1
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Mu H, Zou J, Zhang H. Simultaneous Extraction of Bone Marrow RNA and DNA from Patients with Hematologic Diseases Using a Combined Magnetic Bead Method within 1 Hour. J Appl Lab Med 2024; 9:1004-1013. [PMID: 39135431 DOI: 10.1093/jalm/jfae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 06/17/2024] [Indexed: 11/05/2024]
Abstract
BACKGROUND TRIzolTM is widely used for RNA and DNA extraction. However, this method is laborious and time-consuming. The objective of this study was to validate a time-effective and labor-saving protocol. METHODS The TRIzol method was used to separate the aqueous phase, protein, and phenol layer of bone marrow samples from 12 patients with hematological diseases. Subsequently, RNA and DNA were extracted from the aqueous layer containing RNA and phenol layer containing DNA, respectively, using magnetic bead extraction kits. The quantity and purity of extracted RNA and DNA were examined using a NanoDrop spectrophotometer. Quantitative fluorescence PCR amplification of the ABL1 gene was performed to verify the effectiveness of the extracted RNA and DNA for downstream experiments. RNA and DNA from another 16 bone marrow samples were extracted to compare the performance of the two methods. RESULTS Co-extraction of RNA and DNA was completed within 1 h. The data showed that RNA and DNA yield ranged from 13.1 to 204.5 ng/µL and 33.1 to 228.8 ng/µL, respectively. The A260/A280 ratios of RNA and DNA samples ranged from 1.82 to 2.01 and 1.73 to 1.91, respectively. RNA and DNA extracted using this scheme exhibited ideal performance in quantitative fluorescence PCR. The present protocol showed better quality and effectiveness in extracting RNA and DNA compared to the TRIzol method. CONCLUSIONS This protocol for RNA and DNA co-extraction is fast, labor-saving, and high throughput. It can be adopted for routine molecular biology analyses, particularly for non-reproducible specimens.
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Affiliation(s)
- Huijun Mu
- Department of Clinical Laboratory, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, P.R. China
| | - Jian Zou
- Department of Clinical Laboratory, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, P.R. China
| | - Haiping Zhang
- Department of Dermatology, Wuxi No. 2 People's Hospital, Wuxi, P.R. China
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2
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Evans DT, Nelson DJ, Pask ME, Haselton FR. A safer framework to evaluate characterization technologies of exhaled biologic materials using electrospun nanofibers. NANOSCALE 2023; 15:14822-14830. [PMID: 37655643 PMCID: PMC10530601 DOI: 10.1039/d3nr01859h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Exhaled biologic material is the source for the spread of many respiratory tract infections. To avoid the high-level of biosafety required to manage dangerous pathogens, we developed a safer framework using the endogenous surrogate targets RNase P and Streptococcus mitis as a means to sample exhaled biologics. Our exhalation collection scheme uses nanoscale fibrous poly(vinyl alcohol) substrates as facemask inserts. After a period of breathing or speaking, the inserts are removed and dissolved. RNase P RNA and S. mitis DNA are extracted for quantification by multiplexed RT-qPCR. Both surrogate biomarkers were detected in all samples obtained during breathing for at least five minutes or speaking for one minute. Phrases repeated 30 times had the most copies with 375 ± 247 of S. mitis and 54 ± 33 of RNase P. When the phrases were repeated just 5 times, the S. mitis copies collected were still detectable but at a significantly lower level of 11 ± 5 for S. mitis and 12 ± 9 for RNase P. These results demonstrate a collection and quantification framework that can be readily adapted to further characterize the exhalation of nanoscale biologic materials from healthy individuals, explore new collection designs safely, and serve as a method to incorporate sample controls for future pathogen exhalation studies.
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Affiliation(s)
- David T Evans
- Department of Biomedical Engineering, 5824 Stevenson Center, Vanderbilt University, Nashville, TN 37232, USA.
| | - Dalton J Nelson
- Department of Biomedical Engineering, 5824 Stevenson Center, Vanderbilt University, Nashville, TN 37232, USA.
| | - Megan E Pask
- Department of Biomedical Engineering, 5824 Stevenson Center, Vanderbilt University, Nashville, TN 37232, USA.
| | - Frederick R Haselton
- Department of Biomedical Engineering, 5824 Stevenson Center, Vanderbilt University, Nashville, TN 37232, USA.
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3
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Politza AJ, Liu T, Guan W. Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need. LAB ON A CHIP 2023; 23:3882-3892. [PMID: 37551930 PMCID: PMC11218199 DOI: 10.1039/d3lc00545c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These processes are critical for ensuring the accuracy and sensitivity of downstream nucleic acid amplification and detection. However, current sample preparation methods are often laboratory-based, requiring specialized equipment, trained personnel, and several hours of processing time. As a result, sample preparation often limits the speed, portability, and cost-effectiveness of point-of-need nucleic acid testing. A universal, field-deployable sample preparation device is highly desirable for this critical need and unmet challenge. Here we reported a handheld, battery-powered, reconfigurable, and field-deployable nucleic acid sample preparation device. A programmable electromagnetic actuator was developed to drive a magnetic robot (ProMagBot) in X/Y 2D space, such that various magnetic bead-based sample preparations can be readily translated from the laboratory to point-of-need settings. The control of the electromagnetic actuator requires only a 3-phase unipolar voltage in X and Y directions, and therefore, the motion space is highly scalable. We validated the ProMagBot device with a model application by extracting HIV viral RNAs from plasma samples using two widely used magnetic bead kits: ChargeSwitch and MagMAX beads. In both cases, the ProMagBot could successfully extract viral RNAs from 50 μL plasma samples containing as low as 102 copies of viral RNAs in 20 minutes. Our results demonstrated the ability of ProMagBot to prepare samples from complex mediums at the point of need. We believe such a device would enable rapid and robust sample preparation in various settings, including resource-limited or remote environments, and accelerate the development of next-generation point-of-need nucleic acid testing.
