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Abafogi AT, Lee J, Kim J, Lee SW, Jang S, Park S. Automated sepsis detection with vancomycin- and allantoin-polydopamine magnetic nanoparticles. Sci Rep 2024; 14:3693. [PMID: 38355732 PMCID: PMC10867076 DOI: 10.1038/s41598-024-54236-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/10/2024] [Indexed: 02/16/2024] Open
Abstract
Rapid and accurate identification of the bacteria responsible for sepsis is paramount for effective patient care. Molecular diagnostic methods, such as polymerase chain reaction (PCR), encounter challenges in sepsis due to inhibitory compounds in the blood, necessitating their removal for precise analysis. In this study we present an innovative approach that utilizes vancomycin (Van) and allantoin (Al)-conjugated polydopamine (PDA)-coated magnetic nanoparticles (MNPs) for the rapid and automated enrichment of bacteria and their DNA extraction from blood without inducing clumping and aggregation of blood. Al/Van-PDA-MNPs, facilitated by IMS, eliminate the need for preliminary sample treatments, providing a swift and efficient method for bacterial concentration and DNA extraction within an hour. Employing Al/Van-PDA-MNPs within an automated framework has markedly improved our ability to pre-concentrate various Gram-negative and Gram-positive bacteria directly from blood samples. This advancement has effectively reduced the detection threshold to 102 colony-forming unit/mL by both PCR and quantitative PCR. The method's expedited processing time, combined with its precision, positions it as a feasible diagnostic tool for diverse healthcare settings, ranging from small clinics to large hospitals. Furthermore, the innovative application of nanoparticles for DNA extraction holds promising potential for advancing sepsis diagnostics, enabling earlier interventions and improving patient outcomes.
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Affiliation(s)
| | - Jinyeop Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
- KingoBio Inc., Seoul, 08390, Korea
| | - Joochan Kim
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea
| | - Sei Won Lee
- Department of Pulmonology and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Seongsoo Jang
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, 05505, Korea
| | - Sungsu Park
- School of Mechanical Engineering, Sungkyunkwan University, Suwon, 16419, Korea.
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2
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Bazyar H. On the Application of Microfluidic-Based Technologies in Forensics: A Review. SENSORS (BASEL, SWITZERLAND) 2023; 23:5856. [PMID: 37447704 PMCID: PMC10346202 DOI: 10.3390/s23135856] [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: 05/17/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023]
Abstract
Microfluidic technology is a powerful tool to enable the rapid, accurate, and on-site analysis of forensically relevant evidence on a crime scene. This review paper provides a summary on the application of this technology in various forensic investigation fields spanning from forensic serology and human identification to discriminating and analyzing diverse classes of drugs and explosives. Each aspect is further explained by providing a short summary on general forensic workflow and investigations for body fluid identification as well as through the analysis of drugs and explosives. Microfluidic technology, including fabrication methodologies, materials, and working modules, are touched upon. Finally, the current shortcomings on the implementation of the microfluidic technology in the forensic field are discussed along with the future perspectives.
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Affiliation(s)
- Hanieh Bazyar
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Leeghwaterstraat 39, 2628CB Delft, The Netherlands
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3
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Turiello R, Nouwairi RL, Landers JP. Taking the microfluidic approach to nucleic acid analysis in forensics: Review and perspectives. Forensic Sci Int Genet 2023; 63:102824. [PMID: 36592574 DOI: 10.1016/j.fsigen.2022.102824] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/02/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Forensic laboratories are universally acknowledged as being overburdened, underfunded, and in need of improved analytical methods to expedite investigations, decrease the costs associated with nucleic acid (NA) analysis, and perform human identification (HID) at the point of need (e.g., crime scene, booking station, etc.). In response, numerous research and development (R&D) efforts have resulted in microfluidic tools that automate portions of the forensic genetic workflow, including DNA extraction, amplification, and short tandem repeat (STR) typing. By the early 2000 s, reports from the National Institute of Justice (NIJ) anticipated that microfluidic 'swab-in-profile-out' systems would be available for use at the crime scene by 2015 and the FBI's 2010 'Rapid DNA' Initiative, approved by Congress in 2017, directed this effort by guiding the development and implementation of maturing systems. At present, few fully-automated microfluidic DNA technologies are commercially available for forensic HID and their adoption by agencies interested in identification has been limited. In practice, the integration of complex laboratory processes to produce one autonomous unit, along with the highly variable nature of forensic input samples, resulted in systems that are more expensive per sample and not comparable to gold-standard identification methods in terms of sensitivity, reproducibility, and multiplex capability. This Review and Perspective provides insight into the contributing factors to this outcome; namely, we focus on the complications associated with the tremendous undertaking that is developing a sample-in-answer-out platform for HID. For context, we also describe the intricate forensic landscape that contributes to a nuanced marketplace, not easily distilled down to cases of simple supply and demand. Moving forward and considering the trade-offs associated with developing methods to compete, sometimes directly, with conventional ones, we recommend a focus shift for microfluidics developers toward the creation of innovative solutions for emerging applications in the field to increase the bandwidth of the forensic investigative toolkit. Likewise, we urge case working personnel to reframe how they conceptualize the currently available Rapid DNA tools; rather than comparing these microfluidic methods to gold-standard procedures, take advantage of their rapid and integrated modes for those situations requiring expedited identifications in an informed manner.
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4
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Grosjean F, Favre M, Castella V. Comparison between MACSprep™ forensic sperm microbead kit and Erase Sperm Isolation kit for the enrichment of sperm fractions recovered from sexual assault samples. Int J Legal Med 2023; 137:267-278. [PMID: 35773355 PMCID: PMC9816209 DOI: 10.1007/s00414-022-02861-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 06/21/2022] [Indexed: 01/11/2023]
Abstract
Sexual assault samples often contain mixtures of cells coming from at least two donors. Ideally, one would need to separate the cells into two cellular fractions: one consisting of the alleged aggressor's spermatozoa (the sperm fraction) and the other containing the victim's epithelial cells (the non-sperm fraction). This separation increases the probability of obtaining the alleged offender's autosomal DNA profile. However, spermatozoa are often collected along with an excess of biological material originating from the victim, and with unfavorable male:female biological material ratios, the absence of separation could result in the PCR amplification of the victim's DNA profile only. Several approaches are available to enrich/purify the spermatozoa present on sexual assault samples. In this paper, we compare a new method, the MACSprep™ Forensic Sperm MicroBead Kit (MACSprep, based on microbeads conjugated with antibodies bound to spermatozoa and their retention within a magnetic column) with the Erase Sperm Isolation Kit (Erase, a standard differential lysis separation procedure combined with a specific removal of free DNA) routinely used in our lab. The performance of both kits was tested using sets of vaginal and buccal swabs loaded with different dilutions of sperm, or azoospermic semen, representing a total of 120 independent samples. For the samples containing undiluted sperm, an average recovery of 58% was observed for the MACSprep's sperm fractions and 43% for Erase's. Significantly better recovery of azoospermic semen was observed in MACSprep's non-sperm fractions (~ 85%) compared to Erase (~ 28%). Erase performed significantly better than MACSprep in terms of recovery for diluted sperm samples (1:10 to 1:800 sperm dilutions) in the presence of vaginal cells, while the purities of the achieved sperm fractions were in favor of MACSprep for the highest sperm dilutions tested. Similar trends were observed with buccal swabs loaded with 1:200 sperm dilutions. Increased sperm dilutions on vaginal swabs resulted in higher variability in the male material recovered, whatever the separation method used. Both methods were easy to perform and resulted in male DNA extracts ready to use in less than 2 h. Both kits showed their specificities in terms of recovery efficiency and purity of the sperm fractions. Ideally, additional experiments should be performed in different laboratories, using workflow and chemistries different than ours, to better define the peculiarities observed with MACSprep for high dilutions. Improving the recovery of MACSprep for diluted samples, in addition to its better purity observed in the experiments performed, could make it a method of choice for laboratory workflow, despite MACSprep's current price per sample being about twice the price of Erase's.
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Affiliation(s)
- Frederic Grosjean
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Marylou Favre
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
| | - Vincent Castella
- grid.411686.c0000 0004 0511 8059Forensic Genetics Unit, University Center of Legal Medicine, Lausanne – Geneva, Lausanne University Hospital and University of Lausanne, Chemin de la Vulliette 4, 1000 Lausanne 25, Switzerland
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5
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Lerin-Morales KM, Olguín LF, Mateo-Martí E, Colín-García M. Prebiotic Chemistry Experiments Using Microfluidic Devices. Life (Basel) 2022; 12:life12101665. [PMID: 36295100 PMCID: PMC9605377 DOI: 10.3390/life12101665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/15/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Microfluidic devices are small tools mostly consisting of one or more channels, with dimensions between one and hundreds of microns, where small volumes of fluids are manipulated. They have extensive use in the biomedical and chemical fields; however, in prebiotic chemistry, they only have been employed recently. In prebiotic chemistry, just three types of microfluidic devices have been used: the first ones are Y-form devices with laminar co-flow, used to study the precipitation of minerals in hydrothermal vents systems; the second ones are microdroplet devices that can form small droplets capable of mimic cellular compartmentalization; and the last ones are devices with microchambers that recreate the microenvironment inside rock pores under hydrothermal conditions. In this review, we summarized the experiments in the field of prebiotic chemistry that employed microfluidic devices. The main idea is to incentivize their use and discuss their potential to perform novel experiments that could contribute to unraveling some prebiotic chemistry questions.
