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Wranne MS, Karami N, Kk S, Jaén-Luchoro D, Yazdanshenas S, Lin YL, Kabbinale A, Flach CF, Westerlund F, Åhrén C. Comparison of CTX-M encoding plasmids present during the early phase of the ESBL pandemic in western Sweden. Sci Rep 2024; 14:11880. [PMID: 38789462 PMCID: PMC11126669 DOI: 10.1038/s41598-024-62663-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024] Open
Abstract
Plasmids encoding blaCTX-M genes have greatly shaped the evolution of E. coli producing extended-spectrum beta-lactamases (ESBL-E. coli) and adds to the global threat of multiresistant bacteria by promoting horizontal gene transfer (HGT). Here we screened the similarity of 47 blaCTX-M -encoding plasmids, from 45 epidemiologically unrelated and disperse ESBL-E. coli strains, isolated during the early phase (2009-2014) of the ESBL pandemic in western Sweden. Using optical DNA mapping (ODM), both similar and rare plasmids were identified. As many as 57% of the plasmids formed five ODM-plasmid groups of at least three similar plasmids per group. The most prevalent type (28%, IncIl, pMLST37) encoded blaCTX-M-15 (n = 10), blaCTX-M-3 (n = 2) or blaCTX-M-55 (n = 1). It was found in isolates of various sequence types (STs), including ST131. This could indicate ongoing local HGT as whole-genome sequencing only revealed similarities with a rarely reported, IncIl plasmid. The second most prevalent type (IncFII/FIA/FIB, F1:A2:B20) harboring blaCTX-M-27, was detected in ST131-C1-M27 isolates, and was similar to plasmids previously reported for this subclade. The results also highlight the need for local surveillance of plasmids and the importance of temporospatial epidemiological links so that detection of a prevalent plasmid is not overestimated as a potential plasmid transmission event in outbreak investigations.
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Affiliation(s)
- Moa S Wranne
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Nahid Karami
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden.
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden.
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden.
| | - Sriram Kk
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Daniel Jaén-Luchoro
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Shora Yazdanshenas
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Yii-Lih Lin
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Arpitha Kabbinale
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Christina Åhrén
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Guldhedsgatan 10A, 413 46, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden
- Swedish Strategic Program Against Antimicrobial Resistance (Strama), Region Västra Götaland, Gothenburg, Sweden
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2
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Yang J, Kamai H, Wang Y, Xu Y. Nanofluidic Aptamer Nanoarray to Enable Stochastic Capture of Single Proteins at Normal Concentrations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2301013. [PMID: 37350189 DOI: 10.1002/smll.202301013] [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: 02/04/2023] [Revised: 05/18/2023] [Indexed: 06/24/2023]
Abstract
Single-molecule experiments allow understanding of the diversity, stochasticity, and heterogeneity of molecular behaviors and properties hidden by conventional ensemble-averaged measurements. They hence have great importance and significant impacts in a wide range of fields. Despite significant advances in single-molecule experiments at ultralow concentrations, the capture of single molecules in solution at normal concentrations within natural biomolecular processes remains a formidable challenge. Here, a high-density, well-defined nanofluidic aptamer nanoarray (NANa) formed via site-specific self-assembly of well-designed aptamer molecules in nanochannels with nano-in-nano gold nanopatterns is presented. The nanofluidic aptamer nanoarray exhibits a high capability to specifically capture target proteins (e.g., platelet-derived growth factor BB; PDGF-BB) to form uniform protein nanoarrays under optimized nanofluidic conditions. Owing to these fundamental features, the nanofluidic aptamer nanoarray enables the stochastic capture of single PDGF-BB molecules at a normal concentration from a sample with an ultrasmall volume equivalent to a single cell by following Poisson statistics, forming a readily addressable single-protein nanoarray. This approach offers a methodology and device to surpass both the concentration and volume limits of single-protein capture in most conventional methodologies of single-molecule experiments, thus opening an avenue to explore the behavior of individual biomolecules in a manner close to their natural forms, which remains largely unexplored to date.
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Affiliation(s)
- Jinbin Yang
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
| | - Hiroki Kamai
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
| | - Yong Wang
- Department of Biomedical Engineering, The Pennsylvania State University, 26 CBEB, University Park, PA, 16802-6804, USA
| | - Yan Xu
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Prefecture University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
- Department of Chemical Engineering, Graduate School of Engineering, Osaka Metropolitan University, 1-2, Gakuen-cho, Naka-ku, Sakai, Osaka, 599-8570, Japan
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
- Japan Science and Technology Agency (JST), CREST, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
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3
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Nyblom M, Johnning A, Frykholm K, Wrande M, Müller V, Goyal G, Robertsson M, Dvirnas A, Sewunet T, KK S, Ambjörnsson T, Giske CG, Sandegren L, Kristiansson E, Westerlund F. Strain-level bacterial typing directly from patient samples using optical DNA mapping. COMMUNICATIONS MEDICINE 2023; 3:31. [PMID: 36823379 PMCID: PMC9950433 DOI: 10.1038/s43856-023-00259-z] [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: 05/26/2022] [Accepted: 02/09/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Identification of pathogens is crucial to efficiently treat and prevent bacterial infections. However, existing diagnostic techniques are slow or have a too low resolution for well-informed clinical decisions. METHODS In this study, we have developed an optical DNA mapping-based method for strain-level bacterial typing and simultaneous plasmid characterisation. For the typing, different taxonomical resolutions were examined and cultivated pure Escherichia coli and Klebsiella pneumoniae samples were used for parameter optimization. Finally, the method was applied to mixed bacterial samples and uncultured urine samples from patients with urinary tract infections. RESULTS We demonstrate that optical DNA mapping of single DNA molecules can identify Escherichia coli and Klebsiella pneumoniae at the strain level directly from patient samples. At a taxonomic resolution corresponding to E. coli sequence type 131 and K. pneumoniae clonal complex 258 forming distinct groups, the average true positive prediction rates are 94% and 89%, respectively. The single-molecule aspect of the method enables us to identify multiple E. coli strains in polymicrobial samples. Furthermore, by targeting plasmid-borne antibiotic resistance genes with Cas9 restriction, we simultaneously identify the strain or subtype and characterize the corresponding plasmids. CONCLUSION The optical DNA mapping method is accurate and directly applicable to polymicrobial and clinical samples without cultivation. Hence, it has the potential to rapidly provide comprehensive diagnostics information, thereby optimizing early antibiotic treatment and opening up for future precision medicine management.
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Affiliation(s)
- My Nyblom
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Anna Johnning
- grid.5371.00000 0001 0775 6028Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96 Sweden ,grid.452079.dDepartment of Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, 412 88 Sweden ,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30 Sweden
| | - Karolin Frykholm
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Marie Wrande
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Vilhelm Müller
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Gaurav Goyal
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Miriam Robertsson
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Albertas Dvirnas
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Tsegaye Sewunet
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden
| | - Sriram KK
- grid.5371.00000 0001 0775 6028Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96 Sweden
| | - Tobias Ambjörnsson
- grid.4514.40000 0001 0930 2361Department of Astronomy and Theoretical Physics, Lund University, Lund, 223 62 Sweden
| | - Christian G. Giske
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Stockholm, 141 86 Sweden ,grid.24381.3c0000 0000 9241 5705Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, 171 76 Sweden
| | - Linus Sandegren
- grid.8993.b0000 0004 1936 9457Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 23 Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology & University of Gothenburg, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
| | - Fredrik Westerlund
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, 412 96, Sweden. .,Centre for Antibiotic Resistance Research in Gothenburg (CARe), Gothenburg, 405 30, Sweden.
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4
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Brakta S, Hawkins ZA, Sahajpal N, Seman N, Kira D, Chorich LP, Kim HG, Xu H, Phillips JA, Kolhe R, Layman LC. Rare structural variants, aneuploidies, and mosaicism in individuals with Mullerian aplasia detected by optical genome mapping. Hum Genet 2023; 142:483-494. [PMID: 36797380 DOI: 10.1007/s00439-023-02522-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/06/2023] [Indexed: 02/18/2023]
Abstract
The molecular basis of Mayer-Rokitansky-Kuster-Hauser (MRKH) syndrome remains largely unknown. Pathogenic variants in WNT4 and HNF1B have been confirmed in a small percent of individuals. A variety of copy number variants have been reported, but causal gene(s) remain to be identified. We hypothesized that rare structural variants (SVs) would be present in some individuals with MRKH, which could explain the genetic basis of the syndrome. Large molecular weight DNA was extracted from lymphoblastoid cells from 87 individuals with MRKH and available parents. Optical genome mapping (OGM) was performed to identify SVs, which were confirmed by another method (quantitative PCR, chromosomal microarray, karyotype, or fluorescent in situ hybridization) when possible. Thirty-four SVs that overlapped coding regions of genes with potential involvement in MRKH were identified, 14 of which were confirmed by a second method. These 14 SVs were present in 17/87 (19.5%) of probands with MRKH and included seven deletions, three duplications, one new translocation in 5/50 cells-t(7;14)(q32;q32), confirmation of a previously identified translocation-t(3;16)(p22.3;p13.3), and two aneuploidies. Of interest, three cases of mosaicism (3.4% of probands) were identified-25% mosaicism for trisomy 12, 45,X(75%)/46,XX (25%), and 10% mosaicism for a 7;14 translocation. Our study constitutes the first systematic investigation of SVs by OGM in individuals with MRKH. We propose that OGM is a promising method that enables a comprehensive investigation of a variety of SVs in a single assay including cryptic translocations and mosaic aneuploidies. These observations suggest that mosaicism could play a role in the genesis of MRKH.
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Affiliation(s)
- Soumia Brakta
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia.
| | - Zoe A Hawkins
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Nikhil Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.,Department of Genetics, Greenwood Genetics Center, Greenwood, SC, USA
| | - Natalie Seman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Dina Kira
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Lynn P Chorich
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Hongyan Xu
- Department of Population Health Sciences, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - John A Phillips
- Division of Medical Genetics and Genomic Medicine, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility, & Genetics, Department of Obstetrics & Gynecology, Medical College of Georgia, Augusta University, Augusta, Georgia. .,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, Georgia. .,Department of Physiology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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5
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Rehel DA, Polson JM. Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries. SOFT MATTER 2023; 19:1092-1108. [PMID: 36625101 DOI: 10.1039/d2sm01413k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules in box-like cavities with strong confinement in one direction and with square and elliptical cross sections in the lateral plane. Motivated by these experiments, we employ Monte Carlo and Brownian dynamics simulations to study the physical behaviour of two polymers confined to small cavities with shapes comparable to those used in the experiments. We quantify the effects of varying the following polymer properties and confinement dimensions on the organization and dynamics of the polymers: the polymer width, the polymer contour length ratio, the cavity cross-sectional area, and the degree of cavity elongation for cavities with rectangular and elliptical cross sections. We find that the tendency for polymers to segregate is enhanced by increasing polymer width. For sufficiently small cavities, increasing cavity elongation promotes segregation and localization of identical polymers to opposite sides of the cavity along its long axis. A free-energy barrier controls the rate of polymers swapping positions, and the observed dynamics are roughly in accord with predictions of a simple theoretical model. Increasing the contour length difference between polymers significantly affects their organization in the cavity. In the case of a large linear polymer co-trapped with a small ring polymer in an elliptical cavity, the small polymer tends to lie near the lateral confining walls, and especially at the cavity poles for highly elongated ellipses.
