1
|
Yang W, Pu X, Xie W, Li L, Ding Z, Jia L. Isopropanol-promoted DNA extraction by polydopamine functionalized magnetic particles based on metal coordination. Talanta 2024; 275:126115. [PMID: 38663068 DOI: 10.1016/j.talanta.2024.126115] [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] [Received: 01/04/2024] [Revised: 04/08/2024] [Accepted: 04/13/2024] [Indexed: 05/30/2024]
Abstract
High-quality DNA is an important guarantee to start downstream experiments in many biological and medical research areas. Magnetic particle-based DNA extraction methods from blood mainly depend on electrostatic adsorption in a low-pH environment. However, the strong acidic environment can influence the DNA stability. Herein, a polydopamine-functionalized magnetic particle (PDA@Fe3O4)-based protocol was developed for DNA extraction from whole blood samples. In the protocol, Mg2+ and Ca2+ were utilized to bridge the adsorption of DNA by PDA@Fe3O4 via the metal-mediated coordination. Isopropanol was found to efficiently promote DNA adsorption by triggering the change of the conformation of DNA from B-form to more compact A-form. In 50 % isopropanol solution, the DNA adsorption efficiency was nearly 100 % in the presence of 0.5 mM Ca2+ or 1.5 mM Mg2+. The role of metal ions and isopropanol in DNA adsorption was explored. The protocol averts the strong acidic environment and PCR inhibitors, such as high concentrations of salt or polyethylene glycol. It demonstrates superiority in DNA yield (59.13 ± 3.63 ng μL-1) over the commercial kit (27.33 ± 4.98 ng μL-1) and phenol-chloroform methods (37.90 ± 0.47 ng μL-1). In addition, to simplify the operastion, an automated nucleic acid extraction device was designed and fabricated to extract whole genomic DNA from blood. The feasibility of the device was verified by extracting DNA from cattle and pig blood samples. The extracted DNA was successfully applied to discriminate the beef authenticity by a duplex PCR system. The results demonstrate that the DNA extraction protocol and the automated device have great potential in blood samples.
Collapse
Affiliation(s)
- Wenjuan Yang
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Xiaoxiao Pu
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Wenting Xie
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Ling Li
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Zixuan Ding
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Li Jia
- Ministry of Education Key Laboratory of Laser Life Science & Guangdong Provincial Key Laboratory of Laser Life Science & Guangzhou Key Laboratory of Spectral Analysis and Functional Probes, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
| |
Collapse
|
2
|
Peng Y, Hu R, Xue S, He Y, Tian L, Pang Z, He Y, Dong Y, Shi Y, Wang S, Hong B, Liu K, Wang R, Song L, Fan H, Li M, Tong Y. Rapid and highly sensitive colorimetric LAMP assay and integrated device for visual detection of monkeypox virus. Anal Chim Acta 2024; 1311:342720. [PMID: 38816155 DOI: 10.1016/j.aca.2024.342720] [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] [Received: 01/03/2024] [Revised: 04/30/2024] [Accepted: 05/12/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND The monkeypox virus (MPXV) is a linear double-stranded DNA virus with a large genome that causes tens of thousands of infections and hundreds of deaths in at least 40 countries and regions worldwide. Therefore, timely and accurate diagnostic testing could be an important measure to prevent the ongoing spread of MPXV and widespread epidemics. RESULTS Here, we designed multiple sets of primers for the target region of MPXV for loop-mediated isothermal amplification (LAMP) detection and identified the optimal primer set. Then, the specificity in fluorescent LAMP detection was verified using the plasmids containing the target gene, pseudovirus and other DNA/RNA viruses. We also evaluated the sensitivity of the colorimetric LAMP detection system using the plasmid and pseudovirus samples, respectively. Besides, we used monkeypox pseudovirus to simulate real samples for detection. Subsequent to the establishment and introduction of a magnetic beads (MBs)-based nucleic acid extraction technique, an integrated device was developed, characterized by rapidity, high sensitivity, and remarkable specificity. This portable system demonstrated a visual detection limit of 137 copies/mL, achieving sample-to-answer detection within 1 h. SIGNIFICANCE The device has the advantages of integration, simplicity, miniaturization, and visualization, which help promote the realization of accurate, rapid, portable, and low-cost testing. Meanwhile, this platform could facilitate efficient, cost-effective and easy-operable point-of-care testing (POCT) in diverse resource-limited settings in addition to the laboratory.
Collapse
Affiliation(s)
- Yadan Peng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ruolan Hu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuang Xue
- College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yugan He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lili Tian
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zehan Pang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yuqi Dong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Yinghan Shi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Shuqi Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Bixia Hong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ke Liu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Ruixue Wang
- College of Mechanical and Electrical Engineering, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; School of Life Sciences, Tianjin University, Tianjin, 300072, China.
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, 100029, China.
| |
Collapse
|
3
|
Sugishita Y, Moriuchi R, Ishii Y. External quality assessment survey for SARS-CoV-2 nucleic acid amplification tests in clinical laboratories in Tokyo, 2021. J Infect Chemother 2024; 30:633-641. [PMID: 38325625 DOI: 10.1016/j.jiac.2024.01.016] [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] [Received: 11/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
INTRODUCTION Nucleic acid amplification tests (NAATs) play a pivotal role in clinical laboratories for diagnosing COVID-19. This study aimed to elucidate the accuracy of these tests. METHODS In 2021, an external quality assessment of NAATs for SARS-CoV-2 was conducted in 47 laboratories in Tokyo, Japan. In open testing, where the laboratories knew that the samples were intended for the survey, a simulated nasopharyngeal swab suspension sample was used, featuring a positive sample A with a viral concentration of 50 copies/μL, positive sample B with 5 copies/μL, and a negative sample. Laboratories employing real-time RT-PCR were required to report cycle threshold (Ct) values. In blind testing, where the samples were processed as normal test samples, a positive sample C with 50 copies/μL was prepared using a simulated saliva sample. RESULTS Of the 47 laboratories, 41 were engaged in open testing. For sample A, all 41 laboratories yielded positive results, whereas for sample B, 36 laboratories reported positive results, 3 laboratories reported "test decision pending", 1 laboratory reported "suspected positive", and 1 laboratory did not respond. All 41 laboratories correctly identified the negative samples as negative. The mean Ct values were 32.2 for sample A and 35.2 for sample B. In the blind test, six laboratories received samples. Sample C was identified as positive by five laboratories and negative by one laboratory. CONCLUSIONS The nature of the specimen, specifically the saliva, may have influenced the blind test outcomes. The identified issues must be meticulously investigated and rectified to ensure accurate results.
Collapse
Affiliation(s)
- Yoshiyuki Sugishita
- Quality Control Section, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan.
| | - Rie Moriuchi
- Quality Control Section, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-cho, Shinjuku-ku, Tokyo 169-0073, Japan.
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, 5-21-16 Omori-nishi, Ota-ku, Tokyo 143-8540, Japan.
| |
Collapse
|
4
|
Zeleňáková A, Zeleňák V, Beňová E, Kočíková B, Király N, Hrubovčák P, Szűcsová J, Nagy Ľ, Klementová M, Mačák J, Závišová V, Bednarčík J, Kupčík J, Jacková A, Volavka D, Košuth J, Vilček Š. The surface modification of the silica-coated magnetic nanoparticles and their application in molecular diagnostics of virus infection. Sci Rep 2024; 14:14427. [PMID: 38910140 PMCID: PMC11194262 DOI: 10.1038/s41598-024-64839-2] [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: 06/16/2023] [Accepted: 06/13/2024] [Indexed: 06/25/2024] Open
Abstract
The study presents a series of examples of magnetic nanoparticle systems designed for the diagnosis of viral diseases. In this interdisciplinary work, we describe one of the most comprehensive synthetic approaches for the preparation and functionalization of smart nanoparticle systems for rapid and effective RT-PCR diagnostics and isolation of viral RNA. Twelve different organic ligands and inorganic porous silica were used for surface functionalization of the Fe3O4 magnetic core to increase the number of active centres for efficient RNA binding from human swab samples. Different nanoparticle systems with common beads were characterized by HRTEM, SEM, FT-IR, XRD, XPS and magnetic measurements. We demonstrate the application of the fundamental models modified to fit the experimental zero-field cooling magnetization data. We discuss the influence of the nanoparticle shell parameters (morphology, thickness, ligands) on the overall magnetic performance of the systems. The prepared nanoparticles were tested for the isolation of viral RNA from tissue samples infected with hepatitis E virus-HEV and from biofluid samples of SARS-CoV-2 positive patients. The efficiency of RNA isolation was quantified by RT-qPCR method.
Collapse
Affiliation(s)
- A Zeleňáková
- Institute of Physics, Faculty of Science, P.J. Šafárik University, Park Angelinum 9, 04001, Košice, Slovakia.
| | - V Zeleňák
- Institute of Chemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 04001, Košice, Slovakia
| | - E Beňová
- Institute of Chemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 04001, Košice, Slovakia
| | - B Kočíková
- Department of Epizootiology, Parasitology and Public Health Protection, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 04181, Košice, Slovakia
| | - N Király
- Institute of Chemistry, Faculty of Science, P.J. Šafárik University, Moyzesova 11, 04001, Košice, Slovakia
| | - P Hrubovčák
- Institute of Physics, Faculty of Science, P.J. Šafárik University, Park Angelinum 9, 04001, Košice, Slovakia
| | - J Szűcsová
- Institute of Physics, Faculty of Science, P.J. Šafárik University, Park Angelinum 9, 04001, Košice, Slovakia
| | - Ľ Nagy
- Institute of Physics, Faculty of Science, P.J. Šafárik University, Park Angelinum 9, 04001, Košice, Slovakia
| | - M Klementová
- Institute of Physics of the CAS, v.v.i., Na Slovance 1999/2, 182 21, Praha 8, Czech Republic
| | - J Mačák
- Synlab Slovakia s. r. o Department of Clinical Microbiology, Opatovská Cesta 10, 04001, Košice, Slovakia
| | - V Závišová
- Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 04001, Košice, Slovakia
| | - J Bednarčík
- Institute of Physics, Faculty of Science, P.J. Šafárik University, Park Angelinum 9, 04001, Košice, Slovakia
| | - J Kupčík
- Institute of Physics of the CAS, v.v.i., Na Slovance 1999/2, 182 21, Praha 8, Czech Republic
| | - A Jacková
- Department of Epizootiology, Parasitology and Public Health Protection, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 04181, Košice, Slovakia
| | - D Volavka
- Institute of Physics, Faculty of Science, P.J. Šafárik University, Park Angelinum 9, 04001, Košice, Slovakia
| | - J Košuth
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University, Šrobárova 2, 04154, Košice, Slovakia
| | - Š Vilček
- Department of Epizootiology, Parasitology and Public Health Protection, University of Veterinary Medicine and Pharmacy in Košice, Komenského 73, 04181, Košice, Slovakia
| |
Collapse
|
5
|
Li Z, Zhang S, Zhang J, Avery L, Banach D, Zhao H, Liu C. Palm-Sized Lab-In-A-Magnetofluidic Tube Platform for Rapid and Sensitive Virus Detection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310066. [PMID: 38634211 PMCID: PMC11187901 DOI: 10.1002/advs.202310066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/12/2024] [Indexed: 04/19/2024]
Abstract
Simple, sensitive, and accurate molecular diagnostics are critical for preventing rapid spread of infection and initiating early treatment of diseases. However, current molecular detection methods typically rely on extensive nucleic acid sample preparation and expensive instrumentation. Here, a simple, fully integrated, lab-in-a-magnetofluidic tube (LIAMT) platform is presented for "sample-to-result" molecular detection of virus. By leveraging magnetofluidic transport of micro/nano magnetic beads, the LIAMT device integrates viral lysis, nucleic acid extraction, isothermal amplification, and CRISPR detection within a single engineered microcentrifuge tube. To enable point-of-care molecular diagnostics, a palm-sized processor is developed for magnetofluidic separation, nucleic acid amplification, and visual fluorescence detection. The LIAMT platform is applied to detect SARS-CoV-2 and HIV viruses, achieving a detection sensitivity of 73.4 and 63.9 copies µL-1, respectively. Its clinical utility is further demonstrated by detecting SARS-CoV-2 and HIV in clinical samples. This simple, affordable, and portable LIAMT platform holds promise for rapid and sensitive molecular diagnostics of infectious diseases at the point-of-care.
