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de la Fuente J, Contreras M. Quantum vaccinomics platforms to advance in vaccinology. Front Immunol 2023; 14:1172734. [PMID: 37398646 PMCID: PMC10307952 DOI: 10.3389/fimmu.2023.1172734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
The opinion flows from Introduction to the immunological quantum that requires a historical perspective, to Quantum vaccine algorithms supported by a bibliometric analysis, to Quantum vaccinomics describing from our perspective the different vaccinomics and quantum vaccinomics algorithms. Finally, in the Discussion and conclusions we propose novel platforms and algorithms developed to further advance on quantum vaccinomics. In the paper we refer to protective epitopes or immunological quantum for the design of candidate vaccine antigens, which may elicit a protective response through both cellular and antibody mediated mechanisms of the host immune system. Vaccines are key interventions for the prevention and control of infectious diseases affecting humans and animals worldwide. Biophysics led to quantum biology and quantum immunology reflecting quantum dynamics within living systems and their evolution. In analogy to quantum of light, immune protective epitopes were proposed as the immunological quantum. Multiple quantum vaccine algorithms were developed based on omics and other technologies. Quantum vaccinomics is the methodological approach with different platforms used for the identification and combination of immunological quantum for vaccine development. Current quantum vaccinomics platforms include in vitro, in music and in silico algorithms and top trends in biotechnology for the identification, characterization and combination of candidate protective epitopes. These platforms have been applied to different infectious diseases and in the future should target prevalent and emerging infectious diseases with novel algorithms.
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Affiliation(s)
- José de la Fuente
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Marinela Contreras
- SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM, Ciudad Real, Spain
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McCartney AM, Hilario E, Choi S, Guhlin J, Prebble JM, Houliston G, Buckley TR, Chagné D. An exploration of assembly strategies and quality metrics on the accuracy of the rewarewa (Knightia excelsa) genome. Mol Ecol Resour 2021; 21:2125-2144. [PMID: 33955186 PMCID: PMC8362059 DOI: 10.1111/1755-0998.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/18/2021] [Accepted: 04/20/2021] [Indexed: 12/17/2022]
Abstract
We used long read sequencing data generated from Knightia excelsa, a nectar-producing Proteaceae tree endemic to Aotearoa (New Zealand), to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome reconstruction. Establishing a high-quality genome for this species has specific cultural importance to Māori and commercial importance to honey producers in Aotearoa. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Subsampling highlighted that input data with longer read lengths but perhaps lower coverage constructed more contiguous, kmers and gene-complete assemblies than short read length input data with higher coverage. The final genome assembly was constructed into 14 pseudochromosomes using an initial flye long read assembly, a racon/medaka/pilon combined polishing strategy, salsa2 and allhic scaffolding, juicebox curation, and Macadamia linkage map validation. We highlighted the importance of developing assembly workflows based on the volume and read length of sequencing data and established a robust set of quality metrics for generating high-quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by Hi-C data and that assembly scaffolding was more successful when the underlying contig assembly was of higher accuracy. These findings provide insight into how quality assessment tools can be implemented throughout genome assembly pipelines to inform the de novo reconstruction of a high-quality genome assembly for nonmodel organisms.
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Affiliation(s)
- Ann M. McCartney
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
| | - Elena Hilario
- Genomics AotearoaDunedinNew Zealand
- The New Zealand Institute for Plant and Food Research (Plant & Food Research)SandringhamNew Zealand
| | - Seung‐Sub Choi
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Joseph Guhlin
- Genomics AotearoaDunedinNew Zealand
- University of OtagoDunedinNew Zealand
| | - Jessica M. Prebble
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Gary Houliston
- Genomics AotearoaDunedinNew Zealand
- Manaaki Whenua Landcare ResearchLincolnNew Zealand
| | - Thomas R. Buckley
- Manaaki Whenua ‐ Landcare ResearchAucklandNew Zealand
- Genomics AotearoaDunedinNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - David Chagné
- Genomics AotearoaDunedinNew Zealand
- Plant & Food ResearchFitzherbert, Palmerston NorthNew Zealand
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Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases. MOLECULAR BIOSYSTEMS 2017; 12:2318-41. [PMID: 27303926 DOI: 10.1039/c6mb00240d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
It has been well-recognized that inflammation alongside tissue repair and damage maintaining tissue homeostasis determines the initiation and progression of complex diseases. Albeit with the accomplishment of having captured the most critical inflammation-involved molecules, genetic susceptibilities, epigenetic factors, and environmental factors, our schemata on the role of inflammation in complex diseases remain largely patchy, in part due to the success of reductionism in terms of research methodology per se. Omics data alongside the advances in data integration technologies have enabled reconstruction of molecular and genetic inflammation networks which shed light on the underlying pathophysiology of complex diseases or clinical conditions. Given the proven beneficial role of anti-inflammation in coronary heart disease as well as other complex diseases and immunotherapy as a revolutionary transition in oncology, it becomes timely to review our current understanding of the molecular and genetic inflammation networks underlying major human diseases. In this review, we first briefly discuss the complexity of infectious diseases and then highlight recently uncovered molecular and genetic inflammation networks in other major human diseases including obesity, type II diabetes, coronary heart disease, late onset Alzheimer's disease, Parkinson's disease, and sporadic cancer. The commonality and specificity of these molecular networks are addressed in the context of genetics based on genome-wide association study (GWAS). The double-sword role of inflammation, such as how the aberrant type 1 and/or type 2 immunity leads to chronic and severe clinical conditions, remains open in terms of the inflammasome and the core inflammatome network features. Increasingly available large Omics and clinical data in tandem with systems biology approaches have offered an exciting yet challenging opportunity toward reconstruction of more comprehensive and dynamic molecular and genetic inflammation networks, which hold great promise in transiting network snapshots to video-style multi-scale interplays of disease mechanisms, in turn leading to effective clinical intervention.