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Affiliation(s)
- Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
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4
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Liu F, Hu L, Sheng J, Sun Y, Xia Q, Tang Y, Jiang P, Wei S, Hu J, Lin H, Xu Z, Guo W, Gu Y, Feng N. Can antibiotics for enteritis or for urinary tract infection disrupt the urinary microbiota in rats? Front Cell Infect Microbiol 2023; 13:1169909. [PMID: 37448775 PMCID: PMC10338079 DOI: 10.3389/fcimb.2023.1169909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 05/08/2023] [Indexed: 07/15/2023] Open
Abstract
Background To establish antibiotic preregimes and administration routes for studies on urinary microbiota. Methods and materials Antibiotics for enteritis (Abx-enteritis) and UTIs (Abx-UTI) were administered via gavage and/or urinary catheterisation (UC) for 1 and/or 2 weeks. The effects of these Abx on the urinary microbiota of rats were examined via 16S rRNA sequencing and urine culture, including anaerobic and aerobic culture. Additionally, the safety of the Abx was examined. Results Abx-enteritis/Abx-UTI (0.5 g/L and 1 g/L) administered via gavage did not alter the microbial community and bacterial diversity in the urine of rats (FDR > 0.05); however, Abx-UTI (1 g/L) administered via UC for 1 and 2 weeks altered the urinary microbial community (FDR < 0.05). Rats administered Abx-UTI (1 g/L) via UC for 1 week demonstrated a distinct urinary microbiota in culture. Abx-enteritis/Abx-UTI administered via gavage disrupted the microbial community and reduced bacterial diversity in the faeces of rats (FDR < 0.05), and Abx-UTI administered via UC for 2 weeks (FDR < 0.05) altered the fecal microbiota. Abx-UTI (1 g/L) administered via UC did not alter safety considerations. In addition, we noticed that UC did not induce infections and injuries to the bladder and kidney tissues. Conclusions Administration of Abx-UTI via UC for 1 week can be considered a pre-treatment option while investigating the urinary microbiota.
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Affiliation(s)
- Fengping Liu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
- Jiangnan University Medical Center, Wuxi, Jiangsu, China
| | - Lei Hu
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Jiayi Sheng
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yifan Sun
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Qiang Xia
- Department of Urology, Wuxi 9 People’s Hospital Affiliated to Soochow University, Wuxi, Jiangsu, China
| | - Yifan Tang
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Peng Jiang
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Shichao Wei
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Jialin Hu
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Hao Lin
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Zhenyi Xu
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Wei Guo
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
| | - Yifeng Gu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, School of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ninghan Feng
- Department of Urology, Affiliated Wuxi No. 2 Hospital, Nanjing Medical University, Wuxi, Jiangsu, China
- Jiangnan University Medical Center, Wuxi, Jiangsu, China
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5
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Liu W, Lee LP. Toward Rapid and Accurate Molecular Diagnostics at Home. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2206525. [PMID: 36416278 DOI: 10.1002/adma.202206525] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/14/2022] [Indexed: 05/26/2023]
Abstract
The global outbreaks of infectious diseases have significantly driven an imperative demand for rapid and accurate molecular diagnostics. Nucleic acid amplification tests (NAATs) feature high sensitivity and high specificity; however, the labor-intensive sample preparation and nucleic acid amplification steps remain challenging in order to carry out rapid and precision molecular diagnostics at home. This review discusses the advances and challenges of automatic solutions of sample preparation integrated with on-chip nucleic acid amplification for effective and accurate molecular diagnostics at home. The sample preparation methods of whole blood, urine, saliva/nasal swab, and stool on chip are examined. Then, the repurposable integrated sample preparation on a chip using various biological samples is investigated. Finally, the on-chip NAATs that can be integrated with automated sample preparation are evaluated. The user-friendly approaches with combined sample preparation and NAATs can be the game changers for next-generation rapid and precision home diagnostics.
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Affiliation(s)
- Wenpeng Liu
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
| | - Luke P Lee
- Harvard Medical School, Harvard University, Boston, MA, 02115, USA
- Division of Engineering in Medicine and Renal Division, Department of Medicine, Brigham Women's Hospital, Boston, MA, 02115, USA
- Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, CA, 94720, USA
- Department of Biophysics, Institute of Quantum Biophysics, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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6
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Rodriguez-Mateos P, Ngamsom B, Iles A, Pamme N. Microscale immiscible phase magnetic processing for bioanalytical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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7
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Trumpff C, Rausser S, Haahr R, Karan KR, Gouspillou G, Puterman E, Kirschbaum C, Picard M. Dynamic behavior of cell-free mitochondrial DNA in human saliva. Psychoneuroendocrinology 2022; 143:105852. [PMID: 35834882 PMCID: PMC9880596 DOI: 10.1016/j.psyneuen.2022.105852] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/20/2022] [Accepted: 06/23/2022] [Indexed: 01/31/2023]
Abstract
Mitochondria contain their own genome that can be released in multiple biofluids such as blood and cerebrospinal fluid, as cell-free mitochondrial DNA (cf-mtDNA). In clinical studies, blood cf-mtDNA predicts mortality and higher cf-mtDNA levels are associated with mental and physical stress. However, the dynamics of cf-mtDNA has not been defined, and whether it can be measured non-invasively like other neuroendocrine markers in saliva has not been examined. Here we report cf-mtDNA in human saliva and establish its natural within-person dynamic behavior across multiple weeks. In a small proof-of-principle cohort of healthy adults, we first develop an approach to rapidly quantify salivary cf-mtDNA without DNA isolation, and demonstrate the existence of salivary cf-mtDNA. We then deploy this approach to perform an intensive repeated-measures analysis of two healthy men studied at 4 daily timepoints over 53-60 consecutive days (n = 212-220 observations each) with parallel measures of steroid hormones, self-reported daily mood, and health-related behaviors. Salivary cf-mtDNA exhibited a robust awakening response reaching up to two orders of magnitude 30-45 min after awakening, varied from day-to-day, and moderately correlated with the cortisol awakening response. In exploratory analyses, no consistent association with self-reported daily mood/health-related behaviors were found, although this requires further examination in future studies. Dynamic variation in cf-mtDNA was inversely related with salivary interleukin 6 (IL-6), inconsistent with a pro-inflammatory effect of salivary cf-mtDNA. The highly dynamic behavior of salivary cf-mtDNA opens the door to non-invasive studies examining the relevance of mtDNA signaling in relation to human health.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Shannon Rausser
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Rachel Haahr
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Gilles Gouspillou
- Département des Sciences de l'Activité Physique, Faculté des Sciences, Université du Québec à Montréal (UQAM), Montreal, Québec, Canada
| | - Eli Puterman
- School of Kinesiology, University of British Columbia, Vancouver, Canada
| | | | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA; Department of Neurology, H. Houston Merritt Center, Columbia University Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, USA; New York State Psychiatric Institute, New York, USA.