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Affiliation(s)
- Desiree A Rehel
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada.
| | - James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada.
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6
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KK S, Wranne MS, Sewunet T, Ekedahl E, Coorens M, Tangkoskul T, Thamlikitkul V, Giske CG, Westerlund F. Identification and characterization of plasmids carrying the mobile colistin resistance gene mcr-1 using optical DNA mapping. JAC Antimicrob Resist 2023; 5:dlad004. [PMID: 36743530 PMCID: PMC9891347 DOI: 10.1093/jacamr/dlad004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Objectives Colistin is a last-resort antibiotic, but there has been a rapid increase in colistin resistance, threatening its use in the treatment of infections with carbapenem-resistant Enterobacterales (CRE). Plasmid-mediated colistin resistance, in particular the mcr-1 gene, has been identified and WGS is the go-to method in identifying plasmids carrying mcr-1 genes. The goal of this study is to demonstrate the use of optical DNA mapping (ODM), a fast, efficient and amplification-free technique, to characterize plasmids carrying mcr-1. Methods ODM is a single-molecule technique, which we have demonstrated can be used for identifying plasmids harbouring antibiotic resistance genes. We here applied the technique to plasmids isolated from 12 clinical Enterobacterales isolates from patients at a major hospital in Thailand and verified our results using Nanopore long-read sequencing. Results We successfully identified plasmids encoding the mcr-1 gene and, for the first time, demonstrated the ability of ODM to identify resistance gene sites in small (∼30 kb) plasmids. We further identified bla CTX-M genes in different plasmids than the ones encoding mcr-1 in three of the isolates studied. Finally, we propose a cut-and-stretch assay, based on similar principles, but performed using surface-functionalized cover slips for DNA immobilization and an inexpensive microscope with basic functionalities, to identify the mcr-1 gene in a plasmid sample. Conclusions Both ODM and the cut-and-stretch assay developed could be very useful in identifying plasmids encoding antibiotic resistance in hospitals and healthcare facilities. The cut-and-stretch assay is particularly useful in low- and middle-income countries, where existing techniques are limited.
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Affiliation(s)
- Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Moa S Wranne
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Maarten Coorens
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | | | | | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden,Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
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7
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Levin S, Lerch S, Boje A, Fritzsche J, KK S, Ström H, Moth-Poulsen K, Sundén H, Hellman A, Westerlund F, Langhammer C. Nanofluidic Trapping of Faceted Colloidal Nanocrystals for Parallel Single-Particle Catalysis. ACS NANO 2022; 16:15206-15214. [PMID: 36054658 PMCID: PMC9527799 DOI: 10.1021/acsnano.2c06505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/31/2022] [Indexed: 06/15/2023]
Abstract
Catalyst activity can depend distinctly on nanoparticle size and shape. Therefore, understanding the structure sensitivity of catalytic reactions is of fundamental and technical importance. Experiments with single-particle resolution, where ensemble-averaging is eliminated, are required to study it. Here, we implement the selective trapping of individual spherical, cubic, and octahedral colloidal Au nanocrystals in 100 parallel nanofluidic channels to determine their activity for fluorescein reduction by sodium borohydride using fluorescence microscopy. As the main result, we identify distinct structure sensitivity of the rate-limiting borohydride oxidation step originating from different edge site abundance on the three particle types, as confirmed by first-principles calculations. This advertises nanofluidic reactors for the study of structure-function correlations in catalysis and identifies nanoparticle shape as a key factor in borohydride-mediated catalytic reactions.
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Affiliation(s)
- Sune Levin
- Department
of Biology and Biological Engineering, Chalmers
University of Technology; SE-412 96 Gothenburg, Sweden
| | - Sarah Lerch
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology; SE-412 96 Gothenburg, Sweden
| | - Astrid Boje
- Department
of Physics, Chalmers University of Technology; SE-412 96 Gothenburg, Sweden
| | - Joachim Fritzsche
- Department
of Physics, Chalmers University of Technology; SE-412 96 Gothenburg, Sweden
| | - Sriram KK
- Department
of Biology and Biological Engineering, Chalmers
University of Technology; SE-412 96 Gothenburg, Sweden
| | - Henrik Ström
- Department
of Mechanics and Maritime Sciences, Chalmers
University of Technology; SE-412 96 Gothenburg, Sweden
- Department
of Energy and Process Engineering, Norwegian
University of Science and Technology; NO-7034 Trondheim, Norway
| | - Kasper Moth-Poulsen
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology; SE-412 96 Gothenburg, Sweden
- Institute
of Materials Science of Barcelona, ICMAB-CSIC, Bellaterra, ES-08193 Barcelona, Spain
- Catalan
Institution for Research and Advanced Studies, ICREA; ES-08010 Barcelona, Spain
| | - Henrik Sundén
- Department
of Chemistry and Chemical Engineering, Chalmers
University of Technology; SE-412 96 Gothenburg, Sweden
- Department
of Chemistry & Molecular Biology, University
of Gothenburg; SE-412 96 Gothenburg, Sweden
| | - Anders Hellman
- Department
of Physics, Chalmers University of Technology; SE-412 96 Gothenburg, Sweden
- Competence
Centre for Catalysis, Chalmers University
of Technology; SE-412 96 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department
of Biology and Biological Engineering, Chalmers
University of Technology; SE-412 96 Gothenburg, Sweden
| | - Christoph Langhammer
- Department
of Physics, Chalmers University of Technology; SE-412 96 Gothenburg, Sweden
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8
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Esmek FM, Erichlandwehr T, Brkovic N, Pranzner NP, Teuber JP, Fernandez-Cuesta I. Pillar-structured 3D inlets fabricated by dose-modulated e-beam lithography and nanoimprinting for DNA analysis in passive, clogging-free, nanofluidic devices. NANOTECHNOLOGY 2022; 33:385301. [PMID: 35696945 DOI: 10.1088/1361-6528/ac780d] [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: 02/09/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
We present the fabrication of three-dimensional inlets with gradually decreasing widths and depths and with nanopillars on the slope, all defined in just one lithography step. In addition, as an application, we show how these micro- and nanostructures can be used for micro- and nanofluidics and lab-on-a-chip devices to facilitate the flow and analyze single molecules of DNA. For the fabrication of 3D inlets in a single layer process, dose-modulated electron beam lithography was used, producing depths between 750 nm and 50 nm along a 30 μm long inlet, which is additionally structured with nanometer-scale pillars randomly distributed on top, as a result of incomplete exposure and underdevelopment of the resist. The fabrication conditions affect the slope of the inlet, the nanopillar density and coverage. The key parameters are the dose used for the electron beam exposure and the development conditions, like the developer's dilution, stirring and development time. The 3D inlets with nanostructured pillars were integrated into fluidic devices, acting as a transition between micro and nanofluidic structures for pre-stretching and unfolding DNA molecules, avoiding the intrusion of folded molecules and clogging the analysis channel. After patterning these structures in silicon, they can be replicated in polymer by UV nanoimprinting. We show here how the inlets with pillars slow down the molecules before they enter the nanochannels, resulting in a 3-fold decrease in speed, which would translate to an improvement in the resolution for DNA optical mapping.
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Affiliation(s)
- Franziska M Esmek
- Universität Hamburg, Institute of Nanostructure and Solid State Physics, HARBOR Bldg 610, Luruper Chaussee 149, Hamburg D-22761, Germany
| | - Tim Erichlandwehr
- Universität Hamburg, Institute of Nanostructure and Solid State Physics, HARBOR Bldg 610, Luruper Chaussee 149, Hamburg D-22761, Germany
| | - Nico Brkovic
- Universität Hamburg, Institute of Nanostructure and Solid State Physics, HARBOR Bldg 610, Luruper Chaussee 149, Hamburg D-22761, Germany
| | - Nathalie P Pranzner
- Universität Hamburg, Institute of Nanostructure and Solid State Physics, HARBOR Bldg 610, Luruper Chaussee 149, Hamburg D-22761, Germany
| | - Jeremy P Teuber
- Universität Hamburg, Institute of Nanostructure and Solid State Physics, HARBOR Bldg 610, Luruper Chaussee 149, Hamburg D-22761, Germany
| | - Irene Fernandez-Cuesta
- Universität Hamburg, Institute of Nanostructure and Solid State Physics, HARBOR Bldg 610, Luruper Chaussee 149, Hamburg D-22761, Germany
- Hamburg Centre for Ultrafast Imaging, Germany
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9
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DuBose CO, Daum JR, Sansam CL, Gorbsky GJ. Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells. Genes (Basel) 2022; 13:genes13071157. [PMID: 35885940 PMCID: PMC9318709 DOI: 10.3390/genes13071157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) hold great potential for regenerative medicine. By reprogramming a patient′s own cells, immunological rejection can be avoided during transplantation. For expansion and gene editing, iPSCs are grown in artificial culture for extended times. Culture affords potential danger for the accumulation of genetic aberrations. To study these, two induced pluripotent stem (iPS) cell lines were cultured and periodically analyzed using advanced optical mapping to detect and classify chromosome numerical and segmental changes that included deletions, insertions, balanced translocations and inversions. In one of the lines, a population trisomic for chromosome 12 gained dominance over a small number of passages. This appearance and dominance of the culture by chromosome 12 trisomic cells was tracked through intermediate passages by the analysis of chromosome spreads. Mathematical modeling suggested that the proliferation rates of diploid versus trisomic cells could not account for the rapid dominance of the trisomic population. In addition, optical mapping revealed hundreds of structural variations distinct from those generally found within the human population. Many of these structural variants were detected in samples obtained early in the culturing process and were maintained in late passage samples, while others were acquired over the course of culturing.
