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Eitzmann DR, Anderson JL. Facile Preconcentration of Cell-Free DNA in Human Plasma by Ion-Specific Poly Ionic Sorbents Featuring an Anion Exchange Mechanism. Anal Chem 2024; 96:11942-11950. [PMID: 38985898 DOI: 10.1021/acs.analchem.4c01683] [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: 07/12/2024]
Abstract
The expanding horizon of diagnostic and therapeutic applications involving nucleic acids (NA) requires novel tools for purification, including minimal sample preparation. In this work, thin-film microextraction devices featuring five poly ionic sorbents were examined as anion exchange extraction phases for the rapid purification of NAs. Each sorbent is composed of a nonionic cross-linker and a methacrylate monomer containing a core tetra-alkyl ammonium moiety with an alkyl, anionic, or cationic residue. Extraction devices were produced through the application of the prepolymer sorbent mixture onto a functionalized nitinol metal support followed by photoinduced free-radical polymerization. The miniaturized extraction devices (10 mm × 3.5 mm) were directly immersed into aqueous samples to isolate NAs via electrostatic interactions with the polycation. The ammonium methacrylate (AMA) monomer containing a propyl trimethylammonium group (AMA-C3N(CH3)3) exhibited the highest affinity for DNA, with 80 ± 10% of DNA being isolated. Recovery of DNA from the sorbents required the introduction of ions in an aqueous solution to exchange the anionic biopolymer from the polycationic moiety. An investigation of three anion species revealed that the AMA-C3N(CH3)3 sorbent showed the highest recoveries, with the perchlorate anion producing a preconcentration factor of 4.36 ± 0.86 while requiring only 250 mM NaClO4. A directly compatible quantitative polymerase chain reaction assay was developed to quantify the recovery of spiked DNA with lengths of 830, 204, and 98 base pairs in heat-treated human plasma. The AMA-C3N(CH3)3 sorbent was uninhibited by the complex human plasma matrix and enabled high preconcentration factors for the spiked DNA at a biologically relevant concentration of 10 pg/mL. While Qiagen's circulating cell-free DNA MinElute extraction kit enabled higher preconcentration of all analytes, the methodology described in this work requires fewer steps, less user intervention, and minimal equipment requirements to isolate DNA, making it more amenable for high-throughput and low resource applications.
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Affiliation(s)
- Derek R Eitzmann
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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2
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Palmblad M, Vleugels R, Bergquist J. Text mining and computational chemistry reveal trends in applications and applicability of capillary electrophoresis. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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3
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From First to Second: How Stickler’s Diagnostic Genetics Has Evolved to Match Sequencing Technologies. Genes (Basel) 2022; 13:genes13071123. [PMID: 35885907 PMCID: PMC9319459 DOI: 10.3390/genes13071123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 02/05/2023] Open
Abstract
Diagnostic genetics within the United Kingdom National Health Service (NHS) has undergone many stepwise improvements in technology since the completion of the human genome project in 2003. Although Sanger sequencing has remained a cornerstone of the diagnostic sequencing arena, the human genome reference sequence has enabled next-generation sequencing (more accurately named ‘second-generation sequencing’), to rapidly surpass it in scale and potential. This mini review discusses such developments from the viewpoint of the Stickler’s higher specialist service, detailing the considerations and improvements to diagnostic sequencing implemented since 2003.
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Cheng A, Harikrishna JA, Redwood CS, Lit LC, Nath SK, Chua KH. Genetics Matters: Voyaging from the Past into the Future of Humanity and Sustainability. Int J Mol Sci 2022; 23:ijms23073976. [PMID: 35409335 PMCID: PMC8999725 DOI: 10.3390/ijms23073976] [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: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
The understanding of how genetic information may be inherited through generations was established by Gregor Mendel in the 1860s when he developed the fundamental principles of inheritance. The science of genetics, however, began to flourish only during the mid-1940s when DNA was identified as the carrier of genetic information. The world has since then witnessed rapid development of genetic technologies, with the latest being genome-editing tools, which have revolutionized fields from medicine to agriculture. This review walks through the historical timeline of genetics research and deliberates how this discipline might furnish a sustainable future for humanity.
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Affiliation(s)
- Acga Cheng
- Institute of Biological Science, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (J.A.H.)
| | - Jennifer Ann Harikrishna
- Institute of Biological Science, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Charles S. Redwood
- Radcliffe Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK;
| | - Lei Cheng Lit
- Department of Physiology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Swapan K. Nath
- Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA
- Correspondence: (S.K.N.); (K.H.C.)
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (S.K.N.); (K.H.C.)
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5
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Arter WE, Saar KL, Herling TW, Knowles TPJ. Microchip Free-Flow Electrophoresis for Bioanalysis, Sensing, and Purification. Methods Mol Biol 2022; 2394:249-266. [PMID: 35094333 DOI: 10.1007/978-1-0716-1811-0_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The separation of complex mixtures is ubiquitous throughout molecular biology, and techniques such as gel-based electrophoresis are common laboratory practice. Such methods are not without their drawbacks, however, which include non-specific interactions between analyte and the separation matrix, poor yields in purification and non-continuous analyte throughput. Microfluidic techniques, which exploit physical phenomena unique to the microscale, promise to improve many aspects of traditional laboratory procedures. These methods offer a quantitative, solution-based alternative to traditional gel electrophoresis, with rapid measurement times enabling the analysis of transient or weak biomolecular interactions that would be challenging to observe with traditional methods. Here, we present a protocol for the lithographic fabrication and operation of microfluidic chips capable of free-flow electrophoretic (FFE) fractionation and analysis of biological analytes. We demonstrate the efficacy of our approach through a protein-sensing methodology based on FFE fractionation of DNA-protein mixtures. In addition, the FFE technique described here can be readily adapted to suit a variety of preparative and analytical applications, providing information on the charge, zeta-potential, and interactions of analytes.
