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Gyasi H, Curry J, Browning J, Ha K, Thomas PJ, O'Brien JM. Microsatellite mutation frequencies in river otters (Lontra Canadensis) from the Athabasca Oil Sands region are correlated to polycyclic aromatic compound tissue burden. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2022; 63:172-183. [PMID: 35452555 DOI: 10.1002/em.22482] [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: 02/24/2022] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Mining activities in the Athabasca oil sands region (AOSR) have contributed to an increase of polycyclic aromatic compounds (PACs) locally. However, many PACs found in the AOSR, and the combined effects of PAC mixtures have not been evaluated for genotoxicity in wildlife. Here, we examine whether mutation frequencies in AOSR river otters are correlated to PAC tissue burdens. We used single-molecule polymerase chain reaction (SM-PCR) to measure the mutant frequency of unstable DNA microsatellite loci in the bone marrow of wild river otters (n = 11) from the AOSR. Microsatellite mutation frequencies were regressed against liver PAC burden (total, low/high molecular weight [LMW/HMW], and parent/alkylated PACs), and to the distances from where the samples were collected to nearby bitumen upgraders. We found that microsatellite mutation frequency was positively correlated with total liver PAC burden. LMW and alkylated PACs were detected at higher levels and had a stronger positive relationship with mutation frequency than HMW (alkylated and parent) PACs. There were no significant relationships detected between mutation frequency and LMW parent PACs or the distance from bitumen upgraders. Furthermore, pyrogenic and petrogenic signatures suggest PACs in animals with high mutation frequencies were associated with combustion processes; although further investigation is warranted, due to limitations of diagnostic ratio determination with biotic models. Our findings support the hypothesis that PACs found in the AOSR increase mutation frequency in wildlife. Further investigation is required to determine if the elevated PAC levels associated with higher mutation frequency are due to natural exposure or elevated human activity.
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Affiliation(s)
- Helina Gyasi
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Jory Curry
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
| | - Jared Browning
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Kelsey Ha
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Philippe J Thomas
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
| | - Jason M O'Brien
- Ecotoxicology and Wildlife Health Division, National Wildlife Research Centre, Environment and Climate Change Canada, Ottawa, Ontario, Canada
- Department of Biology, Carleton University, Ottawa, Ontario, Canada
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2
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Pszona M, Gawinkowski S, Jäger R, Kamińska I, Waluk J. Influence of bulky substituents on single-molecule SERS sensitivity. J Chem Phys 2022; 156:014201. [PMID: 34998322 DOI: 10.1063/5.0074840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The surface-enhanced Raman spectroscopy (SERS) detection limit strongly depends on the molecular structure, which we demonstrate for a family of tert-butyl-substituted porphycenes. Even though the investigated species present very similar photophysical properties, the ratio between the SERS signal and fluorescence background depends on the number of bulky tert-butyl groups. Moreover, the probability of single molecule detection systematically drops with the number of the moieties attached to the pyrrole ring. As steric hindrance is the only significantly changing feature among the studied chromophores, we attribute the observed phenomena to the spatial structure. We also show that the sensitivity of the SERS technique can be improved by lowering the temperature. We managed to observe single-molecule spectra for derivatives for which this was unattainable at room temperature.