Collapse
Affiliation(s)
- Ziyue Li
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
- Department of Biomedical EngineeringUniversity of ConnecticutStorrsConnecticut06269USA
| | - Shuo Zhang
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
- Department of Biomedical EngineeringUniversity of ConnecticutStorrsConnecticut06269USA
| | - Jiongyu Zhang
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
- Department of Biomedical EngineeringUniversity of ConnecticutStorrsConnecticut06269USA
| | - Lori Avery
- Department of Pathology and Laboratory MedicineUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
| | - David Banach
- Department of MedicineDivision of Infectious DiseasesUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
| | - Hui Zhao
- Department of Mechanical EngineeringUniversity of NevadaLas VegasNevada89154USA
| | - Changchun Liu
- Department of Biomedical EngineeringUniversity of Connecticut Health CenterFarmingtonConnecticut06030USA
| |
Collapse
|
6
|
Gambarino S, Galliano I, Clemente A, Calvi C, Montanari P, Pau A, Dini M, Bergallo M. Characteristics of RNA Stabilizer RNApro for Peripheral Blood Collection. Diagnostics (Basel) 2024; 14:971. [PMID: 38786269 PMCID: PMC11120318 DOI: 10.3390/diagnostics14100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
Peripheral blood is the most practical tissue for human immune system gene expression profiling because it is easily accessible, whereas the site of primary infection in certain diseases may not be easily accessible. Due to the ex vivo instability of RNA transcripts, a key challenge in the gene expression analysis of blood samples is the rapid sample handling and stabilization of the mRNA by adding an RNA preservative (PAXgeneTM Blood RNA Tubes, TempusTM Blood RNA tubes, RNAlater Stabilization Reagent, RNAgard® Blood Tubes). BioMole (Turin, Italy) has developed a novel blood stabilizer, called RNApro, in which RNA is stabilized during phlebotomy and sample storage. In this study, RNApro performance intended as RNA yield, integrity, and stability was evaluated. Our results show that blood samples stored at -80 °C and re-extracted after 7 years show no differences in terms of quantity, quality, and amplificability. The samples in the RNAlater stabilization solution can be stored at room temperature for up to one week or at 4 °C for up to one month. Similar results can also be observed for PAXgene tubes, Tempus tubes, and RNAgard tubes. In agreement with these data, the RNApro stabilization solution preserves the RNA from degradation for up to 1 month at 4 °C and 1 week at room temperature. RNApro can be stored indifferently at -80, -20, 4 °C, or room temperature for up to 2 months after, and then could be stored at -80 °C for up to seven years. In summary, our study is the first to analyze the performance of an RNA stabilizer called RNApro. We can conclude that several studies have shown significant differences in gene expression analysis when the sample was preserved in different RNA stabilizers. Therefore, it is desirable to standardize the method of nucleic acid conservation when comparing data from transcriptomic analyses.
Collapse
Affiliation(s)
- Stefano Gambarino
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Ilaria Galliano
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Clemente
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Cristina Calvi
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Paola Montanari
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Anna Pau
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
| | - Maddalena Dini
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| | - Massimiliano Bergallo
- Department of Public Health and Pediatric Sciences, Immunopathology Laboratory, Medical School, University of Turin, Piazza Polonia, 94, 10126 Turin, Italy; (S.G.); (I.G.); (A.C.); (C.C.); (P.M.); (A.P.); (M.D.)
- BioMole srl, Via Quarello 15/A, Turin, 10135, Italy
| |
Collapse
|
7
|
Lak A, Wang Y, Kolbeck PJ, Pauer C, Chowdhury MS, Cassani M, Ludwig F, Viereck T, Selbach F, Tinnefeld P, Schilling M, Liedl T, Tavacoli J, Lipfert J. Cooperative dynamics of DNA-grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami. NANOSCALE 2024; 16:7678-7689. [PMID: 38533617 DOI: 10.1039/d3nr06253h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
Magnetic nanoparticles (MNPs) provide new opportunities for enzyme-free biosensing of nucleic acid biomarkers and magnetic actuation by patterning on DNA origami, yet how the DNA grafting density affects their dynamics and accessibility remains poorly understood. Here, we performed surface functionalization of MNPs with single-stranded DNA (ssDNA) via click chemistry with a tunable grafting density, which enables the encapsulation of single MNPs inside a functional polymeric layer. We used several complementary methods to show that particle translational and rotational dynamics exhibit a sigmoidal dependence on the ssDNA grafting density. At low densities, ssDNA strands adopt a coiled conformation that results in minor alterations to particle dynamics, while at high densities, they organize into polymer brushes that collectively influence particle dynamics. Intermediate ssDNA densities, where the dynamics are most sensitive to changes, show the highest magnetic biosensing sensitivity for the detection of target nucleic acids. Finally, we demonstrate that MNPs with high ssDNA grafting densities are required to efficiently couple to DNA origami. Our results establish ssDNA grafting density as a critical parameter for the functionalization of MNPs for magnetic biosensing and functionalization of DNA nanostructures.
Collapse
Affiliation(s)
- Aidin Lak
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Yihao Wang
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Pauline J Kolbeck
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Christoph Pauer
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Mohammad Suman Chowdhury
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Marco Cassani
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic
| | - Frank Ludwig
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Thilo Viereck
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Florian Selbach
- Department of Chemistry and Center for NanoScience, LMU Munich, 81377 Munich, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, LMU Munich, 81377 Munich, Germany
| | - Meinhard Schilling
- Institute for Electrical Measurement Science and Fundamental Electrical Engineering and Laboratory for Emerging Nanometrology (LENA), Hans-Sommer-Str. 66, Braunschweig, 38106, Germany.
| | - Tim Liedl
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Joe Tavacoli
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Jan Lipfert
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
- Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| |
Collapse
|
8
|
Karagianni K, Bibi A, Madé A, Acharya S, Parkkonen M, Barbalata T, Srivastava PK, de Gonzalo-Calvo D, Emanueli C, Martelli F, Devaux Y, Dafou D, Nossent AY. Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102085. [PMID: 38192612 PMCID: PMC10772297 DOI: 10.1016/j.omtn.2023.102085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
RNA editing, a common and potentially highly functional form of RNA modification, encompasses two different RNA modifications, namely adenosine to inosine (A-to-I) and cytidine to uridine (C-to-U) editing. As inosines are interpreted as guanosines by the cellular machinery, both A-to-I and C-to-U editing change the nucleotide sequence of the RNA. Editing events in coding sequences have the potential to change the amino acid sequence of proteins, whereas editing events in noncoding RNAs can, for example, affect microRNA target binding. With advancing RNA sequencing technology, more RNA editing events are being discovered, studied, and reported. However, RNA editing events are still often overlooked or discarded as sequence read quality defects. With this position paper, we aim to provide guidelines and recommendations for the detection, validation, and follow-up experiments to study RNA editing, taking examples from the fields of cardiovascular and brain disease. We discuss all steps, from sample collection, storage, and preparation, to different strategies for RNA sequencing and editing-sensitive data analysis strategies, to validation and follow-up experiments, as well as potential pitfalls and gaps in the available technologies. This paper may be used as an experimental guideline for RNA editing studies in any disease context.
Collapse
Affiliation(s)
- Korina Karagianni
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - Alessia Bibi
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Alisia Madé
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Shubhra Acharya
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
| | - Mikko Parkkonen
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
| | - Teodora Barbalata
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
| | | | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | | | - Fabio Martelli
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Dimitra Dafou
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
| | - A. Yaël Nossent
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
| | - on behalf of EU-CardioRNA COST Action CA17129
- Department of Genetics, Development, and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Molecular Cardiology Laboratory, IRCCS Policlinico San Donato, Via Morandi 30, San Donato Milanese, 20097 Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
- Cardiovascular Research Unit, Luxembourg Institute of Health, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-alzette, Luxembourg
- Research Unit of Biomedicine and Internal Medicine, Department of Pharmacology and Toxicology, University of Oulu, Oulu, Finland
- Lipidomics Department, Institute of Cellular Biology and Pathology “Nicolae Simionescu” of the Romanian Academy, 8, B. P. Hasdeu Street, 050568 Bucharest, Romania
- National Heart & Lung Institute, Imperial College London, London, UK
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
- Department of Surgery, Leiden University Medical Center, Leiden, the Netherlands
- Department of Nutrition, Exercise and Sports (NEXS), University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
9
|
Wang Q, Ren Y, Meng T, Yang X, Lu L, Yang H, Hou H, Negahdary M, Wan Y, Song F, Li J. Cas14a1-advanced LAMP for ultrasensitive and visual Pathogen diagnostic. Talanta 2024; 269:125458. [PMID: 38008027 DOI: 10.1016/j.talanta.2023.125458] [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] [Received: 04/12/2023] [Revised: 09/06/2023] [Accepted: 11/20/2023] [Indexed: 11/28/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas enzymes have been widely applied for biosensor development, combined with various isothermal amplification strategies (IAS) to boost sensitivity and specificity. Currently, the unstable assay and tedious manipulation usually hinder its practical applications. Here, a Cas14a1-advanced LAMP assay (CALA) combined with Rapid Extraction of Bacterial Genomic DNA (REBGD) is proposed for pathogen detection. For rapid CALA, a single stranded fluorescence reporter and ssDNA-gold nanoparticles (AuNPs) are used as signal indicators to establish ultrasensitive and visual platforms. This assay displays precise detection of bacteria, which can achieve an ultrasensitive limit of detection (LOD) 10 aM target genomic DNA. Furthermore, the high reliability of pathogen diagnostic for contrived samples is validated through the rapid visual CALA platform, demonstrating the promising practical testing availability of pathogen detection.
Collapse
Affiliation(s)
- Qingwei Wang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Yihua Ren
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Tian Meng
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Xiufen Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Lin Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Hao Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision & Test Center, Zhengzhou 450001, China, Beijing Institute of Life Science and Technology, Beijing, China
| | - Masoud Negahdary
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil
| | - Yi Wan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
| | - Fengge Song
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, 570228, China.
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
10
|
Wang Z, Liu M, Lin H, Zhu G, Dong Z, Wu N, Fan Y, Xu G, Chang L, Wang Y. An Ion Concentration Polarization Microplatform for Efficient Enrichment and Analysis of ctDNA. ACS NANO 2024; 18:2872-2884. [PMID: 38236597 DOI: 10.1021/acsnano.3c07137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Strategies for rapid, effective nucleic acid processing hold tremendous significance to the clinical analysis of circulating tumor DNA (ctDNA), a family of important markers indicating tumorigenesis and metastasis. However, traditional techniques remain challenging to achieve efficient DNA enrichment, further bringing about complicated operation and limited detection sensitivity. Here, we developed an ion concentration polarization microplatform that enabled highly rapid, efficient enrichment and purification of ctDNA from a variety of clinical samples, including serum, urine, and feces. The platform demonstrated efficiently separating and enriching ctDNA within 30 s, with a 100-fold improvement over traditional methods. Integrating an on-chip isothermal amplification module, the platform further achieved 100-fold enhanced sensitivity in ctDNA detection, which significantly eliminated false-negative results in the serum or urine samples due to the low abundance of ctDNA. Such a simple-designed platform offers a user-friendly yet powerful diagnosis technique with a wide applicability, ranging from early tumor diagnosis to infection screening.