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8
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Magnetic Nylon 6 Nanocomposites for the Microextraction of Nucleic Acids from Biological Samples. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8080085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Magnetic Fe3O4 nanoparticles (MNPs) have great potential for nucleic acid separation, detection, and delivery. MNPs are considered a valuable tool in biomedicine due to their cost-effectiveness, stability, easy surface functionalization, and the possibility of the manipulations under a magnetic field. Herein, the synthesis of magnetic nylon 6 nanocomposites (MNPs@Ny6) was investigated. Transmission electron microscopy (TEM) was used for morphology and size analysis. A new method of UV-induced immobilization of oligonucleotides on MNPs@Ny6 for nucleic acid magnetic separation was proposed. MNPs@Ny6 shows a high oligonucleotide binding capacity of 2.2 nmol/mg with 73.3% loading efficiency. The proposed system has been applied to analyze model mixtures of target RNA on the total yeast RNA background. The RNA target isolation efficiency was 60% with high specificity. The bind RNA release was 88.8% in a quantity of 0.16 nmol/mg. The total RNA capture efficiency was 53%. Considering this, the MNPs@Ny6 is an attractive candidate for nucleic acids-specific magnetic isolation.
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9
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Khimova E, Gonzalo X, Popova Y, Eliseev P, Andrey M, Nikolayevskyy V, Broda A, Drobniewski F. Urine biomarkers of pulmonary tuberculosis. Expert Rev Respir Med 2022; 16:615-621. [PMID: 35702997 DOI: 10.1080/17476348.2022.2090341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Sputum-based tuberculosis diagnosis does not address the needs of certain categories of patients. Active development of a noninvasive urine-based diagnosis could provide an alternative approach. We reviewed publications covering more than 30 urine biomarkers proposed as significant for TB diagnosis. Analytical approaches were heterogeneous in design and methods; few studies on diagnostic outcome prediction described a formal specificity and sensitivity analysis. AREAS COVERED This review describes studies of non-sputum diagnostic approaches of pulmonary TB based on urine using specific TB biomarkers. The search was performed until December 2021, using terms [Tuberculosis] + [urine] + [biomarkers] in PubMed and Cochrane databases. Publications concerning LAM urine diagnostics were excluded as they have been described elsewhere. EXPERT OPINION Microbiological culture of sputum is considered to be the 'gold standard' diagnostic for pulmonary TB but the methodology is slow due to the slow growth of the TB bacteria. Urine provides a large volume of sample. Investigators have evaluated urine for either TB pathogen biomarkers or host biomarkers with some success as the review demonstrates. Detection sensitivity remains a significant problem. In future, combination of host and pathogen biomarkers could increase the sensitivity and specificity of TB diagnosis.
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Affiliation(s)
- Elena Khimova
- Department of Phthisiopulmonology, Northern State Medical University, Arkhangelsk, Russia
| | - Ximena Gonzalo
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Yulia Popova
- Department of Phthisiopulmonology, Northern State Medical University, Arkhangelsk, Russia
| | - Platon Eliseev
- Department of Phthisiopulmonology, Northern State Medical University, Arkhangelsk, Russia
| | - Maryandyshev Andrey
- Department of Phthisiopulmonology, Northern State Medical University, Arkhangelsk, Russia
| | | | - Agnieszka Broda
- Department of Infectious Diseases, Imperial College London, London, UK
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10
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Zimmers ZA, Adams NM, Haselton FR. Addition of mirror-image L-DNA elements to DNA amplification circuits to distinguish leakage from target signal. Biosens Bioelectron 2021; 188:113354. [PMID: 34034212 DOI: 10.1016/j.bios.2021.113354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
DNA amplification circuits that rely on thermodynamically-driven hybridization events triggered by a target nucleic acid are becoming increasingly utilized due to their relative simplicity. A drawback of these circuits is that non-specific amplification, or circuit leakage, must be estimated using a separate "no-target" control reaction to eliminate false positives. Aside from requiring an additional reaction, the problem with this approach is the difficulty of creating a no-target control for biological specimens. To overcome this limitation, we propose a strategy that combines both reactions into the same tube using naturally-occurring right-handed D-DNA circuit elements for the target detection reaction and identical synthetic mirror-image left-handed L-DNA circuit elements for the no-target control reaction. We illustrate this approach using catalyzed hairpin assembly (CHA), one of the most studied DNA amplification circuits. In a dual-chirality CHA design, the right-handed circuit signal is produced by target-specific amplification and circuit leakage, whereas the left-handed circuit signal is produced only by circuit leakage. The target-specific amplification is calculated as the difference between the two signals. The limit of detection of this dual-chirality CHA reaction was found to be similar to that of traditional CHA (81 vs 92 pM, respectively). Furthermore, the left-handed no-target signal matched the right-handed leakage across a wide range of sample conditions including background DNA, increased salt concentration, increased temperature, and urine. These results demonstrate the robustness of a dual-chirality design and the potential utility of left-handed DNA in the development of new DNA amplification circuits better-suited for target detection applications in biological samples.
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Affiliation(s)
- Zackary A Zimmers
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Nicholas M Adams
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, 37240, USA.
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11
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Hu J, Wei Z, Kowalchuk GA, Xu Y, Shen Q, Jousset A. Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development. Environ Microbiol 2020; 22:5005-5018. [PMID: 32458448 DOI: 10.1111/1462-2920.15097] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/18/2020] [Accepted: 05/23/2020] [Indexed: 11/29/2022]
Abstract
The rhizosphere microbiome is essential for plant growth and health, and numerous studies have attempted to link microbiome functionality to species and trait composition. However, to date little is known about the actual ecological processes shaping community composition, complicating attempts to steer microbiome functionality. Here, we assess the development of microbial life history and community-level species interaction patterns that emerge during plant development. We use microbial phenotyping to experimentally test the development of niche complementarity and life history traits linked to microbiome performance. We show that the rhizosphere microbiome assembles from pioneer assemblages of species with random resource overlap into high-density, functionally complementary climax communities at later stages. During plant growth, fast-growing species were further replaced by antagonistic and stress-tolerant ones. Using synthetic consortia isolated from different plant growth stages, we demonstrate that the high functional diversity of 'climax' microbiomes leads to a better resistance to bacterial pathogen invasion. By demonstrating that different life-history strategies prevail at different plant growth stages and that community-level processes may supersede the importance of single species, we provide a new toolbox to understand microbiome assembly and steer its functionality at a community level.
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Affiliation(s)
- Jie Hu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, People's Republic of China
| | - George A Kowalchuk
- Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Yangchun Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, People's Republic of China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, People's Republic of China
| | - Alexandre Jousset
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, Key Lab of Plant Immunity, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Weigang 1, Nanjing, 210095, People's Republic of China.,Institute for Environmental Biology, Ecology and Biodiversity, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
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12
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Chen Y, Liu Y, Shi Y, Ping J, Wu J, Chen H. Magnetic particles for integrated nucleic acid purification, amplification and detection without pipetting. Trends Analyt Chem 2020; 127:115912. [PMID: 32382202 PMCID: PMC7202819 DOI: 10.1016/j.trac.2020.115912] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleic acid amplification based detection plays an important role in food safety, environmental monitoring and clinical diagnosis. However, traditional nucleic acid detection process involves transferring liquid from one tube to another by pipetting. It requires trained persons, equipped labs and consumes lots of time. The ideal nucleic acid detection is integrated, closed, simplified and automated. Magnetic particles actuated by magnetic fields can efficiently adsorb nucleic acids and promote integrated nucleic acid assays without pipetting driven by pumps and centrifuges. We will comprehensively review magnetic particles assisted integrated system for nucleic acid detection and hope it can inspire further related study.