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Affiliation(s)
- Karen Melissa Lerin-Morales
- Posgrado en Ciencias de la Tierra, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
- Correspondence: (K.M.L.-M.); (M.C.-G.); Tel.: +52-(55)-5622-4300 (ext. 164) (M.C.-G.)
| | - Luis F. Olguín
- Laboratorio de Biofisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
| | - Eva Mateo-Martí
- Centro de Astrobiología (CAB), CSIC-INTA, Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850 Madrid, Spain
| | - María Colín-García
- Instituto de Geología, Universidad Nacional Autónoma de México, Ciudad de Mexico 04510, Mexico
- Correspondence: (K.M.L.-M.); (M.C.-G.); Tel.: +52-(55)-5622-4300 (ext. 164) (M.C.-G.)
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6
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Rapid DNA from a Disaster Victim Identification Perspective: is it a game changer? Forensic Sci Int Genet 2022; 58:102684. [DOI: 10.1016/j.fsigen.2022.102684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 02/03/2022] [Accepted: 03/03/2022] [Indexed: 11/18/2022]
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7
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Cong H, Zhang N. Perspectives in translating microfluidic devices from laboratory prototyping into scale-up production. BIOMICROFLUIDICS 2022; 16:021301. [PMID: 35350441 PMCID: PMC8933055 DOI: 10.1063/5.0079045] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/23/2022] [Indexed: 05/05/2023]
Abstract
Transforming lab research into a sustainable business is becoming a trend in the microfluidic field. However, there are various challenges during the translation process due to the gaps between academia and industry, especially from laboratory prototyping to industrial scale-up production, which is critical for potential commercialization. In this Perspective, based on our experience in collaboration with stakeholders, e.g., biologists, microfluidic engineers, diagnostic specialists, and manufacturers, we aim to share our understanding of the manufacturing process chain of microfluidic cartridge from concept development and laboratory prototyping to scale-up production, where the scale-up production of commercial microfluidic cartridges is highlighted. Four suggestions from the aspect of cartridge design for manufacturing, professional involvement, material selection, and standardization are provided in order to help scientists from the laboratory to bring their innovations into pre-clinical, clinical, and mass production and improve the manufacturability of laboratory prototypes toward commercialization.
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Affiliation(s)
- Hengji Cong
- Centre of Micro/Nano Manufacturing Technology (MNMT-Dublin), School of Mechanical & Materials Engineering, University College Dublin, Dublin 4, Ireland
| | - Nan Zhang
- Author to whom correspondence should be addressed:
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8
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Boelens D, Fogliatto Mariot R, Ghemrawi M, Kloosterman AD, McCord BR. The development of miniSTRs as a method for high-speed direct PCR. Electrophoresis 2021; 42:1352-1361. [PMID: 33811666 DOI: 10.1002/elps.202100066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 12/17/2022]
Abstract
There are situations in which it would be very valuable to have a DNA profile within a short time; for example, in mass disasters or airport security. In previous work, we have promoted reduced size STR amplicons for the analysis of degraded DNA. We also noticed that shorter amplicons are more robust during amplification, making them inhibition resistant, and potentially applicable to high-speed direct PCR. Here, we describe a set of miniSTRs capable of rapid direct PCR amplification. The selected markers are a subset of the Combined DNA Index System (CODIS) loci modified to permit high-speed amplification. Using the proposed protocol, the amplification of eight loci plus amelogenin directly from a saliva sample can be completed in 7 min and 38 s using a two-step PCR with 30 cycles of 98°C for 2 s and 62°C for 7 s on a Streck Philisa thermocycler. Selection of DNA polymerase, optimization of the two-step PCR cycling conditions, the primer concentrations, and the dilution of saliva is described. This method shows great potential as a quick screening method to obtain a presumptive DNA profile when time is limited, particularly when combined with high-speed separation and detection methods.
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Affiliation(s)
- Dide Boelens
- Department of Chemistry, Florida International University (FIU), Miami, Florida, USA
| | | | - Mirna Ghemrawi
- Department of Chemistry, Florida International University (FIU), Miami, Florida, USA
| | - Ate D Kloosterman
- CLHC, Amsterdam Center for Forensic Science and Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Bruce R McCord
- Department of Chemistry, Florida International University (FIU), Miami, Florida, USA
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9
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Wu J, Jiang K, Mi H, Qiu Y, Son J, Park HJ, Nam JM, Lee JH. A rapid and sensitive fluorescence biosensor based on plasmonic PCR. NANOSCALE 2021; 13:7348-7354. [PMID: 33889912 DOI: 10.1039/d1nr00102g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Plasmonic PCR utilizing metallic nanoparticles has shown great advantages compared to the commercial thermocycler equipment in terms of cost, size and processing time. However, due to the strong fluorescence quenching, plasmonic nanoparticle-based PCR requires additional post-processing steps such as centrifugation and gel electrophoresis. This process increases the overall diagnostic time, offsetting the benefits of fast thermocycling. Here, we report a rapid and sensitive plasmonic photothermal PCR (PPT-PCR) assay method based on in situ end-point fluorescence detection. By using plasmonic magnetic bi-functional nanoparticles, PPT-PCR involving 30 thermocycles and fluorescence detection following magnetic separation has successfully shown that DNA targets can be detected within 5.5 minutes. The limit of detection (3.3 copies per μL) is comparable with that of the conventional real-time quantitative PCR; however, the assay time is about 5.5 times shorter for the PPT-PCR. The strategy of combining the photothermal effect and magnetic separation into a single particle will open new horizons in the development of fast and sensitive PCR-based biosensors for point-of care testing.
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Affiliation(s)
- Jingrui Wu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China.
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10
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Abdel Hady RH, Thabet HZ, Ebrahem NE, Yassa HA. Thermal Effects on DNA Degradation in Blood and Seminal Stains: Forensic View. Acad Forensic Pathol 2021; 11:7-23. [PMID: 34040682 PMCID: PMC8129487 DOI: 10.1177/1925362121998547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/25/2021] [Indexed: 11/16/2022]
Abstract
Forensic investigations using DNA analysis have been grown rapidly. Samples retrieved from crime scene may be exposed to different conditions before proceeding. This study aimed to evaluate the effect of different grades of temperature and burn on DNA extraction and typing. METHODS Seven mL of blood and four mL of semen were collected from each volunteer. Effects of temperature grades (100 °C, 50 °C, 37 °C, 4 °C, -20 °C, and burn) on blood and seminal stain were tested. RESULTS Bloodstains exposed to temperature grades 100 °C, 50 °C, 37 °C, 4 °C, and -20 °C can be identified using preliminary test while burnt blood stain cannot. Seminal stains exposed to temperature grades 37 °C, 4 °C, and -20 °C can be identified by Florence test while those exposed to 100 °C, 50 °C, and burn cannot. Blood and seminal stains exposed to temperature grades 100 °C, 50 °C, and burn show marked reduction in DNA concentration while maximum DNA conc could be recovered from stains exposed to temperature grade temperature. Both blood and seminal DNA was affected only in case of burn without significant difference between THO1 and Amelogenin primers. CONCLUSION High environmental temperature affect the quantity of extracted DNA from different stains but less effect on the quality of extracted DNA. Burn affects both preliminary test, DNA quantity, and quality in stains.
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Affiliation(s)
| | | | | | - Heba A. Yassa
- Heba A. Yassa, Professor of Forensic Medicine and Clinical Toxicology Department, Assiut Governorate, Egypt; or
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11
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12
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Naghdi T, Faham S, Mahmoudi T, Pourreza N, Ghavami R, Golmohammadi H. Phytochemicals toward Green (Bio)sensing. ACS Sens 2020; 5:3770-3805. [PMID: 33301670 DOI: 10.1021/acssensors.0c02101] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Because of numerous inherent and unique characteristics of phytochemicals as bioactive compounds derived from plants, they have been widely used as one of the most interesting nature-based compounds in a myriad of fields. Moreover, a wide variety of phytochemicals offer a plethora of fascinating optical and electrochemical features that pave the way toward their development as optical and electrochemical (bio)sensors for clinical/health diagnostics, environmental monitoring, food quality control, and bioimaging. In the current review, we highlight how phytochemicals have been tailored and used for a wide variety of optical and electrochemical (bio)sensing and bioimaging applications, after classifying and introducing them according to their chemical structures. Finally, the current challenges and future directions/perspective on the optical and electrochemical (bio)sensing applications of phytochemicals are discussed with the goal of further expanding their potential applications in (bio)sensing technology. Regarding the advantageous features of phytochemicals as highly promising and potential biomaterials, we envisage that many of the existing chemical-based (bio)sensors will be replaced by phytochemical-based ones in the near future.
