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Berkovich AK, Pyshkina OA, Zorina AA, Rodin VA, Panova TV, Sergeev VG, Zvereva ME. Direct Determination of the Structure of Single Biopolymer Molecules Using Nanopore Sequencing. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:S234-S248. [PMID: 38621753 DOI: 10.1134/s000629792414013x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/21/2023] [Accepted: 09/01/2023] [Indexed: 04/17/2024]
Abstract
This review highlights operational principles, features, and modern aspects of the development of third-generation sequencing technology of biopolymers focusing on the nucleic acids analysis, namely the nanopore sequencing system. Basics of the method and technical solutions used for its realization are considered, from the first works showing the possibility of creation of these systems to the easy-to-handle procedure developed by Oxford Nanopore Technologies company. Moreover, this review focuses on applications, which were developed and realized using equipment developed by the Oxford Nanopore Technologies, including assembly of whole genomes, methagenomics, direct analysis of the presence of modified bases.
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Affiliation(s)
- Anna K Berkovich
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Olga A Pyshkina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Anna A Zorina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir A Rodin
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Tatyana V Panova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vladimir G Sergeev
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maria E Zvereva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
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2
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MacKenzie M, Argyropoulos C. An Introduction to Nanopore Sequencing: Past, Present, and Future Considerations. MICROMACHINES 2023; 14:459. [PMID: 36838159 PMCID: PMC9966803 DOI: 10.3390/mi14020459] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
There has been significant progress made in the field of nanopore biosensor development and sequencing applications, which address previous limitations that restricted widespread nanopore use. These innovations, paired with the large-scale commercialization of biological nanopore sequencing by Oxford Nanopore Technologies, are making the platforms a mainstay in contemporary research laboratories. Equipped with the ability to provide long- and short read sequencing information, with quick turn-around times and simple sample preparation, nanopore sequencers are rapidly improving our understanding of unsolved genetic, transcriptomic, and epigenetic problems. However, there remain some key obstacles that have yet to be improved. In this review, we provide a general introduction to nanopore sequencing principles, discussing biological and solid-state nanopore developments, obstacles to single-base detection, and library preparation considerations. We present examples of important clinical applications to give perspective on the potential future of nanopore sequencing in the field of molecular diagnostics.
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Affiliation(s)
- Morgan MacKenzie
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Christos Argyropoulos
- Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
- Clinical & Translational Science Center, Department of Internal Medicine, Division of Nephrology, School of Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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3
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von Reumont BM, Anderluh G, Antunes A, Ayvazyan N, Beis D, Caliskan F, Crnković A, Damm M, Dutertre S, Ellgaard L, Gajski G, German H, Halassy B, Hempel BF, Hucho T, Igci N, Ikonomopoulou MP, Karbat I, Klapa MI, Koludarov I, Kool J, Lüddecke T, Ben Mansour R, Vittoria Modica M, Moran Y, Nalbantsoy A, Ibáñez MEP, Panagiotopoulos A, Reuveny E, Céspedes JS, Sombke A, Surm JM, Undheim EAB, Verdes A, Zancolli G. Modern venomics-Current insights, novel methods, and future perspectives in biological and applied animal venom research. Gigascience 2022; 11:giac048. [PMID: 35640874 PMCID: PMC9155608 DOI: 10.1093/gigascience/giac048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/10/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Venoms have evolved >100 times in all major animal groups, and their components, known as toxins, have been fine-tuned over millions of years into highly effective biochemical weapons. There are many outstanding questions on the evolution of toxin arsenals, such as how venom genes originate, how venom contributes to the fitness of venomous species, and which modifications at the genomic, transcriptomic, and protein level drive their evolution. These questions have received particularly little attention outside of snakes, cone snails, spiders, and scorpions. Venom compounds have further become a source of inspiration for translational research using their diverse bioactivities for various applications. We highlight here recent advances and new strategies in modern venomics and discuss how recent technological innovations and multi-omic methods dramatically improve research on venomous animals. The study of genomes and their modifications through CRISPR and knockdown technologies will increase our understanding of how toxins evolve and which functions they have in the different ontogenetic stages during the development of venomous animals. Mass spectrometry imaging combined with spatial transcriptomics, in situ hybridization techniques, and modern computer tomography gives us further insights into the spatial distribution of toxins in the venom system and the function of the venom apparatus. All these evolutionary and biological insights contribute to more efficiently identify venom compounds, which can then be synthesized or produced in adapted expression systems to test their bioactivity. Finally, we critically discuss recent agrochemical, pharmaceutical, therapeutic, and diagnostic (so-called translational) aspects of venoms from which humans benefit.