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Key Words
- ATP, adenosine triphosphate
- DLS, dynamic light scattering
- FMR, ferromagnetic resonance
- GTC, guanidinium thiocyanate
- ICP-AES, inductively coupled plasma atomic emission spectroscopy
- IFAST, immiscible filtration assisted by surface tension
- Immiscible interface
- Integrated detection
- LAMP, loop-mediated isothermal amplification
- Magnetic particles
- Nucleic acid
- PCR, polymerase chain reaction
- PEG, polyethylene glycol
- POCT, point-of-care testing
- RPA, recombinase polymerase amplification
- SQUID, superconducting quantum interference device magnetometer
- TEM, transmission electron microscopy
- XRD, X-Ray diffraction
- qPCR, quantitative PCR
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Affiliation(s)
- Yanju Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Yang Liu
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Ya Shi
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
- Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China
| | - Huan Chen
- Key Laboratory of Microbiol Technology and Bioinformatics of Zhejiang Province, Zhejiang Institute of Microbiology, Hangzhou, 310012, China
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13
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Lee EY, Lee EJ, Yoon H, Lee DH, Kim KH. Comparison of Four Commercial Kits for Isolation of Urinary Cell-Free DNA and Sample Storage Conditions. Diagnostics (Basel) 2020; 10:diagnostics10040234. [PMID: 32325682 PMCID: PMC7236016 DOI: 10.3390/diagnostics10040234] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/16/2020] [Accepted: 04/16/2020] [Indexed: 12/25/2022] Open
Abstract
Urinary cell-free DNA (cfDNA) is an attractive body fluid for liquid biopsy. In this study, we compared the efficiencies of four commercial kits for urinary cell-free DNA (cfDNA) isolation and of various sample storage conditions. Urinary cfDNA was isolated from 10 healthy individuals using four commercial kits: QIAamp Circulating Nucleic Acid Kit (QC; Qiagen), MagMAX™ Cell-Free DNA Isolation Kit (MM; Applied Biosystems), Urine Cell-Free Circulating DNA Purification Midi Kit (NU; Norgen Biotek), and Quick-DNA™ Urine Kit (ZQ; Zymo Research). To assess the isolation efficiency, an Agilent 2100 Bioanalyzer with High Sensitivity DNA chips was used, and cfDNA yield was defined as the amount of cfDNA obtained from 1 mL of urine. MM and QC provided the highest cfDNA yield in the 50–300 bp range, and MM and NU gave the highest cfDNA yield in the 50–100 bp range. In particular, the NU kit was efficient for isolation of more fragmented cfDNA in the range of 50–100 bp with the lowest cellular genomic DNA contamination. ZQ had the best cost-efficiency for isolating the same amount of urinary cfDNA. Samples stored at −70 °C with the addition of 10 mM EDTA resulted in the highest cfDNA yield 3 months after sample collection.
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Affiliation(s)
- Eun Young Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Eun-Ju Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Ewha Medical Research Institute, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Hana Yoon
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Dong Hyeon Lee
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
| | - Kwang Hyun Kim
- Department of Urology, College of Medicine, Ewha Womans University, Seoul 07804, Korea; (E.Y.L.); (E.-J.L.); (H.Y.); (D.H.L.)
- Correspondence: ; Tel.: +82-2-6986-1685; Fax: +82-2-6986-3258
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14
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Pearlman S, Leelawong M, Richardson KA, Adams NM, Russ PK, Pask ME, Wolfe AE, Wessely C, Haselton FR. Low-Resource Nucleic Acid Extraction Method Enabled by High-Gradient Magnetic Separation. ACS APPLIED MATERIALS & INTERFACES 2020; 12:12457-12467. [PMID: 32039572 PMCID: PMC7082792 DOI: 10.1021/acsami.9b21564] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/10/2020] [Indexed: 05/26/2023]
Abstract
Nucleic acid-based diagnostic tests often require isolation and concentration of nucleic acids from biological samples. Commercial purification kits are difficult to use in low-resource settings because of their cost and insufficient laboratory infrastructure. Several recent approaches based on the use of magnetic beads offer a potential solution but remain limited to small volume samples. We have developed a simple and low-cost nucleic acid extraction method suitable for isolation and concentration of nucleic acids from small or large sample volumes. The method uses magnetic beads, a transfer pipette, steel wool, and an external magnet to implement high-gradient magnetic separation (HGMS) to retain nucleic acid-magnetic bead complexes within the device's steel wool matrix for subsequent processing steps. We demonstrate the method's utility by extracting tuberculosis DNA from both sputum and urine, two typical large volume sample matrices (5-200 mL), using guanidine-based extraction chemistry. Our HGMS-enabled extraction method is statistically indistinguishable from commercial extraction kits when detecting a spiked 123-base DNA sequence. For our HGMS-enabled extraction method, we obtained extraction efficiencies for sputum and urine of approximately 10 and 90%, whereas commercial kits obtained 10-17 and 70-96%, respectively. We also used this method previously in a blinded sample preparation comparison study published by Beall et al., 2019. Our manual extraction method is insensitive to high flow rates and sample viscosity, with capture of ∼100% for flow rates up to 45 mL/min and viscosities up to 55 cP, possibly making it suitable for a wide variety of sample volumes and types and point-of-care users. This HGMS-enabled extraction method provides a robust instrument-free method for magnetic bead-based nucleic acid extraction, potentially suitable for field implementation of nucleic acid testing.
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Affiliation(s)
- Stephanie
I. Pearlman
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Mindy Leelawong
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kelly A. Richardson
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Nicholas M. Adams
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Patricia K. Russ
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Megan E. Pask
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Anna E. Wolfe
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Cassandra Wessely
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R. Haselton
- Department
of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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15
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Chatterjee T, Li Z, Khanna K, Montoya K, Tewari M, Walter NG, Johnson-Buck A. Ultraspecific analyte detection by direct kinetic fingerprinting of single molecules. Trends Analyt Chem 2020; 123:115764. [PMID: 32863484 PMCID: PMC7451408 DOI: 10.1016/j.trac.2019.115764] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The detection and quantification of biomarkers have numerous applications in biological research and medicine. The most widely used methods to detect nucleic acids require amplification via the polymerase chain reaction (PCR). However, errors arising from the imperfect copying fidelity of DNA polymerases, limited specificity of primers, and heat-induced damage reduce the specificity of PCR-based methods, particularly for single-nucleotide variants. Furthermore, not all analytes can be amplified efficiently. While amplification-free methods avoid these pitfalls, the specificity of most such methods is strictly constrained by probe binding thermodynamics, which for example hampers detection of rare somatic mutations. In contrast, single-molecule recognition through equilibrium Poisson sampling (SiMREPS) provides ultraspecific detection with single-molecule and single-nucleotide sensitivity by monitoring the repetitive interactions of a fluorescent probe with surface-immobilized targets. In this review, we discuss SiMREPS in comparison with other analytical approaches, and describe its utility in quantifying a range of nucleic acids and other analytes.