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Affiliation(s)
- William E Arter
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Kadi L Saar
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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6
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Novel frameshift variant of the CFTR gene: S511Lfs*2 from phenotype to molecular predictions. Mol Biol Rep 2020; 47:6463-6469. [DOI: 10.1007/s11033-020-05677-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 07/09/2020] [Accepted: 07/19/2020] [Indexed: 11/28/2022]
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7
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Feng J, Cao X, Pan Q, He Y. Direct observation of single plasmonic metal nanoparticle reaction in microcolumn with chromatic‐aberration‐free LASER light‐sheet scattering imaging. Electrophoresis 2019; 40:2227-2234. [DOI: 10.1002/elps.201900071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/31/2019] [Accepted: 06/02/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Jingjing Feng
- Department of chemistry Tsinghua University Beijing P. R. China
| | - Xuan Cao
- College of pharmacy, Institute of pharmacy and pharmacology University of South China Hengyang Hunan P. R. China
| | - Qi Pan
- Department of chemistry Tsinghua University Beijing P. R. China
| | - Yan He
- Department of chemistry Tsinghua University Beijing P. R. China
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Szarka M, Szigeti M, Guttman A. Imaging Laser-Induced Fluorescence Detection at the Taylor Cone of Electrospray Ionization Mass Spectrometry. Anal Chem 2019; 91:7738-7743. [DOI: 10.1021/acs.analchem.9b01028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Máte Szarka
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt, Debrecen 4032, Hungary
| | - Márton Szigeti
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt, Debrecen 4032, Hungary
- Translational Glycomics Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem 8200, Hungary
| | - András Guttman
- Horváth Csaba Memorial Laboratory of Bioseparation Sciences, Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt, Debrecen 4032, Hungary
- Translational Glycomics Laboratory, Research Institute of Biomolecular and Chemical Engineering, University of Pannonia, 10 Egyetem Street, Veszprem 8200, Hungary
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Frickmann H, Künne C, Hagen RM, Podbielski A, Normann J, Poppert S, Looso M, Kreikemeyer B. Next-generation sequencing for hypothesis-free genomic detection of invasive tropical infections in poly-microbially contaminated, formalin-fixed, paraffin-embedded tissue samples - a proof-of-principle assessment. BMC Microbiol 2019; 19:75. [PMID: 30961537 PMCID: PMC6454699 DOI: 10.1186/s12866-019-1448-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/28/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The potential of next-generation sequencing (NGS) for hypothesis-free pathogen diagnosis from (poly-)microbially contaminated, formalin-fixed, paraffin embedded tissue samples from patients with invasive fungal infections and amebiasis was investigated. Samples from patients with chromoblastomycosis (n = 3), coccidioidomycosis (n = 2), histoplasmosis (n = 4), histoplasmosis or cryptococcosis with poor histological discriminability (n = 1), mucormycosis (n = 2), mycetoma (n = 3), rhinosporidiosis (n = 2), and invasive Entamoeba histolytica infections (n = 6) were analyzed by NGS (each one Illumina v3 run per sample). To discriminate contamination from putative infections in NGS analysis, mean and standard deviation of the number of specific sequence fragments (paired reads) were determined and compared in all samples examined for the pathogens in question. RESULTS For matches between NGS results and histological diagnoses, a percentage of species-specific reads greater than the 4th standard deviation above the mean value of all 23 assessed sample materials was required. Potentially etiologically relevant pathogens could be identified by NGS in 5 out of 17 samples of patients with invasive mycoses and in 1 out of 6 samples of patients with amebiasis. CONCLUSIONS The use of NGS for hypothesis-free pathogen diagnosis from contamination-prone formalin-fixed, paraffin-embedded tissue requires further standardization.
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Affiliation(s)
- Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, Bernhard-Nocht Str. 74, 20359, Hamburg, Germany. .,Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany.
| | - Carsten Künne
- Department of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad Nauheim, Parkstraße 1, 61231, Bad Nauheim, Germany
| | - Ralf Matthias Hagen
- Department of Preventive Medicine, Bundeswehr Medical Academy, Neuherbergstraße 11, 80937, Munich, Germany
| | - Andreas Podbielski
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Jana Normann
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
| | - Sven Poppert
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051, Basel, Switzerland.,Faculty of Medicine, University Basel, Socinstrasse 57, 4051, Basel, Switzerland
| | - Mario Looso
- Department of Bioinformatics, Max-Planck Institute for Heart and Lung Research Bad Nauheim, Parkstraße 1, 61231, Bad Nauheim, Germany
| | - Bernd Kreikemeyer
- Institute for Microbiology, Virology and Hygiene, University Medicine Rostock, Schillingallee 70, 18057, Rostock, Germany
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Zascavage RR, Thorson K, Planz JV. Nanopore sequencing: An enrichment-free alternative to mitochondrial DNA sequencing. Electrophoresis 2019; 40:272-280. [PMID: 30511783 PMCID: PMC6590251 DOI: 10.1002/elps.201800083] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 10/25/2018] [Accepted: 11/03/2018] [Indexed: 12/31/2022]
Abstract
Mitochondrial DNA sequence data are often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require several rounds of PCR enrichment during Sanger or MPS protocols followed by fairly tedious assembly and analysis. Here we describe an efficient approach to sequencing directly from genomic DNA samples without prior enrichment or extensive library preparation steps. A comparison is made between libraries sequenced directly from native DNA and the same samples sequenced from libraries generated with nine overlapping mtDNA amplicons on the Oxford Nanopore MinION™ device. The native and amplicon library preparation methods and alternative base calling strategies were assessed to establish error rates and identify trends of discordance between the two library preparation approaches. For the complete mtGenome, 16 569 nucleotides, an overall error rate of approximately 1.00% was observed. As expected with mtDNA, the majority of error was detected in homopolymeric regions. The use of a modified basecaller that corrects for ambiguous signal in homopolymeric stretches reduced the error rate for both library preparation methods to approximately 0.30%. Our study indicates that direct mtDNA sequencing from native DNA on the MinION™ device provides comparable results to those obtained from common mtDNA sequencing methods and is a reliable alternative to approaches using PCR-enriched libraries.
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Affiliation(s)
- Roxanne R. Zascavage
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
- Department of Criminology and Criminal JusticeUniversity of Texas at ArlingtonArlingtonTXUSA
| | - Kelcie Thorson
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
- Zoetis Inc.ParsippanyNJUSA
| | - John V. Planz
- Department of MicrobiologyImmunology and GeneticsUniversity of North Texas Health Science CenterFort WorthTXUSA
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11
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Gauthier J, Vincent AT, Charette SJ, Derome N. A brief history of bioinformatics. Brief Bioinform 2018; 20:1981-1996. [DOI: 10.1093/bib/bby063] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/22/2018] [Indexed: 02/06/2023] Open
Abstract
AbstractIt is easy for today’s students and researchers to believe that modern bioinformatics emerged recently to assist next-generation sequencing data analysis. However, the very beginnings of bioinformatics occurred more than 50 years ago, when desktop computers were still a hypothesis and DNA could not yet be sequenced. The foundations of bioinformatics were laid in the early 1960s with the application of computational methods to protein sequence analysis (notably, de novo sequence assembly, biological sequence databases and substitution models). Later on, DNA analysis also emerged due to parallel advances in (i) molecular biology methods, which allowed easier manipulation of DNA, as well as its sequencing, and (ii) computer science, which saw the rise of increasingly miniaturized and more powerful computers, as well as novel software better suited to handle bioinformatics tasks. In the 1990s through the 2000s, major improvements in sequencing technology, along with reduced costs, gave rise to an exponential increase of data. The arrival of ‘Big Data’ has laid out new challenges in terms of data mining and management, calling for more expertise from computer science into the field. Coupled with an ever-increasing amount of bioinformatics tools, biological Big Data had (and continues to have) profound implications on the predictive power and reproducibility of bioinformatics results. To overcome this issue, universities are now fully integrating this discipline into the curriculum of biology students. Recent subdisciplines such as synthetic biology, systems biology and whole-cell modeling have emerged from the ever-increasing complementarity between computer science and biology.
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Affiliation(s)
- Jeff Gauthier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030, av. de la Médecine, Québec, Canada
| | - Antony T Vincent
- INRS-Institut Armand-Frappier, Bacterial Symbionts Evolution, 531 boul. des Prairies, Laval, QC, Canada
| | - Steve J Charette
- Centre de Recherche de l'Institut, Universitaire de Cardiologie et de Pneumologie de Québec (CRIUCPQ), 2725 Chemin Sainte-Foy, Québec, QC, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, Québec, Canada
| | - Nicolas Derome
- Institut de Biologie Intégrative et des Systèmes (IBIS), Département de Biologie, Université Laval, 1030, av. de la Médecine, Québec, Canada
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12
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Kumar Jadav K, Pratap Singh A, Srivastav AB, Sarkhel BC. Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus). Anim Biotechnol 2018; 30:186-191. [DOI: 10.1080/10495398.2018.1469506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
| | | | - A. B. Srivastav
- School of Wildlife Forensic and Health, Nanaji Deshmukh Veterinary Science University, NDVSU, Jabalpur, India
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13
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Isaac C, Patel TR, Zovoilis A. Non-coding RNAs in virology: an RNA genomics approach. Biotechnol Genet Eng Rev 2018; 34:90-106. [PMID: 29865927 DOI: 10.1080/02648725.2018.1471642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Advances in sequencing technologies and bioinformatic analysis techniques have greatly improved our understanding of various classes of RNAs and their functions. Despite not coding for proteins, non-coding RNAs (ncRNAs) are emerging as essential biomolecules fundamental for cellular functions and cell survival. Interestingly, ncRNAs produced by viruses not only control the expression of viral genes, but also influence host cell regulation and circumvent host innate immune response. Correspondingly, ncRNAs produced by the host genome can play a key role in host-virus interactions. In this article, we will first discuss a number of types of viral and mammalian ncRNAs associated with viral infections. Subsequently, we also describe the new possibilities and opportunities that RNA genomics and next-generation sequencing technologies provide for studying ncRNAs in virology.