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Affiliation(s)
- Bjoern M von Reumont
- Goethe University Frankfurt, Institute for Cell Biology and Neuroscience, Department for Applied Bioinformatics, 60438 Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Gregor Anderluh
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Agostinho Antunes
- CIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Naira Ayvazyan
- Orbeli Institute of Physiology of NAS RA, Orbeli ave. 22, 0028 Yerevan, Armenia
| | - Dimitris Beis
- Developmental Biology, Centre for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation Academy of Athens, Athens 11527, Greece
| | - Figen Caliskan
- Department of Biology, Faculty of Science and Letters, Eskisehir Osmangazi University, TR-26040 Eskisehir, Turkey
| | - Ana Crnković
- Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, 1000 Ljubljana, Slovenia
| | - Maik Damm
- Technische Universität Berlin, Department of Chemistry, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Goran Gajski
- Institute for Medical Research and Occupational Health, Mutagenesis Unit, Ksaverska cesta 2, 10000 Zagreb, Croatia
| | - Hannah German
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Beata Halassy
- University of Zagreb, Centre for Research and Knowledge Transfer in Biotechnology, Trg Republike Hrvatske 14, 10000 Zagreb, Croatia
| | - Benjamin-Florian Hempel
- BIH Center for Regenerative Therapies BCRT, Charité - Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Tim Hucho
- Translational Pain Research, Department of Anesthesiology and Intensive Care Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Nasit Igci
- Nevsehir Haci Bektas Veli University, Faculty of Arts and Sciences, Department of Molecular Biology and Genetics, 50300 Nevsehir, Turkey
| | - Maria P Ikonomopoulou
- Madrid Institute for Advanced Studies in Food, Madrid,E28049, Spain
- The University of Queensland, St Lucia, QLD 4072, Australia
| | - Izhar Karbat
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Maria I Klapa
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
| | - Ivan Koludarov
- Justus Liebig University Giessen, Institute for Insectbiotechnology, Heinrich Buff Ring 26-32, 35396 Giessen, Germany
| | - Jeroen Kool
- Amsterdam Institute of Molecular and Life Sciences, Division of BioAnalytical Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081HV Amsterdam, The Netherlands
| | - Tim Lüddecke
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Frankfurt, Senckenberganlage 25, 60235 Frankfurt, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, 35392 Gießen, Germany
| | - Riadh Ben Mansour
- Department of Life Sciences, Faculty of Sciences, Gafsa University, Campus Universitaire Siidi Ahmed Zarrouk, 2112 Gafsa, Tunisia
| | - Maria Vittoria Modica
- Dept. of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Via Po 25c, I-00198 Roma, Italy
| | - Yehu Moran
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ayse Nalbantsoy
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 Bornova, Izmir, Turkey
| | - María Eugenia Pachón Ibáñez
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alexios Panagiotopoulos
- Metabolic Engineering and Systems Biology Laboratory, Institute of Chemical Engineering Sciences, Foundation for Research & Technology Hellas (FORTH/ICE-HT), Patras GR-26504, Greece
- Animal Biology Division, Department of Biology, University of Patras, Patras, GR-26500, Greece
| | - Eitan Reuveny
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Javier Sánchez Céspedes
- Unit of Infectious Diseases, Microbiology, and Preventive Medicine, Virgen del Rocío University Hospital, Institute of Biomedicine of Seville, 41013 Sevilla, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Andy Sombke
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Eivind A B Undheim
- University of Oslo, Centre for Ecological and Evolutionary Synthesis, Postboks 1066 Blindern 0316 Oslo, Norway
| | - Aida Verdes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Giulia Zancolli
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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4
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Chen Z, Wang Z, Xu Y, Zhang X, Tian B, Bai J. Controlled movement of ssDNA conjugated peptide through Mycobacterium smegmatis porin A (MspA) nanopore by a helicase motor for peptide sequencing application. Chem Sci 2021; 12:15750-15756. [PMID: 35003607 PMCID: PMC8654031 DOI: 10.1039/d1sc04342k] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
The lack of an efficient, low-cost sequencing method has long been a significant bottleneck in protein research and applications. In recent years, the nanopore platform has emerged as a fast and inexpensive method for single-molecule nucleic acid sequencing, but attempts to apply it to protein/peptide sequencing have resulted in limited success. Here we report a strategy to control peptide translocation through the MspA nanopore, which could serve as the first step toward strand peptide sequencing. By conjugating the target peptide to a helicase-regulated handle-ssDNA, we achieved a read length of up to 17 amino acids (aa) and demonstrated the feasibility of distinguishing between amino acid residues of different charges or between different phosphorylation sites. Further improvement of resolution may require engineering MspA-M2 to reduce its constriction zone's size and stretch the target peptide inside the nanopore to minimize random thermal motion. We believe that our method in this study can significantly accelerate the development and commercialization of nanopore-based peptide sequencing technologies.