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Affiliation(s)
- Tanmay Chatterjee
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zi Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kunal Khanna
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Karen Montoya
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
- Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nils G Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alexander Johnson-Buck
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan 48109, United States
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16
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Raimondo TM, McCalla SE. Adsorption and desorption of DNA-functionalized beads in glass microfluidic channels. BIOMICROFLUIDICS 2019; 13:054104. [PMID: 31592058 PMCID: PMC6768795 DOI: 10.1063/1.5115160] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Integrated microfluidic devices for the purification, amplification, and detection of nucleic acids are a prevalent area of research due to their potential for miniaturization, assay integration, and increased efficiency over benchtop assays. These devices frequently contain micrometer-sized magnetic beads with a large surface area for the capture and manipulation of biological molecules such as DNA and RNA. Although magnetic beads are a standard tool for many biological assays, beads functionalized with biological molecules can adhere to microchannel walls and prevent further manipulation of the beads within the channel. Here, we analyze the effects of solution composition, microchannel hydrophobicity, and bead surface hydrophobicity on DNA-functionalized bead adhesion in a borosilicate glass microfluidic device. Bead adhesion is primarily a result of adsorption of the bead-linked DNA molecule to the microchannel wall; >81% of beads are consistently removed when not functionalized with DNA. Hydrophobicities of both the microchannel walls and the microbead surface are the primary determinants of bead adhesion, rather than electrostatic interactions and ion bridging. Surprisingly, DNA-functionalized bead adhesion in a standard RNA amplification solution was virtually eliminated by using hydrophobic microbeads with hydrophobic microchannel walls; under such conditions, 96.6 ± 1.6% of the beads were removed in one 43 nl/s, 10-min wash. The efficiency of a downstream RNA amplification reaction using DNA-functionalized beads did not appear to be affected by the hydrophobicity of the microbead surface. These findings can be applied to assays that require the efficient use of magnetic beads in DNA-based microfluidic assays.
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Affiliation(s)
- Theresa M. Raimondo
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Stephanie E. McCalla
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana 59717, USA
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17
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Park HJ, Cho H, Jung HS, Cho BH, Lee MY. Development of a DNA isolation device using poly(3,4-dihydroxy-L-phenylalanine)-coated swab for on-site molecular diagnostics. Sci Rep 2019; 9:8144. [PMID: 31148558 PMCID: PMC6544620 DOI: 10.1038/s41598-019-44527-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/15/2019] [Indexed: 12/19/2022] Open
Abstract
For on-site molecular diagnostics, a pre-treatment step for isolation of nucleic acid from clinical samples on site is desired. However, conventional commercialized silica-based nucleic acid isolation kits require repetitive pipetting and a centrifugation or permanent magnet for buffer exchange. In this study, we developed a poly(3,4-dihydroxy-L-phenylalanine) (L-DOPA)-coated swab that can absorb and desorb DNA depending on pH of buffers and a portable integrated DNA isolation device that comprises integrated chambers containing DNA isolation buffers. The poly(L-DOPA)-coated swab interacts with each buffer by passing through the membrane between the integrated chambers. Our device involves a simple operation and does not require any large equipment or skilled experts. By connecting the device with an automated polymerase chain reaction system, an isothermal amplification system, or a non-amplified DNA detection method, on-site molecular diagnosis of various diseases can be quickly realized.
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Affiliation(s)
- Hyun-Ju Park
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, 06351, Korea
| | - Heesoo Cho
- Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, 81, Irwon-ro, Gangnam-gu, Seoul, 06351, Korea
| | - Ho Sang Jung
- Advanced Nano-Surface Department, Korea Institute of Materials Science (KIMS), Changwon, Gyeongnam, 51508, Republic of Korea
| | - Baek Hwan Cho
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, 06351, Korea. .,Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, 81, Irwon-ro, Gangnam-gu, Seoul, 06351, Korea.
| | - Min-Young Lee
- Department of Medical Device Management and Research, Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Sungkyunkwan University, Seoul, 06351, Korea. .,Smart Healthcare Research Institute, Biomedical Engineering Research Center, Samsung Medical Center, 81, Irwon-ro, Gangnam-gu, Seoul, 06351, Korea.
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18
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Zhang H, Huang F, Cai G, Li Y, Lin J. Rapid and sensitive detection of Escherichia coli O157:H7 using coaxial channel-based DNA extraction and microfluidic PCR. J Dairy Sci 2018; 101:9736-9746. [DOI: 10.3168/jds.2018-14730] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 07/21/2018] [Indexed: 01/09/2023]
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19
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Masters C, Dolphin J, Maschmann A, McGill K, Moore M, Thompson D, Kounovsky-Shafer KL. Development of 3D printed mesofluidic devices to elute and concentrate DNA. Electrophoresis 2018; 40:810-816. [PMID: 30367503 DOI: 10.1002/elps.201800309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 11/08/2022]
Abstract
To understand structural variation for personal genomics, an extensive ensemble of large DNA molecules will be required to span large structural variations. Nanocoding, a whole-genome analysis platform, can analyze large DNA molecules for the construction of physical restriction maps of entire genomes. However, handling of large DNA is difficult and a system is needed to concentrate large DNA molecules, while keeping the molecules intact. Insert technology was developed to protect large DNA molecules during routine cell lysis and molecular biology techniques. However, eluting and concentrating DNA molecules has been difficult in the past. Utilizing 3D printed mesofluidic device, a proof of principle system was developed to elute and concentrate lambda DNA molecules at the interface between a solution and a poly-acrylamide roadblock. The matrix allowed buffer solution to move through the pores in the matrix; however, it slowed down the progression of DNA in the matrix, since the molecules were so large and the pore size was small. Using fluorescence intensity of the insert, 84% of DNA was eluted from the insert and 45% of DNA was recovered in solution from the eluted DNA. DNA recovered was digested with a restriction enzyme to determine that the DNA molecules remained full length during the elution and concentration of DNA.