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Affiliation(s)
- Casey O. DuBose
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
| | - John R. Daum
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
| | - Christopher L. Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Gary J. Gorbsky
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA; (C.O.D.); (J.R.D.)
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Correspondence:
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10
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A simple cut and stretch assay to detect antimicrobial resistance genes on bacterial plasmids by single-molecule fluorescence microscopy. Sci Rep 2022; 12:9301. [PMID: 35660772 PMCID: PMC9166776 DOI: 10.1038/s41598-022-13315-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Antimicrobial resistance (AMR) is a fast-growing threat to global health. The genes conferring AMR to bacteria are often located on plasmids, circular extrachromosomal DNA molecules that can be transferred between bacterial strains and species. Therefore, effective methods to characterize bacterial plasmids and detect the presence of resistance genes can assist in managing AMR, for example, during outbreaks in hospitals. However, existing methods for plasmid analysis either provide limited information or are expensive and challenging to implement in low-resource settings. Herein, we present a simple assay based on CRISPR/Cas9 excision and DNA combing to detect antimicrobial resistance genes on bacterial plasmids. Cas9 recognizes the gene of interest and makes a double-stranded DNA cut, causing the circular plasmid to linearize. The change in plasmid configuration from circular to linear, and hence the presence of the AMR gene, is detected by stretching the plasmids on a glass surface and visualizing by fluorescence microscopy. This single-molecule imaging based assay is inexpensive, fast, and in addition to detecting the presence of AMR genes, it provides detailed information on the number and size of plasmids in the sample. We demonstrate the detection of several β-lactamase-encoding genes on plasmids isolated from clinical samples. Furthermore, we demonstrate that the assay can be performed using standard microbiology and clinical laboratory equipment, making it suitable for low-resource settings.
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11
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Yang J, Xu Y. Nanofluidics for sub-single cellular studies: Nascent progress, critical technologies, and future perspectives. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Label-free nanofluidic scattering microscopy of size and mass of single diffusing molecules and nanoparticles. Nat Methods 2022; 19:751-758. [PMID: 35637303 PMCID: PMC9184284 DOI: 10.1038/s41592-022-01491-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 04/12/2022] [Indexed: 12/18/2022]
Abstract
Label-free characterization of single biomolecules aims to complement fluorescence microscopy in situations where labeling compromises data interpretation, is technically challenging or even impossible. However, existing methods require the investigated species to bind to a surface to be visible, thereby leaving a large fraction of analytes undetected. Here, we present nanofluidic scattering microscopy (NSM), which overcomes these limitations by enabling label-free, real-time imaging of single biomolecules diffusing inside a nanofluidic channel. NSM facilitates accurate determination of molecular weight from the measured optical contrast and of the hydrodynamic radius from the measured diffusivity, from which information about the conformational state can be inferred. Furthermore, we demonstrate its applicability to the analysis of a complex biofluid, using conditioned cell culture medium containing extracellular vesicles as an example. We foresee the application of NSM to monitor conformational changes, aggregation and interactions of single biomolecules, and to analyze single-cell secretomes. Nanofluidic scattering microscopy enables label-free, quantitative measurements of the molecular weight and hydrodynamic radius of biological molecules and nanoparticles freely diffusing inside a nanofluidic channel.
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13
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Fernandez-Cuesta I, Llobera A, Ramos-Payán M. Optofluidic systems enabling detection in real samples: A review. Anal Chim Acta 2022; 1192:339307. [DOI: 10.1016/j.aca.2021.339307] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/20/2022]
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14
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Sriram KK, Ekedahl E, Hoang NTB, Sewunet T, Berglund B, Lundberg L, Nematzadeh S, Nilsson M, Nilsson LE, Le NK, Tran DM, Hanberger H, Olson L, Larsson M, Giske CG, Westerlund F. High diversity of bla NDM-1-encoding plasmids in Klebsiella pneumoniae isolated from neonates in a Vietnamese hospital. Int J Antimicrob Agents 2021; 59:106496. [PMID: 34921976 DOI: 10.1016/j.ijantimicag.2021.106496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/08/2021] [Accepted: 12/01/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVES The carbapenemase-encoding gene blaNDM-1 has been reported in Vietnam over the last ten years, and blaNDM-producing Enterobacteriaceae are now silently and rapidly spreading. A key factor behind dissemination of blaNDM-1 are plasmids, mobile genetic elements that commonly carry antibiotic resistance genes and spread via conjugation. Here, we characterized the diversity of blaNDM-1-encoding plasmids from neonates at a large Vietnamese hospital . METHODS 18 fecal Klebsiella pneumoniae and Klebsiella quasipneumoniae isolates collected from 16 neonates at a large pediatric hospital in Vietnam were studied with optical DNA mapping (ODM) and next-generation sequencing (NGS). We identified the plasmid(s) carrying blaNDM-1 by combining ODM with Cas9 restriction. By comparing the plasmids between isolates, we could investigate if the same plasmid was present in different patients. RESULTS Although the same plasmid was found among some isolates, ODM confirmed that there were at least 10 different plasmids encoding blaNDM-1 among the 18 isolates collected from 16 neonates, suggesting a large plasmid diversity. The ODM results were in large agreement with the NGS data. Interestingly, some isolates had two distinct plasmids encoding blaNDM-1, which could be readily detected with ODM. Thus far, the coexistence of different plasmids carrying the same carbapenem resistance gene in an isolate encoding blaNDM-1 has rarely been reported, likely due to limitations in existing plasmid characterization techniques. CONCLUSIONS Our results show that the plasmids encoding blaNDM-1 in this cohort were very diverse, suggesting a similar picture in the Vietnamese society. The study also highlights important aspects of the usefulness of ODM for plasmid analysis.
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Affiliation(s)
- K K Sriram
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Elina Ekedahl
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ngoc Thi Bich Hoang
- Department of Microbiology, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden
| | - Björn Berglund
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Ludwig Lundberg
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden; Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden
| | - Maud Nilsson
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Lennart E Nilsson
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Ngai Kien Le
- Department of Surgery, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Dien Minh Tran
- Department of Infection Control, Vietnam National Children's Hospital, Hanoi, Vietnam
| | - Håkan Hanberger
- Department of Biomedical and Clinical Sciences, Faculty of medicine, Linköping University, Linköping, Sweden
| | - Linus Olson
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden; Department of Women and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Mattias Larsson
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory medicine, Karolinska Institutet, Stockholm, Sweden; Clinical microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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15
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Torstensson E, Goyal G, Johnning A, Westerlund F, Ambjörnsson T. Combining dense and sparse labeling in optical DNA mapping. PLoS One 2021; 16:e0260489. [PMID: 34843574 PMCID: PMC8629184 DOI: 10.1371/journal.pone.0260489] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/10/2021] [Indexed: 11/19/2022] Open
Abstract
Optical DNA mapping (ODM) is based on fluorescent labeling, stretching and imaging of single DNA molecules to obtain sequence-specific fluorescence profiles, DNA barcodes. These barcodes can be mapped to theoretical counterparts obtained from DNA reference sequences, which in turn allow for DNA identification in complex samples and for detecting structural changes in individual DNA molecules. There are several types of DNA labeling schemes for ODM and for each labeling type one or several types of match scoring methods are used. By combining the information from multiple labeling schemes one can potentially improve mapping confidence; however, combining match scores from different labeling assays has not been implemented yet. In this study, we introduce two theoretical methods for dealing with analysis of DNA molecules with multiple label types. In our first method, we convert the alignment scores, given as output from the different assays, into p-values using carefully crafted null models. We then combine the p-values for different label types using standard methods to obtain a combined match score and an associated combined p-value. In the second method, we use a block bootstrap approach to check for the uniqueness of a match to a database for all barcodes matching with a combined p-value below a predefined threshold. For obtaining experimental dual-labeled DNA barcodes, we introduce a novel assay where we cut plasmid DNA molecules from bacteria with restriction enzymes and the cut sites serve as sequence-specific markers, which together with barcodes obtained using the established competitive binding labeling method, form a dual-labeled barcode. All experimental data in this study originates from this assay, but we point out that our theoretical framework can be used to combine data from all kinds of available optical DNA mapping assays. We test our multiple labeling frameworks on barcodes from two different plasmids and synthetically generated barcodes (combined competitive-binding- and nick-labeling). It is demonstrated that by simultaneously using the information from all label types, we can substantially increase the significance when we match experimental barcodes to a database consisting of theoretical barcodes for all sequenced plasmids.
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Affiliation(s)
- Erik Torstensson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Gaurav Goyal
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers Centre, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
- * E-mail:
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16
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Sano H, Kazoe Y, Kitamori T. Stable Formation of Aqueous/Organic Parallel Two-phase Flow in Nanochannels with Partial Surface Modification. ANAL SCI 2021; 37:1611-1616. [PMID: 34054008 DOI: 10.2116/analsci.21p138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In microfluidics, various chemical processes can be integrated utilizing parallel multiphase flows. Our group has extended this research to nanofluidics, and recently performed the extraction of lipids using parallel two-phase flow in nanochannels. Although this was achieved in surface-modified nanochannels, a stable condition of parallel two-phase flow remains unknown due to difficulties in device fabrication, for a suitable method of bonding surface-modified substrates is lacking. Therefore, research on parallel two-phase flow in nanochannels has been limited. Herein, a new bonding method which improves the wash process for the substrates and increases the bonding rate to ∼100% is described. The conditions to achieve parallel organic/aqueous two-phase flow were then studied. It was revealed that in nanochannels, higher capillary numbers for the organic phase flow were required compared to that in microchannels. The newly developed fabrication process and flow regimes will contribute to realize integrated nanofluidic devices capable of analyzing single molecules/cells.