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Affiliation(s)
- Zhijie Chen
- School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Zhenqin Wang
- School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Yang Xu
- School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Xiaochun Zhang
- School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Boxue Tian
- School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
| | - Jingwei Bai
- School of Pharmaceutical Sciences, Tsinghua University 100084 Beijing China
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5
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Wang Y, Zhao Y, Bollas A, Wang Y, Au KF. Nanopore sequencing technology, bioinformatics and applications. Nat Biotechnol 2021; 39:1348-1365. [PMID: 34750572 PMCID: PMC8988251 DOI: 10.1038/s41587-021-01108-x] [Citation(s) in RCA: 505] [Impact Index Per Article: 168.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/22/2021] [Indexed: 12/13/2022]
Abstract
Rapid advances in nanopore technologies for sequencing single long DNA and RNA molecules have led to substantial improvements in accuracy, read length and throughput. These breakthroughs have required extensive development of experimental and bioinformatics methods to fully exploit nanopore long reads for investigations of genomes, transcriptomes, epigenomes and epitranscriptomes. Nanopore sequencing is being applied in genome assembly, full-length transcript detection and base modification detection and in more specialized areas, such as rapid clinical diagnoses and outbreak surveillance. Many opportunities remain for improving data quality and analytical approaches through the development of new nanopores, base-calling methods and experimental protocols tailored to particular applications.
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Affiliation(s)
- Yunhao Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yue Zhao
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA
| | - Audrey Bollas
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yuru Wang
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kin Fai Au
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
- Biomedical Informatics Shared Resources, The Ohio State University, Columbus, OH, USA.
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6
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Lüth T, Wasner K, Klein C, Schaake S, Tse R, Pereira SL, Laß J, Sinkkonen L, Grünewald A, Trinh J. Nanopore Single-Molecule Sequencing for Mitochondrial DNA Methylation Analysis: Investigating Parkin-Associated Parkinsonism as a Proof of Concept. Front Aging Neurosci 2021; 13:713084. [PMID: 34650424 PMCID: PMC8506010 DOI: 10.3389/fnagi.2021.713084] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/01/2021] [Indexed: 01/08/2023] Open
Abstract
Objective: To establish a workflow for mitochondrial DNA (mtDNA) CpG methylation using Nanopore whole-genome sequencing and perform first pilot experiments on affected Parkin biallelic mutation carriers (Parkin-PD) and healthy controls. Background: Mitochondria, including mtDNA, are established key players in Parkinson's disease (PD) pathogenesis. Mutations in Parkin, essential for degradation of damaged mitochondria, cause early-onset PD. However, mtDNA methylation and its implication in PD is understudied. Herein, we establish a workflow using Nanopore sequencing to directly detect mtDNA CpG methylation and compare mtDNA methylation between Parkin-related PD and healthy individuals. Methods: To obtain mtDNA, whole-genome Nanopore sequencing was performed on blood-derived from five Parkin-PD and three control subjects. In addition, induced pluripotent stem cell (iPSC)-derived midbrain neurons from four of these patients with PD and the three control subjects were investigated. The workflow was validated, using methylated and unmethylated 897 bp synthetic DNA samples at different dilution ratios (0, 50, 100% methylation) and mtDNA without methylation. MtDNA CpG methylation frequency (MF) was detected using Nanopolish and Megalodon. Results: Across all blood-derived samples, we obtained a mean coverage of 250.3X (SD ± 80.5X) and across all neuron-derived samples 830X (SD ± 465X) of the mitochondrial genome. We detected overall low-level CpG methylation from the blood-derived DNA (mean MF ± SD = 0.029 ± 0.041) and neuron-derived DNA (mean MF ± SD = 0.019 ± 0.035). Validation of the workflow, using synthetic DNA samples showed that highly methylated DNA molecules were prone to lower Guppy Phred quality scores and thereby more likely to fail Guppy base-calling. CpG methylation in blood- and neuron-derived DNA was significantly lower in Parkin-PD compared to controls (Mann-Whitney U-test p < 0.05). Conclusion: Nanopore sequencing is a useful method to investigate mtDNA methylation architecture, including Guppy-failed reads is of importance when investigating highly methylated sites. We present a mtDNA methylation workflow and suggest methylation variability across different tissues and between Parkin-PD patients and controls as an initial model to investigate.