Collapse
Affiliation(s)
- Zhiying Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Ming Liu
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Haocheng Lin
- Department of Urology, Peking University Third Hospital, Beijing, 100191, China
| | - Guiying Zhu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Zaizai Dong
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Nan Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Thoracic Surgery II, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yubo Fan
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X, Research Institute, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Shanghai Sci-Tech InnoCenter for Infection & Immunity, Shanghai, 200000, China
| | - Lingqian Chang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, China
- School of Engineering Medicine, Beihang University, Beijing 100083, China
| |
Collapse
|
11
|
Malburet C, Carboni A, Guinamand S, Naik H, Fertier-Prizzon S. mRNA extraction from lipid nanoparticles. J Chromatogr A 2024; 1714:464545. [PMID: 38070303 DOI: 10.1016/j.chroma.2023.464545] [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] [Received: 10/03/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024]
Abstract
Messenger RiboNucleic Acid (mRNA) vaccines have recently shown considerable promises for both prophylactic and therapeutic vaccines. These vaccines do not carry an antigen but the information for producing it using the cell machinery, turning the human body into an antigen factory. However, mRNA is an unstable molecule, susceptible to physical, chemical and enzymatic degradation by exo- and endonucleases. If the mRNA is degraded, it can no longer be translated correctly into the antigen of interest and the vaccine lose its efficacy. To protect from nucleases degradation and allow it to get into the cells, mRNA can be encapsulated in lipid nanoparticles (LNPs). As part of the manufacturing process, the quality of the mRNAs should be controlled before the encapsulation (at the drug substance stage) as well as after formulation on the final vaccine product (at the drug product stage). Therefore, it is necessary to be able to extract the mRNA from the LNPs, that is to deformulate the final vaccine product. In this work, different deformulation methods have been compared: spin column extraction, magnetic particle extraction, organic extraction, and direct disruption. Advantages and disadvantages of each of these methods are highlighted.
Collapse
Affiliation(s)
- Camille Malburet
- Sanofi, 1541 Avenue Marcel Mérieux, 69280 Marcy l'Etoile, France.
| | - Aurelien Carboni
- Sanofi, 1541 Avenue Marcel Mérieux, 69280 Marcy l'Etoile, France
| | | | | | | |
Collapse
|
12
|
Kendir S, Franzreb M. Synergies of pH-induced calcium phosphate precipitation and magnetic separation for energy-efficient harvesting of freshwater microalgae. BIORESOURCE TECHNOLOGY 2024; 391:129964. [PMID: 37926356 DOI: 10.1016/j.biortech.2023.129964] [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: 09/18/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/07/2023]
Abstract
Energy- and time-consuming concentration steps currently limit the industrial application of microalgae. Compared to state-of-the-art technologies, magnetic separation shows a high potential for efficient harvesting of microalgae. This study presents a novel approach to combine pH-induced calcium phosphate precipitation with cheap natural magnetite microparticles for magnetic separation of the freshwater microalgae Chlorella vulgaris. Harvesting efficiencies up to 98% were achieved at moderate pH and low particle and calcium phosphate concentrations in a model medium. However, cultivation-dependent high loads of algogenic organic matter can severely inhibit flocculation and particle/algae interactions, requiring higher salt concentrations or pH. Harvesting efficiencies above 90% were still attainable at moderate pH with increased calcium phosphate concentrations of 10mM. Acidification of the suspension to pH 5 allows for simple and reversible particle recycling. The presented process provides a promising path to universal and cost-effective harvesting, advancing the utilization of microalgae as a sustainable bioresource.
Collapse
Affiliation(s)
- Sefkan Kendir
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Matthias Franzreb
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany.
| |
Collapse
|
13
|
Robledo D, Ogwang J, Byakora E, Schulze JN, Benda KK, Fraslin C, Salisbury S, Solimo M, Mayega JF, Peter B, Masembe C, Houston R, Mukiibi R. Genetic diversity and population structure of farmed and wild Nile tilapia (Oreochromis niloticus) in Uganda: The potential for aquaculture selection and breeding programs. Genomics 2024; 116:110781. [PMID: 38182036 DOI: 10.1016/j.ygeno.2024.110781] [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] [Received: 09/15/2023] [Revised: 12/17/2023] [Accepted: 01/01/2024] [Indexed: 01/07/2024]
Abstract
Nile tilapia is one of the most important aquaculture species globally, providing high-quality animal protein for human nutrition and a source of income to sustain the livelihoods of many people in low- and middle-income countries. This species is native to Africa and nowadays farmed throughout the world. However, the genetic makeup of its native populations remains poorly characterized. Additionally, there has been important introgression and movement of farmed (as well as wild) strains connected to tilapia aquaculture in Africa, yet the relationship between wild and farmed populations is unknown in most of the continent. Genetic characterization of the species in Africa has the potential to support the conservation of the species as well as supporting selective breeding to improve the indigenous strains for sustainable and profitable aquaculture production. In the current study, a total of 382 fish were used to investigate the genetic structure, diversity, and ancestry within and between Ugandan Nile tilapia populations from three major lakes including Lake Albert (L. Albert), Lake Kyoga (L. Kyoga) and Lake Victoria (L. Victoria), and 10 hatchery farms located in the catchment regions of these lakes. Our results showed clear genetic structure of the fish sourced from the lakes, with L. Kyoga and L. Albert populations showing higher genetic similarity. We also observed noticeable genetic structure among farmed populations, with most of them being genetically similar to L. Albert and L. Kyoga fish. Admixture results showed a higher (2.55-52.75%) contribution of L. Albert / L. Kyoga stocks to Uganda's farmed fish than the stock from L. Victoria (2.12-28.02%). We observed relatively high genetic diversity across both wild and farmed populations, but some farms had sizable numbers of highly inbred fish, raising concerns about management practices. In addition, we identified a genomic region on chromosome 5, harbouring the key innate immune gene BPI and the key growth gene GHRH, putatively under selection in the Ugandan Nile tilapia population. This region overlaps with the genomic region previously identified to be associated with growth rate in farmed Nile tilapia.
Collapse
Affiliation(s)
- Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Joel Ogwang
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Ezra Byakora
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Jennifer Nascimento Schulze
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK; Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, Kiel 24105, Germany
| | - Katali Kirungi Benda
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Clemence Fraslin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK
| | - Moses Solimo
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Johnson Francis Mayega
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, P.O. Box, 7062, Kampala, Uganda
| | - Beine Peter
- National Animal Genetics Resources Centre and Data Bank (NAGRC&DB), P.O. Box 183, Nsamizi Road, Entebbe, Uganda
| | - Charles Masembe
- Department of Zoology, Entomology and Fisheries Sciences, College of Natural Sciences, Makerere University, P.O. Box, 7062, Kampala, Uganda
| | - Ross Houston
- Benchmark Genetics, 1 Pioneer Building, Edinburgh Technopole, Penicuik EH26 0GB, United Kingdom
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh EH25 9RG, UK.
| |
Collapse
|
14
|
Keuthan CJ, Zack DJ. RNA Isolation from Human Stem Cell-Derived Retinal Organoids. Methods Mol Biol 2024; 2822:3-11. [PMID: 38907907 DOI: 10.1007/978-1-0716-3918-4_1] [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: 06/24/2024]
Abstract
RNA isolation is an essential first step for many types of molecular analyses, including reverse transcription PCR (RT-PCR)/quantitative RT-PCR (qRT-PCR), Northern blotting, microarrays, and RNA-sequencing. While many RNA purification methods have been reported, it can be challenging to extract sufficient quantity, and suitable quality, of RNA from very small amounts of tissue and/or samples containing low numbers of cells. Here we outline a total RNA isolation method that reproducibly yields high-quality RNA from human stem cell-derived retinal organoids for downstream transcriptomic analysis.
Collapse
Affiliation(s)
- Casey J Keuthan
- Department of Ophthalmology | Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Donald J Zack
- Department of Ophthalmology | Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| |
Collapse
|
15
|
Hu J, Ren W, Liu H, Xie C, Li D, Yang L, Liao F, Jiang L, Pu Q, Chen W. Immunomultiple PCR-based electrochemical and lateral flow strategy for the simultaneous detection of liver cancer tumor markers. Mikrochim Acta 2023; 191:27. [PMID: 38091092 DOI: 10.1007/s00604-023-06098-y] [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: 07/11/2023] [Accepted: 11/08/2023] [Indexed: 12/18/2023]
Abstract
The current use of the single serum biomarker α-fetoprotein (AFP) in clinical practice has limitations in terms of specificity and sensitivity. We propose a strategy that combines antigen capture polymerase chain reaction (AC-PCR), lateral flow assay (LFA), and electrochemical biosensors to detect both AFP and circulating tumor cells (CTCs) in liver cancer serum. First, we used the AC-PCR technique to achieve target separation, purification, signal conversion, and amplification, eliminating target heterogeneity. Then, we achieved rapid results through the LFA and electrochemical biosensor platforms. As a result, the proposed assay has limits of 5 cells/mL for CTCs and 5 µg/L for AFP. The proposed method was applied effectively to simulated blood samples. This method has the potential to play a role in early liver cancer and provide a potential application for the diagnosis and precision treatment of liver cancer.
Collapse
Affiliation(s)
- Juan Hu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China
- The Experimental Medicine Center, The First Affiliated Hospital of Chongqing Medical and Pharmaceutical College, Chongqing, 400060, People's Republic of China
| | - Wubo Ren
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China
| | - Han Liu
- Department of Neurology, Jiulongpo District People's Hospital, Chongqing, 400050, People's Republic of China
| | - Cong Xie
- Department of Clinical Laboratory, The People's Hospital of Chongqing Liang Jiang New Area, Chongqing, 401122, People's Republic of China
| | - Dandan Li
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China
| | - Liping Yang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China
| | - Fangli Liao
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China
| | - Linshan Jiang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China
| | - Qinli Pu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China.
| | - Weixian Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, No. 74 Linjiang Road, Yuzhong, Chongqing, 400010, People's Republic of China.
| |
Collapse
|
16
|
Bruand P, Tijunelyte I, Castinel A, Donnadieu C, Joseph P, Bancaud A. Size Fractionation of Milliliter DNA Samples in Minutes Controlled by an Electric Field of ∼10 V. Anal Chem 2023; 95:18099-18106. [PMID: 38047372 DOI: 10.1021/acs.analchem.3c03187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
DNA size fractionation is an essential tool in molecular biology and is used to isolate targets in a mixture characterized by a broad molecular-weight distribution. Microfluidics was thought to provide the opportunity to create devices capable of enhancing and speeding up the classical fractionation processes. However, this conjecture met limited success due to the low mass or volume throughput of these technologies. We describe the μLAF (μ-laboratory for DNA fractionation) technology for DNA size selection based on the stacking of molecules on films of ∼100 μm in thickness with 105 cm-2 pores ∼2 μm in diameter. Size selection is achieved by controlling the regime of electrohydrodynamic migration through the temporal modulation of an electric field. This technology allows the processing of milliliter-scale samples containing a DNA mass of several hundreds of ng within ∼10 min and the selection of DNA in virtually any size window spanning 200 to 1000 bp. We demonstrate that one operation suffices to fractionate sheared genomic DNA in up to six fractions with collection efficiencies of ∼20-40% and enrichment factors of ∼1.5-3-fold. These performances compare favorably in terms of speed and versatility to those of the current standards.
