre for Dentistry Amsterdam (ACTA)AmsterdamThe Netherlands
- TEC‐MMG LIS labEuropean Space Agency (ESA), European Space Research and Technology Center (ESTEC)NoordwijkThe Netherlands
| | - Chiara Ippolito
- Department of Clinical and Experimental Medicine, Biology and Genetics UnitUniversità di PisaPisaItaly
| | - Sandra Ghelardoni
- Department of Pathology, Biochemistry UnitUniversità di PisaPisaItaly
| | - Eric Ghigo
- Institut Hospitalo‐Universitaire Méditerranée InfectionMarseilleFrance
- Techno JouvenceMarseilleFrance
| | - Luca Leoncino
- Istituto Italiano di TecnologiaElectron Microscopy FacilityGenoaItaly
| | - Mirko Prato
- Istituto Italiano di TecnologiaMaterials Characterization FacilityGenoaItaly
| | - Leonardo Rossi
- Università di Pisa, Department of Clinical and Experimental MedicineBiology and Genetics unitPisaItaly
| | - Gianni Ciofani
- Istituto Italiano di TecnologiaCenter for Materials Interfaces, Smart Bio‐InterfacesPisaItaly
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Beheshti A, Miller J, Kidane Y, Berrios D, Gebre SG, Costes SV. NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies. Radiat Res 2018; 189:553-559. [DOI: 10.1667/rr15062.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Afshin Beheshti
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Jack Miller
- Lawrence Berkeley National Laboratory, Berkeley, California, 94720
| | - Yared Kidane
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Daniel Berrios
- USRA, NASA Ames Research Center, Moffett Field, Calfornia 94035
| | - Samrawit G. Gebre
- Wyle Labs, NASA Ames Research Center, Moffett Field, California, 94035
| | - Sylvain V. Costes
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, California 94035
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Ogneva IV, Belyakin SN, Sarantseva SV. The Development Of Drosophila Melanogaster under Different Duration Space Flight and Subsequent Adaptation to Earth Gravity. PLoS One 2016; 11:e0166885. [PMID: 27861601 PMCID: PMC5115863 DOI: 10.1371/journal.pone.0166885] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/05/2016] [Indexed: 12/20/2022] Open
Abstract
In prospective human exploration of outer space, the need to preserve a species over several generations under changed gravity conditions may arise. This paper demonstrates our results in the creation of the third generation of fruit fly Drosophila melanogaster (third-stage larvae) during the 44.5-day space flight (Foton-M4 satellite (2014, Russia)), then the fourth generation on Earth and the fifth generation again in conditions of the 12-day space flight (2014, in the Russian Segment of the ISS). The species preserves fertility despite a number of changes in the level of expression and content of cytoskeletal proteins, which are the key components of the cleavage spindle and the contractile ring of cells. The results of transcriptome screening and space analysis of cytoskeletal proteins show that the exposure to weightless conditions leads to the increased transcription of metabolic genes, cuticle components and the decreased transcription of genes involved in morphogenesis, cell differentiation, cytoskeletal organization and genes associated with the plasma membrane. "Subsequent" exposure to the microgravity for 12 days resulted in an even more significant increase/decrease in the transcription of the same genes. On the contrary, the transition from the microgravity conditions to the gravity of Earth leads to the increased transcription of genes whose products are involved in the morphogenesis, cytoskeletal organization, motility of cells and transcription regulation, and to the decreased transcription of cuticle genes and proteolytic processes.
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Affiliation(s)
- Irina V. Ogneva
- Cell Biophysics Group, State Scientific Center of Russian Federation Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
- I. M. Sechenov First Moscow State Medical University, Moscow, Russia
- * E-mail:
| | | | - Svetlana V. Sarantseva
- B. P. Konstantinov Petersburg Nuclear Physics Institute National Research Centre "Kurchatov Institute", Gatchina, Russia
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Hateley S, Hosamani R, Bhardwaj SR, Pachter L, Bhattacharya S. Transcriptomic response of Drosophila melanogaster pupae developed in hypergravity. Genomics 2016; 108:158-167. [PMID: 27621057 DOI: 10.1016/j.ygeno.2016.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/12/2016] [Accepted: 09/08/2016] [Indexed: 12/20/2022]
Abstract
Altered gravity can perturb normal development and induce corresponding changes in gene expression. Understanding this relationship between the physical environment and a biological response is important for NASA's space travel goals. We use RNA-Seq and qRT-PCR techniques to profile changes in early Drosophila melanogaster pupae exposed to chronic hypergravity (3g, or three times Earth's gravity). During the pupal stage, D. melanogaster rely upon gravitational cues for proper development. Assessing gene expression changes in the pupae under altered gravity conditions helps highlight gravity-dependent genetic pathways. A robust transcriptional response was observed in hypergravity-treated pupae compared to controls, with 1513 genes showing a significant (q<0.05) difference in gene expression. Five major biological processes were affected: ion transport, redox homeostasis, immune response, proteolysis, and cuticle development. This outlines the underlying molecular and biological changes occurring in Drosophila pupae in response to hypergravity; gravity is important for many biological processes on Earth.
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Affiliation(s)
- Shannon Hateley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States.
| | - Ravikumar Hosamani
- Space Biosciences Division, NASA Ames Research Center, Mountain View, CA 94035, United States.
| | - Shilpa R Bhardwaj
- Space Biosciences Division, NASA Ames Research Center, Mountain View, CA 94035, United States.
| | - Lior Pachter
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, United States; Departments of Mathematics and Computer Science, University of California, Berkeley, CA 94720, United States.
| | - Sharmila Bhattacharya
- Space Biosciences Division, NASA Ames Research Center, Mountain View, CA 94035, United States.
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Moskalev A, Zhikrivetskaya S, Krasnov G, Shaposhnikov M, Proshkina E, Borisoglebsky D, Danilov A, Peregudova D, Sharapova I, Dobrovolskaya E, Solovev I, Zemskaya N, Shilova L, Snezhkina A, Kudryavtseva A. A comparison of the transcriptome of Drosophila melanogaster in response to entomopathogenic fungus, ionizing radiation, starvation and cold shock. BMC Genomics 2015; 16 Suppl 13:S8. [PMID: 26694630 PMCID: PMC4686790 DOI: 10.1186/1471-2164-16-s13-s8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The molecular mechanisms that determine the organism's response to a variety of doses and modalities of stress factors are not well understood. Results We studied effects of ionizing radiation (144, 360 and 864 Gy), entomopathogenic fungus (10 and 100 CFU), starvation (16 h), and cold shock (+4, 0 and -4°C) on an organism's viability indicators (survival and locomotor activity) and transcriptome changes in the Drosophila melanogaster model. All stress factors but cold shock resulted in a decrease of lifespan proportional to the dose of treatment. However, stress-factors affected locomotor activity without correlation with lifespan. Our data revealed both significant similarities and differences in differential gene expression and the activity of biological processes under the influence of stress factors. Conclusions Studied doses of stress treatments deleteriously affect the organism's viability and lead to different changes of both general and specific cellular stress response mechanisms.
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Gravity sensing by cells: mechanisms and theoretical grounds. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2014. [DOI: 10.1007/s12210-013-0281-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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