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Kshirsagar A, Choi G, Santosh V, Harvey T, Bernhards RC, Guan W. Handheld Purification-Free Nucleic Acid Testing Device for Point-of-Need Detection of Malaria from Whole Blood. ACS Sens 2023; 8:673-683. [PMID: 36696460 PMCID: PMC11214673 DOI: 10.1021/acssensors.2c02169] [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] [Indexed: 01/26/2023]
Abstract
World Health Organization's aim to eliminate malaria from developing/resource-limited economies requires easy access to low-cost, highly sensitive, and specific screening. We present a handheld nucleic acid testing device with on-chip automated sample preparation to detect malaria (Plasmodium falciparum) infection from a whole blood sample as a feasibility study. We used a simple two-reagent-based purification-free protocol to prepare the whole blood sample on a piezo pump pressure-driven microfluidic cartridge. The cartridge includes a unique mixing chamber for sample preparation and metering structures to dispense a predetermined volume of the sample lysate mixture into four chambers containing a reaction mix. The parasite genomic DNA concentration can be estimated by monitoring the fluorescence generated from the loop-mediated isothermal amplification reaction in real time. We achieved a sensitivity of ∼0.42 parasite/μL of whole blood, sufficient for detecting asymptomatic malaria parasite carriers.
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Affiliation(s)
- Aneesh Kshirsagar
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
| | - Gihoon Choi
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
| | - Vishaka Santosh
- U.S. Army, DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Tara Harvey
- U.S. Army, DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Robert Cory Bernhards
- U.S. Army, DEVCOM Chemical Biological Center, Aberdeen Proving Ground, MD, 21010, USA
| | - Weihua Guan
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA
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Heng ZS, Koh DW, Yeo JY, Ooi C, Gan SK. Effects of different delivery modes on teaching biomedical science practical skills in higher education during the 2021 pandemic measures. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:403-413. [PMID: 35621717 PMCID: PMC9347998 DOI: 10.1002/bmb.21637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 04/28/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
The COVID-19 pandemic related measures had augmented the rise of online education. While online teaching had mitigated the negative impacts from educational institutional closures, it was unable to displace hands-on biomedical laboratory practical lessons effectively. Without practical sessions, there was concern over the imparting of laboratory skills even with video demonstrations. To investigate the effectiveness of different delivery modes in imparting laboratory skills, theoretical and practical student assessments were analyzed alongside an anonymous survey on their motivation and prior experience. The undergraduate students were exposed to (1) instructor-live demonstration; (2) video demonstration or (3) no demonstration prior to the practical test which was a plasmid extraction. Significantly higher mini-prep yields and purity were found for both instructor-live and video demonstrations compared to no demonstration. Comparison with pre-pandemic theoretical assessment performance showed no significant differences despite longer contact hours during pre-pandemic times. Prior lab experience and motivation for selecting the course did not significantly affect student mini-prep yields. In conclusion, our findings suggest that video demonstrations were as effective as instructor-live demonstrations during the pandemic without noticeably compromising the teaching and learning of biomedical laboratory skills.
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Affiliation(s)
- Zealyn Shi‐Lin Heng
- Antibody & Product Development (APD) Lab, EDDC‐BII, Agency for ScienceTechnology and Research (A*STAR)SingaporeSingapore
| | - Darius Wen‐Shuo Koh
- Antibody & Product Development (APD) Lab, EDDC‐BII, Agency for ScienceTechnology and Research (A*STAR)SingaporeSingapore
| | - Joshua Yi Yeo
- Antibody & Product Development (APD) Lab, EDDC‐BII, Agency for ScienceTechnology and Research (A*STAR)SingaporeSingapore
| | - Chui‐Ping Ooi
- School of Science and TechnologySingapore University of Social Sciences (SUSS)SingaporeSingapore
| | - Samuel Ken‐En Gan
- Antibody & Product Development (APD) Lab, EDDC‐BII, Agency for ScienceTechnology and Research (A*STAR)SingaporeSingapore
- School of Science and TechnologySingapore University of Social Sciences (SUSS)SingaporeSingapore
- APD SKEG Pte LtdSingaporeSingapore
- James Cook UniversitySingaporeSingapore
- Wenzhou Municipal Key Lab of Applied Biomedical and Biopharmaceutical InformaticsWenzhou‐Kean UniversityWenzhouZhejiang ProvinceChina
- Zhejiang Bioinformatics International Science and Technology Cooperation CenterWenzhou‐Kean UniversityWenzhouZhejiang ProvinceChina
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Chen ZL, Xu JQ. Purification of quantum dot-based bioprobes with a salting out strategy. NANOSCALE ADVANCES 2022; 4:393-396. [PMID: 36132697 PMCID: PMC9417310 DOI: 10.1039/d1na00569c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 12/08/2021] [Indexed: 06/16/2023]
Abstract
A salting out strategy is reported for purification of IgG-conjugated QD (IgG-QD) bioprobes. Adding NaCl can precipitate free IgG selectively, while the IgG-QD maintains good colloidal stability. The dynamic light scattering technique reveals that this is due to the relatively positive zeta potential of free IgG than that of the IgG-QD.