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Affiliation(s)
- Maria Pszona
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Kasprzaka 44/52, Poland
| | - Sylwester Gawinkowski
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Kasprzaka 44/52, Poland
| | - Regina Jäger
- Institute of Physical and Theoretical Chemistry and LISA, University of Tübingen, Auf der Morgenstelle 18, D-72076 Tübingen, Germany
| | - Izabela Kamińska
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Kasprzaka 44/52, Poland
| | - Jacek Waluk
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Kasprzaka 44/52, Poland
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3
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Poon AFY, Prodger JL, Lynch BA, Lai J, Reynolds SJ, Kasule J, Capoferri AA, Lamers SL, Rodriguez CW, Bruno D, Porcella SF, Martens C, Quinn TC, Redd AD. Quantitation of the latent HIV-1 reservoir from the sequence diversity in viral outgrowth assays. Retrovirology 2018; 15:47. [PMID: 29976219 PMCID: PMC6034329 DOI: 10.1186/s12977-018-0426-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 06/14/2018] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The ability of HIV-1 to integrate into the genomes of quiescent host immune cells, establishing a long-lived latent viral reservoir (LVR), is the primary obstacle to curing these infections. Quantitative viral outgrowth assays (QVOAs) are the gold standard for estimating the size of the replication-competent HIV-1 LVR, measured by the number of infectious units per million (IUPM) cells. QVOAs are time-consuming because they rely on culturing replicate wells to amplify the production of virus antigen or nucleic acid to reproducibly detectable levels. Sequence analysis can reduce the required number of culture wells because the virus genetic diversity within the LVR provides an internal replication and dilution series. Here we develop a Bayesian method to jointly estimate the IUPM and variant frequencies (a measure of clonality) from the sequence diversity of QVOAs. RESULTS Using simulation experiments, we find our Bayesian approach confers significantly greater accuracy over current methods to estimate the IUPM, particularly for reduced numbers of QVOA replicates and/or increasing actual IUPM. Furthermore, we determine that the improvement in accuracy is greater with increasing genetic diversity in the sample population. We contrast results of these different methods applied to new HIV-1 sequence data derived from QVOAs from two individuals with suppressed viral loads from the Rakai Health Sciences Program in Uganda. CONCLUSIONS Utilizing sequence variation has the additional benefit of providing information on the contribution of clonality of the LVR, where high clonality (the predominance of a single genetic variant) suggests a role for cell division in the long-term persistence of the reservoir. In addition, our Bayesian approach can be adapted to other limiting dilution assays where positive outcomes can be partitioned by their genetic heterogeneity, such as immune cell populations and other viruses.
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Affiliation(s)
- Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada.
| | - Jessica L Prodger
- Department of Microbiology and Immunology, Western University, London, ON, Canada.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Briana A Lynch
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA
| | - Jun Lai
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Steven J Reynolds
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.,Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Adam A Capoferri
- Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | | | - Daniel Bruno
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Stephen F Porcella
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Craig Martens
- Genomics Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Thomas C Quinn
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew D Redd
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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4
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Pang B, Ding X, Wang G, Zhao C, Xu Y, Fu K, Sun J, Song X, Wu W, Liu Y, Song Q, Hu J, Li J, Mu Y. Rapid and Quantitative Detection of Vibrio parahemolyticus by the Mixed-Dye-Based Loop-Mediated Isothermal Amplification Assay on a Self-Priming Compartmentalization Microfluidic Chip. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:11312-11319. [PMID: 29198118 DOI: 10.1021/acs.jafc.7b03655] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Vibrio parahemolyticus (VP) mostly isolated from aquatic products is one of the major causes of bacterial food-poisoning events worldwide, which could be reduced using a promising on-site detection method. Herein, a rapid and quantitative method for VP detection was developed by applying a mixed-dye-loaded loop-mediated isothermal amplification (LAMP) assay on a self-priming compartmentalization (SPC) microfluidic chip, termed on-chip mixed-dye-based LAMP (CMD-LAMP). In comparison to conventional approaches, CMD-LAMP was advantageous on the limit of detection, which reached down to 1 × 103 CFU/mL in food-contaminated samples without the pre-enrichment of bacteria. Additionally, as a result of the use of a mixed dye and SPC chip, the quantitative result could be easily acquired, avoiding the requirement of sophisticated instruments and tedious operation. Also, CMD-LAMP was rapid and cost-effective. Conclusively, CMD-LAMP has great potential in realizing the on-site quantitative analysis of VP for food safety.