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Affiliation(s)
- Tina Naghdi
- Nanosensor Bioplatforms Laboratory, Chemistry and Chemical Engineering Research Center of Iran, Tehran 14335-186, Iran
| | - Shadab Faham
- Chemometrics Laboratory, Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Tohid Mahmoudi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Nahid Pourreza
- Chemistry Department, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz 6153753843, Iran
| | - Raouf Ghavami
- Chemometrics Laboratory, Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj 66177-15175, Iran
| | - Hamed Golmohammadi
- Nanosensor Bioplatforms Laboratory, Chemistry and Chemical Engineering Research Center of Iran, Tehran 14335-186, Iran
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13
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Hudson BC, Cox JO, Seashols-Williams SJ, Dawson Cruz T. The effects of dithiothreitol (DTT) on fluorescent qPCR dyes. J Forensic Sci 2020; 66:700-708. [PMID: 33284476 DOI: 10.1111/1556-4029.14637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 11/28/2022]
Abstract
DNA extractions of semen samples commonly utilize dithiothreitol (DTT) to reduce and disrupt disulfide bonds. Although traditional extraction techniques remove DTT before downstream analyses, the forensic DNA community has recently explored Y-screening, direct amplification, and direct cell lysis assays that omit purification but employ reducing agents to lyse spermatozoa. This study examined the impact of residual DTT on downstream processes involving fluorescent dyes. Quantification using Investigator® Quantiplex HYres revealed a significant increase in the male DNA yield (p = 0.00056) and a >150,000,000-fold increase in the male:human DNA ratio when DTT remained in extracts versus when it was filtered out using a traditional purification method. When DTT was present with Quantifiler™ Trio, the true mean DNA yield for the large autosomal target significantly increased (p = 0.038) and the average reported DNA yields increased 1.1-fold, >9.5-fold, and 1.3-fold for the small autosomal, large autosomal, and male targets, respectively. DTT-spiked DNA standards from both kits were impacted similarly to samples with residual DTT, demonstrating that observed effects were related to DTT and not the extraction method. This study corroborates other reports that DTT adversely affects multiple dyes (e.g., Cy5, Quasar 670, SYBR Green I, TMR, and Mustang Purple® ). Overall, DTT causes inaccurate quantities and, consequently, inaccurate calculated male:female ratios when used in conjunction with these kits. Thus, implementation of newer direct-to-PCR assays incorporating DTT should either be avoided or used only with carefully evaluated, compatible dyes.
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Affiliation(s)
- Brittany C Hudson
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.,Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Tracey Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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14
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Terán JE, Millbern Z, Shao D, Sui X, Liu Y, Demmler M, Vinueza NR. Characterization of synthetic dyes for environmental and forensic assessments: A chromatography and mass spectrometry approach. J Sep Sci 2020; 44:387-402. [PMID: 33047882 DOI: 10.1002/jssc.202000836] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/07/2022]
Abstract
Dyes have become common substances since they are employed in mostly all objects surrounding our daily activities such as clothing and upholstery. Based on the usage and disposal of these objects, the transfer of the dyes to other media such as soil and water increases their prevalence in our environment. However, this prevalence could help to solve crimes and pollution problems if detection techniques are proper. For that reason, the detection and characterization of dyes in complex matrices is important to determine the possible events leading to their deposition (natural degradation, attempts of removal, possible match with evidence, among others). Currently, there are several chromatographic and mass spectrometric approaches used for the identification of these organic molecules and their derivatives with high specificity and accuracy. This review presents current chromatographic and mass spectrometric methods that are used for the detection and characterization of disperse, acid, basic, and reactive dyes, and their derivatives.
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Affiliation(s)
- Julio E Terán
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Zoe Millbern
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Dongyan Shao
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Xinyi Sui
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Yixin Liu
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Morgan Demmler
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, North Carolina, USA
| | - Nelson R Vinueza
- Department of Textile Engineering, Chemistry, and Science, North Carolina State University, Raleigh, North Carolina, USA
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15
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Gnaim R, Golberg A, Sheviryov J, Rubinsky B, González CA. Detection and differentiation of bacteria by electrical bioimpedance spectroscopy. Biotechniques 2020; 69:384-394. [PMID: 32486835 DOI: 10.2144/btn-2019-0080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Detecting bacteria in samples and differentiating between Gram-negative and Gram-positive species is an important challenge, and the most common method, Gram staining, is very time consuming. The aim of this study was to evaluate the electrical bioimpedance spectroscopy (EBIS) technique as an inexpensive and practical tool for real-time detection of bacteria and differentiation between Gram-positive and Gram-negative species. The relevant sensitivity for differentiating between species was found in the magnitude and phase at frequencies of 158,489 and 5248 Hz, respectively, at a bacterial concentration of 1 μg/μl. Subsequently, the sensitivity was estimated as a function of bacterial concentration. Our results demonstrated that EBIS can potentially distinguish between presence and absence of bacteria as well as between different types of bacteria.
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Affiliation(s)
- Rima Gnaim
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel.,The Triangle Regional Research & Development Center, Kfar Qari' 30075, Israel
| | - Alexander Golberg
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel
| | - Julia Sheviryov
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel
| | - Boris Rubinsky
- Mechanical Engineering Department, University of California-Berkeley, CA, USA
| | - César A González
- Porter School of Environment & Earth Sciences, Tel Aviv University. Tel Aviv-Yafo, Israel.,Escuela Superior de Medicina-Instituto Politécnico Nacional, Mexico City, Mexico
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16
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Romsos EL, French JL, Smith M, Figarelli V, Harran F, Vandegrift G, Moreno LI, Callaghan TF, Brocato J, Vaidyanathan J, Pedroso JC, Amy A, Stoiloff S, Morillo VH, Czetyrko K, Johnson ED, de Tagyos J, Murray A, Vallone PM. Results of the 2018 Rapid DNA Maturity Assessment. J Forensic Sci 2020; 65:953-959. [PMID: 31985834 PMCID: PMC11034630 DOI: 10.1111/1556-4029.14267] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/25/2019] [Accepted: 12/12/2019] [Indexed: 01/27/2023]
Abstract
Three commercially available integrated rapid DNA instruments were tested as a part of a rapid DNA maturity assessment in July of 2018. The assessment was conducted with sets of blinded single-source reference samples provided to participants for testing on the individual rapid platforms within their laboratories. The data were returned to the National Institute of Standards and Technology (NIST) for review and analysis. Both FBI-defined automated review (Rapid DNA Analysis) and manual review (Modified Rapid DNA Analysis) of the datasets were conducted to assess the success of genotyping the 20 Combined DNA Index System (CODIS) core STR loci and full profiles generated by the instruments. Genotype results from the multiple platforms, participating laboratories, and STR typing chemistries were combined into a single analysis. The Rapid DNA Analysis resulted in a success rate of 80% for full profiles (85% for the 20 CODIS core loci) with automated analysis. Modified Rapid DNA Analysis resulted in a success rate of 90% for both the CODIS 20 core loci and full profiles (all attempted loci per chemistry). An analysis of the peak height ratios demonstrated that 95% of all heterozygous alleles were above 59% heterozygote balance. For base-pair sizing precision, the precision was below the standard 0.5 bp deviation for both the ANDE 6C System and the RapidHIT 200.