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Affiliation(s)
- Hiroki Sano
- Department of Applied Chemistry, School of Engineering, The University of Tokyo
| | - Yutaka Kazoe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo.,Department of System Design Engineering, Faculty of Science and Technology, Keio University
| | - Takehiko Kitamori
- Department of Applied Chemistry, School of Engineering, The University of Tokyo.,Collaborative Research Organization for Micro and Nano Multifunctional Devices, The University of Tokyo.,Institute of NanoEngineering and MicroSystems, Department of Power Mechanical Engineering, National Tsing Hua University
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17
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Dvirnas A, Stewart C, Müller V, Bikkarolla SK, Frykholm K, Sandegren L, Kristiansson E, Westerlund F, Ambjörnsson T. Detection of structural variations in densely-labelled optical DNA barcodes: A hidden Markov model approach. PLoS One 2021; 16:e0259670. [PMID: 34739528 PMCID: PMC8570516 DOI: 10.1371/journal.pone.0259670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/22/2021] [Indexed: 11/19/2022] Open
Abstract
Large-scale genomic alterations play an important role in disease, gene expression, and chromosome evolution. Optical DNA mapping (ODM), commonly categorized into sparsely-labelled ODM and densely-labelled ODM, provides sequence-specific continuous intensity profiles (DNA barcodes) along single DNA molecules and is a technique well-suited for detecting such alterations. For sparsely-labelled barcodes, the possibility to detect large genomic alterations has been investigated extensively, while densely-labelled barcodes have not received as much attention. In this work, we introduce HMMSV, a hidden Markov model (HMM) based algorithm for detecting structural variations (SVs) directly in densely-labelled barcodes without access to sequence information. We evaluate our approach using simulated data-sets with 5 different types of SVs, and combinations thereof, and demonstrate that the method reaches a true positive rate greater than 80% for randomly generated barcodes with single variations of size 25 kilobases (kb). Increasing the length of the SV further leads to larger true positive rates. For a real data-set with experimental barcodes on bacterial plasmids, we successfully detect matching barcode pairs and SVs without any particular assumption of the types of SVs present. Instead, our method effectively goes through all possible combinations of SVs. Since ODM works on length scales typically not reachable with other techniques, our methodology is a promising tool for identifying arbitrary combinations of genomic alterations.
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Affiliation(s)
- Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
- * E-mail:
| | - Callum Stewart
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Vilhelm Müller
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Erik Kristiansson
- Department of Mathematical Sciences, Chalmers University of Technology and the University of Gothenburg, Gothenburg, Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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18
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KK S, Lin YL, Sewunet T, Wrande M, Sandegren L, Giske CG, Westerlund F. A Parallelized Nanofluidic Device for High-Throughput Optical DNA Mapping of Bacterial Plasmids. MICROMACHINES 2021; 12:1234. [PMID: 34683285 PMCID: PMC8538381 DOI: 10.3390/mi12101234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 12/03/2022]
Abstract
Optical DNA mapping (ODM) has developed into an important technique for DNA analysis, where single DNA molecules are sequence-specifically labeled and stretched, for example, in nanofluidic channels. We have developed an ODM assay to analyze bacterial plasmids-circular extrachromosomal DNA that often carry genes that make bacteria resistant to antibiotics. As for most techniques, the next important step is to increase throughput and automation. In this work, we designed and fabricated a nanofluidic device that, together with a simple automation routine, allows parallel analysis of up to 10 samples at the same time. Using plasmids encoding extended-spectrum beta-lactamases (ESBL), isolated from Escherichiacoli and Klebsiellapneumoniae, we demonstrate the multiplexing capabilities of the device when it comes to both many samples in parallel and different resistance genes. As a final example, we combined the device with a novel protocol for rapid cultivation and extraction of plasmids from fecal samples collected from patients. This combined protocol will make it possible to analyze many patient samples in one device already on the day the sample is collected, which is an important step forward for the ODM analysis of plasmids in clinical diagnostics.
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Affiliation(s)
- Sriram KK
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Yii-Lih Lin
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Marie Wrande
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, 752 37 Uppsala, Sweden; (M.W.); (L.S.)
| | - Christian G. Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden; (S.K.); (Y.-L.L.)
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19
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KK S, Sewunet T, Wangchinda W, Tangkoskul T, Thamlikitkul V, Giske CG, Westerlund F. Optical DNA Mapping of Plasmids Reveals Clonal Spread of Carbapenem-Resistant Klebsiella pneumoniae in a Large Thai Hospital. Antibiotics (Basel) 2021; 10:antibiotics10091029. [PMID: 34572611 PMCID: PMC8466775 DOI: 10.3390/antibiotics10091029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/26/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CR-KP) in patients admitted to hospitals pose a great challenge to treatment. The genes causing resistance to carbapenems are mostly found in plasmids, mobile genetic elements that can spread easily to other bacterial strains, thus exacerbating the problem. Here, we studied 27 CR-KP isolates collected from different types of samples from 16 patients admitted to the medical ward at Siriraj Hospital in Bangkok, Thailand, using next generation sequencing (NGS) and optical DNA mapping (ODM). The majority of the isolates belonged to sequence type (ST) 16 and are described in detail herein. Using ODM, we identified the plasmid carrying the blaNDM-1 gene in the ST16 isolates and the plasmids were very similar, highlighting the possibility of using ODM of plasmids as a surrogate marker of nosocomial spread of bacteria. We also demonstrated that ODM could identify that the blaCTX-M-15 and blaOXA-232 genes in the ST16 isolates were encoded on separate plasmids from the blaNDM-1 gene and from each other. The other three isolates belonged to ST147 and each of them had distinct plasmids encoding blaNDM-1.
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Affiliation(s)
- Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
| | - Tsegaye Sewunet
- Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
| | - Walaiporn Wangchinda
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Teerawit Tangkoskul
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Visanu Thamlikitkul
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (W.W.); (T.T.); (V.T.)
| | - Christian G. Giske
- Department of Laboratory Medicine, Karolinska Institute, 141 52 Stockholm, Sweden; (T.S.); (C.G.G.)
- Department of Clinical Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden;
- Correspondence: ; Tel.: +46-31-772-3049
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20
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Lin YL, Sewunet T, KK S, Giske CG, Westerlund F. Optical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital. J Antimicrob Chemother 2021; 75:2804-2811. [PMID: 32653928 PMCID: PMC7678893 DOI: 10.1093/jac/dkaa258] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/24/2020] [Accepted: 05/14/2020] [Indexed: 01/09/2023] Open
Abstract
Objectives MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control. Methods Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria. Results ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles. Conclusions ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.
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Affiliation(s)
- Yii-Lih Lin
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tsegaye Sewunet
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- School of Laboratory Sciences, Department of Microbiology, Jimma University, Jimma, Ethiopia
| | - Sriram KK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Corresponding author. E-mail:
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21
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Polson JM, Rehel DA. Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement. SOFT MATTER 2021; 17:5792-5805. [PMID: 34028486 DOI: 10.1039/d1sm00308a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity. The polymers are modeled as flexible bead-spring chains, and the box has a square cross-section of side length L and a height that is small enough to compress the polymers in that dimension. For sufficiently large L, the system behaviour approaches that of an isolated polymer in a slit. However, the combined effects of crowding and confinement on the polymer organization, conformation and equilibrium dynamics become significant when where is the transverse radius of gyration for a slit geometry. In this regime, the centre-of-mass probability distribution in the transverse plane exhibits a depletion zone near the centre of the cavity (except at very small L) and a 4-fold symmetry with quasi-discrete positions. Reduction in polymer size with decreasing L arises principally from confinement rather than inter-polymer crowding. By contrast, polymer diffusion and internal motion are strongly affected by inter-polymer crowding. The two polymers tend to occupy opposite positions relative to the box centre, about which they diffuse relatively freely. Qualitatively, this static and dynamical behaviour differs significantly from that previously observed for confinement of two polymers to a narrow channel. The simulation results for a suitably chosen box width are qualitatively consistent with results from a recent experimental study of two λ-DNA chains confined to a nanofluidic cavity.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.
| | - Desiree A Rehel
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada.
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22
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Wei Y, Huang Q, Tian X, Zhang M, He J, Chen X, Chen C, Deng Z, Li Z, Chen S, Wang L. Single-molecule optical mapping of the distribution of DNA phosphorothioate epigenetics. Nucleic Acids Res 2021; 49:3672-3680. [PMID: 33764453 PMCID: PMC8053081 DOI: 10.1093/nar/gkab169] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/13/2021] [Accepted: 03/02/2021] [Indexed: 12/13/2022] Open
Abstract
DNA phosphorothioate (PT) modifications, with the nonbridging phosphate oxygen replaced by sulfur, governed by DndABCDE or SspABCD, are widely distributed in prokaryotes and have a highly unusual feature of occupying only a small portion of available consensus sequences in a genome. Despite the presence of plentiful non-PT-protected consensuses, DNA PT modification is still employed as a recognition tag by the restriction cognate, for example, DndFGH or SspE, to discriminate and destroy PT-lacking foreign DNA. This raises a fundamental question about how PT modifications are distributed along DNA molecules to keep the restriction components in check. Here, we present two single-molecule strategies that take advantage of the nucleophilicity of PT in combination with fluorescent markers for optical mapping of both single- and double-stranded PT modifications across individual DNA molecules. Surprisingly, PT profiles vary markedly from molecule to molecule, with different PT locations and spacing distances between PT pairs, even in the presence of DndFGH or SspE. The results revealed unprecedented PT modification features previously obscured by ensemble averaging, providing novel insights into the riddles regarding unusual target selection by PT modification and restriction components.
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Affiliation(s)
- Yue Wei
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China.,Department of Burn and Plastic Surgery, Division of Wound Repair, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Qinqin Huang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,Department of Molecular Pathology, The Second Affiliated Hospital, Academy of Medical Sciences of Zhengzhou University, Zhengzhou 450000, China
| | - Xihao Tian
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Mingmin Zhang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Junkai He
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xingxiang Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Chao Chen
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Shi Chen
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,Department of Burn and Plastic Surgery, Division of Wound Repair, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China
| | - Lianrong Wang
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China.,Department of Burn and Plastic Surgery, Division of Wound Repair, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen 518035, China.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
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23
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Jeffet J, Margalit S, Michaeli Y, Ebenstein Y. Single-molecule optical genome mapping in nanochannels: multidisciplinarity at the nanoscale. Essays Biochem 2021; 65:51-66. [PMID: 33739394 PMCID: PMC8056043 DOI: 10.1042/ebc20200021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/12/2022]
Abstract
The human genome contains multiple layers of information that extend beyond the genetic sequence. In fact, identical genetics do not necessarily yield identical phenotypes as evident for the case of two different cell types in the human body. The great variation in structure and function displayed by cells with identical genetic background is attributed to additional genomic information content. This includes large-scale genetic aberrations, as well as diverse epigenetic patterns that are crucial for regulating specific cell functions. These genetic and epigenetic patterns operate in concert in order to maintain specific cellular functions in health and disease. Single-molecule optical genome mapping is a high-throughput genome analysis method that is based on imaging long chromosomal fragments stretched in nanochannel arrays. The access to long DNA molecules coupled with fluorescent tagging of various genomic information presents a unique opportunity to study genetic and epigenetic patterns in the genome at a single-molecule level over large genomic distances. Optical mapping entwines synergistically chemical, physical, and computational advancements, to uncover invaluable biological insights, inaccessible by sequencing technologies. Here we describe the method's basic principles of operation, and review the various available mechanisms to fluorescently tag genomic information. We present some of the recent biological and clinical impact enabled by optical mapping and present recent approaches for increasing the method's resolution and accuracy. Finally, we discuss how multiple layers of genomic information may be mapped simultaneously on the same DNA molecule, thus paving the way for characterizing multiple genomic observables on individual DNA molecules.
