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Zhang P, Wang M, Zhou T, Chen D. SeqWiz: a modularized toolkit for next-generation protein sequence database management and analysis. BMC Bioinformatics 2023; 24:201. [PMID: 37194023 DOI: 10.1186/s12859-023-05334-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/11/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Current proteomic technologies are fast-evolving to uncover the complex features of sequence processes, variations and modifications. Thus, protein sequence database and the corresponding softwares should also be improved to solve this issue. RESULTS We developed a state-of-the-art toolkit (SeqWiz) for constructing next-generation sequence databases and performing proteomic-centric sequence analyses. First, we proposed two derived data formats: SQPD (a well-structured and high-performance local sequence database based on SQLite), and SET (an associated list of selected entries based on JSON). The SQPD format follows the basic standards of the emerging PEFF format, which also aims to facilitate the search of complex proteoform. The SET format is designed for generating subsets with with high-efficiency. These formats are shown to greatly outperform the conventional FASTA or PEFF formats in time and resource consumption. Then, we mainly focused on the UniProt knowledgebase and developed a collection of open-source tools and basic modules for retrieving species-specific databases, formats conversion, sequence generation, sequence filter, and sequence analysis. These tools are implemented by using the Python language and licensed under the GNU General Public Licence V3. The source codes and distributions are freely available at GitHub ( https://github.com/fountao/protwiz/tree/main/seqwiz ). CONCLUSIONS SeqWiz is designed to be a collection of modularized tools, which is friendly to both end-users for preparing easy-to-use sequence databases as well as bioinformaticians for performing downstream sequence analysis. Besides the novel formats, it also provides compatible functions for handling the traditional text based FASTA or PEFF formats. We believe that SeqWiz will promote the implementing of complementary proteomics for data renewal and proteoform analysis to achieve precision proteomics. Additionally, it can also drive the improvement of proteomic standardization and the development of next-generation proteomic softwares.
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Affiliation(s)
- Ping Zhang
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China
| | - Min Wang
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China
| | - Tao Zhou
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China.
- Wuxi Maternity and Child Health Care Hospital, Wuxi School of Medicine, Jiangnan University, Wuxi, China.
| | - Daozhen Chen
- Research Institute for Reproductive Medicine and Genetic Diseases, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University, Wuxi, 214002, China.
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Hendy J, Warinner C, Bouwman A, Collins MJ, Fiddyment S, Fischer R, Hagan R, Hofman CA, Holst M, Chaves E, Klaus L, Larson G, Mackie M, McGrath K, Mundorff AZ, Radini A, Rao H, Trachsel C, Velsko IM, Speller CF. Proteomic evidence of dietary sources in ancient dental calculus. Proc Biol Sci 2018; 285:20180977. [PMID: 30051838 PMCID: PMC6083251 DOI: 10.1098/rspb.2018.0977] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/25/2018] [Indexed: 12/18/2022] Open
Abstract
Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (eighth century BC to nineteenth century AD) in England, as well as 14 dental calculus samples from contemporary dental patients and recently deceased individuals, to characterize the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detect proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches and authentication strategies in the identification of dietary proteins from archaeological dental calculus. This study demonstrates that proteomic approaches can robustly identify foodstuffs in the archaeological record that are typically under-represented due to their poor macroscopic preservation.