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Affiliation(s)
- Christopher Isaac
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada
| | - Trushar R Patel
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada.,b Department of Microbiology, Immunology and Infectious Diseases , Cumming School of Medicine, University of Calgary , Calgary , Canada.,c DiscoveryLab, Faculty of Medicine & Dentistry , University of Alberta , Edmonton , Canada
| | - Athanasios Zovoilis
- a Department of Chemistry and Biochemistry , Alberta RNA Research and Training Institute, University of Lethbridge , Lethbridge , Canada
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Kylie J, Weese JS, Turner PV. Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi). BMC Vet Res 2018; 14:143. [PMID: 29703196 PMCID: PMC5924505 DOI: 10.1186/s12917-018-1464-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 04/18/2018] [Indexed: 01/09/2023] Open
Abstract
Background Rabbits are cecotrophic, hindgut-fermenters that rely heavily on their gastrointestinal microbiota for optimal digestion of plant-based diets. Dysbiosis, caused by disruption of the gastrointestinal microbiota, is known to predispose rabbits to rabbit enteritis complex (REC), a major cause of morbidity and mortality. The objectives of this study were to describe the fecal microbiota of domestic rabbits from a variety of settings (commercial meat, companion, laboratory, and shelter) and to identify how factors such as age, season, and routine antimicrobial use affect the fecal microbiota composition. Results A total of 86 pooled commercial meat, 54 companion, 14 pooled laboratory, and 14 shelter rabbit fecal samples were evaluated using 16S rRNA gene sequencing of the V4 region. In all sample types, the predominant bacterial phylum was Firmicutes. Other commonly identified phyla (composing ≥ 1% of the total microbiota composition) were Verrucomicrobia, Proteobacteria, and Bacteroidetes. Significant differences in composition were noted between commercial, companion, laboratory, and shelter rabbit samples for proportions of Verrucomicrobia (P < 0.01), Proteobacteria (P < 0.01), and Lentisphaerae (P = 0.01) within the total microbiota. Within the commercial meat rabbit samples, significant differences between the microbiota composition of growers (n = 42) and does (n = 44) were limited to one unclassified Firmicutes (P = 0.03) and no differences were identified at the phylum level. Significant differences were present between fecal samples taken from rabbits during the summer (n = 44) compared to the winter (n = 42), with Firmicutes (P = 0.04), Verrucomicrobia (P = 0.03), Proteobacteria (P = 0.02), Deinococcus-Thermus (P = 0.04), Armatimonadates (P = 0.003), and Actinobacteria (P = 0.03) forming significantly different proportions of the microbiota. The only significant difference in composition between those farms that routinely reported antimicrobial use and those that did not was in one unclassified Bacteroidetes (P < 0.05) and no differences were identified at the phylum level. Conclusions Rabbit husbandry and diet, in addition to season, significantly influence the fecal microbiota composition of domestic rabbits, while age of the rabbit post-weaning has minimal impact. Electronic supplementary material The online version of this article (10.1186/s12917-018-1464-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer Kylie
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - J Scott Weese
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Patricia V Turner
- Department of Pathobiology, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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15
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Hebert PDN, Braukmann TWA, Prosser SWJ, Ratnasingham S, deWaard JR, Ivanova NV, Janzen DH, Hallwachs W, Naik S, Sones JE, Zakharov EV. A Sequel to Sanger: amplicon sequencing that scales. BMC Genomics 2018; 19:219. [PMID: 29580219 PMCID: PMC5870082 DOI: 10.1186/s12864-018-4611-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 03/20/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Although high-throughput sequencers (HTS) have largely displaced their Sanger counterparts, the short read lengths and high error rates of most platforms constrain their utility for amplicon sequencing. The present study tests the capacity of single molecule, real-time (SMRT) sequencing implemented on the SEQUEL platform to overcome these limitations, employing 658 bp amplicons of the mitochondrial cytochrome c oxidase I gene as a model system. RESULTS By examining templates from more than 5000 species and 20,000 specimens, the performance of SMRT sequencing was tested with amplicons showing wide variation in GC composition and varied sequence attributes. SMRT and Sanger sequences were very similar, but SMRT sequencing provided more complete coverage, especially for amplicons with homopolymer tracts. Because it can characterize amplicon pools from 10,000 DNA extracts in a single run, the SEQUEL can reduce greatly reduce sequencing costs in comparison to first (Sanger) and second generation platforms (Illumina, Ion). CONCLUSIONS SMRT analysis generates high-fidelity sequences from amplicons with varying GC content and is resilient to homopolymer tracts. Analytical costs are low, substantially less than those for first or second generation sequencers. When implemented on the SEQUEL platform, SMRT analysis enables massive amplicon characterization because each instrument can recover sequences from more than 5 million DNA extracts a year.
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Affiliation(s)
- Paul D N Hebert
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Thomas W A Braukmann
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Sean W J Prosser
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | | | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Natalia V Ivanova
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Daniel H Janzen
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-6018, USA
| | - Winnie Hallwachs
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104-6018, USA
| | - Suresh Naik
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Jayme E Sones
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Evgeny V Zakharov
- Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Nasir IA, Emeribe AU, Ojeamiren I, Aderinsayo Adekola H. Human Immunodeficiency Virus Resistance Testing Technologies and Their Applicability in Resource-Limited Settings of Africa. Infect Dis (Lond) 2017; 10:1178633717749597. [PMID: 29308013 PMCID: PMC5751912 DOI: 10.1177/1178633717749597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 11/26/2017] [Indexed: 01/03/2023] Open
Abstract
There has been tremendous breakthrough in the development of technologies and protocols for counselling, testing, and surveillance of resistant human immunodeficiency virus strains for efficient prognosis and clinical management aimed at improving the quality of life of infected persons. However, we have not arrived at a point where services rendered using these technologies can be made affordable and accessible to resource-limited settings. There are several technologies for monitoring antiretroviral resistance, each with unique merits and demerits. In this study, we review the strengths and limitations of prospective and affordable technologies with emphasis on those that could be used in resource-limited settings.