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Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sapir Margalit
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Center for Nanoscience and Nanotechnology, Center for Light Matter Interaction, Tel Aviv University, Tel Aviv 6997801, Israel
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24
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Pan M, Cai J, Li S, Xu L, Ma W, Xu C, Kuang H. Aptamer-Gated Ion Channel for Ultrasensitive Mucin 1 Detection. Anal Chem 2021; 93:4825-4831. [PMID: 33688720 DOI: 10.1021/acs.analchem.0c04137] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Detection of cancer markers is important for early diagnosis and timely treatment of cancer. In this study, we fabricated a tailorable gold nanofilm-anodized aluminum oxide (Au-AAO) ion channel through nanoparticle self-assembly and proposed a highly sensitive and selective Mucin 1 (MUC1) detection method. By engineering the optimal layers of the Au-AAO ion channel and encoding the aptamer between the interlayers, a highly controllable ion rectification phenomenon was observed. From this, the relationship between the rectification ratio (RR) and the concentration of MUC1 was established and the highly sensitive detection of MUC1 is achieved. We found that the aptamer-modified Au-AAO ion channel has a good linear range within the MUC1 concentration of 1-104 fg mL-1 and the limit of detection (LOD) was as low as 0.0364 fg mL-1 (0.0025 aM). Thus, this research opens a new horizon for fabricating multi-functional ion channels as well as developing ultrasensitive detection technologies.
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Affiliation(s)
- Mengying Pan
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Jiarong Cai
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Si Li
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Liguang Xu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Wei Ma
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Chuanlai Xu
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
| | - Hua Kuang
- International Joint Research Laboratory for Biointerface and Biodetection, State Key Lab of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, P. R. China
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25
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Ferreira C, Bikkarolla SK, Frykholm K, Pohjanen S, Brito M, Lameiras C, Nunes OC, Westerlund F, Manaia CM. Polyphasic characterization of carbapenem-resistant Klebsiella pneumoniae clinical isolates suggests vertical transmission of the blaKPC-3 gene. PLoS One 2021; 16:e0247058. [PMID: 33635888 PMCID: PMC7909683 DOI: 10.1371/journal.pone.0247058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/30/2021] [Indexed: 11/18/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae are a major global threat in healthcare facilities. The propagation of carbapenem resistance determinants can occur through vertical transmission, with genetic elements being transmitted by the host bacterium, or by horizontal transmission, with the same genetic elements being transferred among distinct bacterial hosts. This work aimed to track carbapenem resistance transmission by K. pneumoniae in a healthcare facility. The study involved a polyphasic approach based on conjugation assays, resistance phenotype and genotype analyses, whole genome sequencing, and plasmid characterization by pulsed field gel electrophoresis and optical DNA mapping. Out of 40 K. pneumoniae clinical isolates recovered over two years, five were carbapenem- and multidrug-resistant and belonged to multilocus sequence type ST147. These isolates harboured the carbapenemase encoding blaKPC-3 gene, integrated in conjugative plasmids of 140 kbp or 55 kbp, belonging to replicon types incFIA/incFIIK or incN/incFIIK, respectively. The two distinct plasmids encoding the blaKPC-3 gene were associated with distinct genetic lineages, as confirmed by optical DNA mapping and whole genome sequence analyses. These results suggested vertical (bacterial strain-based) transmission of the carbapenem-resistance genetic elements. Determination of the mode of transmission of antibiotic resistance in healthcare facilities, only possible based on polyphasic approaches as described here, is essential to control resistance propagation.
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Affiliation(s)
- Catarina Ferreira
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Santosh K. Bikkarolla
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Karolin Frykholm
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Saga Pohjanen
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | | | - Olga C. Nunes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail: (CMM); (FW)
| | - Célia M. Manaia
- CBQF - Centro de Biotecnologia e Química Fina – Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
- * E-mail: (CMM); (FW)
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26
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Yamamoto K, Ota N, Tanaka Y. Nanofluidic Devices and Applications for Biological Analyses. Anal Chem 2021; 93:332-349. [PMID: 33125221 DOI: 10.1021/acs.analchem.0c03868] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Koki Yamamoto
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Nobutoshi Ota
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yo Tanaka
- Laboratory for Integrated Biodevice, Center for Biosystems Dynamics Research (BDR), RIKEN, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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27
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Zhang Y, Nunoura T, Nishiura D, Hirai M, Shimamura S, Kurosawa K, Ishiwata C, Deguchi S. A single-molecule counting approach for convenient and ultrasensitive measurement of restriction digest efficiencies. PLoS One 2020; 15:e0244464. [PMID: 33382779 PMCID: PMC7775078 DOI: 10.1371/journal.pone.0244464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
Restriction endonucleases play a central role in the microbial immune system against viruses and are widely used in DNA specific cleavage, which is called restriction digestion, for genetic engineering. Herein, we applied digital cell-free protein synthesis as an easy-to-use orthogonal readout means to assess the restriction digest efficiency, a new application of digital bioassays. The digital counting principle enabled an unprecedentedly sensitive trace analysis of undigested DNA at the single-molecule level in a PCR-free manner. Our approach can quantify the template DNA of much lower concentrations that cannot be detected by ensemble-based methods such as gold-standard DNA electrophoresis techniques. The sensitive and quantitative measurements revealed a considerable variation in the digest efficiency among restriction endonucleases, from less than 70% to more than 99%. Intriguingly, none of them showed truly complete digestion within reasonably long periods of reaction time. The same rationale was extended to a multiplexed assay and applicable to any DNA-degrading or genome-editing enzymes. The enzyme kinetic parameters and the flanking sequence-dependent digest efficiency can also be interrogated with the proposed digital counting method. The absolute number of residual intact DNA molecules per microliter was concluded to be at least 107, drawing attention to the residual issue of genetic materials associated with the interpretation of nucleases’ behaviors and functions in daily genetic engineering experiments.
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Affiliation(s)
- Yi Zhang
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- * E-mail:
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience, Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Daisuke Nishiura
- Center for Mathematical Science and Advanced Technology, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Miho Hirai
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Shimamura
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Kanako Kurosawa
- SUGAR Program, X-star, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Chieko Ishiwata
- Center for Mathematical Science and Advanced Technology, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Shigeru Deguchi
- Research Center for Bioscience and Nanoscience, Research Institute for Marine Resources Utilization, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
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28
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Basak R, Rosencrans W, Yadav I, Yan P, Berezhnoy NV, Chen Q, van Kan JA, Nordenskiöld L, Zinchenko A, van der Maarel JRC. Internal Motion of Chromatin Fibers Is Governed by Dynamics of Uncompressed Linker Strands. Biophys J 2020; 119:2326-2334. [PMID: 33121944 PMCID: PMC7732777 DOI: 10.1016/j.bpj.2020.10.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/23/2020] [Accepted: 10/13/2020] [Indexed: 11/25/2022] Open
Abstract
Chromatin compaction and internal motion are fundamental aspects of gene expression regulation. Here, we have investigated chromatin fibers comprising recombinant histone octamers reconstituted with double-stranded bacteriophage T4-DNA. The size of the fibers approaches the typical size of genomic topologically associated domains. Atomic force and fluorescence (correlation) microscopy have been used to assess the structural organization, histone-induced compaction, and internal motion. In particular, the fibers are stretched on arrays of nanochannels, each channel with a diameter of 60 or 125 nm. Major intrafiber segregation and fast internal fluctuations are observed. Full compaction was only achieved by triggering an attractive nucleosome interaction through the addition of magnesium cations. Besides compaction, histone complexation results in a dramatic decrease in the fiber's relaxation time. The relaxation times are similar to those of naked DNA with a comparable stretch, which indicates that internal motion is governed by the dynamics of uncompressed linker strands. Furthermore, the main reorganization process is association-dissociation of individually compacted regions. We surmise that the modulation of chromatin's internal motion by histone complexation might have implications for transcriptional bursting.
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Affiliation(s)
- Rajib Basak
- Department of Physics, National University of Singapore, Singapore, Republic of Singapore
| | - William Rosencrans
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Indresh Yadav
- Department of Physics, National University of Singapore, Singapore, Republic of Singapore
| | - Peiyan Yan
- Department of Physics, National University of Singapore, Singapore, Republic of Singapore
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore, Republic of Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Republic of Singapore
| | - Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Nagoya, Japan
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29
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Polson JM, Hastie CG. Free energy of a knotted polymer confined to narrow cylindrical and conical channels. Phys Rev E 2020; 102:052502. [PMID: 33327190 DOI: 10.1103/physreve.102.052502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/16/2020] [Indexed: 06/12/2023]
Abstract
Monte Carlo simulations are used to study the conformational behavior of a semiflexible polymer confined to cylindrical and conical channels. The channels are sufficiently narrow that the conditions for the Odijk regime are marginally satisfied. For cylindrical confinement, we examine polymers with a single knot of topology 3_{1}, 4_{1}, or 5_{1}, as well as unknotted polymers that are capable of forming S loops. We measure the variation of the free energy F with the end-to-end polymer extension length X and examine the effect of varying the polymer topology, persistence length P, and cylinder diameter D on the free-energy functions. Similarly, we characterize the behavior of the knot span along the channel. We find that increasing the knot complexity increases the typical size of the knot. In the regime of low X, where the knot/S-loop size is large, the conformational behavior is independent of polymer topology. In addition, the scaling properties of the free energy and knot span are in agreement with predictions from a theoretical model constructed using known properties of interacting polymers in the Odijk regime. We also examine the variation of F with the position of a knot in conical channels for various values of the cone angle α. The free energy decreases as the knot moves in a direction where the cone widens, and it also decreases with increasing α and with increasing knot complexity. The behavior is in agreement with predictions from a theoretical model in which the dominant contribution to the change in F is the change in the size of the hairpins as the knot moves to the wider region of the channel.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada
| | - Cameron G Hastie
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada
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30
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Yadav I, Basak R, Yan P, van Kan JA, Arluison V, van der Maarel JRC. Role of Internal DNA Motion on the Mobility of a Nucleoid-Associated Protein. J Phys Chem Lett 2020; 11:8424-8429. [PMID: 32930601 DOI: 10.1021/acs.jpclett.0c02251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Protein transport on DNA is at the core of the machinery of life. Here we investigated the influence of DNA internal motion on the mobility of Hfq, which is involved in several aspects of nucleic acid metabolism and is one of the nucleoid-associated proteins that shape the bacterial chromosome. Fluorescence microscopy was used to follow Hfq on double-stranded DNA that was stretched by confinement to a channel with a diameter of 125 nm. The protein mobility shows a strong dependence on the internal motion of DNA in that slower motion results in faster protein diffusion. A model of released diffusion is proposed that is based on three-dimensional diffusion through the interior of the DNA coil interspersed by periods in which the protein is immobilized in a bound state. We surmise that the coupling between DNA internal motion and protein mobility has important implications for DNA metabolism and protein-binding-related regulation of gene expression.