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Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
- Institute for Evolutionary Medicine, ETH-Zürich, University of Zürich, Zürich, Switzerland
- Department of Periodontology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Abigail Bouwman
- Institute for Evolutionary Medicine, ETH-Zürich, University of Zürich, Zürich, Switzerland
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, UK
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Fiddyment
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Roman Fischer
- Discovery Proteomics Facility, Target Discovery Institute, University of Oxford, Oxford, UK
| | - Richard Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
| | - Malin Holst
- BioArCh, Department of Archaeology, University of York, York, UK
- York Osteoarchaeology Ltd, Bishop Wilton, York, UK
| | - Eros Chaves
- Department of Periodontology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
- Pinellas Dental Specialties, Largo, FL 33776, USA
| | - Lauren Klaus
- Laboratories of Molecular Anthropology and Microbiome Research, Department of Anthropology, University of Oklahoma, Norman, USA
- Department of Periodontology, College of Dentistry, University of Oklahoma Health Sciences Center, Oklahoma, OK, USA
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Meaghan Mackie
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Krista McGrath
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Amy Z Mundorff
- Department of Anthropology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Anita Radini
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Huiyun Rao
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Christian Trachsel
- Functional Genomics Center, ETH-Zürich, University of Zürich, Zürich, Switzerland
| | - Irina M Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, UK
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Anthropology, University of British Columbia, Vancouver, BC, Canada
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Bioinformatics Analysis of Transcriptomic Data Reveals Refined Functional Networks for the Self-Renewal of Mouse Spermatogonial Stem Cells. Stem Cells Int 2018; 2018:5842714. [PMID: 30123288 PMCID: PMC6079398 DOI: 10.1155/2018/5842714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 05/17/2018] [Accepted: 05/30/2018] [Indexed: 01/15/2023] Open
Abstract
Spermatogonial stem cells (SSCs) are exquisitely regulated to reach a balance between proliferation and differentiation in the niche of seminiferous epithelium. Several extrinsic factors such as GDNF are reported to switch the transition, activating various intrinsic signaling pathways. Transcriptomics analysis could provide a comprehensive landscape of gene expression and regulation. Here, we reanalyzed a previously published transcriptome of two cell types (standing for self-renewing and differentiating SSCs correspondingly). First, we proposed a new parameter, the expression index, to sort the genes considering both absolute and relative expression levels. Using a dynamic statistical model, we identified a list of 1119 candidate genes for SSC self-renewal with the best enrichment of canonical markers. Finally, based on interaction relations, we further optimized the list and constructed a refined network containing integrated information of interactions, expression alternations, biological functions, and disease associations. Further annotation of the 521 refined genes involved in the network revealed an enrichment of well-studied signaling pathways. We believe that the refined network could help us better understand the regulation of SSCs' fates, as well as find novel regulators or targets for SSC self-renewal or preservation of male fertility.
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da Costa JP, Vitorino R, Silva GM, Vogel C, Duarte AC, Rocha-Santos T. A synopsis on aging-Theories, mechanisms and future prospects. Ageing Res Rev 2016; 29:90-112. [PMID: 27353257 PMCID: PMC5991498 DOI: 10.1016/j.arr.2016.06.005] [Citation(s) in RCA: 209] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/23/2016] [Accepted: 06/23/2016] [Indexed: 12/31/2022]
Abstract
Answering the question as to why we age is tantamount to answering the question of what is life itself. There are countless theories as to why and how we age, but, until recently, the very definition of aging - senescence - was still uncertain. Here, we summarize the main views of the different models of senescence, with a special emphasis on the biochemical processes that accompany aging. Though inherently complex, aging is characterized by numerous changes that take place at different levels of the biological hierarchy. We therefore explore some of the most relevant changes that take place during aging and, finally, we overview the current status of emergent aging therapies and what the future holds for this field of research. From this multi-dimensional approach, it becomes clear that an integrative approach that couples aging research with systems biology, capable of providing novel insights into how and why we age, is necessary.
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Affiliation(s)
- João Pinto da Costa
- CESAM and Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
| | - Rui Vitorino
- Department of Medical Sciences, Institute for Biomedicine-iBiMED, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; Department of Physiology and Cardiothoracic Surgery, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Gustavo M Silva
- Department of Biology, Center for Genomics and Systems Biology, NY, NY 10003, USA
| | - Christine Vogel
- Department of Biology, Center for Genomics and Systems Biology, NY, NY 10003, USA
| | - Armando C Duarte
- CESAM and Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
| | - Teresa Rocha-Santos
- CESAM and Department of Chemistry, University of Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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