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Affiliation(s)
- Theresa Lüth
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Kobi Wasner
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Susen Schaake
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Ronnie Tse
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Sandro L. Pereira
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Joshua Laß
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine, University of Luxembourg, Belvaux, Luxembourg
| | - Anne Grünewald
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Joanne Trinh
- Institute of Neurogenetics BMF, University of Lübeck and University Hospital Schleswig-Holstein Campus Lübeck, Lübeck, Germany
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7
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Yu M, Si W, Zeng T, Chen C, Lin X, Ji Z, Guo F, Li Y, Sha J, Dong Y. Unveiling the Microscopic Mechanism of Current Variation in the Sensing Region of the MspA Nanopore for DNA Sequencing. J Phys Chem Lett 2021; 12:9132-9141. [PMID: 34523927 DOI: 10.1021/acs.jpclett.1c02414] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Different nucleotides generate specific ionic currents that discriminate between the nucleotides while they are passing through the nanopore constriction. MspA is a commonly used nanopore for DNA sequencing. However, the reasons of the current variation remain ambiguous. Our work unveils the microscopic mechanism of current variation for an ssDNA passing through the MspA nanopore by all-atom molecular dynamic simulations. Besides the physical rigidity and dimensions of the nucleotides, nucleotide orientation is observed to induce nonignorable current variation. Besides the generally considered MspA nanopore constriction, it is also found that the region below constriction could be used to detect and differentiate single nucleotides when the single-stranded DNA translocates in the form of base-constriction-base meshing and ratcheting across the nanopore constriction compared to other regions. The work provides a novel insight into facilitating the development of low-cost and high-throughput nanopore DNA sequencing.
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Affiliation(s)
- Meng Yu
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Wei Si
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Tao Zeng
- BGI-ShenZhen, Shenzhen 518103, China
| | - Chang Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | - Xiaojing Lin
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
| | | | - Fei Guo
- BGI-ShenZhen, Shenzhen 518103, China
| | | | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, China
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8
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Liefting LW, Waite DW, Thompson JR. Application of Oxford Nanopore Technology to Plant Virus Detection. Viruses 2021; 13:v13081424. [PMID: 34452290 PMCID: PMC8402922 DOI: 10.3390/v13081424] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 12/13/2022] Open
Abstract
The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.
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9
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Puchtler TJ, Johnson K, Palmer RN, Talbot EL, Ibbotson LA, Powalowska PK, Knox R, Shibahara A, M S Cunha P, Newell OJ, Wu M, Chana J, Athanasopoulou EN, Waeber AM, Stolarek M, Silva AL, Mordaka JM, Haggis-Powell M, Xyrafaki C, Bush J, Topkaya IS, Sosna M, Ingham RJ, Huckvale T, Negrea A, Breiner B, Šlikas J, Kelly DJ, Dunning AJ, Bell NM, Dethlefsen M, Love DM, Dear PH, Kuleshova J, Podd GJ, Isaac TH, Balmforth BW, Frayling CA. Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets. Nucleic Acids Res 2021; 48:e132. [PMID: 33152076 PMCID: PMC7736801 DOI: 10.1093/nar/gkaa987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 11/12/2022] Open
Abstract
Despite remarkable progress in DNA sequencing technologies there remains a trade-off between short-read platforms, having limited ability to sequence homopolymers, repeated motifs or long-range structural variation, and long-read platforms, which tend to have lower accuracy and/or throughput. Moreover, current methods do not allow direct readout of epigenetic modifications from a single read. With the aim of addressing these limitations, we have developed an optical electrowetting sequencing platform that uses step-wise nucleotide triphosphate (dNTP) release, capture and detection in microdroplets from single DNA molecules. Each microdroplet serves as a reaction vessel that identifies an individual dNTP based on a robust fluorescence signal, with the detection chemistry extended to enable detection of 5-methylcytosine. Our platform uses small reagent volumes and inexpensive equipment, paving the way to cost-effective single-molecule DNA sequencing, capable of handling widely varying GC-bias, and demonstrating direct detection of epigenetic modifications.
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Affiliation(s)
- Tim J Puchtler
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Kerr Johnson
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Rebecca N Palmer
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Emma L Talbot
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Lindsey A Ibbotson
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Paulina K Powalowska
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Rachel Knox
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Aya Shibahara
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Pedro M S Cunha
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Oliver J Newell
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Mei Wu
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Jasmin Chana
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | | | - Andreas M Waeber
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Magdalena Stolarek
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Ana-Luisa Silva
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Justyna M Mordaka
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | | | - Christina Xyrafaki
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - James Bush
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Ibrahim S Topkaya
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Maciej Sosna
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Richard J Ingham
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Thomas Huckvale
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Aurel Negrea
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Boris Breiner
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Justinas Šlikas
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Douglas J Kelly
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Alexander J Dunning
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Neil M Bell
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Mark Dethlefsen
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - David M Love
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Paul H Dear
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Jekaterina Kuleshova
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Gareth J Podd
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Tom H Isaac
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Barnaby W Balmforth
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
| | - Cameron A Frayling
- Base 4 Innovation Ltd, Broers Building, JJ Thomson Avenue, Cambridge CB3 0FA, UK
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10
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Crnković A, Srnko M, Anderluh G. Biological Nanopores: Engineering on Demand. Life (Basel) 2021; 11:life11010027. [PMID: 33466427 PMCID: PMC7824896 DOI: 10.3390/life11010027] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/31/2020] [Indexed: 12/17/2022] Open
Abstract
Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.