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Affiliation(s)
- Idris Abdullahi Nasir
- Department of Medical Microbiology and Parasitology, College of Health Sciences, University of Ilorin, Ilorin, Nigeria.,Department of Medical Laboratory Services, University of Abuja Teaching Hospital, FCT Abuja, Nigeria.,Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Maiduguri, Nigeria
| | | | - Iduda Ojeamiren
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Hafeez Aderinsayo Adekola
- Department of Medical Microbiology and Parasitology, College of Health Sciences, University of Ilorin, Ilorin, Nigeria
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18
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Gramelsberger G. [Big Data Revolution or Data Hubris? : On the Data Positivism of Molecular Biology]. NTM 2017; 25:459-483. [PMID: 29058018 DOI: 10.1007/s00048-017-0179-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Genome data, the core of the 2008 proclaimed big data revolution in biology, are automatically generated and analyzed. The transition from the manual laboratory practice of electrophoresis sequencing to automated DNA-sequencing machines and software-based analysis programs was completed between 1982 and 1992. This transition facilitated the first data deluge, which was considerably increased by the second and third generation of DNA-sequencers during the 2000s. However, the strategies for evaluating sequence data were also transformed along with this transition. The paper explores both the computational strategies of automation, as well as the data evaluation culture connected with it, in order to provide a complete picture of the complexity of today's data generation and its intrinsic data positivism. This paper is thereby guided by the question, whether this data positivism is the basis of the big data revolution of molecular biology announced today, or it marks the beginning of its data hubris.
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Affiliation(s)
- Gabriele Gramelsberger
- Zentrum für interdisziplinäre Wissenschafts- und Technikforschung, RWTH Aachen, Theaterplatz 14, 52062, Aachen, Deutschland.
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19
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Lewis EL, Leconte AM. DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis. J Vis Exp 2017. [PMID: 29053685 DOI: 10.3791/56228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
For any enzyme, robust, quantitative methods are required for characterization of both native and engineered enzymes. For DNA polymerases, DNA synthesis can be characterized using an in vitro DNA synthesis assay followed by polyacrylamide gel electrophoresis. The goal of this assay is to quantify synthesis of both natural DNA and modified DNA (M-DNA). These approaches are particularly useful for resolving oligonucleotides with single nucleotide resolution, enabling observation of individual steps during enzymatic oligonucleotide synthesis. These methods have been applied to the evaluation of an array of biochemical and biophysical properties such as the measurement of steady-state rate constants of individual steps of DNA synthesis, the error rate of DNA synthesis, and DNA binding affinity. By using modified components including, but not limited to, modified nucleoside triphosphates (NTP), M-DNA, and/or mutant DNA polymerases, the relative utility of substrate-DNA polymerase pairs can be effectively evaluated. Here, we detail the assay itself, including the changes that must be made to accommodate nontraditional primer DNA labeling strategies such as near-infrared fluorescently labeled DNA. Additionally, we have detailed crucial technical steps for acrylamide gel pouring and running, which can often be technically challenging.
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Affiliation(s)
- Eliza L Lewis
- Department of Chemistry, W.M. Keck Science Department of Claremont Mckenna, Pitzer, and Scripps College
| | - Aaron M Leconte
- Department of Chemistry, W.M. Keck Science Department of Claremont Mckenna, Pitzer, and Scripps College;
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20
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Keifer DZ, Pierson EE, Jarrold MF. Charge detection mass spectrometry: weighing heavier things. Analyst 2017; 142:1654-1671. [DOI: 10.1039/c7an00277g] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Charge detection mass spectrometry (CDMS) is a single molecule method where the mass of each ion is directly determined from individual measurements of its mass-to-charge ratio and charge.
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Affiliation(s)
| | - Elizabeth E. Pierson
- Department of Analytical Sciences
- Pharmaceutical Sciences and Clinical Supplies
- Merck Research Laboratories
- Merck & Co
- Inc
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21
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Cloete KW, Ristow PG, Kasu M, D'Amato ME. Design, installation, and performance evaluation of a custom dye matrix standard for automated capillary electrophoresis. Electrophoresis 2016; 38:617-623. [PMID: 27859383 DOI: 10.1002/elps.201600257] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 11/01/2016] [Accepted: 11/03/2016] [Indexed: 12/17/2022]
Abstract
CE equipment detects and deconvolutes mixtures containing up to six fluorescently labeled DNA fragments. This deconvolution is done by the collection software that requires a spectral calibration file. The calibration file is used to adjust for the overlap that occurs between the emission spectra of fluorescence dyes. All commercial genotyping and sequencing kits require the installation of a corresponding matrix standard to generate a calibration file. Due to the differences in emission spectrum overlap between fluorescent dyes, the application of existing commercial matrix standards to the electrophoretic separation of DNA labeled with other fluorescent dyes can yield undesirable results. Currently, the number of fluorescent dyes available for oligonucleotide labeling surpasses the availability of commercial matrix standards. Therefore, in this study we developed and evaluated a customized matrix standard using ATTO 633, ATTO 565, ATTO 550, ATTO Rho6G, and 6-FAM dyes for which no commercial matrix standard is available. We highlighted the potential genotyping errors of using an incorrect matrix standard by evaluating the relative performance of our custom dye set using six matrix standards. The specific performance of two genotyping kits (UniQTyper™ Y-10 version 1.0 and PowerPlex® Y23 System) was also evaluated using their specific matrix standards. The procedure we followed for the construction of our custom dye matrix standard can be extended to other fluorescent dyes.
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Affiliation(s)
- Kevin Wesley Cloete
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Peter Gustav Ristow
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Mohaimin Kasu
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
| | - Maria Eugenia D'Amato
- Forensic DNA Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, Western Cape, South Africa
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22
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Bacterial surface layer proteins as a novel capillary coating material for capillary electrophoretic separations. Anal Chim Acta 2016; 923:89-100. [DOI: 10.1016/j.aca.2016.04.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 03/31/2016] [Accepted: 04/02/2016] [Indexed: 11/22/2022]
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23
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Jarvas G, Kerekgyarto M, Guttman A. On the electromigration of charged fluorophore-labeled oligosaccharides in polyethylene oxide solutions. Electrophoresis 2016; 37:2347-51. [PMID: 27159236 DOI: 10.1002/elps.201600183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 04/28/2016] [Accepted: 04/28/2016] [Indexed: 11/10/2022]
Abstract
The separation mechanism of charged fluorophore (aminopyrenetrisulfonate)-labeled maltooligosaccharides with α1-4 linkages was studied in polyethylene oxide (PEO) solutions (MW 300 000 Da) with special interest to possible analyte and/or network deformations as well as potential solute-matrix interactions. The electrophoretic mobilities of the 8-aminopyrene-1,3,6-trisulfonate-labeled maltooligosaccharides were found proportional with their MW(-2/3) . The Arrhenius function was used to determine the activation energy needed by the labeled sugars to migrate through the separation media. With increasing solute size, the activation energy (Ea ) values decreased in polymer concentrations above the entanglement threshold of the PEO, while showed apparently independent function at the entanglement threshold. The observed phenomenon was considered as a result of solute-matrix interaction, which could be alleviated by the addition of an organic modifier to the BGE.
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Affiliation(s)
- Gabor Jarvas
- Horváth Csaba Laboratory of Bioseparation Sciences, Regional Centre for Molecular Medicine, University of Debrecen, Debrecen, Hungary.,MTA-PE Translational Glycomics Research Group, University of Pannonia, Veszprem, Hungary
| | - Marta Kerekgyarto
- Horváth Csaba Laboratory of Bioseparation Sciences, Regional Centre for Molecular Medicine, University of Debrecen, Debrecen, Hungary
| | - András Guttman
- Horváth Csaba Laboratory of Bioseparation Sciences, Regional Centre for Molecular Medicine, University of Debrecen, Debrecen, Hungary. .,MTA-PE Translational Glycomics Research Group, University of Pannonia, Veszprem, Hungary.