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Affiliation(s)
- Indresh Yadav
- Department of Physics, National University of Singapore, Singapore 117542
| | - Rajib Basak
- Department of Physics, National University of Singapore, Singapore 117542
| | - Peiyan Yan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Jeroen A van Kan
- Department of Physics, National University of Singapore, Singapore 117542
| | - Véronique Arluison
- Université de Paris, UFR SDV, 75006 Paris, France
- Laboratoire Léon Brillouin, CEA, CNRS, Université Paris Saclay, 91191 Gif-sur-Yvette, France
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31
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Solgi H, Nematzadeh S, Giske CG, Badmasti F, Westerlund F, Lin YL, Goyal G, Nikbin VS, Nemati AH, Shahcheraghi F. Molecular Epidemiology of OXA-48 and NDM-1 Producing Enterobacterales Species at a University Hospital in Tehran, Iran, Between 2015 and 2016. Front Microbiol 2020; 11:936. [PMID: 32547503 PMCID: PMC7270168 DOI: 10.3389/fmicb.2020.00936] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Accepted: 04/20/2020] [Indexed: 01/09/2023] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) is an increasing problem worldwide. Here, we examined the clonal relatedness of 71 non-repetitive CRE isolates collected in a university hospital in Tehran, Iran, between February 2015 and March 2016. Pulsed-field gel electrophoresis (PFGE) and MLST were used for epidemiological analysis. Screening for antibiotic resistance genes, PCR-based replicon typing, conjugation experiments, and optical DNA mapping were also performed. Among all 71 isolates, 47 isolates of Klebsiella pneumoniae (66.2%), eight Escherichia coli (11.2%), five Serratia marcescens (7%), and two Enterobacter cloacae (2.8%) harbored blaNDM–1 and blaOXA–48 genes together or alone. PFGE analysis revealed that most of the OXA-48- and NDM-1-producing K. pneumoniae and all of OXA-48-producing S. marcescens were clonally related, while all eight E. coli and two E. cloacae isolates were clonally unrelated. The predominant clones of carbapenemase-producing K. pneumoniae associated with outbreaks within the hospital were ST147 (n = 13) and ST893 (n = 10). Plasmids carrying blaNDM–1 and blaOXA–48 were successfully transferred to an E. coli K12-recipient strain. The blaOXA–48 gene was located on an IncL/M conjugative plasmid, while the blaNDM–1 gene was located on both IncFII ∼86-kb to ∼140-kb and IncA/C conjugative plasmids. Our findings provide novel epidemiologic data on carbapenemase-producing Enterobacterales (CPE) in Iran and highlight the importance of horizontal gene transfer in the dissemination of blaNDM–1 and blaOXA–48 genes. The occurrence and transmission of distinct K. pneumoniae clones call for improved infection control to prevent further spread of these pathogens in Iran.
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Affiliation(s)
- Hamid Solgi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Amin Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shoeib Nematzadeh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Christian G Giske
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Fredrik Westerlund
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Yii-Lih Lin
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Gaurav Goyal
- Division of Chemical Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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32
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Müller V, Nyblom M, Johnning A, Wrande M, Dvirnas A, KK S, Giske CG, Ambjörnsson T, Sandegren L, Kristiansson E, Westerlund F. Cultivation-Free Typing of Bacteria Using Optical DNA Mapping. ACS Infect Dis 2020; 6:1076-1084. [PMID: 32294378 PMCID: PMC7304876 DOI: 10.1021/acsinfecdis.9b00464] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 01/06/2023]
Abstract
A variety of pathogenic bacteria can infect humans, and rapid species identification is crucial for the correct treatment. However, the identification process can often be time-consuming and depend on the cultivation of the bacterial pathogen(s). Here, we present a stand-alone, enzyme-free, optical DNA mapping assay capable of species identification by matching the intensity profiles of large DNA molecules to a database of fully assembled bacterial genomes (>10 000). The assay includes a new data analysis strategy as well as a general DNA extraction protocol for both Gram-negative and Gram-positive bacteria. We demonstrate that the assay is capable of identifying bacteria directly from uncultured clinical urine samples, as well as in mixtures, with the potential to be discriminative even at the subspecies level. We foresee that the assay has applications both within research laboratories and in clinical settings, where the time-consuming step of cultivation can be minimized or even completely avoided.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - My Nyblom
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Anna Johnning
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Systems and Data Analysis, Fraunhofer-Chalmers
Centre, Chalmers Science
Park, 412 88 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Marie Wrande
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Sriram KK
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
| | - Christian G. Giske
- Department of Laboratory Medicine, Karolinska
Institutet, Alfred Nobels
Allé 8, 141 86 Stockholm, Sweden
- Department of Clinical
Microbiology, Karolinska University Hospital, 171 76 Stockholm, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, 223 62 Lund, Sweden
| | - Linus Sandegren
- Department of Medical
Biochemistry and Microbiology, Uppsala University, Husargatan 3, Box
582, 751 23 Uppsala, Sweden
| | - Erik Kristiansson
- Department of Mathematical
Sciences, Chalmers University of Technology
and the University of Gothenburg, 412 96 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research,
CARe, University of Gothenburg, Box 440, 405 30 Gothenburg, Sweden
| | - Fredrik Westerlund
- Department of Biology
and Biological Engineering, Chalmers University
of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden
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33
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Single-molecule analysis of nucleic acid biomarkers - A review. Anal Chim Acta 2020; 1115:61-85. [PMID: 32370870 DOI: 10.1016/j.aca.2020.03.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 12/11/2022]
Abstract
Nucleic acids are important biomarkers for disease detection, monitoring, and treatment. Advances in technologies for nucleic acid analysis have enabled discovery and clinical implementation of nucleic acid biomarkers. However, challenges remain with technologies for nucleic acid analysis, thereby limiting the use of nucleic acid biomarkers in certain contexts. Here, we review single-molecule technologies for nucleic acid analysis that can be used to overcome these challenges. We first discuss the various types of nucleic acid biomarkers important for clinical applications and conventional technologies for nucleic acid analysis. We then discuss technologies for single-molecule in vitro and in situ analysis of nucleic acid biomarkers. Finally, we discuss other ultra-sensitive techniques for nucleic acid biomarker detection.
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34
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Wand NO, Smith DA, Wilkinson AA, Rushton AE, Busby SJW, Styles IB, Neely RK. DNA barcodes for rapid, whole genome, single-molecule analyses. Nucleic Acids Res 2020; 47:e68. [PMID: 30918971 PMCID: PMC6614835 DOI: 10.1093/nar/gkz212] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 02/13/2019] [Accepted: 03/18/2019] [Indexed: 01/01/2023] Open
Abstract
We report an approach for visualizing DNA sequence and using these ‘DNA barcodes’ to search complex mixtures of genomic material for DNA molecules of interest. We demonstrate three applications of this methodology; identifying specific molecules of interest from a dataset containing gigabasepairs of genome; identification of a bacterium from such a dataset and, finally, by locating infecting virus molecules in a background of human genomic material. As a result of the dense fluorescent labelling of the DNA, individual barcodes of the order 40 kb pairs in length can be reliably identified. This means DNA can be prepared for imaging using standard handling and purification techniques. The recorded dataset provides stable physical and electronic records of the total genomic content of a sample that can be readily searched for a molecule or region of interest.
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Affiliation(s)
- Nathaniel O Wand
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,Physical Sciences of Imaging in the Biomedical Sciences Centre for Doctoral Training, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Darren A Smith
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Andrew A Wilkinson
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ashleigh E Rushton
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Iain B Styles
- School of Computer Science, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Robert K Neely
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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35
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Zrehen A, Huttner D, Meller A. On-Chip Stretching, Sorting, and Electro-Optical Nanopore Sensing of Ultralong Human Genomic DNA. ACS NANO 2019; 13:14388-14398. [PMID: 31756076 PMCID: PMC6933818 DOI: 10.1021/acsnano.9b07873] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 11/22/2019] [Indexed: 05/22/2023]
Abstract
Solid-state nanopore sensing of ultralong genomic DNA molecules has remained challenging, as the DNA must be controllably delivered by its leading end for efficient entry into the nanopore. Herein, we introduce a nanopore sensor device designed for electro-optical detection and sorting of ultralong (300+ kilobase pair) genomic DNA. The fluidic device, fabricated in-silicon and anodically bonded to glass, uses pressure-induced flow and an embedded pillar array for controllable DNA stretching and delivery. Extremely low concentrations (50 fM) and sample volumes (∼1 μL) of DNA can be processed. The low height profile of the device permits high numerical aperture, high magnification imaging of DNA molecules, which remain in focus over extended distances. We demonstrate selective DNA sorting based on sequence-specific nick translation labeling and imaging at high camera frame rates. Nanopores are fabricated directly in the assembled device by laser etching. We show that uncoiling and stretching of the ultralong DNA molecules permits efficient nanopore capture and threading, which is simultaneously and synchronously imaged and electrically measured. Furthermore, our technique provides key insights into the translocation behavior of ultralong DNA and promotes the development of all-in-one micro/nanofluidic platforms for nanopore sensing of biomolecules.