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Affiliation(s)
- Bo Pang
- Department of Hygienic Inspection, School of Public Health, Jilin University , Changchun, Jilin 130021, People's Republic of China
| | - Xiong Ding
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Guoping Wang
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Chao Zhao
- Department of Hygienic Inspection, School of Public Health, Jilin University , Changchun, Jilin 130021, People's Republic of China
| | - Yanan Xu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Kaiyue Fu
- Department of Hygienic Inspection, School of Public Health, Jilin University , Changchun, Jilin 130021, People's Republic of China
| | - Jingjing Sun
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Xiuling Song
- Department of Hygienic Inspection, School of Public Health, Jilin University , Changchun, Jilin 130021, People's Republic of China
| | - Wenshuai Wu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Yushen Liu
- Department of Hygienic Inspection, School of Public Health, Jilin University , Changchun, Jilin 130021, People's Republic of China
| | - Qi Song
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Jiumei Hu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
| | - Juan Li
- Department of Hygienic Inspection, School of Public Health, Jilin University , Changchun, Jilin 130021, People's Republic of China
| | - Ying Mu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University , Hangzhou, Zhejiang 310058, People's Republic of China
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5
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Cao L, Cui X, Hu J, Li Z, Choi JR, Yang Q, Lin M, Ying Hui L, Xu F. Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications. Biosens Bioelectron 2016; 90:459-474. [PMID: 27818047 DOI: 10.1016/j.bios.2016.09.082] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/18/2022]
Abstract
Since the invention of polymerase chain reaction (PCR) in 1985, PCR has played a significant role in molecular diagnostics for genetic diseases, pathogens, oncogenes and forensic identification. In the past three decades, PCR has evolved from end-point PCR, through real-time PCR, to its current version, which is the absolute quantitive digital PCR (dPCR). In this review, we first discuss the principles of all key steps of dPCR, i.e., sample dispersion, amplification, and quantification, covering commercialized apparatuses and other devices still under lab development. We highlight the advantages and disadvantages of different technologies based on these steps, and discuss the emerging biomedical applications of dPCR. Finally, we provide a glimpse of the existing challenges and future perspectives for dPCR.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Xingye Cui
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jie Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jane Ru Choi
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Qingzhen Yang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Min Lin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Li Ying Hui
- Foundation of State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, PR China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
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6
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Lund HL, Hughesman CB, McNeil K, Clemens S, Hocken K, Pettersson R, Karsan A, Foster LJ, Haynes C. Initial diagnosis of chronic myelogenous leukemia based on quantification of M-BCR status using droplet digital PCR. Anal Bioanal Chem 2015; 408:1079-94. [DOI: 10.1007/s00216-015-9204-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 11/11/2015] [Accepted: 11/18/2015] [Indexed: 01/25/2023]
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7
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Zota VE, Magliocco AM. Molecular Technologies in the Clinical Diagnostic Laboratory. Cancer Control 2015; 22:142-51. [PMID: 26068758 DOI: 10.1177/107327481502200204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND New technologies for molecular analysis are increasing our ability to diagnose cancer. METHODS Several molecular analysis technologies are reviewed and their use in the clinical laboratory is discussed. RESULTS Select key technologies, including polymerase chain reaction and next-generation sequencing, are helping transform our ability to analyze cancer specimens. As these technological advances become more and more incorporated into routine diagnostic testing, our classification systems are likely to be impacted and our approach to treatment transformed. The routine use of such technology also brings challenges for analysis and reimbursement. CONCLUSION These advances in technology will change the way we diagnose, monitor, and treat patients with cancer.
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Affiliation(s)
- Victor E Zota
- Department of Anatomic Pathology, Moffitt Cancer Center, Tampa, FL 33612, USA.
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8
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Variation in transcriptome size: are we getting the message? Chromosoma 2014; 124:27-43. [DOI: 10.1007/s00412-014-0496-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 12/30/2022]
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9
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Zhu Q, Qiu L, Yu B, Xu Y, Gao Y, Pan T, Tian Q, Song Q, Jin W, Jin Q, Mu Y. Digital PCR on an integrated self-priming compartmentalization chip. LAB ON A CHIP 2014; 14:1176-85. [PMID: 24481046 DOI: 10.1039/c3lc51327k] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
An integrated on-chip valve-free and power-free microfluidic digital PCR device is for the first time developed by making use of a novel self-priming compartmentalization and simple dehydration control to realize 'divide and conquer' for single DNA molecule detection. The high gas solubility of PDMS is exploited to provide the built-in power of self-priming so that the sample and oil are sequentially sucked into the device to realize sample self-compartmentalization based on surface tension. The lifespan of its self-priming capability was about two weeks tested using an air-tight packaging bottle sealed with a small amount of petroleum jelly, which is significant for a practical platform. The SPC chip contains 5120 independent 5 nL microchambers, allowing the samples to be compartmentalized completely. Using this platform, three different abundances of lung cancer related genes are detected to demonstrate the feasibility and flexibility of the microchip for amplifying a single nucleic acid molecule. For maximal accuracy, within less than 5% of the measurement deviation, the optimal number of positive chambers is between 400 and 1250 evaluated by the Poisson distribution, which means one panel can detect an average of 480 to 4804 template molecules. This device without world-to-chip connections eliminates the constraint of the complex pipeline control, and is an integrated on-chip platform, which would be a significant improvement to digital PCR automation and more user-friendly.
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Affiliation(s)
- Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, PR China.