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11
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Assessing Nanopore Sequencing for Clinical Diagnostics: a Comparison of Next-Generation Sequencing (NGS) Methods for Mycobacterium tuberculosis. J Clin Microbiol 2020; 59:JCM.00583-20. [PMID: 33055186 DOI: 10.1128/jcm.00583-20] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing technologies are being rapidly adopted as a tool of choice for diagnostic and outbreak investigation in public health laboratories. However, costs of operation and the need for specialized staff remain major hurdles for laboratories with limited resources for implementing these technologies. This project aimed to assess the feasibility of using Oxford Nanopore MinION whole-genome sequencing data of Mycobacterium tuberculosis isolates for species identification, in silico spoligotyping, detection of mutations associated with antimicrobial resistance (AMR) to accurately predict drug susceptibility profiles, and phylogenetic analysis to detect transmission between cases. The results were compared prospectively in real time to those obtained with our current clinically validated Illumina MiSeq sequencing assay for M. tuberculosis and phenotypic drug susceptibility testing results when available. Our assessment of 431 sequenced samples over a 32-week period demonstrates that, when using the proper quality controls and thresholds, the MinION can achieve levels of genotyping analysis and phenotypic resistance predictions comparable to those of the Illumina MiSeq at a very competitive cost per sample. Our results indicate that nanopore sequencing can be a suitable alternative to, or complement, currently used sequencing platforms in a clinical setting and has the potential to be widely adopted in public health laboratories in the near future.
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12
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Ramírez-Carreto S, Miranda-Zaragoza B, Rodríguez-Almazán C. Actinoporins: From the Structure and Function to the Generation of Biotechnological and Therapeutic Tools. Biomolecules 2020; 10:E539. [PMID: 32252469 PMCID: PMC7226409 DOI: 10.3390/biom10040539] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/19/2020] [Accepted: 03/21/2020] [Indexed: 12/22/2022] Open
Abstract
Actinoporins (APs) are a family of pore-forming toxins (PFTs) from sea anemones. These biomolecules exhibit the ability to exist as soluble monomers within an aqueous medium or as constitutively open oligomers in biological membranes. Through their conformational plasticity, actinoporins are considered good candidate molecules to be included for the rational design of molecular tools, such as immunotoxins directed against tumor cells and stochastic biosensors based on nanopores to analyze unique DNA or protein molecules. Additionally, the ability of these proteins to bind to sphingomyelin (SM) facilitates their use for the design of molecular probes to identify SM in the cells. The immunomodulatory activity of actinoporins in liposomal formulations for vaccine development has also been evaluated. In this review, we describe the potential of actinoporins for use in the development of molecular tools that could be used for possible medical and biotechnological applications.
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Affiliation(s)
| | | | - Claudia Rodríguez-Almazán
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico; (S.R.-C.); (B.M.-Z.)
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13
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Adir O, Poley M, Chen G, Froim S, Krinsky N, Shklover J, Shainsky-Roitman J, Lammers T, Schroeder A. Integrating Artificial Intelligence and Nanotechnology for Precision Cancer Medicine. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901989. [PMID: 31286573 PMCID: PMC7124889 DOI: 10.1002/adma.201901989] [Citation(s) in RCA: 121] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/17/2019] [Indexed: 05/13/2023]
Abstract
Artificial intelligence (AI) and nanotechnology are two fields that are instrumental in realizing the goal of precision medicine-tailoring the best treatment for each cancer patient. Recent conversion between these two fields is enabling better patient data acquisition and improved design of nanomaterials for precision cancer medicine. Diagnostic nanomaterials are used to assemble a patient-specific disease profile, which is then leveraged, through a set of therapeutic nanotechnologies, to improve the treatment outcome. However, high intratumor and interpatient heterogeneities make the rational design of diagnostic and therapeutic platforms, and analysis of their output, extremely difficult. Integration of AI approaches can bridge this gap, using pattern analysis and classification algorithms for improved diagnostic and therapeutic accuracy. Nanomedicine design also benefits from the application of AI, by optimizing material properties according to predicted interactions with the target drug, biological fluids, immune system, vasculature, and cell membranes, all affecting therapeutic efficacy. Here, fundamental concepts in AI are described and the contributions and promise of nanotechnology coupled with AI to the future of precision cancer medicine are reviewed.