Collapse
Affiliation(s)
- Paul Bruand
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France
- Adelis, 478 Rue de la Découverte, 31670 Labège, France
| | - Inga Tijunelyte
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France
| | - Adrien Castinel
- GeT-PlaGe, US 1426, Genotoul, INRAE, 31320 Castanet-Tolosan, France
| | - Cécile Donnadieu
- GeT-PlaGe, US 1426, Genotoul, INRAE, 31320 Castanet-Tolosan, France
| | - Pierre Joseph
- CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France
| | | |
Collapse
|
17
|
Wang Z, Jacobus EJ, Stirling DC, Krumm S, Flight KE, Cunliffe RF, Mottl J, Singh C, Mosscrop LG, Santiago LA, Vogel AB, Kariko K, Sahin U, Erbar S, Tregoning JS. Reducing cell intrinsic immunity to mRNA vaccine alters adaptive immune responses in mice. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102045. [PMID: 37876532 PMCID: PMC10591005 DOI: 10.1016/j.omtn.2023.102045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The response to mRNA vaccines needs to be sufficient for immune cell activation and recruitment, but moderate enough to ensure efficacious antigen expression. The choice of the cap structure and use of N1-methylpseudouridine (m1Ψ) instead of uridine, which have been shown to reduce RNA sensing by the cellular innate immune system, has led to improved efficacy of mRNA vaccine platforms. Understanding how RNA modifications influence the cell intrinsic immune response may help in the development of more effective mRNA vaccines. In the current study, we compared mRNA vaccines in mice against influenza virus using three different mRNA formats: uridine-containing mRNA (D1-uRNA), m1Ψ-modified mRNA (D1-modRNA), and D1-modRNA with a cap1 structure (cC1-modRNA). D1-uRNA vaccine induced a significantly different gene expression profile to the modified mRNA vaccines, with an up-regulation of Stat1 and RnaseL, and increased systemic inflammation. This result correlated with significantly reduced antigen-specific antibody responses and reduced protection against influenza virus infection compared with D1-modRNA and cC1-modRNA. Incorporation of m1Ψ alone without cap1 improved antibodies, but both modifications were required for the optimum response. Therefore, the incorporation of m1Ψ and cap1 alters protective immunity from mRNA vaccines by altering the innate immune response to the vaccine material.
Collapse
Affiliation(s)
- Ziyin Wang
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | | | - David C. Stirling
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | | | - Katie E. Flight
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Robert F. Cunliffe
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | | | - Charanjit Singh
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | - Lucy G. Mosscrop
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| | | | | | | | - Ugur Sahin
- BioNTech SE, An der Goldgrube 12, 55131 Mainz, Germany
| | | | - John S. Tregoning
- Department of Infectious Disease, Imperial College London, London W2 1PG, UK
| |
Collapse
|
18
|
Ziegenhals T, Frieling R, Wolf P, Göbel K, Koch S, Lohmann M, Baiersdörfer M, Fesser S, Sahin U, Kuhn AN. Formation of dsRNA by-products during in vitro transcription can be reduced by using low steady-state levels of UTP. Front Mol Biosci 2023; 10:1291045. [PMID: 38146535 PMCID: PMC10749352 DOI: 10.3389/fmolb.2023.1291045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/27/2023] [Indexed: 12/27/2023] Open
Abstract
Introduction: Exogeneous messenger ribonucleic acid (mRNA) can be used as therapeutic and preventive medication. However, during the enzymatic production process, commonly called in vitro transcription, by-products occur which can reduce the therapeutic efficacy of mRNA. One such by-product is double-stranded RNA (dsRNA). We therefore sought to limit the generation of dsRNA by-products during in vitro transcription. Materials and methods: In vitro transcription was performed with a DNA template including a poly(A)-tail-encoding region, dinucleotide or trinucleotide cap analogs for cotranscriptional capping, and relevant nucleoside triphosphates. Concentrations of UTP or modified UTP (m1ΨTP) and GTP were reduced and fed over the course of the reaction. mRNA was analyzed for dsRNA contamination, yield of the reaction, RNA integrity, and capping efficiency before translational activity was assessed. Results: Limiting the steady-state level of UTP or m1ΨTP during the enzymatic reaction reduced dsRNA formation, while not affecting mRNA yield or RNA integrity. Capping efficiency was optimized with the use of a combined GTP and UTP or m1ΨTP feed, while still reducing dsRNA formation. Lower dsRNA levels led to higher protein expression from the corresponding mRNAs. Discussion: Low steady-state concentrations of UTP and GTP, fed in combination over the course of the in vitro transcription reaction, produce mRNA with high capping and low levels of dsRNA formation, resulting in high levels of protein expression. This novel approach may render laborious purification steps to remove dsRNA unnecessary.
Collapse
|
19
|
Starheim EJ, Ravlo E, Schjølberg JO, Solvang V, Wang W, Scrimgeour NR, Manaf A, Erlandsen SE, Aas PA, Hagen L, de Sousa MML, Bjørås M. NAxtra magnetic nanoparticles for low-cost, efficient isolation of mammalian DNA and RNA. Sci Rep 2023; 13:20836. [PMID: 38012172 PMCID: PMC10682382 DOI: 10.1038/s41598-023-46868-5] [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: 07/28/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023] Open
Abstract
A cost-effective, viral nucleic acid (NA) isolation kit based on NAxtra magnetic nanoparticles was developed at the Norwegian University of Science and Technology in response to the shortage of commercial kits for isolation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA during the coronavirus disease 2019 (COVID-19) pandemic. This method showed comparable sensitivity to available kits at significantly reduced cost, making its application for other biological sources an intriguing prospect. Thus, based on this low-cost nucleic acid extraction technology, we developed a simple, low- and high-throughput, efficient method for isolation of high-integrity total NA, DNA and RNA from mammalian cell lines (monolayer) and organoids (3D-cultures). The extracted NA are compatible with downstream applications including (RT-)qPCR and next-generation sequencing. When automated, NA isolation can be performed in 14 min for up to 96 samples, yielding similar quantities to available kits.
Collapse
Affiliation(s)
- Eirin Johannessen Starheim
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Erlend Ravlo
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Jørn-Ove Schjølberg
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Vanessa Solvang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Wei Wang
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Nathan Robert Scrimgeour
- Department of Circulation and Medical Imaging (ISB), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Adeel Manaf
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0372, Oslo, Norway
| | | | - Per Arne Aas
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Proteomics and Modomics Experimental Core Facility (PROMEC) at NTNU, 7491, Trondheim, Norway
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
- Centre for Embryology and Healthy Development, University of Oslo, 0373, Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
- Department of Microbiology, Oslo University Hospital and University of Oslo, 0372, Oslo, Norway.
- Centre for Embryology and Healthy Development, University of Oslo, 0373, Oslo, Norway.
| |
Collapse
|
20
|
Chen Y, Wang Y, Ma C, Li Y, Zuo D, Huang X, Tian X, Wang W. Advances in the authentication of collagen products based on DNA technology. Crit Rev Food Sci Nutr 2023:1-12. [PMID: 37983141 DOI: 10.1080/10408398.2023.2283278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Collagenous products are making their way into consumer markets such as foods, nutraceuticals, cosmetics and pharmaceuticals increasingly. Collagen in a large family of proteins is ubiquitous in metazoan. The most effective way to identify biological samples including collagen is DNA technology indisputably. However, the DNA content of collagen mostly derived from connective tissue is relatively less, and commercial collagen products are usually subjected to some harsh treatments in the production process, which makes DNA damage more serious, thus tracing their origin becomes a huge challenge. At present, DNA enrichment mainly relies on silica based centrifugal columns after extraction by classical phenol chloroform method. For improving the amplification of DNA fragments, small amplicons are designed based on more stable mitochondrial genes, such as cytochrome b gene (cytb). In addition to conventional PCR for DNA amplification, some new PCR techniques have also been developed, such as DNA barcoding techniques, PCR-Southern hybridization and fluorescent PCR. These PCR techniques have their pros and cons, and are mainly used in the identification of gelatin at present. The development of a complete set of DNA authentication is of great significance for the control of collagen products quality and will contribute to sustainable development of collagen industry.
Collapse
Affiliation(s)
- Yuan Chen
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Yang Wang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Chenwei Ma
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Yangshuai Li
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Doudou Zuo
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaoli Huang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Xiaojing Tian
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Wenhang Wang
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
- RandD Centre of Collagen Products, Xingjia Biotechnology Co. LTD, Tianjin, China
| |
Collapse
|
21
|
Delgado SL, Perilla PM, Salgado DM, Rojas MC, Narváez CF. Efficiency of Automated Viral RNA Purification for Pediatric Studies of Dengue and Zika in Hyperendemic Areas. J Trop Med 2023; 2023:1576481. [PMID: 37810169 PMCID: PMC10560119 DOI: 10.1155/2023/1576481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/10/2023] Open
Abstract
The isolation of nucleic acids is a critical and limiting step for molecular assays, which prompted the arrival in Colombia of automated purification instruments during the SARS-CoV-2 pandemic. The local application of this technology in the study of tropical diseases, such as dengue and zika, is beginning to be tested. We evaluated the efficiency of the automated extraction of viral RNA for studies of pediatric dengue and zika. Clinical samples of children with dengue that were well characterized through RNA isolation by silica columns and serotype-specific nested RT-PCR (DENV-1 n = 7, DENV-2 n = 5, and negatives n = 8) in addition to 40 pediatric plasma samples spiked with ZIKV (strain PRVA BC59) and 209 from negative pre-epidemic children were analyzed. RNA from patients was extracted by two automated standard and high-throughput protocols on the KingFisher™ Flex instrument. The isolated RNA was evaluated for concentration and purity by spectrophotometry, for structural and functional integrity by electrophoresis and expression of the RNase P gene, and usefulness in serotype-specific DENV detection by conventional and real-time RT-PCR. For the evaluation of ZIKV RNA, the commercial TaqMan Triplex® assay was used, along with a well-tested in-house RT-qPCR assay. The concentration of RNA (5.2 vs. 7.5 ng/μL, P=0.03) and the number of integral bands (9 vs. 11) were higher with the high-throughput protocol. However, the number of specimens serotyped for DENV by RT-qPCR was comparable for both protocols. The cycle thresholds of the TaqMan Triplex® commercial kit and the in-house assay for the detection of plasma ZIKV RNA isolated with the standard protocol showed a strong association (r = 0.93, P < 0.0001) and a Cohen Kappa index of 0.98 when all 249 samples were analyzed. These preliminary results suggest that automated instruments could be used in studies of cocirculating flaviviruses that have represented a public health problem in recent decades in Colombia. They boast advantages such as efficiency, precision, time savings, and lower risk of cross-contamination.
Collapse
Affiliation(s)
- Sandra L. Delgado
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Huila, Colombia
| | - Piedad M. Perilla
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Huila, Colombia
| | - Doris M. Salgado
- Área de Pediatría, Universidad Surcolombiana, Neiva, Huila, Colombia
| | - María Clemencia Rojas
- Laboratorio de Salud Pública, Secretaría de Salud Departamental del Huila, Neiva, Huila, Colombia
| | - Carlos F. Narváez
- División de Inmunología, Programa de Medicina, Facultad de Salud, Universidad Surcolombiana, Neiva, Huila, Colombia
- Área de Pediatría, Universidad Surcolombiana, Neiva, Huila, Colombia
| |
Collapse
|
22
|
Khaleghi N, Mojtabapour Z, Rashvandi Z, Mohammadi A, Forouzandeh-Malati M, Ganjali F, Zarei-Shokat S, Kashtiaray A, Taheri-Ledari R, Maleki A. Fast synthesis of [1,2,3]-triazole derivatives on a Fe/Cu-embedded nano-catalytic substrate. NANOSCALE ADVANCES 2023; 5:4911-4924. [PMID: 37705809 PMCID: PMC10496887 DOI: 10.1039/d3na00326d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 08/06/2023] [Indexed: 09/15/2023]
Abstract
Triazoles are biologically important compounds that play a crucial role in biomedical applications. In this study, we present an innovative and eco-friendly nanocatalyst system for synthesizing compounds via the click reaction. The system is composed of Arabic gum (AG), iron oxide magnetic nanoparticles (Fe3O4 MNPs), (3-chloropropyl) trimethoxysilane (CPTMS), 2-aminopyridine (AP), and Cu(i) ions. Using AP as an anchor for Cu(i) ions and Fe3O4 MNPs allows facile separation using an external magnet. The hydrophilic nature of the Fe3O4@AG/AP-Cu(i) nanocomposite makes it highly efficient in water as a green solvent. The highest reaction efficiency (95.0%) was achieved in H2O solvent with 50.0 mg of nanocatalyst for 60 min at room temperature. The reaction yield remained consistent for six runs, demonstrating the stability and effectiveness of the catalyst.