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24
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Heemskerk AAM, Deelder AM, Mayboroda OA. CE-ESI-MS for bottom-up proteomics: Advances in separation, interfacing and applications. MASS SPECTROMETRY REVIEWS 2016; 35:259-271. [PMID: 24852088 DOI: 10.1002/mas.21432] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 03/27/2014] [Indexed: 06/03/2023]
Abstract
With the development of more sensitive hyphenation strategies for capillary electrophoresis-electrospray-mass spectrometry the technique has reemerged as technique with high separation power combined with high sensitivity in the analysis of peptides and protein digests. This review will discuss the newly developed hyphenation strategies for CE-ESI-MS and their application in bottom-up proteomics as well as the applications in the same time span, 2009 to present, using co-axial sheathliquid. Subsequently all separate aspects in the development of a CE-ESI-MS method for bottom-up proteomics shall be discussed, highlighting certain applications and discussing pros and cons of the various choices. The separation of peptides in a capillary electrophoresis system is discussed including the great potential for modeling of this migration of peptides due to the simple electrophoretic separation process. Furthermore, the technical aspects of method development are discussed, namely; background electrolyte choice, coating of the separation capillary and chosen loading method. Finally, conclusions and an outlook on future developments in the field of bottom-up proteomics by CE-ESI-MS will be provided.
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Affiliation(s)
- Anthonius A M Heemskerk
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
| | - Oleg A Mayboroda
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2300, RC, Leiden, The Netherlands
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25
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Abstract
Inborn errors of metabolism are single gene disorders resulting from the defects in the biochemical pathways of the body. Although these disorders are individually rare, collectively they account for a significant portion of childhood disability and deaths. Most of the disorders are inherited as autosomal recessive whereas autosomal dominant and X-linked disorders are also present. The clinical signs and symptoms arise from the accumulation of the toxic substrate, deficiency of the product, or both. Depending on the residual activity of the deficient enzyme, the initiation of the clinical picture may vary starting from the newborn period up until adulthood. Hundreds of disorders have been described until now and there has been a considerable clinical overlap between certain inborn errors. Resulting from this fact, the definite diagnosis of inborn errors depends on enzyme assays or genetic tests. Especially during the recent years, significant achievements have been gained for the biochemical and genetic diagnosis of inborn errors. Techniques such as tandem mass spectrometry and gas chromatography for biochemical diagnosis and microarrays and next-generation sequencing for the genetic diagnosis have enabled rapid and accurate diagnosis. The achievements for the diagnosis also enabled newborn screening and prenatal diagnosis. Parallel to the development the diagnostic methods; significant progress has also been obtained for the treatment. Treatment approaches such as special diets, enzyme replacement therapy, substrate inhibition, and organ transplantation have been widely used. It is obvious that by the help of the preclinical and clinical research carried out for inborn errors, better diagnostic methods and better treatment approaches will high likely be available.
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26
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Greenough L, Schermerhorn KM, Mazzola L, Bybee J, Rivizzigno D, Cantin E, Slatko BE, Gardner AF. Adapting capillary gel electrophoresis as a sensitive, high-throughput method to accelerate characterization of nucleic acid metabolic enzymes. Nucleic Acids Res 2015; 44:e15. [PMID: 26365239 PMCID: PMC4737176 DOI: 10.1093/nar/gkv899] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 08/28/2015] [Indexed: 01/26/2023] Open
Abstract
Detailed biochemical characterization of nucleic acid enzymes is fundamental to understanding nucleic acid metabolism, genome replication and repair. We report the development of a rapid, high-throughput fluorescence capillary gel electrophoresis method as an alternative to traditional polyacrylamide gel electrophoresis to characterize nucleic acid metabolic enzymes. The principles of assay design described here can be applied to nearly any enzyme system that acts on a fluorescently labeled oligonucleotide substrate. Herein, we describe several assays using this core capillary gel electrophoresis methodology to accelerate study of nucleic acid enzymes. First, assays were designed to examine DNA polymerase activities including nucleotide incorporation kinetics, strand displacement synthesis and 3′-5′ exonuclease activity. Next, DNA repair activities of DNA ligase, flap endonuclease and RNase H2 were monitored. In addition, a multicolor assay that uses four different fluorescently labeled substrates in a single reaction was implemented to characterize GAN nuclease specificity. Finally, a dual-color fluorescence assay to monitor coupled enzyme reactions during Okazaki fragment maturation is described. These assays serve as a template to guide further technical development for enzyme characterization or nucleoside and non-nucleoside inhibitor screening in a high-throughput manner.
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Affiliation(s)
| | | | | | - Joanna Bybee
- From New England Biolabs, Inc., Ipswich, MA 01938, USA
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27
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Feist P, Hummon AB. Proteomic challenges: sample preparation techniques for microgram-quantity protein analysis from biological samples. Int J Mol Sci 2015; 16:3537-63. [PMID: 25664860 PMCID: PMC4346912 DOI: 10.3390/ijms16023537] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 01/29/2015] [Indexed: 12/22/2022] Open
Abstract
Proteins regulate many cellular functions and analyzing the presence and abundance of proteins in biological samples are central focuses in proteomics. The discovery and validation of biomarkers, pathways, and drug targets for various diseases can be accomplished using mass spectrometry-based proteomics. However, with mass-limited samples like tumor biopsies, it can be challenging to obtain sufficient amounts of proteins to generate high-quality mass spectrometric data. Techniques developed for macroscale quantities recover sufficient amounts of protein from milligram quantities of starting material, but sample losses become crippling with these techniques when only microgram amounts of material are available. To combat this challenge, proteomicists have developed micro-scale techniques that are compatible with decreased sample size (100 μg or lower) and still enable excellent proteome coverage. Extraction, contaminant removal, protein quantitation, and sample handling techniques for the microgram protein range are reviewed here, with an emphasis on liquid chromatography and bottom-up mass spectrometry-compatible techniques. Also, a range of biological specimens, including mammalian tissues and model cell culture systems, are discussed.
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Affiliation(s)
- Peter Feist
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Integrated Biomedical Sciences Program, and the Harper Cancer Research Institute, 251 Nieuwland Science Hall, University of Notre Dame, Notre Dame, IN 46556, USA.
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28
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Zautner AE, Masanta WO, Hinz R, Hagen RM, Frickmann H. Artificially designed pathogens - a diagnostic option for future military deployments. Mil Med Res 2015; 2:17. [PMID: 26157585 PMCID: PMC4495699 DOI: 10.1186/s40779-015-0045-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 06/24/2015] [Indexed: 01/01/2023] Open
Abstract
Diagnostic microbial isolates of bio-safety levels 3 and 4 are difficult to handle in medical field camps under military deployment settings. International transport of such isolates is challenging due to restrictions by the International Air Transport Association. An alternative option might be inactivation and sequencing of the pathogen at the deployment site with subsequent sequence-based revitalization in well-equipped laboratories in the home country for further scientific assessment. A literature review was written based on a PubMed search. First described for poliovirus in 2002, de novo synthesis of pathogens based on their sequence information has become a well-established procedure in science. Successful syntheses have been demonstrated for both viruses and prokaryotes. However, the technology is not yet available for routine diagnostic purposes. Due to the potential utility of diagnostic sequencing and sequence-based de novo synthesis of pathogens, it seems worthwhile to establish the technology for diagnostic purposes over the intermediate term. This is particularly true for resource-restricted deployment settings, where safe handling of harmful pathogens cannot always be guaranteed.