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Affiliation(s)
- Cody Masters
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Jocelyn Dolphin
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - April Maschmann
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Keegan McGill
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Matthew Moore
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
| | - Drew Thompson
- Department of Chemistry, University of Nebraska - Kearney, Kearney, NE, 68849, USA
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20
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Plasmid-normalized quantification of relative mitochondrial DNA copy number. Sci Rep 2018; 8:15347. [PMID: 30337569 PMCID: PMC6194030 DOI: 10.1038/s41598-018-33684-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/02/2018] [Indexed: 02/08/2023] Open
Abstract
Alterations of mitochondrial DNA (mtDNA) copy number have been associated with a wide variety of phenotypes and diseases. Unfortunately, the literature provides scarce methodical information about duplex targeting of nuclear and mtDNA that meets the quality criteria for qPCR. Therefore, we established a method for mtDNA copy number quantification using a quantitative PCR assay that allows for simultaneous targeting of a single copy nuclear gene (beta-2-microglobulin) and the t-RNALeu gene on the mtDNA. We include a plasmid containing both targets in order to normalize against differences in emission intensities of the fluorescent dyes Yakima Yellow and FAM. Applying the plasmid calibrator on an internal control reduced the intra-assay variability from 21% (uncorrected) to 7% (plasmid-corrected). Moreover, we noted that DNA samples isolated with different methods revealed different numbers of mtDNA copies, thus highlighting an important influence of the pre-analytical procedures. In summary, we developed a precise assay for mitochondrial copy number detection relative to nuclear DNA. Our method is applicable to comparative mitochondrial DNA copy number studies since the use of the dual insert plasmid allows correcting for the unequal emission intensities of the different fluorescent labels of the two targets.
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21
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Uehara M. Development of a Novel and Rapid Fully Automated Genetic Testing System. ANAL SCI 2018; 32:1375-1379. [PMID: 27941272 DOI: 10.2116/analsci.32.1375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have developed a rapid genetic testing system integrating nucleic acid extraction, purification, amplification, and detection in a single cartridge. The system performs real-time polymerase chain reaction (PCR) after nucleic acid purification in a fully automated manner. RNase P, a housekeeping gene, was purified from human nasal epithelial cells using silica-coated magnetic beads and subjected to real-time PCR using a novel droplet-real-time-PCR machine. The process was completed within 13 min. This system will be widely applicable for research and diagnostic uses.
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Affiliation(s)
- Masayuki Uehara
- Core Technology Development Center, Corporate Research and Development Div., Seiko Epson Corporation
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22
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Scherr TF, Markwalter CF, Bauer WS, Gasperino D, Wright DW, Haselton FR. Application of mass transfer theory to biomarker capture by surface functionalized magnetic beads in microcentrifuge tubes. Adv Colloid Interface Sci 2017; 246:275-288. [PMID: 28595937 DOI: 10.1016/j.cis.2017.02.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 02/15/2017] [Accepted: 02/15/2017] [Indexed: 12/11/2022]
Abstract
In many diagnostic assays, specific biomarker extraction and purification from a patient sample is performed in microcentrifuge tubes using surface-functionalized magnetic beads. Although assay binding times are known to be highly dependent on sample viscosity, sample volume, capture reagent, and fluid mixing, the theoretical mass transport framework that has been developed and validated in engineering has yet to be applied in this context. In this work, we adapt this existing framework for simultaneous mass transfer and surface reaction and apply it to the binding of biomarkers in clinical samples to surface-functionalized magnetic beads. We discuss the fundamental fluid dynamics of vortex mixing within microcentrifuge tubes as well as describe how particles and biomolecules interact with the fluid. The model is solved over a wide range of parameters, and we present scenarios when a simplified analytical expression would be most accurate. Next, we review of some relevant techniques for model parameter estimation. Finally, we apply the mass transfer theory to practical use-case scenarios of immediate use to clinicians and assay developers. Throughout, we highlight where further characterization is necessary to bridge the gap between theory and practical application.
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23
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Design and use of mouse control DNA for DNA biomarker extraction and PCR detection from urine: Application for transrenal Mycobacterium tuberculosis DNA detection. J Microbiol Methods 2017; 136:65-70. [PMID: 28285168 DOI: 10.1016/j.mimet.2017.02.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/24/2017] [Indexed: 11/22/2022]
Abstract
Urine samples are increasingly used for diagnosing infections including Escherichia coli, Ebola virus, and Zika virus. However, extraction and concentration of nucleic acid biomarkers from urine is necessary for many molecular detection strategies such as polymerase chain reaction (PCR). Since urine samples typically have large volumes with dilute biomarker concentrations making them prone to false negatives, another impediment for urine-based diagnostics is the establishment of appropriate controls particularly to rule out false negatives. In this study, a mouse glyceraldehyde 3-phosphate dehydrogenase (GAPDH) DNA target was added to retrospectively collected urine samples from tuberculosis (TB)-infected and TB-uninfected patients to indicate extraction of intact DNA and removal of PCR inhibitors from urine samples. We tested this design on surrogate urine samples, retrospective 1milliliter (mL) urine samples from patients in Lima, Peru and retrospective 5mL urine samples from patients in Cape Town, South Africa. Extraction/PCR control DNA was detectable in 97% of clinical samples with no statistically significant differences among groups. Despite the inclusion of this control, there was no difference in the amount of TB IS6110 Tr-DNA detected between TB-infected and TB-uninfected groups except for samples from known HIV-infected patients. We found an increase in TB IS6110 Tr-DNA between TB/HIV co-infected patients compared to TB-uninfected/HIV-infected patients (N=18, p=0.037). The inclusion of an extraction/PCR control DNA to indicate successful DNA extraction and removal of PCR inhibitors should be easily adaptable as a sample preparation control for other acellular sample types.
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24
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Munaz A, Kamble H, Shiddiky MJA, Nguyen NT. Magnetofluidic micromixer based on a complex rotating magnetic field. RSC Adv 2017. [DOI: 10.1039/c7ra08073e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We report a magnetically actuated micromixer for mixing non-magnetic microparticles in a microfluidic system.
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Affiliation(s)
- Ahmed Munaz
- Queensland Micro- and Nanotechnology Centre
- Griffith University
- Brisbane
- Australia
| | - Harshad Kamble
- Queensland Micro- and Nanotechnology Centre
- Griffith University
- Brisbane
- Australia
| | - Muhammad J. A. Shiddiky
- Queensland Micro- and Nanotechnology Centre
- Griffith University
- Brisbane
- Australia
- School of Natural Sciences
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre
- Griffith University
- Brisbane
- Australia
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25
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Uehara M, Hanamura M, Yamada K, Yamaguchi A, Murayama T, Saito Y, Idegami K, Honda T. A Rapid and Automated Device for Purifying Nucleic Acids. ANAL SCI 2016; 32:371-4. [PMID: 26960621 DOI: 10.2116/analsci.32.371] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We have developed a rapid, automated nucleic acid purification device in a single cartridge containing silica-coated magnetic beads. We succeeded in extracting the matrix protein gene of influenza A virus from pharyngeal swab samples within 3 min. The device will be widely applicable to detect a specific gene from the various samples for clinical diagnosis and genetic research.