Collapse
Affiliation(s)
- Nima Khaleghi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Zahrasadat Mojtabapour
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Zahra Rashvandi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Adibeh Mohammadi
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Mohadeseh Forouzandeh-Malati
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Fatemeh Ganjali
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Simindokht Zarei-Shokat
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Amir Kashtiaray
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Reza Taheri-Ledari
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| | - Ali Maleki
- Catalysts and Organic Synthesis Research Laboratory, Department of Chemistry, Iran University of Science and Technology Tehran 16846-13114 Iran +98 2173021584 +98 21 77240640-50
| |
Collapse
|
23
|
Politza AJ, Liu T, Guan W. Programmable magnetic robot (ProMagBot) for automated nucleic acid extraction at the point of need. LAB ON A CHIP 2023; 23:3882-3892. [PMID: 37551930 PMCID: PMC11218199 DOI: 10.1039/d3lc00545c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Upstream sample preparation remains the bottleneck for point-of-need nucleic acid testing due to its complexity and time-consuming nature. Sample preparation involves extracting, purifying, and concentrating nucleic acids from various matrices. These processes are critical for ensuring the accuracy and sensitivity of downstream nucleic acid amplification and detection. However, current sample preparation methods are often laboratory-based, requiring specialized equipment, trained personnel, and several hours of processing time. As a result, sample preparation often limits the speed, portability, and cost-effectiveness of point-of-need nucleic acid testing. A universal, field-deployable sample preparation device is highly desirable for this critical need and unmet challenge. Here we reported a handheld, battery-powered, reconfigurable, and field-deployable nucleic acid sample preparation device. A programmable electromagnetic actuator was developed to drive a magnetic robot (ProMagBot) in X/Y 2D space, such that various magnetic bead-based sample preparations can be readily translated from the laboratory to point-of-need settings. The control of the electromagnetic actuator requires only a 3-phase unipolar voltage in X and Y directions, and therefore, the motion space is highly scalable. We validated the ProMagBot device with a model application by extracting HIV viral RNAs from plasma samples using two widely used magnetic bead kits: ChargeSwitch and MagMAX beads. In both cases, the ProMagBot could successfully extract viral RNAs from 50 μL plasma samples containing as low as 102 copies of viral RNAs in 20 minutes. Our results demonstrated the ability of ProMagBot to prepare samples from complex mediums at the point of need. We believe such a device would enable rapid and robust sample preparation in various settings, including resource-limited or remote environments, and accelerate the development of next-generation point-of-need nucleic acid testing.
Collapse
Affiliation(s)
- Anthony J Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
| | - Tianyi Liu
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
| | - Weihua Guan
- Department of Biomedical Engineering, Pennsylvania State University, University Park 16802, USA.
- Department of Electrical Engineering, Pennsylvania State University, University Park 16802, USA
- School of Electrical Engineering and Computer Science, Pennsylvania State University, University Park 16802, USA
| |
Collapse
|
24
|
Ruiz M, Vo AD, Becker JO, Roose ML. Real-Time PCR to Phenotype Resistance to the Citrus Nematode Tylenchulus semipenetrans Cobb. PLANTS (BASEL, SWITZERLAND) 2023; 12:2543. [PMID: 37447106 DOI: 10.3390/plants12132543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
As pest management options, such as nematicides, become more restrictive, developing rootstocks resistant to the citrus nematode is fundamental for citrus production. This study provides an updated methodology to screen for citrus nematode resistance in rootstock-breeding programs. We developed a novel method to extract female citrus nematodes from roots that is suitable for molecular work and a real-time-PCR-based nematode quantification method for Tylenchulus semipenetrans. These procedures allow scaling up screening to high-throughput workflows, increasing the chances of finding rootstock candidates that combine all the desired traits. Our results contribute to the growing literature supporting quantification of nematodes with molecular methods.
Collapse
Affiliation(s)
- Marta Ruiz
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Annie Du Vo
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - J Ole Becker
- Department of Nematology, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| |
Collapse
|
25
|
Poles M, Meggiolaro A, Cremaschini S, Marinello F, Filippi D, Pierno M, Mistura G, Ferraro D. Shaking Device for Homogeneous Dispersion of Magnetic Beads in Droplet Microfluidics. SENSORS (BASEL, SWITZERLAND) 2023; 23:5399. [PMID: 37420565 DOI: 10.3390/s23125399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/26/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Magnetic beads (or particles) having a size between 1 and 5 µm are largely used in many biochemical assays devoted to both purification and quantification of cells, nucleic acids, or proteins. Unfortunately, the use of these beads within microfluidic devices suffers from natural precipitation because of their size and density. The strategies applied thus far to cells or polymeric particles cannot be extended to magnetic beads, mainly due to their magnetization and their higher densities. We report an effective shaking device capable of preventing the sedimentation of beads that are stored in a custom PCR tube. After the characterization of the operating principle, the device is validated for magnetic beads in droplets, leading to an equal distribution between the droplets, barely affecting their generation.
Collapse
Affiliation(s)
- Maria Poles
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Alessio Meggiolaro
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Sebastian Cremaschini
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Filippo Marinello
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Daniele Filippi
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Matteo Pierno
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Giampaolo Mistura
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| | - Davide Ferraro
- Department of Physics and Astronomy, University of Padua, Via Marzolo 8, 35131 Padua, Italy
| |
Collapse
|
26
|
Liu D, Li Q, Luo J, Huang Q, Zhang Y. An SPRI beads-based DNA purification strategy for flexibility and cost-effectiveness. BMC Genomics 2023; 24:125. [PMID: 36927488 PMCID: PMC10022144 DOI: 10.1186/s12864-023-09211-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Current solid-phase reversible immobilization (SPRI) beads technology is widely used in molecular biology due to its convenience for DNA manipulation. However, the high performance commercial SPRI beads have no price advantage over our method. Furthermore, the use of commercially available SPRI beads standards does not provide the flexibility required for a number of specific nucleic acid handling scenarios. RESULTS We report an efficient DNA purification strategy by combining home-made beads-suspension buffer with SPRI beads. The method tests the critical concentrations of polyethylene glycol (PEG) 8000 and beads to maximise recovery. And the composition of the SPRI beads DNA purification system (SDPS) was determined at 20% PEG 8000, 2 M NaCl and 16.3 mM MgCl2, and 1.25 mg/ml beads (1/8th original concentration). Then, we tested the DNA recovery of the SDPS, and the result showed that it was comparable to the control (AMPure XP beads). In the study, we have also developed an adjustment SPRI beads DNA purification system (ASDPS), the volume of ASDPS per reaction is 0.6× reaction volume (beads/samples). The performance of ASDPS is similar to SDPS and the control. But the cost of our methods is only about 1/24th of the control. To further assess its performance, we prepare the DNA-seq libraries to evaluate the yield, library quality, capture efficiency and consistency. We have compared all these results with the performance of the control and confirmed its efficiency. CONCLUSION We have proposed an alternative DNA purification approach with great flexibility, allowing researchers to manipulate DNA in different conditions. And ultimately, its application will benefit molecular biology research in the future.
Collapse
Affiliation(s)
- Danli Liu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qiujia Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Jing Luo
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
| | - Qitong Huang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, 6708PB, Netherlands
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng, Shenzhen, 518120, China.
- College of Life Science and Engineering, Foshan University, Foshan, China.
| |
Collapse
|
27
|
Calvo Chica LE, Aguilar-Mora F, Ramirez Cando LJ, Proaño-Bolaños C, Carrera-Gonzales A. Cost and performance analysis of efficiency, efficacy, and effectiveness of viral RNA isolation with commercial kits and Heat Shock as an alternative method to detect SARS-CoV-2 by RT-PCR. BIONATURA 2023. [DOI: 10.21931/rb/2023.08.01.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
In late 2019 a new virus reported in Wuhan, China, identified as SARS-CoV-2 spread rapidly challenging the healthcare system around the world. The need for rapid, timely and accurate detection was critical to the prevention of community outbreaks of the virus. However, the high global demand for reagents during the years 2020 and 2021 generated a bottleneck in kits used for detection, greatly affecting developing countries, lagging their ability to diagnose and control the virus in the population. The difficulty in importing reagents, high costs and limited public access to the SARS-CoV-2 detection test led to the search for alternative methods. In this framework, different commercial nucleic acid extraction methodologies were evaluated and compared against heat shock as an alternative method for SARS-CoV-2 detection by RT-PCR, in order to determine the diagnostic yield and its possible low-cost compared to other methodologies. Nasopharyngeal samples were used where the diagnostic efficiency of the alternative method was 70 to 73%. The evaluation of the discriminatory efficacy of the method took the sensitivity and specificity to establish its cut-off point, being 0.73 to 0.817, which allows discriminating between COVID-19 positives and negatives. As for the diagnostic effectiveness expressed as the proportion of subjects correctly classified, it is between 80 and 84%. On the other hand, in terms of the costs necessary to carry out the detection, the alternative method is more economical and accessible in terms of direct cost close to 47 and 49 USD, and indirect cost around 35 and 50 USD compared to the commercial methods available in this comparison and evaluation, being possible its implementation in developing countries with high infection rates, allowing access to the diagnostic test with a reliable and low-cost method.
Keywords: COVID-19, RT-PCR, Viral RNA.
Collapse
Affiliation(s)
| | - Fabian Aguilar-Mora
- Faculty of Life Sciences, Universidad Regional Amazonica Ikiam, Tena, Ecuador. ; Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Mendoza, Argentina
| | - Lenin Javier Ramirez Cando
- School of Biological Sciences and Engineering. Yachay University for Experimental Technology and Research, San Miguel de Urcuquí, Proyecto Yachay, Ecuador
| | | | | |
Collapse
|
28
|
Gall-David SL, Boudry G, Buffet-Bataillon S. Comparison of four DNA extraction kits efficiency for 16SrDNA microbiota profiling of diverse human samples. Future Sci OA 2023; 9:FSO837. [PMID: 37006230 PMCID: PMC10051199 DOI: 10.2144/fsoa-2022-0072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/14/2023] [Indexed: 03/11/2023] Open
Abstract
Aim: The current study investigated the performance of 4 widely used DNA extraction kits using different types of high (stool) and low biomass samples (chyme, broncho alveolar lavage and sputum). Methods: Qiagen Powerfecal Pro DNA kit, Macherey Nucleospin Soil kit, Macherey Nucleospin Tissue Kit and MagnaPure LC DNA isolation kit III were evaluated in terms of DNA quantity, quality, diversity and composition profiles. Results: The quantity and quality of DNA varied among the four kits. The microbiota of the stool samples showed similar diversity and compositional profiles for the 4 kits. Conclusion: Despite differences in DNA quality and quantity, the 4 kits yielded similar results for stool samples, while all kits were not sensitive enough for low biomass samples.
Collapse
Affiliation(s)
| | - Gaëlle Boudry
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France
| | - Sylvie Buffet-Bataillon
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France
- Bacteriology, Pontchaillou University Hospital, Rennes, France
| |
Collapse
|
29
|
Özbek MA, Bereli N, Özgür E, Denizli A. Human serum albumin depletion based on dye ligand affinity chromatography via magnetic microcryogels. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2023; 34:449-462. [PMID: 36123323 DOI: 10.1080/09205063.2022.2127142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
One of the primary purposes of proteomic studies is to analyze the proteins in the blood to be considered as biomarkers. Albumin, which constitutes the majority of total serum proteins, complicates the discovery of low-density proteins that are important for the diagnosis of diseases. Based on this, an alternative approach for albumin depletion was developed in this study by covalently attached Cibacron Blue 3GA (CB) to magnetic microcryogels. After detailed characterization of CB attached magnetic microcryogels synthesized via a microstencil array chip, albumin adsorption studies were performed to examine the optimum depletion conditions. In the presented study, the maximum albumin adsorption capacity (Qmax) was calculated as 149.25 mg/mL in pH 5.0 acetate buffer solution, which is the optimum pH value for albumin. Experimental studies have demonstrated that CB-attached magnetic microcryogels can be reused without loss of performance for albumin depletion after 10 adsorption-desorption cycles.