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10
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Day E, Dear PH, McCaughan F. Digital PCR strategies in the development and analysis of molecular biomarkers for personalized medicine. Methods 2013; 59:101-7. [DOI: 10.1016/j.ymeth.2012.08.001] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 07/30/2012] [Accepted: 08/02/2012] [Indexed: 12/18/2022] Open
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11
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Zhelev DV, Hunt M, Le A, Dupuis C, Ren S, Gibbons HS. Effect of the Bacillus atrophaeus subsp. globigii Spo0F H101R mutation on strain fitness. Appl Environ Microbiol 2012; 78:8601-10. [PMID: 23042165 PMCID: PMC3502920 DOI: 10.1128/aem.01922-12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 09/24/2012] [Indexed: 11/20/2022] Open
Abstract
Sporulation is a critical developmental process in Bacillus spp. that, once initiated, removes the possibility of further growth until germination. Therefore, the threshold conditions triggering sporulation are likely to be subject to evolutionary constraint. Our previous studies revealed two spontaneous hypersporulating mutants of Bacillus atrophaeus subsp. globigii, both containing point mutations in the spo0F gene. One of these strains (Detrick-2; contains the spo0F101 allele with a C:T [His101Arg] substitution) had been deliberately selected in the early 1940s as an anthrax surrogate. To determine whether the experimental conditions used during the selection of the "military" strains could have supported the emergence of hypersporulating variants, the relative fitness of strain Detrick-2 was measured in several experimental settings modeled on experimental conditions employed during its development in the 1940s as a simulant. The congenic strain Detrick-1 contained a wild-type spo0F gene and sporulated like the wild-type strain. The relative fitness of Detrick-1 and Detrick-2 was evaluated in competition experiments using quantitative single nucleotide polymorphism (SNP)-specific real-time PCR assays directed at the C:T substitution. The ancestral strain Detrick-1 had a fitness advantage under all conditions tested except when competing cultures were subjected to frequent heat shocks. The hypersporulating strain gained the maximum fitness advantage when cultures were grown at low oxygen tension and when heat shock was applied soon after the formation of the first heat-resistant spores. This is interpreted as gain of fitness by the hypersporulating strain in fast-changing fluctuating environments as a result of the increased rate of switching to the sporulating phenotype.
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Affiliation(s)
- Doncho V. Zhelev
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Mia Hunt
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Anna Le
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Christopher Dupuis
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Suelynn Ren
- Sensors and Electron Devices Directorate, Army Research Laboratory, Adelphi, Maryland, USA
| | - Henry S. Gibbons
- Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
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12
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Zhu Q, Gao Y, Yu B, Ren H, Qiu L, Han S, Jin W, Jin Q, Mu Y. Self-priming compartmentalization digital LAMP for point-of-care. LAB ON A CHIP 2012; 12:4755-63. [PMID: 22986619 DOI: 10.1039/c2lc40774d] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Digital nucleic acid amplification provides unprecedented opportunities for absolute nucleic acid quantification by counting of single molecules. This technique is useful for molecular genetic analysis in cancer, stem cell, bacterial, non-invasive prenatal diagnosis in which many biologists are interested. This paper describes a self-priming compartmentalization (SPC) microfluidic chip platform for performing digital loop-mediated amplification (LAMP). The energy for the pumping is pre-stored in the degassed bulk PDMS by exploiting the high gas solubility of PDMS; therefore, no additional structures other than channels and reservoirs are required. The sample and oil are sequentially sucked into the channels, and the pressure difference of gas dissolved in PDMS allows sample self-compartmentalization without the need for further chip manipulation such as with pneumatic microvalves and control systems, and so on. The SPC digital LAMP chip can be used like a 384-well plate, so, the world-to-chip fluidic interconnections are avoided. The microfluidic chip contains 4 separate panels, each panel contains 1200 independent 6 nL chambers and can be used to detect 4 samples simultaneously. Digital LAMP on the microfluidic chip was tested quantitatively by using β-actin DNA from humans. The self-priming compartmentalization behavior is roughly predictable using a two-dimensional model. The uniformity of compartmentalization was analyzed by fluorescent intensity and fraction of volume. The results showed that the feasibility and flexibility of the microfluidic chip platform for amplifying single nucleic acid molecules in different chambers made by diluting and distributing sample solutions. The SPC chip has the potential to meet the requirements of a general laboratory: power-free, valve-free, operating at isothermal temperature, inexpensive, sensitive, economizing labour time and reagents. The disposable analytical devices with appropriate air-tight packaging should be useful for point-of-care, and enabling it to become one of the common tools for biology research, especially, in point-of-care testing.