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Affiliation(s)
- Zhi-Liang Chen
- School of Pharmacy, Shaoyang University Shaoyang 422000 P. R. China
| | - Jia-Quan Xu
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology Nanchang 330013 China +86-739-5308282
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Resmi PE, Suneesh PV, Ramachandran T, Babu TGS. Paper based micro/nanofluidics devices for biomedical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 186:159-190. [PMID: 35033283 DOI: 10.1016/bs.pmbts.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This chapter details the significance, fabrication and biomedical applications of paper-based microfluidic devices. The first part of the chapter describes the importance of paper diagnostic devices, highlighting pretreatment, dipsticks, lateral flow assays, and microPADs. Various methods followed for the fabrication of the paper analytical devices are discussed in the second part. The last part is about some of the important biomedical applications of paper analytical devices. Finally, the challenges and research gaps in the paper microfluidics for biomedical applications are presented.
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Affiliation(s)
- P E Resmi
- Amrita Biosensor Research Lab, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India
| | - P V Suneesh
- Amrita Biosensor Research Lab, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India; Department of Sciences, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India
| | - T Ramachandran
- Department of Sciences, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India
| | - T G Satheesh Babu
- Amrita Biosensor Research Lab, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India; Department of Sciences, Amrita School of Engineering Coimbatore, Amrita Vishwa Vidyapeetham, Coimbatore, India.
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Thean RKR, Ong DXY, Heng ZSL, Gan SKE, Yeo JY. To Plate or to Simply Unfreeze, That Is the Question for Optimal Plasmid Extraction. J Biomol Tech 2021; 32:57-62. [PMID: 34121935 PMCID: PMC8174125 DOI: 10.7171/jbt.20-3203-001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Many molecular biology applications require fast plasmid DNA extraction, spurring multiple studies on how to speed up the process. It is regularly instructed in standard laboratory protocols to plate out frozen glycerol bacterial stocks prior to bacteria incubation in liquid media and subsequent plasmid extraction, although the rationale for this is often unexplained (other than for the isolation of single colonies). Given the commonality and importance of this laboratory operation, such a practice is time-consuming and laborious. To study the impact of this practice and the alternative direct culturing method, we investigated the association between bacterial cell mass and its potential influence on plasmid yields from the 2 methods. Our results showed no difference with preplating for 7 out of 8 plasmid constructs used in the study, suggesting that direct glycerol recovery would not lead to poorer plasmid yields. The findings support the rationale for direct glycerol recovery for plasmid extraction, without the need of an intermediate preplating step.
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Affiliation(s)
| | | | | | - Samuel Ken-En Gan
- Antibody & Product Development Lab, A*STAR, Singapore 138671, Singapore
- Experimental Drug Development Centre, A*STAR, Singapore 138670, Singapore; and
- p53 Laboratory, A*STAR, Singapore 138648, Singapore
| | - Joshua Yi Yeo
- Antibody & Product Development Lab, A*STAR, Singapore 138671, Singapore
- Experimental Drug Development Centre, A*STAR, Singapore 138670, Singapore; and
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Lu Y, Bianco P. High-yield purification of exceptional-quality, single-molecule DNA substrates. J Biol Methods 2021; 8:e145. [PMID: 33889652 PMCID: PMC8054919 DOI: 10.14440/jbm.2021.350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/10/2020] [Accepted: 01/02/2021] [Indexed: 12/13/2022] Open
Abstract
Single-molecule studies involving DNA or RNA, require homogeneous preparations of nucleic acid substrates of exceptional quality. Over the past several years, a variety of methods have been published describing different purification methods but these are frustratingly inconsistent with variable yields even in the hands of experienced bench scientists. To address these issues, we present an optimized and straightforward, column-based approach that is reproducible and produces high yields of substrates or substrate components of exceptional quality. Central to the success of the method presented is the use of a non-porous anion exchange resin. In addition to the use of this resin, we encourage the optimization of each step in the construction of substrates. The fully optimized method produces high yields of a hairpin DNA substrate of exceptional quality. While this substrate is suitable for single-molecule, magnetic tweezer experiments, the described method is readily adaptable to the production of DNA substrates for the majority of single-molecule studies involving nucleic acids ranging in size from 70–15000 bp.