Collapse
Affiliation(s)
- Merve Asena Özbek
- Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Nilay Bereli
- Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Erdoğan Özgür
- Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, Turkey
| | - Adil Denizli
- Faculty of Science, Department of Chemistry, Hacettepe University, Ankara, Turkey
| |
Collapse
|
30
|
Lavorato GC, de Almeida AA, Vericat C, Fonticelli MH. Redox phase transformations in magnetite nanoparticles: impact on their composition, structure and biomedical applications. NANOTECHNOLOGY 2023; 34:192001. [PMID: 36825776 DOI: 10.1088/1361-6528/acb943] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Magnetite nanoparticles (NPs) are one of the most investigated nanomaterials so far and modern synthesis methods currently provide an exceptional control of their size, shape, crystallinity and surface functionalization. These advances have enabled their use in different fields ranging from environmental applications to biomedicine. However, several studies have shown that the precise composition and crystal structure of magnetite NPs depend on their redox phase transformations, which have a profound impact on their physicochemical properties and, ultimately, on their technological applications. Although the physical mechanisms behind such chemical transformations in bulk materials have been known for a long time, experiments on NPs with large surface-to-volume ratios have revealed intriguing results. This article is focused on reviewing the current status of the field. Following an introduction on the fundamental properties of magnetite and other related iron oxides (including maghemite and wüstite), some basic concepts on the chemical routes to prepare iron oxide nanomaterials are presented. The key experimental techniques available to study phase transformations in iron oxides, their advantages and drawbacks to the study of nanomaterials are then discussed. The major section of this work is devoted to the topotactic oxidation of magnetite NPs and, in this regard, the cation diffusion model that accounts for the experimental results on the kinetics of the process is critically examined. Since many synthesis routes rely on the formation of monodisperse magnetite NPs via oxidation of wüstite counterparts, the modulation of their physical properties by crystal defects arising from the oxidation process is also described. Finally, the importance of a precise control of the composition and structure of magnetite-based NPs is discussed and its role in their biomedical applications is highlighted.
Collapse
Affiliation(s)
- Gabriel C Lavorato
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, C. C. 16, Suc. 4, 1900 La Plata, Argentina
| | - Adriele A de Almeida
- Instituto de Física 'Gleb Wataghin' (IFGW), Universidade Estadual de Campinas-UNICAMP, R. Sérgio Buarque de Holanda, 777-CEP: 13083-859, Campinas - SP, Brazil
| | - Carolina Vericat
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, C. C. 16, Suc. 4, 1900 La Plata, Argentina
| | - Mariano H Fonticelli
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, C. C. 16, Suc. 4, 1900 La Plata, Argentina
| |
Collapse
|
31
|
Xu J, Ma Y, Song Z, Sun W, Liu Y, Shu C, Hua H, Yang M, Liang Q. Evaluation of an automated CRISPR-based diagnostic tool for rapid detection of COVID-19. Heliyon 2023; 9:e13190. [PMID: 36712915 PMCID: PMC9868009 DOI: 10.1016/j.heliyon.2023.e13190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
The performance of an automated commercial CRISPR/Cas based technology was evaluated and compared with routine RT-PCR testing to diagnose COVID-19. Suspected and discharged COVID-19 cases were included and tested with CRISPR-based SARS-CoV-2 test and RT-PCR assay using throat swab and sputum specimens. The diagnostic yield was calculated and compared using the McNemar test. A total of 437 patients were included for analysis, including COVID-19 (n = 171), discharged cases (n = 155), and others (n = 111). For the diagnosis of COVID-19, the CRISPR-SARS-CoV-2 test had a sensitivity and specificity of 98.2% (168/171) and 100.0% (266/266), respectively; the RT-PCR test had a sensitivity and specificity of 100.0% (171/171) and 100.0% (266/266), respectively. No significant difference was found in the sensitivity of CRISPR-SARS-CoV-2 and RT-PCR. In conclusion, the CRISPR-SARS-CoV-2 test had a comparable performance with RT-PCR and showed several advantages, such as short assay time, low cost, and no requirement for expensive equipment.
Collapse
Affiliation(s)
- Jun Xu
- Department for Viral Disease Control and Prevention, Heilongjiang Provincial Center for Disease Control and Prevention, Harbin 150030, China
| | - Yuanyuan Ma
- Department of Drug Clinical Trial, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Zhigang Song
- Pathogen Detection and Biosafety Department, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China,Corresponding author
| | - Wei Sun
- Department for Viral Disease Control and Prevention, Heilongjiang Provincial Center for Disease Control and Prevention, Harbin 150030, China,Corresponding author
| | - Yi Liu
- Pathogen Detection and Biosafety Department, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Chang Shu
- Department for Viral Disease Control and Prevention, Heilongjiang Provincial Center for Disease Control and Prevention, Harbin 150030, China
| | - Hua Hua
- Department for Viral Disease Control and Prevention, Heilongjiang Provincial Center for Disease Control and Prevention, Harbin 150030, China
| | - Ming Yang
- Department for Viral Disease Control and Prevention, Heilongjiang Provincial Center for Disease Control and Prevention, Harbin 150030, China
| | - Qi Liang
- Department for Viral Disease Control and Prevention, Heilongjiang Provincial Center for Disease Control and Prevention, Harbin 150030, China
| |
Collapse
|
32
|
Gerzsenyi TB, Ilosvai ÁM, Szilágyi G, Szőri M, Váradi C, Viskolcz B, Vanyorek L, Szőri-Dorogházi E. A Simplified and Efficient Method for Production of Manganese Ferrite Magnetic Nanoparticles and Their Application in DNA Isolation. Int J Mol Sci 2023; 24:ijms24032156. [PMID: 36768483 PMCID: PMC9917137 DOI: 10.3390/ijms24032156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/25/2023] Open
Abstract
A simplified, fast, and effective production method has been developed for the synthesis of manganese ferrite (MnFe2O4) magnetic nanoparticles (MNPs). In addition to the wide applicability of MnFe2O4 MNPs, this work also reports their application in DNA isolation for the first time. An ultrasonic-cavitation-assisted combustion method was applied in the synthesis of MnFe2O4 MNPs at different furnace temperatures (573 K, 623 K, 673 K, and 773 K) to optimize the particles' properties. It was shown that MnFe2O4 nanoparticles synthesized at 573 K consist of a spinel phase only with adequate size and zeta potential distributions and superparamagnetic properties. It was also demonstrated that superparamagnetic manganese ferrite nanoparticles bind DNA in buffer with a high NaCl concentration (2.5 M), and the DNA desorbs from the MNPs by decreasing the NaCl concentration of the elution buffer. This resulted in a DNA yield comparable to that of commercial DNA extraction products. Both the DNA concentration measurements and electrophoresis confirmed that a high amount of isolated bacterial plasmid DNA (pDNA) with adequate purity can be extracted with MnFe2O4 (573 K) nanoparticles by applying the DNA extraction method proposed in this article.
Collapse
Affiliation(s)
- Tímea B. Gerzsenyi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
| | - Ágnes M. Ilosvai
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - Gergely Szilágyi
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - Milán Szőri
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - Csaba Váradi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
| | - Béla Viskolcz
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
| | - László Vanyorek
- Institute of Chemistry, Faculty of Materials and Chemical Engineering, University of Miskolc, 3515 Miskolc, Hungary
- Correspondence: (L.V.); (E.S.-D.)
| | - Emma Szőri-Dorogházi
- Higher Education and Industrial Cooperation Centre, University of Miskolc, 3515 Miskolc, Hungary
- Correspondence: (L.V.); (E.S.-D.)
| |
Collapse
|
33
|
Kanies OS, Kremer KR, Mason BM, Dudley MG, Hlavay JM, Miller CT, Spero RC, Fisher JK. A modular microfluidic device that uses magnetically actuatable microposts for enhanced magnetic bead-based workflows. LAB ON A CHIP 2023; 23:330-340. [PMID: 36597964 PMCID: PMC10158497 DOI: 10.1039/d2lc00859a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Magnetic beads have been widely and successfully used for target enrichment in life science assays. There exists a large variety of commercially available magnetic beads functionalized for specific target capture, as well as options that enable simple surface modifications for custom applications. While magnetic beads are ideal for use in the macrofluidic context of typical laboratory workflows, their performance drops in microfluidic contexts, such as consumables for point-of-care diagnostics. A primary cause is the diffusion-limited analyte transport in these low Reynolds number environments. A new method, BeadPak, uses magnetically actuatable microposts to enhance analyte transport, improving yield of the desired targets. Critical parameters were defined for the operation of this technology and its performance characterized in canonical life-science assays. BeadPak achieved up to 1000× faster capture than a microfluidic chamber relying on diffusion alone, enabled a significant specimen concentration via volume reduction, and demonstrated compatibility with a range of biological specimens. The results shown in this work can be extended to other systems that utilize magnetic beads for target capture, concentration, and/or purification.
Collapse
|
34
|
Kifaro EG, Kim MJ, Jung S, Jang YH, Moon S, Lee DH, Song CS, Misinzo G, Kim SK. Microparticles as Viral RNA Carriers from Stool for Stable and Sensitive Surveillance. Diagnostics (Basel) 2023; 13:diagnostics13020261. [PMID: 36673071 PMCID: PMC9857651 DOI: 10.3390/diagnostics13020261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/29/2022] [Accepted: 01/02/2023] [Indexed: 01/13/2023] Open
Abstract
Since its discovery, polymerase chain reaction (PCR) has emerged as an important technology for the diagnosis and identification of infectious diseases. It is a highly sensitive and reliable nucleic acids (NA) detection tool for various sample types. However, stool, which carries the most abundant micro-organisms and physiological byproducts, remains to be the trickiest clinical specimen for molecular detection of pathogens. Herein, we demonstrate the novel application of hydrogel microparticles as carriers of viral RNA from stool samples without prior RNA purification for real-time polymerase chain reaction (qPCR). In each microparticle of primer-incorporated network (PIN) as a self-sufficient reaction compartment, immobilized reverse transcription (RT) primers capture the viral RNA by hybridization and directly initiate RT of RNA to generate a pool of complementary DNA (PIN-cDNA pool). Through a simple operation with a portable thermostat device, a PIN-cDNA pool for influenza A virus (IAV) was obtained in 20 min. The PIN-cDNA pools can be stored at room temperature, or directly used to deliver cDNA templates for qPCR. The viral cDNA templates were freely released in the subsequent qPCR to allow amplification efficiency of over 91%. The assay displayed good linearity, repeatability, and comparable limit of detection (LoD) with a commercialized viral RNA purification kit. As a proof of concept, this technology carries a huge potential for onsite application to improve human and animal infectious disease surveillance activities using stool samples without the need for a laboratory or centrifuge for sample preparation.
