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Akash A, Bencurova E, Dandekar T. How to make DNA data storage more applicable. Trends Biotechnol 2024; 42:17-30. [PMID: 37591721 DOI: 10.1016/j.tibtech.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
The storage of digital data is becoming a worldwide problem. DNA has been recognized as a biological solution due to its ability to store genetic information without alteration over long periods. The first demonstrations of high-capacity long-lasting DNA digital data storage have been shown. However, high storage costs and slow retrieval of the data must be overcome to make DNA data storage more applicable and marketable. Herein, we discuss the issues and recent advances in DNA data storage methods and highlight pathways to make this technology more applicable to real-world digital data storage. We envision that a combination of molecular biology, nanotechnology, novel polymers, electronics, and automation with systematic development will allow DNA data storage sufficient for everyday use.
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Affiliation(s)
- Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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2
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Kabiraz MP, Majumdar PR, Mahmud MC, Bhowmik S, Ali A. Conventional and advanced detection techniques of foodborne pathogens: A comprehensive review. Heliyon 2023; 9:e15482. [PMID: 37151686 PMCID: PMC10161726 DOI: 10.1016/j.heliyon.2023.e15482] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/13/2023] [Accepted: 04/11/2023] [Indexed: 05/09/2023] Open
Abstract
Foodborne pathogens are a major public health concern and have a significant economic impact globally. From harvesting to consumption stages, food is generally contaminated by viruses, parasites, and bacteria, which causes foodborne diseases such as hemorrhagic colitis, hemolytic uremic syndrome (HUS), typhoid, acute, gastroenteritis, diarrhea, and thrombotic thrombocytopenic purpura (TTP). Hence, early detection of foodborne pathogenic microbes is essential to ensure a safe food supply and to prevent foodborne diseases. The identification of foodborne pathogens is associated with conventional (e.g., culture-based, biochemical test-based, immunological-based, and nucleic acid-based methods) and advances (e.g., hybridization-based, array-based, spectroscopy-based, and biosensor-based process) techniques. For industrial food applications, detection methods could meet parameters such as accuracy level, efficiency, quickness, specificity, sensitivity, and non-labor intensive. This review provides an overview of conventional and advanced techniques used to detect foodborne pathogens over the years. Therefore, the scientific community, policymakers, and food and agriculture industries can choose an appropriate method for better results.
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Affiliation(s)
- Meera Probha Kabiraz
- Department of Biotechnology, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Priyanka Rani Majumdar
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, 2052, Australia
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | - M.M. Chayan Mahmud
- CASS Food Research Centre, School of Exercise and Nutrition Sciences, Deakin University, 221 Burwood Highway, VIC, 3125, Australia
| | - Shuva Bhowmik
- Department of Fisheries and Marine Science, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand
- Department of Food Science, University of Otago, Dunedin, 9054, New Zealand
- Corresponding author. Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand.
| | - Azam Ali
- Centre for Bioengineering and Nanomedicine, Faculty of Dentistry, Division of Health Sciences, University of Otago, Dunedin, 9054, New Zealand
- Corresponding author.
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Krämer S, Moritz A, Stehl L, Hutt M, Hofmann M, Wagner C, Bunk S, Maurer D, Roth G, Wöhrle J. An ultra-high-throughput screen for the evaluation of peptide HLA-Binder interactions. Sci Rep 2023; 13:5290. [PMID: 37002335 PMCID: PMC10066226 DOI: 10.1038/s41598-023-32384-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 04/04/2023] Open
Abstract
Peptide human leukocyte antigen (pHLA) targeting therapeutics like T-cell receptor based adoptive cell therapy or bispecific T cell engaging receptor molecules hold great promise for the treatment of cancer. Comprehensive pre-clinical screening of therapeutic candidates is important to ensure patient safety but is challenging because of the size of the potential off-target space. By combining stabilized peptide-receptive HLA molecules with microarray printing and screening, we have developed an ultra-high-throughput screening platform named ValidaTe that enables large scale evaluation of pHLA-binder interactions. We demonstrate its potential by measuring and analyzing over 30.000 binding curves for a high-affinity T cell Engaging Receptor towards a large pHLA library. Compared to a dataset obtained by conventional bio-layer interferometry measurements, we illustrate that a massively increased throughput (over 650 fold) is obtained by our microarray screening, paving the way for use in pre-clinical safety screening of pHLA-targeting drugs.