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Affiliation(s)
- Adam Zrehen
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Diana Huttner
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
| | - Amit Meller
- Department
of Biomedical Engineering, Technion −
IIT, Haifa 32000, Israel
- Russell
Berrie Nanotechnology Institute, Technion
− IIT, Haifa 32000, Israel
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36
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Müller V, Dvirnas A, Andersson J, Singh V, Kk S, Johansson P, Ebenstein Y, Ambjörnsson T, Westerlund F. Enzyme-free optical DNA mapping of the human genome using competitive binding. Nucleic Acids Res 2019; 47:e89. [PMID: 31165870 PMCID: PMC6735870 DOI: 10.1093/nar/gkz489] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/22/2019] [Indexed: 01/24/2023] Open
Abstract
Optical DNA mapping (ODM) allows visualization of long-range sequence information along single DNA molecules. The data can for example be used for detecting long range structural variations, for aiding DNA sequence assembly of complex genomes and for mapping epigenetic marks and DNA damage across the genome. ODM traditionally utilizes sequence specific marks based on nicking enzymes, combined with a DNA stain, YOYO-1, for detection of the DNA contour. Here we use a competitive binding approach, based on YOYO-1 and netropsin, which highlights the contour of the DNA molecules, while simultaneously creating a continuous sequence specific pattern, based on the AT/GC variation along the detected molecule. We demonstrate and validate competitive-binding-based ODM using bacterial artificial chromosomes (BACs) derived from the human genome and then turn to DNA extracted from white blood cells. We generalize our findings with in-silico simulations that show that we can map a vast majority of the human genome. Finally, we demonstrate the possibility of combining competitive binding with enzymatic labeling by mapping DNA damage sites induced by the cytotoxic drug etoposide to the human genome. Overall, we demonstrate that competitive-binding-based ODM has the potential to be used both as a standalone assay for studies of the human genome, as well as in combination with enzymatic approaches, some of which are already commercialized.
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Affiliation(s)
- Vilhelm Müller
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Albertas Dvirnas
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - John Andersson
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Vandana Singh
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kk
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Pegah Johansson
- Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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37
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Esmek FM, Bayat P, Pérez-Willard F, Volkenandt T, Blick RH, Fernandez-Cuesta I. Sculpturing wafer-scale nanofluidic devices for DNA single molecule analysis. NANOSCALE 2019; 11:13620-13631. [PMID: 31290915 DOI: 10.1039/c9nr02979f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present micro- and nanofluidic devices with 3D structures and nanochannels with multiple depths for the analysis of single molecules of DNA. Interfacing the nanochannels with graded and 3D inlets allows the improvement of the flow and controls not only the translocation speed of the DNA but also its conformation inside the nanochannels. The complex, multilevel, multiscale fluidic circuits are patterned in a simple, two-minute imprinting step. The stamp, the key of the technology, is directly milled by focused ion beam, which allows patterning nanochannels with different cross sections and depths, together with 3D transient inlets, all at once. Having such a variety of structures integrated in the same sample allows studying, optimizing and directly comparing their effect on the DNA flow. Here, DNA translocation is studied in long (160 µm) and short (5-40 µm) nanochannels. We study the homogeneity of the stretched molecules in long, meander nanochannels made with this technology. In addition, we analyze the effect of the different types of inlet structures interfacing short nanochannels. We observe pre-stretching and an optimal flow, and no hairpin formation, when the inlets have gradually decreasing widths and depths. In contrast, when the nanochannels are faced with an abrupt transition, we observe clogging and hairpin formation. In addition, 3D inlets strongly decrease the DNA molecules' speed before they enter the nanochannels, and help capturing more DNA molecules. The robustness and versatility of this technology and DNA testing results evidence the potential of imprinted devices in biomedical applications as low cost, disposable lab-on-a-chip devices.
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Affiliation(s)
- Franziska M Esmek
- Institut für Nanostruktur- und Festkörperphysik (INF)/Center for Hybrid Nanostructures (CHyN), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Parisa Bayat
- Institut für Nanostruktur- und Festkörperphysik (INF)/Center for Hybrid Nanostructures (CHyN), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | | | - Tobias Volkenandt
- Carl Zeiss Microscopy GmbH, Carl-Zeiss-Str. 22, 73447 Oberkochen, Germany
| | - Robert H Blick
- Institut für Nanostruktur- und Festkörperphysik (INF)/Center for Hybrid Nanostructures (CHyN), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Irene Fernandez-Cuesta
- Institut für Nanostruktur- und Festkörperphysik (INF)/Center for Hybrid Nanostructures (CHyN), University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
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38
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Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak. mBio 2019; 10:mBio.00347-19. [PMID: 31289171 PMCID: PMC6747713 DOI: 10.1128/mbio.00347-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
This study presents how a novel method, based on visualizing single plasmids using sequence-specific fluorescent labeling, could be used to analyze the genetic dynamics of an outbreak of resistant bacteria in a neonatal intensive care unit at a Swedish hospital. Plasmids are a central reason for the rapid global spread of bacterial resistance to antibiotics. In a single experimental procedure, this method replaces many traditional plasmid analysis techniques that together provide limited details and are slow to perform. The method is much faster than long-read whole-genome sequencing and offers direct genetic comparison of patient samples. We could conclude that no transfer of resistance plasmids had occurred between different bacteria during the outbreak and that secondary cases of ESBL-producing Enterobacteriaceae carriage were instead likely due to influx of new strains. We believe that the method offers potential in improving surveillance and infection control of resistant bacteria in hospitals. The global spread of antibiotic resistance among Enterobacteriaceae is largely due to multidrug resistance plasmids that can transfer between different bacterial strains and species. Horizontal gene transfer of resistance plasmids can complicate hospital outbreaks and cause problems in epidemiological tracing, since tracing is usually based on bacterial clonality. We have developed a method, based on optical DNA mapping combined with Cas9-assisted identification of resistance genes, which is used here to characterize plasmids during an extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae outbreak at a Swedish neonatal intensive care unit. The outbreak included 17 neonates initially colonized with ESBL-producing Klebsiella pneumoniae (ESBL-KP), some of which were found to carry additional ESBL-producing Escherichia coli (ESBL-EC) in follow-up samples. We demonstrate that all ESBL-KP isolates contained two plasmids with the blaCTX-M-15 gene located on the smaller one (~80 kbp). The same ESBL-KP clone was present in follow-up samples for up to 2 years in some patients, and the plasmid carrying the blaCTX-M-15 gene was stable throughout this time period. However, extensive genetic rearrangements within the second plasmid were observed in the optical DNA maps for several of the ESBL-KP isolates. Optical mapping also demonstrated that even though other bacterial clones and species carrying blaCTX-M group 1 genes were found in some neonates, no transfer of resistance plasmids had occurred. The data instead pointed toward unrelated acquisition of ESBL-producing Enterobacteriaceae (EPE). In addition to revealing important information about the specific outbreak, the method presented is a promising tool for surveillance and infection control in clinical settings.
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39
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Slatko BE, Gardner AF, Ausubel FM. Overview of Next-Generation Sequencing Technologies. ACTA ACUST UNITED AC 2019; 122:e59. [PMID: 29851291 DOI: 10.1002/cpmb.59] [Citation(s) in RCA: 374] [Impact Index Per Article: 74.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High throughput DNA sequencing methodology (next generation sequencing; NGS) has rapidly evolved over the past 15 years and new methods are continually being commercialized. As the technology develops, so do increases in the number of corresponding applications for basic and applied science. The purpose of this review is to provide a compendium of NGS methodologies and associated applications. Each brief discussion is followed by web links to the manufacturer and/or web-based visualizations. Keyword searches, such as with Google, may also provide helpful internet links and information. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | | | - Frederick M Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
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40
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Jahromi S, Amani E, Movahed S. An improved hybrid continuum-atomistic four-way coupled model for electrokinetics in nanofluidics. Electrophoresis 2019; 40:1678-1690. [PMID: 30903627 DOI: 10.1002/elps.201800307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 02/17/2019] [Accepted: 03/18/2019] [Indexed: 12/13/2022]
Abstract
In this study, an efficient hybrid continuum-atomistic method is proposed to study electrokinetic transport of aqueous solutions in nanofluidics. The aqueous phase is considered as a continuous phase containing immersed ion particles. The behavior of the system is then simulated through utilization of an improved hybrid continuum-atomistic four-way coupled approach, including the MultiPhase Particle-In-Cell method for the short-ranged interaction between the ion particles, the Brownian force for the collision between the aqueous phase molecules and the ion particles, and a wall force accounting for the short-ranged interaction of ions and walls. The validation of the proposed model with the results of Molecular Dynamics simulations suggests that this model can be a promising approach for studying the electrokinetic phenomena in more complicated geometries where the Molecular Dynamics approach is computationally prohibitive. Finally, the effects of electrokinetic parameters, such as the height of the channel, the external electric field, and bulk ionic concentration, on the electroosmotic flow in a nanochannel are investigated and discussed.
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Affiliation(s)
- Saeed Jahromi
- Mechanical Engineering Department, Amirkabir University of Technology, Tehran, Iran
| | - Ehsan Amani
- Mechanical Engineering Department, Amirkabir University of Technology, Tehran, Iran
| | - Saeid Movahed
- Mechanical Engineering Department, Amirkabir University of Technology, Tehran, Iran
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41
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Basak R, Liu F, Qureshi S, Gupta N, Zhang C, de Vries R, van Kan JA, Dheen ST, van der Maarel JRC. Linearization and Labeling of Single-Stranded DNA for Optical Sequence Analysis. J Phys Chem Lett 2019; 10:316-321. [PMID: 30615463 DOI: 10.1021/acs.jpclett.8b03465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Genetic profiling would benefit from linearization of ssDNA through the exposure of the unpaired bases to gene-targeting probes. This is compromised by ssDNA's high flexibility and tendency to form self-annealed structures. Here, we demonstrate that self-annealing can be avoided through controlled coating with a cationic-neutral diblock polypeptide copolymer. Coating does not preclude site-specific binding of fluorescence labeled oligonucleotides. Bottlebrush-coated ssDNA can be linearized by confinement inside a nanochannel or molecular combing. A stretch of 0.32 nm per nucleotide is achieved inside a channel with a cross-section of 100 nm and a 2-fold excess of polypeptide with respect to DNA charge. With combing, the complexes are stretched to a similar extent. Atomic force microscopy of dried complexes on silica revealed that the contour and persistence lengths are close to those of dsDNA in the B-form. Labeling is based on hybridization and not limited by restriction enzymes. Enzyme-free labeling offers new opportunities for the detection of specific sequences.