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Affiliation(s)
- Qiangyuan Zhu
- Research Center for Analytical Instrumentation, Institute of Cyber-Systems and Control, State Key Laboratory of Industrial Control Technology, Zhejiang University, Hangzhou, PR China
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13
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Innovative Diagnostic Technologies and Their Significance for Personalized Medicine. Mol Diagn Ther 2012; 14:141-7. [DOI: 10.1007/bf03256366] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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14
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Ceulemans S, van der Ven K, Del-Favero J. Targeted screening and validation of copy number variations. Methods Mol Biol 2012; 838:311-28. [PMID: 22228019 DOI: 10.1007/978-1-61779-507-7_15] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The accessibility of genome-wide screening technologies considerably facilitated the identification and characterization of copy number variations (CNVs). The increasing amount of available data describing these variants, clearly demonstrates their abundance in the human genome. This observation shows that not only SNPs, but also CNVs and other structural variants strongly contribute to genetic variation. Even though not all structural variants have an obvious phenotypic effect, there is evidence that CNVs influence gene dosage and hence can have profound effects on human disease susceptibility, disease manifestation, and disease severity. Therefore, CNV screening and analysis methodologies, specifically focusing on disease-related CNVs are actively progressing. This chapter specifically describes different techniques currently available for the targeted screening and validation of CNVs. We not only provide an overview of all these CNV analysis methods, but also address their strong and weak points. Methods covered include fluorescence in situ hybridization (FISH), quantitative real-time PCR (qPCR), paralogue ratio test (PRT), molecular copy-number counting (MCC), and multiplex PCR-based approaches, such as multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), multiplex PCR-based real-time invader assay (mPCR-RETINA), quantitative multiplex PCR of short fluorescent fragments (QMPSF), and multiplex amplicon quantification (MAQ). We end with some general remarks and conclusions, furthermore briefly addressing the future perspectives.
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Affiliation(s)
- Shana Ceulemans
- Applied Molecular Genomics Unit, VIB, Department of Molecular Genetics, Flanders, Belgium
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15
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Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang S, Stumbo DP, Hodges SP, Romine S, Milanovich FP, White HE, Regan JF, Karlin-Neumann GA, Hindson CM, Saxonov S, Colston BW. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 2011. [PMID: 22035192 DOI: 10.1021/ac202028g+[doi]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ~2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100,000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.
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Affiliation(s)
- Benjamin J Hindson
- Bio-Rad Laboratories, Inc., Pleasanton, California 94566, United States.
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16
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Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang S, Stumbo DP, Hodges SP, Romine S, Milanovich FP, White HE, Regan JF, Karlin-Neumann GA, Hindson CM, Saxonov S, Colston BW. High-throughput droplet digital PCR system for absolute quantitation of DNA copy number. Anal Chem 2011; 83:8604-10. [PMID: 22035192 PMCID: PMC3216358 DOI: 10.1021/ac202028g] [Citation(s) in RCA: 1852] [Impact Index Per Article: 142.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Accepted: 10/05/2011] [Indexed: 11/30/2022]
Abstract
Digital PCR enables the absolute quantitation of nucleic acids in a sample. The lack of scalable and practical technologies for digital PCR implementation has hampered the widespread adoption of this inherently powerful technique. Here we describe a high-throughput droplet digital PCR (ddPCR) system that enables processing of ~2 million PCR reactions using conventional TaqMan assays with a 96-well plate workflow. Three applications demonstrate that the massive partitioning afforded by our ddPCR system provides orders of magnitude more precision and sensitivity than real-time PCR. First, we show the accurate measurement of germline copy number variation. Second, for rare alleles, we show sensitive detection of mutant DNA in a 100,000-fold excess of wildtype background. Third, we demonstrate absolute quantitation of circulating fetal and maternal DNA from cell-free plasma. We anticipate this ddPCR system will allow researchers to explore complex genetic landscapes, discover and validate new disease associations, and define a new era of molecular diagnostics.
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Affiliation(s)
- Benjamin J Hindson
- Bio-Rad Laboratories, Inc., Pleasanton, California 94566, United States.