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Affiliation(s)
- Erica L Romsos
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
| | | | - Mark Smith
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Vincent Figarelli
- Arizona Department Public Safety, 2102 West Encanto Blvd, Phoenix, AZ, 85009
| | - Frederick Harran
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Glenn Vandegrift
- Bensalem Township Police Department, 2400 Byberry Road, Bensalem, PA, 19020
| | - Lilliana I Moreno
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Thomas F Callaghan
- Federal Bureau of Investigation Laboratory, 2501 Investigation Parkway, Quantico, VA, 22135
| | - Joanie Brocato
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Janaki Vaidyanathan
- Louisiana State Police Crime Laboratory, 376 East Airport Drive, Baton Rouge, LA, 70806
| | - Juan C Pedroso
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Andrea Amy
- Miami Beach Police Department, 1100 Washington Ave, Miami Beach, FL, 33139
| | - Stephanie Stoiloff
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Victor H Morillo
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Karina Czetyrko
- Miami-Dade Police Department, Forensic Services Bureau, 9105 NW 25th Street, Doral, FL, 33172
| | - Elizabeth D Johnson
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Jessica de Tagyos
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Ashley Murray
- United States Army Criminal Investigation Laboratory Defense Forensic Science Center, 4930 North 31st Street, Forest Park, GA, 30297
| | - Peter M Vallone
- Applied Genetics Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-8314
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17
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Ansari N, Trambadiya N, Lodha A, Menon SK. A portable microfluidic paper-based analytical device for blood detection and typing assay. AUST J FORENSIC SCI 2020. [DOI: 10.1080/00450618.2020.1740321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Niha Ansari
- Institute of Forensic Science, Gujarat Forensic Science University, Gadhinagar, India
| | - Nehal Trambadiya
- Department of Forensic Science, School of Sciences, Gujarat University, Ahmedabad, India
| | - Anand Lodha
- Department of Forensic Science, School of Sciences, Mody University of Science and Technology, Sikar, India
| | - S. K. Menon
- Department of Forensic Science, School of Sciences, Gujarat University, Ahmedabad, India
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18
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Sreejith KR, Gorgannezhad L, Jin J, Ooi CH, Takei T, Hayase G, Stratton H, Lamb K, Shiddiky M, Dao DV, Nguyen NT. Core-Shell Beads Made by Composite Liquid Marble Technology as A Versatile Microreactor for Polymerase Chain Reaction. MICROMACHINES 2020; 11:E242. [PMID: 32111025 PMCID: PMC7142426 DOI: 10.3390/mi11030242] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/21/2020] [Accepted: 02/25/2020] [Indexed: 01/16/2023]
Abstract
Over the last three decades, the protocols and procedures of the DNA amplification technique, polymerase chain reaction (PCR), have been optimized and well developed. However, there have been no significant innovations in processes for sample dispersion for PCR that have reduced the amount of single-use or unrecyclable plastic waste produced. To address the issue of plastic waste, this paper reports the synthesis and successful use of a core-shell bead microreactor using photopolymerization of a composite liquid marble as a dispersion process. This platform uses the core-shell bead as a simple and effective sample dispersion medium that significantly reduces plastic waste generated compared to conventional PCR processes. Other improvements over conventional PCR processes of the novel dispersion platform include increasing the throughput capability, enhancing the performance and portability of the thermal cycler, and allowing for the contamination-free storage of samples after thermal cycling.
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Affiliation(s)
- Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
| | - Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia
| | - Jing Jin
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
| | - Chin Hong Ooi
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
| | - Takayuki Takei
- Department of Chemical Engineering, Graduate School of Science and Engineering, Kagoshima University, 1-21-40 Korimoto, Kagoshima 890-0065, Japan;
| | - Gen Hayase
- Frontier Research Institute for Interdisciplinary Science, Tohoku University, 6-3 Aramaki aza Aoba-ku, Sendai, Miyagi 980-8578, Japan;
| | - Helen Stratton
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia
| | - Krystina Lamb
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
| | - Muhammad Shiddiky
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
| | - Dzung Viet Dao
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Nathan Campus, Griffith University, 170 Kessels Road, Brisbane, QLD 4111, Australia; (K.R.S.); (L.G.); (J.J.); (C.H.O.); (H.S.); (K.L.); (M.S.); (D.V.D.)
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19
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Veltkamp HW, Akegawa Monteiro F, Sanders R, Wiegerink R, Lötters J. Disposable DNA Amplification Chips with Integrated Low-Cost Heaters. MICROMACHINES 2020; 11:E238. [PMID: 32106462 PMCID: PMC7143804 DOI: 10.3390/mi11030238] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/20/2020] [Accepted: 02/22/2020] [Indexed: 01/03/2023]
Abstract
Fast point-of-use detection of, for example, early-stage zoonoses, e.g., Q-fever, bovine tuberculosis, or the Covid-19 coronavirus, is beneficial for both humans and animal husbandry as it can save lives and livestock. The latter prevents farmers from going bankrupt after a zoonoses outbreak. This paper describes the development of a fabrication process and the proof-of-principle of a disposable DNA amplification chip with an integrated heater. Based on the analysis of the milling process, metal adhesion studies, and COMSOL MultiPhysics heat transfer simulations, the first batch of chips has been fabricated and successful multiple displacement amplification reactions are performed inside these chips. This research is the first step towards the development of an early-stage zoonoses detection device. Tests with real zoonoses and DNA specific amplification reactions still need to be done.
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Affiliation(s)
- Henk-Willem Veltkamp
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Fernanda Akegawa Monteiro
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Remco Sanders
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Remco Wiegerink
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
| | - Joost Lötters
- Department of Integrated Devices and Systems, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands; (F.A.M.); (R.S.); (R.W.); (J.L.)
- Bronkhorst High-Tech BV, Nijverheidsstraat 1A, 7261 AK Ruurlo, The Netherlands
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20
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Sreejith KR, Gorgannezhad L, Jin J, Ooi CH, Stratton H, Dao DV, Nguyen NT. Liquid marbles as biochemical reactors for the polymerase chain reaction. LAB ON A CHIP 2019; 19:3220-3227. [PMID: 31464317 DOI: 10.1039/c9lc00676a] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The polymerase chain reaction (PCR) is a popular and well-established DNA amplification technique. Technological and engineering advancements in the field of microfluidics have fuelled the progress of polymerase chain reaction (PCR) technology in the last three decades. Advances in microfluidics-based PCR technology have significantly reduced the sample volume and thermal cycling time. Further advances led to novel and accurate techniques such as the digital PCR. However, contamination of PCR samples, lack of reusability of the microfluidic PCR platforms, complexity in instrumentation and operation remain as some of the significant drawbacks of conventional microfluidic PCR platforms. Liquid marbles, the recently emerging microfluidic platform, could potentially resolve these drawbacks. This paper reports the first liquid marble based polymerase chain reaction. We demonstrated an experimental setup for the liquid-marble based PCR with a humidity-controlled chamber and an embedded thermal cycler. A concentrated salt solution was used to control the humidity of the PCR chamber which in turn reduces the evaporation rate of the liquid marble. The successful PCR of microbial source tracking markers for faecal contamination was achieved with the system, indicating potential application in water quality monitoring.
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Affiliation(s)
- Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
| | - Lena Gorgannezhad
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia. and School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, 4111 Queensland, Australia
| | - Jing Jin
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
| | - Chin Hong Ooi
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
| | - Helen Stratton
- School of Environment and Science, Nathan Campus, Griffith University, 170 Kessels Road, 4111 Queensland, Australia
| | - Dzung Viet Dao
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
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21
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Gu Y, Zhuang B, Han J, Li Y, Song X, Zhou X, Wang L, Liu P. Modular-Based Integrated Microsystem with Multiple Sample Preparation Modules for Automated Forensic DNA Typing from Reference to Challenging Samples. Anal Chem 2019; 91:7435-7443. [PMID: 31050401 DOI: 10.1021/acs.analchem.9b01560] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The realization of an automated short tandem repeat (STR) analysis for forensic investigations is facing a unique challenge, that is DNA evidence with wide disparities in sample types, quality, and quantity. We developed a fully integrated microsystem in a modular-based architecture to accept and process various forensic samples in a "sample-in-answer-out" manner for forensic STR analysis. Two sample preparation modules (SPMs), the direct and the extraction SPM, were designed to be easily assembled with a capillary array electrophoresis (CAE) chip using a chip cartridge to efficiently achieve an adequate performance to different samples at a low cost. The direct SPM processed buccal swabs to produce STR profiles without DNA extraction in about 2 h. The extraction SPM analyzed more challenging blood samples based on chitosan-modified quartz filter paper for DNA extraction. This newly developed quartz filter provided a 90% DNA extraction efficiency and the "in situ" PCR capability, which enabled DNA extraction and PCR performed within a single chamber with all the DNA concentrated in the filter. We demonstrated that minute amounts of blood (0.25 μL), highly diluted blood (0.5 μL blood in 1 mL buffer), and latent bloodstains (5-μL bloodstain on cloth washed with detergent) can be automatically analyzed using our microsystem, reliably producing full STR profiles with a 100% calling of all the alleles. This modular-based microsystem with the capability of analyzing a wide range of samples should be able to play an increasing role in both urgent situations and routine forensic investigations, dramatically extending the applications and utility of automated DNA typing.
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Affiliation(s)
- Yin Gu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , Beijing , 100084 , China.,State Key Laboratory of Space Medicine Fundamentals and Application , China Astronaut Research and Training Center , Beijing , 100094 , China
| | - Bin Zhuang
- Beijing CapitalBio Technology Ltd. Co. , Beijing , 101111 , China
| | - Junping Han
- Technology Department of Chaoyang Sub-bureau , Beijing Public Security Bureau , Beijing , 100102 , China
| | - Yi Li
- Beijing CapitalBio Technology Ltd. Co. , Beijing , 101111 , China
| | - Xiaoyu Song
- Beijing CapitalBio Technology Ltd. Co. , Beijing , 101111 , China
| | - Xinying Zhou
- CapitalBio Corporation , Beijing , 102206 , China
| | - Lei Wang
- CapitalBio Corporation , Beijing , 102206 , China
| | - Peng Liu
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Tsinghua University , Beijing , 100084 , China
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22
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Yang J, Hurth C, Nordquist A, Smith S, Zenhausern F. Integrated Microfluidic System for Rapid DNA Fingerprint Analysis: A Miniaturized Integrated DNA Analysis System (MiDAS)-Swab Sample-In to DNA Profile-Out. Methods Mol Biol 2019; 1906:207-224. [PMID: 30488395 DOI: 10.1007/978-1-4939-8964-5_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A fully automated rapid DNA analysis system requires integrating several operational elements performing multiple steps onto one single microfluidic platform. The functions to include on the microfluidic platform consist of substrate lysis, lysate DNA extraction, single or multiplexed PCR amplification, amplicon separation, and product readout. Here we describe a fully automated integrated system for forensic short tandem repeat (STR) analysis of reference samples, achieving buccal swab-in and DNA profile-out.