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Affiliation(s)
- Omer Adir
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
- The Norman Seiden Multidisciplinary Program for Nanoscience and Nanotechnology, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Maria Poley
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Gal Chen
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Sahar Froim
- Department of Physical Electronics, School of Electrical Engineering, Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Nitzan Krinsky
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Jeny Shklover
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Janna Shainsky-Roitman
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Twan Lammers
- Institute for Experimental Molecular Imaging, RWTH Aachen University Hospital, Aachen, 52074, Germany
| | - Avi Schroeder
- Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
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14
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Fragasso A, Schmid S, Dekker C. Comparing Current Noise in Biological and Solid-State Nanopores. ACS NANO 2020; 14:1338-1349. [PMID: 32049492 PMCID: PMC7045697 DOI: 10.1021/acsnano.9b09353] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 05/16/2023]
Abstract
Nanopores bear great potential as single-molecule tools for bioanalytical sensing and sequencing, due to their exceptional sensing capabilities, high-throughput, and low cost. The detection principle relies on detecting small differences in the ionic current as biomolecules traverse the nanopore. A major bottleneck for the further progress of this technology is the noise that is present in the ionic current recordings, because it limits the signal-to-noise ratio (SNR) and thereby the effective time resolution of the experiment. Here, we review the main types of noise at low and high frequencies and discuss the underlying physics. Moreover, we compare biological and solid-state nanopores in terms of the SNR, the important figure of merit, by measuring translocations of a short ssDNA through a selected set of nanopores under typical experimental conditions. We find that SiNx solid-state nanopores provide the highest SNR, due to the large currents at which they can be operated and the relatively low noise at high frequencies. However, the real game-changer for many applications is a controlled slowdown of the translocation speed, which for MspA was shown to increase the SNR > 160-fold. Finally, we discuss practical approaches for lowering the noise for optimal experimental performance and further development of the nanopore technology.
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Affiliation(s)
- Alessio Fragasso
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Sonja Schmid
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University
of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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15
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Soneson C, Yao Y, Bratus-Neuenschwander A, Patrignani A, Robinson MD, Hussain S. A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes. Nat Commun 2019; 10:3359. [PMID: 31366910 PMCID: PMC6668388 DOI: 10.1038/s41467-019-11272-z] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/04/2019] [Indexed: 11/29/2022] Open
Abstract
A platform for highly parallel direct sequencing of native RNA strands was recently described by Oxford Nanopore Technologies, but despite initial efforts it remains crucial to further investigate the technology for quantification of complex transcriptomes. Here we undertake native RNA sequencing of polyA + RNA from two human cell lines, analysing ~5.2 million aligned native RNA reads. To enable informative comparisons, we also perform relevant ONT direct cDNA- and Illumina-sequencing. We find that while native RNA sequencing does enable some of the anticipated advantages, key unexpected aspects currently hamper its performance, most notably the quite frequent inability to obtain full-length transcripts from single reads, as well as difficulties to unambiguously infer their true transcript of origin. While characterising issues that need to be addressed when investigating more complex transcriptomes, our study highlights that with some defined improvements, native RNA sequencing could be an important addition to the mammalian transcriptomics toolbox.
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Affiliation(s)
- Charlotte Soneson
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, 8057, Zurich, Switzerland.
- Friedrich Miescher Institute for Biomedical Research and SIB Swiss Institute of Bioinformatics, Basel, Switzerland.
| | - Yao Yao
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland
- SIB Swiss Institute of Bioinformatics, 8057, Zurich, Switzerland
| | | | - Andrea Patrignani
- Functional Genomics Centre Zurich, ETHZ/University of Zurich, 8057, Zurich, Switzerland
| | - Mark D Robinson
- Institute of Molecular Life Sciences, University of Zurich, 8057, Zurich, Switzerland.
- SIB Swiss Institute of Bioinformatics, 8057, Zurich, Switzerland.
| | - Shobbir Hussain
- Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.
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16
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Lang C, Ye D, Song W, Yao C, Tu YM, Capparelli C, LaNasa JA, Hickner MA, Gomez EW, Gomez ED, Hickey RJ, Kumar M. Biomimetic Separation of Transport and Matrix Functions in Lamellar Block Copolymer Channel-Based Membranes. ACS NANO 2019; 13:8292-8302. [PMID: 31251576 DOI: 10.1021/acsnano.9b03659] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Cell membranes control mass, energy, and information flow to and from the cell. In the cell membrane a lipid bilayer serves as the barrier layer, with highly efficient molecular machines, membrane proteins, serving as the transport elements. In this way, highly specialized transport properties are achieved by these composite materials by segregating the matrix function from the transport function using different components. For example, cell membranes containing aquaporin proteins can transport ∼4 billion water molecules per second per aquaporin while rejecting all other molecules including salts, a feat unmatched by any synthetic system, while the impermeable lipid bilayer provides the barrier and matrix properties. True separation of functions between the matrix and the transport elements has been difficult to achieve in conventional solute separation synthetic membranes. In this study, we created membranes with distinct matrix and transport elements through designed coassembly of solvent-stable artificial (peptide-appended pillar[5]arene, PAP5) or natural (gramicidin A) model channels with block copolymers into lamellar multilayered membranes. Self-assembly of a lamellar structure from cross-linkable triblock copolymers was used as a scalable replacement for lipid bilayers, offering better stability and mechanical properties. By coassembly of channel molecules with block copolymers, we were able to synthesize nanofiltration membranes with sharp selectivity profiles as well as uncharged ion exchange membranes exhibiting ion selectivity. The developed method can be used for incorporation of different artificial and biological ion and water channels into synthetic polymer membranes. The strategy reported here could promote the construction of a range of channel-based membranes and sensors with desired properties, such as ion separations, stimuli responsiveness, and high sensitivity.