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Affiliation(s)
- Yongzhong Zhao
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Christian V Forst
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
| | - Camil E Sayegh
- Vertex Pharmaceuticals (Canada) Incorporated, 275 Armand-Frappier, Laval, Quebec H7V 4A7, Canada
| | - I-Ming Wang
- Informatics and Analysis, Merck Research Laboratories, Merck & Co., Inc., 770 Sumneytown Pike, West Point, PA 19486, USA.
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, CA 90025, USA.
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA. and Institute of Genomics and Multiscale Biology, Mount Sinai School of Medicine, 1425 Madison Avenue, NY 10029, USA
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Song DH, Kim WK, Gu SH, Lee D, Kim JA, No JS, Lee SH, Wiley MR, Palacios G, Song JW, Jeong ST. Sequence-Independent, Single-Primer Amplification Next-Generation Sequencing of Hantaan Virus Cell Culture-Based Isolates. Am J Trop Med Hyg 2016; 96:389-394. [PMID: 27895275 DOI: 10.4269/ajtmh.16-0683] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/16/2016] [Indexed: 01/11/2023] Open
Abstract
Hantaan virus (HTNV), identified in the striped field mouse (Apodemus agrarius), belongs to the genus Hantavirus of the family Bunyaviridae and contains tripartite RNA genomes, small (S), medium (M), and large (L) segments. HTNV is a major causative for hemorrhagic fever with renal syndrome (HFRS) with fatality rates ranging from 1% to 15% in the Republic of Korea (ROK) and China. Defining of HTNV whole-genome sequences and isolation of the infectious particle play a critical role in the characterization and preventive and therapeutic strategies of hantavirus outbreaks. Next-generation sequencing (NGS) provides an advanced tool for massive genomic sequencing of viruses. However, the isolation of viral infectious particles is a huge obstacle to investigate and develop anti-virals for hantaviruses. Here, we report 12 HTNV isolates from lung tissues of the striped field mouse in the highly HFRS-endemic areas. Sequence-independent, single-primer amplification (SISPA) NGS was attempted to recover the genomic sequences of HTNV isolates. The nucleotide sequence of HTNV S, M, and L segments were covered up to 99.4-100%, 97.5-100%, and 95.6-99.8%, respectively, based on the full length of the prototype HTNV 76-118. The whole-genome sequencing of HTNV isolates was accomplished by additional reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification cDNA ends (RACE) PCR. In conclusion, this study will lead to the attempt and usage of SISPA NGS technologies to delineate the whole-genome sequence of hantaviruses, providing a new era of viral genomics for the surveillance, trace, and disease risk management of HFRS incidents.
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Affiliation(s)
- Dong Hyun Song
- The 5th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Se Hun Gu
- The 5th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Daesang Lee
- The 5th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea
| | - Jeong-Ah Kim
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Jin Sun No
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Seung-Ho Lee
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea
| | - Michael R Wiley
- The Center for Genome Science, U.S. Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland
| | - Gustavo Palacios
- The Center for Genome Science, U.S. Army Medical Research Institute of Infectious Disease, Fort Detrick, Maryland
| | - Jin-Won Song
- Department of Microbiology, College of Medicine, Korea University, Seoul, Republic of Korea.
| | - Seong Tae Jeong
- The 5th R&D Institute, Agency for Defense Development, Daejeon, Republic of Korea.
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Linnik JE, Egli A. Impact of host genetic polymorphisms on vaccine induced antibody response. Hum Vaccin Immunother 2016; 12:907-15. [PMID: 26809773 DOI: 10.1080/21645515.2015.1119345] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Many host- and vaccine-specific factors modulate an antibody response. Host genetic polymorphisms, in particular, modulate the immune response in multiple ways on different scales. This review article describes how information on host genetic polymorphisms and corresponding immune cascades may be used to generate personalized vaccine strategies to optimize the antibody response.
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Affiliation(s)
- Janina E Linnik
- a Applied Microbiology Research , Department of Biomedicine, University Basel , Basel , Switzerland.,b Department of Biosystems Science and Engineering , ETH Zürich , Basel , Switzerland.,c Swiss Institute of Bioinformatics , Basel , Switzerland
| | - Adrian Egli
- a Applied Microbiology Research , Department of Biomedicine, University Basel , Basel , Switzerland.,d Clinical Microbiology, University Hospital Basel , Basel , Switzerland
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Barbosa EGV, Aburjaile FF, Ramos RTJ, Carneiro AR, Le Loir Y, Baumbach J, Miyoshi A, Silva A, Azevedo V. Value of a newly sequenced bacterial genome. World J Biol Chem 2014; 5:161-168. [PMID: 24921006 PMCID: PMC4050110 DOI: 10.4331/wjbc.v5.i2.161] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Accepted: 04/03/2014] [Indexed: 02/05/2023] Open
Abstract
Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the “scientific value” of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.
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