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Affiliation(s)
- Masayuki Uehara
- Core Technology Development Center, Corporate Research and Development Div., Seiko Epson Corporation
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26
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Russ PK, Karhade AV, Bitting AL, Doyle A, Solinas F, Wright DW, Haselton FR. A Prototype Biomarker Detector Combining Biomarker Extraction and Fixed Temperature PCR. ACTA ACUST UNITED AC 2016; 21:590-8. [DOI: 10.1177/2211068216634072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Indexed: 11/16/2022]
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27
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Scherr TF, Ryskoski HB, Doyle AB, Haselton FR. A two-magnet strategy for improved mixing and capture from biofluids. BIOMICROFLUIDICS 2016; 10:024118. [PMID: 27158286 PMCID: PMC4833749 DOI: 10.1063/1.4946014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/30/2016] [Indexed: 05/25/2023]
Abstract
Magnetic beads are a popular method for concentrating biomolecules from solution and have been more recently used in multistep pre-arrayed microfluidic cartridges. Typical processing strategies rely on a single magnet, resulting in a tight cluster of beads and requiring long incubation times to achieve high capture efficiencies, especially in highly viscous patient samples. This report describes a two-magnet strategy to improve the interaction of the bead surface with the surrounding fluid inside of a pre-arrayed, self-contained assay-in-a-tube. In the two-magnet system, target biomarker capture occurs at a rate three times faster than the single-magnet system. In clinically relevant biomatrices, we find a 2.5-fold improvement in biomarker capture at lower sample viscosities with the two-magnet system. In addition, we observe a 20% increase in the amount of protein captured at high viscosity for the two-magnet configuration relative to the single magnet approach. The two-magnet approach offers a means to achieve higher biomolecule extraction yields and shorter assay times in magnetic capture assays and in self-contained processor designs.
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Affiliation(s)
- Thomas F Scherr
- Department of Biomedical Engineering, Vanderbilt University , Nashville, Tennessee 37235, USA
| | - Hayley B Ryskoski
- Department of Biomedical Engineering, Vanderbilt University , Nashville, Tennessee 37235, USA
| | - Andrew B Doyle
- Department of Biomedical Engineering, Vanderbilt University , Nashville, Tennessee 37235, USA
| | - Frederick R Haselton
- Department of Biomedical Engineering, Vanderbilt University , Nashville, Tennessee 37235, USA
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28
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Roy S, Rahman IA, Ahmed MU. Paper-based rapid detection of pork and chicken using LAMP–magnetic bead aggregates. ANALYTICAL METHODS 2016; 8:2391-2399. [DOI: 10.1039/c6ay00274a] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Magnetic beads (MBs) have been widely used for DNA quantification.
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Affiliation(s)
- Sharmili Roy
- Biosensors and Biotechnology Laboratory
- Chemical Science Programme
- Faculty of Science
- Universiti Brunei Darussalam
- Gadong
| | - Ibrahim Abd Rahman
- Biosensors and Biotechnology Laboratory
- Chemical Science Programme
- Faculty of Science
- Universiti Brunei Darussalam
- Gadong
| | - Minhaz Uddin Ahmed
- Biosensors and Biotechnology Laboratory
- Chemical Science Programme
- Faculty of Science
- Universiti Brunei Darussalam
- Gadong
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29
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Bitting AL, Bordelon H, Baglia ML, Davis KM, Creecy AE, Short PA, Albert LE, Karhade AV, Wright DW, Haselton FR, Adams NM. Automated Device for Asynchronous Extraction of RNA, DNA, or Protein Biomarkers from Surrogate Patient Samples. ACTA ACUST UNITED AC 2015; 21:732-742. [DOI: 10.1177/2211068215596139] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 11/16/2022]
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30
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Zhang F, Cheng X, Yuan Y, Wu J, Gao Y. Urinary microRNA can be concentrated, dried on membranes and stored at room temperature in vacuum bags. PeerJ 2015. [PMID: 26213651 PMCID: PMC4512770 DOI: 10.7717/peerj.1082] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Urine accumulates traces of changes that occur in the body and can potentially serve as a better biomarker source. Urinary microRNA is a promising class of non-invasive disease biomarkers. However, long-term frozen human urine samples are not a good source for the extraction of urinary microRNA. In this paper, we demonstrate that urinary microRNA can be concentrated, dried on membranes and stored in vacuum bags at room temperature for several months. The amount of total RNA on the membranes after storage at room temperature for three months was unchanged. The levels of miR-16 and miR-21 exhibited no significant differences (P = 0.564, 0.386). This simple and economical method makes the large-scale storage of clinical samples of urinary microRNA or other nucleic acids possible.
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Affiliation(s)
- Fanshuang Zhang
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College , Beijing , China
| | - Xiaoyu Cheng
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College , Beijing , China
| | - Yuan Yuan
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College , Beijing , China
| | - Jianqiang Wu
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College , Beijing , China
| | - Youhe Gao
- Department of Pathophysiology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College , Beijing , China ; Department of Biochemistry and Molecular Biology, Gene Engineering and Biotechnology Beijing Key Laboratory, Beijing Normal University , Beijing , China
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31
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Creecy A, Russ PK, Solinas F, Wright DW, Haselton FR. Tuberculosis Biomarker Extraction and Isothermal Amplification in an Integrated Diagnostic Device. PLoS One 2015; 10:e0130260. [PMID: 26132307 PMCID: PMC4488445 DOI: 10.1371/journal.pone.0130260] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 05/19/2015] [Indexed: 11/19/2022] Open
Abstract
In this study, we integrated magnetic bead-based sample preparation and isothermal loop mediated amplification (LAMP) of TB in a single tube. Surrogate sputum samples produced by the Program for Appropriate Technology in Health containing inactivated TB bacteria were used to test the diagnostic. In order to test the sample preparation method, samples were lysed, and DNA was manually extracted and eluted into water in the tube. In a thermal cycler, LAMP amplified TB DNA from 103 TB cells/mL of sputum at 53.5 ± 3.3 minutes, 104 cells/mL at 46.3 ± 2.2 minutes, and 105 cells/mL at 41.6 ± 1.9 minutes. Negative control samples did not amplify. Next, sample preparation was combined with in-tubing isothermal LAMP amplification by replacing the water elution chamber with a LAMP reaction chamber. In this intermediate configuration, LAMP amplified 103 cells/mL at 74 ± 10 minutes, 104 cells/mL at 60 ± 9 minutes, and 105 TB cells/mL of sputum at 54 ± 9 minutes. Two of three negative controls did not amplify; one amplified at 100 minutes. In the semi-automated system, DNA was eluted directly into an isothermal reaction solution containing the faster OptiGene DNA polymerase. The low surrogate sputum concentration, 103 TB cells/mL, amplified at 52.8 ± 3.3 minutes, 104 cells/mL at 45.4 ± 11.3 minutes, and 105 cells/mL at 31.8 ± 2.9 minutes. TB negative samples amplified at 66.4 ± 7.4 minutes. This study demonstrated the feasibility of a single tube design for integrating sample preparation and isothermal amplification, which with further development could be useful for point-of-care applications, particularly in a low-resource setting.