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Affiliation(s)
- Jianing Yang
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.
| | - Cedric Hurth
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Alan Nordquist
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Stan Smith
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA
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23
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Sreejith KR, Ooi CH, Jin J, Dao DV, Nguyen NT. Digital polymerase chain reaction technology - recent advances and future perspectives. LAB ON A CHIP 2018; 18:3717-3732. [PMID: 30402632 DOI: 10.1039/c8lc00990b] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has remained a "hot topic" in the last two decades due to its potential applications in cell biology, genetic engineering, and medical diagnostics. Various advanced techniques have been reported on sample dispersion, thermal cycling and output monitoring of digital PCR. However, a fully automated, low-cost and handheld digital PCR platform has not been reported in the literature. This paper attempts to critically evaluate the recent developments in techniques for sample dispersion, thermal cycling and output evaluation for dPCR. The techniques are discussed in terms of hardware simplicity, portability, cost-effectiveness and suitability for automation. The present paper also discusses the research gaps observed in each step of dPCR and concludes with possible improvements toward portable, low-cost and automatic digital PCR systems.
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Affiliation(s)
- Kamalalayam Rajan Sreejith
- Queensland Micro- and Nanotechnology Centre, Griffith University, 170 Kessels Road, 4111 Queensland, Australia.
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24
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Lipic SG, Giordullo LM, Fredericks JD. A novel FTA™ elute card collection method that improves direct DNA amplification from bloodstained concrete. Sci Justice 2018; 58:303-307. [PMID: 30193655 DOI: 10.1016/j.scijus.2018.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/18/2018] [Accepted: 03/23/2018] [Indexed: 11/16/2022]
Abstract
Concrete is a common construction material found in residential and commercial buildings, bridges and parking lots that is a composite matrix containing aggregate held together with cement. The porous nature of concrete can make the collection and genotyping of biological fluids, such as blood, challenging. Forensic evidence can become embedded within the matrix, potentially reducing the amount of DNA available for analysis. In forensic science, "direct" amplification refers to a genotyping method that amplifies a DNA profile directly from a sample without DNA extraction, saving time and money. We investigated a novel application of Whatman™ FTA™ Elute cards in their ability to directly amplify PowerPlex® Fusion and Y23 profiles from minute amounts of blood that had been deposited on different concrete structures. In comparison to traditional collection methods, directly profiling blood stained construction materials using FTA™ Elute cards increased the percentage loci amplified and significantly improved both allele peak height and peak height ratio while reducing allelic drop-out. FTA™ Elute cards can provide a reliable, inexpensive and superior alternative to traditional methods.
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Affiliation(s)
- Stephen G Lipic
- Department of Chemistry, Eastern Kentucky University, 521 Lancaster Avenue, Richmond, KY 40475, United States.
| | - Lucille M Giordullo
- Department of Chemistry, Eastern Kentucky University, 521 Lancaster Avenue, Richmond, KY 40475, United States.
| | - Jamie D Fredericks
- Department of Chemistry, Eastern Kentucky University, 521 Lancaster Avenue, Richmond, KY 40475, United States.
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25
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Highly efficient DNA extraction and purification from olive oil on a washable and reusable miniaturized device. Anal Chim Acta 2018; 1020:30-40. [DOI: 10.1016/j.aca.2018.02.079] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/19/2018] [Accepted: 02/23/2018] [Indexed: 01/21/2023]
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26
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Han J, Gan W, Zhuang B, Sun J, Zhao L, Ye J, Liu Y, Li CX, Liu P. A fully integrated microchip system for automated forensic short tandem repeat analysis. Analyst 2018; 142:2004-2012. [PMID: 28513665 DOI: 10.1039/c7an00295e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have successfully developed an integrated microsystem that combines two plastic microchips for DNA extraction and PCR amplification with a glass capillary array electrophoresis chip together in a compact control and detection instrument for automated forensic short tandem repeat (STR) analysis. DNA extraction followed by an "in situ PCR" was conducted in a single reaction chamber of the microchip based on a filter paper-based extraction methodology. PCR products were then mixed with sizing standards by an injection electrode and injected into the electrophoresis chip for four-color confocal fluorescence detection. The entire STR analysis can be completed in about two hours without any human intervention. Since the 15-plex STR system has a more stringent requirement for PCR efficiency, we optimized the structure of the plastic DNA extraction and amplification chip, in which the reaction chamber was formed by sandwiching a hollow structure layer with two blank cover layers, to reduce the adsorption of PCR reagents to the surfaces. In addition, PCR additives, bovine serum albumin, poly(ethylene glycol), and more magnesium chloride were included into the on-chip multiplex STR system. The limit-of-detection study demonstrated that our microsystem was able to produce full 15-plex STR profiles from 3.75 ng standard K562 DNA. Buccal swab and whole blood samples were also successfully typed by our system, validating the feasibility of performing rapid DNA typing in a "sample-in-answer-out" manner for on-site forensic human identification.
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Affiliation(s)
- Junping Han
- Department of Biomedical Engineering, School of Medicine, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing, 100084, China.
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27
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Stokes NA, Stanciu CE, Brocato ER, Ehrhardt CJ, Greenspoon SA. Simplification of complex DNA profiles using front end cell separation and probabilistic modeling. Forensic Sci Int Genet 2018; 36:205-212. [PMID: 30055432 DOI: 10.1016/j.fsigen.2018.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/26/2018] [Accepted: 07/02/2018] [Indexed: 12/22/2022]
Abstract
Forensic samples comprised of cell populations from multiple contributors often yield DNA profiles that can be extremely challenging to interpret. This frequently results in decreased statistical strength of an individual's association to the mixture and the loss of probative data. The purpose of this study was to test a front-end cell separation workflow on complex mixtures containing as many as five contributors. Our approach involved selectively labelling certain cell populations in dried whole blood mixture samples with fluorescently labeled antibody probe targeting the HLA-A*02 allele, separating the mixture using Fluorescence Activated Cell Sorting (FACS) into two fractions that are enriched in A*02 positive and A*02 negative cells, and then generating DNA profiles for each fraction. We then tested whether antibody labelling and cell sorting effectively reduced the complexity of the original cell mixture by analyzing STR profiles quantitatively using the probabilistic modeling software, TrueAllele® Casework. Results showed that antibody labelling and FACS separation of target populations yielded simplified STR profiles that could be more easily interpreted using conventional procedures. Additionally, TrueAllele® analysis of STR profiles from sorted cell fractions increased statistical strength for the association of most of the original contributors interpreted from the original mixtures.
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Affiliation(s)
- Nancy A Stokes
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, United States
| | - Cristina E Stanciu
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, United States
| | - Emily R Brocato
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, United States
| | - Christopher J Ehrhardt
- Department of Forensic Science, Virginia Commonwealth University, 1015 Floyd Avenue, Richmond, VA, 23284, United States.
| | - Susan A Greenspoon
- Virginia Department of Forensic Science, 700 N. 5th St, Richmond, VA, 23219, United States
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28
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Sheathless coupling of microchip electrophoresis to ESI-MS utilising an integrated photo polymerised membrane for electric contacting. Anal Bioanal Chem 2018; 410:5741-5750. [PMID: 29974150 DOI: 10.1007/s00216-018-1226-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/12/2018] [Accepted: 06/22/2018] [Indexed: 10/28/2022]
Abstract
In this article, we present a novel approach for the sheathless coupling of microchip electrophoresis (MCE) with electrospray mass spectrometry (ESI-MS). The key element is an ion-conductive hydrogel membrane, placed between the separation channel and an adjacent microfluidic supporting channel, contacted via platinum electrodes. This solves the persistent challenge in hyphenation of mass spectrometry to chip electrophoresis, to ensure a reliable electrical connection at the end of the electrophoresis channel without sacrificing separation performance and sensitivity. Stable electric contacting is achieved via a Y-shaped supporting channel structure, separated from the main channel by a photo polymerised, ion permeable hydrogel membrane. Thus, the potential gradient required for performing electrophoretic separations can be generated while simultaneously preventing gas formation due to electrolysis. In contrast to conventional make-up or sheathflow approaches, sample dilution is also avoided. Rapid prototyping allowed the study of different chip-based approaches, i.e. sheathless, open sheathflow and electrode support channel designs, for coupling MCE to ESI-MS. The performance was evaluated with fluorescence microscopy and mass spectrometric detection. The obtained results revealed that the detection sensitivity obtained in such Y-channel chips with integrated hydrogel membranes was superior because sample dilution or loss was prevented. Furthermore, band broadening is reduced compared to similar open structures without a membrane.