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Affiliation(s)
- Andreas E Zautner
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Wycliffe O Masanta
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Rebecca Hinz
- Fachbereich Tropenmedizin am Bernhard-Nocht Institut, Bundeswehrkrankenhaus Hamburg, Hamburg, Germany
| | - Ralf Matthias Hagen
- Fachbereich Tropenmedizin am Bernhard-Nocht Institut, Bundeswehrkrankenhaus Hamburg, Hamburg, Germany
| | - Hagen Frickmann
- Fachbereich Tropenmedizin am Bernhard-Nocht Institut, Bundeswehrkrankenhaus Hamburg, Hamburg, Germany ; Institut für Mikrobiologie, Virologie und Hygiene, Universitätsmedizin Rostock, Rostock, Germany
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29
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Fetal mesenchymal stromal cells from cryopreserved human chorionic villi: cytogenetic and molecular analysis of genome stability in long-term cultures. Cytotherapy 2014; 15:1340-51. [PMID: 24094486 DOI: 10.1016/j.jcyt.2013.06.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 06/21/2013] [Accepted: 06/27/2013] [Indexed: 12/24/2022]
Abstract
BACKGROUND AIMS First-trimester chorionic villi (CV) are an attractive source of human mesenchymal stromal cells (hMSC) for possible applications in cellular therapy and regenerative medicine. Human MSC from CV were monitored for genetic stability in long-term cultures. METHODS We set up a good manufacturing practice cryopreservation procedure for small amounts of native CV samples. After isolation, hMSC were in vitro cultured and analyzed for biological end points. Genome stability at different passages of expansion was explored by karyotype, genome-wide array-comparative genomic hybridization and microsatellite genotyping. RESULTS Growth curve analysis revealed a high proliferative potential of CV-derived cells. Immunophenotyping showed expression of typical MSC markers and absence of hematopoietic markers. Analysis of multilineage potential demonstrated efficient differentiation into adipocytes, osteocytes, chondrocytes and induction of neuro-glial commitment. In angiogenic experiments, differentiation in endothelial cells was detected by in vitro Matrigel assay after vascular endothelial growth factor stimulation. Data obtained from karyotyping, array-comparative genomic hybridization and microsatellite genotyping comparing early with late DNA passages did not show any genomic variation at least up to passage 10. Aneuploid clones appeared in four of 14 cases at latest passages, immediately before culture growth arrest. CONCLUSIONS Our findings indicate that hCV-MSC are genetically stable in long-term cultures at least up to passage 10 and that it is possible to achieve clinically relevant amounts of hCV-MSC even after few stages of expansion. Genome abnormalities at higher passages can occasionally occur and are always associated with spontaneous growth arrest. Under these circumstances, hCV-MSC could be suitable for therapeutic purposes.
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30
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Oliveira FV, Gurgel CV, Kobayashi TY, Dionísio TJ, Neves LT, Santos CF, Machado MAAM, Oliveira TM. Amelogenesis imperfecta and screening of mutation in amelogenin gene. Case Rep Dent 2014; 2014:319680. [PMID: 25045544 PMCID: PMC4089840 DOI: 10.1155/2014/319680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/01/2014] [Indexed: 11/30/2022] Open
Abstract
The aim of this study was to report the clinical findings and the screening of mutations of amelogenin gene of a 7-year-old boy with amelogenesis imperfecta (AI). The genomic DNA was extracted from saliva of patient and his family, followed by PCR and direct DNA sequencing. The c.261C>T mutation was found in samples of mother, father, and brother, but the mutation was not found in the sequence of the patient. This mutation is a silent mutation and a single-nucleotide polymorphism (rs2106416). Thus, it is suggested that the mutation found was not related to the clinical presence of AI. Further research is necessary to examine larger number of patients and genes related to AI.
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Affiliation(s)
- Fernanda Veronese Oliveira
- Department of Pediatric Dentistry, Orthodontics and Community Health, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
| | - Carla Vecchione Gurgel
- Department of Pediatric Dentistry, Orthodontics and Community Health, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
| | - Tatiana Yuriko Kobayashi
- Department of Pediatric Dentistry, Orthodontics and Community Health, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
| | - Thiago José Dionísio
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
| | - Lucimara Teixeira Neves
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
- Hospital for the Rehabilitation of Craniofacial Anomalies, University of São Paulo, Rua Silvio Marchione, No. 3-20, 17012-900 Bauru, SP, Brazil
| | - Carlos Ferreira Santos
- Department of Biological Sciences, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
| | - Maria Aparecida Andrade Moreira Machado
- Department of Pediatric Dentistry, Orthodontics and Community Health, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
| | - Thais Marchini Oliveira
- Department of Pediatric Dentistry, Orthodontics and Community Health, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, No. 9-75, 17012-901 Bauru, SP, Brazil
- Hospital for the Rehabilitation of Craniofacial Anomalies, University of São Paulo, Rua Silvio Marchione, No. 3-20, 17012-900 Bauru, SP, Brazil
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31
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Ezgu F, Divanoglu Y, Polat M, Bahceci S, Hasanoglu A, Desnick RJ. Rapid Molecular Diagnosis of Genetic Diseases by High Resolution Melting Analysis: Fabry and Glycogen Storage 1A Diseases. Genet Test Mol Biomarkers 2014; 18:3-7. [DOI: 10.1089/gtmb.2013.0371] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Fatih Ezgu
- Department of Pediatric Metabolic Disorders and Pediatric Genetics, Gazi University Faculty of Medicine, Ankara, Turkey
| | | | - Murat Polat
- Department of Pediatric Metabolic Disorders and Pediatric Genetics, Gazi University Faculty of Medicine, Ankara, Turkey
| | | | - Alev Hasanoglu
- Department of Pediatric Metabolic Disorders and Pediatric Genetics, Gazi University Faculty of Medicine, Ankara, Turkey
| | - Robert J. Desnick
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York
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32
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Németh N, Kerékgyártó M, Sasvári-Székely M, Rónai Z, Guttman A. Rapid identification of human SNAP-25 transcript variants by a miniaturized capillary electrophoresis system. Electrophoresis 2013; 35:379-84. [DOI: 10.1002/elps.201300221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/28/2013] [Accepted: 05/29/2013] [Indexed: 12/25/2022]
Affiliation(s)
- Nóra Németh
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry, Semmelweis University; Budapest Hungary
| | - Márta Kerékgyártó
- Horváth Laboratory of Bioseparation Sciences; University of Debrecen; Debrecen Hungary
| | - Mária Sasvári-Székely
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry, Semmelweis University; Budapest Hungary
| | - Zsolt Rónai
- Department of Medical Chemistry; Molecular Biology and Pathobiochemistry, Semmelweis University; Budapest Hungary
| | - András Guttman
- Horváth Laboratory of Bioseparation Sciences; University of Debrecen; Debrecen Hungary
- MTA-PE Translational Glycomics Group; University of Pannonia; Veszprém Hungary
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33
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Churko JM, Mantalas GL, Snyder MP, Wu JC. Overview of high throughput sequencing technologies to elucidate molecular pathways in cardiovascular diseases. Circ Res 2013; 112:1613-23. [PMID: 23743227 PMCID: PMC3831009 DOI: 10.1161/circresaha.113.300939] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
High throughput sequencing technologies have become essential in studies on genomics, epigenomics, and transcriptomics. Although sequencing information has traditionally been elucidated using a low throughput technique called Sanger sequencing, high throughput sequencing technologies are capable of sequencing multiple DNA molecules in parallel, enabling hundreds of millions of DNA molecules to be sequenced at a time. This advantage allows high throughput sequencing to be used to create large data sets, generating more comprehensive insights into the cellular genomic and transcriptomic signatures of various diseases and developmental stages. Within high throughput sequencing technologies, whole exome sequencing can be used to identify novel variants and other mutations that may underlie many genetic cardiac disorders, whereas RNA sequencing can be used to analyze how the transcriptome changes. Chromatin immunoprecipitation sequencing and methylation sequencing can be used to identify epigenetic changes, whereas ribosome sequencing can be used to determine which mRNA transcripts are actively being translated. In this review, we will outline the differences in various sequencing modalities and examine the main sequencing platforms on the market in terms of their relative read depths, speeds, and costs. Finally, we will discuss the development of future sequencing platforms and how these new technologies may improve on current sequencing platforms. Ultimately, these sequencing technologies will be instrumental in further delineating how the cardiovascular system develops and how perturbations in DNA and RNA can lead to cardiovascular disease.