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Affiliation(s)
| | | | - Luca Stehl
- BioCopy GmbH, 79312, Emmendingen, Germany
| | - Meike Hutt
- Immatics Biotechnologies GmbH, 72076, Tübingen, Germany
| | | | | | | | | | - Günter Roth
- BioCopy GmbH, 79312, Emmendingen, Germany
- BioCopy AG, 4123, Basel, Switzerland
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Bencurova E, Akash A, Dobson RC, Dandekar T. DNA storage-from natural biology to synthetic biology. Comput Struct Biotechnol J 2023; 21:1227-1235. [PMID: 36817961 PMCID: PMC9932295 DOI: 10.1016/j.csbj.2023.01.045] [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: 11/19/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).
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Affiliation(s)
- Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany,Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Corresponding author at: Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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Sánchez-Costa M, López-Gallego F. Solid-Phase Cell-Free Protein Synthesis and Its Applications in Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:21-46. [PMID: 37306703 DOI: 10.1007/10_2023_226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free systems for the in vitro production of proteins have revolutionized the synthetic biology field. In the last decade, this technology is gaining momentum in molecular biology, biotechnology, biomedicine and even education. Materials science has burst into the field of in vitro protein synthesis to empower the value of existing tools and expand its applications. In this sense, the combination of solid materials (normally functionalized with different biomacromolecules) together with cell-free components has made this technology more versatile and robust. In this chapter, we discuss the combination of solid materials with DNA and transcription-translation machinery to synthesize proteins within compartments, to immobilize and purify in situ the nascent protein, to transcribe and transduce DNAs immobilized on solid surfaces, and the combination of all or some of these strategies.
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Affiliation(s)
- Mercedes Sánchez-Costa
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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Bencurova E, Shityakov S, Schaack D, Kaltdorf M, Sarukhanyan E, Hilgarth A, Rath C, Montenegro S, Roth G, Lopez D, Dandekar T. Nanocellulose Composites as Smart Devices With Chassis, Light-Directed DNA Storage, Engineered Electronic Properties, and Chip Integration. Front Bioeng Biotechnol 2022; 10:869111. [PMID: 36105598 PMCID: PMC9465592 DOI: 10.3389/fbioe.2022.869111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of green and sustainable materials opens up new possibilities in the field of applied research. Such materials include nanocellulose composites that can integrate many components into composites and provide a good chassis for smart devices. In our study, we evaluate four approaches for turning a nanocellulose composite into an information storage or processing device: 1) nanocellulose can be a suitable carrier material and protect information stored in DNA. 2) Nucleotide-processing enzymes (polymerase and exonuclease) can be controlled by light after fusing them with light-gating domains; nucleotide substrate specificity can be changed by mutation or pH change (read-in and read-out of the information). 3) Semiconductors and electronic capabilities can be achieved: we show that nanocellulose is rendered electronic by iodine treatment replacing silicon including microstructures. Nanocellulose semiconductor properties are measured, and the resulting potential including single-electron transistors (SET) and their properties are modeled. Electric current can also be transported by DNA through G-quadruplex DNA molecules; these as well as classical silicon semiconductors can easily be integrated into the nanocellulose composite. 4) To elaborate upon miniaturization and integration for a smart nanocellulose chip device, we demonstrate pH-sensitive dyes in nanocellulose, nanopore creation, and kinase micropatterning on bacterial membranes as well as digital PCR micro-wells. Future application potential includes nano-3D printing and fast molecular processors (e.g., SETs) integrated with DNA storage and conventional electronics. This would also lead to environment-friendly nanocellulose chips for information processing as well as smart nanocellulose composites for biomedical applications and nano-factories.
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Affiliation(s)
- Elena Bencurova
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russia
| | - Dominik Schaack
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Kaltdorf
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Edita Sarukhanyan
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alexander Hilgarth
- Aerospace Information Technology, University of Würzburg, Würzburg, Germany
| | - Christin Rath
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
| | - Sergio Montenegro
- Aerospace Information Technology, University of Würzburg, Würzburg, Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
- BioCopy GmbH, Emmendingen, Germany
| | - Daniel Lopez
- Centro Nacional de Biotecnologia CNB, Universidad Autonoma de Madrid, Madrid, Spain
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- *Correspondence: Thomas Dandekar,
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Wells PK, Smutok O, Guo Z, Alexandrov K, Katz E. Nanostructured Interface Loaded with Chimeric Enzymes for Fluorimetric Quantification of Cyclosporine A and FK506. Anal Chem 2022; 94:7303-7310. [PMID: 35543230 DOI: 10.1021/acs.analchem.2c00650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Advances in protein engineering resulted in increased efforts to create protein biosensors that can replace instrumentation-heavy analytical and diagnostic methods. Sensitivity, amenability to multiplexing, and manufacturability remain to be among the key issues preventing broad utilization of protein biosensors. Here, we attempt to address these by constructing arrays utilizing protein biosensors based on the artificial allosteric variant of PQQ-glucose dehydrogenase (GDH). We demonstrated that the silica nanoparticle-immobilized GDH protein could be deposited on fiberglass sheets without loss of activity. The particle-associated GDH activity could be monitored using changes in the fluorescence of the commonly used electron mediator phenazine methosulfate. The constructed biosensor arrays of macrocyclic immunosuppressant drugs cyclosporine A and FK-506 displayed very low background and a remarkable dynamic range exceeding 300-fold that resulted in a limit of detection of 2 pM for both analytes. This enabled us to quantify both drugs in human blood, serum, urine, and saliva. The arrays could be stored in dry form and quantitatively imaged using a smartphone camera, demonstrating the method's suitability for field and point-of-care applications. The developed approach provides a generalizable platform for biosensor array development that is compatible with inexpensive and potentially scalable manufacturing.