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Mapes AA, Stoel RD, de Poot CJ, Vergeer P, Huyck M. Decision support for using mobile Rapid DNA analysis at the crime scene. Sci Justice 2018; 59:29-45. [PMID: 30654966 DOI: 10.1016/j.scijus.2018.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 04/17/2018] [Accepted: 05/02/2018] [Indexed: 11/17/2022]
Abstract
Mobile Rapid DNA technology is close to being incorporated into crime scene investigations, with the potential to identify a perpetrator within hours. However, the use of these techniques entails the risk of losing the sample and potential evidence, because the device not only consumes the inserted sample, it is also is less sensitive than traditional technologies used in forensic laboratories. Scene of Crime Officers (SoCOs) therefore will face a 'time/success rate trade-off' issue when making a decision to apply this technology. In this study we designed and experimentally tested a Decision Support System (DSS) for the use of Rapid DNA technologies based on Rational Decision Theory (RDT). In a vignette study, where SoCOs had to decide on the use of a Rapid DNA analysis device, participating SoCOs were assigned to either the control group (making decisions under standard conditions), the Success Rate (SR) group (making decisions with additional information on DNA success rates of traces), or the DSS group (making decisions supported by introduction to RDT, including information on DNA success rates of traces). This study provides positive evidence that a systematic approach for decision-making on using Rapid DNA analysis assists SoCOs in the decision to use the rapid device. The results demonstrated that participants using a DSS made different and more transparent decisions on the use of Rapid DNA analysis when different case characteristics were explicitly considered. In the DSS group the decision to apply Rapid DNA analysis was influenced by the factors "time pressure" and "trace characteristics" like DNA success rates. In the SR group, the decisions depended solely on the trace characteristics and in the control group the decisions did not show any systematic differences on crime type or trace characteristic. Guiding complex decisions on the use of Rapid DNA analyses with a DSS could be an important step towards the use of these devices at the crime scene.
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Affiliation(s)
- A A Mapes
- Amsterdam University of Applied Sciences (HvA), PO Box 1025, Amsterdam BA 1000, The Netherlands.
| | - R D Stoel
- Netherlands Forensic Institute, Postbus 24044, Den Haag 2490 AA, The Netherlands.
| | - C J de Poot
- Amsterdam University of Applied Sciences (HvA), PO Box 1025, Amsterdam BA 1000, The Netherlands.
| | - P Vergeer
- Netherlands Forensic Institute, Postbus 24044, Den Haag 2490 AA, The Netherlands.
| | - M Huyck
- New York Police Department, Forensic Investigative Division, United States.
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31
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Gibson-Daw G, Crenshaw K, McCord B. Optimization of ultrahigh-speed multiplex PCR for forensic analysis. Anal Bioanal Chem 2017; 410:235-245. [DOI: 10.1007/s00216-017-0715-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/04/2017] [Accepted: 10/17/2017] [Indexed: 11/29/2022]
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DuVall JA, Le Roux D, Thompson BL, Birch C, Nelson DA, Li J, Mills DL, Tsuei AC, Ensenberger MG, Sprecher C, Storts DR, Root BE, Landers JP. Rapid multiplex DNA amplification on an inexpensive microdevice for human identification via short tandem repeat analysis. Anal Chim Acta 2017. [PMID: 28622802 DOI: 10.1016/j.aca.2017.04.051] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Forensic DNA analysis requires several steps, including DNA extraction, PCR amplification, and separation of PCR fragments. Intuitively, there are numerous situations where it would be beneficial to speed up the overall DNA analysis process; in this work, we focus on the most time-consuming component in the analysis pipeline, namely the polymerase chain reaction (PCR). Primers were specially designed to target 10 human genomic loci, all yielding amplicons shorter than 350 bases, for ease of downstream integration with on-board microchip electrophoresis. Primer concentrations were adjusted specifically for microdevice amplification, resulting in well-balanced short tandem repeat (STR) profiles. Furthermore, studies were performed to push the limits of the DNA polymerase to achieve rapid, multiplexed PCR on various substrates, including transparent and black polyethylene terephthalate (Pe), and with two distinct adhesives, toner and heat sensitive adhesive (HSA). Rapid STR-based multiplexed PCR amplification is demonstrated in 15 min on a Pe microdevice using a custom-built system for fluid flow control and thermocycling for the full 10-plex, and in 10 min for a smaller multiplex consisting of six core CODIS loci plus Amelogenin with amplicons shorter than 200bp. Lastly, preliminary studies indicate the capability of this PCR microdevice platform to be integrated with both upstream DNA extraction, and downstream microchip electrophoresis. This, coupled to the use of reagents that are compatible with lyophilization (lyo-compatible) for PCR, represents the potential for a fully integrated rotationally-driven microdevice for complete forensic DNA analysis.
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Affiliation(s)
- Jacquelyn A DuVall
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Delphine Le Roux
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Brandon L Thompson
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Christopher Birch
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Daniel A Nelson
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Jingyi Li
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | - Daniel L Mills
- TeGrex Technologies, Charlottesville, VA 22904, United States
| | - An-Chi Tsuei
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States
| | | | | | | | - Brian E Root
- Applied Research Institute, University of Virginia, Charlottesville, VA 22904, United States
| | - James P Landers
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, United States; Department of Mechanical and Aerospace Engineering, University of Virginia, Charlottesville, VA 22904, United States; Department of Pathology, University of Virginia Health Science Center, Charlottesville, VA 22904, United States; TeGrex Technologies, Charlottesville, VA 22904, United States.
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33
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Katevatis C, Fan A, Klapperich CM. Low concentration DNA extraction and recovery using a silica solid phase. PLoS One 2017; 12:e0176848. [PMID: 28475611 PMCID: PMC5419563 DOI: 10.1371/journal.pone.0176848] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/18/2017] [Indexed: 11/18/2022] Open
Abstract
DNA extraction from clinical samples is commonly achieved with a silica solid phase extraction column in the presence of a chaotrope. Versions of these protocols have been adapted for point of care (POC) diagnostic devices in miniaturized platforms, but commercial kits require a high amount of input DNA. Thus, when the input clinical sample contains less than 1 μg of total DNA, the target-specific DNA recovery from most of these protocols is low without supplementing the sample with exogenous carrier DNA. In fact, many clinical samples used in the development of POC diagnostics often exhibit target DNA concentrations as low as 3 ng/mL. With the broader goal of improving the yield and efficiency of nucleic acid-based POC devices for dilute samples, we investigated both DNA adsorption and recovery from silica particles by using 1 pg- 1 μg of DNA with a set of adsorption and elution buffers ranging in pH and chaotropic presence. In terms of adsorption, we found that low pH and the presence of chaotropic guanidinium thiocyanate (GuSCN) enhanced DNA-silica adsorption. When eluting with a standard low-salt, high-pH buffer, > 70% of DNA was unrecoverable, except when DNA was initially adsorbed with 5 M GuSCN at pH 5.2. Unrecovered DNA was either not initially adsorbed or irreversibly bound on the silica surface. Recovery was improved when eluting with 95°C formamide and 1 M NaOH, which suggested that DNA-silica-chaotrope interactions are dominated by hydrophobic interactions and hydrogen bonding. While heated formamide and NaOH are non-ideal elution buffers for practical POC devices, the salient results are important for engineering a set of optimized reagents that could maximize nucleic acid recovery from a microfluidic DNA-silica-chaotrope system.
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Affiliation(s)
- Constantinos Katevatis
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Andy Fan
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
| | - Catherine M. Klapperich
- Division of Materials Science and Engineering, Boston University, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, United States of America
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Ma S, Murphy TW, Lu C. Microfluidics for genome-wide studies involving next generation sequencing. BIOMICROFLUIDICS 2017; 11:021501. [PMID: 28396707 PMCID: PMC5346105 DOI: 10.1063/1.4978426] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/16/2017] [Indexed: 05/11/2023]
Abstract
Next-generation sequencing (NGS) has revolutionized how molecular biology studies are conducted. Its decreasing cost and increasing throughput permit profiling of genomic, transcriptomic, and epigenomic features for a wide range of applications. Microfluidics has been proven to be highly complementary to NGS technology with its unique capabilities for handling small volumes of samples and providing platforms for automation, integration, and multiplexing. In this article, we review recent progress on applying microfluidics to facilitate genome-wide studies. We emphasize on several technical aspects of NGS and how they benefit from coupling with microfluidic technology. We also summarize recent efforts on developing microfluidic technology for genomic, transcriptomic, and epigenomic studies, with emphasis on single cell analysis. We envision rapid growth in these directions, driven by the needs for testing scarce primary cell samples from patients in the context of precision medicine.