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Affiliation(s)
- Jared M. Churko
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Departments of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Gary L. Mantalas
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joseph C. Wu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Departments of Medicine and Radiology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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Ban E, Song EJ. Recent developments and applications of capillary electrophoresis with laser-induced fluorescence detection in biological samples. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 929:180-6. [DOI: 10.1016/j.jchromb.2013.04.028] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 04/18/2013] [Accepted: 04/20/2013] [Indexed: 12/15/2022]
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Dorfman KD, King SB, Olson DW, Thomas JDP, Tree DR. Beyond gel electrophoresis: microfluidic separations, fluorescence burst analysis, and DNA stretching. Chem Rev 2013; 113:2584-667. [PMID: 23140825 PMCID: PMC3595390 DOI: 10.1021/cr3002142] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Scott B. King
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Daniel W. Olson
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Joel D. P. Thomas
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
| | - Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota — Twin Cities, 421 Washington Ave. SE, Minneapolis, MN 55455, Phone: 1-612-624-5560. Fax: 1-612-626-7246
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Nguyen TV, Chen JK, Murray V. Bleomycin DNA damage: Anomalous mobility of 3'-phosphoglycolate termini in an automated capillary DNA sequencer. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 913-914:113-22. [PMID: 23277328 DOI: 10.1016/j.jchromb.2012.11.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/20/2012] [Accepted: 11/27/2012] [Indexed: 01/22/2023]
Abstract
An automated capillary DNA sequencer with laser-induced fluorescence detection can be utilised for DNA fragment analysis. The precise mobilities of DNA fragments with different chemical termini are especially important in the determination of the sequence specificity of DNA damaging agents. The aim of this study was to examine the electrophoretic mobility profile of DNA fragments with different 3'-termini. The nature of the 3'-teminal residue was found to have a major effect on the electrophoretic mobility of the DNA fragment, especially for 3'-phosphoglycolate termini that migrated anomalously by 3-6 nucleotides. Using the automated capillary sequencer, the electrophoretic mobilities of DNA fragments with different 3'-termini including 3'-hydrogen, 3'-hydroxyl, 3'-phosphate, and 3'-phosphoglycolate were extensively quantified and compared relative to each other. The 3'-hydrogen termini were generated by dideoxy sequencing; 3'-hydroxyl ends by minus sequencing; 3'-phosphate by Maxam-Gilbert chemical sequencing; and 3'-phosphoglycolate by bleomycin cleavage. The mobilities of these DNA fragments with different 3'-termini were found to be: (slowest) 3'-hydroxyl<3'-hydrogen<3'-phosphate<3'-phosphoglycolate (fastest); with average relative mobilities of 0.00<0.12<0.63<4.42 nucleotides, respectively. The possible causes of the unusual electrophoretic mobility of the 3'-phosphoglycolate termini were discussed.
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Affiliation(s)
- Trung V Nguyen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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Kerékgyártó M, Kerekes T, Tsai E, Amirkhanian VD, Guttman A. Light-emitting diode induced fluorescence (LED-IF) detection design for a pen-shaped cartridge based single capillary electrophoresis system. Electrophoresis 2012; 33:2752-8. [DOI: 10.1002/elps.201200139] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Márta Kerékgyártó
- Horváth Laboratory of Bioseparation Sciences; University of Debrecen; Hungary
| | - Tamás Kerekes
- Clinical Genomics Centre; Medical and Health Science Center; University of Debrecen; Hungary
| | - Eric Tsai
- BiOptic, Inc.; New Taipei City; Taiwan; Republic of China
| | | | - András Guttman
- Horváth Laboratory of Bioseparation Sciences; University of Debrecen; Hungary
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38
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Nguyen TV, Murray V. The electrophoretic mobility of DNA fragments differing by a single 3'-terminal nucleotide in an automated capillary DNA sequencer. Biomed Chromatogr 2012; 27:390-5. [PMID: 22911138 DOI: 10.1002/bmc.2804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/16/2012] [Accepted: 07/25/2012] [Indexed: 12/15/2022]
Abstract
The electrophoretic mobility of DNA fragments that differ by a single 3'-terminal nucleotide was assessed by capillary electrophoresis. This was accomplished using dideoxy sequencing with a 5'-fluorescently labelled primer to generate DNA fragments with 3'-hydrogen ends. The resulting DNA fragments were electrophoresed on the ABI 3730 automated capillary sequencer, and the data were analysed with the GeneMapper software to determine the electrophoretic mobility differences on addition of a 3'-terminal nucleotide. It was found that the 3'-terminal nucleotide gave rise to different electrophoretic mobility profiles depending on the identity of the terminal nucleotide. The apparent electrophoretic mobility was (faster) -C > -A > -T > -G (slower). The C-terminated fragments were the fastest and the G-terminated fragments the slowest, relative to other nucleotides. It was proposed that the terminal nucleotide effect was due to changes in partial net charges on the nucleotides that resulted in alterations in the electrophoretic mobility of the DNA fragments in the automated capillary DNA sequencer. Other alternative explanations are also discussed.
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Affiliation(s)
- Trung V Nguyen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
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Stranneheim H, Lundeberg J. Stepping stones in DNA sequencing. Biotechnol J 2012; 7:1063-73. [PMID: 22887891 PMCID: PMC3472021 DOI: 10.1002/biot.201200153] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 06/21/2012] [Accepted: 07/04/2012] [Indexed: 12/11/2022]
Abstract
In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid technological advances have enormously expanded sequencing opportunities and applications, but also imposed strains and challenges on steps prior to sequencing and in the downstream process of handling and analysis of these massive amounts of sequence data. Traditionally, sequencing has been limited to small DNA fragments of approximately one thousand bases (derived from the organism's genome) due to issues in maintaining a high sequence quality and accuracy for longer read lengths. Although many technological breakthroughs have been made, currently the commercially available massively parallel sequencing methods have not been able to resolve this issue. However, recent announcements in nanopore sequencing hold the promise of removing this read-length limitation, enabling sequencing of larger intact DNA fragments. The ability to sequence longer intact DNA with high accuracy is a major stepping stone towards greatly simplifying the downstream analysis and increasing the power of sequencing compared to today. This review covers some of the technical advances in sequencing that have opened up new frontiers in genomics.