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17
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Hindson BJ, Ness KD, Masquelier DA, Belgrader P, Heredia NJ, Makarewicz AJ, Bright IJ, Lucero MY, Hiddessen AL, Legler TC, Kitano TK, Hodel MR, Petersen JF, Wyatt PW, Steenblock ER, Shah PH, Bousse LJ, Troup CB, Mellen JC, Wittmann DK, Erndt NG, Cauley TH, Koehler RT, So AP, Dube S, Rose KA, Montesclaros L, Wang S, Stumbo DP, Hodges SP, Romine S, Milanovich FP, White HE, Regan JF, Karlin-Neumann GA, Hindson CM, Saxonov S, Colston BW. High-Throughput Droplet Digital PCR System for Absolute Quantitation of DNA Copy Number. Anal Chem 2011. [DOI: 10.1021/ac202028g [doi]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Benjamin J. Hindson
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Kevin D. Ness
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Donald A. Masquelier
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Phillip Belgrader
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Nicholas J. Heredia
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Anthony J. Makarewicz
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Isaac J. Bright
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Michael Y. Lucero
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Amy L. Hiddessen
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Tina C. Legler
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Tyler K. Kitano
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Michael R. Hodel
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Jonathan F. Petersen
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Paul W. Wyatt
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Erin R. Steenblock
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Pallavi H. Shah
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Luc J. Bousse
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Camille B. Troup
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Jeffrey C. Mellen
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Dean K. Wittmann
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Nicholas G. Erndt
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Thomas H. Cauley
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Ryan T. Koehler
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Austin P. So
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Simant Dube
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Klint A. Rose
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Luz Montesclaros
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Shenglong Wang
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - David P. Stumbo
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Shawn P. Hodges
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Steven Romine
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Fred P. Milanovich
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Helen E. White
- National Genetics Reference Laboratory, Wessex Regional Genetics, Salisbury District Hospital, Odstock, Salisbury, Wiltshire, SP2 8BJ, United Kingdom
| | - John F. Regan
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - George A. Karlin-Neumann
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Christopher M. Hindson
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Serge Saxonov
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
| | - Bill W. Colston
- Bio-Rad Laboratories, Inc., 7068 Koll Center Parkway, Pleasanton, California 94566, United States
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18
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Pole JCM, McCaughan F, Newman S, Howarth KD, Dear PH, Edwards PAW. Single-molecule analysis of genome rearrangements in cancer. Nucleic Acids Res 2011; 39:e85. [PMID: 21525129 PMCID: PMC3141271 DOI: 10.1093/nar/gkr227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Rearrangements of the genome can be detected by microarray methods and massively parallel sequencing, which identify copy-number alterations and breakpoint junctions, but these techniques are poorly suited to reconstructing the long-range organization of rearranged chromosomes, for example, to distinguish between translocations and insertions. The single-DNA-molecule technique HAPPY mapping is a method for mapping normal genomes that should be able to analyse genome rearrangements, i.e. deviations from a known genome map, to assemble rearrangements into a long-range map. We applied HAPPY mapping to cancer cell lines to show that it could identify rearrangement of genomic segments, even in the presence of normal copies of the genome. We could distinguish a simple interstitial deletion from a copy-number loss at an inversion junction, and detect a known translocation. We could determine whether junctions detected by sequencing were on the same chromosome, by measuring their linkage to each other, and hence map the rearrangement. Finally, we mapped an uncharacterized reciprocal translocation in the T-47D breast cancer cell line to about 2 kb and hence cloned the translocation junctions. We conclude that HAPPY mapping is a versatile tool for determining the structure of rearrangements in the human genome.
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Affiliation(s)
- Jessica C M Pole
- Hutchison/MRC Research Centre and Department of Pathology, University of Cambridge, Hills Road, Cambridge, CB2 0XZ, UK
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19
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Saldanha G, Potter L, Dyall L, Bury D, Hathiari N, Ehdode A, Hollox E, Pringle JH. Detection of Copy Number Changes in DNA from Formalin Fixed Paraffin Embedded Tissues Using Paralogue Ratio Tests. Anal Chem 2011; 83:3484-92. [DOI: 10.1021/ac200153j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Gerald Saldanha
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
| | - Linda Potter
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
| | - Lovesh Dyall
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
| | - Danielle Bury
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
| | - Nisreen Hathiari
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
| | - Abdlrzag Ehdode
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
| | - Edward Hollox
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
| | - James Howard Pringle
- Department of Cancer Studies and Molecular Medicine, University of Leicester, LE2 7LX, United Kingdom
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20
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Abstract
Single-molecule sequencing enables DNA or RNA to be sequenced directly from biological samples, making it well-suited for diagnostic and clinical applications. Here we review the properties and applications of this rapidly evolving and promising technology.