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17
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Malla MA, Dubey A, Kumar A, Yadav S, Hashem A, Abd_Allah EF. Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment. Front Immunol 2019; 9:2868. [PMID: 30666248 PMCID: PMC6330296 DOI: 10.3389/fimmu.2018.02868] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/21/2018] [Indexed: 12/12/2022] Open
Abstract
The interaction between the human microbiome and immune system has an effect on several human metabolic functions and impacts our well-being. Additionally, the interaction between humans and microbes can also play a key role in determining the wellness or disease status of the human body. Dysbiosis is related to a plethora of diseases, including skin, inflammatory, metabolic, and neurological disorders. A better understanding of the host-microbe interaction is essential for determining the diagnosis and appropriate treatment of these ailments. The significance of the microbiome on host health has led to the emergence of new therapeutic approaches focused on the prescribed manipulation of the host microbiome, either by removing harmful taxa or reinstating missing beneficial taxa and the functional roles they perform. Culturing large numbers of microbial taxa in the laboratory is problematic at best, if not impossible. Consequently, this makes it very difficult to comprehensively catalog the individual members comprising a specific microbiome, as well as understanding how microbial communities function and influence host-pathogen interactions. Recent advances in sequencing technologies and computational tools have allowed an increasing number of metagenomic studies to be performed. These studies have provided key insights into the human microbiome and a host of other microbial communities in other environments. In the present review, the role of the microbiome as a therapeutic agent and its significance in human health and disease is discussed. Advances in high-throughput sequencing technologies for surveying host-microbe interactions are also discussed. Additionally, the correlation between the composition of the microbiome and infectious diseases as described in previously reported studies is covered as well. Lastly, recent advances in state-of-the-art bioinformatics software, workflows, and applications for analysing metagenomic data are summarized.
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Affiliation(s)
- Muneer Ahmad Malla
- Department of Zoology, Dr. Harisingh Gour Central University, Sagar, India
| | - Anamika Dubey
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour Central University, Sagar, India
| | - Ashwani Kumar
- Metagenomics and Secretomics Research Laboratory, Department of Botany, Dr. Harisingh Gour Central University, Sagar, India
| | - Shweta Yadav
- Department of Zoology, Dr. Harisingh Gour Central University, Sagar, India
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, Agriculture Research Center, Giza, Egypt
| | - Elsayed Fathi Abd_Allah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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18
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Rouse SL, Stylianou F, Wu HYG, Berry JL, Sewell L, Morgan RML, Sauerwein AC, Matthews S. The FapF Amyloid Secretion Transporter Possesses an Atypical Asymmetric Coiled Coil. J Mol Biol 2018; 430:3863-3871. [PMID: 29886016 PMCID: PMC6173795 DOI: 10.1016/j.jmb.2018.06.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/09/2018] [Accepted: 06/04/2018] [Indexed: 12/28/2022]
Abstract
Gram-negative bacteria possess specialized biogenesis machineries that facilitate the export of amyloid subunits, the fibers of which are key components of their biofilm matrix. The secretion of bacterial functional amyloid requires a specialized outer-membrane protein channel through which unfolded amyloid substrates are translocated. We previously reported the crystal structure of the membrane-spanning domain of the amyloid subunit transporter FapF from Pseudomonas. However, the structure of the periplasmic domain, which is essential for amyloid transport, is yet to be determined. Here, we present the crystal structure of the N-terminal periplasmic domain at 1.8-Å resolution. This domain forms a novel asymmetric trimeric coiled coil that possesses a single buried tyrosine residue as well as an extensive hydrogen-bonding network within a glutamine layer. This new structural insight allows us to understand this newly described functional amyloid secretion system in greater detail.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - H Y Grace Wu
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Lee Sewell
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - R Marc L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Andrea C Sauerwein
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK.
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19
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Abstract
Real-time sequencing of short DNA reads has a wide variety of clinical and research applications including screening for mutations, target sequences and aneuploidy. We recently demonstrated that MinION, a nanopore-based DNA sequencing device the size of a USB drive, could be used for short-read DNA sequencing. In this study, an ultra-rapid multiplex library preparation and sequencing method for the MinION is presented and applied to accurately test normal diploid and aneuploidy samples’ genomic DNA in under three hours, including library preparation and sequencing. This novel method shows great promise as a clinical diagnostic test for applications requiring rapid short-read DNA sequencing.