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Affiliation(s)
- Henrik Stranneheim
- Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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40
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Ramautar R, Heemskerk AAM, Hensbergen PJ, Deelder AM, Busnel JM, Mayboroda OA. CE-MS for proteomics: Advances in interface development and application. J Proteomics 2012; 75:3814-28. [PMID: 22609513 DOI: 10.1016/j.jprot.2012.04.050] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/23/2012] [Accepted: 04/30/2012] [Indexed: 12/25/2022]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) has emerged as a powerful technique for the analysis of proteins and peptides. Over the past few years, significant progress has been made in the development of novel and more effective interfaces for hyphenating CE to MS. This review provides an overview of these new interfacing techniques for coupling CE to MS, covering the scientific literature from January 2007 to December 2011. The potential of these new CE-MS interfacing techniques is demonstrated within the field of (clinical) proteomics, more specifically "bottom-up" proteomics, by showing examples of the analysis of various biological samples. The relevant papers on CE-MS for proteomics are comprehensively summarized in tables, including, e.g. information on sample type and pretreatment, interfacing and MS detection mode. Finally, general conclusions and future perspectives are provided.
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Affiliation(s)
- Rawi Ramautar
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, The Netherlands.
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Liao YM, Lin SK, Liu TC, Chiou SS, Lu HC, Kao CF, Chang JG. Rapid identification of the copy number of α-globin genes by capillary electrophoresis analysis. Clin Biochem 2012; 45:798-805. [PMID: 22374170 DOI: 10.1016/j.clinbiochem.2012.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 01/19/2012] [Accepted: 02/09/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVES The current study aimed at the rapid identification of the copy number of α-globin genes for the diagnosis of α-thalassemia. DESIGN AND METHODS To identify the copy number of α-globin genes in α-thalassemia, we developed a novel method using a multiplex polymerase chain reaction (PCR) in combination with the CE analysis. RESULTS The proposed method provides a rapid detection of the common α-globin gene deletions. Sixty-six patients with α-thalassemia and 46 normal controls were included in the present study. The obtained results showed good correlation with those obtained by gap PCR. Moreover, a low amount of maternal cell contamination in the fetus specimen for the prenatal diagnosis of hemoglobin Barts hydrops fetalis as well as the rare multiplicated α-globin genes can be identified using this method. CONCLUSION This method provides a convenient and efficient tool for the rapid identification of the copy number of α-globin genes in α-thalassemia and the individuals with α-globin gene multiplication.
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Affiliation(s)
- Yu-Mei Liao
- Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
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42
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Qian JX, Chen ZG. A novel electromagnetic induction detector with a coaxial coil for capillary electrophoresis. CHINESE CHEM LETT 2012. [DOI: 10.1016/j.cclet.2011.10.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Ban E, Park SH, Kang MJ, Lee HJ, Song EJ, Yoo YS. Growing trend of CE at the omics level: The frontier of systems biology - An update. Electrophoresis 2011; 33:2-13. [DOI: 10.1002/elps.201100344] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Revised: 08/16/2011] [Accepted: 08/16/2011] [Indexed: 02/03/2023]
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Huang J, Zheng Z, Andersson AF, Engstrand L, Ye W. Rapid screening of complex DNA samples by single-molecule amplification and sequencing. PLoS One 2011; 6:e19723. [PMID: 21625543 PMCID: PMC3098247 DOI: 10.1371/journal.pone.0019723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 04/08/2011] [Indexed: 11/19/2022] Open
Abstract
Microbial cloning makes Sanger sequencing of complex DNA samples possible but is labor intensive. We present a simple, rapid and robust method that enables laboratories without special equipment to perform single-molecule amplicon sequencing, although in a low-throughput manner, from sub-picogram quantities of DNA. The method can also be used for quick quality control of next-generation sequencing libraries, as was demonstrated for a metagenomic sample.
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Affiliation(s)
- Jiaqi Huang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Zongli Zheng
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
| | - Anders F. Andersson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Swedish Institute for Communicable Infectious Disease Control, Solna, Sweden
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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Cheng HL, Chiou SS, Liao YM, Chen YL, Wu SM. Genotyping of single nucleotide polymorphism in γ-glutamyl hydrolase gene by capillary electrophoresis. Electrophoresis 2011; 32:2021-7. [DOI: 10.1002/elps.201000422] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 11/03/2010] [Accepted: 11/16/2010] [Indexed: 12/14/2022]
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46
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Lee A, Whitesides GM. Analysis of inorganic polyphosphates by capillary gel electrophoresis. Anal Chem 2010; 82:6838-46. [PMID: 20704373 DOI: 10.1021/ac1008018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This paper describes the development of a method that uses capillary gel electrophoresis (CGE) to analyze mixtures of inorganic polyphosphate ((P(i))(n)). Resolution of (P(i))(n) on the basis of n, the number of residues of dehydrated phosphate, is accomplished by CGE using capillaries filled with solutions of poly(N,N-dimethylacrylamide) (PDMA) and indirect detection by the UV absorbance of a chromophore, terephthalate, added to the running buffer. The method is capable of resolving peaks representing (P(i))(n) with n up to approximately 70; preparation and use of authentic standards enables the identification of peaks for (P(i))(n) with n = 1-10. The main advantages of this method over previously reported methods for analyzing mixtures of (P(i))(n) (e.g., gel electrophoresis, CGE using polyacrylamide-filled capillaries) are its resolution, convenience, and reproducibility; gel-filled capillaries are easily regenerated by pumping in fresh, low-viscosity solutions of PDMA. The resolution is comparable to that of ion-exchange chromatography and detection of (P(i))(n) by suppressed conductivity. The method is useful for analyzing (P(i))(n) generated by the dehydration of P(i) at low temperature (125-140 degrees C) with urea, in a reaction that may have been important in prebiotic chemistry. The method should also be useful for characterizing mixtures of other anionic, oligomeric, or polymeric species without an intrinsic chromophore (e.g., sulfated polysaccharides, oligomeric phospho-diesters).
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Affiliation(s)
- Andrew Lee
- Department of Chemistry and Chemical Biology, Harvard University,12 Oxford Street, Cambridge, MA, USA
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47
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Klepárník K, Boček P. Electrophoresis today and tomorrow: Helping biologists' dreams come true. Bioessays 2010; 32:218-226. [PMID: 20127703 DOI: 10.1002/bies.200900152] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Intensive research and development of electrophoresis methodology and instrumentation during past decades has resulted in unique methods widely implemented in bioanalysis. While two-dimensional electrophoresis and denaturing polyacrylamide gel electrophoresis in sodium dodecylsulfate are still the most frequently used electrophoretic methods applied to analyses of proteins, new miniaturized capillary and microfluidic versions of electromigrational methods have been developed. High-throughput electrophoretic instruments with hundreds of capillaries for parallel separations and laser-induced fluorescence detection of labeled DNA strands have been of key importance for the scientific and commercial success of the Human Genome Project. Another powerful method, capillary isoelectric focusing with pressurized and pH-driven mobilization, provides efficient separations and on-line sensitive detection of proteins, bacteria and viruses. Electrophoretic microfluidic devices can integrate single-cell injection, cell lysis, separation of its components and fluorescence or mass spectrometry detection. These miniaturized devices also proved the capability of single-molecule detection.
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
| | - Petr Boček
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Veveří 97, CZ-602 00 Brno, Czech Republic
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Nilsson C, Harwigsson I, Birnbaum S, Nilsson S. Cationic and anionic lipid-based nanoparticles in CEC for protein separation. Electrophoresis 2010; 31:1773-9. [DOI: 10.1002/elps.200900725] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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49
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Simionato AVC, Carrilho E, Maggi Tavares MF. CE-MS and related techniques as a valuable tool in tumor biomarkers research. Electrophoresis 2010; 31:1214-1226. [DOI: 10.1002/elps.200900671] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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50
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Oberacher H. Frontiers of mass spectrometry in nucleic acids analysis. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2010; 16:351-365. [PMID: 20530841 DOI: 10.1255/ejms.1045] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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