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Affiliation(s)
- Amy Creecy
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States of America
| | - Patricia K. Russ
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States of America
| | - Francesca Solinas
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States of America
| | - David W. Wright
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
| | - Frederick R. Haselton
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, United States of America
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States of America
- * E-mail:
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Adams NM, Bordelon H, Wang KKA, Albert LE, Wright DW, Haselton FR. Comparison of three magnetic bead surface functionalities for RNA extraction and detection. ACS APPLIED MATERIALS & INTERFACES 2015; 7:6062-9. [PMID: 25710198 DOI: 10.1021/am506374t] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Magnetic beads are convenient for extracting nucleic acid biomarkers from biological samples prior to molecular detection. These beads are available with a variety of surface functionalities designed to capture particular subsets of RNA. We hypothesized that bead surface functionality affects binding kinetics, processing simplicity, and compatibility with molecular detection strategies. In this report, three magnetic bead surface chemistries designed to bind nucleic acids, silica, oligo (dT), and a specific oligonucleotide sequence were evaluated. Commercially available silica-coated and oligo (dT) beads, as well as beads functionalized with oligonucleotides complementary to respiratory syncytial virus (RSV) nucleocapsid gene, respectively recovered ∼75, ∼71, and ∼7% target RSV mRNA after a 1 min of incubation time in a surrogate patient sample spiked with the target. RSV-specific beads required much longer incubation times to recover amounts of the target comparable to the other beads (∼77% at 180 min). As expected, silica-coated beads extracted total RNA, oligo (dT) beads selectively extracted total mRNA, and RSV-specific beads selectively extracted RSV N gene mRNA. The choice of bead functionality is generally dependent on the target detection strategy. The silica-coated beads are most suitable for applications that require nucleic acids other than mRNA, especially with detection strategies that are tolerant of a high concentration of nontarget background nucleic acids, such as RT-PCR. On the other hand, oligo (dT) beads are best-suited for mRNA targets, as they bind biomarkers rapidly, have relatively high recovery, and enable detection strategies to be performed directly on the bead surface. Sequence-specific beads may be best for applications that are not tolerant of a high concentration of nontarget nucleic acids that require short RNA sequences without poly(A) tails, such as microRNAs, or that perform RNA detection directly on the bead surface.
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Affiliation(s)
- Nicholas M Adams
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hali Bordelon
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Kwo-Kwang A Wang
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Laura E Albert
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - David W Wright
- ‡Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Frederick R Haselton
- †Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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Robinson AM, Zhao L, Shah Alam MY, Bhandari P, Harroun SG, Dendukuri D, Blackburn J, Brosseau CL. The development of “fab-chips” as low-cost, sensitive surface-enhanced Raman spectroscopy (SERS) substrates for analytical applications. Analyst 2015; 140:779-85. [DOI: 10.1039/c4an01633e] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Modification of metal-coated zari fabric chips with silver nanoparticles results in sensitive, affordable SERS substrates which are useful for a wide range of chemical sensing applications.
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Affiliation(s)
| | - Lili Zhao
- Department of Chemisty
- Saint Mary's University
- Halifax
- Canada
| | | | | | | | | | - Jonathan Blackburn
- Institute of Infectious Disease & Molecular Medicine
- Division of Medical Biochemistry
- University of Cape Town
- Faculty of Health Sciences
- Cape Town
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Chan BD, Icoz K, Huang W, Chang CL, Savran CA. On-demand weighing of single dry biological particles over a 5-order-of-magnitude dynamic range. LAB ON A CHIP 2014; 14:4188-4196. [PMID: 25162712 DOI: 10.1039/c4lc00765d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We report a simple and highly versatile system to select and weigh individual dry biological particles. The system is composed of a microtweezer to pick and place individual particles and a cantilever-based resonator to weigh them. The system can weigh entities that vary from a red blood cell (~10(-11) g) to the eye-brain complex of an insect (~10(-6) g), covering a 5-order-of-magnitude mass range. Due to its versatility and ease of use, this weighing method is highly compatible with established laboratory practices. The system can provide complementary mass information for a wide variety of individual particles imaged using scanning electron microscopy and determine comparative weights of individual biological entities that are attached to microparticles as well as weigh fractions of individual biological entities that have been subjected to focused ion beam milling.
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Affiliation(s)
- Bin-Da Chan
- School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.
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Adams NM, Wang KKA, Caprioli AC, Thomas LC, Kankia B, Haselton FR, Wright DW. Quadruplex priming amplification for the detection of mRNA from surrogate patient samples. Analyst 2014; 139:1644-52. [PMID: 24503712 DOI: 10.1039/c3an02261g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Simple and rapid methods for detecting mRNA biomarkers from patient samples are valuable in settings with limited access to laboratory resources. In this report, we describe the development and evaluation of a self-contained assay to extract and quantify mRNA biomarkers from complex samples using a novel nucleic acid-based molecular sensor called quadruplex priming amplification (QPA). QPA is a simple and robust isothermal nucleic acid amplification method that exploits the stability of the G-quadruplex nucleotide structure to drive spontaneous strand melting from a specific DNA template sequence. Quantification of mRNA was enabled by integrating QPA with a magnetic bead-based extraction method using an mRNA-QPA interface reagent. The assay was found to maintain >90% of the maximum signal over a 4 °C range of operational temperatures (64-68 °C). QPA had a dynamic range spanning four orders of magnitude, with a limit of detection of ~20 pM template molecules using a highly controlled heating and optical system and a limit of detection of ~250 pM using a less optimal water bath and plate reader. These results demonstrate that this integrated approach has potential as a simple and effective mRNA biomarker extraction and detection assay for use in limited resource settings.
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Affiliation(s)
- N M Adams
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA.
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