Collapse
Affiliation(s)
- Emmanuel George Kifaro
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Mi Jung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Seungwon Jung
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Yoon-ha Jang
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Sungyeon Moon
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
| | - Dong-Hun Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Chang-Seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Gerald Misinzo
- Department of Veterinary Microbiology, Parasitology, and Biotechnology, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3019, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture (SUA), Morogoro P.O. Box 3297, Tanzania
| | - Sang Kyung Kim
- Molecular Recognition Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea
- KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Republic of Korea
- Correspondence:
| |
Collapse
|
35
|
Turner SA, Abou Shaar R, Yang Z. The basics of commonly used molecular techniques for diagnosis, and application of molecular testing in cytology. Diagn Cytopathol 2023; 51:83-94. [PMID: 36345929 PMCID: PMC10098847 DOI: 10.1002/dc.25067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
Molecular diagnostics has expanded to become the standard of care for a variety of solid tumor types. With limited diagnostic material, it is often desirable to use cytological preparations to provide rapid and accurate molecular results. This review covers important pre-analytic considerations and limitations, and a description of common techniques that the modern cytopathologist should understand when ordering and interpreting molecular tests in practice.
Collapse
Affiliation(s)
- Scott A Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Rand Abou Shaar
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Zhongbo Yang
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| |
Collapse
|
36
|
Ahmed FK, Alghuthaymi MA, Abd-Elsalam KA, Ravichandran M, Kalia A. Nano-Based Robotic Technologies for Plant Disease Diagnosis. NANOROBOTICS AND NANODIAGNOSTICS IN INTEGRATIVE BIOLOGY AND BIOMEDICINE 2023:327-359. [DOI: 10.1007/978-3-031-16084-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
|
37
|
Huang X, Fu R, Qiao S, Zhang J, Xianyu Y. Nanotechnology-based diagnostic methods for coronavirus: From nucleic acid extraction to amplification. Biosens Bioelectron 2022; 13:100289. [PMID: 36530849 PMCID: PMC9733970 DOI: 10.1016/j.biosx.2022.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/25/2022] [Accepted: 12/03/2022] [Indexed: 12/13/2022]
Abstract
The recent emergence of human coronaviruses (CoVs) causing severe acute respiratory syndrome (SARS) is posing a great threat to global public health. Therefore, the rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Nucleic acids, including deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), are natural biopolymers composed of nucleotides that store, transmit, and express genetic information. Applications of nucleic acid detection range from genotyping and genetic prognostics, to expression profiling and detection of infectious disease. The nucleic acid detection for infectious diseases is widely used, as evidenced by the widespread use of COVID-19 tests for the containment of the pandemic. Nanotechnology influences all medical disciplines and has been considered as an essential tool for novel diagnostics, nanotherapeutics, vaccines, medical imaging, and the utilization of biomaterials for regenerative medicine. In this review, the recent advances in the development of nanotechnology-based diagnostic methods for coronavirus, and their applications in nucleic acid detection are discussed in detail. The techniques for the amplification of nucleic acids are summarized, as well as the use of magnetic nanoparticles for nucleic acid extraction. Besides, current challenges and future prospects are proposed, along with the great potential of nanotechnology for the effective diagnosis of coronavirus.
Collapse
Affiliation(s)
- Xucheng Huang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ruijie Fu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China,State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Sai Qiao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Zhang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China,Corresponding author
| | - Yunlei Xianyu
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China,State Key Laboratory of Fluid Power and Mechatronic Systems, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China,Corresponding author. Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
38
|
Dunn MJ, Shazib SUA, Simonton E, Slot JC, Anderson MZ. Architectural groups of a subtelomeric gene family evolve along distinct paths in Candida albicans. G3 (BETHESDA, MD.) 2022; 12:jkac283. [PMID: 36269198 PMCID: PMC9713401 DOI: 10.1093/g3journal/jkac283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 10/09/2022] [Indexed: 12/08/2023]
Abstract
Subtelomeres are dynamic genomic regions shaped by elevated rates of recombination, mutation, and gene birth/death. These processes contribute to formation of lineage-specific gene family expansions that commonly occupy subtelomeres across eukaryotes. Investigating the evolution of subtelomeric gene families is complicated by the presence of repetitive DNA and high sequence similarity among gene family members that prevents accurate assembly from whole genome sequences. Here, we investigated the evolution of the telomere-associated (TLO) gene family in Candida albicans using 189 complete coding sequences retrieved from 23 genetically diverse strains across the species. Tlo genes conformed to the 3 major architectural groups (α/β/γ) previously defined in the genome reference strain but significantly differed in the degree of within-group diversity. One group, Tloβ, was always found at the same chromosome arm with strong sequence similarity among all strains. In contrast, diverse Tloα sequences have proliferated among chromosome arms. Tloγ genes formed 7 primary clades that included each of the previously identified Tloγ genes from the genome reference strain with 3 Tloγ genes always found on the same chromosome arm among strains. Architectural groups displayed regions of high conservation that resolved newly identified functional motifs, providing insight into potential regulatory mechanisms that distinguish groups. Thus, by resolving intraspecies subtelomeric gene variation, it is possible to identify previously unknown gene family complexity that may underpin adaptive functional variation.
Collapse
Affiliation(s)
- Matthew J Dunn
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Shahed U A Shazib
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Emily Simonton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Jason C Slot
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA
| |
Collapse
|
39
|
Minkner R, Boonyakida J, Park EY, Wätzig H. Oligonucleotide separation techniques for purification and analysis: What can we learn for today's tasks? Electrophoresis 2022; 43:2402-2427. [PMID: 36285667 DOI: 10.1002/elps.202200079] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Nucleic acids are the blueprint of life. They are not only the construction plan of the single cell or higher associations of them, but also necessary for function, communication and regulation. Due to the pandemic, the attention shifted in particular to their therapeutic potential as a vaccine. As pharmaceutical oligonucleotides are unique in terms of their stability and application, special delivery systems were also considered. Oligonucleotide production systems can vary and depend on the feasibility, availability, price and intended application. To achieve good purity, reliable results and match the strict specifications in the pharmaceutical industry, the separation of oligonucleotides is always essential. Besides the separation required for production, additional and specifically different separation techniques are needed for analysis to determine if the product complies with the designated specifications. After a short introduction to ribonucleic acids (RNAs), messenger RNA vaccines, and their production and delivery systems, an overview regarding separation techniques will be provided. This not only emphasises electrophoretic separations but also includes spin columns, extractions, precipitations, magnetic nanoparticles and several chromatographic separation principles, such as ion exchange chromatography, ion-pair reversed-phase, size exclusion and affinity.
Collapse
Affiliation(s)
- Robert Minkner
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Jirayu Boonyakida
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Enoch Y Park
- Department of Bioscience, Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan.,Laboratory of Biotechnology, Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan
| | - Hermann Wätzig
- Institute of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| |
Collapse
|
40
|
Hin S, Paust N, Rombach M, Lüddecke J, Specht M, Zengerle R, Mitsakakis K. Magnetophoresis in Centrifugal Microfluidics at Continuous Rotation for Nucleic Acid Extraction. MICROMACHINES 2022; 13:2112. [PMID: 36557411 PMCID: PMC9787563 DOI: 10.3390/mi13122112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Centrifugal microfluidics enables fully automated molecular diagnostics at the point-of-need. However, the integration of solid-phase nucleic acid extraction remains a challenge. Under this scope, we developed the magnetophoresis under continuous rotation for magnetic bead-based nucleic acid extraction. Four stationary permanent magnets are arranged above a cartridge, creating a magnetic field that enables the beads to be transported between the chambers of the extraction module under continuous rotation. The centrifugal force is maintained to avoid uncontrolled spreading of liquids. We concluded that below a frequency of 5 Hz, magnetic beads move radially inwards. In support of magnetophoresis, bead inertia and passive geometrical design features allow to control the azimuthal bead movement between chambers. We then demonstrated ferrimagnetic bead transfer in liquids with broad range of surface tension and density values. Furthermore, we extracted nucleic acids from lysed Anopheles gambiae mosquitoes reaching comparable results of eluate purity (LabDisk: A260/A280 = 1.6 ± 0.04; Reference: 1.8 ± 0.17), and RT-PCR of extracted RNA (LabDisk: Ct = 17.9 ± 1.6; Reference: Ct = 19.3 ± 1.7). Conclusively, magnetophoresis at continuous rotation enables easy cartridge integration and nucleic acid extraction at the point-of-need with high yield and purity.
Collapse
Affiliation(s)
- Sebastian Hin
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Nils Paust
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- IMTEK—Laboratory for MEMS Applications, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Markus Rombach
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Jan Lüddecke
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Mara Specht
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- IMTEK—Laboratory for MEMS Applications, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - Konstantinos Mitsakakis
- Hahn-Schickard, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
- IMTEK—Laboratory for MEMS Applications, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| |
Collapse
|
41
|
Sofiev M, Sofieva S, Palamarchuk J, Šaulienė I, Kadantsev E, Atanasova N, Fatahi Y, Kouznetsov R, Kuula J, Noreikaite A, Peltonen M, Pihlajamäki T, Saarto A, Svirskaite J, Toiviainen L, Tyuryakov S, Šukienė L, Asmi E, Bamford D, Hyvärinen AP, Karppinen A. Bioaerosols in the atmosphere at two sites in Northern Europe in spring 2021: Outline of an experimental campaign. ENVIRONMENTAL RESEARCH 2022; 214:113798. [PMID: 35810819 DOI: 10.1016/j.envres.2022.113798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
A coordinated observational and modelling campaign targeting biogenic aerosols in the air was performed during spring 2021 at two locations in Northern Europe: Helsinki (Finland) and Siauliai (Lithuania), approximately 500 km from each other in north-south direction. The campaign started on March 1, 2021 in Siauliai (12 March in Helsinki) and continued till mid-May in Siauliai (end of May in Helsinki), thus recording the transition of the atmospheric biogenic aerosols profile from winter to summer. The observations included a variety of samplers working on different principles. The core of the program was based on 2- and 2.4--hourly sampling in Helsinki and Siauliai, respectively, with sticky slides (Hirst 24-h trap in Helsinki, Rapid-E slides in Siauliai). The slides were subsequently processed extracting the DNA from the collected aerosols, which was further sequenced using the 3-rd generation sequencing technology. The core sampling was accompanied with daily and daytime sampling using standard filter collectors. The hourly aerosol concentrations at the Helsinki monitoring site were obtained with a Poleno flow cytometer, which could recognize some of the aerosol types. The sampling campaign was supported by numerical modelling. For every sample, SILAM model was applied to calculate its footprint and to predict anthropogenic and natural aerosol concentrations, at both observation sites. The first results confirmed the feasibility of the DNA collection by the applied techniques: all but one delivered sufficient amount of DNA for the following analysis, in over 40% of the cases sufficient for direct DNA sequencing without the PCR step. A substantial variability of the DNA yield has been noticed, generally not following the diurnal variations of the total-aerosol concentrations, which themselves showed variability not related to daytime. An expected upward trend of the biological material amount towards summer was observed but the day-to-day variability was large. The campaign DNA analysis produced the first high-resolution dataset of bioaerosol composition in the North-European spring. It also highlighted the deficiency of generic DNA databases in applications to atmospheric biota: about 40% of samples were not identified with standard bioinformatic methods.