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Affiliation(s)
- Yue Lu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
| | - Piero Bianco
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, Omaha, NE 68198-6025, USA
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Continuous Microfluidic Purification of DNA Using Magnetophoresis. MICROMACHINES 2020; 11:mi11020187. [PMID: 32054004 PMCID: PMC7074667 DOI: 10.3390/mi11020187] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Automatic microfluidic purification of nucleic acid is predictable to reduce the input of original samples and improve the throughput of library preparation for sequencing. Here, we propose a novel microfluidic system using an external NdFeB magnet to isolate DNA from the polymerase chain reaction (PCR) mixture. The DNA was purified and isolated when the DNA-carrying beads transported to the interface of multi-laminar flow under the influence of magnetic field. Prior to the DNA recovery experiments, COMSOL simulations were carried out to study the relationship between trajectory of beads and magnet positions as well as fluid velocities. Afterwards, the experiments to study the influence of varying velocities and input of samples on the DNA recovery were conducted. Compared to experimental results, the relative error of the final position of beads is less than 10%. The recovery efficiency decreases with increase of input or fluid velocity, and the maximum DNA recovery efficiency is 98.4% with input of l00 ng DNA at fluid velocity of 1.373 mm/s. The results show that simulations significantly reduce the time for parameter adjustment in experiments. In addition, this platform uses a basic two-layer chip to realize automatic DNA isolation without any other liquid switch value or magnet controller.
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Ling WL, Ng YL, Wipat A, Lane DP, Gan SKE. The quantification of antibody elements and receptors subunit expression using qPCR: The design of VH, VL, CH, CL, FcR subunits primers for a more holistic view of the immune system. J Immunol Methods 2019; 476:112683. [PMID: 31682797 DOI: 10.1016/j.jim.2019.112683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/20/2019] [Accepted: 10/09/2019] [Indexed: 12/18/2022]
Abstract
The expression levels of immunoglobulin elements and their receptors are important markers for health and disease. Within the immunoglobulin locus, the constant regions and the variable region families are associated with certain pathologies, yet a holistic view of the interaction between the expressions of the multiple genes remain to be fully characterized. There is thus an important need to quantify antibody elements, their receptors and the receptor subunits in blood (PBMC cDNA) for both screening and detailed studies of such associations. Leveraging on qPCR, we designed primers for all Vκ1-6, VH1-7, Vλ1-11, nine CH isotypes, Cκ, Cκ, Cλ1 &3, FcεRI α,β, and γ subunits, all three FcγR and their subunits, and FcαR. Validating this on a volunteer PBMC cDNA, we report a qPCR primer set repertoire that can quantify the relative expression of all the above genes to the GAPDH housekeeping gene, with implications and uses in both clinical monitoring and research.
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Affiliation(s)
- Wei-Li Ling
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; Newcastle Research and Innovation Institute (NewRIIS), Singapore.
| | - Yuen-Ling Ng
- Newcastle Research and Innovation Institute (NewRIIS), Singapore.
| | - Anil Wipat
- School of Computing, Newcastle University, UK.
| | - David Philip Lane
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore.
| | - Samuel Ken-En Gan
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore; p53 Laboratory, Agency for Science, Technology and Research (A*STAR), Singapore.
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Mandal G, Das S, Padmanabhan S. Development of a Membrane-Based Method for Isolation of Genomic DNA from Human Blood. J Biomol Tech 2018; 29:46-53. [PMID: 29623006 DOI: 10.7171/jbt.18-2902-001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
High quality and sufficient quantity of genomic DNA (gDNA) are the primary requisites of several molecular biologic applications, including clinical studies related to genetics, genomics, gene polymorphism, and DNA fingerprinting. Whole blood is the primary source of gDNA in most of the clinical investigations. Currently, commercial kits are primarily used to achieve these goals. However, the use of kits is limited by the cost and involvement of several centrifugal steps. Other methods reported are either laborious or do not produce high quality or quantity of gDNA or both. Here, we present the data on the development of a centrifugation-free, cost-effective, and user-friendly method for the isolation of human gDNA from the buffy coat of human blood that involves limited numbers of steps with about 15 min of hands-on time per sample.
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Affiliation(s)
- Goutam Mandal
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
| | - Subhasish Das
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
| | - Sriram Padmanabhan
- Cancyte Technologies Pvt. Ltd., Sri Shankara Research Center, Rangadore Memorial Hospital, Bangalore 560004, India
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Tang R, Yang H, Choi JR, Gong Y, Hu J, Wen T, Li X, Xu B, Mei Q, Xu F. Paper-based device with on-chip reagent storage for rapid extraction of DNA from biological samples. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2225-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Tang RH, Yang H, Choi JR, Gong Y, Feng SS, Pingguan-Murphy B, Huang QS, Shi JL, Mei QB, Xu F. Advances in paper-based sample pretreatment for point-of-care testing. Crit Rev Biotechnol 2016; 37:411-428. [DOI: 10.3109/07388551.2016.1164664] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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