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20
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Ton KNT, Cree SL, Gronert-Sum SJ, Merriman TR, Stamp LK, Kennedy MA. Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples. Front Genet 2018; 9:152. [PMID: 29760718 PMCID: PMC5936980 DOI: 10.3389/fgene.2018.00152] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/12/2018] [Indexed: 11/13/2022] Open
Abstract
The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been associated with adverse drug reactions (ADRs) and disease susceptibility. The frequency of such HLA-B alleles varies by ethnicity, and therefore it is important to understand the prevalence of such alleles in different population groups. Research into HLA involvement in ADRs would be facilitated by improved methods for genotyping key HLA-B alleles. Here, we describe an approach to HLA-B typing using next generation sequencing (NGS) on the MinION™ nanopore sequencer, combined with data analysis with the SeqNext-HLA software package. The nanopore sequencer offers the advantages of long-read capability and single molecule reads, which can facilitate effective haplotyping. We developed this method using reference samples as well as individuals of New Zealand Māori or Pacific Island descent, because HLA-B diversity in these populations is not well understood. We demonstrate here that nanopore sequencing of barcoded, pooled, 943 bp polymerase chain reaction (PCR) amplicons of 49 DNA samples generated ample read depth for all samples. HLA-B alleles were assigned to all samples at high-resolution with very little ambiguity. Our method is a scaleable and efficient approach for genotyping HLA-B and potentially any other HLA locus. Finally, we report our findings on HLA-B genotypes of this cohort, which adds to our understanding of HLA-B allele frequencies among Māori and Pacific Island people.
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Affiliation(s)
- Kim N T Ton
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simone L Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - Tony R Merriman
- Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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21
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Henning-Knechtel A, Knechtel J, Magzoub M. DNA-assisted oligomerization of pore-forming toxin monomers into precisely-controlled protein channels. Nucleic Acids Res 2017; 45:12057-12068. [PMID: 29088457 PMCID: PMC5716084 DOI: 10.1093/nar/gkx990] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 10/11/2017] [Indexed: 01/12/2023] Open
Abstract
We have developed a novel approach for creating membrane-spanning protein-based pores. The construction principle is based on using well-defined, circular DNA nanostructures to arrange a precise number of pore-forming protein toxin monomers. We can thereby obtain, for the first time, protein pores with specifically set diameters. We demonstrate this principle by constructing artificial alpha-hemolysin (αHL) pores. The DNA/αHL hybrid nanopores composed of twelve, twenty or twenty-six monomers show stable insertions into lipid bilayers during electrical recordings, along with steady, pore size-dependent current levels. Our approach successfully advances the applicability of nanopores, in particular towards label-free studies of single molecules in large nanoscaled biological structures.
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Affiliation(s)
- Anja Henning-Knechtel
- Biology Program, Division of Science, New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, UAE
| | - Johann Knechtel
- Division of Engineering, New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, UAE
| | - Mazin Magzoub
- Biology Program, Division of Science, New York University Abu Dhabi, PO Box 129188, Saadiyat Island, Abu Dhabi, UAE
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22
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Quainoo S, Coolen JPM, van Hijum SAFT, Huynen MA, Melchers WJG, van Schaik W, Wertheim HFL. Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. Clin Microbiol Rev 2017; 30:1015-1063. [PMID: 28855266 PMCID: PMC5608882 DOI: 10.1128/cmr.00016-17] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Outbreaks of multidrug-resistant bacteria present a frequent threat to vulnerable patient populations in hospitals around the world. Intensive care unit (ICU) patients are particularly susceptible to nosocomial infections due to indwelling devices such as intravascular catheters, drains, and intratracheal tubes for mechanical ventilation. The increased vulnerability of infected ICU patients demonstrates the importance of effective outbreak management protocols to be in place. Understanding the transmission of pathogens via genotyping methods is an important tool for outbreak management. Recently, whole-genome sequencing (WGS) of pathogens has become more accessible and affordable as a tool for genotyping. Analysis of the entire pathogen genome via WGS could provide unprecedented resolution in discriminating even highly related lineages of bacteria and revolutionize outbreak analysis in hospitals. Nevertheless, clinicians have long been hesitant to implement WGS in outbreak analyses due to the expensive and cumbersome nature of early sequencing platforms. Recent improvements in sequencing technologies and analysis tools have rapidly increased the output and analysis speed as well as reduced the overall costs of WGS. In this review, we assess the feasibility of WGS technologies and bioinformatics analysis tools for nosocomial outbreak analyses and provide a comparison to conventional outbreak analysis workflows. Moreover, we review advantages and limitations of sequencing technologies and analysis tools and present a real-world example of the implementation of WGS for antimicrobial resistance analysis. We aimed to provide health care professionals with a guide to WGS outbreak analysis that highlights its benefits for hospitals and assists in the transition from conventional to WGS-based outbreak analysis.
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Affiliation(s)
- Scott Quainoo
- Department of Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Jordy P M Coolen
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Sacha A F T van Hijum
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
- NIZO, Ede, The Netherlands
| | - Martijn A Huynen
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem J G Melchers
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Willem van Schaik
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Heiman F L Wertheim
- Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
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