Collapse
Affiliation(s)
- Mikhail Sofiev
- Finnish Meteorological Institute, Helsinki, Finland; Vilnius University, Vilnius, Lithuania.
| | - Svetlana Sofieva
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Nina Atanasova
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | - Yalda Fatahi
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Joel Kuula
- Finnish Meteorological Institute, Helsinki, Finland
| | | | - Martina Peltonen
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | - Julija Svirskaite
- Finnish Meteorological Institute, Helsinki, Finland; University of Helsinki, Helsinki, Finland
| | | | | | | | - Eija Asmi
- Finnish Meteorological Institute, Helsinki, Finland
| | | | | | | |
Collapse
|
42
|
Lokras A, Chakravarty A, Rades T, Christensen D, Franzyk H, Thakur A, Foged C. Simultaneous quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems. Int J Pharm 2022; 626:122171. [PMID: 36070841 DOI: 10.1016/j.ijpharm.2022.122171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/17/2022]
Abstract
Robust, sensitive, and versatile analytical methods are essential for quantification of RNA drug cargos loaded into nanoparticle-based delivery systems. However, simultaneous quantification of multiple RNA cargos co-loaded into nanoparticles remains a challenge. Here, we developed and validated the use of ion-pair reversed-phase high-performance liquid chromatography combined with UV detection (IP-RP-HPLC-UV) for simultaneous quantification of single- and double-stranded RNA cargos. Complete extraction of RNA cargo from the nanoparticle carrier was achieved using a phenol:chloroform:isoamyl alcohol mixture. Separations were performed using either a C18 or a PLRP-S column, eluted with 0.1 M triethylammonium acetate (TEAA) solution as ion-pairing reagent (eluent A), and 0.1 M TEAA containing 25 % (v/v) CH3CN as eluent B. These methods were applied to quantify mRNA and polyinosinic:polycytidylic acid co-loaded into lipid-polymer hybrid nanoparticles, and single-stranded oligodeoxynucleotide donors and Alt-R CRISPR single guide RNAs co-loaded into lipid nanoparticles. The developed methods were sensitive (limit of RNA quantification < 60 ng), linear (R2 > 0.997), and accurate (≈ 100 % recovery of RNA spiked in nanoparticles). Hence, the present study may facilitate convenient quantification of multiple RNA cargos co-loaded into nanoparticle-based delivery systems.
Collapse
Affiliation(s)
- Abhijeet Lokras
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Akash Chakravarty
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Thomas Rades
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Dennis Christensen
- Department of Infectious Disease Immunology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen Ø, Denmark
| | - Aneesh Thakur
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Camilla Foged
- Department of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark.
| |
Collapse
|
43
|
Cavalcante EHM, de Oliveira HP. Magnetite‐doped electrospun fibers for
DNA
adsorption. J Appl Polym Sci 2022. [DOI: 10.1002/app.53198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Helinando Pequeno de Oliveira
- Institute of Materials Science Federal University of São Francisco Valley, Avenida Antônio Carlos Magalhães Juazeiro Brazil
| |
Collapse
|
44
|
Yang R, Li J, Wu Y, Jiang X, Qu S, Wang Q, Liang H, Zen K. A novel method to purify small RNAs from human tissues for methylation analysis by LC-MS/MS. Front Mol Biosci 2022; 9:949181. [PMID: 36111135 PMCID: PMC9468635 DOI: 10.3389/fmolb.2022.949181] [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: 05/20/2022] [Accepted: 07/28/2022] [Indexed: 11/23/2022] Open
Abstract
Methylation modification of small RNAs, including miRNA, piRNA, and tsRNA, is critical for small RNA biogenesis and biological function. Methylation of individual small RNA can be defined by liquid chromatography-coupled with mass spectrometry (LC-MS/MS). However, LC-MS/MS analysis requires a high purity of individual small RNA. Due to the difficulty of purifying specific small RNA from tissues or cells, the progress in characterizing small RNA methylation by LC-MS/MS is limited. Here, we report a novel method that can efficiently purify small RNA from human tissues for LC-MS/MS analysis. This method includes two steps: 1) pull down the target small RNA by incubating total small RNAs (18–24 nt) extracted from human tissues with a biotinylated antisense oligonucleotide of the target small RNA, followed by capturing the binding duplex of biotinylated antisense and small RNA via streptavidin magnetic beads, and 2) protect the target small RNA by pairing it with a single-strand DNA, which sequence is complementary to the target small RNA, to form a DNA/RNA hybrid double-strand, followed by sequential digestion with exonuclease I, nuclease S1, and DNase I, respectively. Furthermore, employing a mixture of four pairs of synthetic methylated and non-methylated small RNAs, we further refined this two-step method by optimizing the nuclease S1 treatment condition. With this method, we successfully purified miR-21-5p, miR-26-5p, piR-020485, and tsRNA from human lung and sperm tissue samples and analyzed their 2′-O-methylation modification at the 3′-end by LC-MS/MS.
Collapse
Affiliation(s)
- Rong Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Jianfeng Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Yifan Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Xinli Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Shuang Qu
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Qiang Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Ke Zen, ; Hongwei Liang, ; Qiang Wang,
| | - Hongwei Liang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
- *Correspondence: Ke Zen, ; Hongwei Liang, ; Qiang Wang,
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
- *Correspondence: Ke Zen, ; Hongwei Liang, ; Qiang Wang,
| |
Collapse
|
45
|
Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
Collapse
Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
| |
Collapse
|
46
|
Oligonucleotides Isolation and Separation—A Review on Adsorbent Selection. Int J Mol Sci 2022; 23:ijms23179546. [PMID: 36076941 PMCID: PMC9455468 DOI: 10.3390/ijms23179546] [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: 07/26/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Oligonucleotides have many important applications, including as primers in polymerase chain reactions and probes for DNA sequencing. They are proposed as a diagnostic and prognostic tool for various diseases and therapeutics in antisense therapy. Accordingly, it is necessary to develop liquid chromatography and solid phase extraction methods to separate oligonucleotides and isolate them from biological samples. Many reviews have been written about the determination of these compounds using the separation technique or sample preparation for their isolation. However, presumably, there are no articles that critically review the adsorbents used in liquid chromatography or solid phase extraction. The present publication reviews the literature from the last twenty years related to supports (silica, polymers, magnetic nanoparticles) and their modifications. The discussed issues concern reversed phase (alkyl, aromatic, cholesterol, mixed ligands), ion-exchange (strong and weak ones), polar (silica, polyhydroxy, amide, zwitterionic), and oligonucleotide-based adsorbents.
Collapse
|
47
|
Rapid and inexpensive method of PCR ready DNA isolation from human peripheral blood and saliva. Anal Biochem 2022; 655:114852. [PMID: 35964732 DOI: 10.1016/j.ab.2022.114852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND The isolation of nucleic acids is a frequently performed procedure in the molecular biology area. Although several rapid DNA isolation techniques from human peripheral blood and saliva have been developed, there are still some disadvantages - volume, time, cost, and yield are a few notable ones. OBJECTIVE We aim to develop a rapid and inexpensive method to isolate high-molecular-weight genomic DNA from human peripheral blood and saliva that can be used for molecular biology experiments. METHODS Five DNA isolation methods with slightly varying protocols were used. High-quality DNA obtained from one specific method was further amplified by PCR and the template with good amplification was further used for performing RFLP and sequencing. RESULTS Out of 5 different isolation methods (R1 to R5), DNA obtained from the R4 was of good quality (molecular weight is > 10 kb and 260/280 ratio is 1.89 ± 0.2), which allows successful PCR amplification and good separation in Restriction Fragment Length Polymorphism analysis. Sequencing by the Sanger Sequencing produced a good readable sequence of an amplified fragment from Method R4 DNA. CONCLUSION In the present study we have developed a simple, rapid, and cost-effective DNA isolation method, which uses low sample volume and yields good quantity and high-quality product. The DNA obtained is highly fit for molecular genetics research applications.
Collapse
|
48
|
Tamáš M, Potocarova A, Konecna B, Klucar Ľ, Mackulak T. Wastewater Sequencing-An Innovative Method for Variant Monitoring of SARS-CoV-2 in Populations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:9749. [PMID: 35955106 PMCID: PMC9367975 DOI: 10.3390/ijerph19159749] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 05/14/2023]
Abstract
The SARS-CoV-2 outbreak has already affected more than 555 million people, and 6.3 million people have died. Due to its high infectivity, it is crucial to track SARS-CoV-2 outbreaks early to prevent the spread of infection. Wastewater monitoring appears to be a powerful and effective tool for managing epidemiological situations. Due to emerging mutations of SARS-CoV-2, there is a need to monitor mutations in order to control the pandemic. Since the sequencing of randomly chosen individuals is time-consuming and expensive, sequencing of wastewater plays an important role in revealing the dynamics of infection in a population. The sampling method used is a crucial factor and significantly impacts the results. Wastewater can be collected as a grab sample or as a 24 h composite sample. Another essential factor is the sample volume, as is the method of transport used. This review discusses different pretreatment procedures and RNA extraction, which may be performed using various methods, such as column-based extraction, TRIzol, or magnetic extraction. Each of the methods has its advantages and disadvantages, which are described accordingly. RT-qPCR is a procedure that confirms the presence of SARS-CoV-2 genes before sequencing. This review provides an overview of currently used methods for preparing wastewater samples, from sampling to sequencing.
Collapse
Affiliation(s)
- Michal Tamáš
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
- Institute of Physiology, Faculty of Medicine, Comenius University in Bratislava, 81372 Bratislava, Slovakia
| | - Alena Potocarova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Barbora Konecna
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University in Bratislava, Sasinkova 4, 81108 Bratislava, Slovakia
| | - Ľubos Klucar
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia
| | - Tomas Mackulak
- Department of Environmental Engineering, Institute of Chemical and Environmental Engineering, Faculty of Chemical and Food Technology, Slovak University of Technology, Radinského 9, 81237 Bratislava, Slovakia
| |
Collapse
|
49
|
Thi Nguyen LT, Thi Le NH, Thi Ta HK, Dang Nguyen K. Isolation of DNA from Arthrospira platensis and whole blood using magnetic nanoparticles (Fe3O4@OA and Fe3O4@OA@SiO2). J Anal Sci Technol 2022. [DOI: 10.1186/s40543-022-00337-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
AbstractMagnetic nanoparticles (MNPs) provide a fast, cost-effective, and organic-free method for DNA isolation. In this paper, we synthesized MNP coated with oleic acid (Fe3O4@OA) and silica nanoparticles (Fe3O4@OA@SiO2), characterized the properties of MNP using TEM, VSM, and FTIR, and investigated their efficiency in DNA isolation from cyanobacteria. The yield and quality of isolated DNA were evaluated and compared with those from animal blood and those obtained by the silica column or organic solvents. The results showed the successful preparations of Fe3O4@OA and Fe3O4@OA@SiO2 with superparamagnetic behaviors and a mean diameter of 7 nm and 106 nm, respectively. The FTIR spectra of Fe3O4@OA confirmed the bonding of OA to the surface of iron oxide, while those of Fe3O4@OA@SiO2 showed the exposed silanol groups. Although MNPs yielded a lower quantity of DNA compared with phenol/chloroform extraction, they showed the potential protection of the integrity of DNA against centrifugal and shear forces. Fe3O4@OA@SiO2 favored more nucleic acid absorption than Fe3O4@OA, producing a 1.2 and 1.6 times greater amount of DNA from Arthrospira platensis and animal blood respectively. The purity of DNA isolated from Arthrospira platensis was also higher than that of animal blood. These findings indicate a new and simple approach for the isolation of DNA from Arthrospira genus.
Graphical Abstract
Collapse
|
50
|
Magnetic Nylon 6 Nanocomposites for the Microextraction of Nucleic Acids from Biological Samples. MAGNETOCHEMISTRY 2022. [DOI: 10.3390/magnetochemistry8080085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Magnetic Fe3O4 nanoparticles (MNPs) have great potential for nucleic acid separation, detection, and delivery. MNPs are considered a valuable tool in biomedicine due to their cost-effectiveness, stability, easy surface functionalization, and the possibility of the manipulations under a magnetic field. Herein, the synthesis of magnetic nylon 6 nanocomposites (MNPs@Ny6) was investigated. Transmission electron microscopy (TEM) was used for morphology and size analysis. A new method of UV-induced immobilization of oligonucleotides on MNPs@Ny6 for nucleic acid magnetic separation was proposed. MNPs@Ny6 shows a high oligonucleotide binding capacity of 2.2 nmol/mg with 73.3% loading efficiency. The proposed system has been applied to analyze model mixtures of target RNA on the total yeast RNA background. The RNA target isolation efficiency was 60% with high specificity. The bind RNA release was 88.8% in a quantity of 0.16 nmol/mg. The total RNA capture efficiency was 53%. Considering this, the MNPs@Ny6 is an attractive candidate for nucleic acids-specific magnetic isolation.
Collapse
|