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Affiliation(s)
- Rajib Basak
- Department of Physics , National University of Singapore , Singapore 117542
| | - Fan Liu
- Department of Physics , National University of Singapore , Singapore 117542
| | - Sarfraz Qureshi
- Department of Physics , National University of Singapore , Singapore 117542
| | - Neelima Gupta
- Department of Anatomy , National University of Singapore , Singapore 117594
| | - Ce Zhang
- Institute of Photonics and Photon-Technology , Northwest University , Xi'an , China 710069
| | - Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science , Wageningen University , 6708 Wageningen , The Netherlands
| | - Jeroen A van Kan
- Department of Physics , National University of Singapore , Singapore 117542
| | - S Thameem Dheen
- Department of Anatomy , National University of Singapore , Singapore 117594
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42
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Scheler O, Postek W, Garstecki P. Recent developments of microfluidics as a tool for biotechnology and microbiology. Curr Opin Biotechnol 2019; 55:60-67. [DOI: 10.1016/j.copbio.2018.08.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/13/2018] [Accepted: 08/09/2018] [Indexed: 02/07/2023]
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43
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Krog J, Alizadehheidari M, Werner E, Bikkarolla SK, Tegenfeldt JO, Mehlig B, Lomholt MA, Westerlund F, Ambjörnsson T. Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis. J Chem Phys 2019; 149:215101. [PMID: 30525714 DOI: 10.1063/1.5051319] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.
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Affiliation(s)
- Jens Krog
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | | | - Erik Werner
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Santosh Kumar Bikkarolla
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Bernhard Mehlig
- Department of Physics, Gothenburg University, Gothenburg, Sweden
| | - Michael A Lomholt
- MEMPHYS-Center for Biomembrane Physics, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense, Denmark
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
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44
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Asenso J, Wang L, Du Y, Liu QH, Xu BJ, Guo MZ, Tang DQ. Advances in detection and quantification of methylcytosine and its derivatives. J Sep Sci 2018; 42:1105-1116. [PMID: 30575277 DOI: 10.1002/jssc.201801100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/21/2018] [Accepted: 12/16/2018] [Indexed: 11/08/2022]
Abstract
Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification of four cytosine modifications, based on which, the development, diagnosis, and prognosis of diseases could be monitored through non-invasive procedures.
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Affiliation(s)
- James Asenso
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, P. R. China
| | - Yan Du
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Qing-Hua Liu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Bing-Ju Xu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Meng-Zhe Guo
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Dao-Quan Tang
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
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45
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Johnning A, Karami N, Tång Hallbäck E, Müller V, Nyberg L, Buongermino Pereira M, Stewart C, Ambjörnsson T, Westerlund F, Adlerberth I, Kristiansson E. The resistomes of six carbapenem-resistant pathogens - a critical genotype-phenotype analysis. Microb Genom 2018; 4. [PMID: 30461373 PMCID: PMC6321870 DOI: 10.1099/mgen.0.000233] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Carbapenem resistance is a rapidly growing threat to our ability to treat refractory bacterial infections. To understand how carbapenem resistance is mobilized and spread between pathogens, it is important to study the genetic context of the underlying resistance mechanisms. In this study, the resistomes of six clinical carbapenem-resistant isolates of five different species – Acinetobacter baumannii, Escherichia coli, two Klebsiella pneumoniae, Proteus mirabilis and Pseudomonas aeruginosa – were characterized using whole genome sequencing. All Enterobacteriaceae isolates and the A. baumannii isolate had acquired a large number of antimicrobial resistance genes (7–18 different genes per isolate), including the following encoding carbapenemases: blaKPC-2, blaOXA-48, blaOXA-72, blaNDM-1, blaNDM-7 and blaVIM-1. In addition, a novel version of blaSHV was discovered. Four new resistance plasmids were identified and their fully assembled sequences were verified using optical DNA mapping. Most of the resistance genes were co-localized on these and other plasmids, suggesting a risk for co-selection. In contrast, five out of six carbapenemase genes were present on plasmids with no or few other resistance genes. The expected level of resistance – based on acquired resistance determinants – was concordant with measured levels in most cases. There were, however, several important discrepancies for four of the six isolates concerning multiple classes of antibiotics. In conclusion, our results further elucidate the diversity of carbapenemases, their mechanisms of horizontal transfer and possible patterns of co-selection. The study also emphasizes the difficulty of using whole genome sequencing for antimicrobial susceptibility testing of pathogens with complex genotypes.
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Affiliation(s)
- Anna Johnning
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Nahid Karami
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erika Tång Hallbäck
- 3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Vilhelm Müller
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lena Nyberg
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Mariana Buongermino Pereira
- 1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
| | - Callum Stewart
- 5Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Tobias Ambjörnsson
- 5Department of Astronomy and Theoretical Physics, Lund University, Lund, Sweden
| | - Fredrik Westerlund
- 4Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ingegerd Adlerberth
- 2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden.,3Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- 1Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.,2Centre for Antibiotic Resistance Research, CARe, University of Gothenburg, Gothenburg, Sweden
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46
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Heck C, Michaeli Y, Bald I, Ebenstein Y. Analytical epigenetics: single-molecule optical detection of DNA and histone modifications. Curr Opin Biotechnol 2018; 55:151-158. [PMID: 30326408 DOI: 10.1016/j.copbio.2018.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 09/12/2018] [Accepted: 09/16/2018] [Indexed: 12/13/2022]
Abstract
The field of epigenetics describes the relationship between genotype and phenotype, by regulating gene expression without changing the canonical base sequence of DNA. It deals with molecular genomic information that is encoded by a rich repertoire of chemical modifications and molecular interactions. This regulation involves DNA, RNA and proteins that are enzymatically tagged with small molecular groups that alter their physical and chemical properties. It is now clear that epigenetic alterations are involved in development and disease, and thus, are the focus of intensive research. The ability to record epigenetic changes and quantify them in rare medical samples is critical for next generation diagnostics. Optical detection offers the ultimate single-molecule sensitivity and the potential for spectral multiplexing. Here we review recent progress in ultrasensitive optical detection of DNA and histone modifications.
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Affiliation(s)
- Christian Heck
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel; Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Yael Michaeli
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany; BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str. 11, 12489 Berlin, Germany.
| | - Yuval Ebenstein
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel.
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Jiang K, Rocha S, Westling A, Kesarimangalam S, Dorfman KD, Wittung-Stafshede P, Westerlund F. Alpha-Synuclein Modulates the Physical Properties of DNA. Chemistry 2018; 24:15685-15690. [PMID: 30102440 PMCID: PMC6217799 DOI: 10.1002/chem.201803933] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Indexed: 11/06/2022]
Abstract
Fundamental research on Parkinson's disease (PD) most often focuses on the ability of α-synuclein (aS) to form oligomers and amyloids, and how such species promote brain cell death. However, there are indications that aS also plays a gene-regulatory role in the cell nucleus. Here, the interaction between monomeric aS and DNA in vitro has been investigated with single-molecule techniques. Using a nanofluidic channel system, it was discovered that aS binds to DNA and by studying the DNA-protein complexes at different confinements we determined that aS binding increases the persistence length of DNA from 70 to 90 nm at high coverage. By atomic force microscopy it was revealed that at low protein-to-DNA ratio, the aS binding occurs as small protein clusters scattered along the DNA; at high protein-to-DNA ratio, the DNA is fully covered by protein. As DNA-aS interactions may play roles in PD, it is of importance to characterize biophysical properties of such complexes in detail.
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Affiliation(s)
- Kai Jiang
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sandra Rocha
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Alvina Westling
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Sriram Kesarimangalam
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, Minneapolis, Minnesota, USA
| | | | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Restrepo-Pérez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. NATURE NANOTECHNOLOGY 2018; 13:786-796. [PMID: 30190617 DOI: 10.1038/s41565-018-0236-6] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/16/2018] [Indexed: 05/22/2023]
Abstract
Proteins are major building blocks of life. The protein content of a cell and an organism provides key information for the understanding of biological processes and disease. Despite the importance of protein analysis, only a handful of techniques are available to determine protein sequences, and these methods face limitations, for example, requiring a sizable amount of sample. Single-molecule techniques would revolutionize proteomics research, providing ultimate sensitivity for the detection of low-abundance proteins and the realization of single-cell proteomics. In recent years, novel single-molecule protein sequencing schemes that use fluorescence, tunnelling currents and nanopores have been proposed. Here, we present a review of these approaches, together with the first experimental efforts towards their realization. We discuss their advantages and drawbacks, and present our perspective on the development of single-molecule protein sequencing techniques.
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Affiliation(s)
- Laura Restrepo-Pérez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Chirlmin Joo
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
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Transverse dielectrophoretic-based DNA nanoscale confinement. Sci Rep 2018; 8:5981. [PMID: 29654238 PMCID: PMC5899125 DOI: 10.1038/s41598-018-24132-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/26/2018] [Indexed: 11/19/2022] Open
Abstract
Confinement of single molecules within nanoscale environments is crucial in a range of fields, including biomedicine, genomics, and biophysics. Here, we present a method that can concentrate, confine, and linearly stretch DNA molecules within a single optical field of view using dielectrophoretic (DEP) force. The method can convert an open surface into one confining DNA molecules without a requirement for bonding, hydrodynamic or mechanical components. We use a transverse DEP field between a top coverslip and a bottom substrate, both of which are coated with a transparent conductive material. Both layers are attached using double-sided tape, defining the chamber. The nanofeatures lie at the “floor” and do not require any bonding. With the application of an alternating (AC) electric field (2 Vp-p) between the top and bottom electrodes, a DEP field gradient is established and used to concentrate, confine and linearly extend DNA in nanogrooves as small as 100-nm in width. We also demonstrate reversible loading/unloading of DNA molecules into nanogrooves and nanopits by switching frequency (between 10 kHz to 100 kHz). The technology presented in this paper provides a new method for single-molecule trapping and analysis.
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Abstract
The output from whole genome sequencing is a set of contigs, i.e. short non-overlapping DNA sequences (sizes 1-100 kilobasepairs). Piecing the contigs together is an especially difficult task for previously unsequenced DNA, and may not be feasible due to factors such as the lack of sufficient coverage or larger repetitive regions which generate gaps in the final sequence. Here we propose a new method for scaffolding such contigs. The proposed method uses densely labeled optical DNA barcodes from competitive binding experiments as scaffolds. On these scaffolds we position theoretical barcodes which are calculated from the contig sequences. This allows us to construct longer DNA sequences from the contig sequences. This proof-of-principle study extends previous studies which use sparsely labeled DNA barcodes for scaffolding purposes. Our method applies a probabilistic approach that allows us to discard “foreign” contigs from mixed samples with contigs from different types of DNA. We satisfy the contig non-overlap constraint by formulating the contig placement challenge as a combinatorial auction problem. Our exact algorithm for solving this problem reduces computational costs compared to previous methods in the combinatorial auction field. We demonstrate the usefulness of the proposed scaffolding method both for synthetic contigs and for contigs obtained using Illumina sequencing for a mixed sample with plasmid and chromosomal DNA.
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