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Affiliation(s)
- Paulina K Wells
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia.,Bioeconomy, Centre for Genomics and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, New York 13699, United States
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Heine V, Dey C, Bojarová P, Křen V, Elling L. Methods of in vitro study of galectin-glycomaterial interaction. Biotechnol Adv 2022; 58:107928. [DOI: 10.1016/j.biotechadv.2022.107928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/07/2022] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
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Fruncillo S, Su X, Liu H, Wong LS. Lithographic Processes for the Scalable Fabrication of Micro- and Nanostructures for Biochips and Biosensors. ACS Sens 2021; 6:2002-2024. [PMID: 33829765 PMCID: PMC8240091 DOI: 10.1021/acssensors.0c02704] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Since the early 2000s, extensive research has been performed to address numerous challenges in biochip and biosensor fabrication in order to use them for various biomedical applications. These biochips and biosensor devices either integrate biological elements (e.g., DNA, proteins or cells) in the fabrication processes or experience post fabrication of biofunctionalization for different downstream applications, including sensing, diagnostics, drug screening, and therapy. Scalable lithographic techniques that are well established in the semiconductor industry are now being harnessed for large-scale production of such devices, with additional development to meet the demand of precise deposition of various biological elements on device substrates with retained biological activities and precisely specified topography. In this review, the lithographic methods that are capable of large-scale and mass fabrication of biochips and biosensors will be discussed. In particular, those allowing patterning of large areas from 10 cm2 to m2, maintaining cost effectiveness, high throughput (>100 cm2 h-1), high resolution (from micrometer down to nanometer scale), accuracy, and reproducibility. This review will compare various fabrication technologies and comment on their resolution limit and throughput, and how they can be related to the device performance, including sensitivity, detection limit, reproducibility, and robustness.
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Affiliation(s)
- Silvia Fruncillo
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Xiaodi Su
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
- Department of Chemistry, National University of Singapore, Block S8, Level 3, 3 Science Drive, Singapore 117543, Singapore
| | - Hong Liu
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, #08-03, Innovis, Singapore 138634, Singapore
| | - Lu Shin Wong
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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Hariharan G, Prasannath K. Recent Advances in Molecular Diagnostics of Fungal Plant Pathogens: A Mini Review. Front Cell Infect Microbiol 2021; 10:600234. [PMID: 33505921 PMCID: PMC7829251 DOI: 10.3389/fcimb.2020.600234] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 11/25/2020] [Indexed: 12/18/2022] Open
Abstract
Phytopathogenic fungal species can cause enormous losses in quantity and quality of crop yields and this is a major economic issue in the global agricultural sector. Precise and rapid detection and identification of plant infecting fungi are essential to facilitate effective management of disease. DNA-based methods have become popular methods for accurate plant disease diagnostics. Recent developments in standard and variant polymerase chain reaction (PCR) assays including nested, multiplex, quantitative, bio and magnetic-capture hybridization PCR techniques, post and isothermal amplification methods, DNA and RNA based probe development, and next-generation sequencing provide novel tools in molecular diagnostics in fungal detection and differentiation fields. These molecular based detection techniques are effective in detecting symptomatic and asymptomatic diseases of both culturable and unculturable fungal pathogens in sole and co-infections. Even though the molecular diagnostic approaches have expanded substantially in the recent past, there is a long way to go in the development and application of molecular diagnostics in plant diseases. Molecular techniques used in plant disease diagnostics need to be more reliable, faster, and easier than conventional methods. Now the challenges are with scientists to develop practical techniques to be used for molecular diagnostics of plant diseases. Recent advancement in the improvement and application of molecular methods for diagnosing the widespread and emerging plant pathogenic fungi are discussed in this review.
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Affiliation(s)
- Ganeshamoorthy Hariharan
- Department of Agricultural Biology, Faculty of Agriculture, Eastern University, Chenkalady, Sri Lanka
| | - Kandeeparoopan Prasannath
- Department of Agricultural Biology, Faculty of Agriculture, Eastern University, Chenkalady, Sri Lanka
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