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Affiliation(s)
- Sai Ma
- Department of Biomedical Engineering and Mechanics, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Travis W Murphy
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, USA
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35
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Enzyme Logic Systems: Biomedical and Forensic Biosensor Applications. SPRINGER SERIES ON CHEMICAL SENSORS AND BIOSENSORS 2017. [DOI: 10.1007/5346_2017_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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36
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Campbell R, Pierce SJ, Sharma DB, Shaw J, Feeney H, Nye J, Schelling K, Fehler-Cabral G. Comparing Standard and Selective Degradation DNA Extraction Methods: Results from a Field Experiment with Sexual Assault Kits,. J Forensic Sci 2016; 62:213-222. [DOI: 10.1111/1556-4029.13251] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/18/2016] [Accepted: 04/24/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Rebecca Campbell
- Department of Psychology; Michigan State University; East Lansing MI
| | - Steven J. Pierce
- Center for Statistical Training & Consultation; Michigan State University; East Lansing MI
| | - Dhruv B. Sharma
- Center for Statistical Training & Consultation; Michigan State University; East Lansing MI
| | - Jessica Shaw
- Department of Social Work; Boston College; Chestnut Hill MA
| | - Hannah Feeney
- Department of Psychology; Michigan State University; East Lansing MI
| | - Jeffrey Nye
- Michigan State Police; Forensic Science Division; Lansing MI
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37
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Cox JO, DeCarmen TS, Ouyang Y, Strachan B, Sloane H, Connon C, Gibson K, Jackson K, Landers JP, Cruz TD. A novel, integrated forensic microdevice on a rotation-driven platform: Buccal swab to STR product in less than 2 h. Electrophoresis 2016; 37:3046-3058. [PMID: 27620618 DOI: 10.1002/elps.201600307] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/25/2016] [Accepted: 09/01/2016] [Indexed: 11/08/2022]
Abstract
This work describes the development of a novel microdevice for forensic DNA processing of reference swabs. This microdevice incorporates an enzyme-based assay for DNA preparation, which allows for faster processing times and reduced sample handling. Infrared-mediated PCR (IR-PCR) is used for STR amplification using a custom reaction mixture, allowing for amplification of STR loci in 45 min while circumventing the limitations of traditional block thermocyclers. Uniquely positioned valves coupled with a simple rotational platform are used to exert fluidic control, eliminating the need for bulky external equipment. All microdevices were fabricated using laser ablation and thermal bonding of PMMA layers. Using this microdevice, the enzyme-mediated DNA liberation module produced DNA yields similar to or higher than those produced using the traditional (tube-based) protocol. Initial microdevice IR-PCR experiments to test the amplification module and reaction (using Phusion Flash/SpeedSTAR) generated near-full profiles that suffered from interlocus peak imbalance and poor adenylation (significant -A). However, subsequent attempts using KAPA 2G and Pfu Ultra polymerases generated full STR profiles with improved interlocus balance and the expected adenylated product. A fully integrated run designed to test microfluidic control successfully generated CE-ready STR amplicons in less than 2 h (<1 h of hands-on time). Using this approach, high-quality STR profiles were developed that were consistent with those produced using conventional DNA purification and STR amplification methods. This method is a smaller, more elegant solution than current microdevice methods and offers a cheaper, hands-free, closed-system alternative to traditional forensic methods.
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Affiliation(s)
- Jordan O Cox
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Yiwen Ouyang
- Departments of Chemistry, Mechanical and Aerospace Engineering, & Pathology, University of Virginia, Charlottesville, VA, USA
| | - Briony Strachan
- Departments of Chemistry, Mechanical and Aerospace Engineering, & Pathology, University of Virginia, Charlottesville, VA, USA
| | - Hillary Sloane
- Departments of Chemistry, Mechanical and Aerospace Engineering, & Pathology, University of Virginia, Charlottesville, VA, USA
| | - Cathey Connon
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Kemper Gibson
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Kimberly Jackson
- Departments of Chemistry, Mechanical and Aerospace Engineering, & Pathology, University of Virginia, Charlottesville, VA, USA
| | - James P Landers
- Departments of Chemistry, Mechanical and Aerospace Engineering, & Pathology, University of Virginia, Charlottesville, VA, USA
| | - Tracey Dawson Cruz
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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38
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Jackson K, Borba J, Meija M, Mills D, Haverstick D, Olson K, Aranda R, Garner G, Carrilho E, Landers J. DNA purification using dynamic solid-phase extraction on a rotationally-driven polyethylene-terephthalate microdevice. Anal Chim Acta 2016; 937:1-10. [DOI: 10.1016/j.aca.2016.06.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 12/21/2022]
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39
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Krauss ST, Remcho TP, Lipes SM, Aranda R, Maynard HP, Shukla N, Li J, Tontarski RE, Landers JP. Objective Method for Presumptive Field-Testing of Illicit Drug Possession Using Centrifugal Microdevices and Smartphone Analysis. Anal Chem 2016; 88:8689-97. [DOI: 10.1021/acs.analchem.6b01982] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shannon T. Krauss
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - Thomas P. Remcho
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - Shelby M. Lipes
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - Roman Aranda
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - Henry P. Maynard
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - Nishant Shukla
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - Jingyi Li
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - Richard E. Tontarski
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
| | - James P. Landers
- Department of Chemistry, ∥Department of Computer
Science, ⊥Department of Mechanical and Aerospace
Engineering, and #Department of Pathology, University of Virginia, Charlottesville, Virginia 22904, United States
- Office of the Chief
Scientist and §Forensic Exploitation Directorate, Defense Forensic Science Center, Forest
Park, Georgia 30297, United States
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40
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Microfluidic Devices for Forensic DNA Analysis: A Review. BIOSENSORS-BASEL 2016; 6:bios6030041. [PMID: 27527231 PMCID: PMC5039660 DOI: 10.3390/bios6030041] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/07/2016] [Accepted: 07/25/2016] [Indexed: 12/16/2022]
Abstract
Microfluidic devices may offer various advantages for forensic DNA analysis, such as reduced risk of contamination, shorter analysis time and direct application at the crime scene. Microfluidic chip technology has already proven to be functional and effective within medical applications, such as for point-of-care use. In the forensic field, one may expect microfluidic technology to become particularly relevant for the analysis of biological traces containing human DNA. This would require a number of consecutive steps, including sample work up, DNA amplification and detection, as well as secure storage of the sample. This article provides an extensive overview of microfluidic devices for cell lysis, DNA extraction and purification, DNA amplification and detection and analysis techniques for DNA. Topics to be discussed are polymerase chain reaction (PCR) on-chip, digital PCR (dPCR), isothermal amplification on-chip, chip materials, integrated devices and commercially available techniques. A critical overview of the opportunities and challenges of the use of chips is discussed, and developments made in forensic DNA analysis over the past 10–20 years with microfluidic systems are described. Areas in which further research is needed are indicated in a future outlook.
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41
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Roux C, Talbot-Wright B, Robertson J, Crispino F, Ribaux O. The end of the (forensic science) world as we know it? The example of trace evidence. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0260. [PMID: 26101285 DOI: 10.1098/rstb.2014.0260] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The dominant conception of forensic science as a patchwork of disciplines primarily assisting the criminal justice system (i.e. forensics) is in crisis or at least shows a series of anomalies and serious limitations. In recent years, symptoms of the crisis have been discussed in a number of reports by various commentators, without a doubt epitomized by the 2009 report by the US National Academies of Sciences (NAS 2009 Strengthening forensic science in the United States: a path forward). Although needed, but viewed as the solution to these drawbacks, the almost generalized adoption of stricter business models in forensic science casework compounded with ever-increasing normative and compliance processes not only place additional pressures on a discipline that already appears in difficulty, but also induce more fragmentation of the different forensic science tasks, a tenet many times denounced by the same NAS report and other similar reviews. One may ask whether these issues are not simply the result of an unfit paradigm. If this is the case, the current problems faced by forensic science may indicate future significant changes for the discipline. To facilitate broader discussion this presentation focuses on trace evidence, an area that is seminal to forensic science both for epistemological and historical reasons. There is, however, little doubt that this area is currently under siege worldwide. Current and future challenges faced by trace evidence are discussed along with some possible answers. The current situation ultimately presents some significant opportunities to re-invent not only trace evidence but also forensic science. Ultimately, a distinctive, more robust and more reliable science may emerge through rethinking the forensics paradigm built on specialisms, revisiting fundamental forensic science principles and adapting them to the twenty-first century.