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Affiliation(s)
- John F Thompson
- Helicos BioSciences Corporation, Building 200LL, One Kendall Square, Cambridge, MA 02139, USA.
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21
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Jain KK. Nanobiotechnology and personalized medicine. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 104:325-54. [PMID: 22093223 DOI: 10.1016/b978-0-12-416020-0.00008-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This chapter will start with a definition and scope of personalized medicine and describe how various nanobiotechnologies will contribute to its development. Nanodiagnostics and its combination with therapeutics as well as nanoparticle-based drug delivery will play an important role. The most important applications of nanobiotechnology will be personalized management of cancer, neurological disorders, and cardiovascular diseases.
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Affiliation(s)
- K K Jain
- Jain PharmaBiotech, Basel, Switzerland
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22
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Taylor BS, Ladanyi M. Clinical cancer genomics: how soon is now? J Pathol 2010; 223:318-26. [DOI: 10.1002/path.2794] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 09/17/2010] [Accepted: 09/21/2010] [Indexed: 12/14/2022]
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23
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Mitochondrial DNA variant discovery and evaluation in human Cardiomyopathies through next-generation sequencing. PLoS One 2010; 5:e12295. [PMID: 20808834 PMCID: PMC2924892 DOI: 10.1371/journal.pone.0012295] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 07/26/2010] [Indexed: 11/19/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In heteroplasmy there is a mixture of normal and mutant copies of mtDNA. The clinical phenotype of an affected individual depends on the type of genetic defect and the ratios of mutant and normal mtDNA in affected tissues. We aimed at determining the sensitivity of next-generation sequencing compared to Sanger sequencing for mutation detection in patients with mitochondrial cardiomyopathy. We studied 18 patients with mitochondrial cardiomyopathy and two with suspected mitochondrial disease. We “shotgun” sequenced PCR-amplified mtDNA and multiplexed using a single run on Roche's 454 Genome Sequencer. By mapping to the reference sequence, we obtained 1,300× average coverage per case and identified high-confidence variants. By comparing these to >400 mtDNA substitution variants detected by Sanger, we found 98% concordance in variant detection. Simulation studies showed that >95% of the homoplasmic variants were detected at a minimum sequence coverage of 20× while heteroplasmic variants required >200× coverage. Several Sanger “misses” were detected by 454 sequencing. These included the novel heteroplasmic 7501T>C in tRNA serine 1 in a patient with sudden cardiac death. These results support a potential role of next-generation sequencing in the discovery of novel mtDNA variants with heteroplasmy below the level reliably detected with Sanger sequencing. We hope that this will assist in the identification of mtDNA mutations and key genetic determinants for cardiomyopathy and mitochondrial disease.
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24
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Stapleton JA, Swartz JR. A cell-free microtiter plate screen for improved [FeFe] hydrogenases. PLoS One 2010; 5:e10554. [PMID: 20479937 PMCID: PMC2866662 DOI: 10.1371/journal.pone.0010554] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2010] [Accepted: 04/09/2010] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND [FeFe] hydrogenase enzymes catalyze the production and dissociation of H(2), a potential renewable fuel. Attempts to exploit these catalysts in engineered systems have been hindered by the biotechnologically inconvenient properties of the natural enzymes, including their extreme oxygen sensitivity. Directed evolution has been used to improve the characteristics of a range of natural catalysts, but has been largely unsuccessful for [FeFe] hydrogenases because of a lack of convenient screening platforms. METHODOLOGY/PRINCIPAL FINDINGS Here we describe an in vitro screening technology for oxygen-tolerant and highly active [FeFe] hydrogenases. Despite the complexity of the protocol, we demonstrate a level of reproducibility that allows moderately improved mutants to be isolated. We have used the platform to identify a mutant of the Chlamydomonas reinhardtii [FeFe] hydrogenase HydA1 with a specific activity approximately 4 times that of the wild-type enzyme. CONCLUSIONS/SIGNIFICANCE Our results demonstrate the feasibility of using the screen presented here for large-scale efforts to identify improved biocatalysts for energy applications. The system is based on our ability to activate these complex enzymes in E. coli cell extracts, which allows unhindered access to the protein maturation and assay environment.
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Affiliation(s)
- James A. Stapleton
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - James R. Swartz
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
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