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Affiliation(s)
- Claude Roux
- Centre for Forensic Science, University of Technology Sydney, Broadway, New South Wales 2007, Australia
| | - Benjamin Talbot-Wright
- Centre for Forensic Science, University of Technology Sydney, Broadway, New South Wales 2007, Australia
| | - James Robertson
- National Centre for Forensic Studies, University of Canberra, Australian Capital Territory 2601, Australia
| | - Frank Crispino
- Département Chimie, biochimie et physique, Laboratoire de recherche en criminalistique, Université du Québec à Trois-Rivières, et Centre international de criminologie comparée, Canada
| | - Olivier Ribaux
- Ecole des Sciences Criminelles, University of Lausanne, 1015 Lausanne, Switzerland
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42
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Introducing curcumin as an electrochemical DNA hybridization indicator and its application for detection of human interleukin-2 gene. J Solid State Electrochem 2016. [DOI: 10.1007/s10008-016-3168-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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43
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Evaluation of samples comprising minute amounts of DNA. Sci Justice 2015; 55:316-22. [DOI: 10.1016/j.scijus.2015.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/01/2015] [Accepted: 05/04/2015] [Indexed: 01/31/2023]
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44
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Romsos EL, Vallone PM. Rapid PCR of STR markers: Applications to human identification. Forensic Sci Int Genet 2015; 18:90-9. [DOI: 10.1016/j.fsigen.2015.04.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/03/2015] [Accepted: 04/21/2015] [Indexed: 10/23/2022]
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45
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Kim YT, Heo HY, Oh SH, Lee SH, Kim DH, Seo TS. Microchip-based forensic short tandem repeat genotyping. Electrophoresis 2015; 36:1728-37. [DOI: 10.1002/elps.201400477] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Revised: 03/06/2015] [Accepted: 04/20/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Yong Tae Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Hyun Young Heo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Shin Hye Oh
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Seung Hwan Lee
- DNA Analysis Laboratory, Division of Forensic DNA; Supreme Prosecutors’ Office; Seoul Republic of Korea
| | - Do Hyun Kim
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
| | - Tae Seok Seo
- Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon Republic of Korea
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46
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Moreira Gabriel EF, Tomazelli Coltro WK, Garcia CD. Fast and versatile fabrication of PMMA microchip electrophoretic devices by laser engraving. Electrophoresis 2015; 35:2325-32. [PMID: 25113407 DOI: 10.1002/elps.201470140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This paper describes the effects of different modes and engraving parameters on the dimensions of microfluidic structures produced in PMMA using laser engraving. The engraving modes included raster and vector, while the explored engraving parameters included power, speed, frequency, resolution, line-width, and number of passes. Under the optimum conditions, the technique was applied to produce channels suitable for CE separations. Taking advantage of the possibility to cut-through the substrates, the laser was also used to define solution reservoirs (buffer, sample, and waste) and a PDMS-based decoupler. The final device was used to perform the analysis of a model mixture of phenolic compounds within 200 s with baseline resolution.
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47
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Bartsch MS, Edwards HS, Lee D, Moseley CE, Tew KE, Renzi RF, Van de Vreugde JL, Kim H, Knight DL, Sinha A, Branda SS, Patel KD. The rotary zone thermal cycler: a low-power system enabling automated rapid PCR. PLoS One 2015; 10:e0118182. [PMID: 25826708 PMCID: PMC4380418 DOI: 10.1371/journal.pone.0118182] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 01/09/2015] [Indexed: 12/17/2022] Open
Abstract
Advances in molecular biology, microfluidics, and laboratory automation continue to expand the accessibility and applicability of these methods beyond the confines of conventional, centralized laboratory facilities and into point of use roles in clinical, military, forensic, and field-deployed applications. As a result, there is a growing need to adapt the unit operations of molecular biology (e.g., aliquoting, centrifuging, mixing, and thermal cycling) to compact, portable, low-power, and automation-ready formats. Here we present one such adaptation, the rotary zone thermal cycler (RZTC), a novel wheel-based device capable of cycling up to four different fixed-temperature blocks into contact with a stationary 4-microliter capillary-bound sample to realize 1-3 second transitions with steady state heater power of less than 10 W. We demonstrate the utility of the RZTC for DNA amplification as part of a highly integrated rotary zone PCR (rzPCR) system that uses low-volume valves and syringe-based fluid handling to automate sample loading and unloading, thermal cycling, and between-run cleaning functionalities in a compact, modular form factor. In addition to characterizing the performance of the RZTC and the efficacy of different online cleaning protocols, we present preliminary results for rapid single-plex PCR, multiplex short tandem repeat (STR) amplification, and second strand cDNA synthesis.
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Affiliation(s)
- Michael S. Bartsch
- Sandia National Laboratories, Livermore, CA, United States of America
- * E-mail:
| | | | - Daniel Lee
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Karen E. Tew
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Ronald F. Renzi
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Hanyoup Kim
- Sandia National Laboratories, Livermore, CA, United States of America
| | | | - Anupama Sinha
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Steven S. Branda
- Sandia National Laboratories, Livermore, CA, United States of America
| | - Kamlesh D. Patel
- Sandia National Laboratories, Livermore, CA, United States of America
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48
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DNA copy number concentration measured by digital and droplet digital quantitative PCR using certified reference materials. Anal Bioanal Chem 2015; 407:1831-40. [PMID: 25600685 PMCID: PMC4336415 DOI: 10.1007/s00216-015-8458-z] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 12/19/2014] [Accepted: 01/05/2015] [Indexed: 01/31/2023]
Abstract
The value assignment for properties of six certified reference materials (ERM-AD623a–f), each containing a plasmid DNA solution ranging from 1 million to 10 copies per μL, by using digital PCR (dPCR) with the BioMark™ HD System (Fluidigm) has been verified by applying droplet digital PCR (ddPCR) using the QX100 system (Bio-Rad). One of the critical factors in the measurement of copy number concentrations by digital PCR is the partition volume. Therefore, we determined the average droplet volume by optical microscopy, revealing an average droplet volume that is 8 % smaller than the droplet volume used as the defined parameter in the QuantaSoft software version 1.3.2.0 (Bio-Rad) to calculate the copy number concentration. This observation explains why copy number concentrations estimated with ddPCR and using an average droplet volume predefined in the QuantaSoft software were systematically lower than those measured by dPCR, creating a significant bias between the values obtained by these two techniques. The difference was not significant anymore when the measured droplet volume of 0.834 nL was used to estimate copy number concentrations. A new version of QuantaSoft software (version 1.6.6.0320), which has since been released with Bio-Rad’s new QX200 systems and QX100 upgrades, uses a droplet volume of 0.85 nL as a defined parameter to calculate copy number concentration. Monolayer of droplets generated by the droplet generator and observed under an optical microscope ![]()
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49
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Au nanoparticles enhanced fluorescence detection of DNA hybridization in picoliter microfluidic droplets. Biomed Microdevices 2014; 16:479-85. [PMID: 24599582 DOI: 10.1007/s10544-014-9850-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
This work reports a facile microfluidic device for Au-nanoparticle enhanced fluorescence detection of tiny amount of nucleotides within droplets in a high-throughput way. Droplets containing single strand DNA probe and relevant complementary strands DNA(cDNA) are generated in flow-focusing manner and the hybridization between them is realized in droplets flowing along a long serpentine channel. In order to find the optimal experimental condition, finite element method simulation is used to predict the interface evolution between the two phase liquids. Based on the fluorescence emited by intercalator reacted with the generated double-strand DNA(dsDNA), the target cDNA with a concentration of 1nM can be detected in droplets. And when we adopt Au nanoparticles to immobilize DNA probe which can amplify the fluorescence intensity, 10pM completary DNA could be detected. Due to the advantages in high-throughput and compartmentalization of this droplet platform, the detection procedure can be finished in 3 h. Our method shows good potential application in facile, sensitive, low cost and fast DNA detection for applications in personal health care.
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50
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Luo DB, Duan YX, He Y, Gao B. A novel DC microplasma sensor constructed in a cavity PDMS chamber with needle electrodes for fast detection of methanol-containing spirit. Sci Rep 2014; 4:7451. [PMID: 25502881 PMCID: PMC4264012 DOI: 10.1038/srep07451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 11/20/2014] [Indexed: 11/26/2022] Open
Abstract
A novel microplasma device, for the first time, was constructed in a cavity Poly (dimethylsiloxane) (PDMS) chamber with two normal syringe needles serve as both the gas channels and the electrodes. This device employs argon plasma with direct current for molecular fragmentation and excitation. The microplasma is generated at atmospheric pressure in the PDMS chamber of 0.5 mL (5 × 10 × 10 mm3) volume with a sealable plug. Since the microplasma is maintained in a chamber by separation of the discharge zone and the substrate, stability for a long time of the microplasma is realized which could be observed by argon background emission fluctuation and SEM characterization. This property is beneficial for spectrometric detection of many volatile organics in this chamber. Besides, this kind of microplasma sensor has advantages such as flexibility in replacement of electrodes, convenience in clearance of the discharge chamber, small instrument volume, simple structure, and ease of operation. In addition, methanol-containing spirit samples were chosen to estimate the detecting performance of this microplasma for volatile organic compounds (VOCs) analysis by molecular emission spectrometry. Significant differences are observed upon the introduction of the spirit and the methanol-containing spirit samples. A detection limit of 0.3% is obtained on this microplasma device.
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Affiliation(s)
- Dai-bing Luo
- 1] Analytical &Testing Center, Sichuan University [2] Research Center of Analytical Instrumentation, Key laboratory of bio-resource and eco environment, ministry of education, College of Life Sciences, Sichuan University
| | - Yi-xiang Duan
- Research Center of Analytical Instrumentation, Key laboratory of bio-resource and eco environment, ministry of education, College of Life Sciences, Sichuan University
| | - Yi He
- Analytical &Testing Center, Sichuan University
| | - Bo Gao
- Analytical &Testing Center, Sichuan University
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